gebhart/patrepeval huggingface dataset:
Semi-blind frequency offset synchronization for OFDM (2002)

We address the problem of carrier frequency offset (CFO) synchronization in OFDM-based communications systems in the context of frequency-selective fading channels. A blind CFO estimator was recently developed, which exploits the virtual subcarriers (VSC) in a practical OFDM system. Here, we propose a semi-blind approach where a few (either zero or non-zero) pilots are inserted in the OFDM block. The semi-blind estimator (SBE) is shown to significantly outperform the blind estimator even with a few pilots provided they are equispaced. Further, the SME based on zero pilots consistently outperforms that based on non-zero pilots. Reliable estimation of an unknown frequency-selective channel requires that some (or all) of the pilots be non-zero, since zero pilots are useless for channel estimation. It is shown that if the total number of pilots is (much) larger that the channel order, zero pilots and non-zero pilots lead to almost the same CFO estimation performance. Therefore, in this case, non-zero pilots should be preferred to zero pilots.
Engineering fungal de novo fatty acid synthesis for short chain fatty acid production (2017)

Fatty acids (FAs) are considered strategically important platform compounds that can be accessed by sustainable microbial approaches. Here we report the reprogramming of chain-length control of Saccharomyces cerevisiae fatty acid synthase (FAS). Aiming for short-chain FAs (SCFAs) producing baker's yeast, we perform a highly rational and minimally invasive protein engineering approach that leaves the molecular mechanisms of FASs unchanged. Finally, we identify five mutations that can turn baker's yeast into a SCFA producing system. Without any further pathway engineering, we achieve yields in extracellular concentrations of SCFAs, mainly hexanoic acid (C<sub>6</sub>-FA) and octanoic acid (C<sub>8</sub>-FA), of 464 mg l<sup>-1</sup> in total. Furthermore, we succeed in the specific production of C<sub>6</sub>- or C<sub>8</sub>-FA in extracellular concentrations of 72 and 245 mg l<sup>-1</sup>, respectively. The presented technology is applicable far beyond baker's yeast, and can be plugged into essentially all currently available FA overproducing microorganisms.
Vaccine technologies: view to the future (1994)

The development of vaccines to prevent infectious diseases has been one of the most important contributions of biomedical science. Recent advances in the basic sciences are now fueling the development of a new generation of vaccines that will be based on rational design approaches. Two factors are making this possible: an improved understanding of the microbial factors required for virulence and the nature of the immune response to infection. The status of new vaccine technologies is summarized here.
Synthesis of Phosphorus-Containing Macrocycles and Cryptands (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Phosphorus-Containing Macrocycles and CryptandsAnne-Marie Caminade and Jean Pierre MajoralCite this: Chem. Rev. 1994, 94, 5, 1183–1213Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/cr00029a002https://doi.org/10.1021/cr00029a002research-articleACS PublicationsRequest reuse permissionsArticle Views1371Altmetric-Citations170LEARN 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
<title>Reactive broadcasting protocol for video on demand</title> (1999)

We propose a reactive broadcasting protocol that addresses the problem of distributing moderately popular videos in a more efficient fashion. Like all efficient broadcasting protocols, reactive broadcasting assumes that the customer set-top box has enough local storage to store at least one half of each video being watched. Unlike other broadcasting protocols, reactive broadcasting only broadcasts the later portions of each video. the initial segment of each video is distributed on demand using a stream tapping protocol. Our simulations show that reactive broadcasting outperforms both conventional broadcasting protocols and pure stream tapping for a wide range of video request rates.
Architecture and evolution of the modern web browser (2006)

