Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of the spleen in Plasmodium vivax: a reticulocyte-prone non-lethal malaria

“Plasmodium vivax” es el parasit causant de malaria humana amb mes amplia distribucio i es responsable cada any de 100-300 milions de casos clinics, incloent algunes manifestacions severes i mort. P. vivax envaeix principalment reticulocits I es ampliament acceptat que els reticulocits infectats no citoadhereixen en els capil•lars d'organs interns, tenint un pas obligat per la melsa. Es desconeix com P. vivax escapa del pas per la melsa, el nostre major organ limfoide, i evita aixi ser fagocitat. La nostra hipotesi postula que aquest parasit indueix la formacio de cel•lules de barrera a la melsa, on reticulocits infectats citoadhereixen de manera especifica per protegir-se de l’atac dels macrofags. Per avancar en aquesta hipotesi, hem utilitzat el model muri de malaria en ratolins Balb/c infectats amb una soca noletal que infecta principalment reticulocits, P. yoelii 17X, semblant a P. vivax, i una soca letal amb tropisme per normocits, P. yoelii 17XL, semblant a P. falciparum. Per investigar la funcio i l’estructura de la melsa en la malaria, aixi com les caracteristiques dinamiques dels processos impulsats pel parasit, hem implementat la microscopia intravital i la ressonancia magnetica de la melsa del ratoli en infeccions experimentals. Notablement, hem observat major acumulacio de parasits, motilitat reduida, perdua de direccionalitat, augment en el temps de residencia i ressonancia magnetica alterada nomes a la melsa dels ratolins infectats amb 17X. D'altra banda, aquestes diferencies s’han associat amb la formacio d'una barrera d'origen fibroblastic induida en la polpa vermella de les melses de ratolins infectats amb la soca no-letal, acompanyada d'evasio dels macrofags de la polpa vermella i adherencia dels globuls vermells infectats a la barrera. A mes, hem confirmat l'adhesio de reticulocits infectats per P. vivax de pacients humans a crioseccions de melsa humana i explorat el paper de les proteines Vir en aquesta adhesio. Les nostres dades suggereixen que en la malaria no-letal el pas per la melsa es diferent del que es coneix en altres especies de Plasmodium i obren noves vies per a estudis funcionals i estructurals d'aquest organ limfoide en la malaria.
Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15

This article reports and analyzes the results of protein complex model accuracy estimation by our methods (DeepUMQA3 and GraphGPSM) in the 15th Critical Assessment of techniques for protein Structure Prediction (CASP15). The new deep learning‐based multimeric complex model accuracy estimation methods are proposed based on the ensemble of three‐level features coupling with deep residual/graph neural networks. For the input multimeric complex model, we describe it from three levels: overall complex features, intra‐monomer features, and inter‐monomer features. We designed an overall ultrafast shape recognition (USR) to characterize the relationship between local residues and the overall complex topology, and an inter‐monomer USR to characterize the relationship between the residues of one monomer and the topology of other monomers. DeepUMQA3 (Group name: GuijunLab‐RocketX) ranked first in the interface residue accuracy estimation of CASP15. The Pearson correlation between the interface residue Local Distance Difference Test (lDDT) predicted by DeepUMQA3 and the real lDDT is 0.570, the only method that exceeds 0.5. Among the top 5 methods, DeepUMQA3 achieved the highest Pearson correlation of lDDT on 25 out of 39 targets. GraphGPSM (Group name: GuijunLab‐PAthreader) has TM‐score Pearson correlations greater than 0.9 on 14 targets, showing a good ability to estimate the overall fold accuracy. The DeepUMQA3 server is available at http://zhanglab-bioinf.com/DeepUMQA/ and the GraphGPSM server is available at http://zhanglab-bioinf.com/GraphGPSM/.
Cancer drug response prediction with surrogate modeling-based graph neural architecture search

