gebhart/patrepeval huggingface dataset:
Regional Expression and Androgen Regulation of Carbonic Anhydrase IV and IIin the Adult Rat Epididymis1 (1999)

Carbonic anhydrase (CA) is implicated in the acidification of epididymal fluid and thereby in the regulation of sperm maturation and motility. Among the CA isoenzymes, CA IV and II have been shown to be present in the rat epididymal duct epithelium. In the present study, we examined the expression and androgen regulation of CA IV and II mRNAs along the epididymal duct. Northern blot analysis revealed the presence of CA II mRNA in all regions of the epididymis with the strongest signal in the corpus region, while CA IV mRNA was expressed predominantly in the corpus epididymidis. Three days after bilateral castration, CA IV and II mRNAs were decreased by 80-90% in the corpus epididymidis. Testosterone (T) replacement maintained the expression of CA mRNAs at 50-60% of the control levels, indicating that circulating androgens alone are not sufficient to recover the CA expression in the corpus region. However, unilateral castration did not affect the mRNA levels of CA IV and II, suggesting that factors in testicular fluid do not play a major role in the regulation of CA expression in the corpus epididymidis. Immunoblot analysis showed that CA IV protein levels decreased 3 days after castration, while T administration maintained the protein expression virtually at the precastration levels. These data demonstrate that mRNAs for CA IV and II are predominantly expressed in the corpus region of the rat epididymis and can be regulated by androgens in that region. The present data suggest that the regulation of CA expression in the corpus epididymidis by androgens contributes to the known androgen effects on epididymal acidification.
Virtual Metrology Technique for Semiconductor Manufacturing (2006)

IC metrology is a necessary means for measuring the fabrication performance in the semiconductor industry. It is significant for yield enhancement and process control. However, real-time monitoring of wafer production is required in recent years especially for the 300mm semiconductor manufacturing. Therefore, virtual metrology (VM) is developed for the tide of demand. It is a novel technology to predict the process results based on the previous metrology measurements, instead of measuring practically. Consequently it can assist in achieving total quality management and enable run-to-run control. In this paper a systematic methodology for virtual metrology is proposed. This VM system which is mainly designed for the process subject to linear process drift consists of a piecewise linear neural network and a fuzzy neural network. Because many semiconductor processes exhibit inevitable steady drifts in nature, the design of piecewise linear neural network is to approximate the drift trend. In addition, the influence of process recipe on fabrication outcome is learned using the fuzzy neural network. The system has good generalization capability and performance. Thus, it provides an effective and economical solution for metrology prediction.
Mediator of Hepatic Amino Acid Flux in Infected Rats (1972)

SummaryLive D. pneumoniae, but not endotoxin or double-stranded polynucleotides, stimulated a flux of cycloleucine into liver. Sterile, 2-hr serum from D. pneumoniae-infected rats and secretions obtained from rat peritoneal leukocytes can also mediate a flux of cycloleucine into liver of normal recipient rats. The data were interpreted as evidence that one or more proteins synthesized and excreted by leukocytes can act as humoral intermediates in the stimulation of amino acid flux into liver tissue.
A Continuous‐Flow Microcapillary Reactor for the Preparation of a Size Series of CdSe Nanocrystals (2003)

A microcapillary flow reactor has been used to prepare a size series of colloidal CdSe nanocrystals (NCs). The continuous‐flow method (see Figure for schematic) produces samples with size distributions and quantum yields comparable to those prepared in conventional batch processes. The results obtained from the reactor provide insight into the kinetics of nucleation and growth for NC systems.
High-level expression in Escherichia coli of enzymatically active fusion proteins containing the domains of mammalian cytochromes P450 and NADPH-P450 reductase flavoprotein. (1992)

