Miracle-dz/UniFAR-FTUs huggingface dataset:
Cumulative effects of piscivorous colonial waterbirds on juvenile salmonids: A multi predator-prey species evaluation

We investigated the cumulative effects of predation by piscivorous colonial waterbirds on the survival of multiple salmonid (Oncorhynchus spp.) populations listed under the U.S. Endangered Species Act (ESA) and determined what proportion of all sources of fish mortality (1 –survival) were due to birds in the Columbia River basin, USA. Anadromous juvenile salmonids (smolts) were exposed to predation by Caspian terns (Hydroprogne caspia), double-crested cormorants (Nannopterum auritum), California gulls (Larus californicus), and ring-billed gulls (L. delawarensis), birds known to consume both live and dead fish. Avian consumption and survival probabilities (proportion of available fish consumed or alive) were estimated for steelhead trout (O. mykiss), yearling Chinook salmon (O. tshawytscha), sub-yearling Chinook salmon, and sockeye salmon (O. nerka) during out-migration from the lower Snake River to the Pacific Ocean during an 11-year study period (2008–2018). Results indicated that probabilities of avian consumption varied greatly across salmonid populations, bird species, colony location, river reach, and year. Cumulative consumption probabilities (consumption by birds from all colonies combined) were consistently the highest for steelhead, with annual estimates ranging from 0.22 (95% credible interval = 0.20–0.26) to 0.51 (0.43–0.60) of available smolts. The cumulative effects of avian consumption were significantly lower for yearling and sub-yearling Chinook salmon, with consumption probabilities ranging annually from 0.04 (0.02–0.07) to 0.10 (0.07–0.15) and from 0.06 (0.3–0.09) to 0.15 (0.10–0.23), respectively. Avian consumption probabilities for sockeye salmon smolts was generally higher than for Chinook salmon smolts, but lower than for steelhead smolts, ranging annually from 0.08 (0.03–0.22) to 0.25 (0.14–0.44). Although annual consumption probabilities for birds from certain colonies were more than 0.20 of available smolts, probabilities from other colonies were less than 0.01 of available smolts, indicating that not all colonies of birds posed a substantial risk to smolt mortality. Consumption probabilities were lowest for small colonies and for colonies located a considerable distance from the Snake and Columbia rivers. Total mortality attributed to avian consumption was relatively small for Chinook salmon (less than 10%) but was the single greatest source of mortality for steelhead (greater than 50%) in all years evaluated. Results suggest that the potential benefits to salmonid populations of managing birds to reduce smolt mortality would vary widely depending on the salmonid population, the species of bird, and the size and location of the breeding colony.
The interplay of long noncoding RNAs and hepatitis B virus

Hepatitis B Virus (HBV) infections remain a major global health burden with an estimated 296 million people living with a chronic infection and 884,000 HBV‐related deaths annually. Notably, patients with a chronic hepatitis B (CHB) infection are at a 30‐fold greater risk of developing hepatocellular carcinoma (HCC), the most common type of primary liver cancer, which is the 3rd deadliest cancer worldwide. Several groups have assessed HBV‐related aberrant expression of host‐cell long noncoding RNAs (lncRNAs) and how altered expression of specific lncRNAs affects HBV replication and progression to associated disease states. Given the challenges in establishing effective HBV models and analyzing transcriptomic data, this review focuses on lncRNA expression data primarily collected from clinical patient samples and primary human hepatocytes, with the subsequent mechanism of action analysis in cell lines or other model systems. Ultimately, understanding HBV‐induced lncRNA‐expression dysregulation could lead to new treatments and biomarkers for HBV infection and its associated diseases.
The state of anesthesia in South Korea: a national survey of the status of anesthetic service activity in 2014–2016

