gebhart/patrepeval huggingface dataset:
Primary structure and nuclear localization of a murine homeodomain protein. (1987)

The murine homeobox Hox 1.1 (m6) is the first of a cluster of six boxes on chromosome 6. Using probes and synthetic peptides derived from the Hox 1.1 sequence, we were able to isolate cDNAs and antibodies that allowed us to characterize the product of this homeobox-containing gene. From the open reading frame on the cDNA clone B21, a protein could be predicted, made up of 229 amino acids and having a calculated molecular weight of 25,740. A unique feature of this protein is that it has 15 glutamic acid residues as its carboxyl terminus, which gives it a very hydrophilic and acidic carboxyl terminal structure, most probably folding onto an alpha-helix. A second domain of six amino acids is present on the Hox 1.1 protein, which is conserved in other homeodomain proteins. Antibodies generated against synthetic peptides from the homeobox region were used in the immunoblotting procedure and revealed a major protein band of Mr 31,000 in extracts from 3T3 cells and F9 teratocarcinoma cells induced by retinoic acid and cAMP. The nuclear location of the protein was established by immunofluorescence. The presence of this protein in F9 cell nuclei is in faithful accordance with the kinetics established for the 2.4-kilobase Hox 1.1 transcript during differentiation into parietal endoderm cells.
Pathogenicity of a QX strain of infectious bronchitis virus in specific pathogen free and commercial broiler chickens, and evaluation of protection induced by a vaccination programme based on the Ma5 and 4/91 serotypes (2008)

The aims of this study were firstly to evaluate the pathogenicity of an Italian isolate of the QX strain of infectious bronchitis (IB) virus using 1-day-old female specific pathogen free chicks (layer type) and 1-day-old female commercial broiler type chickens, and secondly to assess the level of protection induced in these birds by a vaccination programme including the IB Massachusetts and 4/91 serotype live attenuated vaccines. Unvaccinated birds showed clinical signs of varying severity, predominantly affecting the upper respiratory tract. Vaccinated birds appeared healthy, with the exception of a very mild conjunctivitis affecting a limited number of the broilers. Vaccination fully protected specific pathogen free birds, since no histopathological lesions were observed, nor was virus detected following challenge. In broilers, replication of the challenge virus was not prevented but was significantly reduced. This study confirms that vaccination at 1 day old and at 14 days of age using the Ma5 and 4/91 IB vaccines may be instrumental in reducing the economic impact of QX IB virus infections in layer and broiler farms.
Characteristics of Wheat‐Flour Dough Using Enterobacter cloacae GAO With and Without Yeast (1991)

ABSTRACT The Leavening bacterium Enterobacter cloacae GAO made dough rise, without shrinkage or flattening due to refrigeration. The GAO plus yeast mixture was allowed to ferment from 20 to 25% of the time for the GAO alone. The ratio of 0.5% yeast volume to wheat flour was acceptable. The yeast was used in the dough to make mantou (a type of bun). Both mantou volume and pH declined after 3 days refrigeration. The GAO and yeast mixture could withstand 5‐7 days refrigeration before falling.
Repression of human papillomavirus oncogenes in HeLa cervical carcinoma cells causes the orderly reactivation of dormant tumor suppressor pathways (2000)

Most cervical carcinomas express high-risk human papillomaviruses (HPVs) E6 and E7 proteins, which neutralize cellular tumor suppressor function. To determine the consequences of removing the E6 and E7 proteins from cervical cancer cells, we infected HeLa cells, a cervical carcinoma cell line that contains HPV18 DNA, with a recombinant virus that expresses the bovine papillomavirus E2 protein. Expression of the E2 protein resulted in rapid repression of HPV E6 and E7 expression, followed approximately 12 h later by profound inhibition of cellular DNA synthesis. Shortly after E6/E7 repression, there was dramatic posttranscriptional induction of p53. Two p53-responsive genes, mdm2 and p21, were induced with slightly slower kinetics than p53 and appeared to be functional, as assessed by inhibition of cyclin-dependent kinase activity and p53 destabilization. There was also dramatic posttranscriptional induction of p105(Rb) and p107 after E6/E7 repression, followed shortly thereafter by induction of p130. By 24 h after infection, only hypophosphorylated p105(Rb) was detectable and transcription of several Rb/E2F-regulated genes was dramatically repressed. Constitutive expression of the HPV16 E6/E7 genes alleviated E2-induced growth inhibition and impaired activation of the Rb pathway and repression of E2F-responsive genes. This dynamic response strongly suggests that the p53 and Rb tumor suppressor pathways are intact in HeLa cells and that repression of HPV E6 and E7 mobilizes these pathways in an orderly fashion to deliver growth inhibitory signals to the cells. Strikingly, the major alterations in the cell cycle machinery underlying cervical carcinogenesis can be reversed by repression of the endogenous HPV oncogenes.
Abnormal Connexin Expression Underlies Delayed Wound Healing in Diabetic Skin (2007)

