gebhart/patrepeval huggingface dataset:
Adjuvant Activities of Novel Cytokines, Interleukin-23 (IL-23) and IL-27, for Induction of Hepatitis C Virus-Specific Cytotoxic T Lymphocytes in HLA-A*0201 Transgenic Mice (2004)

Searching the sequence databases has revealed two novel cytokines: interleukin-23 (IL-23) and IL-27. These cytokines are quite similar to, but clearly distinct from IL-12 in their structures and T-cell stimulatory fashions. In contrast to IL-12, however, little is known about the roles of IL-23 and IL-27 in the immune regulation. Previously, we evaluated the prime-boost immunization consisting of priming and the first boosting with the hepatitis C virus (HCV)-core expression plasmid, followed by a second boosting with recombinant adenovirus expressing HCV core for induction of HCV core-specific cytotoxic T lymphocytes (CTLs) in BALB/c mice. The present study demonstrates that HCV-specific CTL induction was greatly enhanced by coinoculation of an IL-12 expression plasmid in the prime-boost immunization, indicating the potent adjuvant activity of IL-12. We investigated whether similar adjuvant effects could be exerted by either IL-23 or IL-27 in a prime-boost immunization with HLA-A*0201 transgenic mice. Coadministration of either an IL-23 or an IL-27 expression plasmid, as well as an IL-12 expression plasmid, in a prime-boost immunization enhanced induction of HCV-specific CTLs and led to dramatic increases in the numbers of gamma interferon (IFN-gamma)-producing, HCV-specific CD8+ cells. Further, preinjections of IL-12, IL-23, or IL-27 expression plasmids before immunization resulted in great increases in the number of IFN-gamma-producing, HCV-specific CD8+ cells in response to immunization with recombinant adenovirus. These data revealed that both IL-23 and IL-27, as well as IL-12, are potent adjuvants for epitope-specific CTL induction. The two novel cytokines might offer new prophylactic and therapeutic strategies against infectious pathogens such as HCV.
Gold nanoparticles in biomedical applications: recent advances and perspectives (2011)

Gold nanoparticles (GNPs) with controlled geometrical, optical, and surface chemical properties are the subject of intensive studies and applications in biology and medicine. To date, the ever increasing diversity of published examples has included genomics and biosensorics, immunoassays and clinical chemistry, photothermolysis of cancer cells and tumors, targeted delivery of drugs and antigens, and optical bioimaging of cells and tissues with state-of-the-art nanophotonic detection systems. This critical review is focused on the application of GNP conjugates to biomedical diagnostics and analytics, photothermal and photodynamic therapies, and delivery of target molecules. Distinct from other published reviews, we present a summary of the immunological properties of GNPs. For each of the above topics, the basic principles, recent advances, and current challenges are discussed (508 references).
Spectrally-efficient elastic optical path networks (2010)

We describe spectrum-efficient and scalable optical transport network architecture called spectrum-sliced “elastic optical path” network (SLICE). The architecture enables sub-wavelength, super-wavelength, and distance-adaptive spectrum allocation in a highly spectrum-efficient manner.
Correlation between Site ll‐Specific Human Serum Albumin (HSA) Binding Affinity and Murine in vivo Photosensitizing Efficacy of Some Photofrin Components (1997)

Human serum albumin (HSA) is one of the key components in human blood that may influence drug distribution. As such, it is important to know the affinity of any drug for albumin. Previously, Photofrin, a mixture of monomeric, dimeric and oligomeric porphyrins, has been subjected to HSA binding studies. However, due to its complex nature, binding studies on Photofrin or other hematoporphyrin derivatives with HSA are inconclusive. In this report, the binding properties of some components (dimers and trimers) of Photofrin and the relationship between murine photosensitizing efficacy and those binding properties were investigated. The interaction of these porphyrins with HSA was investigated by direct ultrafiltration and fluorescent titration techniques with fluorescent probes such as dansyl-L-proline (DP), which is known to interact selectively with site II on HSA. Porphyrins also were tested for antitumor activity in a mouse model following intravenous administration and exposure to laser light. Together, the results suggest that the photosensitizers that were preferentially bound to site II of HSA were most effective at controlling murine tumor regrowth.
SINNET: Social Interaction Network Extractor from Text (2013)

