gebhart/patrepeval huggingface dataset:
Correlation between electronic and molecular structure distortions and vibrational properties. II. Amide I modes of NMA–nD2O complexes (2003)

Hydration effects on the molecular structure and amide I mode frequency of a prototype peptide molecule, N-methylacetamide (NMA), when it is solvated by a few water molecules, were investigated by carrying out ab initio calculations for a number of NMA–water complexes. The harmonic frequency shift of the amide I mode in NMA–nD2O (n=1–5) complex was found to originate from the combination of the molecular cubic anharmonicity and displacement of the amide I coordinate when the NMA is hydrated. Using a multivariate least-square fitting method, the effective transition charges of six NMA sites were determined. A brief discussion on how this empirical model can be used to quantitatively describe solvatochromic frequency shift of the NMA amide I mode in solution is presented.
Digital watermarks: Shedding light on the invisible (1998)

Digital media promise rewards-and risk, chiefly in the potential for unauthorized replication and distribution. In the content protection debate, digital watermarks offer one solution.
The hepatitis C virus NS3 serine proteinase and NS4A cofactor: establishment of a cell-free trans-processing assay. (1995)

The hepatitis C virus RNA genome encodes a long polyprotein that is proteolytically processed into at least 10 products. The order of these cleavage products in the polyprotein is NH2-C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B -COOH. A serine proteinase domain located in the N-terminal one-third of nonstructural protein NS3 mediates cleavage at four downstream sites (the 3/4A, 4A/4B, 4B/5A, and 5A/5B sites). In addition to the proteinase catalytic domain, the NS4A protein is required for processing at the 4B/5A site but not at the 5A/5B site. These cleavage events are likely to be essential for virus replication, making the serine proteinase an attractive antiviral target. Here we describe an in vitro assay where the NS3-4A polyprotein, NS3, the serine proteinase domain (the N-terminal 181 residues of NS3), and the NS4A cofactor were produced by cell-free translation and tested for trans-processing of radiolabeled substrates. Polyprotein substrates, NS4A-4B or truncated NS5A-5B, were cleaved in trans by all forms of the proteinase, whereas NS4A was also required for NS4B-5A processing. Proteolysis was abolished by substitution mutations previously shown to inactivate the proteinase or block cleavage at specific sites in vivo. Furthermore, N-terminal sequence analysis established that cleavage in vitro occurred at the authentic 4A/4B site. Translation in the presence of microsomal membranes enhanced processing for some, but not all, proteinase-substrate combinations. Trans-processing was both time and temperature dependent and was eliminated by treatment with a variety of detergents above their critical micelle concentrations. Among many common proteinase inhibitors tested, only high (millimolar) concentrations of serine proteinase inhibitors tosyllysyl chloromethyl ketone and 4-(2-aminoethyl)benzenesulfonyl fluoride inactivated the NS3 proteinase. This in vitro assay should facilitate purification and further characterization of the viral serine proteinase and identification of molecules which selectively inhibit its activity.
Constitutive overexpression of a novel 21 kDa protein by Hodgkin Lymphoma and Aggressive Non-Hodgkin Lymphomas (2008)

The 21 kDa protein detected by clone R23.1 and clone R24.1 mabs is a novel membrane-associated protein that may be a potential marker for the diagnosis and targeted therapy of HL and aggressive T and B cell NHL.
Amplification of Antioxidant Activity of Catechin by Polycondensation with Acetaldehyde (2003)

Catechin exhibits numerous biological and pharmacological effects attributed to antioxidant action. The synthetic poly(catechin)s condensed through acetaldehyde with different molecular weights were assessed in terms of antioxidant activity and enzyme inhibitory activity on the basis of a catechin repeating unit and compared with monomeric catechin. The poly(catechin)s showed great amplification of superoxide scavenging activity, xanthine oxidase (XO) inhibitory activity, and inhibition effects on human low-density lipoprotein oxidation initiated by 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH) as a radical generator on the catechin unit level, compared to monomeric catechin: these activities were proportional to their molecular weights. The reducing power of the polymer was lower than that of monomeric catechin, which decreased with increasing the molecular weight. The polymer also protected endothelial cells from oxidative injury induced by AAPH, with a greater effect expressed on a catechin unit basis than that of the monomer. These results demonstrate that the poly(catechin)s are more potent antioxidant agents and enzyme inhibitors.
Synthesis and Acid Hydrolysis of Monophosphate and Pyrophosphate Esters of Phytanol and Phytol (1973)

