gebhart/patrepeval huggingface dataset:
Fine-structure deletion analysis of the transcriptional silencer of the proU operon of Salmonella typhimurium (1995)

Transcriptional control of the osmotically regulated proU operon of Salmonella typhimurium is mediated in part by a transcriptional silencer downstream from the promoter (D.G. Overdier and L.N. Csonka, Proc. Natl. Acad. Sci. USA 89:3140-3144, 1992). We carried out a fine-structure deletion analysis to determine the structure and the position of the silencer, which demonstrated that this regulatory element is located between nucleotide positions +73 to +274 downstream from the transcription start site. The silencer appears to be made up of a number of components which have cumulative negative regulatory effects. Deletions or insertions of short nucleotide sequences (< 40 bp) between the proU promoter and the silencer do not disrupt repression exerted by the silencer, but long insertions (> or = 0.8 kbp) result in a high level of expression from the proU promoter, similar to that imparted by deletion of the entire silencer. The general DNA-binding protein H-NS is required for the full range of repression of the proU operon in media of low osmolality. Although in the presence of the silencer hns mutations increased basal expression from the proU promoter three- to sixfold, in the absence of the silencer they did not result in a substantial increase in basal expression from the proU promoter. Furthermore, deletion of the silencer in hns+ background was up to 10-fold more effective in increasing basal expression from the proU promoter than the hns mutations. These results indicate that osmotic control of the proU operon is dependent of some factor besides H-NS. We propose that the transcriptional regulation of this operon is effected in media of low osmolality by a protein which makes the promoter inaccessible to RNA polymerase by forming a complex containing the proU promoter and silencer.
Endocrine Fibroblast Growth Factor FGF19 Promotes Prostate Cancer Progression (2013)

Prostate cancer is the most common visceral malignancy and the second leading cause of cancer deaths in US men. There is broad evidence that fibroblast growth factor (FGF) receptors are important in prostate cancer initiation and progression, but the contribution of particular FGFs in this disease is not fully understood. The FGF family members FGF19, FGF21, and FGF23 comprise a distinct subfamily that circulate in serum and act in an endocrine manner. These endocrine FGFs require α-Klotho (KL) and/or β-Klotho (KLB), two related single-pass transmembrane proteins restricted in their tissue distribution, to act as coreceptors along with classic FGF receptors (FGFR) to mediate potent biologic activity. Here we show that FGF19 is expressed in primary and metastatic prostate cancer tissues, where it functions as an autocrine growth factor. Exogenous FGF19 promoted the growth, invasion, adhesion, and colony formation of prostate cancer cells at low ligand concentrations. FGF19 silencing in prostate cancer cells expressing autocrine FGF19 decreased invasion and proliferation in vitro and tumor growth in vivo. Consistent with these observations, KL and/or KLB were expressed in prostate cancer cells in vitro and in vivo, raising the possibility that additional endocrine FGFs may also exert biologic effects in prostate cancer. Our findings support the concept that therapies targeting FGFR signaling may have efficacy in prostate cancer and highlight FGF19 as a relevant endocrine FGF in this setting.
Location Aided Cooperative Detection of Primary User Emulation Attacks in Cognitive Wireless Sensor Networks Using Nonparametric Techniques (2015)

Primary user emulation (PUE) attacks are a major security challenge to cognitive wireless sensor networks (CWSNs). In this paper, we propose two variants of the PUE attack, namely, the relay and replay attacks. Such threats are conducted by malicious nodes that replicate the transmissions of a real primary user (PU), thus making them resilient to many defensive procedures. However, we show that those PUE attacks can be effectively detected by a set of cooperating secondary users (SUs), using location information and received signal strength (RSS) measurements. Two strategies for the detection of PUE relay and replay attacks are presented in the paper: parametric and nonparametric. The parametric scheme is based on the likelihood ratio test (LRT) and requires the existence of a precise path loss model for the observed RSS values. On the contrary, the nonparametric procedure is not tied to any particular propagation model; so, it does not require any calibration process and is robust to changing environmental conditions. Simulations show that the nonparametric detection approach is comparable in performance to the LRT under moderate shadowing conditions, specially in case of replay attacks.
High-modulation efficiency silicon Mach-Zehnder optical modulator based on carrier depletion in a PN Diode (2009)

