nils-herrmann/clean_scirepeval huggingface dataset:
Joint optimization of segmentation and shape prior from level set based statistical shape model, and its application to the automated segmentation of abdominal organs
Venue: Medical Image Anal.

The goal of this study is to provide a theoretical framework for accurately optimizing the segmentation energy considering all of the possible shapes generated from the level set based statistical shape model (SSM) The proposed algorithm solves the well known open problem, in which a shape prior may not be optimal in terms of an objective functional that needs to be minimized during segmentation. The algorithm allows the selection of an optimal shape prior from among all possible shapes generated from an SSM by conducting a branch and bound search over an eigenshape space. The proposed algorithm does not require predefined shape templates or the construction of a hierarchical clustering tree before graph cut segmentation. It jointly optimizes an objective functional in terms of both the shape prior and segmentation labeling, and finds an optimal solution by considering all possible shapes generated from an SSM. We apply the proposed algorithm to both pancreas and spleen segmentation using multiphase computed tomography volumes, and we compare the results obtained with those produced by a conventional algorithm employing a branch and bound search over a search tree of predefined shapes, which were sampled discretely from an SSM. The proposed algorithm significantly improves the segmentation performance in terms of the Jaccard index and Dice similarity index. In addition, we compare the results with the state of the art multiple abdominal organs segmentation algorithm, and confirmed that the performances of both algorithms are comparable to each other. We discuss the high computational efficiency of the proposed algorithm, which was determined experimentally using a normalized number of traversed nodes in a search tree, and the extensibility of the proposed algorithm to other SSMs or energy functionals.
Liquid biopsy in the practice of neo oncology.
Venue: Journal of thoracic disease

Selecting the optimal platform for molecular diagnostic profiling is a crucial step in the management of patients with advanced lung adenocarcinomas. With an ever expanding number of targetable oncogenic drivers, there was an evolution of molecular diagnostic platforms. Molecular testing previously followed a one driver one test approach, with the use of Sanger sequencing, reverse transcription polymerase chain reaction (RT PCR) fluorescence in situ hybridization (FISH) or Immunohistochemistry. Multiplex PCR based platforms were developed to simultaneously interrogate multiple oncogenes, however these assays only detect the expression of selected known hotspot mutations and oncogenes and do not have the ability to discover new or additional drug targets (1,2) Nextgeneration sequencing (NGS) also known as massively parallel sequencing, represents an effective way to capture a large amount of genomic information about a cancer (3) In addition to known hotspot oncogenic mutations or gene rearrangements in non small cell lung cancer (NSCLC) NGS has also identified genetic abnormalities that are previous known in other cancer types as well and uncovered many novel genetic abnormalities without knowledge of their biologic functions (2) The use of NGS has also resulted in the identification of new actionable genomic alterations as well as uncovered false negative tests in close to two thirds of lung adenocarcinomas that previously tested "negative" for known alterations by multiple conventional non NGS tests (1,4 6)
Liquid biopsy in patients with adenocarcinoma of the lung and its correlation with their tumor tissue molecular profile: 3PD
Venue: Journal of thoracic oncology official publication of the International Association for the Study of Lung Cancer

