gebhart/patrepeval huggingface dataset:
Speech recognition in noise as a function of the number of spectral channels: Comparison of acoustic hearing and cochlear implants (2001)

Speech recognition was measured as a function of spectral resolution (number of spectral channels) and speech-to-noise ratio in normal-hearing (NH) and cochlear-implant (CI) listeners. Vowel, consonant, word, and sentence recognition were measured in five normal-hearing listeners, ten listeners with the Nucleus-22 cochlear implant, and nine listeners with the Advanced Bionics Clarion cochlear implant. Recognition was measured as a function of the number of spectral channels (noise bands or electrodes) at signal-to-noise ratios of + 15, + 10, +5, 0 dB, and in quiet. Performance with three different speech processing strategies (SPEAK, CIS, and SAS) was similar across all conditions, and improved as the number of electrodes increased (up to seven or eight) for all conditions. For all noise levels, vowel and consonant recognition with the SPEAK speech processor did not improve with more than seven electrodes, while for normal-hearing listeners, performance continued to increase up to at least 20 channels. Speech recognition on more difficult speech materials (word and sentence recognition) showed a marginally significant increase in Nucleus-22 listeners from seven to ten electrodes. The average implant score on all processing strategies was poorer than scores of NH listeners with similar processing. However, the best CI scores were similar to the normal-hearing scores for that condition (up to seven channels). CI listeners with the highest performance level increased in performance as the number of electrodes increased up to seven, while CI listeners with low levels of speech recognition did not increase in performance as the number of electrodes was increased beyond four. These results quantify the effect of number of spectral channels on speech recognition in noise and demonstrate that most CI subjects are not able to fully utilize the spectral information provided by the number of electrodes used in their implant.
Recognition of Planar and Nonplanar Ligands in the Malachite Green–RNA Aptamer Complex (2003)

Ribonucleic acids are an attractive drug target owing to their central role in many pathological processes. Notwithstanding this potential, RNA has only rarely been successfully targeted with novel drugs. The difficulty of targeting RNA is at least in part due to the unusual mode of binding found in most small-molecule-RNA complexes: the ligand binding pocket of the RNA is largely unstructured in the absence of ligand and forms a defined structure only with the ligand acting as scaffold for folding. Moreover, electrostatic interactions between RNA and ligand can also induce significant changes in the ligand structure due to the polyanionic nature of the RNA. Aptamers are ideal model systems to study these kinds of interactions owing to their small size and the ease with which they can be evolved to recognize a large variety of different ligands. Here we present the solution structure of an RNA aptamer that binds triphenyl dyes in complex with malachite green and compare it with a previously determined crystal structure of a complex formed with tetramethylrosamine. The structures illustrate how the same RNA binding pocket can adapt to accommodate both planar and nonplanar ligands. Binding studies with single- and double-substitution mutant aptamers are used to correlate three-dimensional structure with complex stability. The two RNA-ligand complex structures allow a discussion of structural changes that have been observed in the ligand in the context of the overall complex structure. Base pairing and stacking interactions within the RNA fold the phosphate backbone into a structure that results in an asymmetric charge distribution within the binding pocket that forces the ligand to adapt through a redistribution of the positive partial charge.
Roles of IL-1 and TNF-alpha in endotoxin-induced activation of nitric oxide synthase in cultured rat brain cells (1996)

In astrocytes and microglia, bacterial lipopolysaccharide (LPS) stimulates production and release of interleukin-1 beta (IL-1 beta), tumor necrosis factor-alpha (TNF-alpha), and nitric oxide (NO). Although IL-1 beta and TNF-alpha are themselves capable of inducing NO synthase (NOS) in glia, the specific factors mediating LPS induction of NOS in brain have not been identified. To determine whether LPS induction of NOS in brain cells is mediated by IL-1 or TNF-alpha, acting alone or in concert, the effects of IL-1-receptor antagonist (IL-1Ra) and of TNF-soluble receptor (TNFsRp55), presented individually and in combination, on LPS-induced NOS activity were tested. In glial-enriched mixed primary cultures of neonatal rat telencephalic cells, LPS (0.1-100 ng/ml), IL-1 beta (0.01-10 nM), and TNF-alpha (0.1-100 nM) each concentration dependently stimulated accumulation of nitrite, an indicator of NO production. Induction of nitrite accumulation by LPS and by IL-1 was blocked by N omega-nitro-L-arginine methyl ester and N omega-monomethyl-L-arginine, indicating that it was mediated by NOS. TNF-alpha alone induced NO production weakly as compared with IL-1, but combined submaximal concentrations of IL-1 beta (1 nM) and TNF-alpha (10 nM) induced NOS synergistically. Furthermore, TNFsRp55 and IL-1Ra each produced a dose-dependent partial inhibition of the NO response to LPS, and the effect of TNFsRp55 was equal to or greater than that of IL-1Ra. TNFsRp55 and IL-1Ra in combination were not significantly more effective than TNF-sRp55 alone. The results indicate that LPS induction of NOS activity in brain cells is mediated in part by both IL-1 beta and TNF-alpha.
Self-Ordering of Cell Configuration of Anodic Porous Alumina with Large-Size Pores in Phosphoric Acid Solution (1998)

