Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in the Body Composition and Nutritional Status after Long-term Rifaximin Therapy for Hyperammonemia in Japanese Patients with Hepatic Encephalopathy

Objective Rifaximin has become available for treating hyperammonemia in patients with hepatic encephalopathy. This study analyzed the changes in the body composition and nutritional status after long-term rifaximin therapy. Methods Twenty-one patients who underwent rifaximin therapy at 1,200 mg/day for more than 24 weeks were evaluated for the changes in the controlling nutritional status (CONUT) scores for the nutritional assessment, albumin-bilirubin (ALBI) scores for the liver function assessment, and skeletal muscle index (SMI) for the body composition assessment. Results There were 17 men and 4 women, with a mean age of 67.14±8.32 years. Eleven cases had a portosystemic shunt (52.3%), and 10 had hepatocellular carcinoma (47.6%). The Child-Pugh class was A in 9 cases (42.9%), B in 9 cases (42.9%), and C in 3 cases (14.2%). The blood ammonia levels in the rifaximin group improved significantly upon rifaximin therapy, from 124.76±28.68 μg/dL at baseline to 47.00±14.43 μg/dL after 2 weeks (p<0.001) and 49.81±15.02 μg/dL after 24 weeks (p<0.001). The CONUT scores improved significantly during rifaximin therapy, from 6.47±3.25 at baseline to 3.33±2.65 after 24 weeks (p=0.0007). The ALBI scores also improved significantly from -0.39±1.89 at baseline to -2.20±0.55 after 24 weeks (p=0.0002). The SMI scores showed that the body composition had been maintained in response to rifaximin therapy (50.20±7.67 at baseline and 51.29±7.62 after 24 weeks). Conclusion Rifaximin administration for hepatic encephalopathy improved the CONUT and ALBI scores. It may have a secondary effect on the improvement in the nutritional status and hepatic reserve.
Response to the Comment on "Intracorporeal or Extracorporeal Ileocolic Anastomosis After Laparoscopic Right Colectomy. A Double-blinded Randomized Controlled Trial".

Reply: We thank Dr. Pringle et al. for their letter to the Annals of Surgery focused on our randomized controlled trial (RCT) that was designed to detect possible clinically relevant differences in outcomes between laparoscopic right colectomy (LRC) with intracorporeal ileocolic anastomosis (IIA) and LRC with extracorporeal IA (EIA). LRC with IIA was associated with earlier recovery of postoperative bowel func-
Experiences of self-management support in patients with diabetes and multimorbidity: a qualitative study in Norwegian general practice

Abstract Aim: The purpose of this study was to explore how patients with diabetes and multimorbidity experience self-management support by general practitioners (GPs), nurses and medical secretaries in Norwegian general practice. Background: Self-management support is recognised as an important strategy to improve the autonomy and well-being of patients with long-term conditions. Collaborating healthcare professionals (cHCPs), such as nurses and medical secretaries, may have an important role in the provision of self-management support. No previous study has explored how patients with diabetes and multimorbidity experience self-management support provided by cHCPs in general practice in Norway. Methods: Semi-structured interviews with 11 patients with type 1 diabetes mellitus (T1DM) or type 2 diabetes mellitus (T2DM) with one or more additional long-term condition were performed during February–May 2017. Findings: Patients experienced cHCPs as particularly attentive towards the psychological and emotional aspects of living with diabetes. Compared to GPs, whose appointments were experienced as stressful, patients found cHCPs more approachable and more likely to address patients’ questions and worries. In this sense, cHCPs complemented GP-led diabetes care. However, neither cHCPs nor GPs were perceived to involve patients’ in clinical decisions or goal setting during consultations.
Cannabidiol (CBD) modulation of apelin in acute respiratory distress syndrome

