Miracle-dz/UniFAR-FTUs huggingface dataset:
Antiflagellin antibodies suggest infective participation in irritable bowel syndrome pathogenesis

Evaluation of: Schoepfer AM, Schaffer T, Seibold-Schmid B et al. Antibodies to flagellin indicate reactivity to bacterial antigens in IBS patients. Neurogastroenterol. Motil. 20(10), 1110–1118 (2008). Irritable bowel syndrome (IBS) is a functional disorder of multifactorial origin. Recent attention has been paid to the potential role of immune activation in intestinal sensorimotor dysfunction and symptom generation in patients with IBS. The link between immune activation and IBS is further supported by the evidence that IBS may develop after an acute episode of infectious gastroenteritis, IBS-like symptoms may precede the diagnosis or accompany a period of remission of inflammatory bowel disease (IBD), and quantitative histopathologic data demonstrate the presence of low-grade mucosal immune infiltration in a large subset of patients with IBS. These data also suggest some areas of potential overlap between IBS and IBD. The present study explored the possibility that, similarly to IBD patients, IBS patients have antibodies directed against certain components of indigenous flora, such as flagellin (the primary structural component of bacterial flagella). The authors demonstrated that, compared with healthy controls, antibodies against flagellin were recognized more frequently in patients with IBS. Furthermore, these antibodies were found more frequently in postinfectious compared with unspecific IBS. In patients with Crohn’s disease, antiflagellin antibodies were detected with an increased frequency and at higher concentrations than in patients with IBS. All together, these results indicated the presence of a systemic immune activation in IBS patients, characterized by specific antibodies directed against luminal bacterial antigens. Furthermore, these results support the hypothesis that a subset of IBS presents an immune activation with pathogenic features common with IBD.
Investigation of H Pylori Colonization in Adenotonsillectomy Specimens by Means of Rapid Urease (CLO) Test

This prospective clinical study was performed to investigate the colonization of H pylori in adenoid and tonsil tissues by using the Campylobacter-like organism (CLO) test. Included in the study were 56 patients aged 3 to 43 yrs who had undergone adenoidectomy, tonsillectomy or adenotonsille ctomy procedures under general anesthesia. Two-mm diameter tissue pieces of adenoid and tonsil specimens were placed in urease solution. Color changes were noted after 30 min and 24 hrs. 27 (48.2%) of the patients were shown to be H pylori positive and 29 (51.8%) were negative, regardless of the type of specimen. There was a high rate of H pylori colonization in tonsil and adenoid tissues. The cause of recurrent H pylori infections of the gastric mucosa may be the result of colonization in the adenotonsillar tissues. Prevention of H pylori colonization may reduce the recurrences of the disease. Iran J Med Sci 2005; 30(3): 138-140.
High-dose bevacizumab improves survival when combined with FOLFOX4 in previously treated advanced colorectal cancer: Results from the Eastern Cooperative Oncology Group (ECOG) study E3200

2 Background: The humanized monoclonal antibody bevacizumab (BEV) binds VEGF, inhibits angiogenesis, and improves survival when combined with chemotherapy for advanced colorectal cancer. Methods: E3200 is a randomized phase 3 trial of high-dose BEV (10 mg/kg, IV, biweekly) either alone, or in combination with FOLFOX4 (biweekly administration of: oxaliplatin 85 mg/m2, day 1; leucovorin 200 mg/m2 IV 2hrs and fluorouracil 400 mg/m2 IV bolus followed by fluorouracil 600 mg/m2 CIV for 22hrs, days 1 & 2), compared to FOLFOX4 alone, in patients with previously treated advanced colorectal cancer. Eligible patients had an ECOG PS of 0–2 and must have been treated with a fluoropyrimidine and an irinotecan-based regimen used either alone or in combination. Prior BEV use was not allowed. The endpoints of E3200 include survival (OS), progression free survival (PFS) and response rate (RR). Results: 829 patients were accrued from November 2001 to April 2003. The bevacizumab alone arm of the study was closed in March 200.
Burden and pattern of cancer in the Sudan, 2000-2006.

