gebhart/patrepeval huggingface dataset:
Harnessing phytochrome's glowing potential (2004)

Directed evolution of a cyanobacterial phytochrome was undertaken to elucidate the structural basis of its light sensory activity by remodeling the chemical environment of its linear tetrapyrrole prosthetic group. In addition to identifying a small region of the apoprotein critical for maintaining phytochrome's native spectroscopic properties, our studies revealed a tyrosine-to-histidine mutation that transformed phytochrome into an intensely red fluorescent biliprotein. This tyrosine is conserved in all members of the phytochrome superfamily, implicating direct participation in the primary photoprocess of phytochromes. Fluorescent phytochrome mutants also hold great promise to expand the present repertoire of genetically encoded fluorescent proteins into the near infrared.
Complement system in psoriatic arthritis: a useful marker in response prediction and monitoring of anti-TNF treatment. (2012)

PsA patients with moderate to severe disease show elevated C3 and C4 levels, reverted by anti-TNF treatment. High C3 may be considered a hallmark of inflammation and C3 revealed the highest predictive value for response to anti-TNF.
Glycogen Synthase Kinase-3β Facilitates Staurosporine- and Heat Shock-induced Apoptosis (2000)

The potential role of glycogen synthase kinase-3beta in modulating apoptosis was examined in human SH-SY5Y neuroblastoma cells. Staurosporine treatment caused time- and concentration-dependent increases in the activities of caspase-3 and caspase-9 but not caspase-1, increased proteolysis of poly(ADP-ribose) polymerase, and induced morphological changes consistent with apoptosis. Overexpression of glycogen synthase kinase-3beta to levels 3.5 times that in control cells did not alter basal indices of apoptosis but potentiated staurosporine-induced activation of caspase-3, caspase-9, proteolysis of poly(ADP-ribose) polymerase, and morphological changes indicative of apoptosis. Inhibition of glycogen synthase kinase-3beta by lithium attenuated the enhanced staurosporine-induced activation of caspase-3 in cells overexpressing glycogen synthase kinase-3beta. In cells subjected to heat shock, caspase-3 activity was more than three times greater in glycogen synthase kinase-3beta-transfected than control cells, and this potentiated response was inhibited by lithium treatment. Thus, glycogen synthase kinase-3beta facilitated apoptosis induced by two experimental paradigms. These findings indicate that glycogen synthase kinase-3beta may contribute to pro-apoptotic-signaling activity, that inhibition of glycogen synthase kinase-3beta can contribute to anti-apoptotic-signaling mechanisms, and that the neuroprotective actions of lithium may be due in part to its inhibitory modulation of glycogen synthase kinase-3beta.
A New Class of Reverse Signaling Costimulators Belongs to the TNF Family (2007)

Recent evidence shows that many molecules of the TNF family serve as counter-receptors, inducing costimulation through reverse signals in addition to delivering signals through their respective TNF receptors. In this review, we will discuss this new class of costimulators with a focus on the mechanism of costimulation transduced by reverse signaling through Fas ligand.
Low cost and compact quantum key distribution (2006)

Abstract. We present the design of a novel free-space quantum cryptography system, complete with purpose-built software, that can operate in daylight conditions. The transmitter and receiver modules are built using inexpensive off-the-shelf components. Both modules are compact allowing the generation of renewed shared secrets on demand over a short range of a few metres. An analysis of the software is shown as well as results of error rates and therefore shared secret yields at varying background light levels. As the system is designed to eventually work in short-range consumer applications, we also present a use scenario where the consumer can regularly ‘top up’ a store of secrets for use in a variety of one-time-pad and authentication protocols. Low Cost and Compact Quantum Key Distribution 2 1.
Metabolic engineering of Arabidopsis to produce nutritionally important DHA in seed oil (2005)

Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are nutritionally important long-chain (≥ C<sub>20</sub>) omega-3 polyunsaturated fatty acids (ω3 LC-PUFA) currently obtained mainly from marine sources. A set of genes encoding the fatty acid chain elongation and desaturation enzymes required for the synthesis of LC-PUFA from their C<sub>18</sub> PUFA precursors was expressed seed-specifically in Arabidopsis thaliana. This resulted in the synthesis of DHA, the most nutritionally important ω3 LC-PUFA, for the first time in seed oils, along with its precursor EPA and the ω6 LC-PUFA arachidonic acid (ARA). The assembled pathway utilised Δ5 and Δ6 desaturases that operate on acyl-CoA substrates and led to higher levels of synthesis of LC-PUFA than previously reported with acyl-PC desaturases. This demonstrates the potential for development of land plants as alternative sources of DHA and other LC-PUFA to meet the growing demand for these nutrients.
Regiocontrol in MnIII‐Mediated Oxidative Heterobicyclizations: Access to the Core Skeletons of Oroidin Dimers (2006)

Unter Kontrolle: Die Cyclisierung eines allylischen β-Imidazolinonyl-β-ketoesters 1 wird in Form einer MnIII-vermittelten Radikalkaskade durchgeführt. Dabei kann der Reaktionsverlauf (5-exo/6-endo oder 5-exo/5-exo) in Richtung der zentralen Cyclopentyl- und Cyclohexenylgerüste (3 bzw. 2) zweier Klassen von Oroidindimeren gesteuert werden. 2 kann auch durch oxidative Umlagerung in 3 überführt werden. PG=Schutzgruppe. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z601208_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Visible Light and Sunlight Photoinduced ATRP with ppm of Cu Catalyst (2012)

Photochemically induced ATRP was performed with visible light and sunlight in the presence of parts per million (ppm) copper catalysts. Illumination of the reaction mixture yielded polymerization in case of 392 and 450 nm light but not for 631 nm light. Sunlight was also a viable source for the photoinduced ATRP. Control experiments suggest photoreduction of the Cu<sup>II</sup> complex (ligand to metal charge transfer in the excited state), yielding a Cu<sup>I</sup> complex, and a bromine radical that can initiate polymerization. No photoactivation of Cu<sup>I</sup> complex was detected. This implies that the mechanism of ATRP in the presence of light is a hybrid of ICAR and ARGET ATRP. The method was also used to synthesize block copolymers and polymerizations in water.
Ethanol-Induced Activation of Myosin Light Chain Kinase Leads to Dysfunction of Tight Junctions and Blood-Brain Barrier Compromise (2005)

These results suggest that EtOH activates MLCK leading to phosphorylation of MLC, occludin and claudin-5. Cytoskeletal alterations (MLC) and TJ changes (occludin and claudin-5 phosphorylation) result in BBB impairment (decrease in TEER). TJ compromise is associated with increased monocyte migration across the BBB.
T cells expressing CD123-specific chimeric antigen receptors exhibit specific cytolytic effector functions and antitumor effects against human acute myeloid leukemia (2013)

Induction treatments for acute myeloid leukemia (AML) have remained largely unchanged for nearly 50 years, and AML remains a disease of poor prognosis. Allogeneic hematopoietic cell transplantation can achieve cures in select patients and highlights the susceptibility of AML to donor-derived immunotherapy. The interleukin-3 receptor α chain (CD123) has been identified as a potential immunotherapeutic target because it is overexpressed in AML compared with normal hematopoietic stem cells. Therefore, we developed 2 chimeric antigen receptors (CARs) containing a CD123-specific single-chain variable fragment, in combination with a CD28 costimulatory domain and CD3-ζ signaling domain, targeting different epitopes on CD123. CD123-CAR-redirected T cells mediated potent effector activity against CD123+ cell lines as well as primary AML patient samples. CD123 CAR T cells did not eliminate granulocyte/macrophage and erythroid colony formation in vitro. Additionally, T cells obtained from patients with active AML can be modified to express CD123 CARs and are able to lyse autologous AML blasts in vitro. Finally, CD123 CAR T cells exhibited antileukemic activity in vivo against a xenogeneic model of disseminated AML. These results suggest that CD123 CAR T cells are a promising immunotherapy for the treatment of high-risk AML.
Celiac plexus neurolysis with the modified transaortic approach. (1990)

