gebhart/patrepeval huggingface dataset:
IL-33 induces IL-13 production by mouse mast cells independently of IgE-FcεRI signals (2007)

The IL-1-related molecules, IL-1 and IL-18, can promote Th2 cytokine production by IgE/antigen-FcepsilonRI-stimulated mouse mast cells. Another IL-1-related molecule, IL-33, was identified recently as a ligand for T1/ST2. Although mouse mast cells constitutively express ST2, the effects of IL-33 on mast cell function are poorly understood. We found that IL-33, but not IL-1beta or IL-18, induced IL-13 and IL-6 production by mouse bone marrow-derived, cultured mast cells (BMCMCs) independently of IgE. In BMCMCs incubated with the potently cytokinergic SPE-7 IgE without specific antigen, IL-33, IL-1beta, and IL-18 each promoted IL-13 and IL-6 production, but the effects of IL-33 were more potent than those of IL-1beta or IL-18. IL-33 promoted cytokine production via a MyD88-dependent but Toll/IL-1R domain-containing adaptor-inducing IFN-beta-independent pathway. By contrast, IL-33 neither induced nor enhanced mast cell degranulation. At 200 ng/ml, IL-33 prolonged mast cell survival in the absence of IgE and impaired survival in the presence of SPE-7 IgE, whereas at 100 ng/ml, IL-33 had no effect on mast cell survival in the absence of IgE and reduced mast cell survival in the presence of IgE. These observations suggest potential roles for IL-33 in mast cell- and Th2 cytokine-associated immune responses and disorders.
Photoresponsive Monolayers Containing In-Chain Azobenzene (1996)

Azobenzene monolayers on silicon have been prepared by two synthetic methods: (1) chemisorption of triethoxysilanes, and (2) acylation of amine-functionalized self-assembled monolayers with acid chloride derivatives. A series of films were prepared with different methylene spacer lengths and different terminal end groups (pentyl vs hydrogen). The resulting films were characterized using water contact angles, X-ray photoelectron spectroscopy, attenuated total reflectance infrared spectroscopy, and X-ray reflectivity (XR). Despite evidence for successful attachment of azobenzene to the surfaces, film thicknesses as determined by XR suggest uniform, but incomplete, monolayers. Irradiation of the films with 354 nm light effected a decrease in the water contact angle. The largest photoinduced changes in contact angles (9°) were observed for films prepared by acylation and with terminal pentyl groups; for one of these films, XR monitoring of film thicknesses showed a 1 Å increase in film thickness during 354 nm irradiation.
Cyclic alternating pattern: a new marker of sleep alteration in patients with fibromyalgia? (2004)

The increase of CAP rate indicates a worse quality of sleep in patients with FM. These data are strongly correlated to the severity of symptoms.
Synergistic induction of apoptosis by combination of BTK and dual mTORC1/2 inhibitors in diffuse large B cell lymphoma (2014)

Diffuse large B cell lymphoma is generally treated by chemotherapy and there is an unmet medical need for novel targeted therapies or combination therapies. Using in vitro screening, we have identified the combination of ibrutinib, an inhibitor of the tyrosine kinase BTK, and AZD2014, an mTOR catalytic inhibitor, as being highly synergistic in killing ABC-subtype DLBCL cell lines. Simultaneous inhibition of BTK and mTOR causes apoptosis both in vitro and in vivo and results in tumor regression in a xenograft model. We identify two parallel mechanisms that underlie apoptosis in this setting: cooperative inhibition of cap-dependent translation, and the inhibition of an NF-κB/IL10/STAT3 autocrine loop. Combined disruption of these pathways is required for apoptosis. These data represent a rational basis for the dual inhibition of BTK and mTOR as a potential treatment for ABC-subtype DLBCL.
Reductive Carbonylation − an Efficient and Practical Catalytic Route for the Conversion of Aryl Halides to Aldehydes (2006)

