Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the MALDI Biotyper System Using Sepsityper Specimen Processing to Routine Microbiological Methods for Identification of Bacteria from Positive Blood Culture Bottles

ABSTRACT Bloodstream infections are a leading cause of admissions to hospital intensive care units and carry a high mortality rate. Clinical outcome can be greatly improved by early effective antibiotic therapy; therefore, broad-spectrum antimicrobial therapy is often initiated when there is a clinical suspicion of bloodstream infection. Unfortunately, this method may not always be effective when dealing with inherently resistant organisms and can also result in iatrogenic infection and the development of resistant isolates. Rapid identification of the infecting organism may aid in choosing appropriate antimicrobial therapy, thereby reducing these potential adverse events. We compared the matrix-assisted laser desorption ionization (MALDI) Biotyper system with Sepsityper specimen processing (Bruker Daltonics, Billerica, MA) to routine methods for the identification of microorganisms from 164 positive blood cultures. The MALDI Biotyper/Sepsityper identified 85.5% of bacterial isolates directly from positive monomicrobial blood cultures with 97.6% concordance to genus and 94.1% concordance to species with routine identification methods. Gram-negative isolates were more likely to produce acceptable confidence scores (97.8%) than Gram-positive isolates (80.0%); however, genus and species concordance with routine identification methods were similar in both groups. Reanalysis of collected spectra using modified blood culture-specific parameters resulted in an improved overall identification rate for Gram-positive bacteria (89.0%). Median times to identification using the MALDI Biotyper/Sepsityper were 23 to 83 h faster than routine methods for Gram-positive isolates and 34 to 51 h faster for Gram-negative isolates.
Angiotensin gene polymorphism as a determinant of posttransplantation renal dysfunction and hypertension.

BACKGROUND Polymorphism of the genes associated with angiotensin, including angiotensin-converting enzyme (ACE), angiotensinogen (AGT), and the type 1 (AT1) and type 2 (AT2) angiotensin II receptors, has been implicated in the pathophysiology of hypertension, ischemic heart disease, and progression of chronic renal disease. METHODS We investigated the impact of the ACE, AGT, AT1, and AT2 genotypes on renal allograft function in 148 patients (77 men, 71 women) who underwent transplantation over a 5-year period. Patients were genotyped using polymerase chain reaction sequence-specific primers and polymerase chain reaction followed by restriction fragment length polymorphism analysis. RESULTS ACE (D) and AGT (A/A) genotypes were associated with poorer chronic renal transplant function and more rapid chronic progression, defined as an increase of serum creatinine level with time. In addition, mean diastolic blood pressure at 3 years was significantly (P<0.02) correlated with C gene dose of AT1 (A-->C, 1166), with levels of 79+/-10 mmHg, 82+/-8.6 mmHg, and 95+/-8.3 mmHg for the A/A, A/C, and C/C genotypes, respectively. An apparent AT2 homozygote disadvantage could be an epiphenomenon because AT2 maps to the X chromosome, and males are homozygous for just one of the AT2 alleles (A/- or G/-). CONCLUSIONS Pretransplantation testing of the ACE, AGT, and AT1 genotypes may assist clinicians in identifying patients at risk for chronic renal transplant dysfunction and hypertension.
A Study Into Commanders’ Understanding Of, And Attitudes To, Stress And Stress-Related Problems

