gebhart/patrepeval huggingface dataset:
An optical frequency scale in exact multiples of 100 GHz for standardization of multifrequency communications (1996)

Absolute laser frequency assignment in projected dense wavelength division multiplexing (DWDM) networks has become a very important issue for standardization purposes. Recently, a proposal was made to the International Telecommunication Union suggesting a set of standard wavelengths in the 1550 mn communications band. It recommended the use of a krypton line at 193.68625 THz as an absolute frequency reference and a set of 32 wavelengths evenly spaced by 100 GHz around that value. In this paper, we propose the use of an optical frequency scale with markers at exact multiples of 100 GHz for standardization. Our proposed scale is independent of the atomic or molecular species used for calibration (and thus accessible to any user), and moreover is uniformly applicable to all spectral regions. We show one way of implementing such a scale in the 1550 nm band through the use of an absolutely calibrated Fabry-Perot resonator set with a free spectral range of 100 GHz.
The role of binding kinetics in therapeutically useful drug action. (2009)

Binding kinetics help define how a medicine will communicate with physiology to produce a desired therapeutic response. Clinical efficacy, duration of action, clinical differentiation and safety may all be influenced by binding kinetics. The optimization of binding kinetics can be used to maximize a drug's therapeutic index and thereby decrease drug attrition. The gap between basic scientific principles and the potential medical value of a drug is currently bridged by the use of empirical assays. The value of binding kinetics to drug discovery will be increased through an improved ability to identify optimal kinetic mechanisms and define kinetic structure activity relationships.
Mouse extraembryonic arterial vessels harbor precursors capable of maturing into definitive HSCs (2013)

During mouse development, definitive hematopoietic stem cells (dHSCs) emerge by late E10.5 to E11 in several hematopoietic sites. Of them, the aorta-gonad-mesonephros (AGM) region drew particular attention owing to its capacity to autonomously initiate and expand dHSCs in culture, indicating its key role in HSC development. The dorsal aorta contains characteristic hematopoietic clusters and is the initial site of dHSC emergence, where they mature through vascular endothelial (VE)-cadherin(+)CD45(-)CD41(low) (type 1 pre-HSCs) and VE-cadherin(+)CD45(+) (type 2 pre-HSCs) intermediates. Although dHSCs were also found in other embryonic niches (placenta, yolk sac, and extraembryonic vessels), attempts to detect their HSC initiating potential have been unsuccessful to date. Extraembryonic arterial vessels contain hematopoietic clusters, suggesting that they develop HSCs, but functional evidence for this has been lacking. Here we show that umbilical cord and vitelline arteries (VAs), but not veins, contain pre-HSCs capable of maturing into dHSCs in the presence of exogenous interleukin 3, although in fewer numbers than the AGM region, and that pre-HSC activity in VAs increases with proximity to the embryo proper. Our functional data strongly suggest that extraembryonic arteries can actively contribute to adult hematopoiesis.
Blocking of heart allograft rejection by intercellular adhesion molecule-1 antisense oligonucleotides alone or in combination with other immunosuppressive modalities. (1994)

