bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction for yield and malting traits in barley using metabolomic and near-infrared spectra
Authors: Raffo Miguel A. , Sarup Pernille , Jensen Just , Guo Xiangyu , Jensen Jens D. , Orabi Jihad , Jahoor Ahmed , Christensen Ole F. 
Published: January 2025

Abstract

Key message
Genetic variation for malting quality as well as metabolomic and near-infrared features was identified. However, metabolomic and near-infrared features as additional omics-information did not improve accuracy of predicted breeding values.

Abstract
Significant attention has recently been given to the potential benefits of metabolomics and near-infrared spectroscopy technologies for enhancing genetic evaluation in breeding programs. In this article, we used a commercial barley breeding population phenotyped for grain yield, grain protein content, and five malting quality traits: extract yield, wort viscosity, wort color, filtering speed, and β-glucan, and aimed to: (i) investigate genetic variation and heritability of metabolomic intensities and near-infrared wavelengths originating from leaf tissue and malted grain, respectively; (ii) investigate variance components and heritabilities for genomic models including metabolomics (GOBLUP-MI) or near-infrared wavelengths (GOBLUP-NIR); and (iii) evaluate the developed models for prediction of breeding values for traits of interest. In total, 639 barley lines were genotyped using an iSelect9K-Illumina barley chip and recorded with 30,468 metabolomic intensities and 141 near-infrared wavelengths. First, we found that a significant proportion of metabolomic intensities and near-infrared wavelengths had medium to high additive genetic variances and heritabilities. Second, we observed that both GOBLUP-MI and GOBLUP-NIR, increased the proportion of estimated genetic variance for grain yield, protein, malt extract, and β-glucan compared to a genomic model (GBLUP). Finally, we assessed these models to predict accurate breeding values in fivefold and leave-one-breeding-cycle-out cross-validations, and we generally observed a similar accuracy between GBLUP and GOBLUP-MI, and a worse accuracy for GOBLUP-NIR. Despite this trend, GOBLUP-MI and GOBLUP-NIR enhanced predictive ability compared to GBLUP by 4.6 and 2.4% for grain protein in leave-one-breeding-cycle-out and grain yield in fivefold cross-validations, respectively, but differences were not significant (P-value > 0.01).
Gradient-based smoothing parameter estimation for neural P-splines
Authors: Dammann Lea M. , Freitag Marei , Thielmann Anton , Säfken Benjamin 
Published: January 2025

Abstract
Due to the popularity of deep learning models there have recently been many attempts to translate generalized additive models to neural nets. Generalized additive models are usually regularized by a penalty in the loss function and the magnitude of penalization is controlled by one or more smoothing parameters. In the statistical literature these smoothing parameters are estimated by criteria such as generalized cross-validation or restricted maximum likelihood. While the estimation of the primary regression coefficients is well calibrated and investigated for neural net based additive models, the estimation of smoothing parameters is often either based on testing data (and grid search), implicitly estimated or completely neglected. In this paper, we address the issue of explicit smoothing parameter estimation in neural net-based additive models fitted via gradient-based methods, such as the well-known Adam algorithm. We therefore investigate the data-driven smoothing parameter selection via gradient-based optimization of generalized cross-validation and restricted maximum likelihood. Thus we do not need to calculate Hessian information of the smoothing parameters. As an additive model structure, we use a translation of P-splines to neural nets, so-called neural P-splines. The fitting process of neural P-splines as well as the gradient-based smoothing parameter selection are investigated in a simulation study and an application.
Association Between Cesarean Scar and Pelvic Floor Muscle Tone at 6–8 Weeks Postpartum
Authors: Xiao Li , Huang Nan , Zhong Yanbiao , Luo Yun , Wang Maoyuan 
Published: January 2025

Abstract
Introduction and Hypothesis
The relationship between cesarean section scars and active pelvic floor muscle tone lacks sufficient evidence. This study is aimed at investigating the relationship between the severity of cesarean section scars and active pelvic floor muscle tone in postpartum women.

