gebhart/patrepeval huggingface dataset:
Structure and conformation of the hypermodified purine nucleoside wyosine and its isomers: A comparison of coupling constants and distance geometry solutions (1991)

Abstract The structural determination of modified mononucleosides is important for understanding the chemistry, structure and functional changes that they impart to the nucleic acids in which they occur. Empirical analyses of J ( HH ) couplings have been used to describe nucleoside conformational equilibria for the glycosidic angle ( syn ‐ anti ), the C‐4′C‐5′ exocyclic rotamers ( gauche +, gauche − and trans ) and the sugar pucker (N–S). Distance geometry calculations with distance constraints determined from nuclear Overhauser effects (NOE) should provide equally satisfactory structural information. Proton and carbon chemical shifts and coupling constants were used to describe structural parameters for the tricyclic nucleosides wyosine, 4,9‐dihydro‐4,6‐dimethyl‐9‐oxo‐3‐(β‐D‐ribofuranosyl)imidazo(1,2‐ a )purine, and three of its isomers. Using distance geometry calculations with the 14‐19 observed NOEs per nucleoside as distance constraints, multiple structures could be produced with less than 1 Å relative mean standard deviation for the positioning of all atoms. The two methods of structural determination were consistent in their qualitative determination of syn ‐ anti conformation and sugar pucker.
Indium as a surfactant: Effects on growth morphology and background impurity in GaN films grown by ammonia-assisted molecular beam epitaxy (2022)

We report on the improvement of the surface morphology of c-plane GaN films grown at high growth rates (∼1 µm/h) using ammonia molecular beam epitaxy through a series of growth optimizations as well as the introduction of indium as a surfactant. The indium surfactant was expected to help with the adatom mobility and, thus, provide smoother growth surfaces. Through a combination of varying V/III ratios, In flux, and growth temperatures, an optimal condition for surface morphology, characterized by atomic force microscopy, was achieved. At higher Ga fluxes for fast growth rates (∼1 µm/h and beam equivalent pressures of ∼5 × 10−7 Torr), higher ammonia flows were necessary to preserve the surface morphology. In addition, indium was an effective surfactant—reducing the roughness and improving the overall surface morphology. However, excessive indium causes the surface morphology to degrade, potentially due to the enhancement of the Ga desorption from the surface as a result of the reaction of indium with ammonia for high indium fluxes. The indium surfactant also resulted in a reduction of background Si impurity concentrations in the film. These effects allow for the growth of thick drift layers with low background dopant concentrations for vertical GaN power devices.
Extracellular adenosine regulates colitis through effects on lymphoid and nonlymphoid cells (2014)

Adenosine is a purine metabolite that can mediate anti-inflammatory responses in the digestive tract through the A(2A) adenosine receptor (A(2A)AR). We examined the role of this receptor in the control of inflammation in the adoptive transfer model of colitis. Infection of A(2A)AR(-/-) mice with Helicobacter hepaticus increased colonic inflammation scores compared with uninfected A(2A)AR controls. Comparison of T cell subsets in wild-type and A(2A)AR(-/-) mice revealed differences in markers associated with activated helper T (Th) cells and regulatory T (Treg) cells. Previous studies showed that expression of A(2A)AR on CD45RB(HI) and CD45RB(LO) Th cells is essential for the proper regulation of colonic inflammation. Adoptive transfer of CD45RB(HI) with CD45RB(LO) from wild-type mice into RAG1(-/-)/A(2A)AR(-/-) mice induced severe disease within 3 wk, although transfer of the same subsets into RAG1(-/-) mice does not induce colitis. This suggests that the presence of A(2A)AR on recipient cells is also important for controlling colitis. To investigate the role of A(2A)AR in myeloid cells, chimeric recipients were generated by injection of bone marrow from RAG1(-/-) or RAG1(-/-)/A(2A)AR(-/-) mice into irradiated RAG1(-/-) mice. After adoptive transfer, these recipients did not develop colitis, regardless of A(2A)AR expression by the donor. Together, our results suggest that the control of inflammation in vivo is dependent on A(2A)AR signaling through multiple cell types that collaborate in the regulation of colitis by responding to extracellular adenosine.
ChemInform Abstract: Transition Metal Complexes Containing Arsenic‐Sulfur and Phosphorus‐ Sulfur Ligands (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Distributed Robust Power Minimization for the Downlink of Multi-Cloud Radio Access Networks (2017)

