Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovering research articles containing evolutionary timetrees by machine learning

Abstract Motivation Timetrees depict evolutionary relationships between species and the geological times of their divergence. Hundreds of research articles containing timetrees are published in scientific journals every year. The TimeTree (TT) project has been manually locating, curating and synthesizing timetrees from these articles for almost two decades into a TimeTree of Life, delivered through a unique, user-friendly web interface (timetree.org). The manual process of finding articles containing timetrees is becoming increasingly expensive and time-consuming. So, we have explored the effectiveness of text-mining approaches and developed optimizations to find research articles containing timetrees automatically. Results We have developed an optimized machine learning system to determine if a research article contains an evolutionary timetree appropriate for inclusion in the TT resource. We found that BERT classification fine-tuned on whole-text articles achieved an F1 score of 0.67, which we increased to 0.88 by text-mining article excerpts surrounding the mentioning of figures. The new method is implemented in the TimeTreeFinder (TTF) tool, which automatically processes millions of articles to discover timetree-containing articles. We estimate that the TTF tool would produce twice as many timetree-containing articles as those discovered manually, whose inclusion in the TT database would potentially double the knowledge accessible to a wider community. Manual inspection showed that the precision on out-of-distribution recently published articles is 87%. This automation will speed up the collection and curation of timetrees with much lower human and time costs. Availability and implementation https://github.com/marija-stanojevic/time-tree-classification. Supplementary information Supplementary data are available at Bioinformatics online.
Urinary cadmium concentrations and intake of nutrients, food groups and dietary patterns in women from Northern Mexico

Abstract Cadmium (Cd) is a toxic metal found in some foods. There is limited evidence about the relationship of Cd exposure with nutrient and food groups consumption, and almost no information regarding dietary patterns. The objective was to evaluate the association between diet and urinary Cd, and to explore whether metal concentrations vary according to the intake of some nutrients. Urinary Cd concentrations of 891 female residents of northern Mexico were determined by tandem mass spectrometry. We obtained food consumption through a food frequency questionnaire and we used previously defined food groups and estimated dietary patterns by factor analysis. We found positive associations between Cd and daily consumption of non-starchy vegetables (ß = 0.067, 95% CI 0.030, 0.1023), legumes (ß = 0.139, 95% CI 0.065, 0.213) and processed meats (ß = 0.163, 95% CI 0.035.0.291), as well as the Western (ß = 0.083, 95% CI: 0.027.0.139) and Prudent dietary patterns (ß = 0.035, 95% CI: −0.020, 0.091). In contrast, we observed a negative association with the vegetable oil group (ß = −0.070, 95% CI −0.125, −0.014). In addition, we found higher concentrations of Cd in women under 50 years of age with a lower iron intake than recommended. Food is a source of exposure to this metal and at the same time provides nutrients that modulate its metabolism. It is important to generate dietary guidelines to reduce the health effects of Cd exposure.
The mother-to-child transmission of HIV-1 and profile of viral reservoirs in pediatric population: A systematic review with meta-analysis of the Cameroonian studies

Background The mother-to-child transmission of HIV-1 (MTCT) remains on the major route of HIV-transmission among pediatric populations in Africa. Though a prevention of MTCT (PMTCT) high-priority country, data on the MTCT burdens in Cameroon remains fragmented. Objective We sought to assess the pooled MTCT rate, its risk-factors, and to characterize viral reservoirs of infected-children in Cameroon. Methods All relevant observational cohort and cross-sectional studies conducted in Cameroon were searched from PubMed, African Journals Online, Google scholar, ScienceDirect and academic medical education databases. Heterogeneity and publication bias were respectively assessed by the I2 statistic and the Egger/funnel plot test. Meta-analysis was performed using the random effects model. MTCT rate >5% was considered as “high”. This review was registered in the Prospero database, CRD42021224497. Results We included a total of 29 studies and analyzed 46 684 children born from HIV-positive mothers. The overall rate of MTCT was 7.00% (95% CI = 6.07–8.51). According to regions, the highest burden was in Adamaoua-region (17.51% [95% CI:14.21–21.07]) with only one study found. PMTCT option-B+ resulted in about 25% reduction of MTCT (8.97% [95% CI: 8.71–9.24] without option-B+ versus 2.88% [95% CI: 5.03–9.34] with option-B+). Regarding risk-factors, MTCT was significantly associated with the absence of PMTCT-interventions both in children (OR:5.40 [95% CI: 2.58–11.27]) and mothers (OR: 3.59 [95% CI: 2.15–5.99]). Regarding viral reservoirs, a pro-viral DNA mean of 3.34±1.05 log10/mL was observed among 5/57 children and archived HIV drug resistance mutations were identified in pro-viral DNA marker among 21/79 infected-children. Conclusion In spite of the dropdown in MTCT following option-B+ implementation, MTCT remains high in Cameroon, with substantial disparities across regions. Thus, in this era of option-B+, achieving MTCT elimination requires interventions in northern-Cameroon. The variation in pro-viral load in infected-children underlines the relevance of characterizing viral reservoirs for possible infection control in tropical settings.
SARS‐CoV‐2 spike mRNA vaccine sequences circulate in blood up to 28 days after COVID‐19 vaccination