Cx expression in diabetic skin is abnormal, as is the dynamic response of Cx43 to injury, which may underlie the delayed healing of diabetic wounds. Preventing the upregulation of Cx43 in diabetic wounds significantly improves the rate of healing and clearly has potential therapeutic value.
Orally absorbable cephalosporin antibiotics. 2. Structure-activity studies of bicyclic glycine derivatives of 7-aminodeacetoxycephalosporanic acid (1985)

Three positional analogues (4-, 5-, and 7-) of benzothienylglycine and (N-acetylindolinyl)-5-glycine were prepared and coupled to 7-aminodeacetoxycephalosporanic acid (7-ADCA) to give the cephalosporins 17a-c. In addition two isomeric (2,3-b and 3,2-b) thienothiopheneglycines were synthesized and coupled to 7-ADCA to yield cephalosporins 30d and 30e. In vitro testing of these new cephalosporins indicates good activity against Gram-positive bacteria. Against Streptococcus pneumoniae infections compound 25 displayed better mouse protection (both orally and subcutaneously) than cephalexin.
Motion corrected compressed sensing for free‐breathing dynamic cardiac MRI (2012)

Compressed sensing (CS) has been demonstrated to accelerate MRI acquisitions by reconstructing sparse images of good quality from highly undersampled data. Motion during MR scans can cause inconsistencies in k‐space data, resulting in strong motion artifacts in the reconstructed images. For CS to be useful in these applications, motion correction techniques need to be combined with the undersampled reconstruction. Recently, joint motion correction and CS approaches have been proposed to partially correct for effects of motion. However, the main limitation of these approaches is that they can only correct for affine deformations. In this work, we propose a novel motion corrected CS framework for free‐breathing dynamic cardiac MRI that incorporates a general motion correction formulation directly into the CS reconstruction. This framework can correct for arbitrary affine or nonrigid motion in the CS reconstructed cardiac images, while simultaneously benefiting from highly accelerated MR acquisition. The application of this approach is demonstrated both in simulations and in vivo data for 2D respiratory self‐gated free‐breathing cardiac CINE MRI, using a golden angle radial acquisition. Results show that this approach allows for the reconstruction of respiratory motion corrected cardiac CINE images with similar quality to breath‐held acquisitions. Magn Reson Med 70:504–516, 2013. © 2012 Wiley Periodicals, Inc.
Factors affecting the adenosine triphosphate induced release of iron from transferrin (1978)

The release of iron from transferrin was investigated by incubating the diferric protein in the presence of potential iron-releasing agents. The effective chemical group appears to be pyrophosphate, which is present in blood cells as nucleoside di- and triphosphates, notably adenosine triphosphate (ATP). An alternative structure with comparable activity is represented by 2,3-diphosphoglycerate. Neither 1 mM adenosine monophosphate (AMP) nor 1 mM orthophosphate released iron from transferrin. The ATP-induced iron-releasing activity was dependent on weak acidic conditions and was sensitive to temperature and sodium chloride concentration. The rate of iron release rapidly increased as transferrin was titrated with HCl from pH 6.8 to 6.1 in the presence of 1 mM ATP and 160 mM NaCl at 20 degrees C. Iron release from transferrin without ATP was observed below pH 5.5. Ascorbate (10(-4) M) reduced Fe(III), but only after iron release from transferrin by a physiological concentration of ATP. A proposal for the mechanism of iron release from transferrin by ATP and the utilization of reduced iron by erythroid cells is described.
Bacterial Adherence to Plain and Tobramycin-Laden Polymethylmethacrylate Beads (1992)

Antibiotic-impregnated polymethylmethacrylate (PMMA) bead chains are in current clinical use for prophylaxis and management of osteomyelitis. The in vivo interaction between PMMA beads and an experimentally infected wound is examined. Two modes of bacterial adherence to plain PMMA beads are demonstrated. In this report, tobramycin-sensitive bacteria did not attach to tobramycin-laden beads. Therefore, implanted PMMA beads should contain an antibiotic to which the infecting bacteria is sensitive.
Effective Arrestin–Specific Immunotherapy of Experimental Autoimmune Uveitis with RTL: A Prospect for Treatment of Human Uveitis (2013)

