Miracle-dz/UniFAR-FTUs huggingface dataset:
H pylori antibiotic resistance: prevalence, importance, and advances in testing

The discovery that Helicobacter pylori infection is the main cause of most gastroduodenal diseases has been a major breakthrough in gastroenterology. It has dramatically changed the management of these diseases which are now considered as infectious diseases and are treated with antibiotics. Triple therapy, including two antibiotics, amoxicillin and clarithromycin, and a proton pump inhibitor given for a week has been recommended as the treatment of choice at several consensus conferences.1–6 However, this treatment may fail for several reasons, as reported elsewhere.7 In fact, the main reason for failure was found to be H pylori resistance to one of the antibiotics used (that is, clarithromycin). Other treatments have also been proposed, including metronidazole, a drug for which resistance is also a problem although to a lesser extent, as well as tetracycline, fluoroquinolones, and rifamycins for which resistance has become an emerging issue.8,9 Our aim was to review the prevalence of H pylori resistance to these various antibiotics, their clinical importance, and methods of testing, especially in light of the resistance mechanism which allows application of molecular methods. Numerous studies have been performed to determine the prevalence of H pylori resistance to antibiotics. However, many of them have drawbacks, in particular concerning the number and representativeness of the strains tested. Most of the studies were performed in specialised centres, with recruitment of special cases which are not always representative of patients as a whole and, because these studies are monocentric, the number of patients may be low, leading to wide confidence intervals of the prevalence rates obtained. Ideal studies involving patients who are representative of a given region are few. An alternative has been to analyse prevalence data obtained from clinical trials aiming to evaluate new regimens. As prevalence is in essence an evolving phenomenon, only …
A Novel Transcriptional Mechanism of Cell Type–Specific Regulation of Vascular Gene Expression by Glucose

Objective—Vascular diabetic complications are associated with abnormal extracellular matrix and dysfunction of vascular cells, which later result in aberrant angiogenesis and development of atherosclerotic lesions. The tissue and cell specificity of the effects of high glucose are well recognized, but the underlying cell type–specific molecular mechanisms controlled by glucose are still unclear. We sought to identify cell type–specific mechanisms by which high glucose regulates transcription of genes in vascular cells. Methods and Results—Thrombospondin-1 is a potent antiangiogenic protein associated with development of several diabetic complications and regulated by high glucose in multiple cell types. We report that distinct cell type–specific mechanisms regulate thrombospondin-1 gene (THBS1) transcription in endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) in response to high glucose: although a proximal fragment of 280 nucleotides is sufficient to drive transcription in ECs, THBS1 was regulated cooperatively by interaction between proximal (−272 to −275) and distal (−1016 to −1019) promoter elements in VSMCs. Transcription factors activated by high glucose in VSMCs were cell type–specific. The formation of a single complex interacting with both distal and proximal glucose-responsive elements of THBS1 promoter in VSMCs was confirmed using gel-shift assays, binding sequence decoy oligomers, and specific mutant promoter fragments. Conclusion—Transcriptional response of vascular cells to high glucose is cell type–specific and involves activation of distinct transcription factors, providing a basis for tissue-specific changes of vasculature in diabetics.
Seiberg-Witten Equations on Three-manifolds with Euclidean Ends

We construct the Seiberg-Witten theory on 3-manifolds with Euclidean ends (connected sums of $\R^3$ and a compact manifold) with perturbations which approximate $*dx_3$ at infinity, and describe the structure of the moduli spaces. The setup is inspired by Taubes's program of relating the 4-dimensional Seiberg-Witten invariant with `singular Gromov invariants' and has related applications.
International prognostic index is the best prognostic factor for survival in patients with AIDS-related non-Hodgkin's lymphoma treated with CHOP. A multivariate study of 46 patients.

