gebhart/patrepeval huggingface dataset:
Thermodynamics of the Size and Shape of Nanocrystals: Epitaxial Ge on Si(001) (2000)

The growth and evolution of strained epitaxial Ge on a Si(001) surface provides a rich system for exploring the behavior of strongly interacting nanocrystals. In the temperature regime above 500 degrees C, there are two different (metastable) shapes of defect-free nanocrystals, termed pyramids and domes, that dominate the system depending on the temperature of the substrate during growth and the amount of Ge deposited. In contrast to the usual case considered in nucleation theory, the relaxation of the strain energy at the surface of the nanocrystals makes those surfaces stabilizing, i.e. the surface contribution to the free energy of the Ge nanocrystals is negative. Given that the edges of the nanocrystals are destabilizing (positive free energy), the interaction of the surfaces and edges of the nanocrystals in an ensemble renders an internal free energy for the system that has a local minimum with respect to the size (volume) of the nanocrystal. At finite temperatures, this free energy yields a size distribution with a characteristic centroid, width, and skewness for each nanocrystal shape. The smaller pyramids transform into domes when they grow to the point where they can surmount a kinetic energy barrier between the two structures. However, the Ge nanocrystals also effectively repel one another strongly via the strain fields that are produced in the Si substrate. This repulsive interaction makes the ensemble of Ge nanocrystals a highly nonideal thermodynamic system and, in turn, makes the free energies of the nanocrystals a function of their number density, or equivalently a function of the amount of Ge deposited. The interplay of the stabilizing effect of the nanocrystal surfaces and the destabilizing influence of their repulsive interactions yields a complex behavior for the nanocrystal-size distributions that can nonetheless be modeled using simple thermodynamic expressions.
Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations (2010)

The MM-GB/SA scoring technique has become an important computational approach in drug design. We, and others, have demonstrated that for congeneric molecules the correlation with experimental data obtained with the physics-based scoring is usually superior to scoring functions from typical docking algorithms. Despite showing good accuracy when applied within a series, much work is necessary to improve the MM-GB/SA method in order to gain greater efficiency in drug design. Here, we investigate the poor estimation of protein desolvation provided by the GB/SA solvation model and the large dynamic range observed in the MM-GB/SA scoring compared to that of the experimental data. In the former, replacing the GB/SA protein desolvation in the MM-GB/SA method by the free energy associated with displacing binding site waters upon ligand binding estimated by WaterMap provides the best results when ranking congeneric series of factor Xa and cyclin-dependent kinase 2 (CDK2) inhibitors. However, the improvement is modest over results obtained with the MM-GB/SA and WaterMap methods individually, apparently due to the high correlation between the free energy liberation of the displaced solvent and the protein-ligand van der Waals interactions, which in turn may be interpretable as estimates of the hydrophobic effect and hydrophobic-like interactions, respectively. As for the large dynamic range, comparisons between MM-GB/SA and FEP calculations indicate that for the factor Xa test set this problem has its origin in the lack of shielding effects of protein--ligand electrostatic interactions; that overly favors ligands that engage in hydrogen bonds with the protein.
Terahertz-wave generation using graphene: toward the creation of graphene injection lasers (2013)

This paper reviews recent advances in terahertz-wave generation in graphene toward the creation of new types of graphene terahertz lasers. Fundamental basis of the optoelectronic properties of graphene is first introduced. Second, nonequilibrium carrier relaxation/recombination dynamics and resultant negative terahertz conductivity in optically or electrically pumped graphene are described. Third, recent theoretical advances toward the creation of current-injection graphene terahertz lasers are described. Fourth, unique terahertz dynamics of the two-dimensional plasmons in graphene are discussed. Finally, the advantages of graphene materials and devices for terahertz-wave generation are summarized.
Vitamin D and Weight Change: A Mendelian Randomization, Prospective Study (2022)

