gebhart/patrepeval huggingface dataset:
Using a neural network to backtranslate amino acid sequences (1998)

A neural network (NN) was trained on amino and nucleic acid sequences to test the NN’s ability to predict a nucleic acid sequence given only an amino acid sequence. A multi-layer backpropagation network of one hidden layer with 5 to 9 neurons was used. Different network configurations were used with varying numbers of input neurons to represent amino acids, while a constant representation was used for the output layer representing nucleic acids. In the besttrained network, 93% of the overall bases, 85% of the degenerate bases, and 100% of the fixed bases were correctly predicted from randomly selected test sequences. The training set was composed of 60 human sequences in a window of 10 to 25 codons at the coding sequence start site. Different NN configurations involving the encoding of amino acids under increasing window sizes were evaluated to predict the behavior of the NN with a significantly larger training set. This genetic data analysis effort will assist in understanding human gene structure. Benefits include computational tools that could predict more reliably the backtranslation of amino acid sequences useful for Degenerate PCR cloning, and may assist the identification of human gene coding sequences (CDS) from open reading frames in DNA databases.
Train performance and simulation (1999)

Article Train performance and simulation Share on Author: Paul Martin Comreco Rail Ltd, St Marys Court, 39 Blossom Street, York, YO24 1AQ, U.K. Comreco Rail Ltd, St Marys Court, 39 Blossom Street, York, YO24 1AQ, U.K.View Profile Authors Info & Claims WSC '99: Proceedings of the 31st conference on Winter simulation: Simulation---a bridge to the future - Volume 2December 1999 Pages 1287–1294https://doi.org/10.1145/324898.325068Online:01 December 1999Publication History 3citation566DownloadsMetricsTotal Citations3Total Downloads566Last 12 Months10Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Si Photonics and Fiber to the Home (2009)

This paper describes Si photonics and the key application to fiber-to-the-home (FTTH). Mass production in terms of complementary metal-oxide-semiconductor technology is a prerequisite for Si photonics to provide a cost-effective solution, and FTTH should meet this requirement. We describe a design of the FTTH chip architecture with wavelength-division multiplexing based on ring-resonator demultiplexers and multiplexers. The grand challenge of Si photonics for this application is the production of Ge photodetectors and modulators.
PiQASso: Pisa Question Answering system (2001)

In this 42-year-old-man with suspected cholelithiasis the following finding of the serosal surface of the gallbladder was discovered by laparoscopic examination: Smooth serosal elevation, dark-greenish in color in a size of the small bean; No hypervascularity in the surrounding serosa. This finding was confirmed to be due to intramural gallstones. This is the first description of the laparoscopic finding of the intramural stones of the gallbladder, which may assist in establishing the clinical characteristics of the intramural gallstones.
Electrochemical engineering of hollow nanoarchitectures: pulse/step anodization (Si, Al, Ti) and their applications (2013)

Hollow nanoarchitectured materials with straight channels play a crucial role in the fields of renewable energy, environment and biotechnology due to their one-dimensional morphology and extraordinary properties. The current challenge is the difficulty on tailoring hollow nanoarchitectures with well-controlled morphology at a relatively low cost. As a conventional technique, electrochemistry exhibits its unique advantage on machining nanostructures. In this review, we present the progress of electrochemistry as a valuable tool in construction of novel hollow nanoarchitectures through pulse/step anodization, such as surface pre-texturing, modulated, branched and multilayered pore architectures, and free-standing membranes. Basic principles for electrochemical engineering of mono- or multi-ordered nanostructures as well as free-standing membranes are extracted from specific examples (i.e. porous silicon, aluminum and titanium oxide). The potential of such nanoarchitectures are further demonstrated for the applications of photovoltaics, water splitting, organic degradation, nanostructure templates, biosensors and drug release. The electrochemical techniques provide a powerful approach to produce nanostructures with morphological complexity, which could have far-reaching implications in the design of future nanoscale systems.
A novel error control scheme for video streaming over IEEE802.11 network (2004)

In this paper, we propose a novel error control scheme. The scheme, also known as hybrid dynamic packet shuffling (HOPS), consists of three parts: hybrid unequal error protection (HUEP), dynamic packet length adjustment and packets shuffling. HUEP with adaptive parity codes can correct bit error in short time with controllable redundancy. Dynamic packet length adjustment module is a mechanism to generate different size packets along with the varying network situation. The main idea of packets shuffling is to tradeoff continuous error (the unacceptable bursty error) against average error (the acceptable error). Simulation results indicate that these three modules maintain an acceptable video quality at very high rate of bursty error without retransmission.
Magnetoencephalographic localization in pediatric epilepsy surgery: Comparison with invasive intracranial electroencephalography (1999)

