nils-herrmann/clean_scirepeval huggingface dataset:
Thymoglobulin-Associated Cd 4 + T-Cell Depletion and Infection Risk in HIV-Infected Renal Transplant Recipients

HIV-infected patients are increasingly referred for kidney transplantation, and may be at an increased risk for rejection. Treatment for rejection frequently includes thymoglobulin. We studied thymoglobulin’s effect on CD4+ T-cell count, risk of infection and rejection reversal in 20 consecutive HIV-infected kidney recipients. All patients used antiretroviral therapy and opportunistic infection prophylaxis. Maintenance immunosuppression consisted of prednisone, mycophenolate mofetil and cyclosporine. Eleven patients received thymoglobulin (7 for rejection and 4 for delayed/slow graft function) while 9 did not. These two groups were similar in age, gender, race, donor characteristics and immunosuppression. Mean CD4+ T-cell counts remained stable in patients who did not receive thymoglobulin, but became profoundly suppressed in those who did, decreasing from 475 ± 192 to 9 ± 10 cells/lL (p < 0.001). Recovery time ranged from 3 weeks to 2 years despite effective HIV suppression. Although opportunistic infections were successfully suppressed, low CD4+ T-cell count was associated with increased risk of serious infections requiring hospitalization. Rejection reversed in 6 of 7 patients receiving thymoglobulin. We conclude that thymoglobulin reverses acute rejection in HIV-infected kidney recipients, but produces profound and long-lasting suppression of the CD4+ T-cell count associated with increased risk of infections requiring hospitalization.
Time-series analysis of MRI intensity patterns in multiple sclerosis

In progressive neurological disorders, such as multiple sclerosis (MS), magnetic resonance imaging (MRI) follow-up is used to monitor disease activity and progression and to understand the underlying pathogenic mechanisms. This article presents image postprocessing methods and validation for integrating multiple serial MRI scans into a spatiotemporal volume for direct quantitative evaluation of the temporal intensity profiles. This temporal intensity signal and its dynamics have thus far not been exploited in the study of MS pathogenesis and the search for MRI surrogates of disease activity and progression. The integration into a four-dimensional data set comprises stages of tissue classification, followed by spatial and intensity normalization and partial volume filtering. Spatial normalization corrects for variations in head positioning and distortion artifacts via fully automated intensity-based registration algorithms, both rigid and nonrigid. Intensity normalization includes separate stages of correcting intra- and interscan variations based on the prior tissue class segmentation. Different approaches to image registration, partial volume correction, and intensity normalization were validated and compared. Validation included a scan-rescan experiment as well as a natural-history study on MS patients, imaged in weekly to monthly intervals over a 1-year follow-up. Significant error reduction was observed by applying tissue-specific intensity normalization and partial volume filtering. Example temporal profiles within evolving multiple sclerosis lesions are presented. An overall residual signal variance of 1.4% +/- 0.5% was observed across multiple subjects and time points, indicating an overall sensitivity of 3% (for axial dual echo images with 3-mm slice thickness) for longitudinal study of signal dynamics from serial brain MRI.
Birth defects among a cohort of infants born to HIV-infected women on antiretroviral medication.

To determine rate of and risk factors for birth defects in infants born to HIV-infected women receiving nucleoside and protease inhibitor antiretroviral (ARV) therapy.



Birth defects were evaluated among infants on the Pediatric AIDS Clinical Trials Group 316 trial that studied addition of peripartum nevirapine to established ARV regimen for prevention of mother-to-child transmission. Maternal therapy was categorized by trimester of earliest exposure. Birth defects were coded using conventions of the Antiretroviral Pregnancy Registry.



Birth defects were detected in 60/1414 (4.2%; 95% CI 3.3-5.4%) infants including 30/636 (4.7%; 95% CI 3.2-6.7%) with first trimester ARV exposure and 30/778 (3.9%; 95% CI 2.6-5.5%) with exposure only after the first trimester (P=0.51). Rates of classes of defects were similar between first trimester compared to later exposure groups except heart defects which occurred in 16 (2.5%; 95% CI 1.4-4.1%) with first trimester ARV exposure and in six (0.8%; 95% CI 0.3-1.7%) infants with later exposure (P=0.02). Exposure to ARV was not associated with specific types of heart defects. Two cases of cardiomyopathy were noted.



