gebhart/patrepeval huggingface dataset:
Data from Early Noninvasive Detection of Response to Targeted Therapy in Non–Small Cell Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;With the advent of precision oncology, there is an urgent need to develop improved methods for rapidly detecting responses to targeted therapies. Here, we have developed an ultrasensitive measure of cell-free tumor load using targeted and whole-genome sequencing approaches to assess responses to tyrosine kinase inhibitors in patients with advanced lung cancer. Analyses of 28 patients treated with anti-EGFR or HER2 therapies revealed a bimodal distribution of cell-free circulating tumor DNA (ctDNA) after therapy initiation, with molecular responders having nearly complete elimination of ctDNA (&gt;98%). Molecular nonresponders displayed limited changes in ctDNA levels posttreatment and experienced significantly shorter progression-free survival (median 1.6 vs. 13.7 months, &lt;i&gt;P&lt;/i&gt; &lt; 0.0001; HR = 66.6; 95% confidence interval, 13.0–341.7), which was detected on average 4 weeks earlier than CT imaging. ctDNA analyses of patients with radiographic stable or nonmeasurable disease improved prediction of clinical outcome compared with CT imaging. These analyses provide a rapid approach for evaluating therapeutic response to targeted therapies and have important implications for the management of patients with cancer and the development of new therapeutics.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; Cell-free tumor load provides a novel approach for evaluating longitudinal changes in ctDNA during systemic treatment with tyrosine kinase inhibitors and serves an unmet clinical need for real-time, noninvasive detection of tumor response to targeted therapies before radiographic assessment.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Zou and Meyerson, p. 1038&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Portable, Low-Field Magnetic Resonance Imaging Sensitively Detects and Accurately Quantifies Multiple Sclerosis Lesions (2022)

Abstract Magnetic resonance imaging is a fundamental tool in the diagnosis and management of neurological diseases such as multiple sclerosis (MS). New portable, low-field MRI scanners could potentially lower financial and technical barriers to neuroimaging and reach underserved or disabled populations. However, the sensitivity of low-field MRI for MS lesions is unknown. We sought to determine if white matter lesions can be detected on a 64mT low-field MRI, compare automated lesion segmentations and total lesion burden between paired 3T and 64mT scans, and identify features that contribute to lesion detection accuracy. In this prospective, cross-sectional study, same-day brain MRI (FLAIR, T1, and T2) scans were collected from 36 adults (32 women; mean age, 50 ± 14 years) with known or suspected MS using 3T (Siemens) and 64mT (Hyperfine) scanners at two centers. Images were reviewed by neuroradiologists. MS lesions were measured manually and segmented using an automated algorithm. Statistical analyses assessed accuracy and variability of segmentations across scanners and systematic scanner biases in automated volumetric measurements. Lesions were identified on 64mT scans in 94% (31/33) of patients with confirmed MS. The smallest lesions manually detected were 5.7 ± 1.3 mm in maximum diameter at 64mT vs 2.1 ± 0.6 mm at 3T. Automated lesion burden estimates were highly correlated between 3T and 64mT scans (r = 0.89, p &lt; 0.001). Bland-Altman analysis identified bias in 64mT segmentations (mean = 1.6 ml, standard error = 5.2 ml, limits of agreement = -19.0–15.9 ml), which over-estimated low lesion burden and under-estimated high burden (r = 0.74, p &lt; 0.001). Visual inspection revealed over-segmentation was driven by flow-related hyperintensities in veins on 64mT FLAIR. Lesion size drove segmentation accuracy, with 93% of lesions &gt;1.0 ml and all lesions &gt;1.5 ml being detected. These results demonstrate that in established MS, a portable 64mT MRI scanner can identify white matter lesions, and disease burden estimates are consistent with 3T scans. Highlights Paired, same-day 3T and 64mT MRI studies were collected in 36 patients 64mT MRI showed 94% sensitivity for detecting any lesions in established MS cases The diameter of the smallest detected lesion was larger at 64mT compared to 3T Disease burden estimates were strongly correlated between 3T and 64mT scans Low-field MRI can detect white matter lesions, though smaller lesions may be missed
Immunization with lytic polysaccharide monooxygenase CbpD induces protective immunity against Pseudomonas aeruginosa pneumonia (2023)

