gebhart/patrepeval huggingface dataset:
A Novel Method for the Determination of Isokinetic Ratios and Its Application in the Synthesis of Two New Positional Scanning Libraries (2012)

A novel method for the direct evaluation of the equimolarity of the compounds contained in a mixture is presented. We applied the method toward calculating isokinetic ratios for the reaction between the amine termini of a resin bound peptide fragment and a sulfonyl chloride to produce equal molar mixtures of sulfonamides. The results of this study and the application of the method to the synthesis of two new positional scanning synthetic combinatorial libraries (PS-SCL) are discussed.
Surface‐active properties of antifungal lipopeptides produced by<i>Bacillus subtilis</i> (1992)

The interfacial behavior of antifungal lipopetides of the iturinic group was studied in comparison with that of surfactin, an anionic lipopeptide. All these lipopeptides were isolated from various strains of Bacillus subtilis ; each strain produced surfactin and one antifungal compound. The iturinic compounds differ from surfactin by their lower surfactant properties. The critical micelle concentration (CMC) values were dependent on the nature of the peptide moiety in the iturinic compounds. The highest values were observed for anionic antibiotics. The arrangement of lipopeptides at the air‐water interface was largely dependent on the size of the lipid moiety; surfactin, which has a C 14 or C 15 β‐hydroxy fatty acid, iturins A, C, and bacillomycins D, L, which have a C 14 or C 15 β‐amino fatty acid, occupied a smaller area than mycosubtilin and bacillomycin F, which have a C 16 or C 17 β‐amino fatty acid. These data can be related to bioactivity of these lipopeptides.
Transgenic mouse model of familial amyloidotic polyneuropathy. (1989)

Familial amyloidotic polyneuropathy (FAP) is a dominantly inherited disorder, characterized by the extracellular deposition of amyloid fibrils composed of variant transthyretin (TTR), and by prominent peripheral nerve involvement. We demonstrate that the main cause of this disease is the presence of a point mutation in the TTR gene. However, neither the time of onset nor the clinical course is predictable. To elucidate the molecular pathogenesis of this disease, we constructed transgenic mice carrying and expressing the human mutant TTR gene. In these mice, amyloid is deposited in the alimentary tract as early as age six months, and becomes more remarkable with aging. These transgenic mice should be useful in elucidating factors which modulate the time of onset and the clinical course of FAP, and in establishing therapy for this intractable disorder.
Isolation and characterization of heparan sulfate proteoglycans produced by cloned rat microvascular endothelial cells. (1992)

We have isolated heparan sulfate proteoglycans (HSPGs) from cloned rat microvascular endothelial cells using a combination of ion-exchange chromatography, affinity fractionation with antithrombin III (AT III), and gel filtration in denaturing solvents. The anticoagulantly active heparan sulfate proteoglycans (HSPGact) which bind tightly to AT III bear mainly anticoagulantly active heparan sulfate (HSact) whereas the anticoagulantly inactive heparan sulfate proteoglycans (HSPGinact) possess mainly anticoagulantly inactive heparan sulfate (HSinact). HSact and HSinact were also isolated by a combination of ion-exchange chromatography, treatment with protease and chondroitin ABC lyase, and affinity fractionation with AT III. HSact and HSinact have molecular sizes of about 25-30 kDa with the same overall composition of monosaccharides except that HSact exhibits about nine glucuronsyl 3-O-sulfated glucosamines/chain whereas HSinact possesses about three glucuronsyl 3-O-sulfated glucosamines/chain. Direct isolation of the AT III-binding site of HSact by exposing carbohydrate chains to Flavobacterium heparitinase in the presence of protease inhibitor revealed only a single interaction site which contained two to three glucuronsyl 3-O-sulfated glucosamine residues. The core proteins of HSPGact and HSPGinact were isolated by treatment with Flavobacterium heparitinase and purification by ion-exchange chromatography. The molecular sizes of the core proteins were established by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and their primary structures were examined by cleavage with trypsin or endopeptidase Glu-C as well as separation of peptides by reverse-phase high performance liquid chromatography. The results showed that both sets of core proteins exhibited three major components with molecular sizes of 50, 30, and 25 kDa, respectively. The 25-kDa species appears to be a proteolytic degradation product of the 30-kDa species. The peptide mapping revealed that HSPGact and HSPGinact possess extremely similar core proteins.
The Genesis of Voltaire's Micromegas (1957)

