Miracle-dz/UniFAR-FTUs huggingface dataset:
Variant analysis in Chinese families with hereditary hemorrhagic telangiectasia

Hereditary hemorrhagic telangiectasia (HHT) is a vascular dysplasia disorder characterized by epistaxis, mucocutaneous telangiectasias and arteriovenous malformations in internal organs. Recurrent epistaxis is the primary complaint in 90%‐96% of HHT patients and the other symptoms come with age. The aim of this study was to analyze HHT‐associated gene variant spectrum in Chinese HHT patients and to assess whether genetic testing could contribute to the early diagnosis.
Genetically Engineered Proteins to Improve Biomass Conversion: New Advances and Challenges for Tailoring Biocatalysts

Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass are being used for the production of biofuels and fine chemicals. Since most of the enzymes used in the biorefinery industry act in suboptimal conditions, modification of their catalytic properties through protein rational design and in vitro evolution techniques allows the improvement of enzymatic parameters such as specificity, activity, efficiency, secretability, and stability, leading to better yields in the production lines. This review focuses on the current application of protein engineering techniques for improving the catalytic performance of enzymes used to break down lignocellulosic polymers. We discuss the use of both classical and modern methods reported in the literature in the last five years that allowed the boosting of biocatalysts for biomass degradation.
[Incidental discovery of DMD gene deletions by chromosomal microarray analysis].

OBJECTIVE To discuss the value of chromosomal microarray analysis (CMA) for the identification of DMD gene deletions during prenatal diagnosis. METHODS G-banded karyotyping and CMA were performed on fetuses with ultrasonographic soft markers but no family history for Duchenne/Becker muscular dystrophy (DMD/BMD). Denaturing high-performance liquid chromatograghy (DHPLC) was used to detect DMD gene mutations in umbilical cord blood and peripheral blood samples from the mothers. RESULTS For fetus 1, analysis of amniocytes showed a normal karyotype, while CMA detected a 119 kb deletion at Xp21.1 (32 565 489 - 32 681 461), which encompassed exons 10 to 16 of the DMD gene. The result was confirmed by DHPLC analysis. The mother was found to have loss of heterozygosity in the same region. For fetus 2, karyotyping of amniocytes also showed a normal male karyotype, while CMA detected a 254 kb deletion at Xp21.1 (32 104 604 - 32 358 874), which encompassed exons 41 to 44 of the DMD gene. The same deletion was not detected in the mother. DHPLC analysis confirmed the presence of both deletions. CONCLUSION Two fetuses harboring DMD gene deletions but without a family history were discovered. CMA can improve the efficiency for detecting single gene diseases caused by deletions.
Green Synthesis of Privileged Benzimidazole Scaffolds Using Active Deep Eutectic Solvent

The exploitation and use of alternative synthetic methods, in the face of classical procedures that do not conform to the ethics of green chemistry, represent an ever-present problem in the pharmaceutical industry. The procedures for the synthesis of benzimidazoles have become a focus in synthetic organic chemistry, as they are building blocks of strong interest for the development of compounds with pharmacological activity. Various benzimidazole derivatives exhibit important activities such as antimicrobial, antiviral, anti-inflammatory, and analgesic activities, and some of the already synthesized compounds have found very strong applications in medicine praxis. Here we report a selective and sustainable method for the synthesis of 1,2-disubstituted or 2-substituted benzimidazoles, starting from o-phenylenediamine in the presence of different aldehydes. The use of deep eutectic solvent (DES), both as reaction medium and reagent without any external solvent, provides advantages in terms of yields as well as in the work up procedure of the reaction.
Pavlovian-To-Instrumental Transfer and Alcohol Consumption in Young Male Social Drinkers: Behavioral, Neural and Polygenic Correlates

