Miracle-dz/UniFAR-FTUs huggingface dataset:
Expandable metal stents versus laser combined with radiotherapy for palliation of unresectable esophageal cancer: a prospective randomized trial.

BACKGROUND/AIMS Because of the short life expectancy of patients with esophageal cancer, relief of dysphagia associated with low morbidity and mortality must be the aim of any therapeutic strategy. METHODOLOGY A total of 39 patients with unresectable esophageal cancer were randomly allocated to either receive combined laser-percutaneous radiotherapy (group 1, n = 21) or to have a self-expanding metal stent placed (group 2, n = 18). Some patients in group 2 required initial laser therapy (group 2a, n = 8). Treatment efficacy was evaluated on the basis of improved dysphagia, restenosis, hospital stay, survival time and costs. RESULTS Both treatments were able to significantly improve dysphagia. Restenosis occurred in 43% of group 1 and 22% of group 2 patients. In group 1, 2 patients had severe bleeding episodes and 2 patients developed esophago-tracheal fistulas. One group 1 patient died due to uncontrollable bleeding and 1 patient to recurrent aspiration. No treatment-related death was observed in group 2. Hospital stay was 30.0 (mean: 5.4) days in group 1, 18.9 (mean: 4.2) days in group 2a and 7.1 (mean: 3.1) days in group 2b. There was no statistical difference between the 3 groups with regard to survival. Costs were highest in group 1 and lowest in group 2b. CONCLUSIONS The treatment of unresectable esophageal cancer with self-expanding metal stents appears to be simple, safe, as good as laser combined with radiotherapy and cost efficient.
A Global Human Settlement Layer From Optical HR/VHR RS Data: Concept and First Results

A general framework for processing high and very-high resolution imagery in support of a Global Human Settlement Layer (GHSL) is presented together with a discussion on the results of the first operational test of the production workflow. The test involved the mapping of 24.3 million km2 of the Earth surface spread in four continents, corresponding to an estimated population of 1.3 billion people in 2010. The resolution of the input image data ranges from 0.5 to 10 meters, collected by a heterogeneous set of platforms including satellite SPOT (2 and 5), CBERS 2B, RapidEye (2 and 4), WorldView (1 and 2), GeoEye 1, QuickBird 2, Ikonos 2, and airborne sensors. Several imaging modes were tested including panchromatic, multispectral and pan-sharpened images. A new fully automatic image information extraction, generalization and mosaic workflow is presented that is based on multiscale textural and morphological image features extraction. New image feature compression and optimization are introduced, together with new learning and classification techniques allowing for the processing of HR/VHR image data using low-resolution thematic layers as reference. A new systematic approach for quality control and validation allowing global spatial and thematic consistency checking is proposed and applied. The quality of the results are discussed by sensor, band, resolution, and eco-regions. Critical points, lessons learned and next steps are highlighted.
Trans-species learning of cellular signaling systems with bimodal deep belief networks

MOTIVATION Model organisms play critical roles in biomedical research of human diseases and drug development. An imperative task is to translate information/knowledge acquired from model organisms to humans. In this study, we address a trans-species learning problem: predicting human cell responses to diverse stimuli, based on the responses of rat cells treated with the same stimuli. RESULTS We hypothesized that rat and human cells share a common signal-encoding mechanism but employ different proteins to transmit signals, and we developed a bimodal deep belief network and a semi-restricted bimodal deep belief network to represent the common encoding mechanism and perform trans-species learning. These 'deep learning' models include hierarchically organized latent variables capable of capturing the statistical structures in the observed proteomic data in a distributed fashion. The results show that the models significantly outperform two current state-of-the-art classification algorithms. Our study demonstrated the potential of using deep hierarchical models to simulate cellular signaling systems. AVAILABILITY AND IMPLEMENTATION The software is available at the following URL: http://pubreview.dbmi. pitt.edu/TransSpeciesDeepLearning/. The data are available through SBV IMPROVER website, https://www.sbvimprover. com/challenge-2/overview, upon publication of the report by the organizers. CONTACT xinghua@pitt.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Phylogeny, taxonomy, genetics and global heritage ranks of an imperilled, freshwater snail genus Lithasia (Pleuroceridae)

