gebhart/patrepeval huggingface dataset:
Role of NKG2D in tumor cell lysis mediated by human NK cells: cooperation with natural cytotoxicity receptors and capability of recognizing tumors of nonepithelial origin (2001)

NKG2D is a recently described activating receptor expressed by both NK cells and CTL. In this study we investigated the role of NKG2D in the natural cytolysis mediated by NK cell clones. The role of NKG2D varied depending on the type of target cells analyzed. Lysis of various tumors appeared to be exclusively natural cytotoxicity receptors (NCR) dependent. In contrast, killing of another group of target cells, including not only the epithelial cell lines HELA and IGROV-1, but also the FO-1 melanoma, the JA3 leukemia, the Daudi Burkitt lymphoma and even normal PHA-induced lymphoblasts, involved both NCR and NKG2D. Notably, NK cell clones expressing low surface densities of NCR (NCR(dull)) could lyse these tumors in an exclusively NKG2D-dependent fashion. Remarkably, not all of these targets expressed MICA/B, thus implying the existence of additional ligands recognized by NKG2D, possibly represented by GPI-linked molecules. Finally, we show that the engagement of different HLA class I-specific inhibitory receptors by either specific antibodies or the appropriate HLA class I ligand led to inhibition of NKG2D-mediated NK cell triggering.
Estimating Router ICMP Generation Delays (2002)

A number of Internet measurement techniques rely on eliciting ICMP replies from routers inside the network [7], [9]. One question regarding the accuracy of these techniques concerns whether routers introduce delays when generating the ICMPs. We present a technique for estimating these delays. The approach is based on sending packets with spoofed source addresses, some with sufficient TTL to travel all the way to the destination (“direct”), others with a limited TTL that will cause them to be transformed at a given hop into an ICMP Time Exceeded (TE) packet. By spoofing the source address of the probes to match the destination, these TEs are routed identically to how the direct probes are routed. The technique thus allows us to factor out effects due to asymmetric routing or conditions on the return path from a given router back to the source. We have implemented the technique in a tool, fsd (fast-path/slow-path discriminator). In this paper, we discuss an analysis of a set of measurements made using fsd on the NIMI measurement infrastructure [13]. Our analyses provide helpful insight into the question of “what proportion of routers in today’s Internet are slow at generating TE replies?” Our results indicate that the answer to this question is “few” which implies that tools such as pathchar and treno will not in practice suffer greatly from slow-path/fast-path differences, as has been a concern.
Synthesis of C-glucosides by reactions of glucosyl halides with organocuprates (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of C-glucosides by reactions of glucosyl halides with organocupratesRon Bihovsky, Caryn Selick, and Irena GiustiCite this: J. Org. Chem. 1988, 53, 17, 4026–4031Publication Date (Print):August 1, 1988Publication History Published online1 May 2002Published inissue 1 August 1988https://pubs.acs.org/doi/10.1021/jo00252a027https://doi.org/10.1021/jo00252a027research-articleACS PublicationsRequest reuse permissionsArticle Views1374Altmetric-Citations54LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Monitoring of Regulatory T Cell Frequencies and Expression of CTLA-4 on T Cells, before and after DC Vaccination, Can Predict Survival in GBM Patients (2012)

Our results suggest that monitoring the change in regulatory T cell frequencies and dynamic expression of the negative co-stimulatory molecules on peripheral blood T cells, before and after DC vaccination, may predict survival. The cut-off point generated from these data can be utilized in future prospective immunotherapy trials to further evaluate its predictive validity.
Biological Roles of Fibroblast Growth Factor-2* (1997)