Abstract Motivation Understanding drug–response differences in cancer treatments is one of the most challenging aspects of personalized medicine. Recently, graph neural networks (GNNs) have become state-of-the-art methods in many graph representation learning scenarios in bioinformatics. However, building an optimal handcrafted GNN model for a particular drug sensitivity dataset requires manual design and fine-tuning of the hyperparameters for the GNN model, which is time-consuming and requires expert knowledge. Results In this work, we propose AutoCDRP, a novel framework for automated cancer drug–response predictor using GNNs. Our approach leverages surrogate modeling to efficiently search for the most effective GNN architecture. AutoCDRP uses a surrogate model to predict the performance of GNN architectures sampled from a search space, allowing it to select the optimal architecture based on evaluation performance. Hence, AutoCDRP can efficiently identify the optimal GNN architecture by exploring the performance of all GNN architectures in the search space. Through comprehensive experiments on two benchmark datasets, we demonstrate that the GNN architecture generated by AutoCDRP surpasses state-of-the-art designs. Notably, the optimal GNN architecture identified by AutoCDRP consistently outperforms the best baseline architecture from the first epoch, providing further evidence of its effectiveness. Availability and implementation https://github.com/BeObm/AutoCDRP.
Performance Characteristics of Candidate Criteria for Hemodialysis Arteriovenous Fistula Maturation

Visual Abstract Background Twenty to 60% of newly created hemodialysis arteriovenous fistulas do not mature adequately for use. One barrier to developing interventions to improve fistula outcomes is a lack of standardized criteria for maturation. Methods Using data from the multicenter, prospective Hemodialysis Fistula Maturation (HFM) Study, we determined sensitivities, specificities, and positive and negative predictive values of multiple candidate maturation criteria using the HFM Study maturation criteria as the reference. We also compared, across the maturation criteria, relationships between maturation and fistula survival using Cox proportional hazards models. Results We included 535 of the 602 HFM Study participants. The median (interquartile range) age was 57 (47–65) years, 70% were men, and 45% were Black participants. Depending on the criterion and time frame for ascertainment (3, 4, 5, 6, or 9 months), sensitivities ranged from 57% to 100%, specificities ranged from 85% to 100%, positive predictive values ranged from 88% to 100%, and negative predictive values ranged from 65% to 100%. For all criteria, areas under the curve for the 6-month (0.90–0.97 for unassisted maturation and 0.89–0.95 for overall maturation) and 9-month time frames were similar. Attainment of unassisted maturation was associated with lower risks of fistula abandonment, with hazard ratios ranging from 0.10 to 0.40 depending on the criterion and time frame. Eliminating dialysis adequacy indicators, or simplifying the criteria in other ways, had little effect on performance characteristics. Conclusions High performance characteristics are maintained with maturation criteria that are simpler and less burdensome to ascertain than the HFM Study outcome measure.
Dynamic Study of Intercalation/Deintercalation of Ionic Liquids in Multilayer Graphene Using an Alternating Current Raman Spectroscopy Technique

We report Raman spectra and infrared (IR) imaging collected during the intercalation–deintercalation half cycles in a multilayer graphene (MLG) device (∼100 layers) operating at 0.2–10 Hz. The device consists of a MLG/alumina membrane/copper stack, in which the alumina membrane is filled with ionic liquid [DEME][TFSI], forming an electrochemical cell. Upon the application of a positive voltage, the TFSI– anions intercalate into the interstitial spaces in the MLG. The incident laser light is modulated using an optical chopper wheel that is synchronized with (and delayed with respect to) a 0.2–10 Hz alternating current (AC) voltage signal. Raman spectra taken just 200 ms apart show the emergence and disappearance of the intercalated G band mode at around 1610 cm–1. By integration of over hundreds of cycles, a significant Raman signal can be obtained. The intercalation/deintercalation is also monitored with thermal imaging via voltage-induced changes in the carrier density, complex dielectric function ε(ω), and thermal emissivity of the device.
Youth intentions to provide social support to a peer with a concussion

