bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors
Authors: McQuarrie David W. J. , Alizada Azad , Czech Nicholson Benjamin , Soller Matthias 
Published: November 2023

AbstractBackgroundThe piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent inheritance of novel invaders. InDrosophila, this pathway relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine and Piwi) that associate with 23-28 nucleotide piRNAs, directing the silencing of transposon-derived transcripts. Transposons constitute a primary driver of genome evolution, yet the evolution of piRNA pathway factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact piRNA processing, exhibit regions of rapid evolution in their promoters. Consequently, the question arises whether such a mode of evolution is a general feature of transposon silencing pathways.ResultsBy employing genomic analysis of coding and promoter regions within genes that function in transposon silencing inDrosophila, we demonstrate that the promoters of germ cell-specific piRNA factors are undergoing rapid evolution. Our findings indicate that rapid promoter evolution is a common trait among piRNA factors engaged in germline silencing across insect species, potentially contributing to gene expression divergence in closely related taxa. Furthermore, we observe that the promoters of genes exclusively expressed in germ cells generally exhibit rapid evolution, with some divergence in gene expression.ConclusionOur results suggest that increased germline promoter evolution, in partnership with other factors, could contribute to transposon silencing and evolution of species through differential expression of genes driven by invading transposons.
Diffusion of DNA on Atomically Flat 2D Material Surfaces
Authors: Shin Dong Hoon , Kim Sung Hyun , Coshic Kush , Watanabe Kenji , Taniguchi Takashi , Verbiest Gerard , Caneva Sabina , Aksimentiev Aleksei , Steeneken Peter G. , Joo Chirlmin 
Published: November 2023

ABSTRACTAccurate localization of biomolecules is pivotal for understanding biological processes. Utilizing the atomically flat surface of 2D materials offers a promising route to achieve this without the need for tethering or constraining. Here we comprehensively investigate the binding and diffusion of DNA on hexagonal boron nitride (hBN) surfaces. Our findings reveal non-specific binding of DNA to pristine hBN, with subsequent diffusion and confinement within the 2D plane. Through single-molecule experiments and computational techniques, we explore DNA dynamics, and the effects of defects, step edges and domain boundaries on the motion, which gives insights on the interactions between solid-state surfaces and biomolecules. By engineering a narrow hBN ribbon structure, we enhance confinement, demonstrating its potential in nanofluidic guiding of biomolecules. Our 2D platform serves as a proving ground for next generation high-throughput single-molecule manipulation techniques for enabling applications in biotechnology and nanotechnology.
The genome and transcriptome of the snailBiomphalaria sudanica s.l.: Immune gene diversification and highly polymorphic genomic regions in an important African vector ofSchistosoma mansoni
Authors: Pennance Tom , Calvelo Javier , Tennessen Jacob A. , Burd Ryan , Cayton Jared , Bollmann Stephanie R. , Blouin Michael S. , Spaan Johannie M. , Hoffmann Federico G , Ogara George , Rawago Fredrick , Andiego Kennedy , Mulonga Boaz , Odhiambo Meredith , Loker Eric S. , Laidemitt Martina R. , Lu Lijun , Iriarte Andrés , Odiere Maurice , Steinauer Michelle L. 
Published: November 2023

AbstractBackgroundControl and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interruptSchistosoma mansonitransmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genusBiomphalaria. Few complete genomic resources exist, with AfricanBiomphalariaspecies being particularly underrepresented despite this being where the majority ofS. mansoniinfections occur. Here we generate and annotate the first genome assembly ofBiomphalaria sudanicasensu lato, a species responsible forS. mansonitransmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vectorB. glabrataand present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs).ResultsDe novogenome and transcriptome assembly of inbredB. sudanicaoriginating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ∼944.2 Mb (6732 fragments, N50=1.067 Mb), comprising 23,598 genes (BUSCO=93.6% complete). TheB. sudanicagenome contains orthologues to all described immune genes/regions tied to protection againstS. mansoniinB. glabrata. TheB. sudanica PTC2candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown inB. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen inPTC2, as well as in regions linked toPTC1andRADresorthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set ofB. sudanicagenes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes were seen in African compared to South American lineages.ConclusionsTheB. sudanicagenome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.
Structural basis of saccharine derivative inhibition of carbonic anhydrase IX
Authors: Leitans Janis , Kazaks Andris , Bogans Janis , Supuran Claudiu T. , Akopjana Inara , Ivanova Jekaterina , Zalubovskis Raivis , Tars Kaspars 
Published: November 2023

