bluuebunny/crossref_metadata_2025 huggingface dataset:
Trans‐Amazonian natal homing in giant catfish
Authors: Duponchelle Fabrice , Pouilly Marc , Pécheyran Christophe , Hauser Marilia , Renno Jean‐François , Panfili Jacques , Darnaude Audrey M. , García‐Vasquez Aurea , Carvajal‐Vallejos Fernando , García‐Dávila Carmen , Doria Carolina , Bérail Sylvain , Donard Ariane , Sondag Francis , Santos Roberto V. , Nuñez Jesus , Point David , Labonne Maylis , Baras Etienne
Published: April 2016

Knowledge of fish migration is a prerequisite to sustainable fisheries management and preservation, especially in large international river basins. In particular, understanding whether a migratory lifestyle is compulsory or facultative, and whether adults home to their natal geographic area is paramount to fully appraise disruptions of longitudinal connectivity resulting from damming.

In the Amazon, the large migratory catfishes of the Brachyplatystoma genus are apex predators of considerable interest for fisheries. They are believed to use the entire length of the basin to perform their life cycle, with hypothesized homing behaviours. Here, we tested these hypotheses, using the emblematic B. rousseauxii as a model species.

We sampled adults close to major breeding areas in the Amazon basin (upper Madeira and upper Amazonas) and assessed their lifetime movements by measuring variations in 87Sr/86Sr along transverse sections of their otoliths (ear stones) using laser ablation multicollector mass spectrometry (LA‐MC‐ICPMS).

We demonstrate that larvae migrate downstream from the Andean piedmont to the lower Amazon, where they grow over a protracted period before migrating upstream as adults. Contrary to prevailing inferences, not all fish spend their nursery stages in the Amazon estuary. By contrast, the passage in the lower or central Amazon seems an obligate part of the life cycle. We further evidence that most adults home to their natal geographic area within the Madeira sub‐basin. Such long‐distance natal homing is exceptional in purely freshwater fishes.

Synthesis and applications. By using otolith microchemistry, we were able to demonstrate a seemingly compulsory basin‐wide migratory life cycle of large Amazonian catfishes. This makes them the organisms performing the longest migrations (>8000 km) in fresh waters. This exceptional life history is already jeopardized by two dams recently built in the Madeira River, which block a major migration route and access to a substantial part of their spawning grounds. Major impacts can be anticipated from the current and forthcoming hydroelectric development in the Amazon basin, not only on the populations and fisheries of this apex predator, but also on Amazonian food webs through trophic cascades.
Evolutionary responses of invasive grass species to variation in precipitation and soil nitrogen
Authors: Nguyen Monica A. , Ortega Amy E. , Nguyen Kurt Q. , Kimball Sarah , Goulden Michael L. , Funk Jennifer L.
Published: April 2016

Global climate models suggest that many ecosystems will experience reduced precipitation over the next century and the consequences for invasive plant performance are largely unknown. Annual invasive species may be able to quickly evolve traits associated with drought escape or tolerance through rapid genetic changes.

We investigated the influence of 5 years of water and nitrogen manipulations on trait values in a southern California grassland system. Seeds from two annual grass species (Avena barbataandBromus madritensis) were collected from experimental plots and grown in a common environment over two generations. We measured 14 physiological, morphological, phenological and reproductive traits.

Both species displayed phenotypic differences depending on the water treatment from which they were collected, but not depending on the nitrogen treatment. Both species displayed trait values characteristic of drought escape (e.g. earlier flowering inA. barbataandB. madritensis, lower water‐use efficiency inB. madritensis) when grown from the seeds collected from plots that experienced five years of reduced precipitation. Furthermore,A. barbataindividuals grown from the seeds collected from drought plots had higher reproductive output and higher photosynthetic performance than individuals grown from water addition plots, with individuals grown from ambient plots displaying intermediate trait values. Notably, we found no phenotypic variation among treatments for six root traits.

