Miracle-dz/UniFAR-FTUs huggingface dataset:
TOPORS as a novel causal gene for Joubert syndrome

Joubert syndrome (JBTS) is a Mendelian disorder of the primary cilium defined by the clinical triad of hypotonia, developmental delay, and a distinct cerebellar malformation called the molar tooth sign. JBTS is inherited in an autosomal recessive, autosomal dominant, or X‐linked recessive manner. Though over 40 genes have been identified as causal for JBTS, molecular diagnosis is not made in 30%–40% of individuals who meet clinical criteria. TOPORS encodes topoisomerase I‐binding arginine/serine‐rich protein, and homozygosity for a TOPORS missense variant (c.29C > A; p.(Pro10Gln)) was identified in individuals with the ciliopathy oral‐facial‐digital syndrome in two families of Dominican descent. Here, we report an additional proband of Dominican ancestry with JBTS found by exome sequencing to be homozygous for the identical p.(Pro10Gln) TOPORS missense variant. Query of the Mount Sinai BioMe biobank, which includes 1880 individuals of Dominican ancestry, supports a high carrier frequency of the TOPORS p.(Pro10Gln) variant in individuals of Dominican descent. Our data nominates TOPORS as a novel causal gene for JBTS and suggests that TOPORS variants should be considered in the differential of ciliopathy‐spectrum disease in individuals of Dominican ancestry.
Epidemiological Investigation, Risk Factors, Spatial-Temporal Cluster, and Epidemic Trend Analysis of Pseudorabies Virus Seroprevalence in China (2017 to 2021)

PRV is a critical pathogen threatening the global swine industry. Our research fills knowledge gaps regarding PRV prevalence, infection risk factors, spatial-temporal clustering of high PRV gE seroprevalence, and the epidemic trend of PRV gE seroprevalence in China in recent years. These findings are valuable for the clinical prevention and control of PRV infection and suggest that PRV infection is likely to be successfully controlled in China. ABSTRACT Pseudorabies virus (PRV) is a double-stranded linear DNA virus capable of infecting various animals, including humans. We collected blood samples from 14 provinces in China between December 2017 and May 2021 to estimate PRV seroprevalence. The PRV gE antibody was detected using the enzyme-linked immunosorbent assay (ELISA). Logistic regression analysis identified potential risk factors associated with PRV gE serological status at the farm level. Spatial-temporal clusters of high PRV gE seroprevalence were explored using SaTScan 9.6 software. Time-series data of PRV gE seroprevalence were modeled using the autoregressive moving average (ARMA) method. A Monte Carlo sampling simulation based on the established model was performed to analyze epidemic trends of PRV gE seroprevalence using @RISK software (version 7.0). A total of 40,024 samples were collected from 545 pig farms across China. The PRV gE antibody positivity rates were 25.04% (95% confidence interval [CI], 24.61% to 25.46%) at the animal level and 55.96% (95% CI, 51.68% to 60.18%) at the pig farm level. Variables such as farm geographical division, farm topography, African swine fever (ASF) outbreak, and porcine reproductive and respiratory syndrome virus (PRRSV) control in pig farms were identified as risk factors for farm-level PRV infection. Five significant high-PRV gE seroprevalence clusters were detected in China for the first time, with a time range of 1 December 2017 to 31 July 2019. The monthly average change value of PRV gE seroprevalence was −0.826%. The probability of a monthly PRV gE seroprevalence decrease was 0.868, while an increase was 0.132. IMPORTANCE PRV is a critical pathogen threatening the global swine industry. Our research fills knowledge gaps regarding PRV prevalence, infection risk factors, spatial-temporal clustering of high PRV gE seroprevalence, and the epidemic trend of PRV gE seroprevalence in China in recent years. These findings are valuable for the clinical prevention and control of PRV infection and suggest that PRV infection is likely to be successfully controlled in China.
Spatial–temporal patterns of brain disconnectome in Alzheimer's disease

