Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial inactivation using pulsed light

Pulsed light is a new method intended for the decontamination of food surfaces using short, high frequency pulses of an intense broad spectrum. The effects of broad spectrum pulsed light on the survival of Listeria monocytogenes Scott A, Listeria monocytogenes CNL, Pseudomonas fluorescens MF37 and Photobacterium phosphoreum SF680 populations on agar and in a liquid medium were investigated during this study. The sterilisation system generated 1.5 J cm –2 per pulse with eight lamps for 300 µs. In the case of surface-seeded cells, a 7.8, 8.14 and >7.14 log reduction was obtained for L. monocytogenes, Ps. fluorescens MF37 and Ph. phosphoreum, respectively, after a single pulse of treatment. Inactivation levels were lower for depth-plated cells: indeed, 10 pulses of treatment achieved 1.6, 2.03 and 4.78 log reductions for L. monocytogenes ScottA, L. monocytogenes CNL and Ps. fluorescens MF37, respectively. After 5 pulses, Ph. phosphoreum exhibited a 4.6 log reduction. Similarly, bacterial cells in suspension treated with 3 pulses were reduced by 0.52, 0.8, 2.07 and 2.05 for L. monocytogenes ScottA, L. monocytogenes CNL, Ps. fluorescens MF37 and Ph. phosphoreum, respectively. No resistance to pulsed light was observed during our experiments.
Trainability of Health-Related and Motor Performance Fitness in Adults with Cystic Fibrosis within a 12-Month Partially Supervised Exercise Program

Background Regular physical activity plays an important role in the treatment of patients with cystic fibrosis (CF). This study is aimed at investigating the effects of a 12-month partially supervised exercise program on attributes of health-related and motor performance fitness, lung function (ppFEV1), BMI, and habitual physical activity (HPA, steps/day) in adults with CF. Methods Attributes of health-related and motor performance fitness were examined at the beginning (T0), after 6 (T1), and 12 months (T2) on the basis of five test items: forward bend (FB), bent knee hip extension (HE), plank leg raise (PLR), standing long jump (SLJ), and standing on one leg (OLS). Additionally, we recorded HPA by accelerometry, peak exercise performance (Wpeak) by an incremental cycle test, ppFEV1, and BMI. During the first six months, there was close supervision by an experienced sport therapist. Results 26 CF patients (8 female, mean age 26.5 ± 7.9 years; ppFEV1 53.7 ± 21.0) completed the exercise program. Significant improvements were recorded from T0 to T1 (FB: p ≤ 0.05; PLR, OLS: p ≤ 0.01) and from T0 to T2 (FB, PLR: p ≤ 0.01 and HE, OLS: p ≤ 0.05). Wpeak, ppFEV1, BMI, and HPA showed no significant improvement between the single test points and over the entire study period (all p > 0.05). Conclusion Our results show trainability of adults with CF in aspects of health-related and motor performance fitness during a partially supervised exercise program. Close supervision positively influences the results. Using a simple test setup seems to be a promising tool for evaluating the effects of exercise programs in CF and could serve as an additional outcome parameter in future clinical trials. Trial registration: ClinicalTrials.gov (retrospectively registered May 8, 2018).
Risk factors for SARS-CoV-2 infection and course of COVID-19 disease in patients with IBD in the Veterans Affair Healthcare System

