Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial Activity of Essential Oils Obtained from Aromatic Plants of Argentina

ABSTRACT The aim of this work was to evaluate the antibacterial and antifungal activity of essential oils obtained from medicinal plants of the Argentine Republic. The antimicrobial activity of the essential oils of 14 plants collected from different zones was analyzed. The microorganisms used were Staphylococcus aureus. , Staphylococcus epidermidis. , Bacillus cereus. , Micrococcus luteus. , Enterococcus faecalis. , Escherichia coli. , Klebsiella. sp. , Proteus mirabilis. , Pseudomonas aeruginosa. , and the yeast Candida albicans. The disk diffusion method was performed to test antimicrobial activity. B. cereus. and S. aureus. were inhibited by most of the essential oils. Aloysia triphylla. , Psila spartoides. , and Anemia tomentosa. were the most effective compounds against B. cereus. , while A. triphylla. and Baccharis flabellata. were effective against S. aureus. None of the oils inhibited P. aeruginosa. B. flabellata. and Pectis odorata. were active only against Gram-positive bacteria. A. triphylla. and P. spartoides. inhibited all tested microorganism, and the remaining essential oils showed variable activity. The minimum inhibitory concentration (MIC) of A. triphylla. and P. spartoides. essential oils were determined using the disk diffusion method. The lowest MICs were against S. aureus. (1/16), B. cereus. (1/16), S. epidermidis. (1/8), and C. albicans. (1/32) for A. triphylla. The lowest MICs were against S. aureus. (1/32), B. cereus. (1/32), P. mirabilis. (1/32), and C. albicans. (1/64) with P. spartoides. The results showed that B. cereus. and S. aureus. were the most sensitive microorganisms, and P. aeruginosa. was the most resistant microorganism. This study may contribute to improve ethnobotanical knowledge and would help to discover substances with potential therapeutical uses, as food preservants or as food-borne pathogen inhibitors.
Spleen Stiffness Measurements Predict the Risk of Hepatic Decompensation After Direct-Acting Antivirals in HCV Cirrhotic Patients

Abstract Purpose Little evidence is available regarding the risk of hepatic decompensation (HD) after direct-acting antivirals (DAAs) in patients with advanced chronic liver disease. Our aim was to assess the risk of decompensation and the prognostic role of noninvasive tests, such as liver (LSM) and spleen (SSM) stiffness measurements, in the prediction of decompensation after sustained virologic response (SVR) by DAAs. Materials and Methods A cohort study involving 146 cirrhotic patients treated with DAAs in our tertiary center with LSM and SSM available both before and six months after treatment (SVR24). A historical cohort of 92 consecutive cirrhotic patients with active HCV was used as a control group. A propensity score inverse probability weighting method was used to account for differences between the groups. Time-dependent models for the prediction of decompensation were applied to account for changes in noninvasive tests after therapy. Results The decompensation incidence in the DAA cohort was 7.07 (4.56–10.96) per 100 person-years (PYs), which was significantly lower than in the active HCV cohort. The DAA therapy was an independent protective factor for HD development (SHR: 0.071, 95 %-CI: 0.015–0.332). SSM ≥ 54 kPa was independently associated with decompensation despite SVR achievement (SHR: 4.169, 95 %-CI: 1.050–16.559), alongside with a history of decompensation (SHR: 7.956, 95 %-CI: 2.556–24.762). SSM reduction < 10 % also predicted the risk of decompensation after SVR24. Conclusion The risk of decompensation was markedly reduced after DAA therapy, but it was not eliminated. Paired SSM values stratified the risk of decompensation after SVR better than other noninvasive tests.
High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria

Significance Bacteriophages (phages), viruses that infect bacteria, are the most abundant microbes on Earth. Extreme specificity to host species or even strains of bacteria makes phages amenable to particular biotechnical applications. This specificity is partially governed by the surface-expressed structures of bacteria that phages use as cell-binding receptors. However, these receptors remain less-studied in phage biology, because their discovery relies on laborious methods utilizing well-characterized bacteria. Here we present INSeq screens as a rapid, high-throughput tool to identify candidate phage receptors. This method was successful in identifying receptors for previously well-characterized phages T2, T4, T6, and T7 as well as identifying receptors for newly isolated phages R3, U115, EC14, EC35, and 8S. As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage–bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of Escherichia coli (phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere.
Understanding Health and Social Challenges for Aging and Long-Term Care in China

