gebhart/patrepeval huggingface dataset:
Performance of the general amber force field in modeling aqueous POPC membrane bilayers (2007)

The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.
The Golgi Complex Is a Microtubule-organizing Organelle (2001)

We show that the Golgi complex can directly stimulate microtubule nucleation in vivo and in vitro and thus behaves as a potent microtubule-organizing organelle in interphase cells. With the use of nocodazole wash-out experiments in hepatic cells, we found that the occurrence of noncentrosomal, early stabilized microtubules is highly correlated with the subcellular localization of Golgi membranes. With the use of in vitro reconstituted microtubule assembly systems with or without cytosol, we also found that, in contrast to centrosomally attached microtubules, the distal ends of Golgi-attached microtubules are remotely stabilized in a way that requires additional cytosolic component(s). Finally, we demonstrate that Golgi-based microtubule nucleation is direct and involves a subset of gamma-tubulin bound to the cytoplasmic face of the organelle.
Reductive Hydrolysis of the 59,60-Amide Bond of Teicoplanin Antibiotics: A Key Step from Natural to Synthetic Glycopeptides (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReductive Hydrolysis of the 59,60-Amide Bond of Teicoplanin Antibiotics: A Key Step from Natural to Synthetic GlycopeptidesAdriano Malabarba and Romeo CiabattiCite this: J. Med. Chem. 1994, 37, 19, 2988–2990Publication Date (Print):September 16, 1994Publication History Published online1 May 2002Published inissue 16 September 1994https://pubs.acs.org/doi/10.1021/jm00045a002https://doi.org/10.1021/jm00045a002research-articleACS PublicationsRequest reuse permissionsArticle Views110Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Biotinylestradiol for purification of estrogen receptor. (1990)

Publisher Summary Affinity resins suitable for purification of different steroid hormone receptors have been synthesized. They were necessarily used empirically, in contrast to soluble ligands, which could be utilized under controlled conditions in terms of affinity and concentration. Purification of the estrogen receptor by the avidin–biotin system is based on the high affinity of both avidin and the receptor for biotinylestradiol derivatives. It is known that chemical modification of the carboxyl group of biotin does not affect the binding of biotin to avidin and that avidin can be linked to solid supports without losing its binding capacity. Amide bonds are obtained by the mixed anhydride procedure using isobutyl chloroformate in tri- n -butylamine-containing medium. This procedure is more efficient than the most commonly used techniques using carbodiimide or N -hydroxybenzotriazole in the presence of dicyclohexylcarbodiimide and those using Nethoxycarbonyl-2-ethoxy-l,2-dihydroquinoline as coupling agent. When nonradioactive ligand is present in the extract, the total number of binding sites is determined using a liquid-phase exchange. Samples are incubated with 1 μM nonradioactive ligand until equilibrium is reached.
A novel anisotropic dry etching technique (1981)

We have developed a dry etching technique in which the chemically reactive species and the energetic ions are independently controlled. This technique, which we call ion beam assisted etching (IBAE), is accomplished by impinging a chemically reactive gas from a jet and an ion beam from a Kaufman ion source upon the sample. It is based upon the work of Coburn et al., 1 and differs fundamentally from reactive ion etching (RIE), which relies upon a plasma to produce both the chemically active species and the energic ions. In IBAE the partial pressure of the reactive gas can be as high as several Pa (tens of microns) at the sample surface while the chamber pressure can easily be maintained at about 1×10−2 Pa (10−4 Torr). Although a variety of reactive gases and sample materials have been characterized, the presentation will concentrate on using Cl2 as a reactive gas and an argon ion beam. The anisotropic character of this etching technique has been found to depend on the angles that the gas jet and the ion beam make with the surface of the sample. Etching rates as high as a few micrometers per minute have been obtained with GaAs and Al samples and anisotropic etching aspect ratios as large as 50 were easily obtained with GaAs. The etched surface of the GaAs was also electrically characterized in two ways: first, by fabricating Schottky diodes on it and measuring the ideality factor, and secondly, by growing VPE GaAs on the etched surface and profiling the traps at the interface between the etched surface and the VPE GaAs using deep level transient spectroscopy (DLTS). The quality of the etched surface was found to improve as the reactive gas flux varied from about 1×1017 to 5×1018 atoms cm−2 s−1. Measured ideality factors of the Schottky diodes fabricated on GaAs etched under high reactive gas flux conditions were equivalent to diodes fabricated on virgin GaAs. The density of traps at the interface between the etched GaAs and the VPE GaAs was less than 1×1015 cm−3 which is low enough for many GaAs device applications. The independent parameter control afforded by this technique has enabled us to achieve desirable anisotropic etching characteristics while producing etched GaAs surfaces with acceptable electrical quality.
Human eosinophil major basic protein, a mediator of allergic inflammation, is expressed by alternative splicing from two promoters (1995)