This report describes the properties of two mammalian cytochromes P450 that have been expressed at high levels in Escherichia coli as enzymatically active fusion proteins containing the flavoprotein domain of rat NADPH-cytochrome P450 reductase (EC 1.6.2.4). Fusion proteins were prepared by engineering the cDNAs for the steroid-metabolizing bovine adrenal P450 17A with the cDNA for rat liver NADPH-P450 reductase with the introduction of a Ser-Thr linker to give a protein we have named rF450[mBov17A/mRatOR]L1. Similarly, the cDNA for the omega-hydroxylase of rat liver (P450 4A1) was linked with the cDNA for rat liver NADPH-P450 reductase to give rF450[mRat4A1/mRatOR]L1. A procedure involving disruption of transformed E. coli by sonication, isolation of membranes by differential centrifugation, solubilization with detergent, and affinity chromatography provided significant amounts of purified fusion proteins of approximately 118 kDa. The purified fusion proteins had turnover numbers for the metabolism of steroids (rF450[mBov17A/mRatOR]L1) or fatty acids (rF450[mRat4A1/mRatOR]L1) ranging from 10/min to 30/min in the absence of added phospholipid. Addition of purified rat liver cytochrome b5 stimulated the 17,20-lyase reaction for the conversion of 17-hydroxypregnenolone to dehydroepiandrosterone, and addition of purified rat NADPH-cytochrome P450 reductase enhanced the formation of omega--1 metabolites from lauric and arachidonic acids. NADPH oxidation was tightly coupled to substrate hydroxylation with the purified fusion proteins.
Interaction of terminal transferase with single-stranded DNA. (1987)

A 58-kDa monomer of terminal transferase was isolated from calf thymus using a monoclonal antibody affinity column. The enzymatic activity was comparable to that of the 44-kDa alpha beta dimer isolated by conventional methods. Binding of the two enzyme forms to single-stranded DNA was monitored by fluorescence. The site size of both forms was approximately 11 +/- 2 nucleotides. Binding of the 44-kDa alpha beta dimer to polydeoxyadenosine was examined under several conditions. The cooperativity parameter increased from about 90 in the presence of Mg2+ to 300-400 in the absence of Mg2+. The observed dissociation constant of 3-5 microM was essentially independent of salt concentration, whereas the intrinsic dissociation constant decreased about 5-fold in the presence of Mg2+. The binding parameters of the 58-kDa monomer were independent of buffer composition and were similar to those of the 44-kDa alpha beta dimer in the presence of Mg2+. These results indicate that the additional 14-kDa peptide sequences present in the high molecular mass monomer form are not part of the DNA-binding site of terminal transferase.
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures (2008)

A new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromolecular structure. Protonate3D considers side-chain "flip," rotamer, tautomer, and ionization states of all chemical groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titration effects. The results of computational validation experiments suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromolecular structures.
Intradermal ras peptide vaccination with granulocyte-macrophage colony-stimulating factor as adjuvant: Clinical and immunological responses in patients with pancreatic adenocarcinoma (2001)

K-RAS mutations are frequently found in adenocarcinomas of the pancreas, and induction of immunity against mutant ras can therefore be of possible clinical benefit in patients with pancreatic cancer. We present data from a clinical phase I/II trial involving patients with adenocarcinoma of the pancreas vaccinated by i.d. injection of synthetic mutant ras peptides in combination with granulocyte-macrophage colony-stimulating factor. Forty-eight patients (10 surgically resected and 38 with advanced disease) were treated on an outpatient basis. Peptide-specific immunity was induced in 25 of 43 (58%) evaluable patients, indicating that the protocol used is very potent and capable of eliciting immune responses even in patients with end-stage disease. Patients followed-up for longer periods showed evidence of induction of long-lived immunological memory against the ras mutations. CD4(+) T cells reactive with an Arg12 mutation also present in the tumor could be isolated from a tumor biopsy, demonstrating that activated, ras-specific T cells were able to selectively accumulate in the tumor. Vaccination was well tolerated in all patients. Patients with advanced cancer demonstrating an immune response to the peptide vaccine showed prolonged survival from the start of treatment compared to non-responders (median survival 148 days vs. 61 days, respectively; p = 0.0002). Although a limited number of patients were included in our study, the association between prolonged survival and an immune response against the vaccine suggests that a clinical benefit of ras peptide vaccination may be obtained for this group of patients.
Lysophosphatidic Acid (LPA) Induces Plasma Exudation and Histamine Release in Mice via LPA Receptors (2006)

