nils-herrmann/clean_scirepeval huggingface dataset:
DNA copy number alterations and expression of relevant genes in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is defined by a lack of expression of estrogen, progesterone, and HER2 receptors, and genetically most of them fall into the basal subgroup of breast cancer. The important issue of TNBC is poorer clinical outcome and absence of effective targeted therapy. In this study, we sought to identify DNA copy number alterations and expression of relevant genes characteristic of TNBC to discover potential therapeutic targets. Frozen tissues from 114 breast cancers were analyzed using high-resolution array comparative genomic hybridization. The classification into subtype was determined by estrogen and progesterone receptor expression, and by the presence or absence of gain on the ERBB2 containing clone. The ACE algorithm was used for calling gain and loss of clones. Twenty-eight cases (25%) were classified as TNBC. Recurrent gains (> or =25%) unique to TNBC were 9p24-p21, 10p15-p13, 12p13, 13q31-q34, 18q12, 18q21-q23, and 21q22. Two published gene expression array data sets comparing basal subtype versus other subtype breast cancers were used for searching candidate genes. Of the genes upregulated in the basal subtype, 45 of 686 genes in one data set and 59 of 1,428 in the second data set were found to be located in the gained regions. Of these candidate genes, gain of NFIB (9p24.1) was specific for TNBC in a validation set by real-time PCR. In conclusion, we have identified recurrently gained regions characteristic of TNBC, and found that NFIB copy number and expression is increased in TNBC across the data sets. This article contains Supplementary Material available at .
Self-as-doer for diabetes: development and validation of a diabetes-specific measure of doer identification.

The purpose of this study was to develop and validate a scale to measure the level of self-care behavior "doer identity" in persons with diabetes.



Persons with diabetes (N = 355) completed questionnaires assessing self-as-doer identity and other related constructs. Principle components and parallel analyses and tests of reliability and validity were performed.



A 7 factor solution explained 55.24% of the total variance on behaviors. Cronbach's alpha was .93 for the overall scale. Extracted components moderately correlated with one another and theoretically similar constructs. Self-as-doer identity significantly predicted all self-care behaviors (except for blood glucose monitoring) and glycemic control over and above related variables for persons with type 1 diabetes. Self-as-doer identity also predicted diet behaviors for persons with type 2 diabetes.



Evidence for a reliable and valid factor structure of the Self-as-doer-Diabetes measure was demonstrated.
The Influence of Metabolic Factors for Nonalcoholic Fatty Liver Disease in Women

Women after menopause have increased insulin resistance and visceral fat, which may increase the prevalence of nonalcoholic fatty liver disease (NAFLD). However, the pathogenesis of NAFLD in women has not been clearly defined. In this study, we aimed to determine the risk factors for NAFLD in women.



A retrospective cohort study was conducted. Women who underwent abdominal ultrasonography and blood sampling for routine health check-ups were recruited.



Among 1,423 subjects, 695 women (48.9%) were in a menopausal state. The prevalence of NAFLD was higher in postmenopausal women than in premenopausal women (27.2% versus 14.4%, P < 0.001). In premenopausal women, low HDL-cholesterol, central obesity, and homeostasis model assessment-estimated insulin resistance showed a significant association with the increased risk of NAFLD in multivariate analysis. In postmenopausal women, the presence of diabetes, triglyceridemia, and central obesity showed a significant association with the risk of NAFLD. The presence of menopause and hormone replacement therapy in postmenopausal women were not risk factors for NAFLD.



Our findings showed different metabolic factors for NAFLD in pre- and postmenopausal women. However, the key issues are the same: central obesity and insulin resistance. These results reemphasize the importance of metabolic factors irrespective of menopausal status in the pathogenesis of NAFLD in women.
Myocardial CT perfusion imaging in a large animal model: comparison of dynamic versus single-phase acquisitions.

This study sought to compare dynamic versus single-phase high-pitch computed tomography (CT) acquisitions for the assessment of myocardial perfusion in a porcine model with adjustable degrees of coronary stenosis.