In this paper we present a demo of our system: Social Interaction Network Extractor from Text (SINNET). SINNET is able to extract a social network from unstructured text. Nodes in the network are people and links are social events.
Programmable Control of Nucleation for Algorithmic Self-Assembly (2006)

Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure consists of a set of molecular `tiles' designed to have specific binding interactions. A key challenge to making algorithmic self-assembly practical is designing tile set programs that make assembly robust to errors that occur during initiation and growth. One method for the controlled initiation of assembly, often seen in biology, is the use of a seed or catalyst molecule that reduces an otherwise large kinetic barrier to nucleation. Here we show how to program algorithmic self-assembly similarly, such that seeded assembly proceeds quickly but there is an arbitrarily large kinetic barrier to unseeded growth. We demonstrate this technique by introducing a family of tile sets for which we rigorously prove that, under the right physical conditions, linearly increasing the size of the tile set exponentially reduces the rate of spurious nucleation. Simulations of these `zig-zag' tile sets suggest that under plausible experimental conditions, it is possible to grow large seeded crystals in just a few hours such that less than 1 percent of crystals are spuriously nucleated. Simulation results also suggest that zig-zag tile sets could be used for detection of single DNA strands. Together with prior work showing that tile sets can be made robust to errors during properly initiated growth, this work demonstrates that growth of objects via algorithmic self-assembly can proceed both efficiently and with an arbitrarily low error rate, even in a model where local growth rules are probabilistic.
New chemically reactive dsDNAs containing single internucleotide monophosphoryldithio links: reactivity of 5′-mercapto-oligodeoxyribonucleotides (2001)

Novel modified DNA duplexes with single bridging 5'-SS-monophosphoryldithio links [-OP(=O)-O(-)-SS-CH(2)-] were synthesized by autoligation of an oligonucleotide 3'-phosphorothioate and a 5'-mercapto-oligonucleotide previously converted to a 2-pyridyldisulfide adduct. Monophosphoryldisulfide link formation is not a stringent template-dependent process under the conditions used and does not require strong binding of the reactive oligomers to the complementary strand. The modified internucleotide linkage, resembling the natural phosphodiester bond in size and charge density, is stable in water, easily undergoes thiol-disulfide exchange and can be specifically cleaved by the action of reducing reagents. DNA molecules containing an internal -OP(=O)-O(-)-SS-CH(2)- bridge are stable to spontaneous exchange of disulfide-linked fragments (recombination) even in the single-stranded state and are promising reagents for autocrosslinking with cysteine-containing proteins. The chemical and supramolecular properties of oligonucleotides with 5'-sulfhydryl groups were further characterized. We have shown that under the conditions of chemical ligation the 5'-SH group of the oligonucleotide has a higher reactivity towards N-hydroxybenzotriazole-activated phosphate in an adjacent oligonucleotide than does the OH group. This autoligation, unlike disulfide bond formation, proceeds only in the presence of template oligonucleotide, necessary to provide the activated phosphate in close proximity to the SH-, OH- or phosphate function.
[Radiosensitivity of a thymocyte subpopulation capable of stimulating erythropoiesis in locally irradiated animals]. (1985)

It was shown that, in contrast to intact thymocytes and to those irradiated with a dose of 0.25 Gy, thymocytes exposed in vivo to doses from 0.5 to 1.5 Gy and transplanted to locally irradiated (7 Gy) thymectomized BALB/c mice failed to stimulate the recovery of the erythron.
1-nm Spatial Resolution in Carrier Profiling of Ultrashallow Junctions by Scanning Spreading Resistance Microscopy (2008)

Recently, we reported significantly improved spatial resolution in scanning spreading resistance microscopy (SSRM) by measuring in a vacuum. In this paper, we demonstrate the 1-nm spatial resolution of SSRM in carrier profiling by comparing with the 3-D device simulation. The simulation results show that the accuracy of ultrashallow-junction delineation depends on the effective radius of the probe. The precisely measured junction depth corresponds to an effective probe radius of 0.5 nm. We attribute the high resolution to the elimination of parasitic resistances of the whole measuring circuit. Application to failure analysis of n-type metal-oxide-semiconductor field-effect transistors clarified the impact of halo-carrier profiles on Vth-roll-off characteristics.
Sora: high performance software radio using general purpose multi-core processors (2009)