Objectives To undertake a tri-Service questionnaire survey to examine the commanders’ understanding of, and attitudes to, stress and stress-related problems. Methods A questionnaire was designed to elicit information on: Personal experience of stress and stress-related problems; Stress education; Pre-deployments briefings; and Post-incident stress debriefing. A total of 9,020 questionnaires were distributed between the three Services based on their proportional manning contribution to the Armed Forces as a whole. The population sampled ranged in rank from Corporal/Leading Rate up to, and including, Colonel/Captain RN/Group Captain (ranks below Leading Rate/Corporal were excluded because of their lack of command experience). The overall response rate was 55.8%. The study was carried out between September and December 2001 (i.e. pre-OP TELIC). Results Chronic work-based stressors were seen as most stressful when compared with family and health stressors. Most respondents accepted that stress and stress-related problems exist, but were reluctant to disclose their own stressrelated problems or seek help for fear that it might be detrimental both personally and professionally. There was found to be little support from peers or commanders. Little stress training was provided during recruit training, there were gaps in pre-deployment briefings and little in the way of post-deployment stress support. Conclusions Some of the more negative findings could have implications in terms of seeking help for stress-related problems at an early stage, which is counterproductive to the military’s genuine attempts to foster the psychological welfare of its employees. Some concerns could be alleviated by better and more timely stress education, preferably early on in a commander’s career, so that positive attitudes to stress and stressrelated problems can be formed and any negative attitudes changed, thereby bringing about a change in organisational culture in relation to stress. Some of the study’s concerns were addressed by the Operational Health Strategic Surveillance Committee which advised on operational health aspects of OP TELIC.
The Europe 2020 social inclusion indicators: main conclusions of the ImPRovE project on validity, methodological robustness and interrelationships

In 2010, heads of state and government agreed on the Europe 2020 poverty reduction target. The target is measured on the basis of a composite indicator, including income poverty, severe material deprivation and very low work intensity. In this paper, we summarise the main findings and conclusions of a series of studies carried out in the ImPRovE project, with regard to the quality of the three underlying indicators and their cross-sectional, longitudinal and dynamic relationships. By doing so, we point to relevant policy conclusions and areas for further improvement of the indicators and poverty research.
Accuracy of primary health care statistics reported by community based lady health workers in district Lahore.

OBJECTIVE To determine the accuracy of monthly reports submitted by lady health workers of National program for family planning and primary health care in district Lahore. METHODS A cross sectional descriptive study was conducted in district Lahore from November 2008 to February 2009. Forty lady health workers were selected using stratified random technique. Four monthly reports (one from each quarter of year 2008) submitted in health facilities by each lady health worker were retrieved from respective health facilities. These reports were then audited for accuracy using registers in health houses and verification of primary health care information in their respective communities. A scoring system was devised to grade reports for accuracy as good (80% and above score), satisfactory (60-70% score) and unsatisfactory (less than 60% score). RESULTS Out of 40 lady health workers (LHWs) interviewed, 32 (80%) had good knowledge, 6 (15%) had satisfactory knowledge, while 2 (5%) had unsatisfactory knowledge regarding data recording and reporting tools. Based on our scoring system, only 47.5% of reports were found accurate. In addition, 35% of reports contained missed entries, misreported data and factitious information. CONCLUSION There are significant gaps in recording and reporting of primary health care data in National programme for family planning and primary health care in district Lahore. Considering the utility of this data for health planning at district, provincial and national levels, adequate supervision and regular auditing should be carried out at health facility and district levels before onward transmission primary health care data to provincial and national levels.
A Customizable MT Evaluation Metric for Assessing Adequacy Machine Translation Term Project

This project describes a customizable MT evaluation metric that provides system-dependent scores for the purposes of tuning an MT system. The features presented focus on assessing adequacy over uency. Rather than simply examining features, this project frames the MT evaluation task as a classi cation question to determine whether a given sentence was produced by a human or a machine. Support Vector Machines are applied to the classi cation task and their con dence score forms the basis of the evaluation score. In addition, syntactic features are introduced via headword chain precision and recall features derived from dependency parses. Results are presented showing higher sentence-level correlation with adequacy than BLEU as well as an analysis of which features contribute most to assessing adequacy.
Spelling With a Small Mobile Brain-Computer Interface in a Moving Wheelchair