Celiac plexus block with alcohol was performed to relieve pain in 124 patients with abdominal malignancies. A transaortic technique was employed in which a single needle was advanced from a left posterior paramedian approach through the aorta to deposit anesthetic agent directly onto the celiac plexus. Ninety-one percent of patients experienced marked pain relief. No major hemorrhagic or neurologic complications were encountered. The transaortic method of celiac block is as effective as, easier to perform, and may be safer than the classic two-needle technique.
Osteoid-Mimicking Dense Collagen/Chitosan Hybrid Gels (2011)

Bone extracellular matrix (ECM) is a 3D network, composed of collagen type I and a number of other macromolecules, including glycosaminoglycans (GAGs), which stimulate signaling pathways that regulate osteoblast growth and differentiation. To model the ECM of bone for tissue regenerative approaches, dense collagen/chitosan (Coll/CTS) hybrid hydrogels were developed using different proportions of CTS to mimic GAG components of the ECM. MC3T3-E1 mouse calvaria preosteoblasts were seeded within plastically compressed Coll/CTS hydrogels with solid content approaching that of native bone osteoid. Dense, cellular Coll/CTS hybrids were maintained for up to 8 weeks under either basal or osteogenic conditions. Higher CTS content significantly increased gel resistance to collagenase degradation. The incorporation of CTS to collagen gels decreased the apparent tensile modulus from 1.82 to 0.33 MPa. In contrast, the compressive modulus of Coll/CTS hybrids increased in direct proportion to CTS content exhibiting an increase from 23.50 to 55.25 kPa. CTS incorporation also led to an increase in scaffold resistance to cell-induced contraction. MC3T3-E1 viability, proliferation, and matrix remodeling capability (via matrix metalloproteinase expression) were maintained. Alkaline phosphatase activity was increased up to two-fold, and quantification of phosphate mineral deposition was significantly increased with CTS incorporation. Thus, dense Coll/CTS scaffolds provide osteoid-like models for the study of osteoblast differentiation and bone tissue engineering.
Neuronal Circuits Involved in Learning: The Use of Modifiable Synapses in the Simulation of Behavior (1976)

Our present knowledge of brain structure and function requires that any model of neuronal circuitry designed to account for learning must satisfy three conditions. It must (1) meet economy restrictions on the number of cells in the brain, (2) use the same set of cells to account for a number of different behaviors, and (3) not require a detailed embryological specification of its connections. Previously published models have failed to meet one or more of these conditions. In this paper, a model is presented which does satisfy them, and in doing so accounts in detail for classical conditioning, operant conditioning, and other learning tasks. The model employs the types of synapses proposed by Burke and Hebb in simple modular circuits as a means of providing independent storage of information at each modifiable synapse.
Mapping of Antigenic Determinants of Purified, Lipid‐Free Human Serum Amyloid A Proteins (1998)

Serum amyloid A (SAA) is the major apolipoprotein of high-density lipoproteins (HDL) present during the acute-phase reaction. To map specific epitopes on purified, lipid-free SAA, sequence-specific antibodies raised against synthetic peptides corresponding to amino acid residues 1-17, 14-30, 27-44, 40-63, 59-72, 68-84, 79-94 and 89-104 of human SAA1 were studied. Using the indirect sandwich dissociation-enhanced lanthanide fluorescence immunoassay, antibodies raised against epitopes comprising residues 1-17, 14-30, 40-63 and 79-94 failed to recognize the corresponding domains on isolated human SAA1/SAA2 or a mixture of both isoforms, indicating that these epitopes are masked, apparently because of specific folding and/or self-aggregation (dimerization). The accessible antigenic determinants of isolated SAA are epitopes comprising residues 31-39, 64-78 and 95-104. The present findings indicate that: (i) the same epitopes are exposed, irrespective whether SAA is HDL-associated or in its lipid-free form and that (ii) monomeric and dimeric SAA co-exist to a similar extent in the lipid-free form, irrespective of whether conditions are non-denaturating, denaturating, acidic or basic. From our studies it is proposed that isolated, purified SAA may serve as a reliable standard for quantification of HDL-associated SAA and for mimicking the interaction of acute-phase HDL particles with peripheral tissues in vitro.
Adaptive blind interference cancellation in CDMA systems (2003)