Synthesis. Trait differences were observed following two generations in a common garden, suggesting that treatment differences were genetically based. This suggests that populations were responding to selection over the 5 years of water manipulations, a remarkably short time period. The rapid evolutionary responses observed here may help these two widespread invasive grass species thrive under reduced precipitation scenarios, which could have important implications for fire dynamics, invasive species management and native plant restoration in communities invaded by annual grasses.
Normalising desistance: contextualising marijuana and cocaine use careers in young adults
Authors: Roussell Aaron , Omori Marisa
Published: April 2016

Although there is a vast literature on drug use and addiction, there is little work that addresses the long‐term use of drugs within the general population. We take a more contextual look in examining longitudinal drug use patterns over the course of 14 years for a representative sample of young adults in their late teens and early twenties in the United States using the National Longitudinal Survey of Youth (NLSY). We use a growth trajectory modelling approach for cocaine and marijuana users to determine general use careers. Using contextual and life‐course variables, we then estimate a multinomial logistic regression model to predict group membership. In addition to establishing general use career groups, we ask how well mainstream theories comport with our findings and how the different chemical makeup of cocaine and marijuana influence our findings. We find four general use career groups: (i) high use/late desistance; (ii) peaked use/strong desistance; (iii) low use; and (iv) stable use/gradual desistance. Our results suggest similar careers for users of both drugs, with desistance over time as the rule for all groups. We also find some support for life‐course and contextual factors in drug using patterns, but our findings challenge other psychological and criminological theories.
Interaction of Government Tiers and Central Banks in a Federation: An Empirical Test
Authors: Claeys Peter , Ramos Raul , Suriñach Jordi
Published: April 2016

Fiscal rules are necessary to protect monetary policy from the consequences of unsustainable or active fiscal policy for inflation. Monetary unions, such as the Economic and Monetary Union (EMU), require even stronger fiscal rules to avoid free riding by regional fiscal authorities on the common monetary policy. By contrast, in a fiscal federation, the federal government internalises the effect of active regional policies on the overall price level. Federal fiscal policy contributes to price stability either by enforcing fiscal rules or by adjusting its own stance. Following Canzoneri, Cumby and Diba (2001), we test whether federal and regional governments in Germany behave in an active or passive way. We find evidence of a spillover effect of unsustainable policies on other regions. The German federal government offsets the effect on the price level by running passive policies. The Bundesbank's prime objective of price stability is therefore endorsed by fiscal policy. The results have implications for the regulation of fiscal policies in the EMU.
Investigation of Ballistic Evidence through an Automatic Image Analysis and Identification System
Authors: Kara Ilker
Published: April 2016

Automated firearms identification (AFI) systems contribute to shedding light on criminal events by comparison between different pieces of evidence on cartridge cases and bullets and by matching similar ones that were fired from the same firearm. Ballistic evidence can be rapidly analyzed and classified by means of an automatic image analysis and identification system. In addition, it can be used to narrow the range of possible matching evidence. In this study conducted on the cartridges ejected from the examined pistol, three imaging areas, namely the firing pin impression, capsule traces, and the intersection of these traces, were compared automatically using the image analysis and identification system through the correlation ranking method to determine the numeric values that indicate the significance of the similarities. These numerical features that signify the similarities and differences between pistol makes and models can be used in groupings to make a distinction between makes and models of pistols.
The Corpus Callosum and Forensic Issues—An Overview
Authors: Byard Roger W.
Published: April 2016

The 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.
Devolving authority: the impact of giving public schools power to hire staff
Authors: Gavin Mihajla , McGrath‐Champ Susan
Published: April 2016

Governments in the western world are increasingly experimenting with education policies that devolve responsibility for hiring and staffing to the local school level. Driven by forces of neoliberalism, marketisation and decentralisation, such reforms differentially affect schools as a result of various geographic and socio‐spatial factors. This article presents the findings of a recent study of public schools in the Australian state of New South Wales, and the impact that the government's Local schools, local decisions policy has had on staffing and hiring decisions within schools considered ‘hard‐to‐staff’. Drawing on interviews conducted with school principals and representatives of industrial bodies, this article reveals the differential and geographically diverse impact of devolutionary reform on ‘hard‐to‐staff’ schools. It posits that while the reforms facilitate the augmentation of staffing composition and enhanced decision‐making flexibility, the interaction of the policy with existing staffing processes undermines the reform's potential.
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

Aim

This 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.

