Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Features of Scleroderma Patients With or Without Prior or Current Ischemic Digital Ulcers: Post-Hoc Analysis of a Nationwide Multicenter Cohort (ItinérAIR-Sclérodermie)

Objective. Digital ulcers are the most frequent vascular manifestations of systemic sclerosis (SSc). Clinical features of patients with prior or current digital ulcers have not been extensively described. This cross-sectional analysis of a large multicenter cohort compared the characteristics of SSc patients with prior or current digital ulcers with those never affected. Methods. Patients with prior/current digital ulcers or never affected were identified in the cohort of SSc patients enrolled in the French ItinérAIR-Sclérodermie registry. Rodnan skin scores, pulmonary function test results, and clinical and immunological data were analyzed to identify digital ulcerassociated clinical features. Results. Of 599 SSc patients, 317 had prior or current digital ulcers. These patients were more frequently male, with impaired diffusing capacity for carbon monoxide (DLCO), and higher Rodnan skin scores than patients never affected by digital ulcers. In a multivariate analysis, male gender, early onset of SSc, increased duration of SSc, high Rodnan skin score, and presence of anti-topoisomerase I antibodies (anti-topo I) were associated with prior or current digital ulcers. Comparison of patients with current digital ulcers versus patients never affected indicated that affected patients had increased duration of SSc, impaired DLCO, increased Rodnan score, and younger age at onset of SSc. Conclusion. Male patients with early onset SSc, more severe skin fibrosis, impaired DLCO, and anti-topo I were most likely to exhibit prior or current digital ulcers. Confirmation of these results in a prospective longitudinal study may enable identification of patients at greatest risk of developing digital ulcers, facilitating management of this disabling complication.
Clinical Profile of Fever with Thrombocytopenia in Tertiary Hospital, Nellore

Authors Aakash Teja Durbesula, Chetan Reddy K B, Dr Gangaram Usham, Rohith Karnati Department of General Medicine Narayana Medical College & Hospital, Nellore, Andhra Pradesh, India Abstract Objective: Infection is the commonest cause of thrombocytopenia. Definite diagnosis helps to manage the patients effectively. The objective was to determine possible infective etiology for fever with thrombocytopenia and to study the presentation and complications of thrombocytopenia. Methodology: This prospective study was conducted in Narayana Medical College and Hospital, Nellore between May 2015 – June 2016. 150 patients aged 15 years and above with fever and thrombocytopenia were included for this study. A detailed history, general and systemic examination was done and recorded. Results: Out of 150 cases of fever with thrombocytopenia, 88(58.7%) were males and 62(41.3%) were females and the most common age group was between 15-30 years 67(44.7%). The most common presentation was fever 150(100%), followed by myalgia 52(34.7%),headache 46(30.7%),cough 24(16%), hepatomegaly 35(23.3%), splenomegaly 26(17.3%) and bleeding manifestations in 18(12%). 45(30%) patients had bleeding manifestations of which malena in 18 (40%) was the commonest followed by petechiae/ purpura/ecchymosis in 13(28.8%), hematuria 5(11.1%), epistaxis 3(6.7%),gum bleed 3(6.7%) and hematemesis in 3 (6.7%). Common range of platelet count at the time of admission was in the range of 50000 – 1Lakh/cumm in 72(48%). Infection was the commonest cause of thrombocytopenia and the commonest infection was dengue 68 (45.3%), followed by viral fever other than dengue 22(14.7%), septicemia 19 (12.7%), malaria 17(11.3%), undiagnosed 13(8.7%), enteric fever 9(6%) and leptospirosis 2(1.3%). 140(93.3%) of them had good recovery and 10(6.7%) patients have expired. Of those 10 mortality cases, 6 died due to septicemia,3 due to dengue and 1 had malaria. Conclusion: Infections, particularly dengue fever was the commonest cause of fever with thrombocytopenia. Majority of the patients with thrombocytopenia are asymptomatic but in significant number of cases there were bleeding manifestations also. Malena was the common bleeding manifestations. On treating the specific cause drastic improvement in platelet count was noted.
DECOMPOSITION AND RELEASE OF NUTRIENTS FROM SUGARCANE TRASH IN TWO AGRICULTURAL ENVIRONMENTS IN BRAZIL