Objective Our aim was to explore the risk of infection with all classes of inflammatory bowel disease (IBD) medications and the impact of these medications on the disease course in a nationwide cohort of patients with IBD. Design This was a retrospective national cohort study of patients with IBD in the Veterans Affairs Healthcare System. We categorised IBD medication use immediately prior to the COVID-19 pandemic and used survival analysis methods to study associations with SARS-CoV-2 infection, as well as a combined secondary outcome of COVID-19 hospitalisation or COVID-19-related mortality. Results The analytical cohort of 30 911 patients was primarily male (90.9%), white (78.6%) and with ulcerative colitis (58.8%). Over a median follow-up of 10.7 months, 649 patients (2.1%) were diagnosed with SARS-CoV-2 infection and 149 (0.5%) met the combined secondary outcome. In adjusted models, vedolizumab (VDZ) use was significantly associated with infection relative to mesalazine alone (HR 1.70, 95% CI 1.16 to 2.48, p=0.006). Patients on no IBD medications had increased risk of the combined secondary outcome relative to mesalazine alone (sub-HR 1.64, 95% CI 1.12 to 2.42, p=0.01), however, no other IBD medication categories were significantly associated with this outcome, relative to mesalazine alone (each p>0.05). Corticosteroid use was independently associated with both SARS-CoV-2 infection (HR 1.60, 95% CI 1.23 to 2.09, p=0.001) and the combined secondary outcome (sub-HR 1.90, 95% CI 1.14 to 3.17, p=0.01). Conclusion VDZ and corticosteroid were associated with an increased risk of SARS-CoV-2 infection. Except for corticosteroids no medications including mesalazine were associated with an increased risk of severe COVID-19.
Energy Steepened States of the Taylor-Culick Profile

The Taylor-Culick solution for a porous cylinder has long been used to describe the bulk gas motion in idealized representations of solid rocket motors. By superimposing an arbitrary headwall injection velocity, a modified form of this solution can be extended to hybrid rocket applications and to solids with reactive headwall. However, the Taylor-Culick solution appears not to be unique for a prescribed set of boundary conditions. Other solutions may be found that satisfy the same fundamental constraints. As alluded to in the literature, steeper or smoother profiles can be observed in both experimental and numerical tests, particularly in the presence of intense levels of acoustic energy. In this study, we present the system of equations that leads to multiple solutions. We then search for the extreme states that require the least or the most kinetic energy. These solutions are derived and found to be dependent on the chamber aspect ratio and the headwall injection profile. They are evaluated for several baseline cases and compared to numerical simulations. By assuming a sufficiently large aspect ratio, simple expressions are obtained over a finite range of kinetic energies. Some exhibit steep, turbulent-like features that confirm the experimental and numerical findings by CSAR, ATK Thiokol, and ONERA investigators who have often reported steeper profiles than predicted by Taylor-Culick’s basic cold flow model. The solutions presented here are quasi-viscous, specifically in their ability to secure the no slip condition at the sidewall. They are evaluated for several headwall injection patterns and cataloged based on their kinetic energies. In practice, the steepening/dampening process can be sustained through acoustic energy buildup and release, a common occurrence in rocket chambers. In this vein, the advent of energysensitive mean flow solutions enables us to conceptualize a two-way coupling theory connecting the mean flow to the unsteady wave motion.
Sensorimotor predictions shape reported conscious visual experience in a breaking continuous flash suppression task

Abstract Accounts of predictive processing propose that conscious experience is influenced not only by passive predictions about the world, but also by predictions encompassing how the world changes in relation to our actions—that is, on predictions about sensorimotor contingencies. We tested whether valid sensorimotor predictions, in particular learned associations between stimuli and actions, shape reports about conscious visual experience. Two experiments used instrumental conditioning to build sensorimotor predictions linking different stimuli with distinct actions. Conditioning was followed by a breaking continuous flash suppression task, measuring the speed of reported breakthrough for different pairings between the stimuli and prepared actions, comparing those congruent and incongruent with the trained sensorimotor predictions. In Experiment 1, counterbalancing of the response actions within the breaking continuous flash suppression task was achieved by repeating the same action within each block but having them differ across the two blocks. Experiment 2 sought to increase the predictive salience of the actions by avoiding the repetition within blocks. In Experiment 1, breakthrough times were numerically shorter for congruent than incongruent pairings, but Bayesian analysis supported the null hypothesis of no influence from the sensorimotor predictions. In Experiment 2, reported conscious perception was significantly faster for congruent than for incongruent pairings. A meta-analytic Bayes factor combining the two experiments confirmed this effect. Altogether, we provide evidence for a key implication of the action-oriented predictive processing approach to conscious perception, namely that sensorimotor predictions shape our conscious experience of the world.
Complete mitochondrial genome of the H3 haplotype Argentine ant Linepithema humile (Mayr, 1868) (Formicidae; Hymenoptera)

