gebhart/patrepeval huggingface dataset:
Cyclostationary noise analysis of large RF circuits with multitone excitations (1998)

This paper introduces a new, efficient technique for analyzing noise in large RF circuits subjected to true multitone excitations. Noise statistics in such circuits are time-varying, hence cyclostationary stochastic processes, characterized by harmonic power spectral densities (HPSDs), are used to describe noise. HPSDs are used to devise a harmonic-balance-based noise algorithm with the property that required computational resources grow almost linearly with circuit size and nonlinearity. Device noises with arbitrary spectra (including thermal, shot, and flicker noises) are handled, and input and output correlations, as well as individual device contributions, can be calculated. HPSD-based analysis is also used to establish the nonintuitive result that bandpass filtering of cyclostationary noise can result in stationary noise. Results from the new method are validated against Monte Carlo simulations. A large RF integrated circuit (>300 nodes) driven by a local oscillator (LO) tone and a strong RF signal is analyzed in less than two hours. The analysis predicts correctly that the presence of the RF tone leads to noise folding, affecting the circuit's noise performance significantly.
Lighting Up Biochemiluminescence by the Surface Self‐Assembly of DNA–Hemin Complexes (2004)

Illuminating DNA: The assembly of two tailored nucleic acids (colored blue and brown in the scheme) in the presence of hemin yields a G-quadruplex that exhibits peroxidase-like activity and catalyzes the generation of chemiluminescence in the presence of H2O2 and luminol. The DNAzyme is employed for the analysis of DNA (green) in solution and on surfaces.
First experimental demonstration of a Fresnel axicon (2008)

Nondiffracting or Bessel beams find applications in diverse fields like optical tweezers/spanners, microscopy, super-resolution and optical coherence tomography. An axicon, energywise, is the most efficient method for generating a diffraction-free beam. Yet one of the impediments to wide use of these optical elements is the cost related to the way they are manufactured. Recently we proposed a novel optical element - Fresnel axicon (Opt. Lett. 31, 1890, 2006) - which enables to overcome this problem while providing advantages such as compactness and very low bulk absorption. Prototypes of the Fresnel axicon were manufactured. In the present work we report the first experimental results characterising the optical properties of this novel device, which bridges the gap between diffractive axicons and their refractive counterparts.
Analysis of a large-scale VOD architecture for broadband operators: a P2P-based solution (2008)

VOD services distribution is gaining unprecedented interest from the consumer communication industry due to its growing success in both the Internet and residential broadband market. In this article we present a scalable VOD distribution architecture for broadband operators. The solution is based on a P2P streaming concept in which a VOD streaming session requested by a given STB is actually provisioned via a multisource streaming session. This solution has the advantage of scaling naturally with the number of STBs in the network. In this article we focus on efficiently translating the popularity distribution into content availability in the network. Different aspects related to this issue are analyzed and challenges highlighted.
A verified sliding window protocol with variable flow control (1986)

We present a verified sliding window protocol which uses modulo- N sequence numbers to achieve reliable flow-controlled data transfer between a source and a destination. Communication channels are assumed to lose, duplicate and reorder messages in transit. The destination's data needs are represented by a receive window whose size can vary with time. The destination entity uses acknowledgement messages to inform the source entity of the current receive window size and the sequence number of the data word next expected. The source entity responds by sending segments of data words that lie within the allowed window. Each data segment is accompanied by an identifying sequence number and the size of the data segment. The destination entity also uses selective acknowledgement and selective reject messages to inform the source entity of the reception or lack of reception, respectively, of out-of-sequence data segments. Thus, this protocol is a proper extension of the Arpanet's TCP. We have obtained the minimum value of N that ensures correct data transfer and flow control, in terms of the minimum message transmission time, the maximum message lifetime, and the maximum receive window size. The protocol imposes no constraints on the retransmissions of messages or on the data segment sizes; thus, any retransmission policy that optimizes the protocol's performance can be used.
Understanding the Self-Assembly of Proteins onto Gold Nanoparticles and Quantum Dots Driven by Metal-Histidine Coordination (2013)

