nils-herrmann/clean_scirepeval huggingface dataset:
Relationship between in vitro drug sensitivity and clinical response of patients to treatment in chronic lymphocytic leukemia.

To improve the efficacy of therapeutic options in chronic lymphocytic leukemia (CLL) an in vitro system to determine the response of mononuclear blood cells from blood of patients was elaborated. The study combines four approaches, i.e., cell viability, apoptosis rate, differential scanning calorimetry (DSC), and immunoblotting to develop personalized therapy protocols based on the cell sensitivity to drug exposure of individual CLL patients. The complementary analyses were performed on 28 peripheral blood samples from previously untreated CLL patients before therapy. The induction and progress of apoptosis in CLL cells exposed in vitro to purine analogs combined with mafosfamide, i.e., cladribine + mafosfamide (CM) and fludarabine + mafosfamide (FM) were assessed using the above approaches. The changes in thermal profiles (decrease/loss of transition at 95±5˚C) coincided with an accumulation of apoptotic cells, a decrease in the number of viable cells, and differences in the expression of the apoptosis‑related protein PARP‑1. No significant changes were observed in the thermal profiles of nuclei isolated from CLL cells resistant to the treatment. The complementary assays revealed a strong relationship between both the in vitro sensitivity of leukemia cells to drugs and the clinical response of the patients, determined usually after the sixth course of treatment (after ~6 months of therapy). As a summary of studies followed by complementary tests, our findings demonstrate the value of in vitro exposure of CLL cell samples to drugs intended to treat CLL patients, before their administration in order to recommend the most suitable and effective therapy for individual patients.
A multi-stage language with intensional analysis

This paper presents the definition of a language with reflection primitives. The language is a homogeneous multi-stage language that provides the capacity of code analysis by the inclusion of a pattern matching mechanism that permits inspection of the structure of quoted expressions and their destruction into component subparts. Quoted expressions include an explicit annotation of their context which is used for dynamic inference of type, where a dynamic typing discipline based on Hinze and Cheney's approach is used for typing quoted expressions.This paper follows the approach of Sheard and Pasalic about the use of the meta-language Ωmega as a tool for language design. In this sense, it is shown how to represent the syntax, the static as well as the dynamic semantics of the proposed language in terms of Ωmega constructs.
Efficacy of Integrated Rehabilitation Techniques of Traditional Chinese Medicine for ischemic stroke: a randomized controlled trial.

This study aimed to determine the efficacy of Integrated Rehabilitation Techniques of Traditional Chinese Medicine (IRT-TCM) on patients with ischemic stroke as an alternative therapy to conventional rehabilitation techniques. Sixty-nine patients with ischemic stroke were randomly assigned to receive either IRT-TCM (intervention group, n = 46) or conventional rehabilitation techniques (control group, n = 23). The IRT-TCM consisted of a sequential combination of acupuncture and massage techniques. The Fugl-Meyer Assessment (FMA), National Institutes of Health Stroke Scale (NIHSS), Barthel index (BI) and modified Rankin Scale (mRS) were measured on day 0 (baseline, before treatment), day 21, and day 90. We observed that the scores in FMA and BI were increased, and NIHSS were decreased in both groups on day 21 and 90, compared with the baseline (day 0). Furthermore, significantly better scores in FMA of lower limbs and NIHSS were found in patients treated with IRT-TCM on day 21 and 90. For mRS, the percentage of patients ranking 0 and 1 in the intervention group presented a striking contrast to the control group on day 90 but with no significant difference. The results indicated that, as a feasible alternative therapy, IRT-TCM is beneficial for patients with ischemic stroke. Further research with larger sample size, long-term observation, and strict blinding are still in need to confirm the efficacy of IRT-TCM.
Efficacy, safety and effect on biomarkers of AZD9668 in cystic fibrosis.

