gebhart/patrepeval huggingface dataset:
Analysis of Shared Finite Storage in a Computer Network Node Environment Under General Traffic Conditions (1980)

Nodal storage limitations in a store and forward computer network lead to blocking; this results in degradation of network performance due to the loss or retransmission of blocked messages. In this paper, we consider several schemes for sharing a pool of buffers among a set of communication channels emanating from a given node in a network environment so as to make effective use of storage in a variety of applications. Five sharing schemes are examined, analyzed, and displayed in a fashion which permits one to establish the tradeoffs among blocking probability, utilization, throughput, and delay. The key to the analysis lies in the observation that the equilibrium joint probability distribution of the buffer occupancy obeys the well-known product form solution for networks of queues. The study indicates advantages and pitfalls of each of the sharing schemes. We observe, in general, that sharing with appropriate restrictions on the contention for space is very much desirable.
Contributions of the Na+/K+‐ATPase, NKCC1, and Kir4.1 to hippocampal K+ clearance and volume responses (2014)

Network activity in the brain is associated with a transient increase in extracellular K(+) concentration. The excess K(+) is removed from the extracellular space by mechanisms proposed to involve Kir4.1-mediated spatial buffering, the Na(+)/K(+)/2Cl(-) cotransporter 1 (NKCC1), and/or Na(+)/K(+)-ATPase activity. Their individual contribution to [K(+)]o management has been of extended controversy. This study aimed, by several complementary approaches, to delineate the transport characteristics of Kir4.1, NKCC1, and Na(+)/K(+)-ATPase and to resolve their involvement in clearance of extracellular K(+) transients. Primary cultures of rat astrocytes displayed robust NKCC1 activity with [K(+)]o increases above basal levels. Increased [K(+)]o produced NKCC1-mediated swelling of cultured astrocytes and NKCC1 could thereby potentially act as a mechanism of K(+) clearance while concomitantly mediate the associated shrinkage of the extracellular space. In rat hippocampal slices, inhibition of NKCC1 failed to affect the rate of K(+) removal from the extracellular space while Kir4.1 enacted its spatial buffering only during a local [K(+)]o increase. In contrast, inhibition of the different isoforms of Na(+)/K(+)-ATPase reduced post-stimulus clearance of K(+) transients. The astrocyte-characteristic α2β2 subunit composition of Na(+)/K(+)-ATPase, when expressed in Xenopus oocytes, displayed a K(+) affinity and voltage-sensitivity that would render this subunit composition specifically geared for controlling [K(+)]o during neuronal activity. In rat hippocampal slices, simultaneous measurements of the extracellular space volume revealed that neither Kir4.1, NKCC1, nor Na(+)/K(+)-ATPase accounted for the stimulus-induced shrinkage of the extracellular space. Thus, NKCC1 plays no role in activity-induced extracellular K(+) recovery in native hippocampal tissue while Kir4.1 and Na(+)/K(+)-ATPase serve temporally distinct roles.
Broadband Epsilon-Near-Zero Perfect Absorption in the Near-Infrared (2015)

Perfect absorption (PA) of incident light is important for both fundamental light-matter interaction studies and practical device applications. PA studies so far have mainly used resonant nanostructures that require delicate structural patterning. Here, we realize tunable and broadband PA in the near-infrared region using relatively simple thin film coatings. We adjust the growth condition of an ITO film and control its epsilon-near-zero (ENZ) wavelength. We show that this results in highly tunable PA in the telecommunication window. Then, using an ITO multilayer of different ENZ wavelengths, we demonstrate broadband PA that covers a wide range of near-infrared wavelengths. The use of ENZ coatings makes PA adjustable during the film growth and does not require any structural patterning afterward. It also facilitates the chip-scale integration of perfect absorbers with other device components. Broadband PA relaxes the single wavelength condition in previous PA studies, and thus it is suitable for many practical device applications, including sensors, photodetectors, and energy harvesting devices.
Enlargement of Deinococcus grandis spheroplasts requires Mg2+ or Ca2+ (2018)

