bluuebunny/crossref_metadata_2025_split huggingface dataset:
What Can Genome Sequence Data Reveal About Population Viability?
Authors: Kardos Marty , Keller Lukas F. , Funk W. Chris 
Published: December 2024

ABSTRACTBiologists have long sought to understand the impacts of deleterious genetic variation on fitness and population viability. However, our understanding of these effects in the wild is incomplete, in part due to the rarity of sufficient genetic and demographic data needed to measure their impact. The genomics revolution is promising a potential solution by predicting the effects of deleterious genetic variants (genetic load) bioinformatically from genome sequences alone bypassing the need for costly demographic data. After a historical perspective on the theoretical and empirical basis of our understanding of the dynamics and fitness effects of deleterious genetic variation, we evaluate the potential for these new genomic measures of genetic load to predict population viability. We argue that current genomic analyses alone cannot reliably predict the effects of deleterious genetic variation on population growth, because these depend on demographic, ecological and genetic parameters that need more than just genome sequence data to be measured. Thus, while purely genomic analyses of genetic load promise to improve our understanding of the composition of the genetic load, they are currently of little use for evaluating population viability. Demographic data and ecological context remain crucial to our understanding of the consequences of deleterious genetic variation for population fitness. However, when combined with such demographic and ecological data, genomic information can offer important insights into genetic variation and inbreeding that are crucial for conservation decision making.
Different Effects of Fixed Appliances and Clear Aligners on the Microbiome and Metabolome of Dental Plaque
Authors: Gong Wuyi , Zhou Kaiyong , Li Sijin , Yue Zhihang , Zhang Qiongyu , Li Yongming , Mi Xiaohui 
Published: December 2024

ABSTRACTObjectiveThis study aimed to uncover the microbial and metabolic changes in dental plaque during orthodontic treatments with fixed appliances (FAs) and clear aligners (CAs).Materials and MethodsTwenty participants were grouped by the treatment modality they received, with 10 participants each in the FA and CA groups. Supragingival plaques were collected before orthodontic treatment (T0), after 1–3 months (T1) and more than 6 months (T2) of orthodontic treatment. 16S rRNA gene sequencing and liquid chromatography–tandem mass spectrometry were employed to analyse the plaque samples.ResultsNo significant change was observed in the alpha and beta diversity at different time points and between the two treatment modalities. The relative abundance of genera Veillonella, Mogibacterium and unclassified_c__Actinobacteria, and species Actinomyces massiliensis, Prevotella pallens and Prevotella jejuni experienced the most significant changes. The most differential metabolites were amino acids, nucleosides and organoheterocyclic compounds. Compared to T0, downregulation of nucleotide metabolism at T1 and upregulation of amino acid metabolism at T2 were found in the FA group. Compared with the FA group, the CA group experienced metabolite enrichment in several immune pathways at T1, while linoleic acid metabolism, riboflavin metabolism and nucleotide metabolism were downregulated at T2 in the CA group. Significant correlations were identified between most differential plaque microorganisms and metabolites.ConclusionThis study implied that exposure to FAs for more than 6 months resulted in the accumulation of oral disease‐related bacteria in dental plaque and a metabolic shift towards a cariogenic state, whereas CAs could lead to a transient proinflammatory state.
The master relation for polynomiality and equivalences of integrable systems
Authors: Blot Xavier , Sauvaget Adrien , Shadrin Sergey 
Published: December 2024

AbstractWe prove the so‐called master relation in the tautological ring of the moduli space of curves that implies polynomial properties of the Dubrovin–Zhang hierarchies associated to different versions of cohomological field theories as well as their equivalences to the corresponding double ramification hierarchies.
MSEval: A Dataset for Material Selection in Conceptual Design to Evaluate Algorithmic Models
Authors: Patawari Jain Yash , Grandi Daniele , Groom Allin , Cramer Brandon , McComb Christopher 
Published: December 2024

