Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim

Trimethoprim is a synthetic antibacterial agent that targets folate biosynthesis by competitively binding to the di-hydrofolate reductase enzyme (DHFR). Trimethoprim is often administered synergistically with sulfonamide, another chemotherapeutic agent targeting the di-hydropteroate synthase (DHPS) enzyme in the same pathway. Clinical resistance to both drugs is widespread and mediated by enzyme variants capable of performing their biological function without binding to these drugs. These mutant enzymes were assumed to have arisen after the discovery of these synthetic drugs, but recent work has shown that genes conferring resistance to sulfonamide were present in the bacterial pangenome millions of years ago. Here, we apply phylogenetics and comparative genomics methods to study the largest family of mobile trimethoprim-resistance genes (dfrA). We show that most of the dfrA genes identified to date map to two large clades that likely arose from independent mobilization events. In contrast to sulfonamide resistance (sul) genes, we find evidence of recurrent mobilization in dfrA genes. Phylogenetic evidence allows us to identify novel dfrA genes in the emerging pathogen Acinetobacter baumannii , and we confirm their resistance phenotype in vitro. We also identify a cluster of dfrA homologues in cryptic plasmid and phage genomes, but we show that these enzymes do not confer resistance to trimethoprim. Our methods also allow us to pinpoint the chromosomal origin of previously reported dfrA genes, and we show that many of these ancient chromosomal genes also confer resistance to trimethoprim. Our work reveals that trimethoprim resistance predated the clinical use of this chemotherapeutic agent, but that novel mutations have likely also arisen and become mobilized following its widespread use within and outside the clinic. Hence, this work confirms that resistance to novel drugs may already be present in the bacterial pangenome, and stresses the importance of rapid mobilization as a fundamental element in the emergence and global spread of resistance determinants.
Top predators in the Benguela ecosystem — implications of their trophic position

Many top predators in the Benguela ecosystem feed on prey species targeted by commercial fisheries. Their roles as indicators of the state of exploited prey resources, as competitors with commercial fisheries for resources, and as susceptible to impact from commercial fishing on those resources are briefly considered. Trends in the occurrence of anchovy Engraulis capensis and pilchard Sardinops ocellatus in the diet of Cape gannets Morus capensis off South Africa's west coast are related significantly to survey estimates of the abundance of these fish species, and they provide useful confirmation of those estimates. In the 1980s, anchovy decreased in the diet of Cape gannets, but pilchard increased. In both the northern and southern portions of the Benguela system, groundfish were thought to eat most (66–73%) of the total quantity of cephalopods and vertebrates consumed by predators and man in the 1980s. South African fur seals Arctocephalus pusillus pusillus, predatory pelagic fish and man removed roughl.
Role of Prophylactic Vitrectomy in Acute Retinal Necrosis in Preventing Rhegmatogenous Retinal Detachment: Systematic Review and Meta-analysis

ABSTRACT Purpose To evaluate the effects of prophylactic vitrectomy for rhegmatogenous retinal detachment (RRD) risk and visual outcome in acute retinal necrosis (ARN). Methods A systematic search of online databases was performed for articles published between 1994 June and 2020 March. The main outcomes that were assessed by a fixed effects model were RRD risk and visual outcome during a follow up period. Results A total of 7 trials involving 265 eyes (121 prophylactic vitrectomy eyes vs 144 routine antiviral treatment eyes) were analyzed in this study. RRD risk significantly decreased in the prophylactic vitrectomy group compared to the routine antiviral treatment group (P < .001, OR = 0.27, 95% CI: 0.16–0.46, I 2 = 35.3%). Significantly deteriorated visual outcome was observed in the prophylactic vitrectomy group in comparison with the routine antiviral treatment group (P < .001, WMD = 0.47, 95%CI: 0.26–0.67, I 2 = 32.2%). Conclusion This meta-analysis of retrospective cohort studies revealed that prophylactic vitrectomy could reduce the risk of RRD. The silicone oil tamponade and long-term complications may result in deteriorated visual outcome.
Early diagnosis and population prevention of coronavirus disease 2019

