gebhart/patrepeval huggingface dataset:
Semi-automated assembly of high-quality diploid human reference genomes (2022)

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society<sup>1,2</sup>. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals<sup>3,4</sup>. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome<sup>5</sup>. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity<sup>6</sup>. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.
Retinal Arteriolar Diameter and Risk for Hypertension (2004)

Smaller retinal arteriolar diameters are independently associated with incident hypertension, which suggests that arteriolar narrowing may be linked to the occurrence and development of hypertension.
Velocity-resolved single-pass volumetric retinal flow imaging spectral domain optical coherence tomography (2009)

Advances in Doppler spectral domain optical coherence tomography (SDOCT) have demonstrated several image acquisition schemes that enable real-time, high-resolution, volumetric display of blood flow maps. Current generation Doppler SDOCT systems use phase differences between sequential A-scans acquired at a single spatial position to calculate the velocity of moving scatterers. Recently, several methods for optical angiography have been developed which resolve moving scatterers by imposing a spatial frequency modulation across a lateral scan dimension. The carrier frequency is generated by adding a reference phase delay using a moving reference arm or an off-pivot scanning beam. The resulting data is spatial frequency windowed such that all moving scatterers (flow) modulating the carrier frequency can be separated from non-moving scatterers (structure). However, spatial frequency modulation requires precise synchronization of the reference arm delay with B-scan acquisition and multiple B-scans are required to image bidirectional flow into and out-of the A-scan axis. Here we demonstrate single-pass volumetric bidirectional blood flow imaging (SPFI) SDOCT using a modified Hilbert transform without the use of spatial frequency modulation. By windowing low-spatial frequency scatterers across a B-scan, bidirectionally moving scatterers centered at Doppler frequencies outside of the frequency window are resolved. Additionally, 3D velocimetry maps can be constructed by setting the spatial frequency window to a corresponding velocity range and shifting it across all spatial frequencies to image scatterers moving within a particular velocity range. We show that SPFI SDOCT allows for 3D imaging of in vivo human retinal microvasculature down to 20&#956;m, thus providing information about vessel morphology and dynamics.
Adenosine inhibits arginine vasopressin-stimulated chloride secretion in a mouse IMCD cell line (mIMCD-K2) (1995)

Previously, we demonstrated that a mouse inner medullary collecting duct cell line (mIMCD-K2) secretes Cl- by an electrogenic mechanism via cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channels [N. L. Kizer, B. Lewis, and B. A. Stanton. Am. J. Physiol. 268 (Renal Fluid Electrolyte Physiol. 37): F347-F355, 1995; N. L. Kizer, D. Vandorpe, B. Lewis, B. Bunting, J. Russell, and B. A. Stanton. Am. J. Physiol. 268 (Renal Fluid Electrolyte Physiol. 37): F854-F861, 1995; D. Vandorpe, N. Kizer, F. Ciampolillo-Bates, B. Moyer, K. Karlson, W. B. Guggino, and B. A. Stanton. Am. J. Physiol. 269 (Cell Physiol. 38): C683-C689, 1995]. The objective of the present study was to determine whether adenosine, and adenosine A1 receptors (A1AR) specifically, regulate electrogenic Cl- secretion (IscCl) in mIMCD-K2 cells. Neither N6-cyclohexyladenosine (CHA), a specific A1AR agonist, nor 8-cyclopentyl-1,3-dipropylxanthine (DPCPX), a specific A1AR antagonist, altered basal, unstimulated IscCl in monolayers of mIMCD-K2 cells mounted in Ussing-type chambers. In contrast, DPCPX increased arginine vasopressin (AVP)-stimulated IscCl, an effect that was reversed by CHA. Adenosine deaminase (ADA), which oxidatively deaminates adenosine to inosine, increased AVP-stimulated IscCl. CHA reversed the stimulatory effect of ADA on AVP-stimulated IscCl. These results suggest that adenosine, via A1AR, inhibits AVP-stimulated IscCl. To identify the source(s) of extracellular adenosine, we examined the effects of dipyridamole, an inhibitor of nucleoside transport, and alpha,beta-methyleneadenosine 5'-diphosphate (AOPCP), an inhibitor of ecto-5'-nucleotidase, on AVP-stimulated IscCl. Both compounds increased AVP-stimulated IscCl. CHA reversed the stimulatory effect of dipyridamole and AOPCP on IscCl. Neither ADA nor CHA had an effect on 8-(4-chlorophenylthio)-adenosine 3',5'-cyclic monophosphate (CPT-cAMP)-stimulated IscCl. Moreover, U-73122, an inhibitor of phospholipase C, failed to attenuate the increase in AVP-stimulated IscCl elicited by dipyridamole and AOPCP or the decrease in AVP-stimulated IscCl elicited by CHA. We conclude that adenosine, released by a nucleoside transporter and formed extracellularly by the breakdown of AMP, binds to A1AR, and decreases AVP-stimulated IscCl in mIMCD-K2 cells by reducing intracellular cAMP levels.
Migration of Mn cations in delithiated lithium manganese oxides (2014)

