bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades
Authors: Wren Jonathan D. 
Published: May 2016

AbstractMotivation : To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades.Results : When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher ( P  &lt; 4.5 × 10 −29 ). The 20-year trend in the average JIF between the two groups suggests the gap does not appear to be significantly narrowing. For a sampling of the journals producing top papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat ‘hit or miss’. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success.Contact : jdwren@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip
Authors: Niu Liang , Xu Zongli , Taylor Jack A. 
Published: May 2016

Abstract
Motivation: The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes—Infinium I (type I) and Infinium II (type II)—in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis.
Results: Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ.
Availability: We incorporated the method into the R package ENmix , which is freely available from the Bioconductor website ( https://www.bioconductor.org/packages/release/bioc/html/ENmix.html ).
Contact: niulg@ucmail.uc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Metallo-β-Lactamase (MBL)-Producing Enterobacteriaceae in United States Children
Authors: Logan Latania K. , Bonomo Robert A. 
Published: May 2016

Abstract
Metallo-β-lactamases (MBLs) are emerging as the most notable resistance determinants in Enterobacteriaceae. In many cases, the genes encoding MBLs are part of complex, mobile genetic elements that carry other resistance determinants. In the United States, there are increasing reports of MBL-producing Enterobacteriaceae, with New Delhi MBLs (NDMs) accounting for the majority of transmissible MBL infections. Many infections caused by NDM-producing bacteria are associated with international travel and medical tourism. However, little recognition of the introduction of MBL-producing Enterobacteriaceae into the pediatric community has followed. Reports suggest that this occurred as early as 2002. Here, we reflect on the unwelcome emergence of MBL-producing Enterobacteriaceae in US children and the available clinical and molecular data associated with spread. Since 2002, there have been disturbing reports that include the most readily transmissible MBLs, blaIMP, blaVIM, and blaNDM types. In the majority of children with available data, a history of foreign travel is absent.
Genetic evidence for natural selection in humans in the contemporary United States
Authors: Beauchamp Jonathan 
Published: May 2016

AbstractRecent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals’ genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about -1.5 months of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Though they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving—albeit slowly, especially when compared to the rapid secular changes that have occurred over the past few generations due to cultural and environmental factors.
Estimating effective population size from temporal allele frequency changes in experimental evolution
Authors: Jónás Ágnes , Taus Thomas , Kosiol Carolin , Schlötterer Christian , Futschik Andreas 
Published: May 2016

AbstractThe effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-termNe. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related toNe. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-Seq). Pool-Seq is cost-effective and outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling increasing the estimated allele frequency variance. We propose a new estimator ofNe, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurateNeestimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wideNeestimates, we extend our method using a recursive partitioning approach to estimateNelocally along the chromosome. Since type I error is accounted for, our method permits the identification of genomic regions that differ significantly inNe. We present an application to Pool-Seq data from experimental evolution withDrosophila, and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R-package athttps://github.com/ThomasTaus/Nest.
Public Information Precision and Coordination Failure: An Experiment
Authors: BANERJEE SANJAY , MAIER MICHAEL 
Published: May 2016

ABSTRACTMore precise public disclosure reduces uncertainty about economic fundamentals, but it can increase uncertainty about other agents' actions, leading to coordination failure. We conducted a laboratory experiment to study the effects of public information precision and strategic complementarity on coordination failure. Information precision is operationalized in terms of “granularity” (level of detail). We found that (1) granular public disclosure, which is disaggregated and precise, increases the likelihood of coordination failure and decreases coordination efficiency when public information is pessimistic about future economic prospects; (2) the deleterious effect of granular disclosure is stronger when strategic complementarity is high; and (3) higher levels of strategic complementarity decrease coordination efficiency. Overall, the observed likelihood of coordination failure is higher and coordination efficiency is lower than predicted by theory. Our findings have implications for the Federal Reserve's decision to publicly disclose detailed stress test results for distressed banks, and the debate on whether the Public Company Accounting Oversight Board should publicly release reports on firm‐specific quality‐control deficiencies of audit firms.
Who's Afraid of Rural Poverty? The Story Behind America's Invisible Poor
Authors: Gurley Lauren 
Published: May 2016

