Miracle-dz/UniFAR-FTUs huggingface dataset:
Importance of estimating matrix quality for modeling species distribution in complex tropical landscapes: a test with Atlantic forest small mammals

Information to guide decision making is especially urgent in human dominated landscapes in the tropics, where urban and agricultural frontiers are still expanding in an unplanned manner. Nevertheless, most studies that have investigated the influence of landscape structure on species distribution have not considered the heterogeneity of altered habitats of the matrix, which is usually high in human dominated landscapes. Using the distribution of small mammals in forest remnants and in the four main altered habitats in an Atlantic forest landscape, we investigated 1) how explanatory power of models describing species distribution in forest remnants varies between landscape structure variables that do or do not incorporate matrix quality and 2) the importance of spatial scale for analyzing the influence of landscape structure. We used standardized sampling in remnants and altered habitats to generate two indices of habitat quality, corresponding to the abundance and to the occurrence of small mammals. For each remnant, we calculated habitat quantity and connectivity in different spatial scales, considering or not the quality of surrounding habitats. The incorporation of matrix quality increased model explanatory power across all spatial scales for half the species that occurred in the matrix, but only when taking into account the distance between habitat patches (connectivity). These connectivity models were also less affected by spatial scale than habitat quantity models. The few consistent responses to the variation in spatial scales indicate that despite their small size, small mammals perceive landscape features at large spatial scales. Matrix quality index corresponding to species occurrence presented a better or similar performance compared to that of species abundance. Results indicate the importance of the matrix for the dynamics of fragmented landscapes and suggest that relatively simple indices can improve our understanding of species distribution, and could be applied in modeling, monitoring and managing complex tropical landscapes.
A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks

Until 1972, Uganda's national parks boasted of large numbers of large mammal species. Following the breakdown of law and order between 1972 and 1985, large‐scale poaching led to an unprecedented decline in numbers of most large mammals in Uganda's national parks. However, the extent of decline varied in the different parks across different animal species. We have investigated the genetic effects of these reductions in four mammalian species (the common warthog, African savannah elephant, savannah buffalo and common river hippopotamus) from the three major parks of Uganda using both microsatellite loci (for elephant and warthog populations) and mitochondrial control sequence variation in the warthogs, elephants, buffaloes and hippopotamuses. Queen Elizabeth National Park showed extreme reduction in nucleotide diversity for two species, the common warthog (π= 0.0%) and African elephant (π= 0.4%); no such decrease was found for the two other species, the buffalo (π= 3.7–5.4%) and hippopotamus (π= 1.7–1.9%), in the three parks. Nuclear microsatellite markers on the other hand showed high gene diversity in all populations in the common warthog (mean He 0.66–0.78) and the African savannah elephant (mean He 0.68–0.72). We interpret these results in terms of varying poaching pressure in the different parks, susceptibility of different species to poaching and differences in effective population sizes at the mitochondrial and nuclear loci.
A Surface Coating that Rapidly Inactivates SARS-CoV-2

SARS-CoV-2, the virus that causes the disease COVID-19, remains viable on solids for periods of up to 1 week, so one potential route for human infection is via exposure to an infectious dose from a solid. We have fabricated and tested a coating that is designed to reduce the longevity of SARS-CoV-2 on solids. The coating consists of cuprous oxide (Cu2O) particles bound with polyurethane. After 1 h on coated glass or stainless steel, the viral titer was reduced by about 99.9% on average compared to the uncoated sample. An advantage of a polyurethane-based coating is that polyurethane is already used to coat a large number of everyday objects. Our coating adheres well to glass and stainless steel as well as everyday items that people may fear to touch during a pandemic, such as a doorknob, a pen, and a credit card keypad button. The coating performs well in the cross-hatch durability test and remains intact and active after 13 days of being immersed in water or after exposure to multiple cycles of exposure to the virus and disinfection.
Forestomach ciliate Protozoa in Egyptian dromedary camels (Camelus dromedarius)

