bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biophysically Realistic Neuron Models for Simulation of Cortical Stimulation
Authors: Aberra Aman S. , Peterchev Angel V. , Grill Warren M. 
Published: May 2018

1.AbstractObjectiveWe implemented computational models of human and rat cortical neurons for simulating the neural response to cortical stimulation with electromagnetic fields.ApproachWe adapted model neurons from the library of Blue Brain models to reflect biophysical and geometric properties of both adult rat and human cortical neurons and coupled the model neurons to exogenous electric fields (E-fields). The models included 3D reconstructed axonal and dendritic arbors, experimentally-validated electrophysiological behaviors, and multiple, morphological variants within cell types. Using these models, we characterized the single-cell responses to intracortical microstimulation (ICMS) and uniform E-field with dc as well as pulsed currents.Main resultsThe strength-duration and current-distance characteristics of the model neurons to ICMS agreed with published experimental results, as did the subthreshold polarization of cell bodies and axon terminals by uniform dc E-fields. For all forms of stimulation, the lowest threshold elements were terminals of the axon collaterals, and the dependence of threshold and polarization on spatial and temporal stimulation parameters was strongly affected by morphological features of the axonal arbor, including myelination, diameter, and branching.SignificanceThese results provide key insights into the mechanisms of cortical stimulation. The presented models can be used to study various cortical stimulation modalities while incorporating detailed spatial and temporal features of the applied E-field.
Rapid alignment-free phylogenetic identification of metagenomic sequences
Authors: Linard Benjamin , Swenson Krister , Pardi Fabio 
Published: May 2018

AbstractMotivationTaxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, phylogenetic placement (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However,likelihood-based PP algorithms struggle to scale with the ever-increasing throughput of DNA sequencing.ResultsWe have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach, removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers that may be present with non-negligible probability in relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than competing likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP for the era of routine metagenomic diagnostics.AvailabilityProgram and sources freely available for download at gite.lirmm.fr/linard/RAPPAS.Contactbenjamin.linard@lirmm.fr
Genetic diversity in twoPlasmodium vivaxprotein ligands for reticulocyte invasion
Authors: Roesch Camille , Popovici Jean , Bin Sophalai , Run Vorleak , Kim Saorin , Ramboarina Stéphanie , Rakotomalala Emma , Rakotoarison Rado Lalaina , Rasoloharimanana Tsikiniaina , Andriamanantena Zo , Kumar Anuj , Guillotte-Blisnick Micheline , Huon Christèle , Serre David , Chitnis Chetan E. , Vigan-Womas Inès , Menard Didier 
Published: May 2018

AbstractThe interaction betweenPlasmodium vivaxDuffy binding protein (PvDBP) and Duffy antigen receptor for chemokines (DARC) has been described as critical for the invasion of human reticulocytes, although increasing reports ofP. vivaxinfections in Duffy-negative individuals questions its unique role. To investigate the genetic diversity of the two main protein ligands for reticulocyte invasion, PvDBP andP. vivaxErythrocyte Binding Protein (PvEBP), we analyzed 458 isolates collected in Cambodia and Madagascar. First, we observed a high proportion of isolates with multiple copies PvEBP from Madagascar (56%) where Duffy negative and positive individuals coexist compared to Cambodia (19%) where Duffy-negative population is virtually absent. Whether the gene amplification observed is responsible for alternate invasion pathways remains to be tested. Second, we found that thePvEBPgene was less diverse thanPvDBPgene (12vs.33 alleles) but provided evidence for an excess of nonsynonymous mutations with the complete absence of synonymous mutations. This finding reveals that PvEBP is under strong diversifying selection, and confirms the importance of this protein ligand in the invasion process of the human reticulocytes and as a target of acquired immunity. These observations highlight how genomic changes in parasite ligands improve the fitness ofP. vivaxisolates in the face of immune pressure and receptor polymorphisms.
Molecular determinants of WNT9b responsiveness in nephron progenitor cells
Authors: Dickinson Kyle K. , Hammond Leah C. , Karner Courtney M. , Hastie Nicholas D. , Carroll Thomas J. , Goodyer Paul R. 
Published: May 2018