ARV use in early pregnancy was not associated with an increased risk of birth defects overall. The possible association of ARV exposure with heart defects requires further surveillance.
Pilot study evaluating the interaction between paclitaxel and protease inhibitors in patients with human immunodeficiency virus-associated Kaposi’s sarcoma: an Eastern Cooperative Oncology Group (ECOG) and AIDS Malignancy Consortium (AMC) trial

Paclitaxel, a cytotoxic agent metabolized by cytochrome P450 hepatic enzymes, is active for the treatment of human immunodeficiency (HIV) associated Kaposi’s sarcoma. Protease inhibitors are commonly used to treat HIV infection and are known to inhibit cytochrome P450. We sought to determine whether protease inhibitors alter the pharmacokinetics of paclitaxel. Patients with advanced HIV-associated KS received paclitaxel (100 mg/m2) by intravenous infusion over 3 h, and plasma samples were collected to measure paclitaxel concentration. The area under the curve (AUC) was calculated using a combination of the log and linear trapezoidal rule, and clearance was calculated as the dose/AUC. Pharmacokinetics were compared with respect to antiretroviral therapy and toxicity, Thirty-four patients received paclitaxel, of whom 20 had no prior paclitaxel therapy and were assessable for response. Twenty-seven had pharmacokinetic studies performed. Paclitaxel exposure was higher in patients taking protease inhibitors compared to those who were not taking protease inhibitors. The increased exposure did not correlate with efficacy or toxicity. Of the 20 patients assessable for response, 6 (30%) had an objective response and median progression-free survival was 7.8 months (95% confidence interval, 5.6, 21.0 months). Despite higher exposure to paclitaxel, patients on protease inhibitors did not experience enhanced toxicity or efficacy.
Comparison of the prognostic value of cardiopulmonary exercise testing between male and female patients with heart failure.

Cardiopulmonary exercise testing (CPX) clearly holds prognostic value in the heart failure (HF) population. Studies investigating the prognostic value of CPX in individuals with HF have consistently examined predominantly male groups. The purpose of the present study was to examine the prognostic value of CPX in a female HF group.



Seventy-five female and 337 male subjects diagnosed with HF participated in this study. The ability of peak oxygen consumption (VO(2)) and the minute ventilation/carbon dioxide production (VE/VCO(2)) slope to predict cardiac-related events were assessed.



In the year following CPX, the female group suffered 26 cardiac-related events (8 deaths/18 hospitalizations), while the male group suffered 89 cardiac-related events (20 deaths/69 hospitalizations). The hazard ratios for peak VO(2) and the VE/VCO(2) slope were 4.0 (95% confidence interval: 2.6-6.1, p<0.001) and 4.2 (95% confidence interval: 2.7-6.6, p<0.001) in the male group and 3.8 (95% confidence interval: 1.7-8.5, p<0.001) and 4.3 (95% confidence interval: 1.8-9.8, p<0.001) in the female group. In both the male and female groups, Cox multivariate analysis revealed VE/VCO(2) slope was the strongest predictor of cardiac-related events while peak VO(2) added significant predictive value and was retained in the regression.



The results of the present study indicate that the prognostic value of peak VO(2) and the VE/VCO(2) slope are similar in men and women diagnosed with HF. In both men and women, the prognostic power of the VE/VCO(2) slope is greater than that of peak VO(2).
A novel tool for reliable and accurate prediction of renal complications in patients undergoing percutaneous coronary intervention.

The aim of the study was to develop and validate a tool for predicting risk of contrast-induced nephropathy (CIN) in patients undergoing contemporary percutaneous coronary intervention (PCI).



CIN is a common complication of PCI and is associated with adverse short- and long-term outcomes. Previously described risk scores for predicting CIN either have modest discrimination or include procedural variables and thus cannot be applied for pre-procedural risk stratification.



Random forest models were developed using 46 pre-procedural clinical and laboratory variables to estimate the risk of CIN in patients undergoing PCI. The 15 most influential variables were selected for inclusion in a reduced model. Model performance estimating risk of CIN and new requirement for dialysis (NRD) was evaluated in an independent validation data set using area under the receiver-operating characteristic curve (AUC), with net reclassification improvement used to compare full and reduced model CIN prediction after grouping in low-, intermediate-, and high-risk categories.



