gebhart/patrepeval huggingface dataset:
The optimization of an ultra-sensitive single molecule assay for the multiplexed detection of SARS-CoV-2 antigens (2021)

Abstract Introduction/Objective SARS-CoV-2 antigens, including the nucleocapsid (N) protein, spike protein, and its S1 subunit have served as key biomarkers for research and diagnostic purposes. We previously developed quantitative single molecule array (Simoa) assays to measure the concentration of spike, S1 subunit and N protein in plasma samples with femtomolar limits of detection. We aimed to test antibodies that were not available early in the pandemic, reduce assay cross-reactivity, develop a multiplexed assay for spike, S1, and N protein in order to minimize the sample volume needed. Methods/Case Report Using the Simoa platform, a bead-based digital enzyme-linked immunosorbent assay, we cross-tested 17 S1 subunit and spike antibodies for a total of 130 antibody-pair combinations, we performed dilution linearity experiments to determine the ideal dilution factor, spike and recovery experiments, tested the assay using S1 subunit from other human coronavirus HKV1, NL63, and 229E, pre-pandemic plasma samples from patients that were sick with viral or bacterial respiratory infections. We then used the best antibody pairs to measure S1 and spike in plasma samples collected from patients with severe SARS-CoV-2. Lastly, we conjugated the best-performing capture antibodies for spike, S1 and N to beads labeled with different fluorophores to test if the assay for all three antigens could be multiplexed. Results (if a Case Study enter NA) We observed no cross-reactivity with S1 from other coronavirus strains, no detection of S1 or spike in a cohort of 30 pre-pandemic samples and successfully developed a multiplexed assay for the detection of spike, S1, and N protein, enabling us to use 50% less sample volume. Conclusion Reduction of necessary sample volume is important for studies involving multisystem inflammatory syndrome in children (MIS-C), and possible adverse effects of SARS-CoV-2 vaccinations on children and young adults. An improved assay with minimal cross-reactivity will also be useful to study individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).
Effect of changing tumor oxygenation on glycolytic metabolism in a murine C3H mammary carcinoma assessed by in vivo nuclear magnetic resonance spectroscopy. (2001)

The rate of conversion of D-[1-(13)C]glucose into [3-(13)C]lactate (apparent glycolytic rate) has been determined in C3H murine mammary carcinomas in vivo using tumor-selective (13)C nuclear magnetic resonance spectroscopy with (1)H-(13)C cross-polarization. Under conditions of acute hypoxia induced by breathing carbon monoxide at 660 ppm, the apparent glycolytic rate was 0.0239 +/- 0.0019 min(-1). The proportion of (13)C label incorporated into [4-(13)C]glutamate (measured in tumor extracts) was 25-fold lower than that incorporated into [3-(13)C]lactate, reflecting a very limited oxidative metabolism during this hypoxic episode. For animals breathing air or carbogen (95% O(2) + 5% CO(2)), the calculated glycolytic rates were correspondingly lower (0.0160 +/- 0.0021 min(-1) and 0.0050 +/- 0.0011 min(-1), respectively). Although (13)C labeling of glutamate at C4 was still an order of magnitude lower than that for lactate at C3 (11-fold for air and 9-fold for carbogen), these ratios did show a greater degree of oxidative metabolism than that seen in animals breathing carbon monoxide at 660 ppm. The marked difference in apparent glycolytic rate for this tumor model between well-oxygenated and hypoxic conditions demonstrates a substantial Pasteur effect (inhibition of glycolysis by oxygen). Dynamic (13)C nuclear magnetic resonance spectroscopy provides a noninvasive estimate of tumor glycolysis that can be used to evaluate the relationship between oxygenation and energy metabolism, and this has potential consequences for the sensitivity of hypoxic cells to treatment and their ability to promote angiogenesis.
Handheld confocal laser endomicroscopic imaging utilizing tumor-specific fluorescent labeling to identify experimental glioma cells in vivo (2016)

These data suggest that <i>in vivo</i> CLE of selectively tagged neoplasms could allow specific interactive identification of tumoral areas. Imaging of GFP and FITC-EGFR provides real-time histologic information precisely related to the site of microscopic imaging of tumor.
Continuous Cooling Curve Diagrams of Isotactic-Polypropylene/Polyethylene Blends: Mutual Nucleating Effects under Fast Cooling Conditions (2021)

