gebhart/patrepeval huggingface dataset:
A Molecular Beacon Strategy for the Thermodynamic Characterization of Triplex DNA:  Triplex Formation at the Promoter Region of Cyclin D1 (2001)

We studied the formation of triplex DNA in the purine-pyrimidine-rich promoter site sequence of cyclin D1, located at -116 to -99 from the transcription initiation site, with a molecular beacon comprised of a G-rich 18-mer triplex forming oligodeoxyribonucleotide. Formation of triplex DNA was monitored by enhanced fluorescence of the beacon, due to the weakening of fluorescence energy transfer, upon its binding to the target duplex. Electrophoretic mobility shift assay confirmed triplex DNA formation by these oligonucleotides. In low salt buffer (10 mM Na(+)), triplex DNA formation was not observed in the absence of a ligand such as spermine. At room temperature (22 degrees C), the equilibrium association constant (K(a)) calculated in the presence of 1 microM spermine and 10 mM Na(+) was 3.2 x 10(8) M(-1). The K(a) value was 1.0 x 10(9) M(-1) in the presence of 150 mM Na(+), and it increased by 10-fold by the addition of 1 mM spermine. Delta H, Delta S, and Delta G of triplex DNA formation, calculated from the temperature dependence of K(a) in the range of 20--45 degrees C, were -35.9 kcal/mol, -77 cal/(mol.K), and -13 kcal/mol, respectively, in the presence of 150 mM NaCl. The corresponding values were -52.9 kcal/mol, -132.5 cal/(mol.K), and -13.4 kcal/mol in the presence of 150 mM NaCl and 1 mM spermine. Structurally related polyamines exerted different degrees of triplex DNA stabilization, as determined by binding constant measurements. Comparison of spermine versus hexamine showed a 17-fold increase in the equilibrium association constant, whereas bis(ethyl) derivatization lead to a 4-fold decrease of this value. In the absence of added duplex and polyamines, the molecular beacon dissociated with a melting temperature of 67 degrees C. Thermodynamic parameters of beacon melting were calculated from the melting curve, and the Delta H, Delta S, and Delta G values were 37.8 kcal/mol, 112 cal/(mol.K), and 4.4 kcal/mol, respectively. These results demonstrate that molecular beacons can be used for the direct determination of the equilibrium association constants and thermodynamic parameters of triplex DNA formation in the presence of ligands such as polyamines.
ATP-driven stepwise rotation of F o F 1 -ATP synthase (2005)

FoF1-ATP synthase (FoF1) is a motor enzyme that couples ATP synthesis/hydrolysis with a transmembrane proton translocation. F1, a water-soluble ATPase portion of FoF1, rotates by repeating ATP-waiting dwell, 80 degrees substep rotation, catalytic dwell, and 40 degrees -substep rotation. Compared with F1, rotation of FoF1 has yet been poorly understood, and, here, we analyzed ATP-driven rotations of FoF1. Rotation was probed with an 80-nm bead attached to the ring of c subunits in the immobilized FoF1 and recorded with a submillisecond fast camera. The rotation rates at various ATP concentrations obeyed the curve defined by a Km of approximately 30 microM and a Vmax of approximately 350 revolutions per second (at 37 degrees C). At low ATP, ATP-waiting dwell was seen and the kon-ATP was estimated to be 3.6 x 10(7) M(-1) x s(-1). At high ATP, fast, poorly defined stepwise motions were observed that probably reflect the catalytic dwells. When a slowly hydrolyzable substrate, adenosine 5'-[gamma-thio]triphosphate, was used, the catalytic dwells consisting of two events were seen more clearly at the angular position of approximately 80 degrees . The rotational behavior of FoF1 resembles that of F1. This finding indicates that "friction" in Fo motor is negligible during the ATP-driven rotation. Tributyltin chloride, a specific inhibitor of proton translocation, slowed the rotation rate by 96%. However, dwells at clearly defined angular positions were not observed under these conditions, indicating that inhibition by tributyltin chloride is complex.
Oxathiaphospholane Method of Stereocontrolled Synthesis of Diribonucleoside 3‘,5‘-Phosphorothioates (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTOxathiaphospholane Method of Stereocontrolled Synthesis of Diribonucleoside 3',5'-PhosphorothioatesAgnieszka Sierzchała, Andrzej Okruszek, and Wojciech J. StecView Author Information Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Łódź, Poland Cite this: J. Org. Chem. 1996, 61, 19, 6713–6716Publication Date (Web):September 20, 1996Publication History Received3 May 1996Published online20 September 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo960811ehttps://doi.org/10.1021/jo960811ebrief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views442Altmetric-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 InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Absolute configuration,High-performance liquid chromatography,Hydrolysis,Molecular structure,Phosphorus Get e-Alerts
Dietary Cholesterol Worsens Adipose Tissue Macrophage Accumulation and Atherosclerosis in Obese LDL Receptor–Deficient Mice (2008)

