gebhart/patrepeval huggingface dataset:
Subcortical brain iron deposition and cognitive performance in older women with breast cancer receiving adjuvant chemotherapy: A pilot MRI study (2018)

As the number of older adults in the U.S. increases, so too will the incidence of cancer and cancer-related cognitive impairment (CRCI). However, the exact underlying biological mechanism for CRCI is not yet well understood. We utilized susceptibility-weighted imaging with quantitative susceptibility mapping, a non-invasive MRI-based technique, to assess longitudinal iron deposition in subcortical gray matter structures and evaluate its association with cognitive performance in women age 60+ with breast cancer receiving adjuvant chemotherapy and age-matched women without breast cancer as controls. Brain MRI scans and neurocognitive scores from the NIH Toolbox for Cognition were obtained before chemotherapy (time point 1) and within one month after the last infusion of chemotherapy for the patients and at matched intervals for the controls (time point 2). There were 14 patients age 60+ with breast cancer (mean age 66.3 ± 5.3 years) and 13 controls (mean age 68.2 ± 6.1 years) included in this study. Brain iron increased as age increased. There were no significant between- or within- group differences in neurocognitive scores or iron deposition at time point 1 or between time points 1 and 2 (p &amp;gt; 0.01). However, there was a negative correlation between iron in the globus pallidus and the fluid cognition composite scores in the control group at time point 1 (r = -0.71; p &amp;lt; 0.01), but not in the chemotherapy group. Baseline iron in the putamen was negatively associated with changes in the oral reading recognition scores in the control group (r = 0.74, p &amp;lt; 0.01), but not in the chemotherapy group. Brain iron assessment did not indicate cancer or chemotherapy related short-term differences, yet some associations with cognition were observed. Studies with larger samples and longer follow-up intervals are warranted.
Intracytoplasmic maturation of the human immunodeficiency virus type 1 reverse transcription complexes determines their capacity to integrate into chromatin (2006)

These results suggest that RTC maturation occurs predominantly in the cytoplasm. Immature RTCs containing RT and incomplete DNA can translocate into the nucleus during mitosis and complete reverse transcription, but are defective for integration.
Membrane‐binding peptides for extracellular vesicles on‐chip analysis (2020)

ABSTRACT Small extracellular vesicles (sEVs) present fairly distinctive lipid membrane features in the extracellular environment. These include high curvature, lipid‐packing defects and a relative abundance in lipids such as phosphatidylserine and ceramide. sEV membrane could be then considered as a “universal” marker, alternative or complementary to traditional, characteristic, surface‐associated proteins. Here, we introduce the use of membrane‐sensing peptides as new, highly efficient ligands to directly integrate sEV capturing and analysis on a microarray platform. Samples were analysed by label‐free, single‐particle counting and sizing, and by fluorescence co‐localisation immune staining with fluorescent anti‐CD9/anti‐CD63/anti‐CD81 antibodies. Peptides performed as selective yet general sEV baits and showed a binding capacity higher than anti‐tetraspanins antibodies. Insights into surface chemistry for optimal peptide performances are also discussed, as capturing efficiency is strictly bound to probes surface orientation effects. We anticipate that this new class of ligands, also due to the versatility and limited costs of synthetic peptides, may greatly enrich the molecular toolbox for EV analysis.
Prebiotic Colloidal Oat Supports the Growth of Cutaneous Commensal Bacteria Including S. epidermidis and Enhances the Production of Lactic Acid (2021)

Colloidal oat directly affects the growth, metabolism, lactic acid production, and gene expression of skin commensal bacteria, as shown via in vitro studies. The increased production of lactic acid reflects clinical observations with colloidal oat-containing skin moisturizers. Our findings suggest a new mechanism for colloidal oat as a skin prebiotic, which may contribute to improvements in skin and microbiome diversity in various skin conditions, including dry/itchy skin and atopic dermatitis.
FINITE ELEMENT ANALYSIS OF A MOVING PACKED-BED PARTICLE-TO-sCO2 HEAT EXCHANGER. (2021)

Abstract not provided.
Heme Stoichiometry of Heterodimeric Soluble Guanylate Cyclase (1995)