BACKGROUND AND OBJECTIVE The management of non-Hodgkin's lymphomas (NHL) in AIDS is difficult because of the poor bone marrow reserve and immunosuppression of these patients. Combination chemotherapy is the treatment of choice in the subset of patients with good performance status and mild immunosuppression. Several combination chemotherapy regimens have been used in these patients but the results have been poor. We have studied the clinical and biological features, response to treatment, outcome and prognostic factors of 46 patients with NHL and HIV infection, diagnosed in a single institution between January 1988 and June 1997. DESIGN AND METHODS Forty-six patients with NHL and HIV infection were treated with CHOP. Patients with previously treated systemic NHL, primary CNS NHL, performance status > 2 and active AIDS-defining opportunistic or neoplastic diseases were excluded. The parameters evaluated were: age, sex, risk activity, basic hematologic and biochemical parameters, CD4 lymphocyte count, B symptoms, stage (Ann Arbor), histologic subtype (REAL classification), International Prognostic Index (IPI), response to treatment, relative dose intensity (RDI), relapse free survival (RFS) and overall survival (OS). Uni- and multivariate analyses of prognostic factors were performed. RESULTS Median age was 35 years and 40 patients were male. CD4 lymphocyte count was lower than 0.1 x 10(9)/L in 18 out of 38 cases, hypoalbuminemia was registered in 24 (52%), serum LDH was higher than 400 U/L in 20 (43%) and beta 2-microglobulin was higher than the normal range in 9 out of 20 patients (45%). Complete response was achieved in 18 patients (40%). Twenty-six patients received G-CSF after chemotherapy. Grade 4 neutropenia and fever were significantly more frequent in patients who did not receive G-CSF. Serum LDH > 400 U/L and hypoalbuminemia were the only parameters associated with a lower probability to achieve complete response (p = 0.015 and p = 0.025, respectively). The median RFS was 26 (6-47) months and no variable was found to have statistically significant influence on it. The median OS was 9.2 (4.5-14) months, and IPI score 1 and ESR < 60 mm/h were the only parameters identified as good prognostic factors in the multivariate analysis (p = 0.03 and 0.049, respectively). INTERPRETATION AND CONCLUSIONS In spite of patient selection, the response to CHOP treatment in patients with NHL and HIV infection remains poor. Episodes of neutropenic fever are less frequent when G-CSF is administered after CHOP. The IPI score 1 is the most important favorable prognostic factor for survival.
The Johnny 2 Standardized Secure Messaging Scenario

We present a scenario for user testing secure messaging tools and anti-phishing technology. The scenario, Johnny 2, is loosely based on the scenario that Whitten and Tygar presented in their acclaimed paper “Why Johnny Can’t Encrypt,”[14], but provided with significantly refined detail and automation. We recently used this scenario successfully in a user test with 43-subjects. We hope that by developing and using standardized user test scenarios, research conducted by researchers in the field of usability and security can be more easily compared and contrasted.
Prognostic Importance of Pathophysiologic Markers in Patients With Heart Failure and Preserved Ejection Fraction

Background— Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome associated with multiple pathophysiologic abnormalities, including left ventricular (LV) diastolic dysfunction, longitudinal LV systolic dysfunction, abnormal ventricular-arterial coupling, pulmonary hypertension, and right ventricular (RV) remodeling/dysfunction. However, the relative prognostic significance of each of these pathophysiologic abnormalities in HFpEF is unknown. Methods and Results— We prospectively studied 419 patients with HFpEF using echocardiography and sphygmomanometry to assess HFpEF pathophysiologic markers. Cox proportional hazards analyses were used to determine the associations between pathophysiologic markers and outcomes. Mean age was 65±12 years; 62% were women; 39% were black; comorbidities were common; and study participants met published criteria for HFpEF. RV abnormalities were frequent: 28% had abnormal tricuspid annular plane systolic excursion, 15% had reduced RV fractional area change, and 34% had RV hypertrophy. During a median follow-up time of 18 months, 102 (24%) were hospitalized for HF and 175 (42%) experienced the composite end point of cardiovascular hospitalization or death. Decreased LV compliance, measured as reduced LV end-diastolic volume at an idealized LV end-diastolic pressure of 20 mm Hg (EDV20), and RV remodeling, as indicated by increased RV wall thickness, were the 2 pathophysiologic markers most predictive of worse outcomes: adjusted hazard ratio per 1 SD decrease in EDV20=1.39 (95% confidence interval [CI], 1.10–1.75; P=0.006), and hazard ratio per 1 SD increase in RV wall thickness=1.37 (95% CI, 1.16–1.61; P<0.001). These associations persisted after additional adjustment for markers of HF severity. By contrast, markers of LV relaxation, longitudinal LV systolic dysfunction, and ventricular-arterial coupling were not significantly associated with adverse outcomes. Conclusions— In patients with HFpEF, reduced LV compliance and RV remodeling are the strongest pathophysiologic predictors of adverse outcomes.
The design and analysis of split‐mouth studies: What statisticians and clinicians should know