Li2MnO3 is an integrated component in lithium-manganese-rich nickel manganese cobalt oxides, and the conversion of Li2MnO3 to a spinel-like structure after electrochemical activation has been associated with the continuous potential decay of the material. Delithiated Li2MnO3 and delithiated LiMn2O4 were used as model materials to investigate the mechanism of forming the spinel-like structure. An in situ high-energy X-ray diffraction technique was used to trace the structural change of materials at elevated temperatures, a procedure to mimic the structural transformation during the normal cycling of batteries. It was also found that the migration of Mn atoms from the octahedral sites to tetrahedral sites is the key step for phase transformation from a monoclinic structure to a spinel structure.
Simulation of Small-Angle X-ray Scattering from Single-Particle Systems (1998)

Elastic small-angle scattering is sensitive to morphology on the colloidal length scale. In order to make better use of this technique to probe microstructure, a computer program is being developed that will calculate scattering patterns for objects whose shapes and arrangements in space are arbitrary. This program utilizes X-ray diffraction first principles and its only requirement is that the scattering object is centrosymmetric. The simulated data can then be used to extract morphological information from multiphase anisotropic materials, such as polymers, polymer composites and metal alloys. This paper demonstrates the accuracy of this modeling technique for three single-particle morphologies. These simulations are compared to their analytical solution counterparts to show the level of accuracy that can be obtained as a function of simulation time or number of simulated scattering points. This method can be easily adapted to simulate small-angle scattering for single particles whose orientations or geometries make analytical solution extremely difficult or impossible. This is demonstrated with simulations of scattering from a nonideally oriented cylinder, from an elongated hexagon and from a bundle of cylinders.
Use of laser diodes in cavity ring-down spectroscopy (1997)

We have demonstrated that cavity ring-down spectroscopy (CRDS), a highly sensitive absorption technique, is versatile enough to serve as a complete diagnostic for materials process control. In particular, we have used CRDS in the ultraviolet to determine the concentration profile of methyl radicals in a hot-filament diamond reactor; we have applied CRDS in the mid-infrared to detect 50 ppb of methane in a N{sub 2} environment; and, we have extended CRDS so that we can use continuous-wave diode laser sources. Using a laser diode at 810 nm, we were able to achieve a sensitivity of 2 x 10{sup -8} cm{sup -1}. Thus, CRDS can be used not only as an in situ diagnostic for investigating the chemistry of diamond film deposition, but it can also be used as a gas purity diagnostic for any chemical vapor deposition system.
Microbiological Health Risk Assessment of Water Conservation Strategies: A Case Study in Amsterdam (2021)

The aim of this study was to assess the health risks that may arise from the implementation of greywater reuse and rainwater harvesting for household use, especially for toilet flushing. In addition, the risk of cross connections between these systems and the drinking water system was considered. Quantitative microbial risk assessment (QMRA) is a method that uses mathematical modelling to estimate the risk of infection when exposure to pathogens happens and was used in this study to assess the health risks. The results showed that using rainwater without prior treatment for toilet flushing poses an annual infection risk from <i>L. pneumophila</i> at 0.64 per-person-per-year (pppy) which exceeds the Dutch standard of 10<sup>-4</sup> pppy. The use of untreated greywater showed a risk that is below the standard. However, treatment is recommended due to the ability of <i>P. aeruginosa</i> to grow in the reuse system. Moreover, showering and drinking with cross-connected water has a high annual infection risk that exceeds the standard due to contact with <i>Staphylococcus aureus</i> and <i>E. coli</i> O157:H7. Several measures can be implemented to mitigate the risks such as treating the greywater and rainwater with a minimum of 5-log removal, closing the toilet lid while flushing, good design of greywater and rainwater collection systems, and rigorous plumbing installation procedures.
Researcher and user interfaces for studies of hearing-aid self-adjustment (2019)

