nils-herrmann/clean_scirepeval huggingface dataset:
The effects of mastery on pain and fatigue resolution.

To determine whether mastery, the personal control felt over occurrences perceived to have an important effect on one's life, influences the resolution of pain and fatigue severity.



Secondary data analysis of two randomized clinical trials.



Accrual from two comprehensive cancer centers, one community oncology program, and six hospital-affiliated ambulatory oncology centers.


SAMPLE
330 patients with solid tumors who were undergoing chemotherapy and receiving a nurse-presented, six-contact, eight-week intervention for symptom management.



Analysis included baseline and interventional data. Logistic regression and survival analysis methods were used to explain relationships between mastery and time to resolution and resolution of pain and fatigue severity.



Mastery, pain and fatigue severity resolution, and time to resolution.



No significant differences in mastery were found among key socioeconomic and cancer-related variables. Mastery was a significant predictor of pain resolution status but did not significantly decrease time to resolution. Mastery did not have a significant effect on fatigue resolution status or time to fatigue resolution after adjusting for other covariates.



Mastery was symptom specific, predicting pain resolution but not fatigue. Cancer may have an equalizing effect on mastery early in diagnosis and treatment.



Nurses should develop interventions that increase mastery in patients with cancer, which may lead to improved resolution of pain. Additional research is needed to explore how mastery may affect resolution of pain severity and other symptoms experienced by people with cancer.
Evidence for the absence of enzymatic reactions in the glassy state. A case study of xanthophyll cycle pigments in the desiccation-tolerant moss Syntrichia ruralis

Desiccation-tolerant plants are able to withstand dehydration and resume normal metabolic functions upon rehydration. These plants can be dehydrated until their cytoplasm enters a 'glassy state' in which molecular mobility is severely reduced. In desiccation-tolerant seeds, longevity can be enhanced by drying and lowering storage temperature. In these conditions, they still deteriorate slowly, but it is not known if deteriorative processes include enzyme activity. The storage stability of photosynthetic organisms is less studied, and no reports are available on the glassy state in photosynthetic tissues. Here, the desiccation-tolerant moss Syntrichia ruralis was dehydrated at either 75% or <5% relative humidity, resulting in slow (SD) or rapid desiccation (RD), respectively, and different residual water content of the desiccated tissues. The molecular mobility within dry mosses was assessed through dynamic mechanical thermal analysis, showing that at room temperature only rapidly desiccated samples entered the glassy state, whereas slowly desiccated samples were in a 'rubbery' state. Violaxanthin cycle activity, accumulation of plastoglobules, and reorganization of thylakoids were observed upon SD, but not upon RD. Violaxanthin cycle activity critically depends on the activity of violaxanthin de-epoxidase (VDE). Hence, it is proposed that enzymatic activity occurred in the rubbery state (after SD), and that in the glassy state (after RD) no VDE activity was possible. Furthermore, evidence is provided that zeaxanthin has some role in recovery apparently independent of its role in non-photochemical quenching of chlorophyll fluorescence.
Genetics in Genomic Era

Genetics is a relatively young science compared to many other fields in biology, for example, evolutionary biology or physiology. However, genetics is a central theme in many fields, especially the medical sciences, because genetic studies can provide explanations and may even allow predictions to be made, in the context of a range of biological problems including the field of inherited human disorders. This has become especially important during the last decade as we have entered the " genomic era. " With the dramatic improvement of sequencing technologies and the enormous reduction in the cost of sequencing, biologists are faced with a " data avalanche. " Next generation whole exome or genome sequencing has provided us with an arsenal of tools to study human, animal, and plant genetics. The underlying genetic lesions responsible for Mendelian diseases may now be found and mapped with even a limited number (as few as one) of affected individuals (rare and neglected diseases), with the help of large quantities of " control " genome data such as those emanating from the 1000 Genomes Project. Genomic data analysis may also be useful for the dissection of the genetic mechanisms underlying complex polygenic diseases or in exploring the role of modifiers genes in influencing the age of onset or clinical severity of a given Mendelian disease entity. Although we have acquired new research capabilities, we are also encountering new problems with the analysis of genomic data and the reanalysis of already published (deposited in databases) data. Such problems of genomic data presentation, format, sharing, and reanalysis are now starting to be addressed. This special issue is dedicated to problems of genetics in the genomic era and comprises five articles: three review articles and two research articles. In the first review article, entitled " Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement, " A. P. Dhanapal and M. Govindaraj discuss the use of crop plant databases in advancing research in the genomic era. The major focus of this review is to provide knowledge on platforms for comparative genomics of agriculturally important crop plants with industrial and environmental significance. Recent advances in sequencing and resequencing of plant genomes have potentiated new analyses of genomic variation and gene function. Genetic variation databases could facilitate research that helps to improve the efficiency of plant breeding programs. This review should aid …
Efficacy and safety of single fecal microbiota transplantation for Japanese patients with mild to moderately active ulcerative colitis

