gebhart/patrepeval huggingface dataset:
Conformational analysis of josamycin, a 16-membered macrolide free in solution and bound to bacterial ribosomes (1999)

The potent 14-membered macrolide antibiotics displayed a strong NMR response in the TRNOESY experiments whereas their metabolites which do not retain antimicrobial activity gave essentially blank TRNOESY spectra. These TRNOESY experiments are here extended to a macrolide (josamycin) belonging to the 16-atom macrolide class in order to compare responses according to the macrocycle size. Analysis of transferred nuclear Overhauser effect (TRNOE) experiments resulted in a set of constraints for all proton pairs. These constraints were used in structure determination procedures based on molecular modelling to obtain a bound structure compatible with the experimental NMR data. This study allowed us to identify the binding structure at the ribosome for the active 16-membered macrolide. The different conformations existing in solution for this antibiotic in the free state will be compared and correlated with the binding conformation at the ribosome obtained with TRNOE experiments so as to establish a structure–activity relationship. The comparative results indicate that one conformation (called S3) pre-existing in the conformational equilibrium of macrocycle in solution and close to the major one S5, is preferred in the bound state.
Locally weighted regression and scatter correction for near-infrared reflectance data (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLocally weighted regression and scatter correction for near-infrared reflectance dataTormod. Naes, Tomas. Isaksson, and Bruce. KowalskiCite this: Anal. Chem. 1990, 62, 7, 664–673Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ac00206a003https://doi.org/10.1021/ac00206a003research-articleACS PublicationsRequest reuse permissionsArticle Views944Altmetric-Citations247LEARN 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
Odd-Even Pattern Observed in Polyaniline/(Au<sub>0</sub>– Au<sub>8</sub>) Composites (2012)

Theoretically predicted effect of odd-even pattern of electron pairing on behavior of gold clusters in polyaniline/AuN (N = 0 to 8) has been confirmed experimentally. In these composites the atomic Au clusters with even number of atoms exhibit higher catalytic activity for electrochemical oxidation of n-propanol in 1 M NaOH than the odd-number atoms clusters. Also, infrared spectroscopy shows that even numbered PANI/AuN composites affect the N-H stretching vibration more strongly than the corresponding odd numbered ones. This behavior matches the theoretically predicted variations of HOMO-LUMO gap energy and the stability of the atomic Au clusters. It also agrees with the earlier experimental work in which the UPS spectra of isolated, mass-selected Au clusters have been reported.
Flow Cytometric Evaluation of Urological Malignancy (1988)

No AccessJournal of UrologyEditorial1 Feb 1988Flow Cytometric Evaluation of Urological Malignancy Charles B. Brendler Charles B. BrendlerCharles B. Brendler More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)42406-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Flow Cytometric Evaluation of Urological Malignancy." The Journal of Urology, 139(2), pp. 342–343 © 1988 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 139Issue 2February 1988Page: 342-343 Advertisement Copyright & Permissions© 1988 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Charles B. Brendler More articles by this author Expand All Advertisement PDF DownloadLoading ...
Mutagenesis and carcinogenesis induced by dibenzo[<i>a,l</i>]pyrene in the mouse oral cavity: a potential new model for oral cancer (2011)

Cancer of the oral cavity is a serious disease, affecting about 30,000 individuals in US annually. There are several animal models of oral cancer, but each has certain disadvantages. As a new model, we investigated whether topical application of the tobacco smoke carcinogen, dibenzo[a,l]pyrene (DB[a,l]P) is mutagenic and carcinogenic in the oral cavity of the B6C3F1 lacI and B6C3F1 mouse, respectively. B6C3F1 lacI mice received DB[a,l]P (0, 3, 6, 12 nmol) 3× per week. B6C3F1 mice received the same doses and also 24 nmol. At 38 weeks mutagenesis was measured in oral tissues in lacI mice. For the high dose group, the mutant fraction (MF) in upper mucosa and tongue increased about twofold relative to that in vehicle-alone. The increases were statistically significant. The mutational profile in the DB[a,l]P-induced mutants was compared with that induced by benzo[a]pyrene (BaP) in oral tissue. BaP is mutagenic in many tissues when administered by gavage. The mutational profile for DB[a,l]P was more similar to that reported for p53 mutations in head and neck cancers than was that of BaP. At 47 weeks, oral squamous cell carcinomas (OSCC) were found in 31% of the high-dose B6C3F1 group. Elevations of p53 and COX-2 protein were observed in tumor and dysplastic tissue. As DB[a,l]P induces mutations and tumors in the oral cavity, and has a mutational profile in oral tissue similar to that found in p53 in human OSCC, the treatment protocol described here may represent a new and relevant model for cancer of the oral cavity.
Artificial immune system based methods for spam filtering (2013)

