gebhart/patrepeval huggingface dataset:
The molecular basis for the chemical denaturation of proteins by urea (2003)

Molecular dynamics simulations of the protein chymotrypsin inhibitor 2 in 8 M urea at 60 degrees C were undertaken to investigate the molecular basis of chemical denaturation. The protein unfolded rapidly under these conditions, but it retained its native structure in a control simulation in water at the same temperature. The overall process of unfolding in urea was similar to that observed in thermal denaturation simulations above the protein's T(m) of 75 degrees C. The first step in unfolding was expansion of the hydrophobic core. Then, the core was solvated by water and later by urea. The denatured structures in both urea and at high temperature contained residual native helical structure, whereas the beta-structure was completely disrupted. The average residence time for urea around hydrophilic groups was six times greater than around hydrophobic residues and in all cases greater than the corresponding water residence times. Water self-diffusion was reduced 40% in 8 M urea. Urea altered water structure and dynamics, thereby diminishing the hydrophobic effect and encouraging solvation of hydrophobic groups. In addition, through urea's weakening of water structure, water became free to compete with intraprotein interactions. Urea also interacted directly with polar residues and the peptide backbone, thereby stabilizing nonnative conformations. These simulations suggest that urea denatures proteins via both direct and indirect mechanisms.
Clinical Features, Etiology and Outcomes of Community-Acquired Pneumonia in Patients with Chronic Obstructive Pulmonary Disease (2014)

CAP in patients with COPD presents specific characteristics and risk factors for mortality. Prior pneumococcal vaccine has a beneficial effect on outcomes. P. aeruginosa pneumonia is associated with low FEV1 values and poor prognosis.
Empirical high-resolution wind field and gust model in mountainousand hilly terrain based on the dense WegenerNet station networks (2018)

Abstract. A weather diagnostic application for automatic generation of gridded wind fields in near-real time, recently developed by the authors (Schlager et al., 2017), is applied to the WegenerNet Johnsbachtal (JBT) meteorological station network. This station network contains eleven meteorological stations at elevations from about 600 m to 2200 m in a mountainous region in the north of Styria, Austria. The application generates, based on meteorological observations with a temporal resolution of 10 minutes from the WegenerNet JBT, mean wind and wind gust fields at 10 m and 50 m height levels with a high spatial resolution of 100 × 100 m and a temporal resolution of 30 minutes. These wind field products are automatically stored to the WegenerNet data archives, which also include long-term averaged weather and climate datasets from post-processing. A main purpose of these empirically modeled products is the evaluation of convection-permitting dynamical climate models as well as investigating weather and climate variability on a local scale. The application's performance is evaluated against the observations from meteorological stations for representative weather conditions, for a month including mainly thermally induced wind events (July 2014) and a month with frequently occurring strong wind events (December 2013). The overall statistical agreement, estimated for the vector-mean wind speed, shows a reasonably good modeling performance with somewhat better values for the strong wind conditions. The difference between modeled and observed wind directions depends on the station location, where locations along mountain slopes are particularly challenging. Furthermore, the seasonal statistical agreement was investigated from five-year climate data of the WegenerNet JBT in comparison to nine-year climate data from the high-density WegenerNet meteorological station network Feldbach Region (FBR) analyzed by Schlager et al., (2017)In general, the five-year statistical evaluation for the JBT indicates similar performance as the shorter-term evaluations of the two representative months. Because of the denser WegenerNet FBR network, the statistical results show better performance for this station network. The application can now serve as a valuable tool for intercomparison with and evaluation of wind fields from high-resolution dynamical climate models in both the WegenerNet FBR and JBT regions.
Gaussian functions are optimal for waveguided nonlinear-quantum-optical processes (2018)

