gebhart/patrepeval huggingface dataset:
Residues in the Stalk Domain of the Hendra Virus G Glycoprotein Modulate Conformational Changes Associated with Receptor Binding (2008)

Hendra virus (HeV) is a member of the broadly tropic and highly pathogenic paramyxovirus genus Henipavirus. HeV is enveloped and infects cells by using membrane-anchored attachment (G) and fusion (F) glycoproteins. G possesses an N-terminal cytoplasmic tail, an external membrane-proximal stalk domain, and a C-terminal globular head that binds the recently identified receptors ephrinB2 and ephrinB3. Receptor binding is presumed to induce conformational changes in G that subsequently trigger F-mediated fusion. The stalk domains of other attachment glycoproteins appear important for oligomerization and F interaction and specificity. However, this region of G has not been functionally characterized. Here we performed a mutagenesis analysis of the HeV G stalk, targeting a series of isoleucine residues within a hydrophobic alpha-helical domain that is well conserved across several attachment glycoproteins. Nine of 12 individual HeV G alanine substitution mutants possessed a complete defect in fusion-promotion activity yet were cell surface expressed and recognized by a panel of conformation-dependent monoclonal antibodies (MAbs) and maintained their oligomeric structure. Interestingly, these G mutations also resulted in the appearance of an additional electrophoretic species corresponding to a slightly altered glycosylated form. Analysis revealed that these G mutants appeared to adopt a receptor-bound conformation in the absence of receptor, as measured with a panel of MAbs that preferentially recognize G in a receptor-bound state. Further, this phenotype also correlated with an inability to associate with F and in triggering fusion even after receptor engagement. Together, these data suggest the stalk domain of G plays an important role in the conformational stability and receptor binding-triggered changes leading to productive fusion, such as the dissociation of G and F.
Nanostructuring and coherency strain in multicomponent hard coatings (2014)

Lattice resolved and quantitative compositional characterizations of the microstructure in TiCrAlN wear resistant coatings emerging at elevated temperatures are performed to address the spinodal decomposition into nanometer-sized coherent cubic TiCr-and Al-rich domains. The domains coarsen during annealing and at 1100 C, the Al-rich domains include a metastable cubic Al(Cr)N phase containing 9 at. % Cr and a stable hexagonal AlN phase containing less than 1 at. % Cr. The cubic and the hexagonal phases form strained semi-coherent interfaces with each other.
Bidirectional propagation of cold atoms in a “stadium”-shaped magnetic guide (2004)

We demonstrate the bidirectional propagation of more than ${10}^{7}\phantom{\rule{0.3em}{0ex}}\mathrm{atoms}$ ${(}^{87}\mathrm{Rb})$ around a ``stadium''-shaped magnetic ring that encloses an area of $10.9\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{2}$, with a flux density exceeding ${10}^{11}\phantom{\rule{0.3em}{0ex}}\text{atom}\phantom{\rule{0.2em}{0ex}}{\text{s}}^{\ensuremath{-}1}\phantom{\rule{0.2em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}2}$. Atoms are loaded into the guide from a two-dimensional (and higher) magneto-optical trap at one side of the ``stadium.'' An optical standing wave pulse is applied to increase the propagation velocity of atoms along the waveguide. The atom sample fills the entire ring in $200\phantom{\rule{0.3em}{0ex}}\mathrm{ms}$ when counterpropagating atom sections of the original atom cloud recombine at their initial positions after a full revolution.
Physicochemical and immunohistological studies of a sulfobromophthalein- and bilirubin-binding protein from rat liver plasma membranes. (1983)

