Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Chlamydia trachomatis Infection, Serovar Distribution and Co-Infections with Seven High-Risk HPV Types among Italian Women with a Recent History of Abnormal Cervical Cytology

Chlamydia trachomatis (Ct) and human papillomavirus (HPV) are the most prevalent sexually transmitted infections throughout the world. Despite the serious complications associated with chronic Ct infections in sexually active women, a screening program is not yet available in Italy. Moreover, HPV/Ct co-infections are also known to occur frequently, increasing the risk of HPV-induced carcinogenesis. The aim of this study was to evaluate the prevalence of Ct infections, the distribution of Ct serovars, and the incidences of Ct/HPV co-infections among women with a recent history of abnormal cervical cytology. Cervical samples were collected from 199 women referred for a gynecological visit following an abnormal Pap test results. All samples were tested for the presence of Ct and HPV DNA using real-time PCR assays; Ct typing of positive samples was performed by PCR–RFLP (restriction fragment length polymorphism) targeting the ompA gene. A high percentage of these women (12.8% and 21.7% with or without abnormal cytology on “retesting”, respectively) were found to be Ct positive. Serovar F was the most prevalent type in Ct positive women, followed by E and K. Ct/HPV co-infections were detected in 7% (14/199) of enrolled women, with HPV-16, HPV-51, and HPV-52 being most frequently identified in co-infections. This study provides new epidemiological data on the prevalence of Ct and associated HPV infection in women with a recent history of abnormal cervical cytology in Italy, where notification of cases is not mandatory.
Reducing hazards for humans from animals: emerging and re-emerging zoonoses

Pathogens that are capable of infecting more than one host, more than one taxonomic order and wild hosts, all present a higher relative risk of (re-)emergence. A long environmental persistence gives pathogens a more selective advantage. In case of an emerging or re-emerging zoonosis, the prevalence of infection in animals and the exposure determine the incidence in humans. Human exposure to zoonotic agents depends on lifestyle and occupation (e.g., veterinarians and farmers are more at risk for zoonoses related to livestock). Efforts to increase awareness, provide information on prevention, and apply biosecurity are essential. Moreover, a substantial decline in the incidence of human disease implies the prevention, the control or the elimination of zoonoses in the animal compartments. The only way to prevent health hazards is to adapt the existing systems of health governance at global, regional, national and local levels in a harmonised and coordinated manner. To achieve such a goal, the One Health strategy was recently developed to expand interdisciplinary collaborations and communications on all aspects of health care for humans and animals, veterinary, human medical, public health professionals and stakeholders.
Infection/inflammation-associated preterm delivery within 14 days of presentation with symptoms of preterm labour: A multivariate predictive model

Multi-marker tests hold promise for identifying symptomatic women at risk of imminent preterm delivery (PTD, <37 week’s gestation). This study sought to determine the relationship of inflammatory mediators and metabolites in cervicovaginal fluid (CVF) with spontaneous PTD (sPTD) and delivery within 14 days of presentation with symptoms of preterm labour (PTL). CVF samples from 94 (preterm = 19, term = 75) singleton women with symptoms of PTL studied between 19+0–36+6 weeks’ gestation were analysed for cytokines/chemokines by multiplexed bead-based immunoassay, while metabolites were quantified by enzyme-based spectrophotometry in a subset of 61 women (preterm = 16, term = 45). Prevalence of targeted vaginal bacterial species was determined for 70 women (preterm = 14, term = 66) by PCR. Overall, 10 women delivered within 14 days of sampling. Predictive capacities of individual biomarkers and cytokine-metabolite combinations for sPTD and delivery within 14 days of sampling were analysed by logistic regression models and area under the receiver operating characteristic curve. Fusobacterium sp. , Mubiluncus mulieris and Mycoplasma hominis were detected in more preterm-delivered than term women (P<0.0001), while, M. curtisii was found in more term-delivered than preterm women (P<0.0001). RANTES (0.91, 0.65–1.0), IL-6 (0.79, 0.67–0.88), and Acetate/Glutamate ratio (0.74, 0.61–0.85) were associated with delivery within 14 days of sampling (AUC, 95% CI). There were significant correlations between cytokines and metabolites, and several cytokine-metabolite combinations were associated with sPTD or delivery within 14 days of sampling (e.g. L/D-lactate ratio+Acetate/Glutamate ratio+IL-6: 0.84, 0.67–0.94). Symptomatic women destined to deliver preterm and within 14 days of sampling express significantly higher pro-inflammatory mediators at mid to late gestation. In this cohort, IL-6, Acetate/Glutamate ratio and RANTES were associated with delivery within 14 days of sampling, consistent with their roles in modulating infection-inflammation-associated preterm labour in women presenting with symptoms of preterm birth. Replication of these observations in larger cohorts of women could show potential clinical utility.
Evaluating the Outcome of Two Different Regimes in Adhesive Capsulitis: A Prospective Clinical Study

