bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison between low-cost library preparation kits for low coverage sequencing
Authors: Stewart Caitlin M. , Gibson Matthew JS , Parsa Jahan-Yar , Li Jeremiah H. 
Published: January 2024

ABSTRACTIn the fields of human health and agricultural research, low coverage whole-genome sequencing followed by imputation to a large haplotype reference panel has emerged as a cost-effective alternative to genotyping arrays for assaying large numbers of samples. However, a systematic comparison of library preparation methods tailored for low coverage sequencing remains absent in the existing literature. In this study, we evaluated one full sized kit from IDT and miniaturized and evaluated three Illumina-compatible library preparation kits—the KAPA HyperPlus kit (Roche), the DNA Prep kit (Illumina), and an IDT kit—using 96 human DNA samples. Metrics evaluated included imputation concordance with high-depth genotypes, coverage, duplication rates, time for library preparation, and additional optimization requirements. Despite slightly elevated duplication rates in IDT kits, we find that all four kits perform well in terms of imputation accuracy, with IDT kits being only marginally less performant than Illumina and Roche kits. Laboratory handling of the kits was similar: thus, the choice of a kit will largely depend on (1) existing or planned infrastructure, such as liquid handling capabilities, (2) whether a specific characteristic is desired, such as the use of full-length adapters, shorter processing times, or (3) use case, for instance, long vs short read sequencing. Our findings offer a comprehensive resource for both commercial and research workflows of low-cost library preparation methods suitable for high-throughput low coverage whole genome sequencing.
The evolutionary origins of the lysosome-related organelle sorting machinery reveal fundamental homology in post-endosome trafficking pathways
Authors: More Kiran J. , Dacks Joel B. , Manna Paul T. 
Published: January 2024

AbstractThe major organelles and pathways of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (∼1.5 billion years ago) and their acquisition were defining milestones during the process of eukaryogenesis itself. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct inter-organelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of new cellular compartments, infer ancestral states pre-dating LECA, and can even provide insight into the process of eukaryogenesis itself. Here we undertake a molecular evolutionary analysis, including providing a transcriptome of the jakobid flagellateReclinomonas americana,exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles, the so-called Biogenesis of Lysosome-related Organelle Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery, and by inference the corresponding sorting pathway, was likely in place prior to the divergence of eukaryotes and is found in a much more diverse array of eukaryotes than is currently assumed. As such, this sorting pathway is likely an underappreciated facet of broader eukaryotic cellular function. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1/MON1, and a newly identified relationship with HOPS/CORVET) offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LRO biogenesis machinery from prokaryotic origins to current eukaryotic diversity, Asgard archaea to animals, integrating it into the larger mechanistic framework describing endomembrane evolution.
Functional magnetic resonance imaging of the lumbosacral cord during a lower extremity motor task
Authors: Kündig Christian W. , Finsterbusch Jürgen , Freund Patrick , David Gergely 
Published: January 2024

AbstractBlood-oxygen-level dependent (BOLD) functional magnetic resonance imaging (fMRI) can be used to map neuronal function in the cervical cord, yet conclusive evidence supporting its applicability in the lumbosacral cord is still lacking. This study aimed to (i) demonstrate the feasibility of BOLD fMRI in mapping neuronal activation in the lumbosacral cord during a unilateral lower extremity motor task and (ii) investigate the impact of echo time (TE) on the BOLD effect size. Twelve healthy volunteers underwent BOLD fMRI using four reduced-field-of-view single-shot gradient-echo echo planar imaging sequences, all with the same geometry but different TE values ranging from 20 to 42 ms. Each sequence was employed to acquire a single 6-minute rest run and two 10-minute task runs, which included alternating 15-second blocks of rest and unilateral ankle dorsi- and plantar flexion. We detected lateralized task-related neuronal activation at neurological levels S4 to L1, centered at the ipsilateral (right) ventral spinal cord but also extending into the ipsilateral dorsal spinal cord. This pattern of activation is consistent with our current understanding of spinal cord organization, wherein lower motor neurons are located in the ventral gray matter horn, while sensory neurons of the proprioceptive pathway, activated during the movement, are located in the dorsal horns. At the subject level, BOLD activation showed considerable variability but was lateralized in all participants. The highest BOLD effect size within the ipsilateral ventral spinal cord was observed at TE=42 ms. Sequences with a shorter TE (20 and 28 ms) also detected activation in the medioventral part of the spinal cord, likely representing a large vein effect. In summary, our results demonstrate the feasibility of detecting neuronal activation in the lumbosacral cord induced by voluntary lower limb movements. BOLD fMRI in the lumbosacral cord has significant implications for assessing motor function and its alterations in disease or after spinal cord injury.
Recording γ-secretase activity in living mouse brains
Authors: Hou Steven S. , Ikegawa Yuya , Kwon Yeseo , Wieckiewicz Natalia , Houser Mei C.Q. , Lundin Brianna , Bacskai Brian J. , Berezovska Oksana , Maesako Masato 
Published: January 2024

