bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Corpus Callosum and Forensic Issues—An Overview
Authors: Byard Roger W. 
Published: April 2016

AbstractThe corpus callosum is a large central white matter tract that connects the right and left cerebral hemispheres. It permits placental mammals to have a more sophisticated interhemispheric integration of sensory cortices and allows communication between cortical and subcortical neurons. Search of the literature and the pathology archives at The University of Adelaide was undertaken to identify lesions and injuries within the corpus callosum that may have forensic significance. These include developmental/congenital lesions with agenesis/dysgenesis, vascular malformations, and lipomas; inherited syndromes such as neurofibromatosis; and acquired lesions involving trauma, neoplasia, demyelination, vascular conditions, infections, fat embolism, aging/dementia, and the effects of toxins. The finding of lesions within the corpus callosum should initiate careful examination of the adjacent brain and other organ systems for related phenomena as this may shed some light on the nature of the underlying condition, and also help to determine whether there are any forensic implications.
School canteens: A systematic review of the policy, perceptions and use from an Australian perspective
Authors: Lawlis Tanya , Knox Melissa , Jamieson Maggie 
Published: April 2016

AimThis review aimed to identify current research related to the use of school canteens in Australia, with a focus on their food and drink policy. In Australia, approximately 25% of 5–17‐year olds are considered overweight and obese. Up to 41% of energy intake for children aged between 4 and 18 years is found to come from discretionary foods. The structured nature of the school environment provides an ideal environment to address childhood obesity and encourage a culture of healthy eating.MethodsA systematic review of three key nutrition databases: ‘CINAHL’, ‘Academic search complete’ and ‘Medline’ (inception to 2015) was conducted. Inclusion criteria were: Australian, peer‐reviewed studies; studies regarding the purchase of food from school canteens; canteen studies involving students aged 5–18 years, school principals, parents, canteen managers, Parent and Citizen Association members and teachers.ResultsThe search identified 2741 studies with 12 meeting the inclusion criteria. In the main, studies were descriptive in nature with data summarised into four categories: (i) characteristics of canteens; (ii) canteen use and food availability; (iii) stakeholder perceptions and the role of school canteens; and (iv) compliance with policies and the barriers to healthy food implementation. Overall, compliance with healthy canteen policies was low, guidelines were rarely adhered to in terms of product provision and children had preferences for non‐healthy foods.ConclusionsStrategies to improve compliance, overcome the challenges and encourage stakeholder buy‐in are necessary if food habits are to be changed and healthy cultures developed within the school environment.
Instrumental and Sensory Texture Attributes of High‐Protein Nutrition Bars Formulated with Extruded Milk Protein Concentrate
Authors: Banach J.C. , Clark S. , Lamsal B.P. 
Published: April 2016

AbstractPrevious instrumental study of high‐protein nutrition (HPN) bars formulated with extruded milk protein concentrate (MPC) indicated slower hardening compared to bars formulated with unmodified MPC. However, hardness, and its change during storage, insufficiently characterizes HPN bar texture. In this study, MPC80 was extruded at 2 different conditions and model HPN bars were prepared. A trained sensory panel and instrumental techniques were used to measure HPN bar firmness, crumbliness, fracturability, hardness, cohesiveness, and other attributes to characterize texture change during storage. Extrusion modification, storage temperature, and storage time significantly affected the instrumental and sensory panel measured texture attributes. The HPN bars became firmer and less cohesive during storage. When evaluated at the same storage conditions, the texture attributes of the HPN bars formulated with the different extrudates did not differ significantly from each other. However, textural differences were noted most of the time between the control and the HPN bars formulated with extruded MPC80. An adapted HPN bar crumbliness measurement technique produced results that were correlated with sensory panel measured crumbliness (r = 0.85) and cohesiveness (r = –0.84). Overall, the HPN bars formulated with extruded MPC80 were significantly softer, less crumbly, and more cohesive than the control during storage.
Antihypertensive Properties of a Pea Protein Hydrolysate during Short‐ and Long‐Term Oral Administration to Spontaneously Hypertensive Rats
Authors: Girgih Abraham T. , Nwachukwu Ifeanyi D. , Onuh John O. , Malomo Sunday A. , Aluko Rotimi E. 
Published: April 2016

