Miracle-dz/UniFAR-FTUs huggingface dataset:
Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway

Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested one crucial HGT event. We studied the evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows this pathway to be present in more lineages than previously proposed and that nitrate assimilation is restricted to autotrophs and to distinct osmotrophic groups. Our phylogenies show a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. Our results, based on a larger dataset, differ from the previously proposed transfer of a nitrate assimilation cluster from Oomycota (Stramenopiles) to Dikarya (Fungi, Opisthokonta). We propose a complex HGT path involving at least two cluster transfers between Stramenopiles and Opisthokonta. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, and of a novel nitrate reductase in Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.
Effect of acute heat stress and slaughter processing on poultry meat quality and postmortem carbohydrate metabolism

&NA; This study investigated the effects of acute heat stress and slaughter processing on poultry meat quality and carbohydrate metabolism. Broilers (200) were randomly divided into 2 groups receiving heat stress (HS; 36°C for one h), compared to a non‐stressed control (C). At slaughter, each group was further divided into 2 groups for slaughter processing (L = laboratory; F = commercial factory). L group breasts were removed immediately after bleeding without carcass scalding or defeathering, and stored at 4°C. F group broilers were scalded (60°C, 45 s) after bleeding and defeathering. Then the breasts were removed and cooled in ice water until the core temperature was ≤4°C. Rates of Pectoralis core temperature and pH decline were changed by slaughter processing, but only HS affected ultimate pH in group L. HS muscles had higher L* values (P < 0.05) than controls at 24 h postmortem. Laboratory processing “hot‐deboning” increased drip loss, which resulted in a lower cooked loss (P < 0.05). Postmortem glycolysis was affected only by HS. The speed of lactic acid accumulation and glycogen degradation was faster in the HS group than controls at 5 min postmortem. During storage the glycolysis rates were not different (P > 0.05). Sarcoplasmic protein solubility was higher in F processed birds (P < 0.05). HS decreased the solubility of myofibrillar and total protein in the L‐slaughtered birds. Thus, HS caused a higher frequency of accelerated muscle glycolysis than controls. Factory processing (chilling) could not completely eliminate the effects of accelerated glycolysis caused by pre‐slaughter HS.
Optimization of Municipal Waste Collection Routing: Impact of Industry 4.0 Technologies on Environmental Awareness and Sustainability

The accelerated movement of people towards cities led to the fact that the world’s urban population is now growing by 60-million persons per year. The increased number of cities’ population has a significant impact on the produced volume of household waste, which must be collected and recycled in time. The collection of household waste, especially in downtown areas, has a wide range of challenges; the collection system must be reliable, flexible, cost efficient, and green. Within the frame of this paper, the authors describe the application possibilities of Industry 4.0 technologies in waste collection solutions and the optimization potential in their processes. After a systematic literature review, this paper introduces the waste collection process of downtowns as a cyber-physical system. A mathematical model of this waste collection process is described, which incorporates routing, assignment, and scheduling problems. The objectives of the model are the followings: (1) optimal assignment of waste sources to garbage trucks; (2) scheduling of the waste collection through routing of each garbage truck to minimize the total operation cost, increase reliability while comprehensive environmental indicators that have great impact on public health are to be taken into consideration. Next, a binary bat algorithm is described, whose performance is validated with different benchmark functions. The scenario analysis validates the model and then evaluates its performance to increase the cost-efficiency and warrant environmental awareness of waste collection process.
Multilevel Factors Predicting Cardiac Rehabilitation Attendance and Adherence in Underserved Patients at a Safety-Net Hospital

