bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heritability and pre-adult survivorship costs of ectoparasite resistance in the naturally occurringDrosophila-Gamasodesmite system
Authors: Polak Michal , Bose Joy , Benoit Joshua B. , Singh Harmanpreet 
Published: December 2022

AbstractOur understanding of the evolutionary significance of ectoparasites in natural communities is limited by a paucity of information concerning the mechanisms and heritability of resistance to this ubiquitous and diverse assemblage of organisms. Here, we report the results of artificial selection for increasing ectoparasite resistance in replicate lines ofDrosophila melanogasterderived from a field-fresh population. Resistance, as ability to avoid infestation by naturally occurringGamasodes queenslandicusmites, increased significantly in response to selection, and realized heritability (s.e.) was estimated to be 0.11 (0.0090). Ability to deploy energetically expensive bursts of flight from the substrate was a main mechanism of resistance that responded to selection, aligning with previously documented metabolic costs of fly behavioral defenses. Host body size, which affects parasitism rate in some fly-mite systems, was not shifted by selection. In contrast, resistant lines expressed significant reductions in larva-to-adult survivorship with increasing toxic (ammonia) stress, identifying an environmentally modulated pre-adult cost of resistance. Flies resistant toG. queenslandicuswere also more resistant to a different mite,Macrocheles subbadius, suggesting that we documented genetic variation and a pleiotropic cost of broad-spectrum behavioral immunity against ectoparasites. This study demonstrates significant evolutionary potential of an ecologically important trait.
Genome-wide association study reveals loci with sex-specific effects on plasma bile acids
Authors: Landini Arianna , Ghasemi-Semeskandeh Dariush , Johansson Åsa , Ahmad Shahzad , Liebisch Gerhard , Gnewuch Carsten ,   Regeneron Genetics Center, Tzoneva Gannie , Shuldiner Alan R. , Hicks Andrew A. , Pramstaller Peter , Pattaro Cristian , Campbell Harry , Polašek Ozren , Pirastu Nicola , Hayward Caroline , Ghanbari Mohsen , Gyllensten Ulf , Fuchsberger Christian , Wilson James F. , Klarić Lucija 
Published: December 2022

AbstractBile acids are essential for food digestion and nutrient absorption, but also act as signalling molecules involved in hepatobiliary diseases, gastrointestinal disorders and carcinogenesis. While many studies have focused on the genetic determinants of blood metabolites, research focusing specifically on genetic regulation of bile acids in the general population is currently lacking. Here we investigate the genetic architecture of primary and secondary bile acids in blood plasma, reporting associations with both common and rare variants. By performing genome-wide association analysis (GWAS) of plasma blood levels of 18 bile acids (N = 4923) we identify two significantly associated loci, a common variant mapping toSLCO1B1(encoding a liver bilirubin and drug transporter) and a rare variant inPRKG1(encoding soluble cyclic GMP-dependent protein kinase). For these loci, in the sex-stratified GWAS (N♂ = 820, N♀ = 1088), we observe sex-specific effects (SLCO1B1β ♂ = -0.51,P= 2.30×10−13, β♀ = -0.3,P= 9.90×10−07;PRKG1β ♂ = -0.18,P= 1.80×10−01, β ♀ = -0.79,P= 8.30×10−11), corroborating the contribution of sex to bile acid variability. Using gene-based aggregate tests and whole exome sequencing, we identify rare pLoF and missense variants potentially associated with bile acid levels in 3 genes (OR1G1, SART1andSORCS2), some of which have been linked with liver diseases.
COVID-19 Convalescent Plasma Outpatient Therapy to Prevent Outpatient Hospitalization: A Meta-analysis of Individual Participant Data From Five Randomized Trials
Authors: Levine Adam C. , Fukuta Yuriko , Huaman Moises A. , Ou Jiangda , Meisenberg Barry R. , Patel Bela , Paxton James H. , Hanley Daniel F. , Rijnders Bart JA , Gharbharan Arvind , Rokx Casper , Zwaginga Jaap Jan , Alemany Andrea , Mitjà Oriol , Ouchi Dan , Millat-Martinez Pere , Durkalski-Mauldin Valerie , Korley Frederick K. , Dumont Larry J. , Callaway Clifton W. , Libster Romina , Marc Gonzalo Perez , Wappner Diego , Esteban Ignacio , Polack Fernando , Sullivan David J. 
Published: December 2022

