bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast, robust and precise 3D localization for arbitrary point spread functions
Authors: Li Yiming , Mund Markus , Hoess Philipp , Matti Ulf , Nijmeijer Bianca , Sabinina Vilma Jimenez , Ellenberg Jan , Schoen Ingmar , Ries Jonas 
Published: August 2017

AbstractWe present a fitter for 3D single-molecule localization of arbitrary, experimental point spread functions (PSFs) that reaches minimum uncertainty for EMCCD and sCMOS cameras, and achieves more than 105fits/s. We provide tools to robustly model experimental PSFs and correct for depth induced aberrations, which allowed us to achieve an unprecedented 3D resolution with engineered astigmatic PSFs, and acquire high quality 3D superresolution images even on standard microscopes without 3D optics.
Fear extinction requires infralimbic cortex projections to the basolateral amygdala
Authors: Bloodgood Daniel W. , Sugam Jonathan A. , Holmes Andrew , Kash Thomas L. 
Published: August 2017

AbstractFear extinction involves the formation of a new memory trace that attenuates fear responses to a conditioned aversive memory, and extinction impairments are implicated in trauma- and stress-related disorders. Previous studies in rodents have found that the infralimbic prefrontal cortex (IL) and its glutamatergic projections to the basolateral amygdala (BLA) and basomedial amygdala (BMA) instruct the formation of fear extinction memories. However, it is unclear whether these pathways are exclusively involved in extinction, or whether other major targets of the IL, such as the nucleus accumbens (NAc) also play a role. To address this outstanding issue, the current study employed a combination of electrophysiological and chemogenetic approaches in mice to interrogate the role of IL-BLA and IL-NAc pathways in extinction. Specifically, we used patch-clamp electrophysiology coupled with retrograde tracing to examine changes in neuronal activity of the IL and prelimbic cortex (PL) projections to both the BLA and NAc following fear extinction. We found that extinction produced a significant increase in the intrinsic excitability of IL-BLA projection neurons, while extinction appeared to reverse fear induced changes in IL-NAc projection neurons. To establish a causal counterpart to these observations, we then used a pathway-specific Designer Receptors Exclusively Activated by Designer Drugs (DREADD) strategy to selectively inhibit PFC-BLA projection neurons during extinction acquisition. Using this approach, we found that DREADD-mediated inhibition of PFC-BLA neurons during extinction acquisition impaired subsequent extinction retrieval. Taken together, our findings provide further evidence for a critical contribution of the IL-BLA neural circuit to fear extinction.
Human hippocampal replay during rest prioritizes weakly-learned information and predicts memory performance
Authors: Schapiro Anna C. , McDevitt Elizabeth A. , Rogers Timothy T. , Mednick Sara C. , Norman Kenneth A. 
Published: August 2017

AbstractThere is now extensive evidence that the hippocampus replays experiences during quiet rest periods, and that this replay benefits subsequent memory. A critical open question is how memories are prioritized for replay during these offline periods. We addressed this question in an experiment in which participants learned the features of 15 objects and then underwent fMRI scanning to track item-level replay in the hippocampus using pattern analysis during a rest period. Objects that were remembered less well were replayed more during the subsequent rest period, suggesting a prioritization process in which weaker memories—memories most vulnerable to forgetting—are selected for wake replay. Participants came back for a second session, either after a night of sleep or a day awake, and underwent another scanned rest period followed by a second memory test. In the second session, more hippocampal replay of a satellite during the rest period predicted better subsequent memory for that satellite. Only in the group with intervening sleep did rest replay predict improvement from the first to second session. Our results provide the first evidence that replay of individual memories occurs during rest in the human hippocampus and that this replay prioritizes weakly learned information, predicts subsequent memory performance, and relates to memory improvement across a delay with sleep.
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun meta-genomic data
Authors: Oñate Florian Plaza , Le Chatelier Emmanuelle , Almeida Mathieu , Cervino Ales-sandra C. L. , Gauthier Franck , Magoulès Frédéric , Ehrlich S. Dusko , Pichaud Matthieu 
Published: August 2017

AbstractMotivationAnalysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained fromde novoassembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.ResultsWe introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1 661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.AvailabilityThe binary is freely available for non-commercial users at enterome.fr/site/downloads/ Contact:florian.plaza-onate@inra.frSupplementary informationAvailable in the file namedSupplementary Information.pdf
Functional limb muscle innervation prior to cholinergic transmitter specification during early metamorphosis inXenopus
Authors: Lambert F. M. , Cardoit L. , Courty E. , Bougerol M. , Thoby-Brisson M. , Simmers J. , Tostivint H. , Le Ray D. 
Published: August 2017