Methods

A 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.

Results

The 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.

Conclusions

Strategies 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

Previous 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

This 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

Background

Insulin‐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.

Methods

A 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.

Results

Addition 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.

Conclusion

Functional 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

Background

The 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.

Methods

In 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).

Results

Serum 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.

Conclusions

Serum 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

Crickets (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

Environmental 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

The 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

Endophytes 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

This 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

The 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

N‐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

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.
Nitrogen efficiency and leaf nitrogen remobilisation of oilseed rape lines and hybrids
Authors: Wang L. , Mühling K.‐H. , Schulte auf'm Erley G.
Published: April 2016

Improved nitrogen (N) efficiency of oilseed rape is crucial for reducing environmental N surpluses. In this study, a 2‐year field experiment as well as a hydroponic experiment were performed with four hybrids and their corresponding lines. Seed yield and N efficiency parameters of oilseed rape cultivars grown at low N (0 kg N ha−1) and high N (150 kg N ha−1) supply were investigated in the field experiments. Hybrids showed higher seed yield than lines, especially at low N supply, because of a superior N uptake. Moreover, hybrids showed higher N harvest index (NHI) across N rates, which also contributed to higher seed yields. Results from the hydroponic experiment showed significant genotypic variation in leaf N remobilisation efficiency (NRE), but no hybrid‐versus‐line difference was found. Cultivars differed significantly in specific N content in senescent leaves, and leaf NRE was negatively correlated with specific N content in senescent leaves. When linking the hydroponic results with the field results, no relationship was found between leaf NRE and NHI. In conclusion, hybrids were superior to their corresponding lines in N efficiency because of higher N uptake and NHI. The higher NHI was, however, not related to genotypic variation in leaf NRE.
The interrelationship between attentional and executive deficits in major depressive disorder
Authors: Nilsson J. , Thomas A. J. , Stevens L. H. , McAllister‐Williams R. H. , Ferrier I. N. , Gallagher P.
Published: April 2016

Objective

Cognitive dysfunction is an established feature of major depressive disorder (MDD). However, it remains unclear whether deficits in different cognitive domains are relatively independent or originate from a circumscribed ‘primary deficit’. This study tested the hypothesis that a deficit in attention represents a primary deficit in depression.

Method

Neuropsychological function was assessed in 30 depressed patients with MDD and 34 control participants. Cognitive composites were derived from a minimum of three tests and included attention, executive function, visuospatial memory and verbal memory. A multivariate analysis of variance was used to assess group differences in overall cognitive performance, and multiple regression models were used to evaluate the role of attention in deficits in other domains.

Results

The cognitive deficit in the depressed sample was found to be characterized by poorer performance in attention and executive function. When evaluating the interrelationship between the two deficits, the attentional deficit was found to persist when variability in executive function was statistically accounted for, whilst the executive deficit was eliminated when attention was accounted for.

Conclusion

The results demonstrated that the attentional deficit could not be explained by deficits in executive function, which provides support for a primary attention deficit in depression.
Differences in health‐related quality of life between European and Asian patients with hepatocellular carcinoma
Authors: Chie Wei‐Chu , Blazeby Jane M , Hsiao Chin‐Fu , Chiu Herng‐Chia , Poon Ronnie T , Mikoshiba Naoko , Al‐Kadhim Gillian , Heaton Nigel , Calara Jozer , Collins Peter , Caddick Katharine , Costantini Anna , Vilgrain Valerie ,   Chieh Chiang, on behalf of the EORTC Quality of Life Group
Published: April 2016

Aim

The aim of this study is to explore the possible effects of clinical and cultural characteristics of hepatocellular carcinoma on patients’ health‐related quality of life (HRQoL).