In animals and humans, behavior can be influenced by irrelevant stimuli, a phenomenon called Pavlovian-to-instrumental transfer (PIT). In subjects with substance use disorder, PIT is even enhanced with functional activation in the nucleus accumbens (NAcc) and amygdala. While we observed enhanced behavioral and neural PIT effects in alcohol-dependent subjects, we here aimed to determine whether behavioral PIT is enhanced in young men with high-risk compared to low-risk drinking and subsequently related functional activation in an a-priori region of interest encompassing the NAcc and amygdala and related to polygenic risk for alcohol consumption. A representative sample of 18-year old men (n = 1937) was contacted: 445 were screened, 209 assessed: resulting in 191 valid behavioral, 139 imaging and 157 genetic datasets. None of the subjects fulfilled criteria for alcohol dependence according to the Diagnostic and Statistical Manual of Mental Disorders-IV-TextRevision (DSM-IV-TR). We measured how instrumental responding for rewards was influenced by background Pavlovian conditioned stimuli predicting action-independent rewards and losses. Behavioral PIT was enhanced in high-compared to low-risk drinkers (b = 0.09, SE = 0.03, z = 2.7, p < 0.009). Across all subjects, we observed PIT-related neural blood oxygen level-dependent (BOLD) signal in the right amygdala (t = 3.25, pSVC = 0.04, x = 26, y = −6, z = −12), but not in NAcc. The strength of the behavioral PIT effect was positively correlated with polygenic risk for alcohol consumption (rs = 0.17, p = 0.032). We conclude that behavioral PIT and polygenic risk for alcohol consumption might be a biomarker for a subclinical phenotype of risky alcohol consumption, even if no drug-related stimulus is present. The association between behavioral PIT effects and the amygdala might point to habitual processes related to out PIT task. In non-dependent young social drinkers, the amygdala rather than the NAcc is activated during PIT; possible different involvement in association with disease trajectory should be investigated in future studies.
Exploring the Phylogeography of Ancient Platycladus orientalis in China by Specific-Locus Amplified Fragment Sequencing

Platycladus orientalis (i.e., Chinese thuja) is famous for its lifespan spanning hundreds, and even thousands, of years. Most ancient P. orientalis populations are widely distributed in China, with accessible historical records, making them valuable genetic resources. In this study, the distribution pattern of ancient P. orientalis in China was analyzed based on 13 bioclimatic factors. Additionally, a specific-locus amplified fragment (SLAF) sequencing method was applied to detect single nucleotide polymorphisms (SNPs) in the genomes of 100 accessions from 13 populations. The resulting data revealed that the suitable areas for the distribution of ancient P. orientalis populations were accurately predicted with four main climatic factors. A total of 81,722 SNPs were identified from 461,867 SLAFs for 100 individuals, with an average sequencing depth of 10.11-fold and a Q30 value of 82.75%. The pair-wise genetic distance and genetic differentiation of 13 populations indicated that the BT-T population exhibited the largest divergence from the other populations. A neighbor-joining phylogenetic tree suggested the relationship between many individuals was inconsistent with the geographical location, possibly indicative of a history of transplantation and cultivation. All individuals were clustered into nine genotypes according to a structural analysis and the relationships between individuals were clarified in phylogenetic trees. This study highlights the importance of the de novo genome sequencing of ancient P. orientalis and may provide the basis for the conservation of P. orientalis genetic resources, the identification of supergene families, and the evaluation of related genetic resources.
Intakes and Food Sources of Dietary Fibre and Their Associations with Measures of Body Composition and Inflammation in UK Adults: Cross-Sectional Analysis of the Airwave Health Monitoring Study

The purpose of this study was to investigate the associations between intakes of fibre from the main food sources of fibre in the UK diet with body mass index (BMI), percentage body fat (%BF), waist circumference (WC) and C-reactive protein (CRP). Participants enrolled in the Airwave Health Monitoring Study (2007–2012) with 7-day food records (n = 6898; 61% men) were included for cross-sectional analyses. General linear models evaluated associations across fifths of fibre intakes (total, vegetable, fruit, potato, whole grain and non-whole grain cereal) with BMI, %BF, WC and CRP. Fully adjusted analyses showed inverse linear trends across fifths of total fibre and fibre from fruit with all outcome measures (ptrend < 0.0001). Vegetable fibre intake showed an inverse association with WC (ptrend 0.0156) and CRP (ptrend 0.0005). Fibre from whole grain sources showed an inverse association with BMI (ptrend 0.0002), %BF (ptrend 0.0007) and WC (ptrend 0.0004). Non-whole grain cereal fibre showed an inverse association with BMI (Ptrend 0.0095). Direct associations observed between potato fibre intake and measures of body composition and inflammation were attenuated in fully adjusted analyses controlling for fried potato intake. Higher fibre intake has a beneficial association on body composition, however, there are differential associations based on the food source.
Incidence, patterns of progression, and outcomes of preexisting and newly discovered brain metastases during treatment with anti–PD‐1 in patients with metastatic melanoma

