nils-herrmann/clean_scirepeval huggingface dataset:
Update on hepatitis E virology: Implications for clinical practice.
Venue: Journal of hepatology

Hepatitis E virus (HEV) is a positive strand RNA virus transmitted by the fecal oral route. The 7.2kb genome encodes three open reading frames (ORF) which are translated into (i) the ORF1 polyprotein, representing the viral replicase, (ii) the ORF2 protein, corresponding to the viral capsid, and (iii) the ORF3 protein, a small protein involved in particle secretion. Although HEV is a non enveloped virus in bile and feces, it circulates in the bloodstream wrapped in cellular membranes. HEV genotypes 1 and 2 infect only humans and cause mainly waterborne outbreaks. HEV genotypes 3 and 4 are widely represented in the animal kingdom and are transmitted as a zoonosis mainly via contaminated meat. HEV infection is usually self limited but may persist and cause chronic hepatitis in immunocompromised patients. Reduction of immunosuppressive treatment or antiviral therapy with ribavirin have proven effective in most patients with chronic hepatitis E but therapy failures have been reported. Alternative treatment options are needed, therefore. Infection with HEV may also cause a number of extrahepatic manifestations, especially neurologic complications. Progress in the understanding of the biology of HEV should contribute to improved control and treatment of HEV infection.
Principles And Practice Of Clinical Virology

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An Introduction to the Social and Political Philosophy of Bertolt Brecht: Revolution and Aesthetics
Venue: Leonardo

we have collaborated ever since. When I first met Martha she had just completed a project in which she interviewed a number of clairvoyants in order to give conscious shape to the concept of an angel something that for most academics sat between kitsch and fantasy. However, in this work she gave such intellectual substance to the discussions of those who spoke with her that their visions had dignity and authority. In the same way she captured the concept of the technological imaginary at Transtechnology Research at Plymouth University in ways that attracted the minds of researchers who were looking for new paradigms, and through that group worked on dozens of projects, including Leonardo Reviews and L|R|Q. We published joint papers and shared a large research grant that allowed us to work with people that she valued at the EYE Film Institute, the Institute for Sound and Vision and the Angewandte in Vienna. She also worked independently on projects, such as the anthology Light Image and Imagination, in collaboration with Gustave Deutsch and Hannah Schimek. At the time of her death we were working with a large group of researchers from the cognitive sciences, the arts and the humanities on creativity and cognitive innovation. We also set up a small laboratory project to revisit the psychological experiments that were important to media in the late 19th century, and we were working with hospitals and the Dental School at Plymouth to build a new center dealing with health and creativity. We also established a network of researchers from across many disciplines, including Roger Malina, to work on methodological issues in particular those that involve questions about transdisciplinarity and academic collaboration. It seems today as I write this that the answers to many of our questions about academic collaboration were hidden in plain sight. Martha was a natural collaborator or perhaps, more precisely, she made it very easy for others to collaborate with her. At this distance it is clear to me that this was not simply a consequence of her intellectual qualities and her natural compassion for the world around her, but rather was the legacy of her refusal to acknowledge the dichotomy between matter and spirit as an irrefutable given. For her this refusal was a gift of personal freedom and intellectual grace; the irrevocable continuity of time, memory and perception In MeMorIaM: Martha BlassnIgg, 08 septeMBer 1969 27 septeMBer 2015
The impact of Thailand's public health response to the HIV epidemic 1984 2015: understanding the ingredients of success
Venue: Journal of virus eradication