Numerous aquatic species are threatened with extinction from habitat elimination or modification. One particularly imperilled group is the freshwater gastropod family Pleuroceridae. Pleurocerids reach their greatest diversity in the southeastern United States, and many species are currently considered extinct, endangered or threatened. One issue hindering efforts to implement conservation management plans for imperilled pleurocerid species is that the taxonomy is in an abysmal state. The taxonomy of pleurocerids is currently based on late 19th‐ and early 20th‐century studies, which used a typological or morphospecies concept. Most biologists today doubt the validity of many of the currently recognized species; however, this does not stop them from assigning conservation ranks in an attempt to determine which species are imperilled or currently stable. We conducted a phylogenetic analysis of the pleurocerid genus Lithasia using morphological and mitochondrial DNA sequence (mtDNA) data in an attempt to delimit species boundaries and test previous taxonomic schemes. We found that the current taxonomy of Lithasia does not reflect species diversity adequately within the genus, with two new undescribed species being discovered. The conservation status ranks of the new, undescribed species are imperilled and would have been overlooked had we relied on the conventional taxonomy. Additionally, the undescribed species’ conservation ranks that were previously apparently secure became vulnerable due to being inappropriately assigned as members of formerly widely distributed species instead of the imperilled status they warrant and vice versa, as some taxa that were considered imperilled are now thought to be modestly stable. Our study suggests that conservation ranks should be considered suspect at best in taxonomically poorly known groups until the taxa are reviewed using modern systematic methods.
Adaptive Salt-&-Pepper Noise Removal: A Function Level Evolution based Approach

Noise removal is an important procedure before ongoing further image processing. In this paper, a two-stage adaptive noise removal scheme is proposed. The first stage of the scheme is noise detection; the second stage is functional level evolution based noise cancellation. This cancellation only operates on the noise candidates detected in the first stage. Additionally, the proposed method acquires local information to suppress noise from the noisy pixelspsila neighbors rather than from original images. These features enable the scheme to preserve more image details with less computation effort, and make it able to be the basic frame for EHW based implementation of on-line adaptive impulse noise removal system. Simulation results show that the proposed approach provides at least equal performance to the adaptive median filter, and can cope with the corrupted images with up to 70% noise density.
Hodgkin's disease, lymphomatoid papulosis, and cutaneous T-cell lymphoma derived from a common T-cell clone.

BACKGROUND Lymphomatoid papulosis is a benign cutaneous eruption that in 10 to 20 percent of patients is associated with the development of lymphoma. The atypical cells of lymphomatoid papulosis histologically resemble the malignant cells of cutaneous T-cell lymphoma or the Reed-Sternberg cells of Hodgkin's disease. We studied a patient in whom lymphomatoid papulosis developed in 1971, Hodgkin's disease in 1975, and cutaneous T-cell lymphoma in 1985, to determine whether these diseases are clonally related. METHODS The T-cell-receptor alpha-chain gene was cloned and sequenced from a cell line derived from the advanced-stage cutaneous T-cell lymphoma, and the polymerase chain reaction was used to search for this rearrangement of the alpha-chain gene in tissues obtained earlier that were affected by Hodgkin's disease or lymphomatoid papulosis. RESULTS The tumor-specific rearrangement of the alpha-chain gene was detected in the patient's earlier tissues affected by lymphomatoid papulosis and Hodgkin's disease, but not in control tissue, including uninvolved tissues from the staging laparotomy for Hodgkin's disease. Cytogenetic studies revealed a translocation, t(8;9)(p22;p24), in cutaneous T-cell lymphoma lines and in a dermatopathic lymph node removed two years before the clinical onset of the cutaneous T-cell lymphoma. Immunohistochemical findings were consistent with an activated T-cell phenotype for the atypical cells of lymphomatoid papulosis, the Reed-Sternberg cells of Hodgkin's disease, and the malignant cells of the T-cell lymphoma. CONCLUSIONS Lymphomatoid papulosis, Hodgkin's disease, and cutaneous T-cell lymphoma can be derived from a single T-cell clone. A t(8;9) genetic translocation may be involved in the pathogenesis of lymphomatoid papulosis or its progression to malignant disease.
Pulmonary vascular collagen content, not cross-linking, contributes to right ventricular pulsatile afterload and overload in early pulmonary hypertension.

