nils-herrmann/clean_scirepeval huggingface dataset:
Overcoming HBV immune tolerance to eliminate HBsAg positive hepatocytes via pre administration of GM CSF as a novel adjuvant for a hepatitis B vaccine in HBV transgenic mice
Venue: Cellular and Molecular Immunology

Granulocyte macrophage colony stimulating factor (GM CSF) is known to be a potential vaccine adjuvant despite contradictory results from animal and human studies. The discrepancies may be due to the different doses and regimens of GM CSF that were used, given that either mature or immature dendritic cells (DCs) could be induced under different conditions. To test the hypothesis that GM CSF can be used as a novel adjuvant for a hepatitis B virus (HBV) therapeutic vaccine, we administered GM CSF once per day for three days prior to vaccination with recombinant HBV vaccine (rHBVvac) in mice. We observed greater DC maturation in these pre treated animals at day 3 as compared to day 1 or day 2 of daily GM CSF administration. This strategy was further investigated for its ability to break the immune tolerance established in hepatitis B surface antigen transgenic (HBsAg Tg) animals. We found that the levels of induced anti HBsAg antibodies were significantly higher in animals following three days of GM CSF pre treatment before rHBV vaccination after the third immunization. In addition to the increase in anti HBsAg antibody levels, cell mediated anti HBsAg responses, including delayed type hypersensitivity, T cell proliferation, interferon g production, and cytotoxic T lymphocytes, were dramatically enhanced in the three day GM CSF pre treated group. After adoptive transfers of CD8+ T cells from immunized animals, antigen specific CD8+ T cells were observed in the livers of recipient HBsAg Tg animals. Moreover, the three day pre treatments with GM CSF prior to rHBVvac vaccination could significantly eliminate HBsAg positive hepatocytes, suggesting beneficial therapeutic effects. Therefore, this protocol utilizing GM CSF as an adjuvant in combination with the rHBVvac vaccine has the potential to become a novel immunotherapy for chronic hepatitis B patients.
The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos.
Venue: Cell reports

Hibernation is an adaptation that helps many animals to conserve energy during food shortage in winter. Brown bears double their fat depots during summer and use these stored lipids during hibernation. Although bears seasonally become obese, they remain metabolically healthy. We analyzed the microbiota of free ranging brown bears during their active phase and hibernation. Compared to the active phase, hibernation microbiota had reduced diversity, reduced levels of Firmicutes and Actinobacteria, and increased levels of Bacteroidetes. Several metabolites involved in lipid metabolism, including triglycerides, cholesterol, and bile acids, were also affected by hibernation. Transplantation of the bear microbiota from summer and winter to germ free mice transferred some of the seasonal metabolic features and demonstrated that the summer microbiota promoted adiposity without impairing glucose tolerance, suggesting that seasonal variation in the microbiota may contribute to host energy metabolism in the hibernating brown bear.
Raising the legal gambling age in Finland: problem gambling prevalence rates in different age groups among past year gamblers pre and post implementation

This article reports on the frequency of problem gambling, measured with the Lie/Bet instrument, in different age groups among Finnish past year gamblers in 2011 (n 2984) and 2014 (n 2326) The data highlights the situation before, and three years after, the implementation of a raised minimum age limit for gambling from 15 to 18 years. The difference in problem gambling frequency when comparing all age groups was statistically significant in 2011, but not in 2014. A significantly lower frequency of problem gambling was found among 18 19 year olds in 2014 (3.4% compared to 2011 (16.3% The results regarding problem gambling prevalence among 15 17 year olds (8.0% in 2011, 0.0% in 2014) are somewhat inconclusive as the number of respondents fulfilling the criteria for problem gambling was zero in 2014, thus affecting the analysis. No statistically significant difference in problem gambling frequency was found among 20 21 year olds (a group less affected by the policy implementation) or other older age groups between the survey years. While the findings should be viewed with caution, they do support recommendations regarding a minimum gambling age of 18 years or higher as an effective harm minimization measure.
Acceptance of multiple injectable vaccines in a single immunization visit in The Gambia pre and post introduction of inactivated polio vaccine.
Venue: Vaccine