While the cell wall strictly controls cell size and morphology in bacteria, spheroplasts lack cell walls and can become enlarged in growth medium under optimal conditions. Optimal conditions depend on the bacterial species. We frequently observed extreme enlargement of spheroplasts of the radiation-resistant bacterium Deinococcus grandis in Difco Marine Broth 2216, but not in TGY broth (a commonly used growth medium for Deinococcus). Thorough investigation of media components showed that the presence of Mg<sup>2+</sup> or Ca<sup>2+</sup> promoted extreme spheroplast enlargement, synthesizing the outer membrane. Our findings strongly suggest that Mg<sup>2+</sup> or Ca<sup>2+</sup> enlarges spheroplasts, which could change the lipid composition of the spheroplast membrane.
A Prototypical Service For Real-Time Access To Local Context-Based Music Information. (2004)

[TODO] Add abstract here.
Modelocking and femtosecond pulse generation in chip-based frequency combs (2013)

We investigate simultaneously the temporal and optical and radio-frequency spectral properties of parametric frequency combs generated in silicon-nitride microresonators and observe that the system undergoes a transition to a mode-locked state. We demonstrate the generation of sub-200-fs pulses at a repetition rate of 99 GHz. Our calculations show that pulse generation in this system is consistent with soliton modelocking. Ultimately, such parametric devices offer the potential of producing ultra-short laser pulses from the visible to mid-infrared regime at repetition rates from GHz to THz.
The prognostic value of circulating cell-free DNA in breast cancer (2018)

Our meta-analysis indicates that cfDNA is a strong predictive and prognostic marker in patients with BC.
Fabrication of high-radiance LEDs by epitaxial lift-off (1991)

Fully processed A1GaAs/GaAs LEDs were lifted off their GaAs substrates and grafted to various host substrates. Due to a metallic back reflector beneath the epitaxial structure, the LED output power was 2 to 3 times increased compared to LEDs still on a GaAs substrate. Output power and spectral responses were significantly influenced by the thermal properties of the host material.
General 04 (2002)

Intraoperative placement of feeding jejunostomy is a well-established method of providing access to enteral feeding. A retrospective study was undertaken to look at the technical complications related to the procedure. Patients undergoing feeding jejunostomy in the thoracic and upper gastrointestinal surgical units at the Royal Victoria Hospital from January 1998 to December 1998 were included in the study. The charts of all the patients were studied retrospectively. Forty-two patients underwent a feeding jejunostomy in the time period studied. Thirty-one patients had a jejunostomy as an adjunct to major oesophageal or gastric surgery. In five patients, feeding jejunostomy was performed in conjunction with other palliative procedures and in six patients it was performed as a sole procedure. Nine (21.4 per cent) patients had procedure-related complications. Of these, seven (16.7 per cent) were minor including dislodgement of the tube (n = 4), blocked tube (n = 2), and intraoperative catheter damage (n = 1). Two (4.7 per cent) patients had major complications requiring emergency laparotomy. A single patient died as a result of a procedure-related complication. Feeding jejunostomy should not be considered as a benign surgical procedure. Proper attention to surgical technique and postoperative management is essential to prevent serious or life-threatening complications.
Protein kinase C-θ is specifically localized on centrosomes and kinetochores in mitotic cells (1999)

In this study we provide evidence that the protein kinase C (PKC)-θ isoenzyme is recruited on to the mitotic spindle in dividing murine erythroleukaemia (MEL) cells and associates specifically with centrosome and kinetochore structures. None of the other PKC isoenzymes (-α, -δ, -ε, -µ and -ζ) expressed by MEL cells shows this localization on the mitotic spindle. An identical subcellular distribution of PKC-θ is also observed in dividing murine P3 myeloma cells and human LAN-5 neuroblastoma cells, indicating that this PKC isoenzyme interacts with the mitotic apparatus in mammalian cells. In phorbol-ester-treated non-growing MEL cells, a rapid change in the intracellular distribution of PKC-θ occurs. Under these conditions, PKC-θ is translocated from the nuclear to the cytosolic cell compartment, an event that is accompanied by phosphorylation of the PKC-θ molecule and is followed by its down-regulation. The recovery of cell growth capacity results in the concomitant reappearance of PKC-θ. Furthermore, when MEL cells acquire the differentiated non-growing phenotype, the level of PKC-θ is reduced to less than 5%, suggesting that this PKC isoenzyme is no longer required. We propose that, unlike other members of the PKC family, PKC-θ may play a role in cell proliferation.
Tissue reactions to subcutaneously implanted, surface‐modified silicones (1993)

