gebhart/patrepeval huggingface dataset:
The FbaB-type fibronectin-binding protein of Streptococcus pyogenes promotes specific invasion into endothelial cells (2011)

Invasive serotype M3 Streptococcus pyogenes are among the most frequently isolated organisms from patients suffering from invasive streptococcal disease and have the potential to invade primary human endothelial cells (EC) via a rapid and efficient mechanism. FbaB protein, the fibronectin-binding protein expressed by M3 S. pyogenes, was herein identified as a potent invasin for EC. By combining heterologous gene expression with allelic replacement, we demonstrate that FbaB is essential and sufficient to trigger EC invasion via a Rac1-dependent phagocytosis-like uptake. FbaB-mediated uptake follows the classical endocytic pathway with lysosomal destination. FbaB is demonstrated to be a streptococcal invasin exhibiting EC tropism. FbaB thus initiates a process that may contribute to the deep tissue tropism and spread of invasive S. pyogenes isolates into the vascular EC lining.
Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents (1999)

The effect of alkyltrimethylammonium ions on the thermostability of natural and modified DNA duplexes has been investigated. We have shown that the use of tetramethylammonium ions TMA+along with the chemical modification of duplexes allow the fine adjustment of T m and the possibility of obtaining several duplex systems with varied isostabilizedtemperatures, some of which show greater stability than those of natural DNA. This approach could be very useful for DNA sequencing by hybridization.
Efficacy of liposomal curcumin in a human pancreatic tumor xenograft model: inhibition of tumor growth and angiogenesis. (2013)

These data clearly establish the efficacy of liposomal curcumin in reducing human pancreatic cancer growth in the examined model. The therapeutic curcumin-based effects, with no limiting side-effects, suggest that liposomal curcumin may be beneficial in patients with pancreatic cancer.
Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA (2011)

Hemophilia is a bleeding disorder with X-linked inheritance. Current prenatal diagnostic methods for hemophilia are invasive and pose a risk to the fetus. Cell-free fetal DNA analysis in maternal plasma provides a noninvasive mean of assessing fetal sex in such pregnancies. However, the disease status of male fetuses remains unknown if mutation-specific confirmatory analysis is not performed. Here we have developed a noninvasive test to diagnose whether the fetus has inherited a causative mutation for hemophilia from its mother. The strategy is based on a relative mutation dosage approach, which we have previously established for determining the mutational status of fetuses for autosomal disease mutations. In this study, the relative mutation dosage method is used to deduce whether a fetus has inherited a hemophilia mutation on chromosome X by detecting whether the concentration of the mutant or wild-type allele is overrepresented in the plasma of heterozygous women carrying male fetuses. We correctly detected fetal genotypes for hemophilia mutations in all of the 12 studied maternal plasma samples obtained from at-risk pregnancies from as early as the 11th week of gestation. This development would make the decision to undertake prenatal testing less traumatic and safer for at-risk families.
An approach to data visualization and interpretation for sensor networks (2004)

With the increase in applications for sensor networks, data manipulation and representation have become a crucial component of sensor networks. This paper explores an approach to process and interpret the data gathered by sensor networks. We have built sensor networks which consist of a series of sensor and communication units ("pods") deployed to monitor rare plants or other endangered species. The environmental data, such as temperature, rainfall, and sunlight, around the plants are sent by the wireless sensor networks to a base station which is able to access the Internet. The approach presented in this paper combines database management technology, geographic information system and Web development technology to visualize the data gathered by the wireless sensor networks. The resulting maps created by a GIS system, GRASS, connect the environmental data with the pods' geographic positions obtained from GPS (the global positioning system). Voronoi diagrams are used to partition the map into areas holding different weather attributes based on the data collected by the pods. The Web development technology /sub y/namic Web programming - is also adopted in this system to make the data available via the Internet. Finally, we sketch the design of an asynchronous collaborative discussion environment which supports online communities among the end users of our information interpretation system. The integration of our data visualization tools and the online collaborative discussion environment makes the system useful to different communities of potential users.
Statistical Post-Editing for a Statistical MT System (2011)

