nils-herrmann/clean_scirepeval huggingface dataset:
TrajMetrix: a trajectory compression benchmarking framework

Trajectory compression algorithms enable efficient transmission, storage, and processing of trajectory data by eliminating redundant information. While a large number of compression algorithms have been developed, there is no comprehensive and convenient benchmarking system for evaluating these algorithms. We will demonstrate TrajMetrix, our system that meets the above need. We will show how TrajMetrix can be used to gain insights into the benefits and drawbacks of various compression algorithms given different compression requirements.
 From the knowledge attained by using TrajMetrix, we developed SQUISH-E (Spatial QUalIty Simplification Heuristic - Extended). This algorithm uses a priority queue to preferentially remove points based on the error introduced by their removal. Through live demonstrations that use both synthetic and real data sets, we will show the ability of SQUISH-E to effectively bound compression error with low computational overhead.
UGT1A1 polymorphism can predict hematologic toxicity in patients treated with irinotecan.

Irinotecan (CPT-11) is approved in metastatic colorectal cancer treatment and can cause severe toxicity. The main purpose of our study was to assess the role of different polymorphisms on the occurrence of hematologic toxicities and disease-free survival in high-risk stage III colon cancer patients receiving 5-fluorouracil (5FU) and CPT-11 adjuvant chemotherapy regimen in a prospective randomized trial.



Four hundred patients were randomized in a phase III trial comparing LV5FU2 to LV5FU2 + CPT-11. DNA from 184 patients was extracted and genotyped to detect nucleotide polymorphism: 3435C>T for ABCB1, 6986A>G for CYP3A5, UGT1A1*28 and -3156G>A for UGT1A1.



Genotype frequencies were similar in both treatment arms. In the test arm, no significant difference was observed in toxicity or disease-free survival for ABCB1 and CYP3A5 polymorphisms. 28 homozygous patients showed more frequent severe hematologic toxicity (50%) than UGT1A1*1 homozygous patients (16.2%), P = 0.06. Moreover, patients homozygous for the mutant allele of -3156G>A UGT1A1 polymorphism showed more frequent severe hematologic toxicity (50%) than patients homozygous for wild-type allele (12.5%), P = 0.01. This toxicity occurred significantly earlier in homozygous mutant than wild-type homozygous patients (P = 0.043). In a Cox model, the hazard ratio for severe hematologic toxicity is significantly higher for patients with the A/A compared with the G/G genotype [hazard ratio, 8.4; 95% confidence interval, 1.9-37.2; P = 0.005].



This study supports the clinical utility of identification of UGT1A1 promoter polymorphisms before LV5FU2 + CPT-11 treatment to predict early hematologic toxicity. The -3156G>A polymorphism seems to be a better predictor than the UGT1A1 (TA)(6)TAA>(TA)(7)TAA polymorphism.
Perceived risk as a moderator of the effectiveness of framed HIV-test promotion messages among women: a randomized controlled trial.

Researchers argue that gain-framed messages should be more effective for prevention behaviors, while loss frames should be more effective for detection behaviors (Rothman & Salovey, 1997). Evidence for this taxonomy has been mixed. This study examines whether the effects of gain- and loss-framed messages on HIV-testing intentions is moderated by perceived risk of a positive result.



This experiment was conducted online and utilized a single factor (frame: gain/loss) between subjects design, with a separate HIV-test promotion control and a no message control to examine whether perceived risk of a positive test result moderates the effects of framed messages on intentions to seek an HIV test in the next 3 months. The sample (N = 1052; M age = 22, SD = 2.22), recruited through Survey Sampling International, included 51% Black women (49% White women).



HIV-test promotion messages were more effective than no message, but there were no other main effects for condition. Results also demonstrated a significant interaction between message frame and perceived risk, which is mediated through elaborative processing of the message. The interaction demonstrated an advantage for the loss-framed message among women with some perceived risk and an advantage for the gain-framed message among women with low perceived risk.



