Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Mechanisms of Tissue Fibrosis Role of Smad 3 in platelet-derived growth factor-C-induced liver fibrosis

Jung Il Lee, Jocelyn H. Wright, Melissa M. Johnson, Renay L. Bauer, Kristina Sorg, Sebastian Yuen, Brian J. Hayes, Lananh Nguyen, Kimberly J. Riehle, and Jean S. Campbell Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea; Department of Pathology, University of Washington, Seattle, Washington; and Department of Surgery, University of Washington, Seattle, Washington
Human cortico‐hippocampal activity related to auditory discrimination revealed by neuromagmetic field

WE carried out multi-dipole estimation and pursued spatio-temporal brain activity on a time scale of several milliseconds during an auditory discrimination task using a whole-cortex type SQUID system. Neuronal activities were estimated in the medial (hippocampus, parahippocampal gyrus, etc.) and lateral temporal cortices (superior and middle temporal gyri, etc.), the dorsolateral prefrontal cortex (middle and inferior frontal gyri, etc.) and the parietal cortex (supramarginal gyrus, etc.) in the 280–400 ms latency range. The activity in the posterior hippocampal region was the most prominent and long-lasting in parallel with the activities in the other regions. Therefore, the posterior hippocampal region is a central structure engaged in auditory discrimination. The whole-cortex neuromagnetic measurements provided the possibility of imaging the time-varying activities of the human cortico-hippocampal neural networks.
Assessment of the three factors affecting Myanmar's forest cover change using Landsat and MODIS vegetation continuous fields data

ABSTRACT Long-term observation of the earth is essential for studying the factors affecting global environmental changes. Digital earth technology can facilitate the monitoring of global environmental change with its ability to process vast amounts of information. In this study, we map the forest cover change of Myanmar from 2000 to 2005 using a training data automation procedure and support vector machines algorithm. Our results show that Myanmar's forests have declined 0.68% annually over this six-year period. We validated our derived change results and found the overall accuracy to be greater than 88%. We also assessed forest loss from protected areas, areas close to roads, and areas subject to fire, which were most likely to lose forested area. The results revealed the main reasons for forest losses in some hotspots to be increased agricultural conversion, fire, and the construction of highways. This information is useful for identifying the driving forces behind forest changes and to support environmental policy development in Myanmar.
G20210A Prothrombin Gene Polymorphism and Extent of Coronary Disease

In the 389 pts not on OAC therapy, factor II activity was determined coagulometrically using factor II-deficient plasma (Dade-Behring). Median factor II activity in the overall group was 110% (minimum 62%, maximum 179%); no significant correlation with age was found in the overall group (Spearman coefficient r = 0.004; p = 0.20). A trend towards lower factor II activities in older pts was noted, which was more pronounced in pts with the heterozygous variation compared to pts with the wild-type allele (median factor II activities in pts <30 years at diagnosis were 132 (n = 97) vs 110% (n = 6); 30–50 years 126 (n = 147) vs. 109% (n = 7); >50 years 110.5 (n = 126) vs. 108% (n = 6). In the pts homozygous for the wild-type allele (GG20210), median factor II activity was 109.5% (min. 62%, max. 179%), median factor II activity in the pts heterozygous for the G20210A allele was 126% (min. 93%, max. 157%) (Fig. 1), again no significant correlation with age was found for either gene status (Spearman coefficient for GG20210: r = 0.003; p = 0.29; for G20210A: r = 0.028, p = 0.49). Median factor II activities in females (n = 216; 111.5%, min. 62%, max. 179%) were higher compared to male pts (n = 173; 109%, min. 63%, max. 168%) (p = 0.035; Wilcoxon test), probably due to the lower median age of female pts (34.5 years vs. 49 years in males). The difference of median factor II activities remained significant between the two genders for the wild-type allele (female 111%, male 107.5%; p = 0.033; Wilcoxon test); no significant difference between the two genders was found for the heterozygous allele (female 120%, male 127%; p = 0.77; Wilcoxon test). A non-significant trend towards lower factor II activities in older pts was found in our overall group. Interestingly, this trend was more pronounced in pts expressing the heterozygous prothrombin allele G20210A, resulting in similar median factor II activities in pts >50 years irrespective of the gene status (GG20210: 108%; G20210A: 110.5%). Median factor II activity in our population was significantly higher (p = 0.002; Wilcoxon test) in pts with the G20210A prothrombin gene allele compared to pts homozygous for the wild-type allele. However, there is a wide overlap of coagulation factor II activities of pts homozygous for the wild-type prothrombin gene allele with pts heterozygous for the G20210A variation; only factor II activities <90% were found exclusively in the wild-type group. As only 9.8% of pts (38/389) had factor II activities <90%, coagulation factor II activity determination is not considered useful as a screening tool for the G20210A prothrombin gene allele.
CUNI submission in WMT17: Chimera goes neural

