bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset
Authors: Zhou Yong , Kathiresan Nagarajan , Yu Zhichao , Rivera Luis F. , Yang Yujian , Thimma Manjula , Manickam Keerthana , Chebotarov Dmytro , Mauleon Ramil , Chougule Kapeel , Wei Sharon , Gao Tingting , Green Carl D. , Zuccolo Andrea , Xie Weibo , Ware Doreen , Zhang Jianwei , McNally Kenneth L. , Wing Rod A. 
Published: January 2024

AbstractBackgroundSingle-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable.ResultsHere we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a “subpopulation aware” 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq).ConclusionsThis study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.
Interpretable artificial intelligence-based app assists inexperienced radiologists in diagnosing biliary atresia from sonographic gallbladder images
Authors: Zhou Wenying , Ye Zejun , Huang Guangliang , Zhang Xiaoer , Xu Ming , Liu Baoxian , Zhuang Bowen , Tang Zijian , Wang Shan , Chen Dan , Pan Yunxiang , Xie Xiaoyan , Wang Ruixuan , Zhou Luyao 
Published: January 2024

Abstract
Background
A previously trained deep learning-based smartphone app provides an artificial intelligence solution to help diagnose biliary atresia from sonographic gallbladder images, but it might be impractical to launch it in real clinical settings. This study aimed to redevelop a new model using original sonographic images and their derived smartphone photos and then test the new model’s performance in assisting radiologists with different experiences to detect biliary atresia in real-world mimic settings.

Methods
A new model was first trained retrospectively using 3659 original sonographic gallbladder images and their derived 51,226 smartphone photos and tested on 11,410 external validation smartphone photos. Afterward, the new model was tested in 333 prospectively collected sonographic gallbladder videos from 207 infants by 14 inexperienced radiologists (9 juniors and 5 seniors) and 4 experienced pediatric radiologists in real-world mimic settings. Diagnostic performance was expressed as the area under the receiver operating characteristic curve (AUC).

Results
The new model outperformed the previously published model in diagnosing BA on the external validation set (AUC 0.924 vs 0.908, P = 0.004) with higher consistency (kappa value 0.708 vs 0.609). When tested in real-world mimic settings using 333 sonographic gallbladder videos, the new model performed comparable to experienced pediatric radiologists (average AUC 0.860 vs 0.876) and outperformed junior radiologists (average AUC 0.838 vs 0.773) and senior radiologists (average AUC 0.829 vs 0.749). Furthermore, the new model could aid both junior and senior radiologists to improve their diagnostic performances, with the average AUC increasing from 0.773 to 0.835 for junior radiologists and from 0.749 to 0.805 for senior radiologists.

Conclusions
The interpretable app-based model showed robust and satisfactory performance in diagnosing biliary atresia, and it could aid radiologists with limited experiences to improve their diagnostic performances in real-world mimic settings.
Dysfunction in endocannabinoids, palmitoylethanolamide, and degradation of tryptophan into kynurenine in individuals with depressive symptoms
Authors: Comai Stefano , Nunez Nicolas , Atkin Tobias , Ghabrash Maykel F. , Zakarian Rita , Fielding Allan , Saint-Laurent Marie , Low Nancy , Sauber Garrett , Ragazzi Eugenio , Hillard Cecilia J. , Gobbi Gabriella 
Published: January 2024

AbstractBackgroundThe endocannabinoid (eCB) system and the serotonin (5-HT) are both implicated in the severity of the depression. 5-HT is synthesized from the amino acid tryptophan (Trp), which is also a precursor for kynurenine (Kyn) whose production is increased at the expense of 5-HT in depressed patients. No clinical studies have investigated the crosstalk between the eCB system and the Trp/5-HT/Kyn pathways. Here, we hypothesized that the eCB system is associated with an enhanced Kyn production in relation to the severity of depressive symptoms.MethodsEighty-two subjects (51 patients with a diagnosis of depressive disorder (DSM-5) and 31 healthy volunteers), were assessed with the Montgomery-Åsberg Depression Rating Scale (MADRS), Beck Depression Scale, and Global Clinical Impression. Serum concentrations of eCBs (N-arachidonoylethanolamine (AEA) and 2-arachidonoylglycerol (2-AG)); structurally related fatty acyl compounds 2-oleoylglycerol (2-OG), oleoylethanolamide (OEA), and palmitoylethanolamide (PEA); Trp, Kyn, Kyn/Trp ratio (an index of Trp degradation into Kyn) and 5-HT were also determined.ResultsFollowing a principal component analysis including the severity of depression, Kyn and the Kyn/Trp ratio appear to be directly associated with 2-AG, AEA, and PEA. Interestingly, these biomarkers also permitted to distinguish the population into two main clusters: one of individuals having mild/severe depressive symptoms and the other with an absence of depressive symptoms. Using parametric analysis, higher serum levels of 2-AG, Kyn, and the ratio Kyn/Trp and lower levels of Trp and 5-HT were found in individuals with mild/severe depressive symptoms than in those without depressive symptoms. While in asymptomatic people, PEA was directly associated to Trp, and OEA indirectly linked to 5-HT, in individuals with depressive symptoms, these correlations were lost, and instead, positive correlations between AEA and 2-AG, PEA and AEA, and PEA vs 2-AG and OEA concentrations were found.ConclusionsParametric and non-parametric analyses suggest a possible association between eCBs, tryptophan/kynurenine biomarkers, and severity of depression, confirming a likely interplay among inflammation, stress, and depression. The enhanced relationships among the biomarkers of the 2-AG and AEA pathways and related lipids seen in individuals with depressive symptoms, but not in asymptomatics, suggest an altered metabolism of the eCB system in depression.
Predicting cognitive scores from wearable-based digital physiological features using machine learning: data from a clinical trial in mild cognitive impairment
Authors: Rykov Yuri G. , Patterson Michael D. , Gangwar Bikram A. , Jabar Syaheed B. , Leonardo Jacklyn , Ng Kok Pin , Kandiah Nagaendran 
Published: January 2024

