bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of vaccination with SCB-2019 COVID-19 vaccine on transmission of SARS-CoV-2 infection: a household contact study in the Philippines
Authors: Tadesse Birkneh Tilahun , Bravo Lulu , Marks Florian , Aziz Asma Binte , You Young Ae , Sugimoto Jonathan , Li Ping , Garcia Joyce , Rockhold Frank , Clemens Ralf ,   the HHC study group
Published: August 2022

ABSTRACTBackgroundAn exploratory household transmission study was nested in SPECTRA, the phase 2/3 efficacy study of the adjuvanted recombinant protein-based COVID-19 vaccine SCB-2019. We compared occurrence of confirmed COVID-19 infections between households and household contacts of infected SPECTRA participants who were either placebo or SCB-2019 recipients.MethodsSPECTRA trial participants at eight study sites in the Philippines who developed rRT-PCR-confirmed COVID-19 were contacted by a study team blinded to assignment of index cases to vaccine or placebo groups to enroll in this household transmission study. Enrolled households and household contacts were monitored for three weeks using rRT-PCR and rapid antigen testing to detect new COVID-19 infections.ResultsObservation of the households of 154 eligible COVID-19 index cases, 130 symptomatic and 24 asymptomatic at diagnosis, revealed household secondary attack rates for any COVID-19 infection of SCB-2019 index cases of 0.76% (90% CI: 0.15–3.90) compared with 5.88% (90% CI: 3.20–10.8) in placebo index case households, a relative risk reduction of 79% (90% CI: -28–97). The relative risk reduction of symptomatic COVID-19 was 84% (90% CI: 28–97) for household contacts of all COVID-19 infected index cases, and 80% (90% CI: 7–96) for household contacts of index cases with symptomatic COVID-19.ConclusionsIn this prospective household contact study vaccination with SCB-2019 reduced SARS-CoV-2 transmission in households, so decreasing infections of household contacts, compared with placebo.
Costing analysis to introduce a Contrast Enhanced Mammography service in place of existing breast MRI service for local staging of breast cancer
Authors: Savaridas Sarah L , Jin Huajie 
Published: August 2022

AbstractIntroductionContrast-enhanced spectral mammography (CESM) is a functional imaging technique with comparable accuracy to MRI for loco-regional staging of breast cancer. This study assesses the cost impact of switching from CE-MRI to CESM for loco-regional staging of breast cancer from a public healthcare perspective.MethodsThe CE-MRI cost was obtained from NHS reference cost. The CESM cost was calculated using a bottom-up approach including use of the machine, pump injector, contrast, image storage and clinical staff’s time for reporting and cannulation. The cost of upgrading existing machines to CESM or purchasing new mammographic machines were obtained via national procurement. Other costs were obtained from local pharmacy, published unit cost data, or estimated based on surveys.ResultsFor large health boards in Scotland (≥500 cancers diagnosed/annum), the cost savings of switching from CE-MRI to CESM range from £64,069 to £81,570. For small health boards (<500 cancers diagnosed/annum), the cost savings of switching from CE-MRI to CESM range from £6,453 to £23,953. The cost savings are most sensitive to the number of tests conducted per year, and whether the existing mammography machine can be upgraded to CESM or not.ConclusionSwitching from CE-MRI to CESM for loco-regional staging of breast cancer is likely to be cost saving for both large and small health boards in Scotland. Further research is urgently needed to confirm the non-inferiority of CESM to CE-MRI as a locoregional staging technique. The input data of this analysis can be updated when such results become available.HighlightsSwitching from CE-MRI to CESM for locoregional staging is likely to be cost savingFor large health boards, estimated annual savings range from £64,069 to £81,570For a small health boards, estimated annual savings range from £6,453 to £23,953Cost is driven by number of imaging studies and equipment upgrade vs replacementResearch to confirm the non-inferiority of CESM for locoregional staging is needed
Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression
Authors: Liu Chengyu , Wang Wei 
Published: August 2022

AbstractDeveloping models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using a new approach based on the interpretable neural network model called contextual regression model. We showed that this linear model could predict gene expression levels using promoter sequences with a performance comparable to deep neural network models. We uncovered a list of 300 motifs with important regulatory roles on gene expression and showed that they also had significant contributions to cell-type specific gene expression in 154 diverse cell types. This work illustrates the possibility of deriving formulas to represent biology laws that may not be easily elucidated. (https://github.com/Wang-lab-UCSD/Motif_Finding_Contextual_Regression)
Transcriptional landscapes and signaling pathways of chloroquine-treated Esophageal squamous cell carcinoma
Authors: Wang Wei (David) , Qian Zhiwen 
Published: August 2022