Large cell-sized anodic porous alumina with long-range ordering was fabricated using phosphoric acid solution. Self-ordering of the anodic alumina took place under long-period constant voltage anodization at 195 V, which generated the self-ordered anodic porous alumina with a cell size of 500 nm.
Accelerating Smart Speaker Service with Content Prefetching and Local Control (2020)

Smart speakers like Amazon Echo or Google Home are popular because they provides intelligent virtual assistant services. However, smart speakers should be connected through the Internet to the voice server in the cloud that utilizes the powerful computing resources, which may cause the additional latency. In this paper, we propose a content prefetching and local control method to improve the response time of voice commands to smart speakers. Our proposal consists of local user intent detection on the device, content prefetching, and local text-to-speech processing. We select the popular voice commands regarding weather, music, news and time services, and implement a smart speaker prototype that can execute user intent detection at the device and play the prefetched contents with Google API. We compare our speaker prototype with five smart speakers by Amazon, Google, Kakao, Naver, and SKT. From five representative voice commands, we show that our local control of prefetched contents significantly improves the response time. For instance, in music and news services, the response time is reduced from 4.88 seconds to 0.11 seconds and 8.54 seconds to 0.13 seconds, respectively.
Native oligodeoxynucleotides specifically active against human immunodeficiency virus type 1 in vitro: a G-quartet-driven effect? (1996)

Among a series of unmodified phosphodiester (PO)-oligodeoxynucleotides (PO-ODNs) complementary to some of the human immunodeficiency virus type 1 (HIV-1) regulatory genes, several PO-ODN sequences complementary to the vpr gene (PO-ODNs-a-vpr, where a-vpr is the antisense vpr sequence) emerged as potent inhibitors (at concentrations of 0.8 to 3.3 microM) of HIV-1 multiplication in de novo infected MT-4 cells, while they showed no cytotoxicity for uninfected cells at concentrations up to 100 microM. Unlike phosphorothioate counterparts, PO-ODN-a-vpr sequences were not inhibitory to HIV-2 multiplication in de novo infected C8166 cells and neither prevented the fusion between chronically infected and bystander CD4+ cells nor inhibited the activity of the HIV-1 reverse transcriptase in enzyme assays. Moreover, they were not inhibitory to HIV-1 multiplication in chronically infected cells. Delayed addition experiments showed that PO-ODNs-a-vpr inhibit an event in the HIV-1 replication cycle following adsorption to the host cell, but preceding reverse transcription. Structure-activity relationship studies indicated that the antiviral activity of the test PO-ODN-a-vpr sequences is not related to an antisense mechanism but to the presence, within the active sequences, of contiguous guanine residues. Physical characterization of the test PO-ODNs suggested that the active structure is a tetramer stabilized by G quartets (i.e., four G residues connected by eight hydrogen bonds).
Using a depth camera as a touch sensor (2010)

We explore the application of depth-sensing cameras to detect touch on a tabletop. Limits of depth estimate resolution and line of sight requirements dictate that the determination of the moment of touch will not be as precise as that of more direct sensing techniques such as capacitive touch screens. However, using a depth-sensing camera to detect touch has significant advantages: first, the interactive surface need not be instrumented. Secondly, this approach allows touch sensing on non-flat surfaces. Finally, information about the shape of the users and their arms and hands above the surface may be exploited in useful ways, such as determining hover state, or that multiple touches are from same hand or from the same user. We present techniques and findings using Microsoft Kinect.
The Centrosomal Protein C-Nap1 Is Required for Cell Cycle–Regulated Centrosome Cohesion (2000)

