gebhart/patrepeval huggingface dataset:
Semaphorin 4D provides a link between axon guidance processes and tumor-induced angiogenesis (2006)

Tumor progression and metastasis depend on the ability of cancer cells to initiate angiogenesis and ensure delivery of oxygen, nutrients, and growth factors to rapidly dividing transformed cells and provide access to the systemic circulation. In addition to well established growth factors and inflammatory mediators that promote capillary sprouting and endothelial cell growth and migration, an emerging body of evidence supports a previously unrecognized function for axon guidance molecules in regulation of blood vessel development. Here we show that semaphorin 4D (Sema4D), a protein originally shown to regulate axonal growth cone guidance in the developing central nervous system through its receptor, plexin-B1, is highly expressed in cell lines derived from head and neck squamous cell carcinomas (HNSCCs) at both the protein and message level. Immunohistochemical analysis of a large collection of HNSCC specimens revealed high levels of Sema4D in a cell surface pattern in invading islands of transformed epithelial cells, but not in normal and noninvasive dysplastic epithelium. A similar pattern was observed in malignant cells from prostate, colon, breast, and lung cancer tissues. When shed from HNSCC cells, Sema4D stimulates endothelial cell migration, which can be prevented by Sema4D-blocking antibodies and by Sema4D knockdown. Furthermore, knocking down Sema4D by lentiviral expression of Sema4D shRNA reduces dramatically the size and vascularity of HNSCC tumor xenografts. These findings indicate that expression of Sema4D is a frequently used strategy by which a wide variety of carcinomas may promote angiogenesis, and therefore is a possible therapeutic target for the treatment of these malignancies.
Knowledge management capability based competitive advantage of the firm: toward an empirical study (2007)

The role of knowledge management as a powerful means of sustaining competitive advantage has been strongly emphasised in strategic management literature. Although a variety of knowledge management factors have been investigated, only a limited number of studies have explored the resource-based view of knowledge management and analyses to date have focused mostly on infrastructure elements. It is proposed that an absence of knowledge management processes may hinder a valuable integrated contribution of the two major components that constitute knowledge management capability, namely infrastructure and process to organisational competitive advantage. This paper reports progress from the early stages of a large research project aimed at filling this perceived gap in the literature. Adopting the resource-based theory of the firm blended with knowledge and dynamic capability-based approaches, this paper attempts to develop a comprehensive theoretical model. The next stage of the research project will be an empirical examination and validation of this proposed theoretical model.
Mutations and thrombosis in essential thrombocythemia: prognostic interaction with age and thrombosis history (2014)

The favorable impact of mutational status on thrombosis-free survival in ET might be most evident for JAK2, CALR, and MPL wild type patients, whereas the favorable effect from CALR mutations might be confined to young patients.
Achieving Polymorphic and Stoichiometric Diversity in Cocrystal Formation:  Importance of Solid-State Grinding, Powder X-ray Structure Determination, and Seeding (2005)

Solid-state grinding is explored as a means of selectively preparing specific stoichiometric or polymorphic modifications of crystalline supramolecular complexes, or cocrystals. In research involving cocrystals of the model pharmaceutical compound caffeine prepared via solid-state grinding and solution crystallization, it has been demonstrated that these two methods of preparation are not always coterminous with respect to the cocrystal product obtained. Examined herein are the structures of five previously unreported caffeine cocrystals with monocarboxylic acids, including formic acid, acetic acid, and trifluoroacetic acid. This system illustrates three different possibilities in performing cocrystal preparation via the dual methods of solid-state grinding and solution crystallization: (1) the same cocrystal can result from both methods; (2) different cocrystal stoichiometries can result from each method; (3) different cocrystal polymorphs can result from each method. Materials that at first could be prepared only by solid-state grinding were later induced to crystallize from solution by seeding with the grinding material. Because some cocrystals from grinding contained minor residual unreacted starting components, a phase-subtraction method was used to enable subsequent crystal structure determination from powder X-ray diffraction data. The findings herein assign a significance to solid-state grinding as a technique of choice in widespread screening efforts for novel supramolecular materials.
Improved Intraoperative Visualization of Nerves through a Myelin-Binding Fluorophore and Dual-Mode Laparoscopic Imaging (2015)

