bluuebunny/crossref_metadata_2025 huggingface dataset:
New Unified Classification for Fine Grained Sedimentary Siliciclastic Material Based on Atterberg Limits
Authors: Erlangga Bernado Sakti Hakim , Bahagiarti Kusumayudha Sari , Nurcholis M. , Soesilo Joko , Bachtiar Andang
Published: February 2025

Fine-grained (argillaceous) sedimentary material comprising unconsolidated (i.e., argillaceous sediment and soil) and consolidated (argillaceous rock) is the most abundant sedimentary material. Argillaceous rock is further divided into argillaceous stone and shale based on structure, and into siltrock and clayrock based on grain size. However, the nomenclature of these materials is frequently inconsistent, and there is no unified classification system for these materials. This is due to the difficulty and expense of particle size analysis (PSA), particularly in silt and clay fractions. AIPEA and CMS have proposed using plasticity parameters, i.e., plasticity index (PI) and liquid limits (LL), to differentiate between silt and clay. In engineering geology, a quantitative limitation on unconsolidated and consolidated argillaceous materials is necessary. This is defined as the slake durability index after two cycles (Id2) value, which is argillaceous rock with a Id2 ≥ 2%. Argillaceous stone and shale can be distinguished based on the ease with which a fissility plane structure can be formed with a maximum thickness of 1 cm. The term shale is defined as a fine-grained sedimentary rock that is easily fissile, whereas argillaceous stone is defined as a rock that is not fissile (massive). This article presents a new unified classification for fine-grained sedimentary materials, including loose sediments, soils, and sedimentary rocks. This new unified classification is expected to facilitate the nomenclature of argillaceous sedimentary materials and the prediction of clay and silt fractions based on their plasticity, as an alternative to using PSA. To illustrate the utilisation of the novel unified classification, a series of samples of unconsolidated sediments, soils, and sedimentary rocks were employed, sourced from Lower Kutai Basin, East Kalimantan, Indonesia.
Petrogenesis of Sadakeling – Karaha Volcanic Complex, Tasikmalaya, West Java, Indonesia: Argoland Contamination
Authors: Ezziat Putera Muhammad Azrie , Abdurrachman Mirzam , Nugraha Kartadinata Mochammad , Banggur Wilfridus FS
Published: February 2025

The Sadakeling Karaha Volcano Complex is part of a Tertiary Magmatic Arc in West Java enclosed with several active volcanoes. Based on the tectonics, this area can be a continuous fragment of the Australian Continent Argoland, which controls the magmatism process. This study aims to determine the magma series, tectonic setting, and the continuity of Argoland contamination using petrogenesis study. The type of data for this study uses nine primary data from geochemical content (major, minor, and trace elements) using XRF analysis. The geochemical studies reveal that the Sadakeling Karaha Volcanic Complex points to the insignificant content in total alkali (3,59 - 4,85 wt.%), yet with positive correlations with increasing SiO2 content (52,48 - 61,8 wt.%). The value range can be categorized into basaltic–andesite with sub-alkaline magma series characteristics, and magma alkalinity was identified as a medium-K series group. Other than that, there is a slight enrichment in FeO compounds, but the trend shifts towards alkaline, representing the tholeiitic magma series. Based on a triangular and bivariate diagram from trace and minor elements, Sadakeling-Karaha Volcanic Complex is categorized as Volcanic Arc Basalt. Due to the strong influence of continental crust from major elements and the bivariate diagram between Zr and Zr/Y, supported by the spider-diagram pattern, this area belongs to the active continental margin. The detailed explanation about the magma source allegedly originates from the contamination between the Sundaland crust in the north and Gondwana in the south. The part of Gondwana or Argoland presence influences is strengthened with an identical Trace element content (Sr and Nd) with the SE Australian Granite.
Investigation of Mining Management Based on Green Mining Integrated with the Potential and Exploration of Mineral Resource Using the AHP Method in Jember East Java
Authors: Fery Irawan Januar , Fanteri A. D. S. , Haeruddin  , Aminah S. , Ulum M.
Published: February 2025

Policies regarding mineral and coal exploitation are implemented in designated mining areas, and are carried out by applying good mining principles by paying attention to and considering national and global climate changes which are significant in the management and utilization of the mining sector. Policies for the management and use of rocks as mining potential require measurement in evaluating and monitoring hummock mining activities. In Jember Regency, the rock mined from hummocks and limestone hills is used as a source of building construction materials and to support vital industries. Therefore, an investigative study of its management and utilization is needed so that the existence of hummocks can be managed effectively and efficiently. This investigative study was carried out by observing the environmental conditions of the hummocks and the ongoing and post-mining rock mining patterns. Measurement of rock management and utilization was carried out using the AHP (Analytical Hierarchy Process) method based on 5 Mineral and Coal Policy criteria. The research results show that the management and utilization of rocks in Jember Regency was categorized into moderate criteria, meaning that improvements need to be made so that mining can be carried out in accordance with the national mineral and coal policy based on green mining.
Seismic Microzonation Using the Deterministic Seismic Hazard Analysis (DSHA) Method to Identify Earthquake Vulnerability in Ulu Belu Subdistrict of Tanggamus Regency
Authors: Tristi Maryudhaningrum Santika , Muhammad Zulqarnain Andi
Published: February 2025

