gebhart/patrepeval huggingface dataset:
Center for Advanced Signal and Imaging Sciences Workshop 2004 (2004)

Welcome to the Eleventh Annual C.A.S.I.S. Workshop, a yearly event at the Lawrence Livermore National Laboratory, presented by the Center for Advanced Signal & Image Sciences, or CASIS, and sponsored by the LLNL Engineering Directorate. Every November for the last 10 years we have convened a diverse set of engineering and scientific talent to share their work in signal processing, imaging, communications, controls, along with associated fields of mathematics, statistics, and computing sciences. This year is no exception, with sessions in Adaptive Optics, Applied Imaging, Scientific Data Mining, Electromagnetic Image and Signal Processing, Applied Signal Processing, National Ignition Facility (NIF) Imaging, and Nondestructive Characterization.
Increased Plasma Soluble PD-1 Concentration Correlates with Disease Progression in Patients with Cancer Treated with Anti-PD-1 Antibodies (2021)

Immune checkpoint inhibitors (ICIs) confer remarkable therapeutic benefits to patients with various cancers. However, many patients are non-responders or develop resistance following an initial response to ICIs. There are no reliable biomarkers to predict the therapeutic effect of ICIs. Therefore, this study investigated the clinical implications of plasma levels of soluble anti-programmed death-1 (sPD-1) in patients with cancer treated with ICIs. In total, 22 patients (13 with non-small-cell lung carcinoma, 8 with gastric cancer, and 1 with bladder cancer) were evaluated for sPD-1 concentration using enzyme-linked immunosorbent assays for diagnostic and anti-PD-1 antibody analyses. sPD-1 levels were low before the administration of anti-PD-1 antibodies. After two and four cycles of anti-PD-1 antibody therapy, sPD-1 levels significantly increased compared with pretreatment levels (<i>p</i> = 0.0348 vs. 0.0232). We observed an increased rate of change in plasma sPD-1 concentrations after two and four cycles of anti-PD-1 antibody therapy that significantly correlated with tumor size progression (<i>p</i> = 0.024). sPD-1 may be involved in resistance to anti-PD-1 antibody therapy, suggesting that changes in sPD-1 levels can identify primary ICI non-responders early in treatment. Detailed analysis of each cancer type revealed the potential of sPD-1 as a predictive biomarker of response to ICI treatment in patients with cancer.
Optical properties of GaN nanopillar and nanostripe arrays with embedded InGaN/GaN multi quantum wells (2007)

Abstract GaN nanopillar and nanostripe arrays with embedded InGaN/GaN multi quantum wells (MQWs) were fabricated from planar wafers with different quantum well widths using holographic lithography and subsequent reactive ion etching. Although the etching process led to a reduction in the MQW related luminescence, the etch related damage was successfully healed through annealing in NH 3 /N 2 mixtures under optimized conditions, and the annealed nanopatterned samples exhibited enhanced photoluminescence (PL) compared to the planar wafers. Angular‐resolved PL measurements revealed extraction of guided modes from the nanopillar and nanostripe arrays (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Shrinkage and Warpage (2022)

No AccessInjection Mold Design EngineeringOct 2022Shrinkage and WarpageDavid O. KazmerDavid O. KazmerSearch for more papers by this authorhttps://doi.org/10.3139/9781569908921.010SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetails 2022Pages: 353-394Print ISBN: 978-1-56990-891-4eISBN: 978-1-56990-892-1 Copyright & Permissions© 2022 Carl Hanser Verlag GmbH & Co. KGPDF downloadLoading ...
Behavioral Abnormalities in Knockout and Humanized Tau Mice (2020)

Microtubule-associated protein tau assists in stabilizing microtubules and has been particularly implicated in Alzheimer's disease (AD). Given the importance of tau to AD pathogenesis and therapies, it is important to understand non-classic physiological functions for this protein inside and outside the central nervous system (CNS). Our group has previously shown that tau ablation triggers glucose intolerance and pancreatic dysfunction in mice, suggesting that tau plays a role in peripheral metabolic regulation. Little is known about the role of tau in anxiety. Moreover, inconsistent results have been generated regarding the effects of tau deletion in memory. Here, we characterize systemic insulin resistance, anxiety-related behavior and memory in 15 to 20 weeks old Wild-Type (WT), Tau knockout (TauKO) and a distinct hTau mouse model consisting of tau knockout expressing the longest isoform (2N4R) of a non-mutant WT human Tau protein under the prion promoter (hTau). Our findings demonstrate that tau deletion leads to anxiety-related behavior, impaired contextual and cued fear memory. The presence of a human Tau transgene did not ameliorate the phenotypes observed in animals lacking the mouse tau protein and it elicited impairments in learning, memory, and peripheral insulin sensitivity. Our results suggest that tau protein plays a role in memory and anxiety-related behavior. Our findings also indicate that previously unrecognized functions for tau protein may be a complicating factor in using animal models on the TauKO background. Understanding the link between tau pathophysiology and cognitive and metabolic alterations is of great importance to establish the complete contribution of tau protein to AD pathogenesis.
Recurrence of renal lithiasis (2003)

