Miracle-dz/UniFAR-FTUs huggingface dataset:
Interferon α2b increases MMP-13 and IL-10 expression in Kupffer cells through MAPK signaling pathways.

BACKGROUND/AIMS Kupffer cells play critical roles in both progression and resolution of liver fibrosis. Interferon α2b is an important immunoregulator which has anti-fibrotic effect in addition to its antiviral effect. It remained unclear whether the anti-fibrotic effect of interferon α2b is mediated by regulating functions of Kupffer cells. METHODOLOGY Primary isolated Kupffer cells were cultured with interferon α2b and the expression of matrix metalloproteinase-13, interleukin-10, transforming growth factor -β1 and tumor necrosis factor-α were measured. To investigate the role of mitogen-activated protein kinase pathways in regulating cytokines production by interferon α2b-stimulated Kupffer cells, inhibitors were given before cells were treated with interferon a2b. RESULTS Cell purity was more than 98%. Stimulating Kupffer cells with interferon α2b led to a dramatic increase in matrix metalloproteinase-13 and interleukin-10 expression. In contrast, the values of tumor necrosis factor-α and transforming growth factor -β1 remained unchanged throughout the 24-hour observation period. Inhibited ERK1/2 pathway prevented interferon α2b-triggered matrix metalloproteinase-13 production, while inhibited p38MAPK, ERK1/2 or JNK signaling pathways all blocked interleukin-10 expression. CONCLUSIONS Interferon α2b may exert anti-fibrotic effect by elevating the level of matrix metalloproteinase-13 and interleukin-10 in Kupffer cells, in a mitogen-activated protein kinase signaling pathways-dependent manner.
Easier threading through web-based comparisons and cross-validations

UNLABELLED We have developed a WWW server for the integration and comparison of protein structure predictions performed by five different servers. Users submit an amino acid sequence to a selected set of these prediction methods. Results are gathered on a web-based page in order to facilitate comparison and analysis. All the alignments are further evaluated through a common threading tool making their comparisons easier. AVAILABILITY The meta-server is available free at http://www.infobiosud. cnrs.fr/bioserver SUPPLEMENTARY INFORMATION http://www.infobiosud. cnrs.fr/bioserver/hah1.html
Affective response to eye contact and face recognition ability in children with ASD

Abstract This study tested the hypothesis that affective arousal in response to eye contact is negatively associated with face identification skills in children with autism spectrum disorder (ASD). Participants were 20 children and adolescents with ASD and 20 age- and IQ-matched typically developing (TD) children. Skin conductance response (SCR), a psychophysiological measure of autonomic arousal, was collected while participants viewed faces with gaze directed toward them and faces with gaze averted away from them. Participants also completed an independent match-to-sample face recognition test. Children with ASD exhibited significantly larger SCRs than TD children to faces with direct and averted gaze. There were no differences between SCRs to direct gaze and averted gaze in either group. Children with ASD exhibited a marginally significant decrease in face recognition accuracy relative to TD children, particularly when face recognition depended on the eye region of the face. Face recognition accuracy among children with ASD was negatively correlated with the amplitude of SCRs to direct gaze but not to averted gaze. There was no association between face recognition accuracy and SCRs to gaze in the TD group. These findings suggest that autonomic reactivity to eye contact may interfere with face identity processing in some children with ASD. (JINS, 2008, 14, 947–955.)
Organic Aerosol Formation Downwind from the Deepwater Horizon Oil Spill

Organic compounds of intermediate volatility play an important role in the formation of secondary organic aerosols. A large fraction of atmospheric aerosols are derived from organic compounds with various volatilities. A National Oceanic and Atmospheric Administration (NOAA) WP-3D research aircraft made airborne measurements of the gaseous and aerosol composition of air over the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico that occurred from April to August 2010. A narrow plume of hydrocarbons was observed downwind of DWH that is attributed to the evaporation of fresh oil on the sea surface. A much wider plume with high concentrations of organic aerosol (>25 micrograms per cubic meter) was attributed to the formation of secondary organic aerosol (SOA) from unmeasured, less volatile hydrocarbons that were emitted from a wider area around DWH. These observations provide direct and compelling evidence for the importance of formation of SOA from less volatile hydrocarbons.
Hidden messages: A polysemic reading of tourist brochures

