Miracle-dz/UniFAR-FTUs huggingface dataset:
The epidemiological profile of tuberculosis in southern Brazil in times of AIDS.

SETTING Urban area in southern Brazil. OBJECTIVE To investigate human immunodeficiency virus (HIV) co-infection among new cases of tuberculosis recorded in 2000 in Porto Alegre, Brazil. DESIGN Cross-sectional population-based study. RESULTS Among 1713 new tuberculosis cases, HIV testing was not available for 29.8% and results were unknown for 1.8%. Of 1171 with known results, 47% had HIV co-infection. HIV seropositivity was 44% higher in males. The 15-59 years age group had 3.4 times more seropositive cases than the group aged >59 years. Individuals with <8 years of schooling presented 57% more co-infection. HIV positivity was twice as frequent in extra-pulmonary and combined forms of tuberculosis as in pulmonary forms. Hospitalization was 2.4 times more common in HIV-positive individuals. The overall cure rate was 69.8%, while in co-infected patients it was 43.9%. The determinants of risk of death from tuberculosis included <8 years of schooling (PR 2.2, 95%CI 1.2-3.7), HIV seropositivity (PR 8.0, 95%CI 5.0-12.9), combined pulmonary and extra-pulmonary tuberculosis (PR 1.7, 95%CI 1.2-2.5) and diagnosis during admission rather than in out-patient clinics (PR 5.4, 95%CI 2.9-10.1). CONCLUSIONS The co-occurrence of tuberculosis and HIV/AIDS indicates a need to integrate the control programs for these two diseases. The health care system should invest in early diagnosis and adherence to treatment for both diseases.
Vascular dementia in a population-based autopsy study.

BACKGROUND The validity of the clinical diagnosis of vascular dementia (VaD) remains suboptimal. OBJECTIVE To investigate clinicopathologic correlations in VaD. METHODS We used the medical records-linkage system of the Rochester Epidemiology Project to identify incident cases of dementia in Rochester, Minn, from January 1, 1985, through December 31, 1989. Dementia and Alzheimer disease (AD) were defined by the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition. Vascular dementia was defined by criteria including imaging results. Pathological characteristics of AD were quantified by means of standard scoring methods for neurofibrillary tangles and neuritic plaques. Vascular pathological findings were assessed by expert neuropathological opinion. RESULTS Of 419 patients with dementia who died before the study, neuropathological examination results were available in 89 (21%) with median age at onset of 80 years (range, 50-96 years; 52 [58%] women). Pathological diagnoses were AD in 45 patients (51%), pure VaD in 12 (13%), combined AD and VaD in 11 (12%), and other diagnoses in the remaining 21 patients. Criteria for VaD that required either a temporal relationship between a stroke and dementia onset or worsening, or bilateral infarctions in specified locations demonstrated on imaging results (Mayo Clinic criteria) had 75% sensitivity and 81% specificity for pure VaD (positive likelihood ratio, 3.9; 95% confidence interval, 2.2-6.7). Five cases of pure VaD lacked the temporal relationship and accounted for the imperfect sensitivity of the criteria. CONCLUSIONS In this population-based autopsy study, the presence of vascular pathological characteristics in the absence of major AD pathological findings was common. Pure VaD without overt clinical strokes remains a challenge for antemortem diagnosis.
Understanding the Dynamic Evolution of Cyclic Variability at the Operating Limits of HCCI Engines with Negative Valve Overlap

An experimental study is performed for homogeneous charge compression ignition (HCCI) combustion focusing on late phasing conditions with high cyclic variability (CV) approaching misfire. High CV limits the feasible operating range and the objective is to understand and quantify the dominating effects of the CV in order to enable controls for widening the operating range of HCCI. A combustion analysis method is developed for explaining the dynamic coupling in sequences of combustion cycles where important variables are residual gas temperature, combustion efficiency, heat release during re-compression, and unburned fuel mass. The results show that the unburned fuel mass carries over to the re-compression and to the next cycle creating a coupling between cycles, in addition to the well known temperature coupling, that is essential for understanding and predicting the HCCI behavior at lean conditions with high CV.
Poxvirus Exploitation of the Ubiquitin-Proteasome System