Methods
We conducted a prospective cross-sectional study of 604 women at 6–8 weeks postpartum. Active pelvic floor muscle tone was assessed using the Glazer protocol, and scar severity was categorized as no scar, normal scar, and hypertrophic scar. We collected data on demographic and clinical variables, including age, body mass index (BMI), and comorbidities. Linear regression analysis was employed to assess the association between scar severity and active pelvic floor muscle tone, adjusting for potential confounders.

Results
Compared with the no scar group, the normal scar group exhibited higher levels of active pelvic floor muscle tone (β = 1.68 and 1.47), and the hypertrophic scar group had the highest levels of active pelvic floor muscle tone (β = 5.09 and 5.03). Active pelvic floor muscle tone was significantly higher in women with scars than in those without scars. The association remained significant after adjusting for age, BMI, and comorbidities. Moreover, women with hypertrophic scars exhibited higher active pelvic floor muscle tone than those with normal scars.

Conclusions
Cesarean section scar severity is positively associated with increased active pelvic floor muscle tone in postpartum women. This finding highlights the importance of scar management and targeted pelvic floor rehabilitation to optimize postpartum recovery.
Hybrid Pennisetum colonization by Bacillus megaterium BM18-2 labeled with green fluorescent protein (GFP) under Cd stress
Authors: Kamal Nehal , Qian Chen , Hao Huanhuan , Wu Juanzi , Liu Zhiwei , Zhong Xiaoxian , Ghanem Osama M. , Salem Ali , Orban Zoltan , Elwakeel Abdallah Elshawadfy , Mahmoud Samy F. , Said Alaa F. 
Published: January 2025

Abstract
Researchers have reported that Bacillus megaterium BM18-2 reduces Cd toxicity in Hybrid Pennisetum, but understanding the interaction between plants and associated endophytes is crucial for understanding phytoremediation strategies under heavy metal stress. The current study aims to monitor the colonization patterns of GFP-labeled endophytic bacteria BM18-2 on Hybrid Pennisetum grass. Additionally, it will monitor Cd’s effect on plant bacterial colonization. Confocal laser scanning microscopy of plant roots infected with gfp tagged BM18-2 revealed that the bacterium colonised root hairs and epidermal cells at the early stage of colonization, and over time, the bacteria penetrated to the internal tissues following their colonization of the stem and leaf. The roots, stems, and leaves of H. Pennisetum grown in Cd-contaminated soil contained a higher number of bacteria than those grown in normal soil. The result of Cd translocation indicated the condensation of heavy metals in the root cells and stem, while no Cd was found in the leaf. The study will also look for the enzymatic activity of bacteria BM18-2 and use Leadmium Green AM dye to track how Cd is taken up and moved through the plant. The enzymatic activity results showed that BM18-2 can produce catalase and amylase, but did not record any cellulase or lipase activity. As a result, the pattern of useful endophytic BM18-2 colonization through H. Pennisetum grass will aid in the application and maintenance of these bacteria in farming, and it presents new opportunities for the development of innovative strategies in the fields of agriculture and biotechnology.
Copulation interruption decreases female reproductive success in a false widow spider
Authors: Dong Yuting , Harvey Jeffrey A. , van den Hengel Marijn , Zwanenburg Annemie , Rowe Melissah , Gols Rieta 
Published: January 2025

