bluuebunny/crossref_metadata_2025_split huggingface dataset:
MinLinMo: a minimalist approach to variable selection and linear model prediction
Authors: Bohlin Jon , Håberg Siri E. , Magnus Per , Gjessing Håkon K. 
Published: December 2024

AbstractGenerating prediction models from high dimensional data often result in large models with many predictors. Causal inference for such models can therefore be difficult or even impossible in practice. The stand-alone software package MinLinMo emphasizes small linear prediction models over highest possible predictability with a particular focus on including variables correlated with the outcome, minimal memory usage and speed. MinLinMo is demonstrated on large epigenetic datasets with prediction models for chronological age, gestational age, and birth weight comprising, respectively, 15, 14 and 10 predictors. The parsimonious MinLinMo models perform comparably to established prediction models requiring hundreds of predictors.
Revealing genes related teat number traits via genetic variation in Yorkshire pigs based on whole-genome sequencing
Authors: Wei Jialin , Sun Jingchun , Pan Yi , Cao Minghao , Wang Yulong , Yuan Tiantian , Guo Ao , Han Ruihua , Ding Xiangdong , Yang Gongshe , Yu Taiyong , Ding Rongrong 
Published: December 2024

Abstract
Background
Teat number is one of the most important indicators to evaluate the lactation performance of sows, and increasing the teat number has become an important method to improve the economic efficiency of farms. Therefore, it is particularly important to deeply analyze the genetic mechanism of teat number traits in pigs. In this study, we detected Single Nucleotide Ploymorphism (SNP), Insertion-Deletion (InDel) and Structural variant (SV) by high-coverage whole-genome resequencing data, and selected teat number at birth and functional teat number as two types of teat number traits for genome-wide association study (GWAS) to reveal candidate genes associated with pig teat number traits.

Results
In this study, we used whole genome resequencing data from 560 Yorkshire sows to detect SNPs, InDels and SVs, and performed GWAS for the traits of born teat number and functional teat number, and detected a total of 85 significant variants and screened 214 candidate genes, including HEG1, XYLT1, SULF1, MUC13, VRTN, RAP1A and NPVF. Among them, HEG1 and XYLT1 were the new candidate genes in this study. The co-screening and population validation of multiple traits suggested that HEG1 may have a critical effect on the born teat number.

Conclusion
Our study shows that more candidate genes associated with pig teat number traits can be identified by GWAS with different variant types. Through large population validation, we found that HEG1 may be a new key candidate gene affecting pig teat number traits. In conclusion, the results of this study provide new information for exploring the genetic mechanisms affecting pig teat number traits and genetic improvement of pigs.
Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet
Authors: Luo Wei , Sun Min , Zhang Ailing , Lin Chuang , Jin Yarong , Wang Xiaoshan , Huang Linkai 
Published: December 2024

Abstract
Background
Pearl millet (Pennisetum glaucum (L.) R. Br.) is a vital cereal crop, predominantly cultivated in arid and semi-arid regions of Asia and Africa. It serves as a staple food for millions, while also being utilized as forage and an energy crop. The crop’s resistance to heat and drought, coupled with its high biomass, positions it as a promising candidate for climate-resilient agriculture. A detailed understanding of its gene expression patterns across various tissues and developmental stages is essential for enhancing its yield and quality. This study aims to fill this knowledge gap by employing RNA-seq to identify housekeeping genes (HKGs) and tissue-specific genes (TSGs) in pearl millet.

Results
Our analysis of RNA-seq data from nine tissues (seed, germ, radicle, leaf, root, tillering tissue, stem, spike, and grain) across eight developmental stages in pearl millet accession Tifleaf3 revealed a comprehensive gene expression profile. We identified 461 HKGs that exhibited stable expression across all tissues and stages, providing robust internal references for RT-qPCR. Additionally, 8091 TSGs were discovered, many of which showed distinctive expression patterns in tissues such as spike, stem, and leaf. Functional enrichment analysis of these genes using GO and KEGG pathways highlighted their roles in key biological processes and pathways, indicating their potential in crop trait enhancement. Protein-protein interaction networks constructed for stem and leaf tissues further illuminated the regulatory mechanisms underlying the transition from vegetative to reproductive growth stages.

