gebhart/patrepeval huggingface dataset:
Vibrational Assignment of Torsional Normal Modes of Rhodopsin:  Probing Excited-State Isomerization Dynamics along the Reactive C11C12 Torsion Coordinate (1998)

The resonance Raman spectrum of the 11-cis retinal protonated Schiff base chromophore in rhodopsin exhibits low-frequency normal modes at 93, 131, 246, 260, 320, 446, and 568 cm-1. Their relatively strong Raman activities reveal that the photoexcited chromophore undergoes rapid nuclear motion along torsional coordinates that may be involved in the 200-fs isomerization about the C11C12 bond. Resonance Raman spectra of rhodopsins regenerated with isotopically labeled retinal derivatives and demethyl retinal analogues were obtained in order to determine the vibrational character of these low-frequency modes and to assign the C11C12 torsional mode. 13C substitutions of atoms in the C12−C13 or C13C14 bond cause the 568-cm-1 mode to shift by ∼8 cm-1, and deuteration of the C11C12 bond downshifts the 568- and 260-cm-1 modes by ∼35 and 5 cm-1, respectively. The magnitudes of these shifts are consistent with those calculated for modes containing significant C11C12 torsional character. Thus, we assign the 568-cm-1 mode to a localized C11C12 torsion and the 260-cm-1 mode to a more delocalized torsional vibration involving coordinates from C10 to C13. Consistent with these assignments, these two modes are not Raman active in 13-demethyl, 11-cis rhodopsin which has a planar C10···C13 geometry. Furthermore, the relative Raman scattering strengths of the 260- and 568-cm-1 modes are ∼2-fold higher with preresonant excitation. These data quantitate the instantaneous torsional dynamics of the chromophore about its C11C12 bond on the S1 surface and indicate that the isomerization process is facilitated by vibronic coupling of the S1 and S2 surfaces via C11C12 torsional distortion, which reduces the excited-state barrier along the reaction trajectory. We have also examined the low-frequency Raman spectrum of the trans primary photoproduct, bathorhodopsin, and discuss the relevance of its low-frequency torsional modes at ∼54, 92, 128, 151, 262, 276, 324, and 376 cm-1 to the observed femtosecond photochemical dynamics.
Binding Mode of CpG Oligodeoxynucleotides to Nanoparticles Regulates Bifurcated Cytokine induction via Toll-like Receptor 9 (2012)

The interaction of cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs) with Toll-like receptor 9 (TLR9) activates the immune system. Multimeric class A CpG ODNs induce interferon-α (IFN-α) and, to a lesser extent, interleukin-6. By contrast, monomeric class B CpG ODNs induce interleukin-6 but not IFN-α. This difference suggests that the multimerization of CpG ODN molecules is a key factor in IFN-α induction. We multimerized class B CpG ODN2006x3-PD molecules that consist entirely of a phosphodiester backbone onto quantum dot silicon nanoparticles with various binding modes. Herein, we present the binding mode-dependent bifurcation of cytokine induction and discuss its possible mechanism of CpG ODN and TLR9 interaction. Our discoveries also suggest that nanoparticles play roles in not only delivery of CpG ODNs but also control of CpG ODN activity.
Security in service-oriented vehicular networks (2009)

Service-oriented vehicular networks support diverse infrastructure-based commercial services including Internet access, real-time traffic concerns, video streaming, and content distribution. The success of service delivery in vehicular networks depends on the underlying communication system to enable the user devices to connect to a large number of communicating peers and even to the Internet. This poses many new research challenges, especially in the aspects of security, user privacy, and billing. In this article we first identify the key requirements of authentication, privacy preservation, and billing for service delivery in vehicular networks. We then review the existing industrial and academic efforts on service- oriented vehicular networks. We also point out two security challenges, minimizing vehicleto- infrastructure authentication latency and distributed public key revocation, which are considered among the most challenging design objectives in service-oriented vehicular networks. A novel fast vehicle-to-infrastructure authentication based on a vehicle mobility prediction scheme and an infrastructure-based short-time certificate management scheme are then proposed to address these two challenges.
Cardiac sodium channel mutations in patients with long QT syndrome, an inherited cardiac arrhythmia (1995)