I. Introduction II. Structure of FGF-2 III. Mechanisms of Action of FGF-2: Extra- and Intracellular Signaling A. Exogenous 18-kDa FGF-2 B. Endogenous 18-kDa FGF-2 and HMW FGF-2 IV. Release of FGF-2 V. Roles of FGF-2 in Development and Differentiation in Various Organ Systems A. Mesoderm induction B. Angiogenesis C. Vessel wall D. Lung E. Hematopoiesis F. Nervous system G. Reproductive system H. Skin I. Eye J. Muscle and skeleton K. Digestive system VI. Conclusions
Sequence analysis of clonal immunoglobulin and T-cell receptor gene rearrangements in children with acute lymphoblastic leukemia at diagnosis and at relapse: implications for pathogenesis and for the clinical utility of PCR-based methods of minimal residual disease detection (2003)

Immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements provide clonal markers useful for diagnosis and measurement of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL). We analyzed the sequences of Ig and TCR gene rearrangements obtained at presentation and relapse in 41 children with ALL to study clonal stability, which has important implications for monitoring MRD, during the course of the disease. In 42%, all original Ig and/or TCR sequences were conserved. In 24%, one original sequence was preserved but the other lost, and in 14% the original sequences were conserved with new sequences identified at relapse. In 20% only new sequences were found at relapse. Using primers designed from the novel relapse sequences, the relapse clone could be identified as subdominant clones in the diagnostic sample in 8 of 14 patients. Alteration of these clonal gene rearrangements is a common feature in childhood ALL. MRD detection should include multiple gene targets to minimize false-negative samples or include also multicolor flow cytometry. In some cases the leukemic progenitor cell might arise earlier in lineage before DHJH recombination but retain the capacity to further differentiate into cells capable of altering the pattern of Ig and/or TCR rearrangements.
Characterization of Subdomain IIA Binding Site of Human Serum Albumin in its Native, Unfolded, and Refolded States Using Small Molecular Probes (2008)

Subdomain IIA binding site of human serum albumin (HSA) was characterized by examining the change in HSA fluorescence in the native, unfolded, and refolded states. The study was carried out in the absence and presence of small molecular probes using steady-state and time-resolved fluorescence measurements. 2-Pyridone, 3-pyridone, and 4-pyridone bear similar molecular structures to those found in many drugs and are used here as probes. They are found to specifically bind in subdomain IIA and cause a reduction in the fluorescence intensity and lifetime of the Trp-214 residue in native HSA which is located in the same subdomain. The efficiency of energy transfer from Trp-214 fluorescence to the probes was found to depend on the degree of the spectral overlap between the donor's fluorescence and the acceptor's absorption. After probe binding in subdomain IIA, the distance between the donor and acceptor was calculated using Forster theory. The calculated quenching rate constants and binding constants were also shown to depend on the degree of spectral overlap. The results point to a static quenching mechanism operating in the complexes. Denaturation of HSA in the presence of guanidine hydrochloride (GdnHCl) starts at [GdnHCl] > 1.0 M and is complete at [GdnHCl] > or = 6.0 M. Upon unfolding, two fluorescence peaks were observed. One peak was assigned to the fluorescence of Trp-214 in a polar environment, and the other peak was assigned to tyrosine fluorescence. A reduction of the fluorescence intensity of the two peaks upon binding of the probes to the denatured HSA indicates that Tyr-263 in subdomain IIA is one of the tyrosine residues responsible for the second fluorescence peak. The results were confirmed by measuring the fluorescence spectra and lifetimes of denatured HSA at different excitation wavelengths, and of L-tryptophan and L-tyrosine free in buffer. The measured lifetimes of denatured HSA are typical of tryptophan in a polar environment and are slightly reduced upon probe binding. Dilution of the denatured HSA by buffer results in a partial refolding of subdomain IIA. This partial refolding is attributed to some swelling of the binding site caused by water. The swelling prevents a full recovery from the denatured state.
Optical coherence tomography: a review of clinical development from bench to bedside (2007)