AbstractPrimed nephron progenitor cells (NPCs) appear in metanephric mesenchyme by Ell.5 and differentiate in response to the inductive WNT9b signal from the ureteric bud. However, the NPC WNT-receptor complex is unknown. We obtained M15 cells from E10.5 mesonephric mesenchyme and systematically analyzed components required for canonical WNT9b-responsiveness. When M15 cells were transfected with a (β-catenin luciferase reporter plasmid, exposure to recombinant WNT9b resulted in minimal luciferase activity. We then analyzed mRNA-expression of WNT-pathway components and identifiedFzdl-6andLrp6transcripts but notRSPO1.When M15 cells were treated with recombinant RSPO1 the response to transfected WNT9b was augmented 4.8-fold. Co-transfection of M15 cells withFzd5(but no otherFzdfamily member) further increased the WNT9b signal to 16.8-fold and siRNA knockdown ofFzd5reduced the signal by 52%. Knockdown ofLrp6resulted in 60% WNT9b signal reduction. We confirmedFzd5, Lrp6andRSPO1rrtRNA expression in CITED1(+) NPCs from E15.5 embryonic mouse kidney. Thus, while many WNT signaling-pathway components are present by E10.5, optimum responsiveness of Ell.5 cap mesenchyme requires that NPCs acquire RSPO1, FZD5 and LRP6.Summary StatementResponsiveness to the inductive WMT9b signal from ureteric bud is crucial for nephrogenesis. Here we analyze the molecules needed to prime nephron progenitor cells in embryonic mouse kidney.
Measuring behavioural biases affecting real estate investment decisions in India: using IRT
Authors: Pandey Richa , Jessica V. Mary 
Published: May 2018

Purpose
This study aims to investigate the behavioural biases influencing the real estate market investing decisions of normal non-professional investors in India.

Design/methodology/approach
As the study involves the behavioural data with polytomous response format, psychometric test- graded response model (IRT approach) was used for the study with the help of STATA 14. Multi-stage stratified sampling was used to collect a sample of 560 respondents. The study used a 14-item scale representing behavioural biases derived from two broad behavioural theories, i.e. heuristics and prospect theories. Sample characteristics were checked using SPSS 20. Pre-required assumptions for IRT (i.e. local independence and unidimensionality) were tested by CFA using AMOS 20.

Findings
Five items, four of which belong to heuristics (anchoring – 2, representativeness – 1 and availability bias – 1) and one belong to prospect theory (regret aversion) are sufficient to measure the behavioural attitude of real estate investors in the Indian scenario. Item discrimination ai ranged from 0.95 to 1.52 (average value 1.29), showing moderate discrimination power of the items. The items have done a pretty good job of assessing the lower level of agreement. For the higher level of agreement, the scale came out to be less precise, with less information and higher standard error of measurement.

Research limitations/implications
As the behavioural biases are often false, the study suggests the investors not to repeat these nasty biases to improve investment strategies. As they are shared and not easily changeable, understanding these biases may also help them in beating the market by acting as “noise traders”.

Practical implications
The traditional price index is incomplete in some essential respects. The inclusion of these behavioural biases into the construction of price index will greatly improve the traditional price index, policymakers should seriously think about it.

Social implications
Shelter is one of the basic needs; a dwelling unit is needed for one to stay in, develop and contribute to economy and society. If investors try to minimise these biases and policymakers keep a track of these while making strategies, mispricing in this sector can be controlled to some extent, which will ultimately help in the well-being of society.

Originality/value
This study contributes to the limited research by investigating the behavioural biases influencing the real estate market investment decisions of normal non-professional investors. It contributes to the lacking academe on real estate market in India. The study has used a psychometric test, i.e. the item response theory, for evaluating the quality of the items.
What doesn’t kill you makes you stronger: The burdens and benefits of toxin sequestration in a milkweed aphid
Authors: Züst Tobias , Mou Sophie , Agrawal Anurag A. 
Published: May 2018

Abstract

Specialized insect herbivores commonly co‐opt plant defences for protection against predators, but the costs, benefits and mechanisms of sequestration are poorly understood.