Purpose of review To discuss the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by nucleic acid and antibody testing as well as its contribution to mitigating the spread of coronavirus disease 2019. Recent findings Nucleic acid testing (NAT) is the firstly developed and most widely used diagnostic technique for SARS-CoV-2 infection. However, the sensitivity of SARS-CoV-2 RNA NAT assays is always unsatisfactory, mainly due to insufficient viral RNA in samples, especially when upper respiratory samples were used. Compared with NAT assays, serological tests are more convenient and less dependent on the quality of sample collection. But the sensitivity of antibody assays varies largely to test samples collected at different time after onset of symptoms. The diagnostic sensitivity can be significantly improved by combination of RNA and antibody testing. Due to the lack of effective drugs and vaccines, population prevention results mainly from timely triage and quarantine of SARS-CoV-2 infected individuals. Thus, extensive testing with NAT and antibody assays simultaneously is very important to constrain coronavirus disease 2019 epidemic. Summary Viral RNA testing combining with serological testing could improve the early diagnosis of SARS-CoV-2 infection, which has great value for clinical practice and public health.
Rejecting impulsivity as a psychological construct: A theoretical, empirical, and sociocultural argument.

We demonstrate through theoretical, empirical, and sociocultural evidence that the concept of impulsivity fails the basic requirements of a psychological construct and should be rejected as such. Impulsivity (or impulsiveness) currently holds a central place in psychological theory, research, and clinical practice and is considered a multifaceted concept. However, impulsivity falls short of the theoretical specifications for hypothetical constructs by having meaning that is not compatible with psychometric, neuroscience, and clinical data. Psychometric findings indicate that impulsive traits and behaviors (e.g., response inhibition, delay discounting) are largely uncorrelated and fail to load onto a single, superordinate latent variable. Modern neuroscience has also failed to identify a specific and central neurobehavioral mechanism underlying impulsive behaviors and instead has found separate neurochemical systems and loci that contribute to a variety of impulsivity types. Clinically, these different impulsivity types show diverging and distinct pathways and processes relating to behavioral and psychosocial health. The predictive validity and sensitivity of impulsivity measures to pharmacological, behavioral, and cognitive interventions also vary based on the impulsivity type evaluated and clinical condition examined. Conflation of distinct personality and behavioral mechanisms under a single umbrella of impulsivity ultimately increases the likelihood of misunderstanding at a sociocultural level and facilitates misled hypothesizing and artificial inconsistencies for clinical translation. We strongly recommend that, based on this comprehensive evidence, psychological scientists and neuroscientists reject the language of impulsivity in favor of a specific focus on the several well-defined and empirically supported factors that impulsivity is purported to cover. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
In Vitro Inhibition of Phosphodiesterase 3B (PDE 3B) by Anthocyanin-Rich Fruit Juice Extracts and Selected Anthocyanins

Phosphodiesterases (PDEs) are essential enzymes for the regulation of pathways mediated by cyclic adenosine monophosphate (cAMP). Secondary plant compounds like anthocyanins (ACs) can inhibit PDE activity and, consequently, may be beneficial for lipid metabolism. This study investigated 18 AC-rich juice extracts and pure reference compounds from red fruits for potential inhibitory effects on PDE 3B activity. Extracts were obtained through adsorption on Amberlite® XAD 7 resin. Based on this screening, the chokeberry, blueberry, pomegranate, and cranberry extracts were active, with half maximal inhibitory concentrations (IC50) ranging from 163 ± 3 µg/mL to 180 ± 3 µg/mL. The ACs in these extracts, peonidin-3-glucoside and cyanidin-3-arabinoside, were the most active single compounds (IC50 = 56 ± 20 µg/mL, 108 ± 6 µg/mL). All extracts comprised high amounts of phenolic compounds, as determined by the Folin–Ciocalteu assay, ranging from 39.8 ± 1.5 to 73.5 ± 4.8 g gallic acid equivalents (GAE)/100 g extract. Pomegranate and chokeberry extracts exhibited the largest amounts of polyphenols (72.3 ± 0.7 g GAE/100 g, 70.6 ± 4.1 g GAE/100 g, respectively). Overall, our results showed that fruit juice extracts and their ACs can inhibit PDE activity. Any potential health benefits in vivo will be investigated in the future.
Cascaded Attention Guidance Network for Single Rainy Image Restoration

