Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-genotoxic hepatocarcinogenesis in vitro: the FaO hepatoma line responds to peroxisome proliferators and retains the ability to undergo apoptosis.

A range of hepatoma cell lines (RH1, HTC, FaO, 7800C1 and MH1C1), has been studied with the aim of establishing an in vitro model to investigate the molecular mechanisms of hepatocarcinogenicity induced by the peroxisome proliferator class of non-genotoxic carcinogens. In view of speculation that peroxisome proliferators suppress hepatocyte apoptosis in vivo, we have placed particular emphasis on evaluating whether hepatoma cell lines retain the ability to undergo apoptotic cell death. Expression of the liver-specific differentiation marker albumin and the peroxisome proliferator-activated receptor (PPAR) was highest in the Reuber hepatoma cell line, FaO. This cell line also demonstrated the most marked response to the peroxisome proliferator nafenopin with a 2.2-fold induction of the microsomal enzyme cytochrome p450IVA1. This response was found to display intercellular heterogeneity by immunocytochemistry. Thus, the FaO cell line maintained characteristics of hepatocytes, both in vivo and in vitro, in terms of expression of constitutive and inducible markers. However, none of the cell lines tested mirrored the hyperplastic response of hepatocytes to nafenopin, since no increase in cell growth kinetics was observed on addition of nafenopin to the growth medium. The mode of cell death in confluent FaO cultures was characterised as apoptosis, by fluorescence microscopy and agarose gel electrophoresis of extracted DNA. Cells detaching from confluent FaO cultures exhibited chromatin condensation and DNA fragmentation patterns characteristic of cels undergoing apoptotic death.Interestingly, no apoptosis was seen in monolayer cells, suggesting that apoptosis in vitro is associated with cell shrinkage and detachment similar to that documented for the liver in vivo. (ABSTRACT TRUNCATED AT 250 WORDS)
Stability analysis and reduction of gene transcription models

The aim of this paper is to analyze the dynamical behaviour of models of gene transcription in a cell, developed in [1], which are a detailed representation of transcription process from DNA to RNA with action of polymerase. Using monotone system theory and compartmental systems theory, we study several versions of these models. We use our results of global stability of the fast part of the full system to show that, under assumptions of time scales separation, it is possible to reduce the full models to much smaller ones.
Demographic characteristics and intravenous drug use among hepatitis C patients in the Kota Setar district, Kedah, Malaysia

OBJECTIVES: This study explored the demographic characteristics of hepatitis C patients in the Kota Setar (KS) district, Kedah, Malaysia, the prevalence of intravenous drug use (IVDU) as a risk factor among these patients, and the associations between IVDU and demographic characteristics. METHODS: Retrospective data pertaining to 713 patients from January 2009 to December 2013 were retrieved from hospital and disease notification records for analysis. The risk factors for hepatitis C virus (HCV) infection were grouped into IVDU and non-IVDU risk factors for analysis using multiple logistic regression. RESULTS: Of the hepatitis C patients included in this study, the most common age group was 31 to 40 years (30.2%), and male patients (91.2%) made up the overwhelming majority. Ethnic Malays constituted approximately 80.4% of the patients, and IVDU was the main risk factor (77.8%) for HCV infection. Multiple logistic regression showed that male patients were 59 times more likely to have IVDU as a risk factor for HCV infection. Single patients were 2.5 times more likely to have IVDU as a risk factor. Patients aged ≥71 years were much less likely than patients aged ≤30 years to have IVDU as a risk factor for HCV infection. CONCLUSIONS: IVDU was found to be an important risk factor for HCV infection among patients in the KS district. The factors associated with IVDU included age, sex, and marital status. Appropriate preventive measures should be developed to target the groups in which IVDU is most likely to be a risk factor for HCV infection.
Inferring class level specifications for distributed systems

