gebhart/patrepeval huggingface dataset:
Temporal-Relational Classifiers for Prediction in Evolving Domains (2008)

Many relational domains contain temporal information and dynamics that are important to model (e.g., social networks, protein networks). However, past work in relational learning has focused primarily on modeling static "snapshots" of the data and has largely ignored the temporal dimension of these data. In this work, we extend relational techniques to temporally-evolving domains and outline a representational framework that is capable of modeling both temporal and relational dependencies in the data. We develop efficient learning and inference techniques within the framework by considering a restricted set of temporal-relational dependencies and using parameter-tying methods to generalize across relationships and entities. More specifically, we model dynamic relational data with a two-phase process, first summarizing the temporal-relational information with kernel smoothing, and then moderating attribute dependencies with the summarized relational information. We develop a number of novel temporal-relational models using the framework and then show that the current approaches to modeling static relational data are special cases within the framework. We compare the new models to the competing static relational methods on three real-world datasets and show that the temporal-relational models consistently outperform the relational models that ignore temporal information - achieving significant reductions in error ranging from 15% to 70%.
Factors producing bile infarction and bile duct proliferation in biliary obstruction (1990)

To clarify the factors producing bile infarction and bile duct proliferation in obstructive jaundice, the incidence of the hepatic lesions and the serum levels of the bile constituents were examined in three rat models. (1) Ligation of the common bile duct induced bile infarction, bile duct proliferation, retention of bile in the liver, and elevation of the serum levels of total bilirubin and total bile acids. (2) The rats treated by choledochotomy had bile in the abdominal cavity, but there was no retention of bile in the liver. The degree of development of bile infarction was similar to that of the common bile duct ligation group, but bile duct proliferation was not found: the serum levels of total bilirubin and total bile acids were elevated. (3) In the rats subjected to partial bile duct ligation, bile infarction and bile duct proliferation were seen only in the lobes with ligation of the hepatic ducts: only slight or no elevation of the serum levels of total bilirubin and total bile acids was found. These data suggest that bile infarction is caused by the toxic action of bile constituents other than bilirubin and bile acids, absorbed into the blood from the obstructed biliary system, and that bile duct proliferation is due to mechanical factors following bile retention or direct actions of retained bile in the liver.
Racial Differences in Susceptibility to Infection byMycobacterium tuberculosis (1990)

The prevalence of tuberculosis among blacks is known to be about twice that among whites. When we looked at infection rates among the initially tuberculin-negative residents of 165 racially integrated nursing homes in Arkansas, we were stimulated to investigate whether this difference could be due in part to racial differences in susceptibility to Mycobacterium tuberculosis infection. A new infection was defined by an increase of ≥12 mm of induration after a tuberculin skin test (5 tuberculin units) administered at least 60 days after a negative two-step test.
Advancing solar cells to the limit with energy cascading (2013)

An analysis of six-junction (6J) concentrated photovoltaic (CPV) solar cells and modules versus combined cycle power plants is presented in order to determine if the power conversion efficiency of 6J CPV modules can equal or exceed the power conversion efficiency of combined gas turbine/steam turbine power plants. The 6J CPV solar cells are modeled with a realistic DNI solar spectrum at Phoenix, AZ, USA and then CPV cell efficiency and module system efficiency is calculated. Six junction CPV cells and modules will have to be pushed close to their limits in order to approach the performance of combined cycle power plants. If this is the case, it may be possible to realize ~ 50% CPV module AC efficiency with advanced 6J CPV cells and optimized balance of systems.
Basis for selective incorporation of glycoproteins into the influenza virus envelope (1993)

The ability of mutant or chimeric A/Japan hemagglutinins (HAs) to compete for space in the envelope of A/WSN influenza viruses was investigated with monkey kidney fibroblasts that were infected with recombinant simian virus 40 vectors expressing the Japan proteins and superinfected with A/WSN influenza virus. Wild-type Japan HA assembled into virions as well as WSN HA did. Japan HA lacking its cytoplasmic sequences, HAtail-, was incorporated into influenza virions at half the efficiency of wild-type Japan HA. Chimeric HAs containing the 11 cytoplasmic amino acids of the herpes simplex virus type 1gC glycoprotein or the 29 cytoplasmic amino acids of the vesicular stomatitis virus G protein were incorporated into virions at less than 1% the efficiency of HAtail-. Thus, the cytoplasmic domain of HA was not required for the selection process; however, foreign cytoplasmic sequences, even short ones, were excluded. A chimeric HA having the gC transmembrane domain and the HA cytoplasmic domain (HgCH) was incorporated at 4% the efficiency of HAtail-. When expressed from simian virus 40 recombinants in this system, vesicular stomatitis virus G protein with or without (Gtail-) its cytoplasmic domain was essentially excluded from influenza virions. Taken together, these data indicate that the HA transmembrane domain is required for incorporation of HA into influenza virions. The slightly more efficient incorporation of HgCH than G or Gtail- could indicate that the region important for assembling HA into virions extends into part of the cytoplasmic domain.
Highly Efficient Formation of Visible Light Tunable TiO2-xNx Photocatalysts and Their Transformation at the Nanoscale (2003)

