gebhart/patrepeval huggingface dataset:
Increased AKT Activity Contributes to Prostate Cancer Progression by Dramatically Accelerating Prostate Tumor Growth and Diminishing p27Kip1 Expression (2000)

The PTEN tumor suppressor gene is frequently inactivated in human prostate cancers, particularly in more advanced cancers, suggesting that the AKT/protein kinase B (PKB) kinase, which is negatively regulated by PTEN, may be involved in human prostate cancer progression. We now show that AKT activation and activity are markedly increased in androgen-independent, prostate-specific antigen-positive prostate cancer cells (LNAI cells) established from xenograft tumors of the androgen-dependent LNCaP cell line. These LNAI cells show increased expression of integrin-linked kinase, which is putatively responsible for AKT activation/Ser-473 phosphorylation, as well as for increased phosphorylation of the AKT target protein, BAD. Furthermore, expression of the p27(Kip1) cell cycle regulator was diminished in LNAI cells, consistent with the notion that AKT directly inhibits AFX/Forkhead-mediated transcription of p27(Kip1). To assess directly the impact of increased AKT activity on prostate cancer progression, an activated hAKT1 mutant was overexpressed in LNCaP cells, resulting in a 6-fold increase in xenograft tumor growth. Like LNAI cells, these transfectants showed dramatically reduced p27(Kip1) expression. Together, these data implicate increased AKT activity in prostate tumor progression and androgen independence and suggest that diminished p27(Kip1) expression, which has been repeatedly associated with prostate cancer progression, may be a consequence of increased AKT activity.
Forecasting return volatility in the presence of microstructure noise (2010)

Measuring and forecasting volatility of asset returns is very important for asset trading and risk management. There are various forms of volatility estimates, including implied volatility, realized volatility and volatility assumed under stochastic volatility models and GARCH models. Research has shown that these different methods are closely related but have different perspectives, strengths and weaknesses. In order to exploit their connections and take advantage of their different strengths, in this paper, we propose to jointly model them with a vector fractionally integrated autoregressive and moving average (VARFIMA) model. The model is also used for forecasting purpose. In addition, we investigate the impacts of the two realized volatility estimators obtained from intra-daily high frequency data on the forecasts of return volatility. Our methods are applied to five individual stocks and forecasting performances are compared with those from a GARCH(1,1) model and a basic stochastic volatility (SV) model and their extended versions. The proposed VARFIMA model outperforms other volatility forecasting models in this study. Our results show that including the two different realized volatility estimators obtained from the intra-daily high frequency data in the VARFIMA model imposes significant impacts on the forecasting precision for return volatility.
T cell receptor vβ repertoire of double‐negative α/β t cells in patients with systemic sclerosis (1992)

The V beta repertoire on DN alpha/beta T cells in PBL from patients with SSc is rather restricted.
Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are bIL170, AF009630; bIL120, AY054975; bIL15, AY054976; bIL191, AY054977; bIL77, AY054978. (2002)

The complete 31754 bp genome of bIL170, a virulent bacteriophage of Lactococcus lactis belonging to the 936 group, was analysed. Sixty-four ORFs were predicted and the function of 16 of them was assigned by significant homology to proteins in databases. Three putative homing endonucleases of the HNH family were found in the early region. An HNH endonuclease with zinc-binding motif was identified in the late cluster, potentially being part of the same functional module as terminase. Three putative structural proteins were analysed in detail and show interesting features among dairy phages. Notably, gpl12 (putative fibre) and gpl20 (putative baseplate protein) of bIL170 are related by at least one of their domains to a number of multi-domain proteins encoded by lactococcal or streptococcal phages. A 110- to 150-aa-long hypervariable domain flanked by two conserved motifs of about 20 aa was identified. The analysis presented here supports the participation of some of these proteins in host-range determination and suggests that specific adsorption to the host may involve a complex multi-component system. Divergences in the genome of phages of the 936 group, that may have important biological properties, were noted. Insertions/deletions of units of one or two ORFs were the main source of divergence in the early clusters of the two entirely sequenced phages, bIL170 and sk1. An exchange of fragments probably affected the regions containing the putative origin of replication. It led to the absence in bIL170 of the direct repeats recognized in sk1 and to the presence of different ORFs in the ori region. Shuffling of protein domains affected the endolysin (putative cell-wall binding part), as well as gpl12 and gpl20.
Green Synthetic Method for 1,5‐Disubstituted Carbohydrazones (2006)

