gebhart/patrepeval huggingface dataset:
Structural Basis for Shikimate-Binding Specificity of<i>Helicobacter pylori</i>Shikimate Kinase (2005)

Shikimate kinase (EC 2.7.1.71) catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP. As the fifth key step in the shikimate pathway for aromatic amino acid biosynthesis in bacteria, fungi, and plants, but not mammals, shikimate kinase represents an attractive target for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here, we report the 1.8-Angstroms crystal structure of Helicobacter pylori shikimate kinase (HpSK). The crystal structure shows a three-layer alpha/beta fold consisting of a central sheet of five parallel beta-strands flanked by seven alpha-helices. An HpSK-shikimate-PO(4) complex was also determined and refined to 2.3 Angstroms, revealing induced-fit movement from an open to a closed form on substrate binding. Shikimate is located above a short 3(10) helix formed by a strictly conserved motif (GGGXV) after beta(3). Moreover, several highly conserved charged residues including Asp33 (in a conserved DT/SD motif), Arg57, and Arg132 (interacting with shikimate) are identified, guiding the development of novel inhibitors of shikimate kinase.
Prolonged ventricular bypass with intrathoracic pumps. (1964)

DeBakey et al. reported on the progress of their left ventricular assist device, and proposed that using two LVADs would be
 preferable to replacing the entire heart with a total artificial heart.
Circuit board integrated patch transition between microstrip and rectangular waveguide, optimised for producibility (2006)

An angular transition between microstrip and rectangular waveguide is presented. Based on the known patch transition type, it demonstrates a design where both the patch and the waveguide backshort are integrated in the circuit board. Thereby, no parts are required except the circuit board and the waveguide. The assembly of circuit board and waveguide can be either galvanic or nongalvanic. The transition shows good electrical performance and generous mechanical tolerances.
Cloning and Characterization of the 5′-Flanking Region of the Human Growth Hormone-releasing Hormone Receptor Gene (1999)

We cloned the 5'-flanking region of the human growth hormone-releasing hormone receptor (GHRH-R) gene and determined the nucleotide sequence of 2.7 kilobases upstream from the translation start site. RNase protection analysis showed the major transcription start site is 122 base pairs upstream from the translation start site. The 5'-end of the longest product of 5'-rapid amplification of cDNA ends was close to the site. There were no typical TATA homologies but several putative regulatory elements including Pit-1-binding site-like element. Transient transfection studies using a luciferase reporter gene demonstrated that 5'-flanking region had promoter activity in GH3 cells (derived from rat pituitary tumor) but not in nonpituitary cells, BeWo and HeLa cells. However, co-transfection of Pit-1 expression vector increased luciferase activity in BeWo cells. Deletion study showed that the regions from -310 to -130 and from -130 to -120 were important for the GHRH-R gene expression in GH3 cells, although the latter contributed less to the gene expression. In BeWo cells co-transfected with Pit-1 expression vector, the region from -310 to -130 was essential for the Pit-1-dependent expression of GHRH-R gene. The region from -310 to -120 has two putative Pit-1-binding sites, P1 and P2, located from -129 to -123 and from -171 to -160, respectively. Both mobility shift assay and DNase-I footprint analysis showed that P2 had much higher Pit-1 binding affinity than P1. Mutation of P2 decreased GHRH-R gene expression in GH3 cells. These findings were consistent with the results that the region from -310 to -130 is an important element for Pit-1-dependent expression of GHRH-R gene.
Biosynthesis of silver nanoparticles using the extract of Alternanthera sessilis—antiproliferative effect against prostate cancer cells (2013)