The association between 25-hydroxyvitamin D and 5-, 10-, or 15-year weight change were assessed in a population-based, prospective study conducted in Lausanne, Switzerland. Data from the first (2009−2012, N = 3527, 51.3% women), second (2014−2017, N = 3237, 53.8% women), and third (2018−2021, N = 2567, 54.2% women) follow-ups were used. A weighted genetic risk score (GRS) of 115 SNPs associated with vitamin D levels was constructed. At baseline, the GRS correlated positively with 25-hydroxyvitamin D levels based on a Spearman rank correlation and 95% confidence interval: 0.198 (0.166; 0.231), p < 0.001; and with body mass index: 0.036 (0.004; 0.068), p = 0.028. No association was found between quartiles of GRS and weight changes at 5, 10, or 15 years: multivariate-adjusted weight changes ± SEM at 5-years follow-up were 1.39 ± 0.17, 1.13 ± 0.17, 1.24 ± 0.17, and 1.00 ± 0.17 kg for the first to the fourth quartile of the GRS, respectively (p = 0.401). Two-step linear regression showed a significant but clinically meaningless association between GRS-derived vitamin D and weight change at 5- and 15-years: slope and 95% confidence interval for a 5 nmol/L increase in GRS-derived 25-hydroxyvitamin D levels: 0.082 (0.013; 0.150) and 0.130 (0.018; 0.243) kg, respectively. We conclude that there is little association between genetically determined 25-hydroxyvitamin D levels and weight gain.
Electrocatalytic hydrocracking. Final report (1992)

This report describes an electrocatalytic method for the chemical addition of hydrogen to a model hydrocarbon compound. In the method, hydrogen formed by water electrolysis at the counter electrode of an electrochemical cell is delivered via conduction through a proton-conducting solid electrolyte. The working electrode of the cell is, at the same time, a hydrocracking catalyst and therefore promotes the reaction of the hydrogen with the hydrocarbon. This process would have clear and distinct advantages over conventional hydroprocessing technologies in that the hydrogen concentration at the catalyst surface could be controlled and maintained by the applied electromotive force. This control would allow operation of the electrocatalytic reactor at ambient pressures instead of the extremely high hydrogen partial pressures required of conventional reactors. In addition, the direct delivery of hydrogen to the catalyst surface should inhibit coke formation and thus prolong the life of the catalyst. Finally, hydrogen utilization efficiencies should be greatly improved since the hydrogen is delivered directly to the reaction site thereby eliminating hydrogen solubility loss in the effluent stream. This report details the demonstration of (a) the ability of a solid electrolyte to perform as a catalyst, (b) the conduction of hydrogen through a solid electrolyte and (c) the simultaneous exploitation of these two properties. Hence, the essential concept of electrocatalytic hydrocracking has been demonstrated. An objective of future work in this area should be to determine whether the hydrocracking or hydrogenation reactions are actually enhanced during the electrocatalytic process when compared to the conventional catalytic process.
Syntheses and Catalytic Properties of Titanium Nitride Nanoparticles (2006)

This chapter contains sections titled: Introduction Synthesis of TiN Nanoparticles Titanium Nitride Nanoparticles in Hydrogen Storage Applications Catalytic Properties of TiN Nanoparticles in Solution Catalytic Properties References
Pilot-scale NOx and SOx removal from boiler emission using indirect plasma and chemical hybrid process (2005)

The pilot-scale simultaneous NO/sub x/ and SO/sub x/ removal from boiler emission was performed using an indirect plasma and a chemical hybrid process. The flue gas flow rate was in the range of 450-1,470 Nm/sup 3//hr, the gas temperature of 280 /spl deg/C, and NO/sub x/ concentration of 30 ppm for city gas firing, and 70 ppm of NO/sub x/ and 35 ppm of SO/sub x/ for heavy oil firing, respectively. The radical injection by the indirect plasma was demonstrated to be extremely effective for NO oxidation especially when the flue gas temperature is in the range of 300 /spl deg/C where NO/sub x/ is generated at this temperature. The produced NO/sub 2/ was further reduced to N/sub 2/ and nontoxic and water soluble Na/sub 2/SO/sub 4/ by Na/sub 2/SO/sub 3/ chemical scrubber. For the case of oil firing boiler SO/sub 2/ was simultaneously adsorbed by NaOH solution. The NO/sub x/ removal efficiency for gas firing exceeds 90% but NO/sub x/ removal efficiency for oil firing was in the range of 60% due to the lack of ozone concentration with the present pulse power supply. The removal efficiency of SO/sub 2/ was in the range of 85-90% The NO/sub x/ removal efficiency was evaluated by the ratio of the radical flow rate by the indirect plasma to the primary flue gas flow rate, specific energy density, and Na/sub 2/SO/sub 3/ concentration and chemical flow rate. Finally, the quality of disposed water was investigated and proved to be disposable.
Bulk Fill Composites: An Anatomic Sculpting Technique (2015)