Results imply that the prevention/detection function of the behavior may be an inadequate distinction in the consideration of the effectiveness of framed messages promoting HIV testing. Rather, this study demonstrates that risk perceptions are an important moderator of framing effects.
Daily electronic monitoring of subjective and objective measures of illness activity in bipolar disorder using smartphones– the MONARCA II trial protocol: a randomized controlled single-blind parallel-group trial

Patients with bipolar disorder often show decreased adherence with mood stabilizers and frequently interventions on prodromal depressive and manic symptoms are delayed. Recently, the MONARCA I randomized controlled trial investigated the effect of electronic self-monitoring using smartphones on depressive and manic symptoms. The findings suggested that patients using the MONARCA system had more sustained depressive symptoms than patients using a smartphone for normal communicative purposes, but had fewer manic symptoms during the trial. It is likely that the ability of these self-monitored measures to detect prodromal symptoms of depression and mania may be insufficient compared to automatically generated objective data on measures of illness activity such as phone usage, social activity, physical activity, and mobility. The Monsenso system, for smartphones integrating subjective and objective measures of illness activity was developed and will be tested in the present trial.



The MONARCA II trial uses a randomized controlled single-blind parallel-group design. Patients with bipolar disorder according to ICD-10 who previously have been treated at the Copenhagen Clinic for Affective Disorder, Denmark are included and randomized to either daily use of the Monsenso system including an feedback loop between patients and clinicians (the intervention group) or to the use of a smartphone for normal communicative purposes (the control group) for a 9-month trial period. The trial was started in September 2014 and recruitment is ongoing. The outcomes are: differences in depressive and manic symptoms; rate of depressive and manic episodes (primary); automatically generated objective data on measures of illness activity; number of days hospitalized; psychosocial functioning (secondary); perceived stress; quality of life; self-rated depressive symptoms; self-rated manic symptoms; recovery; empowerment and adherence to medication (tertiary) between the intervention group and the control group during the trial. Ethical permission has been obtained. Positive, neutral and negative findings will be published.



If the system is effective in reducing depressive and/or manic symptoms (and other symptoms of bipolar disorder) and the rate of episodes, there will be basis for extending the use to the treatment of bipolar disorder in general and in larger scale.
Predictors of early death risk in older patients treated with first-line chemotherapy for cancer.

Objective factors for making choices about the treatment of elderly patients with cancer are lacking. This investigation aimed to help physicians select appropriate treatments through the identification of factors that predict early death (< 6 months) after initiation of chemotherapy treatment.



Previously untreated patients greater than 70 years of age who were scheduled for first-line chemotherapy for various types of cancer were included. Baseline abbreviated comprehensive geriatric assessment (aCGA), including the Mini-Mental State Exam, Timed Get Up and Go (GUG), Activities of Daily Living (ADL), Instrumental Activities in Daily Living (IADL), Mini Nutritional Assessment (MNA), Geriatric Depression Scale (GDS15), and comorbidities index (Cumulative Index Rating Scale-Geriatric), was carried out. Prognostic factors of early death were sought from aCGA results and traditional oncology measures.



A total of 348 patients were included across 12 centers in Southwest France (median age, 77.45 years; ratio of men to women, 1.47; advanced disease, 65%). Abnormal aCGA scores were observed for 18.1% of patients on the ADL, 73.0% of patients on the IADL, 24.1% of patients on the GUG, 19.0% of patients on the MMS, 44.0% of patients on the GDS15, and 64.9% of patients on the MNA. Advanced disease (odds ratio [OR], 3.9; 95% CI, [1.58 to 9.73]), a low MNA score (OR 2.77; 95% CI, [1.24 to 6.18]), male sex (OR, 2.40; 95% CI, [1.2 to 4.82]), and long GUG (OR, 2.55; 95% CI, [1.32 to 4.94] were associated with higher risk of early death.



In patients greater than 70 years of age with cancer, advanced disease, a low MNA score, and poor mobility predicted early death. We recommend that the MNA and GUG, performed by a trained nurse, be maintained as part of routine pretreatment workup in these patients to identify at-risk patients and to inform the decision-making process for chemotherapy.
Effects of bronchodilator particle size in asthmatic patients using monodisperse aerosols.