The ability to visualize and spare nerves during surgery is critical for avoiding chronic morbidity, pain, and loss of function. Visualization of such critical anatomic structures is even more challenging during minimal access procedures because the small incisions limit visibility. In this study, we focus on improving imaging of nerves through the use of a new small molecule fluorophore, GE3126, used in conjunction with our dual-mode (color and fluorescence) laparoscopic imaging instrument. GE3126 has higher aqueous solubility, improved pharmacokinetics, and reduced non-specific adipose tissue fluorescence compared to previous myelin-binding fluorophores. Dosing and kinetics were initially optimized in mice. A non-clinical modified Irwin study in rats, performed to assess the potential of GE3126 to induce nervous system injuries, showed the absence of major adverse reactions. Real-time intraoperative imaging was performed in a porcine model. Compared to white light imaging, nerve visibility was enhanced under fluorescence guidance, especially for small diameter nerves obscured by fascia, blood vessels, or adipose tissue. In the porcine model, nerve visualization was observed rapidly, within 5 to 10 minutes post-intravenous injection and the nerve fluorescence signal was maintained for up to 80 minutes. The use of GE3126, coupled with practical implementation of an imaging instrument may be an important step forward in preventing nerve damage in the operating room.
Standards of Medical Care in Diabetes—2008 (2008)

The American Diabetes Association (ADA) has released a Standards of Medical Care in Diabetes Position Statement for 2008 (1). In this document, it is stated that aspirin therapy should be used as a primary prevention strategy in diabetic patients at increased cardiovascular (CV) risk, including those who are >40 years old or have additional risk factors. The recommendation is based on evidence graded “A,” which is defined by the ADA as “evidence from well-conducted, randomized controlled trials that are adequately powered or compelling nonexperimental evidence.” As this indication seemed very …
The 5′-Exonuclease Activity of Bacteriophage T4 RNase H Is Stimulated by the T4 Gene 32 Single-stranded DNA-binding Protein, but Its Flap Endonuclease Is Inhibited (1997)

Bacteriophage T4 RNase H is a 5'- to 3'-nuclease that has exonuclease activity on RNA.DNA and DNA.DNA duplexes and can remove the pentamer RNA primers made by the T4 primase-helicase (Hollingsworth, H. C., and Nossal, N. G. (1991) J. Biol. Chem. 266, 1888-1897; Hobbs, L. J., and Nossal, N. G. (1996) J. Bacteriol. 178, 6772-6777). Here we show that this exonuclease degrades duplex DNA nonprocessively, releasing a single oligonucleotide (nucleotides 1-4) with each interaction with the substrate. Degradation continues nonprocessively until the enzyme stops 8-11 nucleotides from the 3'-end of the substrate. T4 gene 32 single-stranded DNA-binding protein strongly stimulates the exonuclease activity of T4 RNase H, converting it into a processive nuclease that removes multiple short oligonucleotides with a combined length of 10-50 nucleotides each time it binds to the duplex substrate. 32 protein must bind on single-stranded DNA behind T4 RNase H for processive degradation. T4 RNase H also has a flap endonuclease activity that cuts preferentially on either side of the junction between single- and double-stranded DNA in flap and fork DNA structures. In contrast to the exonuclease, the endonuclease is inhibited completely by 32 protein binding to the single strand of the flap substrate. These results suggest an important role for T4 32 protein in controlling T4 RNase H degradation of RNA primers and adjacent DNA during each lagging strand cycle.
A Versatile Precompiler for Nonstandard Arithmetics (1979)

article Free Access Share on A Versatile Precompiler for Nonstandard Arithmetics Author: Fred D. Crary 7750 31st Ave, N.E., Seattle, WA 7750 31st Ave, N.E., Seattle, WAView Profile Authors Info & Claims ACM Transactions on Mathematical SoftwareVolume 5Issue 2June 1979 pp 204–217https://doi.org/10.1145/355826.355834Published:01 June 1979Publication History 21citation209DownloadsMetricsTotal Citations21Total Downloads209Last 12 Months9Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Prediction of an HLA B8-restricted influenza epitope by motif. (1993)