Adequate quantity of tumor tissue for molecular analysis is a major handicap to deliver personalized medicine. Reasons such as difficulty to perform tumor biopsy (TBX) either because of tumor location, patient's co morbid conditions or the fact we need to repeat the TBX are among the common factors for lack of molecular profiling results (MPR) Hence, liquid biopsy (LBX) has emerged as a potential alternative to detect these genomic alterations.  We analyzed 59 patients with stage IV or recurrent adenocarcinoma of the lung (ADENO) using Guardant 360 test; sample collections were done at Lynn Cancer Institute and Memorial Cancer Institute. Alterations detected by this test include single nucleotide variations, amplifications, ALK, FGFR2, FGFR3, RET, ROS1, NTRK1 genes, and short insertions/duplications/deletions in exons 19 and 20 of the EGFR and ERBB2 genes as well as exon 14 skipping of the MET gene. We compared these results with their tumor tissue MPR in each individual, to assess their correlation.  41/59 pts were females; median age 75 (range, 27 99) 44 pts (75% had at least 1 genomic alteration by LBX (range, 1 10) Most common abnormalities found in LBX: EGFR (20 pts) TP53 (19 pts) and NF1 (11 pts) From this 44 pts with LBX results, 29 pts (66% had tumor tissue MPRs for comparison. Major reason for lack of tumor tissue MPRs: insufficient tumor (11/17; 65% For comparison between the 2 modalities, we considered all pts with available results in both tests (n 42 pts) 20 pts (48% had at least 1 genomic abnormality or no abnormality identify in both type of "biopsies" Most of the concordance was in EGFR mutations; LBX caught 12/17 (71% EGFR mutations in TBX. Nonetheless, LBX caught 11 EGFR alterations not present or available by TBX MPR.  Insufficient amount of tumor is the reason for lacking tumor MPRs. LBX offers an alternative/complementary way to identify genomic alterations in a much easy way. Our cohort had 48% concordance between LBX and TBX; however, for EGFR mutation, correlation was higher (71% Discrepancies between both modalities could be explained by timing when samples were taken and tumor heterogeneity. Updated data with 90 pts will be presented at the meeting. Legal entity responsible for the study: Lynn Cancer Institute Research Department Funding: Lynn Cancer Institute Research Department Disclosure: L. Raez, B.   Liquid Genomics;  All other authors have declared no conflicts of interest. 4P Co amplifications of PD L1/PD L2 genes (9p24.1) and PD L1 protein expression in NSCLC patients
Self medication and its Effective Modifiable Factors among Elderly Referred Health Care Centers in Shahr e Kord in 2015
Venue: Electronic physician

Drug overuse is a serious problem for health care, and one of the biggest problems for the socio economic well being of different communities. The elderly tend to use more drugs due to changes in their cognitive and physiological factors. One of the best ways to evaluate the health level of elderly people is to evaluate their self medication. This study was conducted to investigate self medication among the elderly in Shahr e Kord.  This cross sectional study was conducted on 350 people older than 65 in Shahr e Kord in 2015. Sampling was done in two stages. In the first stage, the city of Shahr e Kord was divided into four areas using geographical maps. Eighty eight people were selected from each area. The research instrument was a questionnaire called the Health Belief Model (HBM) The data were analyzed using SPSS version 20, the chi squared test, the independent samples t test, and the Pearson correlation coefficient.  No significant relationship was observed between the prevalence of self medication with demographic variables and level of awareness. But there was a significant difference between sensitivity, perceived severity, and perceived barriers and educational level. There also was a significant difference between the perceived benefits and their income level. There also was a significant difference between the level of awareness, sensitivity, severity, benefits, and barriers of people with and without a history of self medication (p 0.05)  Due to the adverse effects of self medication and the high prevalence of this activity among the elderly, it is recommended that a training program be developed and implemented to change the knowledge and beliefs of the elderly about self medication.
Epidemiology of brucellosis in Shahr e Kord from 2010 to 2014

Zoonosis, common diseases between humans and animals, is still one of the most important health problems. Brucellosis is a zoonosis with special health, economic and social importance.  This cross sectional prospective study was conducted on data recorded from 2010 to 2014 in health centers and laboratories of Shahr e kord city.  A total of 267 cases of brucellosis were registered from 2010 to 2014, with 27.3% female and 72.7% male, and a mean age of 33.68+ 17.46 years. The most common jobs of the participants with brucellosis were livestock and agriculture (38.8% and housekeeping (21.1% The most frequent clinical symptom was fever (73% and the most frequent risk factor was a history of contact with animals (75.5% The overall prevalence was 14.67 per 100000 during the years 2010 2014.  Considering the high prevalence of brucellosis in Shahr e kord, especially in rural areas and the high frequency of consuming non pasteurized dairy products, it is important to train people about consumption of pasteurized dairy products.
Investigating the Relationship between Talent Management Strategy and Career Path of Principals of Schools in Shahr e Kord

