title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1623 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Ecosystem functional response across precipitation extremes in a sagebrush steppe link: https://peerj.com/articles/4485 last-modified: 2018-03-13 description: BackgroundPrecipitation is predicted to become more variable in the western United States, meaning years of above and below average precipitation will become more common. Periods of extreme precipitation are major drivers of interannual variability in ecosystem functioning in water limited communities, but how ecosystems respond to these extremes over the long-term may shift with precipitation means and variances. Long-term changes in ecosystem functional response could reflect compensatory changes in species composition or species reaching physiological thresholds at extreme precipitation levels.MethodsWe conducted a five year precipitation manipulation experiment in a sagebrush steppe ecosystem in Idaho, United States. We used drought and irrigation treatments (approximately 50% decrease/increase) to investigate whether ecosystem functional response remains consistent under sustained high or low precipitation. We recorded data on aboveground net primary productivity (ANPP), species abundance, and soil moisture. We fit a generalized linear mixed effects model to determine if the relationship between ANPP and soil moisture differed among treatments. We used nonmetric multidimensional scaling to quantify community composition over the five years.ResultsEcosystem functional response, defined as the relationship between soil moisture and ANPP, was similar among irrigation and control treatments, but the drought treatment had a greater slope than the control treatment. However, all estimates for the effect of soil moisture on ANPP overlapped zero, indicating the relationship is weak and uncertain regardless of treatment. There was also large spatial variation in ANPP within-years, which contributes to the uncertainty of the soil moisture effect. Plant community composition was remarkably stable over the course of the experiment and did not differ among treatments.DiscussionDespite some evidence that ecosystem functional response became more sensitive under sustained drought conditions, the response of ANPP to soil moisture was consistently weak and community composition was stable. The similarity of ecosystem functional responses across treatments was not related to compensatory shifts at the plant community level, but instead may reflect the insensitivity of the dominant species to soil moisture. These species may be successful precisely because they have evolved life history strategies that buffer them against precipitation variability. creator: Andrew T. Tredennick creator: Andrew R. Kleinhesselink creator: J. Bret Taylor creator: Peter B. Adler uri: https://doi.org/10.7717/peerj.4485 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tredennick et al. title: An overview on the interplay between nutraceuticals and gut microbiota link: https://peerj.com/articles/4465 last-modified: 2018-03-13 description: BackgroundNowadays, growing attention was being given to the alternative ways to prevent or treat diseases. Nutraceuticals are used increasingly for this purpose. Many of these are being used as alternative therapy. Classic therapy with synthetic drugs, although very effective, has many side effects. The term “nutraceuticals” refers to the link between the nutritional and pharmaceutical domains. Also, lately, many studies have been done to investigate the role of microbiota in maintaining health. There is the hypothesis that some of the health benefits of nutraceuticals are due to their ability to change the microbiota. The aim of this review was to emphasize the link between the most commonly used nutraceuticals, the microbiota and the health benefits.MethodsWe selected the articles in PubMed, published up to July 2017, that provided information about most used nutraceuticals, microbiota and health benefits. In this review, we incorporate evidence from various types of studies, including observational, in vitro and in vivo, clinical studies or animal experiments.ResultsThe results demonstrate that many nutraceuticals change the composition of microbiota and can interfere with health status of the patients.DiscussionThere is evidence which sustains the importance of nutraceuticals in people’s health through microbiota but further studies are needed to complete the assessment of nutraceuticals in health benefit as a consequence of microbiota’s changing. creator: Adrian Catinean creator: Maria Adriana Neag creator: Dana Maria Muntean creator: Ioana Corina Bocsan creator: Anca Dana Buzoianu uri: https://doi.org/10.7717/peerj.4465 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Catinean et al. title: Establishment and quality evaluation of a glioma biobank in Beijing Tiantan Hospital link: https://peerj.com/articles/4450 last-modified: 2018-03-13 description: BackgroundWe established a glioma biobank at Beijing Tiantan