Considering lack of target‐specific antiviral treatment and vaccination for COVID‐19, it is absolutely exigent to have an effective therapeutic modality to reduce hospitalization and mortality rate as well as to improve COVID‐19‐infected patient outcomes. In a follow‐up study to our recent findings indicating the potential of Cannabidiol (CBD) in the treatment of acute respiratory distress syndrome (ARDS), here we show for the first time that CBD may ameliorate the symptoms of ARDS through up‐regulation of apelin, a peptide with significant role in the central and peripheral regulation of immunity, CNS, metabolic and cardiovascular system. By administering intranasal Poly (I:C), a synthetic viral dsRNA, while we were able to mimic the symptoms of ARDS in a murine model, interestingly, there was a significant decrease in the expression of apelin in both blood and lung tissues. CBD treatment was able to reverse the symptoms of ARDS towards a normal level. Importantly, CBD treatment increased the apelin expression significantly, suggesting a potential crosstalk between apelinergic system and CBD may be the therapeutic target in the treatment of inflammatory diseases such as COVID‐19 and many other pathologic conditions.
Suppression of Metacaspase- and Autophagy-Dependent Cell Death Improves Stress-Induced Microspore Embryogenesis in Brassica napus

Abstract Microspore embryogenesis is a biotechnological process that allows us to rapidly obtain doubled-haploid plants for breeding programs. The process is initiated by the application of stress treatment, which reprograms microspores to embark on embryonic development. Typically, a part of the microspores undergoes cell death that reduces the efficiency of the process. Metacaspases (MCAs), a phylogenetically broad group of cysteine proteases, and autophagy, the major catabolic process in eukaryotes, are critical regulators of the balance between cell death and survival in various organisms. In this study, we analyzed the role of MCAs and autophagy in cell death during stress-induced microspore embryogenesis in Brassica napus. We demonstrate that this cell death is accompanied by the transcriptional upregulation of three BnMCA genes (BnMCA-Ia, BnMCA-IIa and BnMCA-IIi), an increase in MCA proteolytic activity and the activation of autophagy. Accordingly, inhibition of autophagy and MCA activity, either individually or in combination, suppressed cell death and increased the number of proembryos, indicating that both components play a pro-cell death role and account for decreased efficiency of early embryonic development. Therefore, MCAs and/or autophagy can be used as new biotechnological targets to improve in vitro embryogenesis in Brassica species and doubled-haploid plant production in crop breeding and propagation programs.
Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA)

Biological and medical sciences are increasingly acknowledging the significance of gene co-expression-networks for investigating complex-systems, phenotypes or diseases. Typically, complex phenotypes are investigated under varying conditions. While approaches for comparing nodes and links in two networks exist, almost no methods for the comparison of multiple networks are available and—to best of our knowledge—no comparative method allows for whole transcriptomic network analysis. However, it is the aim of many studies to compare networks of different conditions, for example, tissues, diseases, treatments, time points, or species. Here we present a method for the systematic comparison of an unlimited number of networks, with unlimited number of transcripts: Co-expression Differential Network Analysis (CoDiNA). In particular, CoDiNA detects links and nodes that are common, specific or different among the networks. We developed a statistical framework to normalize between these different categories of common or changed network links and nodes, resulting in a comprehensive network analysis method, more sophisticated than simply comparing the presence or absence of network nodes. Applying CoDiNA to a neurogenesis study we identified candidate genes involved in neuronal differentiation. We experimentally validated one candidate, demonstrating that its overexpression resulted in a significant disturbance in the underlying gene regulatory network of neurogenesis. Using clinical studies, we compared whole transcriptome co-expression networks from individuals with or without HIV and active tuberculosis (TB) and detected signature genes specific to HIV. Furthermore, analyzing multiple cancer transcription factor (TF) networks, we identified common and distinct features for particular cancer types. These CoDiNA applications demonstrate the successful detection of genes associated with specific phenotypes. Moreover, CoDiNA can also be used for comparing other types of undirected networks, for example, metabolic, protein-protein interaction, ecological and psychometric networks. CoDiNA is publicly available as an R package in CRAN (https://CRAN.R-project.org/package=CoDiNA).
Population dynamics of Capercaillie in a North-east Scottish glen

