bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural insight into bacterial co-transcriptional translation initiation
Authors: Yokoyama Takeshi , Murayama Yuko , Uchikubo-Kamo Tomomi , Tomabechi Yuri , Nagao Asuteka , Suzuki Tsutomu , Shirouzu Mikako , Sekine Shun-ichi 
Published: March 2024

AbstractIn bacteria, transcription and translation are tightly coupled, forming a transcription-translation complex (TTC) between RNA polymerase (RNAP) and the ribosome. As nascent mRNA emerging from RNAP is susceptible to ribonuclease digestion, undesired RNA folding, and R-loop formation, immediate TTC formation is important. Here, we report the cryo-electron microscopy structures that capture the translation initiation complex assembly on transcribing RNAP. As a short mRNA emerging from RNAP, the 30S ribosomal subunit binds the RNAP on its inter-subunit side, interacting with the mRNA 5’-region and the initiator tRNA. The RNAP could relocate to the canonical mRNA-entry site of 30S, threading the mRNA into a path formed between RNAP and 30S. The subsequent 50S joining establishes a TTC. These structures illustrate the transcription-coupled translation initiation, while protecting mRNA.One-Sentence SummaryCryo-EM captures the ribosome assembly on transcribing RNA polymerase in the presence of translation initiation factors.
Gene-based Hardy–Weinberg equilibrium test using genotype count data identifies novel cancer-related genes
Authors: Nishino Jo , Miya Fuyuki , Kato Mamoru 
Published: March 2024

AbstractBackgroundAn alternative approach to investigate associations between genetic variants and disease is to examine deviations from the Hardy–Weinberg equilibrium (HWE) in genotype frequencies within a case population, instead of case-control association analysis. The HWE analysis distinctively requires disease cases without the need for controls and demonstrates a notable ability in mapping recessive variants. Allelic heterogeneity is a common phenomenon in diseases. While gene-based case-control association analysis successfully incorporates this heterogeneity, there are no such approaches for HWE analysis. Therefore, we proposed a gene-based HWE test (gene-HWT) by aggregating single-nucleotide polymorphism (SNP)-level HWE test statistics in a gene to address allelic heterogeneity.ResultsThis method used only genotype count data and publicly available linkage disequilibrium information and has a very low computational cost. Extensive simulations demonstrated that gene-HWT effectively controls the type I error at a low significance level and outperforms SNP-level HWE test in power when there are multiple causal variants within a gene. Using gene-HWT, we analyzed genotype count data from genome-wide association study for six types of cancers in Japanese individuals and found that most of the genes detected are associated with cancers. In addition, we identified novel genes (AGBL3andPSORS1C1), novel variants inCTSOknown to be associated with breast cancer prognosis and drug sensitivity, and novel genes as germline factors, which have associations in gene expression or methylation status with cancers in the combined analysis of six types of cancers.ConclusionsThese findings indicate the potential of gene-HWT to elucidate the genetic basis of complex diseases, including cancer.
The role of etiology in the identification of clinical markers of consciousness: comparing EEG alpha power, complexity, and spectral exponent
Authors: Maschke Charlotte , Belloli Laouen , Manasova Dragana , Sitt Jacobo D. , Blain-Moraes Stefanie 
Published: March 2024

1AbstractIn the search for EEG markers of human consciousness, alpha power has long been considered a reliable marker which is fundamental for the assessment of unresponsive patients from all etiologies. However, recent evidence questioned the role of alpha power as a marker of consciousness and proposed the spectral exponent and spatial gradient as more robust and generalizable indexes. In this study, we analyzed a large-scale dataset of 260 unresponsive patients and investigated etiology-specific markers of level of consciousness, responsiveness and capacity to recover. We compare a set of candidate EEG makers: 1) absolute, relative and flattened alpha power; 2) spatial ratios; 3) the spectral exponent; and 4) signal complexity. Our results support the claim that alpha power is an etiology-specific marker, which has higher diagnostic value for anoxic patients. Meanwhile, the spectral slope showed diagnostic value for non-anoxic patients only. Changes in relative power and signal complexity were largely attributable to changes in the spectral slope. Grouping unresponsive patients from different etiologies together can confound or obscure the diagnostic value of different EEG markers of consciousness. Our study highlights the importance of analyzing different etiologies independently and emphasizes the need to develop clinical markers which better account for inter-individual and etiology-dependent differences.
Dissociation of white matter bundles in different recovery measures in post-stroke aphasia
Authors: Osa García Alberto , Brambati Simona Maria , Brisebois Amélie , Houzé Bérengère , Bedetti Christophe , Desautels Alex , Marcotte Karine 
Published: March 2024

