gebhart/patrepeval huggingface dataset:
The Boolean Solution to the Congested IP Link Location Problem: Theory and Practice (2007)

Like other problems in network tomography or traffic matrix estimation, the location of congested IP links from end-to-end measurements requires solving a system of equations that relate the measurement outcomes with the variables representing the status of the IP links. In most networks, this system of equations does not have a unique solution. To overcome this critical problem, current methods use the unrealistic assumption that all IP links have the same prior probability of being congested. We find that this assumption is not needed, because these probabilities can be uniquely identified from a small set of measurements by using properties of Boolean algebra. We can then use the learnt probabilities as priors to find rapidly the congested links at any time, with an order of magnitude gain in accuracy over existing algorithms. We validate our results both by simulation and real implementation in the PlanetLab network.
Study on natural head motion in waiting state with receptionist robot SAYA that has human-like appearance (2009)

Android robots that have a human-like appearance have been developed recently. The purpose of android robots is to realize realistic communication between human and robot by implementation of human-like behaviors. Then knowledge and techniques for generating human-like natural motions and behaviors with android robot are required. In human, head and body are moved consciously or unconsciously even while waiting. Therefore it is thought that moving SAYA's head and body in waiting state like human beings improves humanity of SAYA. Thus, in this study, we tried to realize human-like head motion in waiting state with SAYA. Firstly, we measured human head motion and time-dependent three head rotation angles were obtained in waiting state by using motion capture system. We then analyzed human head motions and we proposed random walk model based on characteristics of human head motions for SAYAs motions. Then we implemented natural head motions to SAYA. Finally, we verified that head motions in waiting state affected the humanity of SAYA, and it greatly enhanced emotional impression of human by subjective experiment
A micromass culture method for rat embryonic neural cells (1983)

A method of culturing early (13-day) rat embryo neural cells is described. Undifferentiated neural epithelium is disaggregated and cultured in small discrete islands. Cells that destined to differentiate as neurons actively segregate from the other cells in the island and aggregate together into small clumps. Other cells flatten and attach to the substrate and resemble typical fibroblasts throughout the culture period. The clumps of preneuron cells spread out forming large irregular foci. Spreading is mediated by active cell movements. Cells in the foci differentiate as a pure population of neurons identifiable by specific inhibition of 3H-labelled gamma-amino butyric acid incorporation or by labelling with a monoclonal antibody to GQ-ganglioside. The ganglioside is not found on the cell surface at the start of culture after trypsinization, but emerges during the 5 days of culture. The antigen is similarly not present in the embryonic mesencephalon in vivo at 13 days post coitum, only emerging later in the differentiated midbrain. There is thus an apparent de novo synthesis, which is paralleled in vivo and in vitro.
Determination of pectin content of eucalyptus wood (2011)

Abstract Very little is known about the occurrence of pectin in wood and it is speculated that between 10 mg g -1 and 40 mg g -1 of wood consists of pectin. The present study aimed to quantify pectin in eucalyptus wood and to determine the influence of tree species, yield potential of the site, tree age class and wood tissue type on its occurrence. Wood was hydrolysed using the Saeman procedure and the neutral and acidic monosaccharides quantified with high-performance liquid chromatography (HPLC). The d -galacturonic acid was the predominant pectic monosaccharide followed by d -galactose, l -arabinose and l -rhamnose. Through the addition of all pectic monosaccharides, it was determined that eucalyptus wood contained between 15.2 mg g -1 and 25.8 mg g -1 pectin. Wood tissue type had a major influence on the total pectin content of the samples. The cambium contained the highest concentration of pectin, reflecting more active growth. These results contribute to the understanding of wood biochemistry and can be useful in the industries producing biofuels or paper.
Automated field-programmable compute accelerator design using partial evaluation (2002)

This paper describes a compiler that generates both hardware and controlling software for field-programmable compute accelerators. By analyzing a source program together with part of its input, the compiler generates VHDL descriptions of functional units that are mapped on a set of FPGA chips and an optimized sequence of control constructions that run on the customized machine. The primary technique employed in the compiler is partial evaluation, which is used to transform an application program together with part of its input into an optimized program. Further phases in the compiler identify pieces of the program that can be realized in hardware and schedule computations to execute on the resulting hardware. Finally, a set of specialized functional units generated by the compiler for a timing simulation program is used to demonstrate the approach.
11q Deletions Identify a New Subset of B-Cell Chronic Lymphocytic Leukemia Characterized by Extensive Nodal Involvement and Inferior Prognosis (1997)

