nils-herrmann/clean_scirepeval huggingface dataset:
Phase III randomized equivalence trial of early breast cancer treatments with or without axillary clearance in post-menopausal patients results after 5 years of follow-up.

Axillary lymph node clearance (ALNC) improves locoregional control and provides prognostic information for early breast cancer treatment, but effects on survival are controversial. This multicentre, randomized pragmatic equivalence trial compares outcomes for post-menopausal early invasive breast cancer patients after locoregional treatment with ALNC and adjuvant therapies to outcomes after locoregional treatment without ALNC and adjuvant therapies.



From 1995-2005, women aged ≥ 50 years with early breast cancer (tumor ≤ 10 mm) and clinically-negative axillary nodes were randomized to receive treatment with ALNC (Ax) or without (no-Ax). Adjuvant therapies were prescribed according to hormonal receptor status and individual histological results. The primary endpoint was overall survival (OS); secondary endpoints were event-free survival (EFS) and functional outcomes. The trial was terminated due to lack of equivalence and low accrual after first interim analyses.



Of 625 patients, 297 no-Ax and 310 Ax patients were maintained for final per-protocol analyses. OS and EFS at five years were not equivalent (Ax vs. no-Ax: 98% vs. 94% and 96% vs. 90% respectively). Recurrence was higher for no-Ax, particularly in the first five years after surgery. Axillary nodes were positive for 14% Ax patients but only 2% no-Ax patients experienced axillary node recurrence. Functional impairments were greater after ALNC.



Our results fail to demonstrate equivalence of outcomes when ALNC is omitted from post-menopausal early breast cancer patient treatment. However the low locoregional recurrence rates warrant further examination over a longer duration, in particular to consider whether these would impact on survival.
[Development of an algorithm to predict the incidence of major depression among primary care consultants].

The reduction of major depression incidence is a public health challenge.



To develop an algorithm to estimate the risk of occurrence of major depression in patients attending primary health centers (PHC).



Prospective cohort study of a random sample of 2832 patients attending PHC centers in Concepción, Chile, with evaluations at baseline, six and twelve months. Thirty nine known risk factors for depression were measured to build a model, using a logistic regression. The algorithm was developed in 2,133 patients not depressed at baseline and compared with risk algorithms developed in a sample of 5,216 European primary care attenders. The main outcome was the incidence of major depression in the follow-up period.



The cumulative incidence of depression during the 12 months follow up in Chile was 12%. Eight variables were identified. Four corresponded to the patient (gender, age, depression background and educational level) and four to patients' current situation (physical and mental health, satisfaction with their situation at home and satisfaction with the relationship with their partner). The C-Index, used to assess the discriminating power of the final model, was 0.746 (95% confidence intervals (CI = 0,707-0,785), slightly lower than the equation obtained in European (0.790 95% CI = 0.767-0.813) and Spanish attenders (0.82; 95% CI = 0.79-0.84).



Four of the factors identified in the risk algorithm are not modifiable. The other two factors are directly associated with the primary support network (family and partner). This risk algorithm for the incidence of major depression provides a tool that can guide efforts towards design, implementation and evaluation of effectiveness of interventions to prevent major depression.
De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway

The entire world is facing a deteriorating environment. Understanding the mechanisms underlying plant responses to external abiotic stresses is important for breeding stress-tolerant crops and herbages. Phytohormones play critical regulatory roles in plants in the response to external and internal cues to regulate growth and development. Medicago falcata is one of the stress-tolerant candidate leguminous species and is able to fix atmospheric nitrogen. This ability allows leguminous plants to grow in nitrogen deficient soils. We performed Illumina sequencing of cDNA prepared from abiotic stress treated M. falcata. Sequencedreads were assembled to provide a transcriptome resource. Transcripts were annotated using BLASTsearches against the NCBI non-redundant database and gene ontology definitions were assigned. Acomparison among the three abiotic stress treated samples was carried out. The expression of transcriptswas confirmed with qRT-PCR. We present an abiotic stress-responsive M. falcata transcriptome using next-generation sequencing data from samples grown under standard, dehydration, high salinity, and cold conditions. We combined reads from all samples and de novo assembled 98,515 transcripts to build the M. falcata gene index. A comprehensive analysis of the transcriptome revealed abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. We identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses. Additionally, a global comparison of homology between the M. falcata and M. truncatula transcriptomes, along with five other leguminous species, revealed a high level of global sequence conservation within the family. M. falcata is shown to be a model candidate for studying abiotic stress-responsive mechanisms in legumes. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to abiotic stresses. Our data provides many gene candidates that might be used for herbage and crop breeding. Additionally, FalcataBase ( http://bioinformatics.cau.edu.cn/falcata/ ) was built for storing these data.
Clinical trial: the effects of the proton pump inhibitor dexlansoprazole MR on daytime and nighttime heartburn in patients with non-erosive reflux disease.

