gebhart/patrepeval huggingface dataset:
The Contribution of Blood Lactate to Brain Energy Metabolism in Humans Measured by Dynamic<sup>13</sup>C Nuclear Magnetic Resonance Spectroscopy (2010)

To determine whether plasma lactate can be a significant fuel for human brain energy metabolism, infusions of [3-(13)C]lactate and (1)H-(13)C polarization transfer spectroscopy were used to detect the entry and utilization of lactate. During the 2 h infusion study, (13)C incorporation in the amino acid pools of glutamate and glutamine were measured with a 5 min time resolution. With a plasma concentration ([Lac](P)) being in the 0.8-2.8 mmol/L range, the tissue lactate concentration ([Lac](B)) was assessed as well as the fractional contribution of lactate to brain energy metabolism (CMRlac). From the measured relationship between unidirectional lactate influx (V(in)) and plasma and brain lactate concentrations, lactate transport constants were calculated using a reversible Michaelis-Menten model. The results show that (1) in the physiological range, plasma lactate unidirectional transport (V(in)) and concentration in tissue increase close to linearly with the lactate concentration in plasma; (2) the maximum potential contribution of plasma lactate to brain metabolism is 10% under basal plasma lactate conditions of ∼1.0 mmol/L and as much as 60% at supraphysiological plasma lactate concentrations when the transporters are saturated; (3) the half-saturation constant K(T) is 5.1 ± 2.7 mmol/L and V(MAX) is 0.40 ± 0.13 μmol · g(-1) · min(-1) (68% confidence interval); and (4) the majority of plasma lactate is metabolized in neurons similar to glucose.
Influence of the polyamines spermine and spermidine on yeast tRNAphe as revealed from its imino proton NMR spectrum (1986)

A comparison of imino proton NMR spectra of yeast tRNAPhe recorded at various solution conditions indicates, that polyamines have a limited effect on the structure of this tRNA molecule. Polyamines are found to catalyse the solvent exchange of several imino protons in yeast tRNAPhe not only of non hydrogen bonded imino protons, but also of imino protons of the GU and of some AU and tertiary base pairs. It is concluded that at low levels of catalysing components the exchange rates of the latter protons are not determined by the base pair lifetime. In the presence of high levels of spermidine the solvent exchange rates of imino protons of several base pairs in the molecule were assessed as a function of the temperature. Apparent activation energies derived from these rates were found to be less than 80 kJ/mol, which is indicative for (transient) independent opening of the corresponding base pairs. In the acceptor helix the GU base pair acts as a dynamic dislocation. The AU base pairs at one side of the GU base pair exhibit faster transient opening than the GC base pairs on the other side of this wobble pair. The base pairs m2GC10 and GC11 from the D stem and GC28 from the anticodon stem show relatively slow opening up to high temperatures. Model studies suggest that 1-methyladenosine, an element of tRNA itself, catalyses imino proton solvent exchange in a way similar to polyamines.
Assessing energy functions for flexible docking (1998)

A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that a correctly docked structure can be identified quickly. We assess the selectivity and efficiency of a broad spectrum of energy functions, derived from systematic modifications of the CHARMM param19/toph19 energy function. In particular, we examine the effects of the dielectric constant, the solvation model, the scaling of surface charges, reduction of van der Waals repulsion, and nonbonded cutoffs. Based on an assessment of the energy functions for the docking of five different ligand–receptor complexes, we find that selective energy functions include a variety of distance-dependent dielectric models together with truncation of the nonbonded interactions at 8 Å. We evaluate the docking efficiency, the mean number of docked structures per unit of time, of the more selective energy functions, using a simulated annealing molecular dynamics protocol. The largest improvements in efficiency come from a reduction of van der Waals repulsion and a reduction of surface charges. We note that the most selective potential is quite inefficient, although a hierarchical approach can be employed to take advantage of both selective and efficient energy functions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1612–1622, 1998
On-site fluorine chamber cleaning for semiconductor thin-film processes: Shorter cycle times, lower greenhouse gas emissions, and lower power requirements (2016)