Hypoxic pulmonary hypertension (HPH) is associated with pulmonary artery (PA) remodeling and right ventricular (RV) overload. We have previously uncovered collagen-mediated mechanisms of proximal PA stiffening in early HPH by manipulating collagen degradation and cross-linking using a transgenic mouse strain and a potent collagen cross-link inhibitor, β-aminopropionitrile (BAPN). However, the roles of collagen in distal PA remodeling, overall RV afterload, and RV hypertrophy in HPH remain unknown. Here, we used the same experimental strategy to investigate the effect of pulmonary vascular collagen content and cross-linking on steady and pulsatile RV afterload and on RV hypertrophy in early HPH. Collagenase-resistant mice (Col1a1R/R) and their littermate controls (Col1a1+/+) were exposed to normobaric hypoxia for 10 days with or without BAPN treatment. In vivo pulmonary vascular impedance, a comprehensive measure of RV afterload, was measured via simultaneous RV catheterization and echocardiography. Morphology and collagen accumulation were examined using histological techniques and ELISA in lungs and RVs. In both mouse strains, BAPN did not limit increases in pulmonary arterial pressure or pulmonary vascular resistance, indicating a negligible effect of either collagen content or cross-linking on steady RV afterload. However, BAPN prevented the increase in pulse pressure and RV hypertrophy in Col1a1+/+ mice and these effects were absent in Col1a1R/R mice, suggesting a role for PA collagen content, not cross-linking, in the pulsatile RV afterload. Moreover, we found a significant correlation between pulse pressure and RV hypertrophy, indicating an important role for pulsatile RV afterload in RV overload in early HPH. NEW & NOTEWORTHY The present study found an important role for collagen content, but not collagen cross-linking, in the pulsatile right ventricular (RV) afterload, which is correlated with RV hypertrophy. These results uncover a new collagen-mediated mechanical mechanism of RV dysfunction in early pulmonary hypertension progression. Furthermore, our results suggest that measures and metrics of pulsatile hemodynamics such as pulse pressure and pulse wave velocity are potentially important to cardiovascular mortality in patients with pulmonary hypertension.
Kupffer cells and neutrophils as paracrine regulators of the heme oxygenase-1 gene in hepatocytes after hemorrhagic shock.

Heme oxygenase (HO) plays a pivotal role for the maintenance of liver blood flow and hepatocellular integrity after hemorrhagic shock. We investigated the role of Kupffer cells and neutrophils as paracrine modulators of hepatocellular HO-1 gene expression in a rat model of hemorrhage and resuscitation. Male Sprague-Dawley rats (n = 6-10/group) were anesthetized (pentobarbital, 50 mg/kg intraperitonal) and subjected to hemorrhagic shock (mean arterial blood pressure: 35 mmHg for 60 min) or a sham protocol. Based on the time course of HO-1 gene expression, the effect of various antioxidants, Kupffer cell blockade [gadolinium chloride (GdCl3); 10 mg/kg; 24 h prior to hemorrhage or dichloromethylene diphosphonate (Cl2MDP); 1 mg/kg; 2 days prior to hemorrhage], or neutrophil depletion (vinblastine, 0.5 mg/kg, 5 days prior to hemorrhage) on induction of the HO-1 gene was assessed at 5 h of resuscitation, i.e., the time point of maximal induction. Kupffer cell blockade and antioxidants abolished HO-1 mRNA and protein induction after hemorrhage, while neutrophil depletion failed to affect hepatocellular HO-1 gene expression. In addition, Kupffer cell blockade aggravated hepatocellular injury. N-formyl-methionine-leucyl-phenylalanin (fMLP) induced a substantial influx of neutrophils into the liver but failed to induce hepatocellular HO-1 mRNA expression. These data suggest that Kupffer cells but not neutrophils induce an adaptive hepatocellular stress response after hemorrhage and resuscitation. Oxygen-free radicals released by Kupffer cells may serve as paracrine regulators of a hepatocellular stress gene which is necessary to maintain liver blood flow and integrity under stress conditions.
Intelligent operation of a base transceiver station-microgrid EMS with unreliable grid supply

