gebhart/patrepeval huggingface dataset:
Iron acquisition and its control in pseudomonas aeruginosa many roads lead to rome (2003)

Iron plays an important role in the pathogenesis and rhizosphere competence of the fluorescent group of pseudomonads and it is, thus, fitting that the characteristic fluorescence of these organisms is attributable to an iron-chelating molecule, pyoverdine. Pseudomonas aeruginosa is likely the best-studied member of this group, and while it synthesizes two siderophores, pyochelin and pyoverdine, it is also able to use a number of heterologous siderophores of fungal and bacterial origin and its genome is rich with homologues of iron-siderophore receptor genes, reflecting the enormous flexibility of the organism vis-a-vis iron carriers that it can use in nature. The ability to utilize a variety of heterologous siderophores is shared by other fluorescent pseudomonads and likely reflects both the importance of this vital nutrient for growth and survival and the need to compete with other microorganisms in the aquatic and terrestrial environments that they inhabit. Expression of the various receptors is, however, regulated, with receptor production responding positively to available siderophores only, and selection from multiple available siderophores based on their successful chelation of iron and subsequent transport. Thus, the superior siderophore in a given environment will upregulate the cognate receptor at the expense of other receptors. Such siderophore-dependent regulation of receptor gene expression is common in bacteria, particularly the fluorescent pseudomonads, and typically requires a signal transduction cascade that involves the receptor itself, whose binding to the siderophore initiates the cascade, as well as a regulatory protein pair that includes an environmentally-responsive so-called extracytoplasmic function (ECF) sigma factor, which activates receptor gene expression, and an anti-sigma factor that controls sigma factor activity. Despite the plethora of ferric siderophore receptors in P. aeruginosa, its genome sequence reveals a striking lack of obvious periplasmic and cytoplasmic membrane transport components capable of accommodating these molecules. Unlike e.g. Escherichia coli, then, where ferric siderophore permeases providing transport to the cytoplasm are clearly in evidence, iron-siderophore complexes in P. aeruginosa may be dissociated in the periplasm, with a common iron carrier then responsible for iron uptake into the cell interior.
Speed of Intracranial Clot Lysis With Intravenous Tissue Plasminogen Activator Therapy (2001)

Rapid arterial recanalization is associated with better short-term improvement, mostly likely because of faster and more complete clot breakup with low resistance of the distal circulatory bed. Slow (>/=30 minutes) flow improvement and dampened flow signal are less favorable prognostic signs. These findings may be evaluated to assist with selection of patients for additional pharmacological or interventional treatment.
Chemically modified peptides and proteins - critical considerations for oral delivery (2016)

Numerous approaches have been explored to date in the pursuit of delivering peptides or proteins via the oral route. One such example is chemical modification, whereby the native structure of a peptide or protein is tailored to provide a more efficient uptake across the epithelial barrier of the gastrointestinal tract via incorporation of a chemical motif or moiety. In this regard, a diverse array of concepts have been reported, ranging from the exploitation of endogenous transport mechanisms to incorporation of physicochemical modifications in the molecule, which promote more favorable interactions with the absorptive membrane at the cell surface. This review provides an overview of the modification technologies described in the literature and offers insights into some pragmatic considerations pertaining to their translation into clinically viable concepts.
Everything you always wanted to know about synchronization but were afraid to ask (2013)

This paper presents the most exhaustive study of synchronization to date. We span multiple layers, from hardware cache-coherence protocols up to high-level concurrent software. We do so on different types of architectures, from single-socket -uniform and nonuniform -to multi-socket -directory and broadcastbased -many-cores. We draw a set of observations that, roughly speaking, imply that scalability of synchronization is mainly a property of the hardware.
Preparation of Large Freestanding GaN Substrates by Hydride Vapor Phase Epitaxy Using GaAs as a Starting Substrate (2001)

