gebhart/patrepeval huggingface dataset:
Multiplicative nonnegative greph embedding (2009)

In this paper, we study the problem of nonnegative graph embedding, originally investigated in [14] for reaping the benefits from both nonnegative data factorization and the specific purpose characterized by the intrinsic and penalty graphs [13]. Our contributions are two-fold. On the one hand, we present a multiplicative iterative procedure for nonnegative graph embedding, which significantly reduces the computational cost compared with the iterative procedure in [14] involving the matrix inverse calculation of an M-matrix. On the other hand, the nonnegative graph embedding framework is expressed in a more general way by encoding each datum as a tensor of arbitrary order, which brings a group of byproducts, e.g., nonnegative discriminative tensor factorization algorithm, with admissible time and memory cost. Extensive experiments compared with the state-of-the-art algorithms on nonnegative data factorization, graph embedding, and tensor representation demonstrate the algorithmic properties in computation speed, sparsity, discriminating power, and robustness to realistic image occlusions.
Intravenous Administration of Thioredoxin Decreases Brain Damage Following Transient Focal Cerebral Ischemia in Mice (2004)

Thioredoxin (TRX) is induced by a variety of oxidative stimuli and shows cytoprotective roles against oxidative stress. To clarify the possibility of clinical application, we examined the effects of intravenously administered TRX in a model of transient focal cerebral ischemia in this study. Mature male C57BL/6j mice received either continuous intravenous infusion of recombinant human TRX (rhTRX) over a range of 1-10 mg/kg, bovine serum albumin, or vehicle alone for 2 h after 90-min transient middle cerebral artery occlusion (MCAO). Twenty-four hours after the transient MCAO, the animals were evaluated neurologically and the infarct volumes were assessed. Infarct volume, neurological deficit, and protein carbonyl contents, a marker of protein oxidation, in the brain were significantly ameliorated in rhTRX-treated mice at the dose of 3 and 10 mg/kg versus these parameters in control animals. Moreover, activation of p38 mitogen-activated protein kinase, whose pathway is involved in ischemic neuronal death, was suppressed in the rhTRX-treated mice. Further, rhTRX was detected in the ischemic hemisphere by western blot analysis, suggesting that rhTRX was able to permeate the blood-brain barrier in the ischemic hemisphere. These data indicate that exogenous TRX exerts distinct cytoprotective effects on cerebral ischemia/reperfusion injury in mice by means of its redox-regulating activity.
Theoretical Quality Assessment of Myocardial Elastography with In Vivo Validation (2007)

Myocardial elastography (ME), a radio frequency (RF)-based speckle tracking technique with one-dimensional (1-D) cross correlation and novel recorrelation methods in a 2-D search was proposed to estimate and fully image 2-D transmural deformation field and to detect abnormal cardiac function. A theoretical framework was first developed in order to evaluate the performance of 2-D myocardial elastography based on a previously developed 3-D finite-element model of the canine left ventricle. A normal (control) and an ischemic (left-circumflex, LCx) model, which more completely represented myocardial deformation than a kinematic model, were considered. A 2-D convolutional image formation model was first used to generate RF signals for quality assessment of ME in the normal and ischemic cases. A 3-D image formation model was further developed to investigate the effect of the out-of-plane motion on the 2-D, in-plane motion estimation. Both orthogonal, in-plane displacement components (i.e., lateral and axial) between consecutive RF frames were iteratively estimated. All the estimated incremental 2-D displacements from end-diastole (ED) to end-systole (ES) were then accumulated to acquire the cumulative 2-D displacements, which were further used to calculate the cumulative 2-D systolic finite strains. Furthermore, the cumulative systolic radial and circumferential strains, which were angle- and frame-rate independent, were obtained from the 2-D finite-strain components and imaged in full view to detect the ischemic region. We also explored the theoretical understanding of the limitations of our technique for the accurate depiction of disease and validated it in vivo against tagged magnetic resonance imaging (tMRI) in the case of a normal human myocardium in a 2-D short-axis (SA) echocardiographic view. The theoretical framework succeeded in demonstrating that the 2-D myocardial elastography technique was a reliable tool for the complete estimation and depiction of the in-plane myocardial deformation field as well as for accurate identification of pathological mechanical function using established finite-element, left-ventricular canine models. In a preliminary study, the 2-D myocardial elastography was shown capable of imaging myocardial deformation comparable to equivalent tMRI estimates in a clinical setting.
Isolation and Characterization of RNA-Directed DNA Polymerase from a B-Type RNA Tumor Virus (1974)

