bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-field whole plant maize architecture characterized by Latent Space Phenotyping
Authors: Gage Joseph L. , Richards Elliot , Lepak Nicholas , Kaczmar Nicholas , Soman Chinmay , Chowdhary Girish , Gore Michael A. , Buckler Edward S. 
Published: September 2019

AbstractCollecting useful, interpretable, and biologically relevant phenotypes in a resource-efficient manner is a bottleneck to plant breeding, genetic mapping, and genomic prediction. Autonomous and affordable sub-canopy rovers are an efficient and scalable way to generate sensor-based datasets of in-field crop plants. Rovers equipped with light detection and ranging (LiDar) can produce three-dimensional reconstructions of entire hybrid maize fields. In this study, we collected 2,103 LiDar scans of hybrid maize field plots and extracted phenotypic data from them by Latent Space Phenotyping (LSP). We performed LSP by two methods, principal component analysis (PCA) and a convolutional autoencoder, to extract meaningful, quantitative Latent Space Phenotypes (LSPs) describing whole-plant architecture and biomass distribution. The LSPs had heritabilities of up to 0.44, similar to some manually measured traits, indicating they can be selected on or genetically mapped. Manually measured traits can be successfully predicted by using LSPs as explanatory variables in partial least squares regression, indicating the LSPs contain biologically relevant information about plant architecture. These techniques can be used to assess crop architecture at a reduced cost and in an automated fashion for breeding, research, or extension purposes, as well as to create or inform crop growth models.
Brettanomyces bruxellensis wine isolates show high geographical dispersal and long remanence in cellars
Authors: Cibrario Alice , Avramova Marta , Dimopoulou Maria , Magani Maura , Miot-Sertier Cécile , Mas Albert , Portillo Maria C. , Ballestra Patricia , Albertin Warren , Masneuf-Pomarede Isabelle , Dols-Lafargue Marguerite 
Published: September 2019

AbstractBrettanomyces bruxellensis is the main wine spoiler yeast all over the world, yet the structuration of the populations associated with winemaking remains elusive. In this work, we considered 1411 wine isolates from 21 countries that were genotyped using twelve microsatellite markers. We confirmed that B. bruxellensis isolates from wine environments show high genetic diversity, with 58 and 42% of triploid and diploid individuals respectively distributed in 5 main genetic groups. The distribution in the genetic groups varied greatly depending on the country and/or the wine-producing region. However, the two wine triploid groups showing sulfite resistance/tolerance were identified in almost all regions/countries. Genetically identical isolates were also identified. The analysis of these clone groups revealed that a given genotype could be isolated repeatedly in the same winery over decades, demonstrating unsuspected remanence ability. Besides cellar residency, a great geographic dispersal was also evidenced, with some genotypes isolated in wines from different continents. Finally, the study of old isolates and/or isolates from old vintages revealed that only the diploid groups were identified prior 1990 vintages. The triploid groups were identified in subsequent vintages, and their proportion has increased steadily these last decades, suggesting adaptation to winemaking practices such as sulfite use. A possible evolutionary scenario explaining these results is discussed.
Visualization and Analysis of the Interaction Network of Proteins Associated with Blood-cell targeting Autoimmune Diseases
Authors: Amanatidou Athina I. , Nastou Katerina C. , Tsitsilonis Ourania E. , Iconomidou Vassiliki A. 
Published: September 2019

AbstractBlood-cell targeting Autoimmune Diseases (BLADs) are complex diseases that affect blood cell formation or prevent blood cell production. Since these clinical conditions are gathering growing attention, experimental approaches are being used to investigate the mechanisms behind their pathogenesis and to identify proteins associated with them. However, computational approaches have not been utilized extensively in the study of BLADs. This study aims to investigate the interaction network of proteins associated with BLADs (BLAD interactome) and to identify novel associations with other human proteins. The method followed in this study combines information regarding protein-protein interaction network properties and autoimmune disease terms. Proteins with high network scores and statistically significant autoimmune disease term enrichment were obtained and 14 of them were designated as candidate proteins associated with BLADs. Additionally, clustering analysis of the BLAD interactome was used and allowed the detection of 17 proteins that act as “connectors” of different BLADs. We expect our findings to further extend experimental efforts for the investigation of the pathogenesis and the relationships of BLADs.
On the delay in propagation of action potentials
Authors: Xu J. , Xu S. , Wang F. , Xu S. 
Published: September 2019

