gebhart/patrepeval huggingface dataset:
Image reconstruction: An overview for clinicians (2014)

Image reconstruction plays a critical role in the clinical use of magnetic resonance imaging (MRI). The MRI raw data is not acquired in image space and the role of the image reconstruction process is to transform the acquired raw data into images that can be interpreted clinically. This process involves multiple signal processing steps that each have an impact on the image quality. This review explains the basic terminology used for describing and quantifying image quality in terms of signal-to-noise ratio and point spread function. In this context, several commonly used image reconstruction components are discussed. The image reconstruction components covered include noise prewhitening for phased array data acquisition, interpolation needed to reconstruct square pixels, raw data filtering for reducing Gibbs ringing artifacts, Fourier transforms connecting the raw data with image space, and phased array coil combination. The treatment of phased array coils includes a general explanation of parallel imaging as a coil combination technique. The review is aimed at readers with no signal processing experience and should enable them to understand what role basic image reconstruction steps play in the formation of clinical images and how the resulting image quality is described.
T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response (2018)

The delayed availability of vaccine during the 2009 H1N1 influenza pandemic created a sense of urgency to better prepare for the next influenza pandemic. Advancements in manufacturing technology, speed and capacity have been achieved but vaccine effectiveness remains a significant challenge. Here, we describe a novel vaccine design strategy called immune engineering in the context of H7N9 influenza vaccine development. The approach combines immunoinformatic and structure modeling methods to promote protective antibody responses against H7N9 hemagglutinin (HA) by engineering whole antigens to carry seasonal influenza HA memory CD4<sup>+</sup> T cell epitopes - without perturbing native antigen structure - by galvanizing HA-specific memory helper T cells that support sustained antibody development against the native target HA. The premise for this vaccine concept rests on (i) the significance of CD4<sup>+</sup> T cell memory to influenza immunity, (ii) the essential role CD4<sup>+</sup> T cells play in development of neutralizing antibodies, (iii) linked specificity of HA-derived CD4<sup>+</sup> T cell epitopes to antibody responses, (iv) the structural plasticity of HA and (v) an illustration of improved antibody response to a prototype engineered recombinant H7-HA vaccine. Immune engineering can be applied to development of vaccines against pandemic concerns, including avian influenza, as well as other difficult targets.
Synthesis of Polymers Composed of Alternating Diphenylenedithienosilole and Diethynylenesilylene Units and Their Applications to Hole Transport in Double-Layer EL Devices (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSynthesis of Polymers Composed of Alternating Diphenylenedithienosilole and Diethynylenesilylene Units and Their Applications to Hole Transport in Double-Layer EL DevicesJoji Ohshita, Tomohisa Sumida, Atsutaka Kunai, Akira Adachi, Koichi Sakamaki, and Koichi OkitaView Author Information Department of Applied Chemistry, Faculty of Engineering, Hiroshima University, Higashi-Hiroshima 739-8527, Japan Japan Chemical Innovation Institute, 2-5-3 Kuramae, Taito-Ku, Tokyo 111-0051, Japan Cite this: Macromolecules 2000, 33, 23, 8890–8893Publication Date (Web):October 25, 2000Publication History Received21 March 2000Revised7 September 2000Published online25 October 2000Published inissue 1 November 2000https://doi.org/10.1021/ma0005062Copyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views304Altmetric-Citations27LEARN 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 Read OnlinePDF (57 KB) Get e-AlertsSUBJECTS:Layers,Materials,Nucleic acid structure,Polymer films,Polymers Get e-Alerts
Luminescent Polyaminocarboxylate Chelates of Terbium and Europium: The Effect of Chelate Structure (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLuminescent Polyaminocarboxylate Chelates of Terbium and Europium: The Effect of Chelate StructureMin Li and Paul R. SelvinCite this: J. Am. Chem. Soc. 1995, 117, 31, 8132–8138Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/ja00136a010https://doi.org/10.1021/ja00136a010research-articleACS PublicationsRequest reuse permissionsArticle Views2419Altmetric-Citations255LEARN 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
Distinct mechanisms underlie distinct polyphenol‐induced neuroprotection (2006)

