Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Profiling in Behcet's Disease Indicates an Autoimmune Component in the Pathogenesis of the Disease and Opens New Avenues for Targeted Therapy

Behçet disease (BD) is a chronic inflammatory multisystem disease characterized by oral and genital ulcers, uveitis, and skin lesions. Disease etiopathogenesis is still unclear. We aim to elucidate some aspects of BD pathogenesis and to identify specific gene signatures in peripheral blood cells (PBCs) of patients with active disease using novel gene expression and network analysis. 179 genes were modulated in 10 PBCs of BD patients when compared to 10 healthy donors. Among differentially expressed genes the top enriched gene function was immune response, characterized by upregulation of Th17-related genes and type I interferon- (IFN-) inducible genes. Th17 polarization was confirmed by FACS analysis. The transcriptome identified gene classes (vascular damage, blood coagulation, and inflammation) involved in the pathogenesis of the typical features of BD. Following network analysis, the resulting interactome showed 5 highly connected regions (clusters) enriched in T and B cell activation pathways and 2 clusters enriched in type I IFN, JAK/STAT, and TLR signaling pathways, all implicated in autoimmune diseases. We report here the first combined analysis of the transcriptome and interactome in PBCs of BD patients in the active stage of disease. This approach generates useful insights in disease pathogenesis and suggests an autoimmune component in the origin of BD.
Linking Neuroinflammation and Neurodegeneration in Parkinson's Disease

Neurodegenerative diseases such as Parkinson's disease (PD) and Alzheimer's disease (AD) impose a pressing burden on our developed and consequently aging society. Misfolded protein aggregates are a critical aspect of several neurodegenerative diseases. Nevertheless, several questions remain unanswered regarding the role of misfolded protein aggregates and the cause of neuronal cell death. Recently, it has been postulated that neuroinflammatory processes might play a crucial role in the pathogenesis of PD. Numerous postmortem, brain imaging, epidemiological, and animal studies have documented the involvement of the innate and adaptive immunity in neurodegeneration. Whether these inflammatory processes are directly involved in the etiology of PD or represent secondary consequences of nigrostriatal pathway injury is the subject of intensive research. Immune alterations in response to extracellular α-synuclein may play a critical role in modulating Parkinson's disease progression. In this review, we address the current concept of neuroinflammation and its involvement in PD-associated neurodegeneration.
Data Integration and Machine Learning: A Natural Synergy

There is now more data to analyze than ever before. As data volume and variety have increased, so have the ties between machine learning and data integration become stronger. For machine learning to be effective, one must utilize data from the greatest possible variety of sources; and this is why data integration plays a key role. At the same time machine learning is driving automation in data integration, resulting in overall reduction of integration costs and improved accuracy. This tutorial focuses on three aspects of the synergistic relationship between data integration and machine learning: (1) we survey how state-of-the-art data integration solutions rely on machine learning-based approaches for accurate results and effective human-in-the-loop pipelines, (2) we review how end-to-end machine learning applications rely on data integration to identify accurate, clean, and relevant data for their analytics exercises, and (3) we discuss open research challenges and opportunities that span across data integration and machine learning.
Structure of triaquatris(1,1,1-trifluoro-4-oxopentan-2-olato)cerium(III) as a possible fluorescent compound

The title complex has two kinds of ligands, trifluoroacetylacetonate and water. As a result of the presence of F atoms in the 1,1,1-trifluoro-4-oxopentan-2-olate ligand, the metal–metal distance is longer than in the case of the analogous yttrium complex containing an acetylacetonato ligand and also for the analogous lanthanum complex containing acetylacetonate.
A new frog of the genus Mantidactylus from the rainforests of north-eastern Madagascar, and its karyological affinities

