gebhart/patrepeval huggingface dataset:
Occurrence and Detection of Phosphopeptide Isomers in Large-Scale Phosphoproteomics Experiments (2012)

The past decade has been marked by the emergence of selective affinity media and sensitive mass spectrometry instrumentation that facilitated large-scale phosphoproteome analyses and expanded the repertoire of protein phosphorylation. Despite these remarkable advances, the precise location of the phosphorylation site still represents a sizable challenge in view of the labile nature of the phosphoester bond and the presence of neighboring phosphorylatable residues within the same peptide. This difficulty is exacerbated by the combinatorial distribution of phosphorylated residues giving rise to different phosphopeptide isomers. These peptides have similar physicochemical properties, and their separation by LC is often problematic. Few studies have described the frequency and distribution of phosphoisomers in large-scale phosphoproteomics experiments, and no convenient informatics tools currently exist to facilitate their detection. To address this analytical challenge, we developed two algorithms to detect separated and co-eluting phosphopeptide isomers and target their subsequent identification using an inclusion list in LC-MS/MS experiments. Using these algorithms, we determined that the proportion of isomers present in phosphoproteomics studies from mouse, rat, and fly cell extracts represents 3-6% of all identified phosphopeptides. While conventional analysis can identify chromatographically separated phosphopeptides, targeted LC-MS/MS analyses using inclusion lists provided complementary identification and expanded the number of phosphopeptide isomers by at least 52%. Interestingly, these analyses revealed that the occurrence of phosphopeptides isomers can also correlate with the presence of extended phosphorylatable amino acids that can act as a "phosphorylation switch" to bind complementary domains such as those present in SR proteins and ribonucleoprotein complexes.
Developing parallel applications using high-performance simulation (1993)

Article Developing parallel applications using high-performance simulation Share on Authors: Eric A. Brewer MIT Laboratory for Computer Science MIT Laboratory for Computer ScienceView Profile , William E. Weihl MIT Laboratory for Computer Science MIT Laboratory for Computer ScienceView Profile Authors Info & Claims PADD '93: Proceedings of the 1993 ACM/ONR workshop on Parallel and distributed debuggingDecember 1993 Pages 158–168https://doi.org/10.1145/174266.168848Online:01 December 1993Publication History 16citation296DownloadsMetricsTotal Citations16Total Downloads296Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Two-stage optical parametric generator with multi-Watt outputs in ultrashort pulses around 800 nm and 1450 nm (2004)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text F. Brunner, E. Innerhofer, T. Südmeyer, R. Paschotta, U. Keller, T. Usami, H. Ito, M. Nakamura, and K. Kitamura, "Two-stage optical parametric generator with multi-Watt outputs in ultrashort pulses around 800 nm and 1450 nm," in Advanced Solid-State Photonics, OSA Technical Digest (Optica Publishing Group, 2004), paper TuC1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Iterative Backpropagation Disturbance Observer with Forward Dynamics Model (2021)

Disturbance Observer (DOB) has been widely used for robotic applications to eliminate various kinds of disturbances. Recently, learning-based DOB has attracted significant attention as it can deal with complex robotic systems. In this study, we propose the Iterative Backpropagation Disturbance Observer (IB-DOB) method. IB-DOB learns the forward model with a neural network, and calculates disturbances via iterative backpropagations, which behaves like the inverse model. Our method can not only improve estimation performances owing to the iterative calculation but also be applied to both model-free and -based learning control. We conducted experiments for two manipulation tasks: the cart pole with Deep Deterministic Policy Gradient (DDPG) and the pushing object task with Deep Model Predictive Control (DeepMPC). Our method demonstrated better task performances than the baselines without DOB and with DOB using a learned inverse model even though disturbances of external forces and model errors were provided.
Exact Mass (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Abstract 5534: Liposome accumulation within leukemia engrafted bone marrow is significantly enhanced when the formulation contains cytarabine plus daunorubicin (2010)

