gebhart/patrepeval huggingface dataset:
Molecular analysis of the leukotoxin determinants from Pasteurella haemolytica serotypes 1 to 16 (1993)

All sixteen serotypes of Pasteurella haemolytica were shown to produce a leukotoxin protein which is immunologically related to the well-characterized serotype 1 leukotoxin. All of the leukotoxins were weakly hemolytic and were able to bind to BL-3 target cells. The leukotoxin determinants were characterized by Southern blot hybridization by use of the previously cloned serotype 1 determinant as the probe, and a number of distinct classes were identified. The leukotoxin determinants from serotypes 2, 3, and 11 were cloned. Nucleotide sequence analysis of the lktC and lktA genes of the serotype 3 and 11 determinants revealed nucleotide substitutions throughout the coding sequences. A comparison of the lktC and lktA genes and deduced proteins of serotypes 1, 3, and 11 showed that they are highly homologous.
Review of Optical Transmission Using Rapidly-Dispersed Signals (2001)

As the operating bit rate of a system increases, the signal-to-noise ratio (SNR) requirement increases, necessitating higher launched signal power, which can increase signal degradation from fiber nonlinearities such as self-phase modulation (SPM). The short-pulse return-to-zero (RZ) [1-8] modulation format offers significant advantages for transmission at 40 Gb/s and beyond in dispersive fibers. The idea is to disperse the pulses as quickly as possible, thereby creating an intensity pattern due to overlapping pulses that varies rapidly with fiber position. The accumulated effect of the fiber nonlinearity is averaged out over many bit slots and the overall signal degradation is reduced. This concept is distinctly different from soliton or standard dispersion-managed approaches, which attempt to control the nonlinear degradation by reducing pulse interactions. In fact, in order to differentiate it from other approaches, it has been called “pseudo-linear transmission” [3] or “tedon transmission” [7] after the verb “to ted,” meaning “to scatter; to dissipate”. In this paper, we review the theoretical and experimental work that has been done in this area. We also report computer simulations showing the effectiveness of the short-pulse RZ format in mitigating nonlinear effects.
Solving Planted-Motif Problem A New Approach (2007)

This paper presents a new method for solving planted-motif problem, which is a well-known motif-finding problem in the field of computational molecular biology. Motif-finding problem is considered to be a NP-complete problem and constant research is being carried out to solve the stated problem using some deterministic algorithm in polynomial time. This paper is an attempt to solve the plated-motif problem using a deterministic method in polynomial time. The method presented is not an exact algorithm but the probability of success is quite high. Significance of the technique is its simplicity and time efficiency. The presented technique is implemented as one of the modules in our general-purpose tool by the name "Sequence Comparison and Analysis Tool" for solving a number of sequence comparison problems encountered in the field of bioinformatics.
Abstract 1602: Generation of anti-IL-17B antibodies neutralizing IL-17B-mediated alterations of the immune microenvironment, promotion of tumor cell initiating capacity and chemoresistance (2017)

Abstract Interleukin 17B (IL-17B) is a pro-inflammatory cytokine that belongs to a family encompassing 6 interleukins (IL-17A to F) and binds to the IL-17 receptor B (IL-17RB). Recently, amplified IL-17B/IL-17RB signaling was found critical for breast and pancreatic tumorigenesis and elevated expression of IL-17RB has been associated with the shortest survival rates in patients with breast or pancreatic cancer. Using IL-17B knock-out (IL-17B KO) mice we demonstrate here that melanoma, fibrosarcoma and breast cancer cell tumorigenicity is strongly impaired in immunocompetent IL-17B KO mice compared to WT littermates, including a large number of tumor free mice. Reduced tumor incidence in IL-17B KO mice is associated with alterations of the immune tumor microenvironment especially within innate lymphocyte and myeloid sub-populations. We further demonstrate that IL-17B is a key cytokine shaping the tumor initiating cancer cell niche. Indeed, MDA-MB-468 human breast cancer cells overexpressing IL-17B exhibit 10 times higher frequency of tumor initiating cells when xenografted at a serial limiting dilution in nude mice. Tumor progression is, again, associated with alterations of NK cells within the tumor microenvironment and with increased percentages of CD44hi/CD24lo tumor cells, a phenotype associated with breast cancer stem cells (CSC). This is associated with resistance to conventional chemotherapeutic agents such as taxol, an effect that is totally abrogated by disrupting IL-17B-IL-17RB signaling with a neutralizing antibody. Altogether our results point out the key role of IL-17B in regulating the immune microenvironment as well as cardinal features of CSC, one of the alleged causes of resistance to therapy and tumor relapse. Thereby, IL-17B and its receptor appear as potential therapeutic targets for cancer immunotherapy. Collectively, these data support the ongoing development of IL-17B neutralizing antibodies. Citation Format: Emilie Laprevotte, Aurélie Docquier, Jeremy Bastid, Cécile Déjou, Marion Lapierre, Gilles Alberici, Armand Bensussan, Jean-François Eliaou, Nathalie Bonnefoy. Generation of anti-IL-17B antibodies neutralizing IL-17B-mediated alterations of the immune microenvironment, promotion of tumor cell initiating capacity and chemoresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1602. doi:10.1158/1538-7445.AM2017-1602
A New Technique for Low Concentration Diffusion of Boron into Silicon (1976)

