bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evaluation of RNA-Seq de novo assembly by PacBio long read sequencing
Authors: Yang Yifan , Gribskov Michael 
Published: August 2019

AbstractRNA-Seq de novo assembly is an important method to generate transcriptomes for non-model organisms before any downstream analysis. Given many great de novo assembly methods developed by now, one critical issue is that there is no consensus on the evaluation of de novo assembly methods yet. Therefore, to set up a benchmark for evaluating the quality of de novo assemblies is very critical. Addressing this challenge will help us deepen the insights on the properties of different de novo assemblers and their evaluation methods, and provide hints on choosing the best assembly sets as transcriptomes of non-model organisms for the further functional analysis. In this article, we generate a “real time” transcriptome using PacBio long reads as a benchmark for evaluating five de novo assemblers and two model-based de novo assembly evaluation methods. By comparing the de novo assmblies generated by RNA-Seq short reads with the “real time” transcriptome from the same biological sample, we find that Trinity is best at the completeness by generating more assemblies than the alternative assemblers, but less continuous and having more misassemblies; Oases is best at the continuity and specificity, but less complete; The performance of SOAPdenovo-Trans, Trans-AByss and IDBA-Tran are in between of five assemblers. For evaluation methods, DETONATE leverages multiple aspects of the assembly set and ranks the assembly set with an average performance as the best, meanwhile the contig score can serve as a good metric to select assemblies with high completeness, specificity, continuity but not sensitive to misassemblies; TransRate contig score is useful for removing misassemblies, yet often the assemblies in the optimal set is too few to be used as a transcriptome.
Progression from feature-specific brain activity to hippocampal binding during episodic encoding
Authors: Cooper Rose A. , Ritchey Maureen 
Published: August 2019

ABSTRACTThe hallmark of episodic memory is recollecting multiple perceptual details tied to a specific spatial-temporal context. To remember an event, it is therefore necessary to integrate such details into a coherent representation during initial encoding. Here we tested how the brain encodes and binds multiple, distinct kinds of features in parallel, and how this process evolves over time during the event itself. We analyzed data from 27 human subjects (16 females, 11 males) who learned a series of objects uniquely associated with a color, a panoramic scene location, and an emotional sound while functional magnetic resonance imaging data were collected. By modeling how brain activity relates to memory for upcoming or just-viewed information, we were able to test how the neural signatures of individual features as well as the integrated event changed over the course of encoding. We observed a striking dissociation between early and late encoding processes: left inferior frontal and visuo-perceptual signals at the onset of an event tracked the amount of detail subsequently recalled and were dissociable based on distinct remembered features. In contrast, memory-related brain activity shifted to the left hippocampus toward the end of an event, which was particularly sensitive to binding item color and sound associations with spatial information. These results provide evidence of early, simultaneous feature-specific neural responses during episodic encoding that predict later remembering and suggest that the hippocampus integrates these features into a coherent experience at an event transition.SIGNIFICANCE STATEMENTUnderstanding and remembering complex experiences is crucial for many socio-cognitive abilities, including being able to navigate our environment, predict the future, and share experiences with others. Probing the neural mechanisms by which features become bound into meaningful episodes is a vital part of understanding how we view and reconstruct the rich detail of our environment. By testing memory for multimodal events, our findings show a functional dissociation between early encoding processes that engage lateral frontal and sensory regions to successfully encode event features, and later encoding processes that recruit hippocampus to bind these features together. These results highlight the importance of considering the temporal dynamics of encoding processes supporting multimodal event representations.
Chemotaxis and topotaxis add vectorially for amoeboid cell migration
Authors: Wondergem Joeri A. J. , Mytiliniou Maria , Wit Falko C. H. de , Reuvers Thom G. A. , Holcman David , Heinrich Doris 
Published: August 2019