Since its introduction, optical coherence tomography (OCT) technology has advanced from the laboratory bench to the clinic and back again. Arising from the fields of low coherence interferometry and optical time- and frequency-domain reflectometry, OCT was initially demonstrated for retinal imaging and followed a unique path to commercialization for clinical use. Concurrently, significant technological advances were brought about from within the research community, including improved laser sources, beam delivery instruments, and detection schemes. While many of these technologies improved retinal imaging, they also allowed for the application of OCT to many new clinical areas. As a result, OCT has been clinically demonstrated in a diverse set of medical and surgical specialties, including gastroenterology, dermatology, cardiology, and oncology, among others. The lessons learned in the clinic are currently spurring a new set of advances in the laboratory that will again expand the clinical use of OCT by adding molecular sensitivity, improving image quality, and increasing acquisition speeds. This continuous cycle of laboratory development and clinical application has allowed the OCT technology to grow at a rapid rate and represents a unique model for the translation of biomedical optics to the patient bedside. This work presents a brief history of OCT development, reviews current clinical applications, discusses some clinical translation challenges, and reviews laboratory developments poised for future clinical application.
Conductive Core–Sheath Nanofibers and Their Potential Application in Neural Tissue Engineering (2009)

We have prepared conductive core-sheath nanofibers via a combination of electrospinning and aqueous polymerization. Specifically, nanofibers electrospun from poly(ε-caprolactone) (PCL) and poly((L)-lactide) (PLA) were employed as templates to generate uniform sheaths of polypyrrole (PPy) via in situ polymerization. These conductive core-sheath nanofibers offer a unique system for studying the synergistic effect of different cues on neurite outgrowth in vitro. We found that explanted dorsal root ganglia (DRG) adhered well to the conductive core-sheath nanofibers and generated neurites across the surface when there was a nerve growth factor in the medium. Furthermore, the neurites could be oriented along one direction and enhanced by 82% in terms of maximum length when uniaxially aligned conductive core-sheath nanofibers are compared with their random counterparts. Electrical stimulation, when applied through the mats of conductive core-sheath nanofibers, was found to further increase the maximum length of neurite for random and aligned samples by 83% and 47%, respectively, relative to the controls without electrical stimulation. Combined together, these results suggest the potential use of the conductive core-sheath nanofibers as scaffolds in applications such as neural tissue engineering.
Defined System for In Vitro Production of Porcine Embryos Using a Single Basic Medium (2008)

We have previously indicated that porcine blastocysts can be produced by in vitro fertilization (IVF) and culture (IVC) in chemically defined porcine gamete medium (PGM) and porcine zygote medium (PZM)-5, respectively, In the present study, the effects of basic media and macromolecular components on in vitro maturation (IVM) were investigated to develop a defined system for in vitro embryo production using a single basic medium through IVM, IVF and IVC. Porcine immature oocytes were matured in porcine oocyte medium (POM) or modified North Carolina State University (mNCSU) 37, which were supplemented with either 10% (v/v) porcine follicular fluid (pFF) or 3 mg/ml polyvinyl alcohol (PVA) as a macromolecular component (designated POM+pFF, POM+PVA, mNCSU37+pFF and mNCSU37+PVA). In the maturation with mNCSU37+PVA, the percentages of oocytes that reached the metaphase II stages were significantly lower than those in the other treatments. Following IVM with the above media, oocytes were treated with an electrical stimulus and cycloheximide for parthenogenetic activation and were cultured in PZM-5 for 5 days. The rates of cleavage and blastocyst formation of parthenogenetic oocytes were significantly lowered for maturation with mNCSU37+PVA compared with the other treatments, while there were no significant differences in the total numbers of cells in blastocysts among the treatments. Following IVF and IVC, the rates of penetration, male pronucleus formation, cleavage and blastocyst formation were significantly lower when oocytes were matured in mNCSU37+PVA than in other maturation media. The normal fertilization rate was significantly higher in POM+PVA compared with the other treatments, although the total number of cells in blastocysts was reduced with the addition of PVA to both POM and mNCSU37 compared with pFF supplementation. These results demonstrate that porcine blastocysts can be produced by the defined system using a single basic medium.
Methods for the in vitro determination of an individual disposition towards TH1- or TH2-reactivity by the application of appropriate stimulatory antigens (2003)

