bluuebunny/crossref_metadata_2025_split huggingface dataset:
A universal metric for ferroic energy materials
Authors: Brück Ekkes , Yibole Hargen , Zhang Lian 
Published: July 2016

After almost 20 years of intensive research on magnetocaloric effects near room temperature, magnetic refrigeration with first-order magnetocaloric materials has come close to real-life applications. Many materials have been discussed as potential candidates to be used in multicaloric devices. However, phase transitions in ferroic materials are often hysteretic and a metric is needed to estimate the detrimental effects of this hysteresis. We propose the coefficient of refrigerant performance, which compares the net work in a reversible cycle with the positive work on the refrigerant, as a universal metric for ferroic materials. Here, we concentrate on examples from magnetocaloric materials and only consider one barocaloric experiment. This is mainly due to lack of data on electrocaloric materials. It appears that adjusting the field-induced transitions and the hysteresis effects can minimize the losses in first-order materials.This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
Thermodynamics of multicaloric effects in multiferroic materials: application to metamagnetic shape-memory alloys and ferrotoroidics
Authors: Planes Antoni , Castán Teresa , Saxena Avadh 
Published: July 2016

We develop a general thermodynamic framework to investigate multicaloric effects in multiferroic materials. This is applied to the study of both magnetostructural and magnetoelectric multiferroics. Landau models with appropriate interplay between the corresponding ferroic properties (order parameters) are proposed for metamagnetic shape-memory and ferrotoroidic materials, which, respectively, belong to the two classes of multiferroics. For each ferroic property, caloric effects are quantified by the isothermal entropy change induced by the application of the corresponding thermodynamically conjugated field. The multicaloric effect is obtained as a function of the two relevant applied fields in each class of multiferroics. It is further shown that multicaloric effects comprise the corresponding contributions from caloric effects associated with each ferroic property and the cross-contribution arising from the interplay between these ferroic properties.
This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
(Magneto)caloric refrigeration: is there light at the end of the tunnel?
Authors: Pecharsky Vitalij K. , Cui Jun , Johnson Duane D. 
Published: July 2016

Caloric cooling and heat pumping rely on reversible thermal effects triggered in solids by magnetic, electric or stress fields. In the recent past, there have been several successful demonstrations of using first-order phase transition materials in laboratory cooling devices based on both the giant magnetocaloric and elastocaloric effects. All such materials exhibit non-equilibrium behaviours when driven through phase transformations by corresponding fields. Common wisdom is that non-equilibrium states should be avoided; yet, as we show using a model material exhibiting a giant magnetocaloric effect, non-equilibrium phase-separated states offer a unique opportunity to achieve uncommonly large caloric effects by very small perturbations of the driving field(s).This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
Influence of the transition width on the magnetocaloric effect across the magnetostructural transition of Heusler alloys
Authors: Cugini F. , Porcari G. , Fabbrici S. , Albertini F. , Solzi M. 
Published: July 2016

We report a complete structural and magneto-thermodynamic characterization of four samples of the Heusler alloy Ni-Co-Mn-Ga-In, characterized by similar compositions, critical temperatures and high inverse magnetocaloric effect across their metamagnetic transformation, but different transition widths. The object of this study is precisely the sharpness of the martensitic transformation, which plays a key role in the effective use of materials and which has its origin in both intrinsic and extrinsic effects. The influence of the transition width on the magnetocaloric properties has been evaluated by exploiting a phenomenological model of the transformation built through geometrical considerations on the entropy versus temperature curves. A clear result is that a large temperature span of the transformation is unfavourable to the magnetocaloric performance of a material, reducing both isothermal entropy change and adiabatic temperature change obtainable in a given magnetic field and increasing the value of the maximum field needed to fully induce the transformation. The model, which is based on standard magnetometric and conventional calorimetric measurements, turns out to be a convenient tool for the determination of the optimum values of transformation temperature span in a trade-off between sheer performance and amplitude of the operating range of a material.This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
Large electrocaloric effects in single-crystal ammonium sulfate
Authors: Crossley S. , Li W. , Moya X. , Mathur N. D. 
Published: July 2016

Electrocaloric (EC) effects are typically studied near phase transitions in ceramic and polymer materials. Here, we investigate EC effects in an inorganic salt, namely ammonium sulfate (NH
4
)
2
SO
4
, with an order–disorder transition whose onset occurs at 223 K on cooling. For a single crystal thinned to 50 μm, we use a Maxwell relation to find a large isothermal entropy change of 30 J K
−1
kg
−1
in response to a field change of 400 kV cm
−1
. The Clausius–Clapeyron equation implies a corresponding adiabatic temperature change of 4.5 K.