Alternative routes for the introduction of aldehyde functionality are particularly desirable for fine chemical and pharmaceutical intermediates because of the wide range of further transformations that are possible. Catalytic processes are of particular interest for minimising waste, and therefore the reductive carbonylation of aryl halides has been explored. We have shown that high yields of aldehydes may be obtained for a wide selection of aryl iodides and bromides using mild conditions (3 bar of CO, temperatures 60−120 °C) and silanes as hydride source. A choice of conditions (catalyst, base, solvent) is required to cover the range of aryl substituents varying in electron donation and steric influence. This is related to the competing needs of the several steps of this reaction, including oxidative addition, CO substitution, CO insertion, hydride transfer, and reductive elimination.
Cryptographic support for secure logs on untrusted machines (1998)

In many real-world applications, sensitive information must be kept in log files on an untrusted machine. In the event that an attacker captures this machine, we would like to guarantee that he will gain little or no information from the log files and to limit his ability to corrupt the log files. We describe a computationally cheap method for making all log entries generated prior to the logging machine&amp;apos;s compromise impossible for the attacker to read, and also impossible to undetectably modify or destroy.
A Gene Encoding Phosphatidylethanolamine N-Methyltransferase from Acetobacter aceti and Some Properties of its Disruptant (2001)

Phosphatidylcholine (PC) is a major component of membranes not only in eukaryotes, but also in several bacteria, including Acetobacter. To identify the PC biosynthetic pathway and its role in Acetobacter sp., we have studied Acetobacter aceti IFO3283, which is characterized by high ethanol oxidizing ability and high resistance to acetic acid. The pmt gene of A. aceti, encoding phosphatidylethanolamine N-methyltransferase (Pmt), which catalyzes methylation of phosphatidylethanolamine (PE) to PC, has been cloned and sequenced. One recombinant plasmid that complemented the PC biosynthesis was isolated from a gene library of the genomic DNA of A. aceti. The pmt gene encodes a polypeptide with molecular mass of either 25125, 26216, or 29052 for an about 27-kDa protein. The sequence of this gene showed significant similarity (44.3% identity in the similar sequence region) with the Rhodobacter sphaeroides pmtA gene which is involved in PE N-methylation. When the pmt gene was expressed in E. coli, which lacks PC, the Pmt activity and PC formation were clearly demonstrated. A. aceti strain harboring an interrupted pmt allele, pmt::Km, was constructed. The pmt disruption was confirmed by loss of Pmt and PC, and by Southern blot analyses. The null pmt mutant contained no PC, but tenfold more PE and twofold more phosphatidylglycerol (PG). The pmt disruptant did not show any dramatic effects on growth in basal medium supplemented with ethanol, but the disruption caused slow growth in basal medium supplemented with acetate. These results suggest that the lack of PC in the A. aceti membrane may be compensated by the increases of PE and PG by an unknown mechanism, and PC in A. aceti membrane is related to its acetic acid tolerance.
CD8+ T cell-mediated control of distant tumours following local photodynamic therapy is independent of CD4+ T cells and dependent on natural killer cells (2007)

Cancer survival rates decrease in the presence of disseminated disease. However, there are few therapies that are effective at eliminating the primary tumour while providing control of distant stage disease. Photodynamic therapy (PDT) is an FDA-approved modality that rapidly eliminates local tumours, resulting in cure of early disease and palliation of advanced disease. Numerous pre-clinical studies have shown that local PDT treatment of tumours enhances anti-tumour immunity. We hypothesised that enhancement of a systemic anti-tumour immune response might control the growth of tumours present outside the treatment field. To test this hypothesis we delivered PDT to subcutaneous (s.c.) tumours of mice bearing both s.c. and lung tumours and monitored the growth of the untreated lung tumours. Our results demonstrate that PDT of murine tumours provided durable inhibition of the growth of untreated lung tumours. The inhibition of the growth of tumours outside the treatment field was tumour-specific and dependent on the presence of CD8(+) T cells. This inhibition was accompanied by an increase in splenic anti-tumour cytolytic activity and by an increase in CD8(+) T cell infiltration into untreated tumours. Local PDT treatment led to enhanced anti-tumour immune memory that was evident 40 days after tumour treatment and was independent of CD4(+) T cells. CD8(+) T cell control of the growth of lung tumours present outside the treatment field following PDT was dependent upon the presence of natural killer (NK) cells. These results suggest that local PDT treatment of tumours lead to induction of an anti-tumour immune response capable of controlling the growth of tumours outside the treatment field and indicate that this modality has potential in the treatment of distant stage disease.
Optoelectronic integrated systems based on free-space interconnects with an arbitrary degree of space variance (1994)