In this study we performed several methods for the determination of cytokines (RT-PCR for the demonstration of cytokine mRNA and flow cytometry for the analysis of intracellular cytokines) and compared them with a recently established test system stimulating peripheral blood mononuclear cells (PBMC) with TH1- and TH2-relevant recall antigens and analysing type 1 and type 2 cytokines by ELISA. Aim of the study was therefore to evaluate the reliability of TH1/TH2 cytokine profiles in two individuals with different types of an allergic/atopic disposition: one of them showed a strong TH1/type 1-mediated tuberculin-reaction (subject A), the other (subject B) revealed elevated IgE-levels and eosinophil counts (TH2/type 2-mediated). PBMC were incubated with the type 1-antigen purified protein derivative (PPD) and the type 2-antigen tetanus-toxoid (TT) for seven days. From the comparison of ELISA with RT-PCR and flow cytometry-analysis it became evident that all three methods allowed the definition of subject A as a 'type 1-responder'. Subject B showed a pure type 2-response in the ELISA method; PCR and flow cytometry analysis revealed the simultaneous production of type 1- and type 2-cytokines resulting in a mixed type 1/type 2-profile. Active immunization of subject A with TT at the end of the observation period of 12 months resulted in a transient shift from type 1- to a mixed type 1/type 2-profile (simultaneous PPD-induced IFN-gamma- and TT-induced IL-5 production). From this pilot study based on clear cut clinical criteria concerning either a humoral or cellular immunological reactivity towards allergens/antigens it is suggested that the determination of type 1/type 2-cytokines by ELISA in supernatants of PBMC stimulated with type 1/type 2-relevant antigens is a useful approach for a better classification of 'type1-' or 'type 2-responder'.
Interactions Involving Allelopathy in Cropping Systems (1996)

Abstract Allelopathic inhibition typically results from the combined action of a group of allelochemicals which, collectively, interfere with several physiological processes. The objectives of this paper are to summarize research that illustrates the joint action of allelochemicals, and to provide evidence that both the amount and detrimental action of these compounds depends on the extent of associated abiotic and biotic stresses. Allelopathy is strongly coupled with other stresses of the crop environment, including insects and disease, temperature extremes, nutrient and moisture variables, radiation, and herbicides. These stress conditions often enhance allelochemical production, thus increasing the potential for allelopathic interference. In the paradigm of interactions, the data indicate that crops are more sensitive to allelopathy when moisture, temperature, or nutrient conditions are less than optimal. For example, the inhibition threshold concentration for ferulic acid to affect seedling growth was reduced with even minor moisture stress (Ψ = − 0.15 MPa) or a growth temperature at the higher end of the normal range for a species. Under greenhouse conditions, additive inhibition resulted from the joint action of ferulic acid with low levels of alachlor [2‐chloro‐ N ‐(2,6‐diethylphenyl)‐ N ‐(methoxymethyl)acetamide], atrazine [6‐chloro‐ N ‐ethyl‐ N ’‐(1‐methylethyl)‐1,3,5‐triazine‐2,4‐diamine], or trifluralin [2,6‐dinitro‐ N , N ‐dipropyl‐4‐(trifluoromethyl)benzenamine]. Interactions of multiple stresses in crop environments will determine the relative impact of allelopathy. Allelopathystress interactions also have implications for herbicide and residue management strategies, crop rotations, biological control measures, and tillage practices that can contribute to a more sustainable agriculture.
A programmable architecture for scalable and real-time network traffic measurements (2008)

Accurate and real-time traffic measurement is becoming increasingly critical for large variety of applications including accounting, bandwidth provisioning and security analysis. Existing network measurement techniques, however, have major difficulty dealing with large number of flows in today's high-speed networks and offer limited scalability with increasing link speeds. Consequently, the current state of the art solutions have to resort to conservative sampling of the traffic stream and/or accounting for only a few frequent flows that often fail to provide accurate estimates of traffic features.In this paper, we present a novel hardware-software co-designed solution that is programmable and adaptable to runtime situations offering high-throughputs that can easily match current link-speeds. The key to our design is orthogonalization of memory lookups from traffic measurements through our query-driven measurement scheme. We have prototyped our approach on a Xilinx platform using Microblaze soft-core processors integrated with Virtex-II Pro FPGA fabric. We demonstrate the scalability of our architecture and also compare it with a recent offline (non real-time) sampling-based software alternative. The comparison shows that our architecture performs orders better in terms of speed and throughput even while being used as an offline solution.
Animal models of soft-tissue sarcoma (2010)

