Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Bayesian Network Learning to Infer Sparse Models From Time Series Gene Expression Data

One of the key challenges in systems biology is to derive gene regulatory networks (GRNs) from complex high-dimensional sparse data. Bayesian networks (BNs) and dynamic Bayesian networks (DBNs) have been widely applied to infer GRNs from gene expression data. GRNs are typically sparse but traditional approaches of BN structure learning to elucidate GRNs often produce many spurious (false positive) edges. We present two new BN scoring functions, which are extensions to the Bayesian Information Criterion (BIC) score, with additional penalty terms and use them in conjunction with DBN structure search methods to find a graph structure that maximises the proposed scores. Our BN scoring functions offer better solutions for inferring networks with fewer spurious edges compared to the BIC score. The proposed methods are evaluated extensively on auto regressive and DREAM4 benchmarks. We found that they significantly improve the precision of the learned graphs, relative to the BIC score. The proposed methods are also evaluated on three real time series gene expression datasets. The results demonstrate that our algorithms are able to learn sparse graphs from high-dimensional time series data. The implementation of these algorithms is open source and is available in form of an R package on GitHub at https://github.com/HamdaBinteAjmal/DBN4GRN, along with the documentation and tutorials.
Risk of Anogenital Warts in Renal Transplant Recipients Compared with Immunocompetent Controls: A Cross-sectional Clinical Study

Renal transplant recipients have increased risk of human papilloma virus-related anogenital (pre)cancers. Less is known about their risk of anogenital warts. The aim of this study was to estimate the prevalence and odds of anogenital warts in renal transplant recipients compared with immunocompetent controls, and to assess risk factors for intra- and perianal warts in renal transplant recipients. The study examined 248 renal transplant recipients and 250 controls for cutaneous and mucosal anogenital warts. Participants completed a questionnaire on lifestyle and sexual habits. For external anogenital warts (including penile, vulvar and perianal warts), renal transplant recipients had higher prevalence and odds than controls, both in men (8.1% vs 1.6%, adjusted odds ratio (ORadjusted)=5.09, 95% confidence interval (95% CI), 1.03–25.04) and women (11.3% vs 1.6%, ORadjusted=8.09, 95% CI 1.69–38.82). For intra-anal warts, there was no clear pattern of higher odds in renal transplant recipients than controls. Current smoking and having had receptive anal sex increased the risk of intra-/perianal warts in renal transplant recipients. In conclusion, renal transplant recipients in this study had higher odds of external anogenital warts than controls.
Comparing the frequency of CD33+ pSTAT3+ myeloid‐derived suppressor cells and IL‐17+ lymphocytes in patients with prostate cancer and benign prostatic hyperplasia

Prostate cancer (PCa) is one of the most epidemic types of cancer in men. The tumor microenvironment (TME) of PCa is involved in the emergence of immunosuppressive factors such as myeloid‐derived suppressor cells (MDSC), which regulate the immune system by several mechanisms, including interleukin (IL)‐10 production. On the other hand, IL‐17+ helper T cells (Th17) induce MDSCs and chronic inflammation in TME by producing IL‐17. This study demonstrated that the frequency of CD33+ pSTAT3+ MDSC and IL‐17+ lymphocyte as well as IL‐10 messenger RNA (mRNA) expression were significantly higher in the PCa patients than in the benign prostatic hyperplasia (BPH) group. Moreover, there was no significant relationship between the frequency of CD33+ pSTAT3+ MDSC, and IL‐17+ lymphocyte with Gleason scores in the PCa group. We suggested that the higher frequency of CD33+ pSTAT3+ MDSC and IL‐17+ lymphocyte and the more frequent expression of IL‐10 mRNA in PCa patients may play roles in tumor progression from BPH to PCa.
Mucin‐Like Glycoproteins Modulate Interfacial Properties of a Mimetic Ocular Epithelial Surface

Dry eye disease (DED) has high personal and societal costs, but its pathology remains elusive due to intertwined biophysical and biochemical processes at the ocular surface. Specifically, mucin deficiency is reported in a subset of DED patients, but its effects on ocular interfacial properties remain unclear. Herein a novel in vitro mucin‐deficient mimetic ocular surface (Mu‐DeMOS) with a controllable amount of membrane‐tethered mucin molecules is developed to represent the diseased ocular surfaces. Contact angle goniometry on mimetic ocular surfaces reveals that high surface roughness, but not the presence of hydrophilic mucin molecules, delivers constant hydration over native ocular surface epithelia. Live‐cell rheometry confirms that the presence of mucin‐like glycoproteins on ocular epithelial cells reduces shear adhesive strength at cellular interfaces. Together, optimal surface roughness and surface chemistry facilitate sustainable lubrication for healthy ocular surfaces, while an imbalance between them contributes to lubrication‐related dysfunction at diseased ocular epithelial surfaces. Furthermore, the restoration of low adhesive strength at Mu‐DeMOS interfaces through a mucin‐like glycoprotein, recombinant human lubricin, suggests that increased frictional damage at mucin‐deficient cellular surfaces may be reversible. More broadly, these results demonstrate that Mu‐DeMOS is a promising platform for drug screening assays and fundamental studies on ocular physiology.
Dietary supplementation of a Saccharomyces cerevisiae fermentation product attenuates exercise-induced stress markers in young horses

