nils-herrmann/clean_scirepeval huggingface dataset:
Circulating microRNA Signatures in Patients With Idiopathic and Postmenopausal Osteoporosis and Fragility Fractures.
Venue: The Journal of clinical endocrinology and metabolism

Established bone turnover markers do not reflect fracture risk in idiopathic male and premenopausal osteoporosis and the role of microRNAs (miRNAs) in these patients is currently unclear. miRNAs are a class of small non coding RNAs that regulate gene expression and bone tissue homeostasis. They are considered a new class of endocrine regulators with promising potential as biomarkers.  Evaluation of circulating miRNA signatures in male and female subjects with idiopathic and postmenopausal osteoporotic low traumatic fractures.  This was a case control study of cross sectional design of 36 patients with prevalent low traumatic fractures and 39 control subjects  One hundred eighty seven miRNAs were quantified in serum by qPCR, compared between groups and correlated with established bone turnover markers.  Significant differences in serum levels of circulating miRNAs were identified in all three subgroups (46 in premenopausal, 52 in postmenopausal, 55 in male) A set of 19 miRNAs was consistently regulated in all three subgroups. Eight miRNAs [miR 152 3p, miR 30e 5p, miR 140 5p, miR 324 3p, miR 19b 3p, miR 335 5p, miR 19a 3p, miR 550a 3p] were excellent discriminators of patients with low traumatic fractures, regardless of age and sex, with area under the curve values 0.9. The 11 remaining miRNAs showed area under the curve values between 0.81 and 0.89. Correlation analysis identified significant correlations between miR 29b 3p and P1NP, and miR 365 5p and iPTH, TRAP5b, P1NP and Osteocalcin, as well as BMDL1 L4 and miR 19b 3p, miR 324 3p, miR 532 5p, and miR 93 5p.  Specific serum miRNA profiles are strongly related to bone pathologies. Therefore miRNAs might be directly linked to bone tissue homeostasis. In particular, miR 29b 3p has previously been reported as regulator of osteogenic differentiation and could serve as a novel marker of bone turnover in osteoporotic patients as a member of a miRNA signature.
Tissue specific mutation accumulation in human adult stem cells during life
Venue: Nature

The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life is associated with various age related diseases, including cancer. Extreme variation in cancer risk across tissues was recently proposed to depend on the lifetime number of ASC divisions, owing to unavoidable random mutations that arise during DNA replication. However, the rates and patterns of mutations in normal ASCs remain unknown. Here we determine genome wide mutation patterns in ASCs of the small intestine, colon and liver of human donors with ages ranging from 3 to 87 years by sequencing clonal organoid cultures derived from primary multipotent cells. Our results show that mutations accumulate steadily over time in all of the assessed tissue types, at a rate of approximately 40 novel mutations per year, despite the large variation in cancer incidence among these tissues. Liver ASCs, however, have different mutation spectra compared to those of the colon and small intestine. Mutational signature analysis reveals that this difference can be attributed to spontaneous deamination of methylated cytosine residues in the colon and small intestine, probably reflecting their high ASC division rate. In liver, a signature with an as yet unknown underlying mechanism is predominant. Mutation spectra of driver genes in cancer show high similarity to the tissue specific ASC mutation spectra, suggesting that intrinsic mutational processes in ASCs can initiate tumorigenesis. Notably, the inter individual variation in mutation rate and spectra are low, suggesting tissue specific activity of common mutational processes throughout life.
Taxes and Technological Determinants of Wage Inequalities: France 1976 2010

This paper makes two simple points. First, labour demand depends on product wage or labour cost. Hence, demand side explanations for the rise in inequalities such as skill biased technical change and job polarization should be tested using data on labour cost and not net wage or posted wage. Contrary to previous studies, we find evidence of skill biased technical change in France when we measure wage inequality in terms of labour cost. In that respect, France is no exception. Second, the French case provides a clear evidence that changes in taxation can have very significant effect in converting market inequalities into consumption or net wages inequalities. In France, net wage inequalities have decreased by about 10% while labour cost inequalities have increased by 15% over the 1976 2010 period. This fact provides support both for the supporters of the skill biased technical change explanations of the secular increase in wage inequalities, as well to those who believe that institutions could have significant impact on inequalities in disposable incomes.
Adjust Me if I Can't: The Effect of Firm Incentives on Labor Supply Responses to Taxes

