gebhart/patrepeval huggingface dataset:
How can the solvent affect enzyme enantioselectivity? (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHow can the solvent affect enzyme enantioselectivity?Paul A. Fitzpatrick and Alexander M. KlibanovCite this: J. Am. Chem. Soc. 1991, 113, 8, 3166–3171Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/ja00008a054https://doi.org/10.1021/ja00008a054research-articleACS PublicationsRequest reuse permissionsArticle Views1050Altmetric-Citations316LEARN 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
Geometrically Controlled Endothelial Tubulogenesis in Micropatterned Gels (2010)

We present a novel approach to control endothelial tubulogenesis by spatially patterning cells within micromolded collagen gels. Endothelial cells cultured within microscale channels that were filled with collagen gel organized into tubes with lumens within 24-48 h of seeding. These tubes extended up to 1 cm in length, and exhibited cell-cell junction formation characteristic of early stage capillary vessels. Tube diameter could be controlled by varying collagen concentrations or channel width. The geometry of the microfabricated template also could be used to guide the development of branches during tube formation, allowing for the generation of more complex capillary architectures. Time-lapse imaging of tube formation revealed a highly dynamic process involving coalescence of endothelial cells, reorganization and alignment of collagen fibers into a central core, and arrangement of cells into cords. This platform may be of use to generate geometrically defined vascular networks for tissue engineering applications as well as a means to better understand the process of endothelial tubulogenesis.
Remote ischemic preconditioning (2012)

Since cardiac surgery began, surgeons have aimed to find methods of minimizing myocardial injury resulting from ischemia and reperfusion. The concept of somehow conditioning the heart in order to attenuate ischemia and reperfusion-related injury has evolved in cardiovascular research over decades, from ischemic preconditioning and postconditioning to, more recently, remote ischemic preconditioning (and postconditioning). Although many strategies have proven to be beneficial in the experimental arena, a few have been successfully translated into clinical practice. Remote ischemic preconditioning, with the use of brief episodes of ischemia and reperfusion of vascular territories remote from the heart, has been shown convincingly to decrease myocardial injury. To date, the translation of this powerful innate mechanism of myocardial and/or multiorgan protection from the animal lab to the operating theatre, using transient occlusion of blood flow to the upper limb with a blood-pressure cuff before cardiac surgery, has shown promising results, with several proof-of-principle and first randomized controlled clinical trials reporting benefits for patients undergoing cardiac surgery. If the efficacy of remote ischemic preconditioning can be conclusively proven, the clinical applications in cardiac surgery could be almost infinite, providing multiorgan protection in various surgical scenarios.
Lithium Assisted “Dissolution–Alloying” Synthesis of Nanoalloys from Individual Bulk Metals (2016)

We report new fundamental chemistry involved in the synthesis of bimetallic nanoalloys via dissolving the pure bulk transition metals in molten lithium. It is revealed at the atomic level that when two pure bulk transition metals such as Pd and Pt are placed in molten lithium (∼200 °C), they undergo a dissolution process in which the metal–metal bonds in pure bulk transition metals are completely ruptured, which results in the existence of individual Pd and Pt atoms surrounded by lithium atoms, as is evident by synchrotron X-ray adsorption techniques. Then, upon the conversion of metal lithium to LiOH in humid air, the Pd and Pt atoms undergo an alloying process to aggregate into nanoalloys. This method was further expanded to include PdZn, which is notoriously difficult to prepare via traditional nanoalloy synthesis methods due to the easily oxidizable Zn component. The constantly reducing environment of metallic Li allowed for preparation of PdZn nanoalloys with minimal Zn oxidation via dissolution-alloying of individual bulk transition metals in molten lithium. Additionally, this lithium assisted “dissolution-alloying” method bypasses many complications intrinsic to conventional ion reduction-based nanoalloy synthesis including the necessity of ligated metal ions, the use of proper reducing agents and dispersing surfactants, and the presence of segregated phases due to different reduction potentials of the constituent metal ions.
Molecular dissection of nucleolin's role in growth and cell proliferation: new insights (1999)