The incremental value of the 2 different approaches to CT-based myocardial perfusion imaging remains unclear.



Country pigs received stent implantation in the left anterior descending coronary artery, in which an adjustable narrowing (50% and 75% stenoses) was created using a balloon catheter. All animals underwent CT-based rest and adenosine-stress myocardial perfusion imaging using dynamic and single-phase high-pitch acquisitions at both degrees of stenosis. Fluorescent microspheres served as a reference standard for myocardial blood flow. Segmental CT-based myocardial blood flow (MBFCT) was derived from dynamic acquisitions. Segmental single-phase enhancement (SPE) was recorded from high-pitch, single-phase examinations. MBFCT and SPE were compared between post-stenotic and reference segments, and receiver-operating characteristic curve analysis was performed.



Among 6 animals (28 ± 2 kg), there were significant differences of MBFCT and SPE between post-stenotic and reference segments for all acquisitions at 75% stenosis. By contrast, although for 50% stenosis at rest, MBFCT was lower in post-stenotic than in reference segments (0.65 ± 0.10 ml/g/min vs. 0.75 ± 0.16 ml/g/min, p < 0.05), there was no difference for SPE (128 ± 27 Hounsfield units vs. 137 ± 35 Hounsfield units, p = 0.17), which also did not significantly change under adenosine stress. In receiver-operating characteristic curve analyses, segmental MBFCT showed significantly better performance for ischemia prediction at 75% stenosis and stress (area under the curve: 0.99 vs. 0.89, p < 0.05) as well as for 50% stenosis, regardless of adenosine administration (area under the curve: 0.74 vs. 0.57 and 0.88 vs. 0.61, respectively, both p < 0.05).



At higher degrees of coronary stenosis, both MBFCT and SPE permit an accurate prediction of segmental myocardial hypoperfusion. However, accuracy of MBFCT is higher than that of SPE at 50% stenosis and can be increased by adenosine stress at both degrees of stenosis.
Effects on motor development of kicking and stepping exercise in preterm infants with periventricular brain injury: a pilot study.

Preterm infants with periventricular brain injury (PBI) have a high incidence of atypical development and leg movements.



Determine whether kicking and treadmill stepping intervention beginning at 2 months corrected age (CA) in children with PBI improves motor function at 12 months CA when compared with control subjects.



In a multi-center pilot study for a controlled clinical trial, sixteen infants with PBI were randomly assigned to home exercise consisting of kicking and treadmill stepping or a no-training control condition. Development was assessed at 2, 4, 6, 10, and 12 months CA with the Alberta Infant Motor Scale (AIMS). At 12 months children were classified as normal, delayed, or with cerebral palsy (CP).



At 12 months CA 3 of 7 (43%) of the exercise group children walked alone or with one hand held versus 1 of 9 (11%) in the control group (p=0.262), but no significant differences in AIMS scores were found at any age. Half of the subjects had CP or delay; the outcomes of these infants were not improved by exercise. Compliance with the home program was lower than requested and may have affected results.



Although not statistically significant with a small sample size, self-produced kicking and treadmill exercise may lower age at walking in infants with normal development following PBI, but improvements of the protocol to increase and document compliance are needed before a larger study is implemented.
Intravenous aminophylline in patients admitted to hospital with non-acidotic exacerbations of chronic obstructive pulmonary disease: a prospective randomised controlled trial.

Intravenous aminophylline is commonly used in the treatment of exacerbations of chronic obstructive pulmonary disease (COPD), despite limited evidence for its efficacy and known risks of toxicity. We hypothesised that adding intravenous aminophylline to conventional treatment would not produce clinically important changes in the speed of spirometric or symptomatic recovery or shorten hospital stay in patients with exacerbations of COPD.