The central government is required to have more detailed spatial planning in the Ulu Belu sub-district based on the regulation of the Minister of Agrarian Affairs and Spatial Planning/National Land Agency Number 11 of 2021 contained in the Regional Spatial Plan of Tanggamus Regency. The region has a considerable investment potential estimated at 5 trillion Rupiah. However, earthquake disasters often cause significant damages to the infrastructure and buildings and also serve as a platform for the occurrence of other calamities. The map on earthquake-prone areas in Lampung Province also categorizes Ulu Belu sub-district as highly vulnerable. Therefore, there is a need for a comprehensive earthquake hazard microzonation study. This was achieved through earthquake hazard assessment using the Deterministic Seismic Hazard Analysis (DSHA) method which was used to determine the peak value of acceleration at the bedrock. Furthermore, a Site-Specific Analysis (SSA) was adopted to predict PGA values on the surface with a focus on the East Semangko Fault located about 12 km from the Ulu Belu sub-district and a maximum magnitude of M7.1. It was observed that the class of sites in the region varied between soft soil (SE) and rock (SB). The DSHA analysis results also showed that the PGA bedrock varied between 0.08 and 0.53 g. Meanwhile, the distribution of surface PGA values ranged from 0.10 to 0.87 g, leading to the classification of the area as MMI VI to XXI scale. The shaking of soil at this intensity was believed to have the capacity to cause damage ranging from mild to severe.
Highly efficient terahertz dark-field imaging system with 3D-printed components
Authors: Chung Bryce , Lees Harrison , Ibrahim Matthew , Headland Daniel , Withayachumnankul Withawat
Published: February 2025

Non-destructive testing and evaluation of targets with low contrast and sub-wavelength features tends to be challenging. By illuminating the target off-axis, dark-field imaging techniques can resolve diffracted or scattered features that are typically challenging to discern with conventional bright-field imaging, which relies on specular reflection exclusively. Traditional dark-field methods achieve off-axis illumination by blocking the central portion of the incident beam, but this unfortunately incurs significant power losses of up to 99%. This level of power loss is unfavorable at terahertz frequencies where source power is relatively scarce. To address this, we propose a terahertz dark-field imaging system that makes use of a double axicon beam expander to create an annular beam, which is then focused down upon the target through an objective. The system permits simultaneous bright and dark-field imaging in reflection without modifying the optical train, making greater use of raster scan time while achieving an average transmission efficiency of 33.15% and bright-field spatial resolution of 0.391 lp/mm. The proposed dark-field imaging system is able to enhance the detection of fine features such as growth rings in wood, superficial imperfections on bulk materials, and defects in fiberglass. This approach to achieve dark-field imaging will be valuable for biomedical imaging at the terahertz range that harbors interesting molecular vibration activities.
Ergodic dichotomy for subspace flows in higher rank
Authors: Kim Dongryul , Oh Hee , Wang Yahui
Published: February 2025

In this paper, we study the ergodicity of a one-parameter diagonalizable subgroup of a connected semisimple real algebraic group

G
G

acting on a homogeneous space or, more generally, a homogeneous-like space, equipped with a Bowen-Margulis-Sullivan type measure. These flow spaces are associated with Anosov subgroups of

G
G

, or more generally, with transverse subgroups of

G
G

.

We obtain an ergodicity criterion similar to the Hopf-Tsuji-Sullivan dichotomy for the ergodicity of the geodesic flow on hyperbolic manifolds. In addition, we extend this criterion to the action of any connected diagonal subgroup of arbitrary dimension. Our criterion provides a codimension dichotomy on the ergodicity of a connected diagonalizable subgroup for general Anosov subgroups. This generalizes an earlier work by Burger-Landesberg-Lee-Oh for Borel Anosov subgroups.
Yiddish Translations of Classical Texts
Authors: Shalev Donna
Published: February 2025

This chapter introduces two early twentieth-century Yiddish translators of Plato: Yankev Milkh, whose translations of the Apology, Phaedo, and Crito came out in 1919, and N. Shaynberg, whose translation of the Gorgias probably came out in the 1920s. Both were born and bred on Polish soil, neither from elite backgrounds, and both approached their translations not through the original Greek, but through intermediaries. Yet their lives and modes of translation reflect different trajectories. The chapter explores the distinct approaches of these two translators to Greek culture and to their mandate as purveyors to the Yiddish-speaking consumers of classical culture which they presume to address.
Intellectual Perseverance, Grit, and Growth Mindset
Authors: King Nathan L
Published: February 2025