Abstract CPX-351 is a liposome formulation designed to deliver a synergistic, fixed ratio of cytarabine and daunorubicin in vivo. It has been shown to be highly efficacious against a variety of mouse leukemia models and encouraging evidence of anti-leukemic activity has been observed in clinical trials. In this report we investigate liposome biodistribution properties that may contribute to the enhanced efficacy of CPX-351. In order to model bone marrow leukemia development, we utilized the human leukemia CCRF-CEM tumor which has been shown to efficiently engraft to the bone marrow of SCID Rag2M mice. Liposomes were prepared in the presence or absence of cytarabine and daunorubicin to compare the plasma clearance and biodistribution to bone marrow, liver, lung, spleen and kidney following multiple treatments. The plasma clearance of empty liposomes and CPX-351 were similar in both leukemia and non-leukemia bearing mice. Both liposomal formulations had similar organ distribution profiles in the presence or absence of leukemia; however lipid delivery to the bone marrow was markedly augmented by the presence of encapsulated drug. Accumulation of CPX-351 lipid in the bone marrow was 20 to 50% higher than for empty liposomes and this phenomenon was further enhanced in leukemia bearing mice. Leukemia-laden bone marrow accumulated 75% more CPX-351 lipid than the empty liposomes on the first injection and accumulation increased an additional 20% with subsequent injections. We attribute the increased efficacy of CPX-351 over the free drug cocktail of cytarabine and daunorubicin to elevated exposure of the tumor tissue to chemotherapeutic agents. This increased exposure is not only due to the prolonged circulation of the drug in the liposomes, but also due to the increased bone marrow uptake of the liposomes when drugs are present. Additionally the lipid accumulation is further increased with successive treatments of the leukemia. The results suggest that the liposomal drugs alter either the bone marrow microenvironment or resident cell populations in a manner that facilitates subsequent uptake and/or retention of CPX-351. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5534.
Syntactic alignment models for large-scale statistical machine translation (2012)

Word alignment, the process of inferring the implicit links between words across two languages, serves as an integral piece of the puzzle of learning linguistic translation knowledge. It enables us to acquire automatically from data the rules that govern the transformation of words, phrases, and syntactic structures from one language to another. Word alignment is used in many tasks in Natural Language Processing, such as bilingual dictionary induction, cross-lingual information retrieval, and distilling parallel text from within noisy data. In this dissertation, we focus on word alignment for statistical machine translation. 
We advance the state-of-the-art in search, modeling, and learning of alignments and show empirically that, when taken together, these contributions significantly improve the output quality of large-scale statistical machine translation, outperforming existing methods. We show results for Arabic-English and Chinese-English translation. 
Ultimately, the work we describe herein may be used for any language-pair, supporting arbitrary and overlapping features from varied sources. Finally, our features are learned automatically without any human intervention, facilitating rapid deployment for new language-pairs.
Scatter plot of age versus biomarker summary score for men and women from the Estonian Biobank cohort. (2015)

&lt;p&gt;The lines indicate a fit of age against the biomarker summary score, with dashed lines denoting 95% prediction intervals. Persons who died within the 5-y follow-up period are marked by red dots, and persons who were alive after 5 y are marked by open gray circles. Persons with less than 5 y of follow-up are marked in light gray.&lt;/p&gt;
Light-triggered release of conventional local anesthetics from a macromolecular prodrug for on-demand local anesthesia (2020)

An on-demand anesthetic that would only take effect when needed and where the intensity of anesthesia could be easily adjustable according to patients' needs would be highly desirable. Here, we design and synthesize a macromolecular prodrug (P407-CM-T) in which the local anesthetic tetracaine (T) is attached to the polymer poloxamer 407 (P407) via a photo-cleavable coumarin linkage (CM). P407-CM-T solution is an injectable liquid at room temperature and gels near body temperature. The macromolecular prodrug has no anesthetic effect itself unless irradiated with a low-power blue light emitting diode (LED), resulting in local anesthesia. By adjusting the intensity and duration of irradiation, the anesthetic effect can be modulated. Local anesthesia can be repeatedly triggered.
Semaphorin 3F and Neuropilin-2 Control the Migration of Human T-Cell Precursors (2014)

Neuropilins and semaphorins are known as modulators of axon guidance, angiogenesis, and organogenesis in the developing nervous system, but have been recently evidenced as also playing a role in the immune system. Here we describe the expression and role of semaphorin 3F (SEMA3F) and its receptor neuropilin-2 (NRP2) in human T cell precursors. NRP2 and SEMA3F are expressed in the human thymus, in both lymphoid and non-lymphoid compartments. SEMA3F have a repulsive effect on thymocyte migration and inhibited CXCL12- and sphingosine-1-phosphate (S1P)-induced thymocyte migration by inhibiting cytoskeleton reorganization prior to stimuli. Moreover, NRP2 and SEMA3F are expressed in human T-cell acute lymphoblastic leukemia/lymphoma primary cells. In these tumor cells, SEMA3F also blocks their migration induced by CXCL12 and S1P. Our data show that SEMA3F and NRP2 are further regulators of human thymocyte migration in physiological and pathological conditions.
POROUS TITANIUM PHOSPHATE GLASS-CERAMICS WITH BACTERIOSTATIC ACTIVITIES (1996)

