bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domestication signatures in the non-conventional yeastLachancea cidri
Authors: Villarreal Pablo , O’Donnell Samuel , Agier Nicolas , Muñoz-Guzmán Felipe , Benavides-Parra José , Urbina Kamila , Peña Tomas A. , Solomon Mark , Nespolo Roberto F. , Fischer Gilles , Varela Cristian , Cubillos Francisco A. 
Published: June 2023

AbstractEvaluating domestication signatures beyond model organisms is essential for thoroughly understanding the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in aLachancea cidriyeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (∼16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role on the strain’s phenotypic variation. The set of SVs identified directly impacts dozens of genes, and likely underpins the greater fermentation performance in theL. cidriCBS2950. Additionally, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higherPUT4transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to an anthropogenic habitat and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.ImportanceThe exploration of domestication signatures associated with anthropogenic niches has predominantly focused on studies conducted on model organisms, such asSaccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomycesspecies. In our research, employing a combination of long– and short-read data, we found domestication signatures inL. cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication hallmarks result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.
Methodological considerations for behavioral studies relying on response time outcomes through online crowdsourcing platforms
Authors: McConnell Patrick A. , Finetto Christian , Heise Kirstin-Friederike 
Published: June 2023

AbstractThis study explored challenges associated with online crowdsourced data collection, particularly focusing on longitudinal tasks with time-sensitive outcomes like response latencies. The research identified two significant sources of bias: technical shortcomings such as low, variable frame rates, and human factors, contributing to high attrition rates. The study also explored potential solutions to these problems, such as enforcing hardware acceleration and defining study-specific frame rate thresholds, as well as pre-screening participants and monitoring hardware performance and task engagement over each experimental session. This study provides valuable insights into improving the quality and reliability of data collected via online crowdsourced platforms and emphasizes the need for researchers to be cognizant of potential pitfalls in online research.
Tip of the iceberg? Three novel TOPLESS interacting effectors of the gall-inducing fungusUstilago maydis
Authors: Khan Mamoona , Uhse Simon , Bindics Janos , Kogelmann Benjamin , Nagarajan Nithya , Ingole Kishor D. , Djamei Armin 
Published: June 2023

SummaryUstilago maydisis a biotrophic pathogen causing smut disease in maize. It secretes a cocktail of effector proteins during its biotrophic stages in the host plant, which target different host proteins. One such class of proteins we identified previously is TOPLESS (TPL) and TOPLESS RELATED (TPR) transcriptional corepressors.Here we screen 297 U.maydiseffector candidates for their ability to interact with maize TPL protein RAMOSA 1 ENHANCER LOCUS 2 Like 2 (RELK2) and their ability to induce auxin signaling and thereby identified three novel TPL /TPR interacting effector proteins (Tip6, Tip7 and Tip8). Two of them, Tip6 and Tip7 contain a classical ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif and interact with maize TPL protein RELK2 in nuclear compartments, whereas Tip8 lacks known TPL interaction motifs and its overexpressioninnon-host plant leads to cell death indicating recognition of the effector.By using structural modeling, we show an interaction of Tip6 and Tip7 with the previously crystallized EAR motif binding domain of RELK2. Furthermore, by infection assays with an octuple deletion mutant ofU. maydis, we demonstrate a role of Tips inU. maydisvirulence. Our findings suggest the TOPLESS class of corepressors as a major hub ofU. maydiseffector proteins.
EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment
Authors: Shen Chengze , Liu Baqiao , Williams Kelly P , Warnow Tandy 
Published: June 2023

AbstractBackgroundAdding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity.ResultsWe present EMMA (Extending Multiple alignments using MAFFT-add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT-add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide-and-conquer framework to scale its most accurate version, MAFFT-linsi--add, to constraint alignments with many sequences. We show that EMMA has an accuracy advantage over other techniques for adding sequences into alignments under many realistic conditions and can scale to large datasets with high accuracy (hundreds of thousands of sequences). EMMA is available athttps://github.com/c5shen/EMMA.ConclusionsEMMA is a new tool that provides high accuracy and scalability for adding sequences into an existing alignment.
SAD-1 kinase controls presynaptic phase separation by relieving SYD-2/Liprin-α autoinhibition
Authors: McDonald Nathan A. , Tao Li , Dong Meng-Qiu , Shen Kang 
Published: June 2023

