gebhart/patrepeval huggingface dataset:
Engineering antigens for in situ erythrocyte binding induces T-cell deletion (2012)

Antigens derived from apoptotic cell debris can drive clonal T-cell deletion or anergy, and antigens chemically coupled ex vivo to apoptotic cell surfaces have been shown correspondingly to induce tolerance on infusion. Reasoning that a large number of erythrocytes become apoptotic (eryptotic) and are cleared each day, we engineered two different antigen constructs to target the antigen to erythrocyte cell surfaces after i.v. injection, one using a conjugate with an erythrocyte-binding peptide and another using a fusion with an antibody fragment, both targeting the erythrocyte-specific cell surface marker glycophorin A. Here, we show that erythrocyte-binding antigen is collected much more efficiently than free antigen by splenic and hepatic immune cell populations and hepatocytes, and that it induces antigen-specific deletional responses in CD4(+) and CD8(+) T cells. We further validated T-cell deletion driven by erythrocyte-binding antigens using a transgenic islet β cell-reactive CD4(+) T-cell adoptive transfer model of autoimmune type 1 diabetes: Treatment with the peptide antigen fused to an erythrocyte-binding antibody fragment completely prevented diabetes onset induced by the activated, autoreactive CD4(+) T cells. Thus, we report a translatable modular biomolecular approach with which to engineer antigens for targeted binding to erythrocyte cell surfaces to induce antigen-specific CD4(+) and CD8(+) T-cell deletion toward exogenous antigens and autoantigens.
Interleukin 10 (IL‐10) gene variants and susceptibility for paediatric onset Crohn’s disease (2009)

Our gene-wide analysis replicates recent findings of associations between IL-10 and adult CD, and suggests that these associations extend to paediatric-onset CD as well.
An Adenovirus-Based HIV Subtype B Prime/Boost Vaccine Regimen Elicits Antibodies Mediating Broad Antibody-Dependent Cellular Cytotoxicity Against Non-Subtype B HIV Strains (2006)

Although HIV subtype B predominates in North America and Western Europe, most HIV infections worldwide are non-subtype B. Globally effective AIDS vaccines need to elicit broad immunity against multiple HIV strains. In this study, 10 chimpanzees were intranasally primed sequentially with adenovirus type 5 (Ad5)- and Ad7-HIVMNenv/rev recombinants and boosted twice intramuscularly with heterologous oligomeric HIVSF162 gp140DeltaV2 protein in MF59 adjuvant. Sera were evaluated for binding, neutralizing, and antibody-dependent cellular cytotoxicity (ADCC) against HIV clades A, B, C, and CRF01_AE. The vaccine regimen elicited high-titered HIV subtype A, B, C and CRF01_AE gp120-binding antibodies. Sera from 7 of 10 vaccinated chimpanzees cross-neutralized the heterologous South African subtype C primary HIVTV-1 isolate. Significant cross-clade neutralization against other subtype A, C and E isolates was not observed. Sera from all animals mediated ADCC of cells coated with gp120 from HIV subtypes A and B. Nine of 10 animals also exhibited ADCC activity against HIV subtype C and CRF01_AE gp120-coated targets. This subtype B Ad-HIV recombinant prime/envelope protein boost regimen is a promising approach for eliciting broad ADCC activity against diverse HIV clades. Incorporating additional non-subtype B envelope genes and protein boosts in a multivalent strategy may be required to elicit broader neutralizing antibodies against non-subtype B HIV strains.
Clinical significance of clusterin expression in pancreatic adenocarcinoma (2012)

Abstract Background Clusterin is known to be expressed in many human neoplasms, and is believed to participate in the regeneration, migration, and anti-apoptosis of tumor cells. However, few reports have addressed the relationship between the manifestation of clusterin and clinicopathologic parameters in pancreas cancer patients. In the present study, the authors investigated the expression of clusterin and its clinical significance in pancreatic adenocarcinoma. Methods Immunohistochemical staining was performed for clusterin in tumor tissues obtained from patients who received pancreatic resection with radical intent, and the associations of clusterin expression with various clinicopathologic parameters were analyzed in addition to the relation between its expression and survival. Results Immunoreactivity for clusterin was observed in 17 of the 52 (33%) pancreatic adenocarcinomas examined. In addition, clusterin positivity was found to be associated with preoperative serum carcinoembryonic antigen level, perineural invasion, and, most strongly, lymph node metastasis. The survival analysis identified tumor differentiation and lymph node metastasis as the only significant prognostic factors. Conclusion Although not an independent prognostic factor, clusterin immunoreactivity can be used in conjunction with lymph node metastasis to predict survival in cases of pancreatic adenocarcinoma.
Selected values of the thermodynamic properties of binary alloys (1973)

