nils-herrmann/clean_scirepeval huggingface dataset:
Scoring System Based on BI-RADS Lexicon to Predict Probability of Malignancy in Suspicious Microcalcifications

To develop a scoring system allowing quantification of the probability of malignancy of suspicious microcalcifications based on Breast Imaging Reporting and Data System (BI-RADS). A total of 163 microcalcification lesions surgically excised in 147 women (aged 28–65 years) were included. Two radiologists independently reviewed each lesion with BI-RADS (4th edition). The interobserver agreement and positive predictive value (PPV) for each descriptor were determined and multivariate analysis was used to develop a scoring system. The scores were compared between benign and malignant lesions and among BI-RADS categories by using the two-sample t-test or the analysis of variance. To assess the discriminative power of the scoring system, the area under the receiver–operating characteristic curve (AUC) and cutoff values for categorization were determined. For the test of the scoring system, the validation data set from a different facility was applied. Interobserver agreement was fair to moderate for distribution, morphology, and category (κ = 0.45, 0.40, and 0.37). PPVs were significantly different among BI-RADS descriptors and categories (P < 0.0001). Of the scoring system developed, the AUC was 0.75. The scores between benign and malignant lesions were significantly different. By means of cutoff values, PPV in category 4a, 4b, 4c, and 5 was 7.0%, 15.0%, 44.8%, and 83.3%, respectively. For the validation data set, the AUC was 0.79 and the PPV in category 4a, 4b, 4c, and 5 was 9.4%, 24.1%, 62.5%, and 80.0%, respectively. In suspicious microcalcifications, our scoring system based on BI-RADS (4th edition) could help to derive a specific final category with good stratification of the probability of malignancy.
Polymorphism of the CYP3A5 gene and its effect on tacrolimus blood level.

Tacrolimus is the cornerstone for immunosuppression in renal transplant and is metabolized by the cytochrome P 450 3A (CYP3A) subfamily of enzymes in the liver and small intestine. A polymorphism in intron 3 of the CYP3A5 gene affects the expression of this enzyme and tacrolimus trough blood levels. The purpose of this study was to identify the proportion of CYP3A5 gene polymorphisms in South Indian renal transplant patients and determine the effect of CYP3A5 gene polymorphisms on tacrolimus trough blood levels in patients with and without CYP3A5 expression.



We included 25 adult patients who underwent renal transplant at Government Medical College, Trivandrum. All patients received tacrolimus (dose, 0.1 mg/kg/body weight, in 2 divided doses). Tacrolimus trough blood levels were determined on postoperative day 6. The CYP3A5 genotype analysis was performed by polymerase chain reaction amplification of target and detection by restriction fragment length polymorphism analysis.



The CYP3A5*1/*1 genotype was detected in 5 recipients (20%), *1/*3 genotype in 5 recipients (20%), and *3/*3 genotypes in 15 recipients (60%) of the total 25 graft recipients. Mean tacrolimus level in the CYP3A5*1/*1 group was 5.154 ng/mL (range, 4.42 to 6.5 ng/mL), CYP3A5*1/*3 group was 5.348 ng/mL (range, 3.1 to 9.87 ng/mL), and CYP3A5*3/*3 group was 9.483 ng/mL (range, 4.5 to14.1 ng/mL). Acute rejection episodes were significantly more frequent for CYP3A5*1/*1 homozygous patients (40%) than patients with CYP3A5*1/*3 (20%) or CYP3A5*3/*3 (13%) genotypes.



Most patients carried the mutant allele CYP3A5*3 (A6986G). Tacrolimus drug level correlated well with presence or absence of CYP3A5 polymorphisms. Acute rejection episodes were more frequent in expressors, and they may require higher doses of tacrolimus. Similarly, tacrolimus nephrotoxicity was more frequent in non-expressors. Therefore, CYP3A5 polymorphism analysis before renal transplant may help determine the optimal dose of tacrolimus in this population and prevent acute rejection episodes or tacrolimus toxicity.
Phase I trial of nelarabine in indolent leukemias.

To test whether nelarabine is an effective agent for indolent leukemias and to evaluate whether there is a relationship between cellular pharmacokinetics of the analog triphosphate and clinical responses.



