title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1093
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Exploring the socio-economic and environmental components of infectious diseases using multivariate geovisualization: West Nile Virus
link: https://peerj.com/articles/9577
last-modified: 2020-07-27
description: BackgroundThis study postulates that underlying environmental conditions and a susceptible population’s socio-economic status should be explored simultaneously to adequately understand a vector borne disease infection risk. Here we focus on West Nile Virus (WNV), a mosquito borne pathogen, as a case study for spatial data visualization of environmental characteristics of a vector’s habitat alongside human demographic composition for understanding potential public health risks of infectious disease. Multiple efforts have attempted to predict WNV environmental risk, while others have documented factors related to human vulnerability to the disease. However, analytical modeling that combines the two is difficult due to the number of potential explanatory variables, varying spatial resolutions of available data, and differing research questions that drove the initial data collection. We propose that the use of geovisualization may provide a glimpse into the large number of potential variables influencing the disease and help distill them into a smaller number that might reveal hidden and unknown patterns. This geovisual look at the data might then guide development of analytical models that can combine environmental and socio-economic data.MethodsGeovisualization was used to integrate an environmental model of the disease vector’s habitat alongside human risk factors derived from socio-economic variables. County level WNV incidence rates from California, USA, were used to define a geographically constrained study area where environmental and socio-economic data were extracted from 1,133 census tracts. A previously developed mosquito habitat model that was significantly related to WNV infected dead birds was used to describe the environmental components of the study area. Self-organizing maps found 49 clusters, each of which contained census tracts that were more similar to each other in terms of WNV environmental and socio-economic data. Parallel coordinate plots permitted visualization of each cluster’s data, uncovering patterns that allowed final census tract mapping exposing complex spatial patterns contained within the clusters.ResultsOur results suggest that simultaneously visualizing environmental and socio-economic data supports a fuller understanding of the underlying spatial processes for risks to vector-borne disease. Unexpected patterns were revealed in our study that would be useful for developing future multilevel analytical models. For example, when the cluster that contained census tracts with the highest median age was examined, it was determined that those census tracts only contained moderate mosquito habitat risk. Likewise, the cluster that contained census tracts with the highest mosquito habitat risk had populations with moderate median age. Finally, the cluster that contained census tracts with the highest WNV human incidence rates had unexpectedly low mosquito habitat risk.
creator: Abhishek K. Kala
creator: Samuel F. Atkinson
creator: Chetan Tiwari
uri: https://doi.org/10.7717/peerj.9577
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Kala et al.

title: Viable bacterial communities on hospital window components in patient rooms
link: https://peerj.com/articles/9580
last-modified: 2020-07-27
description: Previous studies demonstrate an exchange of bacteria between hospital room surfaces and patients, and a reduction in survival of microorganisms in dust inside buildings from sunlight exposure. While the transmission of microorganisms between humans and their local environment is a continuous exchange which generally does not raise cause for alarm, in a hospital setting with immunocompromised patients, these building-source microbial reservoirs may pose a risk. Window glass is often neglected during hospital disinfection protocols, and the microbial communities found there have not previously been examined. This pilot study examined whether living bacterial communities, and specifically the pathogens Methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile (C. difficile), were present on window components of exterior-facing windows inside patient rooms, and whether relative light exposure (direct or indirect) was associated with changes in bacterial communities on those hospital surfaces. Environmental samples were collected from 30 patient rooms in a single ward at Oregon Health & Science University (OHSU) in Portland, Oregon, USA. Sampling locations within each room included the window glass surface, both sides of the window curtain, two surfaces of the window frame, and the air return grille. Viable bacterial abundances were quantified using qPCR, and community composition was assessed using Illumina MiSeq sequencing of the 16S rRNA gene V3/V4 region. Viable bacteria occupied all sampled locations, but was not associated with a specific hospital surface or relative sunlight exposure. Bacterial communities were similar between window glass and the rest of the room, but had significantly lower Shannon Diversity, theorized to be related to low nutrient density and resistance to bacterial attachment of glass compared to other surface materials. Rooms with windows that were facing west demonstrated a higher abundance of viable bacteria than those facing other directions, potentially because at the time of sampling (morning) west-facing rooms had not yet been exposed to sunlight that day. Viable C. difficile was not detected and viable MRSA was detected at very low abundance. Bacterial abundance was negatively correlated with distance from the central staff area containing the break room and nursing station. In the present study, it can be assumed that there is more human traffic in the center of the ward, and is likely responsible for the observed gradient of total abundance in rooms along the ward, as healthcare staff both deposit more bacteria during activities and affect microbial transit indoors. Overall, hospital window components possess similar microbial communities to other previously identified room locations known to act as reservoirs for microbial agents of hospital-associated infections.
creator: Patrick F. Horve
creator: Leslie G. Dietz
creator: Suzanne L. Ishaq
creator: Jeff Kline
creator: Mark Fretz
creator: Kevin G. Van Den Wymelenberg
uri: https://doi.org/10.7717/peerj.9580
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Horve et al.