ABSTRACTBackgroundPost-stroke aphasia (PSA) recovery shows high variability across individuals and at different moments during recovery. Although diffusion biomarkers from the ventral and dorsal streams have demonstrated strong predictive power for language outcomes, it is still unclear how these biomarkers relate to the various stages of PSA recovery. In this study, we aim to compare diffusion metrics and language measures as predictors of language recovery in a longitudinal cohort of participants with PSA.MethodsTwenty-four participants (mean age = 73 years, 8 women) presenting PSA were recruited in an acute stroke unit. Participants underwent diffusion MRI scanning and language assessment within 3 days (acute phase) after stroke, with a behavioral follow-up at subacute (10±3 days) and chronic phases (> 6 months). We used regression analyses on language performance (cross-sectional) and Δscores at subacute and chronic timepoints (difference between acute and subacute, and subacute and chronic respectively), with language baseline scores, diffusion metrics from language-related white matter tracts, lesion size and demographic predictors.ResultsBest prediction model of performance scores used axial diffusivity (AD) from the left arcuate fasciculus (AF) in both subacute (R2= 0.785) and chronic timepoints (R2= 0.626). Moreover, prediction of change scores depended on AD from left inferior frontal-occipital fasciculus (IFOF), in subacute stage (R2= 0.5), and depended additionally on AD from right IFOF in the chronic stages (R2= 0.68). Mediation analyses showed that lesion load of left AF mediated the relationship between AD from left AF and chronic language performance.ConclusionLanguage performance in subacute and chronic timepoints depends on the integrity of left AF, whereas Δscores of subacute and chronic phases depends on left IFOF, showing a dissociation of the white matter pathways regarding language outcomes. These results support the hypothesis of a functional differentiation of the dual-stream components in PSA recovery.
Utilizing LLMs for Enhanced Argumentation and Extraction of Causal Knowledge from Scientific Literature
Authors: Wang Shuang , Chen Wenjie , Zhang Yang , Chen Ting , Du Jian 
Published: March 2024

AbstractCurrent semantic extraction tools have limited performance in identifying causal relations, neglecting variations in argument quality, especially persuasive strength across different sentences. The present study proposes a five-element based (evidence cogency, concept, relation stance, claim-context relevance, conditional information) causal knowledge mining framework and automatically implements it using large language models (LLMs) to improve the understanding of disease causal mechanisms. As a result, regarding cogency evaluation, the accuracy (0.84) of the fine-tuned Llama2-7b largely exceeds the accuracy of GPT-3.5 turbo with few-shot. Regarding causal extraction, by combining PubTator and ChatGLM, the entity first-relation later extraction (recall, 0.85) outperforms the relation first-entity later means (recall, 0.76), performing great in three outer validation sets (a gestational diabetes-relevant dataset and two general biomedical datasets), aligning entities for further causal graph construction. LLMs-enabled scientific causality mining is promising in delineating the causal argument structure and understanding the underlying mechanisms of a given exposure-outcome pair.
A Novel Method to Visualize Active Small GTPases Unveils Distinct Sites of Sar1 Activation During Collagen Secretion
Authors: Maeda Miharu , Arakawa Masashi , Komatsu Yukie , Saito Kota 
Published: March 2024