AbstractBackgroundMonoclonal antibody and antiviral treatments for COVID-19 disease remain largely unavailable worldwide, and existing monoclonal antibodies may be less active against circulating omicron variants. Although treatment with COVID-19 convalescent plasma (CCP) is promising, randomized clinical trials (RCTs) among outpatients have shown mixed results.MethodsWe conducted an individual participant data meta-analysis from all outpatient CCP RCTs to assess the overall risk reduction for all-cause hospitalizations by day 28 in all participants who had transfusion initiated. Relevant trials were identified by searching MEDLINE, Embase, MedRxiv, WHO, Cochrane Library, and Web of Science from January 2020 to September 2022.ResultsFive included studies from four countries enrolled and transfused 2,620 adult patients. Comorbidities were present in 1,795 (69%). The anti-Spike or virus neutralizing antibody titer range across all trials was broad. 160 (12.2%) of 1315 control patients were hospitalized, versus 111 (8.5%) of 1305 CCP-treated patients, yielding a 3.7% (95%CI: 1.3%-6.0%; p=.001) ARR and 30.1% RRR for all-cause hospitalization. The effect size was greatest in those with both early transfusion and high titer with a 7.6% ARR (95%CI: 4.0%-11.1%; p=.0001) accompanied by at 51.4% RRR. No significant reduction in hospitalization was seen with treatment > 5 days after symptom onset or in those receiving CCP with antibody titers below the median titer.ConclusionsAmong outpatients with COVID-19, treatment with CCP reduced the rate of all-cause hospitalization. CCP may be most effective when given within 5 days of symptom onset and when antibody titer is higher.Key PointsWhile the outpatient COVID-19 randomized controlled trial meta-analysis indicated heterogeneity in participant risk factors and convalescent plasma, the combined CCP efficacy for reducing hospitalization was significant, improving with transfusion within 5 days of symptom onset and high antibody neutralization levels.
A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms
Authors: Niarakis Anna , Ostaszewski Marek , Mazein Alexander , Kuperstein Inna , Kutmon Martina , Gillespie Marc E. , Funahashi Akira , Acencio Marcio Luis , Hemedan Ahmed , Aichem Michael , Klein Karsten , Czauderna Tobias , Burtscher Felicia , Yamada Takahiro G. , Hiki Yusuke , Hiroi Noriko F. , Hu Finterly , Pham Nhung , Ehrhart Friederike , Willighagen Egon L. , Valdeolivas Alberto , Dugourd Aurelien , Messina Francesco , Esteban-Medina Marina , Peña-Chilet Maria , Rian Kinza , Soliman Sylvain , Aghamiri Sara Sadat , Puniya Bhanwar Lal , Naldi Aurélien , Helikar Tomáš , Singh Vidisha , Fernández Marco Fariñas , Bermudez Viviam , Tsirvouli Eirini , Montagud Arnau , Noël Vincent , de Leon Miguel Ponce , Maier Dieter , Bauch Angela , Gyori Benjamin M. , Bachman John A. , Luna Augustin , Pinero Janet , Furlong Laura I. , Balaur Irina , Rougny Adrien , Jarosz Yohan , Overall Rupert W. , Phair Robert , Perfetto Livia , Matthews Lisa , Rex Devasahayam Arokia Balaya , Orlic-Milacic Marija , Cristobal Monraz Gomez Luis , De Meulder Bertrand , Ravel Jean Marie , Jassal Bijay , Satagopam Venkata , Wu Guanming , Golebiewski Martin , Gawron Piotr , Calzone Laurence , Beckmann Jacques S. , Evelo Chris T. , D’Eustachio Peter , Schreiber Falk , Saez-Rodriguez Julio , Dopazo Joaquin , Kuiper Martin , Valencia Alfonso , Wolkenhauer Olaf , Kitano Hiroaki , Barillot Emmanuel , Auffray Charles , Balling Rudi , Schneider Reinhard ,   the COVID-19 Disease Map Community
Published: December 2022