The decomposition and release of nutrients from unburned and mechanically harvested sugar-cane trash was evaluated under two agricultural environments in Sao Paulo State, Brazil. In the first agricultural environment (AE 1), part of a rain fed commercial field was used in the Ribeirao Preto region. In the second agricultural environment (AE 2), the study was conducted on an irrigated experimental area of the Escola Superior de Agricultura ‘Luiz de Queiroz’ in Piracicaba county. At this site, the influence of application of urea, potassium chloride and vinasse upon the decomposition of sugarcane trash was evaluated in lysimeters. Trash mass reductions of about 20% and 70% were observed at AE 1 and AE 2, respectively, after one year. Nutrient treatments did not affect trash decomposition or nutrient cycling at AE 2. The highest carbon losses, in both agricultural environments, came from decarboxilation of cellular contents and hemicellulose. Potassium was the most labile nutrient in crop residues, with 85– 93% of the total potassium being released across sites in the study period. Only 20% of the total nitrogen was released. The release of calcium and magnesium ranged from 40% to 60%, across sites. In AE 1, there was no release of phosphorus and only 11% of the sulfur was released. However, in AE 2 the release of these nutrients reached 60%. The higher nutrient release and sugarcane trash decomposition in AE 2, comparative to AE 1, was due to greater decomposition of cellular contents and this may have been associated with protection of labile organics at AE 1 by higher lignin content and a consistent moisture regime provided by irrigation at AE 2.
SHORT COMMUNICATION PHENOTYPIC CHARACTERIZATION OF PSEUDOMONAS AVELLANAE (PSALLIDAS) JANSE ET AL. AND OCCURRENCE OF COLONY VARIANTS

SUMMARY Thirty-seven strains of Pseudomonas avellanae from northern Greece, northern Italy and two different areas of central Italy were assessed for some morphological and physiological properties. Whole-cell protein profile analysis was performed by means of UPGMA. The occurrence and induction of transparent colonies of P. avellanae sometimes observed on nutrient sucrose agar (NSA) isolation plates, is described. P. avellanae strains showed variability in morphological characteristics, gelatin liquefaction and maximum temperature of growth. Cluster analysis of whole-cell protein profiles indicated that strains from northern Italy differ from those from northern Greece and central Italy and that strains from the provinces of Viterbo and Rome clustered in the same group. All strains were negative in icenucleation activity and accumulation of poly-β-hydroxybutyrate, and positive in production acid from sucrose. All strains were copper-sensitive. The production of fluorescent pigments on media was influenced by subculture on NSA, and strains from Italy lost this feature after a number of transfers. The existence of populations of the pathogen seems possible. Transparent colonies of P. avellanae were also frequently obtained by incubation for three days at supraoptimal growth temperature, by adding 7% sucrose to the nutrient agar and by subculturing 30 day-old colonies on NSA. Such P. avellanae colony variants were encapsulated and did not induce hypersensitivity in tobacco leaves.
The Differences of Students Learning Outcomes and Metacognitive Skills by Using PBL and Metacognitive-PBL

This study aims to determine the differences of cognitive learning outcome and metacognitive skills between class taught by using PBL and metacognitive-PBL model in salt hydrolysis material. This quasi-experimental research employed the nonequivalent control group design and was conducted at class XI-MIA of SMAN 1 Banjarmasin. The data were collected by using test, questionnaire and interview. They were analyzed using t-test and descriptive analysis. The result of this research showed that there are differences in cognitive learning and metacognitive skills significantly between students who learned by using PBL and metacognitive-PBL model. The students who learned by using metacognitive-PBL model cognitive learning achivement were better than those who learned by using PBL model. Keywords— Cognitive Learning Achievement, MetacognitivePBL Model, Metacognitive Skill, PBL Model, Salt Hydrolysis
Impact of changing crop rotation to continuous wheat on soil characteristics in semiarid areas