Background Because the quality of anesthesia affects the surgical outcome, the aim of this study was to investigate the current status of anesthetic services performed by anesthesiologists and non-anesthesiologists in South Korea from 2014 to 2016 and to compare the results with data from 2011 to 2013. Methods The claimed anesthesia services at medical institutions with employed anesthesiologists and the claims for an invitation fee for an anesthesiologist at medical institutions without employed anesthesiologists were regarded as anesthetic services performed by an anesthesiologist. From 2014 to 2016, the employment of anesthesiologists according to the type of medical institution, the status of anesthetic services according to the presence or absence of employed anesthesiologists, and status of anesthetic services at medical institutions without employed anesthesiologists were analyzed. Results The proportion of medical institutions that employed anesthesiologists slightly increased from 27.8% in 2014 to 28.8% in 2016. General anesthesia was more concentrated at higher medical institutions, and most anesthesias were performed by an anesthesiologist. The proportion of spinal anesthesia, epidural anesthesia, and brachial plexus performed by non-anesthesiologists was 11%, 15%, and 16.5%, respectively. Intravenous anesthesia performed by non-anesthesiologists was 58% and has increased compared to the past. Conclusions The employment of anesthesiologists has increased with time, and general anesthesiology was mostly performed by anesthesiologists. However, since the proportion of anesthetic services performed by non-anesthesiologists in regional anesthesia and intravenous anesthesia was maintained high, it is necessary to find ways to expand the safety of anesthetic services.
Within-Person Dynamics of Objective and Subjective Social Isolation in Midlife and Later Life

Objectives To investigate the within-person dynamics of objective and subjective social isolation among U.S. middle-aged and older adults and to explore gender differences in this relationship. Methods: Four waves of data from the Health and Retirement Study (HRS, 2006–2018, N = 5437) and the multiple group random intercept cross-lagged panel model were used. Results: Within-person deviation in expected subjective isolation predicted deviation in expected objective isolation years later. No corresponding cross-lagged effect of objective isolation on subjective isolation was found. Gender differences were detected: the within-person cross-lagged positive effect of subjective isolation on objective isolation was significant for men but not for women. Discussion: This study provides evidence for a unidirectional relationship between subjective and objective isolation at the within-person level: higher than expected increase in subjective isolation predicts higher than expected increase in subsequent objective isolation. This within-person process is more salient in men than in women.
Mitochondrial organization and structure are compromised in fibroblasts from patients with Huntington’s disease

ABSTRACT Huntington´s disease (HD) is a progressive neurodegenerative disease with onset in adulthood that leads to a complete disability and death in approximately 20 years after onset of symptoms. HD is caused by an expansion of a CAG triplet in the gene for huntingtin. Although the disease causes most damage to striatal neurons, other parts of the nervous system and many peripheral tissues are also markedly affected. Besides huntingtin malfunction, mitochondrial impairment has been previously described as an important player in HD. This study focuses on mitochondrial structure and function in cultivated skin fibroblasts from 10 HD patients to demonstrate mitochondrial impairment in extra-neuronal tissue. Mitochondrial structure, mitochondrial fission, and cristae organization were significantly disrupted and signs of elevated apoptosis were found. In accordance with structural changes, we also found indicators of functional alteration of mitochondria. Mitochondrial disturbances presented in fibroblasts from HD patients confirm that the energy metabolism damage in HD is not localized only to the central nervous system, but also may play role in the pathogenesis of HD in peripheral tissues. Skin fibroblasts can thus serve as a suitable cellular model to make insight into HD pathobiochemical processes and for the identification of possible targets for new therapies.
Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins

Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study we present a comparative analysis of regulatory element sequences and accessibility throughout embryogenesis in three sea urchin species with divergent life histories: a lecithotroph Heliocidaris erythrogramma, a closely related planktotroph H. tuberculata, and a distantly related planktotroph Lytechinus variegatus. We identified distinct epigenetic and mutational signatures of evolutionary modifications to the function of putative cis-regulatory elements in H. erythrogramma that have accumulated non-uniformly throughout the genome, suggesting selection, rather than drift, underlies many modifications associated with the derived life history. Specifically, regulatory elements composing the sea urchin developmental gene regulatory network are enriched for signatures of positive selection and accessibility changes which may function to alter binding affinity and access of developmental transcription factors to these sites. Furthermore, regulatory element changes often correlate with divergent expression patterns of genes involved in cell type specification, morphogenesis, and development of other derived traits, suggesting these evolutionary modifications have been consequential for phenotypic evolution in H. erythrogramma. Collectively, our results demonstrate that selective pressures imposed by changes in developmental life history rapidly reshape the cis-regulatory landscape of core developmental genes to generate novel traits and embryonic programs.
ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins

General-purpose protein structure embedding can be used for many important protein biology tasks, such as protein design, drug design and binding affinity prediction. Recent researches have shown that attention-based encoder layers are more suitable to learn high-level features. Based on this key observation, we propose a two-level general-purpose protein structure embedding neural network, called ContactLib-ATT. On local embedding level, a biologically more meaningful contact context is introduced. On global embedding level, attention-based encoder layers are employed for better global representation learning. Our general-purpose protein structure embedding framework is trained and tested on the SCOP40 2.07 dataset. As a result, ContactLib-ATT achieves a SCOP superfamily classification accuracy of 82.4% (i.e., 6.7% higher than state-of-the-art method). On the same dataset, ContactLib-ATT is used to simulate a structure-based search engine for remote homologous proteins, and our top-10 candidate list contains at least one remote homolog with a probability of 91.9%.
Insulin prevents fatty acid induced increase of adipocyte size

ABSTRACT Metabolic disorders related to obesity are largely dependent on adipose tissue hypertrophy, which involves adipocyte hypertrophy and increased adipogenesis. Adiposize is regulated by lipid accumulation as a result of increased lipogenesis (mainly lipid uptake in mature adipocytes) and reduced lipolysis. Using realtime 2D cell culture analyses of lipid uptake, we show (1) that high glucose concentration (4.5 g/L) was required to accumulate oleic acid increasing lipid droplet size until unilocularization similar to mature adipocytes in few days, (2) oleic acid reduced Peroxisome-Proliferator Activated Receptor Gamma (PPARG) gene transcription and (3) insulin counteracted oleic acid-induced increase of lipid droplet size. Although the lipolytic activity observed in high versus low glucose (1 g/L) conditions was not altered, insulin was found to inhibit oleic acid induced gene transcription required for lipid storage such as Cell Death Inducing DFFA Like Effectors (CIDEC) and G0S2 (G0 switch gene S2), possibly through PPARA activity. Although this signalling pathway requires more detailed investigation, the results point out the differential mechanisms involved in the pro-adipogenic effect of insulin in absence versus its protective effect on adiposity in presence of oleic acid uptake. Abbreviations: AICAR, 5-Aminoimidazole-4-carboxamide-1-D-ribofuranoside; AMPK, AMP-Activated protein kinase, ASCs, adipose stem cell; ATGL, adipose triglyceride lipase; BSA, Bovine serum albumin; CEBPA, CCAAT enhancer binding protein alpha; CIDEs, Cell Death Inducing DFFA Like Effectors; dA, differentiated adipocyte; DMEM, Dulbecco’s Modified Eagle’s Medium; FABPs, Fatty Acid Binding Proteins; FAT/CD36, Fatty acid translocase; FCS, Foetal calf serum; FN1, fibronectin 1; FFA, free fatty acid; G0S2, G0 switch gene S2; GLUTs, Glucose transporters; GPR120, G protein-coupled receptor 120; HG, high glucose; HSL, hormone sensitive lipase; INSR, insulin receptor; LG, low glucose; OA, oleic acid; PBS, Phosphate buffer saline; PPARs, Peroxisome-Proliferator Activated Receptors; PKA, Protein kinase cyclic AMP-dependent; PKG, Protein kinase cyclic GMP dependent; PTGS2, cytochrome oxidase 2; RTCA, realtime cell analysis; TG, triglyceride. Graphical Abstract
Favorable Management of Repeated Serous Retinal Detachment with Continued Tumor Response in a Patient with Intrahepatic Cholangiocarcinoma during Treatment with Pemigatinib