AbstractSmall GTPases are essential in various cellular signaling pathways, and detecting their activation within living cells is crucial for understanding cellular processes. Fluorescence resonance energy transfer is widely used to study the interaction between activated small GTPases and their effectors, but it is limited to those with well-defined effectors, excluding Sar1. Here, we present a novel method, SAIYAN (Small GTPase ActIvitY ANalyzing), for detecting the activation of endogenous small GTPases via fluorescent signals utilizing a split mNeonGreen system. We demonstrated Sar1 activation at the endoplasmic reticulum (ER) exit site and successfully detected its activation state in various cellular conditions. Utilizing the SAIYAN system in collagen-secreting cells, we discovered activated Sar1 localized both at ER exit sites and ER-Golgi intermediate compartment (ERGIC) regions. Additionally, impaired collagen secretion led to the confinement of activated Sar1 at the ER exit sites, underscoring the significance of Sar1 activation through the ERGIC in collagen secretion.
Clinical benefits of modifying the evening light environment in an acute psychiatric unit: A single-centre, two-arm, parallel-group, pragmatic effectiveness randomised controlled trial
Authors: Kallestad Håvard , Langsrud Knut , Simpson Melanie Rae , Vestergaard Cecilie Lund , Vethe Daniel , Kjørstad Kaia , Faaland Patrick , Lydersen Stian , Morken Gunnar , Ulsaker-Janke Ingvild , Saksvik Simen Berg , Scott Jan 
Published: March 2024

AbstractBackgroundThe impact of light exposure on mental health is increasingly recognized. Modifying inpatient evening light exposure may be a low-intensity intervention for mental disorders, but few randomized controlled trials (RCTs) exist. We report a large-scale pragmatic effectiveness RCT exploring whether individuals with acute psychiatric illnesses experience additional benefits from admission to an inpatient ward where changes in the evening light exposure are integrated into the therapeutic environment.Methods and findingsAll adults admitted for acute inpatient psychiatric care over eight months were randomly allocated to a ward with a blue-depleted evening light environment or a ward with standard light environment. Baseline and outcome data from individuals who provided deferred informed consent were used to analyze the primary outcome measure (differences in duration of hospitalization) and secondary measures (differences in key clinical outcomes). The Intent to Treat sample comprised 476 individuals (mean age 37; 41% were male). There were no differences in the mean duration of hospitalization (6.7 vs. 7.1 days). Inpatients exposed to the blue-depleted evening light showed higher improvement during admission (Clinical Global Impressions scale-Improvement: 0.28, 95% CI: 0.02 to 0.54; p=0.035, Number Needed to Treat for clinically meaningful improvement (NNT): 12); lower illness severity at discharge (Clinical Global Impressions Scale-Severity: –0.18, 95% CI: –0.34 to – 0.02; p=0.029, NNT for mild severity at discharge: 7); and lower levels of aggressive behaviour (Broset Violence Checklist difference in predicted serious events per 100 days: –2.98; 95% CI: –4.98 to –0.99; p=0.003, NNT: 9). Incidents of harm to self or others, side effects, and patient satisfaction did not differ between the lighting conditions.ConclusionsModifying the evening light environment in acute psychiatric hospitals according to chronobiological principles does not change duration of hospitalizations, but can have clinically significant benefits without increasing side effects, reducing patient satisfaction or requiring additional clinical staff.
The effect of non-genetic determinants of human milk oligosaccharide profiles in milk of Ugandan mothers
Authors: Owalla Tonny Jimmy , Mwangi Victor Irungu , Moukarzel Sara , Okurut Emmanuel , Yonemitsu Chloe , Bode Lars , Egwang Thomas G. 
Published: March 2024