Lysophosphatidic acid (LPA), the simplest of the water-soluble phospholipids, can evoke various biological responses. The present study examined the activity of LPA to induce plasma exudation and histamine release in mice. Plasma exudation was assessed by extravasation of Evans blue. Subcutaneous administration of LPA (1 - 100 microg/site) led to increased plasma exudation in the skin. The LPA-induced plasma exudation was inhibited by ketotifen, a histamine H1-receptor antagonist, and diacylglycerol pyrophosphate (DGPP), a LPA1/LPA3-receptor antagonist. Moreover, pretreatment with pertussis toxin and DGPP inhibited the histamine release from peritoneal mast cells induced by LPA. These findings indicate that plasma exudation induced by LPA is mediated by histamine release from mast cells via LPA receptor(s), presumably LPA1 and/or LPA3, coupled to G(i/o) proteins. Moreover, these findings point to a role of LPA in the pathomechanisms of various allergic disorders.
Miniature Swine Expressing Human CD47 to Enhance Bone Marrow Engraftment in Non-Human Primates (2012)

Background: Tolerance induction via bone marrow chimerism has been successfully applied to small and large allogeneic models. However, in xenogenic models (pig-to-primate) host macrophages participate in the clearance of porcine bone marrow cells when transplanted into baboons, hindering the ability to achieve mixed chimerism. CD47 interacts with SIRPa receptors on macrophages to inhibit their activation, but this interaction is species-specific. Recent experiments indicate that expression of human CD47 on porcine cells can inhibit phagocytosis by primate macrophages. We report the generation of hCD47 transgenic miniature swine as potential pig-to-primate bone marrow donors. Methods: We constructed a knock-in vector for expression of the human CD47 gene from EF1a promoter with concomitant disruption of the a-1,3-galactosyltransferase (GalT) locus. Selectable targeted cells, with loss of gal epitope and gain of hCD47 expression were generated by transfecting GalT heterozygous fibroblast cells. Somatic cell cloned embryos were generated using Chromatin Transfer technology and transferred into recipient sows at Minitube International Center for Biotechnology. Two early trimester pregnancies were terminated for fetal collection and analysis. Established secondary fetal fibroblasts were then used for a second embryo reconstruction and transfer. Results: RT-PCR and Fluorescent Activated Cell Scan (FACS) analysis of fetal fibroblast lines showed that all fetuses expressed hCD47 and were GalT null. Further, genomic PCR of fetal DNA confirmed proper transgenic locus structure in the cloned fetuses. Transfer of embryos reconstructed using transgenic fetal fibroblasts has resulted in the birth of two healthy transgenic piglets to date. The newborn transgenic piglets also had the desired phenotype; GalT null and hCD47 expression on all peripheral white blood cell lineages. Colony forming unit assay (CFU) analysis of transgenic piglets also confirmed the expression of hCD47 in bone marrow progenitor cells. Also, in preliminary transplant experiments of ckit+ bone marrow progenitors from transgenic piglets in NOD scid IL2 receptor gamma chain knockout mice (NSG) we could detect porcine cells that were hCD47 positive in the peripheral blood and bone marrow of the recipients. Conclusion: We have been able to successfully generate the first transgenic piglets with widespread expression of the human CD47 gene. The animals appear to be healthy and have normal development. Initial transplant experiments in NSG mice recipients show that hCD47 is advantageous for porcine cells to engraft in the bone marrow.
<title>High bit rate and terabytes optical memory in a disk system</title> (1997)

A very high density optical disk system is newly proposed. The system uses a laser diode array consisting of 100 X 100 (equals 10 thousands) VCSELs (vertical cavity surface emitting lasers) with a very small center hole on each output mirror of each cavity. Each 10 thousand laser diodes can emit evanescent wave on a surface of optical disk medium and can write information bits on it. Each 10 thousand tracks can be written and read at once, by inclining the array about 0.57 degrees toward to a tangential direction of the rotating disk. The Each track that is about 20 nm width doesn't has any borderline between tracks, which means that the total 10 thousand tracks can be traced electrically at once with 199 micron meter width. The new system enable us to write and read information as rapidly as 10 GByte/sec and to store data up to 2 Tera Bytes on one surface of 5.25' disk.
Proteomics in thyroid cytopathology: Relevance of MALDI‐imaging in distinguishing malignant from benign lesions (2016)

