bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomics Characteristics Reveal the Risk of T1 Colorectal Cancer Metastasis to Lymph Nodes
Authors: Zhuang Aojia , Zhuang Aobo , Qin Zhaoyu , Zhu Dexiang , Ren Li , Wei Ye , Zhou Pengyang , Yue Xuetong , He Fuchu , Xu Jianming , Ding Chen 
Published: September 2022

AbstractBackgroundThe presence of lymph node metastasis (LNM) affects treatment strategy decisions in T1NxM0 colorectal cancer (CRC), but the currently used clinicopathological-based risk stratification cannot predict LNM accurately. In this study, we established a classifier for predicting LNM in T1 CRC.MethodsWe detected proteins in formalin-fixed paraffin-embedded (FFPE) tumor samples from 143 LNM-negative and 78 LNM-positive patients with T1 CRC and revealed changes in molecular and biological pathways by label-free LC-MS/MS. An effective prediction model was built and validated in a training cohort (N=132) and two validation cohorts (VC1, N=42; VC2, N=47) by machine learning. We further built a simplified classifier with 9 proteins. The expression patterns of 13 proteins were confirmed by immunohistochemistry, and the IHC score of 5 proteins were used to build a IHC predict model.ResultPatients with or without LNM have different molecular signatures. The 55-proteins prediction model achieved an impressive AUC of 1.00 in the training cohort, 0.96 in VC1 and 0.93 in VC2. The 9-protein classifier achieved an AUC of 0.824, and the calibration plot was excellent. We found that 5 biomarkers could predict LNM by the IHC score, with an AUC of 0.825. RHOT2 silence significantly enhanced migration and invasion of colon cancer cells.ConclusionsOur study explored the mechanism of metastasis in T1 CRC and can be used to facilitate the individualized prediction of LNM in patients with T1 CRC, which may provide a guidance for clinical practice in T1 CRC.
Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance
Authors: Takao Sumiko , Morell Victor , Uni Masahiro , Slavit Alicia , Rha Sophia , Cheng Shuyuan , Schmalbrock Laura K , Brown Fiona C , Beneyto-Calabuig Sergi , Koche Richard P , Velten Lars , Kentsis Alex 
Published: September 2022

AbstractMany human cancers, including acute myeloid leukemia (AML), arise from mutations of stem and progenitor cells. Immunophenotypic profiling has shown that leukemias develop hierarchically, with mutations in leukemia stem cells associated with disease propagation and relapse1,2. Although leukemia initiating cells can be enriched using cell surface markers, their frequency tends to be variable and low, obscuring mechanisms and hindering effective therapies3,4. To define AML stem cells in human patients, we performed functional genomic profiling of diverse leukemias using label tracing techniques designed to preserve hematopoietic stem cell (HSC) function in vivo. We found that propagation of human AML is mediated by a rare but distinct quiescent label-retaining cell (LRC) population that evades detection by currently known immunophenotypic markers. We show that human AML LRC quiescence is reversible, sparing genetic clonal competition that maintains its epigenetic inheritance. LRC quiescence is defined by distinct promoter-centered chromatin and gene expression dynamics and controlled by a distinct AP-1/ETS transcription factor network, including JUN in particular, which is associated with disease persistence and chemotherapy resistance in diverse patients. These results enable prospective isolation and functional genetic manipulation of immunophenotypically-varied leukemia stem cells in human patient specimens, as well as establish key functions of epigenetic plasticity in leukemia development and therapy resistance. We anticipate that these findings will lead to the elucidation of essential properties of leukemia stem cell quiescence and the design of therapeutic strategies for their clinical identification and control.
The immune response to lumpy skin disease virus in cattle is influenced by inoculation route
Authors: Fay Petra C. , Wijesiriwardana Najith , Munyanduki Henry , Sanz-Bernardo Beatriz , Lewis Isabel , Haga Ismar R. , Moffat Katy , van Vliet Arnoud H. M. , Hope Jayne , Graham Simon , Beard Philippa M. 
Published: September 2022