Pemigatinib is a fibroblast growth factor receptor inhibitor (FGFRi) approved for the treatment of patients with previously treated biliary tract cancer with FGFR2 fusion. Although infrequent, ocular toxicity manifested as serous retinal detachment (SRD) has been observed and is regarded as a serious side effect. We herein report the case of a 54-year-old woman with unresectable cholangiocarcinoma-initiated pemigatinib after failure of gemcitabine plus S-1 (GS). Although the patient experienced repeated SRD after pemigatinib, dose interruption and dose reduction of pemigatinib from 13.5 mg to 9 mg, and from 9 mg to 4.5 mg led to complete recovery of SRD, and continued tumor shrinkage.
Effectiveness of oral health promotion interventions for people with type 2 diabetes delivered by non-dental health care professionals: a systematic review

ABSTRACT Background Oral health problems among people with diabetes mellitus are an emerging public health problem. Despite the rising concerns of oral health and diabetes mellitus comorbidity, there is a lack of dental health care professionals such as dentists, to address this problem, especially at the primary care level in low- and middle-income countries. Objective This review systematically synthesizes the current evidence in terms of the involvement of non-dental health care professionals in promoting oral health among people with type 2 diabetes mellitus and assessed the effectiveness of such programs. Methods Six electronic databases (CINAHL, Cochrane, Embase, PsycINFO, PubMed, and Scopus) and Google Scholar were systematically searched. The inclusion criteria were: 1) had an intervention promoting oral health; 2) targeted but not limited to people with type 2 diabetes mellitus; 3) intervention led but not limited to by non-dental health care professionals; 4) published in English language between January 2000 and July 2021. This review was registered in PROSPERO (#CRD42021248213). Results A total of five studies from four countries (Finland, Thailand, Iran, and the Netherlands) met the inclusion criteria. The interventions included oral health education, a dental care reminder system, and the implementation of oral health care protocols in general practices, all of which were mainly implemented by nurses. All interventions improved clinical outcomes, including decreased probing depth, attachment loss, and plaque index scores, and non-clinical outcomes such as enhanced knowledge, attitudes, and behaviors. Three studies also reported an improvement in diabetes mellitus outcomes. Conclusion This review suggests that non-dental health care professionals play a promising role in promoting oral health among people with type 2 diabetes mellitus. Our findings support the potential for integrating oral health promotion programs in primary health care, as such programs could bring better oral health and diabetes mellitus outcomes.
Tremor, finger and hand dexterity and force steadiness, do not change after mental fatigue in healthy humans

The effects of mental fatigue have been studied in relation to specific percentages of maximal aerobic or anaerobic efforts, maximal voluntary contractions or the performance of sport specific skills. However, its effects on tremor, dexterity and force steadiness have been only marginally explored. The present work aimed at filling this gap. In twenty-nine young individuals, measurement of postural, kinetic and isometric tremor, pinch force steadiness and finger and hand dexterity were performed before and after either 100 min of mental fatigue or control tasks. During the interventions blood pressure, oxygen saturation and heart rate and perceived effort in continuing the task were recorded every 10 minutes. Tremor was analysed in both time (standard deviation) and frequency domain (position, amplitude and area of the dominant peak) of the acceleration signal. Finger dexterity was assessed by Purdue pegboard test and hand dexterity in terms of contact time in a buzz wire exercise. Force steadiness was quantified as coefficient of variation of the force signal. Postural, kinetic and isometric tremors, force steadiness and dexterity were not affected. Higher oxygen saturation values and higher variability of heart rate and blood pressure were found in the intervention group during the mental fatigue protocol (p < .001). The results provide no evidence that mental fatigue affects the neuromuscular parameters that influence postural, kinetic or isometric tremor, force steadiness and dexterity when measured in single-task conditions. Increased variability in heart rate may suggest that the volunteers in the intervention group altered their alert/stress state. Therefore, it is possible that the alterations that are commonly observed during mental fatigue, and that could have affected tremor, steadiness and dexterity only last for the duration of the cognitive task and are not detectable anymore soon after the mental task is terminated.
Factors associated with hepatitis B and C among adults in Buea, Cameroon: A community‐based cross‐sectional study

Viral hepatitis is a major cause of death in Africa. A paucity of community‐based studies on the determinants of viral hepatitis in Africa impedes efforts to appropriately target prevention, screening, and treatment interventions. We assessed factors associated with hepatitis B virus (HBV) and hepatitis C virus (HCV) in a semi‐urban health district in Cameroon.
Co-occurrence of non-communicable disease risk factors and its determinants among school-going adolescents of Kathmandu Metropolitan City