I provide theoretical and empirical evidence on the importance of statu tory incidence in labor markets in the presence of asymmetric frictions. Using a theoretical model I show that labor supply responses are stronger when the statutory incidence of taxes or labor rules falls on firms, even when wages can adjust freely. I explore these mechanisms by studying labor responses to incentives generated by the "Mini Job" program aimed at increasing labor supply of low income individuals in Germany. Using administrative data, I show evidence of a strong behavioral response in the form of sharp bunching to the mini job threshold that generates large discontinuous changes both in the marginal tax rates and in the total in come and payroll tax liability of individuals in Germany. Sharp bunching translates into elasticity estimates that are an order of magnitude larger than has been previously estimated using the bunching approach. To ex plain the magnitude of the observed response, I show that in addition to tax rates, fringe benefit payments also change at the threshold. Mini job workers receive smaller yearly bonuses and fewer vacation days but are paid higher gross wages than regular workers. These results indicate that lower fringe benefits make mini jobs attractive to employers, thus facilitating labor supply responses in accordance with the model's predictions.
Macroeconomic shocks, forward looking dynamics, and the behavior of hedge funds

We investigate how hedge funds' strategies react, as a group, to macroeconomic risk and uncertainty. Adopting the methodology of Beaudry et al. (2001) we track the behavior of the cross sectional dispersions of hedge fund strategies' returns, market betas and alphas over the business cycle. The pattern of strategies' betas supports Beaudry et al.'s conjecture: hedge funds reduce their risk taking (betas) during times of macroeconomic uncertainty, which makes their strategies more homogeneous and thus contributes to increased systemic risk in the financial system. However, the cyclical behavior of the cross sectional dispersions of strategies' returns and strategies' alphas is not in line with Beaudry et al.'s conjecture. These dispersions tend to increase during episodes of rising macroeconomic uncertainty, which suggests the prevalence of the Black's (1976) leverage effect during financial turmoil and the fact that the exposure of hedge fund strategies to risk factors is quite different from each other. Finally, although remaining important, procyclicality seems to have declined through time in the hedge fund industry, which suggests that a learning process is at play.
Synergy of subgroup J avian leukosis virus and Eimeria tenella to increase pathogenesis in specific pathogen free chickens.
Venue: Veterinary immunology and immunopathology

To investigate the effects of co infections of subgroup J avian leukosis virus (ALV J) and Eimeria tenella on the pathogenesis in specific pathogen free (SPF) white leghorn chickens, groups of chickens were infected with ALV J strain NX0101 at one day of age or with E. tenella at 14 days of age or both. The control group was left uninfected and was mock inoculated with phosphate buffer saline (PBS) Mortality rates, body weights, cecal lesions, and viremia of infected chickens in each group were evaluated. Immune status was evaluated by measuring several parameters: immune organ weight/body weight index, specific humoral responses to inactivated NDV vaccine and to inoculated E. tenella, proportions of blood CD3+CD4+ and CD3+CD8a+ lymphocytes and transcriptional levels of cytokines in blood and cecal tonsils. The results show that co infections of ALV J and E. tenella induced a higher mortality rate and a lower body weight in SPF chickens compared to single pathogen infection. In co infected chickens, ALV J accelerated the disease symptoms induced by E. tenella, and the E. tenella extended the ALV J viremia. Thymus atrophy, decrease in the humoral response levels to pathogens and the NDV vaccine, modifications in the blood lymphocyte sub populations and transcriptional cytokine disorders were found in co infected chickens compared to chickens infected with one pathogen alone and to controls. We underline a synergy between ALV J and E. tenella that results in increasing pathogenesis in SPF chickens.
Rescue of avian leukosis subgroup J associated acutely transforming viruses carrying different lengths of the v fps oncogene and analysis of their tumorigenicity
Venue: Archives of Virology