title: Food sources of energy and nutrients among Canadian adults following a gluten-free diet
link: https://peerj.com/articles/9590
last-modified: 2020-07-27
description: BackgroundThe gluten-free diet (GFD) involves the elimination of wheat and related grains. Wheat is a key fortification vehicle for nutrients such as iron and B vitamins. While there is growing evidence of low nutrients intake and poor diet quality amongst people following long-term GFD, few studies have used a dietary pattern approach to analyse top food sources of nutrients in today’s complex food environment. Thus, the purpose of this study was to identify food sources of energy and nutrients from previously collected diet records of adults following a GFD.MethodsThree, 3-day food records were collected from 35 participants in a lifestyle intervention study (n = 240 records). All food items were categorised according to the Bureau of Nutritional Sciences Food Group Codes. Percentages of total dietary intakes from food groups were ranked.ResultsMean intakes of dietary fibre, calcium and iron (females) were lower than recommended, with half the sample consuming below the recommended proportion of energy as carbohydrate. Meat, poultry and fish were the top source of energy (19.5%) in the diet. Gluten-free (GF) grain products were the top source of carbohydrate, fibre and iron and second greatest source of energy. Amongst grains, breakfast/hot cereals, yeast breads, and mixed grain dishes were the greatest nutrient contributors, despite most commercial cereals and breads (65%) being unenriched. Legumes were not frequently consumed.ConclusionsGF grains were the top food source of carbohydrate, fibre and iron, despite few brands being enriched or fortified. It is a challenge to assess and monitor nutrient intakes on GFD due to the lack of nutrient composition data for B vitamins and minerals (other than iron). Dietary planning guidance for the appropriate replacement of nutrients provided by wheat is warranted.
creator: Jennifer A. Jamieson
creator: Anna Neufeld
uri: https://doi.org/10.7717/peerj.9590
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Jamieson and Neufeld

title: An analysis of the perceived causes leading to task-failure in resistance-exercises
link: https://peerj.com/articles/9611
last-modified: 2020-07-27
description: BackgroundWhile reaching task-failure in resistance-exercises is a topic that attracts scientific and applied interest, the underlying perceived reasons leading to task-failure remain underexplored. Here, we examined the reasons subjects attribute to task-failure as they performed resistance-exercises using different loads.MethodsTwenty-two resistance-trained subjects (11-females) completed one Repetition-Maximum (RM) tests in the barbell squat and bench-press. Then, in the next two counterbalanced sessions, subjects performed two sets to task-failure in both exercises, using either 70% or 83% of 1RM. Approximately 30 seconds after set-completion, subjects verbally reported the reasons they perceived to have caused them to reach task-failure. Their answers were recorded, transcribed, and thematically analyzed. The differences between the frequencies of the identified categories were then tested using a mixed logistic regression model.ResultsThe most commonly reported reason was muscle fatigue (54%, p < 0.001), mostly of the target muscles involved in each exercise. However, remote muscles involved to a lesser extent in each exercise were also reported. Approximately half of the remaining reasons included general fatigue (26%), pain (12%), cardiovascular strain (11%), and negative affect (10%), with the latter three reported more often in the squat (p = 0.022).ConclusionsIn contrast to our expectations, task-failure was perceived to be caused by a range of limiting factors other than fatigue of the target muscles. It now remains to be established whether different perceived limiting factors of resistance-exercises lead to different adaptations, such as muscular strength and hypertrophy.
creator: Aviv Emanuel
creator: Isaac Isur Rozen Smukas
creator: Israel Halperin
uri: https://doi.org/10.7717/peerj.9611
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Emanuel et al.