Abstract A green synthetic method for 1,5‐disubstituted carbohydrazones is described. The reaction of dimethyl carbonate with hydrazine hydrate first gave carbohydrazide, which further reacted with various aromatic aldehydes or aliphatic ketones under solvent‐free conditions to efficiently afford 1,5‐disubstituted carbohydrazone. This protocol has the advantages of using nontoxic dimethyl carbonate as starting material, no use of organic solvents, short reaction time, high yield, and simple workup procedure.
Dexmedetomidine to treat opioid withdrawal in infants following prolonged sedation in the pediatric ICU (2006)

This retrospective study aims to report on the use of dexmedetomidine to treat opioid withdrawal following sedation during mechanical ventilation in a cohort of infants. Seven infants in the pediatric intensive care unit of a tertiary care center, ranging in age from three to 24 months (12.4 +/- 8.2 months) and in weight from 4.6 to 15.4 kgs (9.9 +/- 4.2 kgs), had received a continuous fentanyl infusion, supplemented with intermittent doses of midazolam for sedation, during mechanical ventilation. Withdrawal was documented by a Finnegan score > or = 12. Dexmedetomidine was administered as a loading dose of 0.5 microg/kg/hr, followed by an infusion of 0. 5 microg/kg/hr. Dexmedetomidine effectively controlled the signs and symptoms of withdrawal in the seven patients. Subsequent Finnegan scores were < or = 7 at all times (median 4, range 1 to 7). Two patients required a repeat of the loading dose and an increase of the infusion to 0.7 microg/kg/hr. These two patients had received higher doses of fentanyl than the other five patients (8.5 +/- 0.7 versus 4.6 +/- 0.5 microg/kg/hr, p < 0.0005). No adverse hemodynamic or respiratory effects related to dexmedetomidine were noted. This report involves the largest cohort of patients to receive dexmedetomidine in the treatment of withdrawal following opioid and benzodiazepine sedation during mechanical ventilation. We conclude that dexmedetomidine offers a viable option for such issues in the pediatric intensive care unit (PICU) setting.
Asymmetric Morita−Baylis−Hillman Reaction Catalyzed by Isophoronediamine-Derived Bis(thio)urea Organocatalysts (2006)

New and improved bis(thio)urea catalysts were synthesized from isophoronediamine (IPDA) and tested in the Morita-Baylis-Hillman reaction. The best results were achieved in the reaction of 2-cyclohexen-1-one with cyclohexanecarbaldehyde, using the catalyst depicted above, in combination with a novel base (N,N,N',N'-tetramethylisophoronediamine, TMIPDA) in toluene. The desired Morita-Baylis-Hillman product was obtained in 75% yield and 96% ee.
Quantitative approaches to computational vaccinology (2002)

This article reviews the newly released JenPep database and two new powerful techniques for T-cell epitope prediction: (i) the additive method; and (ii) a 3D-Quantitative Structure Activity Relationships (3D-QSAR) method, based on Comparative Molecular Similarity Indices Analysis (CoMSIA). The JenPep database is a family of relational databases supporting the growing need of immunoinformaticians for quantitative data on peptide binding to major histocompatibility complexes and to the Transporters associated with Antigen Processing (TAP). It also contains an annotated list of T-cell epitopes. The database is available free via the Internet (http://www.jenner.ac.uk/JenPep). The additive prediction method is based on the assumption that the binding affinity of a peptide depends on the contributions from each amino acid as well as on the interactions between the adjacent and every second side-chain. In the 3D-QSAR approach, the influence of five physicochemical properties (steric bulk, electrostatic potential, local hydrophobicity, hydrogen-bond donor and hydrogen-bond acceptor abilities) on the affinity of peptides binding to MHC molecules were considered. Both methods were exemplified through their application to the well-studied problem of peptides binding to the human class I MHC molecule HLA-A*0201.
[Detection of methicillin-resistant Staphylococcus aureus using PCR and non-radioactive DNA probes (II)]. (1993)

