gebhart/patrepeval huggingface dataset:
Sequence diversity of NanA manifests in distinct enzyme kinetics and inhibitor susceptibility (2016)

Streptococcus pneumoniae is the leading pathogen causing bacterial pneumonia and meningitis. Its surface-associated virulence factor neuraminidase A (NanA) promotes the bacterial colonization by removing the terminal sialyl residues from glycoconjugates on eukaryotic cell surface. The predominant role of NanA in the pathogenesis of pneumococci renders it an attractive target for therapeutic intervention. Despite the highly conserved activity of NanA, our alignment of the 11 NanAs revealed the evolutionary diversity of this enzyme. The amino acid substitutions we identified, particularly those in the lectin domain and in the insertion domain next to the catalytic centre triggered our special interest. We synthesised the representative NanAs and the mutagenized derivatives from E. coli for enzyme kinetics study and neuraminidase inhibitor susceptibility test. Via molecular docking we got a deeper insight into the differences between the two major variants of NanA and their influence on the ligand-target interactions. In addition, our molecular dynamics simulations revealed a prominent intrinsic flexibility of the linker between the active site and the insertion domain, which influences the inhibitor binding. Our findings for the first time associated the primary sequence diversity of NanA with the biochemical properties of the enzyme and with the inhibitory efficiency of neuraminidase inhibitors.
Adsorption of Oxygen on YBa<sub>2</sub>Cu<sub>3</sub>O<sub>7</sub><sub>-</sub><i><sub>x</sub></i> and (Bi,Pb)<sub>2</sub>Sr<sub>2</sub>Ca<sub>2</sub>Cu<sub>3</sub>O<i><sub>x</sub></i> Superconducting Adsorbents (1999)

The adsorption of oxygen on a high-temperature superconductor is not inhibited by superconducting forces. The equilibrium adsorption isotherms of oxygen and nitrogen on superconducting YBa2Cu3O7-x and (Bi,Pb)2Sr2Ca2Cu3Ox at 77 K are equivalent. Moreover, the equilibrium adsorption of oxygen on superconducting YBa2Cu3O7-x and (Bi,Pb)2Sr2Ca2Cu3Ox and on nonsuperconducting SiO2 at 77 K are equivalent. These results agree with theoretical arguments that predict the magnetic repulsion of oxygen from a superconductor to be significant over a distance of angstroms. At these distances, the magnetic forces are constrained by the superconductor's penetration depth and no Meissner effect is observed, contrary to the results of past reports.
Hard X-Ray Spectro Microprobe Analysis of Inhomogeneous Solids: A Case Study. Element Distribution and Speciation in Selected Iron Meteorites (2004)

The hard X‐ray microprobe provides an effective methodology for the non‐destructive analysis of inhomogeneous materials. Application of X‐ray absorption/fluroescence spectroscopy techniques (XANES and EXAFS) permits the speciation of the elements and yields information about the local structural environment. Microfocussed, monochromatic, tunable X‐rays allows examination of small areas of micrometer dimensions with spectroscopic procedures. Typically the materials which are presented are thick and cannot be altered for the experiment. This condition introduces difficulties which may compromise the results. Herein we discuss those difficulties and show that the system can yield reliable results in spite of the compromises. Some results are presented on the two iron meteorites we have examined. These specimens are representative of highly inhomogeneous materials and illustrate the difficulties encountered with compositional variations which may occur at sub‐millimeter dimensions and also illustrate the difficulties presented by the need to analyze components present at ppm concentration levels in a concentrated matrix. In these particular samples the major constituent is Fe which ranges from 90% to 70%, balanced by Ni which ranges from 10% to 30%. The critical diagnostic trace elements Ga and Ge which must also be analyzed are present at the 80 and 340 ppm level respectively. These diagnostic elements have been shown by EXAFS to be substitutionally placed in the matrix of the major element species in these meteorite samples.
Mammographic Density and Estrogen Receptor Status of Breast Cancer (2004)

Surprisingly, women with high mammographic density have an increased risk of both ER-positive and ER-negative breast cancers. The association between mammographic density and breast cancer may be due to factors besides estrogen exposure.
P2O-8 Single-Element PLZT Transducer for Wide-Bandwidth Imaging of Solid Materials (2006)