Long QT syndrome (LQT) is an inherited cardiac disorder that causes syncope, seizures and sudden death from ventricular tachyarrhythmias. We used single-strand conformation polymorphism (SSCP) and DNA sequence analyses to identify mutations in the cardiac sodium channel gene, SCN5A, in affected members of four LQT families. These mutations include two identical intragenic deletions and two missense mutations. These data suggest that SCN5A mutations cause LQT. The location and character of these mutations suggest that this form of LQT results from a delay in cardiac sodium channel fast inactivation or altered voltage-dependence of inactivation.
Crystal structures of diketopiperazines containing α‐aminoisobutyric acid: Cyclo(Aib‐Aib) and cyclo(Aib‐L‐Ile) (1982)

Abstract The crystal and molecular structures of two α‐aminoisobutyric acid (Aib)‐containing diketopiperazines, cyclo(Aib‐Aib) 1 and cyclo(Aib‐ L ‐Ile) 2 , are reported. Cyclo(Aib‐Aib) crystallizes in the space group P 1 with a = 5.649(3), b = 5.865(2), c = 8.363(1), α = 69.89(6), β = 113.04(8), γ = 116.0(3), and Z = 1, while 2 occurs in the space group P2 1 2 1 2 1 with a = 6.177(1), b = 10.791(1), c = 16.676(1), and Z = 4. The structures of 1 and 2 have been refined to final R factors of 0.085 and 0.086, respectively. In both structures the diketopiperazine ring shows small but significant deviation from planarity. A very flat chair conformation is adopted by 1, in which the C α atoms are displaced by 0.07 Å on each side of the mean plane, passing through the other four atoms of the ring. Cyclo(Aib‐Ile) favors a slight boat conformation, with Aib C α and Ile C α atoms displaced by 0.11 and 0.05 Å on the same side of the mean plane formed by the other ring atoms. Structural features in these two molecules are compared with other related diketopiperazines.
[Effect of smoking on enzyme composition and neutrophil function]. (1991)

51 BALFs from HIV positive patients were analysed. In 16 of them Pneumocystis carinii organisms were found. Two methods detecting Pneumocystis carinii were used: Grocott-Gomori, fluorescence Papanicolaou stain. The best staining method turned out to be Grocott-Gomori. The differential count was carried out in 40 BALFs. In patients with Pneumocystis carinii detected by BAL neutrophilia was always present. In some of these patients lymphocytosis was also present. In 4 patients with high lymphocytosis immunocytochemical examinations with monoclonal antibodies against CD4, CD8 T cells showed a marked decrease of the CD4/CD8 ratio.
A biochemical translinear principle with weak inversion ISFETs (2005)

A weak inversion region is shown to exist in ion-sensitive field effect transistor (ISFET) sensors. It is therefore proposed that the ISFET and its chemically sensitive (ChemFET) counterparts be used as translinear elements in the synthesis of novel biochemical input stages which perform real-time mathematical manipulation of biochemical signals. A Biochemical Translinear Principle using weakly inverted ChemFETs is presented. A low-power current-mode input stage circuit is presented as an application of the principle. This yields a linear relation between drain current and hydrogen ion concentration valid over four decades. This paper demonstrates an important and necessary step toward biochemical VLSI.
Localization optimization algorithm of maximum likelihood estimation based on received signal strength (2017)

In this paper, we propose a method to improve localization algorithm of maximum likelihood estimation; the localization scheme relies on the distance threshold. In order to suppress effectively the effects of received signal strength error to node localization precision. This paper presents an indoor localization algorithm based on received signal strength to select anchor nodes. Compared with the traditional localization algorithm, this scenario not only improve the localization accuracy, but also reduce the calculation complexity of nodes. The simulation results show that the average error of the proposed method is less than 0.15m. Moreover, when there are a large number of anchor nodes, the computational complexity is effectively reduced. Verification result verifies the effectiveness and reliability of the algorithm.
Carbon-11-thymidine and FDG to measure therapy response. (1998)

Images show a decline in both cellular energetics and proliferative rate after successful chemotherapy. In the two patients with progressive disease, thymidine uptake was unchanged 1 wk after therapy. In our limited series, K(TdR) measurements showed a complete shutdown in tumor proliferation in patients in whom FDG showed a more limited decrease in glucose metabolism.
Rapid Liquid Chromatographic Method to Distinguish Wild Salmon from Aquacultured Salmon Fed Synthetic Astaxanthin (1997)