AbstractNeuronal development orchestrates the formation of an enormous number of synapses that connect the nervous system. In developing presynapses, the core active zone structure has been found to assemble through a liquid-liquid phase separation. Here, we find that the phase separation of SYD-2/Liprin-α, a key active zone scaffold, is controlled by phosphorylation. Using phosphoproteomics, we identify the SAD-1 kinase to phosphorylate SYD-2 and a number of other substrates. Presynaptic assembly is impaired insad-1mutants and increased by overactivation of SAD-1. We determine SAD-1 phosphorylation of SYD-2 at three sites is critical to activate its phase separation. Mechanistically, phosphorylation relieves a binding interaction between two folded SYD-2 domains that inhibits phase separation by an intrinsically disordered region. We find synaptic cell adhesion molecules localize SAD-1 to nascent synapses upstream of active zone formation. We conclude that SAD-1 phosphorylates SYD-2 at developing synapses, enabling its phase separation and active zone assembly.
Targeting lipid nanoparticles to the blood brain barrier to ameliorate acute ischemic stroke
Authors: Nong Jia , Glassman Patrick M. , Reyes-Esteves Sahily , Descamps Helene C. , Shuvaev Vladimir V. , Kiseleva Raisa Y. , Papp Tyler E. , Alameh Mohamad-Gabriel , Tam Ying K. , Mui Barbara L. , Omo-Lamai Serena , Zamora Marco E. , Shuvaeva Tea , Arguiri Evguenia , Thaiss Christoph A , Myerson Jacob W. , Weissman Drew , Kasner Scott E. , Parhiz Hamideh , Muzykantov Vladimir R. , Brenner Jacob S. , Marcos-Contreras Oscar A. 
Published: June 2023

AbstractAfter more than 100 failed drug trials for acute ischemic stroke (AIS), one of the most commonly cited reasons for the failure has been that drugs achieve very low concentrations in the at-risk penumbra. To address this problem, here we employ nanotechnology to significantly enhance drug concentration in the penumbra’s blood-brain barrier (BBB), whose increased permeability in AIS has long been hypothesized to kill neurons by exposing them to toxic plasma proteins. To devise drug-loaded nanocarriers targeted to the BBB, we conjugated them with antibodies that bind to various cell adhesion molecules on the BBB endothelium. In the transient middle cerebral artery occlusion (tMCAO) mouse model, nanocarriers targeted with VCAM antibodies achieved the highest level of brain delivery, nearly 2 orders of magnitude higher than untargeted ones. VCAM-targeted lipid nanoparticles loaded with either a small molecule drug (dexamethasone) or mRNA (encoding IL-10) reduced cerebral infarct volume by 35% or 73%, respectively, and both significantly lowered mortality rates. In contrast, the drugs delivered without the nanocarriers had no effect on AIS outcomes. Thus, VCAM-targeted lipid nanoparticles represent a new platform for strongly concentrating drugs within the compromised BBB of penumbra, thereby ameliorating AIS.Graphical abstractAcute ischemic stroke induces upregulation of VCAM. We specifically targeted upregulated VCAM in the injured region of the brain with drug- or mRNA-loaded targeted nanocarriers. Nanocarriers targeted with VCAM antibodies achieved the highest brain delivery, nearly orders of magnitude higher than untargeted ones. VCAM-targeted nanocarriers loaded with dexamethasone and mRNA encoding IL-10 reduced infarct volume by 35% and 73%, respectively, and improved survival rates.
Decoding Root Biogeography: Building Reduced Complexity Functional Rhizosphere Microbial Consortia
Authors: Chen Mingfei , Acharya Shwetha , Yee Mon Oo , Cabugao Kristine Grace , Chakraborty Romy 
Published: June 2023