Deletions of the long arm of chromosome 11 (11q) are one of the most frequent structural chromosome aberrations in various types of lymphoproliferative disorders. However, in most conventional chromosome banding studies of B-cell chronic lymphocytic leukemia (B-CLL), 11q deletions were not identified as a frequent aberration. The objective of this study was to analyze the frequency and clinical impact of 11q deletions in B-CLL by interphase cytogenetics using fluorescence in situ hybridization (FISH). Mononuclear cells from 214 patients with B-CLL were studied by FISH using the yeast artificial chromosome (YAC) clone 755b11 from chromosome region 11q22.3-q23.1; we previously showed that this clone was contained within a 2- to 3-Mb sized segment of 11q commonly deleted in lymphoproliferative disorders. Forty-three of the 214 (20%) tumors exhibited 11q deletions; 11q deletions were the second most frequent chromosome aberration following 13q14 (RB1 and/or D13S25) deletions (45%); they were more frequent than trisomy 12 (15%) or deletion of 17p (TP53 gene) (10%). Patients with 11q deletions were younger (P = .01) and had more advanced clinical stages (P = .01). 11q deletions were associated with extensive peripheral, abdominal, and mediastinal lymphadenopathy (P < .001). Patients with 11q deletions had a more rapid disease progression as shown by a shorter treatment-free interval (9 months v 43 months; P < .001). The prognostic effect of 11q deletion on survival strongly depended on the age: in patients less than 55 years old, the median survival time was significantly shorter in the deletion group (64 months v 209 months; P < .001), whereas in patients > or = 55 years old there was no significant difference (94 months v 111 months; P = .82). 11q deletions identify a new clinical subset of B-CLL characterized by extensive lymph node involvement. In younger B-CLL patients, this aberration is an important predictor of survival.
The Xerox Star: a retrospective (1989)

A description is given of the Xerox 8010 Star information system, which was designed as an office automation system. The idea was that professionals in a business or organization would have workstations on their desks and would use them to produce, retrieve, distribute, and organize documentation, presentations, memos, and reports. All of the workstations in an organization would be connected via Ethernet and would share access to file servers, printers, etc. The distinctive features of Star are identified, and changes to the original design are examined. A history of Star development is included. Some lessons learned from designing Star are related.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Microwave nanotube transistor operation at high bias (2006)

We measure the small signal, 1GHz source-drain dynamical conductance of a back-gated single-walled carbon nanotube field effect transistor at both low and high dc bias voltages. At all bias voltages, the intrinsic device dynamical conductance at 1GHz is identical to the low frequency dynamical conductance, consistent with the prediction of a cutoff frequency much higher than 1GHz. This work represents a significant step towards a full characterization of a nanotube transistor for rf and microwave amplifiers.
Fungal beta-glucan interacts with vitronectin and stimulates tumor necrosis factor alpha release from macrophages (1996)

beta-Glucans are polymers of D-glucose which represent major structural components of fungal cell walls. It was shown previously that fungi interact with macrophages through beta-glucan receptors, thereby inducing release of tumor necrosis factor alpha (TNF-alpha). Additional studies demonstrated that vitronectin, a host adhesive glycoprotein, binds to fungi and enhances macrophage recognition of these organisms. Since vitronectin contains a carbohydrate-binding region, we postulated that vitronectin binds fungal beta-glucans and subsequently augments macrophage TNF-alpha release in response to this fungal component. To study this, we first determined the release of TNF-alpha from alveolar macrophages stimulated with fungal beta-glucan. Maximal TNF-alpha release occurred with moderate concentrations of beta-glucan (100 to 200 micrograms/ml), whereas higher concentrations of beta-glucan (> or = 500 micrograms/ml) caused apparent suppression of the TNF-alpha activity released. This suppression of TNF-alpha activity by high concentrations of beta-glucan was mediated by the particulate beta-glucan binding soluble TNF-alpha, through the lectin-binding domain of the cytokine, rendering the TNF-alpha less available for measurement. Next, we assessed the interaction of vitronectin with beta-glucan. Binding of 125I-vitronectin to particulate fungal beta-glucan was dose dependent and specifically inhibitable by unlabeled vitronectin. Furthermore, treatment of beta-glucan with vitronectin substantially augmented macrophage TNF-alpha release in response to this fungal component. These findings demonstrate that fungal beta-glucan can directly modulate TNF-alpha release from macrophages. Further, these studies indicate that the host adhesive glycoprotein vitronectin specifically binds beta-glucan and augments macrophage cytokine release in response to this fungal element.
Cell and organ printing 1: Protein and cell printers (2003)