Several proteomic strategies are used extensively for the purpose of biomarker discovery and in order to obtain insights into the molecular aspects of cancers, using either body fluids or tissue as samples. Among them, MALDI-imaging can be applied to cytological thyroid specimens to investigate the molecular signatures of different pathological conditions and highlight differences in the proteome that are of relevance for diagnostic and pathogenetic research. In this study, 26 ex-vivo fine needle aspirations from benign thyroid nodules (n = 13) and papillary thyroid carcinomas (n = 13) were analyzed by MALDI-imaging. Based on the specific protein signatures capable of distinguishing the aforementioned patients, MALDI-imaging was able to correctly assign, in blind, the specimens from ten additional FNABs to a malignant or benign class, as later confirmed by the morphological classification. Moreover, some proteins presented a progressive overexpression in malignant phenotypes when compared with Hashimoto's thyroiditis and hyperplastic/follicular adenoma. This data not only suggests that a MALDI-imaging based approach can be a valuable tool in the diagnosis of thyroid lesions but also in the detection of proteins that have a possible role in the promotion of tumorigenic activity.
Coupled-resonator optical waveguides for biochemical sensing of nanoliter volumes of analyte in the terahertz region (2005)

We present a detailed study of coupled-resonator optical waveguide (CROW) based sensors for biochemical sensing. The sensitivity dependence on the CROW structure parameters, such as intercavity distance and cavity type, is investigated for the effects in the THz region of the EM spectrum of introducing small quantities of molecules, such as DNA, in the holes. Introducing the absorptive material into the low-index medium greatly affects the shape of the propagating modes of the CROW and the transmitted E-field. The shift of the resonant frequency also depends linearly on the refractive index changes for off-resonant case (dispersive effect).
High quality aluminum nitride epitaxial layers grown on sapphire substrates (1994)

In this letter we report the growth of high quality AlN epitaxial layers on sapphire substrates. The AlN grown on (00⋅1) sapphire exhibited a better crystalline quality than that grown on (01⋅2) sapphire. An x-ray rocking curve of AlN on (00⋅1) Al2O3 yielded a full width at half-maximum of 97.2 arcsec, which is the narrowest value reported to our knowledge. The AlN peak on (01⋅2) Al2O3 was about 30 times wider. The absorption edge measured by ultraviolet transmission spectroscopy for AlN grown on (00⋅1) Al2O3 was about 197 nm.
Modeling bone morphogenetic protein and bisphosphonate combination therapy in wild‐type and Nf1 haploinsufficient mice (2007)

Recombinant bone morphogenetic proteins (BMPs) show promise in treating the orthopedic complications associated with neurofibromatosis type 1 (NF1), such as congenital pseudarthrosis of the tibia. Minimal scientific information regarding the effects of BMP in the context of NF1 is available. As abnormalities in both bone formation and resorption have been documented in Nf1-deficient mice, we hypothesized that inadequate BMP-induced bone formation could be augmented by cotreatment with the bisphosphonate zoledronic acid (ZA). First, primary osteoblasts isolated from wild type (Nf1(+/+)) and Nf1-deficient (Nf1(+/-)) mice were cultured in the presence and absence of BMP-2. While Nf1(+/-) cells exhibited less osteogenic potential than Nf1(+/+) cells, alkaline phosphatase expression and matrix mineralization for both genotypes were enhanced by BMP-2 treatment. To model this response in vivo, 20 microg BMP-2 was implanted intramuscularly into the quadriceps of mice to induce heterotopic bone. Radiographs revealed significantly less net bone formation in Nf1(+/-) mice compared to Nf1(+/+) controls. To test the effect of an antiresorptive agent, mice were cotreated twice weekly from postoperative day 3 with 0.02 mg/kg ZA or with saline. ZA treatment led to a synergistic increase in the amount of heterotopic bone in both Nf1(+/+) and Nf1(+/-) mice compared with saline controls, as measured by DEXA and histomorphometry. Thus, the anabolic deficiency noted in Nf1(+/-) mice is amenable to stimulation by BMP-2, but mineralized tissue formation remains below that of Nf1(+/+) controls. Bisphosphonate combination therapy is superior to BMP therapy alone in terms of net bone production in vivo in both wild-type and Nf1-deficient mice.
A pathogen‐ and salicylic acid‐induced WRKY DNA‐binding activity recognizes the elicitor response element of the tobacco class I chitinase gene promoter (1999)

