bluuebunny/crossref_metadata_2025 huggingface dataset:
EpimiRBase: a comprehensive database of microRNA-epilepsy associations
Authors: Mooney Catherine , Becker Brett A. , Raoof Rana , Henshall David C.
Published: February 2016

Summary: MicroRNAs are short non-coding RNA which function to fine-tune protein levels in all cells. This is achieved mainly by sequence-specific binding to 3′ untranslated regions of target mRNA. The result is post-transcriptional interference in gene expression which reduces protein levels either by promoting destabilisation of mRNA or translational repression. Research published since 2010 shows that microRNAs are important regulators of gene expression in epilepsy. A series of microRNA profiling studies in rodent and human tissue has revealed that epilepsy is associated with wide ranging changes to microRNA levels in the brain. These are thought to influence processes including cell death, inflammation and re-wiring of neuronal networks. MicroRNAs have also been identified in the blood after injury to the brain and therefore may serve as biomarkers of epilepsy. EpimiRBase is a manually curated database for researchers interested in the role of microRNAs in epilepsy. The fully searchable database includes information on up- and down-regulated microRNAs in the brain and blood, as well as functional studies, and covers both rodent models and human epilepsy.

Availability and implementation: EpimiRBase is available at http://www.epimirbase.eu

Contact:  catherinemooney@rcsi.ie
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts
Authors: Cavalcante Raymond G. , Patil Snehal , Weymouth Terry E. , Bendinskas Kestutis G. , Karnovsky Alla , Sartor Maureen A.
Published: February 2016

Motivation: Capabilities in the field of metabolomics have grown tremendously in recent years. Many existing resources contain the chemical properties and classifications of commonly identified metabolites. However, the annotation of small molecules (both endogenous and synthetic) to meaningful biological pathways and concepts still lags behind the analytical capabilities and the chemistry-based annotations. Furthermore, no tools are available to visually explore relationships and networks among functionally related groups of metabolites (biomedical concepts). Such a tool would provide the ability to establish testable hypotheses regarding links among metabolic pathways, cellular processes, phenotypes and diseases.

Results: Here we present ConceptMetab, an interactive web-based tool for mapping and exploring the relationships among 16 069 biologically defined metabolite sets developed from Gene Ontology, KEGG and Medical Subject Headings, using both KEGG and PubChem compound identifiers, and based on statistical tests for association. We demonstrate the utility of ConceptMetab with multiple scenarios, showing it can be used to identify known and potentially novel relationships among metabolic pathways, cellular processes, phenotypes and diseases, and provides an intuitive interface for linking compounds to their molecular functions and higher level biological effects.

Availability and implementation:  http://conceptmetab.med.umich.edu

Contacts:  akarnovsky@umich.edu or sartorma@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MuCor: mutation aggregation and correlation
Authors: Kroll Karl W. , Eisfeld Ann-Katherin , Lozanski Gerard , Bloomfield Clara D. , Byrd John C. , Blachly James S.
Published: February 2016

Motivation: There are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting and summarizing variants and effects across a cohort is often done with ad hoc scripts that must be re-written for every new project. In response, we have written MuCor, a tool to gather variants from a variety of input formats (including multiple files per sample), perform database lookups and frequency calculations, and write many types of reports. In addition to use in large studies with numerous samples, MuCor can also be employed to directly compare variant calls from the same sample across two or more platforms, parameters or pipelines. A companion utility, DepthGauge, measures coverage at regions of interest to increase confidence in calls.

Availability and implementation: Source code is freely available at https://github.com/blachlylab/mucor and a Docker image is available at https://hub.docker.com/r/blachlylab/mucor/

Contact:  james.blachly@osumc.edu

Supplementary data:  Supplementary data are available at Bioinformatics online.
PAA: an R/bioconductor package for biomarker discovery with protein microarrays
Authors: Turewicz Michael , Ahrens Maike , May Caroline , Marcus Katrin , Eisenacher Martin
Published: February 2016

Summary: The R/Bioconductor package Protein Array Analyzer (PAA) facilitates a flexible analysis of protein microarrays for biomarker discovery (esp., ProtoArrays). It provides a complete data analysis workflow including preprocessing and quality control, uni- and multivariate feature selection as well as several different plots and results tables to outline and evaluate the analysis results. As a main feature, PAA’s multivariate feature selection methods are based on recursive feature elimination (e.g. SVM-recursive feature elimination, SVM-RFE) with stability ensuring strategies such as ensemble feature selection. This enables PAA to detect stable and reliable biomarker candidate panels.

Availability and implementation:  PAA is freely available (BSD 3-clause license) from http://www.bioconductor.org/packages/PAA/.

