Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for (p)ppGpp-mediated inhibition of the GTPase RbgA

Efficient adaptation to environmental changes is pivotal for all bacterial cells. Almost all bacterial species depend on the conserved stringent response system to prompt timely transcriptional and metabolic responses according to stress conditions and nutrient depletion. The stringent response relies on the stress-dependent synthesis of the second messenger nucleotides and alarmones (p)ppGpp, which pleiotropically target and reprogram processes that consume cellular resources, such as ribosome biogenesis. Here we show that (p)ppGpp acts on the ribosome biogenesis GTPase A (RbgA) of Gram-positive bacteria. Using X-ray crystallography, hydrogen–deuterium exchange MS (HDX-MS) and kinetic analysis, we demonstrate that the alarmones (p)ppGpp bind to RbgA in a manner similar to that of binding by GDP and GTP and thereby act as competitive inhibitors. Our structural analysis of Staphylococcus aureus RbgA bound to ppGpp and pppGpp at 1.8 and 1.65 Å resolution, respectively, suggested that the alarmones (p)ppGpp prevent the active GTPase conformation of RbgA by sterically blocking the association of its G2 motif via their 3′-pyrophosphate moieties. Taken together, our structural and biochemical characterization of RbgA in the context of the alarmone-mediated stringent response reveals how (p)ppGpp affects the function of RbgA and reprograms this GTPase to arrest the ribosomal large subunit.
Genetic diversity, virulence genotype and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from sows

Abstract Background: Urinary tract infections (UTI) cause severe losses to the swine industry worldwide and uropathogenic Escherichia coli (UPEC) are the main agent isolated from UTI in sows. Objective: The aim of this study was to investigate the virulence genes, assess the phylogenetic background, clonal diversity, and the pattern of resistance to antimicrobials in 186 isolates of UPEC isolated from sows in Brazil. Materials and methods: Urine samples from 300 sows of three herds with clinical signs from São Paulo State (Brazil) were screened for UTI; samples with suggestive results were submitted to bacterial isolation. E. coli strains isolated were characterized using disk diffusion technique, polymerase chain reaction and Single-enzyme amplification fragment length polymorphism (SE-AFLP). Results: Virulence genes focH and papC were present in 78.5% and 58% of strains, respectively, followed by cnf1 (23.2%), afa (13.4%), sfa (11.3%), iucD (6.9%), and hlyA (1.6%). No clonal relatedness was found by SE-AFLP. A total of 98% of isolates (182/186) were multidrug resistant, and the highest levels of resistance were to sulfonamides, tetracycline, florfenicol, and ampicillin. Isolates were classified in phylogenetic group B1 (34.4%), followed by D (33.9%), E (30.1%) and A (1.6%). Conclusions: The data obtained suggest that pigs from clinically affected herds may serve as a reservoir of uropathogenic and multidrug-resistant E. coli strains.
Self-Reported Moral Emotions and Physical and Relational Aggression in Early Childhood: A Social Domain Approach.

This study examined discrepancies between 4- and 7-year-olds' (n = 135; Mage = 5.65) self-reported affect following hypothetical moral versus social-conventional transgressions and their associations with teacher-rated physical and relational aggression concurrently and 9-months later. Negative emotion ratings in response to prototypical moral transgressions were not associated with children's aggression. When transgressions were described as no longer prohibited by rules and authority figures, children reporting more negative affect in response to moral as compared to conventional violations were less physically aggressive at Wave 1 and showed relative and mean-level declines in physical aggression over time. Relational aggression was not associated with self-reported emotions. Findings indicate the importance of distinguishing between types of transgressions and forms of aggression in studying moral emotions.
Predicting Bleeding Events in Anticoagulated Patients With Atrial Fibrillation: A Comparison Between the HAS‐BLED and GARFIELD‐AF Bleeding Scores