Objective: Adhesive capsulitis or frozen shoulder is a painful condition affecting up to 5% of the general population. We conducted this study with the aim of evaluating the results of physiotherapy plus intra-articular methylprednisolone injection versus physiotherapy alone in idiopathic frozen shoulder. Methods: This prospective clinical study was conducted in a tertiary care center between August 2016 and August 2018. Patients who were diagnosed with idiopathic frozen shoulder were included in the study, and each patient was randomly allocated to one of two groups: physiotherapy alone (group A) and physiotherapy plus intra-articular steroid injection (group B). Results: A total of 52 cases diagnosed with idiopathic frozen shoulder were included and treated with the two modalities. There was a significant improvement in group B compared to group A at 6 weeks and 3 months in the range of flexion, abduction, and external rotation. The Shoulder Pain and Disability Index showed improvement in both pain and disability score in group B compared to group A, and improvement was significant at 6 weeks and 3 months. Conclusion: The results demonstrate the advantages of physiotherapy plus intra-articular steroid injection in idiopathic frozen shoulder. The predictability of results with physiotherapy plus intra-articular steroid injection in selected patients is excellent, and it is a better modality of treatment compared to physiotherapy alone.
Annexin A5 regulates surface αvβ5 integrin for retinal clearance phagocytosis

ABSTRACT Diurnal clearance phagocytosis by the retinal pigment epithelium (RPE) is a conserved efferocytosis process whose binding step is mediated by αvβ5 integrin receptors. Two related annexins, A5 (ANXA5) and A6 (ANXA6), share an αvβ5 integrin-binding motif. Here, we report that ANXA5, but not ANXA6, regulates the binding capacity for spent photoreceptor outer segment fragments or apoptotic cells by fibroblasts and RPE. Similar to αvβ5-deficient RPE, ANXA5−/− RPE in vivo lacks the diurnal burst of phagocytosis that follows photoreceptor shedding in wild-type retina. Increasing ANXA5 in cells lacking αvβ5 or increasing αvβ5 in cells lacking ANXA5 does not affect particle binding. Association of cytosolic ANXA5 and αvβ5 integrin in RPE in culture and in vivo further supports their functional interdependence. Silencing ANXA5 is sufficient to reduce levels of αvβ5 receptors at the apical phagocytic surface of RPE cells. The effect of ANXA5 on surface αvβ5 and on particle binding requires the C-terminal ANXA5 annexin repeat but not its unique N-terminus. These results identify a novel role for ANXA5 specifically in the recognition and binding step of clearance phagocytosis, which is essential to retinal physiology. This article has an associated First Person interview with the first author of the paper. Summary: Cytosolic annexin A5 regulates the particle binding step of clearance phagocytosis by increasing levels of apical surface αvβ5 integrin receptors of retinal pigment epithelial cells.
Impact of Donor Hepatitis C Virus on Kidney Transplant Outcomes for Hepatitis C-positive Recipients in the Direct-acting Antiviral Era: Time to Revise the Kidney Donor Risk Index?