Cells require optimum protein synthetic activity in order to support cell proliferation, maintain homeostatic and metabolic integrity, and repair damage. Since growth depends on protein synthesis through ribosome biogenesis, the control of biosynthesis of ribosomes is necessarily a key element for control of growth. Nucleolin is a major nucleolar protein of exponentially growing eukaryotic cells, which is directly involved in the regulation of ribosome biogenesis and maturation. The highly conserved nucleolin contains three major domains through which it controls the organization of nucleolar chromatin, packaging of pre-RNA, rDNA transcription, and ribosome assembly. Numerous reports have implicated the involvement of nucleolin either directly or indirectly in the regulation of cell proliferation and growth, cytokinesis, replication, embryogenesis, and nucleogenesis. Nucleolin, an RNA binding protein, is also an autoantigen, a transcriptional repressor, and a switch region targeting factor. In addition, nucleolin exhibits autodegradation, DNA and RNA helicase activities, and DNA-dependent ATPase activity. An interesting aspect of nucleolin action is that it is a target for regulation by proteolysis, methylation, ADP-ribosylation, and phosphorylation by CKII, cdc2, PKC-xi, cyclic AMP-dependent protein kinase, and ecto-protein kinase. For these and other reasons, nucleolin is fundamental to the survival and proliferation of cells. Considerable progress has been made in recent years with the identification of new nucleolin binding proteins that may mediate these many nucleolin-dependent functions. Nucleolin also functions as a cell surface receptor, where it acts as a shuttling protein between cytoplasm and nucleus, and thus can even provide a mechanism for extracellular regulation of nuclear events. Exploration of the regulation of this multifaceted protein in a remarkable number of diverse functions is challenging.
Sperm from a Variety of Mammalian Species Express β1,4-Galactosyltransferase on their Surface1 (1997)

In mice, initial gamete recognition is mediated by the binding of sperm surface beta1,4-galactosyltransferase (GalTase) to a glycoprotein of the zona pellucida, ZP3. When sperm bind to the zona pellucida, ZP3 induces the acrosome reaction by aggregating GalTase. The acrosome reaction releases acrosomal enzymes allowing sperm to pass through the zona pellucida, bind to the egg membrane, and activate development. In addition to GalTase, there is evidence that other sperm proteins may also bind ZP3. Although fertilization in the mouse is morphologically similar to fertilization in most other mammalian species, the degree of parallelism at the molecular level is not well defined. Less information is available about the molecular details of fertilization in other species. The aim of this work was to determine whether sperm from other mammalian species express GalTase on their surface. We performed GalTase enzyme assays on sperm from six species, and all six expressed GalTase on their surface. The amounts of GalTase varied between species. Guinea pig, mouse, and rat sperm had higher levels of GalTase than bovine, porcine, and rabbit sperm. GalTase was localized by immunofluorescence on live and fixed sperm to the anterior portion of the sperm head in all species examined. This is the expected location for a receptor that binds the zona pellucida. Biotinylation of sperm surface proteins confirmed that GalTase detected by immunofluorescence and enzyme assay was expressed on the sperm surface. These results demonstrate that various mammalian species express GalTase on their surface and that it is found in the proper location to bind to the zona pellucida.
Visual arrestins in olfactory pathways of Drosophila and the malaria vector mosquito Anopheles gambiae (2002)

Arrestins are important components for desensitization of G protein-coupled receptor cascades that mediate neurotransmission as well as olfactory and visual sensory reception. We have isolated AgArr1, an arrestin-encoding cDNA from the malaria vector mosquito, Anopheles gambiae, where olfaction is critical for vectorial capacity. Analysis of AgArr1 expression revealed an overlap between chemosensory and photoreceptor neurons. Furthermore, an examination of previously identified arrestins from Drosophila melanogaster exposed similar bimodal expression, and Drosophila arrestin mutants demonstrate impaired electrophysiological responses to olfactory stimuli. Thus, we show that arrestins in Drosophila are required for normal olfactory physiology in addition to their previously described role in visual signaling. These findings suggest that individual arrestins function in both olfactory and visual pathways in Dipteran insects; these genes may prove useful in the design of control strategies that target olfactory-dependent behaviors of insect disease vectors.
Rapid, sequence-specific detection of unpurified PCR amplicons via a reusable, electrochemical sensor (2006)

We report an electrochemical method for the sequence-specific detection of unpurified amplification products of the gyrB gene of Salmonella typhimurium. Using an asymmetric PCR and the electrochemical E-DNA detection scheme, single-stranded amplicons were produced from as few as 90 gene copies and, without subsequent purification, rapidly identified. The detection is specific; the sensor does not respond when challenged with control oligonucleotides based on the gyrB genes of either Escherichia coli or various Shigella species. In contrast to existing sequence-specific optical- and capillary electrophoresis-based detection methods, the E-DNA sensor is fully electronic and requires neither cumbersome, expensive optics nor high voltage power supplies. Given these advantages, E-DNA sensors appear well suited for implementation in portable PCR microdevices directed at, for example, the rapid detection of pathogens.
Human genome contains four genes homologous to transforming genes of Harvey and Kirsten murine sarcoma viruses. (1982)

