bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey ofcisregulatory non-coding RNA involved in bacterial virulence
Authors: Naghdi Mohammad Reza , Djerroud Samia , Smail Katia , Perreault Jonathan 
Published: November 2021

AbstractStudy of pathogenesis in bacteria is important to find new drug targets to treat bacterial infections. Pathogenic bacteria, including opportunists, express numerous so-called virulence genes to escape the host natural defenses and immune system. Regulation of virulence genes is often required for bacteria to infect their host. Such regulation can be achieved bycis-regulatory RNAs, like the metabolite-binding riboswitches or thermoregulators. In spite of the hundreds of RNA families annotated as cis-regulatory, there are relatively few examples of non-coding RNAs (ncRNAs) in 5′-UnTranslated Regions (UTRs) of bacteria described to regulate downstream virulence genes. To reassess the potential roles of such regulatory elements in bacterial pathogenesis, we collected genes important for virulence from different databases and evaluated the presence of ncRNAs in their UTRs to highlight the potential role of this type of gene regulation for virulence and, at the same time, get insight on some of the physical and chemical triggers of virulence.
A molecular network of conserved factors keeps ribosomes dormant in the egg
Authors: Leesch Friederike , Lorenzo-Orts Laura , Pribitzer Carina , Grishkovskaya Irina , Matzinger Manuel , Roitinger Elisabeth , Belačić Katarina , Kandolf Susanne , Lin Tzi-Yang , Mechtler Karl , Meinhart Anton , Haselbach David , Pauli Andrea 
Published: November 2021

AbstractRibosomes are produced in large quantities during oogenesis and stored in the egg. However, the egg and early embryo are translationally repressed. Using mass-spectrometry and cryo-EM analyses of ribosomes isolated from zebrafish and Xenopus eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules and occupy functionally important sites of the ribosome: a Habp4-eEF2 module that stabilizes ribosome levels and a Dap1b/Dapl1-eIF5a module that represses translation. Dap1b/Dapl1 is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Thus, a developmentally programmed, conserved ribosome state plays a key role in ribosome storage and translational repression in the egg.
Intact Drosophila Central Nervous System Cellular Quantitation reveals Sexual Dimorphism
Authors: Jiao Wei , Spreemann Gard , Ruchti Evelyne , Banerjee Soumya , Vernon Samuel , Shi Ying , Stowers R. Steven , Hess Kathryn , McCabe Brian D. 
Published: November 2021

ABSTRACTEstablishing with precision the quantity and identity of the cell types of the brain is a prerequisite for a detailed compendium of gene and protein expression in the central nervous system. Currently however, strict quantitation of cell numbers has been achieved only for the nervous system ofC.elegans. Here we describe the development of a synergistic pipeline of molecular genetic, imaging, and computational technologies designed to allow high-throughput, precise quantitation with cellular resolution of reporters of gene expression in intact whole tissues with complex cellular constitutions such as the brain. We have deployed the approach to determine with exactitude the number of functional neurons and glia in the entire intact larvalDrosophilacentral nervous system (CNS), revealing fewer neurons and more glial cells than previously predicted. We also discover an unexpected divergence between the sexes at this juvenile developmental stage, with the female CNS having significantly more neurons than that of males. Topological analysis of our data establishes that this sexual dimorphism extends to deeper features of CNS organisation. We additionally extended our analysis to quantitate the expression of voltage-gated potassium channel family genes throughout the CNS and uncover substantial differences in abundance. Our methodology enables robust and accurate quantification of the number and positioning of cells within intact organs, facilitating sophisticated analysis of cellular identity, diversity, and gene expression characteristics.
Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos
Authors: Guo Yixuan , Gert Krista R. , Lebedeva Svetlana , Potok Magdalena E. , Wike Candice L. , Grow Edward J. , Ketting René F. , Pauli Andrea , Cairns Bradley R. 
Published: November 2021

