Miracle-dz/UniFAR-FTUs huggingface dataset:
Beo v1.0: numerical model of heat flow and low-temperature thermochronology in hydrothermal systems

Abstract. Low-temperature thermochronology can provide records of the thermal history of the upper crust and can be a valuable tool to quantify the history of hydrothermal systems. However, existing model codes of heat flow around hydrothermal systems do not include low-temperature thermochronometer age predictions. Here I present a new model code that simulates thermal history around hydrothermal systems on geological timescales. The modelled thermal histories are used to calculate apatite (U–Th)∕He (AHe) ages, which is a thermochronometer that is sensitive to temperatures up to 70 ∘C. The modelled AHe ages can be compared to measured values in surface outcrops or borehole samples to quantify the history of hydrothermal activity. Heat flux at the land surface is based on equations of latent and sensible heat flux, which allows more realistic land surface and spring temperatures than models that use simplified boundary conditions. Instead of simulating fully coupled fluid and heat flow, the code only simulates advective and conductive heat flow, with the rate of advective fluid flux specified by the user. This relatively simple setup is computationally efficient and allows running larger numbers of models to quantify model sensitivity and uncertainty. Example case studies demonstrate the sensitivity of hot spring temperatures to the depth, width and angle of permeable fault zones, and the effect of hydrothermal activity on AHe ages in surface outcrops and at depth.
The effect of antenatal magnesium sulfate on intraventricular hemorrhage in premature infants: a systematic review and meta-analysis

Objective The aim of this systematic review and meta-analysis study was to determine the pooled estimate of the effect of antenatal magnesium sulfate (MgSO4) on intraventricular hemorrhage (IVH) in premature infants. Methods Two review authors independently searched all randomized clinical trials from international databases, including Medline (PubMed), Web of Sciences, Scopus, Cochrane Central Register of Controlled Trials (CENTRAL), and Research Registers of ongoing trials (ClinicalTrials.gov), from January 1989 to August 2017. Two independent review authors were responsible for data collection. After extracting the necessary information from the evaluated articles, metaanalysis of the data was performed using Stata version 14. Also, sources of heterogeneity among studies were determined by Meta regression. Results In this study, among 126 articles that were extracted from primary studies, 7 papers that evaluated the effect of MgSO4 on IVH were eligible for inclusion in the meta-analysis. The results of the meta-analysis showed that pooled relative risk (95% confidence interval [CI]) was 0.80 (95% CI, 0.63 to 1.03) for the effect of MgSO4 on IVH. Conclusion Results of this study showed that although MgSO4 had a protective effect on IVH in premature infants, this effect was not statistically significant. Further studies are needed to determine the best dosage, timing, and gestational age to achieve the optimum effect of MgSO4 on IVH. Systematic Review Registration International Prospective Register of Systematic Reviews (PROSPERO) Identifier: CRD42019119610
Assessment of antioxidant traits and protective action of Egyptian acacia pods extracts against paracetamol-induced liver toxicity in rats.

This study investigates the protective effect of Egyptian acacia pod extracts against overdose of paracetamol-induced liver damage. Egyptian acacia green and brown pods were extracted by mixture of ethanol 80%: HCl (6 M) (99:1 v/v). In extracts of green and brown pods, total phenolic content in hydrolyzed ethyl acetate fraction (HEF) at pH 4, was 649.89 and 712.14 mg GAE/g while antioxidant activity was 95.55% and 97.35%, both being the highest than any fraction. HEF (pH 4) in brown pods was analyzed by HPLC, there were 22 phenolic compounds rich in ethyl vanillin about 227 mg/g and 11 flavonoids rich in catechin 48.70 mg/g. A biological experiment was conducted using HEF (pH4) in brown pods against overdose of paracetamol in albino rats induced to hepatotoxicity. Thirty rats were divided into five groups; a control group, a paracetamol group, and the other three received paracetamol plus silymarin or two doses of HEF. Animals were received paracetamol and treated with either silymarin or HEF showed reduced levels of liver (ALT, AST, and ALP) and kidney (urea, creatinine, and uric acid) markers compared with the control group as well as reduction of oxidative stress and increment antioxidant enzyme activity in liver tissue when compared with the paracetamol group. It could be concluded that both HEF and silymarin are considerably high hepatoprotector against paracetamol-induced hepatotoxicity in rats due to their strong antioxidant activity. PRACTICAL APPLICATIONS: Both HEF and silymarin improved liver functions and exerted strong antioxidant activities. This antioxidant activity would have a positive effect against oxidative liver damage caused by parcetamol. Thus, it may be concluded that the liver plasma membranes were protected and the regenerative and reparative capacity of liver by phenolic compound in HEF treatment. The study demonstrated the HEF hepatoprotective activity and recommends using Egyptian acacia pods for treatment of liver disorders.
Clinical guidance on pharmacotherapy for the treatment of attention-deficit hyperactivity disorder (ADHD) for people with intellectual disability