Methicillin resistance in staphylococci is primarily due to the presence of a mec A gene which encodes the novel penicillin-binding protein 2'. Some chromosomal factors, fem A and fem B, also participate in the expression of methicillin resistance in S. aureus. This study was designed to detect mec A, fem A and fem B genes for identification of staphylococcal species and for discrimination of methicillin-resistant cells. Three different pairs of DNA primers (PBP2'AF-PBP2'AR, fem AF-fem AR and fem BF-fem BR) complementary to unique regions of mec A, fem A and fem B genes were synthesized for use in polymerase chain reaction with DNAs of methicillin-sensitive S. aureus (MSSA), S. epidermidis, methicillin-resistant S. aureus (MRSA) and S. epidermidis. Amplified target DNAs of 630, 509, and 651 bp were resolved on ethidium bromide-stained gel, and hybridized to DNA probes conjugated to alkaline phosphatase. When applied to pure cultures on the MRSA screen agar, all three DNA probes tested detected MRSA in 47 of 61 culture-positive specimens (77.1%); the detection ratio of MRSA with mec A and either fem A or fem B probes was increased to 95.9%. By contrast, the fem A and fem B probes did not detect S. epidermidis. The result of detecting these species streaked on mannitol-salt agar were similar, while the detection of MSSA with the fem A and fem B probes was incomplete irrespective of the presence or absence of mec A. These findings suggest a good correlation between cultivation and DNA probe assay with respect to MRSA detection.
Platelet glycoprotein IIb. Chromosomal localization and tissue expression. (1987)

The GPIIb-IIIa complex functions as a receptor for cytoadhesive proteins on the platelet surface. Both GPIIb and GPIIIa are synthesized by a human erythroleukemia (HEL) cell line. We isolated several cDNA clones by screening a HEL cell cDNA library with an oligonucleotide derived from amino acid sequence of GPIIb. Nucleotide and amino acid sequences were determined from 703 bp of one of these clones. Amino acid sequence of purified platelet GPIIb peptides confirmed the identity of the clone. The cDNA encodes the carboxyl terminus of the large (alpha) subunit of GPIIb and all of the smaller (beta) subunit of GPIIb. By hybridizing the cDNA directly to chromosomes separated by dual laser chromosome sorting, the gene for GPIIb was mapped to chromosome 17. Northern blot analysis showed a approximately 3.4-kb GPIIb mRNA in HEL cells. We also compared the amino acid sequences determined from eight additional platelet GPIIb peptides with the derived amino acids from a published HEL cell GPIIb cDNA, and the platelet and HEL cell proteins appear to be the same. Despite previous reports that vascular endothelial cells and monocytes contain GPIIb, no GPIIb mRNA was observed in either type of cell. Thus, GPIIb appears to be specific for the platelet-megakaryocyte membrane and is distinct from the alpha subunits of the adhesion receptors in other normal tissues.
The effect of synthetic peptides corresponding to Fc sequences in human IgG 1 on various steps in the B cell activation pathway (1988)