The object of this study was to determine the concordance of the anatomical location of interictal magnetoencephalographic (MEG) spike foci with the location of ictal onset zones identified by invasive ictal intracranial electroencephalographic recordings in children undergoing evaluation for epilepsy surgery. MEG was performed in 11 children with intractable, nonlesional, extratemporal, localization-related epilepsy. Subsequently, chronic invasive intracranial electroencephalographic monitoring was performed by using subdural electrodes to localize the ictal onset zone and eloquent cortex. Based on the invasive monitoring data, all children had excision of, or multiple subpial transections through, ictal onset cortex and surrounding irritative zones. In 10 of 11 patients, the anatomical location of the epileptiform discharges as determined by MEG corresponded to the ictal onset zone established by ictal intracranial recordings. In all children, the anatomical location of the somatosensory hand area, determined by functional mapping through the subdural electrode array, was the same as that delineated by MEG. Nine of 11 patients became either seizure-free or had a greater than 90% reduction in seizures after surgery, with a mean follow-up of 24 months. MEG is a powerful and accurate tool in the presurgical evaluation of children with refractory nonlesional extratemporal epilepsy.
A negative feedback loop attenuates EGF-induced morphological changes. (1991)

Activation of the EGF receptor tyrosine kinase by ligand indirectly activates a series of other cellular enzymes, including protein kinase C. To test the hypothesis that phosphorylation of the EGF receptor by protein kinase C provides an intracellular negative feedback loop to attenuate EGF receptor signaling, we used scanning EM to follow the characteristic EGF-induced retraction of lamellipodia and concomitant cell shape changes. Wild type and mutant EGF receptors were expressed in receptor-deficient NR6 cells. The mutant receptors were prepared by truncation at C' terminal residue 973 (c'973) to provide resistance to ligand-induced down regulation that strongly attenuates receptor signaling and by replacement of threonine 654 (T654) with alanine (A654) to remove the site of phosphorylation by protein kinase C. Cells expressing WT and c'973 EGF receptors demonstrated characteristic lamellipodial retraction after exposure to EGF, with the non-down regulating c'973 EGF receptors responding more rapidly. Exposure of cells to TPA blocked this response. Replacement of T654 by alanine resulted in EGF receptors that were resistant to TPA. Cells expressing the A654 mutation underwent more rapid and more extensive morphologic changes than cells with the corresponding T654 EGF receptor. In cells expressing T654 EGF receptors, down regulation of protein kinase C resulted in more rapid and extensive EGF-induced changes similar to those seen in cells expressing A654 EGF receptors. These data indicate that activation of protein kinase C and subsequent phosphorylation of the EGF receptor at T654 lead to rapid physiological attenuation of EGF receptor signaling.
The parasympathetic secretory nerves of the lacrimal gland of the cat (1971)

1. Electrical stimulation of the brain stem of the anaesthetized cat induces a secretion from the lacrimal gland.2. The secretion is abolished either by Vidian nerve section or by the application of nicotine to the sphenopalatine ganglion.3. In contrast to stimulation of the peripheral end of the cut Vidian nerve, stimulation of the central end induces lacrimal secretion.4. A new pathway is proposed in the light of the experimental findings.
One-pot synthesis of stabilizer-free Ag-Graphene Nanocomposite and its potential application on photodegradation of RhB (2013)

Simultaneous reduction of graphene oxide (GO) and silver nitrate (AgNO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ) into stabilizer-free Ag-Graphene Naoncomposite (AGN) using DMAc-assisted thermal reduction method with controllable density of Ag nanoparticles (Ag NPs) is reported. Microscopy techniques (scanning electron microscopy and high-resolution transmission electron microscopy) have been employed to probe the morphological characteristics of AGN and the lattice plane of Ag NPs. We observed a significant improvement on adsorption ability of AGN-P25 mixture compared with bare P25, indicating potential application on photocatalysis of AGN.
Elicitation of Neutralizing Antibodies Directed against CD4-Induced Epitope(s) Using a CD4 Mimetic Cross-Linked to a HIV-1 Envelope Glycoprotein (2012)

