nils-herrmann/clean_scirepeval huggingface dataset:
The performance of MRI-based cerebral blood flow measurements in acute and subacute stroke compared with 15O-water positron emission tomography: identification of penumbral flow.

Perfusion-weighted MRI-based maps of cerebral blood flow (CBF(MRI)) are considered a good MRI measure of penumbral flow in acute ischemic stroke but are seldom used in clinical routine due to methodical issues. We validated CBF(MRI) on quantitative CBF measurement by 15O-water positron emission tomography (CBF(PET)).



Comparative CBF(MRI) and CBF(PET) were performed in patients with acute and subacute stroke. In a voxel-based seed-growing technique, predefined CBF(MRI) thresholds (<40, <30, <20, <10 mL/100 g/min) were applied and the resulting volumes were compared with the hypoperfusion volume detected by the penumbral threshold (<20 mL/100 g/min) on CBF(PET). The volumetric comparison was expressed as the C-ratio (volume CBF(MRI)/volume CBF(PET)) to identify the best MRI threshold. The influence of vessel pathology, hypoperfusion size, and time point of imaging was described. The proportion of voxels correctly classified as hypoperfused and the proportion of voxel correctly classified as nonhypoperfused of the best CBF(MRI) threshold was calculated and a Bland-Altman plot illustrated the method-specific differences.



In 24 patients (median time MRI to PET: 68 minutes; 16 patients imaged within 24 hours after stroke), the median volume of hypoperfusion <20 mL/100 g/min (CBF(PET)) was 78.5 cm(3). Median hypoperfusion volume on CBF(MRI) ranged from 245.9 cm(3) (<40 mL/100 g/min) to 35.5 cm(3) (<10 mL/10 g/min). On visual inspection, an excellent qualitative congruence was found. The quantitative congruence was best for the MRI-CBF threshold <20 mL/100 g/min (median C-ratio: 1.0), reaching a proportion of voxels correctly classified as hypoperfused of 76% and a proportion of voxel correctly classified as nonhypoperfused of 96%, but a wide interindividual range (C-ratio 0.3 to 3.5) was found. Ipsilateral vessel pathology, time point of imaging, and size of hypoperfusion did not significantly influence the C-ratio. The Bland-Altman analysis for the volumetric difference of CBF(MRI) and CBF(PET) found a good overall agreement but a large SD.



Hypoperfusion areas below the CBF(PET) penumbral threshold can be well identified by the CBF(MRI) threshold <20 mL/10 g/min at a group level, but a large individual variance (exceeding 20% of volume in nearly half of the patients) could not be explained. Our results support a prudent use of MRI-based quantitative CBF measurement in clinical routine.
BK polyomavirus reactivation after reduced-intensity double umbilical cord blood cell transplantation.

Serial serum samples from 27 patients who underwent double umbilical cord blood transplantation (dUCBT) were analyzed for BK polyomavirus (BKPyV) DNA by real-time PCR and BKPyV-specific immune globulin by ELISA. Clinical data were collected on all patients. All pre-transplant sera had detectable anti-BKPyV IgG. Fifteen patients (56%) had detectable serum BKPyV DNA (median 8.9 × 10(4) copies/ml; range 4.1 × 10(3)-7.9 × 10(6) copies/ml) a median of 40 days (range, 27-733 days) after dUCBT, with highest viral loads on Day 100 assessment. The cumulative probability of developing BKPyV viremia by Day 100 was 0.52 (95% CI, 0.33-0.71). Six of 15 patients with BKPyV viremia experienced hemorrhagic cystitis by Day 100. By Day 100, there was a trend towards higher BKPyV viral loads in sera of patients with hemorrhagic cystitis than in those BKPyV viremic patients without hemorrhagic cystitis (p = 0.06). BKPyV viremia was associated with significantly higher anti-BKPyV IgM values at 6 months post-dUCBT (P = 0.003). BKPyV viremia occurs early after dUBCT and is associated with a detectable humoral immune response by 6 months post-dUBCT.
Prosthetic fitting, use, and satisfaction following lower-limb amputation: a prospective study.