Microporous glass-ceramics with the surface phase of AgTi2(PO4)3 crystal and the interior phase of LiTi2(PO4)3 crystal were prepared by exchange of Ag+ ions for Li+ ions. The mean pore diameter and specific surface area are 150 nm and 10 m2/g, respectively. The glass-ceramics showed excellent bacteriostatic properties. The amount of Ag+ ions released from the materials into the phosphate buffer solution is extremely small.
Plasma etching of quartz for the fabrication of alternating aperture phase-shift photomasks: etch rate uniformity study utilizing a next-generation ICP source (2001)

As on-glass line widths shrink and exposure wavelengths approach the physical limitations of optical lithographic printing, the adoption of newer technology such as Off-Axis Illumination and Phase Shift Photomask technologies will substantially expand the operating life of DUV lithographic tools. In this article, the dry etch processes and Inductively Coupled Plasma (ICP) hardware iterations associated with the etch optimization of Levenson-style hard shifters are explored. These Alternating Aperture Hard Shifters currently adopt a single material form, with Levenson-style photomasks making use of a precise removal of quartz material between the Cr lines of a standard Photomask, improving the resolution of the exposed features. This precise quartz removal is performed utilizing dry etch technologies, with the use of high density, de-coupled plasmas such as ICP preferred. We explore Inductively Coupled Plasma shaping techniques along with newer etch processes for these materials, offering a Next Generation ICP Source design. Process conditions are verified and on-mask results are reported.
Antibody‐virus co‐evolution in HIV infection: paths for HIV vaccine development (2017)

Induction of HIV-1 broadly neutralizing antibodies (bnAbs) to date has only been observed in the setting of HIV-1 infection, and then only years after HIV transmission. Thus, the concept has emerged that one path to induction of bnAbs is to define the viral and immunologic events that occur during HIV-1 infection, and then to mimic those events with a vaccine formulation. This concept has led to efforts to map both virus and antibody events that occur from the time of HIV-1 transmission to development of bnAbs. This work has revealed that a virus-antibody "arms race" occurs in which a HIV-1 transmitted/founder (TF) Env induces autologous neutralizing antibodies that can not only neutralize the TF virus but also can select virus escape mutants that in turn select affinity-matured neutralizing antibodies. From these studies has come a picture of bnAb development that has led to new insights in host-pathogen interactions and, as well, led to insight into immunologic mechanisms of control of bnAb development. Here, we review the progress to date in elucidating bnAb B cell lineages in HIV-1 infection, discuss new research leading to understanding the immunologic mechanisms of bnAb induction, and address issues relevant to the use of this information for the design of new HIV-1 sequential envelope vaccine candidates.
1123: Natural History and Growth Characteristics of Oncocytomas Under Active Surveillance (2006)

You have accessJournal of UrologyDiscussed Poster, Tuesday, May 23, 2006, 9:00 am - 12:00 pm1 Apr 20061123: Natural History and Growth Characteristics of Oncocytomas Under Active Surveillance Paul L. Crispen, Rosalia Viterbo, Richard E. Greenberg, David Y.T. Chen, and Robert G. Uzzo Paul L. CrispenPaul L. Crispen More articles by this author , Rosalia ViterboRosalia Viterbo More articles by this author , Richard E. GreenbergRichard E. Greenberg More articles by this author , David Y.T. ChenDavid Y.T. Chen More articles by this author , and Robert G. UzzoRobert G. Uzzo More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)33348-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1123: Natural History and Growth Characteristics of Oncocytomas Under Active Surveillance." The Journal of Urology, 175(4S), p. 361 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 4SApril 2006Page: 361 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Paul L. Crispen More articles by this author Rosalia Viterbo More articles by this author Richard E. Greenberg More articles by this author David Y.T. Chen More articles by this author Robert G. Uzzo More articles by this author Expand All Advertisement PDF DownloadLoading ...
LCST Phase Behavior and Complexation with Water of an Ionic Liquid Incorporating the 5‐Phenyltetrazolate Anion (2017)

The use of 5-phenyltetrazole, a bioisostere of benzoic acid, as an anion source to prepare an ionic liquid is described for the first time. Tetrabutylphosphonium 5-phenyltetrazolate undergoes phase separation from water with lower critical solution temperature phase behavior, in contrast to completely water miscible tetrabutylphosphonium benzoate, and also exhibits strong complexation with water with both eutectic and peritectic behavior that has not previously been observed in ionic liquid+water systems. The anhydrous and trihydrate salts were isolated and characterized by single crystal X-ray diffraction.
Speaker recognition using dynamic synapse-based neural networks with wavelet preprocessing (2002)