Aerosol particle size influences airway drug deposition. Current inhaler devices are inefficient, delivering a heterodisperse distribution of drug particle sizes where, at best, 20% reaches the lungs. Monodisperse aerosols are the appropriate research tools to investigate basic aerosol science concepts within the human airways. We hypothesized that engineering such aerosols of albuterol would identify the ideal bronchodilator particle size, thereby optimizing inhaled therapeutic drug delivery. Eighteen stable mildly to moderately asthmatic patients [mean forced expiratory volume in 1 s (FEV1) 74.3% of predicted] participated in a randomized, double-blind, crossover study design. A spinning-top aerosol generator was used to produce monodisperse albuterol aerosols that were 1.5, 3, and 6 microm in size, and also a placebo, which were inhaled at cumulative doses of 10, 20, 40, and 100 microg. Lung function changes and tolerability effects were determined. The larger particles, 6 and 3 microm, were significantly more potent bronchodilators than the 1.5-microm and placebo aerosols for FEV1 and for the forced expiratory flow between exhalation of 25 and 75% of forced vital capacity. A 20-microg dose of the 6- and 3-microm aerosols produced FEV1 bronchodilation comparable to that produced by 200 microg from a metered-dose inhaler. No adverse effects were observed in heart rate and plasma potassium. The data suggest that in mildly to moderately asthmatic patients there is more than one optimal beta2-agonist bronchodilator particle size and that these are larger particles in the higher part of the respirable range. Aerosols delivered in monodisperse form can enable large reductions of the inhaled dose without loss of clinical efficacy.
Conservative treatment of spontaneous osteonecrosis of the knee in the early stage: pulsed electromagnetic fields therapy.

pulsed electromagnetic fields treatment might improve symptoms in the early stage of spontaneous osteonecrosis of the knee.



Twenty-eight patients (19M/9F, age 49.8±16.4 years) suffering from symptomatic (pain) Koshino stage I spontaneous osteonecrosis of the knee, confirmed by magnetic resonance imaging (MRI) were treated with local pulsed electromagnetic fields therapy (6 h daily for 90 days).  baseline, 6- and 24-month follow-up by VAS for pain, knee society score (KSS), Tegner and EQ-5D scales. MRI evaluation: baseline and 6-month follow-up, measuring bone marrow lesion's areas and grading these lesions by WORMS score.  patients undergoing knee arthroplasty.



Pain significantly reduced at 6 months (from 73.2±20.7 to 29.6±21.3, p<0.0001), which remained almost unchanged at final follow-up (27.0±25.1). KSS significantly increased in first 6 months (from 34.0±13.3 to 76.1±15.9, p<0.0001) and was slightly reduced at final follow-up (72.5±13.5, p=0.0044). Tegner median level increased from baseline to 6-month follow-up (1(1-1) and 3(3-4), respectively, p<0.0001) and remained stable. EQ-5D improved significantly throughout the 24 months (0.32±0.33, baseline; 0.74±0.23, 6-month follow-up (p<0.0001); 0.86±0.15, 24-month follow-up (p=0.0071)). MRI evaluation: significant reduction of total WORMS mean score (p<0.0001) and mean femoral bone marrow lesion's area (p<0.05). This area reduction was present in 85% and was correlated to WORMS grading both for femur, tibia and total joint (p<0.05). Four failures (14.3%) at 24-month follow-up.



Pulsed electromagnetic fields stimulation significantly reduced knee pain and necrosis area in Koshino stage I spontaneous osteonecrosis of the knee already in the first 6 months, preserving 86% of knees from prosthetic surgery at 24-month follow-up. No correlation was found between MRI and clinical scores.
Verapamil in angina: a double-blind trial.

Three cases of multiple sclerosis are reported, all of which developed chorea, choreo-athetosis, or athetosis during the course of their illness. The diagnoses were based on the association of diffuse and disseminated neurological lesions, a history of remission and relapse, a strongly paretic Lange curve in the C.S.F. with a negative Wassermann reaction, together with marked increase in the gammaglobulin fraction. Two cases responded well to corticotrophin and one improved spontaneously. Follow-up showed satisfactory remission of the whole clinical picture and of voluntary movements in particular. I am grateful to Dr. J. MacDonald Holmes for permission to report his cases. I am indebted to Dr. E. R. Bickerstaff for permission to publish the case under his care and for his criticism and guidance in preparing this paper. I am thankful to Miss G. M. Griffiths and Miss S. Ray for their help at various stages.
Quality risk analysis at sampling stations crossed by one monitored product and an unmonitored flow