Providing a satisfactory, functional prosthesis following lower-limb amputation is a primary goal of rehabilitation. The objectives of this study were to describe the rate of successful prosthetic fitting over a 12 mo period; describe prosthetic use after amputation; and determine factors associated with greater prosthetic fitting, function, and satisfaction. The study design was a multicenter prospective cohort study of individuals undergoing their first major lower-limb amputation because of vascular disease and/or diabetes. At 4 mo, unsuccessful prosthetic fitting was significantly associated with depression, prior arterial reconstruction, diabetes, and pain in the residual limb. At 12 mo, 92% of all subjects were fit with a prosthetic limb and individuals with transfemoral amputation were significantly less likely to have a prosthesis fit. Age older than 55 yr, diagnosis of a major depressive episode, and history of renal dialysis were associated with fewer hours of prosthetic walking. Subjects who were older, had experienced a major depressive episode, and/or were diagnosed with chronic obstructive pulmonary disease had greater functional restriction. Thus, while most individuals achieve successful prosthetic fitting by 1 yr following a first major nontraumatic lower-limb amputation, a number of medical variables and psychosocial factors are associated with prosthetic fitting, utilization, and function.
The US7 score is sensitive to change in a large cohort of patients with rheumatoid arthritis over 12 months of therapy

To determine the sensitivity to change of the US7 score among RA patients under various therapies and to analyze the effect of each therapeutic option over 1 year. To estimate predictors for development of destructive bone changes.



Musculoskeletal ultrasound (US7 score), DAS28, CRP and ESR were performed in 432 RA patients at baseline and after 3, 6 and 12 months. The cohort was divided into four sub-groups: first-line DMARDs (Group 1; 27.3%), therapy switch: DMARDs to second DMARDs (Group 2; 25.0%), first-line biologic after DMARDs therapy (Group 3; 35.4%) and therapy change from biologic to second biologic (Group 4; 12.3%).



The US7 synovitis and tenosynovitis sum scores in grey-scale (GSUS) and power Doppler ultrasound (PDUS) as well as ESR, CRP decreased significantly (p<0.05) after 12 months in group 1 to 3. Group 1+2 also illustrated a significant change of DAS28 after 1 year (p<0.001). Only in Group 4, the US7 erosion sum score decreased significantly from 4.3 to 3.6 (p=0.008) after 1 year. Predictors capable of forecasting US erosions after one year were: higher score of US7 synovitis (p<0.001), of US7 erosions in GSUS (p<0.001), as well as of DAS28 (p<0.001) at baseline.



The comparable developments of the US7 score with clinical and laboratory data illustrates its potential to reflect therapeutic response. Therefore, the novel US7 score is sensitive to change. Patients who switched from one biologic to another exhibited a significant decline in erosions after 12 months, while the erosions scores in the other groups were stable.
Phase I dose escalation trial of feverfew with standardized doses of parthenolide in patients with cancer

Feverfew is a botanical product that contains parthenolide. Parthenolide has in vitro and in vivo anti-tumor and anti-angiogenic activity. Feverfew has been used extensively without any formal pharmacokinetic analysis. A Phase I trial was conducted to evaluate the pharmacokinetics and toxicity of parthenolide given as a component of “feverfew.”  Feverfew (Tanacet™) was administered as a daily oral tablet in a 28-day cycle. A starting dose of 1 mg per day was explored with subsequent dose escalations to 2, 3, and 4 mg. Assessment of plasma pharmacokinetics was performed on patients accrued to the trial. Solid phase extraction and mass spectroscopy were used to evaluate parthenolide plasma concentrations. The limit of detection for parthenolide in plasma was 0.5 ng/ml. Patients were evaluated for response after every two cycles.  Feverfew given on this schedule had no significant toxicity, and the maximum tolerated dose was not reached. When parthenolide was administered at doses up to 4 mg as a daily oral capsule in the feverfew preparation, there was not detectable concentration in the plasma. Because of this, parthenolide pharmacokinetics were not able to be completed.  Feverfew, with up to 4 mg of parthenolide, given daily as an oral tablet is well tolerated without dose-limiting toxicity, but does not provide detectable plasma concentrations. Purification of parthenolide for administration of higher doses will be needed.
Minimally invasive total disc replacement: surgical technique and preliminary clinical results