Distributed systems often contain many behaviorally similar processes, which are conveniently grouped into classes. In system modeling, it is common to specify such systems by describing the class level behavior, instead of object level behavior. While there have been techniques that mine specifications of such distributed systems from their execution traces, these methods only mine object-level specifications involving concrete process objects. This leads to specifications which are large, hard to comprehend, and sensitive to simple changes in the system (such as the number of objects). In this paper, we develop a class level specification mining framework for distributed systems. A specification that describes interaction snippets between various processes in a distributed system forms a natural and intuitive way to document their behavior. Our mining method groups together such interactions between behaviorally similar processes, and presents a mined specification involving “symbolic” Message Sequence Charts. Our experiments indicate that our mined symbolic specifications are significantly smaller than mined concrete specifications, while at the same time achieving better precision and recall.
The E. coli BtuCD Structure: A Framework for ABC Transporter Architecture and Mechanism

The ABC transporters are ubiquitous membrane proteins that couple adenosine triphosphate (ATP) hydrolysis to the translocation of diverse substrates across cell membranes. Clinically relevant examples are associated with cystic fibrosis and with multidrug resistance of pathogenic bacteria and cancer cells. Here, we report the crystal structure at 3.2 angstrom resolution of theEscherichia coli BtuCD protein, an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and appears to represent a conserved motif among the ABC transporters.
Sprouting of crossed entorhinodentate fibers after a unilateral entorhinal lesion: Anterograde tracing of fiber reorganization with Phaseolus vulgaris‐leucoagglutinin (PHAL)

Fibers from the contralateral entorhinal cortex (EC) to the dentate gyrus partially replace the input lost after an ipsilateral EC lesion. To study the morphology and course of single sprouted crossed entorhinodentate fibers, the anterograde tracer Phaseolus vulgaris‐leucoagglutinin (PHAL) was used. Rats that survived for 4 to 8 weeks after a unilateral entorhinal lesion received PHAL deposits into the entorhinal cortex contralateral to the lesion. Control animals received a similar PHAL deposit. Single PHAL‐labeled fibers in the molecular layer of the contralateral (EC lesion) fascia dentata were drawn with a camera lucida, and an axon‐branching index (branch points/100 μm axon length) was calculated for these crossed entorhinodentate fibers in controls and operated animals.
Sildenafil (Viagra) Protective Effects on Neuroinflammation: The Role of iNOS/NO System in an Inflammatory Demyelination Model

We recently demonstrated that sildenafil reduces the expression of cytokines, COX-2, and GFAP in a demyelinating model induced in wild-type (WT) mice. Herein, the understandings of the neuroprotective effect of sildenafil and the mediation of iNOS/NO system on inflammatory demyelination induced by cuprizone were investigated. The cerebella of iNOS−/− mice were examined after four weeks of treatment with cuprizone alone or combined with sildenafil. Cuprizone increased GFAP, Iba-1, TNF-α, COX-2, IL-1β, and IFN-γ expression, decreased expression of glutathione S-transferase pi (GSTpi), and damaged myelin in iNOS−/− mice. Sildenafil reduced Iba-1, IFN-γ, and IL-1β levels but had no effect on the expression of GFAP, TNF-α, and COX-2 compared to the cuprizone group. Sildenafil elevated GSTpi levels and improved the myelin structure/ultrastructure. iNOS−/− mice suffered from severe inflammation following treatment with cuprizone, while WT mice had milder inflammation, as found in the previous study. It is possible that inflammatory regulation through iNOS-feedback is absent in iNOS−/− mice, making them more susceptible to inflammation. Sildenafil has at least a partial anti-inflammatory effect through iNOS inhibition, as its effect on iNOS−/− mice was limited. Further studies are required to explain the underlying mechanism of the sildenafil effects.
Fluid flow and heat transfer in liquid cooled foam heat sinks for electronic packages