It is self-evident that tourist brochures are selling a positive and attractive destination to travellers; what is not as clear are the hidden messages conveyed by the selection of certain pictures in the brochures produced. By coding each picture appearing in a series of tourist brochures according to their content this research aims at showing how the brochures are overtly aimed at different groups of travellers, while they simultaneously are reinforcing certain hegemonic views of society. The suggestion that hegemonic messages appear is not an accusation against the producers of the brochures of covert propaganda, but rather that taken-for-granted views of society as unproblematic truths portrayed in the brochures is not correct-the brochures should rather be viewed as highly sensitive polysemic constructs.
Renewed Avenues through Exercise Muscle Contractility and Inflammatory Status

Physical inactivity leads to the accumulation of visceral fat and, consequently, to the activation of a network of inflammatory pathways which may promote development of insulin resistance, atherosclerosis, neurodegeneration, and tumour growth. These conditions belong to the “diseasome of physical inactivity”. In contrast, the protective effect of regular exercise against diseases associated with chronic inflammation may to some extent be ascribed to an anti-inflammatory effect. The so called “acute exercise threshold”, the complex mixture of several variables involved in exercise, such as type, volume, frequency, and intensity range is capable of inducing positive physiological adaptations and has been specifically addressed in the recent literature. The major concern is related to the level of the threshold: “exercise training shifts from a therapeutic adaptive intervention to one with potential pathological consequences”. Nonetheless, if the mechanical stimulus is too weak to disrupt cellular homeostasis, training adaptations will not occur. Answering these questions could present practical applications, especially during inflammatory diseases associated with detrimental muscle effects and could theoretically constitute a “new” therapeutic approach to treat/improve an inflammatory state. This paper aims to describe specific data from the literature regarding the effects of exercise on inflammatory diseases in order to promote a more sophisticated perspective on the anti-inflammatory effects of exercise.
The comparative effectiveness of sponsored and nonsponsored links for Web e-commerce queries

The predominant business model for Web search engines is sponsored search, which generates billions in yearly revenue. But are sponsored links providing online consumers with relevant choices for products and services? We address this and related issues by investigating the relevance of sponsored and nonsponsored links for e-commerce queries on the major search engines. The results show that average relevance ratings for sponsored and nonsponsored links are practically the same, although the relevance ratings for sponsored links are statistically higher. We used 108 ecommerce queries and 8,256 retrieved links for these queries from three major Web search engines: Yahoo! , Google, and MSN. In addition to relevance measures, we qualitatively analyzed the e-commerce queries, deriving five categorizations of underlying information needs. Product-specific queries are the most prevalent (48%). Title (62%) and summary (33%) are the primary basis for evaluating sponsored links with URL a distant third (2%). To gauge the effectiveness of sponsored search campaigns, we analyzed the sponsored links from various viewpoints. It appears that links from organizations with large sponsored search campaigns are more relevant than the average sponsored link. We discuss the implications for Web search engines and sponsored search as a long-term business model and as a mechanism for finding relevant information for searchers.
Prevalence and antimicrobial susceptibility of virulent and avirulent multidrug-resistant Escherichia coli isolated from diarrheic neonatal calves.