When inspection economies are implemented in multi-product, multi-stage, parallel processing manufacturing systems, there exists a significant risk of losing control of the monitoring efficacy of the sampling strategy adopted. For a product-based sampling decision limited to a particular station in a production segment, the randomness of the departure process and the merging of different product flows at the machines of the different stations subvert the regularity of deterministic sampling. The risk of not regularly monitoring any machine in the segment can be measured in terms of maximum number of consecutive unsampled items. In this study, the distribution of this measure at sampling station machines is developed for a production scenario characterized by one monitored product and an unmonitored flow and compared with the behavior of the same measure at non-sampling station machines. The prediction models illustrated prove fundamental pragmatic tools for quality management involved in sampling strategy-related decisions.
Association of BDNF Val66Met polymorphism with both baseline HRQOL scores and improvement in HRQOL scores in Chinese major depressive patients treated with fluoxetine.

To explore the association of brain-derived neurotrophic-factor (BDNF) Val66Met polymorphism with both baseline health related quality of life (HRQOL) scores and improvement in HRQOL scores in Chinese major depressive patients treated with fluoxetine.



Patients with major depressive disorder (MDD) took fluoxetine (20 mg/day) for 6 weeks. The HRQOL was measured with the Medical Outcomes Study Short Form-36 (SF-36) at baseline and at 6th week. Patients were genotyped for Val66Met polymorphism of BDNF gene.



There was a significant association between social function (SF) and BDNF Val66Met polymorphism, and patients with Met/Met genotype had better SF (compared with Val/Val P = 0.004; compared with Val/Met P = 0.005). A significant association was found between improvement in SF and BDNF Val66Met polymorphism, and patients with Met/Met genotype had poorer improvement in SF (compared with Val/Val P = 0.010; compared with Val/Met P = 0.001). Similar association was found between improvement in mental component summary (MCS) and BDNF Val66Met polymorphism, and patients with Met/Met genotype had poorer improvement in MCS (compared with Val/Val P = 0.066; compared with Val/Met P = 0.006).



These results indicate that there may be association between BDNF Val66Met polymorphism and both baseline HRQOL (SF) scores and improvement in HRQOL (SF, MCS) scores in Chinese major depressive patients treated with fluoxetine.
Reliability and validity of the Brief COPE Scale (English version) among women with breast cancer undergoing treatment of adjuvant chemotherapy: a Malaysian study.

This paper validates the Brief COPE Scale in Malaysian women with breast cancer. Test-retest evaluation was undertaken at two/three weeks and ten weeks following surgery. Internal consistencies ranged from 0.25 to 1.00. Meanwhile, the Intraclass Correlation Coefficient (ICC) ranged from 0.05 to 1.00. Sensitivity of the scale was indicated by the mean differences as observed in most of the domains with Effect Size Index (ESI) ranged from 0 to 0.53. Significant differences between mastectomy and lumpectomy were observed for Active coping, Planning and Acceptance. Brief COPE Scale showed fairly good reliability and validity.
PHLECO: a multicenter study of the fate of 1647 hospital patients treated conservatively without fibrinolysis and surgery

