gebhart/patrepeval huggingface dataset:
Identification of trypsin‐inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor (2009)

Human serine proteinase inhibitor Kazal-type 2 (SPINK2) functions as a trypsin/acrosin inhibitor and is synthesized mainly in the testis and seminal vesicle where its activity is engaged in fertility. The SPINK2 protein contains a typical Kazal domain composed by six cysteine residues forming three disulfide bridges. The expression of SPINK2 is closely related to cancer such as lymphomas, in that a high transcript level of SPINK2 in patients with primary cutaneous follicle center cell lymphomas have better prognosis with lower mortality. To clarify the role of SPINK2 in cancer, we performed quantitative real-time PCR and showed that the expression level of SPINK2 is significantly elevated in most leukemia cell lines except B-lymphoblast TK-6 cells. The molecular function and structural features of SPINK2 were also investigated by employing the recombinant active and mutant inactive SPINK2 proteins to determine its key P2-P2' (Pro(23)-Arg(24)-His(25)-Phe(26)) active site. The inhibition assay results demonstrated that Arg(24) at the P1 site is crucial for the specificity of SPINK2 on target enzyme. Although His(25) at the P1' and Phe(26) at the P2' residues are also involved in trypsin-SPINK2 interaction, Pro(23) at the P2 site may not be directly participated in interacting with trypsin. In addition, we determined the 3D solution structure of SPINK2 and used this structure to predict the SPINK2-proteinase complex structure and binding properties. These studies not only provide critical information about the structural properties and biophysical features of the SPINK2 proteinase inhibitor, but also suggest its important role in tumor progression and response to treatment.
Unveiling the Surface Epitopes That Render Tissue Inhibitor of Metalloproteinase-1 Inactive against Membrane Type 1-Matrix Metalloproteinase (2003)

Membrane type 1-matrix metalloproteinase (MT1-MMP) is a zinc-dependent, membrane-associated endoproteinase of the metzincin family. The enzyme regulates extracellular matrix remodeling and is capable of cleaving a wide variety of transmembrane proteins. The enzymatic activity of MT1-MMP is regulated by endogenous inhibitors, the tissue inhibitor of metalloproteinases (TIMP). To date, four variants of mammalian TIMP have been identified. Whereas TIMP-2-4 are potent inhibitors against MT1-MMP, TIMP-1 displays negligible inhibitory activity against the enzyme. The rationale for such selectivity is hitherto unknown. Here we identify the surface epitopes that render TIMP-1 inactive against MT1-MMP. We show that TIMP-1 can be transformed into an active inhibitor against MT1-MMP by the mutation of a single residue, namely threonine 98 to leucine (T98L). The resultant mutant displayed inhibitory characteristics of a typical slow, tight binding inhibitor. The potency of the mutant could be further enhanced by the introduction of valine 4 to alanine (V4A) and proline 6 to valine (P6V) mutations. Indeed, the inhibitory profile of the triple mutant (V4A/P6V/T98L) is indistinguishable from those of other TIMPs. Our findings suggest that threonine 98 is critical in initiating MMP binding and complex stabilization. Our findings also provide a potential mechanistic explanation for MMP-TIMP selectivity.
High expression of L-type amino acid transporter 1 (LAT1) predicts poor prognosis in pancreatic ductal adenocarcinomas (2012)

LAT1 aberrant overexpression in PDAC predicts poor prognosis, independent of Ki-67 LI, and offers a potential target for future anticancer therapy with its inhibitors.
Detection of hepatitis A virus RNA in oyster meat (1997)

Detection of low concentrations of viruses in shellfish is possible with nucleic acid amplification by PCR. Hepatitis A virus (HAV) has been detected in oyster meat by reverse transcription-PCR (RT-PCR). We developed a method to identify HAV RNA by RT-PCR of total RNA extracted from oyster meat contaminated by adsorption, bioaccumulation, or injection. With dot blot hybridization detection of amplicons from the RT-PCR, rapid screening of a large number of samples is feasible. As few as 8 PFU of HAV/g of oyster meat can be detected.
Application of Antigen Retrieval by Heating for Double-label Fluorescent Immunohistochemistry with Identical Species-derived Primary Antibodies (2004)