Conventional cloud radio access networks (CRANs) assume single cloud processing and treat inter-cloud interference as background noise. This paper considers the downlink of a multi-CRAN where each cloud is connected to several base-stations (BSs) through limited-capacity wireline backhaul links. The set of BSs connected to each cloud, called cluster, serves a set of pre-known mobile users. The performance of the system becomes therefore a function of both inter-cloud and intra-cloud interference, as well as the compression schemes of the limited capacity backhaul links. This paper assumes independent compression scheme and imperfect channel state information (CSI) where the CSI errors belong to an ellipsoidal bounded region. The problem of interest becomes one of minimizing the network total transmit power subject to BS power and quality of service constraints, as well as backhaul capacity and CS! error constraints. This paper suggests solving the problem using the alternating direction method of multipliers (ADMMs). One highlight of this paper is that the proposed ADMM-based algorithm can be implemented in a distributed fashion across the multi-cloud network by allowing a limited amount of information exchange between the coupled clouds. Simulation results show that the proposed distributed algorithm provides a similar performance to the centralized algorithm in a reasonable number of iterations.
All Fiber Technology for High-Energy Petawatt Front End Laser Systems (2003)

We are developing an all fiber front end for the next generation high-energy petawatt (HEPW) laser at Lawrence Livermore National Laboratory (LLNL). The ultimate goal of the LLNL HEPW effort is to generate 5-kJ pulses capable of compression to 5ps at 1053nm, enabling advanced x-ray backlighters and possible demonstration of fast ignition. We discuss the front-end of the laser design from the fiber master oscillator, which generates the mode-locked 20nm bandwidth initial pulses through the 10mJ output of the large flattened mode (LFM) fiber amplifier. Development of an all fiber front end requires technological breakthroughs in the key areas of the master oscillator and fiber amplification. Chirped pulse amplification in optical fibers has been demonstrated to 1mJ. Further increase is limited by the onset of stimulated Raman scattering (SRS). We have recently demonstrated a new flattened mode fiber technology, which reduces peak power for a given energy and thus the onset of SRS. Controlled experiments with 1st generation fibers yielded 0.5mJ of energy while significantly increasing the point at which nonlinear optical effects degrade the amplified pulse. In this paper we will discuss our efforts to extend this work to greater than 20mJ using our large flattened mode fiber amplifier.
Proactive pedestrian safety evaluation at urban road network level, an experience in Kolkata City, India (2021)

In developing nations, road traffic crashes involving pedestrians have become a foremost worry. Presently, most of the road safety assessment projects and selection of interventions are still restricted to traditional methods that depend on historical crash data. However, in low and middle-income countries such as India, the availability, reliability, and accuracy of crash data are uncertain. Alternatively, Post Encroachment Time (PET) has added attention as a proximal indicator to examine pedestrian-vehicular potential crashes and address pedestrian risk under mixed traffic conditions. Hence, it will be meaningful to examine if the PET is a good substitute for pedestrian-vehicular crashes and if so, what built environment and pedestrian-level factors influence PET. In this background, the present study establishes a mathematical association between the average PET value of the urban road network level and actual crashes. Afterward, multiple linear regression models are developed to study the impact of the built environment, traffic parameters, and pedestrian-level attributes on PET. The outcomes indicate that vehicle speed, lack of enforcement, absence of traffic signal (for traffic as well as pedestrians), land use type, slum population, inadequate sight distance, pedestrian's state of crossing, and pedestrian's risky crossing behaviour substantially affect the average PET at road network-level.
Pathology-Driven Comprehensive Proteomic Profiling of the Prostate Cancer Tumor Microenvironment (2017)

Prostate cancer is the second most common cancer in men worldwide. Gleason grading is an important predictor of prostate cancer outcomes and is influential in determining patient treatment options. Clinical decisions based on a Gleason score of 7 are difficult as the prognosis for individuals diagnosed with Gleason 4+3 cancer is much worse than for those diagnosed with Gleason 3+4 cancer. Laser capture microdissection (LCM) is a highly precise method to isolate specific cell populations or discrete microregions from tissues. This report undertook a detailed molecular characterization of the tumor microenvironment in prostate cancer to define the proteome in the epithelial and stromal regions from tumor foci of Gleason grades 3 and 4. Tissue regions of interest were isolated from several Gleason 3+3 and Gleason 4+4 tumors using telepathology to leverage specialized pathology expertise to support LCM. Over 2,000 proteins were identified following liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of all regions of interest. Statistical analysis revealed significant differences in protein expression (>100 proteins) between Gleason 3 and Gleason 4 regions-in both stromal and epithelial compartments. A subset of these proteins has had prior strong association with prostate cancer, thereby providing evidence for the authenticity of the approach. Finally, validation of these proteins by immunohistochemistry has been obtained using an independent cohort of prostate cancer tumor specimens.<b>Implications:</b> This unbiased strategy provides a strong foundation for the development of biomarker protein panels with significant diagnostic and prognostic potential. <i>Mol Cancer Res; 15(3); 281-93. ©2017 AACR</i>.
Lidar-Radiometer Inversion Code (LIRIC) for the retrieval of vertical aerosol properties from combined lidar/radiometer data: development and distribution in EARLINET (2015)

