nils-herrmann/clean_scirepeval huggingface dataset:
Muon decay: an old, yet alive experiment in the university physics curriculum

The classic experiment on muon decay is proposed in the undergraduate or master physics curriculum, making use of a single scintillation detector and observing in coincidence the delayed signal due to the electron following muon decay. Two experimental setups, with different geometries and scintillation materials, were considered, making use of standard equipment available in most undergraduate labs. The results obtained in the two cases were compared and discussed. For a better understanding of the results, and to also evaluate the possible effect of material surrounding the detector, detailed GEANT simulations were carried out for both experimental setups. Such simulations are also intended as an additional student activity to virtually exploit in a short time the effect of modifying detector and material configuration, which cannot be achieved during a single student session. The results of this experiment and its interpretation also proved to be a useful way to discuss with students many topics of interest in modern physics, such as among others the time dilation, the dependence of muon lifetime in matter, the Fermi weak interaction coupling constant and the parity violation in weak interactions.
Curriculum Development in Studio Style University Physics and Implications for Dissemination of Research Based Reforms.

Over the past few decades, a growing body of evidence demonstrates that students learn best in engaging, interactive, collaborative, and inquiry based environments. However, most college science classes are still taught with traditional methods suggesting the existing selection of research based instructional materials has not widely transformed undergraduate education. SCALE UP is a renovated pedagogy and classroom environment that has achieved a greater impact than most, used extensively throughout the United States and abroad. SCALE UP is not a simple collection of lesson plans or a textbook that can be easily adopted, and instead instructors are encouraged to customize main pedagogical principles to their unique instructional situation. This flexibility along with promotion of instructor autonomy may have assisted its spread. This paper uses case studies of five successful secondary implementations in the United States to examine how instructors gather information about reform, create a curriculum, and achieve sustained use. Many people learned about research based resources that formed the composite of their curricula through interpersonal connections. Time constraints and misunderstandings between developers and instructors limited which resources were chosen and how they were used. Once instructors created a "working form" of the curriculum, three out of five instructors did not make significant changes. This could lead to the preservation of a more conservative curriculum. Implications include that disseminators should articulate core principles of the reform that should be retained to uphold the integrity of the reform as well as the areas where adopters have flexibility to innovate. Strategically involving other secondary users in the dissemination process could facilitate important interpersonal exchanges that could provide an additional layer of support for faculty.
Retrospective study
Venue: Medicine

AbstractConventional forceps biopsy (CFB) is the most popular way to screen for gastric epithelial neoplasia (GEN) and adenocarcinoma of gastric epithelium. The aim of this study was to compare the diagnostic accuracy between conventional forceps biopsy and endoscopic submucosal dissection (ESD).Four hundred forty four patients who finally undertook ESD in our hospital were enrolled from Jan 1, 2009 to Sep 1, 2015. We retrospectively assessed the characteristics of pathological results of CFB and ESD.The concordance rate between CFB and ESD specimens was 68.92% (306/444) Men showed a lower concordance rate (63.61% vs 79.33% P 0.001) and concordance patients were younger (P 0.048) In multivariate analysis, men significantly had a lower concordance rate (coefficient 0.730, P 0.002) and a higher rate of pathological upgrade (coefficient 0.648, P 0.015) Locations of CFB did not influence the concordance rate statistically.The concordance rate was relatively high in our hospital. According to our analysis, old men plus gastric fundus or antrum of CFB were strongly suggested to perform ESD if precancerous lesions were found. And young women with low grade intraepithelial neoplasia could select regular follow up.
Association between Zika virus and microcephaly in French Polynesia, 2013 15: a retrospective study
Venue: The Lancet

The emergence of Zika virus in the Americas has coincided with increased reports of babies born with microcephaly. On Feb 1, 2016, WHO declared the suspected link between Zika virus and microcephaly to be a Public Health Emergency of International Concern. This association, however, has not been precisely quantified.  We retrospectively analysed data from a Zika virus outbreak in French Polynesia, which was the largest documented outbreak before that in the Americas. We used serological and surveillance data to estimate the probability of infection with Zika virus for each week of the epidemic and searched medical records to identify all cases of microcephaly from September, 2013, to July, 2015. Simple models were used to assess periods of risk in pregnancy when Zika virus might increase the risk of microcephaly and estimate the associated risk.  The Zika virus outbreak began in October, 2013, and ended in April, 2014, and 66% (95% CI 62 70) of the general population were infected. Of the eight microcephaly cases identified during the 23 month study period, seven (88% occurred in the 4 month period March 1 to July 10, 2014. The timing of these cases was best explained by a period of risk in the first trimester of pregnancy. In this model, the baseline prevalence of microcephaly was two cases (95% CI 0 8) per 10,000 neonates, and the risk of microcephaly associated with Zika virus infection was 95 cases (34 191) per 10,000 women infected in the first trimester. We could not rule out an increased risk of microcephaly from infection in other trimesters, but models that excluded the first trimester were not supported by the data.  Our findings provide a quantitative estimate of the risk of microcephaly in fetuses and neonates whose mothers are infected with Zika virus.
How obesity affects the neutrophil/lymphocyte and platelet/lymphocyte ratio, systemic immune inflammatory index and platelet indices: a retrospective study.
Venue: European review for medical and pharmacological sciences