Purpose: This study examined multilevel factors as predictors of cardiac rehabilitation (CR) attendance and adherence among underserved patients at a safety-net hospital (SNH). Methods: Participants were recruited during hospitalization for a cardiac procedure or event. Participants responded to a questionnaire, and outcome data (including CR attendance and adherence) were extracted from medical records at baseline and 6 mo post-discharge. Results: Data were collected from 171 participants, 92 (53.8%) of whom attended CR. On average, participants completed 24 CR sessions (66.7% adherence) and 40 (43.5%) participants fully adhered to the 36 prescribed sessions. Bivariate comparisons showed that participants who attended CR were more likely to have insurance (P = .002), perceive CR as important (P = .008), believe they needed CR (P = .005), and endorsed fewer barriers to CR (P = .005) than their nonattending counterparts. After controlling for insurance status, a regression analysis to predict attendance revealed only 1 predictor; perceived lack of time (P = .04). Bivariate analyses showed that only 1 clinical factor, treatment during hospitalization, was significantly related to adherence (P = .03). Patients with medical management alone (no revascularization) showed less adherence than their counterparts with revascularization. Conclusions: Although access to insurance is a significant predictor of attendance, psychological barriers that are amenable to being addressed by CR staff are also important. Findings suggest that perceived lack of time is important in SNH patient decision making to attend CR. This psychological barrier is a subject on which CR staff can intervene to educate patients about the life expectancy increases and decreased personal health care expenditures because of attendance.
Ex Vivo Signaling Protein Mapping in T Lymphocytes in the Psoriatic Arthritis Joints

We assessed signaling protein mapping in total T cells, to analyze the proportions of T regulatory (Treg) and TCD4+ effector (Teff) cell phenotypes, and the respective interleukin 6Rα (IL-6Rα) expression in the inflammatory microenvironment of synovial fluid (SF) of patients with sustained psoriatic arthritis (PsA). Our approach was to measure the IL-6 level in SF using a multiplex bead immunoassay. Reverse-phase protein array was used to assess Janus kinase (JAK) 1 and JAK2, extra-cellular regulated kinase (ERK) 1 and 2, protein kinase Cδ (PKCδ), signal transducer and activator and transcription (STAT) 1, STAT3, and STAT5 phosphoproteins in total T cell lysates from SF of patients with PsA. Frequencies of CD4+IL-17A-F+IL-23+ CD4+ Th cells producing IL-17A and IL-17F (Th17) and CD4+CD25high intracellular forkhead box transcription factor+ (FOXP3+) phenotypes, and the percentage of Treg– and Teff– cells were quantified in SF and matched peripheral blood (PB) of patients with PsA and PB of healthy controls (HC) by flow cytometry. Our results were the following: In PsA SF samples, a coordinate increase of JAK1, ERK1/2, STAT1, STAT3, and STAT5 phosphoproteins was found in total T cells in SF of PsA; where IL-6 levels were higher than in PB from HC. Expanded CD4+IL-17A–F+IL-23+ Th17, CD4+ CD25– Teff– and CD4+CD25high FoxP3+Treg subsets, showing similar levels of enhanced IL-6Rδ expression, were confined to PsA joints. In our studies, the transcriptional network profile identified by ex vivo signaling protein mapping in T lymphocytes in PsA joints revealed the complex interplay between IL-1, IL-6, and IL-23 signaling and differentiation of Th17 cells and CD4+Tregs in sustained joint inflammation in PsA.
Epidemiology of Macular Edema in Uveitis

ABSTRACT Purpose: To describe the epidemiology of macular edema (ME) in patients with uveitis. Methods: Review of articles listed on PubMed pertaining to uveitic ME. Results: Reported rates of uveitic ME ranging from 20% to 70%, depending on the ancillary tests used (fundus examination, fluorescein angiography, optical coherence tomography). Macular edema might develop due to uveitis itself, or occur as an adverse effect of drugs taken for different diseases. It is more frequently observed in adults than in children, in chronic uveitis, and in intermediate uveitis. Males with ankylosing spondylitis are more prone to develop ME than females. Three patterns of uveitic ME are observed, either isolated or in combination: cystoid ME, the most frequently encountered pattern seen in up to 80% of cases, diffuse ME and serous retinal detachment. Conclusion: Older age, chronicity of uveitis and intermediate uveitis are risk factors for the development of ME in patients with uveitis.
Inhibition of PAI (Plasminogen Activator Inhibitor)-1 Improves Brain Collateral Perfusion and Injury After Acute Ischemic Stroke in Aged Hypertensive Rats

