gebhart/patrepeval huggingface dataset:
Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors (2010)

Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of 3508 exons from 577 cancer-related genes using next generation sequencing. Focal homozygous deletions were detected at 8p22, 10q23.31, 13q13.1, 13q14.11, and 13q14.12. Key genes mapping within these deleted regions include PTEN, BRCA2, C13ORF15, and SIAH3. Focal high-level amplifications were detected at 5p13.2-p12, 14q21.1, 7q22.1, and Xq12. Key amplified genes mapping within these regions include SKP2, FOXA1, and AR. Furthermore, targeted mutational analysis of normal-tumor pairs has identified somatic mutations in genes known to be associated with prostate cancer including AR and TP53, but has also revealed novel somatic point mutations in genes including MTOR, BRCA2, ARHGEF12, and CHD5. Finally, in one patient where multiple independent metastatic tumors were available, we show common and divergent somatic alterations that occur at both the copy number and point mutation level, supporting a model for a common clonal progenitor with metastatic tumor-specific divergence. Our study represents a deep genomic analysis of advanced metastatic prostate tumors and has revealed candidate somatic alterations, possibly contributing to lethal prostate cancer.
Linkage-specific Action of Endogenous Sialic Acid -Acetyltransferase in Chinese Hamster Ovary Cells (1996)

9-O-Acetylation of sialic acids shows cell type-specific and developmentally regulated expression in various systems. In a given cell type, O-acetylation can also be specific to a particular type of glycoconjugate. It is assumed that this regulation is achieved by control of expression of specific 9-O-acetyltransferases. However, it has been difficult to test this hypothesis, as these enzymes have so far proven intractable to purification or molecular cloning. During a cloning attempt, we discovered that while polyoma T antigen-positive Chinese hamster ovary cells (CHO-Tag cells) do not normally express cell-surface 9-O-acetylation, they do so when transiently transfected with a cDNA encoding the lactosamine-specific alpha2-6-sialyltransferase (Galbeta1-4GlcNAc:alpha2-6-sialyltransferase (ST6Gal I); formerly ST6N). This phenomenon is reproducible by stable expression of ST6Gal I in parental CHO cells, but not upon transfection of the competing lactosamine-specific alpha2-3-sialyltransferase (Galbeta1-(3)4GlcNAc:alpha2-3-sialyltransferase; (ST6Gal III) formerly ST3N) into either cell type. Further analyses of stably transfected parental CHO-K1 cells indicated that expression of the ST6Gal I gene causes selective 9-O-acetylation of alpha2-6-linked sialic acid residues on N-linked oligosaccharides. In a similar manner, while the alpha2-3-linked sialic acid residue of the endogenous GM3 ganglioside of CHO cells is not O-acetylated, transfection of an alpha2-8-sialyltransferase (GM3:alpha2-8-sialyltransferase (ST8Sia I); formerly GD3 synthase) caused expression of 9-O-acetylation of the alpha2-8-linked sialic acid residues of newly synthesized GD3. These data indicate either that linkage-specific sialic acid O-acetyltransferase(s) are constitutively expressed in CHO cells or that expression of these enzymes is secondarily induced upon expression of certain sialyltransferases. The former explanation is supported by a low level of background 9-O-acetylation found in parental CHO-K1 cells and by the finding that O-acetylation is not induced when the ST6Gal I or ST8Sia I cDNAs are overexpressed in SV40 T antigen-expressing primate (COS) cells. Taken together, these results indicate that expression of sialic acid 9-O-acetylation can be regulated by the action of specific sialyltransferases that alter the predominant linkage of the terminal sialic acids found on specific classes of glycoconjugates.
Rolling-Circle Replication of Mitochondrial DNA in the Higher Plant <i>Chenopodium album</i> (L.) (1996)

