bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of bovine tuberculosis and characterization of the members of the Mycobacterium tuberculosis complex from slaughtered cattle in Rwanda
Authors: Ntivuguruzwa Jean B. , Michel Anita , Kolo Francis B. , Mwikarago Ivan E. , Ngabonziza Jean C. S. , VanHeerden Henriette 
Published: November 2021

AbstractBackgroundBovine tuberculosis (bTB) is an endemic disease in Rwanda, but little is known about its prevalence and causative mycobacterial species. The disease causes tremendous losses in livestock and wildlife and remains a significant threat to public health.Materials and methodsA cross-sectional study employing a systematic random sampling of cattle (n=300) with the collection of retropharyngeal lymph nodes and tonsils (n=300) irrespective of granulomatous lesions was carried out in six abattoirs to investigate the prevalence and identify mycobacterial species using culture, acid-fast bacteria staining, polymerase chain reaction, and GeneXpert assay. Individual risk factors and the origin of samples were analysed for association with the prevalence.FindingsOf the 300 samples, six were collected with visible TB-like lesions. Our findings demonstrated the presence of Mycobacterium tuberculosis complex (MTBC) in 1.7% (5/300) of sampled slaughtered cattle. M. bovis was isolated from 1.3% (4/300) animals while one case was caused by a rifampicin-resistance (RR) M. tuberculosis. Non-tuberculous mycobacteria were identified in 12.0% (36/300) of the sampled cattle. There were no significant associations between the prevalence and abattoir category, age, sex, and breeds of slaughtered cattle.ConclusionsThis study is the first in Rwanda to isolate both M. bovis and RR M. tuberculosis in slaughtered cattle indicating that bTB is prevalent in Rwanda with a low prevalence. The isolation of RR M. tuberculosis from cattle indicates possible zooanthroponotic transmission of M. tuberculosis and close human-cattle contact. To protect humans against occupational zoonotic diseases, it is essential to control bTB in cattle and raise the awareness among all occupational groups as well as reinforce biosafety at the farm level and in the abattoirs.Author’s summaryTuberculosis in cattle (bTB) causes financial losses to livestock owners and is a disease transmissible to humans especially those with an occupational risk through exposure to infected animals and animal products. This study aimed to identify the prevalence of bTB and characterize the mycobacterial species from cattle slaughtered in the six abattoirs in Rwanda. Four M. bovis, as well as one rifampicin-resistant (RR) M. tuberculosis, were identified from slaughtered cattle and, thus, the apparent bTB prevalence was 1.7% (5/300). Likely, the RR M. tuberculosis isolate was mostly likely of human origin and transmitted to cattle during close human-cattle contact. It is therefore essential to control bTB in cattle and reinforce the protection of farmworkers and abattoir workers who are always exposed to infected animals.
ProDCoNN-server: a web server for protein sequence prediction and design from a three-dimensional structure
Authors: Zhang Yuan , Mandal Arunima , Cui Kevin , Liu Xiuwen , Zhang Jinfeng 
Published: November 2021

AbstractWe present ProDCoNN-server, a web server for protein sequence design and prediction from a given protein structure. The server is based on a previously developed deep learning model for protein design, ProDCoNN, which achieved state-of-the-art performance when tested on large numbers of test proteins and benchmark datasets. The prediction is very fast compared with other protein sequence prediction servers - it takes only a few minutes for a query protein on average. Two models could be selected for different purposes: BBO for full sequence prediction, extendable for multiple sequence generation, and BBS for single position prediction with the type of other residues known. ProDCoNN-server outputs the predicted sequence and the probability matrix for each amino acid at each predicted residue. The probability matrix can also be visualized as a sequence logos figure (BBO) or probability distribution plot (BBS). The server is available at: https://prodconn.stat.fsu.edu/.
Scrutiny of human lung infection by SARS-CoV-2 and associated human immune responses in humanized mice
Authors: Sun Renren , Zhao Zongzheng , Fu Cong , Wang Yixin , Guo Zhendong , Zhang Chunmao , Liu Lina , Zhang Cheng , Shu Chang , He Jin , Hua Shucheng , Gao Yuwei , Hu Zheng 
Published: November 2021