Obesity-induced macrophage accumulation in adipose tissue is exacerbated by dietary cholesterol. These local inflammatory changes in adipose tissue are associated with insulin resistance, systemic inflammation, and increased atherosclerosis in this mouse model.
Cell adhesion or integrin clustering increases phosphorylation of a focal adhesion-associated tyrosine kinase. (1992)

We have recently shown that changes in tyrosine phosphorylation of a 130-kDa protein(s) (pp130) may be involved in integrin signaling (Kornberg, L., Earp, H.S., Turner, C., Prokop, and Juliano, R. L. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 8392-8396). One component of the pp130 protein complex reacts with an antibody generated against p125fak, which is a focal contact-associated tyrosine kinase (Schaller, M.D., Borgman, C. A., Cobb, B. S., Vines, R. R., Reynolds, A. B., and Parsons, J. T. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5192-5196). Both antibody-mediated integrin clustering and adhesion of KB cells to fibronectin leads to increased tyrosine phosphorylation of p125fak. The phosphorylation of p125fak is coincident with adhesion of cells to fibronectin and is maximal prior to cell spreading. Tyrosine phosphorylation of p125fak is induced when KB cells are allowed to adhere to fibronectin, collagen type IV, or laminin, but is not induced on polylysine. When KB cells are subjected to indirect immunofluorescence microscopy, p125fak colocalizes with talin in focal contacts. These data provide additional evidence that tyrosine kinases are involved in integrin signaling.
D538G Mutation in Estrogen Receptor-α: A Novel Mechanism for Acquired Endocrine Resistance in Breast Cancer (2013)

Resistance to endocrine therapy occurs in virtually all patients with estrogen receptor α (ERα)-positive metastatic breast cancer, and is attributed to various mechanisms including loss of ERα expression, altered activity of coregulators, and cross-talk between the ERα and growth factor signaling pathways. To our knowledge, acquired mutations of the ERα have not been described as mediating endocrine resistance. Samples of 13 patients with metastatic breast cancer were analyzed for mutations in cancer-related genes. In five patients who developed resistance to hormonal therapy, a mutation of A to G at position 1,613 of ERα, resulting in a substitution of aspartic acid at position 538 to glycine (D538G), was identified in liver metastases. Importantly, the mutation was not detected in the primary tumors obtained prior to endocrine treatment. Structural modeling indicated that D538G substitution leads to a conformational change in the ligand-binding domain, which mimics the conformation of activated ligand-bound receptor and alters binding of tamoxifen. Indeed, experiments in breast cancer cells indicated constitutive, ligand-independent transcriptional activity of the D538G receptor, and overexpression of it enhanced proliferation and conferred resistance to tamoxifen. These data indicate a novel mechanism of acquired endocrine resistance in breast cancer. Further studies are needed to assess the frequency of D538G-ERα among patients with breast cancer and explore ways to inhibit its activity and restore endocrine sensitivity.
Predictability and unpredictability in Kalman filtering (1991)

