gebhart/patrepeval huggingface dataset:
Protein/Polymer‐Based Dual‐Responsive Gold Nanoparticles with pH‐Dependent Thermal Sensitivity (2012)

Abstract This article presents the synthesis and physicochemical behavior of dual‐responsive plasmonic nanoparticles with reversible optical properties based on protein‐coated gold nanoparticles grafted with thermosensitive polymer brushes by means of surface‐initiated atom transfer radical polymerization (SI‐ATRP) that exhibit pH‐dependent thermo‐responsive behavior. Spherical gold NPs of two different sizes (15 nm and 60 nm) and with different stabilizing agents (citrate and cetyltrimethylammonium bromide (CTAB), respectively) were first capped with bovine serum albumin (BSA). The resulting BSA‐capped NPs (Au@BSA NPs) exhibited not only extremely high colloidal stability under physiological conditions, but also a reversible U‐shaped pH‐responsive behavior, similar to pure BSA. The ϵ‐amine of the L‐lysine in the protein coating was then used to covalently bind an ATRP‐initiator, allowing for the SI‐ATRP of thermosensitive polymer brushes of oligo(ethylene glycol) methacrylates with an LCST of 42 °C in pure water and around 37 °C under physiological conditions. Such protein coated nanoparticles grafted with thermosensitive polymers exhibit a smart pH‐dependent thermosensitive behavior.
Depth from Diffusion (2010)

An optical diffuser is an element that scatters light and is commonly used to soften or shape illumination. In this paper, we propose a novel depth estimation method that places a diffuser in the scene prior to image capture. We call this approach depth-from-diffusion (DFDiff). We show that DFDiff is analogous to conventional depth-from-defocus (DFD), where the scatter angle of the diffuser determines the effective aperture of the system. The main benefit of DFDiff is that while DFD requires very large apertures to improve depth sensitivity, DFDiff only requires an increase in the diffusion angle-a much less expensive proposition. We perform a detailed analysis of the image formation properties of a DFDiff system, and show a variety of examples demonstrating greater precision in depth estimation when using DFDiff.
Anticariogenicity of Casein Phosphopeptide-amorphous Calcium Phosphate: A Review of the Literature (2009)

Use of CPP-ACP based compounds offers a potential for use in the prevention of dental caries.
Preparation and Improved Stability of N-Boc-α-amino-5-acyl Meldrum's Acids, a Versatile Class of Building Blocks for Combinatorial Chemistry (2002)

The preparation of novel N-Boc-alpha-amino-5-acyl Meldrum's acids is described. The synthetic inaccessibility and instability of several of these products have led to the development of a protocol that allows the synthesis of their corresponding 4-(dimethylamino)pyridine (DMAP) salts (5-AMA-DMAP's), which exhibit superior stability compared to that of the free 5-AMA. A simple and expedient ion-exchange method was developed for the quantitative removal of DMAP to liberate the synthetically useful DMAP-free form when needed.
Regulation of Tiam1 Nucleotide Exchange Activity by Pleckstrin Domain Binding Ligands (2000)

Rho family GTPases play roles in cytoskeletal organization and cellular transformation. Tiam1 is a member of the Dbl family of guanine nucleotide exchange factors that activate Rho family GTPases. These exchange factors have in common a catalytic Dbl homology and adjacent pleckstrin homology domain. Previous structural studies suggest that the pleckstrin domain, a putative phosphoinositide-binding site, may serve a regulatory function. We identified ascorbyl stearate as a compound that binds to the pleckstrin domain of p120 Ras GTPase-activating protein. Furthermore, ascorbyl stearate appears to be a general pleckstrin domain ligand, perhaps by mimicking an endogenous amphiphilic ligand. Tiam1 nucleotide exchange activity was greatly stimulated by ascorbyl stearate. Certain phosphoinositides also stimulated Tiam1 activity but were less potent than ascorbyl stearate. Tiam1 contains an additional N-terminal pleckstrin domain, but only the C-terminal pleckstrin domain was required for activation. Our results suggest that the pleckstrin domains of Dbl-type proteins may not only be involved in subcellular localization but may also directly regulate the nucleotide exchange activity of an associated Dbl homology domain. In addition, this paper introduces ascorbyl stearate as a pleckstrin domain ligand that can modulate the activity of certain pleckstrin domain-containing proteins.
Security Programmers — not all the same (2003)

Introduction Networks dominate today's computing landscape and commercial technical protection is lagging behind attack technology. As a result, protection programme success depends more on prudent management decisions than on the selection of technical safeguards. Managing Network Security takes a management view of protection and seeks to reconcile the need for security with the limitations of technology.
Esophageal squamous cell carcinoma (ESCC): advance in genomics and molecular genetics (2013)

