nils-herrmann/clean_scirepeval huggingface dataset:
Coherent diffraction of single Rice Dwarf virus particles using hard X rays at the Linac Coherent Light Source
Venue: Scientific data

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) RDV was chosen as it is a well characterized model system, useful for proof of principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mm diameter focused hard X ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Angstrom were recorded. The diffraction data are available through the Coherent X ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
Linac Coherent Light Source data analysis using psana

Psana (Photon Science Analysis) is a software package that is used to analyze data produced by the Linac Coherent Light Source X ray free electron laser at the SLAC National Accelerator Laboratory. The project began in 2011, is written primarily in C+ with some Python, and provides user interfaces in both C+ and Python. Most users use the Python interface. The same code can be run in real time while data are being taken as well as offline, executing on many nodes/cores using MPI for parallelization. It is publicly available and installable on the RHEL5/6/7 operating systems.
The Prognostic Role of Androgen Receptor in Patients with Early Stage Breast Cancer: A Meta analysis of Clinical and Gene Expression Data
Venue: Clinical Cancer Research

Androgen receptor (AR) expression has been observed in about 70% of patients with breast cancer, but its prognostic role remains uncertain.  To assess the prognostic role of AR expression in early stage breast cancer, we performed a meta analysis of studies that evaluated the impact of AR at the protein and gene expression level on disease free survival (DFS) and/or overall survival (OS) Eligible studies were identified by systematic review of electronic databases using the MeSH terms "breast neoplasm" and "androgen receptor" and were selected after a qualitative assessment based on the REMARK criteria. A pooled gene expression analysis of 35 publicly available microarray data sets was also performed from patients with early stage breast cancer with available gene expression and clinical outcome data.  Twenty two of 33 eligible studies for the clinical meta analysis, including 10,004 patients, were considered as evaluable for the current study after the qualitative assessment. AR positivity defined by IHC was associated with improved DFS in all patients with breast cancer [multivariate (M) analysis, HR 0.46; 95% confidence interval (CI) 0.37 0.58, P 0.001] and better OS [M HR 0.53; 95% CI, 0.38 0.73, P 0.001] Thirty five datasets including 7,220 patients were eligible for the pooled gene expression analysis. High AR mRNA levels were found to confer positive prognosis overall in terms of DFS (HR 0.82; 95% CI 0.72 0.92;P 0.0007) and OS (HR 0.84; 95% CI, 0.75 0.94; P 0.02) only in univariate analysis.  Our analysis, conducted among more than 17,000 women with early stage breast cancer included in clinical and gene expression analysis, demonstrates that AR positivity is associated with favorable clinical outcome.
Bioinformatics programs are 31 fold over represented among the highest impact scientific papers of the past two decades
Venue: Bioinform.

To analyze the relative proportion of bioinformatics papers and their non bioinformatics counterparts in the top 20 most cited papers annually for the past two decades.  When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34% of the most cited papers in science were bioinformatics papers, which is approximately a 31 fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5 year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non bioinformatics papers was 25.8, significantly higher (P 4.5 x 10( 29) The 20 year trend in the average JIF between the two groups suggests the gap does not appear to be significantly narrowing. For a sampling of the journals producing top papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat 'hit or miss' That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success. CONTACT jdwren@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Opportunities and Challenges of Indian Pharmaceutical Sector: An overview

The global pharmaceutical market size is estimated to reach USD 1.4 trillion and the Indian pharmaceutical market size is estimated as USD 55 billion by the year 2020. The Indian pharmaceutical sector is expected to grow with faster compound annual growth rate (CAGR) compared to global growth rate during the period 2015 2020. The world market will be dominated by countries like USA, EU and Japan and the contribution of Phrmerging countries is expected to be more in coming years. The future of the world pharmaceutical sector will be dominated by medicines for non communicable diseases and original branded medicines. The Indian pharmaceutical sector evolved in different phases from pre independence era to post Trade Related Aspects of Intellectual Property Rights (TRIPS) Presently, Indian pharmaceutical sector is dominated by the generics drugs and more drugs are sold in anti infective category. The Indian pharmaceutical industry is having opportunities in the domestic market with growing demand for quality health care. More opportunities are seen in the area of Contract Research and Manufacturing Services (CRAMS) by Mergers and Acquisitions (M&A) and Biogenic market. The government of India has taken measures to boost pharmaceutical sector, even though, the pharmaceutical sector is facing challenges in patent rights and methods used for fixing ceiling price for drugs. More challenges are expected due to immature clinical trial regulations and ethical aspects.
Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz
Venue: Genome biology and evolution