Glutamate excitotoxicity is mediated by intracellular Ca(2+) overload, caspase-3 activation, and ROS generation. Here, we show that curcumin, tannic acid (TA) and (+)-catechin hydrate (CA) all inhibited glutamate-induced excitotoxicity. Curcumin inhibited PKC activity, and subsequent phosphorylation of NR1 of the NMDA receptor. As a result, glutamate-mediated Ca(2+) influx was reduced. TA attenuated glutamate-mediated Ca(2+) influx only when simultaneously administered, directly interfering with Ca(2+). Both curcumin and TA inhibited glutamate-induced caspase-3 activation. Although Ca(2+) influx was not attenuated by CA, caspase-3 was reduced by direct inhibition of the enzyme. All polyphenols reduced glutamate-induced generation of ROS.
Effect of Differential Polyadenylation and Cell Growth Phase on Dihydrofolate Reductase mRNA Stability (1999)

We have constructed tetracycline-responsive dhfr minigenes and transferred them to a Chinese hamster ovary cell DHFR-deficient deletion mutant to obtained cells in which dhfr transcription can be repressed by tetracycline (tet-off). DHFR mRNA half-life measured after the repression of transcription by tetracycline in these transfectants is about 1.5 h, which is significantly shorter than previously reported. In addition, we observed that DHFR mRNA is less stable in serum-starved cells than in exponentially growing cells. Given that the dhfr gene contains multiple polyadenylation sites, we analyzed the role of polyadenylation site usage on the stability of the resultant mRNA molecules. We found that DHFR mRNA is more stable when a strong polyadenylation site is used. Finally, we have observed that the relative lengths of the poly(A) tails for the different DHFR mRNA species correlated with their relative stability in growing versus resting cells.
Down-Regulated Xanthine Oxidoreductase Is a Feature of Aggressive Breast Cancer (2005)

Loss of XOR identifies breast cancer patients with unfavorable prognosis.
Hepatitis C Virus Induces E6AP-Dependent Degradation of the Retinoblastoma Protein (2007)

Hepatitis C virus (HCV) is a positive-strand RNA virus that frequently causes persistent infections and is uniquely associated with the development of hepatocellular carcinoma. While the mechanism(s) by which the virus promotes cancer are poorly defined, previous studies indicate that the HCV RNA-dependent RNA polymerase, nonstructural protein 5B (NS5B), forms a complex with the retinoblastoma tumor suppressor protein (pRb), targeting it for degradation, activating E2F-responsive promoters, and stimulating cellular proliferation. Here, we describe the mechanism underlying pRb regulation by HCV and its relevance to HCV infection. We show that the abundance of pRb is strongly downregulated, and its normal nuclear localization altered to include a major cytoplasmic component, following infection of cultured hepatoma cells with either genotype 1a or 2a HCV. We further demonstrate that this is due to NS5B-dependent ubiquitination of pRb and its subsequent degradation via the proteasome. The NS5B-dependent ubiquitination of pRb requires the ubiquitin ligase activity of E6-associated protein (E6AP), as pRb abundance was restored by siRNA knockdown of E6AP or overexpression of a dominant-negative E6AP mutant in cells containing HCV RNA replicons. E6AP also forms a complex with pRb in an NS5B-dependent manner. These findings suggest a novel mechanism for the regulation of pRb in which the HCV NS5B protein traps pRb in the cytoplasm, and subsequently recruits E6AP to this complex in a process that leads to the ubiquitination of pRb. The disruption of pRb/E2F regulatory pathways in cells infected with HCV is likely to promote hepatocellular proliferation and chromosomal instability, factors important for the development of liver cancer.
The AMP-activated protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans (2004)

Although limiting energy availability extends lifespan in many organisms, it is not understood how lifespan is coupled to energy levels. We find that the AMP:ATP ratio, a measure of energy levels, increases with age in Caenorhabditis elegans and can be used to predict life expectancy. The C. elegans AMP-activated protein kinase alpha subunit AAK-2 is activated by AMP and functions to extend lifespan. In addition, either an environmental stressor that increases the AMP:ATP ratio or mutations that lower insulin-like signaling extend lifespan in an aak-2-dependent manner. Thus, AAK-2 is a sensor that couples lifespan to information about energy levels and insulin-like signals.
FDA, Producers Moving toward Mammalian Cell-Based Flu Vaccines (2006)

