gebhart/patrepeval huggingface dataset:
Targeting Cancer Stem Cells and Vasculature by a Novel Anti-Delta-Like 4 Ligand (DLL4) Antibody for Treatment of Triple Negative Breast Cancer. (2009)

Abstract Triple negative (ER-, PR- Her2-) breast cancer accounts for 10% of all types of breast cancer and is known to particularly aggressive and refractory to current therapies. Chemotherapeutic agents, such as taxanes, are currently the only treatment option for this type of breast cancer, however, these treatments often result in high rates of local and systemic relapse. It has been suggested that cancer stem cells drive tumor growth and progression and are preferentially resistant to many current therapies. Delta-like 4 ligand (DLL4) is an important component of the Notch signaling pathway which is known to mediate stem cell self-renewal and vascular development. We hypothesized that targeting cancer stem cells and the tumor vasculature by interfering with the DLL4/Notch pathway will improve treatment outcome. We developed anti-DLL4 antibodies that recognize either the human or murine protein and have potent binding and antagonist activities. We have used these antibodies to investigate the role of DLL4 in triple negative breast cancer and to probe the mechanism in tumor and stromal cells in xenograft models derived from primary breast tumors. These studies showed that anti-DLL4 was efficacious as a single agent and in combination with paclitaxel (Taxol) against triple negative breast tumors including a tumor that developed paclitaxel resistance. Gene expression analysis showed that anti-DLL4 affected vascular-related genes in the stroma and Notch target genes in the tumor and stroma. Furthermore, inclusion of anti-DLL4 delayed breast tumor recurrence following termination of paclitaxel treatment. A tumorigenicity study indicated that treatment with anti-DLL4 decreased cancer stem cell frequency as measured by in vivo limiting dilution assay, whereas paclitaxel alone was ineffective. The combination of anti-DLL4 and paclitaxel further decreased cancer stem cell frequency compared to single agents. Our findings provide a rationale for targeting cancer stem cells and tumor vasculature through inhibition of the DLL4/Notch signaling for breast cancer treatment. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5071.
Inhibition of the oncogene product p185erbB-2 in vitro and in vivo by geldanamycin and dihydrogeldanamycin derivatives (1995)

The erbB-2 oncogene encodes a transmembrane protein tyrosine kinase which plays a pivotal role in signal transduction and has been implicated when overexpressed in breast, ovarian, and gastric cancers. Naturally occurring benzoquinoid ansamycin antibiotics herbimycin A, geldanamycin (GDM), and dihydrogeldanamycin were found to potently deplete p185, the erbB-2 oncoprotein, in human breast cancer SKBR-3 cells in culture. Chemistry efforts to modify selectively the quinoid moiety of GDM afforded derivatives with greater potency in vitro and in vivo. Analogs demonstrated inhibition of p185 phosphotyrosine in cell culture and in vivo after systemic drug administration to nu/nu nude mice bearing Fisher rat embryo cells transfected with human erbB-2 (FRE/erbB-2). Specifically, dosed intraperitoneally at 100 mg/kg, 17-(allylamino)-17-demethoxygeldanamycin and other 17-amino analogs were effective at reducing p185 phosphotyrosine in subcutaneous flank FRE/erbB-2 tumors. Modifications to the 17-19-positions of the quinone ring revealed a broad structure-activity relationship in vitro.
Antennapedia homeobox peptide regulates neural morphogenesis. (1991)

We synthesized the 60-amino acid polypeptide corresponding to the sequence of the Drosophila antennapedia gene homeobox. This peptide (pAntp) recognized the consensus motif for binding to the promoter region of Hox-1.3. pAntp mechanically introduced into mammalian nerve cells provoked a dramatic morphological differentiation of the neuronal cultures. Moreover, pAntp directly added to already differentiated neuronal cultures penetrated the cells and further augmented their morphological differentiation. Examination of live and fixed neurons in classical and confocal fluorescence microscopy demonstrated that pAntp was captured at all regions of the nerve cells and accumulated in the nuclei. In addition, the effect of pAntp on neurite extension was blocked in the presence of the protein synthesis inhibitor cycloheximide. Thus, our results demonstrate that neurons possess an efficient uptake system for the antennapedia homeobox peptide and suggest that binding of pAntp to consensus motifs present in nerve cell nuclei influences neuronal morphogenetic programs.
Antiplatelet medications and their indications in preventing and treating coronary thrombosis (2000)