The mitochondrial genomes of higher plants are larger and more complex than those of all other groups of organisms. We have studied the in vivo replication of chromosomal and plasmid mitochondrial DNAs prepared from a suspension culture and whole plants of the dicotyledonous higher plant Chenopodium album (L.). Electron microscopic studies revealed sigma-shaped, linear, and open circular molecules (subgenomic circles) of variable size as well as a minicircular plasmid of 1.3 kb (mp1). The distribution of single-stranded mitochondrial DNA in the sigma structures and the detection of entirely single-stranded molecules indicate a rolling-circle type of replication of plasmid mp1 and subgenomic circles. About half of the sigma-like molecules had tails exceeding the lengths of the corresponding circle, suggesting the formation of concatemers. Two replication origins (nicking sites) could be identified on mpl by electron microscopy and by a new approach based on the mapping of restriction fragments representing the identical 5' ends of the tails of sigma-like molecules. These data provide, for the first time, evidence for a rolling-circle mode of replication in the mitochondria of higher plants.
Laboratory Evaluation of Pyriproxyfen and Spinosad, Alone and in Combination, Against <I>Aedes aegypti</I> Larvae (2006)

In this study, the efficacy of pyriproxyfen and spinosad, alone and in combination, was evaluated against the dengue vector Aedes aegypti (L.). Larval bioassays were carried out on susceptible mosquito larvae to determine the concentration-mortality responses of mosquitoes exposed to each insecticide alone and in mixture. Synergism between pyriproxyfen and spinosad was determined by the calculation of a combination index (CI) by using the isobologram method. For pyriproxyfen, LC50 and LC95 were 1.1 x 10(-4) (1.0 x 10(-4)-1.1 x 10(-4)) and 3.2 x 10(-4) (2.9 x 10(-4)-3.6 x 10(-4)) mg/liter, respectively. Pyriproxyfen acted at very low concentrations by inhibiting the adult emergence of Ae. aegypti (97% inhibition rates at 3.3 x 10(-4) mg/liter). Spinosad activity was -500 times lower than that of pyriproxyfen against the Bora strain, with LC50 and LC95 values estimated at 0.055 (0.047-0.064) and 0.20 (0.15-0.27) mg/liter, respectively. A binary mixture of pyriproxyfen and spinosad was realized at the ratio 1:500 by considering the values of the LC50 obtained for each product. The LC50 and LC95 of the mixture were 0.019 (0.016 - 0.022) and 0.050 (0.040 - 0.065) mg/liter, respectively. The mixture combined both the larvicidal activity of spinosad and the juvenoid action of pyriproxyfen. From the LC70 to LC99 a significant synergism effect was observed between the two insecticides (CI ranged from 0.74 to 0.31). This strong synergism observed at high concentrations allows a reduction by five and nine-fold of pyriproxyfen and spinosad amounts to kill almost 100% mosquitoes. Combination of pyriproxyfen and spinosad may then represent a promising strategy to improve mosquito control in situations with insecticide-resistant Aedes dengue vectors.
Expression and modulation of a retrovirus-associated antigen by murine melanoma cells. (1988)

The antigen recognized by the monoclonal antibody MM2-9B6 is specific for melanomas originating in C57BL/6 mice. It is expressed by three melanomas of independent origin and not by normal or fetal tissues, by a wide variety of other nonmelanoma tumors in C57BL/6 mice, or even by melanomas syngeneic to other strains of mice. We have demonstrated that the expression of the relevant antigen is dependent on the replication and budding of a B-tropic ecotropic murine retrovirus. The relationship between the expression of this virus and carcinogenic progression may yield important insights into the cascade of events leading to neoplastic transformation.
High-Dose Therapy in Lymphomas: A Review of the Current Status of Allogeneic and Autologous Stem Cell Transplantation in Hodgkin's Disease and Non-Hodgkin's Lymphoma (2001)

Autologous stem cell transplantation has proven to be beneficial in selected patients with Hodgkin's disease (HD) and non-Hodgkin's lymphoma (NHL). In patients with HD, transplantation appears to increase event-free survival in patients who fail to enter complete remission with initial therapy. When a patient relapses after a complete remission, transplantation is probably the best option and particularly so if the remission lasted less than 1 year. Transplantation as part of primary therapy for very high-risk patients may be beneficial, but is not standard therapy at this time. For patients with diffuse large-cell NHL, transplantation can be considered standard therapy for relapsed patients if they have chemotherapy-sensitive disease. The use of transplantation for high-risk patients in complete remission is promising, but definite recommendations cannot be made at this time. For follicular lymphomas, selected patients seem to benefit and studies are ongoing. Finally, the use of allogeneic stem cell transplantation can be useful in a select group of younger patients.
Social Influence Does Matter: User Action Prediction for In-Feed Advertising (2020)