AbstractCells encounter a wide variety of physical and chemical cues when navigating their native environments. However, their response to multiple simultaneous cues is not yet clear. In particular, the influence of topography, in the presence of a chemotactic gradient, on their migratory behavior is understudied. Here, we investigate the effects of topographical guidance on highly motile amoeboid cell migration (topotaxis) generated by asymmetrically placed micropillars. The micropillar field allows for an additional, natural chemotactic gradient in two different directions, thereby revealing the relevance of topotaxis in the presence of cell migration directed by chemical gradients (chemotaxis). Interestingly, we found that the topotactic drift generated by the pillar field is conserved during chemotaxis. We show that the drifts generated by both these cues add up linearly. A coarse-grained analysis as a function of pillar spacing subsequently revealed that the strength and direction of the topotactic drift is determined by (i) the pore size, (ii) space between pores, and (iii) the effective diffusion constant of the cells. Finally, we argue that topotaxis must be conserved during chemotaxis, as it is an emergent property of both the asymmetric properties of the pillar field and the inherent stochasticity of (biased) amoeboid migration.
Neurons that Function within an Integrator to Promote A Persistent Behavioral State in Drosophila
Authors: Jung Yonil , Kennedy Ann , Chiu Hui , Mohammad Farhan , Claridge-Chang Adam , Anderson David J. 
Published: August 2019

SUMMARYInnate behaviors involve both reflexive motor programs and internal states. In Drosophila, optogenetic activation of male-specific P1 interneurons triggers courtship song, as well as a persistent behavioral state that prolongs courtship and enhances aggressiveness. Here we identify pCd neurons as persistently activated by repeated P1 stimulation. pCd neurons are required for P1-evoked persistent courtship and aggression, as well as for normal social behavior. Activation of pCd neurons alone is inefficacious, but enhances and prolongs courtship or aggression promoted by female cues. Transient female exposure induced persistent increases in male aggressiveness, an effect suppressed by transiently silencing pCd neurons. Transient silencing of pCd also disrupted P1-induced persistent physiological activity, implying a requisite role in persistence. Finally, P1 activation of pCd neurons enhanced their responsiveness to cVA, an aggression-promoting pheromone. Thus, pCd neurons function within a circuit that integrates P1 input, to promote a persistent internal state that enhances multiple social behaviors.
Potentiating antibiotic treatment using fitness-neutral gene expression perturbations
Authors: Otoupal Peter B. , Erickson Keesha E. , Eller Kristen A. , Campos Jocelyn , Aunins Thomas R. , Chatterjee Anushree 
Published: August 2019

AbstractThe rapid proliferation of multidrug-resistant (MDR) bacteria poses a critical threat to human health, for which new antimicrobial strategies are desperately needed. Here we outline a strategy for combating bacterial infections by administering fitness neutral gene expression perturbations as co-therapies to potentiate antibiotic lethality. We systematically explored the fitness of 270 gene knockout-drug combinations in Escherichia coli, identifying 114 synergistic interactions. Genes revealed in this screen were subsequently perturbed at the transcriptome level via multiplexed CRISPR-dCas9 interference to induce antibiotic synergy. These perturbations successfully sensitized E. coli to antibiotic treatment without imposing a separate fitness cost. We next administered these fitness neutral gene perturbations as co-therapies to potentiate antibiotic killing of Salmonella enterica in intracellular infections of HeLa epithelial cells, demonstrating therapeutic applicability. Finally, we utilized these results to design peptide nucleic acid (PNA) co-therapies for targeted gene expression reduction in four MDR, clinically isolated bacteria. Two isolates of Klebsiella pneumoniae and E. coli were each exposed to PNAs targeting homologs of the genes csgD, fnr, recA and acrA in the presence of sub-minimal inhibitory concentrations of trimethoprim. We successfully increased each strain’s susceptibility to trimethoprim treatment and identified eight cases in which re-sensitization occurred without a direct fitness impact of the PNA on MDR strains. Our results highlight a promising approach for combating MDR bacteria which could extend the utility of our current antibiotic arsenal.
Dynamic regulation of immunity through post-translational control of defense transcript splicing
Authors: Dressano Keini , Weckwerth Philipp R , Poretsky Elly , Takahashi Yohei , Villarreal Carleen , Shen Zhouxin , Schroeder Julian I. , Briggs Steven P. , Huffaker Alisa 
Published: August 2019