ABSTRACTThere is an urgent need for animal models of COVID-19 to study immunopathogenesis and test therapeutic intervenes. In this study we showed that NSG mice engrafted with human lung (HL) tissue (NSG-L mice) could be infected efficiently by SARS-CoV-2, and that live virus capable of infecting Vero cells was found in the HL grafts and multiple organs from infected NSG-L mice. RNA-seq examination identified a series of differentially expressed genes, which are enriched in viral defense responses, chemotaxis, interferon stimulation, and pulmonary fibrosis between HL grafts from infected and control NSG-L mice. Furthermore, when infecting humanized mice with human immune system (HIS) and autologous HL grafts (HISL mice), the mice had bodyweight loss and hemorrhage and immune cell infiltration in HL grafts, which were not observed in immunodeficient NSG-L mice, indicating the development of anti-viral immune responses in these mice. In support of this possibility, the infected HISL mice showed bodyweight recovery and lack of detectable live virus at the later time. These results demonstrate that NSG-L and HISL mice are susceptible to SARS-CoV-2 infection, offering a useful in vivo model for studying SARS-CoV-2 infection and the associated immune response and immunopathology, and testing anti-SARS-CoV-2 therapies.
Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits
Authors: Olasege Babatunde S. , Porto-Neto Laercio R. , Tahir Muhammad S. , Gouveia Gabriela C. , Cánovas Angela , Hayes Ben J. , Fortes Marina R. S. 
Published: November 2021

AbstractReproductive traits are often genetically correlated. Yet, we don’t fully understand the complexities, synergism, or trade-offs between male and female fertility. Here, we introduce correlation scan, a novel framework for identifying the drivers or antagonizers of the genetic correlation between male and female fertility traits across the bovine genome. The identification of these regions facilitates the understanding of the complexity of these traits. Although the methodology was applied to cattle phenotypes, using high-density SNP genotypes, the general framework developed can be applied to any species or traits, and it can easily accommodate genome sequence data.
Outer Membrane Vesicles from the gut microbiome contribute to tumor immunity by eliciting cross-reactive T cells
Authors: Tomasi M. , Caproni E. , Benedet M. , Zanella I. , Giorgetta S. , Dalsass M. , König E. , Gagliardi A. , Fantappiè L. , Berti A. , Tamburini S. , Croia L. , Di Lascio G. , Bellini E. , Valensin S. , Licata G. , Sebastiani G. , Dotta F. , Armanini F. , Cumbo F. , Asnicar F. , Blanco-Míguez A. , Ruggiero E. , Segata N. , Grandi G. , Grandi A. 
Published: November 2021

AbstractThe gut microbiome plays a key role in cancer immunity. One proposed mechanism is through the elicitation of T cells, which incidentally recognize neo-epitopes arising from cancer mutations (“molecular mimicry (MM)” hypothesis). To support MM,Escherichia coliNissle was engineered with the SIINFEKL epitope (OVA) and orally administered to C57BL/6 mice. The treatment elicited OVA-specific CD8+T cells in thelamina propriaand inhibited the growth of OVA-B16F10 tumors. Importantly, the administration of Outer Membrane Vesicles (OMVs) engineered with different T cell epitopes elicited epitope-specific T cells and inhibited tumor growth. Microbiome shotgun sequencing and TCR sequencing provided evidence that cross-reacting T cells were induced at the mucosal level and subsequently reached the tumor site. Overall, our data support the role of MM in tumor immunity, assign a new role to OMVs and pave the way to new probiotics/OMV-based anti-cancer immunotherapies.
Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum
Authors: Martin Annalie , Babbitt Anne , Pickens Allison G. , Pickett Brett E. , Hill Jonathon T. , Suli Arminda 
Published: November 2021

SUMMARYThe optic tectum (OT) is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus, the OT is responsible for the reception and integration of stimuli, followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades, less is known concerning specific cell types, microcircuitry, and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however, a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single-cell RNA-sequencing (scRNA-seq) to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Et(cfos:Gal4;UAS:Kaede). We sequenced 13,320 cells, a 4X cellular coverage, and identified 25 putative OT cell populations. Within those cells, we identified several mature and developing neuronal populations, as well as non-neuronal cell types including oligodendrocytes, microglia, and radial glia. Although most mature neurons demonstrate GABAergic activity, several glutamatergic populations are present, as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes, and computed RNA velocity to infer current and future transcriptional cell states. Finally, we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion, the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge, this is the first time scRNA-seq has been applied to explore the OT alone and in depth.
Mitochondrial DNA variants segregate during human preimplantation development into genetically different cell lineages that are maintained postnatally
Authors: Mertens Joke , Regin Marius , De Munck Neelke , de Deckersberg Edouard Couvreu , Belva Florence , Sermon Karen , Tournaye Herman , Blockeel Christophe , Van de Velde Hilde , Spits Claudia 
Published: November 2021