To evaluate the effect of crop rotation on soil structural properties and aggregate fractal dimension, three locations were selected in Maragheh and Hashtroud areas, northwest of Iran. Four crop rotations were implemented and several soil physical and chemical properties were evaluated. In wheat-chickpea and wheat-fallow rotation treatments (T2 and T4) average bulk density (BD) of 1.155 g cm-3 was significantly (P< 0.01) lower than continuous wheat cropping (T1) and wheat-fallow-wheat-wheat-wheat (T3) treatments with BD of 1.29 g cm-3. Water aggregate stability (WAS) in T4 became significantly (P<0.01) greater than other rotations. Saturated water content (θs) of T1 and T3 (0.39 cm3cm-3) was significantly (P< 0.01) lower than T2 and T4 (nearly equal to 0.55 cm3cm-3). The lowest saturated hydraulic conductivity (KS) of about 2.0 cm h-1 occurred in T1 and T3, and the highest (5.27 cm h-1) in T4. Soil moisture content (θm) in T2 and T4 during GS21 growth stage significantly exceeded those of T1 and T3. Biological yields in T2 and T4 were nearly equal (3.05 t ha-1) and were significantly (P< 0.05) greater than T1 and T3 (1.5 t ha-1). During growth stages of GS54 and GS87, θm and other measured properties were not significantly affected by crop rotations. It appears that substitution of wheat-follow or wheat-chickpea rotations by continuous wheat cropping would gradually degrade the soils and thus should be abandoned. Key words: Crop rotation, fractal dimension, mean weight diameter, soil structure, water aggregate stability.
High-endurance megahertz electrical self-oscillation in Ti/NbO x bilayer structures

Electrical self-oscillation is reported for a Ti/NbOx negative differential resistance device incorporated in a simple electric circuit configuration. Measurements confirm stable operation of the oscillator at source voltages as low as 1.06 V, and demonstrate frequency control in the range from 2.5 to 20.5 MHz for voltage changes as small as ∼1 V. Device operation is reported for >6.5 × 1010 cycles, during which the operating frequency and peak-to-peak device current decreased by ∼25%. The low operating voltage, large frequency range, and high endurance of these devices makes them particularly interesting for applications such as neuromorphic computing.
Lawrence Berkeley National Laboratory Recent Work Title Variant profiling of evolving prokaryotic populations Permalink

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb. univie.ac. at. Subjects Bioinformatics, Computational Biology, Evolutionary Studies, Genomics, Microbiology
MACROSCOPIC AND MICROSCOPIC FINDINGS IN THE LIVER, GALLBLADDER, SPLEEN AND KIDNEYS OF CAPTIVE RETICULATED PYTHONS (Python reticulatus, Schneider, 1801) (Reptilia: Pythonidae) WITH PNEUMONIA

The macroscopic and microscopic findings in the liver, gallbladder, spleen and kidneys of 12 reticulated pythons with pneumonia were described through gross and histopathological examinations. Gross findings in the liver observed were lesions on the surface (milliary white nodules and adhesions) and within the parenchyma of the organ. The gallbladder had a circumference of 15.71 ± 4.75 cm and length of 6.28 ± 2.01 cm. Gross lesions in the kidneys include congestion, thickened capsule and web-like adhesions. Twenty-five percent of the animals were found to have spleen that was irregularly shaped, oblate-spheroid organs with varying discolorations. Histopathological examination revealed signs of hepatitis, nephritis and nephrosis, splenitis and hyperplasia of the pseudostratified epithelium of the gallbladder. Significant histopathologic findings include presence of visceral larva migrans in the liver and kidneys, granuloma formation, presence of intracytoplasmic eosinophilic round inclusion bodies within the hepatocytes and renal tubule as well as presence of lipid vacuoles and cholesterol crystals in the splenic parenchyma. Macroscopic and microscopic findings suggest that presence of lesions in other organ systems is highly likely in snakes with pneumonia.
Exosomal MicroRNAs Released by Pediatric Cardiac Progenitor Cells.