ABSTRACT Introduction ADHD causes significant distress and functional impairment in multiple domains of daily life. Therefore, diagnosis and treatment are important to improve the quality of life of people. The pharmacotherapy for ADHD is well established but needs systematic evaluation in Intellectual Disability (ID) populations. Areas covered This paper reviews the ADHD pharmacological treatment in people with ID using the PRISMA guidance for scoping reviews to help identify the nature and strength of evidence. Expert opinion In the last 20 years, seven randomized controlled trials have evaluated pharmacotherapies for ADHD in people with ID; five looking at methylphenidate. Generally, studies were underpowered; all but two had less than 25 participants. Of the two larger trials one was single blinded and therefore open to bias. Only two used a parallel-group method, the remainder were mostly short crossover trials; not ideal when measuring behavioral and psychological parameters which are long standing. The remaining evidence is made up of observational studies. Methylphenidate and atomoxetine, particularly at higher doses, have shown clear benefits in people with ID. Most people with ID tolerated ADHD medications well. Benefits were seen in behavioral and/or cognitive domains. The evidence base is limited, though promising, for dexamfetamine, clonidine, and guanfacine.
Development of a robust genetic test for hyperkalemic periodic paralysis (HYPP) in quarter horses

A single nucleotide substitution from cysteine to guanine in a region of the skeletal muscle sodium channel gene (SCN4A) is known to cause an equine genetic disorder known as Hyperkalemic Periodic Paralysis (HYPP). The clinical effects of this disorder range from little or no symptoms to frequent episodes of muscle tremors, weakness, and/or complete collapse. Oligonucleotide primer pairs were designed for both the wild type and mutant alleles of the SCN4A gene for use in Amplification Refractory Mutation System‐PCR (ARMS‐PCR). Genomic DNA from both whole blood and saliva swab samples were isolated from horses with wild type phenotypes for HYPP. As expected for an unaffected individual, our test showed the expected PCR product using the wild type specific primer pair, while the mutant specific primer pair did not generate a product. We then varied annealing temperatures and magnesium concentrations to optimize the PCR and found a temperature of 60°C and 3 mM magnesium to be optimal. We next plan to obtain DNA from both carrier horses and individuals expressing the full‐blown mutant phenotype. DNA isolated from HYPP animals should produce a PCR product with only the mutant specific primer pairs, and carriers for HYPP should produce a product in both wild type and mutant specific PCR reactions.
Calcium-triggered fusion of lipid membranes is enabled by amphiphilic nanoparticles