Abstract
Background
Continuous assessment and remote monitoring of cognitive function in individuals with mild cognitive impairment (MCI) enables tracking therapeutic effects and modifying treatment to achieve better clinical outcomes. While standardized neuropsychological tests are inconvenient for this purpose, wearable sensor technology collecting physiological and behavioral data looks promising to provide proxy measures of cognitive function. The objective of this study was to evaluate the predictive ability of digital physiological features, based on sensor data from wrist-worn wearables, in determining neuropsychological test scores in individuals with MCI.

Methods
We used the dataset collected from a 10-week single-arm clinical trial in older adults (50–70 years old) diagnosed with amnestic MCI (N = 30) who received a digitally delivered multidomain therapeutic intervention. Cognitive performance was assessed before and after the intervention using the Neuropsychological Test Battery (NTB) from which composite scores were calculated (executive function, processing speed, immediate memory, delayed memory and global cognition). The Empatica E4, a wrist-wearable medical-grade device, was used to collect physiological data including blood volume pulse, electrodermal activity, and skin temperature. We processed sensors’ data and extracted a range of physiological features. We used interpolated NTB scores for 10-day intervals to test predictability of scores over short periods and to leverage the maximum of wearable data available. In addition, we used individually centered data which represents deviations from personal baselines. Supervised machine learning was used to train models predicting NTB scores from digital physiological features and demographics. Performance was evaluated using “leave-one-subject-out” and “leave-one-interval-out” cross-validation.

Results
The final sample included 96 aggregated data intervals from 17 individuals. In total, 106 digital physiological features were extracted. We found that physiological features, especially measures of heart rate variability, correlated most strongly to the executive function compared to other cognitive composites. The model predicted the actual executive function scores with correlation r = 0.69 and intra-individual changes in executive function scores with r = 0.61.

Conclusions
Our findings demonstrated that wearable-based physiological measures, primarily HRV, have potential to be used for the continuous assessments of cognitive function in individuals with MCI.
Prognostic significance and survival benefits of postoperative adjuvant chemotherapy in patients with stage IA lung adenocarcinoma with non-predominant micropapillary components
Authors: Li Rongyang , Qiu Jianhao , Li Zhenyi , Li Haiming , Tang Zhanpeng , Yu Wenhao , Tian Hui , Sun Zhenguo 
Published: January 2024

Abstract
Background
The prognostic significance of adjuvant chemotherapy (ACT) for patients with stage IA micropapillary non-predominant (MPNP) lung adenocarcinoma (LUAD) remains unknown. This study aimed to investigate the effects of postoperative ACT in patients with stage IA MPNP-LUAD.

Methods
A total of 149 patients with pathological stage IA MPNP-LUAD who underwent surgery at our center were retrospectively analyzed. Propensity score matching (PSM) analysis was conducted to reduce potential selection bias. Kaplan–Meier analyses were used to assess the impact of ACT on recurrence-free survival (RFS), overall survival (OS), and disease-specific survival (DSS). Subgroup analyses were performed for the survival outcomes based on the percentage of micropapillary components. Cox proportional hazards regression analyses were applied to identify risk factors associated with survival.