Recent developments in psychology and philosophy highlight the role of effort in intellectual achievement, to the relative de-emphasis of notions like raw intelligence and innate ability. In psychology, Angela Duckworth’s work on grit lauds the importance of passion and perseverance in the achievement of long-term goals, including intellectual goals. Carol Dweck’s research on growth mindset suggests that our capacities for achievement—and even intelligence itself—are malleable in response to effort. Indeed, the belief that one’s capacities are malleable in this way is an important predictor for both effort and achievement. Finally, a small cadre of philosophers has drawn attention to the concept of intellectually virtuous perseverance (IVP), an excellence of cognitive character that often plays a prominent role in agents’ gaining, keeping, and sharing epistemic goods. Discussions of grit, growth mindset, and IVP all underscore the fact that when it comes to achieving intellectual goals, effort matters. To date, however, theorists have paid relatively little attention to explaining how these concepts are related to each other. The present chapter aims to fill this void.
Cultivating Persistence
Authors: Costa Arthur L , Kallick Bena
Published: February 2025

Persisting is a disposition that is essential for success in life. Human beings are born with the capacity to persist; however, some environments deter its development. Modeling by respected adults, discussing its meanings and importance, recognizing and reinforcing the behavior when it is performed, teaching the skills and strategies of persisting directly, and creating nurturing environments at school and at home can instill this trait in the mind and behaviors of young people as they grow into efficacious adults. As a result of continuous attention to the development of this behavior, they build a habit that builds hope, confidence and the capacity to think through and meet the challenges of an ever-changing environment.
Perseverance in the Religious Life
Authors: McKaughan Daniel J , Howard-Snyder Daniel
Published: February 2025

Life presents us with no shortage of difficulty and, in light of the experience of people of faith, the pursuit of a religious life will also involve its share. This chapter briefly explores the place that ancient Jewish and early Christian communities envisioned for perseverance through difficulty in a life oriented around individual and communal relationship with God. It also finds perseverance at the heart of the relational faith and faithfulness commended by these communities. This chapter offers a theory of faith and faithfulness that accommodates this finding, as well as several other items of religious data any such theory should accommodate.
John of Salisbury on Natural Law, Natural Rights, and Liberty
Authors: Nederman Cary J
Published: February 2025

One of the most striking developments in the study of medieval political and legal philosophy has been the recognition that the idea of individual natural rights has a pedigree that can be traced back to the work of the twelfth-century canonists. Scholars now maintain that the theory of natural (sometimes called “subjective”) rights arose from the canonist interpretation of natural law. In turn, such rights confer upon human beings a sphere of personal liberty in their actions. The defense of individual rights might also be found in an alternative formulation in the writings of the mid-twelfth-century philosopher and churchman John of Salisbury. John’s knowledge of canonistic doctrines was seemingly marginal at best and he virtually never uses Stoic terms such as ius naturale and lex naturale. Yet John too articulates a conception of subjective rights that draws a direct connection between ius and liberty but without appealing to natural law at all. The connection between nature and rights that necessitated liberty instead arises from John’s reliance on the moderate skepticism of the New Academy, which advocated a probabilistic approach to human claims to knowledge.
Ockham on Group Reality and Group Action
Authors: Pelletier Jenny
Published: February 2025

This contribution explores the conceptual connection between group reality and group action in William of Ockham’s political writings, with supporting metaphysical considerations drawn from his academic writings. Against John XXII, Ockham argues that (1) groups are real in part because (2) groups can act, and this is in turn why (3) groups can bear certain political and economic rights. (The contribution leaves aside the question of group rights.) The principal claim of the contribution is that group action is the theoretical anchor underpinning group reality, and one of its central aims is to render Ockham’s understanding of group action intelligible. An ontology of group action is reconstructed with an analysis of two types of group act that is consistent with his individualist and nominalist metaphysics. His discussion bears witness to a lively medieval debate on philosophical questions about groups and group agents that are by no means exclusively contemporary.
Nominalism’s Modal Paradise Lost
Authors: Pasnau Robert
Published: February 2025

Nominalism in all of its manifestations, from Abelard to Quine, grows out of ontological scruples. For William Ockham and his followers in the fourteenth century, nominalism was centrally concerned with a more parsimonious treatment of the ten Aristotelian categories of being. But when it came to the alethic modalities of possibility and necessity, the nominalist program suddenly turned expansive—or so it has seemed to recent commentators, who have found in the nominalists a commitment to vast realms of merely possible beings, and even to a possible-worlds semantics for modality. This contribution argues that quite contrary to how the nominalists are generally read, they take particular care to avoid an ontological commitment to possibilia. Indeed, although their broader semantic views make it quite natural for them to analyze modal sentences in terms of possible worlds, they deliberately eschew this way of proceeding, even at the cost of forgoing the explanatory power that their semantic theories have in other domains.
Dynamic reconfiguration of brain functional networks in world class gymnasts: a resting-state functional MRI study
Authors: Cao Bolin , Guo Yu , Xia Fengguang , Li Lunxiong , Ren Zhanbing , Lu Min , Wang Jun , Huang Ruiwang
Published: February 2025