Thailand has been heralded as a global leader in HIV prevention and treatment, and its experience with the HIV/AIDS epidemic holds valuable lessons for public health. This paper documents Thailand's response to its HIV epidemic from the late 1980s until today, and analyses its epidemiological impact (incidence and mortality) We discuss the association between the trajectory of HIV incidence and mortality rates over time, and the programmatic investments, policies and interventions that were implemented in the last three decades.  This is a review paper that draws on published literature, unpublished sources and routine behavioural and serological surveillance data since 1989. It is informed by the modelling of epidemiological impacts using the AIDS Epidemic Model. The AIDS Epidemic Model and Spectrum were used to assess the impact on incidence and mortality. Apart from epidemiological data, National AIDS Spending Assessment and programme data were also used to assess financial investments.  Thailand is well on its way to meeting the 90 90 90 targets, the goal that by 2020, 90% of people living with HIV know their HIV status, 90% of people with diagnosed HIV infection receive sustained antiretroviral therapy, and 90% of people receiving antiretroviral therapy (ART) are virally suppressed. In Thailand, 89% of people living with HIV know their status, 72% receive ART and 82% have viral load testing 99% of whom are suppressed. The public health response to HIV in Thailand has averted 5.7 million infections since 1991. If Thailand had not responded in 1991 to the HIV epidemic, and had there been no prevention and ART provision, the country would have experienced an estimated 158,000 225,000 deaths in the 2001 2006 period. This figure would have risen to 231,000 268,924 in the 2007 2014 period. A total of 196,000 deaths were averted between 2001 and 2014. If ART scale up had not occurred in 2001, Thailand would have experienced between 50,000 and 55,000 deaths per year in the period 2001 2006, and 31,000 46,000 annual deaths between 2007 and 2014. The main impact in terms of deaths averted is seen from 2004 onwards, reflecting treatment scale up.  Thailand's AIDS response has prevented needless morbidity and mortality due to the HIV epidemic. In the context of Thailand's ageing population, it is faced with the twin challenges of maintaining life long quality services among HIV patients and sustaining behaviour change to maintain primary prevention gains. Keeping the focus of the policy makers and health administrators on 'Ending the HIV epidemic' will require consistent advocacy, and evidence based, innovative and efficient approaches.
Life cycle assessment of shipping container home: A sustainable construction

Shipping containers are manufactured exceedingly rigid and strong complying specifications for freight purposes. After ending freight spell at sea and road, shipping containers are just occupying huge spaces at ports and other places. Among all the reuses, the recent technology and construction practices have set the containers for home building purposes. This research investigates the recent usage of containers for home buildings, and determines its constructability in Australian building industry. It also investigates the effects of carbon footprint and other life cycle environmental impacts (LCEI) Life cycle assessment (LCA) approach was used to evaluate 6 LCEI category indicators: cumulative energy demand (CED) water use, solid waste, global warming potential (GWP) acidification potential, and eutrophication potential. A container framed house is used as the base case to compare with other previous studies to evaluate the differences in those LCEI. According to Building Code Australia, the container house was complied with 6 star energy rating. Results show that operation phase has the most dominating impact for all the indicators except water use and solid waste generation. For all the impact categories, the overall contributions of the whole life cycle impacts have increased significantly if the design life of a building is increased to 100 years.
On two door three dimensional container packing problem under home delivery service

This paper considers the three dimensional container packing problem (3DCPP) under home delivery service, which predetermines an ordering of delivering ordered cargo boxes to customers, and aims to load a subset of those boxes according to the delivery ordering into a 3D car container with maximal utilization ratio of the container space while prohibiting the process of delivering cargos to each customer from unloading and subsequent reloading of boxes. In practice, cargos can be taken out from not only the rear door of the delivery container but also the side door. Nonetheless, the previous research only considered the case with only a single door. Therefore, this paper establishes the model for the two door 3DCPP under home delivery service. Furthermore, the rule of invisible and untouchable items and the subvolume based approach for the one door problem are extended to resolve the two door problem. Last, simulation analysis verifies performance of our approach.
The home stretch: developing automated solutions for legacy container list data at the Cuban Heritage Collection, University of Miami Libraries

Legacy finding aids in formats other than standardized EAD XML encoding are problematic for archivists wishing to provide deep access to and interoperability of their archival description and metadata. This case study will detail the project development, implementation, and outcomes for the legacy PDF container list conversion project as implemented at Cuban Heritage Collection (CHC) at the University of Miami, which seeks to provide innovative automation solutions based on the tenant of iterative processing and description of archival collections.
Drivers of University Industry Links: The Case of Knowledge Intensive Business Service Firms in Rural Locations

Johnston A. and Huggins R. Drivers of university industry links: the case of knowledge intensive business service firms in rural locations, Regional Studies. Establishing collaborative links with universities is a difficult task with an uncertain outcome and influenced by many factors including location, geographic distance, compatibility of interests, shared understanding and prior experience of collaboration. Drawing on an analysis of knowledge intensive business service firms (KIBS) located in predominantly rural districts of the UK, this paper examines the influences on partner selection when developing formal university linkage through knowledge transfer partnerships. The findings indicate that both geographic and organizational proximity are significantly associated with partner choice, indicating that the formation of university industry links is the result not only of spatial factors but also of prior experience of collaboration.
University industry collaboration and firms' R&D effort

