gebhart/patrepeval huggingface dataset:
Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome (2009)

Visibly fluorescent proteins (FPs) from jellyfish and corals have revolutionized many areas of molecular and cell biology, but the use of FPs in intact animals, such as mice, has been handicapped by poor penetration of excitation light. We now show that a bacteriophytochrome from Deinococcus radiodurans, incorporating biliverdin as the chromophore, can be engineered into monomeric, infrared-fluorescent proteins (IFPs), with excitation and emission maxima of 684 and 708 nm, respectively; extinction coefficient >90,000 M(-1) cm(-1); and quantum yield of 0.07. IFPs express well in mammalian cells and mice and spontaneously incorporate biliverdin, which is ubiquitous as the initial intermediate in heme catabolism but has negligible fluorescence by itself. Because their wavelengths penetrate tissue well, IFPs are suitable for whole-body imaging. The IFPs developed here provide a scaffold for further engineering.
Structure−Affinity Relationships of a Unique Nicotinic Ligand:  N-Dimethyl-N4-phenylpiperazinium Iodide (DMPP) (2001)

DMPP is a well-known nicotinic agonist that does not fit any proposed pharmacophore for nicotinic binding and represents a unique ligand among the hundreds of nicotinic agonists studied in the past decades. A systematic modulation of the chemical structure of DMPP, aimed to establish its structure-affinity relationships, is reported. The research has allowed to identify molecules such as 11c, 13c, 14c, and 28c, with affinities for alpha(4)beta(2) receptors in the low nanomolar range, some 2 orders of magnitude lower than the lead compound. The agonistic properties of the most interesting compounds have been assessed by measuring their analgesic activity on mice (hot-plate test). Another result of the research was the identification of DMPP analogues, such as 3a (K(i) = 90 nM) and 14b (K(i) = 180 nM), that maintain affinity for the central nicotinic receptor when the ammonium function is changed into an aminic one and are therefore possible leads for drug development in neurodegenerative diseases.
Retroviral gene transfer induced constitutive expression of interleukin- 2 or interferon-gamma in irradiated human melanoma cells (1992)

Cytokines are important modulators of host antitumor responses. Two of these cytokines, interleukin-2 (IL-2) and interferon gamma (IFN-gamma), are produced after antigen-induced activation of helper lymphocytes. The cytokines are released into the immediate vicinity where they either interact with the appropriate receptors on effector cell populations or are rapidly degraded. To mimic this physiologic release of cytokines at the effector-target site, we used retroviral vectors to transduce melanoma cells with the IL-2 or IFN-gamma cDNA. Five melanoma cell lines were transduced with IL-2- or IFN-gamma-containing vectors and secreted IL-2 at 1 to 40 U/mL/10(6) cells/24 h or IFN-gamma 1 to 8 U/mL/10(6) cells/24 h, respectively. After gamma irradiation, these cells continued to secrete cytokines for about 3 to 4 weeks. Secretion of IFN-gamma induced upregulation of major histocompatibility complex class I molecules in a subset of melanoma cell lines. IL-2 production by human melanoma xenografts induced tumor rejection in BALB/c nu/nu mice, showing the in vivo effect of this cytokine. This study shows that (1) human melanoma cells can be stably transduced with cytokine-containing retroviral vectors; (2) cytokines are secreted constitutively by the transduced tumor cells and have the expected biologic effects in vitro and in vivo; and (3) after gamma irradiation, cytokines continue to be secreted for several weeks. These data suggest that irradiated cytokine-secreting allogenic or autologous tumor cells can be used in vaccination protocols for cancer patients.
Rearrangement of 3,3-Disubstituted 1-Aryl-4,5-dihydro-5-oxo-3H-1,2,4-triazolium Tetrafluoroborates; Part 1. A Versatile Synthesis of 1,5-Disubstituted 2-Aryl-1,2-dihydro-3H-1,2,4-triazol-3-one Tetrafluoroborates (1990)

α-(Arylazo)alkyl isocyanates 3 react with tetrafluoroboric acid to yield 3, 3-disubstituted 1-aryl-4,5-dihydro-5-oxo-3H-1,2,4-triazo-lium tetrafluoroborates 4. These compounds rearrange under mild conditions and in good yields to the tetrafluoroborates of 1,5 disubstituted 2-aryl-1,2-dihydro-3H-1,2, 4-triazol-3-ones 5. Our results show that the nature of the substituents determines their migratory aptitude for the rearrangement.
Influence of ruminal protozoa on site and extent of starch digestion and ruminal fermentation (1993)