Thirty-five patients with relapsed/refractory leukemias (n = 24, B-cell chronic lymphocytic leukemia and n = 11, T-cell prolymphocytic leukemia) were entered onto three different protocols. For schedule A, patient received nelarabine daily for 5 days, whereas for schedule B, nelarabine was administered on days 1, 3, and 5. Schedule C was similar to schedule B except that fludarabine was also infused. Plasma and cellular pharmacokinetics were studied during the first cycle.



Responses were achieved in 20%, 15%, and 63% of patients receiving schedule A, B, and C, respectively. Histologic category, number of prior therapies, and fludarabine refractoriness did not influence the response rate. The most common nonhematologic toxicity was peripheral neuropathy. Grade 4 neutropenia and thrombocytopenia complicated 23% and 26% of courses respectively, and were significantly more frequent among patients with pre-existing marrow failure. Pharmacokinetics of plasma nelarabine and arabinosylguanine (ara-G) and of cellular ara-G triphosphate (ara-GTP) were similar in the two groups of diagnoses, and the elimination of ara-GTP from leukemia cells was slow (median, > 24 hours). The median peak intracellular concentrations of ara-GTP were significantly different (P = .0003) between responders (440 micromol/L; range, 35 to 1,438 micromol/L; n = 10) and nonresponders (50 micromol/L; range, 22 to 178 micromol/L; n = 15).



Nelarabine is an effective regimen against indolent leukemias, and combining it with fludarabine was most promising. Determination of tumor cell ara-GTP levels may provide a predictive test for response to nelarabine.
Chromium treatment has no effect in patients with type 2 diabetes in a Western population: a randomized, double-blind, placebo-controlled trial.

Chromium treatment has been reported to improve glycemic control in patients with type 2 diabetes. However, concern exists about the possible toxic effects of chromium picolinate. The aim of this study was to determine the effect of chromium treatment in the form of chromium yeast on glycemic control in a Western population of patients with type 2 diabetes who were being treated with oral hypoglycemic agents.



In this 6-month, double-blind study, patients with moderate glycemic control, being treated with oral hypoglycemic agents, were randomly assigned to receive either a placebo or treatment with 400 microg of chromium daily in the form of chromium yeast. The primary efficacy parameter was a change in A1C. Secondary end points were changes in lipid profile, BMI, blood pressure, body fat, and insulin resistance.



No differences were found for the change in A1C between the intervention and placebo groups, nor were any differences found between the groups for the secondary end points.



There is no evidence that chromium in the form of chromium yeast is effective in improving glycemic control in Western patients with type 2 diabetes who are taking oral hypoglycemic agents.
Immune control of HIV-1 after early treatment of acute infection

Virus-specific T-helper cells are considered critical for the control of chronic viral infections. Successful treatment of acute HIV-1 infection leads to augmentation of these responses, but whether this enhances immune control has not been determined. We administered one or two supervised treatment interruptions to eight subjects with treated acute infection, with the plan to restart therapy if viral load exceeded 5,000 copies of HIV-1 RNA per millilitre of plasma (the level at which therapy has been typically recommended) for three consecutive weeks, or 50,000 RNA copies per ml at one time. Here we show that, despite rebound in viraemia, all subjects were able to achieve at least a transient steady state off therapy with viral load below 5,000 RNA copies per ml. At present, five out of eight subjects remain off therapy with viral loads of less than 500 RNA copies per ml plasma after a median 6.5 months (range 5–8.7 months). We observed increased virus-specific cytotoxic T lymphocytes and maintained T-helper-cell responses in all. Our data indicate that functional immune responses can be augmented in a chronic viral infection, and provide rationale for immunotherapy in HIV-1 infection.
Acoustic Correlates of Compensatory Adjustments to the Glottic and Supraglottic Structures in Patients with Unilateral Vocal Fold Paralysis

The goal of this study was to analyse perceptually and acoustically the voices of patients with Unilateral Vocal Fold Paralysis (UVFP) and compare them to the voices of normal subjects. These voices were analysed perceptually with the GRBAS scale and acoustically using the following parameters: mean fundamental frequency (F0), standard-deviation of F0, jitter (ppq5), shimmer (apq11), mean harmonics-to-noise ratio (HNR), mean first (F1) and second (F2) formants frequency, and standard-deviation of F1 and F2 frequencies. Statistically significant differences were found in all of the perceptual parameters. Also the jitter, shimmer, HNR, standard-deviation of F0, and standard-deviation of the frequency of F2 were statistically different between groups, for both genders. In the male data differences were also found in F1 and F2 frequencies values and in the standard-deviation of the frequency of F1. This study allowed the documentation of the alterations resulting from UVFP and addressed the exploration of parameters with limited information for this pathology.
Efficacy of electroacupuncture in the treatment of functional constipation: A randomized controlled pilot trial.

