Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of protection from light-induced retinal degeneration by the synthetic antioxidant phenyl-N-tert-butylnitrone.

PURPOSE A prior study demonstrated that pretreatment with phenyl-N-tert-butylnitrone (PBN), a synthetic antioxidant and free radical trapping agent, protects rats from light-induced photoreceptor cell death. The objective of the present study was to elucidate the molecular mechanism of PBN neuroprotection. METHODS Sprague-Dawley rats (5-6 weeks old) raised in dim (5 lux) cyclic light (12 hours ON/OFF) from birth were injected intraperitoneally with PBN or water 30 minutes before exposure to three columns of fluorescent light (approximately 2700 lux intensity) for 0, 3, 6, 12, or 24 hours. mRNA levels were measured by RNase protection assay and DNA fragmentation by TUNEL assay. Activator protein (AP)-1 complex was determined by electrophoretic mobility shift assay. Immunocytochemistry and Western blots were used to measure changes in c-fos levels. RESULTS Typical apoptotic features (TUNEL staining and DNA laddering) were seen in rat retinas after 24 hours of continuous exposure to light, but not in PBN-injected rats. FasL, Bax, and caspase-3 were upregulated in a time-dependent manner. PBN treatment markedly inhibited caspase-3 gene expression, but neither PBN nor bright light exposure had any effect on caspase-3 activity. AP-1 activation by exposure to light was inhibited by PBN. Western blot analysis showed that the c-fos protein level increased in the nuclear fraction after a 6-hour exposure to light, but was decreased in PBN-treated rats. CONCLUSIONS Inhibition of c-fos activation by PBN may be the key event in protection. The involvement of oxygen free radicals has been suggested in c-fos activation and the action of PBN could be through its antioxidant activity.
BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Exopolysaccharide biosynthesis and biodegradation by a marine hydrothermal Alteromonas sp . strain

Alteromonas macleodii subsp. fijiensis biovar deepsane is a deep-sea ecotype exopolysaccharide-producing bacteria isolated from the polychaete annelid Alvinella pompejana. The high molecular weight biopolymer HYD657 produced by this strain, is the first marine exopolysaccharide (EPS) to be commercialized for cosmetic use. Depolymerization methods are necessary to elucidate the complete structure of this EPS and to generate potentially bioactive oligosaccharides. Enzymatic methods are useful for elucidating polysaccharide structure because they specifically cleave glycosidic bonds and do not require harsh chemical conditions. The HYD657 EPS is structurally complex and no commercially available enzymes are able to effectively degrade it. Here, we present the first results on the endogenous enzymatic depolymerization of a marine EPS of biotechnological interest by the producing strain. Enzymatic activity was detected in the bacterial lysate and was able to decrease the apparent molecular size of the EPS, releasing mainly oligosaccharides. The reduced form of the native polysaccharide showed a slightly modified osidic composition, particularly in terms of molar ratio. Several exoglycosidase activities were measured in the bacterial lysate using paranitrophenyl-osides.
Understanding BGP Session Failures in a Large ISP

The current global Internet routing frequently suffers from cascading routing changes and slow routing convergence. Such instability can significantly affect the performance of real-time Internet applications such as VoIP, multimedia conferencing and online gaming. One major cause of routing instability is the failure of BGP peering sessions, but there has been little understanding of the factors that contribute to the failures of operational BGP sessions. In this paper, we present a systematic study on the failures of a few hundred BGP sessions using data collected in a tier-1 ISP network over a 9-month period. We first quantify the impact of the session failures on both the control plane and the data plane. We then use syslog events to identify the direct triggers of session failures. Furthermore, we use several heuristics, including link failure information, session down time and traffic level, to identify the root problems that led to these session failures. We found that the major root causes are administrative session resets and link failures, each contributing to 46.1% and 30.4% of the observed session failures.
Effects of the black tea polyphenol theaflavin-2 on apoptotic and inflammatory pathways in vitro and in vivo.

