title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2015-07
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: On the challenges of drawing conclusions from p-values just below 0.05
link: https://peerj.com/articles/1142
last-modified: 2015-07-30
description: In recent years, researchers have attempted to provide an indication of the prevalence of inflated Type 1 error rates by analyzing the distribution of p-values in the published literature. De Winter & Dodou (2015) analyzed the distribution (and its change over time) of a large number of p-values automatically extracted from abstracts in the scientific literature. They concluded there is a ‘surge of p-values between 0.041–0.049 in recent decades’ which ‘suggests (but does not prove) questionable research practices have increased over the past 25 years.’ I show the changes in the ratio of fractions of p-values between 0.041–0.049 over the years are better explained by assuming the average power has decreased over time. Furthermore, I propose that their observation that p-values just below 0.05 increase more strongly than p-values above 0.05 can be explained by an increase in publication bias (or the file drawer effect) over the years (cf. Fanelli, 2012; Pautasso, 2010, which has led to a relative decrease of ‘marginally significant’ p-values in abstracts in the literature (instead of an increase in p-values just below 0.05). I explain why researchers analyzing large numbers of p-values need to relate their assumptions to a model of p-value distributions that takes into account the average power of the performed studies, the ratio of true positives to false positives in the literature, the effects of publication bias, and the Type 1 error rate (and possible mechanisms through which it has inflated). Finally, I discuss why publication bias and underpowered studies might be a bigger problem for science than inflated Type 1 error rates, and explain the challenges when attempting to draw conclusions about inflated Type 1 error rates from a large heterogeneous set of p-values.
creator: Daniël Lakens
uri: https://doi.org/10.7717/peerj.1142
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lakens

title: Ligature-induced peri-implant infection in crestal and subcrestal implants: a clinical and radiographic study in dogs
link: https://peerj.com/articles/1139
last-modified: 2015-07-30
description: Objective. The aim of this study was to assess the influence of implant–abutment interface (IAI) placement depths on peri-implant tissues in the presence of ligature-induced peri-implant inflammation.Materials and Methods. Two implants with screwed-in IAIs (SI) and two implants with tapped-in IAIs (TI) were inserted in one side of the mandible in six dogs eight weeks after tooth extraction. Four experimental groups were constituted: SI placed crestally, SI placed 1.5 mm subcrestally, TI placed crestally and TI placed 1.5 mm subcrestally. After 12 weeks, the healing abutments were connected. Four weeks later, cotton floss ligatures were placed around the abutments to promote plaque accumulation. Clinical and radiographic examinations were performed at 0, 6 and 12 weeks after ligature placement. The effects of the IAI placement depths on clinical and radiographic parameters were assessed.Results. The alterations of peri-implant probing depths, clinical attachment levels, distances from the IAI to the first bone-implant contact (IAI-fBIC) and depths of infrabony defect were significant larger in the subcrestal groups compared with the crestal groups during the plaque accumulation period. The alterations of clinical attachment levels, IAI-fBIC, depth of the infrabony defect and horizontal bone loss were not significantly different between the SI and TI groups after ligature placement.Conclusion. Tissue destruction in subcrestal implants may be more serious than that in crestal implants in the presence of inflamed peri-implant mucosa.
creator: Baoxin Huang
creator: Muzi Piao
creator: Li Zhang
creator: Xian’e Wang
creator: Li Xu
creator: Weidong Zhu
creator: Huanxin Meng
uri: https://doi.org/10.7717/peerj.1139
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Huang et al.

title: Spectrum of tablet computer use by medical students and residents at an academic medical center
link: https://peerj.com/articles/1133
last-modified: 2015-07-30
description: Introduction. The value of tablet computer use in medical education is an area of considerable interest, with preliminary investigations showing that the majority of medical trainees feel that tablet computers added value to the curriculum. This study investigated potential differences in tablet computer use between medical students and resident physicians.Materials & Methods. Data collection for this survey was accomplished with an anonymous online questionnaire shared with the medical students and residents at Southern Illinois University School of Medicine (SIU-SOM) in July and August of 2012.Results. There were 76 medical student responses (26% response rate) and 66 resident/fellow responses to this survey (21% response rate). Residents/fellows were more likely to use tablet computers several times daily than medical students (32% vs. 20%, p = 0.035). The most common reported uses were for accessing medical reference applications (46%), e-Books (45%), and board study (32%). Residents were more likely than students to use a tablet computer to access an electronic medical record (41% vs. 21%, p = 0.010), review radiology images (27% vs. 12%, p = 0.019), and enter patient care orders (26% vs. 3%, p < 0.001).Discussion. This study shows a high prevalence and frequency of tablet computer use among physicians in training at this academic medical center. Most residents and students use tablet computers to access medical references, e-Books, and to study for board exams. Residents were more likely to use tablet computers to complete clinical tasks.Conclusions. Tablet computer use among medical students and resident physicians was common in this survey. All learners used tablet computers for point of care references and board study. Resident physicians were more likely to use tablet computers to access the EMR, enter patient care orders, and review radiology studies. This difference is likely due to the differing educational and professional demands placed on resident physicians. Further study is needed better understand how tablet computers and other mobile devices may assist in medical education and patient care.
creator: Robert Robinson
uri: https://doi.org/10.7717/peerj.1133
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Robinson

title: Distinct mechanical behavior of HEK293 cells in adherent and suspended states
link: https://peerj.com/articles/1131
last-modified: 2015-07-30
description: The mechanical features of individual animal cells have been regarded as indicators of cell type and state. Previously, we investigated the surface mechanics of cancer and normal stromal cells in adherent and suspended states using atomic force microscopy. Cancer cells possessed specific mechanical and actin cytoskeleton features that were distinct from normal stromal cells in adherent and suspended states. In this paper, we report the unique mechanical and actin cytoskeletal features of human embryonic kidney HEK293 cells. Unlike normal stromal and cancer cells, the surface stiffness of adherent HEK293 cells was very low, but increased after cell detachment from the culture surface. Induced actin filament depolymerization revealed that the actin cytoskeleton was the underlying source of the stiffness in suspended HEK293 cells. The exclusive mechanical response of HEK293 cells to perturbation of the actin cytoskeleton resembled that of adherent cancer cells and suspended normal stromal cells. Thus, with respect to their special cell-surface mechanical features, HEK293 cells could be categorized into a new class distinct from normal stromal and cancer cells.
creator: Seyed Mohammad Ali Haghparast
creator: Takanori Kihara
creator: Jun Miyake
uri: https://doi.org/10.7717/peerj.1131
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Haghparast et al.

title: Frailty as a predictor of short-term adverse outcomes
link: https://peerj.com/articles/1121
last-modified: 2015-07-30
description: The objectives of this study were to compare how different frailty measures (Frailty Phenotype/FP, Groningen Frailty Indicator/GFI and Tilburg Frailty Indicator/TFI) predict short-term adverse outcomes. Secondarily, adopting a multidimensional approach to frailty (integral conceptual model–TFI), this study aims to compare how physical, psychological and social frailty predict the outcomes. A longitudinal study was carried out with 95 community-dwelling elderly. Participants were assessed at baseline for frailty, determinants of frailty, and adverse outcomes (healthcare utilization, quality of life, disability in basic and instrumental activities of daily living/ADL and IADL). Ten months later the outcomes were assessed again. Frailty was associated with specific healthcare utilization indicators: the FP with a greater utilization of informal care; GFI with an increased contact with healthcare professionals; and TFI with a higher amount of contacts with a general practitioner. After controlling for the effect of life-course determinants, comorbidity and adverse outcome at baseline, GFI predicted IADL disability and TFI predicted quality of life. The effect of the FP on the outcomes was not significant, when compared with the other measures. However, when comparing TFI’s domains, the physical domain was the most significant predictor of the outcomes, even explaining part of the variance of ADL disability. Frailty at baseline was associated with adverse outcomes at follow-up. However, the relationship of each frailty measure (FP, GFI and TFI) with the outcomes was different. In spite of the role of psychological frailty, TFI’s physical domain was the determinant factor for predicting disability and most of the quality of life.
creator: Tiago Coelho
creator: Constança Paúl
creator: Robbert J.J. Gobbens
creator: Lia Fernandes
uri: https://doi.org/10.7717/peerj.1121
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Coelho et al.

title: Suffering and mental health among older people living in nursing homes—a mixed-methods study
link: https://peerj.com/articles/1120
last-modified: 2015-07-30
description: Background. Knowledge about mixed-methods perspectives that examine anxiety, depression, social support, mental health and the phenomenon of suffering among cognitively intact NH residents is scarce. We aimed to explore suffering and mental health among cognitively intact NH residents.Methods. This study used a mixed-methods design to explore different aspects of the same phenomena of interest to gain a more comprehensive understanding. The qualitative core component comprised a qualitative interview from 18 nursing home residents (≥65 years) about experiences related to pain, grief and loss. The supplementary component comprised interview from the same respondents using the SF-36 Health Survey subscales, the Hospital Anxiety and Depression Scale and the Social Provisions Scale.Results. The individual descriptions reveal suffering caused by painful experiences during life. The quantitative results indicated that symptoms of anxiety and depression were related to mental health and symptoms of anxiety were related to bodily pain and emotional role limitations. Attachment and social integration were associated with vitality and social functioning.Discussion. To improve the situation, more attention should be paid to the residents’ suffering related to anxiety, depression and psychosocial relations.
creator: Jorunn Drageset
creator: Elin Dysvik
creator: Birgitte Espehaug
creator: Gerd Karin Natvig
creator: Bodil Furnes
uri: https://doi.org/10.7717/peerj.1120
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Drageset et al.