Platelets play a pivotal role in the pathophysiology of unstable angina, acute myocardial infarction, and complications following percutaneous coronary intervention. Three classes of platelet-inhibiting drugs, aspirin, thienopyridines and platelet glycoprotein IIb/ IIIa inhibitors, are now commonly used for the prevention and treatment of disorders of coronary artery thrombosis. For the last several decades aspirin has been the sole option for antiplatelet therapy in the treatment and prevention of the manifestations of cardiovascular disease. However, a wider selection of antiplatelet agents, including the thienopyridines (ticlopidine and clopidogrel) and the platelet glycoprotein (GP)IIb/IIIa receptor antagonists, are now available and provide clinicians with the opportunity to potentially improve upon the previous gold standard of aspirin. This review summarizes these drugs and the scientific data that have led to their use in primary and secondary prevention, unstable angina, myocardial infarction, and percutaneous coronary intervention.
Expression in Escherichia coli of a Chemically Synthesized Gene for the Hormone Somatostatin (1977)

A gene for somatostatin, a mammalian peptide (14 amino acid residues) hormone, was synthesized by chemical methods. This gene was fused to the Escherichia coli beta-galactosidase gene on the plasmid pBR322. Transformation of E. coli with the chimeric plasmid DNA led to the synthesis of a polypeptide including the sequence of amino acids corresponding to somatostatin. In vitro, active somatostatin was specifically cleaved from the large chimeric protein by treatment with cyanogen bromide. This represents the first synthesis of a functional polypeptide product from a gene of chemically synthesized origin.
Migraine prevalence, disease burden, and the need for preventive therapy (2007)

Compared with previous studies, the epidemiologic profile of migraine has remained stable in the United States during the past 15 years. More than one in four migraineurs are candidates for preventive therapy, and a substantial proportion of those who might benefit from prevention do not receive it.
Double-Layered TiO2−SiO2 Nanostructured Films with Self-Cleaning and Antireflective Properties (2006)

Dual function of self-cleaning and antireflection can be created in double-layered TiO2-SiO2 nanostructured films. The film were prepared by (1) layer-by-layer deposition of multilayered SiO2 nanoparticles with polydiallyldimethylammonium (PDDA) cations, (2) layer-by-layer deposition of multilayered titanate nanosheets with polications on PDDA/SiO2 multilayer films, and (3) burning out the polymer and converting titanate nanosheets into TiO2 by hearing at 500 degrees C. The as-prepared films, consisting of a porous SiO2 bottom layer and a dense TiO2 top layer, improved the transmittance of glass or quartz substrates, as demonstrated by transmission spectra collected at normal incidence. The photocatalytic properties of the films were studied by the change of the water contact angle together with the decay of the IR absorption of the hydrocarbon chain of octadecylphosphonic-acid-modified films under 2.6 mW cm-2 UV illumination. Both the antireflective and the photocatalytic properties of the films were dependent on the number of PDDA/nanosheet bilayers deposited. however, excellent surface wettability of the films for water was obtained, independent of the preparation conditions. The experimental findings are discussed in terms of the special structure of the double-layered nanostructured film.
A new flow focusing technique to produce very thin jets (2013)

A new technique is proposed in this paper to produce jets, droplets, and emulsions with sizes ranging from tens of microns down to the submicrometer scale. Liquid is injected at a constant flow rate through a hypodermic needle to form a film over the needle's outer surface. This film flows toward the needle tip until a liquid ligament is steadily ejected. Both the film motion and the liquid ejection are driven by the viscous and pressure forces exerted by a coflowing fluid stream. If this stream is a high-speed gas current, the outcome is a capillary jet which breaks up into droplets due to the Rayleigh instability. Micrometer emulsions are also produced by this instability mechanism when the injected liquid is focused by a viscous liquid stream. The minimum flow rates reached with the proposed technique are two orders of magnitude lower than those of the standard flow focusing configuration. This sharp reduction of the minimum flow rate allows one to form steady jets with radii down to the submicrometer scale. The stability of this new configuration is analyzed experimentally for both gas-liquid and liquid-liquid systems. In most of the cases, the loss of stability must be attributed to the liquid source because the critical Weber (capillary) number for the gas-liquid (liquid-liquid) case was significantly greater than the value corresponding to the convective/absolute instability transition in the jet.
The impact of MPI queue usage on message latency (2004)

