gebhart/patrepeval huggingface dataset:
Criteria for Selecting PEGylation Sites on Proteins for Higher Thermodynamic and Proteolytic Stability (2014)

PEGylation of protein side chains has been used for more than 30 years to enhance the pharmacokinetic properties of protein drugs. However, there are no structure- or sequence-based guidelines for selecting sites that provide optimal PEG-based pharmacokinetic enhancement with minimal losses to biological activity. We hypothesize that globally optimal PEGylation sites are characterized by the ability of the PEG oligomer to increase protein conformational stability; however, the current understanding of how PEG influences the conformational stability of proteins is incomplete. Here we use the WW domain of the human protein Pin 1 (WW) as a model system to probe the impact of PEG on protein conformational stability. Using a combination of experimental and theoretical approaches, we develop a structure-based method for predicting which sites within WW are most likely to experience PEG-based stabilization, and we show that this method correctly predicts the location of a stabilizing PEGylation site within the chicken Src SH3 domain. PEG-based stabilization in WW is associated with enhanced resistance to proteolysis, is entropic in origin, and likely involves disruption by PEG of the network of hydrogen-bound solvent molecules that surround the protein. Our results highlight the possibility of using modern site-specific PEGylation techniques to install PEG oligomers at predetermined locations where PEG will provide optimal increases in conformational and proteolytic stability.
A Review of Passive Wireless Sensors for Structural Health Monitoring (2013)

Wireless sensors for Structural Health Monitoring (SHM) is an emerging new technology that promises to overcome many disadvantages pertinent to conventional, wired sensors. The broad field of SHM has experienced significant growth over the past two decades, with several notable developments in the area of sensors such as piezoelectric sensors and optical fibre sensors. Although significant improvements have been made on damage monitoring techniques using these smart sensors, wiring remains a significant challenge to the practical implementation of these technologies. Wireless SHM has recently attracted the attention of researchers towards un-powered and more effective passive wireless sensors. This article presents a review of some of the underlying technologies in the field of wireless sensors for SHM - with a focus on the research progress towards the development of simple, powerless, yet effective and robust wireless damage detection sensors. This review examines the development of passive wireless sensors in two different categories: (1) use of oscillating circuits with the help of inductors, capacitors and resistors for damage detection; and (2) use of antennas, Radio Frequency Identification (RFID) tags and metamaterial resonators as strain sensors for wireless damage monitoring. An assessment of these electromagnetic techniques is presented and the key issues involved in their respective design configurations are discussed.
Improved serodiagnosis of tuberculosis using two assay test. (1986)

An antigen capture immunoassay was developed for the detection of mycobacterial antigens in sera from patients with tuberculosis. The assay was evaluated together with an antibody measuring enzyme immunoassay in a clinical trial for serodiagnosis of tuberculosis. Sensitivity of the antibody assay for active pulmonary tuberculosis, including relapsed infections, was 75%, and specificity with other lung diseases was 97%. Sensitivity for extrapulmonary tuberculosis was 84.5% and specificity 84%. Sensitivity of the antigen assay for active tuberculosis was 45% with no false positive reactions. Combination of the results from the two assays increased total sensitivity to 96.5% with a positive predictive value of 0.81 and a negative value of 0.98. The two assay test was relatively simple to perform and offered improved serological diagnosis of tuberculosis over a single antibody test.
Millisecond autothermal steam reforming of cellulose for synthetic biofuels by reactive flash volatilization (2008)

Three biomass-to-liquid process steps (volatilization of cellulose, tar-cleaning of organic products, and water-gas-shift of the gaseous effluent) have been integrated into a single autothermal catalytic reactor for the production of high quality synthesis gas at millisecond residence times (∼30 ms). Particles of cellulose (∼300 μm) were directly impinged upon the hot, catalytic bed of Rh–Ce/γ-Al2O3 catalyst on 1.3 mm α-Al2O3 spheres in the presence of O2, N2, and steam in a continuous flow fixed-bed reactor at 500–1100 °C. Complete conversion to gases was observed for all experimental parameters including N2/O2, S/C, the total flow rate of cellulose, and the fuel-to-oxygen ratio (C/O). The addition of steam increased the selectivity to H2 and decreased the selectivity to CO in agreement with water-gas-shift equilibrium. Optimal conditions produced a clean gaseous effluent which exhibited ∼80% selectivity to H2 at a synthesis gas ratio of H2/CO = 2.3 with no dilution from N2 at a fuel efficiency of ∼75%. Carbon-free processing was explained by relating the domain of experimental parameters to the thermodynamic prediction for the formation of solid carbon, CS.
Processing and Fabrication of Advanced Materials for High Temperature Applications (1992)

