gebhart/patrepeval huggingface dataset:
Cyclic ADP-Ribose Mediates Formyl Methionyl Leucyl Phenylalanine (fMLP)-Induced Intracellular Ca2+ Rise and Migration of Human Neutrophils (2008)

Although cyclic ADP-ribose (cADPR), a novel Ca(2+)-mobilizing mediator, is suggested to be involved in the functions of neutrophils in rodents, its role in human neutrophils remains unclear. The present study examined the ability of cADPR to mobilize Ca(2+) and mediate formyl methionyl leucyl phenylalanine (fMLP)-stimulated increase in cytosolic free Ca(2+) concentration ([Ca(2+)](i)) and migration in human neutrophils. cADPR induced Ca(2+) release from digitonin-permeabilized neutrophils, and the release was blocked by 8Br-cADPR, an antagonist of cADPR. Immunophilin ligands, FK506 and rapamycin, but not cyclosporine A, inhibited cADPR-induced Ca(2+) release. 8Br-cADPR partially reduced fMLP-induced [Ca(2+)](i) rise and abolished the rise in combination with 2APB, an IP(3)-receptor antagonist. Anti-CD38Ab and NADase that interfere with cADPR formation, reduced the fMLP-induced [Ca(2+)](i) rise. When beta-NAD(+), a substrate of ADP-ribosyl cyclase, and cADPR were added to the medium, the former gradually increased [Ca(2+)](i) and the latter potentiated the fMLP-induced [Ca(2+)](i) rise. The beta-NAD(+)-induced [Ca(2+)](i) rise in Ca(2+)-free medium was inhibited by anti-CD38Ab, 8Br-cADPR, FK506, ruthenium red, and thapsigargin. mRNAs of nucleoside transporter (NT), ENT1, ENT2, CNT, and CNT3 were expressed in neutrophils; and their inhibitors, inosine, uridine, and s-(4-nitrobenzyl)-6-thioinosine, reduced the [Ca(2+)](i) rise induced by beta-NAD(+) and fMLP. fMLP-timulated migration was inhibited by the removal of Ca(2+) from the medium or by the addition of 8Br-cADPR, anti-CD38Ab, NADase, and NT inhibitors. These results suggest that cADPR was synthesized extracellularly by CD38, transported into the cells through NTs, and then Ca(2+) was mobilized by FK506-binding protein-dependent process. This process may be involved in fMLP-induced intracellular Ca(2+) signaling and migration in human neutrophils.
Simultaneous Determination of Paroxetine, Risperidone and 9-Hydroxyrisperidone in Human Plasma by High-Performance Liquid Chromatography with Coulometric Detection (2000)

A method for the simultaneous determination of paroxetine, risperidone and its main metabolite 9-hydroxyrisperidone in human plasma has been developed. The procedure involved a multistep solid-phase liquid extraction with an internal standard. The drugs were separated on a cyano column followed by coulometric detection. This method described here has sufficient sensitivity to quantitate paroxetine accurately in the range 5-500 ng/ml with a lower limit of detection of 1 ng/ml and risperidone and its main metabolite 9-hydroxyrisperidone in the range 2-100 ng/ml with a lower limit of detection of 1 ng/ml when 1 ml of plasma was used for the analysis. The precision, accuracy and specificity have been proven, and show that the method is reliable for clinical studies and routine drug monitoring.
An Overview of Cyclophosphamide and Ifosfamide Pharmacology (1997)

Cyclophosphamide and ifosfamide are alkylating agents administered to treat malignant disease. They are prodrugs and require activation by hepatic microsomal enzymes before being metabolized to their respective cytotoxic species, phosphoramide mustard and ifosfamide mustard. These species alkylate DNA, forming DNA-DNA cross-links that result in inhibition of DNA synthesis and cell death. Resistance to oxazaphosphorines is poorly understood, although increased aldehyde dehydrogenase activity may be a significant factor. Although both compounds share a common metabolic pathway, 4-hydroxylation of ifosfamide occurs at a slower rate and to a lesser extent than that of cyclophosphamide. This difference significantly alters the toxicity profile of ifosfamide. Leukopenia is the dose-limiting toxicity of cyclophosphamide, and neurotoxicity is the dose-limiting toxicity of ifosfamide when preventive measures are taken to reduce urotoxicity. With recent findings concerning their basic and clinical pharmacology, the therapeutic index of these compounds can be improved.
On "Shooting" a Moving Vehicle with Data Flows (2007)