Aims: The aim of this study is to determine the number of newly diagnosed cancer cases and their distribution in two cancer-care providing facilities in Sudan. Study Design: This is a retrospective descriptive study. Methodology: Data was retrieved from patients’ records that were diagnosed and treated at the Radiation Isotope Center in Khartoum (RICK) and National Cancer Institute at Wadmadani (NCI -UG) in Sudan over the period between 2000 and 2006 and then statistically analyzed. Results: A total of 26652 cancer cases were retrieved with a noticeable increase in numbers from year 2000 to 2006. The maximum cancer number was observed in 45-64 year age group in both male and female patients with a male to female ratio of 1.3:1.0. The most common cancer sites for females were: the breast (29.3%), cervix uteri (8.2%), leukemia (7.2%), ovary (6.8%), and esophagus (5.9%) and for males: were Original Research Article British Journal of Medicine & Medical Research, 4(5): 1231-1243, 2014 1232 prostate (7.6%), followed by leukemia, (7.0%), NHL (6.8%), esophagus (5.4%) and bladder (4.4), while leukemia (25.2%), NHL (12.4%), lymphoma (10.8%), retinoblastoma (6.6%) and brain tumors (3.3%) dominated in younger patients (<14 years old). Conclusions: This study provided some knowledge about the cancer situation in two institutions providing cancer care in Sudan that may draw attention of policy maker and aid in formulating appropriate cancer-control strategies in the country.
Decision Making at the End of Life in Dementia: How Family Caregivers Perceive Their Interactions With Health Care Providers in Long-Term-Care Settings

Makingend-of-lifecare decisions in the context of dementiais complex. As people with advanced dementia are in capable of deciding about their own care, family caregivers often become involved with health care providers in the decision-making process to ensure the best care for their loved one. Using a grounded theory approach, the experience of family caregivers in making such end-of-life care decisions was explored. Twenty-four caregivers were interviewed. The results show that caregivers evoke five dimensions when considering these decisions. One dimension, the relationship with health care providers, emerged as vital to their experience. Four elements of this relationship are presented in this article: quality of the relationship, frequency of contact, congruence of their values and beliefs with those of health care providers, and the level of trust. In an era that promotes partnership with families in long-term-care settings, care standards are needed in order to guarantee family participation in achieving quality dementia care.
Advances in ventilator-associated lung injury: prevention is the target

Mechanical ventilation (MV) is the main supportive treatment in respiratory failure due to different etiologies. However, MV might aggravate ventilator-associated lung injury (VALI). Four main mechanisms leading to VALI are: 1) increased stress and strain, induced by high tidal volume (VT); 2) increased shear stress, i.e. opening and closing, of previously atelectatic alveolar units; 3) distribution of perfusion and 4) biotrauma. In severe acute respiratory distress syndrome patients, low VT, higher levels of positive end expiratory pressure, long duration prone position and neuromuscular blockade within the first 48 hours are associated to a better outcome. VALI can also occur by using high VT in previously non injured lungs. We believe that prevention is the target to minimize injurious effects of MV. This review aims to describe pathophysiology of VALI, the possible prevention and treatment as well as monitoring MV to minimize VALI.
Chikungunya in West Bengal, India

Fever of unknown origin broke out in several districts of West Bengal, from August 2007 to December 2007. The cases were suffering from high fever, severe joint pain lasting for several weeks after clinical cure and appearance of skin rashes. Patients’ sera were collected at least five days after fever and were analyzed to detect specific IgM antibodies. A total of 800 patients were investigated and 321 (40.13%) were found to be reactive for Chikungunya antibodies. Of the patients, 66% were male. Predominant signs and symptoms observed in the sero-positive cases were fever (100%), arthralgia (96%) and diffuse erythematous skin rash (94%). Of the patients, 3% had haemorrhagic manifestations. Re-emerging Chikungunya virus spread in epidemic form in several districts of West Bengal after a gap of four decades.
FOREIGN BODY IN THE AIRWAY. A REVIEW OF 200 CASES

