Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening of crows and waterfowls for Salmonella and Listeria monocytogenes infection

Background and Aim: Wild birds can carry a number of potential human and animal pathogens. These birds can intrude into human habitats giving the opportunity to transmission of such infection. Therefore, the current study was designed to investigate the role of crows and waterfowls as vectors of Salmonella and Listeria monocytogenes and to compare cultivation methods with direct polymerase chain reaction (PCR) for the detection of infection. Materials and Methods: A total of 200 fecal dropping samples were collected. Salmonella was cultivated by three step method (Universal Pre-enrichment Broth [UPB], Rappaport-Vassiliadis Broth, and Xylose Lysine Desoxycholate agar). The recovered isolates were characterized by biotyping, serotyping, and PCR detection of enterotoxin (stn) gene. The antibiogram pattern of isolates against a panel of 8 antibiotics was recorded. L. monocytogenes was cultivated on UPB, then on Listeria Oxford Agar and Listeria CHROMagar. The recovered isolates were characterized by biotyping and PCR detection of listeriolysin (hylA) gene. Results: The percentages of Salmonella infection in crows and waterfowls were 10 and 20, respectively. The most frequently recovered serovars were Typhimurium, Potengi, Enteritidis, and Kentucky. Antimicrobial susceptibility analysis of Salmonella isolates showed that the resistance rates for gentamicin were the highest (92%), followed by amoxicillin (88%) and cefixime (60%). Resistance to 8 antibiotics was recorded in 60% (15/25) of Salmonella isolates. The percentages of L. monocytogenes infection in crows and waterfowls were 1.3 and 2, respectively. Direct PCR applied to UPB revealed that 12% and 3% of samples were positive for Salmonella and L. monocytogenes, respectively, and there was no significant difference between direct PCR and cultivation method for the detection of infection. Conclusion: The present findings indicate that wild birds can harbor zoonotic enteric pathogens and this necessitates monitoring the epidemiologic status of these pathogens among wild birds and humans and applying the appropriate intervention measures to prevent the spread of infection.
Strengthening the integration of eye care into the health system: methodology for the development of the WHO package of eye care interventions

Objective To describe the rational for, and the methods that will be employed to develop, the WHO package of eye care interventions (PECI). Methods and analysis The development of the package will be conducted in four steps: (1) selection of eye conditions (for which interventions will be included in the package) based on epidemiological data on the causes of vision impairment and blindness, prevalence estimates of eye conditions and health facility data; (2) identification of interventions and related evidence for the selected eye conditions from clinical practice guidelines and high-quality systematic reviews by a technical working group; (3) expert agreement on the inclusion of eye care interventions in the package and the description of resources required for the provision of the selected interventions; and (4) peer review. The project will be led by the WHO Vision Programme in collaboration with Cochrane Eyes and Vision. A Technical Advisory Group, comprised of public health and clinical experts in the field, will provide technical input throughout all stages of development. Results After considering the feedback of Technical Advisory Group members and reviewing-related evidence, a final list of eye conditions for which interventions will be included in the package has been collated. Conclusion The PECI will support Ministries of Health in prioritising, planning, budgeting and integrating eye care interventions into health systems. It is anticipated that the PECI will be available for use in 2021.
Association Between Work‐Related Hyperthermia Emergency Department Visits and Ambient Heat in Five Southeastern States, 2010–2012—A Case‐Crossover Study

The objective of this study is to assess ambient temperatures' and extreme heat events' contribution to work‐related emergency department (ED) visits for hyperthermia in the southeastern United States to inform prevention. Through a collaborative network and established data framework, work‐related ED hyperthermia visits in five participating southeastern U.S. states were analyzed using a time stratified case‐crossover design. For exposure metrics, day‐ and location‐specific measures of ambient temperatures and county‐specific identification of extreme heat events were used. From 2010 to 2012, 5,017 work‐related hyperthermia ED visits were seen; 2,298 (~46%) of these visits occurred on days when the daily maximum heat index was at temperatures the Occupational Safety and Health Administration designates as having “lower” or “moderate” heat risk. A 14% increase in risk of ED visit was seen for a 1°F increase in average daily mean temperature, modeled as linear predictor across all temperatures. A 54% increase in risk was seen for work‐related hyperthermia ED visits during extreme heat events (two or more consecutive days of unusually high temperatures) when controlling for average daily mean temperature. Despite ambient heat being a well‐known risk to workers' health, this study's findings indicate ambient heat contributed to work‐related ED hyperthermia visits in these five states. Used alone, existing OSHA heat‐risk levels for ambient temperatures did not appear to successfully communicate workers' risk for hyperthermia in this study. Findings should inform future heat‐alert communications and policies, heat prevention efforts, and heat‐illness prevention research for workers in the southeastern United States.
Spatial Patterns of Spread of Dengue with Human and Vector Mobility