To solve the spam problem, many statistical learning methods and AIS methods have been proposed and applied. In essence, statistical learning methods and AIS methods have quite different origins, and they try to find the solutions from distinct aspects. In recent works, we proposed several hybrid methods, which combined immune theory with statistical methods in spam filtering. In this paper, we briefly review and analyze these works and possible extensions, and demonstrate the rationality of building hybrid immune models for spam filtering. In addition, a generic framework of an immune based model is presented, and online implementation strategies are given. It is well demonstrated that how to apply the immune based model to building an intelligent email server.
Accelerated computation using runtime partial reconfiguration (2013)

Runtime reconfigurable architectures, which integrate a hard processor core along with a reconfigurable fabric on a single device, allow to accelerate a computation by means of hardware accelerators implemented in the reconfigurable fabric. Runtime partial reconfiguration provides the flexibility to dynamically change these hardware accelerators to adapt the computing capacity of the system. This thesis presents the evaluation of design paradigms which exploit partial reconfiguration to implement compute intensive applications on such runtime reconfigurable architectures. For this purpose, image processing applications are implemented on Zynq-7000, a System on a Chip (SoC) from Xilinx Inc. which integrates an ARM Cortex A9 with a reconfigurable fabric. This thesis studies different image processing applications to select suitable candidates that benefit if implemented on the above mentioned class of reconfigurable architectures using runtime partial reconfiguration. Different Intellectual Property (IP) cores for executing basic image operations are generated using high level synthesis for the implementation. A software based scheduler, executed in the Linux environment running on the ARM core, is responsible for implementing the image processing application by means of loading appropriate IP cores into the reconfigurable fabric. The implementation is evaluated to measure the application speed up, resource savings, power savings and the delay on account of partial reconfiguration. The results of the thesis suggest that the use of partial reconfiguration to implement an application provides FPGA resource savings. The extent of resource savings depend on the granularity of the operations into which the application is decomposed. The thesis could also establish that runtime partial reconfiguration can be used to accelerate the computations in reconfigurable architectures with processor core like the Zynq-7000 platform. The achieved computational speed-up depends on factors like the number of hardware accelerators used for the computation and the used reconfiguration schedule. The thesis also highlights the power savings that may be achieved by executing computations in the reconfigurable fabric instead of the processor core.
Detection and localization of emitters in the presence of multipath using a uniform linear antenna array (2008)

In this paper, we present a new application of the likelihood ratio test to solve the problem of enumeration and localization of multiple emitters (sources) with a uniform linear antenna array in a multi-path environment. First, spatial smoothing is applied to the antenna array data to decorrelate signals corresponding to each path in the estimated correlation matrix and the number of paths is then counted using an information theoretic criterion. Then, MUSIC is applied with this correlation matrix to estimate the angle of arrival of all possible incident paths. In our signal model, we assume that the correlation between signals from two paths is one if they originate from the same source but zero if they are from different sources. The likelihood ratio test is then applied to each path pair using this correlation model and the angles of arrival estimated by MUSIC in order to find out if the path pair originates from the same emitter, and hence the number of emitters and their angles of arrival are estimated. The proposed algorithm on the likelihood ratio test is compared with the correlation coefficient algorithm based on minimum variance beamforming with a performance analysis.
Software Defined SSD: An Architecture to Generalize Data Processing in SSDs (2013)

With the advances in non-volatile memory technologies, the access latencies and bandwidth of storage class memories such as PCM, spin-transfer torque RAMs, have improved three orders of magnitude compared to hard disks. Along with these improvements, internal bandwidth of the solid state drives (SSDs) has increased and has exceeded the bandwidth on the Host Interface. Thus the Host Interface is the performance bottleneck when the SSDs are treated as simple block IO devices. With the decrease in access latency of the new memory technologies, the memory latency is a small fraction of the total access latency from the host. These observations indicate that treating SSDs made of fast memories as just block IO devices will restrict the system performance gains. In this work, we propose an Software-Defined SSD (SDSSD) Architecture that expands the scope of an SSD to a smart device with compute logic. By moving computations inside the SSD, the amount of data transferred to the host is reduced, thereby reducing the impact of the host interface bottleneck. The compute logic is made software programmable enabling different host applications to make use of it. The compute logic and the host applications interact using a generic RPC Interface, thus making programming simple. The proposed architecture is designed and implemented on a FPGA prototyping board. The results from the IO benchmarks run on the SDSSD prototype indicate that, bandwidth and latency of SDSSD Architecture matches closely to the performance of the SSD Architecture with IO specific logic for large access sizes
Chimerism after organ transplantation (1997)

Recent evidence suggests that passenger leukocytes migrate after organ transplantation and produce persistent chimerism, which is essential for sustained survival of the allograft. Here, we describe how this hematolymphopoietic chimerism provides an important framework for interpretation of post-transplant phenomena and for initiation of therapeutically oriented transplantation research.
Clinical development of novel proteasome inhibitors for cancer treatment (2009)