Abstract The argentine ant, Linepithema humile (Mayr, 1867), is an invasive ant species that has spread across the world. We have determined the mitochondrial genome of L. humile collected in South Korea, which is 15,934 bp containing 10 SNPs and 5 INDELs compared to the previous mitogenome. Most SNPs were found in cox3, followed by cytb. From SNPs our mitogenome was identified as a H3 haplotype, which was previously recorded in Japan and the U.S. while the previous mitogenome was H1 haplotype. Phylogenetic analysis was congruent to previous study within the tribe Leptomyrmecini but not between other tribes of subfamily Dolichoderinae.
Lack of Synergy Between β-Agonist Treatment and a Blockage of Sarcoplasmic Calcium Flow in a Rat Cancer Cachexia Model

Background During cancer cachexia, both skeletal muscle and adipose tissue losses take place. The use of β2-agonists, formoterol in particular, has proven to be very successful in the treatment of the syndrome in pre-clinical models. The object of the present research was to study the effects of a combination of formoterol and dantrolene, an inhibitor of the ryanodine receptor 1 (RyR1), on body weight loss and cachexia in tumour-bearing animals. Methods Rats were separated into two groups: controls (C) and tumour bearing (TB). TB group was further subdivided into four groups: untreated (saline as a vehicle), treated with Formoterol (TF) (0,3 mg/kg body weight in saline, subcutaneous (s.c.), daily), treated with Dantrolene (TD) (5 mg/kg body weight in saline, subcutaneous (s.c.), daily), and double-treated treated (TFD) with Formoterol (0,3 mg/kg body weight, subcutaneous (s.c.), daily) and Dantrolene (5 mg/kg body weight, subcutaneous (s.c.), daily). 7 days after tumour transplantation, muscle weight, grip force, and total physical activity were specified in all experimental groups. Results While formoterol had, as in previous studies, a very positive effect in reducing muscle weight loss, dantrolene had no effects, neither on skeletal muscle nor on any of the parameters studied. Finally, the combined treatment (formoterol and dantrolene) did not result in any significant benefit on the action of the β2-agonist. Conclusion It is concluded that, in the preclinical cachectic model used, no synergy exists between β2-agonist treatment and the blockade of sarcoplasmic-calcium flow.
PARTICLE CHARACTERIZATION FOR OIL SAND PROCESSING 2: PARTICLE SIZE MEASUREMENTS BY LASER DIFFRACTION

ABSTRACT Particle size measurements of oil sands solids by laser diffraction are reviewed together with the process used at Syncrude to replace old laser diffraction instruments with current ones. The new instrument has a much broader measurement range and by accounting for fine particles (smaller than 1 μm) it addresses a major limitation of earlier instruments. Results from both laser diffraction instruments are compared so that new results can be related to our historic database. Results from the new instrument are also compared with those from a disc centrifuge and the hydrometer method. It is concluded that the new instrument can be used for samples that were previously analyzed by these other techniques and so is the preferred particle size method for almost all oil sand processing solids.
Chinese Herbal Medicine for Weight Management: A Systematic Review and Meta-Analyses of Randomised Controlled Trials

