gebhart/patrepeval huggingface dataset:
Assembly and secretion of fibrinogen. Degradation of individual chains (1992)

Hep G2 cells produce surplus A alpha and gamma fibrinogen chains. These excess chains, which are not secreted, exist primarily as free gamma chains and as an A alpha-gamma complex. We have determined the intracellular location and the degradative fate of these polypeptides by treatment with endoglycosidase-H and by inhibiting lysosomal enzyme activity, using NH4Cl, chloroquine, and leupeptin. Free gamma chain and the gamma component of A alpha-gamma are both cleaved by endoglycosidase-H, indicating that the gamma chains accumulate in a pre-Golgi compartment. Lysosomal enzyme inhibitors did not affect the disappearance of free gamma chains but inhibited A alpha-gamma by 50%, suggesting that A alpha-gamma is degraded in lysosomes. The degradative fate of individual chains was determined in transfected COS cells which express but do not secrete single chains. Leupeptin did not affect B beta chain degradation, had very little affect on gamma chain, but markedly inhibited A alpha chain degradation. Antibody to immunoglobulin heavy chain-binding protein (GRP 78) co-immunoprecipitated B beta but not A alpha or gamma chains. Preferential binding of heavy chain-binding protein to B beta was also noted in Hep G2 cells and in chicken hepatocytes. Taken together these studies indicate that B beta and gamma chains are degraded in the endoplasmic reticulum, but only B beta is bound to BiP. By contrast A alpha chains and the A alpha-gamma complex undergo lysosomal degradation.
Clean and Convenient One-Pot Synthesis of 4-Hydroxycoumarin and 4-Hydroxy-2-quinolinone Derivatives (2010)

A simple, efficient, and environmentally friendly procedure has been developed for the reaction of Meldrum's acid with phenol, substituted phenols, aniline, or substituted anilines with Eaton's reagent (phosphoric anhydride + methylsulfonic acid) as cyclization reagent. 4-Hydroxycoumarins and 4-hydroxy-2-quinolinones were synthesized in moderate yields by carrying out the reaction in solvent-free, convenient, and clean one-pot preparation.
Chronic human immunodeficiency virus type 1 infection stimulates distinct NF-kappa B/rel DNA binding activities in myelomonoblastic cells (1993)

The relationship between human immunodeficiency virus type 1 (HIV-1) infection and the induction of NF-kappa B binding activity was examined in a myeloid cell model of HIV-1 infection derived from the PLB-985 cell line. Chronic infection of PLB-985 cells led to increased monocyte-specific surface marker expression, increased c-fms gene transcription, and morphological alterations consistent with differentiation along the monocytic pathway. PLB-IIIB cells displayed a constitutive NF-kappa B-like binding activity that was distinct from that induced by tumor necrosis factor alpha or phorbol 12-myristate 13-acetate treatment of the parental PLB-985 cell line. This unique DNA binding activity consisted of proteins of 70, 90, and 100 kDa with a high degree of binding specificity for the NF-kappa B site within the PRDII domain of beta interferon. In this report, we characterize the nature of these proteins and demonstrate that binding of these proteins is also induced following Sendai paramyxovirus infection. The 70-kDa protein corresponds to the NF-kappa B RelA (p65) subunit, which is activated in response to an acute paramyxovirus infection or a chronic HIV-1 infection. Virus infection does not appear to alter the amount of RelA (p65) or NFKB1 (p50) but rather affects the capacity of I kappa B alpha to sequester RelA (p65), therefore leading to constitutive levels of RelA DNA binding activity and to increased levels of NF-kappa B-dependent gene activity. The virally induced 90- to 100-kDa proteins have a distinct binding specificity for the PRDII domain and an AT-rich sequence but do not cross-react with NF-kappa B subunit-specific antisera directed against NFKB1 (p105 or p50), NFKB2 (p100 or p52), RelA (p65), or c-rel. DNA binding of the 90- to 100-kDa proteins was not inhibited by recombinant I kappa B alpha/MAD-3 and was resistant to tryptic digestion, suggesting that these proteins may not be NF-kappa B related. Transient cotransfection experiments demonstrated that RelA and NFKB1 expression maximally stimulated HIV-1 LTR- and NF-kappa B-dependent reporter genes; differences in NF-kappa B-like binding activity were also reflected in higher constitutive levels of NF-kappa B-regulated gene expression in HIV-1-infected myeloid cells.
Characterization of the Sperm Penetration Bioassay (1982)

