gebhart/patrepeval huggingface dataset:
Variance-Reduced Decentralized Stochastic Optimization With Accelerated Convergence (2020)

This paper describes a novel algorithmic framework to minimize a finite-sum of functions available over a network of nodes. The proposed framework, that we call GT-VR, is stochastic and decentralized, and thus is particularly suitable for problems where large-scale, potentially private data, cannot be collected or processed at a centralized server. The GT-VR framework leads to a family of algorithms with two key ingredients: (i) local variance reduction, that enables estimating the local batch gradients from arbitrarily drawn samples of local data; and, (ii) global gradient tracking, which fuses the gradient information across the nodes. Naturally, combining different variance reduction and gradient tracking techniques leads to different algorithms of interest with valuable practical tradeoffs and design considerations. Our focus in this paper is on two instantiations of the GT-VR framework, namely GT-SAGA and GT-SVRG, that, similar to their centralized counterparts (SAGA and SVRG), exhibit a compromise between space and time. We show that both GT-SAGA and GT-SVRG achieve accelerated linear convergence for smooth and strongly convex problems and further describe the regimes in which they achieve non-asymptotic, network-independent linear convergence rates that are faster with respect to the existing decentralized first-order schemes. Moreover, we show that both algorithms achieve a linear speedup in such regimes compared to their centralized counterparts that process all data at a single node. Extensive simulations illustrate the convergence behavior of the corresponding algorithms.
Development of Laser-Ion Beam Photodissociation Methods (2004)

OAK-B135 Our BES funded research is aimed at determining structure(s) of model gas-phase ions and understanding how structure influences unimolecular reactivity. The model gas-phase ions include positional isomers of di- and tri-amino acids synthesized in my laboratory, i.e., RGG, GRG, and GGR, to peptides derived from proteolytic digestion of biologically relevant proteins. We are especially interested in understanding the role of intramolecular interactions in the stabilizing ion structure and how changing the charge-site affects structure. The location of charge of gas-phase ions can be manipulated by changing the position of the charge carrying amino acid (basic vs. acidic side chains) and by derivatization of the N- and/or C-terminus. For example, the proton of [M + H]+ ions is mobile and migrates over the entire molecule, whereas Li+, Na+, and to some extent K+ prefers to bind to the C-terminal or side-chain carboxylic acid groups, and Cu+ binds exclusively to the N-terminus and/or basic side-chains such as H, K, and R. The studies are carried out using tandem TOF mass spectrometry, viz. 193 nm (6.43 eV) photodissociation, low (Elab = 10-100 eV) and high kinetic energy (Elab = 1-10 keV) collision-induced dissociation (CID) and surface-induced dissociation (SID)(Elab = 20-70 eV). These techniques are used to probe the structure of model gas-phase ions, i.e., to determine the amino acid sequence of the peptide ions or metal ion (alkali metal and/or transition metal ions) binding site(s) or the site(s) of other charge-carrying functional groups, i.e., oxidized side-chains as well as phosphate or sulfate groups. We are especially interested in understanding how metal ion binding alters the secondary/tertiary (2o/3o) structure of the peptide, i.e., intra-molecular interactions. We have also combine these studies with solution-phase studies and ion mobility spectrometry (IMS)), which can be used to study 2o/3o structure of low-internal energy (collisionally stabilized) ions. It is difficult to probe 2o/3o structure of gas-phase ions using fragmentation chemistry, because the energy barriers to inter-conversion of different structural forms lie below the fragmentation threshold, studies of low internal energy ions are more suited for these studies. A major challenge for gas-phase ion research is the design of experimental structural probes that can be used in parallel with computational chemistry, molecular modeling and/or classical structural diagnostic tools to aid interpretation of the experimental data. Our experimental design and selection of research problems is guided by this philosophy. The following section of the progress report focus on three main issues: (i) technique and instrument development, and (ii) studies of ion structure and ion chemistry.
Revisiting the Stability of Hexacenes (2007)

The Strating-Zwanenberg photodecarbonylation was used to prepare hexacene (1). Compound 1 was found to be extremely unstable in solution, undergoing dimerization and oxidation. However, when generated in a polymer matrix, 1 survived for more than 12 h under ambient conditions. Hexacenes substituted at the 6 and 15 positions with the phenyl, p-tert-butylphenyl, and mesityl groups were synthesized using the quinone reduction method, but these compounds were also shown to be unstable in solution.
Meningococcal factor H binding protein as immune evasion factor and vaccine antigen (2020)