Long-term intensive training has enabled world class gymnasts to attain exceptional skill levels, inducing notable neuroplastic changes in their brains. Previous studies have identified optimized brain modularity related to long-term intensive training based on resting-state functional MRI, which is associated with higher efficiency in motor and cognitive functions. However, most studies assumed that functional topological networks remain static during the scans, neglecting the inherent dynamic changes over time. This study applied a multilayer network model to identify the effect of long-term intensive training on dynamic functional network properties in gymnasts. The imaging data were collected from 13 gymnasts and 14 age- and gender-matched non-athlete controls. We first construct dynamic functional connectivity matrices for each subject to capture the temporal information underlying these brain signals. Then, we applied a multilayer community detection approach to analyze how brain regions form modules and how this modularity changes over time. Graph theoretical parameters, including flexibility, promiscuity, cohesion, and disjointedness, were estimated to characterize the dynamic properties of functional networks across global, network, and nodal levels in the gymnasts. The gymnasts showed significantly lower flexibility, cohesion, and disjointedness at the global level than the controls. Then, we observed lower flexibility and cohesion in the auditory, dorsal attention, sensorimotor, subcortical, cingulo-opercular, and default mode networks in the gymnasts than in the controls. Furthermore, these gymnasts showed decreased flexibility and cohesion in several regions associated with motor function. Together, we found brain functional neuroplasticity related to long-term intensive training, primarily characterized by decreased flexibility of brain dynamics in the gymnasts, which provided new insights into brain reorganization in motor skill learning.
Examining the Accuracy and Reproducibility of Responses to Nutrition Questions Related to Inflammatory Bowel Disease by Generative Pre-trained Transformer-4 (GPT-4)
Authors: Samaan Jamil S , Issokson Kelly , Feldman Erin , Fasulo Christina , Rajeev Nithya , Ng Wee Han , Hollander Barbara , Yeo Yee Hui , Vasiliauskas Eric
Published: February 2025

Background and Aims

Generative Pre-trained Transformer-4 (GPT-4) is a large language model (LLM) trained on a vast corpus of data, including the medical literature. Nutrition plays an important role in managing inflammatory bowel disease (IBD), with an unmet need for nutrition-related patient education resources. This study examines the accuracy, comprehensiveness, and reproducibility of responses by GPT-4 to patient nutrition questions related to IBD.

Methods

Questions were obtained from adult IBD clinic visits, Facebook, and Reddit. Two IBD-focused registered dieticians independently graded the accuracy and reproducibility of GPT-4’s responses while a third senior IBD-focused registered dietitian arbitrated. Each question was inputted twice into the model.

Results

88 questions were selected. The model correctly responded to 73/88 questions (83.0%), with 61 (69.0%) graded as comprehensive. 15/88 (17%) responses were graded as mixed with correct and incorrect/outdated data. The model comprehensively responded to 10 (62.5%) questions related to “Nutrition and diet needs for surgery”, 12 (92.3%) “Tube feeding and parenteral nutrition”, 11 (64.7%) “General diet questions”, 10 (50%) “Diet for reducing symptoms/inflammation” and 18 (81.8%) “Micronutrients/supplementation needs”. The model provided reproducible responses to 81/88 (92.0%) questions.

Conclusion

GPT-4 comprehensively answered most questions, demonstrating the promising potential of LLMs as supplementary tools for IBD patients seeking nutrition-related information. However, 17% of responses contained incorrect information, highlighting the need for continuous refinement prior to incorporation into clinical practice. Future studies should emphasize leveraging LLMs to enhance patient outcomes and promoting patient and healthcare professional proficiency in using LLMs to maximize their efficacy.
No-touch vein grafts in coronary artery bypass surgery: a registry-based randomized clinical trial
Authors: Thelin Stefan , Modrau Ivy Susanne , Duvernoy Olov , Dalén Magnus , Dreifaldt Mats , Ericsson Anders , Friberg Örjan , Holmgren Anders , Hostrup Nielsen Per , Hultkvist Henrik , Jensevik Eriksson Karin , Jeppsson Anders , Lidén Mats , Nozohoor Shahab , Ragnarsson Sigurdur , Sartipy Ulrik , Ternström Lisa , Themudo Raquel , Vikholm Per , James Stefan
Published: February 2025

Background and Aims

No-touch saphenous vein harvesting may enhance graft patency and improve clinical outcomes after coronary artery bypass grafting (CABG).

Methods

In this registry-based, randomized trial, patients undergoing CABG were randomly assigned to no-touch or conventional harvesting. The primary composite outcome was the proportion of patients with occluded/stenosed >50% vein graft on coronary computed tomography angiography, or who underwent percutaneous coronary intervention to a vein graft, or died. Secondary outcomes included clinical outcomes and leg wound complications.

Results

A total of 902 patients were enrolled with a mean total number of distal vein anastomoses of 2.0 (SD 0.87). The primary endpoint occurred in 90/454 (19.8%) of patients randomized to no-touch and in 107/446 (24.0%) of patients randomized to the conventional technique [difference, −4.3 percentage points; 95% confidence interval (CI) −10.1–1.6; P = .15] at a mean follow-up time of 3.5 (SD 0.1) years. The composite of death, myocardial infarction, or repeat revascularization at 4.4 (SD 1.3) years occurred in 57/454 (12.6%) and 44/446 (9.9%) in the no-touch and conventional groups, respectively (hazard ratio 1.3; 95% CI, 0.87–1.93). Leg wound complications were more common in patients assigned to no-touch harvesting at 3 months [107/433 (24.7%) vs. 59/427 (13.8%); difference, 10.9 percentage points; 95% CI 5.7–16.1]. At 2 years, 189/381 (49.6%) vs. 91/361 (25.2%) had remaining leg symptoms (difference, 24.4 percentage points; 95% CI 17.7–31.1).