During a nine-year study of Capercaillie almost twice as many female as male chicks were reared, but there were no more hens than cocks in the adult population. Both the proportion of male chicks in late summer each year, and mean brood size, were related to the chicks' condition in July. Condition was related to the number of days with rain in early June, during and just after hatching. The breeding density of hens each year varied between 4.0 and 8.0 km-2 but was related neither to their density in the previous year nor to the production of female chicks in the intervening summer. The best predictive model was simply that breeding densities would return to their mean each year. It was inferred that breeding densities were determined by densitydependent losses and gains involving emigration and immigration. Autumn densities of young and old birds were not related to breeding densities and breeding success, but were inversely related to the proportion of broods which disappeared, and probably emigrated, during the summer.
Melatonin ameliorates microvessel abnormalities in the cerebral cortex and hippocampus in a rat model of Alzheimer’s disease

Melatonin can attenuate cardiac microvascular ischemia/reperfusion injury, but it remains unclear whether melatonin can also ameliorate cerebral microvascular abnormalities. Rat models of Alzheimer’s disease were established by six intracerebroventricular injections of amyloid-beta 1–42, administered once every other day. Melatonin (30 mg/kg) was intraperitoneally administered for 13 successive days, with the first dose given 24 hours prior to the first administration of amyloid-beta 1–42. Melatonin ameliorated learning and memory impairments in the Morris water maze test, improved the morphology of microvessels in the cerebral cortex and hippocampus, increased microvessel density, alleviated pathological injuries of cerebral neurons, and decreased the expression of vascular endothelial growth factor and vascular endothelial growth factor receptors 1 and 2. These findings suggest that melatonin can improve microvessel abnormalities in the cerebral cortex and hippocampus by lowering the expression of vascular endothelial growth factor and its receptors, thereby improving the cognitive function of patients with Alzheimer’s disease. This study was approved by the Animal Care and Use Committee of Jinzhou Medical University, China (approval No. 2019015) on December 6, 2018.
Persistence of an intact HIV reservoir in phenotypically naive T cells

Despite the efficacy of antiretroviral therapy (ART), HIV persists in a latent form and remains a hurdle to eradication. CD4+ T lymphocytes harbor the majority of the HIV reservoir, but the role of individual subsets remains unclear. CD4+ T cells were sorted into central, transitional, effector memory, and naive T cells. We measured HIV DNA and performed proviral sequencing of more than 1900 proviruses in 2 subjects at 2 and 9 years after ART initiation to estimate the contribution of each subset to the reservoir. Although our study was limited to 2 subjects, we obtained comparable findings with publicly available sequences. While the HIV integration levels were lower in naive compared with memory T cells, naive cells were a major contributor to the intact proviral reservoir. Notably, proviral sequences isolated from naive cells appeared to be unique, while those retrieved from effector memory cells were mainly clonal. The number of clones increased as cells differentiated from a naive to an effector memory phenotype, suggesting naive cells repopulate the effector memory reservoir as previously shown for central memory cells. Naive T cells contribute substantially to the intact HIV reservoir and represent a significant hurdle for HIV eradication.
Combining fixation and lateral masking training enhances perceptual learning effects in patients with macular degeneration

Macular degeneration (MD), a retinal disease affecting central vision, represents the leading cause of visual impairment in the Western world, and MD patients face severe limitations in daily activities like reading and face recognition. A common compensation strategy adopted by these patients involves the use of a region in the spared peripheral retina as a new fixation spot and oculomotor reference (preferred retinal locus, or PRL). Still, peripheral vision is characterized by poorer visual acuity, fixation stability, and larger crowding zones that further hinder processes like object recognition, visual search, and reading. Perceptual learning (PL) has been successfully used to improve visual acuity in mild visual conditions (e.g., presbyopia, amblyopia and myopia), but results in MD are less clear, often showing limited generalization of learning, unlike what is observed in a healthy population. A possible reason is the suboptimal fixation in the PRL that might prevent patients from processing the briefly presented training stimuli. Following this hypothesis, we trained five MD patients and four age- and eccentricity-matched controls with a protocol that combined contrast detection and a task previously used to train fixation stability. Results showed transfer of learning to crowding reduction, reading speed, and visual acuity in both MD patients and controls. These results suggest that in the case of central vision loss, PL training might benefit from the integration of oculomotor components to optimize the effect of training and promote transfer of learning to other visual functions.
Systematic revisit of Sparsitubus (Basidiomycota, Aphyllophorales), an unusual cyphelloid polypore from China