Background Patients with atrial fibrillation (AF) treated with oral anticoagulants may be exposed to an increased risk of bleeding events. The HAS‐BLED (Hypertension, Abnormal renal and liver function, Stroke, Bleeding, Labile INRs, Elderly, Drugs or alcohol) score is a simple, well‐established, clinical bleeding‐risk prediction score. Recently, a new algorithm‐based score was proposed, the GARFIELD‐AF (Global Anticoagulant in the Field–AF) bleeding score. We compared HAS‐BLED and GARFIELD‐AF scores in predicting adjudicated bleeding events in a clinical trial cohort of patients with AF taking anticoagulants, in the first external comparative validation of both scores. Methods and Results We analyzed patients from the SPORTIF (Stroke Prevention Using an Oral Thrombin Inhibitor in Patients With AF) III and V trials. All patients assigned to the warfarin arm with information to calculate the scores were considered. Outcomes were major, major/clinically relevant nonmajor, and any bleeding. A total of 3550 warfarin‐treated patients were available for analysis. Of these patients, 2519 (71.0%) had a HAS‐BLED score ≥3, whereas based on GARFIELD‐AF median value, 2056 (57.9%) were categorized as “high score. ” Both HAS‐BLED and GARFIELD‐AF C‐indexes showed modest predictive value (C‐index [95% confidence interval] for major bleeding, 0.58 [0.56–0.60] and 0.56 [0.54–0.57], respectively); however, GARFIELD‐AF was not predictive of any bleeding. The GARFIELD‐AF bleeding score had a significantly lower sensitivity and a negative reclassification for any bleeding compared with HAS‐BLED, assessed by integrated discrimination improvement and net reclassification improvement (both P<0.001). HAS‐BLED showed a 5% net benefit for any bleeding occurrence. Conclusions The algorithm‐based GARFIELD‐AF bleeding score did not show any significant improvement in major and major/clinically relevant nonmajor prediction compared with the simple HAS‐BLED score. For clinical usefulness in prediction of any bleeding, the HAS‐BLED score showed a significant net benefit compared with the GARFIELD‐AF.
Automating the Development of High-Performance Multigrid Solvers

The purpose of a domain-specific language (DSL) is to enable the application programmer to specify a problem, or an abstract algorithm description, in his/her domain of expertise without being burdened by implementation details. The ideal scenario is that the implementation detail is added in an automatic process of program translation and code generation. The approach of domain-specific program generation has lately received increasing attention in the area of computational science and engineering. In this paper, we introduce the new code generation framework Athariac. Its goal is to support the quick implementation of a language processing and program optimization platform for a given DSL based on stepwise term rewriting. We demonstrate the framework’s use on our DSL ExaSlang for the specification and optimization of multigrid solvers. On this example, we provide evidence of Athariac’s potential for making domain-specific software engineering more productive.
Digital Control of Multistep Hydrothermal Synthesis by Using 3D Printed Reactionware for the Synthesis of Metal–Organic Frameworks

Abstract Hydrothermal‐synthesis‐based reactions are normally single step owing to the difficulty of manipulating reaction mixtures at high temperatures and pressures. Herein we demonstrate a simple, cheap, and modular approach to the design reactors consisting of partitioned chambers, to achieve multi‐step synthesis under hydrothermal conditions, in digitally defined reactionware produced by 3D printing. This approach increases the number of steps that can be performed sequentially and allows an increase in the options available for the control of hydrothermal reactions. The synthetic outcomes of the multi‐stage reactions can be explored by varying reaction compositions, number of reagents, reaction steps, and reaction times, and these can be tagged to the digital blueprint. To demonstrate the potential of this approach a series of polyoxometalate (POM)‐containing metal–organic frameworks (MOFs) unavailable by “one‐pot” methods were prepared as well as a set of new MOFs.
IPS-WASEDA system at CoNLL–SIGMORPHON 2018 Shared Task on morphological inflection

This paper presents the system submitted by IPS-WASEDA University for CoNLL– SIGMORPHON 2018 Shared Task 1: Type level inﬂection. We develop a system based on a holistic approach which considers whole-word form as a unit, instead of breaking them into smaller pieces (e,g. morphemes) like the baseline systems does. We also implement an encoder-decoder model which has recently become the new standard in many natural language processing (NLP) tasks. The results show that the neural approach outperforms the baseline and our holistic approach on bigger resources settings. The use of data augmentation helps to improve the performance of the model in lower resources settings, although it still cannot beat the other systems. In the end, for the low resources setting, our holistic approach performs best in comparison to the baseline and the neural approach (even with data augmentation).
Severe acute alcoholic hepatitis and liver transplant: A never-ending mournful story