Parameters influencing the zona‐free hamster egg bioassay for human sperm fertility potential were evaluated. Egg recovery from hamsters superovulated at random with respect to their estrous cycle was enhanced when the PMS‐HCG time interval was lengthened. Prolonged egg exposure to trypsin during zona removal did not adversely affect egg viability. A swim‐up procedure for washing human sperm was superior to a centrifugation‐resuspension technique, although the yield of washed cells was low. The kinetics of sperm capacitation were examined for six different donors over a 22‐hour time period. Capacitation in 0.3% albumin was maximal after 6.5 hours, and penetration scores in five of the six donors declined thereafter. In 3.5% albumin, capacitation was slower with peak penetration levels observed at 13.5 hours. Much higher penetration was noted when sperm, capacitated in 3.5% albumin, were compared with those exposed to 0.3%. Specific recommendations for optimizing bioassay outcome are summarized.
Index of plant hosts of Sclerotinia sclerotiorum (1994)

(1994). Index of plant hosts of Sclerotinia sclerotiorum. Canadian Journal of Plant Pathology: Vol. 16, No. 2, pp. 93-108.
Glucagon and Glucagon-Like Peptide Receptors as Drug Targets (2006)

Glucagon and the glucagon-like peptides are derived from a common proglucagon precursor, and regulate energy homeostasis through interaction with a family of distinct G protein coupled receptors. Three proglucagon-derived peptides, glucagon, GLP-1, and GLP-2, play important roles in energy intake, absorption, and disposal, as elucidated through studies utilizing peptide antagonists and receptor knockout mice. The essential role of glucagon in the control of hepatic glucose production, taken together with data from studies employing glucagon antagonists, glucagon receptor antisense oligonucleotides, and glucagon receptor knockout mice, suggest that reducing glucagon action may be a useful strategy for the treatment of type 2 diabetes. GLP-1 secreted from gut endocrine cells controls glucose homeostasis through glucose-dependent enhancement of beta-cell function and reduction of glucagon secretion and gastric emptying. GLP-1 administration is also associated with reduction of food intake, prevention of weight gain, and expansion of beta-cell mass through stimulation of beta-cell proliferation, and prevention of apoptosis. GLP-1R agonists, as well as enzyme inhibitors that prevent GLP-1 degradation, are in late stage clinical trials for the treatment of type 2 diabetes. Exenatide (Exendin-4) has been approved for the treatment of type 2 diabetes in the United States in April 2005. GLP-2 promotes energy absorption, inhibits gastric acid secretion and gut motility, and preserves mucosal epithelial integrity through enhancement of crypt cell proliferation and reduction of epithelial apoptosis. A GLP-2R agonist is being evaluated in clinical trials for the treatment of inflammatory bowel disease and short bowel syndrome. Taken together, the separate receptors for glucagon, GLP-1, and GLP-2 represent important targets for developing novel therapeutic agents for the treatment of disorders of energy homeostasis.
Dendritic Cells Transduced with an Adenoviral Vector Encoding a Model Tumor-Associated Antigen for Tumor Vaccination (1997)

Evaluation of the potential role of dendritic cells (DCs) as adjuvants for tumor vaccination has focused primarily on techniques that load DCs with peptide tumor antigens. Our aim has been to optimize the induction of antitumor immunity by enhancing the ability of DCs to present tumor-associated antigens endogenously to the afferent lymphatic system in the appropriate major histocompatibility complex (MHC)-restricted context. We have used replication-defective adenovirus vectors (Ads) to transduce DCs with various genes, including tumor antigen genes. We found that 90% of murine bone marrow derived-DCs could be infected with an Ad vector expressing the beta-galactosidase gene and still retain their physiologic and phenotypic characteristics. Furthermore, we demonstrated that transgene expression was detectable in the spleen for at least 3 days following intravenous injection of Ad-transduced DCs. Using a polyoma middle T (PymT) transgenic murine mammary carcinoma model, we have shown that a single injection of 10(5)-4 x 10(6) DCs transduced with an Ad vector expressing PymT provided complete and specific protection against tumor cell challenge in 100% of vaccinated animals. Immunization against the PymT tumor by injection with the PymT expressing Ad vector alone resulted in varying degrees of effectiveness, was highly dependent upon the route of administration, and led to significant hepatic toxicity that was not seen in mice immunized with DC transduced with the Ad vector. Our results suggest that: (i) DCs can be very efficiently modified by ex vivo Ad transduction to express tumor-specific antigens, (ii) such modified DCs appear nontoxic and stimulate a potent antitumor response.
Biomechanical characteristics of the human anterior lens capsule in relation to age. (1997)