AbstractThe signal delay during the propagation of action potentials is one of the key issues in understanding the mechanisms of generation and propagation of neural signals. Here we reanalyzed related experimental data to demonstrate that action potentials in the propagation process along a myelinated axon are highly overlapped in the time scale. The shift in time of two successive signals from neighboring nodes, defined as delay time τ in this work, is only tens of microseconds (16.3-87.0 μs), thus is only ~ 0.8-4.4 % of the measured average duration of an action potential, ~ 2 ms. This fact may reveal a huge gap to the commonly accepted picture for propagation of neural signal. We could apply the electromagnetic soliton-like model to well explain this phenomenon, and attribute τ to the waiting time that one signal source (i.e., ion channel cluster at one node) needs to take when it generates an electromagnetic neural pulse with increasing intensity until the intensity is higher than a certain point so as to activate neighboring signal source. This viewpoint may shed some light on a better understanding of the exact physical mechanism of neural signal communication in a variety of biosystems.Statement of SignificanceThe delay time during the propagation of action potentials is an important term in understanding the mechanisms of generation and propagation of neural signals. In this article we analyzed published experimental data and showed that action potentials from two neighboring Ranvier nodes are highly overlapped in time, with an average shift of tens of microseconds, which occupied only ~ 0.8-4.4 % of the average duration of an action potential (2 ms). The electromagnetic soliton-model seemed the best model to explain this phenomenon.The viewpoint of this article may shed some light on a better understanding of the exact physical mechanism of neural signal communication, and be tractive to researchers in a variety of fields, such as neuroscience, brain-computer interface, etc..
Genomic Characterization of Posttraumatic Stress Disorder in a Large US Military Veteran Sample
Authors: Stein Murray B. , Levey Daniel F. , Cheng Zhongshan , Wendt Frank R. , Harrington Kelly , Cho Kelly , Quaden Rachel , Radhakrishnan Krishnan , Girgenti Matthew J. , Anne Ho Yuk-Lam , Posner Daniel ,   PTSD Working Group of the Psychiatric Genomics Consortium (PGC),   Traumatic Stress Brain Research Study Group,   VA Million Veteran Program,   VA Cooperative Studies Program, Aslan Mihaela , Duman Ronald S. , Zhao Hongyu , Polimanti Renato , Concato John , Gelernter Joel 
Published: September 2019

ABSTRACTIndividuals vary in their liability to develop Posttraumatic Stress Disorder (PTSD), the symptoms of which are highly heterogeneous, following exposure to life-threatening trauma. Understanding genetic factors that contribute to the biology of PTSD is critical for refining diagnosis and developing new treatments. Using genetic data from more than 250,000 participants in the Million Veteran Program, genomewide association analyses were conducted using a validated electronic health record-based algorithmically-defined PTSD diagnosis phenotype (48,221 cases and 217,223 controls), and PTSD quantitative symptom phenotypes (212,007 individuals). We identified several genome-wide significant loci in the case-control analyses, and numerous such loci in the quantitative trait analyses, including some (e.g., MAD1L1; TCF4; CRHR1) that were associated with multiple symptom sub-domains and total symptom score, and others that were more specific to certain symptom sub-domains (e.g., CAMKV to re-experiencing; SOX6 to hyperarousal). Genetic correlations between all pairs of symptom sub-domains and their total were very high (rg 0.93 – 0.98) supporting validity of the PTSD diagnostic construct. We also demonstrate strong shared heritability with a range of traits, show that heritability persists when conditioned on other major psychiatric disorders, present independent replication results, provide support for one of the implicated genes in postmortem brain of individuals with PTSD, and use this information to identify potential drug repositioning candidates. These results point to the utility of genetics to inform and validate the biological coherence of the PTSD syndrome despite considerable heterogeneity at the symptom level, and to provide new directions for treatment development.
TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells
Authors: Vendrame Elena , Seiler Christof , Ranganath Thanmayi , Zhao Nancy Q. , Vergara Rosemary , Alary Michel , Labbé Annie-Claude , Guédou Fernand , Poudrier Johanne , Holmes Susan , Roger Michel , Blish Catherine A. 
Published: September 2019

