Miracle-dz/UniFAR-FTUs huggingface dataset:
Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress

Abstract Listeria monocytogenes is the causative agent of the highly fatal foodborne disease listeriosis and can persist in food production environments. Recent research highlights the involvement of L. monocytogenes plasmids in different stress response mechanisms, which contribute to its survival in food production facilities. Ultraviolet (UV) light in the UVC spectrum (200–280 nm) is used in food production to control microbial contamination. Although plasmid-encoded UV resistance mechanisms have been described in other bacteria, no research indicates that L. monocytogenes plasmids contribute to the UV stress response. The plasmids of L. monocytogenes strains 6179, 4KSM and R479a are genetically distinct and were utilized to study the roles of plasmids in the UV response. Wild-type and plasmid-cured variant cells were grown to logarithmic or late-stationary phase, plated on agar plates and exposed to UVC for 60 or 90 s, and colony-forming units (CFUs) were determined. CFUs of 6179 and 4KSM, bearing pLM6179 and p4KSM, respectively, were significantly (P-value < 0.05) higher than those of the plasmid-cured strains in both logarithmic and stationary phases. No difference in survival was observed for the R479a strain. Our data show for the first time that certain L. monocytogenes plasmids contribute to the survival of UVC light stress.
Diagnostic accuracy of focused deep venous, lung, cardiac and multiorgan ultrasound in suspected pulmonary embolism: a systematic review and meta-analysis

Objective To determine the diagnostic accuracy of point-of-care ultrasound in suspected pulmonary embolism. Design Systematic review and meta-analysis. Data sources MEDLINE, Embase, CINAHL and Cochrane library were searched on 2 July 2020 with no restrictions on the date of publication. Subject headings or subheadings combined with text words for the concepts of pulmonary embolism, ultrasound and diagnosis were used. Eligibility criteria and data analysis Eligible studies reported sensitivity and specificity of deep venous, lung, cardiac or multiorgan ultrasound in patients with suspected pulmonary embolism, using an adequate reference-test. Prospective, cross-sectional and retrospective studies were considered for eligibility. No restrictions were made on language. Studies were excluded if a control group consisted of healthy volunteers or if transesophageal or endobronchial ultrasound was used. Risk of bias was assessed using quality assessment of diagnostic accuracy studies-2. Meta-analysis of sensitivity and specificity was performed by construction of hierarchical summary receiver operator curves. I2 was used to assess the study heterogeneity. Main outcome measures The primary outcome was overall sensitivity and specificity of reported ultrasound signs, stratified by organ approach (deep venous, lung, cardiac and multiorgan). Secondary outcomes were stratum-specific sensitivity and specificity within subgroups defined by pretest probability of pulmonary embolism. Results 6378 references were identified, and 70 studies included. The study population comprised 9664 patients with a prevalence of pulmonary embolism of 39.9% (3852/9664). Risk of bias in at least one domain was found in 98.6% (69/70) of included studies. Most frequently, 72.8% (51/70) of studies reported >24 hours between ultrasound examination and reference test or did not disclose time interval at all. Level of heterogeneity ranged from 0% to 100%. Most notable ultrasound signs were bilateral compression of femoral and popliteal veins (22 studies; 4708 patients; sensitivity 43.7% (36.3% to 51.4%); specificity 96.7% (95.4% to 97.6%)), presence of at least one hypoechoic pleural-based lesion (19 studies; 2134 patients; sensitivity 81.4% (73.2% to 87.5%); specificity 87.4% (80.9% to 91.9%)), D-sign (13 studies; 1579 patients; sensitivity 29.7% (24.6% to 35.4%); specificity 96.2% (93.1% to 98.0%)), visible right ventricular thrombus (5 studies; 995 patients; sensitivity 4.7% (2.7% to 8.1%); specificity 100% (99.0% to 100%)) and McConnell’s sign (11 studies; 1480 patients; sensitivity 29.1% (20.0% to 40.1%); specificity 98.6% (96.7% to 99.4%)). Conclusion Several ultrasound signs exhibit a high specificity for pulmonary embolism, suggesting that implementation of ultrasound in the initial assessment of patients with suspected pulmonary embolism may improve the selection of patients for radiation imaging. PROSPERO registration number CRD42020184313.
Coxsackievirus B Vaccines Prevent Infection-Accelerated Diabetes in NOD Mice and Have No Disease-Inducing Effect

