gebhart/patrepeval huggingface dataset:
Protonation state of Asp (Glu)-85 regulates the purple-to-blue transition in bacteriorhodopsin mutants Arg-82----Ala and Asp-85----Glu: the blue form is inactive in proton translocation. (1990)

Previous studies with site-specific mutants of bacteriorhodopsin have demonstrated that replacement of Asp-85 or Arg-82 affects the absorption spectrum. Between pH 5.5 and 7, the Asp-85----Glu and Arg-82----Ala mutants exist in a pH-dependent equilibrium between purple (lambda max approximately 550/540 nm) and blue (lambda max approximately 600/590 nm) forms of the pigment. Measurement of proton transport as a function of wavelength in reconstituted vesicles shows that proton-pumping activities for the above mutants reside exclusively in their respective purple species. For both mutants, formation of the blue form with decreasing pH is accompanied by loss of proton transport activity. The Asp-85----Asn mutant displays a blue chromophore (lambda max approximately 588 nm), is inactive in proton translocation from pH 5 to 7.5, and shows no transition to the purple form. In contrast, the Asp-212----Asn mutant is purple (lambda max approximately 555 nm) and shows no transition to a blue chromophore with decreasing pH. The experiments suggest that (i) the pKa of the purple-to-blue transition is directly influenced by the pKa of the carboxylate at residue 85 and (ii) the relative strengths of interaction between the protonated Schiff base, Asp-85, Asp-212, and Arg-82 make a major contribution to the regulation of color and function of bacteriorhodopsin.
Inorganic Solid-State Electrolytes for Lithium Batteries: Mechanisms and Properties Governing Ion Conduction (2015)

This Review is focused on ion-transport mechanisms and fundamental properties of solid-state electrolytes to be used in electrochemical energy-storage systems. Properties of the migrating species significantly affecting diffusion, including the valency and ionic radius, are discussed. The natures of the ligand and metal composing the skeleton of the host framework are analyzed and shown to have large impacts on the performance of solid-state electrolytes. A comprehensive identification of the candidate migrating species and structures is carried out. Not only the bulk properties of the conductors are explored, but the concept of tuning the conductivity through interfacial effects-specifically controlling grain boundaries and strain at the interfaces-is introduced. High-frequency dielectric constants and frequencies of low-energy optical phonons are shown as examples of properties that correlate with activation energy across many classes of ionic conductors. Experimental studies and theoretical results are discussed in parallel to give a pathway for further improvement of solid-state electrolytes. Through this discussion, the present Review aims to provide insight into the physical parameters affecting the diffusion process, to allow for more efficient and target-oriented research on improving solid-state ion conductors.
Toward QoS-capable virtual private networks (2002)

What is a virtual private network (VPN)? This paper analyzes the various definitions that exist and explains the different viewpoints that have led to their emergence. Furthermore, it describes an evolution from today's Internet-based VPNs to emerging solutions by which quality of service (QoS) for a variety of service classes can be guaranteed. Specifically, this paper discusses two methods of implementing QoS-capable VPNs - one defined over a pure asynchronous transfer mode (ATM) infrastructure and another based on multiprotocol label switching (MPLS), a new protocol that offers a connection-oriented approach to Internet protocol (IP) transport over a variety of infrastructures. In the near term, it might make sense for a service provider to offer VPN services over an existing ATM infrastructure. However, in the long term, as this paper proposes, evolution toward the MPLS-based approach is the course to follow.
Chimeric NKG2D CAR-Expressing T Cell-Mediated Attack of Human Ovarian Cancer Is Enhanced by Histone Deacetylase Inhibition (2013)

NKG2D ligands (NKG2DLs) are widely expressed on ovarian cancers to various degrees, making them attractive targets for immunotherapy. Here, we applied a chimeric antigen receptor (CAR) approach for the targeting of NKG2DLs expressed on human ovarian cancer cells and evaluated the impact of pharmacological upregulation of NKG2DLs on immune recognition. Various NKG2DLs, including MICA/B and ULBP-1, -2, -3, and -4, were expressed at various levels on the surface of all established ovarian cancer cell lines and primary ovarian cancer samples tested. To redirect human T cells against NKG2DLs, an NKG2DL-specific CAR was generated by fusing the extracellular domain of the NKG2D receptor to the 4-1BB costimulatory and CD3-ζ chain signaling domains. In vitro expansion of chimeric NKG2D CAR T cells was delayed compared with untransduced T cells and control CAR T cells; the likely result of fratricide among activated T cells expressing NKG2DLs. However, NKG2D CAR T cells did expand and were selectively enriched during prolonged culture. In coculture, CD4(+) and CD8(+) NKG2D CAR T cells specifically recognized and killed NKG2DL-expressing ovarian cancer cell lines but not NKG2DL-negative cells. Notably, pretreatment of ovarian cancer cells expressing moderate to low levels of NKG2DLs with the histone deacetylase inhibitor sodium valproate (VPA) upregulated NKG2DL cell surface expression and consequently enhanced their immune recognition by chimeric NKG2D CAR T cells. Our results demonstrate that VPA-induced upregulation of NKG2DL expression enhances the immune recognition of ovarian cancer cells by engineered NKG2D CAR T cells, and rationalizes the use of VPA in combination with NKG2DL-targeted immunotherapy in ovarian cancer.
Role of CD4+ T-Lymphocytes in Rejection by Mice of Fetal Pig Proislet Xenografts (1989)

