gebhart/patrepeval huggingface dataset:
Tradeoffs between Convergence Speed and Reconstruction Accuracy in\n Inverse Problems (2016)

Solving inverse problems with iterative algorithms is popular, especially for\nlarge data. Due to time constraints, the number of possible iterations is\nusually limited, potentially affecting the achievable accuracy. Given an error\none is willing to tolerate, an important question is whether it is possible to\nmodify the original iterations to obtain faster convergence to a minimizer\nachieving the allowed error without increasing the computational cost of each\niteration considerably. Relying on recent recovery techniques developed for\nsettings in which the desired signal belongs to some low-dimensional set, we\nshow that using a coarse estimate of this set may lead to faster convergence at\nthe cost of an additional reconstruction error related to the accuracy of the\nset approximation. Our theory ties to recent advances in sparse recovery,\ncompressed sensing, and deep learning. Particularly, it may provide a possible\nexplanation to the successful approximation of the l1-minimization solution by\nneural networks with layers representing iterations, as practiced in the\nlearned iterative shrinkage-thresholding algorithm (LISTA).\n
ChemInform Abstract: Isolated Redox Centers within Microporous Environments. Part 1. Cobalt‐Containing Aluminophosphate Molecular Sieve Five (1990)

Abstract (CoAPO‐5) is synthesized by heating a gel of composition 1.5 Et 3 N·0.8 Al 2 O 3 ·0.4 CoO·P 2 O 5 ·40 H 2 O to 200 °C at autogeneous pressure.
Generation of large libraries (1999)

DNA is one of the most efficient and fascinating “information storage systems” known to mankind. A few pg of DNA encodes the information in the form of genes necessary for development of an oocyte into a complex organism, for example a human. It is estimated that there are about 80000–100000 genes in a vertebrate genome. However, only a small proportion of the DNA present in the cell encodes genes, which are transcribed to mRNA and then translated into proteins or other non-translated RNAs such as rRNAs and tRNAs. This 1–5% of the genome is usually referred to as coding DNA.
Luminance Enhancement of Flip-Chip Light-Emitting Diodes by Geometric Sapphire Shaping Structure (2008)

The flip-chip light-emitting diodes (FC-LEDs) with geometric sapphire shaping structure were investigated. The sapphire shaping structure was formed on the bottom side of the sapphire substrate by a chemical wet etching technique for light extraction purpose. The crystallography-etched facets were (1010) M-plane, (1102) R-plane, and (1120) A-plane against the (0001) c-axis with the angles range between 29deg~60deg. These large slope oblique sidewalls are useful for light extraction efficiency enhancement. The light-output power of sapphire shaping FC-LEDs was increased 55% (at 350-mA current injection) compared to that of conventional FC-LEDs.
Diversity Analysis of Symbol-by-Symbol Linear Equalizers (2011)

In frequency-selective channels linear receivers enjoy significantly-reduced complexity compared with maximum likelihood receivers at the cost of performance degradation which can be in the form of a loss of the inherent frequency diversity order or reduced coding gain. This paper demonstrates that the minimum mean-square error symbol-by-symbol linear equalizer incurs no diversity loss compared to the maximum likelihood receivers. In particular, for a channel with memory ν, it achieves the full diversity order of (ν+1) while the zero-forcing symbol-by-symbol linear equalizer always achieves a diversity order of one.
Complete Laser System for Strontium Lattice Clock Based on Frequency Comb (2020)

We report the development of a complete turn-key 5 × 10 -16 ultra-stable laser system for operating neutral strontium atoms for optical lattice clocks or for quantum computing.
3 GHz-band superconducting wide-band filter for small microwave receiver (2014)

