bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reductive Analytics on Big MS Data leads to tremendous reduction in time for peptide deduction
Authors: Awan Muaaz Gul , Saeed Fahad 
Published: September 2016

AbstractIn this paper we present a feasibility of using a data-reductive strategy for analyzing big MS data. The proposed method utilizes our reduction algorithm MS-REDUCE and peptide deduction is accomplished using Tide with hiXcorr. Using this approach we were able to process 1 million spectra in under 3 hours. Our results showed that running peptide deduction with smaller amount of selected peaks made the computations much faster and scalable with increasing resolution of MS data. Quality assessment experiments performed on experimentally generated datasets showed good quality peptide matches can be made using the reduced datasets. We anticipate that the proteomics and systems biology community will widely adopt our reductive strategy due to its efficacy and reduced time for analysis.
Trends in DNA methylation with age replicate across diverse human populations
Authors: Gopalan Shyamalika , Carja Oana , Fagny Maud , Patin Etienne , Myrick Justin W. , McEwen Lisa , Mah Sarah M. , Kobor Michael S. , Froment Alain , Feldman Marcus W. , Quintana-Murci Lluis , Henn Brenna M. 
Published: September 2016

AbstractAging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva and whole blood derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rainforest and the ≠Khomani San of the South African Kalahari Desert. We identify hundreds of CpG sites whose methylation levels are significantly associated with age, thousands that are significant in a meta-analysis, and replicate trends previously reported in populations of non-African descent. We confirm that an age-associated site in the gene ELOVL2 shows a remarkably congruent relationship with aging in humans, despite extensive genetic and environmental variation across populations. We also demonstrate that genotype state at methylation quantitative trait loci (meQTLs) can affect methylation trends at some known age-associated CpG sites. Our study explores the relationship between CpG methylation and chronological age in populations of African hunter-gatherers, who rely on different diets across diverse ecologies. While many age-related CpG sites replicate across populations, we show that considering common genetic variation at meQTLs further improves our ability to detect previously identified age associations.
Zika virus replication in the mosquitoCulex quinquefasciatusin Brazil
Authors: Guedes D. R. D. , Paiva M. H. S. , Donato M. M. A. , Barbosa P. P. , Krokovsky L. , Rocha S. W. dos S. , Saraiva K. L. A. , Crespo M. M. , Barbosa R. M. R. , Oliveira C. M. F. , Melo-Santos M. A. V. , Pena L. , Cordeiro M. T. , França R. F. de O. , Oliveira A. L. S, de , Leal W. S. , Peixoto C. A. , Ayres C. F. J. 
Published: September 2016

AbstractZika virus (ZIKV) is a flavivirus that has recently been associated with increased incidence of neonatal microcephaly and other neurological disorders. The virus is primarily transmitted by mosquito bite, although other routes of infection have been implicated in some cases. TheAedes aegyptimosquito is considered to be the main vector to humans worldwide, but there is evidence of other mosquito species, includingCulex quinquefasciatus, playing a role in the Brazilian outbreak. To test this hypothesis, we experimentally compared the vectorial competence of laboratory-rearedA. aegyptiandC. quinquefasciatus. We found ZIKV in the midgut, salivary glands, and saliva of artificially fedC. quinquefasciatus. Additionally, we collected ZIKV-infectedC. quinquefasciatusfrom urban areas of high microcephaly incidence in Recife, Brazil. Take into account; these findings indicate that there may be a wider range of vectors for ZIKV than anticipated.
Biotic drivers of seedling establishment in Neotropical savannas: selective granivory and seedling herbivory by leaf‐cutter ants as an ecological filter
Authors: Costa Alan N. , Vasconcelos Heraldo L. , Bruna Emilio M. 
Published: September 2016

Summary

Herbivory has been shown to have prominent top‐down effects on vegetation in Paleotropical savannas, where consumers of early stages of life history act as demographic bottlenecks. Such impact has been largely ignored in Neotropical savannas, however, despite insect consumption being linked to reduced recruitment of woody species.

We hypothesize that Atta leaf‐cutter ants – the prevalent herbivores in the Neotropics – alter the establishment of woody plant seedlings in the Brazilian Cerrado by reducing seed availability and seedling survival. We also hypothesize that the demographic effects will be species‐specific.

