gebhart/patrepeval huggingface dataset:
Citrobacter rodentium translocated intimin receptor (Tir) is an essential virulence factor needed for actin condensation, intestinal colonization and colonic hyperplasia in mice (2003)

Summary Citrobacter rodentium infection of mice serves as a relevant small animal model to study enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) infections in man. Enteropathogenic E. coli and EHEC translocate Tir into the host cytoplasmic membrane, where it serves as the receptor for the bacterial adhesin intimin and plays a central role in actin condensation beneath the adherent bacterium. In this report, we examined the function of C. rodentium Tir both in vitro and in vivo . Similar to EPEC, C. rodentium Tir is tyrosine phosphorylated and is essential for actin condensation. Citrobacter Tir and EPEC Tir are functionally interchangeable and both require tyrosine phosphorylation to mediate actin rearrangements. In contrast, Citrobacter Tir supports actin nucleation in EHEC independent of tyrosine phosphorylation, while EHEC Tir cannot replace Citrobacter Tir for this function. This indicates that C. rodentium and EPEC use an actin nucleating mechanism different from EHEC. We also found that Tir is expressed and translocated into mouse enterocytes in vivo by C. rodentium during infections. This represents the first direct demonstration of a type III effector translocated in vivo into a natural host by any pathogen. In addition, we showed that Tir, but not its tyrosine phosphorylation, is essential for C. rodentium to colonize the large bowel and induce attaching/effacing (A/E) lesions and colonic hyperplasia in mice, and that both EPEC Tir and EHEC Tir can substitute for Citrobacter Tir for these activities in vivo . These results thus demonstrate that Tir is an essential virulence factor in this infection model. The data also show that the function of Tir tyrosine phosphorylation and its subsequent actin nucleating activity are not essential for C. rodentium colonization of the mouse gut nor for inducing A/E lesions and colonic hyperplasia, thereby uncoupling colonization and disease from actin condensation for this A/E pathogen.
Human T lymphocyte cell line producing colony-stimulating activity (1978)

We derived a permanent human T lymphocyte cell line that elaborates a potent colony-stimulating activity (CSA). The line was established with spleen cells from a patient with a T lymphocyte variant of hairy-cell leukemia. These cells form rosettes with sheep erythrocytes, show a proliferative response to phytohemagglutinin, and are lysed by antithymocyte globulin. They do not synthesize immunoglobulin, nor do they contain Epstein-Barr virus. CSA is regularly detected in the supernatant medium after 3 days culture. In the presence of PHA there is augmented elaboration of CSA; maximal activity is reached by 2 days and is 20% greater than that produced by a feeder layer of 1 X 10(6) peripheral blood leukocytes. One microliter of the supernatant material stimulated colony formation from the light-density nonadherent fraction of human bone marrow; there was maximal activity between 10 and 50 microliter/ml. Conditioned medium from these cells has little effect in stimulating CFU-C from murine bone marrow. The availability of a human T lymphocyte line producing CSA will provide a source for large quantities of the lymphocyte-derived hormone and permit a definition of factors modulating the interaction of T lymphocytes with granulocyte and monocyte stem cells.
Fetal fibronectin: A new screening-marker for bladder cancer? (2001)

Early detection of transitional cell carcinoma (TCC) of the urinary bladder is essential for effective treatment. While several serum markers have been evaluated, none have been widely accepted for practical clinical use. Thus, urinary markers have been introduced and investigated to detect the evidence of bladder cancer. But sensitivity and specificity range around 80% respectively. In a prospective study we evaluated fetal fibronectin in the urine of patients with TCC of the urinary bladder. The positivity of oncofetal fibronectin was measured in morning urine samples by membrane immunoassay. This FFN membrane immunoassay is a qualitative test, a solid-phase immunogold assay. A positive sample will result in a single spot after binding of the oncofetal fibronectin-immunogold complex to the membrane containing a monoclonal antibody specific to oncofetal fibronectin (FDC-6, which specifically recognizes III-CS region). The morning urine samples were collected from patients with TCC before they underwent transurethral resection (n=40, 34 non-invasive and 6 invasive carcinomas) and healthy controls (n=20). Oncofetal fibronectin was investigated in the surgical samples by immunohistochemistry (antibody FDC-6, APAAP technique). We found a positive result for oncofetal fibronectin in 38/40 patients with transitional cell carcinoma of the urinary bladder. Two patients with a small pTaG1-TCC showed negative results. In the urine of healthy controls no positive results were detected. Thus, there is a sensitivity of 95% and a specificity of 100%. The TCC was demonstrated as a source of oncfn. To our knowledge this is the first study showing that patients with an evident TCC have a demonstrable amount of oncofetal fibronectin in the urine. We conclude that a positive result is common in TCC-patients. The sensitivity and specificity of this test seems to be extraordinarily high. Because of the small number of cases further studies are required.
Gelonin analogs with engineered cysteine residues form antibody immunoconjugates with unique properties (1994)