It is appealing to contemplate how VLSI or wafer-scale integrated systems incorporating free-space optical interconnection might outperform purely electrically interconnected systems. This paper first provides a uniform treatment of a general class of optical interconnects based on a Fourier-plane imaging system with an array of sources in the object plane and an array of receptors in the image plane. Sources correspond to data outputs of processing "cells," and receptors to their data inputs. A general abstract optical imaging model, capable of representing a large class of real systems, is analyzed to yield constructive upper bounds on system volume that are comparable to those arising from "3-D VLSI" computational models. These bounds, coupled with technologically derived constraints, form the heart of a design methodology for optoelectronic systems that uses electronic and optical elements each to their greatest advantage, and exploits the available spatial volume and power in the most efficient way. Many of these concepts are embodied in a demonstration project that seeks to implement a bit-serial, multiprocessing system with a radix-2 butterfly topology, and incorporates various new technology developments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-performance liquid chromatography patterns of mycolic acids as criteria for identification of Mycobacterium chelonae, Mycobacterium fortuitum, and Mycobacterium smegmatis (1990)

Rapidly growing mycobacteria of clinical significance were identified by mycolic acids detected with high-performance liquid chromatography. Mycolic acids from whole cells were extracted, derivatized, and detected by a modified high-performance liquid chromatography procedure in less than 3 h. Use of an internal standard allowed differentiation of Mycobacterium chelonae and Mycobacterium fortuitum by comparison of relative retention times. Peak height ratios were used for subidentification of M. chelonae strains; however, M. fortuitum and Mycobacterium smegmatis could not be separated by this system.
2,4-Diamino-5-benzylpyrimidines and analogs as antibacterial agents. 9. Lipophilic trimethoprim analogs as antigonococcal agents (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2,4-Diamino-5-benzylpyrimidines and analogs as antibacterial agents. 9. Lipophilic trimethoprim analogs as antigonococcal agentsB. Roth, D. P. Baccanari, C. W. Sigel, J. P. Hubbell, J. Eaddy, J. C. Kao, M. E. Grace, and B. S. RauckmanCite this: J. Med. Chem. 1988, 31, 1, 122–129Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/jm00396a018https://doi.org/10.1021/jm00396a018research-articleACS PublicationsRequest reuse permissionsArticle Views506Altmetric-Citations27LEARN 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
Thermal Response and Ablation Characteristics of Carbon Fiber Reinforced Composite with Novel Silicon Containing Polymer MSP (2002)

Polymer composites are widely used for high temperature thermal protection (TPS)materials for spacecraft heat shields, and nozzle liners for solid propellant rocket motors. Newly developed silicon containing polymer, abbreviated MSP (Mitsui Silicon Containing Polymer), possesses high decomposition temperature (500 C), and high char yield (&gt;94% at 1000 C)after pyrolysis. Therefore, the MSP polymer has potential as matrix resin of high performance ablative composites compared with conventional phenolic resins. In this study, thermal performance and ablation characteristics of a carbon composite with the MSP polymer (CF/MSP) were investigated under supersonic plasma air stream. The cold wall heat fluxes ranged from 1.2 to 11.0MW/m2. Conventional carbon fiber phenolic (CF/PR) composite was tested at the similar conditions for direct comparison. The mass loss of the CF/MSP composite was far less than that of the CF/PR composite, which is due to higher char yield and consequent high density of char layer. On the other hand, higher internal temperature was measured in the CF/MSP composite.
Predictive Biomarkers of Chemotherapy Efficacy in Colorectal Cancer: Results From the UK MRC FOCUS Trial (2008)