AbstractThis scientific study explores the binding mechanisms of saccharine derivatives with human carbonic anhydrase IX (hCA IX), an antitumor drug target, with the aim of facilitating the design of potent and selective inhibitors. Through the use of crystallographic analysis, we investigate the structures of hCA IX - saccharine derivative complexes, unveiling their unique binding modes that exhibit both similarities to sulfonamides and distinct orientations of the ligand tail. Our comprehensive structural insights provide information regarding the crucial interactions between the ligands and the protein, shedding light on interactions that dictate inhibitor binding and selectivity. Through a comparative analysis of the binding modes observed in hCA II and hCA IX, isoform-specific interactions are identified, offering promising strategies for the development of isoform-selective inhibitors that specifically target tumor-associated hCA IX. The findings of this study significantly deepen our understanding of the binding mechanisms of hCA inhibitors, laying a solid foundation for the rational design of more effective inhibitors.
Social health and subsequent cognitive functioning in people aged 50 years and above: examining the mediating roles of depressive symptoms and inflammatory biomarkers
Authors: Stafford Jean , Dekhtyar Serhiy , Welmer Anna-Karin , Vetrano Davide L , Grande Giulia , Marseglia Anna , Moulton Vanessa G , Mansfield Rosie , Liu Yiwen , Ning Ke , Wolf-Ostermann Karin , Brodaty Henry , Samtani Suraj , Ikram Mohammad Arfan , Melis René , Rymaszewska Joanna , Szcześniak Dorota , Gessa Giorgio Di , Richards Marcus , Davis Daniel , Patalay Praveetha , Maddock Jane 
Published: November 2023

AbstractBackgroundSocial health markers, including marital status, contact frequency, network size, and social support, have shown associations with cognition. However, the underlying mechanisms remain poorly understood. We investigated whether depressive symptoms and inflammation mediated associations between social health and subsequent cognition.MethodsIn the English Longitudinal Study of Ageing (ELSA; n=7,136; aged 50+), we used four-way decomposition to examine to what extent depressive symptoms, C-reactive protein (CRP) and fibrinogen (assessed at an intermediate time point) mediated associations between social health and subsequent standardised cognition (verbal fluency, delayed and immediate recall) including cognitive change, with slopes derived from multilevel models (ELSA: 12-year slope). We examined whether findings replicated in the Swedish National Study of Aging and Care in Kungsholmen (SNAC-K; n=2,846; aged 60+; 6-year slope).FindingsWe found indirect effects via depressive symptoms of network size, positive support and less negative support on subsequent verbal fluency, and positive support on subsequent immediate recall (pure indirect effect (PIE)=0.002 [0.000-0.003]). The positive support-verbal fluency mediation finding replicated in SNAC-K. Depressive symptoms partially mediated associations between less negative support and slower immediate (PIE=0.001 [0.000-0.002]) and delayed recall decline (PIE=0.001 [0.000-0.002]), and between positive support and slower immediate recall decline (PIE=0.001, [0.000-0.001]), which replicated in SNAC-K. We did not observe mediation by inflammatory biomarkers.InterpretationFindings provide new insights into mechanisms linking social health with cognition, suggesting that associations between cognition and interactional aspects of social health in particular, such as social support, are partly underpinned by depressive symptoms.
Sustainable strategies and firm performance in manufacturing industry of Coahuila, Mexico
Authors: Lara-Pérez Jorge Alfonso , Aguilera-Tovar Alberto , Hernandez-Rodriguez Alejandra 
Published: November 2023

PurposeAdoption and implementation of sustainable strategies (SS) in firms have been widely studied; however, there is scarce evidence of factors that affect the overall firm performance (FP). Therefore, in this research the variables knowledge management (KM) and professionalization (PR) toward the adoption of SS and their impact on FP are promoted.Design/methodology/approachData from 120 firms in manufacturing industry in Coahuila, Mexico, were collected, and the study is based on the PLS-SEM technique.FindingsThe results revealed that (1) KM and PR present a positive impact on SS and (2) SS are positively related to FP.Practical implicationsFor manufacturing managers, it is necessary to implement SS that meet the expectations of stakeholders, in addition to training human resources with the ability to achieve the aims of the firm and at the same time take care of the environment. As for corporate policymakers, it is essential that they promote global environmental care strategies based on collaborative business.Originality/valueThis research contributes to literature on business management, mainly to the incorporation of SS that allow boosting the economic aspect, but without neglecting social and environmental part.
Model predictive control for smart buildings: a simulation approach within Indian context
Authors: Pandey Kamal , Basu Bhaskar 
Published: November 2023