This paper presents a robust and optimal operation tracking Energy Management System (EMS) for Mobile Base Transceiver Station (BTS) Microgrid equipped with Battery, PV panels and Diesel Engine Generator (DEG) for unreliable grid. The contribution is particularly focused on minimizing the DEG fuel (with DEG ON/OFF frequency) at the time of power-grid outage (i.e. Blackout). The EMS is designed to work with less sophisticated local BTS controller. The prediction (load predictor, PV power generator predictor and blackout duration predictor) modules and the optimization modules are envisioned to be hosted in a server. The optimization module provides optimal battery control policies that are robust against the temporal uncertainty imposed by unknown blackout duration while minimizing the expected DEG fuel cost. The blackout duration predictor is facilitated by combining Linear Logistic Regression classifier and blackout duration frequency distribution. The load predictor utilizes Support Vector Regression for creating predictive models. The optimizer performs a local search over candidate solution space to seek the optimal control policy. Numerical simulation corroborates that the designed EMS, applied on 14 BTS sites in India, is capable of reducing 26% (on average) of DEG fuel compared to that of current operation over 7-Days.
Automated Cinematography with Unmanned Aerial Vehicles

The rise of Unmanned Aerial Vehicles and their increasing use in the cinema industry calls for the creation of dedicated tools. Though there is a range of techniques to automatically control drones for a variety of applications, none have considered the problem of producing cinematographic camera motion in real-time for shooting purposes. In this paper we present our approach to UAV navigation for autonomous cinematography. The contributions of this research are twofold: (i) we adapt virtual camera control techniques to UAV navigation; (ii) we introduce a drone-independent platform for high-level user interactions that integrates cinematographic knowledge. The results presented in this paper demonstrate the capacities of our tool to capture live movie scenes involving one or two moving actors.
ADAM15 adds to apoptosis resistance of synovial fibroblasts by modulating focal adhesion kinase signaling.

OBJECTIVE To study the contribution of ADAM15, a disintegrin metalloproteinase that is up-regulated in the rheumatoid arthritis (RA) synovial membrane, to the characteristic resistance of RA synovial fibroblasts (RASFs) to apoptosis induction by genotoxic stress or stimulation with proapoptotic FasL, which is present at high concentrations in RA synovial fluid. METHODS Caspase 3/7 activity and the total apoptosis rate in RASFs upon exposure to the DNA-damaging agent camptothecin or FasL were determined using enzyme assays and annexin V staining. Phosphorylated signaling proteins were analyzed by immunoblotting. RNA interference was used to silence ADAM15 expression. NF-κB activity was determined by enzyme-linked immunosorbent assay. RESULTS RASFs displayed significantly higher caspase 3/7 activity upon camptothecin and FasL exposure when ADAM15 had been down-regulated by specific small interfering RNAs. Upon FasL stimulation, RASFs phosphorylated focal adhesion kinase (FAK) and c-Src (Src), and activated phosphatidylinositol 3-kinase as well as the transcription factor NF-κB. This ADAM15-dependent, FasL-induced activation of antiapoptotic kinases and NF-κB was demonstrated by a marked reduction of apoptosis upon knockdown of ADAM15 protein expression. Inhibitors specifically interfering with FAK and Src signaling, such as FAK inhibitor 14 and dasatinib, potently induce apoptosis in RASFs, with significant enhancement by the silencing of ADAM15. CONCLUSION ADAM15 contributes to apoptosis resistance in RASFs by activating the Src/FAK pathway upon FasL exposure, rendering the FAK/Src signaling pathway an interesting target for potential therapeutic intervention in RA.
Dabigatran Effects on the International Normalized Ratio, Activated Partial Thromboplastin Time, Thrombin Time, and Fibrinogen: A Multicenter, In Vitro Study

Background: Patients receiving the direct thrombin inhibitor dabigatran may have selected anticoagulation assays performed as part of routine care. The effect of dabigatran on the international normalized ratio (INR), activated partial thromboplastin time (aPTT), thrombin time (TT), and fibrinogen requires clarification. Objective: To describe the effect of dabigatran on selected assays in North America and the United Kingdom. Methods: Pooled normal plasma enriched with dabigatran at concentrations of 25, 50, 75, 100, 125, 150, 200, 300, 400, and 500 ng/mL were sent blinded to 19 centers in the US, the UK, and Canada to assess the effect of dabigatran on routine coagulation screening tests, the INR, aPTT, TT, and fibrinogen. Results: Data were returned from 16 centers. For effects on INR, Neoplastine CI Plus and Simplastin HTF were the most sensitive and Thromborel S the least sensitive to increasing dabigatran concentrations. For the aPTT, all reagents demonstrated decreasing sensitivity to increasing dabigatran concentrations. Measured fibrinogen either demonstrated no change or factitious decrease with increasing dabigatran concentrations. Commercial TT methods were very sensitive to low concentrations of dabigatran, with 9 of 10 reporting sites exceeding test limits at dabigatran concentrations of 100 ng/mL. Conclusions: The INR, aPTT, and TT rise as dabigatran concentrations increase. Both the INR and aPTT increase in a linear pattern with marginal slopes, creating challenges in using these assays as reliable means for assessing the amount of dabigatran present. The commercial TT assay is very sensitive at low concentrations of dabigatran. Fibrinogen test results may be either unaffected or lower in the presence of dabigatran.
Episodic Secretion of Parathyroid Hormone in Postmenopausal Women: Assessment by Deconvolution Analysis and Approximate Entropy