Green synthesis of silver nanoparticles was carried out using the aqueous extract of <i>Alternanthera sessilis</i> under various experimental conditions. The aqueous extract of <i>Alternanthera sessilis</i> showed significant potential for the quick reduction of silver ions. The synthesized silver nanoparticles were characterized with UV-visible absorption spectrophotometer, XRD, SEM, and FTIR analysis. The average crystallite size as calculated from x-ray diffraction studies and SEM analysis was found to be less than 100 nm. The cytotoxic activity of synthesized nanosilver was carried out against prostate cancer cells (PC3) by MTT assay and found to show significant activity. The present work of biosynthesis of silver nanoparticles using <i>Alternanthera sessilis</i> appears to be cost effective, eco-friendly, and an alternative to conventional method of synthesis.
Stability of a threshold-recall control self-organizing recurrent neural network (2003)

The stability of a recurrent neural network that is made up of neurons that show the activation recall dependent excitation threshold is studied. The activation function of every neuron in the network is adjusted based on the neuron activation recall. The activation threshold of the neuron is considered to be a function of the neuron activation response. Bias-adjusting neurons and activation-threshold-adjusting neurons are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
TORC1 Suppression Predicts Responsiveness to RAF and MEK Inhibition in <i>BRAF-</i> Mutant Melanoma (2013)

RAF and MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) inhibitors are effective in treating patients with BRAF-mutant melanoma. However, most responses are partial and short-lived, and many patients fail to respond at all. We found that suppression of TORC1 activity in response to RAF or MEK inhibitors, as measured by decreased phosphorylation of ribosomal protein S6 (P-S6), effectively predicted induction of cell death by the inhibitor in BRAF-mutant melanoma cell lines. In resistant melanomas, TORC1 activity was maintained after treatment with RAF or MEK inhibitors, in some cases despite robust suppression of mitogen-activated protein kinase (MAPK) signaling. In in vivo mouse models, suppression of TORC1 after MAPK inhibition was necessary for induction of apoptosis and tumor response. Finally, in paired biopsies obtained from patients with BRAF-mutant melanoma before treatment and after initiation of RAF inhibitor therapy, P-S6 suppression predicted significantly improved progression-free survival. Such a change in P-S6 could be readily monitored in real time by serial fine-needle aspiration biopsies, making quantitation of P-S6 a valuable biomarker to guide treatment in BRAF-mutant melanoma.
TALENs Mediate Efficient and Heritable Mutation of Endogenous Genes in the Marine Annelid <i>Platynereis dumerilii</i> (2014)

Platynereis dumerilii is a marine polychaete and an established model system for studies of evolution and development. Platynereis is also a re-emerging model for studying the molecular basis of circalunar reproductive timing: a biological phenomenon observed in many marine species. While gene expression studies have provided new insight into patterns of gene regulation, a lack of reverse genetic tools has so far limited the depth of functional analyses in this species. To address this need, we established customized transcriptional activator-like effector nucleases (TALENs) as a tool to engineer targeted modifications in Platynereis genes. By adapting a workflow of TALEN construction protocols and mutation screening approaches for use in Platynereis, we engineered frameshift mutations in three endogenous Platynereis genes. We confirmed that such mutations are heritable, demonstrating that TALENs can be used to generate homozygous knockout lines in P. dumerilii. This is the first use of TALENs for generating genetic knockout mutations in an annelid model. These tools not only open the door for detailed in vivo functional analyses, but also can facilitate further technical development, such as targeted genome editing.
Cancer Neoantigens (2018)

Malignant transformation of cells depends on accumulation of DNA damage. Over the past years we have learned that the T cell-based immune system frequently responds to the neoantigens that arise as a consequence of this DNA damage. Furthermore, recognition of neoantigens appears an important driver of the clinical activity of both T cell checkpoint blockade and adoptive T cell therapy as cancer immunotherapies. Here we review the evidence for the relevance of cancer neoantigens in tumor control and the biological properties of these antigens. We discuss recent technological advances utilized to identify neoantigens, and the T cells that recognize them, in individual patients. Finally, we discuss strategies that can be employed to exploit cancer neoantigens in clinical interventions.
Molten Sulfur Chemistry. II. The Solubility of Sulfur Dioxide in Molten Sulfur (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolten Sulfur Chemistry. II. The Solubility of Sulfur Dioxide in Molten SulfurF. J. Touro and T. K. WiewiorowskiCite this: J. Phys. Chem. 1966, 70, 11, 3531–3534Publication Date (Print):November 1, 1966Publication History Published online1 May 2002Published inissue 1 November 1966https://pubs.acs.org/doi/10.1021/j100883a028https://doi.org/10.1021/j100883a028research-articleACS PublicationsRequest reuse permissionsArticle Views224Altmetric-Citations14LEARN 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 options Get e-Alerts
Monoclonal antibodies to the peplomer glycoprotein of coronavirus mouse hepatitis virus identify two subunits and detect a conformational change in the subunit released under mild alkaline conditions (1990)