The clinical utility of fecal microbiota transplantation (FMT) in patients with ulcerative colitis (UC) is still controversial. We investigated the efficacy and safety of single FMT for patients with mild to moderately active UC in a Japanese population. Fifty-seven patients were evaluated for eligibility, and 16 patients were excluded. Forty-one patients with UC refractory to standard medical therapy were treated with single FMT by colonoscopic administration. Changes in the fecal microbiota were assessed by 16S ribosomal DNA based terminal restriction fragment length polymorphism analysis. At 8 weeks after FMT, no patient achieved clinical remission, and 11 of 41 patients (26.8 %) showed clinical response.  Mayo score and the Mayo clinical score significantly decreased at week 8 [full Mayo score 5.5 ± 2.4 (mean ± standard deviation) at initiation and 4.6 ± 2.2 at week 8, P < 0.004; Mayo clinical score 4.0 ± 2.0 at initiation and 3.0 ± 1.9 at week 8, P < 0.001], but there were no statistically significant effects on the Mayo endoscopic score. No adverse events occurred after FMT or during the follow-up period of 8 weeks. The proportion of Bifidobacterium was significantly higher in the donor feces used for responders than in the donor feces used for nonresponders. The proportion of Lactobacillales and Clostridium cluster IV were significantly higher in the donor feces used for nonresponders. Single FMT by colonoscopy was performed safely in all patients, but sufficient clinical efficacy and microbial restoration were not confirmed in patients with mild to moderately active UC.
NAD(P)H oxidase and multidrug resistance protein genetic polymorphisms are associated with doxorubicin-induced cardiotoxicity.

A significant number of patients treated with anthracyclines develop cardiotoxicity (anthracycline-induced cardiotoxicity [ACT]), mainly presenting as arrhythmias (acute ACT) or congestive heart failure (chronic ACT). There are no data on pharmacogenomic predictors of ACT.



We genotyped participants of the German non-Hodgkin lymphoma study (NHL-B) who were followed up for the development of heart failure for a median of >3 years. Single-nucleotide polymorphisms (SNPs) were selected from 82 genes with conceivable relevance to ACT. Of 1697 patients, 55 developed acute and 54 developed chronic ACT (cumulative incidence of either form, 3.2%). We detected 5 significant associations with polymorphisms of the NAD(P)H oxidase and doxorubicin efflux transporters. Chronic ACT was associated with a variant of the NAD(P)H oxidase subunit NCF4 (rs1883112, -212A-->G; symbols with right-pointing arrows, as edited?' odds ratio [OR], 2.5; 95% CI, 1.3 to 5.0). Acute ACT was associated with the His72Tyr polymorphism in the p22phox subunit (rs4673; OR, 2.0; 95% CI, 1.0 to 3.9) and with the variant 7508T-->A (rs13058338; OR, 2.6; 95% CI, 1.3 to 5.1) of the RAC2 subunit of the same enzyme. In agreement with these results, mice deficient in NAD(P)H oxidase activity, unlike wild-type mice, were resistant to chronic doxorubicin treatment. In addition, acute ACT was associated with the Gly671Val variant of the doxorubicin efflux transporter multidrug resistance protein 1 (MRP1) (OR, 3.6; 95% CI, 1.6 to 8.4) and with the Val1188Glu-Cys1515Tyr (rs8187694-rs8187710) haplotype of the functionally similar MRP2 (OR, 2.3; 95% CI, 1.0 to 5.4). Polymorphisms in adrenergic receptors previously demonstrated to be predictive of heart failure were not associated with ACT.