A reference architecture for a domain captures the fundamental subsystems common to systems of that domain, as well as the relationships between these subsystems. A reference architecture can be useful both at design time and during maintenance: it can improve understanding of a given system, aid in analyzing trade-offs between different design options, or serve as a template for designing new systems and reengineering existing ones. We examine the history of the web browser domain and identify several underlying forces that have contributed to its evolution. We develop a reference architecture for web browsers based on two well-known open source implementations, and we validate it against five additional implementations. We discuss the maintenance implications of different strategies for code reuse and identify several underlying evolutionary phenomena in the web browser domain; namely, emergent domain boundaries, convergent evolution, and tension between open and closed source development approaches. Key words: software architecture, software evolution, reverse engineering, reference architecture, web browser
Irreversible binding of the fluorescent beta-adrenoceptor probes alprenolol-NBD and pindolol-NBD to specific and non-specific binding sites. (1988)

The fluorescent 4-nitrobenzo-2-oxa-1,3-diazolyl (NBD) derivatives of alprenolol and pindolol bind irreversible to beta-adrenoceptors and non-receptor binding sites. This was established in functional experiments on the guinea pig right atrium and trachea smooth muscle, and by radioligand binding assay of beta-adrenoceptors on Chang liver cells in culture. The pD2'-values of alprenolol-NBD and pindolol-NBD for the beta-adrenoceptors on the right atrium were: 8.3 +/- 0.1 and 8.5 +/- 0.1; on the tracheal smooth muscle strip: 8.2 +/- 0.1 and 8.8 +/- 0.1; and its pKd on Chang liver cells: 8.5 +/- 0.1 and 8.9 +/- 0.1 respectively. The results indicated that no selectivity for the beta-adrenoceptor subtypes was introduced by the addition of NBD. The irreversible binding characteristic to beta-adrenoceptors and non-receptor binding sites of the fluorescent NBD derivatives of alprenolol and pindolol makes these drugs unsuitable to label beta-adrenoceptors specifically. As the irreversible binding is introduced by the coupling of the drug with NBD, it is concluded that NBD derivatives of beta-adrenoceptor antagonists are not suitable to visualize the two-dimensional motion of beta-adrenoceptors during challenge with agonists.
Lithium Phenolates Solvated by Tetrahydrofuran and 1,2-Dimethoxyethane: Structure Determination Using the Method of Continuous Variation (2009)

The method of continuous variation in conjunction with (6)Li NMR spectroscopy was used to characterize lithium phenolates solvated by tetrahydrofuran and 1,2-dimethoxyethane. The strategy relies on the formation of ensembles of homo- and heteroaggregated phenolates. The symmetries and concentration dependencies of the heteroaggregates attest to the aggregation numbers of the homoaggregates. The structurally diverse phenols afford substrate- and solvent-dependent combinations of lithium phenolate monomers, dimers, trimers, tetramers, and pentamers. We discuss the refinement of protocols for characterizing O-lithiated species. Computational studies examine further the substituent and solvent dependencies of aggregation.
A mutation in the beta-globin gene detected in the progeny of a female mouse treated with ethylnitrosourea. (1985)

A mouse with a variant hemoglobin was discovered during electrophoretic screening of (C57BL/6J X DBA/2J)F1 progeny of females treated with ethylnitrosourea. The variant trait was transmitted as a simple Mendelian alternate at the Hbb locus in all crosses except those involving the original carrier of the mutation. The proband mouse which received the mutation directly from the mutagen-treated parent was a germinal mosaic for the mutant and normal Hbbs alleles. The mutant allele was designated Hbbs2. The mutant haplotype specifies both an electrophoretically fast hemoglobin band and a hemoglobin band in the normal beta single hemoglobin position. Thus, the mutation has altered one of the tandemly duplicated genes at the Hbbs locus. A comparison of the relative concentrations of the two hemoglobins in Hbbs2 mice demonstrates preferential expression of the mutant gene, possibly analogous to the enhanced expression of Hbbdmaj in the Hbbd haplotype. Analysis of the amino acid sequence of the variant beta-globin revealed that the valine at position 60 was changed to glutamic acid. The simplest mutation mechanism for such an alteration is an A X T----T X A transversion.
Identification of candidate predisposing copy number variants in familial and early‐onset colorectal cancer patients (2010)

