Miracle-dz/UniFAR-FTUs huggingface dataset:
Dyslipidemia and Associated Factors in Tenofovir Disoproxil Fumarate-Based Regimen Among Human Immunodeficiency Virus-Infected Ethiopian Patients: A Hospital-Based Observational Prospective Cohort Study

Background Studies showed conflicting results regarding the effect of broadly used tenofovir disoproxil fumarate (TDF)-based regimen on lipid profiles, and in Ethiopia, there is no data regarding the magnitude of dyslipidemia and its associated factors. Objective The aim of this study was to determine the magnitude of dyslipidemia and its associated factors among adult human immunodeficiency virus (HIV)-infected patients in TDF-based regimen in Tikur Anbessa Specialized Hospital (TASH) in Ethiopia. Methods A hospital-based observational prospective cohort study was conducted on conveniently selected 63 patients in TASH from January to September, 2019. The data was analyzed by using SPSS version 21.0, and multivariate logistic regression was used to determine associated factors with dyslipidemia. Results The overall dyslipidemia was 73% and 77.8% at baseline and six months, respectively. The prevalence of total cholesterol (TC) ≥200 mg/d, triglyceride (TG) ≥150 mg/dL, low density lipoprotein cholesterol (LDL-c) ≥130 mg/dL, and high density lipoprotein cholesterol (HDL-c) <40 mg/dL was 38.1% vs 42.9%, 23.8% vs 31.7%, 17.5% vs 22.2%, and 41.3% vs 41.3% at baseline and six month follow-up, respectively. Age ≥50 years old (AOR = 0.6, 95% CI: 0.004–0.71, p = 0.026) and body mass index (BMI) ≥25 kg/m2 (AOR = 6.44, 95% CI: 1.34–30.9, p = 0.02) were significantly associated with TC ≥200 mg/dL. Having cancer (AOR = 0.04, 95% CI: 0.01–0.6, p = 0.019) and education level below diploma (AOR = 9.47, 95% CI: 1.15–77.96, p = 0.037) were significantly associated with overall dyslipidemia. Conclusion In this study, the proportion of patients with dyslipidemia was higher at six month follow-up but there was no significant difference when compared to baseline. The mean LDL-c was significantly higher at six months compared to its baseline mean. The associated factors with dyslipidemia were age, BMI, having cancer and low level of education. Lipid profile monitoring is recommended in patients with a younger age and higher BMI.
Traumatic abdominal wall hernias: a single-center case series of surgical management

Background Traumatic abdominal wall hernias (TAWHs) are a rare clinical entity that can be difficult to diagnose and manage. There is no consensus on management of TAWH due to its low incidence and complex concomitant injury patterns. We hereby present the largest single-center case series in the USA to characterize associated injury patterns, identify optimal strategies for hernia management, and determine outcomes. Methods Patients who presented with a TAWH from blunt trauma requiring operative management were retrospectively identified over a 14-year period. Demographic data, Injury Severity Score (ISS), associated injuries, type of repair, durability of repair, and complications were collected, and descriptive statistics were calculated. Results Fifteen patients were identified. The average age was 31±11 years, ISS 15±9, and body mass index 33.4±7.1 kg/m2. Mechanisms included falls (13%), motor vehicle collisions (60%), motorcycle accidents (20%), and pedestrian versus motor vehicle collisions (7%). The most commonly associated injuries included colonic injuries (53%), long bone fractures (47%), pelvic fractures (40%), and small bowel injuries (33%). Nineteen hernia repairs were performed: 6 underwent primary suture repair (32%) and 13 used mesh (68%). There were four recurrences. We could not find any significant relationship between contamination and mesh use or recurrence. There was one mortality related to sepsis. Discussion TAWHs have an associated injury pattern involving fractures and abdominopelvic visceral injuries where a tailored approach is advisable. Without hollow viscous injuries and gross contamination, these hernias can be repaired safely with mesh in the acute setting. However, in patients with gross contamination or hemodynamic instability, the risk of recurrence with primary repair must be weighed against the risk of infection and prolonged surgery with mesh repair. In those cases, a delayed reconstruction in the elective setting may be optimal.
Transcranial Ultrasound Innovations Ready for Broad Clinical Application

