Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographical differences in survival of dogs with non‐Hodgkin lymphoma treated with a CHOP based chemotherapy protocol

BACKGROUND In humans geographical differences in the incidence and presentation of various cancers have been reported. However, much of this information has not been collected in veterinary oncology. AIM The purpose of this study was to determine if a geographic difference in progression free survival exists for dogs with lymphoma treated within the US. MATERIALS AND METHODS Medical records of 775 cases of canine lymphoma from 3 US regions (west, south and north), treated with CHOP chemotherapy, were retrospectively evaluated. Cases were collected from referral institutions and were required to have received at least one doxorubicin treatment and have follow up information regarding time to progression. RESULTS Significant differences in sex (p = 0.05), weight (p = 0.049), stage (p < 0.001), immunophenotype (p = <0.001), and number of doxorubicin doses (p = 0.001) were seen between regions. Upon univariate analysis, progression free survival (PFS) differed by region (p = 0.006), stage (p = 0.009), sub-stage (p = 0.0005), and immunophenotype (p = 0.001). A multivariable Cox regression model showed that dogs in the western region had a significantly shorter PFS when compared to the south and east. CONCLUSION PFS was significantly affected by stage, sub-stage and phenotype.
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples

Abstract Motivation As more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. These enable researchers to leverage vast datasets that would otherwise be difficult to obtain. Results Snaptron is a search engine for summarized RNA sequencing data with a query planner that leverages R-tree, B-tree and inverted indexing strategies to rapidly execute queries over 146 million exon-exon splice junctions from over 70 000 human RNA-seq samples. Queries can be tailored by constraining which junctions and samples to consider. Snaptron can score junctions according to tissue specificity or other criteria, and can score samples according to the relative frequency of different splicing patterns. We describe the software and outline biological questions that can be explored with Snaptron queries. Availability and implementation Documentation is at http://snaptron.cs. jhu.edu. Source code is at https://github.com/ChristopherWilks/snaptron and https://github.com/ChristopherWilks/snaptron-experiments with a CC BY-NC 4.0 license. Supplementary information Supplementary data are available at Bioinformatics online.
Mechanisms of deficient interferon‐γ production in atopic diseases

The mechanisms responsible for an imbalanced cytokine response in atopic diseases are still not understood. While impaired interferon‐gamma (IFN‐γ) production may be the result of a pathological T‐cell/antigen‐presenting cell (APC) interaction, evidence was provided that the T cell itself may have an intrinsic defect to produce IFN‐γ.
Asthma in Elite Athletes

There is a high prevalence of asthma among elite performance athletes, particularly those who train and compete with high ventilation rates in austere environments, such as cross country skiers and swimmers. How best to assess, diagnose, and treat asthma or exercise-induced bronchoconstriction (EIB) in athletes remains controversial. The underlying high cardiorespiratory fitness levels of athletes make the diagnostic process more complex as do a variety of both common and rare alternative diagnoses that must be considered. To add to this, the pathophysiology of EIB in athletes is believed to differ significantly from the exercise-induced asthma seen in clinical patients, with less allergic inflammation and less steroid responsive airways pathology. This review aims to examine the underlying differences in EIB and exercise-induced asthma, to discuss diagnostic testing, and to look at the evidence that suggests how we should direct management and therapy. This discussion raises a number of questions about the diagnosis and treatment of airways symptoms in athletes, and it also suggests how future research should be targeted to answer these questions.
Reacciones adversas a medicamentos en pacientes que acudieron a un hospital general: un meta-análisis de resultados

Objectives The aim of this study was to present the results of a meta-analysis on adverse drug reactions (ADR) in spanish patients admitted to hospital and presenting to emergency department over the past 20 years. Patients and methods An exhaustive review was undertaken of relevant articles in the IME (Spanish Medical Index) and MEDLINE databases and published between 1985 and 2006, rigorously selecting 12 out of 30 publications after applying inclusion and exclusion criteria. Information was required on: symptomatology, prognosis, type, drugs involved, imputability and admissions for ADR; and factors associated with ADR onset, e.g., age, sex, number of drugs, previous history of ADR, method used for ADR detection, and length of study period. A random-effects model (DerSimonian and Laird) and the STATA 9.1 programme were used for the meta-analysis. Results The combined estimation of the percentage of Spanish patients with ADR was 13% (95% CI); with severe ADR, 12 % (95% CI) and with fatal ADR, 0.1% (95% CI). ADR diagnosis was definite in 36% (95% CI), probable in 49.6% (95% CI), and type A in 71% (95% CI) of cases. Among patients in the Emergency Department for ADR, 5.1% (95% IC) were hospitalized. No association was found with number of prescriptions or previous history. Association was established with advanced age and female sex. Digestive, skin, nervous and cardiovascular systems were those most affected by ADR. The drugs most frequently implicated included NSAIDs, digoxin, IACE, calcium antagonists, furosemide, i.v. metamizol, antidiabetics, benzodiazepines, adrenergic bronchodilators and classic antipsychotics. Conclusions ADRs constitute a major medical and economic problem with aspects that have yet to be defined. Greater efforts are warranted to unify criteria for the publication of results in observational studies on ARD and to determine the role played by some factors associated with their onset, e.g., sex, previous history and comorbidities.
Uncovering recurrent microdeletion syndromes and subtelomeric deletions/duplications through non‐selective application of a MLPA‐based extended prenatal panel in routine prenatal diagnosis