Many nonlinear optical technologies require the two-mode spectral amplitude function that describes them---the joint spectral amplitude (JSA)---to be separable. We prove that the JSA factorizes only when the incident pump field and phase-matching function are Gaussian functions. We show this by mapping our problem to a known result, in continuous variable quantum information, that only squeezed states remain unentangled when combined on a beam splitter. We then conjecture that only a squeezed state minimizes entanglement when sent through a beam splitter with another prespecified ket. This implies that to maximize JSA separability when one of the (pump or nonlinear medium) functions is non-Gaussian, the other function must be Gaussian. This answers an outstanding question about optimal design of certain nonlinear processes and is of practical interest to researchers using waveguide nonlinear optics to generate and manipulate quantum light.
Conformation dependence of DNA electrophoretic mobility in a converging channel (2010)

The electrophoresis of lambda-DNA is observed in a microscale converging channel where the center-of-masses trajectories of DNA molecules are tracked to measure instantaneous electrophoretic (EP) mobilities of DNA molecules of various stretch lengths and conformations. Contrary to the usual assumption that DNA mobility is a constant, independent of field and DNA length in free solution, we find DNA EP mobility varies along the axis in the contracting geometry. We correlate this mobility variation with the local stretch and conformational changes of the DNA, which are induced by the electric field gradient produced by the contraction. A "shish-kebab" model of a rigid polymer segment is developed, which consists of aligned spheres acting as charge and drag centers. The EP mobility of the shish-kebab is obtained by determining the electrohydrodynamic interactions of aligned spheres driven by the electric field. Multiple shish-kebabs are then connected end-to-end to form a freely jointed chain model for a flexible DNA chain. DNA EP mobility is finally obtained as an ensemble average over the shish-kebab orientations that are biased to match the overall stretch of the DNA chain. Using physically reasonable parameters, the model agrees well with experimental results for the dependence of EP mobility on stretch and conformation. We find that the magnitude of the EP mobility increases with DNA stretch, and that this increase is more pronounced for folded conformations.
In-Line Extrusion/Thermoforming Techniques for Deep Draw Polyolefin Containers (1989)

Requirements for thermoformed containers are described and con sideration is given to the merits of several production systems. Results are presented for an in-line extrusion and thermoforming system that has been developed for the production of deep draw polyolefin containers.
A Self-referencing Digital Error Correction Method for Dual-comb Interferometer (2020)

We present a self-referencing digital error correction method for dual-comb interferometry. Fully mutual coherence of a dual-comb interferometer is reconstructed and 1 Hz theoretical linewidth in 1 second acquisition time is achieved.
Magnetic resonance imaging of gadolinium-labeled monoclonal antibody polymers directed at human T lymphocytes implanted in canine brain (1987)

Two different murine monoclonal anti-human T cell antibodies, that were coupled to gadolinium (Gd), bind specifically to human T lymphocyte cells implanted in canine brain. This binding was at a concentration of Gd sufficient to detect the implanted cells and to distinguish them from the surrounding brain tissue with magnetic resonance imaging (MRI) at a field strength of 1.5 Tesla. These Gd-labeled immunoglobulin preparations did not bind bovine T cells at a concentration sufficient to be detected on MRI. A protein solution containing the immunoglobulins (100 micrograms), gelatin (2 mg), and bovine serum albumin (2.5 mg) was reacted with the dianhydride of diethylenetriaminepentaacetic acid (DTPA); the DTPA serves as a metal chelator and as a protein crosslinking agent. The DTPA-protein complex was reacted with Gd chloride. There were approximately 10 DTPA residues per protein molecule in the modified protein mixture. Isolated human or bovine monocytes (approximately 12 million cells) were implanted in the brains of anesthetized dogs in a volume of 40 microliters. The blood-brain barrier was then disrupted by the intra-arterial injection of hyperosmotic mannitol, and the Gd-labeled antibodies were injected through a catheter placed at the branch of the internal and external carotid arteries. The brains were imaged 48 to 72 hours later. The MRI scans revealed a markedly decreased T1 relaxation time with a high signal intensity (TE = 25 msec, TR = 200 msec) related to the human T cell implants. There was no evidence of decreased T1 at the site of the bovine T cells. Neither control murine gamma globulin coupled to Gd-DTPA nor anti-human T cell antibodies uncoupled to Gd modified the MRI contrast of the human T cells in the brain.
Susceptibility weighted imaging in acute cerebral ischemia: review of emerging technical concepts and clinical applications (2017)