In healthy young subjects, parathyroid hormone (PTH) is secreted presumptively in a dual fashion, with low amplitude pulses apparently superimposed on tonic secretion. In contrast, PTH secretion has not been as well characterized in postmenopausal women, and relationships among bone density, estrogen status, and PTH release have not been explored. It is possible that a pulsatile pattern of PTH secretion is important for bone remodeling, since exogenous PTH administered in a pulsatile manner stimulates bone formation. To assess the importance of pulsatile PTH secretion as a determinant of bone mass, we measured PTH in blood sampled every 2 minutes for 6 h in four groups of older women: (1) high bone density receiving estrogen (n = 6), (2) high bone density not receiving estrogen (n = 5), (3) low bone density receiving estrogen (n = 6), and (4) low bone density not receiving estrogen (n = 8). The plasma PTH release profiles were subjected to deconvolution analysis, which resolves measured hormone concentrations into secretion and clearance components, and to an approximate entropy (ApEn) estimate, which provides an ensemble measure of the serial regularity or orderliness of the release process. In postmenopausal subjects, PTH was secreted in a fashion similar to that observed in young adults, with significant tonic secretion and PTH pulse occurrences averaging every 18–19 minutes. Pulsatile PTH secretion accounted for approximately 25% of the total secreted PTH. There were no differences in the amplitude or frequency of pulsatile PTH secretory parameters or in ApEn values among the four groups or compared with young controls. We conclude that in postmenopausal women, PTH secretory patterns and temporal organization are similar to those in healthy young subjects and are not altered in states of low bone density or estrogen deficiency. This suggests that abnormalities in orderly pulsatile PTH secretion are unlikely to play a major role in established postmenopausal osteoporosis.
Polycystic Ovary Syndrome among Obese Adolescents

Abstract Background and aims: In adolescence and obesity, the pathophysiology of polycystic ovary syndrome (PCOS) is very difficult to distinguish. We aimed to assess the diagnosis of PCOS in the population of obese adolescent. Methods: Cross-sectional study. Setting: Pediatric Endocrinology Weight and Management Clinic from Children's Institute, São Paulo, Brazil. Participants: Forty-nine post-menarcheal obese adolescents with mean age of 14.7 years. Interventions: Anthropometric assessment and review of medical records were done. Clinical and laboratory hyperandrogenism were quantified using Ferriman–Gallwey index and androgenic dosages, respectively. Ovarian morphology was evaluated through suprapubic ultrasonography. Results: By the 2015 Witchel et al. guideline for PCOS in adolescence, 18.4% were diagnosed as having PCOS. When assessed by Rotterdam, Androgen Excess and PCOS Society, and American National Institute of Health criteria's, 26.4%, 22.4%, and 20.4% had PCOS, respectively. Irregular menstrual cycles were found in 65.3% of patients. Clinical hyperandrogenism was observed in 16.3% of girls and 18.4% had elevated serum androgen values. Suprapubic ultrasonography revealed enlarged ovaries in 18.4% of the adolescents. Conclusions: PCOS in all-comers obese adolescents from a Weight and Management Clinic in a quaternary hospital is more frequent when compared to adult women showed in the literature.
Modeling of spectral broadening in second-harmonic generation

A highly efficient modeling method for SHG is devised by studying the quasi phase matching (QPM) SHG in periodically poled potassium titanyl phosphate (PPKTP). The model can be used for monochromatic and multifrequency SHG. The bandwidth of the pump can be a limiting factor, intensified by its hardly studied spectral coherence.