gebhart/patrepeval huggingface dataset:
Extensive feature detection of N-terminal protein sorting signals (2002)

We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules.
Physicochemical Evaluation of Nanoparticles Assembled from Poly(lactic acid)−Poly(ethylene glycol) (PLA−PEG) Block Copolymers as Drug Delivery Vehicles (2001)

Nanoparticles assembled from poly(d,l-lactic acid)−poly(ethylene glycol) (PLA−PEG) block copolymers may have a therapeutic application in site-specific drug delivery. A series of AB block copolymers based on a fixed PEG block (5 kDa) and a varying PLA segment (2−110 kDa) have been synthesized by the ring-opening polymerization of d,l-lactide using stannous octoate as a catalyst. These copolymers assembled to form spherical nanoparticles in aqueous media following precipitation from a water-miscible organic solvent. 1H NMR studies of the PLA−PEG nanoparticles in D2O confirmed their core−shell structure, with negligible penetration of the hydrated PEG chains into the PLA core. The influence of the PLA block molecular weight on the hydrodynamic size and micellar aggregation number of the assemblies was determined by dynamic and static light scattering techniques. The hydrodynamic radius of the PLA−PEG 2:5−30:5 nanoparticles was solely dependent on the copolymer architecture and scaled linearly as NPLA1/3, where NPLA is the number of monomeric units in the PLA block. The PEG chains of the small PLA−PEG 2:5 and 3:5 assemblies appeared to be fairly splayed as a consequence of their relatively low aggregation number and high surface coverage. However, as NPLA was increased to 6 kDa the area available per PEG chain at the periphery of the shell decreased significantly and then remained fairly constant with further increases in the molecular weight of the PLA block. The aggregation number and hence particle size of nanoparticles produced from copolymers with a PLA block of 45 kDa or more was found to also depend on the concentration of copolymer dissolved in the organic phase during preparation. This suggested that that the PEG chains had little influence on the assembly of the higher molecular weight copolymers.
Digital coding of speech in sub-bands (2005)

A rationale is advanced for digitally coding speech signals in terms of sub-bands of the total spectrum. The approach provides a means for controlling and reducing quantizing noise in the coding. Each sub-band is quantized with an accuracy (bit allocation) based upon perceptual criteria. As a result, the quality of the coded signal is improved over that obtained from a single full-band coding of the total spectrum. In one implementation, the individual sub-bands are low-pass translated before coding. In another, "integer-band" sampling is employed to alias the signal in an advantageous way before coding. Other possibilities extend to complex demodulation of the sub-bands, and to representing the subband signals in terms of envelopes and phase-derivatives. In all techniques, adaptive quantization is used for the coding, and a parsimonious allocation of bits is made across the bands. Computer simulations are made to demonstrate the signal qualities obtained for codings at 16 and 9.6 Kbits/sec.
Figure detection and part label extraction from patent drawing images (2012)

The US Patent and Trademark Office, together with the NASA Tournament Lab, launched a contest to develop spe-cialized algorithms to help bring the seven million patents presently in the patent archive into the digital age. The contest was hosted by TopCoder.com, the largest competitive online software developer community. The challenge was to detect, segment and recognize figures, captions and part labels from patent drawing images. The solution presented in this work was the winning submission. Index Terms — Image analysis, Character recognition, Image segmentation, Document image analysis
The U1 RNA-binding site of the U1 small nuclear ribonucleoprotein (snRNP)-associated A protein suggests a similarity with U2 snRNPs. (1989)

The site of interaction between human U1 RNA and one of its uniquely associated proteins, A, was examined with in vitro binding assays. The A protein bound directly to stem-loop II of U1 RNA in a region which exhibits sequence similarity to U2 RNA. The similarity with U2 RNA was in a region that has been shown to interact with a U2 RNA-associated protein. The A protein-binding site on U1 RNA overlapped a previously described epitope for an RNA-specific human autoantibody (S. L. Deutscher and J. D. Keene, Proc. Natl. Acad. Sci. USA 85:3299-3303, 1988), supporting the hypothesis that the anti-RNA antibody originated as an anti-idiotypic response to A protein-specific autoantibodies.
Direct Cellular Responses to Platinum-Induced DNA Damage (2007)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTDirect Cellular Responses to Platinum-Induced DNA DamageYongwon Jung and Stephen J. LippardView Author Information Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307 Cite this: Chem. Rev. 2007, 107, 5, 1387–1407Publication Date (Web):April 25, 2007Publication History Received18 October 2006Published online25 April 2007Published inissue 1 May 2007https://pubs.acs.org/doi/10.1021/cr068207jhttps://doi.org/10.1021/cr068207jresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views9405Altmetric-Citations1220LEARN 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 SUBJECTS:Adducts,Antineoplastic agents,Genetics,Peptides and proteins,Platinum Get e-Alerts
Space Time Block Coding HARQ scheme for Highly Frequency Selective Channels (2007)