Conclusion
This study presents a detailed transcriptomic landscape of pearl millet, identifying a set of HKGs and TSGs that are crucial for understanding the molecular basis of its growth and development. We provided valuable options for transcript normalization and crucial targets for exploring gene function for the plant growth and development in pearl millet. The insights gained from this work are instrumental for breeding programs aimed at enhancing the productivity of pearl millet, thereby contributing to food and energy security.
Genomic analyses revealed low genetic variation in the intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso
Authors: Kientega Mahamadi , Morianou Ioanna , Traoré Nouhoun , Kranjc Nace , Kaboré Honorine , Zongo Odette N , Millogo Abdoul-Azize , Epopa Patric Stephane , Yao Franck A. , Belem Adrien M G , Austin Burt , Diabaté Abdoulaye 
Published: December 2024

Abstract
Background
The recent success of a population control gene drive targeting the doublesex gene in Anopheles gambiae paved the way for developing self-sustaining and self-limiting genetic control strategies targeting the sex determination pathway to reduce and/or distort the reproductive capacity of insect vectors. However, targeting these genes for genetic control requires a better understanding of their genetic variation in natural populations to ensure effective gene drive spread. Using whole genome sequencing (WGS) data from the Ag1000G project (Ag3.0, 3.4 and 3.8), and Illumina pooled amplicon sequencing, we investigated the genetic polymorphism of the intron-4–exon-5 boundary of the doublesex gene in the natural populations of An. gambiae sensu lato (s.l.).

Results
The analyses showed a very low variant density at the gRNA target sequence of the Ag(QFS)1 gene drive (previously called dsxFCRISPRh) within the populations of West and East Africa. However, populations from the forest area in Central Africa exhibited four SNP at frequencies ranging from 0.011 to 0.26. The SNP (2R:48714641[C > T]) at high frequencies, i.e. 0.26 is identified within the An. coluzzii population from Angola. The analyses also identified 90 low frequency (1 − 5%) SNPs in the genomic region around the gRNA target sequence (intron-4–exon-5 boundary). Three of these SNPs (2R:48714472 A > T; 2R:48714486 C > A; 2R:48714516 C > T) were observed at frequencies higher than 5% in the UTR region of the doublesex gene. The results also showed a very low variant density and constant nucleotide diversity over a five-year survey in natural An. gambiae s.l. populations of Burkina Faso.

Conclusion
These findings will guide the implementation of doublesex-targeted gene drives to support the current control tools in malaria elimination efforts. Our methods can be applied to efficiently monitor the evolution of any sequence of interest in a natural population via pooled amplicon sequencing, surpassing the need for WGS.
Accuracy of symptom checker for the diagnosis of sexually transmitted infections using machine learning and Bayesian network algorithms
Authors: Soe Nyi Nyi , Towns Janet M , Latt Phyu Mon , Woodberry Owen , Chung Mark , Lee David , Ong Jason J , Chow Eric P.F. , Zhang Lei , Fairley Christopher K. 
Published: December 2024

Abstract
Background
A significant proportion of individuals with symptoms of sexually transmitted infection (STI) delay or avoid seeking healthcare, and digital diagnostic tools may prompt them to seek healthcare earlier. Unfortunately, none of the currently available tools fully mimic clinical assessment or cover a wide range of STIs.

Methods
We prospectively invited attendees presenting with STI-related symptoms at Melbourne Sexual Health Centre to answer gender-specific questionnaires covering the symptoms of 12 common STIs using a computer-assisted self-interviewing system between 2015 and 2018. Then, we developed an online symptom checker (iSpySTI.org) using Bayesian networks. In this study, various machine learning algorithms were trained and evaluated for their ability to predict these STI and anogenital conditions. We used the Z-test to compare their average area under the ROC curve (AUC) scores with the Bayesian networks for diagnostic accuracy.