Mounting evidences have shown that progression of white matter hyperintensities (WMHs) with vascular origin might cause cognitive dysfunction symptoms through their effects on brain networks. However, the vulnerability of specific neural connection related to WMHs in Alzheimer's disease (AD) still remains unclear. In this study, we established an atlas‐guided computational framework based on brain disconnectome to assess the spatial–temporal patterns of WMH‐related structural disconnectivity within a longitudinal investigation. Alzheimer's Disease Neuroimaging Initiative (ADNI) database was adopted with 91, 90 and 44 subjects including in cognitive normal aging, stable and progressive mild cognitive impairment (MCI), respectively. The parcel‐wise disconnectome was computed by indirect mapping of individual WMHs onto population‐averaged tractography atlas. By performing chi‐square test, we discovered a spatial–temporal pattern of brain disconnectome along AD evolution. When applied such pattern as predictor, our models achieved highest mean accuracy of 0.82, mean sensitivity of 0.86, mean specificity of 0.82 and mean area under the receiver operating characteristic curve (AUC) of 0.91 for predicting conversion from MCI to dementia, which outperformed methods utilizing lesion volume as predictors. Our analysis suggests that brain WMH‐related structural disconnectome contributes to AD evolution mainly through attacking connections between: (1) parahippocampal gyrus and superior frontal gyrus, orbital gyrus, and lateral occipital cortex; and (2) hippocampus and cingulate gyrus, which are also vulnerable to Aβ and tau confirmed by other researches. All the results further indicate that a synergistic relationship exists between multiple contributors of AD as they attack similar brain connectivity at the prodromal stage of disease.
Sexual Assault, Posttraumatic Stress, Alcohol Use, and Suicidality Among Diverse College Students

Suicide is the second leading cause of death among college-aged populations. This study examined the association of demographics (sexual orientation, gender identity, age, and race), sexual assault, posttraumatic stress symptoms (PTSS), and alcohol use with suicidality, current urge to self-harm, and current suicidal intent among a diverse sample of college students (n = 2,160) from two universities. Over half of participants reported any suicidality (63.5%), 12% reported current urge to harm themselves, and 5% reported current suicidal intent. A linear regression indicated that participants who identified as a sexual minority, gender minority, consumed more drinks per week, and had more severe PTSS reported higher levels of suicidality. University also was associated with suicidality. A negative binomial regression demonstrated that participants who identified as a sexual minority and had more severe PTSS had more current urge to harm themselves. Further, a negative binomial regression demonstrated that first-generation college students, students with more severe sexual assault histories, and students with more severe PTSS had higher current suicidal intent. Findings suggest that risk factors may differ for college students’ general suicidality, self-harm urges, and suicidal intent, suggesting that these may be separate constructs. More comprehensive models, incorporating multiple risk factors and multiple ways of assessing suicidality, are needed to better understand the range of college student suicidal behavior and risks.
Differentiable Histogram Loss Functions for Intensity-based Image-to-Image Translation

We introduce the HueNet - a novel deep learning framework for a differentiable construction of intensity (1D) and joint (2D) histograms and present its applicability to paired and unpaired image-to-image translation problems. The key idea is an innovative technique for augmenting a generative neural network by histogram layers appended to the image generator. These histogram layers allow us to define two new histogram-based loss functions for constraining the structural appearance of the synthesized output image and its color distribution. Specifically, the color similarity loss is defined by the Earth Mover's Distance between the intensity histograms of the network output and a color reference image. The structural similarity loss is determined by the mutual information between the output and a content reference image based on their joint histogram. Although the HueNet can be applied to a variety of image-to-image translation problems, we chose to demonstrate its strength on the tasks of color transfer, exemplar-based image colorization, and edges <inline-formula><tex-math notation="LaTeX">$\to$</tex-math><alternatives><mml:math><mml:mo>→</mml:mo></mml:math><inline-graphic xlink:href="aviaharon-ieq1-3278287.gif"/></alternatives></inline-formula> photo, where the colors of the output image are predefined. The code is available at <uri>https://github.com/mor-avi-aharon-bgu/HueNet.git</uri>.
On the possible locus of the liquid-liquid critical point in real water from studies of supercooled water using the TIP4P/Ice model.