Abstract Mitigation of exercise-induced stress is of key interest in determining ways to optimize performance horse health. To test the hypothesis that dietary supplementation of a Saccharomyces cerevisiae fermentation product would decrease markers of exercise-induced stress and inflammation in young horses, Quarter Horse yearlings (mean ± SD; 9 ± 1 mo) were randomly assigned to receive either no supplementation (CON; n = 8) or 21 g/d S. cerevisiae fermentation product (10.5 g/feeding twice daily; SCFP; n = 10) top-dressed on a basal diet of custom-formulated grain as well as ad libitum Coastal bermudagrass hay. After 8 wk of dietary treatments, horses underwent a 2-h submaximal exercise test (SET) on a free-stall mechanical exerciser. Serum was collected before dietary treatment supplementation (week 0), at week 8 pre-SET, and 0, 1, and 6 h post-SET and analyzed for concentrations of cortisol and serum amyloid A (SAA) by commercial enzyme-linked immunosorbent assay (ELISA) and for cytokine concentrations by commercial bead-based ELISA. Data were analyzed using linear models with repeated measures in SAS v9.4. From week 0 to 8 (pre-SET), serum cortisol decreased (P = 0.01) and SAA did not change, but neither were affected by diet. Serum concentrations of all cytokines decreased from week 0 to 8 (P ≤ 0.008), but granulocyte colony-stimulating factor (G-CSF), granulocyte-macrophage colony-stimulating factor, and interleukin-8 (IL-8) decreased to a greater extent in CON than in SCFP horses (P ≤0.003). In response to the week 8 SET, serum cortisol increased in all horses (P < 0.0001) but returned to pre-SET levels by 1 h post-SET in horses receiving SCFP. At 6 h post-SET, cortisol concentrations in CON horses returned to pre-SET concentrations, whereas cortisol declined further in SCFP horses to below pre-SET levels (P = 0.0002) and lower than CON (P = 0.003) at that time point. SAA increased at 6 h post-SET in CON (P < 0.0001) but was unchanged through 6 h in SCFP horses. All cytokines except G-CSF increased in response to the SET (P < 0.0001) but showed differing response patterns. Concentrations of IL-1β, IL-6, and tumor necrosis factor-alpha were lesser (P ≤ 0.05), and concentrations of G-CSF and IL-18 tended to be lesser (P ≤ 0.09) in SCFP compared with CON horses throughout recovery from the SET. In summary, 8 wk of dietary supplementation with 21 g/d of SCFP may mitigate cellular stress following a single, prolonged submaximal exercise bout in young horses.
Disclosures of harming others during their most recent drinking session: Findings from a large national study of heavy-drinking adolescents.

INTRODUCTION The extant Alcohol's Harms to Others (AHTO) literature is largely comprised of reports from victims. We investigated AHTO from perpetrators' perspectives, including how harms were associated with individual characteristics, and alcohol quantities consumed during the perpetration incident. METHODS Participants (N = 2932) were 14-19 years old, recruited primarily through social media and screened as risky drinkers. They completed face-to-face (n = 594) or self-administered (n = 2338) surveys. They self-reported whether during their last risky drinking session (LRDS) they had perpetrated any verbal abuse, physical abuse or property damage. A multinomial logistic regression examined whether nine factors were associated with perpetrating zero, one or 2+ categories of AHTO. RESULTS Eleven percent (n = 323) reported perpetrating at least one form of AHTO (7.5% verbal, 1.9% physical and 4.6% property). Perpetration of AHTO at LRDS was uniquely associated with: younger age, male gender, experiences of childhood physical punishment, greater perpetration incident-specific drinking, concurrent illicit drug use, and less frequent use of safety strategies while drinking in the past 12 months. Controlling for the other variables, an increase of six Australian standard drinks (60 g of alcohol) increased the odds of perpetration by 15% [95% confidence interval (CI) adjusted odds ratio (AOR) 1.08, 1.23], and an increase of 15 Australian standard drinks increased the odds by 42% (95% CI AOR 1.20, 1.69). DISCUSSION AND CONCLUSIONS Individual characteristics, larger quantities of alcohol consumed, and a disinclination to practice harm reduction amplified risk of AHTO perpetration. This has implications for health promotion and risk prevention/reduction strategies.
Regions of genetic divergence in depth‐separated Sebastes rockfish species pairs: Depth as a potential driver of speciation

Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation‐driving adaptations, particularly along a depth gradient. A reduced‐representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black‐and‐yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation‐with‐gene‐flow evolutionary model followed by post‐speciation selective sweeps within each species. Limited whole‐genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.
Atom Probe Tomography Investigations of Ag Nanoparticles Embedded in Pulse-Electrodeposited Ni Films

Abstract Atomic mapping of nanomaterials, in particular nanoparticles, using atom probe tomography (APT) is of great interest, as their properties strongly depend on shape, size, and composition. However, APT analyses of nanoparticles are extremely challenging, and there is an urgent need for developing robust and universally applicable sample preparation methods. Herein, we explored a method based on pulse electrodeposition to embed Ag nanoparticles in a Ni matrix and prepare APT specimens from the resulting composite film. By systematically varying the duty cycle during pulse electrodeposition, the dispersion and number density of the nanoparticles within the matrix was significantly enhanced as compared to DC electrodeposition. Several Ag nanoparticles were analyzed with APT from such samples. Shape distortions and biased compositions were observed for the Ag nanoparticles after applying a standard data reconstruction protocol. Numerical simulations of the field evaporation process showed that such artifacts were caused by a difference in the evaporation field of Ni and Ag and a local magnification effect. We expect such detrimental effects to be mitigated by a careful selection of the matrix material, matching the evaporation field of the nanoparticles. Furthermore, we anticipate that the method presented herein can be extended to a wider range of nanomaterials.
Vulnerability of agriculture to climate change increases the risk of child malnutrition: Evidence from a large-scale observational study in India

Introduction The impact of climate change on agriculture and food security has been examined quite thoroughly by researchers globally as well as in India. While existing studies provide evidence on how climate variability affects the food security and nutrition, research examining the extent of effect vulnerability of agriculture to climate change can have on nutrition in India are scarce. This study examined a) the association between the degree of vulnerability in agriculture to climate change and child nutrition at the micro-level b) spatial effect of climate vulnerability on child nutrition, and c) the geographical hotspots of both vulnerability in agriculture to climate change and child malnutrition. Methods The study used an index on vulnerability of agriculture to climate change and linked it to child malnutrition indicators (stunting, wasting, underweight and anaemia) from the National Family Health Survey 4 (2015–16). Mixed-effect and spatial autoregressive models were fitted to assess the direction and strength of the relationship between vulnerability and child malnutrition at macro and micro level. Spatial analyses examined the within-district and across-district spill-over effects of climate change vulnerability on child malnutrition. Results Both mixed-effect and spatial autoregressive models found that the degree of vulnerability was positively associated with malnutrition among children. Children residing in districts with a very high degree of vulnerability were more like to have malnutrition than those residing in districts with very low vulnerability. The analyses found that the odds of a child suffering from stunting increased by 32%, wasting by 42%, underweight by 45%, and anaemia by 63% if the child belonged to a district categorised as very highly vulnerable when compared to those categorised as very low. The spatial analysis also suggested a high level of clustering in the spatial distribution of vulnerability and malnutrition. Hotspots of child malnutrition and degree of vulnerability were mostly found to be clustered around western-central part of India. Conclusion Study highlights the consequences that vulnerability of agriculture to climate change can have on child nutrition. Strategies should be developed to mitigate the effect of climate change on areas where there is a clustering of vulnerability and child malnutrition.
Time‐Efficient Inspiratory Muscle Strength Training Lowers Blood Pressure and Improves Endothelial Function, NO Bioavailability, and Oxidative Stress in Midlife/Older Adults With Above‐Normal Blood Pressure