The aim of this study was to evaluate the safety and effect on clinical outcomes and biomarkers of inflammation and tissue damage of the neutrophil elastase inhibitor AZD9668 (60 mg twice daily orally for 4 weeks) in cystic fibrosis. This was a randomised, double-blind, placebo-controlled study. Primary outcome measures were sputum neutrophil count, lung function, 24-h sputum weight, BronkoTest® diary card data and health-related quality-of-life (revised cystic fibrosis quality-of-life questionnaire). Secondary end-points included sputum neutrophil elastase activity, inflammatory biomarkers in sputum and blood, urine and plasma desmosine (an elastin degradation marker), AZD9668 levels and safety parameters (adverse events, routine haematology, biochemistry, electrocardiogram and sputum bacteriology). 56 patients were randomised, of which 27 received AZD9668. There was no effect for AZD9668 on sputum neutrophil counts, neutrophil elastase activity, lung function or clinical outcomes, including quality of life. In the AZD9668 group, there was a trend towards reduction in sputum inflammatory biomarkers with statistically significant changes in interleukin-6, RANTES and urinary desmosine. The pattern of adverse events was similar between groups. Consistent reductions in sputum inflammatory biomarkers were seen in the AZD9668 group, and reduction in urinary desmosine suggests that AZD9668 impacts elastin cleavage by neutrophil elastase.
Preliminary results of ON/OFF detection using an integrated system for Parkinson's disease monitoring

This paper describes the experimental set up of a system composed by a set of wearable sensors devices for the recording of the motion signals and software algorithms for the signal analysis. This system is able to automatically detect and assess the severity of bradykinesia, tremor, dyskinesia and akinesia motor symptoms. Based on the assessment of the akinesia, the ON-OFF status of the patient is determined for each moment. The assessment performed through the automatic evaluation of the akinesia is compared with the status reported by the patients in their diaries. Preliminary results with a total recording period of 32 hours with two PD patients are presented, where a good correspondence (88.2 +/- 3.7 %) was observed. Best (93.7%) and worst (87%) correlation results are illustrated, together with the analysis of the automatic assessment of the akinesia symptom leading to the status determination. The results obtained are promising, and if confirmed with further data, this automatic assessment of PD motor symptoms will lead to a better adjustment of medication dosages and timing, cost savings and an improved quality of life of the patients.
Efficacy of fluticasone propionate/formoterol fumarate in the treatment of asthma: a pooled analysis.

Fluticasone propionate and formoterol fumarate have been combined in a single inhaler (fluticasone/formoterol; flutiform(®)) for the maintenance treatment of asthma. This pooled analysis assessed the efficacy of fluticasone/formoterol versus fluticasone in patients who previously received inhaled corticosteroids.



Data were pooled from five randomised studies in patients with asthma (aged ≥12 years) treated for 8 or 12 weeks with fluticasone/formoterol (100/10, 250/10 or 500/20 μg b.i.d.; n = 528 delivered via pMDI) or fluticasone alone (100, 250 or 500 μg b.i.d.; n = 527).



Fluticasone/formoterol provided significantly greater increases than fluticasone alone in mean morning forced expiratory volume in 1 second (FEV1) from pre-dose at baseline to 2 hours post-dose at study end (least-squares mean [LSM] treatment difference: 0.146L; p < 0.001) and in pre-dose FEV1 from baseline to study end (LSM treatment difference: 0.048 L; p = 0.043). Compared with fluticasone, fluticasone/formoterol provided greater increases in the percentage of asthma control days (no symptoms, no rescue medication use and no sleep disturbance due to asthma) from baseline to study end (LSM treatment difference: 8.6%; p < 0.001), and was associated with a lower annualised rate of exacerbations (rate ratio: 0.71; p = 0.014).



In summary, fluticasone/formoterol provides clinically significant improvements in lung function and asthma control measures, with a lower incidence of exacerbations than fluticasone alone.
Microbiome Dynamics of a Polychlorobiphenyl (PCB) Historically Contaminated Marine Sediment under Conditions Promoting Reductive Dechlorination