Monoclonal antibodies (MAbs) directed against the E2 glycoprotein of mouse hepatitis virus (MHV) have been classified according to their ability to bind to either of the two purified 90,000-molecular-weight subunits (90K subunits) of the 180K peplomeric glycoprotein E2. Correlation with previously reported information about these MAbs suggest that both of the subunits of E2 are important for viral infectivity and cell fusion. Incubation of trypsin-treated virions at pH 8.0 and 37 degrees C released only the E2N subunit from virions. The pattern of MAb reactions suggested that a conformational change occurred in the E2N subunit in association with its release from virions under mildly alkaline conditions at 37 degrees C, the same conditions which are optimal for coronavirus-induced cell fusion.
Paraxial matrix description of astigmatic and cylindrical mirror resonators with twisted axes for laser spectroscopy (2007)

A complete matrix description of ray-optic propagation in an astigmatic multipass cell is presented, with expressions for the coupling of coordinates. A pair of transforms puts the 4 x 4 paraxial system matrix into block-diagonal form, allowing a solution using Sylvester's theorem. A variation on the Jones matrix calculus is employed wherein the ray coordinates on both resonator mirrors are simultaneously represented as a single state of the system. The formulations are applicable to resonators with any degree of astigmatism and axial twist. Examples are presented of beam paths and the boundary shapes of beam spots. The shape of the pattern boundaries, as a function of the coordinate coupling coefficient, influences the practical availability of patterns.
Active learning guided interactions for consistent image segmentation with reduced user interactions (2011)

Interactive techniques leverage the expert knowledge of users to produce accurate image segmentations. However, the segmentation accuracy varies with the users. Additionally, users may also require training with the algorithm and its exposed parameters to obtain the best segmentation with minimal effort. Our work combines active learning with interactive segmentation and (i) achieves as good accuracy compared to a fully user guided segmentation but with significantly lower number of user interactions (on average 50%), and (ii) achieves robust segmentation by reducing segmantation variability with user inputs. Our approach interacts with user to suggest gestures or seed point placements. We present extensive experimental evaluation of our results on two different publicly available datasets.
Overlapping and non-redundant functions of the <i>Arabidopsis</i> auxin response factors <i>MONOPTEROS</i> and <i>NONPHOTOTROPIC HYPOCOTYL 4</i> (2004)

Transcription factors of the auxin response factor (ARF) family have been implicated in auxin-dependent gene regulation, but little is known about the functions of individual ARFs in plants. Here, interaction assays, expression studies and combinations of multiple loss- and gain-of-function mutants were used to assess the roles of two ARFs, NONPHOTOTROPIC HYPOCOTYL 4 (NPH4/ARF7) and MONOPTEROS (MP/ARF5), in Arabidopsis development. Both MP and NPH4 interact strongly and selectively with themselves and with each other, and are expressed in vastly overlapping domains. We show that the regulatory properties of both genes are far more related than suggested by their single mutant phenotypes. NPH4 and MP are capable of controlling both axis formation in the embryo and auxin-dependent cell expansion. Interaction of MP and NPH4 in Arabidopsis plants is indicated by their joint requirement in a number of auxin responses and by synergistic effects associated with the co-overexpression of both genes. Finally, we demonstrate antagonistic interaction between ARF and Aux/IAA gene functions in Arabidopsis development. Overexpression of MP suppresses numerous defects associated with a gain-of-function mutation in BODENLOS (BDL)/IAA12. Together these results provide evidence for the biological relevance of ARF-ARF and ARF-Aux/IAA interaction in Arabidopsis plants and demonstrate that an individual ARF can act in both invariantly programmed pattern formation as well as in conditional responses to external signals.
Single Adult Kidney Stem/Progenitor Cells Reconstitute Three-Dimensional Nephron Structures In Vitro (2014)

