nils-herrmann/clean_scirepeval huggingface dataset:
Novel Protein Based Pneumococcal Vaccines Administered with the Th1 Promoting Adjuvant IC31 Induce Protective Immunity against Pneumococcal Disease in Neonatal Mice
Venue: Infection and Immunity
Year: 2011

Streptococcus pneumoniae is responsible for many vaccine preventable deaths, annually causing around 1 million deaths in children younger than 5 years of age. A new generation of pneumococcal vaccines based on conserved proteins is being developed. We evaluated the immunogenicities and protective efficacies of four pneumococcal protein vaccine candidates, PcsB, StkP, PsaA, and PspA, in a neonatal mouse model. Mice were immunized three times and challenged intranasally with virulent pneumococci. All four proteins were immunogenic in neonatal mice, and antibody (Ab) responses were significantly enhanced by the novel adjuvant IC31, which consists of an antibacterial peptide (KLKL5KLK) and a synthetic oligodeoxynucleotide, ODN1a, that signals through Toll like receptor 9 (TLR9) Two single proteins, StkP and PspA, combined with IC31 significantly reduced pneumococcal bacteremia but had no effects on lung infection. Three proteins, PcsB, StkP, and PsaA, were evaluated with alum or IC31. IC31 enhanced Ab responses and avidity to all three proteins, whereas alum enhanced Ab responses and avidity to StkP and PsaA only. Mice receiving the trivalent protein formulation with IC31 had significantly reduced bacteremia and lung infection compared to unvaccinated mice, but the level of protection was dependent on the dose of IC31. When PspA was added to the trivalent protein formulation, the dose of IC31 needed to obtain protective immunity could be reduced. These results demonstrate that a novel pneumococcal protein based vaccine is immunogenic at an early age of mice and emphasize the benefits of using a combination of conserved proteins and an effective adjuvant to elicit potent protective immunity against invasive pneumococcal disease.
Automatic playlist continuation using a hybrid recommender system combining features from text and audio
Venue: RecSys Challenge
Year: 2018

The ACM RecSys Challenge 2018 focuses on music recommendation in the context of automatic playlist continuation. In this paper, we describe our approach to the problem and the final hybrid system that was submitted to the challenge by our team Cocoplaya. This system consists in combining the recommendations produced by two different models using ranking fusion. The first model is based on Matrix Factorization and it incorporates information from tracks' audio and playlist titles. The second model generates recommendations based on typical track co occurrences considering their proximity in the playlists. The proposed approach is efficient and achieves a good overall performance, with our model ranked 4th on the creative track of the challenge leaderboard.
Structural basis for the multitasking nature of the potato virus Y coat protein
Venue: Science Advances
Year: 2019

Structural and functional studies of the coat protein regions of potato virus Y reveal crucial roles in viral infectivity. Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl terminal regions of the coat protein units and viral RNA. RNA coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near atomic structure of RNA free virus like particles. The structures offer the first evidence for plasticity of the coat protein's amino and carboxyl terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
Antibacterial and Antifungal Activity of the Aqueous and Methanolic Extracts and Essential Oils of Red Beets Beta vulgaris Leaves
Year: 2020

The aim of this study was to investigate the antimicrobial properties of aqueous and methanolic extracts, as well as essential oils of red beet leaves. The leaves were purchased from local farms in Isfahan province, Iran. After drying the leaves, their extracts were obtained by water and methanol as solvent, and also essential oils of the leaves were extracted through the hydro distillation method. Antibacterial activity of the extracts and essential oils was determined against five foodborne bacteria by disc diffusion assay and minimum inhibitory concentration method. Moreover, the antifungal activity of the samples was examined by the contact phase method against five fungi species. The aqueous extract of red beet leaves did not show any antimicrobial activity against the studied species, whereas the methanolic extract inhibited the growth of four strains of the bacteria, including Escherichia coli, Bacillus cereus, Staphylococcus aureus, Salmonella enteritidis. Essential oil had an inhibitory effect against B. cereus, S. enteritidis, and S. aureus. Furthermore, the aqueous and methanolic extracts and essential oils had a variable degree of antifungal activity against all tested fungi. However, the methanolic extract and essential oils had a stronger antifungal effect than the aqueous extract.
Types of urbanization and economic growth
Year: 2020

What is the relationship between urbanization and economic growth? Though many scholars have long documented the impact of urbanization on economic growth, others find no relationship has been established between rates of urbanization and rates of growth. While urbanization has typically been theorized as the product of a Harris Todaro push and pull framework that encourages migration to urban areas for economic opportunity, recent works indicate that growth in urban areas stems from several distinct mechanisms. By re conceptualizing urbanization as resulting from two distinct mechanisms natural increase and residual increase, respectively we examine the impact of types of urbanization on economic growth. We find that while urban residual increase is corelated to economic growth, urbanization due to natural births and deaths is not. The results contribute to existing literature by providing an important insight into the factors behind economic growth and the effects of urbanization.
Detection of the sul2 strA strB gene cluster in an ice core from Dome Fuji Station, East Antarctica.
Venue: Journal of global antimicrobial resistance
Year: 2019