AbstractBackgroundHuman milk oligosaccharides (HMOs) protect against infection and promote growth and cognitive development in breastfeeding children. Non-genetic factors which influence HMO composition in breastfeeding mothers in rural Africa have not been investigated.ObjectiveWe undertook a cross-sectional study to determine the association between HMO profiles and non-genetic maternal factors and children’s sex in Ugandan mother-children pairs.MethodHuman milk was collected from 127 breastfeeding mothers by manual expression. HMO analysis was by high performance liquid chromatography. The proportion of each HMO per total HMO concentration was calculated. Spearman’s correlation and Mann-Whitney U test were used to assess the relationship between individual HMOs and maternal factors and infant sex.ResultNineteen HMOs were assayed. The prevalence of secretor and non-secretor status, based on the proportion of mothers with high milk concentrations of 2’FL and LNFP 1, was 80.3 % and 19.7 %, respectively. In secretor mothers, 2’FL, DFLac and LNFP I constituted > 57 % while in non-secretor mothers LNT and LNFPII constituted 46.9 % of the measured total HMOs. The median 3’SL concentration in milk of all mothers of male children was significantly higher than that in all mothers of female children. The median DFLac concentration in all mothers was significantly higher in multiparous mothers compared to primiparous mothers. Higher FDSLNH and lower LNH concentrations were observed in overweight secretor and non-secretor mothers, respectively. Median concentrations of LNFP I and DSLNT were significantly higher in all mothers < 18 years old compared all mothers > 18 years old. Concentrations of specific HMOs increased, decreased, or remained unchanged with increasing lactation duration in secretor and non-secretor mothers.ConclusionsSpecific HMOs were associated with infant sex and maternal age, parity and post-partum BMI in Ugandan mothers but were different from those reported in other populations.
The ciliary kinesin KIF7 controls the development of the cerebral cortex by acting differentially on SHH-signaling in dorsal and ventral forebrain
Authors: Pedraza María , Grampa Valentina , Scotto-Lomassese Sophie , Puech Julien , Muzerelle Aude , Mohammad Azka , Renier Nicolas , Métin Christine , Masson Justine 
Published: March 2024

ABSTRACTMutations ofKIF7, a key ciliary component of Sonic hedgehog (SHH) pathway, are associated in humans with cerebral cortex malformations and clinical features suggestive of cortical dysfunction. KIF7 regulates the processing of GLI-A and GLI3-R transcription factors in a SHH-dependent manner both in humans and mice. Here, we examine the embryonic cortex development of a mouse model that lacks the expression of KIF7 (Kif7-/-). The cortex is composed of principal neurons generated locally in the dorsal telencephalon where SHH expression is low and inhibitory interneurons (cIN) generated in the ventral telencephalon where SHH expression is high. We observe a strong impact ofKif7deletion on the dorsal cortex development whose abnormalities resemble those of GLI3R mutants: subplate cells are absent, the intermediate progenitor layer and cortical plate do not segregate properly, and corticofugal axons do not develop timely, leading to a delayed colonization of the telencephalon by thalamo-cortical axons. These structural defects alter the cortical distribution of cIN, which moreover exhibit intrinsic migration defects resembling those of cyclopamine-treated cIN. Our results show thatKif7deletion impairs the cortex development in multiple ways, exhibiting opposite effects on SHH pathway activity in the developing principal neurons and inhibitory interneurons.
The role of individualism, collectivism, and promotional reward type on consumer response to amplified word-of-mouth strategies
Authors: Rawal Monika , Saavedra Torres Jose Luis , Bagherzadeh Ramin , Rani Suchitra , Melancon Joanna 
Published: March 2024

Purpose
This study aims to understand the effect of cultural dimension (individualism/ collectivism) on promotional rewards (social or economic) resulting in incentivizing consumers to engage in electronic word-of-mouth (eWOM), further impacting their repurchase intentions.

Design/methodology/approach
In Study 1, a 2 (culture: individualism vs collectivism) × 2 (promotional rewards: social vs economic) between-subjects design was used. Structural equation modeling was used to test the hypotheses. In Study 2, culture was measured instead of just being manipulated. The authors used regression analysis in this study.

Findings
Owing to the characteristics of collectivistic individuals, consumers in collectivistic cultures were more likely to respond to social rewards as an incentive to engage in eWOM. However, consumers in individualistic cultures were more motivated to engage in eWOM when economic rewards were offered.

