bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abundant and rare bacterial taxa structuring differently in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau
Authors: Ren Ze , Zhang Cheng , Li Xia , Ma Kang , Cui Baoshan 
Published: May 2021

AbstractThermokarst lakes are forming from permafrost thaw and severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remain largely unknow, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided to abundant and rare according to their relative abundance, and the Sorensen dissimilarity (βsor) was partitioned into turnover (βturn) and nestedness (βnest). The whole bacterial communities as well as the abundant and rare subcommunities differed substantially between sediment and water, in terms of taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. Abundant taxa had significantly higher relative abundances but lower α-diversity and β-diversity than rare taxa. Moreover, bacterial communities are predominantly governed by strong turnover processes (βturn/βsorratio of 0.925). Abundant subcommunities were significantly lower in βturn/βsorratio compared to rare subcommunities. Bacterial communities in sediment had a significantly higher βturn/βsorratio than in water. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by environmental filtering and geographical isolation, leading to compositional distinct. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapid changing and vulnerable ecosystems.
Distinct REV-ERBα Conformational State Predicted by GaMD Simulations Leads to the Structure-Based Discovery of Novel REV-ERBα Antagonist
Authors: Hegazy Lamees , Valfort Aurore-Cecile , Burris Thomas P. , Elgendy Bahaa 
Published: May 2021

ABSTRACTREV-ERBα is a nuclear hormone receptor that plays important role in the regulation of many physiological processes such as circadian clock regulation, inflammation, and metabolism. Despite its importance, few chemical tools are available to study this receptor. In addition, there is no available X-ray crystal structures of REV-ERB bound with synthetic ligands, hampering the development of targeted therapeutics. SR8278 is the only identified synthetic antagonist of REV-ERB. We have performed Gaussian accelerated molecular dynamics (GaMD) simulations to sample the binding pathway of SR8278 and associated conformational changes to REV-ERBα. The simulations revealed a novel and more energetically favorable conformational state than the starting conformation. The new conformation allows ligand binding to the orthosteric binding site in a specific orientation. This state is reached after a tryptophan (Trp436) rotameric switch coupled with H3-H6 distance change. We used the newly identified GaMD conformational state in structure-based virtual screening of one million compounds library which led to the identification of novel REV-ERBα antagonist. This study is the first that demonstrates a synthetic ligand binding pathway to REV-ERBα, which provided important insights into the REV-ERBα functional mechanism and lead to the discovery of novel REV-ERBα antagonists. This study further emphasizes the power of computational chemistry methods in advancing drug discovery research.
Age and infectious dose significantly affect disease progression after RHDV2 infection in naïve domestic rabbits
Authors: Hall Robyn N. , King Tegan , O’Connor Tiffany , Read Andrew J. , Arrow Jane , Trought Katherine , Duckworth Janine , Piper Melissa , Strive Tanja 
Published: May 2021

AbstractRabbit haemorrhagic disease virus 2 (RHDV2 or GI.2, referring to any virus with lagovirus GI.2 structural genes) is a recently emerged calicivirus that causes generalised hepatic necrosis and disseminated intravascular coagulation leading to death in susceptible lagomorphs (rabbits and hares). Previous studies investigating the virulence of RHDV2 have reported conflicting results, with case fatality rates ranging from 0% to 100% even within a single study. Lagoviruses are of particular importance in Australia and New Zealand where they are used as biocontrol agents to manage wild rabbit populations; wild rabbits threaten over 300 native species and result in economic impacts in excess of $200 million AUD to Australian agricultural industries. It is critically important that any pest control method is both highly effective (i.e., virulent, in the context of viral biocontrols) and has minimal animal welfare impacts. To determine whether RHDV2 might be a suitable candidate biocontrol agent, we investigated the virulence and disease progression of a naturally occurring Australian recombinant RHDV2 in both 5-week-old and 11-week-old New Zealand White laboratory rabbits after either high or low dose oral infection. Objective measures of disease progression were recorded through continuous body temperature monitoring collars, continuous activity monitors, and twice daily observations. We observed a 100% case fatality rate in both infected kittens and adult rabbits after either high dose or low dose infection. Clinical signs of disease, such as pyrexia, weight loss, and reduced activity, were evident in the late stages of infection. Clinical disease, i.e., welfare impacts, were limited to the period after the onset of pyrexia, lasting on average 12 hours and increasing in severity as disease progressed. These findings confirm the high virulence of this RHDV2 variant in naïve rabbits. While age and infectious dose significantly affected disease progression, the case fatality rate was consistently 100% under all conditions tested.
The Hox gene Antennapedia regulates wing development through 20-hydroxyecdysone in insect
Authors: Fang Chunyan , Xin Yaqun , Sun Tao , Monteiro Antónia , Ye Zhanfeng , Dai Fangyin , Lu Cheng , Tong Xiaoling 
Published: May 2021

