gebhart/patrepeval huggingface dataset:
Viral and immunological determinants of hepatitis C virus clearance, persistence, and disease (2002)

To define the early events that determine the outcome of acute hepatitis C virus (HCV) infection, we compared the course of viremia with the peripheral and intrahepatic T cell response and intrahepatic cytokine profile in six acutely infected chimpanzees. Three different outcomes were observed after peak viral titers were reached: sustained viral clearance, transient viral clearance followed by chronic infection, and chronic infection that persisted at initial peak titers. The results indicate that HCV spread outpaces the T cell response and that HCV rapidly induces but is not controlled by IFN-alphabeta; that viral clearance follows the entry and accumulation of HCV-specific IFN-gamma-producing T cells in the liver; and that it may not require the destruction of infected cells.
Pilocarpine treatment in a mixed cohort of xerostomic patients (2006)

Treatment with pilocarpine hydrochloride tablets may improve saliva secretion in patients taking xerogenic medications and/or suffering from metabolic sialosis expanding the beneficial potential of this sialogogue.
Characterization of the essential cell division gene ftsL (yllD ) of Bacillus subtilis and its role in the assembly of the division apparatus (1998)

We have identified the Bacillus subtilis homologue of the essential cell division gene, ftsL, of Escherichia coli. Repression of ftsL in a strain engineered to carry a conditional promoter results in cell filamentation, with a near immediate arrest of cell division. The filaments show no sign of invagination, indicating that division is blocked at an early stage. FtsL is also shown to be required for septation during sporulation, and depletion of FtsL blocks the activation but not the synthesis of the prespore-specific sigma factor, sigmaF. Immunofluorescence microscopy shows that depletion of FtsL has little or no effect on FtsZ ring formation, but the assembly of other division proteins, DivIB and DivIC, at the site of division is prevented. Repression of FtsL also results in a rapid loss of DivIC protein, indicating that DivIC stability is dependent on the presence of FtsL, in turn suggesting that FtsL is intrinsically unstable. The instability of one or more components of the division apparatus may be important for the cyclic assembly/disassembly of the division apparatus.
Protein kinase C inhibitor and irradiation-induced apoptosis: relevance of the cytochrome c-mediated caspase-9 death pathway. (2000)

Caspases are a family of cysteine proteases that constitute the apoptotic cell death machinery. We report the importance of the cytochrome c-mediated caspase-9 death pathway for radiosensitization by the protein kinase C (PKC) inhibitors staurosporine (STP) and PKC-412. In our genetically defined tumor cells, treatment with low doses of STP or the conventional PKC-specific inhibitor PKC-412 in combination with irradiation (5 Gy) potently reduced viability, enhanced mitochondrial cytochrome c release into the cytosol, and specifically stimulated the initiator caspase-9. Whereas treatment with each agent alone had a minimal effect, combined treatment resulted in enhanced caspase-3 activation. This was prevented by broad-range and specific caspase-9 inhibitors and absent in caspase-9-deficient cells. The tumor suppressor p53 was required for apoptosis induction by combined treatment but was dispensable for dose-dependent STP-induced caspase activation. These results demonstrate the requirement for an intact caspase-9 pathway for apoptosis-based radiosensitization by PKC inhibitors and show that STP induces apoptosis independent of p53.
A Unique Human B Lymphocyte Antigen Defined by a Monoclonal Antibody (1984)

We produced a hybridoma designated 4G7 from a mouse immunized with chronic lymphocytic leukemia cells. The 4G7 hybridoma secretes an IgG1 antibody that is specific for normal and malignant B lymphocytes. Using dual color immunofluorescence staining, this antibody reacted with all immunoglobulin-positive cells but no T cells in normal peripheral blood. There was no detectable 4G7 antigen on monocytes, platelets, red cells, granulocytes, or phytohemagglutinin-activated T cells. When PBL were depleted of 4G7 positive cells and stimulated with pokeweed mitogen, secreted immunoglobulin levels fell to less than 10% of control values on Day 5 and less than 1% of control on Day 7. This antibody was reactive with 155 of 176 B lineage neoplasms on which it was screened. Thirty-five cases of myeloid or T-lymphoid malignancy were negative. Our studies show that the 4G7 antigen modulates in the presence of excess antibody. Free 4G7 antigen was not found circulating in human serum. The cell surface antigen identified by 4G7 was sensitive to pronase proteolysis but resistant to trypsin and chymotrypsin digestion. A comparison of 4G7 with other known B-cell antibodies indicates that the 4G7 antigen has not been previously identified. This antibody is of use for the identification of normal B lymphocytes, the study of B-cell differentiation, and the characterization of lymphoid malignancies.
Complex regional pain syndrome in adults (2011)