As the World Health Organization (WHO) currently recommends that children be protected against 11 different pathogens, it is becoming increasingly necessary to administer multiple injectable vaccines during a single immunization visit. In this study we assess Gambian healthcare providers' and infant caregivers' attitudes and practices related to the administration of multiple injectable vaccines to a child at a single immunization visit before and after the 2015 introduction of inactivated polio vaccine (IPV) IPV introduction increased the number of injectable vaccines recommended for the 4 month immunization visit from two to three in The Gambia.  We conducted a cross sectional questionnaire based survey before and after the introduction of IPV at 4months of age in a representative sample of all health facilities providing immunizations in The Gambia. Healthcare providers who administer vaccines at the selected health facilities and caregivers who brought infants for their 4month immunization visit were surveyed.  Prior to IPV introduction, 9.9% of healthcare providers and 35.7% of infant caregivers expressed concern about a child receiving more than 2 injections in a single visit. Nevertheless, 98.8% and 90.9% of infants received all required vaccinations for the visit before and after IPV introduction, respectively. The only reason why vaccines were not received was vaccine stock outs. Infant caregivers generally agreed that vaccinators could be trusted to provide accurate information regarding the number of vaccines that a child needed.  Healthcare providers and infant caregivers in this resource limited setting accepted an increase in the number of injectable vaccines administered at a single visit even though some expressed concerns about the increase.
The Gothenburg congestion charge scheme: A pre post analysis of commuting behavior and travel satisfaction

The article uses the Gothenburg congestion charge scheme, implemented in 2013, as a case study to analyze the effects and perceptions of a policy instrument directly aimed to change the travel behavior of individuals. For the study, a survey was conducted including measures of commuting habits, attitudes (toward the congestion charge, the environment, automobility, and public transport) and satisfaction with travel, along with socio demographic and geographical variables. The survey was distributed to a panel of 3500 car owners in the Gothenburg region before the implementation of the scheme, with a follow up one year later. The analysis use group comparisons and a binary logistic regression analysis and results show that the difference in accessibility of different societal functions using private versus public transport affected the propensity to reduce car travel, whereas socio demographic variables had a low statistical significance, with the exception of women who were twice as likely to reduce their car travel than men. All studied groups reported a more positive view of the scheme at follow up, although this effect was more pronounced among those adapting their commuting behavior. In none of the studied groups did the implementation of the congestion charge scheme correlate with any significant change in satisfaction with travel.
A Pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform.
Venue: FEMS microbiology letters

Biological production in heterologous hosts is of interest for the production of the C4 alcohol (butanol) and other chemicals. However, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. Pseudomonas putida is a potential host for solvent production; in order to further adapt P. putida to this role, we generated mini Tn5 mutant libraries in strain BIRD 1 that do not consume butanol. We analyzed the insertion site of the mini Tn5 in a mutant that was deficient in assimilation of butanol using arbitrary PCR followed by Sanger sequencing and found that the transposon was inserted in the malate synthase B gene. Here, we show that in a second round of mutagenesis a double mutant unable to take up butanol had an insertion in a gene coding for a multisensor hybrid histidine kinase. The genetic context of the histidine kinase sensor revealed the presence of a set of genes potentially involved in butanol assimilation; qRT PCR analysis showed induction of this set of genes in the wild type and the malate synthase mutant but not in the double mutant.
In silico Driven Metabolic Engineering Towards Enhancing Biofuel and Biochemical Production

The development of a secure and sustainable energy economy is likely to require the production of fuels and commodity chemicals in a renewable manner. There has been renewed interest in biological commodity chemical production recently, in particular focusing on non edible feedstocks. The fields of metabolic engineering and synthetic biology have arisen in the past 20 years to address the challenge of chemical production from biological feedstocks. Metabolic modeling is a powerful tool for studying the metabolism of an organism and predicting the effects of metabolic engineering strategies. Various techniques have been developed for modeling cellular metabolism, with the underlying principle of mass balance driving the analysis. In this dissertation, two industrially relevant organisms were examined for their potential to produce biofuels. First, Saccharomyces cerevisiae was used to create biodiesel in the form of fatty acid ethyl esters (FAEEs) through expression of a heterologous acyl transferase enzyme. Several genetic manipulations of lipid metabolic and or degradation pathways were rationally chosen to enhance FAEE production, and then culture conditions were modified to enhance FAEE production further. The results were used to identify the rate limiting step in FAEE production, and provide insight to further optimization of FAEE production. Next, Clostridium thermocellum, a cellulolytic thermophile with great potential for consolidated bioprocessing but a weakly understood metabolism, was investigated for enhanced ethanol production. To accomplish the analysis, two models were
ZIKA virus elicits P53 activation and genotoxic stress in human neural progenitors similar to mutations involved in severe forms of genetic microcephaly and p53
Venue: Cell Death and Disease