Abstract
Material selection plays a pivotal role in many industries, from manufacturing to construction. Material selection is usually carried out after several cycles of conceptual design, during which designers iteratively refine the design solution and the intended manufacturing approach. In design research, material selection is frequently modeled as a structured decision-making process, where optimization techniques, whether single-objective or multiobjective, are employed to identify solutions that best meet the design requirements. However, traditional approaches can be limited by their reliance on existing knowledge and data, which may not adequately capture the full range of considerations involved in material selection. In this article, we introduce MSEval, a novel dataset comprised expert material evaluations across a variety of design briefs and criteria. This dataset is designed to serve as a benchmark to facilitate the evaluation and modification of machine learning models in the context of material selection for conceptual design. By focusing on a diverse set of design tasks and criteria, MSEval enables a more nuanced understanding of the material selection and the thought process, providing valuable insights for both human designers and AI systems.
Nonlinear Pressure Evolution in Wellbore During the Tubing Conveyed Perforation Process
Authors: Ding Liangliang , Wang Kejie , Zhang Lin , Lei Qisong , Peng Geng , Wang Min , Chen Wenkang 
Published: December 2024

Abstract
With increasing wellbore depth, the environmental conditions become progressively more severe, characterized by elevated temperatures and pressures. Consequently, the pressure variations within the well induced by Tubing Conveyed Perforation (TCP) operations exhibit a more pronounced intensity. These nonlinear pressure fluctuations generate significant impact loads at the bottom of the perforating gun, which can cause failure of the perforating tubing. A transient nonlinear pressure field model of perforation explosion was established based on hydraulic-mechanical coupling to effectively control the risk of accidents. The model considers the effects of several hundred perforation charges and their precise placement in relation to blind holes, thus taking into account the impact of shot density. As a result, the model more accurately reflects actual field conditions. The study investigated the evolution of nonlinear pressure fields at different positions of the entire tubing under perforation explosion and analyzed the influence of different factors on nonlinear pressure fluctuations at the bottom of the perforating gun. The results showed that the peak pressure of the perforation section was much higher than that of the tubing section and the rathole section, maintaining at approximately 200 MPa. The pressure wave attenuated to the initial wellbore pressure of about 80 MPa only seven meters away from the perforation section center. The peak pressure at the bottom of the perforating gun was positively correlated with the initial wellbore pressure, perforating fluid density, shot density, and quantity of explosive. When the explosive mass was the same, RDX explosive in RDX, HMX, HNS, and TNT caused the largest peak pressure at the bottom of the perforating gun, with TNT causing the smallest. These results provided guidance for the prediction of TCP wellbore nonlinear pressure fluctuation.
Biot Number Error in Low-Temperature Inconel Overall Effectiveness Experiments
Authors: Hopkins Bailey W. , Hughes Jacob A. , Bryant Carol E. , Rutledge James L. 
Published: December 2024

Abstract
To predict the performance of turbine materials at engine conditions, experiments are often performed at low-temperature laboratory conditions. In order to ensure the low-temperature, laboratory results accurately predict the nondimensionalized surface temperature at engine conditions, several nondimensional parameters must be matched in the experiment, including the Biot number. Matching the Biot number requires that the ratio of the thermal conductivity of the material to the thermal conductivity of the air must be matched between laboratory experiments and engine conditions. With traditional nickel alloys such as Inconel, it is sometimes assumed that the Biot number is matched since Inconel's thermal conductivity variation with temperature scales relatively closely with that of air. However, the thermal conductivity ratio does not scale perfectly and therefore some Biot number error does indeed exist, with the problem exacerbated at lower testing temperatures. To date, there has been no experimentally verified quantification of the error in the overall effectiveness, ϕ, that might be caused by this Biot number error. Ti-6Al-4V is predicted to allow for a better Biot number match, thereby better simulating Inconel at engine conditions in typical low-temperature experiments. In this research, we utilized geometrically identical models constructed of Ti-6Al-4V and Inconel 718 to evaluate the error in overall effectiveness that might occur through simply using an actual engine nickel alloy part at experimental conditions. While the Ti-6Al-4V model has a nearly perfectly matched Biot number, the Inconel model's Biot number was 73% higher than appropriate. The results demonstrate that ϕ measured in low-temperature tests performed on an Inconel turbine component do not suffer markedly from Biot number error. The theoretically more Biot number appropriate Ti-6Al-4V model produced area-averaged overall effectiveness values that differed by only 0.01 from its Inconel counterpart. These results suggest that typical nickel superalloys used in turbine components may be tested at low temperature without the use of a surrogate material to better match Biot number.
Genome sequences of bacteriophages that infect
Salmonella
Typhi from Bangladesh
Authors: Islam Shuborno , Kabiraj Rathindranath , Sarkar Himadree , Dev Preonath Chondrow , Tanni Afroza Akter , Keya Deb Purna , Malakar Apurba Rajib , Tanmoy Arif Mohammad , Saha Samir K. , Hooda Yogesh , Saha Senjuti 
Published: December 2024