AbstractLumpy skin disease virus (LSDV) causes severe disease in cattle and water buffalo and is transmitted by hematophagous arthropod vectors. Detailed information of the adaptive and innate immune response to LSDV is limited, hampering the development of tools to control the disease. This study provides an in-depth analysis of the immune responses of calves experimentally inoculated with LSDV via either needle-inoculation or arthropod-inoculation using virus-positive Stomoxys calcitrans and Aedes aegypti vectors. Seven out of seventeen needle-inoculated calves (41%) developed clinical disease characterised by multifocal necrotic cutaneous nodules. In comparison 8/10 (80%) of the arthropod-inoculated calves developed clinical disease. A variable LSDV-specific IFN-γ immune response was detected in the needle-inoculated calves from 5 days post inoculation (dpi) onwards, with no difference between clinical calves (developed cutaneous lesions) and nonclinical calves (did not develop cutaneous lesions). In contrast a robust and uniform cell-mediated immune response was detected in all eight clinical arthropod-inoculated calves, with little response detected in the two nonclinical arthropod-inoculated calves. Neutralising antibodies against LSDV were detected in all inoculated cattle from 5-7 dpi. Comparison of the production of anti-LSDV IgM and IgG antibodies revealed no difference between clinical and nonclinical needle-inoculated calves, however a strong IgM response was evident in the nonclinical arthropod-inoculated calves but absent in the clinical arthropod-inoculated calves. This suggests that early IgM production is a correlate of protection in LSD. This study presents the first evidence of differences in the immune response between clinical and nonclinical cattle and highlights the importance of using a relevant transmission model when studying LSD.
Integrated cardio-behavioural defensive states
Authors: Signoret-Genest Jérémy , Schukraft Nina , Reis Sara L. , Segebarth Dennis , Tovote Philip 
Published: September 2022

AbstractFear and anxiety are brain states that evolved to mediate defensive responses to threat. While it is clear that the defense reaction includes multiple interacting behavioural, autonomic and endocrine adjustments, their integrative nature is poorly understood. In particular, threat has been associated with various cardiac changes, yet a clear consensus on their relevance for the integrated defense reaction is missing. We here define rapid microstates associated with specific behaviours and heart rate dynamics, both affected by long-lasting macrostates and reflecting context-dependent threat levels. In addition, we demonstrate that one of the most commonly used defensive behavioural responses, freezing measured by immobility, is part of an integrated cardio-behavioural microstate mediated by specific midbrain circuit elements. Our work puts forth a framework for systematic integration of cardiac and behavioural readouts that presents the basis for a better understanding of complex neural defensive states and their associated systemic functions.
A dramatic impairment of the antitumor activity of human Vγ9Vδ2 T cells is induced by TGF-β through significant phenotype, transcriptomic and metabolic changes
Authors: Rafia Chirine , Loizeau Clément , Renoult Ophélie , Harly Christelle , Pecqueur Claire , Joalland Noémie , Scotet Emmanuel 
Published: September 2022

AbstractDespite significant advances, the eradication of cancer remains a clinical challenge which justifies the urgent exploration of additional therapeutic strategies such as immunotherapies. Human peripheral Vγ9Vδ2 T cells represent an attractive candidate subset for designing safe, feasible and effective adoptive T cell transfer-based therapies. However, following their infiltration within tumors, γδ T cells are exposed to various regulating constituents and signals from the tumor microenvironment (TME), which severely alter their antitumor functions. Here, we show that TGF-β, whose elevated production in some solid tumors is linked to a poor prognosis, interferes with the antigenic activation of human Vγ9Vδ2 T cells in vitro. This regulatory cytokine strongly impairs their cytolytic activity, which is accompanied by the induction of particular phenotypic, transcriptomic and metabolic changes. Collectively, these observations provide informations for better understanding and targeting the impact of TME components to regulate the antitumor activity of human T cell effectors.
Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation
Authors: Bala Pratyusha , Rennhack Jonathan P. , Aitymbayev Daulet , Morris Clare , Moyer Sydney M. , Duronio Gina N. , Doan Paul , Li Zhixin , Liang Xiaoyan , Hornick Jason L. , Yurgelun Matthew B. , Hahn William C. , Sethi Nilay S. 
Published: September 2022

