Miracle-dz/UniFAR-FTUs huggingface dataset:
Frailty and risk of adverse outcomes among community-dwelling older adults in China: a comparison of four different frailty scales

Background Data on which frailty scales are most suitable for estimating risk in Chinese community populations remain limited. Herein we examined and compared four commonly used frailty scales in predicting adverse outcomes in a large population-based cohort of Chinese older adults. Methods A total of 5402 subjects (mean age 66.3 ± 9.6 years, 46.6% male) from the WHO Study on global AGEing and adult health (SAGE) in Shanghai were studied. Frailty was measured using a 35-item frailty index (FI), the frailty phenotype (FP), FRAIL, and Tilburg Frailty Indicator (TFI). Multivariate logistic regression models were performed to evaluate the independent association between frailty and outcomes including 4-year disability, hospitalization, and 4- and 7-year all-cause mortality. The accuracy for predicting these outcomes was determined by evaluating the area under the curve (AUC). The prevalence of frailty, sensitivity, and specificity were calculated using our proposed cut-off points and other different values. Results Prevalence of frailty ranged from 4.2% (FRAIL) to 16.9% (FI). FI, FRAIL and TFI were comparably associated with 4-year hospitalization, and 4- and 7-year mortality (adjusted odds ratios [aORs] 1.44–1.69, 1.91–2.22 and 1.85–2.88, respectively). FRAIL conferred the greatest risk of 4-year disability, followed by FI and TFI (aOR 5.55, 3.50, and 1.91, respectively). FP only independently predicted 4- and 7-year mortality (aOR 1.57 and 2.21, respectively). AUC comparisons showed that FI, followed by TFI and FRAIL, exhibited acceptable predictive accuracy for 4-year disability, 4- and 7-year mortality (AUCs 0.76–0.78, 0.71–0.71, 0.65–0.72, respectively), whereas all scales poorly predicted 4-year hospitalization (AUCs 0.53–0.57). For each scale, while specificity estimates (85.3–97.3%) were high and similar across all outcomes, their sensitivity estimates (6.3–56.8%) were not sufficient yet. Prevalence of frailty, sensitivity, and specificity varied considerably when different cut-off points were used. Conclusion Frailty defined using any of the four scales was associated with an increased risk of adverse outcomes. Although FI, FRAIL and TFI exhibited fair-to-moderate predictive accuracy and high specificity estimates, their sensitivity estimates were not sufficient yet. Overall, FI performed best in estimating risk, while TFI and FRAIL were additionally useful, the latter perhaps being more applicable to Chinese community-dwelling older adults.
Performance-related physiological changes induced by one year of endurance training in young athletes

Introduction Although maximal oxygen uptake (VO2max) is generally recognized as the single best indicator of aerobic fitness in youth, interpretation of this parameter and the extent to which it can be improved by training remain controversial, as does the relative importance of VO2max for performance in comparison to other factors such as power production. Here, we examined the influence of endurance training on the VO2max, muscle power and sports-related performance of cross-country skiers attending a school specializing in sports, as well as potential relationships between any changes observed to one another and/or to perceived stress scale (Cohen) and certain blood parameters. Methods On two separate occasions, prior to the competition season and separated by one year of endurance training, the 12 participants (5 males, 7 females, 17 ± 1 years) carried out tests for VO2max on a treadmill, explosive power utilizing countermovement jumps (CMJ) and ski-specific maximal double pole performance (DPP) employing roller skis on a treadmill. Blood levels of ferritin (Fer), vitamin D (VitD) and hemoglobin (Hg) were monitored, and stress assessed with a questionnaire. Results DPP improved by 10 ± 8% (P < 0.001), but no other significant changes were observed. There were no significant correlations between the changes in DPP and any other variable. Discussion Whereas one year of endurance training improved the cross-country ski-specific performance of young athletes significantly, the increase in their maximal oxygen uptake was minimal. Since DPP was not correlated with VO2max, jumping power or the levels of certain blood parameters, the improvement observed probably reflected better upper-body performance.
The influence of student factors on students’ achievement in the Trends in International Mathematics and Science Study in Abu Dhabi Emirate Schools

