gebhart/patrepeval huggingface dataset:
Analysis of the Human Casein Phosphoproteome by 2-D Electrophoresis and MALDI-TOF/TOF MS Reveals New Phosphoforms (2008)

Mammalian breast milk contains an array of proteins and other nutrients essential for the development of the newborn. In human milk, the caseins (alpha S1, beta and kappa) are a major class of proteins; however, the dynamic range of concentrations in which the various isoforms of each casein exist presents challenges in their characterization. To study human milk casein phosphoforms, we applied traditional two-dimensional polyacrylamide gel electrophoretic (2-DE) separation combined with matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) tandem mass spectroscopic analysis. The abundant beta-casein was resolved as a train of 6 spots differing in phosphorylation level with 0-5 phosphates attached. To study the less abundant alpha S1-casein, a cysteine-tagging enrichment treatment was used prior to 2-DE. A train of 9 spots with 4.4 < p I < 5.3 were identified as alpha S1-casein. This included five previously uncharacterized phosphoforms with up to 8 phosphate groups located in two serine-rich tryptic phosphopeptides ( (27)L-R (51), (69)N-K (98)) consistent with alpha-caseins from various ruminant species. MS/MS analysis of the phosphopeptides released by tryptic digestion enabled identification of the residue-specific order of phosphorylation among the 6 beta-casein and 9 alpha S1-casein phosphoforms. Deamidation of N (47) of alpha S1-casein was also a feature of the MS analysis. This study represents the first comprehensive analysis of the human casein phosphoproteome and reveals a much higher level of phosphorylation than previously recognized. It also highlights the advantages of 2-DE for examining the global pattern of protein phosphoforms and the limitations of attempting to estimate phosphorylation site occupancies from "bottom-up" studies.
Characterizing Solid Electrolyte Interphase on Sn Anode in Lithium Ion Battery (2015)

Tin (Sn) nanoparticle electrodes have been prepared and battery cycling performance has been investigated with 1.2 M LiPF6 in ethylene carbonate (EC) / diethyl carbonate (DEC) electrolyte (1:1, w/w) with and without added vinylene carbonate (VC) or fluoroethylene carbonate (FEC). Incorporation of either VC or FEC improves the capacity retention of Sn nanoparticle electrodes although incorporation of VC also results in a significant increase in cell impedance. The best electrochemical performance was observed with electrolyte containing 10% of added FEC. In order to develop a better understanding of the role of the electrolyte in capacity retention and solid electrolyte interface (SEI) structure, ex-situ surface analysis has been performed on cycled electrodes with infrared (IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and Hard XPS (HAXPES). The ex-situ analysis reveals a correlation between electrochemical performance, electrolyte composition, and SEI structure.
[N-(3-Aminopropyl)-N-methyl-1,3-propanediamine-κ3N]dichlorocopper(II) (1998)

The preparation and crystal structure of the title complex, [CuCl2(C7H19N3)], are described. The CuII ion has distorted tetragonal pyramidal geometry, with Cl axial; the axial Cu—Cl distance [2.505 (1) Å] is elongated compared with the basal Cu—Cl distance [2.400 (1) Å]. In the basal plane, Cu—N(tertiary) [2.138 (3) Å] is considerably longer than Cu—N(primary) [1.985 (4) Å mean], presumably reflecting the reduced basicity of the ligand atom.
Dimension Reduction in Location Estimation—the Need for Variable Propagation Speed (2020)