AbstractThe rhizosphere microbiome plays a crucial role in supporting plant productivity and contributes to ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, characterizing their functional attributes and microbial relationships remains challenging due to their complex taxonomic and functional compositions. To enable such studies, the development of reduced complexity microbial consortia derived from the rhizosphere microbiome of the natural ecosystem is highly desirable. Designing and assembling reduced complexity consortia that mimic natural communities with consistent, stable, predictable features are highly sought after but is challenging to deliver. Here we present our systematic controlled design towards successful assembly of several such rhizosphere derived reduced complexity consortia. FromBrachypodiumgrown in natural soil under controlled lab conditions, we enriched the root-associated microbes, utilizing carbon compounds prevalent in Brachypodium root exudates. By transferring the enrichments every 3 or 7 days for 9 generations, we developed both fast and slow-growing microbial communities. 16S rRNA amplicon analysis revealed that both inoculum and carbon substrates significantly influence microbial community composition. For example, 1/10 R2A preferentially enriched Amplicon Sequence Variants (ASVs) from slow growing taxa vital to plant including Acidobacteria and Verrucomicrobia. Network analysis revealed that although fast and slow growing microbial consortia have distinct key taxa, the key hubs (keystone taxa) for both belong to genera with plant growth promoting (PGP) traits. This suggests that PGP bacteria might play a central role in controlling the microbial networks among rhizospheric microbiomes. Based on the stability and richness results from different transfers, most carbon substrates lead to microbial consortia with reduced complexity and high stability after a few transfers. The stability tests of the derived microbial consortia also showed high stability, reproducibility, and revivability of the constructed microbial consortia. Our study represents a significant step towards understanding and harnessing the potential of rhizosphere microbiomes, with implications for sustainable agriculture and environmental management.
Groundwater redox dynamics across the terrestrial-aquatic interface of Lake Erie coastal ecosystems
Authors: Machado-Silva Fausto , Weintraub Michael , Ward Nicholas , Doro Kennedy O. , Regier Peter J. , Ehosioke Solomon , Thomas Shan Pushpajom , Peixoto Roberta B. , Sandoval Leticia , Forbrich Inke , Kemner Kenneth M. , O’Loughlin Edward J. , Setten Lucie , Spanbauer Trisha , Bridgeman Thomas B. , O’Meara Teri , Rod Kenton A. , Patel Kaizad , McDowell Nate G. , Bond-Lamberty Ben P. , Megonigal J. Patrick , Rich Rich L. , Bailey Vanessa L 
Published: June 2023

ABSTRACTGroundwater biogeochemistry in coastal areas is spatially and temporally dynamic because fluctuations in groundwater level may cause alternate redox between distinct hydrological conditions. Recent studies have proposed connections between biogeochemistry and large-scale hydrological processes, specifically focusing on the role of redox-active compounds in changing the oxidation state during flooding and draining events. While water saturation generally results in a shift of redox-active compounds from electron donors to acceptors, the specific mechanisms underlying the transition of groundwater between oxidizing and reducing conditions in response to water level fluctuations are uncertain. To determine the effects of groundwater levels on redox dynamics, we monitored groundwater redox potential across the terrestrial-aquatic interface in Lake Erie coastal areas throughout the high and low-water seasons. In contrast to previously observed responses to flooding in soils, our results revealed patterns of oxidizing redox potentials during high-water and reducing during low-water periods. Furthermore, short-term fluctuations in water table levels significantly impacted the redox potential of groundwater when dissolved oxygen increased, and redox dynamics displayed voltage hysteresis in most events. Based on these findings, we propose that for improved predictions of microbial functions and biogeochemical cycles, redox-informed models should incorporate the antagonistic changes in groundwater redox balance compared to soils and consider the time lags in redox fluctuations.Graphical AbstractConceptual diagram of groundwater redox fluctuations in coastal ecosystems. Large redox fluctuations are derived by dissolved oxygen inputs and smaller more frequent redox fluctuations are led by redox sensitive species leaching from topsoil.
Discovery ofThetaRibozymes in Gut Phages–Implications for tRNA and Alternative Genetic Coding
Authors: Kienbeck Kasimir , Malfertheiner Lukas , Zelger-Paulus Susann , Johannsen Silke , von Mering Christian , Sigel Roland K.O. 
Published: June 2023

AbstractRibozymes, relics of the “RNA world”, are essential across all domains of life. Nonetheless, the functions and genomic contexts of recently discovered small ribozymes, such as minimal hepatitis delta virus (HDV)-like ribozymes, remain elusive. Using bioinformatic analyses, we identified a novel subfamily of minimal HDV-like ribozymes, coinedthetaribozymes. Hundreds of unique examples were found adjacent to viral tRNAs withinCaudoviricetesbacteriophages of the mammalian gut virome.In vitroexperiments confirm site-specific self-scission activity, suggesting their involvement in processing tRNA 3’-trailers.Intriguingly, a significant fraction ofthetaribozymes is associated with viral suppressor tRNAs, potentially regulating the late-stage assembly of recoded bacteriophages. These findings advance the understanding of RNA-based mechanisms underlying the intricate interplay between the bacterial and viral parts of the mammalian gut microbiome.One-Sentence SummaryNewly unveiledthetaribozymes associate with suppressor tRNAs of alternatively coded gut phages: a potential lytic switch.
Matlab sensitivity analysis toolbox: an application on faults identification in induction motors
Authors: Aswad Raya A.K. , Jassim Bassim M.H. 
Published: June 2023

Purpose
This paper aims to introduce the usage of sensitivity analysis (SA) for the problem of faults identification in three-phase induction motors (IMs). These motors are susceptible to different kinds of faults that should be detected in a proper time to keep the systems working in a safety environment.

