Miracle-dz/UniFAR-FTUs huggingface dataset:
GeneWeb II: Sequence Analysis Tools on Web Server Using Java API

In recent years, the computer network, including Internet, came into wide use and researchers in many elds came to utilize it routinely. World Wide Web (WWW) and its browser software such as Netscape or Internet Explorer are probably the most powerful and useful tools for researchers who search documents or retrieve information from remote computers distributed over Internet. Especially in molecular and genome biology, researchers need to access to the various extremely large biological database on the network and to retrieve them. Therefore, the researchers are expected to be accustomed to use Web browser, even if they are not familiar with the computer operation other than Web browser. In this aspect, we had been developing sequence analysis tools on Web server named GeneWeb I in 1995 [1]. This system provided sequence analysis tools which was available on Web browser in any kind of computers. For improving graphical user interface (GUI), we have been developing new software named GeneWeb II (Fig. 1) which is developed by using Java Application Programming Interface (Java API) for GUI and for interfacing external applications with Web server.
Prevalence and correlates of alcohol use in a central Nepal district: secondary analysis of a population-based cross-sectional study

Background. As reported from studies conducted in Nepal, between 15% and 57% of adults had ever consumed alcohol and between 1.5% and 25% of adults have alcohol use disorders (AUD). Few studies in Nepal have identified the correlates of consumption or described the help-seeking patterns and stigma among those affected with AUD. Methods. Interviewers administered the Alcohol Use Disorders Identification Test (AUDIT) as part of population-based surveys of adults in Chitwan District between 2013 and 2017. We conducted a secondary analysis to identify sociodemographic and health-related correlates of recent alcohol consumption using the χ2 test, to identify correlates of total AUDIT scores among men who drink using negative binomial regression, and to describe the treatment-seeking and stigma beliefs of men with AUD. Results. Over half (53.7%, 95% CI 50.4–57.0) of men (n = 1130) recently consumed alcohol, and there were associations between being a drinker with age, religion, caste, education, occupation and tobacco use. Nearly one in four (23.8%, 95% CI 20.2–27.8%) male drinkers screened positive for AUD, and AUDIT scores were associated with age, caste, marital status, occupation, tobacco use, depression, functional status and suicidal ideation. Few (13.3%, 95% CI 11.7–15.0) women (n = 2352) recently consumed alcohol, and 5.3% (95% CI 3.0–9.1) of female drinkers screened positive for AUD. Among AUDIT-positive men, 38% spoke to another person about their problems and 80% had internalized stigma. Conclusions. This study revealed that nearly one in four men who drink likely have AUD. Higher AUDIT scores were associated with depression, suicidality, dysfunctionality and internalized stigma.
Follicular dendritic cell sarcoma detected in hepatogastric ligament: A case report and review of the literature

The most common organ where follicular dendritic cell sarcoma (FDCS) occurs is in cervical lymph nodes, while few cases are found in extranodal organs such as liver, spleen, and soft tissue. This is a case report that FDCS occurs in the hepatogastric ligament. To our knowledge, there is no such case that has been reported previously. A 47-year-old male patient was found to have an intraabdominal mass during an annual physical examination. Computed tomography showed a 4.2 cm × 4.1 cm mass located at the lesser curvature of the stomach, above the pancreas. During operation, a tumor mass was found in the hepatogastric ligament and a radical resection was performed. The tumor was diagnosed as FDCS by pathology and immunohistochemical testing. The patient had a favorable recovery, and no obvious abnormality was found 3 months post-operation.
Acaulosproa koreana, a New Species of Arbuscular Mycorrhizal Fungi (Glomeromycota) Associated with Roots of Woody Plants in Korea

Abstract A new species of arbuscular mycorrhizal fungi (Glomeromycota), Acaulospora koreana, was isolated from forest soils in South Korea. This novel fungus was collected from the rhizosphere of Lindera obtusiloba and Styrax obassia in forest and propagated with Sorghum bicolor in pot. Morphological characteristics of spores of A. koreana are rarely distinguished from Acaulospora mellea, which is reported as one of the most abundant mycorrhizal species in Korea. However, molecular evidence of rDNA sequence using improved primers for glomeromycotan fungal identification strongly supported that A. koreana is different from A. mellea but also any other species belonging to the genus Acaulospora. This is the first novel glomeromycatan fungus introduced in South Korea, but it suggests that there is a high possibility for discovering new arbuscular mycorrhizal fungi considering the abundance of plant species and advanced phylogenetic analysis technique.
Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis

Abstract Whole-genome sequencing of Flammulina ononidis, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of de novo genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one F. ononidis gene. In addition, 11,252 (89.5%) of 12,586 genes for F. ononidis proteins had orthologs among the Dikarya, and F. ononidis contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the F. ononidis genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus F. ononidis.
Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

ABSTRACT The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.
Insulin-like Growth Factor-1 Receptor Dictates Beneficial Effects of Treadmill Training by Regulating Survival and Migration of Neural Stem Cell Grafts in the Injured Spinal Cord

Survival and migration of transplanted neural stem cells (NSCs) are prerequisites for therapeutic benefits in spinal cord injury. We have shown that survival of NSC grafts declines after transplantation into the injured spinal cord, and that combining treadmill training (TMT) enhances NSC survival via insulin-like growth factor-1 (IGF-1). Here, we aimed to obtain genetic evidence that IGF-1 signaling in the transplanted NSCs determines the beneficial effects of TMT. We transplanted NSCs heterozygous (+/−) for Igf1r, the gene encoding IGF-1 receptor, into the mouse spinal cord after injury, with or without combining TMT. We analyzed the influence of genotype and TMT on locomotor recovery and survival and migration of NSC grafts. In vitro experiments were performed to examine the potential roles of IGF-1 signaling in the migratory ability of NSCs. Mice receiving +/− NSC grafts showed impaired locomotor recovery compared with those receiving wild-type (+/+) NSCs. Locomotor improvement by TMT was more pronounced with +/+ grafts. Deficiency of one allele of Igf1r significantly reduced survival and migration of the transplanted NSCs. Although TMT did not significantly influence NSC survival, it substantially enhanced the extent of migration for only +/+ NSCs. Cultured neurospheres exhibited dynamic motility with cytoplasmic protrusions, which was regulated by IGF-1 signaling. IGF-1 signaling in transplanted NSCs may be essential in regulating their survival and migration. Furthermore, TMT may promote NSC graft-mediated locomotor recovery via activation of IGF-1 signaling in transplanted NSCs. Dynamic NSC motility via IGF-1 signaling may be the cellular basis for the TMT-induced enhancement of migration.
Usability testing of bed information management system: A think-aloud method

Not considering the usability in designing clinical information systems causes problems in human–computer interaction and patient dissatisfaction. Therefore, in this study, the usability of the bed information management system (BIMS) was examined by think-aloud method. This cross-sectional study was conducted on the BIMS in 50 noneducational hospitals. Participants consisted of three groups including users, facilitators, and technical support. To carry out the study, a scenario consisting of four tasks was designed. Three researchers analyzed the recorded files to identify the usability problems and their severity. The mean time of the evaluation process was 20:33 ± 4:47 s. The total number of the problems identifies by users was 80 cases. Data entry and layout problems with 38 (48%) and 33 (41%) cases were the most frequently found problems, respectively. About 61% and 55% of the data entry and layout problems had a minor severity (Severity 2), respectively. Furthermore, 43 (54%) cases of the problems were resolved by the users and 32 (40%) cases by the facilitator assistance. This study showed that a large number of the problems were due to the system poor design. Furthermore, by increasing the users' level of knowledge about the system, it is possible to enhance user-system interaction. It is recommended that before designing and implementing a system, the system should be evaluated for usability, and the users should be educated in clinical information systems.
Association of markers of systemic and local inflammation with prognosis of patients with rectal cancer who received neoadjuvant radiotherapy

Purpose The inflammatory status of patients with cancer appears to affect cancer progression and patient prognosis. We examined the characteristics of cancer-associated systemic and local inflammation and its impact on the overall survival (OS) of patients with locally advanced rectal cancer (LARC) who received neoadjuvant radiotherapy (nRT). Patients and methods Seventy-six consecutive LARC patients who received nRT from February 2012 to September 2015 were retrospectively analyzed. The peripheral neutrophil-to-lymphocyte ratio (NLR) was determined at diagnosis, and the CD8+ T-cell count was determined from surgical specimens. Factors associated with OS were identified by univariate and multivariate Cox regression. Results The median follow-up time was 23.0 months (range: 2–59), and the overall 5-year OS rate was 68.6% (95% CI =46.06–91.14). Patients with a high NLR (≥2.0) and a low CD8+ T-cell count (<9%) had a significantly worse 5-year OS than those with a low NLR and a high CD8+ T-cell count (P=0.005). NLR was also associated with lymphovascular invasion (P=0.014) and T stage (P=0.047), and the CD8+ T-cell count was associated with mucinous adenocarcinoma (P=0.005) and T stage (P=0.049). An NLR <2.0 was associated with pathological complete regression after nRT (P=0.039). Multivariate Cox regression indicated that NLR (P=0.025), CD8+ T-cell count (P=0.018), age (P=0.020), lymphovascular invasion (P=0.038), and T stage (P=0.011) were independently associated with OS. Conclusion A high NLR and a low CD8+ T-cell count were significantly associated with poor survival in our population of patients with LARC. Measurement of markers of systemic and local inflammation might help to predict the prognosis of patients with LARC after nRT.
Versatility of cell-penetrating peptides for intracellular delivery of siRNA