Genetic variants in doxorubicin transport and free radical metabolism may modulate the individual risk to develop ACT.
Effect of a nurse-coordinated prevention programme on cardiovascular risk after an acute coronary syndrome: main results of the RESPONSE randomised trial

To quantify the impact of a practical, hospital-based nurse-coordinated prevention programme on cardiovascular risk, integrated into the routine clinical care of patients discharged after an acute coronary syndrome, as compared with usual care only.



RESPONSE (Randomised Evaluation of Secondary Prevention by Outpatient Nurse SpEcialists) was a randomised clinical trial.



Multicentre trial in secondary and tertiary healthcare settings.



754 patients admitted for acute coronary syndrome.



A nurse-coordinated prevention programme, consisting of four outpatient nurse clinic visits, focusing on healthy lifestyles, biometric risk factors and medication adherence, in addition to usual care.



The main outcome was 10-year cardiovascular mortality risk as estimated by Systematic Coronary Risk Evaluation at 12 months follow-up. Secondary outcomes included Framingham Coronary Risk Score at 12 months, in addition to changes in individual risk factors. Risk factor control was classified as 'poor' if 0 to 3 factors were on target, 'fair' if 4 to 6 factors were on target, and 'good' if 7 to 9 were on target.



The mean Systematic Coronary Risk Evaluation at 12 months was 4.4 per cent (SD 4.5) in the intervention group and 5.4 per cent (SD 6.2) in the control group (p=0.021), representing a 17.4% relative risk reduction. At 12 months, risk factor control classified as 'good' was achieved in 35% of patients in the intervention group compared with 25% in the control group (p=0.003). Attendance to the nurse-coordinated prevention programme was 92%. In the intervention group, 86 rehospitalisations were observed against 132 in the control group (relative risk reduction 34.8%, p=0.023).



The nurse-coordinated hospital-based prevention programme in addition to usual care is a practical, yet effective method for reduction of cardiovascular risk in patients with coronary disease. Our data suggest that the counselling component of the programme may lead to a reduction in hospital readmissions.
Topical mitomycin C chemotherapy for conjunctival melanoma and PAM with atypia.

To evaluate topical mitomycin C (MMC) chemotherapy in the treatment of conjunctival melanoma and primary acquired melanosis with atypia.



In a phase I clinical trial, 10 patients with conjunctival melanoma and/or primary acquired melanosis with atypia were treated with topical MMC 0.04% four times daily. Four patients were given MMC for 28 days as a primary treatment. Six patients were treated with MMC for 7 days after excision and cryotherapy in an effort to improve local control. In this series, 10 patients have been followed for an average of 29 months.



All patients were noted to develop transient keratoconjunctivitis during treatment. One patient also developed a transient corneal epithelial defect. Decreased conjunctival pigmentation was noted in the four patients where topical chemotherapy was used as a primary treatment. Nodular tumours were resistant to topical MMC chemotherapy. Of the six patients treated within 2 weeks after primary excision and cryotherapy, there has been no tumour recurrence or symblepharon formation. Nine of the 10 study patients have maintained within one line of their pretreatment visual acuity. No retinal or optic nerve toxicity was noted.



Since no complications which might preclude further investigation of topical MMC chemotherapy occurred, it was concluded that topical MMC chemotherapy was tolerated as a treatment for conjunctival melanoma and primary acquired melanosis with atypia.
Clinical measurement of the thoracic kyphosis. A study of the intra-rater reliability in subjects with and without shoulder pain