To evaluate the efficacy and safety of electroacupuncture at Tianshu (ST25) for patients with functional constipation (FC).



Ninety-six patients with FC were randomized to receive deep needling on bilateral ST25 (group A, 48 cases) or shallow needling on bilateral ST25 (group B, 48 cases) with electroacupuncture once daily for 4 weeks. The proportion of patients with four or more complete spontaneous bowel movements (CSBMs) per week, and scores of constipation symptoms and satisfaction with treatment were compared between two groups. Safety was also assessed.



The proportion of patients with four or more CSBMs per week was 52.1% in group A, significantly higher than 25.0% in group B during the 4-week treatment (P<0.05). The constipation symptom score of patients were significantly improved in group A as compared with group B at week 2-4 (P<0.05). Patients in group A were more satisfied with their treatment compared with those in group B at week 1-4 (P<0.05). Five patients in group A felt significant pain and discomfort. No other adverse reaction was observed in both groups.



Using electroacupuncture at ST25 to treat patients with FC is effectively, and deep needling had more stable effect than shallow needling.
Fungal colonization in neutropenic patients: a randomized study comparing itraconazole solution and amphotericin B solution

We assessed the impact of prophylaxis with the oral itraconazole solution and amphotericin B solution on fungal colonization and infection in a randomized study among patients with hematological malignancies and neutropenia. Infecting and colonizing Candida strains of patients suffering from candidiasis were genotyped by random amplification of polymorphic DNA (RAPD) analysis. A total of 106 patients were evaluated in this study: 52 patients in the itraconazole and 54 in the amphotericin B arm. During neutropenia fungal colonization in the oropharynx occurred in 11 (19.6%) and 24 (40.6%) and in the rectum in 11 (19.6%) and 23 (38.9%) courses in the itraconazole and amphotericin B groups (P<0.05), respectively. Candida albicans was the most prevalent species in both study groups. Mixed fungal colonization with Candida krusei and Candida glabrata was increased in the amphotericin B group, yet without clinical importance since infections were due to C. albicans. The occurrence of invasive candidiasis was significantly increased in multicolonized compared to monocolonized patients. In the amphotericin B group 20 and in the itraconazole group 2 neutropenic patients showed multicolonization with Candida spp. (P<0.05). Overall fungal infections were 3.8% in the itraconazole and 14.8% in the amphotericin B group (P<0.05). RAPD typing showed oropharynx strains involved in superficial infections in four of five patients. In all four patients with deep fungal infections, it appears that the colonizing rectum strains were identical to infecting strains of Candida spp. Itraconazole solution significantly reduced Candida colonization and infection compared to amphotericin B solution. Most patients remained infected with the colonized strains for the entire study period, irrespective of antifungal prophylaxis.
Effectiveness of a Chronic Disease Surveillance Systems for Blood Pressure Monitoring

Information Technology (IT) enables health care providers to manage patients with chronic conditions through identification, follow up and administration of specific interventions. In our setting, we developed a surveillance system for chronic diseases. The aim of this study was to show its efficacy on monitoring blood pressure throughout a cluster randomized controlled trial. Patients without blood pressure registries (condition 1) or with high blood pressure measurements (condition 2) were randomized to be detected by the surveillance system or to receive usual care. The proportion of patients with at least one blood pressure measurement within three months of follow up was 49.9% (207 patients) in the intervention group and 37% (195) in the control group (p<0.001) for condition 1. And 61% (224) vs. 50% (239) respectively (p=0.002) for condition 2. Patients under the surveillance system have higher proportion of blood pressure measurements, showing this study an improvement on the process of care with this IT tool.
Clinical consequences of generic substitution of lamotrigine for patients with epilepsy.

To measure the proportions of patients switching from generic to branded drugs among users of antiepileptic drugs (AED) compared to other therapeutic areas and to investigate medical services utilization associated with generic switching of lamotrigine.