The Yiddish language is over 1,000 years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographical origin of Yiddish speaking Ashkenazic Jews (AJs) An analysis of 393 Ashkenazic, Iranian, and mountain Jews and over 600 non Jewish genomes demonstrated that Greeks, Romans, Iranians, and Turks exhibit the highest genetic similarity with AJs. The Geographic Population Structure analysis localized most AJs along major primeval trade routes in northeastern Turkey adjacent to primeval villages with names that may be derived from "Ashkenaz." Iranian and mountain Jews were localized along trade routes on the Turkey's eastern border. Loss of maternal haplogroups was evident in non Yiddish speaking AJs. Our results suggest that AJs originated from a Slavo Iranian confederation, which the Jews call "Ashkenazic" (i.e. "Scythian" though these Jews probably spoke Persian and/or Ossete. This is compatible with linguistic evidence suggesting that Yiddish is a Slavic language created by Irano Turko Slavic Jewish merchants along the Silk Roads as a cryptic trade language, spoken only by its originators to gain an advantage in trade. Later, in the 9th century, Yiddish underwent relexification by adopting a new vocabulary that consists of a minority of German and Hebrew and a majority of newly coined Germanoid and Hebroid elements that replaced most of the original Eastern Slavic and Sorbian vocabularies, while keeping the original grammars intact.
Fatigue Crack Growth in Specimens with Rectangular Section under Torsion and Bending with Torsion

The paper presents the test results on the fatigue crack growth under torsion and proportional bending with torsion in the aluminium alloy EN AW 2017A T4. The tests were performed at the fatigue test stand MZGS 100 at the constant amplitude of moment MB MT MBT 15.84 Nm and stress ratio R 1. Plane specimens with stress concentrators in form of the external one sided blunt notch were tested. The results of experiments were described on graphs of the fatigue crack length ,a" versus numbers of cycles N. A non uniform fatigue cracks growth on both lateral surfaces of specimens was observed during experimental tests.
Sustainable Thinking and Environmental Awareness through Design Education

Environmentally aware design aims to convert global socio environmental concerns to investigate ecological principles and interactions with design decisions, which determine levels of sustainable usage of environmental resources. The aim of this study is to analyze the changing role and responsibility of designers and the importance of environmentally aware design education as crucial factors to acquire knowledge through the viewpoint of sustainability. The outputs and findings of the workshop conducted with design professionals and educators will be analyzed to consider the obstacles and fundamentals of sustainable design education for developing countries to create environments, buildings and products in a sustainable way.
Scaffolding practices: A study of design practitioner engagement in design education

The paper presents a study of tutor student design reviews that form part of formal Industrial Design education. It is motivated by interests in how design expertise is acquired through experiences of designing and how novice designers are assisted to develop their own positions as designers. It explores the ways a professional designer tutor directs, guides and encourages students' engagement with a design task, and presents them with opportunities to develop their own design values, preferences, and design sensibilities. It uses the empirical data to draw attention to how the potential of design proposals as rhetorical instruments to serve both designers 'own thinking and the presentation of their designs to others is a prominent theme in the professional designer tutor's engagement.
A novel approach for similarity and indexing based ontology for semantic web educational system
Venue: Int. J. Intell. Eng. Informatics