SCOPE Theaflavin-2 (TF-2), a major component of black tea extract, induces apoptosis of human colon cancer cells and suppresses serum-induced cyclooxygenase-2 (COX-2) expression 1. Here, we explored the mechanisms for activation of apoptosis, evaluated the impact on inflammatory genes in a broader panel of cells and tested whether topical anti-inflammatory effects could be observed in vivo. METHODS AND RESULTS TF-2 triggered apoptosis in five other transformed cancer cell lines, inducing cell shrinkage, membrane blebbing, and mitochondrial clustering within 3 h of treatment. Among a set of pro-apoptotic genes, TF-2 quickly induced the up-regulation of P53 and BAX, suggesting mitochondria as the primary target. Using a cell model for inflammatory response, we showed that TF-2 suppressed the 12-O-tetradecanoylphorbol-13-acetate-induced COX-2 gene expression, and also down-regulated TNF-α, iNOS, ICAM-1, and NFκB. A reporter gene assay showed that TF-2 down-regulated COX-2 at the transcriptional level. We also demonstrated that TF-2 exhibited anti-inflammatory activity in two mouse models of inflammation. Topical application with TF-2 significantly reduced ear edema and produced a pattern of gene down-regulation similar to that observed in the cell model. CONCLUSION These results suggest that the anti-inflammatory and pro-apoptotic activity of TF-2 may be exploited therapeutically in cancer and other diseases associated with inflammation.
Capturing Consumer Preference in System Requirements Through Business Strategy

A core concern within Business-IT alignment is coordinating strategic initiatives and plans with Information Systems IS. Substantial work has been done on linking strategy to requirements for IS development, but it has usually been focused on the core value exchanges offered by the business, and thus overlooking other aspects that influence the implementation of strategy. One of these, consumer preferences, has been proven to influence the successful provisioning of the business's customer value proposition, and this study aims to establish a conceptual link between both strategy and consumer preferences to system requirements. The core contention is that reflecting consumer preferences through business strategy in system requirements allows for the development of aligned systems, and therefore systems that better support a consumer orientation. The contribution of this paper is an approach to establish such alignment, with this being accomplished through the proposal of a consumer preference meta-model mapped to a business strategy meta-model further linked to a system requirements technique. The validity of this proposal is demonstrated through a case study carried out within an institution of higher education in Sweden.
Improvement of color quality with modified linear multi-scale retinex

With popular of Digital Still Camera-DSC, higher image quality is required. One of the subjects is that image quality at shadow area caused by the narrow dynamic range of the CCD devices is improved automatically. Conventionally, gamma transformation, histogram equalization, and etc. have been utilized for this improvement, but these are not always enough improvement. Recently, examinations applying to retinex theory taking into account of human eyes characteristics proposed by Land are paid attention. This algorithm renders image at shadow area clearly and effectively using spatial information between surrounding pixels arranged into two dimensions. Typical methods are Single-scale retinex(SSR) and Multi-Scale Retinex(MSR). These methods, however, does not always work on practical use in terms of color correction of the printed images with different RGB density distribution. In order to improve the issues of MSR, we propose the Modified Linear Multi-scale retinex (ML-MSR) method. A modified method consists of (a) linear computation processing and (b) synthesis both the original images and the images obtained by the linear MSR. By the simulation for the images printed by DSC, we show that ML-MSR can improve the visibility at shadow areas keeping with both the color balance and saturation, comparing with the conventional methods, such as histogram equalization and MSR proposed by Jobson. In general, a processing time of MSR remarkably increases with the size of Gaussian averaging filter to compute the weighted average. We describe about faster processing method of the ML-MSR algorithm, which has been shorten by using the thinning out of surrounding pixels and simplicity of average processing.
Data structures for mobile data

Computer systems commonly cache the values of variables to gain efficiency. In applications where the goal is to track attributes of a continuously moving or deforming physical system over time, caching relations between variables works better than caching individual values. The reason is that, as the system evolves, such relationships are more stable than the values of individual variables. Kinetic data structures (KDSs) are a novel formal framework for designing and analyzing sets of assertions to cache about the environment, so that these assertion sets are at once relatively stable and tailored to facilitate or trivialize the computation of the attribute of interest. Formally, a KDS is a mathematical proof animated through time, proving the validity of a certain computation for the attribute of interest. KDSs have rigorous associated measures of performance and their design shares many qualities with that of classical data structures. The KDS framework has led to many new and promising algorithms in applications where the efficient modeling of motion is essential. Among these are collision detection for moving rigid and deformable bodies, connectivity maintenace in ad-hoc networks, local environment tracking for mobile agents, and visibility/occlusion maintenance. This talk will survey the general ideas behind KDSs and illustrate their application to simple geometric problems that arise in virtual and physical environments.
PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