Bacteria harbouring antimicrobial resistance genes (ARGs) have been isolated from various locations, including ancient microbiomes, indicating that these genes pre date the discovery of antibiotics. To gain further information regarding ARGs in the pre antibiotic era, ice samples derived from Dome Fuji Station, Eastern Antarctica, were examined.  DNA was extracted from firn or ice core samples (n=3; 1200 1400ybp, 1700 2100ybp and 2200 2800ybp, respectively) under sterile conditions. Whole genome amplification and PCR analyses were utilised to detect ARGs.  A 2764 bp gene cluster containing the type II dihydropteroate synthase gene sul2 and the aminoglycoside phosphotransferase genes strA and strB was detected in the 1200 1400 year old Antarctic ice core (DF 63.5) The sul2 strA strB gene cluster is frequently associated with plasmid RSF1010 and transposon Tn5393; however, these elements were not detected in sample DF 63.5. The gene cluster exhibited a high level of sequence identity to sequences harboured in present day bacteria, although there were sequence polymorphisms in the strA gene. Furthermore, expression of this gene cluster in Escherichia coli resulted in reduced susceptibility to dihydrostreptomycin and sulfamethoxazole.  The results of this study provide further evidence that certain ARGs existed in the pre antibiotic era. Because the sul2 gene confers resistance to the synthetic compound sulfamethoxazole, these findings suggest that ARGs against synthetic antimicrobials emerged in bacteria during the pre antibiotic era.
A review of the business case for CSR in the hospitality industry
Year: 2020

Despite prolific research on corporate social responsibility (CSR) in its various forms in the hospitality industry, there is no consensus regarding the business case for CSR initiatives. Using a stakeholder lens, we review the research on CSR and its rationale by analyzing its impact on the environment, employees, customers, community, and investors in the hospitality industry. Our review analyzes 170 articles published between 1990 and 2017 covering different conceptual frameworks, measures, and samples to evaluate the current state of the field, integrate findings, identify gaps, and suggest avenues for future research. Our review calls for a) more studies that examine hospitality specific CSR initiatives to examine impact on firm performance, b) greater theory driven research, and c) expansion of contexts both in terms of different sectors of the industry and geographical locations, than is covered by existing studies. Future research directions are provided.
Exposure to diagnostic radiation and risk of breast cancer among carriers of BRCA1/2 mutations: retrospective cohort study (GENE RAD RISK)
Venue: BMJ British Medical Journal
Year: 2012

To estimate the risk of breast cancer associated with diagnostic radiation in carriers of BRCA1/2 mutations.  Retrospective cohort study (GENE RAD RISK) Setting Three nationwide studies (GENEPSO, EMBRACE, HEBON) in France, United Kingdom, and the Netherlands, Participants 1993 female carriers of BRCA1/2 mutations recruited in 2006 09.  Risk of breast cancer estimated with a weighted Cox proportional hazards model with a time dependent individually estimated cumulative breast dose, based on nominal estimates of organ dose and frequency of self reported diagnostic procedures. To correct for potential survival bias, the analysis excluded carriers who were diagnosed more than five years before completion of the study questionnaire.  In carriers of BRCA1/2 mutations any exposure to diagnostic radiation before the age of 30 was associated with an increased risk of breast cancer (hazard ratio 1.90, 95% confidence interval 1.20 to 3.00) with a dose response pattern. The risks by quarter of estimated cumulative dose <0.0020 Gy, =0.0020 0.0065 Gy, =0.0066 0.0173 Gy, and =0.0174 Gy were 1.63 (0.96 to 2.77) 1.78 (0.88 to 3.58) 1.75 (0.72 to 4.25) and 3.84 (1.67 to 8.79) respectively. Analyses on the different types of diagnostic procedures showed a pattern of increasing risk with increasing number of radiographs before age 20 and before age 30 compared with no exposure. A history of mammography before age 30 was also associated with an increased risk of breast cancer (hazard ratio 1.43, 0.85 to 2.40) Sensitivity analysis showed that this finding was not caused by confounding by indication of family history.  In this large European study among carriers of BRCA1/2 mutations, exposure to diagnostic radiation before age 30 was associated with an increased risk of breast cancer at dose levels considerably lower than those at which increases have been found in other cohorts exposed to radiation. The results of this study support the use of non ionising radiation imaging techniques (such as magnetic resonance imaging) as the main tool for surveillance in young women with BRCA1/2 mutations.
Problem gambling and family violence in the Asian context: a review
Year: 2015