To present the application of multiplex ligation‐dependent probe amplification (MLPA)‐based screening approach in 1550 typical prenatal cases, for the simultaneous targeted detection of 23 recurrent microdeletion syndromes as well as subtelomeric copy number assessment for all chromosomes and discuss the implications in routine prenatal chromosomal diagnosis (PCD).
Integrative data mining to identify novel candidate serum biomarkers for pre‐eclampsia screening

Pre‐eclampsia (PE) is a serious complication that affects approximately 2% of pregnant women worldwide. At present, there is no sufficiently reliable test for early detection of PE in a screening setting that would allow timely intervention. To help future experimental identification of serum biomarkers for early onset PE, we applied a data mining approach to create a set of candidate biomarkers.
Peritoneal endometriosis, ovarian endometriosis and adenomyotic nodules of the rectovaginal septum: a different histopathogenesis?

Morphological and morphometric data showed similarities between eutopic endometrium and red peritoneal lesions, suggesting that these lesions are the first stage of early implantation of endometrial glands and stroma. An inflammatory reaction provokes scarification and the lesions become black. The subsequent fibrosis leads to areas of white opacification which are probably inactive. Three different types of ovarian endometriosis were described: superficial haemorrhagic lesions; haemorrhagic cysts, and deeply infiltrating ovarian endometriosis. We showed that the mesothelium covering the ovary can invaginate in the ovarian cortex pushing back the primordial follicles. These mesothelial invaginations were in a continuum with endometriotic tissue, strongly suggesting the metaplasia theory as an explanation for the pathogenesis of ovarian endometriomas. Endometriotic rectovaginal nodules were histologically similar to adenomyomas, consisting of smooth muscle hyperplasia with active glandular epithelium and scanty stroma. Immunocytochemical results showed the poor differentiation and the hormonal independence of these lesions and indicated a close relationship with their mesodermal Mullerian origin. These three types of lesions, peritoneal, ovarian and rectovaginal, must be considered as three different entities with different pathogeneses.
Argon plasma coagulation ablation versus endoscopic surveillance of Barrett’s esophagus: late outcomes from two randomized trials

Background and study aim: Argon plasma coagulation (APC) has been used to ablate dysplastic and nondysplastic Barrett’s esophagus. We determined the longer-term efficacy of APC ablation within two randomized controlled trials of APC versus surveillance for Barrett’s esophagus in patients in whom gastroesophageal reflux was controlled by either surgery or proton pump inhibitors. Patients and methods: 129 patients (surgical trial 70, medical trial 59) with Barrett’s esophagus (nondysplastic or low grade dysplasia) were randomly allocated to either ablation using APC or to continuing endoscopy surveillance. Outcomes were determined at three time points: short-term (12 months), mid-term (42 – 75 months) and long-term (> 84 months). Results: In the APC groups, initial ablation of > 95 % of the Barrett’s esophagus was achieved in 61 of 63 patients; the > 95 % ablation persisted in 47 of 56 patients at short-term follow-up, in 33 of 49 at mid-term and in 21 of 32 at long-term follow-up. In the surveillance groups, the length of Barrett’s esophagus reduced from a mean of 4.2 cm to 2.7 cm at long-term follow-up. High grade dysplasia (HGD) developed in 1 patient in the APC groups and in 3 in the surveillance groups. Low grade dysplasia developed in 1 APC patient and in 6 surveillance patients. Conclusions: APC ablation reduced the extent of Barrett’s esophagus, and this reduction was maintained in some patients at longer-term follow-up. However, progression to HGD can still occur despite APC ablation, suggesting endoscopic surveillance is still required. Clinical trial registration: ACTRN012607000293460 and ACTRN12607000292471 (Australian Clinical Trials Registry).
Deferasirox, an oral chelator in the treatment of iron overload