Restoring a rainy image with raindrops or rainstreaks of varying scales, directions, and densities is an extremely challenging task. Recent approaches attempt to leverage the rain distribution (e.g., location) as prior to generate satisfactory results. However, concatenation of a single distribution map with the rainy image or with intermediate feature maps is too simplistic to fully exploit the advantages of such priors. To further explore this valuable information, an advanced cascaded attention guidance network, dubbed as CAG-Net, is formulated and designed as a three-stage model. In the first stage, a multi-task learning network is constructed for producing the attention map and coarse de-raining results simultaneously. Subsequently, the coarse results and the rain distribution map are concatenated and fed to the second stage for results refinement. In this stage, the attention map generation network from the first stage is used to formulate a novel semantic consistency loss for better detail recovery. In the third stage, a novel pyramidal “where-and-how” learning mechanism is formulated. At each pyramid level, a two-branch network is designed to take the features from previous stages as inputs to generate better attention-guidance features and de-raining features, which are then combined via a gating scheme to produce the final de-raining results. Moreover, the uncertainty maps are also generated in this stage for more accurate pixel-wise loss calculation. Extensive experiments are carried out for removing raindrops or rainstreaks from both synthetic and real rainy images, and CAG-Net is demonstrated to produce significantly better results than state-of-the-art models. Codes are available at <<uri>https://github.com/RobinCSIRO/CAGNet>.
Effects of chronic exposure to Cu2+ and Zn2+ on growth and survival of juvenile Apostichopus japonicus

Abstract Juvenile Apostichopus japonicus were cultured in seawater containing Cu2+ and Zn2+ for 75 days at 10–13 °C. The effects of Cu2+ and Zn2+ accumulation on the growth and survival of juvenile A. japonicus were investigated. Juvenile A. japonicus were poisoned at 0.050 mg L-1 Cu2+ and survival was just 65.33±8.33%, while the length and weight growth rates of the survivors were very low. Cu2+ accumulation in the 0.050 mg L-1 group increased with exposure time and this resulted in poisoning and death. However, at 0.5 mg L-1 Zn2+, the length and weight growth rates and survival of juvenile A. japonicus were reduced significantly, and the accumulation rate in each group stressed with Zn2+ was greater than in the control group (P<0.05). There were no significant differences in the body composition of juvenile A. japonicus in any of the treatment groups (P>0.05). The present study demonstrates that exposure to Cu2+ and Zn2+ can affect growth, survival and accumulation in juvenile A. japonicus; however, different mechanisms are used by these organisms to resist the effects of these heavy metals.
Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities

Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.
Modeling of an immune response: Queuing network analysis of the impact of zinc and cadmium on macrophage activation