<i>Pseudomonas aeruginosa</i> (PA) CbpD belongs to the lytic polysaccharide monooxygenases (LPMOs), a family of enzymes that cleave chitin or related polysaccharides. Here, we demonstrate a virulence role of CbpD in PA pneumonia linked to impairment of host complement function and opsonophagocytic clearance. Following intratracheal challenge, a PA ΔCbpD mutant was more easily cleared and produced less mortality than the wild-type parent strain. The x-ray crystal structure of the CbpD LPMO domain was solved to subatomic resolution (0.75Å) and its two additional domains modeled by small-angle X-ray scattering and Alphafold2 machine-learning algorithms, allowing structure-based immune epitope mapping. Immunization of naive mice with recombinant CbpD generated high IgG antibody titers that promoted human neutrophil opsonophagocytic killing, neutralized enzymatic activity, and protected against lethal PA pneumonia and sepsis. IgG antibodies generated against full-length CbpD or its noncatalytic M2+CBM73 domains were opsonic and protective, even in previously PA-exposed mice, while antibodies targeting the AA10 domain were not. Preexisting antibodies in PA-colonized cystic fibrosis patients primarily target the CbpD AA10 catalytic domain. Further exploration of LPMO family proteins, present across many clinically important and antibiotic-resistant human pathogens, may yield novel and effective vaccine antigens.
Apache Airavata: Design and Directions of a Science Gateway Framework (2014)

This paper provides an overview of the Apache Airavata software system for science gateways. Gateways use Airavata to manage application and workflow executions on a range of backend resources (grids, computing clouds, and local clusters). Airavata's design goal is to provide component abstractions for major tasks required to provide gateway application management. Components are not directly accessed but are instead exposed through a client Application Programming Interface. This design allows gateway developers to take full advantage of Airavata's capabilities, and Airavata developers (including those interested in middleware research) to modify Airavata's implementations and behavior. This is particularly important as Airavata evolves to become a scalable, elastic "platform as a service" for science gateways. We illustrate the capabilities of Airavata through the discussion of usage vignettes. As an Apache Software Foundation project, Airavata's open community governance model is as important as its software base. We discuss how this works within Airavata and how it may be applicable to other distributed computing infrastructure and cyber infrastructure efforts.
Cardiovascular Effects of Xenon in Isoflurane-anesthetized Dogs with Dilated Cardiomyopathy (1998)

The results indicate that xenon produces minimal cardiovascular actions in the presence of isoflurane in dogs with and without experimental dilated cardiomyopathy.
Fabrication of polymer photonic crystal superprism structures using polydimethylsiloxane soft molds (2007)

We presented a soft lithography technique of fabricating polymer photonic crystal superprism structures using elastomeric polydimethylsiloxane templates. Dense two-dimensional photonic crystal superprism structures with feature sizes of 150–500nm and aspect ratios of up to 1.25 were replicated. Large field size and easy fabrication are two major advantages when compared with other imprint technology. Atomic force microscopy images showed that the molded structures had high fidelity to the masters. Less than 3% reduction of the depth in the molded structures was achieved with respect to the master. The increase of the surface roughness from the master to the molded structures is minimal. The issue of pattern collapse during pattern transfer of submicron structures was analyzed against the pattern dimensions and aspect ratios; and the experimental results were found in agreement with a prior theory. We also experimentally demonstrated the superprism effect in two-dimensional photonic crystal structure at near-infrared wavelength. The propagation beam changed 39° in the photonic crystal with respect to the input wavelength varying from 1546to1572nm. Such an effective, low cost, and high throughput soft lithography technique could find wide use in making photonic crystal based nanostructures.
Contrasting the EXAFS obtained under air and H2 environments to reveal details of the surface structure of Pt–Sn nanoparticles (2021)