AbstractA long-standing view in the field of evo-devo is that insect forewings develop without any Hox gene input. The Hox gene Antennapedia (Antp), despite being expressed in the thoracic segments of insects, has no effect on wing development. This view has been obtained from studies in two main model species, Drosophila and Tribolium. Here, we show that partial loss of function of Antp resulted in reduced and malformed adult wings in Bombyx, Drosophila, and Tribolium. Antp mediates wing growth in Bombyx by directly regulating the ecdysteriod biosynthesis enzyme gene (shade) in the wing tissue, which leads to local production of the growth hormone 20E. In turn, 20E signaling also up-regulates Antp. Additional targets of Antp are wing cuticular protein genes CPG24, CPH28, and CPG9, essential for wing development. We propose, thus, that insect wing development occurs in an Antp-dependent manner.
Notch controls the cell cycle to define leader versus follower identities during collective cell migration
Authors: Alhashem Zain , Feldner-Busztin Dylan , Revell Christopher , Portillo Macarena Alvarez-Garcillan , Richardson Joanna , Rocha Manuel , Gauert Anton , Corbeaux Tatianna , Prince Victoria E , Bentley Katie , Linker Claudia 
Published: May 2021

SUMMARYCoordination of cell proliferation and migration is fundamental for life, and its dysregulation has catastrophic consequences, as cancer. How cell cycle progression affects migration, and vice-versa, remains largely unknown. We address these questions by combining in silico modelling and in vivo experimentation in the zebrafish Trunk Neural Crest (TNC). TNC migrate collectively, forming chains with a leader cell directing the movement of trailing followers. We show that the acquisition of migratory identity is autonomously controlled by Notch signalling in TNC. High Notch activity defines leaders, while low Notch determines followers. Moreover, cell cycle progression is required for TNC migration and is regulated by Notch. Cells with low Notch activity stay longer in G1 and become followers, while leaders with high Notch activity quickly undergo G1/S transition and remain in S-phase longer. We propose that migratory behaviours are defined through the interaction of Notch signalling and cell cycle progression.
Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction
Authors: Turzo SM Bargeen Alam , Seffernick Justin T. , Rolland Amber D. , Donor Micah T. , Heinze Sten , Prell James S. , Wysocki Vicki , Lindert Steffen 
Published: May 2021

AbstractAmong a wide variety of mass spectrometry (MS) methodologies available for structural characterizations of proteins, ion mobility (IM) provides structural information about protein shape and size in the form of an orientationally averaged collision cross-section (CCS). While IM data have been predominantly employed for the structural assessment of protein complexes, CCS data from IM experiments have not yet been used to predict tertiary structure from sequence. Here, we are showing that IM data can significantly improve protein structure determination using the modeling suite Rosetta. The Rosetta Projection Approximation using Rough Circular Shapes (PARCS) algorithm was developed that allows for fast and accurate prediction of CCS from structure. Following successful rigorous testing for accuracy, speed, and convergence of PARCS, an integrative modelling approach was developed in Rosetta to use CCS data from IM experiments. Using this method, we predicted protein structures from sequence for a benchmark set of 23 proteins. When using IM data, the predicted structure improved or remained unchanged for all 23 proteins, compared to the predicted models in the absence of CCS data. For 15/23 proteins, the RMSD (root-mean-square deviation) of the predicted model was less than 5.50 Å, compared to only 10/23 without IM data. We also developed a confidence metric that successfully identified near-native models in the absence of a native structure. These results demonstrate the ability of IM data inde novostructure determination.
MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula
Authors: Carrère Sébastien , Verdier Jérôme , Gamas Pascal 
Published: May 2021

AbstractAlthough RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs.Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers.Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.
Anin vivoapproach to characterize novel variants associated with musculoskeletal disorders
Authors: McAdow Jennifer , Yang Shuo , Ou Tiffany , Huang Gary , Dobbs Matthew B. , Gurnett Christina A. , Johnson Aaron N. 
Published: May 2021