The aim of the present study is to investigate the relationship between talent management strategy and career path in principals of schools in Shahr e Kord. The study is a descriptive correlational one and its population includes all principals of high schools in Areas 1 and 2 of Shahr e Kord equal as 103 individuals in the academic year 2014 2015. A number of 81 principals were selected as participants via the simple random sampling and using Chochrane's formula. To measure talent management, the Sweem standard questionnaire and to measure career path, the Schaufeli standard questionnaire were used. The reliability coefficients for the questionnaires were calculated using Chronbach's alpha coefficients as 0.85 and 0.84 respectively. Data analysis was conducted using Pearson correlation coefficient and regression coefficient by SPSS. The results indicated that talent management strategy has a positive and significant correlation with principals' career path of principals of schools in Shahr e Kord. In addition, there is a direct and significant correlation between components of communication, performance management, training the staff and in acknowledgment of individuals with career path.
Palladium catalyzed direct C H arylation of pyridine N oxides with potassium aryl and heteroaryltrifluoroborates.
Venue: Organic biomolecular chemistry

An efficient ligand free Pd(OAc)2 catalyzed selective arylation of pyridine N oxides using potassium (hetero)aryltrifluoroborates as coupling partners via C H bond activation was achieved in the presence of TBAI. This approach has a broad substrate scope and shows moderate to high yields.
Aprendizaje de las reacciones quimicas a traves de actividades de indagacion en el laboratorio sobre cuestiones de la vida cotidiana

En aquest article s'examinen els acompliments de l'alumnat de secundaria durant la resolucio de dues activitats d'indagacio sobre les reaccions quimiques, en les quals han de planificar com resoldre questions relacionades amb la vida quotidiana. Els participants son estudiants de 3r. d'ESO que cursen la materia de Fisica i Quimica i que treballen en petits grups. Per a l'analisi es recullen les respostes escrites de cada petit grup relatives a la planificacio de la recerca, presa de dades i elaboracio de l'informe final per a cada tasca. Els resultats principals apunten a una evolucio en els acompliments de l'alumnat relatius a algunes operacions d'indagacio, aixi com tambe a certes dificultats relatives al disseny de les recerques.
La guerra cotidiana y la cotidianidad en el exilio. Representaciones sociales de la vida cotidiana de los gitanos conquenses en tiempos de la Guerra Civil.

Son multiples los estudios e investigaciones que han tenido y tienen como objeto de estudio la guerra civil, asi como sobre los gitanos como cultura o como pueblo pero resultan mas escasos los estudios donde confluyen ambos. Menos por no decir nulos cuando el eje en el que se articulan es la vida cotidiana como perspectiva de un analisis valido y legitimo en la investigacion. El presente trabajo pretende desde una perspectiva antropologica por un lado, hacer inteligible el pasado de una comunidad, la gitana, el discurso generado en la vida cotidiana contada su dia a dia experiencias, pensamientos, hechos deseos y palabras, en tiempos de la guerra, luchados mas alla del 36 al 39. Por otro lado, queremos aportar como es construida dicha cotidianidad a traves de los discursos de fuentes orales no gitanas y fuentes escritas, historiograficas, bibliograficas y prensa, ademas del discurso en tesis doctorales actuales. No hay pueblos sin historia, porque quedan las palabras que construyen historia e historias. El pueblo gitano tiene mucha historia que escribir de su puno y letra, ya que su historia ha sido escrita en tercera persona y, lamentablemente con intencionalidades, como se vera en el presente estudio, donde se ha tomado como referencia tiempos pasados y su reverberacion en los tiempos presentes, y que ha constituido la agrafia de dicha historia, lo escrito muestra lo no escrito, esa cotidianidad que ha sido exiliada. Muchas palabras con necesidad de ser articuladas e historias y realidades gitanas que piden ser estudiadas desde otro prisma.
Human computer interaction (hci) and internet residency: implications for both personal life and teaching/learning

