gebhart/patrepeval huggingface dataset:
Interactive design and synthesis of a novel antibacterial agent (1994)

β-Lactam compounds act on penicillin-recognizing enzymes via acylation of the hydroxyl group of an active site serine. When the resulting acyl enzyme is kinetically stable, as in the case of a penicillin-binding protein (PBP), the biosynthesis of a bacterial cell wall is inhibited, and death of the organism results. The de novo design of an antibacterial agent targeted to a PBP might be possible if the three-dimensional structural requirements of the equilibrium (i.e, fit) and catalytic (i.e. reactivity) steps of the aforementioned enzymatic process could be determined. For a model of the active site of a PBP from Streptomyces R61, the use of molecular mechanics calculations to treat "fit," and ab initio molecular orbital calculations to treat "reactivity," leads to the idea that the carboxyl group (G 1 ) and the amide N-H (G 2 ) of the antibiotic are hydrogen bonded to a lysine amino group and a valine carbonyl group in the enzyme–substrate complex. These two hydrogen bonds place the serine hydroxyl group on the convex face of the antibiotic, in position for attack on the β-lactam ring by a neutral reaction, catalyzed by water, that involves a direct proton transfer to the β-lactam nitrogen. Molecular orbital calculations of structure–reactivity relations associated with this mechanism suggest that C=N is bioisosteric to the β-lactam N-C(=O), comparable to a β-lactam in its reactivity with an alcohol, and that the product RO(C-N)H is formed essentially irreversibly (−ΔE &gt; 10 kcal/mol). Accordingly, structures containing a G 1 and a G 2 separated by a C=N, and positioned in different ways with respect to this functional group, have been synthesized computationally and examined for their ability to fit to the PBP model. This strategy identified a 2H-5,6-dihydro-1,4-thiazine substituted by hydroxyl and carboxyl groups as a target for chemical synthesis. However, exploratory experiments suggested that the C=N of this compound equilibrates with endocyclic and exocyclic enamine tautomers. This required that the C2 position be substituted, and that the hydroxyl group not be attached to the carbon atom adjacent to the C=N. These conditions are met in a 2,2-dimethyl-3-(2-hydroxypropyl)-1,4-thiazine, which also exhibits the necessary fit to the PBP model. Two epimers of this compound have been synthesized, from D- and L-serine. The compound derived from L-serine is not active. The compound derived from D-serine exhibits antibacterial activity, but is unstable, and binding studies with PBP's have not been performed. It is hoped that these studies can be carried out if modification of the lead structure leads to compounds with improved chemical stability.
Use of Dual-Energy CT for Quantification of Essential Trace Metals (Iron, Copper, and Zinc): Proof of Concept (2020)

<b>OBJECTIVE.</b> Altered concentrations of essential trace metals have been associated with the development of abdominal tumors. We developed a method to quantify trace metals (iron, copper, and zinc) using monochromatic data from commercially available dual-energy CT (DECT) implementations. <b>CONCLUSION.</b> Our data provide a foundation for the use of DECT for noninvasive quantification of essential trace metals. Minimum detectable concentrations of iron and zinc estimated with DECT overlap with in vivo hepatic concentrations reported in the literature.
Exploration of 4D MRI Blood Flow using Stylistic Visualization (2010)

Insight into the dynamics of blood-flow considerably improves the understanding of the complex cardiovascular system and its pathologies. Advances in MRI technology enable acquisition of 4D blood-flow data, providing quantitative blood-flow velocities over time. The currently typical slice-by-slice analysis requires a full mental reconstruction of the unsteady blood-flow field, which is a tedious and highly challenging task, even for skilled physicians. We endeavor to alleviate this task by means of comprehensive visualization and interaction techniques. In this paper we present a framework for pre-clinical cardiovascular research, providing tools to both interactively explore the 4D blood-flow data and depict the essential blood-flow characteristics. The framework encompasses a variety of visualization styles, comprising illustrative techniques as well as improved methods from the established field of flow visualization. Each of the incorporated styles, including exploded planar reformats, flow-direction highlights, and arrow-trails, locally captures the blood-flow dynamics and may be initiated by an interactively probed vessel cross-section. Additionally, we present the results of an evaluation with domain experts, measuring the value of each of the visualization styles and related rendering parameters.
Large nonlinear phase shift in Epsilon-near-zero materials: the effect of group and phase velocity (2020)

