Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity.

De novo heterozygous loss-of-function mutations in PTEN are strongly associated with Autism spectrum disorders (ASD); however, it is unclear how heterozygous mutations in this gene affects different cell types during human brain development, and how these effects vary across individuals. Here, we used human cortical organoids from different donors to identify cell-type-specific developmental events that are affected by heterozygous mutations in PTEN. We profiled individual organoids by single-cell RNA-seq, proteomics, and spatial transcriptomics, and revealed abnormalities in developmental timing in human outer radial glia progenitors and deep layer cortical projection neurons, which varied with the donor genetic background. Calcium imaging in intact organoids showed that both accelerated and delayed neuronal development phenotypes resulted in similar abnormal activity of local circuits, irrespective of genetic background. The work reveals donor-dependent, cell-type specific developmental phenotypes of PTEN heterozygosity that later converge on disrupted neuronal activity.
Occurrence of pre- and postharvest multi-mycotoxins in durum wheat grains collected in 2020 and 2021 in two climatic regions of Tunisia

ABSTRACT Twenty two mycotoxins in 136 durum wheat collected from Tunisia in 2020 and 2021 were investigated. Mycotoxins were analyzed by UHPLCMS/MS. In 2020, 60.9% of the samples were contaminated with Aflatoxin B1 (AFB1) and/or enniatin. Whereas, in 2021, 34.4% were contaminated by enniatins. AFB1 was detected only in 2020, in the continental region (6/46) and all samples exceeded limits. AFB1 was detected in stored wheat (24-37.8 µg/kg) but also in pre-stored wheat (17-28.4 µg/kg) and in one sample collected in the field (21 µg/kg). Enniatin A1, enniatin B and enniatin B1 were detected in wheat collected in the field (30-7684 µg/kg), pre-storage (42-1266 µg/kg) and storage (65.8-498.2 µg/kg) from the continental region also, in sample collected in pre-storage (31.3-1410 µg/kg) and at harvest (48- 1060 µg/kg). Samples had a water activity less than 0.7 and moisture content ranged between 09-14%. AFB1 level represent a health risk to the Tunisian consumers.
Interdecadal variability in the thermal difference between western and eastern China and its association with rainfall anomalies

This study investigated the spring thermal difference between western and eastern China and its association with the rainfall anomalies using station and reanalysis data from 1960 to 2006. The spring thermal difference between western and eastern China underwent an obvious interdecadal shift around 1979. The thermal difference between western and eastern China was small during 1960–1978, which strengthened the southwesterly wind anomalies in line with the thermal wind. This enhanced the East Asian summer monsoon. In addition, the increase in rainfall over North China and decrease in rainfall over the Yangtze River were associated with the strong East Asian summer monsoon. However, during 1979–2006, the thermal difference between western and eastern China was large, which strengthened the northeasterly wind anomalies in line with the thermal wind. This supports the notion of weakened East Asian summer monsoon associated with the decrease in rainfall over North China and increase in rainfall over the Yangtze River.
Quality assessment of red blood cell concentrates from blood donors at the extremes of the age spectrum: The BEST collaborative study

Blood donors at the extremes of the age spectrum (16–19 years vs. ≥75 years) are characterized by increased risks of iron deficiency and anemia, and are often underrepresented in studies evaluating the effects of donor characteristics on red blood cells (RBC) transfusion effectiveness. The aim of this study was to conduct quality assessments of RBC concentrates from these unique age groups.
Wearable AI Reveals the Impact of Intermittent Fasting on Stress Levels in School Children During Ramadan

Intermittent fasting has been practiced for centuries across many cultures globally. Recently many studies have reported intermittent fasting for its lifestyle benefits, the major shift in eating habits and patterns is associated with several changes in hormones and circadian rhythms. Whether there are accompanying changes in stress levels is not widely reported especially in school children. The objective of this study is to examine the impact of intermittent fasting during Ramadan on stress levels in school children as measured using wearable artificial intelligence (AI). Twenty-nine school children (aged 13-17 years and 12M / 17F ratio) were given Fitbit devices and their stress, activity and sleep patterns analyzed 2 weeks before, 4 weeks during Ramadan fasting and 2 weeks after. This study revealed no statistically significant difference on stress scores during fasting, despite changes in stress levels being observed for 12 of the participants. Our study may imply intermittent fasting during Ramadan poses no direct risks in terms of stress, suggesting rather it may be linked to dietary habits, furthermore as stress score calculations are based on heart rate variability, this study implies fasting does not interfere the cardiac autonomic nervous system.
Attachment-Based Family Therapy to Improve Family Functioning in Adolescent Binge-Spectrum Eating Disorders: An Initial Evaluation Via Case Series Design