The forestomach contents of 20 dromedary camels were examined for total, generic and species composition of ciliate protozoa. The geometric mean value of total ciliate protozoa was 13.9 X 10 4 / ml with values ranging from 4.9 to 109.4 X 10 4 / ml. A total of ten genera containing 31 species and 16 forms were identified. Five species of Entodinium (E. biconcavum, E. bimastus, E. ekendrae, E. parvum and E. tsunodai) and Ostracodinium trivesticulatum represent a new host record. Two new spinated forms of Diplodinium cameli were observed, one has a single spine arising from the left lateral surface near the posterior end and the second has an additional spine on the posterior right lateral surface. Previous reports on concentration and species composition in the camel are summarized and compared to the present results.
The Role of Laparoscopic Cholecystectomy After Severe and/or Necrotic Pancreatitis in the Setting of Modern Minimally Invasive Management of Pancreatic Necrosis

Objectives The trend toward minimally invasive procedures (MIP) in necrotizing pancreatitis is increasing. The optimal timing and technique of cholecystectomy in severe/necrotizing pancreatitis is unclear. This study aims to determine the role of laparoscopic cholecystectomy after severe/necrotizing pancreatitis in the context of MIP. Methods Retrospective analysis of a prospective database was performed for consecutive patients after cholecystectomy for gallstone pancreatitis between January 2011 and January 2018 at Monash Health, Melbourne, Australia. Results Three hundred fifty-five patients with gallstone pancreatitis underwent laparoscopic cholecystectomy with 2 conversions. Patients with severe pancreatitis were older (P = 0.002), with a more even sex distribution when compared with mild pancreatitis. Females predominated in the mild pancreatitis group. Patients with moderate/severe pancreatitis (P = 0.002) and necrosis (P > 0.001) were more likely to have delayed cholecystectomy compared with mild pancreatitis. There was no increase in biliary presentations while awaiting cholecystectomy. Length of stay for patients with severe/necrotizing pancreatitis (P = 0.001) was increased, surgical complications appeared similar. Conclusions Laparoscopic cholecystectomy can be performed safely and effectively for pancreatitis, irrespective of severity. The paradigm shift in the management of severe necrotizing pancreatitis away from open necrosectomy toward MIP can be extended to encompass laparoscopic cholecystectomy.
Progressive fibrosing interstitial lung disease: treatable traits and therapeutic strategies.

PURPOSE OF REVIEW In this review, the authors describe therapeutic strategies for a disease group called progressive fibrosing interstitial lung disease (PF-ILD) and highlight the importance of the definition of progression, prognosis, and treatment response. RECENT FINDINGS Although it is a relatively new concept, the term PF-ILD has been increasingly applied in clinical research and practice. Three domains commonly used to detect the disease progression include clinical symptoms, rate of forced vital capacity (FVC) decline and the extent of fibrosis on imaging. Although details of the pathogenesis of PF-ILD are still unclear, it has become apparent that genetic predisposition and an abnormal tissue microenvironment and host response are involved in the nature of the disease. Antifibrotic agents recently showed their efficacy on the treatment of PF-ILD. Both nintedanib and pirfenidone can slow the disease progression, as defined by a decline of FVC from baseline, of PF-ILD whenever compared with placebo, similar to the results in idiopathic pulmonary fibrosis (IPF) trials. This effect seems consistent irrespective of the underlying ILD diagnosis. SUMMARY Recent evidence supports the use of antifibrotic therapy in the management of the phenotype progressive non-IPF ILD. Ongoing studies exploring genetic and other molecular biomarkers could identify at-risk individuals or predict treatment response and prognosis (endotypes). This would support the concept of 'treatable traits' in the field of ILD.
Meta-analysis of Proportions Using Generalized Linear Mixed Models

Supplemental Digital Content is available in the text. Epidemiologic research often involves meta-analyses of proportions. Conventional two-step methods first transform each study’s proportion and subsequently perform a meta-analysis on the transformed scale. They suffer from several important limitations: the log and logit transformations impractically treat within-study variances as fixed, known values and require ad hoc corrections for zero counts; the results from arcsine-based transformations may lack interpretability. Generalized linear mixed models (GLMMs) have been recommended in meta-analyses as a one-step approach to fully accounting for within-study uncertainties. However, they are seldom used in current practice to synthesize proportions. This article summarizes various methods for meta-analyses of proportions, illustrates their implementations, and explores their performance using real and simulated datasets. In general, GLMMs led to smaller biases and mean squared errors and higher coverage probabilities than two-step methods. Many software programs are readily available to implement these methods.
Differences in executive function of the attention network between athletes from interceptive and strategic sports