We present a high phase-shift efficiency Mach-Zehnder silicon optical modulator based on the carrier-depletion effect in a highly-doped PN diode with a small waveguide cross-sectional area. The fabricated modulator show a V(pi)L(pi) of 1.8 V x cm and phase shifter loss of 4.4 dB/mm. A device using a 750 microm-long phase-shifter exhibits an eye opening at 12.5 Gbps with an extinction ratio of 3 dB. Also, an extinction ratio of 7 dB is achieved at 4 Gbps for a device with a 2 mm-long phase shifter. Further enhancement of the extinction ratio at higher operating speed can be achieved using a travelling-wave electrode design and the optimal doping.
Dapagliflozin Is Effective as Add-on Therapy to Sitagliptin With or Without Metformin: A 24-Week, Multicenter, Randomized, Double-Blind, Placebo-Controlled Study (2013)

These results suggest that in patients with type 2 diabetes, inadequately controlled on sitagliptin with or without metformin, add-on treatment with dapagliflozin provides additional clinical benefit and is well tolerated.
Immunofluorescence analysis of IgA binding by human mononuclear cells in blood and lymphoid tissue. (1989)

The nature of IgA-binding cells and their tissue distribution was examined by an indirect immunofluorescence assay with the use of IgA1 and IgA2 paraproteins and fluorochrome- or biotin-labeled F(ab')2 fragments of idiotype-specific antibodies. The frequency of IgA-binding mononuclear cells was approximately 13% in blood and spleen samples but less than 1% in tonsil samples. IgA binding could be visualized by flow immunocytometry on monocyte/macrophages, but not on T and B cells. IgA polymers were bound better than IgA dimers and monomers. Nonhomologous IgA myelomas of both IgA1 and IgA2 subclasses inhibited the IgA-binding to monocytes, whereas aggregated normal serum IgG, IgM paraproteins, and an IgG myeloma did not. IgA binding was relatively insensitive to changes in temperature or cation concentration. IgA-binding monocytes were found in IgA-deficient patients at the same frequency as in normal individuals. The results indicate that monocytes constitutively express class-specific binding sites for both IgA1 and IgA2 molecules.
AdTorrent: Digital Billboards for Vehicular Networks (2005)

One of the most important sources of revenue for big Internet-based companies are advertisements. With vehicular networks poised to become part of the Internet, this new &quot;edge&quot; of the Internet represents the next frontier that advertising companies will be striving to reach. In this paper we investigate the feasibility of targeted dissemination of ad content in a car network. We present Digital Billboards, a scalable &quot;push&quot; model architecture for ad content delivery. We then propose, AdTorrent, an integrated system for search, ranking and content delivery in this architecture. We evaluate our design using a realistic vehicular mobility model which captures mobility characteristics such as temporal and spatial dependencies and geographic restrictions.
Regulation of protein-synthesis elongation-factor-2 kinase by cAMP in adipocytes (1998)

Treatment of primary rat epididymal adipocytes or 3T3-L1 adipocytes with various agents which increase cAMP led to the phosphorylation of eukaryotic translation elongation factor-2 (eEF-2). The increase in eEF-2 phosphorylation was a consequence of the activation of eEF-2 kinase (eEF-2K), which is a Ca2+/calmodulin-dependent kinase. eEF-2K was shown to be essentially inactive at less than 0.1 microM free Ca2+ when measured in cell-free extracts. Treatment of adipocytes with isoproterenol induced Ca2+-independent eEF-2K activity, and an 8-10-fold activation of eEF-2K was observed at Ca2+ concentrations of less than 0.1 microM. Increased cAMP in 3T3-L1 adipocytes led to the inhibition of total protein synthesis and decreased the rate of polypeptide-chain elongation. We also show that the phosphorylation of eEF-2 and the activity of eEF-2K are insulin-regulated in adipocytes. These results demonstrate a novel mechanism for the control of protein synthesis by hormones which act by increasing cytoplasmic cAMP.
Lymphokines and Platelets Promote Human Monocyte Adherence to Fibrinogen and Fibronectin In Vitro (1987)