• Two hundred children aged 6 months to 12 years were admitted to the hospital with a foreign body in the airway. Food materials constituted 93% of all foreign bodies. A positive history of foreign body aspiration was obtained in 88% of the cases. The most common symptoms of laryngotracheal foreign bodies were dyspnea, cough, and stridor, whereas those of bronchial foreign bodies were cough, decreased air entry, wheezing, and dyspnea. Chest fluoroscopy contributed to the diagnosis in 90% of the cases of bronchial foreign bodies, but only 32% of those in the laryngotracheal area. Of the foreign bodies removed, 98½% were done by laryngoscopy, tracheoscopy, and/or bronchoscopy. Complications were involved in 6% of the cases, including one death. History of recurrent intractable pneumonia should make one consider a foreign body in the airway. Removal of one foreign body does not exclude the existence of another. The condition may be fatal; thus immediate removal of the foreign body is mandatory. (Am J Dis Child134:68-71, 1980)
Graph-of-word and TW-IDF: new approach to ad hoc IR

In this paper, we introduce novel document representation (graph-of-word) and retrieval model (TW-IDF) for ad hoc IR. Questioning the term independence assumption behind the traditional bag-of-word model, we propose a different representation of a document that captures the relationships between the terms using an unweighted directed graph of terms. From this graph, we extract at indexing time meaningful term weights (TW) that replace traditional term frequencies (TF) and from which we define a novel scoring function, namely TW-IDF, by analogy with TF-IDF. This approach leads to a retrieval model that consistently and significantly outperforms BM25 and in some cases its extension BM25+ on various standard TREC datasets. In particular, experiments show that counting the number of different contexts in which a term occurs inside a document is more effective and relevant to search than considering an overall concave term frequency in the context of ad hoc IR.
Impact of sleep quality on functional capacity, peripheral muscle strength and quality of life in patients with chronic obstructive pulmonary disease

Purpose: The purpose of this study was to assess the impact of quality of sleep on functional capacity, peripheral muscle strength and quality of life in patients with chronic obstructive pulmonary disease (COPD). Materials and Methods: Forty patients with COPD (61.6 ± 8.28 years) were included in this study. Subjective sleep quality (Pittsburgh sleep quality index), quality of life (Nottingham health profile), quadriceps muscle strength (QMS) and functional capacity (6-min walk test) were assessed. Results: Poor sleep quality (Pittsburgh sleep quality index total >5) was present in 57% of the patients. Patients with a poor sleep quality had significantly lower QMS and higher exercise heart rate (p < 0.05). The Pittsburgh sleep quality index total score was associated with QMS, Nottingham health profile physical mobility and sleep scores, exercise fatigue and dyspnea (p < 0.05). Conclusion: Sleep quality is affected in a majority of patients with COPD. It is related with symptoms, functional capacity, peripheral muscle strength and general quality of life.
Clinical manifestations of patients with novel H1N1 infection hospitalized in Infectious Disease ward, Sina hospital, Tabriz, Iran

Background: Novel H1N1 influenza virus is a unique type of an influenza virus which is built due to abrupt structural alterations. This virus created a pandemic disease. The manifestations and severity may be affected by environmental, cultural and economical condition. Patients and Methods: From October 2009 until December 2009, we had recruited 40 patients with H1N1 infection documented with RT-PCR. Their demographic features and presenting signs and symptoms as well as their associated laboratory data were recorded. Results: During the study period, 40 patients were studied with a mean age of 36.8±13.0 years of whom 21 were admitted to ICU. Totally, 37.5% of patients had risk factors. Pneumonia was the most frequent lung involvement. The most prominent radiographic findings were bilateral ground glass opacity and ARDS (25%). Cough and fever was the most prevalent presenting clinical symptoms. Unfortunately, 8 patients died. Independent risk factor of death was ICU admission and mechanical ventilation. Conclusion: Our findings were more or less the same as other centers, however, most of the studied subjects did not have an underlying risk factor. Except for pneumonia and ARDS, bilateral pulmonary thromboembolism were detected in patients all of whom discharged after complete recovery.
Prevalence of hepatitis A in Iranian patients with chronic liver disease.