We describe a new species of the genus Mantidactylus found during e eld inventories in the north- eastern rainforests of Madagascar. Mantidactylus salegy sp. n. reaches a snout-vent length of 45-50 mm, has evident dorsolateral ridges and whitish spots on the upper jaws (mainly in females). The vocal sacs in males are distinctly visible and paired subgular, without strongly ine atable areas recognizable between the blackish lateral skin e aps on the throat. This frog exhibits a mosaic of characters previously thought to be typical for either the subgenera Gephyromantis or Phylacomantis. Therefore, it is a crucial discovery towards better understanding of the relationships between the taxa included in these two subgenera, supporting previous molecular results which indicated their paraphyly. The call of M. salegy consists of a rapid series of 8-11 rattling notes emitted at 1000-3500 Hz. We also provide karyological data for M. salegy, and for several related species, M. granulatus , M. leucomaculatus , M. moseri, M. redimitus , M. zavona, and M. pseudoasper (attributed to the subgenus Phylacomantis ) and M. luteus (subgenus Gephyromantis ). In terms of general chromosome morphology and structure, NOR localisation and heterochromatin characteristics, M. salegy shows similarities to M. redimitus , M. zavona and M. leucomaculatus , all included within Phylacomantis . Our data cone rm that NOR position is a phylogenetically informative character.
Study of Clinical Profile and Outcome of Acute Respiratory Distress Syndrome in Intensive Care Unit

DOI: 10.21276/sjams.2018. 6.4. 61 Abstract: Acute respiratory distress syndrome (ARDS) is a clinical syndrome of severe dyspnea of rapid onset, hypoxemia and diffuse pulmonary infiltrates leading to respiratory failure. ARDS is associated with significant morbidity and mortality. A prospective study to evaluate the clinical features, etiology, factors influencing survivors and non survivors, predictors of outcome of patients with ARDS admitted in ICU of tertiary care hospital this study encompassed 100 cases of ARDS admitted to ICU as per AECC guidelines. Patients excluded were with cardiac failure, significant underlying lung disease, and age below 14 years. There were more males 52% than females 48% with a total mortality of 61 %. In the present study the main etiological factor for ARDS was infective 84%. Most common cause being sepsis 45(53%). ARDS due to noninfective cause accounted for 16% of cases. Sepsis with multiorgan failure was seen in 26% with mortality of 61.5%. APACHE II score among survivors was 12.3 ± 5.3 compared to non survivors 18.9 ± 5.7. APACHE III score among survivors was 53.6 ± 14.9 compared to non survivors 94.1 ±19.8. The PaO2/FiO2 at admission was109.9 ± 35.5 for survivors compared to 75.5 ± 36.3 for non survivors. Dengue, Malaria, pneumonia, scrub typhus and undiagnosed fever were the main etiologies. PaO2/ FiO2 ratio, APACHE II and III score at the time of admission were significant predictors of the outcome. Sepsis, acidosis, hypotension, and multiorgan failure were individual predictors of mortality in patients with ARDS.
T‐NET, a dynamic model for simulating daily stream temperature at the regional scale based on a network topology

Currently, the distribution areas of aquatic species are studied by using air temperature as a proxy of water temperature, which is not available at a regional scale. To simulate water temperature at a regional scale, a physically based model using the equilibrium temperature concept and including upstream‐downstream propagation of the thermal signal is proposed. This model, called Temperature‐NETwork (T‐NET), is based on a hydrographical network topology and was tested at the Loire basin scale (105 km2). The T‐NET model obtained a mean root mean square error of 1.6 °C at a daily time step on the basis of 128 water temperature stations (2008–2012). The model obtained excellent performance at stations located on small and medium rivers (distance from headwater <100 km) that are strongly influenced by headwater conditions (median root mean square error of 1.8 °C). The shading factor and the headwater temperature were the most important variables on the mean simulated temperature, while the river discharge influenced the daily temperature variation and diurnal amplitude. The T‐NET model simulates specific events, such as temperature of the Loire during the floods of June 1992 and the thermal regime response of streams during the heatwave of August 2003, much more efficiently than a simple point‐scale heat balance model. The T‐NET model is very consistent at a regional scale and could easily be transposed to changing forcing conditions and to other catchments. Copyright © 2016 John Wiley & Sons, Ltd.
Outcomes of Delayed Sternal Closure in Pediatric Heart Surgery: Single-Center Experience