This paper proposes an ITS system that uses not only integrated cellular and ad hoc relaying technologies, but also users' mobility profiles. It focuses on a subsystem where cellular bandwidth is used mostly for control signals, and an ad hoc distribution network (ADN) is used for file downloading and video streaming. The paper formulates an optimization problem with the objective being to maximize the amount of data to be delivered to a moving vehicles via the ADN, and thereby minimizing the usage of the costly cellular bandwidth for data transfer. Three approaches based on non-linear and linear programs are described and compared, and simulation results indicate that a satisfying performance for file download applications can be achieved.
An SoC With 1.3 Gtexels/s 3-D Graphics Full Pipeline for Consumer Applications (2005)

A high-speed three-dimensional (3-D) graphics SoC for consumer applications is presented. A 166-MHz 3-D graphics full pipeline engine with performance of 33 Mvertices/s and 1.3Gtexels/s, and 333-MHz ARM11 RISC processor, and video composition IPs are integrated together on a single chip. The geometry part of 3-D graphics IP provides full programmability in vertex and triangle level, and two-level multi-texturing with trilinear MIPMAP filtering are realized in the rasterization part. Per-pixel effects such as fog effects, alpha blending, and stencil test are also implemented in the proposed 3-D graphics IP. The rasterization architecture is designed for reducing external memory accesses to achieve the peak performance. The chip is fabricated using 0.13/spl mu/m CMOS technology and its area is 7.1/spl times/7.0mm/sup 2/.
Secure OpenID Authentication Model by Using Trusted Computing (2014)

The growth of Internet online services has been very quick in recent years. Each online service requires Internet users to create a new account to use the service. The problem can be seen when each user usually needs more than one service and, consequently, has numerous accounts. These numerous accounts have to be managed in a secure and simple way to be protected against identity theft. Single sign-on (SSO) and OpenID have been used to decrease the complexity of managing numerous accounts required in the Internet identity environment. Trusted Platform Module (TPM) and Trust Multitenancy are great trusted computing-based technologies to solve security concerns in the Internet identity environment. Since trust is one of the pillars of security in the cloud, this paper analyzes the existing cloud identity techniques in order to investigate their strengths and weaknesses. This paper proposes a model in which One Time Password (OTP), TPM, and OpenID are used to provide a solution against phishing as a common identity theft in cloud environment.
Light-Weight Protocols for Wire-Speed Ordering (2018)

We describe light-weight protocols for selective packet ordering in out-of-order networks that carry memory traffic. The protocols are designed for heterogeneous high-performance systems, in particular, accelerated systems with end-points that have few resources available for interfacing the network. The protocols preserve the semantics of a relaxed memory ordering model as adopted by highly-threaded many-core processors and accelerators. The protocols achieve link-rate performance through the following techniques: (1) Speculative connection setup avoids round-trip delays found in protocols with little knowledge about endpoint resources, (2) target-side ordering avoids round-trip delays found in source-side ordering mechanisms, (3) fine-grained ordering removes dependencies unwarranted by program code avoiding cumulative ordering dependencies caused by coarse-grained ordering, (4) ordering relaxations and optimizations for producer/consumer communication patterns. We describe two ordering protocols that provide (1) strict sequential ordering and (2) relaxed ordering for multi-packet transfers. The protocols impose no restrictions on routing, including multipath routing.
Dynamic DNA Templates for Discrete Gold Nanoparticle Assemblies:  Control of Geometry, Modularity, Write/Erase and Structural Switching (2007)