The split‐mouth design is a popular design in oral health research. In the most common split‐mouth study, each of two treatments are randomly assigned to either the right or left halves of the dentition. The attractiveness of the design is that it removes a lot of inter‐individual variability from the estimates of the treatment effect. However, already about 20 years ago the pitfalls of the design have been reported in the oral health literature. Yet, many clinicians are not aware of the potential problems with the split‐mouth design. Further, it is our experience that most statisticians are not even aware of the existence of this design. Since most of the critical remarks appeared in the oral health literature, we argue that it is necessary to introduce the split‐mouth design to a statistical audience, so that both clinicians and statisticians clearly understand the advantages, limitations, statistical considerations, and implications of its use in clinical trials and advise them on its use in practice. Copyright © 2009 John Wiley & Sons, Ltd.
Radiotherapy and short-term androgen deprivation for localized prostate cancer.

BACKGROUND It is not known whether short-term androgen-deprivation therapy (ADT) before and during radiotherapy improves cancer control and overall survival among patients with early, localized prostate adenocarcinoma. METHODS From 1994 through 2001, we randomly assigned 1979 eligible patients with stage T1b, T1c, T2a, or T2b prostate adenocarcinoma and a prostate-specific antigen (PSA) level of 20 ng per milliliter or less to radiotherapy alone (992 patients) or radiotherapy with 4 months of total androgen suppression starting 2 months before radiotherapy (radiotherapy plus short-term ADT, 987 patients). The primary end point was overall survival. Secondary end points included disease-specific mortality, distant metastases, biochemical failure (an increasing level of PSA), and the rate of positive findings on repeat prostate biopsy at 2 years. RESULTS The median follow-up period was 9.1 years. The 10-year rate of overall survival was 62% among patients receiving radiotherapy plus short-term ADT (the combined-therapy group), as compared with 57% among patients receiving radiotherapy alone (hazard ratio for death with radiotherapy alone, 1.17; P=0.03). The addition of short-term ADT was associated with a decrease in the 10-year disease-specific mortality from 8% to 4% (hazard ratio for radiotherapy alone, 1.87; P=0.001). Biochemical failure, distant metastases, and the rate of positive findings on repeat prostate biopsy at 2 years were significantly improved with radiotherapy plus short-term ADT. Acute and late radiation-induced toxic effects were similar in the two groups. The incidence of grade 3 or higher hormone-related toxic effects was less than 5%. Reanalysis according to risk showed reductions in overall and disease-specific mortality primarily among intermediate-risk patients, with no significant reductions among low-risk patients. CONCLUSIONS Among patients with stage T1b, T1c, T2a, or T2b prostate adenocarcinoma and a PSA level of 20 ng per milliliter or less, the use of short-term ADT for 4 months before and during radiotherapy was associated with significantly decreased disease-specific mortality and increased overall survival. According to post hoc risk analysis, the benefit was mainly seen in intermediate-risk, but not low-risk, men. (Funded by the National Cancer Institute; RTOG 94-08 ClinicalTrials.gov number, NCT00002597.).
Aligning clinical practice to PTSD treatment guidelines: medication prescribing by provider type.