Ubiquitination plays a critical role in many cellular processes. A growing number of viruses have evolved strategies to exploit the ubiquitin-proteasome system, including members of the Poxviridae family. Members of the poxvirus family have recently been shown to encode BTB/kelch and ankyrin/F-box proteins that interact with cullin-3 and cullin-1 based ubiquitin ligases, respectively. Multiple members of the poxvirus family also encode ubiquitin ligases with intrinsic activity. This review describes the numerous mechanisms that poxviruses employ to manipulate the ubiquitin-proteasome system.
An assay combining cell culture with reverse transcriptase PCR to detect and determine the infectivity of waterborne Cryptosporidium parvum

The presence of Cryptosporidium in drinking water supplies is a significant problem faced by the water industry. Although a variety of methods exist for the detection of waterborne oocysts, water utilities currently have no way of assessing the infectivity of detected oocysts and consequently are unable to accurately determine the risks posed to public health by waterborne Cryptosporidium. In this paper, the development of an infectivity assay for waterborne Cryptosporidium parvum is described. Oocysts were inoculated onto monolayers of Caco-2 cells and grown on microscope slides, and infections were detected by C. parvum specific reverse transcriptase PCR of extracted mRNA, targeting the heat shock protein 70 (hsp70) gene. A single infectious oocyst was detected by this experimental procedure. The use of concentrated samples obtained from 250 liters of finished water had no observable effect on the integrity of cell monolayers or on the infectivity of oocysts seeded into the concentrate. Intracellular developmental stages of the parasite were also detected by using fluorescently labeled antibodies. One pair of PCR primers targeting the hsp70 gene was specific for C. parvum, while a second pair recognized all species of Cryptosporidium tested. The C. parvum-specific primers amplified DNA from 1 to 10 oocysts used to seed 65 to 100 liters of concentrated environmental water samples and were compatible with multiplex PCR for the simultaneous detection of C. parvum and Giardia lambia. This paper confirms the utility of PCR for the detection of waterborne C. parvum and, most importantly, demonstrates the potential of an in vitro infectivity assay.
Analytical Evaluation of iSTAT Portable Clinical Analyzer and Use by Nonlaboratory Health-Care Professionals

We evaluated the performance of the i-STAT Portable Clinical Analyzer, a hand-held instrument that, with its current cartridge, analyzes for electrolytes, urea nitrogen, glucose, and hematocrit in -60 jL of whole blood in -90 s. Accuracy, imprecision, and linearity studies were performed with aqueous controls and standards and by split-sample analysis. Intrarun imprecision (CV) ranged from 0.34% to 3.97%. Total imprecision over a 2-month period ranged from 0.42% to 4.83%, with urea nitrogen and glucose analyses generating the higher values. Patients’ results from the Portable Clinical Analyzer correlated well with those obtained for whole blood or plasma by the Nova Stat ProfIle 5, the Beckman Synchron CX3, or the Technicon Hi Hematology Analyzer, with S values <0.2 mmol/L for potassium; <1.5 mmol/L for sodium, glucose, and urea nitrogen;<2.4 mmol/L for chloride; and <2.4% for hematocrit. We also ascertained imprecision and accuracy of the system placed in a cardiothoracic intensive-care unit and operated by nurses. There were no significantdifferences in either the imprecision or accuracy of the system in this setting. We conclude that operator technique is not a factor in the analytical performance of the system and that it can be used by nonlaboratorians with a high degree of confidence that reliable results will be obtained.
Cognitive demand and cognitive effort in post-editing