To test these hypotheses, we experimentally (i) compared seed removal in areas with and without Atta foraging and (ii) compared the survivorship of seedlings exposed to or protected from Atta foraging. Both experiments were performed with the same common Cerrado species which allowed us to evaluate the potential net effects of consumers at the population and community levels.

Overall seed removal rates in sites with Atta foraging were greater than those where ants were absent (59.2% and 39.2% of seeds removed, respectively). There were differences in removal for 10 of the 12 tested species, with per species removal 1.1‐ to 3.8‐fold greater in areas with Atta foraging. On transplanted plants, 45% of seedlings exposed to Atta were attacked, resulting in a survival 7.6% lower than that of protected seedlings. Seedling survival was 11.8–31.5% lower in five species, with the largest differences in survival between treatments during the dry season.

Taken together, these results support the hypothesis that consumers can lead to demographic bottlenecks in Neotropical savanna plant species, with effects varying among life‐history stages and between species.

Synthesis. Granivory by ants has been linked to reduced seedling recruitment of woody species in the Brazilian Cerrado. Our results show that leaf‐cutter ants may largely limit early seedling establishment of woody species by reducing seed availability and seedling survival with differential species‐specific effects. Atta ants may therefore be acting as an ecological filter, which coupled with potential selectivity in foraging on reproductive life‐history stages, may ultimately influence the relative abundance of different species and hence the structure and composition of Cerrado vegetation.
Do Alcohol Relapse Episodes During Treatment Predict Long‐Term Outcomes? Investigating the Validity of Existing Definitions of Alcohol Use Disorder Relapse
Authors: Maisto Stephen A. , Roos Corey R. , Hallgren Kevin A. , Moskal Dezarie , Wilson Adam D. , Witkiewitz Katie 
Published: September 2016

BackgroundThe construct of relapse is used widely in clinical research and practice of alcohol use disorder (AUD) treatment. The purpose of this study was to test the predictive validity of commonly appearing definitions of AUD relapse in the empirical literature.MethodsSecondary analyses of data from Project MATCH and COMBINE were conducted using 7 definitions of “relapse” based on drinking quantity within a single drinking episode: any drinking; at least 4/5 drinks for women/men; at least 4.3/7.1 drinks for women/men; at least 6/7 drinks for women/men; at least 6 drinks; at least 7/9 drinks for women/men; and at least 8/10 drinks for women/men. Relapse was used to predict alcohol consumption, related consequences, and nonconsumption outcomes (quality of life, psychosocial functioning) at the end of treatment and up to 1 year posttreatment.ResultsRegression analyses indicated within‐treatment relapse definitions significantly predicted end‐of‐treatment alcohol consumption and alcohol‐related consequences. Heavy drinking definitions were generally more predictive than the any drinking definition, but no single heavy drinking definition was consistently a better predictor of outcomes. Relapse definitions were less predictive of longer‐term alcohol‐related outcomes and both shorter‐ and longer‐term nonconsumption outcomes, including health and psychosocial functioning.ConclusionsOne particular definition of relapse did not consistently stand out as the best predictor. Advances in AUD research may require reconceptualization of relapse as a multifaceted dynamic process and may consider a wider range of relevant behaviors (e.g., health and psychosocial functioning) when examining the change process in individuals with AUD.
Human papillomavirus test with cytology triage in organized screening for cervical cancer
Authors: Veijalainen Olga , Kares Saara , Kujala Paula , Tirkkonen Mika , Vuento Risto , Kholová Ivana , Luukkaala Tiina , Osuala Veronika , Mäenpää Johanna 
Published: September 2016

