gebhart/patrepeval huggingface dataset:
IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis (2004)

IMGT/V-QUEST, for 'V-QUEry and STandardization', is an integrated software program which analyses the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. The extraordinary diversity of the IG and TR repertoires (10(12) antibodies and 10(12) TR per individual) results from several mechanisms at the DNA level: the combinatorial diversity of the variable (V), diversity (D) and joining (J) genes, the N-diversity and, for IG, the somatic mutations. IMGT/V-QUEST identifies the V, D and J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. IMGT/V-QUEST delimits the structurally important features, frameworks and complementarity-determining regions (the last of these forming the antigen binding site), on the basis of the IMGT unique numbering. The tool localizes the somatic mutations of the IG rearranged sequences. IMGT/V-QUEST also dynamically displays a graphical two-dimensional representation, or IMGT Collier de Perles, of the IG and TR variable regions. Moreover, IMGT/V-QUEST can interact with IMGT/JunctionAnalysis for the detailed description of the V-J and V-D-J junctions, and with IMGT/PhyloGene for the construction of phylogenetic trees. IMGT/V-QUEST is currently available for human and mouse, and partly for non-human primates, sheep, chondrichthyes and teleostei. IMGT/V-QUEST is freely available at http://imgt.cines.fr.
Molecular and Structural Basis of Target Recognition by Calmodulin (1995)

Calmodulin (CaM) acts as an intracellular calcium sensor that translates the Ca2+ signal into a variety of cellular processes. Ca(2+)-CaM recognition of a short polypeptide segment in target proteins induces conformational changes in both CaM and the target, enabling the target protein to become functionally active. The solution and crystal structures of Ca(2+)-CaM bound to peptides derived from three CaM-dependent enzymes reveal structural features that are common in target recognition by Ca(2+)-CaM. Phosphorylation of the target proteins at sites in or near the CaM-binding region modulates binding of CaM, thereby providing an additional mechanism of functional regulation. The structural aspects of target recognition by Ca(2+)-CaM are discussed using mainly the three-dimensional structural information obtained with nuclear magnetic resonance spectroscopy and X-ray diffraction methods.
Phase I Dose-Escalation Study of Intravenous Aflibercept in Combination with Docetaxel in Patients with Advanced Solid Tumors (2012)

On the basis of findings from this study, aflibercept (6 mg/kg) was the dose recommended for further clinical development.
View Matching for Outer-Join Views (2005)

Prior work on computing queries from materialized views has focused on views defined by expressions consisting of selection, projection, and inner joins, with an optional aggregation on top (SPJG views). This paper provides the first view matching algorithm for views that may also contain outer joins (SPOJG views).
Variation of inflammatory indexes after electrical cardioversion of persistent atrial fibrillation. Is there an association with early recurrence rates? (2005)

Inflammation has been recently implicated in the pathophysiology of atrial fibrillation (AF). The aim of this study was to examine the variation of inflammatory indexes during the first week after successful electrical cardioversion of persistent AF. Successive measurements of white blood cell (WBC) count, C-reactive protein (CRP) and fibrinogen levels were performed in 30 cardioverted patients. At the end of the 7-day follow-up period, AF had recurred in 30% of patients. A significant variance was found in serial measurements of fibrinogen levels in the two groups (non-relapse and relapse, p = 0.005). Fibrinogen levels increased significantly in patients who relapsed into AF, but remained stable in patients who remained in sinus rhythm. In the latter patients, CRP values tended to decrease post-cardioversion, but WBC count was significantly lower (p < 0.001) on the 7th day (6083 +/- 1335), compared with baseline values (6648 +/- 1395). The variation of inflammatory indices post-cardioversion might have prognostic implications with regard to sinus rhythm maintenance.
Influenzal Vaccine Response in Systemic Lupus Erythematosus (1978)

The response of patients with systemic lupus erythematosus and normal subjects to systemic immunization and boosting with influenza A vaccines was studied. Symptoms after vaccination were somewhat more frequent in the patients than in the normal subjects; however, all symptoms were minor and no major flare of illness occurred. No significant induction or increase of pre-existing autoantibodies among the patients was detected after vaccination. The immunogenecity of the vaccinations, as assessed by antibody titers, was similar in the patient and control groups. No correlation between serologic response to influenzal antigens and HLA was found. Thus, in this group of patients with systemic lupus erythematosus, who were either in remission or had mild-to-moderate disease activity, killed influenzal vaccination caused no apparent worsening of disease activity.
A distributed control system for an automatic mechanical transmission of a fuel cell city bus (2012)