Human eosinophil major basic protein (MBP) is one of the principal mediators of injury to parasites and tissues in allergic inflammation. MBP is stored in eosinophil crystalloid granules and released with other granule constituents during eosinophil action. Previous studies have identified an MBP gene promoter that generates a 1.0 kb mRNA transcript encoding MBP preproprotein which undergoes processing to the mature storage form. To investigate how the MBP gene is regulated, we have examined the identity and levels of the MBP transcripts both in precursor cells and in blood eosinophils. It was found that the gene was expressed from two upstream promoters, a distal promoter P1 in addition to the previously described promoter P2. Evidence for the second promoter was initially provided by isolation from a human HL-60 leukaemic cell cDNA library of a novel 1.6 kb MBP cDNA that was distinct from the known 1.0 kb cDNA. The complete nucleotide sequence of the 1.6 kb cDNA was determined, and showed that the two cDNAs had identical coding and 3' untranslated regions but differed in their 5' sequences. By isolating and sequencing MBP genomic clones from an arrayed chromosome 11 library, it was demonstrated that the MBP gene is composed of nine upstream exons and five coding exons. The 1.6 and 1.0 kb cDNAs arise by differential splicing of alternate MBP transcripts from promoters P1 and P2 respectively, located 32 kb apart in the genomic DNA. Primer extension analysis identified two transcription start sites at P1, neither associated with a typical TATA box motif. Northern blotting and reverse-transcription PCR analysis showed that the 1.0 kb mRNA was present at higher levels than the 1.6 kb species in immature cells including HL-60 and bone-marrow cells. By contrast, low levels of 1.6 kb mRNA transcripts predominated in differentiated blood eosinophils. The results are compatible with differential use of P1 and P2 promoters as a mechanism for regulation of MBP expression during eosinophil maturation.
Fiber-FISH: Fluorescence <I> In Situ</I> Hybridization on Stretched DNA (2004)

High-resolution fluorescence in situ hybridization (FISH) on deproteinized, stretched DNA prepared by in situ extraction of whole cells immobilized on microscope glass slides allows the visualization of individual genes or other small DNA elements on chromosomes with a resolution of approx 1000 bp. Applications of fiber-FISH range from the determination of numbers of repetitive genes to establishing the physical order of cloned DNA fragments along continuous sections of individual chromosomes. Particularly in organisms with relatively small and gene dense genomes, such as protozoan parasites, fiber-FISH can easily be used as a complementary technique to classical in vitro mapping approaches.
Cyclic changes in composition and volume of the breast during the menstrual cycle, measured by magnetic resonance imaging (1990)

The volumes and spin-lattice (T1) relaxation times of breast tissues and parenchymal water content were measured non-invasively by magnetic resonance imaging (MRI) in eight healthy women during four to eight consecutive menstrual cycles. Total breast volume, and parenchymal volume, T1 relaxation time and water content were lowest between days 6 and 15. Between days 16 and 28, parenchymal volume, T1 relaxation time and water content rose sharply by 38.9%, 15.1% and 24.5%, respectively, and peaked after day 25. Within 5 days of the onset of menses, parenchymal volume fell sharply by 30.3%, while water content declined by 17.5%. Rising parenchymal volume in the second half of the menstrual cycle is not solely due to increased tissue water content and provides in vivo evidence for both growth and increased tissue fluid at this time.
The effects of Beta-Endorphin: state change modification (2015)

Beta-endorphin (β-END) is an opioid neuropeptide which has an important role in the development of hypotheses concerning the non-synaptic or paracrine communication of brain messages. This kind of communication between neurons has been designated volume transmission (VT) to differentiate it clearly from synaptic communication. VT occurs over short as well as long distances via the extracellular space in the brain, as well as via the cerebrospinal fluid (CSF) flowing through the ventricular spaces inside the brain and the arachnoid space surrounding the central nervous system (CNS). To understand how β-END can have specific behavioral effects, we use the notion behavioral state, inspired by the concept of machine state, coming from Turing (Proc London Math Soc, Series 2,42:230-265, 1937). In section 1.4 the sequential organization of male rat behavior is explained showing that an animal is not free to switch into another state at any given moment. Funneling-constraints restrict the number of possible behavioral transitions in specific phases while at other moments in the sequence the transition to other behavioral states is almost completely open. The effects of β-END on behaviors like food intake and sexual behavior, and the mechanisms involved in reward, meditation and pain control are discussed in detail. The effects on the sequential organization of behavior and on state transitions dominate the description of these effects.
An Efficient Real Time Focusing Delay Calculation in Ultrasonic Imaging Systems (1994)