A new technique is proposed for doped-oxide diffusion of boron into silicon, providing a controlled surface concentration in a wide range from 1015 to 1020 cm-3. The principle is based on our finding that if the source borosilicate film deposited is heat-treated in an NH3 ambient prior to the drive-in step, the transfer of boron into silicon is remarkably suppressed. The concentration of boron diffused in silicon is strongly dependent on the temperature and/or time of the NH3-heat-treatment. It is also found that an undoped SiO2 or Si3N4 film deposited on the source film works as a mask against the NH3 ambient. As a result, a simultaneous local diffusion of boron can be performed from a single film source to plural regions where different boron profiles are desired.
P2P Video Live Streaming with MDC: Providing Incentives for Redistribution (2007)

In this paper, we consider applying multiple description coding in mesh-pull P2P live streaming networks to provide incentives for redistribution. In our system, a video is encoded into multiple descriptions with each description having equal importance. We consider a heterogeneous system with peers having different uplink bandwidths. We design a distributed protocol in which a peer contributing more uplink bandwidth receives more descriptions and consequently better video quality. Previous approaches consider single-layer video, where each peer receives the same video quality no matter how much bandwidth it contributes to the system. The simulation results show that our approach can provide differentiated video quality commensurate with a peer's contribution to other peers.
Addressable High-Performance Multi-junction VCSEL Arrays for Automotive and Mobile LiDAR (2021)

We demonstrate VCSEL arrays for LiDAR applications with high peak optical power densities >1.5kW per mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of die area, and high slope efficiency, >6W/A, under pulsed operation. Arrays are contacted electrically as a single-section or multiple stripes of emitters or as a 2D matrix-addressable grid.
Simulation of free-space optical guiding structure based on colliding gas flows (2015)

Preformed plasma channels with parabolic radial density profiles enable the extended and stable optical guiding of high-intensity laser pulses. High-voltage discharge capillaries, commonly used for channel formation, have limited guiding length and opaque walls, complicating the diagnosis of the plasma within. This paper proposes a free-space gas channel produced by the collision of several gas flows. The collision of the gas flows forms an on-axis density depression surrounded by higher density walls. By offsetting the flows, we demonstrated the creation of what we believe is a novel vortex structure that exhibits a long-lived parabolic density profile. Once ionized, the resulting plasma density profile has a near-parabolic dependence appropriate for guiding. We then performed detailed two-dimensional (2D) fluid dynamics simulations to examine the properties and stability of the guiding structure.
Synthesis and complexation properties of a new macrocyclic polyaza polyphosphinate ligand, DOTEP (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methyleneethylphosphinate)) (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and complexation properties of a new macrocyclic polyaza polyphosphinate ligand, DOTEP (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methyleneethylphosphinate))Istvan Lazar, A. Dean Sherry, Ravichandran Ramasamy, Erno Brucher, and Robert KiralyCite this: Inorg. Chem. 1991, 30, 26, 5016–5019Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/ic00026a030https://doi.org/10.1021/ic00026a030research-articleACS PublicationsRequest reuse permissionsArticle Views223Altmetric-Citations50LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Non-contact detection of mechanical properties of intact cellular nucleus by Brillouin flow cytometry (Conference Presentation) (2018)