Abstract The plasma membrane is a large barrier to systemic drug delivery into cells, and it limits the efficacy of drug cargo. This issue has been overcome using cell-penetrating peptides (CPPs). CPPs are short peptides (6–30 amino acid residues) that are potentially capable of intracellular penetration to deliver drug molecules. CPPs broadened biomedical applications and provide a means to deliver a range of biologically active molecules, such as small molecules, proteins, imaging agents, and pharmaceutical nanocarriers, across the plasma membrane with high efficacy and low toxicity. This review is focused on the versatility of CPPs and advanced approaches for siRNA delivery.
Pre-saccadic remapping relies on dynamics of spatial attention

Each eye movement shifts the projections of the visual scene on the retina. It has been proposed that the receptive fields of neurons in oculomotor areas are remapped pre-saccadically to account for these shifts. While remapping of the whole visual scene seems prohibitively complex, selection by visual attention may limit these processes to a subset of attended locations. Because attentional selection consumes time, remapping of attended locations should evolve in time, too. In our study, we cued a spatial location by presenting an attention capturing cue at different times before a saccade and constructed detailed maps of attentional allocation across the visual field. We observed no remapping when the cue appeared shortly before saccade. In contrast, when the cue appeared sufficiently early before saccade, attentional resources were reallocated to the remapped location. Our results suggest that pre-saccadic remapping is an attentional process relying on the spatial and temporal dynamics of visual attention.
Evaluation of transfer factor protective efficacy against Tuberculosis in Guinea Pigs

Transfer factor has been prepared from sensitized guinea pigs against heat killed Mycobacterium bovis antigen and protective efficacy were evaluated in guinea pigs that gave 1 ml of transfer factor equivalent 5x10 8 cell / ml of sensitized and normal cell donor; then challenged with dose 0.01 mg / animal of virulent Mycobacterium bovis, After 40 days of challenge all animals were sacrificied. Histologically: TFs recipient group showed a mono-nuclear cells infiltration’s (Lymphocytes & Macrophages) with a mild emphysema of lungs, and liver showed mononuclear cells ,a small necrotic foci in the lymphocytic organs (spleen & lymph nodes); the kidney showed mononuclear cells in glomeruli and urinary tubules ;While the TFn recipient group were an areas of caseated necrotic materials surrounded by macrophages &Lymphocytes, congestion of internal organs (Liver and Spleen) and Sever congestion with hemorrhage of alveoli tissue, sever emphysema & consolidation in lung kidney showed tuberculle foci in glomeruli and around urinary tubules . There were no pathgenomic changes in heart muscles of TFs recipient group while a mild congestion in TFn recipient group.
Insomnia is associated with increased mortality in patients with first-ever stroke: a 6-year follow-up in a Chinese cohort study

Objective Insomnia is a highly prevalent disorder among patients suffering from stroke. The association between insomnia and stroke mortality is less studied, particularly using the latest diagnostic criteria. The current study examined the relationship between insomnia and mortality among patients with first-evonal hazard models were used to calculate HRs for stroke er stroke in China. Methods Patients with acute cerebrovascular diseases (stroke) were recruited from 56 hospitals in mainland China. Insomnia was defined as difficulty falling asleep, or difficulty staying asleep or waking up early, for at least two consecutive visits. Demographic data, medical history and clinical data were collected. Four follow-up visits occurred within the first year after stroke, and the last follow-up call was conducted 6 years later. Cox proportional hazard models were used to calculate HRs for stroke mortality. Results Insomnia was reported by 38.4% (489/1273) of patients at baseline. During the 6 years of follow-up, after adjusting for all confounders, insomnia was found to be associated with increased mortality (HR=1.66, 95% CI 1.10 to 2.48). Old age (HR=1.08, 95% CI 1.06 to 1.10), stroke recurrence in the first year of follow-up (HR=2.53, 95% CI 1.48 to 4.31) and stroke survivors with hypertension (HR=1.62, 95% CI 1.04 to 2.53) had substantially higher risk of mortality. Conclusions Besides old age, stroke recurrence in the first year of follow-up and hypertension, insomnia is associated with increased risk of mortality in patients with first-ever stroke in China. More studies about prompt and efficient interventions for insomnia are expected in the future. Trial registration number rctn62169508.
Candelaria asiatica, an Ignored New Species from South Korea