The “Goldilocks” explore-and-select protocol of Boothroyd and Mackersie was adapted for field studies of hearing-aid self-fitting and incorporated into the wearable UCSD open-source speech-processing platform (OSP). A researcher interface allows adjustment of hearing aid parameters, including starting response for self-adjustment; compression parameters; and number, consequence, and step size of listener controls. The listener-interface provides for adjustment of level and spectrum using either three controls (overall gain plus low- and high-frequency tilt) or two controls (overall gain and overall spectral tilt). Response selections made in specific acoustic environments can be saved, named, and recalled. Both interfaces are accessible via web-browser on any web-enabled device, including a listener’s smart-phone. Every listener-adjustment is logged and options are available for logging information about the ambient noise plus the listener’s reasons for, and satisfaction with, response modifications. These interfaces were created using HTML, CSS, and Javascript, and use PHP to communicate information with the embedded webserver on the wearable platform. This web framework is faster and easier to customize than is a native application, and it supports the iterative design required in research. Instructions for customizing the interface are included. They vary in challenge, from editing a text document to modifying documented, readable code.
Intrinsic Response Control of Moment Resisting Frames Utilizing Advanced Composite Materials and Structural Elements (2003)

Peer Reviewed
A Case of Omental Metastasis from Pleomorphic Carcinoma of the Lung with Resection (2012)

症例は62歳の男性で，膵管内乳頭粘液性腫瘍でフォロー中にCEAの上昇を認め，精査で右鎖骨上窩リンパ節転移を伴う左肺多形癌と診断された．化学療法によりいったんCT上complete response（以下，CRと略記）となったが，半年後に縦隔リンパ節に再発し同部位に放射線療法を施行した．再度CRになったが，その2年7か月後にCEAが再上昇しFDG-PETで腹腔内に集積を認めた．CTでは，腫瘤は下行結腸近傍に存在し，肺癌の孤立性大網転移と診断し手術を施行した．開腹時に左側大網に腫瘤を認め周囲の大網を含めて腫瘤を摘出した．病理組織学的検査では，以前の右鎖骨上窩リンパ節生検像と同様に，大型異型細胞が増生し，免疫染色検査で肺原発を示すThyroid transcription factor-1，NapsinAが陽性であり，肺多形癌の大網転移と最終診断された．術後8か月経過した現在，無再発生存中である．
Cofactor-specific Anchoring of Horseradish Peroxidase onto a Polythiophene-modified Electrode (2017)

Horseradish peroxidase apoprotein (apoHRP) was immobilized on a heme-modified polythiophene film, which was electropolymerized on an indium tin oxide surface to yield immobilized and reconstituted HRP. The HRP-immobilized electrode exhibits a 6-fold enhanced electrochemical response toward hydrogen peroxide reduction relative to having the protein randomly immobilized on the polythiophene electrode. This indicates that the insertion of the heme moiety into the heme pocket of HRP leads to an increase in the electrocatalytic current.
<title>Eight-level programmable binary optics system using cascaded ferroelectric liquid crystal spatial light modulators</title> (1995)

We present a novel method for producing arbitrary valued, binary phase-only modulation from a commercially available ferroelectric liquid crystal spatial light modulator (FLCSLM) used in conjunction with simple polarization components. Three such stages can be cascaded together in an instrument capable of producing up to eight discrete, equally spaced levels of phase modulation. By using 128 by 128 pixel FLCSLMs a reconfigurable, pixellated, eight-level, optical phase modulator has been constructed which we refer to here as a programmable phase transformer (PPT). We report on the near diffraction limited performance of such an instrument when stopped down to 64 by 64 pixels in producing simple diffraction patterns and when used to generate asymmetric spot arrays in the Fourier plane of a lens. We also discuss the limitations of the current system and the projected improvements that will result from current and future developments in device technology and modulation schemes.
Distributed Enactment of Multiagent Flows (2003)