Binge-spectrum eating disorders (EDs; bulimia nervosa, binge eating disorder) often develop during adolescence and are associated with serious psychological and physical consequences. Current treatments for adolescents are highly behavioral in nature and while efficacious, many patients do not reach remission indicating that current treatments fail to target a key maintenance factor for EDs. One potential maintenance factor is poor family functioning (FF). In particular, high family conflict (e.g., arguing, critical comments) and low family cohesion (e.g., warmth, support) are known to maintain ED behaviors. Poor FF can (1) cause or exacerbate an adolescent’s use of ED behaviors to cope with life stress and/or (2) inhibit parents from being a resource to adolescents during ED treatment. Attachment-Based Family Therapy (ABFT) is specifically designed to improve FF, and thus may be a promising adjunct to behavioral ED intervention strategies. ABFT, however, has not been tested in adolescents with binge-spectrum EDs. Thus, the current study is the first to evaluate a 16-week adapted ABFT treatment for adolescents with EDs (N = 8, Mage = 16.00, 71.43% female, 71.43% White) fusing together behavioral treatment for EDs with ABFT for highest possible impact. Eight families were treated in an open pilot trial to examine treatment feasibility, acceptability, and preliminary efficacy on FF and eating pathology. Overall, findings were promising. ABFT + B treatment was feasible and acceptable and showed preliminary evidence that it could improve FF and ED behaviors. Future research will test this intervention in a larger sample and further examine the role of FF in maintaining ED symptoms.
Ten-Year Performance of Posterior 6-mm Implants with Single-Tooth Restorations: A Randomized Controlled Trial

The aim of the study was to compare the clinical and radiographic outcomes of short dental implants (6-mm test group, TG) to longer implants (10-mm control group, CG) with single crown restorations after 10 y of loading. Patients requiring single-tooth replacement in the posterior jaws were randomly assigned to TG or CG. Implants were loaded with screw-retained single crowns after a healing period of 10 wk. Follow-up appointments were scheduled yearly and comprised patient-adapted oral hygiene reinstructions and polishing of all teeth and implants. After 10 y, clinical and radiographical parameters were assessed again. Out of initially 94 patients (47 in TG and CG, each), 70 (36 TG and 34 CG) could be reassessed. Survival rates accounted for 85.7% (TG) and 97.1% (CG), without significant intergroup difference (P = 0.072). All but 1 lost implant had been located in the lower jaw. These implants were not lost due to peri-implantitis but due to a late loss of osseointegration without signs of inflammation and with actually stable marginal bone levels (MBLs) over the investigation period. In general, MBLs were stable with medians (interquartile ranges) of 0.13 (0.78) mm and 0.08 (1.2) mm, for TG and CG, without significant intergroup differences. Crown-to-implant ratio showed a highly significant intergroup difference of 1.06 ± 0.18 mm and 0.73 ± 0.17 mm (P < 0.001). Few technical complications (i.e., screw loosening or chipping) were registered during the investigation period. In conclusion, given stringent professional maintenance, short dental implants with single-crown restorations show a slightly worse but statistically not different survival rate after 10 y, especially in the lower jaw, but can still be considered a valuable alternative, especially when vertical bone dimensions are limited (German Clinical Trials Registry: DRKS00006290).
Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures

Abstract Motivation Non-canonical (or non-B) DNA are genomic regions whose three-dimensional conformation deviates from the canonical double helix. Non-B DNA play an important role in basic cellular processes and are associated with genomic instability, gene regulation, and oncogenesis. Experimental methods are low-throughput and can detect only a limited set of non-B DNA structures, while computational methods rely on non-B DNA base motifs, which are necessary but not sufficient indicators of non-B structures. Oxford Nanopore sequencing is an efficient and low-cost platform, but it is currently unknown whether nanopore reads can be used for identifying non-B structures. Results We build the first computational pipeline to predict non-B DNA structures from nanopore sequencing. We formalize non-B detection as a novelty detection problem and develop the GoFAE-DND, an autoencoder that uses goodness-of-fit (GoF) tests as a regularizer. A discriminative loss encourages non-B DNA to be poorly reconstructed and optimizing Gaussian GoF tests allows for the computation of P-values that indicate non-B structures. Based on whole genome nanopore sequencing of NA12878, we show that there exist significant differences between the timing of DNA translocation for non-B DNA bases compared with B-DNA. We demonstrate the efficacy of our approach through comparisons with novelty detection methods using experimental data and data synthesized from a new translocation time simulator. Experimental validations suggest that reliable detection of non-B DNA from nanopore sequencing is achievable. Availability and implementation Source code is available at https://github.com/bayesomicslab/ONT-nonb-GoFAE-DND.
Numerical Investigation of the Fluid Flow around and Past a Circular Cylinder by Ansys Simulation

