gebhart/patrepeval huggingface dataset:
van der Waals Surface Graphs and the Shape of Small Rings (1998)

A van der Waals surface graph is the graph defined on the van der Waals surface of a molecule by the intersections of the atomic van der Waals spheres. This is a discrete invariant of three-dimensional molecular shape. Two applications of these graphs to the study of small ring molecules are described: the basic shapes of rings up to order six are classified, and the results of a substructure search are analyzed, indicating how substructures with a specified three-dimensional shape may be identified.
Setting standards - uphill work (1990)

June Girvin describes the problems encountered when attempting to write and implement standards of care
NCBI’s Database of Genotypes and Phenotypes: dbGaP (2013)

The Database of Genotypes and Phenotypes (dbGap, http://www.ncbi.nlm.nih.gov/gap) is a National Institutes of Health-sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents. Publicly accessible metadata about submitted studies, summary level data, and documents related to studies can be accessed freely on the dbGaP website. Individual-level data are accessible via Controlled Access application to scientists across the globe.
Vaccination Using Recombinants Influenza and Adenoviruses Encoding Amastigote Surface Protein-2 Are Highly Effective on Protection against Trypanosoma cruzi Infection (2013)

In the present study we evaluated the protection raised by immunization with recombinant influenza viruses carrying sequences coding for polypeptides corresponding to medial and carboxi-terminal moieties of Trypanosoma cruzi ´s amastigote surface protein 2 (ASP2). Those viruses were used in sequential immunization with recombinant adenovirus (heterologous prime-boost immunization protocol) encoding the complete sequence of ASP2 (Ad-ASP2) in two mouse strains (C57BL/6 and C3H/He). The CD8 effector response elicited by this protocol was comparable to that observed in mice immunized twice with Ad-ASP2 and more robust than that observed in mice that were immunized once with Ad-ASP2. Whereas a single immunization with Ad-ASP2 sufficed to completely protect C57BL/6 mice, a higher survival rate was observed in C3H/He mice that were primed with recombinant influenza virus and boosted with Ad-ASP2 after being challenged with T. cruzi. Analyzing the phenotype of CD8+ T cells obtained from spleen of vaccinated C3H/He mice we observed that heterologous prime-boost immunization protocol elicited more CD8+ T cells specific for the immunodominant epitope as well as a higher number of CD8+ T cells producing TNF-α and IFN-γ and a higher mobilization of surface marker CD107a. Taken together, our results suggest that immunodominant subpopulations of CD8+ T elicited after immunization could be directly related to degree of protection achieved by different immunization protocols using different viral vectors. Overall, these results demonstrated the usefulness of recombinant influenza viruses in immunization protocols against Chagas Disease.
MPS1 and MPS2: novel yeast genes defining distinct steps of spindle pole body duplication. (1991)

It is crucial to the eucaryotic cell cycle that the centrosome undergo precise duplication to generate the two poles of the mitotic spindle. In the budding yeast Saccharomyces cerevisiae, centrosomal functions are provided by the spindle pole body (SPB), which is duplicated at the time of bud emergence in G1 of the cell cycle. Genetic control of this process has previously been revealed by the characterization of mutants in CDC31 and KAR1, which prevent SPB duplication and lead to formation of a monopolar spindle. Newly isolated mutations described here (mps1 and mps2, for monopolar spindle) similarly cause monopolar mitosis but their underlying effects on SPB duplication are unique. The MPS1 gene is found by electron microscopy to be essential for proper formation of the site at which the new SPB normally arises adjacent to the existing one. By contrast, a mutation in MPS2 permits duplication to proceed, but the newly formed SPB is structurally defective and unable to serve as a functional spindle pole. Distinct temporal requirements for the CDC31, MPS1, and MPS2 gene functions during the SPB duplication cycle further demonstrate the individual roles of these genes in the morphogenetic pathway.
The Neil Bibby Lecture 2006: From Archimedes to limits: understanding real analysis (2006)

Neil Bibby made many substantial contributions to history of mathematics education in the UK and to the BSHM in particular. He and his mother each left generous legacies to the Society. His former colleague Bob Burn was invited to give a lecture in his memory to the History of Mathematics in Education (HIMED) meeting in Loughborough in March 2006.
Polyanion Inhibitors of Human Immunodeficiency Virus and Other Viruses. Part 2. Polymerized Anionic Surfactants Derived from Amino Acids and Dipeptides (1996)