Abstract. This paper presents a detailed description of LIRIC (LIdar-Radiometer Inversion Code) algorithm for simultaneous processing of coincident lidar and radiometric (sun photometric) observations for the retrieval of the aerosol concentration vertical profiles. As the lidar/radiometric input data we use measurements from European Aerosol Research Lidar Network (EARLINET) lidars and collocated sun-photometers of Aerosol Robotic Network (AERONET). The LIRIC data processing provides sequential inversion of the combined lidar and radiometric data by the estimations of column-integrated aerosol parameters from radiometric measurements followed by the retrieval of height-dependent concentrations of fine and coarse aerosols from lidar signals using integrated column characteristics of aerosol layer as a priori constraints. The use of polarized lidar observations allows us to discriminate between spherical and non-spherical particles of the coarse aerosol mode. The LIRIC software package was implemented and tested at a number of EARLINET stations. Intercomparison of the LIRIC-based aerosol retrievals was performed for the observations by seven EARLNET lidars in Leipzig, Germany on 25 May 2009. We found close agreement between the aerosol parameters derived from different lidars that supports high robustness of the LIRIC algorithm. The sensitivity of the retrieval results to the possible reduction of the available observation data is also discussed.
First observation of forces on three-level atoms in Raman resonant standing-wave optical fields (1992)

A sodium atomic beam is deflected by two optical standing-wave fields which excite near resonance Raman transitions. Observed deflections are consistent with theoretical predictions of a long-range dc component of the force on a three-level atom in the \ensuremath{\Lambda} configuration. The low laser intensities (and small detunings) used, combined with observed evidence of damping in the three-level \ensuremath{\Lambda} system, may ultimately lead to the design of high-density, all optical traps wherein the atoms would be mostly in the dark state.
Supplementary Figure S5 from Preclinical Antitumor Efficacy of BAY 1129980—a Novel Auristatin-Based Anti-C4.4A (LYPD3) Antibody–Drug Conjugate for the Treatment of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Binding of C4.4A-Ab.&lt;/p&gt;
Rate Splitting with Finite Constellations: The Benefits of Interference\n Exploitation vs Suppression (2019)

Rate-Splitting (RS) has been proposed recently to enhance the performance of\nmulti-user multiple-input multiple-output (MU-MIMO) systems. In RS, a user\nmessage is split into a common and a private part, where the common part is\ndecoded by all users, while the private part is decoded only by the intended\nuser. In this paper, we study RS under a phase-shift keying (PSK) input\nalphabet for multi-user multi-antenna system and propose a constructive\ninterference (CI) exploitation approach to further enhance the sum-rate\nachieved by RS under PSK signaling. To that end, new analytical expressions for\nthe ergodic sum-rate are derived for two precoding techniques of the private\nmessages, namely, 1) a traditional interference suppression zero-forcing (ZF)\nprecoding approach, 2) a closed-form CI precoding approach. Our analysis is\npresented for perfect channel state information at the transmitter (CSIT), and\nis extended to imperfect CSIT knowledge. A novel power allocation strategy,\nspecifically suited for the finite alphabet setup, is derived and shown to lead\nto superior performance for RS over conventional linear precoding not relying\non RS (NoRS). The results in this work validate the significant sum-rate gain\nof RS with CI over the conventional RS with ZF and NoRS.\n
Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system (2022)

Bacteriophage exclusion ('BREX') phage restriction systems are found in a wide range of bacteria. Various BREX systems encode unique combinations of proteins that usually include a site-specific methyltransferase; none appear to contain a nuclease. Here we describe the identification and characterization of a Type I BREX system from Acinetobacter and the effect of deleting each BREX ORF on growth, methylation, and restriction. We identified a previously uncharacterized gene in the BREX operon that is dispensable for methylation but involved in restriction. Biochemical and crystallographic analyses of this factor, which we term BrxR ('BREX Regulator'), demonstrate that it forms a homodimer and specifically binds a DNA target site upstream of its transcription start site. Deletion of the BrxR gene causes cell toxicity, reduces restriction, and significantly increases the expression of BrxC. In contrast, the introduction of a premature stop codon into the BrxR gene, or a point mutation blocking its DNA binding ability, has little effect on restriction, implying that the BrxR coding sequence and BrxR protein play independent functional roles. We speculate that elements within the BrxR coding sequence are involved in cis regulation of anti-phage activity, while the BrxR protein itself plays an additional regulatory role, perhaps during horizontal transfer.
Mastocytosis: a paradigmatic example of a rare disease with complex biology and pathology. (2013)