BackgroundFew empirical studies have specifically evaluated the causal connection between problem gambling and domestic or family violence within East and South East Asian populations. Evidence from qualitative and quantitative studies suggests that at the very least, an association exists. Lifetime prevalence of intimate partner violence has been drawn from various Asian communities, and ranges from 15.4 to 61.1% which is generally higher than in western countries such as US, UK and Australia (17 26% Problem gambling rates are similarly higher in certain Asian countries (3.8 6% when compared to the international average (2.3% The aim of this review was to evaluate the available literature on problem gambling and family violence in East and South East Asian populations, and to highlight any consistencies between the two phenomena. The authors conducted an online literature search using the terms: "Asia" "gambling" "domestic violence" "family violence" and "abuse" and accessed physical libraries for literature not available online.DiscussionAs evidenced by qualitative and quantitative studies, it is reasonable to suggest that a link does indeed exist between family violence and problem gambling in certain Asian communities. The authors argue that there may be specific cultural factors that underpin the acceptance, maintenance, and under reporting of both problem gambling and family violence in some Asian communities. Such cultural factors include: patriarchal family systems, low help seeking and under reporting, the impact of collectivist culture on gambling normalisation, and immigration and acculturation stresses.SummaryThis paper concludes East and South East Asian communities display high rates of problem gambling and family violence. At the very least, there is some evidence to suggest a relationship between these two issues; however, immigration stresses and cultural beliefs may mediate this effect amongst migrant samples. The current state of research in this area is incomplete and requires rigorous methodological inquiry. Given strong preliminary evidence of a problem gambling family violence link, it is recommended that future research endeavours focus on accurately assessing a causal relationship between problem gambling and family violence. Further research should be longitudinal, carried out in Asian countries, and use local resident populations to consider whether or not underlying cultural traditions and beliefs engender or contribute to problem gambling and family violence. These findings have implications for the field of problem gambling and family violence by informing prevention and treatment strategies and services within the public health and welfare sectors.
Magnification of Video Signals of Engineering and Medical Applications
Year: 2019

Magnifying micro movements from natural video has recently been investigated by several Computer Vision and Image Processing researchers, due to its impact in numerous applications. In this paper we analyze video signals and try to magnify micro movements/vibrations to make them visible. These micro movements are typically undetectable and cannot be seen by basic human vision. We utilize Complex Wavelets to analyze sequential frames and detect any minor change in object's spatial position. We magnify some specific complex wavelet frequency bands by a multiplication factor and reconstruct back the video signal after some manipulation and modification to make these micro movements seen and observable. We compare our work with recent techniques in micro motion magnification (Freeman et. and try to show the merits of each technique. We finally apply the proposed technique of micro motion magnification on medical videos to disease diagnosis.
Bioarchaeology of Southeast Asia
Year: 2006

Preface Foreword 1.  Southeast Asian bioarchaeology: past and present Nancy Tayles and Marc Oxenham 2. The population history of Southeast Asia viewed from morphometric analyses of human skeletal and dental remains Hirofumi Matsumura 3. A multivariate craniometric study of the prehistoric and modern inhabitants of Southeast Asia, East Asia and surrounding regions: a human kaleidoscope? Michael Pietrusewsky 4. Interpretation of craniofacial variation and diversification of East and Southeast Asians Tsunehiko Hanihara 5. New perspectives on the human peopling of Southeast and East Asia during the late upper Pleistocene Fabrice Demeter 6. Human variation and evolution in Holocene Peninsular Malaysia David Bulbeck and Adam Lauer 7. Batak dentition, Palawan Island,  Southeast Asian Negrito origins Christy G. Turner II and James F. Eder 8. Non Nok Tha people: an assessment of dental pathological conditions Michele Toomay Douglas 9. Human biology from the bronze age to the iron age in the Mun River Valley of Northeast Thailand Kate Domett and Nancy Tayles 10. Paleodietary change among pre state metal age societies in Northeast Thailand: a study using bone stable isotopes Christopher King and Lynette Norr 11. The oral health consequences of the adoption and intensification of agriculture in Southeast Asia Marc Oxenham, Nguyen Lan Cuong and Nguyen Kim Thuy 12. Cranial lesions on the late Pleistocene Indonesian Homo erectus Ngandong 7 Etty Indriati 13. 'The predators within' investigating the relationship between malaria and health in the prehistoric Pacific Islands Hallie Buckley 14.  synthesising Southeast Asian population history and paleohealth Marc Oxenham and Nancy Tayles.
Draft Genome Sequence of the Human Pathogen Streptomyces somaliensis, a Significant Cause of Actinomycetoma
Venue: Journal of bacteriology
Year: 2012

