gebhart/patrepeval huggingface dataset:
Real-time monitoring of nucleic acid ligation in homogenous solutions using molecular beacons (2003)

Nucleic acids ligation is a vital process in the repair, replication and recombination of nucleic acids. Traditionally, it is assayed by denatured gel electrophoresis and autoradiography, which are not sensitive, and are complex and discontinuous. Here we report a new approach for ligation monitoring using molecular beacon DNA probes. The molecular beacon, designed in such a way that its sequence is complementary with the product of the ligation process, is used to monitor the nucleic acid ligation in a homogeneous solution and in real-time. Our method is fast and simple. We are able to study nucleic acids ligation kinetics conveniently and to determine the activity of DNA ligase accurately. We have studied different factors that influence DNA ligation catalyzed by T4 DNA ligase. The major advantages of our method are its ultrasensitivity, excellent specificity, convenience and real-time monitoring in homogeneous solution. This method will be widely useful for studying nucleic acids ligation process and other nucleic acid interactions.
Improving brain–machine interface performance by decoding intended future movements (2013)

This study is the first to characterize the effects of control delays in a BMI and to show that decoding the user's future intent can compensate for the negative effect of control delay on BMI performance.
All-trans-retinyl Esters Are the Substrates for Isomerization in the Vertebrate Visual Cycle (2003)

The identification of the critical enzyme(s) that carries out the trans to cis isomerization producing 11-cis-retinol during the operation of the visual cycle remains elusive. Confusion exists in the literature as to the exact nature of the isomerization substrate. At issue is whether it is an all-trans-retinyl ester or all-trans-retinol (vitamin A). As both putative substrates interconvert rapidly in retinal pigment epithelial membranes, the choice of substrate can be ambiguous. The two enzymes that effect interconversion of all-trans-retinol and all-trans-retinyl esters are lecithin retinol acyl transferase (LRAT) and retinyl ester hydrolase (REH). The retinyl ester or all-trans-retinol pools are radioactively labeled separately in the presence of inhibitors of LRAT and REH, effectively preventing their interconversion. Pulse-chase experiments unambiguously demonstrate that all-trans-retinyl esters, and not all-trans-retinol, are the precursors of 11-cis-retinol. When the all-trans-retinyl ester pool is radioactively labeled, the resulting 11-cis-retinol is labeled with the same specific activity as the precursor ester. The converse is true with vitamin A. These data unambiguously establish all-trans-retinyl esters as the precursors of 11-cis-retinol.
Liquid Transport and Colloidal Self Assembly in Thin Wetting Films Driven by Electric Fields. (2013)

KLEINERT, JAIRUS MATTHEW.Liquid Transport and Colloidal Self Assembly in Thin Wetting Films Driven by Electric Fields.(Under the direction of Dr
Façade: virtual storage devices with performance guarantees (2003)

High-end storage systems, such as those in large data centers, must service multiple independent workloa&amp;amp;. Workloa&amp;amp; often require predictable quality of service, deslite the fact that they have to compete with other rapidly-changing workloads for access to common storage resources. We present a novel approach to providing performance guarantees in this highly-volatile scenario, in an efficient and cost-effective way. Facade, a virtual store controller, sits between hosts and storage devices in the network, and throttles individual I/0 requests from multiple clients so that devices do not saturate. We implemented a prototype, and evaluated it using real workloads on an enterprise storage system. We also instantiated it to the particular case of emulating commercial disk arrays. Our results show that Facade satisfies performance objectives while making efficient use of the storage resources---even in the presence of of failures and bursty workloads with stringent performance requirements.
Limiting factors of room-temperature nonradiative photoluminescence lifetime in polar and nonpolar GaN studied by time-resolved photoluminescence and slow positron annihilation techniques (2005)

Room-temperature nonradiative lifetime (τnr) of the near-band-edge excitonic photoluminescence (PL) peak in {0001} polar, (112¯0), (11¯00), and (001) nonpolar GaN was shown to increase with the decrease in density or size of Ga vacancies (VGa) and with the decrease in gross density of point defects including complexes, leading to the increase in the PL intensity. As the edge threading dislocation density decreased, density or size of VGa tended to decrease and τnr tended to increase. However, there existed remarkable exceptions. The results indicate that nonradiative recombination process is governed not by single point defects, but by certain defects introduced with the incorporation of VGa, such as VGa-defect complexes.
Highly Alpha‐Selective Sialyl Phosphate Donors for Efficient Preparation of Natural Sialosides (2010)