Monophytanyl phosphate was synthesized by phosphorylation of phytanol with diphenylphosphoryl monochloride followed by catalytic hydrogenolysis of the phenyl groups; the product was isolated as the dipotassium salt. The phytanyl pyrophosphate was prepared by phosphorylation of phytanol with monophenylphosphoryl dichloride followed by aminolysis and saponification of the resulting phytanylmonophenylphosphoryl monochloride to the phytanyl phosphoramidate. The latter, as the cyclohexylamine salt, was reacted with dioxane diphosphate in the presence of pyridine to give the desired phytanyl pyrophosphate isolated as the tripotassium salt. Alternatively, the phytanyl pyrophosphate was made from phytanyl monophosphate via the phosphomorpholidate. The 2-phytenyl (phytyl) pyrophosphate was synthesized more directly by phosphorylation of phytol with di-(triethylammonium) phosphate in the presence of trichloroacetonitrile in acetonitrile as solvent. The phytyl pyrophosphate and the accompanying phytyl monophosphate were isolated as tri- and diammonium salts, respectively. These mono- and pyrophosphates were characterized by elementary analysis, infrared spectra, and behavior towards acid hydrolysis; the hydrolysis products formed are characteristic of the phytyl or phytanyl phosphate hydrolyzed and may be used for their identification.
Activation of the Keap1/Nrf2 pathway for neuroprotection by electrophillic phase II inducers (2006)

Electrophilic neurite outgrowth-promoting prostaglandin (NEPP) compounds protect neurons from oxidative insults. At least part of the neuroprotective action of NEPPs lies in induction of hemeoxygenase-1 (HO-1), which, along with other phase II enzymes, serve as a defense system against oxidative stress. Here, we found that, by using fluorescent tags and immunoprecipitation assays, NEPPs are taken up preferentially into neurons and bind in a thiol-dependent manner to Keap1, a negative regulator of the transcription factor Nrf2. By binding to Keap1, NEPPs prevent Keap1-mediated inactivation of Nrf2 and, thus, enhance Nrf2 translocation into the nucleus of cultured neuronal cells. In turn, Nrf2 binds to antioxidant/electrophile-responsive elements of the HO-1 promoter to induce HO-1 expression. Consistent with this notion, NEPP induction of an HO-1 reporter construct is prevented if the antioxidant-responsive elements are mutated. We show that NEPPs are neuroprotective both in vitro from glutamate-related excitotoxicity and in vivo in a model of cerebral ischemia/reperfusion injury (stroke). Our results suggest that NEPPs prevent excitotoxicity by activating the Keap1/Nrf2/HO-1 pathway. Because NEPPs accumulate preferentially in neurons, they may provide a category of neuroprotective compounds, distinct from other electrophilic compounds such as tert-butylhydroquinone, which activates the antioxidant-responsive element in astrocytes. NEPPs thus represent a therapeutic approach for stroke and neurodegenerative disorders.
Signal enhancement using beamforming and nonstationarity with applications to speech (2001)