ABSTRACTHumans present remarkable mitochondrial DNA (mtDNA) variant mosaicism, not only across tissues but even across individual cells within one person. The timing of the first appearance of this mosaicism has not yet been established. In this study, we hypothesized it occurs during preimplantation development. To investigate this, we deep-sequenced the mtDNA of 254 oocytes from 85 donors, 158 single blastomeres of 25 day-3 embryos, 17 inner cell mass and trophectoderm samples of 7 day-5 blastocysts, 142 bulk DNA and 68 single cells of different adult tissues. We found that day-3 preimplantation embryos already present blastomeres that carry variants unique to that cell, showing that the first events of mtDNA mosaicism happen very early in human development. We classified the mtDNA variants based on their recurrence or uniqueness across sibling oocytes and embryos, and between single cells and samples from the same embryos or adult individuals. Variants that recurred across samples had higher heteroplasmic loads and more frequently resulted in synonymous changes or were located in non-coding regions than variants that were unique to one oocyte or single embryonic cell. These differences were maintained through developmental stages, suggesting that the mtDNA mosaicism arising in preimplantation development is maintained into adulthood. Further, the results support a model in which close clustering of mitochondria carrying specific mtDNA variants in the ooplasm leads to asymmetric distribution of these mitochondria throughout the cell divisions of the preimplantation embryo, resulting in the appearance of the first form of mtDNA mosaicism in human development.
Regulation of ERK2 activity by dynamic S-acylation
Authors: Azizi Saara-Anne , Qiu Tian , Brookes Noah , Dickinson Bryan C. 
Published: November 2021

AbstractThe extracellular signal-regulated kinases (ERK1/2) are key effector proteins of the mitogen-activated protein kinase pathway, choreographing essential processes of cellular physiology. Critical in regulating these regulators are a patchwork of mechanisms, including post-translational modifications (PTMs) such as MEK-mediated phosphorylation. Here, we discover that ERK1/2 are subject to S-palmitoylation, a reversible lipid modification of cysteine residues, at C271/C254. Moreover, the levels of ERK1/2 S-acylation are modulated by epidermal growth factor (EGF) signaling, mirroring its phosphorylation dynamics, and palmitoylation-deficient ERK2 displays altered phosphorylation patterns at key sites. We find that chemical inhibition of either lipid addition or removal significantly alters ERK1/2’s EGF-triggered transcriptional program. We also identify a subset of “writer” protein acyl transferases (PATs) and an “eraser” acyl protein thioesterase (APT) that drive ERK1/2’s cycle of palmitoylation and depalmitoylation. Finally, we examine ERK1/2 S-acylation in a mouse model of metabolic syndrome, correlating changes in its lipidation levels with alterations in writer/eraser expression and solidifying the link between ERK1/2 activity, ERK1/2 lipidation, and organismal health. This study not only presents a previously undescribed mode of ERK1/2 regulation and a node to modulate MAPK pathway signaling in pathophysiological conditions, it also offers insight into the role of dynamic S-palmitoylation in cell signaling more generally.
Enteroendocrine cell types that drive food reward and aversion
Authors: Bai Ling , Sivakumar Nilla , Mesgarzadeh Sheyda , Ding Tom , Ly Truong , Corpuz Timothy V. , Grove James C.R. , Jarvie Brooke C. , Knight Zachary A. 
Published: November 2021

AbstractAnimals must learn through experience which foods are nutritious and should be consumed, and which are toxic and should be avoided. Enteroendocrine cells (EECs) are the principal chemosensors in the GI tract, but investigation of their role in behavior has been limited by the difficulty of selectively targeting these cells in vivo. Here we describe an intersectional genetic approach for manipulating EEC subtypes in behaving mice. We show that multiple EEC subtypes inhibit food intake but have different effects on learning. Conditioned flavor preference is driven by release of cholecystokinin whereas conditioned taste aversion is mediated by serotonin and substance P. These positive and negative valence signals are transmitted by vagal and spinal afferents, respectively. These findings establish a cellular basis for how chemosensing in the gut drives learning about food.
Deep time structural evolution of retroviral and filoviral surface envelope proteins
Authors: Hötzel Isidro 
Published: November 2021

AbstractThe retroviral surface envelope protein subunit (SU) mediates receptor binding and triggers membrane fusion by the transmembrane subunit (TM). SU evolves rapidly under strong selective conditions, resulting in seemingly unrelated SU structures in highly divergent retroviruses. Structural modeling of the SU of several retroviruses and related endogenous retroviral elements with AlphaFold identifies a TM-proximal SU β-sandwich structure that has been conserved in the orthoretroviruses for at least 110 million years. The SU of orthoretroviruses diversified by differential expansion of the β -sandwich core to form domains involved in virus-host interactions. The β-sandwich domain is also conserved in the SU equivalent GP1 of Ebola virus although with a significantly different orientation in the trimeric envelope protein structure. The unified structural view of orthoretroviral SU and filoviral GP1 identifies an ancient, structurally conserved and evolvable domain underlying the structural diversity of orthoretroviral SU and filoviral GP1.
Inflation targeting and economic performance over the crisis: evidence from emerging market economies
Authors: Duong Thuy Hang 
Published: November 2021