   Social in-feed advertising delivers ads that seamlessly fit inside a user’s feed, and allows users to engage in social actions (likes or comments) with the ads. Many businesses pay higher attention to “engagement marketing” that maximizes social actions, as social actions can effectively promote brand awareness. This paper studies social action prediction for in-feed advertising. Most existing works overlook the social influence as a user’s action may be affected by her friends’ actions. This paper introduces an end-to-end approach that leverages social influence for action prediction, and focuses on addressing the high sparsity challenge for in-feed ads. We propose to learn influence structure that models who tends to be influenced. We extract a subgraph with the near neighbors a user interacts with, and learn topological features of the subgraph by developing structure-aware graph encoding methods. We also introduce graph attention networks to learn influence dynamics that models how a user is influenced by neighbors’ actions. We conduct extensive experiments on real datasets from the commercial advertising platform of WeChat and a public dataset. The experimental results demonstrate that social influence learned by our approach can significantly boost performance of social action prediction.
Partial Dynamic Reconfiguration: The Caronte Approach. A New Degree of Freedom in the HW/SW Codesign (2006)

The design of embedded systems is rapidly changed during the last decade. It is possible to identify two main factors that are involved in this process: HW/WS codesign and dynamic reconfigurable architecture. This work aims at introducing an innovative methodology that allows to easily implement on an FPGA a system specification, taking as input its high-level description, such as C or SystemC, and exploiting the capabilities of partial dynamic reconfiguration and HW/SW codesign methodologies. In order to meet the software requirements of complex systems, the solution is also provided with the porting of a real-time GNU/Linux OS, CLinux, which allows software processes to exploit a rich set of features, and with a Linux module that simplifies the handling of reconfiguration
Trichomonas vaginalis: a review of epidemiologic, clinical and treatment issues (2015)

Trichomonas vaginalis (TV) is likely the most common non-viral sexually transmitted infection (STI) in the world. It is as an important source of reproductive morbidity, a facilitator of HIV transmission and acquisition, and thus it is an important public health problem. Despite its importance in human reproductive health and HIV transmission, it is not a reportable disease and surveillance is not generally done. This is problematic since most persons infected with TV are asymptomatic. Metronidazole (MTZ) has been the treatment of choice for women for decades, and single dose has been considered the first line of therapy. However, high rates of retest positive are found among TV infected persons after single dose MTZ treatment. This has not been explained by drug resistance since in vitro resistance is only 2-5 %. Treatment failure can range from 7-10 % and even higher among HIV+ women. Treatment efficacy may be influenced by vaginal ecology. The origins of repeat positives need further explanation and better treatment options are needed.
Formation and Properties of Blended Nonwovens Produced by Cellulose-Cellulose Bonding (1975)

A series of self-bonded nonwoven fabrics have been produced from cellulosic fibers and from cellulose fiber/noncellulose (natural or manmade) fiber blends by treatment of cross-laid card webs with concentrated zinc chloride solutions. The cellulosic fibers become cohesively bonded during the treatment. If noncellulosic fibers have been blended in during the carding operation, their mechanical entanglement will be enhanced by this bonding. A number of parameters, such as zinc chloride concentration, can be varied to produce a range of desired physical properties and aesthetic characteristics. Usefulness of these nonwovens in filtration studies has been demonstrated.
Performance of the Trans-Alaska Pipeline in the November 3, 2002 Denali Fault Earthquake (2003)

The magnitude 7.9 earthquake that occurred in south-central Alaska on November 3, 2002 ruptured a 336-km long segment of the Denali Fault. The epicenter was located about 88 km west of the Trans-Alaska Pipeline, and the rupture propagated to the east across the pipeline right-of-way. The above-ground segments of the pipeline were subjected to violent near-fault ground shaking approaching or exceeding design criteria, and liquefaction was observed at a number of locations along the pipeline, including a remote gate valve location. The performance of the pipeline was in line with original project design requirements, and there was no oil leakage. The paper presents a high-level overview of the seismic design of the Trans-Alaska Pipeline, performance of the pipeline system during the magnitude 7.9 event, and a brief commentary on post-event emergency response.
Analysis of Cordycepin in Cordyceps Militaris(L. Fr)Link by High Performance Liquid Chromatography (2004)

