gebhart/patrepeval huggingface dataset:
Designed SARS‐CoV‐2 receptor binding domain variants form stable monomers (2022)

The receptor binding domain (RBD) of the SARS-CoV-2 spike (S)-protein is a prime target of virus-neutralizing antibodies present in convalescent sera of COVID-19 patients and thus is considered a key antigen for immunosurveillance studies and vaccine development. Although recombinant expression of RBD has been achieved in several eukaryotic systems, mammalian cells have proven particularly useful. The authors aimed to optimize RBD produced in HEK293-6E cells towards a stable homogeneous preparation and addressed its O-glycosylation as well as the unpaired cysteine residue 538 in the widely used RBD (319-541) sequence. The authors found that an intact O-glycosylation site at T323 is highly relevant for the expression and maintenance of RBD as a monomer. Furthermore, it was shown that deletion or substitution of the unpaired cysteine residue C538 reduces the intrinsic propensity of RBD to form oligomeric aggregates, concomitant with an increased yield of the monomeric form of the protein. Bead-based and enzyme-linked immunosorbent assays utilizing these optimized RBD variants displayed excellent performance with respect to the specific detection of even low levels of SARS-CoV-2 antibodies in convalescent sera. Hence, these RBD variants could be instrumental for the further development of serological SARS-CoV-2 tests and inform the design of RBD-based vaccine candidates.
Electrical Stimulation of the Urethra Evokes Bladder Contractions in a Woman With Spinal Cord Injury (2010)

This is the first report of an excitatory urethra-spinal-bladder reflex in a woman with SCI. Future studies will determine whether this reflex can produce bladder emptying.
B-5-245 A Prospective Mesh Network Based Platform for Universal Mobile Communication Services (2004)

Styrene is a widely used industrial solvent associated with acute neurotoxicity. To investigate the relationships between exposure, blood concentrations, and the appearance of neurotoxic effects, four healthy males were exposed to styrene concentrations of 5-200 ppm in four different exposure-time profiles. A digit recognition test and P300 event-related evoked potential were used to measure neurologic function. A physiologically based kinetic (PBK) model generated close predictions of measured styrene blood concentrations, in the range of 0.01-12 mg/L, from this and 21 previous studies. Simulated peak brain concentration, durationXaverage exposure, and peak exposure level were predictive of toxicity. Central nervous system effects were expected at a blood concentration near 2.4 mg/L. A standard of 20 ppm was expected to protect styrene-exposed workers from acute central nervous system toxicity under light work conditions.
The finite element boundary integral method accelerated using a graphics processing unit (2013)

An implementation of the finite element boundary integral method with GPU accelerated code was developed to provide a significant improvement in computation time over the standard method.
Supplementary Table 7 from Use of Angiotensin System Inhibitors Is Associated with Immune Activation and Longer Survival in Nonmetastatic Pancreatic Ductal Adenocarcinoma (2023)

&lt;p&gt;Genes differentially expressed in ACEi alone treated group compared to control group&lt;/p&gt;
Explicit Navier-Stokes computation of cascade flows using the k-epsilon turbulence model (1992)

A fully explicit two-dimensional flow solver, based on a four-stage Runge-Kutta scheme, has been developed and used to predict two-dimensional viscous flow through turbomachinery cascades for which experimental data are available. The formulation is applied to the density-weighted time-averaged Navier-Stokes equations. Several features of the technique improve the ability of the code to predict high Reynolds number flows on highly stretched grids. These include a low Reynolds number compressible form of the A-e turbulence model, anisotropic scaling of artificial dissipation terms, and locally varying timestep evaluation based on hyperbolic and parabolic stability considerations. Comparisons between computation and experiment are presented for both a supersonic and a low-subsonic compressor cascade. These results indicate that the code is capable of predicting steady two-dimensional viscous cascade flows over a wide range of Mach numbers in reasonable computation times.
Evolution beyond LTE-advanced with Full Dimension MIMO (2013)

In this paper, we study the overall development of Full Dimension MIMO (FD-MIMO) technology in the context of next generation evolution towards B4G and 5G cellular systems. FD-MIMO relies on a large number of antennas placed in a 2-dimensional antenna array panel at base stations (BSs). Utilizing the 2-dimensional antenna array, FD-MIMO simultaneously transmits to a large number of mobile stations (MSs) effectively realizing high order multi-user MIMO (MU-MIMO) well beyond what is possible today. This paper discusses the research and standardization effort in 3GPP to incorporate the features and performance benefits of FD-MIMO in the next evolution of LTE standards. In order to demonstrate the potential performance benefits of FD-MIMO, system level evaluation results are provided using the 3GPP evaluation methodology. Evaluation results show that FD-MIMO can provide vast improvement over conventional LTE networks.
Reinforcement Learning for Efficient and Tuning-Free Link Adaptation (2021)