We engineered the ribosome inactivating-protein gelonin (Gel) to generate a family of Gel analogs, each with a single unpaired cysteine residue. The cysteine sites coincide with surface-accessible loops in the probable three-dimensional structure of Gel, or with the positions of endogenous cysteine residues. In most cases, enzymatic activity in vitro was unaltered by this modification. The rGel analogs were conjugated via their unpaired cysteine residue to the anti-CD5 antibody H65, or to H65 Fab and F(ab')2. Several rGel analogs formed immunoconjugates that were up to 6-fold more cytotoxic to antigen-bearing cells than those made with linker-modified rGel, whereas others were less potent. In the rat, the in vivo clearance rates of whole antibody conjugates correlated with their relative in vitro disulfide bond stability, and deconjugation to intact antibody and rGel was the predominant clearance mechanism. Fab conjugates to rGel analogs which differed in their in vitro disulfide bond stability had similar serum clearance rates, suggesting that clearance occurs mainly by removal of intact immunoconjugate from the serum, and is less dependent on deconjugation. Our results demonstrate that rGel analogs with a single cysteine at various positions on the solvent exposed surface are produced efficiently in Escherichia coli (>1 g/liter), and that the position of the cysteine greatly influences the potency and stability of the resulting immunoconjugates.
Dispersion compensation using a planar lightwave circuit optical equalizer (1994)

We successfully demonstrate the effectiveness of a planar lightwave circuit (PLC) optical dispersion equalizer in a 2.5 Gb/s transmission experiment with a 40 km-long 1.3 μm zero-dispersion fiber at 1.55 μm. The dispersion equalizer consists of 5 Mach-Zehnder interferometers with asymmetrical arm lengths cascaded in series. The total insertion loss is 3.5 dB and the maximum dispersion value is 836 psec/nm in the 1.55 μm region.
Important issues for perioperative systemic antimicrobial prophylaxis in surgery (2014)

Most frequently, anaesthesiologists administer perioperative antimicrobial prophylaxis. Identification of core principles and harmonization of protocols should facilitate this task and thus help to improve patient safety and to monitor compliance. However, local and regional epidemiology have to be taken into account in order to establish local protocols.
Production of nerve growth factor by cultured vascular smooth muscle cells from spontaneously hypertensive and Wistar???Kyoto rats (1993)

In contrast to the reports of increased NGF in SHR tissues, our data demonstrate that NGF secretion was lower in VSMC from SHR, and was equivalent in mesenteric artery and thoracic aorta segments from SHR and WKY rats. We have no clear explanation for these observations, but the present results indicate that upregulation of NGF in SHR tissues is not responsible for a simple enhancement of NGF synthesis in VSMC, and suggest a breakdown of the regulatory mechanism or mechanisms of NGF gene expression in SHR tissues.
In Vivo Identification of the Posttrabecular Aqueous Outflow Pathway Using Swept-Source Optical Coherence Tomography (2016)

The continuous posttrabecular aqueous outflow pathway could be identified from a single B-scan and quantitatively analyzed using SS-OCT with en face imaging and volume scan reslicing.
The Role of Surface Carbohydrates in the Hepatic Recognition and Transport of Circulating Glycoproteins (1974)

Introduction Tritiation of Asialoglycoproteins Specificity of Galactose Locus of Uptake and Catabolism Enzymatic Replacement of Sialic Acid Residues Quantitation of the Galactose Requirement Generality of the Phenomenon Differentiation from Phagocytosis Mechanism of Hormone Inactivation Chemical Coupling of Glycopeptides to Proteins New Method of Labeling Glycoproteins Binding by Plasma Membranes Quantitation of Binding Solubilization of Binding Protein Summary
cDNA cloning, expression and characterization of an allergenic L3 ribosomal protein of Aspergillus fumigatus (2003)