Abstract : This volume, together with its companion, Selected Values of Thermodynamic Properties of the Elements, represents a complete revision of the work, Selected Values of Thermodynamic Properties of Metals and Alloys, by Hultgren, Orr, Anderson, and Kelley, published in 1963 by John Wiley and Sons, New York. The work should cover pertinent data available at the date printed on the first page of each system. Inspection will show that many or most of the selected values differ from the 1963 edition; many of the differences are substantial. This shows progress in measurement and, at the same time, hints of uncertainties still present.
Effects of RNA secondary structure on cellular antisense activity (2000)

The secondary and tertiary structures of a mRNA are known to effect hybridization efficiency and potency of antisense oligonucleotides in vitro. Additional factors including oligonucleotide stability and cellular uptake are also thought to contribute to antisense potency in vivo. Each of these factors can be affected by the sequence of the oligonucleotide. Although mRNA structure is presumed to be a critical determinant of antisense activity in cells, to date little direct experimental evidence has addressed the significance of structure. In order to determine the importance of mRNA structure on antisense activity, oligonucleotide target sites were cloned into a luciferase reporter gene along with adjoining sequence to form known structures. This allowed us to study the effect of target secondary structure on oligonucleotide binding in the cellular environment without changing the sequence of the oligonucleotide. Our results show that structure does play a significant role in determining oligonucleotide efficacy in vivo. We also show that potency of oligonucleotides can be improved by altering chemistry to increase affinity for the mRNA target even in a region that is highly structured.
Highly Potent, Selective, and Orally Active Phosphodiesterase 10A Inhibitors (2011)

The identification of highly potent and orally active phenylpyrazines for the inhibition of PDE10A is reported. The new analogues exhibit subnanomolar potency for PDE10A, demonstrate high selectivity against all other members of the PDE family, and show desired druglike properties. Employing structure-based drug design approaches, we methodically explored two key regions of the binding pocket of the PDE10A enzyme to alter the planarity of the parent compound 1 and optimize its affinity for PDE10A. Bulky substituents at the C9 position led to elimination of the mutagenicity of 1, while a crucial hydrogen bond interaction with Glu716 markedly enhanced its potency and selectivity. A systematic assessment of the ADME and PK properties of the new analogues led to druglike development candidates. One of the more potent compounds, 96, displayed an IC(50) for PDE10A of 0.7 nM and was active in predictive antipsychotic animal models.
Inhibition of aldose reductase enhances HeLa cell sensitivity to chemotherapeutic drugs and involves activation of extracellular signal-regulated kinases (2002)

Changes in glucose metabolism during diabetes are linked to an increased risk for the development of cancer. Increased activity of aldose reductase, the rate-limiting polyol pathway enzyme that converts glucose into sorbitol, mediates pathologies associated with diabetes and is thought to be involved in increased resistance to chemotherapeutic drugs. Thus, increased intracellular sorbitol levels may serve a protective function in cancer cells. In these studies we determined whether an inhibitor of aldose reductase could enhance the effectiveness of anticancer agents. Our findings indicate that treatment with the aldose reductase inhibitor, ethyl 1-benzyl-3-hydroxy-2(5H)-oxopyrrole-4-carboxylate (EBPC), enhances the cytotoxic effects of the anticancer agents doxorubicin and cisplatin in HeLa cervical carcinoma cells. To establish a mechanistic basis for the increased cytotoxicity by EBPC, we examined the activity of the extracellular signal-regulated kinase (ERK) pathway, which is an important regulator of cell growth. Interestingly, treatment with EBPC in combination with the chemotherapeutic drugs increased ERK activity as compared to treatment with the chemotherapeutic drugs, suggesting a possible role for the ERK pathway in mediating doxorubicin- or cisplatin-induced cell death. Consistent with this possibility, inhibition of ERK activation by the MEK inhibitor, U0126, reversed the EBPC-mediated enhancement of cell death. In summary, these data provide evidence that adjuvant therapy with aldose reductase inhibitors improves the effectiveness of chemotherapeutic drugs, possibly through an ERK pathway-mediated mechanism.
The amination of 3‐nitro‐1,5‐naphthyridines by liquid ammonia/potassium permanganate. A new and convenient amination method (1983)

