bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control of N2 fixation and NH3 excretion in Azorhizobium caulinodans ORS571
Authors: Haskett Timothy L , Karunakaran Ramakrishnan , Batista Marcelo Bueno , Dixon Ray , Poole Philip S 
Published: April 2022

AbstractDue to the costly energy demands of N2 fixation, diazotrophic bacteria have evolved complex regulatory networks that permit expression of the N2-fixing catalyst nitrogenase only under conditions of N starvation, whereas the same condition stimulates upregulation of high-affinity NH3 assimilation by glutamine synthetase (GS), preventing excess release of excess NH3 for plants. Diazotrophic bacteria can be engineered to excrete NH3 by interference with GS, however control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target plants. Here, we attempted two strategies to control GS regulation and NH3 excretion in our model cereal symbiont Azorhizobium caulinodans AcLP, a derivative of ORS571. We first attempted to recapitulate previous work where mutation of both PII homologues glnB and glnK stimulated GS shutdown but found that one of these genes was essential for growth. Secondly, we expressed unidirectional adenylyltransferases (uATs) in a ΔglnE mutant of AcLP which permitted strong GS shutdown and excretion of NH3 derived from N2 fixation and completely alleviated negative feedback regulation on nitrogenase expression. We placed a uAT allele under control of the NifA-dependent promoter PnifH, permitting GS shutdown and NH3 excretion specifically under microaerobic conditions, the same cue that initiates N2 fixation, then deleted nifA and transferred a rhizopine-inducible nifAL94Q/D95Q-rpoN controller plasmid into this strain, permitting coupled rhizopine-dependent activation of N2 fixation with NH3 excretion. In future, this highly sophisticated and multi-layered control circuitry could be used to activate N2 fixation and NH3 excretion specifically by AcLP colonising transgenic rhizopine producing cereals, targeting delivery of fixed N to the crop, and preventing interaction with non-target plants.Author SummaryInoculation of cereal crops with associative “diazotrophic” bacteria that convert atmospheric N2 to NH3 could be used to sustainably improve delivery of nitrogen in agriculture. However, due to the costly energy demands of N2 fixation, natural diazotrophic bacteria have evolved to conserve energy by preventing excess production of NH3 and release to the plants. Diazotrophs can be engineered for excess NH3 production and release, however genetic control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target weed species. Here, we engineer control of N2 fixation and NH3 excretion in response to the signalling molecule rhizopine which is produced by transgenic barley. This control could be used to establish plant host-specific activation of N2 fixation and NH3 release following root colonisation in the field, minimising bacterial energy requirements in the bulk soil and preventing provision of NH3 to non-target plants.
Dimensionality of genomic information and its impact on GWA and variant selection: a simulation study
Authors: Jang Sungbong , Tsuruta Shogo , Leite Natalia Galoro , Misztal Ignacy , Lourenco Daniela 
Published: April 2022

AbstractBackgroundIdentifying true-positive variants in genome-wide associations (GWA) depends on several factors, including the number of genotyped individuals. The limited dimensionality of the genomic information may give insights into the optimal number of individuals to use in GWA. This study investigated different discovery set sizes in GWA based on the number of largest eigenvalues explaining a certain proportion of variance in the genomic relationship matrix (G). An additional investigation included the change in accuracy by adding variants, selected based on different set sizes, to the regular SNP chips used for genomic prediction.MethodsSequence data were simulated containing 500k SNP with 200 or 2000 quantitative trait nucleotides (QTN). A regular 50k panel included one every ten simulated SNP. Effective population size (Ne) was 20 and 200. The GWA was performed with the number of genotyped animals equivalent to the number of largest eigenvalues ofG(EIG) explaining 50, 60, 70, 80, 90, 95, 98, and 99% of the variance. In addition, the largest discovery set consisted of 30k genotyped animals. Limited or extensive phenotypic information was mimicked by changing the trait heritability. Significant and high effect size SNP were added to the 50k panel and used for single-step GBLUP with and without weights.ResultsUsing the number of genotyped animals corresponding to at least EIG98 enabled the identification of QTN with the largest effect sizes whenNewas large. Smaller populations required more than EIG98. Furthermore, using genotyped animals with higher reliability (i.e., higher trait heritability) helped better identify the most informative QTN. The greatest prediction accuracy was obtained when the significant or the high effect SNP representing twice the number of simulated QTN were added to the 50k panel. Weighting SNP differently did not increase prediction accuracy, mainly because of the size of the genotyped population.ConclusionsAccurately identifying causative variants from sequence data depends on the effective population size and, therefore, the dimensionality of genomic information. This dimensionality can help identify the suitable sample size for GWA and could be considered for variant selection. Even when variants are accurately identified, their inclusion in prediction models has limited implications.
Synaptic wiring motifs in posterior parietal cortex support decision-making
Authors: Kuan Aaron T. , Bondanelli Giulio , Driscoll Laura N. , Han Julie , Kim Minsu , Hildebrand David G. C. , Graham Brett J. , Thomas Logan A. , Panzeri Stefano , Harvey Christopher D. , Lee Wei-Chung A. 
Published: April 2022