Using a simple nanoscale exclusive synthesis route, TiO2-xNx photocatalysts that can be tuned to absorb across the visible region are produced in seconds at room temperature. The photocatalysts are formed by employing the direct nitridation of anatase TiO2 nanostructures with alkylammonium salts. Depending on the degree of TiO2 nanoparticle agglomeration, catalytically active TiO2-xNx anatase structured particles are obtained whose absorption onset extends well into the visible region at λ ∼ 550 nm. The introduction of a small quantity of palladium in the form of the chloride or nitrate facilitates further nitrogen uptake, appears to lead to a partial phase transformation, displays a counterion effect when compared also to the acetate, and produces a material absorbing well into the near-infrared. The introduction of palladium via the chloride also facilitates the formation of small tetrahedral and octahedral palladium-based crystallites throughout the TiO2-xNx lattice. Surprisingly, no organics appear to be incorporated into the final TiO2-xNx products. The resulting photocatalysts readily photodegrade methylene blue and lead to the catalytic oxidation of ethylene as they are placed as gels on surfaces. In contrast to the current nitridation process, which is quite facile at the nanoscale, we observe a much slower nitration of Degussa P25 nanopowders and little or no direct nitridation of micrometer-sized anatase or rutile TiO2 powders at room temperature. We thus demonstrate an example of how a traversal to the nanoscale can vastly improve the efficiency for producing important submicron materials.
Parallax: managing storage for a million machines (2005)

OS virtualization is drastically changing the face of system administration for large computer installations such as commercial datacenters and scientific clusters. A recent report by Gartner predicts that commercial use of
Late-life rapamycin treatment reverses age-related heart dysfunction (2013)

Rapamycin has been shown to extend lifespan in numerous model organisms including mice, with the most dramatic longevity effects reported in females. However, little is known about the functional ramifications of this longevity-enhancing paradigm in mammalian tissues. We treated 24-month-old female C57BL/6J mice with rapamycin for 3 months and determined health outcomes via a variety of noninvasive measures of cardiovascular, skeletal, and metabolic health for individual mice. We determined that while rapamycin has mild transient metabolic effects, there are significant benefits to late-life cardiovascular function with a reversal or attenuation of age-related changes in the heart. RNA-seq analysis of cardiac tissue after treatment indicated inflammatory, metabolic, and antihypertrophic expression changes in cardiac tissue as potential mechanisms mediating the functional improvement. Rapamycin treatment also resulted in beneficial behavioral, skeletal, and motor changes in these mice compared with those fed a control diet. From these findings, we propose that late-life rapamycin therapy not only extends the lifespan of mammals, but also confers functional benefits to a number of tissues and mechanistically implicates an improvement in contractile function and antihypertrophic signaling in the aged heart with a reduction in age-related inflammation.
Medical Imaging on the Semantic Web: Annotation and Image Markup. (2008)

Medical images are proliferating at an explosive pace, similar to other types of data in e-Science. Technological solutions are needed to enable machines to help researchers and physicians access and use these images optimally. While Semantic Web technologies are showing promise in tackling the information challenges in biomedicine, less attention is focused on leveraging similar technologies in imaging. We are developing methods and tools to enable the transparent discovery and use of large distributed collections of medical images in cyberspace as well as within hospital information systems. Our approach is to make the human and machine descriptions of image pixel content machine-accessible through annotation using ontologies. We created an ontology of image annotation and markup, specifying the entities and relations necessary to represent the semantics of medical image pixel content. We are creating a toolkit to collect the annotations directly from researchers and physicians as they view the images on medical imaging workstations. Image annotations, represented as instances in the ontology can be serialized to a variety of formats, enabling interoperability among a variety of systems that contain images: medical records systems, image archives in hospitals, and the Semantic Web. The ontology-based annotations will enable images to be related to non-image data having related semantics and relevance. Our ultimate goal is to enable semantic integration of images and all the related scientific data pertaining to their content so that researchers and physicians can have the best understanding of the biological and physiological significance of image content.
Viscoelastic Surfactants: A New Horizon in Fracturing Fluids for Pennsylvania (2007)