ABSTRACT

This report presents near-complete genome sequences of 14 bacteriophages that infect
Salmonella
Typhi, identified through environmental surveillance in Bangladesh between August 2021 and June 2022. The bacteriophages, belonging to the genera
Kayfunavirus
,
Macdonaldcampvirus
, and
Teseptimavirus
, exhibit high degrees of sequence similarity and conserved genetic features with previously reported Typhi bacteriophages.
Whole-genome sequence of non-rhizobial strain
Tardiphaga
sp. 709 isolated from the root nodule of
Astragalus inopinatus
Borris., growing on the Kamchatka Peninsula
Authors: Guro Polina , Kuznetsova Irina , Sazanova Anna , Belimov Andrey , Safronova Vera 
Published: December 2024

ABSTRACT

We report the whole-genome sequence of the non-rhizobial endosymbiotic bacteria
Tardiphaga
sp. strain 709, which was isolated from the root nodule of
Astragalus inopinatus
Borris. on the Kamchatka Peninsula, Russia. The genome consists of one chromosome and one plasmid with a total length of 6,359,564 bp and 61.5% of GC content.
Multimedia: multimodal mediation analysis of microbiome data
Authors: Jiang Hanying , Miao Xinran , Thairu Margaret W. , Beebe Mara , Grupe Dan W. , Davidson Richard J. , Handelsman Jo , Sankaran Kris 
Published: December 2024

ABSTRACT

Mediation analysis has emerged as a versatile tool for answering mechanistic questions in microbiome research because it provides a statistical framework for attributing treatment effects to alternative causal pathways. Using a series of linked regressions, this analysis quantifies how complementary data relate to one another and respond to treatments. Despite these advances, existing software’s rigid assumptions often result in users viewing mediation analysis as a black box. We designed the multimedia R package to make advanced mediation analysis techniques accessible, ensuring that statistical components are interpretable and adaptable. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis, enabling experimentation with various mediator and outcome models while maintaining a simple overall workflow. The software includes modules for regularized linear, compositional, random forest, hierarchical, and hurdle modeling, making it well-suited to microbiome data. We illustrate the package through two case studies. The first re-analyzes a study of the microbiome and metabolome of Inflammatory Bowel Disease patients, uncovering potential mechanistic interactions between the microbiome and disease-associated metabolites, not found in the original study. The second analyzes new data about the influence of mindfulness practice on the microbiome. The mediation analysis highlights shifts in taxa previously associated with depression that cannot be explained indirectly by diet or sleep behaviors alone. A gallery of examples and further documentation can be found at
https://go.wisc.edu/830110
.

IMPORTANCE
Microbiome studies routinely gather complementary data to capture different aspects of a microbiome’s response to a change, such as the introduction of a therapeutic. Mediation analysis clarifies the extent to which responses occur sequentially via mediators, thereby supporting causal, rather than purely descriptive, interpretation. Multimedia is a modular R package with close ties to the wider microbiome software ecosystem that makes statistically rigorous, flexible mediation analysis easily accessible, setting the stage for precise and causally informed microbiome engineering.
Trichobezoar, a Cause of Nonspecific Acute Abdominal Pain: Four Case Reports and Bibliographic Review
Authors: Perez Lopez Ruben Daniel , Carbajal Cabrera Pabel Ruben , Sempere Alvarado Laura Gabriela , Narváez González Hugo Fernando , Avila Rosales Angel , Velázquez Jaimes Ashley Zulema , Figueroa Morales Daniela , Flores de la Canal Cintia , Embriz Sánchez Alejandro Juan , Reyna Marzano Julio Federico 
Published: December 2024