OBJECTIVE To determine the prevalence of selected virulence genes and the antimicrobial susceptibility of multidrug-resistant (MDR) Escherichia coli isolated from diarrheic neonatal calves. SAMPLE 97 E coli isolates from diarrheic neonatal calves. PROCEDURES E coli isolates were tested via PCR assay for 6 virulence genes and susceptibility to 17 drugs belonging to 9 classes. A 2-sample test of proportions was used to make comparisons between proportions of virulent and avirulent MDR isolates. RESULTS 23 of 97 (23.7%) isolates were virulent, and 74 (76.3%) were avirulent. Of the 23 virulent isolates, 15 (65.2%) were positive for K99, 14 (60.9%) for F41, 12 (52.2%) for STa, 9 (39.1%) for Stx1, 6 (26.1%) for intimin, and 0 (0%) for Stx2. Twenty of 23 (87.0%) virulent isolates expressed ≥ 2 virulence genes, and 3 of 23 (13.0%) were positive for 1 virulence factor. Eight of 23 (34.8%) virulent isolates expressed STa, K99, and F41, whereas 1 of 23 (4.4%) was positive for STa, F41, intimin, and Stx1. The second most frequent gene pattern was Stx1 and intimin. Twenty of 23 (87.0%) virulent isolates were MDR; the highest prevalence of resistance was recorded for the macrolide-lincosides, followed by the tetracyclines and penicillins. Also, 17 of 23 (74.0%) virulent isolates were resistant to sulfadimethoxine, and 10 of 23 (43.5%) were resistant to trimethoprim-sulfamethoxazole. Additionally, 60 of 74 (81.0%) avirulent isolates were MDR. CONCLUSIONS AND CLINICAL RELEVANCE The prevalence of multidrug resistance was comparable for virulent and avirulent E coli isolated from diarrheic neonatal calves. Cephalosporins and aminoglycosides had reasonable susceptibility.
Rab11 in Disease Progression

Membrane/protein trafficking in the secretory/biosynthetic and endocytic pathways is mediated by vesicles. Vesicle trafficking in eukaryotes is regulated by a class of small monomeric GTPases: the Rab protein family. Rab proteins represent the largest branch of the Ras superfamily GTPases, and have been concerned in a variety of intracellular vesicle trafficking and different intracellular signalling pathways. Rab11 (a subfamily of the Ypt/Rab gene family), an evolutionarily conserved ubiquitously expressed subfamily of Rab GTPases, has been implicated in regulating vesicular trafficking through the recycling of endosomes. Rabs have been grouped into different subfamilies based on the distinct unambiguous sequence motifs. Three members: Rab11a, Rab11b and Rab25 make up the Rab11 GTPase subfamily. In this review article, we describe an overview over Rab11 subfamily with a brief structural aspect and its roles in implicating different disease progression.
Ensembles of Region Based Classifiers

In machine learning, ensemble classifiers have been introduced for more accurate pattern classification than single classifiers. We propose a new ensemble learning method that employs a set of region based classifiers. Since the distribution of data can be different in different regions in the feature space, we split the data and generate classifiers based on each region and apply a weighted voting among the classifiers. We used 11 data sets from the UCI Machine Learning Repository to compare the performance of our new ensemble method with that of individual classifiers as well as other ensemble methods such as bagging and boosting. As a result, we found that our method improve performance, particularly when the base learner is Naive Bayes or SVM.
A Low-Voltage 13T Latch-Type Sense Amplifier with Regenerative Feedback for Ultra Speed Memory Access

Sense amplifiers provide amplification to the very small voltage change in the memory datapath in near-zero access time. The sub-micron technology demands high performance sensing at extreme noise margins. In this paper, a state of the art latch-type storage element is proposed to provide a strong positive feedback for the small change in the differential sense input. A well synchronized 4T controlling circuit has been used to speed up the latch operation by dissipating minimal sense energy. The 13T ultra speed latch-type sense amplifier has been designed using predictive 45-nm CMOS technology and simulated in SPECTRE. The results show that the proposed design dissipates 0.152 fJ with extremely low sense time of 58.6 ps at 0.6 V. The design can function up to a supply voltage scaling of 0.4 V with an average sensing delay variation of just 29%.
A MODULATION-DEMODULATION MODEL FOR SPEECH COMMUNICATION AND ITS EMERGENCE

Perceptual invariance against large acoustic variability in speech has been a long-discussed question in speech science and engineering (Perkell & Klatt, 2002), and it is still an open question (Newman, 2008; Furui, 2009). Recently, we proposed a candidate answer based on mathematically-guaranteed relational invariance (Minematsu et al., 2010; Qiao & Minematsu, 2010). Here, transform-invariant features, f -divergences, are extracted from the speech dynamics in an utterance to form an invariant topological shape which characterizes and represents the linguistic message conveyed in that utterance. In this paper, this representation is interpreted from a viewpoint of telecommunications, linguistics, and evolutionary anthropology. Speech production is often regarded as a process of modulating the baseline timbre of a speaker’s voice by manipulating the vocal organs, i.e., spectrum modulation. Then, extraction of the linguistic message from an utterance can be viewed as a process of spectrum demodulation. This modulation-demodulation model of speech communication has a strong link to known morphological and cognitive differences between humans and apes.
New Colorimetric Method for Lipases Activity Assay in Microbial Media