Regular removal of thin-film deposits in chemical vapor deposition (CVD) reaction chambers is an important requirement in semiconductor manufacturing technology. Most often plasma etching using fluorine-containing gases like sulfur hexafluoride SF6 and nitrogen trifluoride NF3 is widely applied, because of the efficient reactions of fluorine radicals with the residues and the high volatility of the resulting fluoride products. Concerns have been expressed, however, about the global warming impact of such gases: SF6 and NF3 exhibit global warming potentials of 22,600 and 17,200 times that of CO2 as measured over 100 years [1] [2]. While previous work has shown that NF3 may be preferred to SF6 because of a gas utilization near 100% for small area scale reactors [3], significantly lower gas usage was measured for commercial reactors. Weiss et al. estimate that 16% of the global production of NF3 is released in the atmosphere, with atmospheric concentration rising 11% per year [4]. Alternative chemical cleaning using environmentally friendly processes exist, however. Molecular fluorine has been already used for chamber cleaning in other applications such as semiconductor thermal oxide / nitride, atomic layer deposition (ALD), and plasma enhanced chemical vapor deposition (PeCVD), and LCD display manufacturing. As a non-polar gas, it has no global warming potential [5]. Besides environmental advantages, molecular fluorine offers process and consumption advantages over other cleaning gases. In particular, F2 requires low energy to be dissociated. While 79.5 kJ are sufficient to obtain 1 mole of atomic fluorine from F2, 281 kJ and 329 kJ are necessary from NF3 and SF6 respectively. Thus much more F2 can be activated per unit time, resulting in a faster clean. Another advantage is the gain in mass efficiency. Because the nitrogen atoms from NF3 do not contribute to the cleaning process, molecular fluorine needs 20% less mass to supply the same amount of atomic fluorine radicals as NF3. The absence of the spectator nitrogen atom will be shown to also reduce deleterious temperature effects at the remote plasma source (RPS) as well as the process chamber, resulting in shorter overall clean cycles due to stabilized cleaning temperatures, and significant energy savings. Here we report an effective cleaning process of various process chambers using a variety of deposition techniques and chemistries - PECVD for amorphous silicon; ALD for ultra-low temperature silicon oxide, and thermal diffusion for doped poly-silicon. Fluorine cleaning performances are compared to NF3. Several parameters, such as clean rate, temperature rise at the remote plasma source and chamber during cleaning, and power consumption, are measured. We illustrate with data from various production chambers and explain the underlying thermodynamics and kinetics. Finally, process benefits of faster cleaning times, faster cycle times, temperature stability, and lower material use are demonstrated.
Low Temperature Electrochemical Synthesis and Dielectric Characterization of Barium Titanate Films Using Nonalkali Electrolytes (1995)

Polycrystalline thin films of approximately 1 μm thickness have been synthesized on Ti substrates by an electrochemical process using nonalkali electrolytes, at temperatures as low as 55°C. The effect of various processing parameters, such as solution chemistry, atmosphere, quality of substrate surface, applied voltage, temperature, and reaction time have been discussed. Film thickness and uniformity increase with reaction time up to 24 h. The quantity of total electric charge passed through the electrolytic cell is found to govern the film thickness and uniformity. Dielectric characteristics of the as‐prepared and heat‐treated films have also been reported. Use of tetraethylammonium hydroxide, a nonalkali base reagent to adjust solution pH, has resulted in films having improved dielectric properties as opposed to the films prepared with alkali metal bases such as . Heat‐treatment further improves the dielectric properties through a phase transition to the thermodynamically stable tetragonal phase from the as‐prepared pseudo‐cubic phase as confirmed by the x‐ray diffraction data.
Velocity profile measurement in oil/gas flows (1995)

This paper describes a capacitance tomography system for imaging oil/gas flows in circular pipes. The system is capable of computing the distribution of each component of a flow at two adjacent cross-sections in real-time. These two images are then cross-correlated off-line to obtain velocity profile measurements of the gaseous component. Extensive tests have been performed on a 3 inch diameter, two-phase flow loop; superficial oil velocities ranged from 0.1 to 0.8 m/s, and superficial gas velocities ranged from 0.05 to 0.5 m/s. Some typical component distribution and velocity profile measurements are presented. (6 pages)
Direct downstream targets of proneural activators in the imaginal disc include genes involved in lateral inhibitory signaling. (1994)

