gebhart/patrepeval huggingface dataset:
GenK-Catalyzed C-6′ Methylation in the Biosynthesis of Gentamicin: Isolation and Characterization of a Cobalamin-Dependent Radical SAM Enzyme (2013)

The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-l-methionine (SAM) superfamily was previously predicted on the basis of bioinformatic analysis. A number of these are Cbl-dependent methyltransferases, but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp(3) carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that 1 equiv each of 5'-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. On the basis of these results, one mechanistic possibility for the GenK reaction can be ruled out, and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed.
ATM Is Required for Efficient Recombination between Immunoglobulin Switch Regions (2004)

Ataxia telangiectasia mutated (ATM) kinase is critical for initiating the signaling pathways that lead to cell cycle checkpoints and DNA double strand break repair. In the absence of ATM, humans and mice show a primary immunodeficiency that includes low serum antibody titers, but the role of ATM in antigen-driven immunoglobulin gene diversification has not been defined. Here, we show that although ATM is dispensable for somatic hypermutation, it is required for efficient class switch recombination (CSR). The defect in CSR is not due to alterations in switch region transcription, accessibility, DNA damage checkpoint protein recruitment, or short-range intra-switch region recombination. Only long-range inter-switch recombination is defective, indicating an unexpected role for ATM in switch region synapsis during CSR.
Programming applications for Microsoft Windows (1999)

An update to a bestselling, practical Windows programming guide, this title is a comprehensive inside look at the Windows 2000 and 64-bit Windows environments. It provides detailed system information that's unavailable elsewhere, including architectural and implementation details and sample code.
Operative Nephroscopy (1976)

Renal endoscopy has been made possible, practical and safe by technical advances in instrumentation. Operative nephroscopy has become a uniquely valuable adjunct to stone operations, especially for caliceal calculi, but does not permit the surgeon to dispense with operative x-rays. Furthermore, it has extended our horizons in the management of intrarenal hematuria and of low grade tumors of the renal collecting system. We suggest that the rigid right-angled nephroscope in use today be referred to as the Leadbetter nephroscope in recognition of that pioneer's original conception for its design.
An Evaluation of the Navy Periodontal Screening Examination (1977)

Ninety-eight young adult patients were examined and scored according to the criteria of the Navy Periodontal Screening Examination. The population examined had a 98% incidence of inflammatory periodontal disease. The relationship of the Navy Periodontal Disease Index and the Navy Plaque Index total scores was determined to +0.55 (P 0.01). The relationship of the gingival score of the NPDI and the NPI was found to be +0.75 (P 0.01). The Navy Plaque Index, like others reported, has a better relationship to a reversible index of inflammatory periodontal disease. The use of the NPDI total is recommended as an aid in determining treatment recommendations.
F-logic: a higher-order language for reasoning about objects, inheritance, and scheme (1989)

We propose a database logic which accounts in a clean declarative fashion for most of the “object-oriented” features such as object identity, complex objects, inheritance, methods, etc. Furthermore, database schema is part of the object language, which allows the user to browse schema and data using the same declarative formalism. The proposed logic has a formal semantics and a sound and complete resolution-based proof procedure, which makes it also computationally attractive.
Fine-grained channel access in wireless LAN (2010)

Modern communication technologies are steadily advancing the physical layer (PHY) data rate in wireless LANs, from hundreds of Mbps in current 802.11n to over Gbps in the near future. As PHY data rates increase, however, the overhead of media access control (MAC) progressively degrades data throughput efficiency. This trend reflects a fundamental aspect of the current MAC protocol, which allocates the channel as a single resource at a time.
Dynamic properties of actin. Structural changes induced by beryllium fluoride. (1994)