Wireless links adapt the data transmission parameters to the dynamic channel state – this is called <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">link adaptation</i> . Classical link adaptation relies on tuning parameters that are challenging to configure for optimal link performance. Recently, reinforcement learning has been proposed to automate link adaptation, where the transmission parameters are modeled as discrete arms of a multi-armed bandit. In this context, we propose a latent learning model for link adaptation that exploits the correlation between data transmission parameters. Further, motivated by the recent success of Thompson sampling for multi-armed bandit problems, we propose a latent Thompson sampling (LTS) algorithm that quickly learns the optimal parameters for a given channel state. We extend LTS to fading wireless channels through a tuning-free mechanism that automatically tracks the channel dynamics. In numerical evaluations with fading wireless channels, LTS improves the link throughout by up to 100% compared to the state-of-the-art link adaptation algorithms.
Ultrasonic tissue characterization parameter presentations in three dimensions (1990)

Ultrasonic tissue characterization based on spectrum analysis of radio-frequency (rf) echo signals is proving to be clinically useful in ophthalmology and abdominal studies. Parameters computed using spectrum analysis can be theoretically related to scattering properties of tissue such as scatterer size and impedance and therefore to histology. Such parameters can also be correlated empirically with clinical features, histopathology, treatment history, etc. They appear to be useful for clinical evaluation of disease, particularly detecting, diagnosing, staging, and monitoring cancer. Although parameters can be presented graphically or numerically, two-dimensional parameter images significantly facilitate the interpretation provided by tissue characterization. The portrayal of parameters in three dimensions further enhances the visualization of parameter distributions, and provides an even more powerful tool for tissue evaluation. In addition, three-dimensional (3-D) presentations of the surfaces of tissue structures permit assessment of spatial relationships and quantitative estimation of volume. These methods have been applied fruitfully in a number of medical applications, including evaluation of intraocular tumors, cancers of the liver, clots and thrombi, skin lesions, and prostate tissue. [This research has been supported by NIH Grants EY01212, EY01480, CA38400, and RR05853.]
XT-PRAGGMA: Crosstalk Pessimism Reduction Achieved with GPU Gate-level Simulations and Machine Learning (2022)

Accurate crosstalk-aware timing analysis is critical in nanometerscale process nodes. While today’s VLSI flows rely on static timing analysis (STA) techniques to perform crosstalk-aware timing signoff, these techniques are limited due to their static nature as they use imprecise heuristics such as arbitrary aggressor filtering and simplified delay calculations. This paper proposes XT-PRAGGMA, a tool that uses GPU-accelerated dynamic gate-level simulations and machine learning to eliminate false aggressors and accurately predict crosstalk-induced delta delays. XT-PRAGGMA reduces STA pessimism and provides crucial information to identify crosstalk-critical nets, which can be considered for accurate SPICE simulation before signoff. The proposed technique is fast (less than two hours to simulate 30,000 vectors on million-gate designs) and reduces falsely-reported total negative slack in timing signoff by 70%.
Metabolic Prosthesis for Oxygenation of Ischemic Tissue (2009)

This communication discloses new ideas and preliminary results on the development of a metabolic prosthesis for local oxygenation of ischemic tissue under physiologically neutral conditions. We report for the first time selective electrolysis of physiological saline by repetitively pulsed, charge-limited electrolysis for the production of oxygen and suppression of free chlorine. Using 800-microA amplitude current pulses and < 200 micros pulse duration, we demonstrate prompt oxygen production and delayed chlorine production at the surface of a fused 0.85-mm diameter spherical platinum electrode. The data, interpreted in terms of the ionic structure of the electric double layer, suggest a strategy for in situ production of metabolic oxygen via a new class of "smart" prosthetic implants for ischemic disease such as diabetic retinopathy. We also present data indicating that collateral pH drift, if any, can be held constant using a feedback-controlled three-electrode electrolysis system that chooses an anode and cathode pair based on pH data provided by a local sensor.
Betulin Attenuates TGF-β1- and PGE<sub>2</sub>-Mediated Inhibition of NK Cell Activity to Suppress Tumor Progression and Metastasis in Mice (2022)