The role of T-lymphocyte subpopulations in the rejection of fetal pig proislet (islet precursor) xenografts in mice was examined with in vivo administration of monoclonal antibodies (MoAbs) to CD4+ (GK 1.5) and CD8+ (49-11.1) T-lymphocyte subsets. The data indicate that the rejection process is T-lymphocyte dependent and mediated by CD4+ T-lymphocytes. The in vivo administration of MoAbs specific for graft-borne pig leukocytes failed to prevent xenograft rejection in fully immunocompetent transplant recipients.
Color constancy under varying illumination (2002)

Illumination is rarely constant in intensity or color throughout a scene. Multiple light sources with different spectra-sun and sky, direct and interreflected light-are the norm. Nonetheless, almost all color constancy algorithms assume that the spectrum of the incident illumination remains constant across the scene. We assume the converse, that illumination does vary, in developing a new algorithm for color constancy. Rather than creating difficulties, varying illumination is in fact a very powerful constraint. Indeed tests of our algorithm using real images of an office scene show excellent results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficiently secure data privacy on hybrid cloud (2013)

The growing concerns about the privacy of data stored in public cloud have hindered the widespread adoption of cloud. On one hand, large part of data, such as medical data, has a lot of images, and this kind of data may be private. On the other hand, the cloud service providers have the full access of data, and they may bleach the data for financial or other reasons. The traditional method to protect the privacy of data is to employ cryptographic algorithms, which unavoidably introduces heavy computation. Another way is hybrid cloud consisting of public and private cloud. The sensitive data is separated from non-sensitive data, and only the non-sensitive data is outsourced to public cloud. If we use hybrid cloud method directly, all the private images have to be stored in private cloud, which makes the adoption of cloud computing meaningless. Besides achieving data privacy, we should reduce computation and storage overhead in private cloud, as well as communication overhead between private and public cloud. In this paper, we propose a novel scheme to achieve the above goals. We test our scheme in real network environments (including Amazon EC2). We also propose a novel algorithm to process private image data. Our experimental results show that: (1) Our algorithm achieves data privacy but only takes about 1/1,000 the time of the AES algorithm. (2) The delay of our hybrid cloud approach (including the private and public cloud communications) is only 3%-5% more compared to the traditional public-cloud-only approach.
Engineering and functional immobilization of opioid receptors (2005)

Opioid receptors, like many G protein-coupled receptors (GPCRs), are notoriously unstable in detergents. We have now developed a more stable variant of the mu-opioid receptor (MOR) and also a method for the immobilization of solubilized, functional opioid receptors on a solid phase (magnetic beads). Starting with the intrinsically more stable kappa-opioid receptor (KOR), we optimized the conditions (i.e. detergents and stabilizing ligands) for receptor extraction from lipid bilayers of HEK293T cells to obtain maximal amounts of functional, immobilized receptor. After immobilization, the ligand binding profile remains the same as observed for the membrane-embedded receptor. For the immobilized wild-type mu-opioid receptor, however, no conditions were found under which ligand binding capacity was retained. To solve this problem, we engineered the receptor chimera KKM where the N-terminus and the first transmembrane helix (TM1) of wild-type MOR is exchanged for the homologous receptor parts of the wild-type KOR. This hybrid receptor behaves exactly as the wild-type MOR in functional assays. Interestingly, the modified MOR is expressed at six times higher levels than wild-type MOR and is similarly stable as wild-type KOR after immobilization. Hence the immobilized MOR, represented by the chimera KKM, is now also amenable for biophysical characterization. These results are encouraging for future stability engineering of GPCRs.
Designing Acceptor Polymers for Organic Photovoltaic Devices (2011)

One of the challenges in the field of organic photovoltaics is developing alternatives to the family of fullerene derivatives that are commonly used as acceptor material but that generally lack strong optical absorption coefficient. We describe the synthesis and optoelectronic properties of three new acceptor electron acceptor polymers that use the alternation of thiophene units and electron-deficient units as a common design theme. The acceptor polymers are combined with poly(3-hexylthiophene) as electron donor material in bulk heterojunction solar cells. The performance of the photovoltaic devices is limited by incomplete exciton dissociation and a sluggish separation of the photogenerated electrons and holes at low fields. The separation is in competition with charge recombination to the triplet state. In addition, the low electron mobility in the acceptor polymers hampers charge collection.
The Splash 2 software environment (2002)