Total disc replacement has become an option for the treatment of degenerative disc disease of the lumbar spine. A new generation of implants has been developed that can be implanted through minimally invasive anterior approaches to the lumbar levels L2/3, L3/4, L4/5 and L5/S1. However mid- and long-term data are still lacking. This paper describes the minimally invasive surgical approach – techniques as well as the preliminary results of our first 34 consecutive patients. The intervertebral spaces L5/S1, L4/5, L3/4 and L2/3 were each approached through slightly different, but standardized, mini-laparotomies either through a retroperitoneal or a transperitoneal route. The clinical results with a follow-up of up to 1 year show satisfactory outcomes in about 80% of the patients. Oswestry score as well as VAS values show significant changes during the postoperative course. There have been three complications (8.8%), two of which were specific to the implantation process, but were resolved with a good clinical outcome in both patients. The preliminary results suggest that total disc replacement may become a reasonable alternative to spinal fusion under the selection criteria used in this study.
The relationship between mitral regurgitation and ejection fraction as predictors for the prognosis of patients with heart failure.

To study whether there is interaction between mitral regurgitation (MR) and left ventricular ejection fraction (LVEF) in the mortality risk of heart failure (HF) patients.



We studied a large group of patients hospitalized for symptoms and clinical signs of HF in the period 2001-02. Mitral regurgitation was diagnosed on echocardiography and qualitatively graded as no/trace, mild, moderate, and severe using the colour Doppler method. Median follow-up time was 4.5 years. Three thousand and seventy-eight patients with HF were included, of whom 1890 patients (61%) had no/trace MR, 628 (20%) had mild MR, 452 (15%) had moderate MR, and 108 (4%) had severe MR. During follow-up, 1660 deaths (54%) were registered. In univariate analysis, increasing severity of MR carried an increasing mortality risk, hazard ratio (HR) 1.10, 95% confidence interval (CI) 1.04-1.16, P = 0.0006 for each increasing degree of MR. In multivariable analysis, with adjustments made for age, sex, ejection fraction, serum creatinine, presence of ischaemic heart disease, chronic obstructive pulmonary disease, diabetes, and stroke, similar results were found, but only in patients with LVEF<25%, HR 1.14, 95% CI 1.03-1.26, P = 0.01 for each increasing degree of MR. This risk was driven by moderate and severe MR. For patients with LVEF≥25% the HR was 0.91, 95% CI 0.82-1.03, P = 0.2 for each increasing degree of MR.



Mitral regurgitation has a negative effect on prognosis of patients with HF, but only in patients with severely reduced LVEF.
Evolution of the clinical manifestations of infection during the course of febrile neutropenia in patients with malignancy

The impact of a standardized set of diagnostic interventions on the further management of 968 episodes of fever in neutropenic cancer patients who did not respond to initial therapy was assessed prospectively. At the onset of fever, 65% of patients had no additional signs of infection, whereas skin and soft tissue infections were present in 12% and clinical sepsis and gastrointestinal infections in 8% each. After 72h, 41% of the fevers still remained unexplained. New foci of infection emerged in 11% of the cases involving mainly the lungs, skin and soft tissues, and urinary tract. The presence of a lower respiratory tract infection or a microbiologically defined infection of any sort was associated with higher mortality than other types of infection were. Changes in initial antibiotic therapy were, based on the results of the diagnostic measures specified in the protocol in only 15% of the cases.
RADAR – A randomised, multi-centre, prospective study comparing best medical treatment versus best medical treatment plus renal artery stenting in patients with haemodynamically relevant atherosclerotic renal artery stenosis

Prospective, international, multi-centre, randomised (1:1) trial to evaluate the clinical impact of percutaneous transluminal renal artery stenting (PTRAS) on the impaired renal function measured by the estimated glomerular filtration rate (eGFR) in patients with haemodynamically significant atherosclerotic renal artery stenosis.