This paper presents Sora, a fully programmable software radio platform on commodity PC architectures. Sora combines the performance and fidelity of hardware SDR platforms with the programmability and flexibility of general-purpose processor (GPP) SDR platforms. Sora uses both hardware and software techniques to address the challenges of using PC architectures for highspeed SDR. The Sora hardware components consist of a radio front-end for reception and transmission, and a radio control board for high-throughput, low-latency data transfer between radio and host memories. Sora makes extensive use of features of contemporary processor architectures to accelerate wireless protocol processing and satisfy protocol timing requirements, including using dedicated CPU cores, large low-latency caches to store lookup tables, and SIMD processor extensions for highly efficient physical layer processing on GPPs. Using the Sora platform, we have developed a demonstration radio system called SoftWiFi. SoftWiFi seamlessly interoperates with commercial 802.11a/b/g NICs, and achieves equivalent performance as commercial NICs at each modulation. 1
Comment on "Tunable Spin-Flip Laser and Infrared Spectroscopy" (1971)

The tunable spin-flip Raman laser has been proposed as a potentially useful instrument for high-resolution spectroscopic and heterodyne applications in the infrared. On the basis of the published experimental data, however, the effective linewidth of this laser may be too broad for such applications, and attempts to reduce it could destroy the continuous tunability.
Combined Effects of Tamoxifen and a Chimeric Humanized Single Chain Antibody against the Type I IGF Receptor on Breast Tumor GrowthIn vivo (2003)

Proliferative and anti-apoptotic actions of IGFs are mediated by the IGF-I receptor (IGF-IR), to which both IGF-I and -II bind with high affinity. We previously reported that alphaIGF-IR scFv-Fc (scFv-Fc) consisting of the alphaIGF-IR scFv and human IgG (1) Fc domain retained general characteristics of the parental 1H7 monoclonal antibody, and significantly suppressed MCF-7 tumor growth. We proposed IGF-IR down-regulation as a possible mechanism for inhibition of MCF-7 tumor growth. To further determine the therapeutic potentials of this approach, in vivo effects of this antibody on breast tumor growth were evaluated in the absence or presence of tamoxifen (Tam) using a T61 human breast tumor model. T61 xenograft growth in athymic mice was compared under five conditions, PBS, scFv-Fc, Tam, scFv-Fc+Tam, and control antibody. While treatment with PBS and control antibody did not affect T61 tumor growth, scFv-Fc, Tam, and scFv-Fc+Tam treatments significantly suppressed the tumor growth during the first two weeks of treatment. Although the growth inhibitory effect of scFv-Fc during the first two weeks was significant, the tumor grew as rapidly as PBS-treated tumors thereafter. This rapid tumor growth was suppressed when scFv-Fc was combined with Tam. Throughout four weeks, the combined Tam+scFv-Fc treatment was more effective in inhibiting the T61 tumor growth than scFv-Fc or Tam treatment alone. scFv-Fc treatment down-regulated IGF-IR which appears to contribute to tumor growth inhibition. This study provides evidence that simultaneous targeting of IGF-IR and the estrogen receptor may enhance the therapeutic effect.
Characterization of Tyrosylprotein Sulfotransferase from Rat Liver and Other Tissues (1989)