Analytical methods are needed to determine the presence of color additives in fish. We report a liquid chromatographic (LC) method developed to identify the synthetic form of the color additive astaxanthin in salmon, based on differences in the relative ratios of the configurational isomers of astaxanthin. The distributions of configurational isomers of astaxanthin in the flesh of wild Atlantic and wild Pacific salmon are similar, but significantly different from that in aquacultured salmon. Astaxanthin is extracted from the flesh of salmon, passed through a silica gel Sep-Pak cartridge, and analyzed directly by LC on a Pirkle covalent L-leucine column. No derivatization of the astaxanthin is required-an important advantage of our approach, which is a modification of our previously described method. This method can be used to distinguish between aquacultured and wild salmon. The method has general applicability and can also be used to identify astaxanthins derived from other sources such as Phaffia yeast and Haematococcus pluvialis algae.
All About Analytics (2013)

To understand and be successful with analytics, it is important to be precise in understanding what analytics means, the different targets or approaches that companies can take to using analytics, and the drivers that lead to the use of analytics. For companies that use advanced analytics, the keys to success include a clear business need; strong, committed sponsorship; a fact-based decision making culture; a strong data infrastructure; the right analytic tools; and strong analytical personnel in an appropriate organizational structure. These are the same factors for success for business intelligence in general, but there are important nuances when implementing advanced analytics, such as with the data infrastructure, analytical tools, and personnel. Companies like Amazon.com, Overstock.com, Harrah’s Entertainment, and First American Corporation are exemplars that illustrate concepts and best practices.
Structure-Function Studies of the Adipocyte-secreted Hormone Acrp30/Adiponectin (2003)

Acrp30/adiponectin is an adipocyte-specific secretory protein that has recently been implicated as a mediator of systemic insulin sensitivity with liver and muscle as target organs. Acrp30 is found as two forms in serum, as a lower molecular weight trimer-dimer and a high molecular weight complex. Little is know about the regulation and significance of these Acrp30 complexes in serum and about the events that lead to the generation of the bioactive ligand. Here, we show that there is a profound sexual dimorphism of Acrp30 levels and complex distribution in serum. Female mice display significantly higher levels of the high molecular weight complex in serum than males. In both females and males, levels of the high molecular weight complex are significantly reduced in response to a systemic increase of insulin. The ratio of the two complexes is restored upon normalization of glucose levels. Structurally, we show that oligomer formation of Acrp30 critically depends on disulfide bond formation mediated by Cys-39. Mutation of Cys-39 results in trimers that are subject to proteolytic cleavage in the collagenous domain. Surprisingly, Acrp30(C39S) or wild-type Acrp30 treated with dithiothreitol are significantly more bioactive than the higher order oligomeric forms of the protein with respect to reduction of serum glucose levels. Furthermore, treatment of primary hepatocytes with trimeric and higher order forms of Acrp30 confirms that the increased bioactivity seen in vivo is reflected in an augmented potency to reduce glucose output in the presence of gluconeogenic stimuli. Combined, these results shed new light on the regulation of this complex protein and suggest a new model for in vivo activation of the protein, implicating a serum reductase activity.
Breaking Up is Hard to Do: Creating Hydraulic Fracture Complexity in the Bakken Central Basin (2013)

Abstract The Bakken drilling boom in North Dakota has seen a frenzy of activity over the past several years as operators sought to hold acreage and create value with the drill bit. This has been particularly true in the Central Basin portion of the Williston Basin where initial wells drilled prior to 2008 were uneconomic. However, advances in completion technology caused such a fundamental shift in economics that the whole Central Basin area of over 2500 square miles has been opened to economic development with ~100 rigs currently drilling in the region. The most fundamental change in completion design has been the incorporation of "high-intensity" multi-stage fracturing. What makes Bakken completion design fundamentally different from recent shale gas developments has been the widespread use of uncemented liners with external packers in the open-hole lateral in order to create the multi-stage zonal isolation. As operators have advanced the application of multi-stage completion techniques there has been a wide variety of completion equipment used and stimulation designs that have been pumped. This operator decided to employ a completion design that comprised: An open-hole "uncemented" liner section;Annular zonal isolation created by swell packers;The use of "plug and perf" technology to individually open successive zones to stimulation;The pumping of slickwater fracture treatment fluids at high rate;The use of high-quality ceramic proppant to generate the required fracture conductivity. Production data are presented from 58 wells in which this completion and stimulation design has been conducted, which show that the use of this approach has resulted in well performance that is 25-45% superior to any other Bakken completion technique.
Identification and determination of fat‐soluble vitamins and metabolites in human serum by liquid chromatography/triple quadrupole mass spectrometry with multiple reaction monitoring (2007)

