Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Tool for the Generation of Conditional Knockouts To Study Gene Function across the Plasmodium falciparum Life Cycle

One of the major limitations in studying P. falciparum is that so far only asexual stages are amenable to rapid conditional genetic modification. The most promising drug targets and vaccine candidates, however, have been refractory to genetic modification because they are essential during the blood stage or for transmission in the mosquito vector. This leaves a major gap in our understanding of parasite proteins in most life cycle stages and hinders genetic validation of drug and vaccine targets. Here, we describe a method that supports conditional gene deletion across the P. falciparum life cycle for the first time. We demonstrate its potential by deleting essential and nonessential genes at different parasite stages, which opens up completely new avenues for the study of malaria and drug development. It may also allow the realization of novel vaccination strategies using attenuated parasites. ABSTRACT Plasmodium falciparum has a complex life cycle that involves interaction with multiple tissues inside the human and mosquito hosts. Identification of essential genes at all different stages of the P. falciparum life cycle is urgently required for clinical development of tools for malaria control and eradication. However, the study of P. falciparum is limited by the inability to genetically modify the parasite throughout its life cycle with the currently available genetic tools. Here, we describe the detailed characterization of a new marker-free P. falciparum parasite line that expresses rapamycin-inducible Cre recombinase across the full life cycle. Using this parasite line, we were able to conditionally delete the essential invasion ligand AMA1 in three different developmental stages for the first time. We further confirm efficient gene deletion by targeting the nonessential kinase FIKK7.1. IMPORTANCE One of the major limitations in studying P. falciparum is that so far only asexual stages are amenable to rapid conditional genetic modification. The most promising drug targets and vaccine candidates, however, have been refractory to genetic modification because they are essential during the blood stage or for transmission in the mosquito vector. This leaves a major gap in our understanding of parasite proteins in most life cycle stages and hinders genetic validation of drug and vaccine targets. Here, we describe a method that supports conditional gene deletion across the P. falciparum life cycle for the first time. We demonstrate its potential by deleting essential and nonessential genes at different parasite stages, which opens up completely new avenues for the study of malaria and drug development. It may also allow the realization of novel vaccination strategies using attenuated parasites.
Bioactivation of Napabucasin Triggers Reactive Oxygen Species–Mediated Cancer Cell Death

Purpose: Napabucasin (2-acetylfuro-1,4-naphthoquinone or BBI-608) is a small molecule currently being clinically evaluated in various cancer types. It has mostly been recognized for its ability to inhibit STAT3 signaling. However, based on its chemical structure, we hypothesized that napabucasin is a substrate for intracellular oxidoreductases and therefore may exert its anticancer effect through redox cycling, resulting in reactive oxygen species (ROS) production and cell death. Experimental Design: Binding of napabucasin to NAD(P)H:quinone oxidoreductase-1 (NQO1), and other oxidoreductases, was measured. Pancreatic cancer cell lines were treated with napabucasin, and cell survival, ROS generation, DNA damage, transcriptomic changes, and alterations in STAT3 activation were assayed in vitro and in vivo. Genetic knockout or pharmacologic inhibition with dicoumarol was used to evaluate the dependency on NQO1. Results: Napabucasin was found to bind with high affinity to NQO1 and to a lesser degree to cytochrome P450 oxidoreductase (POR). Treatment resulted in marked induction of ROS and DNA damage with an NQO1- and ROS-dependent decrease in STAT3 phosphorylation. Differential cytotoxic effects were observed, where NQO1-expressing cells generating cytotoxic levels of ROS at low napabucasin concentrations were more sensitive. Cells with low or no baseline NQO1 expression also produced ROS in response to napabucasin, albeit to a lesser extent, through the one-electron reductase POR. Conclusions: Napabucasin is bioactivated by NQO1, and to a lesser degree by POR, resulting in futile redox cycling and ROS generation. The increased ROS levels result in DNA damage and multiple intracellular changes, one of which is a reduction in STAT3 phosphorylation.
The Effect of a Single Dose of Dark Chocolate on Cardiovascular Parameters and Their Reactivity to Mental Stress

