gebhart/patrepeval huggingface dataset:
Genomic Rearrangements Considered as Quantitative Traits (2016)

Abstract To understand the population genetics of structural variants (SVs), and their effects on phenotypes, we developed an approach to mapping SVs, particularly transpositions, segregating in a sequenced population, and which avoids calling SVs directly. The evidence for a potential SV at a locus is indicated by variation in the counts of short-reads that map anomalously to the locus. These SV traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between an SV trait at one locus and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3x) population sequence data from 488 recombinant inbred Arabidopsis genomes, we identified 6,502 segregating SVs. Remarkably, 25% of these were transpositions. Whilst many SVs cannot be delineated precisely, PCR validated 83% of 44 predicted transposition breakpoints. We show that specific SVs may be causative for quantitative trait loci for germination, fungal disease resistance and other phenotypes. Further we show that the phenotypic heritability attributable to sequence anomalies differs from, and in the case of time to germination and bolting, exceeds that due to standard genetic variation. Gene expression within SVs is also more likely to be silenced or dysregulated. This approach is generally applicable to large populations sequenced at low-coverage, and complements the prevalent strategy of SV discovery in fewer individuals sequenced at high coverage.
Revisiting the nanoformulation design approach for effective delivery of topotecan in its stable form: an appraisal of its in vitro Behavior and tumor amelioration potential (2015)

Topotecan (TPT) is indicated against a variety of solid tumors, but has restricted clinical use owing to associated pharmaceutical caveats. This study is focused at formulating a successful TPT PLGA nanosystem which ameliorates the rapid conversion of active lactone form of drug to its inactive carboxylate form and consequently improvises its efficacy. TPT PLGA nanoparticles were formulated by a double emulsion-solvent evaporation technique with sequential optimization to obtain desired particle size, PDI, zeta potential, and entrapment efficiency. Stability of TPT was ensured by maintaining an acidic pH in the drug-containing phase and the system was evaluated for in vitro-in vivo performance including cytotoxic potency. The optimized nanosystem had a particle size of 187.33 ± 7.50 nm, a PDI of 0.179 ± 0.05, and an entrapment efficiency of 56 ± 1.2%. Low pH in the interior of nanoparticles stabilized the drug to remain in its active lactone form and revealed a biphasic release pattern till 15 d. Additionally, an in vitro cytotoxicity testing as well as in vivo antitumor efficacy demonstrated a significant potential of higher proliferation inhibition as compared with neat drug (TPT). Thus, the investigation summarized an innovative simple tool for developing stable TPT NPs for effective delivery for treating solid tumors.
Stabilin‐1 protects against adverse inflammation and injury during viral myocarditis (2012)

Stabilin‐1 is a transmembrane glycoprotein expressed on activated macrophages and endothelial cells of new capillaries during tissue remodeling. In the coxsackie B3 (CVB3) murine model of viral myocarditis, stabilin‐1 expression increased significantly and was primarily expressed in macrophages. This was also seen in endomyocardial biopsies from patients with fulminant myocarditis, where stabilin‐1 was expressed by CD‐68+ macrophages, forming a protective barrier around the healthy tissue. When challenged with the CVB3 virus, Stabilin‐1 null mice showed increased cardiac related mortality as compared to wild‐type mice (p&lt;0,001, n=19). Histological analysis showed that the stabilin‐1 null mice had increased cardiac necrosis due to CD3+ T‐lymphocyte infiltration, and lower F4/80+ macrophages as compared to their wild‐type littermates, suggesting that stabilin‐1 may be important for monocytes recruitment. Thioglycolate induced peritonitis in stabilin‐1 WT and null mice also resulted in fewer monocytes recruited. Depletion of circulating monocytes with clodronate liposomes in wild‐type mice induced a similar phenotype after CVB3 infection. We identify stabilin‐1 as an important upregulated protein during VM in both mice and humans and that absence of stabilin‐1 results in increased cardiac inflammation, injury and mortality, demonstrating a novel cardio‐protective effect of stabilin‐1.
Substructuring approach to optimization of matching structures for photonic crystal waveguides (2004)