title: Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam
link: https://peerj.com/articles/9612
last-modified: 2020-07-27
description: This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.
creator: Tong Jia
creator: Tingyan Guo
creator: Baofeng Chai
uri: https://doi.org/10.7717/peerj.9612
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Jia et al.

title: How “dirty” is the Dark Triad? Dark character profiles, swearing, and sociosexuality
link: https://peerj.com/articles/9620
last-modified: 2020-07-27
description: Malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy) are associated to emotional frigidity, antagonism, immoral strategic thinking, betrayal, exploitation, and sexual promiscuity. Despite the fact that character is a complex adaptive system, almost every study has solely investigated the linear association between malevolent character and attitudes towards both swearing and sociosexual orientation (i.e., behavior, attitude, and desire regarding promiscuous sexual behavior). In contrast, the aim in this set of studies was to evaluate these associations in relation to specific profiles of malevolent character (i.e., the Dark Cube). In two studies participants responded to the Dark Triad Dirty Dozen, the Taboo Words’ Offensiveness and Usage Inventories (i.e., attitudes towards 30 swear words’ level of offensiveness and usage) (Study 1: N1 = 1,000) and the Sociosexual Orientation Inventory Revised (Study 2: N2 = 309). Participants were clustered according to all eight possible combinations based on their dark trait scores (M/m = high/low Machiavellianism; N/n = high/low narcissism; P/p = high/low psychopathy). The results of this nonlinear approach suggested that the frequent usage, not level of offensiveness, of swear words was associated to Machiavellianism and narcissism. In other words, individuals with high levels in these traits might swear and are verbally offensive often, because they do not see swearing as offensive (cf. with the attitude-behavior-cognition-hypothesis of taboo words; Rosenberg, Sikström & Garcia, 2017). Moreover, promiscuous sociosexual attitude and desire were related to each dark trait only when the other two were low. Additionally, promiscuous sociosexual behavior was not associated to these malevolent character traits. That is, individuals high in the dark traits are willing to and have the desire to engage in sexual relations without closeness, commitment, and other indicators of emotional bonding. However, they do not report high levels of previous sexual experience, relationships, and infidelity. Hence, they approve and desire for it, but they are not actually doing it. The use of person-centered and non-linear methods, such as the Dark Character Cube, seem helpful in the advancement of a coherent theory of a biopsychosocial model of dark character.
creator: Danilo Garcia
uri: https://doi.org/10.7717/peerj.9620
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Garcia

title: Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy
link: https://peerj.com/articles/9621
last-modified: 2020-07-27
description: We aimed to identify prognostic signature based on autophagy-related genes (ARGs) for breast cancer patients. The datasets of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to construct multiple-ARG risk signature. In total, 32 ARGs were identified as differentially expressed between tumors and adjacent normal tissues based on TCGA. Six ARGs (IFNG, TP63, PPP1R15A, PTK6, EIF4EBP1 and NKX2-3) with non-zero coefficient were selected from the 32 ARGs using LASSO regression. The 6-ARG signature divided patients into high-and low-risk group. Survival analysis indicated that low-risk group had longer survival time than high-risk group. We further validated the 6-ARG signature using dataset from GEO and found similar results. We analyzed the associations between ARGs and breast cancer survival in TCGA and nine GEO datasets, and obtained 170 ARGs with significant associations. EIF4EBP1, FOS and FAS were the top three ARGs with highest numbers of significant associations. EIF4EBP1 may be a key ARG which had a higher expression level in patients with more malignant molecular subtypes and higher grade breast cancer. In conclusion, our 6-ARG signature was of significance in predicting of overall survival of patients with breast cancer. EIF4EBP1 may be a key ARG associated with breast cancer survival.
creator: Shanliang Zhong
creator: Huanwen Chen
creator: Sujin Yang
creator: Jifeng Feng
creator: Siying Zhou
uri: https://doi.org/10.7717/peerj.9621
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Zhong et al.