Manufacturers and officials of the Food and Drug Administration (FDA) are planning a major shift in how subunit influenza vaccines are produced—discarding chicken eggs in favor of cultured mammalian cells (Microbe, January 2006, p. 4). Several factors are adding momentum to this pending shift, including concerns over pandemic flu, a pledge by President Bush for new resources to support research on producing vaccines in cell cultures, and a general move to eliminate bottlenecks embedded in the traditional approach to making flu vaccines using eggs. Despite this momentum, however, vaccine producers will need to surmount safety concerns before FDA officials approve vaccines made using this approach (ASM News, May 2004, p. 210).
4-1BBL Cooperates with B7-1 and B7-2 in Converting a B Cell Lymphoma Cell Line into a Long-Lasting Antitumor Vaccine (1999)

A20 is a B cell lymphoma that constitutively expresses the costimulatory molecule B7-2 yet grows readily as a tumor in syngeneic BALB/c mice. We have compared the tumorigenicity of A20 variants expressing either B7-1 (A20/B7-1) or B7-2 (A20/B7-2) with an A20 variant expressing B7-1 and B7-2 with 4-1BBL (A20/4-1BBL), a costimulatory member of the TNF family. Mice injected with tumors expressing the vector backbone (A20/CMV) or B7-1 developed tumors within 25 days of s.c. injection. In contrast, mice injected with A20/4-1BBL were tumor free for the 150-day follow-up period, while 25% of mice injected with A20/B7-2 developed tumors. Tumorigenicity experiments using nude mice indicated the requirement for T cells for variant rejection. Almost all mice that resisted the initial tumor challenge were resistant to further challenge with the parental tumor. Splenocytes from these mice showed high CTL lytic activity against the parental tumor, A20, as well as the syngeneic BALB/c lymphoma K46J, but showed background levels of lytic activity against the congenic SCID thymoma line ST-D2 or the allogeneic EL4 thymoma. In vitro blocking experiments with anti-B7-1 plus anti-B7-2 and/or soluble 4-1BB receptor showed B7-1, B7-2, and 4-1BBL all contributed to the CTL activity. Thus, the data show that neither B7-1 or B7-2 alone can confer full immunogenicity to the A20 lymphoma but that the addition of 4-1BBL results in a tumor that is highly immunogenic and can confer long-lasting protection against challenge with parental tumor in vivo.
Mechanism of the Attenuation of Proteolysis-Inducing Factor Stimulated Protein Degradation in Muscle by β-Hydroxy-β-Methylbutyrate (2004)

The leucine metabolite beta-hydroxy-beta-methylbutyrate (HMB) prevents muscle protein degradation in cancer-induced weight loss through attenuation of the ubiquitin-proteasome proteolytic pathway. To investigate the mechanism of this effect, the action of HMB on protein breakdown and intracellular signaling leading to increased proteasome expression by the tumor factor proteolysis-inducing factor (PIF) has been studied in vitro using murine myotubes as a surrogate model of skeletal muscle. A comparison has been made of the effects of HMB and those of eicosapentaenoic acid (EPA), a known inhibitor of PIF signaling. At a concentration of 50 mumol/L, EPA and HMB completely attenuated PIF-induced protein degradation and induction of the ubiquitin-proteasome proteolytic pathway, as determined by the "chymotrypsin-like" enzyme activity, as well as protein expression of 20S proteasome alpha- and beta-subunits and subunit p42 of the 19S regulator. The primary event in PIF-induced protein degradation is thought to be release of arachidonic acid from membrane phospholipids, and this process was attenuated by EPA, but not HMB, suggesting that HMB might act at another step in the PIF signaling pathway. EPA and HMB at a concentration of 50 mumol/L attenuated PIF-induced activation of protein kinase C and the subsequent degradation of inhibitor kappaBalpha and nuclear accumulation of nuclear factor kappaB. EPA and HMB also attenuated phosphorylation of p42/44 mitogen-activated protein kinase by PIF, thought to be important in PIF-induced proteasome expression. These results suggest that HMB attenuates PIF-induced activation and increased gene expression of the ubiquitin-proteasome proteolytic pathway, reducing protein degradation.
Antigen-Specific IgG Responses from Naive Human Splenocytes: In Vitro Priming Followed by Antigen Boost in the SCID Mouse (1998)