Transforming growth factor (TGF)-β1 and prostaglandin E<sub>2</sub> (PGE<sub>2</sub>) are humoral factors critically involved in the induction of immunosuppression in the microenvironment of various types of tumors, including melanoma. In this study, we identified a natural compound that attenuated TGF-β1- and PGE<sub>2</sub>-induced immunosuppression and examined its effect on B16 melanoma growth in mice. By screening 502 natural compounds for attenuating activity against TGF-β1- or PGE<sub>2</sub>-induced suppression of cytolysis in poly(I:C)-stimulated murine splenocytes, we found that betulin was the most potent compound. Betulin also reduced TGF-β1- and PGE<sub>2</sub>-induced downregulation of perforin and granzyme B mRNA expression and cell surface expression of NKG2D and CD69 in natural killer (NK) cells. Cell depletion and coculture experiments showed that NK cells, dendritic cells, B cells, and T cells were necessary for the attenuating effects of betulin. Structure-activity relationship analysis revealed that two hydroxyl groups at positions C3 and C28 of betulin, their cis-configuration, and methyl group at C30 played crucial roles in its attenuating activity. In a subcutaneous implantation model of B16 melanoma in mice, intratumor administration of betulin and LY2157299, a TGF-β1 type I receptor kinase inhibitor, significantly retarded the growth of B16 melanoma. Notably, betulin increased significantly the number of CD69 positive NK cells in tumor sites at early stages of post-tumor cell injection. Our data suggest that betulin inhibits the growth of B16 melanoma by enhancing NK cell activity through attenuating the immunosuppressive tumor microenvironment.
Evidence that the Density of Self Peptide-MHC Ligands Regulates T-Cell Receptor Signaling (2012)

Noncognate or self peptide-MHC (pMHC) ligands productively interact with T-cell receptor (TCR) and are always in a large access over the cognate pMHC on the surface of antigen presenting cells. We assembled soluble cognate and noncognate pMHC class I (pMHC-I) ligands at designated ratios on various scaffolds into oligomers that mimic pMHC clustering and examined how multivalency and density of the pMHCs in model clusters influences the binding to live CD8 T cells and the kinetics of TCR signaling. Our data demonstrate that the density of self pMHC-I proteins promotes their interaction with CD8 co-receptor, which plays a critical role in recognition of a small number of cognate pMHC-I ligands. This suggests that MHC clustering on live target cells could be utilized as a sensitive mechanism to regulate T cell responsiveness.
Neprilysin Peptidase‐Independent Complex Formation In Pulmonary Artery Smooth Muscle Cells (2010)

Pulmonary hypertension (PHTN) results from vasoconstriction and remodeling of pulmonary arteries (PA), including accumulation and migration of smooth muscle cells (SMCs). We found that the activity/expression of the transmembrane peptidase neprilysin (NEP) is decreased in chronic hypoxic PHTN, and that chronically hypoxic NEP null mice have increased pulmonary vascular remodeling. We hypothesize that, besides peptidase effects, the peptidase‐independent mechanisms of NEP, mediated through coupling of NEP to intracellular proteins, are important in mediating the effects of NEP in PA SMCs. Silver‐stained gels of C57BL/6 wt mouse PA SMCs, co‐immunoprecipitated with an antibody to NEP, show bands of 40, 55, 65, 75, 90 and 150 kD. Western analyses (n=2–5) show that NEP forms complexes with the MAPK ERK1/2 and the protein kinase Lyn. Human PA SMCs show similar results. Future studies will investigate the growth‐ and migratory‐inhibitory properties of these complexes, as well as characterize NEP complexes with other proteins. These findings indicate that peptidase‐independent mechanisms may contribute to the mechanisms of action of NEP and may aid in understanding NEP's involvement in preventing/reversing pulmonary vascular remodeling, and in designing treatment and prevention strategies for PHTN. Research Support: NHLBI RO1 HL‐078929‐01 and PPG HL‐014985, UCD Dept. of Medicine, and the VA.
CVD Material Processing. Nanometer-Sized Silver Particle Measurements by Low Pressure Differential Mobility Analyzer and its Classification Performance. (2000)