Materials with vanishing real part of permittivity, also known as epsilon-near-zero (ENZ), have emerged as a new paradigm to obtain large optical nonlinearities. Transparent conducting oxides such as indium tin oxide (ITO) naturally exhibit an ENZ condition in the near-infrared and close to their plasma frequency. The peculiarity of ENZ materials is their highly dispersive nature explained by Drude model, allowing to obtain reduced group velocity at frequencies where the phase velocity is enhanced. This condition can dramatically increase the phase sensitivity caused by any given changes in material permittivity. To accurately address the NLO mechanism in such materials, we present a generalized formalism for the nonlinear phase shift for a dispersive material, where it includes contributions from both group velocity and phase velocity. We experimentally demonstrate that the nonlinear phase can reach to the values close to &pi;/2 when the probe beam is at ENZ, while the index change in the conventional definition is not enhanced necessarily. In this work, we present nonlinear optical measurements using the nondegenerate Beam Deflection (BD) methodology at normal incident together with cross-phase modulation experiments. BD is a pump-probe method that directly characterizes the ultrafast response of the nonlinear phase-shift, hence nonlinear refraction. We see no polarization dependence proving that bound electronic third-order nonlinearities are negligible compared to the sub-picosecond fast carrier effects. We also present that frequency shift is highly sensitive to the temporal dynamics of the nonlinear phase shift suggesting that short pulses may help to improve the magnitude of frequency shift.
Supplementary Figure S6 from Blocking Angiopoietin-2 Promotes Vascular Damage and Growth Inhibition in Mouse Tumors Treated with Small Doses of Radiation (2023)

&lt;p&gt;Supplementary Figure S6&lt;/p&gt;
Analysis of Lewis fucosyltransferase genes from the human gastric mucosa of Lewis-positive and -negative individuals (1993)

The expression of Lewis fucosyltransferase (FT) mRNA was examined in gastric mucosa from two Lewis-positive [Le(+)] and two Lewis-negative [Le(-)] individuals. Northern blot analysis demonstrated that levels of mRNA were similar in both Le(+) and Le(-) gastric mucosa. We isolated the protein-coding region of the Lewis FT cDNA from Le(+) and Le(-) gastric mucosa by polymerase chain reaction (PCR) amplification. The sequence of cDNA from the Le(-) gastric mucosa shows two single-base substitutions of G for T at position 59 and of A for G at position 508 from the A of the initiation codon of cDNA. These substitutions may be the cause of changes in two amino acid residues, Arg for Leu at position 20 and Ser for Gly at position 170 from the N-terminal. To determine whether either or both of these base substitutions is responsible for the Le(-) gene, we constructed chimera cDNAs and expressed them in COS cells. Those COS cells transfected with a chimera cDNA containing a mutation of the 508th nucleotide did not express Lewis antigen, whereas those cells transfected with a chimera cDNA containing the 59th nucleotide mutation expressed Lewis antigen, indicating that a single-base change from G to A at position 508 is responsible for the Le(-) gene. The G to A transition at position 508 created a new site for PvuII endonuclease. The digestion by PvuII endonuclease of PCR products between the 386th and 612th nucleotides of Lewis FT cDNA from one of the Le(-) individuals proved to be homozygous for the PvuII site. However, the other Le(-) individual was heterozygous for the PvuII site, suggesting the presence of other Le(-) allele(s). Thus, we isolated one of the silent Lewis genes (le).
Sequence and Chromosomal Assignment of a Novel cDNA Identified by Immunoscreening of a Thyroid Expression Library: Similarity to a Family of Mitochondrial Solute Carrier Proteins (1989)