Abstract Objective: This study investigated the effect of a single administration of dark or milk chocolate on blood pressure (BP), heart rate (HR), and double product (DP) in young healthy women at rest and during acute mental stress. Method: Measurements consisted of anthropometry, BP, and HR. Mean arterial BP (MAP) and DP were computed. The relative reactivity of individual variables was quantified as to their percentage change during the rest or test of mental arithmetic (MA) with respect to the respective baseline value. All subjects underwent two tests of MA—one before chocolate administration and the second one 2 hours after chocolate (1 mg/g of body weight) ingestion. Results: Two hours after ingestion at rest, dark chocolate administration resulted in a significant increase in relative values of systolic BP and DP by 5.1% ± 1.4% and 13.7% ± 3.2%, respectively, compared to the responses in the milk chocolate group (−2.4% ± 1.6% and 0.6% ± 3.4%, respectively, p < 0.04 for both comparisons) without changes in diastolic BP, HR, and MAP. During MA-induced acute stress, the relative magnitude of the reactivity of diastolic BP, HR, MAP, and DP decreased by about 10, 16, 8, and 23 percentage points, respectively, 2 hours after ingestion of dark chocolate compared to the relative reactivity determined before dark chocolate ingestion. Milk chocolate failed to affect any of the above-mentioned parameters at rest or during stress. Conclusions: The single oral intake of 85% dark chocolate increased relative values of systolic BP and DP at rest but buffered the reactivity of diastolic BP, HR, MAP, and DP during mental stress, which was not found after ingestion of milk chocolate. Thus, dark chocolate might have a beneficial effect during acute stress due to its ability to buffer cardiovascular reactivity in young healthy women.
Differential Risk for Drug Use by Sexual Minority Status among Electronic Dance Music Party Attendees in New York City

Abstract Background: Drug use among electronic dance music (EDM) party attendees is common; however, studies are needed to examine associations between drug use and sexual orientation as this can inform prevention and harm reduction efforts in the lesbian, gay, and bisexual (LGB) community. Methods: Data were examined from a repeated cross-sectional study of 3066 young adult EDM party attendees surveyed entering nightclubs and dance festivals in New York City between 2016 and 2018. Of these participants, 277 identified as gay/lesbian, 293 identified as bisexual, and 83 identified as other sexuality. We examined how sexual orientation relates to past-year use of various ‘traditional’ drugs (e.g., ecstasy/MDMA/Molly) and new psychoactive substances (NPS; e.g., “bath salts”) in a bivariable and multivariable manner, stratified by sex. Results: Compared to heterosexual males, gay males were at higher odds for use of ecstasy, GHB, and methamphetamine; bisexual males were at higher odds for use of LSD and unknown powders, and males identifying as “other” sexuality were at higher odds for use of mushrooms and 2C drugs. Compared to heterosexual females, lesbians were at higher odds for use of mushrooms and GHB; bisexual females were at higher odds for use of cocaine, LSD, mushrooms, and tryptamines, and females identifying as “other” sexuality were at higher odds for use of cocaine and tryptamines. Conclusions: We determined differential risk of use of different drugs among those who attend EDM parties according to sexual orientation. Findings can be used to tailor prevention messaging to specific groups within the LGB community.
Paediatric Barcelona Olfactory Test-6 (pBOT-6): Validation of a Combined Odour Identification and Threshold Screening Test in Healthy Spanish Children and Adolescents.

BACKGROUND AND OBJECTIVES Few odour tests have been created for children. Objectives: The aim of the present study was to develop and validate a simple and quick olfactory test, suitable for the evaluation of odour identification and threshold in a Spanish paediatric population, the paediatric Barcelona Olfactory Test-6 (pBOT-6). METHODS The pBOT-6 consisted in a set of 6 odorants for a forced-choice identification test (IT), and a 6 dilutions phenyl ethyl alcohol geometric series for the threshold test (TT). The pBOT-6 was compared with the U-sniff test (a validated international paediatric smell test) in 131 Spanish healthy volunteers aged 6-17 years. A Bland-Altman plot was used to determine the agreement between two tests. Reliability was analyzed in fifteenvolunteers using the intraclass correlation coefficient (ICC). Normative data was obtained and 8 children diagnosed with subjective smell loss were tested for validation. RESULTS Bland-Altman analysis demonstrated a minimal bias of -1.71% with upper and lower limit of agreement of -31.1% and 27.6%, respectively. The ICC was 0.83 (95% CI 0.6-0.96) for the IT and 0.73 (95% CI 0.36-0.9) for the TT, showing excellent and good consistency between measurements over time. Mean pBOT-6 scores were significantly higher in healthy volunteers compared with patients with smell loss. Discrimination between normosmia and smell loss was achieved with a sensitivity of 96.9% and a specificity of 100%. CONCLUSIONS The pBOT-6 offers an effectiveand fast method useful in clinical routine to distinguish, with high sensitivity and specificity, between paediatric patients with normosmia and those with smell dysfunction.
Effectiveness in clinical practice versus efficacy of dipeptidyl peptidase-4 inhibitors in clinical trials for type 2 diabetes: protocol for systematic review