Research into brain-computer interfaces (BCIs), which spell words using brain signals, has revealed that a desktop version of such a speller, the edges paradigm, offers several advantages: This edges paradigm outperforms the benchmark row-column paradigm in terms of accuracy, bitrate, and user experience. It has remained unknown whether these advantages prevailed with a new version of the edges paradigm designed for a mobile device. This paper investigated and evaluated in a rolling wheelchair a mobile BCI, which implemented the edges paradigm on small displays with which visual crowding tends to occur. How the mobile edge paradigm outperforms the mobile row-column paradigm has implications for understanding how principles of visual neurocognition affect BCI speller use in a mobile context. This investigation revealed that all the advantages of the edges paradigm over the row-column paradigm prevailed in this setting. However, the reduction in adjacent errors for the edges paradigm was unprecedentedly limited to horizontal adjacent errors. The interpretation offered is that dimensional constraints of visual interface design on a smartphone thus affected the neurocognitive processes of crowding.
Smokeless Tobacco and Severe Active Periodontal Disease, NHANES III

Whereas smoking is a major risk factor for periodontal disease, the role of smokeless tobacco is unclear. The purpose of this US population-based study of 12,932 adults participating in the Third National Health and Nutrition Examination Survey was to evaluate the association between smokeless tobacco use and severe active periodontal disease. Univariable and multivariable logistic regression modeling quantified the associations between tobacco use and severe active periodontal disease. All adults and never-smokers who currently used smokeless tobacco were twice as likely to have severe active periodontal disease at any site [respective odds ratios (ORAdj) and 95% confidence intervals: ORAdj = 2.1; 1.2–3.7 and ORAdj = 2.1; 1.0–4.4] or restricted to any interproximal site [respective ORAdj = 2.1; 1.0–4.2 and ORAdj = 2.3; 0.9–6.3], simultaneously adjusted for smoking, age, race, gender, diabetes, and having a dental visit in the past year. These results indicate that smokeless tobacco may also be an important risk factor for severe active periodontal disease.
Newly Reported p.Asp240Asn Mutation in UBIAD1 Suggests Central Discoid Corneal Dystrophy Is a Variant of Schnyder Corneal Dystrophy

Purpose: To determine whether central discoid corneal dystrophy (CDCD), previously reported as a novel corneal dystrophy, is actually Schnyder corneal dystrophy (SCD) through screening of the UBIAD1 gene in the members of the family in which CDCD was reported. Methods: Genetic analysis was performed in 3 affected members and 1 unaffected member of a pedigree with CDCD including the affected 31-year-old proband. Results: All 4 affected members of the described pedigree demonstrated discoid central corneal clouding, with subtle, superficial, crystalline deposits noted in one of the affected individuals. Screening of UBIAD1 in the affected individuals demonstrated a previously unreported missense mutation, p.Asp240Asn, which was not identified in an unaffected family member or in 100 control individuals. Conclusions: The clinical findings of the family reported to have CDCD were indistinguishable from those found in SCD. However, CDCD was originally thought to be distinct from SCD because of the absence of positive lipid staining and the presence of alcian blue staining consistent with glycosaminoglycans in the proband's cornea. Our recent investigation has revealed that corneal specimens from other patients with SCD have also demonstrated staining for glycosaminoglycans. Discovery that mutations in UBIAD1 caused SCD allowed genetic testing of this CDCD family. Our newly reported UBIAD1 mutation suggests that CDCD is actually a variant of SCD. This report underscores the utility of genetic testing in determining whether newly described corneal dystrophies are in fact unique entities or just variants of well-known diseases.
Accountability and Accreditation: Putting Information Systems Accreditation into Perspective