In Drosophila imaginal discs, the spatially restricted activities of the achaete (ac) and scute (sc) proteins, which are transcriptional activators of the basic-helix-loop-helix class, define proneural clusters (PNCs) of potential sensory organ precursor (SOP) cells. Here, we report the identification of several genes that are direct downstream targets of ac-sc activation, as judged by the following criteria. The genes are expressed in the PNCs of the wing imaginal disc in an ac-sc-dependent manner; the proximal promoter regions of all of these genes contain one or two high-affinity ac-sc binding sites, which define the novel consensus GCAGGTG(T/G)NNNYY; where tested, these binding sites are required in vivo for PNC expression of promoter-reporter fusion genes. Interestingly, these ac-sc target genes, including Bearded, Enhancer of split m7, Enhancer of split m8, and scabrous, are all known or believed to function in the selection of a single SOP from each PNC, a process mediated by inhibitory cell-cell interactions. Thus, one of the earliest steps in adult peripheral neurogenesis is the direct activation by proneural proteins of genes involved in restricting the expression of the SOP cell fate.
Electro-Optic Frequency Beam Splitters and Tritters for High-Fidelity Photonic Quantum Information Processing (2018)

We report the experimental realization of high-fidelity photonic quantum gates for frequency-encoded qubits and qutrits based on electro-optic modulation and Fourier-transform pulse shaping. Our frequency version of the Hadamard gate offers near-unity fidelity (0.99998±0.00003), requires only a single microwave drive tone for near-ideal performance, functions across the entire C band (1530-1570 nm), and can operate concurrently on multiple qubits spaced as tightly as four frequency modes apart, with no observable degradation in the fidelity. For qutrits, we implement a 3×3 extension of the Hadamard gate: the balanced tritter. This tritter-the first ever demonstrated for frequency modes-attains fidelity 0.9989±0.0004. These gates represent important building blocks toward scalable, high-fidelity quantum information processing based on frequency encoding.
Uncooled infrared detectors based on MEMS technologies (2007)

Uncooled infrared (IR) detectors are gaining importance over the HgCdTe based IR photon detectors because of their room temperature operation, low power consumption and smaller in size. Silicon micromachining has made it possible to make micro bolometer base IR detector. In a focal plane array (FPA), there is a two dimensional assembly of bolometers and each bolometer acts as a thermally sensitive pixel. The detector element consists of thermal sensitive material suspended above the readout electronics having an air gap of 2 micron and supported by thermally isolated hinges. The most important task is to design the structure of the sensor having the lowest possible thermal conductance. The characterization gives that thermal conductance and thermal mass are the deciding factors for the higher responsivity and detectivity. This paper presents a modified design based on thermal characterization of the membranes of micro bolometer. Based on our theoretical analysis, the required thermal conductance can be achieved even with short hinges. This can be done by reducing the thermal conductivity of the material of hinges. Our experimental investigations are in good agreement with this concept. This will also enhance the fill factor of the two dimensional IR array.
A Two-Tier Coordination System against DDoS Attacks (2013)

We present a two-tier coordination approach for detecting and mitigating DDoS attacks. The first tier traffic filter (1st-TF) filters suspicious traffic for possible flooding. This is achieved by using proactive tests to identify and isolate the malicious traffic. The second tier traffic filter (2nd-TF), which is deployed on network routers, performs online monitoring on queue length status with RED/Droptail mechanism for any incoming traffic. The simulation shows that the scheme can detect attacks accurately and effectively.
Direct measurement of the absorption coefficient for the <i>P</i>1(7) transition in HF (1975)