Coupling of polyhistidine-appended biomolecules to inorganic nanocrystals driven by metal-affinity interactions is a greatly promising strategy to form hybrid bioconjugates. It is simple to implement and can take advantage of the fact that polyhistidine-appended proteins and peptides are routinely prepared using well established molecular engineering techniques. A few groups have shown its effectiveness for coupling proteins onto Zn- or Cd-rich semiconductor quantum dots (QDs). Expanding this conjugation scheme to other metal-rich nanoparticles (NPs) such as AuNPs would be of great interest to researchers actively seeking effective means for interfacing nanostructured materials with biology. In this report, we investigated the metal-affinity driven self-assembly between AuNPs and two engineered proteins, a His7-appended maltose binding protein (MBP-His) and a fluorescent His6-terminated mCherry protein. In particular, we investigated the influence of the capping ligand affinity to the nanoparticle surface, its density, and its lateral extension on the AuNP-protein self-assembly. Affinity gel chromatography was used to test the AuNP-MPB-His7 self-assembly, while NP-to-mCherry-His6 binding was evaluated using fluorescence measurements. We also assessed the kinetics of the self-assembly between AuNPs and proteins in solution, using time-dependent changes in the energy transfer quenching of mCherry fluorescent proteins as they immobilize onto the AuNP surface. This allowed determination of the dissociation rate constant, Kd(-1) ∼ 1-5 nM. Furthermore, a close comparison of the protein self-assembly onto AuNPs or QDs provided additional insights into which parameters control the interactions between imidazoles and metal ions in these systems.
Improving locality of reference in a garbage-collecting memory management system (1988)

Modern Lisp systems make heavy use of a garbage-collecting style of memory management. Generally, the locality of reference in garbage-collected systems has been very poor. In virtual memory systems, this poor locality of reference generally causes a large amount of wasted time waiting on page faults or uses excessively large amounts of main memory. An adaptive memory management algorithm, described in this article, allows substantial improvement in locality of reference. Performance measurements indicate that page-wait time typically is reduced by a factor of four with constant memory size and disk technology. Alternately, the size of memory typically can be reduced by a factor of two with constant performance.
PTC124 is an orally bioavailable compound that promotes suppression of the human CFTR -G542X nonsense allele in a CF mouse model (2008)

Nonsense mutations inactivate gene function and are the underlying cause of a large percentage of the individual cases of many genetic disorders. PTC124 is an orally bioavailable compound that promotes readthrough of premature translation termination codons, suggesting that it may have the potential to treat genetic diseases caused by nonsense mutations. Using a mouse model for cystic fibrosis (CF), we show that s.c. injection or oral administration of PTC124 to Cftr-/- mice expressing a human CFTR-G542X transgene suppressed the G542X nonsense mutation and restored a significant amount of human (h)CFTR protein and function. Translational readthrough of the premature stop codon was demonstrated in this mouse model in two ways. First, immunofluorescence staining showed that PTC124 treatment resulted in the appearance of hCFTR protein at the apical surface of intestinal glands in Cftr-/- hCFTR-G542X mice. In addition, functional assays demonstrated that PTC124 treatment restored 24-29% of the average cAMP-stimulated transepithelial chloride currents observed in wild-type mice. These results indicate that PTC124 can effectively suppress the hCFTR-G542X nonsense mutation in vivo. In light of its oral bioavailability, safety toxicology profile in animal studies, and efficacy with other nonsense alleles, PTC124 has the potential to be an important therapeutic agent for the treatment of inherited diseases caused by nonsense mutations.
Antimicrobial activity and antibiotic resistance of Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus strains isolated from Turkish homemade yoghurts (2011)