This paper proposes a study on the distributed control system of a non-clutch automatic mechanical transmission for an electrified power-train applied on a fuel cell city bus. The control system is composed of three electronic controllers, the vehicle control unit (VCU), the electric motor control unit (MCU) and the transmission control unit (TCU). The vehicle can accelerate or decelerate, the electric motor can drive, slide or brake, and the transmission can upshift or downshift. Therefore, there are twelve possible operation modes. Removing the unreasonable modes, four modes need to be considered. A two-layer control strategy based on the four modes is designed, including a two-parameter optimal shift decision strategy and a shift process control strategy with a sliding mode control algorithm. Simulation results show that, compared to the energy consumption in a non-shift strategy, the energy consumption can be reduced by 5.3% and 7.0% with the AMT system in cases of being without and with automatic shifting strategies in the braking process, respectively. Experiments on test bench show that, the upshifting process lasts about 2.09s, and the downshifting process lasts about 1.59s. The time can be reduced by enlarging the torque rate limitations of the electric motor during dynamic process, and by improving the performance of the stepping motor and the mechanical system of the transmission.
Pulse shaping of octave spanning femtosecond laser pulses (2006)

Characterization and pulse shaping of octave spanning femtosecond lasers poses a significant challenge. We have constructed a grating-based pulse shaper for an ultra-broad-bandwidth (620-1020 nm)femtosecond laser, and used it to compensate the phase distortions of the laser, spatial-light modulator and optics within 0.1 rad accuracy accross the entire bandwidth using Multiphoton Intrapulse Interference Phase Scan (MIIPS) without a precompressor. The compensated transform limited pulses generated a second harmonic spectrum with a 12,260 cm(-1) spectral width. Binary phase modulation was introduced by this pulse shaping system to demonstrate high resolution control of the second harmonic generation spectrum.
A genetic mouse model of adult-onset, pervasive central nervous system demyelination with robust remyelination (2010)

Adult-onset demyelinating disorders of the central nervous system represent the most common neurological abnormalities in young adults. Nevertheless, our understanding of disease pathogenesis and recovery in demyelinating disorders remains incomplete. To facilitate investigation into these processes, we have developed a new mouse model system that allows for the induction of dipththeria toxin A subunit expression in adult oligodendrocytes, resulting in widespread oligodendrocyte loss and demyelination of the central nervous system. These mice develop severe ataxia and tremor that correlates with impaired axonal conduction in the spinal cord. Strikingly, these animals fully recover from their motor and physiological defects and display extensive oligodendrocyte replenishment and widespread remyelination. This model system demonstrates the robust reparative potential of myelin in the central nervous system and provides a promising model for the quantitative assessment of therapeutic interventions that promote remyelination.
Formation of dibenzo[b,f]azecines by the reaction of 1-halogenophenethyl-1H-2-benzazepines with dimsylsodium. (1977)

Treatment of 1-(2-bromo-4, 5-dimethoxyphenethyl)-2, 3, 4, 5-tetrahydro-7, 8-dimethoxy-2-methyl-1H-2-benzazepine (7a) with dimsylsodium afforded 5, 6, 7, 8, 13, 14-hexahydrotrans-13, 14-methano-2, 3, 10, 11-tetramethoxy-5-methyldibenzo [b, f] azecine (8) and its cisisomer (9). The structure of the former was confirmed by direct comparison with the authentic sample prepared by the Simmons-Smith reaction of the 13, 14-trans-5, 6, 7, 8-tetrahydrodibenzo [b, f] azecine (11). 5, 6, 7, 8, 13, 14-Hexahydro-11-hydroxy-cis-13, 14-methano-2, 3, 10-trimethoxy-5-methyldibenzo [b, f] azecine (15) was obtained by the reaction of 1-(2-bromo-4, 5-dimethoxyphenethyl)-2, 3, 4, 5-tetrahydro-8-hydroxy-7-methoxy-2-methyl-1H-2-benzazepine (7b) with dimsylsodium. The same reaction by the use of 1-(2-bromo-4, 5-dimethoxyphenethyl)-2, 3, 4, 5-tetrahydro-7-hydroxy-8-methoxy-2-methyl-1H-2-benzazepine (7e) afforded the 13-(methylsulfinyl) methyl-5H-dibenzo [b, g] azacycloundecine (16).
Reduced-intensity conditioning allogeneic hematopoietic stem cell transplantation. (2007)