Background : Dengue is a vector borne disease transmitted to humans by Aedes Aegypti mosquitoes carrying Dengue virus of different serotypes. Primarily an urban epidemic, Dengue exhibits complex spatial and temporal dynamics, influenced by many biological, human and environmental factors. However, most of the existing models neglect the spatial factors influencing the spread of Dengue. This work sheds light on how Dengue parameters and human mobility changes the spatial spread of the infection and size of the epidemic. Methodology/Principal findings: We model the Dengue as a stochastic Cellular Automata (CA) process following Susceptible, Exposed, Infected, Recovered (SEIR) -Susceptible, Exposed, Infected (SEI)for human and vector dynamics respectively in each cell, and analyze the spatial and temporal spreading disease using parameters from field studies. We use the data on mosquito density from Ahmedabad city of India as input to our model to predict the dynamics of Dengue incidence and compare it to the reported data on the prevalence of the disease from 2006-2012. We find that for certain infection rates, CA model closely reproduces observed peaks and intensity. We used data based statistical models of human mobility such as exponential step length and super diffusive Lévy flight to study mobility effects on Dengue spreading within the city. We find an interesting result that inclusion of human mobility in many cases can decrease the incidence of Dengue, and may suppress the infection completely. The scale and intensity of reduction depend on the relative strengths of infection ∗endurimuralikrishna@iitgn.ac. in †shiva.jolad@iitgn.ac. in transmission rate and mobility step length. The primarily reason for decline can be attributed to the significant fraction of the susceptible and exposed population moving to the regions where majority have already recovered and can no longer be infected. Conclusions/Significance: The current study is aimed at more realistic model of spatial spread of Dengue and understand how human mobility factors in the spread of vector borne diseases. It highlights certain counter intuitive results such as suppression of Dengue spreading when we include statistical patterns of human mobility. In supplementary information, we show that even for Lévy flight broadly same conclusions hold hood. The random mobility pattern produces large peak initially, but suppresses Dengue completely within a short period of time even for large infection rate, deviating largely from the observed pattern.
Improved algorithms for discovery of transcription factor binding sites in DNA sequences

Improved Algorithms for Discovery of Transcription Factor Binding Sites in DNA Sequences. (December 2010) Xiaoyan Zhao, B.S., Beijing Normal University Chair of Advisory Committee: Dr. Sing-Hoi Sze Understanding the mechanisms that regulate gene expression is a major challenge in biology. One of the most important tasks in this challenge is to identify the transcription factors binding sites (TFBS) in DNA sequences. The common representation of these binding sites is called “motif” and the discovery of TFBS problem is also referred as motif finding problem in computer science. Despite extensive efforts in the past decade, none of the existing algorithms perform very well. This dissertation focuses on this difficult problem and proposes three new methods (MotifEnumerator, PosMotif, and Enrich) with excellent improvements. An improved pattern-driven algorithm, MotifEnumerator, is first proposed to detect the optimal motif with reduced time complexity compared to the traditional exact pattern-driven approaches. This strategy is further extended to allow arbitrary don’t care positions within a motif without much decrease in solvable values of motif length. The performance of this algorithm is comparable to the best existing motif finding algorithms on a large benchmark set of samples.
Efficacy of Gastrointestinal Endoscopy in 398 Patients With Iron Deficiency Anemia Who Lack Gastrointestinal Symptoms: Basrah Experience