One of the most accepted hypothesis to explain the anomalous behavior of water is the presence of a critical point between two liquids, the liquid-liquid critical point (LLCP), buried within the deep supercooled regime. Unfortunately, such hypothesis is hard to be experimentally confirmed due to fast freezing. Here, we show that the TIP4P/Ice water potential shifted by 400 bar can reproduce with unprecedented accuracy the experimental isothermal compressibility of water and its liquid equation of state for a wide pressure and temperature range. We find, both by extrapolation of response function maxima and by a Maxwell construction, that the location of the model LLCP is consistent with previous calculations. According to the pressure shift needed to recover the experimental behavior of supercooled water, we estimate the experimental LLCP to be located around 1250 bar and 195 K. We use the model to estimate the ice nucleation rate (J) in the vicinity of the hypothesized LLCP experimental location and obtain J = 1024 m-3 s-1. Thereby, experiments where the ratio between the cooling rate and the sample volume is equal or larger than the estimated nucleation rate could probe liquid-liquid equilibrium before freezing. Such conditions are not accessible in common experiments with microdroplets cooled at a few kelvin per second, but they could be, for instance, using nanodroplets of around 50 nm radius observed in a millisecond timescale.
Subthalamic Nucleus Activity during Cognitive Load and Gait Dysfunction in Parkinson's Disease

Gait freezing is a common, disabling symptom of Parkinson's disease characterized by sudden motor arrest during walking. Adaptive deep brain stimulation devices that detect freezing and deliver real‐time, symptom‐specific stimulation are a potential treatment strategy. Real‐time alterations in subthalamic nucleus firing patterns have been demonstrated with lower limb freezing, however, whether similar abnormal signatures occur with freezing provoked by cognitive load, is unknown.
Robust Image Hashing Based on Selective

Robust image hashing, which maps the perceptual contents of image to a short digest, is a key technique for tackling the challenges of content-based indexing, searching and copyright protection.In this letter, wepropose a quaternion invariance based hashing algorithm that can fuse complementary visua lf eatures to compact hash. The proposed algorithm leverages quaternion polar cosine transform to holistically capture the spatial and chromatic characteristicsofdigitalimage,androtation-invariantfeaturesare derived from the phase information in the quaternion frequency domain. In addition, we also propose an information theoretic based metric for feature quality assessment and ag reedy strategy to select the optimal subset of features for hash computation. Extensive experiments over a large database demonstrate that the proposed work shows higher content identification accuracy than most competing algorithms, and the resulting hash is compact and easy to compute.
Antibacterial and anti-Toxoplasma activities of Aspergillus niger endophytic fungus isolated from Ficus retusa: in vitro and in vivo approach

Abstract Emergent records propose that Aspergillus niger endophytic fungus is a vital source for various bioactive molecules possessing many biological properties. The current study was designed to inspect the antibacterial and anti-Toxoplasma potentials of Ficus retusa-derived endophytic fungi. After isolation and identification (using 18S rRNA gene sequencing) of A. niger endophytic fungus, LC/MS was utilized for identification and authentication of the chemical profile of the A. niger endophyte extract. Then, the fungal extract was assessed for its antibacterial and antibiofilm activities against Klebsiella pneumoniae clinical isolates. Additionally, its efficacy against Toxoplasma gondii was elucidated in vivo. The fungal extract displayed antibacterial activity against K. pneumoniae isolates with minimum inhibitory concentration values of 64–512 µg/mL. It also possessed a membrane potential dissipating effect using flow cytometry. Moreover, it formed distorted cells with rough surfaces and deformed shapes using a scanning electron microscope (SEM). Regarding its antibiofilm activity, it resulted in a dysregulation of the genes encoding biofilm formation (fimH, mrkA and mrkD) using qRT-PCR in nine K. pneumoniae isolates. The in vivo anti-Toxoplasma potential was demonstrated by decreasing the mortality rate of mice and reducing the tachyzoites’ count in the peritoneal fluids and liver impression smears of mice. In addition, the deformities of the parasite decreased, as revealed by SEM and the inflammation in tissues diminished. Thus, A. niger endophytic fungi could be a valuable source of antibacterial and anti-Toxoplasma compounds.
Optimizing the design and implementation of question prompt lists to support person‐centred care: A scoping review