Hubble, bubble, toil, and trouble: The use of a new sialyl phosphate donor allows the stereoselective, one-pot multicomponent synthesis of α-sialooligosaccharides (see scheme).
Mechanisms Underlying Burst and Regular Spiking Evoked by Dendritic Depolarization in Layer 5 Cortical Pyramidal Neurons (1999)

Apical dendrites of layer 5 pyramidal cells in a slice preparation of rat sensorimotor cortex were depolarized focally by long-lasting glutamate iontophoresis while recording intracellularly from their soma. In most cells the firing pattern evoked by the smallest dendritic depolarization that evoked spikes consisted of repetitive bursts of action potentials. During larger dendritic depolarizations initial burst firing was followed by regular spiking. As dendritic depolarization was increased further the duration (but not the firing rate) of the regular spiking increased, and the duration of burst firing decreased. Depolarization of the soma in most of the same cells evoked only regular spiking. When the dendrite was depolarized to a critical level below spike threshold, intrasomatic current pulses or excitatory postsynaptic potentials also triggered bursts instead of single spikes. The bursts were driven by a delayed depolarization (DD) that was triggered in an all-or-none manner along with the first Na+ spike of the burst. Somatic voltage-clamp experiments indicated that the action current underlying the DD was generated in the dendrite and was Ca2+ dependent. Thus the burst firing was caused by a Na+ spike-linked dendritic Ca2+ spike, a mechanism that was available only when the dendrite was adequately depolarized. Larger dendritic depolarization that evoked late, constant-frequency regular spiking also evoked a long-lasting, Ca2+-dependent action potential (a "plateau"). The duration of the plateau but not its amplitude was increased by stronger dendritic depolarization. Burst-generating dendritic Ca2+ spikes could not be elicited during this plateau. Thus plateau initiation was responsible for the termination of burst firing and the generation of the constant-frequency regular spiking. We conclude that somatic and dendritic depolarization can elicit quite different firing patterns in the same pyramidal neuron. The burst and regular spiking observed during dendritic depolarization are caused by two types of Ca2+-dependent dendritic action potentials. We discuss some functional implications of these observations.
Suppression of calcium-dependent membrane currents in human fibroblasts by replicative senescence and forced expression of a gene sequence encoding a putative calcium-binding protein. (1994)

Human diploid fibroblasts (HDFs) possess Ca(2+)-dependent membrane currents. These currents were suppressed in late-passage normal (senescent) HDFs and prematurely senescent HDFs derived from a subject with Werner syndrome (WS), compared with early-passage normal (young) HDFs. When young HDFs were microinjected with mRNA transcribed in vitro from a cDNA (WS3-10) which encodes a protein bearing a putative Ca(2+)-binding site and whose endogenous gene is overexpressed in senescent and WS HDFs, membrane currents fell to levels present in senescent and WS HDFs. Thus, both replicative senescence and forced expression of the WS3-10 gene sequence lead to suppression of Ca(2+)-dependent membrane currents, which suggests that a causal connection exists between these two processes.
GPU accelerated toolbox for real-time beam-shaping in multimode fibres (2014)

We present a GPU accelerated toolbox for shaping the light propagation through multimode fibre using a spatial light modulator (SLM). The light is modulated before being coupled to the proximal end of the fibre in order to achieve arbitrary light patterns at the distal end of the fibre. First, the toolbox optimises the acquisition time of the transformation matrix of the fibre by synchronous operation of CCD and SLM. Second, it uses the acquired transformation matrix retained within the GPU memory to design, in real-time, the desired holographic mask for on-the-fly modulation of the output light field. We demonstrate the functionality of the toolbox by acquiring the transformation matrix at the maximum refresh rate of the SLM - 204 Hz, and using it to display an on-demand oriented cube, at the distal end of the fibre. The user-controlled orientation of the cube and the corresponding holographic mask are obtained in 20 ms intervals. Deleterious interference effects between the neighbouring points are eliminated by incorporating an acousto-optic deflector (AOD) into the system. We remark that the usage of the toolbox is not limited to multimode fibres and can be readily used to acquire transformation matrix and implement beam-shaping in any other linear optical system.
WWOX, a novel WW domain-containing protein mapping to human chromosome 16q23.3-24.1, a region frequently affected in breast cancer. (2000)