This volume is divided into the following sections: (1) processing and fabrication of intermetallics; (2) intermetallic and metal matrix composites; (3) ceramics and SHS processing; (4) carbon-carbon composites and high temperature coatings; and (5) novel processing routes. Separate abstracts were prepared for 43 papers in this volume.
Green Enzymatic Synthesis of L-Ascorbyl Fatty Acid Ester: An Antioxidant (2009)

Abstract In green chemistry, biocatalysis using microwaves is a very attractive tool for various regioselective syntheses. L-Ascorbyl fatty acid esters were synthesized by an immobilized lipase from Bulkholderia multivorans using microwaves, with a dynamically enhanced rate of reaction and appreciable yield of around 80%. Microwave radiation had no effect on enzymic inactivation, however, synergism between microwaves and biocatalyst was observed.
Exfoliating pristine black phosphorus down to the monolayer: photo-oxidation and electronic confinement effects (2014)

Thin layers of black phosphorus have recently raised interest for their two-dimensional (2D) semiconducting properties, such as tunable direct bandgap and high carrier mobilities. This lamellar crystal of P atoms stacked together by weak van der Waals forces can be exfoliated down to the stratophosphane monolayer (also called phosphorene) using procedures similar to those used for graphene. Properties of this 2D material are however challenging to probe due to a fast and ubiquitous degradation upon exposure to ambient conditions. Herein, we investigate the crystal degradation using in-situ Raman and transmission electron spectroscopies and highlight a process involving a photo-induced oxidation reaction with adsorbed oxygen in water. The experimental conditions to prepare and preserve mono-, bi- and multilayers of stratophosphane in their pristine states were determined. Study on these 2D layers provides new insights on the effect of confinement on the chemical reactivity and the vibrational modes of black phosphorus.
Manchester encoded bandpass sigma–delta modulation for RF class D amplifiers (2007)

An analysis of a continuous-time bandpass sigma–delta modulator in a configuration with an upconverter is given for a RF class D amplifier application. The upconverter multiplies the modulator pulse train with a synchronised clock signal and maps each modulator bit to an integer multiple k of a (+1, −1) or (−1, +1) pattern depending on the sign of the modulator bit. The upconversion is equivalent to an extension of Manchester encoding, which is usually defined for k=1. The analysis focuses on evaluating the impact of upconversion on the modulator coding efficiency and the average pulse period. A design equation is derived, which shows that coding efficiency is dependent only on the upconversion frequency ratio, while the average pulse period depends only on k. The equations provide a designer with a way of evaluating the trade-offs in the amplifier system and show that encoding with k=1 is the most efficient configuration for maximising coding efficiency and minimising switching power loss.
A virtual office environment for home office worker based on 3D virtual space (2002)

Describes a system that provides a "work-at-home" environment based on a virtual shared room built on a 3D graphics workstation. We realize an "awareness space" on the system to avoid the tradeoff between providing a facility for informal communication and keeping one's workspace information private from other people's awareness. Also, this system provides users with a feeling of their presence at a virtual office by using a so-called "around view" and sound effects.
Chronic Sex Steroid Exposure Increases Mean Plasma Growth Hormone Concentration and Pulse Amplitude in Men with Isolated Hypogonadotropic Hypogonadism (1987)

Sex steroid administration can increase the GH response to provocative stimuli, but the relationship of sex steroids to spontaneous GH secretion is still controversial. We sought to characterize the effect of sex steroids on the plasma GH concentration by examining the 24-h pattern of episodic GH secretion in nine previously untreated adult men with isolated hypogonadotropic hypogonadism before and during long term testosterone, gonadotropin, or pulsatile GnRH treatment. After chronic sex steroid exposure, the mean 24-h plasma GH level, mean GH pulse amplitude, and mean area under the curve of pulses were significantly increased compared to pretreatment values [3.2 +/- 1.8 ( +/- SD) vs. 1.8 +/- 1.2 ng/mL (P less than 0.01); 11.4 +/- 7.2 vs. 5.5 +/- 4.4 ng/mL (P less than 0.05); and 720 +/- 547 vs. 316 +/- 371 ng/mL X 20 min (P less than 0.05), respectively], while mean 24-h pre- and posttreatment GH pulse frequencies were indistinguishable (5.7 +/- 2.1 posttreatment vs. 5.0 +/- 3.2 pretreatment; P = NS). The mean posttreatment plasma somatomedin-C level also rose significantly during treatment (1.89 +/- 0.65 vs. 1.28 +/- 0.48 U/mL; P less than 0.01). We conclude that the increase in the mean plasma GH level during chronic sex steroid exposure is due mainly to augmentation of GH pulse amplitude, and that sex steroids probably increase spontaneous GH secretion.
Source signature determination by inversion (1992)