It is well known that traditional microbenchmarks do not fully capture the salient architectural features that impact application performance. Even worse, microbenchmarks that target MPI and the communications subsystem do not accurately represent the way that applications use MPI. For example, traditional MPI latency benchmarks time a ping-pong communication with one send and one receive on each of two nodes. The time to post the receive is never counted as part of the latency. This scenario is not even marginally representative of most applications. Two new microbenchmarks are presented here that analyze network latency in a way that more realistically represents the way that MPI is typically used. These benchmarks are used to evaluate modern high-performance networks, including Quadrics, InfiniBand, and Myrinet.
A Primer on Oils Processing Technology (2020)

Abstract In the last couple of decades, the emphasis has been placed from stand‐alone operations toward the integrated manufacturing facility, producing a more complete range of value‐added products from the raw seed to the dinner table. During this transition, operations have become more dependent on each other, as the individual functions involved must now consider the impact of their actions on the total process. At the same time, the scope of knowledge each operation must have of other functions has expanded, and it is important that at least a basic understanding of the “big overall picture” be available to the decision‐maker. The purpose of this article is to provide an overview of the typical processes and interrelations associated with a total integrated facility.
Electron-spin decoherence in bulk and quantum-well zinc-blende semiconductors (2001)

A theory for longitudinal ${(T}_{1})$ and transverse ${(T}_{2})$ electron spin coherence times in zinc-blende semiconductor quantum wells is developed based on a nonperturbative nanostructure model solved in a fourteen-band restricted basis set. Distinctly different dependences of coherence times on mobility, quantization energy, and temperature are found from previous calculations. Quantitative agreement between our calculations and measurements is found for GaAs/AlGaAs, InGaAs/InP, and GaSb/AlSb quantum wells.
Neuropilins (2007)

It is now well established that neuropilins (NRP1 and NRP2), first described as mediators of neuronal guidance, are also mediators of angiogenesis and tumor progression. NRPs are receptors for the class-3 semaphorin (SEMA) family of axon guidance molecules and also for the vascular endothelial growth factor (VEGF) family of angiogenic factors. VEGF-NRP interactions promote developmental angiogenesis as shown in mouse knockout and zebrafish knockdown studies. There is also evidence that NRPs mediate tumor progression. For example, overexpression of NRP1 enhances tumor growth whereas NRP1 antagonists, such as soluble NRP1 and anti-NRP1 antibodies, inhibit tumor growth. Furthermore, some class-3 SEMAs acting via NRPs inhibit tumor angiogenesis, progression and metastasis. Clinical data suggest that high NRP levels correlate with poor prognosis and survival in a variety of cancer types. Taken together, these results suggest that NRPs are potentially valuable targets for new anti-cancer therapies. We analyze here the current knowledge on NRPs and their role in angiogenesis and tumor progression and enumerate strategies for targeting these receptors.
Impaired Expression of the Cell Cycle Regulator BTG2 Is Common in Clear Cell Renal Cell Carcinoma (2004)

The prognosis of patients with renal cell carcinoma (RCC) is poor. A full understanding of the molecular genetics and signaling pathways involved in renal cancer development and in the metastatic process is of central importance for developing innovative and novel treatment options. In this study, BD Atlas Human Cancer 1.2 cDNA microarrays were used to identify genes involved in renal tumorigenesis. By analyzing gene expression patterns of four clear cell RCC (cRCC) cell lines and normal renal tissue, 25 genes were found differentially expressed. To determine the relevance of these genes, RNA in situ hybridization was performed on a tissue microarray generated from 61 snap-frozen primary renal cell carcinomas and 12 normal renal cortex biopsies. B-cell translocation gene 2 (BTG2), a negative cell cycle regulator, which was expressed in normal renal tissue but down-regulated in cRCC cell lines and primary cRCCs, was selected for additional experiments. Quantitative BTG2 mRNA expression analysis in 42 primary cRCCs and 18 normal renal cortex biopsies revealed up to 44-fold reduced expression in the tumor tissues. Decrease of BTG2 expression was not associated with tumor stage, grade, and survival. Cell culture experiments demonstrated that BTG2 expression was weakly inducible by the phorbolester 12-O-tetradecanoylphorbol-13-acetate in one of four cRCC cell lines. In contrast, increasing cell density led to elevated BTG2 mRNA expression in three of four cRCC cell lines. In both experiments, BTG2 mRNA levels did not reach values observed in normal renal tissue. These data suggest that down-regulation of BTG2 is an important step in renal cancer development.
Using Blood Lactate to Predict Prognosis in Emergency Shock Patients (2001)