Studies were conducted with the final goal of identifying genes of interest mapping to the chromosome region 16q23.3-24.1, an area commonly affected by allelic losses in breast cancer. To this end we generated a detailed physical map of the genomic region spanning between sequence-tagged site markers D16S518 and D16S516. To identify candidate genes, we used shotgun genomic sequencing as well as isolation and analysis of transcripts mapping to the area of interest. We identified and cloned a novel gene, the genomic structure of which spans the whole region of interest. We named this gene WWOX because it contains two WW domains coupled to a region with high homology to the short-chain dehydrogenase/reductase family of enzymes. The ORF of WWOX is 1245 bp long, encoding a 414-amino acid protein. This gene is composed of nine exons. We performed a mutation screening of WWOX exons in a panel of breast cancer lines, most of which are hemizygous for the 16q genomic region indicated. We found no evidence of mutations, thus indicating that WWOX is probably not a tumor suppressor gene. However, we observed that one case of homozygous deletion as well as two previously described translocation breakpoints map to intronic regions of this gene. We speculate that WWOX may span the yet uncharacterized common fragile site FRA16D region. In expression studies we found overexpression of WWOX in breast cancer cell lines when compared with normal breast cells and tissues. The highest normal expression of WWOX was observed in hormonally regulated tissues such as testis, ovary, and prostate. This expression pattern and the presence of a short-chain dehydrogenase/reductase domain and specific amino acid features suggest a role for WWOX in steroid metabolism. Interestingly, the presence of WW domains in the structure of WWOX indicate the likelihood that this protein physically interacts with other proteins. The unique features of WWOX and its possible association with cancer processes make it an interesting target for further investigation.
Biosynthesis of the Glycolipid Anchor in Lipoteichoic Acid of Staphylococcus aureus RN4220: Role of YpfP, the Diglucosyldiacylglycerol Synthase (2001)

In Staphylococcus aureus RN4220, lipoteichoic acid (LTA) is anchored in the membrane by a diglucosyldiacylglycerol moiety. The gene (ypfP) which encodes diglucosyldiacylglycerol synthase was recently cloned from Bacillus subtilis and expressed in Escherichia coli (P. Jorasch, F. P. Wolter, U. Zahringer, and E. Heinz, Mol. Microbiol. 29:419-430, 1998). To define the role of ypfP in this strain of S. aureus, a fragment of ypfP truncated from both ends was cloned into the thermosensitive replicon pVE6007 and used to inactivate ypfP. Chloramphenicol-resistant (ypfP::cat) clones did not synthesize the glycolipids monoglucosyldiacylglycerol and diglucosyldiacylglycerol. Thus, YpfP would appear to be the only diglucosyldiacylglycerol synthase in S. aureus providing glycolipid for LTA assembly. In LTA from the mutant, the glycolipid anchor is replaced by diacylglycerol. Although the doubling time of the mutant was identical to that of the wild type in Luria-Bertani (LB) medium, growth of the mutant in LB medium containing 1% glycine was not observed. This inhibition was antagonized by either L- or D-alanine. Moreover, viability of the mutant at 37 degrees C in 0.05 M phosphate (pH 7.2)-saline for 12 h was reduced to <0.1%. Addition of 0.1% D-glucose to the phosphate-saline ensured viability under these conditions. The autolysis of the ypfP::cat mutant in the presence of 0.05% Triton X-100 was 1.8-fold faster than that of the parental strain. Electron microscopy of the mutant revealed not only a small increase in cell size but also the presence of pleomorphic cells. Each of these phenotypes may be correlated with either (or both) a deficiency of free glycolipid in the membrane or the replacement of the usual glycolipid anchor of LTA with diacylglycerol.
Analysis of the HLA-restricted influenza-specific cytotoxic T lymphocyte response in transgenic mice carrying a chimeric human-mouse class I major histocompatibility complex. (1991)

