nils-herrmann/clean_scirepeval huggingface dataset:
Morphologic, Molecular, and Taxonomic Evolution of Renal Cell Carcinoma: A Conceptual Perspective With Emphasis on Updates to the 2016 World Health Organization Classification.
Venue: Archives of pathology laboratory medicine

Molecular and morphologic interrogation has driven a much needed reexamination of renal cell carcinoma (RCC) Indeed, the recently released 2016 World Health Organization classification now recognizes 12 distinct RCC subtypes, as well as several other emerging/provisional RCC entities. From a clinical perspective, accurate RCC classification may have important implications for patients and their families, including prognostic risk stratification, targeted therapeutics selection, and identification for genetic testing. In this review, we provide a conceptual framework for approaching RCC diagnosis and classification by categorizing RCCs as tumors with clear cytoplasm, papillary architecture, and eosinophilic (oncocytic) cytoplasm. The currently recognized 2016 World Health Organization classification for RCC subtypes is briefly discussed, including new diagnostic entities (clear cell papillary RCC, hereditary leiomyomatosis and RCC associated RCC, succinate dehydrogenase deficient RCC, tubulocystic RCC, and acquired cystic disease associated RCC) and areas of evolving RCC classification, such as transcription elongation factor B subunit 1 (TCEB1) mutated RCC/RCC with angioleiomyoma like stroma/RCC with leiomyomatous stroma, RCC associated with anaplastic lymphoma receptor tyrosine kinase (ALK) gene rearrangement, thyroidlike follicular RCC, and RCC in neuroblastoma survivors. For each RCC subtype, relevant clinical, molecular, gross, and microscopic findings are reviewed, and ancillary studies helpful for its differential diagnosis are presented, providing a practical approach to modern RCC classification.
Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region
Venue: Molecular ecology

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.
Proteome Profile and Quantitative Proteomic Analysis of Buffalo (Bubalusbubalis) Follicular Fluid during Follicle Development
Venue: International journal of molecular sciences

Follicular fluid (FF) accumulates in the antrum of the ovarian follicle and provides the microenvironment for oocyte development. FF plays an important role in follicle growth and oocyte maturation. The FF provides a unique window to investigate the processes occurring during buffalo follicular development. The observed low quality of buffalo oocytes may arise from the poor follicular microenvironment. Investigating proteins found in buffalo FF (BFF) should provide insight into follicular development processes and provide further understanding of intra follicular maturation and oocytes quality. Here, a proteomic based approach was used to analyze the proteome of BFF. SDS PAGE separation combined with mass spectrometry was used to generate the proteomic dataset. In total, 363 proteins were identified and classified by Gene Ontology terms. The proteins were assigned to 153 pathways, including signaling pathways. To evaluate difference in proteins expressed between BFF with different follicle size (small, <4 mm; and large, >8 mm) a quantitative proteomic analysis based on multi dimensional liquid chromatography pre fractionation tandem Orbitrap mass spectrometry identification was performed. Eleven differentially expressed proteins (six downregulated and five upregulated in large BFF) were identified and assigned to a variety of functional processes, including serine protease inhibition, oxidation protection and the complement cascade system. Three differentially expressed proteins, Vimentin, Peroxiredoxin 1 and SERPIND1, were verified by Western blotting, consistent with the quantitative proteomics results. Our datasets offers new information about proteins present in BFF and should facilitate the development of new biomarkers. These differentially expressed proteins illuminate the size dependent protein changes in follicle microenvironment.
Gut microbiota, metabolites and host immunity
Venue: Nature Reviews Immunology

The microbiota the collection of microorganisms that live within and on all mammals provides crucial signals for the development and function of the immune system. Increased availability of technologies that profile microbial communities is facilitating the entry of many immunologists into the evolving field of host microbiota studies. The microbial communities, their metabolites and components are not only necessary for immune homeostasis, they also influence the susceptibility of the host to many immune mediated diseases and disorders. In this Review, we discuss technological and computational approaches for investigating the microbiome, as well as recent advances in our understanding of host immunity and microbial mutualism with a focus on specific microbial metabolites, bacterial components and the immune system.
Preventie van seksueel grensoverschrijdend gedrag in de sport

