Miracle-dz/UniFAR-FTUs huggingface dataset:
The association between consuming bivalves, and acute gastroenteritis and norovirus in Tokyo, Japan

A prospective matched case‐control study was conducted to evaluate associations between dietary histories, including consumption of bivalves, diarrhea, and norovirus positive diarrhea in adult ambulatory patients at an outpatient clinic of a hospital in Tokyo, Japan. Ambulatory cases with diarrhea were matched with nondiarrheal control patients, who visited the same clinic. A standardized questionnaire was used to obtain patients’ information, including histories of food consumption and clinical information. Norovirus infection was confirmed using real‐time reverse transcription polymerase chain reaction. A total of 207 patients, including 69 diarrheal cases and 138 nondiarrheal cases were included in the analysis. Among them, 60 (29.0%) participants reported consuming bivalves. Norovirus was detected in 35% (24/69) of diarrheal cases. Of those, 10 (41.7%) reported consumption of bivalves and of those, 6 (60.0%) consumed raw bivalves. The proportion of those who consumed raw bivalves was significantly higher in norovirus‐positive diarrheal cases than in norovirus‐negative diarrheal cases (25.0% vs 6.7%; odds ratio [OR], 4.67; 95% confidence interval [CI], 1.1‐20.7) and matched nondiarrheal controls (25.0% vs 6.3%, OR: 5.00; 95% CI, 1.1‐22.2). The attributable fraction of consuming raw bivalves for norovirus‐associated diarrhea to matched nondiarrheal controls was 20.0%. Consuming raw bivalves was substantially attributed to norovirus‐associated diarrhea in adult ambulatory patients and preventive measures for reducing the risk associated with consumption of raw bivalves could decrease the incidence of norovirus‐associated diarrhea.
Targeting CD74 in multiple myeloma with the novel, site-specific antibody-drug conjugate STRO-001

STRO-001 is a site-specific, predominantly single-species, fully human, aglycosylated anti-CD74 antibody-drug conjugate incorporating a non-cleavable linker-maytansinoid warhead with a drug-antibody ratio of 2 which was produced by a novel cell-free antibody synthesis platform. We examined the potential pharmacodynamics and anti-tumor effects of STRO-001 in multiple myeloma (MM). CD74 expression was assessed in MM cell lines and primary bone marrow (BM) MM biopsies. CD74 mRNA was detectable in CD138+ enriched plasma cells from 100% (892/892) of patients with newly diagnosed MM. Immunohistochemistry confirmed CD74 expression in 35/36 BM biopsies from patients with newly diagnosed and relapsed/refractory MM. Cytotoxicity assays demonstrated nanomolar STRO-001 potency in 4/6 MM cell lines. In ARP-1 and MM.1S tumor-bearing mice, repeat STRO-001 dosing provided significant antitumor activity with eradication of malignant hCD138+ BM plasma cells and prolonged survival. In a luciferase-expressing MM.1S xenograft model, dose-dependent STRO-001 efficacy was confirmed using bioluminescent imaging and BM tumor burden quantification. Consistent with the intended pharmacodynamic effect, STRO-001 induced dose-responsive, reversible B-cell and monocyte depletion in cynomolgus monkeys, up to a maximum tolerated 10 mg/kg, with no evidence of off-target toxicity. Collectively, these data suggest that STRO-001 is a promising therapeutic agent for the treatment of MM.
Single-Walled Carbon Nanotubes Toxicity to the Freshwater Amphipod Hyalella Azteca: Influence of to the Freshwater Amphipod Sediment and Exposure Duration

Carbon nanomaterials are present in various industrial applications and therefore their release into the environment including freshwater ecosystem is expected to increase. The aim of the present study was to investigate the influence of several parameters on the toxicity of single-walled carbon nanotubes (SWCNT) to the freshwater amphipod, Hyalella azteca. The effect of period of exposure, sediment presence and possible impurities released during SWCNT preparation on survival and/or growth of such organism was evaluated. We measured a reduction of survival at concentrations ranging from 10 to 40 mg/L after 96-h exposure, while no mortality was observed with the same concentrations and in the presence of artificial sediment after 14 days of exposure. It is possible that SWCNT are adsorbed on the organic matter from the artificial sediment leading to a decrease of SWCNT bioavailability. The survival and growth toxicity tests revealed a stronger effect at 28 days compared to the 14 days of exposure, and full mortality of organisms at 1000 mg/L for both exposure times. The presence of SWCNT in the gut of survived organisms was observed. The present study demonstrates that the interaction with sediment should be considered when carbon nanotubes toxicity through water exposure is investigated.
Complete Genome Sequence of Mycolicibacterium hassiacum DSM 44199