Melanoma brain metastases (MBM) occur in up to 50% of patients with metastatic melanoma (MM) and represent a frequent site of systemic treatment failure for targeted therapies. However, to the authors' knowledge, little is known regarding the incidence, patterns of disease progression, and outcomes of MBM in patients treated with anti–PD‐1 immunotherapy.
A Study on Exfoliation of Expanded Graphite Stacks in Candelilla Wax

A novel, green route for pre-exfoliation of graphite based on a biodegradable polymer and high-power ultrasound is presented. Candelilla wax (CW), derived from the leaves of the candelilla plant, has been used for the first time as a natural non aqueous medium to induce the pre-exfoliation of expanded graphite (EG) under ultrasonic irradiation in an economical way. The proposed method uses also D-limonene as a natural organic solvent for reducing viscosity and increasing the affinity between the polar groups of EG and candelilla wax, thus improving the intercalation/exfoliation of EG. The quality of dispersion of the nanofiller in the natural wax matrix has been evaluated using multiple techniques. The addition of EG to wax and use of ultrasonic treatment leads to a reduced crystallinity, probably due to restrictions of the molecular movements, improved thermal stability of wax, and to an increased shear thinning exponent, which are all indicative of a high degree of EG dispersion. The ultrasonic dynamic mechanical results suggest a reduction in the cluster size and a better filler dispersion in the wax matrix promoted by polar or chemical reactions between the CW fractions and the graphite stacks, which was observed by XPS analysis. The results were compared to those obtained with paraffin, a synthetic wax, and confirmed the dispersion improvement obtained by using natural wax as a pre-exfoliating medium.
A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis.

Soybean (Glycine max) production is severely affected in unfavorable environments. Identification of regulatory factors conferring stress tolerance would facilitate soybean breeding. In this study, through coexpression network analysis of salt-tolerant wild soybeans, together with molecular and genetic approaches, we unraveled a previously unidentified function of a class B heat shock factor, HSFB2b, in soybean salt stress response. We showed that HSFB2b improves salt tolerance through the promotion of flavonoid accumulation by activating one subset of flavonoid biosynthesis-related genes and by inhibiting the repressor gene GmNAC2 to release another subset of genes in the flavonoid biosynthesis pathway. Moreover, four promoter haplotypes of HSFB2b were identified from wild and cultivated soybeans. Promoter haplotype II from salt-tolerant wild soybean Y20, with high promoter activity under salt stress, is likely selected for during domestication. Another promoter haplotype, haplotype III, from salt-tolerant wild soybean Y55, had the highest promoter activity under salt stress, had a low distribution frequency and may be subjected to the next wave of selection. Together, our results revealed the mechanism of HSFB2b in soybean salt stress tolerance. Its promoter variations were identified, and the haplotype with high activity may be adopted for breeding better soybean cultivars that are adapted to stress conditions. This article is protected by copyright. All rights reserved.
Adaptation of the DEMQOL-Proxy for routine use in care homes: a cross-sectional study of the reliability and validity of DEMQOL-CH