The nucleus is the largest and stiffest organelle of eukaryotic cells, and as such, its mechanical properties are tightly related to various cell functions. Many efforts have been devoted to characterize the mechanical properties of nucleus, but the current techniques generally need physical contact of the cell and staining of the nucleus and thus cannot acquire the mechanical information directly. Brillouin microscope is an integration of a confocal microscope and a Brillouin spectrometer, which measures the spectral shift due to the spontaneous Brillouin light scattering, and from that the longitudinal modulus of the sample can be quantified. In this work, by combining the standard Brillouin microscope with the microfluidic technique, we developed a Brillouin flow cytometry that can quantify the mechanical properties of the intact cellular nucleus in a non-contact and label-free manner. As cell flows through a microfluidic channel, its mechanical property at different regions will be sampled by a sub-micron beam spot of the Brillouin microscope. The mechanical information of the nucleus from the cell population can then be identified and extracted via data post-processing, which is further confirmed by co-registering Brillouin data with fluorescence data from the same cell. Currently, the overall throughput of this technique is about 200 cells per hour, mainly relies on the acquisition speed of the spectrometer, which could be readily improved with available technology. We verified the capability of this all-optical technique by distinguishing the stiffness changes of the nucleus that are relevant to physiological and pathological phenomena.
Pharmacophore‐Based Design of Novel Oxadiazoles as Selective Sphingosine‐1‐phosphate (S1P) Receptor Agonists with in vivo Efficacy (2015)

Sphingosine-1-phosphate (S1P) receptor agonists have shown promise as therapeutic agents for multiple sclerosis (MS) due to their regulatory roles within the immune, central nervous system, and cardiovascular system. Here, the design and optimization of novel [1,2,4]oxadiazole derivatives as selective S1P receptor agonists are described. The structure-activity relationship exploration was carried out on the three dominant segments of the series: modification of the polar head group (P), replacement of the oxadiazole linker (L) with different five-membered heterocycles, and the use of diverse 2,2'-disubstituted biphenyl moieties as the hydrophobic tail (H). All three segments have a significant impact on potency, S1P receptor subtype selectivity, physicochemical properties, and in vitro absorption, distribution, metabolism, excretion and toxicity (ADMET) profile of the compounds. From these optimization studies, a selective S1P1 agonist, N-methyl-N-(4-{5-[2-methyl-2'-(trifluoromethyl)biphenyl-4-yl]-1,2,4-oxadiazol-3-yl}benzyl)glycine (45), and a dual S1P1,5 agonist, N-methyl-N-(3-{5-[2'-methyl-2-(trifluoromethyl)biphenyl-4-yl]-1,2,4-oxadiazol-3-yl}benzyl)glycine (49), emerged as frontrunners. These compounds distribute predominantly in lymph nodes and brain over plasma and induce long lasting decreases in lymphocyte count after oral administration. When evaluated head-to-head in an experimental autoimmune encephalomyelitis mouse model, together with the marketed drug fingolimod, a pan-S1P receptor agonist, S1P1,5 agonist 49 demonstrated comparable efficacy while S1P1 -selective agonist 45 was less potent. Compound 49 is not a prodrug, and its improved property profile should translate into a safer treatment of relapsing forms of MS.
Integrated Optic Laser Emitting at 905, 1057, and 1356 nm (1993)

Integrated optic lasers and amplifiers have been demonstrated in neodymium-doped glasses. These devices have operated near 1057 nm in silicate glasses and 1057 and 1355 nm in phosphate glasses [1,2,3]. Laser action at 905 nm has been realized in neodymium-doped-silica fiber lasers but not in glass integrated optic devices [4]. Ion exchange from silver films is attractive for integrated optic waveguide fabrication since it is a dry process which does not use molten salts. We have fabricated low-loss waveguides in a neodymium-doped phosphate glass by ion exchange from silver films. CW lasing was achieved at 905, 1057 and 1356 nm in the same device.
FAST, MEMS-BASED, PHASE-SHIFTING INTERFEROMETER (2006)

We demonstrate a MEMS-based, phase-shifting interferometer (MBPSI) that is much faster than conventional phase-shifting interferometers (PSI). For phase shifting, our system employs a comb-driven vertically resonating micromachined mirror illuminated by synchronized laser pulses ( =660nm). Our MBPSI employs a four-frame phase-shifting technique (four CMOS-imager frames per one profile measurement), at a rate of 23 profile measurements-per-second (23Hz, 43.5msec per measurement). At this rate, the MBPSI can continuously capture more than 500 profile measurements of a transient phenomenon over 21.7 seconds. The MBPSI in Twyman-Green configuration has accurately tracked in real time the fast-changing, transient motion of a PZT actuator, within /110 ( 6nm).
BRAF mutation in thyroid carcinogenesis and its clinical implications (2006)