Contact:  michael.turewicz@rub.de or martin.eisenacher@rub.de
Optimization of alignment-based methods for taxonomic binning of metagenomics reads
Authors: Jaillard Magali , Tournoud Maud , Meynier Faustine , Veyrieras Jean-Baptiste
Published: February 2016

Motivation: Alignment-based taxonomic binning for metagenome characterization proceeds in two steps: reads mapping against a reference database (RDB) and taxonomic assignment according to the best hits. Beyond the sequencing technology and the completeness of the RDB, selecting the optimal configuration of the workflow, in particular the mapper parameters and the best hit selection threshold, to get the highest binning performance remains quite empirical.

Results: We developed a statistical framework to perform such optimization at a minimal computational cost. Using an optimization experimental design and simulated datasets for three sequencing technologies, we built accurate prediction models for five performance indicators and then derived the parameter configuration providing the optimal performance. Whatever the mapper and the dataset, we observed that the optimal configuration yielded better performance than the default configuration and that the best hit selection threshold had a large impact on performance. Finally, on a reference dataset from the Human Microbiome Project, we confirmed that the optimized configuration increased the performance compared with the default configuration.

Availability and implementation: Not applicable.

Contact:  magali.dancette@biomerieux.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications
Authors: Cui Ya , Chen Xiaowei , Luo Huaxia , Fan Zhen , Luo Jianjun , He Shunmin , Yue Haiyan , Zhang Peng , Chen Runsheng
Published: February 2016

Summary: We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions.

Availability and implementation: BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/.

Contact:  rschen@ibp.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
ASDB: a resource for probing protein functions with small molecules
Authors: Liu Zhihong , Ding Peng , Yan Xin , Zheng Minghao , Zhou Huihao , Xu Yuehua , Du Yunfei , Gu Qiong , Xu Jun
Published: February 2016

Summary: Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets.

Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/with the major web browsers.

Contact:  junxu@biochemomes.com or xujun9@mail.sysu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
MOCCASIN: converting MATLAB ODE models to SBML
Authors: Gómez Harold F. , Hucka Michael , Keating Sarah M. , Nudelman German , Iber Dagmar , Sealfon Stuart C.
Published: February 2016

Summary: MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging—especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format.

Availability and implementation: MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin.

Contact: mhucka@caltech.edu

Supplementary information: More information is available at https://github.com/sbmlteam/moccasin.
Managing research and surveillance projects in real-time with a novel open-source
e
Management tool designed for under-resourced countries
Authors: Steiner Andreas , Hella Jerry , Grüninger Servan , Mhalu Grace , Mhimbira Francis , Cercamondi Colin I , Doulla Basra , Maire Nicolas , Fenner Lukas
Published: February 2016

Objective A software tool is developed to facilitate data entry and to monitor research projects in under-resourced countries in real-time.

Methods The e Management tool “odk_planner” is written in the scripting languages PHP and Python. The odk_planner is lightweight and uses minimal internet resources. It was designed to be used with the open source software Open Data Kit (ODK). The users can easily configure odk_planner to meet their needs, and the online interface displays data collected from ODK forms in a graphically informative way. The odk_planner also allows users to upload pictures and laboratory results and sends text messages automatically. User-defined access rights protect data and privacy.

Results We present examples from four field applications in Tanzania successfully using the e Management tool: 1) clinical trial; 2) longitudinal Tuberculosis (TB) Cohort Study with a complex visit schedule, where it was used to graphically display missing case report forms, upload digitalized X-rays, and send text message reminders to patients; 3) intervention study to improve TB case detection, carried out at pharmacies: a tablet-based electronic referral system monitored referred patients, and sent automated messages to remind pharmacy clients to visit a TB Clinic; and 4) TB retreatment case monitoring designed to improve drug resistance surveillance: clinicians at four public TB clinics and lab technicians at the TB reference laboratory used a smartphone-based application that tracked sputum samples, and collected clinical and laboratory data.

Conclusions The user friendly, open source odk_planner is a simple, but multi-functional, Web-based e Management tool with add-ons that helps researchers conduct studies in under-resourced countries.
Triclosan Exposure is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish
Authors: Gaulke Christopher A. , Barton Carrie L. , Proffitt Sarah , Tanguay Robert L. , Sharpton Thomas J.
Published: February 2016