ABSTRACTIn vertebrates, functional motoneurons are defined as differentiated neurons that are connected to a central premotor network and activate peripheral muscle using acetylcholine. Generally, motoneurons and muscles develop simultaneously during embryogenesis. However, duringXenopusmetamorphosis, developing limb motoneurons must reach their target muscles through the already established larval cholinergic axial neuromuscular system. Here, we demonstrate that at metamorphosis onset, spinal neurons retrogradely labeled from the emerging hindlimbs initially express neither choline acetyltransferase nor vesicular acetylcholine transporter. Nevertheless, they are positive for the motoneuronal transcription factor Islet1/2 and exhibit intrinsic and axial locomotor-driven electrophysiological activity. Moreover, the early appendicular motoneurons activate developing limb musclesvianicotinic antagonist-resistant, glutamate antagonist-sensitive, neuromuscular synapses. Coincidently, the hindlimb muscles transiently express glutamate, but not nicotinic receptors. Subsequently, both pre- and postsynaptic neuromuscular partners switch definitively to typical cholinergic transmitter signaling. Thus, our results demonstrate a novel context-dependent re-specification of neurotransmitter phenotype during neuromuscular system development.
FastID: Extremely Fast Forensic DNA Comparisons
Authors: Ricke Darrell O. 
Published: August 2017

AbstractRapid analysis of DNA forensic samples can have a critical impact on time sensitive investigations. Analysis of forensic DNA samples by massively parallel sequencing is creating the next gold standard for DNA forensic analysis. This technology enables the expansion of forensic profiles from the current 20 short tandem repeat (STR) loci to tens of thousands of single nucleotide polymorphism (SNP) loci. A forensic search scales by the product of the number of loci and the number of profile comparisons. This paper introduces a method (FastID) to address the need for rapid scalable analysis of DNA forensic samples (patent pending)[1]. FastID can search a profile of 2,500 SNP loci against 20 million profiles in 5.08 seconds using a single computational thread on a laptop (Intel i7 4.0 GHz).
Fast P(RMNE): Fast Forensic DNA Probability of Random Man Not Excluded Calculation
Authors: Ricke Darrell O. , Schwartz Steven 
Published: August 2017

AbstractHigh throughput sequencing (HTS) of DNA forensic samples is expanding from the sizing of short tandem repeats (STRs) to massively parallel sequencing (MPS). HTS panels are expanding from the FBI 20 core Combined DNA Index System (CODIS) loci to include SNPs. The calculation of random man not excluded, P(RMNE), is used in DNA mixture analysis to estimate the probability that a person is present in a DNA mixture. This calculation encounters calculation artifacts with expansion to larger panel sizes. Increasing the floating-point precision of the calculations allows for increased panel sizes but with a corresponding increase in computation time. The Taylor series higher precision libraries used fail on some input data sets leading to algorithm unreliability. Herein, a new formula is introduced for calculating P(RMNE) that scales to larger SNP panel sizes while being computationally efficient (patent pending)[1].
Impacts of residential construction defects on customer satisfaction
Authors: Milion Raphael Negri , Alves Thaís da C.L. , Paliari José Carlos 
Published: August 2017

Purpose
The purpose of this paper is to investigate the impact of defects on the satisfaction of residential construction customers. Three working hypotheses were tested: first, defects in residential construction impact the customer satisfaction; second, different defects have different impacts on customer satisfaction; and third, interviewing customers about defects in their residential units is not a reliable method to collect data.

Design/methodology/approach
The research investigated correlations between data on defects and customer satisfaction surveys carried out by a construction company on its projects. Data were cross-checked to determine what kinds of defects have the worse impact on customer satisfaction.

Findings
The occurrence of defects does not necessarily jeopardize customer satisfaction, although it appears to be a concern to the customers who responded to the survey. When the occurrence of defects did interfere with customer satisfaction, it was found that the worse impacts resulted from the occurrence of multiple defects in a single unit, the inability of the construction company to communicate with the customer after a claim was filed, and the occurrence of functional defects. Results suggest that interviewing customers about the defect occurrence in their units is not a reliable method to collect data for research purposes.