A simple, rapid and precise method has been developed for determination of lipase activity in microbial media. The method is based on using phenyl acetate as substrate for lipase and determination of liberated phenol by Folin Ciocalteu reagent. Reaction mixture containing substrate 2.4 ml of phenyl acetate 165 μM in Tris HCl buffer, 0.1 M and pH 7, with 1% (v/v) Triton X-100) and 0.1 ml lipase is incubated at 40? C during 10 minutes and the absorbance was measured at 750 nm. Linearity was observed in the concentration range 0-0.8 g/L lipase.
Joint routing tree construction and centralized scheduling in WiMAX mesh networks

The rapid growth of demand for high speed internet access services has ignited worldwide in standardization and deployment of broadband wireless access (BWA). WiMAX is a leading technology for wireless metropolitan area networks, which aim to provide broadband wireless access and high speed data rates. In this paper we develop a novel joint dynamic routing tree construction and centralized scheduling algorithm for WiMAX mesh networks based on feedback from network. The proposed algorithms incorporate cross layer concept between MAC and network layers. We consider both transmission overhead and spatial reuse for efficient employment of radio resources. In comparison with basic routing tree and standard scheduling, our simulation results show considerable improvement in terms of the scheduling length, average delay, and throughput of the system.
In vitro assays for evaluating the cellular responses to DNA damage induced by solar UV

Solar UV induces dimeric photolesions in the genome of human skin cells, which potentially cause cutaneous abnormalities including cancer and aging. Normal human cells possess various systems to protect their genome from the harmful DNA lesions and nucleotide excision repair plays a dominant role in removing and fixing those DNA lesions. Measuring DNA lesions induced in the cells as well as monitoring the activity of cellular repair activity are helpful for evaluating the risk suffered from solar UV. We have previously established several monoclonal antibodies specifically recognizing UV-induced DNA lesions and developed in vitro immunoassays using the antibodies. Here I show various applications of the immunoassays to evaluate the cellular responses to UV-induced DNA lesions.
Characterization of the non‐sexual flocculation of fission yeast cells that results from the deletion of ribosomal protein L32

We recently reported that deleting either of the two paralogous rpl32 genes resulted in non‐sexual flocculation in fission yeast. This study represents the first report that these non‐sexually flocculating fission yeast cells exhibit a thicker cell wall, an increased wall protein content with smeared glycosylated wall proteins, and increased cell wall polysaccharide content and adhesin‐binding sugar residues (i.e. glucose, mannose and galactose). These changes reflect the wall features of flocculating cells that mediate recognition and connections between cells. Furthermore, this study demonstrates that this non‐sexual flocculation is an adhesin‐mediated process: (a) the transcription levels of several members of the Mam3/Map4 family of adhesins (i.e. PFL3, PFL7 and PFL6) and a Flo11‐like adhesin protein are upregulated in rpl32‐1Δ and rpl32‐2Δ cells; (b) this non‐sexual flocculation of rpl32‐1Δ and rpl32‐2Δ cells was eliminated by heating or enzyme digestion; (c) this non‐sexual flocculation of rpl32‐1Δ and rpl32‐2Δ cells was enhanced by Ca2+ and some other divalent metal ions, which stabilize the active conformation of adhesins; and (d) this non‐sexual flocculation of rpl32‐1Δ and rpl32‐2Δ cells was competitively inhibited by glucose, galactose or mannose rather than only by galactose, as reported previously. Although different adhesin genes are selectively expressed under particular physiological or environmental conditions, the functions of these adhesins are the same and are interchangeable. Copyright © 2015 John Wiley & Sons, Ltd.
Using mutation to assess fault detection capability of model review