AbstractIntroductionIn randomized studies, testing for high‐risk (HR) human papillomavirus (hrHPV) has been more sensitive than conventional cytology in detecting cervical intraepithelial neoplasia (CIN). The aim of this study was to evaluate the performance of HPV testing in the setting of an organized routine screening program.Material and methodsSince 2012, 35‐ to 60‐year‐old women living in the city of Tampere have been screened with the Abbott RealTime hrHPV test. HPV‐negative women are referred to the next screening round in five years. HPV‐positive women are triaged with conventional cytology, and women with at least low‐grade squamous intraepithelial lesion (LSIL+) are referred to colposcopy. The remaining HPV‐positive women are referred for re‐testing after 12 months, and then all HPV‐positive women are referred to colposcopy. The data from the last cohort with cytological screening (screened in 2011) is presented for comparison.ResultsA total 5637 (70%) women attended the first round of HPV screening, and 369 were HPV‐positive. Of them, 54 women LSIL+ were referred to colposcopy, resulting in 16 CIN2+ lesions found. Of the remaining HPV‐positive women, 66% were still positive one year later, and were referred to colposcopy, with 18 additional CIN2+ lesions found. The attendance rate to the last round of cytological screening was 71% (5814 women). Sixty‐four women with LSIL+ cytology were referred to colposcopy, and 11 CIN2+ lesions were found. Of the 777 women with borderline cytology and scheduled for reflex screening in the following year, 109 (19%) had ASC‐US+, and 57 underwent colposcopy, resulting in six additional CIN2+ lesions found. The total detection rate of CIN2+ was significantly higher in the HPV‐screened cohort (6.0/1000 vs. 2.9/1000, p = 0.015). However, the total colposcopy rate was 4% vs. 2%, respectively (p < 0.001).ConclusionHuman papillomavirus testing also seems to be more sensitive than cytology in detecting CIN2+ lesions in the setting of a routine organized screening program, besides in the context of randomized trials. The problem of an increased colposcopy rate needs to be addressed in the future.
T‐cell immunity in myocardial inflammation: pathogenic role and therapeutic manipulation
Authors: Stephenson E , Savvatis K , Mohiddin S A , Marelli‐Berg F M 
Published: September 2016

T‐cell‐mediated immunity has been linked not only to a variety of heart diseases, including classic inflammatory diseases such as myocarditis and post‐myocardial infarction (Dressler's) syndrome, but also to conditions without an obvious inflammatory component such as idiopathic dilated cardiomyopathy and hypertensive cardiomyopathy. It has been recently proposed that in all these conditions, the heart becomes the focus of T‐cell‐mediated autoimmune inflammation following ischaemic or infectious injury. For example, in acute myocarditis, an inflammatory disease of heart muscle, T‐cell responses are thought to arise as a consequence of a viral infection. In a number of patients, persistent T‐cell‐mediated responses in acute viral myocarditis can lead to autoimmunity and chronic cardiac inflammation resulting in dilated cardiomyopathy. In spite of the major progress made in understanding the mechanisms of pathogenic T‐cell responses, effective and safe therapeutic targeting of the immune system in chronic inflammatory diseases of the heart has not yet been developed due to the lack of specific diagnostic and prognostic biomarkers at an early stage. This has also prevented the identification of targets for patient‐tailored immunomodulatory therapies that are both disease‐ and organ‐selective. In this review, we discuss current knowledge of the development and functional characteristics of pathogenic T‐cell‐mediated immune responses in the heart, and, in particular, in myocarditis, as well as recent advances in experimental models which have the potential to translate into heart‐selective immunomodulation.Linked ArticlesThis article is part of a themed section on Targeting Inflammation to Reduce Cardiovascular Disease Risk. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.22/issuetoc and http://onlinelibrary.wiley.com/doi/10.1111/bcp.v82.4/issuetoc
Vascular actions of relaxin: nitric oxide and beyond
Authors: Leo C H , Jelinic M , Ng H H , Marshall S A , Novak J , Tare M , Conrad K P , Parry L J 
Published: September 2016