The soluble form of guanylate cyclase (sGC) is to date the only definitive receptor for the novel signaling agent nitric oxide (.NO). .NO increases the Vmax of sGC by 100-200-fold, and it has been proposed that this activation occurs subsequent to the binding of .NO to a heme moiety on the enzyme. It has previously been demonstrated that the enzyme can be purified in a state containing as much as 1 heme per heterodimer. However, since the two subunits of the heterodimer display considerable homology, and the enzyme routinely loses heme upon purification, it has been unclear whether the native heme stoichiometry is 1 per heterodimer or 2 per heterodimer. Using a novel procedure, the enzyme has been purified to homogeneity from bovine lung in a state containing 1.52 +/- 0.10 equiv of heme per heterodimer, indicating that the native heme stoichiometry is 2 per heterodimer. The .NO-activated specific activity of this enzyme is increased by 50% over that of enzyme containing 1 heme per heterodimer and is the highest specific activity ever observed for sGC. Spectrally only one type of heme is observed, indicating that both hemes in the heterodimer are in similar environments. It is concluded that each subunit of the heterodimer binds 1 equiv of heme at a site conserved between the two subunits. Alignment of the nine published cDNA sequences for sGC indicates that the heme binding domain is the central portion of each subunit, corresponding to residues 213-370 in the bovine beta 1 sequence.
Semisynthetic glycopeptide antibiotics derived from LY264826 active against vancomycin-resistant enterococci (1996)

Certain derivatives of the glycopeptide antibiotic LY264826 with N-alkyl-linked substitutions on the epivancosamine sugar are active against glycopeptide-resistant enterococci. Six compounds representing our most active series were evaluated for activity against antibiotic-resistant, gram-positive pathogens. For Enterococcus faecium and E. faecalis resistant to both vancomycin and teicoplanin, the MICs of the six semisynthetic compounds for 90% of the strains tested were 1 to 4 micrograms/ml, compared with 2,048 micrograms/ml for vancomycin and 256 micrograms/ml for LY264826. For E. faecium and E. faecalis resistant to vancomycin but not teicoplanin, the MICs were 0.016 to 1 micrograms/ml, compared with 64 to 1,024 micrograms/ml for vancomycin. The compounds were highly active against vancomycin-susceptible enterococci and against E. gallinarum and E. casseliflavus and showed some activity against isolates of highly vancomycin-resistant leuconostocs and pediococci. The MICs for 90% of the strains of methicillin-resistant Staphylococcus aureus tested were typically 0.25 to 1 micrograms/ml, compared with 1 microgram/ml for vancomycin. Against methicillin-resistant S. epidermidis MICs ranged from 0.25 to 2 micrograms/ml, compared with 1 to 4 micrograms/ml for vancomycin and 4 to 16 micrograms/ml for teicoplanin. The spectrum of these new compounds included activity against teicoplanin-resistant, coagulase-negative staphylococci. The compounds exhibited exceptional potency against pathogenic streptococci, with MICs of < or = 0.008 microgram/ml against Streptococcus pneumoniae, including penicillin-resistant isolates. In in vivo studies with a mouse infection model, the median effective doses against a challenge by S. aureus, S. pneumoniae, or S. pyogenes were typically 4 to 20 times lower than those of vancomycin. Overall, these new glycopeptides, such as LY307599 and LY333328, show promise for use as agents against resistant enterococci, methicillin-resistant S. aureus, and penicillin-resistant pneumococci.
Layer removal from triso-coated particles with a cold plasma (2010)

Summary form only given. Generation IV nuclear reactors generally use small spherical UO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> particles that are coated with a multitude of layers including graphite and SiC. These particles are called TRISO-particles. During the manufacturing process some of the particles are scrapped because of defective layer formation or layer densities and are therefore outside the prescribed specifications. In order to recover the uranium contained inside such particles, a process was developed where the carbon and SiC layers was removed by oxidizing and etching it in a non-thermal plasma.
Enhancement of temporal cues to pitch in cochlear implants: Effects on pitch ranking (2012)