Abstract A new method for estimating the pressure wavefield generated by a marine air-gun array is presented. It is assumed that data is acquired at a ministreamer located below the source array. Effective source signatures for each air gun are estimated by an inversion algorithm. The forward modeling scheme used in the inversion algorithm is based upon a physical modeling of the air bubble generated by each air gun. This means that typical inversion parameters are: gun depths, empirical damping coefficients, and reflection coefficient of the sea surface. Variations in streamer depth are also taken into account by the inversion scheme. The algorithm has been successfully tested on examples with unknown streamer positions, gun parameters, reflection coefficient of sea surface, and ministreamer data contaminated with white noise.
Antike Metrik für den Schulgebrauch. Erstes Heft: Griechische Metrik von Dr.F. Eckstein; S. 37. Zweites Heft: Römische Metrik von Dr. P. Fleig und E. Wohleb; S. 24. Bielefeld und Leipzig: Velhagen und Klasing, 1926. (1928)

Antike Metrik für den Schulgebrauch. Erstes Heft: Griechische Metrik von Dr.F. Eckstein; S. 37. Zweites Heft: Römische Metrik von Dr. P. Fleig und E. Wohleb; S. 24. Bielefeld und Leipzig: Velhagen und Klasing, 1926. - Volume 42 Issue 1
Curie-temperature depth estimation using a self-similar magnetization model (1997)

The Earth's crust is magnetized down to the Curie-temperature depth at about 10 to 50 km. This limited depth extent of the crustal magnetization is discernible in the power spectra of magnetic maps of South Africa and Central Asia. At short wavelengths, the power increases as rapidly towards longer wavelengths as expected for a self-similar magnetized crust with unlimited depth extent. Above wavelengths of about 100 km the power starts increasing less rapidly, indicating the absence of deep-seated sources. To quantify this effect we derive the theoretical power spectrum due to a slab carved out of a self-similar magnetization distribution. This model power spectrum matches the power spectra of South Africa and Central Asia for a self-similarity parameter of β = 4 and Curie temperature depths of 15 to 20 km.
Continuous hidden process model for time series expression experiments (2007)

Supplementary data are available at Bioinformatics online.
Syntheses of 8‐aminoimidazo[4′,5′:5,6]pyrido[2,3‐<i>d</i>]pyrimiciines: Linear tricyclic analogs of adenine (1996)

Abstract The syntheses of 8‐aminoimidazo[4′,5′:5,6]pyrido[2,3‐ d ]pyrimidines (7), stretched‐out versions of the naturally occuring nucleoside base adenine, are reported. Their preparation involves conversion of purine into 5‐arninoimidazo[4,5‐ b ]pyrimidine‐6‐carbonitrile ( 1 ) by reaction with malononitrile, followed by construction of the pyrimidine ring in two steps via the ethoxymethylene derivative 3 . 8‐Azapurine can be converted to 8‐amino‐1,2,3‐triazolo[4′,5′:5,6]pyrido[2,3‐ d ]pyrimidines 8 in a similar fashion.
Protein Expression, Aggregation, and Triggered Release from Polymersomes as Artificial Cell‐like Structures (2012)

Bringing droplets to life: A cytoskeletal protein (red dots, see scheme) is expressed in artificial cells composed of biocompatible polymersomes, which encapsulate expression machinery and amino acid building blocks. Release of the expressed proteins can be triggered by a negative osmotic shock.
Simultaneous involvement of all six predicted antigen binding loops of the T cell receptor in recognition of the MHC/antigenic peptide complex. (1993)