Affinity chromatography over bilirubinagarose and sulfobromophthalein (BSP)-agarose was used to isolate two proteins, with high affinities for bilirubin and BSP, respectively, from Triton X-100-solubilized rat liver plasma membranes. The protein eluted from either affinity column migrated as a single band of approximately 55,000 D on sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, and either protein cochromatographed with both [14C]bilirubin and [35S]BSP on Sephadex G-75. On gradient gels without reduction or SDS, or on Sephadex G-150, the native BSP-binding protein had an estimated molecular mass of approximately 100,000 D. After incubation with SDS, an additional Sephadex G-150 peak of molecular mass of 56,000 D was observed. Both, the 100,000- and 56,000-D G-150 peaks cochromatographed with [35S]BSP. The native protein had an isoelectric point of 3.5, stained with periodic acid-Schiff but not Sudan black, and contained 4 mol of sialic acid per mol of protein. A rabbit antibody to the BSP-binding protein gave a line of identity with both the BSP- and bilirubin-binding antigens, and inhibited the binding of [14C]bilirubin and [35S]BSP, but not [14C]oleate or [14C]taurocholate, to rat liver plasma membranes. Immunohistochemical studies revealed the presence of the antigen on all surface domains of rat hepatocytes, but not on other cell populations from normal rat liver. It was not found in other organs. These data are compatible with the hypothesis that a specific liver cell plasma membrane protein mediates the hepatocytic sequestration of bilirubin and BSP.
Cystathionine γ-lyase regulates arteriogenesis through NO-dependent monocyte recruitment (2015)

Endogenous CSE/H2S regulates ischaemic vascular remodelling mediated during hind limb ischaemia through NO-dependent monocyte recruitment and cytokine induction revealing a previously unknown mechanism of arteriogenesis.
The Four-Connected Net in the CeCu2 Structure and Its Ternary Derivatives. Its Electronic and Structural Properties (1996)

The crystallochemistry of and the bonding in the orthorhombic four-connected nets of BaIn(2) (CeCu(2) structure) and of CaPtSn (TiNiSi structure, a derivative of the CeCu(2) structure) are analyzed with approximate molecular orbital calculations. Following the Zintl concept, in BaIn(2) the In(-) ions are isoelectronic with group IV tin and should adopt a four-connected structure. In contrast to alpha-tin, which has a cubic diamond structure, the indium ions in BaIn(2) build up an orthorhombic three-dimensional four-connected net containing distorted tetrahedra and ladder polymers of four-membered rings. In the CeCu(2) structure (space group Imma) two bond angles in these distorted tetrahedra are fixed at 90 degrees. The four-connected net in the CeCu(2) structure is topologically related to the layers in black phosphorus (space group Cmca). In CaPtSn (TiNiSi structure) the orthorhombic four-connected net is formed by (PtSn)(2)(-) ions in an ordered arrangement. Calculations on BaIn(2) and CaPtSn show that the four-connected nets are increasingly stabilized as the valence electron count is increased from 16 to 30 valence electrons per 4 formula units. For more than 30e, the nets are destabilized due to filling of M-E antibonding states. Structural data obtained by precise single crystal investigations for the TiNiSi series CaPdIn (20e), CaPdSn (24e), CaPdSb (28e), and CaAgSb (32e), confirm the results of the extended Hückel calculations. We find an interesting and understandable angular asymmetry of the tetrahedral sites in these ternary compounds.
Averaged and Cluster DPDs for Beamforming Applications (2022)

This paper addresses the problem of beam angle dependence of the Digital Predistortion (DPD) algorithm in the case of beamforming 5G transmitters. While a beam dependent DPD solution based on characterizing the system for each beam angle can offer good linearity performance, its implementation in practice requires continuous and fast adaptation of the DPD coefficients given that the beam forming vector is set to change every few milliseconds. This work proposes two alternative DPD solutions, the averaged DPD (A-DPD) and the cluster DPD (C-DPD), that trade-off signal quality for reduced dependence on the beamforming angle. Experimental results using a developed MIMO/beamforming test bed using 16 element phased array antenna operating at 2.35 GHz, demonstrates that the proposed C-DPD method is able to maintain an ACPR level within 5 dB of best-case scenario obtained by beam-dependent DPD, while using only a set of 3 DPDs over 90 degrees beam angle range.
Glycosphingolipid antigens from Leishmania (L.) amazonensis amastigotes: Binding of anti-glycosphingolipid monoclonal antibodies in vitro and in vivo (1997)

