bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of COVID-19 in Africa
Authors: Kogan Nicole E. , Gantt Shae , Swerdlow David , Viboud Cécile , Semakula Muhammed , Lipsitch Marc , Santillana Mauricio 
Published: July 2022

AbstractBackgroundThe COVID-19 pandemic has had a devastating impact on global health, the magnitude of which appears to differ intercontinentally: for example, reports suggest 271,900 per million people have been infected in Europe versus 8,800 per million people in Africa. While Africa is the second largest continent by population, its reported COVID-19 cases comprise <3% of global cases. Although social, environmental, and environmental explanations have been proposed to clarify this discrepancy, systematic infection underascertainment may be equally responsible.MethodsWe seek to quantify magnitude of underascertainment in COVID-19’s cumulative incidence in Africa. Using serosurveillance and postmortem surveillance, we constructed multiplicative factors estimating ratios of true infections to reported cases in African nations since March 2020.ResultsMultiplicative factors derived from serology data – in a subset of 12 nations – suggested a range of COVID-19 reporting rates, from 1 in 630 infections reported in Kenya (May 2020) to 1 in 15 infections reported in South Africa (November 2021). The largest multiplicative factor, 3,795, corresponded to Malawi (June 2020), suggesting <0.05% of infections captured. A similar set of multiplicative factors for all nations derived from postmortem data points toward the same conclusion: reported COVID-19 cases are unrepresentative of true infections, suggesting a key reason for low case burden in many African nations is significant underdetection and underreporting.ConclusionsWhile estimating COVID-19’s exact burden is challenging, the multiplicative factors we present provide incidence curves reflecting likely-to-worst-case ranges of infection. Our results stress the need for expansive surveillance to allocate resources in areas experiencing severe discrepancies between reported cases, projected infections, and deaths.SummaryHere we present a range of estimates quantifying the extent of underascertainment of COVID-19 cumulative incidence in Africa. These estimates, constructed from serology and mortality data, suggest that systematic underdetection and underreporting may be contributing to the seemingly low burden of COVID-19 reported in Africa.
Short repeat RNA reduces cytotoxicity by preventing the aggregation of TDP-43 and its 25 kDa carboxy-terminal fragment
Authors: Fujimoto Ai , Kinjo Masataka , Kitamura Akira 
Published: July 2022

AbstractTAR DNA/RNA-binding protein 43 kDa (TDP-43) proteinopathy is a hallmark of neurodegenerative disorders such as amyotrophic lateral sclerosis, in which cytoplasmic aggregates containing TDP-43 and its C-terminal fragments, such as TDP25, are observed in degenerative neuronal cells. However, few reports have focused on small molecules that can reduce their aggregation and cytotoxicity. Here, we show that short RNA repeats of GGGGCC and AAAAUU are aggregation-suppressors of TDP-43 and TDP25. TDP25 interacts with these RNAs, as well as TDP-43, despite the lack of major RNA-recognition motifs, using fluorescence cross-correlation spectroscopy. Expression of these RNAs significantly decreases the cells harboring cytoplasmic aggregates of TDP-43 and TDP25 and ameliorates rounded and shrinking cells by mislocalized TDP-43; furthermore, the cellular transcriptome is not altered. Consequently, these RNAs can maintain proteostasis by preventing aggregation of TDP-43 and TDP25.
Waning of SARS-CoV-2 vaccine-induced immunity: A systematic review and secondary data analysis
Authors: Menegale Francesco , Manica Mattia , Zardini Agnese , Guzzetta Giorgio , Marziano Valentina , d’Andrea Valeria , Trentini Filippo , Ajelli Marco , Poletti Piero , Merler Stefano 
Published: July 2022