Results
The study population included 6,162 men (median age 30, IQR: 26–38; approximately 40% of whom had sex with men in the past 12 months) and 4,358 women (median age 27, IQR: 24–31). Non-gonococcal urethritis (NGU) (23.6%, 1447/6121), genital warts (11.7%, 718/6121) and balanitis (8.9%, 546/6121) were the most common conditions in men. Candidiasis (16.6%, 722/4538) and bacterial vaginosis (16.2%, 707/4538) were the most common conditions in women. During evaluation with unseen datasets, machine learning models performed well for most male conditions, with the AUC ranging from 0.81 to 0.95, except for urinary tract infections (UTI) (AUC 0.72). Similarly, the models achieved AUCs ranging from 0.75 to 0.95 for female conditions, except for cervicitis (AUC 0.58). Urethral discharge and other urinary symptoms were important features for predicting urethral gonorrhoea, NGU and UTIs. Similarly, participants selected skin images that were similar to their own lesions, and the location of the anogenital skin lesions were also strong predictors. The vaginal discharge (odour, colour) and itchiness were important predictors for bacterial vaginosis and candidiasis. The performance of the machine learning models was significantly better than Bayesian models for male balanitis, molluscum contagiosum and genital warts (P < 0.05) but was similar for the other conditions.

Conclusions
Both machine learning and Bayesian models could predict correct diagnoses with reasonable accuracy using prospectively collected data for 12 STIs and other common anogenital conditions. Further work should expand the number of anogenital conditions and seek ways to improve the accuracy, potentially using patient collected images to supplement questionnaire data.
Differential somatic coding variant landscapes between laser microdissected luminal epithelial cells from canine mammary invasive ductal solid carcinoma and comedocarcinoma
Authors: Deckwirth Vivi , Hundi Sruthi , Hytönen Marjo K. , Hannula Sari , Ellonen Pekka , Björkenheim Pia , Sukura Antti , Lohi Hannes 
Published: December 2024

Abstract
Background
Breast cancer (BC) is the most common cancer in women. Likewise, canine mammary tumors (CMT) represent the most common cancer in intact female dogs and develop in the majority spontaneously. Similarities exist in clinical presentation, histopathology, biomarkers, and treatment. However, CMT subtype-specific genomic background is less investigated. Here, we assess the genetic etiology of two histomorphological (HM) subtypes with BC counterparts, the CMT invasive ductal simple solid carcinoma (SC) and comedocarcinoma (CC), and compare the results with BC data.

Methods
Groups of 11–13 transformed ductal luminal epithelial cells were laser-capture microdissected from snap-frozen invasive mammary SC and CC subtypes of one intact female dog. HM unaffected lobular luminal epithelial cells were controls. Single-cell whole genome libraries were generated using PicoPLEX and sequenced to compare the subtypes’ somatic coding variant landscapes with each other and with BC data available in COSMIC-CGC and KEGG. Furthermore, HM and immunohistochemical (IHC) subtype characteristics were compared with the genomic results.

Results
The CC had six times more variants than the SC. The SC showed variants in adherens junction genes and genes of the MAPK, mTOR and NF-kappa-B signaling pathways. In the CC, the extracellular matrix (ECM) receptor interaction, cell adhesion, PI3K-Akt and cGMP-PKG pathways were enriched, reflecting the higher cellular malignancy. Affected pathways in both CMT subtypes overlapped with BC pathways in KEGG. Additionally, we identified ATP6V1C2, GLYATL3, CARMIL3, GATAD2B, OBSCN, SIX2, CPEB3 and ZNF521 as potential new subtype-distinct driver genes. Furthermore, our results revealed biomarker alterations in IHC in the basal/myoepithelial cell layer without respective genetic mutations, suggesting changes to their complex signaling pathways, disturbed regulative feedback loops or other silencing mechanisms.