Harvey and Kirsten murine sarcoma viruses each encode a structurally and functionally related 21-kilodalton protein (p21), which is the transforming protein of each virus. Using probes from the 0.9-kilobase (kb) p21-coding region of each virus (called v-Ha-ras and v-Ki-ras, respectively), we have molecularly cloned from normal human genomic DNA the sequences that hybridize to these probes. Four evolutionarily divergent restriction endonuclease fragments were isolated. Two hybridized preferentially to v-Ha-ras and were designated human c-Ha-ras1 and c-Ha-ras2; two hybridized preferentially to v-Ki-ras and were called c-Ki-ras1 and c-Ki-ras2. Human c-Ha-ras1 contained 0.9 kb of sequence homologous with v-Ha-ras interspersed with three intervening sequences; this gene was closely related to a previously cloned rat c-Ha-ras gene that also contained intervening sequences. Human c-Ha-ras2 was more divergent from v-Ha-ras and also hybridized poorly to human c-Ha-ras1. One c-Ki-ras gene contained 0.9 kb homologous to v-Ki-ras and had one intervening sequence, whereas the other contained only 0.3 kb homologous to v-Ki-ras. The results indicated that human DNA contains several copies of the c-ras family and that c-Ha-ras1 (with intervening sequences) was more highly conserved evolutionarily than was c-Ha-ras2.
Characterizing Driving Styles with Deep Learning (2016)

Characterizing driving styles of human drivers using vehicle sensor data, e.g., GPS, is an interesting research problem and an important real-world requirement from automotive industries. A good representation of driving features can be highly valuable for autonomous driving, auto insurance, and many other application scenarios. However, traditional methods mainly rely on handcrafted features, which limit machine learning algorithms to achieve a better performance. In this paper, we propose a novel deep learning solution to this problem, which could be the first attempt of extending deep learning to driving behavior analysis based on GPS data. The proposed approach can effectively extract high level and interpretable features describing complex driving patterns. It also requires significantly less human experience and work. The power of the learned driving style representations are validated through the driver identification problem using a large real dataset.
HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis (2013)

The ten-eleven translocation (TET) family of methylcytosine dioxygenases initiates demethylation of DNA and is associated with tumorigenesis in many cancers; however, the mechanism is mostly unknown. Here we identify upstream activators and downstream effectors of TET1 in breast cancer using human breast cancer cells and a genetically engineered mouse model. We show that depleting the architectural transcription factor high mobility group AT-hook 2 (HMGA2) induces TET1. TET1 binds and demethylates its own promoter and the promoter of homeobox A (HOXA) genes, enhancing its own expression and stimulating expression of HOXA genes including HOXA7 and HOXA9. Both TET1 and HOXA9 suppress breast tumor growth and metastasis in mouse xenografts. The genes comprising the HMGA2-TET1-HOXA9 pathway are coordinately regulated in breast cancer and together encompass a prognostic signature for patient survival. These results implicate the HMGA2-TET1-HOX signaling pathway in the epigenetic regulation of human breast cancer and highlight the importance of targeting methylation in specific subpopulations as a potential therapeutic strategy.
Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis. (1991)

Processing of the putative structural proteins of hepatitis C virus was examined by using an in vitro expression system. An RNA transcript for cell-free translation was prepared from a cDNA construct that encompasses the region encoding the 980 amino-terminal residues of the viral polyprotein precursor. Processing of the in vitro translation product proceeded cotranslationally in the presence of microsomal membranes and generated four major membrane-associated products. Two of these four major products, named gp35 and gp70, were shown to be transported into microsomes and heavily glycosylated, suggesting that the processing events are partly mediated by the signal peptidase of the endoplasmic reticulum. The other two products, p19 and p21, were probably associated with the outer surface of the microsomal membrane. Analysis of processed proteins translated from a series of truncated forms of the cDNA construct as well as determination of amino-terminal amino acid sequences of gp35 and gp70 indicated that these four products are arranged from the amino-terminal end of the polyprotein precursor in the order: NH2-p22-gp35-gp70-p19. Both gp35 and gp70 could be candidates of initially processed forms of envelope proteins of the hepatitis C virus.
zFabric: How to virtualize lossless ethernet? (2014)

Converged Enhanced Ethernet (CEE) is a crucial step in embracing storage, cluster, and high-performance computing fabrics under a common network. However, the adoption of lossless CEE in virtualized clusters is hindered by the lack of network hypervisor software that addresses the major issues of losslessness, i.e., head-of-line blocking and saturation trees. Our objective is to design a hypervisor that prevents miscon-figured or malicious virtual machines from filling the lossless network with stalled packets, thus compromising tenant isolation. Furthermore, we observe that current hypervisors perform compulsory isolation, management, and mobility functions, but introduce new bottlenecks on the data-path. By taking advantage of the lossless fabric, we deconstruct the existing virtualized networking stack into its core functions and consolidate them into zFabric, an efficient hypervisor that meets our aforementioned goals. To demonstrate zFabric's benefits, we evaluate a prototype implementation on a datacenter testbed. Besides resolving head-of-line blocking, zFabric improves throughputs for long flows by up to 56%, lowers CPU utilization by up to 63%, and shortens completion times by up to 7x for partition-aggregate queries when compared with current virtualized TCP stacks.
Receptor imaging: application to MR imaging of liver cancer. (1990)