Severe acute alcoholic liver disease (SAAH) unresponsive to medical therapy shows one-year-mortality rates of up to 90%. Most transplant centers request six months of alcohol abstinence prior to transplantation, the so-called “6-month rule. ” This regulation is not based on strong evidence, repeatedly making it a topic of controversial debates. The majority of patients with SAAH will die before fulfilling the 6-month rule. Therefore, liver transplantation (LT) protocols are becoming more flexible towards the rigid abstinence regulation, especially concerning SAAH patients. We conducted a literature review regarding LT in SAAH and its outcomes, including post-transplant mortality and recidivism. We studied available data on PubMed from 2011 and onwards whilst including articles dealing with genetic components, medical therapy and historic snapshots of alcoholism. Emerging studies recommend LT in SAAH not responding to medical therapies even without realizing the required abstinence period, since the majority of these patients would die within 6 months. SAAH without response to medical therapy has one-year-mortality rates of up to 90%. The 6-month rule is not based on strong evidence and is repeatedly a topic of controversial debates. There is genetic linkage to alcoholism and medical therapy is not as effective as estimated, yet. The 6-months-regulation has not shown to evidently decrease the risk of recidivism post-LT, which is a lifesaving treatment in SAAH patients. Insisting on rigid sobriety rules results in excluding patients with a low risk of recidivism from being transplanted. Moreover, the genetic linkage of alcoholism must be recognized.
Biomarker Profiling in Stage 5 Chronic Kidney Disease Identifies the Relationship between Angiopoietin-2 and Atrial Fibrillation

Atrial fibrillation (AF) is prevalent in nearly 27% of patients with stage 5 chronic kidney disease on hemodialysis (CKD5-HD), suggesting a strong association between these 2 pathologies. It is hypothesized that the relationship between these 2 diseases may be mediated by inflammation. Angiopoietin-2 (Ang-2), a pro-inflammatory biomarker of endothelial instability, inflammation, and vascular remodeling, is elevated in CKD5-HD and AF, yet has not been evaluated in patients with concomitant AF and CKD5-HD. The aim of this study is to analyze circulating levels of inflammatory and thrombotic biomarkers in patients with concomitant AF and CKD5-HD. Plasma levels of Ang-2 were measured via sandwich enzyme-linked immunosorbent assay method in CKD5-HD patients (n = 96), patients with AF (n = 38), and controls (n = 50). Angiopoietin-2 was markedly elevated in CKD5-HD with comorbid AF as compared to CKD5-HD alone, and AF alone, respectively (13.05 ± 1.56 vs 9.57 ± 0.71 ng/mL; P = .00169; vs 2.48 ± 0.57 ng/mL; P < .0001). The results of this study suggest an additive effect of Ang-2 with coexistence of AF and CKD5-HD, which may be useful in the detection of AF within this patient population.
Chronic periodontitis impairs polymorphonuclear leucocyte–endothelium cell interactions and oxidative stress in humans

AIM To evaluate the relationship between oxidative stress parameters in polymorphonuclear leucocytes (PMNs) and PMN-endothelial cell interactions in patients with chronic periodontitis (CP) according to different degrees of severity of the disease. MATERIALS AND METHODS For this cross-sectional study, 182 subjects were divided into four groups according to degree of CP: without CP (n = 37), mild CP (n = 59), moderate CP (n = 51), and severe CP (n = 35). We determined anthropometric and biochemical variables, periodontal parameters, inflammatory markers, oxidative stress parameters (superoxide and mitochondrial membrane potential), and PMN-endothelium cell interactions (rolling flux, velocity, and adhesion). RESULTS Systemic inflammatory markers-C-reactive protein, leucocyte count, TNFα, and retinol-binding protein 4-were altered in the group with CP. Total superoxide was augmented in patients with moderate and severe periodontitis, whereas mitochondrial membrane potential did not change. Furthermore, PMNs adhesion and rolling flux were increased in subjects with CP. CONCLUSION In a systemic proinflammatory environment, PMNs from patients with CP exhibit hyperactivity and produce higher amounts of superoxide. In parallel with this, an increase in PMNs rolling flux and cell adhesion to the endothelium suggests the presence of alterations of PMN-endothelium interactions in patients with CP that can lead to atherosclerosis and cardiovascular complications.
Advanced Practice Provider Versus Physician‐Only Outpatient Follow‐Up After Acute Myocardial Infarction