In our previous study, six subgroup J strains of avian leukosis virus (ALV J) associated acutely transforming viruses carrying different lengths of the v fps oncogene, designated as Fu J and Fu J1 5, were isolated and characterized from fibrosarcomas in ALV J infected chickens. In the present study, the oncogenic potential of Fu J and Fu J1 5 was investigated using a reverse genetics technique. Six replication defective viruses, named rFu J and rFu J1 5, were rescued with the replication competent rescued ALV J strain rSDAU1005 as a helper virus by co transfection of chicken embryo fibroblast monolayers with infectious clone plasmids. Experimental bird studies were performed, demonstrating that only the rescued rFu J virus carrying the complete v fps oncogene with rSDAU1005 as the helper virus could induce acute fibrosarcoma after inoculation in specific pathogen free (SPF) chickens. These results provide direct evidence that the replication defective acutely transforming Fu J virus, with the complete v fps oncogene, was associated with acute fibrosarcoma in chickens infected with ALV J in the field, as reported previously.
Anticoagulant therapy for symptomatic calf deep vein thrombosis (CACTUS) a randomised, double blind, placebo controlled trial.
Venue: The Lancet. Haematology

The efficacy and safety of anticoagulant treatment is not established for patients with acute symptomatic deep vein thrombosis (DVT) of the calf. We aimed to assess whether therapeutic anticoagulation is superior to placebo in patients with symptomatic calf DVT.  In this randomised, double blind, placebo controlled trial, we enrolled low risk outpatients (without active cancer or previous venous thromboembolic disease) with a first acute symptomatic DVT in the calf from 23 university medical centres or community medical clinics in Canada, France, and Switzerland. We randomly assigned (1:1) patients to receive either the low molecular weight heparin nadroparin (171 UI/kg, subcutaneously, once a day) or placebo (saline 0*9% subcutaneously, once a day) for 6 weeks (42 days) Central randomisation was done using a computer generated randomisation list, stratified by study centre. Random allocation sequences of variable block size were centrally determined by an independent research clinical centre. Study staff, patients, and outcome assessors (central adjudication committee) were masked to group assignment. Numbered boxes of active drug or placebo were provided to pharmacies in identical packaging. All patients were prescribed compression stockings and followed up for 90 days. The primary efficacy outcome was a composite measure of extension of calf DVT to proximal veins, contralateral proximal DVT, and symptomatic pulmonary embolism at day 42 in the modified intention to treat population. The primary safety outcome was major or clinically relevant non major bleeding at day 42.   Between Feb 1, 2008, and Nov 30, 2014, we screened 746 patients, enrolling 259 patients (50% of the prespecified sample size) before the trial steering committee terminated the trial because of expiry of study drug and slow recruitment. The intention to treat analysis population comprised 122 patients in the nadroparin group and 130 in the placebo group. There was no significant difference between the groups in the composite primary outcome, which occurred in four patients (3% in the nadroparin group and in seven (5% in the placebo group (risk difference 2*1% 95% CI 7*8 to 3*5; p=0*54) Bleeding occurred in five patients (4% in the nadroparin group and no patients in the placebo group (risk difference 4*1, 95% CI 0*4 to 9*2; p=0*0255) In the nadroparin group one patient died from metastatic pancreatic cancer and one patient was diagnosed with heparin induced thrombocytopenia type 2.  Nadroparin was not superior to placebo in reducing the risk of proximal extension or venous thromboembolic events in low risk outpatients with symptomatic calf DVT, but did increase the risk of bleeding. Avoidance of systematic anticoagulation for calf DVT could have a substantial impact on individual patients and from a public health perspective.
The discourse of language learning strategies: towards an inclusive approach