AbstractTransposable elements threaten genome stability, and the Piwi-piRNA system has evolved to silence transposons in the germline1–6. However, it remains largely unknown what mechanisms are utilized in early vertebrate embryos prior to germline establishment and ‘ping-pong’ piRNA production. To address this, we first characterized small RNAs in early zebrafish embryos and detected abundant maternally-deposited, Ziwi-associated, antisense piRNAs that map largely to evolutionarily young long terminal repeat (LTR) retrotransposons. Notably, the focal establishment of the repressive modification H3K9me2/3 coincides with these young LTR elements, is deposited independent of transcription, and is required for LTR silencing. We find piRNAs highly enriched and maintained in primordial germ cells (PGCs), which display lower LTR expression than somatic cells. To examine the consequences of piRNA loss, we used reciprocal zebrafish-medaka hybrids, which display selective activation of LTRs that lack maternally-contributed targeting piRNAs. Thus, the Piwi-piRNA system actively antagonizes transposons in the soma and PGCs during early vertebrate embryogenesis.
Integrative Modelling of Signalling Network Dynamics Identifies Cell Type-selective Therapeutic Strategies for FGFR4-driven Cancers
Authors: Shin Sung-Young , Chew Nicole J , Ghomlaghi Milad , Chüeh Anderly C , Jeong Yunhui , Nguyen Lan K. , Daly Roger J 
Published: November 2021

AbstractOncogenic FGFR4 signalling represents a potential therapeutic target in various cancer types, including triple negative breast cancer (TNBC) and hepatocellular carcinoma (HCC). However, resistance to FGFR4 single-agent therapy remains a major challenge, emphasizing the need for effective combinatorial treatments. Our study sought to develop a comprehensive computational model of FGFR4 signalling and provide network-level insights into resistance mechanisms driven by signalling dynamics. Our integrated approach, combining computational network modelling with experimental validation, uncovered potent AKT reactivation following FGFR4 targeting in the TNBC cell line MDA-MB-453. By systematically simulating the model to analyse the effects of co-targeting specific network nodes, we were able to predict, and subsequently confirm through experimental validation, the strong synergy of co-targeting FGFR4 and AKT or specific ErbB kinases, but not PI3K. Incorporating protein expression data from hundreds of cancer cell lines, we then adapted our model to diverse cellular contexts. This revealed that while AKT rebound is common, it is not a general phenomenon. ERK reactivation, for example, occurs in certain cell types, including the FGFR4-driven HCC cell line Hep3B, where there is a synergistic effect of co-targeting FGFR4 and MEK, but not AKT. In summary, our study offers key insights into drug-induced network remodelling and the role of protein expression heterogeneity in targeted therapy responses. We underscore the utility of computational network modelling for designing cell type-selective combination therapies and enhancing precision cancer treatment.SignificanceThis study underscores the potential of computational predictive modelling in deciphering mechanisms of cancer cell resistance to targeted therapies and in designing more effective, cancer type-specific combination treatments.
Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction
Authors: Dimitrova Emilia , Feldmann Angelika , van der Weide Robin H. , Flach Koen D. , Lastuvkova Anna , de Wit Elzo , Klose Robert J. 
Published: November 2021

ABSTRACTPrecise control of gene expression underpins normal development. This relies on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs), the CDK-Mediator (CDK-MED) complex has been reported to physically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here we discover that CDK-MED contributes little to 3D genome organisation in ESCs, but has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by Polycomb repressive complexes (PRCs). These interactions are established by the canonical PRC1 (cPRC1) complex but rely on CDK-MED, which facilitates binding of cPRC1 to its target sites. Importantly, through separation of function experiments, we reveal that this collaboration between CDK-MED and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on an interaction-independent mechanism whereby the CDK module supports core Mediator engagement with gene promoters to enable gene activation.
Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
Authors: Lensch Sarah , Herschl Michael H. , Ludwig Connor H. , Sinha Joydeb , Hinks Michaela M. , Mukund Adi , Fujimori Taihei , Bintu Lacramioara 
Published: November 2021