A method for determination of fat-soluble vitamins K(1), K(3), A, D(2), D(3) and E (as alpha- and delta-tocopherol) and metabolites 25-hydroxyvitamin D(2) and D(3) and 1,25-dihydroxyvitamin D(3) in human serum by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in positive mode is proposed. Highly selective identification of the target compounds in serum was confirmed by the most representative transitions from precursor ion to product ion. Quantitative MS/MS analysis was carried out by multiple reaction monitoring optimizing the most sensitive transition for each analyte in order to achieve low detection limits (from 0.012 to 0.3 ng/mL estimated with serum). The analysis was performed with 1 mL of serum, which was subjected to protein precipitation, liquid-liquid extraction to an organic phase, evaporation to dryness and reconstitution with methanol. The precision of the overall method ranged from 3.17-6.76% as intra-day variability and from 5.07-11.53% as inter-day variability. The method, validated by the standard addition method, provides complete information on the fat-soluble vitamins profile, which is of interest in clinical and metabolomics studies.
Silk fibroin: Structural implications of a remarkable amino acid sequence (2001)

The amino acid sequence of the heavy chain of Bombyx mori silk fibroin was derived from the gene sequence. The 5,263-residue (391-kDa) polypeptide chain comprises 12 low-complexity "crystalline" domains made up of Gly-X repeats and covering 94% of the sequence; X is Ala in 65%, Ser in 23%, and Tyr in 9% of the repeats. The remainder includes a nonrepetitive 151-residue header sequence, 11 nearly identical copies of a 43-residue spacer sequence, and a 58-residue C-terminal sequence. The header sequence is homologous to the N-terminal sequence of other fibroins with a completely different crystalline region. In Bombyx mori, each crystalline domain is made up of subdomains of approximately 70 residues, which in most cases begin with repeats of the GAGAGS hexapeptide and terminate with the GAAS tetrapeptide. Within the subdomains, the Gly-X alternance is strict, which strongly supports the classic Pauling-Corey model, in which beta-sheets pack on each other in alternating layers of Gly/Gly and X/X contacts. When fitting the actual sequence to that model, we propose that each subdomain forms a beta-strand and each crystalline domain a two-layered beta-sandwich, and we suggest that the beta-sheets may be parallel, rather than antiparallel, as has been assumed up to now.
Symptoms and Satisfaction of Patients in the Patient-Reported Outcomes With Laser In Situ Keratomileusis (PROWL) Studies (2016)

The systematic administration of a questionnaire to patients who have undergone LASIK surgery is a new approach to assess symptoms and satisfaction. Our findings support the need for adequate counseling about the possibility of developing new symptoms after LASIK surgery.
Statistical properties of MPEG video traffic and their impact on traffic modeling in ATM systems (2002)

MPEG video traffic is expected to cause several problems in ATM networks, both from performance and from architectural viewpoint. For the solution of these difficulties, appropriate video traffic models are needed. A detailed statistical analysis of newly generated long MPEG encoded video sequences is presented and the results are compared to those of existing data sets. Based on the results of the analysis, a layered modeling scheme for MPEG video traffic is suggested which will simplify the finding of appropriate models for a lot of performance analysis techniques.
Aberrant expression of c‐met mRNA in human gastric carcinomas (1993)