RNA-directed DNA polymerase was isolated from milk-borne B-type murine mammary tumor virus of the RIII mouse strain. The several hundred-fold-purified enzyme sediments at 5.5 to 5.7S with an average molecular weight of approximately 100,000. The purified enzyme is completely template dependent and responds to RNA, DNA, and synthetic templates. Stability studies indicate differential lability dependent on the exogenous template used to monitor activity.
Efficient distributed quantum computing (2013)

Abstract We provide algorithms for efficiently moving and addressing quantum memory in parallel. These imply that the standard circuit model can be simulated with a low overhead by a more realistic model of a distributed quantum computer. As a result, the circuit model can be used by algorithm designers without worrying whether the underlying architecture supports the connectivity of the circuit. In addition, we apply our results to existing memory-intensive quantum algorithms. We present a parallel quantum search algorithm and improve the time–space trade-off for the element distinctness and collision finding problems.
Glyceraldehyde 3-Phosphate and Pyruvate as Precursors of Isoprenic Units in an Alternative Non-mevalonate Pathway for Terpenoid Biosynthesis (1996)

Incorporation of 13C-labeled glycerol or pyruvate into the ubiquinone Q8 of Escherichia coli mutants lacking enzymes of the triose phosphate metabolism and of (U-13C6)glucose into the triterpenoids of the hopane series of Zymomonas mobilis showed that glyceraldehyde 3-phosphate (or eventually glyceraldehyde) and a C2 unit derived from pyruvate decarboxylation were the only precursors of the C5 skeleton of isoprenic units in a novel non-mevalonate pathway for isoprenoid biosynthesis in these bacteria.
Ethanol Content of Various Foods and Soft Drinks and their Potential for Interference with a Breath-Alcohol Test (1998)

A variety of breads and soft drinks were tested and found to contain low concentrations of alcohol. The potential for these products to generate false readings on an evidential breath-alcohol instrument was evaluated. Alcohol-free subjects ingested these products and then provided breath samples into a DataMaster. It was found that breath samples provided immediately after consumption of some of these products, or with them still present in the mouth, did produce low levels of apparent breath alcohol, which may or may not be rejected as invalid by the breath-test instrument. If the subject swallowed or expectorated the food or beverage and then observed a 15-min deprivation period during which nothing was introduced into the mouth, the apparent effect was eliminated. These findings emphasize the need for the mandatory pretest alcohol-deprivation period and the benefits of duplicate breath sampling.
Interleukin 8: the major neutrophil chemotaxin in a case of pseudogout. (1993)

A patient with traumatic osteoarthritis secondary to a pinning procedure, developed monoarthritis following gall bladder surgery. Although the neutrophil count within the synovial fluid (SF) (> 36,000 cells/microliters) suggested an infectious arthritis, there was no improvement following antibiotic therapy. Radiographs indicated the presence of chondrocalcinosis, and calcium pyrophosphate dihydrate crystals were detected within the granulocytes of the SF. The condition was alleviated after administration of colchicine. Before the treatment with colchicine, the neutrophil chemotactic and activating peptide, interleukin 8 (IL-8), was the major neutrophil chemotaxin within the SF. During the course of the treatment, the IL-8 concentration continued to rise in the synovium, while the neutrophil count decreased. Our data indicate that IL-8 was the major neutrophil chemotaxin in the SF, and that while the condition was alleviated with colchicine, the underlying disorder still existed, with the potential that discontinuance of the colchicine would result in the unrestrained action of the IL-8.
Ion-Selective Electrode for Transmembrane pH Difference Measurements (2001)

