gebhart/patrepeval huggingface dataset:
Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics (2019)

Within the last several years, top-down proteomics has emerged as a high throughput technique for protein and proteoform identification. This technique has the potential to identify and characterize thousands of proteoforms within a single study, but the absence of accurate false discovery rate (FDR) estimation could hinder the adoption and consistency of top-down proteomics in the future. In automated identification and characterization of proteoforms, FDR calculation strongly depends on the context of the search. The context includes MS data quality, the database being interrogated, the search engine, and the parameters of the search. Particular to top-down proteomics-there are four molecular levels of study: proteoform spectral match (PrSM), protein, isoform, and proteoform. Here, a context-dependent framework for calculating an accurate FDR at each level was designed, implemented, and validated against a manually curated training set with 546 confirmed proteoforms. We examined several search contexts and found that an FDR calculated at the PrSM level under-reported the true FDR at the protein level by an average of 24-fold. We present a new open-source tool, the TDCD_FDR_Calculator, which provides a scalable, context-dependent FDR calculation that can be applied post-search to enhance the quality of results in top-down proteomics from any search engine.
ChemInform Abstract: Synthesis of Pyridines by [2 + 2 + 2]‐Cyclotrimerization of Alkynes with Nitriles (2010)

Abstract Review: 109 refs.
Primary Structure of the N-Terminal Portion of D-Amino Acid Oxidase (1974)

The primary structure of the N-terminal portion of D-amino acid oxidase [D-amino acid: O2 oxidoreductase (deaminating), EC 1.4.3.3] was studied in the form of its S-carboxymethylated apoprotein by the automatic Edman degradation method. The structure was found to be Met-Arg-Val-Val-Val-Ile-Gly-Ala-Gly-Val-Ile-Gly-Leu-Ser-Thr-Ala-Leu-Ser-Ile-His-Glx……
The pH of wounds during healing and infection: A descriptive literature review (2017)

Introduction: Infection is difficult to detect and diagnose in chronic wounds. Misdiagnosis of wound infection risks inappropriate antibiotic prescribing, antibiotic resistance and unnecessary treatment side effects. Alternatively, waiting for the results of microbiological investigations can delay treatment risking spreading or/and systemic infection. There is a need for simple and objective measures of wound infection that provide real-time indication of infection that is accessible to the majority of clinical settings. Methods: A literature review was conducted that explored existing evidence regarding the association between the pH of a wound and wound healing and infection to determine whether a wound pH scale could be used as a marker of infection. Results: The literature review found evidence to suggest that wound pH, and specifically an 'Alkaline pH', is conducive to bacterial bio-burden and reflective of the specific physiological processes of the healing cascade. Conclusions: As such, while pH is not sufficiently understood to be translated into current practice as a metric for infection, the pH scale does have potential as a diagnostic and management indicator and merits exploration.
Integrated refrigeration and storage of LNG for compositional stability (2020)

Abstract Growing interest in liquefied natural gas (LNG) as a rocket fuel necessitates a greater technical understanding of the compositional changes due to preferential boil-off (or weathering) that occurs during long duration storage. The purity of methane in LNG can range from 90 to 98%, and is subject to preferential boil-off due to its low boiling point compared to other constituents despite the use of high-performance thermal insulation systems. Active heat extraction (i.e. refrigeration) is required to completely eliminate weathering. For future operational safety and reliability, and to better understand the quality and efficiency of the LNG as a cryofuel, a 400-liter Cryostat vessel was designed and constructed to measure the composition and temperatures of the LNG at a number of different liquid levels over long durations. The vessel is the centerpiece of a custom-designed lab-scale integrated refrigeration and storage (IRaS) system employing a pulse tube cryocooler capable of roughly 50 W of lift at 100 K. Instrumentation includes ten temperature sensors mounted on a vertical rake and five liquid sample tubes corresponding to five liquid levels. Two modes of operation are studied. The first is without refrigeration in order to determine a baseline in the change in composition, and to study stratification of the LNG. The second is performed with the cryocooler active to determine the operational parameters of the IRaS system for eliminating the weathering as well as stratification effects in the bulk liquid. The apparatus design and test method, as well as preliminary test results are presented in this paper. As a bonus in cost-saving and operational efficiency, the capability of the IRaS system to provide zero-loss capabilities such as zero boil-off (ZBO) keeping of the LNG and zero-loss filling/transfer operations are also discussed.
In vivo magnetic resonance imaging of single cells in mouse brain with optical validation (2005)