Chemotherapy and radiotherapy administered in preparation for allogeneic hematopoietic progenitor cell transplantation serve the dual role of providing antitumor activity as well as immunosuppression to prevent graft rejection. Conditioning regimens were initially designed to provide dose-intense therapy in order to overcome tumor resistance. These forms of transplants, referred to as ablative regimens, often result in significant extramedullary toxicity, limiting its applicability to younger, fitter patients. Reduced-intensity conditioning (RIC) transplants are a direct result of an understanding of the immunotherapeutic potential of the donated hematopoietic stem cells. These forms of transplants administer chemoradiotherapy with the intent of allowing for donor cell engraftment with less of an emphasis on dose intensity. In so doing, treatment-related mortality has been reduced, and older-aged patients and those with co-morbidities are now frequently offered this therapy. In the decade since its creation, RIC transplantation has changed the spectrum of patients with malignancies who may benefit from this therapy. For the first time, transplant patients are becoming more representative of the populations most at risk for diseases requiring this therapy. This article reviews the science behind RIC transplants and provides a concise summary of the current body of evidence for the major indications for which it is most commonly employed. The data presented will demonstrate that age should no longer be the sole deciding factor for referral for allogeneic transplant.
Survey of network-based defense mechanisms countering the DoS and DDoS problems (2007)

This article presents a survey of denial of service attacks and the methods that have been proposed for defense against these attacks. In this survey, we analyze the design decisions in the Internet that have created the potential for denial of service attacks. We review the state-of-art mechanisms for defending against denial of service attacks, compare the strengths and weaknesses of each proposal, and discuss potential countermeasures against each defense mechanism. We conclude by highlighting opportunities for an integrated solution to solve the problem of distributed denial of service attacks.
Uptake and presentation of hepatitis C virus-like particles by human dendritic cells (2005)

Hepatitis C virus (HCV) is a major cause of chronic hepatitis worldwide. Interaction of dendritic cells (DCs) with viral particles may play an important role in the immunopathogenesis of HCV infection. Since the synthesis or purification of infectious virions is limited, we used HCV-like particles (HCV-LPs) to study the interaction of HCV with human DCs. Immature DCs exhibited an envelope-specific and saturable binding of HCV-LPs, indicating receptor-mediated DC-HCV-LP interaction. Confocal microscopy revealed that HCV-LPs were rapidly taken up by DCs in a temperature-dependent manner. Competition experiments demonstrated that C-type lectins such as mannose receptor or DC-SIGN (DC-specific intercellular adhesion molecule 3-grabbing nonintegrin) were not sufficient for mediating HCV-LP binding. HCV-LP uptake was followed by DC activation. DCs pulsed with HCV-LPs stimulated HCV core-specific CD4(+) T cells, indicating that uptake of HCV-LPs by DCs leads to antigen processing and presentation on major histocompatibility complex (MHC) class II molecules. Finally, HCV-LP-derived antigens were efficiently cross-presented to HCV core-specific CD8(+) T cells. These findings demonstrate that HCV-LPs represent a novel model system to study HCV-DC interaction allowing definition of the molecular mechanisms of HCV uptake, DC activation, and antigen presentation to T cells. Furthermore, HCV-LP-mediated DC activation and efficient antigen presentation may explain the marked immunogenicity of HCV-LPs in vivo.
Beneficial effects of alkaline phosphatase in septic shock (2006)

In this clinically relevant septic shock model, alkaline phosphatase administration improved gas exchange, decreased interleukin-6 concentrations, and prolonged survival time.
Idiotypes: structure and immunogenicity 1 (1993)

