Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Airborne Mushroom Damaging Trichoderma spp. from Indoor Air of Cultivation Houses Used for Oak Wood Mushroom Production Using Sawdust Media

Some species of the Trichoderma genus are reported as the major problem in oak wood mushroom production in Korea. In spite of economic loss by the fungi, scientific information on airborne Trichoderma species is not much available. To generate information for disease management development we analyzed airborne Trichoderma. A total of 1,063 fungal isolates were purely obtained from indoor air sampling of cultivation houses used for oak wood mushroom using sawdust media. Among the obtained isolates, 248 isolates were identified as Trichoderma fungi including T. harzianum, T. atroviride, T. citrinoviride, and T. pseudokoningii, by morphological and molecular analysis. T. harzianum was dominant among the four identified species. All the four Trichoderma species grew fast on solid nutrient media tested (potato dextrose agar [PDA], malt extract agar [MEA], Czapek’s Dox + yeast extract agar [CYA] and cornmeal dextrose agar). Compact mycelia growth and mass spore production were better on PDA and CYA. In addition, T. harzianum and T. citrinoviride formed greenish and yellowish mycelium and spores on PDA and CYA. Greenish and yellowish pigment was saturated into PDA only by T. pseudokoningii. These four Trichoderma species could produce extracellular enzymes of sawdust substrate degradation such as β-glucosidase, avicelase, CM-cellulase, amylase, pectinase, xylanase, and protease. Their mycelia inhibited the growth of oak wood mushroom mycelia of two tested cultivars on dual culture assay. Among of eleven antifungal agents tested, benomyl was the best to inhibit the growth of the four Trichoderma species. Our results demonstrate that the airborne Trichoderma fungi need to be properly managed in the cultivation houses for safe mushroom production.
To the Editor

We have recently put forward a hypothesis, based on complement activation, as to how Creutzfeldt-Jakob disease, and related prion disorders, can become rapidly progressive encephalopathies (Oken and McGeer, 1995). The hypothesis does not bear on how the transmissible agent is initially acquired. Several accidental methods for transmitting the agent have been identified, including re-use of formalintreated brain electrodes (Gibbs et al., 1994), transplantation of affected corneal (Bernoulli et al., 1977) and dura mater tissue (Nisbett et al., 1989), and injection of growth hormone from human pituitary extracts (Rappaport, 1987). This letter is to draw attention to the possibility that contaminated surgical instruments, including dental drills, might be yet another accidental method of transmission, since animals receiving intracerebral injections of blood or urine from afflicted patients developed the disease (Manuelidis et al., 1985; Tateishi, 1985). As with all spongiform encephalopathies, CreutzfeldtJakob is a rare disorder, occurring at a rate of about 1 per million population per year. However, the transmissible agent may be much more prevalent than these figures would suggest. Manuelidis and Manuelidis (1993) injected buffy coat homogenates from non-demented volunteers directly into the brains of recipient hamsters. In 26 out of 30 cases, Creutzfeldt-Jakob-like spongiform changes were observed in the hamster brains from 200 to 500 days post-inoculation. The implication is that these 26 cases were asymptomatic carriers of the transmissible agent and that such carriers may be more common than previously suggested. Given such evidence, it might be prudent to emphasize the desirability of using sterilization procedures known to decontaminate instruments from this as-yet-unidentified agent. Treatment with formalin, alcohol, or autoclaving at 121°C for 30 minutes will not suffice (Steelman, 1994). Autoclaving at 132°C for 30 minutes is reported to be effective (Taguchi et al., 1991). Manuelidis et al. (1995) have recently reported that the titer of infectious material can be reduced more than 99.5% by solubilization with 2.5 M guanidine hydrochloride. Such a treatment prior to routine autoclaving would be an extremely simple procedure, which would be non-corrosive to instruments, and would require no special protection of personnel. The transmissible agent in Creutzfeldt-Jakob disease is still controversial. One theory holds that it is an infectious prion protein (Prusiner and DeArmond, 1994), while another is that it is an unusual virus (Manuelidis et al., 1995). From a practical point of view, the important objective is to reduce transmissions by all possible means. -Robert J. Oken, MD P.O. Box 412 Hopatcong, NJ 07843
California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.
Mapping of a Novel H3-Specific Broadly Neutralizing Monoclonal Antibody Targeting the Hemagglutinin Globular Head Isolated from an Elite Influenza Virus-Immunized Donor Exhibiting Serological Breadth

