Miracle-dz/UniFAR-FTUs huggingface dataset:
Cancer patients’ acceptability of incorporating an epidemiology questionnaire within a clinical trial

Background/aims Understanding the influence or impact of epidemiological factors on cancer outcomes in clinical trials can broaden our knowledge of disease, trial populations and therapeutic effects thus leading to improved patient care. However, there is a lack of data on cancer patients’ compliance with an epidemiology questionnaire in the context of a clinical trial. Patients and methods Cancer patients were provided with a hypothetical scenario and surveyed regarding their willingness and preferences to complete an epidemiology questionnaire if incorporated into a cancer therapy trial. Patient compliance with completing a voluntary epidemiology questionnaire and trial coordinators perceptions therein were separately determined in the NCIC Clinical Trials Group HN.6 clinical trial, an ongoing randomized phase III trial comparing two first-line treatment regimens in patients with locoregionally advanced head and neck cancer. Results Of 617 cancer patients from community, academic and tertiary cancer centres, the majority were willing to complete an epidemiology questionnaire either unconditionally (45%), or provided it did not inconvenience them (31%); 4% would refuse. Patients preferred shorter questionnaires of 30–50 questions requiring 10–20 min to complete, administered over 1–3 sessions. Patients were less willing, but still compliant, to answer questions relating to sexual history (71%) and annual household income (66%) relative to other questions (>90%). Eighteen percent thought that the questionnaire should be mandatory, with 31% believing that they may benefit personally from such research. In the HN.6 trial, compliance averaged 94.8% per question. Conclusions Cancer patients are very willing to complete epidemiology questions in clinical trials.
A Chlamydia-Specific C-Terminal Region of the Stress Response Regulator HrcA Modulates Its Repressor Activity

ABSTRACT Chlamydial heat shock proteins have important roles in Chlamydia infection and immunopathogenesis. Transcription of chlamydial heat shock genes is controlled by the stress response regulator HrcA, which binds to its cognate operator CIRCE, causing repression by steric hindrance of RNA polymerase. All Chlamydia spp. encode an HrcA protein that is larger than other bacterial orthologs because of an additional, well-conserved C-terminal region. We found that this unique C-terminal tail decreased HrcA binding to CIRCE in vitro as well as HrcA-mediated transcriptional repression in vitro and in vivo. When we isolated HrcA from chlamydiae, we only detected the full-length protein, but we found that endogenous HrcA had a higher binding affinity for CIRCE than recombinant HrcA. To examine this difference further, we tested the effect of the heat shock protein GroEL on the function of HrcA since endogenous chlamydial HrcA has been previously shown to associate with GroEL as a complex. GroEL enhanced the ability of HrcA to bind CIRCE and to repress transcription in vitro, but this stimulatory effect was greater on full-length HrcA than HrcA lacking the C-terminal tail. These findings demonstrate that the novel C-terminal tail of chlamydial HrcA is an inhibitory region and provide evidence that its negative effect on repressor function can be counteracted by GroEL. These results support a model in which GroEL functions as a corepressor that interacts with HrcA to regulate chlamydial heat shock genes.
Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354T

ABSTRACT Campylobacter fetus subsp. venerealis is the etiologic agent of bovine genital campylobacteriosis, a sexually transmitted disease of cattle that is of worldwide importance. The complete sequencing and annotation of the genome of the type strain C. fetus subsp. venerealis NCTC 10354T are reported.
Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings

ABSTRACT A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species displaying a high level of resistance to zinc and cadmium, is presented here. The genome contains a large number of genes encoding proteins predicted to be involved in conferring metal resistance. Many of these genes appear to have been acquired through horizontal gene transfer.
A stabilizing receding horizon regulator for nonholonomic mobile robots

This paper presents a receding horizon (RH) controller used for regulating a nonholonomic mobile robot. The RH control stability is guaranteed by adding a terminal-state penalty to the cost function and a terminal-state region to optimization constraints. A suboptimal solution to the optimization problem is sufficient to achieve stability. A new terminal-state penalty and its corresponding terminal-state constraints are found. Implementation and simulation results are provided to verify the proposed control strategy.
The implementation methodology for a CD-ROM English document database

Producing a database of scanned document images for development or evaluation of OCR and document image understanding algorithms is neither easy nor inexpensive. The authors first briefly describe the makeup of a database of scanned document images of scientific and technical documents written in English which are being produced in a CD-ROM format. Then, the authors concentrate on the implementation methodology used to prepare the database. The methodology gives the protocols for each step of the database preparation, and the error model used for the estimation of the ground-truth errors that may exist in the database is discussed. <<ETX>>
A informática no consultório médico