Splash 2 is an attached special purpose parallel processor in which the computing elements are user programmable FPGA devices. The architecture of Splash 2 is designed to accelerate the solution of problems which exhibit at least modest amounts of temporal or data parallelism. Applications are developed by writing behavioral descriptions of algorithms in VHDL, which are then iteratively refined and debugged within the Splash 2 simulator. Once an application is determined to be functionally correct in simulation, it is compiled to a gate list and optimized by logic synthesis. The gate list is then mapped onto the FPGA architecture by automatic placement and routing tools to form a loadable FPGA object module. A C language library and a symbolic debugger comprise the execution environment. The Splash 2 system has been shown to be effective on a variety of applications, including text searching, sequence analysis, and image processing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of human tumor necrosis factor .alpha. derived from recombinant DNA (1987)

Recombinant DNA derived tumor necrosis factor alpha, when expressed at a high level in Escherichia coli, appeared in the pellet and soluble fractions of disrupted cells. The protein was purified from the pellet fraction by solubilizing it in urea and reducing agent and was refolded into a buffer without these additives. The structure of the protein was identical with that purified from the soluble fraction without exposure to both reducing and denaturing agents, as demonstrated by circular dichroism, gel filtration, and sulfhydryl titration. As a reflection of the structural similarity, both purified proteins showed identical cytolytic activity on mouse L929 cells. The protein was characterized as an essentially nonhelical and beta-sheet-rich structure and possibly as a noncovalently associating oligomer. Two cysteine residues form an intrapolypeptide disulfide bond.
Cortically coupled computer vision for rapid image search (2006)

We describe a real-time electroencephalography (EEG)-based brain-computer interface system for triaging imagery presented using rapid serial visual presentation. A target image in a sequence of nontarget distractor images elicits in the EEG a stereotypical spatiotemporal response, which can be detected. A pattern classifier uses this response to reprioritize the image sequence, placing detected targets in the front of an image stack. We use single-trial analysis based on linear discrimination to recover spatial components that reflect differences in EEG activity evoked by target versus nontarget images. We find an optimal set of spatial weights for 59 EEG sensors within a sliding 50-ms time window. Using this simple classifier allows us to process EEG in real time. The detection accuracy across five subjects is on average 92%, i.e., in a sequence of 2500 images, resorting images based on detector output results in 92% of target images being moved from a random position in the sequence to one of the first 250 images (first 10% of the sequence). The approach leverages the highly robust and invariant object recognition capabilities of the human visual system, using single-trial EEG analysis to efficiently detect neural signatures correlated with the recognition event.
Poly[(ι-hydroxyalkyl)thio-α-cyanocinnamates]. Linear polyesters with NLO-phores in the main chain (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPoly[(ι-hydroxyalkyl)thio-α-cyanocinnamates]. Linear polyesters with NLO-phores in the main chainFrancesco Fuso, Anne Buyle Padias, and H. K. HallCite this: Macromolecules 1991, 24, 8, 1710–1713Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/ma00008a002https://doi.org/10.1021/ma00008a002research-articleACS PublicationsRequest reuse permissionsArticle Views87Altmetric-Citations44LEARN 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
Inorganic Janus Nanosheets (2011)

Another face to Janus particles: Silica Janus nanosheets were synthesized by crushing Janus hollow spheres formed by self-assembled materialization of an amphiphilic emulsion interface. The Janus nanosheets serve as solid surfactants and can be used collecting oil or hazardous chemical spills. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Synthesis and Application of Imidazole Derivatives. Synthesis of Pyrrolo[1,2-a]benzimidazoles and Azepino[1,2-a]benzimidazoles. (1991)

4-Methyl-4H-pyrrolo[1, 2-a]benzimidazol-2(1H)-one derivatives (11a-d) were synthesized by intramolecular acylation of 1-carboxymethyl-2, 3-dimethylbenzimidazolium halides (9a and 8b-d) in good yields. Treatment of the iodide (8a) with an excess of refluxing thionyl chloride gave 1, 1, 3-trichloro-4-methyl-4H-pyrrolo[1, 2-a]benzimidazol-2(1H)-one (14). Introduction of electrophiles into the 1-position of 11d and 6-position of 5-methyl-9, 10-dihydro-5H-azepino[1, 2-a]benzimidazol-7(8H)-one (2a) was achieved by successive treatment with lithium diisopropylamide and electrophiles such as methyl iodide and ketones. The azepinone 2a was reacted with various electrophiles to give 6-substituted products in good yields.
Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study (2019)

