bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversities of Mycobacterium tuberculosis complex species in Western Kenya
Authors: Chelimo Charles Komen , Angienda Paul Oyieng , Olwal Charles Ochieng , Nyamogoba Henry 
Published: December 2023

Background. Tuberculosis (TB) remains a high burden infectious disease worldwide. Mycobacterium tuberculosiscomplex (MTBC) is the etiological agent of TB.
Research Gap. TB burden is majorly linked to development of drug resistant strains. Thus, there is urgent need for close surveillance of MTBC circulating in a given region like Western Kenya for treatment of TB.
Aim. To determine the proportion of MTBC species, strains and genetic diversities in circulation in an HIV/AIDS prevalent regions especially in Western Kenya. The clinical MTBC isolates were collected from Moi Teaching and Referral Hospital (MTRH) at Eldoret-Kenya during 2013-14. All clinical MTBC isolates were confirmed by the gold standard method (i.e. Lowenstein-Jensen medium culture) before inclusion in the investigation.
Methodology. A 12-loci of Mycobacterium Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) genotyping was performed to determine the circulating species/strains of MTBC using www. MIRU-VNTRplus web platform. Allelic diversity was calculated using the Hunters-Gaston Diversity Index (HGDI).
Results. The species M. tuberculosis, M. bovis, M. africanum, M. pinnipedii, M. microti, M. caprae and M. canettiwere identified in the MTBC population. These strains were found in the Beijing, Latin American Mediterranean, Uganda 1/2, East African Indian, Ilama, West African 1/2, Harlem, URAL, Ghana, Seal, Cameroon and Vole etc. regions of Western Kenya. Notably, some isolates had unknown (new/unassigned) species. The strains were grouped into nine clusters with a clustering rate of 31.18% and a high allelic diversity index of 0.53 was observed.
Conclusion. The present findings suggest that there is an urgent need for more awareness among healthcare and stakeholders on the existence of foreign MTBC species/strains in Kenya. Furthermore, 12-loci MIRU-VNTR may not be suitable for the surveillance of MTBC strains in the circulation in Kenya. Thus, high-resolution techniques i.e., Whole Genome Sequencing needs to be adopted to resolve the genetic diversity to establish evolutionary trends for future and archived samples. This knowledge will be crucial in restraining TB, giving insights into new drug development, and prevention, control, and treatment strategies of TB.
Primary cilia in osteoblasts and osteocytes are required for skeletal development and mechanotransduction
Authors: Moraes de Lima Perini Mariana , Pugh Julie N , Scott Elizabeth M , Bhula Karan , Chirgwin Austin , Reul Olivia N , Berbari Nicolas F , Li Jiliang 
Published: December 2023

1.AbstractPrimary cilia have been involved in the development and mechanosensation of various tissue types, including bone. In this study, we explored the mechanosensory role of primary cilia in bone growth and adaptation by examining two cilia specific genes, IFT88 and MKS5, required for proper cilia assembly and function. To analyze the role of primary cilia in osteoblasts, Osx1-GFP:Cre mice were bred with IFT88LoxP/LoxPto generate mice with a conditional knockout of primary cilia in osteoblasts. A significant decrease in body weight was observed in both male (p=0.0048) and female (p=0.0374) conditional knockout (cKO) mice compared to the wild type (WT) controls. The femurs of cKO mice were significantly shorter than that of the WT mice of both male (p=0.0003) and female (p=0.0019) groups. Histological analysis revealed a significant difference in MAR (p=0.0005) and BFR/BS (p<0.0001) between female cKO and WT mice. The BFR/BS of male cKO mice was 58.03% lower compared to WT mice. To further investigate the role of primary cilia in osteocytes, Dmp1-8kb-Cre mice were crossed with MKS5LoxP/LoxPto generate mice with defective cilia in osteocytes. In vivo axial ulnar loading was performed on 16-week-old mice for 3 consecutive days. The right ulnae were loaded for 120 cycles/day at a frequency of 2Hz with a peak force of 2.9N for female mice and 3.2N for male mice. Load-induced bone formation was measured using histomorphometry. The relative values of MS/BS, MAR and BFR/BS (loaded ulnae minus nonloaded ulnae) in male MKS5 cKO mice were decreased by 24.88%, 46.27% and 48.24%, respectively, compared to the controls. In the female groups, the rMS/BS was 52.5% lower, the rMAR was 27.58% lower, and the rBFR/BS was 41.54% lower in MKS5 cKO mice than the WT group. Histological analysis indicated that MKS5 cKO mice showed significantly decreased response to mechanical loading compared to the controls. Taken together, these data highlight a critical role of primary cilia in bone development and mechanotransduction, suggesting that the presence of primary cilia in osteoblasts play an important role in skeletal development, and primary cilia in osteocytes mediate mechanically induced bone formation.
A functional parcellation of the whole brain in individuals with autism spectrum disorder reveals atypical patterns of network organization
Authors: Persichetti Andrew S. , Shao Jiayu , Gotts Stephen J. , Martin Alex 
Published: December 2023

