nils-herrmann/clean_scirepeval huggingface dataset:
Nuclear Receptor CAR Represses TNFα-Induced Cell Death by Interacting with the Anti-Apoptotic GADD45B

Phenobarbital (PB) is the most well-known among numerous non-genotoxic carcinogens that cause the development of hepatocellular carcinoma (HCC). PB activates nuclear xenobiotic receptor Constitutive Active/Androstane Receptor (CAR; NR1I3) and this activation is shown to determine PB promotion of HCC in mice. The molecular mechanism of CAR-mediated tumor promotion, however, remains elusive at the present time. Here we have identified Growth Arrest and DNA Damage-inducible 45beta (GADD45B) as a novel CAR target, through which CAR represses cell death.



PB activation of nuclear xenobiotic receptor CAR is found to induce the Gadd45b gene in mouse liver throughout the development of HCC as well as in liver tumors. Given the known function of GADD45B as a factor that represses Mitogen-activated protein Kinase Kinase 7 - c-Jun N-terminal Kinase (MKK7-JNK) pathway-mediated apoptosis, we have now demonstrated that CAR interacts with GADD45B to repress Tumor Necrosis Factor alpha ( TNFalpha)-induced JNK1 phosphorylation as well as cell death. Primary hepatocytes, prepared from Car(+/+), Car(-/-), Gadd45b(+/+) and Gadd45b(-/-) mice, were treated with TNFalpha and Actinomycin D to induce phosphorylation of JNK1 and cell death. Co-treatment with the CAR activating ligand TCPOBOP (1,4 bis[2-(3,5-dichloropyridyloxy)]benzene) has resulted in repression of both phosphorylation and cell death in the primary hepatocytes from Car(+/+) but not Car(-/-) mice. Repression by TCPOBOP was not observed in those prepared from Gadd45b(-/-) mice. In vitro protein-protein interaction and phosphorylation assays have revealed that CAR interacts with MKK7 and represses the MKK7-mediated phosphorylation of JNK1.



CAR can form a protein complex with GADD45B, through which CAR represses MKK7-mediated phosphorylation of JNK1. In addition to activating the Gadd45b gene, CAR may repress death of mouse primary hepatocytes by forming a GADD45B complex and repressing MKK7-mediated phosphorylation of JNK1. The present finding that CAR can repress cell death via its interaction with GADD45B provides an insight for further investigations into the CAR-regulated molecular mechanism by which PB promotes development of HCC.
Negotiate, reciprocate, or cooperate? The impact of exchange modes on inter-employee knowledge sharing

Alexander Serenko is a Professor at Faculty of Business Administration, Lakehead University, Thunder Bay, Canada. Nick Bontis is an Associate Professor at DeGroote School of Business, McMaster University, Hamilton, Canada.  The purpose of this paper is to investigate the impact of exchange modes – negotiated, reciprocal, generalized, and productive – on inter-employee knowledge sharing.  Based on the affect theory of social exchange, a theoretical model was developed and empirically tested using a survey of 691 employees from 15 North American credit unions.  The negotiated mode of knowledge exchange, i.e. when a knowledge contributor explicitly establishes reciprocation conditions with a recipient, develops negative knowledge sharing attitude. The reciprocal mode, i.e. when a knowledge donor assumes that a receiver will reciprocate, has no effect on knowledge sharing attitude. The generalized exchange form, i.e. when a knowledge contributor believes that other organizational members may reciprocate, is weakly related to knowledge sharing attitude. The productive exchange mode, i.e. when a knowledge provider assumes he or she is a responsible citizen within a cooperative enterprise, strongly facilitates the development of knowledge sharing attitude, which, in turn, leads to knowledge sharing intentions.  To facilitate inter-employee knowledge sharing, managers should focus on the development of positive knowledge sharing culture when all employees believe they contribute to a common good instead of expecting reciprocal benefits.  This is one of the first studies to apply the affect theory of social exchange to study knowledge sharing.
Role of statistical symmetries in sensory coding: an optimal scale invariant code for vision