OBJECTIVE: currently, information technology is part of several aspects of our daily life. The objective of this paper is to analyze and discuss the use of information technology in both medical education and/or medical practice. SOURCES OF DATA: information was gathered through nonsystematic bibliographic review, including articles, official regulations, book chapters and annals. Direct search and search of electronic databanks in Medline and Lilacs databases were also performed. SUMMARY OF THE FINDINGS: this paper was structured in topics. First, there is a discussion on the electronic medical record. The following aspects are presented: history, functions, costs, benefits, ethical and legal issues, and positive and negative characteristics. Medical decision-support systems are also evaluated in view of the huge amount of information produced every year regarding healthcare. The impact of the Internet on the production and diffusion of knowledge is also analyzed. Telemedicine is assessed, since it presents new challenges to medical practice, and raises important ethical issues such as "virtual medical consultation". Finally, a practical experience of modernization of a pediatric outpatient center by the introduction of computers and telecommunication tools is described. CONCLUSIONS: medical computing offers tools and instruments that support the administrative organization of medical visits, gather, store and process patient's data, generate diagnoses, provide therapeutical advice and access to information in order to improve medical knowledge and to make it available whenever and wherever adequate decision-making is required.
Genome-Wide Definition of the SigF Regulon in Mycobacterium tuberculosis

ABSTRACT In Mycobacterium tuberculosis the alternative sigma factor SigF controls the expression of a particular subset of genes by altering RNA polymerase specificity. Here, we utilize two genome-wide approaches to identify SigF-binding sites: chromatin immunoprecipitation (ChIP-on-chip) and microarray analysis of SigF-mediated transcripts. Since SigF is not an abundant protein in the logarithmic phase of growth, a pristinamyin IA-inducible system was used to control its expression. We identified 67 high-affinity SigF-binding sites and 16 loci where a SigF promoter directs the expression of a transcript. These loci include sigF itself, genes involved in lipid and intermediary metabolism and virulence, and at least one transcriptional regulator (Rv2884), possibly acting downstream of SigF. In addition, SigF was also found to direct the transcription of the gene for small RNA F6. Many loci were also found where SigF may be involved in antisense transcription, and in two cases (Rv1358 and Rv1870c) the SigF-dependent promoter was located within the predicted coding sequence. Quantitative PCR confirmed the microarray findings and 5′-rapid amplification of cDNA ends was used to map the SigF-specific transcriptional start points. A canonical SigF consensus promoter sequence GGTTT-N(15-17)-GGGTA was found prior to 11 genes. Together, these data help to define the SigF regulon and show that SigF not only governs expression of proteins such as the virulence factor, HbhA, but also impacts novel functions, such as noncoding RNAs and antisense transcripts.
Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103

ABSTRACT Sinorhizobium fredii HH103 is a fast-growing rhizobial strain that is able to nodulate legumes that develop determinate nodules, e.g., soybean, and legumes that form nodules of the indeterminate type. Here we present the genome of HH103, which consists of one chromosome and five plasmids with a total size of 7.22 Mb.
Importance of Hemodynamic Factors in the Prognosis of Symptomatic Carotid Occlusion

Context. —The relative importance of hemodynamic factors in the pathogenesis and treatment of stroke in patients with carotid artery occlusion remains controversial.Objective. —To test the hypothesis that stage II cerebral hemodynamic failure (increased oxygen extraction measured by positron emission tomography [PET]) distal to symptomatic carotid artery occlusion is an independent risk factor for subsequent stroke in medically treated patients.Design and Setting. —Prospective, blinded, longitudinal cohort study of patients referred from a group of regional hospitals between 1992 and 1996.Patients. —From 419 subjects referred, 81 with previous stroke or transient ischemic attack in the territory of an occluded carotid artery were enrolled. All were followed up to completion of the study, with average follow-up of 31.5 months.Main Outcome Measures. —Telephone contact every 6 months recorded the subsequent occurrence of all stroke, ipsilateral ischemic stroke, and death.Results. —Stroke occurred in 12 of 39 patients with stage II hemodynamic failure and in 3 of 42 patients without (P=.005); stroke was ipsilateral in 11 of 39 patients with stage II hemodynamic failure and in 2 of 42 patients without (P=.004). Six deaths occurred in each group (P=.94). The age-adjusted relative risk conferred by stage II hemodynamic failure was 6.0 (95% confidence interval [CI], 1.7-21.6) for all stroke and 7.3 (95% CI, 1.6-33.4) for ipsilateral stroke.Conclusions. —Stage II hemodynamic failure defines a subgroup of patients with symptomatic carotid occlusion who are at high risk for subsequent stroke when treated medically. A randomized trial evaluating surgical revascularization in this high-risk subgroup is warranted.
Four out of ten patients are not taking statins regularly during the 12 months after an acute coronary event

