gebhart/patrepeval huggingface dataset:
Identification and characterization of two Alcaligenes eutrophus gene loci relevant to the poly(beta-hydroxybutyric acid)-leaky phenotype which exhibit homology to ptsH and ptsI of Escherichia coli (1991)

From genomic libraries of Alcaligenes eutrophus H16 in lambda L47 and in pVK100, we cloned DNA fragments which restored the wild-type phenotype to poly(beta-hydroxybutyric acid) (PHB)-leaky mutants derived from strains H16 and JMP222. The nucleotide sequence analysis of a 4.5-kb region of one of these fragments revealed two adjacent open reading frames (ORF) which are relevant for the expression of the PHB-leaky phenotype. The 1,799-bp ORF1 represented a gene which was referred to as phbI. The amino acid sequence of the putative protein I (Mr, 65,167), which was deduced from phbI, exhibited 38.9% identity with the primary structure of enzyme I of the Escherichia coli phosphoenolpyruvate:carbohydrate phosphotransferase system (PEP-PTS). The upstream 579-bp ORF2 was separated by 50 bp from ORF1. It included the 270-bp phbH gene which encoded protein H (Mr, 9,469). This protein exhibited 34.9% identity to the HPr protein of the E. coli PEP-PTS. Insertions of Tn5 in different PHB-leaky mutants were mapped at eight different positions in phbI and at one position in phbH. Mutants defective in phbH or phbI exhibited no pleiotropic effects and were not altered with respect to the utilization of fructose. However, PHB was degraded at a higher rate in the stationary growth phase. The functions of these HPr- and enzyme I-like proteins in the metabolism of PHB are still unknown. Evidence for the involvement of these proteins in regulation of the metabolism of intracellular PHB was obtained, and a hypothetical model is proposed.
Polymerization of fibrin: direct observation and quantification of individual B:b knob-hole interactions (2006)

The polymerization of fibrin occurs primarily through interactions between N-terminal A- and B-knobs, which are exposed by the cleavage of fibrinopeptides A and B, respectively, and between corresponding a- and b-holes in the gamma- and beta-modules. Of the potential knob-hole interactions--A:a, B:b, A:b, and B:a--the first has been shown to be critical for fibrin formation, but the roles of the others have remained elusive. Using laser tweezers-based force spectroscopy, we observed and quantified individual B:b and A:b interactions. Both desA-fibrin with exposed A-knobs and desB-fibrin bearing B-knobs interacted with fragment D from the gammaD364H fibrinogen containing b-holes but no functional a-holes. The strength of single B:b interactions was found to be 15 to 20 pN, approximately 6-fold weaker than A:a interactions. B:b binding was abrogated by B-knob mimetic peptide, the (beta15-66)2 fragment containing 2 B-knobs, and a monoclonal antibody against the beta15-21 sequence. The interaction of desB-fibrin with fragment D containing a- and b-holes produced the same forces that were insensitive to A-knob mimetic peptide, suggesting that B:a interactions were absent. These results directly demonstrate for the first time B:b binding mediated by natural B-knobs exposed in a fibrin monomer.
CD70 Exacerbates Blood Pressure Elevation and Renal Damage in Response to Repeated Hypertensive Stimuli (2016)

Our findings illustrate a previously undefined role of CD70 and long-lived T(EM) cells in the development of blood pressure elevation and end-organ damage that occur on delayed exposure to mild hypertensive stimuli. Interventions to prevent repeated hypertensive surges could attenuate formation of hypertension-specific T(EM) cells.
Vacuum sealed MEMS package with an optical window (2008)