A triethylammonium-sensitive electrode was constructed using sodium tetrakis[3,5-bis(2-methoxyhexafluoro-2-propyl)phenyl]borate as an ion-exchanger and benzyl 2-nitrophenyl ether as a solvent mediator in a poly(vinylchloride) membrane matrix and was used to determine the pH difference across a cell membrane. The method is based on monitoring of the pH gradient-induced uptake of triethylammonium in situ. The triethylammonium electrode exhibited a near-Nernstian response to triethylammonium in the concentration range of 5 x 10(-6)-1 x 10(-2) M with a slope of 58.5 mV per concentration decade in a buffer solution composed of 150 mM NaCl and 10 mM NaH2PO4/Na2HPO4 (pH 7.5). The limit of detection was 1 microM. In experiments using liposomes, the uptake of triethylammonium into liposomes was quantitatively induced according to the pH difference across the liposomal membrane. The transmembrane pH differences in Escherichia coli cells and the light-induced pH differences across the envelope vesicles of Halobacterium halobium were successfully determined by the present method.
Development and demise of Plasmodium liver stage parasites - The hunt for a Genetically Attenuated Malaria Vaccine (2013)

A considerable effort is currently underway to develop a malaria vaccine based on live Plasmodium falciparum sporozoites. The first requisite of a sporozoite vaccine is the guarantee of parasite arrest prior to the onset of the pathogenic blood stage. Immunisation with genetically attenuated parasites (GAP) that arrest in the liver forms a promising approach. Work in this thesis describes the development and characterisation of a P. berghei Δb9Δslarp GAP that fully arrests in the liver. Immunisation of multiple mouse strains with low numbers of Δb9Δslarp GAP resulted in sterile protection. The Δb9Δslarp GAP is there-fore the leading GAP vaccine candidate. Work in this the-sis further describes the effect of varying the parameters of sporozoite inoculation on parasite liver load. These findings provide a rationale for the design of clinical trials aimed at the administration of live attenuated P. falciparum sporozoites.
Wideband Parametric Frequency Comb as Coherent Optical Carrier (2013)

We report the first use of the CW-seeded parametric comb as a multiwavelength source for coherent channel transmitters. The new comb source relies on a multistage parametric mixer design seeded by a single kilohertz-linewidth master laser. The resultant frequency comb provides more than 120 tones in a 100-nm-wide continuous band, all possessing kilohertz-scale linewidth inherited from the master laser. The applicability of the new comb source as a coherent channel carrier was quantified by error-vector magnitude and bit-error rate metrics of individual spectral lines modulated by QPSK signaling. The performance of the new source exceeded that of the standard tunable coherent transmitter while providing a qualitatively lower frequency uncertainty and drift.
Detection of Hepatitis C Virus in the Corneas of Seropositive Donors (2001)

This is the first study in the literature that demonstrates a significant correlation between HCV seropositivity and the presence of HCV in the corneas. Routine HCV serologic testing for all potential corneal donors and rejection of corneal tissues based on HCV seropositivity is certainly justifiable.
Stable, High‐Efficiency Ionic‐Liquid‐Based Mesoscopic Dye‐Sensitized Solar Cells (2007)

Efficient and stable mesoscopic dye-sensitized solar cells (DSCs) introducing a low-viscosity binary ionic liquid (1-propyl-3-methyl-imidazolium iodide (PMII) and 1-ethyl-3-methyl-imidazolium tetracyanoborate (EMIB(CN)(4))) electrolyte in combination with a new high-molar-extinction-coefficient ruthenium complex, Ru(2,2'-bipyridine-4,4'-dicarboxylic acid)(4,4'-bis(2-(4-tert-butyloxy -phenyl)ethenyl) -2,2'-bipyridine) (NCS)(2), are demonstrated. The dependence of photovoltaic performance, charge transport and electron lifetime on the composition of the binary ionic-liquid electrolyte with different ratios of PMII/EMIB(CN)(4) were investigated by electrochemical impedance and photovoltage transient techniques. A photovoltaic conversion efficiency of 7.6 % was obtained under simulated full sunlight illumination, which is a record for solvent-free DSCs. These devices exhibit excellent stability at 80 degrees C in the dark or under visible-light soaking at 60 degrees C during 1000 h of accelerated tests.
Newcastle disease virus f glycoprotein expressed from a recombinant vaccinia virus vector protects chickens against live‐virus challenge (1988)