The toxicity of polychlorinated biphenyls (PCB) can be efficiently reduced in contaminated marine sediments through the reductive dechlorination (RD) process lead by anaerobic organohalide bacteria. Although the process has been extensively investigated on PCB-spiked sediments, the knowledge on the identity and metabolic potential of PCB-dechlorinating microorganisms in real contaminated matrix is still limited. Aim of this study was to explore the composition and the dynamics of the microbial communities of the marine sediment collected from one of the largest Sites of National Interest (SIN) in Italy (Mar Piccolo, Taranto) under conditions promoting the PCBs RD. A long-term microcosm study revealed that autochthonous bacteria were able to sustain the PCB dechlorination at a high extent and the successive addition of an external fermentable organic substrate (lactate) caused the further depletion of the high-chlorinated PCBs (up to 70%). Next Generation Sequencing was used to describe the core microbiome of the marine sediment and to follow the changes caused by the treatments. OTUs affiliated to sulfur-oxidizing ε-proteobacteria, Sulfurovum, and Sulfurimonas, were predominant in the original sediment and increased up to 60% of total OTUs after lactate addition. Other OTUs detected in the sediment were affiliated to sulfate reducing (δ-proteobacteria) and to organohalide respiring bacteria within Chloroflexi phylum mainly belonging to Dehalococcoidia class. Among others, Dehalococcoides mccartyi was enriched during the treatments even though the screening of the specific reductive dehalogenase genes revealed the occurrence of undescribed strains, which deserve further investigations. Overall, this study highlighted the potential of members of Dehalococcoidia class in reducing the contamination level of the marine sediment from Mar Piccolo with relevant implications on the selection of sustainable bioremediation strategies to clean-up the site.
Intensive referral to 12-Step self-help groups and 6-month substance use disorder outcomes.

This study implemented and evaluated procedures to help clinicians make effective referrals to 12-Step self-help groups.



Randomized controlled trial. Setting Out-patient substance use disorder treatment. Participants Individuals with substance use disorders (SUDs) entering a new treatment episode (n = 345) who were assigned randomly to a standard referral- or an intensive referral-to-self-help condition.



Self-reports of 12-Step group attendance and involvement and substance use at baseline and a 6-month follow-up.



The intensive referral intervention focused on encouraging patients to attend 12-Step meetings by connecting them to 12-Step volunteers.



Among patients with relatively less previous 12-Step meeting attendance, intensive referral was associated with more meeting attendance during follow-up than was standard referral. Among all patients, compared with those who received standard referral, those who received intensive referral were more likely to be involved with 12-Step groups during the 6-month follow-up (i.e. had provided service, had a spiritual awakening and currently had a sponsor). Intensive referral patients also had better alcohol and drug use outcomes at 6 months. Twelve-Step involvement mediated part of the association between referral condition and alcohol outcomes.



The brief intensive referral intervention was associated with improved 12-Step group involvement and substance use outcomes even among patients with considerable previous 12-Step group exposure and formal treatment. Future 12-Step intensive referral procedures should focus on encouraging 12-Step group involvement in addition to attendance to benefit patients most effectively.
Back-of-device authentication on smartphones

This paper presents BoD Shapes, a novel authentication method for smartphones that uses the back of the device for input. We argue that this increases the resistance to shoulder surfing while remaining reasonably fast and easy-to-use. We performed a user study (n=24) comparing BoD Shapes to PIN authentication, Android grid unlock, and a front version of our system. Testing a front version allowed us to directly compare performance and security measures between front and back authentication. Our results show that BoD Shapes is significantly more secure than the three other approaches. While performance declined, our results show that BoD Shapes can be very fast (up to 1.5 seconds in the user study) and that learning effects have an influence on its performance. This indicates that speed improvements can be expected in long-term use.
The use of energy drinks in sport: perceived ergogenicity and side effects in male and female athletes.