The proportion of patients who respond to proton pump inhibitor (PPI) therapy is about 20% lower in those with non-erosive reflux disease (NERD) than in those with erosive oesophagitis.



To assess efficacy and safety of dexlansoprazole MR, a PPI using Dual Delayed Release technology, in NERD patients.



In this 4-week, double-blind, placebo-controlled study, 947 NERD patients randomly received dexlansoprazole MR 30 mg, 60 mg or placebo once daily (QD). The percentages of 24-h heartburn-free days (primary) and nights without heartburn (secondary) were assessed from patients' daily diaries. Investigators also assessed symptoms. Patients completed validated quality of life and symptom severity questionnaires.



Dexlansoprazole MR provided significantly greater median percentages of 24-h heartburn-free days (54.9% and 50.0% for the 30- and 60-mg doses vs. 17.5% for placebo, P < 0.00001) and nights without heartburn (80.8% and 76.9% vs. 51.7%, P < 0.00001 vs. placebo). Dexlansoprazole MR also reduced symptom severity. Quality of life improvements in patients receiving dexlansoprazole MR were consistent with clinical efficacy endpoints. Percentages of patients experiencing treatment-emergent adverse events were similar among groups.



Dexlansoprazole MR 30 and 60 mg were superior to placebo in providing 24-h heartburn-free days and nights in NERD patients. Treatment was well tolerated.
Patient knowledge of atrial fibrillation: 3-month follow-up after an emergency room visit.

This paper is a report of a study to assess patient knowledge about atrial fibrillation, its determinants and evolution during 3 months after a visit to the emergency room.



Atrial fibrillation is one of the most common single diagnoses in the emergency room, and care often results in treatment modifications after which most patients are discharged home.



A knowledge test was developed to measure patients' knowledge of atrial fibrillation. Patient data from 200 patients were assessed by examining quartiles and medians. The statistical significance of changes was tested with the Sign test. A logistic regression model was built to identify variables possibly related to patient knowledge. The data were collected in 2003 in three emergency rooms in Finland.



Patients had only moderate knowledge about atrial fibrillation in the emergency room, and their knowledge showed only limited improvement 3 months after the visit. They had best knowledge of the symptoms of atrial fibrillation and its effects on everyday life. There were gaps in their knowledge about this disease and how it is treated, including anticoagulation, detection of symptoms and when to seek treatment, both during the emergency room visit and 3 months thereafter. Male gender, previous atrial fibrillation diagnosis and sense of good coping with the disease were statistically significantly associated with better knowledge.



Informational support should be available for patients with atrial fibrillation during and after the emergency room visit. The knowledge test introduced in this paper could be developed to evaluate the educational needs of individual patients.
Performance of Spanish speakers on the Mattis dementia rating scale (MDRS).