We report the draft genome sequence of the human pathogen Streptomyces somaliensis (DSM 40738) a pathogen within a genus of largely saprophytic organisms. S. somaliensis causes severe and debilitating deep tissue and bone infections. The genome sequence is deposited in DDBJ/EMBL/GenBank with the accession number AJJM01000000.
A novel media properties based material removal rate model for magnetic field assisted finishing
Year: 2018

Magnetic field assisted finishing (MFAF) is a category of non conventional finishing processes that use magnetic field to manipulate finishing media typically consisting of magnetic particles and non magnetic abrasives suspended in a carrier fluid. In order to better control the process, an improved understanding of the actual removal process is needed. This paper introduces a new material removal rate model for magnetic field assisted finishing (MFAF) that aims to do so. The model considers the complexity of finishing media used in MFAF processes, where two different types of particles are present and interact with each other. The proposed material removal rate expression is based on contact mechanics and is a function of number of active magnetic particles, number of active abrasives, force per magnetic particle, and force per abrasive. Expressions for particle numbers were developed by considering an ideal face centred cubic configuration for the magnetic particle network, while expressions for forces were developed based on a proposed framework for the particle interactions. The model was verified experimentally for a double magnet MFAF process by varying the abrasive size and abrasive concentration. When the abrasive size was increased from 0.6 mm to 15 mm, the material removal rate decreased, consistent with the theoretical trend given by the model. Then, when abrasive concentration, given by the abrasives to carbonyl iron volumetric ratio, was increased from 0 to 0.768, the material removal rate initially increased and then reached a maximum when the volume ratio is 0.259 before decreasing with further increase of the volume ratio. This is also in agreement with the theoretical trend given by the model.
Developing Plugin e DDC as an Additional Application for Senayan Library Management System with PHP Language Programming and MySQL Database
Year: 2016

Senayan Library Management System, usually called as SLiMS dan e DDC (electronic Dewey Decimal Classification) is an application for library that now is used widely because it is easy to use, guaranteed of updating from the provider, and free. SLiMs and e DDC is actually two separated application, but in the practice, it is possible and recommended to be used together. SLiMS is used as a tool of library automation, meanwhile e DDC functions to help finding collection classification number. Some users of SLiMS and e DDC have suggested to develop SLiMS that is integral with e DDC, so the use of both application can be practical which can make the librarian easier to manage the library. Based on the suggestion, the writer and e DDC team finally created and designed additional application which is called plugin in SLiMS automation system that contained e DDC. The plugin was created using PHP MySQL and MySQL database. The purpose of this paper is to enrich the reference of library application development, especially that is based on Free Open Source Software (FOSS) The method used is Research and Development method. The result was the Plugin e DDC for SLiMS was finished and released on May 2, 2015 to celebrate National Education Day.
Making Online Teaching Effective: A Few Suggestions from a Developing Country's Perspective
Venue: Academia Letters
Year: 2021

In this letter, five broad suggestions are made to improve the effectiveness of online teaching in Bangladesh. They are: using state of the art digital tools, holding classes regularly and creating a conducive learning environment, developing an online evaluation system, indirect or direct financial support and lastly, other issues like health support and career counselling. If these steps are taken, online teaching and classes would be effective in Bangladesh. These policies would be relevant for other developing countries that are experiencing similar obstacles.
Big data driven outlier detection for soybean straw near infrared spectroscopy
Venue: J. Comput. Sci.
Year: 2018

In near infrared spectroscopy (NIRS) analysis, the prediction ability of the model is seriously affected by outliers that may be the result of errors related to the spectral measurements, the chemical analysis, or a combination of both. In this paper, an outlier detection method is described based on the NIRS analysis data of soybean straw. We improved the resampling by half mean (RHM) method by including a confidence interval (IRHM) and combined the IRHM and Cook's distance methods (IRHM COOK) to detect outlier samples in the NIRS data. The confidence interval is an important parameter in the IRHM COOK method and the optimal confidence intervals for the IRHM and Cook's distance methods are combined and used as the confidence interval for the IRHM COOK method. The selection process for the confidence interval is aimed at relative independence between the detection of the spectrum outliers and the chemical outliers. The experimental results show that the IRHM COOK method is superior to the traditional Mahalanobis distance method, the IRHM method, and the Cook's distance method using a partial least squares regression (PLS) model. The determination coefficient (R2) of a hemicellulose PLS calibration model increased from 0.4397918 to 0.5333039 and the root mean square error (RMSE) decreased from 0.7926415 to 0.7287254. The PLS models for lignin and cellulose performed better using the IRHM COOK method than the original model. The results show that the IRHM COOK method can effectively identify spectrum outliers and chemical outliers for soybean straw biomass. In addition, it is an effective method to handle NIRS analysis data with one type of outlier, which is proven based on an NIRS analysis of starch.