Cell-based therapies have been intensively studied as promising treatments for the diseased heart, although the mechanisms underlying the modest beneficial effects to date are far from being clear. In this issue of Circulation Research , Agarwal et al1 suggest that both oxygen levels and age of donors are able to influence the beneficial effects of pediatric cardiac progenitor cell (CPC)–derived exosomes. In addition, the change of miRNA content in hypoxic/normoxic preconditioned exosomes from different age groups are found to be associated with differences in reparative effects in a rat model of ischemia–reperfusion injury based on a computational modeling approach. The authors found at day 3 after ischemia–reperfusion injury that exosomes derived from neonatal cells led to a significant improvement of ejection fraction (no matter pretreated by hypoxic condition or not), whereas hypoxic exosomes from infant- and child-derived CPCs showed improvement at day 28 after ischemia–reperfusion injury. Reduced fibrosis and increased angiogenesis in the infarcted region were observed after treatment with hypoxic exosomes from all age groups. To predict and further explore the underlying mechanisms, the authors took an unbiased multivariate modeling approach that they used before2 to establish a connection between donor age and oxygen content, miRNAs, and the functional consequences. A partial least squares regression model was created and tested for the capability of predicting miRNAs with functional relevance. To prove the predicted miRNAs derived from the partial least squares regression modeling approach, several angiogenesis-associated miRNAs without known related function were tested in vitro. Article, see p 701 Numerous studies have suggested an improvement of cardiac function after delivery of cardiac stem cells including human CPC in animal models; however, the mechanisms behind the observed therapeutic effects are not fully elucidated. Paracrine signaling pathways play an essential role in the repair action via activation of the adjacent …
Full-sky Ray-tracing Simulation of Weak Lensing Using ELUCID Simulations: Exploring Galaxy Intrinsic Alignment and Cosmic Shear Correlations

The intrinsic alignment of galaxies is an important systematic effect in weak-lensing surveys, which can affect the derived cosmological parameters. One direct way to distinguish different alignment models and quantify their effects on the measurement is to produce mock weak-lensing surveys. In this work, we use the full-sky ray-tracing technique to produce mock images of galaxies from the ELUCID N-body simulation run with WMAP9 cosmology. In our model, we assume that the shape of the central elliptical galaxy follows that of the dark matter halo, and that of the spiral galaxy follows the halo spin. Using the mock galaxy images, a combination of galaxy intrinsic shape and the gravitational shear, we compare the predicted tomographic shear correlations to the results of the Kilo-Degree Survey (KiDS) and Deep Lens Survey (DLS). We find that our predictions stay between the KiDS and DLS results. We rule out a model in which the satellite galaxies are radially aligned with the center galaxy; otherwise, the shear correlations on small scales are too high. Most importantly, we find that although the intrinsic alignment of spiral galaxies is very weak, they induce a positive correlation between the gravitational shear signal and the intrinsic galaxy orientation (GI). This is because the spiral galaxy is tangentially aligned with the nearby large-scale overdensity, contrary to the radial alignment of the elliptical galaxy. Our results explain the origin of the detected positive GI term in the weak-lensing surveys. We conclude that in future analyses, the GI model must include the dependence on galaxy types in more detail.
Redox-mediated polymerization and removal of benzidine from model wastewater catalyzed by immobilized peroxidase