We have developed a low-insertion-loss and wideband bandpass filter using a superconducting microstrip filter, in order to reduce the noise of a small microwave receiver in the 3 GHz band. For the superconducting microstrip filter, it is necessary to suppress the radiation loss of the resonator in order to achieve low insertion loss and to couple resonators strongly with each other to achieve wide passband, too. Therefore, by adopting an interdigital hairpin resonator whose ends are both comb-shaped, we have aimed to suppress the radiation loss and to strengthen the coupling between resonators. Using the interdigital hairpin resonators, we designed and fabricated a 5th-order Chebyshev filter and evaluated its frequency characteristics. As a result, it is confirmed that the insertion loss is less than 0.06 dB and the fractional passband width is 26.8%.
Pressure–Enhanced Liquid Chromatography as a Suitable Approach to Improve Selectivity for Large Molecule Separations (2023)

This work describes the application of a pressure-enhanced liquid chromatography (PE-LC) setup to tune the separation of various large molecules comprised of nucleic acids (oligonucleotides, messenger ribonucleic acid [mRNA], and deoxyribonucleic acid [DNA]). When adding pressure as a method development parameter, it indeed becomes possible to modify retention, selectivity, and peak width. As an example, the separation of oligonucleotides having sizes comprised between 40 and 100-mer in ion-pairing reversed-phase liquid chromatography (IP-RPLC) was drastically improved by using a stepwise pressure gradient to selectively shift the retention of a peak or group of peaks. Resolution was increased from 1.5 to 11.8 when setting a rapid high pressure step (twofold increased pressure) during the run. On the other hand, it was also possible to improve the separation of erythropoietin (EPO) mRNA and related impurities under ion-exchange chromatography (IEX). However, with this biomolecule, the best separation was achieved by reducing the pressure in the system. Finally, for another sample (DNA ladder) under IEX conditions, the pressure was found to have a limited impact on the overall selectivity. As highlighted in this work, pressure is an additional parameter that can be successfully used to develop LC methods of large biomolecules.
Hyperglucagonemia Mitigates the Effect of Metformin on Glucose Production in Prediabetes (2016)

The therapeutic mechanism of metformin action remains incompletely understood. Whether metformin inhibits glucagon-stimulated endogenous glucose production (EGP), as in preclinical studies, is unclear in humans. To test this hypothesis, we studied nine prediabetic individuals using a randomized, placebo-controlled, double-blinded, crossover study design. Metformin increased glucose tolerance, insulin sensitivity, and plasma glucagon. Metformin did not alter average basal EGP, although individual variability in EGP correlated with plasma glucagon. Metformin increased basal EGP in individuals with severe hyperglucagonemia (>150 pg/ml). Decreased fasting glucose after metformin treatment appears to increase glucagon to stimulate EGP and prevent further declines in glucose. Similarly, intravenous glucagon infusion elevated plasma glucagon (>150 pg/ml) and stimulated a greater increase in EGP during metformin therapy. Metformin also counteracted the protein-catabolic effect of glucagon. Collectively, these data indicate that metformin does not inhibit glucagon-stimulated EGP, but hyperglucagonemia may decrease the ability of the metformin to lower EGP in prediabetic individuals.
ChemInform Abstract: SELECTIVITY IN THE ACID CATALYZED REDUCTION OF CARBONYL COMPOUNDS TO ALCOHOLS BY BIS(TRIPHENYLPHOSPHINE)COPPER(I) TETRAHYDROBORATE: REDUCTION OF ALDEHYDES IN THE PRESENCE OF KETONES (1981)

Abstract Aldehyde der verschiedensten Art (I) reagieren mit dem komplexierten Kupfer‐boranat (II) in Gegenwart von sauren Komponenten wie HCl, Zinkchlorid oder Aluminiumchlorid zu den Reduktionsprodukten (III).
Artificial Blood (2006)