Double-label fluorescent immunohistochemistry (IHC) is frequently used to identify cellular and subcellular co-localization of independent antigens. In general, primary antibodies for double labeling should be derived from independent species. However, such convenient pairs of antibodies are not always available. To overcome this problem, several methods for double labeling with primary antibodies from identical species have been proposed. Among them are methods using monovalent secondary antibodies, such as Fab fragments. Soluble immune complexes consisting of primary and monovalent secondary antibodies are first formed. After absorption of the excess secondary antibody with nonspecific immunoglobulin, the immune complexes are applied to sections. By this procedure, unwanted cross-reaction between false pairs of antibodies is avoidable. However, soluble immune complexes often show reduced or no immunoreactivity to antigens on sections. I noted that antigen retrieval (AR) of tissues by heating often but not always showed improved immunoreactivity for soluble immune complexes. Here I demonstrate the examination of conditions for this soluble immune complex method using AR-treated sections and show examples of double-label fluorescent IHC with identical species-derived primary antibodies.
DNA end resection and its role in DNA replication and DSB repair choice in mammalian cells (2020)

DNA end resection has a key role in double-strand break repair and DNA replication. Defective DNA end resection can cause malfunctions in DNA repair and replication, leading to greater genomic instability. DNA end resection is initiated by MRN-CtIP generating short, 3'-single-stranded DNA (ssDNA). This newly generated ssDNA is further elongated by multiple nucleases and DNA helicases, such as EXO1, DNA2, and BLM. Effective DNA end resection is essential for error-free homologous recombination DNA repair, the degradation of incorrectly replicated DNA and double-strand break repair choice. Because of its importance in DNA repair, DNA end resection is strictly regulated. Numerous mechanisms have been reported to regulate the initiation, extension, and termination of DNA end resection. Here, we review the general process of DNA end resection and its role in DNA replication and repair pathway choice.
Synthesis and field emission properties of TiSi2 nanowires (2005)

TiSi 2 is a high-melting compound with excellent conductivity ∼severalμΩcm. TiSi2 nanowires were fabricated in large scale by a simple vapor phase deposition method. The as-synthesized TiSi2 nanowires were investigated using x-ray diffraction, scanning electron microscopy, transmission electron microscopy, and Raman scattering. Field emission property of TiSi2 nanowires was studied and an emission current density of 5mA∕cm2 was obtained and no obvious degradation was observed in a life stability experiment period for over ∼40h. The cathodoluminescence images were very bright and homogenous. The remarkable performance reveals that the TiSi2 nanowires can serve as a good candidate for commercial application in vacuum microelectronic devices, particularly flat panel displays.
The σE‐mediated response to extracytoplasmic stress in Escherichia coli is transduced by RseA and RseB, two negative regulators of σE (1997)

The extracytoplasmic stress response in Escherichia coli is controlled by the alternative sigma factor, sigma(E). sigma(E) activity is uniquely induced by the accumulation of outer membrane protein precursors in the periplasmic space, and leads to the increased production of several proteins, including the periplasmic protease DegP, that are thought to be required for maintaining cellular integrity under stress conditions. Genetic and biochemical experiments show that sigma(E) activity is under the control of three genes, rseABC (for regulator of sigma E), encoded immediately downstream of the sigma factor. Deletion of rseA leads to a 25-fold induction of sigma(E) activity. RseA is predicted to be an inner membrane protein, and the purified cytoplasmic domain binds to and inhibits sigma(E)-directed transcription in vitro, indicating that RseA acts as an anti-sigma factor. Deletion of rseB leads to a slight induction of sigma(E), indicating that RseB is also a negative regulator of sigma(E). RseB is a periplasmic protein and was found to co-purify with the periplasmic domain of RseA, indicating that RseB probably exerts negative activity on sigma(E) through RseA. Deletion of rseC, in contrast, has no effect on sigma(E) activity under steady-state conditions. Under induction conditions, strains lacking RseB and/or C show wild-type induction of sigma(E) activity, indicating either the presence of multiple pathways regulating sigma(E) activity, or the ability of RseA alone to both sense and transmit information to sigma(E).
Effect of Administration of Bifidobacteria and Lactic Acid Bacteria to Newborn Calves and Piglets (1995)

