gebhart/patrepeval huggingface dataset:
Reduced transition probabilities along the yrast line in W166 (2017)

Lifetimes of excited states in the yrast band of the neutron-deficient nuclide $^{166}\mathrm{W}$ have been measured utilizing the DPUNS plunger device at the target position of the JUROGAM II $\ensuremath{\gamma}$-ray spectrometer in conjunction with the RITU gas-filled separator and the GREAT focal-plane spectrometer. Excited states in $^{166}\mathrm{W}$ were populated in the $^{92}\mathrm{Mo}(^{78}\mathrm{Kr},4p$) reaction at a bombarding energy of 380 MeV. The measurements reveal a low value for the ratio of reduced transitions probabilities for the lowest-lying transitions $B(E2;\phantom{\rule{0.16em}{0ex}}{4}^{+}\phantom{\rule{0.16em}{0ex}}\ensuremath{\rightarrow}\phantom{\rule{0.16em}{0ex}}{2}^{+})/B(E2;\phantom{\rule{0.16em}{0ex}}{2}^{+}\phantom{\rule{0.16em}{0ex}}\ensuremath{\rightarrow}\phantom{\rule{0.16em}{0ex}}{0}^{+})=0.33(5)$, compared with the expected ratio for an axially deformed rotor (${B}_{4/2}$ = 1.43).
Downregulation of cyclin D1 sensitizes cancer cells to MDM2 antagonist Nutlin-3 (2016)

The MDM2-p53 pathway has a prominent oncogenic function in the pathogenesis of various cancers. Nutlin-3, a small-molecule antagonist of MDM2-p53 interaction, inhibits proliferation in cancer cells with wild-type p53. Herein, we evaluate the expression of MDM2, both the full length and a splicing variant MDM2-A, and the sensitivity of Nutlin-3 in different cancer cell lines. Included are seven cell lines with wild-type p53 (four mesothelioma, one breast cancer, one chondrosarcoma, and one leiomyosarcoma), two liposarcoma cell lines harboring MDM2 amplification and wild-type p53, and one mesothelioma cell line harboring a p53 point mutation. Nutlin-3 treatment increased expression of cyclin D1, MDM2, and p53 in cell lines with wild-type p53. Additive effects were observed in cells containing wild-type p53 through coordinated attack on MDM2-p53 binding and cyclin D1 by lentivirual shRNA knockdown or small molecule inhibition, as demonstrated by immunoblots and cell viability analyses. Further results demonstrate that MDM2 binds to cyclin D1, and that an increase in cyclin D1 expression after Nutlin-3 treatment is correlated with expression and ubiquitin E3-ligase activity of MDM2. MDM2 and p53 knockdown experiments demonstrated inhibition of cyclin D1 by MDM2 but not p53. These results indicate that combination inhibition of cyclin D1 and MDM2-p53 binding warrants clinical evaluation as a novel therapeutic strategy in cancer cells harboring wild-type p53.
Automated extraction of chemical structure information from digital raster images (2009)

The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles.
ChemInform Abstract: GEM‐DICHLORALLYLLITHIUM, A SEEMINGLY AMBIDENT NUCLEOPHILE (1974)

Abstract Dichlorallyllithium (II) kann durch Reaktion von (I) oder (III) mit Butyllithium bei tiefen Temperaturen in THF dargestellt werden.
Throughput analysis of tree-based protocols for many-to-many reliable multicast (2003)

Tree-based reliable multicast protocols are known to be most scalable for one-to-many sessions. However, there is still an open question whether these protocols are also scalable for many-to-many sessions. We categorize existing tree-based protocols into four classes according to the feedback/retransmission policies employed, and analyze and compare them on the basis of a proposed spatial loss model. This model considers the correlation of packet loss events for more realistic analysis, unlike previous work. The analysis reveals that, in many-to-many cases, a tree-based protocol with unicast NACK, unicast retransmission and periodic polling is most scalable with respect to throughput for practical session sizes. The protocol is also simple to implement.
Volcanic ash detection and retrievals using MODIS data by means of neural networks (2011)

