Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymerase chain reaction for detection of mucosal cytomegalovirus infection in patients with acute ulcerative colitis

Background Cytomegalovirus (CMV) infection is associated with acute exacerbations of ulcerative colitis (UC) but its clinical relevance remains uncertain. The primary aim of this study was to assess the prevalence of CMV infection in UC patients using viral polymerase chain reaction (PCR) analysis of mucosal biopsy samples. Secondary aims were to establish whether the disease was due to a primary infection or reactivation and to note associated risk factors and clinical outcomes. Methods Since 2011, a policy of biopsy for CMV infection was adopted for severe UC patients in a large tertiary center. A retrospective review was undertaken to identify patients with mucosal biopsies for exacerbations of UC from October 2011 through January 2014. Results Sixty biopsies for CMV PCR were obtained from 52 patients, 15 of whom were positive. In these patients, 9/9 tested were seropositive for anti-CMV IgG, while none were seropositive for anti-CMV IgM. Steroid refractory disease was a significant predictor of CMV positivity; however, there was no difference between the CMV-positive and -negative groups in rates of immunosuppression, or clinical and endoscopic severity. Six patients in the CMV-positive group received infliximab; all received concurrent antiviral therapy and did not require surgery. Conclusions PCR of mucosal biopsies detected CMV infection due to viral reactivation in almost a third of patients with deteriorating or acute severe UC. Steroid refractory disease was significantly associated with CMV positivity, but no significant relationship was demonstrated with either disease severity or immunosuppression in our cohort. Treatment with anti-tumor necrosis factor agents was administered safely in combination with antiviral drugs.
Toll-like receptor 4 in acute viral infection: Too much of a good thing

Although a well-regulated inflammatory response is a vital defense mechanism against viral infection, too much inflammation can be detrimental. Excessive inflammatory responses, which are characterized by elevated levels of a broad array of pro-inflammatory cytokines and chemokines, have been observed in a wide variety of viral diseases associated with serious morbidity and mortality. Examples of this include acute lung injury caused by infections with respiratory syncytial virus (RSV), influenza A virus (IAV), or severe acute respiratory syndrome coronavirus (SARS-CoV). Excessive inflammatory responses induced by viral infections are not restricted to the lung but can be systemic, as reported for Ebola virus (EBOV) disease and severe dengue [1–5]. The reasons leading to an unbalanced inflammatory response in certain viral infections are not well understood and are most likely multifactorial. Here, we explore the role of toll-like receptor 4 (TLR4) in the induction of damaging inflammatory responses during acute viral infections.
Lung Ultrasound and Blood Gas-Based Classification of Critically Ill Patients with Dyspnea: A Pathophysiologic Approach

Introduction: The objective of this study was to classify dyspneic patients and to evaluate outcome variables on the basis of lung ultrasound (LUS) and arterial blood gas (ABG) findings. Methods: We performed a retrospective chart-based review in which we included patients with dyspnea admitted to our intensive care unit (ICU) between March 2015 and August 2016. On the basis of LUS (presence of A-lines/B-lines) and ABG (hypoxia/hypercarbia), patients were classified into six groups: (i) metabolic defect (dry lung, no hypoxia); (ii) perfusion defect (dry lung, hypoxia); (iii) ventilation defect (dry lung, hypoxia, and hypercarbia); (iv) ventilation and alveolar defect (wet lung, hypoxia, and hypercarbia); (v) alveolar defect-consolidation ([wet lung] hypoxia, no echocardiographic [ECG] abnormality); (vi) alveolar defect-pulmonary edema (wet lung [usually bilateral], hypoxia, ECG abnormality). The patient's demographic data, sequential organ failure assessment (SOFA) score, need for intubation, vasopressors, form of mechanical ventilation, ICU outcome, and length of stay were noted. Results: A total of 244 out of 435 patients were eligible for inclusion in the study. The median age was 56 years. 132 patients (54.1%) required mechanical ventilation, and median SOFA score was 7. Noninvasive ventilation was required in 87.5% of patients with ventilation defect as compared to 9.2% with alveolar defect-consolidation (P < 0.0001). We had 21.7% mortality in patients with alveolar defect-consolidation, 10.8% mortality in patients with metabolic defect, and 8.7% mortality in patients with alveolar defect-pulmonary edema (P < 0.0001). Conclusion: This classification gives an organized approach in managing patients with dyspnea. It predicts that patients with alveolar defect-consolidation are most sick of all the groups and need immediate intervention.
Testes mass in the livebearing fish Brachyrhaphis rhabdophora (Poeciliidae) varies hypoallometrically with body size but not between predation environments