Eight ruminally, duodenally, and ileally fistulated sheep were used to study the effects of protozoa on ruminal fermentation and starch digestion in the rumen and intestines. The experimental diet (75% grain DM basis) was based on a mixture of 67% high-moisture corn (HMC) and 33% dry-rolled grain sorghum (DRGS). Protozoa were reduced from 51,286 to 13,987 organisms/mL of ruminal fluid by feeding a diet (13 d) containing 9% tallow and monensin at 27 mg/kg (DM basis). Three sheep were defaunated by intraruminal infusions of lactic acid (20 to 30 g/d) and one sheep by washing the rumen and heating ruminal contents (60 degrees C for 20 min). No differences were observed in DM or starch intake, ruminal fluid pH, lactate concentration, or total tract starch digestibility. Molar proportion of acetate was reduced (48.6 vs 58.3%; P < .01) and propionate was increased (32.2 vs 23.4%; P < .03) by defaunation. Total VFA tended (P = .20) to be lower in faunated sheep (118.5 vs 139.2 mM). In situ rate of starch digestion of HMC (22.3 vs 14.7 %/h; P < .02) and DRGS (5.1 vs 3.3 %/h; P < .009) was increased by defaunation. Starch digestibility (percentage of intake) in the rumen was increased (P < .001) by defaunation (84.2 vs 93.7%) and was reduced (P < .002) in the small intestine (5.2 vs 13.6%). Defaunation increased (P < .03) amylolytic activity (.40 vs .17 units/mg of protein; P < .03) and osmotic pressure (321 vs 245 mOsm/kg; P < .006).(ABSTRACT TRUNCATED AT 250 WORDS)
Ultrastructural vascular changes in pressure zones of rat molar periodontium incident to orthodontic movement (1972)

abstract – Changes in the vasculature of the periodontal ligament of teeth subjected to orthodontic forces have been described. The purpose of the present study was to characterize these changes at the ultrastructural Ievel. In 55 rats, one maxillary first molar was moved buccally by means of a fixed appliance, using forces of 5–25 g. Animals were sacrificed after periods of 30 min to 28 d. The experimental teeth with surrounding periodontal tissues were obtained and processed for electron microscopy. Retardation and stasis of the blood flow occurred within 30 min after force application. After 2 h the vessels in the pressure zone appeared extended and packed with red blood cells which often attained a polygonal shape. After 2 h to 3 d, fragmentation of the erythrocytes occurred. Various patterns of erythrocyte breakdown were observed. Most often the erythrocytes changed into irregularly contoured fragments of various electron densities. Occasionally the fragments exhibited a substructure indicating transformation to a crystalline substance. Also, disintegration of the walls of the blood vessels and release of their contents into the surrounding fibrous tissue was observed after 1–7 d. Regenerative processes were predominating in the 7–28 day specimens.
DNA sequencing using biotinylated dideoxynucleotides and mass spectrometry (2001)

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) has been explored widely for DNA sequencing. The major requirement for this method is that the DNA sequencing fragments must be free from alkaline and alkaline earth salts as well as other contaminants for accurately measuring the masses of the DNA fragments. We report here the development of a novel MS DNA sequencing method that generates Sanger-sequencing fragments in one tube using biotinylated dideoxynucleotides. The DNA sequencing fragments that carry a biotin at the 3'-end are made free from salts and other components in the sequencing reaction by capture with streptavidin-coated magnetic beads. Only correctly terminated biotinylated DNA fragments are subsequently released and loaded onto a mass spectrometer to obtain accurate DNA sequencing data. Compared with gel electrophoresis-based sequencing systems, MS produces a very high resolution of DNA-sequencing fragments, fast separation on microsecond time scales, and completely eliminates the compressions associated with gel electrophoresis. The high resolution of MS allows accurate mutation and heterozygote detection. This optimized solid-phase DNA-sequencing chemistry plus future improvements in detector sensitivity for large DNA fragments in MS instrumentation will further improve MS for DNA sequencing.
Role of Inflammatory Mediators in Angiogenesis (2005)