Originality/value
Despite the global nature of eWOM, little research has explored the effects of cultural traits on consumer response to amplified eWOM strategy. Additionally, though many organizations now offer various promotional incentives to reviewers, little research has explored the effects of promotional offers on a reviewer’s subsequent behavior, and no research has explored the relationship between cultural dimensions and current and future response to promotional eWOM rewards.
Influences of critical success factors on nonprofit outcomes of ODA education construction projects: a case of Vietnam
Authors: Le Duc-Anh , Dang Chau Ngoc , Le-Hoai Long , Hoang Viet Quoc 
Published: March 2024

Purpose
Official development assistance (ODA) education projects have played a crucial role in improving education and training fields in developing countries, but are often facing several considerable challenges (e.g. long implementation time). Thus, this study aims to identify critical success factors (CSFs) in ODA education projects and investigate the influences of CSFs on ODA project performance measured by 11 nonprofit outcomes (NPOs).

Design/methodology/approach
A comprehensive literature review and expert interviews were conducted to compile a list of 35 potential success factors for ODA education projects. Using a survey questionnaire, 143 valid responses were collected from practitioners joining ODA projects in Vietnam. Various statistical methods (e.g. mean score method, Spearman rank correlation test, analysis of variance test, factor analysis and regression analysis) were used to analyze the collected data.

Findings
This research identified seven CSFs for ODA education projects in Vietnam: comprehensive project management competency (C1), clarity and compliance in project execution (C2), transparency and committed funding (C3), external context conditions (C4), well-controlled design and project management procedures (C5), preparations in equipment and complexity insight (C6) and punctual site delivery (C7). Furthermore, the results of regression analysis indicated that comprehensive project management competency (C1) and transparency and committed funding (C3) could significantly affect various NPOs.

Originality/value
This study offers significant insights for practitioners (e.g. project managers) to improve ODA projects’ performance and effectiveness in the education and training sector of a developing country context (like Vietnam).
Assessing the environmental and economic impacts of adopting circular economy for sustainable resource management in the Indian construction sector
Authors: Mhatre-Shah Purva , Gedam Vidyadhar , Unnikrishnan Seema 
Published: March 2024

Purpose
The aim of this study is to understand the environmental benefits and economic savings associated with adoption of circular economy in the construction sector. The research findings will support different stakeholders and decision makers to develop business models based on responsible consumption of resources and build sustainable business models.

Design/methodology/approach
The research uses mixed methodology wherein inventory for life cycle assessment and life cycle costing for environmental and economic impacts is based on primary data using on-site visits for qualitative and quantitative data.

Findings
Different types of land transportation infrastructures are compared for their environmental impacts. It is found that bridges have the highest environmental impacts as compared to tunnels, roads and railways. Further, the results affirm the environmental and economic benefits of adopting circular economy practices.

Originality/value
This is one of a kind research that compares the environmental and economic tradeoffs of adopting circular economy in different types of land transportation infrastructures.
Entrepreneurial leadership in online freelancing: bricolage and project success
Authors: Ahmed Mansoor , Lucianetti Lorenzo 
Published: March 2024

PurposeThe research study provides empirical insights on the relationship between entrepreneurial leadership (EL), entrepreneurial passion for founding (EPF), entrepreneurial bricolage (EB) and project success (PS), in the case of freelancers. The study aims to get a better understanding of whether freelancers, who behave like entrepreneurial leaders, can successfully complete projects through EB.Design/methodology/approachThe study collected data from 209 freelancers through snowball sampling, in two waves, with a time-lag of fourteen days, to better examine the causality of variables. Data were analyzed by Model No. 4 and 7 (i.e. mediation and moderation, respectively) of Process macro.FindingsDrawing on the effectuation theory, the results show that EB mediates the relationship between EL and PS and EPF moderates this relationship.Practical implicationsThe freelancers can formally establish businesses later, after knowing whether they can complete these new types of projects. These online freelancing platforms can provide special services to freelancers who first want to test their skills on unrelated projects. In sum, the paper suggests that freelancers can be successful entrepreneurial leaders.Originality/valueThe EL, EPF, EB and PS are studied in the context of the informal sector, i.e. freelancing, which is the emerging working style in the world. It provides an in-depth understanding of phenomena in freelancers that lacks background literature.