Methods

Patients with hepatocellular carcinoma from Asian and European countries completed the EORTC QLQ‐C30 and the EORTC QLQ‐HCC18. Comparisons were made using Student's t‐test and Wilcoxon rank‐sum test with method of false discovery to correct multiple comparisons. Multiway analysis of variance and model selection were used to assess the effects of clinical characteristics and geographic areas.

Results

Two hundred and twenty‐seven patients with hepatocellular carcinoma completed questionnaires. After adjusting for demographic and clinical characteristics, Asian patients still had significantly better HRQoL scores in emotional functioning, insomnia, (QLQ‐C30) and in sexual interest (QLQ‐HCC18). We also found an interaction in physical functioning (QLQ‐C30) and fatigue (QLQ‐HCC18) between geographic region and marital status, married European had worse HRQoL scores than Asian singles.

Conclusions

Both clinical characteristics and geographic areas affected the HRQoL in with hepatocellular carcinoma. Cultural differences and clinical differences in the pattern of disease due to active surveillance of Asian countries may explain the results.
The Angioedema Quality of Life Questionnaire (AE‐QoL) – assessment of sensitivity to change and minimal clinically important difference
Authors: Weller K. , Magerl M. , Peveling‐Oberhag A. , Martus P. , Staubach P. , Maurer M.
Published: April 2016

Background

The Angioedema Quality of Life Questionnaire (AE‐QoL) has recently been developed and validated as the first specific patient‐reported outcome tool to assess quality of life (QoL) impairment in recurrent angioedema patients. As of yet, its sensitivity to change and minimal clinically important difference (MCID) have not been established.

Methods

Recurrent angioedema patients with chronic spontaneous urticaria or hereditary angioedema were repeatedly asked to complete the AE‐QoL along with the SF‐12 and other anchors for QoL impairment and disease activity during routine care visits. The sensitivity to change of AE‐QoL was determined by correlating changes in its scores over time with changes in the applied anchors. In addition, the MCID was determined using anchor‐based and distributional criterion‐based approaches.

Results

Two hundred and seventy‐eight patients contributed data sets for analysis. Baseline AE‐QoL values were found to correlate well with SF‐12 results as well as all other applied anchors for angioedema‐related QoL impairment and disease activity. In addition, AE‐QoL score changes over time correlated significantly with changes in the above anchors, thus demonstrating its sensitivity to change. The MCID of the AE‐QoL total score was found to be six points.

Conclusion

The AE‐QoL is a valuable tool to assess changes of QoL impairment in recurrent angioedema patients over time, including changes due to treatment.
Deceleration Capacity of Heart Rate Predicts Arrhythmic and Total Mortality in Heart Failure Patients
Authors: Arsenos Petros , Manis George , Gatzoulis Konstantinos A. , Dilaveris Polychronis , Gialernios Theodoros , Angelis Athanasios , Papadopoulos Achileas , Venieri Erifili , Trikas Athanasios , Tousoulis Dimitris
Published: April 2016

Background

Deceleration capacity (DC) of heart rate proved an independent mortality predictor in postmyocardial infarction patients. The original method (DCorig) may produce negative values (9% in our analyzed sample). We aimed to improve the method and to investigate if DC also predicts the arrhythmic mortality.

Methods

Time series from 221 heart failure patients was analyzed with DCorig and a new variant, the DCsgn, in which decelerations are characterized based on windows of four consecutive beats and not on anchors. After 41.2 months, 69 patients experienced sudden cardiac death (SCD) surrogate end points, while 61 died.