Aging of the human anterior lens capsule is associated with a progressive loss of mechanical strength. The young capsule is strong, tough, and highly extensible, whereas the older, thicker capsule is less extensible and much more brittle, and it has a markedly reduced breaking strength.
Novel MHC Class I Structures on Exosomes (2009)

Exosomes are nanometer-sized vesicles released by a number of cell types including those of the immune system, and often contain numerous immune recognition molecules including MHC molecules. We demonstrate in this study that exosomes can display a significant proportion of their MHC class I (MHC I) content in the form of disulfide-linked MHC I dimers. These MHC I dimers can be detected after release from various cell lines, human monocyte-derived dendritic cells, and can also be found in human plasma. Exosome-associated dimers exhibit novel characteristics which include 1) being composed of folded MHC I, as detected by conformational-dependent Abs, and 2) dimers forming between two different MHC I alleles. We show that dimer formation is mediated through cysteine residues located in the cytoplasmic tail domains of many MHC I molecules, and is associated with a low level of glutathione in exosomes when compared with whole cell lysates. We propose these exosomal MHC I dimers as novel structures for recognition by immune receptors.
Micromotor endoscope catheter for in vivo, ultrahigh-resolution optical coherence tomography (2004)

A distally actuated, rotational-scanning micromotor endoscope catheter probe is demonstrated for ultrahigh-resolution in vivo endoscopic optical coherence tomography (OCT) imaging. The probe permits focus adjustment for visualization of tissue morphology at varying depths with improved transverse resolution compared with standard OCT imaging probes. The distal actuation avoids nonuniform scanning motion artifacts that are present with other probe designs and can permit a wider range of imaging speeds. Ultrahigh-resolution endoscopic imaging is demonstrated in a rabbit with <4-microm axial resolution by use of a femtosecond Cr:forsterite laser light source. The micromotor endoscope catheter probe promises to improve OCT imaging performance in future endoscopic imaging applications.
Structural biology of tissue factor, the initiator of thrombogenesis in vivo 1 (1994)

Thromboembolic disorders are commonly associated with cardiovascular, infectious, and neoplastic disease. A major link in the pathophysiology of thrombosis is the excessive triggering of the coagulation pathways by the initiating cofactor molecule termed tissue factor, an integral membrane glycoprotein. The tissue factor extracellular ligand binding domain is predicted to fold in an architecture similar to the cytokine receptor homology module. Functional sites in tissue factor have been defined by a combination of antibody, chemical cross-linking, and mutational analyses providing a model for cofactor function that involves discrete interactions with both enzyme and substrate. The understanding of the structural basis of tissue factor function promises to facilitate rational design of inhibitor molecules for defined functional sites, eventually leading to effective in vivo therapeutics.
Reducing deviations from trajectory components with input shaping (2005)

Input shaping, a technique for reducing residual vibration, was evaluated for use with trajectory following applications. The performance of input shaping for trajectory following was investigated by simulating the response of a two-dimensional system with orthogonal modes. Due to the difficulty of predicting the response of a flexible system to an arbitrary trajectory command, the investigation is limited to the two most common trajectory components: corners and arcs. For a wide range of parameter values the shaped inputs result in better trajectory following than unshaped inputs. The improvements in trajectory following are shown to be robust to parameter uncertainty.
Quality of Service for Ad hoc On-Demand Distance Vector Routing (2001)