Abstract. Volcanic ash clouds detection and retrieval represent a key issue for aviation safety due to the harming effects on aircraft. A lesson learned from the recent Eyjafjallajokull eruption is the need to obtain accurate and reliable retrievals on a real time basis. In this work we have developed a fast and accurate Neural Network (NN) approach to detect and retrieve volcanic ash cloud properties from the Moderate Resolution Imaging Spectroradiometer (MODIS) data in the Thermal InfraRed (TIR) spectral range. Some measurements collected during the 2001, 2002 and 2006 Mt. Etna volcano eruptions have been considered as test cases. The ash detection and retrievals obtained from the Brightness Temperature Difference (BTD) algorithm are used as training for the NN procedure that consists in two separate steps: ash detection and ash mass retrieval. The ash detection is reduced to a classification problem by identifying two classes: "ashy" and "non-ashy" pixels in the MODIS images. Then the ash mass is estimated by means of the NN, replicating the BTD-based model performances. A segmentation procedure has also been tested to remove the false ash pixels detection induced by the presence of high meteorological clouds. The segmentation procedure shows a clear advantage in terms of classification accuracy: the main drawback is the loss of information on ash clouds distal part. The results obtained are very encouraging; indeed the ash detection accuracy is greater than 90%, while a mean RMSE equal to 0.365 t km−2 has been obtained for the ash mass retrieval. Moreover, the NN quickness in results delivering makes the procedure extremely attractive in all the cases when the rapid response time of the system is a mandatory requirement.
Low Frequency Raman Active Vibrations in Fullerenes. 2. Quadrupolar Modes (2000)

The lowest frequency Raman active (molecular) vibrations of known fullerenes are quadrupolar in nature (QP modes). They can be simply rationalized in terms of the 5-fold degenerate Dg oscillation of an isotropic spherical shell. Symmetry distortion away from spherical leads to lifting of the degeneracy and correspondingly up to five vibrational features may be resolved in the QP-mode regions of the Raman spectra of high fullerenes. The energy splitting is a measure of fullerene cage topology.
A Fiber‐Optic System for Measuring Single Excitation‐Dual Emission Fluorescence Ratios in Real Time (1992)

Abstract The development and subsequent evaluation of a fiber‐optic system for measuring single excitation—dual emission fluorescence ratios in real time is described. The design of the flashlamp excitation source, optics, electronics, and computer software is discussed. The dual emission pH sensitive fluorophore 1, 4‐dihydroxyphthalonitrile (1, 4‐DHPN) was used to test the performance of this system. The flexible design of this modular system permits the use of other single excitation—dual emission fluorophores by simply changing the appropriate optical filters. Upon a single 340–380‐nm excitation, pH‐sensitive emissions were monitored at 488 nm and 434 nm. The ratio of these emissions (488/434) was then computed in real time, for a 2 mM solution of 1, 4‐DHPN, while the pH was titrated over the range 5–9. The nonlinear, system‐dependent, calibration curve of pH versus the ratio of emission wavelengths was empirical fit by a fourth‐order polynomial (r 2 = 0.995). Reliable pH measurements in the range 6–8 were obtained using concentrations of 1, 4‐DHPN as low as 50 μM. The standard deviation of pH measurements using a 1 mM solution of 1, 4‐DHPN, near neutral pH, was found to be approximately 0.1 pH unit.
Code division and time division multiple access networks for vehicle-to-vehicle communications at 60 GHz (2002)

A new analytical methodology for outage probability evaluation of a vehicle-to-vehicle packet radio communication system at 60 GHz, is presented. Propagation characteristics, co-channel interference and thermal noise are taken into account, in the context of an highway traffic model. Both code division and time division multiple access schemes are analysed: results as a function of offered traffic and useful link distance are discussed. The analytical procedure is general, and can also be applied to bi-dimensional cellular structures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Emergence and Molecular Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates from the Delhi Region in India (2010)