The effect of oral administration of bifidobacteria and lactic acid bacteria on newborn livestock was investigated. Oral administration of Bifidobacterium pseudolongum or Lactobacillus acidophilus to calves improved BW gain and feed conversion over that of untreated controls. The frequency of diarrhea occurrence was decreased in the group fed probiotics. However, there was no significant difference between calves administered B. pseudolongum and those administered L. acidophilus. Under conditions of feeding without antibiotics, the frequency of diarrhea was decreased markedly by administration of probiotics. The BW gain of piglets was significantly greater during both the suckling and weaning periods for the group fed probiotics than for the control group. The effect was more evident during the suckling period than during the weaning period. Under conditions of feeding without antibiotics, the frequency of piglet mortality was decreased markedly by administration of probiotics. The probiotics tested here had useful effects, including improved BW gain, feed conversion, and fecal condition of both newborn calves and piglets.
Human P3450: cDNA and complete amino acid sequence (1986)

Journal Article Human P 3 450: cDNA and complete amino acid sequence Get access Anil K. Jaiswal, Anil K. Jaiswal Search for other works by this author on: Oxford Academic PubMed Google Scholar Daniel W. Nebert, Daniel W. Nebert Search for other works by this author on: Oxford Academic PubMed Google Scholar Frank J. Gonzalez Frank J. Gonzalez 1Laboratory of Molecular Carcinogenesis, National Cancer Institute, National Institutes of HealthBethesda, MD 20892, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 14, Issue 16, 26 August 1986, Pages 6773–6774, https://doi.org/10.1093/nar/14.16.6773 Published: 26 August 1986 Article history Received: 23 May 1986 Published: 26 August 1986
Depth image-based rendering from multiple cameras with 3D propagation algorithm (2009)

This paper proposes a new 3D propagation algorithm for the depth image-based rendering problem with multiple color and range cameras at arbitrary positions. The proposed algorithm efficiently renders novel images at arbitrary virtual views by propagating all available depth information from range ca
Denoising array-based comparative genomic hybridization data using wavelets (2005)

Array-based comparative genomic hybridization (array-CGH) provides a high-throughput, high-resolution method to measure relative changes in DNA copy number simultaneously at thousands of genomic loci. Typically, these measurements are reported and displayed linearly on chromosome maps, and gains and losses are detected as deviations from normal diploid cells. We propose that one may consider denoising the data to uncover the true copy number changes before drawing inferences on the patterns of aberrations in the samples. Nonparametric techniques are particularly suitable for data denoising as they do not impose a parametric model in finding structures in the data. In this paper, we employ wavelets to denoise the data as wavelets have sound theoretical properties and a fast computational algorithm, and are particularly well suited for handling the abrupt changes seen in array-CGH data. A simulation study shows that denoising data prior to testing can achieve greater power in detecting the aberrant spot than using the raw data without denoising. Finally, we illustrate the method on two array-CGH data sets.
Stability of polyatomic molecules in degenerate electronic states - I—Orbital degeneracy (1937)

Abstract In the following we investigate the conditions under which a polyatomic molecule can have a stable equilibrium configuration when its electronic state has orbital degeneracy, i. e. degeneracy not arising from the spin. We shall show that stability and degeneracy are not possible simultaneously unless the molecule is a linear one, i. e. unless all the nuclei in the equilibrium configuration lie on a straight line. We shall see also that the instability is only slight if the degeneracy is due solely to electrons having no great influence on the binding of the molecule. We first note that if accidental degeneracy (i. e. degeneracy not caused by symmetry) is disregarded then a degenerate electronic state necessarily entails a symmetrical nuclear configuration. Thus in order to cover all cases we may first consider each possible type of symmetry separately and discuss what nuclear configurations are consistent with each symmetry. A given molecule will possess a continuous set of configurations consistent with one definite type of symmetry, and among these configurations there may be one with a minimum electronic energy. This configuration is then stable with respect to all totally symmetrical nuclear displacements (i. e. displacements which do not disturb the symmetry). We shall have to investigate its stability with respect to all other nuclear displacements.
Formulation Technology: Emulsions, Suspensions, Solid Forms (2001)