Influenza viruses escape immunity through continuous antigenic changes that occur predominantly on the viral hemagglutinin (HA). Induction of broadly neutralizing antibodies (bnAbs) targeting conserved epitopes following vaccination is a goal of universal influenza vaccines and advantageous in protecting hosts against virus evolution and antigenic drift. To date, most of the discovered bnAbs bind either to conserved sites in the stem region or to the sialic acid-binding pocket. Generally, antibodies targeting the stem region offer broader breadth with low potency, while antibodies targeting the sialic acid-binding pocket cover narrower breadth but usually have higher potency. In this study, we identified a novel neutralizing epitope in the head region recognized by a broadly neutralizing human antibody against a broad range of H3N2 with high potency. This epitope may provide insights for future universal vaccine design. ABSTRACT The discovery of potent and broadly protective influenza virus epitopes could lead to improved vaccines that are resistant to antigenic drift. Here, we describe human antibody C585, isolated from a vaccinee with remarkable serological breadth as measured by hemagglutinin inhibition (HAI). C585 binds and neutralizes multiple H3N2 strains isolated between 1968 and 2016, including strains that emerged up to 4 years after B cells were isolated from the vaccinated donor. The crystal structure of C585 Fab in complex with the HA from A/Switzerland/9715293/2013 (H3N2) shows that the antibody binds to a novel and well-conserved epitope on the globular head of H3 HA and that it differs from other antibodies not only in its epitope but in its binding geometry and hypermutated framework 3 region, thereby explaining its breadth and ability to mediate hemagglutination inhibition across decades of H3N2 strains. The existence of epitopes such as the one elucidated by C585 has implications for rational vaccine design. IMPORTANCE Influenza viruses escape immunity through continuous antigenic changes that occur predominantly on the viral hemagglutinin (HA). Induction of broadly neutralizing antibodies (bnAbs) targeting conserved epitopes following vaccination is a goal of universal influenza vaccines and advantageous in protecting hosts against virus evolution and antigenic drift. To date, most of the discovered bnAbs bind either to conserved sites in the stem region or to the sialic acid-binding pocket. Generally, antibodies targeting the stem region offer broader breadth with low potency, while antibodies targeting the sialic acid-binding pocket cover narrower breadth but usually have higher potency. In this study, we identified a novel neutralizing epitope in the head region recognized by a broadly neutralizing human antibody against a broad range of H3N2 with high potency. This epitope may provide insights for future universal vaccine design.
Gastrointestinal Adverse Events of Cannabinoid 1 Receptor Inverse Agonists suggest their Potential Use in Irritable Bowel Syndrome with Constipation: A Systematic Review and Meta-Analysis.

BACKGROUND AND AIMS Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal (GI) disorders characterized by pain and impaired bowel movements. Currently available drugs show limited efficacy. Cannabinoid 1 receptor (CB1) inverse agonists (CB1-RAN) cause diarrhea and may be candidates for the treatment of constipation-predominant IBS (IBS-C). We evaluated the effects of CB1-RAN in clinical trials for their potential use in IBS-C. METHODS Database search identified all clinical trials published up to May 2018 that reported rimonabant and taranabant treatment for at least one month and detailed the GI adverse events (AEs). Categorical outcomes (subgroups of AEs) were analyzed using the odds ratio (OR). RESULTS Eighteen trials met the inclusion criteria. Rimonabant 20 mg produced significantly more overall AEs (OR=1.35, CI: 1.19-1.52, p<0.0001), psychiatric events (OR=1.79, CI: 1.46-2.21, p<0.001) and GI AEs (OR=2.05, CI: 1.65-2.55, p<0.001) compared to placebo. Taranabant at doses ranging from 0.5 to 8 mg produced significantly more overall AEs (OR=1.36, CI: 1.13-1.64, p<0.002), psychiatric AEs (1.82, CI: 1.54-2.16, p<0.001) and GI AEs (OR=1.75, CI: 1.29-2.37, p<0.001) compared to placebo. CONCLUSIONS The approach to target CB1 in the gut for the treatment of IBS-C or chronic constipation seems a promising therapeutic option. Prospective clinical trials on the possible targeting of CB1 and the endocannabinoid system are warranted.
Thyroid-disrupting effects of chlorpyrifos in female Wistar rats

