Miracle-dz/UniFAR-FTUs huggingface dataset:
Reversibility of GERD Ultrastructural Alterations and Relief of Symptoms After Omeprazole Treatment

BACKGROUND:Dilation of intercellular spaces (DIS) of human esophageal epithelium, evident at transmission electron microscopy (TEM), is an early marker of damage caused by gastroesophageal reflux, but its reversibility after therapy has not been investigated.AIM:To evaluate whether omeprazole can induce the healing of DIS.METHODS:Thirty-eight symptomatic patients, 22 with nonerosive reflux disease (NERD) and 16 with erosive esophagitis (EE), classified on the basis of 24-h pH monitoring, were enrolled. During upper gastrointestinal endoscopy, six biopsies from apparently normal mucosa were taken within the lower 5 cm of the esophagus for histological and TEM analysis. One hundred computer measurements were taken on TEM photomicrographs of the specimens in each patient. After 3 months of omeprazole 40 mg/die a further endoscopy with biopsies was performed. In patients with persistent heartburn and/or incomplete ultrastructural recovery of esophageal epithelium, a new endoscopy was performed after 3 more months of treatment.RESULTS:After 3 months of therapy, 35 patients (92.1%) showed a complete recovery of DIS and resolution of heartburn. Three patients required 3 more months of therapy because of an incomplete recovery of the epithelium correlated with sporadic heartburn. Healing of the mucosa was achieved in two patients, whereas one had an incomplete recovery of DIS with persistent heartburn.CONCLUSIONS:Three and six months of omeprazole therapy led to a complete recovery of DIS in 92.1% and 97.4% of cases, respectively. No significant differences of DIS between NERD and EE were noted. Complete recovery of DIS was accompanied by regression of heartburn in all cases.
Role of Combined Post-Operative Venous Lactate and 48 Hours C-Reactive Protein Values on the Etiology and Predictive Capacity of Organ-Space Surgical Site Infection after Elective Colorectal Operation

Background: C-reactive protein (CRP) has been assessed to detect organ-space surgical site infection (OSI). Nevertheless, data about peri-operative oxygen debt and surgical stress-elicited biologic markers to explain and allow for the early detection of OSI are lacking. We analyzed immediate post-operative venous lactate, early CRP levels, and intra-operative hemodynamic values on the capacity to predict OSI after elective colorectal operation. Patients and Methods: Patients undergoing an elective colorectal surgical procedure with anastomosis between March 2013 and August 2014 were included and assessed prospectively. Post-operative lactate values at L-0, L-6, and L-24 hours, CRP (basal and 48 h), and the percentage of operative time (POT) with systolic blood pressure below 100 mm Hg and heart rate above 90 beats per minute in patients with and without OSI were compared. Binary logistic regression was constructed for L-0 and CRP-48, and receiver-operating characteristic (ROC) was analyzed for sensitivity (S), specificity (Sp), positive (PPV) and negative (NPV) predictive values. Results: Patients with OSI (11 of 100) showed higher L-0 and L-24 (3.2 – 2.5 vs. 1.6 – 0.8; p = 0.025 and 1.9 – 1.2 vs. 1.2 – 0.4 mmol/L; p = 0.025) and CRP-48 (188 – 80 vs. 74 – 52 mg/L; p = 0.001). The ROC from logistic regression showed area under the curve of 0.899 (95% confidence interval [CI] 0.805–0.992), S of 72% (95% CI 43.2%–90.5%), Sp of 95% (95% CI 88.6%–98.4%), PPV of 66% (95% CI 38.9%–86.4%) and NPV of 0.96 (95% CI 90%–99%). L-0 was higher in those patients with hypotension during more than 60% of the POT (2.4 – 2.1 vs. 1.6 – 0.8; p = 0.038). Patients with OSI had a higher POT with hypotension (50 – 28% vs. 30 – 28%; p = 0.032) and tachycardia (18 – 27% vs. 5 – 16%; p = 0,024). Conclusions: The combination of immediate post-operative lactate and CRP at 48 hours proved to be useful in predicting OSI after elective colorectal operation. Assessment of peri-operative lactate is a potential target for intra-operative goal-oriented management aimed at improving post-operative outcomes.
Critically Ill patients with 2009 influenza A(H1N1) in Mexico.