In our retrospective study, we show that a CNN can assess the human tumor microenvironment and predict prognosis directly from histopathological images.
Efficient oligonucleotide probe selection for pan-genomic tiling arrays (2009)

PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on a single microarray chip. These unique pan-genome tiling arrays provide maximum flexibility for the analysis of both known and uncharacterized strains.
Endostatin, an antiangiogenic drug, induces tumor stabilization after chemotherapy or anti-CD20 therapy in a NOD/SCID mouse model of human high-grade non-Hodgkin lymphoma (2000)

Both chemotherapy and chimeric anti-CD20 monoclonal antibodies are effective agents against B-cell non-Hodgkin lymphoma (NHL). However, patients achieving remission are at risk of relapse. To evaluate the effect of the antiangiogenic drug endostatin used alone and after the administration of cyclophosphamide (CTX) or the anti-CD20 antibody rituximab, we generated a new model of human NHL by transplanting Namalwa cells intraperitoneally into nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. First, we determined the most effective treatment schedule for the drugs assessed. When administered alone, CTX (3 courses of 75 mg/kg of body weight given intraperitoneally), rituximab (3 courses of 25 mg/kg given intraperitoneally), and endostatin (5 courses of 50 μg given subcutaneously) delayed tumor growth, and CTX was the most effective in controlling bulky disease. When given after chemotherapy or immunotherapy, endostatin effectively induced tumor stabilization. When mice given CTX or rituximab on days 3, 5, and 7 after transplantation were randomly assigned to receive endostatin or phosphate-buffered saline on days 15 to 19, tumor growth was prevented in endostatin-treated mice as long as the drug was administered. Furthermore, administration of endostatin on days 25 to 29 after tumor regrowth still induced significant tumor regression, whereas CTX and rituximab were not effective. The specific antiangiogenic action of endostatin was confirmed by in vitro and in vivo studies indicating that the drug inhibited proliferation and induced apoptosis of endothelial (but not of NHL) cells. In conclusion, sequential administration of chemotherapy and endostatin seems promising for treating bulky NHL, and the less toxic sequential administration of rituximab and endostatin is promising for treating limited disease.
The Science of Breeding and Its Application to the Breeder Genetic Algorithm (BGA) (1993)

The breeder genetic algorithm (BGA) models artificial selection as performed by human breeders. The science of breeding is based on advanced statistical methods. In this paper a connection between genetic algorithm theory and the science of breeding is made. We show how the response to selection equation and the concept of heritability can be applied to predict the behavior of the BGA. Selection, recombination, and mutation are analyzed within this framework. It is shown that recombination and mutation are complementary search operators. The theoretical results are obtained under the assumption of additive gene effects. For general fitness landscapes, regression techniques for estimating the heritability are used to analyze and control the BGA. The method of decomposing the genetic variance into an additive and a nonadditive part connects the case of additive fitness functions with the general case.
Combined Genetic and Chemical Capsid Modifications Enable Flexible and Efficient De- and Retargeting of Adenovirus Vectors (2005)

Numerous attempts to target viral gene therapy vectors to specific cells have met with limited success. Here we describe a novel virus vector-targeting platform based on a unique combination of genetic and chemical vector particle modifications to overcome typical restrictions in virus vector targeting. We genetically introduced cysteines at solvent-exposed positions of the adenovirus capsid. The corresponding thiol groups were highly reactive, and we established procedures for controlled covalent coupling to them of protein and nonprotein ligands. After the coupling of transferrin, the particles were efficiently targeted to the transferrin receptor pathway. Depending on the chemistry used, ligands could be coupled under the formation of thioether or disulfide bonds, the latter allowing for separation of ligand and particle after cell entry in the endosome. Furthermore, this technology could be efficiently combined with vector shielding for true retargeting: after amino-PEGylation of the vector particles the genetically introduced thiols were still accessible for ligand coupling, and particles could be retargeted to the transferrin receptor. Since this platform is robust, can be scaled, is compatible with industrial standards, and can integrate chemically diverse molecules as ligands, it may be used for clinical gene therapy and, potentially, also for vaccination.
The link between angiotensin II-mediated anxiety and mood disorders with NADPH oxidase-induced oxidative stress. (2012)

The renin-angiotensin system (RAS) and its active peptide angiotensin II (AngII) have major involvements not only in hypertension but also in mood and anxiety disorders. Substantial evidence supports the notion that AngII acts as a neuromodulator in the brain. In this review, we provide an overview of the link between the RAS and anxiety or mood disorders, and focus on recent advances in the understanding of AngII-linked, NADPH oxidase-derived oxidative stress in the central nervous system, which may underlie pathogenesis of mood and anxiety disorders.