Brain diseases are one of the most important problems in our rapidly ageing society. Currently, there are not many effective medications and surgical options are limited due to invasiveness and non‐invasive brain stimulation techniques cannot be well targeted and cannot access deep brain areas. A novel therapy is transcranial ultrasound which allows a variety of treatments without opening of the skull. Recent technological developments generated three revolutionary options including 1) targeted non‐invasive surgery, 2) highly targeted drug, antibody, or gene therapy via local opening of the blood–brain barrier, and 3) highly targeted brain stimulation to improve pathological brain functions. This progress report summarizes the current state of the art for clinical application and the results of recent patient investigations.
Bisecting GlcNAc modification diminishes the pro‐metastatic functions of small extracellular vesicles from breast cancer cells

Abstract Small extracellular vesicles (sEVs) are enriched in glycoconjugates and display specific glycosignatures. Aberrant expression of surface glycoconjugates is closely correlated with cancer progression and metastasis. The essential functions of glycoconjugates in sEVs are poorly understood. In this study, we observed significantly reduced levels of bisecting GlcNAc in breast cancer. Introduction of bisecting GlcNAc into breast cancer cells altered the bisecting GlcNAc status on sEVs, and sEVs with diverse bisecting GlcNAc showed differing functions on recipient cells. Carcinogenesis and metastasis of recipient cells were enhanced by sEVs with low bisecting GlcNAc, and the pro‐metastatic functions of sEVs was diminished by high bisecting GlcNAc modification. We further identified vesicular integrin β1 as a target protein bearing bisecting GlcNAc. Metastasis of recipient cells was strongly suppressed by high bisecting GlcNAc levels on vesicular β1. Our findings demonstrate the important roles of glycoconjugates on sEVs. Modification of sEV glycosylation may contribute to development of novel targets in breast cancer therapy.
Demineralization study of Indian Assam coking coal by sodium hydroxide leaching

The purpose of this study was to examine the ash removal efficiency of sodium hydroxide leaching from Assam coking coal so that it could be used for the manufacture of graphite electrodes. The parameters tested were sodium hydroxide concentration, panicle size of coal, NaOH solution / coal ratio, leaching temperature and time, and heat treatment of coal. Increase in NaOH concentration up to 500 gL −1 was found to increase the extent of ash removal. The ash content of the leached coal decreased with decrease in particle size, but very finely ground (− 72 mesh) particles reduced the ash removal rate. Increase in leaching temperature (50-120°C) and time (30-180 min) considerably reduced the ash content of the leached coal. Heat-treated (at 1300°C) coal (i.e., coke) has much lower ash removal efficiency than raw coal.
Application of remote sensing technology to estimate productivity and assess phylogenetic heritability

PREMISE Measuring plant productivity is critical to understanding complex community interactions. Many traditional methods for estimating productivity, such as direct measurements of biomass and cover, are resource intensive, and remote sensing techniques are emerging as viable alternatives. METHODS We explore drone‐based remote sensing tools to estimate productivity in a tallgrass prairie restoration experiment and evaluate their ability to predict direct measures of productivity. We apply these various productivity measures to trace the evolution of plant productivity and the traits underlying it. RESULTS The correlation between remote sensing data and direct measurements of productivity varies depending on vegetation diversity, but the volume of vegetation estimated from drone‐based photogrammetry is among the best predictors of biomass and cover regardless of community composition. The commonly used normalized difference vegetation index (NDVI) is a less accurate predictor of biomass and cover than other equally accessible vegetation indices. We found that the traits most strongly correlated with productivity have lower phylogenetic signal, reflecting the fact that high productivity is convergent across the phylogeny of prairie species. This history of trait convergence connects phylogenetic diversity to plant community assembly and succession. DISCUSSION Our study demonstrates (1) the importance of considering phylogenetic diversity when setting management goals in a threatened North American grassland ecosystem and (2) the utility of remote sensing as a complement to ground measurements of grassland productivity for both applied and fundamental questions.
Use of artificial structures to enhance fish diversity in the Youjiang River, a dammed river of the Pearl River in China