Beryllium fluoride (BeFx) has been widely used as a phosphate analogue in nucleotide-binding proteins. It was found to bind tightly to F- but not G-actin (Combeau C., and Carlier M. F. (1988) J. Biol. Chem. 263, 17429-17436) and to affect the three-dimensional structure of filaments by stabilizing the subdomain 2 region of the actin promoter (Orlova, A., and Egelman, E. H. (1992) J. Mol. Biol. 227, 1043-1053). In this work we examined the BeFx-induced structural and functional changes in G- and F-actin by using proteolysis, chemical modifications, ATPase, and in vitro motility assays. The results of proteolysis studies show that BeFx binds also to MgADP-G-actin and renders its subdomain 2 region more similar to that in MgATP-G-actin. This is manifested in enhanced subtilisin and decreased tryptic digestions in subdomain 2 of G-actin. BeFx had a strong effect on the proteolysis of MgADP-F-actin: both the tryptic and subtilisin digestions in subdomain 2 were completely inhibited. Significant protection against proteolysis in this region was observed even at 1:14 molar ratios of BeFx to actin indicating cooperative effects on the structure of the actin filament. A similar although milder effect of phosphate on the proteolysis of F-actin suggests that BeFx acts as a phosphate analogue in this system. BeFx also induces changes in the subdomain 1 region of F-actin. This is revealed via reduced rates of Cys-374 alkylation with 7-diethylamino-3-(4'-maleimidylphenyl)-4-methylcoumarin and an increased subtilisin cleavage near the C terminus of actin in the presence of BeFx. The BeFx-induced structural changes in actin have little effect on its interactions with myosin. BeFx inhibits only slightly the actin-activated ATPase activity of S1 by decreasing Vmax without affecting KM. Additionally, the binding of BeFx to actin does not change the sliding velocity of actin filaments in the in vitro motility assays. The BeFx-induced specific and distinct changes in G- and F-actin point to the dynamic nature of actin structure and the local differences between monomeric and polymeric forms of actin.
The Bordoni Relaxation in High Purity Copper Single Crystals at Low Frequencies (1996)

The aim of this work is to explore the low-frequency spectrum of 5N pure copper in a subresonant pendulum which allows "in situ" cycled torsion deformation and recovery. Samples were taken from the same single crystals used for ultrasonic attenuation studies in order to compare both results in an Arrhenius plot. In one sample prepared by electro-erosion, polished with nitric acid, recovered 4 hours at 650°C in preliminary vacuum and 1,4 and 9% deformed at room temperature, the spectra show a main Bordoni peak whose height increases with deformation, and additional peaks in the 40-65K range, as important as the Bordoni peak, which are due to impurities generated during the preparation of the sample. In an uncontaminated sample cut by diamond disk, polished with a mixture of nitric, phosphoric and glacial acetic acids, and water, recovered in 5.10-6 mmHg vacuum, deformed 3 and 5%, the internal friction spectra show the main Bordoni peak as the principal effect, accompanied by a defect modulus. The study of the influence of different parameters such as the amount of deformation, the amplitude and frequency of oscillation, the temperature rate and the recoveries may be an interesting contribution to the characterization of the Bordoni peak.
The Quantitative Analysis of Super-Low Phosphorus Content of SUS316L Type Stainless Steel With EPMA Calibration Curve Method (2008)

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008
Heterogenous humoral and cellular immune responses with distinct trajectories post-SARS-CoV-2 infection in a population-based cohort (2022)

To better understand the development of SARS-CoV-2-specific immunity over time, a detailed evaluation of humoral and cellular responses is required. Here, we characterize anti-Spike (S) IgA and IgG in a representative population-based cohort of 431 SARS-CoV-2-infected individuals up to 217 days after diagnosis, demonstrating that 85% develop and maintain anti-S responses. In a subsample of 64 participants, we further assess anti-Nucleocapsid (N) IgG, neutralizing antibody activity, and T cell responses to Membrane (M), N, and S proteins. In contrast to S-specific antibody responses, anti-N IgG levels decline substantially over time and neutralizing activity toward Delta and Omicron variants is low to non-existent within just weeks of Wildtype SARS-CoV-2 infection. Virus-specific T cells are detectable in most participants, albeit more variable than antibody responses. Cluster analyses of the co-evolution of antibody and T cell responses within individuals identify five distinct trajectories characterized by specific immune patterns and clinical factors. These findings demonstrate the relevant heterogeneity in humoral and cellular immunity to SARS-CoV-2 while also identifying consistent patterns where antibody and T cell responses may work in a compensatory manner to provide protection.
Bioenergy crop greenhouse gas mitigation potential under a range of management practices (2014)