Patients will be randomised to receive either PTRAS using the Dynamic Renal Stent system plus best medical treatment or best medical treatment. Renal stenting will be performed under angiographic imaging. For patients randomised to best medical treatment the degree of stenosis measured by renal duplex sonography (RDS) will be confirmed by MR angio or multi-slice CT where possible. Best medical treatment will be initiated at randomisation or post procedure (for PTRAS arm only), and adjusted as needed at all visits. Best medical treatment is defined as optimal drug therapy for control of the major risk factors (blood pressure < or = 125/80 mmHg, LDL cholesterol < or = 100 mg/dL, HbA1c < or = 6.5%). Data recordings include serum creatinine values, eGFR, brain natriuretic peptide, patients' medical history and concomitant medication, clinical events, quality of life questionnaire (SF-12v2), 24 hour ambulatory blood pressure measurement, renal artery duplex ultrasound and echocardiography. Follow-up intervals are at 2, 6, 12 and 36 months following randomisation.The primary endpoint is the difference between treatments in change of eGFR over 12 months. Major secondary endpoints are technical success, change of renal function based on the eGFR slope change between pre-treatment and post-treatment (i.e. improvement, stabilisation, failure), clinical events overall such as renal or cardiac death, stroke, myocardial infarction, hospitalisation for congestive heart failure, progressive renal insufficiency (i.e. need for dialysis), need of target vessel revascularisation or target lesion revascularisation, change in average systolic and diastolic blood pressure, change in left ventricular mass index calculated from echocardiography, difference in the size of kidney (pole to pole length) measured by renal duplex sonography, total number, drug name, drug class, daily dose, regimen and Defined Daily Dose (DDD), of anti-hypertensive drugs, and change in New York Heart Association (NYHA) classification. Approximately 30 centres in Europe and South America will enrol patients. Duration of enrolment is expected to be 12 months resulting in study duration of 48 months.
A concept lattice-based event model for Cyber-Physical Systems

Cyber-Physical Systems (CPS) involve communication, computation, sensing, and actuating through heterogeneous and widely distributed physical devices and computational components. The close interactions of these systems with the physical world places events as the major building blocks for the realization of CPS. More specifically, the system components and design principles should be revisited with a strictly event-based approach. In this paper, a concept lattice-based event model for CPS is introduced. Under this model, a CPS event is uniformly represented by three components: event type, its internal attributes, and its external attributes. The internal and external attributes together characterize the type, spatiotemporal properties of the event as well as the components that observe it. A set of event composition rules are defined where the CPS event composition is based on a CPS concept lattice. The resulting event model can be used both as an offline analysis tool as well as a run-time implementation model due to its distributed nature. A real-life smart home example is used to illustrate the proposed event model. To this end, a CPS event simulator is implemented to evaluate the developed event model and compare with the existing Java implementation of the smart home application. The comparison result shows that the event model provides several advantages in terms of flexibility, QoS support, and complexity. The proposed event model lay the foundations of event-based system design in CPS.
Demographic and social profile of epilepsy in a vulnerable low-income population in Bogotá, Colombia.

Very few studies describe the demographic and social profile of epilepsy in vulnerable low-income populations.



Observational, descriptive, cross-sectional study prospectively recording data from all patients diagnosed with epilepsy who attended a specialist neurology consultation between January and March 2014. Data were analysed using descriptive epidemiology tools.



A total of 107 patients were evaluated, of whom 24.2% were illiterate and only 10.2% had completed a higher education programme. Most of the patients (86.8%) had a low socioeconomic status; 73.8% were single and 76.7% were unemployed. The main risk factors for epilepsy in this population were recorded as follows: delayed psychomotor development (n=24, 22.4%), head trauma (n=16, 14.9%), and central nervous system infection (n=13, 12.1%). Most patients (70.1%) responded to antiepileptic drugs (controlled cases) and 15.4% (n=15) had drug-resistant epilepsy (refractory cases).



The demographic and clinical profiles of the patients included in this study resemble those published for high-income populations; differences are mostly limited to aetiological classification and risk factors. The social profile of the patients evaluated in this study shows high rates of unemployment, illiteracy, and single marital status. These findings seem to be more frequent and prevalent in this group than in high income populations.
Clinical experience of strain imaging using DENSE for detecting infarcted cardiac segments

We hypothesised that myocardial deformation determined with magnetic resonance imaging (MRI) will detect myocardial scar.