Results

(SCD+ vs SCD‐group) DCorig: 3.7 ± 1.6 ms versus 4.6 ± 2.6 ms (P = 0.020) and DCsgn: 4.9 ± 1.7 ms versus 6.1 ± 2.2 ms (P < 0.001). After Cox regression (gender, age, left ventricular ejection fraction, filtered QRS, NSVT≥1/24h, VPBs≥240/24h, mean 24‐h QTc, and each DC index added on the model separately), DCsgn (continuous) was an independent SCD predictor (hazard ratio [H.R.]: 0.742, 95% confidence intervals (C.I.): 0.631–0.871, P < 0.001). DCsgn ≤ 5.373 (dichotomous) presented 1.815 H.R. for SCD (95% C.I.: 1.080–3.049, P = 0.024), areas under curves (AUC)/receiver operator characteristic (ROC): 0.62 (DCorig) and 0.66 (DCsgn), P = 0.190 (chi‐square). Results for deceased versus alive group: DCorig: 3.2 ± 2.0 ms versus 4.8 ± 2.4 ms (P < 0.001) and DCsgn: 4.6 ± 1.4 ms versus 6.2 ± 2.2 ms (P < 0.001). In Cox regression, DCsgn (continuous) presented H.R.: 0.686 (95% C.I. 0.546–0.862, P = 0.001) and DCsgn ≤ 5.373 (dichotomous) presented an H.R.: 2.443 for total mortality (TM) (95% C.I. 1.269–4.703, P = 0.008). AUC/ROC: 0.71 (DCorig) and 0.73 (DCsgn), P = 0.402.

Conclusions

DC predicts both SCD and TM. DCsgn avoids the negative values, improving the method in a nonstatistical important level.
Primary trabeculotomy compared to combined trabeculectomy–trabeculotomy in congenital glaucoma: 3‐year study
Authors: Khalil Dalia H. , Abdelhakim Mohamad A. S. E.
Published: April 2016

Purpose

To compare the outcome of primary trabeculotomy with that of combined trabeculectomy–trabeculotomy (CTT) with mitomycin C (MMC) in children with congenital glaucoma.

Methods

This is a prospective comparative study, carried out on a cohort of 28 eyes (28 infants) with congenital glaucoma. Infants with proved congenital glaucoma [based on intra‐ocular pressure (IOP), cup/disc (C/D ratio), corneal diameter and axial length measurements] were randomly allocated to either group A (trabeculotomy) or group B (CTT with MMC). Postoperatively, all patients were followed regularly for 3 years; for IOP and C/D evaluation. Criteria for successful outcome included resolution of corneal oedema, reversal of disc cupping, and IOP 18 mmHg or less.

Results

Success rate in each group was 85.7% (p = 1.00). All preoperative parameters, including horizontal corneal diameter, axial length, IOP and C/D ratio, were not statistically significantly different between the two groups. Also, postoperative C/D ratio, IOP, IOP difference and percentage difference (compared to preoperative values), at different follow‐up visits, were not statistically significantly different between both surgical techniques. Comparing preoperative to postoperative IOP and C/D ratio in each group was statistically significant.

Conclusion

Both primary trabeculotomy and CTT with MMC had similar outcomes, which could mean that trabeculotomy could be resorted to first.
Maternal drug or alcohol abuse is associated with decreased head size from mid‐pregnancy to childhood
Authors: Lehikoinen Anni , Ordén Maija‐Riitta , Heinonen Seppo , Voutilainen Raimo
Published: April 2016

Aim

Maternal alcohol abuse is poorly recognised and causes developmental problems. This study explored the foetal central nervous systems (CNS), head circumference and psychomotor development of children exposed to drugs or alcohol during pregnancy up to 2.5 years of age.