Several web based educational systems have been designed and widely used for the past two decades. However, there are some limitations in the previous systems. The integration of semantic web and artificial intelligence explores new methods for educational concepts. For instance, an educational system based on the semantic web ESBSW which represents the content and the knowledge in the form of ontology and counts on intelligent agents that allow machines to understand the web content. In this paper, a new approach for an educational system based on the semantic web is developed. The architecture of the system and the new mechanism for similarity and indexing based on ontology is proposed and elaborated. This paper also compares the performance evaluation of indexing system in the vector space model VSM and ontology based information retrieval models. The similarity between the concept and document is calculated using semantic similarity measure.
Transforming High School Classrooms with Free/Open Source Software: It 's Time for an Open Source Software Revolution

applications meet many of the software needs of high school science classrooms. In spite of the availability and quality of FOSS tools, they remain unknown to many teachers and utilized by fewer still. In a world where most software has restrictions on copying and use, FOSS is an anomaly, free to use and to redistribute without restrictions. Using FOSS instead of the ubiquitous proprietary applications most commonly used can seem as heretical and as impossible as did Copernicus's suggestion that the Earth was not the center of the universe. This paper suggests one of the factors that keeps schools from adopting or even considering FOSS is that its very existence can be written off as an anomaly. Additionally, it shows similarities between the development of FOSS and the development of scientific knowledge. Moreover, it provides examples of FOSS for high school science classrooms.
3D for the people: multi camera motion capture in the field with consumer grade cameras and open source software
Venue: Biology Open

Ecological, behavioral and biomechanical studies often need to quantify animal movement and behavior in three dimensions. In laboratory studies, a common tool to accomplish these measurements is the use of multiple, calibrated high speed cameras. Until very recently, the complexity, weight and cost of such cameras have made their deployment in field situations risky; furthermore, such cameras are not affordable to many researchers. Here, we show how inexpensive, consumer grade cameras can adequately accomplish these measurements both within the laboratory and in the field. Combined with our methods and open source software, the availability of inexpensive, portable and rugged cameras will open up new areas of biological study by providing precise 3D tracking and quantification of animal and human movement to researchers in a wide variety of field and laboratory contexts.  Argus is a free and open source toolset for using consumer grade cameras to acquire 3D kinematic data in field settings.
Foreign language anxiety levels in Second Life oral interaction
Venue: ReCALL

Virtual worlds have been described as low anxiety environments (Dickey, 2005) where students may feel "shielded" behind their avatars (Rosell Aguilar, 2005: 432) The aim of this article is to analyse the evolution of the Foreign Language Anxiety (FLA) levels experienced by a group of participants who used the virtual world Second Life for oral interaction (VW Group) The data gathered was compared to that of a group of students who completed similar oral interaction activities in the traditional classroom (CR Group) The quantitative and qualitative data analysed indicates that the FLA levels of the VW Group decreased as weeks went by and that they were lower than those experienced by the CR Group. The anonymity afforded by the VW had a positive effect on some of the students, who reported increased self confidence and decreased nervousness. However, the students' comments suggest that this anonymity may wear off once they feel they know their interlocutor. Anonymity may not be the only reason to explain the decrease in FLA.
TASK REPETITION AND SECOND LANGUAGE SPEECH PROCESSING
Venue: Studies in Second Language Acquisition

This study examines the relationship between the repetition of oral monologue tasks and immediate gains in L2 fluency. It considers the effect of aural oral task repetition on speech rate, frequency of clause final and midclause filled pauses, and overt self repairs across different task types and proficiency levels and relates these findings to specific stages of L2 speech production (conceptualization, formulation, and monitoring) Thirty two Japanese learners of English sampled at three levels of proficiency completed three oral communication tasks (instruction, narration, and opinion) six times. Results revealed that immediate aural oral same task repetition was related to gains in oral fluency regardless of proficiency level or task type. Overall gains in speech rate were the largest across the first three performances of each task type but continued until the fifth performance. More specifically, however, clause final pauses decreased until the second performance, midclause pauses decreased up to the fourth, and self repairs decreased only after the fourth performance, indicating that task repetition may have been differentially related to specific stages in the speech production process.
RapIoT Toolkit: Rapid Prototyping of Collaborative Internet of Things Applications
Venue: 2016 International Conference on Collaboration Technologies and Systems (CTS)