Abstract Perennial grasses have been proposed as viable bioenergy crops because of their potential to yield harvestable biomass on marginal lands annually without displacing food and to contribute to greenhouse gas ( GHG ) reduction by storing carbon in soil. Switchgrass, miscanthus, and restored native prairie are among the crops being considered in the corn and agricultural regions of the Midwest and eastern United States. In this study, we used an extensive dataset of site observations for each of these crops to evaluate and improve the DayCent biogeochemical model and make predictions about how both yield and GHG fluxes would respond to different management practices compared to a traditional corn‐soy rotation. Using this model‐data integration approach, we found 30–75% improvement in our predictions over previous studies and a subsequent evaluation with a synthesis of sites across the region revealed good model‐data agreement of harvested yields ( r 2 &gt; 0.62 for all crops). We found that replacement of corn‐soy rotations would result in a net GHG reduction of 0.5, 1.0, and 2.0 Mg C ha −1 yr −1 with average annual yields of 3.6, 9.2, and 17.2 Mg of dry biomass per year for native prairie, switchgrass, and miscanthus respectively. Both the yield and GHG balance of switchgrass and miscanthus were affected by harvest date with highest yields occurring near onset of senescence and highest GHG reductions occurring in early spring before the new crops emergence. Addition of a moderate length rotation (10–15 years) caused less than a 15% change to yield and GHG balance. For policy incentives aimed at GHG reduction through onsite management practices and improvement of soil quality, post‐senescence harvests are a more effective means than maximizing yield potential.
Scatter factor promotes motility of human glioma and neuromicrovascular endothelial cells (1998)

Malignant gliomas are characterized by rapid growth, infiltration of normal brain tissue, and high levels of tumor-associated angiogenesis. The genetic and local environmental tissue factors responsible for the malignant progression from low to high grade gliomas and the highly malignant behavior of glioblastomas are not well understood. In a study of 77 human brain tissue extracts, high grade (III-IV) tumors had significantly greater scatter factor (SF) content than did low grade tumors or non-neoplastic tissue. To investigate the potential significance of SF accumulation in gliomas, we measured the effects of SF on DNA synthesis and motility of cultured human glioma cell lines. SF stimulated DNA synthesis in 7/10 glioma cell lines and in 3/3 neuromicrovascular endothelial cell (NMVEC) lines, consistent with our previous report that SF stimulated cell proliferation of a few human glioma cell lines. SF markedly stimulated the chemotactic migration of 10/10 glioma cell lines as well as 3/3 NMVEC lines. In addition, SF stimulated the 2-dimensional migration of glioma cells on culture surfaces coated with specific extracellular matrix molecules (collagen i.v., laminin, and fibronection). As expected based on these biologic responses to SF, 10/10 glioma lines and 4/4 NMVEC lines expressed mRNA for c-met, the SF receptor. To assess the possible in vivo significance of these migration assays, we compared the chemotactic response of a glioma cell line to human brain cyst fluids and tumor extracts that contained high or low SF concentrations. Fluids and extracts with high SF content tended to induce higher levels of chemotactic migration than did fluids and extracts with low SF content. Addition of anti-SF monoclonal antibody (MAb) inhibited migration induced by fluids and extracts with high SF content by about 30-50%.
Metal-Assisted Chemical Etching and Electroless Deposition for Fabrication of Hard X-ray Pd/Si Zone Plates (2020)

