gebhart/patrepeval huggingface dataset:
Functional Genomic, Biochemical, and Genetic Characterization of the Salmonella pduO Gene, an ATP:Cob(I)alamin Adenosyltransferase Gene (2001)

Salmonella enterica degrades 1,2-propanediol by a pathway dependent on coenzyme B12 (adenosylcobalamin [AdoCb1]). Previous studies showed that 1,2-propanediol utilization (pdu) genes include those for the conversion of inactive cobalamins, such as vitamin B12, to AdoCbl. However, the specific genes involved were not identified. Here we show that the pduO gene encodes a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is apparently the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation. Genetic tests showed that the function of the pduO gene was partially replaced by the cobA gene (a known ATP:corrinoid adenosyltransferase) but that optimal growth of S. enterica on 1,2-propanediol required a functional pduO gene. Growth studies showed that cobA pduO double mutants were unable to grow on 1,2-propanediol minimal medium supplemented with vitamin B(12) but were capable of growth on similar medium supplemented with AdoCbl. The pduO gene was cloned into a T7 expression vector. The PduO protein was overexpressed, partially purified, and, using an improved assay procedure, shown to have cob(I)alamin adenosyltransferase activity. Analysis of the genomic context of genes encoding PduO and related proteins indicated that particular adenosyltransferases tend to be specialized for particular AdoCbl-dependent enzymes or for the de novo synthesis of AdoCbl. Such analyses also indicated that PduO is a bifunctional enzyme. The possibility that genes of unknown function proximal to adenosyltransferase homologues represent previously unidentified AdoCbl-dependent enzymes is discussed.
Improvements in RWTH's System for Off-Line Handwriting Recognition (2013)

In this paper we describe a novel HMM-based system for off-line handwriting recognition. We adapt successful techniques from the domains of large vocabulary speech recognition and image object recognition: moment-based image normalization, writer adaptation, discriminative feature extraction and training, and open-vocabulary recognition. We evaluate those methods and examine their cumulative effect on the recognition performance. The final system outperforms current state-of-the-art approaches on two standard evaluation corpora for English and French handwriting.
Estrogen receptor mutagenesis and hormone resistance (1994)

The authors have detected a truncated receptor that is lacking the majority of the hormone-binding domain because of the deletion of exon 5. This variant acts as a dominant-positive receptor in the absence of hormones. The exon 5 estrogen receptor (ER) variant, although originally identified in ER-negative, progesterone receptor-positive tumors, now has been found to be coexpressed at variable levels with the wild-type receptor in a large number of ER-positive tumors. Therefore, to establish the significance of its coexpression with the wild-type receptor, the authors transfected the variant into ER-positive MCF-7 cells. MCF-7 transfected cells that now express equivalent levels of the variant as compared with the wild-type receptor are resistant to the growth-inhibitory effects of tamoxifen. The authors hypothesize that the exon 5 ER deletion variant may be involved in clinical tamoxifen resistance and hormone independence.
Repair Optimal Erasure Codes Through Hadamard Designs (2013)

<?Pub Dtl=""?> In distributed storage systems that employ erasure coding, the issue of minimizing the total communication required to exactly rebuild a storage node after a failure arises. This repair bandwidth depends on the structure of the storage code and the repair strategies used to restore the lost data. Designing high-rate maximum-distance separable (MDS) codes that achieve the optimum repair communication has been a well-known open problem. Our work resolves, in part, this open problem. In this study, we use Hadamard matrices to construct the first explicit two-parity MDS storage code with optimal repair properties for all single node failures, including the parities. Our construction relies on a novel method of achieving perfect interference alignment over finite fields with a finite number of symbol extensions. We generalize this construction to design <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$m$</tex></formula> -parity MDS codes that achieve the optimum repair communication for single systematic node failures.
Functional properties of an endothelial cell cofactor for thrombin-catalyzed activation of protein C. (1981)