Chickens were immunised using a vaccinia recombinant virus (vaccinia-Italien-F), expressing the F protein of Newcastle disease virus (NDV). Immunisation was successful using either TK" cells infected with the vaccinia-Italien-F virus, the recombinant virus grown in TK7 cells and inoculated intracerebrally in one-day-old chickens or the recombinant virus given by wing-web to adult chickens after adaptation by alternate passage in chick embryo fibroblasts and chickens. The use of recombinant viruses expressing the F protein of NDV as vaccines would allow joint application of vaccination and eradication programmes for NDV. Therefore, recombinant viruses obtained in chickens virus vectors are needed.
Erythropoietin prevents motor neuron apoptosis and neurologic disability in experimental spinal cord ischemic injury (2002)

The cytokine erythropoietin (EPO) possesses potent neuroprotective activity against a variety of potential brain injuries, including transient ischemia and reperfusion. It is currently unknown whether EPO will also ameliorate spinal cord injury. Immunocytochemistry performed using human spinal cord sections showed abundant EPO receptor immunoreactivity of capillaries, especially in white matter, and motor neurons within the ventral horn. We used a transient global spinal ischemia model in rabbits to test whether exogenous EPO can cross the blood-spinal cord barrier and protect these motor neurons. Spinal cord ischemia was produced in rabbits by occlusion of the abdominal aorta for 20 min, followed by saline or recombinant human (rHu)-EPO (350, 800, or 1,000 units/kg of body weight) administered intravenously immediately after the onset of reperfusion. The functional neurological status of animals was better for rHu-EPO-treated animals 1 h after recovery from anesthesia, and improved dramatically over the next 48 h. In contrast, saline-treated animals exhibited a poorer neurological score at 1 h and did not significantly improve. Histopathological examination of the affected spinal cord revealed widespread motor neuron injury associated with positive terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling in control but not in rHu-EPO-treated animals. These observations suggest both an acute as well as a delayed beneficial action of rHu-EPO in ischemic spinal cord injury. Because rHu-EPO is currently used widely with an excellent safety profile, clinical trials evaluating its potential to prevent motor neuron apoptosis and the neurological deficits that occur as a consequence of ischemic injury are warranted.
Allosteric modulators of NR2B‐containing NMDA receptors: molecular mechanisms and therapeutic potential (2009)

N-methyl-D-aspartate receptors (NMDARs) are ion channels gated by glutamate, the major excitatory neurotransmitter in the mammalian central nervous system (CNS). They are widespread in the CNS and are involved in numerous physiological and pathological processes including synaptic plasticity, chronic pain and psychosis. Aberrant NMDAR activity also plays an important role in the neuronal loss associated with ischaemic insults and major degenerative disorders including Parkinson's and Alzheimer's disease. Agents that target and alter NMDAR function may, thus, have therapeutic benefit. Interestingly, NMDARs are endowed with multiple extracellular regulatory sites that recognize ions or small molecule ligands, some of which are likely to regulate receptor function in vivo. These allosteric sites, which differ from agonist-binding and channel-permeation sites, provide means to modulate, either positively or negatively, NMDAR activity. The present review focuses on allosteric modulation of NMDARs containing the NR2B subunit. Indeed, the NR2B subunit confers a particularly rich pharmacology with distinct recognition sites for exogenous and endogenous allosteric ligands. Moreover, NR2B-containing receptors, compared with other NMDAR subtypes, appear to contribute preferentially to pathological processes linked to overexcitation of glutamatergic pathways. The actions of extracellular H+, Mg2+, Zn2+, of polyamines and neurosteroids, and of the synthetic compounds ifenprodil and derivatives ('prodils') are presented. Particular emphasis is put upon the structural determinants and molecular mechanisms that underlie the effects exerted by these agents. A better understanding of how NR2B-containing NMDARs (and NMDARs in general) operate and how they can be modulated should help define new strategies to counteract the deleterious effects of dysregulated NMDAR activity.
Modulation of malignant B cell activation and apoptosis by bcl-2 antisense ODN and immunostimulatory CpG ODN (2002)