The sulfoconjugation of tyrosyl residues is a widespread post-translational modification of biologically active peptides and proteins. In this paper we describe the characterization of a rat liver tyrosylprotein sulfotransferase that is capable of catalyzing the transfer of a sulfate moiety from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the synthetic polymer, poly-(Glu6,Ala3,Tyr1) (EAY; Mr 47,000) using a simple filter paper assay. Following sucrose density gradient centrifugation and comparison with known subcellular marker enzyme activities, rat liver tyrosylprotein sulfotransferase activity was shown to have a distribution similar to the Golgi enzyme, galactosyltransferase. Using the enriched Golgi preparation, rat liver tyrosylprotein sulfotransferase displayed a pH optimum of 6.7 and required the presence of 20 mM Mn2+ for maximal activity. Co2+ (20 mM) was able to produce 26% of the maximal stimulation observed with Mn2+, whereas other metal ions, such as Mg2+, Ca2+, and Co2+, were not effective in stimulating tyrosylprotein sulfotransferase activity. Whereas tyrosylprotein sulfotransferase activity was observed in the native membrane-bound state, EAY sulfation was maximally enhanced 3-fold when assayed in the presence of Lubrol Px. Under the optimal conditions for assaying the sulfation of EAY by a rat liver enriched Golgi fraction, significant degradation of the sulfate donor, PAPS, was observed. The addition of both NaF and 5'-AMP to the incubation mixture was found to effectively prevent PAPS degradation and increase the amount of product formed in the assay by 10-fold. Using the optimized conditions for the sulfation of EAY by rat liver tyrosylprotein sulfotransferase, membrane-bound sulfotransferase activity was also observed in the crude microsomal pellets of a variety of rat tissues, including lung, pituitary, and cerebellum, as well as in livers from different species.
Psychosocial aspects of the functional gastrointestinal disorders (1999)

The functional gastrointestinal disorders (FGID) are the most frequent conditions seen in gastroenterology practice and comprise a major portion of primary care. Psychosocial factors are important in these disorders with regard to: (1) their effects on gut physiology; (2) their modulation of the symptom experience; (3) their influence on illness behavior; (4) their impact on outcome; and (5) the choice of the therapeutic approach. This paper provides a review and consensus of the existing literature by gastroenterologists, psychiatrists, psychologists, physiologists, and health services investigators. Evidence is provided to support the biopsychosocial model as a basis for understanding and treating these disorders, and epidemiological and clinical information on the relations of psychosocial factors to gut physiology, symptom presentation, health behavior, and outcome is offered. Features of motility, personality, abuse history, health concerns, and treatment-seeking differ between patients with FGID and healthy controls, but they are not specific to FGID. They occur in other patients with chronic medical conditions and/or psychiatric disorders. Review of treatment trials indicates clear support for psychotherapeutic treatments, especially in the long term, as well as some evidence for the benefit of antidepressants in FGID, even in the absence of improvements in mood.
Biological activities of Curcuma longa L. (2001)

There are several data in the literature indicating a great variety of pharmacological activities of Curcuma longa L. (Zingiberaceae), which exhibit anti-inflammatory, anti-human immunodeficiency virus, anti-bacteria, antioxidant effects and nematocidal activities. Curcumin is a major component in Curcuma longa L., being responsible for its biological actions. Other extracts of this plant has been showing potency too. In vitro, curcumin exhibits anti-parasitic, antispasmodic, anti-inflammatory and gastrointestinal effects; and also inhibits carcinogenesis and cancer growth. In vivo, there are experiments showing the anti-parasitic, anti-inflammatory potency of curcumin and extracts of C. longa L. by parenteral and oral application in animal models. In this present work we make an overview of the pharmacological activities of C. longa L., showing its importance.
Arterial insufficiency in hemodialysis access procedures: correction by "banding" technique. (1991)

Arterial insufficiency distal to an antecubital access is fortunately an infrequent but disturbing and often debilitating complication resulting in suboptimal access. During an 8 1/2-year period, 335 vascular access procedures were performed, 108 of which were antecubital brachiocephalic Gore-Tex conduits. Of these Gore-Tex conduits, 1.8% (2/108) had developed symptoms of vascular insufficiency 2 to 3 1/2 months after such access surgery. As previously published, arterial steal after the creation of an AV fistula could be corrected by the placement of an interposition Gore-Tex loop that would cure the problem and save the access. We have presented a procedure to correct a steal syndrome once a Gore-Tex conduit is already in place. Proximal banding and distal ligation with division of the cephalic vein below an end-to-side Gore-Tex loop is a simple surgical solution. It is not only curative but the procedure also maintains the existing Gore-Tex graft as a sustained avenue for access.
A Rapid, Specific, and Sensitive Method for the Determination of Acetylation Phenotype using Dapsone (1997)