Background: Acute hepatitis A in patients with chronic liver diseases (CLD) may lead to a more severe outcome for which routine vaccination is recommended in many regions. Nevertheless, studies of HAV seroprevalence and exposure predictors in populations with CLD are scanty in our region. Patients and methods: We studied 200 patients with CLD between September 2005 and September 2006. Patients were stratified on the basis of age, gender, size of family, place of residency and etiology of liver disease. The HAV seroprevalence in patients with CLD was compared with age- and sex-matched controls. Independent predictors of HAV exposure were identified by logistic regression analysis. Results: Of 200 patients, HAV seroprevalence was available for 190 (96.5%). Hepatitis B and C, alcohol, autoimmune hepatitis and Wilson's disease were the causes of CLD. Most of the seronegative patients aged 10-20 years. The overall HAV seroprevalence was 97.3% in controls. None of the risk factors were identified as independent predictors. Conclusion: Age stratified seroprevalence of HAV in patients with CLD is close to that of the general population. High prevalence of HAV must be considered in vulnerable travelers to our country.
Classification of different patterns of pulmonary adenocarcinomas

The epidemic increase of adenocarcinoma histology accounting for more than 50% of primary lung malignancies and the advent of effective molecular targeted-therapies against specific gene alterations characterizing this tumor type have led to the reconsideration of the pathologic classification of lung cancer. The new 2015 WHO classification provided the basis for a multidisciplinary approach emphasizing the close correlation among clinical, radiologic and molecular characteristics and histopathologic pattern of lung adenocarcinoma. The terms ‘bronchioloalveolar carcinoma’ and ‘mixed adenocarcinoma’ have been eliminated, introducing the concepts of ‘adenocarcinoma in situ’, ‘minimally invasive adenocarcinoma’ and the use of descriptive predominant patterns in invasive adenocarcinomas (lepidic, acinar, papillary, solid and micropapillary patterns). ‘Invasive mucinous adenocarcinoma’ is the new definition for mucinous bronchioloalveolar carcinoma, and some variants of invasive adenocarcinoma have been included, namely colloid, enteric and fetal-type adenocarcinomas. A concise update of the immunomorphologic, radiological and molecular characteristics of the different histologic patterns of lung adenocarcinoma is reported here.
Allergic airway inflammation: unravelling the relationship between IL-37, IL-18Rα and Tir8/SIGIRR

The hallmarks of allergic bronchial asthma arise from chronic airway inflammation. Thus, elucidating the mechanisms regulating the maintenance of this chronic inflammatory response is key to understanding asthma pathogenesis. To date, it is not clear whether a predominance of proinflammatory factors or a reduced capacity of counterbalancing anti-inflammatory mediators is the pivotal factor predisposing individuals towards asthma development. The IL-1 cytokine family and its receptor systems comprise a variety of proinflammatory cytokines like IL-1β and IL-18 and anti-inflammatory molecules such as the Toll/interleukin-1 receptor 8/single Ig IL-1 receptor (IL-R)-related molecule (Tir8/SIGIRR) and the recently established cytokine IL-37. This article reviews the functions of these IL-1 cytokine family members in the regulation of allergic airway inflammation and asthma as they have been assessed clinically, in vitro and in mouse models.
Multidrug resistant typhoid fever outbreak in Ercek Village–Van, Eastern Anatolia, Turkey: clinical profile, sensitivity patterns and response to antimicrobials

Summary The present study discusses the clinical features and treatment outcomes during an outbreak caused by multidrug resistant (MDR) Salmonella typhi isolates from Van, Turkey. Of the 867 typhoid fever patients from the same village, 154 (17.8%) were hospitalised. A total of 42 (27.3%) cultures were positive. All S. typhi isolates were resistant to chloramphenicol, ampicillin and co-trimoxazole. Ceftriaxone was the most commonly used antibiotic (89%). It was found that the time-to-fever defervescence and the length of the hospital stay were greater for patients who were treated by ciprofloxacin than ceftriaxone (P <0.001). Inappropriate antibiotic treatment should be discouraged in order to prevent the development of resistant strains of S. typhi.
Bacterial Pathogen Responsible For Urinary Tract Infection.

