gebhart/patrepeval huggingface dataset:
A path towards next generation x-ray gratings: compensation of substrate errors by a variation of the local line density (2021)

Diffraction gratings are key components in experiments with UV, VUV and soft x-ray radiation at synchrotron radiation and free-electron laser (FEL) facilities. They areused in monochromators to produce beams with narrow energy distribution, and in analyzers to provide high-resolution spectral analysis of scattered radiation. Today, such diffraction gratings consist of a large number of periodic grooves (typically tens to thousands per millimeter) arranged on the reflecting surface on a plane or concave substrate. The performance of the grating is also ultimately limited by the surface quality of the substrate. For best spectral resolution, the substrates need to be ultra-precise and superpolished, with typical lengths of 100 – 300 mm and shape errors of 1-2 nanometers, slope errors in the order of 100 nrad, and a roughness in the Ångstrom scale. Today, the line patterns of x-ray gratings are mostly produced either by holographic exposures of interfering laser beams into a photo resist, or by ruling machines that imprint the grating groves in a line-by-line manner into a soft metal layer. As an alternative to these established methods, we present a strategy of grating fabrication by electron-beam lithography (EBL). This technique can expose arbitrary patterns with high resolution and placement accuracy at a speed sufficient for x-ray grating fabrication. We have performed optical metrology of a low-cost grating substrate, which served as the basis for an aligned exposure of a corrected grating pattern to yield a laminar grating with a constant deflection angle along the substrate surface. We have confirmed that the effects of slope errors were strongly compensated over an extended wavelength range by using synchrotron radiation in the soft x-ray range. This work shows a path for circumventing the limited availability of high quality reflective substrates to obtain gratings with performance beyond what is possible today.
Screening of DNA aptamers against multiple proteins in tissue (2005)

We report the development of a novel screening method for DNA aptamers against multiple proteins in the target tissue. Although a purified single protein is generally used in screening of aptamers at present, such a simultaneous selection would be very advantageous in efficiency and selectivity. We first carried out the screening in situ and it was suggested that aptamers against particular target proteins were enriched. We also developed another novel screening method named Aptamer Blotting based on protein separation by PAGE and its visualization with fluorescein labeled aptamers and it was demonstrated that this method allowed the simultaneous selection of specific aptamers against multiple proteins.
Initial Experience With Simultaneous 18F-FDG PET/MRI in the Evaluation of Cardiac Sarcoidosis and Myocarditis (2017)

Simultaneous cardiac PET/MRI is feasible in the evaluation of cardiac sarcoidosis and myocarditis achieving diagnostic image quality.
Novel Approach Toward Plasma Enhancement in Trench-Insulated Gate Bipolar Transistors (2015)

In this letter, a trench-insulated gate bipolar transistor (IGBT) design with local charge compensating layers featured at the cathode of the device is presented and analyzed. The superjunction or reduced surface effect proves to be very effective in overcoming the inherited ON-state versus breakdown tradeoff appearing in conventional devices, such as the soft punch through plus or field stop plus (FS+) IGBTs. This design enhances the ON-state performance of the FS+IGBT by increasing the plasma concentration at the cathode side without affecting either the switching performance or the breakdown rating.
In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design (2018)

Plants are extensively used in traditional medicine, and several plant antimicrobial peptides have been described as potential alternatives to conventional antibiotics. However, after more than four decades of research no plant antimicrobial peptide is currently used for treating bacterial infections, due to their length, post-translational modifications or high dose requirement for a therapeutic effect . Here we report the design of antimicrobial peptides derived from a guava glycine-rich peptide using a genetic algorithm. This approach yields guavanin peptides, arginine-rich α-helical peptides that possess an unusual hydrophobic counterpart mainly composed of tyrosine residues. Guavanin 2 is characterized as a prototype peptide in terms of structure and activity. Nuclear magnetic resonance analysis indicates that the peptide adopts an α-helical structure in hydrophobic environments. Guavanin 2 is bactericidal at low concentrations, causing membrane disruption and triggering hyperpolarization. This computational approach for the exploration of natural products could be used to design effective peptide antibiotics.
Enzymatic Depolymerization of Gum Tragacanth: Bifidogenic Potential of Low Molecular Weight Oligosaccharides (2013)