To evaluate the influence of surface properties on tissue reactions, the surface of a medical-grade silicone elastomer was modified without changing the bulk properties. Surface modifications employed were oxidation by corona discharge in air, graft polymerization of water-soluble monomers, coating a polysaccharide through polyion complex formation, and covalent immobilization of cell-adhesive proteins. Surface-modified silicone sheets were implanted in the subcutaneous tissue of rats, and tissue reactions such as infiltration of inflammatory cells, appearance of foreign-body giant cells, and collagenous capsule formation were studied. It was found that the thickness of collagenous capsules formed after 16 weeks' implantation was in the range of 85-95 microns for the nontreated ones and all the modified silicones except the acrylic acid-grafted and the collagen-immobilized silicones.
Methods for Detection and Classification of Normal Swallowing from Muscle Activation and Sound (2006)

Swallowing is an important part of the dietary process. This paper presents an investigation to detect and classify normal swallowing during eating and drinking from electromyography and microphone sensors. The non-invasive sensors are selected in order to integrate them into a collar-like fabric for continuous monitoring of swallowing activity over a day. We compare methods for the detection of individual swallowing events from continuous sensor data. Furthermore we present a classifier comparison for the swallowing event properties volume and viscosity. The methods are evaluated on experimental data and a performance analysis is shown. Moreover we present a class skew analysis based on the metrics precision and recall
The crystal structure of a plant lectin in complex with the Tn antigen (2003)

The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins. The amino acid moiety of the Tn antigen is largely exposed to the solvent and makes few contacts with the protein. The structure of the complex provides a framework to understand the differences in the strength of VVLB4 binding to different sugars and emphasizes the role of a single protein residue, Tyr127, as a structural determinant of Tn-binding specificity.
Clinical impact of L1CAM expression measured on the transcriptome level in ovarian cancer (2016)

L1CAM mRNA expression appears to play a substantial role in the pathophysiology of ovarian cancer that is translated into poor clinical outcome. Additionally humanized L1CAM antibodies, which can serve as potential future treatment options are under testing.
The synthesis and high‐level expression of a β2‐adrenergic receptor gene in a tetracycline‐inducible stable mammalian cell line (2006)

High-level expression of G-protein-coupled receptors (GPCRs) in functional form is required for structure-function studies. The main goal of the present work was to improve expression levels of beta2-adrenergic receptor (beta2-AR) so that biophysical studies involving EPR, NMR, and crystallography can be pursued. Toward this objective, the total synthesis of a codon-optimized hamster beta2-AR gene suitable for high-level expression in mammalian systems has been accomplished. Transient expression of the gene in COS-1 cells resulted in 18 +/- 3 pmol beta2-AR/mg of membrane protein, as measured by saturation binding assay using the beta2-AR antagonist [3H] dihydroalprenolol. Previously, we reported the development of an HEK293S tetracycline-inducible system for high-level expression of rhodopsin. Here, we describe construction of beta2-AR stable cell lines using the HEK293S-TetR-inducible system, which, after induction, express wild-type beta2-AR at levels of 220 +/- 40 pmol/mg of membrane protein corresponding to 50 +/- 8 microg/15-cm plate. This level of expression is the highest reported so far for any wild-type GPCR, other than rhodopsin. The yield of functional receptor using the single-step affinity purification is 12 +/- 3 microg/15-cm plate. This level of expression now makes it feasible to pursue structure-function studies using EPR. Furthermore, scale-up of beta2-AR expression using suspension cultures in a bioreactor should now allow production of enough beta2-AR for the application of biophysical techniques such as NMR spectroscopy and crystallography.
Synthesis of 8-Substituted Xanthines and Their Oxidative Skeleton Rearrangement to 1-Oxo-2,4,7,9-tetraazaspiro[4,5]dec-2-ene-6,8,10-triones (1999)

The synthesis of a number of 8-(dialkylamino)- and 8-alkoxyxanthines (3 and 6, respectively) is described. Treatment of 3 with m-chloroperoxybenzoic acid (m-CPBA) gave by a novel rearrangement 3-(disubstituted amino)-4,7,9-trimethyl-1-oxo-2,4,7,9-tetraazaspiro[4,5]dec-2-ene-6,8,10-triones 10. Also, the corresponding 3-alkoxy-subtituted spiro compounds 12 were obtained by an analogus treatment of 8-alkoxyxanthines 6. In attempts to elucidate a tentative mechanism for this rearrangement 8-[(dialkylamino)methyl]caffeines 7 when treated with m-CPBA did not undergo the rearrangement but only yielded the expected N-oxide derivatives 16. This result seems to indicate that a necessary structure element for this rearrangement to occur is an atom with an unshared pair of electrons to be attached to the 8-position of the investigated xanthines. In agreement with this statement is the fact that N-oxides of 8-[(dialkylamino)methyl]caffeines 16 do not undergo the novel rearrangement but rather give the expected Meisenheimer rearrangement or the Cope elimination depending upon reaction conditions.
Relationship between interferon‐γ, indoleamine 2,3‐dioxygenase, and tryptophan catabolism (1991)