Recurrent stone-formers can be classified into two large groups: those who always produce the same type of calculus (the most common type of recurrence was calcium oxalate dihydrate, followed by calcium oxalate monohydrate non-papillary and calcium oxalate monohydrate papillary calculi); and those who produce different types of renal calculi (the most frequent recurrences in this group were the changes calcium oxalate dihydrate-->calcium oxalate dihydrate/hydroxyapatite and calcium oxalate monohydrate-->calcium oxalate dihydrate).
N‐terminal myristylation of HBV preS1 domain enhances receptor recognition (2001)

The N-terminal portion of the large envelope protein of the human hepatitis B virus (HBV), the preS1 domain, plays a fundamental role in cell attachment and infectivity. Recent investigations have suggested that myristylation of preS1 Gly2 residue is essential for viral infectivity, but the importance of this post-translational modification on HBV-receptor interaction has not been elucidated completely. In this study we produced, using stepwise solid-phase chemical synthesis, the entire preS1[1-119] domain (adw2 subtype), and compared its receptor binding activity with the myristylated form, myristyl-preS1[2-119] in order to define the importance of fatty acid modification. Both synthetic proteins were fully characterized in terms of structural identity using TOF-MALDI mass spectrometry and analysis of tryptic fragments. Circular dichroism measurements indicated a low content of ordered structure in the preS1 protein, while the propensity of the myristylated derivative to assume a conformationally defined structure was more evident. HBV-receptor binding assays performed with plasma membranes preparations from the hepatocyte carcinoma cell line HepG2 clearly showed that the preS1[1-119] domain recognizes the HBV receptor, and confirmed that binding is occurring through the 21-47 region. The myristylated derivative recognized HBV receptor preparations with higher affinity than the preS1 domain, suggesting that the conformational transitions induced in the preS1 moiety by fatty acid post-translational modification are important for efficient attachment of viral particles to HBV receptors.
Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection (2022)

Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, <i>Batrachochytrium dendrobatidis</i> (Bd) and <i>B. salamandrivorans</i> (Bsal), in four salamander species with different <i>Batrachochytrium</i> susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores <i>in vitro</i>), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. <b>IMPORTANCE</b> How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.
Development and Validation of Noninvasive Magnetic Resonance Relaxometry for the In Vivo Assessment of Tissue-Engineered Graft Oxygenation (2016)

Techniques to monitor the oxygen partial pressure (pO<sub>2</sub>) within implanted tissue-engineered grafts (TEGs) are critically necessary for TEG development, but current methods are invasive and inaccurate. In this study, we developed an accurate and noninvasive technique to monitor TEG pO<sub>2</sub> utilizing proton (<sup>1</sup>H) or fluorine (<sup>19</sup>F) magnetic resonance spectroscopy (MRS) relaxometry. The value of the spin-lattice relaxation rate constant (R<sub>1</sub>) of some biocompatible compounds is sensitive to dissolved oxygen (and temperature), while insensitive to other external factors. Through this physical mechanism, MRS can measure the pO<sub>2</sub> of implanted TEGs. We evaluated six potential MRS pO<sub>2</sub> probes and measured their oxygen and temperature sensitivities and their intrinsic R<sub>1</sub> values at 16.4 T. Acellular TEGs were constructed by emulsifying porcine plasma with perfluoro-15-crown-5-ether, injecting the emulsion into a macroencapsulation device, and cross-linking the plasma with a thrombin solution. A multiparametric calibration equation containing R<sub>1</sub>, pO<sub>2</sub>, and temperature was empirically generated from MRS data and validated with fiber optic (FO) probes in vitro. TEGs were then implanted in a dorsal subcutaneous pocket in a murine model and evaluated with MRS up to 29 days postimplantation. R<sub>1</sub> measurements from the TEGs were converted to pO<sub>2</sub> values using the established calibration equation and these in vivo pO<sub>2</sub> measurements were simultaneously validated with FO probes. Additionally, MRS was used to detect increased pO<sub>2</sub> within implanted TEGs that received supplemental oxygen delivery. Finally, based on a comparison of our MRS data with previously reported data, ultra-high-field (16.4 T) is shown to have an advantage for measuring hypoxia with <sup>19</sup>F MRS. Results from this study show MRS relaxometry to be a precise, accurate, and noninvasive technique to monitor TEG pO<sub>2</sub> in vitro and in vivo.
Time‐Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile (2015)