We address the problem of constructing multiagent systems for service composition by coordinating heterogeneous, autonomous agents, whose internal designs may not be fully known. We develop an approach that (a) takes declarative specifications of the desired interactions, and (b) automatically enacts them. Our approach is based on temporal logic, has a rigorous semantics, and yields a naturally distributed implementation.
Binding of Pu(IV) to galacturonic acid and extracellular polymeric substances (EPS) fromShewanella putrefaciens, Clostridium sp. andPseudomonas fluorescens (2008)

Abstract The conditional stability constants for trace-level concentrations of Pu(IV) complexing with galacturonic acid and EPS, isolated from axenic Clostridium sp., P. fluorescens and Shewanella putrefaciens CN32 cultures, were determined at pH 4 and an ionic strength of 0.1 M NaCl using an ion-exchange technique. The analysis of ion-exchange data with Schubert´s technique indicates that the Pu binding by galacturonic acid and EPS from Clostridium sp. and S. putrefaciens can be described based on the formation of 1:1 Pu(IV)-ligand complexes. However, the accurate description of Pu binding by EPS from P. fluorescens requires postulation of a mixture of 1:1/1:2 complexes between Pu(IV) and ligands under the experimental conditions studied. The results from the ion-exchange experiments were also modeled based on a non-electrostatic, discrete ligand approach in which bacterial EPS is conceptualized as being composed of a suite of monoprotic acids, HL i , of arbitrarily-assigned p K a (i) values ( e.g. , 4, 6 and 8). The examination of ion-exchange data in a chemical model suggested that only the p K a 4 (L 1 ) and 6 (L 2 ) ligands are sufficient to accurately simulate the Pu(IV)/EPS binding, implying that carboxylic groups in EPS are the primary binding sites for complexing with Pu(IV) under the experimental conditions examined. The affinity of EPS for complexing Pu(IV) decreases in the order of Clostridium sp.&gt; S. putrefaciens &gt; P. fluorescens although the concentrations of carboxylic groups in EPS decrease in the order of P. fluorescens &gt; S. putrefaciens &gt; Clostridium sp. This discrepancy may be due to differences in binding affinities between Na + ion in solution and EPS ligands. At I =0.1 M, models demonstrated that the EPS from P. fluorescens exhibits a much stronger affinity for the Na + ion compared to ligands from other EPS; therefore, the deprotonated carboxylic sites of EPS from P. fluorescens are hypothesized to be mostly bound by Na + in solution.
ChemInform Abstract: Au Catalysts for Acetylene Hydrochlorination and Carbon Monoxide Oxidation (2014)

Abstract Review: 25 refs.
Generation of Coherent X-rays in the Water Window Using 5-Femtosecond Laser Pulses (1997)

Coherent extreme-ultraviolet radiation extending to wavelengths below the carbon K edge at 4.37 nanometers (nm) has been generated at a repetition rate of 1 kilohertz by focusing 5-femtosecond near-infrared (780 nm) laser pulses into a helium gas jet. The incident light field performs just a few oscillations, which results in the emission of an x-ray supercontinuum rather than discrete harmonics. Owing to the extremely short rise time of the driving pulses, neutral atoms can be exposed to high fields before they are depleted by ionization. As a result, the observed x-ray radiation extends well into the water window and is delivered in a well-collimated beam (divergence less than 1 milliradian). The high repetition rate and spatial coherence result in a brightness of about 5 × 10 8 photons per square millimeter per square milliradian per second in a 1-percent bandwidth at 4.37 nm, the carbon edge of the water window. The compact laboratory system holds promise as a source for biological holography and nonlinear optics in the x-ray regime.
Table S1 from A Novel HSP90 Inhibitor–Drug Conjugate to SN38 Is Highly Effective in Small Cell Lung Cancer (2023)