Understanding the surface structure of bimetallic nanoparticles is crucial for heterogeneous catalysis. Although surface contraction has been established in monometallic systems, less is known for bimetallic systems, especially of nanoparticles. In this work, the bond length contraction on the surface of bimetallic nanoparticles is revealed by XAS in H2 at room temperature on dealloyed Pt-Sn nanoparticles, where most Sn atoms were oxidized and segregated to the surface when measured in air. The average Sn-Pt bond length is found to be ∼0.09 Å shorter than observed in the bulk. To ascertain the effect of the Sn location on the decrease of the average bond length, Pt-Sn samples with lower surface-to-bulk Sn ratios than the dealloyed Pt-Sn were studied. The structural information specifically from the surface was extracted from the averaged XAS results using an improved fitting model combining the data measured in H2 and in air. Two samples prepared so as to ensure the absence of Sn in the bulk were also studied in the same fashion. The bond length of surface Sn-Pt and the corresponding coordination number obtained in this study show a nearly linear correlation, the origin of which is discussed and attributed to the poor overlap between the Sn 5p orbitals and the available orbitals of the Pt surface atoms.
Poly[1,4-bis(pyrrol-2-yl)phenylene]: A New Electrically Conducting and Electroactive Polymer Containing the Bipyrrole-Phenylene Repeat Unit (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPoly[1,4-bis(pyrrol-2-yl)phenylene]: A New Electrically Conducting and Electroactive Polymer Containing the Bipyrrole-Phenylene Repeat UnitJohn R. Reynolds, Alan R. Katritzky, Jadwiga Soloducho, Sergei Belyakov, Gregory A. Sotzing, and Myoungho PyoCite this: Macromolecules 1994, 27, 24, 7225–7227Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ma00102a038https://doi.org/10.1021/ma00102a038research-articleACS PublicationsRequest reuse permissionsArticle Views256Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Low noise figure, high gain, high conversion efficiency L-band EDFA (1999)

We report a novel L-band EDFA uses in-line tilted fiber Bragg gratings to filter the C-band ASE. This amplifier has a low external noise figure (&lt;4.5 dB), high gain (&gt;27 dB) over a 33 nm bandwidth, and high power conversion efficiency of 24.3%.
Metal‐based nanoparticles for bone tissue engineering (2020)

Tissue is vital to the organization of multicellular organisms, because it creates the different organs and provides the main scaffold for body shape. The quest for effective methods to allow tissue regeneration and create scaffolds for new tissue growth has intensified in recent years. Tissue engineering has recently used some promising alternatives to existing conventional scaffold materials, many of which have been derived from nanotechnology. One important example of these is metal nanoparticles. The purpose of this review is to cover novel tissue engineering methods, paying special attention to those based on the use of metal-based nanoparticles. The unique physiochemical properties of metal nanoparticles, such as antibacterial effects, shape memory phenomenon, low cytotoxicity, stimulation of the proliferation process, good mechanical and tensile strength, acceptable biocompatibility, significant osteogenic potential, and ability to regulate cell growth pathways, suggest that they can perform as novel types of scaffolds for bone tissue engineering. The basic principles of various nanoparticle-based composites and scaffolds are discussed in this review. The merits and demerits of these particles are critically discussed, and their importance in bone tissue engineering is highlighted.
Unravelling the Hydration Barrier of Lignin Oleate Nanoparticles for Acid‐ and Base‐Catalyzed Functionalization in Dispersion State (2021)

Abstract Lignin nanoparticles (LNPs) are promising renewable nanomaterials with applications ranging from biomedicine to water purification. However, the instability of LNPs under acidic and basic conditions severely limits their functionalization for improved performance. Here, we show that controlling the degree of esterification can significantly improve the stability of lignin oleate nanoparticles (OLNPs) in acidic and basic aqueous dispersions. The high stability of OLNPs is attributed to the alkyl chains accumulated in the shell of the particle, which delays protonation/deprotonation of carboxylic acid and phenolic hydroxyl groups. Owing to the enhanced stability, acid‐ and base‐catalyzed functionalization of OLNPs at pH 2.0 and pH 12.0 via oxirane ring‐opening reactions were successfully performed. We also demonstrated these new functionalized particles as efficient pH‐switchable dye adsorbents and anticorrosive particulate coatings.
PEDS: A Parallel Error Detection Scheme for TCAM Devices (2010)