The reaction mechanism of nitrile hydratase (NHase) was investigated using time-resolved crystallography of the mutant NHase, in which βArg56, strictly conserved and hydrogen bonded to the two post-translationally oxidized cysteine ligands, was replaced by lysine, and pivalonitrile was the substrate. The crystal structures of the reaction intermediates were determined at high resolution (1.2-1.3 Å). In combination with FTIR analyses of NHase following hydration in H2 (18) O, we propose that the metal-coordinated substrate is nucleophilically attacked by the O(SO(-) ) atom of αCys114-SO(-) , followed by nucleophilic attack of the S(SO(-) ) atom by a βArg56-activated water molecule to release the product amide and regenerate αCys114-SO(-) .
TiN Films Prepared by Flow Modulation Chemical Vapor Deposition using TiCl4 and NH3 (2001)

We propose a new chemical vapor deposition (CVD) process, the flow modulation chemical vapor deposition (FMCVD) process, to obtain high quality titanium nitride (TiN) films at low deposition temperature in a single CVD chamber. FMCVD uses sequential deposition and reduction processes, such as the deposition of TiN films followed by chlorine reduction. This cycle was repeated to achieve sufficient film thickness. By decreasing the thickness in one cycle, the residual chlorine concentration and the resistivity of the films decreased. Using FMCVD process, we could achieve low resistivity (250 µΩcm), low residual chlorine concentration (2 at.%) with uniform step coverage at low deposition temperature (380°C).
Isolation and Characterization of a Distinct Influenza A Virus from Egyptian Bats (2018)

Recently, two genetically distinct influenza viruses were detected in bats in Guatemala and Peru. We conducted influenza A virus surveillance among four bat species in Egypt. Out of 1,202 swab specimens, 105 were positive by real-time PCR. A virus was successfully isolated in eggs and propagated in MDCK cells in the presence of <i>N</i>-tosyl-l-phenylalanine chloromethyl ketone-treated trypsin. Genomic analysis revealed that the virus was phylogenetically distinct from all other influenza A viruses. Analysis of the hemagglutinin gene suggested a common ancestry with other H9 viruses, and the virus showed a low level of cross-reactivity with serum raised against H9N2 viruses. Bats were seropositive for the isolated viruses. The virus replicated in the lungs of experimentally infected mice. While it is genetically distinct, this virus shares several avian influenza virus characteristics suggesting a more recent avian host origin.<b>IMPORTANCE</b> Through surveillance, we isolated and characterized an influenza A virus from Egyptian fruit bats. This virus had an affinity to avian-like receptors but was also able to infect mice. Our findings indicate that bats may harbor a diversity of influenza A viruses. Such viruses may have the potential to cross the species barrier to infect other species, including domestic birds, mammals, and, possibly, humans.
L'ostéoporose, une pathologie dégénérative : prévention nutritionnelle (2014)

L'ostéoporose, une pathologie dégénérative : prévention nutritionnelle. Conférence du PASRES Programme d'Appui Stratégique à la Recherche Scientifique
Response to Comment on “Nonreciprocal Light Propagation in a Silicon Photonic Circuit” (2012)

Fan et al . raised technical concerns about our study regarding the Lorentz reciprocity theorem, with which we completely agree. Unfortunately, we incorrectly used the term “nonreciprocal” to describe the behavior of electromagnetic propagation in our devices. In our paper, this term does not refer to Lorentz reciprocity but to the asymmetric mode conversion that is experimentally demonstrated.
Pigerne stikker af fra drengene i karakterer til den fællesfaglige prøve: - har det noget med elevernes motivation for den fællesfaglige undervisning at gøre? (2021)

Pigerne høster meget højere karakterer end drengene i den nye fælles prøve i naturfagene, også markant højere end i den tidligere praktiske prøve i fysik/kemi. I denne artikel bruger vi omfattende surveydata fra vores prøvefølgeforskning til at afdække, om denne bias skyldes forskelle i oplevelsen af den fællesfaglige undervisning og i motivation for den nye naturfaglige undervisning. Undersøgelsen peger på, at forklaringen snarere skal søges i den prøveforberedende periode, selve prøven og/eller bias i lærerforventninger. Med inddragelse af selvreguleringsteori formuleres derfor en række forklarende hypoteser, som holdes op imod kvalitativ empiri fra følgeforskningen. Afslutningsvis diskuteres de mest relevante konsekvenser for praksis.
Identification of a class of non-conventional ER-stress-response-derived immunogenic peptides (2021)