Calling mammals, ships, and many other objects have been commonly located during the last century with two-dimensional (2D) models from measurements of a signal’s Time Differences of Arrivals (TDOA) when the objects are not on the 2D surface. The overwhelmingly common method for locating signals with 2D models takes signal speed as constant and location is derived by intersecting hyperbolas. However, when correct locations are required for 2D models, the speed used to derive location must depend on the geodesic distance along the 2D model surface between the object and the instrument. For example, when this distance is zero, the speed needed for correct location must also be zero. The dimension reduction from three to two introduces large errors in 2D models both near and far from the instruments unless the variable speeds induced by the dimensional reduction are explicitly accounted for. In light of these findings, methods are derived for generating extremely reliable confidence intervals for estimated locations in 2D models and identifying regions of the 2D model where a 3D model is needed. Because speeds needed for correct location are spatially inhomogeneous in the extreme, isodiachrons emerge as a natural geometry for interpreting location instead of hyperbolas. These issues are caused by choice of coordinates, and the same phenomena occur when coordinate transformations are applied in other fields of physics.
USING MEASURED 30–150 kVp POLYCHROMATIC TUNGSTEN X-RAY SPECTRA TO DETERMINE ION CHAMBER CALIBRATION FACTORS, Nx (Gy C−1) (2000)

Two methods for determining ion chamber calibration factors (Nx) are presented for polychromatic tungsten x-ray beams whose spectra differ from beams with known Nx. Both methods take advantage of known x-ray fluence and kerma spectral distributions. In the first method, the x-ray tube potential is unchanged and spectra of differing filtration are measured. A primary standard ion chamber with known Nx for one beam is used to calculate the x-ray fluence spectrum of a second beam. Accurate air energy absorption coefficients are applied to the x-ray fluence spectra of the second beam to calculate actual air kerma and Nx. In the second method, two beams of differing tube potential and filtration with known Nx are used to bracket a beam of unknown Nx. A heuristically derived Nx interpolation scheme based on spectral characteristics of all three beams is described. Both methods are validated. Both methods improve accuracy over the current half value layer Nx estimating technique.
Growth of in situ CoSi2 layer by metalorganic chemical vapor deposition on Si tips and its field-emission properties (2001)

We prepared Si emitters coated with a metalorganic chemical vapor deposited CoSi2 layer to improve emission properties. The CoSi2 layer was grown in situ by reactive chemical vapor deposition of cyclopentadienyl dicarbonyl cobalt at 650 °C. The CoSi2 layer was conformally deposited on the Si emitter tips and had a twinned structure at the epitaxial CoSi2/Si interface in the partial region. The CoSi2-coated Si emitters showed an enhanced emission due to the increase in the number of emitting sites from the Fowler–Nordheim plot. The fluctuation of emission current was reduced by the CoSi2 coating. But the long-term stability was not much improved, which may be due to the decrease of the field enhancement factor and the number of emitting sites of the CoSi2-coated Si tip.
The Conversion of Mixed N,O-Diacylated 2-Aminophenols to 2-Substituted Benzoxazoles (1999)

When N,O-diacylated Zaminophenols that have different acyl substituents on nitrogen and oxygen are treated with p-toluenesulfonic acid in refluxing xylenes, mixtures of benzoxazoles are produced.The major product is the benzoxazole in which the substituent at the 2-position is derived from the acyl group on nitrogen.This product may arise from an unusual case of acid-mediated neighboring amido-group assisted hydrolysis.2-Aryl-and Zalkyl-substituted benzoxazoles have received a considerable amount of attention in diverse areas of chemistry.1In our previous paper2 we reported that the synthesis of 2-substituted benzoxazoles can be accomplished by treating N,O-diacylated 2-aminophenols with p-toluenesulfonic acid (TsOH) in refluxing xylenes or toluene.This procedure affords a variety of 2-aryl-and 2-alkyl-benzoxazoles in excellent yields, and is preferable to other methods for the preparation of benzoxazoles bearing electron withdrawing groups.In studying this transformation further, we were interested in examining the fate of N,O-diacylated 2-aminophenols in which the acyl groups on nitrogen and oxygen are not the same (1, R1 # R2).These mixed, N.0-diacylated Zaminophenols are of interest because they are produced in a number of synthetically useful reactions,3 and undergo a facile base-catalyzed acyl exchange ~eaction.~This paper reports the conversion of these mixed N,O-diacylated 2-aminophenols into benzoxazoles under the influence of TsOH.In addition to providing information concerning the potential synthetic utility of this conversion, this study has provided some mechanistic rationale for the conversion of N,O-diacylated 2-aminophenols to benzoxazoles under acidic reaction conditions.
The Environmental Footprint of Data Centers (2009)