Abstract In this study, we considered potential causes of variation in testis size in the livebearing fish Brachyrhaphis rhabdophora. We evaluated variation in testes mass among individual males and among populations that occupy different selective environments. First, we predicted that small males should allocate more to testes mass than large males (i.e., hypoallometric pattern) based on a sperm competition argument. Second, based on life history theory and associated differences in mortality rates between populations that coexist with many fish predators and those with few predators, we predicted that males in high‐predation environments should allocate more to testes mass than males in habitats with few predators. Our results showed that small males allocated proportionally more to testes mass than larger males (slope of testes mass to body mass was hypoallometric). However, there was no effect of predator environment on testes mass independent of body size differences. In this system, size‐specific patterns of reproductive allocation in males (hypoallometry) differ from that seen in females (hyperallometry). Allocation to testes mass may respond to differences in mortality rate through selection on body size.
Consequences of swamp forest fragmentation on assemblages of vascular epiphytes and climbing plants: Evaluation of the metacommunity structure

Abstract Aim Habitat reduction in fragmented landscapes provides an opportunity to study the biogeographic patterns that drive changes in diversity in poorly studied metacommunities. In this study, colonization–extinction dynamics were indirectly evaluated through the analysis of the species–area relationship and the nestedness of vascular epiphytes and climbing plants in 30 swamp forest fragments. Location Coast of the Araucanía Region in Chile. Taxon Vascular epiphytes (16 species, mainly Pteridophytes) and climbing plants (15 species). Methods We used the database in Pincheira‐Ulbrich et al. (New Zealand Journal of Botany, 54, 2016, 458), where 904 trees were sampled and a total abundance of 41,097 fern fronds and 3,098 climbing stems were reported. For the species–area relationship, a simple linear regression model (SLR) and two models that consider the spatial autocorrelation of species richness among fragments, generalized least squares (GLS) and simultaneous autoregressive model (SAR), were compared. For the species nestedness, the nestedness measure based on overlap and decreasing fills (NODF) and weighted nestedness metric based on overlap and decreasing fill (WNODF) indexes were used on presence–absence and abundance matrices, respectively. These matrices were sorted by area size and distance from the largest fragment and then contrasted with the probability distribution of a randomized null model based on 10,000 simulations. Results The results showed that the area size had a significantly positive effect on epiphyte species richness, while spatial autocorrelation played a fundamental role in explaining the richness of climbing plants. Both metacommunities had a general nestedness structure in terms of species incidence, which was determined first by area size and secondly by isolation. Main conclusions Our results indicate that local colonization processes determined by species’ dispersal capacities could be the predominant mechanism for the spatial configuration of climbing plant species composition. On the other hand, selective extinction determined by patch size could characterize the spatial structure of epiphyte species’ composition.
The effect of hydro-alcohol extract of Tribulus terrestris on sexual satisfaction in postmenopause women: A double-blind randomized placebo-controlled trial