Two problems in the field of speaker recognition are noise robustness and low interspeaker variability. This project involved the design of a system that is capable of speaker verification on a closed set of speakers using a wavelet processing technique that allows for a speaker-dependent feature set extraction. Verification is accomplished using a dynamic synapse-based neural network with noise-resistance properties that is trained using a genetic algorithm technique. Using these techniques, the system was able to perform speaker verification without being adversely affected by normal levels of noise, and perform verification despite low variability between speakers.
AICAR Protects Vascular Endothelial Cells from Oxidative Injury Induced by the Long-Term Palmitate Excess (2021)

Hyperlipidemia manifested by high blood levels of free fatty acids (FFA) and lipoprotein triglycerides is critical for the progression of type 2 diabetes (T2D) and its cardiovascular complications via vascular endothelial dysfunction. However, attempts to assess high FFA effects in endothelial culture often result in early cell apoptosis that poorly recapitulates a much slower pace of vascular deterioration in vivo and does not provide for the longer-term studies of endothelial lipotoxicity in vitro. Here, we report that palmitate (PA), a typical FFA, does not impair, by itself, endothelial barrier and insulin signaling in human umbilical vein endothelial cells (HUVEC), but increases NO release, reactive oxygen species (ROS) generation, and protein labeling by malondialdehyde (MDA) hallmarking oxidative stress and increased lipid peroxidation. This PA-induced stress eventually resulted in the loss of cell viability coincident with loss of insulin signaling. Supplementation with 5-aminoimidazole-4-carboxamide-riboside (AICAR) increased endothelial AMP-activated protein kinase (AMPK) activity, supported insulin signaling, and prevented the PA-induced increases in NO, ROS, and MDA, thus allowing to maintain HUVEC viability and barrier, and providing the means to study the long-term effects of high FFA levels in endothelial cultures. An upgraded cell-based model reproduces FFA-induced insulin resistance by demonstrating decreased NO production by vascular endothelium.
Experimental and computational studies of pyridine-assisted post-synthesis modified air stable covalent–organic frameworks (2012)

Pyridine-modified COF-10 exhibits enhanced stability in humid air relative to un-modified COF-10. Solid state NMR and computational studies were used to probe the nature of pyridine interactions with the framework. We propose two models for pyridine-framework interactions with different stabilities.
Supplementary Figure S3 from The Bromodomain Inhibitor JQ1 and the Histone Deacetylase Inhibitor Panobinostat Synergistically Reduce N-Myc Expression and Induce Anticancer Effects (2023)

&lt;p&gt;Combination therapy with JQ1 and panobinostat synergistically reduces neuroblastoma cell viability.&lt;/p&gt;
Regio- and stereoselective synthesis of novel spiropyrrolidines through 1,3-dipolar cycloaddition reactions of azomethine ylides and 2-styrylquinazolin-4(3H)-ones (2014)

Efficient regio- and stereoselective synthesis of novel spiropyrrolidines.
Optical links for cryogenic focal plane array readout (1994)

An optical link can provide an interface channel for a focal plane array that is immune to electro-magnetic interference (EMI) and can lower the heat load on the dewar. Our approach involves the use of fiber optics and an on-focal-plane optical modulator to provide an interface to the focal plane array (FPA). The FPA drives the modulator with an electrical signal. We evaluated specially fabricated AlGaAs/GaAs multiple-quantum-well (MQW) optical modulators, operating near 840 nm, for analog modulation, and we have used the results to calculate the performance of an optical interface link using experimentally determined device parameters. Link noise and dynamic range for an analog link were estimated from a separate experiment using pigtailed fiber components. The performance of the MQW modulator system is compared to alternative strategies. Significant improvement in performance in comparison to conventional electronic interfaces appears to be possible.
Carbon Radical Attack on a Pyrimidine Nitrogen. An Unusual Entry into Polycyclic Aminopyrimidones (2014)

Unprecedented examples of a synthetically useful radical ring closure onto a pyrimidine nitrogen leading to novel, highly functionalized bi- and tricyclic pyrimidone structures are reported. An unexpected hydrogen atom translocation prior to the cyclization step was observed in some cases.
Multi-Task Sensor Resource Balancing Using Lagrangian Relaxation and Policy Rollout (2020)

The sensor resource management problem in a multi-object tracking scenario is considered. In order to solve it, a dynamic budget balancing algorithm is proposed which models the different sensor tasks as partially observable Markov decision processes. Those are being solved by applying a combination of Lagrangian relaxation and policy rollout. The algorithm converges to a solution which is close to the optimal steady-state solution. This is shown through simulations of a two-dimensional tracking scenario. Moreover, it is demonstrated how the algorithm allocates the sensor time budgets dynamically to a changing environment and takes predictions of the future situation into account.