gebhart/patrepeval huggingface dataset:
Disulfide bond assignments and secondary structure analysis of human and murine interleukin 10 (1993)

Interleukin 10 (IL-10), which was first discovered by its ability to inhibit the synthesis of various cytokines, most notably gamma interferon, from Th1 helper cells, displays pleiotropic immunoregulatory properties. Human and murine IL-10 have a high amino acid sequence identity (ca. 73%) which includes the conservation of all four cysteine residues in human IL-10 and the first four out of five cysteine residues for murine IL-10. Chemical analysis was used to determine that both recombinant human and recombinant murine IL-10 contain two disulfide bonds. The disulfide pairs for each were determined by mass spectrometric and reversed-phase HPLC analysis of trypsin-derived polypeptide fragments. The disulfide bond assignments for both species were similar in that the first cysteine residue in the sequence paired with the third and the second paired with the fourth. The fifth cysteine in murine IL-10 was determined by chemical modification to be unpaired. Far-UV circular dichroism analysis indicated that the secondary structure of recombinant human and murine IL-10 are composed of ca. 60% alpha-helix. Reduction of the disulfide bonds structurally destabilized the protein and led to a structure containing only 53% alpha-helix. The reduced protein displayed no in vitro biological activity in a mast cell proliferation assay. These studies indicate that IL-10 is a highly alpha-helical protein containing two disulfide bonds, either one or both of which are critical for its structure and function. In addition, these properties suggest that this interesting cytokine may belong to the alpha helical cytokine class of hematopoietic ligands.
Carbon Dynamics (2017)

The biogeochemical cycle of carbon (C) in the earth system controls fluxes, pools, and transformations associated with life’s most fundamental element. As the most basic building block for all living organisms, organically bound C forms the basis for the overwhelming majority of food chains in ecosystems and global energy flows. The uptake of carbon dioxide (CO2) by autotrophic organisms and photosynthetic transformation of light energy into chemical energy enables conversion of atmospheric CO2 into structural materials for living organisms and ultimately fossil fuels. In the earth system, C exists in different forms and reservoirs, including gaseous, dissolved, and solid forms distributed and continually exchanged among the atmosphere, terrestrial, and aquatic spheres. The most important gaseous forms of C include CO2 and methane (CH4). The liquid phase includes different species of C found in water, including (1) dissolved CO2 and carbonic acid (H2CO3) and its intermediates, (2) dissolved organic compounds (molecules &lt;0.45 µm in size), (3) suspended organic and inorganic colloids/particles (typically &gt;10s nm) containing C, and (4) raw oil. The solid phase comprises C (1) in rocks of organic and inorganic origin, in sedimentary rocks and sediments including coal, (2) on and in soils in the form of carbonates, (3) in dead not dissolved or suspended organic compounds, and (4) in the living biomass of microorganisms, plants, and animals. The C in the atmosphere, terrestrial, and aquatic systems can be characterized according to the amount of C stored in a given reservoir, its mean residence time (i.e., the time needed to exchange each C atom of the considered system or subsystem at least once), and the physical or chemical state of C in a given reservoir or as it exchanges among reservoirs. Different systems can be subdivided into active and inactive drivers of C dynamics based on the C mean residence times. Under natural conditions, almost the entire C stored in sediments or sedimentary rocks, for example, is considered to be inactive with mean residence times longer than 1,000 years. Contrastingly, the C stored in the atmosphere, surface oceans, plant biomass, and soil organic material in the soil is relatively active with residence times ranging from seconds to centuries. However, anthropogenic extractions of fossil fuel C from global sedimentary deposits, for example, have demonstrated how inactive C reservoirs can be rapidly transformed into highly active drivers of global C dynamics.
A Highly Sensitive Capacitive‐Based Soft Pressure Sensor Based on a Conductive Fabric and a Microporous Dielectric Layer (2017)

Abstract In this paper, the design and manufacturing of a highly sensitive capacitive‐based soft pressure sensor for wearable electronics applications are presented. Toward this aim, two types of soft conductive fabrics (knitted and woven), as well as two types of sacrificial particles (sugar granules and salt crystals) to create micropores within the dielectric layer of the capacitive sensor are evaluated, and the combined effects on the sensor's overall performance are assessed. It is found that a combination of the conductive knit electrode and higher dielectric porosity (generated using the larger sugar granules) yields higher sensitivity (121 × 10 −4 kPa −1 ) due to greater compressibility and the formation of air gaps between silicone elastomer and conductive knit electrode among the other design considerations in this study. As a practical demonstration, the capacitive sensor is embedded into a textile glove for grasp motion monitoring during activities of daily living.
Standards of diagnostic colonoscopy for early‐stage neoplasia: Recommendations by an Asian private group (2018)