Nanoparticle assemblies hold great promise as new materials for catalysis, nanoelectronics, and nanophotonics applications. However, many of their properties, which depend on the relative arrangement of the particles within the assembly, are not sufficiently well-understood because of a lack of methods to systematically assemble them into well-defined discrete model systems. We here report a method which uses a minimal set of dynamic DNA templates to generate a large number of discrete gold nanoparticle assemblies. These assemblies are addressable in real time and can undergo structural switching and write/erase functions in response to external agents. More specifically, control of geometry is demonstrated by the facile creation of triangle and square gold nanoparticle assemblies; modularity is shown by positioning two different sizes of gold nanoparticles into all the possible triangular combinations; structural switching is established by the use of the same square template to selectively construct square, trapezoidal, and rectangular assemblies; and a write/erase function is shown by assembling a triangle of three gold nanoparticles, selectively removing one of the particles, followed by the "writing" of a different particle. The study of these systems promises to shed light on the phenomena of single electron transport and optical coupling in nanoparticle assemblies and will lead to the more effective incorporation of nanoparticles in photonic/electronic devices. In principle, our dynamic templates can be used to organize any DNA-labeled nanocomponent into well-defined and addressable structures, and as such, this constitutes a new and economical method to construct discrete nanoparticle materials on the nanoscale.
Performance improvement of metal gate CMOS technologies (2002)

Metal gate CMOS technologies for high speed applications were investigated using the damascene metal gate process (Yagishita et al., 1999). We demonstrated the performance improvement by no gate depletion effect in the metal gate using actual devices. Ti/W was used as a single work function metal gate material and ultra shallow buried channel profile was formed for threshold voltage control. The self-aligned channel structure effectively reduces source/drain junction capacitance. An extremely good metal/SiO/sub 2/ interface with the CVD-TiN gate stack realizes intrinsic channel mobility. The propagation delay time of a CMOS inverter ring oscillator was 20 ps, and projected next generation performance would be better due to the improved technologies.
Cultivation in vitro of cells derived from a human osteosarcoma (1971)

A cell line was derived from an osteosarcoma. Cells grew to high population density in liquid medium and formed colonies in agar medium. The cell line consisted of polygonal or fusiform cells resembling the cells of the original tumor. No collagen fibers or calcium apatite microcrystals could be demonstrated in the cultured cells by electron microscopy nor were virus particles detected. Isoenzyme studies of the cell line revealed the “B” band of glucose-6-phosphate dehydrogenase. Chromosome studies of the cell line revealed a range of stem line number from 58 to 65; chromosome counts ranged from 47 to 183. Some cells had marker chromosome of varied morphology and some had minute chromosomes. Chromosome breaks were found in 30.5% of the cells.
Pervasive domestication of defective prophages by bacteria (2014)

Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have endowed bacteria with molecular systems involved in secretion, defense, warfare, and gene transfer. However, the rates and mechanisms of domestication remain unknown. We used comparative genomics to study the evolution of prophages within the bacterial genome. We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. The size distribution of prophage elements is bimodal, suggestive of rapid prophage inactivation followed by much slower genetic degradation. Accordingly, we observed a pervasive pattern of systematic counterselection of nonsynonymous mutations in prophage genes. Importantly, such patterns of purifying selection are observed not only on accessory regions but also in core phage genes, such as those encoding structural and lysis components. This suggests that bacterial hosts select for phage-associated functions. Several of these conserved prophages have gene repertoires compatible with described functions of adaptive prophage-derived elements such as bacteriocins, killer particles, gene transfer agents, or satellite prophages. We suggest that bacteria frequently domesticate their prophages. Most such domesticated elements end up deleted from the bacterial genome because they are replaced by analogous functions carried by new prophages. This puts the bacterial genome in a state of continuous flux of acquisition and loss of phage-derived adaptive genes.
Classification of Breast Cancer versus Normal Samples from Mass Spectrometry Profiles Using Linear Discriminant Analysis of Important Features Selected by Random Forest (2008)

We present our approach to classifying the processed proteomic data that were made available to the participants of the classification competition. Although classification of the spectra was the goal of the competition we feel that proteomic applications to cancer biomarker studies make certain additional demands. For example, one such requirement should be identification of certain features which collectively could differentiate the two groups of samples. Also ideally, the size of the feature set should be small. To that end we propose a linear discriminant classifier based on nine m/z intensity values. Construction and performance of this classifier are discussed.
Block Description Language (BDL): A Structural Description Language (1984)