Conclusions

No-touch vein graft harvesting for CABG was not superior to conventional open harvesting in reducing vein graft failure or clinical events after CABG but increased leg wound complications. The primary outcome requires cautious interpretation due to a lower-than-expected number of primary events.
May Measurement Month 2022: an analysis of blood pressure screening results from Mozambique
Authors: Jessen Neusa , Govo Valério , Amarcy Sheila , Novela Célia , Antunes Anabela , Nhantumbo Amos , Gelfi Giorgia , Ramirez Lucy , Poulter Neil R , Beaney Thomas , Kerr Gabriele , Damasceno Albertino
Published: February 2025

The May Measurement Month (MMM) campaign was carried out in Mozambique in 2022 with the aim of raising awareness of raised blood pressure (BP). Here, we report on the findings of the campaign.

Adults aged ≥ 18 years were recruited opportunistically at Zambézia, Sofala and Maputo city, in Northern, Central and Southern regions of Mozambique, respectively. Three seated BP readings were taken for each participant, along with completion of a questionnaire on demographics, lifestyle factors, and comorbidities. Hypertension was defined as a systolic BP ≥ 140 mmHg and/or diastolic BP ≥ 90 mmHg or being on antihypertensive medication. Controlled BP was defined as being on antihypertensive medication with a BP <140/90 mmHg. Multiple imputation was used to estimate any missing BP readings. In total, 8276 were screened, with a mean age of 36.9 years and 61.6% of whom were female. Of all participants, 2486 (30.0%) had hypertension, of whom 1122 (45.1%) were aware, and 735 (29.6%) were on antihypertensive medication. Of those on antihypertensive medication, 285 (38.8%) had controlled BP, and of all participants with hypertension, 11.5% had controlled BP. In conclusion, the MMM campaign in Mozambique identified significant numbers of participants with either untreated or inadequately treated hypertension, calling attention to the need to improve the overall hypertension care cascade. There is an urgent need to increase awareness, improve access to appropriate antihypertensive medication and better follow up those on treatment.
The Role of Meaning in the Retirement Transition: Scoping Review
Authors: Wood Rachel E , Pachana Nancy A
Published: February 2025

Background and Objectives

The retirement transition is a period of major change and instability, which may challenge a person’s sense of meaning in life. This scoping review sought to characterize the current research on the role of meaning in the retirement transition.

Research Design and Methods

This scoping review was conducted according to JBI and PRISMA reporting guidelines. Database searches of Scopus, PubMed, PsycINFO, and Social Science Database, and ProQuest Dissertations and Theses Global yielded 738 records (after duplicates removed). Accessory searches yielded an additional 286 records. Eligible articles included peer-reviewed literature and theses (qualitative and quantitative) that explored an aspect of meaning in the context of the retirement transition.

Results

A total of 30 studies (21 qualitative and nine quantitative) were included. These studies examined a broad range of research questions on different aspects of meaning – meaning in life, meaning making, meaningful engagement, and meaning of retirement. Most were single, stand-alone studies (not part of a broader research program) that included only a single time point. Only six studies were longitudinal.

Discussion and Implications

This review revealed a heterogeneous set of studies and identified gaps in reporting of important participant characteristics, lack of conceptual clarity in defining meaning, and few longitudinal studies. There is a need for more theoretically driven, programs of research that include longitudinal designs, ideally using mixed methods approaches, to build a richer understanding of the role of meaning during this major life transition.
Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl
Authors: Wang Gang , Zhang Xinye , Zhao Xiurong , Ren Xufang , Chen Anqi , Dai Wenting , Zhang Li , Lu Yan , Jiang Zhihua , Wang Huie , Liu Yong , Zhao Xiaoyu , Wen Junhui , Cheng Xue , Zhang Yalan , Ning Zhonghua , Ban Liping , Qu Lujiang
Published: February 2025

Introduction

The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation that causes the leucistic plumage of the blue peafowl (also called white peafowl) remains unknown.

Results

In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, and a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes, and 33 peafowl W chromosomes genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found 3 hybrid green peafowls in zoo samples rather than in the wild samples, with a blue peafowl genomic content of 16–34%. Maternal genetic analysis showed that 2 of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in 4 zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP3 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for leucistic plumage of blue peafowl, preventing melanocytes from being transported into plumage, thereby inhibiting melanin deposition.

Conclusion

Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide a valuable resource for blue peafowl genomics-assisted breeding.
VaxBot-HPV: a GPT-based chatbot for answering HPV vaccine-related questions
Authors: Li Yiming , Li Jianfu , Li Manqi , Yu Evan , Rhee Danniel , Amith Muhammad , Tang Lu , Savas Lara S , Cui Licong , Tao Cui
Published: February 2025

Objective

Human Papillomavirus (HPV) vaccine is an effective measure to prevent and control the diseases caused by HPV. However, widespread misinformation and vaccine hesitancy remain significant barriers to its uptake. This study focuses on the development of VaxBot-HPV, a chatbot aimed at improving health literacy and promoting vaccination uptake by providing information and answering questions about the HPV vaccine.