The aim of this study was to determine the inhibitive effect of 25 Lactobacillus delbruecki ssp. bulgaricus and 16 Streptococcus thermophilus strains isolated from 30 different homemade yoghurts on several pathogen and contaminant bacteria. The antibiotic resistance of these bacteria was also determined. All of Lactobacillus bulgaricus strains exhibited antimicrobial activity against Escherichia coli, whereas all of S. thermophilus strains exhibited the same activity against Klebsiella pneumoniae. None of L. bulgaricus strains were resistant to the polymixin-B, only the OL4 strain has shown resistance to bacitracin. While some strains of S. thermophilus like C6 and SL4 exhibited resistance to novobiocin, SY72, M3, C1M, and F1M were shown to optochin. ET6 and SY73 strains were found to be resistant in both novobiocin and optochin.
Generalized contextual recognition of hand-printed documents using semantic trees with lazy evaluation (2002)

Describes a new general-purpose contextual architecture which provides a unified framework for efficiently combining all types and levels of context in hand-print recognition applications. The architecture has been designed and built as a C++ class library and utilised within an initial demonstrator which implements full contextual constraints for a combination of postcode and corresponding postal address. Preliminary evaluation of the demonstrator suggests the system has the potential to achieve genuinely remarkable performance compared with previous context systems: its memory requirements are an order of magnitude less than an equivalent trie-based dictionary; its search speed is at least an order of magnitude faster than the trie, and actually gets faster as the dictionary size increases(!); and its error rate is virtually zero if suitable contextual constraints can be applied. Using this architecture, it appears to be possible to build real-time solutions to large-scale heterogeneous contextual problems.
Enhancement of tumor-specific immune response with plasmid DNA replicon vectors. (2000)

To enhance the immunogenicity of nucleic acid vaccines, we used plasmid DNA vectors that contained replicons derived from the prototype alphavirus, Sindbis, and another alphavirus, Semliki Forest virus. When transfected into cells or injected directly into animal muscle, these plasmids launch a self-replicating RNA vector (replicon) which in turn directs the expression of a model tumor antigen. Immunization with plasmid DNA replicons elicited immune responses at doses 100 to 1000-fold lower than conventional DNA plasmids and effectively treated mice bearing an experimental tumor expressing the model antigen. Significantly, replicon-based DNA plasmids did not produce a greater quantity of antigen; instead, antigen production differed qualitatively. Plasmid DNA replicons mediated antigen production that was homogeneous in all transfected cells and associated with the apoptotic death of the host cells. Because of their safety and efficacy, plasmid DNA replicons may be useful in the development of recombinant vaccines for infectious diseases and cancer.
O-Antigen Diversity among Acinetobacter baumannii Strains from the Czech Republic and Northwestern Europe, as Determined by Lipopolysaccharide-Specific Monoclonal Antibodies (2001)

O-antigen-specific monoclonal antibodies (MAbs) are currently being generated to develop an O-serotyping scheme for the genus Acinetobacter and to provide potent tools to study the diversity of O-antigens among Acinetobacter strains. In this report, Acinetobacter baumannii strains from the Czech Republic and from two clonal groups identified in Northwestern Europe (termed clones I and II) were investigated for their reactivity with a panel of O-antigen-specific MAbs generated against Acinetobacter strains from various species. The bacteria were characterized for their ribotype, biotype, and antibiotic susceptibility and the presence of the 8.7-kb plasmid pAN1. By using the combination of these typing profiles, the Czech strains could be classified into four previously defined groups (A. Nemec, L. Janda, O. Melter, and L. Dijkshoorn, J. Med. Microbiol. 48:287-296, 1999): two relatively homogeneous groups of multiresistant strains (termed groups A and B), a heterogeneous group of other multiresistant strains, and a group of susceptible strains. O-antigen reactivity was observed primarily with MAbs generated against Acinetobacter calcoaceticus and Acinetobacter baumannii strains. A comparison of reaction patterns confirmed the previously hypothesized clonal relationship between group A and clone I strains, which are also similar in other properties. The results show that there is limited O-antigen variability among strains with similar geno- and phenotypic characteristics and are suggestive of a high prevalence of certain A. baumannii serotypes in the clinical environment. It is also shown that O-antigen-specific MAbs are useful for the follow-up of strains causing outbreaks in hospitals.
PRENATAL DIAGNOSIS USING FETAL CELLS IN THE MATERNAL CIRCULATION (1990)