Intercellular adhesion molecule-1 (ICAM-1) binds circulating leukocytes through interactions with beta 2 integrins, LFA-1, and macrophage Ag-1. The phosphorothioate antisense oligodeoxynucleotide, IP-3082, specific for ICAM-1 mRNA inhibited ICAM-1, but not vascular cell adhesion molecule-1, mRNA induction and expression of ICAM-1 molecules by mouse endothelioma cells. Scrambled control oligonucleotides were ineffective. Untreated C3H (H-2k) mice rejected C57BL/10 (H-2b) heart allografts with a mean survival time of 7.7 +/- 1.4 days. Administration i.v. of IP-3082 by a 7-day osmotic pump prolonged the survival of heart allografts in a dose-dependent fashion: 1.25 mg/kg, to 11 +/- 0 days; 2.5 mg/kg, to 12 +/- 2.7 days; 5 mg/kg, to 14.1 +/- 2.7 days; and 10 mg/kg, to 15.3 +/- 5.8 days (all p < 0.01). Control IP-1082 (10 mg/kg) was ineffective (7 +/- 0.8 days). Although 7-day anti-LFA-1 mAb (50 micrograms/day; i.p.) prolonged allograft survival to 14.1 +/- 2.7 days, the addition of IP-3082 (5.0 mg/kg x 7 days) induced donor-specific transplantation tolerance (> 150 days). Furthermore, IP-3082 (5 mg/kg x 7 days) acted synergistically with antilymphocyte serum, rapamycin, and brequinar, but not cyclosporin A: a single antilymphocyte serum (0.2 ml) i.p. injection alone prolonged graft survival to 10 +/- 0.5 days (p < 0.01) and in combination with IP-3082 (5 mg/kg), to 32.2 +/- 8.3 days (p < 0.001); rapamycin (0.1 mg/kg x 7 days; i.v.) alone prolonged survival to 13 +/- 7.5 days (p < 0.01), and with IP-3082, to 32.4 +/- 8.9 days (p < 0.03); brequinar (0.5 mg/kg x 7 days; oral gavage) alone to 12 +/- 2.4 days (p < 0.05), and with IP-3082 (5 mg/kg), to 38.8 +/- 30.2 days (p < 0.01); in contrast, cyclosporin A (5 mg/kg x 7 days; i.v.) alone produced graft survival of 9.8 +/- 1.3 days (p < 0.1 and in combination with IP-3082 (5 mg/kg), produced survival of 7.8 +/- 3.5 days (NS). Thus, antisense oligonucleotides may proffer a selective gene-targeted immunosuppressive therapy for organ transplantation.
A Synthetic Metabolic Pathway for Production of the Platform Chemical Isobutyric Acid (2011)

Go green: Isobutyric acid is a high-volume industrial chemical produced from non-sustainable petroleum feedstocks and toxic materials. A synthetic metabolic pathway is constructed in E. coli to enable the biosynthesis of this compound from glucose, a renewable carbon source. The biosynthetic approach is an attractive option from both an economical and environmental point of view. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Induction of apoptosis in rhabdomyosarcoma cells through down-regulation of PAX proteins (1996)

The expression of a number of human paired box-containing (PAX) genes has been correlated with various types of tumors. Novel fusion genes encoding chimeric fusion proteins have been found in the pediatric malignant tumor alveolar rhabdomyosarcoma (RMS). They are generated by two chromosomal translocations t(2;13) and t(1;13) juxtaposing PAX3 or PAX7, respectively, with a forkhead domain gene FKHR. Here we describe that specific down-regulation of the t(2;13) translocation product in alveolar RMS cells by antisense oligonucleotides results in reduced cellular viability. Cells of embryonal RMS, the other major histiotype of this tumor, were found to express either wild type PAX3 or PAX7 at elevated levels when compared with primary human myoblasts. Treatment of corresponding embryonal RMS cells with antisense olignucleotides directed against the mRNA translational start site of either one of these two transcription factors similarly triggers cell death, which is most likely due to induction of apoptosis. Retroviral mediated ectopic expression of mouse Pax3 in a PAX7 expressing embryonal RMS cell line could partially rescue antisense induced apoptosis. These data suggest that the PAX3/FKHR fusion gene and wild-type PAX genes play a causative role in the formation of RMS and presumably other tumor types, possibly by suppressing the apoptotic program that would normally eliminate these cells.
Nuclear Thyroid Hormone Receptor in the Rat Uterus* (1983)

