gebhart/patrepeval huggingface dataset:
Contribution of oncoproteomics to cancer biomarker discovery (2007)

Oncoproteomics is the study of proteins and their interactions in a cancer cell by proteomic technologies. Proteomic research first came to the fore with the introduction of two-dimensional gel electrophoresis. At the turn of the century, proteomics has been increasingly applied to cancer research with the wide-spread introduction of mass spectrometry and proteinchip. There is an intense interest in applying proteomics to foster an improved understanding of cancer pathogenesis, develop new tumor biomarkers for diagnosis, and early detection using proteomic portrait of samples. Oncoproteomics has the potential to revolutionize clinical practice, including cancer diagnosis and screening based on proteomic platforms as a complement to histopathology, individualized selection of therapeutic combinations that target the entire cancer-specific protein network, real-time assessment of therapeutic efficacy and toxicity, and rational modulation of therapy based on changes in the cancer protein network associated with prognosis and drug resistance. Besides, oncoproteomics is also applied to the discovery of new therapeutic targets and to the study of drug effects. In pace with the successful completion of the Human Genome Project, the wave of proteomics has raised the curtain on the postgenome era. The study of oncoproteomics provides mankind with a better understanding of neoplasia. In this article, the discovery of cancer biomarkers in recent years is reviewed. The challenges ahead and perspectives of oncoproteomics for biomarkers development are also addressed. With a wealth of information that can be applied to a broad spectrum of biomarker research projects, this review serves as a reference for biomarker researchers, scientists working in proteomics and bioinformatics, oncologists, pharmaceutical scientists, biochemists, biologists, and chemists.
NKT Cells Provide Help for Dendritic Cell-Dependent Priming of MHC Class I-Restricted CD8+ T Cells In Vivo (2003)

Dendritic cells (DC) are potent APCs for naive T cells in vivo. This is evident by inducing T cell responses through adoptive DC transfer. Priming specific CTL responses in vivo often requires "help". We study alternative sources of help in DC-dependent priming of MHC class I-restricted CTL. Priming an anti-viral CTL response in naive B6 mice by adoptive transfer of antigenic peptide-pulsed DC required CD4(+) T cell help. CTL priming was facilitated by providing MHC class II-dependent specific help. Furthermore, transfers of MHC class II-deficient pulsed DC into naive, normal hosts, or DC transfers into naive, CD4(+) T cell-depleted hosts primed CTL inefficiently. Pretreatment of DC with immune-stimulating oligodeoxynucleotides rendered them more efficient for CD4(+) T cell-independent priming of CTL. DC copresenting a K(b)-binding antigenic peptide and the CD1d-binding glycolipid alpha-galactosyl-ceramide efficiently primed CTL in a class II-independent way. To obtain NKT cell-dependent help in CTL priming, the same DC had to present both the peptide and the glycolipid. CTL priming by adoptive DC transfer was largely NK cell-dependent. The requirement for NK cells was only partially overcome by recruiting NKT cell help into DC-dependent CTL priming. NKT cells thus are potent helper cells for DC-dependent CTL priming.
A framework design for the next-generation radio access system (2006)

Extensive use of the Internet and huge demands for multimedia services via portable devices require the development of packet-based radio access systems with high transmission efficiency. Advanced radio transmission technologies have recently been proposed to achieve this challenging task. However, few researches have been reported on the design of an integrated system that can efficiently exploit the advantages of these transmission technologies. This paper considers the design of a packet-based cellular system for next-generation radio access. We propose a novel system framework that can incorporate various advanced transmission technologies such as link adaptation, opportunistic packet scheduling, channel coding, and multiantenna techniques. For efficient use of these technologies together, we first investigate the interoperability between these technologies by proposing a so-called cause and effect analysis. Based on this investigation, we design a differentiated-segments-based orthogonal frequency-division multiplexing system, called DiffSeg, to accommodate heterogeneous operating conditions in a seamless manner. Simulation results show that the proposed DiffSeg system can provide a nearly optimum performance with flexible configuration in a wide range of wireless channel conditions.
Ankle Fractures Treated Using Biodegradable Internal Fixation (1989)