ABSTRACT Objectives 1) To describe demographic factors, concussion knowledge, attitudes, subjective norms, self-efficacy and intentions to provide social support to a peer with a concussion and 2) to examine if demographic factors and concussion knowledge are associated with components of the Theory of Planned Behavior. Methods The survey was completed between October 2018 and February 2019 by 200 youth (M = 15.30 years, SD = 1.52). Questions were designed for athletes and non-athletes and inquired about various types of social support. Data analysis included descriptive statistics, Wilcoxon Rank Sum Tests and Spearman’s Rank-Order Correlation Coefficients. Results More favorable attitudes and intentions to provide social support were observed among females (W = 2576, p ≤ 0.001; W = 2411, p ≤ 0.001), older youth (rho = 0.32, p ≤ 0.001; rho = 0.41, p ≤ 0.001) and those with higher concussion knowledge (rho = 0.29, p ≤ 0.001; rho = 0.22; p ≤ 0.001). Participating in sports with a high-risk of concussion was associated with lower attitudes and intentions to provide social support (W = 6677; p ≤ 0.001; W = 6721; p ≤ 0.001). Self-reported concussion history or knowing someone with a concussion history was not significantly associated with social support intentions. Conclusion This study identified characteristics of youth who had positive intentions to provide social support. These findings identify individuals who may model providing social support to a peer, as well as opportunities for future concussion education.
Association of postoperative length of stay with outcomes following orthotopic heart transplantation—A national analysis

Background: In the absence of standardized recovery protocols, there is little evidence to guide postoperative care to ensure optimal in‐hospital and long‐term outcomes following heart transplantation (HT). Using two national databases, we examined the association between postoperative length of stay (LOS) with patient/graft survival, index hospitalization costs, and non‐elective readmissions.
Intravascular hemolysis triggers NAFLD characterized by a deregulation of lipid metabolism and lipophagy blockade

Intravascular hemolysis is a common feature of different clinical entities, including sickle cell disease and malaria. Chronic hemolytic disorders are associated with hepatic damage; however, it is unknown whether heme disturbs lipid metabolism and promotes liver steatosis, thereby favoring the progression to nonalcoholic fatty liver disease (NAFLD). Using an experimental model of acute intravascular hemolysis, we report here the presence of liver injury in association with microvesicular lipid droplet deposition. Hemolysis promoted serum hyperlipidemia and altered intrahepatic triglyceride fatty acid composition, with increments in oleic, palmitoleic, and palmitic acids. These findings were related to augmented expression of transporters involved in fatty acid uptake (CD36 and MSR1) and deregulation of LDL transport, as demonstrated by decreased levels of LDL receptor and increased PCSK9 expression. Hemolysis also upregulated hepatic enzymes associated with cholesterol biosynthesis (SREBP2, HMGC1, LCAT, SOAT1) and transcription factors regulating lipid metabolism (SREBP1). Increased LC3II/LC3I ratio and p62/SQSTM1 protein levels were reported in mice with intravascular hemolysis and hepatocytes stimulated with heme, indicating a blockade of lipophagy. In cultured hepatocytes, cell pretreatment with the autophagy inductor rapamycin diminished heme‐mediated toxicity and accumulation of lipid droplets. In conclusion, intravascular hemolysis enhances liver damage by exacerbating lipid accumulation and blocking the lipophagy pathway, thereby promoting NAFLD. These new findings have a high translational potential as a novel NAFLD‐promoting mechanism in individuals suffering from severe hemolysis episodes. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Association of Aspirin with Dementia or Mild Cognitive Impairment: A Systematic Review and Meta-Analysis of Randomized Trials

Background: At present, the effect of aspirin in preventing dementia or mild cognitive impairment (MCI) is controversial. Clarifying their association is of interest for subsequent relevant clinical trials. Methods: Four databases (PubMed, Embase, Web of Science, and the Cochrane Library) were searched from inception to May 12, 2023, for randomized controlled trials (RCTs) that explored the effects between aspirin and dementia or MCI. Two reviewers independently extracted and analyzed data using Stata software. Discrepancy was resolved by a third reviewer. The primary outcomes were dementia and MCI. The secondary outcomes were cognitive decline and changes in cognitive scores. Results: Five RCTs with 46,804 participants at randomization were included. For the primary outcomes, low-certainty evidence showed that aspirin was not associated with dementia (odds ratio [OR] = 0.93, 95% confidence interval [CI]: [0.85, 1.03], p > 0.05, I2 = 0%) or MCI (OR = 1.00, 95% CI: [0.88, 1.14], p > 0.05, I2 = 3.3%). For the secondary outcomes, moderate-certainty evidence showed that aspirin was not associated with cognitive decline (OR = 1.02, 95% CI: [0.93, 1.11], p > 0.05, I2 = 0%) and a change in global cognitive score (standard mean difference [SMD] = −0.01, 95% CI: [−0.03, 0.02], p > 0.05, I2 = 0%). Low-certainty evidence showed that aspirin was not associated with a change in verbal learning memory score (SMD = −0.04, 95% CI: [−0.09, 0.01], p > 0.05; I2 = 72.5%). Conclusions: Low- and moderate-certainty evidence showed that aspirin was not associated with dementia, MCI, cognitive decline, or better cognitive scores. Future research may need to focus more on subtypes of dementia, mainly vascular dementia or other vascular neurocognitive diseases, and assess whether aspirin has long-term clinical benefits in a large sample of patients with dementia or MCI.
Perceptron sous forme duale tronquée et variantes

