nils-herrmann/clean_scirepeval huggingface dataset:
PyMOL360: Multi user gamepad control of molecular visualization software
Venue: J. Comput. Chem.

Interactive visualization of biomolecular structure is a powerful tool for scientists, students, and audiences from the laboratory to the classroom and beyond. However, existing platforms lack the ability to generate a collaborative environment to engage multiple users simultaneously. To address this need, PyMOL360 is described, which enables control of PyMOL molecular visualization software from multiple gamepad controllers. Extensive modularity enables user defined configurations while default settings ease adoption by new users. A walkthrough of the software demonstrates its ability to select relevant molecules and modify viewing perspectives, molecular styles, colors, highlighted residues, or chains. Provision of source code encourages use and further development.
Diversifying Search Results Using Time An Information Retrieval Method for Historians
Venue: ECIR

Getting an overview of a historic entity or event can be difficult in search results, especially if important dates concerning the entity or event are not known beforehand. For such information needs, users benefit if returned results covered diverse dates, thus giving an overview of what has happened throughout history. Such a method can be a building block for applications, for instance, in digital humanities. We describe an approach to diversify search results using temporal expressions (e.g. 1990s) from their contents. Our approach first identifies time intervals of interest to the given keyword query based on pseudo relevant documents. It then re ranks query results so as to maximize the coverage of identified time intervals. We present a novel and objective evaluation for our proposed approach. We test the effectiveness of our methods on The New York Times Annotated corpus and the Living Knowledge corpus, collectively consisting of around 6 million documents. Using history oriented queries and encyclopedic resources we show that our method is able to present search results diversified along time.
Language Geometry Using Random Indexing
Venue: QI

Random Indexing is a simple implementation of Random Projections with a wide range of applications. It can solve a variety of problems with good accuracy without introducing much complexity. Here we demonstrate its use for identifying the language of text samples, based on a novel method of encoding letter N grams into high dimensional Language Vectors. Further, we show that the method is easily implemented and requires little computational power and space. As proof of the method's statistical validity, we show its success in a language recognition task. On a difficult data set of 21,000 short sentences from 21 different languages, we achieve 97.4% accuracy, comparable to state of the art methods.
A Test of Concept Study of At Home, Self Administered HIV Testing With Web Based Peer Counseling Via Video Chat for Men Who Have Sex With Men
Venue: JMIR public health and surveillance

Men who have sex with men (MSM) particularly MSM who identify as African American or Black (BMSM) are the sociodemographic group that is most heavily burdened by the human immunodeficiency virus (HIV) epidemic in the United States. To meet national HIV testing goals, there must be a greater emphasis on novel ways to promote and deliver HIV testing to MSM. Obstacles to standard, clinic based HIV testing include concerns about stigmatization or recognition at in person testing sites, as well as the inability to access a testing site due to logistical barriers.  This study examined the feasibility of self administered, at home HIV testing with Web based peer counseling to MSM by using an interactive video chatting method. The aims of this study were to (1) determine whether individuals would participate in at home HIV testing with video chat based test counseling with a peer counselor, (2) address logistical barriers to HIV testing that individuals who report risk for HIV transmission may experience, and (3) reduce anticipated HIV stigma, a primary psychosocial barrier to HIV testing.  In response to the gap in HIV testing, a pilot study was developed and implemented via mailed, at home HIV test kits, accompanied by HIV counseling with a peer counselor via video chat. A total of 20 MSM were enrolled in this test of concept study, 80% of whom identified as BMSM.  All participants reported that at home HIV testing with a peer counseling via video chat was a satisfying experience. The majority of participants (13/18, 72% said they would prefer for their next HIV testing and counseling experience to be at home with Web based video chat peer counseling, as opposed to testing in an office or clinic setting. Participants were less likely to report logistical and emotional barriers to HIV testing at the 6 week and 3 month follow ups.  The results of this study suggest that self administered HIV testing with Web based peer counseling is feasible and that MSM find it to be a satisfactory means by which they can access their test results. This study can serve as a general guideline for future, larger scale studies of Web based HIV test counseling for MSM.
INDOOR UWB POSITIONING IN EIGER LOCALIZATION SYSTEM

The EIGER project proposes a global approach for the exploitation of the efficient joint use of Global Navigation Satellite System (GNSS) signals and Ultra Wide Band (UWB) positioning in order to allow permanent and reliable outdoor/indoor localization. This paper is focused on the UWB positioning subsystem designed within the project. The architecture of the subsystem, design of its components and the transmission scheme leading to the time difference of arrival determination are described. Results of system laboratory tests are presented and discussed.
Targeted Gene Deletion Using DNA Free RNA Guided Cas9 Nuclease Accelerates Adaptation of CHO Cells to Suspension Culture.
Venue: ACS synthetic biology