AbstractBackgroundThe emergence of Omicron (B.1.1.529) variant of SARS-CoV-2 in late 2021 was followed by a marked increase of breakthrough infections. Estimates of vaccine effectiveness (VE) in the long term are key to assess potential resurgence of COVID-19 cases in the future.MethodsWe conducted a systematic review of manuscripts published until June 21, 2022 to identify studies reporting the level of protection provided by COVID-19 vaccines against SARS-CoV-2 infection and symptomatic disease at different time points since vaccine administration. An exponential model was used to perform a secondary data analysis of the retrieved data to estimate the progressive waning of VE associated with different vaccine products, numbers of received doses, and SARS-CoV-2 variants.FindingsOur results show that VE of BNT162b2, mRNA-1273, ChAdOx1 nCoV-19 vaccines against any laboratory confirmed infection with Delta might have been lower than 70% at 9 months from second dose administration. We found a marked immune escape associated with Omicron infection and symptomatic disease, both after the administration of two and three doses. The half-life of protection against symptomatic infection provided by two doses was estimated in the range of 178-456 days for Delta, and between 66 and 73 days for Omicron. Booster doses were found to restore the VE to levels comparable to those acquired soon after administration of the second dose; however, a fast decline of booster VE against Omicron was observed, with less than 20% VE against infection and less than 25% VE against symptomatic disease at 9 months from the booster administration.ConclusionsThis study provides a cohesive picture of the waning of vaccine protection; obtained estimates can inform the identification of appropriate targets and timing for future COVID-19 vaccination programs.
Patterns of mortality in domesticated ruminants in Ethiopia
Authors: Innocent Giles T. , Vance Ciara , Ewing David , McKendrick Iain J. , Hailemariam Solomon , Nwankpa Veronica R. , Allan Fiona K. , Schnier Christian , Peters Andrew R. 
Published: July 2022

AbstractBackgroundIn Ethiopia, there are limited data on the causes of ruminant mortality and reproductive losses which is hampering the development of interventions to improve livestock health. The present study aimed to establish the causes and magnitude of mortality and reproductive losses in cattle, sheep and goats across all smallholder production systems in Ethiopia.MethodsThe study, consisting of three data sources, was conducted to collect data on mortality and reproductive losses in cattle, sheep and goats. Nine regional states; Afar, Amhara, Benishangul Gumuz, Gambela, Harari, Oromia, Southern Nations, Nationalities, and Peoples’ Region, Somali, and Tigray were surveyed, as well as the city administrations of Dire Dawa and Addis Ababa. Questionnaire surveys were conducted with farmers and key stakeholders, as well as data collected from regional diagnostic laboratories. Data from the Living Standards Measurement Study were also included. Generalised linear mixed and hurdle models were used for data analysis, with results summarized using predicted outcomes.ResultsAnalyses indicated that most herds experienced zero mortality and reproductive losses, with rare occasions of larger losses. Diseases causing deaths varied greatly both geographically and over time. There was little agreement between the different datasets. While the models aid the understanding of patterns of mortality and reproductive losses, the degree of variation observed limited the predictive scope.ConclusionsThe models revealed some insight into why mortality rates are variable over time and are therefore less useful in measuring production or health status, and it is suggested that alternative measures of productivity, such as young stock mortality, would be more stable over time and likely more indicative.
Paracoccin impacts on Paracoccidioides brasiliensis virulence and susceptibility to antifungal drugs by modifying the expression of genes related to remodeling of the yeasts cell wall
Authors: Pitangui Nayla de Souza , Fernandes Fabrício Freitas , da Silva Thiago Aparecido , Gonçales Relber Aguiar , Roque-Barreira Maria Cristina 
Published: July 2022