Abstract The genus Candelaria is characterized by a micro-foliose to micro-fruticose thallus and contains eight species, two of which were reported in South Korea. During the excursion of a Korean lichen flora investigation, some suspected Candelaria concolor specimens were collected, and their morphological, chemical, molecular phylogenetic, and geographic analyses were conducted. The samples eventually proved to be a new species, Candelaria asiatica, which can be recognized by a small, yellow lobate thallus with a pulverulent surface, and a fragile lobe margin with blastidia or phyllidia-like lobules.
Growth Inhibitory Effect of Lactocare on Vibrio cholerae

Background and Objective: Acute microbial diarrheal diseases are the major public health problems in the developing countries. People affected by diarrheal diseases have the lowest financial resources and poorest hygienic facilities. Children under five, primarily in Asian and African countries, are mostly the subjects affected by microbial diseases transmitted through water.The current study aimed at investigating the comparative inhibitory effect of Lactocare (commercial probiotic) on clinical samples and standard strains of Vibrio cholerae. Methods: A total of 20 clinical samples and a standard strain (ATCC 14035) were provided by Health Reference Laboratory and Biotechnology Institute, respective ly. In order to confirm the samples, biochemical analysis and the polymerase chain reaction (PCR) were performed on intergenic space. Afterward, agar well diffusion method was performed in order to measure the minimum inhibitory concentration to monitor the antimicrobial activity of Lactocare. Results: Colony count of V. cholerae for the standard strain in 30% and mean for clinical samples in 50% concentration of Lactocare treatment revealed that it would propel to death phase. Since the number of colonies decreased to 100, it was considered that higher concentrations of Lactocare would completely inhibit the growth of V. cholera. Conclusion: Probiotics are employed to develop new pharmaceutical preparations and functional foods in order to promote the public health.
A Method of Query Expansion Based on Event Ontology

Aiming at the requirements of getting event information from internet,a method of query expansion based on event ontology was proposed.Two key technologies were mainly introduced concerning this method:matching between query content and field event ontology and selecting extended item based on event ontology.Experiments on the prototype validated the effectiveness of the proposed method in Chinese Event Corpus(CEC).
Evolutionary training of behavior-based self-organizing map

The paper presents a novel idea of a behavior-based self-organizing map. The self-organizing map (SOM) is extended to cover 'objects' that interact with their environment. They are organized based on their behavior instead of parameterized presentation. The original SOM needs a metric to be defined, while in the new self-organizing map no metric between the parameterized presentations is needed. The neighborhood concept of the SOM algorithm is given a probability interpretation that is suitable for evolutionary computing. The behavior based SOM algorithm is presented, and the new concept is demonstrated on linear time-series models, that are identified and organized based on sample data from a simulated system.
Diabetes Self-Management Behaviors among American Indians in the Midwestern United States

The purpose of this study was to understand if American Indian adults with diabetes in the Midwest are similar to American Indian adults nationally in their self-management behaviors. This cross-sectional survey was conducted from May 2009 to April 2010 at powwows, health fairs, and other community events. The convenience sample self-selected into the study and answered questions via touch screen computer about diabetes self-management. Participants were significantly below the national average for American Indians in their adherence to self-management recommendations in daily foot checks (p=0.0035) and having had a dilated eye exam in the previous year (p=0.0002), despite being significantly more likely to have taken a diabetes self-management class (p<0.0001). They were similar to the national average for daily glucose checks and having had one or more hemoglobin A1C tests in the previous year. Participants were less likely to eat 5 or more servings of fruits or vegetables per day (p=0.0001), but more likely to achieve 150 minutes or more of physical activity per week (p=0.0001). Programs addressing self-care issues should be developed to help improve the self-management habits of American Indian adults with diabetes, with particular attention to activities outside of monitoring blood glucose and hemoglobin A1C levels.
An Analysis of the Motives of Ecotourists in Comparison to the General Canadian Population

L'A. compare les attitudes et les motivations des touristes traditionnels et des touristes preoccupes d'ecologie. Il etudie a cette fin les resultats d'une enquete aupres de membres de la Federation des Naturalistes de l'Ontario sur certaines categories de voyages. Les « ecotouristes » privilegient l'activite physique, la rencontre de personnes partageant les memes centres d'interet et le fait de voir un maximum de choses en un minimum de temps