The Ad hoc On-Demand Distance Vector (AODV) routing protocol is
intended for use by mobile nodes in an ad hoc network. It offers quick
adaptation to dynamic link conditions, low processing and memory
overhead, low network utilization, and determines routes between
source and destination addresses. To provide quality of service,
extensions can be added to the messages used during route discovery.
These extensions specify the service requirements which must be met by
nodes rebroadcasting a Route Request or returning a Route Reply for a
destination. This draft describes how service partners discover routes
that can satisfy QoS service conditions by using these extensions.
Immunization of mice against murine mammary tumor virus infection and mammary tumor development. (1978)

Formalin-inactivated whole murine mammary tumor virus (MuMTV), VuMTV membranes, the acid-soluble component of MuMTV, and purified MuMTV glycoprotein with a molecular weight of 55,000 (gp55; also designated as gp52) were used as vaccines in an attempt to identify the MuMTV antigen(s) that can protect mice from exogenous MuMTV infection and subsequent tumor development. Formalin-inactivated whole MuMTV, MuMTV membranes, and purified MuMTV gp55 were effective immunogens, whereas the acid-soluble component of MuMTV (which consists mainly of MuMTV gp55) failed to protect mice from challenge with live virus. These results suggest that (a) MuMTV gp55 is the major immunizing antigen and (b) its native conformation must be maintained for it to be an effective vaccine.
Isolation and Characterization of Homogentisate Phytyltransferase Genes from Synechocystis sp. PCC 6803 and Arabidopsis (2002)

Tocopherols, synthesized by photosynthetic organisms, are micronutrients with antioxidant properties that play important roles in animal and human nutrition. Because of these health benefits, there is considerable interest in identifying the genes involved in tocopherol biosynthesis to allow transgenic alteration of both tocopherol levels and composition in agricultural crops. Tocopherols are generated from the condensation of phytyldiphosphate and homogentisic acid (HGA), followed by cyclization and methylation reactions. Homogentisate phytyltransferase (HPT) performs the first committed step in this pathway, the phytylation of HGA. In this study, bioinformatics techniques were used to identify candidate genes, slr1736 and HPT1, that encode HPT from Synechocystis sp. PCC 6803 and Arabidopsis, respectively. These two genes encode putative membrane-bound proteins, and contain amino acid residues highly conserved with other prenyltransferases of the aromatic type. A Synechocystis sp. PCC 6803 slr1736 null mutant obtained by insertional inactivation did not accumulate tocopherols, and was rescued by the Arabidopsis HPT1 ortholog. The membrane fraction of wild-type Synechocystis sp. PCC 6803 was capable of catalyzing the phytylation of HGA, whereas the membrane fraction from the slr1736 null mutant was not. The microsomal membrane fraction of baculovirus-infected insect cells expressing the Synechocystis sp. PCC 6803 slr1736 were also able to perform the phytylation reaction, verifying HPT activity of the protein encoded by this gene. In addition, evidence that antisense expression of HPT1 in Arabidopsis resulted in reduced seed tocopherol levels, whereas seed-specific sense expression resulted in increased seed tocopherol levels, is presented.
New Simple and Rapid Method for Purification of Mesenchymal Stem Cells from the Human Umbilical Cord Wharton Jelly (2011)

We have developed a simple and rapid method for isolation of human umbilical cord matrix stem cells (hUCMS). The umbilical cord contains a virtual inexhaustible source of adult stem cells. We have substantially modified, simplified, and improved previously reported hUCMS isolation procedures in terms of either used enzyme type, or digestion time, and substantially enhanced the final product yield and purity. The isolated hUCMS were positive for CD90, CD117, and SCF, and negative for CD31 and CD45 surface markers. mRNA and related proteins (i.e., Sox2, Oct4a, Nanog, ABCG2, and c-Myc) that coincide with an uncommitted cell status also were detected. hUCMS express genes and proteins for CD90 and Nestin that are associated with mesenchymal stem cells, as well as other genes that specifically relate to different embryonic germ layers, namely, Vimentin, Sox7, Sox17, FoxA2, E-cadherin, and N-cadherin. hUCMS showed multilineage cell differentiation potential into adipogenic, osteogenic, and neural cell phenotypes, under the influence of lineage-specific, differentiation culture media. Moreover, the basal expression of endocrine cell markers makes these cells seemingly suitable for endocrine cell phenotype differentiation. Noteworthy, Activin A induced hUCMS to acquire definitive endoderm cell markers.
Removal of Trypsin Complexed Alpha-2 Macroglobulin by Plasma Fractionation (1993)