We quantified sequestration of toxic cardenolides by the specialist aphid Aphis nerii when reared on four closely related milkweed (Asclepias) species with >20‐fold variation in cardenolide content, and in the presence or absence of generalist ladybug predators.

Increasing concentrations of apolar plant cardenolides increased sequestered amounts in aphids. High concentrations in plants impaired aphid population growth, but also reduced the top‐down effects of predators. An in vitro enzymatic assay of total cardenolides in aphid bodies using the cardenolides’ target (animal Na+/K+‐ATPase) revealed that the subset of sequestered cardenolides is disproportionally more toxic than cardenolides in leaves.

All aphids accumulated two cardenolides not present in their host plant, even on plants with very low foliar cardenolide concentrations. Sequestration of potent cardenolides by A. nerii thus involves passive, concentration‐dependent uptake from the host plant, as well as a presumably more active mechanism of modification and up‐concentration of plant cardenolides.

The concentration of toxins in the host plant thus not only determines the negative impacts on growth and performance of an aphid, but also the ease and efficiency by which toxins are sequestered for the aphid’s defence, making the costs and benefits of plant toxins highly context‐dependent for both the plant and the herbivore. Therefore, variation in plant toxins is of central importance for co‐evolutionary plant–insect interactions, particularly in environments with variable predator pressure.

A plain language summary is available for this article.
In vivo profiling of four centrally administered opioids for antinociception, constipation and respiratory depression: Between‐colony differences in Sprague Dawley rats
Authors: Kuo Andy , Smith Maree T 
Published: May 2018

SummaryOutbred rodent stocks including Sprague Dawley rats, are known for their genetic diversity and so they are often used to develop animal models of human disease. Although between‐colony differences in pharmaco‐behavioural studies have been published previously, a direct head‐to‐head comparison study, whereby all research was performed in the same laboratory by the same experimenter utilising the supraspinal route of drug administration in the same strain of rat, is lacking. Herein, we report our head‐to‐head comparison study, involving assessment of antinociception, constipation and respiratory depression evoked by single bolus intracerebroventricular (ICV) doses of morphine, buprenorphine, DPDPE and U69,593 using male Sprague Dawley rats sourced from a different breeding colony (BC2) from that (BC1) used by us previously. Our data show that there are marked differences in the potency rank order for morphine and buprenorphine between rats sourced from BC2 and BC1. Although ICV morphine evoked a bell‐shaped dose‐response curve in the constipation test for rats from both colonies, this occurred at higher doses for rats from BC2. In conclusion, our head‐to‐head comparison shows considerable between‐colony differences for the same rat strain, in the potency rank order of two clinically important strong opioid analgesics given by the ICV route.
Bangladeshi children with acute diarrhoea show faecal microbiomes with increased Streptococcus abundance, irrespective of diarrhoea aetiology
Authors: Kieser Silas , Sarker Shafiqul A. , Sakwinska Olga , Foata Francis , Sultana Shamima , Khan Zeenat , Islam Shoheb , Porta Nadine , Combremont Séverine , Betrisey Bertrand , Fournier Coralie , Charpagne Aline , Descombes Patrick , Mercenier Annick , Berger Bernard , Brüssow Harald 
Published: May 2018