Susceptibility weighted imaging (SWI) is an essential magnetic resonance imaging sequence in the assessment of acute ischemic stroke. In this article, we discuss the physics principals and clinical application of conventional SWI and multi-echo SWI sequences. We review the research evidence and practical approach of SWI in acute ischemic stroke by focusing on the detection and characterization of thromboembolism in the cerebral circulation. In addition, we discuss the role of SWI in the assessment of neuroparenchyma by depiction of asymmetric hypointense cortical veins in the ischemic territory (surrogate tissue perfusion), detection of existing microbleeds before stroke treatment and monitoring for hemorrhagic transformation post-treatment. In conclusion, the SWI sequence complements other parameters in the stroke magnetic resonance imaging protocol and understanding of the research evidence is vital for practising stroke neurologists and neuroradiologists.
Accuracy of chimeric proteins in the serological diagnosis of chronic chagas disease – a Phase II study (2017)

Our findings indicate that the IBMP-8.4 antigen can be safely used in serological tests for T. cruzi screening in blood banks and for chronic CD laboratory diagnosis.
Optics for a Read–Write Holographic Memory (1970)

An optical system is described for a read-write holographic memory capable of storage densities on the order of 8000 bits mm(-2). Simplicity is achieved through the use of a normally incident reference beam for both writing and reading.
Derivation and Isolation of NKX2.1-Positive Basal Forebrain Progenitors from Human Embryonic Stem Cells (2013)

Gamma aminobutyric acid (GABA)-expressing interneurons are the major inhibitory cells of the cerebral cortex and hippocampus. These interneurons originate in the medial ganglionic eminence (MGE) and lateral ganglionic eminence of the ventral forebrain during embryonic development and show reduced survival and function in a variety of neurological disorders, including temporal lobe epilepsy. We and others have proposed that embryonic stem cell (ESC)-derived ventral forebrain progenitors might provide a source of new GABAergic interneurons for cell-based therapies. While human ESCs (hESCs) are readily differentiated in vitro into dorsal telencephalic neural progenitors, standard protocols for generating ventral subtypes of telencephalic progenitors are less effective. We now report efficient derivation of GABAergic progenitors using an established hESC reporter line that expresses green fluorescent protein (GFP) under the control of an endogenous NKX2.1 promoter. GABAergic progenitors were derived from this hESC line by a modified monolayer neural differentiation protocol. Consistent with sonic hedgehog (SHH)-dependent specification of NKX2.1-positive progenitors in the embryonic MGE, we show a dose-dependent increase in the generation of NKX2.1:GFP-positive progenitors after SHH treatment in vitro. Characterization of NKX2.1:GFP-positive cells confirms their identity as MGE-like neural progenitors, based on gene expression profiles and their ability to differentiate into GABAergic interneurons. We are also able to generate highly enriched populations of NKX2.1:GFP-positive progenitors, including cells with telencephalic identity, by fluorescence-activated cell sorting. These hESC-derived ventral forebrain progenitors are suitable candidates for cell-based therapies that aim at replacing dysfunctional or damaged cortical or hippocampal GABAergic interneurons.
8.2 A 22.4-to-26.8GHz Dual-Path-Synchronized Quad-Core Oscillator Achieving −138dBc/Hz PN and 193.3dBc/Hz FoM at 10MHz Offset from 25.8GHz (2023)