Among validation techniques, model review is a static analysis approach that can be performed at the early stages of software development, at the specification level, and aims at determining if a model owns certain quality attributes (like completeness, consistency and minimality). However, the model review capability to detect behavioural faults has never been measured. In this paper, a methodology and a supporting tool for evaluating the fault detection capability of a NuSMV model advisor are presented, which performs an automatic static model review of NuSMV models. The approach is based on the use of mutation in a similar way as in mutation testing: several mutation operators for NuSMV models are defined, and the model advisor is used to detect behavioural faults by statically analysing mutated specifications. In this way, it is possible to measure the model advisor ability to discover faults. To improve the quality of the analysis, the equivalence between a NuSMV model and any of its mutants must be checked. To perform this task, this paper proposes a technique based on the concept of equivalent Kripke structures, as NuSMV models are Kripke structures. A number of experiments assess the fault‐detecting capability, precision and accuracy of the proposed approach. Analysis of variance is used to check if the results are statistically significant. Some relationships among mutation operators and model quality attributes are also established. Copyright © 2014 John Wiley & Sons, Ltd.
Diluting the founder effect: cryptic invasions expand a marine invader's range

Most invasion histories include an estimated arrival time, followed by range expansion. Yet, such linear progression may not tell the entire story. The European green crab (Carcinus maenas) was first recorded in the US in 1817, followed by an episodic expansion of range to the north. Its population has recently exploded in the Canadian Maritimes. Although it has been suggested that this northern expansion is the result of warming sea temperatures or cold-water adaptation, Canadian populations have higher genetic diversity than southern populations, indicating that multiple introductions have occurred in the Maritimes since the 1980s. These new genetic lineages, probably from the northern end of the green crab's native range in Europe, persist in areas that were once thought to be too cold for the original southern invasion front. It is well established that ballast water can contain a wide array of nonindigenous species. Ballast discharge can also deliver genetic variation on a level comparable to that of native populations. Such gene flow not only increases the likelihood of persistence of invasive species, but it can also rapidly expand the range of long-established nonindigenous species.
The Role of Periaqueductal Gray and Cingulate Cortex During Suppression of Pain in Complex Regional Pain Syndrome

ObjectiveComplex regional pain syndrome I (CRPS I) is a frequent and debilitating condition with unclear etiology. Hypothesizing that maladaptive central processes play a crucial role in CRPS, the current study set out to explore cerebral activation during a task to suppress the feeling of pain under constant painful stimulation. MethodsTen individuals with CRPS I with symptoms on their left hand were subjected to electrical stimulation of both index fingers subsequently in a functional magnetic resonance imaging experiment. Their data were compared with 15 healthy controls. ResultsConcerning psychophysical measures, patients succeeded similarly as healthy controls in suppressing the feeling of pain. However, during constant painful stimulation and with the task to suppress the feeling of pain, there were significant differences in the interaction analyses of the corresponding cortical activation. DiscussionPatients differ from healthy controls by the activation pattern of cerebral areas that belong to the descending opioid pain suppression pathway: PAG and cingulate cortex are activated significantly less during suppression of pain, regardless of whether the symptomatic or asymptomatic hand was stimulated. Thus, there is a generalized functional change in individuals with CRPS I. However, it cannot be deducted whether the abnormality is causative or merely an effect, possibly maladaptive.
Effects of a low molecular weight superoxide dismutase mimic, 4-hydroxy-tempo on the lipid peroxidation in burned rats

The purpose of the experiment was to check the prevention from ongoing lipid peroxidation by 4-hydroxytempo (Tempol) treatment in the burned rat. The burn disease rat model was used for the estimation of Tempol ability to scavenge increased amounts of free radicals and prevent spreading of lipid peroxidation process. Four groups of male Wistar rats were used in the experiment. Saline or Tempol were administered to scalded and healthy rats. Malonyldialdehyde and 4-hydroxynonenal levels were estimated in plasma, lungs and kidneys as markers of lipid peroxidation. The total antioxidant plasma capacity was assessed with ferric reducing ability of plasma. Intraperitoneal injection of Tempol decreased the level of lipid peroxidation products in plasma and tissues in scalded animals. The results of this study suggest that membrane-permeable radical scavengers, such as Tempol, exert beneficial effects in experimental burn and may, hence, minimise tissue injury due to free radicals.