Esophageal cancer is aggressive and has poor prognosis. Esophageal squamous cell carcinoma (ESCC) is histologically the most prevalent type of esophageal cancer and ranked as the sixth leading cause of cancer death worldwide. In recent years, cancer has been widely regarded as genetic disease, as well as epigenetic abnormalities including DNA methylation, histone deacetylation, chromatin remodeling, gene imprinting and noncoding RNA regulation. In this review, we will provide a general overview of genes, proteins and microRNAs that are involved in the development of ESCC, which aims to enhance our understanding of molecular mechanisms implicated in ESCC development and progression.
Hydrophilic Interaction Chromatography Reduces the Complexity of the Phosphoproteome and Improves Global Phosphopeptide Isolation and Detection (2008)

The diversity and complexity of proteins and peptides in biological systems requires powerful liquid chromatography-based separations to optimize resolution and detection of components. Proteomics strategies often combine two orthogonal separation modes to meet this challenge. In nearly all cases, the second dimension is a reverse phase separation interfaced directly to a mass spectrometer. Here we report on the use of hydrophilic interaction chromatography (HILIC) as part of a multidimensional chromatography strategy for proteomics. Tryptic peptides are separated on TSKgel Amide-80 columns using a shallow inverse organic gradient. Under these conditions, peptide retention is based on overall hydrophilicity, and a separation truly orthogonal to reverse phase is produced. Analysis of tryptic digests from HeLa cells yielded numbers of protein identifications comparable to that obtained using strong cation exchange. We also demonstrate that HILIC represents a significant advance in phosphoproteomics analysis. We exploited the strong hydrophilicity of the phosphate group to selectively enrich and fractionate phosphopeptides based on their increased retention under HILIC conditions. Subsequent IMAC enrichment of phosphopeptides from HILIC fractions showed better than 99% selectivity. This was achieved without the use of derivatization or chemical modifiers. In a 300-microg equivalent of HeLa cell lysate we identified over 1000 unique phosphorylation sites. More than 700 novel sites were added to the HeLa phosphoproteome.
H3N2 Influenza Infection Elicits More Cross-Reactive and Less Clonally Expanded Anti-Hemagglutinin Antibodies Than Influenza Vaccination (2011)

The presence of broadly reactive subdominant antibody responses in some EI subjects suggests that improved vaccine designs that make broadly reactive antibody responses immunodominant could protect against novel influenza strains.
Crowdbrush (2005)

Recent advances in computer graphics techniques and increasing power of graphics hardware made it possible to display and animate large crowds in real-time. Most of the research efforts have been directed towards improving rendering or behavior control; the question how to author crowd scenes in an efficient way is usually not addressed. We introduce a novel approach to create complex scenes involving thousands of animated individuals in a simple and intuitive way. By employing a brush metaphor, analogous to the tools used in image manipulation programs, we can distribute, modify and control crowd members in real-time with immediate visual feedback. We define concepts of operators and instance properties that allow to create and manage variety in populations of virtual humans. An efficient technique allowing to render up to several thousands of fully three-dimensional polygonal characters with keyframed animations at interactive framerates is presented. The potential of our approach is demonstrated by authoring a scenario of a virtual audience in a theater and a scenario of a pedestrian crowd in a city.
A Conceptual Database Model for Genomic Research (1994)

We describe a conceptual model for genome databases that facilitates the process of building, maintaining, and disseminating physically anchored genetic linkage maps. The model has been implemented as a relational database at the Roman L. Hruska U.S. Meat Animal Research Center (MARC). Development of consensus maps using disparate data from different reference pedigrees or laboratories is supported. The model is of use to quantitative and population geneticists interested in loci that affect phenotypes and marker-assisted selection, and it is sufficiently flexible for centralized, species genome databases facilitating comparative mapping. The MARC genome database is used to assemble, maintain, and disseminate physically anchored genetic linkage maps for cattle, swine, and sheep currently based on more than 100,000 genotypes from 1,000 markers. Integrated with linkage analysis software, this database permits frequent updates of physically anchored genetic linkage maps.
CGRP and somatostatin modulate chronic hypoxic pulmonary hypertension (1992)