AbstractBACKGROUNDResearchers studying autism spectrum disorder (ASD) lack a comprehensive map of the functional network topography in the ASD brain. We used high-quality resting state functional MRI (rs-fMRI) connectivity data and a robust parcellation routine to provide a whole-brain map of functional networks in a group of seventy individuals with ASD and a group of seventy typically developing (TD) individuals.METHODSThe rs-fMRI data were collected using an imaging sequence optimized to achieve high temporal signal-to-noise ratio (tSNR) across the whole-brain. We identified functional networks using a parcellation routine that intrinsically incorporates stability and replicability of the networks by keeping only network distinctions that agree across halves of the data over multiple random iterations in each group. The groups were tightly matched on tSNR, in-scanner motion, age, and IQ.RESULTSWe compared the maps from each group and found that functional networks in the ASD group are atypical in three seemingly related ways: 1) whole-brain connectivity patterns are less stable across voxels within multiple functional networks, 2) the cerebellum, subcortex, and hippocampus show weaker differentiation of functional subnetworks, and 3) subcortical structures and the hippocampus are atypically integrated with the neocortex.CONCLUSIONSThese results were statistically robust and suggest that patterns of network connectivity between the neocortex and the cerebellum, subcortical structures, and hippocampus are atypical in ASD individuals.
SleepEEGpy: a Python-based software “wrapper” package to organize preprocessing, analysis, and visualization of sleep EEG data
Authors: Belonosov G. , Falach R , Schmidig J.F. , Aderka M. , Zhelezniakov V. , Shani-Hershkovich R. , Bar E. , Nir Y 
Published: December 2023

AbstractSleep research uses electroencephalography (EEG) to infer brain activity in health and disease. Beyond standard sleep scoring, there is increased interest in advanced EEG analysis that require extensive preprocessing to improve the signal-to-noise ratio, and dedicated analysis algorithms. While many EEG software packages exist, sleep research has specific needs that require dedicated tools (e.g. particular artifacts, event detection). Currently, sleep investigators use different libraries for specific tasks in a ‘fragmented’ configuration that is inefficient, prone to errors, and requires the learning of multiple software environments. This leads to a high initial complexity, creating a crucial barrier for beginners in sleep research. Here, we present SleepEEGpy, an open-source Python software “wrapper” package to facilitate sleep EEG data preprocessing and analysis. SleepEEGpy builds upon MNE-Python, YASA, and SpecParam tools to provide an all-in-one, beginner-friendly package for comprehensive yet straightforward sleep EEG research including (i) cleaning, (ii) independent component analysis, (iii) detection of sleep events, (iv) analysis of spectral features, and associated visualization tools. A dashboard visualization tool provides an overview to evaluate data and its preprocessing, which can be useful as an initial step prior to detailed analysis. We demonstrate the SleepEEGpy pipeline and its functionalities by applying it to overnight high-density EEG data in healthy participants, revealing multiple characteristic activity signatures typical of each vigilance state. These include alpha oscillations in wakefulness, sleep spindle and slow wave activities in NREM sleep, and theta activity in REM sleep. We hope that this software will be embraced and further developed by the sleep research community, and constitute a useful entry point tool for beginners in sleep EEG research.
Fully flexible molecular alignment enables accurate ligand structure modelling
Authors: Wang Zhihao , Zhou Fan , Wang Zechen , Li Yong-Qiang , Wang Sheng , Zheng Liangzhen , Li Weifeng , Peng Xiangda 
Published: December 2023