Topo1 immunohistochemistry identified subpopulations that did or did not benefit from irinotecan, and possibly also from oxaliplatin. If verified independently, this information will contribute to the individualization of treatment for colorectal cancer.
Gastrin Stimulates β-Cell Neogenesis and Increases Islet Mass From Transdifferentiated but Not From Normal Exocrine Pancreas Tissue (2002)

It is still unclear which factors regulate pancreatic regeneration and beta-cell neogenesis and which precursor cells are involved. We evaluated the role of intravenously infused gastrin in regenerating pancreas of duct-ligated rats. The ligation of exocrine ducts draining the splenic half of the pancreas resulted in acinoductal transdifferentiation within the ligated part but not in the unligated part. We found that infusion of gastrin from day 7 to 10 postligation resulted in a doubling of the beta-cell mass in the ligated part as measured by morphometry. This increase in insulin-expressing cells was not associated with increased proliferation, hypertrophy, or reduced cell death of the beta-cells. Furthermore, we found an increased percentage of single, extra-insular beta-cells and small beta-cell clusters induced by gastrin infusion. These changes occurred only in the ligated part of the pancreas, where transdifferentiation of the exocrine acinar cells to ductlike cells (metaplasia) had occurred, and was not found in the normal unaffected pancreatic tissue. In conclusion, we demonstrate that administration of gastrin stimulates beta-cell neogenesis and expansion of the beta-cell mass from transdifferentiated exocrine pancreas.
Guiding endothelial progenitor cell tube formation using patterned fibronectin surfaces (2010)

Engineering vascular networks is a key initiative in regenerative medicine. Moreover, control over the formation of organized vascular networks in vitro may facilitate their rapid and functional integration with the host vasculature after implantation. The extracellular matrix provides a structural platform for endothelial progenitor cells (EPCs) to differentiate and assemble into a tubular structure. We demonstrate that optimized, patterned fibronectin surfaces guide the ordered adhesion of human EPCs, maintain EPC responsiveness to tumor necrosis factor-α, support their elongation along the culture period, and enhance von Willebrand factor expression. Using fibrin gel as the three-dimensional milieu allows the assembly of unidirectional chains and formation of tubular structures. High-resolution analysis shows a distinctive lumen, as well as numerous Weibel Palade bodies and caveolae, all indicating a typical progression in vascular morphogenesis and the angiogenic process. Altogether, this approach allows us to engineer the formation of well-organized vascular structures in vitro.
New Aza-Dipeptide Analogues as Potent and Orally Absorbed HIV-1 Protease Inhibitors:  Candidates for Clinical Development (1998)

On the basis of previously described X-ray studies of an enzyme/aza-dipeptide complex,8 aza-dipeptide analogues carrying N-(bis-aryl-methyl) substituents on the (hydroxethyl)hydrazine moiety have been designed and synthesized as HIV-1 protease inhibitors. By using either equally (12) or orthogonally (13) protected dipeptide isosteres, symmetrically and asymmetrically acylated aza-dipeptides can be synthesized. This approach led to the discovery of very potent inhibitors with antiviral activities (ED50) in the subnanomolar range. Acylation of the (hydroxethyl)hydrazine dipeptide isostere with the L-tert-leucine derivative 29 increased the oral bioavailability significantly when compared to the corresponding L-valine or L-isoleucine derivatives. The bis(L-tert-leucine) derivatives CGP 75355, CGP 73547, CGP 75136, and CGP 75176 combine excellent antiviral activity with high blood concentration after oral administration. Furthermore, they show no cross-resistance with saquinavir-resistant strains and maintain activity against indinavir-resistant ones. Consequently they qualify for further profiling as potential clinical candidates.
139. Heterocyclic imines and amines. Part VIII. Identification of “o-cyanothiobenzamide” as 1-imino-3-thioisoindoline, and its conversion with amines into macrocycles and intermediates (1957)

M. E. Baguley and J. A. Elvidge, J. Chem. Soc., 1957, 709 DOI: 10.1039/JR9570000709
XONN: XNOR-based oblivious deep neural network inference (2019)