title: Preliminary needs assessment of mobile technology use for healthcare among homeless veterans
link: https://peerj.com/articles/1096
last-modified: 2015-07-30
description: Background. Homeless veterans have complex healthcare needs, but experience many barriers to treatment engagement. While information technologies (IT), especially mobile phones, are used to engage patients in care, little is known about homeless veterans’ IT use. This study examines homeless veterans’ access to and use of IT, attitudes toward health-related IT use, and barriers to IT in the context of homelessness.Methods. Qualitative interviews were conducted with 30 homeless veterans in different housing programs in Boston, MA, ranging from emergency shelters to supportive transitional housing that allow stays of up to 2 years. Interviews were conducted in person, audio recorded and then transcribed. Three researchers coded transcripts. Inductive thematic analysis was used.Results. Most participants (90%) had a mobile phone and were receptive to IT use for health-related communications. A common difficulty communicating with providers was the lack of a stable mailing address. Some participants were using mobile phones to stay in touch with providers. Participants felt mobile-phone calls or text messages could be used to remind patients of appointments, prescription refills, medication taking, and returning for laboratory results. Mobile phone text messaging was seen as convenient, and helped participants stay organized because necessary information was saved in text messages. Some reported concerns about the costs associated with mobile phone use (calls and texting), the potential to be annoyed by too many text messages, and not knowing how to use text messaging.Conclusion. Homeless veterans use IT and welcome its use for health-related purposes. Technology-assisted outreach among this population may lead to improved engagement in care.
creator: D. Keith McInnes
creator: Gemmae M. Fix
creator: Jeffrey L. Solomon
creator: Beth Ann Petrakis
creator: Leon Sawh
creator: David A. Smelson
uri: https://doi.org/10.7717/peerj.1096
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Spatio-temporal variability in the distribution of ground-dwelling riparian spiders and their potential role in water-to-land energy transfer along Hong Kong forest streams
link: https://peerj.com/articles/1134
last-modified: 2015-07-28
description: Terrestrial predators have been shown to aggregate along stream margins during periods when the emergence of adult aquatic insects is high. Such aggregation may be especially evident when terrestrial surroundings are relatively unproductive, and there are steep productivity gradients across riparia. In tropical forests, however, the productivity of inland terrestrial habitats may decrease the resource gradient across riparia, thus lessening any tendency of terrestrial predators to aggregate along stream margins. We elucidated the spatio-temporal variability in the distribution of ground-dwelling spiders and terrestrial arthropod prey within the riparia of two forest streams in tropical Hong Kong by sampling arthropods along transects at different distances from the streams during the wet and dry seasons. Environmental variables that may have influenced spider distributions were also measured. The vast majority of ground-dwelling predators along all transects at both sites were spiders. Of the three most abundant spiders captured along stream margins, Heteropoda venatoria (Sparassidae) and Draconarius spp. (Agelenidae) were terrestrially inclined and abundant during both seasons. Only Pardosa sumatrana (Lycosidae) showed some degree of aggregation at the stream banks, indicating a potential reliance on aquatic insect prey. Circumstantial evidence supports this notion, as P. sumatrana was virtually absent during the dry season when aquatic insect emergence was low. In general, forest-stream riparia in Hong Kong did not appear to be feeding hotspots for ground-dwelling predators. The lack of aggregation in ground-dwelling spiders in general may be attributed to the low rates of emergence of aquatic insects from the study streams compared to counterpart systems, as well as the potentially high availability of terrestrial insect prey in the surrounding forest. Heteropoda venatoria, the largest of the three spiders maintained a high biomass (up to 28 mg dry weight/m2) in stream riparia, exceeding the total standing stock of all other spiders by 2–80 times. The biomass and inland distribution of H. venatoria could make it a likely conduit for the stream-to-land transfer of energy.
creator: Elaine Y.L. Yuen
creator: David Dudgeon
uri: https://doi.org/10.7717/peerj.1134
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yuen and Dudgeon

title: Interpreting pathologies in extant and extinct archosaurs using micro-CT
link: https://peerj.com/articles/1130
last-modified: 2015-07-28
description: Palaeopathology offers unique insight to the healing strategies of extinct organisms, permitting questions concerning bone physiology to be answered in greater depth. Unfortunately, most palaeopathological studies are confined to external morphological interpretations due to the destructive nature of traditional methods of study. This limits the degree of reliable diagnosis and interpretation possible. X-ray MicroTomography (micro-CT, XMT) provides a non-destructive means of analysing the internal three-dimensional structure of pathologies in both extant and extinct individuals, at higher resolutions than possible with medical scanners. In this study, we present external and internal descriptions of pathologies in extant and extinct archosaurs using XMT. This work demonstrates that the combination of external/internal diagnosis that X-ray microtomography facilitates is crucial when differentiating between pathological conditions. Furthermore, we show that the use of comparative species, both through direct analysis and from the literature, provides key information for diagnosing between vertebrate groups in the typical pathological conditions and physiological processes. Micro-CT imaging, combined with comparative observations of extant species, provides more detailed and reliable interpretation of palaeopathologies. Micro-CT is an increasingly accessible tool, which will provide key insights for correctly interpreting vertebrate pathologies in the future.
creator: Jennifer Anné
creator: Russell J. Garwood
creator: Tristan Lowe
creator: Philip J. Withers
creator: Phillip L. Manning
uri: https://doi.org/10.7717/peerj.1130
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Anné et al.

title: Mechanistic pathways of mercury removal from the organomercurial lyase active site
link: https://peerj.com/articles/1127
last-modified: 2015-07-28
description: Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H+-assisted cleavage of the Hg–C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg2+ from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we have studied the final steps of the reaction catalyzed by MerB through quantum chemical computations at the combined MP2/CBS//B3PW91/6-31G(d) level of theory. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. The addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal mol−1, determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH3)2 may be removed only after protonation by solvent-provided H3O+. Thiolate addition to the active site (prior to any attack by thiols) leads to pathways where the removal of the first cysteine becomes the rate-determining step, irrespective of whether Cys159 or Cys96 leaves first. Comparisons with the recently computed mechanism of the related enzyme MerA further underline the important role of Asp99 in the energetics of the MerB reaction. Kinetic simulation of the mechanism derived from our computations strongly suggests that in vivo the thiolate-only pathway is operative, and the Asp-assisted pathway (as well as the conversion of intermediates of the thiolate pathway into intermediates of the Cys-assisted pathway) is prevented by steric factors absent from our model and related to the precise geometry of the organomercurial binding-pocket.
creator: Pedro J. Silva
creator: Viviana Rodrigues
uri: https://doi.org/10.7717/peerj.1127
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Silva and Rodrigues

title: Sexual dimorphism and allometry in the sphecophilous rove beetle Triacrus dilatus
link: https://peerj.com/articles/1123
last-modified: 2015-07-28
description: The rove beetle Triacrus dilatus is found in the Atlantic forest of South America and lives in the refuse piles of the paper wasp Agelaia vicina. Adults of T. dilatus are among the largest rove beetles, frequently measuring over 3 cm, and exhibit remarkable variation in body size. To examine sexual dimorphism and allometric relationships we measured the length of the left mandible, ocular distance and elytra. We were interested in determining if there are quantifiable differences between sexes, if there are major and minor forms within each sex and if males exhibit mandibular allometry. For all variables, a t-test was run to determine if there were significant differences between the sexes. Linear regressions were run to examine if there were significant relationships between the different measurements. A heterogeneity of slopes test was used to determine if there were significant differences between males and females. Our results indicated that males had significantly larger mandibles and ocular distances than females, but the overall body length was not significantly different between the sexes. Unlike most insects, both sexes showed positive linear allometric relationships for mandible length and head size (as measured by the ocular distance). We found no evidence of major and minor forms in either sex.
creator: Maxwell H. Marlowe
creator: Cheryl A. Murphy
creator: Stylianos Chatzimanolis
uri: https://doi.org/10.7717/peerj.1123
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Marlowe et al.

title: Diagnostic inertia in dyslipidaemia: results of a preventative programme in Spain
link: https://peerj.com/articles/1109
last-modified: 2015-07-28
description: Others have analysed the relationship between inadequate behaviour by healthcare professionals in the diagnosis of dyslipidaemia (diagnostic inertia) and the history of cardiovascular risk factors. However, since no study has assessed cardiovascular risk scores as associated factors, we carried out a study to quantify diagnostic inertia in dyslipidaemia and to determine if cardiovascular risk scores are associated with this inertia. In the Valencian Community (Spain), a preventive programme (cardiovascular, gynaecologic and vaccination) was started in 2003 inviting persons aged ≥40 years to undergo a health check-up at their health centre. This cross-sectional study examined persons with no known dyslipidaemia seen during the first six months of the programme (n = 16, 905) but whose total cholesterol (TC) was ≥5.17 mmol/L. Diagnostic inertia was defined as lack of follow-up to confirm/discard the dyslipidaemia diagnosis. Other variables included in the analysis were gender, history of cardiovascular risk factors/cardiovascular disease, counselling (diet/exercise), body mass index (BMI), age, blood pressure, fasting blood glucose and lipids. TC was grouped as ≥/<6.20 mmol/L. In patients without cardiovascular disease and <75/≤65 years (n = 15, 778/13, 597), the REGICOR (REgistre GIroní del COr)/SCORE (Systematic COronary Risk Evaluation) cardiovascular risk functions were used to classify risk (high/low). Inertia was quantified and the adjusted odds ratios calculated from multivariate models. In the overall sample, the rate of diagnostic inertia was 52% (95% CI [51.2–52.7]); associated factors were TC ≥ 6.20 mmol/L, high or “not measured” BMI, hypertension, smoking and higher values of fasting blood glucose, systolic blood pressure and TC. In the REGICOR sample, the rate of diagnostic inertia was 51.9% (95% CI [51.1–52.7]); associated factors were REGICOR high and high or “not measured” BMI. In the SCORE sample the rate of diagnostic inertia was 51.7% (95% CI [50.9–52.5]); associated factors were SCORE high and high or “not measured” BMI. Diagnostic inertia existed in over half the patients and was associated with a greater cardiovascular risk.
creator: Antonio Palazón-Bru
creator: Armina Sepehri
creator: Dolores Ramírez-Prado
creator: Felipe Navarro-Cremades
creator: Ernesto Cortés
creator: Mercedes Rizo-Baeza
creator: Vicente Francisco Gil-Guillén
uri: https://doi.org/10.7717/peerj.1109
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Palazón-Bru et al.

title: Using affective knowledge to generate and validate a set of emotion-related, action words
link: https://peerj.com/articles/1100
last-modified: 2015-07-28
description: Emotion concepts are built through situated experience. Abstract word meaning is grounded in this affective knowledge, giving words the potential to evoke emotional feelings and reactions (e.g., Vigliocco et al., 2009). In the present work we explore whether words differ in the extent to which they evoke ‘specific’ emotional knowledge. Using a categorical approach, in which an affective ‘context’ is created, it is possible to assess whether words proportionally activate knowledge relevant to different emotional states (e.g., ‘sadness’, ‘anger’, Stevenson, Mikels & James, 2007a). We argue that this method may be particularly effective when assessing the emotional meaning of action words (e.g., Schacht & Sommer, 2009). In study 1 we use a constrained feature generation task to derive a set of action words that participants associated with six, basic emotional states (see full list in Appendix S1). Generation frequencies were taken to indicate the likelihood that the word would evoke emotional knowledge relevant to the state to which it had been paired. In study 2 a rating task was used to assess the strength of association between the six most frequently generated, or ‘typical’, action words and corresponding emotion labels. Participants were presented with a series of sentences, in which action words (typical and atypical) and labels were paired e.g., “If you are feeling ‘sad’ how likely would you be to act in the following way?” … ‘cry.’ Findings suggest that typical associations were robust. Participants always gave higher ratings to typical vs. atypical action word and label pairings, even when (a) rating direction was manipulated (the label or verb appeared first in the sentence), and (b) the typical behaviours were to be performed by the rater themselves, or others. Our findings suggest that emotion-related action words vary in the extent to which they evoke knowledge relevant for different emotional states. When measuring affective grounding, it may then be appropriate to use categorical ratings in conjunction with unimodal measures, which assess the ‘magnitude’ to which words evoke feelings (e.g., Newcombe et al., 2012). Towards this aim we provide a set of emotion-related action words, accompanied by generation frequency and rating data, which show how strongly each word evokes knowledge relevant to basic emotional states.
creator: Emma Portch
creator: Jelena Havelka
creator: Charity Brown
creator: Roger Giner-Sorolla
uri: https://doi.org/10.7717/peerj.1100
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Portch et al.