Bortezomib, the reversible proteasome inhibitor that first entered clinical trials, has been studied extensively as a single agent and in combination with glucocorticoids, cytotoxic agents, immunomodulatory drugs and radiation as treatment for multiple myeloma and other hematological malignancies. The results in some cases have been impressive. There is less evidence of bortezomib's efficacy in solid tumors. Novel irreversible proteasome inhibitors, NPI-0052 and carfilzomib, have also been developed and clinical trials are underway. Natural products with proteasome-inhibitory effects, such as green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG), soy isoflavone genistein, and the spice turmeric compound curcumin, have been studied alone and in combination with traditional chemotherapy and radiotherapy against various cancers. There is also interest in developing these natural compounds as potential chemopreventive agents.
A synaptic organizing principle for cortical neuronal groups (2011)

Neuronal circuitry is often considered a clean slate that can be dynamically and arbitrarily molded by experience. However, when we investigated synaptic connectivity in groups of pyramidal neurons in the neocortex, we found that both connectivity and synaptic weights were surprisingly predictable. Synaptic weights follow very closely the number of connections in a group of neurons, saturating after only 20% of possible connections are formed between neurons in a group. When we examined the network topology of connectivity between neurons, we found that the neurons cluster into small world networks that are not scale-free, with less than 2 degrees of separation. We found a simple clustering rule where connectivity is directly proportional to the number of common neighbors, which accounts for these small world networks and accurately predicts the connection probability between any two neurons. This pyramidal neuron network clusters into multiple groups of a few dozen neurons each. The neurons composing each group are surprisingly distributed, typically more than 100 μm apart, allowing for multiple groups to be interlaced in the same space. In summary, we discovered a synaptic organizing principle that groups neurons in a manner that is common across animals and hence, independent of individual experiences. We speculate that these elementary neuronal groups are prescribed Lego-like building blocks of perception and that acquired memory relies more on combining these elementary assemblies into higher-order constructs.
Detection of a submerged object insonified by beach noise (1993)

In a previous paper, numerical simulations were performed which demonstrated that a submerged object insonified by surface noise in an ocean waveguide can be detected at low to mid frequency for realistic arrays within about 1-km range [Makris etal., J. Acoust. Soc. Am. 92, 2416 (A) (1992)]. For the present paper, an investigation into the possibility of detecting a submerged object insonified by low- to mid-frequency beach noise in an ocean waveguide was carried out. Model beach noise is defined as a one-dimensional array of uncorrelated surface sources and the detectability of the object is investigated for various orientations of the sensing array axis, beach axis, and object.
Processes of Zinc Attenuation by Biogenic Manganese Oxides Forming in the Hyporheic Zone of Pinal Creek, Arizona (2014)

The distribution and speciation of Zn sorbed to biogenic Mn oxides forming in the hyporheic zone of Pinal Creek, AZ, was investigated using extended X-ray absorption fine structure (EXAFS) and microfocused synchrotron X-ray fluorescence (μSXRF) mapping, and chemical extraction. μSXRF and chemical extractions show that contaminant Zn co-varied with Mn in streambed sediment grain coatings. Bulk and microfocused EXAFS spectra of Zn in the biogenic Mn oxide coating are indicative of Zn forming triple-corner-sharing inner-sphere complexes over octahedral vacancies in the Mn oxide sheet structure. Zn desorbed in response to the decrease in pH in batch experiments and resulted in near-equal dissolved Zn at each pH over a 10-fold range in the solid/solution ratio. The geometry of sorbed Zn was unchanged after 50% desorption at pH 5, indicating that desorption is not controlled by dissolution of secondary Zn phases. In summary, these findings support the idea that Zn attenuation in Pinal Creek is largely controlled by sorption to microbial Mn oxides forming in the streambed during hyporheic exchange. Sorption to biogenic Mn oxides is likely an important process of Zn attenuation in circum-neutral pH reaches of many acid-mine drainage contaminated streams when dissolved Mn is present.
The yeast BDF1 gene encodes a transcription factor involved in the expression of a broad class of genes including snRNAs (1994)

While screening for genes that affect the synthesis of yeast snRNPs, we identified a thermosensitive mutant that abolishes the production of a reporter snRNA at the non-permissive temperature. This mutant defines a new gene, named BDF1. In a bdf1-1 strain, the reporter snRNA synthesized before the temperature shift remains stable at the non-permissive temperature. This demonstrates that the BDF1 gene affects the synthesis rather than the stability of the reporter snRNA and suggests that the BDF1 gene encodes a transcription factor. BDF1 is present in single copy on yeast chromosome XII, and is important for normal vegetative growth but not essential for cell viability. bdf1 null mutants share common phenotypes with several mutants affecting general transcription and are defective in snRNA production. BDF1 encodes a protein of 687 amino-acids containing two copies of the bromodomain, a motif also present in other transcription factors as well as a new conserved domain, the ET domain, also present in Drosophila and human proteins.
Structure of glycolate oxidase from spinach (1985)