OBJECTIVE Veterans with posttraumatic stress disorder (PTSD) are frequently prescribed psychiatric medications that are currently not supported by a guideline developed by the U.S. Department of Veterans Affairs and the U.S. Department of Defense. To better understand this practice, this study examined prescribing frequencies for three classes of psychiatric medications and the proportion of prescribing attributable to various provider types. METHODS This cross-sectional study analyzed fiscal year 2009 electronic pharmacy data from the Veterans Health Administration (VHA) for 356,958 veterans with PTSD who were receiving medications from VHA prescribers. Veterans had at least one VHA encounter with a diagnostic code of PTSD and evidence of continuous medication use. Medications of interest were selective serotonin-norepinephrine reuptake inhibitors (SSRI/SNRIs), second-generation antipsychotic medications, and benzodiazepines. Analyses described the proportion of prescribing attributable to mental health care providers and primary care providers for each medication class. RESULTS In 2009, among all veterans with PTSD who had continuous VA medication use, 65.7% were prescribed SSRI/SNRIs, and 70.2% of this prescribing was attributable to mental health care providers. Second-generation antipsychotics were prescribed for 25.6% of these veterans, and 80.2% of the prescribing was attributable to mental health care providers. Benzodiazepines were prescribed for 37.0% of the sample, and 68.8% of the prescribing was attributable to mental health care providers. CONCLUSIONS The findings indicate that veterans with PTSD were frequently prescribed medications not supported by existing guidelines. Most of these prescriptions were written by mental health care providers. Interventions to align prescribing with PTSD treatment guidelines should emphasize provider type.
▼Ezetimibe – an update

▼Ezetimibe (Ezetrol – MSD-Schering Plough) is a lipid-lowering drug that reduces plasma concentrations of low-density lipoprotein (LDL) cholesterol and total cholesterol when used alone or in combination with a statin.1 In 2004, we could find no evidence on the effects of ezetimibe on cardiovascular morbidity and mortality and concluded that it should not replace a statin in the routine management of patients at increased risk of developing complications of atherosclerotic disease.1 Since then, a fixed-dose combination product, containing simvastatin and ezetimibe (▼Inegy – MSD-Schering Plough), has been launched in the UK, and new evidence on the safety and efficacy of ezetimibe has been published. Here we reconsider ezetimibe in light of the new product and data.
Heterogeneous Decision Diagrams for Applications in Harmonic Analysis on Finite Non-Abelian Groups

Spectral techniques on Abelian groups are a well-established tool in diverse fields such as signal processing, switching theory, multi-valued logic and logic design. The harmonic analysis on finite non-Abelian groups is an extension of them, which has also found applications for particular tasks in the same fields. It takes advantages of the peculiar features of the domain groups and their dual objects. Representing unitary irreducible representations, that are kernels of Fourier transforms on non-Abelian groups, in a compact manner is a key task in this area. These representations are usually specified in terms of rectangular matrices with matrix entries. Therefore, the problem of their efficient representations can be viewed as handling large rectangular matrices with matrix-valued entries. Quantum Multiple-valued Decision Diagrams (QMDDs) and Heterogeneous Decision Diagrams (HDDs) have been used for representation of matrices with numerical values, under some restrictions to the order of matrices to be represented. In this paper, we present a generalization of this concept for the representation of rectangular matrices with matrix-valued entries. We also demonstrate an implementation of an XML-based software package aimed at handling such data structures.
Stimulated Brillouin Scattering in Ultrahigh-Speed In-Phase RZ and CS-RZ OTDM Transmission