The angiogenic process involves several cell types and mediators, which interact to establish a specific microenvironment suitable for the formation of new capillaries from pre-existing vessels. Angiogenesis occurs in several physiological and pathological conditions, such as embryo development and wound healing, diabetic retinopathy and tumours. Inflammatory cells, namely monocytes/macrophages, T lymphocytes and neutrophils, fully participate in the angiogenic process by secreting cytokines that may affect endothelial cell (EC) functions, including EC proliferation, migration and activation. Angiogenesis is the result of a net balance between the activities exerted by positive and negative regulators. With regards to inflammatory cells and endothelium cross-talk, such balance is conceptually very similar to that of pro-inflammatory and anti-inflammatory mediators that modulate an appropriate inflammatory response. In this review we will mainly discuss the relevance of both physiological and pathological inflammatory processes in angiogenesis, with particular regards to microenvironmental contribution. We will also describe some of the most relevant pro-inflammatory cytokines in the modulation of the angiogenic process. Furthermore, we will concentrate on what has been recently reported about the mechanism by which some of these cytokines are induced during inflammation to promote a suitable microenvironment for angiogenesis and tumour progression. Pro-angiogenic cytokines, such as IL-1 and TNF, and anti-angiogenic cytokines such as IFN-gamma and IL-12, will be briefly described. We will try to provide a rationale for the use of both cytokines and cytokine blockades as novel potential pharmaceutical targets to modulate angiogenesis in chronic inflammation as well as in cancer.
Cellular Binding of Hepatitis C Virus Envelope Glycoprotein E2 Requires Cell Surface Heparan Sulfate (2003)

The conservation of positively charged residues in the N terminus of the hepatitis C virus (HCV) envelope glycoprotein E2 suggests an interaction of the viral envelope with cell surface glycosaminoglycans. Using recombinant envelope glycoprotein E2 and virus-like particles as ligands for cellular binding, we demonstrate that cell surface heparan sulfate proteoglycans (HSPG) play an important role in mediating HCV envelope-target cell interaction. Heparin and liver-derived highly sulfated heparan sulfate but not other soluble glycosaminoglycans inhibited cellular binding and entry of virus-like particles in a dose-dependent manner. Degradation of cell surface heparan sulfate by pretreatment with heparinases resulted in a marked reduction of viral envelope protein binding. Surface plasmon resonance analysis demonstrated a high affinity interaction (KD 5.2 x 10-9 m) of E2 with heparin, a structural homologue of highly sulfated heparan sulfate. Deletion of E2 hypervariable region-1 reduced E2-heparin interaction suggesting that positively charged residues in the N-terminal E2 region play an important role in mediating E2-HSPG binding. In conclusion, our results demonstrate for the first time that cellular binding of HCV envelope requires E2-HSPG interaction. Docking of E2 to cellular HSPG may be the initial step in the interaction between HCV and the cell surface resulting in receptor-mediated entry and initiation of infection.
The replication of insect pathogenic viruses (nuclear polyhedrosis viruses) in cell cultures. (1980)

The phenomena and steps of replication of insect pathogenic viruses (baculoviruses : nuclear polyhedrosis viruses) in their natural hosts and in insect cell cultures are described.
Development of Systemic Immunity to Glioblastoma Multiforme Using Tumor Cells Genetically Engineered to Express the Membrane-Associated Isoform of Macrophage Colony-Stimulating Factor (1999)