Introduction Data supporting the use of oral antidiabetic drugs mainly rely on data from premarketing clinical trials. Real-world data studies are crucial to evaluate effectiveness of drugs. The aim of this systematic review is to compare the results obtained for efficacy and effectiveness endpoints on clinical trials and those obtained from routine clinical practice of dipeptidyl peptidase-4 inhibitors. Methods and analysis This systematic review will include randomised controlled trials and observational studies evaluating the efficacy and effectiveness of dipeptidyl peptidase-4 inhibitors, respectively. A literature search will be performed at Medline, Embase, Cochrane Controlled Register of Trials and ClinicalTrials.gov. Search terms comprised the drug name (including the pharmacotherapeutic class and the international non-proprietary name). Data on haemoglobin A1C, blood glucose and body weight will be retrieved. The risk of bias will be independently assessed according to the checklist proposed by Downs and Black. Data will be analysed using descriptive statistics and meta-analysis when applicable. Ethics and dissemination Ethical approval is not required as no primary data are collected. This systematic review will be disseminated through a peer-reviewed publication and at conference meetings.
Discordance in Reporting of Maternal Aggression: Exploring Differences by Characteristics of Children, Mothers, and Their Environments

This study investigated discordant reports of maternal aggression using the Fragile Families and Child Wellbeing Study (N = 1,606). Multinomial logistic regression models predicted discordant reports of hitting and shouting from child, mother, and environmental characteristics. Compared to dyads in which both mothers and children reported aggression, mothers with a college degree had higher child-only and mother-only reports of both hitting and shouting versus mothers with less than a high school diploma. High-income mothers had higher child-only reports of hitting, while families with past Child Protective Services involvement had higher child-only and mother-only reports of hitting. Additionally, children with lower reading test scores and whose fathers had history of incarceration had higher child-only reports of hitting. Families residing in neighborhoods for which mothers were scared to let children play outside also had higher child-only and mother-only reports of hitting and shouting.
The Impacts of Climatic Factors and Vegetation on Hemorrhagic Fever with Renal Syndrome Transmission in China: A Study of 109 Counties

Hemorrhagic fever with renal syndrome (HFRS) is a rodent-borne infectious disease caused by hantaviruses. About 90% of global cases were reported in China. We collected monthly data on counts of HFRS cases, climatic factors (mean temperature, rainfall, and relative humidity), and vegetation (normalized difference vegetation index (NDVI)) in 109 Chinese counties from January 2002 to December 2013. First, we used a quasi-Poisson regression with a distributed lag non-linear model to assess the impacts of these four factors on HFRS in 109 counties, separately. Then we conducted a multivariate meta-analysis to pool the results at the national level. The results of our study showed that there were non-linear associations between the four factors and HFRS. Specifically, the highest risks of HFRS occurred at the 45th, 30th, 20th, and 80th percentiles (with mean and standard deviations of 10.58 ± 4.52 °C, 18.81 ± 17.82 mm, 58.61 ± 6.33%, 198.20 ± 22.23 at the 109 counties, respectively) of mean temperature, rainfall, relative humidity, and NDVI, respectively. HFRS case estimates were most sensitive to mean temperature amongst the four factors, and the lag patterns of the impacts of these factors on HFRS were heterogeneous. Our findings provide rigorous scientific support to current HFRS monitoring and the development of early warning systems.
Ovariectomy increases RANKL protein expression in bone marrow adipocytes of C3H/HeJ mice.

Estrogen deficiency induces bone loss by increasing bone resorption, in part, through upregulation of receptor activator of nuclear factor κB ligand (RANKL). RANKL is secreted by osteoblasts and osteocytes, but more recently also bone marrow (pre-)adipocytes have been shown to express RANKL. Estrogen deficiency increases bone marrow adipose tissue (BMAT). The aim of this study was to determine the effect of ovariectomy on RANKL protein expression by bone marrow adipocytes in C3H/HeJ mice. 14 weeks old, female C3H/HeJ mice (n=20) were randomized to sham surgery (Sham) or ovariectomy (OVX). After 4 weeks animals were euthanized. BMAT volume fraction (Ad.V/Ma.V) was quantified by polyoxometalate-based contrast enhanced nanoCT. The percentage of RANKL positive bone marrow adipocytes (RANKL.Pos.N.Ad/N.Ad) and the percentage of RANKL positive osteoblasts covering the bone surface (RANKL.Pos.B.Pm/B.Pm) were quantified in the distal metaphysis of immunohistochemically stained sections of the left femora. The effects of OVX were analyzed by Student's t-test or Mann-Whitney U test. RANKL was detected in osteoblasts, osteocytes and bone marrow adipocytes. OVX significantly increased mean RANKL.Pos. N.Ad/N.Ad (mean±SD: Sham: 42±18%; OVX: 62±14%; P = 0.029), as well as Ad.V/Ma.V (median (IQR): Sham: 1.4 (4.9)%; OVX: 7.2 (7.3)%: P = 0.008), compared to sham surgery. We show that ovariectomy increased both the percentage of RANKL positive bone marrow adipocytes and the total BMAT volume fraction in C3H/HeJ mice. This way RANKL produced by bone marrow adipocytes could be an important contributor to ovariectomy induced bone loss in C3H/HeJ mice.
Gene pool sharing and genetic bottleneck effects in subpopulations of Eschweilera ovata (Cambess.) Mart. ex Miers (Lecythidaceae) in the Atlantic Forest of southern Bahia, Brazil