Abstract Treatment of a solution of 3‐nitro‐2‐X‐1,5‐naphthyridines (X = H, OC 2 H 5 , Cl, NH 2 , OH) in liquid ammonia with potassium permanganate gives the corresponding 4‐amino‐3‐nitro‐2‐X‐1,5‐naphthyridines in moderate to good yields. From 1 H NMR spectroscopy, good evidence has been obtained for the intermediacy of 4‐amino‐1,4‐dihydro‐3‐nitro‐2‐X‐1,5‐naphthyridines in these amination reactions.
Incorporating speculative execution into scheduling of control-flow intensive behavioral descriptions (1998)

Speculative execution refers to the execution of parts of a computation before the execution of the conditional operations that decide whether it needs to be executed. It has been shown to be a promising technique for eliminating performance bottlenecks imposed by control flow in hardware and software implementations alike. In this paper, we present techniques to incorporate speculative execution in a fine-grained manner into scheduling of control-flow intensive behavioral descriptions. We demonstrate that failing to take into account information such as resource constraints and branch probabilities can lead to significantly sub-optimal performance. We also demonstrate that it may be necessary to speculate simultaneously along multiple paths, subject to resource constraints, in order to minimize the delay overheads incurred when prediction errors occur. Experimental results on several benchmarks show that our speculative scheduling algorithm can result in significant (upto seven-fold) improvements in performance (measured in terms of the average number of clock cycles) as compared to scheduling without speculative execution. Also, the best and worst case execution times for the speculatively performed schedules are the same as or better than the corresponding values for the schedules obtained without speculative execution.
Intercellular adhesion molecule-1 (ICAM-1) and endothelial leucocyte adhesion molecule-1 (ELAM-1) expression in the bronchial mucosa of normal and asthmatic subjects (1992)

Bronchial lavage and biopsy studies suggest the involvement of eosinophils and T-lymphocytes in allergic inflammation in asthma. There is evidence suggesting that the expression of adhesion molecules on endothelial cells and of their receptors on leucocytes is involved in this process. To investigate these mechanisms we have obtained bronchial mucosal biopsies from 10 normal subjects and from 10 symptomatic atopic asthmatics. Six of the asthmatics were re-biopsied after 6 weeks of inhaled beclomethasone dipropionate (BDP) during which time their clinical response was monitored. Frozen sections were stained by the immunoperoxidase method using monoclonal antibody (MoAb) 6.5B5 to identify expression of intercellular adhesion molecule (ICAM-1) and MoAb 1.2B6 for endothelial leucocyte adhesion molecule (ELAM-1). Araldite-embedded sections were also stained for eosinophils using MoAb EG2 to identify eosinophilic cationic protein (ECP). A significant mucosal eosinophilia was apparent in the asthmatic but not in the normal biopsies. Immunostaining for ICAM-1 was observed in both the epithelium and endothelium and ELAM-1 in endothelium, with no significant differences being apparent between the asthmatic and normal subjects. Topical BDP markedly reduced the mucosal eosinophilia without affecting the expression of either adhesion molecule. Using this method, we conclude that there is basal expression of ICAM-1 and ELAM-1 in normal human bronchial mucosa, which is not significantly different from that in asthmatics, and that it is insensitive to suppression with corticosteroids at an inhaled dose that causes clinical improvement.
Design Considerations for an Inhibitive, Stable Water-Based Mud System (1987)

Summary This paper discusses the technique of using high-molecular-weight organic polymers to stabilize troublesome shales through the adsorption of a protective polymer layer. It specifically covers the performance of a partially hydrolyzed Polyacrylamide (PHPA) in respect to shale preservation and in the retardation of cuttings dispersion. Other design factors—e.g., pH control, rheological stability, and lubricity—are also covered.
Skyscraper broadcasting (1997)

