Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular phylogeny of Sarcocystis fayeri (Apicomplexa: Sarcocystidae) from the domestic horse Equus caballus based on 18S rRNA gene sequences and its prevalence

Sarcocystosis is a parasitic disease caused by an intracellular protozoan parasite Sarcocystis belonging to the phylum Apicomplexa. These parasites have a requisite two‐host life cycle. Recently, there are many Sarcocystis species that identified morphologically. In the present study, diaphragmatic muscle samples from the domestic horse (Equus caballus) were examined for Sarcocystis infection. The natural infection with sarcocysts was recorded to be 62·5% for only microcysts in the infected muscles. Molecular analysis using the 18S rRNA gene was conducted to swiftly and accurately identify the recovered species. Studies on the expression of the 18S rRNA gene have confirmed that the present parasite isolates belong to the Sarcocystis genus. The sequence data showed significant identities (>80%) with archived gene sequences from species within the Sarcocystidae family, and a dendrogram showing the phylogenetic relationship was constructed. The most closely related species were the previously described Sarcocystis fayeri and Sarcocystis bertrami. The current data showed that the present species was identified as S. fayeri and deposited in GenBank (accession number MF614956.1). This study highlights the importance of the genetic data in the exact taxonomy within sarcocystid species.
Spoil Heaps From Brown Coal Mining: Technical Reclamation Versus Spontaneous Revegetation

Abstract Vegetation samples from either spontaneously revegetated or technically reclaimed spoil heaps of different ages in one of the largest active brown coal mining districts in Europe were analyzed and compared. The spoil heaps are located in the northwestern part of the Czech Republic and represent ages between 0 and 45 years. Ordination analysis (detrended correspondence analysis) showed that vegetation on technically reclaimed spoil heaps developed in a different way than that on spontaneously revegetated ones. The latter exhibited much higher species diversity in the oldest stages with the number of species doubled that of technically reclaimed sites. The oldest stages were also more advanced along an expected successional gradient as indicated by the ordination. Accelerating the vegetation development by technical reclamation was only of temporal character, whereas spontaneous succession proceeded further over the longer time scale. Spontaneous succession is advocated as an inexpensive and easy alternative to technical reclamation, because it leads to a more natural and rich vegetation cover. Unfortunately, technical reclamation is still the only approach considered in the present reclamation activities for this region.
Are there latitudinal gradients in taxa turnover? A worldwide study with Sciuridae (Mammalia: Rodentia)

Changes in taxa composition among different communities in a landscape or along an environmental gradient are defined as β-diversity. From a biogeographic point of view, it is interesting to analyse patterns of β-turnover across latitudinal bands, and to understand whether P-diversity is significantly associated with endemism at lower latitudes, as predicted by theory. We inspected these issues by using squirrels (Rodentia, Sciuridae) as a study case. Distribution data for each genus were obtained from literature and mapped. The two hemispheres were subdivided into 23 latitudinal bands of equal area, and we calculated a β-turnover index between latitudinal bands with two formulae: Wilson and Shmida’s (1984) and Lennonetal. ’s (2001) indices. We found that the peak of number of Sciuridae genera significantly corresponded to the peak in β-turnover scores at the same latitudes (25–31°N) with Wilson and Shmida’s (1984), but not with Lennon et al.’s (2001) index. We also found that the turnover between ground a.
Online searching platform for antibiotic resistome in bacterial tree of life and global habitats.

BACKGROUND Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. METHODS Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in about 55,000 bacterial genomes, 16,000 bacterial plasmid sequences, 3,000 bacterial integron sequences, and 850 metagenomes using a standard pipeline. RESULTS We found that more than 80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM, and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation to the degree of anthropogenicity. These observations highlight the needs to differentiate ARGs of high clinical relevance. We publish this profile on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as valuable resources for the most challenging topics in this field, such as the risk, evolution, and emergence of ARGs.
Large‐Area Maize Yield Forecasting Using Leaf Area Index Based Yield Model

Large-area yield prediction early in the growing season is important in agricultural decision-making. This study derived maize (Zea mays L.) leaf area index (LAI) estimates from spectral data and used these estimates witha simple LAI-based yield model to forecast yield under irrigated conditions in large areas in Sinaloa, Mexico. Leaf area index was derived from satellite data with the use of an equation developed with LAI measurements from farmers' fields during the 2001-2002 autumn-winter growing season. These measurements were correlated with the normalized difference vegetation index values from 2002 Landsat ETM+ (enhanced thematic mapper) data. The equation was then tested with 2003 Landsat imagery data. A yield model was validated with maximum LAI and yield data measured in farmers' fields in northern and central Sinaloa during three consecutive autumn-winter growing seasons (1999-2000, 2000-2001, and 2001-2002). The yield model was further validated with 2002-2003 autumn-winter ground LAI (gLAI) and satellite-derived LAI (sLAI) data from 71 farmers' fields in northern and central Sinaloa. Grain yield was predicted with a mean error of -9.2% with maximum gLAI and -11.2% with sLAI. Results indicate that the yield model using LAI can forecast yield in large areas in Sinaloa in the middle of the growing season with a mean absolute error of -1.2 Mg ha - 1 . The use of sLAI in place of ground measurements increased the mean absolute error by 0.3 Mg ha - 1 . Nevertheless, the use of sLAI would eliminate laborious LAI measurements for large-area yield prediction in Sinaloa.
Hepatitis C virus alternative reading frame protein (ARFP): Production, features, and pathogenesis