A series of new polyanions was synthesized via gamma-polymerization, in aqueous micellar solution, of omega-unsaturated anionic surfactants whose polar head was derived from amino acids or dipeptides. The obtained polyanions were evaluated for their activity against human immunodeficiency virus (HIV-1, HIV-2) and various other RNA and DNA viruses. All the test compounds proved active against HIV-1 and HIV-2, their 50% inhibitory concentration (IC50) being in the range of 0.04-7.5 micrograms/mL, while they were not toxic to the host cells (CEM-4 or MT-4) at concentrations up to 100 micrograms/mL or higher. The HIV-inhibitory effect increased with the hydrophilic character of the amino acid moiety. The compounds were found to interact with both the viral envelope glycoprotein gp120 and the cellular CD4 receptor, thus blocking virus-cell binding and virus-induced syncytium formation. These polyanions also proved active against human cytomegalovirus at about the same IC50 as for HIV. In addition, they were also active, albeit at somewhat higher IC50 values (0.8-20 micrograms/mL), against other enveloped viruses such as respiratory syncytial virus and arenaviruses (Junin and Tacaribe). At yet higher IC50 values ( > or = 20 micrograms/mL), some of the compounds showed activity against influenza A virus. No activity was observed with any of the compounds against vesicular stomatitis virus, Sindbis virus, Semliki forest virus, influenza B, parainfluenza type 3, and the nonenveloped viruses Coxsackie type B4, polio type 1, and reovirus type 1.
The requirement for basement membrane antigens in the production of human epidermal/dermal composites in vitro (1999)

The importance of a dermal element when providing permanent wound cover for skin loss has become evident as the shortcomings of pure epidermal grafts are recognized. We are developing a skin composite formed from sterilized human de-epidermized acellular dermis, keratinocytes and fibroblasts with the ultimate aim of using this composite to cover full-thickness excised burn wounds. These composites can be prepared with or without basement membrane (BM) antigens initially present on the dermis. This study investigates the importance of retaining BM antigens on the dermis to the production and appearance of these composites in vitro. Skin composites prepared from dermis with BM antigens either present or absent initially were studied throughout 3 weeks. Composites with BM antigens present initially were significantly better than those initially lacking BM antigens in: (i) the degree of epithelial cell attachment to the underlying dermis (hemidesmosomes were seen only in the former); (ii) the morphology of the epithelial layer; (iii) the consistent presence of collagen IV and laminin and the increasing expression of tenascin; and (iv) the amount of soluble collagen IV and fibronectin detected in the conditioned media. We conclude that an initial BM antigen template is vital in this skin composite model for the attachment and differentiation of the epithelial layer and for the subsequent remodelling of the BM in vitro.
Ultrafast Low‐Angle RARE: U‐FLARE (1991)

The subsecond application of the RARE technique is described. Two possible methods of implementation are discussed, one in which T2 contrast is manipulated by temporal reordering of the phase-encoding gradient, and the other in which the phase-encoding order is held constant and the contrast is manipulated by means of a spin-echo preparation experiment. In vivo images obtained with the latter method are presented and applications of the sequence discussed.
Highly miniaturized vertical end-fire antenna array for mmWave wireless communication (2013)

This paper demonstrates a novel end-fire antenna array solution applicable for millimeter (mmWave) wireless communications. Previously existing antenna solutions are either confined to broadside radiation or require a bulky ground fill cut space underneath the antenna which commonly limits the feasibility of end-fire antennas. In contrast, the salient feature of the devised antenna array is in fact that end-fire radiation is retained despite being in very close proximity to the ground plane. The proposed shorted monopole antenna array consists of a series of vias, alleviating the fabrication complexity and form factor. The antenna lamination consists of 10-layered Printed Circuit boards (PCB) with a total thickness of 622um. Simulation results indicate the featured 6dB S11 bandwidth to range from 77.6 – 82.2 GHz with peak gain of 4.45 dBi at 80 GHz. |S21| between identical antenna arrays separated along the horizontal plane by 10mm is determined to be −32 dB at 80 GHz.
Hydrogels based on chemically modified poly(vinyl alcohol) (PVA-GMA) and PVA-GMA/chondroitin sulfate: Preparation and characterization (2012)

This work reports the preparation of hydrogels based on PVA-GMA, PVA-GMA is poly(vinyl alcohol) (PVA) functionalized with vinyl groups from glycidyl methacrylate (GMA), and on PVA-GMA with different content of chondroitin sulfate (CS). The degrees of swelling of PVA-GMA and PVA-GMA/CS hydrogels were evaluated in distilled water and the swelling kinetics was performed in simulated gastric and intestinal fluids (SGF and SIF). PVA-GMA and PVA-GMA/CS hydrogels demonstrated to be resistant on SGF and SIF fluids. The elastic modulus, E, of swollen-hydrogels were determined through compressive tests and, according to the obtained results, the hydrogels presented good mechanical properties. At last, the presence of CS enhances the hydrogel cell compatibility as gathered by cytotoxicity assays. It was concluded that the hydrogels prepared through this work presented characteristics that allow them to be used as biomaterial, as a carrier in drug delivery system or to act as scaffolds in tissue engineering as well.
Depth-directed hardware object detection (2011)