The visual system is the most studied sensory pathway, which is partly because visual stimuli have rather intuitive properties. There are reasons to think that the underlying principle ruling coding, however, is the same for vision and any other type of sensory signal, namely the code has to satisfy some notion of optimality--understood as minimum redundancy or as maximum transmitted information. Given the huge variability of natural stimuli, it would seem that attaining an optimal code is almost impossible; however, regularities and symmetries in the stimuli can be used to simplify the task: symmetries allow predicting one part of a stimulus from another, that is, they imply a structured type of redundancy. Optimal coding can only be achieved once the intrinsic symmetries of natural scenes are understood and used to the best performance of the neural encoder. In this paper, we review the concepts of optimal coding and discuss the known redundancies and symmetries that visual scenes have. We discuss in depth the only approach which implements the three of them known so far: translational invariance, scale invariance and multiscaling. Not surprisingly, the resulting code possesses features observed in real visual systems in mammals.
Principles of Object Perception

Research on human infants has begun to shed light on early-develpping processes for segmenting perceptual arrays into objects. Infants appear to perceive objects by analyzing three-dimensional surface arrangements and motions. Their perception does not accord with a general tendency to maximize figural goodness or to attend-to nonaccidental geometric relations in visual arrays. Object perception does accord with principles governing the motions of material bodies: Infants divide perceptual arrays into units that move as connected wholes, that move separately from one another, that tend to maintain their size and shape over motion, and that tend to act upon each other only on contact. These findings suggest that o general representation of object unity and boundaries is interposed between representations of surfaces and representations of obiects of familiar kinds. The processes that construct this representation may be related to processes of physical reasoning. This article is animated by two proposals about perception and perceptual development. One proposal is substantive: In situations where perception develops through experience, but without instruction or deliberate reflection , development tends to enrich perceptual abilities but not to change them fundamentally. The second proposal is methodological: In the above situations , studies of the origins and early development of perception can shed light on perception in its mature state. These proposals will arise from a discussion of the early development of one perceptual ability: the ability to organize arrays of surfaces into unitary, bounded, and persisting objects. PERCEIVING OBJECTS In recent years, my colleagues and I have been studying young infants' perception of objects in complex displays in which objects are adjacent to other objects, objects are partly hidden behind other objects, of objects move fully
Microblogging during two natural hazards events: what twitter may contribute to situational awareness

We analyze microblog posts generated during two recent, concurrent emergency events in North America via Twitter, a popular microblogging service. We focus on communications broadcast by people who were "on the ground" during the Oklahoma Grassfires of April 2009 and the Red River Floods that occurred in March and April 2009, and identify information that may contribute to enhancing situational awareness (SA). This work aims to inform next steps for extracting useful, relevant information during emergencies using information extraction (IE) techniques.
Fit-for-Purpose Method Development and Validation for Successful Biomarker Measurement

Despite major advances in modern drug discovery and development, the number of new drug approvals has not kept pace with the increased cost of their development. Increasingly, innovative uses of biomarkers are employed in an attempt to speed new drugs to market. Still, widespread adoption of biomarkers is impeded by limited experience interpreting biomarker data and an unclear regulatory climate. Key differences preclude the direct application of existing validation paradigms for drug analysis to biomarker research. Following the AAPS 2003 Biomarker Workshop (J. W. Lee, R. S. Weiner, J. M. Sailstad, et al. Method validation and measurement of biomarkers in nonclinical and clinical samples in drug development. A conference report.  2005), these and other critical issues were addressed. A practical, iterative, “fit-for-purpose” approach to biomarker method development and validation is proposed, keeping in mind the intended use of the data and the attendant regulatory requirements associated with that use. Sample analysis within this context of fit-for-purpose method development and validation are well suited for successful biomarker implementation, allowing increased use of biomarkers in drug development.
A new rail inspection method based on deep learning using laser cameras

Rail systems are one of the most important transportation methods used in today's world. The abnormalities that occur on railway tracks due to various causes result in breakdowns and accidents. For this reason, railway tracks must be periodically inspected. This study proposes a new approach for rail inspection. Today, the railway inspection process is generally performed using computer vision. But the oil and dust residues occurring on railway surfaces can be detected as an false-positive by the image processing software can lead to loss of time and additional costs in the railway maintenance process. In this study, a hardware and software architecture are presented to perform railway surface inspection using 3D laser camera and deep learning. The use of 3D laser cameras in railway inspection process provides high accuracy rates in real time. The reading rate of laser cameras to read up to 25.000 profiles per second is another important advantage provided in real time railway inspection. Consequently, a computer vision-based approach in which 3D laser cameras that could allow for contact-free and fast detection of the railway surface and lateral defects such as fracture, scouring and wear with high accuracy are used in the railway inspection process was proposed in the study.
A Haar wavelet-based perceptual similarity index for image quality assessment