Enteroviruses, including the Coxsackievirus Bs (CVB), have been implicated as causal agents in human type 1 diabetes. Immunization of at-risk individuals with a CVB vaccine provides an attractive strategy for elucidating the role of CVBs in the disease etiology. Previously, we have shown that an inactivated whole-virus vaccine covering all CVB serotypes (CVB1–6) is safe to administer and highly immunogenic in preclinical models, including nonhuman primates. Before initiating clinical trials with this type of vaccine, it was also important to address 1) whether the vaccine itself induces adverse immune reactions, including accelerating diabetes onset in a diabetes-prone host, and 2) whether the vaccine can prevent CVB-induced diabetes in a well-established disease model. Here, we present results from studies in which female NOD mice were left untreated, mock-vaccinated, or vaccinated with CVB1–6 vaccine and monitored for insulitis occurrence or diabetes development. We demonstrate that vaccination induces virus-neutralizing antibodies without altering insulitis scores or the onset of diabetes. We also show that NOD mice vaccinated with a CVB1 vaccine are protected from CVB-induced accelerated disease onset. Taken together, these studies show that CVB vaccines do not alter islet inflammation or accelerate disease progression in an animal model that spontaneously develops autoimmune type 1 diabetes. However, they can prevent CVB-mediated disease progression in the same model.
Outcomes in the ISCHEMIA Trial Based on Coronary Artery Disease and Ischemia Severity

Supplemental Digital Content is available in the text. Background: The ISCHEMIA trial (International Study of Comparative Health Effectiveness With Medical and Invasive Approaches) postulated that patients with stable coronary artery disease (CAD) and moderate or severe ischemia would benefit from revascularization. We investigated the relationship between severity of CAD and ischemia and trial outcomes, overall and by management strategy. Methods: In total, 5179 patients with moderate or severe ischemia were randomized to an initial invasive or conservative management strategy. Blinded, core laboratory–interpreted coronary computed tomographic angiography was used to assess anatomic eligibility for randomization. Extent and severity of CAD were classified with the modified Duke Prognostic Index (n=2475, 48%). Ischemia severity was interpreted by independent core laboratories (nuclear, echocardiography, magnetic resonance imaging, exercise tolerance testing, n=5105, 99%). We compared 4-year event rates across subgroups defined by severity of ischemia and CAD. The primary end point for this analysis was all-cause mortality. Secondary end points were myocardial infarction (MI), cardiovascular death or MI, and the trial primary end point (cardiovascular death, MI, or hospitalization for unstable angina, heart failure, or resuscitated cardiac arrest). Results: Relative to mild/no ischemia, neither moderate ischemia nor severe ischemia was associated with increased mortality (moderate ischemia hazard ratio [HR], 0.89 [95% CI, 0.61–1.30]; severe ischemia HR, 0.83 [95% CI, 0.57–1.21]; P=0.33). Nonfatal MI rates increased with worsening ischemia severity (HR for moderate ischemia, 1.20 [95% CI, 0.86–1.69] versus mild/no ischemia; HR for severe ischemia, 1.37 [95% CI, 0.98–1.91]; P=0.04 for trend, P=NS after adjustment for CAD). Increasing CAD severity was associated with death (HR, 2.72 [95% CI, 1.06–6.98]) and MI (HR, 3.78 [95% CI, 1.63–8.78]) for the most versus least severe CAD subgroup. Ischemia severity did not identify a subgroup with treatment benefit on mortality, MI, the trial primary end point, or cardiovascular death or MI. In the most severe CAD subgroup (n=659), the 4-year rate of cardiovascular death or MI was lower in the invasive strategy group (difference, 6.3% [95% CI, 0.2%–12.4%]), but 4-year all-cause mortality was similar. Conclusions: Ischemia severity was not associated with increased risk after adjustment for CAD severity. More severe CAD was associated with increased risk. Invasive management did not lower all-cause mortality at 4 years in any ischemia or CAD subgroup. Registration: URL: https://www.clinicaltrials. gov. Unique identifier: NCT01471522.
Effect of the combination of astragaloside IV and Panax notoginseng saponins on pyroptosis and necroptosis in rat models of cerebral ischemia-reperfusion

