gebhart/patrepeval huggingface dataset:
Cell cycle dynamics of chromosomal organisation at single-cell resolution (2016)

Summary Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between a highly condensed mitotic structure facilitating chromosome segregation, and a decondensed interphase structure accommodating transcription, gene silencing and DNA replication. These cyclical structural transformations have been evident under the microscope for over a century, but their molecular-level analysis is still lacking. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis -interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological domains (TADs), contact insulation and long-range loops, all defined by ensemble Hi-C maps, are governed by distinct cell cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Analysing whole genome 3D structural models using haploid cell data, we discover a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data creates an essential new paradigm for the re-interpretation of chromosome conformation maps through the prism of the cell cycle.
Enabling hybrid services in emerging data networks (1999)

For a number of years, the network, software, and telecommunication industries have been working on a number of key technical issues dealing with the infrastructure support for hybrid services. From the end users' perspectives, hybrid services utilize various networks while hiding the underlying network technologies such as the wireless networks, phone system, and data networks. To this end, however, the data networks lack necessary power to support next-generation hybrid services. It is now generally understood that there is great value in creating a three-level network model with the middle level supporting a service platform that would contribute certain common services. Such a data network would provide the common services at its edges close to its points of presence (POPs) while maintaining control over all network components belonging to a specific network provider. It would interoperate with other networks to offer a uniform view and management of all hybrid services. This article describes the nature of the enhanced emerging networks and outlines the structure of a service platform that would support its functions.
IPTV, Towards Seamless Infotainment (2009)

IPTV, enabled by aggregating new technologies in computing, networking, and storage, provides a new information access and entertainment platform in the world of digital evolution. From this perspective where information and entertainment are part of each other, we write this paper to address the issues of IPTV towards seamless infotainment. We focus our discussions to explore such IPTV potentials from three aspects: information access and distribution, improving quality of entertainment, and enabling seamless infotainment. In addition, relevant topics such as IPTV standards and future directions are also discussed.
Farnesyltransferase inhibitor tipifarnib inhibits Rheb prenylation and stabilizes Bax in acute myelogenous leukemia cells (2013)

Although farnesyltransferase inhibitors have shown promising activity in relapsed lymphoma and sporadic activity in acute myelogenous leukemia, their mechanism of cytotoxicity is incompletely understood, making development of predictive biomarkers difficult. In the present study, we examined the action of tipifarnib in human acute myelogenous leukemia cell lines and clinical samples. In contrast to the Ras/MEK/ERK pathway-mediated Bim upregulation that is responsible for tipifarnib-induced killing of malignant lymphoid cells, inhibition of Rheb-induced mTOR signaling followed by dose-dependent upregulation of Bax and Puma occurred in acute myelogenous leukemia cell lines undergoing tipifarnib-induced apoptosis. Similar Bax and Puma upregulation occurred in serial bone marrow samples harvested from a subset of acute myelogenous leukemia patients during tipifarnib treatment. Expression of FTI-resistant Rheb M184L, like knockdown of Bax or Puma, diminished tipifarnib-induced killing. Further analysis demonstrated that increased Bax and Puma levels reflect protein stabilization rather than increased gene expression. In U937 cells selected for tipifarnib resistance, neither inhibition of signaling downstream of Rheb nor Bax and Puma stabilization occurred. Collectively, these results not only identify a pathway downstream from Rheb that contributes to tipifarnib cytotoxicity in human acute myelogenous leukemia cells, but also demonstrate that FTI-induced killing of lymphoid versus myeloid cells reflects distinct biochemical mechanisms downstream of different farnesylated substrates. (ClinicalTrials.gov identifier NCT00602771).
The Influence of High Energy Radiation on Cotton (1959)