The second King’s College London Symposium on Ageing and Long-term Care in China was convened from 4 to 5th July 2019 at King’s College London in London. The aim of the Symposium was to have a better understanding of health and social challenges for aging and long-term care in China. This symposium draws research insights from a wide range of disciplines, including economics, public policy, demography, gerontology, public health and sociology. A total of 20 participants from eight countries, seek to identify the key issues and research priorities in the area of aging and long-term care in China. The results published here are a synthesis of the top four research areas that represent the perspectives from some of the leading researchers in the field.
Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach

Abstract Ongoing COVID-19 outbreak has raised a drastic challenge to global public health security. Most of the patients with COVID-19 suffer from mild flu-like illnesses such as cold and fever; however, few percentages of the patients progress from severe illness to death, mostly in an immunocompromised individual. The causative agent of COVID-19 is an RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite these debilitating conditions, no medication to stop the disease progression or vaccination is available till now. Therefore, we aimed to formulate a multi-epitope vaccine against SARS-CoV-2 by utilizing an immunoinformatics approach. For this purpose, we used the SARS-CoV-2 spike glycoprotein to determine the immunodominant T- and B-cell epitopes. After rigorous assessment, we designed a vaccine construct using four potential epitopes from each of the three epitope classes such as cytotoxic T-lymphocytes, helper T-lymphocyte, and linear B-lymphocyte epitopes. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. More importantly, the predicted vaccine structure was similar to the native protein. Further investigations indicated a strong and stable binding interaction between the vaccine and the toll-like receptor (TLR4). Strong binding stability and structural compactness were also evident in molecular dynamics simulation. Furthermore, the computer-generated immune simulation showed that the vaccine could trigger real-life-like immune responses upon administration into humans. Finally, codon optimization based on Escherichia coli K12 resulted in optimal GC content and higher CAI value followed by incorporating it into the cloning vector pET28+(a). Overall, these results suggest that the designed peptide vaccine can serve as an excellent prophylactic candidate against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
The physical activity of children and adolescents in Germany 2003-2017: The MoMo-study

With digitalization and virtual entertainment being the megatrends of the 21st century, there is reasonable concern about the role of physical activity (PA) in the daily life of children and adolescents. To identify risk-groups with insufficient PA and to guide interventions, continuous and representative tracking of PA is crucial. In this paper, representative PA data of children and adolescents from the Motorik-Modul (MoMo) baseline study (2003–2006, N = 4,528) is compared to those of Wave 2 (2014–2017, N = 3,708). Participants aged 4–17 were drawn out of 167 sample points in Germany and the data was weighted to ensure representativeness for Germany. Organized (sports clubs and schools) and unorganized (unorganized sports and playing outside) PA was measured by questionnaire and stratified by sex, age, and socioeconomic status. Contrary to common expectation, overall PA remained stable among youths in the past ten years, however, there is an ongoing trend towards organized forms of PA at the expense of unorganized sports and playing outside. Besides different trends in settings, there is inequality in PA distribution among socioeconomic status and gender, unequally pronounced in different settings.
The Hong Kong Principles for assessing researchers: Fostering research integrity

For knowledge to benefit research and society, it must be trustworthy. Trustworthy research is robust, rigorous, and transparent at all stages of design, execution, and reporting. Assessment of researchers still rarely includes considerations related to trustworthiness, rigor, and transparency. We have developed the Hong Kong Principles (HKPs) as part of the 6th World Conference on Research Integrity with a specific focus on the need to drive research improvement through ensuring that researchers are explicitly recognized and rewarded for behaviors that strengthen research integrity. We present five principles: responsible research practices; transparent reporting; open science (open research); valuing a diversity of types of research; and recognizing all contributions to research and scholarly activity. For each principle, we provide a rationale for its inclusion and provide examples where these principles are already being adopted.
Bis[(E)-N '-(2-nitrobenzylidene)-2-oxidobenzohydrazide]-bis-(pyridine-kappa N)-nickel(II)

The title compound, [Ni(C14H10N3O4)(2)(C5H5N)(2)], contains a Ni atom (site symmetry 2) six-coordinated by two N,O-bidentate Schiff base ligands and two pyridine N atoms, giving a distorted trans-NiN4O2 octa-hedral coordination environment for the metal atom.
Specific and Non-Invasive Fluorescent Labelling of Extracellular Vesicles for Evaluation of Intracellular Processing by Intestinal Epithelial Cells

The presence of extracellular vesicles (EVs) in milk has gained interest due to their capacity to modulate the infant’s intestinal and immune system. Studies suggest that milk EVs are enriched in immune-modulating proteins and miRNA, highlighting their possible health benefits to infants. To assess uptake of milk EVs by intestinal epithelial cells, a method was developed using labelling of isolated EVs with fluorophore-conjugated lactadherin. Lactadherin is a generic and validated EV marker, which enables an effective labelling of phosphatidylserine (PS) exposing EVs. Labelled EVs could effectively be used to describe a dose- and time-dependent uptake into the intestinal epithelial Caco-2 cell line. Additionally, fluorescence microscopy was employed to show that EVs colocalize with endosomal markers and lysosomes, indicating that EVs are taken up via general endocytotic mechanisms. Collectively, a method to specifically label isolated EVs is presented and employed to study the uptake of milk EVs by intestinal epithelial cells.
Precision Oncology in Surgery