A new contrast agent for magnetic resonance (MR) imaging, directed to asialoglycoprotein (ASG) receptors on hepatocytes, was used for detection of liver cancer in rats. Ultrasmall superparamagnetic (mean size, 12 nm) particles of iron oxide (USPIOs) were targeted to ASG receptors by coating particles with arabinogalactan (AG). Liver T2 relaxation times decreased more effectively after a single intravenous administration of AG-USPIO than after an equal dose of a conventional superparamagnetic liver MR contrast agent (AMI-25; mean size, 72 nm). Receptor affinity studies demonstrated that receptor-mediated attachment and subsequent cellular endocytosis do not occur in primary malignant (hepatocellular carcinoma) or metastatic (adenocarcinoma) tumors, because the surface ASG receptors are lost during malignant dedifferentiation. In vitro relaxation and in vivo MR imaging experiments of liver tumors show that targeting USPIO to hepatocytes rather than to the mononuclear phagocytic system allows a considerable dose reduction, increases tumor-liver contrast, and potentially allows distinction of ASG-positive (benign hepatocellular) and ASG-negative (malignant hepatocellular) tumors.
Progresses towards safe and efficient gene therapy vectors (2015)

The emergence of genetic engineering at the beginning of the 1970's opened the era of biomedical technologies, which aims to improve human health using genetic manipulation techniques in a clinical context. Gene therapy represents an innovating and appealing strategy for treatment of human diseases, which utilizes vehicles or vectors for delivering therapeutic genes into the patients' body. However, a few past unsuccessful events that negatively marked the beginning of gene therapy resulted in the need for further studies regarding the design and biology of gene therapy vectors, so that this innovating treatment approach can successfully move from bench to bedside. In this paper, we review the major gene delivery vectors and recent improvements made in their design meant to overcome the issues that commonly arise with the use of gene therapy vectors. At the end of the manuscript, we summarized the main advantages and disadvantages of common gene therapy vectors and we discuss possible future directions for potential therapeutic vectors.
A low-power low-noise direct-conversion front-end with digitally assisted IIP2 background self calibration (2010)

Direct conversion receivers offer a high level of integration for multiband applications. For standards operating in full duplex, like WCDMA, a very high IIP2 is needed due to transmit signal leakage. Several circuit, compensation and calibration techniques to improve the IIP2 have been developed, but they usually result in a trade-off between IIP2, area, power and other specifications [1,2]. The IIP2 is very sensitive to manufacturing variations and operating conditions such as supply voltage, LO power or frequency, and temperature. We present a robust automatic background self-calibration technique with minimal overhead and performance penalties on the receiver front-end or baseband due to its digital implementation (Fig. 3.8.1). Such digital IIP2 calibration is also free of mismatch. The 0.13µm 1.8GHz CMOS RF front-end without external filter between LNA and mixer has an IIP2 better than 60dBm-sufficient for WCDMA applications [3]- with a state-of-the-art noise figure and power consumption.
Absorption of high-energy cosmic photons through double-pair production in photon--photon collisions (1973)

At photon energies above 7.2 x 1020 eV, absorption by γ + γ' → 2 e+ + 2 e– dominates that from the lower-order process γ + γ' → e+ + e– for high-energy photons traversing a 2.8 K blackbody photon gas. Existence of the 2 e+, 2 e– process and the cosmic blackbody radiation thus guarantees that the universe is opaque for all photon energies above 1014 eV. The question of single-pair production in collisions with cosmic radio-wave photons is discussed, and the uncertainty in our knowledge of the important low-frequency end of the radio spectrum is emphasized. Other processes (γ + γ' → muons, hadrons, etc.) are discussed briefly, and it is concluded that they are of minor importance.
Allylbarium Reagents: Unprecedented Regio- and Stereoselective Allylation Reactions of Carbonyl Compounds (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAllylbarium Reagents: Unprecedented Regio- and Stereoselective Allylation Reactions of Carbonyl CompoundsAkira Yanagisawa, Shigeki Habaue, Katsutaka Yasue, and Hisashi YamamotoCite this: J. Am. Chem. Soc. 1994, 116, 14, 6130–6141Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/ja00093a010https://doi.org/10.1021/ja00093a010research-articleACS PublicationsRequest reuse permissionsArticle Views2492Altmetric-Citations145LEARN 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