In the current work we demonstrate, for the first time, that single cells can be detected in mouse brain in vivo using magnetic resonance imaging (MRI). Cells were labeled with superparamagnetic iron oxide nanoparticles and injected into the circulation of mice. Individual cells trapped within the microcirculation of the brain could be visualized with high-resolution MRI using optimized MR hardware and the fast imaging employing steady state acquisition (FIESTA) pulse sequence on a 1.5 T clinical MRI scanner. Single cells appear as discrete signal voids on MR images. Direct optical validation was provided by coregistering signal voids on MRI with single cells visualized using high-resolution confocal microscopy. This work demonstrates the sensitivity of MRI for detecting single cells in small animals for a wide range of application from stem cell to cancer cell tracking.
Scaling concepts in cell physics: paradigms for cell adhesion (2010)

Shapes and lengths are treated differently in cell biology and in physics. In cell biology, morphology is considered a powerful read-out for estimating protein activities and for classifying pathways. Spatial features are often viewed as binary signals, on or off, active or non-active. In contrast, in condensed matter physics, spatial dimensions are generally derived quantitatively with scaling relations using the mechanical properties of matter. This powerful approach allows predicting scales in new experiments. Here, we applied such a type of scaling method for specific organelles in cells: the cell adhesion structures. We show that simple relations allow one to derive measured lengths in a variety of situations and proteic complexes; if the molecular detail is not at play in such an approach, the mesoscopic equations allow one to quantitatively match the experimental observations. Based on these relations, we also predict simple rules for varying lengths of contacts and distances between contacts in future experiments.
Development of a novel laser system for the CZMIL lidar (2010)

The Coastal Zone Mapping and Imaging Lidar (CZMIL) system<sup>1</sup> aims to expand bathymetric lidar performance in shallow water conditions, where high spatial and temporal data resolutions are required. This must be achieved without sacrificing performance in deep water. Very high frequency data collection (as high as 70KHz) utilizing a hybrid flash-point lidar approach is utilized, which places high demands on the transmitted laser beam, namely high pulse power with short duration with very high fidelity beam characteristics. To meet these requirements, we have developed a compact, high-power, short pulse length, high repetition rate laser with beam quality acceptable for use with the hybrid lidar approach employed in CZMIL. The short pulse length is achieved using a CW-pumped Q-switched oscillator, and the required power is achieved by using multiple amplifiers employing fiber coupled, CW end-pumped Nd:YVO<sub>4</sub> crystals prior to doubling the 1064 nm beam. The resulting output power is ~ 30W at 10 kHz with a pulse length of &lt; 2.5 ns FWHM at 532 nm and ~ 20W of residual power at 1064 nm.
Useful polyclonal antibodies against synthetic peptides corresponding to immunoglobulin light chain constant region for immunohistochemical detection of immunoglobulin light chain amyloidosis (2001)