Thrombin-catalyzed activation of Protein C is accelerated by a human endothelial cell surface cofactor. The cofactor occurs also on mouse hemangioma cells (a transformed endothelial cell line), but not on cultured human smooth muscle cells or fibroblasts. The cofactor remains bound to the cell surface during Protein C activation. The cofactor is saturable with respect to both Protein C (Km = 0.72 +/- 0.07 microM) and thrombin (Km = 0.48 +/- 0.05 nM). Diisopropylphosphoryl-thrombin is a competitive inhibitor of the cofactor-dependent reaction with Ki = 0.56 +/- 0.1 nM. Prothrombin Fragment 1, the peptide derived from prothrombin that retains phospholipid binding capacity, does not inhibit activation of Protein C when present in a 7:1 molar excess over Protein C. Platelet Factor 4 (20 microgram/ml) also fails to inhibit Protein C activation. It is concluded that the endothelial cell provides a surface on which Protein C can be activated under physiological conditions.
Line-level incremental resynthesis techniques for FPGAs (2011)

FPGA logic density is roughly doubling at every process generation. Consequently, it is becoming increasingly challenging for FPGA CAD tools to keep up with the growing complexities of high-speed designs while keeping CAD run-times reasonable. In this paper, we present a novel incremental resynthesis tool called Line-Level Incremental reSynthesis (LLIS), integrated within an industrial tool suite, that addresses the problems of timing closure as well as CAD runtime (patent pending). We describe a general framework that can incrementally reuse results from a previous compile based on automatic differencing of HDL changes. We show that it is possible to reduce synthesis runtime by 6.5x for common HDL changes. As compared with complete resynthesis, we preserve known good timing solutions more than 82% of the time. This represents a 3X improvement vs. non-incremental techniques.
Doping superlattices ("n-i-p-i crystals") (1986)

Semiconductors with doing superlattices exhibit a number of unique features by which they differ from uniform bulk crystals as well as from semiconductors with a compositional superlattice. The properties which make them particularly appealing as a new kind of semiconductor are tunability of carrier concentration, bandgap, two-dimensional subband structure, and recombination lifetimes, in combination with an enormous flexibility in tailoring. Moreover, the choice of host materials is not restricted by interface- or lattice-matching problems. The possibility of varying conductivity, absorption coefficient, optical gain, and luminescence spectra by light or external electrical potentials implies new concepts for photodetectors, tunable light sources, optical amplifiers, and modulators. The long recombination lifetimes result in large low-power nonlinearities of the optical absorption coefficient and the refractive index. These properties offer applications for saturable absorbers and bistable optical devices. In this paper the basic concept of doping superlattices and experiments which have provided its verification will be reviewed first. New physical phenomena and possible device applications will then be discussed. Finally, we will report some recent results of extensions of the concept to "hetero n-i-p-i's," obtained by periodic modulation of composition superimposed on the periodic n-i-p-i doping profile.
The Nonamer UUAUUUAUU Is the Key AU-Rich Sequence Motif That Mediates mRNA Degradation (1995)

Labile mRNAs that encode cytokine and immediate-early gene products often contain AU-rich sequences within their 3' untranslated region (UTR). These AU-rich sequences appear to be key determinants of the short half-lives of these mRNAs, although the sequence features of these elements and the mechanism by which they target mRNAs for rapid decay have not been fully defined. We have examined the features of AU-rich elements (AREs) that are crucial for their function as determinants of mRNA instability in mammalian cells by testing the ability of various mutant c-fos AREs and synthetic AREs to direct rapid mRNA deadenylation and decay when inserted within the 3' UTR of the normally stable beta-globin mRNA. Evidence is presented that the pentamer AUUUA, which previously was suggested to be the minimal determinant of instability present in mammalian AREs, cannot direct rapid mRNA deadenylation and decay. Instead, the nonomer UUAUUUAUU is the elemental AU-rich sequence motif that destabilizes mRNA. Removal of one uridine residue from either end of the nonamer (UUAUUUAU or UAUUUAUU) results in a decrease of potency of the element, while removal of a uridine residue from both ends of the nonamer (UAUUUAU) eliminates detectable destabilizing activity. The inclusion of an additional uridine residue at both ends of the nonamer (UUUAUUUAUUU) does not further increase the efficacy of the element. Taken together, these findings suggest that the nonamer UUAUUUAUU is the minimal AU-rich motif that effectively destabilizes mRNA. Additional ARE potency is achieved by combining multiple copies of this nonamer in a single mRNA 3' UTR. Furthermore, analysis of poly(A) shortening rates for ARE-containing mRNAs reveals that the UUAUUUAUU sequence also accelerates mRNA deadenylation and suggests that the UUAUUUAUU motif targets mRNA for rapid deadenylation as an early step in the mRNA decay process.
Functional consequences of dysregulated B7-1 (CD80) and B7-2 (CD86) expression in B or T lymphocytes of transgenic mice (1997)