Medical and pharmacy claims data from Régie de l'Assurance Maladie du Québec database from April 1998 to July 2006 were used. Patients with an epilepsy diagnosis (International Classification of Diseases-9 345) and treated with lamotrigine for >60 of the 90 days before the entry date of generic lamotrigine in Quebec (February 1, 2003) were selected. The proportion of patients switching back to brand were calculated for lamotrigine, for other AEDs (clobazam, carbamazepine CR, gabapentin) and for non-AED chronic medications (carvedilol, fosinopril, simvastatin). Medical resource utilization was compared between periods of branded vs generic use of lamotrigine.



Of 671 patients treated with branded lamotrigine, 187 patients (27.9%) switched to a generic, and 51 of these patients (27.5%) switched back to the branded medication. Rates of switchback were from 20.8% to 44.1% for various AEDs and from 7.7% to 9.1% for non-AEDs. Relative to the branded lamotrigine use period, generic lamotrigine use period was associated with a 5.1% increase in mean daily dose of lamotrigine (239.1 vs 251.4 mg; p = 0.0149), a higher number of dispensations for other AEDs (20.4 vs 23.9 dispensations per person-year; p < 0.001) as well as non-AED drugs (26.4 vs 32.8 dispensations per person-year; p < 0.0001), a higher utilization rate of medical services (8.7 vs 9.8 visits per person-year; p < 0.0001), and a longer hospital length of stay (3.29 days vs 4.86 days per person-year; p < 0.0001).



A higher propensity to switch back to branded medications was observed among antiepileptic drug users compared to users of antihypertensives and antihyperlipidemics, similar to findings from Andermann et al. Switch to generic lamotrigine was significantly associated with increased physician visits and hospitalizations.
FUEL Your Life: A Translation of the Diabetes Prevention Program to Worksites.

To evaluate the effectiveness of FUEL Your Life, a translation of the Diabetes Prevention Program for worksites.



A randomized control group design was conducted in five worksites of a large transportation company. Measures were collected pretest, posttest (6 months), and follow-up (12 months).



Railroad maintenance facilities of Union Pacific Railroad.



Participants consisted of 362 workers (227 treatment, 135 control).



FUEL Your Life was translated from the Diabetes Prevention Program to better fit within the context of the worksite. The primary difference was the use of peer health coaches to provide social support and reinforcement and an occupational nurse to provide lesson content (six sessions of 10 minutes) to participants instead of the lifestyle coaches employed by the Diabetes Prevention Program, resulting in a less structured meeting schedule.



The primary outcomes were weight and body mass index (BMI), with secondary outcomes including eating behaviors, physical activity, and social support.



Latent growth modeling was used to measure changes in the outcomes over time.



Participants in the intervention group maintained weight/BMI (-.1 pounds/-.1 BMI), whereas the control participants gained weight/BMI (+2.6 pounds/+.3 BMI), resulting in a statistically significant difference between groups. Fifty-five percent of intervention participants lost some weight, whereas only 35% of the control group lost weight.



FUEL Your Life, a low intensity intervention, was not effective for promoting weight loss, but was effective for helping workers maintain weight over a 12-month period.
A multi-centre, blinded international trial of the effect of A1 and A2 β-casein variants on diabetes incidence in two rodent models of spontaneous Type I diabetes