Higher education in the United States has recently come under pressure from federal and state legislatures for failing to provide “value for money” because of an alleged lack of accountability and quality [U.S. Department of Education 2006]. This article will argue that, contrary to this view, institutes of higher learning have a rigorous quality assurance and accountability mechanism in place, namely accreditation, and that, moreover, the recent shift in accreditation from an input-based approach to an outcomes-based approach has resulted in improved programs that prepare graduates better than ever before for the workforce and/or further studies. These measures in fact are well applied in the field of information systems. The paper focuses on accreditation and the role of accreditation in ensuring quality in education. The work of agencies that are of most interest to information systems programs, namely the Association to Advance Collegiate Schools of Business (AACSB) and the Computing Accreditation Commission of ABET Inc (ABET CAC) is reviewed. The paper also describes a process to aid those interested in improving educational quality.
Low aerobic capacity and physical activity not associated with fatigue in patients with rheumatoid arthritis: a cross-sectional study.

OBJECTIVE To explore whether low aerobic capacity and physical activity are associated with fatigue, when controlling for age, gender, pain and depressive symptoms in persons with rheumatoid arthritis. METHODS In 60 individuals fatigue (Multidimensional Assessment of Fatigue scale; MAF), disease activity (Disease Activity Score-28; DAS 28), pain, physical and psychological status (Arthritis Impact Measurement Scales 2; AIMS 2), depression (Hospital Anxiety and Depression Scale; HADS), aerobic capacity and physical activity (Short Questionnaire to Assess Health-enhancing physical activity; SQUASH) were measured. Regression was performed to study the variance of fatigue explained by aerobic capacity and physical activity. RESULTS Mean (standard deviation (SD)) age of participants was 51.8 (SD 10.4) years and 73.3% were women. Duration of disease was 10.2 (SD 0-41) years and mean disease activity score was 3.4 (SD 1.4). Mean Global Fatigue Index was 20.3 (SD 10.5). Physical function was 1.6 (SD 1.1) and psychological status 3.1 (SD 0-8) on the AIMS2. Pain score was 4.1 (SD 2.0) and median depression score was 3.2 (range 0-15). Total amount of physical activity was 176.9 (10.6-1,492.3) METhours/week and VO2max was 27.8 (SD 3.8) ml/kg/min. Backward multiple regression showed a statistically significant relationship with depressive symptoms only (t = 5.4, p < 0.001), which explained 33% of variance of fatigue in patients with RA. CONCLUSION Depression, but not aerobic capacity or physical activity, contributed to fatigue. However, no relationship was found between aerobic capacity and fatigue.
Fluorescence In Situ Hybridization (FISH) as Primary Methodology for the Assessment of HER2 Status in Adenocarcinoma of the Breast: A Single Institution Experience

The demand for both reflexed and primary fluorescence in-situ hybridization (FISH) testing in the clinical setting is increasing. Relevant literature has reported the incidence of HER2 overexpression in 20% to 30% of cases, but some reports suggest that HER2 gene amplification rates are substantially lower. Published data, however, on primary FISH assessment from a single institution is limited, especially information about the frequency of the anomalous genotypes defined by FISH. We report our experience with primary FISH testing in 742 consecutive cases of breast cancer, in the calendar year 2006. Eighty percent (595/742) of the breast cancer cases were not amplified for HER2 (HER2/CEP17=0.8-1.9), whereas 19% (142/742) of cases were HER2 amplified (HER2/CEP17≥2.0). Among the HER2-amplified cases, 3% (19/742) were low-level amplified (HER2/CEP17 ratio=2.0–2.5). Genotypic heterogeneity, defined as >5% but <50% of the tumor cells demonstrating HER2 gene amplification, was observed in 5% (40/7242) of the cases. HER2 monoallelic deletion (HER2/CEP17≤0.7) was demonstrated in 2% (12/742) of the cases and CEP17 monosomy (1 CEP17 signal in >80% of tumor cells) was observed in 2% (13/742). Polysomy, if defined as CEP17 spot count 3.0 or more in at least80% of tumor cells, was observed in 3% (20/742) of the cases. These data may be helpful as benchmarks for other institutions initiating primary FISH analysis for HER2 genotyping.
Around-the-dock Attending Radiology Coverage is Essential to Avoid Mistakes in the Care of Trauma Patients