The uterus may be a target organ for T3 action. The present study was done to determine whether uterine nuclei contain receptors for T3 (T3R). Methods were established for the measurement of T3R concentrations in preparations of rat uterine nuclei. The liver was studied concomitantly as a tissue known to contain nuclear T3R. Nuclear fractions were prepared by established procedures and extracted in buffer containing 0.5 M KCl. Specific [125I]T3 binding in the nuclear extract was analyzed by Scatchard plot. In both liver and uterine nuclear extracts, a binding component of high affinity for [125I]T3 (Ka = 1.0-3.0 X 10(9) M-1) was detected. This binding component was lost after heating at 50 C for 10 min. On sucrose density gradients, the principal [125I]T3-binding component in uterine and liver nuclear extracts had a 3.5-4.0 S sedimentation coefficient. Binding specificity was assessed by competition assays for [125I]T3 binding by using stable T3, T4, triiodothyroacetic acid (TRIAC), rT3, and 3,5-diiodothyronine (T2). The order of relative binding affinities (RBAs) in uterine nuclear extracts was T3 greater than TRIAC greater than T4 greater than rT3 greater than T2, and that in liver extracts was TRIAC greater than T3 greater than T4 greater than rT3 greater than T2. In contrast, RBA values derived from dilute serum were distinctly different from both uterine and liver values: T4 greater than T3 greater than rT3 greater than TRIAC greater than T2. The concentrations (femtomoles per mg DNA) of T3R in several tissues were: liver, 595 +/- 162; kidney, 492 +/- 120; uterus, 249 +/- 66; spleen, 48 +/- 10 (mean +/- SE; n = 4). These results provide evidence for the presence of T3R in the nuclear fraction of the rat uterus with properties similar to those of the liver nuclear T3R.
Nanoparticle–Aptamer Conjugates for Cancer Cell Targeting and Detection (2010)

Aptamers are DNA or RNA oligonucleotide sequences that selectively bind to their target with high affinity and specificity. They are obtained using an iterative selection protocol called SELEX. Several small molecules and proteins have been used as targets. Recently, a variant of this methodology, known as cell-SELEX, has been developed for a new generation of aptamers, which are capable of recognizing whole living cells. We have used this methodology for the selection of aptamers, which show high affinity and specificity for several cancer cells. In this chapter, we describe (1) the process followed for the generation of aptamers capable of recognizing acute leukemia cells (CCRF-CEM cells) and (2) the method of enhancing the selectivity and sensitivity of these aptamers by conjugation with a dual-nanoparticle system, which combines magnetic nanoparticles (MNP) and fluorescent silica nanoparticles (FNP). Specifically, the selected aptamers, which showed dissociation constants in the nanomolar range, have been coupled to MNPs in order to selectively collect and enrich cells from complex matrices, including blood samples. The additional coupling of the aptamer to FNPs offers an excellent and highly sensitive method for detecting cancer cells. In order to prove the potential of this rapid and low-cost method for diagnostic purposes, confocal microscopy was used to confirm the specific collection and detection of target cells in concentrations as low as 250 cells. The final fluorescence of the cells labeled with the nanoparticles was quantified using a fluorescence microplate reader.
Cardiac troponin I and T alterations in hearts with severe left ventricular remodeling (1997)

Cardiac troponin T (cTnT) and troponin I (cTnI) have been suggested as new, more specific markers of myocardial cellular damage. The objective of this study was to examine how the distributions of cTnI and cTnT were affected in postinfarction left ventricular remodeled (LVR) myocardium. At 2 months postinfarct in a porcine heart failure model, both Western blot and biochemical assay analyses were performed on left ventricular myocardium remote from the infarct zone in ligation animals (n = 8). Results were compared with data from the left ventricular myocardium from similar sized healthy (control) pigs (n = 7). Autoradiograms from Western blot analysis showed that the protein mass for cTnI and cTnT in LVR hearts decreased 80% (P < 0.001) and 40% (P < 0.02), respectively, when compared with nondiseased tissue. Similarly, the concentrations for cTnI and cTnT in LVR hearts decreased 42% (P < 0.05) and 70% (P < 0.001), respectively, compared with nondiseased normal tissue. The clinical assumption is that the appearance of cTnI and cTnT in the blood is proportional to chronic loss of cTnI and cTnT from injured myocardium associated with left ventricular remodeling.
The cytotoxic T lymphocyte response to multiple hepatitis B virus polymerase epitopes during and after acute viral hepatitis. (1995)