Earlier observation suggests that hepatitis C virus (HCV) is a single‐stranded RNA virus which encodes at least 10 viral proteins. F protein is a novel protein which has been discovered recently. These studies suggest three mechanisms for the production of this protein concerning ribosomal frameshift at codon 10, initial translation at codons 26 and 85 or 87. In this study, the association between protein F and chronicity of hepatocellular carcinoma (HCC) has been reviewed. Evidence suggests that humoral immune system can recognize this protein and produce antibodies against it. By detecting antibodies in infected people, investigators found that F protein might have a role in HCV infection causing chronic cirrhosis and HCC as higher prevalence was found in patients with mentioned complications. The increment of CD4+, CD25+, and FoxP3+ T cells, along with CD8+ T cells with low expression of granzyme B, also leads to weaker responses of the immune system which helps the infection to become chronic. Moreover, it contributes to the survival of the virus in the body through affecting the production of interferon. F protein also might play roles in the disease development, resulting in HCC. The existence of F protein affects cellular pathways through upregulating p53, c‐myc, cyclin D1, and phosphorylating Rb. This review will summarize these effects on immune system and related mechanisms in cellular pathways.
Obesity is Associated with Worse Outcomes in COVID‐19: Analysis of Early Data from New York City

The 2019 novel coronavirus disease (COVID‐19) has triggered a rapidly expanding global pandemic in which patients exhibit a wide spectrum of disease severity. Given the high prevalence of obesity in the United States, we hypothesized that the presence of obesity may play a role in the clinical course of patients with COVID‐19.
Adsorption of Sulfamethazine Drug onto the Modified Derivatives of Carbon Nanotubes at Different pH

The sulfamethazine drug interaction with carbon nanotubes was investigated with the aim of improving the adsorption capacity of the adsorptive materials. Experiments were performed to clarify how the molecular environment affects the adsorption process. Single-walled carbon nanotubes have a higher removal efficiency of sulfamethazine than pristine or functionalized multi-walled carbon nanotubes. Although the presence of cyclodextrin molecules improves the solubility of sulfamethazine, it reduces the adsorption capacity of the carbon nanotube towards the sulfamethazine drug and, therefore, inhibits the removal of these antibiotic pollutants from waters by carbon nanotubes.
Field and laboratory investigations of budding in the tetillid sponge Cinachyrella cavernosa

The budding process of the tetillid sponge Cinachyrella cavernosa was studied for one year in the low intertidal zone near Mhapan (15°55′27.48″N, 73°33′29.89″E), on the central west coast of India. The sponges showed the highest budding frequency when the average water temperature of intertidal rock pools was 32.4±0.23°C (February–March), followed by a significant decrease in budding frequency at 28.2±0.12°C (April–July), and no budding at ≤25.9±0.12°C (August–November). Stepwise multiple regression analysis of physico-chemical factors revealed temperature as the most prominent factor regulating the intensity of budding. Based on size and morphology, three stages of sponge buds were defined. The production of buds was found to be asynchronous, as adult sponges possessed buds of all three stages. Differences among these stages were examined at ultrastructural (in terms of spicules) and molecular (in terms of RNA/DNA) levels. Stage I ( 1 mm) buds contained all spicules characteristic of the adult sponge. There was a significant increase in RNA/DNA ratio from stage I to III, suggestive of a progressive increase in physiological activity during the developmental process. Additionally, we studied post-settlement bud growth under field and laboratory conditions. Newly settled buds displayed a lower average-specific growth rate in the field, owing to variability in environmental conditions, but more rapid growth under controlled conditions in the laboratory. This study highlights the role of abiotic factors in regulating the budding process and stresses the ecological significance of budding in maintaining natural sponge populations. Our data suggest that an increased frequency of budding under stressful conditions, such as high temperature, is an advantageous adaptation for these sponges. Buds showed rapid development, as no metamorphosis is involved, and retained the genotype of the parents, yielding high reproductive outputs and survival rates.
Early warning signals in motion inference