Background Physician shortages and reimbursement changes have led to greater use of advanced practice providers (APPs). Prevalence of and outcomes associated with APP care following myocardial infarction are unknown. Methods and Results We examined outpatient cardiology or primary care visits within 90 days post‐myocardial infarction among 29 477 Medicare‐insured patients aged ≥65 years from 364 hospitals in Acute Coronary Treatment Intervention Outcomes Network Registry. We compared medication adherence, all‐cause readmission risk, mortality, and major adverse cardiovascular events between patients seen by APPs versus physicians only. Overall, 11% of myocardial infarction patients were treated by an APP. Patients seen by APPs were more likely to have diabetes mellitus (37% versus 33%) and heart failure (20% versus 16%), be discharged to a nursing facility (21% versus 13%) and had more outpatient visits within 90 days post‐discharge (median 6 versus 5, P<0.01 for all) than those seen by physicians only. Adherence to evidence‐based medications (adjusted odds ratio, 0.98; 95% confidence interval, 0.89–1.08) and readmission risks (adjusted hazard ratio, 1.11; 95% confidence interval, 0.99–1.26) were similar between patients seen by APPs versus physicians only. Risks of 90‐day mortality (adjusted hazard ratio, 1.18; 95% confidence interval, 0.98–1.42) and major adverse cardiovascular events (adjusted hazard ratio, 1.06; 95% confidence interval, 0.90–1.23) were also similar between patients seen by APPs versus physicians only. Conclusions APPs were likely used to provide more frequent monitoring of high‐risk post‐MI patients. Medication adherence, readmission risk, mortality, and major adverse cardiovascular events did not differ substantially between patients seen by physician‐APP teams than those seen by physicians only.
Going with the Flow: Multiscale Insights into the Composite Nature of Water Transport in Roots1[OPEN]

A bio-physical model of the ”root hydraulic anatomy“ allows testing hypotheses related to radial water transport down to the cell level and proves complementary to current experimental approaches. As water often limits crop production, a more complete understanding of plant water capture and transport is necessary. Here, we developed MECHA, a mathematical model that computes the flow of water across the root at the scale of walls, membranes, and plasmodesmata of individual cells, and used it to test hypotheses related to root water transport in maize (Zea mays). The model uses detailed root anatomical descriptions and a minimal set of experimental cell properties, including the conductivity of plasma membranes, cell walls, and plasmodesmata, which yield quantitative and scale-consistent estimations of water pathways and root radial hydraulic conductivity (kr). MECHA revealed that the mainstream hydraulic theories derived independently at the cell and root segment scales are compatible only if osmotic potentials within the apoplastic domains are uniform. The results suggested that the convection-diffusion of apoplastic solutes explained most of the offset between estimated kr in pressure clamp and osmotic experiments, while the contribution of water-filled intercellular spaces was limited. Furthermore, sensitivity analyses quantified the relative impact of cortex and endodermis cell conductivity of plasma membranes on root kr and suggested that only the latter contributed substantially to kr due to the composite nature of water flow across roots. The explicit root hydraulic anatomy framework brings insights into contradictory interpretations of experiments from the literature and suggests experiments to efficiently address questions pertaining to root water relations. Its scale consistency opens avenues for cross-scale communication in the world of root hydraulics.
The stigmatization of nonsuicidal self-injury.