Statistical post-editing (SPE) techniques have been successfully applied to the output of Rule Based MT (RBMT) systems. In this paper we investigate the impact of SPE on a standard Phrase-Based Statistical Machine Translation (PB-SMT) system, using PB-SMT both for the first-stage MT and the second stage SPE system. Our results show that, while a naive approach to using SPE in a PB-SMT pipeline produces no or only modest improvements, a novel combination of source context modelling and thresholding can produce statistically significant improvements of 2 BLEU points over baseline using technical translation data for French to English. 1
Fracture Toughness of Dental Porcelains Evaluated by IF, SCF, and SEPB Methods (2005)

Fracture toughness of six dental porcelains with leucite content ranging from 0 to 22 vol% was evaluated by indentation fracture (IF), surface crack in flexure (SCF), and single edge pre‐cracked beam (SEPB) methods. The results of the IF method were similar to those of the SCF method for all the porcelains investigated. The results of the SEPB were similar to those of the other two methods only for the glassy porcelains, but for leucite‐based porcelains this method resulted in higher values of K I c . Based on microstructure, fractographic analysis, and an additional single edge V‐notched beam test, it was concluded that the pre‐crack size influences the value of K I c for porcelains reinforced by leucite. For design and failure analysis purposes, the K I c determined by SCF method should be preferred, since fracture of dental restorations usually starts from small surface cracks.
Spherulin skin testing and histoplasmal and coccidioidal serology: lack of effect. (1977)

This study demonstrated that the administration of a spherulin skin test to subjects whose skin-test reactions were either positive or negative, at the dose used (Usual Test Strength), did not elicit an antibody response to antigens of Coccidioides immitis or Histoplasma capsulatum, as determined by standard serologic methods. Of 32 subjects, one developed a seroconversion by the latex agglutination test. The data suggested that spherulin can be used clinically as a diagnostic reagent without affecting the serologic reactions, which are of both prognostic and diagnostic value.
Ferric Dicitrate Transport System (Fec) of Shigella flexneri 2a YSH6000 Is Encoded on a Novel Pathogenicity Island Carrying Multiple Antibiotic Resistance Genes (2001)

Iron uptake systems which are critical for bacterial survival and which may play important roles in bacterial virulence are often carried on mobile elements, such as plasmids and pathogenicity islands (PAIs). In the present study, we identified and characterized a ferric dicitrate uptake system (Fec) in Shigella flexneri serotype 2a that is encoded by a novel PAI termed the Shigella resistance locus (SRL) PAI. The fec genes are transcribed in S. flexneri, and complementation of a fec deletion in Escherichia coli demonstrated that they are functional. However, insertional inactivation of fecI, leading to a loss in fec gene expression, did not impair the growth of the parent strain of S. flexneri in iron-limited culture media, suggesting that S. flexneri carries additional iron uptake systems capable of compensating for the loss of Fec-mediated iron uptake. DNA sequence analysis showed that the fec genes are linked to a cluster of multiple antibiotic resistance determinants, designated the SRL, on the chromosome of S. flexneri 2a. Both the SRL and fec loci are carried on the 66,257-bp SRL PAI, which has integrated into the serX tRNA gene and which carries at least 22 prophage-related open reading frames, including one for a P4-like integrase. This is the first example of a PAI that carries genes encoding antibiotic resistance and the first report of a ferric dicitrate uptake system in Shigella.
Three-dimensional Nanohydroxyapatite/Chitosan Scaffolds as Potential Tissue Engineered Periodontal Tissue (2007)