We examined mRNA expression for c-met encoding hepatocyte growth factor receptor in 8 gastric carcinoma cell lines and 31 surgically resected gastric carcinoma tissues by Northern-blot analysis. Two forms of the transcript, sized 7.0 kb and 6.0 kb, were found in gastric carcinomas. Transcripts of both sizes were detected at various levels in all the gastric carcinoma cell lines except the MKN-74 line, which expressed only the 7.0-kb form. Of the 31 gastric carcinomas, 15 (48%) over-expressed the 7.0-kb transcript when compared with non-neoplastic mucosa. The 6.0-kb transcript of the c-met gene was expressed at considerable levels in 52% of the gastric carcinoma tissues, whereas it was only slightly expressed in non-neoplastic mucosa of a small number of cases. An important finding was that expression of the 6.0-kb transcript was closely correlated with tumor staging, lymph-node metastasis and depth of tumor invasion. These results, overall, suggest that the 6.0-kb transcript of the c-met gene might participate in the development and progression of gastric carcinomas.
Slim binaries (1997)

article Free AccessSlim binaries Authors: Michael Franz assistant professor in the Department of, Information and Computer Science at the University of California, at Irvine assistant professor in the Department of, Information and Computer Science at the University of California, at IrvineView Profile , Thomas Kistler Ph.D. student in the Department of Information, and Computer Science at the University of California at Irvine Ph.D. student in the Department of Information, and Computer Science at the University of California at IrvineView Profile Authors Info & Claims Communications of the ACMVolume 40Issue 12Dec. 1997 pp 87–94https://doi.org/10.1145/265563.265576Published:01 December 1997Publication History 91citation1,072DownloadsMetricsTotal Citations91Total Downloads1,072Last 12 Months90Last 6 weeks10 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Cloning and comparison of the DNA encoding ammelide aminohydrolase and cyanuric acid amidohydrolase from three s-triazine-degrading bacterial strains (1991)

DNA encoding the catabolism of the s-triazines ammelide and cyanuric acid was cloned from Pseudomonas sp. strain NRRLB-12228 and Klebsiella pneumoniae 99 with, as a probe, a 4.6-kb PstI fragment from a third strain, Pseudomonas sp. strain NRRLB-12227, which also encodes these activities. In strains NRRLB-12228 and 99 the ammelide aminohydrolase (trzC) and cyanuric acid amidohydrolase (trzD) genes are located on identical 4.6-kb PstI fragments which are part of a 12.4-kb DNA segment present in both strains. Strain NRRLB-12227 also carries this 12.4-kb DNA segment, except that a DNA segment of 0.8 to 1.85 kb encoding a third enzyme, ammeline aminohydrolase (trzB), has been inserted next to the ammelide aminohydrolase gene with the accompanying deletion of 1.1 to 2.15 kb of DNA. In addition, the s-triazine catabolic genes are flanked in strain NRRLB-12227 by apparently identical 2.2-kb segments that are not present in the other two strains and that seem to cause rearrangements in adjacent DNA.
WHO Classification of Tumours of the Digestive System (2010)

WHO Classification of Tumours of the Digestive System - Libros de Medicina - Gastroenterologia oncologica - 128,25
Oxazole- and Imidazole-Based Ser-Leu Dipeptide Mimetics in Potent Inhibitors of Antigen Presentation by MHC Class II DR Molecules (2002)

Imidazole and oxazole derivatives 1 to 4 were designed and prepared as dipeptide mimetics to replace the Ser-Leu dipeptide sequence of Ro-25-9980 (Ac-(Cha)-RAMA-S-L-NH2), a peptidic inhibitor of antigen binding to major histocompatibility complex (MHC) class II DR molecules linked to rheumatoid arthritis (RA). The most potent analog in binding assays (IC50 = 30 nM in DRB1*0401 binding; 1.6 times as potent as Ro 25-9980) was 16, Ac-(Cha)RAMA-(S)S-psi(oxazole)-L-NH2. The SAR of peptide hybrids 10 to 24, prepared by incorporating the dipeptide mimetics 1 to 4 is discussed. Of these hybrids, 23 and 24, analogs that incorporated the imidazole and oxazole mimetics as well as optimized variants at positions 3 to 5, were found to have 70 to 80 nM binding affinity comparable to the parent peptide in DRB 1*0401 binding and were also active in DRB1*0101 binding, while being resistant to proteolysis by cathepsin B. Both of these compounds showed inhibitory activity in an antigen-stimulated T-cell proliferation assay, indicating their potential to suppress autoimmune responses and as leads for therapeutic agents to treat RA.