Obesity is an important preventable cause of death and is a major risk factor for cardiovascular diseases as well as skeletal system diseases and malignancies. In many studies, complete blood count (CBC) and ratios derived from its results such as the neutrophil/lymphocyte ratio, platelet/lymphocyte ratio and systemic immune inflammatory index have been associated with some diseases and their surveys. In these studies, the body mass index (BMI) and state of obesity of patients and the possible effects of these factors on CBC have not been defined. In this study, our aim was to evaluate the effect of BMI and smoking on CBC and ratios derived from CBC.  In this cross sectional, retrospective study; the data of male and female patients aged between 18 65 years who presented for a routine check up or obesity was collected and subjects were grouped as normal weight, overweight, obese and morbidly obese accordingly BMI. Persons' smoking habits were calculated as pack/years. All complete blood count results were noted. Smoking status and BMI groups were compared to CBC findings and ratios derived from these findings.  After exclusion, 223 participants' data (104 female and 119 male) was included in the study. BMI was found to have a statistically significant positive linear correlation with lymphocyte number, PDW, SII and RDW (p 0.05) and an extremely significant positive linear correlation (p 0.01) was found between BMI and WBC, neutrophil count, PCT and platelet count. When BMI was not considered and 135 smokers were compared to 88 non smokers, leukocytes and neutrophil counts were found to be higher in smokers (p 0.05)  Our study has found that WBC, neutrophil count, lymphocyte count, platelet count, PCT, PDW and SII are significantly affected by BMI status. Future studies that use these parameters and indices must take the participants' BMI and smoking status into account.
Systemic inflammatory and autoimmune manifestations associated with myelodysplastic syndromes and chronic myelomonocytic leukaemia: a French multicentre retrospective study.
Venue: Rheumatology

We describe myelodysplastic syndrome (MDS) associated systemic inflammatory and autoimmune diseases (SIADs) their treatments and outcomes and the impact of SIADs on overall survival in a French multicentre retrospective study.  In this study, 123 patients with MDS and SIADs were analysed.  Mean age was 70 years (s.d. 13) and the male:female ratio was 2. The SIADs were systemic vasculitis in 39 (32% cases, CTD in 31 (25% cases, inflammatory arthritis in 28 (23% cases, a neutrophilic disorder in 12 (10% cases and unclassified in 13 cases (11% The SIADs fulfilled the usual classification criteria in 75 (66% cases, while complete criteria were not reached in 21 (19% cases. A significant association was shown between chronic myelomonocytic leukaemia (CMML) and systemic vasculitis (P 0.0024) One hundred and eighteen (96% SIAD patients were treated (91% with steroids) with an 83% response to first line treatment, including 80% for steroids alone. A second line treatment for SIADs was required for steroid dependence or relapse in 48% of cases. The effect of MDS treatment on SIADs could be assessed in 11 patients treated with azacytidine and SIAD response was achieved in 9/11 (80% and 6/11 (55% patients at 3 and 6 months, respectively. Compared with 665 MDS/CMML patients without SIADs,  male (P 0.03) less often had refractory anaemia with ring sideroblasts (P 0.01) more often had a poor karyotype (16% vs 11% P 0.04) and less frequently belonged to low and intermediate 1 International Prognostic Scoring System categories, but no survival difference was seen between patients with MDS associated SIADs and without SIADs (P 0.5)  The spectrum of SIADs associated to MDS is heterogeneous, steroid sensitive, but often steroid dependent.
Results of a nation wide retrospective study of lymphadenectomy for esophagogastric junction carcinoma
Venue: Gastric Cancer