Abstract The Upper Devonian play within Pennsylvania has been the predominant focus of most operators for many years. These sandstone and siltstone formations are regularly hydraulically fractured with a variety of fluids ranging from high concentration crosslinks, linear gels, polyacrylamide slick waters and even treated fresh water. These fluids, although economical, lack quality and can cause severe damage during the stimulation process. Whether it is leaving behind heavy residual damage or not supplying enough viscosity to carry proppant deep into the created fracture, these fluids do not offer the advantages of an all-inclusive system. Recently, with the development of visco-elastic surfactants (VES's), a standalone, total package fluid is available at an economical cost. VES's offer high quality with no polymers, giving us a completely clean fluid without residual damage. They can be designed to supply a wide range of viscosities with excellent carrying properties to help ensure optimal proppant placement. With the fluid being surfactant based it is a good foaming agent, which provides exceptional water recovery and strong flowbacks. Best of all, these fluids are all-inclusive, removing the need for additional additives. It consists of one on-the-fly additive that is compatible with extremely poor quality water that may have been reused. There is no need for additional clay controls, biocides, surfactants or iron controls, but in extreme cases, their additions do not create any compatibility issues. This allows VES's to deliver a high quality system at a competitive price. This paper will take an in depth look at visco-elastic surfactants and their current applications in the Upper Devonian throughout Pennsylvania. It will highlight the treatment design, operational execution and production results from a variety of wells during the initial application of VES fluids.
Investigation of N-Terminal Domain Charged Residues on the Assembly and Stability of HIV-1 CA (2004)

The human immunodeficiency virus type 1 (HIV-1) capsid protein (CA) plays a crucial role in both assembly and maturation of the virion as well as viral infectivity. Previous in vivo experiments generated two N-terminal domain charge change mutants (E45A and E128A/R132A) that showed an increase in stability of the viral core. This increase in core stability resulted in decreased infectivity, suggesting the need for a delicate balance of favorable and unfavorable interactions to both allow assembly and facilitate uncoating following infection. Purified CA protein can be triggered to assemble into tubelike structures through the use of a high salt buffer system. The requirement for high salt suggests the need to overcome charge/charge repulsion between subunits. The mutations mentioned above lie within a highly charged region of the N-terminal domain of CA, away from any of the proposed protein/protein interaction sites. We constructed a number of charge mutants in this region (E45A, E45K, E128A, R132A, E128A/R132A, K131A, and K131E) and evaluated their effect on protein stability in addition to their effect on the rate of CA assembly. We find that the mutations alter the rate of assembly of CA without significantly changing the stability of the CA monomer. The changes in rate for the mutants studied are found to be due to varying degrees of electrostatic repulsion between the subunits of each mutant.
Trioctylphosphine:  A General Phosphorus Source for the Low-Temperature Conversion of Metals into Metal Phosphides (2007)

Metal phosphides can have important properties such as superconductivity, magnetoresistance, magnetocaloric behavior, catalytic activity, and lithium intercalation capacity, which make them useful for a variety of technological applications. Bulk metal phosphides usually require high temperatures and harsh reaction conditions to form, and metal phosphide nanocrystals can also be challenging to synthesize. Here we elaborate on a recently developed alternative approach for synthesizing metal phosphides, which involves the solution-mediated reaction of pre-formed metals with trioctylphosphine (TOP) at temperatures below 370 °C. This chemical conversion strategy is shown to be general and highly versatile, successfully forming a wide range of transition-metal and post-transition-metal phosphides using a range of both bulk and nanoscale metals as precursors. Metal nanocrystals, bulk powders, foils, wires, thin films, lithographically patterned substrates, and supported nanocrystals can all be converted to metal phosphides by reaction with TOP. Collectively, this represents a general, unified, and robust strategy for forming metal phosphides using readily available reagents and metal precursors.
Schedule Restoration for Single-Armed Cluster Tools (2014)

The idle time between two consecutive tasks may seriously affect the wafer quality in some wafer fabrication processes requiring high temperature and pressure. Hence, a cluster tool provides high wafer quality and predictability when operated at a steady schedule, which means that every cycle repeats the same pattern considering not only a sequence but also timing. However, multiple process modules per step can cause the fluctuation of wafer quality even under the same sequence since different modules have different wafer delays. It is known that a dual-armed cluster tool can always have a steady schedule that can be established via a timed event graph and (max, +) algebra. We extend this result to a single-armed cluster tool and generalize the method to establish its steady schedule. Although a cluster tool is initially set on a steady schedule, the schedule can become unsteady after disruptive events, such as wafer alignment failures, and it cannot always return to it. We develop strategies that change the system dynamics of a cluster tool by appropriately delaying some tasks such that any disrupted schedule pattern is stabilized in a finite time. Finally, we examine how they help to flatten wafer delays after a disruption or when tasks have stochastic time fluctuation.
Mitochondrial pathophysiology in Friedreich's ataxia (2013)

