Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction-Based Formal Verification of SystemC TLM Designs

In this paper we present a formal verification approach for SystemC TLM designs. The approaches allows to check expressive properties and uses induction to cope with the large state space of abstract SystemC programs. The technique is tightly integrated with our SystemC-to-C transformation and generation of monitoring logic to form a complete and efficient method. Properties specifying both hardware and software aspects, e.g. pre- and post-conditions as well as temporal relations of transactions and events, can be specified. As shown by experiments our inductive technique gives significant speed-ups in comparison to simple methods.
Research, part of a Special Feature on Scenarios of global ecosystem services The Future of Vascular Plant Diversity Under Four Global Scenarios

Biodiversity is of crucial importance for ecosystem functioning and human well-being. Using quantitative projections of changes in land use and climate from the four Millennium Ecosystem Assessment (MA) scenarios, we project that reduction of habitat by year 2050 will result in a loss of global vascular plant diversity ranging from 7-24% relative to 1995, after populations have reached equilibrium with the reduced habitat. This range includes both the impact of different scenarios and uncertainty in the SAR relationship. Biomes projected to lose the most species are warm mixed forest, savannahs, shrub, tropical forest, and tropical woodlands. In the 2000-2050 period, land-use change contributes more on a global scale to species diversity loss than does climate change, 7-13% vs. 2-4% loss at equilibrium for different scenarios, respectively. However, after 2050, climate change will become increasingly important.
Gastric but not Renal Amyloid Deposition is Removed by Biologics Therapy in AA Amyloidosis Patients with Rheumatoid Arthritis

Objectives: Several biologics therapy reportedly regress gastric amyloid deposition in AA amyloidosis patients, but it is uncertain whether they can also regress renal amyloid deposition. We carried out serial renal biopsy to clarify the regression of amyloid deposition in kidney by biologics. Methods: After the diagnosis of AA amyloidosis was determined by gastric biopsy to rheumatoid arthritis (RA) patients, renal biopsy was carried out. The patients who had inadequate response by conventional oral medicines for RA were treated with tocilizumab or etanercept for more than two years. After biologics treatment, gastric and renal biopsy was carried out. Results: Six AA amyloidosis patients received biologics and the disease activities of RA were improved significantly. By renal biopsy, four patients were diagnosed with glomerular type and two patients with vascular type. After biologics treatment, amyloid deposition of gastroduodenal tracts was markedly regressed in all six patients. However, amyloid deposition of kidney did not regress significantly in two patients with vascular type whereas four patients with glomerular type could not be carried out renal biopsy due to renal failure. Conclusions: Amyloid deposition of kidney, unlikely to gastric tract, may not regress significantly in AA amyloidosis patients with RA by biologics therapy.
Mutually coherent structural representation for image registration through joint manifold embedding and alignment

In this paper, we introduce mutually coherent structural representations (McSR) for image registration which learns a mapping of local structural descriptors to create a unique scalar representation, which is similar across modalities. The McSR is learnt using joint alignment and embedding of Laplacian eigenmaps using modality-combination specific dense structural descriptors. The resulting alternate image representation offers richer structurally-driven information for registration while being invariant to inter-modal differences in intensities. The proposed formulation has been evaluated for robustness and registration error on standard multimodal brain image datasets. It is observed to demonstrate superior systematic recovery and performance over comparative simultaneous registration methods.
Dataset for a Neural Natural Language Interface for Databases (NNLIDB)

Progress in natural language interfaces to databases (NLIDB) has been slow mainly due to linguistic issues (such as language ambiguity) and domain portability. Moreover, the lack of a large corpus to be used as a standard benchmark has made data-driven approaches difficult to develop and compare. In this paper, we revisit the problem of NLIDBs and recast it as a sequence translation problem. To this end, we introduce a large dataset extracted from the Stack Exchange Data Explorer website, which can be used for training neural natural language interfaces for databases. We also report encouraging baseline results on a smaller manually annotated test corpus, obtained using an attention-based sequence-to-sequence neural network.
Infection Rates and Comparative Population Dynamics of Peregrinus maidis (Hemiptera: Delphacidae) on Corn Plants with and without Symptoms of Maize Mosaic Virus (Rhabdoviridae: Nucleorhabdovirus) Infection