High-throughput oligonucleotide microarrays are commonly employed to investigate genetic disease, including cancer. The algorithms employed to extract genotypes and copy number variation function optimally for diploid genomes usually associated with inherited disease. However, cancer genomes are aneuploid in nature leading to systematic errors when using these techniques. We introduce a preprocessing transformation and hidden Markov model algorithm bespoke to cancer. This produces genotype classification, specification of regions of loss of heterozygosity, and absolute allelic copy number segmentation. Accurate prediction is demonstrated with a combination of independent experimental techniques. These methods are exemplified with affymetrix genome-wide SNP6.0 data from 755 cancer cell lines, enabling inference upon a number of features of biological interest. These data and the coded algorithm are freely available for download.
Corticosteroid Use for Paradoxical Reactions during Antibiotic Treatment for Mycobacterium ulcerans

Buruli or Bairnsdale Ulcer (BU) is a neglected infectious disease caused by Mycobacterium ulcerans and is characterized by necrotic cutaneous lesions. Infection is challenging to treat, and the ideal combination of surgery and antimicrobial therapy continues to evolve. M. ulcerans has been endemic to the Bellarine peninsula in Victoria, Australia, since 1998, with more than 250 cases of infection. Studies have illustrated the safety and efficacy of antimicrobial therapy [1]–[5], and our standard treatment practice has evolved over the last 15 years to comprise limited surgical debridement with combination antimicrobial therapy.
Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific community at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/.
Cold-start Problem in Collaborative Recommender Systems: Efficient Methods Based on Ask-to-rate Technique

To develop a recommender system, the collaborative filtering is the best known approach, which considers the ratings of users who have similar rating profiles or rating patterns. Consistently, it is able to compute the similarity of users when there are enough ratings expressed by users. Therefore, a major challenge of the collaborative filtering approach can be how to make recommendations for a new user, that is called cold-start user problem. To solve this problem, there have been proposed a few efficient methods based on ask-to-rate technique in which the profile of a new user is made by integrating information gained from a quick interview. This paper is a review of these proposed methods and how to use the ask-to-rate technique. Consequently, they are categorized into non-adaptive and adaptive methods. Then, each category is analyzed and their methods are compared.
Characterization of the periodic surface in agricuture by the use of polarimetric signatures

This study investigates the characteristics of periodic surface in agriculture by the use of C-band polarimetric synthetic aperture radar (PolSAR) imagery. The scattering characteristics of the periodic potato fields in different directions are highlighted using a set of polarimetric parameters. Enhanced coherent scattering is observed when the alignment direction of ridging patterns is perpendicular to radar's line of sight (LOS). There are higher copolarized backscattering coefficients and unaffected cross-polarized backscattering coefficient for the coherent scattering. The increased copolarized correlation coefficient, reduced entropy and polarimetric alpha angle indicate that the induced coherent scattering has small scattering randomness and the odd scattering is its dominant scattering mechanism.
Social Emotions in Nature and Artifact

Recent years have seen the rise of a remarkable partnership between the social and computational sciences on the phenomena of emotions. Rallying around the term Affective Computing, this research can be seen as revival of the cognitive science revolution, albeit garbed in the cloak of affect, rather than cognition. Traditional cognitive science research, to the extent it considered emotion at all, cases it as at best a heuristic but more commonly a harmful bias to cognition. More recent scholarship in the social sciences has upended this view. Increasingly, emotions are viewed as a form of information processing that serves a functional role in human cognition and social interactions. Emotions shape social motives and communicate important information to social partners. When communicating face-to-face, people can rapidly detect nonverbal affective cues, make inferences about the other party's mental state, and respond in ways that co-construct an emotional trajectory between participants. Recent advances in biometrics and artificial intelligence are allowing computer systems to engage in this nonverbal dance, on the one hand opening a wealth of possibilities for human-machine systems, and on the other, creating powerful new tools for behavioral science research. Social Emotions in Nature and Artifact reports on the state-of-the-art in both social science theory and computational methods, and illustrates how these two fields, together, can both facilitate practical computer/robotic applications and illuminate human social processes.
Solid Organ Transplantation in Patients with Inflammatory Bowel Diseases (IBD): Analysis of Transplantation Outcome and IBD Activity in a Large Single Center Cohort