In order to reduce the resources needed for the removal of metallic fixation devices in fracture treatment, absorbable implants of biodegradable synthetic polymers were developed using self-reinforced lactide-glycolide copolymer and polyglycolide. In a prospective study 102 patients with displaced unimalleolar or bimalleolar fractures of the ankle were managed using internal fixation devices consisting of cylindrical biodegradable implants 3.2 or 4.5 mm in diameter and 50 or 70 mm in length. After open reduction of the fracture a channel was drilled from the tip of the malleolus into the cancellous bone through the fracture surfaces. A biodegradable rod of the same diameter was then tapped into the drill channel to fix the fracture. Postoperatively, the ankle was immobilized by a plaster cast for six weeks. An anatomic initial reduction was achieved in 93 patients (91%). A slight secondary displacement occurred in four patients. In six patients a sinus formation yielding remnants of the degrading implant was seen two to four months after the operation. This minor complication did not influence the union of the fracture or functional recovery. At the one-year follow-up examination there was no change in the ability to participate in sports and other physical activities in 89 patients (87%). The biodegradable fixation method is now the routine approach of the department in treating displaced unimalleolar and bimalleolar ankle fractures. New clinical applications for the implants are under trial.
CMOS RF Biosensor Utilizing Nuclear Magnetic Resonance (2009)

We report on a CMOS RF transceiver designed for detection of biological objects such as cancer marker proteins. Its main function is to manipulate and monitor RF dynamics of protons in water via nuclear magnetic resonance (NMR). Target objects alter the proton dynamics, which is the basis for our biosensing. The RF transceiver has a measured receiver noise figure of 0.7 dB. This high sensitivity enabled construction of an entire NMR system around the RF transceiver in a 2-kg portable platform, which is 60 times lighter, 40 times smaller, yet 60 times more mass sensitive than a state-of-the-art commercial benchtop system. Sensing 20 fmol and 1.4 ng of avidin (protein) in a 5 muL sample volume, our system represents a circuit designer's approach to pursue low-cost diagnostics in a portable platform.
Fully-differential poly-sic lame-mode resonator and checkerboard filter (2005)

In this paper, we report the first fully-differential, electrostatically transduced RF MEMS resonator. The fully-differential electrode configuration not only cancels capacitive feedthrough between the drive and sense terminals but also eliminates the reduction in electromechanical quality factor (Q) from the large ohmic resistance of the polycrystalline silicon carbide (poly-SiC) suspension and anchor. Using this configuration, we have demonstrated a 173 MHz poly-SiC Lame-mode resonator with a Q of 9,300 in air. By mechanically coupling five Lame-mode resonators into a 2-D checkerboard, we have realized a 173 MHz center frequency band-pass filter with 110 kHz bandwidth and < 2 dB pass-band ripple.
Epidemiology and prevention of meningococcal disease (1995)

From the Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA.
Visualization and ligand-induced modulation of dopamine receptor dimerization at the single molecule level (2016)

G protein-coupled receptors (GPCRs), including dopamine receptors, represent a group of important pharmacological targets. An increased formation of dopamine receptor D2 homodimers has been suggested to be associated with the pathophysiology of schizophrenia. Selective labeling and ligand-induced modulation of dimerization may therefore allow the investigation of the pathophysiological role of these dimers. Using TIRF microscopy at the single molecule level, transient formation of homodimers of dopamine receptors in the membrane of stably transfected CHO cells has been observed. The equilibrium between dimers and monomers was modulated by the binding of ligands; whereas antagonists showed a ratio that was identical to that of unliganded receptors, agonist-bound D2 receptor-ligand complexes resulted in an increase in dimerization. Addition of bivalent D2 receptor ligands also resulted in a large increase in D2 receptor dimers. A physical interaction between the protomers was confirmed using high resolution cryogenic localization microscopy, with ca. 9 nm between the centers of mass.
Selective epitaxial growth of silicon and some potential applications (1990)