ABSTRACT We examined the population dynamics of the corn planthopper Peregrinus maidis (Ashmead) (Hemiptera: Delphacidae) throughout a cycle of corn (Zea mays L.) production on plants with or without symptoms of maize mosaic virus (MMV) (Rhabdoviridae: Nucleorhabdovirus) infection. Our results indicate that the timing of MMV plant infection greatly influenced the planthopper's host plant colonization patterns. Corn plants that expressed symptoms of MMV infection early in the crop cycle (28 d after planting) harbored, on average, 40 and 48% fewer planthoppers than plants that expressed symptoms of MMV infection later in the crop cycle (49 d after planting) and asymptomatic plants, respectively. We also observed a change in the number of brachypterous (short-wing type) and macropterous (long-wing type) winged forms produced; plants expressing early symptoms of MMV infection harbored, on average, 41 and 47% more of the brachypterous form than plants with late infections of MMV and plants with no symptoms of MMV, respectively. Furthermore, we determined the rates of MMV-infected planthoppers relative to their wing morphology (macropterous or brachypterous) and gender. MMV infection was 5 and 12% higher in females than in males in field and greenhouse experiments, respectively; however, these differences were not significantly different. This research provides evidence that MMV similarly infects P. maidis planthoppers regardless of the gender and wing morphotype. These results also suggest that the timing of symptom development greatly affects the population dynamics of the planthopper vector, and likely has important consequences for the dynamics of the disease in the field.
Syphacia muris infection in rats attenuates colorectal carcinogenesis through oxidative stress and gene expression alterations. Implications for modulatory effects by Bryostatin-1

Accumulating evidence suggest that some infectious agents may interfere in the natural progression of neoplasia. This study examined the association between chronic infection with adult Syphacia muris parasites and 1,2-dimethylhydrazine (DMH)-induced colorectal carcinogenesis in rats. In addition, the conceivable therapeutic effect of Bryostatin-1, a potent extract of the marine Bryozoan, Bugulane ritina, was investigated against this combined effect.DMH administration has induced aberrant crypt foci (ACF), surrogate biomarkers for colorectal carcinogenesis, while the S. muris infection combined with DMH has significantly increased the total numbers of ACF. Nonetheless, treatment with Bryostatin-1 after infection has significantly reduced the ACF numbers particularly larger ones. This inhibition was concomitant with significant inhibition in the immunohisto-chemical levels of the ki67, Caspase-3 and IgM levels in colorectal epithelium, as well as serum levels of IgM and IgG. Additionally, treatment with Bryostatin-1 after S. muris + DMH has modulated enzymatic antioxidative markers levels of superoxide dismutase and catalase as well as the non-enzymatic antioxidant markers levels of reduced glutathione, lipid peroxidation, nitric oxide and total antioxidant capacity. Further, treatment with Bryostatin-1 has down-regulated the mRNA expression levels of COX-2 and APC genes in colorectal mucosa. In conclusion, infection with S. muris during colorectal carcinogenesis has significantly modulated the oxidative stress markers in the colorectum, while treatment with Bryostatin-1 has exerted significant curative potential. A mechanism could be explained that Bryostatin-1 treatment has reduced oxidative stress markers activities along with affecting host to parasite immunity possibly leading to changes in the COX-2 and APC expression, retarding cellular proliferation and subsequently reducing the colorectal carcinogenesis events.
Fast Robust and Precise Shadow Algorithm for WebGL 1.0 Platform

This paper presents fast and robust per-sample correct shadows for WebGL platform. The algorithm is based on silhouette shadow volumes and it rivals the standard shadow mapping performance. Our performance is usually superior when compared with high resolution shadow maps. Moreover, it does not suffer from a number of artefacts of shadow mapping and always provides per-pixel correct results. WebGL 1.0 provides just vertex and fragment shaders. Thus, we put all our algorithms evaluating silhouette edges to vertex shaders. Specially precomputed data are fed to the vertex shaders that extrude shadow volume sides just for silhouette edges. Some optimizations are deployed for performance and data size reasons that are important especially on low performance configurations, such as cost-effective tablets and mobile phones. The paper evaluates our solution on number of models. Our solution performs on par with high resolution omnidirectional shadow mapping.
Bacterial Lipopolysaccharide Activates Nuclear Factor-κB through Interleukin-1 Signaling Mediators in Cultured Human Dermal Endothelial Cells and Mononuclear Phagocytes*