Growing evidence indicates that disrupting the microbial community that comprises the intestinal tract, known as the gut microbiome, can contribute to the development or severity of disease. As a result, it is important to discern the agents responsible for microbiome disruption. While animals are frequently exposed to a diverse array of environmental chemicals, little is known about their effects on gut microbiome stability and structure. Here, we demonstrate how zebrafish can be used to glean insight into the effects of environmental chemical exposure on the structure and ecological dynamics of the gut microbiome. Specifically, we exposed forty-five adult zebrafish to triclosan-laden food for four or seven days or a control diet, and analyzed their microbial communities using 16S rRNA amplicon sequencing. Triclosan exposure was associated with rapid shifts in microbiome structure and diversity. We find evidence that several operational taxonomic units (OTUs) associated with the family Enterobacteriaceae appear to be susceptible to triclosan exposure, while OTUs associated with the genusPseudomonasappeared to be more resilient and resistant to exposure. We also found that triclosan exposure is associated with topological alterations to microbial interaction networks and results in an overall increase in the number of negative interactions per microbe in these networks. Together these data indicate that triclosan exposure results in altered composition and ecological dynamics of microbial communities in the gut. Our work demonstrates that because zebrafish afford rapid and inexpensive interrogation of a large number of individuals, it is a useful experimental system for the discovery of the gut microbiome’s interaction with environmental chemicals.
Gene regulation and speciation in house mice
Authors: Mack Katya L. , Campbell Polly , Nachman Michael W.
Published: February 2016

One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproductive isolation. Here, we take advantage of a cross between house mouse subspecies, where hybrid dysfunction is largely unidirectional, to test several key predictions about regulatory divergence and reproductive isolation. Regulatory divergence between Mus musculus musculus and M. m. domesticus was characterized by studying allele-specific expression in fertile hybrid males using mRNA-sequencing of whole testes. We found extensive regulatory divergence between M. m. musculus and M. m. domesticus, largely attributable to cis-regulatory changes. When both cis and trans changes occurred, they were observed in opposition much more often than expected under a neutral model, providing strong evidence of widespread compensatory evolution. We also found evidence for lineage-specific positive selection on a subset of genes related to transcriptional regulation. Comparisons of fertile and sterile hybrid males identified a set of genes that were uniquely misexpressed in sterile individuals. Lastly, we discovered a nonrandom association between these genes and genes showing evidence of compensatory evolution, consistent with the idea that regulatory interactions might contribute to Dobzhansky-Muller incompatibilities and be important in speciation.
De novo pathogenic variants in CHAMP1 are associated with global developmental delay, intellectual disability, and dysmorphic facial features
Authors: Tanaka Akemi J. , Cho Megan T. , Retterer Kyle , Jones Julie R. , Nowak Catherine , Douglas Jessica , Jiang Yong-Hui , McConkie-Rosell Allyn , Schaefer G. Bradley , Kaylor Julie , Rahman Omar A. , Telegrafi Aida , Friedman Bethany , Douglas Ganka , Monaghan Kristin G. , Chung Wendy K.
Published: February 2016

We identified five unrelated individuals with significant global developmental delay and intellectual disability (ID), dysmorphic facial features and frequent microcephaly, and de novo predicted loss-of-function variants in chromosome alignment maintaining phosphoprotein 1 (CHAMP1). Our findings are consistent with recently reported de novo mutations in CHAMP1 in five other individuals with similar features. CHAMP1 is a zinc finger protein involved in kinetochore–microtubule attachment and is required for regulating the proper alignment of chromosomes during metaphase in mitosis. Mutations in CHAMP1 may affect cell division and hence brain development and function, resulting in developmental delay and ID.
Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogenAcinetobacter baumannii
Authors: Sutton Kristin A. , Breen Jennifer , Russo Thomas A. , Schultz L. Wayne , Umland Timothy C.
Published: February 2016

The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the sixth step of the seven-step shikimate pathway. Chorismate, the product of the pathway, is a precursor for the biosynthesis of aromatic amino acids, siderophores and metabolites such as folate, ubiquinone and vitamin K. The shikimate pathway is present in bacteria, fungi, algae, plants and apicomplexan parasites, but is absent in humans. The EPSP synthase enzyme produces 5-enolpyruvylshikimate 3-phosphate and phosphate from phosphoenolpyruvate and shikimate 3-phosphateviaa transferase reaction, and is the target of the herbicide glyphosate. TheAcinetobacter baumanniigene encoding EPSP synthase,aroA, has previously been demonstrated to be essential during host infection for the growth and survival of this clinically important drug-resistant ESKAPE pathogen. Prephenate dehydrogenase is also encoded by the bifunctionalA. baumannii aroAgene, but its activity is dependent upon EPSP synthase since it operates downstream of the shikimate pathway. As part of an effort to evaluate new antimicrobial targets, recombinantA. baumanniiEPSP (AbEPSP) synthase, comprising residues Ala301–Gln756 of thearoAgene product, was overexpressed inEscherichia coli, purified and crystallized. The crystal structure, determined to 2.37 Å resolution, is described in the context of a potential antimicrobial target and in comparison to EPSP synthases that are resistant or sensitive to the herbicide glyphosate.
catena-Poly[silver(I)-μ-[1-(pyridin-2-ylmethyl-κN)-3-(3-sulfonatopropyl)imidazolin-2-ylidene]-κC2]
Authors: Rietzler Barbara , Laus Gerhard , Kahlenberg Volker , Schottenberger Herwig
Published: February 2016