We screened 194 Mycobacterium tuberculosis strains isolated from tuberculosis (TB) patients in Delhi and neighboring regions in India to identify the prevalence of extensive drug resistance (XDR) in clinical isolates. Among these, 104 isolates were found to be multidrug resistant (MDR), and 6 were identified as XDR isolates, which was later confirmed by antimicrobial susceptibility testing against the respective drug screening panel. Genotyping was carried out by amplifying and sequencing the following genes: rpoB (rifampin), katG (isoniazid), gyrA (fluoroquinolones), and rrs (amikacin, kanamycin, and capreomycin). Our analyses indicated that mutations at the hot spots of these genes were positively correlated with drug resistance in clinical isolates. The key mutation observed for rpoB was in the codon for amino acid position 531 (S531L), and other mutations were seen in the hot spot, including those encoding Q510P, L511H, D516V, and H526Y mutations. We identified S315T and R463L substitutions encoded in the katG locus. An S95T substitution encoded in the gyrA locus was the most common mutation observed in fluoroquinolone-resistant isolates. In addition, we saw D94G and D94N mutations encoded in the QRDR region. The 16S rRNA (rrs) gene encoded mainly the A1401G mutation and an additional mutation, G1484T, resulting in ribosomal modifications. Taken together, the data in this report clearly establish the presence of phenotypically distinct XDR strains in India by molecular profiling and further identify specific mutational hot spots within key genes of XDR-TB strains.
Modulation of growth and epidermal growth factor receptor activity by retinoic acid in human glioma cells. (1989)

The growth-inhibitory activity of beta-all-trans-retinoic acid (RA) was examined on seven cultured human gliomas and cells derived from one normal brain. Response in monolayer cultures was heterogenous: three cell lines were completely resistant whereas five cell lines were growth inhibited with 50% inhibitory dose ranging from greater than 10(-5) to 1 x 10(-8) M. Two glioma cell lines capable of forming colonies in soft agar exhibited dose-dependent sensitivity to RA-induced growth inhibition, whereas another cell line was not affected by RA under either growth condition. Cell cycle analysis of the glial-derived cells has shown that the RA-sensitive cells accumulated in the G0-G1 phase. The cell surface expression of epidermal growth factor (EGF) receptors displayed by the various cells was either slightly increased or not affected by RA. In addition, the affinity of binding was slightly decreased in some sensitive cells. The activity of EGF receptor as assessed by immunocomplex-kinase assays revealed a dose-dependent decrease in autophosphorylation activity that appeared to correlate with the growth inhibition. The decrease in phosphokinase activity represented a dose-dependent inhibition of phosphorylation on tyrosine residues on EGF receptor as well as several other substrates. Furthermore, the autophosphorylation of either RA-treated or untreated EGF receptors occurred on similar amino acid residues. These results demonstrate that RA exhibits a heterogeneous growth-inhibitory activity against human glioma cells and suggest that the effects of RA may be mediated, at least in part, by modulation of EGF receptor phosphotyrosine kinase activity.
Diabetes Affects Antibody Response to SARS-CoV-2 Vaccination in Older Residents of Long-term Care Facilities: Data From the GeroCovid Vax Study (2022)

Older residents of LTCFs with diabetes tended to have weaker antibody response to COVID-19 vaccination. Insulin treatment might buffer this effect and establish humoral immunity similar to that in individuals without diabetes.
<title>Active stabilization of interferometers by two-frequency phase modulation</title> (1991)

This paper suggests a new method of active stabilization of interferometers that permits stabilization not only of a majority of interferometer types, but also of holographic interferometers directly during hologram recording without affecting the diffraction efficiency and the quality of holograms.
RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data (2015)

Supplementary data are available at Bioinformatics online.
Viral Nanoparticles for <em>In vivo</em> Tumor Imaging (2012)