BACKGROUND Deferasirox is a once-daily oral iron chelator developed for treating iron overload complicating long-term transfusion therapy in patients with diseases such as beta-thalassemia and myelodysplastic syndromes. Iron overload can damage the liver, pancreas and the heart. Deferoxamine, the only other drug approved for iron chelation, can prevent these effects but requires parenteral administration. Deferasirox has been approved after a one-year, open-label trial in patients ≥ 2 years old with beta-thalassemia and transfusional emosiderosis randomized to once-daily oral 5, 10, 20, 30 mg/kg/day in comparison of subcutaneous deferoxamine 20-60 mg/mg/kg/day x 5/week. CONCLUSIONS Deferasirox 20-30 mg/kg/day produced reductions in liver iron concentration (LIC) similar to those with deferoxamine. Adverse effect of deferasirox (increases of serum creatinine and aminotransferases), including the gastrointestinal ones, are similar but more frequent than those occurring with deferoxamine. Information is lacking on the effects of deferasirox on cardiac iron and cardiac dysfunction which is the most serious complication of transfusional iron overload.
Endoscopic ultrasound-guided therapy of a rectal Dieulafoy lesion

Dieulafoy lesion A 68-year-old manwith stage IV renal cell adenocarcinoma was admitted for severe lower gastrointestinal bleeding and hemodynamic instability. After blood transfusion, colonoscopy revealed fresh blood in the rectum and sigmoid colon but no apparent lesions. At 4 days after admission, the patient experienced another episode of severe bleeding. A repeat colonoscopy showed active pulsatile bleeding from an exposed vessel without mucosal ulceration, consistent with a Dieulafoy lesion located 3cm above the anal verge. An endoscopically administered epinephrine injection (1:10000) stopped the bleeding. After 5 days, recurrence of bleeding was noted from the treated vessel but it ceased with appropriate placement of two hemoclips and another epinephrine injection. However, in spite of this endoscopic treatment, 4 days later the patient had re-bleeding. Endoscopic ultrasound (EUS)-guided vascular treatment was planned prior to considering surgical treatment (●" Video1). The ultrasonographic view showed a persistently widecaliber vessel, that is, without any sign of tapering, coursing directly toward the mucosal surface (●" Fig.1) with arterial flow (●" Fig.2). Under EUS guidance, the rectal wall was punctured the needle tip directed toward the vessel (●" Fig.3) and 6mL of 2% polidocanol was injected, with cessation of bleeding (●" Fig.4). Subsequently, the patient did not experience any new bleeding episodes and was discharged, however, 2 months later he passed away following progression of his oncologic disease. Endoscopic treatment of bleeding Dieulafoy lesions, with epinephrine injection or hemoclips, should be attempted before considering surgery [1,2]. Successful EUS-guided treatment has been described for gastric [3] and duodenal [4] Dieulafoy lesions but to our knowledge it has never been reported for rectal lesions. In this setting, EUS allowed accurate identification of the source of bleeding and precise delivery of the thrombotic agent into the target vessel. This treatment offers a new option for minimally invasive treatment before surgery [4]. Fig.2 Pulsed Doppler study showing arterial flow into the vessel, confirming the provisional diagnosis. The white arrows are pointing towards the muscularis propria of the rectal wall. The arterial vessel is clearly seen entering the rectal wall through the muscularis propria. Fig.1 Endoscopic view in a 68-year-old man with stage IV renal cell adenocarcinoma and lower gastrointestinal bleeding: a widecaliber vessel (arrow) is seen coursing from the perirectal fat tissue entering the rectal wall and reaching the mucosal surface without tapering. This finding is consistent with a rectal Dieulafoy lesion and this area corresponded to the site of bleeding.
Characteristics of students receiving counselling services at the University of Cape Town, South Africa

The aim of the study was to document the correlates of receiving counselling services at the University of Cape Town, South Africa. The 932 students who received counselling over a 3-year period were compared with the other 23,158 students registered at the university. Data were obtained from the university computerised record system. Women, Black people and 20-24-year-olds were significantly more likely to receive counselling services. When adjusting for these demographic variables, non-English speakers, humanities students, undergraduates, first-year students, students who were eligible to receive financial assistance, and students from outside Cape Town were significantly more likely to receive counselling. New research is required to determine the reasons for these findings.
The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies

Maternal plasma contains circulating cell‐free DNA fragments originating from both the mother and the placenta. The proportion derived from the placenta is known as the fetal fraction. When measured between 10 and 20 gestational weeks, the average fetal fraction in the maternal plasma is 10% to 15% but can range from under 3% to over 30%. Screening performance using next‐generation sequencing of circulating cell‐free DNA is better with increasing fetal fraction and, generally, samples whose values are less than 3% or 4% are unsuitable. Three examples of the clinical impact of fetal fraction are discussed. First, the distribution of test results for Down syndrome pregnancies improves as fetal fraction increases, and this can be exploited in reporting patient results. Second, the strongest factor associated with fetal fraction is maternal weight; the false negative rate and rate of low fetal fractions are highest for women with high maternal weights. Third, in a mosaic, the degree of mosaicism will impact the performance of the test because it will reduce the effective fetal fraction. By understanding these aspects of the role of fetal fraction in maternal plasma DNA testing for aneuploidy, we can better appreciate the power and the limitations of this impressive new methodology. © 2013 John Wiley & Sons, Ltd.
Hydrogen bond strength and bond geometry in cyclic dimers of crystalline carboxylic acids.

In a study of 101 crystal structures of carboxylic acids we have observed a clear trend in the difference between the formally single and formally double C-O bond distances, as observed by X-ray diffraction, with a clear-cut distinction between aromatic acids, where the two distances are similar, and non-aromatic acids, where the two distances distinctly differ by 0.06-0.12 A. A tentative energy classification - within the limits of the many assumptions - and a correlation with the O.O separation over the hydrogen bond indicate that the stability of the carboxylic acid dimer increases as the difference between the two apparent C-O distances becomes smaller, owing to an increasing Coulombic contribution to the dimerization energy. No simple hypothesis is adequate for a complete explanation of the origin, of the details and of the variations of this phenomenon. As often happens in crystal chemistry problems, one is presumably confronted with a balance of several subtle intra- and intermolecular factors.
Give a disease a bad name

Diseases may be known by the localities where they were first described or were common. Thus undulant fever, a particularly debilitating illness that often led to rheumatism, became known as Malta fever—to which many Maltese objected. There were many other names for it: Rock or Gibraltar fever, as well as Cyprus, Neapolitan, Italian, and Crimean fever. But Malta fever was the favoured name. Mediterranean fever was recommended by an international congress but was really unsuitable as the fever was found in many other localities. Sir David Bruce discovered the causative organism in the spleen of a soldier who had died in Malta …
Labia Minora Elongation and its Implications on the Health of Women: A Systematic Review

ABSTRACT Objectives: Labia minora elongation (LME) is a female genital modification practice categorized among the types included in the fourth group of female genital mutilation. In this article, we display the results of a systematic review of the evidence-based knowledge published on the health risks and benefits of LME as informed by African female respondents who are insiders of the practice. No other systematic review on this specific topic has been published before. Methods: A methodological bibliographic search was done in scientific databases by manual referencing and by contacting experts on this area of knowledge. Seventeen articles were eligible for this review, which corresponded to nine different studies. Eight of these studies were conducted in Eastern and Southern African countries and one was carried out in Italy. Results: This review concludes that pain at the beginning of the practice, nuisances related to the use of caustic herbs, and stigmatization in failing to comply with the practice are the principal health risks associated with LME. At the same time, there is evidence that labial elongation may benefit the sexual health and well-being of women. Conclusions: More research of a quantitative nature is necessary to determine the prevalence of LME across the practicing cultures and to determine its implications on the sexual and reproductive health of women who engage in this female genital modification.
Clinimetric Properties of Timed Walking Events Among Patient Populations Commonly Encountered in Orthotic and Prosthetic Rehabilitation

Outcomes assessment is becoming increasingly prevalent in healthcare. Many assessment measures involve timed ambulatory events and have been validated among those patient populations most commonly encountered in orthotic and prosthetic rehabilitation. These assessments are described, and the ranges of probable performance values across several patient populations are presented. The populations of cerebral vascular accident, cerebral palsy, multiple sclerosis, lower extremity amputation, traumatic brain injury, spinal cord injury, post polio and peripheral neuropathy are then treated individually, with summaries of current reliability findings and other considerations.
A model of seasonal changes in energy balance

In developing countries, many peasant farmers experience regular seasonal changes of body weight, so that the adequacy of food energy supply cannnot be assessed simply in terms of energy balance and a desirable body weight. A computer simulation model has been devised, which predicts the pattern of changes in body weight which result from the annual cycle of agricultural work load, and the way in which food consumption is regulated over the year. The model also includes the effect of post‐harvest storage losses. The actual observed patterns of food use of farmers in The Gambia, and in Burma, are first of all used to simulate the seasonal changes in body weight and these agree well with observations. The effects of alternative strategies of food use are then tried, ranging from a constant intake throughout the year, to an exaggerated feasting and fasting cycle. The simulations show that the actual food allocation patterns adopted by these two peasant populations constitute an optimum strategy in which the .