This article is part of the themed issue ‘Taking the temperature of phase transitions in cool materials’.
Geo-climatic gradient shapes functional trait variations inSalix eriocephalaMichx
Authors: Shunmugam Arun S.K. , Soolanayakanahally Raju Y. , Guy Robert D. 
Published: July 2016

AbstractIntraspecific variations in seasonal phenology and growth physiology reflect adaptation to local climate. To explore the patterns of local adaptation along latitudinal and longitudinal clines, we used thirty-four populations ofSalix eriocephalasourced from its natural ranges across Canada. The genotypes were examined for 6 phenology and 19 ecophysiology traits over two growing seasons under common garden condition. Photosynthetic assimilation rate (A) increased with increasein latitude when measured during free growth. In spite, the negative correlation between stomatal density and stomatal conductance (gs), higherAis facilitatedvialarger pore length among genotypes from short growing seasons. In addition, higherA, was positively associated with total leafnitrogen and leaf mass per unit area. No population level differences wereobserved for water use-efficiency (Δ13C), however nitrogen isotope discrimination (δ15N) displayed latitudinalclines. Growing season phenological traits considered in this study accounted highheritability (H2= 0.65-0.94).Melampsorarust infestation also displayed a strong latitudinal cline with high-latitude genotypes being more susceptible. Overall, the results support the hypothesis that functional trait variations are largely explained by climate of origin and facilitate selection of parents with superior adaptive traits in the Canadian willow improvement program forbioenergy and environmental applications.
Animals in the Zika virus life cycle: what to expect from megadiverse Latin American countries
Authors: Bueno Marina Galvão , Martinez Nádia , Abdala Lívia , dos Santos Claudia Nunes Duarte , Chame Marcia 
Published: July 2016

ABSTRACTZika virus (ZIKV) was first isolated in 1947 in primates in Uganda, West Africa. The virus remained confined to the equatorial regions of Africa and Asia, cycling between infecting monkeys, arboreal mosquitoes, and occasional humans. The ZIKV Asiatic strain was probably introduced into Brazil in 2013. In the current critical human epidemic in the Americas, ZIKV is transmitted primarily byAedes aegyptimosquitoes, especially where the human population density is combined with poor sanitation. Presently, ZIKV is in contact with the rich biodiversity in all Brazilian biomes, bordering on other Latin American countries. Infections in Brazilian primates have been reported recently, but the overall impact of this virus on wildlife in the Americas is still unknown. The current epidemic in the Americas requires knowledge on the role of mammals, especially non-human primates, in ZIKV transmission to humans. The article discusses the available data on ZIKV in host animals, besides issues of biodiversity, rapid environmental change, and impact on human health in megadiverse Latin American countries. The authors reviewed scientific articles and recent news stories on ZIKV in animals, showing that 47 animal species from three orders (mammals, reptiles, and birds) have been investigated for the potential to establish a sylvatic cycle. The review aims to contribute to epidemiological studies and the knowledge on the natural history of ZIKV. The article concludes with questions that require urgent attention in epidemiological studies involving wildlife in order to understand their role as ZIKV hosts and to effectively control the epidemic.
Allelic spectrum of the RNA guided CRISPR/Cas9 DNA repair events at PAM associated trinucleotide repeat (NGG)n inCaenorhabditis elegans.
Authors: Kapulkin Wadim 
Published: July 2016

AbstractThis work describes the experience with implementation ofStreptococcus pyogenesCas9 nuclease, expressed inC. elegansgermline. The described work utilizes guide RNA-unc-22-1000 (GGAGAAGGAGGCGGTGCTGG) designed to target the polyglycine encoding stretch within theunc-22gene embedding the impure trinucleotide (NGG)n PAM repeat region. We describe the allelic spectrum of mutational events identified at position specified by gRNA-unc-22-1000. Of above experiments we conclude: i. the trinucleotide (NGG)n PAM repeat is a receptive target for the CRISPR/Cas9 experiments inC. elegansii. we conclude the allelic spectrum indicates the gRNA-unc-22-1000 induces fairly frequent NHEJ joining events involving deletions and indels but also, a phenotypically distinct class of small in-frame deletions indicative for microhomology-mediated end-joining (MMEJ) as a result ofS. pyogenesCas9 activity at the trinucleotide (NGG)n PAM repeat region. We demonstrate guide RNA-unc-22-1000 could be used to modify complex transgenicC. elegansline expressing human beta-amyloid protein. We provide the evidence for bi-allelic transaction resulting from Cas9 action recovered in experiment in CB1138him-6background. We contrast the expected performance of gRNA-unc-22-1000 with guide targeting another type ofC. elegansrepeat embeddingS. pyogenesPAM, the telomeric repeat (TTAGGC)n. We propose that preferential frame restoring MMEJ repair of the Cas9 cut at the 'modules' encoding for poly-glycine in +2(NGG)n position could be useful mode of genome engineering at the naturally occurring (NGG)n PAM embedding repeats dispersed across animal genomes.
A DNA-based T cell receptor reveals a role for receptor clustering in ligand discrimination
Authors: Taylor Marcus J. , Husain Kabir , Gartner Zev J. , Mayor Satyajit , Vale Ronald D. 
Published: July 2016