We investigated the ability of Fischer rat T9 glioblastoma cells transduced with cDNA genes for the secreted (s) or membrane-associated (m) isoform of M-CSF to elicit an antitumor response when implanted into syngeneic animals. Intracranial (i.c.) implantation of 1 x 10(5) T9 cells expressing mM-CSF (T9/mM-CSF) resulted in 80% tumor rejection. Electron microscopy of the T9/mM-CSF tumor site, 2-4 days postimplantation, showed marked infiltration by macrophages, many of which were in physical contact with the T9/mM-CSF cells. Animals that rejected T9/mM-CSF cells were resistant to i.c. rechallenge with T9 cells, but not syngeneic MadB106 breast adenocarcinoma cells, suggesting that T9-specific immunity can be generated within the brain via the endogenous APCs. Intracranial injection of parental T9, vector control (T9/LXSN), or T9 cells secreting M-CSF (T9/sM-CSF) was 100% fatal. Subcutaneous injection of 1 x 10(7) T9/sM-CSF, T9/LXSN, or parental T9 cells resulted in progressive tumors. In contrast, T9/mM-CSF cells injected s.c. were destroyed in 7-10 days and animals developed systemic immunity to parental T9 cells. Passive transfer of CD3+ T cells from the spleens of immune rats into naive recipients transferred T9 glioma-specific immunity. In vitro, splenocytes from T9/mM-CSF-immunized rats specifically proliferated in response to various syngeneic glioma stimulator cells. However, only marginal T cell-mediated cytotoxicity was observed by these splenocytes in a CTL assay against T9 target cells, regardless of restimulation with T9 cells. Subcutaneous immunization with viable T9/mM-CSF cells was effective in eradicating i.c. T9 tumors.
Leptin receptor (Ob-R) expression is induced in peripheral blood mononuclear cells byin vitroactivation andin vivoin HIV-infected patients (2002)

Leptin, the Ob gene product, is an adipocyte hormone that centrally regulates weight control. In addition, other effects of leptin in peripheral tissues have been described. Thus, leptin has been found to regulate reproduction, haematopoiesis and immune function. We have found recently that leptin has a stimulatory effect on human peripheral blood mononuclear cells (PBMC). Monocytes are activated by leptin alone whereas T lymphocytes need a suboptimal stimulus of PHA or ConA before further activation by leptin. These effects are mediated by the long isoform of the leptin receptor, which has been shown to trigger signalling in PBMC. In fact, we have found that human leptin stimulates Janus kinase (JAK)-signal transducer and activator of transcription (STAT), phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) pathways in PBMC. In order to assess possible regulation of the long isoform of the leptin receptor (Ob-R) in mononuclear cells upon activation, we have studied the expression of Ob-R by RT-PCR and Western blotting in PBMC activated in vitro by PHA or ConA and in vivo in HIV-infected patients. We have found that in vitro activation and in vivo HIV infection correlates with an increase in leptin receptor expression in PBMC. Moreover, the leptin receptor is tyrosine phosphorylated in PBMC from HIV-infected patients, suggesting that the leptin receptor is activated. These results are consistent with the suggested role of leptin in modulating the immune response.
Screening Mutations of MYBPC3 in 114 Unrelated Patients with Hypertrophic Cardiomyopathy by Targeted Capture and Next-generation Sequencing (2015)

Hypertrophic cardiomyopathy (HCM) is a major cause of sudden cardiac death. Mutations in the MYBPC3 gene represent the cause of HCM in ~35% of patients with HCM. However, genetic testing in clinic setting has been limited due to the cost and relatively time-consuming by Sanger sequencing. Here, we developed a HCM Molecular Diagnostic Kit enabling ultra-low-cost targeted gene resequencing in a large cohort and investigated the mutation spectrum of MYBPC3. In a cohort of 114 patients with HCM, a total of 20 different mutations (8 novel and 12 known mutations) of MYBPC3 were identified from 25 patients (21.9%). We demonstrated that the power of targeted resequencing in a cohort of HCM patients, and found that MYBPC3 is a common HCM-causing gene in Chinese patients. Phenotype-genotype analyses showed that the patients with double mutations (n = 2) or premature termination codon mutations (n = 12) showed more severe manifestations, compared with patients with missense mutations (n = 11). Particularly, we identified a recurrent truncation mutation (p.Y842X) in four unrelated cases (4/25, 16%), who showed severe phenotypes, and suggest that the p.Y842X is a frequent mutation in Chinese HCM patients with severe phenotypes.
Distinction between natural and pathological autoantibodies by immunoblotting and densitometric subtraction: liver-kidney microsomal antibody (LKM) positive sera identify multiple antigens in human liver tissue. (1987)