Micro-cavities formed by local defects within an otherwise perfect photonic crystal can trap light and resonate at wavelengths within the stop-band of the background crystal. An array of equally spaced identical micro-cavities forms the coupled cavity waveguide (CCW), a narrow band waveguide whose central frequency and bandwidth are determined by the form of the micro-cavities and their inter-spacing. Such devices can be used as optical or millimeter wave filters, routers, and (de)multiplexers. We develop a method for matching these devices to external structures. We formulate an optimization problem in which one seeks for the minimum of a properly defined standing wave ratio (SWR), with respect to limited variations of the dielectric structure in the neighborhood of the interface between the sub-system (micro-cavity, CCW) and the external structure. A novel numerical approach to solve this problem is developed and tested on a few examples.
Detecting Glaucoma from Fundus Photographs Using Deep Learning without Convolutions: Transformer for Improved Generalization (2022)

&lt;p&gt; &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Purpose: &lt;/strong&gt;To compare the diagnostic accuracy and explainability of a new Vision Transformer deep learning technique, Data-efficient image Transformer (DeiT), and Resnet-50, trained on fundus photographs from the Ocular Hypertension Treatment Study (OHTS) to detect primary open-angle glaucoma (POAG) and to identify the salient areas of the photographs most important for each model's decision-making process.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Study Design: &lt;/strong&gt;Evaluation of a diagnostic technology&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Subjects, Participants, and/or Controls: &lt;/strong&gt;66,715 photographs from 1,636 OHTS participants and an additional five external datasets of 16137 photographs of healthy and glaucoma eyes. &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Methods, Intervention, or Testing: &lt;/strong&gt;DeiT models were trained to detect five ground truth OHTS POAG classifications: OHTS Endpoint Committee POAG determinations due to disc changes (Model 1), visual field changes (Model 2), or either disc or visual field changes (Model 3) and reading center determinations based on disc (Model 4) and visual fields (Model 5). The best-performing DeiT models were compared to ResNet-50 on OHTS and five external datasets. &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Main Outcome Measures: &lt;/strong&gt;Diagnostic performance was compared using areas under the receiver operating characteristic curve (AUROC) and sensitivities at fixed specificities. The explainability of the DeiT and ResNet-50 models was compared by evaluating the attention maps derived directly from DeiT to 3 gradient-weighted class activation map generation strategies.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Compared to our best-performing ResNet-50 models, the DeiT models demonstrated similar performance on the OHTS test sets for all five-ground truth POAG labels; AUROC ranged from 0.82 (Model 5) to 0.91 (Model 1). However, the AUROC of DeiT was consistently higher than ResNet-50 on the five external datasets. For example, AUROC for the main OHTS endpoint (Model 3) was between 0.08 and 0.20 higher in the DeiT compared to ResNet-50 models. The saliency maps from the DeiT highlight localized areas of the neuroretinal rim, suggesting the use of important clinical features for classification, while the same maps in the ResNet-50 models show a more diffuse, generalized distribution around the optic disc, &lt;/p&gt; &lt;p&gt;&lt;strong&gt;Conclusions:&lt;/strong&gt; Vision transformer has the potential to improve the generalizability and explainability of deep learning models for the detection of eye disease and possibly other medical conditions that rely on imaging modalities for clinical diagnosis and management.&lt;/p&gt;
Charcot–Marie–tooth disease causing mutation (p.R158H) in pyruvate dehydrogenase kinase 3 (PDK3) affects synaptic transmission, ATP production and causes neurodegeneration in a CMTX6C. elegansmodel (2021)

Charcot-Marie-Tooth (CMT) is a commonly inherited, non-fatal neurodegenerative disorder that affects sensory and motor neurons in patients. More than 90 genes are known to cause axonal and demyelinating forms of CMT. The p.R158H mutation in the pyruvate dehydrogenase kinase 3 (PDK3) gene is the genetic cause for an X linked form of axonal CMT (CMTX6). In vitro studies using patient fibroblasts and iPSC-derived motor neurons have shown that this mutation causes deficits in energy metabolism and mitochondrial function. Animal models that recapitulate pathogenic in vivo events in patients are crucial for investigating mechanisms of axonal degeneration and developing therapies for CMT. We have developed a C. elegans model of CMTX6 by knocking-in the p.R158H mutation in pdhk-2, the ortholog of PDK3. In addition, we have developed animal models overexpressing the wild type and mutant form of human PDK3 specifically in the GABAergic motor neurons of C. elegans. CMTX6 mutants generated in this study exhibit synaptic transmission deficits, locomotion defects and show signs of progressive neurodegeneration. Furthermore, the CMTX6 in vivo models display energy deficits that recapitulate the phenotype observed in patient fibroblasts and iPSC-derived motor neurons. Our CMTX6 animals represent the first in vivo model for this form of CMT and have provided novel insights into the cellular function and metabolic pathways perturbed by the p.R158H mutation, all the while closely replicating the clinical presentation observed in CMTX6 patients.
Preface (1991)