A freestanding GaN substrate over 2 inches in size was successfully prepared for the first time by hydride vapor phase epitaxy (HVPE) using GaAs as a starting substrate. In the experiment, a GaAs (111)A substrate with a SiO 2 mask pattern on its surface was used. A thick GaN layer was grown on the GaAs substrate at 1030°C through the openings in the SiO 2 mask. By dissolving the GaAs substrate in aqua regia, a freestanding GaN substrate about 500 µm thick was obtained. The full-width at half maximum (FWHM) in the ω-mode X-ray diffraction (XRD) profile of GaN (0002) plane was 106 arcsec. The dislocation density of the GaN substrate obtained was determined to be as low as 2×10 5 cm -2 by plan-view transmission electron microscopy (TEM). Hall measurements revealed the n-type conductivity of the GaN substrate with typical carrier concentration and carrier mobility of 5×10 18 cm -3 and 170 cm 2 ·V -1 ·s -1 , respectively.
NEURAL NETWORK LICENCE PLATE RECOGNITION (1995)

This article describes Talon, a new automatic license plate recognition system using a new generation of recognition algorithms based on neural network techniques. The system is able to overcome the limitations of conventional template matching techniques and aims to erase previous system skepticism and to produce modular, cost effective systems which yield a high level of performance in a wide range of applications.
Oligonucleotide-Directed Mutagenesis: A Simple Method Using Two Oligonucleotide Primers and a Single-Stranded DNA Template (1984)

This paper presents a simple and efficient method for oligonucleotide-directed mutagenesis using vectors derived from single-stranded phage. This modification of our previously published procedure (Zoller and Smith, 1982) features the use of two primers, one of which is a standard M13 sequencing primer and the other is the mutagenic oligonucleotide. Both primers are simultaneously annealed to single-stranded template DNA, extended by DNA polymerase I (large fragment), and ligated together to form a mutant wild-type gapped heteroduplex. Escherichia coli is transformed directly with this DNA; the isolation of covalently closed circular DNA as in our previous report is not necessary. Mutants are identified by plaque lift hybridization using the mutagenic oligonucleotide as a probe. As an example of the method, a heptadecanucleotide was used to create a T----G transversion in the MATa gene of Saccharomyces cerevisiae cloned into the vector M13mp5. The efficiency of mutagenesis was approximately 50%. Production of the desired mutation was verified by DNA sequencing. The same procedure has been used without modification to create insertions of restriction sites as well as specific deletions of 500 bases.
Common themes in microbial pathogenicity revisited (1997)

Bacterial pathogens employ a number of genetic strategies to cause infection and, occasionally, disease in their hosts. Many of these virulence factors and their regulatory elements can be divided into a smaller number of groups based on the conservation of similar mechanisms. These common themes are found throughout bacterial virulence factors. For example, there are only a few general types of toxins, despite a large number of host targets. Similarly, there are only a few conserved ways to build the bacterial pilus and nonpilus adhesins used by pathogens to adhere to host substrates. Bacterial entry into host cells (invasion) is a complex mechanism. However, several common invasion themes exist in diverse microorganisms. Similarly, once inside a host cell, pathogens have a limited number of ways to ensure their survival, whether remaining within a host vacuole or by escaping into the cytoplasm. Avoidance of the host immune defenses is key to the success of a pathogen. Several common themes again are employed, including antigenic variation, camouflage by binding host molecules, and enzymatic degradation of host immune components. Most virulence factors are found on the bacterial surface or secreted into their immediate environment, yet virulence factors operate through a relatively small number of microbial secretion systems. The expression of bacterial pathogenicity is dependent upon complex regulatory circuits. However, pathogens use only a small number of biochemical families to express distinct functional factors at the appropriate time that causes infection. Finally, virulence factors maintained on mobile genetic elements and pathogenicity islands ensure that new strains of pathogens evolve constantly. Comprehension of these common themes in microbial pathogenicity is critical to the understanding and study of bacterial virulence mechanisms and to the development of new "anti-virulence" agents, which are so desperately needed to replace antibiotics.
Targeting BRAF for patients with melanoma (2010)