Abstract The fragmentation and homogenization of habitats have seriously affected the fishery resources of the Pearl River. To protect the fishery resources, a novel artificial habitat, constructed using bamboo and palm slices, was deployed in the Youjiang River, a tributary of the Pearl River in China. The results of field and laboratory experiments showed that fish abundance, species richness and Shannon–Wiener diversity index were higher in the artificial habitats than at the control sites. There was no significant impact on fish biomass, as the artificial habitats attracted more Cultrinae and Gobioninae fish that are of a smaller size. Artificial habitats can serve as spawning grounds for fish that produce sticky eggs and refuges that improve the survival rates of juvenile fishes. This study revealed that this novel artificial habitat created suitable habitats and suitable spawning substrate for fish, improved fish richness and diversity in the structureless freshwater ecosystem like the Youjiang River.
Comparison of subtyping methods for neuroimaging studies in Alzheimer’s disease: a call for harmonization

Abstract Biological subtypes in Alzheimer’s disease, originally identified on neuropathological data, have been translated to in vivo biomarkers such as structural magnetic resonance imaging and positron emission tomography, to disentangle the heterogeneity within Alzheimer’s disease. Although there is methodological variability across studies, comparable characteristics of subtypes are reported at the group level. In this study, we investigated whether group-level similarities translate to individual-level agreement across subtyping methods, in a head-to-head context. We compared five previously published subtyping methods. Firstly, we validated the subtyping methods in 89 amyloid-beta positive Alzheimer’s disease dementia patients (reference group: 70 amyloid-beta negative healthy individuals) using structural magnetic resonance imaging. Secondly, we extended and applied the subtyping methods to 53 amyloid-beta positive prodromal Alzheimer’s disease and 30 amyloid-beta positive Alzheimer’s disease dementia patients (reference group: 200 amyloid-beta negative healthy individuals) using structural magnetic resonance imaging and tau positron emission tomography. Subtyping methods were implemented as outlined in each original study. Group-level and individual-level comparisons across methods were performed. Each individual subtyping method was replicated, and the proof-of-concept was established. At the group level, all methods captured subtypes with similar patterns of demographic and clinical characteristics, and with similar cortical thinning and tau positron emission tomography uptake patterns. However, at the individual level, large disagreements were found in subtype assignments. Although characteristics of subtypes are comparable at the group level, there is a large disagreement at the individual level across subtyping methods. Therefore, there is an urgent need for consensus and harmonization across subtyping methods. We call for the establishment of an open benchmarking framework to overcome this problem.
Limited contributions of plant pathogens to density‐dependent seedling mortality of mast fruiting Bornean trees

Abstract Fungal pathogens are implicated in driving tropical plant diversity by facilitating strong, negative density‐dependent mortality of conspecific seedlings (C‐NDD). Assessment of the role of fungal pathogens in mediating coexistence derives from relatively few tree species and predominantly the Neotropics, limiting our understanding of their role in maintaining hyper‐diversity in many tropical forests. A key question is whether fungal pathogen‐mediated C‐NDD seedling mortality is ubiquitous across diverse plant communities. Using a manipulative shadehouse experiment, we tested the role of fungal pathogens in mediating C‐NDD seedling mortality of eight mast fruiting Bornean trees, typical of the species‐rich forests of South East Asia. We demonstrate species‐specific responses of seedlings to fungicide and density treatments, generating weak negative density‐dependent mortality. Overall seedling mortality was low and likely insufficient to promote overall community diversity. Although conducted in the same way as previous studies, we find little evidence that fungal pathogens play a substantial role in determining patterns of seedling mortality in a SE Asian mast fruiting forest, questioning our understanding of how Janzen‐Connell mechanisms structure the plant communities of this globally important forest type.
A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa

Abstract Ganoderma P. Karst. is a cosmopolitan genus of white-rot fungi which comprises species with highly-prized pharmaceutical properties, valuable biotechnological applications and of significant phytopathological interest. However, the status of the taxonomy within the genus is still highly controversial and ambiguous despite the progress made through molecular approaches. A metadata analysis of 3908 nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences obtained from GenBank/ENA/DDBJ and UNITE was performed by targeting sequences annotated as Ganoderma, but also sequences from environmental samples and from material examined for the first time. Ganoderma taxa segregated into five main lineages (Clades A to E). Clade A corresponds to the core of laccate species and includes G. shanxiense and three major well-supported clusters: Cluster A.1 (‘G. lucidum sensu lato’) consists of taxa from Eurasia and North America, Cluster A.2 of material with worldwide occurrence including G. resinaceum and Cluster A.3 is composed of species originating from all continents except Europe and comprises G. lingzhi. Clade B includes G. applanatum and allied species with a Holarctic distribution. Clade C comprises taxa from Asia and Africa only. Clade D consists of laccate taxa with tropical/subtropical occurrence, while clade E harbours the highest number of non-laccate species with a cosmopolitan distribution. The 92 Ganoderma-associated names, initially used for sequences labelling, correspond to at least 80 taxa. Amongst them, 21 constitute putatively new phylospecies after our application of criteria relevant to the robustness/support of the terminal clades, intra- and interspecific genetic divergence and available biogeographic data. Moreover, several other groups or individual sequences seem to represent distinct taxonomic entities and merit further investigation. A particularly large number of the public sequences was revealed to be insufficiently and/or incorrectly identified, for example, 87% and 78% of entries labelled as G. australe and G. lucidum, respectively. In general, ITS demonstrated high efficacy in resolving relationships amongst most of the Ganoderma taxa; however, it was not equally useful at elucidating species barriers across the entire genus and such cases are outlined. Furthermore, we draw conclusions on biogeography by evaluating species occurrence on a global scale in conjunction with phylogenetic structure/patterns. The sequence variability assessed in ITS spacers could be further exploited for diagnostic purposes.
Predicting greater sage‐grouse habitat selection at the southern periphery of their range

Abstract Mapping suitable habitat is an important process in wildlife conservation planning. Species distribution reflects habitat selection processes occurring across multiple spatio‐temporal scales. Because habitat selection may be driven by different factors at different scales, conservation planners require information at the scale of the intervention to plan effective management actions. Previous research has described habitat selection processes shaping the distribution of greater sage‐grouse (Centrocercus urophasianus; sage‐grouse) at the range‐wide scale. Finer‐scale information for applications within jurisdictional units inside the species range is lacking, yet necessary, because state wildlife agencies are the management authority for sage‐grouse in the United States. We quantified seasonal second‐order habitat selection for sage‐grouse across the state of Utah to produce spatio‐temporal predictions of their distribution at the southern periphery of the species range. We used location data obtained from sage‐grouse marked with very‐high‐frequency radio‐transmitters and lek location data collected between 1998 and 2013 to quantify species habitat selection in relation to a suite of topographic, edaphic, climatic, and anthropogenic variables using random forest algorithms. Sage‐grouse selected for greater sagebrush (Artemisia spp.) cover, higher elevations, and gentler slopes and avoided lower precipitations and higher temperatures. The strength of responses to habitat variables varied across seasons. Anthropogenic variables previously reported as affecting their range‐wide distribution (i.e., roads, powerlines, communication towers, and agricultural development) were not ranked as top predictors at our focal scale. Other than strong selection for sagebrush cover, the responses we observed differed from what has been reported at the range‐wide scale. These differences likely reflect the unique climatic, geographic, and topographic context found in the southern peripheral area of the species distribution compared to range‐wide environmental gradients. Our results highlight the importance of considering appropriateness of scale when planning conservation actions for wide‐ranging species.
Ecological models for estimating breakpoints and prediction intervals