Purpose
In the context of a developing country, Indian buildings need further research to channelize energy needs optimally to reduce energy wastage, thereby reducing carbon emissions. Also, reduction in smart devices’ costs with sequential advancements in Information and Communication Technology have resulted in an environment where model predictive control (MPC) strategies can be easily implemented. This study aims to propose certain preemptive measures to minimize the energy costs, while ensuring the thermal comfort for occupants, resulting in better greener solutions for building structures.

Design/methodology/approach
A simulation-based multi-input multi-output MPC strategy has been proposed. A dual objective function involving optimized energy consumption with acceptable thermal comfort has been achieved through simultaneous control of indoor temperature, humidity and illumination using various control variables. A regression-based lighting model and seasonal auto-regressive moving average with exogenous inputs (SARMAX) based temperature and humidity models have been chosen as predictor models along with four different control levels incorporated.

Findings
The mathematical approach in this study maintains an optimum tradeoff between energy cost savings and satisfactory occupants’ comfort levels. The proposed control mechanism establishes the relationships of output variables with respect to control and disturbance variables. The SARMAX and regression-based predictor models are found to be the best fit models in terms of accuracy, stability and superior performance. By adopting the proposed methodology, significant energy savings can be accomplished during certain hours of the day.

Research limitations/implications
This study has been done on a specific corporate entity and future analysis can be done on other corporate or residential buildings and in other geographical settings within India. Inclusion of sensitivity analysis and non-linear predictor models is another area of future scope.

Originality/value
This study presents a dynamic MPC strategy, using five disturbance variables which further improves the overall performance and accuracy. In contrast to previous studies on MPC, SARMAX model has been used in this study, which is a novel contribution to the theoretical literature. Four levels of control zones: pre-cooling, strict, mild and loose zones have been used in the calculations to keep the Predictive Mean Vote index within acceptable threshold limits.
Silent alliances and shifting tides: unveiling the hidden pathways to resolving interstate rivalries – the UAE-Israel case
Authors: Schiff Amira , Kertcher Chen 
Published: November 2023

Purpose
This study delves into the transformation of UAE-Israel relations, which transitioned from a long-term rivalry to a formal peace agreement in 2020. It aims to uncover the multifaceted elements that influenced both nations’ pursuit of bilateral negotiations, with a special emphasis on the role of unofficial collaboration.

Design/methodology/approach
Employing a case study approach, the research traces the evolution of the UAE-Israel ties, mapping their progression from covert collaborations to public accords. This exploration is set against a backdrop of political, economic, and societal factors that have historically characterized the broader Israel-Arab conflict. Real-world dynamics and theoretical constructs are analyzed in tandem to derive comprehensive insights.

Findings
Key drivers for the transformation of UAE-Israel relations included the threat from Iran, internal disturbances, economic stresses, and the strategic advantages of discreet diplomacy. Exogenous catalysts like the Covid-19 pandemic and Israel's annexation plans in 2019-2020 played pivotal roles, capitalizing on pre-existing covert collaborations and shared regional interests. Constructive strategies, notably inducements, effectively reshaped their adversarial relationship. The resultant U.S.-mediated agreement conferred strategic, security, economic, and diplomatic benefits to both parties. Importantly, the potency of conengagement conflict management strategy, especially when bolstered by exogenous factors and growing mutual interest, emerged as a game-changer in terminating longstanding rivalries.