The title compound, [Ag(C12H14N3O3S)]n, was obtained by deprotonation and metalation of 1-(pyridin-2-ylmethyl)-3-(3-sulfopropyl)imidazolium, inner salt, using silver(I) oxide in methanol. The title compound is a one-dimensional helical coordination polymer. Several C—H...O hydrogen bonds and a short Ag—O contact are observed. The C—Ag—N angle is 168.3 (1)° and the N—C—N `carbene angle' is 103.8 (3)°.
Women managing women
Authors: Hurst Jane , Leberman Sarah , Edwards Margot
Published: February 2016

Purpose

– The purpose of this paper is to examine the intersections between the way women’s careers develop, the hierarchical relationships between women and the resulting implications for gender equity in the workplace.

Design/methodology/approach

– While a considerable body of research exists on gender in the workplace, the intersection between the way in which women ' s careers develop and the influence hierarchical relationships between women in the workplace have on that career development are under-researched. This paper examines existing relevant research, discusses the implications of these intersecting areas and raises areas for future academic research, as well as the development of organizational practice.

Findings

– The nature of the hierarchical relationships between women in the workplace is an important but under-researched factor when considering the career development of women. Delving into the experiences of women managers and employees, both good and bad, enables a deeper understanding of the role these relationships play in shaping the careers of women. From this, personal and organizational strategies can be developed that enhance workplace relationships and the career development of women.

Originality/value

– This paper encourages academics and practitioners to critically consider the connections between hierarchical workplace relationships and career development as part of organizational practice and further gender equity research.
Supervisor support and work engagement of hotel employees in Malaysia
Authors: Ling Suan Choo , Mohd Nasurdin Aizzat
Published: February 2016

Purpose

– This study aims to examine the impact of supervisor support and to assess the moderating role of gender on employee work engagement in the context of the Malaysian hospitality industry.

Design/methodology/approach

– Data were collected from a sample of 438 customer-contact employees in Malaysian upscale hotels and tested using the partial least squares technique.

Findings

– The findings indicated that supervisor support positively influences work engagement and that this positive relationship was stronger for male employees than female employees.

Research limitations/implications

– The results highlight that supervisor support plays a critical role in fostering greater employee work engagement. In addition, different approaches need to be utilized by supervisors in supporting their male and female subordinates.

Originality/value

– This study extends the existing literature by examining the role of gender in moderating the relationship between supervisor support and work engagement, especially within the context of a developing country (i.e. Malaysia), using structural equation modelling.
Beyond sex
Authors: Cheung Ho Kwan , Lindsey Alex , King Eden , Hebl Michelle R
Published: February 2016

Purpose

– Influence tactics are prevalent in the workplace and are linked to crucial outcomes such as career success and helping behaviours. The authors argue that sex role identity affects women’s choice of influence tactics in the workplace, but they only receive positive performance ratings when their behaviours are congruent with gender role expectation. Furthermore, the authors hypothesize that these relationships may be moderated by occupational continuance commitment. Results suggest that femininity is negatively related to the use of influence tactics overall, and this relationship is moderated by occupational continuance commitment.

Design/methodology/approach

– In all, 657 women working in the construction industry were surveyed for their continuance occupational commitment and sex role identity and 465 supervisors whose responses are linked with the subordinates are surveyed for the women’s influence tactics and performance ratings.

Findings

– Results suggested that femininity was negatively related to the use of influence tactics overall, and this relationship was moderated by occupational continuance commitment. Results also showed that women’s use of influence tactics was only positively received in terms of performance ratings when the influence tactic was congruent with gender role expectations.

Research limitations/implications

– The results of this current study suggest that not all women are equally likely to use influence tactics and not all tactics result in positive perceptions of performance. Feminine women in general refrain from using influence tactics unless they are driven to stay in a given occupation, but they only receive positive results when their behaviours are congruent with society’s gender role expectations.

Originality/value

– Past research has mostly focused on broad differences between males and females, and this study has shown that there are more nuanced differences that can more accurately describe the effects of gender disposition (i.e. sex role identity) on influence tactics. It also emphasizes the importance of occupational commitment as a boundary condition, which influences women to step out of their gender roles even though they may be penalized with lower performance ratings.
Higher education curriculum for sustainability
Authors: Etse Daniel , Ingley Coral
Published: February 2016

Purpose

– The purpose of this study is to determine the degree of attention to and the nature of sustainability issues in the curriculum of the Higher National Diploma (HND) Purchasing and Supply Management programme of Ghana.