Epidemiological evidence from the current outbreak of Zika virus (ZIKV) and recent studies in animal models indicate a strong causal link between ZIKV and microcephaly. ZIKV infection induces cell cycle arrest and apoptosis in proliferating neural progenitors. However, the mechanisms leading to these phenotypes are still largely obscure. In this report, we explored the possible similarities between transcriptional responses induced by ZIKV in human neural progenitors and those elicited by three different genetic mutations leading to severe forms of microcephaly in mice. We found that the strongest similarity between all these conditions is the activation of common P53 downstream genes. In agreement with these observations, we report that ZIKV infection increases total P53 levels and nuclear accumulation, as well as P53 Ser15 phosphorylation, correlated with genotoxic stress and apoptosis induction. Interestingly, increased P53 activation and apoptosis are induced not only in cells expressing high levels of viral antigens but also in cells showing low or undetectable levels of the same proteins. These results indicate that P53 activation is an early and specific event in ZIKV infected cells, which could result from cell autonomous and/or non cell autonomous mechanisms. Moreover, we highlight a small group of P53 effector proteins that could act as critical mediators, not only in ZIKV induced microcephaly but also in many genetic microcephaly syndromes.
Evaluation and prediction of the tensile properties of continuous fiber reinforced 3D printed structures

Three dimensional (3D) printing is a technique conventionally used to manufacture prototypes. Commercial desktop 3D printers have become available which produce functional 3D printed parts. The MarkOne by Mark Forged manufactures printed structures reinforced with continuous Carbon, Fiberglass or Kevlar fibers. The aim of this study is to evaluate the elastic properties of the fiber reinforced 3D printed structures and predict elastic properties using an Average Stiffness (VAS) method. Samples evaluated in this study were produced by varying the volume fraction of fibers within the 3D printed structures (4.04, 8.08 and 10.1% respectively) The experimentally determined elastic modulus was found to be 1767.2, 6920.0 and 9001.2 MPa for fiber volume fractions of 4.04, 8.08 and 10.1% respectively. The predicted elastic moduli were found to be 4155.7, 7380.0 and 8992.1 MPa. The model results differed from experiments by 57.5, 6.2 and 0.1% for the 4.04, 8.08 and 10.1% fiber volume fractions. The predictive model allows for the elastic properties of fiber reinforced 3D printed parts. The model presented will allow for designers to predict the elastic properties of fiber reinforced 3D printed parts to be used for functional components which require specific mechanical properties.
Influence of maximal anaerobic performance on body posture stability in elite senior and junior male judo athletes

The ability to maintain postural stability under the variable conditions of randori and during judo tournaments is one of the most important determinants of a judoka s performance. The aim of this study was to answer the question whether under the maximal anaerobic performance followed there are changes of postural stability (PS) among elite junior and senior male judo athletes. If so, whether the differences concern both visual control and then limb preference and the type of the test used.  Nineteen judo athletes (9 junior, 10 senior category) were tested. The multi sensorial platform was used for posturographic examination. Anaerobic variables were detected using the Wingate test with a Monark 824E mechanical ergometer.  Senior judo athletes achieved significantly better values of PS in comparison to juniors (F(1,34) 11.24, p 0.00, e2 0.25) In the one leg stance test, both groups produced significantly higher values than in the bipedal test (F(1,72) 159.81, p 0.000, e 2 0.69) In the monitored groups, we found a significant effect of the physical load in the bipedal test (F(1,34) 19.56, p 0.00, e 2 0.37) as well as in the one limb test (F(1,34) 49.03, p 0.00, e 2 0.59) Changes in PS after exercise are manifested more in the non preferred limb than in the preferred one.  The effect of maximal anaerobic exercise applied in our study was reflected in both senior and junior participants. Adult athletes appeared to have significantly better postural stability in comparison to juniors.
Advanced notch strain based calculation of S N curves for welded components

The present paper contains an advanced elastic plastic calculation procedure of S N curves of welded joints, taking into account solely standardized cyclic material data. The methodology used is based on the Notch Strain Approach, whereby advanced proposals regarding the means stress relaxation, mean stress sensitivity and residual stress state are introduced. The calculation accuracy of the proposed concept has been verified by means of experimentally determined S N curves of motor truck's axle casings, providing welds with explicit terminations (weld starts and ends) and subjected to cyclic loading at different load ratios and load configurations. Very good agreement between calculated and experimentally determined fatigue lives has been observed in all cases investigated.
Experiences and recommendations for numerical analyses of notch stress intensity factor and averaged strain energy density