Specific glycosphingolipid antigens of Leishmania (L.) amazonensis amastigotes reactive with the monoclonal antibodies (MoAbs) ST-3, ST-4 and ST-5 were isolated, and their structure was partially elucidated by negative ion fast atom bombardment mass spectrometry. The glycan moieties of five antigens presented linear sequences of hexoses and N-acetylhexosamines ranging from four to six sugar residues, and the ceramide moieties were found to be composed by a sphingosine d18:1 and fatty acids 24:1 or 16:0. Affinities of the three monoclonal antibodies to amastigote glycosphingolipid antigens were also analyzed by ELISA. MoAb ST-3 reacted equally well with all glycosphingolipid antigens tested, whereas ST-4 and ST-5 presented higher affinities to glycosphingolipids with longer carbohydrate chains, with five or more sugar units (slow migrating bands on HPTLC). Macrophages isolated from footpad lesions of BALB/c mice infected with Leishmania (L.) amazonensis were incubated with MoAb ST-3 and, by indirect immunofluorescence, labeling was only detected on the parasite, whereas no fluorescence was observed on the surface of the infected macrophages, indicating that these glycosphingolipid antigens are not acquired from the host cell but synthesized by the amastigote. Intravenous administration of 125I-labeled ST-3 antibody to infected BALB/c mice showed that MoAb ST-3 accumulated significantly in the footpad lesions in comparison to blood and other tissues.
Morphology of femtosecond-laser-ablated borosilicate glass surfaces (2003)

We study the morphology of borosilicate glass surface machined by femtosecond laser pulses. Our observations show that a thin rim is formed around ablated craters after a single laser pulse. When multiple laser pulses are overlapped, the crater rims also overlap and produce a surface roughness. The rim appears to be a resolidified splash from a molten layer generated during the ablation process. We estimate that this molten layer is a few micrometers thick and exists for a few microseconds. During this melt lifetime, forces acting on the molten layer move it from the center to the edge of the crater.
Rain rate estimation from attenuation measurements using a 35 GHz dual polarization microwave link (2002)

A 35 GHz dual polarization microwave link has been built at Penn State University. The operating principle of this instrument is essentially that of a pulsed bi-static radar. Rain attenuation measurements are made by placing a corner reflector in the beam of the antennas. Calibration and stability requirements are simplified compared to standard uni-directional propagation links. Taking the ratio of horizontal to vertical attenuation factors also reduces the sensitivity to instrument fluctuations, since receiver drifts which are slower than the polarization switching speed (2200 Hz) will be canceled out. This is a primary motivation for using the differential polarization technique. The results of differential sensitivity measurements by this instrument are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Changes in magnetocardiogram patterns of infarcted-reperfused myocardium after injection of superparamagnetic contrast media. (2004)

The changes in spatio-temporal patterns of magnetocardiograms were investigated following injection of superparamagnetic iron-oxide (SPIO) nanoparticles using a dog model of ischemia/reperfusion. Acute myocardial infarction was induced by ligation of the left anterior descending coronary in two anesthetized open-chest dogs. Following 60 min coronary occlusion and 30 min reperfusion, dogs were subjected to injections of SPIO at a dose of 0.56 mg Fe/kg using a catheter inserted into the left atrium. Magnetocardiograms were measured before coronary occlusion, 15 min after reperfusion and immediately after administration of the SPIO. Magnetic field maps of early reperfused myocardium showed spatio-temporal field distributions consistent with anterior myocardial infarction. Magnetic field distribution measured after injection of SPIO revealed additional spatio-temporal features most prominent during ventricular repolarization due to augmentation/fragmentation of the ST-segment detected at several sensor locations. No significant differences in MCG patterns were noted following contrast agent injections in a dog without coronary occlusion. In conclusion, preliminary experimental evidence appears to support the notion that superparamagnetic contrast agents increase the sensitivity of standard MCG and may have an important implication for magnetocardiography in the assessment of regional myocardial ischemia, infarction and perfusion.
Focused ultrasound stimulation on meibomian glands for the treatment of evaporative dry eye (2021)