Hard tissue medical imaging and other applications such as IC-chip package inspection present a series of challenges for ultrasound imaging, including small feature size, high acoustic clutter, and high acoustic impedances. We report here on the design and performance of a 19 MHz resonant thickness mode, ceramic PLZT (Lead Lanthanum Zirconate Titanate) transducer designed for high acoustic impedance (>10 MRayl) operation in the presence of acoustic clutter. One-dimensional transducer analysis using the Mason model is also presented and is used to predict the expected bandwidth and center operating frequency, and to compare PLZT and PZT-5H in our transducer design. The packaged transducer features a high impedance matching layer and a gallium-indium alloy couplant (17.4 MRayl), which together minimize surface clutter due to impedance mismatches. The transducer has a narrow 8deg -3 dB full beamwidth, a 30% instantaneous bandwidth, and a narrow pulse width (250 ns), resulting in high lateral (210 mum at 1.5 mm) and axial (350 mum in gallium-indium alloy) resolutions for detection of small features. The transducer has been integrated with a match filter receiver, and the system has been demonstrated to obtain a single pulse SNR of 45 dB in detecting a 25 mum thick crack in the highly cluttered environment of a human tooth. The Mason model predicts that the PLZT transducer has a 50% higher bandwidth than an equivalent PZT-5H transducer, in large part because of the increased electromechanical coupling coefficient (PLZT k ap 0.82, and PZT-5H k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> ap 0.65). The tradeoff is ~30% lower acoustic-to-electric responsivity caused primarily by a larger dielectric constant. This is not so significant in the present applications (solid-state imaging), which tend to have clutter-limited environments. However, the improved bandwidth is very useful in improving range resolution and in gating out unwanted echoes, including those from the clutter
Subwavelength nanophotonics: From a new waveguide principle to practical components at telecom wavelengths (2010)

We report on a new waveguide principle using subwavelength gratings. It is known that diffraction effects are suppressed for waves propagating in materials structured at the subwavelength scale. Subwavelength gratings can create artificial media engineered using microscopic inhomogeneities to enact effective macroscopic behaviour. For the high-index-contrast waveguides, a subwavelength grating can be created by the combination of high-refractive-index and low-refractive-index materials, for example single crystal silicon and amorphous silica in silicon-on-insulator platform. These periodic structures frustrate diffraction provided they operate outside the Bragg condition and behave like a homogeneous medium. In a subwavelength grating (SWG) waveguide with a core consisting of a periodic arrangement of segments (Fig. 1), light excites a Bloch mode, which can theoretically propagate through the SWG waveguide with minimal scattering losses. Unlike other periodic waveguides such as line-defects in a 2D photonic crystal lattice, a subwavelength grating waveguide confines the light like a conventional index-guided structure and does not exhibit optically resonant behaviour.
Implementation of coupled mode optimal structural vibration control using approximated eigenfunctions (1998)

With the approximately normalized eigenfunctions and matching modal equations obtained in a differential form, we have implemented the structural vibration control successfully. In applying the steady-state quadratic coupled mode optimal control algorithm for the control structure, i.e. the all-clamped square plate, the non-orthogonalized extra terms are evaluated. By the suitable formulation of a control system, we could simulate the modal responses of the first six modes showing the validity of proposed modal equations and all the control procedures are considered to be reliable as a structural vibration control scheme. Modal responses for single and double actuators are observed and by changing the other control factors such as impulse position and weighting matrices we could compare the control performance. Moreover, these simulation results provide ideas on how to select the optimal number and positions of the actuators.
Transfer of a Malignant Phenotype by Calcium-Mediated DNA Transfection from Human Prostatic Carcinoma Cells to a Cloned Rat Embryo Fibroblast (CREF) Cell Line (1987)

No AccessJournal of Urology1 Jun 1987Transfer of a Malignant Phenotype by Calcium-Mediated DNA Transfection from Human Prostatic Carcinoma Cells to a Cloned Rat Embryo Fibroblast (CREF) Cell Line Wen-Shing Liaw, Ah-Kau Ng, Zhuoru Liu, Gregory J. Duigou, Stephen G. Zimmer, and Paul B. Fisher Wen-Shing LiawWen-Shing Liaw More articles by this author , Ah-Kau NgAh-Kau Ng More articles by this author , Zhuoru LiuZhuoru Liu More articles by this author , Gregory J. DuigouGregory J. Duigou More articles by this author , Stephen G. ZimmerStephen G. Zimmer More articles by this author , and Paul B. FisherPaul B. Fisher More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)75188-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Transfer of a Malignant Phenotype by Calcium-Mediated DNA Transfection from Human Prostatic Carcinoma Cells to a Cloned Rat Embryo Fibroblast (CREF) Cell Line." The Journal of Urology, 137(6), p. 113A © 1987 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 137Issue 6June 1987Page: 113A Advertisement Copyright & Permissions© 1987 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Wen-Shing Liaw More articles by this author Ah-Kau Ng More articles by this author Zhuoru Liu More articles by this author Gregory J. Duigou More articles by this author Stephen G. Zimmer More articles by this author Paul B. Fisher More articles by this author Expand All Advertisement PDF DownloadLoading ...
Generation and statistical mechanical modeling of Z-DNA in the mouse metallothionein I promoter (1987)