The pause to word ratio, the number of pauses per word in a post-edited MT segment, is an indicator of cognitive effort in post-editing (Lacruz and Shreve, 2014). We investigate how low the pause threshold can reasonably be taken, and we propose that 300 ms is a good choice, as pioneered by Schilperoord (1996). We then seek to identify a good measure of the cognitive demand imposed by MT output on the post-editor, as opposed to the cognitive effort actually exerted by the post-editor during post-editing. Measuring cognitive demand is closely related to measuring MT utility, the MT quality as perceived by the post-editor. HTER, an extrinsic edit to word ratio that does not necessarily correspond to actual edits per word performed by the post-editor, is a well-established measure of MT quality, but it does not comprehensively capture cognitive demand (Koponen, 2012). We investigate intrinsic measures of MT quality, and so of cognitive demand, through edited-error to word metrics. We find that the transfer-error to word ratio predicts cognitive effort better than mechanical-error to word ratio (Koby and Champe, 2013). We identify specific categories of cognitively challenging MT errors whose error to word ratios correlate well with cognitive effort.
Morphine Is Associated With a Delayed Activity of Oral Antiplatelet Agents in Patients With ST-Elevation Acute Myocardial Infarction Undergoing Primary Percutaneous Coronary Intervention

Background—Morphine is recommended in patients with ST-segment–elevation myocardial infarction, including those undergoing primary percutaneous coronary intervention. Suboptimal antiplatelet effect during and after primary percutaneous coronary intervention is associated with increased thrombotic complications. It was hypothesized a potential drug–drug interaction between morphine and antiplatelet agents. We sought to assess platelet inhibition after a loading dose of the currently recommended antiplatelet agents in ST-segment–elevation myocardial infarction patients according to morphine use. Methods and Results—Three hundred patients undergoing primary percutaneous coronary intervention receiving either prasugrel (n=95) or ticagrelor (n=205) loading dose had platelet reactivity assessed by VerifyNow 1, 2, and 4 hours after loading dose. Patients treated with morphine (n=95; 32%) had a higher incidence of vomit (15% versus 2%; P=0.001). P2Y12 reactivity units 2 hours after the loading dose was 187 (153–221) and 133 (102–165) in patient with and without morphine (P<0.001); the difference persisted after excluding patients with vomit (P<0.0001). High residual platelet reactivity (P2Y12 reactivity units ≥208) at 2 hours was found in 53% and 29% patients with and without morphine (P<0.001) and without difference between prasugrel and ticagrelor patients. The independent predictors of high residual platelet reactivity at 2 hours were morphine use (odds ratio, 2.91 [1.71–4.97]; P<0.0001) and age (odds ratio, 1.03 [1.01–1.05]; P=0.010). Morphine remained associated with high residual platelet reactivity after propensity score adjustment (c-statistic, 0.68; 95% confidence interval, 0.66–0.70; P=0.879 for Hosmer–Lemeshow test). Conclusions—In patients with ST-segment–elevation myocardial infarction, morphine use is associated with a delayed onset of action of the oral antiplatelet agents. This association persisted after adjusting for the propensity to receive morphine and after excluding patients with vomit.
[Relaxation therapy in patients with anxiety and somatoform disorders in primary care].

OBJECTIVE To study the effect of relaxation therapy on the symptomology of patients with anxiety and somatoform disorders. DESIGN An experimental prospective study, controlled through random assignation, using evaluation scales. SETTING Mn. Jaume Soler Health Centre, Cornellà (Barcelona). PATIENTS 31 patients (8 men and 23 women), diagnosed with anxiety or previously untreated somatoform disorders, for whom combined anti-depressive and relaxation therapy over a 5-month period was established. The results were compared with those of a control group (n = 17) with identical diagnoses, which only received antidepressive medication. MEASUREMENTS AND MAIN RESULTS The STAI tests and two pain scales were administered at 0, 15, 30, 45, 60 and 150 days and the HRS and SCL-90-R at 0 and 150 days. The possible impact of the psychiatric diagnosis, age, gender, married status, existence of concomitant physical illness, SRE, present employment status and the presence of children or not were all considered. The results pointed to a significant improvement over the period in the analogue-visual scale of pain (p = .009) and in the HRS (p = .046) for the group comprised of those complying with the relaxation therapy independently of the psychiatric diagnosis. CONCLUSIONS The benefit of relaxation in anxious and somatoform patients, when pain--and not anxiety--is the principal symptom, was confirmed. Depression improved when antidepressants were administered simultaneously, whereas anxiety varied little, at least during the time the trial lasted.
Evaluation of Hygienic Quality and Labelling of Fish Distributed in Public Canteens of Northeast Italy