Design/methodology/approach

– Documentary research is the approach used to analyse the curriculum document for the programme of study.

Findings

– Findings of this study reveal a low presence of sustainability in the curriculum, and most of the sustainability sub-topics address issues of social justice, while economic sustainability issues feature the least.

Practical implications

– Deliberate and greater efforts should be made to integrate sustainability in the curriculum; all three dimensions of sustainability need to be well represented in the teaching and learning experiences; and there should be training and sensitisation of all relevant stakeholders in issues of sustainability.

Originality/value

– This study provides an analysis of a higher education curriculum in terms of attention given to sustainability and the nature of sustainability issues addressed therein. It sets the research agenda for the study of curricula of other programmes for sustainability, as research literature on higher education curricula for sustainability in Africa, especially Ghana, is scarce (GUNi et al., 2011).
Distinctly un-American: subliminal advertising and the Cold War
Authors: Samuel Lawrence R
Published: February 2016

Purpose

– This paper aims to describe the relationship between subliminal advertising and the Cold War to have a better understanding of the cultural dynamics of postwar America.

Design/methodology/approach

– This paper is a review of primary and secondary materials from the period 1957-1958, primarily popular and trade periodicals that capture the events as they took place.

Findings

– Subliminal advertising both reflected and shaped fears grounded in the Cold War cultural climate, and reveal other key insights related to the postwar psyche.

Research limitations/implications

– Political ideology is readily apparent within consumer culture, a prime example of the insights to be gained by viewing American culture through an interdisciplinary lens.

Practical implications

– Advertisers can effectively tap into consumers’ deeply seated emotions, but should tread carefully lest they be accused of “mind control”.

Social implications

– Subliminal advertising represented a seminal moment in postwar American history by exposing the hyper-paranoia of the times.

Originality/value

– A blow-by-blow account of the subliminal advertising craze and its relationship to the Cold War represents a deep dive into one of the more fascinating sites of mid-century America.
Individual and contextual factors influencing engagement in learning activities after errors at work
Authors: Leicher Veronika , Mulder Regina H.
Published: February 2016

Purpose

– The purpose of this replication study is to identify relevant individual and contextual factors influencing learning from errors at work and to determine if the predictors for learning activities are the same for the domains of nursing and retail banking.

Design/methodology/approach

– A cross-sectional replication study was carried out in retail banking departments of a German bank. In a pre-study, interviews were conducted with experts (N = 4) of retail banking. The pre-study was necessary to develop vignettes describing authentic examples of error situations which were part of the questionnaire. The questionnaire was filled out by 178 employees.

Findings

– Results indicate that the estimation of an error as relevant for learning positively predicts bankers’ engagement in social learning activities. The tendency to cover up an error predicts bankers’ engagement negatively. There are also indirect effects of error strain and the perception of a safe social team climate on the engagement in social learning.

Originality/value

– This paper contributes to the generalization of results by transferring and testing a model of learning from errors in a domain different from the previous domains where this topic was investigated.
Workplace identity as a mediator in the relationship between learning climate and job satisfaction during apprenticeship
Authors: Cortini Michela
Published: February 2016

Purpose

– The purpose of this paper was to explore if and to what extent workplace identity can mediate the relationship between learning climate dimensions and job satisfaction in a group of apprentices.

Design/methodology/approach

– Data were gathered thanks to a non-profit organization devoted to vocational training. Participants (N = 87) were apprentices working in different job contexts in central Italy.

Findings

– Results showed that the relationship between learning climate and job satisfaction was mediated by workplace identity.

Originality/value

– To the author’s knowledge, this is the first attempt to evaluate the effect of learning climate and workplace identity on job satisfaction during apprenticeship.
Exploring the universal ecological responses to climate change in a univoltine butterfly
Authors: Fenberg Phillip B. , Self Angela , Stewart John R. , Wilson Rebecca J. , Brooks Stephen J.
Published: February 2016

Animals with distinct life stages are often exposed to different temperatures during each stage. Thus, how temperature affects these life stages should be considered for broadly understanding the ecological consequences of climate warming on such species. For example, temperature variation during particular life stages may affect respective change in body size, phenology and geographic range, which have been identified as the “universal” ecological responses to climate change. While each of these responses has been separately documented across a number of species, it is not known whether each response occurs together within a species. The influence of temperature during particular life stages may help explain each of these ecological responses to climate change.

Our goal was to determine if monthly temperature variation during particular life stages of a butterfly species can predict respective changes in body size and phenology. We also refer to the literature to assess if temperature variability during the adult stage influences range change over time.