Complex regional pain syndrome (CRPS) is a highly painful, limb-confined condition, which arises usually after trauma. It is associated with a particularly poor quality of life, and large health-care and societal costs. The causes of CRPS remain unknown. The condition's distinct combination of abnormalities includes limb-confined inflammation and tissue hypoxia, sympathetic dysregulation, small fibre damage, serum autoantibodies, central sensitization and cortical reorganization. These features place CRPS at a crossroads of interests of several disciplines including rheumatology, pain medicine and neurology. Significant scientific and clinical advances over the past 10 years hold promise both for an improved understanding of the causes of CRPS, and for more effective treatments. This review summarizes current concepts of our understanding of CRPS in adults. Based on the results from systematic reviews, treatment approaches are discussed within the context of these concepts. The treatment of CRPS is multidisciplinary and aims to educate about the condition, sustain or restore limb function, reduce pain and provide psychological intervention. Results from recent randomized controlled trials suggest that it is possible that some patients whose condition was considered refractory in the past can now be effectively treated, but confirmatory trials are required. The review concludes with a discussion of the need for additional research.
The Prudhoe Cognitive Function Test, a scale to assess cognitive function in adults with Down's syndrome: inter‐rater and test–retest reliability (2003)

The PCFT is a highly reliable instrument when used by either specialist or non-specialist raters. It has excellent temporal stability.
The Dicke model in quantum optics: Dicke model revisited (2011)

A short review of recent developments of the Dicke model in quantum optics is presented. The focus is on the model in a cavity at zero temperature and in the rotating wave approximation. Topics discussed include spectroscopic structures, the giant quantum oscillator, entanglement and phase transitions.
Selective estrogen receptor modulators (SERMs) and selective estrogen receptor degraders (SERDs) in cancer treatment (2017)

Breast cancer is the most frequently diagnosed cancer in women, with estrogen receptor positive (ER+) breast cancer making up approximately 75% of all breast cancers diagnosed. Given the dependence on active ER signaling in these tumors, the predominant treatment strategy has been to inhibit various aspects of this pathway including directly antagonizing ER with the use of selective estrogen receptor modulators (SERMs) and selective estrogen receptor degraders (SERDs). Interestingly, the dependence on ER for breast cancer growth is often retained even after progression through several lines of antiestrogen therapy, making ER a bonafide biomarker for this cancer subtype and driving the continued research and development of novel ER-targeted therapeutics to treat this patient population. This, combined with the continuous discovery of mechanisms underlying endocrine resistance, is resulting in a continually evolving treatment landscape for ER+ breast cancer. This review discusses various ER antagonists investigated for the treatment of breast cancer, outlining their pharmacological and tissue-specific mechanisms of action as well as their specified use within the ER+ breast cancer setting. In addition, mechanisms of resistance to SERMs and SERDs, the use of ER antagonists in combination therapy strategies, and the ongoing development of novel drugs are also reviewed in the context of the changing clinical landscape of ER+ breast cancer. Lastly, the role of SERMs and SERDs in non-breast cancer indications is also discussed.
SUITABILITY AND UTILITY OF COMPUTATIONAL ANALYSIS TOOLS: CHARACTERIZATION OF ERYTHROCYTE PARAMETER VARIATION (2002)