Eighty patients admitted to hospital with non-acidotic exacerbations of COPD were recruited at admission to a randomised, double blind, placebo controlled study comparing intravenous aminophylline 0.5 mg/kg/hour after an appropriate loading dose with an equivalent volume of 0.9% saline. The primary outcome was the change in post-bronchodilator forced expiratory volume in 1 second (FEV(1)) over the first 5 days of the admission. Secondary end points were changes in self-reported breathlessness, arterial blood gas tensions, forced vital capacity (FVC), and length of hospital stay.



There was no difference in the post-bronchodilator FEV(1) over the first 5 days between the aminophylline and placebo groups. In the aminophylline group, 2 hours of treatment produced a small but significant rise in arterial pH (p = 0.001) and a fall in arterial carbon dioxide tension (p = 0.01) compared with placebo treatment. There were no differences in the severity of breathlessness, post-bronchodilator FVC, or length of hospital stay between the groups. Nausea was a more frequent side effect in the aminophylline group (46% v 22%; p<0.05), but palpitations and headache were noted equally in both groups.



Although intravenous aminophylline produced small improvements in acid-base balance, these did not influence the subsequent clinical course. No evidence was found for any clinically important additional effect of aminophylline treatment when used with high dose nebulised bronchodilators and oral corticosteroids. Given its known toxicity, we cannot therefore recommend the use of intravenous aminophylline in the treatment of non-acidotic COPD exacerbations.
Effect of nutritional supplementation of breastfeeding HIV positive mothers on maternal and child health: findings from a randomized controlled clinical trial

It has been well established that breastfeeding is beneficial for child health, however there has been debate regarding the effect of lactation on maternal health in the presence of HIV infection and the need for nutritional supplementation in HIV positive lactating mothers.



To assess the effect of nutritional supplementation to HIV infected lactating mothers on nutritional and health status of mothers and their infants.



A randomized controlled clinical trial to study the impact of nutritional supplementation on breastfeeding mothers. Measurements included anthropometry; body composition indicators; CD4 count, haemoglobin and albumin; as well as incidence rates of opportunistic infections; depression and quality of life scores. Infant measurements included anthropometry, development and rates of infections.



The supplement made no significant impact on any maternal or infant outcomes. However in the small group of mothers with low BMI, the intake of supplement was significantly associated with preventing loss of lean body mass (1.32 kg vs. 3.17 kg; p = 0.026). There was no significant impact of supplementation on the infants.



A 50 g daily nutritional supplement to breastfeeding mothers had no or limited effect on mother and child health outcomes.
Impact of prior treatment on patients with relapsed multiple myeloma treated with carfilzomib and dexamethasone vs bortezomib and dexamethasone in the phase 3 ENDEAVOR study

The randomized phase 3 ENDEAVOR study (N=929) compared carfilzomib and dexamethasone (Kd) with bortezomib and dexamethasone (Vd) in relapsed multiple myeloma (RMM). We performed a subgroup analysis from ENDEAVOR in patients categorized by number of prior lines of therapy or by prior treatment. Median progression-free survival (PFS) for patients with one prior line was 22.2 months for Kd vs 10.1 months for Vd, and median PFS for patients with ⩾2 prior lines was 14.9 months for Kd vs 8.4 months for Vd. For patients with prior bortezomib exposure, the median PFS was 15.6 months for Kd vs 8.1 months for Vd, and for patients with prior lenalidomide exposure the median PFS was 12.9 months for Kd vs 7.3 months for Vd. Overall response rates (Kd vs Vd) were 81.9 vs 65.5% (one prior line), 72.0 vs 59.7% (⩾2 prior lines), 71.2 vs 60.3% (prior bortezomib) and 70.1 vs 59.3% (prior lenalidomide). The safety profile in the prior lines subgroups was qualitatively similar to that in the broader ENDEAVOR population. In RMM, outcomes are improved when receiving treatment with carfilzomib compared with bortezomib, regardless of the number of prior therapy lines or prior exposure to bortezomib or lenalidomide.
Analysis of quality of life among asthmatic individuals with obesity and its relationship with pulmonary function: cross-sectional study.