For the immunohistochemical detection of immunoglobulin (Ig) light chain amyloidosis on formalin-fixed, paraffin-embedded tissue sections, we prepared polyclonal antibodies against synthetic peptides corresponding to positions 118-134 of Ig lambda light chain and positions 116-133 of Ig kappa light chain. Nineteen cases of systemic Ig lambda light chain amyloidosis (Alambda amyloidosis), 10 cases of systemic Ig kappa light chain amyloidosis (Akappa amyloidosis), one case of immunohistochemically unclassified systemic amyloidosis and five cases of localized Alambda amyloidosis were tested with these antibodies. Anti-lambda (118-134) antiserum and the affinity-purified antibody both reacted with 18 of the 19 cases of systemic Alambda amyloidosis and all cases of localized Alambda amyloidosis, although the immunoexpression was somewhat variable in intensity in different areas within the same specimen in both systemic and localized amyloidosis. The signal intensities in plasma cells and serum reacted for anti-lambda (118-134) antiserum were weaker than signals obtained with commercially available anti-Ig lambda light chain antibodies. Anti-kappa (116-133) antiserum and the affinity-purified antibody reacted with nine of the 10 cases of systemic Akappa amyloidosis. We conclude that these antibodies against synthetic peptides corresponding to the Ig light chain constant region are useful for the classification of amyloidosis on formalin-fixed, paraffin-embedded tissue sections.
The cationic cluster Grignard [{MgCl(thf)2}3(μ3-C3H5)2]+ (2006)

The synthesis and structure of [{MgCl(thf)2}3(mu3-C3H5)2]2[Mg(C3H5)4], which contains both a cationic cluster Grignard and a tetraorganomagnesiate dianion, are reported.
(1) AUTOCATALYZED HYDROLYSIS OF ACRYLIC POLYMER COLLOIDS: A KINETIC AND CARBON-13 NMR STUDY. (2) SYNTHESIS OF MONODISPERSE, SPIN-LABELED, AMPHIPHILIC POLYMERS OF STEARIC ACID AND POLY(ETHYLENE GLYCOL) (POLYETHYLENE) (1983)

Methyl acrylate polymer colloids can be hydrolyzed self-catalytically by bound strong acid groups chemically bound to the particle surface which are derived from the polymerization initiator. The kinetics of hydrolysis, after an initial surge are shown to be apparently pseudo-zero order for any given latex, and first order with respect to surface strong acid concentration. A reaction zone model is proposed to explain the kinetics. It also leads to the prediction that the polymer particles will possess a core-shell morphology after some hydrolysis has occurred. This study used ('13)C NMR to investigate the particle morphology in the wet latex, a new application for this method. The temperature-dependence of the ('13)C NMR integrated intensities at various levels of hydrolysis provides strong evidence that the particles do possess core-shell morphology, and that the shell is composed of PAA/PMA copolymer. This shell is swollen and plasticized by water, resulting in greatly enhanced segmental mobility of the polymer chains as evidenced by marked narrowing of the NMR lines. Consistent with the kinetics and NMR results, a quantitative expression based upon a model involving two concentric surface reaction zones was derived.^ In a separate study, methods were developed for the synthesis of monodisperse, spin-labeled, colloidal stabilizers made from 12-keto-stearic acid and poly(ethylene glycol), PEG. The diester was made from a PEG with molecular weight of 4000 and 12-keto-stearyl chloride. In separate experiments it was shown that 12-keto-methyl stearate could react with 2-amino-2-methyl-1-propanol to form the corresponding dimethyl oxazolidine. This was subsequently oxidized to form the nitroxyl free radical spin-label, which exhibited the expected triplet-peak ESR spectrum. ^
A Manganese N‐Heterocyclic Carbene Catalyst for Reduction of Sulfoxides with Silanes (2019)

Abstract The first reduction of sulfoxides catalysed by a well‐defined manganese complex is described. A variety of sulfoxides are reduced to the corresponding sulfides in high yields using phenylsilane, diphenylsilane, and the economically feasible 1,1,3,3‐tetramethyldisiloxane (TMDS) as reducing agents in the presence of a Mn‐NHC complex. The reaction is performed under air and without the need of any additive. The involvement of radicals in the catalytic reaction is probed by spin‐trap experiments.
Thermodynamic Characteristics of Hybrid Solar Microgas Turbine Plants under Tropical Climate (2021)