Peroxidase from Momordica charantia was highly effective, active and stable for the oxidation of benzidine from model wastewater. There was no oxidative polymerization of benzidine without any redox mediator. Various experimental parameters were standardized for the maximum oxidation of benzidine by peroxidase. The maximum oxidation of this pollutant was observed in the presence of 0.05 mM phenol, 0.75 mM H 2 O 2 and 0.2 U mL -1 bitter gourd peroxidase (BGP) in a buffer of pH 5.0 at 40°C. Comparative study was performed by soluble as well as surface immobilized bitter gourd peroxidase on Con A layered calcium alginate-starch beads for the degradation of benzidine from model wastewater. Immobilized bitter gourd peroxidase was used for the successful and effective removal of water polluted with benzidine in batch as well as in continuous reactor. The effect of detergents and some water miscible organic solvent was also reported for the oxidation of benzidine from polluted water. Oxidation of benzidine in batch process by soluble and immobilized peroxidase was highly effective and it could remove 72 and 100% benzidine by soluble and immobilized bitter gourd peroxidase, respectively. The reactor filled with immobilized enzyme retained more than 45% benzidine removal efficiency even after 30 days of its continuous operation. The absorption spectra of the treated benzidine exhibited a marked difference in absorption at its λ max as compared to untreated benzidine polluted water. Keywords: Alginate, bitter gourd peroxidase, concanavalin A, removal, immobilization
Lung nodules: CT-guided placement of microcoils to direct video-assisted thoracoscopic surgical resection.

PURPOSE To prospectively assess the safety and effectiveness of computed tomography (CT)-guided placement of fiber-coated microcoils used to guide video-assisted thoracoscopic surgical (VATS) excision of small peripheral lung nodules, with successful excision as the primary outcome and successful CT-guided microcoil placement and procedural complications as secondary outcomes. MATERIALS AND METHODS The institutional review board approved the study protocol. Informed consent was obtained from all 69 enrolled patients (30 men, 39 women; mean age, 60.7 years +/- 10.1 [standard deviation]) with 75 nodules. At CT, one end of an 80-mm long, 0.018-inch-diameter fiber-coated microcoil was placed deep to the small peripheral lung nodule, and the other end was coiled in the pleural space. VATS excision of lung tissue, nodules, and the microcoil was performed with fluoroscopic guidance. RESULTS Seventy-three (97%) 4-24-mm nodules were successfully removed at fluoroscopically guided VATS excision; two nodules could not be removed. CT-guided microcoil placement was successful in all cases; however, two (3%) of 75 coils were displaced at VATS excision. Pneumothorax requiring chest tube placement occurred in two (3%) patients, and asymptomatic hemothorax occurred in one (1%) patient. The microcoil did not impede intraoperative frozen-section histopathologic analysis, which facilitated accurate clinical management in all patients. For 19 (28%) patients, the preoperative treatment plan based on bronchoscopy, needle biopsy, and positron emission tomography findings changed after VATS excision. CONCLUSION Microcoil localization of small peripheral lung nodules enabled fluoroscopically guided VATS resection of 97% of the nodules, with a low rate of intervention (3%) for procedural complications.
Advection patterns and composition of TSP and PM2.5 samples over south-east Italy

24-hour Total Suspended Particulate (TSP) matter and PM2.5 samples have simultaneously been collected at a suburban site of South-East Italy (40.4° N; 18.1° E) to investigate the dependence of TSP and PM2.5 mass concentrations on long-range transported air masses, and to infer how concentration and composition of sampled particles were dependent on particulate matter (PM) cut-off diameter. The PM chemical composition is quite dependent on particle size and as a consequence, can allow inferring aerosol types and corresponding sources. Ion chromatography (IC) and Organic Carbon/Elemental Carbon (OC/EC) analyses have been performed on some PM2.5 and TSP randomly selected samples, in order to determine mass concentrations of main ionic species and of EC and OC, respectively. In accordance with TSP and PM2.5 mass concentrations and PM2.5/TSP ratios, ion chromatography and OC/EC analyses have revealed that both ionic species and OC/EC concentrations significantly varied from sample to sample, as a consequence of the significant dependence of aerosol properties on regional sources and pathways of the air masses advected over the monitoring site.