Cytotoxic T lymphocytes (CTL) are thought to contribute to viral clearance and liver cell injury during hepatitis B virus (HBV) infection. Using a strategy involving the in vitro stimulation of peripheral blood mononuclear cells (PBMC) with HBV-derived synthetic peptides containing HLA-A2.1, -A31, and -Aw68 binding motifs, we have previously described CTL responses to several epitopes within the HBV nucleocapsid and envelope antigens in patients with acute hepatitis. In this study we define six HLA-A2-restricted CTL epitopes located in the highly conserved reverse transcriptase and RNase H domains of the viral polymerase protein, and we show that the CTL response to polymerase is polyclonal, multispecific, and mediated by CD8+ T cells in patients with acute viral hepatitis, but that it is not detectable in patients with chronic HBV infection or uninfected healthy blood donors. Importantly, the peptide-activated CTL recognize target cells that express endogenously synthesized polymerase protein, suggesting that these peptides represent naturally processed viral epitopes. DNA sequence analysis of the viruses in patients who did not respond to peptide stimulation indicated that CTL nonresponsiveness was not due to infection by viral variants that differed in sequences from the synthetic peptides. CTL specific for one of the epitopes were unable to recognize several naturally occurring viral variants, except at high peptide concentration, underlining the HBV subtype specificity of this response. Furthermore, CTL responses against polymerase, core, and envelope epitopes were detectable for more than a year after complete clinical recovery and seroconversion, reflecting either the persistence of trace amounts of virus or the presence of long lived memory CTL in the absence of viral antigen. Finally, we demonstrated that wild type viral DNA and RNA can persist indefinitely, in trace quantities, in the serum and PBMC after complete clinical and serological recovery, despite a concomitant, vigorous, and sustained polyclonal CTL response. Since viral persistence is not due to escape from CTL recognition under these conditions, the data suggest that HBV may retreat into immunologically privileged sites from which it can seed the circulation and reach CTL-inaccessible tissues, thereby maintaining the CTL response in apparently cured individuals and, perhaps, prolonging the liver disease in patients with chronic hepatitis.
A phase I/II trial of recombinant methionyl human brain derived neurotrophic factor administered by intrathecal infusion to patients with amyotrophic lateral sclerosis (2000)

The intrathecal delivery of r-metHuBDNF in doses of up to 150 microg/day was well tolerated and appears feasible. The reversible CNS effects with higher dose indicate that BDNF can be delivered cranially against CSF flow. The small number of patients and the design of the study did not permit conclusions to be drawn about the efficacy of the treatment.
Optimal motion and structure estimation (2003)

The problem of estimating motion and structure of a rigid scene from two perspective monocular views is studied. The optimization approach presented is motivated by the following observations of linear algorithms: (1) for certain types of motion, even pixel-level perturbations (such as digitization noise) may override the information characterized by epipolar constraint; (2) existing linear algorithms do not use the constraints in the essential parameter matrix E in solving for this matrix. The authors present approaches to estimating errors in the optimal solutions, investigate the theoretical lower bounds on the errors in the solutions and compare them with actual errors, and analyze two types of algorithms of optimization: batch and sequential. The analysis and experiments show that, in general, a batch technique performs better than a sequential technique for any nonlinear problems. A recursive batch processing technique is proposed for nonlinear problems that require recursive estimation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
B cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus–associated acute liver failure (2010)

Hepatitis B virus (HBV)-associated acute liver failure (ALF) is a dramatic clinical syndrome due to a sudden loss of hepatic cells leading to multiorgan failure. The mechanisms whereby HBV induces ALF are unknown. Here, we show that liver tissue collected at the time of liver transplantation in two patients with HBV-associated ALF is characterized by an overwhelming B cell response apparently centered in the liver with massive accumulation of plasma cells secreting IgG and IgM, accompanied by complement deposition. We demonstrate that the molecular target of these antibodies is the hepatitis B core antigen (HBcAg); that these anti-bodies display a restricted variable heavy chain (V(H)) repertoire and lack somatic mutations; and that these two unrelated individuals with ALF use an identical predominant V(H) gene with unmutated variable domain (IGHV1-3) for both IgG and IgM anti-HBc antibodies, indicating that HBcAg is the target of a germline human V(H) gene. These data suggest that humoral immunity may exert a primary role in the pathogenesis of HBV-associated ALF.
The space of all stereo images (2002)