Abstract The possibility of using human blood for transfusion is limited by requirements of blood‐typing, the danger of transmitting certain diseases, and a short shelf life of liquid blood. These limitations and the wide range of applications of blood substitutes have fueled a worldwide search for safe, effective, and universal blood substitute materials. One major route to avoid the problems associated with blood (i.e., AIDS, Hepatitis, etc.) involves the use of isolated human hemoglobin (Hb) because of its high capacity of oxygen and hemocompatibility. However, cell‐free Hb has to be either molecularly modified or encapsulated in order to prevent its dissociation into dimers, decrease the high oxygen affinity, and increase the retention time in circulation. This route of research requires the use of specifically designed cross‐linker reagents necessary to modify the Hb protein. With molecular engineering techniques, a new family of cross‐linking reagents was developed, based on nicotinamide‐adenine dinucleotide (NAD) derivatives. One of the reagents designed, namely oxidized beta‐NAD ( o ‐NAD), was reacted with deoxyHb to produce NAD‐derivatized hemoglobin (HbNAD). The latter was further polymerized to yield poly‐HbNAD. Macroscopic properties of HbNAD and poly‐HbNAD were studied. From the results obtained, it is evident that poly‐HbNAD possesses a physiological oxygen‐carrying capacity and oncotic characteristics similar to whole blood. These properties make poly‐HbNAD a viable potential candidate as a resuscitation fluid.
Hypertension and Genes. (2001)

Under classical strategy, scientists have tried first to find a physiological phenomenon specific for essential hypertension, then to identify the protein underlying the physiological abnormality, and finally to clarify the causative gene which encoded the protein. On the other hand, under the reverse genetic approach, the correlation between hypertension and genetic abnormality is identified first, and then the pathogenesis is clarified-in reverse order. Therefore, it is not extraordinary for unexpected results to be obtained in the correlation between a gene and a disease, suggesting that this approach has a possibility to be a breakthrough in the chaos of hypertension research.
Moiré effect-based Overlay target design for OPO improvements (2021)

As design nodes of advanced semiconductor chips shrink, reduction in on-product overlay (OPO) budget becomes more critical to achieving higher yield. Imaging-based overlay (IBO) targets usually consist of periodic patterns where their pitches are resolvable with visible light microscopy. The difference between the feature dimensions of the device and the optical target is growing as device design nodes shrink. To make the optical target emulate the device as much as possible, the target’s feature periodicity is reduced. Using this approach, the process impact on the device is simulated on the overlay target which enables a more accurate measurement on grid (target) in terms of OPO matching. To further optimize IBO performance, a new moiré effect based robust Advanced Imaging Mode (rAIM™) target design was developed. This rAIM IBO target is implemented using significantly smaller pitches compared to the standard AIM® target, resulting in a more device-like target design. In this paper we investigate the benefits of the optical improvement, manifested as the target gain, and the process compatibility benefits to improve the target accuracy, robustness, and measurability to meet overlay (OVL) basic performance requirements, such as total measurement uncertainty (TMU).
Full-Body Photobiomodulation Therapy Is Associated with Reduced Sleep Durations and Augmented Cardiorespiratory Indicators of Recovery (2022)

Research is emerging on the use of Photobiomodulation therapy (PBMT) and its potential for augmenting human performance, however, relatively little research exists utilizing full-body administration methods. As such, further research supporting the efficacy of whole-body applications of PBMT for behavioral and physiological modifications in applicable, real-world settings are warranted. The purpose of this analysis was to observe cardiorespiratory and sleep patterns surrounding the use of full-body PBMT in an elite cohort of female soccer players. Members of a women's soccer team in a "Power 5 conference" of the National Collegiate Athletic Association (NCAA) were observed across one competitive season while wearing an OURA Ring nightly and a global positioning system (GPS) sensor during training. Within-subject comparisons of cardiorespiratory physiology, sleep duration, and sleep composition were evaluated the night before and after PBMT sessions completed as a standard of care for team recovery. Compared to pre-intervention, mean heart rate (HR) was significantly lower the night after a PBMT session (<i>p</i> = 0.0055). Sleep durations were also reduced following PBMT, with total sleep time (TST) averaging 40 min less the night after a session (<i>p</i> = 0.0006), as well as significant reductions in light sleep (<i>p</i> = 0.0307) and rapid eye movement (REM) sleep durations (<i>p</i> = 0.0019). Sleep durations were still lower following PBMT, even when controlling for daily and accumulated training loads. Enhanced cardiorespiratory indicators of recovery following PBMT, despite significant reductions in sleep duration, suggest that it may be an effective modality for maintaining adequate recovery from the high stress loads experienced by elite athletes.
Novel Cost-Effective Methanephosphonoanilidothioate Approach to the Stereoselective Synthesis of Dinucleoside (3‵,5‵)-Methanephosphonates (1997)