Abstract
Copulation is essential for transferring sperm from males to females in most animals. During copulation, males and females are often static and thus prone to predation or other threats. Its duration should therefore be reduced to minimize costs but sufficient to ensure the fertilization of eggs. Here, we investigated reproductive behavior and success in the false widow spider, Steatoda grossa (Araneae: Theridiidae), when copulation was interrupted after 1, 3, 5, 10, or 20 min or was not experimentally interrupted (control). Copulation duration in this study is defined as the total duration of insertions of male pedipalps into a female’s copulatory openings. In S. grossa, uninterrupted copulations typically last 40 to 60 min. We found that within the first 5 min, copulation interruption negatively affected reproductive success (i.e., number of egg sacs, their total mass, and number of spiderlings), and delayed production of the first egg sac within the first 10 min (in some extreme instances by over 200 days). However, when copulation duration was 10 min or longer, reproductive outcome was unaffected. In the 1-min treatment, the number of egg sacs and their mass varied greatly, which indicates considerable variation among males with respect to the speed and efficiency of sperm transfer. We discuss the costs and benefits of extended copulation duration on female reproduction and on male and female fitness.
Six-Month Outcomes from the Prospective, Multi-Center, Non-Randomized Clinical Study of the COVERA(™) Arterio VeNous (AV) Stent Graft in the Treatment of Stenosis in the VEnous OutfloW of AV Fistula Access Circuits (AVeNEW PAS)
Authors: Dolmatch Bart , Saber Talar , Underwood Margo ,   and AVeNEW PAS trial investigators, Licht Jonah , Makris Angelo , Neyra N. Roxanne , Hoggard Jeffrey , Schultz Scott , Kurbanov Alexander , Margassery Suresh , Molnar Robert , Narayan Rajeev , Lozada Juan Carlos Perez , Talaie Reza 
Published: January 2025

Abstract

Purpose
The AVeNEW Post-Approval Study (AVeNEW PAS) follows upon results from the AVeNEW IDE clinical trial and was designed to provide additional clinical evidence of safety and effectiveness using the Covera™ Vascular Covered Stent to treat arteriovenous fistula (AVF) stenoses in a real-world hemodialysis patient population.

Materials and Methods
One hundred AVF patients were prospectively enrolled at 11 clinical trial sites in the USA and treated with the covered stent after angioplasty of a clinically significant target stenosis. The primary safety outcome was freedom from any adverse event that suggests the involvement of the AV access circuit evaluated at 30 days. The primary efficacy outcome was Target Lesion Primary Patency (TLPP) at six months, determined by an independent core laboratory. Secondary outcome measures included technical success defined as successful deployment to the intended location and access circuit primary patency (ACPP).

Results
Safety was 94.9% with no device-related deaths nor in-patient hospitalization. Technical success was 100%. TLPP rates at 1, 3, and 6 months were 100, 89.7, and 82.2%. ACPP rates at 1, 3, and 6 months were 98, 76.3, and 60.0%. Target stenoses were 81% restenotic, and 75% located in the cephalic vein arch. There were 35% non-target stenoses treated with angioplasty during the index procedure.

Conclusion
The 6-month results of the AVeNEW PAS confirm results from the AVeNEW IDE clinical trial and demonstrate safety and efficacy using the Covera(™) Covered Stent in a real-world US hemodialysis patient population.

Trial Registration
NCT04261686.

Level of Evidence
3 – prospective, multicenter.

Graphical Abstract
Review of the techniques for estimating population size of Adélie penguins (Pygoscelis adeliae)
Authors: Strang Alexandra J. , Cameron Elissa Z. , Anderson Dean P. , Robinson Esme , LaRue Michelle A. 
Published: January 2025

Abstract
Monitoring of sentinel species provides insight into the ecosystems in which they live. In the Southern Ocean, penguins are one such indicator species, where only a limited number of colonies have been monitored extensively for decades around Antarctica. As the Southern Ocean warms and commercial fishing continues, the need for expansion of population monitoring has become paramount. Using Adélie penguins (Pygoscelis adeliae) as a model species, we reviewed methods to estimate colony size including ground and aerial (occupied and unoccupied aircraft) assessment and satellite imagery, with an aim of understanding costs and benefits of each method to inform their future use. Ground assessment includes physically taxing field counts of individuals or nests and was historically the only method used to count penguins in Antarctica. Aerial assessments via occupied and unoccupied aircraft have expanded the spatial extent of monitoring for remote and logistically challenging environments such as Antarctica. Combined with aerial assessment, the more recent use of very high-resolution satellite imagery (VHR) has further expanded Adélie penguin monitoring into previously inaccessible areas. Adélie penguin breeding colonies can be monitored using VHR imagery through the area of their guano stain as a proxy for the number of breeding pairs. Our review provides an overview of the monitoring techniques for Adélie penguins in Antarctica and provides direction for future use and development.
Overlooked and underpowered: a meta-research addressing sample size in radiomics prediction models for binary outcomes
Authors: Zhong Jingyu , Liu Xianwei , Lu Junjie , Yang Jiarui , Zhang Guangcheng , Mao Shiqi , Chen Haoda , Yin Qian , Cen Qingqing , Jiang Run , Song Yang , Lu Minda , Chu Jingshen , Xing Yue , Hu Yangfan , Ding Defang , Ge Xiang , Zhang Huan , Yao Weiwu 
Published: January 2025