Purpose of review Extensive recent research on BRAF mutation in thyroid cancer has advanced understanding of its role in thyroid carcinogenesis and its clinical implications. The purpose of this review is to summarize the recent advances in this exciting area of thyroid cancer medicine. Recent findings Since the initial discovery of the oncogenic T1799A BRAF mutation in papillary thyroid cancer 3 years ago, numerous studies continue to show a high prevalence and specificity of this mutation in papillary thyroid cancer. Recent studies have focused on the role of this mutation, through activation of the Ras → Raf → MEK → MAP kinase pathway, in papillary thyroid cancer carcinogenesis. This role of BRAF mutation is now strongly supported by clinicopathological, in-vitro cell line, and in-vivo animal studies that showed BRAF mutation as an initiator, as well as a promoter of aggressiveness, of papillary thyroid cancer. Summary BRAF mutation represents one of the most important molecular discoveries in thyroid cancer in recent years. Its role in papillary thyroid cancer carcinogenesis and potential as a novel prognostic molecular marker, as well as therapeutic target for papillary thyroid cancer, have been recognized. The recent work on BRAF mutation may have an important impact on thyroid cancer medicine.
Synthesis and structural analysis of curdlan sulfate with a potent inhibitory effect in vitro of AIDS virus infection (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and structural analysis of curdlan sulfate with a potent inhibitory effect in vitro of AIDS virus infectionTakashi Yoshida, Kenichi Hatanaka, Toshiyuki Uryu, Yutaro Kaneko, Eiichiro Suzuki, Hiroshi Miyano, Toru Mimura, Osamu Yoshida, and Naoki YamamotoCite this: Macromolecules 1990, 23, 16, 3717–3722Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/ma00218a001https://doi.org/10.1021/ma00218a001research-articleACS PublicationsRequest reuse permissionsArticle Views399Altmetric-Citations103LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Photonic crystals for long-wavelength single-mode VCSELs (2008)

In this paper, we present the design and manufacturing of photonic-crystal long-wavelength VCSELs. They were developed to provide a high-performance low-cost alternative to Fabry-Perot and DFB lasers for 2.5 Gbps applications within the intermediate range access network. The paper covers photonic-crystal long-wavelength device design, manufacturing process, DC and AC characteristics, as well as reliability studies. The addition of photonic-crystal structures to the long-wavelength vertical-cavity surface-emitting lasers allows us to increase the oxide diameter. This reduces the series resistance as well as the thermal resistance resulting in increased single-mode output-power and an enhanced high-temperature performance of our devices.
Texture-Based Analysis of COPD: A Data-Driven Approach (2011)

This study presents a fully automatic, data-driven approach for texture-based quantitative analysis of chronic obstructive pulmonary disease (COPD) in pulmonary computed tomography (CT) images. The approach uses supervised learning where the class labels are, in contrast to previous work, based on measured lung function instead of on manually annotated regions of interest (ROIs). A quantitative measure of COPD is obtained by fusing COPD probabilities computed in ROIs within the lung fields where the individual ROI probabilities are computed using a k nearest neighbor (kNN ) classifier. The distance between two ROIs in the kNN classifier is computed as the textural dissimilarity between the ROIs, where the ROI texture is described by histograms of filter responses from a multi-scale, rotation invariant Gaussian filter bank. The method was trained on 400 images from a lung cancer screening trial and subsequently applied to classify 200 independent images from the same screening trial. The texture-based measure was significantly better at discriminating between subjects with and without COPD than were the two most common quantitative measures of COPD in the literature, which are based on density. The proposed measure achieved an area under the receiver operating characteristic curve (AUC) of 0.713 whereas the best performing density measure achieved an AUC of 0.598. Further, the proposed measure is as reproducible as the density measures, and there were indications that it correlates better with lung function and is less influenced by inspiration level.
Symmetry within the sequence-pair representation in the context of placement for analog design (2000)

This paper addresses the problem of device-level placement for analog layout, focusing mainly on symmetry-related aspects. Different from most of the existent analog placement approaches, employing basically simulated annealing optimization algorithms operating on flat (absolute) spatial representations, our model uses a more recent topological representation called sequence-pair, which has the advantage of not being restricted to slicing floorplan topologies. In this paper, we explain how specific features essential to analog placement, such as the ability to deal with complex symmetry constraints (for instance, an arbitrary number of symmetry groups of cells), can be easily handled by employing the sequence-pair representation. Several analog examples substantiate the effectiveness of our placement tool, which is already in use in an industrial environment.
Clean Absorption‐Mode NMR Data Acquisition (2009)

Abstract Die phasenverschobene gespiegelte Aufnahme („phase‐shifted mirrored sampling“, PMS) von indirekten Evolutionsperioden vieldimensionaler NMR‐Experimente liegt neuen Datenaufnahmeverfahren zugrunde, die ohne Anwendung einer Phasenkorrektur dispersive Signalkomponenten eliminieren, welche die Signalidentifikation erschweren und deren Maxima verschieben. Die erhöhte Auflösung ist von besonderem Interesse für Systeme mit nahezu entarteten chemischen Verschiebungen. magnified image