We investigate a novel multicast technique, called Skyscraper Broadcasting (SB), for video-on-demand applications. We discuss the data fragmentation technique, the broadcasting strategy, and the client design. We also show the correctness of our technique, and derive mathematical equations to analyze its storage requirement. To assess its performance, we compare it to the latest designs known as Pyramid Broadcasting (PB) and Permutation-Based Pyramid Broadcasting (PPB). Our study indicates that PB offers excellent access latency. However, it requires very large storage space and disk bandwidth at the receiving end. PPB is able to address these problems. However, this is accomplished at the expense of a larger access latency and more complex synchronization. With SB, we are able to achieve the low latency of PB while using only 20% of the buffer space required by PPB.
Shape modification of Gregory patches (1997)

There is an urgent need to identify biomarkers for hepatocellular carcinoma due to limited treatment options and the poor prognosis of this common lethal disease. Whole-transcriptome shotgun sequencing (RNA-Seq) provides new possibilities for biomarker identification. We sequenced ∼250 million pair-end reads from a pair of adjacent normal and tumor liver samples. With the aid of bioinformatics tools, we determined the transcriptome landscape and sought novel biomarkers by further empirical validations in 55 pairs of adjacent normal and tumor liver samples with various viral statuses such as HBV(+), HCV(+) and HBV(-)HCV(-). We identified a novel gene with coding regions, termed DUNQU1, which has a tissue-specific expression pattern in tumor liver samples of HCV(+) and HBV(-)HCV(-) hepatocellular carcinomas. Overexpression of DUNQU1 in Huh7 cell lines enhances the ability to form colonies in soft agar. Also, we identified three novel differentially-expressed protein-coding genes (ALG1L, SERPINA11 and TMEM82) that lack documented expression profiles in liver cancer and showed that the level of SREPINA11 is correlated with pathology stages. Moreover, we showed that the alternative splicing event of FGFR2 is associated with virus infection, tumor size, cirrhosis and tumor recurrence. The findings indicate that these new markers of hepatocellular carcinoma may be of value in improving prognosis and could have potential as new targets for developing new treatment options.
Plasminogen Structural Domains Exhibit Different Functions When Associated with Cell Surface GRP78 or the Voltage-dependent Anion Channel (2007)

Both the voltage-dependent anion channel and the glucose-regulated protein 78 have been identified as plasminogen kringle 5 receptors on endothelial cells. In this study, we demonstrate that kringle 5 binds to a region localized in the N-terminal domain of the glucose-regulated protein 78, whereas microplasminogen does so through the C-terminal domain of the glucose-regulated protein 78. Both plasminogen fragments induce Ca(2+) signaling cascades; however, kringle 5 acts through voltage-dependent anion channel and microplasminogen does so via the glucose-regulated protein 78. Because trafficking of voltage-dependent anion channel to the cell surface is associated with heat shock proteins, we investigated a possible association between voltage-dependent anion channel and glucose-regulated protein 78 on the surface of 1-LN human prostate tumor cells. We demonstrate that these proteins co-localize, and changes in the expression of the glucoseregulated protein 78 affect the expression of voltage-dependent anion channel. To differentiate the functions of these receptor proteins, either when acting singly or as a complex, we employed human hexokinase I as a specific ligand for voltage-dependent anion channel, in addition to kringle 5. We show that kringle 5 inhibits 1-LN cell proliferation and promotes caspase-7 activity by a mechanism that requires binding to cell surface voltage-dependent anion channel and is inhibited by human hexokinase I.
The left ventricular dP/dtmax-end-diastolic volume relation in closed-chest dogs. (1985)