AbstractEsophageal squamous cell carcinoma (ESCC) is one of the human malignancies worldwide, but the mechanism of ESCC development is still unclear. Chloroquine has the anti-tumor function by the inhibition of autophagy and thereby contributing to apoptosis. In our study, we analyzed the RNA-seq data of Chloroquine-treated ESCC cells and identified the transcriptional landscapes. We then used the gene enrichment methods such as KEGG and GO to further analyze the potential signaling pathways. In addition, we constructed the PPI network and Reactome map to further identified the biological processes. We identified the top two signaling pathways that were involved in the chloroquine-treated ESCC: Cell cycle and Glycerophospholipid metabolism. We identified the top ten interactive genes including ATM, CCNB1, FN1, CCT6A, VEGFA, PA2G4, CCT2, CDKN1A, BRIX1, and CDC20. Our study may provide new insights into the mechanisms for the Chloroquine-treated ESCC cells.
Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021
Authors: Molina-Mora Jose Arturo , Reales-González Jhonnatan , Camacho Erwin , Duarte-Martínez Francisco , Tsukayama Pablo , Soto-Garita Claudio , Brenes Hebleen , Cordero-Laurent Estela , dos Santos Andrea Ribeiro , Salgado Cláudio Guedes , Silva Caio Santos , de Souza Jorge Santana , Nunes Gisele , Negri Tatiane , Vidal Amanda , Oliveira Renato , Oliveira Guilherme , Muñoz-Medina José Esteban , Salas Lais Angel Gustavo , Mireles-Rivera Guadalupe , Sosa Ezequiel , Turjanski Adrián , Monzani María Cecilia , Carobene Mauricio G. , Lenicov Federico Remes , Schottlender Gustavo , Do Porto Darío A. Fernández , Kreuze Jan Frederik , Sacristán Luisa , Guevara-Suarez Marcela , Cristancho Marco , Campos-Sánchez Rebeca , Herrera-Estrella Alfredo 
Published: August 2022

AbstractLatin America is one of the regions in which the COVID-19 pandemic has had a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic.To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America.A total of 1534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments.This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.
The Association of Postoperative Anaemia with Outcomes in Cardiac Surgical Patients Eligible for Patient Blood Management: A Single Institution Retrospective Cohort Study
Authors: Bartoszko Justyna , Li Michelle , Callum Jeannie , Yi Sujung , Ouzounian Maral , McCluskey Stuart A. , Miles Sarah , Lin Yulia , Karkouti Keyvan 
Published: August 2022

ABSTRACTBackgroundAnaemia is prognostically important and affects 30-40% of cardiac surgical patients. The objective of this study was to examine the association of pre- and postoperative anaemia with outcomes in cardiac surgical patients.MethodsThis was a single-institution retrospective cohort study including cardiac surgical patients from October 26, 2020 to December 3, 2021. Patients were classified as preoperatively non-anaemic (hemoglobin ≥ 130 g/L), anaemic, or treated with IV Iron. The main predictors of interest were nadir haemoglobin on postoperative days 1-2 and preoperative anaemia and receipt of IV iron therapy. The primary outcome was number of red blood cell units (RBC) transfused on postoperative days 1-7. Secondary outcomes included acute kidney injury, hospital length of stay, and 30 day in-hospital mortality. Regression models, adjusted for demographics, comorbidities, and surgical characteristics, examined the association between predictors and outcomes.ResultsA total of 844 patients were included [528 (63%) non-anaemic, 276 (33%) anaemic, and 40 (5%) anaemic, treated with IV iron]. There was no difference between groups in RBC transfusion or mortality, however anaemic patients had a higher adjusted risk for acute kidney injury [aOR 2.69 (95% CI, 1.37 to 5.30), p=0.004] and longer hospital length of stay [aRR 1.38 (95% CI, 1.24 to 1.54), p<0.0001] compared to non-anaemic patients. Patients treated with IV iron did not have the same increased risk. A lower postoperative haemoglobin nadir was significantly associated with increased risk for all outcomes.ConclusionsPostoperative anaemia confers additional risk regardless of preoperative anaemia status. Further research is needed to better clarify these associations.
Genomic and transcriptional profiling stratifies VQ myeloma lines into two clusters with distinct risk signatures and drug responses
Authors: Flietner Evan , Yu Mei , Rajagopalan Adhithi , Zhou Yun , Feng Yubin , Veltri Anthony J. , Lasho Terra , Wen Zhi , Sun Yuqian , Patnaik Mrinal M. , Callander Natalie S. , Asimakopoulos Fotis , Wang Demin , Zhang Jing 
Published: August 2022