The kidneys are formed during development from two distinct primordial tissues, the metanephric mesenchyme and the ureteric bud. The metanephric mesenchyme develops into the kidney nephron, the minimal functional unit of the kidney. A nephron consists of several segments and regulates water, electrolyte, and acid-base homeostasis in addition to secreting certain hormones. It has been predicted that the kidney will be among the last organs successfully regenerated in vitro due to its complex structure and multiple functions. Here, we show that adult kidney stem/progenitor cells (KS cells), derived from the S3 segment of adult rat kidney nephrons, can reconstitute a three-dimensional kidney-like structure in vitro. Kidney-like structures were formed when a cluster of KS cells was suspended in an extracellular matrix gel and cultured in the presence of several growth factors. Morphological analyses revealed that these kidney-like structures contained every substructure of the kidney, including glomeruli, proximal tubules, the loop of Henle, distal tubules, and collecting ducts, but no vasculature. Our results demonstrate that a cluster of tissue stem/progenitor cells has the ability to reconstitute the minimum unit of its organ of origin by differentiating into specialized cells in the correct location. This process differs from embryonic kidney development, which requires the mutual induction of two different populations of progenitors, metanephric mesenchymal cells and ureteric bud cells.
Epithermal Neutron Capture in Uranium-238 (1977)

Designers of thermal-neutron reactors have always had to adjust microscopic nuclear cross sections to predict neutron multiplication in slightly enriched uranium lattices. It has been surmised that the problem lies in an overestimation of the neutron capture cross section of 238U below 100 eV. We have measured these cross sections by three independent experiments. First, a series of neutron transmission and self-indication measurements were taken on samples of 238U ranging from 10.79 to 11 620 b/atom in inverse thickness. The level parameters were obtained using area analysis and multilevel fits. Next, the capture cross sections deduced from these level parameters were confirmed by direct measurements on both the continuum and discrete line portions of the low-energy gamma-ray spectra. High resolution measurements on the gamma-ray spectra were carried out from 530 to 900 keV over the neutron energy range from near thermal to ∼20 eV. Finally, a further check was made by activating thin samples of 238U with monochromatic neutrons obtained by Bragg scattering. The result is consistent with the capture cross sections obtained by the gamma-ray spectra measurement. Our results reduce, by 25%, the shielded capture integral discrepancy observed in early Bettis Atomic Power Laboratory critical experiments (TRX) with low-235U-enriched uranium rods latticed in water. When they are coupled with refined lattice calculations, much of the long-standing discrepancy is removed.
Design of superachromatic quarter-wave retarders in a broad spectral range (2015)

A superachromatic quarter-wave retarder using an arbitrary number of waveplates in a broadband spectral range has been proposed. Their design is based on the optimization of a merit function, the achromatism degree (AcD), which represents a global behavior metric for the retardation. By means of this technique, the thickness and azimuth of each waveplate is determined. The achromatism degree is a measure of the distance between the overall retardation and a target retardation weighted by the spectrum of the incident light. We report on a particular case where all waveplates are made of quartz. As application examples, the design of a quarter-wave retarder using two, three, and four waveplates in the spectral ranges of 500-700 nm and 400-1000 nm was studied. The numerical results show that for these ranges, the best designs obtained present a maximum difference of 0.013° and 0.010° with respect to the target retardation, respectively. In addition, an analysis of their achromatic stability is presented. These results can be applied in the aerospace industry, spectroscopic ellipsometry, and spectrogoniometry, among others.
Determination of electron energy distribution in a GaAs vertical field-effect transistor with hot-electron injection (1989)