In this paper, the fluid flow and heat transfer of liquid cooled foam heat sinks (FHSs) were experimentally investigated. Eight Open-celled copper foam materials with two pore densities of 60 and 100 PPI (pores per inch) and four porosities varying from 0.6 to 0.9 were bonded onto copper base plates to form the FHSs, which were then assembled on flip chip BGA packages (FBGAs) with a common thermal grease as the thermal interface material. A liquid cooling test loop was established to obtain the pressure drops and overall thermal resistances. For the four 60 PPI FHSs, the one with the lowest porosity of 0.6 is found to possess the lowest thermal resistance level with the largest pressure drop. Generally the FHSs with 100 PPI had slightly lower thermal resistances at the same flowrates but much larger pressure drops than those with 60 PPI. In the overall performance assessment, the thermal resistances of the FHSs are plotted against the pressure drop and the pump power, together with a microchannel heat sink of similar unit cell scale and structural dimensions. The thermal resistances of the FHS with a porosity of 0.8 and pore density of 60 PPI were identified to be the lowest among all the FHSs, which outperformed the microchannel heat sink at large pressure drop and pump power. The reduced heat sink thermal resistance and Nusselt numbers for the present FHSs and microchannel heat sink are also presented and compared with the FHS reported in the literature.
Measuring social capital in creative teams through sociometric sensors

We describe the results of an experiment capturing the face-to-face ‘honest signals’ of knowledge workers through sociometric badges. We find that collective creativity of teams is a function of the aggregated social capital of members. The higher it is, the higher their creative output. We collected communication data of 14 graduate students and their instructor during a one-week seminar, comparing it against the creative output of their teamwork. As a second component of social capital we also measured the level of trust team members show to each other through surveys. We find that the more team members directly interact with each other face-to-face, and the more they trust other team members, the more creative and of higher quality the result of their teamwork is.
MULTI-VIEW 3 D CITY MODEL GENERATION WITH IMAGE SEQUENCES

Rapid texture mapping of buildings and other man-made objects is a key aspect for reconstruction of 3D city landscapes. An effective approach by the way of coarse-to-fine 3D city model generation based on digital photogrammetric theory is proposed. Three image sequences, two oblique photography to buildings’ walls and one vertical photography to building’s roof, acquired by digital video camera on a helicopter, coarse 2D vector data of buildings and LIDAR data are used as sources of information. Automatic aerial triangulation technique for high overlapping image sequences is used to give initial values of camera parameters of each image. The correspondence between the space edge of building and its line feature in image sequences is determined with a coarse-to-fine strategy. Hybrid point-line photogrammetric technique is used for accurate reconstruction of buildings. Reconstructed buildings with fine textures superimposed on DSM and orthoimage are visualized realistically.
The association between emergency department crowding and hospital performance on antibiotic timing for pneumonia and percutaneous intervention for myocardial infarction.

BACKGROUND Antibiotics within four hours of arrival for patients with pneumonia and percutaneous intervention (PCI) within two hours for patients with acute myocardial infarction (AMI) are standard measures of emergency department (ED) quality. OBJECTIVES To assess the institutional-level association between measures of ED crowding and process measures for pneumonia and AMI. METHODS The authors used summary data from 24 academic hospitals in the University Health Consortium. Analysis included the 2004 ED cycle time survey and performance data from January to December 2004 regarding the Joint Commission for Accreditation of Healthcare Organizations' PN-5b (initial antibiotic administration within four hours) for pneumonia and AMI-8a (PCI received within 120 minutes). Spearman correlation coefficients were used to determine associations between crowding and performance measures. RESULTS Across all institutions, 59% (range 43%-77%) of pneumonia patients received antibiotics within four hours, and 57% (range 22%-95%) of AMI patients received PCI within two hours. An increase in overall ED length of stay (-0.44, p = 0.04) and for admitted patients (-0.37, p = 0.08) was associated with a decrease in the proportion of pneumonia patients receiving antibiotics within four hours. An increase in chest x-ray turnaround time (-0.83, p < 0.001) and an increase in the left-without-being-seen rate (-0.51, p = 0.01) were also associated with a decrease in the proportion of pneumonia patients receiving antibiotics within four hours. No measures of crowding exhibited an association with time to PCI for AMI patients. CONCLUSIONS Administrative measures of ED crowding showed an association with poorer performance on pneumonia quality of care measures but not with AMI quality of care measures. Hospitals might consider improving ED throughput, reducing boarding times for admitted patients, and reducing chest x-ray turnaround times to improve pneumonia care.
The induction and characterization of natural porcine interferons alpha and beta.