Aspergillus fumigatus (Afu) is an important fungal pathogen causing allergic and invasive respiratory disorders. A plethora of multi-functional allergens/antigens secreted by Afu have been implicated in pathogenesis. The present study was undertaken to identify and characterize novel Afu allergen/antigen by cDNA library approach. cDNA library of Afu was immunoscreened with pooled sera of allergic bronchopulmonary aspergillosis (ABPA) patients. The cDNA clone, TS1, reacting significantly with specific IgG antibodies, was selected. cDNA was subcloned and expressed in Escherichia coli. Sequencing of the cDNA revealed an open reading frame (ORF) of 1179 bases coding for a protein with an approximate molecular weight of 44 kDa. Immunoreactivity of the recombinant TS1 protein (rTS1) was evaluated by ELISA and Western blot analysis using pooled sera of ABPA patients. The rTS1 exhibited binding to specific IgG and IgE antibodies present in sera of ABPA patients. The deduced amino acid sequence showed homology to 60S ribosomal protein L3 (RpL3) of Aspergillus nidulans, Saccharomyces cerevisiae and Homo sapiens. The RpL3 of S. cerevesiae, tcm1, to which TS1 sequence shows significant homology (72% identity), is known to be responsible for conferring resistance against trichodermin (antibiotic, inhibiting protein synthesis). The present study has led to identification, cloning and expression of a 44-kDa novel allergen/antigen of Afu with sequence homology to L3 ribosomal protein with a probable role in resistance of Afu to antifungal drugs. Sixty-four per cent sequence identity of Afu RpL3 with human RpL3 and common regions in their predicted epitopes suggest a possibility of involvement of Afu RpL3 in autoimmune reactions due to molecular mimicry.
Brachytherapy in oesophageal carcinoma (1995)

Patients with recurrent or locally advanced oesophageal carcinoma have a poor prognosis. Relief of dysphagia is often the goal of any further treatment. Several methods, including laser re-canalization, prosthetic intubation, dilatation, external beam irradiation (EBI) and intraluminal brachytherapy (IBT) can be used to alleviate dysphagia. In this retrospective review of 11 patients, eight with recurrent tumour and three newly diagnosed patients were treated with low dose rate IBT. Relief of dysphagia was achieved in nine patients, all of whom were able to maintain swallowing of at least a semi-solid diet until death or last follow-up. Toxicity was minimal, but survival was poor, with a median survival of only 3 months. IBT presents several advantages over other palliative methods, especially in recurrent tumours where re-treatment with EBI is often difficult because of normal tissue tolerance. Low dose rate IBT takes only 1-2 days to deliver, is highly effective, has little morbidity and the palliation achieved is relatively durable.
Surfactant Protein A Gene Deletion and Prognostics for Patients with Stage I Non–Small Cell Lung Cancer (2005)

Deletions of the SP-A gene are specific genomic aberrations in bronchial epithelial cells adjacent to and within NSCLC, and are associated with tumor progression and a history of smoking. SP-A deletions might be a useful biomarker to identify poor prognoses in patients with NSCLC who might therefore benefit from adjuvant treatment.
Sequence-targeted Cleavage of single- and Double-stranded DNA by Oligothymidylates Covalently Linked to 1,10-Phenanthroline (1989)

The nuclease activity of 1,10-phenanthroline copper ion was targeted to a specific sequence by attachment of the ligand to the 5' or 3' end of octathymidylates. An acridine derivative was also attached to the other end of the oligothymidylate-phenanthroline conjugate. The duplex formed by the oligothymidylate with its complementary sequence was stabilized by intercalation of the acridine derivative. The reaction induced by 3-mercaptopropionic acid led to a very localized cleavage of a 27-nucleotide-long DNA fragment containing a (dA)8 sequence. At high NaCl concentration or in the presence of spermine, cleavage of the single-stranded 27-mer fragment occurred on both sides of the target sequence. This was ascribed to the formation of a triple helix involving two 1,10-phenanthroline-octathymidylate strands that adopt an antiparallel orientation with respect to each other. When a 27-mer duplex was used as a substrate, cleavage sites were observed on both strands. The location of the cleavage sites led us to conclude that the octathymidylate was bound to the (dA)8.(dT)8 sequence in a parallel orientation with respect to the (dA)8-containing strand. This result reflects the ability of thymine to form two hydrogen bonds with an adenine already engaged in a Watson-Crick base pair. This study shows that it is possible to design DNA-binding oligodeoxynucleotides that could selectively recognize and cleave polypurine-polypyrimidine sequences in double-stranded DNA.
Glial-cell-line-derived neurotrophic factor is required for bud initiation from ureteric epithelium (1997)