Clinical sagittal plane assessment of the thoracic kyphosis angle is considered an essential component of the postural examination of patients presenting with upper body pain syndromes. Cervical headaches and conditions involving the shoulder, such as subacromial pain syndrome, have all been associated with an increase in the thoracic kyphosis. Concomitantly a decrease in the thoracic kyphosis as a result of a stretching and strengthening rehabilitation programme is believed to be associated with a reduction in symptoms and pain and improvement in function. Clinicians generally measure the sagittal plane kyphosis angle visually. There is no certainty that this method is reliable or is capable of measuring angular changes over time or in response to intervention. As such a simple and reliable clinical method of measuring the thoracic kyphosis would enable clinicians to record this information. The aim of this investigation was to determine the intra-tester reliability of measuring the thoracic kyphosis angle using a clinical method



Measurements were made in 45 subjects with and 45 subjects without upper body symptoms. Measurements were made with the subjects in relaxed standing. Two gravity dependent inclinometers were used to measure the kyphosis. The first was placed over the region of the 1st and 2nd thoracic spinous processes. The other, over the region of the 12th thoracic and 1st lumbar spinous processes. The angle produced by each inclinometer was measured 3 times in succession. Each set of 3 measurements was made on two occasions (separated by a minimum of 30 minutes and additional data collection involving 46 further measurements of posture and movement on the same and an additional subject before the thoracic kyphosis measurements were re-measured) by one rater. The reliability of the measurements was analyzed using 2-way ANOVA intraclass correlation coefficients (ICC), 95% confidence intervals (CI) and standard error of measurement (SEM) for precision, for a single measurement [ICC(single)] and the average of 3 measures [ICC(average)]. The assessor remained 'blinded' to data input and the measurements were staggered to reduce examiner bias.



The measurement of the thoracic kyphosis as used in this investigation was found to have excellent intra-rater reliability for both subjects with and without symptoms. The ICC(single) results for the subjects without symptoms were, .95; (95% CI .91-.97). The corresponding ICC(average) results were; .97; (95% CI .95-.99). The results for the subjects with symptoms were; 93; (95% CI .88-.96), for ICC(single) and for ICC(average); .97; (95% CI .94-.98). The SEM results for subjects without and with symptoms were 1.0 degrees and 1.7 degrees , respectively.



The findings of this immediate test-retest reliability study suggest that the clinical measurement of the thoracic kyphosis using gravity dependent inclinometers demonstrates excellent intra-rater reliability. Additional research is required to determine the inter-rater reliability of this method.
Changes in EEG power density of non-REM sleep in depressed patients during treatment with trazodone.

Recently, it was hypothesized that acute or cumulative suppression of non-REM sleep intensity might be related to the therapeutic effects of antidepressants. This intensity has been proposed to be expressed in the EEG power density in non-REM sleep. In the present study, the relationship was examined between the changes of EEG power density in non-REM sleep and the changes in clinical state in 8 depressed patients during treatment with trazodone. A 1-week wash-out period was followed by 1 week of placebo administration, a medication period of 5 weeks and a 1-week placebo period. To minimize systematic influences of sleep duration and non-REM-REM sleep alterations, EEG power was measured over the longest common amount of non-REM sleep stages 2-4 (168.5 min), accumulated from sleep onset onwards. During trazodone treatment, the 13- and 14-Hz bins showed a significant reduction in EEG power. No clear-cut change, however, was observed in the EEG power of the delta frequency range (1-4 Hz) which is considered to be the principle manifestation of non-REM sleep intensity. Furthermore, no overall significant relationship between EEG power suppression and clinical improvement could be demonstrated.
Use of a reduced-intensity conditioning regimen for allogeneic transplantation in patients with chronic myeloid leukemia

Reduced-intensity conditioning that harnesses the potential of a graft-versus-tumor (GVT) effect has been proposed as an alternative to conventional myeloablative allogeneic stem cell transplantation. The primary aim is engraftment and this can be achieved with minimal immunosuppression. In this report, we describe the use of such regimens for CML in 17 patients who received human leukocyte antigen (HLA)-matched sibling allografts. Conditioning was with fludarabine, antithymocyte globulin (ATG) and busulfan for the first 11 patients, whereas fludarabine, busulfan and TBI were used for the remaining six patients. Engraftment was prompt in most of the cases. Complications and need for supportive therapy in the immediate post-transplant period were reduced drastically. Only two patients (both in the TBI group) died within the first 100 days. Acute graft-versus-host disease (GVHD) grade II–IV was seen in seven patients. Complications occurred later on. Chronic GVHD was observed in 11/17 patients. Lung infection and GVHD were the major killers. In surviving patients, after a median follow-up of 30 months (range 37–21 months), 6/17 (35.3%) are alive. Five are disease free and one patient is still in relapse even after a second donor lymphocyte infusion. Total treatment time and cost were more than with conventional transplants. We conclude that reduced-intensity transplantation still requires further refinement.
Quantitative evaluation of lower urinary tract symptoms using a visual analog scale in men undergoing permanent brachytherapy.