Transgenic murine lines have been constructed that express a chimeric class I molecule composed of the alpha 1 and alpha 2 domains of HLA-A2.1 and the alpha 3, transmembrane, and cytoplasmic domains of H-2Kb. Upon immunization with influenza virus, transgenic mice developed a strong A2.1Kb-restricted cytotoxic T lymphocyte (CTL) response specific for the same matrix protein epitope that serves as the dominant A2.1-restricted determinant in the equivalent human response. Fine specificity analysis of CTL clones using truncated peptides revealed strong similarity between the response repertoire of transgenic mice and that previously reported using influenza-specific A2.1-restricted CTL clones from humans. This suggests that even when considering T cell responses by different species, the alpha 1 and alpha 2 domains of the restriction element play a dominant role in determining the CTL specific repertoire. Thus, substituting the alpha 3 domain of A2.1 with a murine counterpart has permitted development of a transgenic strain that should serve as an excellent model system in studies of HLA-restricted responses.
Bit-Interleaved Coded Modulation Revisited: A Mismatched Decoding Perspective (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We revisit the information-theoretic analysis of bit-interleaved coded modulation (BICM) by modeling the BICM decoder as a mismatched decoder. The mismatched decoding model is well defined for finite, yet arbitrary, block lengths, and naturally captures the channel memory among the bits belonging to the same symbol. We give two independent proofs of the achievability of the BICM capacity calculated by Caire <etal/>, where BICM was modeled as a set of independent parallel binary-input channels whose output is the bitwise log-likelihood ratio. Our first achievability proof uses typical sequences, and shows that due to the random coding construction, the interleaver is not required. The second proof is based on the random coding error exponents with mismatched decoding, where the largest achievable rate is the generalized mutual information. Moreover, the generalized mutual information of the mismatched decoder coincides with the infinite-interleaver BICM capacity. We show that the error exponent—and hence the cutoff rate—of the BICM mismatched decoder is upper-bounded by that of coded modulation and may thus be lower than in the infinite-interleaved model; for binary reflected Gray mapping in Gaussian channels the loss in error exponent is small. We also consider the mutual information appearing in the analysis of iterative decoding of BICM with extrinsic information transfer (EXIT) charts: if the symbol metric has knowledge of the transmitted symbol, EXIT mutual information admits a representation as a pseudo-generalized mutual information, which is in general not achievable. A different symbol decoding metric, for which the extrinsic side information refers to the hypothesized symbol, induces a generalized mutual information lower than the coded modulation capacity. In this case, perfect extrinsic side information turns the mismatched-decoder error exponent into that of coded modulation. </para>
Mechanical properties of LIGA-deposited nickel for MEMS transducers (2002)

This paper presents a new technique for measuring the stress-strain curve of nickel produced by the LIGA method. The results of nine tests on 200 /spl mu/m thick specimens produced on the 3rd LIGAMUMPS run show a Young's modulus similar to that of pure nickel, but strengths that are considerably higher.
Artificial Chaperone-Assisted Refolding of Denatured-Reduced Lysozyme:  Modulation of the Competition between Renaturation and Aggregation (1996)

Conditions that promote renaturation of an unfolded protein also promote protein aggregation, in many cases, because these competing intramolecular and intermolecular processes are driven by similar networks of noncovalent interactions. The GroEL/GroES system and related biological chaperones facilitate the renaturation of substrate proteins by minimizing the aggregation pathway. We have devised a two-step method in which small molecules, "artificial chaperones," facilitate protein refolding from a chemically denatured state. In the first step, the protein is captured by a detergent as guanidinium chloride is diluted to a non-denaturing concentration; formation of a protein-detergent complex prevents both protein aggregation and proper refolding. In the second step, a cyclodextrin strips detergent from the protein, allowing the protein to refold. Here we describe the first application of this method to a protein that must form disulfides in the native state. Lysozyme (hen egg white) can be refolded from the Gdm-denatured, DTT-reduced state in good yields at final protein concentrations as high as 1 mg/mL with the artificial chaperone method. Several mechanistic aspects of artificial chaperone-assisted refolding have been probed, and a detailed mechanism for the kinetically controlled stripping step is proposed.
Alkali Metal Nitrate-Promoted High-Capacity MgO Adsorbents for Regenerable CO2 Capture at Moderate Temperatures (2015)