Abstractγ-Secretase plays a pivotal role in the central nervous system. Our recent development of genetically encoded Förster resonance energy transfer (FRET)-based biosensors has enabled the spatiotemporal recording of γ-secretase activity on a cell-by-cell basis in live neuronsin culture. Nevertheless, how γ-secretase activity is regulatedin vivoremains unclear. Here we employ the near-infrared (NIR) C99 720-670 biosensor and NIR confocal microscopy to quantitatively record γ-secretase activity in individual neurons in living mouse brains. Intriguingly, we uncovered that γ-secretase activity may influence the activity of γ-secretase in neighboring neurons, suggesting a potential “cell non-autonomous” regulation of γ-secretase in mouse brains. Given that γ-secretase plays critical roles in important biological events and various diseases, our new assayin vivowould become a new platform that enables dissecting the essential roles of γ-secretase in normal health and diseases.
Employers, recruitment and activation programmes experimental evidence from the Czech labour market
Authors: Vyhlídal Jiří 
Published: January 2024

Purpose
The purpose of this paper is to test the impact of selected characteristics of jobseekers on employers’ decisions regarding potential hires (direct and probabilistic signals). The main focus of the study is to test the impact of jobseekers’ participation in selected active labour market programmes on employers’ hiring decisions for three positions: unskilled worker, skilled worker and administrative employee. Other characteristics tested include age, gender, presence of children in the household, state of health, experience of short- and long-term unemployment and indebtedness.

Design/methodology/approach
This study analyses data from a representative survey of employers with five or more employees in the Czech Republic. The survey was conducted in December 2020 using stratified random sampling, combining online questionnaires and personal interviews. The study includes 1,040 employers and uses the factorial survey experiment (FSE) design.

Findings
The results of the FSE suggest that the perceived positive impact of completing one of the activation programmes depends on the position for which the candidate is being recruited. While for the unskilled job category, the completion of any of the tested schemes (training, subsidised jobs or public works) had a positive effect; for the skilled job category, only the training and subsidised jobs schemes had a positive effect; and for the administrative job category, public works programme even had a negative effect.

Research limitations/implications
A somewhat limiting factor in the context of this study seems to be the definitions of the positions tested (unskilled and skilled workers and administrative staff). The decision-making of the respondents was somewhat restricted by such broadly defined categories. Typically, studies with FSE designs have a focus on a specific sector of the economy, which allows for a better definition of the positions or jobs under test. The relationship between position and the impact of individual characteristics is clearly a matter for further research.

Practical implications
The results of the study confirm that completion of the activation programme, as well as other candidate characteristics, constitute differentiating signals for employers that influence their hiring decisions. At the same time, there is evidence that the training programme and the subsidised jobs programme are effective in terms of increasing participants’ chances of employment.

Originality/value
The demand side should be included in the evaluation of activation policies. The design of the FSE provides an appropriate way to test the impact of activation measures on the decision-making of employers.
Adoption of building information modelling for post-construction in Nigeria: examination of barriers and strategies development
Authors: Bello Abdulkabir Opeyemi , Ayegba Calistus 
Published: January 2024

PurposeDespite successfully adopting building information modelling (BIM) for design and construction, its adoption in post-construction is critically lagging. This study aims to investigate the adoption of BIM for post-construction in Nigeria. Specifically, it aims to investigate the barriers hindering BIM adoption, propose strategies to facilitate its integration into the post-construction phase and examine the relationship between the barriers and strategies towards adopting BIM for post-construction.Design/methodology/approachThis study employs a quantitative approach to gather numerical data on BIM perceived barriers among International Facility Management Association (IFMA) members. The study also develops strategies from an extensive literature review and combines them with insights from preliminary investigation. The data were analysed using descriptive and inferential statistics.FindingsThe top perceived barriers among the professionals are lack of BIM awareness, software availability issues and difficulties using new technologies. Institute training/workshops on BIM software for the professionals in the organisation, including BIM software courses in various related professional exams, and encouraging adoption of BIM from the grassroots, such as higher institutions, emerge as the top strategies. The findings further show a significant relationship between the barriers and strategies, emphasising the recognition that understanding barriers prompts the active development and implementation of strategies.Originality/valueThis study holds originality in its examination of the relationship between the barriers and strategies associated with BIM adoption in Nigerian Architecture, Construction, Engineering and Operation.
The impact of high commitment work practices on radical innovation: innovative work behaviour and knowledge sharing as mediators
Authors: Thneibat Motasem M. 
Published: January 2024

