Miracle-dz/UniFAR-FTUs huggingface dataset:
Culture of Intestinal Epithelial Cell Monolayers and Their Use in Multiplex Macromolecular Permeability Assays for In Vitro Analysis of Tight Junction Size Selectivity

Tight junctions form a selectively permeable barrier that limits paracellular flux across epithelial‐lined surfaces. Small molecules (less than ∼8 Å diameter) can traverse the junction via the size‐ and charge‐selective, high‐conductance pore pathway. In contrast, the low‐conductance leak pathway accommodates larger macromolecules (up to ∼100 Å diameter) and is not charge‐selective. Flux across the tight junction–independent, high‐conductance, non‐selective, unrestricted pathway occurs at sites of epithelial damage. Cytokines can regulate each of these pathways, but commonly used measures of barrier function cannot discriminate between tight junction regulation and epithelial damage. This article describes methods for culturing intestinal epithelial cell monolayers and assessing the impact of cytokine treatment on leak and unrestricted pathway permeabilities. © 2020 Wiley Periodicals LLC.
Plastid Engineering of a Marine Alga, Nannochloropsis gaditana, for Co‐Expression of Two Recombinant Peptides

The purpose of this study was to establish a plastid transformation system for expressing recombinant proteins in Nannochloropsis gaditana. On the basis of the sequenced plastid genome, the homologous flanking region, 16S‐trnI/trnA‐23S, and the endogenous regulatory fragments containing the psbA promoter, rbcL promoter, rbcL terminator, and psbA terminator were amplified from N. gaditana as elements of a plastid transformation vector. Then, the herbicide‐resistant gene (bar) was used as a selectable marker, regulated by the psbA promoter and rbcL terminator. Finally, two codon‐optimized antimicrobial peptide‐coding genes linked by endogenous ribosome binding site (RBS) in a polycistron were inserted into the constructed vector under the regulation of the rbcL promoter and psbA terminator. After microparticle bombardment, the positive clones were detected using polymerase chain reaction (PCR), and Southern and Western blotting were used to assess the co‐expression of the two antimicrobial peptides from the plastid. Nannochloropsis gaditana showed the potential to express recombinant proteins for biotechnological applications, for example, for the development of oral vaccines in aquaculture.
The Destructive Fungal Pathogen Botrytis cinerea—Insights from Genes Studied with Mutant Analysis

Botrytis cinerea is one of the most destructive fungal pathogens affecting numerous plant hosts, including many important crop species. As a molecularly under-studied organism, its genome was only sequenced at the beginning of this century and it was recently updated with improved gene annotation and completeness. In this review, we summarize key molecular studies on B. cinerea developmental and pathogenesis processes, specifically on genes studied comprehensively with mutant analysis. Analyses of these studies have unveiled key genes in the biological processes of this pathogen, including hyphal growth, sclerotial formation, conidiation, pathogenicity and melanization. In addition, our synthesis has uncovered gaps in the present knowledge regarding development and virulence mechanisms. We hope this review will serve to enhance the knowledge of the biological mechanisms behind this notorious fungal pathogen.
Channelling carbon flux through the meta‐cleavage route for improved poly(3‐hydroxyalkanoate) production from benzoate and lignin‐based aromatics in Pseudomonas putida H