Summary Using a simple oligo selection procedure, we have previously identified a tobacco sequence‐specific DNA‐binding activity, TDBA12, that increases markedly during the tobacco mosaic virus (TMV)‐induced hypersensitive response (HR). Based on the binding specificity and the two cDNA clones isolated, TDBA12 is related to a novel class of DNA‐binding factors containing WRKY domains. In the present study, we report that TDBA12 could be induced not only by TMV infection but also by treatment with salicylic acid (SA) or its biologically active analogs capable of inducing pathogenesis‐related (PR) genes and enhanced resistance. TDBA12 was sensitive to temperature and the protein dissociating agent sodium deoxycholate, suggesting that it may be a multimeric factor in which protein–protein interaction is important for the enhanced DNA‐binding activity. Pre‐treatment of nuclear extracts with alkaline phosphatase abolished TDBA12, suggesting that protein phosphorylation is important for its high DNA‐binding activity. TDBA12 specifically recognized the elicitor response element of the tobacco class I basic chitinase gene promoter. The increase in the levels of TDBA12 following TMV infection or SA treatment preceded the induced expression of the tobacco chitinase gene. These results strongly suggest that certain WRKY DNA‐binding proteins may be activated by enhanced protein phosphorylation and regulate inducible expression of defense‐related genes during pathogen‐ and SA‐induced plant defense responses.
Closed-loop Continuous Infusions of Etomidate and Etomidate Analogs in Rats (2011)

Our results suggest that methoxycarbonyl etomidate and carboetomidate may have clinical utility as sedative-hypnotic maintenance agents when hemodynamic stability is desirable.
Fuzzy Connectedness and Object Definition: Theory, Algorithms, and Applications in Image Segmentation (1996)

Images are by nature fuzzy. Approaches to object information extraction from images should attempt to use this fact and retain fuzziness as realistically as possible. In past image segmentation research, the notion of “hanging togetherness” of image elements specified by their fuzzy connectedness has been lacking. We present a theory of fuzzy objects forn-dimensional digital spaces based on a notion of fuzzy connectedness of image elements. Although our definitions lead to problems of enormous combinatorial complexity, the theoretical results allow us to reduce this dramatically, leading us to practical algorithms for fuzzy object extraction. We present algorithms for extracting a specified fuzzy object and for identifying all fuzzy objects present in the image data. We demonstrate the utility of the theory and algorithms in image segmentation based on several practical examples all drawn from medical imaging.
Protective effects of an anti‐inflammatory cytokine, interleukin‐4, on motoneuron toxicity induced by activated microglia (2006)

Microglia-mediated cytotoxicity has been implicated in models of neurodegenerative diseases, such as amyotrophic lateral sclerosis, Parkinson's disease and Alzheimer's disease, but few studies have documented how neuroprotective signals might mitigate such cytotoxicity. To explore the neuroprotective mechanism of anti-inflammatory cytokines, we applied interleukin-4 (IL-4) to primary microglial cultures activated by lipopolysaccharide as well as to activated microglia cocultured with primary motoneurons. lipopolysaccharide increased nitric oxide and superoxide (O(2) (.-)) and decreased insulin-like growth factor-1 (IGF-1) release from microglial cultures, and induced motoneuron injury in microglia-motoneuron cocultures. However, lipopolysaccharide had minimal effects on isolated motoneuron cultures. IL-4 interaction with microglial IL-4 receptors suppressed and nitric oxide release, and lessened lipopolysaccharide-induced microglia-mediated motoneuron injury. The extent of nitric oxide suppression correlated directly with the extent of motoneuron survival. Although IL-4 enhanced release of free IGF-1 from microglia in the absence of lipopolysaccharide, it did not enhance free IGF-1 release in the presence of lipopolysaccharide. These data suggest that IL-4 may provide a significant immunomodulatory signal which can protect against microglia-mediated neurotoxicity by suppressing the production and release of free radicals.