Objective: We aimed to define preoperative clinical and molecular characteristics that would allow better patient selection for operative resection. Background: Although we use molecular selection methods for systemic targeted therapies, these principles are not applied to surgical oncology. Improving patient selection is of vital importance for the operative treatment of pancreatic cancer (pancreatic ductal adenocarcinoma). Although surgery is the only chance of long-term survival, 80% still succumb to the disease and approximately 30% die within 1 year, often sooner than those that have unresected local disease. Method: In 3 independent pancreatic ductal adenocarcinoma cohorts (total participants = 1184) the relationship between aberrant expression of prometastatic proteins S100A2 and S100A4 and survival was assessed. A preoperative nomogram based on clinical variables available before surgery and expression of these proteins was constructed and compared to traditional measures, and a postoperative nomogram. Results: High expression of either S100A2 or S100A4 was independent poor prognostic factors in a training cohort of 518 participants. These results were validated in 2 independent patient cohorts (Glasgow, n = 198; Germany, n = 468). Aberrant biomarker expression stratified the cohorts into 3 distinct prognostic groups. A preoperative nomogram incorporating S100A2 and S100A4 expression predicted survival and nomograms derived using postoperative clinicopathological variables. Conclusions: Of those patients with a poor preoperative nomogram score, approximately 50% of patients died within a year of resection. Nomograms have the potential to improve selection for surgery and neoadjuvant therapy, avoiding surgery in aggressive disease, and justifying more extensive resections in biologically favorable disease.
NAFLD in type 2 diabetes mellitus: Still many challenging questions

Epidemiologic data consistently show that in patients with type 2 diabetes (T2DM) the prevalence of non‐alcoholic fatty liver disease (NAFLD), including advanced fibrosis, is double compared to the general population, and it associates with high risk of liver‐related morbidity (advanced fibrosis, hepatocellular carcinoma) and mortality, but also with other systemic consequences, such as cardiovascular (CV) disease, chronic kidney disease, and overall mortality. There are still many answers that need to be clarified regarding NAFLD in T2DM, including deciphering the complex pathogenetic mechanisms, the intertwined relationships with the extrahepatic organs and tissues (mainly heart, kidneys, adipose tissue, gut), the prognostic value of NAFLD for CV risk stratification, and more importantly, what would be the most appropriate screening algorithm, diagnostic method and therapeutic approach. We advocate here for proactive action, in order to identify NAFLD in a timely manner, and suggest a simple algorithm to be used in clinical practice, based on risk stratification and on experts' opinions. We discuss the current therapeutic options for NAFLD in T2DM, for which a multifactorial approach is needed, that concomitantly addresses the liver and the cardio‐reno‐metabolic disturbances.
Relationship between Left Ventricular Outflow Tract Pressure Gradient and Hemoglobin in Patients with Hypertrophic Cardiomyopathy.

Background Anemia caused by left ventricular outflow tract obstruction in patients with hypertrophic obstructive cardiomyopathy (HOCM) has been reported, however, large clinical studies confirming this association are lacking. The objective of the present study was to investigate the relationship between left ventricular outflow tract (LVOT) pressure gradient and hemoglobin in patients with hypertrophic cardiomyopathy (HCM). Methods Patient demographics, laboratory and echocardiography data from 310 patients diagnosed with HCM from our hospital who had undergone echocardiography from July 2014 to March 2019 were collected from medical records. Patients were classified into HOCM and non-HOCM groups. Results Compared to the non-HOCM group, patients in the HOCM group had a lower hemoglobin level (112.2 ± 16.7 vs. 132.9 ± 22.2 g/L, p < 0.001). In addition, significant negative correlations between hemoglobin and LVOT pressure gradient were found in males (r = -0.568, p < 0.001) and females (r = -0.589, p < 0.001). Receiver operating characteristic curve analysis revealed that the best cut-off value for hemoglobin to predict HOCM in male patients was 128 g/L with 74.19% sensitivity and 75.51% specificity (area under the curve: 0.763, p < 0.001). For female patients, the cut-off value was 125 g/L, with a sensitivity and specificity of 89.39% and 48.48%, respectively (area under the curve: 0.718, p < 0.001). Conclusions Our results indicate that hemoglobin level is inversely proportional to the LVOT gradient pressure and has value for predicting outflow tract obstruction in patients with HCM.
Dynamics and allostery of Zika virus non-structural protein 5 methyltransferase