A vacuum sealed package with an optical window is a useful diagnostic tool for MEMS devices as well as a critical component of optical devices, such as imaging bolometers, scanning mirrors and variable wavelength filters. In either of these applications, the package must meet a number of stringent requirements. It cannot contaminate devices by either outgassing or shedding particulates. The window must be optically flat to allow devices to be observed or measured with interferometric tools, when the package is used as a diagnostic tool. When it serves as an integral part of an optical MEMS device, the window must also have the requisite transmissibility over the device's operating wavelength range. The vacuum level in many applications can also be quite challenging to achieve. Typically, pressures less than a few millitorr are necessary to prevent gas damping from limiting attainable Q values. Packages utilized for diagnostic purposes are often subjected to harsh environmental testing to evaluate how MEMS devices respond to mechanical shock, vibration, or thermal shock. Consequently, package robustness, particularly the glass to package seal integrity, is an important design element. We have successfully used a sputtered composite structure of gold over platinum over titanium to fabricate a seal ring on the window. The window is attached to a leadless ceramic chip carrier package by soldering with a 50 microns thick eutectic gold-tin preform. The sealing process is to load package assemblies, preforms and windows into a high vacuum system, degas them, raise the temperature of all components to 325degC, bring them into contact, and cool. We have used finite element analysis to optimize the seal geometry as a function of CTE mismatch, solder material, and window material to meet environmental requirements and optical flatness specifications. We have validated these FEM calculations by subjecting sealed packages to mechanical shock and helium leak testing. The optical flatness of windows was evaluated by direct optical interferometry measurements and high resolution measurements on sealed MEMS devices. The gas permeability of sealed packages was evaluated by measuring the Q of resonant devices over a period of several months. This fundamental understanding of window design, validated by experimental testing, extends our MEMS packaging capability to support the needs of both diagnostic investigations and optical device packaging.
Squeezed state generation in photonic crystal microcavities (2008)

The feasibility of using a parametric down-conversion process to generate squeezed electromagnetic states in three dimensional photonic crystal microcavity structures is investigated for the first time. The spectrum of the squeezed light is theoretically calculated by using an open cavity quantum mechanical formalism. The cavity communicates with two main channels, which model vertical radiation losses and coupling into a single-mode waveguide respectively. The amount of squeezing is determined by the correlation functions relating the field quadratures of light coupled into the waveguide. All of the relevant model parameters are realistically estimated for structures made in Al0.3Ga0.7As, using finite-difference time-domain simulations. Squeezing up to approximately 30% below the shot noise level is predicted for 10 mW average power, 80 MHz repetition, 500 ps excitation pulses using in a [111] oriented wafer.
NIST cold neutron research facility. [NIST (National Institute of Standards and Technology)] (1993)

The Cold Neutron Research Facility (CNRF) at the National Institute of Standards and Technology (NIST) Research Reactor (NBSR) is now coming on line, with the first seven experimental stations operational, and more stations scheduled to be installed during 1992. The present article provides an introduction to the facility, and to other articles in the current issue that give more details on some of the research opportunities that the facility will bring to NIST.
Giving light yet another new twist (2009)

Metamaterials can be designed to rotate light as it passes through them. If the effect is strong enough, it can lead to the material having a negative index of refraction and light bouncing around very differently than expected.
CellAnimation: an open source MATLAB framework for microscopy assays (2011)

Supplementary data available at Bioinformatics online.
An Integrated Raman Spectroscopy and Mass Spectrometry Platform to Study Single-Cell Drug Uptake, Metabolism, and Effects (2020)

Cells are known to be inherently heterogeneous in their responses to drugs. Therefore, it is essential that single-cell heterogeneity is accounted for in drug discovery studies. This can be achieved by accurately measuring the plethora of cellular interactions between a cell and drug at the single-cell level (i.e., drug uptake, metabolism, and effect). This paper describes a single-cell Raman spectroscopy and mass spectrometry (MS) platform to monitor metabolic changes of cells in response to drugs. Using this platform, metabolic changes in response to the drug can be measured by Raman spectroscopy, while the drug and its metabolite can be quantified using mass spectrometry in the same cell. The results suggest that it is possible to access information about drug uptake, metabolism, and response at a single-cell level.
Atomic Layer Deposition of Iridium Thin Films Using Sequential Oxygen and Hydrogen Pulses (2016)