Abstract The differences in the executive attention network and the related blood oxygen characteristics of the right frontal-parietal network brain area between athletes from interceptive and strategic sport were investigated. Strategic athletes had higher accuracy and longer reaction time (RT) compared with interceptive sports athletes, lower flanker conflict effects on accuracy compared to the other two group. It was accompanied by significant activation of the rdLPFC and the rIFG. Strategic athletes had higher flanker conflict effects on RT compared with interception athletes under the invalid cue condition, which was accompanied by significant activation of the right IFG. The strategic athletes complete the task under the condition of invalid clues indicating top-down control, and which is closely related to the activation of the right frontal-parietal network.
A CLADISTIC ANALYSIS OF THE FAMILY TRISTIRIDAE (ORTHOPTERA, ACRIDOIDEA)

Abstract— A cladistic analysis of the endemic South American family Tristiridae was performed using 29 characters from external morphology and the genitalia. Polarity of characters was based on the outgroup comparison method. One most parsimonious cladogram of 54 steps was obtained, from which a classification of the family Tristiridae was constructed. The analysis of phylogenetic relationships showed that the different kinds of characters define taxa at different levels in the cladogram. Those mostly from the phallic complex define suprageneric taxa while those from external morphology characterize genera. It is hypothesized that in Tristiridae differentiation of the phallic complex preceded differentiation of external morphology and that characters from the phallic complex arc less conservative than those from the external morphology.
The 2018 Banff Working Group classification of definitive polyomavirus nephropathy: A multicenter validation study in the modern era

Polyomavirus nephropathy (PVN) remained inadequately classified until 2018 when the Banff Working Group published a new 3‐tier morphologic classification scheme derived from in‐depth statistical analysis of a large multinational patient cohort. Here we report a multicenter “modern‐era” validation study that included 99 patients with definitive PVN transplanted post January 1, 2009 and followed the original 2018 study design. Results validate the PVN classification, that is, the 3 PVN disease classes predicted clinical presentation, allograft function, and outcome independent of therapeutic intervention. PVN class 1 compared to classes 2 and 3 was diagnosed earlier (16.9 weeks posttransplant [median], P = .004), and showed significantly better function at 24 months postindex biopsy (serum creatinine 1.75 mg/dl, geometric mean, vs class 2: P = .037, vs class 3: P = .013). Class 1 presented during long‐term follow‐up with a low graft failure rate: 5% class 1, vs 30% class 2, vs 50% class 3 (P = .009). Persistent PVN was associated with an increased risk for graft failure (and functional decline in class 2 at 24 months postdiagnosis; serum creatinine with persistence: 2.48 mg/dL vs 1.65 with clearance, geometric means, P = .018). In conclusion, we validate the 2018 Banff Working Group PVN classification that provides significant clinical information and enhances comparative data analysis.
Functional divergence of white genes in Henosepilachna vigintioctopunctata revealed by RNA interference

Henosepilachna vigintioctopunctata is a serious pest of Solanaceae and Cucurbitaceae in many Asian countries. RNA interference (RNAi) can effectively reduce transcript abundance in this beetle, offering opportunities to explore the biological function of specific genes. The white gene encodes a half‐type ATP‐binding cassette transporter that plays an essential role in tryptophan, guanine and uric acid transport across membranes. Mutations that disrupt the function of white are known to cause eye pigmentation phenotypes in many insect species. Here, we found evidence for five white gene paralogues present in H. vigintioctopunctata transcriptome datasets sequenced from a range of developmental stages. We individually knocked down each of the five white genes through the injection of corresponding double‐stranded RNAs (dsRNAs) to the fourth‐instar larvae to determine whether functional divergence has occurred. We found that injecting 1 μg dswhite3 caused compound eye colour of pupae and adults to develop as red/brown and brown, respectively, compared with black eyes in control beetles. Injection of 2 μg dswhite3 increased RNAi efficacy and produced a clearer eye colour phenotype. At both doses, the ocular diaphragm (a ring of black pigment surrounding each eye) did not change in the white3 RNAi hypomorphs. Moreover, our data revealed that injection of dswhite2 at the fourth‐instar larval stage impaired the climbing ability of both male and female adults. Our results confirmed, for the first time, functional divergence of duplicated white genes in an insect species.
Clinical Features of COVID-19 in Patients With Essential Hypertension and the Impacts of Renin-angiotensin-aldosterone System Inhibitors on the Prognosis of COVID-19 Patients