Pyroptosis and necroptosis are closely associated with the mechanism underlying cerebral ischemia-reperfusion (I/R) injury. The combination of astragaloside IV (AST IV) and Panax notoginseng saponins (PNS) has remarkable effects on the alleviation of cerebral I/R damage. However, whether inhibition of pyroptosis and necroptosis is the mechanism underlying the beneficial effects of this drug combination on cerebral I/R injury remains unclear. To explore the effects and mechanisms of drug treatment, middle cerebral artery occlusion was performed to induce I/R injury in rats, which was verified based on neurological deficit score (NDS), infarct volume and H&E staining. Activation of pyroptosis and necroptosis was detected by western blot analysis of associated proteins. The results of the present study demonstrated that treatment with AST IV and PNS, either alone or in combination, significantly reduced the NDS, cerebral infarct volume and cell injury rate in the cerebral cortex of rats. The treatments also improved pathological injury to the cerebral cortex and reduced the levels of proteins associated with pyroptosis and necroptosis. These effects were stronger in the combination drug group compared with groups treated with a single drug alone. The findings of the present study suggested that the combination of AST IV and PNS exhibited stronger neuroprotective effects in I/R injury than either drug alone, and that the underlying mechanism was associated with inhibition of pyroptosis and necroptosis.
Effect of Vaccination on Transmission of SARS-CoV-2

Background Decisions around COVID-19 vaccination strategies and non-pharmacological interventions require evidence on the effectiveness of vaccines in protecting individuals vaccinated from infection and severe disease, but also the impact of vaccination on transmission, in real-world contexts. Objectives 1. To determine the real-world efficacy of COVID-19 vaccination in HCWs. 2. To determine the effect of vaccinating HCWs on the risk of COVID-19 in individuals with whom they share a household as such an effect would be consistent with an effect of vaccination on transmission Methods Record linkage of routine healthcare data. Amendments and updates This is the first version of the protocol submitted to ENCEPP. As the ENCEPP server was unavailable when we ready to start the analysis we posted an encrypted version of an SAP on a public github repository (https://github.com/dmcalli2/hcw_vax). We have followed closely the ACCESS template created in ENCEPP. Milestones and timeline This document was created after linking the vaccination data to the healthcare worker/household cohorts but BEFORE these data were linked to the outcome data (except outcomes prior to July 2020 which were already linked). Where this description refers to the “original” analyses this corresponds to the analysis of COVID-19 risk in healthcare workers (HCWs) carried out for the first wave of the pandemic and described in https://www.bmj. com/content/371/bmj.m3582. Rationale and Background Decisions around COVID-19 vaccination strategies and non-pharmacological interventions require evidence on the effectiveness of vaccines in protecting individuals vaccinated from infection and severe disease, but also the impact of vaccination on transmission, in real-world contexts. Healthcare workers and their household members provide an ideal population to address these question since: 1. Healthcare workers are essential to providing health services and so their health is of wider public interest 2. Healthcare workers are a high risk population so the number of events are likely to be higher 3. Healthcare workers have been vaccinated early, allowing us to examine the questions at the earliest possible opportunity 4. Individuals who are household members of healthcare workers are at increased risk compared to people who are not household members of healthcare workers. As such
Effect of Vermicompost in Media on Growth, Yield and Fruit Quality of Cherry Tomato (Lycopersicon esculentun Mill.) Under Net House Conditions