Crystallization kinetics under processing-relevant cooling conditions of polyethylene/isotactic-polypropylene (PE/PP) blends, with compositions similar to real recycled blends, was investigated through an in situ temperature monitoring technique. Continuous Cooling Curve (CCC) diagrams in a large crystallization temperature range were obtained for the two phases, thanks to a new apparatus allowing fast quenching of polymer samples. Using this technique, we found an "inversion point" in the crystallization order of the two polymers, which arises from the difference in crystallization rates between PP and PE with an increasing cooling rate. The order of crystallization of the two polymers at low cooling rates, that is, before the inversion point, can be tuned by employing non-nucleated or nucleated PP. In particular, non-nucleated PP crystallizes after PE above 0.5 degrees C/s, while nucleated PP solidifies before PE until 80 degrees C/s. Interestingly, mutual nucleating effects, previously shown only for ideal systems such as thin-layered films, were found at the interface between the phases, in correlation with the inversion point. During cooling, the phase which crystallizes first can enhance the onset of crystallization of the second lower crystallizing phase through nucleation at the interface. Ex situ morphological and wide-angle X-ray diffraction experiments confirmed the validity of the results shown by CCC diagrams. Our approach to characterize semicrystalline polymer blends with CCC diagrams facilitates tailoring their properties at cooling rates relevant for polymer processing. Moreover, the importance of knowing and controlling the type of components in blends obtained from recycling is demonstrated, given the variety of crystallization behaviors attainable.
Great Expectations: Inflation versus Cyclic Predictions for Spectral Tilt (2003)

We present a simple, nearly model-independent estimate that yields the predictions of the simplest inflationary and ekpyrotic/cyclic models for the spectral tilt of the primordial density inhomogeneities. Remarkably, we find that the simplest models yield an identical result: n_s is approximately 0.95. For inflation, the same estimate predicts a ratio of tensor to scalar contributions to the low multipoles of the microwave background anisotropy of T/S=20 %; the tensor contribution is negligible for ekpyrotic/cyclic models.
ROUND ROBIN TESTING INITIATIVE FOR FIBER REINFORCED POLYMER (FRP) REINFORCEMENT (2011)

An international Round Robin Testing (RRT) programme on FRP reinforcement was conducted within the framework of the Marie Curie Research Training Network, ENCORE, and with the support of Task Group 9.3 of the International Federation for Structural Concrete (fib). Eleven laboratories and six manufacturers and suppliers participated in this exercise. As part of this extensive experimental endeavour, one or more of the following tests were performed by the participating laboratories: 1) tensile tests on FRP bars and strips; 2) tensile tests on FRP laminates; 3) double bond shear tests on FRP laminates (Externally Bonded Reinforcement, EBR) and FRP bars/strip (Near Surface Mounted reinforcement, NSM). This paper will discusses the results of the RRT initiative, among which the experimental results of bond tests on concrete specimens strengthened with EBR and NSM FRP.
Succinimide-mediated pathway for peptide bond cleavage: Kinetic study on an Asn-Sar containing peptide (1996)

The cleavage reaction of the peptide bond next to the Asn residue has been studied in the pH range 7.4–13.8 at 37°C and μ = 1M. This reaction yields an N-terminal peptide fragment having at its C-terminus a succinimide ring, which rapidly hydrolyses to both asparagine and iso-asparagine residues. For both the two consecutive reactions, peptide bond cleavage and the succinimide hydrolysis, the general trend is an increase of the reaction rate with the pH. However, for the hydrolysis reaction there is a small decrease in the pH range 10–11 caused by the deprotonation of the succinimide nitrogen atom. Kinetic evidence indicates that the cleavage reaction is a multistep process with a change in the rate-determining step at pH 8.5–9.0. The mechanism involves preequilibrium deprotonation of the NH2 amide group of the Asn side chain, followed by nucleophilic attack of the nitrogen atom on the carbonyl carbon atom of the same asparagine residue, giving a cyclic intermediate. Then, general acid-catalyzed departure of the leaving group gives the final reaction product. At pH < 8.5, the formation of the cyclic intermediate is rate determining, whereas, at higher pH, it is the departure of the leaving group. © 1997 John Wiley & Sons, Inc. Biopoly 40: 543–551, 1996
EPR and ENDOR study of chiral nitroxides (1989)