The purpose of this study was to define optimum conditions for the production of high concentrations of natural porcine interferon (POIFN)-alpha and POIFN-beta, and to characterize the IFNs which were produced. The inducers used were Newcastle disease virus (NDV), polyinosinic:polycytidylic acid (poly IC), poly IC complexed with diethylaminoethyl dextran (poly IC-DEAEdx) and poly IC complexed with poly-L-lysine and carboxymethylcellulose. The highest yields of POIFN-alpha were obtained from porcine peripheral blood leukocyte (PBL) cultures induced with NDV. The concentrations of both cells and virus were critical for high yields of IFN, which were also enhanced by priming. Poly IC was found to be a relatively poor IFN inducer in PBL, in which low yields were obtained only after priming or in response to poly IC-DEAEdx. POIFN-beta was prepared by induction of the PK-15 cell line with poly IC or poly IC-DEAEdx. The highest yields were obtained from cultures induced 24 h after seeding, although when poly IC-DEAEdx or superinduction was used, the age of the cells was less critical. Priming had little effect on the yields of POIFN-beta. PK-15 cells induced with NDV gave relatively low yields of IFN. Both POIFN-alpha and POIFN-beta were classified as type I IFN on the basis of their resistance or susceptibility to pH 2.0, ultracentrifugation, 56 degrees C and trypsin treatment. Disulphide bonds essential for antiviral activity were demonstrated in both types of IFN by reduction with 2-beta-mercaptoethanol, and anionic exchange chromatography after treatment with dithiothreitol indicated a second disulphide bond in POIFN-alpha which was not essential for antiviral activity. (ABSTRACT TRUNCATED AT 250 WORDS)
Petrified Forest of Lesbos Island (Greece): A Palaeobotanical Puzzle of a Unique Geopark and the New Discoveries.

On November 2015 Lesbos Island has faced an ultimate recognition as one of UNESCO’s Global Geoparks, an honor of its international significance based on its geological treasure as revealed by the existence of the famous early Miocene Petrified Forest and the variety of its geosites. The aim of this study is to draw a holistic approach for the palaeobotany of Lesbos Island through three main subjects: a) The first one is dealing with the past, the recognition of the palaeobotanical importance of Lesbos since the ancient times and the revision of the palaeoxylotomical and foliage material, b) the second theme gives a very brief summary of the recent results from the research by the first author and c) the third one uses the revealing of the historical part of Lesbos palaeofloristic treasure and also the recent botanical legislation and studies highlighting the complexity of Lesbos palaeobotany, which underline the remaining inconsistencies and propose solutions in order to give the perspectives of the future.
Dismantling the Papez circuit for memory in rats

Over the last 50 years, anatomical models of memory have repeatedly highlighted the hippocampal inputs to the mammillary bodies via the postcommissural fornix. Such models downplay other projections to the mammillary bodies, leaving them largely ignored. The present study challenged this dominant view by removing, in rats, the two principal inputs reaching the mammillary bodies: the postcommissural fornix from the hippocampal formation and Gudden's ventral tegmental nucleus. The principal mammillary body output pathway, the mammillothalamic tract, was disconnected in a third group. Only mammillothalamic tract and Gudden's ventral tegmental nucleus lesions impaired behavioral tests of spatial working memory and, in particular, disrupted the use of extramaze spatial landmarks. The same lesions also produced widespread reductions in immediate-early gene (c-fos) expression in a network of memory-related regions, not seen after postcommissural fornix lesions. These findings are inconsistent with previous models of mammillary body function (those dominated by hippocampal inputs) and herald a new understanding of why specific diencephalic structures are vital for memory. DOI: http://dx.doi. org/10.7554/eLife.00736. 001
Climate change and hydrology with emphasis on the Indian subcontinent