In the majority of colorectal cancers (CRCs) under clinical suspicion for a hereditary cause, the disease-causing genetic factors are still to be discovered. To identify such genetic factors we stringently selected a discovery cohort of 41 CRC index patients with microsatellite-stable tumors. All patients were below 40 years of age at diagnosis and/or exhibited an overt family history. We employed genome-wide copy number profiling using high-resolution SNP arrays on germline DNA, which resulted in the identification of novel copy number variants (CNVs) in six patients (15%) encompassing, among others, the cadherin gene CDH18, the bone morphogenetic protein antagonist family gene GREM1, and the breakpoint cluster region gene BCR. In addition, two genomic deletions were encountered encompassing two microRNA genes, hsa-mir-491/KIAA1797 and hsa-mir-646/AK309218. None of these CNVs has previously been reported in relation to CRC predisposition in humans, nor were they encountered in large control cohorts (>1,600 unaffected individuals). Since several of these newly identified candidate genes may be functionally linked to CRC development, our results illustrate the potential of this approach for the identification of novel candidate genes involved in CRC predisposition.
A gesture based user interface prototyping system (1989)

GID, for Gestural Interface Designer, is an experimental system for prototyping gesture-based user interfaces. GID structures an interface as a collection of “controls”: objects that maintain an image on the display and respond to input from pointing and gesture-sensing devices. GID includes an editor for arranging controls on the screen and saving screen layouts to a file. Once an interface is created, GID provides mechanisms for routing input to the appropriate destination objects even when input arrives in parallel from several devices. GID also provides low level feature extraction and gesture representation primitives to assist in parsing gestures.
Endosomal Proteolysis of Glucagon at Neutral pH Generates the Bioactive Degradation Product Miniglucagon-(19–29) (2003)

We have investigated the proteolytic mechanisms of glucagon degradation within hepatic endosomes at neutral pH before lumen acidification. Hepatic endosomes incubated at neutral pH rapidly degraded native glucagon into 13 intermediate products, one of which corresponded to the bioactive fragment glucagon-(19-29) (miniglucagon). The serine protease inhibitor phenylmethylsulfonyl fluoride as well as the nonspecific protease inhibitor bacitracin inhibited the endosomal degradation of glucagon at pH 7. In purified endosomal fractions, miniglucagon endopeptidase was undetectable as evaluated by immunoblotting, and immunoprecipitation with antibodies to insulin-degrading enzyme, cathepsins B and D, or furin failed to remove the endosomal neutral glucagonase activity. Incubation of endosomal fractions and [125I]iodoglucagon with the zero-length bifunctional cross-linker 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide resulted in specific labeling of a 170-kDa polypeptide. The labeling was completely inhibited by unlabeled glucagon (IC50 value, 5 x 10-7 m) and bacitracin (IC50 value, 1 microg/ml), suggesting that it may correspond to a bacitracin-sensitive glucagon-degrading enzyme. Treatment of the 125I-labeled 170-kDa cross-linked polypeptide with N-glycanase demonstrated that the cross-linked complex contained approximately 30 kDa of N-linked oligosaccharides. Specific cross-linking of the 170-kDa polypeptide was also observed using [125I]Tyr12-miniglucagon as the radioligand. Together, these data suggest that the 170-kDa glycoprotein represents a novel glucagon-degrading activity that could mediate glucagon proteolysis within endosomes before the acidification step and generate the bioactive (19-29) miniglucagon peptide.
Heavy Hitter Estimation over Set-Valued Data with Local Differential Privacy (2016)