This consensus provides guidance for carrying out endoscopic diagnosis and characterization for early-stage colorectal neoplasia based on the evidence. This will enhance the quality of endoscopic diagnosis and improve detection of early-stage colorectal neoplasia.
Two-Photon Fluorescence Spectroscopy and Imaging of 4-Dimethylaminonaphthalimide Peptide and Protein Conjugates (2013)

We report detailed photophysical studies on the two-photon fluorescence processes of the solvatochromic fluorophore 4-DMN as a conjugate of the calmodulin (CaM) and the associated CaM-binding peptide M13. Strong two-photon fluorescence enhancement has been observed which is associated with calcium binding. It is found that the two-photon absorption cross-section is strongly dependent on the local environment surrounding the 4-DMN fluorophore in the CaM conjugates, providing sensitivity between sites of fluorophore attachment. Utilizing time-resolved measurements, the emission dynamics of 4-DMN under various environmental (solvent) conditions are analyzed. In addition, anisotropy measurements reveal that the 4-DMN–S38C–CaM system has restricted rotation in the calcium-bound calmodulin. To establish the utility for cellular imaging, two-photon fluorescence microscopy studies were also carried out with the 4-DMN-modified M13 peptide in cells. Together, these studies provide strong evidence that 4-DMN is a useful probe in two-photon imaging, with advantageous properties for cellular experiments.
Diffusion of -lactam antibiotics into proteoliposomes reconstituted with outer membranes of isogenic imipenem-susceptible and -resistant strains of Enterobacter cloacae (1992)

The influence of outer membrane (OM) permeability on carbapenem susceptibility was studied in strains of Enterobacter cloacae, a species in which carbapenem resistance depends upon the conjunction of overproduction of the chromosomal cephalosporinase and reduction of OM permeability. Relative trans-OM diffusion rates were measured using the liposome swelling assay. Proteoliposomes were reconstituted with OM from the members of an isogenic set of E. cloacae strains, selected in vivo or in vitro, which produced either porins F and D (wild-type), or F or D only, or neither. For all but one mutant, and compared with the wild-type strain, the respective increases in MICs and decreases in trans-OM diffusion of carbapenems were: nil and 13 to 18%; 4- to 32-fold and 33 to 50%; > or = 64-fold and > or = 90%. Our results suggest (i) that carbapenems (and other beta-lactam antibiotics) diffuse through porins F and D, but more rapidly through porin F, and (ii) that OM permeability is the critical factor in determining the level of MICs of carbapenems for cephalosporinase-overproducing strains of E. cloacae. The OM of one particular low-level carbapenem-resistant and porin F- and D-deficient mutant was at least five times more permeable to carbapenems than the similarly porin-deficient high-level resistant mutants. We infer from this observation the possible existence of an alternative carbapenem penetration pathway which could be associated with two as yet uncharacterized overproduced OM proteins of about 22 and 47 kDa.
Peak shape variation in fixed-wavelength neutron powder diffraction and its effect on structural parameters obtained by Rietveld analysis (1985)

Analyses of high-resolution neutron powder diffraction data, using both the Pearson VII and pseudo-Voigt peak shape functions, have revealed a range of peak shapes from essentially Gaussian to Lorentzian and beyond. Moreover, the refinements show that the Lorentzian character of the peaks in each pattern increases with increasing diffraction angle. Both kinds of shape change are associated with varying relative contributions to the peak profiles of the instrumental resolution, isotropic crystallite strain and crystallite size effects. Rietveld analysis of powder data with the standard Gaussian form when the peaks have significant Lorentzian character has little effect on atomic positional parameters, but it leads to an overestimation of the thermal vibration coefficients and higher least-squares residuals.
In vitro activity of the killer toxin from yeast Hansenula mrakii against yeasts and molds. (1988)