title: Klebsiella pneumoniae subsp. pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman
link: https://peerj.com/articles/1061
last-modified: 2015-07-28
description: A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages (phages). A lytic phage, named KLPN1, was isolated on a strain identified as Klebsiella pneumoniae subsp. pneumoniae (capsular type K2, rmpA+). This Siphoviridae phage presents a rosette-like tail tip and exhibits depolymerase activity, as demonstrated by the formation of plaque-surrounding haloes that increased in size over the course of incubation. When screened against a panel of clinical isolates of K. pneumoniae subsp. pneumoniae, phage KLPN1 was shown to infect and lyse capsular type K2 strains, though it did not exhibit depolymerase activity on such hosts. The genome of KLPN1 was determined to be 49,037 bp (50.53 %GC) in length, encompassing 73 predicted ORFs, of which 23 represented genes associated with structure, host recognition, packaging, DNA replication and cell lysis. On the basis of sequence analyses, phages KLPN1 (GenBank: KR262148) and 1513 (a member of the family Siphoviridae, GenBank: KP658157) were found to be two new members of the genus “Kp36likevirus.”
creator: Lesley Hoyles
creator: James Murphy
creator: Horst Neve
creator: Knut J. Heller
creator: Jane F. Turton
creator: Jennifer Mahony
creator: Jeremy D. Sanderson
creator: Barry Hudspith
creator: Glenn R. Gibson
creator: Anne L. McCartney
creator: Douwe van Sinderen
uri: https://doi.org/10.7717/peerj.1061
license: http://www.nationalarchives.gov.uk/doc/open-government-licence/
rights: 

title: Early prediction of language and literacy problems: is 18 months too early?
link: https://peerj.com/articles/1098
last-modified: 2015-07-23
description: There is a lack of stability in language difficulties across early childhood: most late talkers (LTs) resolve their difficulties by pre-school; and a significant number of children who were not LTs subsequently manifest language difficulties. Greater reliability in predicting individual outcomes is needed, which might be achieved by waiting until later in development when language is more stable. At 18 months, productive vocabulary scores on the Oxford Communicative Developmental Inventory were used to classify children as LTs or average talkers (ATs). Thirty matched-pairs of LTs and ATs were followed up at school-age (average age 7 years), when language and literacy outcomes were assessed. For 18 children, intermediate testing at age 4 had classified them as showing typical development (TD) or specific language impairment (SLI). After correcting for multiple comparisons, there were no significant differences between the LTs and ATs on any outcome measure, and the LTs were performing in the average range. However, there were large-sized effects on all outcomes when comparing the TD and SLI groups. LT status on its own is not determinative of language and literacy difficulties. It would therefore not be appropriate to use expressive vocabulary measures alone to screen for language difficulties at 18 months. However, children with language impairment at age 4 are at risk of enduring difficulties.
creator: Fiona J. Duff
creator: Kate Nation
creator: Kim Plunkett
creator: DVM Bishop
uri: https://doi.org/10.7717/peerj.1098
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Duff et al.

title: A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef
link: https://peerj.com/articles/1092
last-modified: 2015-07-23
description: Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes to the conservation value of the archipelago. The lack of evidence for genetic erosion, in combination with our observation that the North Keppel Island population samples collected in 2002 and 2008, respectively, exhibited a pairwise genetic distance of zero, supports previous published work indicating that, following bleaching, Acropora corals in the Keppel Islands predominantly recover from regrowth of small amounts of remaining live tissue in apparently dead coral colonies. This is likely supplemented by recruitment of larvae from genetically similar, less disturbed populations at nearby reefs, particularly following extreme flood events.
creator: Madeleine J.H. van Oppen
creator: Vimoksalehi Lukoschek
creator: Ray Berkelmans
creator: Lesa M. Peplow
creator: Alison M. Jones
uri: https://doi.org/10.7717/peerj.1092
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 van Oppen et al.

title: All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality
link: https://peerj.com/articles/1087
last-modified: 2015-07-23
description: More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about “old” samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the “fresh” specimens.
creator: JinHee Choi
creator: HyeJi Lee
creator: Alexey Shipunov
uri: https://doi.org/10.7717/peerj.1087
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Choi et al.

title: Conducting perception research over the internet: a tutorial review
link: https://peerj.com/articles/1058
last-modified: 2015-07-23
description: This article provides an overview of the recent literature on the use of internet-based testing to address important questions in perception research. Our goal is to provide a starting point for the perception researcher who is keen on assessing this tool for their own research goals. Internet-based testing has several advantages over in-lab research, including the ability to reach a relatively broad set of participants and to quickly and inexpensively collect large amounts of empirical data, via services such as Amazon’s Mechanical Turk or Prolific Academic. In many cases, the quality of online data appears to match that collected in lab research. Generally-speaking, online participants tend to be more representative of the population at large than those recruited for lab based research. There are, though, some important caveats, when it comes to collecting data online. It is obviously much more difficult to control the exact parameters of stimulus presentation (such as display characteristics) with online research. There are also some thorny ethical elements that need to be considered by experimenters. Strengths and weaknesses of the online approach, relative to others, are highlighted, and recommendations made for those researchers who might be thinking about conducting their own studies using this increasingly-popular approach to research in the psychological sciences.
creator: Andy T. Woods
creator: Carlos Velasco
creator: Carmel A. Levitan
creator: Xiaoang Wan
creator: Charles Spence
uri: https://doi.org/10.7717/peerj.1058
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Woods et al.

title: From promise to practice: pairing non-invasive sampling with genomics in conservation
link: https://peerj.com/articles/1106
last-modified: 2015-07-21
description: Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 ng. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.
creator: Michael A. Russello
creator: Matthew D. Waterhouse
creator: Paul D. Etter
creator: Eric A. Johnson
uri: https://doi.org/10.7717/peerj.1106
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Russello et al.

title: A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution
link: https://peerj.com/articles/1114
last-modified: 2015-07-21
description: Overdispersion is a common feature of models of biological data, but researchers often fail to model the excess variation driving the overdispersion, resulting in biased parameter estimates and standard errors. Quantifying and modeling overdispersion when it is present is therefore critical for robust biological inference. One means to account for overdispersion is to add an observation-level random effect (OLRE) to a model, where each data point receives a unique level of a random effect that can absorb the extra-parametric variation in the data. Although some studies have investigated the utility of OLRE to model overdispersion in Poisson count data, studies doing so for Binomial proportion data are scarce. Here I use a simulation approach to investigate the ability of both OLRE models and Beta-Binomial models to recover unbiased parameter estimates in mixed effects models of Binomial data under various degrees of overdispersion. In addition, as ecologists often fit random intercept terms to models when the random effect sample size is low (<5 levels), I investigate the performance of both model types under a range of random effect sample sizes when overdispersion is present. Simulation results revealed that the efficacy of OLRE depends on the process that generated the overdispersion; OLRE failed to cope with overdispersion generated from a Beta-Binomial mixture model, leading to biased slope and intercept estimates, but performed well for overdispersion generated by adding random noise to the linear predictor. Comparison of parameter estimates from an OLRE model with those from its corresponding Beta-Binomial model readily identified when OLRE were performing poorly due to disagreement between effect sizes, and this strategy should be employed whenever OLRE are used for Binomial data to assess their reliability. Beta-Binomial models performed well across all contexts, but showed a tendency to underestimate effect sizes when modelling non-Beta-Binomial data. Finally, both OLRE and Beta-Binomial models performed poorly when models contained <5 levels of the random intercept term, especially for estimating variance components, and this effect appeared independent of total sample size. These results suggest that OLRE are a useful tool for modelling overdispersion in Binomial data, but that they do not perform well in all circumstances and researchers should take care to verify the robustness of parameter estimates of OLRE models.
creator: Xavier A. Harrison
uri: https://doi.org/10.7717/peerj.1114
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Harrison

title: Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus)
link: https://peerj.com/articles/1112
last-modified: 2015-07-21
description: Many decapod crustaceans perform escape tailflips with a neural circuit involving giant interneurons, a specialized fast flexor motor giant (MoG) neuron, populations of larger, less specialized fast flexor motor neurons, and fast extensor motor neurons. These escape-related neurons are well described in crayfish (Reptantia), but not in more basal decapod groups. To clarify the evolution of the escape circuit, I examined the fast flexor and fast extensor motor neurons of white shrimp (Litopenaeus setiferus; Dendrobranchiata) using backfilling. In crayfish, the MoGs in each abdominal ganglion are a bilateral pair of separate neurons. In L. setiferus, the MoGs have massive, possibly syncytial, cell bodies and fused axons. The non-MoG fast flexor motor neurons and fast extensor motor neurons are generally found in similar locations to where they are found in crayfish, but the number of motor neurons in both the flexor and extensor pools is smaller than in crayfish. The loss of fusion in the MoGs and increased number of fast motor neurons in reptantian decapods may be correlated with an increased reliance on non-giant mediated tailflipping.
creator: Zen Faulkes
uri: https://doi.org/10.7717/peerj.1112
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Faulkes

title: Not all jellyfish are equal: isotopic evidence for inter- and intraspecific variation in jellyfish trophic ecology
link: https://peerj.com/articles/1110
last-modified: 2015-07-21
description: Jellyfish are highly topical within studies of pelagic food-webs and there is a growing realisation that their role is more complex than once thought. Efforts being made to include jellyfish within fisheries and ecosystem models are an important step forward, but our present understanding of their underlying trophic ecology can lead to their oversimplification in these models. Gelatinous zooplankton represent a polyphyletic assemblage spanning >2,000 species that inhabit coastal seas to the deep-ocean and employ a wide variety of foraging strategies. Despite this diversity, many contemporary modelling approaches include jellyfish as a single functional group feeding at one or two trophic levels at most. Recent reviews have drawn attention to this issue and highlighted the need for improved communication between biologists and theoreticians if this problem is to be overcome. We used stable isotopes to investigate the trophic ecology of three co-occurring scyphozoan jellyfish species (Aurelia aurita, Cyanea lamarckii and C. capillata) within a temperate, coastal food-web in the NE Atlantic. Using information on individual size, time of year and δ13C and δ15N stable isotope values, we examined: (1) whether all jellyfish could be considered as a single functional group, or showed distinct inter-specific differences in trophic ecology; (2) Were size-based shifts in trophic position, found previously in A. aurita, a common trait across species?; (3) When considered collectively, did the trophic position of three sympatric species remain constant over time? Differences in δ15N (trophic position) were evident between all three species, with size-based and temporal shifts in δ15N apparent in A. aurita and C. capillata. The isotopic niche width for all species combined increased throughout the season, reflecting temporal shifts in trophic position and seasonal succession in these gelatinous species. Taken together, these findings support previous assertions that jellyfish require more robust inclusion in marine fisheries or ecosystem models.
creator: Nicholas E.C. Fleming
creator: Chris Harrod
creator: Jason Newton
creator: Jonathan D.R. Houghton
uri: https://doi.org/10.7717/peerj.1110
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Fleming et al.