The abilities to hear changes in pitch for sung vowels and understand speech using an experimental sound coding strategy (eTone) that enhanced coding of temporal fundamental frequency (F0) information were tested in six cochlear implant users, and compared with performance using their clinical (ACE) strategy. In addition, rate- and modulation rate-pitch difference limens (DLs) were measured using synthetic stimuli with F0s below 300 Hz to determine psychophysical abilities of each subject and to provide experience in attending to rate cues for the judgment of pitch. Sung-vowel pitch ranking tests for stimuli separated by three semitones presented across an F0 range of one octave (139-277 Hz) showed a significant benefit for the experimental strategy compared to ACE. Average d-prime (d') values for eTone (d' = 1.05) were approximately three time larger than for ACE (d' = 0.35). Similar scores for both strategies in the speech recognition tests showed that coding of segmental speech information by the experimental strategy was not degraded. Average F0 DLs were consistent with results from previous studies and for all subjects were less than or equal to approximately three semitones for F0s of 125 and 200 Hz.
Membrane Insertion, Glycosylation, and Oligomerization of Inositol Trisphosphate Receptors in a Cell-free Translation System (1997)

In order to study the membrane topology, processing, and oligomerization of inositol trisphosphate receptor (IP3R) isoforms, we have utilized RNA templates encoding putative transmembrane domains to program a cell-free translation system of rabbit reticulocyte lysates supplemented with canine pancreas microsomes. In the absence of microsomes, translation of the RNA templates encoding all the putative transmembrane domains present in the C-terminal segment of the type I (1TM) and type III (3TM) IP3R isoforms resulted in a 62- and 59-kDa polypeptide, respectively. In both cases, an additional band approximately 3 kDa larger was observed upon the addition of microsomes. Both bands in the translation doublet were integrated into microsomal membranes and were full-length translation products, as shown by sedimentation through a sucrose cushion and immunoprecipitation with C-terminal isoform-specific antibodies. With both isoforms, N-glycopeptidase F digestion indicates that the upper band in the doublet corresponds to a glycosylated translation product. A 17-kDa protected fragment was observed after proteinase-K digestion of 1TM translated in the presence of microsomes. The pattern and size of protected fragments was consistent with the current six-transmembrane domain model of IP3R topology. Cotranslation of both 1TM and 3TM RNA templates in the presence of microsomes followed by immunoprecipitation with isoform specific antibodies revealed coimmunoprecipitation of translation products. This was not observed when the isoforms were translated separately and then mixed, suggesting that heteroligomerization occurs cotranslationally. A construct encoding only the first putative transmembrane domain of the type I isoform was found to be sufficient for integration into membranes but was unable to oligomerize with either 1TM or 3TM. Cotranslation experiments using additional constructs indicate that the major structural determinant for homoligomerization lies between putative transmembrane domain 5 and the C terminus. A second oligomerization domain involved in stabilization of heteroligomers is present within the first four transmembrane domains.
A highly versatile beamforming ASIC for application in broad-band fixed wireless access systems (2000)

This paper presents the architecture and implementation of a highly versatile beamforming ASIC (VBASIC) for application in broad-band fixed wireless access systems. The architecture accommodates a large number of user-programmable parameters, which broaden the chip's application base to a variety of present and future systems for fixed wireless access. These features include: (a) a novel structure for variable-rate interpolation that allows operation at any user specified symbol rate from 625 kBaud to 10 MBaud; (b) operation in both the transmit and receive modes; (c) support for arrays consisting of up to 64 elements; (d) a unique shaping filter structure with programmable canonic signed digit coefficients; (e) complete reconfiguration of all parameters on a per-time-slot basis; and f) digital intermediate-frequency interface. The resulting layout measures 7.1 mm on each side in the 0.6-/spl mu/m HPCMOS14 process and consists of a total of 787 987 transistors.
MRI-guided Disruption of the Blood-brain Barrier using Transcranial Focused Ultrasound in a Rat Model (2012)

Focused ultrasound (FUS) disruption of the blood-brain barrier (BBB) is an increasingly investigated technique for circumventing the BBB(1-5). The BBB is a significant obstacle to pharmaceutical treatments of brain disorders as it limits the passage of molecules from the vasculature into the brain tissue to molecules less than approximately 500 Da in size(6). FUS induced BBB disruption (BBBD) is temporary and reversible(4) and has an advantage over chemical means of inducing BBBD by being highly localized. FUS induced BBBD provides a means for investigating the effects of a wide range of therapeutic agents on the brain, which would not otherwise be deliverable to the tissue in sufficient concentration. While a wide range of ultrasound parameters have proven successful at disrupting the BBB(2,5,7), there are several critical steps in the experimental procedure to ensure successful disruption with accurate targeting. This protocol outlines how to achieve MRI-guided FUS induced BBBD in a rat model, with a focus on the critical animal preparation and microbubble handling steps of the experiment.
Slide-Free Microscopy via UV Surface Excitation (2016)