Ternary content-addressable memory (TCAM) devices are increasingly used for performing high-speed packet classification. A TCAM consists of an associative memory that compares a search key in parallel against all entries. TCAMs may suffer from error events that cause ternary cells to change their value to any symbol in the ternary alphabet {”0”,“1”,“*”}. Due to their parallel access feature, standard error detection schemes are not directly applicable to TCAMs; an additional difficulty is posed by the special semantic of the “*” symbol. This paper introduces PEDS, a novel parallel error detection scheme that locates the erroneous entries in a TCAM device. PEDS is based on applying an error-detecting code to each TCAM entry and utilizing the parallel capabilities of the TCAM by simultaneously checking the correctness of multiple TCAM entries. A key feature of PEDS is that the number of TCAM lookup operations required to locate all errors depends on the number of symbols per entry in a manner that is typically orders of magnitude smaller than the number of TCAM entries. For large TCAM devices, a specific instance of PEDS requires only 200 lookups for 100-symbol entries, while a naive approach may need hundreds of thousands of lookups. PEDS allows flexible and dynamic selection of tradeoff points between robustness, space complexity, and number of lookups.
Optical Design for a Head-Mounted Display (1993)

This paper presents a design concept for a head-mounted display, incorporating color stereo vision using commercial LCDs and our own optical relay design. The focus here is on the optical system design, which must meet specifications for a wide field of view, size and cost constraints, and aberration minimization based on human factors. Two multispherical lens systems are presented and compared, one a straight structure and the other a folded structure, which satisfy the design constraints. Their aberrations (distortion, coma, lateral color, field curvature, and astigmatism) have been well corrected, according to human perceptual constraints explicitly discussed. Each has a 20-mm eye relief and an instantaneous field of view greater than 60°; the former has an exit pupil of 10 mm and the latter of 8 mm.
On the plasticizing properties of divalproex sodium: physicochemical and spectroscopic characterization studies (2018)

The objective of the research was to demonstrate the plasticization properties of divalproex sodium, due to its component-valproic acid, on ethyl cellulose, which could prove beneficial for film fabrications or hot melt extrusion based formulations. Films containing 10-50% w/w (DVS/EC) as dry weight were prepared using solvent evaporation method and characterized using texture analyzer, hybrid rheometer, differential scanning calorimetry, thermogravimetry, X-ray diffractometry, polarized microscopy, FTIR, and Raman spectroscopy. It was found that there was a decrease in average peak load, melt viscosity, and glass transition temperature (T<sub>g</sub>) while increase in elongation, with increase in concentration of DVS in the films. These results demonstrate the plasticization tendency of DVS on EC, which was attributed to the presence of valproic acid (fatty acid) in DVS. XRD studies showed amorphous nature of the films; however, polarized microscopy revealed the presence of scattered undissolved sodium valproate crystals. The presence of a single T<sub>g</sub> established complete miscibility between valproic acid and EC. Films showed reasonable physical stability (similar T<sub>g</sub>) at 45 °C/75% RH for 2 weeks (open condition), attributable to the similar solubility parameters of DVS and EC. FTIR and Raman spectroscopy results proved the presence of hydrogen bonding between DVS and EC.
ChemInform Abstract: ABSOLUTE CONFIGURATION OF THE CANCEROSTATIC S(‐)‐CYCLOPHOSPHAMIDE (1977)

Abstract Die absolute Konfiguration und die Konformation der Titelverbindung (I) wird anhand einer Röntgenstrukturanalyse diskutiert und ermittelt.
Capacity, MSE and Secrecy Analysis of Linear Block Precoding for Distributed Antenna Systems in Multi-User Frequency-Selective Fading Channels (2011)