Using historical museum collections paired with monthly temperature records, we show that changes in body size and phenology of the univoltine butterfly, Hesperia comma, are partly dependent upon temporal variation in summer temperatures during key stages of their life cycle. June temperatures, which are likely to affect growth rate of the final larval instar, are important for predicting adult body size (for males only; showing a positive relationship with temperature). July temperatures, which are likely to influence the pupal stage, are important for predicting the timing of adult emergence (showing a negative relationship with temperature). Previous studies show that August temperatures, which act on the adult stage, are linked to range change.

Our study highlights the importance of considering temperature variation during each life stage over historic time‐scales for understanding intraspecific response to climate change. Range edge studies of ectothermic species that have annual life cycles, long time‐series occurrence data, and associated temperature records (ideally at monthly resolutions) could be useful model systems for intraspecific tests of the universal ecological responses to climate change and for exploring interactive effects.
Context‐dependent seed dispersal by a scatter‐hoarding corvid
Authors: Pesendorfer Mario B. , Sillett T. Scott , Morrison Scott A. , Kamil Alan C.
Published: February 2016

Corvids (crows, jays, magpies and nutcrackers) are important dispersers of large‐seeded plants. Studies on captive or supplemented birds suggest that they flexibly adjust their scatter‐hoarding behaviour to the context of social dynamics and relative seed availability. Because many corvid‐dispersed trees show high annual variation in seed production, context‐dependent foraging can have strong effects on natural corvid scatter‐hoarding behaviour.

We investigated how seed availability and social dynamics affected scatter‐hoarding in the island scrub jays (Aphelocoma insularis). We quantified rates of scatter‐hoarding behaviour and territorial defence of 26 colour‐marked birds over a three‐year period with variable acorn crops.

We tested whether caching parameters were correlated with variation in annual seed production of oaks as predicted by the predator dispersal hypothesis, which states that caching rates and distances should vary with seed abundance in ways that benefit tree fitness. We also tested whether antagonistic interactions with conspecifics would affect scatter‐hoarding adversely, as found in experimental studies.

Caching behaviour varied with acorn availability. Caching distances correlated positively with annual acorn crop size, increasing by as much as 40% between years. Caching rates declined over time in years with small acorn crops, but increased when crops were large. Acorn foraging and caching rates were also negatively correlated with rates of territorial aggression. Overall foraging rates, however, were not associated with aggression, suggesting that reduced dispersal rates were not simply due to time constraints.

Our field results support laboratory findings that caching rates and distances by scatter‐hoarding corvids are context‐dependent. Furthermore, our results are consistent with predictions of the predator dispersal hypothesis and suggest that large seed crops and social interactions among scatter‐hoarders affect dispersal benefits for oaks and other masting tree species.
Volatile Retention and Morphological Properties of Microencapsulated Tributyrin Varied by Wall Material and Drying Method
Authors: Donovan Joseph D. , Cadwallader Keith R. , Lee Youngsoo
Published: February 2016

Butyric acid is an important short‐chain fatty acid for intestinal health and has been shown to improve certain intestinal disease states. A triglyceride containing 3 butyric acid esters, tributyrin (TB) can serve as a source of butyric acid; however, the need to target intestinal delivery and mitigate unpleasant sensory qualities has limited its use in food. Microencapsulation, the entrapment of one or more cores within a matrix, may provide a solution to the aforementioned challenge. This research primarily focused on the influence of (1) wall material: whey and soy protein isolate (WPI and SPI, respectively) and gamma‐cyclodextrin (GCD), (2) wall additives: inulin of varying chain length, and (3) processing method: spray or oven drying (SD or OD, respectively) on the morphological properties and volatile retention of TB within microcapsules. SPI‐based microcapsules retained significantly less (P < 0.001) TB compared to WPI‐based microcapsules as measured by gas chromatography. The inclusion of inulin in the SD WPI‐based microcapsules increased (P < 0.001) TB retention over WPI‐based microcapsules without inulin. Inulin inclusion into WPI‐based microcapsules resulted in a smoother, minimally‐dented, circular morphology as compared to noninulin containing WPI‐based microcapsules as shown by scanning electron microscopy. GCD and TB OD microcapsules retained more (P < 0.001) TB (94.5% ± 1.10%) than all other WPI, WPI‐inulin, and GCD TB SD microcapsules. When spray dried, the GCD‐based microcapsules exhibited (P < 0.001) TB retention than all other microcapsules, indicating the GCD may be unsuitable for spray drying. These findings demonstrate that microencapsulated TB in GCD can lead to minimal TB losses during processing that could be utilized in functional food applications for intestinal health.
Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment
Authors: Korenblum Elisa , Jiménez Diego Javier , van Elsas Jan Dirk
Published: February 2016