In Denmark, vaccination against Severe Acute Respiratory Syndrome Corona Virus 2 (SARS‐CoV‐2) has been with the Pfizer‐BioNTech (BTN162b2) or the Moderna (mRNA‐1273) mRNA vaccines. Patients with chronic hepatitis C virus (HCV) infection followed in our clinic received mRNA vaccinations according to the Danish roll‐out vaccination plan. To monitor HCV infection, RNA was extracted from patient plasma and RNA sequencing was performed on the Illumina platform. In 10 of 108 HCV patient samples, full‐length or traces of SARS‐CoV‐2 spike mRNA vaccine sequences were found in blood up to 28 days after COVID‐19 vaccination. Detection of mRNA vaccine sequences in blood after vaccination adds important knowledge regarding this technology and should lead to further research into the design of lipid‐nanoparticles and the half‐life of these and mRNA vaccines in humans.
High flux and high resolution beamline for elliptically polarized radiation in the vacuum ultraviolet and soft x‐ray regions

A dedicated beamline with a broad energy range of photons and with high flux and a high degree of circular polarization has been designed for the ELETTRA storage ring. The beamline exploits the circularly polarized radiation produced by an electromagnetic elliptical wiggler and cover the (5–1200) eV photon energy range using a double‐incidence spherical grating monochromator.
Substitution of gp120 C4 region compensates for V3 loss-of-fitness mutations in HIV-1 CRF01_AE co-receptor switching

ABSTRACT HIV-1 infection is mediated by a viral envelope subsequently binding to CD4 receptor and two main coreceptors, CCR5 (R5) for primary infection and CXCR4 (X4) in chronic infection. Switching from R5 to X4 tropism in HIV-1 infection is associated with increased viral pathogenesis and disease progression. The coreceptor switching is mainly due to variations in the V3 loop, while the mechanism needs to be further elucidated. We systematically studied the determinant for HIV-1 coreceptor switching by substitution of the genes from one R5 and one X4 pseudoviruses. The study results in successfully constructing two panels of chimeric viruses of R5 to X4 forward and X4 to R5 reverse switching. The determinants for tropism switching are the combined substitution of the V3 loop and C4 region of the HIV-1 envelope. The possible mechanism of the tropism switching includes two components, the V3 loop to enable the viral envelope binding to the newly switched coreceptor and the C4 region, to compensate for the loss of fitness caused by deleterious V3 loop mutations to maintain the overall viral viability. The combined C4 and V3 substitution showed at least an eightfold increase in replication activity compared with the pseudovirus with only V3 loop substitution. The site-directed mutations of N425R and S440-I442 with charged amino acids could especially increase viral activity. This study could facilitate HIV-1 phenotype surveillance and select right entry inhibitor, CCR5 or CXCR4 antagonists, for antiviral therapy.
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets.

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation. This article is protected by copyright. All rights reserved.
Graduates' preparedness for the changing doctor‐patient relationship: A qualitative study

A positive doctor‐patient relationship is a crucial part of high‐quality patient care. There is a general perception that it has been changing in recent years; however, there is a lack of evidence for this. Adapting to the changing doctor‐patient relationship has been identified as an important skill doctors of the future must possess. This study explores (1) multiple stakeholder perspectives on how the doctor‐patient relationship is changing and (2) in what ways medical graduates are prepared for working in this changing doctor‐patient relationship.
West meets east: Taking a stab at acupuncture point names

Acupuncture point names written in Chinese Han characters often provide clinically useful information in both their literal and figurative meanings about location and therapeutic use. The World Health Organization (WHO) standard acupuncture nomenclature includes these names in Han characters in an unusual array that includes both “original” forms and, in parentheses, simplified forms. Construction of a multilingual table of acupuncture point names during development of a database revealed that the assumption that the “original” form in the WHO nomenclature was the traditional Chinese character was frequently false. The Han character forms in the pdf of the 2009 reprint of WHO Standard Acupuncture Point Locations were carefully compared with Han characters used in traditional and simplified Chinese, Japanese and Korean writing systems. This work utilized three online tools: UnicodePlus, Unihan Database Lookup, and Wiktionary. Only 48% of the “original” character forms were traditional Chinese characters. The Unicode number was correct in 99%, but in most cases the East Asian font used was not a traditional Chinese one. The issue about Han character forms was also found in all earlier versions of the WHO standard acupuncture nomenclature. Other detected problems included the use of wrong characters for an “original” character form in one name and for a simplified character form in another name. The WHO standard acupuncture nomenclature should be revised with a focus on accuracy in the usage of Han characters.
Broad-spectrum infrared thermography for detection of M2 digital dermatitis lesions on hind feet of standing dairy cattle