Lignin‐based aromatics are attractive raw materials to derive medium‐chain length poly(3‐hydroxyalkanoates) (mcl‐PHAs), biodegradable polymers of commercial value. So far, this conversion has exclusively used the ortho‐cleavage route of Pseudomonas putida KT2440, which results in the secretion of toxic intermediates and limited performance. Pseudomonas putida H exhibits the ortho‐ and the meta‐cleavage pathways where the latter appears promising because it stoichiometrically yields higher levels of acetyl‐CoA. Here, we created a double‐mutant H‐ΔcatAΔA2 that utilizes the meta route exclusively and synthesized 30% more PHA on benzoate than the parental strain but suffered from catechol accumulation. The single deletion of the catA2 gene in the H strain provoked a slight attenuation on the enzymatic capacity of the ortho route (25%) and activation of the meta route by nearly 8‐fold, producing twice as much mcl‐PHAs compared to the wild type. Inline, the mutant H‐ΔcatA2 showed a 2‐fold increase in the intracellular malonyl‐CoA abundance – the main precursor for mcl‐PHAs synthesis. As inferred from flux simulation and enzyme activity assays, the superior performance of H‐ΔcatA2 benefited from reduced flux through the TCA cycle and malic enzyme and diminished by‐product formation. In a benzoate‐based fed‐batch, P. putida H‐ΔcatA2 achieved a PHA titre of 6.1 g l–1 and a volumetric productivity of 1.8 g l–1 day–1. Using Kraft lignin hydrolysate as feedstock, the engineered strain formed 1.4 g l‐ 1 PHA. The balancing of carbon flux between the parallel catechol‐degrading routes emerges as an important strategy to prevent intermediate accumulation and elevate mcl‐PHA production in P. putida H and, as shown here, sets the next level to derive this sustainable biopolymer from lignin hydrolysates and aromatics.
Systematic review: Investigating the prognostic performance of four non‐invasive tests in alcohol‐related liver disease

Mortality of alcohol‐related liver disease (ArLD) is increasing, and liver fibrosis stage is the best mortality predictor. Non‐invasive tests (NITs) are increasingly used to detect fibrosis, but their value as prognostic tests in chronic liver disease, and in particular in ArLD, is less well recognized. We aimed to describe the prognostic performance of four widely used NITs (Fibrosis 4 test [FIB4], Enhanced Liver Fibrosis [ELF] test, FibroScan, and FibroTest) in ArLD.
Internal Consistency of Yesavage Geriatric Depression Scale (GDS 15-Item Version) in Ecuadorian Older Adults

The present study aimed to assess the validity of a Spanish version of the Geriatric Depression-15 Scale (GDS-15) in Ecuadorian adults. Cross-sectional study to validate GDS-15 in its short version (GDS-15). Internal consistency and factor structure were assessed through Kuder Richardson 20 and Confirmatory Factor Analysis. A total of 211 subjects 65 years of age and older participated in the validation process. Internal consistency was adequate, the Kuder Richardson 20 coefficient for the total scale was 0.73. Three factor structure was found for the scale. This study highlights the importance of having a validated scale for screening depression in the elderly. This study provides an evidence for the use of GDS-15 in Ecuadorian elderly population to screen for depression.
Search for New Allergens in Lolium perenne Pollen Growing under Different Air Pollution Conditions by Comparative Transcriptome Study

The relationship between air pollution and the allergenic capacity of pollen is widely accepted, with allergenicity being directly related to air pollution. To our knowledge, this is the first study comparing the differential expression of Lolium perenne pollen genes by RNAseq, in two wild populations with different levels of air pollution. The objective is to search for proteins that are expressed differentially in both situations and to establish a relationship with increased allergenic capacity. Two populations of L. perenne (Madrid and Ciudad Real) have been studied in two consecutive years, under the rationale that overexpressed genes in Madrid, with higher levels of NO2 and SO2, could be a cause for their greater allergenic capacity. Heat shock proteins (HSP), glycoside hydrolases, proteins with leucin-rich repeat motifs, and proteins with EF-HAND motifs were consistently overexpressed in Madrid pollen in the two years studied. Interestingly, some genes were overexpressed only in one of the years studied, such as pectinesterases in the first year, and lipid transfer proteins (LTPs) and thaumatin in the second. Despite the fact that the potential of all these proteins in relation to possible allergies has been reported, this is the first time they are cited as possible allergens of L. perenne. The results found can contribute decisively to the knowledge of the allergens of L. perenne and their relationship with atmospheric pollution, and to the development of much more effective vaccines.
Portable Gait Lab: Estimating Over-Ground 3D Ground Reaction Forces Using Only a Pelvis IMU