Duplicating centrosomes are paired during interphase, but are separated at the onset of mitosis. Although the mechanisms controlling centrosome cohesion and separation are important for centrosome function throughout the cell cycle, they remain poorly understood. Recently, we have proposed that C-Nap1, a novel centrosomal protein, is part of a structure linking parental centrioles in a cell cycle-regulated manner. To test this model, we have performed a detailed structure-function analysis on C-Nap1. We demonstrate that antibody-mediated interference with C-Nap1 function causes centrosome splitting, regardless of the cell cycle phase. Splitting occurs between parental centrioles and is not dependent on the presence of an intact microtubule or microfilament network. Centrosome splitting can also be induced by overexpression of truncated C-Nap1 mutants, but not full-length protein. Antibodies raised against different domains of C-Nap1 prove that this protein dissociates from spindle poles during mitosis, but reaccumulates at centrosomes at the end of cell division. Use of the same antibodies in immunoelectron microscopy shows that C-Nap1 is confined to the proximal end domains of centrioles, indicating that a putative linker structure must contain additional proteins. We conclude that C-Nap1 is a key component of a dynamic, cell cycle-regulated structure that mediates centriole-centriole cohesion.
Purification of murine bone-marrow-derived granulocyte-macrophage colony-forming cells. (1987)

Previous attempts to purify progenitor cells that form colonies and clusters of granulocytes and/or macrophages (CFU-GM) from adult murine bone marrow have had limited success because of the paucity of these cells. In the present paper we report studies with a rapid, reproducible method involving pretreatment of mice, three days prior to sacrifice, with 200 mg/kg of Cytoxan (cyclophosphamide), density separation on Ficoll-Hypaque, and counterflow centrifugal elutriation, that yielded highly enriched populations of CFU-GM. The peak CFU-GM-containing fraction (FR-28) eluted at a flow rate of 28 ml/min and contained very little contamination by other in vitro colony-forming cells (BFU-E, CFU-GEMM, CFU-MK). FR-28 contained 0.54% +/- 0.30% (16 experiments) of the unfractionated post-Cytoxan bone marrow nucleated cells and lacked significant contamination by lymphocytes and monocytes. The mean CFU-GM cloning efficiency of FR-28 was 44% +/- 9% in agar (11 experiments) and 75% +/- 10% in agarose (nine experiments). CFU-GM from FR-28 demonstrated linear plating characteristics even at very low cell density (25 cells), and formed colonies and clusters of granulocytes, macrophages, or both in the same proportions as did unfractionated post-Cytoxan or untreated bone marrow. Approximately 10% (assuming a seeding efficiency of 10%) of FR-28 cells were in vivo spleen colony-forming cells (CFU-S) measured at day 12. These results represent the highest degree of purity (up to 94%) of CFU-GM thus far reported and should prove useful in studies of this cell population.
Structural Basis of Amino Acid α Helix Propensity (1993)

The propensity of an amino acid to form an alpha helix in a protein was determined by multiple amino substitutions at positions 44 and 131 in T4 lysozyme. These positions are solvent-exposed sites within the alpha helices that comprise, respectively, residues 39 to 50 and 126 to 134. Except for two acidic substitutions that may be involved in salt bridges, the changes in stability at the two sites agree well. The stability values also agree with those observed for corresponding amino acid substitutions in some model peptides. Thus, helix propensity values derived from model peptides can be applicable to proteins. Among the 20 naturally occurring amino acids, proline, glycine, and alanine each have a structurally unique feature that helps to explain their low or high helix propensities. For the remaining 17 amino acids, it appears that the side chain hydrophobic surface buried against the side of the helix contributes substantially to alpha helix propensity.
The modern methods of the electrical stimulation for the management of neurogenic disturbances of urination (2015)