In the selective epitaxial growth (SEG) of silicon, growth occurs only on exposed silicon areas of a silicon substrate. Substrate regions on which silicon growth is not desired are masked by a dielectric film, typically silicon dioxide or silicon nitride. Use of the process permits the fabrication of novel silicon devices and integrated-circuit structures. In this paper, an overview is presented of our studies on the SEG process at the IBM Thomas J. Watson Research Center. Aspects covered are the kinetics of the process using a SiCl <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> and H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> gaseous mixture, the associated suppression of deposition on silicon dioxide and silicon nitride, and some potential applications of the process to the fabrication of bipolar devices and dynamic random access memory (DRAM) cells.
Production and Application of Activated Carbons Made from Waste Tire (2005)

Nowadays, waste tires disposal has become a relevant environmental problem. Although pyrolysis processes seem to be a feasible alternative treatment, a proper application for generated residues is a task to be solved. In this context, the aim of this work is to valorize pyrolytic tire char by means of the production of a useful adsorbent for air purification. An activation process with CO2 was chosen to control the process of microporosity generation. The activation reaction and the textural properties were followed to achieve the understanding of porosity evolution. A change in the reaction rate in the first steps of the process was observed, followed by a linear relationship between activation time and burnoff. Microporosity is generated in two main processes. At the beginning, narrow microporosity is formed, and later, a widening of the micropores is taking place. The performance of the new obtained samples for hot gas cleaning was tested by a process of Phenanthrene (Phe) adsorption in a fixed bed reactor with a process temperature of 150 °C at low inlet concentrations. It was concluded that the porosity development, both micro- and nonmicroporosity, increases the Phe adsorption capacity of activated carbons, likely due to a multilayer adsorption process
Levetiracetam in Refractory Pediatric Epilepsy (2002)

Levetiracetam, one of the newer-generation antiepilepsy drugs, is not currently approved for use in children. Given its favorable efficacy, pharmacokinetic, and, particularly, safety profile in adults, we felt that it may be a useful antiepilepsy drug for children with refractory epilepsy. We treated 39 patients (mean age 8.6 years) with open-label levetiracetam for up to 9 months. Seizure frequency, drug dosages, adverse events, and neurologic examinations were documented at baseline and routine follow-up visits. Levetiracetam, as add-on therapy, was effective in reducing seizure frequency in a variety of seizure types but was most effective for partial-onset seizures. Fourteen patients were discontinued for lack of efficacy or adverse events. Ten patients reported improvements in cognition or behavior. Levetiracetam was generally effective and well tolerated in this open-label study. Its apparent positive effects on cognition in some patients are encouraging. Large, well-controlled studies are needed to fully define levetiracetam's potential in children with refractory epilepsy.
Splicing in the immune system: potential targets for therapeutic intervention by antisense-mediated alternative splicing. (2009)

Alternative splicing of pre-mRNA leads to variation in the exons that form the mRNA, and provides eukaryotic organisms with an additional qualitative control of gene expression. Disruptions in the regulation of pre-mRNA splicing caused by heritable genomic mutations or quantitative shifts in the regulation of exon inclusion can lead to disease. Alternative exon inclusion (pre-mRNA splicing) produces different proteins with alternative activities, derived from the same pre-mRNA, and is utilized by the immune system to expand gene function. Recent advances in the delivery of splice switching oligomers to lymphoid cells, combined with the ability to manipulate mRNA splicing to either correct mis-splicing or to alter the balance of different splice forms, holds great promise for the development of new therapeutic strategies for the treatment of immune-related disease. Antisense-based targeted manipulation of various immune modulating molecules as therapeutic approaches are discussed in this review.
Highly Sensitive and Selective Colorimetric Sensors for Uranyl (UO<sub>2</sub><sup>2+</sup>): Development and Comparison of Labeled and Label-Free DNAzyme-Gold Nanoparticle Systems (2008)