Our study cohort comprised 68,573 PCI procedures performed at 46 hospitals between January 2010 and June 2012 in Michigan, of which 48,001 (70%) were randomly selected for training the models and 20,572 (30%) for validation. The models demonstrated excellent calibration and discrimination for both endpoints (CIN AUC for full model 0.85 and for reduced model 0.84, p for difference <0.01; NRD AUC for both models 0.88, p for difference = 0.82; net reclassification improvement for CIN 2.92%, p = 0.06).



The risk of CIN and NRD among patients undergoing PCI can be reliably calculated using a novel easy-to-use computational tool (https://bmc2.org/calculators/cin). This risk prediction algorithm may prove useful for both bedside clinical decision making and risk adjustment for assessment of quality.
Serum sclerostin: the missing link in the bone-vessel cross-talk in hemodialysis patients?

We found for the first time that in maintenance hemodialysis patients, higher sclerostin serum level was associated with severe abdominal aortic calcification (AAC). In addition, cortical bone microarchitecture (density and thickness) assessed by high-resolution peripheral quantitative computed tomography (HR-pQCT) at tibia was also independently associated with severe AAC. These results suggest that sclerostin may be involved in the association of mineral and bone disorder with vascular calcification in hemodialysis patients. Severe abdominal aortic calcifications are predictive of high cardiovascular mortality in maintenance hemodialysis (MHD) patients. In patients with end-stage renal disease, a high aortic calcification score was associated with lower bone turnover on bone biopsies. Thus, we hypothesized that sclerostin, a Wnt pathway inhibitor mainly secreted by osteocytes and acting on osteoblasts to reduce bone formation, may be associated with vascular calcifications in MHD patients. Fifty-three MHD patients, aged 53 years [35–63] (median [Q1–Q3]) were included. Serum was sampled before the MHD session to assay sclerostin. Framingham score was computed and the abdominal aortic calcification (AAC) score was assessed according to Kauppila method on lateral spine imaging using DEXA. Tibia bone status was evaluated by high-resolution peripheral quantitative computed tomography (HR-pQCT). Patients were distributed into two groups according to their AAC score: patients with mild or without AAC (score below 6) versus patients with severe AAC (score of 6 and above). In multivariate analysis, after adjustment on age, dialysis duration and diabetes, serum sclerostin and cortical thickness were independently associated with severe AAC (odds ratio (OR) = 1.43 for each 0.1 ng/mL increase [95 % confidence interval (CI) 1.10–1.83]; p = 0.006 and 0.16 for 1 SD increase [0.03–0.73]; p = 0.018, respectively). A second cardiovascular model adjusted on Framingham score and the above mentioned confounders showed similar results. Elevated sclerostin serum level and poorer tibia cortical bone structure by HR-pQCT were positively and independently associated with higher odds of severe AAC in MHD patients. Serum sclerostin may become a biomarker of mineral and bone disorder and vascular risk in MHD patients.
Current imaging of childhood urinary infections: prospective survey.

To assess whether ultrasonography alone is adequate for routine screening of childhood urinary infection, whether clinical features determine the need for further investigations, and which investigations are most appropriate.



Prospective survey of children with proved urinary infection and a preinvestigation record of clinical features. Ultrasonography and intravenous urography were routine, with choice of further studies determined by ultrasonographic findings.



A children's hospital and two district general hospitals in Mersey region.



Sensitivity and specificity of ultrasonography both generally and in relation to clinical features. Accuracy of intravenous urography compared with radioisotope examinations.



Specificity of ultrasonography was good (99% (95% confidence interval 96% to 100%)) but sensitivity modest (43% (32% to 55%)), principally with respect to detecting vesicoureteric reflux and renal scarring. Among older children (aged 2-10 years) with positive ultrasound results and fever or vomiting the sensitivity in detecting reflux (with and without renal scarring) was 78% (62% to 89%) and the specificity 69% (60% to 78%); in detecting renal scarring (with and without reflux) the sensitivity was 100% (80% to 100%) and specificity 65% (56% to 74%). Renal scarring and obstructive uropathies were better assessed by radioisotope examinations than by intravenous urography.