High titers of Ag-specific human IgG were consistently achieved in SCID mice reconstituted with human splenocytes that had been primed with Ag in vitro and then boosted with Ag after engraftment into SCID mice. Specific human IgG titers in the hu-SPL-SCID mice reached approximately 1:4 x 10(5) when the mice were immunized with a neo-antigen, whereas titers reached 1:2 x 10(6) when recall responses were induced. Booster immunizations with Ag 21 days after the initial in vivo boost further enhanced this response, and specific human IgG titers of 1:17 x 10(6) were achieved. This represented an essentially monospecific IgG population. These responses were CD4+ T cell dependent. In addition, affinity maturation of the human Ab responses was observed. Spleens of hu-SPL-SCID mice with Ag-specific titers < or = 1:1 x 10(6) were often significantly enlarged and often displayed visible tumors. Fourteen of sixteen B cell tumors removed from spleens of five such hu-SPL-SCID mice, produced Abs that were specific for the immunizing Ags. From such tumor, cloned cell lines were established. One such mAb, MLN-7 (gamma1, kappa), was raised to tetanus toxoid and had no identified cross-reactivity.
Glomerular Filtration Rate Estimation in Patients with Advanced Chronic Renal Insufficiency Based on Serum Cystatin C Levels (2003)

The findings suggest that in patients with advanced chronic renal insufficiency (CRI) for the same decrease in GFR the increase of S(cyst) is not significantly higher than that of S(cr), although the tubular secretion of creatinine is significantly increased. Further studies (especially those focused on nonrenal elimination of cystatin C) are needed to elucidate the lack of difference between changes in S(cyst) and S(cr) in patients with CRI.
A 128-Channel 6mW Wireless Neural Recording IC with On-the-Fly Spike Sorting and UWB Tansmitter (2008)

The chip is composed of eight 16-channel front-end blocks, data serializing circuits, a DSP for on-chip spike sorting, digital MUX, encoder, UWB TX, and bias generators. The chip operates in one of the two modes. In sorting mode, a selected channel is connected to the on-the-fly spike sorting block and the extracted features of the spikes are transmitted for off-chip classification. In streaming mode, all the sampled data from the 128 channels are recorded and transmitted without any additional processing.
Methylsulfonylnitrobenzoates, a New Class of Irreversible Inhibitors of the Interaction of the Thyroid Hormone Receptor and Its Obligate Coactivators That Functionally Antagonizes Thyroid Hormone (2011)

Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor (NR) superfamily and regulate development, growth, and metabolism. Upon binding thyroid hormone, TR undergoes a conformational change that allows the release of corepressors and the recruitment of coactivators, which in turn regulate target gene transcription. Although a number of TR antagonists have been developed, most are analogs of the endogenous hormone that inhibit ligand binding. In a screen for inhibitors that block the association of TRβ with steroid receptor coactivator 2 (SRC2), we identified a novel methylsulfonylnitrobenzoate (MSNB)-containing series that blocks this interaction at micromolar concentrations. Here we have studied a series of MSNB analogs and characterized their structure activity relationships. MSNB members do not displace thyroid hormone T3 but instead act by direct displacement of SRC2. MSNB series members are selective for the TR over the androgen, vitamin D, and PPARγ NR members, and they antagonize thyroid hormone-activated transcription action in cells. The methylsulfonylnitro group is essential for TRβ antagonism. Side-chain alkylamine substituents showed better inhibitory activity than arylamine substituents. Mass spectrum analysis suggested that MSNB inhibitors bind irreversibly to Cys-298 within the AF-2 cleft of TRβ to disrupt SRC2 association.
ForC, a novel type of formin family protein lacking an FH1 domain, is involved in multicellular development inDictyostelium discoideum (2003)