Monocytes must accumulate in areas of tissue injury and inflammation to effect phagocytosis, antigen presentation, and monokine production. Fibrinogen/fibronectin matrices have been demonstrated in healing wounds and in delayed-type hypersensitivity skin reactions. We have developed an in vitro system for investigation of the ability of fibrinogen and fibronectin matrices to serve as substrata for human peripheral blood monocyte adherence. Monocyte adherence was greatest on matrices of both fibrinogen and fibronectin, less to fibrinogen alone, and least to fibronectin alone. Lymphokines increased adherence of monocytes to all three surfaces but not to albumin-coated surfaces. Addition of platelets also caused a dose-dependent increase in monocyte adherence to all three surfaces. This increased adherence was not a simple function of arachidonic acid metabolites, stable platelet products, nor monocyte binding sites on the platelet membrane. The effect of platelets was not additive to the effect of lymphokines. We conclude that fibrinogen and fibronectin provide a framework for monocyte adherence and that factors present in areas of inflammation and wound healing, such as lymphokines and platelets, can augment this adherence. Such adherence facilitates the transformation of monocytes into macrophages in vitro and may also foster such transformation in vivo.
Adjoint-Method Retrievals of Low-Altitude Wind Fields from Single-Doppler Wind Data (1994)

The simple adjoint method of Qiu and Xu is extended and used to retrieve the low-altitude horizontal wind field from single-Doppler radial wind data measured during the Phoenix II field experiment. Since the extended method uses only the radial momentum equation on a low-altitude horizontal plane with a weak nondivergence constraint for the horizontal winds, the pressure gradient and vertical advection are treated as an unknown residual forcing. The test results show that (i) the method can retrieve the low-altitude time-mean (or running mean) horizontal winds (averaged over a period of several sequential radar scans) from single-Doppler radial wind data; (ii) retrieving the time-mean part of the unknown residual forcing term improves the wind retrieval; (iii) the detailed data treatments and proper settings of the weights considered in Xu et at. remain useful for improving the retrieval.
Measurement of small strains in a noisy environment (1985)

A simple technique is demonstrated for measuring strains in an electromagnetically noisy environment using electrical strain gauges. For applications in which strains are produced electromagnetically in current-carrying structures, the noise signal can be much larger than the strain signal. Furthermore, the noise signal is at precisely the same frequency as the strain signal, making standard methods of synchronous signal detection difficult. This problem has been surmounted by modulating the detection circuit sensitivity. Bridge circuit modulation has been shown to effectively decouple the strain signal from the noise, even at very low strain levels of ∼10−8 m/m.
Retinal cell death and current strategies in retinal neuroprotection (2014)

With more knowledge of how retinal cells die, further advances are being made in prolonging the cell survival. However, even as basic science discoveries remain promising, clinical utility of neuroprotection is still quite limited at this time.
Ultra-widefield retinal imaging: an update on recent advances (2020)

The development of ultra-widefield retinal imaging has accelerated our understanding of common retinal diseases. As we continue to validate the diagnostic and prognostic significance of pathology in the retinal periphery, the ability to visualize and evaluate these features in an efficient and patient-friendly manner will become more important. Current interest in ultra-widefield imaging includes the development of potential biomarkers of disease progression and indicators of preclinical disease development. This article reviews the current ultra-widefield imaging systems and recent advances in their applications to clinical practice with a focus on diabetic retinopathy, retinal vein occlusion, uveitis, and pediatric retina.
Automatic Construction of Program-Optimized FPGA Memory Networks (2017)

Memory systems play a key role in the performance of FPGA applications. As FPGA deployments move towards design entry points that are more serial, memory latency has become a serious design consideration. For these applications, memory network optimization is essential in improving performance. In this paper, we examine the automatic, program-optimized construction of low-latency memory networks. We design a feedback-driven network compiler, which constructs an optimized memory network based on the target program's memory access behavior measured via a newly designed network profiler. In our test applications, the compiler-optimized networks provide a 45% performance gain on average over baseline memory networks by minimizing the impact of network latency on program performance.
A radiation-hard, low-background multiplexer design for spacecraft imager applications (1992)