Abstract Thousands of chemicals are released into the environment daily, arousing great scientific interest because they can influence the overall function of living organisms. The indiscriminate use of pesticides, especially organophosphate, confers important risks to both public and environmental health. Previous studies showed that chlorpyrifos (CPF) acts as an endocrine disruptor. Nevertheless, CPF is still widely used in many countries. Thus, we evaluated the thyroid-disrupting effects of CPF after short-term low-dose oral exposure in female Wistar rats. A total of 48 female Wistar rats were divided into five experimental groups (n = 8/group) that were treated orally by gavage with vehicle (control) and chlorpyrifos (0.01, 0.1, 1, and 10 mg/kg) for 5 days. Clinical signs of toxicity were observed throughout treatment. On day 6, the animals were weighed. Serum samples were obtained to measure levels of thyroid hormones, alanine aminotransferase, aspartate aminotransferase, bilirubin, glutamyl transpeptidase, and estradiol. The animals were then euthanized by deep anesthesia with isoflurane. The thyroid gland, liver, spleen, and kidneys were collected to determine relative organ weight and perform histopathological analyses. We observed a significant increase in total triiodothyronine (T3) levels in all CPF treatment groups, even at very low doses that corresponded to the Acceptable Daily Intake. Only the highest dose tested significantly increased both total and free T3 levels. In the group that received the highest dose of CPF, thyroid follicles had irregular contours and few or no colloids. The present results indicated that short-term low-dose CPF exposure in female rats induced significant thyroid-disrupting effects.
Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation

Abstract Advances in chromosome conformation capture techniques as well as computational characterization of genomic loci structural dynamics open new opportunities for exploring the mechanistic aspects of genome-scale differences across different cell types. We examined here the dynamic basis of variabilities between different cell types by investigating their chromatin mobility profiles inferred from Hi-C data using an elastic network model representation of the chromatin. Our comparative analysis of sixteen cell lines reveals close similarities between chromosomal dynamics across different cell lines on a global scale, but notable cell-specific variations emerge in the detailed spatial mobilities of genomic loci. Closer examination reveals that the differences in spatial dynamics mainly originate from the difference in the frequencies of their intrinsically accessible modes of motion. Thus, even though the chromosomes of different types of cells have access to similar modes of collective movements, not all modes are deployed by all cells, such that the effective mobilities and cross-correlations of genomic loci are cell-type-specific. Comparison with RNA-seq expression data reveals a strong overlap between highly expressed genes and those distinguished by high mobilities in the present study, in support of the role of the intrinsic spatial dynamics of chromatin as a determinant of cell differentiation.
Influence of the grip width on the reliability and magnitude of different velocity variables during the bench press exercise

Abstract This study aimed to compare the within-session reliability and magnitude of velocity variables recorded against a range of submaximal loads during the bench press (BP) exercise performed in a Smith machine using different grip widths. Sixteen physically active men (BP one-repetition maximum [1RM] relative to body mass = 1.01 ± 0.19 kg·kg−1) were randomly tested on 4 sessions using a close grip width (100% of biacromial width), medium grip width (150% of biacromial width), wide grip width (200% of biacromial width), and self-selected grip width (176 ± 17% of biacromial width). Mean velocity (MV), maximum velocity (Vmax), and vertical displacement were recorded with a linear velocity transducer against the 35%1RM, 55%1RM, and 75%1RM. The main findings revealed that (I) the self-selected was the only grip width with an acceptable reliability for all loads and velocity variables (CV ≤ 7.56%; ICC ≥ 0.82), (II) the medium grip width provided the highest reliability for MV (CV ratio ≥ 1.20), while a comparable reliability was observed for Vmax using the close, medium and self-selected grip widths (CV ratio ≤ 1.08), (III) the Vmax showed the highest reliability for all grip widths (CV ratio = 1.68), and (IV) the MV and vertical displacement of the barbell were generally higher for narrow grip widths (close and medium) compared to the wide and self-selected grip widths, while no significant differences between the grip widths were observed for Vmax (p > .05). Taken together, we recommend the assessment of Vmax using a self-selected grip width during the routine testing of BP performance against submaximal loads.
Salt intake assessed by spot urine on physical examination in Hunan, China.

BACKGROUND AND OBJECTIVES Excessive salt intake is a major public health problem in several countries, especially in China. However, few people are aware of their salt intake. The purpose of this study is to carry out salt intake test in routine physical examination, and to explore the salt intake of different populations and their correlation with diet. METHODS AND STUDY DESIGN Spot urine sample was collected to test urinary sodium and creatinine excretions for each participant recruited from physical examinations at the Third Xiangya Hospital. The Tanaka formula was used to estimate 24-h urinary sodium excretion, which reflects salt intake. In addition to physical and laboratory examination, information including personal details, health-related habits, and selfreported disease histories was obtained from the National Physical Examination Questionnaire. RESULTS In total, 26,406 people completed the salt intake evaluation. After data cleansing, the average salt intake was 8.39±1.80 g/d. Male, middle-aged, overweight and obese, hypertensive, and dyslipidaemic populations, as well as those with non-cardiovascular diseases were more likely to have excessive salt intake. Dietary sources had an effect on salt intake. Salt intake was lower in those who consumed more milk and fruit (both p and p trend<0.01) but was higher in those who consumed more lean meat (both p and p trend<0.05), fatty meat (both p and p trend<0.01) and animal organs (both p and p trend<0.01). CONCLUSIONS The salt intake in this population far surpasses the recommended amount. We strongly recommend salt intake assessment as routine test into physical examination center.
Clinical Application of Next-Generation Sequencing–Based Panel to BRAF Wild-Type Advanced Melanoma Identifies Key Oncogenic Alterations and Therapeutic Strategies

Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid cancers to discover potential therapeutic targets. Here, we describe the results of a clinical NGS panel in patients with advanced melanoma. Thirty-six tumor tissues from patients with BRAF wild-type melanoma at Seoul National University Hospital (SNUH; Seoul, Republic of Korea) were collected and deep-sequenced using the SNUH FIRST-Cancer NGS panel to assess single-nucleotide variants, small insertions/deletions, copy number variations, and structural variations to estimate tumor mutation burden (TMB). We discovered 106 oncogenic alterations and most of the patients (n = 33, 92%) harbored at least one oncogenic alteration, including 2 patients who were initially diagnosed as BRAF V600E–negative but were later confirmed to be positive. Altogether, 36 samples were classified into RAS/BRAF/NF1–mutant (n = 14, 39%) or triple wild-type (n = 22, 61%) melanoma subtypes. The estimated median TMB was 8.2 mutations per Mb, ranging from 0 to 146.67 mutations per Mb. Of the 36 patients, 25 (70%) had actionable alterations with currently developed drugs, and 7 (19.4%) were enrolled in clinical trials with an RAF inhibitor, multiple receptor tyrosine kinase inhibitor, and anti-programmed cell death-1 (PD-1) antibody. TMB tended to associate with progression-free survival (PFS) of treatment with anti-PD-1/PDL-1 antibody (HR, 0.96; 95% confidence interval, 0.92–1.00; P = 0.07). High-TMB (≥13) group was associated with longer PFS than the low-TMB group (median 34.0 vs. 11.0 weeks, P = 0.04). Overall, the clinical use of a NGS panel in patients with advanced melanoma shows association with clinical outcomes and several therapeutic strategies.
Recent 5-Year Trend of Endoscopic Retrograde Cholangiography in Korea Using National Health Insurance Review and Assessment Service Open Data

Background/Aims The utilization of endoscopic retrograde cholangiopancreatography (ERCP) is variable and largely dependent on a patient’s age, sex, and region. Herein we analyzed the publicly available Health Insurance Review and Assessment (HIRA) database with the aim of understanding the current status and trend of ERCP use in Korea. Methods Between 2013 and 2017, information regarding ERCP was acquired from the HIRA database using the procedural codes of the Korean Standard Classification of Disease. We analyzed the annual number of patients according to age in 10-year increments, sex, type of medical institution, and administrative division. Results The total number of patients and number of patients undergoing ERCP per 100,000 people increased from 40,516 and 78.6 in 2013 to 47,027 and 91.3 in 2017, respectively those aged 70 years accounted for the highest number, and the increase was the most prominent in those aged 80 years or older. Men underwent more ERCPs than women, except in younger patients (<40 years). Most ERCPs were performed at tertiary and general hospitals; however, the ratios between the two types of institutions were different according to the procedure. There were different patterns of patients associated with each procedure according to the administrative division. Therapeutic ERCP was performed more frequently than diagnostic ERCP. Conclusions Most procedures in Korea were therapeutic, and the increase in patients was most prominent in those aged 80 years or older. The utilization of ERCP increased markedly and varied depending on age, sex, type of medical institution, and region.
Health-related quality of life of adolescents with type 1 diabetes mellitus

Objective: To evaluate the health-related quality of life of adolescents with type 1 diabetes mellitus, associating it with socio-demographic, clinical and biochemical variables. Method: Cross-sectional study with 92 adolescents with type 1 diabetes mellitus. A form containing socio-demographic, clinical and biochemical variables was used, as well as the Diabetes Quality of Life for Youths questionnaire. Descriptive statistics and logistic regression were used for analysis. Results: Regarding socio-demographic variables, economic class showed statistically significant differences in relation to total Health Related Quality of Life (p-value =0.02) and the impact domain (p-value =0.009). However, the impact domain was more compromised. Diabetes-related complications (p-value =0.004), number of hospitalizations (p-value =0.01), number of daily insulin injections (p-value =0.02), glycated hemoglobin (p-value =0.002) and triglycerides (p-value =0.03) were associated with greater impairment of quality of life related to total health and greater dissatisfaction. Conclusion: Single male adolescents with lower level of education and high glycated hemoglobin levels were more likely to have lower health-related quality of life.