Current treatments for meibomian gland dysfunction have several limitations, creating a necessity for other advanced treatment options. The purpose of this study is to determine the effectiveness of focused ultrasound stimulation for the treatment of dry eye disease caused by meibomian gland dysfunction. An <i>in vivo</i> study of nine Dutch Belted rabbits was conducted with focused ultrasound stimulation of the meibomian glands. A customized line-focused ultrasonic transducer was designed for treatment. Fluorescein imaging, Schirmer's test, and Lipiview II ocular interferometer were used to quantify outcomes from three aspects: safety, tear production, and lipid layer thickness. Both tear secretion and lipid layer thickness improved following ultrasound treatment. Five to 10 min after the ultrasound treatment, the mean values of lipid layer thickness increased from 55.33 ± 11.15 nm to 95.67 ± 22.77 nm (<i>p</i> < 0.05), while the mean values measured with the Schirmer's test increased from 2.0 ± 2.3 to 7.2 ± 4.3 (<i>p</i> < 0.05). Positive effects lasted more than three weeks. Adverse events such as redness, swelling, and mild burn, occurred in two rabbits in preliminary experiments when the eyelids sustained a temperature higher than 42°C. No serious adverse events were found. The results suggest that ultrasound stimulation of meibomian glands can improve both tear production and lipid secretion. Ultimately, ultrasound stimulation has the potential to be an option for the treatment of evaporative dry eye disease caused by meibomian gland dysfunction.
Justifications For A Hybrid Approach To Optical Computing (1988)

A hybrid approach to optical computing is currently studied at the University of California, San Diego for performing parallel processing. Figure 1 shows a promising parallel processing architecture, in which an optical processing array is connected massively in parallel to an optical memory array. An optical processing array consists of an array of electronic logic gates; each cell in the array has at least one photodetector (or phototransistor) and one modulator for optical input/output. Similarly, an optical memory array consists of an array of electronic memory circuits; each cell in the array has also optical input/output. Within the optical processing array or the optical memory array, local interconnections among neighboring cells can be established electronically. Between the optical processing array and the optical memory array, global interconnections among distant cells can be established optically using the optical input/output in each cell. One important application of such a massively interconnected architecture would be to perform matrix-tensor multiplications (Ref. 1) not only for numeric computing, but also for artificial intelligence and neural computing (Ref. 2). There are three unique aspects associated with the parallel architecture of Figure 1, which may serve to justify this hybrid approach toward optical computing: optical interconnection, 3-D computational topology and optical memory.
Direct Acoustics-to-Word Models for English Conversational Speech Recognition (2017)

Recent work on end-to-end automatic speech recognition (ASR) has shown that the connectionist temporal classification (CTC) loss can be used to convert acoustics to phone or character sequences.Such systems are used with a dictionary and separately-trained Language Model (LM) to produce word sequences.However, they are not truly end-to-end in the sense of mapping acoustics directly to words without an intermediate phone representation.In this paper, we present the first results employing direct acoustics-to-word CTC models on two well-known public benchmark tasks: Switchboard and Call-Home.These models do not require an LM or even a decoder at run-time and hence recognize speech with minimal complexity.However, due to the large number of word output units, CTC word models require orders of magnitude more data to train reliably compared to traditional systems.We present some techniques to mitigate this issue.Our CTC word model achieves a word error rate of 13.0%/18.8%on the Hub5-2000 Switchboard/CallHome test sets without any LM or decoder compared with 9.6%/16.0%for phone-based CTC with a 4-gram LM.We also present rescoring results on CTC word model lattices to quantify the performance benefits of a LM, and contrast the performance of word and phone CTC models.
Natural Language Generation at Scale: A Case Study for Open Domain\n Question Answering (2019)

Current approaches to Natural Language Generation (NLG) for dialog mainly\nfocus on domain-specific, task-oriented applications (e.g. restaurant booking)\nusing limited ontologies (up to 20 slot types), usually without considering the\nprevious conversation context. Furthermore, these approaches require large\namounts of data for each domain, and do not benefit from examples that may be\navailable for other domains. This work explores the feasibility of applying\nstatistical NLG to scenarios requiring larger ontologies, such as multi-domain\ndialog applications or open-domain question answering (QA) based on knowledge\ngraphs. We model NLG through an Encoder-Decoder framework using a large dataset\nof interactions between real-world users and a conversational agent for\nopen-domain QA. First, we investigate the impact of increasing the number of\nslot types on the generation quality and experiment with different partitions\nof the QA data with progressively larger ontologies (up to 369 slot types).\nSecond, we perform multi-task learning experiments between open-domain QA and\ntask-oriented dialog, and benchmark our model on a popular NLG dataset.\nMoreover, we experiment with using the conversational context as an additional\ninput to improve response generation quality. Our experiments show the\nfeasibility of learning statistical NLG models for open-domain QA with larger\nontologies.\n
Viability of cells in ethanol. Role of alcohol dehydrogenase. (1976)