Objective This review investigated the effects and safety of Chinese herbal medicine (CHM) formulas on weight management. Methods Eighteen databases in English, Chinese, Korean, and Japanese were searched from their inceptions to September 2019. The treatment groups included CHM formulations, and the control included placebo, Western medication (WM), and lifestyle intervention (LI), with or without cointerventions (WM and/or LI). Quality of studies was assessed using Cochrane Collaboration's risk of bias assessment tool. Body weight and body mass index (BMI) were analysed in RevMan v5.4. 1 and expressed as mean differences with 95% confidence intervals (CI), while adverse events were expressed as risk ratio with 95% CI. Results Thirty-nine RCTs were eligible for qualitative analysis, 34 of which were included in the meta-analyses. The majority of studies had a high or unclear risk of selection, performance, and detection bias. Twenty-five CHM studies involving cointerventions revealed that CHM had significant adjunct effects on body weight and BMI at the end of treatment compared to control. No serious adverse events were reported in the CHM groups. Conclusion CHM indicates a promising adjunct to facilitate WM or lifestyle change for weight management. However, methodological barriers such as lack of allocation concealment and double-blinding may have led to challenges in data synthesis. More rigorously designed RCTs involving cointerventions are warranted.
Heparin-binding protein and procalcitonin in the diagnosis of pathogens causing community-acquired pneumonia in adult patients: a retrospective study

The performance of inflammatory markers in community-acquired pneumonia (CAP) caused by different pathogens has not been fully studied. We sought to find the differences in the concentrations of procalcitonin (PCT) and heparin-binding protein (HBP) between patients with CAP caused by different pathogens. We enrolled 162 patients with CAP, divided into three groups on the basis of bacterial (n = 108), fungal (n = 21) and viral (n = 33) infection. Complete leukocyte counts and the concentration of HBP and PCT were measured, and the differences were compared with nonparametric tests. The receiver operating characteristic (ROC) curve was used to evaluate the significant differences in the sensitivity and specificity of the indicators. The leukocyte and neutrophils counts and the concentrations of HBP and PCT in the viral group were significantly lower than those in the other two groups (p < 0.001). The area under the ROC curve (AUC) of the concentration of HBP and PCT as well as leukocyte and neutrophils counts were 0.927, 0.892, 0.832 and 0.806 for distinguishing bacterial from viral infection, respectively. The best cut-off value was 20.05 ng/mL for HBP, with a sensitivity of 0.861 and specificity of 0.939. The best cut-off value was 0.195 ng/mL for PCT, with a sensitivity of 0.991 and specificity of 0.636. The best cut-off value was 5.195 × 109/L and 4.000 × 109/L for leukocyte and neutrophils counts, with sensitivity of 0.694 and 0.880 and specificity of 0.667 and 0.636, respectively. The AUC of HBP, PCT and leukocyte and neutrophil counts for distinguishing fungal from viral infection were 0.851, 0.883, 0.835 and 0.830, respectively. The best cut-off values were 29.950 ng/mL, 0.560 ng/mL, 5.265 × 109/L and 3.850 × 109/L, with sensitivity of 0.667, 0.714, 0.905 and 0.952 and specificity of 0.970, 0.879 0.667 and 0.606, respectively. There were no significant differences in the three indicators between the bacterial and fungal infection groups. The concentration of CRP showed no significant differences among the three groups. Consequently, the stronger immune response characterized by higher inflammation markers including HBP and PCT can help distinguish bacterial and fungal CAP from viral CAP.
Biopsy-confirmed Genitourinary Tuberculosis in a Secondary Health Care Hospital: An Evidence-based Clinical Review