Flow around a circular cylinder is a fundamental fluid mechanics problem of practical importance. The dynamic characteristics of the pressure and velocity fields of unsteady incompressible laminar and turbulent wakes behind a circular cylinder are investigated numerically and analyzed simulation. The governing equations, written in the velocity pressure formulation are solved using 2-D finite volume method. In the present work is based on the cylinder diameter 10 2 Reynolds number for flow analysis slow and also turbulent based on the diameter of the cylindrical Reynolds number 10 5 as well as for the analysis of the flow around a cylindrical has been considered. The aim of this research is to investigate the influence of Reynolds number on flow parameters and verify the correctness of the calculations carried out by the governing equations of fluid mechanicsflow. Research on the hydraulic parameters of the flow around a cylinder help of ANSYS software. The frequencies of the drag and lift oscillations obtained theoretically agree well with the experimental results. The pressure and drag coefficients for different Reynolds numbers were also computed and compared with experimental and other numerical results. Due to faster convergence, 2-D finite volume method is found very much prospective for turbulent flow as well as laminar flow.
Cognitive assessment after stroke: A qualitative study of patients’ experiences

Objectives Clinical guidelines recommend early cognitive assessment after stroke to inform rehabilitation and discharge decisions. However, little is known about stroke survivors’ experiences of the cognitive assessment process. This qualitative study aimed to explore patients’ experiences of poststroke cognitive assessments. Design Stroke survivors were purposively sampled in an iterative process through a pool of research volunteers who had previously taken part in the Oxford Cognitive Screen Recovery study. Stroke survivors and their family caregivers were invited to participate in a semistructured interview steered by a topic guide. Interviews were audio recorded, transcribed and analysed using reflexive thematic analysis. Demographic, clinical and cognitive data were acquired from patients’ previous research data. Setting Stroke survivors were originally recruited from the acute inpatient unit at Oxford University Hospital (John Radcliffe), UK. Participants were interviewed after discharge either at their homes or via telephone or videocall. Participants Twenty-six stroke survivors and eleven caregivers participated in semi-structured interviews. Results We identified three key phases of the cognitive assessment process and themes pertaining to each phase. The phases (numbered) and themes (lettered) were as follows: (1) before the cognitive assessment: (A) lack of explanation, (B) considering the assessment useless; (2) during the cognitive assessment: varied emotional responses, moderated by (D) perception of the purpose behind cognitive assessment, (E) perception of cognitive impairment, (F) confidence in cognitive abilities, (G) assessment administration style and (3) after the cognitive assessment: (H) feedback can impact self-confidence and self-efficacy, (I) vague feedback and clinical jargon are unhelpful. Conclusions Stroke survivors require clear explanations about the purpose and outcomes of poststroke cognitive assessments, including constructive feedback, to promote engagement with the process and protect their psychological wellbeing.
Smoking, early menopause and multiple sclerosis disease course

Abstract Smoking is associated with an increased risk of multiple sclerosis (MS), and smoking and early menopause are related to poor outcomes in MS. Smoking is also associated with early menopause. To explore this intricate relationship between smoking status, age at menopause and disease course in MS, 137 women with MS and 396 age-matched controls were included in this case–control study. Age at menopause (median 49.0 vs. 50.0 years; p = 0.79) and smoking status (40.3% vs. 47.6%; p = 0.15) were similar among MS and control women. Relapsing MS onset was earlier in ever-smoker women with early menopause compared to the rest of the women (median 30.4 vs. 37.0 years; p = 0.02) and also compared to ever-smoker women with normal age at menopause (median 30.4 vs. 41.0 years; p = 0.008) and never-smoker women with early menopause (median 30.4 vs. 41.5 years; p = 0.004). Progressive MS onset was also earlier in ever-smoker women with early menopause compared to ever-smoker women with normal age at menopause (median 41.1 vs. 49.4 years; p = 0.05) and never-smoker women with early menopause (median 41.1 vs. 50.1 years; p = 0.12). Our results suggest that smoking and menopause associate with MS disease course, including the onset of relapsing and progressive MS in women.
Nutritional aspects of inflammatory bowel disease

ABSTRACT Introduction The number of people diagnosed with inflammatory bowel disease (IBD) continues to increase in most parts of the world. Although the exact etiology of this chronic intestinal disease is not fully understood, nutritional factors appear to play key roles. Furthermore, individuals with IBD are at increased risk of adverse nutritional impacts, including micronutrient deficiencies. Areas covered This review aims to summarize recent reports focusing on nutritional factors relevant to the development of IBD and to also review data on nutritional deficiencies seen in individuals with IBD. Expert opinion The typical western diet, characterized by high-fat/high-sugar foods, along with food additives, appears to contribute to the etiopathogenesis of IBD. In contrast, some reports indicate that some foods are likely protective. However, there are inconsistencies in the currently available data, reflecting study design and other confounding factors. Furthermore, some of the conclusions are inferred from animal or in vitro studies. The presence of IBD can compromise the nutrition of individuals with one of these disorders: ongoing monitoring is critical. Nutrition and diet in the setting of IBD remain key areas for further and ongoing study.
Non coding RNA