The article presents the results obtained during the study of the characteristics of hybrid solar micro-gas turbine units with an integrated parabolocylindrical solar collector. The efficiency of a hybrid solar gas turbine plant depends both on the efficiency of the solar collector and the location of its integration, and on the efficiency of the gas turbine engine. (Research purpose) The research purpose is in studying hybrid solar gas turbine installations based on a parabolocylindrical focusing solar collector in combination with micro-gas turbine engines of various configurations to determine the most suitable match. (Materials and methods) The article considers four basic schemes of gas turbine engines running on organic fuel, their parameters and optimization results. The article presents the main climatic parameters for the study of the focusing solar collector, as well as the parameters of the collector itself and the main dependencies that determine its efficiency and losses. The place of integration of the focusing solar collector into the gas turbine plant was described and justified. (Results and discussion) Hybrid solar micro-gas turbine installations based on micro-gas turbine engines of a simple cycle, a simple cycle with heat recovery, a simple cycle with a turbocharger utilizer, a simple cycle with a turbocharger utilizer and heat recovery for tropical climate conditions were studied on the example of Abu Dhabi. (Conclusions) The most suitable configuration of micro-gas turbine engines for integrating a focusing solar collector is a combination of a simple cycle with a turbocharger utilizer and regeneration. The combination of micro-gas turbine engines of a simple cycle with a turbocharger heat recovery and heat recovery with an integrated focusing solar collector can relatively increase the average annual efficiency of fuel consumption of such installations in a tropical climate by 10-35 percent or more, while maintaining cogeneration capabilities.
Selective tropism of bovine leukemia virus (BLV) for surface immunoglobulin-bearing ovine B lymphocytes. (1987)

Bovine leukemia virus (BLV) is experimentally infectious for sheep. Virus production does not occur in the animals, but only after in vitro cultivation of infected lymphocytes in the presence of phytohemagglutinin. Lipopolysaccharide or dextran sulfate 500 had no effect. After panning separation, it was possible to demonstrate that, in peripheral blood lymphocytes, BLV was integrated in the B lymphocytes only and that BLV expression took place in a fraction of this population. The ovine leukemia may constitute a good experimental model for understanding the virus-induced leukemias of the BLV-human T cell leukemia virus group.
Topical Anesthetic Abuse Ring Keratitis (1997)

Topical anesthetic abuse resulting in sight-threatening keratitis may be seen as a masquerade syndrome in many cases. Because of the often poor outcome, we must be aware of this entity, prevent abuse, and be vigilant in our prohibition of topical anesthetic for any therapeutic use.
An RFID-based Infrastructure for Automatically Determining the Position and Orientation of Game Objects in Tabletop Games1 (2007)

Abstract. Radio Frequency Identification (RFID) technology already plays a major role in many areas. In business applications, for example, the idea of smart shelves or tables equipped with RFID technology has been around for some time now, especially for retailing. Current solutions, however, are designed to only identify objects in range, which is sufficient for most of the envisioned shop applications. For other uses, however, not only the identification, but also the exact position and orientation of objects would be interesting, if not necessary. A good example are miniature war games, where the current game state usually depends on what objects are located where, and, in some cases, how these objects are oriented. In this article, we present an approach to determine the position and orientation of (multi-tagged) objects. We introduce the conceptual idea, as well as the technical realization based on the example of an augmented miniature war game. We then describe our findings so far and summarize our next steps.
PTP-1B is an essential positive regulator of platelet integrin signaling (2005)