Electron energy distribution on the drain edge of a channel in a GaAs nongated vertical field-effect transistor with hot-electron injection has been probed using hot-electron spectroscopy as a function of current density up to about 105 A/cm2. Electrons rapidly accelerated in an n+-i-p+-i-n+ planar-doped barrier source exhibit nonequilibrium transport through a thin channel (130 nm) with deceleration due to scattering and acceleration due to the electric field. The resulting hot-electron energy distribution, determined by using a planar-doped barrier as an analyzer, diverges from the steady-state one. This divergence dramatically increases with increasing the current density.
Pacemaker interference by 60-Hz contact currents (2002)

Contact currents occur when a person touches conductive surfaces at different potentials, thereby completing a path for current flow through the body. Such currents provide an additional coupling mechanism between the human body and external low-frequency fields. The resulting fields induced in the body can cause interference with implanted cardiac pacemakers. Modern computing resources used in conjunction with millimeter-scale human body conductivity models make numerical modeling a viable technique for examining any such interference. An existing well-verified scalar-potential finite-difference frequency-domain code has recently been modified to allow for combined current and voltage electrode sources, as well as to allow for implanted wires. Here, this code is used to evaluate the potential for cardiac pacemaker interference by contact currents in a variety of configurations. These include current injection into either hand, and extraction via: 1) the opposite hand; 2) the soles of both feet; or 3) the opposite hand and both feet. Pacemaker generator placement in both the left and right pectoral areas is considered in conjunction with atrial and ventricular electrodes. In addition, the effects of realistically implanted unipolar pacemaker leads with typical lumped resistance values of either 20 kohms and 100 kohms are investigated. It is found that the 60-Hz contact current interference thresholds for typical sensitivity settings of unipolar cardiac pacemaker range from 24 to 45 microA. Voltage and electric field dosimetry are also used to provide crude threshold estimates for bipolar pacemaker interference. The estimated contact current thresholds range from 63 to 340 microA for bipolar pacemakers.
Arachidonic Acid and Early Human Growth: Is there a Relation? (1991)

Growth failure is a classical sign of essential fatty acid deficiency. We investigated whether birth weight correlates with the postnatal essential fatty acid status in a group of 29 premature infants. A significant and positive correlation between body weight and plasma triglyceride content of arachidonic acid (20:4n-6) (r = 0.47, p = 0.01) and total omega-6 long-chain polyunsaturated fatty acids (r = 0.49, p less than 0.01) was found. In contrast, there was no positive relation to linoleic acid (18:2n-6) or any omega-3 fatty acid but a significant inverse correlation to alpha-linolenic acid (18:3n-3). We propose that during early life arachidonic acid may have a growth-promoting effect which could be related to its role as an eicosanoid precursor or to its structural function in membrane lipids.
Precise Relative Positioning of Formation Flying Spacecraft using GPS (2006)

These visits really helped to shape the dissertation to what it is right now, and provided me with lots of inspiration. To this extent my deepest gratitude also goes to the host
Trifunctional somatostatin-based derivatives designed for targeted radiotherapy using auger electron emitters. (2005)

These encouraging results support our hypothesis that an additional NLS sequence to the DOTA-TOC could not only provide a better carrier for Auger electron-emitting radionuclides but also ensure a longer radioactivity retention time in the tumor cell.
RELEASE OF TRANSFER RNA DURING PEPTIDE CHAIN ELONGATION (1969)

In amino acid polymerization, the tRNA donating its peptidyl moiety to the neighboring aminoacyl-tRNA must be released from the ribosome for further growth of the polypeptide chain. It was not known at what stage of peptide elongation this tRNA is released. To study this question, we prepared ac-C(14)-Phe-H(3)-tRNA using H(3)-tRNA isolated from E. coli strain 15THU grown in the presence of H(3)-uracil, and followed the fate of the H(3)-tRNA during chain growth. Our results indicate that donor tRNA is released during the translocation step, mediated by the soluble factor G and GTP.