gebhart/patrepeval huggingface dataset:
Inhibition of Raf Kinase in the Treatment of Acute Myeloid Leukemia (2002)

Adult acute myeloid leukemia (AML) and the myelodysplastic syndromes (MDS) remain a formidable therapeutic challenge. Although 30-40% of young adults with AML may have prolonged remissions, following either intensive chemotherapy or bone marrow transplantation, the remainder relapse and ultimately die of their disease. Older adults, or those with leukemia following an antecedent hematologic disorder such as MDS, experience only brief remissions with modern chemotherapy, and in this population the rate of long-term disease-free survival is less than 10%. Treatment of MDS consists mainly of supportive care with antibiotics and transfusion therapy, and only a small minority of patients are cured with allogeneic stem cell transplantation. As the biology of the acute leukemias and MDS has unfolded, new potential targets for arresting malignant cell growth and restoring normal hematopoiesis have been identified. This article will discuss the relevance of the ras-raf signaling pathway in the pathogenesis of myeloid leukemia, and describes some early results in the use of novel small molecule inhibitors of farnysltransferase and raf protein kinase in leukemia therapy.
Integrating scale out and fault tolerance in stream processing using operator state management (2013)

As users of "big data" applications expect fresh results, we witness a new breed of stream processing systems (SPS) that are designed to scale to large numbers of cloud-hosted machines. Such systems face new challenges: (i) to benefit from the "pay-as-you-go" model of cloud computing, they must scale out on demand, acquiring additional virtual machines (VMs) and parallelising operators when the workload increases; (ii) failures are common with deployments on hundreds of VMs-systems must be fault-tolerant with fast recovery times, yet low per-machine overheads. An open question is how to achieve these two goals when stream queries include stateful operators, which must be scaled out and recovered without affecting query results.
Mapping of the Sites for Ligand Binding and Receptor Dimerization at the Extracellular Domain of the Vascular Endothelial Growth Factor Receptor FLT-1 (1997)

The vascular endothelial growth factor (VEGF) receptor FLT-1 has been shown to be involved in vasculogenesis and angiogenesis. The receptor is characterized by seven Ig-like loops within the extracellular domain. Upon VEGF binding FLT-1 becomes phosphorylated, which has been thought to be preceded by receptor dimerization. To further investigate high affinity binding of VEGF to FLT-1 and ligand-induced receptor dimerization, we expressed in Sf9 cells the entire extracellular domain comprising all seven Ig-like loops: sFLT-1(7) and several truncated mutants consisting of loop one, one and two, one to three, one to four, and one to five. The corresponding proteins, named sFLT-1(1), (2), (3), (4), and (5) were purified. Only mutants sFLT-1(3) to (7) were able to bind 125I-VEGF with high affinity. No binding of VEGF was observed with sFLT-1(1) and sFLT-1(2), indicating that the first three Ig-like loops are involved in high affinity binding of VEGF. The binding of VEGF to sFLT-1(3) could be competed with placenta growth factor (PlGF), a VEGF-related ligand, suggesting that high affinity binding of VEGF and PlGF is mediated by the same or closely related contact sites on sFLT-1. Deglycosylation of the sFLT-1(3), (4), (5), and (7) did not abolish VEGF binding. Furthermore, unglycosylated sFLT-1(3), expressed in Escherichia coli, was able to bind VEGF with similar affinity as sFLT-1(3) or sFLT-1(7), both expressed in Sf9 cells. This indicates that receptor glycosylation is not essential for high affinity binding. Dimerization of the extracellular domains of FLT-1 upon addition of VEGF was detected with all mutants containing the Ig-like loop four. Although sFLT-1(3) was able to bind VEGF, dimerization of this mutant was inefficient, indicating that sites on Ig-like loop four are essential to stabilize receptor dimers.
A New Paradigm for Type 2 Diabetes Mellitus (1998)

Weight loss is not the reason why GB controls diabetes mellitus. Instead, bypassing the foregut and reducing food intake produce the profound long-term alterations in glucose metabolism and insulin action. These findings suggest that our current paradigms of type 2 diabetes mellitus deserve review. The critical lesion may lie in abnormal signals from the gut.
SDR: a database of predicted specificity-determining residues in proteins (2008)