As an alternative to force plates, an inertial measurement unit (IMU) at the pelvis can offer an ambulatory method for measuring total center of mass (CoM) accelerations and, thereby, the ground reaction forces (GRF) during gait. The challenge here is to estimate the 3D components of the GRF. We employ a calibration procedure and an error state extended Kalman filter based on an earlier work to estimate the instantaneous 3D GRF for different over-ground walking patterns. The GRF were then expressed in a body-centric reference frame, to enable an ambulatory setup not related to a fixed global frame. The results were validated with ForceShoesTM, and the average error in estimating instantaneous shear GRF was 5.2 ± 0.5% of body weight across different variable over-ground walking tasks. The study shows that a single pelvis IMU can measure 3D GRF in a minimal and ambulatory manner during over-ground gait.
Magnesium Sensing Regulates Intestinal Colonization of Enterohemorrhagic Escherichia coli O157:H7

Sensing specific gut metabolites is an important strategy for inducing crucial virulence programs by enterohemorrhagic Escherichia coli (EHEC) O157:H7 during colonization and infection. Here, we identified a virulence-regulating pathway wherein the PhoQ/PhoP two-component regulatory system signals to the O island 119-encoded low magnesium-induced regulator A (LmiA), which, in turn, activates locus of enterocyte effacement (LEE) genes to promote EHEC O157:H7 adherence in the low-magnesium conditions of the large intestine. This regulatory pathway is widely present in a range of EHEC and enteropathogenic E. coli (EPEC) serotypes. Disruption of this pathway significantly decreased EHEC O157:H7 adherence in the mouse intestinal tract. Moreover, mice fed a magnesium-rich diet showed significantly reduced EHEC O157:H7 adherence in vivo, indicating that magnesium may help in preventing EHEC and EPEC infection in humans. ABSTRACT The large intestinal pathogen enterohemorrhagic Escherichia coli (EHEC) O157:H7 detects host cues to regulate virulence gene expression during colonization and infection. However, virulence regulatory mechanisms of EHEC O157:H7 in the human large intestine are not fully understood. Herein, we identified a virulence-regulating pathway where the PhoQ/PhoP two-component regulatory system senses low magnesium levels and signals to the O island 119-encoded Z4267 (LmiA; low magnesium-induced regulator A), directly activating loci of enterocyte effacement genes to promote EHEC O157:H7 adherence in the large intestine. Disruption of this pathway significantly decreased EHEC O157:H7 adherence in the mouse intestinal tract. Moreover, feeding mice a magnesium-rich diet significantly reduced EHEC O157:H7 adherence in vivo. This LmiA-mediated virulence regulatory pathway is also conserved among several EHEC and enteropathogenic E. coli serotypes; therefore, our findings support the use of magnesium as a dietary supplement and provide greater insights into the dietary cues that can prevent enteric infections. IMPORTANCE Sensing specific gut metabolites is an important strategy for inducing crucial virulence programs by enterohemorrhagic Escherichia coli (EHEC) O157:H7 during colonization and infection. Here, we identified a virulence-regulating pathway wherein the PhoQ/PhoP two-component regulatory system signals to the O island 119-encoded low magnesium-induced regulator A (LmiA), which, in turn, activates locus of enterocyte effacement (LEE) genes to promote EHEC O157:H7 adherence in the low-magnesium conditions of the large intestine. This regulatory pathway is widely present in a range of EHEC and enteropathogenic E. coli (EPEC) serotypes. Disruption of this pathway significantly decreased EHEC O157:H7 adherence in the mouse intestinal tract. Moreover, mice fed a magnesium-rich diet showed significantly reduced EHEC O157:H7 adherence in vivo, indicating that magnesium may help in preventing EHEC and EPEC infection in humans.
Management of infection among Medicare beneficiaries with HIV/AIDS: risk of diabetes with protease inhibitors and associated racial disparities using big data approach