This paper aims at providing recommendations for the practical application of relatively novel fatigue assessment approaches. Although the concept of notch stress intensity factor (N SIF) itself was proposed decades ago to provide the analytical solution of the stress field in way of sharp notches, only recently it has been considered as the basis for fatigue strength assessment of welded joints. N SIF itself and derived quantities such as the equivalent peak stress or the averaged strain energy density (SED) can be assumed as fatigue governing parameters and applied in everyday engineering practice being supported by powerful computation facilities. The N SIF approach is still too cumbersome for practical applications; the SED approach seems promising to overcome shortcomings, to be applied flexibly to different joint geometries and possibly to automate the calculation procedure in finite element analysis. Software having different features and different refinement strategies are applied in order to benchmark advantages and disadvantages of possible practical solutions for the approaches based on N SIF and averaged SED, thus offering various element types and modelling strategies. In general, high computational accuracy has been verified, despite relatively coarse meshes, if the element type, shape and mesh pattern is selected properly. However, the approach based on the averaged SED can be unsuitable for studying the notch effect of varying geometries if the averaging area increases more than the local stress concentration rises, as shown for the simplified geometry of a butt joint.
NSCT Based Infrared Image Enhancement Method for Rotating Machinery Fault Diagnosis
Venue: IEEE Transactions on Instrumentation and Measurement

Infrared images are usually subject to low contrast, edge blurring, and high noise. Especially for machinery diagnosis, the range of temperature variation is narrow, which causes the difficulty to diagnose different equipment conditions directly from infrared images. To enhance fault related information extraction and improve diagnosis accuracy, a new infrared image analysis method based on nonsubsampled contourlet transform is investigated with fuzzy enhancement and nonlinear gain. The parameters of fuzzy enhancement and nonlinear gain functions are optimized by particle swarming optimization algorithm, in which the optimization criterion is formulated by information entropy and contrast of infrared image. Feature extraction and dimensionality reduction methods are then applied to select features for further diagnosis. The effectiveness of the presented method is experimentally validated in the infrared image analysis of rotor test stand in laboratory, and the results show that the presented method can effectively enhance the fault information, enlarge the contrast of image under different conditions, and improve the accuracy of machinery fault diagnosis.
A summary of the REVERB challenge: state of the art and remaining challenges in reverberant speech processing research
Venue: EURASIP J. Adv. Signal Process.

In recent years, substantial progress has been made in the field of reverberant speech signal processing, including both single and multichannel dereverberation techniques and automatic speech recognition (ASR) techniques that are robust to reverberation. In this paper, we describe the REVERB challenge, which is an evaluation campaign that was designed to evaluate such speech enhancement (SE) and ASR techniques to reveal the state of the art techniques and obtain new insights regarding potential future research directions. Even though most existing benchmark tasks and challenges for distant speech processing focus on the noise robustness issue and sometimes only on a single channel scenario, a particular novelty of the REVERB challenge is that it is carefully designed to test robustness against reverberation, based on both real, single channel, and multichannel recordings. This challenge attracted 27 papers, which represent 25 systems specifically designed for SE purposes and 49 systems specifically designed for ASR purposes. This paper describes the problems dealt within the challenge, provides an overview of the submitted systems, and scrutinizes them to clarify what current processing strategies appear effective in reverberant speech processing.
Evidence for a limit to human lifespan
Venue: Nature

Driven by technological progress, human life expectancy has increased greatly since the nineteenth century. Demographic evidence has revealed an ongoing reduction in old age mortality and a rise of the maximum age at death, which may gradually extend human longevity. Together with observations that lifespan in various animal species is flexible and can be increased by genetic or pharmaceutical intervention, these results have led to suggestions that longevity may not be subject to strict, species specific genetic constraints. Here, by analysing global demographic data, we show that improvements in survival with age tend to decline after age 100, and that the age at death of the world's oldest person has not increased since the 1990s. Our results strongly suggest that the maximum lifespan of humans is fixed and subject to natural constraints.
Aerodynamic performance of the locust wing in gliding mode at low Reynolds number

Gliding is an important flight mode for insects because it saves energy during long distance flight without ing flapping. In this study, we investigated the influence of locust wing corrugation on the aerodynamic performance in gliding mode at low Reynolds number. Numerical simulations using two dimensional Navier Stokes equations are applied to study the gliding flight, which reveals the interaction between forewing and hindwing. The lift of the corrugated airfoil in a locust wing decreases from the wing root to the tip. Simulation results show that the pressure drags on the forewing and hindwing increase with an increase in wing thickness; while the lift drag ratio of the airfoil is marginally affected by the corrugation on the airfoil. Geometric parameters analysis of the locust wing is also carried out, which includes the corrugation height, the corrugation placement and the shapes of leading and trailing edges.
LIFT: Learned Invariant Feature Transform
Venue: ECCV

We introduce a novel Deep Network architecture that implements the full feature point handling pipeline, that is, detection, orientation estimation, and feature description. While previous works have successfully tackled each one of these problems individually, we show how to learn to do all three in a unified manner while preserving end to end differentiability. We then demonstrate that our Deep pipeline outperforms state of the art methods on a number of benchmark datasets, without the need of retraining.