SummaryNemaline Myopathy (NM) is the most common congenital myopathy, characterized by extreme weakness of the respiratory, limb, and facial muscles. Pathogenic variants inTropomyosin 2(TPM2), which encodes a skeletal muscle specific actin binding protein essential for sarcomere function, cause a spectrum of musculoskeletal disorders that include NM as well as Cap Myopathy, congenital fiber type disproportion, and distal arthrogrypsosis (DA).TPM2-related disorders have not been modeledin vivo, so we expressed a series of dominant, pathogenicTPM2variants inDrosophilaembryos and found two variants, K49Del and E122K, significantly affected muscle morphogenesis and muscle function, in part by disrupting myotube guidance. Transient overexpression of K49Del and E122K also disrupted the morphogenesis of immortalized mouse myoblastsin vitro, and negatively affected zebrafish muscle development and functionin vivo. We used our transient overexpression assays in zebrafish to characterize two novelTPM2variants that we identified in DA patients (V129A and E139K), and found these variants caused musculoskeletal defects similar to those of the known pathogenic variants. In addition, the severity of musculoskeletal phenotypes in zebrafish expressingTPM2variants correlated with the severity of clinical phenotypes observed in DA patients. Our study establishes transient overexpression in zebrafish as an efficient platform to characterize variants of uncertain significance inTPM2 in vivo, and suggests that this method can be used to predict the clinical severity of variants associated with DA and congenital myopathies.
Opportunities and challenges of graduate entrepreneurship in China's Greater Bay Area: cases in Hong Kong and Shenzhen
Authors: Liu Dian 
Published: May 2021

PurposeThis study chooses to look at early-stage entrepreneurship and entrepreneurial activities from the perspective of university graduates. More specially, this study takes the stance of integrated role of structure and agency, examining how university graduate entrepreneurs recognize, review and activate their entrepreneurial opportunities, and what implications can be drawn in response to the integration of the in-building of the Greater Bay Area (GBA).Design/methodology/approachThis article is drawn upon 12 case studies of small-scaled (within five permanent personnel) graduate enterprises based in Shenzhen and Hong Kong. The fieldwork was conducted in 2019, including enterprise visits, analyzing the enterprises documents and interviewing the graduate entrepreneurs. Participants were accessed through snowball sampling, and personal privacy and ethnicity were guaranteed during data collection. All founders of the graduate enterprises are university graduates within five years, regardless of their last achieved academic degree.FindingsIn this study, the objectivity–opportunity is interpreted as external enablers that are recognized by graduate entrepreneurs. Due to lack of experience, graduate entrepreneurs are more dependent on existing external opportunities in the market, instead of creating new inspirations. However, lack of experience does not mean the subjectivity–agency is missing. Instead, the subjectivity–element of entrepreneurial opportunity identification is the continuous evaluation in activating the external enablers, which is interpreted as self-evaluated challenges during entrepreneurial opportunity identification. These challenges function as sources of hesitation, modification and termination during their decision-making, as well as reflections of the current graduate entrepreneurial environment.Originality/valueBy date, no sophisticated study in literature is found analyzing the entrepreneurial opportunity identification of university graduates. Additionally, regardless of the rising attention, no agreement is achieved in the literature on measurement of entrepreneurial opportunity, influential factors of entrepreneurial opportunity and sub-elements of the identification process. This implies that more research to be conducted in diverse contexts, sub-entrepreneurial groups and in-depth analysis of selected variables regarding entrepreneurial opportunity, as elaborated in this article.
Does annual report readability explain the accrual anomaly?
Authors: Liu Ming , Liu Zhefeng 
Published: May 2021