AbstractMultiple myeloma (MM) is a cancer of malignant plasma cells in the bone marrow and extramedullary sites. We previously characterized a VQ model for human high-risk MM. Different VQ lines display distinct disease phenotypes and survivals, suggesting significant intra-model variation. Here, we use whole exome sequencing and copy number variation (CNV) analysis coupled with RNA-Seq to stratify VQ lines into corresponding clusters: Cluster I VQ cells carried recurrent amplification of chromosome (chr) 3 and displayed upregulation of growth pathways and high-risk myeloma gene signatures, whereas Cluster II cells had monosomy chr5 and overexpressed genes and pathways associated with positive response to bortezomib (Btz) treatment in human MM patients. Consistently, in sharp contrast to Cluster II VQ cells that showed short-term response to Btz, Cluster I VQ cells were de novo resistant to Btzin vivo. Our study highlights Cluster I VQ lines as highly representative of human high-risk MM subset.
MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks
Authors: Edrisi Mohammadamin , Ogilvie Huw A. , Li Meng , Nakhleh Luay 
Published: August 2022

AbstractWith the advent of single-cell DNA sequencing, it is now possible to infer the evolutionary history of thousands of tumor cells obtained from a single patient. This evolutionary history, which takes the shape of a tree, reveals the mode of evolution of the specific cancer under study and, in turn, helps with clinical diagnosis, prognosis, and therapeutic treatment. In this study we focus on the question of determining the mode of evolution of tumor cells from their inferred evolutionary history. In particular, we employ recursive neural networks that capture tree structures to classify the evolutionary history of tumor cells into one of four modes—linear, branching, neutral, and punctuated. We trained our model, MoTERNN, using simulated data in a supervised fashion and applied it to a real phylogenetic tree obtained from single-cell DNA sequencing data. MoTERNN is implemented in Python and is publicly available at https://github.com/NakhlehLab/MoTERNN.
Determinants of institutional agricultural credit access and its linkage with farmer satisfaction in India: a moderated-mediation analysis
Authors: Dey Shiladitya , Singh Piyush Kumar , Mhaskar Megha Deepak 
Published: August 2022

PurposeThe study assesses the relationship between institutional credit access and farmer satisfaction using contextual mediating and moderating variables. This study identifies various socioeconomic, service features and service quality determinants impacting institutional credit access.Design/methodology/approachThe authors used the stratified random sampling method and selected 512 farmers from 40 villages in Maharashtra, India. Initially, the study employed probit regression analysis to identify the credit adoption determinants. Subsequently, the relationship between institutional credit and farmer satisfaction is identified through moderated-mediation analysis using the Statistical Package for the Social Sciences and Analysis of a Moment Structures (SPSS - AMOS model).FindingsProbit model's results suggest that socioeconomic variables like education and bank distance; service quality variables like prompt service and employee behavior; and service characteristics variables like the interest rate, loan sanction time, repayment period, and documents for loan application significantly affect institutional credit adoption across the smallholders. Subsequently, the results of the moderating-mediation analysis show that working capital, perceived value and risk perception partially mediate the association between credit adoption and farmer satisfaction. The mediated effects are further moderated by farm advisory services and financial knowledge and skills.Research limitations/implicationsThe study is restricted in opportunity due to primary data, and it considers only farmers' perspectives to measure service quality and service features as constraints for institutional credit access.Practical implicationsThe government, nongovernment organizations, civil societies and private institutions should provide sufficient financial knowledge and training to the farmers via extension services to utilize the borrowed capital effectively to bring economic welfare and mental satisfaction.Originality/valueThe existing literature rarely considered banking service quality and service features (demand side) variables as determinants of credit access. Further, the study brings novelty in examining how the capital management cognitive factors of the formal credit adopters influence the relationship between credit access and satisfaction.
Investment and inclusive growth in sub-Saharan Africa
Authors: Adeosun Opeoluwa Adeniyi , Olomola Philip Akani , Tabash Mosab I. , Anagreh Suhaib 
Published: August 2022