Soft-tissue sarcomas (STSs) are rare mesenchymal tumors that arise from muscle, fat and connective tissue. Currently, over 75 subtypes of STS are recognized. The rarity and heterogeneity of patient samples complicate clinical investigations into sarcoma biology. Model organisms might provide traction to our understanding and treatment of the disease. Over the past 10 years, many successful animal models of STS have been developed, primarily genetically engineered mice and zebrafish. These models are useful for studying the relevant oncogenes, signaling pathways and other cell changes involved in generating STSs. Recently, these model systems have become preclinical platforms in which to evaluate new drugs and treatment regimens. Thus, animal models are useful surrogates for understanding STS disease susceptibility and pathogenesis as well as for testing potential therapeutic strategies.
Enhancement of antibody fragment secretion into the Escherichia coli periplasm by co-expression with the peptidyl prolyl isomerase, FkpA, in the cytoplasm (2013)

Improper protein folding or aggregation can frequently be responsible for low expression and poor functional activity of antibody fragments secreted into the Escherichia coli periplasm. Expression issues also can affect selection of antibody candidates from phage libraries, since antibody fragments displayed on phage also are secreted into the E. coli periplasm. To improve secretion of properly folded antibody fragments into the periplasm, we have developed a novel approach that involves co-expressing the antibody fragments with the peptidyl prolyl cis-trans isomerase, FkpA, lacking its signal sequence (cytFkpA) which consequently is expressed in the E. coli cytosol. Cytoplasmic expression of cytFkpA improved secretion of functional Fab fragments into the periplasm, exceeding even the benefits from co-expressing Fab fragments with native, FkpA localized in the periplasm. In addition, panning and subsequent screening of large Fab and scFv naïve phage libraries in the presence of cytFkpA significantly increased the number of unique clones selected, as well as their functional expression levels and diversity.
A tumor suppressor-dependent inhibitor of angiogenesis is immunologically and functionally indistinguishable from a fragment of thrombospondin. (1990)

A secreted inhibitor of angiogenesis that is controlled by a tumor suppressor gene in hamster cells has been found to be similar to a fragment of the platelet and matrix protein thrombospondin. The two proteins were biochemically similar and immunologically crossreactive and could substitute for one another in two functional assays. Human thrombospondin inhibited neovascularization in vivo and endothelial cell migration in vitro, as does the hamster protein, gp140. gp140 sensitized smooth muscle cells to stimulation by epidermal growth factor, as does human thrombospondin. The thrombospondin gene has been localized on human chromosome 15. These results demonstrate a function for the ubiquitous adhesive glycoprotein thrombospondin that is likely to be important in the normal physiological down-regulation of neovascularization. In addition, they raise the possibility that thrombospondin may be one of a number of target molecules through which a tumor suppressor gene could act to restrain tumor growth.
Nucleic acid detection technologies -- labels, strategies, and formats. (1999)

Currently, no consensus exists on assay formats, labels, or detection reactions for nucleic acid assays. New labels continue to be developed and tested, and recent candidates include acetate kinase, firefly luciferase, and genes for enzymes. An additional trend is toward nonamplification strategies (e.g., branched chain and dendrimer type assays) as alternatives to the popular PCR and related amplification strategies. The new wave of microanalytical devices (microchips, with nanoliter to microliter internal volumes), massively parallel simultaneous test arrays, and the desire to produce hand-held sensors present new challenges and requirements for nucleic acid detection methods (e.g., analysis of large arrays of micrometer-sized spots of nucleic acid with high resolution). Here I review selected developments and new directions in nucleic acid assays.