A high-resolution structure determination of glycolate oxidase from spinach is reported. X-ray data were collected on films at the synchrotron radiation source in Daresbury, England. The structure was solved by using two heavy-atom derivatives and a solvent-flattening procedure developed by B.-C. Wang. The subunit structure is essentially a structure of the eight-stranded alpha/beta-barrel type first described for triosephosphate isomerase. In addition, there are 70 residues at the NH(2) terminus and 45 residues between strand four and helix four of the barrel, which are arranged in a helical domain outside the COOH end of the parallel strands of the barrel. The active site is in a cleft between these domains with the coenzyme FMN essentially bound to the barrel and a substrate analogue, thioglycolate, bound to the helical domain. The molecule is octameric with 422 symmetry and has a 15- to 20-A-wide hole in the middle.
HIV-1 Variation Diminishes CD4 T Lymphocyte Recognition (1998)

Effective long-term antiviral immunity requires specific cytotoxic T lymphocytes and CD4(+) T lymphocyte help. Failure of these helper responses can be a principle cause of viral persistence. We sought evidence that variation in HIV-1 CD4(+) T helper epitopes might contribute to this phenomenon. To determine this, we assayed fresh peripheral blood mononuclear cells from 43 asymptomatic HIV-1(+) patients for proliferative responses to HIV-1 antigens. 12 (28%) showed a positive response, and we went on to map dominant epitopes in two individuals, to p24 Gag restricted by human histocompatibility leukocyte antigen (HLA)-DR1 and to p17 Gag restricted by HLA-DRB52c. Nine naturally occurring variants of the p24 Gag epitope were found in the proviral DNA of the individual in whom this response was detected. All variants bound to HLA-DR1, but three of these peptides failed to stimulate a CD4(+) T lymphocyte line which recognized the index sequence. Antigenic variation was also detected in the p17 Gag epitope; a dominant viral variant present in the patient was well recognized by a specific CD4(+) T lymphocyte line, whereas several natural mutants were not. Importantly, variants detected at both epitopes also failed to stimulate fresh uncultured cells while index peptide stimulated successfully. These results demonstrate that variant antigens arise in HIV-1(+) patients which fail to stimulate the T cell antigen receptor of HLA class II-restricted lymphocytes, although the peptide epitopes are capable of being presented on the cell surface. In HIV-1 infection, naturally occurring HLA class II-restricted altered peptide ligands that fail to stimulate the circulating T lymphocyte repertoire may curtail helper responses at sites where variant viruses predominate.
Reinforcement Learning Based Mobile Offloading for Cloud-Based Malware Detection (2017)

Cloud-based malware detection improves the detection performance for mobile devices that offload their malware detection tasks to security servers with much larger malware database and powerful computational resources. In this paper, we investigate the competition of the radio transmission bandwidths and the data sharing of the security server in the dynamic malware detection game, in which each mobile device chooses its offloading rate of the application traces to the security server. As the Q-learning technique has a slow learning rate in the game with high dimension, we have designed a mobile malware detection based on hotbooting-Q techniques, which initiates the quality values based on the malware detection experience. We propose an offloading strategy based on deep Q-network technique with a deep convolutional neural network to further improve the detection speed, the detection accuracy, and the utility. Preliminary simulation results verify the detection gain of the scheme compared with the Q- learning based strategy.
T and B cell collaboration: induction of motility in small, resting B cells by interleukin 4 (1991)

In this report we investigate if IL 4 can work as a chemoattractant factor by inducing locomotion in B cells. We found that murine recombinant IL 4 (rIL 4) induced motile morphology and migration through polycarbonate micropore filters of murine, splenic B cells at an optimal concentration of 3 ng/ml. Kinetic studies revealed optimal migration at 8-16 h, although a significant response could be detected already after 1 h. Flow cytometric studies confirmed that the migrated cells were indeed B cells. We also compared the activity of small, dense B cells and large, low-density B cells, based on Percoll gradient separation. We found no difference in IL 4-induced motility among the two groups. Furthermore, we looked at B cells activated in vitro by preculture in lipopolysaccharide (LPS) or IL 4. Our data indicate that both LPS and IL 4 can increase the general capacity for motility in B cells after preculture for 24 h. T and B cell collaboration requires close cell-cell contacts in order for T cell help to be administered to the B cell. One way of enhancing such cell contacts could be through directional cell migration induced by helper factors (chemotaxis). We suggest that IL 4 can play a role as a chemoattractant factor that enhances cell contacts between T helper cells and B cells.