Objective To investigate the routine use of a measure of quality of life (QoL) in care homes and assess its psychometric properties when used by care staff. Design A cross-sectional two-phase study. Setting and participants Data were collected from care staff in seven care homes in East Sussex, England. Method Phase I: The ability of care staff from two care homes to use the DEMQOL-Proxy without interviewer administration was assessed using agreement analysis between a self-administered and interviewer-administered version of the instrument. Based on these findings, DEMQOL-Proxy was adapted into a new version, DEMQOL-CH, for use as a self-administered instrument in care homes. We assessed agreement between the new DEMQOL-CH and DEMQOL-Proxy to ensure DEMQOL-CH was used correctly. Phase II: A preliminary assessment of the psychometric properties of DEMQOL-CH when used routinely was completed in a further five care homes. Results Phase I: Nineteen care staff from two care homes completed QoL measurements for residents. Systematic error was identified when staff self-completed the DEMQOL-Proxy without an interviewer. We modified the DEMOoL-Proxy to create DEMQOL-CH; this reduced the error, producing a version that could be used more accurately by care staff. Phase II: Eleven care staff from five care homes rated resident QoL routinely. DEMQOL-CH showed acceptable psychometric properties with satisfactory reliability and validity and a clear factor structure. Conclusions The research presents positive preliminary data on the acceptability, feasibility and performance of routine QoL measurement in care homes using an adapted version of DEMQOL-Proxy, the DEMQOL-CH. Results provide evidence to support the concept that routine measurement of QoL may be possible in care homes. Research is needed to refine and test the methodology and instrument further and to explore the potential for benefits to residents, staff and care homes in larger and more representative populations.
Contribution of CYP27B1 and CYP24A1 Genetic Variations to the Incidence of Acute Coronary Syndrome and to Vitamin D Serum Level.

BACKGROUND Cardiovascular diseases remain a major public health burden worldwide. It was reported that vitamin D protects the cardiovascular system through several mechanisms mainly by hindering atherosclerosis development. Genetic variations in vitamin D metabolic pathway were found to affect vitamin D levels. This study aims at investigating the association between single nucleotide polymorphisms (SNPs) in genes involved in vitamin D metabolism; CYP27B and CYP24A1; 25(OH)D levels, and susceptibility to acute coronary syndrome (ACS). SUBJECTS/METHODS 185 patients and 138 healthy controls were recruited. CYP24A1 rs2762939 was genotyped using Fast Real time PCR, while CYP24A1 rs4809960 and CYP27B1 rs703842 were genotyped using polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP). 25(OH)D3and 25(OH)D2 levels were measured using ultra-performance liquid chromatography tandem mass spectrum (UPLC-MS/MS). RESULTS Vitamin D level was significantly lower in patients than controls (p<0.05). The GG genotype of rs2762939 was significantly associated with the risk of ACS development, but not correlated to the vitamin D level. Rs4809960 and rs703842 genetic variations were not associated with ACS nor with 25(OH)D level. CONCLUSION The genetic variant rs2762939 of CYP24A1 is remarkably associated with ACS. Meanwhile, the variants rs4809960 and rs703842 are not associated with ACS incidence.
BBKNN: fast batch alignment of single cell transcriptomes

Abstract Motivation Increasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through data integration. A number of methods have been developed to combine diverse datasets by removing technical batch effects, but most are computationally intensive. To overcome the challenge of enormous datasets, we have developed BBKNN, an extremely fast graph-based data integration algorithm. We illustrate the power of BBKNN on large scale mouse atlasing data, and favourably benchmark its run time against a number of competing methods. Availability and implementation BBKNN is available at https://github.com/Teichlab/bbknn, along with documentation and multiple example notebooks, and can be installed from pip. Supplementary information Supplementary data are available at Bioinformatics online.
Examining the Factor Structure and Psychometric Properties of the Chinese Version of the Life Orientation Test in Older Chinese Immigrants

The current study examined the factor structure and psychometric properties of the Chinese version of the Revised Life Orientation Test (CLOT-R) in a sample of 342 community-dwelling older Chinese immigrants in Canada (mean age = 71.99, SD = 5.62; 58.5% female). Confirmatory factor analysis demonstrated that the CLOT-R yields a two-factor model with one item cross-loading on two latent constructs of optimism and pessimism. Analysis further revealed poor internal consistency and convergent validity. Evidence for discriminant and convergent validity was found between optimism and perceived stress, as well as optimism and quality of life. Compared with the factor structure reported in previous Chinese-speaking samples, the modified two-factor structure found in the current group of older Chinese immigrants could be attributed to the heterogeneity of the sample and possible configural variance across culture and age. Overall, the current findings suggest that the CLOT-R may not be a reliable and valid measure to assess dispositional optimism and pessimism among older Chinese immigrants. Theoretical implications and suggestions for further scale development and research is discussed.
Body Fat Mass and Risk of Cerebrovascular Lesions: The PRESENT (Prevention of Stroke and Dementia) Project