A theory of stereo image formation is presented that enables a complete classification of all possible stereo views, including non-perspective varieties. Towards this end, the notion of epipolar geometry is generalized to apply to multiperspective images. It is shown that any stereo pair must consist of rays lying on one of three varieties of quadric surfaces. A unified representation is developed to model all classes of stereo views, based on the concept of a quadric view. The benefits include a unified treatment of projection and triangulation operations for all stereo views. The framework is applied to derive new types of stereo image representations with unusual and useful properties.
[Orchids from coffee-plantations in mexico: an alternative for the sustainable use of tropical ecosystems]. (2007)

Life form, endemism, conservation status, and horticultural interest are detailed for orchid species associated to shade coffee-plantations in Mexico. About 11% of the orchid taxa (214 species) found in these agroecosystems are in the Mexican list of species requiring some form of protection. Almost 40% of the species are of horticultural interest. The importance of promoting shaded coffee plantations as an alternative to the conservation of primary plant communities in Mexican and other tropical regions is clear. Long term management plans are recommended.
Detection and identification of Mycobacterium tuberculosis directly from sputum sediments by amplification of rRNA (1993)

Seven hundred fifty-eight processed sputum sediments received for the diagnosis of tuberculosis or other mycobacterial infections were tested by utilizing a rRNA target amplification assay and traditional culture techniques. The results from the rRNA target amplification assay (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test), available in 5 h, were compared with the results from standard culture techniques held for 6 weeks. A total of 119 specimens (16%) were culture positive for Mycobacterium tuberculosis. Overall sensitivity, specificity, positive predictive value, and negative predictive value were 82, 99, 97, and 96%, respectively, for the Gen-Probe assay; 88, 100, 100, and 97%, respectively, for culture; and 53, 99.8, 99.6, and 91%, respectively, for fluorochrome stain. The Gen-Probe assay employs the isothermal enzymatic amplification of M. tuberculosis complex rRNA followed by detection of the amplicon with an acridinium ester-labeled DNA probe. This assay has the potential of reducing the time for diagnosis of tuberculosis to 1 day.
Interleukin-1 and Tumor Necrosis Factor-α Trigger Restriction of Hepatitis B Virus Infection via a Cytidine Deaminase Activation-induced Cytidine Deaminase (AID) (2013)

Virus infection is restricted by intracellular immune responses in host cells, and this is typically modulated by stimulation of cytokines. The cytokines and host factors that determine the host cell restriction against hepatitis B virus (HBV) infection are not well understood. We screened 36 cytokines and chemokines to determine which were able to reduce the susceptibility of HepaRG cells to HBV infection. Here, we found that pretreatment with IL-1β and TNFα remarkably reduced the host cell susceptibility to HBV infection. This effect was mediated by activation of the NF-κB signaling pathway. A cytidine deaminase, activation-induced cytidine deaminase (AID), was up-regulated by both IL-1β and TNFα in a variety of hepatocyte cell lines and primary human hepatocytes. Another deaminase APOBEC3G was not induced by these proinflammatory cytokines. Knockdown of AID expression impaired the anti-HBV effect of IL-1β, and overexpression of AID antagonized HBV infection, suggesting that AID was one of the responsible factors for the anti-HBV activity of IL-1/TNFα. Although AID induced hypermutation of HBV DNA, this activity was dispensable for the anti-HBV activity. The antiviral effect of IL-1/TNFα was also observed on different HBV genotypes but not on hepatitis C virus. These results demonstrate that proinflammatory cytokines IL-1/TNFα trigger a novel antiviral mechanism involving AID to regulate host cell permissiveness to HBV infection.
Alteration of T cell immunity by lentiviral transduction of human monocyte-derived dendritic cells (2004)

DCs transduced with LVs in vitro displayed diminished Th1 functions due to altered DC phenotypes. Our study addresses an important issue concerning lentiviral infection and modification of DC functions, and provides a rational approach using LVs for immunotherapy.