Anaerobic bacteria degrade lignocellulose in various anoxic and organically rich environments, often in a syntrophic process. Anaerobic enrichments of bacterial communities on a recalcitrant lignocellulose source were studied combining polymerase chain reaction–denaturing gradient gel electrophoresis, amplicon sequencing of the 16S rRNA gene and culturing. Three consortia were constructed using the microbiota of lake sediment as the starting inoculum and untreated switchgrass (Panicum virgatum) (acid or heat) or treated (with either acid or heat) as the sole source of carbonaceous compounds. Additionally, nitrate was used in order to limit sulfate reduction and methanogenesis. Bacterial growth took place, as evidenced from 3 to 4 log unit increases in the 16S rRNA gene copy numbers as well as direct cell counts through three transfers on cleaned and reused substrate placed in fresh mineral medium. After 2 days, Aeromonas bestiarum‐like organisms dominated the enrichments, irrespective of the substrate type. One month later, each substrate revealed major enrichments of organisms affiliated with different species of Clostridium. Moreover, only the heat‐treated substrate selected Dysgonomonas capnocytophagoides‐affiliated bacteria (Bacteroidetes). Towards the end of the experiment, members of the Proteobacteria (Aeromonas, Rhizobium and/or Serratia) became dominant in all three types of substrates. A total of 160 strains was isolated from the enrichments. Most of the strains tested (78%) were able to grow anaerobically on carboxymethyl cellulose and xylan. The final consortia yield attractive biological tools for the depolymerization of recalcitrant lignocellulosic materials and are proposed for the production of precursors of biofuels.
Palestine, my love: The ethico‐politics of love and mourning in Jewish Israeli solidarity activism
Authors: WRIGHT FIONA
Published: February 2016

Jewish Israeli left‐wing activists engage in a subversive affective politics when they express love for, and mourn the loss of, Palestinian life. But the affects of love and mourning also bind these solidarity activists to Israeli state violence and sovereignty in various ways, entangling them in the very forms of power they aim to challenge. Loving and mourning the Palestinian Other involves an ambivalent ethics in which the activist subject objectifies the Other, and this objectification is a kind of violence that emerges in the affective becomings of solidarity activism. Activist loving and mourning thus call into question the nature of solidarity and alert us to the difficulty of ethics as troubled relations enmeshed in the violence of politics. [love, mourning, solidarity, ethics, political subjectivity, activism, Israel/Palestine]
“I am a radioactive mutant”: Emergent biological subjectivities at Kazakhstan's Semipalatinsk Nuclear Test Site
Authors: STAWKOWSKI MAGDALENA E.
Published: February 2016

The Semipalatinsk Nuclear Test Site in Kazakhstan was conceived as an experimental landscape where science, technology, Soviet Cold War militarism, and human biology intersected. As of 2015, thousands of people continue to live in rural communities in the immediate vicinity of this polluted landscape. Lacking good economic options, many of them claim to be “mutants” adapted to radiation, while outsiders see them as genetically tainted. In such a setting, how do post‐Soviet social, political, and economic transformations operate with radioactivity to co‐constitute a “mutant” subjectivity? Today, villagers think of themselves as biologically transformed but not disabled, showing that there is no uniform way of understanding the effects of radioactive pollution, including among scientists. [Kazakhstan, Semipalatinsk Nuclear Test Site, subjectivity, toxic environments, low‐dose radiation, nuclear testing]
Cholesterol: A necessary evil from a multiple sclerosis perspective
Authors: Chandra Avinash , Xu Yu Ming
Published: February 2016

Cholesterol and lipid are essential component of nerve cells. They are found in abundant quantities in the brain, with the largest pool of free cholesterol in the myelin sheath, a crucial component taking part in electrochemical conduction along the axons. However, disruption in cholesterol homeostasis becomes detrimental, as seen in multiple sclerosis (MS) at its various stages. MS is a complex disorder that is characterized by ongoing inflammatory, demyelinating and neurodegenerative processes. With an extensive literature search and critical review, we found that emerging epidemiological and molecular evidence suggests that cholesterol might have: (i) a causal relationship with MS; (ii) a positive association with the progression in disability in MS with an increase in cholesterol level; and (iii) an important role to play as a biomarker predicting MS disease course and the therapeutic response. The present review also highlights the possible therapeutic role of cholesterol and lipids in MS.
Contact radiotherapy boost in association with ‘watch and wait’ for rectal cancer: initial experience and outcomes from a shared programme between a district general hospital network and a regional oncology centre
Authors: Smith F. M. , Al‐Amin A. , Wright A. , Berry J. , Nicoll J. J. , Sun Myint A.
Published: February 2016

Aim

Recent data have highlighted the potential of more intensive neoadjuvant protocols to increase and sustain the rate of complete response in rectal cancer managed nonoperatively. This study aimed to review the outcome of all patients from our district general hospitals network who had received standard neoadjuvant therapy and were additionally referred to a centre of excellence for contact X‐ray brachytherapy or high‐dose‐rate brachytherapy boost.