Hospital in November, 2010. Specialized residents have been trained to collect, store and manage the biobank in accordance with standard operating procedures.MethodsOne hundred samples were selected to evaluate the quality of glioma samples stored in the liquid nitrogen tank during different periods (from 2011 to 2015) by morphological examination, RNA integrity determination, DNA integrity determination and housekeeping gene expression determination.ResultsThe majority of samples (95%) had high RNA quality for further analysis with RIN ≥6. Quality of DNA of all samples were stable without significant degradation.ConclusionStorage conditions of our biobank are suitable for long-term (at least five years) sample preservation with high molecular quality. creator: Fanhong Kong creator: Wenli Zhang creator: Lin Qiao creator: Qi Li creator: Haowen Li creator: Jingli Cao creator: Wenyan He creator: Chengya Dong creator: Yanjiao He creator: Lu He creator: Li Liu creator: Weilun Fu creator: Lijun Liu creator: Zirui Li creator: Yajie Wang uri: https://doi.org/10.7717/peerj.4450 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kong et al. title: Spatial–temporal trend for mother-to-child transmission of HIV up to infancy and during pre-Option B+ in western Kenya, 2007–13 link: https://peerj.com/articles/4427 last-modified: 2018-03-13 description: IntroductionUsing spatial–temporal analyses to understand coverage and trends in elimination of mother-to-child transmission of HIV (e-MTCT) efforts may be helpful in ensuring timely services are delivered to the right place. We present spatial–temporal analysis of seven years of HIV early infant diagnosis (EID) data collected from 12 districts in western Kenya from January 2007 to November 2013, during pre-Option B+ use.MethodsWe included in the analysis infants up to one year old. We performed trend analysis using extended Cochran–Mantel–Haenszel stratified test and logistic regression models to examine trends and associations of infant HIV status at first diagnosis with: early diagnosis (<8 weeks after birth), age at specimen collection, infant ever having breastfed, use of single dose nevirapine, and maternal antiretroviral therapy status. We examined these covariates and fitted spatial and spatial–temporal semiparametric Poisson regression models to explain HIV-infection rates using R-integrated nested Laplace approximation package. We calculated new infections per 100,000 live births and used Quantum GIS to map fitted MTCT estimates for each district in Nyanza region.ResultsMedian age was two months, interquartile range 1.5–5.8 months. Unadjusted pooled positive rate was 11.8% in the seven-years period and declined from 19.7% in 2007 to 7.0% in 2013, p < 0.01. Uptake of testing ≤8 weeks after birth was under 50% in 2007 and increased to 64.1% by 2013, p < 0.01. By 2013, the overall standardized MTCT rate was 447 infections per 100,000 live births. Based on Bayesian deviance information criterion comparisons, the spatial–temporal model with maternal and infant covariates was best in explaining geographical variation in MTCT.DiscussionImproved EID uptake and reduced MTCT rates are indicators of progress towards e-MTCT. Cojoined analysis of time and covariates in a spatial context provides a robust approach for explaining differences in programmatic impact over time.ConclusionDuring this pre-Option B+ period, the prevention of mother to child transmission program in this region has not achieved e-MTCT target of ≤50 infections per 100,000 live births. Geographical disparities in program achievements may signify gaps in spatial distribution of e-MTCT efforts and could indicate areas needing further resources and interventions. creator: Anthony Waruru creator: Thomas N.O. Achia creator: Hellen Muttai creator: Lucy Ng’ang’a creator: Emily Zielinski-Gutierrez creator: Boniface Ochanda creator: Abraham Katana creator: Peter W. Young creator: James L. Tobias creator: Peter Juma creator: Kevin M. De Cock creator: Thorkild Tylleskär uri: https://doi.org/10.7717/peerj.4427 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Waruru et al. title: Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA link: https://peerj.com/articles/4315 last-modified: 2018-03-13 description: The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides. creator: I Nyoman Giri Putra creator: Yuliana Fitri Syamsuni creator: Beginer Subhan creator: Made Pharmawati creator: Hawis Madduppa uri: https://doi.org/10.7717/peerj.4315 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Putra et al. title: Repetitive low intensity magnetic field stimulation in a neuronal cell line: a metabolomics study link: https://peerj.com/articles/4501 last-modified: 2018-03-12 description: Low intensity repetitive magnetic stimulation of neural tissue modulates neuronal excitability and has promising therapeutic potential in the treatment of neurological disorders. However, the underpinning cellular and biochemical mechanisms remain poorly understood. This study investigates the behavioural effects