Interferons have been shown to be potential anti-cancer agents and to inhibit tumor cell growth in culture. The in vivo mechanism of the anti-proliferative effect may be direct or indirect through the immune system; however, in vitro a primary mechanism of cytotoxicity is through the depletion of tryptophan. In particular, interferon-gamma (IFN-gamma) induces an enzyme of tryptophan catabolism, indoleamine 2,3-dioxygenase (IDO), which is responsible for conversion of tryptophan and other indole derivatives to kynurenine. The inhibitory effect of interferon on many intracellular parasites such as Toxoplasma gondii and Chlamydia trachomatis is by the same mechanism. Elevated kynurenine levels have been found in humans in a number of diseases and after interferon treatment, and the enzyme is induced in rodents after administration of interferon inducers, or influenza virus. IDO induction also occurs in vivo during rejection of allogeneic tumors, indicating a possible role for this enzyme in the tumor rejection process. The gene for IDO has been cloned and shown to be differentially regulated by IFN-alpha and IFN-gamma. IDO induction has been correlated with induction of GTP-cyclohydrolase, the key enzyme in pteridine biosynthesis. A direct role for IDO in pteridine synthesis has not been shown, and this parallel induction may reflect coordinate regulation of genes induced by IFN-gamma. A possible role for IDO in O2-radical scavenging and in inflammation is discussed.
Natural Cannabinoids Improve Dopamine Neurotransmission and Tau and Amyloid Pathology in a Mouse Model of Tauopathy (2013)

Cannabinoids are neuroprotective in models of neurodegenerative dementias. Their effects are mostly mediated through CB1 and CB2 receptor-dependent modulation of excitotoxicity, inflammation, oxidative stress, and other processes. We tested the effects of Sativex®, a mixture of Δ9-tetrahydrocannabinol and cannabidiol, acting on both CB1 and CB2 receptors, in parkin-null, human tau overexpressing (PK-/-/TauVLW) mice, a model of complex frontotemporal dementia, parkinsonism, and lower motor neuron disease. The animals received Sativex®, 4.63 mg/kg, ip, daily, for one month, at six months of age, at the onset of the clinical symptoms. We evaluated the effects of Sativex® on behavior, dopamine neurotransmission, glial activation, redox state, mitochondrial activity, and deposition of abnormal proteins. PK-/-/TauVLW mice developed the neurological deficits, but those treated with Sativex® showed less abnormal behaviors related to stress, less auto and hetero-aggression, and less stereotypy. Sativex® significantly reduced the intraneuronal, MAO-related free radicals produced during dopamine metabolism in the limbic system. Sativex® also decreased gliosis in cortex and hippocampus, increased the ratio reduced/oxidized glutathione in the limbic system, reduced the levels of iNOS, and increased those of complex IV in the cerebral cortex. With regard to tau and amyloid pathology, Sativex® reduced the deposition of both in the hippocampus and cerebral cortex of PK-/-/TauVLW mice and increased autophagy. Sativex®, even after a short administration in animals with present behavioral and pathological abnormalities, improves the phenotype, the oxidative stress, and the deposition of proteins in PK-/-/TauVLW mice, a model of complex neurodegenerative disorders.
Direct synthesis of functionalized mesoporous silica by non-ionic alkylpolyethyleneoxide surfactant assembly (1998)

The co-condensation of tetraethoxysilane (TEOS) and organotrialkoxysilane [(RO)3SiR′] assembled in the presence of structure-directing non-ionic polyethyleneoxide surfactant micelles provides a convenient neutral pH synthesis methodology for the one-step preparation of organically functionalized mesostructured materials.
Inhibition of extracellular ATP‐mediated lysis of human macrophages by calmodulin antagonists (1995)