The killer phenomenon is widespread among various genera and species of yeasts12). Killer yeast strains so far isolated fall into ll types (Ki to Kn type) (Young and Yagiu2), and Wickner3)) with respect to their killing and immunity cross-reactions.
A simple method for the preparation of 32P-labelled adenosine triphosphate of high specific activity (1964)

32P-labelled ATP of high specific activity is not available commercially.Chemical methods for preparing it (see, for example, Lowenstein & Metzenberg, 1960) are tedious and yield a product
Efficacy of platinum-pemetrexed combination chemotherapy in ALK+ non-small cell lung cancer refractory to second-generation ALK TKIs. (2019)

9067 Background: Second-generation (gen) ALK tyrosine kinase inhibitors (TKIs) are standard first- and second-line therapies in patients (pts) with advanced ALK+ non-small cell lung cancer (NSCLC). After progression on second-gen TKI(s), standard options include platinum (PT)-based chemotherapy (chemo) or the third-gen ALK TKI lorlatinib. The efficacy of PT-based chemo is established in treatment-naive pts but is undefined in pts who have failed prior ALK TKIs. Here we evaluate the efficacy of PT/pemetrexed (pem)-based chemo in pts with ALK+ NSCLC refractory to second-gen TKIs. Methods: A retrospective study was performed at three institutions. Pts were eligible if they had advanced ALK+ NSCLC refractory to ≥1 second-gen TKI, and received PT-pem-based chemo. Medical records and imaging were reviewed to determine outcomes. Results: Among 55 eligible pts, chemo regimens included: PT/pem (31/55, 56%), PT/pem/bevacizumab (bev) (6/55, 11%), PT/pem/PD-1 inhibitor (3/55, 5%), PT/pem with ALK TKI (8/55, 15%), PT/pem/bev with TKI (6/55, 11%), and PT/pem/PD-1 inhibitor with TKI (1/55, 2%). Pts had received one (6/55, 11%), two (38/55, 69%), or more (11/55, 20%) prior TKIs. Six pts (11%) previously received adjuvant or neoadjuvant chemo. Radiographic data for response evaluation was available for 39 pts. Among 36 pts with measurable baseline disease, confirmed ORR was 31% (11/36; 95% CI, 16-48%); 13 (36%) had stable disease. The median duration of response was 5.4 months (95% CI, 1.5-7.1 months). The median progression-free survival (PFS) for the entire cohort was 4.0 months (95% CI, 2.8-4.6 months). Chemo (PT/pem +/- bev or PD-1 inhibitor) plus ALK TKI (n = 15) was associated with a significant increase in PFS compared to chemo without TKI (n = 40) (median PFS 6.8 vs 3.2 months; HR 0.306; p = 0.002). Similarly, PT/pem plus ALK TKI (n = 8) was associated with increased PFS compared to PT/pem without TKI (n = 31) (median PFS 6.8 vs 2.9 months; HR 0.358; p = 0.036). Conclusions: The efficacy of PT-pem-based chemo is limited after failure of second-gen ALK TKIs but may be higher in pts who receive chemo plus ALK TKI, suggesting a potential role for ongoing ALK inhibition. The modest benefit of PT-pem-based chemo highlights the need for other therapeutic strategies for pts refractory to second-gen TKIs.
Theoretical Description of Novel Element for Josephson Spintronics (2013)

D-amino acids (D-AAs) are important signaling molecules due to their ability to bind ionotropic N-methyl-D-aspartate receptors. D-serine (D-Ser), D-alanine (D-Ala), and D-aspartate (D-Asp) have been found individually in the endocrine portion of the pancreas, the islets of Langerhans, and/or their secretions. However, there has been no report of a comprehensive assessment of D-AAs in islet secretions. To evaluate the release of these compounds, the effectiveness of both 1-(9-fluorenyl)-ethyl chloroformate (FLEC reagent) and 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide (Marfey's reagent, MR) in separation of D/L-AA enantiomeric pairs in islet-specific buffers were evaluated. MR-derivatized D/L AAs showed greater than baseline resolution (Rs ≥ 1.5) of 13 enantiomeric pairs when using a non-linear gradient and an acidic mobile phase system, while FLEC-derivatized AAs exhibited limited resolution on both biphenyl and C18 columns. The optimized MR method yielded highly reproducible separations with retention times less than 1% RSD. Excellent linearity between the analyte concentrations and response (R<sup>2</sup> > 0.98) were obtained, with less than 15% RSD for all analyte responses. Most analytes had an LOD at or below 100 nM, except for L-Ala (200 nM). The optimized MR method was used to quantify D-AAs in secretions of 150 murine islets after incubation in 3- and 20-mM glucose. In response to both solutions, D-Ser and D-glutamine were tentatively identified via comparison of retention time and quantifier-to-qualifer ion ratios with standards, and from spiking experiments. Both were secreted in low quantities which did not differ significantly in either low (D-Ser: 44 ± 2 fmol islet<sup>-1</sup>h<sup>-1</sup>; D-Gln: 300 ± 100 fmol islet<sup>-1</sup>h<sup>-1</sup>) or high (D-Ser: 23 ± 1 fmol islet<sup>-1</sup>h<sup>-1</sup>; D-Gln: 120 ± 50 fmol islet<sup>-1</sup>h<sup>-1</sup>) glucose across 3 biological replicates. The method developed is robust and can be applied to further examine the release of D-AAs and their potential roles in islet physiology.
Automated microfluidics for genomics (2005)