The authors study the dynamical behavior of the Kalman filter when the given parameters are allowed to vary in a way which does not necessarily correspond to an underlying stochastic system. This may correspond to situations in which the basic parameters are chosen incorrectly through estimates. The authors show that, as has been suggested by Kalman, the filter equations converge to a limit (corresponding to a steady-state filter) for a subset of the parameter space which is much larger than that corresponding to bona fide stochastic systems. More surprisingly, in the complement of this subset, the filtering equations behave in both a regular and an unpredictable manner, representative of some of the basic aspects of chaotic dynamics. This interesting dynamical behavior occurs already for one-dimensional filters, and a complete phase portrait in this case is given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Exposure to chromium, cobalt and molybdenum from metal-on-metal total hip replacement and hip resurfacing arthroplasty (2006)

During the first 2 years after surgery, the Birmingham hip resurfacing arthroplasty leads to a significantly greater increase in serum chromium and cobalt levels than the 28-mm metal-on-metal MTHR. Observation of patients over a longer period will be necessary in order to evaluate any chronic adverse effects to the system due to elevated chromium and cobalt serum concentrations.
High-performance multilayered phosphorescent OLEDs by solution-processed commercial electron-transport materials (2012)

Highly efficient multilayered polymer-based phosphorescent organic light-emitting diodes (PhOLEDs) are realized by orthogonal sequential solution-processing of commercial small-molecule electron-transport materials (ETMs), including 1,3,5-tri(3-pyrid-3-yl-phenyl)benzene (TmPyPB), 4,7-diphenyl-1,10-phenanthroline (BPhen) and 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (BCP). The performance of PhOLEDs with solution-deposited ETMs is found to be far superior compared to devices with vacuum-deposited ETMs. PhOLEDs with a solution-deposited BPhen electron-transport layer gave a luminous efficiency of 53.8 cd A−1 with an external quantum efficiency of 16.1%. The solution-processed electron-transport layer exhibits a unique rough surface morphology which facilitates charge-injection and transport from the cathode metal. The nanostructured surface morphology and charge carrier mobility of the solution-processed electron-transport layers could be tuned and controlled by the solution concentration. The orthogonal solution-processing demonstrated here is a promising strategy for applications in various solution-processed multilayered organic electronic devices.
Activity distribution of a cobalt‐60 teletherapy source (1991)

In the course of quantifying the effect of radiation source size on the spatial resolution of portal images, a concentric ring structure in the activity distribution of a Cobalt-60 teletherapy source has been observed. The activity distribution was measured using a strip integral technique and confirmed independently by a contact radiograph of an identical but inactive source replica. These two techniques suggested that this concentric ring structure is due to the packing configuration of the small 60Co pellets that constitute the source. The source modulation transfer function (MTF) showed that this ring structure has a negligible influence on the spatial resolution of therapy images when compared to the effect of the large size of the 60Co source.
Human hand modeling from surface anatomy (2006)

The human hand is an important interface with complex shape and movement. In virtual reality and gaming applications the use of an individualized rather than generic hand representation can increase the sense of immersion and in some cases may lead to more effortless and accurate interaction with the virtual world. We present a method for constructing a person-specific model from a single canonically posed palm image of the hand without human guidance. Tensor voting is employed to extract the principal creases on the palmar surface. Joint locations are estimated using extracted features and analysis of surface anatomy. The skin geometry of a generic 3D hand model is deformed using radial basis functions guided by correspondences to the extracted surface anatomy and hand contours. The result is a 3D model of an individual's hand, with similar joint locations, contours, and skin texture.
Aircraft based four-channel thermal dissociation laser induced fluorescence instrument for simultaneous measurements of NO 2 , total peroxy nitrate, total alkyl nitrate, and HNO 3 (2013)