The prognosis of patients with metastatic melanoma is poor and not influenced by systemic therapy with cytotoxic drugs. New targeted agents directed against the RAS-RAF-MEK-ERK pathway show promising activity in early clinical development and particular interest is focused on selective inhibitors of mutant BRAF, which is present in one half of the cases of metastatic melanoma. The majority of patients on early trials of these drugs develop secondary resistance and subsequent disease progression and it is, therefore, critical to understand the underlying escape mechanisms leading to resistance.
Updating the Parameters of a Threshold Scheme by Minimal Broadcast (2005)

Threshold schemes allow secret data to be protected among a set of participants in such a way that only a prespecified threshold of participants can reconstruct the secret from private information (shares) distributed to them on a system setup using secure channels. We consider the general problem of designing unconditionally secure threshold schemes whose defining parameters (the threshold and the number of participants) can later be changed by using only public channel broadcast messages. In this paper, we are interested in the efficiency of such threshold schemes, and seek to minimize storage costs (size of shares) as well as optimize performance in low-bandwidth environments by minimizing the size of necessary broadcast messages. We prove a number of lower bounds on the smallest size of broadcast message necessary to make general changes to the parameters of a threshold scheme in which each participant already holds shares of minimal size. We establish the tightness of these bounds by demonstrating optimal schemes.
Solid lipid nanoparticles: could they help to improve the efficacy of pharmacologic treatments for brain tumors? (2007)

Compared to other vehicules, SLN seem to offer more advantages (such as higher physical stability, greater protection from degradation and better release profile of incorporated drugs, good tolerability and possibility of site-specific targeting) and could be regarded as an effective carrier for chemotherapeutic drugs, gene therapeutical agents, and diagnostic tools in neuro-oncology.
In Vivo Enrichment of Diabetogenic T Cells (2017)

Dysfunctional T cells can mediate autoimmunity, but the inaccessibility of autoimmune tissues and the rarity of autoimmune T cells in the blood hinder their study. We describe a method to enrich and harvest autoimmune T cells in vivo by using a biomaterial scaffold loaded with protein antigens. In model antigen systems, we found that antigen-specific T cells become enriched within scaffolds containing their cognate antigens. When scaffolds containing lysates from an insulin-producing β-cell line were implanted subcutaneously in autoimmune diabetes-prone NOD mice, β-cell-reactive T cells homed to these scaffolds and became enriched. These T cells induced diabetes after adoptive transfer, indicating their pathogenicity. Furthermore, T-cell receptor (TCR) sequencing identified many expanded TCRs within the β-cell scaffolds that were also expanded within the pancreata of NOD mice. These data demonstrate the utility of biomaterial scaffolds loaded with disease-specific antigens to identify and study rare, therapeutically important T cells.
A novel ad hoc routing protocol research based on mobility prediction algorithm (2005)

Mobile ad hoc network (MANET) is a network that every node processes packet routing without infrastructure. The fast equipping and mobile self-organization characters push MANET the hot point in wireless communication research. Based on ad hoc on-demand vector (AODV) routing protocol, this paper provides a novel MAODV routing protocol research based on mobility prediction algorithm. The MAODV controls route discovery, keeping and switch by estimating neighbor node's distance and predicting neighbor node's mobility to suit fast changed network topology. Simulator result demonstrates that, compared with original AODV, MAODV could reduce end-to-end delay effectively and enhance the real-time character.
Cleavage of Amyloid β Peptide During Constitutive Processing of Its Precursor (1990)