This paper describes the neural and phrase-based machine translation systems submitted by CUNI to English-Czech News Translation Task of WMT17. We experiment with synthetic data for training and try several system combination techniques, both neural and phrase-based. Our primary submission CU-C HIMERA ends up being phrase-based backbone which incorporates neural and deep-syntactic candidate translations.
Total Synthesis of the Macrolide Antibiotic Cytovaricin.

A convergent asymmetric synthesis of the antinoeplastic macrolide antibiotic cytovaricin has been achieved through the synthesis and coupling of the illustrated spiroketal and polyol glycoside subunits. All absolute steroechemical relationships within the target structure were ultimately controlled by the use of asymmetric aldol, alkylation, or epoxidation methodology. Union of the two subnits was accomplished by Julia-Lythgoe trans olefination, providing direct access to a suitable macrolactonization substrate
Gene Trap Disruption of the Mouse Heparan Sulfate 6-O-Endosulfatase Gene, Sulf2

ABSTRACT Heparan sulfate (HS) chains are found in the extracellular matrix, covalently linked to core proteins collectively termed heparan sulfate proteoglycans (HSPGs). A wealth of data has demonstrated roles for HSPGs in the regulation of many cell surface signaling pathways that are crucial during development. Variations in the sulfation pattern along the HS chains influence their ability to interact with molecules such as growth factors, chemokines, morphogens, and adhesion molecules. Sulf1 and Sulf2 are members of a class of recently identified genes that encode heparan sulfate 6-O-endosulfatases (Sulf genes). The removal of 6-O-sulfate from HS via SULF activity influences the function of many factors, including Wnt, fibroblast growth factor, hepatocyte growth factor, heparin-binding epidermal growth factor, and bone morphogenetic protein. Given their possible developmental roles, we have examined Sulf gene expression during mouse embryogenesis. The two Sulf genes are expressed in a broad range of tissues throughout development with largely nonoverlapping expression patterns. Sulf2 transcripts are expressed in the lung, heart, placenta, and ribs. We generated a mouse line possessing a gene trap disruption of the Sulf2 gene. Mice homozygous for the Sulf2 gene trap allele are viable and fertile and have no major developmental defects on several genetic backgrounds. However, we observed strain-specific, nonpenetrant defects affecting viability, lung development, and growth in Sulf2 homozygous animals. These data suggest that Sulf2 may have roles in several tissues but that there is compensation by and/or redundancy with Sulf1.
Error Immune Logic for Low-Power Probabilistic Computing

Two novel theorems are developed which prove that certain logic functions are more robust to errors than others. These theorems are used to construct datapath circuits that give an increased immunity to error over other naive implementations. A link between probabilistic operation and ultra-low energy computing has been shown in prior work. These novel theorems and designs will be used to further improve probabilistic design of ultra-low power datapaths. This culminates in an asynchronous design for the maximum amount of energy savings per a given error rate. Spice simulation results using a commercially available and well-tested 0. 25µm technology are given verifying the ultra-low power, probabilistic full-adder designs. Further, close to 6X energy savings is achieved for a probabilistic full-adder over the deterministic case.
CryptoPage : Support matériel pour cryptoprocessus