title: Linear and nonlinear characteristics of the runoff response to regional climate factors in the Qira River basin, Xinjiang, Northwest China
link: https://peerj.com/articles/1104
last-modified: 2015-07-21
description: The inland river watersheds of arid Northwest China represent an example of how, in recent times, climatic warming has increased the complexity of Earth’s hydrological processes. In the present study, the linear and nonlinear characteristics of the runoff response to temperature and precipitation were investigated in the Qira River basin, located on the northern slope of the Kunlun Mountains. The results showed that average temperature on annual and seasonal scales has displayed a significantly increasing trend, but this has not been reflected in accumulated precipitation and runoff. Using path analysis, a positive link between precipitation and runoff was found both annually and in the summer season. Conversely, it was found that the impact of temperature on runoff has been negative since the 1960s, attributable to higher evaporation and infiltration in the Qira River basin. Over the past 50 years, abrupt changes in annual temperature, precipitation and runoff occurred in 1997, 1987 and 1995, respectively. Combined with analysis using the correlation dimension method, it was found that the temperature, precipitation and runoff, both annually and seasonally, possessed chaotic dynamic characteristics, implying that complex hydro-climatic processes must be introduced into other variables within models to describe the dynamics. In addition, as determined via rescaled range analysis, a consistent annual and seasonal decreasing trend in runoff under increasing temperature and precipitation conditions in the future should be taken into account. This work may provide a theoretical perspective that can be applied to the proper use and management of oasis water resources in the lower reaches of river basins like that of the Qira River.
creator: Jie Xue
creator: Dongwei Gui
uri: https://doi.org/10.7717/peerj.1104
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Xue and Gui

title: Indicators of distress in newly diagnosed breast cancer patients
link: https://peerj.com/articles/1107
last-modified: 2015-07-21
description: Background. The diagnosis, treatment, and long-term management of cancer can present individuals with a multitude of stressors at various points in that trajectory. Psychosocial distress may appear early in the diagnostic process and have negative effects on compliance with treatment and subsequent quality of life.Purpose. The aim of the study was to determine early-phase predictors of distress before any medical treatment.Method. Consistent with the goals of the study, 123 newly diagnosed breast cancer patients (20 to 74 years old) completed multiple indicators of knowledge about breast cancer management and treatment, attitudes toward cancer, social support, coping efficacy, and distress.Results. SEM analysis confirmed the hypothesized model. Age was negatively associated with the patient’s knowledge (β = − 0.22), which, in turn, was positively associated with both attitudes toward breast cancer (β = 0.39) and coping self-efficacy (β = 0.36). Self-efficacy was then directly related to psychological distress (β = − 0.68).Conclusions. These findings establish indicators of distress in patients early in the cancer trajectory. From a practical perspective, our results have implications for screening for distress and for the development of early interventions that may be followed by healthcare professionals to reduce psychological distress.
creator: Andrea Chirico
creator: Fabio Lucidi
creator: Luca Mallia
creator: Massimiliano D’Aiuto
creator: Thomas V. Merluzzi
uri: https://doi.org/10.7717/peerj.1107
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Chirico et al.

title: The majority are not performing home-exercises correctly two weeks after their initial instruction—an assessor-blinded study
link: https://peerj.com/articles/1102
last-modified: 2015-07-21
description: Introduction. Time-under-tension (TUT) reflects time under load during strength training and is a proxy of the total exercise dose during strength training. The purpose of this study was to investigate if young participants are able to reproduce TUT and exercise form after two weeks of unsupervised exercises.Material and Methods. The study was an assessor-blinded intervention study with 29 participants. After an initial instruction, all participants were instructed to perform two weeks of home-based unsupervised shoulder abduction exercises three times per week with an elastic exercise band. The participants were instructed in performing an exercise with a predefined TUT (3 s concentric; 2 s isometric; 3 s eccentric; 2 s break) corresponding to a total of 240 s of TUT during three sets of 10 repetitions. After completing two weeks of unsupervised home exercises, they returned for a follow-up assessment of TUT and exercise form while performing the shoulder abduction exercise. A stretch sensor attached to the elastic band was used to measure TUT at baseline and follow-up. A physiotherapist used a pre-defined clinical observation protocol to determine if participants used the correct exercise form.Results. Fourteen of the 29 participants trained with the instructed TUT at follow-up (predefined target: 240 s ±8%). Thirteen of the 29 participants performed the shoulder abduction exercise with a correct exercise form. Seven of the 29 participants trained with the instructed TUT and exercise form at follow-up.Conclusion. The majority of participants did not use the instructed TUT and exercise form at follow-up after two weeks of unsupervised exercises. These findings emphasize the importance of clear and specific home exercise instructions if participants are to follow the given exercise prescription regarding TUT and exercise form as too many or too few exercise stimuli in relation to the initially prescribed amount of exercise most likely will provide a misinterpretation of the actual effect of any given specific home exercise intervention.
creator: Mathilde Faber
creator: Malene H. Andersen
creator: Claus Sevel
creator: Kristian Thorborg
creator: Thomas Bandholm
creator: Michael Rathleff
uri: https://doi.org/10.7717/peerj.1102
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Faber et al.

title: Age, growth, and natural mortality of yellowfin grouper (Mycteroperca venenosa) from the southeastern United States
link: https://peerj.com/articles/1099
last-modified: 2015-07-21
description: Ages of yellowfin grouper (n = 306) from the southeastern United States coast from 1979–2014 were determined using sectioned sagittal otoliths. Opaque zones were annular, forming January–June (peaking in February–March). Yellowfin grouper ranged in age from 3 to 31 years; the largest fish measured 1,000 mm fork length (FL). Body size relationships for yellowfin grouper were: W = 1.22 × 10−5 FL3.03 (n = 229, r2 = 0.92); TL = 1.06 FL − 14.53 (n = 60, r2 = 0.99); and FL = 0.93 TL + 18.63 (n = 60, r2 = 0.99), where W = whole weight in grams, FL in mm, and TL = total length in mm. The von Bertalanffy growth equation was: Lt = 958 (1 − e−0.11(t+2.94)) (n = 306). The point estimate of natural mortality for yellowfin grouper was M = 0.14, while age-specific estimates of M ranged from 1.59 to 0.17 for ages 1–31.
creator: Michael L. Burton
creator: Jennifer C. Potts
creator: Daniel R. Carr
uri: https://doi.org/10.7717/peerj.1099
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Coping with shorter days: do phenology shifts constrain aphid fitness?
link: https://peerj.com/articles/1103
last-modified: 2015-07-16
description: Climate change can alter the phenology of organisms. It may thus lead seasonal organisms to face different day lengths than in the past, and the fitness consequences of these changes are as yet unclear. To study such effects, we used the pea aphid Acyrthosiphon pisum as a model organism, as it has obligately asexual clones which can be used to study day length effects without eliciting a seasonal response. We recorded life-history traits under short and long days, both with two realistic temperature cycles with means differing by 2 °C. In addition, we measured the population growth of aphids on their host plant Pisum sativum. We show that short days reduce fecundity and the length of the reproductive period of aphids. Nevertheless, this does not translate into differences at the population level because the observed fitness costs only become apparent late in the individual’s life. As expected, warm temperature shortens the development time by 0.7 days/°C, leading to faster generation times. We found no interaction of temperature and day length. We conclude that day length changes cause only relatively mild costs, which may not decelerate the increase in pest status due to climate change.
creator: Jens Joschinski
creator: Thomas Hovestadt
creator: Jochen Krauss
uri: https://doi.org/10.7717/peerj.1103
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Joschinski et al.

title: Marked increase in rat red blood cell membrane protein glycosylation by one-month treatment with a cafeteria diet
link: https://peerj.com/articles/1101
last-modified: 2015-07-16
description: Background and Objectives. Glucose, an aldose, spontaneously reacts with protein amino acids yielding glycosylated proteins. The compounds may reorganize to produce advanced glycosylation products, which regulatory importance is increasingly being recognized. Protein glycosylation is produced without the direct intervention of enzymes and results in the loss of function. Glycosylated plasma albumin, and glycosylated haemoglobin are currently used as index of mean plasma glucose levels, since higher glucose availability results in higher glycosylation rates. In this study we intended to detect the early changes in blood protein glycosylation elicited by an obesogenic diet.Experimental Design. Since albumin is in constant direct contact with plasma glucose, as are the red blood cell (RBC) membranes, we analyzed their degree or glycosylation in female and male rats, either fed a standard diet or subjected to a hyper-energetic self-selected cafeteria diet for 30 days. This model produces a small increase in basal glycaemia and a significant increase in body fat, leaving the animals in the initial stages of development of metabolic syndrome. We also measured the degree of glycosylation of hemoglobin, and the concentration of glucose in contact with this protein, that within the RBC. Glycosylation was measured by colorimetric estimation of the hydroxymethylfurfural liberated from glycosyl residues by incubation with oxalate.Results. Plasma glucose was higher in cafeteria diet and in male rats, both independent effects. However, there were no significant differences induced by sex or diet in either hemoglobin or plasma proteins. Purified RBC membranes showed a marked effect of diet: higher glycosylation in cafeteria rats, which was more marked in females (not in controls). In any case, the number of glycosyl residues per molecule were higher in hemoglobin than in plasma proteins (after correction for molecular weight). The detected levels of glucose in RBC were lower than those of plasma, even when expressed in molal units, and were practically nil in cafeteria-diet fed rats compared with controls; there was no effect of sex.Conclusions. RBC membrane glycosylation is a sensitive indicator of developing metabolic syndrome-related hyperglycemia, more sensitive than the general measurement of plasma or RBC protein glycosylation. The extensive glycosylation of blood proteins does not seem to be markedly affected by sex; and could be hardly justified from an assumedly sustained plasma hyperglycemia. The low levels of glucose found within RBC, especially in rats under the cafeteria diet, could hardly justify the extensive glycosylation of hemoglobin and the lack of differences with controls, which contained sizeable levels of intracellular glucose. Additional studies are needed to study the dynamics of glucose in vivo in the RBC to understand how such extensive protein glycosylation could take place.
creator: Laia Oliva
creator: Cristian Baron
creator: José-Antonio Fernández-López
creator: Xavier Remesar
creator: Marià Alemany
uri: https://doi.org/10.7717/peerj.1101
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Oliva et al.

title: Do the effects of crops on skylark (Alauda arvensis) differ between the field and landscape scales?
link: https://peerj.com/articles/1097
last-modified: 2015-07-16
description: The promotion of biodiversity in agricultural areas involves actions at the landscape scale, and the management of cropping patterns is considered an important means of achieving this goal. However, most of the available knowledge about the impact of crops on biodiversity has been obtained at the field scale, and is generally grouped together under the umbrella term “crop suitability.” Can field-scale knowledge be used to predict the impact on populations across landscapes? We studied the impact of maize and rapeseed on the abundance of skylark (Alauda arvensis). Field-scale studies in Western Europe have reported diverse impacts on habitat selection and demography. We assessed the consistency between field-scale knowledge and landscape-scale observations, using high-resolution databases describing crops and other habitats for the 4 km2 grid scales analyzed in the French Breeding Bird Survey. We used generalized linear models to estimate the impact of each studied crop at the landscape scale. We stratified the squares according to the local and geographical contexts, to ensure that the conclusions drawn were valid in a wide range of contexts. Our results were not consistent with field knowledge for rapeseed, and were consistent for maize only in grassland contexts. However, the effect sizes were much smaller than those of structural landscape features. These results suggest that upscaling from the field scale to the landscape scale leads to an integration of new agronomic and ecological processes, making the objects studied more complex than simple “crop ∗ species” pairs. We conclude that the carrying capacity of agricultural landscapes cannot be deduced from the suitability of their components.
creator: Christophe Sausse
creator: Aude Barbottin
creator: Frédéric Jiguet
creator: Philippe Martin
uri: https://doi.org/10.7717/peerj.1097
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Sausse et al.