The amyloid beta peptide (A beta P) is a small fragment of the much larger, broadly distributed amyloid precursor protein (APP). Abundant A beta P deposition in the brains of patients with Alzheimer's disease suggests that altered APP processing may represent a key pathogenic event. Direct protein structural analyses showed that constitutive processing in human embryonic kidney 293 cells cleaves APP in the interior of the A beta P, thus preventing A beta P deposition. A deficiency of this processing event may ultimately prove to be the etiological event in Alzheimer's disease that gives rise to senile plaque formation.
Site Specific Chronotherapeutic Drug Delivery Systems: A Patent Review (2009)

Oral dosage forms are known to provide a zero order or first order release in which the drug is released at a substantially steady rate of release per unit of time. However, there are instances where maintaining a constant blood level of a drug is not desirable. In such cases a pulsatile drug delivery may be more advantageous. Pulsatile drug delivery systems can be classified into site-specific systems in which the drug is released at the desired site within the intestinal tract (e.g., the colon), or time-controlled devices in which the drug is released after a well-defined time period. Environmental factors like pH or enzymes present in the intestinal tract control the release of a site-controlled system whereas the drug release from time-controlled systems is controlled primarily by the delivery system and not by the environment. The delayed liberation of orally administered drugs has been achieved through a range of formulation approaches, including single or multiple unit systems provided with release-controlling coatings, capsular devices and osmotic pumps. Our aim in this review is to outline the rational and prominent design strategies behind site-specific oral pulsatile delivery. The present article provides a good patent review regarding the Site Specific Chronotherapeutic Drug Delivery Systems.
MALDI-TOF Mass Spectrometric Method for Detection of Hybridized DNA Oligomers (2001)

Two new approaches for nucleic acid hybridizations by MALDI-TOF mass spectrometry are described. Hybridization using genomic DNA without polymerase chain reaction was demonstrated. Total genomic DNA of bacteriophages bound to charge-modified nylon membranes was identified by the hybridization of species-specific oligonucleotide probes. lambda-Phage DNA and M13 were used for the test with good success. Since MALDI-TOF mass spectrometry can be used to measure the molecular weights of different probes, mass spectrometry can be used for the detection of hybridizations with multiple probes. We demonstrate that multiple-probe hybridization can be resolved by mass spectrometry. Six probes with different mass tag were used for hybridization on a single spot. MALDI-TOF mass spectrometry was successfully used to measure these probes simultaneously. This provides a simple nonradioactive method for multiplex hybridization analysis. It has the potential to drastically increase the speed for microarray hybridization analysis in the future.
Iterative blind deconvolution algorithm applied to phase retrieval (1990)

The iterative blind deconvolution algorithm proposed by Ayers and Dainty [ Opt. Lett.13, 547 ( 1988)] and improved on by Davey et al. [ Opt. Commun.69, 353 ( 1989)] is applied to the problem of phase retrieval, which is a special case of the blind deconvolution problem. A close relationship between this algorithm and the error-reduction version of the iterative Fourier-transform phase-retrieval algorithm is shown analytically. The performance of the blind deconvolution algorithm is compared with the error-reduction and hybrid input–output versions of the iterative Fourier-transform algorithm by reconstruction experiments on real-valued, nonnegative images with and without noise.
Recognition of hepatitis B surface antigen by human T lymphocytes. Proliferative and cytotoxic responses to a major antigenic determinant defined by synthetic peptides. (1988)

The antigenic sites for human T lymphocytes on hepatitis B surface Ag (HBsAg) were studied by using synthetic oligopeptides. T cell lines of the helper/inducer class, which were isolated from hepatitis B vaccine recipients, were found to react strongly and in an Ag-specific way with peptides corresponding to a sequence of 10 to 30 amino acids near the amino terminus of the HBsAg molecule. Cells with surface expression of the antigenic determinant contained in these synthetic peptides induced both proliferative and cytotoxic responses in the hepatitis B-specific T cells. The results indicate that amino acid residues 24-27 of HBsAg could be directly involved in this T cell determinant. Inhibition studies with mAb to MHC class II Ag and target cells from various HLA-typed individuals suggest that some T cell responses to this determinant of HBsAg might be restricted by the DPw4 molecule. However, the possibility exists that more than one of the MHC class II molecules could be involved as restricting elements of T cell responses to this synthetic peptide. In vivo experiments with synthetic peptides such as those described here are needed to demonstrate the possibility of enhancing HBsAg immune responses in some individuals.
The consequences of stepwise deletions from the signal-processing site of beta-lactamase. (1987)