A possible multiplexer design for the focal plane for the Cassini Visible and Infrared Mapping Spectrometer (VIMS) is reviewed. The instrument's requirements for the multiplexed array are summarized. The VIMS instrument has a modest radiation-hardness requirement due to the trajectory and planetary environments in which the instrument will be required to operate. The total ionizing dose hardness requirement is a few tens of kilorads. A thin-gate oxide of a few hundred angstroms thickness is to be used. Field hardness is to be achieved by guard bands or hardened dielectric isolation. The design is argued to meet the low-noise and radiation-hardness required for imaging at Saturn. The design is versatile enough to provide double-correlated and double-uncorrelated sampling, which is accomplished in the signal processing electronics outside the focal plane.
New .ALPHA.-amylase inhibitor, trestatins. II. structure determination of trestatins A, B and C. (1983)

The structures of trestatins A (C56H94N2O40), B (C37H63NO28) and C (C75H125N3O52), new basic oligosaccharides with potent inhibitory activity against various alpha-amylases, have been shown by spectroscopic and chemical methods to be 1, 2 and 3, respectively.
Functional restoration of human immunodeficiency virus and Epstein-Barr virus-specific CD8+ T cells during highly active antiretroviral therapy is associated with an increase in CD4+ T cells (2002)

To investigate the effect of highly active antiretroviral therapy (HAART) on HIV- and Epstein-Barr virus (EBV)-specific CD8(+) T cells, total number and function of these cells was determined in 16 HIV-infected individuals using tetrameric HLA-peptide complexes and IFN-gamma ELISPOT assays after peptide stimulation, respectively. HAART induced a significant decrease in HIV-specific tetramer(+) T cells, whereas EBV-specific tetramer(+) T cells did not change. In addition, individuals who temporarily failed on therapy showed a temporary increase in the number of HIV-specific T cells, suggesting that differences in the pool size of antigen-specific T cells was determined by the presence of antigen. Interestingly, there was an increase in the ratio of IFN-gamma-producing T cells per total number of both HIV- and EBV-specific T cells in the majority of individuals, suggesting that the function of virus-specific T cells is improved in individuals successfully treated with HAART. Despite this relative functional improvement of EBV-specific T cells, no significant changes were observed in EBV load. In four subjects who temporarily failed on HAART, the percentage of IFN-gamma-producing T cells, both for HIV and EBV, paralleled CD4(+) T cell kinetics, suggesting that function seems to be related to differences in CD4(+) T cell numbers. Overall, these data indicate that HAART improves the antigen responsiveness of both HIV- and EBV-specific T cells, which is associated with an increase in CD4(+) T cells.
Capacity allocation in semiconductor fabrication (2003)

One of the most serious challenges in the semiconductor memory business is the rapid price decline. We develop an allocation scheme that determines the die (chip) allocation among different memory products. The allocation takes into account available die capacity, customer service requirements, as well as price declines and demand distributions among different products.
Genetic Validation of the Protein Arginine Methyltransferase PRMT5 as a Candidate Therapeutic Target in Glioblastoma (2014)

Glioblastoma is the most common and aggressive histologic subtype of brain cancer with poor outcomes and limited treatment options. Here, we report the selective overexpression of the protein arginine methyltransferase PRMT5 as a novel candidate theranostic target in this disease. PRMT5 silences the transcription of regulatory genes by catalyzing symmetric dimethylation of arginine residues on histone tails. PRMT5 overexpression in patient-derived primary tumors and cell lines correlated with cell line growth rate and inversely with overall patient survival. Genetic attenuation of PRMT5 led to cell-cycle arrest, apoptosis, and loss of cell migratory activity. Cell death was p53-independent but caspase-dependent and enhanced with temozolomide, a chemotherapeutic agent used as a present standard of care. Global gene profiling and chromatin immunoprecipitation identified the tumor suppressor ST7 as a key gene silenced by PRMT5. Diminished ST7 expression was associated with reduced patient survival. PRMT5 attenuation limited PRMT5 recruitment to the ST7 promoter, led to restored expression of ST7 and cell growth inhibition. Finally, PRMT5 attenuation enhanced glioblastoma cell survival in a mouse xenograft model of aggressive glioblastoma. Together, our findings defined PRMT5 as a candidate prognostic factor and therapeutic target in glioblastoma, offering a preclinical justification for targeting PRMT5-driven oncogenic pathways in this deadly disease.
Purification of Dehydroascorbate Reductase from Spinach and Its Characterization as a Thiol Enzyme (1984)