Background: In New Zealand, a setting in which national guidelines recommend statins for all patients with coronary heart disease (CHD) and cost barriers are low, patterns of use of these drugs are unknown. We investigated dispensing rates after hospital discharge for acute CHD event. Design: Retrospective cohort study. Methods: Drug dispensing, hospital diagnosis, and mortality records were linked by unique identifier for all New Zealanders aged 35–84 years after discharge following acute CHD event in 2007. We defined the statin dispensing ratio (SDR) as the proportion of days that 15,506 patients aged 35–84 years were dispensed such agents during the 12 months post discharge. An SDR ≥0.8 (80% or more days covered) was considered optimal. Results: Overall, 59% of the cohort had an SDR ≥0.8. Of patients dispensed statins in the 3 months before admission (n = 5506), almost all (99%; 5466) continued treatment during follow up and 82% had an SDR ≥0.8. In contrast, for patients not dispensed statins before admission (n = 8014), only two–thirds started statins during follow up and only 44% had an SDR ≥0.8. Of all patients with low statin dispensing (SDR <0.8), about one–quarter were not dispensed any lipid-lowering drugs, one-quarter received alternative lipid-lowering drugs, one-quarter stopped statins, and the remaining quarter were intermittent statin users. Conclusion: In a setting with few barriers to statin treatment, about 40% of patients had suboptimal statin dispensing during the year after hospital treatment for CHD. This study has identified four significant categories of suboptimal adherence that could inform quality improvement programmes.
Revision of the Dutch clinical algorithm for assessing patient needs in cardiac rehabilitation based on identified implementation problems

Background: Despite all available evidence of its effectiveness, cardiac rehabilitation and secondary prevention (CRSP) is still insufficiently implemented in current clinical practice. Based on an analysis of implementation problems, recently the Dutch clinical algorithm for the assessment of patient’s CRSP needs was revised. The purpose of this paper is to describe the revision process and its results to improve CRSP guideline implementation. Methods: The National Institute for Health and Clinical Excellence (NICE) guidelines manual for conducting guideline revisions was followed. Information on the use of the algorithm in practice was collected from electronic medical records and by conducting semi-structured interviews. Next, an expert advisory group identified the problems for use in daily practice and defined the scope for the revision. A multidisciplinary guideline development group subsequently wrote the revised algorithm. Results: A large variation in assessed patient needs was observed between CRSP clinics. Assessment based on clinical judgement was found to be a source of practice variation and is therefore avoided in the revised algorithm. It was decided to add assessment instruments for anxiety and depression, cardiovascular risk factors, stress, attitude of partner and lifestyle parameters. Conclusion: The Dutch clinical algorithm for assessing patient needs for CRSP was revised using a combination of patient data from routine practice, knowledge from academic experts and experience from field experts. The revised algorithm is a practical tool consisting of assessment instruments to improve CRSP guideline adherence in the Netherlands. This algorithm may also be useful for other Western countries to organize their CRSP needs assessment procedure.
An object-oriented form description language and approach to handwritten form processing

Virtually all form processing systems rely upon a form description file which holds some form design specific information. Such files are written in a form description language. This paper presents a novel form description language and a new approach to form processing which makes full use of the language. The form description language which is presented is novel in two ways: firstly, it allows the comprehensive utilisation of contextual information; secondly, it enables the storage of form models which economically describe the variations in the form design which are allowed for a particular class of forms.
A Model for Human–Human Collaborative Object Manipulation and Its Application to Human–Robot Interaction

During collaborative object manipulation, the interaction forces provide a communication channel through which humans coordinate their actions. In order for the robots to engage in physical collaboration with humans, it is necessary to understand this coordination process. Unfortunately, there is no intrinsic way to define the interaction forces. In this study, we propose a model that allows us to compute the interaction force during a dyadic cooperative object manipulation task. The model is derived directly from the existing theories on human arm movements. The results of a user study with 22 human subjects prove the validity of the proposed model. The model is then embedded in a control strategy that enables the robot to engage in a cooperative task with a human. The performance evaluation of the controller through simulation shows that the control strategy is a promising candidate for a cooperative human-robot interaction.
Table image segmentation