Computers are widely used and interconnected but are not as secure as we could expect. For example, a secure execution cannot even be achieved or proved against a software (the system administrator) or hardware attacker (a logical analyzer on the computer buses). In this article a strong cryptography-based architecture with an operating system support is presented to reach such security levels without reducing the performance. A cache line cipher and a memory verifier based on MERKLE tree hash function is added to the internal cache in order to resist to various attacks and even replay attacks. Then the impact on the operating system and some applications are described.
Effects of total flavonoids from Dracocephalum moldavica on the proliferation, migration, and adhesion molecule expression of rat vascular smooth muscle cells induced by TNF-α

Context: Dracocephalum moldavica Linn (Labiatae) is one of the ethnomedicinal drugs of Uygur in Xinjiang, China. This herb is mainly used in treating cardiovascular diseases, such as atherosclerosis. However, the mechanism of pharmacological activity of D. moldavica has been poorly studied. Objective: To explore the pharmacological mechanism of D. moldavica in treating atherosclerosis by investigating the effects of total flavonoids from the aerial portion of D. moldavica on rat vascular smooth muscle cells (VSMCs). Materials and methods: The proliferation and migration of VSMCs were evaluated via a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and transwell chamber experiment, respectively. The expression of proliferating cell nuclear antigen (PCNA), nuclear factor κB p65 (NF-κB p65), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) of VSMCs was determined using immunohistochemistry staining and quantitative real-time PCR (qRT-PCR). Results: Total flavonoids (IC50 = 145.63 μg/mL) significantly inhibited tumor necrosis factor-α (TNF-α) induced VSMC proliferation at concentrations of 25, 50, and 100 μg/mL. Treatment with 50 and 100 μg/mL of total flavonoids also significantly inhibited TNF-α-induced VSMC migration, whereas 25 μg/mL of total flavonoids did not elicit any significant inhibitory effect. In addition, the effects of total flavonoids on inflammatory molecule expression of cells were tested by immunohistochemistry staining, showing that TNF-α-induced expression of PCNA, NF-κB p65, ICAM-1, and VCAM-1 in VSMCs was dose-dependently suppressed by total flavonoids. Furthermore, qRT-PCR data confirmed the inhibition of mRNA expressions of these inflammatory molecules. Discussion and conclusion: These data suggest that total flavonoids from D. moldavica exhibit anti-inflammatory activities, which is probably one of the underlying mechanisms of D. moldavica for clinical treatment of atherosclerosis.
AToMRS: A Tool to Monitor Recommender Systems

Recommender systems arose in response to the excess of available online information. These systems assign, to a given individual, suggestions of items that may be relevant. These systemâs monitoring and evaluation are fundamental to the proper functioning of many business related services. It is the goal of this paper to create a tool capable of collecting, aggregating and supervising the results obtained from the recommendation systemsâ evaluation. To achieve this goal, a multi-granularity approach is developed and implemented in order to organize the different levels of the problem. This tool also aims to tackle the lack of mechanisms to enable visually assessment of the performance of a recommender systemsâ algorithm. A functional prototype of the application is presented, with the purpose of validating the solutionâs concept.
Electric Vehicles - effects on domestic low voltage networks

Electric Vehicles (EV) charging from a domestic power socket are becoming increasingly popular due to their economic and environmental benefits. The large number of such vehicles presents a significant additional load on existing low voltage (LV) power distribution networks (PDN). Evaluating this impact is essential for distribution network operators (DNO) to ensure normal functioning of the distribution grid. This research uses predictions of EV development and penetration levels to create a stochastic model of aggregate charging demand in a neighbourhood. Combined with historic distribution substations data from the Milton Keynes, UK total loads on the distribution transformers are projected. The results show significant overloading can occur with uncoordinated charging with just 25% of EVs on the road. The traditional way to solve this problem would be upgrading the transformer; however, that could be avoided by implementing coordinated charging to redistribute the load.
Evidence that myocardial Na/I symporter gene imaging does not perturb cardiac function.