Method

A retrospective, chart‐based review of all patients co‐managed in this manner was performed. Patient details were retrieved from a prospectively maintained departmental database. Indications for treatment, patient outcome and serial data from follow‐up clinical and radiological assessment were analysed.

Results

Seventeen patients treated over a 6‐year period were identified. Median follow‐up was 20 (5–54) months. Fourteen patients were clinically staged as T2 or T3 and eight were clinically node positive. Three patients died, of whom only one was initially a surgical candidate but refused an exenteration. Of the 14 patients who remain alive, 11 (79%) have a sustained complete (n = 8) or partial (n = 3) response. Two patients had an incomplete response, one is being palliated and the other awaits salvage surgery. One patient underwent abdominoperineal excision for suspected local recurrence. Currently 13 (93%) surviving patients are stoma free.

Conclusions

This series shows that the addition of a radiotherapy boost offered sustained responses and stoma‐free survival even in advanced disease and adverse patient populations whilst providing the majority of care closer to home.
A randomized controlled trial of web‐based training to increase activity in children with cerebral palsy
Authors: Mitchell Louise E , Ziviani Jenny , Boyd Roslyn N
Published: February 2016

Aim

To determine the efficacy of web‐based training on activity capacity and performance in children with unilateral cerebral palsy (CP).

Method

In a matched‐pairs randomized waitlist controlled trial, independently ambulant children and adolescents with unilateral CP were allocated to receive 30 minutes of training (intervention) 6 days per week, or usual care (waitlist control) for 20 weeks. Activity capacity was assessed using maximal repetitions of functional strength tasks and 6‐minute walk test (6MWT); performance using 4‐day ActiGraph GT3X+ accelerometer records at baseline and 20 weeks. Data were analysed by intention to treat comparing between groups using hierarchical linear modelling.

Results

Participants were n=101, 52 males, mean age 11 years 3 months (SD 2y 4mo). Intervention participants completed a mean 32.4 hours (SD 17.2) of training, associated with significant improvements in functional strength (mean difference 19.3 repetitions; 95% confidence interval [CI] 10.8–27.7; p<0.001) and 6MWT distance (mean difference 38.9m; 95% CI 12.3–51.9; p<0.001) compared with the control group at 20 weeks, although not activity performance (p>0.05).

Interpretation

Training was effective at increasing functional strength and walking endurance in independently ambulant children with unilateral CP. This did not translate into improvements in activity performance.
Off‐road vehicles affect nesting behaviour and reproductive success of American Oystercatchers Haematopus palliatus
Authors: Borneman Tracy E. , Rose Eli T. , Simons Theodore R.
Published: February 2016

As human populations and associated development increase, interactions between humans and wildlife are occurring with greater frequency. The effects of these interactions, particularly on species whose populations are declining, are of great interest to ecologists, conservationists, land managers and natural resource policy‐makers. The American Oystercatcher Haematopus palliatus, a species of conservation concern in the USA, nests on coastal beaches subject to various forms of anthropogenic disturbance, including aircraft overflights, off‐road vehicles and pedestrians. This study assessed the effects of these human disturbances on the incubation behaviour and reproductive success of nesting American Oystercatchers at Cape Lookout National Seashore, on the Atlantic coast of the USA. We expanded on‐going monitoring of Oystercatchers at Cape Lookout National Seashore by supplementing periodic visual observations with continuous 24‐h video and audio recording at nests. Aircraft overflights were not associated with changes in Oystercatcher incubation behaviour, and we found no evidence that aircraft overflights influenced Oystercatcher reproductive success. However, Oystercatchers were on their nests significantly less often during off‐road vehicle and pedestrian events than they were during control periods before the events, and an increase in the number of off‐road vehicles passing a nest during incubation was consistently associated with significant reductions in daily nest survival (6% decrease in daily nest survival for a one‐vehicle increase in the average number of vehicles passing a nest each day; odds ratio = 0.94; 95% confidence interval (CI) 0.90, 0.98) and hatching success (12% decrease in hatching success for a one‐vehicle increase in the average number of vehicles passing a nest each day; odds ratio = 0.88; 95% CI 0.76, 0.97). Management of vehicles and pedestrians in areas of Oystercatcher breeding is important for the conservation of American Oystercatchers.