We consider a sensor array located in an enclosure, where arbitrary transfer functions (TFs) relate the source signal and the sensors. The array is used for enhancing a signal contaminated by interference. Constrained minimum power adaptive beamforming, which has been suggested by Frost (1972) and, in particular, the generalized sidelobe canceler (GSC) version, which has been developed by Griffiths and Jim (1982), are the most widely used beamforming techniques. These methods rely on the assumption that the received signals are simple delayed versions of the source signal. The good interference suppression attained under this assumption is severely impaired in complicated acoustic environments, where arbitrary TFs may be encountered. In this paper, we consider the arbitrary TF case. We propose a GSC solution, which is adapted to the general TF case. We derive a suboptimal algorithm that can be implemented by estimating the TFs ratios, instead of estimating the TFs. The TF ratios are estimated by exploiting the nonstationarity characteristics of the desired signal. The algorithm is applied to the problem of speech enhancement in a reverberating room. The discussion is supported by an experimental study using speech and noise signals recorded in an actual room acoustics environment.
Does Thrombin Activatable Fibrinolysis Inhibitor (TAFI) Contribute to Impairment of Fibrinolysis in Patients with Preeclampsia and/or Intrauterine Fetal Growth Retardation? (2002)

Thrombin Activatable Fibrinolysis Inhibitor (TAFI) is a relatively recently described glycoprotein (MM 55 KDa) that can be converted into its active form by the thrombin/thrombomodulin complex and potentially inhibits fibrinolysis. Since it represents a link between coagulation and fibrinolysis, TAFI can be expected to play a part in various clinical conditions associated with a thrombotic tendency. Preeclampsia (PE) and intrauterine fetal growth retardation (IUFGR) are fairly common complications of pregnancy that are characterized by hemostatic abnormalities. TAFI antigen and its influence on hemostasis was investigated in 46 women with PE and/or IUFGR and in 16 normal pregnancies. We found a significant decrease of TAFI antigen in the patient group. Using the recently described method Overall Hemostatic Potential (OHP) in plasma we measured clot lysis time (CLT) and overall fibrinolytic potential (OFP). We found that CLT is prolonged and OFP decreased in patients with PE and/or IUFGR. Since OFP did not increase after addition of the specific inhibitor of TAFI (potato tuber carboxypeptidase inhibitor), it seems that TAFI does not contribute to the impairment of fibrinolysis in these patients. Since serum albumin was decreased together with presence of proteinuria and aminotransferases were increased in the patients, it seems that one explanation for the decrease in TAFI could be reduced hepatic synthesis and an increased loss in urine. It an be speculated that this mechanism can prevent more serious thrombotic complications in patients with PE and/or IUFGR.
Large-scale vehicle re-identification in urban surveillance videos (2016)

Vehicle, as a significant object class in urban surveillance, attracts massive focuses in computer vision field, such as detection, tracking, and classification. Among them, vehicle re-identification (Re-Id) is an important yet frontier topic, which not only faces the challenges of enormous intra-class and subtle inter-class differences of vehicles in multicameras, but also suffers from the complicated environments in urban surveillance scenarios. Besides, the existing vehicle related datasets all neglect the requirements of vehicle Re-Id: 1) massive vehicles captured in real-world traffic environment; and 2) applicable recurrence rate to give cross-camera vehicle search for vehicle Re-Id. To facilitate vehicle Re-Id research, we propose a large-scale benchmark dataset for vehicle Re-Id in the real-world urban surveillance scenario, named “VeRi”. It contains over 40,000 bounding boxes of 619 vehicles captured by 20 cameras in unconstrained traffic scene. Moreover, each vehicle is captured by 2~18 cameras in different viewpoints, illuminations, and resolutions to provide high recurrence rate for vehicle Re-Id. Finally, we evaluate six competitive vehicle Re-Id methods on VeRi and propose a baseline which combines the color, texture, and highlevel semantic information extracted by deep neural network.
Real time google and live image search re-ranking (2008)

Nowadays, web-scale image search engines (e.g. Google, Live Image Search) rely almost purely on surrounding text features. This leads to ambiguous and noisy results. We propose to use adaptive visual similarity to re-rank the text-based search results. A query image is first categorized into one of several predefined intention categories, and a specific similarity measure is used inside each category to combine image features for re-ranking based on the query image. Extensive experiments demonstrate that using this algorithm to filter output of Google and Live Image Search is a practical and effective way to dramatically improve the user experience. A real-time image search engine is developed for on-line image search with re-ranking: http://mmlab.ie.cuhk.edu.hk/intentsearch
Adenoviral vector type 26 encoding Zika virus (ZIKV) M-Env antigen induces humoral and cellular immune responses and protects mice and nonhuman primates against ZIKV challenge (2018)