Introduction The diagnosis of iron deficiency anemia (IDA) relies heavily on symptom presentation, and patients lacking typical gastrointestinal (GI) symptoms represent a diagnostic challenge. IDA may be the initial manifestation of underlying pathology. This study sought to evaluate the effectiveness of different GI endoscopic studies in patients with IDA who lack GI symptoms. Methods We conducted an observational, multicenter retrospective analysis of 398 asymptomatic IDA patients admitted for GI endoscopic diagnosis from 2006 to 2016. Baseline measurements included hemoglobin, serum ferritin, mean corpuscular volume, serum iron, total iron-binding capacity, and transferrin saturation. We analyzed demographic characteristics, duration of hospital stay, the degree of severity of anemia, and endoscopic findings. Results The mean age of the study population was 52±9 years (range, 23 to 85 years), and 53% were men. Most patients were older than 45 years (n=353, 89%) with mild to moderate IDA. Patients underwent esophagogastroduodenoscopy (EGD, n=102), colonoscopy (n=271), or bidirectional endoscopy (n=25). The mean hospital stay was 2.72±1.66 days. The most common EGD results were atrophic gastritis (n=31), peptic ulcer (n=25), and negative findings (n=25). The most common colonoscopic results were negative findings (n=118), nonspecific colonic inflammatory changes (n=117), and non-bleeding hemorrhoids (n=29). We found no significant association between any endoscopic findings and age, gender, the severity of anemia, and length of hospitalization. Conclusions The presence of symptoms is of limited value in guiding diagnostic procedures concerning GI etiologies. Asymptomatic patients with IDA patients should receive an endoscopic examination irrespective of iron parameters, age, or gender for potentially treatable pathologies, especially for patients with suspected malignancies.
Gluconobacter dominates the gut microbiome of the Asian palm civet Paradoxurus hermaphroditus that produces kopi luwak

Coffee beans derived from feces of the civet cat are used to brew coffee known as kopi luwak (the Indonesian words for coffee and palm civet, respectively), which is one of the most expensive coffees in the world owing to its limited supply and strong market demand. Recent metabolomics studies have revealed that kopi luwak metabolites differ from metabolites found in other coffee beans. To produce kopi luwak, coffee beans are first eaten by civet cats. It has been proposed that fermentation inside the civet cat digestive tract may contribute to the distinctively smooth flavor of kopi luwak, but the biological basis has not been determined. Therefore, we characterized the microbiome of civet cat feces using 16S rRNA gene sequences to determine the bacterial taxa that may influence fermentation processes related to kopi luwak. Moreover, we compared this fecal microbiome with that of 14 other animals, revealing that Gluconobacter is a genus that is, uniquely found in feces of the civet cat. We also found that Gluconobacter species have a large number of cell motility genes, which may encode flagellar proteins allowing colonization of the civet gut. In addition, genes encoding enzymes involved in the metabolism of hydrogen sulfide and sulfur-containing amino acids were over-represented in Gluconobacter. These genes may contribute to the fermentation of coffee beans in the digestive tract of civet cats.
When, why and how tumour clonal diversity predicts survival

The utility of intratumour heterogeneity as a prognostic biomarker is the subject of ongoing clinical investigation. However, the relationship between this marker and its clinical impact is mediated by an evolutionary process that is not well understood. Here, we employ a spatial computational model of tumour evolution to assess when, why and how intratumour heterogeneity can be used to forecast tumour growth rate and progression‐free survival. We identify three conditions that can lead to a positive correlation between clonal diversity and subsequent growth rate: diversity is measured early in tumour development; selective sweeps are rare; and/or tumours vary in the rate at which they acquire driver mutations. Opposite conditions typically lead to negative correlation. In cohorts of tumours with diverse evolutionary parameters, we find that clonal diversity is a reliable predictor of both growth rate and progression‐free survival. We thus offer explanations—grounded in evolutionary theory—for empirical findings in various cancers, including survival analyses reported in the recent TRACERx Renal study of clear‐cell renal cell carcinoma. Our work informs the search for new prognostic biomarkers and contributes to the development of predictive oncology.
Molecular phylogenetic analyses of tissue coccidia (sarcocystidae; apicomplexa) based on nuclear 18s RDNA and mitochondrial COI sequences confirms the paraphyly of the genus Hammondia