Background. Lactic acidosis is frequently caused by systemic hypoperfusion, tissue hypoxia and the severity of shock. The purpose of this study was to investigate whether blood lactate concentration is a useful prognostic parameter in patients with shock in the emergency department (ED).
Methods . The criteria for patient selection were 1) arrival at ED with shock syndrome, 2) blood lactate (BLC1) ＞ 19.6 mg/dL prior to resuscitation. All patients were monitored of blood lactate (BLC2) after resuscitation over a period of four hours prior to being sent to the operation room, intensive care unit or ordinary ward .
Results. Seventy-five shock patients had abnormal blood lactate levels (BLCI ＞ 19.6 mg/dL) before resuscitation. Patients who died (mortality group) had significantly higher BLC2 levels (74.4±72.1 vs 27.0±11.1 mg/dL, p ＜ 0.0001) than patients who survived (survival group). In addition, there was a significantly higher mortality rate in patients with blood lactate concentrations (BLC1) ＞ 100 mg/dL than patients with blood lactate concentrations (BLC2) s 100 mg/dL (87%ω43%, P ＜ 0.005). Patients with blood lactate concentrations (BLC2) ＞50 mg/ dL had a higher mortality rate than patients with blood lactate concentrations (BLC2)≦50 mg/dL (100% vs 36%, P ＜ 0.0001). Patients with changes in blood lactate levels (BLC2-BLC1) ＞ 20 mg/dL had a higher rate of mortality than those with a change of ≦20 mg/ dL (n = 66) (100% us 47%, P ＜ 0.005). 
Conclusions. Blood lactate and its clearance may help emergency physicians predict the prognosis of shock patients in the ED. The detection of the changes in blood lactate concentrations after resuscitation is more valuable than before resuscitation.
Multiple promoters direct the tissue-specific expression of novel N-terminal variant human vitamin D receptor gene transcripts (1998)

The effects of 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3] are mediated by the vitamin D receptor (VDR), a member of the nuclear receptor superfamily of transcriptional regulators. We have identified upstream exons of the human (h) VDR gene that are incorporated into variant transcripts, two of which encode N-terminal variant receptor proteins. Expression of the hVDR gene, which spans more than 60 kb and consists of at least 14 exons, is directed by two distinct promoters. A tissue-specific distal promoter generates unique transcripts in tissues involved in calcium regulation by 1, 25-(OH)2D3 and can direct the expression of a luciferase reporter gene in a cell line-specific manner. These major N-terminal differences in hVDR transcripts, potentially resulting in structural differences in the expressed receptor, may contribute to cellular responsiveness to 1,25-(OH)2D3 through tissue differences in the regulation of VDR expression.
Role of naive-derived T memory stem cells in T-cell reconstitution following allogeneic transplantation (2015)

Early T-cell reconstitution following allogeneic transplantation depends on the persistence and function of T cells that are adoptively transferred with the graft. Posttransplant cyclophosphamide (pt-Cy) effectively prevents alloreactive responses from unmanipulated grafts, but its effect on subsequent immune reconstitution remains undetermined. Here, we show that T memory stem cells (TSCM), which demonstrated superior reconstitution capacity in preclinical models, are the most abundant circulating T-cell population in the early days following haploidentical transplantation combined with pt-Cy and precede the expansion of effector cells. Transferred naive, but not TSCM or conventional memory cells preferentially survive cyclophosphamide, thus suggesting that posttransplant TSCM originate from naive precursors. Moreover, donor naive T cells specific for exogenous and self/tumor antigens persist in the host and contribute to peripheral reconstitution by differentiating into effectors. Similarly, pathogen-specific memory T cells generate detectable recall responses, but only in the presence of the cognate antigen. We thus define the cellular basis of T-cell reconstitution following pt-Cy at the antigen-specific level and propose to explore naive-derived TSCM in the clinical setting to overcome immunodeficiency. These trials were registered at www.clinicaltrials.gov as #NCT02049424 and #NCT02049580.
Preferential Utilization of Imp7/8 in Nuclear Import of Smads (2008)