PurposeThis paper examined the inclusive growth position of sub-Saharan Africa (SSA) through the metrics of poverty-gap, bottom20 and employment. Through these indicators, the study investigated the effects of domestic-investment on inclusive-growth and established the moderating impact of governance in the domestic investment-inclusive growth nexus. It further accounted for potential nonlinearity and investigated the governance threshold that moderates domestic investment-inclusive growth relationships.Design/methodology/approachUsing a sample of 41-SSA countries, the paper employed the fixed effect (FE) with the Driscoll and Kraay nonparametric consistent covariance matrix estimator, the generalized method of moments (GMM) and the dynamic-panel threshold techniques.FindingsThe poverty-gap metric showed that with increasing GDP-growth, the income of the poor falls below the poverty-line, suggesting that GDP-growth episodes may have widened the poverty-gap and contributed minimally to reducing it. Findings revealed insignificant effects of GDP-growth on the bottom-20 metric while the employment-metric indicated that the “jobless-growth” phenomenon remained valid. The authors essentially established that economic growth has not been inclusive but the complementary roles played by domestic-investments and governance are essential requirements for achieving inclusive growth. The threshold-modeling indicated that countries in the upper-regime of governance gained more in reducing poverty gaps, increasing income shared by the bottom-quintile and improving employment for every percentage increase in investment. The authors confirmed nonlinearity and showed that there exists a governance threshold that respective governments in Africa must reach for domestic-investment to enhance inclusive growth.Originality/valueThe paper accounted for cross-sectional dependence, nonlinearity and the governance threshold needed for domestic-investment to stimulate inclusive growth.
Gender differences among teenagers: healthy and unhealthy lifestyle habits and eating behaviours, food involvement and packaging cues
Authors: Kuster-Boluda Ines , Vila-Lopez Natalia 
Published: August 2022

PurposeThe aim of this paper is the analysis of teenage consumers with varying degrees of healthy and unhealthy lifestyle habits and different healthy and unhealthy eating behaviours and food involvement, and its effects on packaging cues. At the same time, the paper tries to analyse the moderating role of gender.Design/methodology/approachWith a sample of 589 (316 girls and 273 boys) young consumers (14–17 years old) and using SEM methodology, this paper tested a theoretical model related to the association between health, food, packaging cues and gender differences.FindingsAmong teenagers, healthy habits (sports) and healthy eating behaviours affect positively food involvement (p < 0.01 in both cases), and food involvement is positively related to informative packaging cues (p < 0.05). There are some differences between girls and boys. For example (1) there is a significant relationship between your consumers' sports activities and food involvement, and young consumers' healthy eating behaviours and food involvement. (2) More food-involved teenagers are those consumers that significantly read more carefully the packaging labels. Or (3) gender could be considered as a variable able to moderate the relationships between health and unhealthy lifestyle habits and eating behaviours, food involvement and packaging decisions.Originality/valueThe present paper tries to fulfil some literature gaps by developing a study with teenage consumers to solve three main questions/objectives: (1) Do healthy behaviours affect teenagers' food involvement? (2) Does teenagers' food involvement affect teenagers' packaging perceptions? and (3) Do girls and boys differ in their food packaging perceptions?
Factors affecting contractors’ bid or no-bid and mark-up decisions: a case of the Jilin province, China
Authors: Zhang Yixi , Oo Bee Lan , Lim Benson Teck-Heng 
Published: August 2022

PurposeContractors of different scales, operating in different construction industries of varying institutional and economic settings, have different considerations when making bid or no-bid and mark-up decisions. Focusing on the large and medium-sized contractors in the Jilin province, China, the purpose of this study is to examine important factors affecting their decision to bid (d2b) and mark-up decisions and investigate differences between large and medium-sized contractors in evaluating the importance of the various factors affecting their d2b and mark-up decisions.Design/methodology/approachThis study used a survey design for timely data collection from a large population. Contractors’ bidding attitudes was collected using an online survey questionnaire with a list of 40 key factors. Statistical analytical methods were applied for comparing the two groups of contractors.FindingsThe results of this study indicate that factors related to client conditions are most critical for both large and medium-sized contractors in their d2b and mark-up decisions. The results also show statistically significant differences between the two groups of contractors on a subset of factors affecting their d2b and mark-up decisions. The large contractors have placed more emphasis on projects' potential financial and strategic benefits. Another notable finding is that both groups of contractors have placed great emphasise on “government legislations” in their d2b and mark-up decisions.Research limitations/implicationsThese findings should be interpreted in consideration of several limitations. Firstly, the sample size is relatively small, and the focus was on a single province in the China construction industry. Next, this study only explores differences between large and medium-sized contractors in evaluating the importance of the various factors affecting their d2b and mark-up decisions.Practical implicationsContractors could refer list of critical factors in competing for jobs in Jilin province or other provinces of similar institutional and economic settings. Construction clients, on the other hand, should consider the list of critical factors in the formulation of their competitive tendering procedures, thus enhancing the efficiency in their procurement of construction services.Originality/valueResearch on contractors’ bidding decision-making in the context of Chinese construction industry remains scarce; the research findings have implications for the industry stakeholders.