In local differential privacy (LDP), each user perturbs her data locally before sending the noisy data to a data collector. The latter then analyzes the data to obtain useful statistics. Unlike the setting of centralized differential privacy, in LDP the data collector never gains access to the exact values of sensitive data, which protects not only the privacy of data contributors but also the collector itself against the risk of potential data leakage. Existing LDP solutions in the literature are mostly limited to the case that each user possesses a tuple of numeric or categorical values, and the data collector computes basic statistics such as counts or mean values. To the best of our knowledge, no existing work tackles more complex data mining tasks such as heavy hitter discovery over set-valued data. In this paper, we present a systematic study of heavy hitter mining under LDP. We first review existing solutions, extend them to the heavy hitter estimation, and explain why their effectiveness is limited. We then propose LDPMiner, a two-phase mechanism for obtaining accurate heavy hitters with LDP. The main idea is to first gather a candidate set of heavy hitters using a portion of the privacy budget, and focus the remaining budget on refining the candidate set in a second phase, which is much more efficient budget-wise than obtaining the heavy hitters directly from the whole dataset. We provide both in-depth theoretical analysis and extensive experiments to compare LDPMiner against adaptations of previous solutions. The results show that LDPMiner significantly improves over existing methods. More importantly, LDPMiner successfully identifies the majority true heavy hitters in practical settings.
The KCl cotransporter, KCC2, is highly expressed in the vicinity of excitatory synapses in the rat hippocampus (2001)

Immunocytochemical visualization of the neuron-specific K+/Cl- cotransporter, KCC2, at the cellular and subcellular level revealed an area- and layer-specific diffuse labelling, and a discrete staining outlining the somata and dendrites of some interneurons in all areas of the rat hippocampus. KCC2 was highly expressed in parvalbumin-containing interneurons, as well as in subsets of calbindin, calretinin and metabotropic glutamate receptor 1a-immunoreactive interneurons. During the first 2 postnatal weeks, an increase of KCC2 staining was observed in the molecular layer of the dentate gyrus, correlating temporally with the arrival of entorhinal cortical inputs. Subcellular localization demonstrated KCC2 in the plasma membranes. Immunoreactivity in principal cells was responsible for the diffuse staining found in the neuropil. In these cells, KCC2 was detected primarily in dendritic spine heads, at the origin of spines and, at a much lower level on the somata and dendritic shafts. KCC2 expression was considerably higher in the somata and dendrites of interneurons, most notably of parvalbumin-containing cells, as well as in the thorny excrescences of CA3 pyramidal cells and in the spines of spiny hilar and stratum lucidum interneurons. The data indicate that KCC2 is highly expressed in the vicinity of excitatory inputs in the hippocampus, perhaps in close association with extrasynaptic GABAA receptors. A high level of excitation is known to lead to a simultaneous net influx of Na+ and Cl-, as evidenced by dendritic swelling. KCC2 located in the same microenvironment may provide a Cl- extrusion mechanism to deal with both ion and water homeostasis in addition to its role in setting the driving force of Cl- currents involved in fast postsynaptic inhibition.
429. 2 : 4 : 3′ : 5′-Tetrahydroxystilbene from Artocarpus lakoocha (1957)

S. Mongolsuk, A. Robertson and R. Towers, J. Chem. Soc., 1957, 2231 DOI: 10.1039/JR9570002231
New Lyophilized Kit for Rapid Radiofluorination of Peptides (2012)