A new method of stereoselective preparation of di(2'-deoxy or 2'-OMe)ribonucleoside (3',5')-methanephosphonate 5 is presented. The DBU/LiCl-assisted reaction of 5'-O-DMT-(2'-deoxy or 2'-OMe)ribonucleoside 3'-O-(S-alkyl methanephosphonothioate) 9 with 5'-OH nucleosides proceeds with full stereospecificity, giving 5 in moderate to good yield. The conversion of 5'-O-DMT-(2'-deoxy or 2'-OMe) ribonucleoside 3'-methanephosphonoanilidothioates 8 and 3'-O-methanephosphonoanilidates 10 by means of NaH/CX2 (X = O,S) followed by S-alkylation leads to monomers 9, with the possibility of use of both separated diastereomers of 8 for the preparation of one selected diastereomer of 5. The relative configuration at the P atom in 2'-OMe and deoxynucleoside derivatives of compounds 9 was established by means of stereoselective degradation of nucleoside 3'-O-methanephosphonothioates 11 (precursors of 9) with nuclease P1.
DNA topoisomerase II sites in the histone H4 gene during the highly synchronous cell cycle of Physarum polycephalum [published erratum appears in Nucleic Acids Res 1998 Oct 15;26(20):following 4789] (1998)

The nearly perfect synchrony of nuclear division in a plasmodium of Physarum polycephalum provides a powerful system to analyze topoisomerase II cleavage sites in the course of the cell cycle. The histone H4 locus, whose schedule of replication and transcription is precisely known, was chosen for this analysis. Drug-induced topoisomerase II sites are clustered downstream of the histone H4 gene and appear highly dependent on cell cycle stage. They were only detected in mitosis and at the very beginning of S phase, precisely at the time of replication of the histone H4 region. The sites, which were absent in G2 phase, reappeared at the next mitosis. Remarkably, DNase I hypersensitive sites occurred in nearly the same location, but their schedule was totally different: they were absent in mitosis and present in G2. This schedule follows H4 transcription, which peaks in mid-S phase and in the second part of G2 phase and is off during mitosis. These results suggest that topoisomerase II may not be involved in transcription, but plays a role in remodeling chromatin structure, both during chromosome condensation in prophase/metaphase to allow their decatenation and during chromosome decondensation after metaphase to allow replication fork passage throughout the region.
Clinical perspectives of concepts on neoplastic stem cells and stem cell-resistance in chronic myeloid leukemia (2008)

In chronic myeloid leukemia (CML), neoplastic stem cells and/or their subclones exhibit resistance against BCR/ABL tyrosine kinase inhibitors (TKIs). Therefore, residual CML stem cells (subclones) in TKI-treated patients are a logical target of therapy, and their elimination is considered a major aim and clue in the development of curative treatment approaches. A number of different mechanisms may underly resistance of CML stem cells against TKIs and other targeted or/and conventional drugs, including stem cell quiescence, expression of drug-transporters, stem cell plasticity, BCR/ABL mutations, overexpression of BCR/ABL and BCR/ABL-independent signalling- and survival-molecules. In this article, possibilities to overcome stem cell resistance in CML by exploiting knowledge on molecular mechanisms that underly the 'stem cell escape' from drug therapy are discussed.
Can Heterocyclic γ‐Peptides Provide Polyfunctional Platforms for Synthetic Glycocluster Construction? (2018)