We have developed several devices for positioning organic molecules, molecular aggregates, cells, and single-cell organisms onto solid supports. These printers can create stable, functional protein arrays using an inexpensive technology. The cell printer allows us to create cell libraries as well as cellular assemblies that mimic their respective position in organs. The printers are derived from commercially available ink-jet printers that are modified to dispense protein or cell solutions instead of ink. We describe here the modifications to the print heads, and the printer hardware and software that enabled us to adapt the ink-jet printers for the manufacture of cell and protein arrays. The printers have the advantage of being fully automated and computer controlled, and allow for the high-throughput manufacture of protein and cell arrays.
Influenza virus‐like particles produced by transient expression in Nicotiana benthamiana induce a protective immune response against a lethal viral challenge in mice (2008)

A strain-specific vaccine represents the best possible response to the threat of an influenza pandemic. Rapid delivery of such a vaccine to the world's population before the peak of the first infection wave seems to be an unattainable goal with the current influenza vaccine manufacturing capacity. Plant-based transient expression is one of the few production systems that can meet the anticipated surge requirement. To assess the capability of plant agroinfiltration to produce an influenza vaccine, we expressed haemagglutinin (HA) from strains A/Indonesia/5/05 (H5N1) and A/New Caledonia/20/99 (H1N1) by agroinfiltration of Nicotiana benthamiana plants. Size distribution analysis of protein content in infiltrated leaves revealed that HA was predominantly assembled into high-molecular-weight structures. H5-containing structures were purified and examination by transmission electron microscopy confirmed virus-like particle (VLP) assembly. High-performance thin layer chromatography analysis of VLP lipid composition highlighted polar and neutral lipid contents comparable with those of purified plasma membranes from tobacco plants. Electron microscopy of VLP-producing cells in N. benthamiana leaves confirmed that VLPs accumulated in apoplastic indentations of the plasma membrane. Finally, immunization of mice with two doses of as little as 0.1 microg of purified influenza H5-VLPs triggered a strong immune response against the homologous virus, whereas two doses of 0.5 microg of H5-VLPs conferred complete protection against a lethal challenge with the heterologous A/Vietnam/1194/04 (H5N1) strain. These results show, for the first time, that plants are capable of producing enveloped influenza VLPs budding from the plasma membrane; such VLPs represent very promising candidates for vaccination against influenza pandemic strains.
Reduced Sequence Variability on the NeoY Chromosome of Drosophila americana americana (1999)

Sex chromosomes are generally morphologically and functionally distinct, but the evolutionary forces that cause this differentiation are poorly understood. Drosophila americana americana was used in this study to examine one aspect of sex chromosome evolution, the degeneration of nonrecombining Y chromosomes. The primary X chromosome of D. a. americana is fused with a chromosomal element that was ancestrally an autosome, causing this homologous chromosomal pair to segregate with the sex chromosomes. Sequence variation at the Alcohol Dehydrogenase (Adh) gene was used to determine the pattern of nucleotide variation on the neo-sex chromosomes in natural populations. Sequences of Adh were obtained for neo-X and neo-Y chromosomes of D. a. americana, and for Adh of D. a. texana, in which it is autosomal. No significant sequence differentiation is present between the neo-X and neo-Y chromosomes of D. a. americana or the autosomes of D. a. texana. There is a significantly lower level of sequence diversity on the neo-Y chromosome relative to the neo-X in D. a. americana. This reduction in variability on the neo-Y does not appear to have resulted from a selective sweep. Coalescent simulations of the evolutionary transition of an autosome into a Y chromosome indicate there may be a low level of recombination between the neo-X and neo-Y alleles of Adh and that the effective population size of this chromosome may have been reduced below the expected value of 25% of the autosomal effective size, possibly because of the effects of background selection or sexual selection.
Monitoring and guidance of minimally-invasive thermal therapy using diagnostic ultrasound (2009)