Background and Purpose— Aging and hypertension, comorbidities prevalent in the stroke population, are associated with poor collateral status and worsened stroke outcome. However, underlying mechanisms by which these conditions affect stroke outcome are not clear. We studied the role of PAI (plasminogen activator inhibitor)-1 that is increased in aging and hypertension on brain and vascular expression of inflammatory factors and perfusion that may contribute to worse stroke outcomes. Methods— Aged (≈50 weeks) and young (≈18 weeks) spontaneously hypertensive rats (SHR) were subjected to ischemia by middle cerebral artery occlusion (2 hours) and reperfusion (2 hours) with or without treatment with the PAI-1 inhibitor TM5441. Changes in middle cerebral artery and collateral perfusion territories were measured by multisite laser Doppler. Reactivity to TM5441 was studied using isolated and pressurized leptomeningeal anastomotic arterioles. Brain injury was determined by 2,3,5-triphenyltetrazolium staining and quantitative immunohistochemistry of amyloid-&bgr;-42, PAI-1, and hemoglobin. Circulating inflammatory factors were measured by ELISA. Results— Changes in cerebral blood flow during middle cerebral artery occlusion were similar between groups, with both having poor collateral perfusion and incomplete reperfusion. However, aged SHR had greater brain injury versus young (41±2 versus 23±2%, P<0.05) as well as increased brain deposition of amyloid-&bgr;-42 and circulating oxLDL (oxidized low-density lipoprotein). Erythrocyte aggregation and hemorrhage within the injured brain was observed in 50% of aged but no young SHR, with increased circulating PAI-1 in this subgroup of aged SHR (16±3 versus 6±2 ng/mL, P<0.05). PAI-1 inhibition with TM5441 improved brain injury but did not affect hemorrhage. TM5441 increased collateral perfusion by 38±7% and dilated leptomeningeal anastomotic arterioles by 44±10%, which was abolished by nitric oxide synthase inhibition. Conclusions— Increased injury in aged SHR seemed to be related to poor collateral perfusion, hemorrhagic transformation, increased amyloid-&bgr;-42, and oxidative stress. PAI-1 inhibition reduced infarction in both groups of SHR that possibly due, in part, to increased collateral perfusion.
Flexural Capacity and Deflection of Fiber-Reinforced Lightweight Aggregate Concrete Beams Reinforced with GFRP Bars

Adding fibers is highly effective to enhance the deflection and ductility of fiber-reinforced polymer (FRP)-reinforced beams. In this study, the stress and strain conditions of FRP-reinforced lightweight aggregate concrete (LWC) beams with and without fibers at ultimate load level were specified. Based on the sectional analyses, alternative equations to predict the balanced reinforcement ratio and flexural capacity for beams failed by balanced failure and concrete crushing were established. A rational equation for estimating the short-term stiffness of FRP–LWC beams at service-load levels was suggested based on Zhu’s model. In addition, the contribution of the steel fibers on the short-term stiffness was quantified incorporating the effects of FRP reinforcement ratio. The proposed short-term stiffness model was validated with measured deflections from an experimental database for fiber-reinforced normal weight concrete (FNWC) beams reinforced with FRP bars. Furthermore, six glass fiber-reinforced polymer (GFRP)-reinforced LWC beams with and without steel fibers were tested under four-point bending. Based on the test results, the proposed models and procedures according to current design codes ACI 440.1R, ISIS-M03, GB 50608, and CSA S806 were linked together by comparing their predictions. The results showed that increasing the reinforcement ratio and adding steel fibers decreased the strain of the FRP bars. The flexural capacity of the LWC beams with and without steel fibers was generally underestimated by the design codes, while the proposed model provided accurate ultimate moment predictions. Moreover, the proposed short-term stiffness model yielded reasonable estimations of deflection for both steel fiber-reinforced lightweight aggregate concrete (SFLWC) and FNWC beams.
Efficacy of hydration in the prevention of contrast material-induced nephropathy.

