gebhart/patrepeval huggingface dataset:
Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain (2001)

A recJ homolog was cloned from the extremely thermophilic bacterium Thermus themophilus HB8. It encodes a 527 amino acid protein that has 33% identity to Escherichia coli RecJ protein and includes the characteristic motifs conserved among RecJ homologs. Although T.thermophilus RecJ protein (ttRecJ) was expressed as an inclusion body, it was purified in soluble form through denaturation with urea and subsequent refolding steps. Limited proteolysis showed that ttRecJ has a protease-resistant core domain, which includes all the conserved motifs. We constructed a truncated ttRecJ gene that corresponds to the core domain (cd-ttRecJ). cd-ttRecJ was overexpressed in soluble form and purified. ttRecJ and cd-ttRecJ were stable up to 60 degrees C. Size exclusion chromatography indicated that ttRecJ exists in several oligomeric states, whereas cd-ttRecJ is monomeric in solution. Both proteins have 5'-->3' exonuclease activity, which was enhanced by increasing the temperature to 50 degrees C. Mg(2+), Mn(2+) or Co(2+) ions were required to activate both proteins, whereas Ca(2+) and Zn(2+) had no effects.
Chicken sarcoma to human cancers: a lesson in molecular therapeutics. (2007)

Much of our current understanding of oncogenesis arose from a 1911 finding by American pathologist Peyton Rous that cell-free extracts of a chicken fibrosarcoma transmitted the disease to other chickens, indicating that the tumor was due to a “transmissible agent.” More than 40 years later, this led to the discovery of Rous sarcoma virus (RSV), named for its discoverer (1). In 1966, at the age of 87, Rous was awarded a Nobel Prize in recognition of his discovery of tumor-inducing viruses. The evidence that RSV is a retrovirus (RNA) tumor came from the Nobel Prize-winning discovery of reverse transcriptase by Howard Temin (2) and David Baltimore (3), which indicates that the viral genome is reverse transcribed into a DNA copy that becomes integrated into the host chromosome DNA as a provirus. This new genetic information acquired by the host serves as a source of virus production.
Cell surface thrombospondin is functionally essential for vascular smooth muscle cell proliferation (1988)

Thrombospondin (TS) is an extracellular glycoprotein whose synthesis and secretion by vascular smooth muscle cells (SMC) is regulated by platelet-derived growth factor. We have used a panel of five monoclonal antibodies against TS to determine an essential role for thrombospondin in the proliferation of cultured rat aortic SMC. All five monoclonal antibodies inhibited SMC growth in 3-d and extended cell number assays; the growth inhibition was specific for anti-TS IgG. The effects of one antibody (D4.6) were examined in detail and were found to be reversable and dose dependent. Cells treated with D4.6 at 50 micrograms/ml (which resulted in a greater than 60% reduction in cell number at day 8) were morphologically identical to control cells. D4.6-treated SMC were analyzed by flow cytofluorimetry and were found to be arrested in the G1 phase of the cell cycle. To determine a possible cellular site of action of TS in cell growth, SMC were examined by immunofluorescence using a polyclonal antibody against TS. TS was observed diffusely bound to the cell surface of serum- or platelet-derived growth factor-treated cells. The binding of TS to SMC was abolished in the presence of heparin, which prevents the binding of TS to cell surfaces and inhibits the growth of SMC. Monoclonal antibody D4.6, like heparin, largely abolished cell surface staining of TS but had no detectable effect on the cellular distribution of fibronectin. These results were corroborated by metabolic labeling experiments. We conclude that cell surface-associated TS is functionally essential for the proliferation of vascular SMC, and that this requirement is temporally located in the G1 phase of the cell cycle. Agents that perturb the interaction of TS with the SMC surface, such as heparin, may inhibit SMC proliferation in this manner.
Complex instruction set computing architecture for performing accurate quantum $Z$ rotations with less magic (2013)