Question prompt lists (QPLs) are lists of questions that patients may want to discuss with clinicians. QPLs support person‐centred care and have been associated with many beneficial outcomes including improved patient question‐asking, and the amount and quality of the information provided by clinicians. The purpose of this study was to review published research on QPLs to explore how QPL design and implementation can be optimized.
Environmental exposure and ecotoxicological properties of a new‐generation fluorosurfactant (cC6O4): A comparison with selected legacy perfluoroalkyl acids

Cyclic C6O4 (cC6O4, CAS number 1190931‐27‐1) is a new‐generation polyfluorinated alkyl substance (PFAS) used as a polymerization aid in the synthesis of fluoropolymers, which has been produced in Italy since 2011. A review of the properties of cC6O4, focused on environmental distribution and ecotoxicology, was conducted. The EQuilibrium Criterion model was applied, using default environmental scenarios, to estimate environmental distribution and fate. In a situation of static thermodynamic equilibrium in a closed system (Level I), cC6O4 distributes mainly to water (97.6%) and in a minimal amount to soil (2.3%). In a more realistic scenario (Level III), with dynamic conditions in an open system, with advection in air and water and with equal emissions in air and water, the major amount of the compound is transported through water advection. Monitoring data, mainly referring to surface and groundwater, are available for water bodies close to the production sites (maximum measured concentration 52 μg/L) as well as for a wider area in the river Po watershed with concentrations generally lower than 1 μg/L. Few values are also available for concentration in biota. Effect data indicate low toxicity on all tested organisms with no observed effect concentration (NOEC) values always higher than the maximum concentrations tested (100 mg/L for acute tests). Bioaccumulation potential is also very low. A comparison with selected widely used PFAS with five to eight C atoms indicates that cC6O4 is substantially less dangerous to aquatic organisms. For the time being, an ecological risk for the aquatic ecosystem may be excluded even in directly exposed ecosystems. However, for a complete assessment of the suitability of cC6O4 as a substitute for other PFAS (namely, perfluorooctanoic acid), more comprehensive chronic experiments are necessary, to produce realistic NOEC, as well as higher tier experiments (e.g., mesocosms) capable of providing ecologically relevant endpoints. Moreover, a more accurate evaluation of the environmental persistence would be necessary. Integr Environ Assess Manag 2023;19:1636–1648. © 2023 SETAC
Prevalence and associated risk factors of intestinal parasites among schoolchildren in Ecuador, with emphasis on the molecular diversity of Giardia duodenalis, Blastocystis sp. and Enterocytozoon bieneusi

Background Intestinal helminths, including Soil-Transmitted Helminth (STH), and Gastrointestinal Protist (GP) infections are major contributors to the global burden of disease, particularly in low-income countries such Ecuador. Their epidemiology in these settings is largely unknown. Methodology This prospective cross-sectional study investigates the carriage of intestinal helminths, including STH, and GP in asymptomatic schoolchildren (3–11 years) in the Chimborazo and Guayas provinces, Ecuador. Single stool samples (n = 372) and epidemiological questionnaires on demographics and potential risk factors were collected from participating schoolchildren. Conventional microscopy examination was used as screening method, and molecular (PCR and Sanger sequencing) assays were used to further investigate the epidemiology of some GP. A multivariate logistic regression analysis was used to evaluate the strength of the association of suspected risk factors with the presence of helminths and GP. Principal findings At least one intestinal parasite species was observed by microscopy in 63.2% (235/372) of the participating schoolchildren. Enterobius vermicularis (16.7%, 62/372; 95% CI: 13.0–20.9) and Blastocystis sp. (39.2%, 146/372; 95% CI: 34.2–44.2) were the most prevalent among helminths and GP, respectively. Assemblages A (50.0%), B (37.5%) and A+B (12.5%) were detected within Giardia duodenalis and ST3 (28.6%), ST1 and ST2 (26.2% each), and ST4 (14.3%) within Blastocystis sp. Three genotypes, two known (A: 66.7%; KB-1: 16.7%) and a novel (HhEcEb1, 16.7%) were identified within Enterocytozoon bieneusi. Municipality of origin, household overcrowding, and poor sanitation and personal hygiene habits were risk factors for childhood intestinal parasites colonization. Conclusions/Significance Despite massive government drug administration programs, STH and GP infection remain a public health concern in paediatric populations living in poor-resource settings. Molecular analytical methods are required to better understand the epidemiology of these intestinal parasites. This study provides novel information on the occurrence of Blastocystis sp. and E. bieneusi genetic variants circulating in Ecuadorian human populations.
Prevalence of non‐accidental burns and related factors in children: A systematic review and meta‐analysis