Over the past few years, the demand for the introduction of fish products in public canteens (schools, hospitals and nursing-homes) has grown due to their good nutritional proprieties. The particular health conditions and sensitivity of some groups of consumers exposes them to greater risks of food poisoning. It is therefore important to monitor the raw materials that end up in mass catering implementing strategies of mass catering control, both with self-monitoring strategies and with regular controls performed by the competent health authorities. The purpose of this study is to assess the overall quality of seafood dealt out from public catering services located in Northeast Italy. In this paper we illustrate the results of microbiological analysis performed on 135 fish samples (58% of samples were raw fishes, 27% cooked fishes, 6% raw fish products, 9% cooked fish products) and species identification performed on 102 fish samples. Additionally, 135 environmental swabs were collected to determine the effectiveness of cleaning and sanitation of food contact (cutting boards, cooking equipment and food processing surfaces) and non-contact (refrigerator wall and handle, tap lever) surfaces. Of raw seafood samples, 24% had total aerobic mesophilic bacteria count >105 CFU/g and for Enterobacteriaceae the faecal contamination was excluded since no Salmonella spp. and Escherichia coli were isolated. Just 3.8% of raw seafood samples resulted positive for Listeria monocytogenes. The results of swab samples of cooking utensils and surfaces showed that sanitation practices should be improved. Molecular analysis for fish species identification revealed a mislabelling for 25% of sampled fishes. The results of this survey can provide valuable information for monitoring and surveillance programmes for the control of quality of fish and fish products.
Iron Chelation Improves Endothelial Function in Patients With Coronary Artery Disease

Background—Some epidemiological studies have shown that increased iron stores are associated with increased cardiovascular events. Redox-active iron may contribute to lipid peroxidation, endothelial cell activation, and generation of reactive oxygen species (especially hydroxyl radical, via Fenton chemistry). Increased oxidative stress is associated with impaired action of endothelium-derived nitric oxide in patients with atherosclerosis. Methods and Results—To test the hypothesis that reducing vascular iron stores would reverse endothelial dysfunction, we examined the effects of the iron chelator deferoxamine (500 mg intra-arterially over 1 hour) on vasomotor function in forearm resistance vessels of patients with coronary artery disease by venous occlusion plethysmography. Patients with coronary artery disease had impaired endothelium-dependent vasodilation in response to methacholine compared with healthy control subjects (P <0.001). Deferoxamine infusion decreased serum iron levels (P <0.001). Deferoxamine improved the blood flow response to methacholine in patients with coronary artery disease (P <0.01 by 2-way repeated-measures ANOVA) but had no effect on the response to sodium nitroprusside. In normal volunteers, deferoxamine had no effect on the response to methacholine. The nitric oxide synthase inhibitor NG-monomethyl-l-arginine abolished augmentation of the methacholine response associated with deferoxamine. The hydroxyl radical scavenger mannitol had no effect on the methacholine response. Conclusions—Deferoxamine improved nitric oxide–mediated, endothelium-dependent vasodilation in patients with coronary artery disease. These results suggest that iron availability contributes to impaired nitric oxide action in atherosclerosis.
Known Allergen Structures Predict Schistosoma mansoni IgE-Binding Antigens in Human Infection