BackgroundEsophagogastric junction (EGJ) carcinoma has attracted considerable attention because of the marked increase in its incidence globally. However, the optimal extent of esophagogastric resection for this tumor entity remains highly controversial.MethodsThis was a questionnaire based national retrospective study undertaken in an attempt to define the optimal extent of lymph node dissection for EGJ cancer. Data from patients with EGJ carcinoma, less than 40 mm in diameter, who underwent R0 resection between January 2001 and December 2010 were reviewed.ResultsClinical records of 2807 patients without preoperative therapy were included in the analysis. There are distinct disparities in terms of the nodal dissection rate according to histology and the predominant tumor location. Nodal metastases frequently involved the abdominal nodes, especially those at the right and left cardia, lesser curvature and along the left gastric artery. Nodes along the distal portion of the stomach were much less often metastatic, and their dissection seemed unlikely to be beneficial. Lower mediastinal node dissection might contribute to improving survival for patients with esophagus predominant EGJ cancer. However, due to low dissection rates for nodes of the middle and upper mediastinum, no conclusive result was obtained regarding the optimal extent of nodal dissection in this region.ConclusionsComplete nodal clearance along the distal portion of the stomach offers marginal survival benefits for patients with EGJ cancers less than 4 cm in diameter. The optimal extent of esophageal resection and the benefits of mediastinal node dissection remain issues to be addressed in managing patients with esophagus predominant EGJ cancers.
Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene Expression Based Retrospective Study
Venue: PLoS medicine

Immune infiltration of breast tumours is associated with clinical outcome. However, past work has not accounted for the diversity of functionally distinct cell types that make up the immune response. The aim of this study was to determine whether differences in the cellular composition of the immune infiltrate in breast tumours influence survival and treatment response, and whether these effects differ by molecular subtype.  We applied an established computational approach (CIBERSORT) to bulk gene expression profiles of almost 11,000 tumours to infer the proportions of 22 subsets of immune cells. We investigated associations between each cell type and survival and response to chemotherapy, modelling cellular proportions as quartiles. We found that tumours with little or no immune infiltration were associated with different survival patterns according to oestrogen receptor (ER) status. In ER negative disease, tumours lacking immune infiltration were associated with the poorest prognosis, whereas in ER positive disease, they were associated with intermediate prognosis. Of the cell subsets investigated, T regulatory cells and M0 and M2 macrophages emerged as the most strongly associated with poor outcome, regardless of ER status. Among ER negative tumours, CD8+ T cells (hazard ratio [HR] 0.89, 95% CI 0.80 0.98; p 0.02) and activated memory T cells (HR 0.88, 95% CI 0.80 0.97; p 0.01) were associated with favourable outcome. T follicular helper cells (odds ratio [OR] 1.34, 95% CI 1.14 1.57; p 0.001) and memory B cells (OR 1.18, 95% CI 1.0 1.39; p 0.04) were associated with pathological complete response to neoadjuvant chemotherapy in ER negative disease, suggesting a role for humoral immunity in mediating response to cytotoxic therapy. Unsupervised clustering analysis using immune cell proportions revealed eight subgroups of tumours, largely defined by the balance between M0, M1, and M2 macrophages, with distinct survival patterns by ER status and associations with patient age at diagnosis. The main limitations of this study are the use of diverse platforms for measuring gene expression, including some not previously used with CIBERSORT, and the combined analysis of different forms of follow up across studies.  Large differences in the cellular composition of the immune infiltrate in breast tumours appear to exist, and these differences are likely to be important determinants of both prognosis and response to treatment. In particular, macrophages emerge as a possible target for novel therapies. Detailed analysis of the cellular immune response in tumours has the potential to enhance clinical prediction and to identify candidates for immunotherapy.
Adverse Events in Robotic Surgery: A Retrospective Study of 14 Years of FDA Data
Venue: PloS one

Use of robotic systems for minimally invasive surgery has rapidly increased during the last decade. Understanding the causes of adverse events and their impact on patients in robot assisted surgery will help improve systems and operational practices to avoid incidents in the future.  By developing an automated natural language processing tool, we performed a comprehensive analysis of the adverse events reported to the publicly available MAUDE database (maintained by the U.S. Food and Drug Administration) from 2000 to 2013. We determined the number of events reported per procedure and per surgical specialty, the most common types of device malfunctions and their impact on patients, and the potential causes for catastrophic events such as patient injuries and deaths.  During the study period, 144 deaths (1.4% of the 10,624 reports) 1,391 patient injuries (13.1% and 8,061 device malfunctions (75.9% were reported. The numbers of injury and death events per procedure have stayed relatively constant (mean 83.4, 95% confidence interval (CI) 74.2 92.7 per 100,000 procedures) over the years. Surgical specialties for which robots are extensively used, such as gynecology and urology, had lower numbers of injuries, deaths, and conversions per procedure than more complex surgeries, such as cardiothoracic and head and neck (106.3 vs. 232.9 per 100,000 procedures, Risk Ratio 2.2, 95% CI, 1.9 2.6) Device and instrument malfunctions, such as falling of burnt/broken pieces of instruments into the patient (14.7% electrical arcing of instruments (10.5% unintended operation of instruments (8.6% system errors (5% and video/imaging problems (2.6% constituted a major part of the reports. Device malfunctions impacted patients in terms of injuries or procedure interruptions. In 1,104 (10.4% of all the events, the procedure was interrupted to restart the system (3.1% to convert the procedure to non robotic techniques (7.3% or to reschedule it (2.5% Conclusions Despite widespread adoption of robotic systems for minimally invasive surgery in the U.S. a non negligible number of technical difficulties and complications are still being experienced during procedures. Adoption of advanced techniques in design and operation of robotic surgical systems and enhanced mechanisms for adverse event reporting may reduce these preventable incidents in the future.
Effect of Combination of Acapella Device and Breathing Exercises on Treatment of Pulmonary Complications After Upper Abdominal Surgeries