Background Currently, limited data of the outcome of inflammatory bowel disease (IBD) in patients after solid organ transplantation (SOT) are available. We aimed to analyze effects of SOT on the IBD course in a large IBD patient cohort. Methods Clinical data from 1537 IBD patients were analyzed for patients who underwent SOT (n = 31) between July 2002 and May 2014. Sub-analyses included SOT outcome parameters, IBD activity before and after SOT, and efficacy of IBD treatment. Results 4.74% of patients with ulcerative colitis (UC) and 0.84% of patients with Crohn’s disease (CD) underwent SOT (p = 2.69 x 10−6, UC vs. CD). 77.4% of patients with SOT underwent liver transplantation (LTx) with tacrolimus-based immunosuppressive therapy after SOT. All LTx were due to primary sclerosing cholangitis (PSC) or PSC overlap syndromes. Six patients (19.4%) required renal transplantation and one patient (3.2%) heart transplantation. A survival rate of 83.9% after a median follow-up period of 103 months was observed. Before SOT, 65.0% of patients were in clinical remission and 5 patients received immunosuppressive therapy (16.1%). After SOT, 61.0% of patients were in remission (p = 1.00 vs. before SOT) and 29.0% required IBD-specific immunosuppressive or anti-TNF therapy (p = 0.54 vs. before SOT). 42.9% of patients with worsening of IBD after SOT were at higher risk of needing steroid therapy for increased IBD activity (p = 0.03; relative risk (RR): 10.29; 95% CI 1.26–84.06). Four patients (13.0%) needed anti-TNF therapy after SOT (response rate 75%). Conclusions SOT was more common in UC patients due to the higher prevalence of PSC-related liver cirrhosis in UC. Despite mainly tacrolimus-based immunosuppressive regimens, outcome of SOT and IBD was excellent in this cohort. In this SOT cohort, concomitant immunosuppressive therapy due to IBD was well tolerated.
Interval type-2 fuzzy image processing expert system for diagnosing brain tumors

The focus of this paper is diagnosing and differentiating Astrocytomas in MRI scans by developing an Interval Type-2 fuzzy image processing expert system. This system consists of three modules: working memory, knowledge base, and inference engine. An image processing method with four steps of preprocessing, segmentation, feature extraction and approximate reasoning is used in inference engine module to enhance the quality of MRI scans, segment them into desired regions, extract the required features, and finally diagnose and differentiate Astrocytomas. The performance of this system is evaluated using 100 MRI scans and the results show good improvement in diagnosing and differentiating Astrocytomas.
MSC Therapy Attenuates Obliterative Bronchiolitis after Murine Bone Marrow Transplant

Rationale Obliterative bronchiolitis (OB) is a significant cause of morbidity and mortality after lung transplant and hematopoietic cell transplant. Mesenchymal stromal cells (MSCs) have been shown to possess immunomodulatory properties in chronic inflammatory disease. Objective Administration of MSCs was evaluated for the ability to ameliorate OB in mice using our established allogeneic bone marrow transplant (BMT) model. Methods Mice were lethally conditioned and received allogeneic bone marrow without (BM) or with spleen cells (BMS), as a source of OB-causing T-cells. Cell therapy was started at 2 weeks post-transplant, or delayed to 4 weeks when mice developed airway injury, defined as increased airway resistance measured by pulmonary function test (PFT). BM-derived MSC or control cells [mouse pulmonary vein endothelial cells (PVECs) or lung fibroblasts (LFs)] were administered. Route of administration [intratracheally (IT) and IV] and frequency (every 1, 2 or 3 weeks) were compared. Mice were evaluated at 3 months post-BMT. Measurements and Main Results No ectopic tissue formation was identified in any mice. When compared to BMS mice receiving control cells or no cells, those receiving MSCs showed improved resistance, compliance and inspiratory capacity. Interim PFT analysis showed no difference in route of administration. Improvements in PFTs were found regardless of dose frequency; but once per week worked best even when administration began late. Mice given MSC also had decreased peribronchiolar inflammation, lower levels of hydroxyproline (collagen) and higher frequencies of macrophages staining for the alternatively activated macrophage (AAM) marker CD206. Conclusions These results warrant study of MSCs as a potential management option for OB in lung transplant and BMT recipients.