Journal Article Slide-Free Microscopy via UV Surface Excitation Get access Richard Levenson, Richard Levenson Dept. of Pathology and Laboratory Medicine, UC Davis Medical Ctr., Sacramento, CA Search for other works by this author on: Oxford Academic Google Scholar Farzad Fereidouni, Farzad Fereidouni Dept. of Pathology and Laboratory Medicine, UC Davis Medical Ctr., Sacramento, CA Search for other works by this author on: Oxford Academic Google Scholar Zachary Harmany, Zachary Harmany Dept. of Pathology and Laboratory Medicine, UC Davis Medical Ctr., Sacramento, CA Search for other works by this author on: Oxford Academic Google Scholar Miao Tan, Miao Tan Dept. of Pathology and Laboratory Medicine, UC Davis Medical Ctr., Sacramento, CA Search for other works by this author on: Oxford Academic Google Scholar Mirna Lechpammer, Mirna Lechpammer Dept. of Pathology and Laboratory Medicine, UC Davis Medical Ctr., Sacramento, CA Search for other works by this author on: Oxford Academic Google Scholar Stavros Demos Stavros Demos Lawrence Livermore National Laboratory, Livermore, CA Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 22, Issue S3, 1 July 2016, Pages 1002–1003, https://doi.org/10.1017/S1431927616005857 Published: 25 July 2016
Tetracysteine Genetic Tags Complexed with Biarsenical Ligands as a Tool for Investigating Gap Junction Structure and Dynamics (2003)

Gap junctions (GJ) are defined as contact regions between two adjacent cells containing tens to thousands of closely packed membrane channels. Cells dynamically modulate communication through GJ by regulating the synthesis, transport and turnover of these channels. Previously, we engineered a recombinant connexin43 (Cx43) by genetically appending a small tetracysteine peptide motif containing the sequence -Cys-Cys-Xaa-Xaa-Cys-Cys- to the carboxy terminus of Cx43 (Cx43-TC) (3). Cx43-TC was stably expressed in HeLa cells and was specifically labeled by exposing the cells to membrane-permeant non-fluorescent ligands, such as FlAsH (a fluorescein derivative) and ReAsH (a resorufin derivative). Direct correlation of live cell images with high resolution EM detection was possible because bound ReAsH not only becomes fluorescent, but can also be used to initiate the photoconversion of diaminobenzidine (DAB) that causes the localized polymerization of an insoluble osmiophilic precipitate then visible by EM. Cx43-TC GJ's could be labeled with ReAsH and photooxidized to give selectively stained channels. Here, how the development of these tetracysteine tags complexed with appropriate ligands are useful for experiments spanning resolution ranges from light microscopy to electron tomography to molecular purification and detection is described.
Preparation of lower-dispersity fractionated novolak resins by ultracentrifugation (1999)

The need to make well characterized resins consistently is paramount to the preparation of high performance photoresists. Solid resins fractionated by selective precipitation have been separated by ultracentrifugation at varying temperatures. At sufficiently high revolutions per minute, solvents and oligomers are efficiently squeezed out leaving behind polymer with higher average molecular weight and lower dispersity than resins obtained by more common isolation techniques. By controlling isolation conditions, resins with desired dissolution rates could be produced. Lithographic test confirmed that resists properties could effectively be controlled by manipulation of process conditions to isolate resins used in the formulations.
Coherent Spin Transfer Between Molecularly Bridged Quantum Dots (2003)

Femtosecond time-resolved Faraday rotation spectroscopy reveals the instantaneous transfer of spin coherence through conjugated molecular bridges spanning quantum dots of different size over a broad range of temperature. The room-temperature spin-transfer efficiency is approximately 20%, showing that conjugated molecules can be used not only as interconnections for the hierarchical assembly of functional networks but also as efficient spin channels. The results suggest that this class of structures may be useful as two-spin quantum devices operating at ambient temperatures and may offer promising opportunities for future versatile molecule-based spintronic technologies.
Sema3E–Plexin D1 signaling drives human cancer cell invasiveness and metastatic spreading in mice (2013)