Introduction This study aimed to investigate student factors affecting performance in mathematics in Abu Dhabi schools in the United Arab Emirates. Method We used the secondary data from the Trends in International Mathematics and Science Study (TIMSS) 2015, which included 4,838 eighth-grade students from 156 schools in Abu Dhabi. Result The data from the student questionnaire in TIMSS 2015 were subjected to principal component analysis (PCA). The 39 questions were reduced to five factors generated from the student questionnaire, including Safety and Behavior, Classroom Mathematics, Environment, Student Attitudes toward Mathematics, and Technology and Resources. The effects of these factors on students’ achievement were examined using multiple regression analysis. Discussion All of these factors had a significant impact on student achievement in the 2015 TIMSS. The pedagogical and policy implications of the findings have been discussed.
Validation of the neuroconnective endophenotype questionnaire (NEQ): a new clinical tool for medicine and psychiatry resulting from the contribution of Ehlers–Danlos syndrome

Introduction The link between anxiety disorders and joint hypermobility syndrome (now under hypermobility spectrum disorders, which include hypermobile Ehlers–Danlos syndrome) has been widely replicated over the past 30 years and has grown beyond the initial nosological limits. To integrate clinical and research progress in this field, a new neuroconnective endophenotype (NE) and its corresponding instrument, the Neuroconnective Endophenotype Questionnaire (NEQ), have been developed. This new clinical construct, created with the active participation of patients, includes both somatic and psychological dimensions and symptoms and resilience items. Methods The NE includes five dimensions: (1) sensorial sensitivity, (2) body signs and symptoms, (3) somatic conditions, (4) polar behavioral strategies, and (5) psychological and psychopathological dimensions. The NEQ information is collected through four self-administered questionnaires (sensorial sensitivity, body signs and symptoms, polar behavioral strategies, and psychological characteristics) and a structured diagnostic part that should be completed by a trained observer. This hetero-administered part incorporates (a) psychiatric diagnoses (using structured criteria, e.g., MINI), (b) somatic disorders diagnosis, using structured criteria, and (c) assessment of joint hypermobility criteria. Results In a sample of 36 anxiety cases with 36 matched controls, the NEQ obtained high scores for test–retest, inter-rater reliability, and internal consistency. As for predictive validity, cases and controls significantly differed in all five dimensions and hypermobility measurements. Discussion We can conclude that the NEQ has achieved acceptable reliability and validity values and, therefore, is ready to be used and tested in different samples. This original and consistent construct including somatic and mental items may improve clinical specificity, the search for more comprehensive therapies, and their genetic and neuroimaging bases.
Evaluating machine-generated explanations: a “Scorecard” method for XAI measurement science

Introduction Many Explainable AI (XAI) systems provide explanations that are just clues or hints about the computational models-Such things as feature lists, decision trees, or saliency images. However, a user might want answers to deeper questions such as How does it work? , Why did it do that instead of something else? What things can it get wrong? How might XAI system developers evaluate existing XAI systems with regard to the depth of support they provide for the user's sensemaking? How might XAI system developers shape new XAI systems so as to support the user's sensemaking? What might be a useful conceptual terminology to assist developers in approaching this challenge? Method Based on cognitive theory, a scale was developed reflecting depth of explanation, that is, the degree to which explanations support the user's sensemaking. The seven levels of this scale form the Explanation Scorecard. Results and discussion The Scorecard was utilized in an analysis of recent literature, showing that many systems still present low-level explanations. The Scorecard can be used by developers to conceptualize how they might extend their machine-generated explanations to support the user in developing a mental model that instills appropriate trust and reliance. The article concludes with recommendations for how XAI systems can be improved with regard to the cognitive considerations, and recommendations regarding the manner in which results on the evaluation of XAI systems are reported.
PUFA and carotenoid producing thraustochytrids and their anti-microbial and antioxidant activities