The peptide hormone relaxin regulates the essential maternal haemodynamic adaptations in early pregnancy through direct actions on the renal and systemic vasculature. These vascular actions of relaxin occur mainly through endothelium‐derived NO‐mediated vasodilator pathways and improvements in arterial compliance in small resistance‐size arteries. This work catalysed a plethora of studies which revealed quite heterogeneous responses across the different regions of the vasculature, and also uncovered NO‐independent mechanisms of relaxin action. In this review, we first describe the role of endogenous relaxin in maintaining normal vascular function, largely referring to work in pregnant and male relaxin‐deficient animals. We then discuss the diversity of mechanisms mediating relaxin action in different vascular beds, including the involvement of prostanoids, VEGF, endothelium‐derived hyperpolarisation and antioxidant activity in addition to the classic NO‐mediated vasodilatory pathway. We conclude the review with current perspectives on the vascular remodelling capabilities of relaxin.Linked ArticlesThis article is part of a themed section on Recent Progress in the Understanding of Relaxin Family Peptides and their Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.10/issuetoc
Total mesorectal excision for cancer: histological and immunohistochemical evidence of nerve removal and risk‐factor analysis
Authors: Moszkowicz D. , Rougier G. , Julié C. , Nyangoh Timoh K. , Beauchet A. , Vychnevskaia K. , Malafosse R. , Nordlinger B. , Peschaud F. 
Published: September 2016

AbstractAimWhether or not nerve‐sparing rectal‐cancer surgery can effectively prevent removal of the pelvic autonomic nerves has not been substantiated microscopically. We aimed to analyse the quality of nerve preservation in female patients by quantifying residual nerve fibres in total mesorectal excision specimens, to analyse pro‐erectile function of the nerve fibres removed and to determine risk factors for pelvic denervation.MethodSerial transverse sections from female patients, 64 ± 18 years of age, were studied after the mesorectal fascia was inked and studied histologically [using anti‐S100 and anti‐neuronal nitric oxide synthase (nNOS) antibodies]. Nerve fibres located within 1 mm of the inked surface were counted and analysed according to type of surgery, tumour location, pT stage, circumferential resection margin and the necessity for a posterior colpectomy.ResultsTwelve specimens were analysed. Per specimen, the mean number of nerve‐fibre sections outside the mesorectum was 5.3 ± 3.6 (range: 1–12). The mean number of fibres per specimen was 6.4 ± 4.1 in patients having a low‐rectal tumour and 4.4 ± 2.9 in those with mid or higher rectal tumours (P = 0.42). The mean number of fibres was higher (9.2) for T4 tumours than for T2/T3 tumours (5.0 ± 3.5), but this difference was not statistically sigmificant (P = 0.25). Patients having abdominoperineal excision, a posterior colpectomy or a circumferential resection margin of less than 1 mm had significantly more nerve fibres in the specimen (10.6 ± 1.9 vs 4.4 ± 2.8; P = .041). Fibres localized at the anterolateral rectum corresponded to branches of the neurovascular bundle, expressing rich pro‐erectile activity (positive anti‐nNOS immunostaining).ConclusionThe neurovascular bundle is a key risk zone for pelvic denervation during total mesorectal excision. Abdominoperineal excision, posterior colpectomy and an invaded circumferential resection margin are associated with perineal denervation.
Head width–body mass equation: facilitating worker termite biomass estimates
Authors: DAHLSJÖ CECILIA A. L. 
Published: September 2016

1. Termites are one of the most important invertebrate ecosystem engineers in tropical regions, which may be quantified using termite biomass data. However, biomass data are particularly difficult to collect as they rely on termites being weighed in the field, which may neither be possible nor convenient. Local scale linear regression models, based on termite head widths (mm) and body masses (mg), have been used in the past to estimate termite biomass using head width and abundance data. However, these models represent very limited numbers of termite taxa from single sites. In the present study, I provide one of the most representative linear regression models available based on 90 samples from three different countries (Peru, Kenya, and Malaysia).2. Although the linear regression model under‐ or overestimated body weights of taxa with characteristic features (e.g. large heads of Odontotermes workers or elongated abdomens of Kalotermitidae) it provides a robust method for estimating termite biomass at the community level. Additionally, while there are limitations related to the general model, which may be solved by focusing on taxa specific data and the use of higher accuracy equipment, it is the first model to facilitate termite biomass estimates using the head with and abundance data only.3. This study encourages the use of termite biomass data to gain a better understanding of termites in ecosystem processes and calls for comparative data to be gathered for the purpose of creating models that may be representative of the variability among termite taxa.
Postnatal light alters hypothalamic‐pituitary‐adrenal axis function and induces a depressive‐like phenotype in adult mice
Authors: Coleman Georgia , Gigg John , Canal Maria Mercè 
Published: September 2016