Numerous evaluation metrics and standards are being proposed across industry and government to measure and monitor the energy efficiency of data centers. However, the energy use of data centers is just one aspect of the environmental impact. In this paper, we explore the overall environmental footprint of data centers beyond just energy efficiency. Building upon established procedures from the environmental sciences, we create an end-to-end life-cycle model of the environmental footprint of data centers across a diverse range of impacts. We test this model in the case study of a hypothetical 2.2-MW data center. Our analysis suggests the need for evaluation metrics that go beyond just operational energy use in order to achieve sustainable data centers.
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008)

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.
Overall survival in patients with re-excision of positive microscopic margins of limb and trunk wall soft tissue sarcoma operated outside of a reference center: a nationwide cohort analysis (2022)

Abstract Background This French nationwide NETSARC exhaustive prospective cohort aims to explore the impact of systematic re-excision (RE) as adjuvant care on overall survival (OS), local recurrence free survival (LRFS), and local and distant control (RFS) in patients with soft tissue sarcoma (STS) with positive microscopic margins (R1) after initial resection performed outside of a reference center. Methods Eligible patients had experienced STS surgery outside a reference center from 2010 to 2017, and had R1 margins after initial surgery. Characteristics and treatment comparisons used chi-square for categorical variables and Kruskall-Wallis test for continuous data. Survival distributions were compared in patients reexcised (RE) or not (No-RE) using a log-rank test. A Cox proportional hazard model was used for subgroup analysis. Results A total of 1,284 patients had experienced initial STS surgery outside NETSARC with R1 margins, including 1,029 patients with second operation documented. Among the latter, 698 patients experienced re-excision, and 331 were not re-excised. Characteristics were significantly different regarding patient age, tumor site, tumor size, tumor depth, and histotype in the population of patients re-excised (RE) or not (No-RE). The study identified RE as an independent favorable factor for OS (HR 0.36, 95%CI 0.23–0.56, p &lt;0.0001), for LRFS (HR 0.45, 95%CI 0.36–0.56, p &lt;0.0001), and for RFS (HR 0.35, 95%CI 0.26–0.46, p &lt;0.0001). Conclusion This large nationwide series shows that RE improved overall survival in patients with STS of extremities and trunk wall, with prior R1 resection performed outside of a reference center. RE as part of adjuvant care should be systematically considered. Level of evidence II
AC Temperature Compensation of Integrated Amplifiers (1962)

Abstract : Effort is expended towards an analytical basis for temperature compensation of the AC performance of transistor small-signal amplifiers. Described is a simple, accurate design theory in which this compensation is analytically determined by imposing the requirement of equality for the values of the individual small-signal fourpole parameters of the amplifier at its operating temperature limits. For values of T between -30 and +100 C in a typical noncompensated circuit, power gain, input impedance and output impedance vary by 99%, 71%, and 22%, respectively, while the comparable compensated circuit variation of each of these quantities is less than 9%. In an integrated circuit a single tapped resistance, properly selected, is the temperature sensitive element required for this compensation. (Author)
ChemInform Abstract: The Rupe Reaction Applied to 3‐(n‐Perfluorobutyl)‐alk‐2‐yn‐1‐ols: An Unexpected Route to 5‐n‐Perfluoropropylfuran‐3(2H)‐ones. (1986)

Abstract I‐Iydratisierung der Alkinole (I) ergibt die Ketone (II) und (III), von denen die Verbindungen (II) in (IV) umgelagert und zu den Furanonen (V) cyclisien werden.
Source-Degenerated Schmitt-Trigger-Based High-Performance Digital Logic for Flexible Organic Thin-Film Transistor Technologies (2023)