AbstractT cells mount an immune response by measuring the binding strength of its T cell receptor (TCR) for peptide-loaded MHCs (pMHC) on an antigen-presenting cell. How T cells convert the lifetime of the extracellular TCR-pMHC interaction into an intracellular signal remains unknown. Here, we developed a synthetic signaling system in which the extracellular domains of the TCR and pMHC were replaced with short hybridizing strands of DNA. Remarkably, T cells can discriminate between DNA ligands differing by a single base pair. Single molecule imaging reveals that signaling is initiated when single ligand-bound receptors are converted into clusters, a time-dependent process requiring ligands with longer bound times. A computation model reveals that receptor clustering serves a kinetic proofreading function, enabling ligands with longer bound times to have disproportionally greater signaling outputs. These results suggest that spatial reorganization of receptors plays an important role in ligand discrimination in T cell signaling.
Schizophrenia hiPSC neurons display expression changes that are enriched for disease risk variants and a blunted activity-dependent response
Authors: Roussos Panos , Guennewig Boris , Kaczorowski Dominik C. , Barry Guy , Brennand Kristen J. 
Published: July 2016

ABSTRACTIMPORTANCESchizophrenia (SCZ) is a common illness with complex genetic architecture where both common genetic variation and rare mutations have been implicated. SCZ candidate genes participate in common molecular pathways that are regulated by activity-dependent changes in neurons, including the signaling network that modulates synaptic strength and the network of genes that are targets of fragile X mental retardation protein. One important next step is to further our understanding on the role of activity-dependent changes of genes expression in the etiopathogenesis of SCZ.OBJECTIVETo examine whether neuronal activity-dependent changes of gene expression is dysregulated in SCZ.DESIGN, SETTING, AND PARTICIPANTSNeurons differentiated from human induced pluripotent stem cells (hiPSCs) derived from 4 cases with SCZ and 4 unaffected controls were depolarized using potassium chloride. RNA was extracted followed by genome-wide profiling of the transcriptome.MAIN OUTCOMES AND MEASURESWe performed differential expression analysis and gene co-expression analysis to identify activity-dependent or disease-specific changes of the transcriptome. Further, we used gene set analyses to identify co-expressed modules that are enriched for SCZ risk genes.RESULTSWe identified 1,669 genes that are significantly different in SCZ-associated vs. control hiPSC-derived neurons and 1,199 genes that are altered in these cells in response to depolarization. We show that the effect of activity-dependent changes of gene expression in SCZ-associated neurons is attenuated compared to controls. Furthermore, these differentially expressed genes are co-expressed in modules that are highly enriched for genes affected by genetic risk variants in SCZ and other neurodevelopmental disorders.CONCLUSIONS AND RELEVANCEOur results show that SCZ candidate genes converge to gene networks that are associated with a blunted effect of activity-dependent changes of gene expression in SCZ-associated neurons. Overall, these findings show that hiPSC neurons demonstrate activity-dependent transcriptional changes that can be utilized to examine underlying mechanisms and therapeutic interventions related to SCZ.
Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays
Authors: Li Bo , Tambe Akshay , Aviran Sharon , Pachter Lior 
Published: July 2016

SUMMARYA number of high-throughput transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and post-transcriptional modifications. Although these assays survey a diverse set of ‘epitranscriptomic’ marks, they share methodological similarities and as such their interpretation is predicated on addressing similar computational challenges. Among these, a key question is how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. In this paper, we propose PROBer, the first rigorous statistical model to handle these challenges for a general set of sequencing-based ‘toeprinting’ assays.
Origins of pandemicVibrio choleraefrom environmental gene pools
Authors: Shapiro B. Jesse , Levade Inès , Kovacikova Gabriela , Taylor Ronald K. , Almagro-Moreno Salvador 
Published: July 2016