Methods

We constructed the knowledge base (KB) for VaxBot-HPV, which consists of 451 documents from biomedical literature and web sources on the HPV vaccine. We extracted 202 question-answer pairs from the KB and 39 questions generated by GPT-4 for training and testing purposes. To comprehensively understand the capabilities and potential of GPT-based chatbots, 3 models were involved in this study: GPT-3.5, VaxBot-HPV, and GPT-4. The evaluation criteria included answer relevancy and faithfulness.

Results

VaxBot-HPV demonstrated superior performance in answer relevancy and faithfulness compared to baselines. For test questions in KB, it achieved an answer relevancy score of 0.85 and a faithfulness score of 0.97. Similarly, it attained scores of 0.85 for answer relevancy and 0.96 for faithfulness on GPT-generated questions.

Discussion

VaxBot-HPV demonstrates the effectiveness of fine-tuned large language models in healthcare, outperforming generic GPT models in accuracy and relevance. Fine-tuning mitigates hallucinations and misinformation, ensuring reliable information on HPV vaccination while allowing dynamic and tailored responses. The specific fine-tuning, which includes context in addition to question-answer pairs, enables VaxBot-HPV to provide explanations and reasoning behind its answers, enhancing transparency and user trust.

Conclusions

This study underscores the importance of leveraging large language models and fine-tuning techniques in the development of chatbots for healthcare applications, with implications for improving medical education and public health communication.
Assessing the use of neonatal sepsis guidelines and antibiotic prescription with large-scale prospective data from Zimbabwe and Malawi
Authors: Khan Nushrat , Chimhini Gwendoline , Shrestha Som Kumar , Cortina-Borja Mario , Chimhuya Simbarashe , Zailani Gloria , Gannon Hannah , Mangiza Marcia , Fitzgerald Felicity , Heys Michelle , Chiume Msandeni
Published: February 2025

Background

Neonatal sepsis is a major cause of mortality in low-resource settings. We assessed how neonatal sepsis guidelines were used in two Zimbabwean hospitals and one Malawian hospital.

Methods

Using routine data collected with the digital health intervention, Neotree, we retrospectively reviewed doctors’ and nurses’ agreement with national and World Health Organization (WHO) guideline recommendations for antibiotic prescription for sepsis. We compared clinical features and outcomes of neonates who should have received antibiotics as per guideline with those who actually received them and fitted a logistic regression model to identify features associated with prescription.

Results

Data were collected between January 2021 and June 2022 from 10,868 neonates: 6,045 admitted to Sally Mugabe Central Hospital (SMCH), 1,094 to Chinhoyi Provincial Hospital (CPH) and 3,729 to Kamuzu Central Hospital (KCH). Complete implementation of national guidelines would increase antibiotics at admission: from 2,188 (38%) to 3,745 (64%) at SMCH, 472 (44%) to 852 (79%) at CPH, and 1,519 (41%) to 3,043 (82%) at KCH. Clinical features of sepsis were frequently not acted on, but the case-fatality rate was lower in those not prescribed antibiotics despite guideline recommendation. Application of WHO guidelines would increase antibiotic prescription to 91% at SMCH, 88% at CPH, and 77% in KCH. Maternal risk factors for sepsis, male gender, low birth weight, older age at admission, and spontaneous vaginal delivery were associated with higher rate of antibiotic prescription.

Conclusion

Guideline-recommended clinical signs for sepsis are inconsistently used, with clinicians using other features for antibiotic decision-making. Work is needed to revise clinical diagnostic algorithms in low-resource settings to ensure they are useful, usable and contextually appropriate.
Can we disentangle between the emission of an accretion disc around a single black hole and a circumbinary disc?
Authors: Varniere Peggy , Mignon-Risse Raphaël , Casse Fabien
Published: February 2025

The detection of gravitational waves from binary black holes (BBHs) started the hunt for their pre-merger electromagnetic emission. In that respect, numerical simulations have been looking for the ‘smoking gun’ signal that could help identify pre-merger systems. Here we study if any of the expected features of circumbinary discs, such as the periodic modulation from the orbiting ‘lump’, could be used to identify pre-merger BBHs or if they could be easily confused with other systems. Indeed, while the timing feature associated with the ‘lump’ seems to be present for a large part of the parameter space defined by the binary separation and mass ratio in circular binaries, it was recently proposed to form thanks to an instability occurring naturally at the edge of accretion discs around single black holes (SBH). In order to check if features of a circumbinary disc could be reproduced by a SBH system, we search for at least one SBH fit able to replicate the given synthetic observations of a circumbinary disc. We found that many of the features from a circumbinary disc can be reproduced by a SBH system with different masses, distances or inner disc positions. Interestingly, while we can always find a SBH model providing a good enough fit to the data, the presence of two variabilities, associated with the lump and the binary, or binary-lump beat, period, is a necessary condition for a wide range of BBH system parameters and should be used as a test to disqualify some BBH candidates.
Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time
Authors: Dong Xiaofeng , Matthews David A , Gallo Giulia , Darby Alistair , Donovan-Banfield I’ah , Goldswain Hannah , MacGill Tracy , Myers Todd , Orr Robert , Bailey Dalan , Carroll Miles W , Hiscox Julian A
Published: February 2025