An efficient real time focusing delay calculation algorithm is proposed for variable sampling clock generation (SCG) with high accuracy needed in digital focusing in ultrasonic imaging systems. The proposed algorithm is an extension of the midpoint drawing algorithm that is well known in the computer graphics area. It can be implemented with simple hardware amenable to VLSI realization, without using a large amount of look-up memory to store the sampling clock information otherwise required.
Stress inducible proteinase inhibitor diversity in Capsicum annuum (2012)

Plants can differentially perceive various kinds of insect attacks and respond appropriately through activating plant defenses including regulation of PIs at transcriptional and post-translational levels. Based on the differentially elicited CanPI accumulation patterns, it is intriguing to speculate that generating sequence diversity in the form of multi-IRD PIs is a part of elaborative plant defense strategy to obtain a diverse pool of functional units to confine insect attack.
Effect of Arsenic Trioxide on QT Interval in Patients With Advanced Malignancies (2003)

This analysis shows that arsenic trioxide can prolong the QTc interval. However, with appropriate ECG monitoring and management of electrolytes and concomitant medications, arsenic trioxide can be safely administered in patients with relapsed APL.
IL-7 reverses NK1<sup>+</sup> Tcell-defective IL-4 production in the non-obese diabetic mouse (1996)

Converging data suggest an important role for IL-7 in T lymphocyte maturation as illustrated by the severe T lymphopenia observed in IL-7-deficient mice. We recently reported that IL-7 preferentially promotes the in vitro expansion of a discrete MHC class I-dependent lymphocyte subset comprising both CD4+ and CD4-CD8- TCR alpha beta + cells bearing several NK cells markers such NK1.1 and Ly-49. These T cells, designated as NK1+ T cells, have the unique property among thymocytes of producing large amounts of IL-4 upon primary stimulation via the TCR. We have further demonstrated that thymic NK1+ T cells of non-obese diabetic (NOD) mice, a spontaneous model of autoimmune type I diabetes, are markedly deficient in maturation both quantitatively and functionally (IL-4 production). In the present experiments, the addition of exogenous IL-7 completely restored IL-4 production by anti-TCR alpha beta-stimulated mature (HSA-CD8-) thymocytes in NOD mice. A short 2 h preincubation with IL-7 was sufficient to restore both the expression of IL-4 mRNA and IL-4 production capacity. This was related to a direct effect on NK1+ thymocytes since: (i) the effect of IL-7 was restricted to the non-mainstream MEL-14- 3G11- TCR alpha beta + subset which mostly concentrates the IL-4-producing capacity and (ii) IL-7 did not restore IL-4 production in class I-deficient mice which lack the NK1+ T cell subset. Importantly, this activity of IL-7 on NK1+ T cells was also demonstrated in non-autoimmune strains of mice. These results were extended in vivo by showing that the IL-7 treatment significantly increased the anti-CD3 triggered IL-4 production by NK1+ T spleen cells. These findings confirm the role of IL-7 in NK1+ T cell maturation and suggest that the NK1+ T cell defect in NOD mice could be related to insufficient intrathymic IL-7 bioavailability.
Plasmid insertion mutagenesis and lac gene fusion with mini-mu bacteriophage transposons (1984)

Small bacteriophage Mu transposable elements containing the lac operon structural genes were constructed to facilitate the isolation and use of Mu insertions and lac gene fusions. These mini-Mu elements have selectable genes for either ampicillin or kanamycin resistance and can be used to form both transcriptional and translational lac gene fusions. Some of the mini-Mu-lac elements constructed are deleted for the Mu A and B transposition genes and form stable insertions that cannot undergo transposition unless complemented for these functions. A procedure was developed for selecting mini-Mu insertions specifically into plasmids, including commonly used high-copy-number cloning vectors such as pBR322. Mu insertions in pBR322 were found to be distributed around the plasmid, but insertions in certain regions occurred more frequently than in others.
Syntheses and X‐ray Crystal Structures of Dichlorobis(tert‐butylimido) Complexes of Molybdenum(VI); Potential Precursors to Molybdenum Nitride and Molybdenum Carbonitride (1994)