The use of nanomaterials has the potential to revolutionize materials science and medicine. Currently, a number of different nanoparticles are being investigated for applications in imaging and therapy. Viral nanoparticles (VNPs) derived from plants can be regarded as self-assembled bionanomaterials with defined sizes and shapes. Plant viruses under investigation in the Steinmetz lab include icosahedral particles formed by Cowpea mosaic virus (CPMV) and Brome mosaic virus (BMV), both of which are 30 nm in diameter. We are also developing rod-shaped and filamentous structures derived from the following plant viruses: Tobacco mosaic virus (TMV), which forms rigid rods with dimensions of 300 nm by 18 nm, and Potato virus X (PVX), which form filamentous particles 515 nm in length and 13 nm in width (the reader is referred to refs. (1) and (2) for further information on VNPs). From a materials scientist's point of view, VNPs are attractive building blocks for several reasons: the particles are monodisperse, can be produced with ease on large scale in planta, are exceptionally stable, and biocompatible. Also, VNPs are "programmable" units, which can be specifically engineered using genetic modification or chemical bioconjugation methods. The structure of VNPs is known to atomic resolution, and modifications can be carried out with spatial precision at the atomic level, a level of control that cannot be achieved using synthetic nanomaterials with current state-of-the-art technologies. In this paper, we describe the propagation of CPMV, PVX, TMV, and BMV in Vigna ungiuculata and Nicotiana benthamiana plants. Extraction and purification protocols for each VNP are given. Methods for characterization of purified and chemically-labeled VNPs are described. In this study, we focus on chemical labeling of VNPs with fluorophores (e.g. Alexa Fluor 647) and polyethylene glycol (PEG). The dyes facilitate tracking and detection of the VNPs, and PEG reduces immunogenicity of the proteinaceous nanoparticles while enhancing their pharmacokinetics. We demonstrate tumor homing of PEGylated VNPs using a mouse xenograft tumor model. A combination of fluorescence imaging of tissues ex vivo using Maestro Imaging System, fluorescence quantification in homogenized tissues, and confocal microscopy is used to study biodistribution. VNPs are cleared via the reticuloendothelial system (RES); tumor homing is achieved passively via the enhanced permeability and retention (EPR) effect. The VNP nanotechnology is a powerful plug-and-play technology to image and treat sites of disease in vivo. We are further developing VNPs to carry drug cargos and clinically-relevant imaging moieties, as well as tissue-specific ligands to target molecular receptors overexpressed in cancer and cardiovascular disease.
Quick Turnaround Technique for Highlighting Defects in Thin Si/SiGe Bilayers (2004)

A chemical defect etching technique is described that permits accurate determination of defect density in thin Si/SiGe bilayer films. The etching technique is capable of distinguishing between isolated defect pits, such as threading defects, and planar defects in the top Si layer within the resolution of optical microscopy. A strained Si layer grown on a silicon-germanium-on-insulator substrate with a 40 atom % Ge content was analyzed using the new etching technique and the measured defect density compared well with plan-view transmission electron microscopy (PV-TEM) and cross-sectional TEM (X-TEM) results. X-TEM revealed that the planar defects observed in the defect etching images correspond to microtwin defects. © 2004 The Electrochemical Society. All rights reserved.
Subthreshold implementation of a 2D CNN Gabor-type focal plane filter (2002)

We describe the implementation of a focal plane CNN array for computing the outputs of orientation selective filters similar to Gabor filters using weak inversion transistor circuits. Both the scale and the orientation selectivity of the filter can be tuned electronically. We exploit the concept of the transistor as a pseudo-conductance or diffuser and use current, rather than voltage to represent signals of interest. This design enables energy efficient computation of the filter responses. Test results from a 12/spl times/14 pixel array fabricated in 1.2 /spl mu/m technology are presented.
Catalytic coupling of nitriles with amines to selectively form imines under mild hydrogen pressure (2012)

Imines are selectively formed by coupling of nitriles and amines under mild hydrogen pressure. The reaction is catalyzed by a bipyridine-based PNN Ru(II) pincer complex and proceeds under mild, neutral conditions at 4 bar of H(2).
Physiological, metabolic and haematological responses in white shrimp Litopenaeus vannamei (Boone) juveniles fed diets supplemented with astaxanthin acclimated to low-salinity water (2007)