PurposeThe purpose of the study is to investigate the possible role of annual report readability in accrual anomaly, shedding light on why investors fail to incorporate accruals information in a timely and unbiased manner beyond the original naive investor fixation explanation.Design/methodology/approachUsing five proxies of annual report readability and available data over 1993–2017, we investigate whether accrual overpricing is more severe when annual reports are less readable.FindingsWe find little (substantive) evidence of accrual overpricing among high (low) readability firms. The readability effects are contingent on the level of business complexity and earnings management.Research limitations/implicationsThis study extends the original naive investor fixation explanation and documents annual report complexity as a market friction in explaining the accrual anomaly, contributing to the mispricing vs risk debate and supporting the efficient market hypothesis.Practical implicationsLow readability of annual reports is a red flag to investors.Social implicationsThis study provides support for regulatory initiatives aimed at enhancing readability of corporate disclosures to address market frictions and improve market efficiency.Originality/valueAccrual anomaly has posed a challenge to the efficient market hypothesis. This study draws on and adds to the line of research indicating that annual report complexity is a friction erecting a barrier to transparency, hindering market efficiency. This study contributes to our understanding of the enigmatic accrual anomaly.
Transformer network-based word embeddings approach for autonomous cyberbullying detection
Authors: Pericherla Subbaraju , Ilavarasan E. 
Published: May 2021

PurposeNowadays people are connected by social media like Facebook, Instagram, Twitter, YouTube and much more. Bullies take advantage of these social networks to share their comments. Cyberbullying is one typical kind of harassment by making aggressive comments, abuses to hurt the netizens. Social media is one of the areas where bullying happens extensively. Hence, it is necessary to develop an efficient and autonomous cyberbullying detection technique.Design/methodology/approachIn this paper, the authors proposed a transformer network-based word embeddings approach for cyberbullying detection. RoBERTa is used to generate word embeddings and Light Gradient Boosting Machine is used as a classifier.FindingsThe proposed approach outperforms machine learning algorithms such as logistic regression, support vector machine and deep learning models such as word-level convolutional neural networks (word CNN) and character convolutional neural networks with short cuts (char CNNS) in terms of precision, recall, F1-score.Originality/valueOne of the limitations of traditional word embeddings methods is context-independent. In this work, only text data are utilized to identify cyberbullying. This work can be extended to predict cyberbullying activities in multimedia environment like image, audio and video.
Recouping proceeds of corruption: is there any need to reverse extant trends by enacting civil forfeiture legal regime in Nigeria?
Authors: Olujobi Olusola Joshua 
Published: May 2021

PurposeThe aim of this study is to investigate how Nigeria can seek legal assistance on recovery of its stolen assets to reduce corruption and to ensure no sheltered havens for incomes from corruption.Design/methodology/approachThe research adopts a conceptual method by using existing literature with the application of doctrinal legal research technique. The research likewise uses primary and secondary sources of legislations such as legislative provisions, case laws and the provisions of Chapter V of the United Nations Convention against Corruption and the process of asset recovery. The study compares the United Kingdom, USA, Hong Kong in China, South Africa and Nigeria proceeds of corruption recovery laws to gain basic legal features that would be beneficial to Nigeria in reforming its anti-corruption laws.FindingsThe principle of territorial sovereignty under the international law makes the offence of corruption not punishable outside the jurisdiction of the state where the offence was committed. As a result, some developed states boost their economy with these proceeds and the developing states are impoverished. There is also an allegation of discrepancies in the figures of funds recovered by the anti-corruption agencies. Thus, there is the need for transparency; law on civil forfeiture of proceeds of corruption; bilateral treaties; and mutual legal assistance on investigation, confiscation among countries for tracing and returning of proceeds of corruption.Research limitations/implicationsThe estimates of the volume of assets looted from Nigeria vary widely because of the complexity of collecting data on proceeds of corruption as official statistics on proceeds of corruption recovered do not exist as each anti-corruption agency occasionally makes pronouncements on the volume of assets recovered without any breakdown in terms of assets seized, nature of assets and their locations and its values. Such data would aid policymakers to measure the effectiveness of the present assets legislations and to enhance its effectiveness.Practical implicationsConsidering the clandestine manners corruption is being committed, it is tasking to correctly evaluate the amount of money stolen so, their economic impacts on the nation’s economy.Social implicationsAbsence of accurate data would aid policymakers to measure the effectiveness of the present assets legislations and to enhance its effectiveness.Originality/valueThe study offers modules on management of proceeds of corruption by establishing “Assets Management Commission” and “Proceeds of Corruption Forfeiture Funds” for reparation of victims’ of corruption. The study suggests the necessity for civil forfeiture of proceeds of corruption, which is presently lacking, and creation of Proceeds of Corruption Recovery and Management Commission to manage such proceeds and advocate establishment of “Proceeds of Corruption Forfeiture Funds” for reparation of victims of corruption.