We proposed a hybrid automatic repeat request (HARQ) packet transmission scheme for a multiple input multiple output (MIMO) system in a frequency selective fading channel. The scheme combines Alamouti space-time block coding with MIMO-HARQ and single-carrier frequency domain equalization (SC-FDE). It is shown that the technique works in a frequency flat fading channel as well.
The adjuvant effect of Vibrio cholerae and Escherichia coli heat‐labile enterotoxins is linked to their ADP‐ribosyltransferase activity (1992)

This study addressed the question of whether the mucosal adjuvant property of cholera toxin (CT) and the structurally closely related Escherichia coli heat-labile toxin (LT) requires the enterotoxic and adenylate cyclase/cAMP activating property of these molecules. Therefore, we investigated the cytotoxic and adjuvant abilities of the enterotoxins and compared the results with those obtained with the non-toxic CT and LT derivatives; recombinant CTB (rCTB) and a mutated LT (mLT), which had a single amino acid substitution in position 112 (Glu----Lys) of the A subunit. Detailed functional studies revealed that, in contrast to the enterotoxins, both rCTB and mLT lacked ADP-ribosylating and cAMP-stimulating abilities. However, similar membrane ganglioside GM1-receptor binding ability of all the putative adjuvants was demonstrated. When the probe antigen, keyhole limpet hemocyanin (KLH), was given perorally together with CT or LT strong gut mucosal anti-KLH immune responses were stimulated, whereas no or very low anti-KLH responses were seen in the groups which received antigen admixed with rCTB or the mLT. Moreover, the specific serum antibody responses to the various immunization protocols closely paralleled the local anti-KLH response in the gut. From these results it appears that the adjuvant mechanism of LT, and probably also of CT, is linked to the ability to ADP-ribosylate and to stimulate cAMP formation. However, this study does not unequivocally rule out other possibilities such as interactions by the A1 fragment of CT or LT with other G-proteins than Gs alpha or events that parallel or precede the effects on the adenylate cyclase/cAMP system. Thus, the levels of ADP-ribosylation and cAMP-induction that are required and the key event or target cell that is responsible for the adjuvant effect of CT and LT remain to be elucidated. Studies are underway to address these issues.
Assessment of cell proliferation and muscular structure following surgical tongue volume reduction in pigs (2010)

Fibrosis without predominant myogenic regeneration was the major histological consequence of surgical tongue volume reduction.
Optimal Large-Angle Single-Axis Rotational Maneuvers of Flexible Spacecraft (1980)

The necessary conditions formulated from Pontryagin's principle for optimal single-axis reorientations of a flexible vehicle having a control system capable of generating a continuous torque (on a rigid part of the structure) are discussed in this paper. The flexural deformations are modeled using the assumed modes method and only small (linear) flexural displacements are considered. A single-stage relaxation process is proposed for solution of the two-point boundary-value problem. Starting iteratives for initial costate variables are obtained by zeroing the kinematic nonlinearity in the state equation, leading to a closed-form solution algorithm. The relaxation process increases the participation of the nonlinearity in a sequence of neighboring optimal solutions, converging finally to the solution of the nonlinear problem.
A comparison of efficient beamforming algorithms (1984)

Time domain and frequency domain concepts which aid in the design and efficient implementation of a digital beamformer have been described at various times in the literature. The numerous beam-former structures that result are discussed with an emphasis on hardware requirements and spectral areas of application. Time domain procedures which include delay-sum, partial-sum, interpolation and shifted-sideband beamforming, and frequency domain techniques which include the application of discrete Fourier transforms and phase shift beam-forming are considered. Hardware considerations are primarily in the areas of analog-to-digital conversion, data storage, and computational throughput requirements.
Prostate-Specific Membrane Antigen as a Potential Novel Vascular Target for Treatment of Glioblastoma Multiforme (2011)

Prostate-specific membrane antigen is expressed in the vasculature of GBM vessels, thus rendering a potential novel therapeutic vascular target. A clinical trial with a cytotoxin-conjugated antibody to PSMA is planned.
The use of human CD68 transcriptional regulatory sequences to direct high‐level expression of class A scavenger receptor in macrophages in vitro and in vivo (2001)