Trafficking of Smad proteins between the cytoplasm and nucleus is a critical component of transforming growth factor beta (TGF-beta) signal transduction. Smad4 translocates into the nucleus either in response to TGF-beta stimulation or when its nuclear export is blocked by leptomycin B (LMB). We demonstrate that both TGF-beta-induced and basal state spontaneous nuclear import of Smad4 require importin 7 and 8 (Imp7,8). Our data suggest that in the nuclear import of Smad4, the role of Imp8 is irreplaceable by Imp7, and that Smads preferentially bind Imp8. Interestingly, in contrast to its mammalian counterpart Smad4, Drosophila Medea appears to utilize different mechanisms for TGF-beta-induced or basal state nuclear accumulation, with the latter independent of Msk (Drosophila Imp7/8) function. In addition, overexpression of Imp8 alone was sufficient to cause an increased concentration of Smad1, 3 and 4 in the nucleus, but had very limited effects on Smad2. These observations suggest selective involvement of Imp8/Msk in nuclear import of different Smads under different conditions.
Induction of Protective Immunity against Herpes Simplex Virus with DNA Encoding the Immediate Early Protein ICP 27 (1995)

Using a mouse zosteriform model that mimics human herpes simplex virus (HSV) infection in several aspects, the effectiveness of plasmid DNA encoding the immediate early protein ICP 27 was evaluated as a vaccine. Animals were immunized intramuscularly twice with DNA, then either challenged with virus or killed, and the nature of the immune response induced was measured. After intramuscular injection with plasmid DNA encoding ICP 27 (pc-ICP 27), solid protection was evident in 70-80% of mice and the lesions were delayed in the remaining animals. Immune splenocytes obtained from pc-ICP 27 immune mice showed HSV-specific lymphoproliferation, MHC-class I restricted cytotoxic T-lymphocyte (CTL) activity, and type 1 cytokine production. These animals also exhibited delayed-type hypersensitivity (DTH) reactions. Adoptive transfer studies conducted on syngeneic nude mice revealed that those recipients of immune CD4+ T cells, but not CD8+ T cells, were protected from subsequent HSV-1 (strain 17) challenge. Thus pc-ICP 27 DNA immunization protected the mice principally by CD4+ T cells and it is likely that these cells were Th-1 type because only type 1 cytokines were detectable after in vitro antigen stimulation. Our results indicate the potential value of DNA encoding nonstructural viral proteins as vaccines against HSV.
Pore formation by LamB of Escherichia coli in lipid bilayer membranes (1986)

Lipid bilayer experiments were performed in the presence of different Escherichia coli LamB preparations. These LamB preparations formed two types of pores in the membranes. Large pores, which had a single-channel conductance of 2.7 nS and comprised about 1 to 6% of the total pores, were presumably contaminants which might have been induced together with LamB. LamB itself formed small pores with a single-channel conductance of 160 pS in 1 M KCl. These pores could be completely blocked by the addition of maltose and maltodextrins. Titration of the pore conductance with maltotriose suggested that there was a binding site inside the pores with a Ks of 2.5 X 10(-4) M for maltotriose. On the basis of our data we concluded that the structure of the LamB channels is quite different from the structures of the channels of general diffusion porins, such as OmpF and OmpC.
Determination of Gossypol Enantiomer Ratio in Cotton Plants by Chiral Higher-Performance Liquid Chromatography (2004)

A celulose tris(3,5-dimethylphenylcarbamate) coated onto APS silica (Nucleosil, particle size, 7 microm; pore size, 500 A) was used under a reversed-phase condition to measure the enantiomeric ratios of gossypol enantiomers in cottonseeds, flowers, and roots in a number of cultivars samples of different Gossipium species. While unidimensional chromatography was used for measuring the enantiomeric ratio of all the samples of G. hirsutum, G. mustelinum, and in the seeds of G. barbadense, multidimensional chromatography was necessary for the analysis of samples of roots and flowers of G. barbadense. In the latter case, an ODS Hypersil column was used in the first dimension for sample clean up, and the enantiomers were resolved on the second dimension by the chiral column. As expected, all the seed samples of G. hirsutum and G. mustelinum showed the (P)-(+)-enantiomer in excess, whereas the seeds of G. barbadense showed the (M)-(-)-enantiomer. However, (P)-(+)-gossypol was found in enantiomeric excess in three samples examined of roots and in one of flower of G. barbadense. These results are discussed in this paper.