Practical implications
Results can be used to help companies better define continuous improvement activities and avoid the occurrence of defects that cause the worse impacts to customer satisfaction.

Originality/value
Data availability is a challenge for studies on defects. This study had direct access to data from a construction company, which made the presented analyses possible.
Barriers to rural women entrepreneurs in Oman
Authors: Ghouse Suhail , McElwee Gerard , Meaton Julia , Durrah Omar 
Published: August 2017

Purpose
The purpose of this paper is to analyse the barriers confronted by rural women entrepreneurs in Oman. The study focusses on women living in rural and mountain areas who aspire to move beyond their traditional family roles. It identifies several problems including accessing funding for new ventures and innovative activities, a lack of skills-based training and limited family support.

Design/methodology/approach
Based on 57 responses to a semi-structured questionnaire, and face to face qualitative interviews with ten women entrepreneurs. Quantitative responses are evaluated and ranked in terms of their mean score, standard deviation and the intensity of each factor shaping rural women entrepreneurship. Five qualitative cases are presented.

Findings
Although Oman is arguably one of the more progressive Arab countries regarding gender equality and women empowerment, the findings exhibit socio-cultural concerns which hamper women entrepreneurial venture creations and their subsequent success. The findings of the research are discussed using the three dimensions of entrepreneurship identified by Wenneker and Thurik (1999). The three dimensions are: conditions leading to entrepreneurship, characteristics of entrepreneurship and outcomes of entrepreneurship.

Practical implications
Suggests that Omani policymakers should consider how women entrepreneurs can be better supported so that they can diversify household income by starting new ventures while simultaneously contributing to the socio-economic development of the region. A number of suggestions on how this can be achieved are presented.

Originality/value
Research on rural women entrepreneurship in the context of an Arab country is scarce and the study can provide an overview of the obstacles and the support required for the development of the rural women entrepreneurship in this region.
Developing a conceptual framework of waste management in the organizational context
Authors: Singh Aarti , Sushil  
Published: August 2017

Purpose
The purpose of this paper is to develop a conceptual framework of waste management by using total interpretive structural modeling (TISM) technique in the Indian organizational context.

Design/methodology/approach
TISM technique has been used to develop a conceptual framework of waste management in the organizational context, where the waste management factors have been identified and verified through content analysis.

Findings
The conceptual framework of waste management in the organization has been developed using TISM that contributes to the development of important links and the hierarchical relationships among the factors. In addition to it, the model also figures out the driving and dependent factors of waste management.

Research limitations/implications
This study has its implication for both organizations and policy makers. It provides the important factors for managing waste in the organization which must be considered before planning the waste management practice in an organization. For policy makers, it highlights the waste management paths and important linkages required for the development of waste management policies in the organizations.

Originality/value
This study has made its contribution by providing the conceptual framework for waste management in the Indian organizational context which has been developed through qualitative modeling technique. The conceptual framework also provides important paths of managing waste in the organization which is a new effort in the Indian organizational context.
Land use change analysis in the urban region of Milan
Authors: Salata Stefano 
Published: August 2017

Purpose
The comparative study between urban regions gathered by the 2010 National Project of Relevant Interest financed by the Italian Ministry of Education, University and Research (MIUR – PRIN 2010) re-opened, in Italy, the debate on regional comparison of data, especially the ones of land use monitoring, which are difficult to collect, and to compare. The purpose of this paper is to illustrate some results of comparative studies based on regional and national data sets of land use indicators. Further considerations of land use change (LUC) assessment and its effect on environmental policies extended to the whole metropolitan area of Milan are outlined.

Design/methodology/approach
The adopted methodology collects different types of information from the existent databases on land uses/land covers (national/regional) and presents an assessment between the selected case of studies (urban regions), leading a shift from a quantitative evaluation to a qualitative one. A comparative study was conducted applying a geographical and statistical difference of land uses among different time thresholds. Subsequently, a cross-tabulation analysis allows an in-depth LUC analysis for the Milan urban region.

Findings
The results of the study display an autonomous pattern for the Milan urban region, which is the most densely populated area in Italy and seems to be the only comparable to other international cases of studies due to its extension and characteristics. Nevertheless, it is not the urban region that is affected by the highest rate of land take, which takes place in the Italian context where densities of settlements are lower and sprawled. According to Soja’s (2011) interpretation, the post-metropolitan condition of Milan seems to be proved.