AbstractThe posterior parietal cortex (PPC) exhibits choice-selective activity during perceptual decision-making tasks. However, it is not known how this selective activity arises from the underlying synaptic connectivity. Here, we combined virtual reality behavior, two-photon calcium imaging, high throughput electron microscopy, and circuit modeling to analyze how synaptic connectivity between neurons in PPC relates to their selective activity. We found that excitatory pyramidal neurons preferentially target inhibitory interneurons with the same selectivity. In turn, inhibitory interneurons preferentially target pyramidal neurons with opposite selectivity, forming an opponent inhibition motif. Using circuit models, we show that opponent inhibition amplifies selective inputs and induces competition between neural populations with opposite selectivity, thereby improving the encoding of trial-type information. These results provide evidence for how synaptic connectivity in cortical circuits supports a learned decision-making task.
A hybrid unsupervised approach for accurate short read clustering and barcoded sample demultiplexing in nanopore sequencing
Authors: Han Renmin , Qi Junhai , Xue Yang , Sun Xiujuan , Zhang Fa , Gao Xin , Li Guojun 
Published: April 2022

AbstractShort nucleic acid sequences are usually attached as DNA barcodes for multiple sample sequencing and single cell protocols, which enables Oxford Nanopore sequencing to sequence multiple barcoded DNA samples on a single flow cell. However, due to the high base-calling error, short reads in Nanopore sequencing are difficult to be accurately identified by traditional tools. Here, we propose a hybrid unsupervised approach for the accurate clustering of short reads and demultiplexing of barcoded samples in Nanopore sequencing. In our approach, both the nucleic base information translated from base-calling and the raw current signal directly outputted by the flow cell are utilized. A GPU-supported parallelization strategy is proposed to ensure the runtime of our hybrid clustering. Comprehensive experiments demonstrate that our approach outperforms all the traditional unsupervised tools in short read clustering, and achieves comparable accuracy in barcoded sample demultiplexing compared with the learning-based methods.
The broad shell colour variation in common cockle (Cerastoderma edule) from Northeast Atlantic relies on a major QTL revealed by GWAS using a new high-density genetic map
Authors: Hermida Miguel , Robledo Diego , Díaz Seila , Costas Damián , Bruzos Alicia L. , Blanco Andrés ,   The Cockle’s Consortium, Martínez Paulino 
Published: April 2022

AbstractShell colour pattern shows broad diversity in molluscs, and both genetic and environmental factors seem to interact to some extent on the final phenotype. Despite information on the genetic component and pathways involved in shell construction and colour has increased in the last decade, more data are needed particularly to understand colour variation and its putative role on adaptation. The European common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives with important variation in colour pattern, but this diversity has never been characterized and the underlying genetic architecture is unknown. In this study, we constructed a high-density genetic map, as an essential tool for genomic screening in common cockle, that was applied to ascertain the genetic basis of colour pattern variation in the species. The consensus map, including 13,874 2b-RAD SNPs, was constituted by the 19 linkage groups (LGs) corresponding to the n = 19 chromosomes of its karyotype and spanned 1,073 cM (730 markers per LG; inter-marker distance of 0.13 cM). Five full-sib families showing segregation for several colour-associated traits were used to perform a GWAS analysis. A major QTL on chromosome 13 explained most of the variation for shell colour patterns. Mining on this genomic region revealed the presence of several candidate genes enriched on Gene Ontology terms such as anatomical structure development, ion transport, membrane transport and cell periphery, closely related to shell architecture, including six chitin-related, one ependymin, several ion binding and transporters, and others related to transit across the cell membrane. Interestingly, this major QTL overlaps with a genomic region previously reported associated with divergent selection in the distribution range of the species, suggesting a putative role on local adaptation.
Development of novel temporal beta-diversity indices for assessing community compositional shifts accounting for changes in the properties of individuals
Authors: Nakadai Ryosuke 
Published: April 2022