Abstract Composite resins have been routinely used for posterior cavities due to a phasedown on amalgam as a restorative option. However, clinical problems related to polymerization shrinkage demands careful and specific techniques for placement of the composite layers. New low shrinkage composites are now marketed for bulk filling of cavities without the need of a traditional layering. With this new concept, the restoration can be built in one or two layers, depending on the classification of the bulk fill material. This article discusses and presents two alternative techniques using the low shrinkage composites, suggesting a called “amalgam‐like sculpting technique,” one using a flowable bulk fill and other a regular bulk fill material. Clinical cases illustrate these two alternatives compared with the layered technique. Clinical Significance New techniques using low shrinkage composites for bulk filling can provide a simpler technical approach for the clinician in sculpting and generating highly esthetic posterior composites.
Development of Subspace-based Hybrid Monte Carlo-Deterministric Algorithms for Reactor Physics Calculations (2014)

The development of hybrid Monte-Carlo-Deterministic (MC-DT) approaches, taking place over the past few decades, have primarily focused on shielding and detection applications where the analysis requires a small number of responses, i.e. at the detector locations(s). This work further develops a recently introduced global variance reduction approach, denoted by the SUBSPACE approach is designed to allow the use of MC simulation, currently limited to benchmarking calculations, for routine engineering calculations. By way of demonstration, the SUBSPACE approach is applied to assembly level calculations used to generate the few-group homogenized cross-sections. These models are typically expensive and need to be executed in the order of 103 - 105 times to properly characterize the few-group cross-sections for downstream core-wide calculations. Applicability to k-eigenvalue core-wide models is also demonstrated in this work. Given the favorable results obtained in this work, we believe the applicability of the MC method for reactor analysis calculations could be realized in the near future.
TT virus - highly prevalent, but still in search of a disease (2000)

Hepatitis B virus (HBV) and hepatitis C virus (HCV) are major risk factors for hepatocellular carcinoma (HCC). The role of a novel DNA virus, designated SEN virus (SENV), in the etiology of liver cancer remains to be established. The aim of this study was to evaluate the association between SENV infection and the risk of HCC by conducting a hospital-based, case–control study among Thai patients.Eighty-six patients with HCC were enrolled and matched individually to a control according to sex, age (± 5 yr), and geographic background. The presences of HBV DNA, HCV RNA, and SENV DNA in stored serum samples were detected with the use of semi-nested polymerase chain reaction amplification.Individuals who were infected with SENV did not have increased risk of developing HCC (OR = 1.49, 95% CI = 0.50–4.42). In contrast, those who were positive for HBV markers (hepatitis B surface antigen and/or HBV DNA) or HCV markers (anti-HCV and/or HCV RNA) had significant risk for HCC (OR = 19.91, 95% CI = 8.26–47.98 and OR = 7.97, 95% CI = 2.15–29.54, respectively). Moreover, coinfection with SENV did not further increase the risk of HCC among patients infected with HBV and/or HCV.Our data suggest that, unlike chronic HBV or HCV infection, SENV infection is not a risk factor for developing HCC in Thai populations.
New insights into the structure of abasic DNA from molecular dynamics simulations (2000)

Abasic (AP) sites constitute a common form of DNA damage, arising from the spontaneous or enzymatic breakage of the N-glycosyl bond and the loss of a nucleotide base. To examine the effects of such damage on DNA structure, especially in the vicinity of the abasic sugar, four 1.5 ns molecular dynamics simulations of double-helical DNA dodecamers with and without a single abasic (tetrahydrofuran, X) lesion in a 5'-d(CXT) context have been performed and analyzed. The results indicate that the abasic site does not maintain a hole or gap in the DNA, but instead perturbs the canonical structure and induces additional flexibility close to the abasic site. In the apurinic simulations (i.e., when a pyrimidine is opposite the AP site), the abasic sugar flipped in and out of the minor groove, and the gap was water filled, except during the occurrence of a novel non-Watson-Crick C-T base pair across the abasic site. The apyrimidinic gap was not penetrated by water until the abasic sugar flipped out and remained extrahelical. Both AP helices showed kinks of 20-30 degrees at the abasic site. The Watson-Crick hydrogen bonds are more transient throughout the DNA double helices containing an abasic site. The abasic sugar displayed an unusually broad range of sugar puckers centered around the northern pucker. The increased motion of the bases and backbone near the abasic site appear to correlate with sequence-dependent helical stability. The data indicate that abasic DNA contorts more easily and in specific ways relative to unmodified DNA, an aspect likely to be important in abasic site recognition and hydrolysis.
Uterine MHC Class I Molecules and β2-Microglobulin Are Regulated by Progesterone and Conceptus Interferons during Pig Pregnancy (2008)