ABSTRACT Association between protease inhibitors (PI) and Type II diabetes mellitus (T2DM) in human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) patients is largely debated. This study examined the odds of developing T2DM among HIV/AIDS Medicare beneficiaries treated with PI and possible racial disparities in the odds. We performed a nested casecontrol study of Medicare database 2013–2017. We included HIV/AIDS positive beneficiaries who were enrolled continuously in Medicare Part A/B with no previous history of T2DM. PI-users were matched to non-PI users and non-anti-retroviral therapies (ART) users using a1:1 greedy propensity score (PS) matching . Multivariablee logistic regressions were performed to assess the odds of developing T2DM. The analysis included 2,353 HIV/AIDS beneficiaries. Matched samples were generated for PI vs. non-PI groups (n = 484) and PI vs. non-ART groups (n = 490). Compared to the non-PI group, the odds of developing T2DM were higher in PI-users (AOR: 1.76; 95% CI: 1.17–2.64), in Caucasian PI-users (AOR: 1.81; 95% CI: 1.02–3.22) and in African-American PI-users (AOR: 1.86; 95% CI: 1.03–3.36). Compared to the non-ART group, the odds of developing T2DM were higher in PI-users (AOR: 1.87; 95% CI: 1.25–2.81), in Caucasian PI-users (AOR: 1.96; 95% CI: 1.14–3.39) and in African-American PI-users (AOR: 2.05; 95% CI: 1.03–4.09). The use of PI is associated with higher odds of T2DM; odds were higher among African-Americans than Caucasians.
Obesity and Diabetes: A Sword of Damocles for Future Generations

Childhood obesity is one of the most challenging problem of the 21st century. The prevalence has increased, reaching an alarming rate. Furthermore, the problem is global and is also affecting low- and middle-income countries. This global obesity epidemic explains how the roots of cardiovascular disease, the most common cause of mortality among adults, begin in childhood. Overweight and obese children are likely to stay obese into adulthood and to develop noncommunicable diseases such as diabetes and cardiovascular diseases at a younger age. Thus, prevention should be the major goal and should start early in life. The aim of this review is to present an updated framework of the current understanding of the cardiovascular and metabolic risks in obese children and adolescents and to discuss the available therapeutic options.
Intra-arterial lidocaine for pain control after uterine artery embolization: a meta-analysis of randomized controlled trials

Abstract Introduction The efficacy of intra-arterial lidocaine for pain control of uterine artery embolization remains controversial. We conduct a systematic review and meta-analysis to explore the influence of intra-arterial lidocaine versus placebo on the postoperative pain intensity of uterine artery embolization. Methods We searched PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases through April 2020 for randomized controlled trials (RCTs) assessing the effect of intra-arterial lidocaine versus placebo on pain control of uterine artery embolization. This meta-analysis is performed using the random-effect model. Results Three RCTs were included in the meta-analysis. Overall, compared with control group for uterine artery embolization, intra-arterial lidocaine was associated with substantially reduced pain scores at 4 h (SMD = −0.85; 95% CI = −1.31 to −0.38; p = .0003) and analgesic consumption (SMD = −0.84; 95% CI = −1.26 to −0.42; p < .0001), but has no obvious influence on pain scores at 7 h (SMD = −0.19; 95% CI = −0.63 to 0.25; p = .40) or pain scores at 24 h (SMD = −0.55; 95% CI = −1.25 to 0.16; p = .13). Conclusions Intra-arterial lidocaine is effective for pain control after uterine artery embolization.
Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry

In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner.
Changes in Non-Nutritive Sweetener Consumption Patterns in Response to a Sugar-Sweetened Beverage Reduction Intervention