We present quantum protocols for executing arbitrarily accurate $π/2^k$ rotations of a qubit about its $Z$ axis. Reduced instruction set computing (\textsc{risc}) architectures typically restrict the instruction set to stabilizer operations and a single non-stabilizer operation, such as preparation of a "magic" state from which $T = Z(π/4)$ gates can be teleported. Although the overhead required to distill high-fidelity copies of this magic state is high, the subsequent quantum compiling overhead to realize $Z$ rotations in a \textsc{risc} architecture can be much greater. We develop a complex instruction set computing (\textsc{cisc}) architecture whose instruction set includes stabilizer operations and preparation of magic states from which $Z(π/2^k)$ gates can be teleported, for $2 \leq k \leq k_{\text{max}}$. This results in a substantial overall reduction in the number of gates required to achieve a desired gate accuracy for $Z$ rotations. The key to our construction is a family of shortened quantum Reed-Muller codes of length $2^{k+2}-1$, whose magic-state distillation threshold shrinks with $k$ but is greater than 0.85% for $k \leq 6$.
Designing Facial Amphiphiles for the Stabilization of Integral Membrane Proteins (2007)

An added dimension: Amphiphiles with two-dimensional hydrophobic and hydrophilic faces represent a departure from traditional one-dimensional polar-head/nonpolar-tail molecules for the stabilization of integral membrane proteins. A prototypical example of this design has been synthesized from cholic acid (see picture), and was successfully used in the stabilization of two integral membrane proteins (represented by the blue/green cylinder).
The Use of Sep‐Pak™ C18 Cartridges During the Isolation of Gangliosides (1980)

The use of Sep-Pak C18 reverse-phase cartridges to adsorb gangliosides from aqueous solutions was studied. When upper phases formed from chloroform-methanol tissue extracts or aqueous salt solutions containing gangliosides are rapidly passed through the cartridges, the lipids are retained and the non-lipid components can be washed through. Gangliosides and other retained lipids can subsequently be eluted with methanol or chloroform-methanol
Ipilimumab in Combination With Paclitaxel and Carboplatin As First-Line Treatment in Stage IIIB/IV Non–Small-Cell Lung Cancer: Results From a Randomized, Double-Blind, Multicenter Phase II Study (2012)

Phased ipilimumab plus paclitaxel and carboplatin improved irPFS and PFS, which supports additional investigation of ipilimumab in NSCLC.
Effects of the Variation of Ferroelectric Properties on Negative Capacitance FET Characteristics (2016)

We study the effects of the variation of ferroelectric material properties (thickness, polarization, and coercivity) on the performance of negative capacitance FETs (NCFETs). Based on this, we propose the concept of conservative design of NCFETs, where any unintentional yet reasonable and simultaneous variation ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\sim \pm 3$ </tex-math></inline-formula> %) in ferroelectric parameters does not result in the emergence of hysteresis and causes only a reasonable variation in the ON-current (≤5%) and, within these constraints, the enhancement of ON-current due to the addition of the ferroelectric gate oxide, which is is maximized.
Active and Realistic Passive Marijuana Exposure Tested by Three Immunoassays and GCIMS in Urine (1988)

Human urine samples obtained before and after active and passive exposure to marijuana were analyzed by immune kits (Roche, Amersham, and Syva) and gas chromatography/mass spectrometry (GC/MS). Seven of eight subjects were positive for the entire five-day test period with one immune kit. The latter correlated with GC/MS in 98% of the samples. Passive inhalation experiments under conditions likely to reflect realistic exposure resulted consistently in less than 10 ng/mL of cannabinoids. The 10-100-ng/mL cannabinoid concentration range essential for detection of occasional and moderate marijuana users is thus unaffected by realistic passive inhalation.
Efficient Monte Carlo Procedures for Generating Points Uniformly Distributed over Bounded Regions (1984)

We consider the Monte Carlo problem of generating points uniformly distributed within an arbitrary bounded (measurable) region. The class of Markovian methods considered generate points asymptotically uniformly distributed within the region. Computational experience suggests the methods are potentially superior to conventional rejection techniques for large dimensional regions.
FAK signaling is critical for ErbB-2/ErbB-3 receptor cooperation for oncogenic transformation and invasion (2005)