Atomic layer deposition (ALD) is an advanced thin-film deposition method based on self-limiting surface reactions that allows for the controlled deposition of conformal, high-quality thin films of various materials. In this study, we aimed to explore how modifying the deposition chemistry affects the growth and properties of iridium films. We demonstrated a new ALD process using sequential pulses of iridium acetylacetonate [Ir(acac)3], oxygen (O2), and hydrogen (H2) and compared this to the established Ir(acac)3 + O2 process in the wide temperature range of 200–350 °C. A reaction scheme is proposed to explain how both oxygen and hydrogen affect the film growth. Comprehensive information on film properties was obtained for both processes. In particular, the strong (111) texture seen in this study has not been reported before for ALD iridium films. Changes in film properties, especially lowered resistivity, stronger (111) texture, and faster nucleation compared to the Ir(acac)3 + O2 process, should motivate further studies on O2 + H2 processes of platinum metals.
Correlated observation error models for assimilating all-sky infrared radiances (2019)

Abstract. The benefit of hyperspectral infrared sounders to weather forecasting has been improved with the representation of inter-channel correlations in the observation error model. A further step would be to assimilate these observations in all-sky conditions. However, in cloudy skies, observation errors exhibit much stronger inter-channel correlations, as well as much larger variances, compared to clear-sky conditions. An observation error model is developed to represent these effects, building from the symmetric error models developed for all-sky microwave assimilation. The combination of variational quality control with correlated errors is also introduced. The new error model is tested in all-sky assimilation of seven water vapour sounding channels from the Infrared Atmospheric Sounding Interferometer (IASI). However, its initial formulation degrades both tropospheric and stratospheric analyses. To explain this, the eigendeparture and eigenjacobian are introduced as a way of understanding the effect of correlated observation errors in data assimilation. The trailing eigenvalues can be problematic because they strongly amplify high-order harmonic combinations of the water vapour channels, which could have at least three consequences. First, if there are small inter-channel biases, these can be greatly amplified. Second, the trailing eigenjacobians map onto features resembling gravity waves that the data assimilation may not be able to handle. Finally, these harmonic combinations can amplify trace sensitivities, for example, revealing a strong upper stratospheric sensitivity over high cloud in what are usually mid- to upper-tropospheric water vapour channels. A likely explanation is the sensitivity to gravity wave features that are present in the observations but hard for the data assimilation to handle. After reducing the sensitivity to the trailing eigenjacobians, the new error covariance matrix gives good results in all-sky infrared assimilation.
Identification and characterization of a new gene from <i>Variovorax paradoxus</i> Iso1 encoding <i>N</i>‐acyl‐<scp>d</scp>‐amino acid amidohydrolase responsible for <scp>d</scp>‐amino acid production (2002)

An N-acyl-d-amino acid amidohydrolase (N-D-AAase) was identified in cell extracts of a strain, Iso1, isolated from an environment containing N-acetyl-d-methionine. The bacterium was classified as Variovorax paradoxus by phylogenetic analysis. The gene was cloned and sequenced. The gene consisted of a 1467-bp ORF encoding a polypeptide of 488 amino acids. The V. paradoxusN-D-AAase showed significant amino acid similarity to the N-acyl-d-amino acid amidohydrolases of the two eubacteria Alcaligenes xylosoxydans A-6 (44-56% identity), Alcaligenes facelis DA1 (54% identity) and the hyperthermophilic archaeon Pyrococcus abyssi (42% identity). After over-expression of the N-D-AAase protein in Escherichia coli, the enzyme was purified by multistep chromatography. The native molecular mass was 52.8 kDa, which agreed with the predicted molecular mass of 52 798 Da and the enzyme appeared to be a monomer protein by gel-filtration chromatography. A homogenous protein with a specific activity of 516 U.mg-1 was finally obtained. After peptide sequencing by LC/MS/MS, the results were in agreement with the deduced amino acid sequence of the N-D-AAase. The pI of the enzyme was 5.12 and it had an optimal pH and temperature of 7.5 and 50 degrees C, respectively. After 30 min heat treatment at 45 degrees C, between pH 6 and pH 8, 80% activity remained. The N-D-AAase had higher hydrolysing activity against N-acetyl-d-amino acid derivates containing d-methionine, d-leucine and d-alanine and against N-chloroacetyl-d-phenylalanine. Importantly, the enzyme does not act on the N-acetyl-l-amino acid derivatives. The enzyme was inhibited by chelating agents and certain metal ions, but was activated by 1 mm of Co2+ and Mg2+. Thus, the N-D-AAase from V. paradoxus can be considered a chiral specific and metal-dependent enzyme.
Advantages of low voltage applications and issues to be solved in SOI technology [DRAMs] (2002)