Zone plates are diffractive optics commonly used in X-ray microscopes. Here, we present a wet-chemical approach for fabricating high aspect ratio Pd/Si zone plate optics aimed at the hard X-ray regime. A Si zone plate mold is fabricated via metal-assisted chemical etching (MACE) and further metalized with Pd via electroless deposition (ELD). MACE results in vertical Si zones with high aspect ratios. The observed MACE rate with our zone plate design is 700 nm/min. The ELD metallization yields a Pd density of 10.7 g/cm 3 , a value slightly lower than the theoretical density of 12 g/cm 3 . Fabricated zone plates have a grid design, 1:1 line-to-space-ratio, 30 nm outermost zone width, and an aspect ratio of 30:1. At 9 keV X-ray energy, the zone plate device shows a first order diffraction efficiency of 1.9%, measured at the MAX IV NanoMAX beamline. With this work, the possibility is opened to fabricate X-ray zone plates with low-cost etching and metallization methods.
Hybrid-view programming of nuclear fusion simulation code in the PGAS parallel programming language XcalableMP (2014)

Recently, the Partitioned Global Address Space (PGAS) parallel programming model has emerged as a usable distributed memory programming model. XcalableMP (XMP) is a PGAS parallel programming language that extends base languages such as C and Fortran with directives in OpenMP-like style. XMP supports a global-view model that allows programmers to define global data and to map them to a set of processors, which execute the distributed global data as a single thread. In XMP, the concept of a coarray is also employed for local-view programming. In this study, we port Gyrokinetic Toroidal Code - Princeton (GTC-P), which is a three-dimensional PIC code developed at Princeton University to study the microturbulence phenomenon in magnetically confined fusion plasmas, to XMP as an example of hybrid memory model coding with the global-view and local-view programming models. In local-view programming, the coarray notation is simple and intuitive compared with Message Passing Interface (MPI) programming while the performance is comparable to that of the MPI version. Thus, because the global-view programming model is suitable for expressing the data parallelism for a field of grid space data, we implement a hybrid-view version using a global-view programming model to compute the field and a local-view programming model to compute the movement of particles. The performance is degraded by 5-25% compared with the original MPI version, but the hybrid-view version facilitates more natural data expression for static grid space data (in global-view model) and dynamic particle data (in local-view model), and it also increases the readability of the code for higher productivity.
Circulating CD21 low B cells in common variable immunodeficiency resemble tissue homing, innate-like B cells (2009)

The homeostasis of circulating B cell subsets in the peripheral blood of healthy adults is well regulated, but in disease it can be severely disturbed. Thus, a subgroup of patients with common variable immunodeficiency (CVID) presents with an extraordinary expansion of an unusual B cell population characterized by the low expression of CD21. CD21(low) B cells are polyclonal, unmutated IgM(+)IgD(+) B cells but carry a highly distinct gene expression profile which differs from conventional naïve B cells. Interestingly, while clearly not representing a memory population, they do share several features with the recently defined memory-like tissue, Fc receptor-like 4 positive B cell population in the tonsils of healthy donors. CD21(low) B cells show signs of previous activation and proliferation in vivo, while exhibiting defective calcium signaling and poor proliferation in response to B cell receptor stimulation. CD21(low) B cells express decreased amounts of homeostatic but increased levels of inflammatory chemokine receptors. This might explain their preferential homing to peripheral tissues like the bronchoalveolar space of CVID or the synovium of rheumatoid arthritis patients. Therefore, as a result of the close resemblance to the gene expression profile, phenotype, function and preferential tissue homing of murine B1 B cells, we suggest that CD21(low) B cells represent a human innate-like B cell population.
Reversible and irreversible colossal barocaloric effects in plastic crystals (2019)

Colossal barocaloric effects were observed in four species of plastic crystals, and two displayed the reversibility required for cooling devices.
A data interchange standard for clinical neurophysiology. (1993)

A Standard Specification for Transferring Digital Neurophysiological Data Between Independent Computer Systems (Designation E 1467-92) has been developed. The specification defines a common representation of all of the data associated with a complete clinical study, including digitized neurophysiological waveforms, textual annotations and interpretive reports. Patterned after existing, related healthcare data interchange standards, it will facilitate data interchange between neurophysiological instruments, computer systems within the neurophysiology laboratory, other information systems in the hospital, and outside healthcare facilities or research laboratories.
Recombination coefficients of GaN-based laser diodes (2011)