&lt;p&gt;Supplemental Table 1&lt;/p&gt;
Resist shrink characterization methodology for more accurate CD metrology (2022)

This work proposes a methodology to characterize the extent of photoresists’ CD shrink from various SEM landing energy and imaging conditions, using both AFM metrology and post-etch pattern transfer as methods to evaluate the true physical CD. The resist shrink for both 1D and 2D features with varying resist volumes can be quantified through the various metrology techniques and post-etch dimensional data. Once characterized, material response during SEM exposure can be accounted for in any CDSEM data comparison or OPC model.
Fault location in High Voltage Multi-terminal dc Networks Using Ensemble Learning (2022)

Precise location of faults for large distance power transmission networks is essential for faster repair and restoration process. High Voltage direct current (HVdc) networks using modular multi-level converter (MMC) technology has found its prominence for interconnected multi-terminal networks. This allows for large distance bulk power transmission at lower costs. However, they cope with the challenge of dc faults. Fast and efficient methods to isolate the network under dc faults have been widely studied and investigated. After successful isolation, it is essential to precisely locate the fault. The post-fault voltage and current signatures are a function of multiple factors and thus accurately locating faults on a multi-terminal network is challenging. In this paper, we discuss a novel data-driven ensemble learning based approach for accurate fault location. Here we utilize the eXtreme Gradient Boosting (XGB) method for accurate fault location. The sensitivity of the proposed algorithm to measurement noise, fault location, resistance and current limiting inductance are performed on a radial three-terminal MTdc network designed in Power System Computer Aided Design (PSCAD)/Electromagnetic Transients including dc (EMTdc).
Design and synthesis of deuterated boceprevir analogs with enhanced pharmacokinetic properties (2011)

As part of an ongoing effort to apply the Deuterated Chemical Entity Platform (DCE Platform™) to clinically validated drugs, the synthesis of deuterated analogs of the hepatitis C virus protease inhibitor boceprevir was carried out. The devised synthetic routes allowed for site‐selective deuterium incorporation with high levels of isotopic purity. Application of the DCE Platform™ to boceprevir enabled the identification of several deuterated analogs that display marked levels of in vitro metabolic stabilization. Most notably, analog 1g exhibits a near doubling of in vitro half‐life in human liver microsomal assays. The details of the convergent synthetic route to the boceprevir isotopologs and the results of the metabolic stability assays are described herein.
Modular Representation of Layered Neural Networks (2017)

Layered neural networks have greatly improved the performance of various applications including image processing, speech recognition, natural language processing, and bioinformatics. However, it is still difficult to discover or interpret knowledge from the inference provided by a layered neural network, since its internal representation has many nonlinear and complex parameters embedded in hierarchical layers. Therefore, it becomes important to establish a new methodology by which layered neural networks can be understood. In this paper, we propose a new method for extracting a global and simplified structure from a layered neural network. Based on network analysis, the proposed method detects communities or clusters of units with similar connection patterns. We show its effectiveness by applying it to three use cases. (1) Network decomposition: it can decompose a trained neural network into multiple small independent networks thus dividing the problem and reducing the computation time. (2) Training assessment: the appropriateness of a trained result with a given hyperparameter or randomly chosen initial parameters can be evaluated by using a modularity index. And (3) data analysis: in practical data it reveals the community structure in the input, hidden, and output layers, which serves as a clue for discovering knowledge from a trained neural network.
High-noise-rejection fiber-optic probe for interferometric applications (1982)

A fiber-optic interferometer with almost total rejection of the noise introduced by the fiber-optic link is reported. The new scheme is based on the passage of the reference and sensing beams through the same path in a single-mode fiber. The experimental results emphasize the excellent noise rejection of the new setup compared with that of a conventional fiber-optic interferometer.
A technique to reduce power and test application time in BIST (2004)

Increased switching activity during testing causes substantial increase in power dissipation. This paper presents an efficient test application procedure for reducing power dissipation in test-per-scan BIST as well as the test application time, while maintaining the fault coverage. Experiments on ISCAS89 benchmarks show promising results - up to 51.8% (63.1%) peak power reduction and an average energy saving of 36.3% (62.3%) in the combinational logic (scan chain) for three partitions.