Recent prevalentieonderzoek bij een steekproef van 4000 Nederlandse en Vlaamse volwassenen toont aan dat 1 op de 7 volwassenen die in kindertijd of jeugd sportten, op z'n minst eenmalig seksueel grensoverschrijdend gedrag ervaart in de sport. Sinds 2012 maakt de Vlaamse sportwereld werk van de preventie van seksueel grensoverschrijdend gedrag in de sport. Het huidige artikel beschrijft een stand van zaken van het preventiebeleid en licht een veelbelovend instrument 'Sport met grenzen' toe. De auteurs doen tevens een oproep aan de sportarts om een actieve rol op te nemen bij het ontwikkelen, installeren en uitdragen van een preventief en curatief beleid in de sportvereniging. Trefwoorden: sexual violence, abuse, harassment, prevention, policy, child protection, organized sport
Gender Differences in Platelet Reactivity in Patients Receiving Dual Antiplatelet Therapy
Venue: Cardiovascular Drugs and Therapy

BackgroundCardiovascular risk is still underestimated in women, experiencing higher mortality and worse prognosis after acute cardiovascular events. Gender differences have been reported in thrombotic and hemorrhagic risk during dual antiplatelet therapy (DAPT) thus suggesting a potential variability in platelet reactivity according to sex. The aim of the present study was to assess the role of gender on platelet function and the prevalence of high on treatment residual platelet reactivity (HRPR) during DAPT in patients with recent acute coronary syndrome or percutaneous coronary revascularization.MethodsPatients treated with DAPT (ASA and clopidogrel or ticagrelor) were scheduled for platelet function assessment at 30 90 days post discharge. By whole blood impedance aggregometry, HRPR was considered for ASPI test >862 AU*min (for ASA) and ADP test values =417 AU*min (for ADP antagonists).ResultsWe included 541 patients on DAPT, 122 (22.6 of whom were females. Females were older (p 0.001) displayed more frequently hypercholesterolemia (p 0.003) renal failure (p 0.04) acute presentation (p 0.001) higher cholesterol levels and platelets count (p 0.001) Inverse association was demonstrated with smoking (p 0.001) previous PCI (p 0.04) and statin use (p 0.03) creatinine and haemoglobin (p 0.001) Female gender did not influence mean platelet reactivity or the prevalence of HRPR for ASA (1.7 vs 1.4 OR[95%CI] 1.14[0.17 4.36] p 0.99, adjusted OR[95%CI] 1.54[0.20 11.6] p 0.68) or ADP antagonists (26.3 vs 22.8 OR[95%CI] 1.17[0.52 1.34] p 0.45, adjusted OR[95%CI] 1.05[0.59 1.86] p 0.87) Results did not change when considering separately the 309 patients treated with clopidogrel (34 vs 31.3 OR[95%CI] 1.13[0.62 2.07] p 0.76, adjusted OR[95%CI] 1.35[0.63 2.9] p 0.44 for females vs males) or patients (n 232) on ticagrelor (20.4 vs 11.1 OR[95%CI] 2.27[0.99 5.17] p 0.06 for females vs males) confirmed after correction for baseline differences (adjusted OR[95%CI] 1.21[0.28 2.29] p 0.68).ConclusionIn patients receiving dual antiplatelet therapy, gender does not impact on the prevalence of high on treatment residual platelet reactivity (HRPR) with the major antiplatelet agents ASA, clopidogrel or ticagrelor.
Motor learning affects car to driver handover in automated vehicles
Venue: Science Robotics

A human driver requires a period of motor adaptation to resume normal steering after taking control of an automated vehicle. Vehicles in the foreseeable future will be required to transition between autonomous driving (without human involvement) and full human control. During this transition period, the human, who has not been actively engaged in the driving process, must resume the motor control necessary to steer the car. The in car study presented here demonstrates that when human drivers are presented with a steering behavior that is different from the last time they were in control, specifically the ratio of hand wheel angle to road wheel angle (emulating a change in vehicle speed) they undergo a significant period of adaptation before they return to their previous steering behavior. However, drivers do not require an adaptation period to return to previous driving behavior after changes in steering torque. These findings have implications for the design of vehicles that transition from automated to manual driving and for understanding of human motor control in real world tasks.
Secure and Safe Automated Vehicle Platooning