An original, simple, specific, and rapid high-performance liquid chromatography assay for the determination of dapsone and monoacetyldapsone in human plasma is presented. The procedure consists of extracting the drugs and the internal standard (phenacetin) from 1 mL plasma with ethyl ether at alkaline pH. A liquid chromatograph equipped with a reversed-phase 5-microm C8 analytical column was used. The drugs were eluted with a mixture of water and methanol (70:30, v/v). Flow rate and wavelength were set at 1 mL/min and 286 nm, respectively. The precision, linearity, and limit of quantitation of the method were within acceptable limits. The method was considered adequate and has been used for the determination of the acetylator phenotype in population studies.
Risk and Prevention of Anti-factor IX Formation in AAV-Mediated Gene Transfer in the Context of a Large Deletion of F9 (2001)

The safety of several gene therapy approaches for treatment of the severe, X-linked bleeding disorder hemophilia is currently being evaluated in early phase clinical trials. One strategy seeks to correct deficiency of functional coagulation factor IX (hemophilia B) by intramuscular (IM) administration of an adeno-associated viral (AAV) vector. A potentially serious complication of any treatment for hemophilia is formation of inhibitory antibodies against the coagulation factor protein, a risk that increases in the setting of null mutations in the factor IX gene (F9). Here, we describe hemophilia B mice with a large F9 deletion that form inhibitors within 1 to 2 months after IM administration of an AAV vector expressing mouse F9 or after repeated intravenous infusion of mouse F9 concentrate. In both cases, inhibitors are primarily IgG1 immunoglobulins representing a Th2-driven humoral immune response. We further demonstrate that anti-mouse F9 antibody formation in the gene-based approach can be reduced by transient immune modulation at the time of vector administration. Moreover, this maneuver resulted in complete absence of anti-mouse F9 and sustained expression of functional mouse F9 in some hemophilia B mice, particularly in those animals treated with the immunosuppressive drug cyclophosphamide. These data have direct relevance for design of clinical trials and strategies aimed at avoiding immune responses against a secreted transgene product.
High level PSMA expression is associated with early psa recurrence in surgically treated prostate cancer (2010)

Based on the high frequency of PSMA overexpression in all stages and grades of prostate cancer and the high prevalence of PSMA overexpression, it can be speculated that increased PSMA expression may be related with prostate cancer development rather than progression. The known function of PSMA activating cell migration would be in line with the suggested role in cancer progression and the missing association between PSMA overexpression and tumor cell proliferation.
Insulin-like growth factor-I and more potent variants restore growth of diabetic rats without inducing all characteristic insulin effects (1993)

The effects of graded doses of insulin-like growth factor-I (IGF-I) and two variants which bind poorly to IGF-binding proteins were investigated in 160 g streptozotocin-induced diabetic rats. The two variants were the truncated form, des(1-3)IGF-I, and another with arginine at residue 3 and an N-terminal extension, termed LR3-IGF-I. The peptides were infused via mini-osmotic pumps. Reference groups received either vehicle or insulin (30 i.u. per day). Treatment led to a marked dose-dependent increase in growth rate and nitrogen balance. The highest dose (695 micrograms/day) of IGF-I increased body weight by 48.1 +/- 1.7 g/7 days, compared with 11.0 +/- 2.8 g/7 days for the vehicle-treated group. The two variants were 2.5-3 times more potent than IGF-I in restoring growth. The insulin-treated group gained more weight (64.5 +/- 1.6 g/7 days), but the added gain was fat (92.5 +/- 4.8 g of fat/kg carcass wet wt., compared with 32.2 +/- 2.1 for all other groups) rather than protein. All peptides increased muscle protein-synthesis rates and RNA levels by up to 50%, with IGF-I the least potent. These high doses of IGFs did not decrease either the glucosuria or the daily excretion rate of N tau-methyl-histidine (N tau-MH). On the other hand, insulin treatment markedly decreased both glucosuria (from 82.7 +/- 5.4 to 4.5 +/- 3.3 mmol/day) and N tau-MH excretion (from 9.3 +/- 0.3 to 7.1 +/- 0.4 mumol/day per kg). This experiment shows that, although IGF-I and variants can restore growth in diabetic rats, other insulin-dependent metabolic processes in liver, muscle and adipose tissue are not restored.