Results
The receipt or non-receipt of postoperative ACT had no significant effect on RFS, OS, and DSS among all enrolled patients with stage IA MPNP-LUAD (P > 0.05). For patients with a micropapillary component > 5%, the 5-year rates of RFS, OS, and DSS were significantly higher in the ACT group compared to the observation group, both before and after PSM (P < 0.05). However, the differences between the two groups were not significant for patients with a micropapillary component ≤ 5% (P > 0.05). The resection range (HR = 0.071; 95% CI: 0.020–0.251; P < 0.001), tumor size (HR = 2.929; 95% CI: 1.171–7.330; P = 0.022), and ACT (HR = 0.122; 95% CI: 0.037–0.403; P = 0.001) were identified as independent prognostic factors for RFS through Cox regression analysis.

Conclusion
Patients with stage IA MPNP-LUAD who have a micropapillary component greater than 5% might benefit from postoperative ACT, while those with a micropapillary component ≤ 5% did not appear to derive the same benefit from postoperative ACT.
Intratumoral microorganisms in tumors of the digestive system
Authors: Xuan Mengjuan , Gu Xinyu , Liu Yingru , Yang Li , Li Yi , Huang Di , Li Juan , Xue Chen 
Published: January 2024

AbstractTumors of the digestive system pose a significant threat to human health and longevity. These tumors are associated with high morbidity and mortality rates, leading to a heavy economic burden on healthcare systems. Several intratumoral microorganisms are present in digestive system tumors, and their sources and abundance display significant heterogeneity depending on the specific tumor subtype. These microbes have a complex and precise function in the neoplasm. They can facilitate tumor growth through various mechanisms, such as inducing DNA damage, influencing the antitumor immune response, and promoting the degradation of chemotherapy drugs. Therefore, these microorganisms can be targeted to inhibit tumor progression for improving overall patient prognosis. This review focuses on the current research progress on microorganisms present in the digestive system tumors and how they influence the initiation, progression, and prognosis of tumors. Furthermore, the primary sources and constituents of tumor microbiome are delineated. Finally, we summarize the application potential of intratumoral microbes in the diagnosis, treatment, and prognosis prediction of digestive system tumors.
Effects of remote coaching following supervised exercise oncology rehabilitation on physical activity levels, physical fitness, and patient-reported outcomes: a randomised controlled trial
Authors: Weemaes Anouk T.R. , Beelen Milou , Weijenberg Matty P. , van Kuijk Sander M. J. , Lenssen Antoine F. 
Published: January 2024

Abstract
Background
Studies have shown that cancer survivors experience difficulties maintaining physical activity levels after participation in a supervised exercise rehabilitation program. This study aimed to assess the effectiveness of a six-month remote coaching intervention, following a supervised exercise oncology rehabilitation program on maintenance of PA levels; and improvement of aerobic capacity, muscle strength and patient-reported outcomes in cancer survivors.

Methods
Ninety-seven participants from a Dutch University Hospital’s exercise rehabilitation program were randomised to the COACH group (n = 46), receiving 6 months of remote coaching after completing the exercise program, or the CONTROL group (n = 50), receiving no additional intervention. Assessment of PA levels; sedentary time; aerobic capacity; muscle strength; fatigue; health-related quality of life (HRQoL); level of anxiety and depression; and return to work (RTW) rates were conducted at baseline (T0) and six months later (T1). Multiple linear regression was used for between-group statistical comparisons of all outcomes measures. Mean differences at T1 were estimated with corresponding 95% confidence intervals (95%CI).

Results
No significant between-group differences were observed for all outcomes at T1. An adjusted mean difference in weekly PA of 45 min (95%CI -50;140) was observed between the COACH group and the CONTROL group, favouring the COACH group, yet lacking statistical or clinical significance.

Conclusions
Our six-month remote coaching intervention did not notably improve PA levels; sedentary time; aerobic capacity; muscle strength; HRQoL; fatigue; anxiety and depression symptoms and RTW rates after participation in a supervised exercise oncology program. Although the participants who received coaching showed slightly higher levels of PA, these differences were not significant. More research is needed to identify patients in need for follow-up interventions following supervised exercise program and to investigate the effectiveness of remote coaching interventions in these patients.

Trial registration
Dutch Trial Register NL7729, registered 13 may 2019, https://trialsearch.who.int/Trial2.aspx?TrialID=NL7729.
The glucocorticoid receptor as a master regulator of the Müller cell response to diabetic conditions in mice
Authors: Pfaller Anna M. , Kaplan Lew , Carido Madalena , Grassmann Felix , Díaz-Lezama Nundehui , Ghaseminejad Farhad , Wunderlich Kirsten A. , Glänzer Sarah , Bludau Oliver , Pannicke Thomas , Weber Bernhard H. F. , Koch Susanne F. , Bonev Boyan , Hauck Stefanie M. , Grosche Antje 
Published: January 2024