ABSTRACTCell state (phenotypic) plasticity is a carefully regulated feature of adult epithelial cells that enables adaptive responses to injury, inflammation, and other forms of stress. Aberrant expansion of the normally restricted capability for cell state plasticity to escape terminal differentiation is a critical aspect of neoplasia. The nongenetic factors and specific programs that mediate aberrant cell state plasticity and impaired differentiation require deeper characterization to understand this elusive aspect of cancer pathogenesis. Using genetically engineered and carcinogen-induced murine models of intestinal neoplasia, we demonstrate that impaired differentiation is a conserved event preceding cancer development. Single cell RNA-sequencing (scRNA-seq) of neoplastic intestinal lesions from both mouse models and a patient with familial adenomatous polyposis revealed that cancer initiates by adopting an aberrant transcriptional state characterized by nonoverlapping expression of a regenerative pathway, marked byLy6a(Sca-1), and a fetal intestinal program, positive forTacstd2(Trop2). Genetic inactivation ofSox9prevented adenoma formation in ApcKOmice, obstructed emergence of aberrant regenerative and fetal intestinal programs, and restored multi-lineage differentiation by scRNA-seq. Expanded chromatin accessibility at regeneration and fetal genes upon Apc inactivation was reduced by concomitant Sox9 suppression. These studies indicate that aberrant cell state plasticity mediated by unabated regenerative activity and developmental reprogramming precedes cancer development.
Deep transfer learning provides aParetoimprovement for multi-ancestral clinico-genomic prediction of diseases
Authors: Gao Yan , Cui Yan 
Published: September 2022

AbstractAccurate genomic predisposition assessment is essential for the prevention and early detection of diseases. Polygenic scores and machine learning models have been developed for disease prediction based on genetic variants and other risk factors. However, over 80% of existing genomic data were acquired from individuals of European descent. As a result, clinico-genomic risk prediction is less accurate for non-European populations. Here we employ a transfer learning strategy to improve the clinico-genomic prediction of disease occurrence for the data-disadvantaged populations. Our multi-ancestral machine learning experiments on clinico-genomic datasets of cancers and Alzheimer’s disease and synthetic datasets with built-in data inequality and subpopulation shift show that transfer learning can significantly improve disease prediction accuracy for data-disadvantaged populations. Under the transfer learning scheme, the prediction accuracy for the data-disadvantaged populations can be improved without compromising the prediction accuracy for other populations. Therefore, transfer learning provides aParetoimprovement toward equitable machine learning for genomic medicine.
Molecular Mechanisms of Holliday Junction Branch Migration Catalyzed by an Asymmetric RuvB Hexamer
Authors: Rish Anthony D. , Shen Zhangfei , Chen Zhenhang , Fu Tian-Min 
Published: September 2022