Upper abdominal surgery alters postoperative pulmonary function, as observed by impairment of lung volumes such as total lung capacity, vital capacity. Impaired clearance of sputum results in a vicious cycle of colonization and infection of bronchi with pathogenic organisms, dilation of bronchi and further production of sputum. The aim was to investigate the effect of combination of Acapella device and breathing exercises on treatment of post operative pulmonary complications after upper abdominal surgeries.  Sixty patients underwent upper abdominal surgery were assigned randomly into two equal groups; their ages ranged from 20 50 years. The study group received breathing exercises, Acapella device and traditional chest physical therapy program (postural drainage. percussion, vibration, cough training and early ambulation) Control group received traditional chest physical therapy program (postural drainage. percussion, vibration, cough training and early ambulation) All groups received three sessions per week for four successful weeks. The data were collected before and after the same period of treatment for both groups. Evaluation procedures were carried out to measure pulmonary function: Forced vital capacity (FVC) and Forced expiratory volume in one second (FEV1) using electronic spirometer.  Post treatment results showed that there was a significant improvement difference in FVC and FEV1 in both groups in favor of the study group. Percentage of improvement of FVC in the study group was 42.28% while it was 16.31%in the control group. Percentage of improvement of FEV1 in the study group was 49.05% while it was 20.79%in the control group.  Combination of Acapella device and breathing exercises were considered to be an effective modality for treatment of postoperative pulmonary complications and removal of secretions after upper abdominal surgeries.
Rapid Delaunay triangulation for randomly distributed point cloud data using adaptive Hilbert curve
Venue: Comput. Graph.

Given the enormous scale and diverse distribution of 2D point cloud data, an adaptive Hilbert curve insertion algorithm which has quasi linear time complexity is proposed to improve the efficiency of Delaunay triangulation. First of all, a large number of conflicting elongated triangles, which have been created and deleted many times, can be reduced by adopting Hilbert curve traversing multi grids. In addition, searching steps for point location can be reduced by adjusting Hilbert curve's opening direction in adjacent grids to avoid the "jumping" phenomenon. Lastly, the number of conflicting elongated triangles can be further decreased by adding control points during traversing grids. The experimental results show that the efficiency of Delaunay triangulation by the adaptive Hilbert curve insertion algorithm can be improved significantly for both uniformly and non uniformly distributed point cloud data, compared with CGAL, regular grid insertion and multi grid insertion algorithms. The order is determined by adaptive Hilbert curve and control points.Conflicting elongated triangles and searching steps are reduced by optimized order.The efficiency of the proposed method is proved to be enhanced by detail experiment.The proposed algorithm is suitable for randomly distributed points.
Skin lesion image segmentation using Delaunay Triangulation for melanoma detection
Venue: Comput. Medical Imaging Graph.

Developing automatic diagnostic tools for the early detection of skin cancer lesions in dermoscopic images can help to reduce melanoma induced mortality. Image segmentation is a key step in the automated skin lesion diagnosis pipeline. In this paper, a fast and fully automatic algorithm for skin lesion segmentation in dermoscopic images is presented. Delaunay Triangulation is used to extract a binary mask of the lesion region, without the need of any training stage. A quantitative experimental evaluation has been conducted on a publicly available database, by taking into account six well known state of the art segmentation methods for comparison. The results of the experimental analysis demonstrate that the proposed approach is highly accurate when dealing with benign lesions, while the segmentation accuracy significantly decreases when melanoma images are processed. This behavior led us to consider geometrical and color features extracted from the binary masks generated by our algorithm for classification, achieving promising results for melanoma detection.
Electrically Tunable Absorption Enhancement with Spectral and Polarization Selectivity through Graphene Plasmonic Light Trapping
Venue: Nanomaterials

In this paper, anisotropic graphene plasmonic structures are explored for light trapping and absorption enhancement in surrounding media. It is shown that electrically tunable and versatile spectral and polarization selectivity can be realized. Particularly, it is possible to control absorption of the incident light's polarization component at a specific wavelength by varying the Fermi energy with suitable geometric designs. It may find applications for new types of infrared and THz photodetectors and will promote the research of other novel polarization devices.