Sliver lap, yarn, and fabric made of the same raw cotton of known composition were irradiated with cathode rays under various conditions. Changes in the chemical and physical properties were investigated. Some yarns also were irradiated with gamma rays. The changes that occurred in these samples were found to be the same as those in samples irradiated with cathode rays. Data for the copper number, the methylene blue number, and the intrinsic viscosity indicated that degradation of the cathode ray irradiated yarn had taken place. A new absorption maximum was found in infrared spectrograms of the cotton irradiated at high dose levels. Direct-dye affinity of the irradiated fabric was similar to oxycellulose. The tensile strength of the yarn decreased with the amount of dose it received. However, at low levels the tensile strength was found to increase to a maximum before it started to decrease; a "natural curve" of tensile strength and a "natural curve" of toughness were defined. Microbiological tests showed that both yarn and fabric were sterilized by a dome of one megarep. A general increase in mildew resistance was noted in irradiated samples compared with unirradiated samples. '
The Food of Kingfishers and Mergansers on the Margaree river, Nova Scotia (1936)

The river, particularly its northeast branch, contains chiefly salmon and trout (Salvelinus fontinalis). Kingfishers shot along the northeast branch contained chiefly salmon remains, but also trout, sticklebacks and suckers. Disgorged kingfisher pellets showed the same food for the northeast branch but consisted chiefly of sticklebacks where that fish abounded. In feeding experiments young kingfishers consumed forty or more fish each per day. The numbers consumed by kingfishers on the Northeast Margaree in 1935 is estimated to have been 330,000 salmon, 50,000 trout, and 40,000 other fishes. They evidently fed upon the food most easily obtained. American mergansers were found frequenting the salmon and trout habitats, rearing their young on the smaller streams. Stomach analyses of 28 birds shot on the Northeast Margaree give as food 82.2% salmon, 6.3% trout, 11.5% other fishes. The estimated consumption on the Northeast Margaree for July to October, 1935, is 390,000 salmon and trout.
Fragmentation of Lignin Samples with Commercial Pd/C under Ambient Pressure of Hydrogen (2016)

We report the reagentless cleavage of prevalent β-O-4 linkages in lignin model compounds, as well as the cleavage of several types of organosolv lignins, catalyzed by commercially available Pd/C. Such lignin fragmentation occurred without added reagent if the indigenous double bonds were reduced first or it occurred under conditions in which just 1 atm of hydrogen was added to the system to reduce C═C bonds of the original lignin sample in situ prior to fragmentation. A detailed view of the sites of cleavage of lignin samples from various sources was gained by HSQC NMR experiments. Complex model compounds were prepared and shown to form simpler arenes and substituted phenols under catalytic conditions without added reagents. The hydrogen generated in situ from alcohol functionalities provides the reductant for concomitant hydrogenolysis of C–O bonds in β aryl ethers. Decarbonylation of primary alcohols also occurred, and this process resulted in significant amounts of aromatic products containing substituents bearing one fewer carbon atom than the original linkages in lignin. The fragmentations of synthetic lignin and several organosolv lignins derived from Miscanthus giganteus and pine tree were conducted. Because the lignins contain alkenes that accept the hydrogen, two procedures involving reduction of the alkenes prior to C–O bond cleavage were developed. The first procedure involves reduction of the alkenes, followed by catalytic cleavage of C–O bonds after saturation of the C–C bonds; a second involves cleavage of lignin samples in the presence of 1 atm of hydrogen to saturate the alkenes before cleavage in situ. These protocols convert solid lignin to monomeric phenolic compounds with 20 mol % catalyst or to an oil (with 5 mol % Pd/C loading) having favorable viscosity parameters upon blending with a renewable organic solvent.
Analytical approach to the single-domain-to-vortex transition in small magnetic disks (2004)

An analytical model to determine the stable configuration of thin ferromagnetic disks as a function of their thickness and diameter is presented. The vortex core energy is fully taken into account. The model includes materials with nonvanishing anisotropy. We find very good agreement with micromagnetic simulations provided that the energy of the finite difference calculation is corrected for the dipolar contribution arising from the discreetness at the edge.
<i>In situ</i> oxidation of a thin layer of Ge on Si(001): Observation of GeO to SiO2 transition (1993)