The combined effect of obesity and asthma may lead to significant impairment of quality of life (QOL). The aim here was to evaluate the prevalence of asthma among obese individuals, characterize the severity of impairment of quality of life and measure its relationship with pulmonary function.



Observational cross-sectional study in public university hospital.



Morbidly obese individuals (body mass index > 40 kg/m2) seen in a bariatric surgery outpatient clinic and diagnosed with asthma, were included. Anthropometric data were collected, the Standardized Asthma Quality of Life Questionnaire (AQLQ(S)) was applied and spirometry was performed. The subjects were divided into two groups based on the median of the score in the questionnaire (worse < 4 and better > 4) and were compared regarding anthropometric data and pulmonary function.



Among the 4791 individuals evaluated, 219 were asthmatic; the prevalence of asthma was 4.57%. Of these, 91 individuals were called to start multidisciplinary follow-up during the study period, of whom 82 answered the questionnaire. The median score in the AQLQ(S) was 3.96 points and, thus, the individuals were classified as having moderate impairment of their overall QOL. When divided according to better or worse QOL, there was a statistically difference in forced expiratory flow (FEF) 25-75%, with higher values in the better QOL group.



The prevalence of asthma was 4.57% and QOL was impaired among the asthmatic obese individuals. The worst QOL domain related to environmental stimuli and the best QOL domain to limitations of the activities. Worse QOL was correlated with poorer values for FEF 25-75%.
The effects of controlled breathing during pulmonary rehabilitation in patients with COPD.

Conventional pulmonary rehabilitation programs improve exercise tolerance but have no effect on pulmonary function in patients with chronic obstructive pulmonary disease (COPD). The role of controlled breathing using respiratory biofeedback during rehabilitation of patients with COPD remains unclear.



To compare the effects of a conventional 4-week pulmonary rehabilitation program with those of rehabilitation plus controlled breathing interventions.



A randomized controlled trial was performed. Pulmonary function (FEV1), exercise capacity (6-min walking distance, 6 MWD), health-related quality of life (chronic respiratory questionnaire, CRQ) and cardiac autonomic function (rMSSD) were evaluated.



Forty COPD patients (mean±SD age 66.1±6.4, FEV1 45.9±17.4% predicted) were randomized to rehabilitation (n=20) or rehabilitation plus controlled breathing (n=20). There were no statistically significant differences between the two groups regarding the change in FEV1 (mean difference -0.8% predicted, 95% CI -4.4 to 2.9% predicted, p=0.33), 6 MWD (mean difference 12.2 m, 95% CI -37.4 to 12.2 m, p=0.16), CRQ (mean difference in total score 0.2, 95% CI -0.1 to 0.4, p=0.11) and rMSSD (mean difference 2.2 ms, 95% CI -20.8 to 25.1 ms, p=0.51).



In patients with COPD undergoing a pulmonary rehabilitation program, controlled breathing using respiratory biofeedback has no effect on exercise capacity, pulmonary function, quality of life or cardiac autonomic function.
Clinical Evaluation and Magnetic Resonance Imaging Assessment of Intradiscal Methylene Blue Injection for the Treatment of Discogenic Low Back Pain.

Low back pain is a common worldwide health problem and has a significant socioeconomic impact on public health. Internal disc disruption has been considered as the most common cause of low back pain. Various therapies, including interbody fusion, disc replacement, injection therapies, and thermal annular procedures have been utilized for the treatment of discogenic low back pain. Recently, a new method of intradiscal methylene blue injection has been introduced to treat discogenic low back pain, but the clinical outcomes are controversial.



To investigate the clinical outcomes and magnetic resonance imaging changes of intradiscal methylene blue injection for the treatment of discogenic low back pain.



Observational study.



An interventional low back pain management practice in a university hospital.



A total of 33 patients were selected to be treated with intradiscal methylene blue injection. The clinical outcomes were evaluated by numeric rating scale and Oswestry Disability Index at pretreatment, one month, 3, 6, and 12 months after treatment. The magnetic resonance imaging changes of involved intervertebral discs were assessed by apparent diffusion coefficient and T2 values at pretreatment, 3, 6, and 12 months after treatment.