Low-effort, reliable diagnostics of digital dermatitis (DD) are needed, especially for lesions warranting treatment, regardless of milking system or hygienic condition of the feet. The primary aim of this study was to test the association of infrared thermography (IRT) from unwashed hind feet with painful M2 lesions under farm conditions, with lesion detection as ultimate goal. Secondary objectives were to determine the association between IRT from washed feet and M2 lesions, and between IRT from unwashed and washed feet and the presence of any DD lesion. A total of 641 hind feet were given an M-score and IRT images of the plantar pastern were captured. Multivariable logistic regression analyses were done with DD status as dependent variable and maximum infrared temperature (IRTmax), lower leg cleanliness score and locomotion score as independent variables, and farm as fixed effect. To further our understanding of IRTmax within DD status, we divided IRTmax into two groups over the median value of IRTmax in the datasets of unwashed and washed feet, respectively, and repeated the multivariable logistic regression analyses. Higher IRTmax from unwashed hind feet were associated with M2 lesions or DD lesions, in comparison with feet without an M2 lesion or without DD, adjusted odds ratio 1.6 (95% CI 1.2–2.2) and 1.1 (95% CI 1.1–1.2), respectively. Washing of the feet resulted in similar associations. Dichotomization of IRTmax substantially enlarged the 95% CI for the association with feet with M2 lesions indicating that the association becomes less reliable. This makes it unlikely that IRTmax alone can be used for automated detection of feet with an M2 lesion. However, IRTmax can have a role in identifying feet at-risk for compromised foot health that need further examination, and could therefore function as a tool aiding in the automated monitoring of foot health on dairy herds.
Corticosteroids and Cancer Immunotherapy.

Despite revolutionizing cancer management, immunotherapies dysregulate the immune system leading to immune-mediated adverse events. These common and potentially dangerous toxicities are often treated with corticosteroids, which are among the most prescribed drugs in oncology for a wide range of cancer and non-cancer indications. While steroids exert several mechanisms to reduce immune activity, immunotherapies, such as immune checkpoint inhibitors (ICI), are designed to enhance the immune system's inherent antitumor activity. Because ICI requires an intact and robust immune response, the immunosuppressive properties of steroids have led to a widespread concern they may interfere with antitumor responses. However, the existing data of the effect of systemic steroids on immunotherapy efficacy remain somewhat conflicted and unclear. To inform clinical decision making and improve outcomes, we review the impact of steroids on antitumor immunity, recent advances in the knowledge of their impact on ICI efficacy in unique populations and settings, associated precautions, and steroid-sparing treatment approaches.
Selenomonas sputigena Interactions with Gingival Epithelial Cells That Promote Inflammation

Increased prevalence and abundance of Selenomonas sputigena have been associated with periodontitis, a chronic inflammatory disease of tooth-supporting tissues, for more than 50 years. Over the past decade, molecular surveys of periodontal disease using 16S and shotgun metagenomic sequencing approaches have confirmed the disease association of classically recognized periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia while highlighting previously underappreciated organisms such as Filifactor alocis and S. sputigena. ABSTRACT Increased prevalence and abundance of Selenomonas sputigena have been associated with periodontitis, a chronic inflammatory disease of tooth-supporting tissues, for more than 50 years. Over the past decade, molecular surveys of periodontal disease using 16S and shotgun metagenomic sequencing approaches have confirmed the disease association of classically recognized periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia while highlighting previously underappreciated organisms such as Filifactor alocis and S. sputigena. Despite abundant clinical association between S. sputigena and periodontal disease, we have little to no understanding of its pathogenic potential, and virulence mechanisms have not been studied. In this study, we sought to characterize the response of gingival epithelial cells to infection with S. sputigena. Here, we show that S. sputigena attaches to gingival keratinocytes and induces expression and secretion of cytokines and chemokines associated with inflammation and leukocyte recruitment. We demonstrate that S. sputigena induces signaling through Toll-like receptor 2 (TLR2) and TLR4 but evades activation of TLR5. Cytokines released from S. sputigena-infected keratinocytes induced monocyte and neutrophil chemotaxis. These results show that S. sputigena-host interactions have the potential to contribute to bacterially driven inflammation and tissue destruction, the hallmark of periodontitis. Characterization of previously unstudied pathogens may provide novel approaches to develop therapeutics to treat or prevent periodontal disease.
The Effect of Coherent Scattering on Radiative Losses in the Solar Ca II K Line