AbstractThe COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.
Dynamic interplay between target search and recognition for the Cascade surveillance complex of type I-E CRISPR-Cas systems
Authors: Aldag Pierre , Rutkauskas Marius , Madariaga-Marcos Julene , Songailiene Inga , Sinkunas Tomas , Kemmerich Felix E , Kauert Dominik J , Siksnys Virginijus , Seidel Ralf 
Published: December 2022

AbstractCRISPR-Cas effector complexes enable the defense against foreign nucleic acids and have recently been exploited as molecular tools for precise genome editing at a target locus. To bind and cleave their target, the CRISPR-Cas effectors first have to interrogate the entire genome for the presence of a matching sequence. Matching is achieved by base-pairing between the crRNA of the complexes and the DNA target strand such that an R-loop is formed. R-loop formation starts at a specific PAM motif and progresses reversibly in single base-pair steps until mismatches stop further progression or until the full target is recognized and destroyed. The reversible nature of this process entails that even a fully matching target should only become recognized with a low probability per target encounter. The details of this process, which directly affect the effectiveness of the target search, remain unresolved.Here we dissect the target search process of the Type I CRISPR-Cas complex Cascade by simultaneously monitoring DNA binding and R-loop formation by the complex. We directly quantify the low target recognition probabilities and show that they increase with increasing negative supercoiling. Furthermore, we demonstrate that Cascade uses a combination of three-dimensional and limited one-dimensional diffusion along the DNA contour for its target search. The latter allows for rapidly scanning the PAM sequences in a given region and, importantly, significantly increasing the overall efficiency of the target search by repeatedly revisiting the sites. Overall we show that target search and target recognition are tightly linked and that DNA supercoiling and limited 1D diffusion need to be considered when understanding target recognition and target search by CRISPR-Cas enzymes and engineering more efficient and precise variants.
Genetic relationships and causality between overall and central adiposity and breast, prostate, lung and colorectal cancer
Authors: Maina Jared G , Pascat Vincent , Zudina Liudmila , Ulrich Anna , Pupko Igor , Demirkan Ayse , Bonnefond Amélie , Balkhiyarova Zhanna , Kaakinen Marika , Froguel Philippe , Prokopenko Inga 
Published: December 2022