Originality/value
This study offers a unique perspective on Israel-UAE relations, emphasizing the significance of covert engagements, inducements, and the innovative conengagement strategy in conflict resolution. By examining a relationship devoid of direct armed conflict, the research underscores the interplay of economic, political, and societal factors in reshaping rivalries. This case study serves as a testament to the potential for transformative change in enduring disputes when the right conditions and strategies align, supplementing conventional perspectives and offering valuable implications for policy and mediation initiatives in the Middle East.
Advancing social procurement: an institutional work perspective
Authors: Razmdoost Kamran , Alinaghian Leila 
Published: November 2023

PurposeThe adoption of social procurement, the emerging practice of using a firm's spending power to generate social value, requires buying firms to navigate conflicts of institutional logics. Adopting an institutional work perspective, this study aims to investigate how buying firms change their existing procurement institutions to adopt and advance social procurement.Design/methodology/approachThe authors conducted an in-depth case study of a social procurement initiative in the UK. This case study comprised of 16 buying firms that were actively participating in the social procurement initiative at the time of data collection (2020–2021). The data were largely captured through a set of 41 semi-structured interviews.FindingsFour types of institutional work were observed: reducing institutional conflicts, crossing institutional boundaries, legitimising institutional change and spreading the new institutional logic. These different types of institutional work appeared in a sequential way.Originality/valueThis study contributes to various strands of literature investigating the role of procurement in generating value and benefits within societies, adopting an institutional lens to investigate the buying firms' purposeful actions to change procurement institutions. Secondly, this study complements the existing literature investigating the conflicts of institutional logics by illustrating the ways firms address such institutional conflicts when adopting and advancing social procurement. Finally, this work contributes to the recently emerging research on institutional work that examines the creation and establishment of new institutions by considering the existing procurement institutions in the examination of institutional work.
Best practice in sexual offender rehabilitation and reintegration programs
Authors: Prenzler Tim , McKillop Nadine , Rayment-McHugh Sue , Christensen Lara 
Published: November 2023

Purpose
This paper aims to report on the results of a global search to identify the characteristics of successful sexual offender treatment programs, with a view to providing guidance for program development.

Design/methodology/approach
A keyword search was conducted of criminology and social science databases. Successful programs were selected on evaluations that used standard scientific designs.

Findings
This study identified 18 evaluations of 16 programs showing significant reductions in reconvictions. Most programs used cognitive behavioural therapy (CBT), with both group and individual sessions; and many evidenced multisystemic therapy (MST) approaches involving families and/or local communities. CBT-based approaches were also common in the 20 unsuccessful programs identified in the study, although fewer MST-oriented features were in evidence. Noncustodial settings, and combined custodial-noncustodial settings, were also more prominent in the successful programs.

Research limitations/implications
There is a shortage of studies focused on the specific components of successful treatment programs for sexual offenders, including for subsets of offenders, such as ethnic minority groups and women.

Practical implications
The findings demonstrate the need for more investment in treatment programs with strict evaluation processes. New and modified programs are likely to benefit from the application of CBT, MST and a community-based reintegration component. More research is needed on effective elements of sexual offender treatment programs.

Originality/value
To the best of the authors’ knowledge, this appears to be the first study that examines features of successful sexual offender treatment programs, compared to unsuccessful programs, using a case-study approach. The findings reinforce the known value of CBT and systemic approaches as core features of programs but raise important questions about what other components are key to activating success.
A count model of financial inclusion in Ghana: evidence from living standards surveys
Authors: Issahaku Haruna , Muhammed Munira Alhassan , Abu Benjamin Musah 
Published: November 2023

PurposeThis paper aims to estimate the determinants of the intensity of use of financial inclusion by households in Ghana.Design/methodology/approachDue to the reality of a household using one or more financial products or services, this study uses the generalised Poisson model applied to GLSS6 and GLSS7 data collected in 2012/2013 and 2016/2017 respectively, to estimate the determinants of the intensity of use of financial inclusion. To deepen the analysis, a multinomial probit model is also applied.FindingsResults show that infrastructural variables such as roads, public transport and banks stimulate the intensity of financial inclusion. In addition, agricultural development characteristics such as markets and cooperatives are essential for the intensity of inclusion.Research limitations/implicationsThere is a need to incorporate how many services or depth of services that people use as part of the conceptualisation of financial inclusion, as this can provide more policy-relevant evidence to enhance priority setting in financial inclusion policies. Also, micro-level financial inclusion studies in agrarian economies should consider exploring agricultural development and infrastructure variables in the modelling framework. As lead to further studies, count models of financial inclusion should consider exploring cross-country analysis, the use of panel data, or other methodological approaches to provide more robust evidence.Originality/valuePrevious studies have not modelled financial inclusion based on a count model as a means of measuring intensity though conceptualisations highlight the fact that people use varied financial products or services. Following from this angle, to the best of the authors’ knowledge, this study provides the first attempt at analysing the underlying determinants of the number of financial products or services used by households.