Gum tragacanth derived from the plant "goat's horn" (Astragalus sp.) has a long history of use as a stabilizing, viscosity-enhancing agent in food emulsions. The gum contains pectinaceous arabinogalactans and fucose-substituted xylogalacturonans. In this work, gum tragacanth from Astragalus gossypinus was enzymatically depolymerized using Aspergillus niger pectinases (Pectinex BE Color). The enzymatically degraded products were divided into three molecular weight fractions via membrane separation: HAG1 < 2 kDa; 2 kDa < HAG2 < 10 kDa; HAG3 > 10 kDa. Compositional and linkage analyses showed that these three fractions also varied with respect to composition and structural elements: HAG1 and HAG2 were enriched in arabinose, galactose, and galacturonic acid, but low in fucose and xylose, whereas HAG3 was high in (terminal) xylose, fucose, and 1,4-bonded galacturonic acid, but low in arabinose and galactose content. The growth-stimulating potential of the three enzymatically produced gum tragacanth fractions was evaluated via growth assessment on seven different probiotic strains in single-culture fermentations on Bifidobacterium longum subsp. longum (two strains), B. longum subsp. infantis (three strains), Lactobacillus acidophilus , B. lactis, and on one pathogenic strain of Clostridium perfringens . The fractions HAG1 and HAG2 consistently promoted higher growth of the probiotic strains than HAG3, especially of the three B. longum subsp. infantis strains, and the growth promotion on HAG1 and HAG2 was better than that on galactan (control). HAG3 completely inhibited the growth of the C. perfringens strain. Tragacanth gum is thus a potential source of prebiotic carbohydrates that exert no viscosity effects and which may find use as natural functional food ingredients.
A phase II trial of risk-adapted treatment for muscle invasive bladder cancer after neoadjuvant accelerated MVAC. (2018)

TPS537 Background: Cisplatin-based neoadjuvant chemotherapy (NAC) followed by cystectomy (Cx) or chemoradiation (CRT) is the standard of care for urothelial carcinoma (UC) pts with muscle invasive bladder cancer (MIBC). Both Cx and CRT carry potential short and long-term toxicity and quality of life implications. Recent work has shown that mutations in DNA damage repair/response genes are predictive of pathologic downstaging after NAC at the time of Cx, with those pts achieving pT0 disease demonstrating excellent long-term survival (Van Allen et al. Cancer Discov. 2014; Plimack et al. Eur Urol. 2015; Liu et al. JAMA Oncol. 2016; Teo et al. CCR. 2017). Sparing pts Cx or CRT after NAC without compromising oncologic outcomes would improve quality of life and decrease morbidity. Methods: A phase II, parallel arm, multi-institutional clinical trial (NCT02710734) is being conducted to evaluate a risk-adapted approach to treatment of MIBC. Pts with cT2-T3N0M0 UC of the bladder, ECOG PS 0-1 and CrCl≥50 mL/min, undergo NAC with accelerated methotrexate, vinblastine, doxorubicin, and cisplatin. Simultaneously, the pre-NAC TURBT specimen is submitted for deep sequencing to identify variants in a panel of cancer-relevant genes (Caris Life Sciences, Phoenix, AZ). Those with an alteration in ATM, RB1, FANCC or ERCC2 and no clinical evidence of disease by restaging TUR and imaging post-NAC will begin a pre-defined active surveillance regimen that includes urinary cytological, cystoscopic, and radiographic evaluations. The remaining pts will undergo bladder-directed therapy at the discretion of the pt and clinician applying either intravesical therapy ( &lt; cT2 post-NAC), CRT or Cx (≤cT2 post-NAC) or Cx (≥cT3 post-NAC). The primary objective is metastasis-free survival (MFS) at 2 years for all enrolled and evaluable pts. The trial has a non-inferiority design with a 14% margin between risk-adapted treatment (MFS = 78%) and standard-of-care (MFS = 64%) with a sample size of 70 pts, 82% power and a type I error of 0.045. Key secondary and translational objectives: assess the rate of UC recurrence in active surveillance pts; validate biomarkers of response to NAC; evaluate urinary biomarkers consistent with persistent UC. Clinical trial information: NCT02710734.
The Johnson-Lindenstrauss Lemma Meets Compressed Sensing (2006)