Abstract. A four-channel thermal dissociation laser induced fluorescence (TD-LIF) instrument has been developed for simultaneous measurements of nitrogen dioxide (NO2), total peroxy nitrate (∑PNs), total alkyl nitrate (∑ANs) and nitric acid (HNO3). NO2 is measured directly by LIF at 532 nm, whereas organic nitrates and nitric acid are thermally dissociated at distinct temperatures in the inlet to form NO2, which is then measured by LIF. The concentrations of each dissociated species are derived by the differences in measured NO2 relative to the reference colder inlet channel. The TD-LIF was adapted to fly on board the UK Facility for Airborne Atmospheric Measurements (FAAM) BAe 146-301 atmospheric research aircraft in summer 2010, and to date has successfully flown in five field campaigns. This paper reports novel improvements in the TD-LIF instrumentations, including (1) the use of a single wavelength laser, which makes the system compact and relatively cheap; (2) the use of a single beam laser that allows easy alignment and optical stability against the vibrational aircraft environment; and (3) the optical assembly of four detection cells that allow simultaneous and fast (time resolution up to 0.1 s) measurements of NO2, ∑PNs, ∑ANs and HNO3. Laboratory-generated mixtures of PNs, ANs and HNO3 in zero air are converted into NO2 and used to fix the dissociation temperatures of each heated inlet to test the selectivity of the instrument and potential interferences due to recombination reactions of the dissociated products. The effectiveness of the TD-LIF was demonstrated during the RONOCO aircraft campaign (summer 2010). A chemiluminescence system that was measuring NO2 and a broadband cavity enhanced absorption spectrometer (BBCEAS) that was measuring one of the PNs (N2O5) were installed on the same aircraft during the campaign. The in-flight intercomparison of the new TD-LIF with the chemiluminescence system for NO2 measurements and the intercomparison between ∑PNs measured by the TD-LIF and N2O5 by the BBCEAS are used to assess the performance of the TD-LIF.
Construction and Characterization of Soluble, Cleaved, and Stabilized Trimeric Env Proteins Based on HIV Type 1 Env Subtype A (2006)

The generation of an antibody response capable of neutralizing a broad range of clinical isolates remains an important goal of human immunodeficiency virus type 1 (HIV-1) vaccine development. Envelope glycoprotein (Env)-based vaccine candidates will also need to take into account the extensive genetic diversity of circulating HIV-1 strains. We describe here the generation of soluble, stabilized, proteolytically cleaved, trimeric forms of Env (SOSIP gp140 proteins) based on contemporary Env subtype A viruses from East Africa. We discuss issues associated with the construction, purification, and characterization of such complex proteins; not all env sequences allow the expression of trimeric proteins. However, stabilized trimers from one such protein, KNH1144 SOSIP gp140, were successfully made. These proteins are now being prepared for preclinical immunogenicity studies.
Spectral Conformal Parameterization (2008)

Abstract We present a spectral approach to automatically and efficiently obtain discrete free‐boundary conformal parameterizations of triangle mesh patches, without the common artifacts due to positional constraints on vertices and without undue bias introduced by sampling irregularity. High‐quality parameterizations are computed through a constrained minimization of a discrete weighted conformal energy by finding the largest eigenvalue/eigenvector of a generalized eigenvalue problem involving sparse, symmetric matrices. We demonstrate that this novel and robust approach improves on previous linear techniques both quantitatively and qualitatively.
Safety Evaluation of Clinical Gene Therapy Using Hepatocyte Growth Factor to Treat Peripheral Arterial Disease (2004)

