Miracle-dz/UniFAR-FTUs huggingface dataset:
Portal hypertensive gastropathy and gastric antral vascular ectasia (GAVE) syndrome

Portal hypertensive gastropathy (PHG) and gastric antral vascular ectasia (GAVE) syndrome are recently characterised entities that can be associated with gastrointestinal blood loss in patients with and without cirrhosis. Up to 65% of patients with portal hypertension from cirrhosis will develop PHG but it can also occur in the setting of non-cirrhotic portal hypertension. In patients with portal hypertension, PHG is often associated with the presence of oesophageal and/or gastric varices. The mechanisms involved in the pathogenesis of PHG have not been fully elucidated. However, regulation of gastric nitric oxide, prostaglandins, tumour necrosis factor α (TNF-α), and epidermal growth factor (EGF) production may be involved. The mechanisms involved in the development of GAVE syndrome are also unclear. The classic features of this syndrome include red, often haemorrhagic, lesions predominantly located in the gastric antrum which can result in significant blood loss. More than 70% of patients with GAVE syndrome do not have cirrhosis or portal hypertension. However, in the setting of cirrhosis, GAVE syndrome can be difficult to differentiate from PHG. This distinction is paramount in that PHG generally responds to a reduction in portal pressures whereas those with GAVE syndrome and coexisting portal hypertension generally do not respond to such therapy. This review will focus on the incidence, clinical importance, aetiology, pathophysiology, and treatment of PHG and GAVE syndrome, including differentiation between GAVE syndrome and PHG in the setting of portal hypertension. ### DIAGNOSIS, INCIDENCE, AND CLINICAL IMPORTANCE The diagnosis of PHG is made endoscopically. The New Italian Endoscopic Club has classified the severity of PHG based on the presence of four elementary lesions: mosaic-like pattern, red point lesions, cherry red spots, and black-brown spots1 (fig 1). In mild PHG the gastric mucosa often looks reddened and oedematous with a snakeskin or mosaic pattern. The term scarletina has also been used to describe the …
Performance Assessment of Multi-Level Ensemble for Multi-Class Problems

—Many supervised machine learning tasks require decision making across numerous different classes. Multi-class classiﬁcation has several applications, such as face recognition, text recognition and medical diagnostics. The objective of this article is to analyze an adapted method of Stacking in multi-class problems, which combines ensembles within the ensemble itself. For this purpose, a training similar to Stacking was used, but with three levels, where the ﬁnal decision-maker (level 2) performs its training by combining outputs from the tree-based pair of meta-classiﬁers (level 1) from Bayesian families. These are in turn trained by pairs of base classiﬁers (level 0) of the same family. This strategy seeks to promote diversity among the ensembles forming the meta-classiﬁer level 2. Three performance measures were used: (1) accuracy, (2) area under the ROC curve, and (3) time for three factors: (a) datasets, (b) experiments and (c) levels. To compare the factors, ANOVA three-way test was executed for each performance measure, considering 5 datasets by 25 experiments by 3 levels. A triple interaction between factors was observed only in time. The accuracy and area under the ROC curve presented similar results, showing a double interaction between level and experiment, as well as for the dataset factor. It was concluded that level 2 had an average performance above the other levels and that the proposed method is especially efﬁcient for multi-class problems when compared to binary problems.
Proving Differential Privacy in Hoare Logic

Differential privacy is a rigorous, worst-case notion of privacy-preserving computation. Informally, a probabilistic program is differentially private if the participation of a single individual in the input database has a limited effect on the program's distribution on outputs. More technically, differential privacy is a quantitative 2-safety property that bounds the distance between the output distributions of a probabilistic program on adjacent inputs. Like many 2-safety properties, differential privacy lies outside the scope of traditional verification techniques. Existing approaches to enforce privacy are based on intricate, non-conventional type systems, or customized relational logics. These approaches are difficult to implement and often cumbersome to use. We present an alternative approach that verifies differential privacy by standard, non-relational reasoning on non-probabilistic programs. Our approach transforms a probabilistic program into a non-probabilistic program which simulates two executions of the original program. We prove that if the target program is correct with respect to a Hoare specification, then the original probabilistic program is differentially private. We provide a variety of examples from the differential privacy literature to demonstrate the utility of our approach. Finally, we compare our approach with existing verification techniques for privacy.
Comparative analysis on information fusion conflict redistribution and driving risk classification