In most practical situations, the compression or transmission of images and videos creates distortions that will eventually be perceived by a human observer. Vice versa, image and video restoration techniques, such as inpainting or denoising, aim to enhance the quality of experience of human viewers. Correctly assessing the similarity between an image and an undistorted reference image as subjectively experienced by a human viewer can thus lead to significant improvements in any transmission, compression, or restoration system. This paper introduces the Haar wavelet-based perceptual similarity index (HaarPSI), a novel and computationally inexpensive similarity measure for full reference image quality assessment. The HaarPSI utilizes the coefficients obtained from a Haar wavelet decomposition to assess local similarities between two images, as well as the relative importance of image areas. The consistency of the HaarPSI with the human quality of experience was validated on four large benchmark databases containing thousands of differently distorted images. On these databases, the HaarPSI achieves higher correlations with human opinion scores than state-of-the-art full reference similarity measures like the structural similarity index (SSIM), the feature similarity index (FSIM), and the visual saliency-based index (VSI). Along with the simple computational structure and the short execution time, these experimental results suggest a high applicability of the HaarPSI in real world tasks.
Large-scale brain network associated with creative insight: combined voxel-based morphometry and resting-state functional connectivity analyses

Creative insight occurs with an “Aha!” experience when solving a difficult problem. Here, we investigated large-scale networks associated with insight problem solving. We recruited 232 healthy participants aged 21–69 years old. Participants completed a magnetic resonance imaging study (MRI; structural imaging and a 10 min resting-state functional MRI) and an insight test battery (ITB) consisting of written questionnaires (matchstick arithmetic task, remote associates test, and insight problem solving task). To identify the resting-state functional connectivity (RSFC) associated with individual creative insight, we conducted an exploratory voxel-based morphometry (VBM)-constrained RSFC analysis. We identified positive correlations between ITB score and grey matter volume (GMV) in the right insula and middle cingulate cortex/precuneus, and a negative correlation between ITB score and GMV in the left cerebellum crus 1 and right supplementary motor area. We applied seed-based RSFC analysis to whole brain voxels using the seeds obtained from the VBM and identified insight-positive/negative connections, i.e. a positive/negative correlation between the ITB score and individual RSFCs between two brain regions. Insight-specific connections included motor-related regions whereas creative-common connections included a default mode network. Our results indicate that creative insight requires a coupling of multiple networks, such as the default mode, semantic and cerebral-cerebellum networks.
Security analysis of Android applications

The now ubiquitous Android platform lacks security features that are considered to be necessary given how easily an application can be uploaded on markets by third-party developers and distributed to a large set of devices. Fortunately, static analysis can help developers, markets and users improve the quality and security of applications at a reasonable cost by being automated. While most existing analyses target specific security properties, we take a step back to build better foundations for the analysis of Android applications. We describe a model and give semantics for a significant part of the system by studying what obstacles existing analyses have faced. We then adapt a classical analysis, known as points-to analysis, to applications. This leads us to design and implement a new form of context-sensitivity for Android, paving the way for further experimentation and more specific security analyses.
Green Diesel from Biomass via Fischer-Tropsch synthesis : New Insights in Gas Cleaning and Process Design