Introduction: Urinary Tract Infection (UTI) is one of the common medical conditions which seek the help of clinician and prompt intervention with suitable antibiotics to prevent morbid conditions. Therefore, identification of causative agent with their antibiotic sensitivity pattern is always mandatory for successful treatment of the cases. The main objective of the study was to identify the common bacterial pathogen responsible for causing Urinary Tract Infection with determination of sensitivity pattern of commonly used antibiotics. Methods: A total of 8270 urine samples were collected from the patient attending Outpatient Department and admitted as Inpatient in ward during the period of January 2011 to December 2011 in Shree Birendra Hospital. The samples were subjected to culture for identification of pathogen with their antibiotic sensitivity pattern following standard methodology. Results: Out of total, only1654 (20%) showed growth of pathogenic organisms. Among them positivity was highest in patient attending Outpatient Department. Eight different species of bacteria was isolated as causative agent. Among them Escherichia coli (67%) was predominantly higher in number followed by Proteus spp (22.24%), Klebsiellaspp (4.07%), Pseudomonas aeruginosa (2.7%) and Citriobacterfreundii (2.3%). Among these organisms sensitivity was highest towards Amikacin (86%) & Gentamycin (69%) followed by Nitrofuranti on (60.5%). Conclusions: Causative agent of Urinary Tract Infection may vary in different situation. Definite identification of pathogen with their antibiotic sensitivity pattern is always key point for success of treatment. Medical Journal of Shree Birendra Hospital; Jan-June 2012/vol.11/Issue1/13-16 DOI: http://dx.doi. org/10.3126/mjsbh.v11i1. 7760
Cardiopulmonary exercise testing in patients with pulmonary hypertension: clinical recommendations based on a review of the evidence

ABSTRACT Pulmonary hypertension (PH) remains an ominous diagnosis despite advances in pharmacological and surgical therapy. Early and effective diagnosis is important for clinicians making treatment determinations and patients wishing to understand the prognostic implications of their illness. Cardiopulmonary exercise testing (CPX) has the power to reveal the underlying pathophysiological consequences of the disease process. Research, especially over the last 10-15 years, has demonstrated the utility of this tool. Several CPX variables have been shown to be consistently altered in patients with PH and more so as severity of disease increases. However, to further enhance clinical application, additional research is needed to better define optimal CPX measures and associated cutoff values. This paper gives class-based recommendations with associated levels of evidence for the use of CPX in the PH patient population.
The line of action

The line of action is a conceptual tool often used by cartoonists and illustrators to help make their figures more consistent and more dramatic. We often see the expression of characters---may it be the dynamism of a super hero, or the elegance of a fashion model---well captured and amplified by a single aesthetic line. Usually this line is laid down in early stages of the drawing and used to describe the body's principal shape. By focusing on this simple abstraction, the person drawing can quickly adjust and refine the overall pose of his or her character from a given viewpoint. In this paper, we propose a mathematical definition of the line of action (LOA), which allows us to automatically align a 3D virtual character to a user-specified LOA by solving an optimization problem. We generalize this framework to other types of lines found in the drawing literature, such as secondary lines used to place arms. Finally, we show a wide range of poses and animations that were rapidly created using our system.
3D self-portraits

We develop an automatic pipeline that allows ordinary users to capture complete and fully textured 3D models of themselves in minutes, using only a single Kinect sensor, in the uncontrolled lighting environment of their own home. Our method requires neither a turntable nor a second operator, and is robust to the small deformations and changes of pose that inevitably arise during scanning. After the users rotate themselves with the same pose for a few scans from different views, our system stitches together the captured scans using multi-view non-rigid registration, and produces watertight final models. To ensure consistent texturing, we recover the underlying albedo from each scanned texture and generate seamless global textures using Poisson blending. Despite the minimal requirements we place on the hardware and users, our method is suitable for full body capture of challenging scenes that cannot be handled well using previous methods, such as those involving loose clothing, complex poses, and props.
25 million flows later: large-scale detection of DOM-based XSS

In recent years, the Web witnessed a move towards sophis- ticated client-side functionality. This shift caused a signifi- cant increase in complexity of deployed JavaScript code and thus, a proportional growth in potential client-side vulnera- bilities, with DOM-based Cross-site Scripting being a high impact representative of such security issues. In this paper, we present a fully automated system to detect and validate DOM-based XSS vulnerabilities, consisting of a taint-aware JavaScript engine and corresponding DOM implementation as well as a context-sensitive exploit generation approach. Using these components, we conducted a large-scale analysis of the Alexa top 5000. In this study, we identified 6167 unique vulnerabilities distributed over 480 domains, show- ing that 9,6% of the examined sites carry at least one DOM- based XSS problem.