Amino acids have been deleted from the processing site of pre-beta-lactamase, either into the signal sequence or into the mature protein. Whereas the loss of more than 2 amino acid residues from the C-terminal end of the signal sequence prevents the translocation of the protein into the periplasm, the removal of two or more amino acids from the beginning of the mature protein has no effect on the translocation of the truncated protein. The insertion of an additional one to three amino acids at the processing site has no detectable phenotypic consequence either. It appears that many sequences for the first few residues of the mature protein allow successful translocation and processing. In sharp contrast, the removal of one (but not both) of the amino acids that flank the processing site results in a severe growth defect in the host cell and very low expression of the protein. Yet removal of two amino acids from either side of the processing site, or removal of both the flanking residues of the processing site, results in normal secretion and signal cleavage. These results illustrate the limits on the amino acid sequence around the processing junction and suggest that interference with the signal cleavage step can lead not only to aborted secretion but also to pleiotropic consequences for the growth of the host organism.
Effect of Chloroquine on Erythematous and Carcinogenic Response to Ultraviolet Light (1960)

During a lifetime, exposed areas of the body are subject to large amounts of irradiation from sunlight. Unna was the first to call attention to the high incidence of skin cancer among sailors exposed to sunlight,<sup>1</sup>and his observation on the relationship between exposure to sunlight and the development of skin cancers has been confirmed by many others. Also, epitheliomas have been produced experimentally by subjecting albino mice, rats, and rabbits to repeated exposures to ultraviolet rays produced by a mercury arc lamp.<sup>2-5</sup>The carcinogenic wave lengths of the spectrum have been determined to be between 2,900 and 3,341 A. In experimental animals, the amount of effective midultraviolet radiant energy necessary to initiate changes which culminate with tumor formation is relatively small (63 to 84×107 ergs/sq. cm.).<sup>5</sup>To a certain extent, the length of the precancerous period varies inversely with the daily dose of irradiation. Carcinogenesis, once
High-frequency piezopolymer transducers with a copper-clad polyimide backing layer (2006)

The effect of a copper-clad polyimide (CCP) backing layer on piezopolymer transducer performance is evaluated. High-frequency, spherically curved polyvinylidene fluoride (PVDF) transducers with and without a CCP backing layer are electrically and acoustically tested. The results showed very similar operating characteristics. B-mode in vivo images of a mouse embryo also showed no qualitative differences, indicating that the CCP backing layer does not affect transducer performance.
End-user controlled group formation and access rights management in a shared workspace system (2004)

Group formation and access rights management become crucial issues when shared workspaces are used to support flexible, emerging group work. End-Users should be able to form groups and adapt access rights for changing groups and workspaces. Current shared workspace systems do not support this sufficiently. Our approach combines a room metaphor-based shared workspace with the key-metaphor for facilitating both, end-user controlled flexible group formation and access rights management. An evaluation of this approach during four month of use has indicated that end-users can form groups and manage the access rights of their shared spaces.
SAGEmap: A Public Gene Expression Resource (2000)

We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of this resource, SAGEmap, are located at http://www.ncbi.nlm.nih. gov/sage and ftp://ncbi.nlm.nih.gov/pub/sage, respectively. We herein describe SAGE data submission procedures, the construction and characteristics of SAGE tags to gene assignments, the derivation and use of a novel statistical test designed specifically for differential-type analyses of SAGE data, and the organization and use of this resource.