bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of transcriptomic datasets identifies ABA-responsive factors as regulators of photomorphogenesis inArabidopsis
Authors: Stafen Cássia Fernanda , Souza Iara , de Oliveira Ben Hur , de Oliveira-Busatto Luísa Abruzzi , Dalmolin Rodrigo Juliani Siqueira , Sánchez Oscar Lorenzo , Maraschin Felipe dos Santos 
Published: July 2022

AbstractFollowing germination, seedlings grown in light show a photomorphogenic development with open and green cotyledons and a robust root system. The light perception by the photoreceptors activate autotrophic photosynthetic metabolism to sustain growth of the whole plant. Several studies have evaluated transcriptional responses to light signals. Nevertheless, evaluating a single source experiment might bias the identificationof general, reproducible light responses. In order to identify widespread light-dependent signaling events that control early seedling photomorphogenesis we performed a survey comparing commonly regulated genes in transcriptomic public datasets derived from etiolated seedlings exposed to short light treatments. By compiling commonly regulated genes from different datasets, we obtained broadly representative regulated processes concerning general light transcriptional response. Our analysis shows that light primarly affects shoot gene expression promoting the assembly of photosynthetic machinery, signaling and redox responses. We observed that Transcriptograms allowed a better comparison among different experiments than DEseq analysis. We also identified that, transcriptional regulation of early light response is centered in the transcription factor ABA-Insensitive5 (ABI5) along with other bZIP transcription factors suggesting a mechanism by which dark expressed transcription factors guide the activation of early photomorphogenic genes.Key MessageComparative analisys of seedling deetiolation transcriptomic datasets identified ABA-responsive bZIP transcription factors as central regulators of early photomorphogenesis
Digitally Predicting Protein Localization and Manipulating Protein Activity in Fluorescence Images Using Four-dimensional Reslicing GAN
Authors: Jiao Yang , Weng Mo , Gu Lingkun , Jiang Yingtao , Yang Mei 
Published: July 2022

AbstractMotivationWhile multi-channel fluorescence microscopy is a vital imaging method in biological studies, the number of channels that can be imaged simultaneously is limited by technical and hardware limitations such as emission spectra cross-talk. One feasible solution is using deep neural networks to model the localization relationship between two proteins so that the localization of a protein can be digitally predicted. Furthermore, the input and predicted localization implicitly reflects the modeled relationship. Accordingly, observing the predictions via repeatedly manipulating input localizations is an explainable and feasible way to analyze the modeled relationships between the input and the predicted proteins.ResultsWe propose a Protein Localization Prediction (PLP) method using a cGAN named Four-dimensional Reslicing Generative Adversarial Network (4DR-GAN) to digitally generate additional channels. 4DR-GAN models the joint probability distribution of imaged and target proteins by simultaneously incorporating the protein localization signals in four dimensions including space and time. Because protein localization often correlates with protein activation state, with accurate PLP, we further propose two novel tools: digital activation (DA) and digital inactivation (DI) to digitally activate and inactivate a protein and observe the response of the predicted protein localization. Compared with genetic approaches, these tools allow precise spatial and temporal control. A comprehensive experiment on four groups of proteins shows that 4DR-GAN achieves higher-quality PLP than Pix2Pix and the DA and DI responses are consistent with the known protein functions. The proposed PLP method helps simultaneously visualize additional proteins and DA and DI provide guidance to study localization-based protein functions.Availability and ImplementationThe open-source code is athttps://github.com/YangJiaoUSA/4DR-GAN.
Single neurons in thalamus and subthalamic nucleus process cardiac and respiratory signals in humans
Authors: De Falco Emanuela , Solcà Marco , Bernasconi Fosco , Babo-Rebelo Mariana , Young Nicole , Sammartino Francesco , Rezai Ali , Krishna Vibhor , Blanke Olaf 
Published: July 2022