The Genomation Laboratory at the University of Washington is developing an automated fluid handling system called "Acapella" to prepare microliter reactions for genome analysis. The system prepares 5,000 samples in 8 hours for general-purpose chemistry analysis including DNA sequencing reaction preparation.
Zinc and Iron Bioavailability of Genetically Modified Soybeans in Rats (2007)

The aim of this work was to evaluate zinc and iron bioavailability of UFV-116, a new variety without 2 lipoxygenases, with better taste and flavor than a commercial variety OCEPAR 19, containing all 3 isozymes. To evaluate zinc absorption using 65Zn whole body retention and femur 65Zn uptake, rats were given 3 g of a 65ZnCl2 labeled test meal (0.25 microCi). The 2 varieties were tested at the level of 9 and 30 ppm of zinc as defatted soy flour. Two other groups (control) received egg white as source of protein and ZnS04.H20 as the zinc source. To evaluate iron absorption, using 59Fe whole body retention, animals were given a 3 g 59FeCl3 labeled test meal (0.2 microCi). The 2 varieties were tested at 12 and 25 ppm iron as defatted soy flour. Whole fat soy flour of variety 1 (UFV-116) was higher (P < 0.05) in Ca, K, Mg, phytic acid, and oxalate than variety 2 (OCEPAR-19). No difference was observed among the soybean varieties (P > 0.05) for femur 65Zn retention, at different levels of zinc. However, whole body retention was lower (P < 0.05) for UFV-116 than for OCEPAR-19. Femur 65Zn uptake was correlated with the whole body retention; however, whole body retention was more sensitive. Whole body 59Fe retention from UFV-116 was lower (P < 0.05) than from OCEPAR-19. Zinc and iron bioavailability was lower for UFV-116, possibly due to its higher content of antinutrient factors, especially phytate.
The cleavage site of C5 from man and animals as a common target for neutralizing human monoclonal antibodies: in vitro and in vivo studies (2002)

The isolation of an anti-C5 single-chain fragment variable (scFv) antibody, TS-A12/22, from a human phage display library, is described. This antibody inhibits the activation of C5 and the assembly of the terminal complement complex implicated in cell and tissue damage. Using antibody-sensitized sheep erythrocytes and rabbit red cells as target cells in hemolytic assays, we found that TS-A12/22 inhibited the activation of C5 by the convertases of both classical and alternative pathways. Western blot analysis and competition experiments with synthetic peptides showed that TS-A12/22 reacted with the alpha chain of C5 and recognized the cleavage site of this complement component by the C5 convertase. As a result, the antibody prevented splitting of C5 and inhibited the generation of C5a and of the terminal complement complex. The identification of the TS-A12/22 recognition site as a conserved sequence in man, mouse, rat and rabbit enabled the demonstration of in vitro inhibition of complement activity in these species. The scFv TS-A12/22 was tested in a rat model of antigen-induced arthritis and proved to be effective in preventing influx of polymorphonuclear cells into the knee joint and C9 deposition on synovial tissue.
Ultrasonic Characterization of Electrochemically Etched Porous Silicon (2014)

International audience
412. Assessment and Capability of SARS-CoV-2 Detection in the Veterans Health Administration (2020)