In this paper, risk level correlation and classification based on the recorded driving activities' data about sharp maneuvering tasks ensuing with the human being who is controlling the technical system, i.e., the car, in traffic is presented. The dataset is constituted by time stamped and geographically referenced driving maneuver information, which is exceptionally occurring when exceeding a given threshold acceleration in both longitudinal and lateral direction and a speed limit given as the static attribute of the road map data. Ground truth risk level is identified in terms of the change in vehicle collision property damage cost for the analyzed time period. Distribution of conflict masses generated by harsh driving activities and overspeeding is studied in order to predict the risk level about making an accident. High risk group is identified by PCR6 method with a level of accuracy of 80%.
A critical role of spinal Shank2 proteins in NMDA-induced pain hypersensitivity

Background Self-injurious behaviors (SIBs) are devastating traits in autism spectrum disorder (ASD). Although deficits in pain sensation might be one of the contributing factors underlying the development of SIBs, the mechanisms have yet to be addressed. Recently, the Shank2 synaptic protein has been considered to be a key component in ASD, and mutations of SHANK2 gene induce the dysfunction of N-methyl-D-aspartate (NMDA) receptors, suggesting a link between Shank2 and NMDA receptors in ASD. Given that spinal NMDA receptors play a pivotal role in pain hypersensitivity, we investigated the possible role of Shank2 in nociceptive hypersensitivity by examining changes in spontaneous pain following intrathecal NMDA injection in Shank2−/− (Shank2 knock-out, KO) mice. Results Intrathecal NMDA injection evoked spontaneous nociceptive behaviors. These NMDA-induced nociceptive responses were significantly reduced in Shank2 KO mice. We also observed a significant decrease of NMDA currents in the spinal dorsal horn of Shank2 KO mice. Subsequently, we examined whether mitogen-activated protein kinase or AKT signaling is involved in this reduced pain behavior in Shank2 KO mice because the NMDA receptor is closely related to these signaling molecules. Western blotting and immunohistochemistry revealed that spinally administered NMDA increased the expression of a phosphorylated form of extracellular signal-regulated kinase (p-ERK) which was significantly reduced in Shank2 KO mice. However, p38, JNK, or AKT were not changed by NMDA administration. The ERK inhibitor, PD98059, decreased NMDA-induced spontaneous pain behaviors in a dose-dependent manner in wild-type mice. Moreover, it was found that the NMDA-induced increase in p-ERK was primarily colocalized with Shank2 proteins in the spinal cord dorsal horn. Conclusion Shank2 protein is involved in spinal NMDA receptor-mediated pain, and mutations of Shank2 may suppress NMDA-ERK signaling in spinal pain transmission. This study provides new clues into the mechanisms underlying pain deficits associated with SIB and deserves further study in patients with ASD.
Learning Individual Moving Preference and Social Interaction for Location Prediction

Location prediction has attracted increasing attention in diverse fields due to its wide applications, such as traffic planning and control, weather forecasting, homeland security, and travel recommendation. Many existing algorithms forecast a user’s next location by learning that user’s past moving patterns. However, the individual moving patterns in many practical applications (e.g., the moving trajectory of a taxi driver) tend to be random, which poses a big challenge for location prediction. In this paper, we propose a new robust location prediction model that considers both individual preferences and social interactions (PSI) at a group level to alleviate the effect of randomness and improve the location prediction performance. Specifically, we first extract hot places of interesting (POIs) and normal POIs, respectively, via a two-stage clustering approach. To characterize exterior social interactions, an associated group is identified, and an outline of group moving patterns is then extracted based on association rule mining. Finally, the next location is predicted by learning the individual’s regular patterns and group moving patterns via a pair-wise ridge regression. In contrast to the traditional approaches, our proposed algorithm has several desirable characteristics: 1) PSI provides an intuitive and quantitative way to model human movement from two aspects: the individual’s internal moving preferences and group-level exterior social interactions; 2) Building upon group-level pattern mining, PSI provides a more robust prediction model by learning both individual and group trend information simultaneously, alleviating the randomness of location prediction from individual historical trajectory data only; and 3) The experimental results demonstrate that PSI achieves a better prediction performance compared to the state-of-the-art methods.
Parallel Partitioned-Rotor Switched flux PM machine for light hybrid/ electric vehicles