This paper examined whether education-, age-, and gender-matched Spanish- and English-speaking normals (n=30 pairs) had comparable scores on the Mattis dementia rating scale (MDRS). It provides preliminary normative data on Spanish-speaking volunteers aged 55-89 years old (n=54). It also compared the MDRS total score with its memory subscale score and the mini-mental state examination (MMSE) score on sensitivity and specificity for distinguishing normals from patients with dementia (n=61). Spanish-speaking normals scored significantly lower than English-speaking normals on MDRS total and its attention, conceptualization, and memory subscales. The area under the receiver operating characteristic curve distinguishing normals from patients with dementia was not significantly different among the MDRS total, its memory subscale, and the MMSE. We conclude that (a) the norms based on English-speaking individuals are not appropriate for use with Spanish-speaking individuals, and (b) to screen for dementia, the shorter MDRS Memory subscale and the MMSE are as good as the entire MDRS.
Exploring the effect of achievements on students attending university orientation

University orientation is a key event for new students that aids in the transition from a school to a university environment. A smartphone orientation application was built to aid students attending the event. Achievements were added to the application in an attempt to engage students further with the orientation activities and application. An exploratory field study was undertaken to evaluate the effect of the achievement system on participants attending orientation. Forty-six new students were recruited to test the orientation application. Twenty-six participants used a gamified version of the orientation application and twenty participants used a non-gamified version. While the gamification was generally well received, no impact on user experience was evident. Some effect on engagement with orientation activities was shown. Participants who used the gamified system reported the game elements as fun, but some negative issues arose, such as cheating.
[Epidemiology of candidemia: a one-year prospective observational study in the west of France].

A one-year prospective, observational study was conducted in the west of France, to evaluate the epidemiology of candidemia.



During the year 2004, each patient with at least one blood culture yielding Candida sp. was included. For each episode of candidemia, mycological, demographical, clinical, and therapeutic data, as well as outcome, were collected.



One hundred and ninety-three strains of Candida sp. were isolated in 186 patients, Candida albicans accounting for 54.9%, Candida glabrata for 18.7%, Candida parapsilosis for 12.9%, Candida tropicalis for 4.7% and Candida krusei for 4.1% of these isolates. A percentage of 84% of the Candida isolates were fully susceptible to fluconazole in vitro. Dose-dependent susceptibility or resistance to fluconazole was detected in more than one third of the Candida glabrata strains, of which 36% were also resistant to voriconazole. Two-thirds of the patients were males, and the mean age was 61.5 years. A percentage of 37% of patients were hospitalized in intensive care units. The main predisposing factors for candidemia were broad-spectrum antibiotics (75.8%), central venous catheter (72.6%), cancer or hematologic malignancy (47.3%), recent surgery (42.5%), total parenteral nutrition (37.6%). One hundred and fifty-four patients were treated with antifungal therapy, two-thirds of whom received fluconazole as first-line agent. Mortality was 49% overall, and was significantly higher in case of septic shock, advanced age, and absence of catheter removal.
The influence of communication goals and physical demands on different dimensions of pain behavior

The purpose of the present research was to examine the influence of communication goals and physical demands on the expression of communicative (e.g., facial grimaces) and protective (e.g., guarding) pain behaviors. Participants with musculoskeletal conditions (N=50) were asked to lift a series of weights under two communication goal conditions. In one condition, participants were asked to estimate the weight of the object they lifted. In a second condition, participants were asked to rate their pain while lifting the same objects. The display of communicative pain behaviors varied as a function of the communication goal manipulation; participants displayed more communicative pain behavior when asked to rate their pain while lifting objects than when they estimated the weight of the object. Protective pain behaviors varied with the physical demands of the task, but not as a function of the communication goals manipulation. Pain ratings and self-reported disability were significantly correlated with protective pain behaviors but not with communicative pain behaviors. The results of this study support the functional distinctiveness of different forms of pain behavior. Findings are discussed in terms of evolutionary and learning theory models of pain behavior. Clinical implications of the findings are addressed.
First-in-Human Phase I Study of GSK2126458, an Oral Pan-Class I Phosphatidylinositol-3-Kinase Inhibitor, in Patients with Advanced Solid Tumor Malignancies.

GSK2126458 (GSK458) is a potent inhibitor of PI3K (α, β, γ, and δ), with preclinical studies demonstrating broad antitumor activity. We performed a first-in-human phase I study in patients with advanced solid tumors.