The IgE response has been associated with both allergic reactions and immunity to metazoan parasites. Recently, we hypothesized that all environmental allergens bear structural homology to IgE-binding antigens from metazoan parasites and that this homology defines the relatively small number of protein families containing allergenic targets. In this study, known allergen structures (Pfam domains) from major environmental allergen families were used to predict allergen-like (SmProfilin, SmVAL-6, SmLipocalin, SmHSP20, Sm triosephosphate isomerase, SmThioredoxin, Sm superoxide dismutase, SmCyclophilin, and Sm phosphoglycerate kinase) and non-allergen-like [Sm dynein light chain (SmDLC), SmAldolase SmAK, SmUbiquitin, and Sm14-3-3] proteins in Schistosoma mansoni. Recombinant antigens were produced in Escherichia coli and IgG1, IgG4, and IgE responses against them measured in a cohort of people (n = 222) infected with S. mansoni. All allergen-like antigens were targeted by IgE responses in infected subjects, whilst IgE responses to the non-allergen-like antigens, SmAK, SmUbiquitin, and Sm14-3-3 were essentially absent being of both low prevalence and magnitude. Two new IgE-binding Pfam domain families, not previously described in allergen family databases, were also found, with prevalent IgE responses against SmDLC (PF01221) and SmAldolase (PF00274). Finally, it was demonstrated that immunoregulatory serological processes typically associated with allergens also occurred in responses to allergen-like proteins in S. mansoni infections, including the production of IgG4 in people responding with IgE and the down-regulation of IgE in response to increased antigen exposure from S. mansoni eggs. This study establishes that structures of known allergens can be used to predict IgE responses against homologous parasite allergen-like molecules (parallergens) and that serological responses with IgE/IgG4 to parallergens mirror those seen against allergens, supporting our hypothesis that allergenicity is rooted in expression of certain protein domain families in metazoan parasites.
A bivalent pneumococcal histidine triad protein D-choline-binding protein A vaccine elicits functional antibodies that passively protect mice from Streptococcus pneumoniae challenge

ABSTRACT Vaccines based on conserved pneumococcal proteins are being investigated because serotype coverage by pneumococcal polysaccharide and polysaccharide conjugate vaccines is incomplete and may eventually decrease due to serotype replacement. Here, we examined the functionality of human antibodies induced by a candidate bivalent choline-binding protein A- pneumococcal histidine triad protein D (PcpA-PhtD) vaccine. Pre- and post-immune sera from subjects who had been vaccinated with the PcpA-PhtD candidate vaccine were tested in an established passive protection model in which mice were challenged by intravenous injection with Streptococcus pneumoniae serotype 3 strain A66.1. Serum antibody concentrations were determined by enzyme-linked immunosorbent assay (ELISA). Bacterial surface binding by serum antibodies was determined by a flow cytometry-based assay. Sera from 20 subjects were selected based on low activity of pre-immune samples in the passive protection model. Bacterial surface binding correlated more strongly with anti-PcpA (0.87; p < 0.0001) than with anti-PhtD (0.71; p < 0.0001). The odds ratio for predicting survival in the passive protection assay was higher for the anti-PcpA concentration (470 [95% confidence interval (CI), 46.8 to >999.9]) than for the anti-PhtD concentration (3.4 [95% CI, 1.9 to 5.6]) or bacterial surface binding (9.4 [95% CI, 3.6 to 24.3]). Pooled post-immune serum also protected mice against a challenge with S. pneumoniae serotype 3 strain WU2. Both anti-PcpA and anti-PhtD antibodies induced by the bivalent candidate vaccine mediate protection against S. pneumoniae. The results also showed that the ELISA titer might be useful as a surrogate for estimating the functional activity of antibodies induced by pneumococcal protein vaccines.
The first implementation of IMRT technique for head & neck and prostate cancer patients in public sector in Greece: feasibility, treatment planning and dose delivery verification using the delta(4PT) Pre-Treatment volumetric quality assurance system.

PURPOSE Intensity Modulated Radiation Therapy (IMRT) is nowadays the treatment of choice, in terms of technique, for either head & neck or prostate cancer. With this paper, we are sharing our experience for the first inplementation of IMRT planning in the public sector in Greece, and especially in the Aretaieion University Hospital of Athens. METHODS From May 2013 until January 2014 four prostate and four head & neck cancer patients were evaluated in the present study. We used the ONCENTRA IMRT treatment planning with a step and shoot technique in a SIEMENS ONCORE Linac. The dose verification method used was based on the delta4(PT) Pre-Treatment volumetric quality assurance system, by Scadidos. RESULTS In all cases, the Relative Standard Deviation between the prescribed and the calculated average dose received by the target volume was less than 5%, while the γ-index was more than 90%. The acute toxicity was low and equivalent to published data with IMRT technique. CONCLUSION In conclusion, the first implementation of IMRT technique in the Medical School of Athens was feasible and safe as well as in terms of dose verification. The IMRT technique is already in clinical use and further results with long term radiation induced toxicity will be reported.