Sugars play key roles in many molecular and cellular communication processes involving a family of proteins named lectins. The low affinity associated with sugar recognition is generally counterbalanced by the multivalent nature of the interaction. While many polyglycosylated architectures have been described, only a few studies focused on the impact of topology variations of the multivalent structures on the interaction with lectin proteins. One major interest of our group concerns the design of new highly predictable and stable molecular pseudo-peptide architectures for therapeutic applications. In such a context, we described a class of constrained heterocyclic γ-amino acids built around a thiazole ring, named ATCs. ATC oligomers are helical molecules resulting from the formation of a highly stable C<sub>9</sub> hydrogen-bonding pattern. Following our program, we herein address the potential of ATC oligomers as tunable scaffolds for the development of original multivalent glycoclusters.
Novel materials for next generation photonic devices (2017)

We show that graphene can provide electro-optic properties to traditionally passive optical materials and enable efficient integrated active nanophotonic devices. We show devices with GHz absorption modulation based on ring resonators. We also report the first experimental demonstration of a graphene electro-refractive modulator with V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">π</sub> L of 0.14 Vcm, and minimal absorption modulation based on graphene capacitor integrated on Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> with embedded high-K and high breakdown dielectric.
Cognitive Radio Techniques Under Practical Imperfections: A Survey (2015)

Cognitive radio (CR) has been considered as a potential candidate for addressing the spectrum scarcity problem of future wireless networks. Since its conception, several researchers, academic institutions, industries, and regulatory and standardization bodies have put their significant efforts toward the realization of CR technology. However, as this technology adapts its transmission based on the surrounding radio environment, several practical issues may need to be considered. In practice, several imperfections, such as noise uncertainty, channel/interference uncertainty, transceiver hardware imperfections, signal uncertainty, and synchronization issues, may severely deteriorate the performance of a CR system. To this end, the investigation of realistic solutions toward combating various practical imperfections is very important for the successful implementation of cognitive technology. In this direction, first, this survey paper provides an overview of the enabling techniques for CR communications. Subsequently, it discusses the main imperfections that may occur in the most widely used CR paradigms and then reviews the existing approaches toward addressing these imperfections. Finally, it provides some interesting open research issues.
Comparative In Vitro Activity of ABT-773, a Novel Antibacterial Ketolide (2001)

The in vitro activities of ABT-773, erythromycin, clarithromycin, and azithromycin were compared. ABT-773 was the most active compound against macrolide-susceptible Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Staphylococcus epidermidis, Listeria monocytogenes, and Enterococcus spp. and multidrug-resistant Streptococcus pneumoniae. It also had good activity against gram-negative and atypical respiratory tract pathogens and Helicobacter pylori.
Mathematics in a Nutshell (2005)

This chapter contains sections titled: Linear Algebra Linear Equations The Gaussian Elimination Algorithm Systematic Solution of Linear Systems Matrices Basic Notions Linear Dependency Basic Matrix Operations Dimension and Rank Eigenvalues and Eigenvectors of a Square Matrix Ordinary Differential Equations Notions Linearization of Autonomous Systems Solution of Linear ODE Systems Stability of Steady States Global Stability of Steady States Limit Cycles Difference Equations Statistics Basic Concepts of Probability Theory Random Variables, Densities, and Distribution Functions Transforming Probability Densities Product Experiments and Independence Limit Theorems Descriptive Statistics Statistics for Sample Location Statistics for Sample Variability Density Estimation Correlation of Samples Testing Statistical Hypotheses Statistical Framework Two-sample Location Tests Linear Models ANOVA Multiple Linear Regression Graph and Network Theory Introduction Regulatory Networks Linear Networks Boolean Networks Bayesian Networks Stochastic Processes Gillespie's Direct Method Other Algorithms Stochastic and Macroscopic Rate Constants First-order Reaction Second-order Reaction
HIV Molecular Immunology 2014 (2015)

HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.