The TCR is predicted to resemble the Fab fragment of an Ig molecule and by analogy to possess six Ag binding loops that contact MHC proteins bound with antigenic peptides. We have identified residues in the predicted Ag binding loops (beta 1, beta 2, and beta 3) on a TCR beta-chain that are important in the recognition of the MHC/antigenic peptide complex. Using site-directed mutagenesis, we altered the residues forming the predicted Ag binding site on the beta-chain expressed by the T lymphocyte clone D5, which specifically recognizes p-azobenzenearsonate-conjugated peptides presented by the class II MHC molecule I-Ad. Amino acid substitution of individual residues in each loop affected Ag recognition, demonstrating that all three putative Ag binding loops of the D5 TCR beta-chain are important in interaction with I-Ad/arsonate-conjugated Ag. Taken together with our previous work on the D5 TCR alpha-chain (Nalefski et al., J. Exp. Med. 175:1553), these results suggest that all six Ag binding loops of the D5 TCR alpha- and beta-chains interact simultaneously with the MHC/peptide complex. Consequently, the area of interaction between the TCR and the MHC/antigenic peptide complex is predicted to be extensive.
Effect of storage temperature and equilibration time on polymethyl methacrylate (PMMA) bone cement polymerization in joint replacement surgery (2015)

This study reflects the extent to which storage temperatures and equilibration times can potentially affect the handling characteristics of PMMA cement. We recommend institutions to have a well-regulated temperature and humidity-controlled facility for storage of bone cements and a protocol to standardize the equilibration time of cements prior to use in the OT to improve consistency and reproducibility of the handling characteristics of PMMA cement.
Design and implementation of FPGA based linear all digital phase-locked loop (2012)

This paper presents a linear all-digital phase locked loop based on FPGA. In this ADPLL the phase detection system is realized by generating an analytic signal using a compact implementation of Hilbert transform and then simply computing the instantaneous phase using CORDIC algorithm in vectoring mode of operation. A 16-bit pipelined CORDIC algorithm is employed in order to obtain the phase information of the signal. All the components used in this phase detection system are realized as digital discrete time components. This design does not involve any class of multipliers thus reducing the complexity of the design. The loop filter of the ADPLL has been designed using PI controller which has a low pass behavior and is used to discard the higher order harmonics of the error signal. The CORDIC algorithm in its rotation mode of operation is used to compute sinusoidal values for the DDS. The ADPLL model has been implemented using Xilinx ISE 12.3 and ModelSim PE Student Edition 10.1a.
USING NEURAL NETWORKS TO IDENTIFY DRIVING STYLE AND HEADWAY CONTROL BEHAVIOR OF DRIVERS (1997)

Abstract This paper illustrates the use of neural network techniques for analyzing headway data collected from a group of 36 driving subjects during normal on-highway driving. Pattern recognition methods are used to identify different types of headway-keeping behavior exhibited by these drivers and their relative distributions. Possibilities for using neural networks to represent longitudinal control behavior of drivers are also considered and discussed.
Fungal Ammonia Fermentation, a Novel Metabolic Mechanism That Couples the Dissimilatory and Assimilatory Pathways of Both Nitrate and Ethanol (2004)

Fungal ammonia fermentation is a novel dissimilatory metabolic mechanism that supplies energy under anoxic conditions. The fungus Fusarium oxysporum reduces nitrate to ammonium and simultaneously oxidizes ethanol to acetate to generate ATP (Zhou, Z., Takaya, N., Nakamura, A., Yamaguchi, M., Takeo, K., and Shoun, H. (2002) J. Biol. Chem. 277, 1892-1896). We identified the Aspergillus nidulans genes involved in ammonia fermentation by analyzing fungal mutants. The results showed that assimilatory nitrate and nitrite reductases (the gene products of niaD and niiA) were essential for reducing nitrate and for anaerobic cell growth during ammonia fermentation. We also found that ethanol oxidation is coupled with nitrate reduction and catalyzed by alcohol dehydrogenase, coenzyme A (CoA)-acylating aldehyde dehydrogenase, and acetyl-CoA synthetase (Acs). This is similar to the mechanism suggested in F. oxysporum except A. nidulans uses Acs to produce ATP instead of the ADP-dependent acetate kinase of F. oxysporum. The production of Acs requires a functional facA gene that encodes Acs and that is involved in ethanol assimilation and other metabolic processes. We purified the gene product of facA (FacA) from the fungus to show that the fungus acetylates FacA on its lysine residue(s) specifically under conditions of ammonia fermentation to regulate its substrate affinity. Acetylated FacA had higher affinity for acetyl-CoA than for acetate, whereas non-acetylated FacA had more affinity for acetate. Thus, the acetylated variant of the FacA protein is responsible for ATP synthesis during fungal ammonia fermentation. These results showed that the fungus ferments ammonium via coupled dissimilatory and assimilatory mechanisms.
Stereotactic radiosurgery for brain metastases: analysis of outcome and risk of brain radionecrosis (2011)