Background Delayed sternal closure (DSC) after cardiac surgery is a therapeutic option in the treatment of the severely impaired heart in pediatric cardiac surgery. Methods A single-center retrospective review of all bypass surgeries performed over a 10-year period (2003–2012). Results Of a total of 2325 patients registered in our database, the DSC group included 259 cases (11%), and the remaining 2066 cases (89%) constituted the control group (PSC). RACHS-1 risk was higher for the DSC group (74% had a score of 3 or 4) than for the PSC group (82% had a score of 2 or 3). The most frequent diagnosis for the DSC group was transposition of the great arteries (28%). We found out that hemodynamic instability was the main indication observed in patients aged ≤ 8 years (63%), while bleeding was the principal indication for patients aged ≥ 8 years (94%) (p ≤ 0.001). The average time between surgery and sternal closure was 2.3 ± 1.4 days. Overall mortality rates were higher for patients of the DSC group (22%) than for the PSC group (8.7%) (OR: 0.4 (95% CI: 0.4 to 0.5), p < 0.05). There were six patients with DSC who developed mediastinitis (2.3%). The risk of mediastinitis was significantly higher when DSC was performed 4 days after the primary surgery. Conclusions DSC is an important management strategy for congenital cardiac surgery in infants and children. The prolonged sternal closure time is associated with an increased rate of postoperative mediastinitis.
Improved Surface Velocity and Trajectory Estimates in the Gulf of Mexico from Blended Satellite Altimetry and Drifter Data

AbstractThis study investigates the results of blending altimetry-based surface currents in the Gulf of Mexico with available drifter observations. Here, subsets of trajectories obtained from the near-simultaneous deployment of about 300 Coastal Ocean Dynamics Experiment (CODE) surface drifters provide both input and control data. The fidelity of surface velocity fields are measured in the Lagrangian frame by a skill score that compares the separation between observed and hindcast trajectories to the observed absolute dispersion. Trajectories estimated from altimetry-based velocities provide satisfactory average results (skill score > 0.4) in large (~100 km) open-ocean structures. However, the distribution of skill score values within these structures is quite variable. In the DeSoto Canyon and on the shelf where smaller-scale structures are present, the overall altimeter skill score is typically reduced to less than 0.2. After 3 days, the dataset-averaged distance between hindcast and drifter trajectorie.
Spectral Clustering for Multiple Sparse Networks: I

Although much of the focus of statistical works on networks has been on static networks, multiple networks are currently becoming more common among network data sets. Usually, a number of network data sets, which share some form of connection between each other are known as multiple or multi-layer networks. We consider the problem of identifying the common community structures for multiple networks. We consider extensions of the spectral clustering methods for the multiple sparse networks, and give theoretical guarantee that the spectral clustering methods produce consistent community detection in case of both multiple stochastic block model and multiple degree-corrected block models. The methods are shown to work under sufficiently mild conditions on the number of multiple networks to detect associative community structures, even if all the individual networks are sparse and most of the individual networks are below community detectability threshold. We reinforce the validity of the theoretical results via simulations too.
Anti-factor Xa levels in obese patients receiving enoxaparin for treatment and prophylaxis indications

Objectives To evaluate the degree of anticoagulation achieved with different enoxaparin dosing regimens used in obese and morbidly obese patients in a hospital setting in Jordan. Methods All obese adult patients who were prescribed enoxaparin for various indications were invited to participate in the study. The anti-factor Xa (anti-Xa) level was checked once after 4–6 hours of the third or fourth dose of enoxaparin (at steady state). Patients were followed daily to evaluate drug efficacy and safety through their hospital course. Results Enoxaparin daily dose used for prophylaxis indications ranged from 0.3 to 0.85 mg/kg and from 0.31 to 2.25 mg/kg in case of certain treatment indications. Most participants who received enoxaparin for treatment indications (76.9%) were on capping dosing regimens, which was <1 mg/kg twice daily. On the other hand, most patients (88.5%) who received enoxaparin for prophylaxis indications were on a fixed 40 mg/d dose. Among the 52 patients who completed the study, 19 patients (36.5%) had therapeutic anti-Xa levels. The results showed no statistically significant associations between regimens that were used and achieving therapeutic anti-Xa level (p>0.05). No bleeding events or thrombocytopenia were noticed, and there was one case of recurrent thrombosis. Conclusion Enoxaparin dosing regimens that were used for obese patients varied based on prescribing physicians. Regardless of the regimen used, the majority of participants had nontherapeutic anti-Xa. Individualized dosing regimens based on anti-Xa levels are warranted for obese patients on enoxaparin.
NTU NLP Lab System at SemEval-2018 Task 10: Verifying Semantic Differences by Integrating Distributional Information and Expert Knowledge