Conclusions
This study contributes to understanding the subtype-specific molecular mechanisms in the canine mammary invasive ductal simple SC and CC, and revealed subtype-specific molecular complexity for phenotypically similar characteristics. Several affected genes and signaling pathways overlapped with BC indicating the potential use of CMT as model for BC. Our findings emphasize the need for thorough characterization of cancer specimens with respect to translational cancer research, but also how insight into tumor heterogeneity will be crucial for the development of targeted prognostics and therapeutic interventions.
Evaluation of N-NOSE as a surveillance tool for recurrence in gastric and esophageal cancers: a prospective cohort study
Authors: Iitaka Sayuri , Kuroda Akihiro , Narita Tomonori , Hatakeyama Hideyuki , Morishita Masayo , Ungkulpasvich Umbhorn , Hirotsu Takaaki , di Luccio Eric , Yagi Koichi , Seto Yasuyuki 
Published: December 2024

Abstract
Objective
Early detection of recurrent gastric and esophageal cancers remains a critical challenge. Innovative and non-invasive cancer screening technologies, such as N-NOSE, can improve early detection. N-NOSE is a urine-based scent test that leverages the olfactory abilities of the nematode C. elegans. For the first time, this prospective study evaluates the efficacy of the N-NOSE chemotaxis index as a novel biomarker for postoperative surveillance and recurrence in patients with upper gastrointestinal cancers.

Methods
A two-year prospective cohort study was conducted at The University of Tokyo Hospital, involving 40 patients with gastric and esophageal cancers. Urine samples were collected pre- and postoperatively and analysed using the N-NOSE technique.

Results
In cases of recurrence with vascular invasion, the chemotaxis index at 100-fold urine dilution was significantly elevated compared to the non-recurrence group.

Conclusion
This study suggests the potential of N-NOSE as an effective follow-up tool for patients with upper gastrointestinal cancer, particularly those with vascular invasion. While N-NOSE has been validated to distinguish between cancer and non-cancer, and its performance compared to traditional markers has been proven, it has not been studied for recurrence. Our data highlights, for the first time, the capability of N-NOSE in the surveillance of cancer recurrence.
The limited clinical utility of a routine creatine kinase (CK) on admission to a psychiatric inpatient unit
Authors: Scott Fraser A. M. , Butler Matt , Rogers Jonathan P. 
Published: December 2024

Abstract
Background
Creatine kinase (CK) is an intracellular enzyme expressed most commonly in tissues such as skeletal muscle. CK can be used as an investigation to support the diagnosis of conditions such as neuroleptic malignant syndrome (NMS), a rare idiosyncratic drug reaction – classically to antipsychotic medications – which can be fatal. Routine screening of CK in psychiatric inpatients is a known practice, but its value is uncertain. We aimed to ascertain whether such screening resulted in new diagnoses of NMS or other conditions, and changes in clinical management.

Methods
Using an electronic case register, we conducted a descriptive retrospective cohort study, identifying all psychiatric inpatient admissions in a South London mental health trust over a four-year period where a CK test was conducted within 48 h of admission. We extracted the demographic and clinical characteristics (e.g., diagnosis) of those who met inclusion criteria. Free-text review was performed on all those with a CK potentially suggestive of NMS (CK ≥ 4x upper limit of normal reference range (ULN)) to determine the impact of this abnormal result on subsequent management and diagnosis (including NMS if identified).

Results
Of 14,236 inpatient episodes in the specified window, 2358 (16.6%) had a CK test within 48 h of admission. This was ≥ 4x ULN in 327 (13.8%) cases (free-text successfully reviewed in 318). There were no cases of NMS identified. An abnormal CK result led to a new alternative diagnosis, such as dehydration or catatonia, in only 14 patients (4.4% raised CK sample, 0.6% total CK sample). Impact on subsequent management appeared limited, with the most common adjustment being an increase in frequency of physical observations in 47 instances (14.8%).