Inhibition of bcl-2 expression by antisense oligodeoxynucleotides (ODN) might render bcl-2 overexpressing malignant B cells more susceptible to chemotherapy. ODN containing unmethylated CG dinucleotides (CpG) are known to activate B cells. We studied the effects of two bcl-2 antisense ODN, with (G3139) or without CG dinucleotides (NOV 2009) within the sequence, and the effects of a nonantisense, CpG-containing ODN (ODN 2006) on activation and apoptosis of malignant B cell lines and primary B-CLL cells. Without cationic lipids, no antisense-mediated inhibition of bcl-2 synthesis was achieved with G3139 and NOV 2009. Instead, G3139, but not NOV 2009, induced similar changes as ODN 2006 in proliferation, expression of costimulatory and antigen-presenting molecules, as well as in bcl-2 and bcl-xL levels of primary B-CLL cells. G3139 and ODN 2006 inhibited in vitro, spontaneous apoptosis in B-CLL cells of patients with high serum thymidine kinase activity (s-TK, marker for proliferative activity of malignant B cells), whereas in patients with low s-TK activity, apoptosis was induced. In conclusion, our results suggest that modulation of malignant B cell apoptosis by G3139 depends on its immunostimulatory properties rather than on antisense-mediated reduction of bcl-2 expression. Immunostimulatory CpG ODN may have a therapeutic potential in patients with B-CLL, especially those with low s-TK activity.
pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010)

De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. However, de novo sequencing can correctly interpret only approximately 30% of high- and medium-quality spectra generated by collision-induced dissociation (CID), which is much less than database search. This is mainly due to incomplete fragmentation and overlap of different ion series in CID spectra. In this study, we show that higher-energy collisional dissociation (HCD) is of great help to de novo sequencing because it produces high mass accuracy tandem mass spectrometry (MS/MS) spectra without the low-mass cutoff associated with CID in ion trap instruments. Besides, abundant internal and immonium ions in the HCD spectra can help differentiate similar peptide sequences. Taking advantage of these characteristics, we developed an algorithm called pNovo for efficient de novo sequencing of peptides from HCD spectra. pNovo gave correct identifications to 80% or more of the HCD spectra identified by database search. The number of correct full-length peptides sequenced by pNovo is comparable with that obtained by database search. A distinct advantage of de novo sequencing is that deamidated peptides and peptides with amino acid mutations can be identified efficiently without extra cost in computation. In summary, implementation of the HCD characteristics makes pNovo an excellent tool for de novo peptide sequencing from HCD spectra.
Differentiation of astrocytes and oligodendrocytes from germinal matrix cells in primary culture (1986)

Primary cultures derived from neonatal rat forebrain grow almost entirely as glial cultures, with a large astrocytic preponderance and smaller numbers of oligodendrocytic cells. Although both astrocytic and oligodendrocytic characteristics are acquired in vitro, the origins of both types of glia in primary cultures have not been determined. We tested the hypothesis that glia differentiate in vitro from immature neuroectodermal cells by following the fate of germinal zone cells in primary cultures. A monoclonal antibody that binds GD3 ganglioside was used as a marker for cells of the subventricular zone (SVZ), since antibody binding in newborn rat forebrain could be detected by immunofluorescence only in the SVZ of newborn rats (Goldman et al., 1984). We followed the expression of glial fibrillary acidic protein (GFAP), an astrocytic marker; galactocerebroside (GC), an oligodendrocytic marker; and GD3 during the first several weeks of culture. Both GFAP and GC expression were first detected in cells that bound the GD3 antibody. Astrocytes developed during the first week in vitro; eventually, they lost the ability to bind the GD3 antibody and most became GD3-/GFAP+ cells. In high-density cultures, a population of small cells that resided on top of the astrocytic monolayer retained GD3 expression. GC-antibody binding was first observed in these cells of the upper layer, although it was not readily apparent until the second week of culture. Few GC+ cells were seen in cultures grown at low density, however.(ABSTRACT TRUNCATED AT 250 WORDS)
I NTRANASAL A DMINISTRATION OF N ALOXONE BY P ARAMEDICS (2002)

Intranasal naloxone may provide a safe, rapid, effective way to manage suspected opioid overdoses in the field. Use of this route may decrease paramedic exposures to blood-borne diseases. The addition of i.n. naloxone administration to prehospital protocols should be considered as an initial therapy for suspected opioid abusers.