The specificity-determining residue database (SDR database) presents residue positions where mutations are predicted to have changed protein function in large protein families. Because the database pre-calculates predictions on existing protein sequence alignments, users can quickly find the predictions by selecting the appropriate protein family or searching by protein sequence. Predictions can be used to guide mutagenesis or to gain a better understanding of specificity changes in a protein family. The database is available on the web at http://paradox.harvard.edu/sdr.
Relative abundance of Alzheimer A beta amyloid peptide variants in Alzheimer disease and normal aging. (1994)

The Alzheimer A beta amyloid peptide (A beta) is the principal proteinaceous component of amyloid associated with Alzheimer disease (AD). We have determined the relative abundance of A beta structural variants present in amyloid from brains of 10 individuals with sporadic AD, 2 individuals with familial AD carrying specific mutations in the Alzheimer amyloid precursor protein gene, and 5 nondemented elderly controls. A procedure of isolation based on the extreme insolubility of A beta amyloid was used. The purified, nondigested A beta was analyzed by N-terminal sequencing and electrospray-ionization mass spectrometry. Three principal A beta variants were detected--A beta-(1-40), A beta-(1-42), and A beta-(11-42)--in all brains analyzed. The predominant variant in sporadic AD was A beta-(1-40), whereas the principal A beta variant in nondemented elderly controls was A beta-(1-42). The ratio A beta-(1-40)/A beta-(1-42) differed by 10-fold between brains from nondemented controls and those with sporadic AD.
Complexity of FGF receptors: genetic basis for structural diversity and functional specificity (1992)

Since 1989, the receptors for fibroblast growth factors (FGFs) were cloned and characterized as a subgroup of the family of receptor tyrosine kinases. Four FGF receptor genes were identified, all of which encode membrane-bound glycoproteins containing three immunoglobulin (Ig) -like domains at the extracellular region, where only two of these domains are involved in ligand binding. Three unique features characterize the FGF receptors: 1) overlapping recognition and redundant specificity, where one receptor may bind with a similar affinity several of the seven known FGFs and one FGF may bind similarly to several distinct receptors. 2) The binding of FGFs to their receptors is dependent on the interaction of FGF with cell surface heparan sulfate proteoglycans. 3) A multitude of isoforms of cell-bound or secreted receptors are produced by the same gene. The gene structure of these receptors revealed two major mechanisms that are responsible for the formation of the diverse forms: alternative mRNA splicing, resulting in deletions or alternate exons usage, and internal polyadenylation, resulting in truncated products. These are reminiscent of mechanisms that also operate in the immunoglobulin family to generate diversity and to produce either secreted or cell-bound molecules. Tissue-specific alternative splicing in FGF receptors allows for the generation of two distinct receptors from a single gene because alternative exons determine the sequence of the COOH-terminal half of the third Ig-like domain involved in ligand binding. This represents a novel genetic mechanism to generate receptor diversity and specificity and to increase receptor repertoire.
Phase-sensitive interferometry with ultrashort optical pulses (1995)

Reliable phase-sensitive time-resolved interferometry with ultrashort pulsed lasers is performed with the use of a closed scanning Michelson interferometer in combination with a fixed Mach–Zehnder interferometer at the front end. The technique is based on measuring the full phase and frequency properties of the pulse distortion of an ultrashort optical pulse introduced by linear or nonlinear interaction with a sample. The necessary stability and reproducibility to perform an interferometric measurement is provided by a commercially available Fourier transform spectrometer enabling time-resolved measurements from the IR well into the visible part of the optical spectrum. The feasibility of the technique is demonstrated by measuring the distortion introduced by an etalon and a surface-plasmon polariton.
An Adenovirus Type 5 Mutant with the Preterminal Protein Gene Deleted Efficiently Provides Helper Functions for the Production of Recombinant Adeno-Associated Virus (1998)

Production of recombinant adeno-associated virus (rAAV) requires helper functions that have routinely been provided by infection of the producer cells with adenovirus. Complete removal and/or inactivation of progeny adenovirus, present in such rAAV preparations, presents significant difficulty. Here, we report that an adenovirus type 5 (Ad5) mutant with the preterminal protein (pTP) gene deleted can provide helper function for the growth of rAAV. At high multiplicity, Ad5dl308DeltapTP was as efficient as the phenotypically wild-type Ad5dl309 in permitting growth of rAAV. Use of Ad5dl308DeltapTP, which is incapable of replication in the absence of complementation for pTP, as a helper avoids the need to remove contaminating adenovirus infectious activity by heat inactivation or by purification. Comparison of the transducing ability of rAAV generated with either Ad5dl308DeltapTP or Ad5dl309 as a helper demonstrated that the heat inactivation protocol generally used does not remove all of the helper Ad5dl309 function.
In silico design of clinical trials: A method coming of age (2004)