Chinese hamster ovary (CHO) cells are the preferred host for the production of a wide array of biopharmaceuticals. Thus, efficient and rational CHO cell line engineering methods have been in high demand to improve quality and productivity. Here, we provide a novel genome engineering platform for increasing desirable phenotypes of CHO cells based upon the integrative protocol of high throughput RNA sequencing and DNA free RNA guided Cas9 (CRISPR associated protein9) nuclease based genome editing. For commercial production of therapeutic proteins, CHO cells have been adapted for suspension culture in serum free media, which is highly beneficial with respect to productivity and economics. To engineer CHO cells for rapid adaptation to a suspension culture, we exploited strand specific RNA seq to identify genes differentially expressed according to their adaptation trajectory in serum free media. More than 180 million sequencing reads were generated and mapped to the currently available 109,152 scaffolds of the CHO K1 genome. We identified significantly downregulated genes according to the adaptation trajectory and then verified their effects using the genome editing method. Growth based screening and targeted amplicon sequencing revealed that the functional deletions of Igfbp4 and AqpI gene accelerate suspension adaptation of CHO K1 cells. The availability of this strand specific transcriptome sequencing and DNA free RNA guided Cas9 nuclease mediated genome editing facilitates the rational design of the CHO cell genome for efficient production of high quality therapeutic proteins.
Sensing Pollution on Online Social Networks: A Transportation Perspective
Venue: Mob. Networks Appl.

Transportation policy and planning strategies, as well as Intelligent Transportation Systems (ITS) can all play important roles in decreasing pollution levels and their negative effects. Interestingly, limited effort has been devoted to exploring the potential of social network analysis in such context. Social networks provide direct feedback from people and, hence, potentially valuable information. A post telling how a person feels about pollution at a given time at a given location, could be useful to policy makers, planners or environmentally aware ITS designers. This work verifies the feasibility of sensing air pollution from social networks and of integrating such information with real sensors feeds, unveiling how people advertise such phenomenon, acting themselves as smart objects, and how online posts relate to true pollution levels. This work explores a new dimension in pollution sensing for the benefit of environmental and transportation research in future smart cities, confronting over 1,500,000 posts and pollution readings obtained from governmental on the field sensors over a one year span.
Known Vulnerabilities of Global Navigation Satellite Systems, Status, and Potential Mitigation Techniques
Venue: Proceedings of the IEEE

Global navigation satellite systems (GNSS) like GPS but also Galileo, GLONASS, and Beidou represent an important infrastructure to our society. They provide position and timing for numerous applications. A GNSS is a rather complex system consisting of around 30 satellites, a number of monitor stations, plus a control center. Billions of GNSS receivers represent the user segment. The receivers and the monitor stations receive a weak satellite radio signal and thus are susceptible to interference like jamming or spoofing. This paper outlines the core operation principles of satellite navigation to describe those kind of interference and to analyze the impacts. Different types of interference attacks result in different effects at the target receiver. The attack schemes are categorized within this paper. Reported incidents are summarized as well as the potential impact of GNSS vulnerability on critical infrastructure. Well known countermeasures at user receiver level or at system level are outlined and discussed for their suitability. The political and socioeconomic context of GNSS vulnerability is described emphasizing the large impact of a potential disruption of the GNSS service.
Comparison of Smartphone based Cyclist GPS Data Sources

It is important for planning agencies to have data on cyclist travel patterns, routes, volumes, and speeds, but access to such data is currently limited and often expensive to obtain. Many regions are looking toward the use of GPS data collected using smartphones to track cyclist trips, both via apps deployed by the agencies and, more recently, fitness based apps providing anonymized user data by roadway segment. As regions begin to collect and purchase GPS based data, there are many questions about potential uses in transportation planning, including the representativeness of the data. This paper provides a comparison of the data obtained from two smartphone based apps, Cycle Atlanta and Strava, to begin to understand how GPS data can be used to map cyclist movements in an urban area. Analysis includes user demographic data and overall trip statistics, time of day, and geographic trips by segment comparisons. Differences between the two populations were found in terms of gender, age, percent commute trips, trip lengths, and preference for bike paths. Cycle Atlanta data was also compared to a set of manual bike counts and it was found that only about 3% of the cyclists counted had recorded their trip in Cycle Atlanta. The usage of GPS based smartphone cycling app data is a promising new data source for transportation planning and design analysis, but should carefully take into account the likely bias from the self selected users of such apps. These apps can supplement, but not replace large scale count programs to establish system wide cyclist volumes.
Design parameter evaluation based on human operation for tip mechanism of forceps manipulator using surgical robot simulation
Venue: Adv. Robotics