Sparsitubus is a monotypic genus found in East Asia that has a bizarre cyphelloid hymenophore. The position of Sparsitubus in the Polyporaceae has been suggested previously based on morphological characters. To study the relationships of Sparsitubus among other Homobasidiomycetes, rDNA sequences of Sparsitubus and polypores representatives were generated or downloaded from GenBank. Parsimony analyses using rDNA data suggest that Sparsitubus is in a clade of polypores producing a white rot and maybe closely related to the Ganodermataceae. Characters of fruiting body, hyphal systems, and basidiospore were compared and discussed between S. nelumbiformis and related polypores or similar cyphelloid fungi.
Cranial Shape and Diet Variation in Myotis Species (Chiroptera: Vespertilionidae): Testing the Relationship between Form and Function

The relationship between cranial morphology and diet has long been investigated in bats. Bats of the genus Myotis include insectivorous, facultatively piscivorous, and piscivorous species. We tested the hypothesis that facultatively piscivorous (five Myotis species) and piscivorous species (M. vivesi) present cranial morphological and functional changes with respect to insectivorous taxa (16 Myotis species). Cranial shapes in skull and mandible modules were described with four geometric landmark configurations in these dietary groups. Gape capacity was measured with the stretch factors for temporal and masseter muscles. Geometric configurations from two skull and two mandible shapes were analyzed to detect differences in cranial morphology in relation to diet. Differences in cranial morphology were found between piscivorous and insectivorous species involving the mandibular process where masticatory muscles are attached. Linear regression analysis of Procrustes distances and gape capacity showed that the shape of the mandibular process region was highly correlated with the stretch factor of the masseter muscle in piscivorous and facultatively piscivorous species. These results suggest differences in cranial morphology and performance among diets but the hypothesis of gradual changes in cranial shape among diets was only accepted for the mandible and not for the skull. Myotis vivesi appears to improve mechanical advantage of masticatory muscles at lower gapes, presumably allowing more efficient chewing of slippery prey.
Thermoregulatory behaviour and thermal tolerance of three species of Conidae in the Eastern Pacific and Gulf of California coasts of Baja California, Mexico

ABSTRACT We investigated three species of Conidae, one on the western shores of Baja California (Californiconus californicus), and two in the Gulf of California (Conasperella perplexus and Conasperella ximenes). In a thermal horizontal gradient trial with day–night cycles, we determined the final thermal preference of three species of snails. Californiconus californicus had a preferred average temperature of 23.3 °C, compared with 22.7 °C for Co. perplexus whereas Co. ximenes had a diel preference of 20.1 °C during the day and 27.2 °C at night. The displacement velocity in Ca. californicus during the day was 12.6 ± 1.9 cm h−1 versus 17.6 ± 2 cm h−1 at night; for Co. perplexus it was 3.8 ± 0.67 cm h−1 in the day and 4.16 ± 0.72 cm h−1 at night; and for Co. ximenes it was 19.3 ± 2.5 cm h−1 during the day and 18.3 ± 2.6 cm h−1 during the night. The critical thermal maximum, the temperature at which at least 50% of the experimental group experiences a loss of attachment, differed between Conasperella species from the Gulf of California and Californiconus californicus from the Eastern Pacific Ocean. The species inhabiting the Gulf of California have a greater thermal tolerance, with this pattern typical of species in tropical seas, whereas some of those that inhabit the Pacific coast of North America can tolerate lower temperatures, reflecting their range in more temperate climates.
Integrating Metapopulation Dynamics into a Bayesian Network Relative Risk Model: Assessing Risk of Pesticides to Chinook Salmon (Oncorhynchus tshawytscha) in an Ecological Context