AbstractThe postnatal light environment that a mouse experiences during the critical first three postnatal weeks has long‐term effects on both its circadian rhythm output and clock gene expression. Furthermore, data from our lab suggest that postnatal light may also impact the hypothalamic‐pituitary‐adrenal (HPA) axis, which is a key regulator of stress. To test the effect of postnatal light exposure on adult stress responses and circadian rhythmicity, we raised mice under either 24‐h light–dark cycles (LD), constant light (LL) or constant dark (DD) during the first three postnatal weeks. After weaning we then exposed all animals to LD cycles (basal conditions), followed by LL (stressed conditions) environments. We examined brain neuropeptide and glucocorticoid receptor (GR) expression, plasma corticosterone concentration rhythm and body temperature rhythm, together with depression‐ and anxiety‐related behaviour. Results showed that LL‐ and DD‐raised mice exhibited decreased GR expression in the hippocampus, increased plasma corticosterone concentration at the onset of the dark phase and a depressive phenotype when exposed to LD cycles later in life. Furthermore, LL‐raised mice showed increased corticotrophin‐releasing hormone mRNA expression in the paraventricular nucleus of the hypothalamus. When exposed to LL as adults, LL‐raised mice showed a significant circadian rhythm of plasma corticosterone concentration, together with a shorter period and stronger circadian rhythm of body temperature compared to DD‐raised mice. Taken together, these data suggest that altered postnatal light environments have long‐term effects on the HPA axis and the circadian system, which can lead to altered stress responses and a depressive phenotype in adulthood.
Leadership Styles and Collaboration Among Members of the American Association of Family and Consumer Sciences
Authors: Saiki Diana , Kandiah Jay , Beard Kate , Jones James J. 
Published: September 2016

The objectives of this study were to examine the degree of collaboration and leadership style related to: levels of leadership position, years of leadership among female members of the American Association of Family and Consumer Sciences, age of members, and types of professions within Family and Consumer Sciences. Two hundred participants were recruited through convenience sampling at an annual conference. The participants completed a printed survey. The results showed that members who were engaged in national/international positions, older than 49, and with 5–25 years of leadership experience exhibited collaborative and participatory leadership styles. The results can be utilized to understand and cultivate effective collaborators and leaders in family and consumer sciences.
The unseen invaders: introduced earthworms as drivers of change in plant communities in North American forests (a meta‐analysis)
Authors: Craven Dylan , Thakur Madhav P. , Cameron Erin K. , Frelich Lee E. , Beauséjour Robin , Blair Robert B. , Blossey Bernd , Burtis James , Choi Amy , Dávalos Andrea , Fahey Timothy J. , Fisichelli Nicholas A. , Gibson Kevin , Handa I. Tanya , Hopfensperger Kristine , Loss Scott R. , Nuzzo Victoria , Maerz John C. , Sackett Tara , Scharenbroch Bryant C. , Smith Sandy M. , Vellend Mark , Umek Lauren G. , Eisenhauer Nico 
Published: September 2016

AbstractGlobally, biological invasions can have strong impacts on biodiversity as well as ecosystem functioning. While less conspicuous than introduced aboveground organisms, introduced belowground organisms may have similarly strong effects. Here, we synthesize for the first time the impacts of introduced earthworms on plant diversity and community composition in North American forests. We conducted a meta‐analysis using a total of 645 observations to quantify mean effect sizes of associations between introduced earthworm communities and plant diversity, cover of plant functional groups, and cover of native and non‐native plants. We found that plant diversity significantly declined with increasing richness of introduced earthworm ecological groups. While plant species richness or evenness did not change with earthworm invasion, our results indicate clear changes in plant community composition: cover of graminoids and non‐native plant species significantly increased, and cover of native plant species (of all functional groups) tended to decrease, with increasing earthworm biomass. Overall, these findings support the hypothesis that introduced earthworms facilitate particular plant species adapted to the abiotic conditions of earthworm‐invaded forests. Further, our study provides evidence that introduced earthworms are associated with declines in plant diversity in North American forests. Changing plant functional composition in these forests may have long‐lasting effects on ecosystem functioning.