A mathematical simulation of anti-TNF therapy identified clear windows of opportunity for this intervention as well as populations that can be harmed by anti-TNF therapy. The construction of an in silico clinical trial could provide profound insight into the design of clinical trials of immunomodulatory therapies, ranging from optimal patient selection to individualized dosage and duration of proposed therapeutic interventions.
Human adult T-cell leukemia virus: molecular cloning of the provirus DNA and the unique terminal structure. (1982)

Adult T-cell leukemia virus (ATLV) is a human retrovirus closely associated with adult T-cell leukemia. The integrated provirus DNA and cDNA from virion RNA were molecularly cloned and their structures were analyzed. Clone lambda ATM-1 of an integrated provirus DNA in the MT-1 cell line, established from adult T-cell leukemia cells by cocultivation with cord lymphocytes, contained DNA about 13,000 base pairs (bp) long and long terminal repeats (LTR) at both ends of the viral sequence that were about 8,000 bp long. These two LTR sequences were linked to cellular sequences with direct repeats of 7 bp. Each LTR consisted of 754 bp including inverted repeats of 2 bp at the ends and the T-A-T-A-A box, characteristics in common with those of LTRs of other known retroviruses. Adjacent to the 5' LTR there was a sequence identical to the tRNAPro binding site in murine leukemia virus, suggesting that tRNAPro is a primer for reverse transcription of the viral genome. From these structural features, the mechanism of ATLV replication was suggested to be the same as that of other known animal retroviruses. However, the length of the small terminal repeats at the ends of the RNA genome, 228 +/- 1 bases, is much longer than the lengths, up to 80 bases, of those in avian, mouse, or primate retroviruses so far analyzed. These findings suggest that ATLV should be classified in a distinct group of retroviruses with bovine leukemia virus which also makes unusually long strong-stop cDNA.
Repair of Mycotic Paravisceral Aneurysm with a Fenestrated Stent-Graft (2000)

Fenestrated stent-graft repair may evolve into a useful technique for the treatment of mycotic paravisceral aneurysms.
The Performance Study on Several Distributed File Systems (2011)

With the development of cloud computing, the distributed file systems are getting more and more attention. In this paper, we introduce the concept and the features of the distributed file system, and analyse several popular systems, such as Hadoop, Moosefs and Lustre. Especially, the tested performance comparison of these systems is given. Finally, we propose the research trends in the future.
Tumoural vascularity as a prognostic factor in cancer patients: the evidence continues to grow (1998)

Accurate prognostic indicators would help in identifying patients at high risk for recurrence and death. Recent and previous studies indicate that intratumoural microvessel density (iMVD) of invasive breast carcinoma (a measure of tumour angiogenesis) is associated with aggressive tumour growth; iMVD may thus be a valuable prognostic indicator. Moreover, the bulk of accumulating data indicates that microvessel density in the area of most intense neovascularization in invasive breast carcinoma is an independent, significant and accurate prognostic indicator in predicting poorer survival. Such an indicator would be useful in the selection of high-risk patients with breast carcinoma for systemic adjuvant therapy. © 1998 John Wiley & Sons, Ltd.
High-sensitivity peptide mapping by capillary zone electrophoresis and microcolumn liquid chromatography using immobilized trypsin for protein digestion (1989)

Procedures for the reduced-scale analysis of proteins by peptide mapping have been developed, allowing peptide maps to be obtained from picomole to femtomole quantities of protein. The use of trypsin immobilized on agarose gel and placed in a small reactor column has made it possible to reproducibility digest as little as 50 ng of protein. This represents a decrease in sample size of approximately 3 orders of magnitude from conventional tryptic digestion schemes. Separations of tryptic digests were accomplished by using either microcolumn high-performance liquid chromatography (HPLC) or capillary zone electrophoresis (CZE). Separations of 100 ng (4 pmol) of tryptic digest samples of beta-casein were achieved with microcolumn HPLC, while separations of approximately 2 ng (80 fmol) of beta-casein tryptic digest (from a total sample size of 50 ng) were possible with CZE. Peptide maps from phosphorylated and dephosphorylated forms of beta-casein were readily distinguishable using both separation methods, demonstrating an ability to detect a single amino acid modification in a protein. Relative standard deviations of peak retention or migration times were less than 3% for microcolumn HPLC and less than 1% for CZE.
Differential phosphorylation of the gap junction protein connexin43 in junctional communication-competent and -deficient cell lines. (1990)