The denser modulation scheme, employed by high-speed wireless communications, such as 5G, demands millimeter-wave (mm-wave) oscillators with low phase noise (PN). Generally, the PN of an LC oscillator can be reduced by downscaling its tank inductance. Yet, an over-shrunk single-turn spiral inductor suffers from <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Q$</tex> degradation [1], impairing the figure-of-merit (FoM) and the minimum-achievable PN of the oscillator. Coupling multiple oscillators together is effective for PN reduction. Ideally, an N-core coupled oscillator can achieve 10log(N) lower PN when compared with a single-core oscillator. Nevertheless, the frequency mismatch between the oscillator cores tends to penalize the PN improvement and FoM of a coupled oscillator (Fig. 8.2.1 upper). Figure 8.2.1 (bottom) depicts two approaches to implement a quad-core oscillator by connecting four cores using: 1) spiral inductors (transformers) in a concentric way [2], [3], or 2) slab inductors (transformers) in a circular way [1], [4]. Since the outputs of either of the two cores in the first approach can be directly connected via a short metal trace with a small resistance, it benefits from a small PN penalty induced by the frequency mismatch. But the poor <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Q$</tex> of the small spiral inductor limits its PN. On the contrary, the latter approach features a circular inductor (transformer) with an improved <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$Q$</tex> but suffers from a large PN penalty due to the frequency mismatch between two non-adjacent cores, i.e., cores #1 (#2) and #3(#4), since the non-adjacent cores are not directly connected and synchronized.
Why Do Sicker Patients Cost More? A Charge-Based Analysis of Patients Undergoing Prostatectomy (1993)

Hospitals are reimbursed a greater amount for Medicare patients undergoing prostate surgery who have comorbid and complicating conditions than for patients without these conditions, since the former have been shown to have higher hospital costs and charges. We attempted to determine whether the higher hospital charges are due to duration of hospital stay and/or intensity of services. We analyzed hospital discharge data from 799 patients undergoing radical or transurethral prostatectomy during a 3-year period (1988 to 1991) at 2 major teaching hospitals by examining length of stay (duration), charges per hospital day (intensity) and total charges per stay. Mean lengths of stay were significantly longer for sicker versus healthier patients undergoing radical prostatectomy (7.4 versus 6.8 days at hospital 1 and 8.9 versus 7.8 days at hospital 2, p < 0.05) and transurethral prostatectomy (3.5 versus 2.8 days at hospital 1 and 3.5 versus 2.5 days at hospital 2, p < 0.05). Total hospital charges were significantly higher for sicker versus healthier patients undergoing radical prostatectomy ($14,557 versus $13,357 at hospital 1 and $17,864 versus $16,080 at hospital 2, p < 0.05) and transurethral prostatectomy ($6,446 versus $5,012 at hospital 1 and $5,468 versus $3,710 at hospital 2, p < 0.05). However, sicker and healthier patients had similar charges per day for radical prostatectomy ($1,959 versus $1,961 at hospital 1 and $2,006 versus $2,073 at hospital 2, p not significant) and for transurethral prostatectomy ($1.839 versus $1,800 at hospital 1 and $1.544 versus $1,488 at hospital 2, p not significant). On specified hospital days the charges per day for room/nursing, medical/surgical supplies, laboratory services and pharmacy services were similar for patients with and without comorbid conditions. Patients who are more ill at admission remain hospitalized longer after prostatectomy. However, they do not receive more intense care during their stays. For these procedures duration and not intensity appears to be the primary determinant of higher hospital charges for sicker patients.
Accurate X-Propagation for Test Applications by SAT-Based Reasoning (2012)

Unknown or X-values during test applications may originate from uncontrolled sequential cells or macros, from clock or A/D boundaries, or from tristate logic. The exact identification of X-value propagation paths in logic circuits is crucial in logic simulation and fault simulation. In the first case, it enables the proper assessment of expected responses and the effective and efficient handling of X-values during test response compaction. In the second case, it is important for a proper assessment of fault coverage of a given test set and consequently influences the efficiency of test pattern generation. The commonly employed <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> -valued logic simulation evaluates the propagation of X-values only pessimistically, i.e., the X-propagation paths found by <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> -valued logic simulation are a superset of the actual propagation paths. This paper presents an efficient method for overcoming this pessimism and for determining accurately the set of signals that carry an X-value for an input pattern. As examples, it investigates the influence of this pessimism on the two applications, X-masking and stuck-at fault coverage assessment. The experimental results on benchmark and industrial circuits assess the pessimism of classic algorithms and show that these algorithms significantly overestimate the signals with X-values. The experiments show that overmasking of test data during test compression can be reduced by an accurate analysis. In stuck-at fault simulation, the coverage of the test set is increased by the proposed algorithm without incurring any overhead.
Extending the semantics of scheduling priorities (2012)