Data are lacking on whether non-nutritive sweeteners (NNS) can be used as a strategy to support decreases in sugar-sweetened beverage (SSB) consumption. The purpose of this secondary analysis of a 6-month SSB-reduction intervention was to explore changes in NNS consumption patterns in Talking Health participants within the SIPsmartER (n = 101) intervention. Additionally, participant characteristics were compared for three SSB-NNS change groups (decrease SSB/increase NNS; decrease SSB/no increase in NNS; increase/no change in SSB/regardless of NNS). There was a significant increase in aspartame and total NNS intake for participants (mean daily mg increases of 37.2 ± 13.9 and 63.7 ± 18.5, respectively). With the exception of sex, no differences in participant characteristics were found between the three SSB-NNS change groups. Furthermore, no significant changes in weight or body mass index (BMI) were demonstrated between SSB-NNS change groups over time. Diet soda was the most commonly consumed source of NNS; however, other dietary sources of NNS also contributed to intake. At 6 months, intake of sucralose and saccharin were primarily from dietary sources other than diet sodas (94% and 100%, respectively). These findings suggest that NNS may be a feasible strategy to help reduce SSB consumption. This study supports the need to consistently quantify and identify NNS intake, beyond using diet soda intake as a proxy for NNS intake and grouping all NNS types into one variable, to more accurately address the potential health effects of NNS.
Measuring Quality of Life in Ovarian Cancer Clinical Trials—Can We Improve Objectivity and Cross Trial Comparisons?

Simple Summary Regarded as the “disease that whispers” ovarian cancer remains difficult to diagnose and treat due to other complex conditions that may occur together. As research into new treatments for ovarian cancer continues, growing efforts to understand how treatments may be impact the day to day lives of women is also growing. Known as Patient Reported Outcomes or PROs and quality of life (QoL), the research community is improving how this important information communicated by women with ovarian cancer is captured across their cancer journey, and importantly, how this information can be used further refine treatments. Understanding the impact treatment has on day to day living is important, as new treatments should not only help control cancer cells, but also help keep women living with ovarian cancer living their lives to the fullest. Abstract Epithelial ovarian cancer (EOC) remains a lethal disease for the majority of women diagnosed with it worldwide. For the majority of patients, diagnosis occurs late, in the advanced setting. Disease-induced as well as treatment-related adverse events can negatively impact quality of life (QoL). Research to date has captured these data through use of patient-related outcomes (PROs) and, increasingly, has become an area of increased attention and focus in clinical trial reporting. QoL/PRO measurements in EOC clinical trials at different transition points in a patient’s journey are increasingly being recognized by patients, clinicians and regulatory agencies as the key determinants of treatment benefit. Various context-specific PROs and PRO endpoints have been described for clinical trials in EOC. Standardized approaches and checklists for incorporating PRO endpoints in clinical trials have been proposed. In a real-world clinical practice setting, PRO/QoL measures, which are meaningful, valid, reliable, feasible and acceptable to patients and clinicians, need to be implemented and used. These may assist by serving as screening tools; helping with the identification of patient preferences to aid in decision making; improving patient–provider communication; facilitating shared decision making. Importantly, they may also improve quality of care through an increasingly patient-centered approach. Potential areas of future research include assessment of anxiety, depression and other mental health issues. In good prognostic groups, such as maintenance clinical trials, following patients beyond progression will capture possible downstream effects related to delaying the psychological trauma of relapse, symptoms due to disease progression and side-effects of subsequent chemotherapy. Identifying PRO endpoints in next-generation-targeted therapies (including immunotherapies) also warrants investigation.
Optogenetic investigation of BMP target gene expression diversity

Signaling molecules activate distinct patterns of gene expression to coordinate embryogenesis, but how spatiotemporal expression diversity is generated is an open question. In zebrafish, a BMP signaling gradient patterns the dorsal-ventral axis. We systematically identified target genes responding to BMP and found that they have diverse spatiotemporal expression patterns. Transcriptional responses to optogenetically delivered high- and low-amplitude BMP signaling pulses indicate that spatiotemporal expression is not fully defined by different BMP signaling activation thresholds. Additionally, we observed negligible correlations between spatiotemporal expression and transcription kinetics for the majority of analyzed genes in response to BMP signaling pulses. In contrast, spatial differences between BMP target genes largely collapsed when FGF and Nodal signaling were inhibited. Our results suggest that, similar to other patterning systems, combinatorial signaling is likely to be a major driver of spatial diversity in BMP-dependent gene expression in zebrafish.