gebhart/patrepeval huggingface dataset:
Adenovirus E4 ORF3 Protein Inhibits the Interferon-Mediated Antiviral Response (2007)

The PML oncogenic domain (POD/ND10/PML body) is a common target of DNA viruses, which replicate their genomes in proximity to this nuclear structure. The adenovirus early protein E4 ORF3 is both necessary and sufficient to rearrange PODs from punctate bodies into track-like structures. Although multiple hypotheses exist, the precise reason for this activity has not yet been elucidated. PML, the protein responsible for nucleating PODs, is an interferon (IFN)-stimulated gene, implicating the participation of this nuclear body in an innate antiviral response. Here, we demonstrate that E4 ORF3 is critical to the replicative success of adenovirus during the IFN-induced antiviral state. When cells are pretreated with either IFN-alpha or IFN-gamma, a mutant virus that does not express E4 ORF3 is severely compromised for replication. This result suggests the functional significance of ORF3 track formation is the inhibition of a POD-mediated, antiviral mechanism. Replication of the E4 ORF3 mutant virus can be rescued following the introduction of E4 ORF3 from evolutionarily divergent adenoviruses, suggesting a conserved function for E4 ORF3 inhibition of the IFN-induced antiviral state. Furthermore, E4 ORF3 inhibition of an IFN-induced response is unrelated to the inhibition of adenovirus replication by the Mre11-Rad50-Nbs1 DNA repair complex. We propose that the evolutionarily conserved function of the adenovirus E4 ORF3 protein is the inhibition of a host interferon response to viral infection via disruption of the PML oncogenic domain.
Fiber Optic Data Bus for the AN/GYQ-21(V). (1981)

Abstract : This report describes the application of fiber optic bus technology to the AN/GYQ-21(V) system with the goal of providing for increased separation distances between peripherals and increased long distance data transfer rates. The ring network and the transmissive star network are described as implementable fiber optic busses which can provide for the following enhancements to the 21(V) system: increased separation distances up to 1 kilometer between peripherals and increased long distance data transfer rates up to 60 Mbps. (Author)
Activating and inhibitory receptors of natural killer cells (2010)

Natural killer (NK) cells are potent immune effector cells that can respond to infection and cancer, as well as allowing maternal adaptation to pregnancy. In response to malignant transformation or pathogenic invasion, NK cells can secrete cytokine and may be directly cytolytic, as well as exerting effects indirectly through other cells of the immune system. To recognize and respond to inflamed or infected tissues, NK cells express a variety of activating and inhibitory receptors including NKG2D, Ly49 or KIR, CD94-NKG2 heterodimers and natural cytotoxicity receptors, as well as co-stimulatory receptors. These receptors recognize cellular stress ligands as well as major histocompatibility complex class I and related molecules, which can lead to NK cell responses. Importantly, NK cells must remain tolerant of healthy tissue, and some of these receptors can also prevent activation of NK cells. In this review, we describe the expression of prominent NK cell receptors, as well as expression of their ligands and their role in immune responses. In addition, we describe the main signaling pathways used by NK cell receptors. Although we now appreciate that NK cell biology is more complicated than first thought, there are still facets of their biology that remain unclear. These will be highlighted and discussed in this review.
Exon-Skipping Antisense Oligonucleotides to Correct Missplicing in Neurogenetic Diseases (2014)

Alternative splicing is an important regulator of the transcriptome. However, mutations may cause alteration of splicing patterns, which in turn leads to disease. During the past 10 years, exon skipping has been looked upon as a powerful tool for correction of missplicing in disease and progress has been made towards clinical trials. In this review, we discuss the use of antisense oligonucleotides to correct splicing defects through exon skipping, with a special focus on diseases affecting the nervous system, and the latest stage achieved in its progress.
Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes (2017)

Proteins are structurally dynamic macromolecules, and it is challenging to quantify the conformational properties of their native state in solution. Nanopores can be efficient tools to study proteins in a solution environment. In this method, an electric field induces electrophoretic and/or electro-osmotic transport of protein molecules through a nanopore slightly larger than the protein molecule. High-bandwidth ion current measurement is used to detect the transit of each protein molecule. First, our measurements reveal a correlation between the mean current blockade amplitude and the radius of gyration for each protein. Next, we find a correlation between the shape of the current signal amplitude distributions and the protein fluctuation as obtained from molecular dynamics simulations. Further, the magnitude of the structural fluctuations, as probed by experiments and simulations, correlates with the ratio of α-helix to β-sheet content. We highlight the resolution of our measurements by resolving two states of calmodulin, a canonical protein that undergoes a conformational change in response to calcium binding.
Cloning of a cDNA encoding the human cation-dependent mannose 6-phosphate-specific receptor. (1987)