T cell activation and tolerance are regulated by interactions between CD28 or CTLA-4 on T cells and B7 costimulatory molecules on APCs. We have generated transgenic mouse strains that constitutively express B7-1 (CD80) at high levels on B cells or T cells or express B7-2 (CD86) on T lymphocytes to examine the consequences of dysregulated B7 expression on T cell responses. The transgene-derived B7 molecules are functional, because B7-1 transgenic B cells are more efficient APCs than are wild-type B cells, and the activation of B7 transgenic T cells is less dependent on exogenous costimulation than that of wild-type T cells. In vivo, constitutive expression of B7 molecules leads to the elimination of immature B cells. The expression of B7 molecules on thymocytes results in the down-regulation of CD28 expression. However, B7 transgenic mice have normal numbers of mature lymphocytes and mount normal T cell responses following immunization with protein Ag. Neither anergy induction nor superantigen-mediated deletion of T cells is altered by the dysregulated expression of B7-1 or B7-2 on B or T lymphocytes in these transgenic strains. Therefore, functionally significant levels of B7 expressed constitutively on mature lymphocytes are not, by themselves, sufficient to abrogate T cell tolerance or induce autoimmune disease.
Evaluation of a Series of Naphthamides as Potent, Orally Active Vascular Endothelial Growth Factor Receptor-2 Tyrosine Kinase Inhibitors (2008)

We have previously shown N-arylnaphthamides can be potent inhibitors of vascular endothelial growth factor receptors (VEGFRs). N-Alkyl and N-unsubstituted naphthamides were prepared and found to yield nanomolar inhibitors of VEGFR-2 (KDR) with an improved selectivity profile against a panel of tyrosine and serine/threonine kinases. The inhibitory activity of this series was retained at the cellular level. Naphthamides 3, 20, and 22 exhibited good pharmacokinetics following oral dosing and showed potent inhibition of VEGF-induced angiogenesis in the rat corneal model. Once-daily oral administration of 22 for 14 days led to 85% inhibition of established HT29 colon cancer and Calu-6 lung cancer xenografts at doses of 10 and 20 mg/kg, respectively.
Expression of vascular permeability factor (vascular endothelial growth factor) and its receptors in adenocarcinomas of the gastrointestinal tract. (1993)

Vascular permeability factor (VPF) is one of the most potent known inducers of microvascular hyperpermeability; in addition, it is a selective endothelial cell growth factor, hence its alternate name, vascular endothelial growth factor. VPF exerts its actions on the microvasculature by interacting with specific endothelial cell receptors. VPF is expressed by many transplantable animal tumors, by tumor cell lines in culture, and by certain normal cells in situ. The purpose of the present investigation was to determine whether and with what consistency VPF and its endothelial cell receptors are expressed in primary autochthonous human tumor of gastrointestinal tract origin, as determined by in situ hybridization and immunohistochemistry. Twenty-one primary adenocarcinomas (17 colon, 2 stomach, 1 small bowel, and 1 pancreas) were studied. The malignant epithelial cells expressed VPF mRNA strongly, in contrast to normal epithelium, hyperplastic polyps, and adenomas, which expressed little or no VPF mRNA. VPF expression was further increased in tumor cells immediately adjacent to zones of tumor necrosis; in such areas, occasional stromal cells also expressed VPF mRNA. In the ten colon carcinomas studied, tumor cells stained for VPF protein by immunohistochemistry. The endothelial cells of nearby stromal blood vessels also stained for VPF by immunohistochemistry and in addition expressed mRNAs encoding the VPF receptors flt-1 and kdr as determined by in situ hybridization. Endothelial cells away from the tumor did not stain for VPF and no definite mRNA expression for flt-1 or kdr was detected by in situ hybridization. The ganglion cells of the myenteric plexus of normal bowel expressed VPF mRNA and protein. These data indicate that primary autochthonous human tumors of gastrointestinal origin regularly express both VPF mRNA and VPF protein and that adjacent stromal vessels express mRNAs for both known VPF receptors. VPF is likely to contribute to tumor growth by promoting angiogenesis and stroma formation, both directly, through its action as an endothelial cell growth factor, and indirectly, by increasing vascular permeability, thereby leading to plasma protein extravasation, fibrin deposition, and the eventual replacement of the resulting matrix with vascularized stroma.
Mutational Spectra of PTEN/MMAC1 Gene: a Tumor Suppressor With Lipid Phosphatase Activity (1999)