The overexpression of members of the ErbB tyrosine kinase receptor family has been associated with cancer progression. We demonstrate that focal adhesion kinase (FAK) is essential for oncogenic transformation and cell invasion that is induced by ErbB-2 and -3 receptor signaling. ErbB-2/3 overexpression in FAK-deficient cells fails to promote cell transformation and rescue chemotaxis deficiency. Restoration of FAK rescues both oncogenic transformation and invasion that is induced by ErbB-2/3 in vitro and in vivo. In contrast, the inhibition of FAK in FAK-proficient invasive cancer cells prevented cell invasion and metastasis formation. The activation of ErbB-2/3 regulates FAK phosphorylation at Tyr-397, -861, and -925. ErbB-induced oncogenic transformation correlates with the ability of FAK to restore ErbB-2/3-induced mitogen-activated protein kinase (MAPK) activation; the inhibition of MAPK prevented oncogenic transformation. In contrast, the inhibition of Src but not MAPK prevented ErbB-FAK-induced chemotaxis. In migratory cells, activated ErbB-2/3 receptors colocalize with activated FAK at cell protrusions. This colocalization requires intact FAK. In summary, distinct FAK signaling has an essential function in ErbB-induced oncogenesis and invasiveness.
ModelingWeb Services using Semantic Graph Transformations to aid Automatic Composition (2007)

In this paper, we propose a novel way of modeling Web services using semantic graph transformations. Each operation supported by a Web service is associated with a semantic annotation that describes the input and output messages using RDF graph patterns. The terms used in these patterns are defined in OWL ontologies that describe the application domain. A key difference between our model and existing semantic Web service models like OWLS is that it describes the inputs and outputs in terms of instance-based graph patterns, rather than in terms of concepts. This allows associating a rich set of constraints on the input and output data in terms of relations between instances. We also propose a composition model for Web service operations, that describes the conditions for composing services into workflows. The composition model includes the notion of semantic propagation, i.e. the semantic description of the output message of an operation depends on the semantics of the input message. We have developed a planner that uses this model to compose services, automatically. The planner uses DLP reasoning to aid plan search. We present performance results for the planner.
Time-domain image processing using dynamic holography (1998)

Coded ultrafast optical pulses can be treated as one-dimensional (1-D) images in the time domain. We have converted spare-domain images into time-domain images using diffraction from dynamic holograms inside a Fourier pulse shaper, with photorefractive quantum wells (QW's) used as the dynamic holographic medium. We present several examples, in which amplitude or phase modulation of the hologram writing beams modifies the complex spectrum of the femtosecond output, resulting in a time-domain image. Both storage and processing of time-domain images can be achieved, depending on the hologram writing geometry and power densities. Time-domain processing operations such as edge enhancement, Fourier transform, and correlation are demonstrated.
Prevention of chronic doxorubicin cardiotoxicity in beagles by liposomal encapsulation. (1983)

Antitumor drugs such as doxorubicin have been encapsulated into liposomes as a means of enhancing activity and reducing toxicity. The present study was initiated to determine whether chronically administered liposome-encapsulated doxorubicin would be less toxic than the free drug. Doxorubicin was prepared in positively charged cardiolipin liposomes, and 1.75 mg/kg was given i.v. to each of five beagles. A second group received the free drug at 1.75 mg/kg. Additional animals received i.v. injections of either doxorubicin-free liposomes or 0.9% NaCl solution. All substances were given at 3-week intervals, and the experiment ended 1 week after the seventh injection (total dose, 12.25 mg/kg). A temporary reduction in food consumption was noted during the first few days after the administration of either form of doxorubicin. The effect was more severe in the dogs given free doxorubicin, and body weight decreased significantly only in this group of animals. Three dogs given free doxorubicin died or were killed before the end of the study because they were in poor condition. Lesions consisting mainly of vacuolization and myofibrillar loss were noted in the hearts of all five dogs given free doxorubicin. The severity of the lesions ranged from 2 to 4 (average, 3.4). In contrast, no abnormalities were found in any of the hearts from dogs given the liposomal doxorubicin. The most obvious general toxic effect caused by administration of free doxorubicin was alopecia, which was entirely prevented when doxorubicin was encapsulated into liposomes. At the dosage regimen utilized, liposomal doxorubicin and free doxorubicin exerted comparable degrees of bone marrow suppression. Thus, liposomal encapsulation of doxorubicin decreased cardiac and other toxic effects elicited by free doxorubicin. Whether this advantage can be translated into effective antineoplastic activity will need further evaluation.
Bernard-Soulier Syndrome (1998)