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Noncoding RNA E. Desgranges, S. Marzi, K. Moreau, P. Romby, Isabelle Caldelari
UNADON: transformer-based model to predict genome-wide chromosome spatial position

Abstract Motivation The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial positioning in a genome-wide manner are not well understood. Results Here, we develop a new transformer-based deep learning model called UNADON, which predicts the genome-wide cytological distance to a specific type of nuclear body, as measured by TSA-seq, using both sequence features and epigenomic signals. Evaluations of UNADON in four cell lines (K562, H1, HFFc6, HCT116) show high accuracy in predicting chromatin spatial positioning to nuclear bodies when trained on a single cell line. UNADON also performed well in an unseen cell type. Importantly, we reveal potential sequence and epigenomic factors that affect large-scale chromatin compartmentalization in nuclear bodies. Together, UNADON provides new insights into the principles between sequence features and large-scale chromatin spatial localization, which has important implications for understanding nuclear structure and function. Availability and implementation The source code of UNADON can be found at https://github.com/ma-compbio/UNADON.
Reference panel-guided super-resolution inference of Hi-C data

Abstract Motivation Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types. Results Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains. Availability and implementation https://github.com/BlanchetteLab/RefHiC.
Strictly-controlled techniques are required in laparoscopic appendectomy for elemental mercury sequestration in the appendix: a case report

Elemental mercury impaction in the appendix can cause subsequent local and systemic complications. We present a case of a teenage boy who ingested approximately 10 mL of elemental mercury, resulting in residual mercury sequestration in the appendix after conservative management. We performed laparoscopic appendectomy to remove the residual mercury. The patient made a complete clinical recovery without adverse events related to mercury poisoning over the 6-month follow-up. We highlight the advantages of laparoscopic appendectomy, abdominal computed tomography (CT), negative pressure operating rooms, and surgeon protection to improve surgical success rates. This case report adds to the literature on the management of elemental mercury impaction in the appendix and provides valuable insights for clinical decision-making.
Pain Outcomes in Patients with Metastatic Castration-Resistant Prostate Cancer Treated with 223Ra: PARABO, a Prospective, Noninterventional Study

223Ra, a targeted α-therapy, is approved for the treatment of patients with metastatic castration-resistant prostate cancer (mCRPC) who have bone metastases. In the phase 3 ALSYMPCA study, 223Ra prolonged survival and improved quality of life versus placebo. Our real-world study, PARABO, investigated pain and bone pain–related quality of life in patients with mCRPC and symptomatic bone metastases receiving 223Ra in clinical practice. Methods: PARABO was a prospective, observational, noninterventional single-arm study conducted in nuclear medicine centers across Germany (NCT02398526). The primary endpoint was a clinically meaningful pain response (≥2-point improvement from baseline for the worst-pain item score in the Brief Pain Inventory–Short Form). Results: The analysis included 354 patients, who received a median of 6 223Ra injections (range, 1–6). Sixty-seven percent (236/354) received 5–6 injections, and 33% (118/354) received 1–4 injections. Of 216 patients with a baseline worst-pain score of more than 1, 59% (128) had a clinically meaningful pain response during treatment. Corresponding rates were 67% (range, 98/146) with 5–6 223Ra injections versus 43% (range, 30/70) with 1–4 injections, 60% (range, 60/100) in patients with no more than 20 lesions versus 59% (range, 65/111) in those with more than 20 lesions, and 65% (range, 69/106) in patients without prior or concomitant opioid use versus 54% (range, 59/110) in those with prior or concomitant opioid use. Mean subscale scores (pain severity and pain interference) on the Brief Pain Inventory–Short Form improved during treatment. Conclusion: 223Ra reduced pain in patients with mCRPC and symptomatic bone metastases, particularly in patients who received 5–6 injections. The extent of metastatic disease did not impact pain response.
Parameterized Complexity of Finding Regular Induced Subgraphs 1

The r-Regular Induced Subgraph problem asks, given a graph G and a nonnegative integer k, whether G contains an r-regular induced subgraph of size at least k, that is, an induced subgraph in which every vertex has degree exactly r. In this paper we examine its parameterization k-Size r-Regular Induced Subgraph with k as parameter and prove that it is W[1]-hard. We also examine the parameterized complexity of the dual parameterized problem, namely, the k-Almost r-Regular Graph problem, which asks for a given graph G and a non-negative integer k whether G can be made r-regular by deleting at most k vertices. For this problem, we prove the existence of a problem kernel of size O(kr(r + k) 2 ).