Algorithm for table image segmentation, a part of complete document recognition system is presented. The proposed approach introduces a concept of table grid which can serve for advanced methods of table structure analysis. It provides a layer of terminal symbols for the table, which is used by syntactical methods. Detailed discussion of grid detection is presented which is performed through the analysis of connected components projection profile. Simple rules for analysis of table structure cover majority of real life tables. The system is implemented, rested, and is now extensively used in FineReader OCR product.
Evaluation of mupA EVIGENE Assay for Determination of High-Level Mupirocin Resistance in Staphylococcus aureus

ABSTRACT Mupirocin is widely used to decolonize patients carrying Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA). The aim of this study was to determine the presence of high-level mupirocin resistance by a new commercially available mupA genotypic diagnostic product, mupA EVIGENE assay (AdvanDx).
Understanding factors that inhibit or promote the utilization of telecare in chronic lung disease

Objectives: To perform a process evaluation of a randomized controlled trial (RCT) of home telecare for the management of acute exacerbations of chronic obstructive pulmonary disease (COPD), using the normalization process model (NPM) as an explanatory framework. Methods: Semi-structured interviews were carried out with patients (n = 9) and nurses (n = 11) participating in a RCT. A framework approach to data analysis was used. Results: The telecare service did not provide an interactional advantage for the nurses providing this service and did not fit with the nurses' views of the most appropriate or preferred use of their skills. The telecare service seemed unlikely to become normalized as part of routine healthcare delivery, because the nursing team lacked confidence that it was a safe way to provide healthcare in this context and it was not perceived as improving efficiency. Discussion: The NPM effectively mapped onto the study findings and explained those factors that inhibited the routine delivery of COPD services by telecare.
The war on cancer – What is the enemy, and are we winning?

The so-called ‘war on cancer’ is now in its fifth decade. This article presents some facts and figures about cancer and the effort to treat it. It outlines updated thinking on the hallmarks and classification of cancer, and draws together published quotes from experts on the state of play in the fight against this disease.
Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

ABSTRACT A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca ). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA, porB, gyrA, and parC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n = 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n = 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n = 100; 13.0%), ST-42 and ST-91 (n = 45; 5.9%), ST-64 (n = 44; 5.72%), and ST-139 (n = 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n = 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n = 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n = 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n = 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains.
The association between metabolic syndrome and coronary artery disease in Jordan

Background: Previous studies in Jordan showed a considerably high prevalence of metabolic syndrome (MeS) and its individual components. However, data about the association between MeS and coronary artery disease (CAD) in Jordan are lacking. Therefore, this study aimed to determine the association between MeS and CAD among Jordanians. Methods: This case-control study included 269 patients diagnosed with CAD and 1026 subjects without CAD. Data collected from cases and controls included socio-demographic and clinical characteristics and anthropometric measurements. Patients were diagnosed with MeS based on the criteria of the National Cholesterol Education Program (NCEP) adult treatment panel (ATP) III. Results: MeS was present in 65.1% of patients with CAD and in 44.0% of those with no CAD (p<0.0005). After adjusting for the important variables in the multivariate analysis, those with MeS were twice more likely to have CAD (OR = 1.94, 95% CI: 1.29, 2.93, p = 0.002) compared to those without MeS. The number of metabolic abnormalities was significantly associated with CAD, when it substituted MeS in the regression model, with a higher number of MeS components led to greater odds for CAD. Conclusions: The MeS, which occurs very frequently in the general population, is associated with CAD in Jordan. The identification of subjects with the MeS is conceivably useful from a clinical standpoint, as it can be anticipated that these individuals should benefit from interventions aimed at reducing cardiovascular risk.
Advanced state clustering for very large vocabulary HMM-based on-line handwriting recognition

The paper presents some novel methods for the introduction of context dependent hidden Markov models (HMM) to online handwriting recognition. The use of these so-called n-graphs can lead to substantially improved modeling accuracy, but requires some intelligent parameter reduction methods (state clustering). This is especially the case for the investigated very large vocabulary system, incorporating an active vocabulary of 200000 words. Switching from context independent models to context dependent models-considering the underlying vocabulary-yields in the worst case to 25000 HMMs and very poor trainability for most of the introduced models. Therefore, the conducted investigations are focused on an appropriate state clustering method which is supported by decision trees and some new self organizing approaches to generate the required trees. The presented comparison takes also the different context dependencies (left, right or both sides) into consideration.