Partial mitochondrial cytochrome c oxidase subunit I (mt COI) sequences were generated from: Toxoplasma gondii (strains CTG, GTI, MAS, ME49, PTG, TgCatBr5, TgCat, Br64, TgCgCal, TgToucan); Neospora caninum (Strain NC1); Hammondia hammondi (Strain H.H–20); H. heydorni; H . cf. triffittae; Cystoisospora felis; C. suis; C. canis; C. rivolta; C . cf. ohioensis; Caryospora bigenetica; Sarcocystis rileyi ; and S. neurona . Nuclear 18S rDNA sequences were generated for H. heydorni, H. hammondi, C. suis, C. canis, C. felis, C. rivolta, C . cf. ohioensis, S. neurona , and S. rileyi . Aligned, concatenated 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I + G for 18S; GTR + I + G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade of Cystoisospora spp. with Nephroisospora eptesici ; and (2) a clade of Toxoplasma, Neospora and Hammondia . Within the latter, Hammondia was shown to be paraphyletic; H. heydorni and H. triffittae were monophyletic with N. caninum [canine definitive hosts (DHs)], whereas H. hammondi was monophyletic with T. gondii (feline DHs). A new genus is erected to resolve the paraphyly of the genus Hammondia confirmed using mt COI and combined 18S/COI sequence datasets.
Prevalence of Enteroparasites Among Non-Saudis in Bahrah, Saudi Arabia

Background Enteroparasitic infections in tropical and subtropical regions of the world are among the most common diseases. The majority of the cases may show no symptoms; however, many untreated cases may experience severe complications. The recent substantial economic development in Saudi Arabia has resulted in an inflow of millions of workers with intestinal parasitic infection, from highly endemic countries, mainly from Asia and Africa. Objective This cross-sectional study aimed to assess for the first time the prevalence and associated factors of intestinal parasitic infestation among non-Saudi residents in Bahrah, western region, Saudi Arabia. Materials and methods A total of 355 stool samples were collected from participants included in this study for several examinations of intestinal parasites. In addition, questionnaires including personal data, sociodemographic data, personal hygiene, health habits and other factors were used. Results The prevalence of intestinal parasitic infections among non-Saudi workers in the present study was 22.3%, and the prevalence of protozoan infection was higher than helminth infection. Most of the workers were from Asian countries and were prevalent with Trichuris trichiura, Blastocystis hominis, Endolimax nana and Ascaris lumbricoides. Single intestinal infections were among 86% of the infected cases. The main significant factors associated with intestinal parasitic infections were personal hygiene practices (such as proper handwashing before meals and after using the toilet), source of drinking water and type of living accommodation. Conclusion Intestinal parasites were slightly more prevalent among non-Saudi workers in Bahrah. There is a need for public health awareness programs to prevent spreading of the infections.
백년초선인장의 ITS(internal transcribed spacer) 유전자 분석

To investigate the origin of backyeoncho (Opuntia ficus-indica var. saboten), we isolated 685 bp clone using ITS primer pairs. The rDNA consists of the genes coding for the partial 54 bp 18S, 162 bp 5.8S, and partial 56 bp 26S. The coding regions are interrupted by two internal transcribed spacers, 193 bp ITS1 and 220 bp ITS2. The ITS2 of backnyeoncho in length was shorter than that previously registered in Cucurbitoideae plants. The GC contents was 66.8% in ITS1, and 67.7% in ITS2. The rDNA of backnyeoncho matched to the previously reported genes and showed a high similarity with the 95% identity with Pereskiopsis porteri (L708037). In the phylogenetic analysis, the backnyeoncho rDNA was clustered with Pereskiopsis porteri (L708037).
A new species of Oomyzus Rondani (Hymenoptera, Eulophidae) reared from the pupae of Coccinella septempunctata (Coleoptera, Coccinellidae) in China