Systems engineering can provide insights into multivariate regulatory networks and pooling in complex biological networks that cannot be fully interpreted through experiments alone. Herein, we analyzed the use of phase planes, modal and time-lagged correlation (TLC) analyses of the human erythrocyte to explore the utility of these techniques for understanding the effect of single parameter changes on the behavior of a metabolic network. Specifically, several parameters in key regulatory steps in erythrocyte glycolysis, Rapoport-Leubering bypass, pentose phosphate pathway, adenosine metabolism, and membrane transport were perturbed. The most sensitive parameters were identified based on the steady-state metabolite concentration changes and were explored further. Modal analysis identified relevant time scales for each parameter change. These time scales were further explored using phase plane and TLC analyses. Phase plane and TLC both inferred pooling changes, while TLC also identified changes in the regulatory network structure that resulted from various parameter changes. Each method has strengths and weaknesses for exploring and gaining insight into complex biological networks.
Preparation of 2-Aryl-4a,5-dihydro-4H-[1.3.4]oxadiazino[4,5-a]indoles as a [a]-Fused Indoles Derivatives (1994)

The formation of 2-aryl-4a,5-dihydro-4H-[1,3,4]oxadiazino[4,5-a]indoles was effected by the intramolecular Mitsunobu reaction between primary hydroxy and NH-amide groups in excellent yield
Homonojirimycin and N-methyl-homonojirimycin inhibit N-Iinked oligosaccharide processing (1997)

Homonojirimycin (HNJ) and N-methylhomonojirimycin (MHNJ) were tested as inhibitors of the purified glycoprotein processing enzymes, glucosidase I and glucosidase II. MHNJ was a reasonably good inhibitor of glucosidase I (Ki = 1 x 10(-6) M) and was about three times as effective on this enzyme as was HNJ. On the other hand, HNJ inhibited glucosidase II with a Ki of about 1 x 10(-6) M, whereas MHNJ was three times less effective (Ki = 3 x 10(-5) M). However, the butyl derivative of HNJ had very low activity toward these two processing glucosidases. HNJ and its methyl derivative were also tested in vivo using influenza virus-infected MDCK cells, and measuring the inhibition of N-linked oligosaccharide processing of the viral envelope glycoproteins. With 100 micrograms/ml of MHNJ in the medium, essentially all of the N-linked oligosaccharide chains of the virus were of the "high-mannose" type with the major structure being characterized as Glc3Man9(GlcNAc)2. Similar results were obtained with HNJ although this compound was less effective in vivo as well as in vitro. These results are in keeping with these inhibitors being effective at the glucosidase I step. Both inhibitors were also tested in MDCK cell cultures to determine whether they affected the in vivo synthesis of proteins, or of lipid-linked saccharides. In contrast to deoxynojirimycin, which has been reported to inhibit the formation of lipid-linked saccharides, no effects were seen on either the incorporation of mannose into lipid-linked saccharides or the incorporation of leucine into protein.
Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor (2007)

The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and formation of spore chains, and coincides with the production of a diverse array of clinically relevant antibiotics and other secondary metabolites. These processes are tightly regulated; however, the genes and signals involved have not been fully elucidated. Here, we report a novel tRNA cleavage event that follows the same temporal regulation as morphological and physiological differentiation, and is growth medium dependent. All tRNAs appear to be susceptible to cleavage; however, there appears to be a bias towards increased cleavage of those tRNAs that specify highly utilized codons. In contrast to what has been observed in eukaryotes, accumulation of tRNA halves in S. coelicolor is not significantly affected by amino acid starvation, and is also not affected by induction of the stringent response or inhibition of ribosome function. Mutants defective in aerial development and antibiotic production exhibit altered tRNA cleavage profiles relative to wild-type strains.
The ROMP toolbox upgraded (2010)

This article features the current state of research in olefin metathesis polymerization techniques towards the synthesis of functional polymeric materials. Emphasis is laid on work making use of ring opening metathesis polymerization (ROMP) initiated by ruthenium complexes published in the last five years. Other techniques such as alternating diene metathesis polymerization (ALTMET) are only covered when appropriate. A survey on polymer architectures accessible via olefin metathesis is presented and illustrated with manifold examples from research fields like life science, optics and electronics, sensorics or energy storage. Important new developments such as end-group functionalization or stereoselective polymerization are addressed. A chapter on using alternative and green solvents in ROMP is disclosed as well as an overview on the use of olefin metathesis polymerization using sustainable substrates. Applications in material science such as porous, liquid crystal or self-healing materials close the work.
Incubator embedded cell culture imaging system (EmSight) based on Fourier ptychographic microscopy (2016)