We measure the charge carrier recombination coefficients of InGaN quantum wells by analyzing the dynamical properties of (Al,In)GaN laser diodes emitting in the violet spectral range. Relaxation oscillations and turn-on delays are fitted to a rate equation model including a charge carrier density dependent recombination rate. Using optical gain spectroscopy we can directly determine the injection efficiency of the devices and thereby separate the effect of charge carrier leakage from that of carrier recombination. We find a third-order recombination coefficient of (4.5±0.9)×10-31cm6s-1 which is in agreement with theoretical predictions for phonon- and alloy-disorder-assisted Auger scattering.
Diamond‐based DNA sensors: surface functionalization and read‐out strategies (2009)

Abstract This article reviews the current state‐of‐the art of diamond‐based DNA sensors. Some general concepts involved in biosensors are introduced and applied to DNA sensors. The properties of chemically vapor deposited (CVD) diamond relevant for this application are summed up, with special attention for the stability and bio‐compatibility of the material. Several routes to functionalize the diamond surface are considered. The physical properties of the obtained DNA layers are discussed in terms of surface density and molecular conformation. Possible read‐out strategies are evaluated, including optical and electronic sensing. With diamond‐based DNA sensors, real‐time and label‐free sensing is achieved. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
A Dynamic Binary Translation Framework Based on Page Fault Mechanism in Linux Kernel (2010)

Dynamic binary translation and optimization is one of the most important essential techniques for computing system virtualization. This paper proposes a new dynamic translation framework for co-designed virtual machines. It generates and handles translation requests based on page fault mechanism provided in Linux kernel. In this new framework, the translation of guest codes and the execution of translated codes can be performed on different processors in parallel. The framework support the coprocessor translating guest code pages and the host CPU executing translated pages simultaneously, thus the translator becomes more efficient. The paper also presents a qualitative analysis of the time cost in our framework on an x86-ARM co-designed dynamic binary translation system, and suggests that the performance of this framework can be further improved if shared memory between host CPU and coprocessor is used. The framework can also be used in a dynamic binary translator on multi-core platforms.
Charakterisierung des tribologischen Verhaltens von keramischen Gleitpaarungen mit moderner Oberflächenanalytik (1991)

Abstract Es werden Ergebnisse von Modellverschleißprüfungen an artgleichen keramischen Gleitpaarungen in einer Stift/Scheibe‐Anordnung bei Festkörperreibung vorgestellt. Die Temperatur wurde zwischen 22 °C und 1000 °C und die Gleitgeschwindigkeit zwischen 0,03 m/s und 3 m/s variiert. Die Versuche wurden in Laboratmosphäre unter konstanten Lasten von 1 N und 10 N durchgeführt. Für die Charakterisierung der Ausgangswerkstoffe, zur Aufklärung von Verschleißhochlage/‐tieflage‐Übergängen sowie der Verschleißmechanismen und der Verschleißerscheinungsformen wurden verschiedene oberflächenanalytische Verfahren – u. a. Lichtmikroskopie. Rasterelektronenmikroskopie. Transmissionselektronenmikroskopie. Infrarot‐Spektroskopie. Elektronenstrahl‐Mikroanalyse, Röntgenbeugung. Auger‐Elektronen‐Spektroskopie und Röntgen‐Photoelektronen‐Spektroskopie – eingesetzt. Auf der Grundlage oberflächenanalytischer Untersuchungen wurden die Werkstoffe tribologisch optimiert. Mit den neu entwickelten Werkstoffen konnten die Reibungszahlen und/oder die Verschleißraten auf Werte gesenkt werden, Wie sie vor allem bei extremen Beanspruchungsbedingungen (hohe Temperatur, aggressives Umgebungsmedium und Festkörperreibung) von anderen Werkstoffgruppen nicht erreicht werden.