Neurological examination indicates that Friedreich's ataxia corresponds to a mixed sensory and cerebellar ataxia, which affects the proprioceptive pathways. Neuropathology and pathophysiology of Friedreich's ataxia involves the peripheral sensory nerves, dorsal root ganglia, posterior columns, the spinocerebellar, and corticospinal tracts of the spinal cord, gracile and cuneate nuclei, dorsal nuclei of Clarke, and the dentate nucleus. Involvement of the myocardium and pancreatic islets of Langerhans indicates that it is also a systemic disease. The pathophysiology of the disease is the consequence of frataxin deficiency in the mitochondria and cells. Some of the biological consequences are currently recognized such as the effects on iron-sulfur cluster biogenesis or the oxidative status, but others deserve to be studied in depth. Among physiological aspects of mitochondria that have been associated with neurodegeneration and may be interesting to investigate in Friedreich's ataxia we can include mitochondrial dynamics and movement, communication with other organelles especially the endoplasmic reticulum, calcium homeostasis, apoptosis, and mitochondrial biogenesis and quality control. Changes in the mitochondrial physiology and transport in peripheral and central axons and mitochondrial metabolic functions such as bioenergetics and energy delivery in the synapses are also relevant functions to be considered. Thus, to understand the general pathophysiology of the disease and fundamental pathogenic mechanisms such as dying-back axonopathy, and determine molecular, cellular and tissue therapeutic targets, we need to discover the effect of frataxin depletion on mitochondrial properties and on specific cell susceptibility in the nervous system and other affected organs.
Retraction: Human telomeric G‐quadruplex: targeting with small molecules (2009)

Retraction: The following review from FEBS Journal , 'Human telomeric G‐quadruplex: targeting with small molecules' by Amit Arora, Niti Kumar, Tani Agarwal and Souvik Maiti, published online on 27 th November 2009 in Wiley InterScience ( www.interscience.wiley.com ), has been retracted by agreement between the authors, the journal Editor‐in‐Chief Professor Richard Perham and Blackwell Publishing Ltd. The retraction has been agreed due to overlap between this review and the following reviews: Published in Organic &amp; Biomolecular Chemistry , 'A hitchhiker's guide to G‐quadruplex ligands' by David Monchaud and Marie‐Paule Teulade‐Fichou. Volume 6 Issue 4, 2008, pages 627‐636. Published in BioChimie , 'Targeting telomeres and telomerase' by Anne De Cian, Laurent Lacroix, Celine Douarre, Nassima Temime‐Smaali, Chantal Trentesaux, Jean‐Francois Riou and Jean‐Louis Mergny. Volume 90 Issue 1, 2008, pages 131‐155.
Polyelectrolytes in Salt Solutions: Molecular Dynamics Simulations (2011)

We present results of the molecular dynamics simulations of salt solutions of polyelectrolyte chains with number of monomers N = 300. Polyelectrolyte solutions are modeled as an ensemble of bead–spring chains of charged Lennard-Jones particles with explicit counterions and salt ions. Our simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I–1/2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ∝ I–1/5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ∝ I–1/2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ∝ cp–1/4, while at high salt concentrations we observed a weaker dependence of the chain size on the solution ionic strength, R ∝ I–1/8. Our simulations also confirmed that the peak position in the polymer scattering function scales with the polymer concentration in dilute polyelectrolyte solutions as cp1/3. In semidilute polyelectrolyte solutions at low salt concentrations the location of the peak in the scattering function shifts toward the large values of q* ∝ cp1/2 while at high salt concentrations the peak location depends on the solution ionic strength as I–1/4. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X(I) in salt solutions and corresponding quantities X(I0) in salt-free solutions, X(I) = X(I0)(I/I0)β. The exponent β = −1/2 for chain persistence length lp, β = 1/4 for solution correlation length ξ, and β = −1/5 and β = −1/8 for chain size R in dilute and semidilute solution regimes, respectively.
A bioactive bone cement containing Bis‐GMA resin and A–W glass‐ceramic as an augmentation graft material on mandibular bone (2003)

The potential of a bioactive bone cement (BABC) as an onlay graft material for the mandible with and without the periosteum was investigated in rabbits. Its matrix consists of bisphenol-alpha-glycidyl methacrylate (Bis-GMA) and triethylene-glycol dimetacrylate (TEGDMA) and its filler is silane-treated CaO-SiO2-P2O5-MgO-CaF2 glass (A-W glass-ceramic) powder. The BABC was pasted onto the mandible under the periosteum in Group 1, and onto the mandible with the periosteum removed in Group 2 and allowed to set in situ. In both groups, the cement-bone interface was filled by new bone at 4, 12 and 48 weeks, and bone grew from adjacent bone tissue into the cement-soft tissue interface at 12 and 48 weeks. There were no differences in the rate of bone formation between the groups. The shearing strength increased progressively from 0.25+/-0.10 MPa (mean+/-SD) at week 1 to 7.98+/-0.62 MPa at week 48. The results suggest that the BABC has good handling properties, a high bonding strength and good biocompatibility, and that it has potential for clinical application as a substitute material for autogenous bone transplantation.