Thraustochytrids contribute to the microbiota of mangrove ecosystem, and they hold promise as a potential source of polyunsaturated fatty acids (PUFAs), antimicrobials and antioxidants for their application in pharmaceutical, aquaculture, and human health sectors. However, the thraustochytrids have not been properly studied in Indian mangrove ecosystems for their PUFAs and biological activities, and hence, the present study was carried to isolate the PUFAs-rich thraustochytrids for their pigments, antimicrobial and antioxidant properties. This work isolated and identified the thraustochytrids that are capable of producing PUFAs from decomposing leaves of mangroves at Pichavaram, southeast coast of India. Two predominant isolates were identified as Thraustochytrium sp. and Aurantiochytrium mangrovei based on morphological and molecular characteristics. Thraustochytrium sp. , produced the biomass of 4.72 g L-1, containing total lipids of 42.36% and docosahexaenoic acid (DHA) of 32.69% of total lipids, whereas, A. mangrovei produced the biomass of 6.25 g L-1 containing total lipids of 49.81% and DHA of 44.71% of total lipids. Astaxanthin pigment accumulated up to 3.2 µg L-1 in A. mangrovei, whereas the pigment was not detected in Thraustochytrium sp. Further, the biomass extracted in organic solvents was tested for antibacterial activity against seven clinical pathogens along with positive control of ampicillin. Thraustochytrium sp. , exhibited the highest antibacterial activity with the zone of inhibition of 78.77% against Staphylococcus aureus and the lowest (20.95%) against Klebsiella pneumonia. Thraustochytrium sp. , also showed minimum inhibitory concentration (MIC) of 40 µg L-1 inhibiting the growth of S. aureus. The antioxidant activity of A. mangrovei was tested by using six assays and noted the highest free radical scavenging (87.37 ± 1.22%) and the lowest nitric oxide radical scavenging (75.12 ± 2.22%) activities. Hence, it is clear that the extracts of Thraustochytrium sp. , and A. mangrovei are promising sources of lead compounds for biopharma and food industries.
Tumor microenvironment promotes lymphatic metastasis of cervical cancer: its mechanisms and clinical implications

Although previous studies have shed light on the etiology of cervical cancer, metastasis of advanced cervical cancer remains the main reason for the poor outcome and high cancer-related mortality rate. Cervical cancer cells closely communicate with immune cells recruited to the tumor microenvironment (TME), such as lymphocytes, tumor-associated macrophages, and myeloid-derived suppressor cells. The crosstalk between tumors and immune cells has been clearly shown to foster metastatic dissemination. Therefore, unraveling the mechanisms of tumor metastasis is crucial to develop more effective therapies. In this review, we interpret several characteristics of the TME that promote the lymphatic metastasis of cervical cancer, such as immune suppression and premetastatic niche formation. Furthermore, we summarize the complex interactions between tumor cells and immune cells within the TME, as well as potential therapeutic strategies to target the TME.
Psychodynamic university counseling: which factors predict psychological functioning after intervention?

Introduction University counseling centers represent important resources for personal development, and students are increasingly turning to them for help. The present study aimed at, first, evaluating changing in psychological functioning before and after a university counseling intervention and, second, exploring which psychological variables predicted the intervention outcome. Methods For this purpose, 122 students who attended university counseling services were administered measures to assess personality traits, and measures to assess state variables - intended as contextual, rather than stable, alterations in functioning - such as anxiety, hopelessness and depression. Several Linear Mixed Models were performed to measure the differences between OQ-45 scores before and after the intervention (one for each OQ dimension and OQ total score); then, two steps of multiple regression analyses were performed. Results Significative reductions between pre-test and post-test OQ-45 scores were found, highlighting increased levels of well-being; personality traits seem not to be predictive of the intervention outcome, while state variables significantly contribute to the psychological wellbeing improvement after counseling intervention. Discussion Our findings highlight the importance of paying attention to the role of affective difficulties in predicting the counseling effectiveness.
Radioimmunotherapy in colorectal cancer treatment: present and future

Colorectal cancer (CRC) is a deadly form of cancer worldwide. Patients with locally advanced rectal cancer and metastatic CRC have a poor long-term prognosis, and rational and effective treatment remains a major challenge. Common treatments include multi-modal combinations of surgery, radiotherapy, and chemotherapy; however, recurrence and metastasis rates remain high. The combination of radiotherapy and immunotherapy (radioimmunotherapy [RIT]) may offer new solutions to this problem, but its prospects remain uncertain. This review aimed to summarize the current applications of radiotherapy and immunotherapy, elaborate on the underlying mechanisms, and systematically review the preliminary results of RIT-related clinical trials for CRC. Studies have identified several key predictors of RIT efficacy. Summarily, rational RIT regimens can improve the outcomes of some patients with CRC, but current study designs have limitations. Further studies on RIT should focus on including larger sample sizes and optimizing the combination therapy regimen based on underlying influencing factors.
Note on Calibration in Stratified and Double Sampling