The mouse metallothionein I promoter has a potential Z-DNA sequence 86-102 bases upstream from the transcription start. The alternating purine/pyrimidine nature of this sequence, d-(GCGCGTGACTATGCGTG), is interrupted by a central d(AC) dinucleotide. We reversed the d(AC) to d(CA) by site-directed mutagenesis and subcloned the wild-type and mutated 218 base pair (bp) SstI-BglII fragment containing this region into pUC12. By two-dimensional chloroquine gel analysis, the mutant promoter clearly underwent a B-Z transition with a resulting loss of at least five twists. Purines within this sequence exhibited diethyl pyrocarbonate (DEP) sensitivity, which extended in both the 5' and 3' direction encompassing a region of approximately 32 base pairs. When subjected to sufficient torsional stress, the wild-type sequence showed weak evidence of a transition on chloroquine gels and clear DEP sensitivity with a similar, yet distinct pattern. Statistical mechanical modeling of the chloroquine gel analysis demonstrated that the average free energy of propagation for the mutant sequence (0.7-0.9 kcal mol-1 bp-1) was approximately twice that for d(CG)n sequences and that the sequence d(GACGCGGGGCGCGTGCATATGCGTGG) forms the core Z-DNA region.
Enabling synthesis in fragment-based drug discovery by reactivity mapping: photoredox-mediated cross-dehydrogenative heteroarylation of cyclic amines (2018)

In fragment-based drug discovery (FBDD), a weakly binding fragment hit is elaborated into a potent ligand by bespoke functionalization along specific directions (growth vectors) from the fragment core in order to complement the 3D structure of the target protein. This structure-based design approach can present significant synthetic challenges, as growth vectors often originate on sp<sup>2</sup> or sp<sup>3</sup> ring carbons which are not the most synthetically accessible points on the fragment. To address this issue and expedite synthesis in FBDD, we established a nanogram-to-gram workflow for the development of enabling synthetic transformations, such as the direct C-H functionalization of heterocycles. This novel approach deploys high-throughput experimentation (HTE) in 1536-well microtiter plates (MTPs) facilitated by liquid handling robots to screen reaction conditions on the nanomolar scale; subsequently the reaction is upscaled in a continuous flow to generate gram-quantities of the material. In this paper, we disclose the use of this powerful workflow for the development of a photoredox-mediated cross-dehydrogenative coupling of fragments and medicinally relevant heterocyclic precursors <i>via</i> Minisci-type addition of α-amino radicals to electron-deficient heteroarenes. The optimized reaction conditions were employed on the milligram-scale on a diverse set of 112 substrates to map out structure-reactivity relationships (SRRs) of the transformation. The coupling exhibits excellent tolerance to a variety of functional groups and N-rich heteroarenes relevant to FBDD and was upscaled in a continuous flow to afford gram-quantities of pharmaceutically relevant sp<sup>2</sup>-sp<sup>3</sup> privileged architectures.
Adoptive immunotherapy after hematopoietic stem cell transplantation (1998)

Adoptive immunotherapy may be performed with either autologous or allogeneic lymphocytes. Autologous cellular immunotherapy is hindered by the inability to break anergy or self-tolerance. Advances in this area have focused on the use of tumor-specific lymphocytes activated by antigen-pulsed or transgene modified dendritic cells. Allogeneic cellular immunotherapy is effective even with the use of non-specific and unactivated donor lymphocytes. Allogeneic cellular therapy is, however, complicated by graft-versus-host disease (GVHD). Advances in allogeneic immunotherapy will require better control of GVHD.
Tandem Amination/Oxetane Ring Opening toward Benzomorpholines (2021)