Supplemental Digital Content is available in the text. Background. Kidneys from donors with hepatitis C virus (HCV) infection are traditionally considered to be at risk for poorer survival outcomes, as reflected in the kidney donor profile index (KDPI). Modern direct-acting antivirals may modify this risk. Methods. Using United Network for Organ Sharing data, HCV-infected adult first-time kidney transplant recipients from 2014 to 2017 were examined. Graft and patient survival were compared in a propensity-matched cohort of recipients of HCV antibody (Ab)(+) kidneys versus Ab(-) kidneys. Subsequent analysis was performed in a propensity-matched cohort of recipients of HCV-viremic (RNA positive) versus HCV-naïve kidneys. Results. There were 379 recipients each in the matched cohort of recipients of HCV Ab(+) versus HCV Ab(-) kidneys. Despite a higher KDPI (58.2% for HCV Ab[+] versus 38.8% for HCV Ab[-]), 1-year patient and graft survival were similar in the HCV(+) and HCV(-) groups (95.4% and 94.9% versus 97.9% and 96.0%, P = 0.543 and P = 0.834, respectively). There were 200 recipients each in the cohort of recipients of HCV-viremic versus HCV-naïve kidneys, with the KDPI again higher in the HCV-viremic group (56.8% versus 35.2%). Baseline hazard ratios (HRs) for graft failure (HR, 4.69; P = 0.009) and death (HR, 7.60; P = 0.003) were significantly elevated in the viremic group, but crossed 1 at 21 and 24 months, respectively. Conclusions. In the modern direct-acting antiviral era, calculated likely KDPI overestimates risk kidneys from HCV (+) donors. Donor viremia conveys an early risk which appears to subside over time. These results suggest that it may be time to revise the kidney donor risk index.
Sera total oxidant/antioxidant status in lung cancer patients

Abstract We investigated oxidative stress parameters in the sera of patients with lung cancer and healthy individuals to evaluate their correlations with lung cancer. Ninety-four lung cancer patients and 64 healthy controls were enrolled after obtaining informed consent. Their sera oxidative stress parameters were measured. Total antioxidant status (TAS), total oxidant status (TOS), and oxidative stress index (OSI) were significantly different between patients and healthy groups (all P < .001). TAS gradually decreased and TOS and OSI gradually increased from stage I to III, but it did not reach statistical significance (all P > .05). TAS and OSI were significantly different between the nonsmoking and smoking groups, radiotherapy and without radiotherapy groups, chemotherapy and without chemotherapy groups (P < .05), but not TOS (P > .05). In a receiver operating characteristic curve analysis comparing patients with lung cancer with healthy controls, the Youden indices of TOS, TAS, and OSI were 0.541, 0.532, and 1, respectively. The oxidative stress may be correlation with lung cancer staging. Smoking, surgery, radiotherapy, and chemotherapy showed correlation with parts oxidative stress parameters.
A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations

Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from 447 human lymphoblastoid cell lines, we show that nonsynonymous editing activities (prevalence/level) are negatively correlated with the deleteriousness of A-to-G genomic changes and positively correlated with that of G-to-A genomic changes within the population. We find a significantly negative correlation between nonsynonymous editing activities and allele frequency of A within the population. This negative editing-allele frequency correlation is particularly strong when editing sites are located in highly important genes/loci. Examinations of deleterious missense variants from the 1000 Genomes Project further show a significantly higher proportion of rare missense mutations for G-to-A changes than for other types of changes. The proportion for G-to-A changes increases with increasing deleterious effects of the changes. Moreover, the deleteriousness of G-to-A changes is significantly positively correlated with the percentage of editing enzyme binding motifs at the variants. Overall, we show that nonsynonymous editing is associated with the increased burden of G-to-A missense mutations in healthy individuals, expanding RNA editing in pathogenomics studies.
Controls on planktonic foraminifera apparent calcification depths for the northern equatorial Indian Ocean