窒素気流中で大気圧場で発生させたAgナノ粒子を対象として, 分級部の短い新しいタイプのウイーン大学型の減圧用微分型静電分級器 (Low Pressure Differential Mobility Analyzer, LPDMA) を用いて, Agナノ粒子のその場サイズ測定および分級特性試験を123～300Torrの減圧場において系統的に行った. 160Torrの減圧場で本LPDMAで測定した体積平均径DV, DMAは, Agナノ粒子の粒径6～15nmの範囲において, LPDMA入口でサンプリングした粒子を透過型電子顕微鏡 (TEM) で観察して求めた体積平均径DV, TEMよりも約7%程度大きいものの, 良い相関を示した.また, 160Torrの減圧場において本LPDMAを用いて6～25nmの範囲で, シースガスとエアロゾルガス流量比を5: 1で分級した際の設定径は, 分級後サンプリングしてTEM観察した粒子から求めた粒径よりも約14%程度大きいものの, 同様に良い相関を示した. その際, 分級前のサンプリング粒子のTEM像から求めた粒径から算出した幾何標準偏差は1.34～1.50の範囲であるのに対して, 分級後のサンプリング粒子像から算出したそれは1.08～1.17の範囲であり, ブラウン拡散による分級のブロードニングを無視してLPDMA流量比から算出した理論値 (1.093) とほぼ一致した. 以上の結果より, 123～300Torrの減圧場における6～25nmのナノ粒子の粒径測定, 分級操作が, 本LPDMAシステムを用いて十分可能であることを実証した.
Noise Reduction Effect of Multiple-Sampling-Based Signal-Readout Circuits for Ultra-Low Noise CMOS Image Sensors (2016)

This paper discusses the noise reduction effect of multiple-sampling-based signal readout circuits for implementing ultra-low-noise image sensors. The correlated multiple sampling (CMS) technique has recently become an important technology for high-gain column readout circuits in low-noise CMOS image sensors (CISs). This paper reveals how the column CMS circuits, together with a pixel having a high-conversion-gain charge detector and low-noise transistor, realizes deep sub-electron read noise levels based on the analysis of noise components in the signal readout chain from a pixel to the column analog-to-digital converter (ADC). The noise measurement results of experimental CISs are compared with the noise analysis and the effect of noise reduction to the sampling number is discussed at the deep sub-electron level. Images taken with three CMS gains of two, 16, and 128 show distinct advantage of image contrast for the gain of 128 (noise(median): 0.29 e<sup>-</sup><sub>rms</sub>) when compared with the CMS gain of two (2.4 e<sup>-</sup><sub>rms</sub>), or 16 (1.1 e<sup>-</sup><sub>rms</sub>).
Process Characterization of MOS devices by Scanning Electron Microscopy with 0.5-1 KV electrons (1981)

A low acceleration voltage scanning electron microscope (SEM) is applied to the inprocess characterization of MOS LSI without any adverse effects. Radiation of electrons having an energy of less than 1 kV does not cause any MOS circuit characteristics to change, e.g., the Vth shift of a MOSFET is less than 0.01 V. A low voltage of 800 V is required to inspect resist patterns on SIO2?Si substrates to avoid charge-up effects.
Rhodium‐Catalyzed Asymmetric Hydroformylation of Unsaturated Nitriles. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Maximum-Entropy Method for EG Source Imaging (1997)

Magnetoencephalographic imaging is the estimation of three-dimensional neuronal current sources on the cortical surface from the measured magnetoencephalogram (MEG). It is a highly under-determined inverse problem as there are many “feasible” images which are consistent with the MEG. Previous approaches to this problem have concentrated on the use of weighted minimum-norm inverse methods [ 1,2]. These methods often produce overly smoothed images and exhibit bias towards surface sources. In this work we explore the maximum-entropy approach [3] to obtain better solutions to the problem. This estimation technique selects, from the possible set of feasible images, the image with the highest entropy permitted by the available information. In order to account for the presence of noise in the data, we have also incorporated a noise rejection term into the maximum-entropy method (MEM). This makes our approach mirror a Bayesian maximum a posteriori probability (MAP) formulation. Additional information from other modalities like functional magnetic resonance imaging (fMRI) can also be incorporated into the proposed method in the form of a prior bias function to improve solutions. We demonstrate the method with experimental phantom data from a clinical 122-channel MEG system.
Novel injectable calcium phosphate scaffold with human periodontal ligament stem cell encapsulation in microbeads for bone regeneration (2022)