The Internet of Things holds huge promises to enhance collaboration in multiple application domains. By bringing Internet connectivity to everyday objects and environments it promotes ubiquitous access to information and integration with third party systems. Further, connected things can be used as physical interfaces to enable users to cooperate leveraging multiple devices via parallel and distributed actions. Yet creating prototypes of IoT systems is a complex task for non experts because it requires dealing with multi layered hardware and software infrastructures. We introduce RapIoT, a software toolkit that facilitates prototyping IoT systems providing an integrated set of developer tools. Our solution abstracts low level details and communication protocols allowing developers to focus on the application logic, facilitating rapid prototyping. RapIoT supports the development of collaborative applications by enabling the definition of high level data types primitives. RapIoT primitives act as a loosely coupled interface between generic IoT devices and applications; simplifying the development of systems that make use of an ecology of devices distributed to multiple users and environments. We illustrate the potential of our toolkit by presenting the development process of a IoT system for crowd sourcing of air quality data. We conclude discussing strength and limitations of our platform highlighting further possible uses for collaborative applications.
Current advances in orthodontic pain
Venue: International Journal of Oral Science

Orthodontic pain is an inflammatory pain that is initiated by orthodontic force induced vascular occlusion followed by a cascade of inflammatory responses, including vascular changes, the recruitment of inflammatory and immune cells, and the release of neurogenic and pro inflammatory mediators. Ultimately, endogenous analgesic mechanisms check the inflammatory response and the sensation of pain subsides. The orthodontic pain signal, once received by periodontal sensory endings, reaches the sensory cortex for pain perception through three order neurons: the trigeminal neuron at the trigeminal ganglia, the trigeminal nucleus caudalis at the medulla oblongata and the ventroposterior nucleus at the thalamus. Many brain areas participate in the emotion, cognition and memory of orthodontic pain, including the insular cortex, amygdala, hippocampus, locus coeruleus and hypothalamus. A built in analgesic neural pathway periaqueductal grey and dorsal raphe has an important role in alleviating orthodontic pain. Currently, several treatment modalities have been applied for the relief of orthodontic pain, including pharmacological, mechanical and behavioural approaches and low level laser therapy. The effectiveness of nonsteroidal anti inflammatory drugs for pain relief has been validated, but its effects on tooth movement are controversial. However, more studies are needed to verify the effectiveness of other modalities. Furthermore, gene therapy is a novel, viable and promising modality for alleviating orthodontic pain in the future.
A conceptual framework of students with visual impairments on website accessibility acceptance
Venue: 2016 International Computer Science and Engineering Conference (ICSEC)

Website accessibility is a key determinant of people with disabilities' acceptance. It is the key of making websites accessible to all, which covers all disabilities who affect access to the web. Web users including students with visual impairments can conveniently undertake a number of tasks that would be difficult or impossible, but many web applications are not accessible to them. Therefore, inaccessible online materials will lead students with visual impairments to fewer opportunities to learn and improve their learning outcomes. Based on many researches, it was found that the acceptance of website accessibility of students with visual impairments included web accessibility and vision impairment level. The purpose of this paper is to build a model based on Unified Theory of Acceptance and Use of Technology, that performance expectancy, effort expectancy, social influence, and facilitating conditions have positive effects on usage intention and acceptance behavior of website accessibility. This proposed model provides more understanding of the factors that could influence user acceptance in website accessibility. It also presents hypotheses and develops a structural equation model for further empirical study.
Development of the Classism Attitudinal Profile (CAP)
Venue: Journal of counseling psychology

Despite increasing interest in social class issues within psychology, there are a limited number of theoretically rooted instruments to measure subjective social class, particularly related to classism. The purpose of this project was to create a brief, psychometrically sound, and theoretically grounded instrument, called the Classism Attitudinal Profile (CAP) designed to measure 2 aspects of classism (downward and upward) defined in Liu's (2011) Social Class World View Model Revised (SCWM R) Data from 2 independent samples (n 608, n 199) provided evidence in support of the consistency (alpha and test retest coefficients) anticipated factor structure, and convergent/discriminant validity of CAP subscale scores. Downward and upward classism scores were only modestly correlated with each other and differentially correlated with other measures, thereby demonstrating that CAP subscales measure distinct constructs rather than opposite ends of the same continuum. Validity of CAP scores was further supported by logically consistent patterns of relationships with measures of subjective social status, materialistic values, Protestant work ethic, life satisfaction, racism, sexism, and key demographic variables.