A previous study showed that a visual analog scale (VAS) that measures quality of life (QOL) in relation to each of the seven items on the International Prostate Symptom Score (IPSS) was found to be significantly more able to identify a patient's chief complaint. The aim of this study was to assess the two questionnaires with special reference to the symptom that the patient most wants treated via the concomitant use of the IPSS and VAS after permanent brachytherapy (PBT).



A total of 156 men undergoing PBT were enrolled. The IPSS and VAS were evaluated at the preimplantation stage and at 1-3 months, 6-9 months, and 1 year after PBT. The correlations between the IPSS-QOL score and the total for the 14 symptoms questions included in the IPSS and VAS were statistically calculated. Multivariate analysis was used to investigate which factors could be used to predict the IPSS-QOL after PBT.



The correlation coefficients between the IPSS-QOL score and the seven questions on the VAS were higher than those between the IPSS-QOL and the seven questions on the IPSS. Multivariate analysis showed that the strongest factor for determining IPSS-QOL at each time point was nocturia on the VAS.



The VAS scale reflected the change in the patients' QOL more precisely than the IPSS, which examines the frequency of lower urinary tract symptoms. Nocturia plays a key role in determining QOL. VAS could be a promising tool for assessing satisfaction in patients with lower urinary tract symptoms after PBT.
The effects of dementia care mapping on nursing home residents’ quality of life and staff attitudes: design of the quasi-experimental study Leben-QD II

The main objective of care for people with dementia is the maintenance and promotion of quality of life (Qol). Most of the residents in nursing homes have challenging behaviors that strongly affect their Qol. Person-centered care (PCC) is an approach that aims to achieve the best possible Qol and to reduce challenging behaviors. Dementia Care Mapping (DCM) is a method of implementing PCC that has been used in Germany for several years. However, there are no data on the effectiveness of DCM or the challenges of implementation of DCM in German nursing homes.



In this quasi-experimental non-randomized cluster-controlled study, the effects of DCM will be compared to 2 comparison groups. 9 nursing homes will take part: 3 will implement DCM, 3 will implement a comparison intervention using an alternative Qol assessment, and 3 have already implemented DCM. The main effect outcomes are Qol, challenging behaviors, staff attitudes toward dementia, job satisfaction and burnout of caregivers. These outcomes will be measured on 3 data points. Different quantitative and qualitative data sources will be collected through the course of the study to investigate the degree of implementation as well as facilitators of and barriers to the implementation process.



This study will provide new information about the effectiveness of DCM and the implementation process of DCM in German nursing homes. The study results will provide important information to guide the national discussion about the improvement of dementia-specific Qol, quality of care in nursing homes and allocation of resources. In addition, the study results will provide information for decision-making and implementation of complex psychosocial interventions such as DCM. The findings will also be important for the design of a subsequent randomized controlled trial (e.g. appropriateness of outcomes and measurements, inclusion criteria for participating nursing homes) and the development of a successful implementation strategy.
The story of set disjointness

The satisfiability problem has emerged as the queen of the complexity zoo. She is the quintessential NP-complete hard-to-find but easy-to-recognize search problem in computer science. There are hundreds if not thousands of problems that are now known to be equivalent to SAT, and our rich theory of complexity classes is centered around its queen. In the world of communication complexity, the set disjointness problem has similarly emerged as the quintessential hard-to-find but easy-to-recognize problem. There is an impressive collection of problems in many diverse areas whose hardness boils down to the hardness of the set disjointness problem in some model of communication complexity. Moreover, we will argue that proving lower bounds for the set disjointness function in a particular communication