With low voltage applications as the main objective, SOI technology has made rapid and substantial progress in recent years. This paper describes the current status of SOI technology with emphasis on analysis of dynamic retention characteristics in low voltage DRAMs, countermeasures regarding the floating-body effect in low voltage region, and reliability issues in state-of-the-art SOI substrate technology.
Can RF Help CMOS Processors? [Topics in Circuits for Communications] (2007)

Digital circuits implemented in CMOS technology have been the workhorses of high performance computer processors for more than a decade, following Moore's law with exponentially increasing integration and performance. Driven by lower cost, increasing performance, and mixed-signal benefits, CMOS technology also has found increasing use in analog, and more recently, RF applications. Now, with transistor performance still improving, wires are becoming the limiting factor for speed and performance by imposing limits on communication bandwidth and latency between processing cores and memories, both off- and on-chip. Communication and circuit techniques, developed mainly for narrow band-wireless RF communication can help increase the wired communication speed in digital systems. This approach, dubbed RF Interconnect (RF-I), picks up speed for on-board and on-chip applications, changing the communication paradigm from the old parallel unidirectional time-shared bus to new transmission lines enabling reconfigurable communication using both frequency and code division multiple access techniques.
TWEAK is expressed at the cell surface of monocytes during multiple sclerosis (2008)

The TNF superfamily ligand, TNF-like weak inducer of apoptosis (TWEAK), regulates cellular responses ranging from proliferation to cell death in a manner highly dependent on the cell type and the microenvironmental context. We have shown previously that treatment of experimental autoimmune encephalomyelitis mice after the priming phase with neutralizing anti-TWEAK antibodies results in a reduction in the severity of the disease and leukocyte infiltration. To further characterize TWEAK/fibroblast growth factor-inducible 14-kDa protein (Fn14) involvement during multiple sclerosis (MS), we evaluated in MS patients and controls: TWEAK and Fn14 expression on PBMC and soluble TWEAK concentration in serum and cerebrospinal fluid (CSF). Thirty-six consecutive patients were enrolled, including 11 patients with relapsing-remitting MS, 11 with a clinical isolated syndrome suggestive of MS (CISSMS), and 14 controls with non-MS diseases. Intracellular TWEAK could be observed in lymphocytes and/or monocytes in all groups of patients. None of the 36 patients displayed TWEAK expression at the cell surface of lymphocytes. In contrast, 12 out of the 36 patients were positive for membrane TWEAK expression on their monocytes. Among these patients, eight were from the CISSMS group. Fn14 was not detected in PBMC. The soluble form of TWEAK is detectable in serum and CSF of patients, and TWEAK concentrations were not statistically different between the disease groups. We demonstrated for the first time that TWEAK is expressed at the cell surface of monocytes during MS, especially in the CISSMS group. Our results support the proposal that TWEAK could be a target for antibody therapy in MS.
Power Optimization of Ultrasonic Friction-Modulation Tactile Interfaces (2014)

Ultrasonic friction-modulation devices provide rich tactile sensation on flat surfaces and have the potential to restore tangibility to touchscreens. To date, their adoption into consumer electronics has been in part limited by relatively high power consumption, incompatible with the requirements of battery-powered devices. This paper introduces a method that optimizes the energy efficiency and performance of this class of devices. It considers optimal energy transfer to the impedance provided by the finger interacting with the surface. Constitutive equations are determined from the mode shape of the interface and the piezoelectric coupling of the actuator. The optimization procedure employs a lumped parameter model to simplify the treatment of the problem. Examples and an experimental study show the evolution of the optimal design as a function of the impedance of the finger.
Epitaxial Growth of Ge on Si(100) and Si(111) Surfaces (1993)