We show how two fundamental results in analysis related to n-widths and Compressed Sensing are intimately related to the Johnson-Lindenstrauss lemma. Our elementary approach is based on the same concentration inequalities for random inner products that have recently provided simple proofs of the Johnson-Lindenstrauss lemma. We show how these ideas lead to simple proofs of Kashin’s theorems on widths of finite balls in Euclidean space (and their improvements due to Gluskin) as well as the existence of optimal Compressed Sensing measurement matrices. In the process we also prove that these measurement matrices are universal with respect to the sparsity-inducing basis.
Controlling the object phase for g‐factor reduction in phase‐Constrained parallel MRI using spatially selective RF pulses (2017)

Combining phase-constrained reconstruction and phase optimization by tailored radiofrequency pulses can provide notable improvement in the signal-to-noise ratio and reconstruction quality of accelerated MRI. Magn Reson Med 79:2113-2125, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
A pocket-factor-triggered conformational switch in the hepatitis B virus capsid (2021)

International audience
A nonsense mutation in the retinal specific guanylate cyclase gene is the cause of Leber congenital amaurosis in a large inbred kindred from Jordan (1999)

Editor—Leber congenital amaurosis (LCA) (MIM 204000) has the earliest onset and is the most severe form of retinal dystrophy.1-3 It is an autosomal recessive condition that is recognised within the first few months of life because of impaired vision and an extinguished electroretinogram.4 Nystagmus, specifically pendular, and eye poking are frequently observed early on,5 while hypermetropia and keratoconus may develop later during the course of the disease.6 7 Genetic heterogeneity was confirmed when the first gene of LCA was mapped to chromosome 17p13.1 ( LCA1 ) by homozygosity mapping in consanguineous Arab families.8 9 Four different mutations in the retinal specific guanylate cyclase gene ( RETGC ) were found in four unrelated probands and thus LCA1 was assumed to result from homozygous alterations in this gene.10 

We report here a nonsense mutation in the RETGC gene, which in the homozygous state is responsible for LCA in a large inbred tribe from Jordan. We had already identified a large, highly inbred family from the Jordan valley consisting of about 2000 living subjects, in which affected members have LCA.11 A 31 member subset of this family was investigated (fig 1). All members were examined by an ophthalmologist and a paediatrician. Four patients had ERG performed (Nos 3, 9, 13, 14). Blood samples were collected from 28 family members …
Prospective study of serum and aqueous humour anti‐Hsp70.1 IgG antibody levels in ocular toxoplasmosis (2020)

While the level of IgG anti-Hsp-70.1 antibody in AH did not improve the laboratory diagnosis of ocular toxoplasmosis, its level in serum was of major significance for retinal damage diagnosis.
Adaptive Sabotage-Tolerant Scheduling for Peer-to-Peer Grids (2009)

Computational grids are an infrastructure to aggregate computing power to support and improve performance of parallel applications. Some of them evolved in the sense of forming free-to-join communities over the Internet and became peer-to-peer (P2P) grids. One of the main problems associated with users freely joining and leaving grid communities is that cheating users may corrupt the final computation. Sabotage tolerance techniques, generally based on replication, tackle this problem by estimating the computation correctness. The use of credibility-based techniques in the task scheduling may promote high confidence levels for the computation results, whilst minimizing replication costs, when compared to the traditional voting technique. This work aims at evaluating the usage of scheduling heuristics that adapt themselves to the machines' confidence level in P2P grids. Three scheduling heuristics were evaluated. They present advantages and disadvantages, leading us to the conclusion that the performance of the scheduling heuristics is deeply influenced by the grid environment.
Technical Considerations for Semantic Segmentation in MRI using Convolutional Neural Networks (2019)

High-fidelity semantic segmentation of magnetic resonance volumes is critical for estimating tissue morphometry and relaxation parameters in both clinical and research applications. While manual segmentation is accepted as the gold-standard, recent advances in deep learning and convolutional neural networks (CNNs) have shown promise for efficient automatic segmentation of soft tissues. However, due to the stochastic nature of deep learning and the multitude of hyperparameters in training networks, predicting network behavior is challenging. In this paper, we quantify the impact of three factors associated with CNN segmentation performance: network architecture, training loss functions, and training data characteristics. We evaluate the impact of these variations on the segmentation of femoral cartilage and propose potential modifications to CNN architectures and training protocols to train these models with confidence.
Lactococcus lactis STRAINS ECTOPICALLY EXPRESS THE INTERNALIN-A PROTEIN FROM Listeria monocytogenes UNDER THE BACTERIAL SEPTUM REGION (2006)