We present specialized ultrasound imaging modes for monitoring and guidance of noninvasive and minimally-invasive thermal therapy. One mode is based on two-dimensional imaging of temperature change using diagnostic ultrasound. We have validated this method both in vivo and in vitro in monitoring the heating patterns produced by noninvasive HIFU source and minimally-invasive RF ablation device, respectively. In addition, a nonlinear method for imaging the quadratic echo components from HIFU-induced lesions has also been developed and tested in vivo. Illustrative results from both modes of imaging are presented. These results demonstrate the unique advantages of ultrasound as an image-guidance modality. Specifically, the high spatial and temporal resolutions that allow for imaging highly-localized short-duration therapeutic and sub-therapeutic HIFU beams. With the advent of highperformance computing hardware, these imaging modes are now implementable in real-time. This will lead to active realtime monitoring and control of a range of thermal therapies in the very near future.
Differentially expressed fibroblast growth factors regulate skeletal muscle development through autocrine and paracrine mechanisms. (1996)

Several FGF family members are expressed in skeletal muscle; however, the roles of these factors in skeletal muscle development are unclear. We examined the RNA expression, protein levels, and biological activities of the FGF family in the MM14 mouse skeletal muscle cell line. Proliferating skeletal muscle cells express FGF-1, FGF-2, FGF-6, and FGF-7 mRNA. Differentiated myofibers express FGF-5, FGF-7, and reduced levels of FGF-6 mRNA. FGF-3, FGF-4, and FGF-8 were not detectable by RT-PCR in either proliferating or differentiated skeletal muscle cells. FGF-I and FGF-2 proteins were present in proliferating skeletal muscle cells, but undetectable after terminal differentiation. We show that transfection of expression constructs encoding FGF-1 or FGF-2 mimics the effects of exogenously applied FGFs, inhibiting skeletal muscle cell differentiation and stimulating DNA synthesis. These effects require activation of an FGF tyrosine kinase receptor as they are blocked by transfection of a dominant negative mutant FGF receptor. Transient transfection of cells with FGF-1 or FGF-2 expression constructs exerted a global effect on myoblast DNA synthesis, as greater than 50% of the nontransfected cells responded by initiating DNA synthesis. The global effect of cultures transfected with FGF-2 expression vectors was blocked by an anti-FGF-2 monoclonal antibody, suggesting that FGF-2 was exported from the transfected cells. Despite the fact that both FGF-l and FGF-2 lack secretory signal sequences, when expressed intracellularly, they regulate skeletal muscle development. Thus, production of FGF-1 and FGF-2 by skeletal muscle cells may act as a paracrine and autocrine regulator of skeletal muscle development in vivo.
Lipase-Catalyzed Regioselective Esterification of Rapamycin:  Synthesis of Temsirolimus (CCI-779) (2005)

A lipase-catalyzed acylation of the immunosuppressant rapamycin with complete regioselectivity is described. The method was successfully applied to the synthesis of 42-hemiesters and temsirolimus (CCI-779), an investigational oncology drug.[reaction: see text]
Electrophilic Fluorination of 5-(Cyanomethyl)imidazole-4-carboxylate Nucleosides: Facile Entry to 3-Fluoro-3-deazaguanosine Analogues (2005)

A facile and efficient methodology is described for the synthesis of 3-fluoro-3-deazaguanosines based on a novel electrophilic fluorination of 5-(cyanomethyl)imidazole-4-carboxylate nucleosides. This general methodology can be readily applied to the synthesis of sugar-modified 3-fluoro-3-deazaguanosine analogues.
Fractal and Image Analysis of the Microvasculature in Normal Intestinal Submucosa and Intestinal Polyps in APCMin/+ Mice (2007)