Successful therapies for autoimmune uveitis must specifically inhibit pathogenic inflammation without inducing generalized immunosuppression. RTLs can offer such an option. The single retina-specific RTLs may have a value as potential immunotherapeutic drug for human autoimmune uveitis because they effectively prevent disease induced by multiple T cell specificities.
The path tracing revolution in the movie industry (2015)

As path tracing allows for more realistic and faster lighting, an increasing number of movies are created the physically based way. With examples from recent movies, the architectures and novel workflows of the next generation of production renderers are introduced to a wide audience including technical directors, artists, and researchers.
Evanescent wave cavity ring-down spectroscopy with a total-internal-reflection minicavity (1997)

A miniature-cavity realization of the cavity ring-down concept, which permits extension of the technique to spectroscopy of surfaces, thin films, liquids, and, potentially, solids, is explored using a wave-optics model. The novel spectrometer design incorporates a monolithic, total-internal-reflection-ring cavity of regular polygonal geometry with at least one convex facet to induce stability. Evanescent waves generated by total-internal reflection probe absorption by matter in the vicinity of the cavity. Optical radiation enters or exits the resonator by photon tunneling, which permits precise control of input and output coupling. The broadband nature of total-internal reflection circumvents the narrow bandwidth restriction imposed by dielectric mirrors in conventional gas-phase cavity ring-down spectroscopy. Following a general discussion of design criteria, calculations are presented for square and octagonal cavity geometries that quantify intrinsic losses and reveal an optimal cavity size for each geometry. Calculated absorption spectra for the NO3 radical from 450 to 750 nm in a nitric acid solution are presented to demonstrate bandwidth and sensitivity.
HTTP: The Definitive Guide (2002)

Web technology has become the foundation for all sorts of critical networked applications and far-reaching methods of data exchange, and beneath it all is a fundamental protocol: HyperText Transfer Protocol, or HTTP. HTTP: The Definitive Guide documents everything that technical people need for using HTTP efficiently. A reader can understand how web applications work, how the core Internet protocols and architectural building blocks interact, and how to correctly implement Internet clients and servers.
The immobilized leukoagglutinin from the seeds of Maackia amurensis binds with high affinity to complex-type Asn-linked oligosaccharides containing terminal sialic acid-linked alpha-2,3 to penultimate galactose residues. (1988)

We recently reported that the purified leukoagglutinin (designated MAL) from the seeds of the leguminous plant Maackia amurensis is a potent leukoagglutinin for the mouse lymphoma cell line BW5147 (Wang, W.-C., and Cummings, R. D. (1987) Anal. Biochem. 161,80). We and others have shown that this lectin is a weak hemagglutinin of human erythrocytes (Kawaguchi, T., Matsumoto, I., and Osawa, T. (1974) J. Biol. Chem. 249, 2786). We now report that leukoagglutination by MAL is inhibited by low concentrations of 2,3-sialyllactose (NeuAc alpha 2,3Gal beta 1,4Glc), but it is not inhibited by either 2,6-sialyllactose (NeuAc alpha 2,6Gal beta-1,4Glc), lactose, or free NeuAc. To further study the carbohydrate-binding specificity of this lectin, we investigated the interactions of immobilized MAL with glycopeptides prepared from the mouse lymphoma cell line BW5147 and from purified glycoproteins. We found that immobilized MAL interacts with high affinity with complex-type tri- and tetraantennary Asn-linked oligosaccharides containing outer sialic acid residues linked alpha 2,3 to penultimate galactose residues. Glycopeptides containing sialic acid linked only alpha 2,6 to penultimate galactose did not interact detectably with the immobilized lectin. Our analyses indicate that the interactions of complex-type Asn-linked chains with the lectin are dependent on sialic acid linkages and are not dependent on either the branching pattern of the mannose residues or the presence of poly-N-acetyllactosamine sequences.
STAT3-induced WNT5A signaling loop in embryonic stem cells, adult normal tissues, chronic persistent inflammation, rheumatoid arthritis and cancer (Review) (2007)