AbstractSurvival of all living organisms requires the ability to detect attack and swiftly counter with protective immune responses. Despite considerable mechanistic advances, interconnectivity of signaling circuits often remains unclear. A newly-characterized protein, IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR), negatively regulates immune responses in both maize and Arabidopsis, with disrupted function resulting in enhanced disease resistance. IRR physically interacts with, and promotes canonical splicing of, transcripts encoding defense signaling proteins, including the key negative regulator of pattern recognition receptor signaling complexes, CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28). Upon immune activation by Plant Elicitor Peptides (Peps), IRR is dephosphorylated, disrupting interaction withCPK28transcripts and resulting in accumulation of an alternative splice variant encoding a truncated CPK28 protein with impaired kinase activity and diminished function as a negative regulator. We demonstrate a novel circuit linking Pep-induced post-translational modification of IRR with post-transcriptionally-mediated attenuation of CPK28 function to dynamically amplify Pep signaling and immune output.One Sentence SummaryPlant innate immunity is promoted by post-translational modification of a novel RNA-binding protein that regulates alternative splicing of transcripts encoding defense signaling proteins to dynamically increase immune receptor signaling capacity through deactivation of a key signal-buffering circuit.
Design of a transcriptional biosensor for the portable, on-demand detection of cyanuric acid
Authors: Liu Xiangyang , Silverman Adam D. , Alam Khalid K. , Iverson Erik , Lucks Julius B. , Jewett Michael C. , Raman Srivatsan 
Published: August 2019

ABSTRACTRapid molecular biosensing is an emerging application area for synthetic biology. Here, we engineer a portable biosensor for cyanuric acid (CYA), an analyte of interest for human and environmental health, using a LysR-type transcription regulator (LTTR) from Pseudomonas within the context of Escherichia coli gene expression machinery. To overcome cross-host portability challenges of LTTRs, we rationally engineered hybrid Pseudomonas-E. coli promoters by integrating DNA elements required for transcriptional activity and ligand-dependent regulation from both hosts, which enabled E. coli to function as whole-cell biosensor for CYA. To alleviate challenges of whole-cell biosensing, we adapted these promoter designs to function within a freeze-dried E. coli cell-free system to sense CYA. This portable, on-demand system robustly detects CYA within an hour from laboratory and real-world samples and works with both fluorescent and colorimetric reporters. This work elucidates general principles to facilitate the engineering of a wider array of LTTR-based environmental sensors.
Classifying T cell activity in autofluorescence intensity images with convolutional neural networks
Authors: Wang Zijie J. , Walsh Alex J. , Skala Melissa C. , Gitter Anthony 
Published: August 2019

ABSTRACTThe importance of T cells in immunotherapy has motivated developing technologies to better characterize T cells and improve therapeutic efficacy. One specific objective is assessing antigen-induced T cell activation because only functionally active T cells are capable of killing the desired targets. Autofluorescence imaging can distinguish T cell activity states of individual cells in a non-destructive manner by detecting endogenous changes in metabolic co-enzymes such as NAD(P)H. However, recognizing robust patterns of T cell activity is computationally challenging in the absence of exogenous labels or information-rich autofluorescence lifetime measurements. We demonstrate that advanced machine learning can accurately classify T cell activity from NAD(P)H intensity images and that those image-based signatures transfer across human donors. Using a dataset of 8,260 cropped single-cell images from six donors, we meticulously evaluate multiple machine learning models. These range from traditional models that represent images using summary statistics or extract image features with CellProfiler to deep convolutional neural networks (CNNs) pre-trained on general non-biological images. Adapting pre-trained CNNs for the T cell activity classification task provides substantially better performance than traditional models or a simple CNN trained with the autofluorescence images alone. Visualizing the images with dimension reduction provides intuition into why the CNNs achieve higher accuracy than other approaches. However, we observe that fine-tuning all layers of the pre-trained CNN does not provide a classification performance boost commensurate with the additional computational cost. Our software detailing our image processing and model training pipeline is available as Jupyter notebooks at https://github.com/gitter-lab/t-cell-classification.
Factors influencing farmers’ use of the warehouse receipt system in Indonesia
Authors: Gunawan Endro , Kuwornu John K.M. , Datta Avishek , Nguyen Loc T. 
Published: August 2019