The ability to infer intention lies at the basis of many social interactions played out via motor actions. We consider a simple paradigm of this ability in humans using data from experiments simulating an antagonistic game between an Attacker and a Blocker. Evidence shows early inference of an Attacker move by as much as 100ms but the nature of the informational cues signaling the impending move remains unknown. We show that the transition to action has the hallmark of a critical transition that is accompanied by early warning signals. These early warning signals occur as much as 130 ms before motion ensues—showing a sharp rise in motion autocorrelation at lag-1 and a sharp rise in the autocorrelation decay time. The early warning signals further correlate strongly with Blocker response times. We analyze the variance of the motion near the point of transition and find that it diverges in a manner consistent with the dynamics of a fold-transition. To test if humans can recognize and act upon these early warning signals, we simulate the dynamics of fold-transition events and ask people to recognize the onset of directional motion: participants react faster to fold-transition dynamics than to its uncorrelated counterpart. Together, our findings suggest that people can recognize the intent and onset of motion by inferring its early warning signals.
Selenium Deficiency Is Widespread and Spatially Dependent in Ethiopia

Selenium (Se) is an essential element for human health and livestock productivity. Globally, human Se status is highly variable, mainly due to the influence of soil types on the Se content of crops, suggesting the need to identify areas of deficiency to design targeted interventions. In sub-Saharan Africa, including Ethiopia, data on population Se status are largely unavailable, although previous studies indicated the potential for widespread Se deficiency. Serum Se concentration of a nationally representative sample of the Ethiopian population was determined, and these observed values were combined with a spatial statistical model to predict and map the Se status of populations across the country. The study used archived serum samples (n = 3269) from the 2015 Ethiopian National Micronutrient Survey (ENMS). The ENMS was a cross-sectional survey of young and school-age children, women and men. Serum Se concentration was measured using inductively coupled plasma mass spectrometry (ICPMS). The national median (Q1, Q3) serum Se concentration was 87.7 (56.7, 123.0) μg L−1. Serum Se concentration differed between regions, ranging from a median (Q1, Q3) of 54.6 (43.1, 66.3) µg L−1 in the Benishangul-Gumuz Region to 122.0 (105, 141) µg L−1 in the Southern Nations, Nationalities, and Peoples’ Region and the Afar Region. Overall, 35.5% of the population were Se deficient, defined as serum Se < 70 µg L−1. A geostatistical analysis showed that there was marked spatial dependence in Se status, with serum concentrations greatest among those living in North-East and Eastern Ethiopia and along the Rift Valley, while serum Se concentrations were lower among those living in North-West and Western Ethiopia. Selenium deficiency in Ethiopia is widespread, but the risk of Se deficiency is highly spatially dependent. Policies to enhance Se nutrition should target populations in North-West and Western Ethiopia.
The influence and added value of a Standardized Assessment and Reporting System for functioning outcomes upon national rehabilitation quality reports

Abstract Objective To demonstrate the influence and added value of a Standardized Assessment and Reporting System (StARS) upon the reporting of functioning outcomes for national rehabilitation quality reports. A StARS builds upon an ICF-based (International Classification of Functioning, Disability and Health) and interval-scaled common metric. Design Comparison of current ordinal-scaled Swiss national rehabilitation outcome reports including an expert-consensus-based transformation scale with StARS-based reports through descriptive statistical methods and content exploration of further development areas of the reports with relevant ICF Core Sets. Setting Swiss national public rehabilitation outcome quality reports on the clinic level. Participants A total of 29 Swiss rehabilitation clinics provided their quality report datasets including 18 047 patients. Interventions Neurological or musculoskeletal rehabilitation. Main outcome measures Functional Independence Measure™ or Extended Barthel Index. Results Outcomes reported with a StARS tended to be smaller but more precise than in the current ordinal-scaled reports, indicating an overestimation of achieved outcomes in the latter. The comparison of the common metric’s content with ICF Core Sets suggests to include ‘energy and drive functions’ or ‘maintaining a basic body position’ to enhance the content of functioning as an indicator. Conclusions A StARS supports the comparison of outcomes assessed with different measures on the same interval-scaled ICF-based common metric. Careful consideration is needed whether an ordinal-scaled or interval-scaled reporting system is applied as the magnitude and precision of reported outcomes is influenced. The StARS’ ICF basis brings an added value by informing further development of functioning as a relevant indicator for national outcome quality reports in rehabilitation.
Effect of sediment type, feeding level, and larval density on growth and development of a midge (Chironomus riparius)