Leukemia inhibitory factor (LIF), oncostatin M, leptin, ciliary neurotrophic factor, cardiotrophin 1, cardiotrophin-like cytokine factor 1, interleukin 6 (IL6), interleukin 11 and interleukin 27 activate the gp130-JAK-STAT3 signaling cascade. Here, WNT5A was characterized as the evolutionarily conserved target of the STAT3 signaling cascade based on 11-bp-spaced tandem STAT3-binding sites within intron 4 of human, chimpanzee, cow, mouse and rat WNT5A orthologs. Canonical WNT5A signaling through Frizzled and LRP5/LRP6 receptors activates FGF20, WISP1, MYC and CCND1 transcription for the maintenance of stem/progenitor cells, while non-canonical WNT5A signaling through Frizzled and ROR2/PTK7/RYK receptors activates the RHOA, JNK, NLK and NFAT signaling cascades for the control of tissue polarity, cell adhesion or movement. LIF-induced Wnt5a activates canonical Wnt signaling in mouse embryonic stem cells for self-renewal. STAT3-induced Wnt5a activates non-canonical Wnt signaling in rat cardiac myocytes for N-cadherin-dependent aggregation. IL6, secreted from epithelial cells or macrophages, induces WNT5A upregulation in mesenchymal cells. WNT5A then activates canonical WNT signaling in epithelial cells. IL6-induced WNT5A activates canonical WNT signaling for autocrine proliferation of human synovial fibroblasts in rheumatoid arthritis. IL-6 signaling is activated during human chronic atrophic gastritis with Helicobacter pylori infection, and aberrant Stat3 signaling activation gives rise to mouse gastric tumors. WNT5A is frequently upregulated in human primary gastric cancer due to tumor-stromal interaction. WNT5A might be downregulated in advanced cancer with poorer prognosis due to genetic alterations compensating WNT5A signaling. Oncogenic WNT5A activates canonical WNT signaling in cancer stem cells for self-renewal, and non-canonical WNT signaling at the tumor-stromal interface for invasion and metastasis. SNP of genes encoding components of the cytokine-induced WNT5A signaling loop is a predicted risk factor for RA and cancer, especially diffuse-type gastric and pancreatic cancer. Humanized anti-IL6 receptor antibody and WNT5A mimetic small-molecule antagonist could be applied to personalized medicine for RA and cancer driven by the IL6-induced WNT5A signaling loop.
Propionibacterium acnes Types I and II Represent Phylogenetically Distinct Groups (2005)

Although two phenotypes of the opportunistic pathogen Propionibacterium acnes (types I and II) have been described, epidemiological investigations of their roles in different infections have not been widely reported. Using immunofluorescence microscopy with monoclonal antibodies (MAbs) QUBPa1 and QUBPa2, specific for types I and II, respectively, we investigated the prevalences of the two types among 132 P. acnes isolates. Analysis of isolates from failed prosthetic hip implants (n = 40) revealed approximately equal numbers of type I and II organisms. Isolates from failed prosthetic hip-associated bone (n = 6) and tissue (n = 38) samples, as well as isolates from acne (n = 22), dental infections (n = 8), and skin removed during surgical incision (n = 18) were predominately of type I. A total of 11 (8%) isolates showed atypical MAb labeling and could not be conclusively identified. Phylogenetic analysis of P. acnes by nucleotide sequencing revealed the 16S rRNA gene to be highly conserved between types I and II. In contrast, sequence analysis of recA and a putative hemolysin gene (tly) revealed significantly greater type-specific polymorphisms that corresponded to phylogenetically distinct cluster groups. All 11 isolates with atypical MAb labeling were identified as type I by sequencing. Within the recA and tly phylogenetic trees, nine of these isolates formed a cluster distinct from other type I organisms, suggesting a further phylogenetic subdivision within type I. Our study therefore demonstrates that the phenotypic differences between P. acnes types I and II reflect deeper differences in their phylogeny. Furthermore, nucleotide sequencing provides an accurate method for identifying the type status of P. acnes isolates.
Bromptonʼs Mixture in Alleviating Pain of Terminal Neoplastic Disease (1980)

We conducted a one-year preliminary study on 107 patients in a hospice for incurable cancer to assess the efficacy of a modified Brompton's Mixture (an oral analgesic solution) in alleviating intractable pain. The results presented indicate that in patients who can tolerate oral medication, the present formulation can be used in lieu of parenteral narcotics, often with superior results and always with cost effectiveness. With Brompton's Misture, side effects of parenteral narcotics such as sedation, lethargy, and nausea are avoided. As documented by four representative case reports, the patient is pain-free, ambulatory, communicating with his environment, and experiencing an improved nutritional status, thereby improving the quality of life. Brompton's Mixture appears to be a valuable adjunct to conventional therapy, giving the patient an effective alternative to parenteral medication for control of pain.
Structure of a glutathione conjugate bound to the active site of aldose reductase (2006)