Abstract Oomyzus spiraculus Song, Fei & Cao sp. nov. (Hymenoptera, Eulophidae) is described and illustrated as a gregarious larval-pupal endoparasitoid of Coccinella septempunctata L. (Coleoptera, Coccinellidae). Differentiation between O. spiraculus and its similar species is discussed and a key to differentiate the female and male of these species is provided. DNA barcodes of O. spiraculus and O. scaposus are analyzed and compared.
Arming Oncolytic Adenoviruses: Effect of Insertion Site and Splice Acceptor on Transgene Expression and Viral Fitness

Oncolytic adenoviruses (OAds) present limited efficacy in clinics. The insertion of therapeutic transgenes into OAds genomes, known as “arming OAds”, has been the main strategy to improve their therapeutic potential. Different approaches were published in the decade of the 2000s, but with few comparisons. Most armed OAds have complete or partial E3 deletions, leading to a shorter half-life in vivo. We generated E3+ OAds using two insertion sites, After-fiber and After-E4, and two different splice acceptors linked to the major late promoter, either the Ad5 protein IIIa acceptor (IIIaSA) or the Ad40 long fiber acceptor (40SA). The highest transgene levels were obtained with the After-fiber location and 40SA. However, the set of codons of the transgene affected viral fitness, highlighting the relevance of transgene codon usage when arming OAds using the major late promoter.
Phylogeography and speciation processes in marine fishes and fishes from large freshwater lakes

Fishes constitute about half of all known vertebrate species and have colonized nearly all available marine and freshwater habitats. The greatest diversity of fishes is found in the marine realm as well as in large (and often old) freshwater lakes such as the East African Great Lakes. Here, we compare the phylogeographic history of fishes in marine and large freshwater ecosystems, with particular emphasis on groups that underwent adaptive radiation, i.e. the emergence of a multitude of species from a single ancestor as a consequence of the adaptation to different ecological niches. Phylogeographic analyses are highly suited to identify and compare causal agents of speciation in rapidly diversifying groups. This is particularly true for fishes, in which distribution ranges and preferred habitat structures can be quantified in a straightforward matter.
Efficient gene delivery into mammalian cells by baculovirus vector in vitro

The recombinant baculovirus vector with EGFP reporter gene under the control of strong CAG promoter cassette was used for transduction of normal (HEK293) and tumor (HeLa) human cell lines. Dependence of transduction efficiency on the virus dose, time of virus incubation, temperature and cell type is shown. Transient reporter gene expression gradually diminished and was detected in single cells on the 15 day after transduction.
Performance of white oat cultivars for grain chemical content

Abstract: The chemical analysis of market-available white oat cultivars allows for their optimized use for processing, consumption, and in blocks of crosses. The purpose of this study was to evaluate the performance of white oat cultivars with regard to grain chemical content, to estimate the correlation between these traits, and to select potential REMAP markers for marker-assisted selection. Fifteen cultivars, grown in three environments, were evaluated for the contents of proteins; lipids; total, insoluble, and soluble dietary fiber; ß-glucan; and carbohydrates. Eight cultivars were analysed with REMAP markers. The cultivars Brisasul and UPFA Gaudéria presented higher contents of ß-glucan, while cultivars URS 21 and URS 22 had higher protein contents. For animal feed, the cultivars Barbarasul and FAPA Louise stood out with high lipid contents. Positive correlations between the contents of lipid and total dietary fiber, protein and insoluble dietary fiber, and total dietary fiber and insoluble dietary fiber were constant in different environments. Also, carbohydrate content was negatively correlated with protein, total dietary fiber, insoluble dietary fiber, and lipid content. A total of thirteen REMAP combinations were selected for variability studies regarding lipid and ß-glucan contents.
Vitality structure of the populations of some weed species in crop sowings

Features of development of populations of weed species ( Cirsium arvense (L.) Scop. , Sonchus arvensis L. , Melandium album (Mill.) Garke, Setaria glauca (L.) Beauv. , Fallopia convolvulus (L.) А. Lоve) in most typical crop s in the forest-steppe zone of the Sumy region. It was studied t he crop sowing s (winter wheat, rye, barley, buckwheat, pea) which was not subjected to the herbicide treatment.