Abstract The methyltransferase (MTase) domain of non-structural protein 5 (NS5) plays a fundamental role in flaviviruses replication, and its inhibition is a strategy for antiviral development. MTase methylates viral RNA cap at guanine N-7 and the ribose 2'OH of the first adenosine. Many structures of Zika virus (ZIKV) and other flaviviruses MTases bound to cofactors, substrates and inhibitor candidates have been solved. Still, the dynamical modulation of MTase binding and catalytic activity yet needs to be clarified. Here, we investigated the structural dynamics of ZIKV NS5 MTase domain free and bound to Guanosine-5'-triphosphate (GTP) and S-Adenosyl-Lmethionine (SAM), to identify the molecular dynamics changes related to ligand binding and methyl transfer reaction. We have observed that the binding of the GTP and SAM individually and GTP-SAM in the ternary complex has induced allostery in the RNA binding site, showing the complexity of ZIKV MTase conformational equilibrium and its impact on viral RNA recognition. We also mapped in molecular dynamics trajectories, conformations of GTP guanine moiety that mimics guanine orientations visualized in human-specific N-methyltransferase structures solved by X-ray crystallography. It is the first time that N-7 methylation-prone guanine orientation has been proposed and modeled in flavivirus MTase. Communicated by Ramaswamy H. Sarma Graphical abstract
Diabetes mellitus association with coronavirus disease 2019 (COVID‐19) severity and mortality: A pooled analysis

Highlights There are ~ 2‐fold increased odds of severe coronavirus disease 2019 (COVID‐19) and a ~ 2‐fold increased risk of odds of mortality in patients with history of diabetes mellitus compared to those without diabetes mellitus. Patients with a history of diabetes mellitus should be closely monitored if they get infected with COVID‐19. Results of meta‐analysis showing association of diabetes mellitus with severity (Panel A) of disease and mortality (Panel B) in coronavirus disease 2019 (COVID‐19) patients
Motor adaptation via distributional learning

Objective. Both artificial and biological controllers experience errors during learning that are probabilistically distributed. We develop a framework for modeling distributions of errors and relating deviations in these distributions to neural activity. Approach. The biological system we consider is a task where human subjects are required to learn to minimize the roll of an inverted T-shaped object with an unbalanced weight (i.e. one side of the object is heavier than the other side) during lift. We also collect BOLD activity during this process. For our experimental setup, we define the state of the system to be the maximum magnitude roll of the object after lift onset and give subjects the goal of achieving the zero state. Main Results. We derive a model for this problem from a variant of Temporal Difference Learning. We then combine this model with Distributional Reinforcement Learning (DRL), a framework that involves defining a value distribution by treating the reward as stochastic. This model transforms the goal of the controller from achieving a target state, to achieving a distribution over distances from the target state. We call it a Distributional Temporal Difference Model (DTDM). The DTDM allows us to model errors in unsuccessfully minimizing object roll using deviations in the value distribution when the center of mass of the unbalanced object is changed. We compute deviations in global neural activity and show that they vary continuously with deviations in the value distribution. Different aspects might contribute to this global shift or signal difference, including a difference in grasp and lift force at lift onset, as well as sensory feedback of error/roll after lift onset. We predict that there exists a coordinated, global response to errors that incorporates all of this information, which is encoding the DTDM objective and used on subsequent trials enabling success. We validate the utility of the DTDM as a model for biological adaptation by using it to engineer a robotic controller to solve a similar problem. Significance. We develop a novel theoretical framework and show that it can be used to model a non-trivial motor learning task. Because this theoretical framework is consistent with state-of-the-art reinforcement learning, we can also use it to program a robot to perform a similar task. These results suggest a way to model the multiple subsystems composing global neural activity in a way that transfers well to engineering artificial intelligence.
Effects of plant growth regulators on callus induction from Cananga odorata flower petal explant

The Cananga odorata callus was initiated from petals of the C. odorata flowers on MS medium and B5 vitamins containing 30 g/L sugar and 3 g/L agar. The medium was also supplemented with different concentrations of 1-naphtalene acetic acid (NAA), and combinations of NAA with 6-benzylaminpurine (BAP) as the plant growth regulators. It was observed that the C. odorata callus could be induced on media containing the combination of 3 mg/L NAA and 0.5 mg/L BAP. High concentration of NAA gave rise to pale, whitish and friable callus after 1 - 2 weeks of culture. The optimum pH for the cell culture was about 5.7 and incubation at 25 ± 2°C, in totally dark condition.