Aldose reductase (AR) is a monomeric NADPH-dependent oxidoreductase that catalyzes the reduction of aldehydes, ketones, and aldo-sugars. AR has been linked to the development of hyperglycemic injury and is a clinical target for the treatment of secondary diabetic complications. In addition to reducing glucose, AR is key regulator of cell signaling through it's reduction of aldehydes derived from lipoproteins and membrane phospholipids. AR catalyzes the reduction of glutathione conjugates of unsaturated aldehydes with higher catalytic efficiency than free aldehydes. The X-ray structure of human AR holoenzyme in complex with the glutathione analogue S-(1,2-dicarboxyethyl) glutathione (DCEG) was determined at a resolution of 1.94 A. The distal carboxylate group of DCEG's dicarboxyethyl moiety interacted with the conserved AR anion binding site residues Tyr48, His110, and Trp111. The bound DCEG's glutathione backbone adopted the low-energy Y-shape form. The C-terminal carboxylate of DCEG glutathione's glycine formed hydrogen bonds to Leu301 and Ser302, while the remaining interactions between DCEG and AR were hydrophobic, permitting significant flexibility of the AR and glutathione (GS) analogue interaction. The observed conformation and interactions of DCEG with AR were consistent with our previously published molecular dynamics model of glutathionyl-propanal binding to AR. The current structure identifies major interactions of glutathione conjugates with the AR active-site residues.
Anatomic Evaluation of Two Different Techniques for the Percutaneous Insertion of Pedicle Screws in the Lumbar Spine (1999)

This in vitro study showed that the percutaneous technique of pedicle screw insertion in the lumbar spine is a safe and reliable procedure. Compared with the well-established Magerl technique, the new modified technique did not decrease the misplacement rate significantly, although less pedicle violations were found in the upper lumbar spine.
Targeting the Cerebrovascular Large Neutral Amino Acid Transporter (LAT1) Isoform Using a Novel Disulfide-Based Brain Drug Delivery System (2006)

We describe a novel strategy to achieve high affinity recognition for the specific, cerebrovascular large neutral amino acid transporter (LAT1) isoform by covalent coupling of small molecules to the amino acid, L-cysteine (L-Cys). L-Cys (as the carrier) was covalently attached via a disulfide bond to either 6-mercaptopurine or 2-methyl-1-propanethiol (IBM) to form the brain-targeted drug delivery systems (BTDS). BTDS were designed for high affinity recognition by LAT1 at the cerebrovasculature. Using an in situ rat brain perfusion technique, competition between BTDS and the radiotracer [14C]L-Leu demonstrated significant inhibition of [14C]L-Leu brain uptake. BTDS possess affinity for cerebrovascular LAT1 in many distinct brain compartments, and the recognition of BTDS by LAT1 is influenced by hydrophobicity of the side-chain in BTDS. Thus, the BTDS strategy may be utilized for rapid shuttling of various neuropharmaceuticals into brain.
Phosphorylation of hydroxyproline in a synthetic peptide catalyzed by cyclic AMP-dependent protein kinase. (1979)

The cyclic AMP-dependent protein kinase catalyzes the phosphorylation of hydroxyproline present in the heptapeptide, Leu-Arg-Arg-Ala-Hyp-Leu-Gly. The Km value for the reaction with this substrate was high (approximately 18 mM) compared to the Km values reported for the analogous threonine and serine-containing peptides, which were 0.59 mM and 0.016 mM, respectively (Kemp, B.E., Graves, D.J., Benjamini, E., and Krebs, E.G. (1977) J. Biol. Chem. 252, 4888-4894). The Vmax value with the hydroxyproline-containing peptide was 1 mumol . min-1 mg-1 in contrast to Vmax values of 6 mumol . min-1 mg-1 and 20 mumol . min-1 mg-1 for the threonine- and serine-containing peptides, respectively. Phosphate esterified to hydroxyproline present in the peptide was relatively stable in hot alkali, only 10% being released as Pi within 30 min in 0.1 N NaOH at 100 degrees C, whereas all of the phosphate was released from the phosphoserine peptide analogue under these conditions. Phosphohydroxyproline in the peptide was also more stable to acid (5.7 N HCl, 110 degrees C) than phosphoserine, the time for 50% release as Pi being 15 h in contrast to 6 h for the latter.