The population level is often the biological endpoint addressed in ecological risk assessments (ERAs). However, ERAs tend to ignore the metapopulation structure, which precludes an understanding of how population viability is affected by multiple stressors (e.g., toxicants and environmental conditions) at large spatial scales. Here we integrate metapopulation model simulations into a regional‐scale, multiple stressors risk assessment (Bayesian network relative risk model [BN‐RRM]) of organophosphate (OP) exposure, water temperature, and DO impacts on Chinook salmon (Oncorhynchus tshawytscha). A matrix metapopulation model was developed for spring Chinook salmon in the Yakima River Basin (YRB), Washington, USA, including 3 locally adapted subpopulations and hatchery fish that interact with those subpopulations. Three metapopulation models (an exponential model, a ceiling density‐dependent model, and an exponential model without dispersal) were integrated into the BN‐RRM to evaluate the effects of population model assumptions on risk calculations. Risk was defined as the percent probability that the abundance of a subpopulation would decline from their initial abundance (500 000). This definition of risk reflects the Puget Sound Partnership's management goal of achieving “no net loss” of Chinook abundance. The BN‐RRM model results for projection year 20 showed that risk (in % probability) from OPs and environmental stressors was higher for the wild subpopulations—the American River (50.9%–97.7%) and Naches (39.8%–84.4%) spring Chinook—than for the hatchery population (CESRF 18.5%–46.5%) and the Upper Yakima subpopulation (21.5%–68.7%). Metapopulation risk was higher in summer (58.1%–68.7%) than in winter (33.6%–53.2%), and this seasonal risk pattern was conserved at the subpopulation level. To reach the management goal in the American River spring Chinook subpopulation, the water temperature conditions in the Lower Yakima River would need to decrease. We demonstrate that 1) relative risk can vary across a metapopulation's spatial range, 2) dispersal among patches impacts subpopulation abundance and risk, and 3) local adaptation within a salmon metapopulation can profoundly impact subpopulation responses to equivalent stressors. Integr Environ Assess Manag 2021;17:95–109. © 2020 SETAC
A Pilot Study on In-Task Affect Predicting Free-Living Adherence to HIIT and MICT

ABSTRACT Purpose: To report pilot test findings on whether in-task affect during a supervised exercise program, where participants were randomized to either moderate-intensity continuous training (MICT) or high-intensity interval training (HIIT), predicts changes in moderate-to-vigorous physical activity (MVPA-Total and MVPA10+ in bouts of ≥ 10 min) at 1- and 6-month post-intervention. Method: This experimental study design randomized 32 inactive adults with prediabetes to complete a 2-week supervised MICT or HIIT plus behavioral counseling exercise intervention and objectively assessed free-living physical activity post-intervention. The Feeling Scale (FS) was used to assess the in-task effect. FS was measured in the middle of four, 1-min intervals in the HIIT condition, corresponding to ~20%, ~50%, ~75%, and ~85% of work out time. For the MICT condition, FS was assessed at similar exercise duration percentage times as HIIT. Accelerometer data evaluated MVPA at 1- and 6-month post-intervention. Results: 32 adults were included in the analyses. Pilot findings indicated in-task affect between the conditions did not predict changes in MVPA-Total from baseline to 1 and 6 months. For MVPA10+, in-task affect negatively predicted MVPA10+ over time in the MICT condition only. Conclusion: This study provides preliminary evidence that affect during MICT negatively predicts MVPA10+ over time, and that there is no difference of in-task affect’s utility in predicting MVPA-Total between HIIT and MICT. Larger studies are required to confirm these findings.