The identification of HIV-1 envelope glycoprotein (Env) structures that can generate broadly neutralizing antibodies (BNAbs) is pivotal to the development of a successful vaccine against HIV-1 aimed at eliciting effective humoral immune responses. To that end, the production of novel Env structure(s) that might induce BNAbs by presentation of conserved epitopes, which are otherwise occluded, is critical. Here, we focus on a structure that stabilizes Env in a conformation representative of its primary (CD4) receptor-bound state, thereby exposing highly conserved "CD4 induced" (CD4i) epitope(s) known to be important for co-receptor binding and subsequent virus infection. A CD4-mimetic miniprotein, miniCD4 (M64U1-SH), was produced and covalently complexed to recombinant, trimeric gp140 envelope glycoprotein (gp140) using site-specific disulfide linkages. The resulting gp140-miniCD4 (gp140-S-S-M64U1) complex was recognized by CD4i antibodies and the HIV-1 co-receptor, CCR5. The gp140-miniCD4 complex elicited the highest titers of CD4i binding antibodies as well as enhanced neutralizing antibodies against Tier 1 viruses as compared to gp140 protein alone following immunization of rabbits. Neutralization against HIV-2(7312/V434M) and additional serum mapping confirm the specific elicitation of antibodies directed to the CD4i epitope(s). These results demonstrate the utility of structure-based approach in improving immunogenic response against specific region, such as the CD4i epitope(s) here, and its potential role in vaccine application.
Characterization of monoclonal antibodies recognizing a Mr 180,000 P-glycoprotein: differential expression of the Mr 180,000 and Mr 170,000 P-glycoproteins in multidrug-resistant human tumor cells. (1989)

P-glycoprotein is a plasma membrane protein believed to mediate resistance to natural product drugs such as vincristine, Adriamycin, and actinomycin D. To facilitate the study of human P-glycoprotein, monoclonal antibodies (designated HYB-612, HYB-241, and HYB-195) were raised against vincristine-resistant human neuroblastoma (SH-SY5Y/VCR) cells. The antibodies recognize a Mr 180,000 plasma membrane phosphoglycoprotein produced in increased amounts in SH-SY5Y/VCR as well as in vincristine-resistant human neuroepithelioma (MC-IXC/VCR), vinblastine-resistant human leukemia (CEM/VLB100), and actinomycin D- or vincristine-resistant Chinese hamster (DC-3F/AD X and DC-3F/VCRd-5L) cells, as compared to control cells. Radioimmunoprecipitation of proteins in cells metabolically labeled with [35S]methionine, 32Pi, or [3H]glucosamine and Western transfer procedures were used for these studies. Characterization of the HYB-612 or HYB-241 antigen by destructive degradation produced a pattern of results typical of a conformation-dependent protein epitope. HYB-612 recognizes complexes of the Mr 180,000 antigen with an iodinated photoaffinity analogue of vinblastine or with tritiated azidopine. Furthermore, pretreatment of MC-IXC and MC-IXC/VCR cells with HYB-612 or HYB-241 before measurement of tritium-labeled actinomycin D or vincristine uptake increases the amount of drug accumulation in resistant, but not in sensitive, cells. Of importance is the fact that the Mr 180,000 protein is expressed in cells which also contain a Mr 170,000 P-glycoprotein. The relative amounts of the Mr 180,000 and 170,000 species vary from one drug-resistant cell line to another. Evidence that the Mr 180,000 protein is a P-glycoprotein and that there is a conserved complex pattern of resistance-related surface proteins in multidrug-resistant cells is presented in this report.
Heterojunction Photocatalysts (2017)

Semiconductor-based photocatalysis attracts wide attention because of its ability to directly utilize solar energy for production of solar fuels, such as hydrogen and hydrocarbon fuels and for degradation of various pollutants. However, the efficiency of photocatalytic reactions remains low due to the fast electron-hole recombination and low light utilization. Therefore, enormous efforts have been undertaken to solve these problems. Particularly, properly engineered heterojunction photocatalysts are shown to be able to possess higher photocatalytic activity because of spatial separation of photogenerated electron-hole pairs. Here, the basic principles of various heterojunction photocatalysts are systematically discussed. Recent efforts toward the development of heterojunction photocatalysts for various photocatalytic applications are also presented and appraised. Finally, a brief summary and perspectives on the challenges and future directions in the area of heterojunction photocatalysts are also provided.
The roles of molecular chaperones in vivo. (1995)