AbstractThis study investigated short‐term (24 h) and long‐term (5 wk) systolic blood pressure (SBP)‐lowering effects in spontaneously hypertensive rats (SHR) of a 5 kDa membrane pea protein hydrolysate permeate (PPH‐5) produced through thermoase hydrolysis of pea protein isolate (PPI). Amino acid analysis showed that the PPH‐5 had lower contents of sulfur‐containing amino acids than the PPI. Size‐exclusion chromatography indicated mainly low molecular weight (<10 kDa) peptides in PPH‐5 but not in the PPI. The PPH‐5 had renin and angiotensin converting enzyme inhibition IC50 values of 0.57 and 0.10 mg/mL (P < 0.05), respectively, and consisted mainly of peptides with 2 to 6 amino acids. Mass spectrometry analysis revealed mainly hydrophilic tetrapeptide sequences. After a single oral administration (100 mg/kg body weight) to SHR, the unheated PPI showed weakest (P < 0.05) SBP‐lowering effect with a –4 mm Hg maximum when compared to –25 mm Hg for heat‐treated PPI and –36 mm Hg for PPH‐5. Incorporation of the PPH‐5 as 0.5% or 1% (w/w) casein substitute in the SHR diet produced maximum SBP reductions of –22 or –26 mm Hg (P < 0.05), respectively after 3 wk. In comparison, the unhydrolyzed PPI produced a maximum SBP reduction of –17 mm Hg also after 3 wk. Potency of the pea products decreased in the 4th and 5th wk, though SBP values of the treated rats were still lower than the untreated control. We conclude that the antihypertensive potency of PPH‐5 may have been due to the presence of easily absorbed hydrophilic peptides.
Efficient generation of functional pancreatic β‐cells from human induced pluripotent stem cells
Authors: Yabe Shigeharu G. , Fukuda Satsuki , Takeda Fujie , Nashiro Kiyoko , Shimoda Masayuki , Okochi Hitoshi 
Published: April 2016

AbstractBackgroundInsulin‐secreting cells have been generated from human embryonic or induced pluripotent stem cells (iPSCs) by mimicking developmental processes. However, these cells do not always secrete glucose‐responsive insulin, one of the most important characteristics of pancreatic β‐cells. We focused on the importance of endodermal differentiation from human iPSCs in order to obtain functional pancreatic β‐cells.MethodsA six‐stage protocol was established for the differentiation of human iPSCs to pancreatic β‐cells using defined culture media without feeders or serum. The effects of CHIR99021, a selective glycogen synthase kinase‐3β inhibitor, were examined in the presence of fibroblast growth factor 2, activin, and bone morphogenetic protein 4 (FAB) during definitive endodermal induction by immunostaining for SRY (sex determining region Y)‐box 17 (SOX17) and Forkhead box protein A2 (FOXA2). Insulin secretion was compared between the last stage of monolayer culture and spheroid culture conditions. Cultured cells were transplanted under kidney capsules of streptozotocin‐diabetic non‐obese diabetic–severe combined immunodeficiency mice, and blood glucose levels were measured once a week. Immunohistochemical analyses were performed 4 and 12 weeks after transplantation.ResultsAddition of CHIR99021 (3 μmol/L) in the presence of FAB for 2 days improved endodermal cell viability, maintaining the high SOX17‐positive rate. Spheroid formation after the endocrine progenitor stage showed more efficient insulin secretion than did monolayer culture. After cell transplantation, diabetic mice had lower blood glucose levels, and islet‐like structures were detected in vivo.ConclusionFunctional pancreatic β‐cells were generated from human iPSCs. Induction of definitive endoderm and spheroid formation may be key steps for producing these cells.
Serum brain‐derived neurotrophic factor levels and sleep disorders in Chinese healthy and newly diagnosed type 2 diabetic subjects
Authors: Wei Huili , Qu Hua , Wang Hang , Ji Baolan , Deng Huacong 
Published: April 2016

AbstractBackgroundThe aims of the present study were to detect serum brain‐derived neurotrophic factor (BDNF) protein concentrations in healthy and diabetic subjects with sleep disorders and to explore correlations among serum BDNF concentrations, metabolic parameters and inflammation.MethodsIn all, 377 eligible subjects were recruited to the study and underwent a 75‐g oral glucose tolerance test. Various clinical parameters of metabolic disorders and cytokines were measured. Sleep disorders were assessed using the Pittsburgh Sleep Quality Index (PSQI). Subjects were grouped into those with normal glucose tolerance (NGT), those with NGT and sleep disorders (NGT‐SDi), those with newly diagnosed type 2 diabetes mellitus (T2DM), and those with newly diagnosed T2DM and sleep disorders (T2DM‐SDi).ResultsSerum BDNF levels were higher in the NGT‐SDi and T2DM‐SDi subgroups than in the NGT and T2DM groups, respectively. Multiple linear regression analysis revealed that serum BDNF concentrations were independently correlated with PSQI scores, homeostasis model assessment of insulin resistance, and HbA1c, interleukin 6 and tumor necrosis factor‐α concentrations (P < 0.05 for all). Binary logistic regression analysis revealed that significant associations remained between serum BDNF concentrations and sleep disorders after adjustment for glucose‐ and metabolic‐related factors in both the NGT‐SDi and T2DM‐SDi subgroups.ConclusionsSerum BDNF concentrations were higher in patients with sleep disorders and were associated with various metabolic parameters and inflammatory cytokines.
A genes eye view of ontogeny:de novoassembly and profiling of theGryllus rubenstranscriptome
Authors: Berdan Emma L. , Blankers Thomas , Waurick Isabelle , Mazzoni Camila J. , Mayer Frieder 
Published: April 2016