Factor H binding protein (fHbp) is a key virulence factor of Neisseria meningitidis and a main component of the two licensed vaccines against serogroup B meningococcus (Bexsero and Trumenba). fHbp is a surface-exposed lipoprotein that enables the bacterium to survive in human blood by binding the human complement regulator factor H (fH). When used as vaccine, the protein induces antibodies with potent bactericidal activity. While the fHbp gene is present in the majority of N. meningitidis serogroup B isolates, the expression level varies up to 15 times between different strains and more than 700 different sequence variants have been described. Antigenically, the protein has been divided into three variants or two subfamilies. The 3D structure of fHbp alone, in combination with fH or in complex with bactericidal antibodies, has been key to understanding the molecular details of the protein. In this article, we will review the biochemical and immunological properties of fHbp, and its key role in meningococcal pathogenesis, complement regulation, and immune evasion.
CCDC 1844735: Experimental Crystal Structure Determination (2019)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
RASSF2 (Ras association (RalGDS/AF-6) domain family member 2) (2011)

Review on RASSF2 (Ras association (RalGDS/AF-6) domain family member 2), with data on DNA, on the protein encoded, and where the gene is implicated.
Reflection field methods (1995)

Field methods for the acquisition of seismic reflection data vary considerably, depending on whether the area is land or marine, on the nature of the geologic problem, and on the accessibility of the area. One of the most important aspects in controlling data costs is avoiding delays such as when some phases of operations have to wait on other phases before work can begin. High-quality field work is essential because nothing done subsequently can remedy defects in the basic data. Evans (1989) and Pritchett (1990) deal with field techniques.
Modulation of DNA/ALVAC/gp120 vaccine immune-response by vaccination with Insulin-Like Growth Factor 1 (IGF-1) (2017)

Abstract ALVAC-SIV/gp120 vaccine reduced the risk of infection in SIVmac251 model. Protection was associated with antibodies (Abs) to V2 region of gp120 protein, mucosal NKp44+ cells, and the expression of 11 genes in the Ras pathway. IGF-1 hormone is a Ras activator and its plasma level diminishes with aging. We hypothesized that IGF-1 might affect the efficacy of the ALVAC-SIV/gp120 platform by modulating the immune responses, particularly when administered in old macaques. In this study we enrolled 25 young (Group 1, av. 3 years) and 34 old macaques (Group 2, av. 9 years) having significantly different plasma levels of IGF-1, and we immunized them with a DNA-SIV/ALVAC-SIV/gp120 vaccine. During immunizations, half of the animals of each group were also administered IGF-1, as recombinant protein (Increlex, Ipsen) and as DNA vaccine. All the animals, including controls, were challenged intra-vaginally with repeated low-doses of SIVmac251. The estimated vaccine efficacy in young macaques of Group 1 was 69%. IGF-1 administration did not increase the efficacy; although, it determined a significant increase of serum Abs titers against V2 and frequency of mucosal NKp44+ cells. Furthermore, IGF-1 treated macaques showed higher frequencies of circulating classical (CCR2+CD14+CD16−) and intermediate (CCR2+CD14+CD16+) monocytes and lower frequencies of mucosal CD4+ T cells expressing α4β7 or CCR5 compared to the untreated animals. These data suggest that IGF-1 administration might improve protective immune responses and decrease possible SIV target cells in the mucosa. Therefore, IGF-1 administration during vaccination might particularly benefit older animals. Challenge exposure of older animals in Group 2 is ongoing.
Tuning solubility and stability of hydrochlorothiazide co-crystals (2013)