A thin layer of Ge grown on Si(001) surface is oxidized in situ and investigated using XPS, AES, RHEED, and MEIS. The samples used are, Ge layer formed by deposition at room temperature and SiGe mixed layer formed by deposition at 550 °C. Oxidation at 250 °C of the RT grown layer leads to the formation of GeO and on heating the surface to 360 °C, oxygen bonds with Si forming SiO2, thereby reducing GeO to elemental Ge. In the epitaxially grown layer (grown at 550 °C), after oxidation, SiO2 and a small amount of GeO are formed. Similar reaction takes place on this surface also, forming SiO2 as the final product on the surface. In the RT grown layer, after oxidation, MEIS shows evidence for the diffusion of Si through the Ge layer towards the surface.
Is There a Fatty Acid Taste? (2009)

Taste is a chemical sense that aids in the detection of nutrients and guides food choice. A limited number of primary qualities comprise taste. Accumulating evidence has raised a question about whether fat should be among them. Most evidence indicates triacylglycerol is not an effective taste stimulus, though it clearly contributes sensory properties to foods by carrying flavor compounds and altering texture. However, there is increasing anatomical, electrophysiological, animal behavior, imaging, metabolic, and psychophysical evidence that free fatty acids are detectable when non-taste cues are minimized. Free fatty acids varying in saturation and chain length are detectable, suggesting the presence of multiple transduction mechanisms and/or a nonspecific mechanism in the oral cavity. However, confirmation of "fatty" as a taste primary will require additional studies that verify these observations are taste specific. Oral exposure to free fatty acids likely serves as a warning signal to discourage intake and influences lipid metabolism.
The ‘Naturally Occurring’ Anti‐E (1970)

Abstract. A study of 146 antenatal patients having anti‐E strongly suggests that most anti‐E's, particularly those of the papain reactive type, are initially due to a ‘natural’ stimulus, and are further stimulated by pregnancy and transfusion.
Prediction of Wax Precipitation Temperature in Petroleum Fluids (2021)

The precipitation and deposition of wax has remained a major challenge that the oil industries is faced with during the production of waxy crude. This problem is simply an issue from the wellbore to the surface facilities. As a result of this, millions of dollars has been invested in remedial operations. In this research, a predictive model that uses thermodynamic relationship in predicting precipitation of wax has been developed. K-values for the solid-liquid equilibrium is described using solubility parameter, melting point temperature, enthalpy of fusion, and the molar volume for the components. The weight fraction was used to describe the wax mixture. Experimental data from three oil mixtures were used in comparing the model predicted wax appearance temperature (WAT). For oil mixA, the experimental value is 294.15K; Pauly et al predicted 302.15K while this work predicted 301.21K. For oil mixB, the experimental value is 300.15K; Pauly et al predicted 310.15K while this work predicted 308.91K. For oil mixC, the experimental value is 298.15K; Pauly et al predicted 302.15K while this work predicted 300.38K. The obtained results from this research confirmed the capability of the model in predicting Wax Appearance Temperature. A more conservative value for the WAT was predicted which is an improvement.
Diagnostic value of elevated serum miRNA-143 levels in sepsis (2016)

Serum miR-143 is elevated in patients with sepsis, and may be a useful biomarker for distinguishing between sepsis and SIRS.
Recent SLC developments (2002)

The SLAC Linear Collider (SLC) is the forerunner of a new generation of high energy accelerators. As such, it incorporates many novel features that must be fully exploited to achieve optimum performance. In this paper we present an overview of the frontiers of collider performance at SLC. Recent developments have centered on polarization, intensity and emittance preservation issues. A polarized source and spin transport system were successfully commissioned in 1992 and operated with high reliability. Practical intensity limits associated with rapid growth (>
The Role of Tau Phosphorylation in the Pathogenesis of Alzheimers Disease (2006)