Complementary DNA clones for the human cation-dependent mannose 6-phosphate-specific receptor have been isolated from a human placenta library in lambda gt11. The nucleotide sequence of the 2463-base-pair cDNA insert includes a 145-base-pair 5' untranslated region, an open reading frame of 831 base pairs corresponding to 277 amino acids (Mr = 30,993), and a 1487-base-pair 3' untranslated region. The deduced amino acid sequence is colinear with that determined by amino acid sequencing of the N-terminus peptide (41 residues) and nine tryptic peptides (93 additional residues). The receptor is synthesized as a precursor with a signal peptide of 20 amino acids. The hydrophobicity profile of the receptor indicates a single membrane-spanning domain, which separates an N-terminal region containing five potential N-glycosylation sites from a C-terminal region lacking N-glycosylation sites. Thus the N-terminal (Mr = 18,299) and C-terminal (Mr less than or equal to 7648) segments of the mature receptor are assumed to be exposed to the extracytosolic and cytosolic sides of the membrane, respectively. Analysis of a panel of somatic cell (mouse-human) hybrids shows that the gene for the receptor is located on human chromosome 12.
Converting a breast cancer microarray signature into a high-throughput diagnostic test (2006)

In this report we demonstrate for the first time that microarray technology can be used as a reliable diagnostic tool. The data clearly demonstrate the reproducibility and robustness of the small custom-made microarray. The array is therefore an excellent tool to predict outcome of disease in breast cancer patients.
Micromagnetic–microfluidic blood cleansing device (2009)

Sepsis is a lethal disease caused by a systemic microbial infection that spreads via the bloodstream to overwhelm the body's defenses. Current therapeutic approaches are often suboptimal, in part, because they do not fully eliminate the pathogen, and hence the source of deadly toxins. Here we describe an extracorporeal blood cleansing device to selectively remove pathogens from contaminated blood and thereby enhance the patient's response to antibiotic therapy. Immunomagnetic microbeads were modified to create magnetic opsonins that were used to cleanse flowing human whole blood of Candida albicans fungi, a leading cause of sepsis-related deaths. The micromagnetic-microfluidic blood cleansing device generates magnetic field gradients across vertically stacked channels to enable continuous and high throughput separation of fungi from flowing whole blood. A multiplexed version of the device containing four parallel channels achieved over 80% clearance of fungi from contaminated blood at a flow rate of 20 mL/h in a single pass, a rate 1000 times faster than a previously described prototype micromagnetic-microfluidic cell separation system. These results provide the first proof-of-principle that a multiplexed micromagnetic-microfluidic separation system can be used to cleanse pathogens from flowing human blood at a rate and separation efficiency that is relevant for clinical applications.
Self-pumped, continuous-wave phase conjugator using internal reflection (1982)

Continuous-wave phase conjugation of an image-bearing beam is demonstrated using a single-domain crystal of BaTiO(3) and nothing else. The device operates by four-wave mixing using the photorefractive effect but without any external pumping beams or external mirrors. The customary pumping beams are derived from the incident beam and are internally reflected inside the crystal adjacent to an edge. The device is self-starting and has a phase-conjugate reflectivity of 30%. Imaging applications are discussed.
Space-scale diagrams (1995)

There is too much to see. They are hard to navigate. An armada of techniques has been proposed to present the many scales of information needed. Space-scale diagrams provide an analytic framework for much of this work. By representing both a spatial world and its different magnifications explicitly, the diagrams allow the direct visualization and analysis of important scale related issues for interfaces.
The role of ADP receptors in platelet function (2006)