Abstract The bistertbutylimido complexes [MoCl(μ‐Cl)(NBu 1 ) 2 (NH 2 Bu 1 )] 2 , 1 , and MoCl 2 (NBu 1 ) 2 (py) 2 , 2 (py = pyridine), were prepared by reacting MoCl 2 (NBu 1 ) 2 (dme) (dme = dimethoxyethane) with excess Bu 1 NH 2 and pyridine, respectively. Their structures were determined by X‐ray crystallography. 1 has a pseudo edge‐shared bioctahedral geometry with two Cl ligands bridging the Mo centers unequally. Pertinent bond distances and angles for 1 , Mo = NBu 1 beut = 1.737(3) Å, ∠Mo = N‐CMe 3 = 154.0(2)°; Mo = NBu 1 linear = 1.725(3) Å, ∠Mo = N‐CMe 3 = 172.4(2)°; Mo‐Bu 1 NH 2 = 2.233(2) Å; Mo‐Cl bridging = 2.575(1) and 2.835(1) Å, and Mo‐Cl terminal = 2.428(1) Å. Crystal data for 1: triclinic, space group P 1, a = 8.897(4) Å, b = 10.518(3) Å, c = 10.663(3) Å, α = 107.68(2)° β = 98.03(3)° γ = 99.26(3)°, V = 919.3(5) Å 3 , Z = 1, D c = 1.381 g/mL. 2 is mononuclear with a distorted octahedral geometry with two trans Cl ligands, two cis ‐oriented Bu 1 N = ligands, and two py ligands trans to the imido groups. Pertinent averaged bond distances and angles for 2 , Mo = NBu t bent = 1.736(4) Å, ∠Mo = N‐CMe 3 = 163.8(4)°; Mo = NBu t linear .= 1.705(5) Å, ∠Mo = N‐CMe 3 = 173.4(4)° Mo‐N(py) = 2.44(1), Mo‐Cl = 2.421(3) Å. Crystal data for 2: orthorhombic, space group P na2 1 a = 16.860(2) Å, b = 8.920(3) Å, c = 15.120(3) Å, V = 2274.1(9) Å 3 , Z = 4, D c = 1.362 g/mL. A potential application of 2 as a single‐source precursor to grow molybdenum nitride and molybdenum carbonitride thin films by low pressure chemical vapor deposition (LPCVD) was explored. Cubic phase thin films (a thin film = 4.16–4.20 Å) were grown at temperatures between 450 °C and 650 °C with hydrogen as carrier gas. At 450 °C, thin films of molybdenum nitride were obtained. With temperature of deposition increased from 450 °C to 650 °C, the ratio C/Mo increased from 0.03 to 0.5 whereas me ratio N/Mo decreased from 0.7 to 0.3. Thus, thin films of molybdenum carbonitride were deposited at 650 °C.
A gripper and sensor system for controlled slip and force (2002)

The paper describes the development of a robot gripper, sensors and associated electronics suitable for controlling slippage and contact force. A typical application is the handling of glass test tubes in an automated medical analysis laboratory. Through force control, the gripper first holds an object, then repeatedly releases and regrasps it for controlled slip. The basic mechanical principle consists of a rolling cylinder in direct contact with the (cylindrical) object, forming a cylinder-cylinder pivot with 5 degrees of freedom. A stable grasp is achieved by a finger/counter-finger arrangement with 3 contact points. In the left finger, contact force is reflected in the pivots of the roll and measured by piezoresistive force sensors. In the right finger, motion is measured by optical encoders. Analog electronics deal with gripper motor control and signal processing for the force sensors. Digital circuits handle the motion measurement from the optical encoders, A/D conversion of force sensor outputs and force feedback for motor control and communications with an external computer. The proposed design has been built and tested using an industrial SCARA robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Downscaling ferroelectric field effect transistors by using ferroelectric Si-doped HfO<sub>2</sub> (2012)

Throughout the 22 nm technology node HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> is established as a reliable gate dielectric in contemporary complementary metal oxide semiconductor (CMOS) technology. The working principle of ferroelectric field effect transistors FeFET has also been demonstrated for some time, for dielectric materials like PZT and SrBi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Ta <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sub> . However, integrating these into contemporary downscaled CMOS technology nodes is not trivial due to the necessity of an extremely thick gate stack. Recent developments have shown HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> to have ferroelectric properties given the proper doping. Moreover, these doped HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thin films only require layer thicknesses similar to the ones already in use in CMOS technology. This work will show how the incorporation of Si induces ferroelectricity in HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> based capacitor structures and finally demonstrate non-volatile storage in nFeFETs down to a gate length of 100 nm.