AbstractRural poverty and rural issues in general remain invisible in the United States to the urban majority. Rural sociologists have tried to raise these issues, but even in the field of sociology, they have been sidelined for several generations. Progressives treat urban poverty with sympathy and rural poverty with contempt because the latter is stereotyped as a problem that afflicts only white families, who are then blamed for failings of the economy as a whole. In fact, persistent rural poverty is concentrated in pockets in Appalachia, the Mississippi Delta, and several other regions, many of which are inhabited by blacks, Hispanics, and Native Americans. Nevertheless, it seems that making rural poverty as much a concern among progressive Democrats as urban poverty has been will require a different political orientation towards rural issues. Such an approach was visible briefly during Barack Obama's 2008 presidential campaign, but it has had little influence on other candidates for high office.
The role of N‐glycosylation in high glucose‐induced upregulation of intercellular adhesion molecule‐1 on bovine retinal endothelial cells
Authors: Liu Kun , Liu Haiyun , Zhang Zhihua , Ye Wen , Xu Xun 
Published: May 2016

AbstractPurposeThe development of diabetic retinopathy has been implicated as a consequence of chronic inflammation. Given the role of the intercellular adhesion molecule‐1 (ICAM‐1) in inflammation, the potential effect of N‐glycosylation on the upregulated expression of ICAM‐1 at the surface of bovine retinal endothelial cells (BRECs) induced by high glucose concentrations was investigated.MethodsGene and protein expression of ICAM‐1 in primary BRECs cultured in medium containing increasing concentrations of mannose or glucose in the presence or absence of tunicamycin were studied with reverse transcription–polymerase chain reaction and Western blot analysis, and the expression level of ICAM‐1 at the surface of BRECs was examined with an immunofluorescence analysis. A lectin blot assay with PHA‐L was performed to explore the level of N‐glycans on cell total proteins or immunoprecipitated ICAM‐1 from cells treated or untreated with high glucose.ResultsBoth the mRNA and protein levels of ICAM‐1, as well as the level of ICAM‐1 on the cell surface, were significantly upregulated by increasing the concentration of glucose in the culture medium, with a peak concentration of 20 mm. Consistent with these results, a dramatic increase in the N‐glycosylation of ICAM‐1 in BRECs cultured with a high concentration of glucose was observed, which could be partially attenuated by tunicamycin treatment.ConclusionHigh glucose‐induced upregulation of ICAM‐1 on the surface of BRECs could be ascribed to the alterations in its N‐glycosylation at least in part, indicating that interference with the glycosylation of ICAM‐1 may contribute to improving the efficiency of current therapies with diabetic retinopathy.
Navigating the challenges of delivering secondary school courses by videoconference
Authors: Rehn Nicole , Maor Dorit , McConney Andrew 
Published: May 2016

AbstractThe purpose of this research is to unpack and learn from the experiences of teachers who deliver courses to remote secondary school students by videoconference. School districts are using videoconferencing to connect students and teachers who are separated geographically through regular live, real‐time conferences. Previous studies have shown the inadequacy of videoconferencing to create effective learning communities when used solely as a lecturing tool, but there is limited research into understanding how to mitigate the challenges in order to leverage the tool for what it affords. This collective case study uses qualitative methods to examine those challenges and propose strategies for overcoming them. Five obstacles were identified (insufficient time, feelings of isolation, scheduling and logistics, unreliable technology and limited personal connection) with the following recommendations: leverage supporting tools, intentionally build presence and prioritize the programming within the district.
Immunohistochemical evaluation of p16 expression in cutaneous histiocytic, fibrohistiocytic and undifferentiated lesions
Authors: Smith Emily H. , Lowe Lori , Harms Paul W. , Fullen Douglas R. , Chan May P. 
Published: May 2016

