gebhart/patrepeval huggingface dataset:
Directionality of Chemical Reaction and Spontaneity of Biological Process in the Context of Entropy (2022)

Chemical and biochemical reactions are carried out either to generate energy or to produce useful macromolecules. Entropy is a well-applied concept in many fields, including physics, chemistry, biology, and medicine. Various perspectives have been used to describe the concept, creating confusion and misconceptions. In chemical and biochemical reactions, entropy plays a significant role in the directionality and spontaneity of the reactions. Potential energy can be used to better understand the concept of entropy. Potential energy represents order, while entropy represents disorder; therefore, they are inversely proportional and intimately linked. Molecules with high potential usually have rich sets of functions and information, which is due to the enrichment of their constitutions, configurations, and conformations. In molecules with low potential, there are greater vibrational, rotational, and translational motions associated with decreased order in their constitution, configuration, and conformation. Distribution of electronic charge changes in macromolecules over time, increasing the rotation of side-chain residues and thus increasing entropy and affecting potential in terms of structure, function, and information. Entropy can thus be defined as a state of spontaneous change, bound to time and constantly increasing, which causes structural changes in the form of constitution, configuration, and conformation, and functional changes in the form of the ability to do work as well as informational changes in the form of the transmission of commands.
LARGE EDDY SIMULATIONS OF TURBULENT LIQUID FLOWS WITH CHEMICAL REACTIONS (2001)

A subgrid-scale (SGS) model for the filtered reaction term is presented to develope large eddy simulations (LES) of nonpremixed, turbulent reacting liquid flows. The SGS model is based on the SGS probability density function (PDF) and SGS conditional expectation. The SGS PDF is assumed to have the beta distribution and the SGS conditional expectation was modeled using the filtered data obtained from direct numerical simulations (DNS) of liquid flows with second-order chemical reactions. To confirm the accuracy of the SGS model, the LES was applied to a liquid mixing layer flow downstream of a turbulence-generating grid with a chemical reaction. The large eddy probability density function (LEPDF) model and the present model were used as the SGS models for a rapid reaction and for a moderately fast reaction, respectively. The predictions of the LES were compared with the measurements by Komori et al. (1993, 1994) to examine the proposed SGS models. The results show that the predictions of the LES are in good areement with the mesurements. Furthermore, to investigate the applicability of the present LES to other reacting liquid flows, both experiment and LES were performed in a turbulent mixing layer with a rapid reaction. The predictions were also in good agreement with the measurements. These results show that the present LES taking account into the SGS distributions can accurately estimate the concentration statistics in various types of reacting liquid flows.
Analysis and improvement of an authenticated key exchange protocol for sensor networks (2005)

In 2003, Huang et al. proposed: an authenticated key exchange protocol for secure communications between a sensor and a security manager in a self-organizing sensor network. The protocol is, based on elliptic curve cryptography. In this letter, we show that a security manager will learn the long-term private key of a sensor after having one normal run of-the protocol with the sensor. This contradicts to some of their security claims. We explain why this is undesirable in practice and also-propose an improvement which solves the problem and makes all of their security claims hold again.
RF power devices for wireless communications (2003)

A wide variety of semiconductor devices are used in wireless power amplifiers. This paper will review the advantages and disadvantages of these devices for handheld and infrastructure applications.
Morphology Control in Mesoporous Carbon Films Using Solvent Vapor Annealing (2013)

Ordered mesoporous (2-50 nm) carbon films were fabricated using cooperative self-assembly of a phenolic resin oligomer with a novel block copolymer template (poly(styrene-block-N,N-dimethyl-n-octadecylamine p-styrenesulfonate), (PS-b-PSS-DMODA)) synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. Due to the high Tg of the PS segment and the strong interactions between the phenolic resin and the PSS-DMODA, the segmental rearrangement is kinetically hindered relative to the cross-linking rate of the phenolic resin, which inhibits long-range ordering and yields a poorly ordered mesoporous carbon with a broad pore size distribution. However, relatively short exposure (2 h) to controlled vapor pressures of methyl ethyl ketone (MEK) yields significant improvements in the long-range ordering and narrows the pore size distribution. The average pore size increases as the solvent vapor pressure during annealing increases, but an upper limit of p/p0 = 0.85 exists above which the films dewet rapidly during solvent vapor annealing. This approach can be extended using mesityl oxide, which has similar solvent qualities to MEK, but is not easily removed by ambient air drying after solvent annealing. This residual solvent can impact the morphology that develops during cross-linking of the films. These results illustrate the ability to fine-tune the mesostructure of ordered mesoporous carbon films through simple changes in the processing without any compositional changes in the initial cast film.
Flow-mediated and reflex changes in large peripheral artery tone in humans. (1989)