Idiotopes are markers on the variable domains of antigen-specific immunological receptors recognized by anti-idiotypic antibodies or T cells. Therefore, a given antibody or T cell receptor can be identified on the basis of a characteristic idiotypic pattern. The structural correlates for idiotopes on antibodies have been studied by competitive binding assays, electron microscopy, site-directed mutagenesis, and X-ray crystallography. Immunoglobulin idiotopes, recognized by antiidiotypic antibodies, can involve amino acid residues from several hypervariable or framework regions and from either or both of the heavy and light chain variable domains. Recent studies suggest that it may be possible to exploit structural knowledge of idiotopes and anti-idiotopes for the design of new ligands for immunological or other cell surface receptors. In one instance, it has been possible to use the inferred structural features of an anti-idiotope, which mimics a viral protein, to design a small organic molecule with functional properties approximating those of the antigen and the native anti-idiotope. An alternative strategy being explored for creating new vaccines or therapeutic agents involves engineering an amino acid sequence, corresponding to a segment of a selected nominal antigen, into an immunoglobulin variable domain.
Transgenic mice expressing rabbit C-reactive protein are resistant to endotoxemia (1997)

C-reactive protein (CRP), the prototypic acute-phase reactant in humans, is synthesized in liver in response to a wide variety of inflammatory stimuli. We have generated a line of transgenic mice that express rabbit CRP from the rat phospho enol pyruvate carboxykinase (PEPCK) promoter in response to gluconeogenic signals. Here we show that transgenic mice expressing high levels of CRP were partially protected from a lethal challenge of bacterial lipopolysaccharide compared with littermates in which CRP expression had been suppressed. Similar protection was observed with challenges from platelet-activating factor (PAF) and the combination of tumor necrosis factor α (TNF-α) plus interleukin 1β, but not with TNF-α alone. We further demonstrate that although PAF was able to bind CRP, the mechanism by which CRP provides protection probably does not involve sequestration of PAF. The biologically inactive precursor of PAF, lyso-PAF, also bound CRP but did not render the transgenic mice sensitive to PAF when CRP-expressing animals were simultaneously challenged with PAF and an excess of lyso-PAF. These results suggest that CRP functions in vivo by modulating host defense systems.
ADHD prevalence and association with hoarding behaviors in childhood-onset OCD (2010)

ADHD rates were elevated in this sample of individuals with childhood-onset OCD compared to the general population rate of ADHD, and there was a strong association between ADHD and clinically significant hoarding behavior. This association is consistent with recent studies suggesting that individuals with hoarding may exhibit substantial executive functioning impairments and/or abnormalities, including attentional problems.
ATHLATES: accurate typing of human leukocyte antigen through exome sequencing (2013)

Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing. This novel approach should be broadly applicable to research and clinical laboratories.
Metastatic potential of B16 melanoma cells after in vitro selection for organ-specific adherence. (1985)

Heterogeneous primary tumors contain subpopulations of cells that differ in ability to metastasize to specific host organs. We have used cryostat sections of host organs to select for metastatic variants of B16 melanoma cells with increased adhesion to specific syngeneic tissues. By repeating the selection procedure with lung tissue, a subpopulation of cells was isolated that demonstrated a specific increase in binding to cryostat sections of mouse lung. This altered binding was reflected by a sixfold increase in the frequency of lung metastasis 21 d after tail vein injection of the tumor cells. In contrast, B16 melanoma cells selected on cryostat sections of mouse brain showed no increase in adhesion to brain or lung tissue and the metastatic pattern in vivo was not significantly different compared with the parent cell line. When cells selected for increased adhesion to cryostat sections of lung were further examined in vitro, they showed altered morphology and increased motility but no change in growth rate. These results demonstrate that alterations in the adhesive interactions between metastatic tumor cells and a specific host tissue can directly affect the frequency of metastasis to that tissue in vivo.
Marked therapeutic efficacy of a novel polyethylene glycol-SN38 conjugate, EZN-2208, in xenograft models of B-cell non-Hodgkin's lymphoma (2009)