Significance Lipid membrane fusion is a critical component of biological transport, communication, and developmental processes. The fusion reaction is kinetically constrained since it contains multiple large energy barriers, so proteins and ions are used by natural systems to intervene and catalyze the reaction toward biologically relevant timescales. Here, we demonstrate how amphiphilic nanoparticles can prime lipid membranes for fusion so that complete fusion proceeds only upon exposure to an excess of calcium or other stimulus that would stress the outer leaflet. This is a major advance in the nascent field of controlled fusion and may unlock new avenues of research on how nanomaterials can be designed from first principles to perform targeted functional roles in biological systems. Lipid membrane fusion is an essential process for a number of critical biological functions. The overall process is thermodynamically favorable but faces multiple kinetic barriers along the way. Inspired by nature’s engineered proteins such as SNAP receptor [soluble N-ethylmale-imide-sensitive factor-attachment protein receptor (SNARE)] complexes or viral fusogenic proteins that actively promote the development of membrane proximity, nucleation of a stalk, and triggered expansion of the fusion pore, here we introduce a synthetic fusogen that can modulate membrane fusion and equivalently prime lipid membranes for calcium-triggered fusion. Our fusogen consists of a gold nanoparticle functionalized with an amphiphilic monolayer of alkanethiol ligands that had previously been shown to fuse with lipid bilayers. While previous efforts to develop synthetic fusogens have only replicated the initial steps of the fusion cascade, we use molecular simulations and complementary experimental techniques to demonstrate that these nanoparticles can induce the formation of a lipid stalk and also drive its expansion into a fusion pore upon the addition of excess calcium. These results have important implications in general understanding of stimuli-triggered fusion and the development of synthetic fusogens for biomedical applications.
High fat diet negatively impacts both metabolic and behavioral health in an outbred rat model.

Obesity is influenced by both genetics and diet and has wide ranging comorbidities, including anxiety and depressive disorders. In this study, outbred Heterogeneous Stock (HS) rats were fed high fat diet (HFD) or low fat diet (LFD) and tested for metabolic and behavioral outcomes. Male HS rats were fed 60% HFD or 10% LFD ad lib for 12-21 weeks. Rats were weighed weekly. We assessed multiple metabolic (glucose tolerance, fasting insulin, fat pad weights) and behavioral (elevated plus maze - EPM, open field test - OFT, splash test - SpT, and forced swim test - FST) measures. We found negative effects of HFD on metabolic outcomes, including increased body weight and fat pad weights, decreased glucose tolerance, and increased fasting insulin. We also found negative effects of HFD on coping response to stress and/or despair- and anxiety-like behaviors, including increased closed arm time and decreased open arm time in the EPM, increased movement and rest episodes and decreased rearing episodes in the OFT, increased SpT grooming time, and increased FST immobility. Positive correlations were found between FST immobility and visceral fat pad weights. We also found diet-dependent correlations between EPM, OFT and SpT measures. HFD negatively affected metabolic and behavioral health in HS rats. Changes in multiple coping/despair-and anxiety-like behaviors, independent of locomotion, indicate a role of HFD on behavioral health beyond just fat mass. This work establishes the HS rat as a model to study gene by diet interactions affecting obesity and behavioral health.
Pre-PCI versus immediate post-PCI Impella initiation in acute myocardial infarction complicated by cardiogenic shock

Background In selected patients with an acute myocardial infarction (AMI) complicated by Cardiogenic shock (CS), mechanical circulatory support with Impella may be beneficial, although conclusive evidence is still lacking. Nevertheless, it has been suggested that Impella initiation prior to primary PCI might improve survival. Objective To investigate the effect pre-PCI versus immediate post-PCI Impella initiation on short term mortality. Methods A prospective, single center, observational study, was performed including all patients with STEMI complicated by CS, treated with primary PCI and Impella. Thirty day mortality was compared between patients with Impella initiation pre-PCI and immediately post-PCI. Results A total of 88 patients were included. In the pre-PCI group (n = 21), admission heart rate was lower (84 versus 94 bpm, p = 0.04) and no IABP was implanted before Impella initiation, versus 17.9% in post-PCI group (n = 67), p = 0.04. Total 30-day all-cause mortality was 58%, and was lower in pre-PCI group, 47.6% versus 61.2% in the post-PCI group, however not statistically significant (HR 0.7, 95% CI 0.3–1.3, p = 0.21). Thirty-day cardiac mortality was significantly lower in the pre-PCI group, 19% versus 44.7% in the post-PCI group (HR 0.3, 95% CI 0.09–0.96, p = 0.042). Conclusion Pre-PCI Impella initiation in AMICS patients was not associated with a statistically significant difference in 30-day all-cause mortality, compared to post-PCI Impella initiation.
Outer membrane vesicles: moving within the intricate labyrinth of assays that can predict risks of reactogenicity in humans