The use of caffeine containing energy drinks has dramatically increased in the last few years, especially in the sport context because of its reported ergogenic effect. The ingestion of low to moderate doses of caffeinated energy drinks has been associated with adverse side effects such as insomnia or increased nervousness. The aim of the present study was to assess psycho-physiological changes and the prevalence of side effects resulting from the ingestion of 3 mg caffeine/kg body mass in the form of an energy drink. In a double-blind and placebo controlled experimental design, ninety experienced and low-caffeine-consuming athletes (fifty-three male and thirty-seven female) in two different sessions were provided with an energy drink that contained 3 mg/kg of caffeine or the same decaffeinated energy drink (placebo; 0 mg/kg). At 60 min after the ingestion of the energy drink, participants completed a training session. The effects of ingestion of these beverages on psycho-physiological variables during exercise and the rate of adverse side effects were measured using questionnaires. The caffeinated energy drink increased self-perceived muscle power during exercise compared with the placebo beverage (6·41 (sd 1·7) v. 5·66 (sd 1·51); P= 0·001). Moreover, the energy drink produced a higher prevalence of side effects such as insomnia (31·2 v. 10·4 %; P< 0·001), nervousness (13·2 v. 0 %; P= 0·002) and activeness (16·9 v. 3·9 %; P= 0·007) than the placebo energy drink. There were no sex differences in the incidence of side effects (P>0·05). The ingestion of an energy drink with 3 mg/kg of caffeine increased the prevalence of side effects. The presence of these side effects was similar between male and female participants.
Phase II multicenter trial of Caphosol for the reduction of mucositis in patients receiving radiation therapy for head and neck cancer.

We conducted a phase II multicenter study evaluating Caphosol in patients receiving head and neck radiation (H/N RT) +/- chemotherapy or biologic sensitizer.



The primary endpoint of the study tested the rate of functional mucositis (WHO grade > or equal to 2) with the hypothesis that <75% of patients would develop > or equal to 2 mucositis with Caphosol compared with a historical rate of >90%. New methods were applied with higher than historic rigor. 5 Institutions were included in this study: Moffitt Cancer Center (MCC), MD Anderson Cancer Center (MDACC), Duke University Cancer Center (DUCC), University of Florida (UF) and Temple University Cancer Center (TUCC). Caphosol was taken by patients at least 4 times a day and up to 10 times per day commencing with day 1 of RT and for a total duration of 8 weeks after completion of RT. Detailed questionnaires were completed weekly by patients and a unique algorithm was used to generate the WHO grade of mucositis.



98 Patients were enrolled in the study. 59/98 (60%) patients were evaluable for the primary endpoint giving us 80% power. All evaluable patients experienced WHO grade > or equal to 2 mucositis and the trial failed to reject the null hypothesis. > or equal to 2 mucositis rates at weeks 2, 4, 6, 11 and 15 were as follows: 45%, 90%, 98%, 71%, 50%.



We were unable to demonstrate that Caphosol significantly reduced WHO grade 2 or higher mucositis below a 90% historic rate. We are not surprised with this finding given our rigorous methodology in grading.
Symptomatic simple renal cyst: comparison of continuous negative-pressure catheter drainage and single-session alcohol sclerotherapy.

The purpose of this study was to evaluate whether continuous percutaneous catheter drainage with negative pressure yields better results than single-session alcohol sclerotherapy in the management of symptomatic simple renal cysts.



Eighty-five patients with 92 simple renal cysts were randomly assigned to two groups in a prospective controlled trial. One group was treated with sonographically guided continuous catheter drainage with negative pressure and the other group with single-session alcohol sclerotherapy. Patient demographics, clinical characteristics, treatment outcome, and complications were analyzed.



The initial volume of the cysts did not differ significantly between the groups, but the final volume was significantly smaller in the continuous drainage group (p = 0.026). During the 24-month follow-up period, 37 (40%) of the cysts disappeared completely: 24 (52%) of the 46 cysts in the drainage group and 13 (28%) of the 46 cysts in the sclerotherapy group (p = 0.033). In the sclerotherapy group, the probability of disappearance of the cysts was highly dependent on cyst size, being less for giant cysts (p = 0.01). Cyst size was not a significant factor in probability of disappearance in the drainage group (p = 0.15). The probability of disappearance of giant cysts (volume > 500 mL) differed significantly between the groups (p = 0.009), but there was no difference in probability of disappearance of moderately large cysts (p = 0.16). Three of 14 patients with giant cysts in the drainage group and 10 of 13 such patients in the sclerotherapy group had recurrences that necessitated additional treatment (p = 0.007). They were successfully treated with continuous catheter drainage.