Originality/value
The study was aimed at creating the first online National Atlas which has been used to overcome traditional problems of homogenization of LUC data in Italy. The quantification and qualification of LUC patterns allow us to understand if, and where, post-metropolis condition occurs. This research gives a clear indication of the kind of ongoing phenomena for policy orientation to planners and administrators, especially the one of the green infrastructure approach at the city-region level to solving the emerging environmental challenges.
Green chicken purchase behavior: the moderating role of price transparency
Authors: Minbashrazgah Morteza Maleki , Maleki Fatemeh , Torabi Maedeh 
Published: August 2017

PurposeDeveloping green consumption, organic and green meat and poultry consumption have been increased recently. The purpose of this paper is to investigate the effect of food’s sensory characteristics (e.g. organic food beliefs) and non-food factors (e.g. price transparency) on consumers’ green purchase behavior. So, according to the moderating role of price transparency, affecting factors on green chicken purchase intention and behavior are examined.Design/methodology/approachEvaluating the model, the authors used measures from previous research. The authors distributed questionnaire in four chain stores in four different geographical regions in Tehran. The structural model and relations were examined by using Smart PLS 2.0 software to simultaneously estimate the measurement and structural models.FindingsStructural equation analysis revealed that level of trust, consumer’s organic food beliefs and perceived environmental responsibility have positive impact on green purchase intention. Also price transparency moderator role confirmed that moderators can affect consumers’ actual behavior.Research limitations/implicationsAs our sample was just from Tehran, the research results may lack generalizability to all people in Iran. Therefore, future researchers are encouraged to retest the proposed model in other cities and also in other countries with different level of economic development.Practical implicationsThis paper includes suggestions for managers and producers to develop green food products consumption especially green chicken. Also it has implications for spreading out green consumption among people with high environmental involvement.Originality/valueDespite conducted research, the moderating role of price transparency has been used only rarely to investigate consumers’ green purchase behavior.
Autophagy in stem cell aging
Authors: Revuelta Miren , Matheu Ander 
Published: August 2017

SummaryAging is responsible for changes in mammalian tissues that result in an imbalance to tissue homeostasis and a decline in the regeneration capacity of organs due to stem cell exhaustion. Autophagy is a constitutive pathway necessary to degrade damaged organelles and protein aggregates. Autophagy is one of the hallmarks of aging, which involves a decline in the number and functionality of stem cells. Recent studies show that stem cells require autophagy to get rid of cellular waste produced during the quiescent stage. In particular, two independent studies in muscle and hematopoietic stem cells demonstrate the relevance of the autophagy impairment for stem cell exhaustion and aging. In this review, we summarize the main results of these works, which helped to elucidate the impact of autophagy in stem cell activity as well as in age‐associated diseases.
Gambling involvement among Native Americans, Blacks, and Whites in the United States
Authors: Barnes Grace M. , Welte John W. , Tidwell Marie‐Cecile O. 
Published: August 2017

Background and ObjectivesThis paper examines risk factors of gambling and problem gambling among racial subgroups in the U.S. population, namely Native Americans and blacks, for whom research data are lacking.MethodsFindings are based on a large representative general population survey (n = 3,474) of gambling in the U.S. with an oversample of Native Americans (n = 549). Multiple domains were assessed including sociodemographic factors; ecological factors (census‐defined neighborhood disadvantage, geocoded density of casinos within 30 miles of respondents’ homes, and perceived gambling convenience); impulsivity; and alcohol abuse.ResultsAfter controlling for all variables in the study, neighborhood disadvantage has a significantly greater effect on overall gambling, frequent gambling, and problem gambling for Native Americans than for the rest of the U.S. population. In addition, the relationship between frequent gambling and heavier drinking is much stronger for blacks than for the rest of the U.S. population.Discussion and ConclusionsThere is a lack of research on gambling involvement among minority groups in the U.S. Blacks and Native Americans are at a higher risk for problem gambling as compared with the rest of the population. Furthermore, social factors and alcohol abuse may show a stronger co‐occurrence with gambling involvement among minority groups than among whites.Scientific SignificanceThis study is a large representative U.S. sample with sizeable numbers of Native Americans and blacks. Thus, prevalence rates and risk factors can be assessed for these important population subgroups. This will allow for targeted intervention programs for Native Americans and blacks with problem gambling and alcohol abuse. (Am J Addict 2017;26:713–721)