Colloids, phases, interfaces Emulsions - properties and production Microemulsions, vesicles and liposomes Foams Production and properties of colloid suspensions and dispersions Solids Rheology Solubility parameters Solubility, crystallization Purification, detergency Cosmetics Pharmaceutical technology Food formulations Agroformulations Pigments and dyes.
Immunosuppressant FK506 promotes neurite outgrowth in cultures of PC12 cells and sensory ganglia. (1994)

The immunosuppressant drug FK506 acts by binding to receptor proteins, FK506-binding proteins (FKBPs), which in turn can bind to and regulate a Ca(2+)-dependent phosphatase, calcineurin, and a Ca2+ release channel, the ryanodine receptor. Based on our findings in regeneration models that levels of FKBPs during neural regeneration parallel those of growth-associated protein GAP43, a calcineurin substrate that regulates neurite extension, we examined effects of FK506 in PC12 rat pheochromocytoma cells and in rat sensory ganglia. FK506 enhances neurite outgrowth in both systems by increasing sensitivity to nerve growth factor. Blockade of FK506 actions in sensory ganglia by rapamycin, an FK506 antagonist, establishes that these effects involve FKBPs. Rapamycin itself stimulates neurite outgrowth in PC12 cells. These drug effects are detected at subnanomolar concentrations, suggesting therapeutic application in diseases involving neural degeneration.
Postburn facial resurfacing with a split ascending neck flap. (1993)

Ninety-eight patients with postburn facial scar deformities were treated by using a split ascending neck flap. Anatomic studies and discovery of axial blood supply to the anterior of the neck are utilized, allowing for wide mobilization, thin flaps, and transfer of neck skin to the face and chest skin to the neck. By leaving the platysma muscle in situ and using vacuum drainage with a large tube in the subflap space, preservation of the chin and neck contours is obtained. There are five varieties of postburn facial scar deformities described and treated. Extensive facial deformity requires a two-stage operation. Neck skin transferred to the face by the described method preserves all natural properties. This method of facial resurfacing is preferable to other methods and is indicated for all cases of scars to the face with healthy neck skin and chest wall.
Wnt3a-/--like phenotype and limb deficiency in Lef1-/-Tcf1-/- mice (1999)

Members of the LEF-1/TCF family of transcription factors have been implicated in the transduction of Wnt signals. However, targeted gene inactivations of Lef1, Tcf1, or Tcf4 in the mouse do not produce phenotypes that mimic any known Wnt mutation. Here we show that null mutations in both Lef1 and Tcf1, which are expressed in an overlapping pattern in the early mouse embryo, cause a severe defect in the differentiation of paraxial mesoderm and lead to the formation of additional neural tubes, phenotypes identical to those reported for Wnt3a-deficient mice. In addition, Lef1(-/-)Tcf1(-/-) embryos have defects in the formation of the placenta and in the development of limb buds, which fail both to express Fgf8 and to form an apical ectodermal ridge. Together, these data provide evidence for a redundant role of LEF-1 and TCF-1 in Wnt signaling during mouse development.
Parametric Study on the CO2 Capture Capacity of CaO-Based Sorbents in Looping Cycles (2008)

An experimental parametric study on the CO2 capture activity of four limestone-derived CaO-based sorbents has been performed. Experiments were done in a thermogravimetric analyzer (TGA) at temperatures ranging from 650 to 850 °C. Three particle-size fractions of Kelly Rock limestone and powders obtained by their grinding were also tested, while the influence of carbonation and calcination durations was examined at 750 and 850 °C. Calcination is typically performed in an atmosphere of N2 and carbonation in 50% CO2 (N2 balance), and the influence of the effective CO2 concentration surrounding reacting particles was examined by changing the sample mass in some experiments. The results indicated that increasing the calcination/carbonation temperature had a negative influence on the sorbent activity, while the influence of particle size was small, although larger particles have higher activity. This was unexpected, but it can be explained by the higher content of impurities in the smaller particles. Grinding enhances sorbent activity, and this appears to be more than simply due to increased external surface area of the sorbent particles in the powdered samples. Prolonged carbonation time has a negative effect on the sorbent performance. The formation and decomposition of CaCO3 as well as its presence on the sorbent surface at higher temperatures appear to be key factors in the loss of surface area (i.e., decrease in sorbent activity). However, it is shown that the prolonged exposure to calcination conditions employed in this work (inert atmosphere) has a slightly beneficial effect on sorbent behavior as a function of the number of calcination/carbonation cycles. Experiments with larger sample masses typically resulted in better conversions. Analysis of scanning electron microscope (SEM) images of spent sorbent particles obtained from different reactor types indicated that thermal stresses are the main cause for sorbent particle fracture and attrition.
Cloning the double-stranded RNA genes of reovirus: sequence of the cloned S2 gene. (1982)