Introduction: Increasing life expectancy in women and having menstrual problems and hormone-associated complications have led people to use complementary and alternative medicine. In menopause, the reduction in estrogen and androgen physiologically leads to a decrease in blood flow in the volvuleous and vaginal zone, resulting in a reduction in sexual desire and arousal. Sexual satisfaction plays an important role in mental health. The aim of this study was to investigate the effect of Tribulus terrestris on sexual satisfaction in postmenopausal women. Methods: This double-blind clinical trial was conducted in 2017 with the aim of investigating the effect of hydro-alcohol extract of T. terrestris on sexual satisfaction of postmenopausal women on 60 women referred to health center number 1 in eastern Ahvaz. A total of 60 postmenopausal women were randomly assigned into two groups of 30 to receive a syrup containing T. terrestris extract at a concentration of 0.9 mg and placebo for 8 weeks. Sexual satisfaction was calculated based on Larsson questionnaire. Data were analyzed by SPSS software (version 22) and t-test was used for comparing two groups in quantitative variables and Chi-square test was used for qualitative variables. P value less than 0.05 was considered significant. Findings: After intervention, the mean of sexual satisfaction in the intervention group was significantly higher than in the preintervention group (P < 0.005), and a significant increase in sexual satisfaction was observed in the tetanus syrup group. Results: Taking T. terrestris syrup increased sexual satisfaction in postmenopausal women.
Five years of fecal microbiota transplantation - an update of the Israeli experience

AIM To evaluate and describe the efficacy of fecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) in a national Israeli cohort. METHODS All patients who received FMT for recurrent (recurrence within 8 wk of the previous treatment) or refractory CDI from 2013 through 2017 in all the five medical centers in Israel currently performing FMT were included. Stool donors were screened according to the Israeli Ministry of Health guidelines. Clinical and laboratory data of patients were collected from patients’ medical files, and they included indications for FMT, risk factors for CDI and disease severity. Primary outcome was FMT success (at least 2 mo free of CDI-related diarrhea post-FMT). Secondary outcomes included initial response to FMT (cessation of diarrhea within 7 d) and recurrence at 6 mo. RESULTS There were 111 FMTs for CDI, with a median age of 70 years [interquartile range (IQR): 53-82], and 42% (47) males. Fifty patients (45%) were treated via the lower gastrointestinal (LGI, represented only by colonoscopy) route, 37 (33%) via capsules, and 24 (22%) via the upper gastrointestinal (UGI) route. The overall success rate was 87.4% (97 patients), with no significant difference between routes of administration (P = 0.338). In the univariant analysis, FMT success correlated with milder disease (P = 0.01), ambulatory setting (P < 0.05) and lower Charlson comorbidity score (P < 0.05). In the multivariant analysis, only severe CDI [odd ratio (OR) = 0.14, P < 0.05] and inpatient FMT (OR = 0.19, P < 0.05) were each independently inversely related to FMT success. There were 35 (32%) patients younger than 60 years of age, and 14 (40%) of them had a background of inflammatory bowel disease. CONCLUSION FMT is a safe and effective treatment for CDI, with capsules emerging as a successful and well-tolerated route. Severe CDI is less likely to respond to FMT.
Awareness of folic acid use among Saudi women attending outpatient clinics at King Fahad Medical City

Context: Women should consume folic acid (FA) during pregnancy to prevent neural tube defects (NTDs) in their children. Awareness of FA use, dosage, and administration can affect the risk of child malformations and other pregnancy complications. Aims: The primary objective of this study was to assess knowledge about the role of FA intake among Saudi women of reproductive age. The secondary objective was to ascertain the use of FA supplements in Saudi Arabia and the age of gestation at which FA is taken. Settings and Design: This cross-sectional study used a simple random sampling method for selecting Saudi women attending outpatient clinics at King Fahad Medical City in Riyadh, Saudi Arabia. Materials and Methods: A random sample of 600 Saudi women aged 18–45 years was evaluated for their awareness of FA use. Participants completed a questionnaire comprising 16 questions. Six questions were demographic, and the remaining 10 fulfilled the study aims. Results: Women had high awareness about FA. Survey responses showed that 42.2% of women knew that FA should be taken before pregnancy, and 80.1% were aware that it prevents NTDs. A total of 46.8% women took FA during preconception. Healthcare professionals provided the information in 69.7% of the cases. Conclusion: We concluded that the lower number of deformities in Saudi Arabia is due to greater awareness of the importance of FA, which can likely be attributed to better education. Doctors and nurses should continue to encourage women to take FA supplements when planning their pregnancies.
Use of auto‐germ to model germination timing in the sagebrush‐steppe