Abstract Background Rapid scale up of testing to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is essential to direct clinical management, optimize infection control actions, and guide public health response efforts to mitigate the spread of Coronavirus Disease 2019 (COVID-19). As the largest integrated health care system in the United States, the Veterans Health Administration (VHA) supported the laboratory-based detection of COVID-19 in a network of 170 medical centers across the country. Methods SARS-CoV-2 testing data from VHA databases were analyzed to assess SARS-CoV-2 detection characteristics. Testing capacity was calculated by multiplying the number of inventoried instruments available for SARS-CoV-2 detection by estimates of instrument-specific maximum throughput with the assumption that instruments would be operational for 16 hours a day and 7 days a week. Results From March 01, 2020 to May 31, 2020, 224,059 Emergency Use Authorization approved RT-PCR tests for SARS-CoV-2 on more than 7 different assay platforms were conducted among 168,761 individuals attending VHA facilities; 10,048 individuals (5.9%) tested positive. During this period, the average rate of tests completed for SARS-CoV-2 increased to more than 4,000 per day (Figure 1A), the percentage of hospitalized individuals who were tested for SARS-CoV-2 increased to approximately 80% (Figure 1B), the median turnaround time from specimen collected to result reported decreased to less than 1 day (Figure 1C), and the percentage of SARS-CoV-2 clinical specimens collected in VHA facilities that were tested at VHA laboratories increased to more than 80% (Figure 1D). Based on inventories of high-throughput and rapid diagnostic instruments (Figure 2), VHA could perform at least 20,000 tests for SARS-CoV-2 per week. Figure 1. Testing metrics for SARS-CoV-2 across VHA facilities. A) Number of daily tests for SARS-CoV-2 completed. B) Percentage of hospitalized Veterans tested for SARS-CoV-2. C). Median turnaround time of completed tests for SARS-CoV-2 from specimen collection to result reported. D) Percentage of SARS-CoV-2 specimens collected in VHA facilities that were tested in VHA laboratories. Figure 2. Distribution of instruments to detect SARS-CoV-2 across VHA facilities. Conclusion Key indicators of laboratory performance for SARS-CoV-2 detection, including test turnaround time, percentage of hospitalized individuals tested, and overall testing volume improved substantially in VHA during the first 3 months of testing during the pandemic. Ongoing efforts seek to enhance just-in-time diagnostic capacity, ensure continuity of specimen collection supplies and laboratory consumables, and identify and minimize gaps in access to testing facilities. Disclosures All Authors: No reported disclosures
Benzocyclobutene interlayer dielectrics for thin film multichip modules (1990)

An organic dielectric derived from benzocyclobutene has been investigated as an interlayer dielectric for thin-film multichip modules. The material is processed using standard semiconductor techniques. Key attributes of the polymer are a low dielectric constant
<italic>DStore</italic>: A Holistic Key-Value Store Exploring Near-Data Processing and On-Demand Scheduling for Compaction Optimization (2018)

Log-structured merge tree (LSM-tree)-based key-value stores are widely deployed in largescale storage systems. The underlying reason is that the traditional relational databases cannot reach the high performance required by big-data applications. As high-throughput alternatives to relational databases, LSM-tree-based key-value stores can support high-throughput write operations and provide high sequential bandwidth in storage systems. However, the compaction process triggers write amplification and is confronted with the degraded write performance, especially under update-intensive workloads. To address this issue, we design a holistic key-value store to explorer near-data processing (NDP) and on-demand scheduling for compaction optimization in an LSM-tree key-value store, named DStore. DStore makes full use of various computing capacities in the host-side and device-side subsystems. DStore dynamically divides the whole host-side compaction tasks into the above two-side subsystems according to two-side different computing capabilities. Meanwhile, the device must be featured with an NDP model. The divided compaction tasks are performed by the host and the device in parallel. In DStore, the NDP-based devices exhibit low-latency and high-bandwidth performance, thus facilitating key-value stores. DStore not only accomplishes compaction for key-value stores but also improves the system performance. We implement our DStore prototype in a real-world platform, and different kinds of testbeds are employed in our experiment. LevelDB and a static compaction optimization using the NDP model (called Co-KV) are used to compare with the DStore in our evaluation. Results show that DStore achieves about 3.7× performance improvement over LevelDB under the db_bench workload. In addition, DStore-enabled key-value stores outperform LevelDB by a factor of about 3.3× and 77% in terms of throughput and latency under YCSB benchmark, respectively.