Multi-day tracking of cells in culture systems can provide valuable information in bioscience experiments. We report the development of a cell culture imaging system, named EmSight, which incorporates multiple compact Fourier ptychographic microscopes with a standard multiwell imaging plate. The system is housed in an incubator and presently incorporates six microscopes. By using the same low magnification objective lenses as the objective and the tube lens, the EmSight is configured as a 1:1 imaging system that, providing large field-of-view (FOV) imaging onto a low-cost CMOS imaging sensor. The EmSight improves the image resolution by capturing a series of images of the sample at varying illumination angles; the instrument reconstructs a higher-resolution image by using the iterative Fourier ptychographic algorithm. In addition to providing high-resolution brightfield and phase imaging, the EmSight is also capable of fluorescence imaging at the native resolution of the objectives. We characterized the system using a phase Siemens star target, and show four-fold improved coherent resolution (synthetic NA of 0.42) and a depth of field of 0.2 mm. To conduct live, long-term dopaminergic neuron imaging, we cultured ventral midbrain from mice driving eGFP from the tyrosine hydroxylase promoter. The EmSight system tracks movements of dopaminergic neurons over a 21 day period.
Tumour-associated carbohydrate antigens in breast cancer (2010)

Glycosylation changes that occur in cancer often lead to the expression of tumour-associated carbohydrate antigens. In breast cancer, these antigens are usually associated with a poor prognosis and a reduced overall survival. Cellular models have shown the implication of these antigens in cell adhesion, migration, proliferation and tumour growth. The present review summarizes our current knowledge of glycosylation changes (structures, biosynthesis and occurrence) in breast cancer cell lines and primary tumours, and the consequences on disease progression and aggressiveness. The therapeutic strategies attempted to target tumour-associated carbohydrate antigens in breast cancer are also discussed.
A significantly impaired natural killer cell activity due to a low activity on a per-cell basis in rheumatoid arthritis (2009)

To elucidate the characterization of peripheral natural killer (NK) cells in patients with rheumatoid arthritis (RA), we investigated the NK cell activity, the expression of NK cell activating receptors and intracellular molecules. The NK activity was analyzed in 27 RA patients, 22 primary Sjögren’s syndrome (SS) patients, and 15 healthy individuals using the 51Chrominium release assay. The expression of NK cell activating receptors (NKG2D, CD244, CD2, and CD16) and intracellular molecules (granzyme B, perforin, and TCR ζ chain) in CD3-CD56+ cells were characterized by flow cytometry. The serum cytokine levels (IL-6, TNFα, and IL-18) were measured using ELISA. Both the NK cell activity and the activity on a per-cell basis were observed to significantly decrease in the RA patients in comparison to the controls. The expression of NKG2D and CD244 also significantly decreased in both the RA and primary SS patients, whereas the significant decrease in the CD16 expression was only observed in the RA patients. The titer of the serum IL-6, TNFα, and IL-18 was significantly higher in the RA patients than in the controls. These data suggest that a low NK activity on a per-cell basis might therefore contribute to an impaired NK activity in the patients with RA.
Identification of amino acid residues in the C-terminal tail of big endothelin-1 involved in processing to endothelin-1 (1998)

Big endothelin-1 (big ET-1) is converted to 21-amino acid residue endothelin-1 (ET-1) via a specific cleavage at Trp21-Val22 by endothelin converting enzyme (ECE). This conversion is an essential step to produce bioactive ET-1 and represents a regulatory site in the biosynthesis of this potent vasoconstrictor. ECE-1a, a unique membrane-bound enzyme, processes big ET-1 more efficiently than other big ET isoforms, which mainly differ in the C-terminal tail (residues 22-38). In this study, each of the highly conserved residues, Val22, Pro25, Pro30, Gly32, Leu33, and Gly34 were replaced with Ala in the preproendothelin-1 (PPET-1) cDNA using site-directed mutagenesis. The mutant and wild-type cDNAs were transiently transfected into Chinese hamster ovary cells along with ECE-1a cDNAs, and concentrations of the resulting recombinant peptides, ET-1 and big ET-1, in the transfection media were then measured. The concentration of immunoreactive ET-1 in the media from Val22, Pro25, Pro30, Gly32, and Leu33 mutant PPET-1-transfected cells was 4- to 6-fold lower than that of wild type and (Gly34-->Ala)PPET-1. Moreover, with the exception of Gly34 there was a corresponding increase in the concentrations of immunoreactive big ET-1 in the media from mutants. Similar results were obtained when His27, Val28, and Ser35 of big ET-1( )were substituted with the corresponding residues in big ET-2 and big ET-3. These findings suggest that the C-terminal tail has an important role in the intracellular processing of big ET-1 by ECE-1a. Herein we also report that a recombinant big ET-1 analog we previously generated and characterized, (Ala21)big ET-1, inhibits ECE-1a activity in a dose-dependent (K i=1 microM) and competitive manner.
A testicular antigen aberrantly expressed in human cancers detected by autologous antibody screening (1997)