THE GENESIS OF VOLTAIRE'S MICROMÉGAS Get access W. H. BARBER W. H. BARBER LONDON Search for other works by this author on: Oxford Academic Google Scholar French Studies, Volume XI, Issue 1, January 1957, Pages 1–15, https://doi.org/10.1093/fs/XI.1.1 Published: 01 January 1957
Expanding the genetic code of mammalian cells (2017)

In the last two decades, unnatural amino acid (UAA) mutagenesis has emerged as a powerful new method to probe and engineer protein structure and function. This technology enables precise incorporation of a rapidly expanding repertoire of UAAs into predefined sites of a target protein expressed in living cells. Owing to the small footprint of these genetically encoded UAAs and the large variety of enabling functionalities they offer, this technology has tremendous potential for deciphering the delicate and complex biology of the mammalian cells. Over the last few years, exciting progress has been made toward expanding the toolbox of genetically encoded UAAs in mammalian cells, improving the efficiency of their incorporation and developing innovative applications. Here, we provide our perspective on these recent developments and highlight the current challenges that must be overcome to realize the full potential of this technology.
Photoimmobilization of Insulin onto Polystyrene Dishes for Protein-Free Cell Culture (1996)

Photoreactive insulin was synthesized by coupling with azidobenzoic acid. The insulin derivative was immobilized onto the wells of polystyrene culture plates by photoir-radiation. The photoimmobilized insulin enhanced the growth of anchorage-dependent cells such as Chinese hamster ovary CHO-K1 and mouse fibroblast STO cells by more than native or azidophenyl-derivatized insulin. A small amount of photoimmobilized insulin (1-10% of the amount of the native or derivatized insulin) enhanced the growth of CHO-K1 and STO cells. In addition, the maximal mitogenic effect of the immobilized insulin was greater than that of native or derivatized insulin. Photoimmobilization could be a universal means of immobilizing growth factors onto the surface of materials devoid of chemical functional groups scaffolding growth factors and providing a new protein-free cell culture system or tissue engineering materials.
Chylomicronemia due to apolipoprotein CIII overexpression in apolipoprotein E-null mice. Apolipoprotein CIII-induced hypertriglyceridemia is not mediated by effects on apolipoprotein E. (1997)

The mechanism of apolipoprotein (apo) CIII-induced hypertriglyceridemia remains uncertain. We crossed apoCIII transgenic and apoE gene knockout (apoE0) mice, and observed severe hypertriglyceridemia with plasma triglyceride levels of 4,521+/-6, 394 mg/dl vs. 423+/-106 mg/dl in apoE0 mice, P < 0.00001 for log(triglycerides [TG]). Cholesterols were 1,181+/-487 mg/dl vs. 658+/-151 mg/dl, P < 0.0001. Lipoprotein fractionation showed a marked increase in triglyceride-enriched chylomicrons+VLDL. This increase was limited to the lowest density (chylomicrons and Sf 100-400) subfractions. Intermediate density lipoproteins (IDL)+LDL increased moderately, and HDL decreased. There was no significant increase in triglyceride production in apoCIII transgenic/apoE0 mice. The clearance of VLDL triglycerides, however, was significantly decreased. Lipoprotein lipase in postheparin plasma was elevated, but activation studies suggested LPL inhibition by both apoCIII transgenic and apoCIII transgenic/apoE0 plasma. ApoCIII overexpression also produced a marked decrease in VLDL glycosaminoglycan binding which was independent of apoE. The predominant mechanism of apoCIII-induced hypertriglyceridemia appears to be decreased lipolysis at the cell surface. The altered lipoprotein profile that was produced also allowed us to address the question of the direct atherogenicity of chylomicrons and large VLDL. Quantitative arteriosclerosis studies showed identical results in both apoCIII transgenic/apoE0 and apoE0 mice, supporting the view that very large triglyceride-enriched particles are not directly atherogenic.
Software Development with Automatic Code Generation: Observations from Novice Developer Viewpoint. (2006)

Abstract — Modern software development methodologies use Model Based Development (MBD) in design and verification practices. A number of software design tools support the use of modeling throughout the development lifecycle. Using appropriate notation the system model is build and verified. Subsequently the software source code can be automatically generated from the design artifacts. The variety of tools on the market and deceptive vendor claims about tool applicability and ease of use leaves industry confused. To explore this, four students of ERAU Master of Software Engineering program were given an assignment: to learn how to use specific software development tool and subsequently develop small project while collecting observations. In addition to give the student opportunity to explore modern tools and technologies, the objective of this exercise was to collect observation on the leading software development tools usability from the perspective of a young software developer.
iScout: an intelligent scout for navigating large image sets (2003)