Abstract Forest loss and fragmentation are the main threats to the maintenance of the Atlantic Forest, an important global biodiversity hotspot. Because of the current critical level of deforestation, ecological corridors are needed to facilitate species dispersion and gene flow among fragments. This study was conducted to investigate the genetic variability and gene pool sharing of Eschweilera ovata in five forest remnants in southern Bahia, Brazil using nuclear simple sequence repeat (nSSR) and plastid simple sequence repeat (cpSSR) microsatellite markers. cpSSR marker analysis revealed the domains of four haplotypes, showing that 80% of the individuals had only four maternal origins, reflecting a founder effect and/or genetic bottleneck. The results of cpSSR and nSSR analyses indicated moderate genetic diversity, particularly in conservation units with full protection, which showed the best parameters of all areas evaluated. Another indication of the susceptibility of these populations to forest loss and fragmentation was the strong genetic bottleneck observed. In contrast, genetic structure analyses (FST and discriminant analysis of principal components) revealed gene pool sharing between the subpopulations, which may reflect the historical gene flow that occurred before forest fragmentation.
Assessing Motivational Differences Between Young and Older Adults When Playing an Exergame.

Background: Currently, exergames are used by different age groups for both recreational and training/rehabilitation purposes. However, little is known about how to design exergames so that they are motivating for specific age groups and health outcomes. Objective: In this article, we compare motivational factors between healthy young and older adults by analyzing their assessments of the same balance training exergame. Materials and Methods: We performed a laboratory-based assessment of a custom-made balance training exergame with 12 healthy young and 10 healthy older adults. Their answers to a semistructured text input questionnaire were analyzed qualitatively. Results: Both age groups were motivated by a combination of intrinsic and extrinsic motivational factors. We found that the young adults tended to be motivated by the game challenge and the in-game reward system (scores). In contrast, the older adults were more motivated by the perceived health effects (both physical and cognitive) and the joy of playing, with less regard for the in-game rewards. Conclusion: The differences in motivational factors that were identified between young and older adults have several design implications. For older adults less effort can be put on designing the in-game reward system and more on showing the player the potential health effects of their play. Furthermore, the competition aspect can be downplayed and more focus placed on simply making the gaming experience itself as joyful as possible.
miR-125a-5p inhibits tumorigenesis in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most prevalent and deadly cancers world-wide. miR-125a-5p is a tumor suppressor in HCC and other cancers, but its mechanisms of action during HCC tumorigenesis remain largely unknown. In this study, we found that miR-125a-5p expression was significantly lower in HCC tissues and cell lines than matched normal tissues and liver cells. miR-125a-5p overexpression inhibited HCC cell proliferation and induced apoptosis in vitro and in vivo, while miR-125a-5p knockdown had the opposite effects. In addition, PTPN1 and MAP3K11 were identified as targets of miR-125a-5p. Knocking down PTPN1 and MAP3K11 activated the JNK MAPK signaling pathway to suppress HCC cell proliferation and induce apoptosis. Our findings suggest that miR-125a-5p may be a useful therapeutic target for treatment of HCC patients.
PEGylated chitosan and PEGylated PLCL for blood vessel repair: An in vitro study

In this study, we fabricated native tissue mimicking a bilayered small-diameter vascular graft based on PEGylated chitosan (PEG–CS) and poly(l-lactic acid-co-ε-caprolactone) (PLCL). PEG–CS possesses good hemocompatibility, and as the inner layer of a vascular graft, it is more likely to swell and deform to debris, causing a blood clot, so the PLCL was added to stabilize it. In order to optimize the performance of the inner layer, PEG–CS blends with different ratios of PLCL (P/C:PLCL) casting films were fabricated, and endothelial cell compatibility and hemocompatibility were tested. The outer layer of the graft was fabricated via electrospinning with PLCL blends with different ratios of water-soluble polyethylene glycol. After water treatment, we tested smooth muscle cell penetration. Designing a two-layer vascular graft structure with an inner layer of P/C:PLCL = 1:6 and an outer layer being composed of a PLCL blend with 12% polyethylene glycol offers very good hemocompatibility and fast cell growth and also reserves well mechanical properties with good cell infiltration. Therefore, this kind of graft has a high potential to be used as an artificial blood vessel.
Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016–2018

ABSTRACT Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016–2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2. 1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3. 4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.