ABSTRACT Outer membrane vesicles (OMV) are exosomes naturally released from the surface of Gram-negative bacteria. Since the ’80s, OMVs have been proposed as powerful vaccine platforms due to their intrinsic self-adjuvanticity and ability to present multiple antigens in natural conformation. However, the presence of several pathogen-associated molecular patterns (PAMPs), especially lipid A, has raised concerns about potential systemic reactogenicity in humans. Recently, chemical and genetic approaches allowed to efficiently modulate the balance between reactogenicity and immunogenicity for the use of OMV in humans. Several assays (monocyte activation test, rabbit pyrogenicity test, limulus amebocyte lysate, human transfectant cells, and toxicology studies) were developed to test, with highly predictive potential, the risk of reactogenicity in humans before moving to clinical use. In this review, we provide a historical perspective on how different assays were and can be used to successfully evaluate systemic reactogenicity during clinical development and after licensure.
The nervous system of amphioxus : structure, development, and evolutionary significance

Amphioxus neuroanatomy is important not just in its own right but also for the insights it provides regarding the evolutionary origin and basic organization of the vertebrate nervous system. This review summarizes the overall layout of the central nervous system (CNS), peripheral nerves, and nerve plexuses in amphioxus, and what is currently known of their histology and cell types, with special attention to new information on the anterior nerve cord. The intercalated region (IR) is of special functional and evolutionary interest. It extends caudally to the end of somite 4, traditionally considered the limit of the brain-like region of the amphioxus CNS, and is notable for the presence of a number of migrated cell groups. Unlike most other neurons in the cord, these migrated cells detach from the ventricular lumen and move into the adjacent neuropile, much as developing neurons do in vertebrates. The larval nervous system is also considered, as there is a wealth of new data on the organization and cell typ.
Comparative histological basis of sun and shade leaf dimorphism in Helianthus annuus

The development processes which give rise to the histological differences between leaves expanding under full daylight and 25% daylight are described for Helianthus annuus. Generally the pattern of cell division and cell enlargement in shaded leaves lags behind that in unshaded leaves by about 2 days. There is no significant difference in the amount of cell enlargement in the paradermal plane in the epidermis and palisade layers of shaded leaves as compared with leaves expanding in full sunlight. However, cell division in all cell layers occurs at greater rates in unshaded leaves, resulting in greater final leaf area. Cell elongation in both palisade layers is of longer duration and occurs at a greater rate in unshaded leaves and is closely correlated with increase in leaf thickness. The volumes of palisade and spongy mesophyll are significantly greater in unshaded leaves than in shaded leaves, but the relative proportions of each tissue type does not change significantly. However, in shaded leaves there .
Detection and Level Estimation of Cavitation in Hydraulic Turbines with Convolutional Neural Networks

In this paper a method for detecting and furthermore estimating the intensity of cavitation occurrences in hydraulic turbines is presented. The method relies on analyzing high frequency signals with a convolutional neural network (CNN). The CNN is trained in an adversarial manner in order to get more robust results. After successful training the obtained network is modified in such a way, that it is possible to obtain estimations of the intensity. For evaluation purposes a separate dataset is investigated.
Systematic Review and Meta-analysis of the Change in Pharyngeal Bacterial Cultures After Pediatric Tonsillectomy