Herein, a tandem approach that allows rapid access to the benzomorpholine scaffold is reported. This operationally simple method allows for valuable heterocycles to be isolated in moderate to high yields. The overall transformation consists of an initial C-N coupling, demonstrated using traditional Ullmann or Buchwald-Hartwig conditions, followed by an <i>in situ</i> oxetane ring opening. A range of functionality is tolerated on the aryl ring, and the cyclization exposes a pendant hydroxymethyl substituent, providing opportunities for further functionalization.
A Thin X-Band Microwave Absorber Using a Center Shorted Spiral Medium (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this letter, the reflection characteristics of a shorted two-arm spiral medium are examined numerically. A magnetic-type phase response zone has been observed at a lower frequency range for both polarizations compared to other magnetic photonic band-gap (PBG) structures, such as the mushroom structure. The proposed structure exhibits good stability on the incident angle. The resonant frequency $(\angle\Gamma=0)$ varies within 1% with respect to the incident angle $(\theta\in(0^{\circ}\ 60^{\circ})$ for both polarizations. An absorption state occurs at the first magnetic-type phase response region. A 0.508-mm-thin X-band microwave absorber is fabricated and verified in a WR90 waveguide. An optimized design with 1.5% absorbing bandwidth is also given. Finally, the absorbing mechanism is discussed. </para>
A Bioresorbable Molding Mesh for Impaction Grafting Revision Hip Surgery (2005)

Impacted morselized allografts are used to treat bone loss in revision surgery. This technique depends on adequate mechanical support of the graft. Metal support devices function well, but there are disadvantages associated with the use of steel meshes. In this cadaveric, surgical simulation model we investigated the surgical and mechanical suitability of a bioresorbable molding mesh for use in impaction grafting revision surgery. Surgical feasibility was assessed, and mechanical deformation of the mesh during the surgical procedure and postoperative cyclic loading of the specimens were measured with strain gauges. All meshes were surgically usable. The exterior surface deformation of the meshes during the surgical procedure and postoperative mechanical loading did not exceed 4500 microm/m, although the meshes were not damaged in a four-point bending test in which deformations higher than 19,000 microm/m were reached. Therefore, results of this study suggest that this type of bioresorbable mesh seems to have sufficient initial mechanical properties to warrant additional preclinical in vivo study.
A preliminary numerical analysis of the differential group delay of a 6-spatial-modes spun fiber (2016)

The differential group delay of a spun fiber supporting the first 4 LP groups (for a total of 12 spatial-polarization modes) has been numerically analyzed. Results&#13;\nsuggest that spin may reduce modal dispersion.
Event related potential during visualizing (1997)

視覚的イメージを想起している時には, 外部刺激の情報処理は視覚的イメージ想起という作業によって影響を受けると考えられる.本研究では, 音刺激によって誘発された事象関連電位 (ERP) の振幅を計測することにより, 視覚的イメージ想起が音刺激に対する注意の配分を減少させるかどうか検討することを目的とした.大学生・大学院生13名が実験に参加した.全被験者は3条件に参加し, 平均刺激間間隔6秒でランダムに呈示される音刺激 (1000Hz) に対してボタソ押しで反応するように教示された.視覚的イメージ条件では日常的な光景の視覚イメージ想起が要求された.呈示映像注意条件では, 呈示された映像に注視するように求められた.聴覚刺激注意条件では音にのみ注意することとした.音刺激に誘発されたERPは, Fz, Cz, Pz, Oz, T5, T6から記録された, P300成分のピーク振幅が3条件について分析された.視覚的イメージ条件の反応時間は他の2条件より長く, 呈示映像注意条件の反応時間は聴覚刺激注意条件より長かった.視覚的イメージ条件のP300成分の振幅は他の2条件よりも低かった.これらの結果は, 視覚的イメージ想起時には, 音刺激への注意配分が, 呈示映像に注意していたときや, 音刺激に注意していたときよりも減少していたことを示唆した.
Pure Signet Ring Cell Type Early Gastric Carcinoma with Extensive Lymph Node Metastases -A Case Report- (1987)