Advancements in deep learning enable cloud servers to provide inference-as-a-service for clients. In this scenario, clients send their raw data to the server to run the deep learning model and send back the results. One standing challenge in this setting is to ensure the privacy of the clients' sensitive data. Oblivious inference is the task of running the neural network on the client's input without disclosing the input or the result to the server. This paper introduces XONN (pronounced /z∧n/), a novel end-to-end framework based on Yao's Garbled Circuits (GC) protocol, that provides a paradigm shift in the conceptual and practical realization of oblivious inference. In XONN, the costly matrixmultiplication operations of the deep learning model are replaced with XNOR operations that are essentially free in GC. We further provide a novel algorithm that customizes the neural network such that the runtime of the GC protocol is minimized without sacrificing the inference accuracy.

We design a user-friendly high-level API for XONN, allowing expression of the deep learning model architecture in an unprecedented level of abstraction. We further provide a compiler to translate the model description from high-level Python (i.e., Keras) to that of XONN. Extensive proof-of-concept evaluation on various neural network architectures demonstrates that XONN outperforms prior art such as Gazelle (USENIX Security'18) by up to 7×, MiniONN (ACM CCS'17) by 93×, and SecureML (IEEE S&P'17) by 37×. State-of-the-art frameworks require one round of interaction between the client and the server for each layer of the neural network, whereas, XONN requires a constant round of interactions for any number of layers in the model. XONN is first to perform oblivious inference on Fitnet architectures with up to 21 layers, suggesting a new level of scalability compared with state-of-the-art. Moreover, we evaluate XONN on four datasets to perform privacy-preserving medical diagnosis. The datasets include breast cancer, diabetes, liver disease, and Malaria.
Induction of the Unfolded Protein Response in Familial Amyotrophic Lateral Sclerosis and Association of Protein-disulfide Isomerase with Superoxide Dismutase 1 (2006)

Mutations in Cu/Zn superoxide dismutase (SOD1) are linked to motor neuron death in familial amyotrophic lateral sclerosis (ALS) by an unclear mechanism, although misfolded SOD1 aggregates are commonly associated with disease. Proteomic analysis of the transgenic SOD1(G93A) ALS rat model revealed significant up-regulation of endoplasmic reticulum (ER)-resident protein-disulfide isomerase (PDI) family members in lumbar spinal cords. Expression of SOD1 mutants (mSOD1) led to an up-regulation of PDI in motor neuron-like NSC-34 cells but not other cell lines. Inhibition of PDI using bacitracin increased aggregate production, even in wild type SOD1 transfectants that do not readily form inclusions, suggesting PDI may protect SOD1 from aggregation. Moreover, PDI co-localized with intracellular aggregates of mSOD1 and bound to both wild type and mSOD1. SOD1 was also found in the microsomal fraction of cells despite being a predominantly cytosolic enzyme, confirming ER-Golgi-dependent secretion. In SOD1(G93A) mice, a significant up-regulation of unfolded protein response entities was also observed during disease, including caspase-12, -9, and -3 cleavage. Our findings therefore implicate unfolded protein response and ER stress-induced apoptosis in the patho-physiology of familial ALS. The possibility that PDI may be a therapeutic target to prevent SOD1 aggregation is also raised by this study.
Second Conserved Domain of gp120 Is Important for HIV Infectivity and Antibody Neutralization (1988)

Rabbit antisera were raised against three overlapping synthetic peptides with sequence homology to the second conserved domain of the external envelope glycoprotein (gp120) of the human immunodeficiency virus (HIV). All of the antisera immunoprecipitated the envelope glycoprotein. In particular, an antiserum directed against amino acids 254 to 274 of env was efficient in neutralizing three different isolates of HIV in vitro, without affecting the binding of the virus to CD4-positive cells. Therefore, this conserved region of gp120 appears to be critical in a postbinding event during virus penetration and may represent a target for antibody neutralization of HIV. These findings may be applicable in the design of a vaccine for the acquired immunodeficiency syndrome.