An immunoglobulin G (IgG) preparation of the serum from a patient with active Graves' disease was used to isolate cDNA clones from a lambda gt11 cDNA library of human thyroid follicular carcinoma tissue by immunoscreening. One of these clones, hML-7, is further characterized herein by sequencing, Northern analysis, and chromosomal mapping. The clone reacted with IgG preparations from the sera of 14 of 19 patients with active Graves' disease but not with IgG preparations from 11 normal individuals, three patients with toxic thyroid adenoma, and three with rheumatoid arthritis. The hML-7 cDNA hybridized to a 3.6 kilobase (kb) mRNA transcript in poly(A+) RNA preparations from human thyroid tissue and continuously cultured rat thyroid cells; expression of this transcript in rat FRTL-5 thyroid cells was positively regulated by TSH. The 3.6 kb transcript was less abundant in rat liver (BRL3A) cells or differentiated rat (L6) myoblasts than in cultured rat thyroid cells and was not detectable in mouse L-M fibroblasts, human IM-9 lymphocytes, Chinese hamster ovary cells, or human cervical carcinoma cells. The cDNA from hML-7 was sequenced and compared with the sequence of cross-hybridizing cDNA clones isolated from human Graves' thyroid and rat FRTL-5 thyroid cell lambda gt11 expression libraries. A 1.05 kb open reading frame, which is highly conserved between human and rat, was defined. The predicted amino acid sequence of 348 residues exhibited a strong homology with the mitochondrial ADP/ATP carrier protein (adenine nucleotide translocase; ADP/ATP translocator) and with two other members of the same mitochondrial protein family, the phosphate carrier and the hydrogen ion uncoupling protein. The gene represented by the hML-7 cDNA has been assigned to human chromosome 10.
Analysis of synchronous intensity modulation control of 40 Gbit/s dispersion-managed soliton transmissions (2002)

Transmission control of dispersion-managed solitons by means of in-line synchronous intensity modulators and no filtering is analyzed. The feasibility of a 40 Gbit/s dispersion-managed transmission over 20 Mm regenerated only intensity modulation is demonstrated.
Total Synthesis of (+)-Neopeltolide (2008)

(+)-Neopeltolide has reasonable activity against several cancer cell lines. The key step in the synthesis is the formal [4+2] allylsilane annulation (E+F) to yield the trisubstituted tetra­hydropyran ring G. The synthesis depicted corrects the stereochemistry assigned to the natural product.
Intraneuronal Aβ42 accumulation in Down syndrome brain (2002)

Alzheimer's disease (AD) brains display A beta (Abeta) plaques, inflammatory changes and neurofibrillary tangles (NFTs). Converging evidence suggests a neuronal origin of Abeta. We performed a temporal study of intraneuronal Abeta accumulation in Down syndrome (DS) brains. Sections from temporal cortex of 70 DS cases aged 3 to 73 years were examined immunohistochemicallyf or immunoreactivity (IR) for the Abeta N-terminal, the Abeta40 C-terminus and the Abeta42 C-terminus. N-terminal antibodies did not detect intracellular Abeta. Abeta40 antibodies did not detect significant intracellular Abeta, but older cases showed Abeta40 IR in mature plaques. In contrast, Abeta42 antibodies revealed clear-cut intraneuronal IR. All Abeta42 antibodies tested showed strong intraneuronal Abeta42 IR in very young DS patients, especially in theyoungest cases studied (e.g., 3 or 4yr. old), but this IR declined as extracellular Abeta plaques gradually accumulated and matured. No inflammatory changes were associated with intraneuronal Abeta. We also studied the temporal development of gliosis and NFT formation, revealing that in DS temporal cortex, inflammation and NFT follow Abeta deposition. We conclude that Abeta42 accumulates intracellularly prior to extracellular Abeta deposition in Down syndrome, and that subsequent maturation of extracellular Abeta deposits elicits inflammatory responses andprecedes NFTs.
Strong coupling of plasmonic bright and dark modes with two eigenmodes of a photonic crystal cavity (2023)

Dark modes represent a class of forbidden transitions or transitions with weak dipole moments between energy states. Due to their low transition probability, it is difficult to realize their interaction with light, let alone achieve the strong interaction of the modes with the photons in a cavity. However, by mutual coupling with a bright mode, the strong interaction of dark modes with photons is possible. This type of mediated interaction is widely investigated in the metamaterials community and is known under the term electromagnetically induced transparency (EIT). Here, we report strong coupling between a plasmonic dark mode of an EIT-like metamaterial with the photons of a 1D photonic crystal cavity in the terahertz frequency range. The coupling between the dark mode and the cavity photons is mediated by a plasmonic bright mode, which is proven by the observation of a frequency splitting which depends on the strength of the inductive interaction between the plasmon bright and dark modes of the EIT-like metamaterial. In addition, since the plasmonic dark mode strongly couples with the cavity dark mode, we observes four polariton modes. The frequency splitting by interaction of the four modes (plasmonic bright and dark mode and the two eigenmodes of the photonic cavity) can be reproduced in the framework of a model of four coupled harmonic oscillators.
IP traffic offloading to elastic optical layer using multi-flow optical transponder (2011)