The PHLECO Study (phlebothrombosis conservative therapy) is a multicenter investigation of patients with deep vein thrombosis receiving conservative nonfibrinolytic hospital treatment. A second study (part II : PHLEFI, phlebothrombosis fibrinolytic treatment) to be published later deals with the outcome of fbrnolytic therapy. In both studies the incidence of life-threatening sequelae, such as pulmonary embolism, is of major interest. The 49 medical departments participating in the study mailed the relevant data to the Duisburg Coordination Center for further data analysis and the following information was gained: (a) In descending order of frequency, the clinical conditions of thrombosis were: immobility, postoperative status, malignancy, hormone treatment, posttraumatic conditions, and pregnancy. (b) In descending order of frequency, the sites of thrombosis were: femoral vein, calf vein, iliac vein, popliteal vein, and subclavian vein. Left-sided thrombosis predominated in the iliac and subclavian vein groups. (c) In descending order of frequency, the treatment regimens employed were: intravenous heparin+ oral anticoagulants, intravenous heparin+subcutaneous heparin, intravenous heparin alone, subcutaneous heparin alone, intravenous heparin+subcutaneous heparin+oral anticoagulants, subcutaneous heparin+oral anticoagulants, intravenous heparin + platelet aggregation inhibitors. (d) The average hospital stay was 23.7 + 15.6 days. No correlation existed between duration of hospital stay and particular types of therapy.  The incidence of nonfatal pulmonary embolism was 16.1% while that of fatal pulmonary embolism was 2.33%. (f) Women outnumbered men in the group with fatal pulmonary embolism, and the death rate among older patients was higher than that among younger patients. (g) Patients with fatal pulmonary embolism had a shorter history of thrombosis than patients in the unselected cohort (patients with and without pulmonary embolism). (h) Iliac vein thrombosis correlated with the highest incidence of fatal pulmonary embolism, with the right iliac vein predominating. (i) Calf vein thrombosis produced pulmonary embolism only very rarely, and pulmonary embolism was not observed in the group of patients with subclavian vein thrombosis.
The impact of high-frequency repetitive transcranial magnetic stimulation on fine motor functions in medication-resistant major depression.

Although high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) over the left dorsolateral prefrontal cortex (DLPFC) has been reported to improve mood symptoms in major depressive disorder (MDD), research on its impact on psychomotor symptoms is scarce. This study assessed the psychomotor effects of 1 and 10 sessions, respectively, of HF-rTMS over the left DLPFC.



Ten HF-rTMS sessions were applied in 21 medication-free MDD patients over a 2-week period. At the beginning, one placebo (sham)-controlled rTMS session was also applied in a cross-over, single-blind design. Psychomotor variables were digitally recorded during completion of a Fitts' task, at baseline, after the first and second real/sham session and at the end point.



The total 10-session treatment period resulted in a decrease of depression severity. One HF-rTMS session resulted in improvements on the Fitts' task, without a difference between active and sham stimulation, however. No further improvements occurred from session 2 to session 10.



No evidence was provided to link the observed psychomotor improvements to HF-rTMS stimulation, as a practice effect could have impacted the significant psychomotor outcomes.
Effect of Lactobacillus plantarum 299v on cardiovascular disease risk factors in smokers.

The short-chain fatty acids formed in the human colon by the bacterial fermentation of fiber may have an antiinflammatory effect, may reduce insulin production, and may improve lipid metabolism. We previously showed in hypercholesterolemic patients that supplementation with the probiotic bacteria Lactobacillus plantarum 299v significantly lowers concentrations of LDL cholesterol and fibrinogen.



We determined the influence of a functional food product containing L. plantarum 299v on lipid profiles, inflammatory markers, and monocyte function in heavy smokers.



Thirty-six healthy volunteers (18 women and 18 men) aged 35-45 y participated in a controlled, randomized, double-blind trial. The experimental group drank 400 mL/d of a rose-hip drink containing L. plantarum 299v (5 x 10(7) colony-forming units/mL); the control group consumed the same volume of product without bacteria. The experiment lasted 6 wk and entailed no changes in lifestyle.



Significant decreases in systolic blood pressure (P < 0.000), leptin (P < 0.000), and fibrinogen (P < 0.001) were recorded in the experimental group. No such changes were observed in the control group. Decreases in F(2)-isoprostanes (37%) and interleukin 6 (42%) were also noted in the experimental group in comparison with baseline. Monocytes isolated from subjects treated with L. plantarum showed significantly reduced adhesion (P < 0.001) to native and stimulated human umbilical vein endothelial cells.



L. plantarum administration leads to a reduction in cardiovascular disease risk factors and could be useful as a protective agent in the primary prevention of atherosclerosis in smokers.
Publish-Subscribe Systems via Gossip: a Study based on Complex Networks

This paper analyzes the adoption of unstructured P2P overlay networks to build publish-subscribe systems. We consider a very simple distributed communication protocol, based on gossip and on the local knowledge each node has about subscriptions made by its neighbours. A mathematical analysis is provided to estimate the number of nodes receiving the event. These outcomes are compared to those obtained via simulation. Results show even when the amount of subscribers represents a very small (yet non-negligible) portion of network nodes, by tuning the gossip probability the event can percolate through the overlay.