The influence of synthetic peptides comrizing sequences in the exposed positions of the Fc region of human IgG1 was tested on B lymphocyte activation. CH2 domain peptides having an inhibitory effect on antibody-dependent cellular cytotoxicity, as well as the whole Fc fragment, induced the appearance of the early signs of activation on resting B lymphocytes such as increase in cell volume and HLA-DR antigen expression or leukocyte migration inhibitory factor production. The peptides did not induce proliferation of resting B cells even when B cell growth factor (BCGF)c-ontaining supernatants were added. Exposure to Fc fragment, however, induced a weak proliferation which was significantly enhanced by BCGF. On the other hand, both the Fc fragment and the CH2 or CH3 domain peptides enhanced the IgM synthesis of human blood mononuclear cells when a suboptimal dose of pokeweed mitogen was present. This effect was lost when Fc fragment or the peptides were added on the third day of culture. These results suggest that the early steps of B cell activation can be induced by Fc fragment and by small molecular weight Fc peptides, which are potential ligands of Fc receptors. The Fc fragment activates B cells to the state where they respond to BCGF, but the peptides do not possess this activity. Furthermore, both Fc fragment and Fc peptides are able to enhance the IgM synthesis, when accessory cells and the appropriate differentiating factors are present.
Demosaicking: color filter array interpolation (2005)

The author begins by discussing the image formation process. The demosaicking methods are examined in three groups: the first group consists of heuristic approaches. The second group formulates demosaicking as a restoration problem. The third group is a generalization that uses the spectral filtering model given in Wandell.
Oriented active shape models for 3D segmentation in medical images (2007)

Active Shape Models (ASM) have been applied to various segmentation tasks in medical imaging, most successfully in 2D segmentation of objects that have a fairly consistent shape. However, several difficulties arise when extending 2D ASM to 3D: (1) difficulty in 3D labeling, (2) the requirement of a large number of training samples, (3) the challenging problem of landmark correspondence in 3D, (4) inefficient initialization and optimization in 3D. This paper addresses the 3D segmentation problem by using a small number of effective 2D statistical models called oriented ASM (OASM). We demonstrate that a small number of 2D OASM models, which are derived from a chunk of a contiguous set of slices, are sufficient to capture the shape variation between slices and individual objects. Each model can be matched rapidly to a new slice by using the OASM algorithm<sup>1</sup>. Our experiments in segmenting breast and bone of the foot in MR images indicate the following: (1) The accuracy of segmentation via our method is much better than that of 2DASM-based segmentation methods.<sup>2</sup> (2) Far fewer landmarks are required compared with thousands of landmarks needed in true 3D ASM. Therefore, far fewer training samples are required to capture details. (3) Our method is computationally slightly more expensive than the 2D method2 owing to its 2 level dynamic programming (2LDP) algorithm.
Repair of articular cartilage defects: part I. Basic Science of cartilage healing. (1999)

Articular cartilage injuries result in numerous clinical symptoms, such as pain and decreased functional levels. The limited reparative capabilities of hyaline cartilage results in the generation of repair tissue that lacks the structure and biomechanical properties of normal cartilage. Chondrocytes are unable to adequately proliferate, migrate, and synthesize high-quality repair tissue in response to blunt, superficial, or deep penetrating trauma. Extensive research has been conducted to understand the healing process and devise techniques that would enhance this response. Part I of this paper will discuss the basic science of cartilage repair. Part II, which will be published in the February issue, will present the treatment options.
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps (2015)

Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless 'geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses. ACSN may also support patient stratification, prediction of treatment response and resistance to cancer drugs, as well as design of novel treatment strategies.
Room-temperature continuous photopumped laser operation of coupled InP quantum dot and InGaP quantum well InP–InGaP–In(AlGa)P–InAlP heterostructures (2001)

Data are presented demonstrating continuous 300 K photopumped InP quantum dot (QD) laser operation (656–679 nm) realized by modifying and coupling, via tunneling, an auxiliary InGaP quantum well (QW) to the QDs of an InP–In(AlGa)P–InAlP heterostructure grown by metalorganic chemical vapor deposition. The In0.49Ga0.51P QW coupled to the InP QDs by a thin (≲20 Å) In0.5Al0.3Ga0.2P barrier overcomes the limitations of carrier collection, lateral transport, and thermalization in the QDs, thus yielding a different form of QD laser.
Flame Retardant Textile Back-Coatings. Part 1: Antimony-Halogen System Interactions and the Effect of Replacement by Phosphorus-Containing Agents (2000)