Financial constraints due to increasing operating cost and decreased reimbursement do not allow many hospitals to maintain coverage by attending radiologists around the clock (CARAC). Preliminary film readings by radiology trainees may be inaccurate. In trauma, decisions are made fast and are often based on these preliminary readings. To examine whether there are significant discrepancies between preliminary readings (PRs) and final readings (FRs) of CT scans of trauma patients we prospectively recorded PRs (done immediately by radiology residents) and FRs (done the following working day by radiology attendings) over a period of 6 months for trauma CT scans done between 5 pm and 7 am on weekdays or weekends. A discrepancy was classified as significant if a change in management was instituted after FR. In 42 of 383 (11%) trauma patients there was a discrepancy between PR and FR. Patients with discrepancies had a higher Injury Severity Score, higher incidence of penetrating trauma, longer hospital stay, higher hospital charges, and higher mortality than patients without any discrepancy. Most of the discrepancies were found on abdominal CT scans. The lower the level of radiology resident doing the PR the higher the likelihood of a discrepancy. In 20 patients (5%) a significant discrepancy was found. We conclude that the absence of CARAC results in inaccurate FRs risking optimal trauma patient care. The institutional savings realized by avoiding CARAC may be offset by the cost of additional care provided to patients who have delayed diagnosis and treatment due to the lack of it.
On updates of epistemic states: belief chance under incomplete information

In this dissertation I present some aspects of belief-change theory and representation of knowledge as one of the main theoretical basis to formulate semantics for updates of logic programs. Firstly, there is an introduction to relevant principles and postulates, like the classical belief-revision formulation and a following proposal to make a difference between belief revision and updates. Next, there is a survey of some few proposals to update logic programs that are the main motivation for this thesis. Finally, I present a progressive approach that overrides the problems pointed out in other alternatives, and that meets most of the principles here introduced. In particular, revising and updating knowledge bases is an important problem in knowledge representation and reasoning. It has led to various proposals for updating logic programs, specifically with respect to the well known answer-sets semantics. However, most of these approaches are based on the causal rejection principle, which leads to counter-intuitive behaviour. The proposed approach in this thesis is a semantics for abduction known as generalised answer sets, which allows one to choose potential models, without changing the semantics of the original given update programs. With generalised answer sets one can actually formulate semantics for updates that consist in choosing between generalised models that satisfy an intended set of properties and overcome certain problems from other approaches. Weak Irrelevance of Syntax and Strong Consistency are two of the main properties an update semantics should manifest, which are a keystone to overcome the mentioned problems. Finally, as an important component of logic programming and as a useful tool in the classroom, this work also provides the research community with online solver prototypes that help close the gap between theory and practice. These automatic testbeds make the semantics more accessible, and open up a path with a solid component for further more-complex prototypes of knowledge management.
Adhesion of Nongerminated Botrytis cinerea Conidia to Several Substrata

Conidia of the plant pathogenic fungus Botrytis cinerea adhered to tomato cuticle and to certain other substrata immediately upon hydration. This immediate adhesion occurred with both living and nonliving conidia. Adhesion was not consistently influenced by several lectins, sugars, or salts or by protease treatment, but it was strongly inhibited by ionic or nonionic detergents. With glass and oxidized polyethylene, substrata whose surface hydrophobicities could be conveniently varied, there was a direct relationship between water contact angle and percent adhesion. Immediate adhesion did not involve specific conidial attachment structures, although the surfaces of attached conidia were altered by contact with a substratum. Freshly harvested conidia were very hydrophobic, with more than 97% partitioning into the organic layer when subjected to a phase distribution test. Percent adhesion of germinated conidia was larger than that of nongerminated conidia. Evidence suggests that immediate adhesion of conidia of B. cinerea depends, at least in part, on hydrophobic interactions between the conidia and substratum.