Alignment of previously identified HLA B8-restricted cytotoxic T-cell (CTL) epitopes revealed a common motif: x, x, K/R, x, R/K, x, W/Y, x, I/L. Of five motif-conforming peptides tested, ELRSRYWAI was found to represent a new epitope from influenza nucleoprotein (NP). High concentrations of some peptides gave cross-reactive stimulation illustrating the requirement to confirm epitope assignment with recombinant vaccinias and highlighting a potential problem of peptide-based CTL vaccines.
Terminal Sialic Acid Residues on Human Glycophorin A Are Recognized by Porcine Kupffer Cells (2005)

Terminal sialic acid on human erythrocytes is a target recognized by porcine Kupffer cells, suggesting a role for a sialic-acid receptor in innate cellular recognition of xenogeneic epitopes. Inasmuch as this work reveals a carbohydrate-recognition mechanism for cellular rejection, we shed light on a potential new boundary that will need to be overcome within xenotransplantation.
Human endothelial cells are target for platelet-activating factor. I. Platelet-activating factor induces changes in cytoskeleton structures. (1987)

Platelet-activating factor (PAF), but not its deacetylated and biologically inactive metabolite lyso-PAF, in a dose dependent-manner (0.1 to 10 nM), induces human endothelial cells (EC) in culture to change their shape. EC retract and tend to lose reciprocal contact, whereas the distribution of stress fibers is changed and the cells tend to assume a migratory phenotype. The normal localization of vinculin at streaks corresponding to adhesion plaques and located at stress fiber endings is mostly lost and replaced by diffuse distribution of this protein related to the cell-substratum adhesion complex. The effects of PAF are appreciable after 10 min, become maximal after 30 min, and are fully reversible. The disappearance of F-actin in stimulated EC was analyzed by measuring the fluorescence of the cells after staining with fluorosceinated phalloidin, PAF, but not lyso-PAF and the enantiomer of PAF ([S] form), decreases in a time- and concentration-dependent fashion the fluorescence of the cells stained with fluoresceinated phalloidin. EC grown on fibronectin-coated polycarbonate filters restrict the diffusion of 125I-albumin; PAF promotes 125I-albumin diffusion with a concentration dependency similar to that for the PAF-induced cytoskeleton changes. Four different PAF-receptor antagonists belonging to four different series, CV-3988 (PAF-related framework), BN52021 (a natural terpenoid), BN53013 (a natural lignan) and 48740 RP (a synthetic antagonist) prevent the alteration induced by PAF. These findings, coupled to the lack of effect of the enantiomer of PAF ([S] form), support the existence of a specific mechanism of PAF-mediated activation of EC, most probably mediated by a putative receptor. These results explain part of the PAF mechanism of action in inducing the increase of vascular permeability in vivo.
siRNA Conjugate Delivery Systems (2008)

Small interfering RNA (siRNA) has been chemically conjugated to a variety of bioactive molecules, lipids, polymers, peptides, and inorganic nanostructured materials to enhance their pharmacokinetic behavior, cellular uptake, target specificity, and safety. To efficiently deliver siRNAs to the target cells and tissues, many different siRNA bioconjugates were synthesized and characterized, and their gene silencing efficiencies were tested in vitro and in vivo. In this review, recent developments of siRNA bioconjugates are summarized.
Gas phase activation energy for unimolecular dissociation of biomolecular ions determined by Focused RAdiation for Gaseous Multiphoton ENergy Transfer (FRAGMENT) (1999)

We present a novel approach for the determination of activation energy for the unimolecular dissociation of a large (>50 atoms) ion, based on measurement of the unimolecular dissociation rate constant as a function of continuous-wave CO(2) laser intensity. Following a short ( approximately 1 s) induction period, CO(2) laser irradiation produces an essentially blackbody internal energy distribution, whose 'temperature' varies inversely with laser intensity. The only currently available method for measuring such activation energies is blackbody infrared radiative dissociation (BIRD). Compared with BIRD, FRAGMENT: (a) eliminates the need to heat the surrounding ion trap and vacuum chamber to each of several temperatures (each requiring hours for temperature equilibration); (b) offers a three-fold wider range of effective blackbody temperature; and (c) extends the range of applications to include initially cold ions (e.g., gas-phase H/D exchange). Our FRAGMENT-determined activation energy for dissociation of protonated bradykinin, 1.2 +/- 0.1 eV, agrees within experimental error to the value, 1.3 +/- 0.1 eV, previously reported by Williams et al. from BIRD experiments. Copyright 1999 John Wiley & Sons, Ltd.
WNK1, the kinase mutated in an inherited high-blood-pressure syndrome, is a novel PKB (protein kinase B)/Akt substrate (2004)