All of the patients got a follow-up period up to 12 months. The mean numeric rating scale scores at pretreatment, one month, 3, 6, and 12 months after treatment were 6.54, 2.98, 3.23, 3.66, and 4.72, respectively. There was a minimum of 2 points reduction at one month, 3, and 6 months after treatment, but less than 2 points reduction at 12 months. There was at least 50% improvement on the Oswestry Disability Index at one month, 3, and 6 months after treatment, but not at 12 months. The mean apparent diffusion coefficient and T2 value were significantly higher at 6 and12 months after treatment compared to pretreatment, but there was no significant difference between pretreatment and 3 months after treatment.



This is an observational study with a relatively small sample size and short-term follow-up.



The intradiscal methylene blue injection might be an effective therapy for discogenic low back pain for the short-term and could improve disc degeneration condition to some extent. Low back pain, discogenic pain, internal disc disruption, provocation discography, methylene blue, intradiscal injection, disc degeneration, magnetic resonance, imaging.
Controlled medial branch anesthetic block in the diagnosis of chronic lumbar facet joint pain: the value of a three-month follow-up

To verify the incidence of facetary and low back pain after a controlled medial branch anesthetic block in a three-month follow-up and to verify the correlation between the positive results and the demographic variables.



Patients with chronic lumbar pain underwent a sham blockade (with a saline injection) and then a controlled medial branch block. Their symptoms were evaluated before and after the sham injection and after the real controlled medial branch block; the symptoms were reevaluated after one day and one week, as well as after one, two and three months using the visual analog scale. We searched for an association between the positive results and the demographic characteristics of the patients.



A total of 104 controlled medial branch blocks were performed and 54 patients (52%) demonstrated >50% improvements in pain after the blockade. After three months, lumbar pain returned in only 18 individuals, with visual analogue scale scores >4. Therefore, these patients were diagnosed with chronic facet low back pain. The three-months of follow-up after the controlled medial branch block excluded 36 patients (67%) with false positive results. The results of the controlled medial branch block were not correlated to sex, age, pain duration or work disability but were correlated with patient age (p<0.05).



Patient diagnosis with a controlled medial branch block proved to be effective but was not associated with any demographic variables. A three-month follow-up is required to avoid a high number of false positives.
S-l combined with cisplatin plus concurrent chemoradiotherapy versus cisplatin plus concurrent chemoradiotherapy for Chinese patients with advanced gastric cancer: a multi-centre randomized controlled trial.

This study aimed to investigate the safety and efficacy of S-l combined with cisplatin plus concurrent chemoradiotherapy (SCCC) versus cisplatin plus concurrent chemoradiotherapy (CCC) for Chinese patients with advanced gastric cancer (AGC).



Between April 2008 and June 2010, 144 eligible patients with AGC were included and divided randomly into 2 groups. Seventy-two patients in the SCCC group received with S-1 on days 1-14 of a 21-day cycle, 24-h cisplatin infusion (70 mg/m(2) on day 1) every 4 weeks for 2 cycles, and concurrent chemoradiotherapy (30-Gy radiotherapy over 4 weeks) beginning on day 1. The other 72 patients in the CCC group were administered cisplatin and concurrent chemoradiotherapy as for SCCC. The primary outcome was overall survival. Secondary outcomes were progression-free survival and adverse events.



The median overall survival durations were 11.7 months (range 1.7-29.7 months) and 9.5 months (range 1.2-25.4 months) in SCCC and CCC groups, respectively (P = 0.041). The median progression-free survival durations were 10.6 months for SCCC (range 1.3-24.7 months) and 8.8 months (range 0.7-22.3 months) for CCC (P = 0.046). The toxicity profile was similar in both groups.



In summary, SCCC showed more promising safety and efficacy than CCC in Chinese patients with AGC. In addition, the toxicities were also acceptable in both groups.