Object detection is a vital task in several emerging applications, requiring real-time detection frame-rate and low energy consumption for use in embedded and mobile devices. This paper proposes a hardware-based, depth-directed search method for reducing the search space involved in object detection, resulting in significant speed-ups and energy savings. The proposed architecture utilizes the disparity values computed from a stereoscopic camera setup, in an attempt to direct the detection classifier to regions that contain objects of interest. By eliminating large amounts of search data, the proposed system achieves both performance gains and reduced energy consumption. FPGA simulation results indicate performance speedups up to 4.7 times and high energy savings ranging from 41-48%, when compared to the traditional sliding window approach.
Eviction of Misbehaving and Faulty Nodes in Vehicular Networks (2007)

Vehicular networks (VNs) are emerging, among civilian applications, as a convincing instantiation of the mobile networking technology. However, security is a critical factor and a significant challenge to be met. Misbehaving or faulty network nodes have to be detected and prevented from disrupting network operation, a problem particularly hard to address in the life-critical VN environment. Existing networks rely mainly on node certificate revocation for attacker eviction, but the lack of an omnipresent infrastructure in VNs may unacceptably delay the retrieval of the most recent and relevant revocation information; this will especially be the case in the early deployment stages of such a highly volatile and large-scale system. In this paper, we address this specific problem. We propose protocols, as components of a framework, for the identification and local containment of misbehaving or faulty nodes, and then for their eviction from the system. We tailor our design to the VN characteristics and analyze our system. Our results show that the distributed approach to contain nodes and contribute to their eviction is efficiently feasible and achieves a sufficient level of robustness.
Activation of TBK1 and IKKε Kinases by Vesicular Stomatitis Virus Infection and the Role of Viral Ribonucleoprotein in the Development of Interferon Antiviral Immunity (2004)

Mounting an immune response to a viral pathogen involves the initial recognition of viral antigens through Toll-like receptor-dependent and -independent pathways and the subsequent triggering of signal transduction cascades. Among the many cellular kinases stimulated in response to virus infection, the noncanonical IKK-related kinases TBK1 and IKKepsilon have been shown to phosphorylate and activate interferon regulatory factor 3 (IRF-3) and IRF-7, leading to the production of alpha/beta interferons and the development of a cellular antiviral state. In the present study, we examine the activation of TBK1 and IKKepsilon kinases by vesicular stomatitis virus (VSV) infection in human lung epithelial A549 cells. We demonstrate that replication-competent VSV is required to induce activation of the IKK-related kinases and provide evidence that ribonucleoprotein (RNP) complex of VSV generated intracellularly during virus replication can activate TBK1 and IKKepsilon activity. In TBK1-deficient cells, IRF-3 and IRF-7 activation is significantly reduced, although transcriptional upregulation of IKKepsilon following treatment with VSV, double-stranded RNA, or RNP partially compensates for the loss of TBK1. Biochemical analyses with purified TBK1 and IKKepsilon kinases in vitro demonstrate that the two kinases exhibit similar specificities with respect to IRF-3 and IRF-7 substrates and both kinases target serine residues that are important for full transcriptional activation of IRF-3 and IRF-7. These data suggest that intracellular RNP formation contributes to the early recognition of VSV infection, activates the catalytic activity of TBK1, and induces transcriptional upregulation of IKKepsilon in epithelial cells. Induction of IKKepsilon potentially functions as a component of the amplification mechanism involved in the establishment of the antiviral state.
Serum Type Iii Procollagen Peptide, Type Iv Collagen 7S Domain, Central Triple–Helix of Type Iv Collagen and Tissue Inhibitor of Metalloproteinases in Patients With Chronic Viral Liver Disease: Relationship to Liver Histology (1994)

To assess the clinical value of serum biochemical markers, the aminoterminal peptide of type III procollagen, type IV collagen 7S domain, the central triple-helix of type IV collagen and tissue inhibitor of metalloproteinases, as a marker of hepatic fibrosis, we measured these four serum markers in 132 patients with chronic viral liver disease and compared these serum markers with liver histological findings. Serum levels of these markers increased closely with the progress of liver disease, and the abnormal percentages of type III procollagen peptide, type IV collagen 7S domain, central triple-helix of type IV collagen and tissue inhibitor of metalloproteinases in patients with cirrhosis were 97%, 95%, 83% and 48%, respectively. These four serum markers strongly correlated with the histological degree of periportal with or without bridging hepatocellular necrosis and of liver fibrosis and correlated weakly with the degree of intralobular degeneration and focal necrosis and the degree of portal inflammation. The correlation coefficients of serum type IV collagen 7S domain with periportal with or without bridging hepatocellular necrosis and with liver fibrosis were the highest among these four serum markers, suggesting that serum type IV collagen 7S domain is the most valuable diagnostic marker to assess the degree of liver fibrosis in chronic viral liver disease. When we assessed the ability of each serum marker to detect cirrhosis with a receiver operating curve, the best test was type IV collagen 7S domain, and the second best was type III procollagen peptide.(ABSTRACT TRUNCATED AT 250 WORDS)
A reconfigurable compute engine for real-time vision automata prototyping (2002)