In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been selected that are more transmissible and capable of partial immune escape. Currently, models for projecting the evolution of SARS-CoV-2 are based on using dominant genome sequences to forecast whether a known mutation will be prevalent in the future. However, novel variants of SARS-CoV-2 (and other viruses) are driven by evolutionary pressure acting on minor variant genomes, which then become dominant and form a potential next wave of infection. In this study, sequencing data from 96 209 patients, sampled over a 3-year period, were used to analyse patterns of minor variant genomes. These data were used to develop unsupervised machine learning clusters to identify amino acids that had a greater potential for mutation than others in the Spike protein. Being able to identify amino acids that may be present in future variants would better inform the design of longer-lived medical countermeasures and allow a risk-based evaluation of viral properties, including assessment of transmissibility and immune escape, thus providing candidates with early warning signals for when a new variant of SARS-CoV-2 emerges.
XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites
Authors: Lin Xiaohui , Leung Kay Sze Karina , Wolfe Kaitlynn F , Call Nicolas , Bhandari Seema Khattri , Huang Xiaoyu , Lee Brian J , Tomkinson Alan E , Zha Shan
Published: February 2025

Poly-ADP-ribose polymerases 1 and 2 (PARP1 and 2) are critical sensors of DNA-strand breaks and targets for cancer therapy. Upon DNA damage, PARP1 and 2 synthesize poly-ADP-ribose (PAR) chains on themselves and other substrates, facilitating DNA single-strand break repair by recruiting PAR-binding DNA repair factors, including X-ray repair cross-complementing group 1 (XRCC1) and aprataxin and polynucleotide kinase phosphatase-like factor (APLF). While diverse DNA lesions activate PARP1, PARP2 is selectively activated by 5′ phosphorylated nicks. They function independently and compensate for each other. Previous studies suggest that PARP1 and its PAR chains act upstream to recruit PARP2 to DNA damage sites. Here, we report that the scaffold protein XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to damage sites. XRCC1-deficiency causes hyperactivation of PARP1 while attenuating micro-irradiation-induced PARP2 foci. Mechanistically, the BRCT1 domain of XRCC1 binds to PAR, while its BRCT2 domain interacts with the PARP2 catalytic domain independently of the PARP2 enzymatic activity and the LIG3 BRCT domain via residues D575 and Y576. This mode of PARP2 enrichment is important for the recruitment of certain PAR-binding proteins, such as APLF, but dispensable for others, such as the XRCC1–BRCT1 domain. These findings highlight the distinct role of PARP1 and PARP2 in PAR synthesis and uncover unexpected hierarchical roles of PARP1 and XRCC1 upstream of PARP2.
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
Authors: Xu Zhiting , Lin Qing , Cai Xiaodian , Zhong Zhanming , Teng Jinyan , Li Bingjie , Zeng Haonan , Gao Yahui , Cai Zexi , Wang Xiaoqing , Shi Liangyu , Wang Xue , Wang Yi , Zhang Zipeng , Lin Yu , Liu Shuli , Yin Hongwei , Bai Zhonghao , Wei Chen , Zhou Jun , Zhang Wenjing , Zhang Xiaoke , Shi Shaolei , Wu Jun , Diao Shuqi , Liu Yuqiang , Pan Xiangchun , Feng Xueyan , Liu Ruiqi , Su Zhanqin , Chang Chengjie , Zhu Qianghui , Wu Yuwei , Zhou Zhongyin , Bai Lijing , Li Kui , Wang Qishan , Pan Yuchun , Xu Zhong , Peng Xianwen , Mei Shuqi , Mo Delin , Liu Xiaohong , Zhang Hao , Yuan Xiaolong , Liu Yang , Liu George E , Su Guosheng , Sahana Goutam , Lund Mogens Sandø , Ma Li , Xiang Ruidong , Shen Xia , Li Pinghua , Huang Ruihua , Ballester Maria , Crespo-Piazuelo Daniel , Amills Marcel , Clop Alex , Karlskov-Mortensen Peter , Fredholm Merete , Tang Guoqing , Li Mingzhou , Li Xuewei , Ding Xiangdong , Li Jiaqi , Chen Yaosheng , Zhang Qin , Zhao Yunxiang , Zhao Fuping , Fang Lingzhao , Zhang Zhe
Published: February 2025

Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted a comprehensive genome-wide association studies (GWAS) followed by cross-breed meta-analysis for 232 complex traits and within-breed meta-analysis for 12 traits, using 28.3 million imputed sequence variants in 70 328 animals across 14 pig breeds. We identified 6 878 quantitative trait loci (QTL) for 139 complex traits. Leveraging the Pig Genotype-Tissue Expression (PigGTEx) resource, we systematically investigated the biological context and regulatory mechanisms behind these trait-QTLs, ultimately prioritizing 14 829 variant-gene-tissue-trait regulatory circuits. For instance, rs344053754 regulates UGT2B31 expression in the liver and intestines, potentially by modulating enhancer activity, ultimately influencing litter weight at weaning in pigs. Furthermore, we observed conservation of certain genetic and regulatory mechanisms underlying complex traits between humans and pigs. Overall, our cross-breed meta-GWAS in pigs provides invaluable resources and novel insights into the genetic regulatory and evolutionary mechanisms of complex traits in mammals.
Financial incentives for substance abstinence: a systematic review and meta-analysis
Authors: Phillips-Chantelois Damon , Sharrad Kelsey , Perveen Shagufta , Gammatopoulos Tahlia , Usmani Nawal , Szumlinski Karen , Carson-Chahhoud Kristin
Published: February 2025

Introduction

Substance Use Disorder (SUD) increased by 45% globally in the past 10 years, representing one of the largest increases in risk factors for disease. Financial incentives (FI) are a promising tool to promote health behavior change, including substance abstinence. We aim to address a 10-year gap in the evidence and identify key characteristics for optimal treatment.

Methods

A meta-analysis of randomized controlled trials (RCTs) was undertaken per Cochrane guidelines and the PRISMA 2020 checklist. Medline, PsycINFO, and EMBASE were searched up to 11th September 2024. Included studies offered FI to substance users in exchange for substance abstinence compared to an alternative intervention control. The primary outcome extracted was substance abstinence at latest follow-up. Secondary outcomes such as cost-effectiveness, adverse events, and motivational assessments were also extracted. Risk of bias was analyzed using the RoB 1 tool.

Results

Of 5,042 studies identified, 246 were shortlisted for full-text review and included 39 RCTs (N = 27,845) for meta-analysis. SUD categories spanning nicotine (n = 30, OR = 1.83; 95%CI = 1.65-2.03, p < .001), alcohol (n = 3, OR = 4.69, 95%CI = 1.59-13.86, p = .005), stimulants (n = 2, OR = 3.52; 95%CI = 0.36-34.18, p = 0.28), and polydrug (n = 2, OR = 3.11, 95%CI = 0.53-18.25, p = 0.21) were meta-analyzed for improving abstinence rates. Cannabis and opioid sub-groups could not be meta-analyzed. Overall effectiveness was significant for FI improving substance abstinence rates (OR=1.93, 95%CI=1.66-2.24, p<.001) with continued significance through 12-month or longer follow-ups (OR=1.78; 95%CI=1.50-2.12, p<.001).

Conclusions

Findings from this meta-analysis suggest that FI are an effective tool for increasing substance abstinence, particularly nicotine and alcohol, however, future research is recommended for other substances such as stimulants and opioids.

Implications

This systematic review and meta-analysis exploring the use of financial incentives for substance use disorders provides the first update on trends in this field since 2014 and the first meta-analysis since 2006. Notably, this review challenges the concerns of sustainability and effects on motivation which have withheld the clinical application of financial incentives for substance use disorders.
Embedded structure in quantum theory, functional operator and multiverse
Authors: Kawamura Yoshiharu
Published: February 2025

We explore a wider theoretical framework that has quantum field theory built-in, taking the fact that quantum mechanics is reconstructed from quantum field theory as a hint. We formulate a quantum theory with an embedded structure by introducing functional operators, and we find that it could describe the level II multiverse. Topics related to a beginning of the universe such as an inflation, the third quantization and the landscape are discussed in our formulation.
Biomaterials for neuroengineering: applications and challenges
Authors: Wu Huanghui , Feng Enduo , Yin Huanxin , Zhang Yuxin , Chen Guozhong , Zhu Beier , Yue Xuezheng , Zhang Haiguang , Liu Qiong , Xiong Lize
Published: February 2025

Neurological injuries and diseases are a leading cause of disability worldwide, underscoring the urgent need for effective therapies. Neural regaining and enhancement therapies are seen as the most promising strategies for restoring neural function, offering hope for individuals affected by these conditions. Despite their promise, the path from animal research to clinical application is fraught with challenges. Neuroengineering, particularly through the use of biomaterials, has emerged as a key field that is paving the way for innovative solutions to these challenges. It seeks to understand and treat neurological disorders, unravel the nature of consciousness, and explore the mechanisms of memory and the brain’s relationship with behavior, offering solutions for neural tissue engineering, neural interfaces and targeted drug delivery systems. These biomaterials, including both natural and synthetic types, are designed to replicate the cellular environment of the brain, thereby facilitating neural repair. This review aims to provide a comprehensive overview for biomaterials in neuroengineering, highlighting their application in neural functional regaining and enhancement across both basic research and clinical practice. It covers recent developments in biomaterial-based products, including 2D to 3D bioprinted scaffolds for cell and organoid culture, brain-on-a-chip systems, biomimetic electrodes and brain–computer interfaces. It also explores artificial synapses and neural networks, discussing their applications in modeling neural microenvironments for repair and regeneration, neural modulation and manipulation and the integration of traditional Chinese medicine. This review serves as a comprehensive guide to the role of biomaterials in advancing neuroengineering solutions, providing insights into the ongoing efforts to bridge the gap between innovation and clinical application.