This paper applies the Parallel Partitioned-Rotor (PR) Switched flux PM (SFPM) machine topology to light hybrid/electric vehicles applications. The design has 12/31 stator and rotor poles combination, that is suitable for direct drive hybrid/electric vehicles. The proposed design is globally optimized for maximum average torque and minimum torque ripples based on genetic algorithm. The electromagnetic performance of the proposed design is investigated and analyzed using the time stepping 2D FEA software. It is found that the key advantages of the proposed design are high torque capability, reduced torque ripples, as well as wide speed control range.
Endothelial Dysfunction in Systemic Lupus Erythematosus: Pathogenesis, Assessment and Therapeutic Opportunities.

BACKGROUND Systemic Lupus Erythematosus (SLE) is characterised by increased mortality secondary to Cardiovascular Diseases (CVD). Despite being common in SLE, traditional cardiovascular risk factors cannot entirely justify such increase in CVD-associated mortality. The endothelium is a key regulator of the vascular homeostasis; lupus-associated persistent systemic inflammation may impair endothelium functionality, thus initiating a cascade of events that, in concert with traditional CVD-risk factors, leads to atherosclerosis development and progression. Numerous methods have been used for the in vivo assessment of the endothelial function; among all, Flow- Mediated Dilatation (FMD) has been widely validated in clinical trials. Quantification of the endothelial dysfunction by FMD has been confirmed to be an early predictor of CVD in multiple studies involving both non-CVD and CVD-population and it may therefore represent a likewise efficient biomarker of CVD in SLE. METHODS Research and online content related to endothelial function in SLE is reviewed in this article with special attention to the pathophysiology and therapeutic opportunities. RESULTS To date, the vast majority of the available data, albeit not all, shows that endotheliumdependent FMD values are lower in SLE patients compared to healthy subjects; further studies, however, will be required in order to confirm the usefulness of the endothelial dysfunction quantification as CVD-predictor in the specific clinical setting of lupus. Notably, FMD variations can also be a sensitive marker for assessing specific therapeutic strategies ability of improving endothelial function in SLE patients. CONCLUSION Endothelial function appears to be affected by SLE potentially contributing to the increased cardiovascular risk observed in SLE patients.
Multicenter study on the safety of bariatric endoscopy.

INTRODUCTION Bariatric endoscopy includes a series of specific techniques focused on the management of obese patients. As a quality criterion, safety as expressed by a minimal incidence of serious complications is required in addition to efficacy. METHODS A descriptive, retrospective, multicenter review of the experience recorded at seven hospitals included in the Grupo Español de Endoscopia Bariátrica (GETTEMO) in order to document the incidence, cause, and resolution (including legal consequences) of serious complications reported for each bariatric technique, and according to endoscopist expertise. RESULTS In all, 6,771 bariatric endoscopic procedures were collected, wherein 57 serious complications (0.84%) were identified. Balloons: Orbera®-Medsil®, 5/5,589; Spatz2® (older model): 44/225; Heliosphere®: 1/70; Obalon®: 0/107. Sutures: POSE®, 5/679; sleeve gastroplasty with Apollo® system: 0/55. Prostheses: Endobarrier®: 2/46. All complications were resolved with medical/endoscopic management except for five cases (0.07%) that required surgery. A single lawsuit occurred (esophageal perforation with Spatz2® balloon), which had a favorable outcome. There was no mortality, and apparently no differences were found according to endoscopist expertise level. CONCLUSIONS In our multicenter experience, bariatric endoscopy may be considered as a safe procedure (0.84% of serious complications in all). However, some devices may induce a higher proportion of complications, such as 19.55% for Spatz2® balloons (already replaced) or 4.34% for Endobarrier® sleeves (at the upper limit of accepted safety), although our experience with the latter is limited. All complications were resolved with conservative medical management, and only exceptionally required surgery (0.07%). No technique-related mortality was seen, and only one lawsuit occurred. Further evolutionary studies are required on the novel endoscopic techniques presently emerging to authenticate our results.
Association of Body Mass Index With Infectious Complications in Free Tissue Transfer for Head and Neck Reconstructive Surgery