AbstractIn mammalian cells genes that are in close proximity are coupled transcriptionally: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also lead to downstream gene silencing, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. We propose a new model of multi-gene regulation, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
Physical Internet deployment in industry: literature review and research opportunities
Authors: Chen Sihua , Su Linlin , Cheng Xusen 
Published: November 2021

PurposeThe Physical Internet (PI) provides solutions to improve the current unsustainable economically logistics systems. This paper aims to identify the key themes and point out the gaps to demonstrate the current state of the PI deployment in the industry. Furthermore, this paper attempts to provide possible opportunities for future research to lead research directions of PI deployment in the industry.Design/methodology/approachThis paper follows the methodology of systematic literature review (SLR) including five processes of (1) identifying the search process; (2) selecting publications following the criteria that include and/or exclude a publication; (3) evaluating and analyzing the chosen literature; (4) reporting findings and (5) synthesizing future research opportunities. A total of 88 papers ranging from 2011 to 2021 were selected and coded for analysis.FindingsThis paper has identified 7 themes, including the PI concepts, assessments of the PI, components of the PI, innovative facilities applied in the PI, collaboration in the PI, the PI implementation and literature review. Meanwhile, five key methodologies including experimental, exploratory, review, design science research as well as mixed-methods have been classified. A framework has been proposed to summarize the results incorporating the real-life industries involved in the existing research. The authors also present the research gaps and future research opportunities for the PI deployment in industries.Originality/valueThis study is one of the first research focusing on the PI real-life implementation and thus contributes to the PI literature differing from other literature review papers. The proposed framework is useful to learn about the current core research themes in the PI. The discussion of future research opportunities may inspire interesting research delving into the field.
Price and volume effects around Islamic index revisions: the case of DJIM-GCC
Authors: Labidi Chiraz , Laribi Dorra , Ureche-Rangau Loredana 
Published: November 2021

PurposeThis study explores the price and trading volume effects around the quarterly Dow Jones Islamic Market-GCC index (DJIM-GCC) revisions and investigates whether these reactions are driven by firms' fundamentals or by investors' perception of ethical screening.Design/methodology/approachThe authors adopt an event study methodology to analyze the price and volume effects of Islamic indices redefinitions.FindingsThe results exhibit a positive (negative) price reaction for added (deleted) stocks. The authors also document an asymmetric volume response for index additions and deletions. The multivariate analysis of the cumulative abnormal returns reveals that the documented market reaction around Islamic index revisions is mainly related to the compliance attribution (withdrawal).Originality/valueThe approach allows to separate the market reaction arising from changes in firms' fundamentals from that induced by investors' perception of the attribution or withdrawal of a compliance certification. Moreover, the focus on the GCC region, where countries share the same cultural traits and perceive Islamic law identically excludes any social effect that would influence the market reaction due to cultural differences between countries.
Unsupervised dual learning for seismic data denoising in the absence of labelled data
Authors: Zhao Yu Xing , Li Yue , Wu Ning 
Published: November 2021

ABSTRACTThe training and updating of the supervised deep learning model are both dependent on labelled data. Unfortunately, the data‐labelling process is usually expensive and time consuming, which makes obtaining labelled data a huge challenge, especially in the field of geophysics. Because of the above‐mentioned factors, some seismic data denoising methods based on supervised deep learning use synthetic seismic data for network training. Since synthetic seismic data are more or less different from real seismic data, the denoising results may have some amount of residual noise and some false signals when dealing with real seismic data. In response to the above problems, this paper introduces an unpaired domain‐to‐domain translation method based on the framework of two‐way generative adversarial networks, which does not need to use labelled data for training, and effectively solves the problem of lacking labelled data in the seismic data denoising tasks. We use an unpaired mixed training set containing synthetic seismic data and real seismic data to train the network, which effectively improves the denoising ability of the network for the real seismic data. The experimental results show that compared with the state‐of‐the‐art denoising methods such as denoising convolutional neural network, the proposed method can suppress the random noise and ground roll more thoroughly, and the denoising results basically would have no false signals.
Late Quaternary Slip Behavior of the Jinqianghe Fault in the Middle Qilian–Haiyuan Fault Zone, Northeastern Tibetan Plateau
Authors: LIANG Shumin , ZHENG Wenjun , CHEN Gan , ZHANG Peizhen , ZHANG Dongli , BI Haiyun , YANG Xue , ZHANG Yipeng , DUAN Lei , LU Bentian 
Published: November 2021