ABSTRACTObjectiveOur objective was to investigate the mechanisms that govern natural killer (NK) cell responses to HIV, with a focus on specific receptor-ligand interactions involved in HIV recognition by NK cells.Design and MethodsWe first performed a mass cytometry-based screen of NK cell receptor expression patterns in healthy controls and HIV+ individuals. We then focused mechanistic studies on the expression and function of T cell immunoreceptor with Ig and ITIM domains (TIGIT).ResultsThe mass cytometry screen revealed that TIGIT is upregulated on NK cells of untreated HIV+ women, but not in antiretroviral-treated women. TIGIT is an inhibitory receptor that is thought to mark exhausted NK cells; however, blocking TIGIT did not improve anti-HIV NK cell responses. In fact, the TIGIT ligands CD112 and CD155 were not upregulated on CD4+ T cells in vitro or in vivo, providing an explanation for the lack of benefit from TIGIT blockade. TIGIT expression marked a unique subset of NK cells that express significantly higher levels of NK cell activating receptors (DNAM-1, NTB-A, 2B4, CD2) and exhibit a mature/adaptive phenotype (CD57hi, NKG2Chi, LILRB1hi, FcRγlo, Syklo). Furthermore, TIGIT+ NK cells had increased responses to mock-infected and HIV-infected autologous CD4+ T cells, and to PMA/ionomycin, cytokine stimulation and the K562 cancer cell line.ConclusionsTIGIT expression is increased on NK cells from untreated HIV+ individuals. Although TIGIT does not participate directly in NK cell recognition of HIV, it marks a population of mature/adaptive NK cells with increased functional responses.
Expression Profile of Circular RNAs in Epicardial Adipose Tissue in Heart Failure
Authors: Zheng Meili , Zhao Lei , Yang Xinchun 
Published: September 2019

AbstractRecent studies have reported circular RNA (circRNA) expression profiles in various tissue types; specifically, a recent work showed a detailed circRNA expression landscape in the heart. However, circRNA expression profile in human epicardial adipose tissue (EAT) remains undefined. RNA-sequencing was carried out to compare circRNA expression patterns in EAT specimens from coronary artery disease (CAD) cases between the heart failure (HF) and non-HF groups. The top highly expressed EAT circRNAs corresponded to genes involved in cell proliferation and inflammatory response, including KIAA0182, RHOBTB3, HIPK3, UBXN7, PCMTD1, N4BP2L2, CFLAR, EPB41L2, FCHO2, FNDC3B and SPECC1. Among the 141 circRNAs substantially different between the HF and non-HF groups (P<0.05;fold change>2), hsa_circ_0005565 stood out, and was mostly associated with positive regulation of metabolic processes and insulin resistancein GO and KEGG pathway analyses, respectively. These data indicate EAT circRNAs contribute to the pathogenesis of metabolic disorders causing HF.
On the mechanism of bilayer separation by extrusion; or, why your large unilamellar vesicles are not really unilamellar
Authors: Scott Haden L. , Skinkle Allison , Kelley Elizabeth G. , Waxham M. Neal , Levental Ilya , Heberle Frederick A. 
Published: September 2019