PurposeInflation targeting has increasingly become a popular monetary framework since its first introduction in New Zealand at the beginning of 1990. However, the causality effects of this policy on economic performance, particularly in periods of economic turmoil remain controversial. Thus, this paper re-examines the treatment effect of inflation targeting on two important macro indicators which are inflation rate and output growth with the focus on emerging market economies. The global financial crisis, which is known as the great recession since the last decade, is investigated as an exogenous shock to test for the effectiveness of this popular regime.Design/methodology/approachThe difference-in-difference approach in the fixed-model is employed for this investigation using a balanced panel data of 54 countries with 15 inflation-targeting countries for the period 2002 to 2010.FindingsThe examination finds that there is no significant difference in terms of the inflation rate and gross domestic product growth over the whole research period between the treatment and control groups. However, the outcome suggests that emerging economies can control the increase in inflation rate when the economy has to cope with the exogenous uncertainties.Research limitations/implicationsThis finding indicates important policy implications for central banks in many countries.Originality/valueInflation targeting can help emerging countries to reduce an increase in inflation rate in the crisis period without many trade-offs in the growth of output.
Deep learning for detecting distresses in buildings and pavements: a critical gap analysis
Authors: Elghaish Faris , Matarneh Sandra T. , Talebi Saeed , Abu-Samra Soliman , Salimi Ghazal , Rausch Christopher 
Published: November 2021

Purpose
The massive number of pavements and buildings coupled with the limited inspection resources, both monetary and human, to detect distresses and recommend maintenance actions lead to rapid deterioration, decreased service life, lower level of service and increased community disruption. Therefore, this paper aims at providing a state-of-the-art review of the literature with respect to deep learning techniques for detecting distress in both pavements and buildings; research advancements per asset/structure type; and future recommendations in deep learning applications for distress detection.

Design/methodology/approach
A critical analysis was conducted on 181 papers of deep learning-based cracks detection. A structured analysis was adopted so that major articles were analyzed according to their focus of study, used methods, findings and limitations.

Findings
The utilization of deep learning to detect pavement cracks is advanced compared to assess and evaluate the structural health of buildings. There is a need for studies that compare different convolutional neural network models to foster the development of an integrated solution that considers the data collection method. Further research is required to examine the setup, implementation and running costs, frequency of capturing data and deep learning tool. In conclusion, the future of applying deep learning algorithms in lieu of manual inspection for detecting distresses has shown promising results.

Practical implications
The availability of previous research and the required improvements in the proposed computational tools and models (e.g. artificial intelligence, deep learning, etc.) are triggering researchers and practitioners to enhance the distresses’ inspection process and make better use of their limited resources.

Originality/value
A critical and structured analysis of deep learning-based crack detection for pavement and buildings is conducted for the first time to enable novice researchers to highlight the knowledge gap in each article, as well as building a knowledge base from the findings of other research to support developing future workable solutions.
Decolonising knowledge production in disaster management: a feminist perspective
Authors: Andrabi Shazana 
Published: November 2021

PurposeThis paper focuses on how feminist research seeks to integrate the inclusion of women in society for them to be active participants in disaster management, and goes on to prove how crucial it is for disaster research to collaborate with feminist research to arrive at a cohesive, interwoven, interdisciplinary field and methodology, while at the same time giving the agency in the hands of local agents for them to bring about change through traditional methods interwoven with broader methodologies. To hand over the process to local agents would result in decolonisation of knowledge production and implementation.Design/methodology/approachThe paper was written using secondary sources, mainly in the form of books, journal articles and news articles. Reports by international organisations were used to augment data and other theoretical frameworks and references in the paper. The secondary sources were selected keeping in view one of the primary objectives of the paper, namely “decolonising knowledge production”. Analysis by postcolonial authors from the global South has been included. Research and literature based in local contexts form an important part of the sources consulted throughout this paper. The ongoing COVID-19 pandemic has been used as a case study to highlight how disasters are still “gendered”; it opens up space for further research on the topic.FindingsEven though women are increasingly recognised as agents of positive change in prevention, mitigation and post-disaster efforts, very little is done at the policy and implementation levels to include their experiences and benefit from them. There is an urgent need for systemic, gender-aware changes at socio-economic and political levels so that hazards may be prevented from turning into disasters by reducing the vulnerability of populations.Originality/valueThe importance of this research lies in its interdisciplinary approach and the integration of three fields of study disaster management, feminist/gender studies and decolonising knowledge production. The attempt is to analyse the interdependence of these fields of study to understand the lacunae in planning and implementation of disaster management policies, and to pave the way for further research by way of this integration.