AbstractAccurate protein-ligand binding poses are the prerequisites of structure-based binding affinity prediction, and also provide the structural basis for in depth lead optimization in small molecule drug design. Ligand-based modeling approaches primarily extract valuable information from the structural features of small molecules to assess their potential as drug candidates against specific targets. However, it is challenging to provide reasonable predictions of binding poses for different molecules, due to the complexity and diversity of the chemical space of small molecules. Similarity-based molecular alignment techniques can effectively narrow the search range, as structurally similar molecules are likely to have similar binding modes, with higher similarity usually correlating to higher success rates. However, molecular similarity isn’t consistently high because molecules often require changes to achieve specific purposes, leading to reduced alignment precision. To address this issue, we propose a new alignment method—Z-align. This method uses topological structural information as a criterion for evaluating similarity, reducing the reliance on molecular fingerprint similarity. Our method has achieved significantly higher success rates than other methods at moderate levels of similarity. Additionally, our approach can comprehensively and flexibly optimize bond lengths and angles of molecules, maintaining high accuracy even when dealing with larger molecules. Consequently, our proposed solution helps in achieving more accurate binding poses in protein-ligand docking problems, facilitating the development of small molecule drugs.
Dynamics and plasticity of stem cells in the regenerating human colonic epithelium
Authors: Oost Koen C. , Kahnwald Maurice , Barbiero Silvia , de Medeiros Gustavo , Suppinger Simon , Kalck Veronique , Meylan Ludivine Challet , Smallwood Sebastien A. , Stadler Michael B. , Liberali Prisca 
Published: December 2023

SummaryThe human intestinal epithelium is a tissue with rapid turnover. Its complex regenerative process and differentiation trajectories have been challenging to study due to its inaccessibility and lack of temporal sampling. To this end, we developed a workflow to culture adult stem cell-derived human intestinal organoids from single cells to maturation. Extensive characterization of our model system indicated a transient regenerative response, followed by differentiation into all mature cell lineages. This switch is accompanied by a transition between two stem cell states. High-content screening and comparison toin vivostudies revealed that an initial fetal-like state is crucial for achieving successful regeneration, while the subsequent adult-like state is vital for maintaining a balance of cell lineages and continuous support of crypt-morphogenesis. Taken together, this study highlights the extensive plasticity of the intestinal epithelium and paves the way for further studies of human intestinal regeneration and its deregulation in pathologies.
A Mathematical Framework for Measuring and Tuning Tempo in Developmental Gene Regulatory Networks
Authors: Manser Charlotte L , Perez-Carrasco Ruben 
Published: December 2023

AbstractEmbryo development is a dynamic process governed by the regulation of timing and sequences of gene expression, which control the proper growth of the organism. While many genetic programs coordinating these sequences are common across species, the timescales of gene expression can vary significantly among different organisms. Currently, substantial experimental efforts are focused on identifying molecular mechanisms that control these temporal aspects. In contrast, the capacity of established mathematical models to incorporate tempo control while maintaining the same dynamical landscape remains less understood. This manuscript addresses this gap by developing a mathematical framework that links the functionality of developmental programs to the corresponding gene expression orbits (or landscapes). This unlocks the ability to find tempo differences as perturbations in the dynamical system that preserve its orbits. We demonstrate that this framework allows for the prediction of molecular mechanisms governing tempo, through both numerical and analytical methods. Our exploration includes two case studies: a generic network featuring coupled production and degradation, and the repressilator. In the latter, we illustrate how altering the dimerisation rates of transcription factors can decouple the tempo from the shape of the resulting orbits. The manuscript concludes by highlighting how the identification of orthogonal molecular mechanisms for tempo control can inform the design of circuits with specific orbits and tempos.
Management accounting for a circular economy: current limits and avenue for a dialogic approach
Authors: Aureli Selena , Foschi Eleonora , Paletta Angelo 
Published: December 2023