The geometrical and electronic structure of epitaxially grown Ge on Si(100) and Si(111) surfaces has been studied by scanning tunneling microscopy. Since Ge atoms could be distinguished from Si atoms by scanning tunneling spectroscopy and voltage dependent STM images, the growth mode of the added layer could be studied. On the (100) surface with a (21) reconstruction, Ge overlayer grow preferentially on the B type step edges at 720K. On the (111) surface, Ge overlayer also grow on the step edges with (77) and (55) structure depending on their coverage and annealing temperature.
Antagonistic Effects of Hydrogen Peroxide and Glutathione on Acclimation to Excess Excitation Energy in Arabidopsis (2000)

The redox status of the quinone B (Q(B)) and plastoquinone (PQ) pools plays a key role in the cellular and systemic signalling processes that control acclimatory responses in plants. In this study, we demonstrate the effects of hydrogen peroxide and glutathione on acclimatory responses controlled by redox events in the proximity of the Q(B)-PQ pools. Our results suggest that the chloroplast is a sink for H2O2 and that, paradoxically, high concentrations of H2O2 in the chloroplast protect the photosynthetic apparatus and the plant cell from photoinhibition and photooxidative damage. Excess glutathione, however, caused an effect antagonistic to that observed for high H2O2. An explanation of this apparent paradox and a hypothetical redox-signalling model are suggested.
Differential effects of short affinity tags on the crystallization of<i>Pyrococcus furiosus</i>maltodextrin-binding protein (2002)

Pyrococcus furiosus maltodextrin-binding protein readily forms large orthorhombic crystals that diffract to high resolution. This protein was used as a model system to investigate the influence of five short affinity tags (His(6), Arg(5), Strep tag II, FLAG tag and the biotin acceptor peptide) on the formation of protein crystals and their ability to diffract X-rays. The results indicate that the amino-acid sequence of the tag can have a profound effect on both of these parameters. Consequently, the ability to obtain diffracting crystals of a particular protein may depend as much on which affinity tag is selected as it does on whether an affinity tag is used at all.
A Crystal Structure of the Complex Between Human Complement Receptor 2 and Its Ligand C3d (2011)

The interaction of complement receptor 2 (CR2)--which is present on B cells and follicular dendritic cells--with its antigen-bound ligand C3d results in an enhanced antibody response, thus providing an important link between the innate and adaptive immune systems. Although a cocrystal structure of a complex between C3d and the ligand-binding domains of CR2 has been published, several aspects of this structure, including the position in C3d of the binding interface, remained controversial because of disagreement with biochemical data. We now report a cocrystal structure of a CR2(SCR1-2):C3d complex at 3.2 angstrom resolution in which the interaction interfaces differ markedly from the previously published structure and are consistent with the biochemical data. It is likely that, in the previous structure, the interaction was influenced by the presence of zinc acetate additive in the crystallization buffer, leading to a nonphysiological complex. Detailed knowledge of the binding interface now at hand gives the potential to exploit the interaction in vaccine design or in therapeutics directed against autoreactive B cells.
CAM and NK Cells (2004)

It is believed that tumor development, outgrowth and metastasis are under the surveillance of the immune system. Although both innate and acquired immune systems play roles, innate immunity is the spearhead against tumors. Recent studies have revealed the critical role of natural killer (NK) cells in immune surveillance and that NK cell activity is considerably influenced by various agents, such as environmental factors, stress, foods and drugs. Some of these NK cell stimulants have been used in complementary and alternative medicine (CAM) since ancient times. Therefore, the value of CAM should be re-evaluated from this point of view. In this review, we overview the intimate correlation between NK cell functions and CAM agents, and discuss possible underlying mechanisms mediating this. In particular, neuro-immune crosstalk and receptors for CAM agents are the most important and interesting candidates for such mechanisms.
Elevated fasting plasma level of islet amyloid polypeptide (IAPP) in chronic alcoholic pancreatitis (CAP). (2003)

Those findings suggest that islet amyloid polypeptide may play a role in the pathogenesis of chronic alcoholic pancreatitis. In addition increased plasma islet amyloid polypeptide level may prove useful as an indicator of an early phase of pancreatic endocrine function impairment and severe parenchymal damage in chronic pancreatitis.