Supplemental Digital Content is available in the text. Hypertension is one of the most common comorbidities in patients with coronavirus disease 2019 (COVID-19). This study aimed to clarify the impact of hypertension on COVID-19 and investigate whether the prior use of renin-angiotensin-aldosterone system (RAAS) inhibitors affects the prognosis of COVID-19. A total of 996 patients with COVID-19 were enrolled, including 282 patients with hypertension and 714 patients without hypertension. Propensity score-matched analysis (1:1 matching) was used to adjust the imbalanced baseline variables between the 2 groups. Patients with hypertension were further divided into the RAAS inhibitor group (n=41) and non-RAAS inhibitor group (n=241) according to their medication history. The results showed that COVID-19 patients with hypertension had more severe secondary infections, cardiac and renal dysfunction, and depletion of CD8+ cells on admission. Patients with hypertension were more likely to have comorbidities and complications and were more likely to be classified as critically ill than those without hypertension. Cox regression analysis revealed that hypertension (hazard ratio, 95% CI, unmatched cohort [1.80, 1.20–2.70]; matched cohort [2.24, 1.36–3.70]) was independently associated with all-cause mortality in patients with COVID-19. In addition, hypertensive patients with a history of RAAS inhibitor treatment had lower levels of C-reactive protein and higher levels of CD4+ cells. The mortality of patients in the RAAS inhibitor group (9.8% versus 26.1%) was significantly lower than that of patients in the non-RAAS inhibitor group. In conclusion, hypertension may be an independent risk factor for all-cause mortality in patients with COVID-19. Patients who previously used RAAS inhibitors may have a better prognosis.
Early events in DNA double strand break repair after damage induction with a laser microbeam

In the present thesis DNA double strand break (DSB) induction and repair are analysed after laser-microbeam irradiation. Live cell imaging of DNA repair proteins fused to Green Fluorescent Protein (GFP) as well as immunofluorescent detection of endogenous protein are used. Laser induced DNA damage, detected by gamma-H2AX foci staining depend on a subtle combination of used laser pulse wavelength, pulse energy and dose. The recruitment times of repair proteins depend inverse linearly on laser pulse energy. By extrapolation to zero, the recruitment time at biological relevant conditions is calculated. Interestingly, considerable spatial dynamics of the foci is found. Two neighbouring foci even can fuse within ~20 min. Recruitment time comparison of molecules representing early and late Non-Homologous end Joining (NHEJ), Homologous Recombination Repair (HRR) and the Mre11-Rad50-NBS1 (MRN) complex reveals that the whole NHEJ machinery is assembled to DSBs within 1 min. Recruitment of latest NHEJ factor (XRCC4) is faster than NBS1 and is not directly influenced by the absence of NBS1. XRCC4 persists at DSBs longer in the G1 cell cycle phase than in G2 where the replacement of NHEJ by HRR molecules occurs. Rad51 is recruited when XRCC4 is released with the complementary kinetics. DNA-PKcs phosphorylation at two sites, known to facilitate DNA end processing, occurs between the recruitment of NHEJ and HRR. A new modification of Comet-assay technique the Immunofluorescent Comet-assay (IFCA) is developed in this work for direct visualisation of DSBs in single cells. IFCA uses the immunofluorescent detection of histone H1 in neutral and alkaline Comet-assay, and enables simple and clear visualisation of details in the comet tail, which are hardly detectable by conventional DNA staining dyes such as SYBR Green. Using IFCA, the fragment size at the end of the neutral comet tail is determined for the first time.
Assessment of Development of Resistance in Cotton Whitefly Gennadius of Guntur Strain