OBJECTIVE Despite the high prevalence of nonsuicidal self-injury (NSSI), no research has systematically studied the occurrence and effects of stigmatization by others towards NSSI scarring. METHODS The current study measured implicit and explicit attitudes among undergraduates towards NSSI scarring using the implicit association test and questionnaires to compare implicit and explicit biases towards NSSI with biases towards tattoos, a culturally sanctioned form of self-determined marking, as well as nonintentional disfigurement. RESULTS Our study demonstrated strong negative implicit and explicit biases towards NSSI when comparing NSSI to tattoos and nonintentional disfigurement. CONCLUSIONS Results extend previous research describing stigma towards mental illness and suggest a large negative bias towards NSSI. The importance of studying how stigma affects those who bear scarring from NSSI is discussed.
Effects of Grape Juice in Superoxide Dismutase and Catalase in Colorectal Cancer Carcinogenesis Induced by Azoxymethane

Background: The intestinal mucosa is commonly exposed to oxidant nutrients and carcinogens, which can lead to the generation of free radicals. The antioxidants present in the diet assume great importance as possible protective agents, reducing the oxidative damage. In this way, we evaluated the antioxidant action of grape juice on preneoplastic lesions induced by azoxymethane (AOM) in Wistar rats. Methods: The colorectal carcinogenesis was induced by two intraperitoneal injections of 15mg/kg of AOM in Wistar rats. The animals were divided in 7 groups and treated with 1 and 2% concentrations of grape juice before and after carcinogen administration. After euthanasia, the expression of antioxidant enzymes catalase (CAT), copper-zinc superoxide dismutase (Cu/Zn-SOD) and manganese superoxide dismutase (Mn-SOD) CAT, SOD1 and SOD2 were evaluated by immunohistochemistry. Results: AOM decreased the expression of CAT and Mn-SOD enzymes, but not for Cu/Zn-SOD. We observed an increase expression of CAT and Mn-SOD after grape juice administration in some concentrations according to the time of administration of the grape juice before the carcinogen or just after the carcinogen. Conclusion: Our results suggest an independent action of each enzyme and a possible antioxidant action of the grape juice components in the diet being able to balance the body to neutralize the superoxide radicals and not leave them in the cell-damaging form.
Exponential Consensus of Multiagent Systems With Lipschitz Nonlinearities Using Sampled-Data Information

In this paper, exponential consensus of general linear multiagent systems with Lipschitz nonlinear dynamics using sampled-data information is investigated. Both leaderless and leader-following consensuses are considered. Using input-delay approach, the resulting sampled-data closed-loop systems are first reformulated as continuous systems with time-varying delay in the control input. Then, decoupled conditions in terms of linear matrix equality (LMI) on the Lipschitz constant, the decay rate, the communication graph parameters, and the control gain matrix to guarantee exponential consensus are derived using novel Lyapunov functionals. Based on the sufficient conditions, controller design methods are also provided in the form of decoupled LMIs. Finally, simulation examples including the consensus of Chua’s circuit systems are given to illustrate the effectiveness of the obtained results.
Increasing Information Reposting Behavior in Online Learning Community

Online learning communities (OLCs) enable their learner to access different types of information through internet based structures anywhere anytime. OLCs are among the strategies used for the production and repost of information by learners interested in a specific area to support asynchronous learning. In this respect, learners become members of a particular domain and begin posting. OLC members consist of different sites with different educational backgrounds as well as different levels of expertise. This causes the sharing of posts which may not be appropriate for different learners. It also reduces data reposting behavior and subsequently decreases participation in information sharing. Furthermore, most learners of these communities take up a lurking position toward the posts. One of the ways proposed to increase information reposts is the selection and display of effective posts for each individual. Effective posts are selected in such a way that they can be more likely to be reposted by learners based on each learner's interests, knowledge and characteristics. The present paper intends to introduce a new method for selecting k effective posts to ensure the increase of information repost and participation in OLCs. In terms of participation in OLCs, learners are divided into two groups of posters and lurkers. Some solutions are proposed to encourage lurking learners to participate in content repostings. Comprehensive evaluations indicated that the proposed method had significantly solved the presented challenges