Abstract Racemic and achiral alkyl aryl nitroxides were examined at various temperatures. The restricted rotation of the aminoxyl substituents was indicated both by the β‐proton coupling constants and by the inequivalence of the aromatic ortho protons. These results are interpreted by the presence of two different rotamers which may lead to two splitting constants for the β‐proton. The capability for inter‐ and intra‐molecular hydrogen bond formation in the nitroxides investigated was demonstrated. However, complexes consisting of chiral radicals and chiral auxiliaries do not show hyperfine structures which unambiguously indicate diastereomeric species. Therefore, hydrogen bonding between chiral molecules is not sufficient for chiral recognition if an alteration of the hyperconjugation angle does not occur. Simple steric interactions can result in the doubling of the β‐proton coupling constant, independently of diastereomeric complex formation.
Polymers for Microelectronics (1993)

A comparative study of polystyrene (PS) with bis(perfluorophenyl) azides 1-2 and the corresponding non-fluorinated bisazides 3-4 as deep-UV resists is reported. Inclusion of as low as 1.2 wt-% of 1 in PS led to 70% retention of film thickness after photolysis and development. PS containing 2.4 wt-% of 1 is &gt; 100 times more sensitive as a deep-UV negative resist than PS itself. The presence of 1 in PS also increased the contrast of the resist. On a molar basis, 1 was about 10 times as effective as non-fluorinated bisazide 3 in cross-linking PS while 2 was about 6 times as effective as 4. PS containing 2.4 wt-% of 1 was found to have a deep-UV sensitivity of 5-10 mJ/sq cm and resolution of about 0.5 micrometer. Polymers, Deep-UV negative resists, Cross-linking.
Studies concerning the antibiotic actinonin. Part I. The constitution of actinonin. A natural hydroxamic acid with antibiotic activity (1975)

J. J. Gordon, J. P. Devlin, A. J. East, W. D. Ollis, I. O. Sutherland, D. E. Wright and L. Ninet, J. Chem. Soc., Perkin Trans. 1, 1975, 819 DOI: 10.1039/P19750000819
Microfluidic Shear Devices for Quantitative Analysis of Cell Adhesion (2004)

We describe the design, construction, and characterization of microfluidic devices for studying cell adhesion and cell mechanics. The method offers multiple advantages over previous approaches, including a wide range of distractive forces, high-throughput performance, simplicity in experimental setup and control, and potential for integration with other microanalytic modules. By manipulating the geometry and surface chemistry of the microdevices, we are able to vary the shear force and the biochemistry during an experiment. The dynamics of cell detachment under different conditions can be captured simultaneously using time-lapse videomicroscopy. We demonstrate assessment of cell adhesion to fibronectin-coated substrates as a function of the shear stress or fibronectin concentration in microchannels. Furthermore, a combined perfusion-shear device is designed to maintain cell viability for long-term culture as well as to introduce exogenous reagents for biochemical studies of cell adhesion regulation. In agreement with established literature, we show that fibroblasts cultured in the combined device reduced their adhesion strength to the substrate in response to epidermal growth factor stimulation.
SIRT1 Contains N- and C-terminal Regions That Potentiate Deacetylase Activity (2011)