of low intensity repetitive magnetic stimulation (LI-rMS) at a cellular and biochemical level. We delivered LI-rMS (10 mT) at 1 Hz and 10 Hz to B50 rat neuroblastoma cells in vitro for 10 minutes and measured levels of selected metabolites immediately after stimulation. LI-rMS at both frequencies depleted selected tricarboxylic acid (TCA) cycle metabolites without affecting the main energy supplies. Furthermore, LI-rMS effects were frequency-specific with 1 Hz stimulation having stronger effects than 10 Hz. The observed depletion of metabolites suggested that higher spontaneous activity may have led to an increase in GABA release. Although the absence of organised neural circuits and other cellular contributors (e.g., excitatory neurons and glia) in the B50 cell line limits the degree to which our results can be extrapolated to the human brain, the changes we describe provide novel insights into how LI-rMS modulates neural tissue. creator: Ivan Hong creator: Andrew Garrett creator: Garth Maker creator: Ian Mullaney creator: Jennifer Rodger creator: Sarah J. Etherington uri: https://doi.org/10.7717/peerj.4501 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hong et al. title: Prognostic value of new-onset right bundle-branch block in acute myocardial infarction patients: a systematic review and meta-analysis link: https://peerj.com/articles/4497 last-modified: 2018-03-12 description: BackgroundPatients with acute myocardial infarction (AMI) and bundle-branch block have poor prognoses. The new European Society of Cardiology guideline suggests a primary percutaneous coronary intervention strategy when persistent ischemic symptoms occur in patients with persistent ischemic symptoms and right bundle-branch block (RBBB), but the level of evidence is not high. In fact, the presence of RBBB may lead to the misdiagnosis of transmural ischemia and mask the early diagnosis of ST-elevation myocardial infarction. Moreover, new-onset RBBB is occasionally caused by AMI. Our study aims to investigate the prognostic value of new-onset RBBB in AMI.Methods and ResultsWe conducted a meta-analysis of studies to evaluate the prognostic value of RBBB in AMI patients. Of 914 primary records, five studies and 874 MI patients were included for meta-analysis. Compared with previous RBBB, AMI patients with new-onset RBBB had a higher risk of long-term mortality (RR, 1.66, 95% CI [1.31–2.09], I2 = 0.0%, p = 0.000, n = 2), ventricular arrhythmia (RR, 4.86, 95% CI [2.10–11.27], I2 = 0.0%, p = 0.000, n = 3), and cardiogenic shock (RR, 2.76, 95% CI [1.66–4.59], I2 = 0.0%, p = 0.000, n = 3), but a lower risk of heart failure (RR, 0.66, 95% CI [0.52–0.85], I2 = 2.50%, p = 0.001, n = 4). Compared with AMI patients with new-onset permanent RBBB, patients with new-onset transient RBBB had a lower risk of short-term mortality (RR, 0.20, 95% CI [0.11–0.37], I2 = 44.1%, p = 0.000, n = 4).ConclusionNew-onset RBBB is likely to increase long-term mortality, ventricular arrhythmia, and cardiogenic shock, but not heart failure in AMI patients. AMI patients with new-onset transient RBBB have a lower risk of short-term mortality than those with new-onset permanent RBBB. Revascularization therapies should be considered when persistent ischemic symptoms occur in patients with RBBB, especially new-onset RBBB. creator: Juntao Wang creator: Hongxing Luo creator: Chunling Kong creator: Shujuan Dong creator: Jingchao Li creator: Haijia Yu creator: Yingjie Chu uri: https://doi.org/10.7717/peerj.4497 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al. title: Chloropid flies (Diptera, Chloropidae) associated with pitcher plants in North America link: https://peerj.com/articles/4491 last-modified: 2018-03-12 description: We review the taxonomy and ecology of Chloropidae (Diptera) associated with pitcher plants (Sarraceniaceae) in North America. Tricimba wheeleri Mlynarek sp.n. is described from the pitchers of Sarracenia alata Alph.Wood and S. leucophylla Raf. in the southeastern United States (Alabama, Mississippi). Aphanotrigonum darlingtoniae (Jones) associated with Darlingtonia californica Torr. in northern California is redescribed, including the first description of male genitalic characters. A lectotype is designated for A. darlingtoniae. Published records of other species of Tricimba Lioy in pitcher plants in North America are considered accidental or facultative occurrences; published records of Aphanotrigonum Duda as pitcher plant associates in eastern North America are probably errors in identification. creator: Julia J. Mlynarek creator: Terry A. Wheeler uri: https://doi.org/10.7717/peerj.4491 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mlynarek and Wheeler title: Clinical impact of albumin in advanced head and neck cancer patients with free flap reconstruction—a retrospective study link: https://peerj.com/articles/4490 last-modified: 2018-03-12 description: BackgroundPoor nutritional status among patients with advanced stage head and neck squamous cell carcinoma (HNSCC) is common. Albumin is a common indicator