In the present investigation, new calibration equations making use of second order moments of the auxiliary character are introduced for estimating the population mean in stratified simple random sampling. Ways for estimating the variance of the proposed estimator are suggested, as well. The resultant new estimator can be more efficient than the combined regression estimator is in stratified sampling. The idea has been extended to double sampling in a stratified population and some simulation results studied.
Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant (Camellia sinensis (L.) Kuntze)

Introduction Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement. Methods In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought. Results The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6). Discussion Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
Resources and tools for rare disease variant interpretation

Collectively, rare genetic disorders affect a substantial portion of the world’s population. In most cases, those affected face difficulties in receiving a clinical diagnosis and genetic characterization. The understanding of the molecular mechanisms of these diseases and the development of therapeutic treatments for patients are also challenging. However, the application of recent advancements in genome sequencing/analysis technologies and computer-aided tools for predicting phenotype-genotype associations can bring significant benefits to this field. In this review, we highlight the most relevant online resources and computational tools for genome interpretation that can enhance the diagnosis, clinical management, and development of treatments for rare disorders. Our focus is on resources for interpreting single nucleotide variants. Additionally, we present use cases for interpreting genetic variants in clinical settings and review the limitations of these results and prediction tools. Finally, we have compiled a curated set of core resources and tools for analyzing rare disease genomes. Such resources and tools can be utilized to develop standardized protocols that will enhance the accuracy and effectiveness of rare disease diagnosis.
Small cardamom genome: development and utilization of microsatellite markers from a draft genome sequence of Elettaria cardamomum Maton

Small cardamom (Elettaria cardamomum Maton), the queen of spices, is the third most expensive spice in the world after saffron and vanilla, valued highly for its aroma and taste. This perennial herbaceous plant is a native of coastal parts of Southern India and displays a significant amount of morphological diversity. Its genetic potential has not been exploited due to lack of genomic resources limiting our understanding of the genome and important metabolic pathways which give it the economic advantage in the spice industry. Here, we report upon the de novo assembled, draft whole genome sequence of cardamom variety, Njallani Green Gold. We used a hybrid assembly strategy using the reads from the Oxford Nanopore, Illumina and 10x Genomics GemCode sequencing chemistries. The assembled genome length was 1.06 Gb (gigabases) which is close to the estimated genome size of cardamom. More than 75% of the genome was captured in 8000 scaffolds with a N50 of 0.15 Mb. The genome appears to have a high repeat content and 68055 gene models were predicted. The genome is close to Musa species and displays an expansion and contraction in different gene families. The draft assembly was used for in silico mining of simple sequence repeats (SSRs). A total of 2,50,571 SSRs were identified of which 2,18,270 were perfect SSRs and 32,301 were compound SSRs. Among the perfect SSRs, trinucleotides were most abundant (1,25,329) and hexanucleotide repeats appear least (2,380). From the 2,50,571 SSRs mined, 2,27,808 primer pairs were designed based on flanking sequence information. Wet lab validation was performed for 246 SSR loci and based on their amplification profiles, 60 SSR markers were used for diversity analysis of a set of 60 diverse cardamom accessions. The average number of alleles detected per locus were 14.57 with a minimum of 4 and maximum of 30 alleles. Population structure analysis revealed the presence of high degree of admixtures which could primarily be due to cross-pollination prevalent in this species. The SSR markers identified would help in the development of gene or trait-linked markers which can be subsequently used for marker-assisted breeding for crop improvement in cardamom. The information on utilization of the SSR loci for generation of markers has been developed into a public database, ‘cardamomSSRdb’ that is freely available for use by the cardamom community.
Functional interrogation of twenty type 2 diabetes-associated genes using isogenic hESC-derived β-like cells

Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined β-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-β cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes (CP, RNASE1, PCSK1N and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.