Dehydroascorbate (DHA) reductase (EC 1.8.5.1) was purified from spinach leaves to nearly a homogeneous state, judging from polyacrylamide gel electrophoresis. The enzyme was found to be a monomer with a molecular weight of 23,000 with apparent Km values for GSH and DHA of 2.5 and 0.07 nu, respectively. Kinetic studies indicated that the reaction proceeds by an ordered or random mechanism involving the formation of a ternary complex. The enzyme was inhibited by thiol reagents and DHA could partly protect the enzyme thiol group. Incubation of the inactivated enzyme with GSH led to slight recovery of the activity. NADH, NADPH, cysteine or reduced thioredoxin could not replace GSH as an electron donor. Thus, the thiol group(s) participates in the reaction of DHA reductase.
Continuous veno–venous haemodialysis with a novel bicarbonate dialysis solution: prospective cross-over comparison with a lactate buffered solution (1999)

During continuous veno venous haemodialysis a bicarbonate buffered dialysis solution provided equal acid-base control but maintained more normal lactate levels than a lactate buffered dialysis solution.
In Vitro Analysis of Integrated Global High-Resolution DNA Methylation Profiling with Genomic Imbalance and Gene Expression in Osteosarcoma (2008)

Genetic and epigenetic changes contribute to deregulation of gene expression and development of human cancer. Changes in DNA methylation are key epigenetic factors regulating gene expression and genomic stability. Recent progress in microarray technologies resulted in developments of high resolution platforms for profiling of genetic, epigenetic and gene expression changes. OS is a pediatric bone tumor with characteristically high level of numerical and structural chromosomal changes. Furthermore, little is known about DNA methylation changes in OS. Our objective was to develop an integrative approach for analysis of high-resolution epigenomic, genomic, and gene expression profiles in order to identify functional epi/genomic differences between OS cell lines and normal human osteoblasts. A combination of Affymetrix Promoter Tilling Arrays for DNA methylation, Agilent array-CGH platform for genomic imbalance and Affymetrix Gene 1.0 platform for gene expression analysis was used. As a result, an integrative high-resolution approach for interrogation of genome-wide tumour-specific changes in DNA methylation was developed. This approach was used to provide the first genomic DNA methylation maps, and to identify and validate genes with aberrant DNA methylation in OS cell lines. This first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression has provided comprehensive evidence of the cumulative roles of epigenetic and genetic mechanisms in deregulation of gene expression networks.
Identification of fibroblast growth factor-5 as an overexpressed antigen in multiple human adenocarcinomas. (2001)

Methodology for identifying tumor-associated antigens recognized by T cells has been successfully used to clone antigens from melanoma cells. Similar efforts for nonmelanoma tumors have had limited success with few antigens identified. To identify potentially relevant tumor-associated antigens expressed in renal cell carcinoma cell lines, a tumor-specific CTL clone was established from tumor-infiltrating lymphocytes from a regressing pulmonary lesion. This CTL recognized nonmutated fibroblast growth factor-5 (FGF-5). Quantitative real-time reverse transcription PCR revealed that FGF-5 was overexpressed in the majority of renal cell carcinomas, as well as in some prostate carcinoma and breast carcinoma lines. FGF-5 expression by quantitative real-time reverse transcription PCR in normal tissues was below the recognition threshold for this CTL. As a normal protein with significant overexpression by multiple adenocarcinomas and little normal tissue expression, FGF-5 represents an immunotherapy target with potential utility against a broad array of nonmelanoma cancers.
Concurrent generation of nitric oxide and superoxide inhibits proteoglycan synthesis in bovine articular chondrocytes: involvement of peroxynitrite. (1998)

The concurrent generation of superoxide anion and NO is required for the action of IL-1 to inhibit proteoglycan synthesis. Peroxynitrite is a candidate for this underlying mechanism.
Optimum Input and Output Filters for a Single-Phase Rectifier Power Supply (1981)

The ``optimum'' output filter inductance Lf and the input filter capacitor Ci for a single-phase uncontrolled bridge rectifier employed for low power de-to-dc converters or inverters is established. The filter Ci is optimized to obtain maximum input power factor, minimum filter inductance, and minimum output dc voltage regulation. A design example is provided and theoretical results have been verified on an experimental model.