Abstract

Objectives
To investigate how studies determine the sample size when developing radiomics prediction models for binary outcomes, and whether the sample size meets the estimates obtained by using established criteria.

Methods
We identified radiomics studies that were published from 01 January 2023 to 31 December 2023 in seven leading peer-reviewed radiological journals. We reviewed the sample size justification methods, and actual sample size used. We calculated and compared the actual sample size used to the estimates obtained by using three established criteria proposed by Riley et al. We investigated which characteristics factors were associated with the sufficient sample size that meets the estimates obtained by using established criteria proposed by Riley et al.

Results
We included 116 studies. Eleven out of one hundred sixteen studies justified the sample size, in which 6/11 performed a priori sample size calculation. The median (first and third quartile, Q1, Q3) of the total sample size is 223 (130, 463), and those of sample size for training are 150 (90, 288). The median (Q1, Q3) difference between total sample size and minimum sample size according to established criteria are −100 (−216, 183), and those differences between total sample size and a more restrictive approach based on established criteria are −268 (−427, −157). The presence of external testing and the specialty of the topic were associated with sufficient sample size.

Conclusion
Radiomics studies are often designed without sample size justification, whose sample size may be too small to avoid overfitting. Sample size justification is encouraged when developing a radiomics model.

Key Points

Question

Sample size justification is critical to help minimize overfitting in developing a radiomics model, but is overlooked and underpowered in radiomics research.

Findings

Few of the radiomics models justified, calculated, or reported their sample size, and most of them did not meet the recent formal sample size criteria.

Clinical relevance

Radiomics models are often designed without sample size justification. Consequently, many models are too small to avoid overfitting. It should be encouraged to justify, perform, and report the considerations on sample size when developing radiomics models.
CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)
Authors: Aspromonte Maria Cristina , Del Conte Alessio , Zhu Shaowen , Tan Wuwei , Shen Yang , Zhang Yexian , Li Qi , Wang Maggie Haitian , Babbi Giulia , Bovo Samuele , Martelli Pier Luigi , Casadio Rita , Althagafi Azza , Toonsi Sumyyah , Kulmanov Maxat , Hoehndorf Robert , Katsonis Panagiotis , Williams Amanda , Lichtarge Olivier , Xian Su , Surento Wesley , Pejaver Vikas , Mooney Sean D. , Sunderam Uma , Srinivasan Rajgopal , Murgia Alessandra , Piovesan Damiano , Tosatto Silvio C. E. , Leonardi Emanuela 
Published: January 2025