In 2015, there was a large outbreak of Zika virus (ZIKV) in Brazil. Despite its relatively mild impact on healthy adults, ZIKV infection during pregnancy has been associated with severe birth defects. Currently, there is no ZIKV vaccine available, but several vaccine candidates based on the ZIKV membrane (M) and envelope (Env) structural proteins showed promising results in preclinical and clinical studies. Here, the immunogenicity and protective efficacy of a non-replicating adenoviral vector type 26 (Ad26) that encodes the ZIKV M-Env antigens (Ad26.ZIKV.M-Env) was evaluated in mice and non-human primates (NHP). Ad26.ZIKV.M-Env induced strong and durable cellular and humoral immune responses in preclinical models. Humoral responses were characterized by Env-binding and ZIKV neutralizing antibody responses while cellular responses were characterized by ZIKV reactive CD4+ and CD8+ T cells. Importantly, a single immunization with a very low dose of 4x107 vp of Ad26.ZIKV.M-Env protected mice from ZIKV challenge. In NHP, a single immunization with a typical human dose of 1x1011 vp of Ad26.ZIKV.M-Env also induced Env-binding and ZIKV neutralizing antibodies and Env and M specific cellular immune responses that associated with complete protection against viremia from ZIKV challenge as measured in plasma and other body fluids. Together these data provide the rationale to progress the Ad26.ZIKV.M-Env candidate vaccine to clinical testing.
Emerging therapies in gastrointestinal cancers (2006)

Members of the receptor tyrosine kinase family, that include EGFR, ErbB-2/HER-2, ErbB-3/HER-3 and ErbB-4/HER-4, are frequently implicated in experimental models of epithelial cell neoplasia as well as in human cancers. Therefore, interference with the activation of these growth factor receptors represents a promising strategy for development of novel and selective anticancer therapies. Indeed, a number of inhibitors that target either EGFR or HER-2, with the exception of a few that target both; have been developed for treatment of epithelial cancers. Since most solid tumors express different ErbB receptors and/or their ligands, identification of inhibitor(s), targeting multiple EGFR family members may provide a therapeutic benefit to a broader patient population. Here we describe the significance of an ErbB family of receptors in epithelial cancers, and summarize different available therapeutics targeting these receptors. It also emphasizes the need to develop pan-ErbB inhibitors and discusses EGF-Receptor Related Protein, a recently isolated negative regulator of EGFR as a potential pan-ErbB therapeutic for a wide variety of epithelial cancers.
Preparation of Size Controlled Nanometric Spheres of Colloidal Silica for Synthetic Opal Manufacture (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Power-conscious design of wireless circuits and systems (2000)

The great importance of power consciousness is well understood in mobile wireless communications. However, with growing experience the fundamental principles underlying power conscious design of RF circuits, systems, and networks are only now becoming known. Using as example ultralow-power wireless devices for messaging such as paging receivers and wireless sensor networks, the first part of this paper presents the relationship between current consumption and dynamic range of low-noise amplifiers, mixers, oscillators, and active filters. The second part of the paper covers issues of modulation, protocols, and networking that would be required in dense networks of wireless sensors, which communicate using very little energy. These ideas are expected to find use in most forms of digital wireless communications.
Covalent structure of a nitrogen mustard-induced DNA interstrand cross-link: an N7-to-N7 linkage of deoxyguanosine residues at the duplex sequence 5'-d(GNC) (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCovalent structure of a nitrogen mustard-induced DNA interstrand cross-link: an N7-to-N7 linkage of deoxyguanosine residues at the duplex sequence 5'-d(GNC)Stacia M. Rink, Marjorie S. Solomon, Matthew J. Taylor, Sharanabasava B. Rajur, Larry W. McLaughlin, and Paul B. HopkinsCite this: J. Am. Chem. Soc. 1993, 115, 7, 2551–2557Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/ja00060a001https://doi.org/10.1021/ja00060a001research-articleACS PublicationsRequest reuse permissionsArticle Views843Altmetric-Citations110LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Type 2 Diabetes Mellitus: Update on Diagnosis, Pathophysiology, and Treatment (1999)