The interest in biomass is increasing in the light of the growing concern about global warming and the resulting climate change. The emission of the greenhouse gas CO2 can be reduced when 'green' biomass-derived transportation fuels are used. One of the most promising routes to produce green fuels is the combination of biomass gasification (BG) and Fischer-Tropsch (FT) synthesis, wherein biomass is gasified and after cleaning the biosyngas is used for FT synthesis to produce long-chain hydrocarbons that are converted into ‘green diesel’. To demonstrate this route, a small FT unit based on Shell technology was operated for in total 650 hours on biosyngas produced by gasification of willow. In the investigated system, tars were removed in a high-temperature tar cracker and other impurities, like NH3 and H2S were removed via wet scrubbing followed by active-carbon and ZnO filters. The experimental work and the supporting system analysis afforded important new insights on the desired gas cleaning and the optimal line-up for biomass gasification processes with a maximised conversion to FT liquids. Two approaches were considered: a front-end approach with reference to the (small) scale of existing CFB gasifiers (1-100 M Wth) and a back-end approach with reference to the desired (large) scale for FT synthesis (500-1000 MWth). In general, the sum of H2 and CO in the raw biosyngas is an important parameter, whereas the H2/CO ratio is less relevant. BTX (i.e . benzene, toluene, and xylenes) are the design guideline for the gas cleaning and with this the tar issue is de-facto solved (as tars are easier to remove than BTX). To achieve high yields of FT products the presence of a tar cracker in the system is required. Oxygen gasification allows a further increase in yield of FT products as a N2-free gas is required for off-gas recycling. The scale of the BG-FT installation determines the line-up of the gas cleaning and the integrated process. It is expected that the future of BG-FT systems will be large plants with pressurised oxygen blown gasifiers and maximised Fischer-Tropsch synthesis.
Hybrid Connectionist-Symbolic Modules: A Report from the IJCAI-95 Workshop on Connectionist-Symbolic Integration

need for such models has been growing slowly but steadily over the past five years. Some new, important approaches have been proposed and developed, some of which were presented at the workshop. In sum, the participants felt that it was definitely worthwhile to further pursue research in this area because it might generate important new ideas and significant new applications in the near future. The basic motivations for research in hybrid connectionist-symbolic models need to be articulated and made clear. These motivations can ■ The Workshop on Connectionist-Symbolic Integration: From Unified to Hybrid Approaches was held on 19 to 20 August 1995 in Montreal, Canada, in conjunction with the Fourteenth International Joint Conference on Artificial Intelligence. The focus of the workshop was on learning and architectures that feature hybrid representations and support hybrid learning. The general consensus was that hybrid connectionist-symbolic models constitute a promising avenue to the development of more robust, more powerful, and more versatile architectures for both cognitive modeling and intelligent systems.
First report of junctional epidermolysis bullosa (JEB) in the Italian draft horse

Epitheliogenesis imperfecta in horses was first recognized at the beginning of the 20th century when it was proposed that the disease could have a genetic cause and an autosomal recessive inheritance pattern. Electron microscopy studies confirmed that the lesions were characterized by a defect in the lamina propria and the disease was therefore reclassified as epidermolysis bullosa. Molecular studies targeted two mutations affecting genes involved in dermal-epidermal junction: an insertion in LAMC2 in Belgians and other draft breeds and one large deletion in LAMA3 in American Saddlebred.



A mechanobullous disease was suspected in a newborn, Italian draft horse foal, which presented with multifocal to coalescing erosions and ulceration on the distal extremities. Histological examination of skin biopsies revealed a subepidermal cleft formation and transmission electron microscopy demonstrated that the lamina densa of the basement membrane remained attached to the dermis. According to clinical, histological and ultrastructural findings, a diagnosis of junctional epidermolysis bullosa (JEB) was made. Genetic tests confirmed the presence of 1368insC in LAMC2 in the foal and its relatives.



This is the first report of JEB in Italy. The disease was characterized by typical macroscopic, histologic and ultrastructural findings. Genetic tests confirmed the presence of the 1368insC in LAMC2 in this case: further investigations are required to assess if the mutation could be present at a low frequency in the Italian draft horse population. Atypical breeding practices are responsible in this case and played a role as odds enhancer for unfavourable alleles. Identification of carriers is fundamental in order to prevent economic loss for the horse industry.
Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

"No plant is an island too…" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method - for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.
Mere Generation: Essential Barometer or Dated Concept?

The computational creativity community (rightfully) takes a dim view of supposedly creative systems that operate by mere generation. However, what exactly this means has never been adequately defined, and therefore the idea of requiring systems to exceed this standard is problematic. Here, we revisit the question of mere generation and attempt to qualitatively identify what constitutes exceeding this threshold. This exercise leads to the conclusion that the question is likely no longer relevant for the field and that a failure to recognize this is likely detrimental to its future health.