Serological analysis of recombinant cDNA expression libraries (SEREX) using tumor mRNA and autologous patient serum provides a powerful approach to identify immunogenic tumor antigens. We have applied this methodology to a case of esophageal squamous cell carcinoma and identified several candidate tumor targets. One of these, NY-ESO-1, showed restricted mRNA expression in normal tissues, with high-level mRNA expression found only in testis and ovary tissues. Reverse transcription-PCR analysis showed NY-ESO-1 mRNA expression in a variable proportion of a wide array of human cancers, including melanoma, breast cancer, bladder cancer, prostate cancer, and hepatocellular carcinoma. NY-ESO-1 encodes a putative protein of Mr 17,995 having no homology with any known protein. The pattern of NY-ESO-1 expression indicates that it belongs to an expanding family of immunogenic testicular antigens that are aberrantly expressed in human cancers in a lineage-nonspecific fashion. These antigens, initially detected by either cytotoxic T cells (MAGE, BAGE, GAGE-1) or antibodies [HOM-MEL-40(SSX2), NY-ESO-1], represent a pool of antigenic targets for cancer vaccination.
Dilated cardiomyopathy in transgenic mice expressing a mutant A subunit of protein phosphatase 2A (2000)

The protein phosphatase 2A (PP2A) holoenzyme consists of a catalytic subunit, C, and two regulatory subunits, A and B. The PP2A core enzyme is composed of subunits A and C. Both the holoenzyme and the core enzyme are similarly abundant in heart tissue. Transgenic mice were generated expressing high levels of a dominant negative mutant of the A subunit (A delta 5) in the heart, skeletal muscle, and smooth muscle that competes with the endogenous A subunit for binding the C subunit but does not bind B subunits. We found that the ratio of core enzyme to holoenzyme was increased in A delta 5-expressing hearts. Importantly, already at day 1 after birth, A delta 5-transgenic mice had an increased heart weight-to-body weight ratio that persisted throughout life. Echocardiographic analysis of A delta 5-transgenic hearts revealed increased end-diastolic and end-systolic dimensions and decreased fractional shortening. In addition, the thickness of the septum and of the left ventricular posterior wall was significantly reduced. On the basis of these findings, we consider the heart phenotype of A delta 5-transgenic mice to be a form of dilated cardiomyopathy that frequently leads to premature death.
Molecular cloning and physical mapping of the otsBA genes, which encode the osmoregulatory trehalose pathway of Escherichia coli: evidence that transcription is activated by katF (AppR) (1992)

It has been shown previously that the otsA and otsB mutations block osmoregulatory trehalose synthesis in Escherichia coli. We report that the transcription of these osmoregulated ots genes is dependent on KatF (AppR), a putative sigma factor for certain stationary phase- and starvation-induced genes. The transcription of the osmoregulated bet and proU genes was not katF dependent. Our genetic analysis showed that katF carries an amber mutation in E. coli K-12 and many of its derivatives but that katF has reverted to an active form in the much-used strain MC4100. This amber mutation in katF leads to strain variations in trehalose synthesis and other katF-dependent functions of E. coli. We have performed a molecular cloning of the otsBA genes, and we present evidence that they constitute an operon encoding trehalose-6-phosphate phosphatase and trehalose-6-phosphate synthase. A cloning and restriction site analysis, performed by comparing the cloned fragments with the known physical map of the E. coli chromosome, revealed that the otsBA genes are situated on a 2.9-kb HindIII fragment located 8 to 11 kb clockwise of tar (41.6 min).