MHC class I molecules and beta(2)-microglobulin (beta(2)m) are membrane glycoproteins that present peptide Ags to TCRs, and bind to inhibitory and activating receptors on NK cells and other leukocytes. They are involved in the discrimination of self from non-self. Modification of these molecules in the placenta benefits pregnancy, but little is known about their genes in the uterus. We examined the classical class I swine leukocyte Ags (SLA) genes SLA-1, SLA-2, and SLA-3, the nonclassical SLA-6, SLA-7, and SLA-8 genes, and the beta(2)m gene in pig uterus during pregnancy. Uterine SLA and beta(2)m increased in luminal epithelium between days 5 and 9, then decreased between days 15 and 20. By day 15 of pregnancy, SLA and beta(2)m increased in stroma and remained detectable through day 40. To determine effects of estrogens, which are secreted by conceptuses to prevent corpus luteum regression, nonpregnant pigs were treated with estradiol benzoate, which did not affect the SLA or beta(2)m genes. In contrast, progesterone, which is secreted by corpora lutea, increased SLA and beta(2)m in luminal epithelium, whereas a progesterone receptor antagonist (ZK137,316) ablated this up-regulation. To determine effects of conceptus secretory proteins (CSP) containing IFN-delta and IFN-gamma, nonpregnant pigs were implanted with mini-osmotic pumps that delivered CSP to uterine horns. CSP increased SLA and beta(2)m in stroma. Cell-type specific regulation of SLA and beta(2)m genes by progesterone and IFNs suggests that placental secretions control expression of immune regulatory molecules on uterine cells to provide an immunologically favorable environment for survival of the fetal-placental semiallograft.
A Study of BER-Optimal ADC-Based Receiver for Serial Links (2016)

Analog-to-digital converter (ADC)-based multi-Gb/s serial link receivers have gained increasing attention in the backplane community due to the desire for higher I/O throughput, ease of design portability, and flexibility. However, the power dissipation in such receivers is dominated by the ADC. ADCs in serial links employ signal-to-noise-and-distortion ratio (SNDR) and effective-number-of-bit (ENOB) as performance metrics as these are the standard for generic ADC design. This paper studies the use of information-based metrics such as bit-error-rate (BER) to design a BER-optimal ADC (BOA) for serial links. Channel parameters such as the $m$ -clustering value and the threshold non-uniformity metric $h_{t}$ are introduced and employed to quantify the BER improvement achieved by a BOA over a conventional uniform ADC (CUA) in a receiver. Analytical expressions for BER improvement are derived and validated through simulations. A prototype BOA is designed, fabricated and tested in a 1.2 V, 90 nm LP CMOS process to verify the results of this study. BOA's variable-threshold and variable-resolution configurations are implemented via an 8-bit single-core, multiple-output passive digital-to-analog converter (DAC), which incurs an additional power overhead of $ 0.1% (approximately 50 $\mu\text{W}$ ). Measurement results show examples in which the BER achieved by the 3-bit BOA receiver is lower by a factor of $10^{9}$ and $10^{10}$ , as compared to the 4-bit and 3-bit CUA receivers, respectively, at a data rate of 4-Gb/s and a transmitted signal amplitude of 180 mVppd.
Neurotrophic factors in diabetic neuropathy (2001)