All current methods of fetal karyotyping are invasive and carry a definite, albeit small, procedure- related risk.Because of this and testing costs, only women older than 35 years who have a greater risk for fetal aneuploidy are currently offered prenatal testing.But this detects only 20% to 25% of fetuses with Down syndrome.It would be a tremendous advance to find a noninvasive technique for prenatal diagnosis that carries no procedure-related risk and could be offered to all pregnant women.We describe a possible technique for noninvasive prenatal diagnosis that aims to identify fetal cells in the peripheral maternal circulation and successfully garner them for pre- natal testing.Early attempts at fetal karyotyping were hampered by inaccurate diagnostic methods and cumbersome cell-counting techniques.Today, improved capabilities of identifying and enriching for fetal cells, coupled with sensitive methods of analysis such as the polymerase chain reaction, bring renewed enthusiasm to this task.Many technical issues, as well as serious questions regarding the test's utility, still exist, however, and must be explored and answered before the capture of fetal cells in the maternal circulation translates into reality for noninvasive prenatal diagnosis.
Smad regulation in TGF-β signal transduction (2001)

Smad proteins transduce signals from transforming growth factor-beta (TGF-beta) superfamily ligands that regulate cell proliferation, differentiation and death through activation of receptor serine/threonine kinases. Phosphorylation of receptor-activated Smads (R-Smads) leads to formation of complexes with the common mediator Smad (Co-Smad), which are imported to the nucleus. Nuclear Smad oligomers bind to DNA and associate with transcription factors to regulate expression of target genes. Alternatively, nuclear R-Smads associate with ubiquitin ligases and promote degradation of transcriptional repressors, thus facilitating target gene regulation by TGF-beta. Smads themselves can also become ubiquitinated and are degraded by proteasomes. Finally, the inhibitory Smads (I-Smads) block phosphorylation of R-Smads by the receptors and promote ubiquitination and degradation of receptor complexes, thus inhibiting signalling.
Human beta-casein. Amino acid sequence and identification of phosphorylation sites. (1984)

The primary structure of human beta-casein has been determined by automated Edman degradation of the intact protein and of peptides derived therefrom by hydrolysis with trypsin and by chemical cleavage with cyanogen bromide. For each form of this multiphosphorylated protein (0-5 P/molecule), phosphorylated sites at specific seryl and threonyl residues have been identified. These are located near the amino terminus, within the first 10 residues of this 212-amino acid molecule. Sequence comparison of human beta-casein with the bovine and ovine proteins reveals 50% identity and a 10-residue shifted alignment relationship. Locations of prolyl and charged residues are generally conserved for the three homologues. The sequence data indicate the existence of genetic polymorphism involving uncharged residues in human beta-casein.
Nanowire Arrays Electrodeposited from Liquid Crystalline Phases (2002)

Crystalline silver nanowire arrays (see Figure) with high aspect ratio are produced here by electrodeposition from a reverse hexagonal liquid-crystalline phase. Enhancement of the alignment is shown to be possible by applying a high electric field gradient during deposition. High-density bundles can be obtained by washing the deposited material and single wires can easily be retrieved by sonication of these bundles.
Activation of microglia and astrocytes by CpG oligodeoxynucleotides (2001)

Bacterial DNA and synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG motifs stimulate cells of the immune system to secrete a variety of cytokines and chemokines. This function can be carried out by microglia and astrocytes in the CNS. To evaluate the effect of CpG ODN on microglia and astrocytes, purified cells were isolated and cultured in vitro. CpG ODN rapidly up-regulated their production of IL-1beta, IL-6, IL-12, TNFalpha, MIP-1alpha and/or MIP-1beta. In vivo, systemically administered CpG ODN up-regulated the expression of mRNA encoding cytokines and chemokines in normal mouse brain. These findings suggest that CpG ODN can directly activate immune cells of the CNS.
A novel feeding strategy for enhanced plasmid stability and protein production in recombinant yeast fedbatch fermentation (1997)