Introduction Tuberculosis (TB) is a worldwide disease and remains a major public health problem in developing countries, with 95% of cases occurring in developing countries, including Indonesia. It is caused by Mycobacterium tuberculosis, an acid-fast aerobic bacillus. When M. tuberculosis infects other than lung, it is called extrapulmonary tuberculosis (EPTB). Among other organs, genitourinary tuberculosis (GUTB) is responsible for 30–40% of all EPTB cases. Methods The study was conducted in a secondary health-care hospital in central Jakarta over a five-year period. We took data from hospital’s medical records and collected all the positive histopathological reports on biopsied tissue of the genitourinary tract from 2014–2019. Results Eleven patients showed positive histopathological results for TB on their biopsied genitourinary tissue. The genitourinary tracts involved were as follows: prostate (n=2), kidney (n=1), ureter (n=2), epididymis (n=1), epididymo-orchitis (n=1), bladder (n=4). All of them presented with specific genitourinary symptoms, such as lower urinary tract symptoms (LUTS) (n=8), dysuria (n=9), urinary retention (n=2), flank pain (n=6), and incontinence (n=1). Nine of 11 patients (81.8%) exhibited systemic manifestations, with fever being the most common (n=8), followed by malaise (n=6), dyspepsia syndrome (n= 4), and weight loss (n=3). Discussion Consistent with other studies, our research found that the prevalence of GUTB is substantially decreased with advancing age. Kidney is the most common site infected in GUTB infection. GUTB is easily overlooked, because its signs and symptoms are usually typical of a conventional bacterial cystitis. Conclusion Because of its insidious nature and late-onset symptoms, diagnosis of GUTB is often late to approach, leading to higher morbidity and even mortality rate. This leads into further complications of the disease, which are largely preventable by a correct and timely diagnosis followed by appropriate therapy.
On the northernmost Orchestina species in China, with a first description of the female of O. zhiwui (Araneae, Oonopidae)

Abstract Orchestina zhiwui Liu, Xu & Henrard, 2019, a species previously known only from males collected in Jiangxi Province, was found in Liaoning, ca 2200 km northeast of the type locality, including specimens of both sexes. The previously unknown female of this species is described, and the male is redescribed. A key to species of the genus Orchestina from China is provided.
Comparison of methods for the quantification of botrytis bunch rot in white wine grapes

Background and Aims: Quantification of botrytis bunch rot (BBR) in wine grapes, caused by Botrytis cinerea , is commonly done by visual estimation of the proportion of the area of individual bunches affected by BBR. Visual estimation was compared with four other quantification methods: digital image analysis, near-infrared and mid-infrared spectroscopy, and quantitative real-time polymerase chain reaction. Methods and Results: Visual estimation was found to vary significantly ( P P Conclusions: Near-infrared and mid-infrared spectroscopy require further calibration to quantify accurately BBR of low severity. Quantitative real-time polymerase chain reaction was the most accurate method but is unsuitable for routine use in the vineyard. RotBot was the most suitable and practical alternative to visual estimation, requiring no specialised equipment. Significance of the Study: Visual estimation was demonstrated to be prone to assessor bias. RotBot software is a suitable alternative that can be implemented immediately for objective quantification of BBR severity in white wine grapes. RotBot could be developed further and deployed in mobile devices for rapid sensing in the vineyard and easy collection of disease assessment data by wineries.
Critique of the tracer‐tracer correlation technique and its potential to analyze polar ozone loss in chemistry‐climate models

The tracer-tracer correlation technique (TRAC) has been widely employed to infer chemical ozone loss from observations. Yet, its applicability to chemistry-climate model (CCM) data is disputed. Here, we report the successful application of TRAC on the results of a CCM simulation. By comparing TRAC-calculated ozone loss to ozone loss derived with the passive ozone method in a chemistry transport model we differentiate effects of internal mixing and cross vortex boundary mixing on a TRAC reference correlation. As a test case, we consider results of a cold Arctic winter/spring episode from an E39/C experiment, where typical features, for example, sufficient polar stratospheric cloud formation potential, denitrification and dehydration, and intermittent and final stratospheric warming events, are simulated. We find that internal mixing does not impact the TRAC-derived reference correlation at all. Mixing across the vortex boundary would lead to an underestimation of ozone loss by ∼10% when calculated with TRAC. We provide arguments that TRAC is a consistent and conservative method to derive chemical ozone loss and can be used to extract its chemical signature also from CCM simulations. As a consequence, we will be able to provide a lower bound for chemical ozone loss for model simulations where a passive ozone tracer is not available.