Regenerable high capacity CO2 sorbents are desirable for the establishment of widespread carbon capture and storage (CCS) systems to reduce global CO2 emissions. We report on the marked effects of molten alkali metal nitrates on CO2 uptake by MgO particles and their impact on the development of highly regenerable CO2 adsorbents with high capacity (>10.2 mmol g–1) at moderate temperatures (∼300 °C) under ambient pressure. The molten alkali metal nitrates are shown to prevent the formation of a rigid, CO2-impermeable, unidentate carbonate layer on the surfaces of MgO particles and promote the rapid generation of carbonate ions to allow the high rate of CO2 uptake.
Systemic Lidocaine to Improve Postoperative Quality of Recovery After Ambulatory Laparoscopic Surgery (2012)

Systemic lidocaine improves postoperative quality of recovery in patients undergoing outpatient laparoscopy. Patients who received lidocaine had less opioid consumption, which translated to a better quality of recovery. Lidocaine is a safe, inexpensive, effective strategy to improve quality of recovery after ambulatory surgery.
The lumigraph (1996)

This paper discusses a new method for capturing the complete appearance of bothsynthetic and real world objects and scenes,representing this information, and then using this representation to render images of the object from new camera positions. Unlike the shape capture process traditionally used in computer vision and the rendering process traditionally used in computer graphics, our approach does not rely on geometric representations. Instead we sample and reconstruct a 4D function. which we call a Lumigraph. The Lumigraph is a subset o f the complete plenoptic fu nction that describes the flow of light at all positions in all directions. With the Lumigraph. new images of the object can be generated very quick]y,independentof the geometric or illumination complexity of the scene or object. The paper discusses a complete working system including the capture of sainples. the construction of the Lumigraph, and thesubsequent rendering of images from this new representation. even i f given accurate geometric models.
The user in experimental computer systems research (2007)

Experimental computer systems research typically ignores the end-user, modeling him, if at all, in overly simple ways. We argue that this (1) results in inadequate performance evaluation of the systems, and (2) ignores opportunities. We summarize our experiences with (a) directly evaluating user satisfaction and (b) incorporating user feedback in different areas of client/server computing, and use our experiences to motivate principles for that domain. Specifically, we report on user studies to measure user satisfaction with resource borrowing and with different clock frequencies in desktop computing, the development and evaluation of user interfaces to integrate user feedback into scheduling and clock frequency decisions in this context, and results in predicting user action and system response in a remote display system. We also present initial results on extending our work to user control of scheduling and mapping of virtual machines in a virtualization-based distributed computing environment. We then generalize (a) and (b) as recommendations for incorporating the user into experimental computer systems research.
Physical Layer Design of High-Performance Wireless Transmission for Critical Control Applications (2017)

The next generations of industrial control systems will require high-performance wireless networks (named WirelessHP) able to provide extremely low latency, ultrahigh reliability, and high data rates. The current strategy toward the realization of industrial wireless networks relies on adopting the bottom layers of general purpose wireless standards and customizing only the upper layers. In this paper, a new bottom-up approach is proposed through the realization of a WirelessHP physical layer specifically targeted at reducing the communication latency through the minimization of packet transmission time. Theoretical analysis shows that the proposed design allows a substantial reduction in packet transmission time, down to 1 μs, with respect to the general purpose IEEE 802.11 physical layer. The design is validated by an experimental demonstrator, which shows that reliable communications up to 20 m range can be established with the proposed physical layer.
RAD001 (Everolimus) inhibits growth of prostate cancer in the bone and the inhibitory effects are increased by combination with docetaxel and zoledronic acid (2008)

RAD001 inhibited growth of C4-2 cells in bone, an effect augmented by addition of docetaxel and zoledronic acid. Moreover RAD001 had a significant impact on maintenance of body weight. RAD001 may hold promise for its effects on both metastatic CaP and the important syndrome of tumor cachexia.