title: Pest control of aphids depends on landscape complexity and natural enemy interactions
link: https://peerj.com/articles/1095
last-modified: 2015-07-16
description: Aphids are a major concern in agricultural crops worldwide, and control by natural enemies is an essential component of the ecological intensification of agriculture. Although the complexity of agricultural landscapes is known to influence natural enemies of pests, few studies have measured the degree of pest control by different enemy guilds across gradients in landscape complexity. Here, we use multiple natural-enemy exclosures replicated in 18 fields across a gradient in landscape complexity to investigate (1) the strength of natural pest control across landscapes, measured as the difference between pest pressure in the presence and in the absence of natural enemies; (2) the differential contributions of natural enemy guilds to pest control, and the nature of their interactions across landscapes. We show that natural pest control of aphids increased up to six-fold from simple to complex landscapes. In the absence of pest control, aphid population growth was higher in complex than simple landscapes, but was reduced by natural enemies to similar growth rates across all landscapes. The effects of enemy guilds were landscape-dependent. Particularly in complex landscapes, total pest control was supplied by the combined contribution of flying insects and ground-dwellers. Birds had little overall impact on aphid control. Despite evidence for intraguild predation of flying insects by ground-dwellers and birds, the overall effect of enemy guilds on aphid control was complementary. Understanding pest control services at large spatial scales is critical to increase the success of ecological intensification schemes. Our results suggest that, where aphids are the main pest of concern, interactions between natural enemies are largely complementary and lead to a strongly positive effect of landscape complexity on pest control. Increasing the availability of seminatural habitats in agricultural landscapes may thus benefit not only natural enemies, but also the effectiveness of aphid natural pest control.
creator: Emily A. Martin
creator: Björn Reineking
creator: Bumsuk Seo
creator: Ingolf Steffan-Dewenter
uri: https://doi.org/10.7717/peerj.1095
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Martin et al.

title: Constant illumination reduces circulating melatonin and impairs immune function in the cricket Teleogryllus commodus
link: https://peerj.com/articles/1075
last-modified: 2015-07-16
description: Exposure to constant light has a range of negative effects on behaviour and physiology, including reduced immune function in both vertebrates and invertebrates. It is proposed that the associated suppression of melatonin (a ubiquitous hormone and powerful antioxidant) in response to the presence of light at night could be an underlying mechanistic link driving the changes to immune function. Here, we investigated the relationship between constant illumination, melatonin and immune function, using a model invertebrate species, the Australian black field cricket, Teleogryllus commodus. Crickets were reared under either a 12 h light: 12 h dark regimen or a constant 24 h light regimen. Circulating melatonin concentration and immune function (haemocyte concentration, lytic activity and phenoloxidase (PO) activity) were assessed in individual adult crickets through the analysis of haemolymph. Constant illumination reduced melatonin and had a negative impact on haemocyte concentrations and lytic activity, but its effect on PO activity was less apparent. Our data provide the first evidence, to our knowledge, of a link between exposure to constant illumination and variation in haemocyte concentration in an invertebrate model, while also highlighting the potential complexity of the immune response following exposure to constant illumination. This study provides insight into the possible negative effect of artificial night-time lighting on the physiology of invertebrates, but whether lower and potentially more ecologically relevant levels of light at night produce comparable results, as has been reported in several vertebrate taxa, remains to be tested.
creator: Joanna Durrant
creator: Ellie B. Michaelides
creator: Thusitha Rupasinghe
creator: Dedreia Tull
creator: Mark P. Green
creator: Therésa M. Jones
uri: https://doi.org/10.7717/peerj.1075
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Durrant et al.

title: Photos provide information on age, but not kinship, of Andean bear
link: https://peerj.com/articles/1042
last-modified: 2015-07-16
description: Using photos of captive Andean bears of known age and pedigree, and photos of wild Andean bear cubs <6 months old, we evaluated the degree to which visual information may be used to estimate bears’ ages and assess their kinship. We demonstrate that the ages of Andean bear cubs ≤6 months old may be estimated from their size relative to their mothers with an average error of <0.01 ± 13.2 days (SD; n = 14), and that ages of adults ≥10 years old may be estimated from the proportion of their nose that is pink with an average error of <0.01 ± 3.5 years (n = 41). We also show that similarity among the bears’ natural markings, as perceived by humans, is not associated with pedigree kinship among the bears (R2 < 0.001, N = 1,043, p = 0.499). Thus, researchers may use photos of wild Andean bears to estimate the ages of young cubs and older adults, but not to infer their kinship. Given that camera trap photos are one of the most readily available sources of information on large cryptic mammals, we suggest that similar methods be tested for use in other poorly understood species.
creator: Russell C. Van Horn
creator: Becky Zug
creator: Robyn D. Appleton
creator: Ximena Velez-Liendo
creator: Susanna Paisley
creator: Corrin LaCombe
uri: https://doi.org/10.7717/peerj.1042
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Van Horn et al.

title: Influence of a hyperlipidic diet on the composition of the non-membrane lipid pool of red blood cells of male and female rats
link: https://peerj.com/articles/1083
last-modified: 2015-07-14
description: Background and objectives. Red blood cells (RBC) are continuously exposed to oxidative agents, affecting their membrane lipid function. However, the amount of lipid in RBCs is higher than the lipids of the cell membrane, and includes triacylglycerols, which are no membrane components. We assumed that the extra lipids originated from lipoproteins attached to the cell surface, and we intended to analyse whether the size and composition of this lipid pool were affected by sex or diet.Experimental design. Adult male and female Wistar rats were fed control or cafeteria diets. Packed blood cells and plasma lipids were extracted and analysed for fatty acids by methylation and GC-MS, taking care of not extracting membrane lipids.Results. The absence of ω3-PUFA in RBC extracts (but not in plasma) suggest that the lipids extracted were essentially those in the postulated lipid surface pool and not those in cell membrane. In cells’ extracts, there was a marked depletion of PUFA (and, in general, of insaturation). Fatty acid patterns were similar for all groups studied, with limited effects of sex and no effects of diet in RBC (but not in plasma) fatty acids. Presence of trans fatty acids was small but higher in RBC lipids, and could not be justified by dietary sources.Conclusions. The presence of a small layer of lipid on the RBC surface may limit oxidative damage to the cell outer structures, and help explain its role in the transport of lipophilic compounds. However, there may be other, so far uncovered, additional functions for this lipid pool.
creator: Xavier Remesar
creator: Arantxa Antelo
creator: Clàudia Llivina
creator: Emma Albà
creator: Lourdes Berdié
creator: Silvia Agnelli
creator: Sofía Arriarán
creator: José Antonio Fernández-López
creator: Marià Alemany
uri: https://doi.org/10.7717/peerj.1083
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Remesar et al.

title: Urinary microRNA can be concentrated, dried on membranes and stored at room temperature in vacuum bags
link: https://peerj.com/articles/1082
last-modified: 2015-07-14
description: Urine accumulates traces of changes that occur in the body and can potentially serve as a better biomarker source. Urinary microRNA is a promising class of non-invasive disease biomarkers. However, long-term frozen human urine samples are not a good source for the extraction of urinary microRNA. In this paper, we demonstrate that urinary microRNA can be concentrated, dried on membranes and stored in vacuum bags at room temperature for several months. The amount of total RNA on the membranes after storage at room temperature for three months was unchanged. The levels of miR-16 and miR-21 exhibited no significant differences (P = 0.564, 0.386). This simple and economical method makes the large-scale storage of clinical samples of urinary microRNA or other nucleic acids possible.
creator: Fanshuang Zhang
creator: Xiaoyu Cheng
creator: Yuan Yuan
creator: Jianqiang Wu
creator: Youhe Gao
uri: https://doi.org/10.7717/peerj.1082
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zhang et al.

title: Using signals associated with safety in avoidance learning: computational model of sex differences
link: https://peerj.com/articles/1081
last-modified: 2015-07-14
description: Avoidance behavior involves learning responses that prevent upcoming aversive events; these responses typically extinguish when the aversive events stop materializing. Stimuli that signal safety from aversive events can paradoxically inhibit extinction of avoidance behavior. In animals, males and females process safety signals differently. These differences help explain why women are more likely to be diagnosed with an anxiety disorder and exhibit differences in symptom presentation and course compared to men. In the current study, we extend an existing model of strain differences in avoidance behavior to simulate sex differences in rats. The model successfully replicates data showing that the omission of a signal associated with a period of safety can facilitate extinction in females, but not males, and makes novel predictions that this effect should depend on the duration of the period, the duration of the signal itself, and its occurrence within that period. Non-reinforced responses during the safe period were also found to be important in the expression of these patterns. The model also allowed us to explore underlying mechanisms for the observed sex effects, such as whether safety signals serve as occasion setters for aversive events, to determine why removing them can facilitate extinction of avoidance. The simulation results argue against this account, and instead suggest the signal may serve as a conditioned reinforcer of avoidance behavior.
creator: Milen L. Radell
creator: Kevin D. Beck
creator: Kevin C.H. Pang
creator: Catherine E. Myers
uri: https://doi.org/10.7717/peerj.1081
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris
link: https://peerj.com/articles/1079
last-modified: 2015-07-14
description: Methylation has previously been associated with allele specific expression in ants. Recently, we found methylation is important in worker reproduction in the bumblebee Bombus terrestris. Here we searched for allele specific expression in twelve genes associated with worker reproduction in bees. We found allele specific expression in Ecdysone 20 monooxygenase and IMP-L2-like. Although we were unable to confirm a genetic or epigenetic cause for this allele specific expression, the expression patterns of the two genes match those predicted for imprinted genes.
creator: Harindra E. Amarasinghe
creator: Bradley J. Toghill
creator: Despina Nathanael
creator: Eamonn B. Mallon
uri: https://doi.org/10.7717/peerj.1079
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Amarasinghe et al.

title: Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox
link: https://peerj.com/articles/1078
last-modified: 2015-07-14
description: Aim. In recent years, connectivity studies using neuroimaging data have increased the understanding of the organization of large-scale structural and functional brain networks. However, data analysis is time consuming as rigorous procedures must be assured, from structuring data and pre-processing to modality specific data procedures. Until now, no single toolbox was able to perform such investigations on truly multimodal image data from beginning to end, including the combination of different connectivity analyses. Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach to brain connectivity.Materials and Methods. The MIBCA toolbox is a fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). It was developed in MATLAB environment and pipelines well-known neuroimaging softwares such as Freesurfer, SPM, FSL, and Diffusion Toolkit. It further implements routines for the construction of structural, functional and effective or combined connectivity matrices, as well as, routines for the extraction and calculation of imaging and graph-theory metrics, the latter using also functions from the Brain Connectivity Toolbox. Finally, the toolbox performs group statistical analysis and enables data visualization in the form of matrices, 3D brain graphs and connectograms. In this paper the MIBCA toolbox is presented by illustrating its capabilities using multimodal image data from a group of 35 healthy subjects (19–73 years old) with volumetric T1-weighted, diffusion tensor imaging, and resting state fMRI data, and 10 subjets with 18F-Altanserin PET data also.Results. It was observed both a high inter-hemispheric symmetry and an intra-hemispheric modularity associated with structural data, whilst functional data presented lower inter-hemispheric symmetry and a high inter-hemispheric modularity. Furthermore, when testing for differences between two subgroups (<40 and >40 years old adults) we observed a significant reduction in the volume and thickness, and an increase in the mean diffusivity of most of the subcortical/cortical regions.Conclusion. While bridging the gap between the high numbers of packages and tools widely available for the neuroimaging community in one toolbox, MIBCA also offers different possibilities for combining, analysing and visualising data in novel ways, enabling a better understanding of the human brain.
creator: Andre Santos Ribeiro
creator: Luis Miguel Lacerda
creator: Hugo Alexandre Ferreira
uri: https://doi.org/10.7717/peerj.1078
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Ribeiro et al.