PurposeThe purpose of this paper is to examine the factors influencing Indonesian farmers’ use of the warehouse receipt system (WRS) and their choice of private and public warehouses.Design/methodology/approachPrimary data were collected through questionnaires administered to 500 farmers in two districts, Subang and Cianjur, in West Java Province in Indonesia. Binary logit regression was employed to examine the factors influencing farmers’ use of the WRS. Binary and bivariate probit regressions were employed to determine the factors influencing farmers’ choice of private and public warehouses.FindingsThe empirical results of the binary logit regression revealed that age, land ownership, selling price, the use of the warehouse receipt as collateral security and the availability of transportation facility positively influenced farmers’ use of the WRS, whereas education, income, farm profit and participation in farmers’ group negatively influenced farmers’ use of the WRS. The results of the binary probit regressions revealed that profit, availability of insurance and processing facility positively influenced the farmers’ decision to use the private WRS, whereas education, production, selling price and distance from the farm to the warehouse negatively influenced farmers’ decision to use the private WRS. Age, education, selling price and distance from the farm to the warehouse positively influenced the farmers’ decision to use the public WRS, whereas production and availability of processing facility negatively influenced the decision of farmers to use the public WRS.Practical implicationsThis study highlights the importance of education and government assistance regarding the provision of facilities and price indemnified insurance for successful implementation of the WRS.Originality/valueThis study provides an empirical contribution to the existing literature on the development of WRS in Indonesia. In terms of methods of analysis, previous studies used purely qualitative and descriptive methods, whereas this study employed econometric techniques (i.e. binary logit, binary probit and bivariate probit regressions) to examine the WRS in Indonesia. In addition, whereas previous studies explored the WRS in general, this study investigated the farmers’ use of the public and private warehouses in addition to exploring the WRS in general. Finally, the finding that the average annual profit of non-users was significantly higher than that of the users of the WRS is striking, and this could be attributed to the current challenges of the implementation of the WRS, including high transportation and warehouse rental costs.
Global sourcing processes in the Italian agricultural breweries
Authors: Francioni Barbara , Curina Ilaria , Masili Giorgia , Viganò Elena 
Published: August 2019

Purpose
The purpose of this paper is to deepen the global sourcing (GS) phenomenon from the acquiring firms’ viewpoint by analyzing the Italian craft beer sector. This industry has been chosen since it represents a perfect context for the GS activities’ analysis. Notably, different features characterizing this business force Italian breweries to turn to suppliers, located outside their national borders, to purchase the necessary raw materials.

Design/methodology/approach
The paper adopts a multiple case study concerning four Italian agricultural breweries located in the Marche region.

Findings
Results identify the main motivations, drivers, risks, obstacles and costs related to the adoption of the GS activities, by corroborating a positive interconnection with the GS literature findings.

Research limitations/implications
The main limitation is related to the fact that the study is based on a survey carried out on a specific region and product category. Therefore, future research could analyze other Italian regions and/or different types of products.

Practical implications
The study identifies different gaps characterizing the Italian supply market. Managerially these gaps can be converted into critical opportunities for the future development of the entire Italian brewing sector. Moreover, the results detect several actions the investigated breweries will seek to develop in the near future, which could strongly support the growth of the Italian beer sector.