Radiolabeling compounds with positron-emitting radionuclides often involves a time-consuming, customized process. Herein, we report a simple lyophilized kit formulation for labeling peptides with (18)F, based on the aluminum-fluoride procedure. The prototype kit contains IMP485, a NODA (1,4,7-triazacyclononane-1,4-diacetate)-MPAA (methyl phenylacetic acid)-di-HSG (histamine-succinyl-glycine) hapten-peptide, [NODA-MPAA-D-Lys(HSG)-D-Tyr-D-Lys(HSG)-NH(2)], used for pretargeting, but we also examined a similar kit formulation for a somatostatin-binding peptide [IMP466, NOTA-D-Phe-Cys-Phe-D-Trp-Lys-Thr-Cys-Throl] bearing a NOTA ligand to determine if the benefits of using a kit can be extended to other AlF-binding peptides. The NODA-MPAA ligand forms a single stable complex with (AlF)(2+) in high yields. In order to establish suitable conditions for a facile kit, the formulation was optimized for pH, peptide to Al(3+) ratio, bulking agent, radioprotectant, and the buffer. For optimal labeling, the kit was reconstituted with an aqueous solution of (18)F(-) and ethanol (1:1), heated at 100-110 °C for 15 min, and then simply and rapidly purified using one of two equally effective solid-phase extraction (SPE) methods. Al(18)F-IMP485 was isolated as a single isomer complex, in high yield (45-97%) and high specific activity (up to 223 GBq/μmol), within 20 min. The labeled product was stable in human serum at 37 °C for 4 h and in vivo, urine samples showed the intact product was eliminated. Tumor targeting of the Al(18)F-IMP485 in nude mice bearing human colon cancer xenografts pretargeted with an anti-CEACAM5 bispecific antibody showed very low uptake (0.06% ± 0.02 ID/g) in bone, further illustrating its stability. At 1 h, pretargeted animals had high Al(18)F-IMP485 tumor uptake (28.1% ± 4.5 ID/g), with ratios of 9 ± 4, 123 ± 38, 110 ± 43, and 120 ± 108 for kidney, liver, blood and bone, respectively. Tumor uptake remained high at 3 h postinjection, with increased tumor/nontumor ratios. The NOTA-somatostatin-binding peptide also was fluorinated with good yield and high specific activity in the same kit formulation. However, yields were somewhat lower than those achieved with IMP485 containing the NODA-MPAA ligand, likely reflecting this ligand's superior binding properties over the simple NOTA. These studies indicate that (18)F-labeled peptides can be reproducibly prepared as stable Al-F complexes with good radiochemical yield and high specific activity using a simple, one-step, lyophilized kit followed by a rapid purification by SPE that provides the (18)F-peptide ready for patient injection within 30 min.
The cell biology of HIV-1 and other retroviruses (2006)

In recognition of the growing influence of cell biology in retrovirus research, we recently organized a Summer conference sponsored by the American Society for Cell Biology (ASCB) on the Cell Biology of HIV-1 and other Retroviruses (July 20-23, 2006, Emory University, Atlanta, Georgia). The meeting brought together a number of leading investigators interested in the interplay between cell biology and retrovirology with an emphasis on presentation of new and unpublished data. The conference was arranged from early to late events in the virus replication cycle, with sessions on viral fusion, entry, and transmission; post-entry restrictions to retroviral infection; nuclear import and integration; gene expression/regulation of retroviral Gag and genomic RNA; and assembly/release. In this review, we will attempt to touch briefly on some of the highlights of the conference, and will emphasize themes and trends that emerged at the meeting. MEETING REPORT: The conference began with a keynote address from W. Sundquist on the biochemistry of HIV-1 budding. This presentation will be described in the section on Assembly and Release of Retroviruses.
Aspect Ratio Determines the Quantity of Mesoporous Silica Nanoparticle Uptake by a Small GTPase-Dependent Macropinocytosis Mechanism (2011)

Although the aspect ratio (AR) of engineered nanomaterials (ENMs) is one of the key physicochemical parameters that could determine biological outcome, not much is understood about how AR contributes to shaping biological outcome. By using a mesoporous silica nanoparticle (MSNP) library that has been constructed to cover a range of different lengths, we could demonstrate that the AR of rod-shaped particles determines the rate and abundance of MSNP uptake by a macropinocytosis process in HeLa and A549 cancer cell lines. MSNPs with an AR of 2.1-2.5 were taken up in larger quantities compared to shorter or longer length rods by a process that is sensitive to amiloride, cytochalasin D, azide, and 4 °C inhibition. The rods with intermediary AR also induced the maximal number of filopodia, actin polymerization, and activation of small GTP-binding proteins (e.g., Rac1, CDC42) that involve assembly of the actin cytoskeleton and filopodia formation. When assessing the role of AR in the delivery of paclitaxel or camptothecin, the rods with AR 2.1-2.5 were clearly more efficient for drug delivery and generation of cytotoxic killing in HeLa cells. All considered, our data suggest an active sensoring mechanism by which HeLa and A549 cells are capable of detecting AR differences in MSNP to the extent that accelerated macropinocytosis can be used to achieve more efficient drug delivery.