of nutritional status and has been shown to be a predictor of oncological outcomes and perioperative morbidity. This study aims to determine the prognostic value of the serum albumin level among patients with advanced HNSCC undergoing surgery with simultaneous free flap reconstruction.Methods A total of 233 patients with advanced head and neck cancer undergoing tumor resection and immediate microvascular free flap reconstruction in a tertiary referral center were enrolled retrospectively between January 2009 and December 2011. Statistical analyses including Pearson’s chi-squared test were used to determine whether there was a significant difference between each selected clinical factors and postoperative major wound infection. Multiple regression analysis was performed to reveal the relationship between postoperative major wound infection and clinical factors. Kaplan–Meier curves and multivariate Cox regression were applied to analyse survival outcome for overall survival (OS), disease-specific survival (DSS) and disease-free survival (DFS).ResultsPostoperative serum albumin level (p < 0.001) and tumor location were both significantly associated with postoperative major wound infection (p = 0.018) in univariate analysis. Multiple regression analysis showed a higher risk of postoperative major wound infection among patients with postoperative hypoalbuminemia than in their counterparts (odds ratio [OR] 9.811, 95% CI [2.288–42.065], p = 0.002). Patients with a tumor located over the hypopharynx experienced increased risk of postoperative major wound infection (OR 2.591, 95% CI [1.095–6.129], p = 0.030). With respect to oncological outcomes, preoperative serum albumin level is a significant independent prognostic factor for overall survival (OS), disease-specific survival (DSS) and disease-free survival (DFS).ConclusionsPostoperative hypoalbuminemia is a useful indicator for the development of postoperative complications. In addition, preoperative hypoalbuminemia is a negative prognostic factor for patients who have undergone tumor excision and free flap reconstruction for the advanced stage of HNSCC. creator: Ming-Hsien Tsai creator: Hui-Ching Chuang creator: Yu-Tsai Lin creator: Hui Lu creator: Wei-Chih Chen creator: Fu-Min Fang creator: Chih-Yen Chien uri: https://doi.org/10.7717/peerj.4490 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tsai et al. title: The anatomy of the foveola reinvestigated link: https://peerj.com/articles/4482 last-modified: 2018-03-12 description: ObjectiveIn the foveola of the eye, photoreceptors and Müller cells with a unique morphology have been described, but little is known about their 3D structure and orientation. Considering that there is an angle-dependent change in the foveolar photoreceptor response for the same light beam, known as the Stiles Crawford Effect of the first kind (SCE I), which is still not fully understood, a detailed analysis of the anatomy of the foveolar cells might help to clarify this phenomenon.MethodsSerial semithin and ultrathin sections, and focused ion beam (FIB) tomography were prepared from 32 foveolae from monkeys (Macaca fascicularis) and humans. Foveolae were also analyzed under the electron microscope. Serial sections and FIB analysis were then used to construct 3D models of central Müller and photoreceptor cells. In addition, we measured the transmission of collimated light under the light microscope at different angles after it had passed through human foveae from flat mounted isolated retinae.ResultsIn monkeys, outer segments of central foveolar cones are twice as long as those from parafoveal cones and do not run completely parallel to the incident light. Unique Müller cells are present in the central foveolae (area of 200 µm in diameter) of humans and monkeys. Light entering the fovea center, which is composed only of cones and Müller cells, at an angle of 0° causes a very bright spot after passing through this area. However, when the angle of the light beam is changed to 10°, less light is measured after transpasssing through the retina, the foveolar center becomes darker and the SCE-like phenomenon is directly visible. Measurements of the intensities of light transmission through the central foveola for the incident angles 0 and 10° resemble the relative luminance efficiency for narrow light bundles as a function of the location where the beam enters the pupil as reported by Stiles and Crawford. The effect persisted after carefully brushing away the outer segments.ConclusionWe show that unique cones and Müller cells with light fibre-like properties are present in the center of the fovea. These unique Müller cells cause an angle dependent, SCE-like drop in the intensity of light guided through the foveola. Outer segments from the foveolar cones of monkeys are not straight. creator: Alexander V. Tschulakow creator: Theo Oltrup creator: Thomas Bende creator: Sebastian Schmelzle creator: Ulrich Schraermeyer uri: https://doi.org/10.7717/peerj.4482 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tschulakow et al.