Background Adolescence is a critical transition in human growth and adolescents tend to engage in various risky behaviors which are likely to continue into adulthood. Co-occurrence of non-communicable disease risk factors has the potential to increase risks of chronic disease comorbidity and increased mortality in later life. Behavioral risk factors are adopted due to changes in lifestyle and adolescents are more prone to acquire them. This study aimed to determine the prevalence and associated factors of co-occurrence of non-communicable disease risk factors among school-going adolescents of Kathmandu Metropolitan City. Methods We conducted a cross-sectional study among school-going adolescents of Kathmandu Metropolitan City in January/February 2020. We used stratified random sampling to select 1108 adolescents studying in 9, 10, 11, and 12 grades. We used Global Schools Health Survey tools to collect data. We entered data in EpiData 3.1 and exported it into Statistical Package for Social Science (SPSS) version 20 for statistical analysis. We estimated prevalence of NCDs risk factors and co-occurrence of risk factors. We applied multivariate multinomial logistic regression analysis adjusting for age, gender, ethnicity, religion, education, type of school, and parental education to determine factors associated with co-occurrence of NCDs risk factors. Results The prevalence of physical inactivity, unhealthy diet, harmful use of alcohol and tobacco among school-going adolescents were 72.3% (95%CI: 69.6–74.9), 41.1% (95%CI: 38.2–44.0), 14.8% (95%CI: 12.8–17.0) and 7.8% (95%CI:6.3–9.5) respectively. The adolescent with co-occurrence of two or more risk factors was 40.7% (95%CI: 37.8–43.7). The school-going adolescents who were in higher age group (AOR = 1.72, 95% CI- 1.06, 2.77), Hindus (AOR = 1.78, 95% CI-1.09, 2.89), other than Brahmin/Chhetri by ethnicity (AOR = 2.11, 95% CI-1.39, 2.22) and with lower education level of mothers (AOR = 2.40, 95% CI- 1.46,3.98) were more likely to have co-occurrence of NCDs risk factors after adjusting for all socio-demographic variables. Conclusion The co-occurrence of non-communicable disease risk factors was high among school going adolescents and was associated with age, religion, ethnicity and mother’s education. Integrated and comprehensive interventional programs should be developed by concerned authorities.
Post-COVID syndrome: A prospective study in a tertiary hospital of Nepal

Introduction The post-coronavirus disease 2019 (COVID-19) syndrome is defined as the persistence of symptoms after viral clearance and the emergence of new symptoms after a few months following recovery from COVID-19. This study aimed to assess the prevalence of post-COVID-19 syndrome and the risk factors that contribute to its development. Methods This study was conducted prospectively in Tribhuvan University Teaching Hospital (TUTH), located in Maharajgunj, Kathmandu. The patients were followed up for three months. Results The post-COVID status of 300 patients admitted to the COVID emergency of TUTH was studied. The mean age of the patients was 46.6±15.7 years, and the proportion of male (56%) was slightly higher than female (44%). Most of the patients (81.7%) had fever on their presentation to the emergency which was followed by fatigue (81.3%) and cough (78.3%). During the post-COVID phase, fatigue was the most common persistent symptom, with 34% experiencing fatigue after 60 days and 28.3% even after 90 days from the onset of symptoms. Univariate logistic regression showed sore throat (OR 4.6; 95% CI (2.8–7.6)), rhinitis (OR 3.6; 95% CI (2.1–5.9)), fatigue (OR 3.7; 95% CI (1.8–7.6)), diarrhea (OR 4.1; 95% CI (2.4–6.9)), anosmia (OR 6.7; 95% CI (3.9–11.3)), ageusia (OR 7.8; 95% CI (4.5–13.4)) and shortness of breath (OR 14.9; 95% CI (1.8–119.6)) at admission were all predictors of post-COVID syndrome after three months. Conclusion Even after recovering from COVID-19, people with COVID-19 may develop symptoms. As a result, COVID-19’s long-term consequences should not be neglected, as they may lead to increased morbidity among patients, consumption of financial resources, and added burden on the health system.