The shapes of different organs can be explained largely by two fundamental characteristics of their epithelial rudiments - the pattern of branching and the rate of proliferation. Glial-cell-line-derived neurotrophic factor (GDNF) has recently been implicated in the development of metanephric ureteric epithelium (Pichel, J. G., Shen, L., Sheng, H. Z., Granholm, A.-C., Drago, J., Grinberg, A., Lee, E. J., Huang, S. P., Saarma, M., Hoffer, B.J., Sariola, H. and Westphal, H. (1996). Nature 382, 73-76; Sánchez, M.P., Silos-Santiago, I., Frisén, J., He, B., Lira, S.A. and Barbacid, M. (1996). Nature 382, 70-73; Vega, Q.C., Worby, C.A., Lechner, M.S., Dixon, J.E. and Dressler, G.R. (1996). Proc. Nat. Acad. Sci. USA 93, 10657-10661). We have analysed the target cells of GDNF and the manner in which it controls ureteric development, and have compared it with other growth factors that have been associated with the regulation of branching morphogenesis, namely hepatocyte growth factor (HGF) and transforming growth factor-beta1 (TGFbeta1). We show that GDNF binds directly to the tips of ureteric bud branches, and that it has the ability to promote primary ureteric buds from various segments of Wolffian duct and to attract ureteric branches towards the source of GDNF. It increases cell adhesion, but is not obviously mitogenic for ureteric cells. The data indicate that GDNF is required primarily for bud initiation. Comparison of GDNF, HGF and TGFbeta1 suggests that the latter act later than GDNF, and may represent a partially redundant set of mesenchyme-derived growth factors that control ureteric development. Thus, GDNF is the first defined inducer in the embryonic metanephric kidney.
Optical Imaging Techniques in Cell Biology (2006)

Since the word microscopy was coined in 1656, the evolution of the instrument has had a long and convoluted history. Plagued with problems of chromatic aberration, spherical aberration, and challenges with illumination and resolution, the microscope's technical progression happened in a series of fits and starts until the late 19th century. After E
The Factorized Distribution Algorithm for additively decomposed functions (2003)

FDA (the Factorized Distribution Algorithm) is an evolutionary algorithm that combines mutation and recombination by using a distribution. First the distribution is estimated from a set of selected points. It is then used to generate new points for the next generation. In general a distribution defined for n binary variables has 2/sup n/ parameters. Therefore it is too expensive to compute. For additively decomposed discrete functions (ADFs) there exists an algorithm that factors the distribution into conditional and marginal distributions, each of which can he computed in polynomial time. The scaling of FDA is investigated theoretically and numerically. The scaling depends on the ADF structure and the specific assignment of function values. Difficult functions on a chain or a tree structure are optimized in about O(n/spl radic/n) function evaluations. More standard genetic algorithms are not able to optimize these functions. FDA is not restricted to exact factorizations. It also works for approximate factorizations.
Sorting microparticles into lateral streams using a two-phase rectangular electrokinetic array (2008)

In this paper, we study microparticles in liquid suspension streaming around a closed rectangular track and present lateral sorting of the particles into focused streams. The track consists of a two-phase interdigitated electrode array with symmetric electrodes but asymmetric electrode spacing. We demonstrate the ability to consistently focus an initially scattered suspension of mono-size polystyrene particles into a single narrow stream traveling around the circuit. We also demonstrate the ability of the device to separate suspensions of multiple sphere sizes into distinct streams according to size. We report that focusing positions are generally consistent for a given particle size, regardless of the presence of other particles in the suspension, and that particles sort by decreasing size from the center to the edge of the track. These results are compared with finite element analysis of the steady-state electric field and analytical approximations of the electrokinetic forces. We hypothesize that the sorting is due to a balance between phase-based and gradient-based dielectrophoretic forces.
A prospective multicenter study on genome wide associations to ranibizumab treatment outcome for age-related macular degeneration (2017)