The absorption coefficient for the P1(7) transition in pure HF gas has been measured using resonant radiation from an HF laser. It was found that the Doppler-broadened absorption coefficient is equal to the pressure-broadened absorption coefficient at a pressure of 16 Torr.
Asymmetric reductinon of carbonyl compounds by yeast. II. Preparation of optically active α- and β-hydroxy carboxylic acid derivatives (1976)

a- and ß-Keto esters and amides are readily reduced by an actively fermenting mutant of Saccharomyces cerevisiae and produce optically active a- and ß-hydroxy esters and amides in moderate yields. Typically, methyl 2-oxo-2-phenylacetate gave methyl (R)-(-)-2-hydroxy- 2-phenyl- acetate; 2-oxo-2-phenylacetamide gave (R)-(-)-2-hydroxy-2- phenylacetamide; ethyl benzoylacetate gave ethyl (S)-(-)-3-hydroxy-3- phenylpropionate, and ethyl 2-oxocyclohexanecarboxylate gave ethyl (1R,2S)-(+)-2-hydroxycyclohexanecarboxylate. In each case, the product obtained was optically pure. However, the reduction of ethyl pyruvate to ethyl lactate produced partially racemized products.
Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination (2016)

We identified genes and pathways that explain in part, and are associated with, neutralizing antibody titers after measles vaccination. This new knowledge could assist in the identification of biomarkers and predictive signatures of protective immunity that may be useful in the design of new vaccine candidates and in clinical studies.
<title>Characteristics And Uses Of X-Radiation From Laser-Heated Plasmas</title> (1984)

Multi-million degree plasmas produced at the foci of powerful lasers efficiently emit short intense pulses of soft x-rays. Recent x-ray measurements obtained with laser-repetition rates up to 10 Hz are reviewed. High average-power solid and gas laser systems with powers sufficient for x-ray generation are now being designed. New laser-plasma x-radiation sources should find extensive use in research and industry. Demonstrated and expected uses of x-rays from laser-heated plasmas are summarized.
How Efficient; Is Current; Infrastructure Spending and Pricing? (1990)

Congested highways and airports, collapsing bridges, deteriorating roads, periodic water shortages, and suspect waste disposal facilities bear silent witness that the infrastructure of our nation, currently valued at close to $1 trillion, is inadequate. To shore up America’s foundations, many economists and policy analysts have urged the federal government to increase spending substantially. The urgency of the problem, however, does not preclude the need to ask whether the current use of facilities is efficient, whether choices about how current facilities are used are possible, and how current use will affect the efficiency of new facilities. In fact, surprisingly large benefits are to be gained from making efficient use of our current infrastructure by pricing it and investing in it efficiently. Efficient pricing and investment will reduce the need for massive public investment and will prevent the recurrence of infrastructure problems. The primary reason why the current facilities are gravely deficient is that they are priced in ways that do not reflect economic costs and designed in ways that result in higher life-cycle costs of use. In their anxiety to address the infrastructure problem, policymakers are pushing policies that, if adopted, would indefinitely foreclose consideration of efficient pricing and investment. Congressional renewal of the gas tax in 1991, for example, would perpetuate a method of *Senior Fellow, The Brookings Institution. This paper draws heavily upon and
A P1-based physical map of the Drosophila euchromatic genome. (1996)

A PCR-based sequence-tagged site (STS) content mapping strategy has been used to generate a physical map with 90% coverage of the 120-Mb euchromatic portion of the Drosophila genome. To facilitate map completion, the bulk of the STS markers was chosen in a nonrandom fashion. To ensure that all contigs were localized in relation to each other and the genome, these contig-building procedures were performed in conjunction with a large-scale in situ hybridization analysis of randomly selected clones from a Drosophila genomic library that had been generated in a P1 cloning vector. To date, the map consists of 649 contigs with an STS localized on average every 50 kb. This is the first whole genome that has been mapped based on a library constructed with large inserts in a vector that is maintained in Escherichia coli as a single-copy plasmid.
A Multicenter Analysis of Axial Femorotibial Rotation after Total Knee Arthroplasty (2004)