This paper critiques discourse surrounding language learning strategies within Teaching English to Speakers of Other Languages (TESOL) and argues for the creation of new definitions of language learning strategies that are rooted in the socio political and socio economic contexts of the marginalized. Section one of this paper describes linguistic imperialism theory and post colonial education's responses to allegations therein: multicultural education theory, critical race theory, and technological egalitarianism. This section also highlights the difference between formal and informal learning in order to validate multiple learning strategies. Section two of this paper then analyses two prominent works by Oxford [2002. Language learning strategies around the world: Cross cultural perspectives. Honolulu: Second Language Teaching Curriculum Center, University of Hawai'i at Manoa. 2013.  What every teacher should know.  Heinle Cengage Learning] This section suggests that even though Oxford [2002. Language learning strategies around the world: Cross cultural perspectives. Honolulu: Second Language Teaching Curriculum Center, University of Hawai'i at Manoa] made attempts to incorporate diverse voices into language learning strategy theory, her efforts in turn potentiate those who already have access to education. Finally, the concluding section postulates five principles for including marginalized voices in the discourse of language learning strategies in order to propose contextualized definitions: (1) incorporate non extractive research among the marginalized, (2) document local knowledges and practices in marginalized communities, (3) confront one's own identity of privilege before, during, and after research, (4) allow those on the margins to define learning strategies, and (5) develop diversity within TESOL.
An unsupervised approach for overlapping cervical cell cytoplasm segmentation
Venue: 2016 IEEE EMBS Conference on Biomedical Engineering and Sciences (IECBES)

The poor contrast and the overlapping of cervical cell cytoplasm are the major issues in the accurate segmentation of cervical cell cytoplasm. This paper presents an automated unsupervised cytoplasm segmentation approach which can effectively find the cytoplasm boundaries in overlapping cells. The proposed approach first segments the cell clumps from the cervical smear image and detects the nuclei in each cell clump. A modified Otsu method with prior class probability is proposed for accurate segmentation of nuclei from the cell clumps. Using distance regularized level set evolution, the contour around each nucleus is evolved until it reaches the cytoplasm boundaries. Promising results were obtained by experimenting on ISBI 2015 challenge dataset.
Generalization of orientational motion in unit quaternion space
Venue: 2016 IEEE RAS 16th International Conference on Humanoid Robots (Humanoids)

A requirement for the humanoid robot's operation in natural environments is that a humanoid robot can effectively adapt to new configurations of the external world. In this paper we address the problem of adaptation, where new robot movements are generated based on data accumulated in related but different situations. Our solution to this challenge is to apply statistical learning, which provides a method to generate robot responses in new situations. Building on our previous work on learning motor primitives  we propose a new methodology for task specific generalization of orientation trajectories, which we encode as Cartesian space Dynamic Movement Primitives. Example trajectories are generalized by applying Locally Weighted Regression in unit quaternion space, using the parameters describing the task as query points into the trajectory database. We show on real world and simulated tasks that the proposed methodology can be used for statistical learning of orientation trajectories.
Dynamic movement primitives in latent space of time dependent variational autoencoders
Venue: 2016 IEEE RAS 16th International Conference on Humanoid Robots (Humanoids)

Dynamic movement primitives (DMPs) are powerful for the generalization of movements from demonstration. However, high dimensional movements, as they are found in robotics, make finding efficient DMP representations difficult. Typically, they are either used in configuration or Cartesian space, but both approaches do not generalize well. Additionally, limiting DMPs to single demonstrations restricts their generalization capabilities. In this paper, we explore a method that embeds DMPs into the latent space of a time dependent variational autoencoder framework. Our method enables the representation of high dimensional movements in a low dimensional latent space. Experimental results show that our framework has excellent generalization in the latent space, e.g. switching between movements or changing goals. Also, it generates optimal movements when reproducing the movements.
Enhancing Initiation Efficiency in Metal Free Surface Initiated Atom Transfer Radical Polymerization (SI ATRP)