ABSTRACTOBJECTIVEDiverse measures of obesity relate to cancer risk differently. Here we assess the relationship between overall and central adiposity and cancer.METHODSWe constructed z-score weighted polygenic scores (PGS) for two obesity-related phenotypes; body mass index (BMI) and BMI adjusted waist-to-hip ratio (WHRadjBMI) and tested for their association with five cancers in the UK Biobank: overall breast (BrC), post-menopausal breast (PostBrC), prostate (PrC), colorectal (CrC) and lung (LungC) cancer. We utilised publicly available data to perform bi-directional Mendelian randomization (MR) between BMI/WHRadjBMI and BrC, PrC and CrC.RESULTSPGSBMIhad significant multiple testing-corrected inverse association with PrC (OR[95%CI]=0.97[0.95-0.99],P=0.0012) but PGSWHRadjBMIwas not associated with PrC. PGSBMIwas associated with PostBrC (OR[95%CI]=0.97[0.96-0.99],P=0.00203) while PGSWHRadjBMIhad nominal association with BrC. PGSBMIhad nominal positive association with LungC. MR analyses showed significant multiple testing-corrected protective causal effect of BMI on PrC (OR[95%CI]=0.993[0.988-0.998],P=4.19×10−3). WHRadjBMI had a nominal causal effect on higher PrC risk (OR[95%CI]=1.022[1.0067-1.038],P=0.0053). We also report nominal causal protective effect of WHRadjBMI on breast cancer (OR[95%CI]=0.99[0.98-0.997],P=0.0068). Neither PGS nor MR analyses were significant for CrC.CONCLUSIONSHigher overall adiposity appears protective from PrC while higher central adiposity is a potential risk factor for PrC but protective from BrC.STUDY IMPORTANCEWhat is already known about this subject?Observational studies suggest obesity is associated with higher risk of certain cancers and at the same time is protective of other cancers. The direction of association is in part influenced by the anthropometric trait used to assess obesity.Higher BMI appears protective from prostate, breast and lung cancers but is a risk factor for post-menopausal breast, pancreatic and colorectal cancers.What are the new findings in your manuscript?We implement Mendelian randomization approach using large scale datasets and show a protective causal effect of higher BMI from prostate cancer but suggest that higher WHRadjBMI is causal for prostate cancer.We also show nominal evidence of WHRadjBMI being causally protective from breast cancer.How might your results change the direction of research or the focus of clinical practice?We demonstrate the importance of partitioning obesity into discrete types depending on the area of fat deposition rather than using an overall measure.Our results show that diverse measures of obesity relate differently to cancer risk. In fact, even for the same type of cancer, overall and central obesity measures may impact in opposite direction in terms of risk to cancer.
Automated 4D BIM development: the resource specification and optimization approach
Authors: Fazeli Abdulwahed , Banihashemi Saeed , Hajirasouli Aso , Mohandes Saeed Reza 
Published: December 2022

PurposeThis research aims to develop an automated and optimization algorithms (OAs)-integrated 4D building information modeling (BIM) approach and a prototype and enable construction managers and practitioners to estimate the time of compound elements in building projects using the resource specification technique.Design/methodology/approachA 4D BIM estimation process was first developed by applying the resource specification and geometric information from the BIM model. A suite of OA including particle swarm optimization, ant colony, differential evolution and genetic algorithm were developed and compared in order to facilitate and automate the estimation process. The developed processes and porotypes were linked and integrated.FindingsThe OA-based automated 4D BIM estimation prototype was developed and validated through a real-life construction project. Different OAs were applied and compared, and the genetic algorithm was found as the best performing one. The prototype was successfully linked with BIM timeliner application. By using this approach, the start and finish dates of all object-based activities are developed, and the project completion time is automatically estimated.Originality/valueUnlike conventional construction estimation methods which need various tools and are error prone and time-consuming, the developed method bypasses the existing time estimation tools and provides the integrated and automated process with BIM and machine learning algorithms. Furthermore, this approach integrates 4D BIM applications into construction design procedures, connected with OA automation.
The interaction effect of government non-financial support and firm's regulatory compliance on firm innovativeness in Sub-Saharan Africa
Authors: Njinyah Sam , Asongu Simplice , Adeleye Ngozi 
Published: December 2022

PurposeThe purpose of this study is to assess the interaction effect of government non-financial support and firms' regulatory compliance on firms' innovativeness. Firms' regulatory compliance with environmental and safety issues has been suggested as one of the reasons why firms innovate. Such compliance provides legitimacy, improves reputation and corporate image, and enhances customer loyalty and competitive advantages, which influence firm innovativeness. However, regulatory compliance is costly and with limited resources, the role of government support is crucial as a moderator, to help firms become more compliant and influence their innovativeness.Design/methodology/approachThe study uses data from the World Bank Enterprise Innovation Survey for seven countries in Sub-Saharan Africa.FindingsRegulatory compliance has a positive and significant effect on firm innovativeness. Increased use of government non-financial support enhances the level of firm regulatory compliance and the effect of regulatory compliance on firm innovativeness.Originality/valueThe study contributes to the literature on compliance and firm innovativeness in Africa by showing how the positive effect of regulatory compliance on firm innovativeness is stronger when firms benefit from government non-financial support.
A new era of the music industry? Blockchain and value co-creation: the Bitsong case study
Authors: Centorrino Giovanna , Naciti Valeria , Rupo Daniela 
Published: December 2022