Studies of peripheral blood vessels in humans have focused primarily on regulation of blood flow and vascular resistance, which are thought to reflect small vessel caliber. Recent studies in animals have identified flow-mediated and neurogenic changes in large artery diameter. This study tested for flow-mediated dilatation and reflex constriction of the brachial artery in humans. A dual-crystal pulsed Doppler system was used to measure brachial artery diameter and blood flow proximal to the antecubital fossa. To test for flow-mediated dilatation, flow through the brachial artery was altered by an occluding cuff placed on the forearm distal to the site of brachial artery flow and diameter measurement. Control blood flow was 123 +/- 20 ml/min, and brachial artery diameter was 4.74 +/- 0.17 mm (mean +/- SEM). By inflating the distal occluding cuff (distal circulatory arrest), flow was reduced through the brachial artery to 21 +/- 5 ml/min (p less than 0.005), and brachial artery diameter was reduced to 4.35 +/- 0.20 mm (p less than 0.001). By deflating the distal occluding cuff after 10 minutes (reactive hyperemia), brachial artery flow was increased to 358 +/- 55 ml/min (p less than 0.001), and diameter was increased to 5.6 +/- 0.19 mm (p less than 0.001). These interventions did not change systemic arterial pressure and, as measured in three subjects, caused only small changes in local brachial artery distending pressure. Thus, both increased and decreased brachial artery blood flow produced significant changes in brachial artery diameter without altering arterial distending pressure. These data provide evidence for flow-mediated dilatation in humans.(ABSTRACT TRUNCATED AT 250 WORDS)
Near-Earth Asteroid Sample Curation (2000)

Curation of Near-Earth Asteroid (NEA) samples returned by spacecraft will require careful planning to ensure that the samples are not contaminated prior to distribution to the research community. In addition, curation and distribution will be required to address a level of planetary protection concerns that depends on the asteroid type. Laboratories and procedures developed for curation of lunar samples and Antarctic meteorites have successfully preserved the integrity of these samples and supported research for decades. Planning for curation to support future asteroid, comet, and Mars sample return encompasses many of the concerns unique to a NEA mission. Additional information is contained in the original extended abstract.
Nanofiltration to remove microparticles and decrease the thrombogenicity of plasma: in vitro feasibility assessment (2015)

Nanofiltration of 75 nm efficiently removes MPs and decreases in vitro thrombogenicity of plasma without affecting the protein content or the hemostatic activity of coagulation factors. Studies are needed to evaluate the impact of MP removal on in vivo thrombogenic risks and hemostatic efficacy.
Distributed optical fiber sensing based on brillouin scattering (2008)

The technique of Brillouin scattering distributed optical fiber sensing has drawn great attention all over the world.The time-domain distributed optical fiber sensing based on Brillouin scattering has mainly two structures,Brillouin optical time-domain reflectometry and Brillouin optical time-domain analysis.Since there have been many research reports about the distributed optical fiber sensing based on the Brillouin optical time-domain reflectometry,the latest researches on the distributed optical fiber sensing based on Brillouin optical time-domain analysis are introduced in detail.Characteristics of the two timedomain sensing technologies are compared and analyzed.Key problems in the applications of Brillouin sensing and their potential solutions are summarized.Prospects in this field are also given.
The crystal structures of some calabash-curare alkaloids and other organic molecules by X-ray methods (1963)