A series of back-coated cotton fabrics comprising varying molar ratios of chlorine, bromine and antimony has been studied using a simulated match ignition test, LOI and thermal analysis (TGA and DTA). Results show that the presence of chlorine alone and in combination with bro mine increases LOI and carbonaceous char values at optimum halogen :anti mony molar ratios of 2.5-3.6:1 and bromine:chlorine molar ratios within the range 0.31-0.42. Only back-coated samples containing bromine pass the simu lated match test although at Br:Sb molar ratios above 4:1, LOI and char residual values decrease. It is evident that condensed and vapour phase flame retardant mechanisms are operating with efficiencies determined by halogen : Sb and Br/Cl molar ratios. Partial and whole replacement of halogen and antimony by phosphorus-containing and other flame retardants in the back-coating formulation that do not function in the vapour phase may be used to pass the simulated match test.
The rabies virus genome: an overview. (1993)

The replication strategy, genome organization and extent of variation within the genome of the genus Lyssavirus is briefly reviewed. Strategies used in the approach to genome studies are discussed.
Oligo(ethylene glycol)-Based Thermosensitive Dendrimers and Their Tumor Accumulation and Penetration (2014)

Dendrimers have several featured advantages over other nanomaterials as drug carriers, such as well-defined structure, specific low-nanometer size, and abundant peripheral derivable groups, etc. However, these advantages have not been fully exploited yet to optimize their biological performance, especially tumor penetration, which is a shortcoming of current nanomaterials. Here we show the syntheses of a new class of oligo(ethylene glycol) (OEG)-based thermosensitive dendrimers up to the fourth generation. Each dendrimer shows monodisperse structure. OEG/poly(ethylene glycol) (PEG) moieties with different precise lengths were introduced to the periphery of the fourth-generation dendrimer followed by an antitumor agent, gemcitabine (GEM). The biodistributions of the GEM-conjugated dendrimers were investigated by micro positron emission tomography and multispectral optoacoustic tomography imaging techniques and compared with that of GEM-conjugated poly(amidoamine) (PAMAM). The GEM-conjugated dendrimer with the longest peripheral PEG segments exhibited the most desirable tumor accumulation and penetration and thus had significantly higher antitumor activity than the GEM-conjugated PAMAM.
CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling (2018)

Mature T-cell lymphomas consisting of an expanded clonal population of T cells that possess common rearrangements of the T-cell receptor (TCR) encoding genes can be identified and monitored using molecular methods of T-cell repertoire analysis. We have developed a hybrid-capture method that enriches DNA sequencing libraries for fragments encoding rearranged TCR genes from all 4 loci in a single reaction. We use this method to describe the TCR repertoires of 63 putative lymphoma clinical isolates, 7 peripheral blood mononuclear cell (PBMC) populations, and a collection of tumor infiltrating lymphocytes. Dominant Variable (V) and Joining (J) gene pair rearrangements in cancer cells were confirmed by polymerase chain reaction (PCR) amplification and Sanger sequencing; clonality assessment of clinical isolates using BIOMED-2 methods showed agreement for 73% and 77% of samples at the β and γ loci, respectively, whereas β locus V and J allele prevalence in PBMCs were well correlated with results from commercial PCR-based DNA sequencing assays (<i>r</i> <sup>2</sup> = 0.94 with Adaptive ImmunoSEQ, 0.77-0.83 with Invivoscribe LymphoTrack TRB Assay). CapTCR-seq allows for rapid, high-throughput and flexible characterization of dominant clones within TCR repertoire that will facilitate quantitative analysis of patient samples and enhance sensitivity of tumor surveillance over time.