Obesity is known to increase the risk of stroke. It is unclear whether high absolute fat mass (FM) increases the risk of stroke independently. We studied the correlation between FM and silent brain infarction/white matter change (SI/WMC) using brain computed tomography. We selected subjects from the local government health promotion project. We randomly selected a target population that had never been diagnosed with stroke or dementia. FM was measured by bioelectrical impedance analysis (BIA). We divided the subjects into three groups according to the FM (gender-specific tertiles [GTx]). Seven hundred and twenty-two subjects (321 men) between 50 and 75 years of age were recruited. The overall odds ratio (OR) of SI/WMC was 2.23 (95% confidence interval (CI), 1.34–3.71; p = 0.002) times higher in the 37th to 100th percentiles (GT3) than in the first to 32nd percentiles (GT1). When men and women were separated, the OR of GT3 was 1.35 (CI, 0.62–2.94; p = 0.45) in men and 3.2 (CI, 1.60–6.40; p = 0.001) in women. The findings were not found to be statistically significant after adjusting for the well-known stroke risk factors. When the subjects were divided into a high FM (HFMG, GT3) and low FM group (LFMG, GT1 + GT2), the HFMG showed an increased OR of SI/WMC in women. Similar results were seen after adjusted (overall: OR, 1.38; CI, 0.85–2.25, p = 0.198; men: OR, 0.93; CI, 0.422–2.051; p = 0.86; women: OR, 2.02; CI, 1.06–3.86; p = 0.03). The findings suggest that high FM may be an independent risk factor for ischemic stroke among adults free from stroke and dementia, especially in women.
Color discrimination thresholds in a cichlid fish: Metriaclima benetos

ABSTRACT Color vision is essential for animals as it allows them to detect, recognize and discriminate between colored objects. Studies analyzing color vision require an integrative approach, combining behavioral experiments, physiological models and quantitative analyses of photoreceptor stimulation. Here, we demonstrate, for the first time, the limits of chromatic discrimination in Metriaclima benetos, a rock-dwelling cichlid from Lake Malawi, using behavioral experiments and visual modeling. Fish were trained to discriminate between colored stimuli. Color discrimination thresholds were quantified by testing fish chromatic discrimination between the rewarded stimulus and distracter stimuli that varied in chromatic distance (ΔS). This was done under fluorescent lights alone and with additional violet lights. Our results provide two main outcomes. First, cichlid color discrimination thresholds correspond with predictions from the receptor noise limited (RNL) model but only if we assume a Weber fraction higher than the typical value of 5%. Second, cichlids may exhibit limited color constancy under certain lighting conditions as most individuals failed to discriminate colors when violet light was added. We further used the color discrimination thresholds obtained from these experiments to model color discrimination of actual fish colors and backgrounds under natural lighting for Lake Malawi. We found that, for M. benetos, blue is most chromatically contrasting against yellows and space-light, which might be important for discriminating male nuptial colorations and detecting males against the background. This study highlights the importance of lab-based behavioral experiments in understanding color vision and in parameterizing the assumptions of the RNL vision model for different species. Summary: Color discrimination thresholds of cichlids can be obtained through visually mediated tasks, enabling investigation of the role of vision in cichlid ecology, sexual selection and speciation.
Use of an Outbred Rat Hepacivirus Challenge Model for Design and Evaluation of Efficacy of Different Immunization Strategies for Hepatitis C Virus

The lack of immunocompetent small animal models for hepatitis C virus (HCV) has greatly hindered the development of effective vaccines. Using rodent hepacivirus (RHV), a homolog of HCV that shares many characteristics of HCV infection, we report the development and application of an RHV outbred rat model for HCV vaccine development.