A 10‐d growth test and an emergence test were performed with Chironomus riparius Meigen in four unpolluted lake sediments (organic carbon content 0.5–57%) using different feeding levels (Tetramin® at 0.03, 0.06, 0.12, or 0.33 mg/larva/d in the growth test and 0, 0.15, or 0.30 mg/larva/d in the emergence test) to study how sediment type and feeding level affect larval growth. To examine effects of larval density on growth, another growth test was performed using densities of one larva per 24, 12, 4.8, or 2.4 cm2 and a feeding level of Tetramin at 0.12 mg/larva/d. Regardless of sediment type, feeding was necessary in the experiments started with first‐instar larvae. The effects of sediment physicochemical characteristics on larval growth and development could not be totally compensated for by food addition. When fed, larvae grew best in sandy sediment with low organic carbon content (0.5%). Acceptable survival was achieved with a very low food dose (0.03 mg/larva/d), but a somewhat higher dose (0.12 mg/larva/d) is recommended. Increment of feeding accelerated larval growth and development. Larval growth was correlated to the food dose per individual and to the density of food particles on the sediment surface.
A pilot randomized trial of incentive strategies to promote HIV retesting in rural Uganda

Background Retesting for HIV is critical to identifying newly-infected persons and reinforcing prevention efforts among at-risk adults. Incentives can increase one-time HIV testing, but their role in promoting retesting is unknown. We sought to test feasibility and acceptability of incentive strategies, including commitment contracts, to promote HIV retesting among at-risk adults in rural Uganda. Methods At-risk HIV-negative adults were enrolled in a pilot trial assessing feasibility and acceptability of incentive strategies to promote HIV retesting three months after enrollment. Participants were randomized (1:1:3) to: 1) no incentive; 2) standard cash incentive (~US$4); and 3) commitment contract: participants could voluntarily make a low- or high-value deposit that would be returned with added interest (totaling ~US$4 including the deposit) upon retesting or lost if participants failed to retest. Contracts sought to promote retesting by leveraging loss aversion and addressing present bias via pre-commitment. Outcomes included acceptability of trial enrollment, contract feasibility (proportion of participants making deposits), and HIV retesting uptake. Results Of 130 HIV-negative eligible adults, 123 (95%) enrolled and were randomized: 74 (60%) to commitment contracts, 25 (20%) to standard incentives, and 24 (20%) to no incentive. Of contract participants, 69 (93%) made deposits. Overall, 93 (76%) participants retested for HIV: uptake was highest in the standard incentive group (22/25 [88%]) and lowest in high-value contract (26/36 [72%]) and no incentive (17/24 [71%]) groups. Conclusion In a randomized trial of strategies to promote HIV retesting among at-risk adults in Uganda, incentive strategies, including commitment contracts, were feasible and had high acceptability. Our findings suggest use of incentives for HIV retesting merits further comparison in a larger trial. Trial registration ClinicalTrials.gov identifier: NCT:02890459
Reproductive cycle and growth of Phyllopteryx taeniolatus

In this study, 36 males, 33 females and 15 juveniles of the common or weedy seadragon Phyllopteryx taeniolatus, a syngnathid fish endemic to the waters of southern Australia, were identified using visual implant fluorescent elastomer tags and pattern of appendages and their reproductive cycle and growth was studied from May 2001 to June 2002. Brooding males were present for a period of >6 months, from June—July to early-January. The percentage of males that were pregnant in the studied areas peaked in November—December, near the end of the breeding season. Two pregnancies were reported for some males. Ten recruits were identified from November to June. Growth rates for young-of-the-year, young of the previous year, males and females were measured. The von Bertalanffy growth constant K was estimated at 0� 098 month � 1 .
Tailored Mental Health Literacy Training Improves Mental Health Knowledge and Confidence among Canadian Farmers

This study evaluated the impact of “In the Know” mental health literacy training for Canadian agriculture. We hypothesized that “In the Know” would significantly increase participants’ knowledge around mental health, confidence in recognizing mental health struggles, confidence in speaking about mental health with others, and confidence in helping someone who may be struggling with mental health. “In the Know” was a 4-h, in-person program delivered by a mental health professional who also had experience in agriculture. Six sessions were offered in Ontario, Canada in 2018. Participants were farmers and/or worked primarily with farmers. A pre-training paper questionnaire was administered, followed by a post-training questionnaire at the end of the session and 3 and 6 month post-training questionnaires via email. Wilcoxon signed-rank tests were performed to compare participants’ self-reported knowledge and confidence across four timepoints. “In the Know” significantly improved participants’ self-reported mental health knowledge and confidence in recognizing mental health struggles, speaking to others, and helping others who are struggling immediately following training and often at 3 and 6 months post-training. This is the first study among farming populations to measure program impact with 3- and 6-month follow-ups. Given the reported associations between mental health literacy and increased help-seeking, disseminating “In the Know” more broadly across farming communities may help to increase mental health literacy and thus increase help-seeking among farmers.