Adenine di-Phosphate (ADP) is an important physiological agonist that plays a vital role in normal hemostasis and thrombosis. The importance of ADP in normal hemostasis is clearly demonstrated in patients suffering from storage pool disease who show excessive bleeding tendencies. It is well established that ADP activates platelets through 3 purinergic receptors, namely P2Y1, P2Y12 and P2X1. The P2Y1 receptor is a Galpha q coupled G-protein receptor that is important for platelet shape change, aggregation, thromboxane A2 generation, procoagulant activity, adhesion to immobilized fibrinogen and thrombus formation under shear conditions. The availability of P2Y1 antagonists and knockout mice have aided in demonstrating the multiple functions of this receptor in platelet function and normal hemostasis. The second ADP receptor, the P2Y12 signals through a Galpha i coupled G-protein receptor and has been shown to be important for platelet functions very similar to the P2Y1 receptor. In addition, the P2Y12 receptor is also important for potentiation of platelet activation mediated by other physiological agonists including collagen, von Willebrand and thromboxane A2. Advances in understanding the importance of the P2Y12 receptor has resulted in the development of drugs like clopidogrel and ticlopidine that is being successfully used clinically in the treatment of thrombotic disorders. The understanding of the function of this receptor has been possible due to the availability of multiple P2Y12 antagonists and the development of the P2Y12 null mice. The third and the final P2X1 receptor is an ion channel that upon activation causes an influx of calcium. Even though the activation of this receptor by itself doesn't lead to aggregation, it causes shape change and aids in the activation process of other agonists. Studies have also shown that it is important for thrombus formation under shear conditions in small arteries. Signaling by this receptor leads to significant ERK activation, which has been shown, to be important for collagen mediated platelet activation. The importance of ADP in hemostasis and thrombosis greatly underscores the significance of understanding the function of these receptors that would enable development of potent and safe anti-thrombotic drugs.
Recent advances in the chemistry of rhenium (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent advances in the chemistry of rheniumGeorge RouschiasCite this: Chem. Rev. 1974, 74, 5, 531–566Publication Date (Print):October 1, 1974Publication History Published online1 May 2002Published inissue 1 October 1974https://doi.org/10.1021/cr60291a002RIGHTS & PERMISSIONSArticle Views1671Altmetric-Citations193LEARN 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 InReddit PDF (4 MB) Get e-Alerts Get e-Alerts
Recovery of a Neurovirulent Human Coronavirus OC43 from an Infectious cDNA Clone (2006)

This study describes the assembly of a full-length cDNA clone of human coronavirus (HCoV)-OC43 in a bacterial artificial chromosome (BAC). The BAC containing the full-length infectious cDNA (pBAC-OC43(FL)) was assembled using a two-part strategy. The first step consisted in the introduction of each end of the viral genome into the BAC with accessory sequences allowing proper transcription. The second step consisted in the insertion of the whole HCoV-OC43 cDNA genome into the BAC. To produce recombinant viral particles, pBAC-OC43(FL) was transfected into BHK-21 cells. Recombinant virus displayed the same phenotypic properties as the wild-type virus, including infectious virus titers produced in cell culture and neurovirulence in mice.
Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one‐cell mouse embryos (2014)

The use of TALEN and CRISPR/CAS nucleases is becoming increasingly popular as a means to edit single target sites in one-cell mouse embryos. Nevertheless, an area that has received less attention concerns the engineering of structural genome variants and the necessary religation of two distant double-strand breaks. Herein, we applied pairs of TALEN or sgRNAs and Cas9 to create deletions in the Rab38 gene. We found that the deletion of 3.2 or 9.3 kb, but not of 30 kb, occurs at a frequency of 6-37%. This is sufficient for the direct production of mutants by embryo microinjection. Therefore, deletions up to ∼10 kb can be readily achieved for modeling human disease alleles. This work represents an important step towards the establishment of new protocols that support the ligation of remote DSB ends to achieve even larger rearrangements.
High-speed resonant-cavity-enhanced silicon photodetectors on reflecting silicon-on-insulator substrates (2002)

We report a resonant-cavity-enhanced Si photodetector fabricated on a reflecting silicon-on-insulator (SOI) substrate. The substrate incorporates a two period distributed Bragg reflector (DBR) fabricated using a commercially available double-SOI process. The buried DBR provides a 90% reflecting surface. The resonant-cavity-enhanced Si photodetectors have 40% quantum efficiency at 860 nm and response time of 29 ps. These devices are suitable for 10-Gb/s data communications.
The Role of Long-Chained Marine N-3 Polyunsaturated Fatty Acids in Cardiovascular Disease (2012)

This paper reviews the current evidence regarding long-chained marine omega-3 polyunsaturated fatty acids (PUFAs) and cardiovascular disease (CVD), their possible mechanisms of action, and results of clinical trials. Also, primary and secondary prevention trials as studies on antiarrhythmic effects and meta-analyses are summarized. However, the individual bioavailability of n-3 PUFAs along with the highly different study designs and estimations of FAs intake or supplementation dosages in patient populations with different background intake of n-3 PUFAs might be some of the reasons for the inconsistent findings of the studies evaluating the impact of n-3 PUFAs on CVD. The question of an optimum dose of n-3 PUFAs or whether there exists a dose-response relation for n-3 PUFA supplementation is widely discussed. Moreover, the difficulties in interpreting meta-analyses are clearly demonstrated by two recently published meta-analyses (Rizos et al. and Delgado Lista et al.), evaluating the efficacy of n-3 PUFAs on CVD, including 12 common studies, but drawing opposite conclusions. We definitely need more large-scale, randomized clinical trials of long duration, also reporting harmful effects of n-3 PUFAs.
INCREASED ENERGY TRANSFER FROM PHYCOBILISOMES TO PHOTOSYSTEM II IN HIGH LIGHT ADAPTED Anabaena cylindrica (1987)