The development of suitable three-dimensional scaffold for the maintenance of cellular viability and differentiation is critical for applications in periodontal tissue engineering. In this work, different ratios of porous nanohydroxyapatite/chitosan (HA/chitosan) scaffolds are prepared through a freeze-drying process. These scaffolds are evaluated in vitro by the analysis of microscopic structure, porosity, and cytocompatibility. The expression of type I collagen and alkaline phosphatase (ALP) activity are detected with real-time polymerase chain reaction (RT-PCR). Human periodontal ligament cells (HPLCs) transfected with enhanced green fluorescence protein (EGFP) are seeded onto the scaffolds, and then these scaffolds are implanted subcutaneously into athymic mice. The results indicated that the porosity and pore diameter of the HA/chitosan scaffolds are lower than those of pure chitosan scaffold. The HA/chitosan scaffold containing 1% HA exhibited better cytocompatibility than the pure chitosan scaffold. The expression of type I collagen and ALP are up-regulated in 1% HA/chitosan scaffold. After implanted in vivo, EGFP-transfected HPLCs not only proliferate but also recruit surrounding tissue to grow in the scaffold. The degradation of the scaffold significantly decreased in the presence of HA. This study demonstrated the potential of HA/ chitosan scaffold as a good substrate candidate in periodontal tissue engineering.
Nucleotide sequence of tobacco mosaic virus RNA. (1982)

Oligonucleotide primers have been used to generate a cDNA library covering the entire tobacco mosaic virus (TMV) RNA sequence. Analysis of these clones has enabled us to complete the viral RNA sequence and to study its variability within a viral population. The positive strand coding sequence starts 69 nucleotides from the 5' end with a reading frame for a protein of Mr 125,941 and terminates with UAG. Readthrough of this terminator would give rise to a protein of Mr 183,253. Overlapping the terminal five codons of this readthrough reading frame is a second reading frame coding for a protein of Mr 29,987. This gene terminates two nucleotides before the initiator codon of the coat protein gene. Potential signal sequences responsible for the capping and synthesis of the coat protein and Mr 29,987 protein mRNAs have been identified. Similar sequences within these reading frames may be used in the expression of sets of proteins that share COOH-terminal sequences.
[Immunosuppression--a tightrope walk between iatrogenic harm and therapy]. (1996)

The therapeutic effect of most immunosuppressive agents is unspecific and therefore often limited by an increased risk of infection by viral, bacterial or fungal organisms as well as by an increased incidence of malignant neoplasms. This short review includes the most commonly used immunosuppressants such as corticosteroids, azathioprine, methotrexate, cyclophosphamide and cyclosporine. The most common risks of long-term corticosteroid treatment are Cushing-like changes, decreased glucose tolerance and the usually benign steroid diabetes. Also clinically important is osteoporosis, since it can be prevented by physical training, calcium supplementation and treatment with vitamin D if necessary. Although there is still no proof of a significantly increased risk of peptic ulcer during steroid therapy, patients may develop gastrointestinal hemorrhage and even perforation without producing pain while being treated with corticosteroids. Mineralocorticoid effects, such as salt and water retention, are seen only with hydrocortisone and prednisone, whereas with synthetic steroids such as dexamethasone, sodium retention is absent despite their strong antiphlogistic activity. The most important side effect of the cytotoxic agents azathioprine, methotrexate and cyclophosphamide is marrow suppression. Due to the high turnover of neutrophils, patients most frequently suffer neutropenia rather than thrombocytopenia or anemia. Neutropenia, as well as impaired humoral and cellular immune mechanisms, are responsible for increased susceptibility to bacterial, viral or parasitic diseases during immunosuppressive therapy. Hepatotoxicity has been reported among patients receiving azathioprine (cholestatic hepatitis) and methotrexate (elevated AST levels and, rarely, liver fibrosis or cirrhosis). Cyclophosphamide causes hemorrhagic cystitis in a substantial proportion of patients, as well as an increased incidence of urothelial neoplasms. Both these side effects may be prevented by Mesna. The most important side effects of cyclosporine are acute and chronic nephrotoxicity usually associated with significantly elevated plasma levels of the drug. It must be borne in mind that severe nephrotoxicity may occur in patients receiving cyclosporine and ketoconazole together, since the latter may inappropriately increase the plasma cyclosporine level.
Quantitative analysis of floating point arithmetic on FPGA based custom computing machines (2002)