Cooperative adaptive cruise control (CACC) or platooning recently becomes promising as vehicles can learn of nearby vehicles' intentions and dynamics through wireless vehicle to vehicle (V2V) communication and advanced on board sensing technologies. The complexity of automated vehicle platoon system opens doors to various malicious cyber attacks. Violation of cybersecurity often results in serious safety issues as been demonstrated in recent studies. However, safety and security in a vehicle platoon so far have been considered separately by different sets of experts. Consequently no existing solution solves both safety and security in a coherent way. In this article, we show cyber attacks on an automated platoon system could have the most severe level of safety impact with large scale car crash and argue the importance of safety security co design for safety critical cyber physical systems (CPS) Based on a deep comprehension on the interrelation of safety and security, we present a safety security co design engineering process to derive functional security requirements for a safe automated vehicle platoon system. Finally we offer a vision of the future research issues on this important area of automated and connected vehicles.
Redox proteomics: Methods for the identification and enrichment of redox modified proteins and their applications
Venue: Proteomics

PTMs are defined as covalent additions to functional groups of amino acid residues in proteins like phosphorylation, glycosylation, S nitrosylation, acetylation, methylation, lipidation, SUMOylation as well as oxidation. Oxidation of proteins has been characterized as a double edged sword. While oxidative modifications, in particular of cysteine residues, are widely involved in the regulation of cellular homeostasis, oxidative stress resulting in the oxidation of biomolecules along with the disruption of their biological functions can be associated with the development of diseases, such as cancer, diabetes, and neurodegenerative diseases, respectively. This is also the case for advanced glycation end products, which result from chemical reactions of keto compounds such as oxidized sugars with proteins. The role of oxidative modifications under physiological and pathophysiological conditions remains largely unknown. Recently, novel technologies have been established that allow the enrichment, identification, and characterization of specific oxidative PTMs (oxPTMs) This is essential to develop strategies to prevent and treat diseases that are associated with oxidative stress. Therefore this review will focus on (i) the methods and technologies, which are currently applied for the detection, identification, and quantification of oxPTMs including the design of high throughput approaches and (ii) the analyses of oxPTMs related to physiological and pathological conditions.
Extraction, Enrichment, Solubilization, and Digestion Techniques for Membrane Proteomics.
Venue: Journal of proteome research

The importance of membrane proteins in biological systems is indisputable; however, their amphipathic nature makes them difficult to analyze. In this study, the most popular techniques for extraction, enrichment, solubilization, and digestion are compared, resulting in an overall improved workflow for the insoluble portion of Saccharomyces cerevisiae cell lysate. Yeast cells were successfully lysed using a French press pressure cell at 20 000 psi, and resulting proteins were fractionated prior to digestion to reduce sample complexity. The proteins were best solubilized with the addition of ionic detergent sodium deoxycholate (1% and through the application of high frequency sonication prior to a tryptic digestion at 37 degC. Overall, the improved membrane proteomic workflow resulted in a 26% increase in membrane protein identifications for baker's yeast. In addition, more membrane protein identifications were unique to the improved protocol. When comparing membrane proteins that were identified in the improved protocol and the standard operating procedure (176 proteins) 93% of these proteins were present in greater abundance (higher intensity) when using the improved method.
Weakly Supervised Localization Using Deep Feature Maps
Venue: ECCV

Object localization is an important computer vision problem with a variety of applications. The lack of large scale object level annotations and the relative abundance of image level labels makes a compelling case for weak supervision in the object localization task. Deep Convolutional Neural Networks are a class of state of the art methods for the related problem of object recognition. In this paper, we describe a novel object localization algorithm which uses classification networks trained on only image labels. This weakly supervised method leverages local spatial and semantic patterns captured in the convolutional layers of classification networks. We propose an efficient beam search based approach to detect and localize multiple objects in images. The proposed method significantly outperforms the state of the art in standard object localization data sets.
ProNet: Learning to Propose Object Specific Boxes for Cascaded Neural Networks
Venue: 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)

This paper aims to classify and locate objects accurately and efficiently, without using bounding box annotations. It is challenging as objects in the wild could appear at arbitrary locations and in different scales. In this paper, we propose a novel classification architecture ProNet based on convolutional neural networks. It uses computationally efficient neural networks to propose image regions that are likely to contain objects, and applies more powerful but slower networks on the proposed regions. The basic building block is a multi scale fully convolutional network which assigns object confidence scores to boxes at different locations and scales. We show that such networks can be trained effectively using image level annotations, and can be connected into cascades or trees for efficient object classification. ProNet outperforms previous state of the art significantly on PASCAL VOC 2012 and MS COCO datasets for object classification and point based localization.
Image Quality Assessment Scheme Based on Structural Contrast Index and Gradient Similarity