The results of the present study provide materials for the characteristic and the comparative analysis of the methods for electrical stimulation applied for the treatment of neurogenic disorders of urination and illustrate the up-to-date requirements to this therapy taking into consideration the neuroanatomical and neurophysiological features of micturition. One of the most advanced non-pharmacological methods is electrical stimulation and neuromodulation of the urinary bladder function and pelvic floor muscles. The objective of this three-step research was to elucidate the mechanisms of action of electrical stimulation and to compare the effects of tibial and pudendal neuromodulation in 22 patients presenting with ischemic lesions in the brain. The first step included the comprehensive clinical and neuroimaging investigations designed to determine the role of functional asymmetry of cortical and subcortical micturition regulatory centers during the recovery process following the ischemic lesions. At the second stage, afferent and central regulation of micturition was investigated by the method of tibial and pudendal somatosensory evoked potentials in the patients presenting with overactive bladder and acute or chronic cerebral ischemia. At the final step, the optimal parameters of neuromodulation were chosen depending on the form of the urination disorder. It is concluded that the study gave evidence of the high therapeutic effectiveness of tibial and pudendal neuromodulation for the treatment of overactive bladder associated with neurological disorders (including ischemic lesions in the brain).
An 8-b 85-MS/s parallel pipeline A/D converter in 1- mu m CMOS (1993)

A new architecture consisting of a time-interleaved array of pipelined analog-to-digital converters (ADCs) is presented. A prototype has been designed consisting of four switched-capacitor (S/C) multistage pipelined ADCs in parallel. Hardware cost is minimized by sharing resistor strings, bias circuitry and clock generation circuitry over the array. Digital error correction is employed to ease comparator accuracy requirements. Techniques are employed to minimize the effect of mismatches across the array. A key circuit issue is the design of a high-speed sample-and-hold (S/H) amplifier: a fully differential, mostly NMOS, non-folded-cascode operational-amplifier topology is used. An experimental chip was implemented in 1- mu m CMOS and 8-b resolution at a sample rate of 85 megasamples per second (MS/s) was obtained. Signal-to-noise plus distortion (S/(N+D)) was 41 dB for an input sinusoid of 40 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functional Links between the Fusion Peptide-proximal Polar Segment and Membrane-proximal Region of Human Immunodeficiency Virus gp41 in Distinct Phases of Membrane Fusion (2007)

The binding of CD4 and chemokine receptors to the gp120 attachment glycoprotein of human immunodeficiency virus triggers refolding of the associated gp41 fusion glycoprotein into a trimer of hairpins with a 6-helix bundle (6HB) core. These events lead to membrane fusion and viral entry. Here, we examined the functions of the fusion peptide-proximal polar segment and membrane-proximal Trp-rich region (MPR), which are exterior to the 6HB. Alanine substitution of Trp(666), Trp(672), Phe(673), and Ile(675) in the MPR reduced entry by up to 120-fold without affecting gp120-gp41 association or cell-cell fusion. The L537A polar segment mutation led to the loss of gp120 from the gp120-gp41 complex, reduced entry by approximately 10-fold, but did not affect cell-cell fusion. Simultaneous Ala substitution of Leu(537) with Trp(666), Trp(672), Phe(673), or Ile(675) abolished entry with 50-80% reductions in cell-cell fusion. gp120-gp41 complexes of fusion-defective double mutants were resistant to soluble CD4-induced shedding of gp120, suggesting that their ability to undergo receptor-induced conformational changes was compromised. Consistent with this idea, a representative mutation, L537A/W666A, led to an approximately 80% reduction in lipophilic fluorescent dye transfer between gp120-gp41-expressing cells and receptor-expressing targets, indicating a block prior to the lipid-mixing phase. The L537A/W666A double mutation increased the chymotrypsin sensitivity of the polar segment in a trimer of hairpins model, comprising the 6HB core, the polar segment, and MPR linked N-terminally to maltose-binding protein. The data indicate that the polar segment and MPR of gp41 act synergistically in forming a fusion-competent gp120-gp41 complex and in stabilizing the membrane-interactive end of the trimer of hairpins.
Correcting Neuromuscular Deficits With Gene Therapy in Pompe Disease (2015)

Our data provide new mechanistic insight into the pathology of Pompe disease and suggest that early systemic correction to both neural and muscle tissues may be essential for successful correction of neuromuscular function in Pompe disease. Ann Neurol 2015;78:222-234.
Requirement of donor-derived stromal cells in the bone marrow for successful allogeneic bone marrow transplantation. Complete prevention of recurrence of autoimmune diseases in MRL/MP-Ipr/Ipr mice by transplantation of bone marrow plus bones (stromal cells) from the same donor. (1994)