We propose introducing a multi-flow optical transponder combined with elastic optical networking to achieve efficient router-bypass at the optical layer. Numerical evaluation shows considerable savings in the required IP router port count and spectral usage.
Correlation measurements on small mobile devices (2012)

Here, analysis of the antenna correlation at the design stage is done, with focus on measurement techniques. Various theoretical definitions of correlations are used with the corresponding measured data required. The problems related to the coaxial measurement cables, when calculating correlation through the radiation patterns, are analyzed and an optical solution proposed. It is shown that using optical cable replacement, repeatable and accurate measurements of the envelope correlation coefficient can be made.
Densely spaced FDM coherent optical star network using monolithic widely frequency-tunable lasers (1989)

The letter presents the results obtained with a densely spaced FDM coherent optical network using monolithic widely frequency-tunable lasers. The system consists of four channels transmitted around 1.53 µm, FSK-modulated at 200Mbit/s and spaced by 2.45GHz. A 16 × 16 fibre star coupler combines the four optical signals. Demultiplexing is performed by a heterodyne FM receiver at an IF frequency of 850 MHz. The minimum received optical power needed to obtain a BER of 10−9 is −55.5dBm or 109 photons/bit, which is 3.4 dB from the shot noise limit.
Microvascular Endothelial Dysfunction and Enhanced Thromboxane and Endothelial Contractility in Patients with HIV (2013)

Premenopausal HIV positive womenhad microvascular oxidative stress with severe endothelial dysfunction and reduced nitric oxide and arginine: assymetric dimethylarginine ratio but enhanced endothelial, thromboxane and endothelin contractions. These microvascular changes may herald later cardiovascular disease.
ON-state Reliability of Cu Atom Switch Under Current–Temperature Stress (2015)

The dc current-stress tolerance of the ON-state Cu atom switch is evaluated at elevated temperature. It is revealed that the reset-direction current stress causes time-dependent failures, which originate from the E-field-driven diffusion of Cu in the conducting bridge. A new empirical lifetime estimation model, including the Joule heating effect, gives an allowable maximum current per atom switch of I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> = 115 μA, which is large enough to satisfy the requirements for signal routing under currents that are average (18 μA) and peak (63 μA) in the reconfigurable switch block operated at 500 MHz at 125 °C.
93–133 GHz Band InP High-Electron-Mobility Transistor Amplifier with Gain-Enhanced Topology (2013)

In this study, we developed a new type of high-frequency amplifier topology using 75-nm-gate-length InP-based high-electron-mobility transistors (InP HEMTs). To enhance the gain for a wide frequency range, a common-source common-gate hybrid amplifier topology was proposed. A transformer-based balun placed at the input of the amplifier generates differential signals, which are fed to the gate and source terminals of the transistor. The amplified signal is outputted at the drain node. The simulation results show that the hybrid topology exhibits a higher gain from 90 to 140 GHz than that of the conventional common-source or common-gate amplifier. The two-stage amplifier fabricated using the topology exhibits a small signal gain of 12 dB and a 3-dB bandwidth of 40 GHz (93–133 GHz), which is the largest bandwidth and the second highest gain reported among those of published 120-GHz-band amplifiers. In addition, the measured noise figure was 5 dB from 90 to 100 GHz.
Identification and Analysis of Precursors to Invasive Pancreatic Cancer (2004)