SummaryWe report streptococcal dysbiosis in acute diarrhoea irrespective of aetiology. Compared with 20 healthy local controls, 71 Bangladeshi children hospitalized with acute diarrhoea (AD) of viral, mixed viral/bacterial, bacterial and unknown aetiology showed a significantly decreased bacterial diversity with loss of pathways characteristic for the healthy distal colon microbiome (mannan degradation, methylerythritol phosphate and thiamin biosynthesis), an increased proportion of faecal streptococci belonging to the Streptococcus bovis and Streptococcus salivarius species complexes, and an increased level of E. coli‐associated virulence genes. No enteropathogens could be attributed to a subgroup of patients. Elevated lytic coliphage DNA was detected in 2 out of 5 investigated enteroaggregative E. coli (EAEC)‐infected patients. Streptococcal outgrowth in AD is discussed as a potential nutrient‐driven consequence of glucose provided with oral rehydration solution.
Assessment of Antibiotic Susceptibility within Lactic Acid Bacteria and Coagulase‐Negative Staphylococci Isolated from Hunan Smoked Pork, a Naturally Fermented Meat Product in China
Authors: Wang Jing , Wei Xinyuan , Fan Mingtao 
Published: May 2018

AbstractThe aim of this study was to evaluate the antibiotic susceptibility of lactic acid bacteria (LAB) and coagulase‐negative staphylococci (CNS) strains isolated from naturally fermented smoked pork produced in Hunan, China. A total of 48 strains were isolated by selective medium and identified at the species level by 16S rRNA gene sequencing as follows: Staphylococcus carnosus (23), Lactobacillus plantarum (12), Lactobacillus brevis (10), Lactobacillus sakei (1), Weissella confusa (1), and Weissella cibaria (1). All strains were typed by RAPD‐PCR, and their susceptibility to 15 antibiotics was determined and expressed as the minimum inhibitory concentration (MIC) using agar dilution method. High resistance to penicillin G, streptomycin, gentamycin, vancomycin, chloramphenicol, norfloxacin, ciprofloxacin, kanamycin, and neomycin was found among the isolates. All the strains were sensitive to ampicillin, while the susceptibility to tetracycline, oxytetracycline, erythromycin, lincomycin, and roxithromycin varied. The presence of relevant resistance genes was investigated by PCR and sequencing, with the following genes detected: str(A), str(B), tet(O), tet(M), ere(A), and catA. Eleven strains, including 3 S. carnosus, 6 L. plantarum, and 2 L. brevis, harbored more than 3 antibiotic resistance genes. Overall, multiple antibiotic resistance patterns were widely observed in LAB and S. carnosus strains isolated from Hunan smoked pork. Risk assessment should be carried out with regard to the safe use of LAB and CNS in food production.Practical ApplicationWe evaluated the antibiotic resistance of lactic acid bacteria and coagulase‐negative staphylococci strains isolated from Chinese naturally fermented smoked pork. Our results may provide important data on establishing breakpoint standards for LAB and CNS and evaluating the safety risk of these strains for commercial use.
A Simple and Portable Screening Method for Adulterated Olive Oils Using the Hand‐Held FTIR Spectrometer and Chemometrics Tools
Authors: Pan Meng , Sun Suqin , Zhou Qun , Chen Jianbo 
Published: May 2018

AbstractExtra virgin olive oil has been one of the most common targets for economically motivated food adulteration. This research employed the hand‐held FTIR spectrometer to develop the simple and portable screening methods for extra virgin olive oils adulterated with other cheaper vegetable oils. With the help of the ATR probe and chemometrics tools, oil samples can be measured directly without any pretreatment, then the spectra can be interpreted automatically to determine the possibility of adulteration and estimate the content of adulterant oil. A feasibility study of the hand‐held FTIR screening method was carried out using olive oils adulterated with canola oil, peanut oil, corn oil, soybean oil, and sunflower oil. The SIMCA model using the hand‐held FTIR spectra can identify different kinds of vegetable oils correctly and recognize olive oils with not less than 10% of adulterant oils. Meanwhile, the content of adulterant oil in the range of 5% to 45% can be estimated by the PLS model using the hand‐held FTIR spectra within an error of 3%. This research shows the potential of the hand‐held FTIR technique in the rapid and field screening of olive oils adulterated with some cheaper vegetable oils.Practical ApplicationThis research provide a rapid and automatic detection method for olive oils adulterated with other cheaper vegetable oils. An oil sample can be measured directly within one minute, and the hand‐held instrument can be used anywhere needed.
Integrating a comprehensive DNA barcode reference library with a global map of yews (Taxus L.) for forensic identification
Authors: Liu Jie , Milne Richard I. , Möller Michael , Zhu Guang‐Fu , Ye Lin‐Jiang , Luo Ya‐Huang , Yang Jun‐Bo , Wambulwa Moses C. , Wang Chun‐Neng , Li De‐Zhu , Gao Lian‐Ming 
Published: May 2018