SIRT1 is one of seven mammalian sirtuin (silent information regulator 2-related) proteins that harbor NAD(+)-dependent protein deacetylase activity and is implicated in multiple metabolic and age-associated pathways and disorders. The sirtuin proteins contain a central region of high sequence conservation that is required for catalytic activity, but more variable N- and C-terminal regions have been proposed to mediate protein specific activities. Here we show that the conserved catalytic core domain of SIRT1 has very low catalytic activity toward several known protein substrates, but that regions N- and C-terminal to the catalytic core potentiate catalytic efficiency by between 12- and 45-fold, with the N-terminal domain contributing predominantly to catalytic rate, relatively independent of the nature of the acetyl-lysine protein substrate, and the C-terminal domain contributing significantly to the K(m) for NAD(+). We show that the N- and C-terminal regions stimulate SIRT1 deacetylase activity intramolecularly and that the C-terminal region stably associates with the catalytic core domain to form a SIRT1 holoenzyme. We also demonstrate that the C-terminal region of SIRT1 can influence the inhibitory activity of some sirtuin inhibitors that are known to function through the catalytic core domain. Together, these studies highlight the unique properties of the SIRT1 member of the sirtuin proteins and have implications for the development of SIRT1-specific regulatory molecules.
Surface planarization of Cu and CuNiSn Micro-bumps embedded in polymer for below 20μm pitch 3DIC applications (2016)

Planarization techniques such as Surface planer (better known as Fly-cut) and chemical-mechanical polishing (CMP) can be used to improve the bump roughness and bump height uniformity within the die and wafer which can be beneficial for solder based bump stacking and Cu-Cu direct bonding [1]. In this paper the influence of both planarization techniques on 20μm pitch Cu and CuNiSn bumps embedded in polymer are studied. The polymer protects the bumps from the shearing force of the planarization process and will later serve as a underfill material for the resulting gap of a 3D stack. The microbump planarization process will be discussed. Furthermore characterization of the bump height uniformity across the wafer using SEM and High Resolution Profilometry (HRP) is reported.
Stress Analysis and Structural Optimization of a Three-Layer Composite Cladding Tube Under Thermo-Mechanical Loads (2012)

A general solution for the stress and strain fields in a three-layer composite tube subjected to internal and external pressures and temperature changes is first derived using thermo-elasticity. The material in each layer is treated as orthotropic, and the composite tube is regarded to be in a generalized plane strain state. A three-layer ZRY4-SiCf/SiC-SiC composite cladding tube under a combined pressure and thermal loading is then analyzed and optimized by applying the general solution. The effects of temperature changes, applied pressures, and layer thickness on the mechanical behavior of the tube are quantitatively studied. The von Mises’ failure criterion for isotropic materials and the Tsai-Wu’s failure theory for composites are used, respectively, to predict the failure behavior of the monolithic ZRY4 (i.e., Zircaloy-4) inner layer and SiC outer layer and the composite SiCf/SiC core layer of the three-layer tube. The numerical results reveal that the maximum radial and circumferential stresses in each layer always occur on the bonding surfaces. By adjusting the thickness of each layer, the effective stress in the three-layer cladding tube under the prescribed thermal-mechanical loading can be changed, thereby making it possible to optimally design the cladding tube.
Transverse priority phase sensitive optical coherence tomography (2006)

A variation on the standard time domain optical coherence tomography (TDOCT) system is presented. Using an inexpensive piezoelectric stack to modulate the reference mirror position, the amplitude and phase of the sample reflection is determined without scanning. With the primary scan in the transverse direction, en face and B-scan OCT images can be readily produced with phase information. This project plans to use the dynamic phase information to add an extra level of contrast to the images, based on the motion of the scatterers.
Adjustment of the multi-biomarker disease activity score to account for age, sex and adiposity in patients with rheumatoid arthritis (2018)

Leptin-adjusted MBDA score significantly adds information to DAS28-CRP and the original MBDA score in predicting radiographic progression. It may offer improved clinical utility for personalized management of RA.
Evolution of GSM into the Next Generation Wireless World (2007)

GSM is the most widely deployed 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> generation digital cellular standard, with over 2 billion subscribers in some 213 countries and adding about 1000 new users per minute! Originally developed in the 1980s, and first deployed in 1991, GSM is a TDMA+FDMA system, providing wide area voice communications using 200 KHz carriers. Subsequently, GSM evolved into a 2.5G standard with the introduction of packet data transmission technology (GPRS) and higher data rates via higher order modulation schemes (EDGE). More recently, GERAN standards organization has been evolving further to coexist with and provide comparable services to 3G technologies. In this paper, we first provide an overview of the traditional 2G and 2.5G GSM, and then discuss the so-called "GERAN Evolution" into the 3G world. We conclude by detailing a few selected aspects of the GERAN Evolution. Overall, we aspire to demonstrate that GERAN is a vibrant, living and growing technology that exploits the latest advances in communications and signal processing.
Evaluating the effectiveness of program data features for guiding memory management (2019)