AbstractRevealing the patterns of temporal biodiversity changes and deciphering the connection between individual life histories and large-scale ecological patterns is essential for improving the mechanistic understanding of macroecology. However, this is challenging because the relationship between individual life history and biodiversity remains unclear. In the present study, in order to link the individual life history and community-level phenomena, I developed novel indices that allow the evaluation of community compositional shifts over time by explicitly considering the contributions of the life histories of individuals (i.e. growth, mortality, and recruitment) in a community. These novel indices are quantitative extensions of the individual-based temporal beta-diversity indices which can include information on individual sizes. The indices were applied to a subset of data from the US Forest Inventory and Analysis database for the state of Rhode Island, USA, to identify changes in the contribution of individual life histories to biodiversity change. The results of this study represent methodological progress in community ecology and macroecology, as well as a conceptual advancement in bridging studies on biodiversity with those on individual life history and physiology. The individual-based diversity indices developed here pave the way for individual-based biodiversity science, which may facilitate the understanding of the effects of climate change across different hierarchies of biological organisation.
Anti-inflammatory therapy with nebulised dornase alfa for severe COVID-19 pneumonia
Authors: Porter Joanna C. , Inshaw Jamie , Solis Vincente Joel , Denneny Emma , Evans Rebecca , Temkin Mia I. , De Vasconcelos Nathalia , Aramburu Iker Valle , Hoving Dennis , Basire Donna , Crissell Tracey , Guinto Jesusa , Webb Alison , Esmail Hanif , Johnston Victoria , Last Anna , Rampling Thomas , Helbig Elisa Theresa , Lippert Lena , Kurth Florian , Williams Bryan , Flynn Aiden , Lukey Pauline T , Birault Veronique , Papayannopoulos Venizelos 
Published: April 2022

ABSTRACTBackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA.MethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC-BAC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors.ResultsBetween June 2020-October 2021 we recruited 39 evaluable patients: 30 randomised to dornase alfa (R-BAC+DA); 9 randomised to BAC (R-BAC); with the addition of 60 CC-BAC participants. Dornase alfa was well tolerated and reduced CRP by 33% compared to combined BAC groups (T-BAC). Least squares (LS) mean post-dexamethasone CRP fell from 101.9mg/L to 23.23 mg/L in the BAC+ dornase alfa group versus a fall from 99.5mg/L to 34.82 mg/L in the T-BAC group at 7 days; P=0.01. This effect of dornase alfa on CRP was confirmed with subgroup and sensitivity analyses that mitigated potential biases associated with the use of the CC-BAC group. Dornase alfa increased the chance of live discharge by 63% (HR 1.63, 95% CI 1.01 to 2.61, P=0.03), increased lymphocyte counts (LS mean: 1.08 vs 0.87, P=0.02) and reduced circulating cf-DNA and the coagulopathy marker D-dimer (LS mean: 570.78 vs 1656.96 μg/mL, P=0.004).ConclusionWe provide proof-of-concept evidence that dornase alfa reduces pathogenic inflammation in hospitalised patients with COVID-19 pneumonia, suggesting that best available care can be improved by the inclusion of anti-inflammatory treatments that target damage-associated molecules.
Social vulnerability and disasters: development and evaluation of a CONVERGE training module for researchers and practitioners
Authors: Adams Rachel Marie , Evans Candace , Wolkin Amy , Thomas Tracy , Peek Lori 
Published: April 2022

PurposeSocial vulnerability in the context of disaster management refers to the sociodemographic characteristics of a population and the physical, social, economic, and environmental factors that increase their susceptibility to adverse disaster outcomes and capacity to anticipate, cope with, resist, and recover from disaster events. Because disasters do not impact people equally, researchers, public health practitioners, and emergency managers need training to meet the complex needs of vulnerable populations.Design/methodology/approachTo address gaps in current education, the CONVERGE initiative, headquartered at the Natural Hazards Center at the University of Colorado Boulder, developed the Social Vulnerability and Disasters Training Module. This free online course draws on decades of research to examine the factors that influence social vulnerability to disasters. Examples of studies and evidence-based programs are included to illuminate common methods for studying social vulnerability and ways that research can guide practice. To evaluate the module, all trainees completed a pre- and post-training questionnaire.FindingsBetween July 2019 and September 2021, 1,089 people completed the module. Wilcoxon signed rank tests demonstrated a significant perceived increase in self-rated knowledge, skills, and attitudes (KSA). Students, members of historically underrepresented populations, and those new to or less experienced in the field, had the greatest perceived increase.Practical implicationsThis training module can help participants understand the specific needs of socially vulnerable populations to help reduce human suffering from disasters.Originality/valueThis article describes a novel web-based training and offers evaluation data showing how it can help educate a broad hazards and disaster workforce on an important topic for disaster management.
Utility optimization-based multi-stakeholder personalized recommendation system
Authors: Shrivastava Rahul , Sisodia Dilip Singh , Nagwani Naresh Kumar 
Published: April 2022