&lt;p&gt;A source-degenerated Schmitt-trigger logic is proposed. Based on this architecture, basic logic-gate architectures, ring oscillators, and edge-sensitive D-type flip-flops were fabricated using low-voltage p-channel organic thin-film transistors and integrated thin-film carbon resistors on flexible polymeric substrates. Mathematical analysis of this logic architecture indicates improved stability against charge-carrier-mobility degradation. A small-signal gain of 83 dB and a noise margin of 92 % of half the supply voltage have been measured. Owing to the intrinsic positive-feedback loop of the source-degenerated Schmitt-trigger logic, the design of the D-flip-flop enables a substantially smaller footprint and a considerably lower energy dissipation compared to previously reported unipolar organic-TFT-based D-flip-flop architectures. &lt;/p&gt;
An Optical Computed Tomography by Means of the Simplified Collimator in Near-infrared Region (2005)

The optical CT unit which was assembled with the laser diode working at the wavelength of 1.3 μm, and a glass optical fiber and a pin-hole with a diameter of the 100 μm yields the collimated near-infrared light through a scattering medium. Because the spatial collimator system needs no fast response time, a high sensitive Ge-PIN photodetector was employed the CT system. The optical CT image is allowed by use of near-infrared absorption characteristic. When the image construction of a grape was performed using projection data, so the comparatively good experimental results was obtained. The places of a grape seed was found without cutting. By means of the difference in characteristics of near-infrared absorption, the image of a cylindrical oil phantom in gelatin was reproduced.
Nucleation and growth in microcellular materials: Supercritical CO2 as foaming agent (1995)

Abstract Bubble growth is a phenomenon encountered in several commercially important processes. A mathematical model presented here describes the growth of bubbles during phase separation of an initially homogeneous polymer‐supercritical fluid mixture, triggered by a sudden pressure drop at constant temperature. It is a modification of the viscoelastic model of Arefmanesh and Advani (1991) in which the polymer is treated as a single relaxation‐time Maxwell fluid. Since properties of the polymer‐fluid mixture vary with the amount of fluid absorbed in the polymer (as a function of fluid pressure), the model needs to be used evaluating system properties as functions of temperature and pressure. The viscosity of polymer/fluid mixture, density of the mixture, diffusivity of CO 2 in the mixture, and relaxation time for poly (methyl methacrylate) swollen by supercritical carbon dioxide are, therefore, predicted as functions of CO 2 pressure and temperature using appropriate model equations at each step of the bubble growth simulation. The model predicts well the trends in equilibrium cell size vs. saturation pressure and temperature.
Identification of live attenuated vaccine candidates for tularemia prophylaxis (166.20) (2012)

Abstract Francisella tularensis (Ft) is the causative agent of a fatal human disease, tularemia. Ft was used in bioweapon programs in the past and is now classified as a category A agent owing to its possible use as a bioterror agent. Despite over a century since its discovery, an effective vaccine is yet to be developed. A live attenuated vaccine strain (LVS) exists; however, an unknown cause of attenuation and adverse effects in immunized individuals eluded its licensing as a vaccine. This study identified potential vaccine candidates for prophylaxis of respiratory tularemia. Five mutants of Ft LVS [FTL_0057, FTL_0291, FTL_0304, FTL_0325 and superoxide dismutase B (SodB)] were tested for their protective efficacy against Ft SchuS4 challenge. BALB/c mice were immunized intranasally (i.n.) with these mutants. Doses as high as 5x10(3) CFU (for SodB) or 1x10(7) CFU (for other mutants) did not cause any adverse reaction in immunized mice. A kinetic experiment revealed that the immunized mice cleared the mutants by days 14-21 post-immunization (PI). I.n. challenge with 100 CFU of Ft SchuS4 30 days PI protected 100% of mice immunized with SodB, FTL_0057, FTL_0291 and FTL_0325 mutants, while all the mice immunized with FTL_0304 mutant succumbed to infection. Mice that survived the challenge cleared Ft SchuS4 by day 45 post-challenge. This study has identified superior, safer and genetically defined live attenuated vaccine candidates for prevention of respiratory tularemia.
Incremental Visual-Inertial 3D Mesh Generation with Structural Regularities (2019)