CONTEXT In March 2009, novel 2009 influenza A(H1N1) was first reported in the southwestern United States and Mexico. The population and health care system in Mexico City experienced the first and greatest early burden of critical illness. OBJECTIVE To describe baseline characteristics, treatment, and outcomes of consecutive critically ill patients in Mexico hospitals that treated the majority of such patients with confirmed, probable, or suspected 2009 influenza A(H1N1). DESIGN, SETTING, AND PATIENTS Observational study of 58 critically ill patients with 2009 influenza A(H1N1) at 6 hospitals between March 24 and June 1, 2009. Demographic data, symptoms, comorbid conditions, illness progression, treatments, and clinical outcomes were collected using a piloted case report form. MAIN OUTCOME MEASURES The primary outcome measure was mortality. Secondary outcomes included rate of 2009 influenza (A)H1N1-related critical illness and mechanical ventilation as well as intensive care unit (ICU) and hospital length of stay. RESULTS Critical illness occurred in 58 of 899 patients (6.5%) admitted to the hospital with confirmed, probable, or suspected 2009 influenza (A)H1N1. Patients were young (median, 44.0 [range, 10-83] years); all presented with fever and all but 1 with respiratory symptoms. Few patients had comorbid respiratory disorders, but 21 (36%) were obese. Time from hospital to ICU admission was short (median, 1 day [interquartile range {IQR}, 0-3 days]), and all patients but 2 received mechanical ventilation for severe acute respiratory distress syndrome and refractory hypoxemia (median day 1 ratio of Pao(2) to fraction of inspired oxygen, 83 [IQR, 59-145] mm Hg). By 60 days, 24 patients had died (41.4%; 95% confidence interval, 28.9%-55.0%). Patients who died had greater initial severity of illness, worse hypoxemia, higher creatine kinase levels, higher creatinine levels, and ongoing organ dysfunction. After adjusting for a reduced opportunity of patients dying early to receive neuraminidase inhibitors, neuraminidase inhibitor treatment (vs no treatment) was associated with improved survival (odds ratio, 8.5; 95% confidence interval, 1.2-62.8). CONCLUSION Critical illness from 2009 influenza A(H1N1) in Mexico occurred in young individuals, was associated with severe acute respiratory distress syndrome and shock, and had a high case-fatality rate.
Strength - Ultrasonic Pulse Velocity Relationship of Thermally Activated Alum Sludge Multiple Blended High Performance Concretes

In this research the performance of ultrasonic pulse velocity in concrete is examined as a nondestructive experiment, in order to estimate compressive strength of thermally activated alum sludge multiple blended high performance concretes (HPC) that contain AAS, silica fume (SF), ground granulated blast furnace slag (GGBS) and palm oil fuel ash (POFA) are determined in both binary and ternary blends of cement. The water/binder ratio and total binder content are fixed at 0.30 and 493 kg/m3 for all types of mixes. The ultrasonic pulse velocity (UPV) of each concrete mix was measured using 100mm cubes after a curing period of ages of 3, 7, 28, 56 and 90 days. The results indicate a very positive exponential relationship between compressive strength and UPV for both binary and ternary blends of HPC mixtures, with coefficient correlation (R2) of 0.889.
Detection of eight Cryptosporidium genotypes in surface and waste waters in Europe

Cryptosporidia are important protozoan parasites of vertebrates, and a number of species and genotypes, with different host ranges, have been described. In this study a protocol was established for the detection and the genetic characterization of Cryptosporidium spp. isolated from various types of surface waters (rivers, creeks, lakes, sewage plant in- and outlets and swimming pools) from the area between Zurich (Switzerland) and Munich (Germany). Cryptosporidium oocysts were isolated by continuous-flow-centrifugation and immunomagnetic separation (IMS). A novel nested PCR combined with direct sequencing of the amplicon which spans a variable region of the 18S rRNA allowed characterization of species and genotypes. Cryptosporidium spp. were detected in 23 of the 68 water samples investigated. Almost half of these isolates represent species and genotypes known to be pathogenic to man, namely C. parvum ‘bovine genotype’ (from 6 samples) and C. parvum ‘human genotype’ (4). Furthermore, we identified C. muris ‘genotype A’ (3), C. muris ‘genotype B’ (6), C. baileyi (1) as well as 3 novel Cryptosporidium genotypes. Our results confirm the ubiquitous presence of Cryptosporidium oocysts in surface waters. The detection of a variety of species and genotypes stresses the importance that molecular characterization is indispensable before drawing conclusions of medical or epidemiological significance.
An Operating System for the Home