Chronic hypoxic pulmonary hypertension (PH), associated with increased pulmonary arterial pressure (PPA) and right ventricular hypertrophy (RVH), correlates significantly with calcitonin gene-related peptide (CGRP) and somatostatin (SOM) levels in lung and blood. CGRP's role in regulation of PPA in chronic hypoxia and its potential interactions with SOM were investigated. CGRP, its antibody (ab) and blocker, CGRP-(8-37), SOM-14, SOM-28, and SOM-ab, respectively, were infused into the pulmonary circulation of hypobaric hypoxia rats for 4, 8, and 16 days. Thereafter, under pentobarbital sodium anesthesia, PPA was measured in the right ventricle and main pulmonary artery. Chronic CGRP infusion prevented PH at all times, whereas immunoneutralization and receptor blocking exacerbated PH. SOM-28 also exacerbated while SOM-14 and SOM-ab decreased PH. RVH generally reflected the PPA. Radioimmunoassay confirmed successful infusion of the peptides with negligible peptide degradation in the pumps throughout 16 days and showed complete immunoneutralization of CGRP with its ab. Peptide levels in lung tissue suggest inhibition of CGRP release by SOM-28 and increased plasma SOM with CGRP infusion. In vitro pharmacological studies suggest that CGRP exerts a receptor-mediated nonadrenergic, nonmuscarinic vasodilatory effect in the lung which is independent of endothelium-derived relaxing factor and does not involve ATP-dependent potassium channels. We conclude that endogenous CGRP plays an important role in pulmonary pressure homeostasis during hypoxia, by directly dilating pulmonary vasculature, thus ameliorating the development of chronic hypoxic pulmonary hypertension in rats.
Towards 3D Structures of G Protein-Coupled Receptors A Multidisciplinary Approach (2000)

Current strategies in pharmaceutical research comprise two methodologically different but complementary approaches for lead finding purposes, namely the random screening of compound libraries and the structure-based effort, commonly termed rational drug design. The structure-based approach is aimed to exploit 3D structure data of the molecular components involved in the molecular recognition event that underlies the attempt to therapeutically modulate the biological function of a macromolecular target with proven pathophysiological relevance for a disease state. In this context, G protein-coupled receptors (GPCRs) constitute the most prominent family of validated drug targets within biomedical research, since approximately 60 % of approved drugs elicit their therapeutic effects by selectively addressing members of that target family. From a 3D structure point of view, these transmembrane signal transduction systems represent the most challenging task for structure determination, which is due to the heterogeneous and fine-balanced environment conditions that are necessary for structural and functional integrity of the receptor protein. This contribution will address the different concepts to derive structurally relevant information on the transmemebrane seven-helix protein (7TM) domain of GPCRs with special emphasis laid on the multidisciplinarity of the applied methodologies. The current status of electron-cryo-microscopy on 2D crystals and even high-resolution x-ray crystallography on 7TM proteins will be introduced highlighting the transferability of the emerging structural principles onto the GPCR superfamily. Special techniques from bioinformatics and homology-related molecular modeling in combination with tailor-made protein simulation methodologies complement the experimentally derived data, in that they facilitate the 3D structure generation and structure validation process. This contribution summarises the most recent results of GPCR structure studies with the aim to underline the impact of structure data not only for the purpose of rationalising structure-activity data on low-molecular weight antagonists within the context of a protein binding pocket, but also for a better understanding of e.g. mutagenesis experiments, thus qualifying GPCR structure models as valid communication platforms establishing a functional link between molecular biology, biophysics, bioinformatics and organic chemistry in a highly efficient manner.
Bigenic Cre/loxP, pu tk conditional genetic ablation (2004)

Genetic ablation experiments are used to resolve problems regarding cell lineages and the in vivo function of certain groups of cells. We describe a two-component conditional ablation technology using a mouse carrying an X-linked puDeltatk transgene, which is only activated in cells expressing Cre. Ablation of the Cre-expressing cells can be temporally regulated by the time of ganciclovir (GCV) administration. This strategy was demonstrated using a Col2Cre transgenic line. Differentiating chondrocytes in bigenic animals could be ablated at different developmental stages resulting in disorganized growth plates and dwarfism. Macrocephaly, macroglossia and umbilical hernia were also observed in ablated 18.5 dpc embryos. Crosses between the puDeltatk selector transgenic line and existing cre lines will facilitate numerous temporally regulated tissue-specific ablation experiments.
Inhibitory Effects of Resveratrol Derivatives from Dipterocarpaceae Plants on Tyrosinase Activity (2003)

Stilbene derivatives, which are resveratrol (3,4',5-trihydroxy-trans-stilbene) oligomers ranging from monomer to tetramer, isolated from Dipterocarpaceae plants were tested for their inhibitory effects against murine tyrosinase activity. The structure-activity relationships obtained in this study suggest that the double bond in the stilbene skeleton is critical for the inhibition, and also that molecular size is important for inhibitory potency.
Fibroblast activation protein α in tumor microenvironment: Recent progression and implications (Review) (2015)

Accumulated evidence has demonstrated that the microenvironment of a given tumor is important in determining its drug resistance, tumorigenesis, progression and metastasis. These microenvironments, like tumor cells, are vital targets for cancer therapy. The cross-talk between tumor cells and cancer-associated fibroblasts (CAFs, alternatively termed activated fibroblasts) is crucial in regulating the drug resistance, tumorigenesis, neoplastic progression, angiogenesis, invasion and metastasis of a tumor. Fibroblast activation protein α (FAPα) is a transmembrane serine protease and is highly expressed on CAFs present in >90% of human epithelial neoplasms. FAPα activity, alongside that of gelatinase and type I collagenase, has become increasingly important in cancer therapy due to its effectiveness in modulating tumor behavior. In this review, recent progression in the knowledge of the role of FAPα in tumor microenvironments is discussed.
In vitro ovarian tissue and organ culture: a review (2002)