There is a reduction in the availability of neurotrophic factors in diabetes. These factors are important for the maintenance of neuron health and the ability to resist apoptosis, and to regenerate damaged nerves. The best studied is nerve growth factor (NGF). Clinical trials with NGF have had variable results. Nerve growth factor still holds promise for sensory and autonomic neuropathies. The insulin-like growth factors (IGFs), IGF-I and IGF-II, exert profound effects on developing neurons and are deficient in certain tissues in diabetes. Their possible role in the treatment of neuropathy in diabetes is obscured by a complex interaction with various binding proteins and the interaction with different receptors whose disposition in diabetes is not yet clearly established. Laminin, a large heterotrimeric protein present in the basal lamina of nerves, appears to be important in nerve regeneration. Laminin also exerts antiapoptotic properties against the neurotoxicity of sera of patients with diabetes. There are new compounds including cytokines, immunophilin ligands, and inhibitors of programed cell death that are capable of affecting the plasticity of nerves. They stimulate the differentiation of nerve cells in culture and the extension of neurite outgrowth or they inhibit apoptosis, but none of these compounds have been evaluated clinically. The development of growth factor therapy for diabetic neuropathies is a genuine possibility.
Necrose gordurosa multinodular mamária: Diagnóstico diferencial com o carcinoma da mama através da citologia por punção aspirativa (2022)

A necrose gordurosa da mama é um processo de desintegração de células adiposas, acompanhado de uma reação granulomatosa de intensidade variável. E decorrente do reconhecimento de lipídios extravasados do citoplasma de adipócitos como substâncias estranhas ao meio extracelular. O quadro clínico-radiológico pode ocasionar dificuldades no diagnóstico diferencial com neoplasias mamárias. Neste relato é descrito um caso de necrose gordurosa multinodular mamária sendo enfatizada a importância da citologia por punção aspirativa com agulha fina para a confirmação do diagnóstico.
An adaptive color transform approach and its application in 4∶4∶4 video coding (2006)

This paper deals with an approach that extends block-based video-coding techniques by an adaptive color space trans-form. The presented technique allows the encoder to switch between several given color space representations with the objective to maximize the overall rate-distortion gain. Simu-lations based on the current draft of the H.264/MPEG4-AVC 4:4:4 extensions demonstrate that our technique guarantees a rate-distortion performance equal or better than that ob-tained when using any of the individual color spaces only. 1.
Ocrelizumab Treatment Effect on Upper Limb Function in PPMS Patients with Disability: Subgroup Results of the ORATORIO Study to Inform the ORATORIO-HAND Study Design (P3.2-091) (2019)

To assess ocrelizumab efficacy on upper limb function in more disabled/older patients with primary progressive multiple sclerosis (PPMS) from the Phase III ORATORIO study (NCT01194570) to inform the design of the Phase IIIb ORATORIO-HAND study.
Involvement of Two Basic Residues (Lys-17 and Arg-39) of Mouse Lung Carbonyl Reductase in NADP(H)-Binding and Fatty Acid Activation: Site-Directed Mutagenesis and Kinetic Analyses (1996)

Mouse lung carbonyl reductase, a member of the short-chain dehydrogenase/reductase (SDR) family, shows a strong coenzyme preference for NADP(H) over NAD(H), and is uniquely activated by fatty acids. Previous chemical modification and X-ray crystallography studies show that interactions responsible for the coenzyme specificity include salt linkages between the 2'-phosphate of NADPH and side-chains of Lys-17 and Arg-39 of the enzyme. Although Arg-39 is highly conserved in NADP(H)-dependent enzymes of the SDR family, Lys-17 is substituted with Arg in about half of the NADP(H)-dependent enzymes. The present study shows that mutations of Lys-17 to His (K17H) or Ser (K17S) and of Arg-39 to Ala (R39A) bring about decreases (from 5 to 90-fold) of the affinities for NADP(H), but minor changes in the affinity for NAD+. The binding energy arising from the mutations on the binding of the 2'-phosphate of NADP+ was decreased by 38-66% from the value of 4.8 kcal/mol calculated for the wild-type enzyme. In contrast, the mutation of Lys-17 to Arg (K17R) had little effect on the kinetic or thermodynamic properties. The activation by fatty acids was completely attenuated by the mutations of K17H and K17S, but not by K17R or R39A. These results indicate that the 2'-phosphate group of NADP(H) is recognized by both Lys-17 and Arg-39, of which Lys-17 is a component of the binding site for the activator, probably interacting with the negatively charged carboxylate group of fatty acids, and also suggest that the existence of a positively charged residue (either Lys or Arg) at position 17 is required for both NADP(H) specificity of the SDR family enzymes and fatty acid activation of the pulmonary carbonyl reductase.