Objective To review all available biomedical literature to assess published data regarding the effect of pediatric tonsillectomy on the culture results of potentially pathogenic respiratory pharyngeal bacteria before and after surgery. Data Sources Biomedical literature databases (PubMed, Embase, Web of Science) from January 1970 to December 2019. Review Methods A systematic review of the literature was performed with the assistance of a medical librarian. Inclusion criteria consisted of pediatric patients and extractable data regarding respiratory bacteria culture data before and after tonsillectomy. Meta-analysis with random effects modeling was used on a limited basis. Results Only 5 studies met the inclusion criteria. The grand mean age was 5.9 years; the sample size range was 31 to 134; and the range of follow-up was 1 to 12 months. Group A beta hemolytic Streptococcus was generally the least commonly cultured pathogenic bacteria on preoperative cultures. Qualitative culture data generally showed an overall decrease in potentially pathogenic bacteria and some increase in nonpathologic respiratory flora after tonsillectomy. Meta-analysis showed significant reductions in postoperative culture rates for group A beta hemolytic Streptococcus (positive post- vs preoperative culture: risk ratio [RR], 0.144; 95% CI, 0-0.342), Haemophilus influenzae (RR, 0.437; 95% CI, 0.266-0.608), and Streptococcus pneumoniae (RR, 0.268; 95% CI, 0-0.567) and mixed results for Moraxella catarrhalis (0.736; 95% CI, 0.446-1.03) but no significant reduction for Staphylococcus aureus (RR, 0.774; 95% CI, 0.157-1.39). Conclusion The majority of published evidence shows that pediatric tonsillectomy appears to reduce the quantity of most cultured potentially pathogenic respiratory bacteria in the pharynx after surgery. The implications and possible benefits of this favorable change in the microbiologic environment after surgery require further study.
Sex-related patterns of intrinsic functional connectivity in children and adolescents with autism spectrum disorders

Although a growing literature highlights sex differences in autism spectrum disorder clinical presentation, less is known about female variants at the neural level. We investigated sex-related patterns of functional connectivity within and between functional networks in children and adolescents with autism spectrum disorders, compared to typically developing peers. Resting-state functional magnetic resonance imaging data for 141 children and adolescents (7–17 years) selected from an in-house sample and four sites contributing to the Autism Brain Imaging Database Exchange (ABIDE I and II) were submitted to group independent component analysis to generate resting-state functional networks. Functional connectivity was estimated by generating resting-state functional network correlation matrices, which were directly compared between males and females, and autism spectrum disorder and typically developing groups. Results revealed greater connectivity within the default mode network in typically developing girls as compared to typically developing boys, while no such sex effect was observed in the autism spectrum disorder group. Correlational analyses with clinical indices revealed a negative relationship between sensorimotor connectivity and history of early autism symptoms in girls, but not in boys with autism spectrum disorder. A lack of neurotypical sex differentiation in default mode network functional connectivity observed in boys and girls with autism spectrum disorder suggests that sex-related differences in network integration may be altered in autism spectrum disorder. Lay summary We investigated whether children and adolescents with autism spectrum disorders show sex-specific patterns of brain function (using functional magnetic resonance imaging) that are well documented in typically developing males and females. We found, unexpectedly, that boys and girls with autism do not differ in their brain functional connectivity, whereas typically developing boys and girls showed differences in a brain network involved in thinking about self and others (the default mode network). Results suggest that autism may be characterized by a lack of brain sex differentiation.
Utility of SNOMED CT in automated expansion of clinical terms in discharge summaries: Testing issues of coverage

Objective: This study tests coverage of SNOMED CT as an expansion source in the process of automated expansion of clinical terms found in discharge summaries. Term expansion is commonly used as a technique in knowledge extraction, query formulation and semantic modelling among other applications. However, characteristics of the sources might affect credibility of outputs, and coverage is one of them. Method: We developed an automated method for testing coverage of more than one source at a time. We used several methods to clean our corpus of discharge summaries before we extracted text fragments as candidates for clinical concepts. We then used Unified Medical Language System (UMLS) sources and UMLS REST API to filter concepts from the pool of text fragments. Statistical measures like true positive rate and false negative rate were used to decide on the coverage of the source. We also tested the coverage of the individual SNOMED CT hierarchies using the same methods. Results: Findings suggest that a combination of four terminologies tested (SNOMED CT, NCI, LNC and MSH) achieves over 90% of coverage for term expansion. We also found that the SNOMED CT hierarchies that hold clinically relevant concepts provided 60% of coverage. Conclusion: We believe that our findings and the method we developed will be of use to both scientists and practitioners working in the domain of knowledge extraction.