Many investigations have utilized techniques for culturing ovarian tissue or isolated follicles in vitro. Whole ovaries from fetal or neonatal rodents have been incubated in organ culture systems. This has been utilized to understand the sequence of follicle formation and its hormonal requirements, activation of quiescent follicles, follicular growth and development, and acquisition of steroidogenic capabilities. Adaptations of this technique include incubation of ovaries in a chamber continuously perfused with medium or perfusion of medium through the intact vasculature. Late follicular development, ovulation, and steroidogenesis can also be examined in these systems. Another approach has been to culture individual follicles isolated by enzymatic or mechanical dissociation. The majority of this research has focused on improving follicular development in vitro. This review will discuss these various culture techniques and some of the results that have been acquired. Recent results from toxicological studies utilizing whole ovarian cultures performed will also be described. Future applications for ovarian and follicular cultures may include in vitro follicular development for eventual production of offspring from frozen ovarian tissue, mechanistic studies related to the impact of endocrine disruptors and ovotoxicants on ovarian function, and further investigations into follicle activation and development.
Vaccine research and developments (1992)

Part 1 Technical advances in vaccine development: lipopeptides and their effects on the immune system - use as vaccine components, Patricia J. Freda Pietrobon and Patrick Kanda HIV-1 virus-like particles as a source of antigen for AIDS vaccines, Anna Aldovini and Richard A. Young chemically defined synthetic immunogens and vaccines by the multiple antigen peptide approach, James P. Tam the use of muramyl peptides as vaccine adjuvants, Gary Ott et al. Part 2 Vaccine development - current status/future directions: contraceptive vaccine development - future prospects, Nancy J. Alexander perspectives in recombinant pertussis toxoid development, W. Neal Burnette. Part 3 Vaccines - clinical and policy development: vaccine clinical trials, John R. La Montagne and George T. Curlin the development of an HIV vaccine - legal and policy aspects, Robert E. Stein.
Inflammatory Mediators and the Failing Heart: A Translational Approach (2003)

Recent studies have identified the importance of proinflammatory mediators in regulating cardiac structure in health and disease. Recent studies suggest that cytokines that are expressed within the myocardium in response to a environmental injury, namely tumor necrosis factor-alpha (TNF), interleukin-1 (IL-1) and the interleukin-6 (IL-6) family of cytokines play an important role in initiating and integrating homeostatic responses within the heart. However, these "stress-activated" cytokines all have the potential to produce cardiac decompensation when expressed at sufficiently high concentrations. Indeed, there is now a growing appreciation that these molecules may play an important role in mediating disease progression in the failing heart. The growing appreciation of the pathophysiological consequences of sustained expression of proinflammatory mediators in pre-clinical and clinical heart failure models culminated in a series of multicenter clinical trials that utilized "targeted" approaches to neutralize tumor necrosis factor (TNF) in patients with moderate to advanced heart failure. However, these targeted approaches have resulted in worsening heart failure, thereby raising a number of important questions about what role, if any, proinflammatory cytokines play in the pathogenesis of heart failure. This review will summarize the tremendous growth of knowledge that has taken place in this field, with a focus on what we have learned from the negative clinical trials, as well as the potential direction of future research in this area.
Structure of an HIV-1–neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer (2014)

The membrane proximal external region (MPER) of HIV-1 glycoprotein (gp) 41 is involved in viral-host cell membrane fusion. It contains short amino acid sequences that are binding sites for the HIV-1 broadly neutralizing antibodies 2F5, 4E10, and 10E8, making these binding sites important targets for HIV-1 vaccine development. We report a high-resolution structure of a designed MPER trimer assembled on a detergent micelle. The NMR solution structure of this trimeric domain, designated gp41-M-MAT, shows that the three MPER peptides each adopt symmetric α-helical conformations exposing the amino acid side chains of the antibody binding sites. The helices are closely associated at their N termini, bend between the 2F5 and 4E10 epitopes, and gradually separate toward the C termini, where they associate with the membrane. The mAbs 2F5 and 4E10 bind gp41-M-MAT with nanomolar affinities, consistent with the substantial exposure of their respective epitopes in the trimer structure. The traditional structure determination of gp41-M-MAT using the Xplor-NIH protocol was validated by independently determining the structure using the DISCO sparse-data protocol, which exploits geometric arrangement algorithms that guarantee to compute all structures and assignments that satisfy the data.