AbstractCrickets (Orthoptera:Gryllidae) are widely used model organisms for developmental, evolutionary, neurobiological and behavioural research. Here, we developed ade novotranscriptome from pooledRNA‐seq Illumina data spanning seven stages in the life cycle ofGryllus rubens. Approximately 705 Mbp of data was assembled and filtered to form 27 312 transcripts. We were able to annotate 52% of our transcripts usingBLASTand assign at least one gene ontology term to 41%. Pooled samples from three different ontogenetic stages were used for transcriptomic profiling revealing patterns of differential gene expression that highlight processes in the different life stages. Embryonic and early instar development was enriched for ecdysteroid metabolism, cytochrome P450s and glutathione production. Late instar development was enriched for regulation of gene expression and many of the genes highly expressed during this stage were involved in conserved developmental signalling pathways suggesting that these developmental pathways are active beyond embryonic development. Adults were enriched for fat transport (mostly relating to egg production) and production of octopamine, an important neurohormone. We also identified genes involved in conserved developmental pathways (Hedgehog, Hippo, Wnt,JAK/STAT,TGF‐beta, Notch, andMEK/ERK). This is the first transcriptome spanning ontogeny inGryllus rubensand a valuable resource for future work on development and evolution in Orthoptera.
The importance of including imperfect detection models in eDNA experimental design
Authors: Willoughby Janna R. , Wijayawardena Bhagya K. , Sundaram Mekala , Swihart Robert K. , DeWoody J. Andrew 
Published: April 2016

AbstractEnvironmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.
Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms
Authors: Yuan Hao , Jiang Jiamei , Jiménez Francisco Agustín , Hoberg Eric P. , Cook Joseph A. , Galbreath Kurt E. , Li Chenhong 
Published: April 2016

AbstractThe Cyclophyllidea is the most diverse order of tapeworms, encompassing species that infect all classes of terrestrial tetrapods including humans and domesticated animals. Available phylogenetic reconstructions based either on morphology or molecular data lack the resolution to allow scientists to either propose a solid taxonomy or infer evolutionary associations. Molecular markers available for the Cyclophyllidea mostly include ribosomalDNAand mitochondrial loci. In this study, we identified 3641 single‐copy nuclear coding loci by comparing the genomes ofHymenolepis microstoma,Echinococcus granulosusandTaenia solium. We designedRNAbaits based on the sequence ofH. microstoma, and applied target enrichment and Illumina sequencing to test the utility of those baits to recover loci useful for phylogenetic analyses. We capturedDNAfrom five species of tapeworms representing two families of cyclophyllideans. We obtained an average of 3284 (90%) of the targets from the test samples and then used captured sequences (2 181 361 bp in total; fragment size ranging from 301 to 6969 bp) to reconstruct a phylogeny for the five test species plus the three species for which genomic data are available. The results were consistent with the current consensus regarding cyclophyllidean relationships. To assess the potential for our method to yield informative genetic variation at intraspecific scales, we extracted 14 074 single nucleotide polymorphisms (SNPs) from alignments of fourArostrilepis macrocirrosaand twoA. cookiand successfully inferred their relationships. The results showed that our target gene tools yield data sets that provide robust inferences at a range of taxonomic scales in the Cyclophyllidea.
Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis
Authors: Bertani Iris , Abbruscato Pamela , Piffanelli Pietro , Subramoni Sujatha , Venturi Vittorio 
Published: April 2016

SummaryEndophytes are harmless or beneficial microorganisms that live inside plants between cells. The relationship they develop with the plant as well as their potential role in plant health is at large unexplored and it is believed that the opportunity to find new and interesting endophytes among the large variety of plants is great. Here, we present the isolation and analysis of a large collection of endophytes from one cultivar of rice grown in Italy. A total 1318 putative endophytes were isolated from roots, leaves and stems from rice grown in submerged and dry conditions and a working collection of 229 isolates was created. Among these, several isolates were confirmed to be endophytes and a few displayed the trait of plant growth promotion. A cultivation independent analysis via 16S rDNA amplicons of the bacterial community of the endosphere was also performed providing information on bacterial diversity in the rice endopshere.
How Peace Agreements Undermine the Rule of Law in New War Settings
Authors: Kaldor Mary 
Published: April 2016