Ultrasonography alone is inadequate for routine screening of childhood urinary infection. Though further investigations remain advisable in infants, in older children they can be restricted to a minority who have positive ultrasound examinations or have had fever or vomiting. Radioisotope examinations largely eliminate the need for intravenous urography.
Phase II trial of CPT-11 in myelodysplastic syndromes with excess of marrow blasts

CPT-11 is an antineoplastic agent which acts as a specific inhibitor of DNA topisomerase 1 and has a broad spectrum of activity in solid tumors. Very few studies have evaluated the activity of CPT-11 in hematological malignancies. We conducted a phase II trial of CPT-11 in 26 patients with high-risk MDS (RAEB 1: n = 4; RAEB 2: n = 9; MDS having progressed to AML: n = 10; CMML: n = 3) who could not receive anthracycline/cytarabine intensive chemotherapy. Induction therapy consisted of four courses of CPT-11 given intravenously at 200 mg/m2 every 2 weeks. Patient characteristics were: median age, 71 (range 51–77); sex, (M/F), 21/5, median % marrow blasts cells, 13.5 (range 7–52). Cytogenetics according to IPSS were: low-risk n = 13, intermediate-risk n = 6, high-risk n = 3, failure or not done n = 4. Six patients stopped treatment after only one or two courses of CPT-11 due to severe infection (n = 2), progressive disease (n = 3), acute lysis syndrome with renal failure (n = 1). In the 20 patients who received at least three cycles of CPT-11, complete remission was achieved in one case, partial remission in four cases, and hematological improvement in three cases with an overall response rate of 33% in the 26 patients. Duration of response was short (median 4 months, range 1–6 months) and median survival was 8 months (range 1–23 months). Digestive toxicity (diarrhea) occurred in 26/89 (29%) courses, but was mild (grade 1, 20% courses; grade 2 or 3, 9% courses). Hematological toxicity was difficult to assess in non-responders because of initial pancytopenia, but all the patients who responded had grade 3/4 hematological toxicity associated with grade ⩾2 infection requiring hospitalization in 18% of the courses. No other major toxicity was observed. Thus CPT-11 has an interesting activity in MDS with excess of blasts; toxicity is easily managed and most patients can be treated in the out-clinic setting. These results suggest that further evaluation of CPT-11 in MDS is warranted.
Prospective evaluation of dietary treatment in childhood constipation: high dietary fiber and wheat bran intake are associated with constipation amelioration.

The aim of the study was to evaluate, over 24 months, the intake of dietary fiber (DF) and the bowel habit (BH) of constipated children advised a DF-rich diet containing wheat bran.



BH and dietary data of 28 children with functional constipation defined by the "Boston criteria" were obtained at visit 1 (V1, n = 28) and at 4 follow-up visits (V2-V5, n = 80). At each visit the BH was rated BAD (worse/unaltered; improved but still complications) or RECOVERY (REC) (improved, no complications; asymptomatic), and a food intake questionnaire was applied. DF intake was calculated according to age (year) + 5 to 10 g/day and bran intake according to international tables. Nonparametric statistics were used.



Median age (range) was 7.25 years (0.25-15.6 years); 21 children underwent bowel washout (most before V1/V2), and 14 had the last visit at V3/V4. DF intake, bran intake, and the BH rate significantly increased at V2 and remained higher than at V1 through V2 to V5. At V1, median DF intake was 29.9% below the minimum recommended and at the last visit 49.9% above it. Twenty-four children accepted bran at 60 visits, at which median bran intake was 20 g/day and median proportion of DF due to bran 26.9%. Children had significantly higher DF and higher bran intake at V2 to V5 at which they had REC than at those at which they presented BAD BH. DF intake > age +10 g/day was associated with bran acceptance and REC. At the last visit 21 children presented REC (75%); 20 of them were asymptomatic and 18 were off washout/laxatives.