The aim of this study is to assess in vitro the efficacy of a plasma f ractionator to remove trypsin complexed α2MG (alpha-2 macroglobulin) from human plasma in a manner analogous to the reticuloendothelial system (RES). Eval filter type “4A” (Kuraray Co., Osaka, Japan) was chosen as a plasma fractionator. Two and one half liters of bovine trypsin spiked human plasma was perfused in vitro through the fractionator in a single pass mode (n=5). The concentrations of complexed α2MG, total α2MG, albumin, and IgM were measured before and after fractionation, and the concentration of free α2MG and the sieving coefficients of each solute were calculated. The concentration of the trypsin complexed a2MG measured by ELISA was significantly decreased by fractionation with Eval “4A” from 103.7 ± 16.7 to 13.8 ± 8.2 mg/L (reduction of 86.7%). Mean sieving coefficients of each solute were 0.133 ± 0.079 in complexed α2MG, 0.203 ± 0.065 in free α2MG, 0.203 ± 0.065 in total α2MG, 0.770 ± 0.130 in albumin, and 0.070 ± 0.010 in IgM. Although in vivo study will be required in patients with acute pancreatitis, in vitro study shows the feasibility of membrane plasma fractionation in eliminating trypsin complexed α2MG.
Cone‐beam computed tomography with a flat‐panel imager: Initial performance characterization (2000)

The development and performance of a system for x-ray cone-beam computed tomography (CBCT) using an indirect-detection flat-panel imager (FPI) is presented. Developed as a bench-top prototype for initial investigation of FPI-based CBCT for bone and soft-tissue localization in radiotherapy, the system provides fully three-dimensional volumetric image data from projections acquired during a single rotation. The system employs a 512 x 512 active matrix of a-Si:H thin-film transistors and photodiodes in combination with a luminescent phosphor. Tomographic imaging performance is quantified in terms of response uniformity, response linearity, voxel noise, noise-power spectrum (NPS), and modulation transfer function (MTF), each in comparison to the performance measured on a conventional CT scanner. For the geometry employed and the objects considered, response is uniform to within 2% and linear within 1%. Voxel noise, at a level of approximately 20 HU, is comparable to the conventional CT scanner. NPS and MTF results highlight the frequency-dependent transfer characteristics, confirming that the CBCT system can provide high spatial resolution and does not suffer greatly from additive noise levels. For larger objects and/or low exposures, additive noise levels must be reduced to maintain high performance. Imaging studies of a low-contrast phantom and a small animal (a euthanized rat) qualitatively demonstrate excellent soft-tissue visibility and high spatial resolution. Image quality appears comparable or superior to that of the conventional scanner. These quantitative and qualitative results clearly demonstrate the potential of CBCT systems based upon flat-panel imagers. Advances in FPI technology (e.g., improved x-ray converters and enhanced electronics) are anticipated to allow high-performance FPI-based CBCT for medical imaging. General and specific requirements of kilovoltage CBCT systems are discussed, and the applicability of FPI-based CBCT systems to tomographic localization and image-guidance for radiotherapy is considered.
The endoplasmic reticular heat shock protein gp96 is transcriptionally upregulated in interferon-treated cells. (1994)

A cDNA clone complementary to an interferon (IFN)-induced mRNA approximately 3 kb in length was identified and sequenced revealing homology with the endoplasmic reticular heat shock protein/ATPase gp96. Both IFN-alpha and -gamma transcriptionally upregulate expression of this gene. gp96 transcripts, protein, and ATPase activity are shown to be enhanced as a result of IFN treatment in two human cell lines and this effect requires de novo protein synthesis. gp96 molecules have recently been implicated in the presentation of endogenous antigens. A number of the key elements in this pathway, the transporter proteins, the major histocompatibility complex (MHC)-linked units of the proteasomes and the MHC class I molecules are known to be IFN inducible. Our results show that yet another molecule suggested to play an accessory role in the endogenous presentation pathway is IFN inducible. Further, our studies represent the first demonstration of modulation of expression of a heat shock protein by a cytokine and identify a new enzymatic activity upregulated in IFN-treated cells.