Multiuser CDMA communication systems experience multiple access interference as well as multipath distortions and require some interference cancellation scheme at the receiver. While blind multiuser receivers have received considerable attention, adaptive versions are often limited to the no multipath case. In this paper, the receiver's output variance is minimized subject to appropriate constraints which take into account the multipath channel of the user of interest. The constraint parameters are also jointly optimized resulting in a min/max problem. Adaptive solutions are proposed based on gradient descent and recursive least squares procedures. It is shown that the proposed method enjoys global convergence and its performance is close to the trained MMSE receiver.
Faecal Calprotectin Shedding after Short-Term Treatment with Non-Steroidal Anti-Inflammatory Drugs (1996)

Although seemingly influenced by concurrent upper airway infections, the study indicates that the calprotectin test may be useful for monitoring the inflammatory response to NSAID treatment, even in short-term setting.
Genome Scan and Congenic Strains for Blood Pressure QTL Using Dahl Salt-Sensitive Rats (1998)

An F2 population (n = 151) derived from Dahl salt-sensitive (S) and Lewis rats was raised on a 8% NaCl diet for 9 weeks and analyzed for blood pressure quantitative trait loci (QTL) by use of a whole genome scan. Chromosomes 5 and 10 yielded lod scores for linkage to blood pressure that were significant; chromosomes 1, 2, 3, 8, 16, 17, and 18 gave lod scores suggestive for linkage. Chromosome 7 gave a significant signal for heart weight with a lesser effect on blood pressure. Congenic strains were constructed by introgressing Lewis low-blood-pressure QTL alleles for chromosomes 1, 5, 10, and 17 into the S genetic background. Congenic strains for chromosomes 1, 5, and 10 had significantly lower blood pressure than S, proving the existence of QTL on these chromosomes, but the chromosome 17 congenic strain failed to trap a contrasting QTL allele. The QTL allele increasing blood pressure originated from S rats for all QTL except those on chromosomes 2 and 7 in which the Lewis allele increased blood pressure. Interactions between each QTL and every other locus in the genome scan yielded significant interactions between chromosomes 10 and 4, and between chromosomes 2 and 3.
Surgical standards in the management of ovarian cancer (2000)

Surgery is the cornerstone of management of epithelial ovarian cancer and has broad applications throughout the clinical course of disease, from initial diagnosis to palliative care. Comprehensive surgical staging is essential for precise prognostic determination and treatment planning for patients with apparent early-stage ovarian cancer. Although randomized trials are lacking, the survival advantage associated with optimal primary cytoreduction has been consistent and reproducible. With increasing radicality of cytoreductive surgical techniques and sophistication of postoperative care, it appears that an "optimal" surgical procedure is that which leaves the patient with no visible residual disease. The survival benefits of cytoreductive surgery are also applicable to women with stage IV ovarian cancer, although the rate of success is somewhat attenuated compared with patients with stage III disease. Recent data also indicate that with appropriate surgical selection criteria, secondary cytoreduction is associated with a significant prolongation of survival for patients with recurrent ovarian cancer. Unfortunately, several recent publications illustrate how the decentralization of health care may have significant ramifications on the ability of women with known or suspected ovarian cancer to avail themselves of the surgical standard of care.
Fast Screening Procedures for Random Transposon Libraries of Cloned Herpesvirus Genomes: Mutational Analysis of Human Cytomegalovirus Envelope Glycoprotein Genes (2000)