Background: A bezoar is defined as a foreign body resulting from the accumulation of ingested material or food in the stomach. However, they can also be found in the duodenum and other segments of the intestine. The average age of occurrence is 11 years, predominantly affecting females. Among its complications, gastric outlet obstruction is the most frequent, though secondary gastric perforation is extremely rare.Material and Methods: Four clinical cases are presented from a third‐level care facility in Mexico City over the period 2022–2024, all resolved surgically.Results: Four clinical cases involved females aged between 11 and 14 years. All cases presented with generalized abdominal pain, an epigastric mass, nausea, and vomiting. In one case, a gastric perforation occurred. Postsurgical complications included superficial surgical site infections in two cases, an average of 5 days of nil per oral (NPO), and an average hospital stay of 9.2 days. All patients were referred to the pediatric psychiatry service for follow‐up after discharge.Conclusion: Trichobezoar is a rare pathology with a marked incidence in our population, having multiple cases within such a short period. This situation provides a new path to establish an epidemiological basis in our Mexican population and to explore the link between these clinical cases, offering insights into their causes, symptoms, and treatment options.
Characteristics and Effectiveness of XP‐Endo Files and Systems: A Narrative Review
Authors: Alkahtany Sarah M. , Alfadhel Rana , AlOmair Aseel , Durayhim Sarah Bin 
Published: December 2024

Background: XP‐endo files are composed of Max‐Wire alloy, which was developed by FKG Dentaire (La Chaux‐de‐Fonds, Switzerland). This alloy, known as Martensite‐Austenite Electropolish Flex, is the first NiTi alloy used in endodontics to combine the shape memory effect with superelasticity for use in clinical practice.Objective: This article aims to provide a comprehensive overview of the existing knowledge and evidence regarding different XP‐endo files and systems, XP‐endo Finisher (XPEF), XP‐endo Shaper (XPES), XP‐endo Retreatment (XPER), XP‐endo Rise (XPE‐Rise), and XPE‐Rise Retreatment (XPE‐Rise‐R), to help clinicians understand their different properties and recommended clinical uses. Moreover, this review aims to identify future research opportunities in this field.Materials and Methods: A search was performed in the PubMed database using the keywords “XP endo” or “XP‐endo”. A total of 309 studies were identified during the initial search, and then initial abstract screening was conducted. The inclusion criteria included any study that aimed to evaluate XP endo files and systems on permanent teeth, either in vivo or in vitro. We excluded studies that were unrelated to the subject, literature reviews, case studies, and studies that employed deciduous teeth. Finally, we performed an extensive review of the selected 130 studies, which we assessed, summarized, and classified based on the specific XP‐endo file used.Conclusion: Overall, XP‐endo files offer significant improvements in endodontic treatment. XPEF excels in irrigation activation and medicament removal, and XPES succeeds in canal cleaning, shaping, and retreatment. The XPER system, which incorporates the XPEF‐R file, shows promise in removing root‐filling materials, but its performance is inconsistent compared to other retreatment systems. We have found limited information regarding the latest XPE‐Rise and XPE‐Rise‐R systems, additional research is required to fully determine their comparative effectiveness and optimize their clinical application.
Young‐Onset Diabetes in Sri Lanka: Experience From the Developing World
Authors: Arambewela Maulee Hiromi , Mathara Diddhenipothage Shani A. D. , Subasinghe Chandrika Jayakanthi , Wijenayake Umesha Nuwanrasee , Jayakody Surangi , Ratnayake Gowri M. , Antonypillai Charles , Abhayaratne Sachith , Garusinghe Chaminda , Katulanda Prasad , Somasundaram Noel , Bulugahapitiya Uditha , Sumanatilleke Manilka , Wijesinghe Achini , Muthukuda Dimuthu , Pathmanathan Sivatharshya , Samarasekara Tharanga , Kaluarachchi V. T. S. , Samarasinghe Gayani , de Silva Nipun Lakshitha , Seneviratne Sumudu Nimali , Suntharesan Jananie , Gunatilake Sonali Sihindi Chapa 
Published: December 2024