MRL/MP-Ipr/Ipr (MRL/Ipr) mice possess radioresistant (9.5 Gy) abnormal stem cells and show a recurrence of autoimmune diseases within 5 mo of conventional allogeneic bone marrow transplantation. We recently have found that the MHC preference exists between hemopoietic stem cells and stromal cells; when bones are engrafted, donor-derived stromal cells present in the engrafted bones can migrate into the recipient bone marrows, which are replaced with both donor-derived stromal cells and hematopoietic cells. Based on these findings, we attempted to prevent the recurrence of autoimmune diseases in MRL/Ipr mice by the transplantation of both bone marrow cells and bone (as a source of stromal cells). MRL/Ipr mice were irradiated (8.5 Gy) and then reconstituted with C57BL/6 bone marrow cells plus bone grafts. The mice survived more than 48 wk after this treatment. Immunohistologic studies revealed that the mice were completely free from both lymphadenopathy and autoimmune diseases such as lupus nephritis and rheumatoid arthritis. Sera from these mice showed normal levels of circulating immune complexes and rheumatoid factors. Normal functions of both T cells and B cells were noted. Abnormal T cells such as Thy-1+B220+ cells present in nontreated MRL/Ipr mice could not be seen in the thus-treated mice. In addition, to our surprise, spleen cells from treated mice showed completely normal in vitro primary anti-SRBC responses. These results indicate that stromal cells in allogeneic bone marrow transplantation play a crucial role not only in the prevention of graft failure but also in the successful cooperation among APCs, T cells, and B cells. Although MRL/Ipr mice are radiosensitive and usually die of interstitial pneumonia or fatty liver due to the side effects of radiation, it should be noted that this strategy allows a reduction in the radiation dose (9.5 Gy-->8.5 Gy), and that these mice can survive more than 48 wk without showing any symptoms of autoimmune diseases.
Plant antitumor agents. 30. Synthesis and structure activity of novel camptothecin analogs (1993)

A large number of camptothecin (CPT) analogs have been prepared in the 20S, 20RS, and 20R configurations with a number of ring A substituents. Topoisomerase I (T-I) inhibition data (IC50) have been obtained by standard procedures. In general, substitution at the 9 or 10 positions with amino, halogeno, or hydroxyl groups in compounds with 20S configuration results in compounds with enhanced T-I inhibition. Compounds in the 20RS configuration were less active in vitro and in vivo and those in the 20R configuration were inactive. Compounds with 10,11-methylenedioxy substitution on ring A displayed a marked increase in potency in the T-I inhibition assay. The activities of some of the analogs as determined in a variety of in vivo assays including the L-1210 mouse leukemia assay were, in general, in accord with T-I inhibition. A number of water-soluble analogs such as 20-glycinate esters, 9-glycinamides, or hydrolyzed lactone salts were prepared and tested in in vitro and in vivo assays. In general, these compounds were less active than CPT both in terms of T-I inhibition and life prolongation in the L-1210 assay. However, certain 20-glycinate esters showed good in vivo activity after iv administration.
Efficient Conjugation of Peptides to Oligonucleotides by “Native Ligation” (2000)

A new strategy has been developed for conjugation of peptides to oligonucleotides. The method is based on the "native ligation" of an N-terminal thioester-functionalized peptide to a 5'-cysteinyl oligonucleotide. Two new reagents were synthesized for use in solid-phase peptide and oligonucleotide synthesis, respectively. Pentafluorophenyl S-benzylthiosuccinate was used in the final coupling step in standard Fmoc-based solid-phase peptide assembly. Deprotection with trifluoracetic acid generated in solution peptides substituted with an N-terminal S-benzylthiosuccinyl moiety. O-trans-4-(N-alpha-Fmoc-S-tert-butylsulfenyl-L-cysteinyl)aminoc yclohe xyl O-2-cyanoethyl-N,N-diisopropylphosphoramidite was used in the final coupling step in standard phosphoramidite solid-phase oligonucleotide assembly. Deprotection with aqueous ammonia solution generated in solution 5'-S-tert-butylsulfenyl-L-cysteinyl functionalized oligonucleotides. Functionalized peptides and oligonucleotides were used without purification in native ligation conjugation reactions in aqueous/organic solution using tris-(2-carboxyethyl)phosphine to remove the tert-butylsulfenyl group in situ and thiophenol as a conjugation enhancer. A range of peptide-oligonucleotide conjugates were prepared by this route and purified by reversed-phase HPLC.