Importance Elevated body mass index (BMI) has been proposed as a risk factor for morbidity and mortality among patients undergoing surgery. Conversely, an elevated BMI may confer a protective effect on perioperative morbidity. Objective To examine whether an elevated BMI is an independent risk factor for perioperative and postoperative infectious complications after free tissue transfer in head and neck reconstructive surgery. Design, Setting, and Participants This cohort study included patients undergoing major head and neck surgery requiring free tissue transfer at a tertiary care center. Data were collected for 415 patients treated from January 1, 2007, through December 31, 2014. Main Outcomes and Measures The outcome of interest was postoperative infection and complications after head and neck surgery using free flaps. Covariates considered for adjustment in the statistical model included alcohol consumption (defined as >5 drinks per day [eg, 360 mL of beer, 150 mL of wine, or 45 mL of 80-proof spirits]), type 2 diabetes, prior radiotherapy, anesthesia time, hypothyroidism, smoking, American Society of Anesthesiologists classification, antibiotic regimen received (defined as a standard regimen of a first- or second-generation cephalosporin with or without metronidazole hydrochloride vs an alternative antibiotic regimen for patients allergic to penicillin), and primary surgeon. A multiple logistic regression model was developed for the incidence of the infection end point as a function of elevated BMI (>30.0). Results Among the 415 patients included in this study (277 men [66.7%] and 138 women [33.2%]; mean [SD] age, 61.5 [13.9] years), type 2 diabetes and use of an alternative antibiotic regimen were found to be independently associated with increased infectious complications after free flap surgery of the head and neck, with estimated odds ratios of 2.78 (95% CI, 1.27-6.09) and 2.67 (95% CI, 1.14-6.25), respectively, in the multiple logistic regression model. However, a high BMI was not found to be statistically significant as an independent risk factor for postoperative infectious complication (estimated odds ratio, 1.19; 95% CI, 0.48-2.92). Conclusions and Relevance Elevated BMI does not seem to play a role as an independent risk factor in postoperative complications in free tissue transfer in head and neck surgery.
Altered functional properties of satellite glial cells in compressed spinal ganglia

The cell bodies of sensory neurons in the dorsal root ganglion (DRG) are enveloped by satellite glial cells (SGCs). In an animal model of intervertebral foraminal stenosis and low‐back pain, a chronic compression of the DRG (CCD) increases the excitability of neuronal cell bodies in the compressed ganglion. The morphological and electrophysiological properties of SGCs were investigated in both CCD and uninjured, control lumbar DRGs. SGCs responded within 12 h of the onset of CCD as indicated by an increased expression of glial fibrillary acidic protein (GFAP) in the compressed DRG but to lesser extent in neighboring or contralateral DRGs. Within 1 week, coupling through gap junctions between SGCs was significantly enhanced in the compressed ganglion. Under whole‐cell patch clamp recordings, inward and outward potassium currents, but not sodium currents, were detected in individual SGCs. SGCs enveloping differently sized neurons had similar electrophysiological properties. SGCs in the compressed vs. control DRG exhibited significantly reduced inwardly rectifying potassium currents (Kir), increased input resistances and positively shifted resting membrane potentials. The reduction in Kir was greater for nociceptive medium‐sized neurons compared to non‐nociceptive neurons. Kir currents of SGCs around spontaneously active neurons were significantly reduced 1 day after compression but recovered by 7 days. These data demonstrate rapid alterations in glial membrane currents and GFAP expression in close temporal association with the development of neuronal hyperexcitability in the CCD model of neuropathic pain. However, these alterations are not fully sustained and suggest other mechanisms for the maintenance of the hyperexcitable state. © 2009 Wiley‐Liss, Inc.
Racial disparities in adoption of axillary sentinel lymph node biopsy and lymphedema risk in women with breast cancer.