AbstractThe study of the paracoccin lectin (PCN) has provided knowledge about its role in the biology of Paracoccidioides brasiliensis and in the pathogenesis of paracoccidioidomycosis (PCM). In this context, PCN has proved to be a promising immunomodulatory agent for the exploration of vaccine target molecules and/or for diagnostic or therapeutic purposes. Previous investigations allowed establishing PCN as a factor of fungal virulence. However, the effect PCN exerts on the yeast’s resistance to antifungal pharmacological agents used to treat human PCM are not known. Therefore, this work characterizes the role of PCN functional duality on virulence and susceptibility of P. brasiliensis to antifungal drugs. We show that the PCN overexpression increases the virulence of P. brasiliensis yeasts in an alternative model of infection, induces high susceptibility in vitro and in vivo of P. brasiliensis yeasts to antifungal therapy, and impact reducing relative mRNA expression of genes encoding proteins related to cell wall degradation. Conversely, PCN silencing minimized the yeasts’ virulence in Galleria mellonella, correlates with the lowest susceptibility to treatment with antifungal agent in vivo and impact differently from the PCN overexpression on the relative expression of markers related to P. brasiliensis yeasts cell wall remodelling. Our study demonstrates the impact of endogenous PCN on the P. brasiliensis yeasts’ virulence vs. susceptibility to antifungal drugs, the fungal biology, and the relationship of the yeasts-host cells.
CHCHD2 mediates glioblastoma cell proliferation, mitochondrial metabolism, hypoxia-induced invasion, and therapeutic resistance
Authors: Lumibao Jan C. , Haak Payton , Kolossov Vladimir L. , Chen Jee-Wei Emily , Stutchman Jeremy , Ruiz Alejandra , Sivaguru Mayandi , Sarkaria Jann N. , Harley Brendan A. C. , Steelman Andrew J. , Gaskins H. Rex 
Published: July 2022

AbstractGlioblastoma (GBM) is the most common and malignant primary brain tumor in adults and remains incurable. The mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 2 (CHCHD2) is demonstrated to mediate mitochondrial respiration, nuclear gene expression, and cell migration, but evidence of this in GBM is lacking. We hypothesized that CHCHD2 would serve a functional role in U87 GBM cells expressing the constitutively active epidermal growth factor receptor variant III (EGFRvIII). Amplification of the CHCHD2 gene was found to be associated with decreased patient overall survival and progression-free survival. CHCHD2 mRNA levels were increased in high-versus low-grade glioma, IDH-wt GBMs, and in tumor versus non-tumor tissue. Additionally, CHCHD2 protein expression was greatest in invasive, EGFRvIII-expressing patient-derived samples. CRISPR-Cas9-mediated knockout of CHCHD2 in EGFRvIII-expressing U87 cells resulted in altered mitochondrial respiration and glutathione status, decreased cell growth and invasion in both normoxia and hypoxia, and increased sensitivity to cytotoxic agents. CHCHD2 was distributed in both mitochondria and nuclei of U87 and U87vIII cells, and U87vIII displayed greater nuclear CHCHD2 compared to isogenic U87 cells. Incubation in hypoxia, serum starvation, and reductive unfolding of CHCHD2 induced nuclear accumulation of CHCHD2 in both cell lines. Collectively, these data indicate that CHCHD2 mediates a variety of GBM cell hallmark characteristics and highlights mitonuclear retrograde signaling as a pathway of interest in GBM cell biology.ImplicationsThese data demonstrate CHCHD2 as a mediator of a number of GBM cell functions representing disease hallmarks, as well as highlight its subcellular distribution in response to metabolic stressors. These results may inspire therapeutic strategies undermining mitochondrial biology to potentially improve GBM tumor management.
Cancer subclone detection based on DNA copy number in single cell and spatial omic sequencing data
Authors: Wu Chi-Yun , Sathe Anuja , Rong Jiazhen , Hess Paul R. , Lau Billy T. , Grimes Susan M. , Ji Hanlee P. , Zhang Nancy R. 
Published: July 2022

AbstractIn cancer, somatic mutations such as copy number alterations (CNAs) accumulate during disease progression and lead to functional intra-tumor heterogeneity that can influence the efficacy of cancer therapy. Therefore, studying the functional characteristics and spatial distribution of genetically distinct subclones is crucial to the understanding of tumor evolution and the design of cancer treatment. Here, we present Clonalscope, a method for subclone detection using copy number profiles that can be applied to spatial transcriptomics (ST) data and data from single-cell sequencing platforms such as scRNA-seq and scATAC-seq. Clonalscope implements a nested Chinese restaurant process to identify de novo subclones within one or multiple samples from the same patient. Clonalscope incorporates prior information from paired whole-genome or whole-exome sequencing (WGS/WES) data to achieve more reliable subclone detection and malignant cell labeling. On scRNA-seq and scATAC-seq data from four gastrointestinal tumor samples, Clonalscope successfully labeled malignant cells and identified genetically different subclones, which were validated in detail using matched scDNA-seq data. On ST data from a squamous cell carcinoma and two invasive ductal carcinoma samples, Clonalscope successfully labelled malignant spots, traced subclones between associated datasets, and identified spatially segregated subclones expressing genes associated with drug resistance and survival.
Attenuated Dengue Virus PV001-DV Induces Oncolytic Cell Death and Potent Anti-Tumor Immunity
Authors: Goldufsky Josef W. , Daniels Preston , Williams Michael D. , Gupta Kajal , Lyday Bruce , Chen Tony , Singh Geeta , Zloza Andrew , Marzo Amanda L. 
Published: July 2022