Chronic obstructive pulmonary disease is characterized by progressive, irreversible airflow obstruction resulting from an abnormal inflammatory response to noxious gases and particles. Alveolar macrophages rely on the transcription factors, nuclear factor κB and mitogen‐activated protein kinase, among others, to facilitate the production of inflammatory mediators designed to help rid the lung of foreign pathogens and noxious stimuli. Building a kinetic model using queuing networks, provides a quantitative approach incorporating an initial number of individual molecules along with rates of the reactions in any given pathway. Accordingly, this model has been shown useful to model cell behavior including signal transduction, transcription, and metabolic pathways. The aim of this study was to determine whether a queuing theory model that involves lipopolysaccharide‐mediated macrophage activation in tandem with changes in intracellular Cd and zinc (Zn) content or a lack thereof, would be useful to predict their impact on immune activation. We then validate our model with biologic cytokine output from human macrophages relative to the timing of innate immune activation. We believe that our results further prove the validity of the queuing theory approach to model intracellular molecular signaling and postulate that it can be useful to predict additional cell signaling pathways and the corresponding biological outcomes.
Induced resistance against fusarium wilt of chickpea by nonpathogenic races of Fusarium oxysporum f. sp. ciceris and nonpathogenic isolates of F. oxysporum

Germinated seeds of chickpea cultivars JG 62 and ICCV 4 were inoculated with a conidial suspension of nonpathogenic races 0 and 1 of Fusarium oxysporum f. sp. ciceris or isolates of F. oxysporum (inducers), then challenged by root dip in a conidial suspension of F. o. f. sp. ciceris race 5. Prior inoculation with the inducers significantly reduced disease incidence and severity caused by race 5. However, the extent of protection decreased when the inoculum concentration of the challenger was close to that of the inducing agent, and it varied with the nature of inducing agent and genotype of the host. Also, resistance induced by race 0 in JG 62 was annulled when more than 3 days elapsed between inoculations with the nonpathogen and the challenger.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) and its effect on gametogenesis and early pregnancy

SARS‐CoV‐2 infection and pregnancy has been the topic of hundreds of publications over the last several months; however, few studies have focused on the implications of infection in early pregnancy and reproductive tissues. Here, we analyzed available evidence pertaining to SARS‐CoV‐2 infection, in early pregnancy, and in reproductive tissues. We searched PubMed and Embase databases in accordance with guidelines of Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) for publications from inception to June 4, 2020. Four reviewers screened titles and abstracts and obtained full‐text articles for analysis. Sixty‐two studies were included in the review. Biological plausibility for infection with SARS‐CoV‐2 exists in testis, ovaries, and placenta as they express ACE2 receptor activity. In males, SARS‐CoV‐2 infection could lead to functional abnormalities leading to spermatogenic failure and male infertility. In females, an alteration of the ACE2 cascade via SARS‐CoV‐2 infection could lead to impairment in important follicular and luteal processes. There is also evidence of significant placental pathology in SARS‐CoV‐2 infection, but it is unclear what effects there may be for early pregnancy, though available data suggest less severe effects compared to other respiratory virus outbreaks. Further investigation is needed regarding SARS‐CoV‐2 in reproductive function and early pregnancy.
Combining Laser-Induced Breakdown Spectroscopy (LIBS) and Visible Near-Infrared Spectroscopy (Vis-NIRS) for Soil Phosphorus Determination

Conventional wet chemical methods for the determination of soil phosphorus (P) pools, relevant for environmental and agronomic purposes, are labor-intensive. Therefore, alternative techniques are needed, and a combination of the spectroscopic techniques—in this case, laser-induced breakdown spectroscopy (LIBS)—and visible near-infrared spectroscopy (vis-NIRS) could be relevant. We aimed at exploring LIBS, vis-NIRS and their combination for soil P estimation. We analyzed 147 Danish agricultural soils with LIBS and vis-NIRS. As reference measurements, we analyzed water-extractable P (Pwater), Olsen P (Polsen), oxalate-extractable P (Pox) and total P (TP) by conventional wet chemical protocols, as proxies for respectively leachable, plant-available, adsorbed inorganic P, and TP in soil. Partial least squares regression (PLSR) models combined with interval partial least squares (iPLS) and competitive adaptive reweighted sampling (CARS) variable selection methods were tested, and the relevant wavelengths for soil P determination were identified. LIBS exhibited better results compared to vis-NIRS for all P models, except for Pwater, for which results were comparable. Model performance for both the LIBS and vis-NIRS techniques as well as the combined LIBS-vis-NIR approach was significantly improved when variable selection was applied. CARS performed better than iPLS in almost all cases. Combined LIBS and vis-NIRS models with variable selection showed the best results for all four P pools, except for Pox where the results were comparable to using the LIBS model with CARS. Merging LIBS and vis-NIRS with variable selection showed potential for improving soil P determinations, but larger and independent validation datasets should be tested in future studies.
Association between Exercise-Induced Changes in Cardiorespiratory Fitness and Adiposity among Overweight and Obese Youth: A Meta-Analysis and Meta-Regression Analysis