Originality/value
The study deepens a topic little explored by literature, especially with reference to the supply activities of the Italian agricultural breweries.
Revisiting the numerical solution of stochastic differential equations
Authors: Hurn Stan , Lindsay Kenneth A. , Xu Lina 
Published: August 2019

Purpose
The purpose of this paper is to revisit the numerical solutions of stochastic differential equations (SDEs). An important drawback when integrating SDEs numerically is the number of steps required to attain acceptable accuracy of convergence to the true solution.

Design/methodology/approach
This paper develops a bias reducing method based loosely on extrapolation.

Findings
The method is seen to perform acceptably well and for realistic steps sizes provides improved accuracy at no significant additional computational cost. In addition, the optimal step size of the bias reduction methods is shown to be consistent with theoretical analysis.

Originality/value
Overall, there is evidence to suggest that the proposed method is a viable, easy to implement competitor for other commonly used numerical schemes.
Dealing with multiple hazards and threats on cultural heritage sites: an assessment of 80 case studies
Authors: Bosher Lee , Kim Dowon , Okubo Takeyuki , Chmutina Ksenia , Jigyasu Rohit 
Published: August 2019

Purpose
Cultural heritage (CH) sites are not only important components of a country’s identity but can also be important drivers of tourism. However, an increasing number of extreme events associated with the impacts of climate change, natural hazards and human-induced threats are posing significant problems in conserving and managing CH worldwide. Consequently, improved climate change adaptation and enhanced hazard/threat mitigation strategies have become critical (but to-date under-researched) considerations. The purpose of this paper is to identify the key hazards and threats to CH sites, the most common types of risks to CH and the strategies being adopted to mitigate or even eradicate those risks.

Design/methodology/approach
This paper reviews 80 CH case studies from around the world, which have been presented at a UNESCO International Training Course between 2006 and 2016. The case studies cover 45 different countries and provide practical insights into the key challenges being encountered in a variety of “at risk” locations.

Findings
The analysis assesses the key natural hazards and human-induced threats to the sites, an overview of the typical impacts to the tangible components of heritage and identifies the types of strategies being adopted to mitigate the risks, some of which could be transferred across cultural and geographical contexts.

Originality/value
The paper provides a wealth of useful information related to how challenges faced by CH sites might be addressed in the future.
Social capacities in fostering water supply resilience in Vanuatu
Authors: Balaei Behrooz , Wilkinson Suzanne , Potangaroa Regan 
Published: August 2019

PurposeIn March 2015 Vanuatu experienced Tropical Cyclone (TC) Pam, a category 5 cyclone with estimated wind speeds of 250 kph and one of the worst disasters in Vanuatu’s history. Prior to the cyclone, one-third of water in Vanuatu was collected by means of rainwater harvesting systems; around one quarter of these systems were damaged due to the cyclone and no longer functional. The purpose of this paper is to investigate social and organisational complexities in the resilience of water systems in Vanuatu following TC Pam, focussing on rural areas.Design/methodology/approachThe resilience of water supply in rural responses to TC Pam was examined using the three following approaches: review of existing documents, a case study of a village and interviews with specialist local and international non-governmental organisation staff working in Vanuatu.FindingsPeople’s reaction to the cyclone and its consequences at the village or community level in Vanuatu was impressive. The capacity of the locals, their involvement in the community and the low level of violence and high level of trust within society contributed to a quicker water supply restoration than expected. Despite severe shortages of water in some areas due to physical vulnerability of the system, the communities dealt with the issue calmly and the country did not experience any chaos due to water shortages.Originality/valueThe research results provide a benchmark for planners and decision makers in the South Pacific based on the social, organisational and technical dimensions of rural areas in Vanuatu that can be generalised to other countries in the region. This study also recommends potential tools to improve assessment of the role of social capital in fostering water supply resilience.