High DF and bran intake are feasible in constipated children and contribute to amelioration of constipation.
Adaptive Bubble Router: A Design to Improve Performance in Torus Networks

A router design for torus networks that significantly reduces message latency over traditional wormhole routers is presented in this paper. This new router implements virtual cut-through switching and fully-adaptive minimal routing. Packet deadlock is avoided by providing escape ways governed by Bubble flow control, a mechanism that guarantees enough free buffer space in the network to allow continuous packet movement. Both deterministic and adaptive Bubble routers have been designed in VLSI using VHDL synthesis tools. Adopting a fair quantitative comparison, we demonstrate that Bubble routers exhibit a reduction in base latency values over 40% with respect to the corresponding wormhole routers, without any penalty in network throughput. With much lower VLSI costs than adaptive wormhole routers, the adaptive Bubble router is even faster than deterministic wormhole routers based on virtual channels.
Resource utilization in patients with schizophrenia who initiated risperidone long-acting therapy: results from the Schizophrenia Outcomes Utilization Relapse and Clinical Evaluation (SOURCE)

Schizophrenia is a chronic mental health disorder associated with increased hospital admissions and excessive utilization of outpatient services and long-term care. This analysis examined health care resource utilization from a 24-month observational study of patients with schizophrenia initiated on risperidone long-acting therapy (RLAT).



Schizophrenia Outcomes Utilization Relapse and Clinical Evaluation (SOURCE) was a 24-month observational study designed to examine real-world treatment outcomes by prospectively following patients with schizophrenia initiated on RLAT. At baseline visit, prior hospitalization and ER visit dates were obtained for the previous 12 months and subsequent hospitalization visit dates were obtained at 3-month visits, if available. The health care resource utilization outcomes measures observed in this analysis were hospitalizations for any reason, psychiatric-related hospitalizations, and emergency room (ER) visits. Incidence density analysis was used to assess pre-event and postevent rates per person-year (PY).



The primary medical resource utilization analysis included 435 patients who had a baseline visit, ≥1 postbaseline visits after RLAT initiation, and valid hospitalization dates. The number of hospitalizations and ER visits per PY declined significantly (p < .0001) after initiation with RLAT. A 41% decrease (difference of -0.29 hospitalizations per PY [95% CI: -0.39 to -0.18] from baseline) in hospitalizations for any reason, a 56% decrease (a difference of -0.35 hospitalizations per PY [95% CI: -0.44 to -0.26] from baseline) in psychiatric-related hospitalizations, and a 40% decrease (-0.26 hospitalizations per PY [95% CI: -0.44 to -0.10] from baseline) in ER visits were observed after the baseline period. The percentage of psychiatric-related hospitalizations decreased significantly after RLAT initiation, and patients had fewer inpatient hospitalizations and ER visits (all p < .0001).



The results suggest that treatment with RLAT may result in decreased hospitalizations for patients with schizophrenia.
The Effects of Infliximab Therapy on Health-Related Quality of Life in Ulcerative Colitis Patients

The impact of infliximab induction and maintenance therapy on health-related quality of life (HRQL) was evaluated in patients with ulcerative colitis (UC).METHODS:In two placebo-controlled, double-blind studies (the Active Ulcerative Colitis Trials 1 and 2 [ACT 1 and 2]), 728 patients were randomized to placebo or infliximab 5 mg/kg or 10 mg/kg. Infusions were administered at weeks 0, 2, 6, and every 8 wk thereafter, up to week 22 (ACT 2) or 46 (ACT 1). Changes in Inflammatory Bowel Disease Questionnaire (IBDQ) and Medical Outcomes Study 36-Item Short Form Health Survey physical and mental component summary (PCS and MCS, respectively) scores were analyzed.Baseline scores for the pooled patient population indicated substantial impairment in HRQL. Improvement at week 8 in the total IBDQ score was significantly greater in the infliximab 5-mg/kg (40, P < 0.001) and 10-mg/kg (36, P < 0.001) groups compared with the placebo group (28). Improvement at week 8 was also significantly greater in the infliximab 5- and 10-mg/kg groups for the PCS (6.8 and 5.9, respectively) and MCS (5.9 and 6.4, respectively) compared with placebo (PCS = 3.7, MCS = 3.0, P < 0.01 for all comparisons). Continued benefit was seen at weeks 30 and 54 with infliximab maintenance therapy (P < 0.001 for all comparisons). Improvement in total IBDQ score correlated significantly (P < 0.001) with improvement in both PCS and MCS scores, and Mayo score.Infliximab therapy substantially improved HRQL in patients with UC. This benefit was sustained through 1 yr with maintenance infliximab therapy.