In the present report, we describe how Lactococcus lactis strains ectopically express the internalin-A protein from Listeria monocytogenes at the cell surface, situated specifically under the bacterial septum region. Such findings provide relevant insights into the spatial expression pattern of exogenous genes in lactic bacteria.
Growth Hormone Receptor Deficiency Protects against Age-Related NLRP3 Inflammasome Activation and Immune Senescence (2016)

The hallmarks of age-related immune senescence are chronic inflammation, aberrant expansion of effector memory, and loss of naive T lymphocytes due in part to systemic activation of innate immune sensor NLRP3 inflammasome in myeloid lineage cells. The endogenous mechanisms that regulate inflammasome activation during aging are unknown. Here, we present evidence that growth hormone receptor (GH-R)-dependent downregulation of NLRP3 inflammasome in macrophages is linked to pro-longevity effects that maintain immune system homeostasis in aging. Deletion of GH-R prevented the macrophage-driven age-related activation of inflammasome in response to NLRP3 ligands and also increased the preservation of naive T cells, even in advanced age and with higher IFNγ secretion from effector cells. The mechanism of inflammasome inhibition is linked to autocrine somatotropic axis as ablation of IGF1R in macrophages lowered the NLRP3 inflammasome activation. Together, our findings show that functional somatotropic axis in macrophages controls inflammation, thus linking NLRP3-mediated innate immune signaling to health span and longevity.
Determining Attributes to Maximize Visibility of Objects (2009)

In recent years, there has been significant interest in the development of ranking functions and efficient top-k retrieval algorithms to help users in ad hoc search and retrieval in databases (e.g., buyers searching for products in a catalog). We introduce a complementary problem: How to guide a seller in selecting the best attributes of a new tuple (e.g., a new product) to highlight so that it stands out in the crowd of existing competitive products and is widely visible to the pool of potential buyers. We develop several formulations of this problem. Although the problems are NP-complete, we give several exact and approximation algorithms that work well in practice. One type of exact algorithms is based on integer programming (IP) formulations of the problems. Another class of exact methods is based on maximal frequent item set mining algorithms. The approximation algorithms are based on greedy heuristics. A detailed performance study illustrates the benefits of our methods on real and synthetic data.
Frequency Measurement of an Optical Lattice Clock (2007)

A frequency measurement system is developed away from a National Metrological Institute with a frequency link to International Atomic Time (TAI). The absolute frequency of the <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> - <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> clock transition of the <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">87</sup> Sr lattice clock is determined to be 429,228,004,229,875(4) Hz. The frequency measurement system is being further improved by introducing an optical fiber link and by upgrading the GPS link.
Table S5 from The Impact of Smoking and TP53 Mutations in Lung Adenocarcinoma Patients with Targetable Mutations—The Lung Cancer Mutation Consortium (LCMC2) (2023)

&lt;p&gt;Supplemental Table 5. All subjects with all molecular results in LCMC2.&lt;/p&gt;
A long-term reliability analysis of a creep-immune RF-MEMS tunable capacitor (2011)

Actuators used in RF-MEMS tunable capacitors have an issue of creep-induced deformation. The creep is caused by a ductile-metal beam which is indispensable to attain the low loss. To avoid this issue, we previously reported an actuator structure that uses a brittle material, silicon nitride (SiN), at the stress-concentrated spring portions. The present paper aims to clarify a long-term creep immunity of the actuator. We first determined parameters of Norton's law by measurements and then carried out Finite Element Method (FEM) simulations. As a result, we found that the shift of the up-state capacitance is 2.2% after keeping the actuator in down-state position for 3 years at 85°C.
Elementary versus composite interfaces in distributed real-time systems (2003)