The main parts of this thesis describe the determinations of the structures of derivatives of two alkaloids of the calabash-curare series, caracurine-II and macusine-A, by X-ray methods. Another two sections deal with the determination of the crystal structure of a derivative of a naturally-occurring sesquiterpenoid lactone , geigerin, and with that of a monohalogenobenzene derivative, 2-chloro-4-nitroaniline. A considerable amount of information regarding the major portion of the chemical structure of caracurine-II was available when the analysis of this structure was begun. Nothing was known of the crystal structure or of the absolute position of the atoms in the molecule. Examinations of crystals of the isomorphous dihalide derivatives, the dimethochloride and the dimethobromide, were made but owing to difficulty in ascertaining the locations of the halide ions the work on these was abandoned at an early stage. The elucidation of the structure of caracurine-II resulted from an analysis of the dimethiodide derivative. Similarly, the greater part of the chemical structure of macusine-A was known when the X-ray analysis of crystals of the iodide derivative of this alkaloid was undertaken. The iodide ion was easily located and the structure was very readily determined. In neither the analysis of caracurine-II dimethiodide nor that of macusine-A iodide was great accuracy of the molecular parameters attempted. Consequently, the results have considerable limitations imposed upon them and the finer details of the molecular dimensions are obscured. A structure and partial stereochemistry of geigerin had been proposed when crystals of bromogeigerin acetate were received from Professor Barton. The X-ray crystal analysis of this derivative of geigerin confirmed the proposed structure. Unfortunately the substitution of the bromine atom into geigerin acetate did not occur at the expected position but at a centre which was of stereochemical interest. The outcome of this was that the relative stereochemistry of the geigerin molecule at that site at which this substitution had taken place could not be inferred from the results of the analysis. The analysis was carried out to a fair degree of accuracy. Some interesting features which can be correlated with those observed in other molecules are evident in the structure. The work on this structure analysis was shared with Miss J. A. Hamilton who performed, as far as possible, alternate series of calculations. The crystal analysis of 2-chloro-4-nitroaniline was undertaken in order to determine the finer details of the molecule, the gross structure being entirely known. The results clearly establish that, in the solid state, the nitro group of the molecule is twisted out of the plane of the benzene ring by a small amount.
Correlation Functions and Multipartite Entanglement in Cavity QED (2007)

We consider the entanglement between a multi-level atom and two cavity modes for a cavity QED system, find that cross-correlations between the two modes are witness to atom-field entanglement. Concurrences and log negativities are also calculated.
A new vitamin K-dependent protein. A phospholipid-binding zymogen of a serine esterase. (1976)

Conclusive evidence is presented that a recently purified (Stenflo, J. (1976) J. Biol. Chem. 251, 355-363) vitamin K-dependent protein (arbitrarily referred to as Protein C) which is not related to prothrombin, Factors IX or X is also unrelated to Factor VII. It therefore appears to be a new, previously unrecognized vitamin K-dependent protein. In contrast to prothrombin, which binds to negatively charged phospholipid only in the presence of Ca2+ ions, Protein C, like the other vitamin K-dependent proteins, is a precursor of a serine esterase, presumably a protease, but it does not seem to be necessary for blood coagulation. Although the lipid-binding properties of Protein C may suggest that it is associated with membrane structures, its biological function remains unknown.
Effect of Wettability on the Agglomeration of Silicon Nanowire Arrays Fabricated by Metal-Assisted Chemical Etching (2014)

The effect of wettability on the undesirable bundling of silicon nanowire (SiNW) arrays fabricated by metal-assisted chemical etching (MACE) method is investigated. This paper reports a simple and low-cost approach to achieve dense SiNW arrays with excellent lateral separation. A hydrophilic pretreatment on the initial wafer substrate prior to the etching procedure, followed by a hydrophobic post-treatment of the fabricated SiNWs, allows the fabrication of large and dense arrays of SiNWs with no agglomeration. These results are discussed within the framework of the detailed balance of forces acting on the nanowires.
Validated five-factor prognostic model for survival of patients (pts) with metastatic urothelial carcinoma (mUC) receiving different post-platinum PD-L1 inhibitors. (2019)