AbstractVisceral signals are constantly processed by our central nervous system, enable homeostatic regulation, and influence perception, emotion, and cognition. While visceral processes at cortical level have been extensively studied using non-invasive imaging techniques, very few studies have investigated how this information is processed at the single neuron level, both in humans and animals. Subcortical regions, relaying signals from peripheral interoceptors to cortical structures, are particularly understudied and how visceral information is processed in thalamic and subthalamic structures remains largely unknown. Here, we took advantage of intraoperative microelectrode recordings in patients undergoing surgery for deep brain stimulation (DBS) to investigate the activity of single neurons related to cardiac and respiratory functions in three subcortical regions: Ventral Intermedius nucleus (Vim) and Ventral caudalis nucleus (Vc) of the thalamus, and subthalamic nucleus (STN). We report that the activity of a large portion of the recorded neurons (about 70%) was modulated by either the heartbeat, the cardiac inter-beat interval, or the respiration. These cardiac and respiratory response patterns varied largely across neurons both in terms of timing and their kind of modulation. We observed neurons with increases or decreases in firing rate in response to either the heartbeat or the inter-beat interval. Peaks of neural activity were found at different phases of the cardiac and respiratory cycles. Whereas most neurons only responded to one of the tested signals, a substantial proportion of these visceral neurons (30%) was responsive to more than one of the tested signals, underlining specialization and integration of cardiac and respiratory signals in STN and thalamic neurons. By extensively describing for the first time single unit activity related to cardiorespiratory function in thalamic and subthalamic neurons, our results highlight the major role of these subcortical regions in the processing of visceral signals.
Genetic architecture of creativity and extensive genetic overlap with psychiatric disorders revealed from genome-wide association analyses of 241,736 individuals
Authors: Kim Hyejin , Ahn Yeeun , Yoon Joohyun , Jung Kyeongmin , Kim Soyeon , Shim Injeong , Park Tae Hwan , Ko Hyunwoong , Jung Sang-Hyuk , Kim Jaeyoung , Park Sanghyeon , Lee Dong June , Choi Sunho , Cha Soojin , Kim Beomsu , Cho Min Young , Cho Hyunbin , Kim Dan Say , Ihm Hong Kyu , Park Woong-Yang , Bakhshi Hasan , O’Connell Kevin S , Andreassen Ole A , Flint Jonathan , Kendler Kenneth S. , Myung Woojae , Won Hong-Hee 
Published: July 2022

AbstractCreativity is heritable and exhibits familial aggregation with psychiatric disorders, but its genomic basis and genetic relationship with psychiatric disorders remain largely unknown. Here, we conducted a genome-wide association study (GWAS) using an expanded, machine learning-based definition of creativity in individuals of European ancestry from the UK Biobank (n= 241,736) and identified 25 creativity-associated loci. Extensive genetic overlap with psychiatric disorders, including schizophrenia, major depression, bipolar I disorder, attention deficit/hyperactivity disorder, and anorexia nervosa, was demonstrated by the genetic correlation, polygenic risk score, and MiXeR analyses. The condFDR and conjFDR analyses identified additional loci for creativity and psychiatric disorders, as well as shared genetic loci between creativity and psychiatric disorders. This GWAS showed significant correlations with GWASs using traditional definitions of creativity and GWASs adjusted for educational attainment. Our findings contribute to the understanding of the genetic architecture of creativity and reveal its polygenic relationships with psychiatric disorders.
mTORC1 is required for differentiation of germline stem cells in the Drosophila melanogaster testis
Authors: Clémot Marie , D’Alterio Cecilia , Kwang Alexa , Jones D. Leanne 
Published: July 2022

AbstractMetabolism participates in the control of stem cell function and subsequent maintenance of tissue homeostasis. How this is achieved in the context of adult stem cell niches in coordination with other local and intrinsic signaling cues is not completely understood. The Target of Rapamycin (TOR) pathway is a master regulator of metabolism and plays essential roles in stem cell maintenance and differentiation. We observe differential expression of the Tor kinase in the Drosophila male germline, which correlates with restriction of mTORC1 activity to germline stem cells (GSCs) and early germ cells. Targeted RNAi-mediated downregulation of Tor in early germ cells causes a block and/or a delay in differentiation, resulting in an accumulation of germ cells with GSC-like features. These early germ cells also contain unusually large and dysfunctional autolysosomes. In addition, downregulation of Tor in adult male GSCs and early germ cells causes non-autonomous activation of mTORC1 in neighboring cyst cells, which correlates with a disruption in the coordination of germline and somatic differentiation. Our study identifies a previously uncharacterized role of the TOR pathway in regulating male germline differentiation.
Escherichia coliSPFH membrane microdomain proteins HflKC contribute to aminoglycoside and oxidative stress tolerance
Authors: Wessel Aimee K. , Yoshii Yutaka , Reder Alexander , Boudjemaa Rym , Szczesna Magdalena , Betton Jean-Michel , Bernal-Bayard Joaquin , Beloin Christophe , Lopez Daniel , Völker Uwe , Ghigo Jean-Marc 
Published: July 2022