ADVERTISEMENT RETURN TO BOOKPREVPrefaceNEXTPrefaceGEORGE GEORGIOUGEORGE GEORGIOUUniversity of Texas Austin, TX 78712More by GEORGE GEORGIOU and ELIANA DE BERNARDEZ-CLARKELIANA DE BERNARDEZ-CLARKTufts University Medford, MA 02155More by ELIANA DE BERNARDEZ-CLARKDOI: 10.1021/bk-1991-0470.pr001 This publication is free to access through this site. Learn MorePublication Date (Print):July 30, 1991Publication History Published online23 July 2009Published inprint 30 July 1991Request reuse permissions Copyright © 1991 American Chemical Society. This publication is available under these Terms of Use. Protein Refoldingp ixACS Symposium SeriesVol. 470ISBN13: 9780841221079eISBN: 9780841213265Chapter Views108Citations-LEARN ABOUT THESE METRICSChapter 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. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (85 KB) Get e-Alerts
Optimized adiabatic spin-lock pulses for robust dynamic glucose enhanced MRI at 3T (2017)

Purpose/Introduction: Adiabatic spin-lock (SL) was shown to enable dynamic glucose enhanced (DGE) imaging at 7T [1–3]. While the proposed pulses are robust against B1 inhomogeneity the mismatch between adiabatic and locking pulses (Fig. 1a) is in principle prone to B0 artifacts. To robustly translate the adiabatic SL to clinical field strength of 3T we want to improve the stability in the presence of B0 inhomogeneity by matching the RF amplitude of tipping and locking pulse. To achieve this a lower (and shorter) adiabatic tilting pulse is proposed and tested in vivo. Subjects and Methods: Simulation. In addition to the commonly used hyperbolic secant (HS) adiabatic pulse [4], we introduced a Blackman windowed HS amplitude modulation in combination with an exponential frequency modulation (HSExp pulse), defined by the maximum amplitude B1, the bandwidth Df, the exponential parameter l, the length of the Blackman window twindow and the pulse duration tadia. Using a compiled Bloch simulation as a mex file in MATLAB, trajectory computation of the adiabatic pulse was performed for more than 380000 different parameter settings: 1 B l B 80; 5 lT B B1 B 15 lT; 500 Hz B Df B 5000 Hz; 0 ms B twindow B 3 ms; 1 ms B tadia B 10 ms. Imaging Imaging of three healthy volunteers was performed on a 3 T MRI scanner (PRISMA, Siemens), using the optimized HSExp pulse, as well as the HS pulses [1]. On resonant SL-prepared imaging consists of an adiabatic SL pulse cluster (Fig. 1a) and a subsequent single-shot centric-spiral reordered 3D GRE readout (680 k-space lines, FA = 6, TE= 1.95 ms, TR = 3.95 ms, Grappa = 2, elliptical scanning, BW = 700 Hz/px, resolution 1.6 9 1.6 9 3 mm3, FOV = 17 9 21 9 4.8 cm3). Results: The optimized HSExp pulse (l = 51; B1 = 7 lT; Df = 4000 Hz; twindow = 2.8 ms; tadia = 5 ms) found by Bloch simulations has a much smaller discontinuity of 2 lT than the HS pulse with 15 lT (Fig. 1a). The simulated magnetization trajectory reveals good performance of the adiabatic SL independent of typical B0 deviations (Fig. 1b). In vivo, also flat T1q -weighted images could be measured with significantly reduced duration and amplitude of the tip pulses (Figs. 2, 3).
<title>Generalized motion compensation for drift reduction</title> (1998)