AbstractThe Qilian–Haiyuan fault zone in the northeastern Tibetan Plateau has been the source of strong earthquakes in the region. In its middle segment, the Jinqianghe fault is an important active fault within the Tianzhu seismic gap; however, little is known about its slip behavior. To present a new horizontal displacement distribution along this fault, we used WorldView‐2 stereo pairs and unmanned aerial vehicle‐based photogrammetry to construct digital elevation models to obtain a detailed tectono‐geomorphic interpretation and geomorphic offsets. The offset marker measurements yielded 135 geomorphic displacements and 8 offset clusters. Radiocarbon dating was used to establish the regional age sequence of the geomorphic units in offset fluvial terraces at four study sites. The displacements and ages linked the offset clusters with the geomorphic unit sequence; the Holocene strike‐slip rate of the Jinqianghe fault was estimated to 4.8–5.6 mm/a at ∼4–12 ka and 2.9–4.7 mm/a from ∼4 ka. Three recent earthquakes (with a recurrence interval of ∼1000 years) represent an active seismic period, revealing the potential seismic hazard along this fault because it has not ruptured in the last 1500 years.
Geological and Geochemical Characteristics of the Zhiluo Formation in the Bayinqinggeli Uranium Deposit, Northern Ordos Basin: Significance for Uranium Mineralization
Authors: CAI Yuqi , HAN Meizhi , ZHANG Chuang , YI Chao , LI Xiaocui , ZHANG Yan , WANG Gui , LI Huaming 
Published: November 2021

AbstractThe Bayinqinggeli deposit in the northern Ordos Basin, northwestern of China, is a recently discovered sandstone‐type uranium deposit. The uranium (U) orebodies are generally hosted in the lower member of the Jurassic Zhiluo Formation (Fm.), and are primarily tabular or irregular in shape. In the study area, 23 sandstone samples were collected from the Zhiluo Fm. and analyzed for major, trace, and rare earth elements (REEs). The geochemical characteristics of these sandstones are used to evaluate the factors controlling U mineralization. The source rocks of the Zhiluo Fm. sandstones are mainly volcanic and felsic magmatic rocks formed in continental arc and active continental‐marginal arc environments, and they provided the material required for the mineralization. The index of compositional variability ranges from 1.02 to 3.29 (average1.38), indicating that the Zhiluo Fm. sandstones are immature and composed of first‐cycle sediments. The corrected chemical index of alteration averages 56, suggesting that the source rocks underwent weak chemical weathering. The ore host rocks are loose, providing favorable conditions for epigenetic oxidation and U precipitation and enrichment. Ferrous iron in minerals such as chlorite, biotite, ilmenite, and pyrite might have played a role either in adsorbing or reducing the uranium.
Maritime Labour, Circulations of Struggle, and Constructions of Transnational Subaltern Agency: The Spatial Politics of the 1939 Indian Seafarers’ Strikes
Authors: Featherstone David 
Published: November 2021