IN 1948, BERNARD AND SOULIER described a young male patient with a severe bleeding disorder that was characterized by a prolonged bleeding time, thrombocytopenia, and extremely large platelets.[1][1] They termed the disorder “la dystrophie thrombocytaire-hemorragipare congenitale.” Since then
Phase III Trial of Two Investigational Schedules of Ifosfamide Compared With Standard-Dose Doxorubicin in Advanced or Metastatic Soft Tissue Sarcoma: A European Organisation for Research and Treatment of Cancer Soft Tissue and Bone Sarcoma Group Study (2007)

Single-agent doxorubicin remains the treatment of choice for patients with advanced soft tissue sarcoma.
Hyperbilirubinemia (2011)

It is estimated that about two thirds of newborns will appear clinically jaundiced during their first weeks of life. As newborns and their mothers spend fewer days in the hospital after birth, the number of infants readmitted yearly in the United States for neonatal jaundice over the last 10 years has increased by 160%. A portion of these infants present to the emergency department, requiring a careful history and physical examination assessing them for the risk factors associated with pathologic bilirubin levels. Although the spectrum of illness may be great, the overwhelming etiology of neonatal jaundice presenting to an emergency department is physiologic and not due to infection or isoimmunization. Therefore, a little more than a good history, physical examination, and indirect/direct bilirubin levels are needed to evaluate an otherwise well-appearing jaundiced newborn. The American Academy of Pediatrics' 2004 clinical practice guidelines for "Management of Hyperbilirubinemia in the Newborn Infant 35 or More Weeks of Gestation" are a helpful and easily accessible resource when evaluating jaundiced newborns (available at http://aappolicy.aappublications.org/cgi/content/full/pediatrics;114/1/297). There are several exciting developments on the horizon for the diagnosis and management of hyperbilirubinemia including increasing use of transcutaneous bilirubin measuring devices and medications such as tin mesoporphyrin and intravenous immunoglobulin that may decrease the need for exchange transfusions.
A 63 element 1.75 dimensional ultrasound phased array for the treatment of benign prostatic hyperplasia (2005)

A 1.75 dimensional array, that overcame the drawbacks associated with one-dimensional arrays, has been designed, built and successfully tested. Design issues, such as cable and ceramic capacitances, were taken into account when designing this array. The final prototype overcame also the problem of generating grating lobes at unwanted locations by tapering the array elements.
Targeted Molecular Probes for Imaging Atherosclerotic Lesions With Magnetic Resonance Using Antibodies That Recognize Oxidation-Specific Epitopes (2008)

Magnetic resonance imaging with micelles containing gadolinium and oxidation-specific antibodies demonstrates specific targeting and excellent image quality of oxidation-rich atherosclerotic lesions.
Acute-phase protein response and survival duration of patients with pancreatic cancer (1995)

Background. Current methods to predict survival duration of patients with pancreatic cancer are limited. The aim of this study was to determine whether certain nutritional indices and the acute-phase protein response are prognostic factors independent of disease stage for patients with unresectable pancreatic cancer. Methods. Variables at the time of diagnosis of 102 patients with unresectable pancreatic cancer were entered into a Cox's proportional hazards model. Included in the analysis were the serum concentration of C-reactive protein (CRP) and albumin, the extent of weight loss, age, sex, and disease stage (International Union Against Cancer criteria). Results. A multivariate analysis in which each factor was adjusted for the influence of the other factors revealed the patient age, disease stage, serum albumin, and serum CRP to be independent predictors of survival. The presence of an acute-phase protein response was the most significant independent predictor of survival duration. The median survival of those with an acute-phase protein response (CRP > 10 mg/L, n = 45) was 66 days compared with 222 days for those with no acute-phase protein response (n = 57, P = 0.001, Mann-Whitney U test). Conclusion. The acute-phase protein response is a useful prognostic indicator for patients with unresectable pancreatic cancer. Moreover, the metabolic disturbances associated with an acute-phase protein response of patients with pancreatic cancer may be a worthwhile therapeutic target.
Tumor Necrosis Factor (TNF) α Increases Collagen Accumulation and Proliferation in Intestinal Myofibroblasts via TNF Receptor 2 (2005)