PurposeBuilding on social exchange theory (SET), the main aim of this paper is to empirically study the impact of high-commitment work practices (HCWPs) systems on radical innovation. Additionally, the paper examines the mediating roles of employee innovative work behaviour (IWB) and knowledge sharing (KS) in the relationship between HCWPs and radical innovation.Design/methodology/approachUsing a survey questionnaire, data were collected from employees working in pharmaceutical, manufacturing and technological industries in Jordan. A total of 408 employees participated in the study. Structural equation modelling (SEM) using AMOS v28 was employed to test the research hypotheses.FindingsThis research found that HCWPs in the form of a bundle of human resource management (HRM) practices are significant for employee IWB and KS. However, similar to previous studies, this paper failed to find a direct significant impact for HCWPs on radical innovation. Rather, the impact was mediated by employee IWB. Additionally, this paper found that HCWPs are significant for KS and that KS is significant for employee IWB.Originality/valueDistinctively, this paper considered the mediating effect of employee IWB on radical innovation. Extant research treated IWB as a consequence of organisational arrangements such as HRM practices; this paper considered IWB as a foundation and source for other significant organisational outcomes, namely radical innovation. Additionally, the paper considered employees' perspectives in studying the relationship between HRM, KS, IWB and radical innovation.
Ownership structure, board characteristics, and performance of Indonesian Islamic rural banks
Authors: Mai Muhamad Umar , Nansuri Ruhadi , Setiawan Setiawan 
Published: January 2024

Purpose
This study aims to examine the influence of ownership structure and board characteristics on the performance of Indonesian Islamic rural banks (IRB) using the system generalized method of moment model.

Design/methodology/approach
This research uses Indonesian IRB unbalanced annual panel data from 2016 to 2022. IRB performance is measured by return on assets (ROA), return on equity (ROE) and nonperforming financing (NPF). The ownership structure is represented by controlling shareholders, ownership of the board of directors (BD) and ownership of the board of commissioners (BC). Meanwhile, board characteristics are represented by the size of the BC, the proportion of female board directors and female president directors.

Findings
The results show that the ownership structure and board characteristics play an important role in improving the IRB’s performance. Technically, the results show that the size of the BC and the ownership of the BD increase all IRB performance measures. Female president directors and controlling shareholders improve IRB’s performance as measured by ROA and ROE. Women’s boards of directors improve IRB performance as measured by NPF. Meanwhile, the ownership of the BC does not show its effect on all IRB performance measures.

Research limitations/implications
This study fills a literature gap on the influence of ownership structure and board characteristics on IRB Indonesia’s performance. In addition, it adds understanding and insight for Islamic bank regulators, management and IRB depositors in Indonesia.

Originality/value
To the best of the authors’ knowledge, this study is one of the first to provide an empirical survey on the influence of controlling shareholders and board characteristics on IRB performance, particularly in Indonesia.
Broadening participation in STEM, caring intelligence as a leadership intelligence: perspectives of HBCU faculty leaders
Authors: Hendrickson Kenny A. , Askew Karyl 
Published: January 2024

PurposeWithin the scope of broadening participation and developing diverse talents in STEM leadership, this paper aims to deliver a research study that explores faculty leaders’ caring intelligence as STEM leadership intelligence. STEM leadership intelligence is the knowledge, skills, traits and aptitude essential to effective leadership in STEM education.Design/methodology/approachA previously developed STEM caring-oriented academic managerial leadership framework (SCAMLF) and a typology of STEM faculty leadership styles were used to thematically analyze the caring intelligence and leadership qualities of STEM faculty leaders. Interview transcripts of 18 STEM faculty leaders at Historically Black Colleges and Universities (HBCUs), provided by the Center for the Advancement of STEM Leadership (CASL), were used as data in this study.FindingsThe empirical evidence gained from this study highlighted important themes, descriptors and narratives for exploring caring intelligence and leadership intelligence of STEM faculty leadership in HBCUs.Research limitations/implicationsAlthough the generalizability of the study is limited because of the sample size, STEM caring was found to be the most common dimension present in the reflections of participating STEM faculty leaders with diverse leadership styles. Implications for future research on STEM leadership intelligence were discussed.Originality/valueStudying caring intelligence as a form of leadership intelligence provides a new and innovative means of assessing STEM leadership intelligence. Caring intelligence can be employed to predict the mindset, performance and behaviors of STEM faculty leaders.
My privacy at risk – my guard is on: a study of SNS use among young adults
Authors: Handa Meenakshi , Bhalla Ronika , Ahuja Parul 
Published: January 2024