Patients received oral GSK458 once or twice daily in a dose-escalation design to define the maximum tolerated dose (MTD). Expansion cohorts evaluated pharmacodynamics, pharmacokinetics, and clinical activity in histologically and molecularly defined cohorts.



One hundred and seventy patients received doses ranging from 0.1 to 3 mg once or twice daily. Dose-limiting toxicities (grade 3 diarrhea,n= 4; fatigue and rash,n= 1) occurred in 5 patients (n= 3 at 3 mg/day). The MTD was 2.5 mg/day (MTD with twice daily dosing undefined). The most common grade ≥3 treatment-related adverse events included diarrhea (8%) and skin rash (5%). Pharmacokinetic analyses demonstrated increased duration of drug exposure above target level with twice daily dosing. Fasting insulin and glucose levels increased with dose and exposure of GSK458. Durable objective responses (ORs) were observed across multiple tumor types (sarcoma, kidney, breast, endometrial, oropharyngeal, and bladder cancer). Responses were not associated withPIK3CAmutations (OR rate: 5% wild-type vs. 6% mutant).



Although the MTD of GSK458 was 2.5 mg once daily, twice-daily dosing may increase duration of target inhibition. Fasting insulin and glucose levels served as pharmacodynamic markers of drug exposure. Select patients achieved durable responses; however,PIK3CAmutations were neither necessary nor predictive of response. Combination treatment strategies and novel biomarkers may be needed to optimally target PI3K.
Expression and New Exon Mutations of the Human Beta Defensins and Their Association on Colon Cancer Development

The development of cancer involves genetic predisposition and a variety of environmental exposures. Genome-wide linkage analyses provide evidence for the significant linkage of many diseases to susceptibility loci on chromosome 8p23, the location of the human defensin gene cluster. Human β-defensins (hBDs) are important molecules of innate immunity. This study was designed to analyze the expression and genetic variations in hBDs (hBD-1, hBD-2, hBD-3 and hBD-4) and their putative association with colon cancer. hBD gene expression and relative protein expression were evaluated by Real-Time polymerase chain reaction (qPCR) and immunohistochemistry, respectively, from 40 normal patients and 40 age-matched patients with colon cancer in Saudi Arabia. In addition, hBD polymorphisms were genotyped by exon sequencing and by promoter methylation.  Several insertion mutations were detected in different exons of the analyzed hBDs. However, no methylation in any hBDs promoters was detected because of the limited number of CpG islands in these regions. We demonstrated for the first time a link between hBD expression and colon cancer. This suggests that there is a significant link between innate immunity deregulation through disruption of cationic peptides (hBDs) and the potential development of colon cancer.
Transrectal periprostatic lidocaine injection anesthesia for transrectal prostate biopsy: a prospective study

Transrectal ultrasound (TRUS)-guided biopsy remains the mainstay of the diagnosis of prostate cancer. Although this diagnostic method is a safe procedure and well tolerated by most patients a significant number of patients report discomfort and pain during prostate biopsy. In order to define the best method of anesthesia, many studies, in which different methods were compared, have been performed. To determine the effectiveness of local injection anesthesia in TRUS-guided prostate biopsy, we designed and performed this prospective study in order to evaluate the utility of periprostatic nerve block for pain management. A total of 100 patients who had elevated total prostate-specific antigen (tPSA) and/or abnormal digital rectal examination (DRE) were included in this study. Half of the patients received periprostatic injection anesthesia (group I) and the remaining half received placebo (group II). Patients received 10 cm3 (5 cm3 each side) 1% lidocaine injected into the periprostatic nerve plexus under transrectal ultrasonic guidance. Pain during biopsy was assessed using a 10-point modified visual analog scale (VAS). In groups I and II, mean patient age was 66.8+2.5 and 65.6+11.5 y, mean tPSA was 7.87±3.6 and 11.3±1.7 ng/ml, mean biopsy duration was 6.5±2.5 and 6.6±2.2 min and mean pain score during TRUS-guided biopsy was 1.46±2.2 and 4.5±2.1, respectively. No statistically significant difference was observed with respect to age, tPSA and mean biopsy duration between these groups. Mean pain VAS score was statistically or significantly better (P=0.0001) in the lidocaine injection group (group I), and furthermore no patient had a VAS pain score ≥5 in this group. Only minor and transient complications occurred in both groups. This study reinforces the usage of periprostatic nerve block as a standard method of pain management during TRUS-guided prostate biopsy, because it is simple, safe, uncostly and significantly effective without requiring additional time.
A Multi-Level Transformation Approach to HW/SW Codesign: A Case Study