BackgroundExpression of p16 is frequently evaluated in melanocytic lesions. Expression of p16 in cutaneous histiocytic, fibrohistiocytic and undifferentiated lesions has not been well characterized.MethodsWe evaluated p16 expression in a cohort of histiocytic (reticulohistiocytoma, Langerhans cell histiocytosis, xanthogranuloma, Rosai Dorfman disease and xanthoma), fibrohistiocytic (dermatofibroma, epithelioid fibrous histiocytoma and dermatofibrosarcoma protuberans) and undifferentiated (atypical fibroxanthoma and pleomorphic undifferentiated sarcoma) lesions. A group of melanocytic lesions (Spitz nevus, ordinary nevus, spitzoid melanoma and non‐spitzoid melanoma) were also evaluated as reference. Each case was scored by the proportion of p16‐positive cells and by staining intensity.ResultsImmunoreactivity for p16 was found in almost all histiocytic (28/30, 93%) and fibrohistiocytic (22/24, 92%) lesions. About half of the undifferentiated lesions also exhibited p16 staining (9/17, 53%). Most of the melanocytic cases examined in this study expressed p16. A wide range of staining intensity and proportion of p16‐positive cells was observed in most groups.ConclusionExpression of p16 is common, albeit variable in proportion and intensity, amongst a wide variety of cutaneous histiocytic, fibrohistiocytic and undifferentiated lesions. Further studies are required to determine if p16 expression is useful in distinguishing benign from malignant neoplasms of these types.
Pathologic features of anogenital precancerous high‐grade squamous intraepithelial lesion (squamous cell carcinoma in situ)
Authors: Xue Ruzeng , Elbendary Amira , Valdebran Manuel , Chaudhari Soham , Elston Dirk 
Published: May 2016

BackgroundPrecancerous high‐grade squamous intraepithelial lesion (HSIL), the current consensus terminology for anogenital squamous cell carcinoma in situ (SCCIS), often presents with distinctive histopathologic findings that may be a function of anatomic site or associated human papillomavirus infection.MethodsFifty‐six specimens of anogenital HSIL were compared with an equal number of specimens of SCCIS from non‐anogenital sites in regard to the presence of parakeratosis, flag sign in the stratum corneum, compact stratum corneum, hypergranulosis, koilocytes, small blue cells, clonal populations of keratinocytes, pagetoid scatter of atypical keratinocytes, clear cell change, glassy red cytoplasm, pigmentation, nuclear/cytoplasmic(N/C) ratio >2/1, nuclear hyperchromasia, pleomorphic nuclei, mitotic figures, abnormal mitotic figures, dyskeratotic keratinocytes, involvement of skin appendages, acantholysis and amyloid deposition.ResultsHypergranulosis, koilocytes, small blue cells, pigmentation, nuclear hyperchromasia, dyskeratotic keratinocytes and amyloid deposition were more frequently noted in anogenital HSIL. Parakeratosis, clear cell change, pleomorphic nuclei, skin appendages involvement and acantholysis were strongly associated with non‐anogenital location. There was no significant difference in the incidence of the remaining features.ConclusionThe strongest predicators of an anogenital location included hypergranulosis, koilocytes, small blue cells and nuclear hyperchromasia. Pigmentation and amyloid deposition were also strongly associated with an anogenital location.
Prolonged vestibular stimulation induces homeostatic plasticity of the vestibulo‐ocular reflex in larval Xenopus laevis
Authors: Dietrich Haike , Straka Hans 
Published: May 2016

AbstractVestibulo‐ocular reflexes (VOR) stabilise retinal images during head/body motion in vertebrates by generating spatio‐temporally precise extraocular motor commands for corrective eye movements. While VOR performance is generally robust with a relatively stable gain, cerebellar circuits are capable of adapting the underlying sensory‐motor transformation. Here, we studied cerebellum‐dependent VOR plasticity by recording head motion‐induced lateral rectus and superior oblique extraocular motor discharge in semi‐intact preparations of Xenopus laevis tadpoles. In the absence of visual feedback, prolonged sinusoidal rotation caused either an increase or decrease of the VOR gain depending on the motion stimulus amplitude. The observed changes in extraocular motor discharge gradually saturated after 20 min of constant rotation and returned to baseline in the absence of motion stimulation. Furthermore, plastic changes in lateral rectus and superior oblique motor commands were plane‐specific for horizontal and vertical rotations, respectively, suggesting that alterations are restricted to principal VOR connections. Comparison of multi‐ and single‐unit activity indicated that plasticity occurs in all recorded units of a given extraocular motor nucleus. Ablation of the cerebellum abolished motoneuronal gain changes and prevented the induction of plasticity, thus demonstrating that both acquisition and retention of this type of plasticity require an intact cerebellar circuitry. In conclusion, the plane‐specific and stimulus intensity‐dependent modification of the VOR gain through the feed‐forward cerebellar circuitry represents a homeostatic plasticity that likely maintains an optimal working range for the underlying sensory‐motor transformation.
Pathways to Climate Change Adaptation: Making Climate Change Action Political
Authors: Eisenhauer David C. 
Published: May 2016