Many algorithms rely on floating point arithmetic for the dynamic range of representations and require millions of calculations per second. Such computationally intensive algorithms are candidates for acceleration using custom computing machines (CCMs) being tailored for the application. Unfortunately, floating point operators require excessive area (or time) for conventional implementations. Instead, custom formats, derived for individual applications, are feasible on CCMs, and can be implemented on a fraction of a single FPGA. Using higher-level languages, like VHDL, facilitates the development of custom operators without significantly impacting operator performance or area. Properties, including area consumption and speed of working arithmetic operator units used in real-time applications, are discussed.
Smart patches: self-monitoring composite patches for the repair of aircraft (2004)

Conventional aircraft repair techniques employ bolted or riveted metallic reinforcements, which frequently introduce additional stress concentrations leading to further cracking and creating areas difficult or impossible to inspect. Bonded composite repairs (“patches”) result in the elimination of stress concentrations caused by additional fastener holes, improved strength to weight ratio and present a sealed interface. This reduces even further the danger of corrosion and fretting under the repair, gives greater flexibility in design and lessens application time while lengthening fatigue life. Embedding optical fibres and sensors into the patch, and combining this with advanced data collection and processing systems, creating a so-called “smart patch”, will enable the real-time assessment of aircraft structural integrity resulting in reliable prediction of maintenance requirements for repaired structures. This paper describes the current state of the art in smart patch technology, and includes a detailed description of the measurement problem and of the work being undertaken to solve it, at both the component and system level. An analysis of typical crack behaviour, based on FE modelling is presented and this demonstrates the need for optical strain sensors having a very short gauge length. The paper discusses the advantages and limitations of very short Fibre Bragg Gratings (FBGs) in this context and also provides early experimental data from 1mm and 2mm gratings which have been fabricated for this purpose. The paper also describes the impact of the measurement and environmental constraints on the design of the FBG interrogation system and presents the results of initial trials. The work is being undertaken in the framework of a collaborative project (ACIDS) which is co-funded by the European Commission.
Phenylbutyrate up-regulates the adrenoleukodystrophy-related gene as a nonclassical peroxisome proliferator (2005)

X-linked adrenoleukodystrophy (X-ALD) is a demyelinating disease due to mutations in the ABCD1 (ALD) gene, encoding a peroxisomal ATP-binding cassette transporter (ALDP). Overexpression of adrenoleukodystrophy-related protein, an ALDP homologue encoded by the ABCD2 (adrenoleukodystrophy-related) gene, can compensate for ALDP deficiency. 4-Phenylbutyrate (PBA) has been shown to induce both ABCD2 expression and peroxisome proliferation in human fibroblasts. We show that peroxisome proliferation with unusual shapes and clusters occurred in liver of PBA-treated rodents in a PPARalpha-independent way. PBA activated Abcd2 in cultured glial cells, making PBA a candidate drug for therapy of X-ALD. The Abcd2 induction observed was partially PPARalpha independent in hepatocytes and totally independent in fibroblasts. We demonstrate that a GC box and a CCAAT box of the Abcd2 promoter are the key elements of the PBA-dependent Abcd2 induction, histone deacetylase (HDAC)1 being recruited by the GC box. Thus, PBA is a nonclassical peroxisome proliferator inducing pleiotropic effects, including effects at the peroxisomal level mainly through HDAC inhibition.
Functional roles of DTX3L and ARTD9 in prostate cancer (2014)