Formins are highly conserved regulators of cytoskeletal organization and share three regions of homology: the FH1, FH2 and FH3 domains. Of the nine known formin genes or pseudogenes carried by Dictyostelium, forC is novel in that it lacks an FH1 domain. Mutant Dictyostelium lacking forC (DeltaforC) grew normally during the vegetative phase and, when starved, migrated normally and formed tight aggregates. Subsequently, however, DeltaforC cells made aberrant fruiting bodies with short stalks and sori that remained unlifted. DeltaforC aggregates were also unable to migrate as slugs, suggesting forC is involved in mediating cell movement during multicellular stages of Dictyostelium development. Consistent with this idea, expression of forC was increased significantly in aggregates of wild-type cells. GFP-ForC expressed in DeltaforC cells was localized at the crowns, which are macropinocytotic structures rich in F-actin, suggesting that, like other formin isoforms, ForC functions in close relation with the actin cytoskeleton. Truncation analysis of GFP-ForC revealed that the FH3 domain is required for ForC localization; moreover, localization of a truncated GFP-ForC mutant at the site of contacts between cells on substrates and along the cortex of cells within a multicellular culminant suggests that ForC is involved in the local actin cytoskeletal reorganization mediating cell-cell adhesion.
Vibration anesthesia: A noninvasive method of reducing discomfort prior to dermatologic procedures (2004)

In some dermatologic and cosmetic procedures, local anesthesia is not sufficient for relieving pain; often patients are averse to injections. We propose vibration anesthesia, the use of vibration delivered with commercially available inexpensive massagers to reduce discomfort. We find the analgesic effect of vibration helpful in minimizing pain in patients undergoing injections of botulinum toxin type A treatment for hyperhidrosis, injection of filler substances such as Restylane and Juvederm, laser therapy for leg veins, nail-fold injections, Q-switched laser treatment of tattoos, incision and drainage of abscesses, and cautery of facial warts, as well as facilitating anesthetic injections for needle-phobic patients. We expect that additional uses will be found as experience with this modality grows. Although the use of vibration anesthesia generally does not eliminate pain completely, it can serve to make the injection or procedure much more tolerable.
Expression of ril, a novel LIM domain gene, is down-regulated in Hras-transformed cells and restored in phenotypic revertants. (1995)

Several candidate genes involved in the maintenance of normal growth control (H-rev) were identified by differential expression cloning on the assumption that they are expressed in phenotypically normal rat cells and repressed in closely related H-ras transformed cells. Previously the genes coding for lysyl oxidase (H-rev142) and for an 18K-protein of unknown function (H-rev107) were recovered as cDNAs by subtraction cloning. Here we describe the identification and expression pattern of ril, a novel member of the heterogeneous group of genes encoding proteins with LIM/double zinc finger domains. The ril gene is expressed in normal fibroblasts and down-regulated in H-ras-transformed derivatives. Expression is restored in several independent phenotypic revertants derived from H-ras transformed cells. The predicted protein product of ril harbors a single LIM domain but lacks a homeodomain. The ril gene is highly conserved during evolution and is transcribed in various normal cell lines. Northern blot analysis and in situ hybridization studies showed that ril is expressed in meiotic spermatocytes, in somites of developing mice, and in a wide variety of tissues of adult mice.
Crystallization and preliminary x-ray investigation of purine-nucleoside phosphorylase from Escherichia coli. (1985)

Crystals of purine-nucleoside phosphorylase from Escherichia coli have been grown from solutions of ammonium sulfate. The crystals are hexagonal with space group P6(1)22 or P6(5)22; the axes are alpha = 106.5 A and c = 241.3 A. The crystals are moderately stable to x-rays and diffract beyond 3.0-A resolution. It appears that the molecule, which is a hexamer, utilizes the 2-fold symmetry of the space group, resulting in three subunits/asymmetric unit.