I thank Dr Hall for his interest in my article (1). Regarding the term “Lazarus syndrome,” he is correct in its dictionary definition. My use of the term was not intended to be a strict medical or Wikipedia definition, but rather a broader, more liberal (dare I say “poetic”) use. As for his comments regarding the general consensus on wasteful medical care, and the paramount need to address it, I heartily agree. My discourse in no way means to suggest that physicians should be invariably aggressive when faced with similar situations. My intent was to describe the innumerable variables in any individual outlier case and the difficulties doctors face balancing concerns such as those expressed by Dr Hall (and the articles he references) versus the conundrum at the individual’s point of service. As mentioned in the article, understanding the utilitarian need for appropriate expenditure of increasingly scarce health care resources versus the needs of any individual patient, even an outlier, requires a first-rate intelligence. Clearly, Dr Hall’s comments demonstrate his.
Feasibility and Preliminary Effects of a Telerehabilitation Program for People Living With HIV: A Pilot Randomized Study

Abstract We investigated feasibility and preliminary effects of telerehabilitation for people living with HIV (PLWH) and taking antiretroviral therapy. We randomized 25 PLWH to either an endurance and resistance training exercise (ERTE) group or a control group. Endurance and resistance training exercise sessions occurred in a public fitness center, with online guidance and weekly telephone advice. The primary outcome was feasibility (recruitment and retention rates and safety). Secondary outcomes were assessed at baseline and 6 weeks according to the three International Classification of Functioning, Disability, and Health domains. Nine patients completed the ERTE program. Recruitment and retention rates were 93% and 69%, respectively. No adverse events occurred. After 6 weeks, percentage change in D-dimer was lower in the ERTE group, but not significantly after the Bonferroni correction. Other parameters were not different between the groups. Therefore, telerehabilitation is feasible in PLWH taking antiretroviral therapy; however, the performance of the program is still questioned, and future research is warranted.
Life Partner Influence on Uptake of Preventive Services: Evidence From Flu Vaccine Adoption Among the Aging Population

Objectives: This study examines how the patterns of life partner concordance on preventive health service uptake vary by a partner’s previous behavioral history and between genders. Method: This study uses 2008 and 2012 waves of Health and Retirement Study (HRS), a nationally representative sample of U.S. aging population, to examine one’s decision to receive a preventive service as a function of the partner’s decision changes over time (N = 2,680). Results: Life partner concordance on preventive service use is different by the partner’s previous use history and gender. Positive partner preventive engagement showed greater association than negative ones. Women are more responsive to the positive health behaviors (of their partners), and men are more sensitive to the negative partner health behaviors. Conclusion: The asymmetric partner concordance by gender and the partner’s previous usage experience provide implications to develop efficient and culturally acceptable interventions to increase the uptake of preventive health services.
PTSD in Children Younger Than the Age of 13: Toward Developmentally Sensitive Assessment and Management

Posttraumatic stress disorder can be more difficult to assess compared to other disorders. The complicated nature of the symptoms contributes to underdetection of the diagnosis in children. The most substantial proposal for the diagnostic criteria is to lower the Criterion C requirement from three to one symptom. Comorbid disorders tend to complicate the clinical picture, but research is reviewed showing that posttraumatic stress disorder is the core, well-defined posttrauma syndrome. Early longitudinal studies have suggested that the course may be more chronic in children than in adults. Caution is urged about how to view the effects of parent–child relationships on children’s symptomatology following trauma. The author organizes advice for interviewing respondents into seven practical suggestions and discusses treatment implications.
Epidemiological links between malaria parasitaemia and hypertension: findings from a population-based survey in rural Côte d’Ivoire