This reported work applies a transformational synthesis approach to hardware/software codesign. In this approach, the process of algorithm design is coupled early on with hardware design to allow for a complete design space exploration. Both the specification and the transformation mechanisms are encoded in a functional notation, called form, which facilitates algorithmic derivation, structural transformation and verification. In the algorithmic derivation phase, possible computational schedules for a given application function are generated from a partial specification of the target architecture. At the hardware level, structural transformations are applied to explore possible datapath designs, where different designs yield different performance and cost. Other design metrics such as interface buffer size, software code size and data size etc. are also included to determine analytically a hardware/ software partition.
Salivary duct carcinoma: the predominance of apocrine morphology, prevalence of histologic variants, and androgen receptor expression.

Salivary duct carcinoma (SDC) is a prototypic aggressive salivary gland carcinoma. Our aim is to determine the prevalence of histologic variants (micropapillary, basal-like) and androgen receptor (AR) expression in a large multi-institutional series of SDC. AR status was determined by immunohistochemistry (IHC). Most SDCs were characterized by an apocrine phenotype and AR expression. Cases with a nonapocrine phenotype and AR-negative status were studied by additional IHC and fluorescence in situ hybridization for ETV6 or MYB/NFIB. The diagnosis of SDC was confirmed in 187 of 199 (94%) cases. Variant morphologies were identified in 12 cases: micropapillary (n=6), sarcomatoid (n=3), mucinous (n=2), and basal-like (n=1). AR IHC was performed in 183 cases, of which 179 (97.8%) showed AR expression. On the basis of morphologic appearance and results of additional studies, 12 cases were reclassified as squamous cell carcinoma (SCC) (n=4), epithelial-myoepithelial carcinoma with high-grade transformation (HGT) (n=2), myoepithelial carcinoma (n=2), mammary analogue secretory carcinoma, high grade (ETV6 translocated; n=1), adenoid cystic carcinoma with HGT (n=1), acinic cell carcinoma with HGT (n=1), and adenosquamous carcinoma (n=1). AR-negative SDC is extremely rare, and the majority of such cases are more accurately classified as other entities. HGTs of other salivary carcinomas and squamous cell carcinoma are the most common mimics of SDC. SDCs with variant morphologies still show at least a minor component of conventional apocrine appearance. Thus, apocrine morphology defines SDC.
The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30): Validation of English version in Singapore

This study aimed to validate the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30, English version 3.0) in Singaporean cancer patients.  In a cross-sectional study, a heterogeneous sample of cancer patients (n = 57) self-administered a questionnaire containing the QLQ-C30, the Short Form 36 Health Survey (SF-36) and assessing health and sociodemographic status. Construct validity was assessed by testing a priori hypotheses that QLQ-C30 scales would be moderately or strongly correlated with SF-36 scales measuring similar dimensions of health-related quality of life (HRQoL) and that subjects reporting mild symptoms would have better HRQoL scores than those reporting severe symptoms. Internal consistency reliability was assessed using Cronbach’s α.  Strength of Spearman’s correlations between the QLQ-C30 and SF-36 scales assessing similar dimensions of HRQoL ranged from 0.35 to 0.67. Subjects with mild symptoms had better scores than those with severe symptoms for all six QLQ-C30 HRQoL scales (p < 0.05 for five scales, Mann–Whitney U tests). Cronbach’s α ranged from 0.19 for the cognitive functioning scale to 0.91 for the global QoL scale.  This study provides preliminary evidence for the validity and reliability of the EORTC QLQ-C30 in English-speaking Singaporean cancer patients.