The Block Description Language (BDL), a language for capturing the structure of an electronic system, is described. The structure of a system may be specified hierarchically in this language. Additional information may be associated with the structural description with general properties. A facility for declaring and using arrays and records of the structure elements is provided.
Pax-5 Expression in Nonhematopoietic Tissues (2006)

We evaluated 123 formalin-fixed, paraffin-embedded samples, including neuroendocrine tumors, adult brain, mesonephric tissues, and from various other sites. A pre-B lymphoma cell line, Daudi, and a small cell carcinoma cell line, NCL-H128, were evaluated by Western blot. All tissues were immunostained by mouse monoclonal anti-Pax-5 antibody by using standard, synthetic polymer-based detection methods. Our study describes for the first time distribution of Pax-5 in adult brain tissue, including periaqueductal gray matter of the midbrain, area postrema of the medulla oblongata, and occasional cells of the spinal trigeminal nucleus (caudal nucleus). We confirm that Pax-5 is expressed regularly in poorly differentiated neuroendocrine tumors but never in well-differentiated classic carcinoid tumors. Pax-5 expression also was found readily in benign and malignant mesonephric tissues and focally in müllerian duct-derived tissues and tumors. Expression of Pax-5 in the Daudi and NCL-H128 cell lines was confirmed by Western blot. Together, these results are important for correct interpretation of results in immunophenotyping of undifferentiated tumors, for diagnosis of mesonephric carcinoma, and, potentially, for correct classification of neuroendocrine tumors in small biopsy samples.
Class based dynamic priority scheduling for uplink to support M2M communications in LTE (2014)

Machine-to-Machine (M2M) communication has emerged as a key technology with huge market potential for cellular service providers deploying LTE networks. Addition of enormous number of M2M devices into the cellular networks poses a heavy competition to existing Human-to-Human (H2H) devices for getting radio resources, thereby affecting the performance of the H2H communications. But, one can not treat all M2M flows as low priority and schedule them after H2H flows, as there are many M2M applications like healthcare and tracking which are of high importance and delay-intolerant. Hence, there is a need for class based priority scheduling of the traffic of M2M and H2H sessions in the network. In this paper, we propose a class based dynamic priority scheduling algorithm for uplink transmission of M2M and H2H traffic in LTE. The performance of the algorithm is evaluated by various metrics such as H2H throughput and system throughput and also compared with existing schedulers.
Expression and purification of tau protein and its frontotemporal dementia variants using a cleavable histidine tag (2016)

Recombinant tau protein is widely used to study the biochemical, cellular and pathological aspects of tauopathies, including Alzheimer's disease and frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTPD-17). Pure tau in high yield is a requirement for in vitro evaluation of the protein's physiological and toxic functions. However, the preparation of recombinant tau is complicated by the protein's propensity to aggregate and form truncation products, necessitating the use of multiple, time-consuming purification methods. In this study, we investigated parameters that influence the expression of wild type and FTPD-17 pathogenic tau, in an attempt to identify ways to maximise expression yield. Here, we report on the influence of the choice of host strain, induction temperature, duration of induction, and media supplementation with glucose on tau expression in Escherichia coli. We also describe a straightforward process to purify the expressed tau proteins using immobilised metal affinity chromatography, with favourable yields over previous reports. An advantage of the described method is that it enables high yield production of functional oligomeric and monomeric tau, both of which can be used to study the biochemical, physiological and toxic properties of the protein.
Controlling Phase Distributions in Macroporous Composite Materials through Particle-Stabilized Foams (2011)

Aqueous foams stabilized by ceramic and thermoplastic polymeric particles provide a general method for producing novel porous materials because their extraordinary stability against disproportionation and drainage allows them to be dried and sintered into solid materials. Here, we report the different microstructures that can be obtained from liquid foams stabilized by binary mixtures of particles when the interfacial energies between the particles and the air-liquid interfaces are manipulated to promote either preferential or competitive self-assembly of the particles at the foam interface. Modification of the interfacial energies was accomplished through surface modification of the particles or by decreasing the surface tension of the aqueous phase. Materials derived from liquid foams stabilized by poly(vinylidene fluoride) (PVDF) and alumina (Al(2)O(3)) particles are investigated. However, as is shown, the method can be extended to other polymeric and ceramic particles and provides the possibility to manufacture a wide range of porous composite materials.
Sterol regulatory element binding proteins (SREBP)-1a and SREBP-2 are linked to the MAP-kinase cascade (2000)