Macrophages (Mphi) play a key role in innate and acquired immunity. The study of Mphi biology has been hampered by the absence of suitable gene regulatory sequences for the overexpression of heterologous genes in Mphi. The human CD68 gene encodes a glycoprotein that is expressed in monocytes and Mphi, and therefore represents an attractive candidate gene for the generation of a Mphi-specific gene-targeting vector. A transgene expression cassette that combines 2.9 kb of CD68 5' flanking sequence with the 83-bp first intron (IVS-1) of the CD68 gene, directed high-level, long-lasting expression of class A human scavenger receptor (hSR-A) isoforms in the murine Mphi cell line, RAW-264. By using this CD68 expression cassette to generate Mphi cell lines that overexpress a soluble secreted form of the extracellular portion of type I human SR-A, we were able to purify significant quantities of this protein and show its ability to inhibit SR-A-mediated endocytosis. Analysis of two independent lines of transgenic mice that expressed type III human SR-A under the control of the CD68 gene sequences revealed transgene mRNA expression in elicited Mphi populations and in mouse tissues in a pattern that was consistent with Mphi-specific gene targeting. These data show that CD68 transcriptional regulatory sequences can be used to direct high-level transgene expression in Mphi in vitro and in vivo.
Imaging of luciferase and GFP‐transfected human tumours in nude mice (2003)

Studies were performed to compare green fluorescent protein (GFP)-transfected and fi re fl y luciferase (Luc)-transfected MCF-7 human breast tumour cells both in vitro and in vivo. For in vitro studies, cells were serially diluted in 96-well microplates and analysed using a NightOwl LB 981 Molecular Light Imager and a Victor multilabel reader. For in vivo studies, nude mice were injected either intraperitoneally, intravenously or subcutaneously with transfected cells and then imaged using the NightOwl Imager after intraperitoneal injection of d-luciferin for Luc tumours, or excitation at 470 nm for GFP tumours. In vitro imaging studies revealed that both GFP and Luc transfectants were quantifiable. However, the Luc-transfected cells were detectable at a significantly lower concentration compared to GFP transfectants. In vivo studies demonstrated that GFP-transfected tumours were detectable as subcutaneous and intraperitoneal tumours but not as deep tissue lesions, whereas Luc-transfected tumours were detectable as subcutaneous and intraperitoneal tumours and as deep tissue lesions resulting from intraperitoneal or intravenous inoculation. These findings demonstrate that GFP-transfected cells may be useful for imaging studies of superficial tumours where both excitation and emission wavelengths are able to penetrate tissues, whereas luciferase-transfected cells appear superior for imaging studies of primary and metastatic tumours in distant sites and deep tissues.
International Debt: The Anatomy of a Financial Crisis, 1973–83 (1992)

Since 1982 the international financial system has been facing a period of profound crisis characterised by the inability of many developing countries to generate sufficient funding to meet their outstanding commitments and to create an environment in which there can be sustained improvements in living standards. Given the increasingly interdependent character of the world economy as it approaches the twenty-first century, these difficulties are not one-sided affecting only the developing world. It is the banks in the major industrial countries which have funded most of the LDC debt and it is they who are bearing the brunt of loan write-offs. Further as developing countries have sought to improve their international cash flow positions, they have followed policies which have led to reductions in imports. This, of course, will have had an adverse effect on output growth and the trade balance positions of the more well-off industrial countries.
Role of G6PD, ABO incompatibility, low birth weight and infection in neonatal hyperbilirubinaemia. (1987)

In a random sample of 1,000 neonates from a Delhi Hospital the incidence of jaundice was 53% and of hyperbilirubinaemia (HB) 6%. Rh incompatibility was detected in 4% of the neonates. In 74 cases of HB (excluding those due to Rh incompatibility) collected from the above series and from subsequent hospital admissions, incidences of different factors contributing to HB were: low birth weight in 54%, G6PD deficiency in 35%, ABO incompatibility in 31% and infection in 31%. In 45% of them a single factor was present and in the remaining more than one factor was present.
Linear complexity algorithms for hierarchical routing (1989)

A hierarchical procedure for net routing on l*m*n grid-graphs, where l is the number of layers, m is the number of rows, and n is the number of columns, is presented. The hierarchy reduces the overall problem to a sequence of subproblems, where each subproblem works on an l*m'*n portion of the overall grid. For each subproblem, an initial constructive placement (CP) of as many nets as possible is used; then a generalized dynamic programming (DP) algorithm to solve the Steiner problem of an l*2*n grid-graph is used for any remaining nets. The CP procedure uses simplistic routing assumptions to route quickly as many nets as possible. If all nets are routed, the subproblem solution is (locally) optimal and the corresponding branch of the binary recursion tree generated by the hierarchy is pruned. For any unrouted nets, the generalized DP procedure is called to route each net, one at a time, with a run time complexity of O(K*n) where n is the number of columns and K is a function of the grid cross section and layer/wiring restrictions. There are no a priori layer restrictions or limitations on the number of layers used; three-layer cases and even some four-layer cases are feasible for the PYRAMID 90-X.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Size Tunable Au@Ag Core–Shell Nanoparticles: Synthesis and Surface-Enhanced Raman Scattering Properties (2013)