Abstract Germination timing has a strong influence on direct seeding efforts, and therefore is a closely tracked demographic stage in a wide variety of wildland and agricultural settings. Predictive seed germination models, based on soil moisture and temperature data in the seed zone are an efficient method of estimating germination timing. We utilized Visual Basic for Applications (VBA) to create Auto‐Germ, which is an Excel workbook that allows a user to estimate field germination timing based on wet‐thermal accumulation models and field temperature and soil moisture data. To demonstrate the capabilities of Auto‐Germ, we calculated various germination indices and modeled germination timing for 11 different species, across 6 years, and 10 Artemisia‐steppe sites in the Great Basin of North America to identify the planting date required for 50% or more of the simulated population to germinate in spring (1 March or later), which is when conditions are predicted to be more conducive for plant establishment. Both between and within the species, germination models indicated that there was high temporal and spatial variability in the planting date required for spring germination to occur. However, some general trends were identified, with species falling roughly into three categories, where seeds could be planted on average in either fall (Artemisia tridentata ssp. wyomingensis and Leymus cinereus), early winter (Festuca idahoensis, Poa secunda, Elymus lanceolatus, Elymus elymoides, and Linum lewisii), or mid‐winter (Achillea millefolium, Elymus wawawaiensis, and Pseudoroegneria spicata) and still not run the risk of germination during winter. These predictions made through Auto‐Germ demonstrate that fall may not be an optimal time period for sowing seeds for most non‐dormant species if the desired goal is to have seeds germinate in spring.
Bilirubin-Induced Oxidative Stress Leads to DNA Damage in the Cerebellum of Hyperbilirubinemic Neonatal Mice and Activates DNA Double-Strand Break Repair Pathways in Human Cells

Unconjugated bilirubin is considered a potent antioxidant when present at moderate levels. However, at high concentrations, it produces severe neurological damage and death associated with kernicterus due to oxidative stress and other mechanisms. While it is widely recognized that oxidative stress by different toxic insults results in severe damage to cellular macromolecules, especially to DNA, no data are available either on DNA damage in the brain triggered by hyperbilirubinemia during the neonatal period or on the activation of DNA repair mechanisms. Here, using a mouse model of neonatal hyperbilirubinemia, we demonstrated that DNA damage occurs in vivo in the cerebellum, the brain region most affected by bilirubin toxicity. We studied the mechanisms associated with potential toxic action of bilirubin on DNA in in vitro models, which showed significant increases in DNA damage when neuronal and nonneuronal cells were treated with 140 nM of free bilirubin (Bf), as determined by γH2AX Western blot and immunofluorescence analyses. Cotreatment of cells with N-acetyl-cysteine, a potent oxidative-stress inhibitor, prevented DNA damage by bilirubin, supporting the concept that DNA damage was caused by bilirubin-induced oxidative stress. Bilirubin treatment also activated the main DNA repair pathways through homologous recombination (HR) and nonhomologous end joining (NHEJ), which may be adaptive responses to repair bilirubin-induced DNA damage. Since DNA damage may be another important factor contributing to neuronal death and bilirubin encephalopathy, these results contribute to the understanding of the mechanisms associated with bilirubin toxicity and may be of relevance in neonates affected with severe hyperbilirubinemia.
Do the oral Staphylococcus aureus strains from denture wearers have a greater pathogenicity potential?