Recent trends have led to the adoption of larger and more complex memory systems, often with multiple tiers of memory performance within the same platform. To utilize complex memory systems efficiently, current data management strategies must be altered to map usage demands to the underlying hardware. Applications, as the generators of memory accesses, are well-suited to guide this process, but building and maintaining separate source code versions for different memory systems is not feasible in most cases. One potential solution is to employ automated program profiling and analysis to facilitate the production of application-based guidance. By attaching memory usage information to static or lightweight program features, compilers and runtime systems can generate fine-grained guidance without additional efforts from users or developers. Recent works have employed this approach with some success, but it is not clear which program features are most useful for guiding data management.
Absolute and Relative Properties in Geographic Referring Expressions (2016)

This paper discusses the importance of computing relative properties and not just retrieving absolute properties when generating geographic referring expressions such as "northern France". We describe an algorithm that computes spatial properties at run-time by means of spatial operations such as intersecting and analyzing parts of wholes. The evaluation of the algorithm suggests that part-whole relations are key in geographic expressions.
Response: Lack of preoperative predictors of surgical complications in patients undergoing endometriosis surgery may be due to lack of adequate preoperative imaging (2019)

Thank you for your interest in our study and commentary.1, 2 We applaud your work to improve the adoption of ultrasound for identifying endometriosis preoperatively. We agree that significant improvements have been made in the detection of endometriosis by ultrasound. At our institution, Dr. Beryl Benacerraf and colleagues are routinely employing ultrasound to assess for deep infiltrating endometriosis.3, 4 Unfortunately, this assessment is not employed by all local radiologists and was not available to many women in our study. We have taken the opportunity to clarify the preoperative imaging reviewed in our study. The practice is largely referral-based, with most women having undergone imaging assessment prior to presentation. Of the entire cohort, 286 (n = 286/397, 72.0%) had preoperative imaging results that were available for review (Table 1). A total of 246 women (n = 246/397, 62.0%) had preoperative ultrasound available for review. Of these women, 132 (n = 132/246, 53.7%) had suspected endometriosis by ultrasound, mostly due to the presence of a suspected endometrioma (n = 122/246, 49.6%). A smaller number of women had an endometriosis implant or nodule identified on pelvic ultrasound (n = 17/246, 6.9%). Although we do not know the radiologic criteria used in the diverse group of radiology practices represented in this cohort, when an implant or nodule was suspected, it was often characterized by an echogenic focus, sometimes with documentation of adherence to adjacent structures. We agree that if a more thorough assessment of the cul-de-sacs were undertaken, then more women would have been identified as having endometriosis preoperatively. This, in turn, could aid in the prediction of perioperative complications. Interestingly, our study did not find that intraoperative identification of advanced endometriosis predicted perioperative complications. This is likely influenced by the expertise of the surgeons included, all of whom completed a fellowship in Minimally Invasive Gynecologic Surgery and frequently perform complex endometriosis surgery.
Implication of RF EMF Exposure Limitations on 5G Data Rates above 6 GHz (2015)

For future 5G devices operating above 6 GHz, a consequence of existing electromagnetic field (EMF) exposure limits is that the maximum transmit power may have to be reduced several dB compared with what is used for the current cellular bands. To understand the consequences of such limitations on the system capacity, an indoor geometry is used to assess the achievable data rates for low power indoor nodes and UEs. The evaluation is performed as a function of the carrier frequency, the Tx power, and the amount of Tx and Rx beamforming. Ray tracing in combination with physical and experimental models or reasonable assumptions of diffraction-, reflection- and penetration-losses are used for modeling. The paper shows that the current exposure limitations might reduce the achievable data rates in non-line-of-sight regions to levels that may be inconsistent with 5G performance expectations. For the currently given maximum transmit power, high order beamforming seems necessary to achieve a good coverage already for carrier frequencies well below 15 GHz.