This paper presents the NTU NLP Lab system for the SemEval-2018 Capturing Discriminative Attributes task. Word embeddings, pointwise mutual information (PMI), ConceptNet edges and shortest path lengths are utilized as input features to build binary classifiers to tell whether an attribute is discriminative for a pair of concepts. Our neural network model reaches about 73% F1 score on the test set and ranks the 3rd in the task. Though the attributes to deal with in this task are all visual, our models are not provided with any image data. The results indicate that visual information can be derived from textual data.
Persistence of Helicobacter pylori Infection: Genetic and Epigenetic Diversity

Helicobacter pylori is a Gram negative bacterium found on the luminal surface of the gastric epithelium. Infection is generally acquired during childhood and persists life-long in the absence of antibiotic treatment. H. pylori has a long period of co-evolution with humans, going back at least since human migration out of Africa about 60, 000 years ago [1, 2]. This coevolution is reflected in DNA sequence signatures observed in H. pylori strains of different geographic origin and has enabled the mapping of human migration out of Africa. This prolonged and intimate relationship is likely to have shaped the large and diverse repertoire of strategies which H. pylori employs to establish robust colonization and persist in the gastric niche. Key challenges that H. pylori encounters are fluctuation of acidic pH of the gastric lumen, peristalsis of the mucus layer leading to washout in the lower intestine, nutrient scarcity, and the innate and adaptive immune responses promoting local inflammation or gastritis [3-8]. These challenges, particularly host immune responses, are likely to represent the selective pressure driving H. pylori micro-evolution during transmission leading to persistence in the human host.
Subcutaneous Eikenella corrodens, Actinomyces sp., and α-Hemolytic Streptococcus Abscess of the Thigh following a Vitamin B12 Injection

This case report describes a 38-year-old female presenting with a thigh abscess caused by Eikenella corrodens, Actinomyces sp. , and α-hemolytic Streptococcus following an intramuscular vitamin B12 injection administered at an outpatient clinic. After failure to improve clinically with intravenous daptomycin and after visualization of the abscess with gas bubbles on CT scan, she was taken to the operating room for three separate surgical irrigation and debridement procedures. Treatment also included intravenous ampicillin/sulbactam followed by oral amoxicillin/clavulanic acid therapy. She remained symptom free and without infection at nine months following hospitalization. It was suspected that poor hygiene played a role in the infection, but a definitive cause was not identified.
Association of Total Fluid Intake and Output with Duration of Hospital Stay in Patients with Acute Pancreatitis

Background/Aims The aim of this study was to evaluate the association of fluid balance with outcomes in patients hospitalized with acute pancreatitis (AP). Methods This was a retrospective study of patients hospitalized between May 2008 and June 2016 with AP and a clinical order for strict recording of intake and output. Data collected included various types of fluid intake and output at 24 and 48 hours after admission. The primary outcome was length of stay (LOS). Analysis was performed using single-variable and multivariable negative binomial regression models. Results Of 1256 patients hospitalized for AP during the study period, only 71 patients (5.6%) had a clinical order for strict recording of intake and output. Increased urine output was associated with a decreased LOS at 24 and 48 hours in univariable analysis. An increasingly positive fluid balance (total intake minus urine output) at 24 hours was associated with a longer LOS in multivariable analysis. Conclusions Few patients hospitalized for AP had a documented order for strict monitoring of fluid intake and output, despite the importance of monitoring fluid balance in these patients. Our study suggests an association between urine output and fluid balance with LOS in AP.
ADC Benchmark Range for Correct Diagnosis of Primary and Recurrent Middle Ear Cholesteatoma