Mycolicibacterium hassiacum is the most thermophilic of all the mycobacteria. A partial sequence based on Illumina technology of around 5 Mbp was published in 2012. ABSTRACT Mycolicibacterium hassiacum is the most thermophilic of all the mycobacteria. A partial sequence based on Illumina technology of around 5 Mbp was published in 2012. Here, we report the 5,269,097-bp complete genome sequence assembled into a single circular chromosome.
Adenoma and advanced neoplasia detection rates increase from 45 years of age

BACKGROUND Colonoscopy is considered a valid primary screening tool for colorectal cancer (CRC). The decreasing risk of CRC observed in patients undergoing colonoscopy is correlated with the adenoma detection rate (ADR). Due to the fact that screening programs usually start from the age of 50, very few data are available on the risk of adenoma between 40 and 49 years. However, the incidence of CRC is increasing in young populations and it is not uncommon in routine practice to detect adenomas or even advanced neoplasia during colonoscopy in patients under 50 years. AIM To compare the ADR and advanced neoplasia detection rate (ANDR) according to age in a large series of patients during routine colonoscopy. METHODS All consecutive patients who were scheduled for colonoscopy were included. Exclusion criteria were as follows: patients scheduled for partial colonoscopy or interventional colonoscopy (for stent insertion or stenosis dilation). Colonoscopies were performed in our unit by a team of 30 gastroenterologists in 2016. We determined the ADR and ANDR in each age group in the whole population and in the population with an average risk of CRC (excluding patients with personal or family history of advanced adenoma or cancer). RESULTS 6027 colonoscopies were performed in patients with a median age of 57 years (range, 15-96). The ADR and ANDR were 28.6% and 9.7%, respectively, in the whole population. When comparing patients aged 40-44 (n = 382) and 45-49 years (n = 515), a strong increase in all parameters from 45 years was observed, with the ADR rising from 9.7% in patients aged 40-44 to 21.2% between 45 and 49 (P < 0.001) and the ANDR increasing from 3.1% in patients aged 40-44 to 6.4% in those aged 45-49 years (P < 0.03). With regard to patients aged 50-54 (n = 849), a statistically significant increase in the ADR and ANDR was not observed between patients aged 45-49 and those aged 50-54 years. In the population with an average risk of CRC, the ADR and ANDR were still significantly higher in patients aged 45-49 compared with those aged 40-44 years. CONCLUSION This study shows a significant two-fold increase in the ADR and ANDR in patients aged 45 years and over.
Demographic, Life Style and Job-Related Determinants of Quality of Life of Industrial Manufacturing Employees: An Application of Multilevel Latent Class Regression on a Large Cross-Sectional Study

Background Employees are one of the key elements of an organization and measure the quality of life (QoL) provides reliable assessment of health and wellbeing in this population. This study aimed at investigating the QoL in a large sample of Iranian industrial manufacturing employees and its determinants. Methods In a cross-sectional study conducted was in 2015, 3063 people were selected among 16000 Esfahan Seal Company's employees using multistage cluster sampling. QoL was evaluated by EQ-5D questionnaire, mental health by GHQ-12, physical activity by IPAQ, job stress by Effort-Reward Imbalance questionnaire. Self-report questionnaire was used for gathering demographic characteristics. Multilevel latent class regression analysis was used for data analysis using R (3.4.3). Results The mean (SD) age of the study participants was 36.74 (7.31), and 91.5% of them were males. The mean (SD) sleep duration was 7.11 (1.17), and 95.4% of the participants had normal mental health. Latent class analysis classified employees into two classes (high (82.4%) and low QoL (17.6%)). Also employees' job categories classified into high and low QoL classes (79.55% and 20.45%, respectively). Latent class regression showed that lower age (OR=0.93; P< 0.0001), being male (OR=1.75; p=0.009), lower levels of education (OR=2.1; P< 0.0001), normal mental health (OR=12.4; P< 0.0001), higher sleep duration (OR=1.2; P< 0.0001) and lower BMI (OR=0.96; P=0.016) were significant predictors of being in high QoL class. Conclusion Our study provides data about the QoL of industrial manufacturing employees along with its significant determinants. The findings picture the ways for improving QoL, finally increasing the efficiency and productivity of workforce by directing health policies appropriately.
A Significant Expansion of Our Understanding of the Composition of the Human Microbiome

Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. ABSTRACT Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. This is particularly true for non-Western populations and for samples that do not originate from the gut. Pasolli et al. (E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, et al., Cell, 2019, https://doi.org/10.1016/j.cell.2019.01.001) perform a grand effort to expand the reference set, and to better classify its members, revealing a wider pangenome of existing species as well as identifying new species of previously unknown taxonomic branches.
The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.
The Local Brain Abnormalities in Patients With Transient Ischemic Attack: A Resting-State fMRI Study