ABSTRACT Effects of VC application on tomato production and media properties can last for the third successive season, which was verified in this study to evaluate effects of VC application on growth, productivity and fruit quality of cherry tomato for the third season. Six treatments were designed similarly in the first and second seasons (unchanged design compared to the previous season), including: VC with rice husk ash (RHS) and coconut fiber (CF) 0% VC+ 50% RHS +50% CF (T1- control), respectively. 20%VC + 40% RHS + 40% CF(T2), 40% VC+ 30% RHS + 30% CF(T3), 60% VC + 20% RHS + 20% CF(T4), 80% VC + 10% RHS + 10% CF(T5), and 100% VC(T6). The results showed that the pH, EC, N, P, K, Ca, and Mg available in media were increased with the addition of VC. This finding revealed that the addition of VC significantly improved the physic-chemical media properties, increasing the EC and also increasing the macronutrients in the media resulting in substantial increased the yield and quality of tomato fruits. It is concluded that EC of VC was the key factor for the positive increase of the productivity and quality of tomato and the salinity (EC at 3.52 dS/m) causing restriction of water to fruits that resulted in the increase of the total soluble solids in tomato fruit and without affecting yield reduction.
Atomistic theory of thermally activated magnetization processes in Nd2Fe14B permanent magnet

ABSTRACT To study the temperature dependence of magnetic properties of permanent magnets, methods of treating the thermal fluctuation causing the thermal activation phenomena must be established. To study finite-temperature properties quantitatively, we need atomistic energy information to calculate the canonical distribution. In the present review, we report our recent studies on the thermal properties of the Nd2Fe14B magnet and the methods of studying them. We first propose an atomistic Hamiltonian and show various thermodynamic properties, for example, the temperature dependences of the magnetization showing a spin reorientation transition, the magnetic anisotropy energy, the domain wall profiles, the anisotropy of the exchange stiffness constant, and the spectrum of ferromagnetic resonance. The effects of the dipole–dipole interaction (DDI) in large grains are also presented. In addition to these equilibrium properties, the temperature dependence of the coercivity of a single grain was studied using the stochastic Landau-Lifshitz-Gilbert equation and also by the analysis of the free energy landscape, which was obtained by Monte Carlo simulation. The upper limit of coercivity at room temperature was found to be about 3 T at room temperature. The coercivity of a polycrystalline magnet, that is, an ensemble of interactinve grains, is expected to be reduced further by the effects of the grain boundary phase, which is also studied. Surface nucleation is a key ingredient in the domain wall depinning process. Finally, we study the effect of DDI among grains and also discuss the distribution of properties of grains from the viewpoint of first-order reversal curve. Graphical abstract
Chief cell plasticity is the origin of metaplasia following acute injury in the stomach mucosa

Objective Metaplasia arises from differentiated cell types in response to injury and is considered a precursor in many cancers. Heterogeneous cell lineages are present in the reparative metaplastic mucosa with response to injury, including foveolar cells, proliferating cells and spasmolytic polypeptide-expressing metaplasia (SPEM) cells, a key metaplastic cell population. Zymogen-secreting chief cells are long-lived cells in the stomach mucosa and have been considered the origin of SPEM cells; however, a conflicting paradigm has proposed isthmal progenitor cells as an origin for SPEM. Design Gastric intrinsic factor (GIF) is a stomach tissue-specific gene and exhibits protein expression unique to mature mouse chief cells. We generated a novel chief cell-specific driver mouse allele, GIF-rtTA. GIF-GFP reporter mice were used to validate specificity of GIF-rtTA driver in chief cells. GIF-Cre-RnTnG mice were used to perform lineage tracing during homoeostasis and acute metaplasia development. L635 treatment was used to induce acute mucosal injury and coimmunofluorescence staining was performed for various gastric lineage markers. Results We demonstrated that mature chief cells, rather than isthmal progenitor cells, serve as the predominant origin of SPEM cells during the metaplastic process after acute mucosal injury. Furthermore, we observed long-term label-retaining chief cells at 1 year after the GFP labelling in chief cells. However, only a very small subset of the long-term label-retaining chief cells displayed the reprogramming ability in homoeostasis. In contrast, we identified chief cell-originating SPEM cells as contributing to lineages within foveolar cell hyperplasia in response to the acute mucosal injury. Conclusion Our study provides pivotal evidence for cell plasticity and lineage contributions from differentiated gastric chief cells during acute metaplasia development.
Current clinical developments in curcumin‐based therapeutics for cancer and chronic diseases