To manage the complexity of large distributed real-time systems, a system must be partitioned into nearly autonomous subsystems that communicate across small well-specified interfaces. The form and placement of these interfaces determines the system structure and its understandability. This paper investigates two different types of unidirectional information-flow interfaces, the elementary interface and the composite interface. It is argued that systems that interact by elementary interfaces support composability, and are easier to understand and validate than systems that are based on composite interfaces.
Kinetics and Mechanism of Oxidation of L‐Cysteine by Bis‐3‐di‐2‐pyridylketone‐2‐thiophenylhydrazone‐iron(III) Complex in Acidic Medium (2010)

The kinetics of oxidation of L ‐cysteine by 3‐di‐2‐pyridylketone‐2‐thiophenylhydrazone‐iron(III), [Fe(DPKTH) 2 ] 3+ complex in acidic medium was studied spectrophotometrically at 36 °C temperature. The molar ratios of DPKTH to iron(III) and iron(II) individually, were found to be [2:1] [DPKTH : iron(III)/(II)]. The reaction was stroked to be first‐order with respect to iron(III) and L ‐cysteine, second‐order with respected to DPKTH ligand and reversed second‐order with respected to hydrogen ion concentration. Added salts did not affect the rate and no free radical was detected when radical detector was placed in the reaction mixture. Ethanol solvent ratio was found to effect both the initial rate and the maximum absorbance (λ max ) of [Fe(DPKTH) 2 ] 2+ complex. The initial rate rose when the temperature was increased which empowered to calculate the activation parameters. A suitable reaction mechanism was proposed.
Antibody to Mol abrogates the increase in neutrophil phagocytosis and degranulation induced by granulocyte‐macrophage colony‐stimulating factor (1989)

We studied the ability of the human hemopoietic growth factors, granulocyte-macrophage colony-stimulating factor (GM-CSF) and granulocyte colony-stimulating factor (G-CSF) to activate polymorphonuclear neutrophils (PMN) for increased phagocytosis of opsonized Candida albicans and enhanced degranulation. Exposure of neutrophils to these two growth factors resulted in an increased number of Candida phagocytosed. Pretreatment of the neutrophils with the monoclonal antibody anti-Mol abrogated the enhanced phagocytosis associated with GM-CSF priming but not that of G-CSF primed PMN. In examining the effect of these two colony-stimulating factors (CSFs) on neutrophil degranulation we found that GM-CSF induced enhanced release of lysozyme from cytochalasin-treated PMN in the presence of Candida; however, G-CSF did not. The effect of GM-CSF on lysozyme release was abrogated by anti-Mol antibody. These data suggest that GM-CSF and G-CSF prime PMN for certain enhanced functional activities by distinct mechanisms. The differential effect of the CSFs on neutrophil degranulation may relate to the more common inflammatory symptoms seen when GM-CSF is used clinically as compared to the experience with G-CSF.
A Strategy for Functional Proteomic Analysis of Glycosidase Activity from Cell Lysates (2004)

Eine Vielzweckmarkierung: Der Desaktivator 1 markiert die katalytischen Nucleophile von konfigurationserhaltenden β-Glycosidasen kovalent unter Bildung von 2. Die kleine Azidgruppe ermöglicht die Markierung von Enzymen mit sterisch belasteten aktiven Zentren. Staudinger-Ligation mit Phosphin-FLAG überführt 2 in 3, das zum Nachweis der Aktivität solcher β-Glycosidasen in komplexen Mischungen und zur Bestimmung ihres Aktivitätsprofils genutzt werden kann.
Clinical outcomes using rhBMP-2 in spinal fusion applications (2008)

Bone morphogenetic proteins (BMPs) are an integral part of new bone formation and are capable of inducing the entire bone formation cascade [, ]. It is this unique property that allows these proteins, when they are combined with a suitable carrier, to be used as a bone graft replacement. The new bone formation occurs in four distinct phases: recruitment and proliferation, differentiation, calcification, and maturation []. During the recruitment and proliferation phase, undifferentiated mesenchymal cells are attracted to the site by chemotaxis. These stem cells divide and increase in number. During the differentiation phase, the mesenchymal stem cells are transformed into osteoblasts. During the calcification phase, the osteoblasts produce matrix, generate callous and form new bone. During the maturation phase, the newly formed bone remodels into trabecular bone and increases in vascularity.