We conducted a genome-wide association study (GWAS) on the outcome of anti-VEGF treatment for exudative age-related macular degeneration (AMD) in a prospective cohort. Four hundred and sixty-one treatment-naïve AMD patients were recruited at 13 clinical centers and all patients were treated with 3 monthly injections of ranibizumab followed by pro re nata regimen treatment for one year. Genomic DNA was collected from all patients for a 2-stage GWAS on achieving dry macula after the initial treatment, the requirement for an additional treatment, and visual acuity changes during the 12-month observation period. In addition, we evaluated 9 single-nucleotide polymorphisms (SNPs) in 8 previously reported AMD-related genes for their associations with treatment outcome. The discovery stage with 256 patients evaluated 8,480,849 SNPs, but no SNPs showed genome-wide level significance in association with treatment outcomes. Although SNPs with P-values of <5 × 10<sup>-6</sup> were evaluated in replication samples of 205 patients, no SNP was significantly associated with treatment outcomes. Among AMD-susceptibility genes, rs10490924 in ARMS2/HTRA1 was significantly associated with additional treatment requirement in the discovery stage (P = 0.0023), and pooled analysis with the replication stage further confirmed this association (P = 0.0013). ARMS2/HTRA1 polymorphism might be able to predict the frequency of injection after initial ranibizumab treatment.
The role of natural killer cells in immunity against multiple myeloma (2012)

Multiple myeloma (MM) is an essentially incurable malignancy associated with profound immune dysregulation. Despite the advent of novel therapies and improvements in survival over the last 10 years, death from progressive disease and infection remains a common outcome. Natural killer (NK) cells are CD56(+)CD3(−) large granular lymphocytes that constitute a key cellular subset of the innate immune system. For over 30 years, the relationship between NK cells and MM has been described in the clinical setting and characterized in the laboratory. Data suggest that NK cells may play a role in the immune response to MM; however, this effect is lost due to immunoevasive strategies utilized by MM. Nevertheless, progress in the understanding of the mechanisms perpetuating this effect have led to new opportunities to recover or augment NK cell function therapeutically in MM. In fact, the novel agents thalidomide, lenalidomide and bortezomib all confer anti-MM effects, in part, through enhancement of NK cell function. Currently, the development of therapies designed specifically to increase NK cell cytotoxicity against MM is under way. The present review summarizes the current understanding of the NK cell versus MM effect and characterizes therapeutic interventions that exert anti-MM efficacy via NK cell function against the disease.
Detection of Proteinases inSaccharomyces cerevisiaeby Flow Cytometry (2005)

The physiological state of a yeast population used for inoculation determines how rapidly the cells adapt to new environmental conditions, begin proliferating and utilising extract. The decision as to whether a yeast culture is suitable for re-pitching should not be based only on viability determinations since this can be misleading. Increased proteolytic activity in a yeast population indicates the onset of senescence. A flow cytometric method has been developed for measuring a wide variety of proteinases in Saccharomyces cerevisiae employing a commercially available casein-dye conjugate. The detection of intracellular proteinase activity gives an early indication of apoptotic events and allows improved assessment of the physiological state of a yeast population. This knowledge will assist the industry to optimize the selection of yeast and its subsequent fermentation performance. Yeast cell autolysis with all its negative consequences for beer quality and stability will thus be minimised.
Calculation of the external quantum efficiency of light emitting diodes with different chip designs (2004)

External quantum efficiency of GaN light emitting diode (LED) with SiO2-coated grating patterned substrate and/or surface-textured structure were calculated theoretically. Our results show that the enhancement of the reflectance coefficient was obtained by a factor of about 30% in LED chip with SiO2-coated grating patterned substrate, compared to conventional LED chip. The grating parameters such as height and width should be optimized above h=w/4. Moreover, by employing surface-textured structure, the loss factor at top surface of LED was reduced dramatically by decreasing of total internal reflectance at GaN-epoxy interface as the incident angle is higher than the critical angle. Therefore, external quantum efficiency can reach up to about 60% if internal quantum efficiency corresponds to about 90% because of reducing the total loss parameter at top and bottom surface of LED. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)