Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammatory markers as mortality predictors in continuous ambulatory peritoneal dialysis patients

Abstract Background/Aim: Besides peritonitis, the most common complication, indicators of chronic inflammation are also present in patients treated by peritoneal dialysis. The aim of this study was to analyze the predictive value of inflammatory parameters on mortality of continuous ambulatory peritoneal dialysis (CAPD) patients. Methods: Eighty-seven patients (57 males), aged from 30 to 85 [62.92 (10.61)] years who had been treated by a chronic program of CAPD for 3–113 months were analyzed. The basal period lasted 3 months with a follow-up of 30 months. Clinical parameters, dialysis adequacy and laboratory parameters including some inflammatory markers: serum amyloid-A (SAA), high sensitive C-reactive protein (hs-CRP), fibrinogen, erythrocyte sedimentation rate (ESR) and leukocytes were determined for each patient. Cox regression analysis selected the parameters of univariate and multivariate survival analysis. Results: During the follow-up period, 37 patients (42.5%) died. Univariate analysis selected the following potential mortality predictors (p < 0.10): age, months on CAPD, residual urine output, presence of cerebrovascular insult (CVI), KT/V, serum urea and albumin concentrations, SAA, hs-CRP, fibrinogen and ESR. In the multivariate survival analysis four models were created, each with a single inflammatory parameter. In all of these models, besides the age and CVI, inflammatory parameters were the most significant mortality predictors. When the inflammatory markers were analyzed altogether, multivariate analysis established that independent mortality predictors in this group of patients were: SAA, age and CVI. Conclusion: It may be concluded that in this studied group treated by CAPD, SAA was the most significant independent mortality predictor among the analyzed inflammatory markers.
Cohort analysis of simulation-based medical training for decision support

Debriefing is the practice of after session review of training performance to enhance self-reflection through feedback. It has been considered as a vital and crucial part of simulation-based medical training. However an accurate, objective and in-depth evaluation of trainee performance has been a significant challenge. To address this we developed a knowledge-based framework in which the criteria of performance for clinical training are distilled into expert rules. These rules are then matched to data streams from a training session to evaluate the strengths and weaknesses of a trainee. We applied the evaluation technology to a dataset collected from two medical cohorts. The cohort characteristics are calculated, visualised, and validated by the medical experts. The cohort analysis results inform decision making at the levels of both the trainers and the enterprise. Trainers can compare and characterise the performance of different student cohorts or the same cohort over a period of time. The course coordinators can use the cohort analysis result to adjust the course design to target the identified common problems in trainee cohorts.
Effects of light and prey availability on nocturnal, lunar and seasonal activity of tropical nightjars

Nightjars and their allies represent the only major group of visually hunting aerial insectivores with a crepuscular andlor nocturnal lifestyle. Our purpose was to examine how both light regime and prey abundance in the tropics, where periods of twilight are extremely short, but nightjar diversity is high, affect activity across different temporal scales. We studied two nightjar species in West African bush savannah, standard-winged nightjars Macrodipteryx longipennis Shaw and long-tailed nightjars Caprimulgus climacurus Vieillot. We measured biomass of potential prey available using a vehicle mounted trap and found that it was highest at dusk and significantly lower at dawn and during the night. Based on direct observations, both nightjars exhibit the most intense foraging behaviour at dusk, less intense foraging at dawn and least at night, as predicted by both prey abundance and conditions for visual prey detection. Nocturnal foraging was positively correlated with lunar light levels and ceased below about 0.03 mW m -2 . Over the course of a lunar cycle, nocturnal light availability varied markedly, while prey abundance remained constant at dusk and at night was slightly higher at full moon. Both species increased twilight foraging activity during new moon periods, compensating for the shorter nocturnal foraging window at that time. Seasonally, the pattern of nocturnal light availability was similar throughout the year, while prey availability peaked shortly after onset of the wet season and then slowly decreased over the following four months. The courtship and breeding phenology of both species was timed to coincide with the peak in aerial insect abundance, suggesting that prey availability rather than direct abiotic factors act as constraints, at least at the seasonal level. Our findings illustrate the peculiar constraints on visually orienting aerial nocturnal insectivores in general and tropical nightjars in particular and highlight the resulting nocturnal, lunar and seasonal allocation of activities.
T Helper Cell Type 2 Cytokine–Mediated Comitogenic Responses and Ccr3 Expression during Differentiation of Human Mast Cells in Vitro