Recent evidence indicates that mutations in the gene encoding the WNK1 [with no K (lysine) protein kinase-1] results in an inherited hypertension syndrome called pseudohypoaldosteronism type II. The mechanisms by which WNK1 is regulated or the substrates it phosphorylates are currently unknown. We noticed that Thr-60 of WNK1, which lies N-terminal to the catalytic domain, is located within a PKB (protein kinase B) phosphorylation consensus sequence. We found that PKB phosphorylated WNK1 efficiently compared with known substrates, and both peptide map and mutational analysis revealed that the major PKB site of phosphorylation was Thr-60. Employing a phosphospecific Thr-60 WNK1 antibody, we demonstrated that IGF1 (insulin-like growth factor) stimulation of HEK-293 cells induced phosphorylation of endogenously expressed WNK1 at Thr-60. Consistent with PKB mediating this phosphorylation, inhibitors of PI 3-kinase (phosphoinositide 3-kinase; wortmannin and LY294002) but not inhibitors of mammalian target of rapamycin (rapamycin) or MEK1 (mitogen-activated protein kinase kinase-1) activation (PD184352), inhibited IGF1-induced phosphorylation of endogenous WNK1 at Thr-60. Moreover, IGF1-induced phosphorylation of endogenous WNK1 did not occur in PDK1-/- ES (embryonic stem) cells, in which PKB is not activated. In contrast, IGF1 still induced normal phosphorylation of WNK1 in PDK1(L155E/L155E) knock-in ES cells in which PKB, but not S6K (p70 ribosomal S6 kinase) or SGK1 (serum- and glucocorticoid-induced protein kinase 1), is activated. Our study provides strong pharmacological and genetic evidence that PKB mediates the phosphorylation of WNK1 at Thr-60 in vivo. We also performed experiments which suggest that the phosphorylation of WNK1 by PKB is not regulating its kinase activity or cellular localization directly. These results provide the first connection between the PI 3-kinase/PKB pathway and WNK1, suggesting a mechanism by which this pathway may influence blood pressure.
The pharmacological basis for the treatment of perennial allergic rhinitis and non‐allergic rhinitis with topical corticosteroids (1997)

The currently available respiratory topical corticosteroids are all effective at reducing the nasal symptoms of itch, sneezing, rhinorrhoea and obstruction associated with allergic rhinitis. The mechanism of action of corticosteroids is related to their anti-inflammatory activities. They have been documented to prevent fluid exudation and reduce the number of circulating inflammatory cells, including lymphocytes, mast cells, basophils, eosinophils, macrophages, and neutrophils. This occurs through multiple mechanisms, e.g. eosinophil infiltration is suppressed by preventing cytokine production, reducing local mechanisms of tissue infiltration, and decreasing eosinophil survival. Furthermore, corticosteroids also reduce preformed and newly-generated mediators (e.g. histamine, tryptase, prostanoids, leukotrienes), and inhibit production of cytokines and chemokines by inflammatory cells (e.g. IL-1 through IL-6, IL-8, RANTES, TNF-alpha, IFN-gamma and GM-CSF). The currently available corticosteroids differ pharmacologically. Fluticasone propionate appears to have the greatest affinity for the glucocorticoid receptor, and binds more quickly and dissociates more slowly from the receptor compared with other corticosteroids, suggesting a more prolonged duration of action. Its increased specificity for respiratory tissue may lead to greater potency with less potential for systemic adverse effects. Fluticasone propionate has been compared with other corticosteroids in animal models for relative topical and systemic potency, and according to these data, it has the most favourable risk-benefit ratio.
Use of Procalcitonin to Shorten Antibiotic Treatment Duration in Septic Patients (2007)