This paper investigates the impact of publicly funded university industry collaboration on UK firms' R&D effort. We test the hypotheses that project participation has a positive effect on firms' R&D expenditure per employee and on their share of R&D employment. The paper exploits a novel source of data made up of a set of U I projects funded by the UK Engineering and Physical Sciences Research Council between 1997 and 2007 and firm level data available through the UK Office for National Statistics. We employ propensity score matching to select an appropriate control group of untreated firms on the basis of the probability that they participate to U I partnerships. We then estimate the impact of participation on firms' R&D effort in two points in time via ordinary least squares regression. The results show a positive and significant impact on the share of R&D employment two years after the end of projects. This is also confirmed by a robustness check. A positive effect on R&D expenditure per employee is found both at the end of the project and two years later. These findings are highly relevant for policy, given that U I collaboration is among the most frequent policy instruments put in place by local and national policy makers to foster pre competitive research and firms' R&D activities.
Prevalence of Work related Musculoskeletal Symptoms among Iranian Workforce and Job Groups
Venue: International journal of preventive medicine

Musculoskeletal disorders (MSDs) are known to cause occupational injuries. This study aimed to collate the existed relevant data and develop a general feature of MSDs problem among Iranian workforce.  In this study, we used the raw data related to 8004 employees from 20 Iranian industrial settings distributed throughout the country. In all studies, participants were selected based on simple random sampling method, and the data were collected using demographic characteristics and Nordic MSDs questionnaires.  The most prevalent MSDs symptoms were reported in the lower back (48.9% shoulders (45.9% neck (44.2% upper back (43.8% and knees (43.8% Prevalence rates of MSDs at least in one body region were found to be the highest (90.3% among health care workers. Prevalence rates of MSDs symptoms in all body regions were higher among workers with dynamic activities as compared to those of workers with static activities.  MSDs symptoms were common among the study population. Health care provider and workers with dynamic activities had the highest rate of MSDs. These results merit attention in planning and implementing ergonomics interventional program in Iranian industrial settings.
A hierarchical clustering of features approach for vehicle tracking in traffic environments
Venue: Int. J. Intell. Comput. Cybern.

Developing algorithms for automated detection and tracking of multiple objects is one challenge in the field of object tracking. Especially in a traffic video monitoring system, vehicle detection is an essential and challenging task. In the previous studies, many vehicle detection methods have been presented. These proposed approaches mostly used either motion information or characteristic information to detect vehicles. Although these methods are effective in detecting vehicles, their detection accuracy still needs to be improved. Moreover, the headlights and windshields, which are used as the vehicle features for detection in these methods, are easily obscured in some traffic conditions. The paper aims to discuss these issues.  First, each frame will be captured from a video sequence and then the background subtraction is performed by using the Mixture of Gaussians background model. Next, the Shi Tomasi corner detection method is employed to extract the feature points from objects of interest in each foreground scene and the hierarchical clustering approach is then applied to cluster and form them into feature blocks. These feature blocks will be used to track the moving objects frame by frame.  Using the proposed method, it is possible to detect the vehicles in both day time and night time scenarios with a 95 percent accuracy rate and can cope with irrelevant movement (waving trees) which has to be deemed as background. In addition, the proposed method is able to deal with different vehicle shapes such as cars, vans, and motorcycles.  This paper presents a hierarchical clustering of features approach for multiple vehicles tracking in traffic environments to improve the capability of detection and tracking in case that the vehicle features are obscured in some traffic conditions.
Forming Social Partnership Policy in Vocational Training of Service Sector Specialists in Germany and Austria

The article deals with the problem of forming social partnership policy in vocational training of service sector specialists in Germany and Austria. The foreign and domestic pedagogical experience in establishing an effective system of social partnership in vocational education has been analyzed. The author has considered main factors of social partnership development in vocational education that influence the forming of normative and legal support; a multilevel structure of government management, powers of employers and trade unions, regional economic development authorities of local government (industrial, commercial, trade, agricultural units) professional orientation of future specialists vocational education institutions and enterprises where specialists are trained; continuous monitoring of labour market needs and dynamic response to its changes; mechanisms of multivariate and multilevel approach to vocational education funding. Based on the analysis of scientific and reference sources the author has concluded that the main feature of vocational education in Germany and Austria is the participation of social partners who make common decisions and bear responsibility for normative and legal support; a multilevel management structure; monitoring of labour market needs and dynamic response to its changes; an optimal combination of theoretical and practical vocational training of future specialists.
A Tutorial Review of Functional Connectivity Analysis Methods and Their Interpretational Pitfalls
Venue: Front. Syst. Neurosci.