Outside-in integrin alphaIIbbeta3 signaling is required for normal platelet thrombus formation and is triggered by c-Src activation through an unknown mechanism. In this study, we demonstrate an essential role for protein-tyrosine phosphatase (PTP)-1B in this process. In resting platelets, c-Src forms a complex with alphaIIbbeta3 and Csk, which phosphorylates c-Src tyrosine 529 to maintain c-Src autoinhibition. Fibrinogen binding to alphaIIbbeta3 triggers PTP-1B recruitment to the alphaIIbbeta3-c-Src-Csk complex in a manner that is dependent on c-Src and specific tyrosine (tyrosine 152 and 153) and proline (proline 309 and 310) residues in PTP-1B. Studies of PTP-1B-deficient mouse platelets indicate that PTP-1B is required for fibrinogen-dependent Csk dissociation from alphaIIbbeta3, dephosphorylation of c-Src tyrosine 529, and c-Src activation. Furthermore, PTP-1B-deficient platelets are defective in outside-in alphaIIbbeta3 signaling in vitro as manifested by poor spreading on fibrinogen and decreased clot retraction, and they exhibit ineffective Ca2+ signaling and thrombus formation in vivo. Thus, PTP-1B is an essential positive regulator of the initiation of outside-in alphaIIbbeta3 signaling in platelets.
Influence of rupture patterns of the medial patellofemoral ligament (MPFL) on the outcome after operative treatment of traumatic patellar dislocation (2012)

Prognostic study, Level IV.
Testing hyperactive faults in asynchronous circuits (2002)

Testing asynchronous circuits is a difficult task, because of two main reasons; first, the absence of a global clock does not allow the use of traditional test generation techniques used for synchronous circuits. Second, correct (i.e, hazard-free) operations of asynchronous circuits an usually obtained by introducing redundancies, that is, sacrificing the testability. The authors present an efficient test generator for asynchronous circuits which is based on a concurrent fault simulator. They also present an extension of the simulator which provides higher fault coverage by taking into consideration the detection of a special class of faults called hyperactive faults. Experimental results on a set of benchmarks has shown the effectiveness of the test generator, and proved that real circuits actually contain instances of such faults.
CogSketch: Sketch Understanding for Cognitive Science Research and for Education (2011)

Sketching is a powerful means of working out and communicating ideas. Sketch understanding involves a combination of visual, spatial, and conceptual knowledge and reasoning, which makes it both challenging to model and potentially illuminating for cognitive science. This paper describes CogSketch, an ongoing effort of the NSF-funded Spatial Intelligence and Learning Center, which is being developed both as a research instrument for cognitive science and as a platform for sketch-based educational software. We describe the idea of open-domain sketch understanding, the scientific hypotheses underlying CogSketch, and provide an overview of the models it employs, illustrated by simulation studies and ongoing experiments in creating sketch-based educational software.
Supplementary Figure Legends 1-4 from Plasma Fibronectin Promotes Lung Metastasis by Contributions to Fibrin Clots and Tumor Cell Invasion (2023)

Supplementary Figure Legends 1-4 from Plasma Fibronectin Promotes Lung Metastasis by Contributions to Fibrin Clots and Tumor Cell Invasion
Case records of the Meshugunah General Hospital (1985)

A 7-year-old female was admitted to the hospital bacause of paralysis and suspicion of a lung lesion.
Plasma levels of free fatty acids correlate with type 2 diabetes mellitus (2018)

FFA levels are elevated in newly diagnosed and long-term controlled T2DM patients, providing high diagnostic accuracy of 87% and 91%, respectively, which improved further when combined with the glycation degree of lysine-141 in haptoglobin. Additionally, FFA showed higher mean fold-changes than HbA1c or FPG in subjects developing T2DM, indicating higher sensitivity towards the progression of the disease.
Mucorales-Specific T Cells in Patients with Hematologic Malignancies (2016)

Mucorales-specific T cells can be detected and monitored in patients with hematologic malignancies at risk for IM. Mucorales-specific T cells polarized to the production of T helper type 2 cytokines are associated with proven IM and may be evaluated as a surrogate diagnostic marker for IM.
Alkylation of pentaerythritol and trimethylolpropane, two very hydrophilic polyols, by phase-transfer catalysis (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylation of pentaerythritol and trimethylolpropane, two very hydrophilic polyols, by phase-transfer catalysisR. M. Nouguier and M. MchichCite this: J. Org. Chem. 1985, 50, 18, 3296–3298Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/jo00218a010https://doi.org/10.1021/jo00218a010research-articleACS PublicationsRequest reuse permissionsArticle Views735Altmetric-Citations33LEARN 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