Network devices for the home such as remotely controllable locks, lights, thermostats, cameras, and motion sensors are now readily available and inexpensive. In theory, this enables scenarios like remotely monitoring cameras from a smartphone or customizing climate control based on occupancy patterns. However, in practice today, such smarthome scenarios are limited to expert hobbyists and the rich because of the high overhead of managing and extending current technology. We present HomeOS, a platform that bridges this gap by presenting users and developers with a PC-like abstraction for technology in the home. It presents network devices as peripherals with abstract interfaces, enables cross-device tasks via applications written against these interfaces, and gives users a management interface designed for the home environment. HomeOS already has tens of applications and supports a wide range of devices. It has been running in 12 real homes for 4-8 months, and 42 students have built new applications and added support for additional devices independent of our efforts.
Phenylpropanoids and Furanocoumarins as Antibacterial and Antimalarial Constituents of the Bhutanese Medicinal Plant Pleurospermum amabile

With the objective of determining safety and verifying the traditional uses of the Bhutanese medicinal plant, Pleurospermum amabile Craib & W. W. Smith, we investigated its crude extracts and the isolated phytochemicals for their biological activities. Four phenylpropanoids [(E)-isomyristicin (1), (E)-isoapiol (2), methyl eugenol (3) and (E)-isoelemicin (4)] and six furanocoumarins [psoralen (5), bergapten (6), isoimperatorin (7), isopimpinellin (8), oxypeucedanin hydrate (9) and oxypeucedanin methanolate (10)] were isolated from this plant. Among the test samples, compound 10 showed weak antibacterial activity against Bacillus subtilis and best antimalarial activity against the Plasmodium falciparum strains, TM4/8.2 (chloroquine and antifolate sensitive) and K1CB1 (multidrug resistant). None of the test samples showed cytotoxicity. This study generated scientific data that support the traditional medical uses of the plant.
Reader reaction on the fast small‐sample kernel independence test for microbiome community‐level association analysis

Zhan et al. ( ) presented a kernel RV coefficient (KRV) test to evaluate the overall association between host gene expression and microbiome composition, and showed its competitive performance compared to existing methods. In this article, we clarify the close relation of KRV to the existing generalized RV (GRV) coefficient, and show that KRV and GRV have very similar performance. Although the KRV test could control the type I error rate well at 1% and 5% levels, we show that it could largely underestimate p‐values at small significance levels leading to significantly inflated type I errors. As a partial remedy, we propose an alternative p‐value calculation, which is efficient and more accurate than KRV p‐value at small significance levels. We recommend that small KRV test p‐values should always be accompanied and verified by the permutation p‐value in practice. In addition, we analytically show that KRV can be written as a form of correlation coefficient, which can dramatically expedite its computation and make permutation p‐value calculation more efficient.
Comparison of Different Approaches to Define the Applicability Domain of QSAR Models

One of the OECD principles for model validation requires defining the Applicability Domain (AD) for the QSAR models. This is important since the reliable predictions are generally limited to query chemicals structurally similar to the training compounds used to build the model. Therefore, characterization of interpolation space is significant in defining the AD and in this study some existing descriptor-based approaches performing this task are discussed and compared by implementing them on existing validated datasets from the literature. Algorithms adopted by different approaches allow defining the interpolation space in several ways, while defined thresholds contribute significantly to the extrapolations. For each dataset and approach implemented for this study, the comparison analysis was carried out by considering the model statistics and relative position of test set with respect to the training space.
Roles of the Basic Helix-Loop-Helix Genes Hes1 and Hes5 in Expansion of Neural Stem Cells of the Developing Brain*