Visual-Inertial Odometry (VIO) algorithms typically rely on a point cloud representation of the scene that does not model the topology of the environment. A 3D mesh instead offers a richer, yet lightweight, model. Nevertheless, building a 3D mesh out of the sparse and noisy 3D landmarks triangulated by a VIO algorithm often results in a mesh that does not fit the real scene. In order to regularize the mesh, previous approaches decouple state estimation from the 3D mesh regularization step, and either limit the 3D mesh to the current frame [1], [2] or let the mesh grow indefinitely [3], [4]. We propose instead to tightly couple mesh regularization and state estimation by detecting and enforcing structural regularities in a novel factor-graph formulation. We also propose to incrementally build the mesh by restricting its extent to the time-horizon of the VIO optimization; the resulting 3D mesh covers a larger portion of the scene than a per-frame approach while its memory usage and computational complexity remain bounded. We show that our approach successfully regularizes the mesh, while improving localization accuracy, when structural regularities are present, and remains operational in scenes without regularities.
Synthesis of Norfijimycin A with Activity against Mycobacterium tuberculosis (2016)

The total synthesis of norfijimycin A, a simplified analogue of the marine natural product fijimycin A, is described. Fijimycin A is a cyclic depsipeptide that has been shown to possess activity against methicillin-resistant Staphylococcus aureus. The natural product contains a rare N,β-dimethyl leucine unit with unknown stereochemistry at the β-carbon. To evaluate the importance of the β-methyl group for antimicrobial activity, we introduced N-methyl leucine into the natural product scaffold. The resulting norfijimycin A was shown to possess significant activity against Mycobacterium tuberculosis, the etiological agent of tuberculosis.
Evaluation of a Temperature-Sensitive Mutant of Respiratory Syncytial Virus in Adults (1971)

Journal Article Evaluation of a Temperature-Sensitive Mutant of Respiratory Syncytial Virus in Adults Get access Peter F. Wright, Peter F. Wright From the Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar John Mills V, John Mills V From the Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert M. Chanock Robert M. Chanock From the Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 124, Issue 5, November 1971, Pages 505–511, https://doi.org/10.1093/infdis/124.5.505 Published: 01 November 1971 Article history Received: 04 May 1971 Revision received: 28 June 1971 Published: 01 November 1971
Phenotypic analysis of bacterial colonies using laser light scatter and pattern-recognition techniques (2008)

The formation of bacterial colonies and biofilms requires coordinated gene expression, regulated cell differentiation, autoaggregation, and intercellular communication. Therefore colonies of bacteria have been recognized as multicellular organisms or "superorganisms." It has consequently been postulated that the phenotype of colonies formed by microorganisms can be automatically recognized and classified using optical systems capable of collecting information related to cellular pattern formation and morphology of colonies. Recently we have reported a first practical implementation of such a system, capable of noninvasive, label-free classification and recognition of pathogenic Listeria species. The design employed computer-vision and pattern-recognition techniques to classify scatter patterns produced by bacterial colonies irradiated with laser light. Herein we report our efforts to extend this system to other genera of bacteria such as <i>Salmonella</i>, <i>Vibrio</i>, <i>Staphylococcus</i>, and <i>E. coli</i>. Application of orthogonal moments, as well as texture descriptors for image feature extraction, provides high robustness in the presence of noise. An improved pattern classification scheme based on an SVM algorithm provides better results than the previously employed neural network system. Low error rates determined by cross-validation, reproducibility of the measurements, and overall robustness of the recognition system prove that the proposed technology can be implemented in automated devices for bacterial detection.