Objectives Magnetic resonance imaging (MRI) and in particular diffusion-weighted imaging (DWI) have been broadly proven to be the reference imaging method to discriminate between cholesteatoma and noncholesteatomatous middle ear lesions, especially when high tissue specificity is required. The aim of this study is to define a range of apparent diffusion coefficient (ADC) values within which the diagnosis of cholesteatoma is almost certain. Methods The study was retrospectively conducted on a cohort of 124 patients. All patients underwent first- or second-look surgery because primary or secondary acquired cholesteatoma was clinically suspected; they all had preoperative MRI examination 15 days before surgery, including DWI from which the ADC maps were calculated. Results Average ADC value for cholesteatomas was 859,4 × 10−6 mm2/s (range 1545 × 10−6 mm2/s; IQR = 362 × 10−6 mm2/s; σ = 276,3 × 10−6 mm2/s), while for noncholesteatomatous inflammatory lesions, it was 2216,3 × 10−6 mm2/s (range 1015 × 10−6 mm2/s; IQR = 372,75 × 10−6 mm2/s; σ = 225,6 × 10−6 mm2/s). Interobserver agreement with Fleiss' Kappa statistics was 0,96. No overlap between two groups' range of values was found and the difference was statistically significant for p < 0.0001. Conclusions We propose an interval of ADC values that should represent an appropriate benchmark range for a correct differentiation between cholesteatoma and granulation tissue or fibrosis of noncholesteatomatous inflammatory lesions.
Flavocoxid, a Natural Antioxidant, Protects Mouse Kidney from Cadmium-Induced Toxicity

Background Cadmium (Cd), a diffused environmental pollutant, has adverse effects on urinary apparatus. The role of flavocoxid, a natural flavonoid with antioxidant activity, on the morphological and biochemical changes induced in vivo by Cd in mice kidney was evaluated. Methods C57 BL/6J mice received 0.9% NaCl alone, flavocoxid (20 mg/kg/day i.p.) alone, Cd chloride (CdCl2) (2 mg/kg/day i.p.) alone, or CdCl2 plus flavocoxid (2 mg/kg/day i.p. plus 20 mg/kg/day i.p.) for 14 days. The kidneys were processed for biochemical, structural, ultrastructural, and morphometric evaluation. Results Cd treatment alone significantly increased urea nitrogen and creatinine, iNOS, MMP-9, and pERK 1/2 expression and protein carbonyl; reduced GSH, GR, and GPx; and induced structural and ultrastructural changes in the glomeruli and in the tubular epithelium. After 14 days of treatment, flavocoxid administration reduced urea nitrogen and creatinine, iNOS, MMP-9, and pERK 1/2 expression and protein carbonyl; increased GSH, GR, and GPx; and showed an evident preservation of the glomerular and tubular structure and ultrastructure. Conclusions A protective role of flavocoxid against Cd-induced oxidative damages in mouse kidney was demonstrated for the first time. Flavocoxid may have a promising antioxidant role against environmental Cd harmful effects on glomerular and tubular lesions.
Template ultraviolet to near-infrared spectra of star-forming galaxies and their application to K-corrections

Template UV-optical spectra of quiescent and starburst galaxies are presented and used to derive Kcorrections as a function of morphological type and redshift. IUE observations and archival data are used for the UV template spectra. The optical spectra are from ground-based observations obtained in apertures that match closely the 200 arcsec 2 IUE aperture. The templates of quiescent galaxies are built according to morphological type, elliptical, bulge, SO, Sa, Sb, and So, and the templates of starburst galaxies according to color excess. The unprecedented characteristics of these templates is that UV and optical spectra have been obtained in matched apertures to produce consistent spectral information from 1200 to 10,000 A. Despite the relatively small IUE aperture, the galaxy stellar populations are well represented in the elliptical, SO, Sa, and Sc, and in the starburst templates. The spectra are available digitally. The UV-optical templates can be applied to the classification of high-redshift galaxies and to the identification of the host galaxies of quasars. The templates predict that observed magnitudes from traditional ground-based photometric surveys can be uniquely interpreted. For example, U, B, and I magnitudes uniquely determine both the redshift and the morphological type of a galaxy. The template spectra are also used to calculate K-corrections for galaxies as a function of morphological type and redshift, up to z = 2. These improved K-corrections are not sufficient to explain the excess counts in faint blue galaxies. A subset of our galaxy templates are linked with published data from the radio to the X-ray for galaxies and quasars. A comparison between the quiescent galaxies and the quasars suggests that, in the optical band, the host galaxy is a factor of 10-100 fainter in flux than the quasar. Subject headings: galaxies: distances and redshifts --galaxies: photometry -galaxies: starburst -galaxies: stellar content -quasars: general