Background: Transient ischemic attack (TIA) is an important risk factor for stroke. Despite the transient episodes of clinical symptoms, brain alterations are still observed in patients with TIA. However, the functional mechanism of transient ischemia is still unclear. Here, we employed resting-state functional magnetic resonance imaging (rs-fMRI) to explore the functional abnormalities in patients with TIA. Methods: 48 TIA patients and 41 age- and sex-matched healthy controls (HCs) were enrolled in the study. For each participant, we collected rs-fMRI data and clinical/physiological/biochemical data. Amplitude of low frequency fluctuation (ALFF), regional homogeneity (ReHo), and degree centrality (DC) were then calculated. Two sample t-tests were performed to compare the ALFF, ReHo, and DC maps between the two groups. Furthermore, a correlation analysis was performed to explore the relationship between local brain abnormalities and clinical/physiological/biochemical characteristics tests in TIA patients. Results: Compared with the HCs, the TIA patients exhibited decreased ALFF in the left middle temporal gyrus, decreased DC in the triangular part of right inferior frontal gyrus, and no significant statistical difference in ReHo. No correlation was found between local abnormalities and clinical/physiological/biochemical scores in the patients with TIA. Conclusion: Collectively, we found decreased ALFF and DC in patients with TIA which provide evidence for local brain dysfunctions and may help to understand the pathological mechanism for the disease.
Editorial: Advances in the Biology and Conservation of Marine Turtles

1 School of Interdisciplinary Arts and Sciences, University of Washington Bothell, Bothell, WA, United States, Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States, Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom, NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA, United States, Marine Science Program, Department of Biodiversity, Conservation and Attractions, Kensington, WA, Australia, Marine Turtle Research, Ecology and Conservation Group, Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, United States, 7 School of Biological Sciences, Monash University, Clayton, VIC, Australia
Humanized Mouse Model Mimicking Pathology of Human Tuberculosis for in vivo Evaluation of Drug Regimens

Human immune system mice are highly valuable for in vivo dissection of human immune responses. Although they were employed for analyzing tuberculosis (TB) disease, there is little data on the spatial organization and cellular composition of human immune cells in TB granuloma pathology in this model. We demonstrate that human immune system mice, generated by transplanted human fetal liver derived hematopoietic stem cells develop a continuum of pulmonary lesions upon Mycobacterium tuberculosis aerosol infection. In particular, caseous necrotic granulomas, which contribute to prolonged TB treatment time, developed, and had cellular phenotypic spatial-organization similar to TB patients. By comparing two recommended drug regimens, we confirmed observations made in clinical settings: Adding Moxifloxacin to a classical chemotherapy regimen had no beneficial effects on bacterial eradication. We consider this model instrumental for deeper understanding of human specific features of TB pathogenesis and of particular value for the pre-clinical drug development pipeline.
Pooled Analysis of Risk Stratification of Spontaneous Type 1 Brugada ECG: Focus on the Influence of Gender and EPS

Aims: Risk stratification of patients with Brugada syndrome (BrS) is vital for accurate prognosis and therapeutic decisions. Spontaneous Type 1 ST segment elevation is generally considered to be an independent risk factor for arrhythmic events. Other risk factors include gender, syncope, sudden cardiac arrest (SCA), and positive electrophysiological study (EPS). However, the further risk stratification of spontaneous type 1 combined with the other risk factors remains unclear. The present study pooled data from 4 large trials aiming to systematically evaluate the risk of spontaneous Type-1 ECG when combined with one or more of these other recognized risk factors. Methods: We searched for related studies published from November 2, 2002 to February 10, 2018 in PubMed, EMBASE, Cochrane Library, MEDLINE, Chinese National Knowledge Infrastructure (CNKI), and Wanfang Databases. The pooled data were evaluated combining each risk factor with the presence of a spontaneous Type-1 ECG. All analyses were performed using Review Manager, version 5.0. 12. Results: Four eligible studies involving 1,338 patients (85% males, mean age: 48.1 ± 18.1 years) were enrolled. Spontaneous Type-1 ECG was associated with higher risk for ventricular tachycardia/fibrillation (VT/VF) than cases with non-Type 1 ECG in males (odds ratio: 95% CI: 1.84–5.17; P < 0.0001), but not in females (P = 0.29). Among spontaneous Type-1 cases with syncope or with positive EPS, the difference was not statistically significant (P = 0.06 and 0.07, respectively). Patients with Type-1 ECGs and positive EPS were at higher risk than those with negative EPS (95% CI: 1.10–5.04; P = 0.03). Pooled analysis showed an association of Spontaneous Type-1 ECG, Type-1 ECGs combined with male, and Type-1 ECGs combined with positive EPS between increased risk of arrhythmic events. Conclusion: Our results indicate that in BrS patients, a spontaneous Type-1 ECG is an independent risk factor for SCD in males, but not in females. A spontaneous Type-1 BrS is associated with a worse prognosis when combined with positive EPS
Vagus Nerve Stimulation for Depression: A Systematic Review