PurposeThis study investigates the implementation of a sustainable circular business model from an accounting perspective. Its goal is to understand if and how decision- makers use management accounting systems, and what changes are needed if these systems are to support the transition toward a circular economy.Design/methodology/approachDialogic accounting theory frames the case study of six companies that built a value network to develop and implement an innovative packaging solution consistent with circular economy principles. Content analysis was utilised to investigate the accounting tools used.FindingsThe findings indicate that circular solutions generate new organisational configurations based on value networks. Interestingly, managers’ decision-making process largely bypassed the accounting function; they relied on informal accounting and life cycle analysis, which stimulated a multi-stakeholder dialogue in a life cycle perspective.Research limitations/implicationsThe research provides theoretical and practical insights into the capability of management accounting systems to support companies seeking circular solutions.Practical implicationsThe authors offer implications for accounting practice, chief financial officers (CFOs) and accounting educators, suggesting that a dialogic approach may support value retention of resources, materials and products, as required by the circular economy.Social implicationsThe research contributes to the debate about the role of accounting in sustainability, specifically the need for connecting for resource efficiency at the corporate level with the rationalisation of resource use within planetary boundaries.Originality/valueThe study contributes to the limited research into the role of management accounting in a company’s transition to circular business models. Dialogic accounting theory frames exploration of how accounting may evolve to help businesses become accountable to all stakeholders, including the environment.
Cooperative management of an initial training program: case study of a Czech production site of a Japanese globalized manufacturing firm
Authors: Nishiwaki Nobuko , Oe Akitsu 
Published: December 2023

PurposeThis study examines the case of an initial training, called “Dojo”, invented and implemented at a production site in the Czech Republic. It clarifies the initial training program implementation process and offers a conceptual framework for cooperative management of subsidiary activities at the site and firm.Design/methodology/approachThis study conducts an in-depth analysis of qualitative data from the Czech production site over a five-year period. The theoretical base is the theorization and labeling phase of management innovation (MI), the final phase of which legitimizes a new management practice. Interview data, archival data, pictures and financial data are used for the analysis.FindingsTo legitimize the Dojo in the operational flow controlled by the site and firm, the Czech production site acquires validation of the Dojo from employees and board members of the Japanese and European headquarters, helping the site build trustful relationships with them. Training programs, process standardization and skills standardization of the workers offer benefits to the trainees, production site and firm.Originality/valueThe authors offer theoretical insights into MI at the subsidiary-level, which past studies have not differentiated at the firm-level. The authors also provide details of the implementation and management of initial training for newly hired blue-collar workers at the production site. The findings complement related literature on human resource management and operational management.
Mobile business apps and employee productivity
Authors: Rokonuzzaman Md , Alhidari Abdullah , Harun Ahasan , Paswan Audhesh , D'Souza Derrick 
Published: December 2023

PurposeHoping to increase the productivity of their employees, firms provide and expect their employees to use approved mobile apps. However, despite an intuitive appeal, the relationship between information technology usage and productivity is still seen as paradoxical. This study examines the relationship between employees' experience and engagement with business mobile apps provided by employers and its effects on employee work productivity.Design/methodology/approachData from respondents who use employer-provided business apps were used to test the hypotheses. Measurement-corrected latent scores extracted from the PLS measurement evaluation were used in regression-centric assessment using PROCESS.FindingsResults indicate that employee-users’ experience-based attributions of the business app, i.e. customization, performance quality and compatibility, have positive effects on productivity mediated by participation intensity. Further, work type (retail vs non-retail) and the depth of the employee user’s experience moderate experience-based attributions' indirect effects on productivity.Originality/valueUnlike previous studies delving into this topic, this study focuses solely on the mediation and moderation effects for hypothesis testing. Specifically, this study investigates effects conditional on work type (retail vs non-retail), which the authors believe has significant implications for retailing. These findings have interesting implications for both future research and managers.
Ethical governance and the board’s moderating role in Zakat avoidance effects on firm value in muslim nations
Authors: Kateb Ines , Ftouhi Khaoula 
Published: December 2023