PurposeIncreasing incidents of privacy invasion on social networking sites (SNS) are intensifying the concerns among stakeholders about the misuse of personal data. However, there seems to be limited research on exploring the impact of specific privacy concerns on users’ intention to engage in various privacy protection behaviors. This study aims to examine the role of social privacy concerns, institutional privacy concerns and privacy self-efficacy as antecedents of privacy protection–related control activities intention among young adults active on SNS.Design/methodology/approachData collected from 284 young adults active on SNS was analyzed through partial least squares structural equation modeling using Smart PLS.FindingsThe results indicate that institutional privacy concerns, social privacy concerns and privacy self-efficacy positively influence the control activities intention of SNS users. The extent of privacy self-efficacy and privacy protection-related control activities intention differs among users based on gender.Research limitations/implicationsThis study is limited to a population of young adults in the age group of 18–25 years.Practical implicationsThe findings of this study form the basis for specific recommendations addressing the different types of privacy concerns experienced by social media users, promoting responsible privacy control behaviors on online platforms and discouraging the possible misuse of information by third parties.Originality/valueThis study validates a theoretical framework that can contribute to future investigations concerning the use of SNS. The study findings form the basis for a set of practical recommendations for policymakers, SNS platforms and users.
Does simultaneous adoption of drought‐tolerant maize varieties and organic fertiliser affect productivity and welfare outcomes? Evidence from rural Nigeria
Authors: Oyetunde‐Usman Zainab , Shee Apurba , Abdoulaye Tahirou 
Published: January 2024

AbstractThe promotion of improved maize varieties and chemical fertilisers underscores many policy approaches addressing multiple production risks such as poor soil fertility and drought. However, the unsustainable use of chemical fertilisers has important implications for soil degradation. The synergies between improved maize varieties and sustainable land use management practices such as the use of organic fertilisers (e.g., manure) are poorly documented, despite the role of manure in enhancing soil organic matter. Employing nationally representative household survey data in Nigeria, this study utilises multivalued inverse probability weighted regression adjustment, entropy balancing and a multinomial endogenous switching regression model to determine the effects of the adoption of drought‐tolerant maize varieties (DTMVs) and organic fertiliser on farm households' productivity, per capita total expenditure and per capita food expenditure. Controlling for farm households' observables and unobservables, the estimation results of the average treatment effects show that the highest pay‐off on productivity and welfare outcomes is achieved when DTMVs and manure are jointly adopted. Also, wealth indicators, access to loans and access to extension services significantly influenced individual and combinatory packages of DTMVs and manure application adoption. This study underlines the significance of the joint adoption of DTMVs and manure application on rural farmers' productivity and welfare and a substantial contribution to achieving sustainable agricultural practices.
Simulating policy options for improving household resilience to food demand shocks in the context of West Africa
Authors: Ansah Isaac Gershon Kodwo , Gardebroek Cornelis , Ihle Rico 
Published: January 2024

AbstractPolicy interest often focuses on specific instruments that effectively enhance household resilience to food security shocks. Based on microeconomic household demand and resilience theory, this paper investigates to what extent increased household resilience capacities result in household food consumption being more robust to adverse food price and income shocks. Using nationally representative household data from the Ghana Living Standards Survey, baseline parameters estimated from a micro‐econometric quadratic almost ideal demand system are used to simulate the impacts of income and price shocks on food demand of urban and rural non‐poor as well as urban and rural poor households. We assess how policy instruments that increase household resilience capacities, proxied by the values of assets owned, livestock, or household crop buffer stocks, affect shocks' impacts on food demand. Results show that a 20% general increase in food prices induces a demand switch from all other foods to basic staples and miscellaneous foods while a 20% reduction in available food expenditure dampens demand for pulses, greens, protein foods, and oils. Policy instruments that increase assets, livestock, and crop stocks of only poor households are more beneficial to the urban poor—increasing their demand for greens, protein foods, and oils—than policy instruments that raise resilience capacities of all households. On the other hand, rural poor households' protein demand tends to be enhanced by a general increase in assets, livestock, and crop buffer stocks. These findings illustrate that governments in low‐income countries should focus their policy efforts on ensuring food affordability by avoiding price peaks for those food commodities playing major roles in typical national diets. We also conclude that the ongoing Investment for Food and Jobs policy in Ghana helps improving poor households' resilience capacities by raising their buffer stocks, boosting their assets, or increasing the number of livestock kept.