ABSTRACTThe Holliday junction (HJ) is a universal DNA intermediate of homologous recombination that is involved in many fundamental physiological processes. In bacteria, RuvB, a motor protein of the AAA+ ATPase superfamily, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here, we report two cryo-EM structures of RuvB in complex with DNA and nucleotides, providing a comprehecomplex, which was further purified nsive understanding of HJ branch migration. Six RuvB protomers assemble into a spiral staircase, in the shape of a ring, with DNA in the central pore. Four protomers of RuvB hexamer interact with the backbone of the DNA substrate, suggesting a pulling-and-revolving mechanism of DNA translocation with a basic step size of 2 nucleotides. Moreover, the variation of nucleotide-binding states in our RuvB hexamer supports a sequential model for ATP hydrolysis, ADP release, and ATP reloading, which occur at specific positions on the RuvB hexamer. Furthermore, the asymmetric assembly of RuvB also explains the 6:4 stoichiometry between RuvB and RuvA, which assembles into a complex to coordinate HJ migration in cells. Taken together, we provide a comprehensive framework for the mechanistic understanding of HJ branch migration facilitated by RuvB motor protein, which may be universally shared in both prokaryotic and eukaryotic organisms.
Cas9-mediated endogenous plasmid loss in Borrelia burgdorferi
Authors: Takacs Constantin N. , Nakajima Yuko , Haber James E. , Jacobs-Wagner Christine 
Published: September 2022

ABSTRACTThe spirochete Borrelia burgdorferi, which causes Lyme disease, has the most segmented genome among known bacteria. In addition to a linear chromosome, the B. burgdorferi genome contains over 20 linear and circular endogenous plasmids. While many of these plasmids are dispensable under in vitro culture conditions, they are maintained during the natural life cycle of the pathogen. Plasmid-encoded functions are required for colonization of the tick vector, transmission to the vertebrate host, and evasion of host immune defenses. Different Borrelia strains can vary substantially in the type of plasmids they carry. The gene composition within the same type of plasmid can also differ from strain to strain, impeding the inference of plasmid function from one strain to another. To facilitate the investigation of the role of specific B. burgdorferi plasmids, we developed a Cas9-based approach that targets a plasmid for removal. As a proof-of-principle, we showed that targeting wild-type Cas9 to several loci on the endogenous plasmids lp25 or lp28-1 of the B. burgdorferi type strain B31 results in sgRNA-specific plasmid loss even when homologous sequences (i.e., potential sequence donors for DNA recombination) are present nearby. Cas9 nickase versions, Cas9D10A or Cas9H840A, also cause plasmid loss, though not as robustly. Thus, sgRNA-directed Cas9 DNA cleavage provides a highly efficient way to eliminate B. burgdorferi endogenous plasmids that are non-essential in axenic culture.
Actomyosin cables position cell cohorts during Drosophila germband retraction by entraining their morphodynamic and mechanical properties
Authors: Nandi Sudeepa , Balse Aanchal , Inamdar Mandar M. , Kumar K. Vijay , Narasimha Maithreyi 
Published: September 2022

AbstractThe unfolding and displacement of the germband during Drosophila germband retraction (GBR) accomplish the straightening of the embryonic anterior-posterior axis. The failure of GBR reduces embryonic viability and results in the mispositioning of the embryonic segments and the gastrointestinal tract. Despite its importance, the cellular, molecular and physical mechanisms that govern the unfolding of the germband and ensure the accurate positioning of cell fields within it remain poorly understood. Here, we uncover the requirement of planar polarized, supracellular, tensile actomyosin cables for entraining cellular morphodynamics, cell field positioning and retraction kinematics. Circumferential, non-constricting cables that form during early retraction ensure the coherence of ‘placode-like’ cell cohorts, pattern medio-lateral gradients in cell shape and sidedness within it, and dampen retraction speed. Linear, constricting cables that power displacement at the end of retraction enable sequential, multi-tissue, collective T1 transitions to reposition medial cell fields to more posterior locations. Together, our results reveal how the spatiotemporally regulated deployment of actomyosin structures, functioning either as barricades or as purse strings, modulate the speed of tissue unfolding and enable cell field positioning by influencing the morphodynamic and mechanical properties of cell cohorts during morphogenesis.
Plzf mediates a switch between Fgf signalling regimes in the developing hindbrain
Authors: Leino Sami A. , Constable Sean C. J. , Streit Andrea , Wilkinson David G. 
Published: September 2022