Conclusions
The clinical utility of untargeted screening using a serum CK for psychiatric inpatients appears limited, with poor specificity in detection of NMS and a minimal impact on subsequent clinical management.
Association between adherence to behavioral intervention and capability well-being among parents of autistic children: a cross-sectional study from China
Authors: Zhang Huanyu , Chen Shanquan , Yu Jiazhou , Niu Xuejing , Wang Xue , Wang Li 
Published: December 2024

Abstract
Background
High adherence to behavioral interventions among parents of autistic children contribute to improvement in children’s behaviors and parental outcomes. However, most of previous studies focused on the effects of intervention adherence on health-related well-being among parents, which is inadequate to capture the multi-dimensional parental burden of caring for autistic children. The aim of this study is to assess the association between parents’ adherence to behavioral intervention and their capability well-being.

Methods
A cross-sectional study was conducted among caregivers of autistic children aged 1–17 years with a confirmed diagnosis in China. A total of 213 parents of autistic children who were currently receiving behavioral intervention were considered in this study. Parental adherence to behavioral intervention was evaluated by the 5-item General Adherence subscale of the Medical Outcome Study. Capability well-being was assessed using the Investigating Choice Experiments Capability Measures for Adults (ICECAP-A), including the domains of stability, attachment, autonomy, achievement, and enjoyment. The index scores for each domain were computed based on the preference-based value set in the United Kingdom, ranging from 0 to 1. Multivariate linear regression analyses were conducted to assess the relationship between intervention adherence and parental well-being. Intervention adherence as well as the variables with p < 0.1 in the univariate analyses were included in multivariate linear regression analyses.

Results
The mean overall score of ICECAP-A was 0.681 (0.205). In the univariate analyses, intervention adherence was positively associated with stability, autonomy, achievement, and enjoyment (p < 0.05), while the relationship between intervention adherence and attachment was not significant (p = 0.07). After controlling for the confounders in the multivariate linear regression analyses, intervention adherence was positively associated with achievement (β = 0.0004) and enjoyment (β = 0.0004).

Conclusions
The overall capability well-being among parents of autistic children was worse than that of the general population and caregivers of adult patients with chronic diseases. Adherence to behavioral interventions was positively associated with parental well-being in terms of achievement and enjoyment. Health professionals should involve parents in behavioral interventions and encourage them to implement therapeutic strategies on a routine basis. Customized interventions are warranted to improve capability well-being targeting at vulnerable groups.
Components of joint health and wellbeing strategies: a pan-London review of all 33 local authorities
Authors: Asmar Marie Line El , Karki Manisha , Mall Bathsheba , Riboli-Sasco Eva , El-Osta Austen 
Published: December 2024

Abstract
Background
In the UK, Health and Wellbeing Strategies (JHWS) were introduced to identify and help address the health needs of local communities. JHWS translate a borough’s Joint Strategic Needs assessment into actionable outcomes and prioritises areas of focus, but the content and approach of JHWS may vary across different local authorities (LAs) due to demographic and priority differences.

Objective
Characterise the key health and wellbeing components of existing and emerging health and wellbeing strategies of 33 local authorities in London.

Design
Scoping review study with content assessment.

Methods
An online search was conducted to identify JHWS documents. This search was supplemented with outreach to health and wellbeing boards to ensure that the latest documents were retrieved. A set of 62 health and wellbeing themes and words to be captured spanning 13 categories was developed by a team of researchers, and data collection was independently carried out by two researchers. Occurrences of words in the strategy documents were recorded, and a configuration matrix was created and used to determine data trends across the local authorities. A broad search of the context in which the search terms appeared was also performed to understand the trends.

Results
Thirty-three JHWS were analysed to identify key search term frequencies. The analysis encompassed strategies from 2015 to 2030, ranging from 7 to 94 pages. Mental health and youth terms emerged as the two top priorities across all strategies. Other frequent terms were related to access to healthcare, inequality, employment, smoking, housing, carers, and elderly individuals. Conversely, terms related to dental health, pollution, nutrition, sexual health, green spaces, breastfeeding, and climate were less cited.

Conclusion
This analysis provides insights into regional health priorities and a comprehensive overview of health and wellbeing strategies across London's local authorities. Despite certain limitations, the findings offer valuable insights for local authorities' strategic planning and future research.