We describe a simple and efficient methodology for the aqueous synthesis of stable, uniform, and size tunable Au@Ag core-shell nanoparticles (NPs) that are stabilized by citrate ions. The synthetic route is based on the stepwise Ag reduction on preformed Au NPs. The final size of the core-shell NPs and therefore their optical properties can be modulated at least from 30 to 110 nm by either tuning the Ag shell thickness or changing the size of the Au core. The optical properties of the Au@Ag core-shell NPs resemble those of pure Ag NPs of similar sizes, which was confirmed by means of Mie extinction calculations. We additionally evaluated the surface-enhanced raman scattering (SERS) enhancing properties of Au@Ag core-shell NP colloids with three different laser lines (532, 633, and 785 nm). Importantly, such core-shell NPs also exhibit a higher SERS efficiency than Ag NPs of similar size under near-infrared excitation. The results obtained here serve as a basis to select Au@Ag core-shell NPs of specific size and composition with maximum SERS efficiency at their respective excitation wavelengths for SERS-based analytical and bioimaging applications.
Potency testing of killed polio vaccine in rats. (1981)

Various laboratory animal species were considered for testing the potency of killed poliovaccine. The rat appeared most suitable for obtaining quantitative information by measuring the titre of the antibody response. There was, in general, a good correlation between antibody response in rats and D-antigen titre. This relationship appeared less clear for heat-degraded or long-stored vaccines.
Structure, spectra, and function of heme sites (2000)

Heme proteins are a class of biologically important macromolecules that have a unique, common active site, an iron–protoporphyrin IX complex. Despite the common active site, heme proteins have three distinct biological functions: reversible oxygen transport, reversible electron transfer, and metabolizing enzymes. Each type of heme protein differs in the specific forms of the heme complexes that are involved in its biological function. Not only the biological activity, but also the spectroscopic properties of the intact heme proteins are largely centered on the heme unit. Thus, for this family of proteins, there is a particularly strong link between structure spectra and function. However, experimental spectroscopic methods cannot, by themselves, yield a detailed molecular description of the heme active site in the many stable and transient forms that it assumes as a part of its function. Missing is a direct correspondence between observable properties and explicit models for these diverse stable and transient forms of the heme active site that can best be provided by computational studies. In the work reported here, the seminal role played by one of these methods, the semiempirical all-valence electron INDO/SCF/CI method, developed in the laboratory of Dr. Michael Zerner, in elucidating the structure, spectra, and function of heme proteins is demonstrated by four examples from work done in our laboratory. The goal of the first study was to elucidate the nature of the important oxyferrous species of the globins and to use it to provide a consistent explanation of the origin of the observed spectroscopic properties. The goal of the second study was to identify the origin of the signature spectrum of the ubiquitous metabolizing heme proteins, the cytochrome P450s, an intense peak at 450 nm giving them their name. The other two studies illustrate the usefulness of this method in identifying transient species in two related families of metabolizing heme proteins. These are the postulated peroxide complex of peroxidases and the putative catalytically active Compound I form of the cytochrome P450s. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 54–70, 2000
Maintenance of Mydriasis with One Bolus of Epinephrine Injection During Phacoemulsification (2001)

Surgically-induced miosis commonly occurs during cataract extraction surgery, complicating removal of lens cortex and placement of a posterior chamber intraocular lens. To maintain intraoperative mydriasis, one bolus of epinephrine injection was used in our study. The pupillary response to various doses of intracameral epinephrine (0.1 ml of 1:25,000, 1:50,000, 1:100,000, 1:200,000, 1:400,000) was assessed in 60 consecutive patients. The pupil size was measured just prior to the incision, one min after epinephrine injection, after phacoemulsification and after irrigation/aspiration. There was no significant difference among the mean mydriatic responses to the epinephrine concentrations we tested. The 1:400,000 concentration appeared to be as effective as 1:25,000, but two cases of the 1:400,000 group failed to maintain the pupil diameter after irrigation/aspiration. In addition, we found that blood pressure did not elevate after injection of any concentration of epinephrine. We concluded that one bolus of an extremely dilute concentration of epinephrine (i.e., 1:400,000) injection might be effective in maintaining mydriasis during cataract surgery without systemic side effects.