AbstractThis paper explores the relations between maritime labour, the circulation of struggles between different sites, and constructions of transnational subaltern agency. It does this through engaging with the interconnected strikes of Indian merchant seafarers in ports and ships across the British Empire in the Autumn of 1939. These strikes broke out after the outbreak of the Second World War and were in part mobilised against the racialised inequalities which structured maritime labour. The paper foregrounds the relations between practices of blockading ships in ports through refusing to crew them and the circulation of the strikes between ships. I argue that this combination of spatial tactics shaped transnational forms of networked subaltern agency (Balachandran 2012,Globalizing Labour? Indian Seafarers and World Shipping, c. 1870−1945). To engage with the dynamics of subaltern agency through the strikes the paper explores the relations between trajectories of organising, the circulation of demands, and the formation of solidarities.
Laparoscopic hemostasis for abdominal brunt massive hemorrhage due to endometriosis
Authors: Seki Shiori , Ito Kyoji , Takemura Nobuyuki , Oikawa Ryo , Koutake Hikaru , Mihara Fuminori , Yagi Junko , Nakanishi Misao , Tomio Kensuke , Oishi Hajime , Kokudo Norihiro 
Published: November 2021

AbstractIn the gynecological literature, a limited number of studies have reported intraperitoneal bleeding due to abdominal blunt trauma. In this report, we describe a rare case of massive intraabdominal hemorrhage from the uterine artery triggered by a fall injury without apparent abdominal bruising in the presence of severe endometriosis and a uterine fibroid. A 28‐year‐old woman who fell from a railway platform was transported to an emergency hospital. Although she did not sustain abdominal bruising and initially had no abdominal symptoms, she complained of gradually worsening abdominal pain. Abdominal CT identified intraabdominal massive hematoma, and emergency exploratory laparoscopy revealed active bleeding from the right uterine artery eroded by endometriosis, which was treated with laparoscopic electrocoagulation. The cause of the intraabdominal bleeding was associated with avulsion of the endometriosis adhesion between the right perimetrium and the right uterine artery due to inertial forces of the uterus during the fall injury. A uterine fibroid discovered during laparoscopy was suspected to strengthen the inertial forces of the uterus. In the case of hemoperitoneum after trauma, gynecological sources of bleeding must be kept in mind, especially for patients with a known history of fibroids or endometriosis.
Eight‐month repellency and efficacy of an imidacloprid/flumethrin (Seresto®) collar against the eastern paralysis tick (Ixodes holocyclus) on cats
Authors: Smith VM , de Burgh SG , Jackson CM , Chambers MA , Page PC 
Published: November 2021

ObjectiveThe objective of this study was to determine the repellency and efficacy of a 10% imidacloprid/4.5% flumethrin (Seresto®, Elanco) collar over an 8‐month period against the eastern paralysis tick (Ixodes holocyclus) on cats.MethodsTwo non‐blinded, open gender, randomised, placebo‐controlled pen studies were conducted, with 26 cats enrolled in each study. Prior to inclusion, cats were immunised with I. holocyclus holocyclotoxin. Cats were treated on Day 0 with either an imidacloprid/flumethrin or placebo collar. Tick infestations with 20 unfed adult female eastern paralysis ticks commenced on Day 7, and were repeated monthly for 8 months. Repellency was determined by comparing the mean number of attached ticks on imidacloprid/flumethrin treated cats, to placebo collar treated cats at 6 and 24 h post infestation. Efficacy was determined by comparing the mean number of live ticks on imidacloprid/flumethrin collar treated cats to placebo collar treated cats at 72 h post infestation.ResultsEfficacy was 100% (P < 0.001) at 72 h, and repellency was greater than 96% (P < 0.001) at 24 h for every tick challenge in each of the two studies, from Day 7 to the final infestation at 8 months for imidacloprid/flumethrin collar treated cats.ConclusionsIn two pen studies, an imidacloprid/flumethrin collar controlled and repelled the eastern paralysis tick (I. holocyclus) on cats for 8‐months. The marked repellency effect in addition to controlling tick paralysis would be beneficial in preventing tick bites and their sequelae.