476 Background: A prognostic model for overall survival (OS) of mUC was previously reported in the setting of post-platinum atezolizumab (Pond GR, GU ASCO 2018). This model was limited by employing only atezolizumab treated pts, small size of the validation dataset and unclear applicability to other PD-1/L1 inhibitors. Hence, we constructed a robust prognostic model utilizing the combined atezolizumab cohort as the discovery dataset and used a validation dataset comprised of post-platinum avelumab-treated pts. Methods: The discovery dataset consisted of pt level data from 2 phase I/II trials (IMvigor210 and PCD4989g) evaluating atezolizumab (n = 405). Pts enrolled on a phase I/II trial that received post-platinum avelumab (n = 242) comprised the validation dataset (EMR 100070-001). Cox regression analyses evaluated the association of candidate prognostic factors with OS. Factors were dichotomized and laboratory values were normalized by logarithmic transformation. Stepwise selection was employed to propose an optimal model using the discovery dataset. Discrimination (via c-statistic) and calibration were assessed in the avelumab dataset following the validation procedure by Royston and Altman (2013). Results: The 5 factors included in the optimal prognostic model in the discovery dataset were ECOG-PS (1 vs. 0; HR 1.80; 95% CI [1.36-2.36]), presence/absence of liver metastasis (HR 1.55; 95% CI [1.20-2.00]), number of platelets (HR 2.22; 95% CI [1.54-3.18]), neutrophil-lymphocyte ratio (NLR; HR 1.94; 95% CI [1.57-2.40]) and lactate dehydrogenase (LDH; HR 1.60; 95% CI [1.28-1.99]). The c-statistic for prediction of survival was 0.692 and 0.671 in the discovery and validation datasets, respectively. Acceptable or good calibration of expected 1-year survival was observed. Conclusions: A 5-factor externally validated prognostic model for OS is proposed employing a large dataset of 647 pts overall in the setting of post-platinum PD-L1 inhibitors for mUC. This model may assist in prognostic stratification and interpreting nonrandomized trials of post-platinum PD1/L1 inhibitors.
Damage in DNA Irradiated with 1.2 MHz Ultrasound and Its Effect on Template Activity of DNA for RNA Synthesis (1985)

When aqueous DNA solution was irradiated with 1.2 MHz continuous ultrasound in the presence of cysteamine, the number of ultrasound-induced double-strand breaks of DNA was not influenced, but the number of ultrasound-induced single-strand breaks of DNA was reduced to about one-fifth that of the irradiated control. When the effect of cysteamine on the template activity of the ultrasound-irradiated DNA was investigated, the cysteamine was found to exert a leveling effect on the linear decrease of the template activity against ultrasonic intensity. Since cysteamine was known as an effective radical scavenger, the results of the experiment were regarded to suggest that (1) the double-strand breaks were exclusively induced by the mechanical effect of ultrasound, (2) the majority of single-strand breaks were produced by water radicals arising from cavitation, (3) the initial part in the decrease of the template activity was due to the double-strand breaks arising from mechanical effect, and (4) the further decrease of the template activity depended mainly on the single-strand breaks arising from water radicals.
6‐phenylpyrrolocytosine as a fluorescent probe to examine nucleotide flipping catalyzed by a DNA repair protein (2020)

Cellular exposure to tobacco-specific nitrosamines causes formation of promutagenic O<sup>6</sup> -[4-oxo-4-(3-pyridyl)but-1-yl]guanine (O<sup>6</sup> -POB-G) and O<sup>6</sup> -methylguanine (O<sup>6</sup> -Me-G) adducts in DNA. These adducts can be directly repaired by O<sup>6</sup> -alkylguanine-DNA alkyltransferase (AGT). Repair begins by flipping the damaged base out of the DNA helix. AGT binding and base-flipping have been previously studied using pyrrolocytosine as a fluorescent probe paired to the O<sup>6</sup> -alkylguanine lesion, but low fluorescence yield limited the resolution of steps in the repair process. Here, we utilize the highly fluorescent 6-phenylpyrrolo-2'-deoxycytidine (6-phenylpyrrolo-C) to investigate AGT-DNA interactions. Synthetic oligodeoxynucleotide duplexes containing O<sup>6</sup> -POB-G and O<sup>6</sup> -Me-G adducts were placed within the CpG sites of codons 158, 245, and 248 of the p53 tumor suppressor gene and base-paired to 6-phenylpyrrolo-C in the opposite strand. Neighboring cytosine was either unmethylated or methylated. Stopped-flow fluorescence measurements were performed by mixing the DNA duplexes with C145A or R128G AGT variants. We observe a rapid, two-step, nearly irreversible binding of AGT to DNA followed by two slower steps, one of which is base-flipping. Placing 5-methylcytosine immediately 5' to the alkylated guanosine causes a reduction in rate constant of nucleotide flipping. O<sup>6</sup> -POB-G at codon 158 decreased the base flipping rate constant by 3.5-fold compared with O<sup>6</sup> -Me-G at the same position. A similar effect was not observed at other codons.
Supplementary Figures from Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons (2023)