title: Retrodeformation and muscular reconstruction of ornithomimosaurian dinosaur crania
link: https://peerj.com/articles/1093
last-modified: 2015-07-09
description: Ornithomimosaur dinosaurs evolved lightweight, edentulous skulls that possessed keratinous rhamphothecae. Understanding the anatomy of these taxa allows for a greater understanding of “ostrich-mimic” dinosaurs and character change during theropod dinosaur evolution. However, taphonomic processes during fossilisation often distort fossil remains. Retrodeformation offers a means by which to recover a hypothesis of the original anatomy of the specimen, and 3D scanning technologies present a way to constrain and document the retrodeformation process. Using computed tomography (CT) scan data, specimen specific retrodeformations were performed on three-dimensionally preserved but taphonomically distorted skulls of the deinocheirid Garudimimus brevipesBarsbold, 1981 and the ornithomimids Struthiomimus altusLambe, 1902 and Ornithomimus edmontonicusSternberg, 1933. This allowed for a reconstruction of the adductor musculature, which was then mapped onto the crania, from which muscle mechanical advantage and bite forces were calculated pre- and post-retrodeformation. The extent of the rhamphotheca was varied in each taxon to represent morphologies found within modern Aves. Well constrained retrodeformation allows for increased confidence in anatomical and functional analysis of fossil specimens and offers an opportunity to more fully understand the soft tissue anatomy of extinct taxa.
creator: Andrew R. Cuff
creator: Emily J. Rayfield
uri: https://doi.org/10.7717/peerj.1093
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Cuff and Rayfield

title: Two new species of fossil Leggadina (Rodentia: Muridae) from Northwestern Queensland
link: https://peerj.com/articles/1088
last-modified: 2015-07-09
description: Only three species of fossil murine have been described to date in Australia even though they are often found in fossil deposits and can be highly useful in understanding environmental change over time. Until now the genus Leggadina, a group of short-tailed mice that is particularly well adapted to an arid environment, was only known from two extant species: L. forresti and L. lakedownensis. Here two new fossil species of the genus are described from sites in northwestern Queensland. Leggadina gregoriensis sp. nov. comes from the Early Pleistocene Rackham’s Roost Site in the Riversleigh World Heritage Area and Leggadina macrodonta sp. nov. is from the Plio-Pleistocene Site 5C at Floraville Station. The evolution of the genus Leggadina and the lineage’s response to palaeoecological factors is considered. Taphonomy of the two fossil deposits is examined and shows marked differences in both faunal composition of the assemblages and preservation. Description of L. gregoriensis and L. macrodonta extends the known temporal range of the Leggadina lineage by over 2 million years.
creator: Ada J. Klinkhamer
creator: Henk Godthelp
uri: https://doi.org/10.7717/peerj.1088
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Klinkhamer and Godthelp

title: Rearing the scuttle fly Megaselia scalaris (Diptera: Phoridae) on industrial compounds: implications on size and lifespan
link: https://peerj.com/articles/1085
last-modified: 2015-07-09
description: Megaselia scalaris (Loew, 1866) (Diptera, phoridae) is a cosmopolitan fly species used in forensic science, and has been developed as a laboratory model species. They feed on decaying corpses as well as a wide variety of organic matter, and previous studies have even found them feeding on liquid paint or shoe polish, suggesting the possibility that they could breakdown industrial compounds. To test this possibility, we fed M. scalaris on a variety of industrially obtained materials and found that it was unable to complete its life cycle, dying at the larval stage, with the majority of compounds tested. However, when fed on modeling clay, a substrate that contains starch and inedible compounds, it was able to complete its life cycle. On this diet we observed increased larval development time, decreased pupal development time and a shortened adult life span. Additionally, pupae and adult flies were smaller than control flies. Contrary to previous reports, we find no evidence that M. scalaris is able to survive on modern formulations of liquid paint.
creator: Anna Alcaine-Colet
creator: Karl R. Wotton
creator: Eva Jimenez-Guri
uri: https://doi.org/10.7717/peerj.1085
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Alcaine-Colet et al.

title: The seasonal reproduction number of dengue fever: impacts of climate on transmission
link: https://peerj.com/articles/1069
last-modified: 2015-07-09
description: Background. Dengue fever is a mosquito-borne viral disease and a regular epidemic in Thailand. The peak of the dengue epidemic period is around June to August during the rainy season. It is believed that climate is an important factor for dengue transmission.Method. A mathematical model for vector–host infectious disease was used to calculate the impacts of climate to the transmission of dengue virus. In this study, the data of climate and dengue fever cases were derived from Chiang Mai during 2004–2014, Thailand. The value of seasonal reproduction number was calculated to evaluate the potential, severity and persistence of dengue infection.Results. The mosquito population was increasing exponentially from the start of the rainy season in early May and reached its the peak in late June. The simulations suggest that the greatest potential for the dengue transmission occurs when the temperature is 28.9 °C. The seasonal reproduction numbers were larger than one from late March to end of August and reaching the peak in June. The highest incidences occurred in August due to the delay of transmission humans-mosquito-humans. Increasing mean temperature by 1 °C, the number of incidences increases 28.1%. However, a very high or very low temperature reduces the number of infection.Discussion and Conclusion. The results show that the dengue infection depends on the seasonal variation of the climate. The rainfall provides places for the mosquitoes to lay eggs and develop to the adult stage. The temperature plays an important role in the life cycle and behavior of the mosquitoes. A very high or very low temperature reduces the risk of the dengue infection.
creator: Sittisede Polwiang
uri: https://doi.org/10.7717/peerj.1069
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Polwiang

title: Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana
link: https://peerj.com/articles/1033
last-modified: 2015-07-09
description: Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus), additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs’ preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana’s agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana’s still large and contiguous cheetah population.
creator: Hanlie E.K. Winterbach
creator: Christiaan W. Winterbach
creator: Lorraine K. Boast
creator: Rebecca Klein
creator: Michael J. Somers
uri: https://doi.org/10.7717/peerj.1033
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Winterbach et al.

title: Competitive interactions between a nonmycorrhizal invasive plant, Alliaria petiolata, and a suite of mycorrhizal grassland, old field, and forest species
link: https://peerj.com/articles/1090
last-modified: 2015-07-07
description: The widespread invasion of the nonmycorrhizal biennial plant, Alliaria petiolata in North America is hypothesized to be facilitated by the production of novel biochemical weapons that suppress the growth of mycorrhizal fungi. As a result, A. petiolata is expected to be a strong competitor against plant species that rely on mycorrhizal fungi for nutrient uptake services. If A. petiolata is also a strong competitor for soil resources, it should deplete nutrients to levels lower than can be tolerated by weaker competitors. Because the negative effect of losing the fungal symbiont for mycorrhizal plants is greatest when nutrients are low, the ability of A. petiolata to simultaneously suppress fungi and efficiently take up soil nutrients should further strengthen its competitive ability against mycorrhizal plants. To test this hypothesis, we grew 27 mycorrhizal tree, forb and grass species that are representative of invaded habitats in the absence or presence of competition with A. petiolata in soils that had previously been experimentally planted with the invader or left as a control. A history of A. petiolata in soil reduced plant available forms of nitrogen by >50% and phosphorus by 17% relative to control soil. Average mycorrhizal colonization of competitor species was reduced by >50% in A. petiolata history versus control soil. Contrary to expectations, competition between A. petiolata and other species was stronger in control than history soil. The invader suppressed the biomass of 70% of competitor species in control soil but only 26% of species in history soil. In addition, A. petiolata biomass was reduced by 56% in history versus control soil, whereas the average biomass of competitor species was reduced by 15%. Thus, our results suggest that the negative effect of nutrient depletion on A. petiolata was stronger than the negative effect of suppressing mycorrhizal colonization on competitor species. These findings indicate that the inhibitory potential of A. petiolata on competitor species via mycorrhizal suppression is not enhanced under nutrient limitation.
creator: Gary T. Poon
creator: Hafiz Maherali
uri: https://doi.org/10.7717/peerj.1090
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Poon and Maherali

title: Taxonomic identification of Lower Pleistocene fossil hominins based on distal humeral diaphyseal cross-sectional shape
link: https://peerj.com/articles/1084
last-modified: 2015-07-07
description: The coexistence of multiple hominin species during the Lower Pleistocene has long presented a challenge for taxonomic attribution of isolated postcrania. Although fossil humeri are well-suited for studies of hominin postcranial variation due to their relative abundance, humeral articular morphology has thus far been of limited value for differentiating Paranthropus from Homo. On the other hand, distal humeral diaphyseal shape has been used to justify such generic distinctions at Swartkrans. The potential utility of humeral diaphyseal shape merits larger-scale quantitative analysis, particularly as it permits the inclusion of fragmentary specimens lacking articular morphology. This study analyzes shape variation of the distal humeral diaphysis among fossil hominins (c. 2-1 Ma) to test the hypothesis that specimens can be divided into distinct morphotypes. Coordinate landmarks were placed on 3D laser scans to quantify cross-sectional shape at a standardized location of the humeral diaphysis (proximal to the olecranon fossa) for a variety of fossil hominins and extant hominids. The fossil sample includes specimens attributed to species based on associated craniodental remains. Mantel tests of matrix correlation were used to assess hypotheses about morphometric relationships among the fossils by comparing empirically-derived Procrustes distance matrices to hypothetical model matrices. Diaphyseal shape variation is consistent with the hypothesis of three distinct morphotypes (Paranthropus, Homo erectus, non-erectus early Homo) in both eastern and southern Africa during the observed time period. Specimens attributed to non-erectus early Homo are unique among hominids with respect to the degree of relative anteroposterior flattening, while H. erectus humeri exhibit morphology more similar to that of modern humans. In both geographic regions, Paranthropus is characterized by a morphology that is intermediate with respect to those morphological features that differentiate the two forms of early Homo. This study demonstrates the utility of the humeral diaphysis for taxonomic identification of isolated postcranial remains and further documents a high degree of postcranial diversity in early Homo.
creator: Michael R. Lague
uri: https://doi.org/10.7717/peerj.1084
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Lague

title: Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs
link: https://peerj.com/articles/1077
last-modified: 2015-07-07
description: The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems.
creator: JHR Burns
creator: D Delparte
creator: RD Gates
creator: M Takabayashi
uri: https://doi.org/10.7717/peerj.1077
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Burns et al.