Histologically distinct noninvasive precursor lesions have been recognized in the pancreas for close to a century. The recent development of a consistent reproducible nomenclature and classification system for these lesions has been a major advance in the study of these noninvasive precursors. The "pancreatic intraepithelial neoplasia" or PanIN system was developed at a National Cancer Institutes sponsored think tank in Park City, Utah. Numerous studies have now demonstrated that genetic alterations in cancer-associated genes are more common in higher grade PanIN lesions then they are in lower grade PanIN lesions, and that higher grade PanIN lesions have many of the same genetic alterations that are found in invasive ductal adenocarcinomas of the pancreas. Thus, just as there is a progression in the colorectal of adenomas to invasive adenocarcinoma, so too is there a progression in the pancreas of histologically low-grade PanIN, to high-grade PanIN to invasive ductal adenocarcinoma.
Adenine Nucleotide Analogues Locked in a Northern Methanocarba Conformation: Enhanced Stability and Potency as P2Y 1 Receptor Agonists (2020)

Preference for the Northern (N) ring conformation of the ribose moiety of nucleotide 5′-triphosphate agonists at P2Y1, P2Y2, P2Y4, and P2Y11 receptors, but not P2Y6 receptors, was established using a ring-constrained methanocarba (a 3.1.0-bicyclohexane) ring as a ribose substitute (Kim et al. J. Med. Chem. 2002, 45, 208–218.). We have now combined the ring-constrained (N)-methanocarba modification of adenine nucleotides with other functionalities known to enhance potency at P2 receptors. The potency of the newly synthesized analogues was determined in the stimulation of phospholipase C through activation of turkey erythrocyte P2Y1 or human P2Y1 and P2Y2 receptors stably expressed in astrocytoma cells. An (N)-methanocarba-2-methylthio-ADP analogue displayed an EC50 at the hP2Y1 receptor of 0.40 nM and was 55-fold more potent than the corresponding triphosphate and 16-fold more potent than the riboside 5′-diphosphate. 2-Cl–(N)-methanocarba-ATP and its N6-Me analogue were also highly selective, full agonists at P2Y1 receptors. The (N)-methanocarba-2-methylthio and 2-chloromonophosphate analogues were full agonists exhibiting micromolar potency at P2Y1 receptors, while the corresponding ribosides were inactive. Although β,γ-methylene-ATP was inactive at P2Y receptors, β,γ-methylene-(N)-methanocarba-ATP was a potent hP2Y1 receptor agonist with an EC50 of 160 nM and was selective versus hP2Y2 and hP2Y4 receptors. The rates of hydrolysis of Northern (N) and Southern (S) methanocarba analogues of AMP by rat 5′-ectonucleotidase were negligible. The rates of hydrolysis of the corresponding triphosphates by recombinant rat NTPDase1 and 2 were studied. Both isomers were hydrolyzed by NTPDase 1 at about half the rate of ATP hydrolysis. The (N) isomer was hardly hydrolyzed by NTPDase 2, while the (S) isomer was hydrolyzed at one-third of the rate of ATP hydrolysis. This suggests that new, more stable and selective nucleotide agonists may be designed on the basis of the (N)-conformation, which greatly enhanced potency at P2Y1 receptors.
Bimodal and multimodal plant biomass particle mixtures (2023)

An industrial feedstock of plant biomass particles having fibers aligned in a grain, wherein the particles are individually characterized by a length dimension (L) aligned substantially parallel to the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L, wherein the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces, and wherein the particles in the feedstock are collectively characterized by having a bimodal or multimodal size distribution.
Infrared-lamp zone melting on the 31 Å BSCCO phase (1992)

An infrared zone melter has been built to produce oriented thick films of the BSCCO 31 Å phase (Tc=80-90 K) on single-crystal MgO, using a feedstock composition of 2.4:1.5:1.0:1.8. Sample sizes were typically 6*25 mm and were superconducting after being traversed at or below 0.8 mu m s-1 in air. Substrate interactions, producing noticeable (Mg,Cu)O dendrites, occurred when traverse speeds were below 0.6 mu m s-1. At higher speeds, samples resembled partially melted BSCCO, and transition temperatures decreased with increasing traverse speeds. From this study, a traverse speed of 0.6 mu m s-1 was found to produce the greatest critical current density at 4.2 K of 2.2*104 A cm-2.
Interorganisatoriska Samarbeten : Struktur och Styrning för Lärande och Kunskapsspridning (2002)

A substantial minority of ADHD children manifests ATs, and those exhibiting ATs have greater severity of illness and dysfunction.