The last decade has seen an unprecedented rise in the prevalence of chronic diseases worldwide. Different mono‐targeted approaches have been devised to treat these multigenic diseases, still most of them suffer from limited success due to the off‐target debilitating side effects and their inability to target multiple pathways. Hence a safe, efficacious, and multi‐targeted approach is the need for the hour to circumvent these challenging chronic diseases. Curcumin, a natural compound extracted from the rhizomes of Curcuma longa, has been under intense scrutiny for its wide medicinal and biological properties. Curcumin is known to manifest antibacterial, antiinflammatory, antioxidant, antifungal, antineoplastic, antifungal, and proapoptotic effects. A plethora of literature has already established the immense promise of curcuminoids in the treatment and clinical management of various chronic diseases like cancer, cardiovascular, metabolic, neurological, inflammatory, and infectious diseases. To date, more than 230 clinical trials have opened investigations to understand the pharmacological aspects of curcumin in human systems. Still, further randomized clinical studies in different ethnic populations warrant its transition to a marketed drug. This review summarizes the results from different clinical trials of curcumin‐based therapeutics in the prevention and treatment of various chronic diseases.
Skull osteology of the holotype of the rhynchosaur Hyperodapedon sanjuanensis (Sill, 1970) from the Upper Triassic Ischigualasto Formation of Argentina

Rhynchosaurs are bulky quadrupedal herbivores that achieved a cosmopolitan distribution during the Middle and Late Triassic. Rhynchosaurids are characterized by a pair of premaxillae modified into an edentulous beak that had a bone‐to‐bone occlusion with the tips of the dentaries, and a specialized masticatory apparatus composed of groove(s) on the maxilla and ridges(s) on the dentary. The Argentinian fossil record of rhynchosaurs is abundant, but only two nominal species have been named so far. One of them, the hyperodapedontine Hyperodapedon sanjuanensis, is the most abundant tetrapod of the Ischigualasto Formation of northwestern Argentina. However, the anatomy of H. sanjuanensis remains poorly studied. The repreparation and computed tomographic (CT) scanning of its holotypic skull (MACN‐Pv 18185) allowed a detailed description of its anatomy. Among the novel anatomical data presented here, we provide the first tridimensional complete reconstruction of a rhynchosaurid palate. This structure is extremely complex in comparison to the plesiomorphic archosauromorph condition, and more data on other rhynchosaurid palates are needed to shed light on the sequence of character states acquisition that resulted in this peculiar anatomy. The presence of a pair of septomaxillae in H. sanjuanensis is the first report of these bones in a rhynchosaurid, and this new information allowed to identify septomaxillae also in the hyperodapedontines Teyumbaita sulcognathus and Hyperodapedon mariensis. The better understanding of the skull anatomy of the holotype of H. sanjuanensis is a first step towards an improved knowledge of the morphology and taxonomy of the South American rhynchosaurs.
Criminal behavior and mental illness in the Arab world

Numerous studies have highlighted significant correlations between major psychiatric disorders and criminal behavior. However, the plethora of literature on criminality among patients with major psychiatric disorders originated in the West. The objective of the present paper is to review criminal behavior among individuals with mental illness in Arab countries. Attributes of individuals assessed by forensic psychiatric committees and identifying various aspects that may reinforce criminality among individuals with mental illness were considered. Following the PRISMA guidelines, a systematic review of literature from three databases (Scopus, PubMed, and Web of Science) was carried out. A total of 20 articles were included. The publications span between 1975 and 2020 and originated in seven different Arab countries including Egypt, Kuwait, Iraq, Saudi Arabia, Tunisia, Jordan, and Algeria. Individuals evaluated by forensic psychiatric committees were predominantly males. Excluding substance use disorder, psychotic disorders were the most commonly diagnosed disorders among individuals evaluated by forensic psychiatry committees. Concerning schizophrenia, concomitant substance use and nonadherence to therapy were significantly associated with increased criminality. The review demonstrates that substance use is certainly linked to violence. There is a significant association between mental illness and criminal behavior. Therefore, awareness of different characteristics and risk factors behind criminal behavior among mentally ill offenders could allow us to design and implement effective preventative measures. The Arab's contribution in this field of forensic psychiatry is relatively small. Indeed, further investigation and contributions from the Arab world are required.