AbstractDiabetic retinopathy (DR) is considered a primarily microvascular complication of diabetes. Müller glia cells are at the centre of the retinal neurovascular unit and play a critical role in DR. We therefore investigated Müller cell-specific signalling pathways that are altered in DR to identify novel targets for gene therapy. Using a multi-omics approach on purified Müller cells from diabetic db/db mice, we found the mRNA and protein expression of the glucocorticoid receptor (GR) to be significantly decreased, while its target gene cluster was down-regulated. Further, oPOSSUM TF analysis and ATAC- sequencing identified the GR as a master regulator of Müller cell response to diabetic conditions. Cortisol not only increased GR phosphorylation. It also induced changes in the expression of known GR target genes in retinal explants. Finally, retinal functionality was improved by AAV-mediated overexpression of GR in Müller cells. Our study demonstrates an important role of the glial GR in DR and implies that therapeutic approaches targeting this signalling pathway should be aimed at increasing GR expression rather than the addition of more ligand.
Graphical Abstract
Exosome-mediated regulation of inflammatory pathway during respiratory viral disease
Authors: Gheitasi Hamidreza , Sabbaghian Mohammad , Shekarchi Ali Akbar , Mirmazhary Amir Ali , Poortahmasebi Vahdat 
Published: January 2024

AbstractViruses have developed many mechanisms by which they can stimulate or inhibit inflammation and cause various diseases, including viral respiratory diseases that kill many people every year. One of the mechanisms that viruses use to induce or inhibit inflammation is exosomes. Exosomes are small membrane nanovesicles (30–150 nm) released from cells that contain proteins, DNA, and coding and non-coding RNA species. They are a group of extracellular vesicles that cells can take up to produce and mediate communication. Intercellular effect exosomes can deliver a broad confine of biological molecules, containing nucleic acids, proteins, and lipids, to the target cell, where they can convey therapeutic or pathogenic consequences through the modulation of inflammation and immune processes. Recent research has shown that exosomes can deliver entire virus genomes or virions to distant target cells, then the delivered viruses can escape the immune system and infect cells. Adenoviruses, orthomyxoviruses, paramyxoviruses, respiratory syncytial viruses, picornaviruses, coronaviruses, and rhinoviruses are mostly related to respiratory diseases. In this article, we will first discuss the current knowledge of exosomes. We will learn about the relationship between exosomes and viral infections, and We mention the inflammations caused by viruses in the airways, the role of exosomes in them, and finally, we examine the relationship between the viruses as mentioned earlier, and the regulation of inflammatory pathways that play a role in causing the disease.
Tailored implementation of national recommendations on fall prevention among older adults in municipalities in Norway (FALLPREVENT trial): a study protocol for a cluster-randomised trial
Authors: Bjerk Maria , Flottorp Signe A. , Pripp Are Hugo , Øien Henning , Hansen Tonya Moen , Foy Robbie , Close Jacqueline , Linnerud Siv , Brovold Therese , Solli Rune , Olsen Nina Rydland , Skelton Dawn A. , Rydwik Elisabeth , Helbostad Jorunn L. , Idland Gro , Kvæl Linda , Vieira Edgar , Taraldsen Kristin 
Published: January 2024

Abstract
Background
Despite substantial research evidence indicating the effectiveness of a range of interventions to prevent falls, uptake into routine clinical practice has been limited by several implementation challenges. The complexity of fall prevention in municipality health care underlines the importance of flexible implementation strategies tailored both to general determinants of fall prevention and to local contexts. This cluster-randomised trial (RCT) investigates the effectiveness of a tailored intervention to implement national recommendations on fall prevention among older home-dwelling adults compared to usual practice on adherence to the recommendations in health professionals.

Methods
Twenty-five municipalities from four regions in Norway will be randomised to intervention or control arms. Each municipality cluster will recruit up to 30 health professionals to participate in the study as responders. The tailored implementation intervention comprises four components: (1) identifying local structures for implementation, (2) establishing a resource team from different professions and levels, (3) promoting knowledge on implementation and fall prevention and (4) supporting the implementation process. Each of these components includes several implementation activities. The Consolidated Framework for Implementation Research (CFIR) will be used to categorise determinants of the implementation process and the Expert Recommendations for Implementing Change (ERIC) will guide the matching of barriers to implementation strategies. The primary outcome measure for the study will be health professionals’ adherence to the national recommendations on fall prevention measured by a questionnaire. Secondary outcomes include injurious falls, the feasibility of the intervention, the experiences of the implementation process and intervention costs. Measurements will be carried out at baseline in August 2023, post-intervention in May 2024 and at a follow-up in November 2024.

Discussion
This study will provide evidence on the effectiveness, intervention costs and underlying processes of change of tailored implementation of evidence-based fall prevention recommendations.

Trial registration
The trial is registered in the Open Science Registry: https://doi.org/10.17605/OSF.IO/JQ9T5. Registered: March 03, 2023.