Displacement Encoding with Stimulated Echoes (DENSE) was used to calculate left ventricular strain in 125 patients (29 women and 96 men) with suspected coronary artery disease. The patients also underwent cine imaging and late gadolinium enhancement. 57 patients had a scar area >1% in at least one segment, 23 were considered free from coronary artery disease (control group) and 45 had pathological findings but no scar (mixed group). Peak strain was calculated in eight combinations: radial and circumferential strain in transmural, subendocardial and epicardial layers derived from short axis acquisition, and transmural longitudinal and radial strain derived from long axis acquisitions. In addition, the difference between strain in affected segments and reference segments, "differential strain", from the control group was analysed.



In receiver-operator-characteristic analysis for the detection of 50% transmurality, circumferential strain performed best with area-under-curve (AUC) of 0.94. Using a cut-off value of -17%, sensitivity was 95% at a specificity of 80%. AUC did not further improve with differential strain. There were significant differences between the control group and global strain circumferential direction (-17% versus -12%) and in the longitudinal direction (-13% versus -10%). Interobserver and scan-rescan reproducibility was high with an intraclass correlation coefficient (ICC) >0.93.



DENSE-derived circumferential strain may be used for the detection of myocardial segments with >50 % scar area. The repeatability of strain is satisfactory. DENSE-derived global strain agrees with other global measures of left ventricular ejection fraction.
Clinical and immunological outcomes according to adherence to first-line HAART in a urban and rural cohort of HIV-infected patients in Burkina Faso, West Africa

Aim of our study is to investigate the clinical and immunological outcomes according to first-line HAART adherence in a large cohort of HIV-infected patients in Burkina Faso.



A retrospective study was conducted between 2001 and 2009 among patients from two urban medical centers [St. Camille Medical Center (CMSC) and "Pietro Annigoni" Biomolecular Research Center (CERBA)] and 1 in the rural District of Nanoro (St. Camille District Hospital). Socio-demographical and clinical data were analyzed. Adherence was evaluated through a questionnaire investigating 5 key points related to drugs, consultations and blood exams, by assigning 0 to 2 points each up to 10 points overall. Data were collected at baseline and regularly thereafter. Adherence score was considered as a continuous variable and classified in optimal (8-10 points) and sub-optimal (0-7 points). Immunological outcome was evaluated as modification in CD4+ T-cell count over time, while predictors of death were explored by a univariate and multivariate Cox model considering adherence score as a time-varying covariate.



A total of 625 patients were included: 455 (72.8%) were females, the median age was 33.3 (IQR 10.2) years, 204 (32.6.%) were illiterates, the median CD4+ T-cell count was 149 (IQR 114) cells/μl at baseline. At the end of the observation period we recorded 60/625 deaths and 40 lost to follow-up. The analysis of immunological outcomes showed a significant variation in CD4+ T-cell count between M12 and M24 only for patients with optimal adherence (Δ=78.2, p<0.001), with a significant Δ between the two adherence groups at M24 (8-10 vs 0-7, Δ=53.8, p=0.004). Survival multivariate analysis revealed that covariates significantly related to death included being followed at CERBA (urban area) or Nanoro (rural area), and receiving a regimen not including fixed dose combinations, (p=0.024, p=0.001 and p<0.001 respectively); conversely, an increasing adherence score as well as an optimal adherence score were significantly related to survival (p<0.001).



Adherence to HAART remains pivotal to build up a good therapeutic outcome. Our results confirm that, according to our adherence system evaluation, less adherent patients have a higher risk of death and of inadequate CD4+ count recovery.
DualKey: Miniature Screen Text Entry via Finger Identification

Fast and accurate access to keys for text entry remains an open question for miniature screens. Existing works typically use a cumbersome two-step selection process, first to zero-in on a particular zone and second to make the key selection. We introduce DualKey, a miniature screen text entry technique with a single selection step that relies on finger identification. We report on the results of a 10 day longitudinal study with 10 participants that evaluated speed, accuracy, and learning. DualKey outperformed the existing techniques on long-term performance with a speed of 19.6 WPM. We then optimized the keyboard layout for reducing finger switching time based on the study data. A second 10 day study with eight participants showed that the new sweqty layout improved upon DualKey even further to 21.59 WPM for long-term speed, was comparable to existing techniques on novice speed and outperformed existing techniques on novice accuracy rate.