In this paper,a HPLC method for determining the contents of cordycepin in cordyceps militaris ( L. Fr) Link was reported. Methods: The column was Waters NOVA - PAK C18 3,9mm×300mm; mobile phase was KH2PO4 - K2HPO4(0.01mol/L,PH =6. 86) + 1% tetrahydrofuran; flow rate 1.0mL/min; detection wavelength 260nm. Results:The linearity range was 3. 23 μg/mL ~ 129. 0μg/mL( r = 0. 9999) for cordycepin. The average recoveries of cordycepin were 97. 5% . The lower limit of detection was 0. 25ng ( SN = 3 ) for cordycepin. Conclusion: This method is easy rapid and accurate. It has been used to determine the cordycepin in cordyceps militaris (L. Fr)Link with satisfactory results.
A potential role for hydrocortisone in the positive regulation of IL-15–activated NK-cell proliferation and survival (2005)

Although glucocorticoids (GCs) have been described as acting mainly as anti-inflammatory and immunosuppressive drugs, they may also positively influence the immune system. In the present study, we demonstrate for the first time that hydrocortisone (HC), in synergy with interleukin-15 (IL-15), induces a dramatic increase in the expansion of peripheral blood-derived CD56+ cells, favoring the preferential outgrowth of classical natural killer (CD56+CD3- NK) over CD56+CD3+ natural killer T (NKT) cells. HC plus IL-15-driven CD56+ cells exhibited an increased potential for cytokine production with no impairment in their NK- and lymphokine-activated killer (LAK) activities. Elevated levels of GC-induced leucine zipper protein (GILZ) messenger RNA (mRNA) were detected in both NK and NKT cells cultured with HC and IL-15, in comparison to IL-15 alone. Phosphorylation status of signal transducer and activator of transcription 5 (STAT5) was not affected by the presence of HC in either of the populations. On the contrary, HC differentially affected the IL-2/IL-15R beta- and gamma-chain surface expression and the phosphorylation levels of extracellular signal-regulated kinases 1/2 (ERK1/2) in IL-15-activated NK and NKT cells. Our data ascribe a novel role to GCs on mature NK-cell expansion and function and open new perspectives for their use in cellular adoptive cancer immunotherapy.
Acoustic propagation in the ocean with a poro-elastic bottom (1983)

The acoustic normal modes in a homogeneous ocean overlying a homogeneous porous elastic bottom half-space are obtained in closed form. The Biot theory is used to model the bottom. The effects of sediment properties on the dispersion and attenuation of acoustic waves are examined numerically. It is found that the shear modulus and the poro-viscous-frequency number ksf/βν are the two most critical bottom parameters for acoustic attenuation. Here, ks is permeability, f is frequency, β is porosity, and ν is the kinematic viscosity. For sediment and rocks having shear modulus larger than 5×107 N/m2, the shear waves and the slow compressional waves become important in acoustic propagation. For hard porous rocks, such as sandstones and corals, the attenuation of acoustic waves by a porous rock increases with frequency. For a given soft sediment, the acoustic wave attenuation decreases with frequency. For a given frequency, the acoustic attenuation becomes maximum when the sediment properties are such that ksf/βν is about 0.1. Near the critical value ksf/βν=0.1 the energy loss is totally due to the fast compressional waves and the fluid bottom model may be used. However, as ksf/βν deviates from 0.1, the error associated with the fluid bottom approximation increases progressively and becomes unacceptable even for soft sediments.
Fair Multiple-bank E-cash in the Standard Model. (2014)

Abstract. Multiple-bank e-cash (electronic cash) model allows users and merchants to open their accounts at different banks which are monitored by the Center Bank. Some multiple-bank e-cash systems were proposed in recent years. However, prior implementations of multiple-bank e-cash all require the random oracle model idealization in their security analysis. We know some schemes are secure in the random oracle model, but are trivially insecure under any instantiation of the oracle. In this paper, based on the automorphic blind signature, the Groth-Sahai proof system and a new group blind signature, we construct a fair multiple-bank e-cash scheme. The new scheme is proved secure in the standard model and provides the following functionalities, such as owner tracing, coin tracing, identification of the double spender and signer tracing. In order to sign two messages at once, we extend Ghadafi’s group blind signature to a new group blind signature. The new signature scheme may be of independent interest. Key words: Fair multiple-bank e-cash; Automorphic blind signature; Groth-Sahai proof; Group blind signature; Standard model.
Noninvasive imaging of 99mtechnetium-labeled low density lipoprotein uptake by tendon xanthomas in hypercholesterolemic patients. (1990)