The legend for Figure
Sliding-Mode Control for a Three-Phase Unity Power Factor Rectifier Operating at Fixed Switching Frequency (2015)

This paper presents an improved variable hysteresis-band current-control in natural frame for a three-phase unity power rectifier. The proposed control algorithm is based on three decoupled sliding-mode controllers combined with three independent Kalman filters. The use of Kalman filters instead of a nonadaptive state observer improves the quality of the estimated signals in presence of noise, increasing the immunity of the control loop in noisy environments. To reduce drastically the computational load in the Kalman algorithm, a reduced bilinear model is derived which allows to use a Kalman filter algorithm instead of an extended Kalman filter. A fast output-voltage control is also presented which avoids output-voltage variations when a sudden change in the load or a voltage sag appears. Moreover, a fixed switching frequency algorithm is proposed which uses a variable hysteresis-band in combination with a switching decision algorithm, ensuring a switching spectrum concentrated around the desired switching frequency. The overall control proposal has been fully integrated into a digital signal processor. Selected experimental results are introduced to validate the theoretical contributions of this paper.
Investigation of the Garnet Solid Electrolyte and Lithium Metal Anode Interface (2020)

Improving the energy density of lithium-ion batteries by replacing a graphite anode with lithium metal anode is heavily desired. 1 The garnet (LLZO) solid electrolytes are promising candidates to protect lithium metal due to their high lithium-ion conductivity and high elastic modulus, however, the interfacial chemistry between LLZO/Li is poorly understood. 2-4 In this work, LLZO electrolytes of &gt;98% theoretical density were prepared with Field Assisted Sintering Technology. The solid state electrochemistry of LLZO with lithium and blocking electrodes is characterized using electrochemical impedance spectroscopy. Further, investigation of interfacial phenomena between LLZO and Li metal using a suite of surface characterization techniques will be discussed in detail. References 1. Liu J., Bao Z., Cui Y., Dufek E. J., Goodenough J. B., Khalifah P., Li Q., Liaw B. Y., Liu P., Manthiram A., Meng Y. S., Subramanian V. R., Toney M. F., Viswanathan V. V., Whittingham M. S., Xiao J., Xu W., Yang J., Yang X. Q., and Zhang J. G., Energy , 4 , 180 (2019). 2. Krauskopf, Hartmann H., Zeier W. G., and Janek J. ACS Appl. Mater. Interfaces , 11 , 14463 (2019). 3. Fu K., GongY., LiuB., ZhuY., Xu S., YaoY., Luo W., Wang C., Lacey S. D., DaiJ., ChenY., MoY., WachsmanE., and Hu L. Sci. Advances , 3 , e1601659 (2017). 4. Sharafi A., KazyakE., DavisA. L., YuS., Thompson T., SiegelD. J., DasguptaN. P., and Sakamoto J. Chem. Mater., 29 , 7961 (2017).
Measurement-Driven Methodology for Evaluating Processor Heterogeneity Options for Power-Performance Efficiency (2016)

It is generally perceived that heterogeneous multicore processors will provide better performance and power efficiency over conventional homogeneous cores. However, heterogeneity can also be achieved within a homogeneous core design, instantiated under different voltage-frequency settings or per-core simultaneous multi-treading (SMT) modes. In this paper, we pursue an architectural study motivated by the question, "Can we get by with a single, complex SMT-equipped core design that can operate at different voltage-frequency points? Or, is it mandatory to invest into two different core types, one complex and the other simple?" We propose a systematic, measurement-driven methodology to evaluate processor heterogeneity options. Our analysis particularly focuses on the domain of real-time constrained embedded processors. The study is based on a direct measurement of two real processors; one that uses simple in-order cores, and another that uses complex out-of-order cores. The effect of heterogeneous core composition (consisting of complex and simple cores in the same chip) is analytically projected from measurements gleaned from the two different systems. Our analysis yields new interesting insights. When dealing with two core types without SMT enabled, true core heterogeneity does not necessarily provide better performance or power efficiency under area and power constraints. If the complex-core homogeneous processor invokes SMT, it outperforms true heterogeneity by offering 28% better power efficiency, assuming that simple cores in the heterogeneous system operate only in single-threaded mode without SMT capability. If the small cores employ SMT, true heterogeneity yields 32% better power efficiency than the homogeneous processor with SMT.