Machine Learning is a part of the artificial intelligence and is used in many fields in science. It is divided into three categories : supervised, not supervised and by reinforcement. This master’s paper will relate only the supervised learning and more precisely the classification of datas. One of the first algorithms in classification, the perceptron, was proposed in the Sixties. We propose an alternative of this algorithm, which we call the truncated dual perceptron, which allows the stop of the algorithm according to a new criterion. We will compare this new alternative with other alternatives of the perceptron. Moreover, we will use the truncated dual perceptron to build more complex classifiers like the «Bayes Point Machines».
Comprehensive viewpoints on heart rate variability at high altitude

ABSTRACT Objectives Hypoxia is a physiological state characterized by reduced oxygen levels in organs and tissues. It is a common clinicopathological process and a major cause of health problems in highland areas. Heart rate variability (HRV) is a measure of the balance in autonomic innervation to the heart. It provides valuable information on the regulation of the cardiovascular system by neurohumoral factors, and changes in HRV reflect the complex interactions between multiple systems. In this review, we provide a comprehensive overview of the relationship between high-altitude hypoxia and HRV. We summarize the different mechanisms of diseases caused by hypoxia and explore the changes in HRV across various systems. Additionally, we discuss relevant pharmaceutical interventions. Overall, this review aims to provide research ideas and assistance for in-depth studies on HRV. By understanding the intricate relationship between high-altitude hypoxia and HRV, we can gain insights into the underlying mechanisms and potential therapeutic approaches to mitigate the effects of hypoxia on cardiovascular and other systems. Methods The relevant literature was collected systematically from scientific database, including PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), Baidu Scholar, as well as other literature sources, such as classic books of hypoxia. Results There is a close relationship between heart rate variability and high-altitude hypoxia. Heart rate variability is an indicator that evaluates the impact of hypoxia on the cardiovascular system and other related systems. By improving the observation of HRV, we can estimate the progress of cardiovascular diseases and predict the impact on other systems related to cardiovascular health. At the same time, changes in heart rate variability can be used to observe the efficacy of preventive drugs for altitude related diseases. Conclusions HRV can be used to assess autonomic nervous function under various systemic conditions, and can be used to predict and monitor diseases caused by hypoxia at high altitude. Investigating the correlation between high altitude hypoxia and heart rate variability can help make HRV more rapid, accurate, and effective for the diagnosis of plateau-related diseases.
Fit for Purpose? The Suitability of Oral Health Outcome Measures to Inform Policy

Measuring outcomes for oral health is frequently undertaken using the decayed, missing, and filled teeth (DMFT) index. DMFT measures dental caries experience. As a condition-specific outcome, it is not relatable to consumers, nor does it capture the impact of dental caries on quality of life or outcomes that matter most to consumers. Efficient resource allocation should include patient values. It is crucial to use measurement instruments that record consumer values or preferences for oral health and oral diseases. These measures are often called patient-reported outcome measures and/or patient-reported experience measures. Outcome measures relevant to patients are recommended to influence and inform policy decision-making for oral health. Knowledge Transfer Statement: Oral health research and program evaluation should consider alternative outcome measures for population oral health other than the DMFT index.
Vitamin D receptor and binding protein genes variants in patients with migraine

Several studies have shown a relationship between vitamin D and migraine, including the association between decreased serum 25‐hydroxyvitamin D in patients with migraine and the positive effects of vitamin D supplementations in the therapy of this disease. Two single‐nucleotide variants (SNVs) vitamin D receptor (VDR) gene, VDR rs2228570, and VDR rs731236 have shown an association with migraine risk in a previous case–control association study, while an exome sequencing study identified a rare variant in GC vitamin D binding protein gene. This study aims to look for the association between several common variants in these two genes and the risk for migraine.
The Impact of Victim Demeanor on Jurors’ Perceptions of a Sexual Harassment Victim