The microtubule-associated protein tau, which is abundantly expressed in neurons, is deposited in cells in an abnormally phosphorylated state as fibrillar lesions in numerous neurodegenerative diseases, with the most notable being Alzheimer's disease. Tau plays a crucial role in the neuron as it binds and stabilizes microtubules, and can regulate axonal transport; functions that are regulated by site-specific phosphorylation events. In pathological conditions such as Alzheimer's disease and other tauopathies, tau is abnormally phosphorylated, and that this contributes to its dysfunction. Given the increasing evidence that a disruption in the normal phosphorylation state of tau followed by conformational changes plays a key role in the pathogenic events that occur in Alzheimer's disease and other tauopathies; it is critical to elucidate the regulation of tau phosphorylation. This review focuses on recent literature pertaining to the regulation of tau phosphorylation and function, and the role that a dysregulation of tau phosphorylation may play in the neuronal dysfunction in Alzheimer's disease.
Effect of porosity and environment on the mechanical behavior of acrylic bone cement modified with acrylonitrile-butadiene-styrene particles: I. Fracture toughness (1999)

The elastomeric copolymer acrylonitrile-butadiene-styrene (ABS) was added to a conventional acrylic bone cement matrix. The results obtained show that although strength and stiffness decreased with an increasing second phase volume fraction, ductility and toughness both increased. The crack propagation became stable for specimens containing over a 5% volume fraction of the second phase. The fracture toughness increased up to 60% when the amount of ABS reached 20% (v/v). For larger amounts linear elastic fracture mechanics techniques could not be used properly. The effects of porosity and environmental conditions on the mechanical behavior were also studied. The mechanisms that control the fracture process were investigated by means of scanning electron microscopy.
Dynamic Stratification in Drying Films of Colloidal Mixtures (2016)

In simulations and experiments, we study the drying of films containing mixtures of large and small colloidal particles in water. During drying, the mixture stratifies into a layer of the larger particles at the bottom with a layer of the smaller particles on top. We developed a model to show that a gradient in osmotic pressure, which develops dynamically during drying, is responsible for the segregation mechanism behind stratification.
Production of Tubular Structures in Vero Cells Infected with Herpes Simplex Virus Type 2: Effects of Ultraviolet Light Irradiation and Antimetabolites (1979)

In order to investigate the nature of tubular structures specifically found in herpes simplex virus type 2 (HSV-2)-infected cells, the multiplication of HSV-2 was studied in Vero cells cultured in the presence of varying concentrations of cytosine arabinoside (Ara-C) and cycloheximide (CH), inhibitors of DNA synthesis and protein synthesis respectively. Ara-C, at a concentration of 60 micrograms/ml, inhibited the multiplication of HSV-2 by more than 99% and also prevented the appearance of tubular structures and virus particles in the nuclei of infected cells. Nevertheless, the synthesis of virus specific surface antigens of HSV-2-infected Vero cells was not reduced, as revealed by the fluorescent antibody technique. On the other hand, 10 micrograms/ml of CH inhibited both the appearance of tubular structures and virus particles and the synthesis of virus specific surface antigens by more than 99%. These observations strongly suggest that the appearance of tubular structures is one of the late events in the process of virus multiplication. To measure the comparative genome size needed to produce membrane antigens, tubular structures and infectious centres, the effect of u.v.-inactivation of HSV-2 on these processes was studied. After u.v.-irradiation, the capacity to induce tubular structures was inactivated at a slower rate than the capacity to form infectious centres, but at a faster rate than the induction of surface antigens. Furthermore, more tubular structures could be induced by u.v.-inactivated virus than by the non-irradiated virus which was diluted to the same infectivity as the u.v.-irradiated virus. These results indicate that expression of the entire genome is not required for the production of tubular structures.
Anodic oxidation of phenolic compounds. Part 5. Anodic methoxylation of phenols. A simple synthesis of quinones, quinone acetals, and 4-methyl-α-methoxycyclohexa-2,5-dienones (1978)