The classic sterol regulatory cis element (sre-1) in the LDL receptor promoter mediates sterol regulatory element binding protein (SREBP)-binding and the effects of insulin and platelet derived growth factor (PDGF). To elucidate whether SREBP-1a and SREBP-2 play a direct role in insulin and PDGF action, stable cell lines of HepG2 deficient in either SREBP-1 or SREBP-2 were used. Transfection of these cells with the wild-type promoter fragment of the low density lipoprotein (LDL) receptor gene showed that the effects of insulin and PDGF were significantly reduced in both, SREBP-1- as well as SREBP-2-deficient cells. Insulin and PDGF action could be reconstituted again in these deficient cell lines by reintroducing SREBP-1a or SREBP-2. Preincubation of cells with either the phosphatidylinositol (PI)-3 kinase inhibitor wortmannin or the mitogen-activated protein (MAP) kinase cascade inhibitor PD 98059 showed that the latter abolished the stimulatory effects of insulin and PDGF on LDL receptor promoter activity completely, whereas wortmannin had no effect. Overexpression of upstream activators of the MAP kinases, like MEKK1 or MEK1, stimulated LDL receptor promoter activity several fold in an sre-1 related manner. These effects could be enhanced by coexpression of the transcriptional active N-terminal domains of SREBP-1a and SREBP-2. Using the heterologous Gal-4 system, we could show that intracellular activation of the MAP kinase cascade by ectopic expression of MEKK1 or MEK1 has a direct stimulatory effect on the transcriptional activity of SREBP-1a and SREBP-2. Experimental evidence for a direct link between MAP kinases and SREBPs was obtained due to the MAP kinases ERK1 and ERK2 phosphorylating recombinant GST-fusion proteins of SREBP-1a and SREBP-2, in vitro. We conclude that SREBP-1a and SREBP-2 mediate different regulatory effects converging at sre-1 and that they appear to be linked to the MAP kinase cascade, possibly being direct substrates of ERK1 and ERK2.
Selective Induction of Apoptosis and Autophagy Through Treatment With Dandelion Root Extract in Human Pancreatic Cancer Cells (2012)

We demonstrate that DRE has the potential to induce apoptosis and autophagy in human pancreatic cancer cells with no significant effect on noncancerous cells. This will provide a basis on which further research in cancer treatment through DRE can be executed.
Cobalt(II) octanoate and cobalt(II) perfluorooctanoate catalyzed atom transfer radical polymerization of styrene in toluene and fluorous media—A versatile route to catalyst recycling and oligomer formation (2005)

Abstract Cobalt(II) perfluorooctanoate‐catalyzed atom transfer radical polymerization (ATRP) and reverse ATRP were developed to prepare oligostyrenes ( M n < 2500) with low polydispersities M w / M n < 1.5. Fluorous biphase catalysis was applied for effective recycling of catalyst and fluorous solvent. The homogeneous polymerization reaction was performed at 90 °C in toluene/cyclohexane/perfluorodecalin mixture (1:1:1) and fluorine‐free solvents. Temperature‐induced phase separation of this fluorous solvent mixture occurred at room temperature and proved to be the key for the very effective separation of the cobalt(II) perfluorooctanoate from the oligostyrene and fluorine‐free solvents. Both the fluorine‐tagged cobalt catalysts and the fluorous media were recycled and reused up to three times without encountering catalyst activity losses. The roles of cobalt catalysts, fluorous media, and monomer/initiator ratio were examined with respect to the polymerization kinetics. Fluorine‐containing and fluorine‐free cobalt(II) octanoate catalyzed controlled styrene oligomerization according to the ATRP mechanism. The molar mass control range was limited in fluorous biphase catalysis most likely because of precipitation of high molar mass polystyrenes in the fluorous reaction medium. To the best of our knowledge, this is the first time temperature‐induced phase separation of fluorous and fluorine‐free solvents has been successfully applied to polymerization processing. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3804–3813, 2005