The most straight-forward approach in obtaining a down- converted image sequence is to decimate each frame after it has been fully encoded. To reduce memory requirements and other costs incurred by this approach, a down-conversion decoder would perform a decimation within the decoding loop. In this way, predictions are made from a low-resolution reference which has experienced a considerable loss of information. Additionally the prediction s must be made from a set of motion vectors which correspond to the full- resolution image sequence. Given these conditions, it is desirable to optimize the performance of the motion compensation process. In this paper we show that the optimal set of filters for performing the low-resolution motion compensation are dependent on the choice of down-conversion are provided. To demonstrate the usefulness of these results, a sample set of motion compensation filters for each class of down-conversion are calculated. The results are incorporated into a low-resolution decoder and comparisons of each down-conversion class are made. Simulation results reveal that the filters which were based on multiple block down-conversion can reduce the amount of prediction drift found in the single block down-conversion by as much as 35 percent.
Hydroxyphenylbenzene derivatives as glass forming molecules for high resolution photoresists (2008)

This paper presents a fundamental study to relate molecular architecture to the amorphous properties of hydroxyphenylbenzene molecular glass derivatives. These studies demonstrates that the branched hydroxyphenylbenzene derivatives can form stable molecular glasses despite the π–π interactions present. Through this research, design concepts to stabilize the amorphous nature and to increase the glass transition temperature (Tg) based on asymmetric molecular structures, bulky substituents, conformation states and molecular size are explored. An understanding of such behavior is important for the development of hydroxyphenylbenzene derivatives as potential molecular photoresists for patterning below 50 nm. This research has helped to identify potential candidates to be evaluated as positive-tone photoresists for lithographic applications for extreme ultraviolet (EUV, λ = 13.4 nm) lithography. The first reported sub-30 nm feature sizes for hydroxyphenylbenzene derivatives were demonstrated with high Tg materials.
Biobased polymers from lignocellulosic sources (2022)

The ongoing threat of global warming has resulted in numerous attempts to reduce greenhouse gas emissions and impede its ramifications. Replacing fossil fuels in products with renewable biobased materials is currently one approach to tackle the climate change crisis. Lignocellulose is the most abundant natural biomass source and is a potential candidate to replace the non-renewable resources currently made with petroleum-based products. Cellulose, hemicellulose, and lignin, which together make up lignocellulose, are all suitable choices for the creation of biobased materials. This review aims to highlight some of the recent efforts towards synthesizing renewable biobased polymers from raw lignocellulose, as well as refined cellulose, hemicellulose, and lignin sources while identifying some of the current applications to which they are suited.
Discontinuous Galerkin discretization for quantum simulation of chemistry (2020)

Abstract All-electron electronic structure methods based on the linear combination of atomic orbitals method with Gaussian basis set discretization offer a well established, compact representation that forms much of the foundation of modern correlated quantum chemistry calculations—on both classical and quantum computers. Despite their ability to describe essential physics with relatively few basis functions, these representations can suffer from a quartic growth of the number of integrals. Recent results have shown that, for some quantum and classical algorithms, moving to representations with diagonal two-body operators can result in dramatically lower asymptotic costs, even if the number of functions required increases significantly. We introduce a way to interpolate between the two regimes in a systematic and controllable manner, such that the number of functions is minimized while maintaining a block-diagonal structure of the two-body operator and desirable properties of an original, primitive basis. Techniques are analyzed for leveraging the structure of this new representation on quantum computers. Empirical results for hydrogen chains suggest a scaling improvement from O ( N 4.5 ) in molecular orbital representations to O ( N 2.6 ) in our representation for quantum evolution in a fault-tolerant setting, and exhibit a constant factor crossover at 15 to 20 atoms. Moreover, we test these methods using modern density matrix renormalization group methods classically, and achieve excellent accuracy with respect to the complete basis set limit with a speedup of 1–2 orders of magnitude with respect to using the primitive or Gaussian basis sets alone. These results suggest our representation provides significant cost reductions while maintaining accuracy relative to molecular orbital or strictly diagonal approaches for modest-sized systems in both classical and quantum computation for correlated systems.
Polycrystalline low index contrast opals: Towards novel multimodal spectroscopy of diffusive sources of light (2004)