ABSTRACTMany eukaryotic membrane-dependent functions are often spatially and temporally regulated by membrane microdomains (FMMs) also known as lipid rafts. These domains are enriched in polyisoprenoid lipids and scaffolding proteins belonging to the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) protein superfamily that was also identified in Gram-positive bacteria. By contrast, little is still known about FMMs in Gram-negative bacteria. InEscherichia coliK12, 4 SPFH proteins, YqiK, QmcA, HflK, and HflC, were shown to localize in discrete polar or lateral inner-membrane locations, raising the possibility thatE. coliSPFH proteins could contribute to the assembly of inner-membrane FMMs and the regulation of cellular processes.Here we studied the determinant of the localization of QmcA and HflC and showed that FMM-associated cardiolipin lipid biosynthesis is required for their native localization pattern. Using Biolog phenotypic arrays, we showed that a mutant lacking all SPFH genes displayed increased sensitivity to aminoglycosides and oxidative stress that is due to the absence of HflKC. Our study therefore provides further insights into the contribution of SPFH proteins to stress tolerance inE. coli.IMPORTANCEEukaryotic cells often segregate physiological processes in cholesterol-rich functional membrane micro-domains. These domains are also called lipid rafts and contain proteins of the Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) superfamily, which are also present in prokaryotes but were mostly studied in Gram-positive bacteria. Here, we showed that the cell localization of the SPFH proteins QmcA and HflKC in the Gram-negative bacteriaE. coliis altered in absence of cardiolipin lipid synthesis. This suggests that cardiolipins contribute toE. colimembrane microdomain assembly. Using a broad phenotypic analysis, we also showed that HflKC contribute toE. colitolerance to aminoglycosides and oxidative stress. Our study, therefore, provides new insights into the cellular processes associated with SPFH proteins inE. coli.
Reducing environmentally mediated transmission to moderate impacts of an emerging wildlife disease
Authors: Hoyt Joseph R. , Parise Katy L. , DePue John E. , Kaarakka Heather M. , Redell Jennifer A. , Scullon William H. , O’Reskie Rich , Foster Jeffrey T. , Kilpatrick A. Marm , Langwig Kate E. , White J. Paul 
Published: July 2022

AbstractEmerging infectious diseases are a serious threat to wildlife communities, and the ability of pathogens to survive in the environment can exacerbate disease impacts on hosts and increase the likelihood of species extinction. Targeted removal or control of these environmental reservoirs could provide an effective mitigation strategy for reducing disease impacts but is rarely used in wildlife disease control.We examined the effectiveness of managing environmental transmission to reduce impacts of an emerging infectious disease of bats, white-nose syndrome. We used a chemical disinfectant, chlorine dioxide (ClO2), to experimentally reducePseudogymnoascus destructans, the fungal pathogen causing WNS, in the environment. We conducted laboratory experiments followed by three years of field trials at four abandoned mines to determine whether ClO2could effectively reduceP. destructansin the environment, reduce host infection, and limit population impacts.ClO2was effective at killingP. destructans in vitroacross a range of concentrations. In field settings, higher concentrations of ClO2treatment sufficiently reduced viableP. destructansconidia in the environment.The reduction in the environmental reservoir at treatment sites resulted in lower fungal loads on bats compared to untreated control populations. Survival following treatment was higher in little brown bats (Myotis lucifugus), and trended higher for tricolored bats (Perimyotis subflavus) compared to untreated sites.These findings support the management of environmental reservoirs as an effective control strategy for wildlife disease and provide a valuable tool for ongoing conservation efforts. More broadly, these results highlight how the intensity of environmental reservoirs can have cascading impacts on host infection and population declines.
Sample pooling inflates error rates in between-sample comparisons: an empirical investigation of the statistical properties of count-based data
Authors: Taylor Megan N. , Vega Nic M. 
Published: July 2022

AbstractHeterogeneity is ubiquitous across individuals in biological data, and sample batching, a form of biological averaging, inevitably loses information about this heterogeneity. The consequences for inference from biologically averaged data are frequently opaque, particularly when the underlying populations are non-normal. Here we investigate a case where biological averaging is common - count-based measurement of bacterial load in individualCaenorhabditis elegans- to empirically determine the consequences of batching. We find that both central measures and measures of variation on individual-based data contain biologically relevant information that is useful for distinguishing between groups, and that batch-based inference readily produces both false positive and false negative results in these comparisons. These results support the use of individual rather than batched samples when possible, illustrate the importance of understanding distributions across individuals within a sample frame, and indicate the need to consider effect size when drawing conclusions from biologically averaged data.
CEO transformational leadership and firm innovation: the role of strategic flexibility and top management team knowledge diversity
Authors: Yin Kui , Li Can , Sheldon Oliver J. , Zhao Jing 
Published: July 2022