AbstractPathway approaches to adaptation highlight the uncertainty of future impacts of climate change and the ongoing, contingent nature of responses to these effects. This article reviews adaptation to climate change literature employing the notion of pathways and argues that these approaches offer a useful framework to spur meaningful adaptation action. After providing an overview of the history of pathway approaches, the paper focuses on four approaches that apply the metaphor of pathways differently: the socioeconomic pathways, dynamic adaptive policy pathways, pathways to resilience, and the social, technology, and environmental pathways to sustainability. Lessons and strengths from each of these approaches are highlighted. Utilizing multiple pathway approaches can further aid in creating useful and usable knowledge. However, the paper concludes by arguing that pathway approaches could be further strengthened by including political concerns and processes. Working to include the broader public within the coproduction of pathways would help achieve this goal.
Honey Bees and Colony Collapse Disorder: A Pluralistic Reframing
Authors: Watson Kelly , Stallins J. Anthony 
Published: May 2016

AbstractScientific narratives surrounding colony collapse disorder (CCD) are often played against one another. However, oppositional knowledge politics do not neatly segregate the materiality and causal properties of the ecological phenomena they represent. Thus the challenge with CCD is not just to describe the partisan character of how knowledge about it is socially produced. It is also about how to integrate these politics through their less antagonistic material ecologies. We review three dominant discourses underlying CCD and honey bee decline and present a synthesis that conveys how their socially embedded perceptions about ecological causality are more compatible. We invoke a theoretical framework from complexity theory to demonstrate how multiple kinds of ecological causality, from the identifiable and addressable to the more emergent and unpredictable, can align under conflicting policy positions. We argue that this continuum of ecological explanations is a more conciliatory framework for responding to CCD. It provides an alternative to the antagonistic politics that tend to reify and defend either a restrictive search for a singular cause, a paralyzing documentation of all possible permutations of CCD, or a return to a utopian agrarian past. Relating how ecological knowledge is socially produced can illuminate stakeholder positions and strategies. But it is also constructive to map out how the ecological suppositions underlying them relate and inform one under.
Negative impact of oral health conditions on oral health related quality of life of community dwelling elders in Mexico city, a population based study
Authors: Castrejón‐Pérez Roberto Carlos , Borges‐Yáñez S. Aída , Irigoyen‐Camacho Ma. Esther , Cruz‐Hervert Luis Pablo 
Published: May 2016

AimOral health in old persons is frequently poor; non‐functional prostheses are common and negatively affect quality of life. The objective of this study was to estimate the impact of oral health problems on oral health related quality of life in a sample of home dwelling Mexican elders.MethodsHousehold survey in 655 persons 70 years old and over residing in one county in Mexico City.VariablesOral Health Related Quality of Life (Short version of the Oral Health Impact Profile validated in Mexico‐OHIP‐14‐sp), self‐perception of general and oral health, xerostomia, utilization of dental services, utilization and functionality of removable dental prostheses, dental and periodontal conditions, age, gender, marital status, schooling, depression, cognitive impairment and independence in activities of daily living (ADL). A negative binomial regression model was fitted.ResultsMean age was 79.2 ± 7.1 years; 54.2% were women. Mean OHIP‐14‐Sp score was 6.8 ± 8.7, median was 4. The final model showed that men (RR = 1.30); persons with xerostomia (RR = 1.41); no utilization of removable prostheses (RR = 1.55); utilization of non‐functional removable prostheses (RR = 1.69); fair self‐perception of general health (RR = 1.34); equal (RR = 1.43) or worse (RR = 2.32) self‐perception of oral health compared with persons of the same age; and being dependent for at least one ADL (RR = 1.71) increased the probability of higher scores of the OHIP‐14‐sp. Age, schooling, depression, cognitive impairment and periodontal conditions showed no association.ConclusionsOral rehabilitation can improve quality of life, health education and health promotion for the elder and their caregivers may reduce the risk of dental problems. Geriatr Gerontol Int 2017; 17: 744–752.