Mast cells (MCs) arise in situ from circulating stem cell factor (SCF)-dependent committed progenitors (PrMCs) and accumulate at sites of allergic mucosal inflammation. We hypothesized that human (h)PrMCs and their mature counterparts might share overlapping patterns of chemokine and cytokine receptor utilization with eosinophils, basophils, and T helper type 2 (Th2) lymphocytes for their homing and allergy-associated hyperplasia. We have characterized committed hPrMCs and fully mature hMCs derived in vitro from cord blood for their functional responses to chemokine and cytokine agonists germane to allergic inflammation and for their maturation-related expression of the corresponding receptors. After 4 wk of culture in the presence of recombinant stem cell factor (SCF), interleukin (IL)-6, and IL-10, the cells were characterized as hPrMCs based upon their uniform surface expression of c-kit and CD13, low-level expression of Fc∈RIα, absence of CD14 and CD16 expression, and immunoreactivity for MC chymase in >80%, and about half were immunoreactive for tryptase and metachromatic with toluidine blue. By week 9, the cells had matured into hMCs, identified by higher levels of c-kit, continued expression of CD13 and low-level Fc∈RIα, uniform toluidine blue metachromasia, and uniform immunoreactivity for both tryptase and chymase. The 4-wk-old hPrMCs expressed four chemokine receptors (CXCR2, CCR3, CXCR4, and CCR5). Each receptor mediated transient rapid calcium fluxes in response to its respective ligand. Both recombinant human eotaxin and stromal cell–derived factor 1α elicited chemotaxis of hPrMCs. Only CCR3 was retained on the mature 9-wk-old hMCs from among these chemokine receptors, and hMCs responded to eotaxin with a sustained calcium flux but without chemotaxis. The Th2 cytokines IL-3, IL-5, IL-6, IL-9, and granulocyte/macrophage colony-stimulating factor each augmented the SCF-dependent proliferation of hPrMCs and hMCs. In contrast, the prototypical Th1 cytokine, interferon γ, suppressed SCF-driven proliferation of both hPrMCs and hMCs. Thus, throughout their development in vitro, hMCs obey SCF-dependent, cytokine-driven mitogenic responses that reflect a Th2-type polarization characteristic of allergy and asthma. Furthermore, committed hPrMCs have a unique profile of chemokine receptor expression from among reported hematopoietic cells, including CCR3, which is shared with the other cells central to allergic inflammation (eosinophils, basophils, and Th2 lymphocytes).
Molecular testing of urine: catching DNA on the way out.

There has been much recent interest in the potential diagnostic use of DNA in plasma and serum for cancer testing (1), prenatal diagnosis (2), and transplantation monitoring (3). It has also been demonstrated that circulating DNA appears to be cleared very rapidly from the circulation (4). The exact mechanism of clearance, however, has remained incompletely understood. In this issue of the Journal, Botezatu et al. (5) describe interesting results indicating that the kidney plays a role in the clearance of plasma DNA and that, excitingly, a proportion of the DNA is excreted in sizes detectable by molecular techniques such as PCR. Botezatu et al. (5) began their investigation by demonstrating that mice injected with either purified bacteriophage DNA or irradiated Raji cells excreted detectable amounts of DNA derived from the injected materials. They went on to show that their observations could also be extended to humans by demonstrating the presence of male DNA in the urine of women transfused with male blood and in women pregnant with male fetuses (5). These authors continued their line of investigation by showing that tumor-associated K- ras mutations were detectable in the urine of pancreatic and colorectal carcinoma patients. Overall, their results have opened up the possibility that urinary DNA analysis may have diverse clinical applications, ranging …
Effects of resveratrol supplementation on risk factors of non-communicable diseases: A meta-analysis of randomized controlled trials