PTEN/MMAC1 (phosphatase, tensin homologue/mutated in multiple advanced cancers) is a tumor suppressor protein that has sequence homology with dual-specificity phosphatases, which are capable of dephosphorylating both tyrosine phosphate and serine/threonine phosphate residues on proteins. The in vivo function of PTEN/MMAC1 appears to be dephosphorylation of phosphotidylinositol 3,4, 5-triphosphate. The PTEN/MMAC1 gene is mutated in the germline of patients with rare autosomal dominant cancer syndromes and in subsets of specific cancers. Here we review the mutational spectra of the PTEN/MMAC1 gene in tumors from various tissues, especially endometrium, brain, prostate, and ovary, in which the gene is inactivated very frequently. Germline and somatic mutations in the PTEN/MMAC1 gene occur mostly in the protein coding region and involve the phosphatase domain and poly(A)(6) stretches. Compared with germline alterations found in the PTEN/MMAC1 gene, there is a substantially increased frequency of frameshift mutations in tumors. Glioblastomas and endometrial carcinomas appear to have distinct mutational spectra, probably reflecting differences in the underlying mechanisms of inactivation of the PTEN/MMAC1 gene in the two tissue types. Also, depending on the tissue type, the gene appears to be involved in the initiation or the progression of cancers. Further understanding of PTEN/MMAC1 gene mutations in different tumors and the physiologic consequences of these mutations is likely to open up new therapeutic opportunities for targeting this critical gene.
Some new results in hybrid acousto-optic processing (2003)

A fully programmable hybrid acousto-optic convolving processor has been designed for transversal and recursive filtering applications. This system is used for specific signal processing tasks. Its performance (computing time, available precision, noise limitations) is characterized for each task. The main results are reported, with emphasis on transformations pertaining to the image processing field (bidimensional convolution, gradient and Laplacian operators, discrete Fourier transform, discrete cosine transform). Future applications are discussed, including the implementation of algorithms of the JPEG and MPEG classes and work toward the design of hybrid acousto-optic neural networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Topical delivery of nucleic acids in the skin (2001)

The skin is an attractive site for the delivery of nucleic acid-based drugs for the treatment of topical and/or systemic diseases as well as for DNA immunization. However, due to the barrier properties of the skin, the penetration of nucleic acids in or across the skin is limited. This review focuses on the chemical, biological or physical methods developed to enhance nucleic acid delivery into the skin. Oligonucleotides have been delivered across the skin using iontophoresis. Potentially therapeutic concentrations were reached in hair follicles using liposomes and in keratinocytes using electroporation. In vivo transfer of genetic material to the skin has been achieved experimentally using dermal injection, topical application of naked DNA, DNA/lipids complexes or viral vectors as well as particle bombardment, puncturing or electroporation of plasmid DNA. Protein expression has been detected in the skin and/or the serum. The localization and duration of expression was affected by the delivery methods. The remaining challenges to address for optimal in vivo gene delivery in the skin are i) duration of expression (more than 1 to 4 weeks for the treatment of inherited skin and systemic diseases requesting protein supplementation), ii) delivery methods (if progress has been achieved, a safe, efficient, patient-friendly, non-invasive method for long-term expression at a high level in the target cells and extensive body area of a patient has not yet been developed), iii) targeted delivery.
FRACTIONAL AND STRUCTURAL CHARACTERIZATION OF ALKALINE LIGNINS FROM CAREX MEYERIANA KUNTH (2012)