Oscillatory neuronal activity may provide a mechanism for dynamic network coordination. Rhythmic neuronal interactions can be quantified using multiple metrics, each with their own advantages and disadvantages. This tutorial will review and summarize current analysis methods used in the field of invasive and non invasive electrophysiology to study the dynamic connections between neuronal populations. First, we review metrics for functional connectivity, including coherence, phase synchronization, phase slope index, and Granger causality, with the specific aim to provide an intuition for how these metrics work, as well as their quantitative definition. Next, we highlight a number of interpretational caveats and common pitfalls that can arise when performing functional connectivity analysis, including the common reference problem, the signal to noise ratio problem, the volume conduction problem, the common input problem, and the sample size bias problem. These pitfalls will be illustrated by presenting a set of MATLAB scripts, which can be executed by the reader to simulate each of these potential problems. We discuss how these issues can be addressed using current methods.
Feature location in models through a genetic algorithm driven by information retrieval techniques
Venue: MoDELS

In this work we propose a feature location approach that targets models as the feature realization artifacts. The approach combines Genetic Algorithms and Information Retrieval techniques. Given a model and a feature description, model fragments extracted from the model are evolved using genetic operations. Then, Formal Concept Analysis is used to cluster the model fragments based on their common attributes into feature realization candidates. Finally, Latent Semantic Analysis is used to rank the candidates based on the similarity with the feature description. As a result, the genetic algorithm evolves the population of model fragments to find the set of most suitable feature realizations. We have evaluated the approach with an industrial case study, locating features with precision and recall values around 90% (baseline obtains less than 40% Finally, we provide recommendations on how to provide the input to the approach to improve the location of features over the models.
Improving biomedical information retrieval by linear combinations of different query expansion techniques
Venue: BMC Bioinformatics

BackgroundBiomedical literature retrieval is becoming increasingly complex, and there is a fundamental need for advanced information retrieval systems. Information Retrieval (IR) programs scour unstructured materials such as text documents in large reserves of data that are usually stored on computers. IR is related to the representation, storage, and organization of information items, as well as to access. In IR one of the main problems is to determine which documents are relevant and which are not to the user's needs. Under the current regime, users cannot precisely construct queries in an accurate way to retrieve particular pieces of data from large reserves of data. Basic information retrieval systems are producing low quality search results. In our proposed system for this paper we present a new technique to refine Information Retrieval searches to better represent the user's information need in order to enhance the performance of information retrieval by using different query expansion techniques and apply a linear combinations between them, where the combinations was linearly between two expansion results at one time. Query expansions expand the search query, for example, by finding synonyms and reweighting original terms. They provide significantly more focused, particularized search results than do basic search queries.ResultsThe retrieval performance is measured by some variants of MAP (Mean Average Precision) and according to our experimental results, the combination of best results of query expansion is enhanced the retrieved documents and outperforms our baseline by 21.06 even it outperforms a previous study by 7.12 .ConclusionsWe propose several query expansion techniques and their combinations (linearly) to make user queries more cognizable to search engines and to produce higher quality search results.
Altered gut microbiota profile in common variable immunodeficiency associates with levels of lipopolysaccharide and markers of systemic immune activation
Venue: Mucosal Immunology

Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency characterized by low immunoglobulin (Ig)G and IgA, and/or IgM. In addition to bacterial infections, a large subgroup has noninfectious inflammatory and autoimmune complications. We performed 16S ribosomal RNA based profiling of stool samples in 44 CVID patients, 45 patients with inflammatory bowel disease (disease controls) and 263 healthy controls. We measured plasma lipopolysaccharide (LPS) and markers of immune cell activation (i.e. soluble (s) CD14 and sCD25) in an expanded cohort of 104 patients with CVID and in 30 healthy controls. We found a large shift in the microbiota of CVID patients characterized by a reduced within individual bacterial diversity (alpha diversity, P<0.001) without obvious associations to antibiotics use. Plasma levels of both LPS (P=0.001) and sCD25 (P<0.0001) were elevated in CVID, correlating negatively with alpha diversity and positively with a dysbiosis index calculated from the taxonomic profile. Low alpha diversity and high dysbiosis index, LPS, and immune markers were most pronounced in the subgroup with inflammatory and autoimmune complications. Low level of IgA was associated with decreased alpha diversity, but not independently from sCD25 and LPS. Our findings suggest a link between immunodeficiency, systemic immune activation, LPS, and altered gut microbiota.