&lt;p&gt;PDF file, 215K, Reconstructing circular amplicons (S1); TCGA-GBM-06-0152 harbors 2 circular amplicons (S2); Cumulative number of peaks called in 264 GBM exomes as a function of the tumor vs. matched normal relative coverage threshold used to define a peak (S3).&lt;/p&gt;
Effects of Excessive Body Fat Accumulation on Long-Term Outcomes during Peritoneal Dialysis (2019)

<i>Background:</i>Significant body fat accumulation is an inevitable but potentially serious problem in peritoneal dialysis (PD) patients. Whether excessive fat gain predicts long-term outcomes in these patients remains unknown.<i>Methods:</i>In this prospective cohort study (<i>n</i> = 297), the associations of excessive fat accumulation with patient survival and PD failure rate were examined. Based on dialysis duration at the time of study enrollment, patients were divided into short- (< 2 years) and long-term (> 2 years) groups. Body weight (BW) and body composition were measured twice, 12.8 ± 4.6 months apart. Excessive fat accumulation was defined as a 1-year change in the percentage of body fat (ΔPBF) over the highest quartile (5.0% for men, 5.4% for women).<i>Results:</i>Substantial 1-year increases in BW and PBF were observed only in the short-term group (<i>p</i> < 0.001 and <i>p</i> = 0.027, respectively); changes were insignificant in the long-term group. In the short-term group, the ΔPBF was associated closely with unfavorable baseline metabolic profiles, including old age, diabetes, obesity, elevated blood pressure, and edema. Accordingly, the mortality rate was significantly higher in patients with, than in those without, excessive fat accumulation (hazard ratio [HR] 3.26, 95% confidence interval [CI], 1.05 - 10.26). It also increased the incident risk of PD failure 2.22-fold (95% CI, 1.08 - 4.54), even after adjustment for diabetes, obesity, and fluid status. In the long-term group, fat gain had no impact on long-term prognosis.<i>Conclusions:</i>Excessive fat accumulation during the early period of PD was associated with baseline unhealthy metabolic profiles, a higher mortality rate, and a higher PD failure rate, independent of baseline obesity and fluid status.
Supplementary Figure 2 from Inhibition of Peroxisome Proliferator-Activated Receptor γ Increases Estrogen Receptor–Dependent Tumor Specification (2023)

Supplementary Figure 2 from Inhibition of Peroxisome Proliferator-Activated Receptor γ Increases Estrogen Receptor–Dependent Tumor Specification
Influence of young adult cognitive ability and additional education on later-life cognition (2019)

How and when education improves cognitive capacity is an issue of profound societal importance. Education and later-life education-related factors, such as occupational complexity and engagement in cognitive-intellectual activities, are frequently considered indices of cognitive reserve, but whether their effects are truly causal remains unclear. In this study, after accounting for general cognitive ability (GCA) at an average age of 20 y, additional education, occupational complexity, or engagement in cognitive-intellectual activities accounted for little variance in late midlife cognitive functioning in men age 56-66 (<i>n</i> = 1009). Age 20 GCA accounted for 40% of variance in the same measure in late midlife and approximately 10% of variance in each of seven cognitive domains. The other factors each accounted for <1% of the variance in cognitive outcomes. The impact of these other factors likely reflects reverse causation-namely, downstream effects of early adult GCA. Supporting that idea, age 20 GCA, but not education, was associated with late midlife cortical surface area (<i>n</i> = 367). In our view, the most parsimonious explanation of our results, a meta-analysis of the impact of education, and epidemiologic studies of the Flynn effect is that intellectual capacity gains due to education plateau in late adolescence/early adulthood. Longitudinal studies with multiple cognitive assessments before completion of education would be needed to confirm this speculation. If cognitive gains reach an asymptote by early adulthood, then strengthening cognitive reserve and reducing later-life cognitive decline and dementia risk may really begin with improving educational quality and access in childhood and adolescence.