A 42-year old man was admitted with indigestion and left upper quadrant pain. A gastrofiberscopic examination revealed a depressed, discolored lesion (1.5 × 1.5 cm) with converging irregular radiating folds in the antral portion, suggestive of early gastric cancer (type IIc). Histologically, signet ring cell carcinoma was seen. A subtotal gastrectomy was performed and the opeartive findings showed a shallow depression in the anterior wall of the greater curvature side in the antrum and multiple perigastric lymph node enlargment.
O-026 Real-world stent retriever thrombectomy for acute ischemic stroke beyond 6 hours of onset: analysis of the combined NASA and track registries (2018)

<h3>Background and purpose</h3> The DEFUSE 3 and DAWN trials have shown the benefit of thrombectomy beyond 6 hours of stroke symptom onset. The purpose of this study is to evaluate the real-world outcomes of patients treated with stent retriever thrombectomy beyond 6 hours of stroke onset using combined individual patient data from the North American Solitiare Stent Retriever Acute Stroke (NASA) and Trevo Stent-Retriever Acute Stroke (TRACK) registries. <h3>Methods</h3> Pooled analysis of individual patient data of all cases of anterior circulation acute ischemic stroke (AIS) from NASA and TRACK was performed to compare radiographic and clinical outcomes of patients presenting within first 6 or beyond 6 hours of stroke symptom onset. <h3>Results</h3> Out of 830 patients with anterior circulation AIS patients from the NASA and TRACK registries, 32.7% (271 patients) underwent thrombectomy beyond the first 6 hours of symptom onset. There was a similar distribution of age and cerebrovascular risk factors in patients arriving within the first 6 and beyond 6 hours of stroke symptom onset. Both groups of patients had similar approaches to thrombectomy using the Solitaire (NASA registry) and Trevo (TRACK registry) stent retrievers, including the use of a balloon-guide catheter, continuous aspiration or general anesthesia (p=0.12, 0.15 and 0.52, respectively). The rates of successful recanalization, defined as TICI 2b/3, were 79.4% in patients within stroke 0–6 hours, 75.6% within 6–16 hours and 85.0% within 16–24 hours (p=0.04). The rates of good clinical outcome, defined as modified Rankin Scale 0–2, mortality and symptomatic Intracerebral hemorrhage were similar: 48.2%, 20.6% and 8.0% within 0–6 hours, 46.2%, 21.6% and 11.02 within 6–16 hours, and 38.9%, 33.3% and 5% within 6­16 hours (p=0.8, 0.6 and 0.5, respectively). <h3>Conclusions</h3> In real world experience with patients who presented with anterior circulation AIS, using the Solitaire and Trevo thrombectomy devices beyond the first 6 hours of symptom onset proved to be equally safe and effective when compared to patients with symptom onset within the first 6 hours. <h3>Disclosures</h3> <b>M. Mokin:</b> 2; C; Canon medical. <b>A. Abou-Chebl:</b> None. <b>A. Castonguay:</b> None. <b>R. Nogueira:</b> 1; C; Stryker, Medtronic, Penumbra. 2; C; Styker Neurovascular, Covidien. <b>J. English:</b> 2; C; Stryker. <b>H. Farid:</b> None. <b>R. Gupta:</b> 2; C; Stryker. <b>C. Martin:</b> None. <b>W. Holloway:</b> None. <b>D. Haussen:</b>None. <b>N. Mueller-Kronast:</b> None. <b>O. Zaidat:</b> 2; C; Stryker, Medtronic.
Gene Expression Profiles following Cardiac Surgery in Diabetic Patients and Their Clinical Correlation (2006)

Restricted accessAbstractFirst published March 2006Gene Expression Profiles following Cardiac Surgery in Diabetic Patients and Their Clinical CorrelationB. Ramlawi, T.A. Khan, […], M. Ruel, P. Voisine, C. Bianchi, M. Boodhwani, and F.W. Sellke+4-4View all authors and affiliationsVolume 54, Issue 2_supplhttps://doi.org/10.1177/108155890605402s135
Conservative simulation of load-balanced routing in a large ATM network model (2002)

With the emerging of broadband networks based on ATM technology, performance evaluation tools that allow the study of large systems are desperately needed. We present our experiments in distributed simulation of large and complex ATM network models with a conservative simulator. The goal here was not to achieve the maximum speedup with well shaped topologies bat rather to see what speedup can be obtained with a realistic model on a "state of the art" parallel computer. A network model with 78 switches is simulated on a Cray T3E using 3 different traffic loads. The performance results show that good speedups can be achieved but they also highlight partitioning problems and bottlenecks in the simulation model that can seriously limit the speedup of realistic model simulations.