Background: Depression is a common mental disorder worldwide. Psychological treatments and antidepressant medication are the usual treatments for depression. However, a large proportion of patients with depression do not respond to the treatments. In 2005, Vagus nerve stimulation was approved for the adjunctive long-term treatment of chronic or recurrent depression in adult patients experiencing a major depressive episode who had failed to respond to four or more adequate antidepressant treatments. However, the efficacy of VNS for treating depression remains unclear. Accordingly, we performed a systematic review to evaluate the efficacy and safety of VNS. Methods: We conducted a systematic review in accordance with the Cochrane Handbook for Systematic Reviews of Interventions. Systematic search was performed in the database of Pubmed, Embase, CENTRAL, and Web of science for identifying the suitable trials. Suicidal rate was considered as the primary outcome in this review. Result: Only two randomized sham controlled add-on studies including 255 cases (134 with VNS treatment and 121 control cases) were included in this review. None of the studies reported suicidal rate. We performed a qualitative analysis and it is suggested that there was no significant statistic difference between VNS and sham VNS on the score of 24-item Hamilton Rating Scale for Depression (HAMD24) (MD: −2.40, 95% CI: −7.90 to 3.10). Similar findings were also reported on improvement percentage of HAMD24 (MD: 1.00, 95%CI: −6.06 to 8.06), Montgomery-Asberg Depression Rating Scale (MADRS) (MD: 4.70, 95%CI: −2.98 to 12.38) and 30 item Inventory of Depressive Symptomalogy-Self-Report (IDS-SR30) (MD: 4.9, 95%CI: −1.89 to 11.69). However, a marginal difference of Beck Depression Inventory self-rating score was detected between the real and sham treatment (MD: 7.80, 95% CI: 0.34 to 15.26). Aminor effect of IDS-SR30was also found in real VNS group (RR: 2.33, 95% CI: 1.07 to 5.10). Conclusion: The efficacy and safety of VNS for depression is still unclear. Further randomized controlled trials are needed to confirm the efficacy and safety of VNS.
Math Anxiety in Combination With Low Visuospatial Memory Impairs Math Learning in Children

Math anxiety impairs academic achievements in mathematics. According to the processing efficiency theory (PET), the adverse effect is the result of reduced processing capacity in working memory (WM). However, this relationship has been examined mostly with correlational designs. Therefore, using an intervention paradigm, we examined the effects of math anxiety on math learning. Twenty-five 5th graders underwent seven training sessions of multiplication over the course of 2 weeks. Children were faster and made fewer errors in solving trained problems than untrained problems after learning. By testing the relationship between math anxiety, WM, and math learning, we found that if children have little or no math anxiety, enough WM resources are left for math learning, so learning is not impeded. If they have high math anxiety and high visuospatial WM, some WM resources are needed to deal with math anxiety but learning is still supported. However, if they have high math anxiety and low visuospatial WM capacity, math learning is significantly impaired. These children have less capacity to learn new math content as cognitive resources are diverted to deal with their math anxiety. We conclude that math anxiety not only hinders children’s performance in the present but potentially has long-lasting consequences, because it impairs not only math performance but also math learning. This intervention study partially supports the PET because only the combination of high math anxiety and low WM capacity seems critical for hindering math learning. Moreover, an adverse effect of math anxiety was observed on performance effectiveness (response accuracy) but not processing efficiency (response time).
Multigrid Backprojection Super-Resolution and Deep Filter Visualization

We introduce a novel deep–learning architecture for image upscaling by large factors (e.g. 4×, 8×) based on examples of pristine high–resolution images. Our target is to reconstruct high–resolution images from their downscale versions. The proposed system performs a multi–level progressive upscaling, starting from small factors (2×) and updating for higher factors (4× and 8×). The system is recursive as it repeats the same procedure at each level. It is also residual since we use the network to update the outputs of a classic upscaler. The network residuals are improved by Iterative Back–Projections (IBP) computed in the features of a convolutional network. To work in multiple levels we extend the standard back– projection algorithm using a recursion analogous to Multi– Grid algorithms commonly used as solvers of large systems of linear equations. We finally show how the network can be interpreted as a standard upsampling–and–filter upscaler with a space–variant filter that adapts to the geometry. This approach allows us to visualize how the network learns to upscale. Finally, our system reaches state of the art quality for models with relatively few number of parameters.