A new intelligent software tool for PACS systems called 'iScout' has been developed that constructs and displays an overview of large series or studies before downloading the set of images to a PACS workstation. The overview consists of two orthogonal cross-section images that allow the user to select and download a subset of images, avoiding long delays that can occur while downloading hundreds or even thousands of images. The iScout also provides a navigational tool, allowing the user to click on anatomical regions and view the relevant slices, while displaying the anatomical location of the image currently being displayed by the PACS workstation software. The construction of an iScout can be done on either a workstation or a server with only minimal overhead that does not significantly affect the speed of loading. A working iScout tool has been integrated with multi-modality PACS workstation software (McKesson Medical Imaging Solutions), and it was found that the iScout can be generated on the workstation with a maximum added overhead of only 3.4 seconds while downloading a study containing 433 512x512 CT images. The iScout is flexible and can generate scouts for virtually all types of CT and MR images, as well as 3D Ultrasound.
Mechanics of structures (1994)

A.Formulations for linear problems of elasticity. - 1.Basic equations : differential form. 2.Principles of virtual work : integral form of the basic. 3.Related variational and energy principles. - B.Solution methods. 4.Structural analysis methods I : beam elements. 5.Structural analysis methods II : structural systems. 6.The finite element method. 7.Direct variational and weighted residual methods : classical trial function methods. 8.The finite difference method. 9.The boundary element method. - C.Formulations for dynamic and stability problems. - 10.Dynamic responses. 11.Stability analysis. - D.Bars and plates. 12.Beams. 13.Plates.
Targeting human vasohibin‐2 by a neutralizing monoclonal antibody for anti‐cancer treatment (2016)

There are two members of the vasohibin (VASH) family, VASH1 and VASH2. VASH1 is expressed mainly in endothelial cells to inhibit angiogenesis, whereas VASH2 is expressed mainly in cancer cells to stimulate tumor growth. The aim of the present study was to establish neutralizing monoclonal antibody (mAb) against human VASH2 and apply it as an anti-cancer treatment. We previously raised mAb against several synthetic peptides of hVASH1, and found that one of them exhibited neutralizing activity against hVASH1. Because of the similarity in the amino acid sequences between VASH1 and VASH2, we hypothesized that they shared the bioactive center. When we mutated four amino acids within the region, the mutant VASH2 lost its pro-angiogenic activity. Therefore, we raised mAb against a synthetic peptide overlapping the mutated amino acids of hVASH2, and isolated one clone (1760) that almost completely inhibited the stimulatory effect of hVASH2 on the migration of and tube formation by endothelial cells. When we used this clone 1760 antibody for cancer treatment, the peritoneal injection of it inhibited both tumor growth and angiogenesis in a mouse xenograft model of human cancer cells. In terms of anti-tumor activity, 25 mg/kg of clone 1760 was equivalent to 5 mg/kg of bevacizmab. From these results, we propose the targeting of human VASH2 with neutralizing mAb as a new strategy for cancer treatment.
Principles of growth and processing of semiconductors (1998)

Developing the essential elements of semiconductor behaviour, this text goes on to provide a conceptual framework and introduction to microelectronics. Topics include semiconductors, devices, defects, evaluation, bulk growth, epitaxial growth, oxidation, diffussion, and ion implantation.
Improving UDP and TCP performance in mobile ad hoc networks with INSIGNIA (2001)

There is a growing need to provide better service differentiation in mobile ad hoc networks; however, this is challenging. These networks are characterized as being multihop in nature where the wireless topology that interconnects mobile hosts/routers can change rapidly in unpredictable ways or remain relatively static over long periods of time. Power and bandwidth constrained, mobile ad hoc networks typically only support best effort communications where the transport protocol's "goodput" is often lower than the maximum radio transmission rate after encountering the effects of multiple access, fading, noise, and interference. We evaluate three routing protocols with INSIGNIA, an in-band signaling system that supports adaptive reservation-based services in mobile ad hoc networks. INSIGNIA represents a general-purpose approach to delivering quality of service in mobile ad hoc network supporting "operational transparency" between a number of IETF mobile ad hoc network routing protocols that include Ad Hoc On-Demand Distance Vector, Dynamic Source Routing, and the Temporally Ordered Routing Algorithm. We evaluate the performance gains delivered when using INSIGNIA with these MANET routing protocols in support of UDP and TCP traffic. The INSIGNIA ns-2 code used for the study reported in this article is available from the Web at comet.columbia.edu/insignia.
Immunoinformatics and Modeling Perspective of T Cell Epitope-Based Cancer Immunotherapy: A Holistic Picture (2009)