IMPORTANCE Racial disparities exist in many aspects of breast cancer care. Sentinel lymph node biopsy (SLNB) was developed to replace axillary lymph node dissection (ALND) for staging early breast cancer to minimize complications. Racial disparities in the use of SLNB remain incompletely characterized, and their effect on lymphedema risk is not known. OBJECTIVE To determine racial differences in SLNB use among patients with pathologically node-negative breast cancer during the period when SLNB became the preferred method for axillary staging as well as whether such differences affect lymphedema risk. DESIGN, SETTING, AND PARTICIPANTS A retrospective study was conducted using the Surveillance, Epidemiology, and End Results-Medicare-linked database from 2002 through 2007 to identify cases of incident, nonmetastatic, pathologically node-negative breast cancer in women aged 66 years or older. MAIN OUTCOMES AND MEASURES Sentinel lymph node biopsy use and 5-year cumulative incidence of lymphedema by race. RESULTS Of 31 274 women identified, 1767 (5.6%) were black, 27 856 (89.1%) were white, and 1651 (5.3%) were of other or unknown race. Sentinel lymph node biopsy was performed in 73.7% of white patients and 62.4% of black patients (P < .001). The use of SLNB increased by year for both black and white patients (P < .001); however, a fixed disparity of approximately 12 percentage points in SLNB use persisted through 2007. In adjusted analysis, black patients were significantly less likely than white patients to undergo SLNB (odds ratio, 0.67; 95% CI, 0.60-0.75; P < .001). Overall, the 5-year cumulative lymphedema risk was 8.2% in whites and 12.3% in blacks (hazard ratio [HR], 1.43; 95% CI, 1.23-1.67; P < .001). When stratified by type of axillary surgery, 5-year lymphedema risk was 6.8% in whites undergoing SLNB (HR, 1 [reference]), 8.8% in blacks undergoing SLNB (HR, 1.28; 95% CI, 1.02-1.60; P = .03), 12.2% in whites undergoing ALND (1.79; 1.63-1.96; P < .001), and 18.0% in blacks undergoing ALND (2.76; 2.25-3.39; P < .001). CONCLUSIONS AND RELEVANCE Although SLNB use increased in both black and white patients with pathologically node-negative breast cancer from 2002 through 2007, the rates of SLNB remained lower in black than white patients during this entire period by approximately 12 percentage points. This racial disparity in SLNB use contributed to racial disparities in lymphedema risk. Improvements in the dissemination of new techniques are needed to avoid disparities in breast cancer care and patient outcomes, particularly in disadvantaged groups.
Nimbus: a design-driven analyses suite for amplicon-based NGS data

Abstract Motivation PCR-based DNA enrichment followed by massively parallel sequencing is a straightforward and cost effective method to sequence genes up to high depth. The full potential of amplicon-based sequencing assays is currently not achieved as analysis methods do not take into account the source amplicons of the detected variants. Tracking the source amplicons has the potential to identify systematic biases, enhance variant calling and improve the designs of future assays. Results We present Nimbus, a software suite for the analysis of amplicon-based sequencing data. Nimbus includes tools for data pre-processing, alignment, single nucleotide polymorphism (SNP), insertion and deletion calling, quality control and visualization. Nimbus can detect SNPs in its alignment seeds and reduces alignment issues by the usage of decoy amplicons. Tracking the amplicons throughout analysis allows easy and fast design optimization by amplicon performance comparison. It enables detection of probable false positive variants present in a single amplicon from real variants present in multiple amplicons and provides multiple sample visualization. Nimbus was tested using HaloPlex Exome datasets and outperforms other callers for low-frequency variants. The variants called by Nimbus were highly concordant between twin samples and SNP-arrays. The Nimbus suite provides an end-to-end solution for variant calling, design optimization and visualization of amplicon-derived next-generation sequencing datasets. Availability and implementation https://github.com/erasmus-center-for-biomics/Nimbus. Supplementary information Supplementary data are available at Bioinformatics online.