Neural stem cells, which differentiate into neurons and glia, are present in the ventricular zone of the embryonal brain. The precise mechanism by which neural stem cells are maintained during embryogenesis remains to be determined. Here, we found that transient misexpression of the basic helix-loop-helix genes Hes1 and Hes5 keeps embryonal telencephalic cells undifferentiated although they have been shown to induce gliogenesis in the retina. These telencephalic cells later differentiate into neurons and astroglia when Hes expression is down-regulated, suggesting that Hes1- andHes5- expressing cells are maintained as neural stem cells during embryogenesis. Conversely, in the absence of Hes1and Hes5, neural stem cells are not properly maintained, generating fewer and smaller neurospheres than the wild type. These results indicate that Hes1 and Hes5 play an important role in the maintenance of neural stem cells but not in gliogenesis in the embryonal telencephalon.
Prevalence and pattern of birth defects in a tertiary health facility in the Niger Delta area of Nigeria

Objective To ascertain the prevalence and pattern of congenital abnormalities that are peculiar to the Niger Delta area of Nigeria. Methods This is a descriptive retrospective cross-sectional study. It involved data from the labor ward and neonatal birth registers of the University of Port Harcourt Teaching Hospital on the total number of births and the babies that were delivered with major birth defects between August 2011 and December 2014. We also conducted a statistical comparison of the prevalence of congenital abnormalities in the Niger Delta with that in other regions of Nigeria and the developed world of Europe. Results Out of the 7,670 deliveries that occurred, 159 maternities had babies with major birth defects giving a prevalence of 20.73 cases per 1,000 live births. This figure is far more than that which was obtained in other regions of Nigeria −4.15:cases per 1,000 live births in the South East (P<0.001), 15.84:1,000 in the South West (P<0.01), and 5.51:1,000 in the North East (P<0.001). Eighty-five (53.46%) of the defects occurred in 1,681 unbooked patients, while 74 (46.54%) happened in 5,989 booked maternities (P<0.001). The predominant abnormalities were those of the central nervous system at 27.0%, gastrointestinal system 11.95%, cardiovascular system 10.69%, anterior abdominal wall 8.18%, skeleton 6.29%, and chromosomal abnormalities at 5.66%. Conclusion The prevalence of major birth defects at the University of Port Harcourt Teaching Hospital was 20.73 cases per 1,000 live births and it was more in the unbooked than the booked maternities. All body systems were affected with those of the central nervous system predominating at 27.0% of the total diagnosed defects.
A Novel Staining Protocol for Multiparameter Assessment of Cell Heterogeneity in Phormidium Populations (Cyanobacteria) Employing Fluorescent Dyes

Bacterial populations display high heterogeneity in viability and physiological activity at the single-cell level, especially under stressful conditions. We demonstrate a novel staining protocol for multiparameter assessment of individual cells in physiologically heterogeneous populations of cyanobacteria. The protocol employs fluorescent probes, i.e., redox dye 5-cyano-2,3-ditolyl tetrazolium chloride, ‘dead cell’ nucleic acid stain SYTOX Green, and DNA-specific fluorochrome 4′,6-diamidino-2-phenylindole, combined with microscopy image analysis. Our method allows simultaneous estimates of cellular respiration activity, membrane and nucleoid integrity, and allows the detection of photosynthetic pigments fluorescence along with morphological observations. The staining protocol has been adjusted for, both, laboratory and natural populations of the genus Phormidium (Oscillatoriales), and tested on 4 field-collected samples and 12 laboratory strains of cyanobacteria. Based on the mentioned cellular functions we suggest classification of cells in cyanobacterial populations into four categories: (i) active and intact; (ii) injured but active; (iii) metabolically inactive but intact; (iv) inactive and injured, or dead.
An Extension of UML Activity Diagram to Model the Behaviour of Context-Aware Systems

The main characteristics of context-aware systems are their ability to sense perpetually the context of the user and adapt their behaviour accordingly in response to changes in the user's context. Modularity is an important property for any design language as it provides ways of decomposing a system into smaller constituents which are then analyzed separately. The activity diagram of the Unified Modelling Language is a powerful language for describing the functions of a system. However it lacks notations for distinctively capturing the context-awareness requirements of context-aware systems. This paper proposes an extension of the activity diagram of Unified Modelling Language with new notations that enable the separation of concerns between the system functions, the context (or environment) constraints, and the adaption actions to be performed in reaction to changes in the system's environment. The pragmatics and flexibility of the proposed extension are demonstrated using a number of real-world case studies.
Influence of Orbital Implant Length and Diameter on Stress Distribution: A Finite Element Analysis