The effects of dietary astaxanthin supplemented at 0, 40, 80 or 150 mg astaxanthin kg−1 on growth, survival, moult frequency, osmoregulatory capacity (OC) and selected metabolic and haematological variables in Litopenaeus vannamei acclimated to low-salinity water (3 g L−1) were evaluated. Supplemented astaxanthin at 80 mg kg−1 improved growth, survival and moult frequency in shrimp. The lowest OC was also exhibited in shrimp fed with dietary astaxanthin at 80 mg kg−1. Shrimp haemolymph concentrations of glucose, lactate, haemocyanin and total haemocyte count were all significantly enhanced by feeding the diet supplemented with 80 mg astaxanthin kg−1 compared with shrimp fed with the other diets. On the basis of these results, dietary astaxanthin supplementation of 80 mg kg−1 is recommended for juvenile L. vannamei cultured in low-salinity water.
Numerical analysis of short-circuit safe operating area for p-channel and n-channel IGBTs (1991)

The mechanisms of destructive failure of an insulated gate bipolar transistor (IGBT) at short-circuit state are discussed. Results from two-dimensional numerical simulation of p-channel and n-channel IGBTs are presented. It is found that there are two types of destructive failure mechanisms: a secondary breakdown and a latchup. Which type is dominant in p-channel and n-channel IGBTs depends on an absolute value of forward voltage mod V/sub CE/ mod . At moderately low mod V/sub CE/ mod , the p-channel IGBT is destroyed by secondary breakdown, and the n-channel IGBT, by latchup. This is due to the difference of a type of flowing carrier crossing a base-collector junction of wide base transistor and ionization rates of electrons and holes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the Extracellular Domain of Tie Receptor Tyrosine Kinases and Localization of the Angiopoietin-binding Epitope (2006)

Angiogenesis is essential for tissue repair and regeneration during wound healing but also plays important roles in many pathological processes including tumor growth and metastasis. The receptor protein tyrosine kinase Tie2 and its ligands, the angiopoietins, have important functions in the regulation of angiogenesis. Here, we report a detailed structural and functional characterization of the extracellular region of Tie2. Sequence analysis of the extracellular domain revealed an additional immunoglobulin-like domain resulting in a tandem repeat of immunoglobulin-like domains at the N terminus of the protein. The same domain organization was also found for the Tie1 receptor that shares a high degree of homology with Tie2. Based on structural similarities to other receptor tyrosine kinases and cell adhesion molecules, we demonstrate that the N-terminal two immunoglobulin-like domains of Tie2 harbor the angiopoietin-binding site. Using transmission electron microscopy we furthermore show that the extracellular domain of Tie receptors consists of a globular head domain and a short rod-like stalk that probably forms a spacer between the cell surface and the angiopoietin-binding site. Mutational analysis demonstrated that the head domain consists of the three immunoglobulin-like domains and the three epidermal growth factor-like modules and that the stalk is formed by the three fibronectin type III repeats. These findings might be of particular interest for drug development because Tie receptors are potential targets for treatment of angiogenesis-associated diseases.
Regulation of the synthesis of glutamine synthetase by the PII protein in Klebsiella aerogenes. (1980)

Certain mutations at the glaB locus result in the failure to fully derepress glutamine synthetase [L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.2] and to convert it to the active nonadenylylated form in response to nitrogen limitation. In these mutants the PII regulatory protein is altered such that it cannot be converted by uridylyltransferase to the form stimulating deadenylylation of glutamine synthetase by adenylyltransferase. Additional mutations as well as insertions of transposon Tn5 at the glnB site result in the loss of PII. The loss of PII does not prevent adenylylation and deadenylylation of glutamine synthetase but reduces the rates of these reactions. Cells lacking PII have a high level of glutamine synthetase even when they are grown with an excess of ammonia and the enzyme is highly adenylylated. The results suggest that the PII protein plays a role, independent of its effect on adenylylation, in the regulation of the level of glutamine synthetase.