Background High‐resistance inspiratory muscle strength training (IMST) is a novel, time‐efficient physical training modality. Methods and Results We performed a double‐blind, randomized, sham‐controlled trial to investigate whether 6 weeks of IMST (30 breaths/day, 6 days/week) improves blood pressure, endothelial function, and arterial stiffness in midlife/older adults (aged 50–79 years) with systolic blood pressure ≥120 mm Hg, while also investigating potential mechanisms and long‐lasting effects. Thirty‐six participants completed high‐resistance IMST (75% maximal inspiratory pressure, n=18) or low‐resistance sham training (15% maximal inspiratory pressure, n=18). IMST was safe, well tolerated, and had excellent adherence (≈95% of training sessions completed). Casual systolic blood pressure decreased from 135±2 mm Hg to 126±3 mm Hg (P<0.01) with IMST, which was ≈75% sustained 6 weeks after IMST (P<0.01), whereas IMST modestly decreased casual diastolic blood pressure (79±2 mm Hg to 77±2 mm Hg, P=0.03); blood pressure was unaffected by sham training (all P>0.05). Twenty‐four hour systolic blood pressure was lower after IMST versus sham training (P=0.01). Brachial artery flow‐mediated dilation improved ≈45% with IMST (P<0.01) but was unchanged with sham training (P=0.73). Human umbilical vein endothelial cells cultured with subject serum sampled after versus before IMST exhibited increased NO bioavailability, greater endothelial NO synthase activation, and lower reactive oxygen species bioactivity (P<0.05). IMST decreased C‐reactive protein (P=0.05) and altered select circulating metabolites (targeted plasma metabolomics) associated with cardiovascular function. Neither IMST nor sham training influenced arterial stiffness (P>0.05). Conclusions High‐resistance IMST is a safe, highly adherable lifestyle intervention for improving blood pressure and endothelial function in midlife/older adults with above‐normal initial systolic blood pressure. Registration URL: https://www.clinicaltrials. gov; Unique identifier: NCT03266510.
A Word Pair Dataset for Semantic Similarity and Relatedness in Korean Medical Vocabulary: Reference Development and Validation

Background The fact that medical terms require special expertise and are becoming increasingly complex makes it difficult to employ natural language processing techniques in medical informatics. Several human-validated reference standards for medical terms have been developed to evaluate word embedding models using the semantic similarity and relatedness of medical word pairs. However, there are very few reference standards in non-English languages. In addition, because the existing reference standards were developed a long time ago, there is a need to develop an updated standard to represent recent findings in medical sciences. Objective We propose a new Korean word pair reference set to verify embedding models. Methods From January 2010 to December 2020, 518 medical textbooks, 72,844 health information news, and 15,698 medical research articles were collected, and the top 10,000 medical terms were selected to develop medical word pairs. Attending physicians (n=16) participated in the verification of the developed set with 607 word pairs. Results The proportion of word pairs answered by all participants was 90.8% (551/607) for the similarity task and 86.5% (525/605) for the relatedness task. The similarity and relatedness of the word pair showed a high correlation (ρ=0.70, P<.001). The intraclass correlation coefficients to assess the interrater agreements of the word pair sets were 0.47 on the similarity task and 0.53 on the relatedness task. The final reference standard was 604 word pairs for the similarity task and 599 word pairs for relatedness, excluding word pairs with answers corresponding to outliers and word pairs that were answered by less than 50% of all the respondents. When FastText models were applied to the final reference standard word pair sets, the embedding models learning medical documents had a higher correlation between the calculated cosine similarity scores compared to human-judged similarity and relatedness scores (namu, ρ=0.12 vs with medical text for the similarity task, ρ=0.47; namu, ρ=0.02 vs with medical text for the relatedness task, ρ=0.30). Conclusions Korean medical word pair reference standard sets for semantic similarity and relatedness were developed based on medical documents from the past 10 years. It is expected that our word pair reference sets will be actively utilized in the development of medical and multilingual natural language processing technology in the future.
Small for Gestational Age Moderate to Late Preterm Children: A Neuropsychological Follow-up

ABSTRACT Determine whether SGA constitutes a neurodevelopmental risk-factor of MLP, exploring if potential developmental difficulties at toddlerhood persist and are related to school-age performance. 109 SGA and 109 adequate for gestational age MLP children were evaluated at 2 and at 6.5 y.o. SGA children obtained poorer results in several areas at both timepoints; and their development at toddlerhood strongly correlated with only some results at school-age. SGA confers vulnerability to MLP, evolving from global/unspecific difficulties in toddlerhood to a domain-specific profile (attentional/dysexecutive) at 6.5. Findings claim the need for neuropsychological follow-up in MLP to identify emerging difficulties.
Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions

Abstract Metazoan transcription factors distinguish their response elements from a large excess of similar sequences. We explored underlying principles of DNA shape read-out and factor cooperativity in chromatin using a unique experimental system. We reconstituted chromatin on Drosophila genomes in extracts of preblastoderm embryos, mimicking the naïve state of the zygotic genome prior to developmental transcription activation. We then compared the intrinsic binding specificities of three recombinant transcription factors, alone and in combination, with GA-rich recognition sequences genome-wide. For MSL2, all functional elements reside on the X chromosome, allowing to distinguish physiological elements from non-functional ‘decoy’ sites. The physiological binding profile of MSL2 is approximated through interaction with other factors: cooperativity with CLAMP and competition with GAF, which sculpts the profile by occluding non-functional sites. An extended DNA shape signature is differentially read out in chromatin. Our results reveal novel aspects of target selection in a complex chromatin environment.