title: Neurodevelopmental problems and extremes in BMI
link: https://peerj.com/articles/1024
last-modified: 2015-07-07
description: Background. Over the last few decades, an increasing number of studies have suggested a connection between neurodevelopmental problems (NDPs) and body mass index (BMI). Attention deficit/hyperactivity disorder (ADHD) and autism spectrum disorders (ASD) both seem to carry an increased risk for developing extreme BMI. However, the results are inconsistent, and there have been only a few studies of the general population of children.Aims. We had three aims with the present study: (1) to define the prevalence of extreme (low or high) BMI in the group of children with ADHD and/or ASDs compared to the group of children without these NDPs; (2) to analyze whether extreme BMI is associated with the subdomains within the diagnostic categories of ADHD or ASD; and (3) to investigate the contribution of genetic and environmental factors to BMI in boys and girls at ages 9 and 12.Method. Parents of 9- or 12-year-old twins (n = 12,496) were interviewed using the Autism—Tics, ADHD and other Comorbidities (A-TAC) inventory as part of the Child and Adolescent Twin Study in Sweden (CATSS). Univariate and multivariate generalized estimated equation models were used to analyze associations between extremes in BMI and NDPs.Results. ADHD screen-positive cases followed BMI distributions similar to those of children without ADHD or ASD. Significant association was found between ADHD and BMI only among 12-year-old girls, where the inattention subdomain of ADHD was significantly associated with the high extreme BMI. ASD scores were associated with both the low and the high extremes of BMI. Compared to children without ADHD or ASD, the prevalence of ASD screen-positive cases was three times greater in the high extreme BMI group and double as much in the low extreme BMI group. Stereotyped and repetitive behaviors were significantly associated with high extreme BMIs.Conclusion. Children with ASD, with or without coexisting ADHD, are more prone to have low or high extreme BMIs than children without ADHD or ASD.
creator: Nóra Kerekes
creator: Armin Tajnia
creator: Paul Lichtenstein
creator: Sebastian Lundström
creator: Henrik Anckarsäter
creator: Thomas Nilsson
creator: Maria Råstam
uri: https://doi.org/10.7717/peerj.1024
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kerekes et al.

title: MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data
link: https://peerj.com/articles/993
last-modified: 2015-07-07
description: As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the advance of next-generation sequencing techniques, it is now possible to qualitatively and quantitatively assess all taxa (features) in a microbial community. A set of taxa with presence/absence or their different abundances could potentially be used as taxonomical biomarkers for identification of the corresponding microbial community’s phenotype. Though there exist some bioinformatics methods for metagenomic biomarker discovery, current methods are not robust, accurate and fast enough at selection of non-redundant biomarkers for prediction of microbial community’s phenotype. In this study, we have proposed a novel method, MetaBoot, that combines the techniques of mRMR (minimal redundancy maximal relevance) and bootstrapping, for discover of non-redundant biomarkers for microbial communities through mining of metagenomic data. MetaBoot has been tested and compared with other methods on well-designed simulated datasets considering normal and gamma distribution as well as publicly available metagenomic datasets. Results have shown that MetaBoot was robust across datasets of varied complexity and taxonomical distribution patterns and could also select discriminative biomarkers with quite high accuracy and biological consistency. Thus, MetaBoot is suitable for robustly and accurately discover taxonomical biomarkers for different microbial communities.
creator: Xiaojun Wang
creator: Xiaoquan Su
creator: Xinping Cui
creator: Kang Ning
uri: https://doi.org/10.7717/peerj.993
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Wang et al.

title: Mice that gorged during dietary restriction increased foraging related behaviors and differed in their macronutrient preference when released from restriction
link: https://peerj.com/articles/1091
last-modified: 2015-07-02
description: Caloric restriction (CR) can trigger gorging behavior. We examined macronutrient choice and behavior in mice that gorged during restriction compared to restricted non-gorgers and controls. Fifty MF1 male mice were restricted to 75% of ad-libitum food intake (FI), while ten controls were fed ad-lib. Body mass (BM) and FI were measured two and 24-h after food inclusion over 14-days. ‘Gorging’ mice were defined as those which ate over 25% of their daily FI in 2-h. The top 11 gorgers and the lowest 9 gorgers, along with 10 controls, had their behavior analysed during restriction, and were then provided with an unrestricted food choice, consisting of three diets that were high in fat, protein or carbohydrate. During restriction gorgers ate on average 51% of their daily FI in the 2-h following food introduction while the non-gorgers ate only 16%. Gorgers lost significantly more BM than non-gorgers possibly due to an increased physical activity linked to anticipation of daily food provision. Controls and non-gorgers spent most of their time sleeping. After restriction, both gorgers and non-gorgers were hyperphagic until their lost weight was regained. All 3 groups favoured high fat food. Gorgers and non-gorgers had a significantly greater high carbohydrate diet intake than controls, and gorgers also had a significantly greater high protein diet intake than non-gorgers and controls. On unrestricted food, they did not continue to gorge, although they still had a significantly greater 2-h FI than the other groups. Elevated protein intake may play an important role in the recovery of the lost lean tissue of gorgers after restriction.
creator: Catherine Hambly
creator: John R. Speakman
uri: https://doi.org/10.7717/peerj.1091
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hambly and Speakman

title: Powerline noise elimination in biomedical signals via blind source separation and wavelet analysis
link: https://peerj.com/articles/1086
last-modified: 2015-07-02
description: The distortion of biomedical signals by powerline noise from recording biomedical devices has the potential to reduce the quality and convolute the interpretations of the data. Usually, powerline noise in biomedical recordings are extinguished via band-stop filters. However, due to the instability of biomedical signals, the distribution of signals filtered out may not be centered at 50/60 Hz. As a result, self-correction methods are needed to optimize the performance of these filters. Since powerline noise is additive in nature, it is intuitive to model powerline noise in a raw recording and subtract it from the raw data in order to obtain a relatively clean signal. This paper proposes a method that utilizes this approach by decomposing the recorded signal and extracting powerline noise via blind source separation and wavelet analysis. The performance of this algorithm was compared with that of a 4th order band-stop Butterworth filter, empirical mode decomposition, independent component analysis and, a combination of empirical mode decomposition with independent component analysis. The proposed method was able to expel sinusoidal signals within powerline noise frequency range with higher fidelity in comparison with the mentioned techniques, especially at low signal-to-noise ratio.
creator: Samuel Akwei-Sekyere
uri: https://doi.org/10.7717/peerj.1086
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Akwei-Sekyere

title: A pilot study to investigate if New Zealand men with prostate cancer benefit from a Mediterranean-style diet
link: https://peerj.com/articles/1080
last-modified: 2015-07-02
description: Carcinoma of the prostate is the most commonly diagnosed malignancy and the third leading cause of mortality in New Zealand men, making it a significant health issue in this country. Global distribution patterns suggest that diet and lifestyle factors may be linked to the development and progression of this cancer. Twenty men with diagnosed prostate cancer adhered to a Mediterranean diet, with specific adaptations, for three months. Prostate-specific antigen, C-reactive protein and DNA damage were evaluated at baseline and after three months of following the diet. Dietary data were collated from diet diaries and an adaptation of a validated Mediterranean diet questionnaire. A significant reduction in DNA damage compared to baseline was apparent, with particular benefit noted for overall adherence to the diet (p = 0.013), increased intake of folate (p = 0.023), vitamin C (p = 0.007), legumes (p = 0.004) and green tea (p = 0.002). Higher intakes of red meat and dairy products were inversely associated with DNA damage (p = 0.003 and p = 0.008 respectively). The results from this small feasibility study suggest that a high-antioxidant diet, modelled on Mediterranean traditions, may be of benefit for men with prostate cancer. Protection against DNA damage appears to be associated with the diet implemented, ostensibly due to reduction in reactive oxidant species. These findings warrant further exploration in a longer trial, with a larger cohort.
creator: Sharon Erdrich
creator: Karen S. Bishop
creator: Nishi Karunasinghe
creator: Dug Yeo Han
creator: Lynnette R. Ferguson
uri: https://doi.org/10.7717/peerj.1080
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Erdrich et al.

title: Community- and population-level changes in diatom size structure in a subarctic lake over the last two centuries
link: https://peerj.com/articles/1074
last-modified: 2015-07-02
description: Climate change over the last two centuries has been associated with significant shifts in diatom community structure in lakes from the high arctic to temperate latitudes. To test the hypotheses that recent climate warming selects for species of smaller size within communities and a decrease in the average size of species within populations, we quantified the size of individual diatom valves from 10 depths in a sediment core covering the last ∼200 years from a pristine subarctic lake. Over the last ∼200 years, changes in the relative abundance of species of different average size and changes in the average valve size of populations of species contribute equally to the changes in community size structure, but are often opposite in sign, compensating for one another and moderating temporal changes in community size structure. In the surface sediments that correspond to the recent decades when air temperatures have warmed, the mean size of valves in the diatom community has significantly decreased due to an increase in the proportion of smaller-sized planktonic diatom species.
creator: Elizabeth A. Kerrigan
creator: Andrew J. Irwin
creator: Zoe V. Finkel
uri: https://doi.org/10.7717/peerj.1074
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Kerrigan et al.

title: Comparing cestode infections and their consequences for host fitness in two sexual branchiopods: alien Artemia franciscana and native A. salina from syntopic-populations
link: https://peerj.com/articles/1073
last-modified: 2015-07-02
description: The American brine shrimp Artemia franciscana is invasive in the Mediterranean region where it has displaced native species (the sexual A. salina, and the clonal A. parthenogenetica) from many salt pond complexes. Artemia populations are parasitized by numerous avian cestodes whose effects have been studied in native species. We present a study from the Ebro Delta salterns (NE Spain), in a salt pond where both A. franciscana and native A. salina populations coexist, providing a unique opportunity to compare the parasite loads of the two sexual species in syntopy. The native species had consistently higher infection parameters, largely because the dominant cestode in A. salina adults and juveniles (Flamingolepis liguloides) was much rarer in A. franciscana. The most abundant cestodes in the alien species were Eurycestus avoceti (in adults) and Flamingolepis flamingo (in juveniles). The abundance of E. avoceti and F. liguloides was higher in the A. franciscana population syntopic with A. salina than in a population sampled at the same time in another pond where the native brine shrimp was absent, possibly because the native shrimp provides a better reservoir for parasite circulation. Infection by cestodes caused red colouration in adult and juvenile A. salina, and also led to castration in a high proportion of adult females. Both these effects were significantly stronger in the native host than in A. franciscana with the same parasite loads. However, for the first time, significant castration effects (for E. avoceti and F. liguloides) and colour change (for six cestode species) were observed in infected A. franciscana. Avian cestodes are likely to help A. franciscana outcompete native species. At the same time, they are likely to reduce the production of A. franciscana cysts in areas where they are harvested commercially.
creator: Stella Redón
creator: Francisco Amat
creator: Marta I. Sánchez
creator: Andy J. Green
uri: https://doi.org/10.7717/peerj.1073
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Redón et al.