Excitation energy transfer from phycobilisomes to photosystem II in high‐light adapted cells of Anabaena cylindrica was studied by fluorescence spectroscopy and compared to that of low‐light adapted cells. Measurements were made on membrane fragments containing phycobilisomes, photosystem I and II, isolated in 0.75 M K‐phosphate. Relative efficiency of 430 to 590 nm light in the excitation of F 680 chlorophyll fluorescence was compared in low and high light adapted cells, respectively. The values indicate that light energy absorbed by phycobilisomes is transferred to photosystem II antenna chlorophylls with higher efficiency in high‐light adapted cells than in low‐light adapted cells. Partial dissociation and uncoupling of energy transfer caused by low ion concentration were different in the membrane fragments isolated from the two kinds of cells and indicated a higher aggregation state of pigment‐protein complexes of phycobilisomes in high‐light adapted A. cylindrica cells.
Classification of mononuclear zinc metal sites in protein structures (1997)

Our study of the extended metal environment, particularly of the second shell, focuses in this paper on zinc sites. Key findings include: (i) The second shell of mononuclear zinc centers is generally more polar than hydrophobic and prominently features charged residues engaged in an abundance of hydrogen bonding with histidine ligands. Histidine-acidic or histidine-tyrosine clusters commonly overlap the environment of zinc ions. (ii) Histidine tautomeric metal bonding patterns in ligating zinc ions are mixed. For example, carboxypeptidase A, thermolysin, and sonic hedgehog possess the same ligand group (two histidines, one unibidentate acidic ligand, and a bound water), but their histidine tautomeric geometries markedly differ such that the carboxypeptidase A makes only Ndelta1 contacts, thermolysin makes only Nepsilon2 contacts, and sonic hedgehog uses one of each. Thus the presence of a similar ligand cohort does not necessarily imply the same topology or function at the active site. (iii) Two close histidine ligands HXmH, m </= 5, rarely both coordinate a single metal ion in the Ndelta1 tautomeric conformation, presumably to avoid steric conflicts. Mononuclear zinc sites can be classified into six types depending on the ligand composition and geometry. Implications of the results are discussed in terms of divergent and convergent evolution.
Oncogenic targeting of an activated tyrosine kinase to the Golgi apparatus in a glioblastoma (2003)

Activating oncogenic mutations of receptor tyrosine kinases (RTKs) have been reported in several types of cancers. In many cases, genomic rearrangements lead to the fusion of unrelated genes to the DNA coding for the kinase domain of RTKs. All RTK-derived fusion proteins reported so far display oligomerization sequences within the 5' fusion partners that are responsible for oncogenic activation. Here, we report a mechanism by which an altered RTK gains oncogenic potential in a glioblastoma cell line. A microdeletion on 6q21 results in the fusion of FIG, a gene coding for a Golgi apparatus-associated protein, to the kinase domain of the protooncogene c-ROS. The fused protein product FIG-ROS is a potent oncogene, and its transforming potential resides in its ability to interact with and become localized to the Golgi apparatus. Thus we have found a RTK fusion protein whose subcellular location leads to constitutive kinase activation and results in oncogenic transformation.
Catheter-Based Radiofrequency Renal Denervation: Location Effects on Renal Norepinephrine (2015)

RF RD lowers renal NE more significantly when performed in branches of the renal artery closer to the kidney. Increased efficacy of RF RD in extrarenal arterial branches may be due to the greater number of nerves in close proximity to the artery lumen in the branches.
Distributed communication services in the Masix system (2002)

Masix is a distributed multi-server operating system based on the Mach microkernel, with multiple personality support. Its main feature is a distributed generic layer (DGL), which offers distributed services to the personalities. The distributed multi-server architecture of Masix grants it a high modularity, but also raises many issues, such as transparency, security and performance, which cannot be solved without adequate communication services. To provide total transparency, we extend the traditional Mach communication model to a workstation network by interposing a generic network server (GNS) between the tasks and the microkernel. We defined a global name service, based on a name resolution protocol, which allows any pair of Mach remote tasks to communicate transparently, using the local Mach IPC semantics. Our name server also provides local and remote authentication mechanisms, based on digital signatures and a secret key algorithm. To prevent eavesdropping, all remote communications are transparently encrypted by the GNS, using a public key algorithm. These security measures can be easily merged into the name service, to yield a secure distributed name resolution protocol. Microkernel based-systems are traditionally criticized for their relatively poor performance. As far as network services are concerned, experiments show that a good performance level can be reached, provided that the distinctive features of microkernels are taken into account.