AbstractDeveloping tissues are sequentially patterned by extracellular signals that are turned on and off at specific times. In the zebrafish hindbrain, fibroblast growth factor (Fgf) signalling has different roles at different developmental stages: in the early hindbrain, transient Fgf3 and Fgf8 signalling from rhombomere 4 is required for correct segmentation, whereas later, neuronal Fgf20 expression confines neurogenesis to specific spatial domains within each rhombomere. How the switch between these two signalling regimes is coordinated is not known. We present evidence that the promyelocytic leukaemia zinc finger (Plzf) transcription factor is required for this transition to happen in an orderly fashion. Plzf expression is high in the early anterior hindbrain, then gradually upregulated posteriorly and confined to neural progenitors. In mutants lacking functional Plzf, fgf3 expression fails to be downregulated and persists until a late stage, resulting in excess and more widespread Fgf signalling during neurogenesis. Accordingly, the spatial pattern of neurogenesis is disrupted in plzf mutants. Our results reveal how the distinct stage-specific roles of Fgf signalling are coordinated in the zebrafish hindbrain.
Statistical learning quantifies transposable element-mediated cis-regulation
Authors: Pulver Cyril , Grün Delphine , Duc Julien , Sheppard Shaoline , Planet Evarist , de Fondeville Raphaël , Pontis Julien , Trono Didier 
Published: September 2022

AbstractBackgroundTransposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryogenesis to innate immune responses. Because of their repetitive nature, TEs have the potential to form CRE platforms enabling the coordinated and genome-wide regulation of protein-coding genes by only a handful of trans-acting transcription factors (TFs).ResultsHere, we directly test this hypothesis through mathematical modeling and demonstrate that differences in expression at protein-coding genes alone are sufficient to estimate the magnitude and significance of TE-contributed cis-regulatory activities, even in contexts where TE-derived transcription fails to do so. We leverage hundreds of overexpression experiments and estimate that, overall, gene expression is influenced by TE-embedded CREs situated within approximately 200kb of promoters. Focusing on the cis-regulatory potential of TEs within the gene regulatory network of human embryonic stem cells, we find that pluripotency-specific and evolutionarily young TE subfamilies can be reactivated by TFs involved in post-implantation embryogenesis. Finally, we show that TE subfamilies can be split into truly regulatorily active versus inactive fractions based on additional information such as matched epigenomic data, observing that TF binding may better predict TE cis-regulatory activity than differences in histone marks.ConclusionOur results suggest that TE-embedded CREs contribute to gene regulation during and beyond gastrulation. On a methodological level, we provide a statistical tool that infers TE-dependent cis-regulation from RNA-seq data alone, thus facilitating the study of TEs in the next-generation sequencing era.
Users’ attitude on perceived security of mobile cloud computing: empirical evidence from SME users in China
Authors: Palanisamy Ramaraj , Shi Yi 
Published: September 2022

Purpose
The purpose of this paper is to rank the users’ attitude on major components of mobile cloud computing (MCC) security and investigate the degree of impact of these components on MCC security as a whole.

Design/methodology/approach
Hypotheses were evolved and tested by data collected through an online survey-questionnaire. The survey was administered to 363 users from Chinese organizations. Statistical analysis was carried out and structural equation model was built to validate the interactions.

Findings
The eight components of MCC security in the order of importance are as follows: mobile device related, user identity related, deployment model related, application-level security issues, data related, virtualization related, network related and service delivery related. The empirical analysis validates that these security issues are having significant impact on perceived security of MCC.

Practical implications
Constant vigilance on these eight issues and improving the level of user awareness on these issues enhance the overall security.

Social implications
These issues can be used for designing and developing secured MCC system.

Originality/value
While several previous research has studied various security factors in the MCC security domain, a consolidated understanding on the different components of MCC security is missing. This empirical research has identified and ranked the major components of MCC security. The degree of impact of each of these components on overall MCC security is identified. This provides a different perspective for managing MCC security by explaining what components are most important.