Technological advances over the last decade have had a significant impact on the teaching and learning experiences students encounter today. We now take technologies such as Web 2.0, mobile devices, cloud computing, podcasts, social networking, super fast broadband, and connectedness for granted. So what about the student use of these types of technologies? Is there a blurring of the distinction between using them for academic purposes versus social use in their everyday lives? If so, what lessons can Higher Education learn from the fields of HCI and User Experience Design (UXD) about improving engagement through using familiar, intuitive and exciting interactions with technology? One of the factors driving the development of new pedagogies associated with the use of technologies for learning is a concern that there may be differences between the way that students use technologies today for socialising, working and learning. This paper describes the experiences of undergraduate students within the School of Engineering and Computing at the University of the West of Scotland. Initially under the auspices of a UK Higher Education Academy (HEA) Digital Literacies project, groups of students have completed activity maps to show how they used modern technologies for educational and personal purposes, and whether Visitor or Resident behaviour is exhibited. An analysis of these maps may prove interesting showing which tools are most popular and which are niche focussed in order to assess the implications for student engagement and enjoyment of learning.
Applications and Derivable Benefits of Cloud Based Mobile Learning Platform in Nigeria Higher Institutions

Mobile computing involves the use of portable handheld devices having network connections to access online resources via the internet. With mobile computing people can collaborate from various remote locations, they can be involved in online forums, conferences, chats and distance learning. Mobile learning or M learning presently is a more efficient, effective and convenient learning method. But as the education contents and resources as well as number of users and services increases, it becomes challenging deploying the m learning technique. This is where cloud computing comes into play as it provides a more reliable, scalable and dynamic computing platform for the end users. In this paper, a new platform for cloud based mobile learning is presented where mobile and wireless devices are used for its implementation. This new learning method can be applied in higher institutions or any other environment where teaching and learning takes place, with particular interest in the Engineering discipline. The various applications and numerous benefits of mobile computing especially in the area of mobile learning are outlined in this paper. This platform can be applied everywhere where there is a need for teaching and learning in higher education with particular interests in the Engineering discipline. The various applications and numerous benefits of mobile computing especially in the area of mobile learning are outlined in this paper. KeywordsCloud, Internet, Learning, Mobile, Wireless, Communication.
Teaching and learning requirements engineering based on mobile devices and cloud: A case study

Organizations have suffered a large (r)evolution at social, economic and technological levels. The increasing number of mobile devices on day to day of the general population and particularly among youth people, leads to the emergence of new paradigms in several areas of activity, particularly in education. As an example of a new paradigm in teaching and learning process, mobile learning supported by cloud environments and Bloom's taxonomy could be appointed. In this paper and in the context of a course of 1st cycle, following the guidelines of courses in Information Systems provided by ACM AIS, it is proposed the use of Google tools, aligned with Bloom's taxonomy, the model Blended Mobile Learning Context Oriented in a Requirements Engineering course.
Dyninst and MRNet: Foundational Infrastructure for Parallel Tools

Parallel tools require common pieces of infrastructure: the ability to control, monitor, and instrument programs, and the ability to massively scale these operations as the application program being studied scales. The Paradyn Project has a long history of developing new technologies in these two areas and producing ready to use tool kits that embody these technologies: Dyninst, which provides binary program control, instrumentation, and modification, and MRNet, which provides a scalable and extensible infrastructure to simplify the construction of massively parallel tools, middleware and applications. We will discuss new techniques that we have developed in these areas, and present examples of current use of these tool kits in a variety of tool and middleware projects. In addition, we will discuss features in these tool kits that have not yet been fully exploited in parallel tool development, and that could lead to advancements in parallel tools.
Afterslip following the 2007 Mw 8.4 Bengkulu earthquake in Sumatra loaded the 2010 Mw 7.8 Mentawai tsunami earthquake rupture zone