Examination of the clinical utility of SN38 (10-hydroxy-7-ethyl-camptothecin), the active metabolite of CPT-11, has not been possible to date due to poor solubility of SN38. Here we evaluated the activity of EZN-2208, a water-soluble polyethyleneglycol-SN38 conjugate, in pre-clinical models of Burkitt's non-Hodgkin's lymphoma (NHL) (Raji and Daudi), and follicular NHL (DoHH2). In vitro, the IC50 of EZN-2208 ranged from 3-24 nM, which was 30- to 45-fold lower than CPT-11 or 2.5- to 3.5-fold higher than SN38. In both an early-disease Raji model and an advanced-disease Daudi model, treatment with multiple doses of EZN-2208 resulted in 90% and 100% cures of animals, respectively (cure defined as no sign of tumors by gross observations at the termination of study). The activity of EZN-2208 was dramatically superior to that of CPT-11 in all three models. The excellent therapeutic efficacy of EZN-2208 in several B-cell NHL xenograft models merits its evaluation in the clinic for lymphoid malignancies.
A mammalian in vitro model to study gangliogenesis from neural crest cells. (1991)

In spite of considerable advances towards understanding lineages derived from neural crest cells using amphibian and avian embryos, the molecular mechanisms involved in the formation of mammalian peripheral ganglia remain largely unknown, mainly because of the lack of experimental systems that will allow their in vitro manipulation. Here, we present a novel mammalian in vitro model permitting to study gangliogenesis from neural crest cells. This model allowed us to manipulate molecules involved in cell-cell interactions. Our data are in favour of the existence of a hierarchy among adhesion molecules.
Bacterial synthesis of a novel human leukocyte interferon (1981)

A novel human leukocyte interferon cDNA clone (LeIF B) was identified in a cDNA library prepared using polyadenylated mRNA of a myeloblastoid cell line. The nucleotide sequence of LeIF B differs significantly from other published leukocyte interferon cDNA sequences. An expression plasmid was constructed which directs the synthesis in E. coli of 8 x 10(7) interferon units per liter of culture. LeIF B exhibits markedly different specificities from another bacterially synthesized human leukocyte interferon, LeIF A.
Search for 150 MHz radio emission from extrasolar planets in the TIFR GMRT Sky Survey (2014)

The ongoing radio continuum TIFR GMRT Sky Survey (TGSS) using the Giant Metrewave Radio Telescope (GMRT) at 150 MHz offers an unprecedented opportunity to undertake a fairly deep search for low-frequency radio emission from nearby extrasolar planets. Currently TGSS images are available for a little over a steradian, encompassing 175 confirmed exoplanetary systems. We have searched for their radio counterparts in the TGSS (150 MHz), supplemented with a search in the NRAO VLA Sky Survey (NVSS) and the VLA FIRST survey at 1.4 GHz. For 171 planetary systems, we find no evidence of radio emission in the TGSS maps, placing a 3 upper limit between 8.7 mJy and 136 mJy (median 24.8 mJy) at 150 MHz. These non-detections include the 55 Cnc system for which we place a 3 upper limit of 28 mJy at 150 MHz. Nonetheless, for four of the extrasolar planetary systems, we find TGSS radio sources coinciding with or located very close to their coordinates. One of these is 61 Vir: for this system a large radio flux density was predicted in the scenario involving magnetosphere-ionosphere coupling and rotation-induced radio emission. We also found 150 MHz emissions toward HD 86226 and HD 164509, where strong radio emission can be produced by the presence of a massive satellite orbiting a rapidly rotating planet. We also detected 150 MHz emission within a synthesized beam from 1RXS1609 b, a pre-main-sequence star harboring a 14 Jupiter mass planet (or a brown dwarf). With a bright X-ray-UV star and a high mass, the planet 1RXS1609 b presents the best characteristics for rotation-induced emissions with high radio power. Deeper high-resolution observations toward these planetary systems are needed to discriminate between the possibilities of background radio-source and radio-loud planets. At 1.4 GHz, radio emission toward the planet-harboring pulsar PSR B1620-26 is detected in the NVSS. Emissions at 1.4 GHz are also detected toward the very-hot-Jupiter WASP-77A b (in the FIRST survey) and the giant planet HD 43197 b in a highly eccentric orbit (in NVSS). We briefly discuss these detections, as well as the non-detection of the vast majority of exoplanets.