Despite the prevalence of sexual harassment in the workplace, little research has investigated the role of victim demeanor in perceptions of sexual harassment cases. The present study varied whether the victim cried while testifying by using drawings of the victim. Participants were presented with a civil trial summary and asked to make trial-related judgments. Overall, factors representing participants’ perceptions of victim credibility and victim negative emotions were higher when the victim cried than when she did not. The factor representing victim credibility also mediated the relationship between victim demeanor and trial outcomes. Finally, cognitive networks demonstrated that victim demeanor was important to participants’ decision-making. The legal implications of the findings are discussed.
Prediction of coexisting invasive carcinoma on ductal carcinoma in situ (DCIS) lesions by mass spectrometry imaging

Due to limited biopsy samples, ~20% of DCIS lesions confirmed by biopsy are upgraded to invasive ductal carcinoma (IDC) upon surgical resection. Avoiding underestimation of IDC when diagnosing DCIS has become an urgent challenge in an era discouraging overtreatment of DCIS. In this study, the metabolic profiles of 284 fresh frozen breast samples, including tumor tissues and adjacent benign tissues (ABTs) and distant surrounding tissues (DSTs), were analyzed using desorption electrospray ionization‐mass spectrometry (DESI‐MS) imaging. Metabolomics analysis using DESI‐MS data revealed significant differences in metabolite levels, including small‐molecule antioxidants, long‐chain polyunsaturated fatty acids (PUFAs) and phospholipids between pure DCIS and IDC. However, the metabolic profile in DCIS with invasive carcinoma components clearly shifts to be closer to adjacent IDC components. For instance, DCIS with invasive carcinoma components showed lower levels of antioxidants and higher levels of free fatty acids compared to pure DCIS. Furthermore, the accumulation of long‐chain PUFAs and the phosphatidylinositols (PIs) containing PUFA residues may also be associated with the progression of DCIS. These distinctive metabolic characteristics may offer valuable indications for investigating the malignant potential of DCIS. By combining DESI‐MS data with machine learning (ML) methods, various breast lesions were discriminated. Importantly, the pure DCIS components were successfully distinguished from the DCIS components in samples with invasion in postoperative specimens by a Lasso prediction model, achieving an AUC value of 0.851. In addition, pixel‐level prediction based on DESI‐MS data enabled automatic visualization of tissue properties across whole tissue sections. Summarily, DESI‐MS imaging on histopathological sections can provide abundant metabolic information about breast lesions. By analyzing the spatial metabolic characteristics in tissue sections, this technology has the potential to facilitate accurate diagnosis and individualized treatment of DCIS by inferring the presence of IDC components surrounding DCIS lesions. © 2023 The Pathological Society of Great Britain and Ireland.
Relation between HLA and copy number variation of steroid 21-hydroxylase in a Swedish cohort of patients with autoimmune Addison's disease.

OBJECTIVE Autoantibodies against the adrenal enzyme 21-hydroxylase is a hallmark manifestation in autoimmune Addison's disease (AAD). Steroid 21-hydroxylase is encoded by CYP21A2, which is located in the HLA region together with the highly similar pseudogene CYP21A1P. A high level of copy number variation is seen for the two genes, and therefore we asked if genetic variation of the CYP21 genes is associated with AAD. METHODS Using next-generation DNA sequencing, we estimated the copy number of CYP21A2 and CYP21A1P together with HLA alleles in 479 Swedish patients with AAD and autoantibodies against 21-hydroxylase, and in 1,393 healthy controls. RESULTS With 95% of individuals carrying two functional 21-hydroxylase genes, no difference in CYP21A2 copy number was found when comparing patients and controls. In contrast, we discovered a lower copy number of the pseudogene CYP21A1P among AAD patients (p = 5 x 10-44) together with associations of additional nucleotide variants in the CYP21 region. However, the strongest association was found for HLA-DQB1*02:01 (p = 9 x 10-63), which in combination with the DRB1*04:04-DQB1*03:02 haplotype imposed the greatest risk of AAD. CONCLUSIONS We identified strong associations between copy number variants in the CYP21 region and risk of AAD, although these associations most likely are due to linkage disequilibrium with disease-associated HLA class II alleles.