The aim of this study was to determine the minimum change in cardiorespiratory fitness (CRF) required to reduce adiposity (percent body fat) in exercise programs for overweight and obese youth. Studies were identified through a systematic search of five databases. Studies were limited to randomized controlled trials (RCTs) of exercise training (e.g., aerobic, strength, concurrent) that assessed percent body fat and CRF for both exercise and control groups in overweight and obese children and adolescents. A series of meta-regressions were conducted to explore links between change in CRF (maximum oxygen consumption, ml/kg/min) and change in percent body fat. Twenty-three RCTs were included (n = 1790, 59% females). Meta-regression analysis suggested that increases of at least 0.38 mL/kg/min in CRF (p < 0.001) were considered to be a clinically important reduction of percent body fat (−2.30%, 95% confidence interval −3.02 to −1.58; p < 0.001; I2 = 92.2%). Subgroup analysis showed that increases of at least 0.17 mL/kg/min in CRF favored a reduction of percent body fat of −1.62% (95% confidence interval −2.04 to −1.20; p < 0.001; I2 = 69.9%). In conclusion, this change in CRF could be considered by pediatric researchers, youth fitness specialists, and health care providers to determine the effectiveness in body fat reductions through exercise.
Bend-Direction and Rotation Plastic Optical Fiber Sensor

A plastic filament of poly (methyl methacrylate) (PMMA) was fabricated by extrusion. The mode confinement was simulated using numerical software. The idea is to study how the light intensity changes inside the plastic optical fiber (POF) when a bending in multiple directions is applied. The results obtained from the simulation were compared to the experimental observations. The non-circular shape of the POF allows sensing a rotation applied as well. The angle of rotation was obtained processing two images of the end facet of the fiber (one with the fiber in a reference position and one with the rotated fiber), using an intensity-based automatic image registration. The accuracy in the rotation calculation was of 0.01°.
The Hannes hand prosthesis replicates the key biological properties of the human hand

A prosthetic hand with human-like grasping behavior outperforms what is required in the execution of activities of daily living. Replacing the human hand with artificial devices of equal capability and effectiveness is a long-standing challenge. Even the most advanced hand prostheses, which have several active degrees of freedom controlled by the electrical signals of the stump’s residual muscles, do not achieve the complexity, dexterity, and adaptability of the human hand. Thus, prosthesis abandonment rate remains high due to poor embodiment. Here, we report a prosthetic hand called Hannes that incorporates key biomimetic properties that make this prosthesis uniquely similar to a human hand. By means of an holistic design approach and through extensive codevelopment work involving researchers, patients, orthopaedists, and industrial designers, our proposed device simultaneously achieves accurate anthropomorphism, biomimetic performance, and human-like grasping behavior that outperform what is required in the execution of activities of daily living (ADLs). To evaluate the effectiveness and usability of Hannes, pilot trials on amputees were performed. Tests and questionnaires were used before and after a period of about 2 weeks, in which amputees could autonomously use Hannes domestically to perform ADLs. Last, experiments were conducted to validate Hannes’s high performance and the human likeness of its grasping behavior. Although Hannes’s speed is still lower than that achieved by the human hand, our experiments showed improved performance compared with existing research or commercial devices.