The diabetes-inducing potential of cows' milk is still debated and there is no consensus on the diabetogenicity of individual milk proteins. A1-β-casein has been associated with increased diabetes frequency in ecological studies and in NOD mice. Our aim was to ascertain whether A1-β-casein was more diabetogenic than A2 and to test the diabetogenicity of a milk-free diet in animals representing different forms of spontaneous Type I (insulin-dependent) diabetes mellitus.  Defined diets were coded and shipped to laboratories in New Zealand (NOD/NZ), Canada (BB) and the UK (NOD/Ba). Base diets were Pregestimil (PG) and ProSobee (PS). Purified fractions of whole casein (WC), A1 or A2-β-casein were added at 10%. A milk-free, wheat-predominant, NTP-2000 diet was the control. Animals were fed from weaning up to 150 or 250 days, and insulitis, diabetes frequency and expression of pancreatic cytokines were assessed.  Diabetes incidence was highest in three locations in animals fed NTP-2000. PG and PS diets were protective except for NOD/Ba mice fed PG+WC where incidence was similar to NTP-2000. A1 and A2 diets were protective in both models, but A1 β-casein was slightly more diabetogenic in PS-fed BB rats. The New Zealand study was confounded by an infection.  A milk-free, wheat-predominant diet was highly diabetogenic in three widely separate locations in both animal models. A previous result that A1 β-casein was more diabetogenic than A2 β-casein in NOD mice was not confirmed; both β-casein variants were protective in BB rats and NOD mice. Whole Casein promoted diabetes in NOD/Ba but protected BB showing that unique diabetes haplotypes react differently to dietary proteins. A1- was more diabetogenic than A2-β-casein only in PS-fed BB rats. Neither the analysis of insulitis nor of pancreatic cytokine gene expression showed a difference between A1 or A2 β-casein fed animals. Milk caseins are unlikely to be exclusive promoters of Type I diabetes, but could enhance the outcome of diabetes in some cases. Other diet components such as wheat could be more important promoters of Type I diabetes.
Clear cell carcinoma of the ovary: a retrospective multicentre experience of 254 patients with complete surgical staging

A retrospective analysis was performed to evaluate the clinical characteristics and prognostic factors in the patients with clear cell carcinoma (CCC) of the ovary. After central pathological review and scanning of the medical records of nine Japanese institutions between 1992 and 2003, a total of 254 patients with CCC of the ovary were enrolled in the present study. Mean age was 52.4 years (range 23–73 years). Tumours were 13% (33/254) stage Ia, 36% (92/254) stage Ic, 13% (33/254) stage II, 30% (80/254) stage III, and 6% (16/254) stage IV. Five-year progression-free survival and overall survival was 84 and 88% in stage I, 57 and 70% in stage II, 25 and 33% in stage III and 0 and 0% in stage IV, respectively. Retroperitoneal lymph node metastasis was observed in 9% in pT1a tumours, 7% in pT1c tumours, 13% in pT2 tumours, and 58% in pT3 tumours, respectively. There was no survival benefit according to chemotherapeutic differences in the patients who received complete surgical staging procedures and conventional chemotherapy. Peritoneal cytological status was an independent prognostic factor in stage Ic patients (P=0.03) and only residual tumour diameter was an independent prognostic factor in stage III, IV patients (P=0.02). Our results suggest that cytoreductive surgery resulting in no residual tumour only could improve the prognosis of advanced CCC patients.
Comparative one-year effectiveness of percutaneous coronary intervention versus coronary artery bypass grafting in patients <75 versus ≥75 years with unprotected left main disease (from the CUSTOMIZE Registry).

There is a lack of knowledge on the interaction between age and left main coronary artery revascularization. The aim of this study was to investigate the comparative effectiveness of percutaneous coronary intervention (PCI) with drug-eluting stents and coronary artery bypass grafting (CABG) in patients with left main coronary artery disease aged <75 versus ≥75 years. Of a total of 894 patients included, 692 (77.4%) were aged <75 years and 202 (23.6%) ≥75 years. PCI was found to be significantly different from CABG with respect to the composite of major adverse cardiac events at 1-year follow-up in patients aged <75 years (15.5% vs 8.5%, p = 0.01) but not in those aged ≥75 years (16.4% vs 13.9%, p = 0.65). This finding was consistent after statistical adjustment for baseline confounders in the 2 groups (adjusted hazard ratio [AHR] 2.2, 95% confidence interval 1.2 to 4.1, p = 0.016 in younger patients; AHR 0.9, 95% confidence interval 0.3 to 3.0, p = 0.88 in older patients). In the 2 groups, PCI and CABG showed similar adjusted risks for all-cause death, cardiac death, and myocardial infarction. Target lesion revascularization occurred more frequently in patients aged <75 years treated with PCI compared to CABG (AHR 5.1, 95% confidence interval 1.9 to 13.6, p = 0.001) but not in those aged ≥75 years. A significant interaction between age and treatment with regard to major adverse cardiac events was identified (adjusted p for interaction = 0.034). In conclusion, compared to younger patients, elderly patients with left main disease are likely to derive the maximal gain from a less invasive procedure such as PCI.