Describes a reconfigurable computer engine called the Data-Flow Functional Computer (DFFC), which is dedicated to rapid prototyping of real-time vision automata. The computer consists of a regular 3D array of very coarse grain application-specific FPGAs, called the 'field-programmable operator array' (FPOA). Each FPOA includes two configurable data paths and ten input/output ports. Specific development tools allow easy and efficient use of the computer. A high-level description (in a functional language) is compiled into a DFFC configuration using an operator library. Several significant applications (connected component labelling, nonlinear filtering, coloured object tracking) have been implemented using our tools. An environment for automatic derivation of vision automata from a DFFC configuration is currently under development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modeling user interactions for conversion rate prediction in M-Commerce (2015)

Recent developments such as the introduction of new mobile banking and mobile payment services represent both an opportunity and a challenge for banks. While there is great potential to increase revenue by providing new services to customers, this goes together with the need to improve the understanding of customer data through deeper analysis, and to react quickly to changes in customer demands. It becomes increasingly important to maintain and update mobile apps with rapid release cycles. However, evaluating the results of changes in data analysis tools and their applications, such as recommender systems, sometimes requires live experiments on deployed systems. In this paper, a model based on stochastic process algebra is described for the interaction between a user and a recommending engine through a mobile app, and quantitative analysis is performed to show how changing features and parameters at the engine side may have an effect on user experience. This activity can be replicated on models representing an existing system, as a way to assess possible impacts before experimenting with live changes.
Lenalidomide Response in Relapsed/Refractory Diffuse Large B-Cell Non-Hodgkin’s Lymphoma. (2007)

Abstract Background: Patients with diffuse large B-cell lymphoma (DLBCL) not cured by first line R-CHOP chemotherapy or second line high-dose chemotherapy with autologous stem cell rescue have a poor prognosis and represent a clear unmet medical need. Lenalidomide (Revlimid®), an immunomodulatory drug, has activity in hematological malignancies including relapsed/refractory multiple myeloma, chronic lymphocytic leukemia and cutaneous T-cell lymphoma. Aim: To determine the activity and safety of lenalidomide monotherapy in relapsed/refractory DLBCL. Methods: Patients with relapsed/refractory DLBCL with measurable disease after at least 1 prior treatment regimen were eligible. Patients received 25 mg lenalidomide orally once daily on Days 1–21 every 28 days and continued therapy for 52 weeks as tolerated or until disease progression. Response and progression were evaluated using the IWLRC methodology. Univariate analyses using Fisher’s exact test was conducted to investigate and characterize associations of prognostic variables with response. Results: Twenty-six patients with DLBCL lymphoma were enrolled. The median age was 66 (45–86) and 13 were female. Median time from diagnosis to lenalidomide was 2.4 (0.5–12) years and median number of prior treatment regimens was 3 (1–6). Three patients (12%) exhibited an objective complete response (1 complete response (CR) and 2 complete responses unconfirmed (CRu)). Two patients had a partial response (PR) for an overall response rate of 19% and 7 had stable disease (SD). Response to lenalidomide was associated with low disease burden (33% for &lt; 50 cm2v 0% for ≥ 50 cm2, P=0.06) and longer time from rituximab to lenalidomide treatment (33% for ≥ 230 days v 0% for &lt; 230 days, P=0.05). Patients with favorable values for both these prognostic factors (N = 10) had a 50% response rate [RR] (30% CR/CRu RR) compared with a 0% RR for patients with unfavorable values (N = 16; P &lt; 0.004) and a progression free survival (ongoing) of 7.4 months v 1.9 months. Although there were no responses in the poor prognosis group, 4 patients exhibited stable disease with an ongoing median PFS of &gt; 4.2 months (&gt; 3.6 - &gt; 6.2). Eight patients (31%) required at least one dose reduction with a median time to first dose reduction of 1.8 months (0.4–2.9). One patient each (4%) had Grade 4 anemia, cauda equinine syndrome, febrile neutropenia, intermittent rash, lymphopenia, neutropenia, pneumonitis and thrombocytopenia. Most common Grade 3 adverse events were neutropenia (19%), thrombocytopenia (15%) and leukopenia (12%). Conclusion: The prognostic factors of tumor burden and time from last dose of rituximab appear to identify relapsed/refractory DLBCL patients with a high likelihood of response to lenalidomide oral monotherapy.