Abstract The results of randomized controlled trials (RCTs) investigating resveratrol supplementation on risk factors of non-communicable diseases (NCDs) have been inconsistent. The present meta-analysis aimed to quantitatively evaluate the effects of resveratrol intervention on risk factors of NCDs. PubMed and Scopus databases were searched up to June 2017. Weighted mean differences were calculated for net changes in risk factors of NCDs by using a random-effects model. Pre-specified subgroup and univariate meta-regression analyses were carried out to explore the sources of heterogeneity. Twenty-nine studies (30 treatment arms) with 1069 participants were identified. Resveratrol supplementation significantly reduced the concentrations of fasting glucose (−4.77 mg/dL; 95% CI: −9.33 to −0.21 mg/dL; P = 0.040), total cholesterol (TC) (−9.75 mg/dL; 95% CI: −17.04 to −2.46 mg/dL; P = 0.009), and C-reactive protein (CRP) (−0.81 mg/L; 95% CI: −1.42 to −0.21 mg/L; P = 0.009). Resveratrol intervention exerted significant reductions in systolic blood pressure (SBP) and diastolic blood pressure (DBP) in subjects with type 2 diabetes mellitus (T2DM). Subgroup analysis also showed that the trials with resveratrol intervention ≥3 months significantly reduced the low-density lipoprotein cholesterol (LDL-C), DBP, and glycated hemoglobin (HbA1c) values. The results did not support that resveratrol intervention had favorable effects in altering high-density lipoprotein cholesterol (HDL-C), triglyceride (TAG), and homeostasis model assessment of insulin resistance (HOMA-IR). The present study provides substantial evidence that resveratrol supplementation has favorable effects on several risk factors of NCDs.
Targeted Degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL Complex Regulates Clock Function and Photomorphogenesis in Arabidopsis thaliana[W]

Circadian clocks comprise several regulatory feedback loops that control gene transcription. However, recent evidence has shown that posttranslational mechanisms are also required for clock function. In Arabidopsis thaliana, members of the PSEUDO-RESPONSE REGULATOR (PRR) family were proposed to be components of the central oscillator. Using a PRR5-specific antibody, we characterized changes in PRR5 protein levels in relation to its mRNA levels under various circadian conditions. Under long-day conditions, PRR5 mRNA levels are undetectable at dusk but PRR5 protein levels remain maximal. Upon dark transition, however, PRR5 levels decrease rapidly, indicating dark-induced, posttranslational regulation. We demonstrated that the Pseudo-Receiver (PR) domain of PRR5 interacts directly with the F box protein ZEITLUPE (ZTL) in vitro and in vivo. Analyses of mutants and transgenic plants revealed an inverse correlation between PRR5 and ZTL levels, which depends on the PR domain. These results indicate that PRR5 is negatively regulated by ZTL, which likely mediates its ubiquitination and degradation. Phenotypic analyses of prr5 ztl double mutants showed that PRR5 is required for ZTL functions. ZTL contains a Light-Oxygen-Voltage domain, and its activity may be directly regulated by blue light. Consistent with this notion, we found that blue light stabilizes PRR5, although it does not alter ZTL levels. Together, our results show that ZTL targets PRR5 for degradation by 26S proteasomes in the circadian clock and in early photomorphogenesis.
High Prevalence of Sinusitis in Children with Henoch-Schönlein Purpura

We evaluated the prevalence and the types of infectious foci in oral as well as ear, nose, and throat diseases, and we examined incidence of renal involvement with active treatment for focal infection in children with Henoch-Schönlein Purpura. A total of 96 children who presented at Aichi Children's Health and Medical Center and were diagnosed as having HSP were evaluated for infectious foci in the ear, nose, throat, and oral cavities. Seventy-one of 96 children (74.0%) had some type of infectious lesion, such as sinusitis or tonsillitis, and the prevalence of sinusitis was the highest (51 cases, 53.7%). In 44 HSP patients without renal involvement at the first examination, the incidence of nephritis was lower (13.6%) than in previous reports (17–54%) due to our aggressive intervention for infectious foci.
Molecular Barcoding of an Atypical Cyprinid Population Assessed by Cytochrome b Gene Sequencing