Hydrochlorothiazide (HCT), C7H8ClN3O4S2, is a diuretic BCS (Biopharmaceutics Classification System) class IV drug which has primary and secondary sulfonamide groups. To modify the aqueous solubility of the drug, co-crystals with biologically safe co-formers were screened. Multi-component molecular crystals of HCT were prepared with nicotinic acid, nicotinamide, succinamide, p-aminobenzoic acid, resorcinol and pyrogallol using liquid-assisted grinding. The co-crystals were characterized by FT-IR spectroscopy, powder X-ray diffraction (PXRD) and differential scanning calorimetry. Single crystal structures were obtained for four of them. The N-H...O sulfonamide catemer synthons found in the stable polymorph of pure HCT are replaced in the co-crystals by drug-co-former heterosynthons. Isostructural co-crystals with nicotinic acid and nicotinamide are devoid of the common sulfonamide dimer/catemer synthons. Solubility and stability experiments were carried out for the co-crystals in water (neutral pH) under ambient conditions. Among the six binary systems, the co-crystal with p-aminobenzoic acid showed a sixfold increase in solubility compared with pure HCT, and stability up to 24 h in an aqueous medium. The co-crystals with nicotinamide, resorcinol and pyrogallol showed only a 1.5-2-fold increase in solubility and transformed to HCT within 1 h of the dissolution experiment. An inverse correlation is observed between the melting points of the co-crystals and their solubilities.
Supplementary Figure 2 from A Central Role for RAF→MEK→ERK Signaling in the Genesis of Pancreatic Ductal Adenocarcinoma (2023)

&lt;p&gt;PDF file - 331K, MEK inhibitor PD325901 inhibits MEK in vivo&lt;/p&gt;
Pyrimidine Ribonucleotides with Enhanced Selectivity as P2Y 6 Receptor Agonists: Novel 4-Alkyloxyimino, (S)-Methanocarba, and 5′-Triphosphate γ-Ester Modifications † (2020)

The P2Y6 receptor is a cytoprotective G protein-coupled receptor (GPCR) activated by UDP (EC50, 0.30 μM). We compared and combined modifications to enhance P2Y6 receptor agonist selectivity, including ribose ring constraint, 5-iodo and 4-alkyloxyimino modifications, and phosphate modifications such as α,β-methylene and extension of the terminal phosphate group into γ-esters of UTP analogues. The conformationally constrained (S)-methanocarba UDP is a full agonist (EC50 0.042 μM). 4-Methoxyimino modification of pyrimidine enhanced P2Y6, preserved P2Y2 and P2Y4, and abolished P2Y14 receptor potency, in the appropriate nucleotide. N4-Benzyloxy-CDP (15, MRS2964) and N4-methoxy-Cp3U (23, MRS2957) were potent, selective P2Y6 receptor agonists (EC50 0.026 μM and 0.012 μM, respectively). A hydrophobic binding region near the nucleobase was explored with receptor modeling and docking. UTP-γ-aryl and cycloalkyl phosphoesters displayed only intermediate P2Y6 receptor potency, but had enhanced stability in acid and cell membranes. UTP-glucose was inactive, but its (S)-methanocarba analogue and N4-methoxy-cytidine 5′-triphospho-γ-[1]glucose were active (EC50 of 2.47 μM and 0.18 μM, respectively). Thus, the potency, selectivity, and stability of pyrimidine nucleotides as P2Y6 receptor agonists may be enhanced by modest structural changes.
Chiral recognition and separation of β2-amino acids using non-covalently molecularly imprinted polymers (2004)

Non-covalently molecularly imprinted polymers (MIPs) for beta2-amino acids were prepared for the first time. N-(2-chlorobenzyloxycarbonyl)-(R)-beta2-homophenylalanine (N-2-ClZ-(R)-beta2-HPhe) was imprinted with methacrylic acid (MAA) and/or 4-vinylpyridine (4-VPy) as the functional monomers, with ethylene glycol dimethacrylate (EDMA) as the cross-linker. The MIPs made with different ratios of MAA:4-VPy were studied in HPLC mode. The results show that MIPs made with 4-VPy yielded the best chiral separation factor (alpha= 1.86) for the template molecule. The importance for an efficient separation of pi-stacking interactions between the MIPs and the template molecule is demonstrated. Racemates of Z-alpha-amino acids and beta-amino acid analogues of the template were either not or poorly resolved by the MIPs, thus demonstrating the close three-dimensional complementarity of the MIPs' recognition sites with the template.
AlCl3-Catalysed trans N-acylation of Acetanilides with α-Chloropropionyl Chloride†‡ (1998)

H. R. Sonawane, A. V. Pol, B. S. Nanjundiah and A. Sudalai, J. Chem. Res. (S), 1998, 90 DOI: 10.1039/A705770I
Effects of alkaline hydrogen peroxide treatment on in vitro degradation of cellulosic substrates by mixed ruminal microorganisms and Bacteroides succinogenes S85 (1988)