Bacterial lipopolysaccharide (LPS)-mediated immune responses, including activation of monocytes, macrophages, and endothelial cells, play an important role in the pathogenesis of Gram-negative bacteria-induced sepsis syndrome. Activation of NF-κB is thought to be required for cytokine release from LPS-responsive cells, a critical step for endotoxic effects. Here we investigated the role and involvement of interleukin-1 (IL-1) and tumor necrosis factor (TNF-α) signal transducer molecules in LPS signaling in human dermal microvessel endothelial cells (HDMEC) and THP-1 monocytic cells. LPS stimulation of HDMEC and THP-1 cells initiated an IL-1 receptor-like NF-κB signaling cascade. In transient cotransfection experiments, dominant negative mutants of the IL-1 signaling pathway, including MyD88, IRAK, IRAK2, and TRAF6 inhibited both IL-1- and LPS-induced NF-κB-luciferase activity. LPS-induced NF-κB activation was not inhibited by a dominant negative mutant of TRAF2 that is involved in TNF signaling. LPS-induced activation of NF-κB-responsive reporter gene was not inhibited by IL-1 receptor antagonist. TLR2 and TLR4 were expressed on the cell surface of HDMEC and THP-1 cells. These findings suggest that a signal transduction molecule in the LPS receptor complex may belong to the IL-1 receptor/toll-like receptor (TLR) super family, and the LPS signaling cascade uses an analogous molecular framework for signaling as IL-1 in mononuclear phagocytes and endothelial cells.
Expression of L protein of Hantaan virus 84FLi strain and its application for recovery of minigenomes  

Hantaan virus (HTNV) is an Old World hantavirus associated with hemorrhagic fever with renal syndrome (HFRS). To visualize the localization of the L protein of HTNV strain 84FLi within cells, a fusion protein composed of enhanced green fluorescent protein and L protein, EGFP‐L, was expressed in Vero cells. The 273 KDa expressed fusion protein of EGFP‐L localized in the perinuclear region. We also described the development of a reverse genetics system for HTNV strain 84FLi. The RNA polymerase I (pol I)‐mediated transcription system was used to generate artificial viral RNA genome segments (minigenomes), which contained the chloramphenicol acetyltransferase (CAT) reporter gene in antisense (virus RNA) or sense (virus‐complementary RNA) orientation flanked by the noncoding regions of HTNV 84FLi L segment. CAT could be detected in cells after transfection, indicating the successful encapsidation, transcription and replication of the pol I‐derived minigenomes. The passaged transfer of CAT demonstrates that recombinant virus containing packaged pol I‐derived minigenomes has been produced. This system may be helpful in studying the gene function and pathogenesis of HTNV.
Tinnitus and hyperacusis are common , burdensome sources of morbidity with a 50 high rate of co-occurrence

1 2 Title: 3 Hyperactivity in the medial olivocochlear efferent system is a common feature of 4 tinnitus and hyperacusis in humans 5 6 Authors: 7 Joshua J. Sturm 2 Catherine JC Weisz. 8 Department of Otolaryngology, University of Pittsburgh School of Medicine 9 Medical Scientist Training Program, University of Pittsburgh School of Medicine 10 11 Contact: 12 Joshua J Sturm: jjs149@pitt.edu 13 Catherine JC Weisz: cjw52@pitt.edu 14 15
Toxicogenomics of Non-viral Vectors for Gene Therapy: A Microarray Study of Lipofectin- and Oligofectamine-induced Gene Expression Changes in Human Epithelial Cells