S million individuals in the United States with type 2 diabetes mellitus and an additional 30–40 million with impaired glucose tolerance result in health care costs exceeding 100 billion dollars annually (1). Treatment is predominantly directed at microvascular and macrovascular complications (2). In type 1 diabetes mellitus the relationship between glycemic control and microvascular complications has been well established (3). The relationship between tight glycemic control and microvascular disease in type 2 diabetes mellitus appears to be established in the recently completed United Kingdom prospective diabetes study (4, 5). Despite the morbidity and mortality associated with retinopathy, nephropathy, and neuropathy, cardiovascular disease remains the leading cause of death in type 2 diabetes mellitus (6, 7). Consequently, the treatment of confounding risk factors of obesity, hypertension, and hyperlipidemia assumes major importance and must be coordinated with good glycemic control for reduction in total mortality in type 2 diabetes mellitus (6–11). Based on the emerging relationship between the degree of glycemic control and microvascular complications as well as the contribution of hyperglycemia in the development of macrovascular disease, it is the purpose of this review to summarize the current state of knowledge to provide a rational basis for the treatment of type 2 diabetes mellitus.
Taking control of gene expression with light-activated oligonucleotides (2007)

The recent development of caged oligonucletides that are efficiently activated by ultraviolet (UV) light creates opportunities for regulating gene expression with very high spatial and temporal resolution. By selectively modulating gene activity, these photochemical tools will facilitate efforts to elucidate gene function and may eventually serve therapeutic aims. We demonstrate how the incorporation of a photocleavable blocking group within a DNA duplex can transiently arrest DNA polymerase activity. Indeed, caged oligonucleotides make it possible to control many different protein-oligonucleotide interactions. In related experiments, hybridization of a reverse complementary (antisense) oligodeoxynucleotide to target mRNA can inhibit translation by recruiting endogenous RNases or sterically blocking the ribosome. Our laboratory recently synthesized caged antisense oligonucleotides composed of phosphorothioated DNA or peptide nucleic acid (PNA). The antisense oligonucleotide, which was attached to a complementary blocking oligonucleotide strand by a photocleavable linker, was blocked from binding target mRNA. This provided a useful method for photomodulating hybridization of the antisense strand to target mRNA. Caged DNA and PNA oligonucleotides have proven effective at photoregulating gene expression in cells and zebrafish embryos.
Golgi Network Targeting and Plasma Membrane Internalization Signals in Vaccinia Virus B5R Envelope Protein (2000)

The vaccinia virus B5R type I integral membrane protein accumulates in the Golgi network, from where it becomes incorporated into the envelope of extracellular virions. Our objective was to determine the domains of B5R responsible for Golgi membrane targeting in the absence of other viral components. Fusion of an enhanced green fluorescent protein to the C terminus of B5R allowed imaging of the chimeric protein without altering intracellular trafficking and Golgi network localization in transfected cells. Deletion or swapping of B5R domains with corresponding regions of the vesicular stomatitis virus G protein, which is targeted to the plasma membrane, indicated that (i) the N-terminal extracellular domain of B5R had no specific role in Golgi apparatus localization, (ii) the transmembrane domain of B5R was sufficient for exiting the endoplasmic reticulum, and (iii) removal of the cytoplasmic tail impaired Golgi network localization and increased the accumulation of B5R in the plasma membrane. Further experiments demonstrated that the cytoplasmic tail mediated internalization of B5R from the plasma membrane, suggesting a retrieval mechanism. Mutagenesis revealed residues required for Golgi membrane localization and efficient plasma membrane retrieval of the B5R protein: a tyrosine at residue 310 and two adjacent leucines at residues 315 and 316.