Intestinal fibrosis is an incurable complication of Crohn's disease involving increased numbers of collagen-producing myofibroblasts. Tumor necrosis factor (TNF) alpha has defined proinflammatory roles in Crohn's disease but its role in fibrosis is unclear. We tested the hypothesis that TNFalpha increases collagen accumulation and proliferation in intestinal myofibroblasts and has additive effects in combination with insulin-like growth factor (IGF) I. The mechanisms, TNF receptor isoform, and downstream signaling pathways were examined. Intestinal myofibroblasts from wild-type (WT) mice or mice homozygous for disruption of genes encoding TNFR1 (TNFR1-/-), TNFR2 (TNFR2-/-), or both (TNFR1/2-/-), were treated with TNFalpha, IGF-I, or both. In WT cells, TNFalpha and IGF-I stimulated type I collagen accumulation and DNA synthesis in an additive manner. IGF-I, but not TNFalpha, stimulated type I collagen gene activation. TNFalpha, but not IGF-I, induced tissue inhibitor of metalloproteinase-1 (TIMP-1) expression and reduced matrix metalloproteinases-2 activity and collagen degradation. TNFalpha also activated ERK1/2. These responses to TNFalpha were absent in TNFR2-/- and TNFR1/2-/- myofibroblasts, whereas TNFR1-/- cells showed similar responses to WT. Inhibition of ERK1/2 diminished TNFalpha induced DNA synthesis in WT and TNFR1-/- cells. Differences in TNFalpha-induced STAT3/DNA binding activity and not NFkappaB and AP-1 transcriptional activation correlated with impaired collagen accumulation/TIMP-1 induction in TNFR2(-/-) cells. Constitutively active STAT3 rescued TIMP-1 expression in TNFR2-/- cells. We conclude that TNFalpha and IGF-I may additively contribute to fibrosis during intestinal inflammation. TNFR2 is a primary mediator of fibrogenic actions of TNFalpha acting through ERK1/2 to stimulate proliferation and through STAT3 to stimulate TIMP-1 and inhibit collagen degradation.
Diels-Alder reactions involving heterocyclic dienophiles. Synthesis of substituted hydroquinazolines and 1,3-diazaspiro[4.5]decadienes (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiels-Alder reactions involving heterocyclic dienophiles. Synthesis of substituted hydroquinazolines and 1,3-diazaspiro[4.5]decadienesJohn F. W. Keana, Jeffrey S. Bland, Paul E. Eckler, Victor Nelson, and J. Z. GougoutasCite this: J. Org. Chem. 1976, 41, 12, 2124–2129Publication Date (Print):June 1, 1976Publication History Published online1 May 2002Published inissue 1 June 1976https://pubs.acs.org/doi/10.1021/jo00874a012https://doi.org/10.1021/jo00874a012research-articleACS PublicationsRequest reuse permissionsArticle Views346Altmetric-Citations12LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
ospC Diversity in Borrelia burgdorferi (2004)

The outer surface protein C (ospC) locus of the Lyme disease bacterium, Borrelia burgdorferi, is at least an order of magnitude more variable than other genes in the species. This variation is classified into 22 ospC major groups, 15 of which are found in the northeastern United States. The frequency distributions of ospC within populations suggest that this locus is under balancing selection. In multiple-niche polymorphism, a type of balancing selection, diversity within a population can be maintained when the environment is heterogeneous and no one genotype has the highest fitness in all environments. Genetically different individuals within vertebrate species and different vertebrate species constitute diverse environments for B. burgdorferi. We examined four important host species of B. burgdorferi and found that the strains that infected each species had different sets of ospC major groups. We found no variation among conspecific hosts in the ospC major groups of their infecting strains. These results suggest multiple niches create balancing selection at the ospC locus.
Lithium Protects against Anesthesia-induced Developmental Neuroapoptosis (2009)

If further testing finds lithium to be safe for use in pediatric/obstetric medicine, administration of a single dose of lithium before anesthesia induction may be a suitable means of mitigating the risk of anesthesia-induced developmental neuroapoptosis.