PurposeDrawing upon a dynamic managerial capabilities perspective, this study aims to unpack how and when chief experience officer (CEO) transformational leadership influences firm innovation. Specifically, a moderated mediation model linking CEO transformational leadership to firm innovation, which includes strategic flexibility as a mediator and top management team (TMT) knowledge diversity as a moderator, is theorized and empirically tested.Design/methodology/approachThe authors conducted a survey of 354 TMT members and 62 CEOs from 62 firms in China’s construction industry to explore these relationships. Path analysis using Mplus 7.4 was undertaken to test our proposed moderated mediation model.FindingsThe results revealed that strategic flexibility mediates the positive relationship between CEO transformational leadership and firm innovation. Additionally, TMT knowledge diversity positively moderates the relationship between CEO transformational leadership and strategic flexibility.Research limitations/implicationsTaken together, these findings help advance and deepen our understanding of the mechanisms through which CEO transformational leadership influences firm innovation and boundary conditions under which CEO transformational leadership influences strategic flexibility. At the same time, this study also contributes to the literature on strategic flexibility and the CEO-TMT interface by revealing the interactive effect of CEO transformational leadership and TMT knowledge diversity on strategic flexibility.Originality/valueAlthough the positive influence of CEO transformational leadership on firm innovation has been widely recognized, the specific mechanisms underlying this effect have yet to be fully theorized. This study proposes and tests a nuanced theoretical framework linking CEO transformational leadership to firm innovation via a firm’s strategic flexibility. It also argues that TMT knowledge diversity enhances the indirect effect of CEO transformational leadership on firm innovation through strategic flexibility; that is, this indirect effect is significant when TMT diversity is high, but not when TMT diversity is low.
Social learning and career navigation in the U.S. Military: the personal experiences, observations and socializations of servicewomen
Authors: Erwin Stephanie K. 
Published: July 2022

Purpose
This paper aims to explore the interactions of social learning and career navigation and their associated implications for women in military service.

Design/methodology/approach
Social learning theory (Bandura, 1977) exposes and aids in understanding the ability of an organization’s members to reconcile their personal experiences, socialization and observations. Drawn from a larger qualitative study of gender in the US military, this study highlights the US military’s rigorous socialization practices and the reliance on communal memory and social learning including matters pertaining to gender including career navigation.

Findings
Military servicewomen use these processes to learn military culture, acceptable behaviors, institutional norms and organizational realities for career navigation reflective of gender.

Originality/value
This article presents a novel exploration of gender in the military as it pertains to social learning and career progression.
Smart tourism destinations really make sustainable cities: Benidorm as a case study
Authors: Aguirre Alexander , Zayas Antonio , Gómez-Carmona Diego , López Sánchez José Antonio 
Published: July 2022

Purpose
Tourism sustainability is a challenge for 21st-century destinations – this paper aims to analyse smart destinations' sustainability through a case study of Benidorm, the first world destination to be certified under the UNE 178501 standard as smart tourism destination (STD).

Design/methodology/approach
The methodological component has been divided into developing a framework for measuring sustainability through economic, social and environmental open data. Moreover, studying the plan's contribution “Benidorm, Destino Turístico Inteligente y Sostenible” to the city's sustainability through a time series analysis.

Findings
The main contribution shows that Benidorm's transformation into an STD leads to more sustainable cities. Thus, the conversion of Benidorm into an STD has a sustained effect in the medium and long term, contributing to the sustainability of the city.

Research limitations/implications
An open question as a limitation is the subjectivity of the distribution of the relative weight of each indicator. However, statistical analyses are developed to explore the relationship between indicators and global sustainability.

Practical implications
The debate to contextualise this paper is bridging the gap between sustainability and tourism intelligence, giving an original framework for measuring destination sustainability that provides a reasonable starting point for comparing tourism sustainability in different destinations.

Social implications
Tourists in the 21st century prefer environmentally friendly tourism. Marketing campaigns based on destination sustainability must be based on data rather than mere slogans.

Originality/value
To the best of the authors’ knowledge, the originality of this paper provides a flexible framework for measuring sustainability from open data sources, being one of the first empirical analyses to study the effects on the sustainability of converting a mature destination into an STD.
Entrepreneurial ecosystems as contested spaces: a case study from the Galapagos islands
Authors: Carrick Oliver James 
Published: July 2022

Purpose
Although research of entrepreneurial ecosystems has mainly focused on urban centers in developed nations, there is an emergent need to study the complexities of rural, regional and development contexts. Ecosystems in such settings are often characterized by the heightened importance assumed by environmental and social factors. This paper aims to document learning from participatory development and economic planning in the Galapagos, a setting in which the interplay between social, economic and ecological factors is critical.

Design/methodology/approach
This case study seeks to elaborate theory with qualitative data from an empirical context.

Findings
Reconstructed theory shows that in participatory development contexts, the entrepreneurial ecosystem constitutes a space in which competing interests contrast and conflict. Results from the Galapagos islands highlight the ability of local actors to successfully affect policy during local collaborative planning. The tensions between the economy, environment and society apparent in participatory dialogue indicate that a more nuanced approach to the interaction within entrepreneurial ecosystems is required.

Originality/value
This case study demonstrates the value of analyzing the processes and mechanisms for collaboration in the entrepreneurial ecosystem in sustainable development contexts. Results suggest implications for scholars researching entrepreneurial ecosystem networks.