Extract Extended abstract of a paper presented at Microscopy and Microanalysis 2007 in Ft. Lauderdale, Florida, USA, August 5 – August 9, 2007
Exudative Age-Related Macular Degeneration: Current Therapies and Potential Treatments (2009)

Strategies for preventing vision loss in patients with neovascular age-related macular degeneration (ARMD) have evolved over the past decade. Whereas earlier treatments were based on thermal destruction of choroidal neovascularization (CNV), new therapies rely on targeted pharmacologic approaches to reduce the harmful effects of CNV treatment. For the first time in the history of neovascular ARMD treatment, anti-VEGF therapies have consistently improved visual acuity in a subset of patients. Clinical trials continue to investigate the optimal dosing strategies and combination therapies to better refine the treatment of this chronic and debilitating disease.
The Presence of IGHG1 in Human Pancreatic Carcinomas Is Associated With Immune Evasion Mechanisms (2011)

The presence of IGHG1 in pancreatic cancer cells might constitute an important element responsible for tumor cell proliferation and immune evasion mechanisms.
Pharmacologic characteristics of statins (2003)

Considerable effort has been devoted to improving the pharmacologic characteristics and clinical effects of statins. Desirable pharmacologic properties include potent inhibition of hydroxymethylglutaryl coenzyme A (HMG-CoA) reductase, selectivity of uptake in hepatocytes, low systemic bioavailability to reduce systemic adverse effects, prolonged elimination half-life, and no or minimal hepatic metabolism to avoid drug-drug interactions. The desirable effects on lipid variables would include increased effectiveness in reducing levels of low-density lipoprotein cholesterol and other atherogenic lipoproteins and measurable beneficial effects on high-density lipoprotein cholesterol levels. As a product of the ongoing efforts regarding statin pharmacology, the new statin rosuvastatin exhibits significant improvements in several of these characteristics.
Reversal of diet-induced hepatic steatosis and hepatic insulin resistance by antisense oligonucleotide inhibitors of acetyl-CoA carboxylases 1 and 2 (2006)

Hepatic steatosis is a core feature of the metabolic syndrome and type 2 diabetes and leads to hepatic insulin resistance. Malonyl-CoA, generated by acetyl-CoA carboxylases 1 and 2 (Acc1 and Acc2), is a key regulator of both mitochondrial fatty acid oxidation and fat synthesis. We used a diet-induced rat model of nonalcoholic fatty liver disease (NAFLD) and hepatic insulin resistance to explore the impact of suppressing Acc1, Acc2, or both Acc1 and Acc2 on hepatic lipid levels and insulin sensitivity. While suppression of Acc1 or Acc2 expression with antisense oligonucleotides (ASOs) increased fat oxidation in rat hepatocytes, suppression of both enzymes with a single ASO was significantly more effective in promoting fat oxidation. Suppression of Acc1 also inhibited lipogenesis whereas Acc2 reduction had no effect on lipogenesis. In rats with NAFLD, suppression of both enzymes with a single ASO was required to significantly reduce hepatic malonyl-CoA levels in vivo, lower hepatic lipids (long-chain acyl-CoAs, diacylglycerol, and triglycerides), and improve hepatic insulin sensitivity. Plasma ketones were significantly elevated compared with controls in the fed state but not in the fasting state, indicating that lowering Acc1 and -2 expression increases hepatic fat oxidation specifically in the fed state. These studies suggest that pharmacological inhibition of Acc1 and -2 may be a novel approach in the treatment of NAFLD and hepatic insulin resistance.
Synapse Pathology in Psychiatric and Neurologic Disease (2010)

Inhibitory and excitatory synapses play a fundamental role in information processing in the brain. Excitatory synapses usually are situated on dendritic spines, small membrane protrusions that harbor glutamate receptors and postsynaptic density components and help transmit electrical signals. In recent years, it has become evident that spine morphology is intimately linked to synapse function--smaller spines have smaller synapses and support reduced synaptic transmission. The relationship between synaptic signaling, spine shape, and brain function is never more apparent than when the brain becomes dysfunctional. Many psychiatric and neurologic disorders, ranging from mental retardation and autism to Alzheimer's disease and addiction, are accompanied by alterations in spine morphology and synapse number. In this review, we highlight the structure and molecular organization of synapses and discuss functional effects of synapse pathology in brain disease.