AbstractThe Genetics of Neurodevelopmental Disorders Lab in Padua provided a new intellectual disability (ID) Panel challenge for computational methods to predict patient phenotypes and their causal variants in the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6). Eight research teams submitted a total of 30 models to predict phenotypes based on the sequences of 74 genes (VCF format) in 415 pediatric patients affected by Neurodevelopmental Disorders (NDDs). NDDs are clinically and genetically heterogeneous conditions, with onset in infant age. Here, we assess the ability and accuracy of computational methods to predict comorbid phenotypes based on clinical features described in each patient and their causal variants. We also evaluated predictions for possible genetic causes in patients without a clear genetic diagnosis. Like the previous ID Panel challenge in CAGI5, seven clinical features (ID, ASD, ataxia, epilepsy, microcephaly, macrocephaly, hypotonia), and variants (Pathogenic/Likely Pathogenic, Variants of Uncertain Significance and Risk Factors) were provided. The phenotypic traits and variant data of 150 patients from the CAGI5 ID Panel Challenge were provided as training set for predictors. The CAGI6 challenge confirms CAGI5 results that predicting phenotypes from gene panel data is highly challenging, with AUC values close to random, and no method able to predict relevant variants with both high accuracy and precision. However, a significant improvement is noted for the best method, with recall increasing from 66% to 82%. Several groups also successfully predicted difficult-to-detect variants, emphasizing the importance of variants initially excluded by the Padua NDD Lab.
Automated Scene-Adaptive Rock Fragment Recognition Based on the Enhanced Segment Anything Model and Fine-Tuning RTMDet
Authors: Tang Yudi , Wang Yulin , Wang Xin , Oh Joung , Si Guangyao 
Published: January 2025

AbstractThe particle-size distribution (PSD) of rock fragments is crucial for various engineering practices. Recently, there has been increasing attention towards new methods for analysing rock fragment PSD based on artificial intelligence and computer vision. However, most existing image-based studies on this topic are case-based, while heavily relying on manual annotation. The proposed algorithms or trained models often exhibit poor performance across different geological and lighting conditions. In this research, an automatic scene-adaptive framework for real-time rock fragment recognition (FragAdaptixAI) is introduced. First, a diverse foundation image set of rock fragments is built, and an automated annotation module based on an improved segment anything model (SAM) is employed to create the foundation rock fragment dataset, which is then utilised for training the foundation model (RTMDet). When faced with new cases, the foundation model is rapidly fine-tuned using a small amount of current case data to derive an application model, supporting real-time automation in rock fragment recognition. FragAdaptixAI was tested using two cases, and the test results demonstrate that (1) the automated annotation module, developed based on the improved SAM, is effective, and (2) FragAdaptixAI achieves excellent results with short tuning time for new cases. The approach introduces a new concept to address the generalisation issues in rock fragment recognition by combining the zero-shot capability of large models with the real-time processing of small models.
The plaque reducing efficacy of oil pulling with sesame oil: a randomized-controlled clinical study
Authors: Zürcher Christine , Vukoje Kristian , Kleiner Eva Maria , Kuster Sophie Martina , Jäger-Larcher Lisa Katharina , Heller Ingrid , Eick Sigrun , Nagl Markus , Kapferer-Seebacher Ines 
Published: January 2025

Abstract

Objectives
To compare the plaque reducing efficacy of oil pulling with sesame oil compared to distilled water in a randomized, controlled, examiner-blinded parallel group study.

Materials and methods
Forty probands without advanced periodontal disease of the University Hospital for Restorative Dentistry and Periodontology, Medical University of Innsbruck (Austria) were randomized allocated to test- (sesame oil) or control group (distilled water) and asked to pull daily in the morning for eight weeks with their allotted fluid for 15 min. Rustogi Modified Navy Plaque Index (RMNPI) and gingival bleeding index were assessed at baseline and after four and eight weeks. Plaque samples underwent microbiological analysis.

Results
Pulling with sesame oil was significantly more effective in reducing full mouth RMNPI compared to distilled water after eight weeks (median reduction 18.98% versus 10.49%; p = 0.023), and was most pronounced in anterior, buccal, and lingual subscales. On approximal surfaces, significantly higher plaque reduction was found in the test group after four (24.07% versus 14.29%) and eight weeks (16.00% versus 5.36%) of intervention (p < 0.05). No significant changes in gingival index and mirobiological analysis could be detected.

Conclusion
Plaque reduction was statistically significantly higher with oil pulling than with distilled water, however, a study bias cannot be ruled out. Further high-quality trials are needed to understand the mechanisms and effectiveness of oil pulling, to finally clarify the evidence.

Clinical relevance
Oil pulling may be recommended as an adjuvant to mechanical dental cleaning. Individuals with keratosis may experience adverse effects.

Trial registration
ClinicalTrials.gov NCT06327841.