We investigate the influence of partial frequency redistribution (PRD) on radiative cooling due to the Ca II K line in a hydrostatic model of the quiet Sun, and in a series of 20 snapshots from a chromospheric radiation-hydrodynamics simulation. The net radiative rates in the K line were calculated through these models with three different frequency-redistribution formalisms: complete redistribution (CRD), angle-averaged PRD, and angle-dependent PRD. It is found that the approximation of CRD generally leads to an overestimate of the net radiative rates because of its neglect of coherent scattering. Compared to the more realistic full angle-dependent solution, angle-averaged PRD provides accurate emergent profiles and cooling rates in the hydrostatic model and also provides accurate instantaneous profiles in the dynamical snapshots, even when considerable macroscopic velocities are present. Instantaneous angle-averaged cooling rates in the dynamical snapshots may be different at times, but on average, cooling is very similar to the angle-dependent case. In the temperature minimum, the Ca II K line provides, on average, more cooling in the dynamic chromosphere at the same column mass than in the hydrostatic model. It provides less cooling in the chromosphere. Finally, we formulate an approximation for angle-averaged redistribution in a moving atmosphere, employing the unshifted redistribution function. This approximation is easy to implement in existing numerical codes and should provide an efficient method for PRD transfer solutions in dynamic models without loss of accuracy in emergent profiles and radiative cooling rates.
Pain Characteristics and Symptom Management in Children with Hypermobile Ehlers–Danlos Syndrome and Hypermobility Spectrum Disorder

Abstract Aims This study aims to investigate pediatric hypermobile Ehlers–Danlos syndrome (hEDS) and hypermobility spectrum disorder (HSD) pain features and management strategies. Methods This is a mixed-methods, cross-sectional study design using patient-reported outcomes in 21 children diagnosed with hEDS/HSD. Children who reported bothersome pain were interviewed for pain features. The Child Activity Limitation Interview-21, the Brief Pain Inventory pain interference items, and the Functional Disability Inventory were used to investigate pain interference. To evaluate psychological symptoms regarding pain, the pediatric version of the Survey of Pain Attitude and the child version of the Pain Catastrophizing Scale were used. Results Nineteen children had bothersome pain and of them, eight children reported constant pain. The most frequently reported regions of pain were at the ankle (mild pain) and the back (moderate-to-severe pain). Children reported mild-to-moderate pain interference and believed medications were beneficial for their pain management. Nineteen children sought treatment and of those 16 children used to exercise and acetaminophen and 13 visited physicians as a means of treatment. Parents were overall satisfied with their child’s treatment (13 out of 19). Conclusions Sufficient awareness of pain-related symptoms and understanding of the treatment strategies in early childhood is needed to prevent deleterious consequences in adulthood.
Real‐time radial reconstruction with domain transform manifold learning for MRI‐guided radiotherapy

Abstract Background MRI‐guidance techniques that dynamically adapt radiation beams to follow tumor motion in real time will lead to more accurate cancer treatments and reduced collateral healthy tissue damage. The gold‐standard for reconstruction of undersampled MR data is compressed sensing (CS) which is computationally slow and limits the rate that images can be available for real‐time adaptation. Purpose Once trained, neural networks can be used to accurately reconstruct raw MRI data with minimal latency. Here, we test the suitability of deep‐learning‐based image reconstruction for real‐time tracking applications on MRI‐Linacs. Methods We use automated transform by manifold approximation (AUTOMAP), a generalized framework that maps raw MR signal to the target image domain, to rapidly reconstruct images from undersampled radial k‐space data. The AUTOMAP neural network was trained to reconstruct images from a golden‐angle radial acquisition, a benchmark for motion‐sensitive imaging, on lung cancer patient data and generic images from ImageNet. Model training was subsequently augmented with motion‐encoded k‐space data derived from videos in the YouTube‐8M dataset to encourage motion robust reconstruction. Results AUTOMAP models fine‐tuned on retrospectively acquired lung cancer patient data reconstructed radial k‐space with equivalent accuracy to CS but with much shorter processing times. Validation of motion‐trained models with a virtual dynamic lung tumor phantom showed that the generalized motion properties learned from YouTube lead to improved target tracking accuracy. Conclusion AUTOMAP can achieve real‐time, accurate reconstruction of radial data. These findings imply that neural‐network‐based reconstruction is potentially superior to alternative approaches for real‐time image guidance applications.