AbstractViral therapies developed for cancer treatment have classically prioritized direct oncolytic effects over their immune activating properties. However, recent clinical insights have challenged this longstanding prioritization and have shifted the focus to more immune-based mechanisms. Through the potential utilization of novel, inherently immune-stimulating, oncotropic viruses there is a therapeutic opportunity to improve anti-tumor outcomes through virus-mediated immune activation. PV001-DV, is an attenuated strain of Dengue virus (DEN-1 #45AZ5) with a favorable clinical safety profile that also maintains the potent immune stimulatory properties known of Dengue virus. In this study, we examined the anti-tumor effects of PV001-DV as a potential novel cancer immunotherapy. In vitro assays demonstrated that PV001-DV possesses the ability to directly kill human melanoma cells lines as well as patient melanoma tissue ex vivo. Importantly, further in vitro work demonstrated that, when patient peripheral blood mononuclear cells (PBMCs) were exposed to PV001-DV, a substantial induction in production of apoptotic factors and immunostimulatory cytokines was detected. When tumor cells were cultured with the resulting soluble mediators from these PBMCs, rapid cell death of melanoma and breast cancer cell lines was observed. The direct tumor-killing and immune-mediated tumor cytotoxicity facilitated by PV001-DV contributes support of its upcoming clinical evaluation in patients with advanced melanoma who have failed prior therapy (NCT03989895).
Cell size regulation and proliferation fluctuations in single-cell derived colonies
Authors: Nieto César , Vargas-García César , Pedraza Juan Manuel , Singh Abhyudai 
Published: July 2022

AbstractExponentially growing cells regulate their size by controlling their timing of division. Since two daughter cells are born as a result of this cell splitting, cell size regulation has a direct connection with cell proliferation dynamics. Recent models found more clues about this connection by suggesting that division occurs at a size-dependent rate. In this article, we propose a framework that couples the stochastic transient dynamics of both the cell size and the number of cells in the initial expansion of a single-cell-derived colony. We describe the population from the two most common perspectives. The first is known as Single Lineage: where only one cell is followed in each colony, and the second is Population Snapshots: where all cells in different colonies are followed. At a low number of cells, we propose a third perspective; Single Colony, where one tracks only cells with a common ancestor. We observe how the statistics of these three approaches are different at low numbers and how the Single Colony perspective tends to Population Snapshots at high numbers. Analyzing colony-to-colony fluctuations in the number of cells, we report an intriguing find: the extent of fluctuations first increases with time and then decreases to approach zero at large numbers of cells. In contrast, in classical size-independent proliferation models, where cell division occurs based on a pure timing mechanism, fluctuations in cell number increase monotonically over time to approach a nonzero value. We systematically study these differences and the convergence speed using different size control strategies.
RNABSdb and 3plex enable deep computational investigation of triplex forming lncRNAs
Authors: Cicconetti Chiara , Lauria Andrea , Proserpio Valentina , Tamburrini Annalaura , Maldotti Mara , Oliviero Salvatore , Molineris Ivan 
Published: July 2022