We have cloned the human cytomegalovirus (HCMV) genome as an infectious bacterial artificial chromosome (BAC) in Escherichia coli. Here, we have subjected the HCMV BAC to random transposon (Tn) mutagenesis using a Tn1721-derived insertion sequence and have provided the conditions for excision of the BAC cassette. We report on a fast and efficient screening procedure for a Tn insertion library. Bacterial clones containing randomly mutated full-length HCMV genomes were transferred into 96-well microtiter plates. A PCR screening method based on two Tn primers and one primer specific for the desired genomic position of the Tn insertion was established. Within three consecutive rounds of PCR a Tn insertion of interest can be assigned to a specific bacterial clone. We applied this method to retrieve mutants of HCMV envelope glycoprotein genes. To determine the infectivities of the mutant HCMV genomes, the DNA of the identified BACs was transfected into permissive fibroblasts. In contrast to BACs with mutations in the genes coding for gB, gH, gL, and gM, which did not yield infectious virus, BACs with disruptions of open reading frame UL4 (gp48) or UL74 (gO) were viable, although gO-deficient viruses showed a severe growth deficit. Thus, gO (UL74), a component of the glycoprotein complex III, is dispensable for viral growth. We conclude that our approach of PCR screening for Tn insertions will greatly facilitate the functional analysis of herpesvirus genomes.
Capillary electrophoresis and sample injection systems integrated on a planar glass chip (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCapillary electrophoresis and sample injection systems integrated on a planar glass chipD. Jed. Harrison, Andreas. Manz, Zhonghui. Fan, Hans. Luedi, and H. Michael. WidmerCite this: Anal. Chem. 1992, 64, 17, 1926–1932Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/ac00041a030https://doi.org/10.1021/ac00041a030research-articleACS PublicationsRequest reuse permissionsArticle Views3707Altmetric-Citations997LEARN 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
GSK3 and Tau: Two Convergence Points in Alzheimer's Disease (2012)

Glycogen synthase kinase 3 (GSK3) is a ubiquitously expressed serine/threonine kinase that plays a key role in the pathogenesis of Alzheimer's disease (AD). GSK3 phosphorylates tau in most serine and threonine residues hyperphosphorylated in paired helical filaments, and GSK3 activity contributes both to amyloid-β production and amyloid-β-mediated neuronal death. Thus, mice generated in our laboratory with conditional overexpression of GSK3 in forebrain neurons (Tet/GSK3β mice) recapitulate aspects of AD neuropathology such as tau hyperphosphorylation, apoptotic neuronal death, and reactive astrocytosis, as well as spatial learning deficit. In this review, we describe recent contributions of our group showing that transgene shutdown in that animal model leads to normal GSK3 activity, normal phospho-tau levels, diminished neuronal death, and suppression of the cognitive deficit, thus further supporting the potential of GSK3 inhibitors for AD therapeutics. In addition, we have combined transgenic mice overexpressing the enzyme GSK3β with transgenic mice expressing tau with a triple FTDP-17 mutation that develop prefibrillar tau-aggregates. Our data suggest that progression of the tauopathy can be prevented by administration of lithium when the first signs of neuropathology appear. Further, it is possible to partially reverse tau pathology in advanced stages of the disease, although the presence of already assembled neurofibrillary tangle-like structures cannot be reversed.
Rev-erbα and Rev-erbβ coordinately protect the circadian clock and normal metabolic function (2012)

The nuclear receptor Rev-erbα regulates circadian rhythm and metabolism, but its effects are modest and it has been considered to be a secondary regulator of the cell-autonomous clock. Here we report that depletion of Rev-erbα together with closely related Rev-erbβ has dramatic effects on the cell-autonomous clock as well as hepatic lipid metabolism. Mouse embryonic fibroblasts were rendered arrhythmic by depletion of both Rev-erbs. In mouse livers, Rev-erbβ mRNA and protein levels oscillate with a diurnal pattern similar to that of Rev-erbα, and both Rev-erbs are recruited to a remarkably similar set of binding sites across the genome, enriched near metabolic genes. Depletion of both Rev-erbs in liver synergistically derepresses several metabolic genes as well as genes that control the positive limb of the molecular clock. Moreover, deficiency of both Rev-erbs causes marked hepatic steatosis, in contrast to relatively subtle changes upon loss of either subtype alone. These findings establish the two Rev-erbs as major regulators of both clock function and metabolism, displaying a level of subtype collaboration that is unusual among nuclear receptors but common among core clock proteins, protecting the organism from major perturbations in circadian and metabolic physiology.
Serotonin and Octopamine in the Nematode Caenorhabditis elegans (1982)

The biogenic amines serotonin and octopamine are present in the nematode Caenorhabditis elegans. Serotonin, detected histochemically in whole mounts, is localized in two pharyngeal neurons that appear to be neurosecretory. Octopamine, identified radioenzymatically in crude extracts, probably is also localized in a few neurons. Exogenous serotonin and octopamine elicit specific and opposite behavioral responses in Caenorhabditis elegans, suggesting that these compounds function physiologically as antagonists.