PurposeIn a multi-stakeholder recommender system (MSRS), stakeholders are the multiple entities (consumer, producer, system, etc.) benefited by the generated recommendations. Traditionally, the exclusive focus on only a single stakeholders' (for example, only consumer or end-user) preferences obscured the welfare of the others. Two major challenges are encountered while incorporating the multiple stakeholders' perspectives in MSRS: designing a dedicated utility function for each stakeholder and optimizing their utility without hurting others. This paper proposes multiple utility functions for different stakeholders and optimizes these functions for generating balanced, personalized recommendations for each stakeholder.Design/methodology/approachThe proposed methodology considers four valid stakeholders user, producer, cast and recommender system from the multi-stakeholder recommender setting and builds dedicated utility functions. The utility function for users incorporates enhanced side-information-based similarity computation for utility count. Similarly, to improve the utility gain, the authors design new utility functions for producer, star-cast and system to incorporate long-tail and diverse items in the recommendation list. Next, to balance the utility gain and generate the trade-off recommendation solution, the authors perform the evolutionary optimization of the conflicting utility functions using NSGA-II. Experimental evaluation and comparison are conducted over three benchmark data sets.FindingsThe authors observed 19.70% of average enhancement in utility gain with improved mean precision, diversity and novelty. Exposure, hit, reach and target reach metrics are substantially improved.Originality/valueA new approach considers four stakeholders simultaneously with their respective utility functions and establishes the trade-off recommendation solution between conflicting utilities of the stakeholders.
Whether, how and why home country environments influence emerging market firm acquisition behavior
Authors: Reddy Rama Krishna , Fabian Frances , Park Sung-Jin 
Published: April 2022

PurposeAccording to the 2019 World Investment Report, recent events in deglobalization have made many countries, especially developed markets, resist inward foreign direct investment (FDI) as ceding control to foreign countries. At the same time, many emerging market firms (EMFs) have been increasing their acquisitions in developed markets. The authors elaborate three unconventional motives that justify such acquisitions, and test whether conditions in home countries related to these motives predict the pursuit of greater or lesser equity control. Understanding how home country conditions may spur seeking greater equity control can help policymakers and business firm decision-makers improve these dynamics.Design/methodology/approachExamining data covering the period 2006–2018, the authors test hypotheses using a sample of 4,130 acquisitions by EMFs into developed markets, and test hypotheses to investigate “How does the institutional and resource environment of an EMF's home country relate to the respective EMF acquisition behavior of seeking equity control?”FindingsThe authors found that higher institutional quality, poorer factor market development, and higher capital market quality in the home country are related to higher equity positions sought.Practical implicationsAcquiring and target firm managers, along with other stakeholders, can gain insights on how to respond to acquisition opportunities by recognizing how home country conditions influence emerging market internationalizing behaviors into developed markets.Originality/valueThe compilation of this data uniquely covers 48 different emerging markets and further concentrates on the relatively less understood pre-deal phase for EMNEs entering developed markets.
Personality effects on WoM and eWoM susceptibilty – a cross-country perspective
Authors: König Tatjana M. , Clarke Theresa B. , Hellenthal Maria , Clarke III Irvine 
Published: April 2022

PurposeThis study utilizes social communication theory as the framework to examine the influence of personality on young word-of-mouth (WoM) and electronic word-of-mouth (eWoM) audiences across the US, France and Germany and explores relationships between personality traits and cultural dimensions.Design/methodology/approachAn adaptation of the consumer susceptibility to interpersonal influence (CSII) scale measured WoM influence in an online review context. After pretesting and validating the consumer susceptibility to online review influence (CSRI) scale in Luxemburg, hypotheses were tested, and research questions were explored in a multi-group structural equation model based on French, German and US samples.FindingsPersonality traits are negatively linked to CSRI as well as to CSII across the three countries. Overall, the stronger the personality traits, the weaker the online and offline WoM influence seems. In contrast to France, results for the US and Germany show that young people are either more susceptible to WoM or to eWoM influence. Results imply tendencies for a potential interaction effect between power distance and openness to new experience on WoM and partially on eWoM.Practical implicationsEarned media is more effective among audiences with weaker personality structures. Stronger personalities may prefer to serve as senders of WoM and eWoM (influencers). The non-uniform results between WoM and eWoM susceptibility across the countries favor earned media strategies optimized on a country basis and psychological targeting when communicating online review results.Originality/valueThis study expands knowledge of individual (personality traits) and country similarities and differences across France, Germany and the US and how they affect earned media (WoM and eWoM) influence.