Rodent cells were found to contain a high level of alcohol dehydrogenase activity which was not inducible. Other hepatoma and nonhepatoma cell lines were tested and found to contain lower but measurable levels of alcohol dehydrogenase.
Coherence-preserving kW-level Tm fiber amplifiers at 2mm (2011)

We review the design and performance of an actively phase-locked, multi-stage Tm-doped fiber amplifier chain, and we discuss the impact of Tm&#8217;s longer emission wavelength on linear and nonlinear limits for coherent fiber combining. Article not available.
A new medical device for in vivo capturing of circulating tumor cells in breast cancer (BC) patients. (2012)

10537 Background: In BC, the number of circulating tumor cells (CTCs) is discussed as a prognostic and stratification biomarker, and could also reflect treatment efficacy. Currently, CTCs are isolated ex vivo from a small volume of blood. Results from a larger volume of blood are scarce. The aim of the study was to assess a functionalized and structured medical wire (FSMW) for in vivo capturing of CTCs directly from the blood stream of BC patients. Methods: The device was inserted in a cubital vein through a standard cannula for thirty minutes. The interaction of target CTCs with the FSMW was mediated by antibodies directed against the epithelial cell adhesion molecule (EpCAM). To confirm binding of CTCs to the wire, the immunohistochemical positive staining against EpCAM as well as negative staining for CD45 was performed. There were 54 applications of the wire in 42 stage I-IV BC patients (12 double applications). Enumeration data from 37 BC patients with 49 applications (5 failed subsequent analyses) were assessed. CTC counts on 23 devices were directly compared to counts by CellSearch. Results: The device was well tolerated in all 54 applications without side effects. We obtained in vivo isolation of CTCs in 44 of 49 applications to BC patients (89.7 %). The sensitivity was similar for early and late stage BC patients. The median (range) of isolated EpCAM-positive CTCs was 5 (0-515). The CellSearch method reached a sensitivity of 18.5%. In all paired samples the number of CTCs detected with the FSMW was higher or equal to CellSearch, regardless of the disease stage. Linear regression of the data of the double application of the FSMW showed a very good concordance (r 2 = 0.97, p&lt;0.0001). Conclusions: Whilst well tolerated without side effects, the CTC detection rate of the FSMW in BC patients was nearly 90 %. CTC detection was obtained in 18.5% by the CellSearch. Double application of FSMWs in the same patient indicates ample precision. This proof of concept study may have important clinical implications, as the device may improve early detection, prognosis and therapy monitoring of BC patients. The molecular analysis of the captured CTCs could become a breakthrough in personalized medicine.
Modifying Rete to reason temporally (2002)

Although researchers stress the importance of relative time representations, most expert system shells with temporal reasoning target real-time domains and use absolute time representations. This ontological assumption limits these systems to domains in which temporal events relate to times of occurrence. A temporal production system (TPS) is a traditional production system augmented with temporal knowledge maintenance routines and a temporal knowledge representation. These additions provide the ability to model relationships between events and they allow, but do not require, events to be associated with times of occurrence. The authors describe a TPS and the modifications of the Rete pattern matching algorithm required to incorporate interval-based temporal semantics and temporal knowledge maintenance routines.
Narrow-Band-Gap Conjugated Chromophores with Extended Molecular Lengths (2012)

The influence of extending the molecular length of donor-acceptor chromophores on properties relevant to organic optoelectronic devices has been studied by using two new narrow-band-gap systems. Most significantly, we find that the higher molecular weight systems exhibit higher thermal stabilities (beyond 200 °C) when introduced into field effect transistor devices. It is also possible to fabricate bulk heterojunction solar cells using PC(61)BM with power conversion efficiencies >6%. These high values are not heavily influenced by the blend composition and are achieved without the influence of solvent additives or postdeposition thermal annealing.