A multicenter analysis was done to determine in vivo femorotibial axial rotation magnitudes and patterns in 1,027 knees (normal knees, nonimplanted ACL-deficient knees, and multiple designs of total knee arthroplasty). All knees were analyzed using fluoroscopy and a three-dimensional computer model-fitting technique during a deep knee bend and/or gait. Normal knees showed 16.5 degrees and 5.7 degrees of internal tibial rotation during a deep knee bend and gait, respectively. Rotation magnitudes and the percent having normal axial rotation patterns decreased in all total knee arthroplasty groups during a deep knee bend. During gait, all knee arthroplasty groups had similar rotational patterns (limited magnitudes). Average axial rotational magnitudes in gait and a deep knee bend were similar among major implant categories (ie, fixed-bearing versus mobile-bearing, etc). Average values in normal knees and ACL-retaining total knee arthroplasty patients (16.5 degrees and 8.1 degrees , respectively) were higher than in groups in which the ACL was absent (< 4.0 degrees ). All total knee arthroplasty groups had at least 19% of patients have a reverse axial rotational pattern during a deep knee bend and at least 31% during gait. Normal axial rotation patterns are essential for good patellar tracking, reduction of patellofemoral shear forces, and maximization of knee flexion.
A microfluidic model for organ-specific extravasation of circulating tumor cells (2014)

Circulating tumor cells (CTCs) are the principal vehicle for the spread of non-hematologic cancer disease from a primary tumor, involving extravasation of CTCs across blood vessel walls, to form secondary tumors in remote organs. Herein, a polydimethylsiloxane-based microfluidic system is developed and characterized for in vitro systematic studies of organ-specific extravasation of CTCs. The system recapitulates the two major aspects of the in vivo extravasation microenvironment: local signaling chemokine gradients in a vessel with an endothelial monolayer. The parameters controlling the locally stable chemokine gradients, flow rate, and initial chemokine concentration are investigated experimentally and numerically. The microchannel surface treatment effect on the confluency and adhesion of the endothelial monolayer under applied shear flow has also been characterized experimentally. Further, the conditions for driving a suspension of CTCs through the microfluidic system are discussed while simultaneously maintaining both the local chemokine gradients and the confluent endothelial monolayer. Finally, the microfluidic system is utilized to demonstrate extravasation of MDA-MB-231 cancer cells in the presence of CXCL12 chemokine gradients. Consistent with the hypothesis of organ-specific extravasation, control experiments are presented to substantiate the observation that the MDA-MB-231 cell migration is attributed to chemotaxis rather than a random process.
Nrf1 and Nrf2 positively and c-Fos and Fra1 negatively regulate the human antioxidant response element-mediated expression of NAD(P)H:quinone oxidoreductase <sub>1</sub>  gene (1996)

Twenty-four base pairs of the human antioxidant response element (hARE) are required for high basal transcription of the NAD(P)H:quinone oxidoreductase1 (NQO1) gene and its induction in response to xenobiotics and antioxidants. hARE is a unique cis-element that contains one perfect and one imperfect AP1 element arranged as inverse repeats separated by 3 bp, followed by a "GC" box. We report here that Jun, Fos, Fra, and Nrf nuclear transcription factors bind to the hARE. Overexpression of cDNA derived combinations of the nuclear proteins Jun and Fos or Jun and Fra1 repressed hARE-mediated chloramphenicol acetyltransferase (CAT) gene expression in transfected human hepatoblastoma (Hep-G2) cells. Further experiments suggested that this repression was due to overexpression of c-Fos and Fra1, but not due to Jun proteins. The Jun (c-Jun, Jun-B, and Jun-D) proteins in all the possible combinations were more or less ineffective in repression or upregulation of hARE-mediated gene expression. Interestingly, overexpression of Nrf1 and Nrf2 individually in Hep-G2 and monkey kidney (COS1) cells significantly increased CAT gene expression from reporter plasmid hARE-thymidine kinase-CAT in transfected cells that were inducible by beta-naphthoflavone and teri-butyl hydroquinone. These results indicated that hARE-mediated expression of the NQO1 gene and its induction by xenobiotics and antioxidants are mediated by Nrf1 and Nrf2. The hARE-mediated basal expression, however, is repressed by overexpression of c-Fos and Fra1.