Lysis of human culture-derived macrophages by extracellular ATP has recently been described, and treatment of macrophages with interferon-gamma rendered those cells significantly more sensitive to lysis. In addition, cell death occurred more rapidly in interferon (IFN)-treated cells than in untreated macrophages. In an attempt to identify the mechanism by which extracellular ATP affects macrophages, as well as to explore the differences between interferon-gamma-treated and untreated macrophages, selected metabolic inhibitors were included in the lytic assays. Of the compounds tested, three antagonists of calmodulin-linked pathways (trifluoperazine, KN-62, and calmidazolium) blocked the ATP-mediated lysis of both interferon-gamma-treated and colony-stimulating factor-treated macrophages in a dose-dependent manner. Early signals of the ATP ligation of the P2Z purinoceptors of human macrophages included increases in cytosolic [Ca2+] and depolarization of the plasma membrane. However, the inclusion of calmodulin antagonists in these assays did not abrogate either effect. These results suggest that the mechanism which mediates the efflux of 51Cr-labeled proteins from ATP-lysed macrophages is distinct from calcium mobilization and membrane depolarization, and may involve the generation of secondary pores/channels in the plasma membrane via a calmodulin-linked pathway.
Site-selected insertion of the transposon Tc1 into a Caenorhabditis elegans myosin light chain gene. (1993)

We used the polymerase chain reaction to detect insertions of the transposon Tc1 into mlc-2, one of two Caenorhabditis elegans regulatory myosin light chain genes. Our goals were to develop a general method to identify mutations in any sequenced gene and to establish the phenotype of mlc-2 loss-of-function mutants. The sensitivity of the polymerase chain reaction allowed us to identify nematode populations containing rare Tc1 insertions into mcl-2. mlc-2::Tc1 mutants were subsequently isolated from these populations by a sib selection procedure. We isolated three mutants with Tc1 insertions within the mlc-2 third exon and a fourth strain with Tc1 inserted in nearby noncoding DNA. To demonstrate the generality of our procedure, we isolated two additional mutants with Tc1 insertions within hlh-1, the C. elegans MyoD homolog. All of these mutants are essentially wild type when homozygous. Despite the fact that certain of these mutants have Tc1 inserted within exons of the target gene, these mutations may not be true null alleles. All three of the mlc-2 mutants contain mlc-2 mRNA in which all or part of Tc1 is spliced from the pre-mRNA, leaving small in-frame insertions or deletions in the mature message. There is a remarkable plasticity in the sites used to splice Tc1 from these mlc-2 pre-mRNAs; certain splice sites used in the mutants are very different from typical eukaryotic splice sites.
Characterization of lysosomes isolated from Dictyostelium discoideum by magnetic fractionation. (1993)

Superparamagnetic particles were prepared with iron oxide cores of congruent to 8 nm diameter and dextran coats. After feeding the probe to the amoeba, Dictyostelium discoideum, for 15 min and chasing for 15 min, a lysosome fraction was isolated magnetically. Isolates contained 76% of ingested iron, 82% of ingested fluorescent dextran, 1.3% of cell protein, 4% of the lipid, 28% of acid phosphatase, and 5% of the vacuolar H(+)-ATPase. Enrichment in endocytic markers was congruent to 60-fold; markers for other organelles were < 0.5%. The lysosomes were homogeneous, round (0.4-1.1 microns in diameter), and frequently adherent to one another through zones of intimate apposition. Cells were also fed the iron probe continuously for 3 h to fill their entire endocytic pathway; in this case, isolates contained 3.3% of cell protein, 11% of lipid, and 49% of cell acid phosphatase. Bis(monoacylglycerol)phosphate (BMP), a lipid characteristic of lysosomes in animal cells, comprised congruent to 6% of biosynthetically labelled cell lipids and up to half of the lipid in the endocytic pathway. Essentially all of the cellular BMP was recovered in isolates prepared after 3 h of feeding. The specificity and abundance of BMP in the endocytic organelles of this early diverged protist suggests that this phospholipid serves a universal and essential function in endocytosis.
The FAST technique: a simplified Agrobacterium-based transformation method for transient gene expression analysis in seedlings of Arabidopsis and other plant species (2009)

The FAST system provides a rapid, efficient and economical assay of gene function in intact plants with minimal manual handling and without dedicated device. This method is potentially ideal for future automated high-throughput analysis.