Mastocytosis is a rare disease characterized by abnormal expansion and accumulation of tissue mast cells (MC) in one or multiple organs. In most adult patients, systemic mastocytosis (SM) is diagnosed. Based on histopathological findings and organ damage, SM is divided into indolent SM (ISM), smoldering SM (SSM), SM with an associated hematologic non-MC-lineage disease (SM-AHNMD), aggressive SM (ASM), and MC leukemia (MCL). The clinical course and prognosis vary greatly among these groups of patients. In all variants of SM and most patients, neoplastic cells display the KIT mutation D816V. This suggests that additional KIT-independent molecular defects cause progression. Indeed, additional oncogenic lesions, including RAS- and TET2 mutations, have recently been identified in advanced SM. In patients with SM-AHNMD, such additional lesions are often detectable in the 'AHNMD-component' of the disease. Clinically relevant symptoms of SM result from i) malignant MC infiltration and the subsequent organ damage seen in advanced SM and/or ii) the release of pro-inflammatory and vasoactive mediators from MC, found in all disease-variants. Therapy of SM has to be adjusted to the individual situation in each patient. In ISM, the aim is to control mediator release and mediator effects. In advanced SM, a major goal is to control MC expansion by using conventional drugs or novel targeted drugs directed against mutant forms of KIT and/or other pro-oncogenic kinase-targets. In rapidly progressing ASM, MCL and drug-resistant AHNMD, chemotherapy and subsequent stem cell transplantation has to be considered.
Investigations on infrared-channel-image quality improvements for multispectral imaging (2018)

Abstract The improvement of image quality in the infrared range on silicon-based sensors is one major topics using these long wavelength channels for geometric measurements. The reason behind the bad quality of infrared images in comparison with the visible sampling range is explained by the wavelength response dependency of the silicon. Photons are able to either to pass the sensitive range of the pixel or can tunnel to the neighbor pixel. This effect leads to blurred images, which will not only increase the uncertainty of measurement, but also the aesthetical quality of the image. In this paper, methods to improve the image quality using blind convolution as well as a special infrared focusing to improve the sharpness will be presented.
Six-component wave type fingerprinting and filtering (2023)

We present a technique to automatically classify the wave type of seismic phases that are recorded on a single six-component recording station (measuring both three components of translational and rotational ground motion) at the earth's surface. We make use of the fact that each wave type leaves a unique 'fingerprint' in the six-component motion of the sensor. This fingerprint can be extracted by performing an eigenanalysis of the data covariance matrix, similar to conventional three-component polarization analysis. To assign a wave type to the fingerprint extracted from the data, we compare it to analytically derived six-component polarization models that are valid for pure-state plane wave arrivals. For efficient classification, we make use of the supervised machine learning method of support vector machines that is trained using data-independent, analytically-derived six-component polarization models. This enables the rapid classification of seismic phases in a fully automated fashion, even for large data volumes, such as encountered in land-seismic exploration or ambient noise seismology. Once the wave-type is known, additional wave parameters (velocity, directionality, and ellipticity) can be directly extracted from the six-component polarization states without the need to resort to expensive optimization algorithms.We illustrate the benefits of our approach on various real and synthetic data examples for applications such as automated phase picking, aliased ground-roll suppression in land-seismic exploration, and the rapid close-to real time extraction of surface wave dispersion curves from single-station recordings of ambient noise. Additionally, we argue that an initial step of wave type classification is necessary in order to successfully apply the common technique of extracting phase velocities from combined measurements of rotational and translational motion.
Risk Analysis of Aseptic Meningitis after Measles-Mumps-Rubella Vaccination in Korean Children by Using a Case-Crossover Design (2003)

Epidemiologic study of a vaccine's adverse events is not easy; so many countries have no reliable data. Vaccines containing the Urabe or Hoshino strain have been withdrawn from use in several countries. However, the data are not strong enough to form the basis of a recommendation not to use specific strains. The authors used a case-crossover design to estimate the relative risk of aseptic meningitis in children after receiving the measles-mumps-rubella vaccine in Korea. Study subjects were hospitalized children aged 8-36 months who had aseptic meningitis in 1998. Cases were confirmed by hospital chart reviews using previously defined criteria. Through a telephone survey, the authors obtained vaccination date and place information from parents' vaccination records. Study results showed that no significant risk was associated with the Jeryl Lynn or Rubini strain of the vaccine (relative risk = 0.6, 95% confidence interval (CI): 0.18, 1.97). For the Urabe or Hoshino strain, the relative risk was 5.5 (95% CI: 2.6, 11.8); the risk increased in the third week after vaccination (relative risk = 15.6, 95% CI: 5.9, 41.2) and was elevated until the sixth week. The case-crossover design was useful in confirming the risk of acute adverse events after receiving vaccines.
Fluidity Evolution of an Al-10%B<sub>4</sub>C Metal Matrix Composite (2007)

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