Background: Young‐onset diabetes (YOD) is characterised by unique diagnostic and management challenges more pronounced in resource‐limited settings like Sri Lanka.Aims: We aimed to ascertain the prevalence, patterns and characteristics of YOD in Sri Lanka and describe the state of care.Methods: Retrospective review of baseline data of all patients enrolled in the prospective multicentre Database for Young‐Onset Diabetes, Sri Lanka (DYOD‐SL), was performed, from April 2021 to April 2023.Results: A total of 2531 patient data were included from 28 centres island‐wide. Females were 57.6%. The median age was 20 years (interquartile range (IQR) 17, 23), and the age at diagnosis was 15 years (IQR 12, 18). Type 1 diabetes (T1D) was the commonest (57.6%), followed by Type 2 diabetes (T2D) at 34.3%. Younger age at disease onset (p < 0.001), lower BMI (p < 0.001), and diabetic ketoacidosis (DKA) at presentation (p < 0.001) favoured T1D. In the total cohort, the median HbA1c was 9.8% (IQR 7.8, 12.1) with younger patients having poorer control (p = 0.001). Prevalence of nephropathy was 8.1%, retinopathy was 6.6%, neuropathy was 4.1%, moderate–high‐risk diabetic foot disease was 1.9%, and macrovascular complications were 0.5%. Hypertension and dyslipidaemia occurred in 2.7% and 14%, respectively. Among patients > 18 years, overweight and obese were 22.2% and 10.4%. Corresponding prevalence in the 5–18‐year age group was 20% and 14.7%. Among the insulin users (76%) in the total cohort, the majority (64.7%) were on premixed‐based insulin regimens delivered by syringes. Self‐monitoring of blood glucose (BG) was reported in 71.3% of the total population. None were on continuous/flash glucose monitoring or insulin pumps.Conclusion: T1D was the commonest subtype of YOD in this hospital‐based population. However, T2D was notably higher and is of significant concern. Overall, suboptimal glycaemic control and high rate of complications were noted along with substandard insulin regimens and BG monitoring.
Cytotoxicity, Antiadipogenic, Low‐Density Lipoprotein Oxidation Inhibitory Activities, and Acute Toxicity Study of Psychotria densinervia Hydroethanolic Leaf and Bark Extracts
Authors: Mba Jean Romuald , Zouheira Djamila , Guetchueng Stephanie Tamdem , Daïrou Hadidjatou , Djouonzo Paul Toukam , Ayong Lawrence , Kuiate Jules-Roger , Agbor Gabriel A. 
Published: December 2024

Background: Obesity is increasingly taking an important stage as a cause of death worldwide, and interventions with a good cost‐effectiveness ratio are needed. Psychotria densinervia is one of these natural products with health benefits. Objective. The present study evaluated the cytotoxicity, antiadipogenic, low‐density lipoprotein (LDL), oxidation inhibitory activities, and acute toxicity of Psychotria densinervia hydroethanolic leaf and bark extracts.Methods: The cytotoxicity evaluation of the extracts (62.5, 125, 250, and 500 μg/mL) using the MTT assay and the antiadipogenic activity (25, 50, 100, and 200 μg/mL) using oleic acid were carried out in SW‐872 cells. Copper sulfate (CuSO4)‐induced oxidation was used in the evaluation of the effect of extracts (0.25, 0.5, and 1 mg/mL) against LDL oxidation. The oral acute toxicity evaluation of a single dose of 2000 mg/kg of the extracts was performed in Wistar albino rats weighing 127 ± 2 g.Results: The leaf and bark extracts did not show any sign of cytotoxicity at the tested concentrations. The best antiadipogenic activity was observed by the standard orlistat (38.45 ± 1.70 μg/mL), followed by the leaf extract (IC50: 41.47 ± 0.50 μg/mL) and the least the bark extract (IC50: 107.50 ± 0.90 μg/mL). At a concentration of 1 mg/mL, the leaf extract presented an oxidation lag time of 130 min, which was higher and better than that of the bark extract (120 min). Quercetin (standard) presented an oxidation lag time longer than 3 h. The oral acute toxicity evaluation did not show any signs of toxicity indicating that the LD50 was greater than 2000 mg/kg.Conclusion: Based on the results obtained, the P. densinervia hydroethanolic leaf extract possesses a better antioxidant and antiadipogenic activities than the bark extract.