Cancer immunotherapy is fast gaining global attention with its unique position as a potential therapy showing promise in cancer prevention and cure. It utilizes the natural system of immunity as opposed to chemotherapy and radiotherapy that utilize chemical drugs and radiation, respectively. Cancer immunotherapy essentially involves treatment and/or prevention with vaccines in the form of peptide vaccines (T and B cell epitopes), DNA vaccines and vaccination using whole tumor cells, dendritic cells, viral vectors, antibodies and adoptive transfer of T cells to harness the body's own immune system towards the targeting of cancer cells for destruction. Given the time, cost and labor involved in the vaccine discovery and development, researchers have evinced interest in the novel field of immunoinformatics to cut down the escalation of these critical resources. Immunoinformatics is a relatively new buzzword in the scientific circuit that is showing its potential and delivering on its promise in expediting the development of effective cancer immunotherapeutic agents. This review attempts to present a holistic picture of our race against cancer and time using the science and technology of immunoinformatics and molecular modeling in T cell epitope-based cancer immunotherapy. It also attempts to showcase some problem areas as well as novel ones waiting to be explored where development of novel immunoinformatics tools and simulations in the context of cancer immunotherapy would be highly welcome.
STORM: A European Platform for Sub-Micron Technology Simulation and Optimisation (1993)

Software for Technology Optimisation in Research and Manufacturing (STORM) is presented and applied to bipolar and cmos silicon technology.
Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment (2017)

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth's biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and "omics" studies in this field.
STRUCTURE-FUNCTION OF THE TUMOR SUPPRESSOR BRCA1 (2012)

BRCA1, a multi-domain protein, is mutated in a large percentage of hereditary breast and ovarian cancers. BRCA1 is most often mutated in three domains or regions: the N-terminal RING domain, exons 11-13, and the BRCT domain. The BRCA1 RING domain is responsible for the E3 ubiquitin ligase activity of BRCA1 and mediates interactions between BRCA1 and other proteins. BRCA1 ubiquitinates several proteins with various functions. The BRCA1 BRCT domain binds to phosphoproteins with specific sequences recognized by both BRCA1 and ATM/ATR kinases. Structural studies of the RING and BRCT domains have revealed the molecular basis by which cancer causing mutations impact the functions of BRCA1. While no structural data is available for the amino acids encoded by exons 11-13, multiple binding sites and functional domains exist in this region. Many mutations in exons 11-13 have deleterious effects on the function of these domains. In this mini-review, we examine the structure-function relationships of the BRCA1 protein and the relevance to cancer progression.
TrueClick (2014)

The ubiquity of Internet advertising has made it a popular target for attackers. One well-known instance of these attacks is the widespread use of trick banners that use social engineering techniques to lure victims into clicking on deceptive fake links, potentially leading to a malicious domain or malware. A recent and pervasive trend by attackers is to imitate the "download" or "play" buttons in popular file sharing sites (e.g., one-click hosters, video-streaming sites, bittorrent sites) in an attempt to trick users into clicking on these fake banners instead of the genuine link.
Cardiovascular Safety of QVA149, a Combination of Indacaterol and NVA237, in COPD Patients (2010)

This study assessed the cardiovascular safety of QVA149, an inhaled, once daily, bronchodilator combination containing two 24-hour bronchodilators, the long-acting β(2)-agonist indacaterol and the long-acting muscarinic antagonist glycopyrronium (NVA237). In this randomised, double-blind, placebo-controlled, parallel-group study, 257 patients with moderate-to-severe chronic obstructive pulmonary disease (COPD) were randomised to receive QVA149 (indacaterol/NVA237) 600/100 microg, 300/100 microg or 150/100 microg, indacaterol 300 μg or placebo, once daily for 14 days. The primary endpoint was change from baseline in 24-h mean heart rate versus placebo on Day 14. 255 patients were included in the safety analysis (mean age 63.8 years, 76.5% male, post-bronchodilator forced expiratory volume in one second [FEV(1)] 53.2% predicted, FEV(1)/FVC [forced vital capacity] 50.0%, mean 24-h heart rate 79.6 bpm). There were no clinically significant differences in the 24-h mean heart rate on Day 14 between the three doses of QVA149 and placebo or indacaterol. The confidence intervals of these treatment differences (contrasts) were within the pre-specified equivalence limit (-5 to 5 bpm). No clinically relevant differences in QTc interval (Fridericia's) were observed between groups on Days 1, 7 and 14. Once-daily QVA149 was well tolerated in COPD patients with a cardiovascular safety profile and overall adverse event rates similar to placebo.