We report that stimulated Brillouin scattering (SBS) plays an important role in ultrahigh-speed bitwise phase-controlled optical time-division multiplexing transmissions such as in-phase and carrier-suppressed return-to-zero (RZ). We show that the optical power can easily exceed the SBS threshold for such high-speed coherent RZ signals. The SBS-induced performance limitation in a 160-Gb/s-520 km transmission is described in detail.
Passive and active nonlinear fault-tolerant control of a quadrotor unmanned aerial vehicle based on the sliding mode control technique

In this paper, an augmented sliding mode-based fault-tolerant control is designed theoretically, implemented practically and tested experimentally in a quadrotor unmanned aerial vehicle testbed under propeller damage and actuator fault conditions for tracking control. In view of the significant feature of robustness inherent to the sliding mode control technique, the developed sliding mode-based fault-tolerant control strategies have been designed and implemented in the two currently and widely used types of fault-tolerant control strategy, i.e. passive and active, with the intention to investigate and compare the advantages, disadvantages and application considerations and limitations of these two different fault-tolerant control strategies in the tracking control problem of a quadrotor unmanned aerial vehicle application. Therefore, these two types of controller have been carried out in both theory and practice with and without the presence of faults. Both theoretical and experimental analyses demonstrated the effectiveness of the two sliding mode-based fault-tolerant control strategies in the application to the quadrotor unmanned aerial vehicle under a small level of actuator faults or damage. Detailed comparisons are also provided in the paper to demonstrate the capabilities, advantages and disadvantages of the two types of fault-tolerant tracking controller under different flight conditions in the presence of actuator faults and propeller damage.
Comparative studies of type X collagen expression in normal and rachitic chicken epiphyseal cartilage

The levels of type X collagen in mineralizing normal chicken epiphyses and nonmineralizing rachitic chicken tibial epiphyses were measured and compared. Qualitative immunoperoxidase studies with anti-chick type X collagen monoclonal antibodies on sections from normal and rachitic cartilage demonstrated that the type X collagen levels in rachitic growth plates are reduced. Northern hybridization of mRNA and biosynthetic studies have confirmed that type X collagen synthesis in rickets is also decreased. In hypocalcemic rickets, the level of type X collagen mRNA is reduced by 80% whereas the level of type X collagen mRNA is only reduced by 50% in normocalcemic rickets. These observations provide additional evidence that type X collagen is involved in the process of cartilage mineralization and also suggest that the partial recovery of type X collagen synthesis in normocalcemic rickets may be related to the elevated plasma concentration of calcium. Calcium concentration may therefore play an important role in the control of type X collagen synthesis.
Contribution of arm swing to dynamic stability based on the nonlinear time series analysis method

It is human nature to swing their arms at the frequency of leg motion during walking, but the contribution of arm swing to dynamic stability of human motion segments was poorly understood. Based on the nonlinear time series analysis method, the objective of this study was to investigate the effects of arm swing in three conditions (natural, active and restricted arm swing) on the dynamic stability of spine and lower extremity joints, and to further assess the contribution of arm swing to the human dynamic stability in relation with age. Gait experiments were carried out for 10 young and 8 middle-aged healthy volunteers while walking with natural, active and restricted arm swing. The maximum finite time lyapunov exponents were calculated to quantify the local dynamic stability of spine and lower extremity joints under three arm swing conditions, and the percentage change of the maximum Lyapunov exponents was compared between two groups to evaluate the effectiveness of active arm swing in relation with age. For both young and middle-aged groups, no significant difference of the maximum lyapunov exponents of all motion segments was found between walking with natural arm swing and with restricted arm swing (P>;0.05). However, the maximum lyapunov exponents of all motion segments while walking with active arm swing was significantly lower than those while walking with natural arm swing and restricted arm swing, respectively (P<;0.05), and the percentage decrease of the maximum lyapunov exponents for all motion segments while walking with active arm swing was significantly higher in middle-aged group than in young group (P<;0.05). These results indicated that active arm swing would help to improve dynamic stability of human motion segments, especially more effective with age.