Our results suggest that a protocol based on serial PCT measurement allows reducing antibiotic treatment duration and exposure in patients with severe sepsis and septic shock without apparent harm.
DNA Damage Promotes Histone Deacetylase 4 Nuclear Localization and Repression of G2/M Promoters, via p53 C-terminal Lysines (2005)

Repression of G(2)/M promoters after DNA damage is an active mechanism that requires the p53 tumor suppressor. We have recently found that histone deacetylase 4 (HDAC4) is recruited on NF-Y-dependent repressed promoters. In this report, we describe the relationship between p53 and HDAC4 recruitment following DNA damage using immunofluorescence, chromatin immunoprecipitation, and transfection experiments. HDAC4 shuttles from the cytoplasm into the nucleus, following DNA damage, independently of the activation of p53 and becomes associated with promoters through a p53-dependent mechanism. The C-terminal lysines of p53, which are acetylated and methylated, are required for HDAC4 recruitment and transcriptional repression. Trichostatin treatment, but not HDAC4 functional inactivation, relieves the adriamycin-mediated repression of G(2)/M promoters. Our results indicate that HDAC4 is a component of the DNA damage response and that post-translational modifications of p53 are important for repression of G(2)/M genes.
Liquid Chromatography–Tandem Mass Spectrometry Analysis of Folate and Folate Catabolites in Human Serum (2009)

This method based on liquid chromatography-tandem mass spectrometry measures the most abundant folate species and 2 folate catabolites in human serum.
Clinical correlations of leukemic clonogenic cell chemosensitivity assessed by in vitro continuous exposure to drugs. (1983)

This study was performed to assess the value of prolonged, as opposed to short-pulse, in vitro exposure of leukemic cells to chemotherapeutic drugs in leukemic clonogenic assay for prediction of clinical response. In 21 patients with acute nonlymphocytic leukemia treated with intensive combination chemotherapy based on an anthracycline and 1-beta-D-arabinofuranosylcytosine infusion, chemotherapy sensitivity of leukemic clonogenic cells was assessed in comparison with that of normal myeloid clonogenic cells by the in vitro continuous exposure to drugs throughout the entire culture period. Analysis of these in vitro data in terms of prediction of achieving clinical complete remission was carried out in comparison with data on 22 cases in which in vitro sensitivity was assessed by the pulse 1-hr exposure. The in vitro sensitivity index, expressed as a log odds ratio, was positive (greater than 0) in 8 of 11 patients achieving complete remission and negative (less than 0) in 7 of 10 patients failing to achieve complete remission, with an overall correlation of 71%. This is at least as good as the pulse exposure method, which has a correlation of 68%. If sensitivity indexes of marginal magnitudes (--1.0 approximately +1.0) are excluded, the correlation increases to 92% (12 of 13 patients). The correlation appears to improve especially for 1-beta-D-arabinofuranosylcytosine by the continuous exposure method (71%) as compared with the pulse method (57%). This study establishes the feasibility of an in vitro chemotherapy sensitivity testing of leukemic clonogenic cells by continuous in vitro drug exposure and suggests that the continuous exposure method may be better than the pulse method for antimetabolites such as 1-beta-D-arabinofuranosylcytosine. The data also suggest that simulation of the in vivo drug schedule may be important in this in vitro test.
Feedback Stabilization Using Two-Hidden-Layer Nets (1991)

This paper concerns itself with the global stabilization of nonlinear systems by means of state feedback laws which can be implemented using feedforward neural networks. The objective here is not to provide a practical stabilization technique, but rather to explore the capabilities and the ultimate limitations of alternative network architectures. It is shown that, contrary to what might have been expected from the well-known representation theorems, three-layer (also called "single hidden layer") nets are not sufficient for stabilization, but four-layer nets are enough - assuming that threshold processors are used.
Comparing Plasma Phospho Tau, Total Tau, and Phospho Tau–Total Tau Ratio as Acute and Chronic Traumatic Brain Injury Biomarkers (2017)

Plasma P-tau levels and P-tau-T-tau ratio outperformed T-tau level as diagnostic and prognostic biomarkers for acute TBI. Compared with T-tau levels alone, P-tau levels and P-tau-T-tau ratios show more robust and sustained elevations among patients with chronic TBI.