Background: Although potential links between malaria parasitaemia and hypertension have been hypothesized, there is paucity of epidemiologic evidence on this link. We investigated in a population-based survey, the association between malaria parasitaemia and hypertension in Ivorian adults. Methods: We estimated the adjusted odds ratios (OR) and 95% confidence intervals (CI) of hypertension in relation to malaria parasitaemia using multinomial regression, in 997 randomly selected adults in the ‘Côte d’Ivoire Dual Burden of Disease Study’ (CoDuBu), in south-central Côte d’Ivoire. We defined malaria parasitaemia as a positive rapid diagnostic test or identification of Plasmodium spp. on microscopy. Using the mean of the last two of three blood pressure (BP) measurements and questionnaire data, we defined hypertension as SBP at least 140 mmHg or DBP at least 90 mmHg or clinician-diagnosed hypertension. Results: Prevalence of malaria parasitaemia and hypertension were 10 and 22%, respectively. Malaria parasitaemia was negatively associated with hypertension in participants with body temperature 36.5 °C or less [OR 0.23 (95% CI 0.06–0.84)]. Contrastingly, microscopic malaria parasitaemia showed positive associations with hypertension in participants with elevated body temperature [>36.5 °C; OR: 2.93 (95% CI 0.94–9.14)]. Participants having microscopic malaria parasitaemia with elevated body temperature had three-fold higher odds of hypertension [OR: 3.37 (95% CI 1.12–10.0)] than malaria parasitaemia-negatives with lower body temperature. Conclusion: Malaria parasitaemia and hypertension are prevalent and seemingly linked comorbidities in African settings. This link may depend on malaria parasitaemia symptomaticity/latency where individuals with more latent/asymptomatic malaria parasitaemia have lower risk of hypertension and those with more acute/symptomatic malaria parasitaemia have a tendency toward higher BP. The cross-sectional nature of the study limited the distinction of short-term BP elevation (interim pathophysiological stress) from hypertension development. Future longitudinal studies considering malaria/hypertension phenotypes and host molecular variations are needed to clarify involved biological mechanisms, toward comorbidity management.
Myricanol rescues dexamethasone‐induced muscle dysfunction via a sirtuin 1‐dependent mechanism

Muscle atrophy and weakness are adverse effects of high dose or the sustained usage of glucocorticoids. Loss of mitochondria and degradation of protein are highly correlated with muscle dysfunction. The deacetylase sirtuin 1 (SIRT1) plays a vital role in muscle remodelling. The current study was designed to identify myricanol as a SIRT1 activator, which could protect skeletal muscle against dexamethasone‐induced wasting.
Highly Oxygenated Organic Molecules (HOM) from Gas-Phase Autoxidation Involving Peroxy Radicals: A Key Contributor to Atmospheric Aerosol

Highly oxygenated organic molecules (HOM) are formed in the atmosphere via autoxidation involving peroxy radicals arising from volatile organic compounds (VOC). HOM condense on pre-existing particles and can be involved in new particle formation. HOM thus contribute to the formation of secondary organic aerosol (SOA), a significant and ubiquitous component of atmospheric aerosol known to affect the Earth’s radiation balance. HOM were discovered only very recently, but the interest in these compounds has grown rapidly. In this Review, we define HOM and describe the currently available techniques for their identification/quantification, followed by a summary of the current knowledge on their formation mechanisms and physicochemical properties. A main aim is to provide a common frame for the currently quite fragmented literature on HOM studies. Finally, we highlight the existing gaps in our understanding and suggest directions for future HOM research.
TGF-β1 polymorphism in American tegumentary leishmaniasis in a Southern Brazilian population.

INTRODUCTION Genetic polymorphisms define the cytokine production leading to susceptibility or resistance to diseases. We studied the cytokine polymorphism in the development of tegumentary leishmaniasis (TL). METHODS Genotyping of TNF-α, TGF-β1, IFN-γ, IL-6, and IL-10 were performed by polymerase chain reaction assay. RESULTS G and C alleles of TGF- β1 (codon 25) were the most common in controls and patients, respectively. G/G was the most frequent genotype in controls, and G/C and C/C in patients. CONCLUSIONS G/G genotype of codon 25 in TGF-β1 appeared to confer resistance, and G/C and C/C genotypes, susceptibility to TL in this population.