Of the non-viral vectors, cationic lipid (CL) formulations are the most widely studied for the delivery of genes, antisense oligonucleotides and gene silencing nucleic acids such as small interfering RNAs. However, little is known about the impact of these delivery systems on global gene expression in target cells. In an attempt to study the geno-compatibility of CL formulations in target cells, we have used microarrays to examine the effect of Lipofectin and Oligofectamine on the gene expression profiles of human A431 epithelial cells. Using the manufacturer's recommended CL concentrations routinely used for gene delivery, cDNA microarray expression profiling revealed marked changes in the expression of several genes for both Lipofectin- and Oligofectamine-treated cells. Data from the 200 spot arrays housing 160 different genes indicated that Lipofectin or Oligofectamine treatment of A431 cells resulted in more than 2-fold altered expression of 10 and 27 genes, respectively. The downstream functional consequences of CL-induced gene expression alterations led to an increased tendency of cells to enter early apoptosis as assessed by annexin V-FITC flow cytometry analyses. This effect was greater for Oligofectamine than Lipofectin. Observed gene expression changes were not sufficient to induce any significant DNA damage as assessed by single cell gel electrophoresis (COMET) assay. These data highlight the fact that inadvertent gene expression changes can be induced by the delivery formulation alone and that these may, ultimately, have important safety implications for the use of these non-viral vectors in gene-based therapies. Also, the induced non-target gene changes should be taken into consideration in gene therapy or gene silencing experiments using CL formulations where they may potentially mask or interfere with the desired genotype and/or phenotype end-points.
Financial Instability, Uncertainty and Banks’ Lending Behaviour

Why do banks squeeze their lending activity? is an oft-repeated question during the times of financial crisis. This study examines an emerging economy’s banking system and contributes to the evolving body of literature on the topic by providing answers as to what causes the sluggish bank credit during the times of recession. By employing cointegration technique, the study shows that bank credit has a significant positive relationship with the borrowing activity of the banks and on the contrary, inverse relationship with investment activity during the financial crisis. Accordingly, we suggest that banks could increase their lending by increasing the borrowings rapidly either from the Central Banks or from Government supported long term lending institutions during recessionary periods.
Lactoferrin Inhibits Porphyromonas gingivalis Proteinases and Has Sustained Biofilm Inhibitory Activity

ABSTRACT Porphyromonas gingivalis is a bacterial pathogen associated with chronic periodontitis that results in destruction of the tooth's supporting tissues. The major virulence determinants of P. gingivalis are its cell surface Arg- and Lys-specific cysteine proteinases, RgpA/B and Kgp. Lactoferrin (LF), an 80-kDa iron-binding glycoprotein found in saliva and gingival crevicular fluid, is believed to play an important role in innate immunity. In this study, bovine milk LF displayed proteinase inhibitory activity against P. gingivalis whole cells, significantly inhibiting both Arg- and Lys-specific proteolytic activities. LF inhibited the Arg-specific activity of purified RgpB, which lacks adhesin domains, and also inhibited the same activity of the RgpA/Kgp proteinase-adhesin complexes in a time-dependent manner, with a first-order inactivation rate constant (kinact) of 0.023 min−1 and an inhibitor affinity constant (KI) of 5.02 μM. LF inhibited P. gingivalis biofilm formation by >80% at concentrations above 0.625 μM. LF was relatively resistant to hydrolysis by P. gingivalis cells but was cleaved into two major polypeptides (53 and 33 kDa) at R284 to S285, as determined by in-source decay mass spectrometry; however, these polypeptides remained associated with each other and retained inhibitory activity. The biofilm inhibitory activity of LF against P. gingivalis was not attributed to direct antibacterial activity, as LF displayed little growth inhibitory activity against planktonic cells. As the known RgpA/B and Kgp inhibitor N-α-p-tosyl-l-lysine chloromethylketone also inhibited P. gingivalis biofilm formation, the antibiofilm effect of LF may at least in part be attributable to its antiproteinase activity.
Solving power flow problems with a Matlab implementation of the power system applications data dictionary

This paper implements a power flow application and variations using the IEEE Power System Application Data Dictionary within a Matlab environment. It describes a number of useful data and implementation techniques for a variety of applications. The techniques include the use of very compact and efficient code for the computation of Power Transfer Distribution Factors. Power Transfer Distribution Factors are all important element of present and proposed congestion management strategies for power systems, particularly, when these systems must operate in a deregulated environment.
Harmonic power flow in unbalanced and polluted radial distribution systems