A fish population of the carp family Cyprinidae with atypical phenotypic characteristics was observed in one of the main catchments of the Pollino National Park, a valuable, protected area in southern Italy. In this area, the Italian roach Rutilus rubilio (Bonaparte, 1837), a native endemic fish of Tyrrhenean regions, has been introduced in sympatric conditions with Squalius squalus (Bonaparte, 1837) and Telestes muticellus (Bonaparte, 1837). A molecular investigation was carried out to assess the genetic identity of the population with a view to conservation. Direct sequencing of a cytochrome b gene fragment was performed based on 30 individuals of cyprinid fish with atypical phenotype, in addition to 30 S. squalus, 10 T. muticellus, and 30 R. rubilio pure individuals collected in different Italian regions, which served as reference samples. Multiple sequence alignments demonstrated that 50% of atypical-cyprinid haplotypes were maternally inherited from either S. squalus or R. rubilio. No contribution by T. muticellus was determined. Our results indicate an intergeneric hybridization event between S. squalus and R. rubilio, as a consequence of trans-introduction activities of alien species.
Effects of Tamsulosin and Tolterodine on double J stent–related symptoms: A double-blind, randomized, placebo-controlled trial

Background: Ureteral double J stent are routinely applied for urologic patients although stent-related symptoms are common. Several attempts have been reported to minimize these symptoms. Objective: To compare Tolterodine, Tamsulosin, and placebo effects on double J stent–related symptoms. Material and method: In all, 125 patients (82 males and 43 females) with double J stent were randomly divided into three groups (group 1, n: 42, group2, n: 40 and group 3, n: 43). Each patient randomly received one pack of drug in different colors by a nurse unaware of the content to take Tamsulosin 0.4 mg before sleep (MODALUSINE), Tolterodine 2 mg twice a day or placebo once daily (capsules filled with starch): group 1 received placebo, group 2 Tamsulosin and group 3 Tolterodine for 1 month in a double-blind manner. Ureteral stent-related morbidity indices which analyzed include urinary symptom, pain, general health, quality of work and sex scores. All of indices measured by Ureteral Symptom Score Questionnaire for first and fourth weeks after drug consumption and the first week after double J stent removal (labeled as w1, w4, and w5, respectively). Result: The mean age was 44.8 years (range: 15–83 years). There was no statistically significant difference in background characteristics between groups (p value > 0.05). The most important and statistically significant results were Tolterodine-reduced urinary symptom score (p value = 0.001) and improved general health score (p value = 0.007) of the fourth week. The pain score in groups of Tamsulosin and Tolterodine significantly reduced between weeks 4 and 1 and 5 and 1 (both with the p value < 0.05), but in other indices, there was no significant difference between them. Conclusion: According to our results, we suggest Tolterodine to minimize stent-related urinary symptom and improve general health in patients with double J stent.
A study on evolutionary design of binary decision trees

For pattern recognition, decision trees (DTs) are more efficient than neural networks (NNs) for two reasons. First, the computations in making decisions are simpler. Second, important features can be selected automatically during the design process. However, the DTs are not adaptable. This problem can be avoided by mapping a DT to an NN. This mapping not only makes a DT adaptable, but also provides a systematic way for determining the NN structure. In addition, since the features are well selected, the NN obtained from this mapping may have much fewer connections than those designed directly. The key point here is to design a DT which is as small as possible. We study the evolutionary design of the decision trees, and investigate some methods to improve the design efficiency.
An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