Technetium-labeled low density lipoproteins (Tc-LDL) appear to be useful for describing LDL biodistribution in normal and dyslipidemic subjects. We injected 99mTc-LDL into subjects with large tendon xanthomas secondary to homozygous familial hypercholesterolemia or sitosterolemia. Rapid (4 hours) accumulation of Tc-99m activity in xanthomas was observed, and this accumulation increased over a 24-hour period. No comparable accumulations of Tc-99m activity were noted in normal subjects or in a subject with heterozygous familial hypercholesterolemia who had very small tendon xanthomas. These findings support previous biopsy data indicating active uptake of LDL by macrophages within xanthoma and suggest that 99mTc-LDL imaging of xanthomas may be useful in studies of the effects of diet and drugs on the accumulation of lipoproteins by atherosclerotic plaques.
Inhibitory effect of valproic acid on bladder cancer in combination with chemotherapeutic agents in vitro and in vivo (2013)

Histone deacetylase inhibitors (HDACIs) are a promising class of drugs that act as antiproliferative agents by promoting differentiation and inducing apoptosis. Valproic acid (VPA) is an HDACI that has been widely used as an anti-convulsant and shows promise as a chemotherapeutic drug for a number of tumor cells. The present study aimed to investigate the inhibitory effect of VPA on the viability of bladder cancer cells and its synergistic effect with chemotherapeutic agents <i>in vitro</i> and <i>in vivo</i>. The cell viability of human bladder cancer cell lines following treatment with VPA and/or VPA in combination with mitomycin C, cisplatin (DDP) and adriamycin were determined using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Hoechst staining was used to observe the morphology of the apoptotic cells. Survivin protein and acetylated histone H3 levels were quantified using western blot analysis. The <i>in vivo</i> tumor growth inhibition of VPA was determined in rats with N-methyl-N-nitrosourea-induced bladder cancer. VPA significantly inhibited the growth of the bladder cancer cells in a concentration- and time-dependent manner. Furthermore, improved results were achieved for tumor inhibition when VPA was combined with chemotherapeutic agents <i>in vitro</i> and <i>in vivo</i>. Survivin expression decreased and acetylated histone H3 expression increased in the bladder cancer cells following the treatment with VPA. Intravesical injections of VPA were able to inhibit tumor progression when combined with DDP. In conclusion, VPA acts as an HDACI that has a direct anticancer effect and markedly enhances the action of several chemotherapy agents. VPA may sensitize bladder cancer to anticancer drugs by downregulating survivin expression.
Severity of Hepatitis C Virus (Genotype-3) Infection Positively Correlates with Circulating MicroRNA-122 in Patients Sera (2014)

The study thus unveiled the role of miR-122 as a plausible diagnostic biomarker during HCV genotype-3 infection in India.
Similarities in sequences and cellular expression between rat CD2 and CD4 antigens. (1987)

The MRC OX-34 antigen of rat T lymphocytes was purified and peptide sequences were obtained. Oligonucleotide probes were synthesized and cDNA clones coding for the antigen were isolated and sequenced to yield a predicted protein sequence for the molecule that fitted the peptide data. Comparison of this sequence with that for human CD2 determined by Sewell et al. showed that OX-34 is rat CD2. The primary structure of the molecule was notable for a moderately large cytoplasmic domain of unusual sequence and also for its highly significant relationship to CD4 antigen in the membrane proximal extracellular region and the transmembrane sequence. A relationship to the Ig superfamily can be argued for the two extra cellular domains of CD2, even though neither fits the standard pattern for Ig-related domains. Within the T lymphocyte lineage, rat CD2 seemed to be present on all stages with the exception of approximately 50% of the thymic CD4-,CD8- cells. In addition, the antigen was prominent on most macrophages in the spleen but not found on peritoneal or liver macrophages. CD4 antigen is also expressed on T lymphocytes and macrophages, and thus CD2 and CD4 appear similar in their cellular expression as well as structural characteristics.