Table 1 summarizes the families of chaperones mentioned in this review, and lists their proposed functions. Many of these proteins are named in the accompanying review of Burston and Clarke. Molecular chaperones are proteins which interact with other proteins and help them to reach their final, active conformation. They appear to do this by binding them in an unfolded or partially folded state and subsequently releasing them in an altered form. This property may endow them with several essential or important roles in addition to helping newly synthesized proteins to fold correctly, such as repairing damaged proteins and assisting proteins in membrane translocation. To confirm that a given protein has molecular chaperone activity in vivo, it is necessary to show that interactions between the chaperone and other proteins do occur in the cell, and that loss of the molecular chaperone leads to the accumulation of inactive or precursor protein. The hsp70 protein family are highly conserved and ubiquitous. Genetic studies confirm that their depletion leads to the accumulation of inactive precursor or other proteins, and immunochemical studies show they associate with nascent polypeptides. They are implicated not only in protein folding, but also in protein transport across membranes and reactivation of heat-damaged proteins. The hsp60 proteins are also ubiquitous and very similar in sequence. Those found in bacteria and organelles, such as mitochondria (the GroEL family), are essential at all temperatures, and particularly after heat shock. Their loss or depletion leads to the formation of protein aggregates and eventual cell death. A co-chaperone protein (GroES) is required for their function. Cytosolic homologues (the TCP1 family) are also essential, though not heat-shock induced; they are believed to have a chaperone role in tubulin assembly and their actual role in the cell may be much broader. Many other proteins may have a chaperone function in vivo. Such a function may be specific to a particular substrate (such as the PapD protein in E. coli); others may be more general (such as hsp90 and SecB). Evidence is still needed to demonstrate whether all those proteins which show chaperone behaviour in vitro actually have such a role in vivo. It seems likely that different classes of chaperone may overlap in their specificity, and it is certain that the various proteins classed as molecular chaperones fulfil a wide variety of roles in the cell.
Structure-Expression Relationship of Tumor Necrosis Factor Receptor Mutants That Increase Expression (2003)

The extracellular domain of the p55 TNF receptor (TNFrED) is an important therapeutic protein for targeting tumor necrosis factor-alpha (TNF-alpha). The expression level of the TNFrED is low for bioproduction, which is presumably associated with the complication of pairing 24 cysteine residues to form correct disulfide bonds. Here we report the application of the yeast display method to study expression of TNFrED, a multimeric receptor. Randomly mutated libraries of TNFrED were screened, and two mutants were identified that express several-fold higher protein levels compared with the wild type while still retaining normal binding affinity for TNF-alpha. The substituted residues responsible for the higher protein expression in both mutants were identified as proline, and both proline residues are adjacent to cysteine residues involved in disulfide bonds. Analysis of the mutant residues revealed that the improved level of expression is due to conformational restriction of the substituted residues to that of the folded state seen in the crystal structures of TNFrED thereby forcing the neighboring cysteine residues into the correct orientation for proper disulfide bond formation.
Long non‐coding <scp>RNA MALAT</scp>1 regulates hyperglycaemia induced inflammatory process in the endothelial cells (2015)

To examine whether the long non-coding RNA (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is altered in the endothelial cells in response to glucose and the significance of such alteration. We incubated human umbilical vein endothelial cells with media containing various glucose levels. We found an increase in MALAT1 expression peaking after 12 hrs of incubation in high glucose. This increase was associated with parallel increase in serum amyloid antigen 3 (SAA3), an inflammatory ligand and target of MALAT1 and was further accompanied by increase in mRNAs and proteins of inflammatory mediators, tumour necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). Renal tissue from the diabetic animals showed similar changes. Such cellular alterations were prevented following MALAT1 specific siRNA transfection. Results of this study indicate that LncRNA MALAT1 regulates glucose-induced up-regulation of inflammatory mediators IL-6 and TNF-α through activation of SAA3. Identification of such novel mechanism may lead to the development of RNA-based therapeutics targeting MALAT1 for diabetes-induced micro and macro vascular complications.
Partitioning of organic compounds in octanol-water systems (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPartitioning of organic compounds in octanol-water systemsCary T. Chiou, David W. Schmedding, and Milton. ManesCite this: Environ. Sci. Technol. 1982, 16, 1, 4–10Publication Date (Print):January 1, 1982Publication History Published online1 May 2002Published inissue 1 January 1982https://pubs.acs.org/doi/10.1021/es00095a005https://doi.org/10.1021/es00095a005research-articleACS PublicationsRequest reuse permissionsArticle Views1275Altmetric-Citations284LEARN 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
Functional Binding of Human Adipose-Derived Stromal Cells (2008)

Human adipose-derived stromal cells (hASCs) were evaluated in vitro for their ability to bind vascular adhesion and extracellular matrix proteins to arrest (firmly adhere) under physiological flow conditions. hASCs were flowed through a parallel plate flow chamber containing substrates presenting immobilized type I collagen, fibronectin, E-selectin, L-selectin, P-selectin, vascular cell adhesion molecule-1 (VCAM-1), or intercellular adhesion molecule-1 (ICAM-1) under static and laminar flow conditions (wall shear stress = 1 dyn/cm). hASCs were able to firmly adhere to type I collagen, fibronectin, VCAM-1, and ICAM-1 substrates, but not to any of the selectins. Pretreatment with hypoxia increased the ability of hASCs isolated by liposuction to adhere to VCAM-1 and ICAM-1, but this effect was not seen in cells isolated by tissue excision. These results indicate that hASCs possess the ability to adhere key adhesion proteins, illustrate the importance of hASC harvest procedure, and suggest mechanisms for homing in a setting where interaction with inflamed or injured tissue is necessary.