Non‐accidental burns (NABs) in children had some adverse effects, such as severe burns, requiring skin grafting, and mortality. Previous studies reported NABs in the form of neglect, suspected abuse, and child abuse. Also, different statistics were estimated for the prevalence of NABs in children. Therefore, the current study aimed to comprehensively review and summarise the literature on the prevalence of NABs in children. Also, factors related to NABs as a secondary aim were considered in this review. Keywords combined using Boolean operators and searches were performed in international electronic databases, such as Scopus, PubMed, and Web of Science. Only studies in English were considered from the earliest to 1 March 2023. The analysis was performed using STATA software version 14. Finally, 29 articles were retrieved for the quantitative analysis. Results found that the prevalence of child abuse, suspected abuse, neglect, ‘child abuse or suspect abused’, and ‘abuse, suspect abused, or neglect’ was 6% (ES: 0.06, 95% confidence interval [CI]: 0.05‐0.07), 12% (ES: 0.12, 95% CI: 0.09‐0.15), 21% (ES: 0.21, 95% CI: 0.07‐0.35), 8% (ES: 0.08, 95% CI: 0.07‐0.09), and 15% (ES: 0.15, 95% CI: 0.13‐0.16) among burns victims, respectively. Also, factors related to NABs are categorised into age and gender, agent and area of burns, and family features. Considering the results of the current study, planning for rapid diagnosis and designing a process to manage NABs in children is necessary.
3D printing to construct in vitro multicellular models of melanoma

Currently, there is a lack of suitable models for in‐vitro studies of malignant melanoma and traditional single cell culture models no longer reproduce tumor structure and physiological complexity well. The tumor microenvironment is closely related to carcinogenesis and it is particularly important to understand how tumor cells interact and communicate with surrounding nonmalignant cells. Three‐dimensional (3D) in vitro multicellular culture models can better simulate the tumor microenvironment due to their excellent physicochemical properties. In this study, 3D composite hydrogel scaffolds were prepared from gelatin methacrylate and polyethylene glycol diacrylate hydrogels by 3D printing and light curing techniques, and 3D multicellular in vitro tumor culture models were established by inoculating human melanoma cells (A375) and human fibroblasts cells on them. The cell proliferation, migration, invasion, and drug resistance of the 3D multicellular in vitro model was evaluated. Compared with the single‐cell model, the cells in the multicellular model had higher proliferation activity and migration ability, and were easy to form dense structures. Several tumor cell markers, such as matrix metalloproteinase‐9 (MMP‐9), MMP‐2, and vascular endothelial growth factor, were highly expressed in the multicellular culture model, which were more favorable for tumor development. In addition, higher cell survival rate was observed after exposure to luteolin. The anticancer drug resistance result of the malignant melanoma cells in the 3D bioprinted construct demonstrated physiological properties, suggesting the promising potential of current 3D printed tumor model in the development of personalized therapy, especially for discovery of more conducive targeted drugs.
Getting ready for real‐world use of electronic patient‐reported outcomes (ePROs) for patients with cancer: A National Comprehensive Cancer Network ePRO Workgroup paper

Memorial Sloan Kettering Cancer Center, New York, New York, USA Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas, USA University of California‐Davis Comprehensive Cancer Center, Sacramento, California, USA Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA University of Wisconsin Carbone Cancer Center, Madison, Wisconsin, USA National Comprehensive Cancer Network, Plymouth Meeting, Pennsylvania, USA University of California‐Los Angeles Jonsson Comprehensive Cancer Center, Los Angeles, California, USA University of Michigan Rogel Cancer Center, Ann Arbor, Michigan, USA Mayo Clinic Comprehensive Cancer Center, Rochester, Minnesota, USA