Within the world’s oceans, regionally distinct ecological niches develop due to differences in water temperature, nutrients, food availability, predation and light intensity. This results in differences in the vertical dispersion of planktonic foraminifera on the global scale. Understanding the controls on these modern-day distributions is important when using these organisms for paleoceanographic reconstructions. As such, this study constrains modern depth habitats for the northern equatorial Indian Ocean, for 14 planktonic foraminiferal species (G. ruber, G. elongatus, G. pyramidalis, G. rubescens, T. sacculifer, G. siphonifera, G. glutinata, N. dutertrei, G. bulloides, G. ungulata, P. obliquiloculata, G. menardii, G. hexagonus, G. scitula) using stable isotopic signatures (δ18O and δ13C) and Mg/Ca ratios. We evaluate two aspects of inferred depth habitats: (1) the significance of the apparent calcification depth (ACD) calculation method/equations and (2) regional species-specific ACD controls. Through a comparison with five global, (sub)tropical studies we found the choice of applied equation and δ18Osw significant and an important consideration when comparing with the published literature. The ACDs of the surface mixed layer and thermocline species show a tight clustering between 73–109 m water depth coinciding with the deep chlorophyll maximum (DCM). Furthermore, the ACDs for the sub-thermocline species are positioned relative to secondary peaks in the local primary production. We surmise that food source plays a key role in the relative living depths for the majority of the investigated planktonic foraminifera within this oligotrophic environment of the Maldives and elsewhere in the tropical oceans.
Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches

Abstract Peptidoglycan recognition proteins (PGRPs) belong to the family of pattern recognition receptor, represent the major constituent of innate immunity. Although PGRPs are structurally conserved through evolution, their involvement in innate immunity is different in vertebrates and invertebrates. They are highly specific towards recognition of ligands and can hydrolyze bacterial peptidoglycans (PGNs). Zebrafish PGRPs (zPGRPs) have both peptidoglycans lytic amidase activity and broad-spectrum bactericidal activity, but far less is known about how these receptors recognize these microbial ligands. Such studies are hindered due to lack of structural and functional configuration of zPGRPs. Therefore, in this study, we predicted the three-dimensional structure of zPGRP2 through theoretical modeling, investigated the conformational and dynamic properties through molecular dynamics simulations. Molecular docking study revealed the microbial ligands, that is, muramyl pentapeptide–DAP , muramyl pentapeptide–LYS, muramyl tripeptide–DAP, muramyl tripeptide–Lys, muramyl tetrapeptide–DAP, muramyl tetrapeptide–LYS and tracheal cytotoxin interacts with the conserved amino acids of the ligand recognition site comprised of β1, α2, α4, β4 and loops connecting β1 − α2, α2 − β2, β3 − β4 and α4 − α5. Conserved His31, His32, Ala34, Ile35, Pro36, Lys38, Asp60, Trp61, Trp63, Ala89, His90, Asp106, His143 and Arg144 are predicted to essential for binding and provides stability to these zPGRP–PGN complexes. Our study provides basic molecular information for further research on the immune mechanisms of PGRP’s in Zebrafish. The plasticity of the zPGRP’s binding site revealed by these microbial ligands suggests an intrinsic capacity of the innate immune system to rapidly evolve specificities to meet new microbial challenges in the future. Communicated by Ramaswamy H. Sarma
Zeaxanthin: Metabolism, Properties, and Antioxidant Protection of Eyes, Heart, Liver, and Skin

Zeaxanthin, a non-provitamin A carotenoid that belongs to the xanthophyll family, has been less studied than its isomer lutein. However, zeaxanthin has also been shown to have a number of beneficial effects for human health due to its ability to quench free radicals, exert antioxidant effects, as well as decrease inflammation. It is the purpose of this review to discuss the metabolism of zeaxanthin, including digestion, absorption, transport, and uptake by tissues, as well as the dietary or other factors which affect zeaxanthin bioavailability. In addition, this review also focuses on specific effects of this carotenoid on eye, skin, liver, and cardiovascular health. Data derived from human interventions, animal models of research, and in vitro and cell studies are discussed in this review.
The Adoption of the Electronic Health Record by Physicians