AbstractSome microbes can transition from an environmental lifestyle to a pathogenic one1–3. This ecological switch typically occurs through the acquisition of horizontally acquired virulence genes4,5. However, the genomic features that must be present in a population prior to the acquisition of virulence genes and emergence of pathogenic clones remain unknown. We hypothesized that virulence adaptive polymorphisms (VAPs) circulate in environmental populations and are required for this transition. We developed a comparative genomic framework for identifying VAPs, usingVibrio choleraeas a model. We then characterized several environmental VAP alleles to show that, while some of them reduced the ability of clinical strains to colonize a mammalian host, other alleles conferred efficient host colonization. These results show that VAPs are present in environmental bacterial populations prior to the emergence of virulent clones. We propose a scenario in which VAPs circulate in the environment, they become selected and enriched under certain ecologicalconditions, and finally a genomic background containing several VAPs acquires virulence factors that allows for its emergence as a pathogenic clone.
Boosting alignment accuracy through adaptive local realignment
Authors: DeBlasio Dan , Kececioglu John 
Published: July 2016

AbstractMotivationWhile mutation rates can vary across the residues of a protein, when computing alignments of protein sequences the same setting of values for substitution score and gap penalty parameters is typically used across their entire length. We provide for the first time a new method calledadaptive local realignmentthat automatically uses diverse parameter settings in different regions of the input sequences when computing multiple sequence alignments. This allows parameter settings to adapt to more closely match the local mutation rate across a protein.MethodOur method builds on our prior work on global alignmentparameter advisingwith theFacetalignment accuracy estimator. Given a computed alignment, in each region that has low estimated accuracy, a collection of candidate realignments is generated using a precomputed set of alternate parameter settings. If one of these alternate realignments has higher estimated accuracy than the original subalignment, the region is replaced with the new realignment, and the concatenation of these realigned regions forms the final alignment that is output.ResultsAdaptive local realignment significantly improves the quality of alignments over using the single best default parameter setting. In particular, this new method oflocal advising, when combined with prior methods forglobal advising, boosts alignment accuracy by as much as 26% over the best default setting on hard-to-align benchmarks (and by 6.4% over using global advising alone).AvailabilityA new version of theOpalmultiple sequence aligner that incorporates adaptive local realignment using Facet for parameter advising, is available free for non-commercial use athttp://facet.cs.arizona.edu.Contactdeblasio@cs.arizona.edu
Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages
Authors: Kutanan Wibhu , Kampuansai Jatupol , Srikummool Metawee , Kangwanpong Daoroong , Ghirotto Silvia , Brunelli Andrea , Stoneking Mark 
Published: July 2016

AbstractThe Tai-Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1,234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity, with 212 haplogroups. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion. Surprisingly, there is significant genetic differentiation within ethnolinguistic groups, calling into question the common assumption that there is genetic homogeneity within ethnolinguistic groups.
Anex vivolung model to study bronchioles infected withPseudomonas aeruginosabiofilms
Authors: Harrison Freya , Diggle Stephen P. 
Published: July 2016

AbstractA key aim in microbiology is to determine the genetic and phenotypic bases of bacterial virulence, persistence and antimicrobial resistance in chronic biofilm infections. This requires tractable, high-throughput models that reflect the physical and chemical environment encountered in specific infection contexts. Such models will increase the predictive power of microbiological experiments and provide platforms for enhanced testing of novel antibacterial or antivirulence therapies. We present an optimisedex vivomodel of cystic fibrosis lung infection:ex vivoculture of pig bronchiolar tissue in artificial cystic fibrosis mucus. We focus on the formation of biofilms byPseudomonas aeruginosa. We show highly repeatable and specific formation of biofilms that resemble clinical biofilms by a commonly-studied lab strain and ten cystic fibrosis isolates of this key opportunistic pathogen.
Molecular and biological characterization of an isolate ofTomato mottle mosaic virus(ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain
Authors: Ambrós S. , Martínez F. , Ivars P. , Hernández C. , de la Iglesia F. , Elena S.F. 
Published: July 2016

AbstractTomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species,Tomato mottle mosaic virus(ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Koch’s postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV andTomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.
Organized chaos
Authors: Fox Robert 
Published: July 2016

Purpose
There are valuable lessons that can be learned from the software industry regarding process improvement. The modern library is now so closely wedded to technology that the way in which services are implemented mirrors that of software development.

Design/methodology/approach
Several methodologies are explored and compared to processes that involve the implementation of digital services in libraries.

Findings
Libraries have reconsidered how they might adopt various business practices to improve service delivery.

Originality/value
This column advocates a study of software development methodologies that have been adopted across the industry with the hope that lessons learned in the corporate world and also in manufacturing could be of value to the digital library.