On a regional scale, some of the most profound impacts of climate change due to increases in greenhouse gases would probably be major changes in the hydrological cycle, in water availability, in agricultural production and in the use of energy. This paper gives a brief overview of studies carried out on climate change and possible impacts on hydrology and water resources in India, covering also the agricultural aspect. The need is emphasized for carrying out further studies in this important subject area at the national level, keeping in view the data and computing facilities available.
Social Context-Aware Trust Network Discovery in Complex Contextual Social Networks

Trust is one of the most important factors for participants' decision-making in Online Social Networks (OSNs). The trust network from a source to a target without any prior interaction contains some important intermediate participants, the trust relations between the participants, and the social context, each of which has an important influence on trust evaluation. Thus, before performing any trust evaluation, the contextual trust network from a given source to a target needs to be extracted first, where constraints on the social context should also be considered to guarantee the quality of extracted networks. However, this problem has been proved to be NP-Complete. Towards solving this challenging problem, we first propose a complex contextual social network structure which considers social contextual impact factors. These factors have significant influences on both social interaction between participants and trust evaluation. Then, we propose a new concept called QoTN (Quality of Trust Network) and a social context-aware trust network discovery model. Finally, we propose a Social Context-Aware trust Network discovery algorithm (SCAN) by adopting the Monte Carlo method and our proposed optimization strategies. The experimental results illustrate that our proposed model and algorithm outperform the existing methods in both algorithm efficiency and the quality of the extracted trust network.
No Evidence for a Saccadic Range Effect for Visually Guided and Memory-Guided Saccades in Simple Saccade-Targeting Tasks

Saccades to single targets in peripheral vision are typically characterized by an undershoot bias. Putting this bias to a test, Kapoula [1] used a paradigm in which observers were presented with two different sets of target eccentricities that partially overlapped each other. Her data were suggestive of a saccadic range effect (SRE): There was a tendency for saccades to overshoot close targets and undershoot far targets in a block, suggesting that there was a response bias towards the center of eccentricities in a given block. Our Experiment 1 was a close replication of the original study by Kapoula [1]. In addition, we tested whether the SRE is sensitive to top-down requirements associated with the task, and we also varied the target presentation duration. In Experiments 1 and 2, we expected to replicate the SRE for a visual discrimination task. The simple visual saccade-targeting task in Experiment 3, entailing minimal top-down influence, was expected to elicit a weaker SRE. Voluntary saccades to remembered target locations in Experiment 3 were expected to elicit the strongest SRE. Contrary to these predictions, we did not observe a SRE in any of the tasks. Our findings complement the results reported by Gillen et al. [2] who failed to find the effect in a saccade-targeting task with a very brief target presentation. Together, these results suggest that unlike arm movements, saccadic eye movements are not biased towards making saccades of a constant, optimal amplitude for the task.
Comparisons of Spore Dosimetry and Spectral Photometry of Solar-UV Radiation at Four Sites in Japan and Europe¶

Abstract In order to develop monitoring and assessment systems of biologically effective doses of solar-UV radiation, concurrent measurements of spectral photometry and spore dosimetry were conducted in summer months at four sites in Japan and Europe. Effectiveness spectra were derived by multiplying spectral irradiance in 0.5 nm steps between 290 and 400 nm with the inactivation efficiency of the spores determined using monochromatic radiation of fine wavelength resolution. Shapes of the effectiveness spectra were very similar at the four sites exhibiting major peaks at 303.5, 305.0, 307.5 and 311.0 nm. The dose rates for spore inactivation from direct survival measurements and from calculations by the integration of the effectiveness spectra were compared for 174 data points. The ratios (observed/calculated) of the two values were concordant with a mean of 1.26 (±0.24 standard deviation [SD]). The possible causes for the variations and slightly larger observed values are discussed.