Abstract Background Health information technology, especially the electronic health record (EHR) systems, improves health care quality and patient safety. Objectives This study's objectives are as follows: first, to explore the adoption of EHR systems among physicians in Saudi Arabia (with King Fahd Military Medical Complex as the location of the pilot study), and second, to identify the factors that influence these physicians' adoption of such systems. Methods This cross-sectional quantitative study is based on a paper survey that was administered to a sample of 213 physicians. The theoretical model is a version of the Technology Acceptance Model (TAM) that features the following additional variables: resistance to change, training, and social influence. Results The sample includes 133 (62%) physicians who used EHRs and 80 (38%) who did not. The main findings show that users and nonusers of the EHR system differ significantly for several factors such as perceived usefulness, perceived ease of use, social influence, and resistance to change. In addition, age, work experience, and medical specialty are significantly associated with physicians' use of the EHR system. Conclusion To increase EHR systems' adoption rate, the following elements should be improved: the systems' design, the social environments, and the physicians' awareness of the systems' benefits. This is the first study to produce a valid and reliable instrument for measuring the factors that influences physicians' use of the EHR system at a Saudi hospital in the Eastern Province. Further studies are needed to measure how these factors influence physicians' use of EHRs in other settings.
Behaviors Characteristic of Autism Spectrum Disorder in a Geriatric Cohort With Mild Cognitive Impairment or Early Dementia

Introduction: Autism spectrum disorder (ASD) represents a heterogenous cluster of clinical phenotypes that are classically diagnosed by the time of adolescence. The possibility of late-life emergence of ASD has been poorly explored. Methods: To more fully characterize the possibility of late-life emergence of behaviors characteristic of ASD in mild cognitive impairment and AD, we surveyed caregivers of 142 older persons with cognitive impairment from the University of Kentucky Alzheimer’s Disease Center Longitudinal Cohort using the Gilliam Autism Rating Scale-2. Results: Participants with high autism index ratings (autism “possible/very likely,” n=23) reported significantly (statistically and clinically) younger age at the onset of cognitive impairment than those who scored in the autism “unlikely” range (n=119): 71.14±10.9 vs. 76.65±8.25 (P=0.034). In addition, those in the autism “possible/very likely” group demonstrated advanced severity of cognitive impairment, indicated by the Clinical Dementia Rating Scale Sum of Boxes scores. Discussion: Data demonstrate that ASD behaviors may seem de novo of degenerative dementia and such behaviors are more prevalent in those with early onset dementia. Further work elucidating a connection between ASD and dementia could shed light on subclinical forms of ASD, identify areas of shared neuroanatomic involvement between ASD and dementias, and provide valuable insights that might hasten the development of therapeutic strategies.
Susceptibility of Rickettsia rickettsii to Tigecycline in a Cell Culture Assay and Animal Model for Rocky Mountain Spotted Fever.

Rocky Mountain spotted fever (RMSF), caused by Rickettsia rickettsii, is a severe tick-borne infection endemic to the Americas. Oral doxycycline is effective, but during severe life-threatening disease, intravenous therapy is recommended. Unfortunately, intravenous formulations of doxycycline are not always available. Therefore, we aimed to determine the susceptibility of R. rickettsii to an alternative parenteral agent, tigecycline, in vitro and in vivo. To determine the minimum inhibitory concentration of tigecycline, R. rickettsii-inoculated Vero cells were incubated with medium containing tigecycline. At various time points, monolayers were collected and R. rickettsii was quantified via real-time PCR. The growth of R. rickettsii was inhibited in the presence of ≥ 0.5 µg/mL of tigecycline. To determine the effectiveness of tigecycline in vivo, guinea pigs were inoculated with R. rickettsii. Five days after inoculation, they were treated twice daily with subcutaneous tigecycline 3.75 mg/kg or subcutaneous doxycycline 5 mg/kg. Treated animals improved, whereas untreated controls remained ill. Tissues were collected for quantitative PCR-determined bacterial loads on day 8. Median bacterial loads in the tigecycline group were less than those in untreated animals: liver (0 versus 2.9 × 104 copies/mg), lung (0 versus 8.3 × 103 copies/mg), skin (2.6 × 102 versus 2.2 × 105 copies/mg), spleen (0 versus 1.3 × 104 copies/mg), and testes (0 versus 1.0 × 105 copies/mg, respectively). There were no significant differences in the bacterial loads between doxycycline-treated versus tigecycline-treated guinea pigs. These data indicate that tigecycline is effective against R. rickettsii in cell culture and in an animal model of RMSF.