The products and yields obtained on anodic oxidation in methanol of a series of phenols (1a–h) have been investigated as a function of anode material, anode potential, methanol concentration, supporting electrolyte, temperature, and substituents. ortho- and para-Methoxylated and dimeric products were observed. However, experimental conditions were found which, in favourable cases, allow selective formation of para-methoxylated products (isolated as a para-dienone or para-benzoquinone), ortho-methoxylated products (isolated as an ortho-dienone or the Diels–Alder adduct of this dienone), or dimeric products. The methoxylated products are formed via nucleophilic attack of methanol on an anodically generated phenoxylium ion; the dimeric products are probably formed by dimerisation of anodically generated phenoxyl radicals.
Oral administration of transgenic barley expressing a <i>Culicoides</i> allergen induces specific antibody response (2016)

This study shows that specific antibody response can be induced in horses not exposed to Culicoides, using oral treatment with transgenic barley expressing an allergen. Further studies will determine whether this approach is a useful alternative for prevention and treatment of equine insect bite hypersensitivity.
TCP performance over mobile ad hoc networks (2004)

TCP is a transport protocol that guarantees reliable ordered delivery of data packets over wired networks. Although it is well tuned for wired networks, TCP performs poorly in mobile ad hoc networks (MANETs). This is because TCP's implicit assumption that any packet loss is due to congestion is invalid in mobile ad hoc networks where wireless channel errors, link contention, mobility and multipath routing may significantly corrupt or disorder packet delivery. If TCP misinterprets such losses as congestion and consequently invokes congestion control procedures, it will suffer from performance degradation and unfairness. To understand TCP behaviour and improve the TCP performance over multi-hop ad hoc networks, considerable research has been carried out. As the research in this area is still active and many problems are still wide open, an in-depth and timely survey is needed. In this paper, the challenges imposed on the standard TCP in the wireless ad hoc network environment are first identified. Then some existing solutions are discussed according to their design philosophy. Finally, some suggestions regarding future research issues are presented.
Glutamate-dependent activation of NF-kappaB during mouse cerebellum development. (1997)

NF-kappaB and activator protein 1 (AP-1) are dimeric transcription factors involved in transcriptional regulation in many cells, including neurons. We have examined their activity during mouse cerebellum development, a postnatal process starting just after birth and completed by the fourth postnatal (PN) week. The activity of these factors was analyzed by binding of nuclear extracts to a synthetic oligonucleotide representing the kappaB site of human immunodeficiency virus or the AP-1 site of the urokinase promoter. NF-kappaB activity was observed from 7 PN, was restricted to the developing cerebellum, and was not observed in the early postnatal neocortex and hippocampus. On the other hand, AP-1 activity was not found in cerebellum but was present in both neocortex and hippocampus. Moreover, a kappaB-driven transgene was found to be increasingly expressed in the cerebellum from 5 PN to 10 PN but not in the adult. The regulation of NF-kappaB activation in mouse cerebellum was analyzed by intraperitoneal injection of glutamate receptor antagonists to 9 PN mice, which abolished NF-kappaB-binding activity, suggesting an endogenous loop of glutamate receptor activation. Glutamate receptor agonists, on the other hand, induced NF-kappaB nuclear translocation in the cerebellum of 5 PN mice, which is a stage in which NF-kappaB is not yet endogenously activated. This effect was specific for NF-kappaB and not observed for AP-1. In adult mice, NF-kappaB activity was absent in the cerebellum and was not induced by intraperitoneal injection of glutamate receptor agonists. These data show that NF-kappaB is specifically activated during cerebellum development and indicate an important role of glutamate receptors in this process.
Robust support vector machine with bullet hole image classification (2002)

This paper proposes a robust support vector machine for pattern classification, which aims at solving the over-fitting problem when outliers exist in the training data set. During the robust training phase, the distance between each data point and the center of class is used to calculate the adaptive margin. The incorporation of the average techniques to the standard support vector machine (SVM) training makes the decision function less detoured by outliers, and controls the amount of regularization automatically. Experiments for the bullet hole classification problem show that the number of the support vectors is reduced, and the generalization performance is improved significantly compared to that of the standard SVM training.