1.AbstractLong non-coding RNAs (lncRNAs) regulate gene expression through different molecular mechanisms, including DNA binding. We curated the first database of RNA Binding Sites (RNABSdb) by harmonising publicly available raw-data of RNA-DNA binding experiments. This resource is crucial to enable systematic studies on transcriptional regulation driven by lncRNAs. Focusing on high quality experiments, we find that the number of binding sites for each lncRNAs varies from hundreds to tens of thousands. Despite being poorly characterised, the formation of RNA:DNA:DNA triple helices (TPXs) is one of the molecular mechanisms that allows lncRNAs to bind the genome and regulate gene expression. We developed 3plex, a software able to predict TPXs in silico. We show that 3plex outperforms previous existing approaches leveraging the data collected in RNABSdb for lncRNAs known to form functional TPXs. Moreover this analysis shows that TPXs tend to be shorter and more degenerated than previously expected. Finally, we applied 3plex to all the lncRNAs collected in RNABSdb and we show that the majority of them could directly bind the genome by TPXs formation.Data and software are available at https://molinerislab.github.io/RNABSdb/ and https://github.com/molinerisLab/3plex.
The snake-inspired robots: a review
Authors: Yang Xiaolong , Zheng Long , Lü Da , Wang Jinhao , Wang Shukun , Su Hang , Wang Zhixin , Ren Luquan 
Published: July 2022

PurposeSnake-inspired robots are of great significance in many fields because of their great adaptability to the environment. This paper aims to systematically illustrate the research progress of snake-inspired robots according to their application environments. It classifies snake-inspired robots according to the numbers of degrees of freedom in each joint and briefly describes the modeling and control of snake-inspired robots. Finally, the application fields and future development trends of snake-inspired robots are analyzed and discussed.Design/methodology/approachThis paper summarizes the research progress of snake-inspired robots and clarifies the requirements of snake-inspired robots for self-adaptive environments and multi-functional tasks. By equipping various sensors and tool modules, snake-inspired robots are developed from fixed-point operation in a single environment to autonomous operation in an amphibious environment. Finally, it is pointed out that snake-inspired robots will be developed in terms of rigid and flexible deformable structure, long endurance and multi-function and intelligent autonomous control.FindingsInspired by the modular and reconfigurable concepts of biological snakes, snake-inspired robots are well adapted to unknown and changing environments. Therefore, snake-inspired robots will be widely used in industrial, military, medical, post-disaster search and rescue applications. Snake-inspired robots have become a hot research topic in the field of bionic robots.Originality/valueThis paper summarizes the research status of snake-inspired robots, which facilitates the reader to be a comprehensive and systematic understanding of the research progress of snake-inspired robots. This helps the reader to gain inspiration from biological perspectives.
Cloud computing applications in library services of Bangladesh: a study on librarians’ perceptions
Authors: Islam Md. Nazmul , Islam Md. Shariful , Anwar Antora , Alam Mohammed Khalid 
Published: July 2022

Purpose
This study aims to find out the current state of cloud-based library services in selected academic and special libraries of Bangladesh. The study also explored some pertinent problems faced by librarians in implementing this new technology in library services and activities.

Design/methodology/approach
The study used a mixed-method approach with a range of exploratory research questions. Purposive sampling technique was used to select the libraries. A set of structured questionnaires was designed to address the objectives of the study. For in-depth analysis, short interviews with the library professionals were also conducted.

Findings
Only four libraries made use of cloud computing services, and they maintained a partial cloud environment. Most responding librarians treated cloud computing as a dynamically scalable infrastructure for applications, data and file storage with charges imposed. Most of the respondents (90%) preferred cloud computing for “Software-as-a-Service”. Due to the high subscription rate (70%), unreliable online payment system (60%) and trading system (60%), librarians treated cloud computing as a burden in providing library services and activities. Respondent librarians were also interviewed for exploring their views on cloud computing in library services. For adopting cloud computing in library services of Bangladesh, “sufficient financial allocation” and “organizations’ positive decision over cloud computing” were mentioned as challenging tasks by the respondents. Finally, the study suggested some solutions to the problem and proposed a model for a cloud-based library system that can be replicated in libraries and information centres of other developing countries too.

Originality/value
This paper encapsulates the overall scenario of cloud-based library activities and services in Bangladesh. Based on the available secondary sources, no empirical study on librarians’ perceptions of cloud computing in library services of Bangladesh has been carried out before this study. Thus, this is perhaps the first attempt to quantitatively measure cloud-based services in Bangladeshi libraries.