Abstract The relationships between an environmental variable and an ecological response are usually estimated by models fitted through the conditional mean of the response given environmental stress. For example, nonparametric loess and parametric piecewise linear regression model (PLRM) are often used to represent simple to complex nonlinear relationships. In contrast, piecewise linear quantile regression models (PQRM) fitted across various quantiles of the response can reveal nonlinearities in its range of variation across the explanatory variable. We assess the number and positions of candidate breakpoints using loess and compare the relative efficiencies of PLRM and PQRM to quantitatively determine the breakpoints' location and precision. We propose a nonparametric method to generate bootstrap confidence intervals for breakpoints using PQRM and prediction bands for loess and PQRM. We illustrated the applications using data from two aquatic studies suspected to exhibit multiple environmental breakpoints: relating a fish multimetric index of community health (MMI) to agricultural activity in wetlands' adjacent drainage basins; and relating cyanobacterial biomass to total phosphorus concentration in Canadian lakes. Two statistically significant breakpoints were detected in each dataset, demarcating boundaries of three linear segments, each with markedly different slopes. PQRM generated less biased, more accurate, and narrower confidence intervals for the breakpoints and narrower prediction bands than PLRM, especially for small samples and large error variability. In both applications, the relationship between the response and environmental variables was weak/nonsignificant below the lower threshold, strong through the midrange of the environmental gradient, and weak/nonsignificant beyond the upper threshold. We describe several advantages of PQRM over PLRM in characterizing environmental relationships where the scatter of points represents natural environmental variation rather than measurement error. The proposed methodology will be useful for detecting multiple breakpoints in ecological applications where the limits of variation are as important as the conditional mean of a function.
NFB-17. MEK INHIBITOR BINIMETINIB SHOWS CLINICAL ACTIVITY IN CHILDREN WITH NEUROFIBROMATOSIS TYPE 1- ASSOCIATED PLEXIFORM NEUROFIBROMAS: A REPORT FROM PNOC AND THE NF CLINICAL TRIALS CONSORTIUM

Abstract BACKGROUND Plexiform neurofibromas (PNs) can cause significant morbidity. In this phase 2 study, we assessed imaging and functional outcomes to the MEK-inhibitor Binimetinib in pediatric patients with PNs. METHODS Children (age 1–17 years) with PN that were progressive or causing significant morbidity were eligible. Binimetinib is dosed twice-daily (starting dose of 32mg/m2) for maximum of 24 four-week courses. Participants with partial response (PR; >20% decrease in PN volume on central MRI review) at cycle 12 may stay on therapy. Participants undergo MRI and functional assessments at baseline and after courses 4, 8, 12, 18 and 24. Functional assessments are based on PN location. RESULTS Here we present 1-year response data. Twenty participants (55% male) with median age 12 years (range 2–16 years) enrolled; 19 are evaluable for response. Median baseline tumor volume was 326 ml (range, 8-6661 ml). Fourteen participants (74%) met criteria for PR, with 11 achieving PR by course 5. Median maximal PN volume reduction was 25.5% (range, 9–54%). As of August 2020, 14 participants received at least 12 cycles of Binimetinib; 10 remain on therapy. Off study reasons include treatment associated toxicities (n=2), subject withdrawal (n=2), non-compliance (n=2), prolonged treatment delay (n=1), and lack of response (n=3). Thirteen participants underwent dose reduction. Institution-reported related grade 3 toxicities included dry skin, weight gain, muscle weakness, rash, paronychia, cellulitis, diarrhea, gastric hemorrhage and CPK increase. CONCLUSIONS Binimetinib appears reasonably well-tolerated and shows promising activity in children with NF1-associated PNs. Outcomes on functional improvement will be reported at the meeting.