The genes of the Dearing strain of reovirus serotype 3, which consist of double-stranded RNA, have been cloned into pBR322 by tailing both strands of each gene with poly(A), transcribing them with reverse transcriptase, self-hybridizing the cognate plus and minus cDNA strands, incubating them with Escherichia coli DNA polymerase I to ensure that they are complete, and cloning the double-stranded cDNA molecules by standard procedures. The sequence of the cloned S2 gene has been determined. The sequence at the termini are exactly the same as those at the ends of the native double-stranded RNA gene. The gene is 1,329 nucleotides long and possesses a single long open reading frame that starts at the first initiation codon (residue 19) and extends for 331 codons, sufficient to encode a protein of the same size as the known S2 gene product, protein sigma 2, a major reovirus core component (Mr, 38,000). A second open reading frame of 85 codons, in a different phase, starts close to where the first ends. The protein translated from this reading frame is unknown.
Molecular cloning and DNA sequence of lacE, the gene encoding the lactose-specific enzyme II of the phosphotransferase system of Lactobacillus casei. Evidence that a cysteine residue is essential for sugar phosphorylation. (1990)

The gene coding for the lactose-specific Enzyme II of the Lactobacillus casei phosphoenolpyruvate-dependent phosphotransferase system, lacE, has been isolated by molecular cloning and expressed in Escherichia coli. The DNA sequence of the lacE gene and the deduced amino acid sequence are presented. The putative translation product comprises a hydrophobic protein of 577 amino acids with a calculated molecular mass of 62,350 Da. The deduced polypeptide has a high degree of sequence similarity with the corresponding lactose-specific enzymes II of Staphylococcus aureus and Lactococcus lactis. The sequence surrounding cysteine 483 was strongly conserved in the three proteins. The identity of the lacE product as the Enzyme IIlacL.casei was demonstrated by in vitro lactose phosphorylation assays using the protein expressed in E. coli. Single replacement of each of the histidine and cysteine residues by site-directed mutagenesis pointed to cysteine 483 as an amino acid residue essential for the phosphoryl group transfer reaction.
Fiber density of electrospun gelatin scaffolds regulates morphogenesis of dermal–epidermal skin substitutes (2007)

Porous, nowoven fibrous gelatin scaffolds were prepared using electrospinning. Electrospun scaffolds with varying fiber diameter, interfiber distance, and porosity were fabricated by altering the concentration of the electrospinning solution. Solution concentration was a significant predictor of fiber diameter, interfiber distance, and porosity with higher solution concentration correlated with larger fiber diameters and interfiber distances. The potential of electrospun gelatin as a scaffolding material for dermal and epidermal tissue regeneration was also evaluated. Interfiber distances >5.5 microm allowed deeper penetration of human dermal fibroblasts into the scaffold, whereas cells in scaffolds with more densely packed fibers were able to infiltrate only into the upper regions. Scaffolds with interfiber distances </=10 microm exhibited well-stratified dermal and epidermal layers including a continuous basal keratinocyte layer. These scaffolds were shown to form a keratinized layer like in normal skin, which acts as a barrier to infection and fluid loss. Interfiber distances between 5 and 10 microm appear to yield the most favorable skin substitute in vitro, demonstrating high cell viability, optimal cell organization, and excellent barrier formation. These results demonstrate the feasibility of electrospun gelatin as a scaffold for dermal-epidermal composite skin substitutes.