Therapeutic angiogenesis using angiogenic growth factors is expected to be a new treatment for patients with critical limb ischemia (CLI). Because hepatocyte growth factor (HGF) has potent angiogenic activity, we investigated the safety and efficiency of HGF plasmid DNA in patients with CLI as a prospective open-labeled clinical trial. Intramuscular injection of naked HGF plasmid DNA was performed in ischemic limbs of 6 CLI patients with arteriosclerosis obliterans (n=3) or Buerger disease (n=3) graded as Fontaine III or IV. The primary end points were safety and improvement of ischemic symptoms at 12 weeks after transfection. Severe complications and adverse effects caused by gene transfer were not detected in any patients. Of particular importance, no apparent edema was observed in any patient throughout the trial. In addition, serum HGF concentration was not changed throughout the therapy period in all patients. In contrast, a reduction of pain scale of more than 1 cm in visual analog pain scale was observed in 5 of 6 patients. Increase in ankle pressure index more than 0.1 was observed in 5 of 5 patients. The long diameter of 8 of 11 ischemic ulcers in 4 patients was reduced >25%. Intramuscular injection of naked HGF plasmid is safe, feasible, and can achieve successful improvement of ischemic limbs. Although the present data are conducted to demonstrate the safety as phase I/early phase IIa, the initial clinical outcome with HGF gene transfer seems to indicate usefulness as sole therapy for CLI.
Dephasing of a Superconducting Qubit Induced by Photon Noise (2005)

We have studied the dephasing of a superconducting flux qubit coupled to a dc-SQUID based oscillator. By varying the bias conditions of both circuits we were able to tune their effective coupling strength. This allowed us to measure the effect of such a controllable and well-characterized environment on the qubit coherence. We can quantitatively account for our data with a simple model in which thermal fluctuations of the photon number in the oscillator are the limiting factor. In particular, we observe a strong reduction of the dephasing rate whenever the coupling is tuned to zero. At the optimal point we find a large spin-echo decay time of .
Wound Botulism in California, 1951–1998: Recent Epidemic in Heroin Injectors (2000)

California has reported most of the world's wound botulism (WB) cases and nearly three-fourths of the cases reported in the United States. We reviewed the clinical, epidemiologic, and laboratory features of WB. From the first case in 1951, through 1998, a total of 127 cases were identified-93 in the last 5 years. The dramatic increase has been due to an epidemic (of WB) in people who inject black tar heroin. Whereas early cases of WB occurred after gross trauma, all but 1 of the last 102 cases occurred in drug users, primarily those who inject drugs subcutaneously ("skin poppers"). Cases are occurring disproportionately in Hispanics and women. Misdiagnosis and diagnostic delays of up to 64 days have occurred. This unprecedented, ongoing epidemic is now being reported in other states. We discuss the clinical and laboratory features that distinguish botulism from conditions that can mimic it, the relative yield of various diagnostic laboratory tests for botulism, and its treatment.
Assessing geoaccuracy of structure from motion point clouds from long-range image collections (2014)

Automatically extracted and accurate scene structure generated from airborne platforms is a goal of many applications in the photogrammetry, remote sensing, and computer vision fields. This structure has traditionally been extracted automatically through the structure-from-motion (SfM) workflows. Although this process is very powerful, the analysis of error in accuracy can prove difficult. Our work presents a method of analyzing the georegistration error from SfM derived point clouds that have been transformed to a fixed Earth-based coordinate system. The error analysis is performed using synthetic airborne imagery which provides absolute truth for the ray-surface intersection of every pixel in every image. Three methods of georegistration are assessed; (1) using global positioning system (GPS) camera centers, (2) using pose information directly from on-board navigational instrumentation, and (3) using a recently developed method that utilizes the forward projection function and SfM-derived camera pose estimates. It was found that the georegistration derived from GPS camera centers and the direct use of pose information from on-board navigational instruments is very sensitive to noise from both the SfM process and instrumentation. The georegistration transform computed using the forward projection function and the derived pose estimates prove to be far more robust to these errors.
Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation (2017)

Programmable sequence-specific genome editing agents such as CRISPR-Cas9 have greatly advanced our ability to manipulate the human genome. Although canonical forms of genome-editing agents and programmable transcriptional regulators are constitutively active, precise temporal and spatial control over genome editing and transcriptional regulation activities would enable the more selective and potentially safer use of these powerful technologies. Here, by incorporating ligand-responsive self-cleaving catalytic RNAs (aptazymes) into guide RNAs, we developed a set of aptazyme-embedded guide RNAs that enable small molecule-controlled nuclease-mediated genome editing and small molecule-controlled base editing, as well as small molecule-dependent transcriptional activation in mammalian cells.