Design/methodology/approach
One of the effective approaches for faults identifications, which is presented in the literature, is a model-based strategy. This strategy mainly depends on using a software model to make an identification decision. Therefore, this work intends to examine the model sensitivity towards variables’ variation. The SA toolbox of Matlab R2017b package is used for this purpose since the Matlab software is a well-known environment, and it is easy for a nonstatistical person to deal with it. As a study case, open-circuit and stator inter-turn faults in the stator windings of a three-phase IM have been chosen.

Findings
The results show that the model-based strategy is considerably speed up by up to 30% when neglecting the trivial model’s parameters with the same accurate identification decision as compared with the results of this strategy without using the SA.

Originality/value
The novelty of this work is summarized in devoting the usage of SA in the field of faults identification to enhance the speed of final decision.
Diversity, equity, and inclusion practices: a Delphi study to build a consensus in hospitality and tourism organizations
Authors: Ponting Sandra Sun-Ah , Dillette Alana 
Published: June 2023

Purpose
The purpose of this study is to explore the development and implementation of diversity, equity and inclusion (DEI) practices in hospitality and tourism organizations through the lens of structuration theory.

Design/methodology/approach
This study deployed a three-stage Delphi technique involving DEI experts in hospitality and tourism organizations to build a consensus. Specifically, individual agency, development and implementation of DEI practices and best DEI practices were explored through the Delphi technique.

Findings
The findings of this study feature a framework for DEI practices and the intersection between individual agency and organizational structure. The results of this study further showcase the theoretical importance of structuration theory in understanding how organizations develop and implement DEI practices.

Originality/value
This study reveals unique perspectives on DEI within hospitality and tourism organizations, pointing to the imperative need for leadership in initiating, developing and implementing change. This study also extends previous research by highlighting how DEI practices are initiated, developed and implemented through individual agency and organizational structure.
Building trust and empowering informed decisions: effects of risk disclosure and call to action on young adults’ responses to dietary supplement advertising
Authors: Zhao Wenqing , Jin Yan , Karinshak Elise 
Published: June 2023

Purpose
This study aims to examine the effects of risk disclosure and call to action (i.e. encouraging individuals to consult a health provider before they make any purchase decision) on young adults’ cognitive and behavioral responses to dietary supplement advertising.

Design/methodology/approach
A 2 (risk disclosure: absence vs presence) × 2 (call to action: absence vs presence) between-subjects online experiment was conducted with 124 college-attending young adults.

Findings
Including risk disclosure in probiotic supplement advertising increased young adults’ perceived message credibility, intentions to ask a medical doctor and sense of confidence in decision-making. The addition of call to action in probiotic supplement advertising improved perceived message credibility, trust in advertised brand, favorable attitude toward brand, intention to ask a medical doctor and purchase intention; however, a significant joint effect was not found between risk disclosure and call to action.

Originality/value
Although risk disclosure and call to action are significant techniques in pharmaceutical and health-care marketing, they have been overlooked by both research and practice of dietary supplement marketing. This study closes this gap by providing empirical evidence to generate a clear idea about the benefits of including risk disclosure and call to action in dietary supplement advertising.
The qualities of data: how nurses and their managers act on patient feedback in an English hospital
Authors: Desai Amit , Zoccatelli Giulia , Donetto Sara , Robert Glenn , Allen Davina , Rafferty Anne Marie , Brearley Sally 
Published: June 2023

PurposeTo investigate ethnographically how patient experience data, as a named category in healthcare organisations, is actively “made” through the co-creative interactions of data, people and meanings in English hospitals.Design/methodology/approachThe authors draw on fieldnotes, interview recordings and transcripts produced from 13 months (2016–2017) of ethnographic research on patient experience data work at five acute English National Health Service (NHS) hospitals, including observation, chats, semi-structured interviews and documentary analysis. Research sites were selected based on performance in a national Adult Inpatient Survey, location, size, willingness to participate and research burden. Using an analytical approach inspired by actor–network theory (ANT), the authors examine how data acquired meanings and were made to act by clinical and administrative staff during a type of meeting called a “learning session” at one of the hospital study sites.FindingsThe authors found that the processes of systematisation in healthcare organisations to act on patient feedback to improve to the quality of care, and involving frontline healthcare staff and their senior managers, produced shifting understandings of what counts as “data” and how to make changes in response to it. Their interactions produced multiple definitions of “experience”, “data” and “improvement” which came to co-exist in the same systematised encounter.Originality/valueThe article's distinctive contribution is to analyse how patient experience data gain particular attributes. It suggests that healthcare organisations and researchers should recognise that acting on data in standardised ways will constantly create new definitions and possibilities of such data, escaping organisational and scholarly attempts at mastery.