UNLABELLED Adenoviral Na/I symporter (NIS) gene transfer has emerged as a promising method for myocardial gene imaging but concern over possible perturbation of cardiac function persists. In this study, we addressed this issue with cultured cardiac cells and serial echocardiography, creatine kinase (CK) measurements, and histologic examination of rats intramyocardially injected with an adenovirus that expresses both NIS and enhanced green fluorescent protein (EGFP) (Ad.EGFP.NIS) or a control virus (Ad.EGFP). METHODS H9C2 cardiac myoblasts differentiated into cardiomyocytes were evaluated for the effect of Ad.EGFP. NIS and Ad.EGFP infection on viable cell number and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. Rats injected intramyocardially with 3 x 10(8) plaque-forming units of Ad.EGFP. NIS (n = 9) or Ad.EGFP (n = 8) underwent serial echocardiographic measurements of heart rate, left ventricular (LV) dimensions, ejection fraction (EF), and fractional shortening (FS) on the day before and on days 4 and 9 after gene transfer. Five Ad.EGFP. NIS rats also underwent repeated (123)I imaging from which ratios of cardiac to mediastinal counts (C/M ratios) were obtained. Separate rats underwent serial measurements of serum CK, myocardial myeloperoxidase assays, and microscopic assessment of inflammation. RESULTS Cultured cardiac cells showed no change in cell viability or proliferation at 4 and 9 d after Ad.EGFP. NIS or Ad.EGFP infection compared with controls. (123)I scintigraphy demonstrated high cardiac radiouptake at Ad.EGFP. NIS injection sites by days 2 and 4 (C/M ratios, 5.0 +/- 0.6 and 5.1 +/- 1.0, respectively), followed by a complete loss of uptake by day 9 (C/M ratio, 1.4 +/- 0.0). Serial echocardiography revealed no difference in heart rate, LV dimensions, or functional parameters between Ad.EGFP. NIS and Ad.EGFP groups at any given time. Mild reductions in LVEF and LVFS by day 9 compared with baseline were similar for both Ad.EGFP (88.2% +/- 6.4% vs. 79.6% +/- 5.0% for LVEF and 0.55 +/- 0.10 vs. 0.44 +/- 0.05 for LVFS) and Ad.EGFP. NIS groups (88.0% +/- 5.4% vs. 78.7% +/- 4.6% for LVEF and 0.54 +/- 0.09 vs. 0.42 +/- 0.05 for LVFS). Serial serum CK and myocardial myeloperoxidase activities were not elevated in either group, in contrast to substantial increases found after ischemia-reperfusion injury. Histology revealed similar mild inflammatory cell infiltration restricted to the injection site for both groups. CONCLUSION The results of this study demonstrate that myocardial NIS gene imaging does not cause significant myocardial injury or perturbed cardiac function, other than mild effects likely due to adenoviral vector-associated host response. Thus, this practical and convenient reporter gene strategy can be used safely for noninvasive myocardial gene imaging in living subjects.
CD46 in Meningococcal Disease

The human-specific bacterial pathogen Neisseria meningitidis is a major cause of sepsis and/or meningitis. The pili of N. meningitidis interact with CD46, a human cell-surface protein involved in regulation of complement activation. Transgenic mice expressing human CD46 were susceptible to meningococcal disease, because bacteria crossed the blood-brain barrier in these mice. Development of disease was more efficient with piliated bacteria after intranasal, but not intraperitoneal, challenge of CD46 transgenic mice, suggesting that human CD46 facilitates pilus-dependent interactions at the epithelial mucosa. Hence, the human CD46 transgenic mice model is a potentially useful tool for studying pathogenesis and for vaccine development against meningococcal disease.
A sequence-ready contig map of the top arm of Arabidopsis thaliana chromosome 3.