Well defined polymer inorganic hybrid materials were prepared via metal free surface initiated atom transfer radical polymerization (SI ATRP) with 10 phenylphenothiazine (PhPTZ) as the photocatalyst and 2 bromo 2 phenylacetate initiator tethered to silica surfaces. Initiation efficiency and, hence, graft density were significantly enhanced by this very reactive initiator. The polymerization kinetics, effect of initiator structures, particle sizes, and catalyst concentrations were investigated. Well defined hybrid particles were prepared at a low catalyst concentration (0.02 mol or 0.1 mol to monomer) Poly(methyl methacrylate) (PMMA) with number average molecular weight of 3.65 x 104, dispersity of 1.43, and graft density of 0.60 chain/nm2 was grafted from the surface of silica nanoparticles. The hybrid materials were characterized with size exclusion chromatography (SEC) thermogravimetric analysis (TGA) dynamic light scattering (DLS) and transmission electron microscopy (TEM)
Modification of cellulose nanocrystal via SI ATRP of styrene and the mechanism of its reinforcement of polymethylmethacrylate.
Venue: Carbohydrate polymers

Cellulose nanocrystal (CNC) is a promising strengthener but is used limitedly since its poor compatibility with organic materials. The graft polymerization of styrene via surface initiated atom transfer radical polymerization (SI ATRP) of cellulose nanocrystal is adopted to modify its thermo stability and compatibility. The modified crystals have been dosed into polymethylmethacrylate (PMMA) nanocomposites by the solution casting. The polymeric layer on the surface of CNCs should improve the thermal stability of CNCs, and provide significant dispersibility and compatibilization for the nanocomposites. Thermogravimetry analysis proved that the initial degrade temperature of CNC was increased 50 degC with the modification. The scanning electronic microscope showed that the modified CNCs homogeneously dispersed in PMMA matrix. Breaking strength and elongation at break of the composites were improved, which was attributed to the reinforcement of CNCs modified with styrene. Transmittance of nanocomposite films measurement showed that the transmittance of PMMA/1%CNC was almost close to that of pure PMMA.
Living CO2 Switchable Latexes Prepared via Emulsion ATRP and AGET Miniemulsion ATRP

Living CO2 switchable poly(methyl methacrylate) (PMMA) latexes were prepared using reverse ATRP emulsion polymerization and AGET ATRP miniemulsion polymerization. The prepared latexes can be switched between the aggregated and dispersed states using only CO2 and any nonacidic gas (e.g. argon, air, nitrogen) as triggers. AGET ATRP miniemulsion polymerizations were enabled by the design and synthesis of a CO2 switchable ATRP inisurf, 1,1 (diethylamino)undecyl 2 bromo 2 methylpropanoate (BrC11N) which can generate stable emulsions under CO2 without requiring the addition of other emulsifiers. The resulting PMMA has controlled molecular weight and low dispersity.
Fruit and vegetable consumption in Vietnam, and the use of a 'standard serving' size to measure intake
Venue: British Journal of Nutrition

The aims of the present study were to provide nationally representative data on fruit and vegetable consumption in Vietnam, and to assess the accuracy of the reported numbers of 'standard servings' consumed. Data analysed were from a multi stage stratified cluster survey of 14 706 participants (46*5 males, response proportion 64*1 aged 25 64 years in Vietnam. Measurements were made in accordance with the WHO STEPwise approach to surveillance of non communicable diseases (STEPS) protocols. Approximately 80 of Vietnamese people reported having less than five servings of fruit and vegetables daily in a typical week. Fruit and vegetable intake reported in 'standard serving' sizes was positively correlated with levels of education completed and household income (P<0*001 for trend) The correlations between summary values for each province reflect some known demographic, geographical and climatic characteristics of the country. For example, provinces at higher latitude had higher mean servings of vegetables (r 0*90) and provinces with higher proportions of urban population had higher mean servings of fruit (r 0*40) In conclusion, about eight in ten Vietnamese people aged 25 64 years did not meet WHO recommendations for daily consumption of at least five servings of fruit and vegetables. On the basis of the consistency of the data collected with other estimates and with physical and demographic characteristics of the country, the WHO STEPS instrument has construct validity for measuring fruit and vegetable intake, but with two issues identified. The issues were seasonal variation in reporting and a limitation on the usefulness of the information for associative analyses.