The main purpose of this paper is the harmonic power flow in multiphase unbalanced radial distribution systems in the presence of non-linear loads and reactive components. It is important to have analytical methodologies to assess the impact and consequences of non-linear loads and shunt capacitors on voltage profile and harmonic distortion in each bus in the power systems. The presented power flow is entirely different from conventional methods applied in transmission power systems. The proposed method in this paper is based on graph theory, and injection current technique. A standard test system, IEEE-13 bus radial unbalanced, is considered for implementation and explanation of the method. To check the accuracy and efficiency of the method, it is also tested on IEEE 34, 37 & 123 bus test feeders. The comparison of results approves robustness and reliability of the method. MATLAB M-file is used to obtain results.
Molecular Studies on the Ecology of Listeria monocytogenes in the Smoked Fish Processing Industry

ABSTRACT We have applied molecular approaches, including PCR-based detection strategies and DNA fingerprinting methods, to study the ecology ofListeria monocytogenes in food processing environments. A total of 531 samples, including raw fish, fish during the cold-smoking process, finished product, and environmental samples, were collected from three smoked fish processing facilities during five visits to each facility. A total of 95 (17.9%) of the samples tested positive forL. monocytogenes using a commercial PCR system (BAX for Screening/Listeria monocytogenes), including 57 (27.7%) environmental samples (n = 206), 8 (7.8%) raw material samples (n = 102), 23 (18.1%) samples from fish in various stages of processing(n = 127), and 7 (7.3%) finished product samples (n= 96). L. monocytogenes was isolated from 85 samples (16.0%) using culture methods. Used in conjunction with a 48-h enrichment in Listeria Enrichment Broth, the PCR system had a sensitivity of 91.8% and a specificity of 96.2%. To track the origin and spread of L. monocytogenes, isolates were fingerprinted by automated ribotyping. Fifteen different ribotypes were identified among 85 isolates tested. Ribotyping data established possible contamination patterns, implicating raw materials and the processing environment as potential sources of finished product contamination. Analysis of the distribution of ribotypes revealed that each processing facility had a unique contamination pattern and that specific ribotypes persisted in the environments of two facilities over time (P ≤ 0.0006). We conclude that application of molecular approaches can provide critical information on the ecology of different L. monocytogenes strains in food processing environments. This information can be used to develop practical recommendations for improved control of this important food-borne pathogen in the food industry.
Understanding Philistine Migration: City Names and Their Implications

The origin of the Philistines, their quantity, quality, and status among the native Canaanite population, have all been the focus of a substantial volume of research. However, limited attention has been paid to the fact that at least four of the five primary Philistine cities—Ashkelon, Ashdod, Gath, and Ekron—have Semitic names. Four of these five toponyms are known from the Bronze Age historical sources (such as the documents from Ugarit and the Amarna tablets and other Egyptian records), while the fifth (Ekron) is mentioned in Iron Age documents. This paper examines the influence of various factors (e.g., migration, conquest, exile, colonial and imperial rule) on the naming of sites settled by immigrants from other periods and cultures. The results of this examination are then applied to the existing theories regarding the settlement of the Philistines, in order to investigate the choice of location of their cities and the reason for adoption of existing toponyms by the immigrants.
The efficacy of relational governance and value-creating relational investments ( VcRIs ) in revenue-enhancement in downstream networks

A conceptual model is presented which integrates and extends insights from relational exchange theory (RET) and value exchange model (VEM) to discuss the efficacy of relational governance and valuecreating relational investments (VcRIs) to affect certain revenue-enhancing (relational) behaviours (ReBs). It is postulated that value-creating relational investments (VcRIs) made in a highly relational environment successful enough to engender high relationship quality (manifested through total partner satisfaction and inter-organizational trust) result in higher interorganizational commitment. This commitment ultimately translates into superior performance of the focal firm since partners exhibit revenue-enhancing behaviours (ReBs) like longevity of relationship, increased business share, positive word-of-mouth and reduced partial defection. It is further argued that the dynamics of model may vary across different phases of relationship life cycle (RLC) and are moderated by the nodes’ relational polygamy.