Block transmission with cyclic prefix is a promising technique to realize high-speed data rates in frequency-selective fading channels. Many popular linear precoding schemes, including orthogonal frequency-division multiplexing (OFDM), single-carrier (SC) block transmission, and time-reversal (TR), can be interpreted as such a block transmission. This paper presents a unified performance analysis that shows how the optimal precoding strategy depends on the optimization criterion such as capacity, mean-square error, and secrecy. We analyze three variants of TR methods (based on maximum-ratio combining, equal-gain combining and selective combining) and two-types of pre-equalization methods (zero-forcing and minimum mean-square error). As one application of our framework, we derive optimal precoding (i.e., OFDM with optimal power and phase control) in the presence of interference limitation for distributed antenna systems; we find that without power/phase control, OFDM does not have any capacity advantage over SC transmissions. When comparing SC and TR, we verify that for single-antenna systems in the high SNR regimes, SC has a capacity advantage; however, TR performs better in the low SNR regime. For distributed multiple-antenna systems, TR always provides higher capacity, and the capacity of TR can approach that of optimal precoders with a large number of distributed antennas. Furthermore, we make an analysis of secrecy capacity which shows how high-rate messages can be transmitted towards an intended user without being decoded by the other users from the viewpoint of information-theoretic security. We demonstrate that TR precoding can be the best candidate among the non-optimal precoders for achieving high secrecy capacity, while the optimal precoder offers a significant gain over those non-optimal precoders.
COMMD1-Mediated Ubiquitination Regulates CFTR Trafficking (2011)

The CFTR (cystic fibrosis transmembrane conductance regulator) protein is a large polytopic protein whose biogenesis is inefficient. To better understand the regulation of CFTR processing and trafficking, we conducted a genetic screen that identified COMMD1 as a new CFTR partner. COMMD1 is a protein associated with multiple cellular pathways, including the regulation of hepatic copper excretion, sodium uptake through interaction with ENaC (epithelial sodium channel) and NF-kappaB signaling. In this study, we show that COMMD1 interacts with CFTR in cells expressing both proteins endogenously. This interaction promotes CFTR cell surface expression as assessed by biotinylation experiments in heterologously expressing cells through regulation of CFTR ubiquitination. In summary, our data demonstrate that CFTR is protected from ubiquitination by COMMD1, which sustains CFTR expression at the plasma membrane. Thus, increasing COMMD1 expression may provide an approach to simultaneously inhibit ENaC absorption and enhance CFTR trafficking, two major issues in cystic fibrosis.
99.3% Efficient Three-Phase Buck-Type All-SiC SWISS Rectifier for DC Distribution Systems (2018)

DC power distribution systems for data centers, industrial applications, and residential areas are expected to provide higher efficiency, higher reliability, and lower cost compared to ac systems and have been an important research topic in recent years. In these applications, an efficient power factor correction (PFC) rectifier, supplying the dc distribution bus from the conventional three-phase ac mains, is typically required. This paper analyzes the three-phase, buck-type, unity power factor SWISS Rectifier for the realization of an ultrahigh-efficiency PFC rectifier stage with a 400-V rms line-to-line ac input voltage and a 400-V dc output voltage. It is shown that the mains current total harmonic distortion of the rectifier can be improved significantly by interleaving two converter output stages. Furthermore, the dc output filter is implemented using a current-compensated integrated common-mode coupled inductor, which ensures equal current sharing between the interleaved half bridges and provides common-mode electromagnetic interference (EMI) filter inductance. Based on a theoretical analysis of the coupled inductor's magnetic properties, the necessary equations and the design procedure for selecting semiconductors, magnetic cores, the number of turns, and the EMI filter are discussed. Based on these results, an ultrahigh-efficient 8-kW 4-kW·dm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> (66-W·in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> ) laboratory-scale prototype converter using 1.2-kV SiC MOSFETs is designed. Measurements taken on the prototype confirm a full power efficiency of 99.16% and a peak efficiency of 99.26%, as well as the compliance to CISPR 11 Class B conducted emission limits.