Increasing parallelism demands new paradigms.
Facile Oxidations under Flow Conditions in Fixed-Bed Reactors (2010)

Flow oxidation with inductive heating inside flow reactors was described. The oxidation reactions of various substrates were carried out in glass flow reactors charged with superparamagnetic nanoparticles and solid oxidants, which were exposed to a magnetic field with an inductive frequency of 25 kHz at 40 psi backpressure to afford the corresponding products.
TW37 enhances the pro-apoptosis and anti-migration ability of gefitinib in Non-Small Cell Lung Cancer (2018)

B cell leukemia-2 (Bcl-2) plays important roles in the development of tumor and drug resistance. The growth of tumor cells can be inhibited by downregulating the abnormal expression of Bcl-2 protein. TW37, an effective inhibitor of Bcl-2 protein, has now been widely studied in many tumors. In our study, it was found that TW37 exerted a significant effect on the proliferation, apoptosis and migration of Non-Small Cell Lung Cancer cells. Bcl-2 is also a key downstream factor of many signaling pathways such as Epidermal Growth Factor Receptor (EGFR). TW37 enhanced the inhibition of tumorigenesis by gefitinib, an EGFR-Tyrosine Kinase Inhibitor drug. Moreover, TW37 can promote apoptosis ability by inhibiting the phosphorylation level of EGFR protein in H1975 cells. Overall, TW37 enhances the pro-apoptosis and anti-migration ability of gefitinib in Non-Small Cell Lung Cancer.
Ocular adaptive optics and the need for higher bandwidths (2003)

We present an adaptive optics system with measured closed-loop bandwidths between 1 and 29 Hz depending on the specific system configuration and the particular subject tested. A pilot analysis of the system performance as a function of the achieved bandwidth showed consistently smaller variability in the correction and higher Strehl ratios with adaptive compensation for higher closed-loop bandwidths. Increased bandwidths not only improved optical quality but also reduced the variability of the wavefront RMS over time.
Inactivation of Cdc2 increases the level of apoptosis induced by DNA damage (1995)

A number of lines of evidence have suggested a possible involvement of the mitosis-promoting protein kinase Cdc2 in the process of apoptotic cell death, and one recent study concluded that premature activation of Cdc2 is required for apoptosis. Here we have used a temperature-sensitive murine Cdc2 mutant cell line and Cdc2 inhibitor compounds to study the effect of inhibition of this protein kinase on apoptosis induced by DNA-damaging drugs. Inhibition of Cdc2 activity before or during exposure to DNA strand break-inducing drugs had the effect of increasing the level of subsequent apoptosis, as assessed by electron microscopy and flow cytometry. We conclude that, far from being required for cell death, a form of mammalian Cdc2 suppresses apoptosis induced by DNA damage. This form of Cdc2 appears to be active in G2-arrested cells and is therefore presumably distinct from the mitosis-promoting Cdc2-cyclin B heterodimer.
Optimization of wireless bandwidth utilization (2003)

On wireless networks, the bandwidth is shared between the clients, which means that the available bandwidth always fluctuates. Adaptive multimedia contents are required because of this fluctuation in order to optimize the wireless available bandwidth. In this article, we describe NetMoVie a new architecture for the management of adaptive streaming based on the RTP standard. NetMoVie optimizes the bandwidth by providing a hybrid encoding solution and also reduces the time needed to change the quality delivered to the clients.