The effects of sodium hydroxide (NaOH) and alkaline hydrogen peroxide (AHP) treatments on wheat straw (WS) and various cellulosic substrates were determined by measuring susceptibility to degradation by mixed ruminal organisms or Bacteroides succinogenes S85. In vitro incubations were used to measure differences in fermentation resulting from each successive step in the AHP treatment process. In vitro incubations through 48 or 108 h were conducted to measure these differences. The AHP treatment of WS increased (P less than 0.05) dry matter, neutral detergent fiber, and acid detergent fiber degradation over control WS when these substrates were incubated with mixed ruminal microorganisms or B. succinogenes S85. Fermentations containing AHP-treated WS had greater (P less than 0.05) microbial purine (RNA) and volatile fatty acid concentrations by 12 h compared with those containing untreated or NaOH-treated WS. Xylose in AHP-treated WS was utilized more extensively (P less than 0.05) by 12 h compared with the xylose of untreated or NaOH-treated WS. Treatment with AHP removed 23% of the alkali-labile phenolic compounds from WS. When substrates with high levels of crystalline cellulose (raw cotton fiber, Solka floc, and Sigmacell-50) were treated with NaOH or AHP and incubated for 108 h with B. succinogenes S85, extent of acid detergent fiber degradation of cotton fiber and Sigmacell-50 was similar to that of their respective controls. Sodium hydroxide and AHP treatments were effective in increasing acid detergent fiber degradation of the Solka floc which contained, on average, 3.3 and 4.8 percentage units more acid detergent lignin and hemicellulose, respectively, than cotton fiber and Sigmacell-50.(ABSTRACT TRUNCATED AT 250 WORDS)
Multiuser gaussianity and constellation randomization for the MIMO multiple access channel: a unified view (2007)

In recent analyses of multiuser MIMO systems and their capacity achieving transmit strategies, Gaussian codebooks are usually used. For the case in which the input signals are constrained to belong to a finite constellation, we study and explain two effects, namely multiuser Gaussianity (MuG) and constellation randomization (CoRa). MuG means that the more users transmit simultaneously, the higher is the similarity of the received density to the optimal Gaussian one. Hence, the instantaneous mutual information is increased by MuG. This leads to a tradeoff between multiuser diversity and MuG. On the other hand, CoRa is done by linear precoding by random unitary matrices. Based on the observations from MuG, we explain why the outage capacity is increased by CoRa. The effects are illustrated by various numerical simulations.
Single-shot Monitoring of Ultrafast Processes via X-ray Streaking at a Free Electron Laser (2017)

The advent of x-ray free electron lasers has extended the unique capabilities of resonant x-ray spectroscopy techniques to ultrafast time scales. Here, we report on a novel experimental method that allows retrieving with a single x-ray pulse the time evolution of an ultrafast process, not only at a few discrete time delays, but continuously over an extended time window. We used a single x-ray pulse to resolve the laser-induced ultrafast demagnetisation dynamics in a thin cobalt film over a time window of about 1.6 ps with an excellent signal to noise ratio. From one representative single shot measurement we extract a spin relaxation time of (130 ± 30) fs with an average value, based on 193 single shot events of (113 ± 20) fs. These results are limited by the achieved experimental time resolution of 120 fs, and both values are in excellent agreement with previous results and theoretical modelling. More generally, this new experimental approach to ultrafast x-ray spectroscopy paves the way to the study of non-repetitive processes that cannot be investigated using traditional repetitive pump-probe schemes.
B-line detection using amplitude modulation-frequency modulation (AM-FM) features (2018)

Pneumonia is one of the most common acute respiratory infections among pediatric populations worldwide. Ultrasound is becoming increasingly important in the diagnosis of lung diseases as a more portable and safer alternative to X-ray imaging. In the current work, we present a new automatic system for detection of B-lines, one of the distinctive features of pneumonic ultrasound scans, using amplitude modulation-frequency modulation (AM-FM). Features are evaluated on 109 videos obtained from 100 pediatric patients using a Verasonics V1 scanner. Further, the results were compared to the ones obtained with a previously published spectral feature (SF) method. Sensitivities of 92% and 83% and specificities of 91% and 70% were obtained on zone-1 and zone-2 of the lungs, respectively. In contrast, the SF method provided sensitivities of 72% and 68% in zone-1 and zone-2, respectively, and specificities of 68% and 46% in zone-1 and zone-2, respectively. In addition, the AM-FM method allowed increasing the F1-score when compared to the SF method from 70% to 87% and from 61% to 78% in zone-1 and zone-2, respectively. The results suggest the proposed method may be useful for the computer assisted diagnosis of pneumonia.
Fractional wave equation for compressional and shear waves. (2010)