Successive extractions with distilled water, 0.25% NaOH-95% ethanol solution, 0.5%, 1%, 1.5% and 2% NaOH aqueous solutions at a solid-liquid ratio of 1:25 (g mL -1 ) at 80 °C for 3 h from Carex meyeriana Kunth released 4.4%, 6.9%, 10.9%, 13.2%, 7.9% and 4.9% of the original lignin, respectively. The physico-chemical properties and structural features of these lignin fractions were comprehensively characterized by HPLC, GPC, NMR spectroscopy, and TGA. The alkali concentration increment had a positive influence on the purity of the lignin fractions, but a negative influence on the average molecular weight and thermal stability. The FT-IR spectra showed that the lignin fractions had similar structural features with those of HGS lignin. The 1 H, 13 C and 2D NMR spectra illustrated that typical lignin fractions had predominantly β-O-4 aryl ether linkages followed by β-β and β-5’ ones.
Large scale validation of an efficient CRISPR/Cas-based multi gene editing protocol in Escherichia coli (2017)

This work defines for the first time the robustness of a CRISPR/Cas9-based protocol based on a large sample size. Since the technical solutions here proposed can be applied to other similar procedures, the data could be of general interest for the scientific community working on bacterial genome editing and, in particular, for those involved in synthetic biology projects requiring high throughput procedures.
Role of FcγRIIa (CD32) in IgG anti‐RhD‐mediated red cell phagocytosis in vitro (1996)

To test the role of Fc gamma RIIa in IgG anti-RhD-mediated phagocytosis three IgG1 and two IgG3 human monoclonal anti-D antibodies were tested for ability to mediate binding/phagocytosis of cDE/cde and -D-/-D- red cells by Fc gamma RIIa-R131 and Fc gamma RIIa-H131 cDNA-transfected 3T6 fibroblasts. Both IgG3 monoclonal antibodies brought about -D-/-D- cell interaction with IIa-transfected fibroblasts, while only one of them, Og3, mediated binding of cDE/cde targets. Although Fc gamma RIIa expression was three times greater on IIa-R131 than on IIa-H131 fibroblasts, the latter bound significantly more Og3-coated cDE/cde- and IgG3 anti-D-sensitized -D-/-D- cells, respectively, than the former effectors and showed some phagocytosis of the -D-/-D- targets. IgG1 anti-D antibodies were inactive in mediating red cell interaction with the fibroblasts. Moreover, monoclonal anti-Fc gamma RII IV.3 partially inhibited the phagocytosis by adult or fetal monocytes of Og3-sensitized cDE/cde cells. Fc gamma RIIa-H/H131 monocytes exhibited higher phagocytic indices towards these targets than monocytes of other IIa allotypes. The results indicate that Fc gamma RIIa can participate in the phagocytosis of red cells coated with IgG3 anti-D; in this case the allotype of the receptor will modify the extent of red cell destruction.
Cardinal sins : fleet management (2016)

Shadab Azeem Rahil explains the intricacies and shortfalls of fuel card payment methods, and how contactless technology may be the way forward.
Magnetic recording: advancing into the future (2002)

In recent years, the stability of recorded data against thermal decay has become an important criterion for judging the performance of magnetic recording systems. Continued growth of storage densities in the presence of thermally activated behaviour, often called the `superparamagnetic effect', requires new innovations in the recording system in general, and the recording media, in particular. This paper reviews some of the recent advances in recording media (e.g. oriented and antiferromagnetically coupled media) that have helped magnetic recording to maintain the areal density growth rate. However, more innovations and novel architectures are needed for the solutions of tomorrow. Among the more promising media approaches, which are discussed in this paper, are perpendicular, patterned and self-assembled nanoparticle media. Additionally, thermally assisted recording is also reviewed as it combines good writeability with high thermal stability.