Colorimetric uranium sensors based on uranyl (UO2(2+)) specific DNAzyme and gold nanoparticles (AuNP) have been developed and demonstrated using both labeled and label-free methods. In the labeled method, a uranyl-specific DNAzyme was attached to AuNP, forming purple aggregates. The presence of uranyl induced disassembly of the DNAzyme functionalized AuNP aggregates, resulting in red individual AuNPs. Once assembled, such a "turn-on" sensor is highly stable, works in a single step at room temperature, and has a detection limit of 50 nM after 30 min of reaction time. The label-free method, on the other hand, utilizes the different adsorption properties of single-stranded and double-stranded DNA on AuNPs, which affects the stability of AuNPs in the presence of NaCl. The presence of uranyl resulted in cleavage of substrate by DNAzyme, releasing a single stranded DNA that can be adsorbed on AuNPs and protect them from aggregation. Taking advantage of this phenomenon, a "turn-off" sensor was developed, which is easy to control through reaction quenching and has 1 nM detection limit after 6 min of reaction at room temperature. Both sensors have excellent selectivity over other metal ions and have detection limits below the maximum contamination level of 130 nM for UO2(2+) in drinking water defined by the U.S. Environmental Protection Agency (EPA). This study represents the first direct systematic comparison of these two types of sensor methods using the same DNAzyme and AuNPs, making it possible to reveal advantages, disadvantages, versatility, limitations, and potential applications of each method. The results obtained not only allow practical sensing application for uranyl but also serve as a guide for choosing different methods for designing colorimetric sensors for other targets.
Routing in a delay tolerant network (2004)

We formulate the delay-tolerant networking routing problem, where messages are to be moved end-to-end across a connectivity graph that is time-varying but whose dynamics may be known in advance. The problem has the added constraints of finite buffers at each node and the general property that no contemporaneous end-to-end path may ever exist. This situation limits the applicability of traditional routing approaches that tend to treat outages as failures and seek to find an existing end-to-end path. We propose a framework for evaluating routing algorithms in such environments. We then develop several algorithms and use simulations to compare their performance with respect to the amount of knowledge they require about network topology. We find that, as expected, the algorithms using the least knowledge tend to perform poorly. We also find that with limited additional knowledge, far less than complete global knowledge, efficient algorithms can be constructed for routing in such environments. To the best of our knowledge this is the first such investigation of routing issues in DTNs.
Room-temperature phosphonium ionic liquids for supercapacitor application (2005)

Ionic liquids (ILs) have been used as electrolytes for supercapacitors. Two phosphonium salts such as trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide (IL1) and trihexyl(tetradecyl) phosphonium dicyanamide (IL2) have been selected for this target. To decrease the viscosity of ILs, a small amount of acetonitrile (from 5 to 25 wt %) was added. Supercapacitor based on activated carbon (AC) as electrodes and IL1 with 25 wt % of acetonitrile supplied capacitance values of 100F∕g at a high operating voltage of 3.4 V. Such a supercapacitor reached a high energy of ∼40Wh∕kg and a good cyclability.
Bulbar Conjunctival and Tenon\'s Layer Thickness Measurement using Optical Coherence Tomography (2014)

Optical coherence tomography conjunctival and Tenon's layer thickness measurements appear to vary significantly between individuals. We postulate that this could infuence the final bleb morphology and may predict the risk of bleb encapsulation and failure or thin avascular blebs. Further assessment could establish cut-offs on which patients should receive intraoperative antimetabolites and/or Tenon's layer excision. How to cite this article: Howlett J, Vahdani K, Rossiter J. Bulbar Conjunctival and Tenon's Layer Thickness Measurement using Optical Coherence Tomography. J Curr Glaucoma Pract 2014;8(2):63-66.
Control strategies for voltage control of a boost type PWM converter (2002)