ABSTRACTExtrusion through porous filters is a widely used method for preparing biomimetic model membranes. Of primary importance in this approach is the efficient production of single bilayer (unilamellar) vesicles that eliminate the influence of interlamellar interactions and strictly define the bilayer surface area available to external reagents such as proteins. Sub-microscopic vesicles produced using extrusion are widely assumed to be unilamellar, and large deviations from this assumption would dramatically impact interpretations from many model membrane experiments. Using three probe-free methods—small-angle X-ray and neutron scattering (SAXS and SANS) and cryogenic electron microscopy (cryoEM)—we report unambiguous evidence of extensive multilamellarity in extruded vesicles composed of neutral phosphatidylcholine lipids, including for the common case of neutral lipids dispersed in physiological buffer and extruded through 100 nm diameter pores. In such preparations, only ~35% of lipids are externally accessible, and this fraction is highly dependent on preparation conditions. Charged lipids promote unilamellarity, as does decreasing solvent ionic strength, indicating the importance of electrostatic interactions in determining the lamellarity of extruded vesicles. Smaller extrusion pore sizes also robustly increase the fraction of unilamellar vesicles, suggesting a role for membrane bending. Taken together, these observations suggest a mechanistic model for extrusion, wherein formation of unilamellar vesicles involves competition between bilayer bending and adhesion energies. The findings presented here have wide-ranging implications for the design and interpretation of model membrane studies, especially ensemble-averaged observations relying on the assumption of unilamellarity.STATEMENT OF SIGNIFICANCEExtruded vesicles are a ubiquitous tool in membrane research. It is widely presumed that extrusion produces unilamellar (i.e., single bilayer) vesicles, an assumption that is often crucial for data analysis and interpretation. Using X-ray and neutron scattering and cryogenic electron microscopy, we show that a substantial amount of lipid remains inaccessible after extrusion due to an abundance of multilamellar vesicles (MLVs). While this is a general phenomenon for neutral lipids, MLV contamination can be reduced by several complementary approaches such as including charged lipids in the mixture, reducing the ionic strength of the aqueous medium, and reducing the extrusion pore size. These observations together suggest a mechanism by which extrusion strips MLVs of their layers.
Memorize-Generalize: An online algorithm for learning higher-order sequential structure with cloned Hidden Markov Models
Authors: Rikhye Rajeev V. , Guntupalli J. Swaroop , Gothoskar Nishad , Lázaro-Gredilla Miguel , George Dileep 
Published: September 2019

AbstractSequence learning is a vital cognitive function and has been observed in numerous brain areas. Discovering the algorithms underlying sequence learning has been a major endeavour in both neuroscience and machine learning. In earlier work we showed that by constraining the sparsity of the emission matrix of a Hidden Markov Model (HMM) in a biologically-plausible manner we are able to efficiently learn higher-order temporal dependencies and recognize contexts in noisy signals. The central basis of our model, referred to as the Cloned HMM (CHMM), is the observation that cortical neurons sharing the same receptive field properties can learn to represent unique incidences of bottom-up information within different temporal contexts. CHMMs can efficiently learn higher-order temporal dependencies, recognize long-range contexts and, unlike recurrent neural networks, are able to natively handle uncertainty. In this paper we introduce a biologically plausible CHMM learning algorithm, memorize-generalize, that can rapidly memorize sequences as they are encountered, and gradually generalize as more data is accumulated. We demonstrate that CHMMs trained with the memorize-generalize algorithm can model long-range structure in bird songs with only a slight degradation in performance compared to expectation-maximization, while still outperforming other representations.
Cryogenic auxiliary drilling of printed circuit boards
Authors: Lin Dantian , Wang Chengyong , Fu Lianyu , Ke Yong , He Yuxing , Fang Gexian , Yao Junxiong , Huang Xin , Zheng Lijuan 
Published: September 2019

Purpose
Large capacity current carrier printed circuit board (PCB) imposes strict control requirements on the hole wall roughness. The key factors are chip removal, drilling temperature and tool wear. This paper aims to find out a cryogenic drilling process to control the chip removal, chip morphology, tool wear and finally reduce the hole wall roughness.

Design/methodology/approach
The chip removal process, chip morphology, tool wear and hole wall roughness of glass fiber epoxy resin copper clad laminate (FR-4) drilling were observed and analyzed. The influence of cold air on the chip removal process, chip morphology, tool wear and hole wall roughness was also investigated. An optimization process of cold air auxiliary drilling was proposed to control the hole wall roughness of FR-4.