It is shown that polycrystalline low index contrast opals with submillimeter domains provide spatio-spectral diversity of scattering images that can be used for measuring the wavelengths of diffusive sources of light with nanometer accuracy.
Abstract CT113: A phase III, multicenter, randomized study evaluating the efficacy and safety and efficacy of erythrocyte encapsulated l-asparaginase (Ery001) versus native l-asparaginase (L-asp) in combination with COOPRALL regimen in patients with first relapse of acut (2015)

Abstract Asparaginases are a cornerstone in the treatment of ALL, but their utility is limited by toxicities including hypersensitivity. ERY001 improves pharmacokinetics and tolerability, while maintaining circulating asparaginase (ASPA) activity due to the protective barrier of the erythrocyte membrane. This phase III study enrolled pts with primary relapsed/refractory Ph- ALL. The co-primary endpoints were the duration of ASPA activity equal or greater than 100IU/L and the incidence of ASPA hypersensitivity during induction. Patients, aged 1-55 years, without prior ASPA hypersensitivity were randomized to ERY001 (150 IU/kg) or L-ASP(10.000IU/m2) in combination with COOPRALL. The patients with prior ASPA hypersensitivity received ERY001. ERY001 significantly reduced the incidence of ASPA hypersensitivity (0% vs 43%; p100IU/l significantly longer than L-ASP (20.5±5.2 vs 9.2±7.5 days; p&amp;lt;0.001). CR and clotting parameters were also significantly improved in the ERY001 arm. Other adverse events were generally similar in. One-year OS was 77% in the ERY001 arm vs 68% in L-ASP arm. ASPA activity was not reduced in hypersensitive patients. These highly encouraging results show that ERY001 is a suitable option for patients with relapsed ALL maintaining ASPA efficacy with improved tolerability. Citation Format: Yves Bertrand, Andre Baruchel, Xavier Thomas, Nicolas Blin, Emmanuelle Tavernier, Yves Perel, Norbert Vey, Virginie Gandemer, Iman ElHariry, Yann Godfrin. A phase III, multicenter, randomized study evaluating the efficacy and safety and efficacy of erythrocyte encapsulated l-asparaginase (Ery001) versus native l-asparaginase (L-asp) in combination with COOPRALL regimen in patients with first relapse of acut [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr CT113. doi:10.1158/1538-7445.AM2015-CT113
Operative and perioperative management of infected arteriovenous grafts (2016)

Vascular graft infections are a particularly troublesome complication for dialysis patients, many of whom are in an already immunocompromised state. The objective of this review is to detail the risk factors, etiology, diagnosis, perioperative and operative management of vascular graft infections.
Supplementary Figure 1 from Inhibition of CCAAT/Enhancer Binding Protein Family DNA Binding in Mouse Epidermis Prevents and Regresses Papillomas (2023)

Supplementary Figure 1 from Inhibition of CCAAT/Enhancer Binding Protein Family DNA Binding in Mouse Epidermis Prevents and Regresses Papillomas
Calditrichales (2021)

Abstract Cal.di.tri.cha'les N.L. masc. n. Caldithrix type genus of the order; ‐ ales ending to denote an order; N.L. fem. pl. n. Calditrichales the Caldithrix order. The order Calditrichales accommodates Gram‐stain‐negative bacteria with rod‐shaped cells. Known members of the order are obligate anaerobes, moderate thermophiles, and neutrophiles, growing either chemoorganoheterotrophically by fermentation of peptides or carbohydrates, or by anaerobic respiration with nitrate, or chemolithoheterotrophically using molecular hydrogen as the electron donor with nitrate as the electron acceptor. Inhabit deep‐sea or shallow‐water submarine hydrothermal environments. The type genus is Caldithrix . The order contains the single family Calditrichaceae and belongs to the class Calditrichia . DNA G + C content (mol %) : 43.3–47.3 ( T m and genome sequence). Type genus : Caldithrix Miroshnichenko et al. 2003 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Calditrichales is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Calditrichota / Calditrichia / Calditrichales The order Calditrichales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Calditrichales (version v220) ** . GTDB classification: d__Bacteria / p__Calditrichota / c__Calditrichia / o__Calditrichales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776