A study was undertaken to assess the degree of resistance acquired by Bemisia tabaci Gennadius of Guntur strain through comparing with the base line data at LC 50 level and with respect to recommended concentration at LC 90 level. It was found that B. tabaci has developed 3.37, 3.12, 1.59 and 1.41 fold resistance to cypermethrin, monocrotophos, acephate and triazophos respectively at LC after 1993. All the six insecticides are less effective against the cotton whitefly of Guntur strain since the LC values of these insecticides are higher than the corresponding recommended concentrations which imply the acquisition of resistance.
Use of Yucca schidigera Extract in Broiler Diets and Its Effects on Performance Results Obtained with Different Coccidiosis Control Methods

SUMMARY A trial was conducted to assess the effects of the dietary supplement Yucca schidigera extract on the performance of broilers subjected to different coccidiosis control methods. Six hundred male broiler chicks were randomly allocated to 1 of 5 treatments with 4 replicates each. The treatments were as follows: T1, vaccinated against coccidiosis; T2, nonvaccinated, a dietary coccidiostat; T3, vaccinated against coccidiosis, diet supplemented with Y. schidigera extract (0.01%); T4, coccidiostat plus Y. schidigera extract added to feed (0.01%); and T5, nonvaccinated, nonsupplemented control. The parameters analyzed were bird performance and morphology of the intestinal mucosal surface. The intestinal villi were higher a t6do f age inbroilers treated with coccidiostats or vaccinated against coccidiosis and supplemented with Y. schidigera extract compared with groups receiving the vaccine only or no treatment. Addition of the Y. schidigera extract to the diet of vaccinated birds improved average daily gain and feed conversion rate at 42 d of age compared with the other treatments, suggesting there might be a beneficial, synergistic effect between the coccidiosis vaccine and the Y. schidigera extract.
Epidemiological Studies of Low-Dose Ionizing Radiation and Cancer: Summary Bias Assessment and Meta-Analysis.

BACKGROUND Ionizing radiation is an established carcinogen, but risks from low-dose exposures are controversial. Since the Biological Effects of Ionizing Radiation VII review of the epidemiological data in 2006, many subsequent publications have reported excess cancer risks from low-dose exposures. Our aim was to systematically review these studies to assess the magnitude of the risk and whether the positive findings could be explained by biases. METHODS Eligible studies had mean cumulative doses of less than 100 mGy, individualized dose estimates, risk estimates, and confidence intervals (CI) for the dose-response and were published in 2006-2017. We summarized the evidence for bias (dose error, confounding, outcome ascertainment) and its likely direction for each study. We tested whether the median excess relative risk (ERR) per unit dose equals zero and assessed the impact of excluding positive studies with potential bias away from the null. We performed a meta-analysis to quantify the ERR and assess consistency across studies for all solid cancers and leukemia. RESULTS Of the 26 eligible studies, 8 concerned environmental, 4 medical, and 14 occupational exposure. For solid cancers, 16 of 22 studies reported positive ERRs per unit dose, and we rejected the hypothesis that the median ERR equals zero (P = .03). After exclusion of 4 positive studies with potential positive bias, 12 of 18 studies reported positive ERRs per unit dose (P = .12). For leukemia, 17 of 20 studies were positive, and we rejected the hypothesis that the median ERR per unit dose equals zero (P = .001), also after exclusion of 5 positive studies with potential positive bias (P = .02). For adulthood exposure, the meta-ERR at 100 mGy was 0.029 (95% CI = 0.011 to 0.047) for solid cancers and 0.16 (95% CI = 0.07 to 0.25) for leukemia. For childhood exposure, the meta-ERR at 100 mGy for leukemia was 2.84 (95% CI = 0.37 to 5.32); there were only two eligible studies of all solid cancers. CONCLUSIONS Our systematic assessments in this monograph showed that these new epidemiological studies are characterized by several limitations, but only a few positive studies were potentially biased away from the null. After exclusion of these studies, the majority of studies still reported positive risk estimates. We therefore conclude that these new epidemiological studies directly support excess cancer risks from low-dose ionizing radiation. Furthermore, the magnitude of the cancer risks from these low-dose radiation exposures was statistically compatible with the radiation dose-related cancer risks of the atomic bomb survivors.