Purpose
This paper aims to examine the impact of Zakat avoidance on firm value and investigates how board characteristics moderate this relationship within the context of Saudi Arabia, a Muslim nation.

Design/methodology/approach
Using panel data from 2009 to 2020, encompassing 78 nonfinancial firms listed on the Saudi Stock Exchange, this study constructs an enhanced measure of Zakat avoidance that integrates insights from tax avoidance research, Shariah principles and the regulations of the Zakat, Tax and Customs Authority. This research uses empirical techniques, including panel data regressions and interaction analysis to investigate how board characteristics may influence this relationship.

Findings
Descriptive analysis reveals pervasive Zakat compliance, underscoring the effectiveness of Saudi Arabia’s robust Zakat system. Regression results indicate a positive association between Zakat payment and firm value. Remarkably, board characteristics exhibit no significant link to Zakat avoidance, emphasizing the potency of the Zakat system and religious adherence. However, the moderation analysis reveals that board independence and meeting frequency positively moderate the relationship between Zakat avoidance and firm value.

Practical implications
The study emphasizes the vital importance of upholding Zakat obligations to cultivate trust among stakeholders and amplify firm value. It advocates for governance frameworks that foster vigilant oversight and independence, ultimately enhancing a firm’s overall worth. Furthermore, the study’s findings provide valuable insights for corporate leaders, investors, policymakers and society as a whole, facilitating the promotion of ethical financial conduct and driving holistic economic development.

Originality/value
This research introduces novel insights by scrutinizing the intricate interplay of Zakat avoidance, board dynamics and firm value within the context of a culturally distinctive emerging economy. The development of a distinct Zakat avoidance metric, along with comprehensive empirical assessment, contributes to the originality of the study. Moreover, the investigation into the moderating influence of board characteristics adds value to the existing body of knowledge.
Capesize time charter equivalent optimization based on speed and environmental regulations
Authors: Apostolou Tamara , Lagoudis Ioannis N. , Theotokas Ioannis N. 
Published: December 2023

PurposeThis paper aims to identify the interplay of standard Capesize optimal speeds for time charter equivalent (TCE) maximization in the Australia–China iron ore route and the optimal speeds as an operational tool for compliance with the International Maritime Organization (IMO) carbon intensity indicator (CII).Design/methodology/approachThe TCE at different speeds have been calculated for four standard Capesize specifications: (1) standard Capesize with ecoelectronic engine; (2) standard Capesize with non-eco engine (3) standard Capesize vessel with an eco-electronic engine fitted with scrubber and (4) standard Capesize with non-eco engine and no scrubber fitted.FindingsCalculations imply that in a highly inflationary bunker price context, the dollar per ton freight rates equilibrates at levels that may push optimal speeds below the speeds required for minimum CII compliance (C Rating) in the Australia–China trade. The highest deviation of optimal speeds from those required for minimum CII compliance is observed for non-eco standard Capesize vessels without scrubbers. Increased non-eco Capesize deployment would see optimal speeds structurally lower at levels that could offer CII ratings improvements.Originality/valueWhile most of the studies have covered the use of speed as a tool to improve efficiency and emissions in the maritime sector, few have been identified in the literature to have examined the interplay between the commercial and operational performance in the dry bulk sector stemming from the freight market equilibrium. The originality of this paper lies in examining the above relation and the resulting optimal speed selection in the Capesize sector against mandatory environmental targets.