The Smith Waterman algorithm for sequence alignment is one of the main tools of bioinformatics. It is used for sequence similarity searches and alignment of similar sequences. The high end Graphical Processing Unit (GPU), used for processing graphics on desktop computers, deliver computational capabilities exceeding those of CPUs by an order of magnitude. Recently these capabilities became accessible for general purpose computations thanks to CUDA programming environment on Nvidia GPUs and ATI Stream Computing environment on ATI GPUs. Here we present an efficient implementation of the Smith Waterman algorithm on the Nvidia GPU. The algorithm achieves more than 3.5 times higher per core performance than previously published implementation of the Smith Waterman algorithm on GPU, reaching more than 70% of theoretical hardware performance. The differences between current and earlier approaches are described showing the example for writing efficient code on GPU.
Crenarchaeal Biofilm Formation under Extreme Conditions

Background Biofilm formation has been studied in much detail for a variety of bacterial species, as it plays a major role in the pathogenicity of bacteria. However, only limited information is available for the development of archaeal communities that are frequently found in many natural environments. Methodology We have analyzed biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus and S. tokodaii. We established a microtitre plate assay adapted to high temperatures to determine how pH and temperature influence biofilm formation in these organisms. Biofilm analysis by confocal laser scanning microscopy demonstrated that the three strains form very different communities ranging from simple carpet-like structures in S. solfataricus to high density tower-like structures in S. acidocaldarius in static systems. Lectin staining indicated that all three strains produced extracellular polysaccharides containing glucose, galactose, mannose and N-acetylglucosamine once biofilm formation was initiated. While flagella mutants had no phenotype in two days old static biofilms of S. solfataricus, a UV-induced pili deletion mutant showed decreased attachment of cells. Conclusion The study gives first insights into formation and development of crenarchaeal biofilms in extreme environments.
Production benefits learning: The production effect endures and improves memory for text

The production effect is the superior retention of material read aloud relative to material read silently during an encoding episode. Thus far it has been explored using isolated words tested almost immediately. The goal of this study was to assess the efficacy of production as a study strategy, addressing: (a) whether the production benefit endures beyond a short session, (b) whether production can boost memory for more complex material, and (c) whether production transfers to educationally relevant tests. In Experiment 1 a 1-week retention interval was included, and a production effect was observed. In Experiment 2 a production effect was observed for both word pairs and sentence stimuli. In Experiment 3 educationally relevant essays were read and tested with a fill-in-the-blanks test: Memory was superior for questions that probed information that had been read aloud relative to information that had been read silently. We conclude that the production benefit is enduring and generalises to text and different test formats, indicating that production constitutes a worthwhile study strategy.
Maternal and birth attendant hand washing and neonatal mortality in southern Nepal.

BACKGROUND More than 95% of neonatal deaths occur in developing countries, approximately 50% at home. Few data are available on the impact of hand-washing practices by birth attendants or caretakers on neonatal mortality. OBJECTIVE To evaluate the relationship between birth attendant and maternal hand-washing practices and neonatal mortality in rural Nepal. DESIGN Observational prospective cohort study. SETTING Sarlahi District in rural southern Nepal. PARTICIPANTS Newborn infants were originally enrolled in a community-based trial assessing the effect of skin and/or umbilical cord cleansing with chlorhexidine on neonatal mortality in southern Nepal. A total of 23,662 newborns were enrolled and observed through 28 days of life. MAIN EXPOSURES Questionnaires were administered to mothers on days 1 and 14 after delivery to identify care practices and risk factors for mortality and infection. Three hand-washing categories were defined: (1) birth attendant hand washing with soap and water before assisting with delivery, (2) maternal hand washing with soap and water or antiseptic before handling the baby, and (3) combined birth attendant and maternal hand washing. OUTCOME MEASURES Mortality within the neonatal period. RESULTS Birth attendant hand washing was related to a statistically significant lower mortality rate among neonates (adjusted relative risk [RR] = 0.81; 95% confidence interval [CI], 0.66-0.99), as was maternal hand washing (adjusted RR = 0.56; 95% CI, 0.38-0.82). There was a 41% lower mortality rate among neonates exposed to both hand-washing practices (adjusted RR = 0.59; 95% CI, 0.37-0.94). CONCLUSIONS Birth attendant and maternal hand washing with soap and water were associated with significantly lower rates of neonatal mortality. Measures to improve or promote birth attendant and maternal hand washing could improve neonatal survival rates.