title: Three dimensional reconstructions of Nummulites tests reveal complex chamber shapes
link: https://peerj.com/articles/1072
last-modified: 2015-07-02
description: Larger benthic foraminifera (LBF) are important and prolific carbonate producers both in modern and ancient shallow tropical seas. During the Paleogene the genus Nummulites was particularly abundant with a global distribution, leading it to be frequently used in biostratigraphy. However, their evolution is poorly understood as classification is Europe-centered and mostly based on external characters and equatorial thin sections. New occurrences from regions outside the northern Tethys which poorly fit in thus reference frame, show that a more rigid framework for the classification of Nummulites is needed. Here we apply micro computed-tomographical scanning, a tool that recently has become available, to visualise 3D chamber shape of Nummulites djokdjokartae and compare these to traditional morphometrical characters. We find that despite the regular shape in equatorial and axial thin section the irregular 3D chamber shape is not predicted by these sections. We argue that 3D reconstructions of Nummulites tests will be a great aid in improving our understanding of lineages within the genus Nummulites, and to elucidate its evolutionary and biogeographical history.
creator: Willem Renema
creator: Laura Cotton
uri: https://doi.org/10.7717/peerj.1072
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Renema and Cotton

title: Depressive symptoms and other risk factors predicting suicide in middle-aged men: a prospective cohort study among Korean Vietnam War veterans
link: https://peerj.com/articles/1071
last-modified: 2015-07-02
description: Background. Few studies have prospectively examined whether depressive symptoms and other risk factors are associated with a higher risk of suicide death in individuals other than high-risk populations such as psychiatric patients and individuals with self-harm histories. The purpose of the study is to prospectively examine whether depressive symptoms assessed by the Beck Depression Inventory (BDI) are associated with greater risk of suicide death and whether depressive symptoms and other risk factors are independent predictors of suicide in general-risk populations. Another aim is to evaluate the sensitivity of the BDI for predicting suicide death.Methods. 10,238 Korean Vietnam War veterans (mean age: 56.3 years) who participated in two surveys in 2001 were followed up for suicide mortality over 7.5 years.Results. 41 men died by suicide. Severely depressed participants had a higher adjusted hazard ratio (aHR = 3.4; 95% CI [1.5–7.7]) of suicide than non-to-moderately depressed ones. Higher suicide risk was associated with more severe depressive symptoms (p for trend = 0.009). After adjustment for depressive symptoms and other factors, very poor health, low education, and past drinking were associated with higher suicide risk, while good health, body mass index, and marital status were not associated with suicide. The sensitivity at the cut-off score of 31 for detecting suicide was higher during the earlier 3.5 years of the follow-up (75%; 95% CI [50–90]) than during the latter 4 years (60%; 95% CI [41–76]).Conclusions. Depressive symptoms are a strong independent predictor and very poor health, low education, and drinking status may be independent predictors of future suicide. The BDI may have acceptable diagnostic properties as a risk assessment tool for identifying people with depression and suicidal potential among middle-aged men.
creator: Sang-Wook Yi
creator: Jae-Seok Hong
uri: https://doi.org/10.7717/peerj.1071
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Yi and Hong

title: Identification of the underlying factor structure of the Derriford Appearance Scale 24
link: https://peerj.com/articles/1070
last-modified: 2015-07-02
description: Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale.Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24.Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker’s Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body.Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale.
creator: Timothy P. Moss
creator: Victoria Lawson
creator: Paul White
uri: https://doi.org/10.7717/peerj.1070
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Moss et al.

title: Metabolic syndrome in hospitalized patients with chronic obstructive pulmonary disease
link: https://peerj.com/articles/1068
last-modified: 2015-07-02
description: Introduction. The metabolic syndrome (MS) affects 21–53% of patients with chronic obstructive pulmonary disease (COPD) with a higher prevalence in the early stages of COPD, with results being highly variable between studies. MS may also affect natural course of COPD—number of exacerbations, quality of life and lung function.Aim. To examine the prevalence of MS and its correlation with comorbidities and COPD characteristics in patients with COPD admitted for exacerbation.Material and methods. 152 patients with COPD admitted for exacerbation were studied for presence of MS. All of them were also assessed for vitamin D status and diabetes mellitus type 2 (DM). Data were gathered for smoking status and exacerbations during the last year. All patients completed CAT (COPD assessment test) and mMRC (Modified Medical Research Council Dyspnea scale) questionnaires and underwent spirometry. Duration of current hospital stay was recorded.Results. 25% of patients have MS. 23.1% of the male and 29.5% of the female patients have MS (p > 0.05). The prevalence of MS in this study is significantly lower when compared to a national representative study (44.6% in subjects over 45 years). 69.1% of all patients and 97.4% from MS patients have arterial hypertension. The presence of MS is associated with significantly worse cough and sleep (1st and 7th CAT questions; p = 0.002 and p = 0.001 respectively) and higher total CAT score (p = 0.017). Average BMI is 27.31. None of the patients have MS and BMI <25. There is a correlation between the presence of MS and DM (p = 0.008) and with the number of exacerbations in the last year (p = 0.015). There is no correlation between the presence of MS and the pulmonary function.Conclusion. This study among hospitalized COPD patients finds comparable but relatively low prevalence of MS (25%) compared to previously published data (21–53%) and lower prevalence compared to general population (44.6%). MS may impact quality of life and the number of exacerbations of COPD. Having in mind that MS is more common in the early stages and decreases with COPD progression, the COPD patients admitted for exacerbation may be considered as having advanced COPD.
creator: Evgeni Mekov
creator: Yanina Slavova
creator: Adelina Tsakova
creator: Marianka Genova
creator: Dimitar Kostadinov
creator: Delcho Minchev
creator: Dora Marinova
uri: https://doi.org/10.7717/peerj.1068
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Mekov et al.

title: Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber
link: https://peerj.com/articles/1067
last-modified: 2015-07-02
description: Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers), to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR) spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene) resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.
creator: Leyla J. Seyfullah
creator: Eva-Maria Sadowski
creator: Alexander R. Schmidt
uri: https://doi.org/10.7717/peerj.1067
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Seyfullah et al.

title: Factor structure of the happiness-increasing strategies scales (H-ISS): activities and coping strategies in relation to positive and negative affect
link: https://peerj.com/articles/1059
last-modified: 2015-07-02
description: Background. Previous research (Tkach & Lyubomirsky, 2006) shows that there are eight general happiness-increasing strategies: social affiliation, partying, mental control, goal pursuit, passive leisure, active leisure, religion, and direct attempts. The present study investigates the factor structure of the happiness-increasing strategies scales (H-ISS) and their relationship to positive and negative affect.Method. The present study used participants’ (N = 1,050 and age mean = 34.21 sd = 12.73) responses to the H-ISS in structural equation modeling analyses. Affect was measured using the Positive Affect Negative Affect Schedule.Results. After small modifications we obtained a good model that contains the original eight factors/scales. Moreover, we found that women tend to use social affiliation, mental control, passive leisure, religion, and direct attempts more than men, while men preferred to engage in partying and clubbing more than women. The H-ISS explained significantly the variance of positive affect (R2 = .41) and the variance of negative affect (R2 = .27).Conclusions. Our study is an addition to previous research showing that the factor structure of the happiness-increasing strategies is valid and reliable. However, due to the model fitting issues that arise in the present study, we give some suggestions for improving the instrument.
creator: Ali Al Nima
creator: Danilo Garcia
uri: https://doi.org/10.7717/peerj.1059
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Al Nima and Garcia

title: Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae
link: https://peerj.com/articles/1041
last-modified: 2015-07-02
description: Accurate identification of protein–protein interactions (PPI) is the key step in understanding proteins’ biological functions, which are typically context-dependent. Many existing PPI predictors rely on aggregated features from protein sequences, however only a few methods exploit local information about specific residue contacts. In this work we present a two-stage machine learning approach for prediction of protein–protein interactions. We start with the carefully filtered data on protein complexes available for Saccharomyces cerevisiae in the Protein Data Bank (PDB) database. First, we build linear descriptions of interacting and non-interacting sequence segment pairs based on their inter-residue distances. Secondly, we train machine learning classifiers to predict binary segment interactions for any two short sequence fragments. The final prediction of the protein–protein interaction is done using the 2D matrix representation of all-against-all possible interacting sequence segments of both analysed proteins. The level-I predictor achieves 0.88 AUC for micro-scale, i.e., residue-level prediction. The level-II predictor improves the results further by a more complex learning paradigm. We perform 30-fold macro-scale, i.e., protein-level cross-validation experiment. The level-II predictor using PSIPRED-predicted secondary structure reaches 0.70 precision, 0.68 recall, and 0.70 AUC, whereas other popular methods provide results below 0.6 threshold (recall, precision, AUC). Our results demonstrate that multi-scale sequence features aggregation procedure is able to improve the machine learning results by more than 10% as compared to other sequence representations. Prepared datasets and source code for our experimental pipeline are freely available for download from: http://zubekj.github.io/mlppi/ (open source Python implementation, OS independent).
creator: Julian Zubek
creator: Marcin Tatjewski
creator: Adam Boniecki
creator: Maciej Mnich
creator: Subhadip Basu
creator: Dariusz Plewczynski
uri: https://doi.org/10.7717/peerj.1041
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Zubek et al.

title: Divergent thermal specialisation of two South African entomopathogenic nematodes
link: https://peerj.com/articles/1023
last-modified: 2015-07-02
description: Thermal physiology of entomopathogenic nematodes (EPN) is a critical aspect of field performance and fitness. Thermal limits for survival and activity, and the ability of these limits to adjust (i.e., show phenotypic flexibility) depending on recent thermal history, are generally poorly established, especially for non-model nematode species. Here we report the acute thermal limits for survival, and the thermal acclimation-related plasticity thereof for two key endemic South African EPN species, Steinernema yirgalemense and Heterorhabditis zealandica. Results including LT50 indicate S. yirgalemense (LT50 = 40.8 ± 0.3 °C) has greater high temperature tolerance than H. zealandica (LT50 = 36.7 ± 0.2 °C), but S. yirgalemense (LT50 = −2.4 ± 0 °C) has poorer low temperature tolerance in comparison to H. zealandica (LT50 = −9.7 ± 0.3 °C), suggesting these two EPN species occupy divergent thermal niches to one another.Acclimation had both negative and positive effects on temperature stress survival of both species, although the overall variation meant that many of these effects were non-significant. There was no indication of a consistent loss of plasticity with improved basal thermal tolerance for either species at upper lethal temperatures. At lower temperatures measured for H. zealandica, the 5 °C acclimation lowered survival until below −12.5 °C, where after it increased survival. Such results indicate that the thermal niche breadth of EPN species can differ significantly depending on recent thermal conditions, and should be characterized across a broad range of species to understand the evolution of thermal limits to performance and survival in this group.
creator: Matthew P. Hill
creator: Antoinette P. Malan
creator: John S. Terblanche
uri: https://doi.org/10.7717/peerj.1023
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Hill et al.

title: Lack of association of vitamin D receptor BsmI gene polymorphism with bone mineral density in Spanish postmenopausal women
link: https://peerj.com/articles/953
last-modified: 2015-07-02
description: Osteoporosis is a polygenic disorder that is determined by the effects of several genes, each with relatively modest effects on bone mass. The aim of this study was to determine whether the vitamin D receptor single nucleotide polymorphism BsmI is associated with bone mineral density (BMD) in Spanish postmenopausal women. A total of 210 unrelated healthy postmenopausal women aged 60 ± 8 years were genotyped using TaqMan® SNP Genotyping Assays. Lumbar and femoral BMD were determined by dual-energy X-ray absorptiometry (DEXA). Daily calcium and vitamin D intake were determined by a food questionnaire. No differences were found in the femoral neck, trochanter, Ward’s Triangle, L2, L3, L4, L2-L4, or between the femoral neck and total hip BMD after further adjustment for potential confounding factors (P > 0.05) (age, BMI, years since menopause and daily calcium intake). The BsmI polymorphism in the VDR gene was not associated with BMD in Spanish postmenopausal women.
creator: Jose M. Moran
creator: Maria Pedrera-Canal
creator: Francisco J. Rodriguez-Velasco
creator: Vicente Vera
creator: Jesus M. Lavado-Garcia
creator: Pilar Fernandez
creator: Juan D. Pedrera-Zamorano
uri: https://doi.org/10.7717/peerj.953
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2015 Moran et al.