Methods

We recruited 23 pregnant women referred to Kuopio University Hospital, Finland, by their family doctor because of drug or alcohol abuse, and 22 control mothers. Foetal CNS parameters were measured by three‐dimensional ultrasonography at the mean gestational age of 20 weeks and the Griffiths Mental Developmental Scales (GMDS), and anthropometric measurements were carried out at the mean ages of one and 2.5 years.

Results

The exposed foetuses had decreased biparietal and occipito‐frontal distances and head circumferences, but unchanged cerebellar volume at 20 weeks, and decreased head circumferences and length and height at birth, one and 2.5 years of age. They scored lower than the controls on the GMDS general quotient and the hearing, language and locomotor subscales at 2.5 years of age.

Conclusion

Maternal alcohol or drug exposure was associated with decreased head size from mid‐pregnancy to childhood and reduced development at 2.5 years. Foetal head circumference at mid‐pregnancy was a useful indicator of substance abuse affecting the CNS.
Vedolizumab induction therapy for inflammatory bowel disease in clinical practice – a nationwide consecutive German cohort study
Authors: Baumgart D. C. , Bokemeyer B. , Drabik A. , Stallmach A. , Schreiber S. ,   the Vedolizumab Germany Consortium
Published: April 2016

Background

Vedolizumab (VDZ) is a humanised monoclonal IgG1 antibody targeting α4β7 integrin.

Aim

To investigate the real‐world efficacy of vedolizumab for the treatment of Crohn's disease (CD) and ulcerative colitis (UC).

Methods

A consecutive cohort of 212 adult IBD patients with active disease (HBI >7/partial Mayo >4) newly receiving VDZ was prospectively recruited from 7 academic and 17 community centres. The primary endpoint was clinical remission (CRM) (CD HBI ≤4, UC pMayo ≤1) in week 14. Secondary endpoints included steroid‐free remission (SFCRM), clinical response (CRS) (HBI/pMayo score drop ≥3), vedolizumab impact on CRP, calprotectin and haemoglobin.

Results

Data of 97 CD (71.1% female, HBI 11) and 115 UC (42.6% female, pMayo 6) patients were analysed. Only 5.2% CD and 24.3% UC were anti‐TNFα naïve. Most had extensive mucosal involvement (Montreal L3 69.1%/E3 53.9%). At week 14, 23.7% vs. 23.5% of CD vs. UC patients achieved CRM, 19.6% vs. 19.1% SFCRM and 60.8% vs. 57.4% CRS, respectively (all based on NRI). Week 14 CRM in CD was significantly associated with no history of extraintestinal manifestations (P = 0.019), no prior adalimumab use (P = 0.011), no hospitalisation in the past 12 months (P = 0.015) and low HBI score (P = 0.02) and in UC with active or previous smoking (P = 0.044/0.028) and no anti‐TNFα (P = 0.023) use. Low HBI (P = 0.019) and no hospitalisation in the past 12 months (P = 0.01) predict CD CRM. The three most common AE were joint pain, acne and nasopharyngitis.

Conclusion

Vedolizumab is effective in routine use.
Edible plants for oral delivery of biopharmaceuticals
Authors: Merlin Matilde , Pezzotti Mario , Avesani Linda
Published: April 2016

Molecular farming is the use of plants for the production of high value recombinant proteins. Over the last 25 years, molecular farming has achieved the inexpensive, scalable and safe production of pharmaceutical proteins using a range of strategies. One of the most promising approaches is the use of edible plant organs expressing biopharmaceuticals for direct oral delivery. This approach has proven to be efficacious in several clinical vaccination and tolerance induction trials as well as multiple preclinical studies for disease prevention. The production of oral biopharmaceuticals in edible plant tissues could revolutionize the pharmaceutical industry by reducing the cost of production systems based on fermentation, and also eliminating expensive downstream purification, cold storage and transportation costs. This review considers the unique features that make plants ideal as platforms for the oral delivery of protein‐based therapeutics and describes recent developments in the production of plant derived biopharmaceuticals for oral administration.