Findings
The results showed that the discharge time of copper foil chips with obvious characteristics can be used as the evaluation criterion for the smoothness of chip removal. The cold air can promote chip removal and reduce tool wear. In addition, the chip removal and cooling performance will be the best when using −4.7 °C cold air with the injection angle consisted with the angle of helical flute of the drill. The hole wall roughness of FR-4 could be controlled by drilling with −4.7°C cold air.

Originality/value
This paper was the first study of the effect of three kinds of cold air on PCB drilling. This provided a reference for the possibility that the cryogenic drilling methods apply to PCB drilling. A new cold air auxiliary drilling process was developed for large capacity current carrier FR-4 manufacturing.
Effect of piston clearance on the lubrication performance in axial piston pump
Authors: Lee Bora , Yu Yonghun , Cho Yong-Joo 
Published: September 2019

Purpose
This paper aims to provide a reliable and efficient numerical piston–cylinder design method and assess the effect of clearance on the piston-cylinder lubrication.

Design/methodology/approach
Numerical analyses of lubrication characteristics were performed for the piston–cylinder interface. The axial piston was numerically modeled, and the film pressure was calculated using the unsteady two-dimensional Reynolds equation. The behavior of the piston was analyzed by calculating the eccentricity satisfying the force and moment balance.

Findings
The secondary motion of the piston included numerically simulated several cycles until the piston behavior converged, and contact with the inner wall of the cylinder and friction region was estimated. Results showed that the piston–cylinder clearance affected the contact force, length of the contact region and leakage flow rate.

Originality/value
This result improves the understanding of the piston–cylinder lubrication and suggests considerations in terms of lubrication in clearance design.
The role of social media in negotiating identity during the process of acculturation
Authors: Yau Amy , Marder Ben , O’Donohoe Stephanie 
Published: September 2019

PurposeThe purpose of this paper is to contribute to an understanding of the role of social media in negotiating and managing identity for transient migrants relating to the home and host culture during the acculturation process.Design/methodology/approachFocussing on international students in the UK, this paper reports on findings from a qualitative study involving interviews with 27 transient migrants about their social media use and the negotiation of their identity online.FindingsThis paper highlights the multifaceted role that social media plays in the identity negotiations of transient migrants and it offers three theoretical contributions. First, the authors show that social media serves as a medium, consequence and determinant of identity. Second, provide four strategies for identity management are provided: boundary management, access management, online content management and offline content management. Third, contextualised support is provided for a reciprocal relationship between the different identity-related roles played by social media.Research limitations/implicationsThe paper highlights the complex role of social media for identity within the acculturation process for transient migrants. Identity contestation may be salient for young student migrants, especially where there is a large cultural distance between the home and host culture. Identity negotiations and struggles may not be salient with older migrants or migrants who have migrated for different reasons or where there is a small cultural distance between the home and host culture.Practical implicationsThis paper offers recommendations for social media site designers for enhancing the users experience during acculturation by guiding the navigation with identity management strategies as well as to highlight the possible predicaments of not managing their identity online.Originality/valueBased on qualitative research with transient migrants using social media during acculturation, the paper provides a theoretical model of the role and reciprocal relationship of social media for identity, serving the role as a medium, consequence and determinant. The paper incorporates four identity management strategies that migrants can use on social media.
‘The Russian Revolution has not yet taken place’: British views of the Soviet economy between the nineteen-fifties and nineteen-seventies
Authors: O'Hara Glen 
Published: September 2019

Abstract
This article examines British officials' and ministers' attitudes towards the Soviet Union's economy in the post-Second World War era. In the nineteen-fifties and early nineteen-sixties, public and some expert commentary posited Soviet economic ‘success’ based on the country's increasingly rapid growth rate, its potential for consumerization, the promise of economic reform, and the Soviet state's emphasis on education, science and the application of computer technology. New evidence from British official archives, presented here, makes clear that Westminster and Whitehall were never persuaded of this view, and always believed that political meddling and microeconomic inefficiencies would ultimately restrain and undermine Soviet growth.