title: Auditory processing in the zebra finch midbrain: single unit responses and effect of rearing experience
link: https://peerj.com/articles/9363
last-modified: 2020-07-24
description: In birds the auditory system plays a key role in providing the sensory input used to discriminate between conspecific and heterospecific vocal signals. In those species that are known to learn their vocalizations, for example, songbirds, it is generally considered that this ability arises and is manifest in the forebrain, although there is no a priori reason why brainstem components of the auditory system could not also play an important part. To test this assumption, we used groups of normal reared and cross-fostered zebra finches that had previously been shown in behavioural experiments to reduce their preference for conspecific songs subsequent to cross fostering experience with Bengalese finches, a related species with a distinctly different song. The question we asked, therefore, is whether this experiential change also changes the bias in favour of conspecific song displayed by auditory midbrain units of normally raised zebra finches. By recording the responses of single units in MLd to a variety of zebra finch and Bengalese finch songs in both normally reared and cross-fostered zebra finches, we provide a positive answer to this question. That is, the difference in response to conspecific and heterospecific songs seen in normal reared zebra finches is reduced following cross-fostering. In birds the virtual absence of mammalian-like cortical projections upon auditory brainstem nuclei argues against the interpretation that MLd units change, as observed in the present experiments, as a result of top-down influences on sensory processing. Instead, it appears that MLd units can be influenced significantly by sensory inputs arising directly from a change in auditory experience during development.
creator: Priscilla Logerot
creator: Paul F. Smith
creator: Martin Wild
creator: M. Fabiana Kubke
uri: https://doi.org/10.7717/peerj.9363
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Logerot et al.

title: The effects of humic substances on DNA isolation from soils
link: https://peerj.com/articles/9378
last-modified: 2020-07-24
description: BackgroundHumic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions.MethodsThe research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV–Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms.ResultsBased on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.
creator: Ewa Wnuk
creator: Adam Waśko
creator: Anna Walkiewicz
creator: Piotr Bartmiński
creator: Romualda Bejger
creator: Lilla Mielnik
creator: Andrzej Bieganowski
uri: https://doi.org/10.7717/peerj.9378
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Wnuk et al.

title: Effectiveness of non-lethal predator deterrents to reduce livestock losses to leopard attacks within a multiple-use landscape of the Himalayan region
link: https://peerj.com/articles/9544
last-modified: 2020-07-24
description: Lethal measures are widely adopted by local communities and governments to manage human-wildlife conflicts. Such measures lead to large scale decline of carnivore populations globally with trophic cascades on ecosystems and questionable impacts on human-wildlife conflicts. Mitigating human-carnivore conflicts through non-lethal measures will protect endangered predators and secure livelihoods. However, information on the effectiveness of such measures are extremely limited and hence cannot be applied in developing scientific evidence. Further to develop human-carnivore coexistence models, it is important for local community members, biologists and wildlife managers to actively participate in conservation programs. We evaluated the response of a non-lethal visual deterrent (i.e. fox lights) to deter leopard attacks on livestock within a multiple-use landscape of western Himalaya through community engagement. We monitored 16 experimental sites and 17 control sites within 27 villages and recorded data on livestock depredation by leopards between April 2018 to April 2019. A multivariate analysis was conducted to determine the influence of landscape predictors and animal husbandry practices on livestock depredation by leopards within the vicinity of human settlements. We found that visual deterrents discouraged common leopards to predate on livestock (cows and goats). We also demonstrated that community based conservation initiatives are successful in mitigating human-carnivore conflicts within large semi-natural landscapes. We suggest developing site specific coexistence strategies and adopting non-lethal measures to safeguard carnivores, livestock and humans within shared landscapes.
creator: Dipanjan Naha
creator: Pooja Chaudhary
creator: Gaurav Sonker
creator: Sambandam Sathyakumar
uri: https://doi.org/10.7717/peerj.9544
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Naha et al.