Using one-dimensional and two-dimensional immunoblotting techniques the reactions of sera from 14 patients with liver-kidney microsomal (LKM) antibody positive chronic active hepatitis (CAH) with human liver microsomal preparations was compared with the reaction of sera from 12 healthy persons and from five patients with systemic lupus erythematosus (SLE). All sera displayed a multiplicity of reactions. This demonstrates the presence of many autoantibodies in normal human sera. It could be shown that all sera react with the cytoskeletal antigens cytokeratin, actin and actomyosin. These reactions were more marked in the autoimmune sera, i.e. LKM-positive CAH and SLE. Densitometric subtraction was found to be a reliable technique to distinguish the natural antigen/autoantibody reactions from pathological, disease-characteristic autoantibodies. It was shown that the pathological LKM autoantibodies recognize non species-specific microsomal proteins at 50 kD of pI 7.5-8.0 at high titres, which are only very weakly recognized by normal or SLE sera. We recommend sensitive immunoblotting techniques and densitometric subtraction as the currently most accurate method to distinguish natural from pathological autoantibodies.
Computer systems and the design of organizational interaction (1988)

The goal of this paper is to relate theory to invention and application in the design of systems for organizational communication and management. We propose and illustrate a theory of design, technology, and action that we believe has been missing in the mainstream of work on office systems. At the center of our thinking is a theory of language as social action, which differs from the generally taken-for-granted understandings of what goes on in an organization. This approach has been presented elsewhere, and our aim here is to examine its practical implications and assess its effectiveness in the design of The Coordinator, a workgroup productivity system that is in widespread commercial use on personal computers.
Assessing the underlying pattern of human germline mutations: lessons from the factor IX gene (1992)

Germline mutations cause or predispose to most disease. Hemophilia B is a useful model for studying the underlying pattern of recent germline mutations in humans because the observed pattern of mutation in factor IX more closely reflects the underlying pattern of mutation than the observed pattern for many other genes. In addition, it is possible to identify and correct for biases inherent in ascertaining only those mutations that cause hemophilia. Aspects of the pattern of germline mutation in the factor IX gene are becoming clear: 1) in the United States, two-thirds of mutations causing mild disease arose from three founders whereas almost all the mutations resulting in either moderate or severe disease arose independently, generally within the past 150 years; 2) direct estimates of the rates of mutation in humans indicate that transitions are more frequent than transversions, which in turn are more frequent than deletions and insertions; 3) transitions at CpG are elevated approximately 24-fold relative to transitions at non-CpG dinucleotides; 4) transversions at CpG are elevated approximately eightfold relative to transversions at non-CpG dinucleotides; 5) the sum total of the dinucleotide mutation rates produces a bias against G and C bases that would be sufficient to maintain the G+C content of the factor IX gene at its evolutionarily conserved level of 40%; and 6) the pattern of mutation is similar for Caucasians residing in the United States and for Asians residing in Asia. Two ideas emerge from this and from an analysis of the pattern of recent deleterious mutations compared with ancient neutral mutations that have been fixed during evolution into the factor IX gene. First, the bulk of germline mutations are likely to arise from endogenous processes rather than environmental mutagens. Second, the factor IX protein is composed mostly of two classes of amino acids: critical residues in which all single-base missense changes will disrupt protein function, and "spacer" residues in which the precise nature of the residue is unimportant but the peptide bond is necessary to keep the critical residues in register. More work is necessary to assess the veracity and generality of these ideas.
Prenatal diagnosis: update on invasive versus noninvasive fetal diagnostic testing from maternal blood (2008)

The modern obstetrics care includes noninvasive prenatal diagnosis testing such as first trimester screening performed between 11 and 14 weeks' gestation and second trimester screening performed between 15 and 20 weeks. In these screening tests, biochemical markers are measured in the maternal blood with or without ultrasound for fetal nuchal translucency with reported accuracy of up to 90%. Invasive procedures, including amniocentesis or chorionic villi sampling, are used to achieve over 99% accuracy. During these procedures direct fetal material is examined and, therefore, these tests are highly accurate with the caveat of a small risk for pregnancy loss. Much research now focuses on other noninvasive highly accurate and risk-free tests that will identify fetal material in the maternal blood. Fetal cells and fetal DNA/RNA provide fetal information but are hard to find in an overwhelming background of maternal cells and in the absence of specific fetal cell markers. The most experience has been accumulated with fetal rhesus and fetal sex determination from maternal blood, with an accuracy of up to 100% by using gene sequences that are absent from maternal blood. Although not clinically applicable yet, fetal cells, fetal DNA/RNA and fetal proteomics in combination with cutting edge technology are described to prenatally diagnose aneuploidies and single-gene disorders.