Connexin43 is a member of the highly homologous connexin family of gap junction proteins. We have studied how connexin monomers are assembled into functional gap junction plaques by examining the biosynthesis of connexin43 in cell types that differ greatly in their ability to form functional gap junctions. Using a combination of metabolic radiolabeling and immunoprecipitation, we have shown that connexin43 is synthesized in gap junctional communication-competent cells as a 42-kD protein that is efficiently converted to a approximately 46-kD species (connexin43-P2) by the posttranslational addition of phosphate. Surprisingly, certain cell lines severely deficient in gap junctional communication and known cell-cell adhesion molecules (S180 and L929 cells) also expressed 42-kD connexin43. Connexin43 in these communication-deficient cell lines was not, however, phosphorylated to the P2 form. Conversion of S180 cells to a communication-competent phenotype by transfection with a cDNA encoding the cell-cell adhesion molecule L-CAM induced phosphorylation of connexin43 to the P2 form; conversely, blocking junctional communication in ordinarily communication-competent cells inhibited connexin43-P2 formation. Immunohistochemical localization studies indicated that only communication-competent cells accumulated connexin43 in visible gap junction plaques. Together, these results establish a strong correlation between the ability of cells to process connexin43 to the P2 form and to produce functional gap junctions. Connexin43 phosphorylation may therefore play a functional role in gap junction assembly and/or activity.
Combined Blockade of IL6 and PD-1/PD-L1 Signaling Abrogates Mutual Regulation of Their Immunosuppressive Effects in the Tumor Microenvironment (2018)

Recently emerging cancer immunotherapies combine the applications of therapeutics to disrupt the immunosuppressive conditions in tumor-bearing hosts. In this study, we found that targeting the proinflammatory cytokine IL6 enhances tumor-specific Th1 responses and subsequent antitumor effects in tumor-bearing mice. IL6 blockade upregulated expression of the immune checkpoint molecule programmed death-ligand 1 (PD-L1) on melanoma cells. This PD-L1 induction was canceled in IFNγ-deficient mice or CD4<sup>+</sup> T cell-depleted mice, suggesting that CD4<sup>+</sup> T cell-derived IFNγ is important for PD-L1 induction in tumor-bearing hosts. In some patients with melanoma, however, treatment with the anti-PD-1 antibody nivolumab increased systemic levels of IL6, which was associated with poor clinical responses. This PD-L1 blockade-evoked induction of IL6 was reproducible in melanoma-bearing mice. We found that PD-1/PD-L1 blockade prompted PD-1<sup>+</sup> macrophages to produce IL6 in the tumor microenvironment. Depletion of macrophages in melanoma-bearing mice reduced the levels of IL6 during PD-L1 blockade, suggesting macrophages are responsible for the IL6-mediated defective CD4<sup>+</sup> Th1 response. Combined blockade of the mutually regulated immunosuppressive activities of IL6 and PD-1/PD-L1 signals enhanced expression of T cell-attracting chemokines and promoted infiltration of IFNγ-producing CD4<sup>+</sup> T cells in tumor tissues, exerting a synergistic antitumor effect, whereas PD-L1 blockade alone did not promote Th1 response. Collectively, these findings suggest that IL6 is a rational immunosuppressive target for overcoming the narrow therapeutic window of anti-PD-1/PD-L1 therapy.<b>Significance:</b> These findings advance our understanding of IL6-PD1/PD-L1 cross-talk in the tumor microenvironment and provide clues for targeted interventional therapy that may prove more effective against cancer. <i>Cancer Res; 78(17); 5011-22. ©2018 AACR</i>.
Elevated blood levels of inflammatory monocytes (CD14+CD16+) in patients with complex regional pain syndrome (2011)