AbstractThis article argues that internationally endorsed peace agreements entrench the restructuring of power relations that take place in ‘new wars’. It characterizes new wars as ‘mutual enterprises’ in which networks of state and nonstate actors engage in violence for economic and/or political gain. The article shows the way in which such networks subvert efforts to implement a rule of law, primarily using the example of Bosnia. It argues that efforts to challenge such networks through transitional justice mechanisms or democratic politics face huge obstacles. It suggests that the role of the international community has been ambiguous, sometimes going with the grain of existing power relations for geo‐political reasons or for stability and sometimes upholding human rights. Only where grass roots actors have directly accessed international justice mechanisms or where local activists have worked with municipalities have there been some openings. The article concludes by suggesting what a ‘new peace’ might involve.
Why We Should Stop Being Surprised that Lightly Regulated Markets Fall Short of the SEC's Goals for Market Quality: A Discussion of “Private Intermediary Innovation and Market Liquidity”
Authors: Bloomfield Robert 
Published: April 2016

AbstractThe stated goals of the SEC are to protect investors, maintain orderly markets and facilitate capital formation. These goals can be achieved with very light regulation if, as assumed by traditional economic theory, investors process information costlessly and protect themselves from informational disadvantages, and firms optimally balance the costs and benefits of committing to make their reports reliable. A growing body of research demonstrates that light regulation fails to achieve the SEC's goals, because investors find information processing costly and fail to protect themselves. After reviewing theory and prior evidence, I discuss new lessons learned from Jiang, Petroni, and Wang (), who show that Pink Sheets® reduced the liquidity of firms with low reporting quality and increased the liquidity of firms with high reporting quality, merely by highlighting the quality of their listed firms’ disclosure. While the Pink Sheets® innovation might have occurred through many causal channels, all of them entail a violation of costless processing and self‐protection, and lead to the conclusion that this lightly regulated market did not initially meet the stated goals of the SEC. I conclude by arguing that markets can achieve the SEC's goals only if they exhibit a particularly strong version of “dynamic” market efficiency, which requires that each individual trade on the path to even incomplete revelation occurs at the then‐optimal price. Because dynamic efficiency is unlikely, we should stop being surprised to see evidence that lightly regulated markets fall short on key dimensions. Instead, we should use our well‐developed understanding of market inefficiency to guide regulation.
Estimating abundance in the presence of species uncertainty
Authors: Chambert Thierry , Hossack Blake R. , Fishback LeeAnn , Davenport Jon M. 
Published: April 2016

SummaryN‐mixture models have become a popular method for estimating abundance of free‐ranging animals that are not marked or identified individually. These models have been used on count data for single species that can be identified with certainty. However, co‐occurring species often look similar during one or more life stages, making it difficult to assign species for all recorded captures. This uncertainty creates problems for estimating species‐specific abundance, and it can often limit life stages to which we can make inference.We present a new extension of N‐mixture models that accounts for species uncertainty. In addition to estimating site‐specific abundances and detection probabilities, this model allows estimating probability of correct assignment of species identity. We implement this hierarchical model in a Bayesian framework and provide all code for running the model inBUGSlanguage programs.We present an application of the model on count data from two sympatric freshwater fishes, the brook stickleback (Culaea inconstans) and the ninespine stickleback (Pungitius pungitius), and illustrate implementation of covariate effects (habitat characteristics). In addition, we used a simulation study to validate the model and illustrate potential sample size issues. We also compared, for both real and simulated data, estimates provided by our model to those obtained by a simple N‐mixture model when captures of unknown species identification were discarded. In the latter case, abundance estimates appeared highly biased and very imprecise, while our new model provided unbiased estimates with higher precision.This extension of the N‐mixture model should be useful for a wide variety of studies and taxa, as species uncertainty is a common issue. It should notably help improve investigation of abundance and vital rate characteristics of organisms’ early life stages, which are sometimes more difficult to identify than adults.
trapper: an open source web‐based application to manage camera trapping projects
Authors: Bubnicki Jakub W. , Churski Marcin , Kuijper Dries P. J. 
Published: April 2016

Summary

Camera trapping is increasingly becoming an important tool in ecological research. However, the organization of large collections of multimedia files and especially efficient searching for subsets of data is a challenging task. While the development of project‐specific software solutions is dominating in the camera trapping community, little attention has been paid to more flexible and open‐source solutions supporting diverse camera trapping research projects.

We used state of the art and well‐recognized open source software components and programming language python to design and implement trapper, a flexible data base driven web application to manage, classify, integrate, share and re‐use data in camera trapping projects.

The main features of trapper are: (i) it is fully open‐source, (ii) it facilitates analysis of videos as well as images, (iii) it provides spatial filtering and web‐mapping, (iv) it allows flexible implementation of specific data collection protocols, (v) it is a multi‐user and role based system which facilitates collaborative work on camera trapping projects, (vi) it supports data re‐use and (re)discovery.

trapper can therefore be widely used by ecologists working with a variety of camera trap studies, alone or in collaboration with each other.