ABSTRACT We used flow cytometry to compare the phagocytic activity of monocytes against Staphylococcus aureus strains (both biofilm and planktonic cells) isolated from denture wearers and non-wearers. Staphylococcal strains were cultured in Brain Heart Infusion broth in both planktonic and biofilm form and were stained with a fluorescent reporter (propidium iodide) and incubated with monocytes. The fluorescence of the monocytes containing phagocytized bacteria was determined by flow cytometry and normalized to that of the bacterial strains used in the experiment. Staphylococcal strains from denture wearers caused greater activation of monocytes but were less prone to phagocytosis. The percentage of monocytes containing bacterial cells after exposition to staphylococcal strains varied from 2.7% to 81.4% for planktonic cells. For biofilm-released cells, this value ranged from 0.6% to 36.2%. The effectiveness of phagocytosis, estimated based on an increase in monocyte fluorescence, amounted to 32.4 and 71 FL2 units for the biofilm and planktonic cells, respectively. The lesser efficiency of phagocytosis against biofilm S. aureus in denture wearers suggests that they might have been colonized with the strains which were less prone to eradication than those from non-wearers.
Temporal changes in Weddell seal dive behavior over winter: Are females increasing foraging effort to support gestation?

Abstract In capital‐breeding marine mammals, prey acquisition during the foraging trip coinciding with gestation must provide energy to meet the immediate needs of the growing fetus and also a store to meet the subsequent demands of lactation. Weddell seals (Leptonychotes weddellii) that give birth following the gestational (winter) foraging period gain similar proportions of mass and lipid as compared to females that fail to give birth. Therefore, any changes in foraging behavior can be attributed to gestational costs. To investigate differences in foraging effort associated with successful reproduction, twenty‐three satellite tags were deployed on post‐molt female Weddell seals in the Ross Sea. Of the 20 females that returned to the area the following year, 12 females gave birth and eight did not. Females that gave birth the following year began the winter foraging period with significantly longer and deeper dives, as compared to non‐reproductive seals. Mid‐ to late winter, reproductive females spent a significantly greater proportion of the day diving, and either depressed their diving metabolic rates (DMR), or exceeded their calculated aerobic dive limit (cADL) more frequently than females that returned without a pup. Moreover, non‐reproductive females organized their dives into 2–3 short bouts per day on average (BOUTshort; 7.06 ± 1.29 hr; mean ± 95% CI), whereas reproductive females made 1–2 BOUTshort per day (10.9 ± 2.84 hr), comprising one long daily foraging bout without rest. The magnitude of the increase in dive activity budgets and depression in calculated DMR closely matched the estimated energetic requirements of supporting a fetus. This study is one of the first to identify increases in foraging effort that are associated with successful reproduction in a top predator and indicates that reproductive females must operate closer to their physiological limits to support gestational costs.
Characterization of Flow Efficiency, Pulsatility, and Respiratory Variability in Different Types of Fontan Circuits Using Quantitative Parameters

Purpose Details on the hemodynamic differences among Fontan operations remain unclear according to respiratory and cardiac cycles. This study was undertaken to investigate hemodynamic characteristics in different types of Fontan circulation by quantification of blood flow with the combined influence of cardiac and respiratory cycles. Materials and Methods Thirty-five patients [10 atriopulmonary connections (APC), 13 lateral tunnels (LT), and 12 extracardiac conduits (ECC)] were evaluated, and parameters were measured in the superior vena cava, inferior vena cava (IVC), hepatic vein (HV), baffles, conduits, and left and right pulmonary artery. Pulsatility index (PIx), respiratory variability index (RVI), net antegrade flow integral (NAFI), and inspiratory/expiratory blood flow (IQ/EQ) were measured by intravascular Doppler echocardiography. Results The PIx between APC and total cavopulmonary connection (TCPC; LT and ECC) showed significant differences at all interrogation points regardless of respiratory cycles. The PIxs of HVs and IVCs in APC significantly increased, compared with that in LT and ECC, and the RVI between APC and TCPC showed significant differences at all interrogation points (p<0.05). The NAFI and IQ/EQ between APC and TCPC showed significant differences at some interrogation points (p<0.05). Conclusion Patients with different types of Fontan circulation show different hemodynamic characteristics in various areas of the Fontan tract, which may lead to different risks causing long-term complications. We believe the novel parameters developed in this study may be used to determine flow characteristics and may serve as a clinical basis of management in patients after Fontan operations.