Objectives: 1) Develop a novel construct of human periodontal ligament stem cells (hPDLSCs) encapsulated in degradable alginate microbeads (DAMB) with human platelet lysate (hPL) and injectable calcium phosphate cement (ICPC); 2) Investigate the proliferation and osteogenic differentiation of hPDLSCs in ICPC with hPL as a xeno-free supplement and animal serum replacement for bone tissue engineering applications. Methods: hPDLSCs were encapsulated in alginate-fibrin microbeads (DAMB + fibrin), alginate-hPL degradable microbeads (DAMB + hPL), or alginate-fibrin-hPL microbeads (DAMB + fibrin + hPL). The proliferation and osteogenic differentiation of hPDLSCs were investigated in culturing with the ICPC scaffold. Results: Flexural strength of ICPC was 8.4 ± 0.91 MPa, and elastic modulus was 1.56 ± 0.1 GPa, exceeding those of cancellous bone. hPDLSCs had higher viability in DAMB + fibrin + hPL group than in DAMB + fibrin. ALP was 69.97 ± 16.96 mU/mg for ICPC + DAMB + fibrin + hPL group, higher than 30.68 ± 2.86 mU/mg of ICPC + DAMB + fibrin ( p &amp;lt; 0.05) and 4.12 ± 1.65 mU/mg of control ( p &amp;lt; 0.01). At 7 days, osteogenic gene expressions ( ALP , RUNX2 , COL1 , and OPN ) in ICPC + DAMB + fibrin + hPL and ICPC + DAMB + fibrin were 4–11 folds that of control. At 21 days, the hPDLSC-synthesized bone mineral amounts in ICPC + DAMB + fibrin + hPL and ICPC + DAMB + fibrin were 13.2 folds and 11.1 folds that of control group, respectively. Conclusion: The novel injectable CPC scaffold encapsulating hPDLSCs and hPL is promising to protect and deliver hPDLSCs. The hPL-based medium significantly enhanced the osteogenic differentiation of hPDLSCs in ICPC + DAMB + fibrin + hPL construct, suggesting a promising xeno-free approach for bone tissue regeneration applications.
DNA Replication: Yeast (2018)

Abstract DNA replication is a complex biological process essential to maintaining the fidelity of genetic information passed to subsequent generations, while allowing for the mutations necessary for natural selection. The cellular machinery required for DNA replication must be precisely controlled throughout the cycle. A variety of DNA polymerases have proofreading and repairing capabilities to avoid catastrophic errors, thus maintaining genomic stability. Much of the mechanism involved in this process is evolutionarily conserved. Because yeast is a relatively simple and inexpensive organism to work with, much of our understanding of DNA replication in eukaryotes originates from experiments with yeast. The most thoroughly characterized model yeast systems are Saccharomyces cerevisiae (budding yeast) and Saccharomyces pombe (fission yeast). Key Concepts Yeast is a good model organism for simplifying and characterising cellular processes, such as DNA replication. The two most commonly used yeast models are S. cerevisiae and S. pombe . DNA replication is a complex biological process essential to genomic replication. DNA replication is a process that involves timely organisation of proteins and is regulated during the cell cycle by cyclin‐dependent protein kinases. Termination of DNA replication in yeast is generally not sequence specific, except in special circumstances in the cellular process.
ChemInform Abstract: Diethyl 3,6‐Dihydro‐2,4‐dimethyl‐2,6‐methano‐1,3‐benzothiazocine‐5,11‐ dicarboxylates as Calcium Entry Antagonists: New Conformationally Restrained Analogues of Hantzsch 1,4‐Dihydropyridines Related to Nitrendipine as Probes for Receptor‐Site Conformation. (1987)

Abstract Oxidation of the thioether (I) yields the corresponding sulfoxide which undergoes a Pummerer rearrangement with sodium acetate, yielding the masked thiol (II).
Labeling metal oxide nanoparticles with optical dyes: Bioimaging applications of corrole-metal oxide nanoconjugates (2014)

Probe development involving nanoscale materials has become increasingly significant and at the forefront in&#13;\nmol. imaging for both diagnosis and drug development based on improved understanding of biol. processes.&#13;\nVarious nanosized probes, namely, quantum dots and superparamagnetic iron oxides, have been explored using&#13;\nappropriate imaging modalities and biomedical studies. Owing to their vast surface area and extensive&#13;\npossibility for surface decoration with multiple groups to attain desirable functionalities, metal oxide&#13;\nnanomaterials, such as TiO_2 and ZnO, offer unique benefits over traditional small mols. and biomols. as contrast&#13;\nagents. Examples of potential near-IR contrast agents involving TiO_2 nanoparticle surfaces covalently decorated&#13;\nwith fluorescent corroles will be presented. Corrole prepn. and conjugation of the corroles to TiO_2&#13;\nnanoparticles will be discussed. Photophys. and imaging studies of the corrole-TiO_2 nanocojugates will be&#13;\naddressed.