A novel feeding strategy in fedbatch recombinant yeast fermentation was developed to achieve high plasmid stability and protein productivity for fermentation using low-cost rich (non-selective) media. In batch fermentations with a recombinant yeast, Saccharomyces cerevisiae, which carried the plasmid pSXR125 for the production of beta-galactosidase, it was found that the fraction of plasmid-carrying cells decreased during the exponential growth phase but increased during the stationary phase. This fraction increase in the stationary phase was attributed to the death rate difference between the plasmid-free and plasmid-carrying cells caused by glucose starvation in the stationary phase. Plasmid-free cells grew faster than plasmid-carrying cells when there were plenty of growth substrate, but they also lysed or died faster upon the depletion of the growth substrate. Thus, pulse additions of the growth substrate (glucose) at appropriate time intervals allowing for significant starvation period between two consecutive feedings during fedbatch fermentation should have positive effects on stabilizing plasmid and enhancing protein production. A selective medium was used to grow cells in the initial batch fermentation, which was then followed with pulse feeding of concentrated non-selective media in fedbatch fermentation. Both experimental data and model simulation show that the periodic glucose starvation feeding strategy can maintain a stable plasmid-carrying cell fraction and a stable specific productivity of the recombinant protein, even with a non-selective medium feed for a long operation period. On the contrary, without glucose starvation, the fraction of plasmid-carrying cells and the specific productivity continue to drop during the fedbatch fermentation, which would greatly reduce the product yield and limit the duration that the fermentation can be effectively operated. The new feeding strategy would allow the economic use of a rich, non-selective medium in high cell density recombinant fedbatch fermentation. This new feeding strategy can be easily implemented with a simple IBM-PC based control system, which monitors either glucose or cell concentration in the fermentation broth.
Randomized Phase II Trial Comparing Bevacizumab Plus Carboplatin and Paclitaxel With Carboplatin and Paclitaxel Alone in Previously Untreated Locally Advanced or Metastatic Non-Small-Cell Lung Cancer (2004)

Bevacizumab in combination with carboplatin and paclitaxel improved overall response and time to progression in patients with advanced or recurrent non-small-cell lung cancer. Patients with nonsquamous cell histology appear to be a subpopulation with improved outcome and acceptable safety risks.
Functional Characterization of Abicipar-Pegol, an Anti-VEGF DARPin Therapeutic That Potently Inhibits Angiogenesis and Vascular Permeability (2018)

These data support the testing of abicipar as a treatment for retinal diseases characterized by neovascularization and vascular leak.
Incidence and Prognosis of Transient Neurological Attacks (2007)

Patients who experience nonfocal TNAs, and especially those with mixed TNAs, have a higher risk of major vascular diseases and dementia than persons without TNA.
Signals from the notochord and floor plate regulate the region-specific expression of two Pax genes in the developing spinal cord (1993)

ABSTRACT Members of the paired box (Pax) gene family are expressed in discrete regions of the developing central nervous system, suggesting a role in neural patterning. In this study, we describe the isolation of the chicken homologues of Pax-3 and Pax-6. Both genes are very highly conserved and share extensive homology with the mouse Pax-3 and Pax-6 genes. Pax-3 is expressed in the primitive streak and in two bands of cells at the lateral extremity of the neural plate. In the spinal cord, Pax-6 is expressed later than Pax-3 with the first detectable expression preceding closure of the neural tube. When the neural tube closes, transcripts of both genes become dorsoventrally restricted in the undifferentiated mitotic neuroepithelium. We show that the removal of the notochord, or implantation of an additional notochord, dramatically alter the dorsoventral (DV) expression patterns of Pax-3 and Pax-6. These manipulations suggest that signals from the notochord and floor plate regulate the establishment of the dorsoventrally restricted expression domains of Pax-3 and Pax-6 in the spinal cord. The rapid changes to Pax gene expression that occur in neural progenitor cells following the grafting of an ectopic notochord suggest that changes to Pax gene expression are an early effect of the notochord on spinal cord patterning.