A fine physical map of the top arm of Arabidopsis thaliana chromosome 3 has been constructed by ordering P1, TAC and BAC clones using the sequences of a variety of DNA markers and end-sequences of clones. The marker sequences used in this study were derived from 58 DNA markers, 93 YAC end-sequences, and 807 end-sequences of P1, TAC and BAC clones. The entire top arm of chromosome 3, except for the centromeric and telomeric regions, was covered by a single contig 13.3 Mb long. This fine physical map will facilitate gene isolation by map-based cloning experiments as well as genome sequencing of the top arm of chromosome 3. The map and end-sequence information are available on the web site KAOS (Kazusa Arabidopsis data Opening Site) at [http://www.kazusa. or.jp/arabi/].
Structural Basis for the De-N-acetylation of Poly-β-1,6-N-acetyl-d-glucosamine in Gram-positive Bacteria*

Background: IcaB is a poly-β-1,6-N-acetyl-d-glucosamine (PNAG) deacetylase required for polysaccharide intercellular adhesion-dependent biofilm formation by staphylococci. Results: The structure of Ammonifex degensii IcaB has been determined and its catalytic mechanism and localization characterized. Conclusion: IcaB is a membrane-associated PNAG deacetylase that uses an altered catalytic mechanism relative to other family 4 carbohydrate esterases. Significance: First structural characterization of a Gram-positive PNAG deacetylase. Exopolysaccharides are required for the development and integrity of biofilms produced by a wide variety of bacteria. In staphylococci, partial de-N-acetylation of the exopolysaccharide poly-β-1,6-N-acetyl-d-glucosamine (PNAG) by the extracellular protein IcaB is required for biofilm formation. To understand the molecular basis for PNAG de-N-acetylation, the structure of IcaB from Ammonifex degensii (IcaBAd) has been determined to 1.7 Å resolution. The structure of IcaBAd reveals a (β/α)7 barrel common to the family four carbohydrate esterases (CE4s) with the canonical motifs circularly permuted. The metal dependence of IcaBAd is similar to most CE4s showing the maximum rates of de-N-acetylation with Ni2+, Co2+, and Zn2+. From docking studies with β-1,6-GlcNAc oligomers and structural comparison to PgaB from Escherichia coli, the Gram-negative homologue of IcaB, we identify Arg-45, Tyr-67, and Trp-180 as key residues for PNAG binding during catalysis. The absence of these residues in PgaB provides a rationale for the requirement of a C-terminal domain for efficient deacetylation of PNAG in Gram-negative species. Mutational analysis of conserved active site residues suggests that IcaB uses an altered catalytic mechanism in comparison to other characterized CE4 members. Furthermore, we identified a conserved surface-exposed hydrophobic loop found only in Gram-positive homologues of IcaB. Our data suggest that this loop is required for membrane association and likely anchors IcaB to the membrane during polysaccharide biosynthesis. The work presented herein will help guide the design of IcaB inhibitors to combat biofilm formation by staphylococci.
Probe Selection for Pathway-Specific Microarray Probe Design Minimizing Melting Temperature Variance

In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus. Keywords—bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection
RETRIEVAL OF EFFECTIVE DIAMETER VARIATIONS IN TROPICAL CUMULONIMBUS

It is of considerable importance to understand the impacts (if any) of aerosols and other atmospheric constituents on clouds. These impacts may include modification of the optical properties, coverage, dynamical behavior, and/or hydrological role of clouds. The most basic variables that must be measured in order to make progress are cloud coverage, optical thicknesses, and size distributions of the cloud hydrometeors. The recent launch of MODIS (Moderate Resolution Imaging Spectroradiometer) on board NASA’s polar orbiting EOS (Earth Observing System) satellites promises significant advances in observation of the size distribution, using several near-infrared wavelengths. Daytime near-IR reflectivity is particularly helpful since it is quite sensitive to ice particle size (see Liou (1992) for further information). Models are required to relate backscattered intensities to cloud properties, due to dependence of intensity on viewing geometry and cloud optical depth . Uncertainties in these models include assumptions about crystal shape, parameterization of the scattering phase function, and other approximations. They are difficult to test rigorously against observations. Here, we present an analysis of a long record of AVHRR (Advanced High Resolution Radiometer) 3.7 m reflectivity off of cumulonimbus clouds (Cb) that can be used to do this.