The 12 September 2007 Mw 8.4 Bengkulu earthquake in Sumatra marked the first in a modern series of large earthquakes along the Mentawai section of the Sunda megathrust. Understanding the spatial distribution of coseismic slip and ensuing afterslip is important for assessing seismic hazard in neighboring unruptured regions of the megathrust. We re estimate the spatial distribution of coseismic slip during this earthquake with improved coseismic offsets from the Sumatran GPS Array (SuGAr) and estimate afterslip following this earthquake with SuGAr postseismic time series spanning ~6.3 years after the earthquake. We invert for the spatio temporal distribution of afterslip with the principal component analysis based inversion method (PCAIM) and we take into account viscoelastic deformation by incorporating into the inversion the estimation of strain within ductile deforming blocks located at asthenospheric depths. Our results suggest cumulative afterslip concentrated within, updip and downdip of the 2007 coseismic rupture area, and shallow afterslip that borders and overlaps the 2010 Mw 7.8 Mentawai earthquake rupture zone. The cumulative contribution of stress changes due to the coseismic event and the ensuing afterslip likely increased strain rates in the shallow portion of the megathrust adjacent to the Mentawai earthquake rupture area, potentially promoting its rupture in 2010.
GNSS R Delay Doppler Map Simulation Based on the 2004 Sumatra Andaman Tsunami Event
Venue: J. Sensors

A new method for simulating Global Navigation Satellite System Reflectometry (GNSS R) delay Doppler maps (DDMs) of a tsunami dominant sea surface is presented. In this method, the bistatic scattering Z V model, the sea surface mean square slope model of Cox and Munk, and the tsunami induced wind perturbation model are employed. The feasibility of the Cox and Munk model under a tsunami scenario is examined by comparing the Cox and Munk model based scattering coefficient with the Jason 1 measurement. A good consistency between these two results is obtained with a correlation coefficient of 0.93. After confirming the applicability of the Cox and Munk model for a tsunami dominated sea, this study provides the simulations of the scattering coefficient distribution and the corresponding DDMs of a fixed region of interest before and during the tsunami. In the final analysis, by subtracting the simulation results that are free of tsunami from those with presence of tsunami, the tsunami induced variations in scattering coefficients and DDMs can be clearly observed. As a result, the tsunami passage can be readily interpreted.
Tsunami Hazard Analysis of Future Megathrust Sumatra Earthquakes in Padang, Indonesia Using Stochastic Tsunami Simulation

This study assesses the tsunami hazard potential in Padang, Indonesia probabilistically using a novel stochastic tsunami simulation method. The stochastic tsunami simulation is conducted by generating multiple earthquake source models for a given earthquake scenario, which are used as input to run Monte Carlo tsunami simulation. Multiple earthquake source models for three magnitude scenarios, i.e. Mw 8.5, Mw 8.75, and Mw 9.0, are generated using new scaling relationships of earthquake source parameters developed from an extensive set of 226 finite fault models. In the stochastic tsunami simulation, the effect of incorporating and neglecting the prediction errors of earthquake source parameters is investigated. In total, 600 source models are generated to assess the uncertainty of tsunami wave characteristics and maximum tsunami wave height profiles along coastal line of Padang. The results highlight the influence of the uncertainty of the scaling relationships on tsunami simulation results and provide a greater range of tsunamigenic scenarios produced from the stochastic tsunami simulation. Additionally, the results show that for the future major earthquakes in the Sunda megathrust, the maximum tsunami wave height in Padang areas can reach 20 m and therefore, significant damage and loss may be anticipated in this region.