Continuous catheter drainage with negative pressure is more efficient than single-session alcohol sclerotherapy in the management of giant cysts. For moderately large cysts, the two methods have similar results.
Factors Associated With Incarceration History Among HIV-Positive Persons Experiencing Homelessness or Imminent Risk of Homelessness

Among persons living with HIV/AIDS (PLWHA) experiencing homelessness or imminent risk of homelessness, a history of incarceration may serve as a marker for ongoing risk behavior or health disparities. We examined factors associated with a history of incarceration among HIV-positive clients of housing agencies in Baltimore, Chicago, and Los Angeles (N = 581). We used logistic regression to conduct analyses. Of the 581 participants, 68% (n = 438) reported a history of incarceration: 32% (n = 182) had spent more than 1 year incarcerated. After adjustment for covariates, incarceration history was associated with having ever injected drugs, ever engaged in sex exchange, and ever experienced physical abuse. Incarceration history was also associated with having a detectable HIV viral load, better mental health, and being a biological parent. It was not associated with current risk behavior. Service providers may explore possible increased need for medical support among homeless PLWHA with a history of incarceration.
The StrongWomen-Healthy Hearts program: reducing cardiovascular disease risk factors in rural sedentary, overweight, and obese midlife and older women.

We tested a community-based intervention designed to reduce cardiovascular disease risk in sedentary midlife and older women who were overweight or obese.



In a randomized controlled trial conducted in 8 counties in Arkansas and Kansas, counties were assigned to the intervention (a 12-week twice-weekly heart health program) group or to the delayed-intervention control group. Ten to fifteen women were selected from each site, and participants' weight, waist circumference, diet, physical activity, and self-efficacy were measured before and after the intervention. Data were analyzed with multiple regressions.



Compared with the control group, participants in the intervention group had a significant decrease in body weight (-2.1 kg; 95% confidence interval [CI] = -3.2, -1.0), waist circumference (-2.3 in; 95% CI = -4.2, -0.5), and energy intake (-390 kcal/day; 95% CI = -598, -183); an increase in activity (+1637 steps/day; 95% CI = 712, 2562); and an increase in self-efficacy for dietary and physical activity behaviors.



Our results suggest that a community-based program can improve self-efficacy, increase physical activity, and decrease energy intake, resulting in decreased waist circumference and body weight among at-risk women.
Competence Driven Case-Base Mining

We present a novel algorithm for extracting a high-quality case base from raw data while preserving and sometimes improving the competence of case-based reasoning. We extend the framework of Smyth and Keane’s case-deletion policy with two additional features. First, we build a case base using a statistical distribution that is mined from the input data so that the case-base competence can be preserved or even increased for future problems. Second, we introduce a nonlinear transformation of the data set so that the case-base sizes can be further reduced while ensuring that the competence be preserved and even increased. We show that Smyth and Keane’s deletion-based algorithm is sensitive to noisy cases, and that our solution solves this problem more satisfactorily. We show the theoretical foundation and empirical evaluation on several data sets.
Mirtazapine augmentation in depressed patients with sexual dysfunction due to selective serotonin reuptake inhibitors.

To evaluate the effect of mirtazapine augmentation in patients with sexual dysfunction induced by current selective serotonin reuptake inhibitor (SSRI) treatment.



Forty-nine outpatients in remission from major depressive disorder with SSRI treatment and experiencing treatment-emergent sexual dysfunction were invited to participate and 33 (25 women and 8 men) were included in this 8-week open-label study. All patients continued her/his current SSRI treatment (dosages unchanged) and started on mirtazapine augmentation of 15 mg/day during the first week and 30 mg/day throughout the rest of the study. The Hamilton rating scale for depression (HAM-D), the psychotropic-related sexual dysfunction questionnaire (PRSexDQ), and the Golombok and Rust Inventory of Sexual Satisfaction (GRISS) were given to all patients at baseline and at each follow-up (end of the first, second, fourth, sixth, and eight weeks).



Mirtazapine augmentation led to significant reductions in HAM-D, PRSexDQ, and GRISS scores throughout the study especially after week 4 and 48.5% of patients (n = 16) reported that they had no overall sexual dysfunction at the end of the study.



Mirtazapine augmentation is a good choice for the treatment of SSRI-induced sexual dysfunction, and the results are typically seen later after 4-8 weeks.