I investigated the relation of the maximum rate of left ventricular pressure rise to the end-diastolic volume and the comparison of the maximum rate of left ventricular pressure rise-end-diastolic volume relation to the end-systolic pressure-volume relation, using the time-varying elastance model. These studies were performed in 11 dogs chronically instrumented to measure left ventricular pressure and determine left ventricular volume from three orthogonal dimensions. During vena caval occlusions, the relations between the maximum rate of left ventricular pressure rise and end-diastolic volume were described by straight lines (r = 0.97 +/- 0.01, mean +/- SD). Dobutamine increased the slope of the maximum rate of left ventricular pressure rise-end-diastolic volume relation to 358 +/- 94% of control. This increase was greater than the 244 +/- 61% increase in the slope of the end-systolic pressure-volume relation (P less than 0.005). The volume intercepts of the maximum rate of left ventricular pressure rise-end-diastolic volume relation and end-systolic pressure-volume relation were similar and were not significantly altered by dobutamine. The ratio of the slope of the maximum rate of left ventricular pressure rise-end-diastolic volume relation to the slope of the end-systolic pressure-volume relation divided by the time from end-diastole to end-systole was similar before (2.2 +/- 0.7) and after dobutamine (2.3 +/- 0.7, P = NS). Angiotensin II did not significantly alter the maximum rate of left ventricular pressure rise-end-diastolic volume relation generated by caval occlusion.(ABSTRACT TRUNCATED AT 250 WORDS)
The interaction index: a measure of drug synergism (2002)

Two drugs used in combination may produce enhanced or reduced effects. The degree of enhancement or reduction is measured from the interaction index (gamma), a quantity that indicates the changed potency of the combination. The index is therefore a quantitative marker for the drug combination and effect metric used. Methodology for measuring the interaction index utilizes the combination and individual drug dose-effect data suitably modeled by regression techniques that most often produce linear plots of effect on log dose from which isobolar analysis is employed. The isobologram provides a simple and convenient graphical assessment of the interaction index but an independent statistical analysis is needed to assess its precision. In some cases, the relative potency of the constituent drugs is the same at all effect levels. When this is so, it is shown that the interaction index can be measured by either an isobolar or an alternate method that is illustrated here. These calculations demonstrate that these different methods of analysis yield the same value of gamma, and do so with comparable precision.
Modulation of an early step in the secretory machinery in hippocampal nerve terminals (1998)

In hippocampal neurons, neurotransmitter release can be regulated by protein kinase A (PKA) through a direct action on the secretory machinery. To identify the site of PKA modulation, we have taken advantage of the ability of the neurotoxin Botulinum A to cleave the synaptic protein SNAP-25. Cleavage of this protein decreases the Ca2+ responsiveness of the secretory machinery by partially uncoupling Ca2+-sensing from fusion per se. This is expressed as a shift toward higher Ca2+ levels of the Ca2+ to neurotransmitter release relationship and as a perturbation of synaptic delay under conditions where secretion induced by the Ca2+-independent secretagogue ruthenium red is unimpaired. We find that SNAP-25 cleavage also perturbs PKA-dependent modulation of secretion; facilitation of ruthenium red-evoked neurotransmitter release by the adenylyl cyclase activator forskolin is blocked completely after Botulinum toxin A action. Together with our observation that forskolin modifies the Ca2+ to neurotransmitter release relationship, our results suggest that SNAP-25 acts as a functional linker between Ca2+ detection and fusion and that PKA modulates an early step in the secretory machinery related to calcium sensing to facilitate synaptic transmission.
Cost-based query scrambling for initial delays (1998)

Remote data access from disparate sources across a wide-area network such as the Internet is problematic due to the unpredictable nature of the communications medium and the lack of knowledge about the load and potential delays at remote sites. Traditional, static, query processing approaches break down in this environment because they are unable to adapt in response to unexpected delays. Query scrambling has been proposed to address this problem. Scrambling modifies query execution plans on-the-fly when delays are encountered during runtime. In its original formulation, scrambling was based on simple heuristics, which although providing good performance in many cases, were also shown to be susceptible to problems resulting from bad scrambling decisions. In this paper we address these shortcomings by investigating ways to exploit query optimization technology to aid in making intelligent scrambling choices. We propose three different approaches to using query optimization for scrambling. These approaches vary, for example, in whether they optimize for total work or response-time, and whether they construct partial or complete alternative plans. Using a two-phase randomized query optimizer, a distributed query processing simulator, and a workload derived from queries of the TPCD benchmark, we evaluate these different approaches and compare their ability to cope with initial delays in accessing remote sources. The results show that cost-based scrambling can effectively hide initial delays, but that in the absence of good predictions of expected delay durations, there are fundamental tradeoffs between risk aversion and effectiveness.