We proposed a design method for pediatric surgical robots that evaluates the workspace and view information in computer simulator before the actual robot is developed. In this study, we investigated a suturing task in a virtual environment using forceps manipulators with different mechanical parameters. We reproduced the surgical workspace for congenital esophageal atresia and measured the working volume and invisible area to obtain suitable parameters for the suturing task. We also calculated the suitable mechanical parameters using Pareto optimal solution method and verified the mechanical parameters in Pareto optimal solution. We verified from the experimental results that there is a trade off between the working volume and invisible area during the suturing task. Moreover, we determined from the calculation results that the mechanical design of the forceps manipulator is influenced by the invisible area during the suturing task. Finally, we confirmed that it is possible to obtain suitable parameters for surgical robots using the proposed method.
Coping, stress, and personality in Spanish nursing students: A longitudinal study.
Venue: Nurse education today

The purpose of this study was to examine the dominant stress coping style in nursing students, its relationships with stressful life events and personality traits, and the students' changes during their academic training. A non experimental two wave longitudinal design was carried out in 199 nursing students recruited from three Spanish nursing schools. The Stressful Life Events Scale, NEO FFI, and COPE questionnaire were administered at the beginning (T1) and end (T2) of their nursing studies. Descriptive statistics, Anova(s) NPar tests, and Pearson correlations were carried out. Results show that nursing students' dominant coping style was emotion focused coping, both at T1 and T2. Highly significant correlations between emotional coping and the neuroticism trait were found. Coping, stress, and personality changed positively during the training program. At T2, the use of problem focused strategies increased, and participants became more extroverted, agreeable, and conscientious. Coping and personality changes experienced by nursing students throughout their degree program seem to mirror the professional competences needed by future licensed nurses.
Pharmaceutical Applications of Electrospraying.
Venue: Journal of pharmaceutical sciences

The electrohydrodynamic atomization technique, or simply called electrospraying, has been extensively studied for biomedical as well as for pharmaceutical applications over the past years. The simplicity, flexibility, and efficiency of producing particles at the microscale or nanoscale, with tailored size, shape, morphology, and microstructure, make electrospraying to become one of the most promising and well practiced approaches to be applied in many biomedical and pharmaceutical fields, from improving the bioavailability of poorly aqueous soluble drugs, preparing targeted drug delivery systems, and controllable drug release systems to delivering sensitive therapeutic agents such as protein based drugs or even living cells. Nevertheless, some issues still remain with respect to low throughput as well as the complex interplay between a great number of processing and formulation factors. A comprehensive understanding of these fundamental aspects is essential for the successful application of electrospraying for the production of particulate formulations with desired properties.
A Multi scale CNN for Affordance Segmentation in RGB Images
Venue: ECCV

Given a single RGB image our goal is to label every pixel with an affordance type. By affordance, we mean an object's capability to readily support a certain human action, without requiring precursor actions. We focus on segmenting the following five affordance types in indoor scenes: 'walkable' 'sittable' 'lyable' 'reachable' and 'movable' Our approach uses a deep architecture, consisting of a number of multi scale convolutional neural networks, for extracting mid level visual cues and combining them toward affordance segmentation. The mid level cues include depth map, surface normals, and segmentation of four types of surfaces namely, floor, structure, furniture and props. For evaluation, we augmented the NYUv2 dataset with new ground truth annotations of the five affordance types. We are not aware of prior work which starts from pixels, infers mid level cues, and combines them in a feed forward fashion for predicting dense affordance maps of a single RGB image.
Understanding payment card fraud through knowledge extraction from neural networks using large scale datasets

A novel approach to knowledge extraction from neural network classifiers when applied to payment card fraud detection is proposed. Existing Fraud Management Systems (FMS) use neural network classifiers but do not have the ability to explain their learnt patterns of fraud. Rule extraction from such classifiers with a high level of abstraction and linguistic simplicity is proposed. Decompositional knowledge extraction methods are found to be too reliant on the architecture of the fraud classifer and current pedagogical rule extraction methods produce rules that are not sufficiently comprehensible. In this thesis the Sparse Oracle based Adaptive Rule (SOAR) pedagogical extraction algorithm is proposed to extract generalising rules that explain patterns of fraud. SOAR uses sensitivity analysis to avoid the exhaustive searches of other pedagogical methods. By projecting into discretised space, polytopes are formed by SOAR covering the class convex hull of the classifier surface. A methodological and verifiable empirical evaluation on publicly available datasets in various domains is undertaken. These results show that SOAR extracts comprehensible rules that are sound from a deep learning neural network. When SOAR is applied to large datasets provided by payment card issuers it discovered new fraud types that were of key interest to payment risk/fraud analysts. SOAR provides an improved understanding of fraud vectors that will lead to a more secure payment process through informed payment fraud prevention steps and this work could therefore alter how fraud management is undertaken in the future.
Precision assessment of public attitudes toward genetic testing
Venue: American journal of medical genetics. Part A