Image quality assessment (Anmin et al. in Image Proc,  2012  is very important for image processing. A good image evaluation algorithm is consistent with subjective evaluations and has low computational complexity. A lot of image quality assessment methods have been proposed in recent years. Structural Contrast Index (SCI) has been proved can effectively reflect the complexity of image texture and model the masking effect of human visual system (HVS) so SCI is used as an important feature. HVS is very sensitive to edge region, however, SCI can't correctly model the edge region structure. So the gradient similarity was incorporated into our method. An image quality assessment scheme based on structural contrast index and gradient similarity was proposed in our paper. Extensive experiments conducted on TID2013 image database demonstrate the performance this scheme is slightly better than the state of art methods not only on prediction accuracy but computational complexity.
Ni(II) decorated nano silicoaluminophosphate molecular sieves modified carbon paste electrode as an electrocatalyst for electrooxidation of methanol
Venue: Bulletin of Materials Science

In this work, we reported a method for the synthesis of nanosized silicoaluminophosphate (SAPO) molecular sieves that are important members of zeolites family. The synthesized SAPO was characterized using X ray diffraction (XRD) field emission scanning electron microscopy (FESEM) as well as infrared (IR) techniques. Then, the modified carbon paste electrode was prepared by nano SAPO molecular sieves and nickel (II) ion incorporated at this electrode. The electrochemical behaviour of the modified electrode (Ni SAPO/CPE) towards the oxidation of methanol was investigated by cyclic voltammetry and chronoamperometry methods. It has been found that the oxidation current is extremely increased by using Ni SAPO/CPE compared to the unmodified Ni CPE, it seems that Ni2+ inclusion into nano SAPO channels provides the active sites for catalysis of methanol oxidation. The effect of some parameters such as scan rate of potential, concentration of methanol, amount of SAPO was investigated on the oxidation of methanol at the surface of modified electrode. The values of electron transfer coefficient, charge transfer rate constant and electrode surface coverage for the Ni(II)/Ni(III) couple in the surface of Ni SAPO/CPE were found to be 0.555, 0.022 s 1 and 5.995 x 10 6 mol cm 2, respectively. Also, the diffusion coefficient and the mean value of catalytic rate constant for methanol and redox sites of modified electrode were obtained to be 1.16 x 10 5 cm2 s 1 and 4.62 x 104 cm3 mol 1 s 1, respectively. The good catalytic activity, high sensitivity, good selectivity and stability and easy in preparation rendered the Ni SAPO/CPE to be a capable electrode for electrocatalytic oxidation of methanol.
The Effect of Market Size on Fuel Saving Technology Adoption in Passenger Vehicles

Although economic theory suggests that market size and fuel costs affect fuel saving technology adoption by vehicle manufacturers, there is very little empirical evidence. We document a strong connection between market size, as measured by a vehicle's sales, and technology adoption. Using a demographics driven demand shifter to instrument for market size, we find that a 10 percent increase in market size raises power train efficiency by 0.2 percent, compared with a mean improvement rate of 1.4 percent per year between 1997 and 2013. Higher fuel prices affect technology adoption directly by influencing willingness to pay for fuel cost savings, and indirectly by influencing market size. The results have two implications: policies promoting alternative fuel vehicles will be less effective than previously thought; and fuel taxes have different effects ontechnology adoption than do fuel economy standards and feebates.
Construction of a neonatal cortical surface atlas using multimodal surface matching
Venue: 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)

In this paper we propose a method for constructing a spatiotemporal cortical surface atlas of neonatal brains aged between 38 and 42 weeks of gestation at the time of scan. The method is based on a spherical registration approach: multimodal surface matching (MSM) registration, where cortical folding patterns were used to drive alignment. Cortical surfaces from 44 subjects were projected onto spheres and grouped into 5 weeks, with all surfaces within each group co registered using pairwise MSM registration in order to avoid bias in the atlas towards any of the subjects. Finally, warps were projected to the anatomical surfaces to allow averaging of white matter surfaces, and folding metrics, in the template space. Our approach improves the sharpness of the templates from what can be achieved using affine alignment alone.