PurposeThe study aims to investigate the impact of technological innovation, such as blockchain, in the music field from a value co-creation perspective, highlighting how it is determining a radical change in the business model and value creation process.Design/methodology/approachTo shed light on how blockchain adoption is reconfiguring the music industry, the authors adopted a qualitative-based approach based on a case study, allowing us to investigate value co-creation at three levels (macro, meso and micro) through exchange and integration of multi-actor resources.Findings The authors found that blockchain adoption in the music industry can singularly shape the business model, representing a powerful tool to enhance inter-organizational cooperation in value creation. It effectively deals with operational and business issues, besides financial transactions, profoundly impacting both the creation and distribution of value within the supply chain.Research limitations/implicationsThe research contributes to a better understanding of innovation adoption in a specific setting, the music industry, giving support and guidance for players working in this ecosystem. The blockchain-music link helps close the gap between music and society through technology, thus providing a foundation for future research.Originality/valueThe paper provides new insights into the antecedents and mechanisms of value co-creation, spanning macro-, meso-, and micro-levels of context. It also illustrates the factors underpinning Bitsong viability to embed the value co-creation perspective in designing the business model within a value network.
The corruption and sustainable development nexus in Africa: a contemporary review and analysis
Authors: Hope, Sr. Kempe Ronald 
Published: December 2022

Purpose
This study aims to re-examine the corruption and sustainable development nexus in Africa and offer a contemporary analytical review and analysis of that relationship in the region.

Design/methodology/approach
Drawing on the available and accessible relevant data from credible sources, this work quantifies, outlines and analyses the nexus between corruption and sustainable development, as it applies primarily to sub-Saharan Africa. It uses the relevant disaggregated data and also complements that with the results of reliable empirical studies to further cross-reference and demonstrate the corruption and sustainable development nexus.

Findings
It is shown that corruption in Africa continues to be negatively associated with sustainable development objectives and that, in turn, will continue to affect the continent’s progress in achieving sustainable development. Undoubtedly, corruption is very damaging to economies across all nations and regions. However, in Africa, this impact on sustainable development has been particularly severe and ongoing. Consequently, the views expressed several decades ago of corruption being able to grease the wheels and potentially contribute to economic development is not valid and, in fact, has been severally discredited over the years.

Originality/value
The main value of the paper is the insights it provides, and with cross-reference to the empirical literature and time series data, on the corruption and sustainable development nexus in Africa.
Improving the waste to energy supply chain through increased overall equipment effectiveness
Authors: Wijesinghe Prashan Bandara , Illankoon Prasanna 
Published: December 2022

Purpose
The purpose of this study was to improve the overall equipment effectiveness (OEE) of the production process of the shredder operation of ABC company, an industrial waste management company which supplies pre-processed industrial waste as alternative fuel to a cement plant.

Design/methodology/approach
This case study investigated all possible availability and performance losses that caused the shredder system’s OEE and various problem-solving techniques, such as root cause analysis and Pareto analysis, were used to find the root cause of the reduced OEE.

Findings
After analysing this case study, three significant loss factors were identified from all the availability and performance losses, which caused the shredder system’s OEE losses. Practical solutions were found for the effect of those loss factors to improve the machine’s OEE and productivity.

Research limitations/implications
This case study has been concentrated on only analysing of losses and improvement of OEE in the production process and not about cost analysis between loss and improvements.

Originality/value
This paper shows how to improve the OEE of a production process through various problem-solving techniques by identifying its losses and how to achieve the best solutions for those losses in a practical manner.