Prostate cancer (PCa) is one of the leading causes of cancer related mortality and morbidity in the aging male population. The B-lymphoma and BAL-associated protein (BBAP) and Deltex (DTX)-3-like E3 ubiquitin ligase (DTX3L), was originally identified as a binding partner of the B-aggressive lymphoma-1 protein and diphtheria-toxin-like ADP-ribosyltransferase-9 (BAL1/ARTD9). Here it is shown, that DTX3L and ARTD9 are both overexpressed in PCa cells. Together with ARTD8 (ADP-ribosyltransferase-8) they mediate proliferation, survival and chemo-resistance of PCa cells. The effects of DTX3L and ARTD9 are dependent on the signal transducer and activator of transcription factor 1 (STAT-1). STAT-1 is known as a tumor suppressor, activated by interferon γ (IFNγ). Its antitumor effects are mainly based on the activation of the transcription of the interferon responding factor 1 (IRF1). New reports showed that a constitutively activated STAT-1 leads to an IFNγ- and chemo-resistance of tumors and acts as an oncogene. Such a situation occurred also in the analyzed PCa cells. The presented study shows that DTX3L and ARTD9 repress the expression of IRF1. DTX3L also mediates migration of PCa cells in a STAT-1 and STAT-3-dependent manner. However, migration is not dependent on IFNy/IRF1. Together, this study suggests that the combined inhibition of STAT-1, ARTD8, ARTD9 and/or DTX3L could increase the efficacy of chemotherapy or radiation treatment in prostate cancer
Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of "conjugal" transfer in the absence of a conjugative plasmid. (1981)

Streptococcus faecalis strain DS16 harbors the conjugative hemolysin-bacteriocin plasmid pAD1 (35 megadaltons) and the nonconjugative R-plasmid pAD2 determining resistance to streptomycin, kanamycin, and erythromycin; a tetracycline resistance (Tetr) determinant is located on the chromosome. When strain DS16 was mated (on membrane filters) with the plasmid-free strain JH2-2, Tetr transconjugants could be obtained at a frequency of about 10(-6) per recipient. Analyses of transconjugants showed that some contained the Tetr determinant linked to pAD1. Subsequent studies showed that the Tetr determinant was located on a 10-megaldalton transposon, designated Tn916, which could insert into two hemolysin plasmids: pAM gamma 1 and pOB1. In addition, derivatives of DS16 devoid of pAD1 were capable of transferring Tetr to recipient strains. Transconjugants (plasmid-free) from such matings could subsequently act as donors in the transfer of Tetr. Both transposition and transfer were found to be rec independent.
Estimation of environment forces and rigid-body velocities using observers (2002)

This paper presents an observer-based approach to the determination of environment forces acting on a rigid body. Actuation forces, measured positions and orientations and identification of inertial parameters are used for this purpose. It is also shown that environment force estimates can be used in turn to correct rigid-body velocity estimates generated by observers, leading to accurate, low-noise estimates during contact tasks. The approach, shown to also apply to general serial mechanisms, is supported by experimental data obtained with a magnetically levitated wrist.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Activation and Regulation of Toll-like Receptor 9: CpGs and Beyond (2008)

Toll-like receptor 9 has been the focus of considerable research attention for the ability to modulate its activity, and subsequent innate immune responses, through DNA-based immunotherapeutics. Nucleic acids are attractive as therapeutics for their low cost, chemical stability and ease of production. While the ability for TLR9 to be differentially regulated by nucleic acids of varying sequences and structures offers flexibility for immunotherapeutic design, it also necessitates a more comprehensive characterization of these agonists in terms of how these structural parameters correlate with the activation of unique cellular responses. Despite the utilization of TLR9 agonists in human trials these issues have not been adequately addressed. While a wealth of cell stimulation experiments demonstrate the preferential ability for nucleic acids which contain unmethylated cytosine-phosphate-guanine (CpG) motifs to initiate innate immune responses this has not been supported by binding investigations from which largely contradictory information has emerged with respect to the ability of TLR9 to bind nucleic acids in a sequence-dependent fashion. Recent models help to reconcile this apparent contradiction by suggesting that while TLR9 activation is specific for CpG-containing nucleic acids, the receptor binds, and is functionally influenced by, nucleic acids in a sequence-independent fashion. We have proposed a model in which the absolute concentration of nucleic acids modulates the sensitivity of the receptor in a sequence-dependent fashion while activation is specifically achieved by CpG-containing ligands. In this review we reconsider the literature from the perspective of this new appreciation of the functional complexity of TLR9 ligand binding and higher-order regulation with discussion of the implications for immunotherapeutic targeting of TLR9.