Public attitudes toward genetic testing are largely unknown. Furthermore, as medical practices vary widely among different regions around the world due to differences in cultural, sociopolitical, and economical environments, people from different regions may have drastically different attitudes. Even for the same individual, the attitude may vary depending on the purpose and type of genetic testing and the disorder to be tested for. It seems to me what is called for is a "precision" approach to gauging people's attitude toward genetic testing. In the current issue of the American Journal of Medical Genetics: Part A, Fu et al. reported a carefully designed study that began to fill this gap, although more work need to be done for different disorders and among other populations.
Public Attitudes toward an Epidemiological Study with Genomic Analysis in the Great East Japan Earthquake Disaster Area
Venue: Prehospital and Disaster Medicine

The Great East Japan Earthquake of March 11, 2011 may have influenced the long term health of those in the disaster area. It is important to collect current and future health information of the people living in the post disaster area to provide appropriate health support and quality oriented care. However, public perceptions of health and genomic studies in the Great East Japan Earthquake disaster area are still unknown.  A questionnaire survey was conducted in one town affected by the Great East Japan Earthquake and subsequent tsunami. The results of the questionnaire were tailed and the differences in responses to each question were assessed by sex and age.  In 284 eligible people (137 men, 147 women) almost all participants agreed to join a health survey investigating the adverse effects of the disaster, and over 80% of the total participants agreed to genomic analysis. Over 70% of the participants wanted to receive pharmacogenetic testing and to receive feedback on which medications were suitable or unsuitable for them.  Most people living in the disaster area are interested in health surveys. Most of the participants also showed interest in genomic analysis.   MetokiH, KikuyaM, TsuchiyaN, NakamuraT, NagamiF, KuriyamaS, HozawaA, the ToMMo Study Group. Public attitudes toward an epidemiological study with genomic analysis in the Great East Japan Earthquake disaster area.  2016;31(3):330 334.
Antibodies and tuberculosis
Venue: Tuberculosis

Tuberculosis (TB) remains a major public health problem internationally, causing 9.6 million new cases and 1.5 million deaths worldwide in 2014. The Bacillus Calmette Guerin vaccine is the only licensed vaccine against TB, but its protective effect does not extend to controlling the development of infectious pulmonary disease in adults. The development of a more effective vaccine against TB is therefore a pressing need for global health. Although it is established that cell mediated immunity is necessary for the control of latent infection, the presupposition that such immunity is sufficient for vaccine induced protection has recently been challenged. A greater understanding of protective immunity against TB is required to guide future vaccine strategies against TB. In contrast to cell mediated immunity, the human antibody response against M.tb is conventionally thought to exert little immune control over the course of infection. Humoral responses are prominent during active TB disease, and have even been postulated to contribute to immunopathology. However, there is evidence to suggest that specific antibodies may limit the dissemination of M.tb, and potentially also play a role in prevention of infection via mucosal immunity. Further, antibodies are now understood to confer protection against a range of intracellular pathogens by modulating immunity via Fc receptor mediated phagocytosis. In this review, we will explore the evidence that antibody mediated immunity could be reconsidered in the search for new vaccine strategies against TB.
High Intensity Exercise in Hypoxia: Is Increased Reliance on Anaerobic Metabolism Important?
Venue: Front. Physiol.

Hypoxic training strategies to optimize physiological exercise responses have been extensively investigated, although often with limited performance benefits over the equivalent normoxic training (Roels et al. 2007) Recently, novel methods including intermittent hypoxic resistance training (IHRT) and repeat sprint training in hypoxia (RSH) have begun to receive research attention. Early results indicate that IHRT can augment muscle hypertrophy and strength compared to normoxic training (Nishimura et al. 2010; Manimmanakorn et al. 2013a,b) while RSH improves fatigue resistance, resulting in an increased capacity for repeated maximal efforts (Galvin et al. 2013; Faiss et al. 2013b) Although performing these high intensity activities in hypoxia appears to provide some benefits for training adaptations, the mechanisms underpinning these responses are not fully understood. The beneficial responses to high intensity exercise in hypoxia may result from a greater reliance on anaerobic metabolism, suggesting that increased metabolic stress may drive (or at least contribute to) these adaptations (Faiss et al. 2013b; Scott et al. 2015a) Considering the likely importance of metabolic stress on adaptation to IHRT and RSH strategies, the purpose of this paper is to briefly discuss the potential benefits of high intensity training in hypoxia with reference to the role of anaerobic processes.