AbstractRapid and accurate identification of endangered species is a critical component of biosurveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or preprocessed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa. Here, we construct a comprehensive DNA barcode reference library and generate distribution maps using species distribution modelling (SDM), for all 15 Taxus species worldwide. We find that trnL‐trnF is the ideal barcode for Taxus: It can distinguish all Taxus species and in combination with ITS identify hybrids. Among five analysis methods tested, NJ was the most effective. Among 4,151 individuals screened for trnL‐trnF, 73 haplotypes were detected, all species‐specific and some population private. Taxonomical, geographical and genetic dimensions of sampling strategy were all found to affect the comprehensiveness of the resulting DNA barcode library. Maps from SDM showed that most species had allopatric distributions, except T. mairei in the Sino‐Himalayan region. Using the barcode library and distribution map data, two unknown forensic samples were identified to species (and in one case, population) level and another was determined as a putative interspecific hybrid. This integrated species identification system for Taxus can be used for biosurveillance, conservation management and to monitor and prosecute illegal trade. Similar identification systems are recommended for other IUCN‐ and CITES‐listed taxa.
Dietary Omega‐3 Fatty Acids Differentially Impact Acute Ethanol‐Responsive Behaviors and Ethanol Consumption in DBA/2J Versus C57BL/6J Mice
Authors: Wolstenholme Jennifer T. , Bowers M. Scott , Pais Alexander B. , Pais A. Christian , Poland Ryan S. , Poklis Justin L. , Davies Andrew G. , Bettinger Jill C. 
Published: May 2018

BackgroundComplex interactions between environmental and genetic factors influence the risk of developing alcohol use disorder (AUD) in humans. To date, studies of the impact of environment on AUD risk have primarily focused on psychological characteristics or on the effects of developmental exposure to ethanol (EtOH). We recently observed that modifying levels of the long‐chain ω‐3 (LC ω‐3) fatty acid, eicosapentaenoic acid (EPA), alters acute physiological responses to EtOH in Caenorhabditis elegans. Because mammals derive ω‐3 fatty acids from their diet, here we asked if manipulating dietary levels of LC ω‐3 fatty acids can affect EtOH‐responsive behaviors in mice.MethodsWe used 2 well‐characterized inbred mouse strains, C57BL/6J (B6) and DBA/2J (D2), which differ in their responses to EtOH. Age‐matched young adult male mice were maintained on isocaloric diets that differed only by being enriched or depleted in LC ω‐3 fatty acids. Animals were subsequently tested for acute EtOH sensitivity (locomotor activation and sedation), voluntary consumption, and metabolism. Fat deposition was also determined.ResultsWe found that dietary levels of LC ω‐3s altered EtOH sensitivity and consumption in a genotype‐specific manner. Both B6 and D2 animals fed high LC ω‐3 diets demonstrated lower EtOH‐induced locomotor stimulation than those fed low LC ω‐3 diets. EtOH sedation and EtOH metabolism were greater in D2, but not B6 mice on the high LC ω‐3 diet. Conversely, LC ω‐3 dietary manipulation altered EtOH consumption in B6, but not in D2 mice. B6 mice on a high LC ω‐3 diet consumed more EtOH in a 2‐bottle choice intermittent access model than B6 mice on a low LC ω‐3 diet.ConclusionsBecause EtOH sensitivity is predictive of risk of developing AUD in humans, our data indicate that dietary LC ω‐3 levels should be evaluated for their impact on AUD risk in humans. Further, these studies indicate that genetic background can interact with fatty acids in the diet to significantly alter EtOH‐responsive behaviors.