Complex regional pain syndrome (CRPS) is a chronic pain disorder. Although its pathophysiology is not completely understood, neurogenic inflammation is thought to play a significant role. Microglia and astrocytes are activated following tissue injury or inflammation and have been reported to be both necessary and sufficient for enhanced nociception. Blood-borne monocytes/macrophages can infiltrate the central nervous system (CNS) and differentiate into microglia resulting in hypersensitivity and chronic pain. The primary aim of this study was to evaluate the proportion of the proinflammatory CD14(+) CD16(+) monocytes as well as plasma cytokine levels in blood from CRPS patients compared to age- and gender-matched healthy control individuals. Forty-six subjects (25 CRPS, 21 controls) were recruited for this study. The percentage of monocytes, T, B or natural killer (NK) cells did not differ between CRPS and controls. However, the percentage of the CD14(+) CD16(+) monocyte/macrophage subgroup was elevated significantly (P<0·01) in CRPS compared to controls. Individuals with high percentage of CD14(+) CD16(+) demonstrated significantly lower (P<0·05) plasma levels on the anti-inflammatory cytokine interleukin (IL)-10. Our data cannot determine whether CD14(+) CD16(+) monocytes became elevated prior to or after developing CRPS. In either case, the elevation of blood proinflammatoty monocytes prior to the initiating event may predispose individuals for developing the syndrome whereas the elevation of blood proinflammatory monocytes following the development of CRPS may be relevant for its maintenance. Further evaluation of the role the immune system plays in the pathogenesis of CRPS may aid in elucidating disease mechanisms as well as the development of novel therapies for its treatment.
Molecular pathogenesis of malignant gliomas (1999)

De novo glioblastomas develop in older patients without prior clinical history of less malignant tumors. Progressive glioblastomas are common among younger patients and arise through progression from lower-grade astrocytomas. CDKN2A deletions, PTEN alterations, and EGFR amplification are more prevalent among de novo glioblastomas, whereas p53 mutations are more common among progressive glioblastomas. Loss of heterozygosity (LOH) for chromosome 10 is seen uniformly among both de novo and progressive high-grade astrocytomas. The inactivation of the PTEN gene is found in approximately 30% to 40% of astrocytomas with chromosome 10 loss, and LOH pattern in the remaining astrocytomas strongly supports the presence of another yet unidentified tumor suppressor gene telomeric to PTEN. More than 80% of oligodendrogliomas exhibit LOH for 1 p and 19q alleles. Oligoastrocytomas with 1p/19q LOH are related to oligodendrogliomas, and those with p53 mutations are related to astrocytomas.
Identification of Extremely Reactive γ-Ketoaldehydes (Isolevuglandins) as Products of the Isoprostane Pathway and Characterization of Their Lysyl Protein Adducts (1999)

Isoprostanes are prostaglandin-like compounds produced by non-enzymatic peroxidation of arachidonic acid. The cyclooxygenase-derived endoperoxide, prostaglandin H2, can undergo rearrangement to highly reactive gamma-ketoaldehyde secoprostanoids (levuglandin E2 and D2). We explored whether isoprostane endoperoxide intermediates also rearrange to levuglandin-like compounds (isolevuglandins). Formation of a series of isolevuglandins during oxidation of arachidonic acid in vitro was established utilizing a number of mass spectrometric analyses. However, these compounds could not be detected in free form in protein-containing biological systems, which we hypothesized was due to extremely rapid adduction to amines. This was supported by the finding that >60% of levuglandin E2 adducted to albumin within 20 s, whereas approximately 50% of 4-hydroxynonenal still remained unadducted after 1 h. By utilizing electrospray tandem mass spectrometry, we established that these compounds form oxidized pyrrole adducts (lactams and hydroxylactams) with lysine. Formation of isolevuglandin-lysine adducts on apolipoprotein B was readily detected during oxidation of low density lipoprotein following enzymatic digestion of the protein to single amino acids. These studies identify a novel series of extremely reactive products of the isoprostane pathway that rapidly form covalent adducts with lysine residues on proteins. This provides the basis to explore the formation of isolevuglandins in vivo to investigate the potential biological ramifications of their formation in settings of oxidant injury.
Entanglement of a Pair of Quantum Bits (1997)

The ``entanglement of formation'' of a mixed state \ensuremath{\rho} of a bipartite quantum system can be defined as the minimum number of singlets needed to create an ensemble of pure states that represents \ensuremath{\rho}. We find an exact formula for the entanglement of formation for all mixed states of two qubits having no more than two nonzero eigenvalues, and we report evidence suggesting that the formula is valid for all states of this system.