This study has been motivated by the observed difference in the range of the power law attenuation exponent for compressional and shear waves. Usually compressional attenuation increases with frequency to a power between 1 and 2, while shear wave attenuation often is described with powers less than 1. Another motivation is the apparent lack of partial differential equations with desirable properties such as causality that describe such wave propagation. Starting with a constitutive equation which is generalized Hooke’s law with a loss term containing a fractional derivative, one can derive a causal fractional wave equation previously given by Caputo (1967) and Wismer (2006). In the low ωτ (low-frequency) case, this equation has an attenuation with a power law in the range from 1 to 2. This is consistent with, e.g., attenuation in tissue. In the often neglected high ωτ (high-frequency) case, it describes attenuation with a power law between 0 and 1, consistent with what is observed in, e.g., dynamic elastography. Thus a unifying wave equation derived properly from constitutive equations can describe both cases. Recent results on fractional random media will also be discussed as they give similar characteristics from a microperspective.
Function of berberine on porcine in vitro fertilization embryo development and differential expression analysis of microRNAs (2018)

The effect of berberine (Ber) on in vitro fertilization (IVF) embryo development in pigs and the associated differential expression of microRNAs (miRNAs) in the embryo were investigated. NCSU-23 embryonic culture medium was used for a control group, while NCSU-23 embryonic culture medium added with Ber was used for a Ber group. The embryo development rates in these groups were determined, and the zygotes, 4- and 8-cell embryos, and blastocysts were collected for cDNA microarray analysis. The development rates of 2-, 4-, 8-cell embryos and blastocysts were significantly higher in the Ber group than those in the control group (p < 0.01). The differentially expressed miRNAs in the 8-cell versus the 4-cell stage in control group as well as in the 8-cell Ber group versus the 8-cell control group overlapped, and it was found that nine miRNAs were commonly upregulated and two of them were downregulated, while there was no overlap among the other groups. The target genes of Ber-regulated miRNAs at the 8-cell stage were mainly associated with the molecular pathway of nucleic acid and protein synthesis. These findings suggest that Ber may regulate the expression of miRNAs at the 8-cell stage, which is beneficial to provide material reserves for the maternal to zygote transition of porcine embryos, thereby increasing the porcine IVF embryo development rate.
A numerical three‐dimensional conditioned/unconditioned stochastic facies type model applied to a remediation well system (1998)

In this study a three‐dimensional stochastic facies‐based aquifer model was developed. The model can be used to numerically simulate flow and solute transport in heterogeneous groundwater aquifers. The stochastic generation process can be conditioned by using available facies information in one vertical plane or two orthogonal vertical ones. In this study the information was obtained from a facies interpretation of a vertical georadar profile in a natural gravel formation in Switzerland. In the domain outside the known profile, unconditioned lenses and layers were generated at random according to statistical information on coherent sedimentary structures based on observations in adjacent gravel pits [ Jussel et al. , 1994a]. The method was applied to a single extraction well designed to capture an initially block‐shaped contaminant plume. A total of 80 conditioned and unconditioned synthetic aquifers was generated. The flow and transport simulations were performed using a finite element flow model and a random walk transport model. The results are presented as the ensemble of integral solute mass recovery curves of single realizations. One would expect conditioning to reduce the bandwidth of the recovery curves representing the uncertainty, but the results show that the bandwidth even increased. This effect was attributed to a discrepancy in the mean volumetric fraction of the different facies types in the conditioned and the unconditioned cases. Moreover, a simulation using a homogeneous model with constant equivalent flow and transport parameters overestimated the remediation efficiency. The influence of a linear, reversible equilibrium sorption on the remediation well efficiency was taken into account by an uncorrelated random field of the retardation factor based on values from the literature. However, the impact of the variability in hydraulic conductivity clearly exceeded the effect of the variability in the retardation factor.