Efforts to overcome resistance to immune checkpoint blockade therapy have focused on vaccination strategies using neoepitopes, although they cannot be applied on a large scale due to the "private" nature of cancer mutations. Here, we show that infection of tumor cells with Salmonella induces the opening of membrane hemichannels and the extracellular release of proteasome-generated peptides by the exacerbation of endoplasmic reticulum (ER) stress. Peptides released by cancer cells foster an antitumor response in vivo, both in mice bearing B16F10 melanomas and in dogs suffering from osteosarcoma. Mass spectrometry analysis on the supernatant of human melanoma cells revealed 12 peptides capable of priming healthy-donor CD8<sup>+</sup> T cells that recognize and kill human melanoma cells in vitro and when xenotransplanted in vivo. Hence, we identified a class of shared tumor antigens that are generated in ER-stressed cells, such as tumor cells, that do not induce tolerance and are not presented by healthy cells.
Effect of gallium focused ion beam milling on preparation of aluminium thin foils (2010)

Focussed ion beam milling has greatly extended the utility of the atom probe and transmission electron microscope because it enables sample preparation with a level of dimensional control never before possible. Using focussed ion beam it is possible to extract the samples from desired and very specific locations. The artefacts associated with this sample preparation method must also be fully understood. In this work, issues specifically relevant to the focussed ion beam milling of aluminium alloys are presented. After using the focussed ion beam as a sample preparation technique it is evident that gallium will concentrate in three areas of the sample: on the surface, on grain boundaries and at interphase boundaries. This work also shows that low-energy Ar ion nanomilling is potentially quite effective for removing gallium implantation layers and gallium from the internal surfaces of aluminium thin foils.
Cole et al. 2021 Endocrinology Supplementary Data (2021)

Tafazzin Deficiency Reduces Basal Insulin Secretion and Mitochondrial Function in Pancreatic Islets from Male Mice Supplementary Data
Forking and the Sustainability of the Developer Community Participation -- An Empirical Investigation on Outcomes and Reasons (2016)

A majority of OSS projects fails due to their inability to garner significant and sustained developer community participation. The problem proliferates when competing projects emerge from the source code of an existing project, a phenomenon called forking of the original project, claiming existing and potential developer community participation. In this study, we empirically analyze the influence of forking on the sustainability of the developer community participation in the original project. Further, we try to explain the observed behavior in terms of the characteristics of the project observed at the time of forking. A large-scale study of 2,217 projects hosted on GitHub shows that 1 in every 5 original projects observes a decline in the sustainability of the developer community participation after forking. We find that the negative effect is more pronounced in projects ported to GitHub from other platforms (≈ 20%), compared to GitHub developed projects (≈ 9%). We also find that the observed behavior can be explained in terms of the characteristics of the competing projects at the time of forking. For instance, in medium sized projects an increase in the maturity of the original project by a year decreases the odds of decline in the sustainability of the developer participation by 23%.
Coherent evolution of signal amplification by reversible exchange in two alternating fields (alt-SABRE) (2021)

Parahydrogen (pH2) is a convenient and cost efficient source for magnetic resonance signal enhancement. Transient interaction of pH2 with a metal organic complex in a signal amplification by reversible exchange (SABRE) experiment enabled more than 10% polarization for some 15N molecules. Here, we analyzed a variant of SABRE, consisting of an outer magnetic field alternating between a low field of ~1 \muT, where a polarization transfer takes place, and a higher field &gt;50 \muT (alt-SABRE). We found effects of both of these fields on amplitude and the frequency of polarization transfer. Deviation of a lower magnetic field from a "perfect" condition of level anti-crossing increases the frequency of polarization transfer that can be exploited for polarization of short-lived transient SABRE complexes i.e. some substrates. Moreover, the coherences responsible for polarization transfer at a lower field persisted during magnetic field variation and continued their spin evolution at higher field with a frequency of 2.5 kHz at 54 \muT. The latter should be taken into consideration for an efficient alt-SABRE.
ChemInform Abstract: New Routes to Alkylidyne‐Bridged Ditungsten Compounds Containing Alkoxide or Siloxide Ligands by the Activation of Ethylene. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Coefficients for Calculating Radiation Impedances and Far-Field Pressures of Free-Flooded Ring Transducers (1974)

Abstract : Tables of coefficients for determining the radiation impedance and far-field pressure of a free-flooded vibrating ring in an arbitrary medium at 45 frequencies for each of 36 ring geometries were produced. The only restriction on the known velocity distribution for using the tables is that the inside, top and bottom, and outside normal surface velocities must be uniform. Simple formulas for determining the normal surface velocity distribution for some special cases and formulas for determining the radiation resistance and far-field pressure in the low-frequency limit were developed. (Author)