This paper addresses the nonlinear problem of regulating the DC link voltage, in a vector controlled three-phase boost type PWM converter with particular emphasis on applications in wind energy systems. The AC side current control is performed in a synchronously rotating reference frame. An analysis of the system is provided and several alternative DC link voltage controller designs are investigated and compared. Fuzzy controllers augmented using a feedforward compensation technique are found to provide excellent performance. A 3 kW experimental set up has been built and experimental results are provided to validate the control designs.
[Expression, purification and immunogenicity of human papillomavirus type 11 virus-like particles from Escherichia coli]. (2009)

We can provide HPV11 VLPs with highly immunogenicity from prokaryote expression system, which may pave a new way for research and development of prophylactic vaccine for HPV11.
Bit-Interleaved Coded Modulation (2007)

Since its introduction, Bit-Interleaved Coded Modulation (BICM) has been regarded as a pragmatic yet powerful scheme to achieve high data rates with general signal constellations. Nowadays, BICM is employed in a wide range of practical communications systems, such as DVB-S2, Wireless LANs, DSL, WiMax, the future generation of high data rate cellular systems (the so-called 4th generation). BICM has become the de-facto standard for coding over the Gaussian channel in modern systems. Bit-Interleaved Coded Modulation provides a comprehensive study of the subject. In particular, it review its information theoretic foundations, and its capacity, cutoff rate and error exponents. It further examines the error probability of BICM, focussing on the union bound and improved bounds to the error probability before turning its attention to iterative decoding of BICM. The underlying design techniques reviewed and improved BICM schemes in a unified framework introduced. Finally, a number of applications of BICM not explicitly elsewhere covered are described. Bit-Interleaved Coded Modulation provides a comprehensive review of one of the most important coding schemes in modern communication systems. It will be of interest to students, practitioners and researchers working on developing 4th generation communication systems.
Serum cytokines in juvenile rheumatoid arthritis: correlation with conventional inflammation parameters and clinical subtypes (1995)

JRA is associated with significant and consistent changes in serum levels of inflammatory cytokines and soluble receptors. For the clinical monitoring of JRA, determination of levels of sTNFR, and to some extent sIL-2R, may be particularly useful, since these determinations yield information about subtype and/or activity of disease that is not available from conventional parameters of inflammation.
Hepatic VLDL Production in <i>ob</i>/<i>ob</i> Mice Is Not Stimulated by Massive De Novo Lipogenesis but Is Less Sensitive to the Suppressive Effects of Insulin (2003)

Type 2 diabetes in humans is associated with increased de novo lipogenesis (DNL), increased fatty acid (FA) fluxes, decreased FA oxidation, and hepatic steatosis. In this condition, VLDL production is increased and resistant to suppressive effects of insulin. The relationships between hepatic FA metabolism, steatosis, and VLDL production are incompletely understood. We investigated VLDL-triglyceride and -apolipoprotein (apo)-B production in relation to DNL and insulin sensitivity in female ob/ob mice. Hepatic triglyceride (5-fold) and cholesteryl ester (15-fold) contents were increased in ob/ob mice compared with lean controls. Hepatic DNL was increased approximately 10-fold in ob/ob mice, whereas hepatic cholesterol synthesis was not affected. Basal rates of hepatic VLDL-triglyceride and -apoB100 production were similar between the groups. Hyperinsulinemic clamping reduced VLDL-triglyceride and -apoB100 production rates by approximately 60% and approximately 75%, respectively, in lean mice but only by approximately 20% and approximately 20%, respectively, in ob/ob mice. No differences in hepatic expression of genes encoding apoB and microsomal triglyceride transfer protein were found. Hepatic expression and protein phosphorylation of insulin receptor and insulin receptor substrate isoforms were reduced in ob/ob mice. Thus, strongly induced hepatic DNL is not associated with increased VLDL production in ob/ob mice, possibly related to differential hepatic zonation of apoB synthesis (periportal) and lipid accumulation (perivenous) and/or relatively low rates of cholesterogenesis. Insulin is unable to effectively suppress VLDL-triglyceride production in ob/ob mice, presumably because of impaired insulin signaling.