Purpose: A mathematical simulation of stress distribution around orbital implants was used to determine which length and diameter of implants would be best to dissipate stress. Methods: An integrated system for computed tomography data was utilized to create a 3-dimensional model of craniofacial structures. The model simulated implants placed in the 7, 11, and 12 o’clock positions of the orbital rim. A load of 2 N was applied to the model along the long axis of the implant (model 1) and an angle of 45° with the long axis of the implant (model 2). A model simulating an implant with a diameter of 3.75 mm and lengths of 3, 4, 6, 8, and 10 mm was developed to investigate the influence of the length factor. The influence of different diameters was modeled using implants with a length of 6 mm and diameters of 3.0, 3.75, 4.2, 5.0, and 6.0 mm. Values of von Mises equivalent stress at the implant–bone interface were computed using the finite element analysis for all variations. Results: The elements exposed to the maximum stress were located around the root of the orbital implant in model 1 or between the neck and the first thread of the orbital implant in model 2. An increase in the orbital implant diameter led to a decrease in the maximum von Mises equivalent stress values. In model 1, the reductions were 45.2% (diameter of 3.0–3.75 mm), 25.3% (diameter of 3.75–4.2 mm), 17.2% (diameter of 4.2–5.0 mm), and 5.4% (diameter of 5.0–6.0 mm). In model 2, the reductions of the maximum stress values were 51.9%, 35.4%, 19.7%, and 8.1% respectively. However, the influence of orbital implant length was not as pronounced as that of diameter. In model 1, the reductions were 28.8% (length of 3–4 mm), 19.2% (length of 4–6 mm), 9.6% (length of 6–8 mm), and 4.3% (length of 8–10 mm). In model 2, the reductions of the maximum stress values were 35.5%, 21.1%, 10.9%, and 5.4% respectively. Conclusions: An increase in the implant diameter decreased the maximum von Mises equivalent stress around the orbital implant more than an increase in the implant length. From a biomechanical perspective, the optimum choice was an orbital implant with no less than 4.2 mm diameter allowed by the anatomy.
Road traffic noise and sleep disturbances in an urban population: cross-sectional study.

AIM To explore the relationship between sleep disturbances caused by traffic noise and relevant personality traits, such as extroversion-introversion, neuroticism, and subjective noise sensitivity. METHODS A cross-sectional study was carried out from January to April 2005 in a central municipality of Belgrade, the capital of Serbia and Montenegro. Noise measurements were performed at 12 measurement sites three times at daytime and twice at night. On the basis of noise measurement results, three streets with the highest and three streets with the lowest values of equivalent sound pressure level (Leq) were chosen to represent noisy (>65 dB(A)) and quiet (<55dB(A)) areas, respectively. The respondents from both areas were asked to fill out the questionnaire on noise-related health problems. The final sample consisted of 310 respondents, 192 from noisy area and 118 from quiet area. RESULTS Respondents from noisy area reported having significantly more difficulties with falling asleep, being woken up by noise at night more often, and having more difficulties with falling back to sleep. They also complained of poorer sleep quality and tiredness after sleep and they slept by an open window in summer less often. Noise annoyance, subjective noise sensitivity, and neuroticism were significantly correlated with difficulties with falling asleep, time needed to fall asleep, poorer sleep quality, tiredness after sleep, and use of sleeping pills. After adjustment for potential modifying personality traits including subjective noise sensitivity, neuroticism, and extroversion, residence in noisy area was shown to be a significant predictor for difficulties with falling asleep (odds ratio [OR], 2.71; 95% confidence interval [CI], 1.27-5.80), difficulties with falling back to sleep (OR, 1.87; 1.02-3.40), waking up at night (OR, 2.60; 1.49-4.52), sleeping by closed windows (OR, 13.51; 5.84-31.25), having poor sleep quality (OR, 2.99; 1.13-7.89), and feeling tired after sleep (OR, 2.50; 1.11-5.63). CONCLUSION Urban population living in noisy area was at higher risk for sleep disturbances than population living in the quiet area. Furthermore, sleep disturbances were significantly and positively related to personality traits of neuroticism, subjective noise sensitivity, and noise annoyance.