SRS alone represents a feasible option as initial treatment for patients with brain metastases, however a significant subset of patients may develop neurological complications. Lesions with V12 Gy >8.5 cm3 carries a risk of radionecrosis >10% and should be considered for hypofractionated stereotactic radiotherapy especially when located in/near eloquent areas.
Optimal Hotspots of Dynamic Surfaced-Enhanced Raman Spectroscopy for Drugs Quantitative Detection (2017)

Surface-enhanced Raman spectroscopy (SERS) as a powerful qualitative analysis method has been widely applied in many fields. However, SERS for quantitative analysis still suffers from several challenges partially because of the absence of stable and credible analytical strategy. Here, we demonstrate that the optimal hotspots created from dynamic surfaced-enhanced Raman spectroscopy (D-SERS) can be used for quantitative SERS measurements. In situ small-angle X-ray scattering was carried out to in situ real-time monitor the formation of the optimal hotspots, where the optimal hotspots with the most efficient hotspots were generated during the monodisperse Au-sol evaporating process. Importantly, the natural evaporation of Au-sol avoids the nanoparticles instability of salt-induced, and formation of ordered three-dimensional hotspots allows SERS detection with excellent reproducibility. Considering SERS signal variability in the D-SERS process, 4-mercaptopyridine (4-mpy) acted as internal standard to validly correct and improve stability as well as reduce fluctuation of signals. The strongest SERS spectra at the optimal hotspots of D-SERS have been extracted to statistics analysis. By using the SERS signal of 4-mpy as a stable internal calibration standard, the relative SERS intensity of target molecules demonstrated a linear response versus the negative logarithm of concentrations at the point of strongest SERS signals, which illustrates the great potential for quantitative analysis. The public drugs 3,4-methylenedioxymethamphetamine and α-methyltryptamine hydrochloride obtained precise analysis with internal standard D-SERS strategy. As a consequence, one has reason to believe our approach is promising to challenge quantitative problems in conventional SERS analysis.
Double-marker analysis of B lymphocyte subsets using a combination of immunofluorescence and rosetting with immunomagnetic beads. (1989)

Double-marker assays were developed for enumerating CD5+ B-cells and CD25+ activated B-cells. To measure CD5+ B-cells, CD19+ (pan B-specific) cells were first isolated from peripheral blood mononuclear cells using anti-Leu12-coated immunomagnetic beads (Dynabeads). Positively selected cells were stained for surface immunoglobulin (sIg) and then incubated with anti-Leu1-coated Dynabeads. Fluorescent cells which also bound Dynabeads could be readily enumerated. The proportion of CD5+ B-cells was found to be significantly elevated in 9 of 20 patients with definite rheumatoid arthritis. B-cells bearing the interleukin-2 receptor (IL-2-R, CD25) were identified in pokeweed mitogen-stimulated PBM by sIg fluorescence and rosetting with anti-Tac-labelled Dynabeads. The kinetics of CD25 expression following activation were found to be different for B- and non-B-cells.
Nanobodies targeting immune checkpoint molecules for tumor immunotherapy and immunoimaging (Review) (2020)

The immune checkpoint blockade is an effective strategy to enhance the anti‑tumor T cell effector activity, thus becoming one of the most promising immunotherapeutic strategies in the history of cancer treatment. Several immune checkpoint inhibitor have been approved by the FDA, such as anti‑CTLA‑4, anti‑PD‑1, anti‑PD‑L1 monoclonal antibodies. Most tumor patients benefitted from these antibodies, but some of the patients did not respond to them. To increase the effectiveness of immunotherapy, including immune checkpoint blockade therapies, miniaturization of antibodies has been introduced. A single‑domain antibody, also known as nanobody, is an attractive reagent for immunotherapy and immunoimaging thanks to its unique structural characteristic consisting of a variable region of a single heavy chain antibody. This structure confers to the nanobody a light molecular weight, making it smaller than conventional antibodies, although remaining able to bind to a specific antigen. Therefore, this review summarizes the production of nanobodies targeting immune checkpoint molecules and the application of nanobodies targeting immune checkpoint molecules in immunotherapy and immunoimaging.