gebhart/patrepeval huggingface dataset:
The secreted IpaB and IpaC invasins and their cytoplasmic chaperone IpgC are required for intercellular dissemination of Shigella flexneri (1999)

Invasion of epithelial cells by Shigella flexneri involves entry and dissemination. The main effectors of entry, IpaB and IpaC, are also required for contact haemolytic activity and escape from the phagosome in infected macrophages. These proteins are stored in the cytoplasm in association with the chaperone IpgC, before their secretion by a type III secretion apparatus is activated by host cells. We used a His-tagged IpgC protein to purify IpgC-containing complexes and showed that only IpaB and IpaC are associated with IpgC. Plasmids expressing His6-IpgC either alone or together with IpaB or IpaC under the control of an IPTG-inducible lac promoter were introduced into ipgC, ipaB or ipaC mutants. Induction of expression of the recombinant plasmid-encoded proteins by IPTG allowed bacteria to enter epithelial cells, and the role of these proteins in dissemination was investigated by incubating infected cells in either the absence or the presence of IPTG. The size of plaques produced by recombinant strains on cell monolayers was regulated by IPTG, indicating that IpgC, IpaB and IpaC were each required for efficient dissemination. Electron microscopy analysis of infected cells indicated that these proteins were necessary for lysis of the membrane of the protrusions during cell-to-cell spread.
Recent advances in the formation of the bacterial peptidoglycan monomer unit (1985 to 2000) (2001)

Covering: 1985–2000.
UV-based nanoimprinting lithography with a fluorinated flexible stamp (2011)

A custom-made copolymer of a perfluoropolyether (PFPE) and a hyperbranched polymer (HP) was employed to prepare an UV-based nanoimprinting lithographic (NIL) flexible HPFPE stamp. The properties of the HP afforded the resultant HPFPE resist with low viscosity, suitable surface energy, high Young’s modulus, and enhanced stability. The HPFPE resist also presented excellent properties of antisticking, and durability, no deformation, or distortion after long time usage; therefore, demonstrating an improvement in the NIL pattern transfer fidelity and resolution. By optimizing the UV-based NIL process with this flexible HPFPE stamp, the imprinting results showed near zero residues at the bottom of the resist grooves, and no sticking over a large area. The structure of the HPFPE flexible stamp was transferred intact onto a soft substrate indium tin oxide/polyethylene terephthalate film with good resolution, achieving a 50 nm linewidth and a 200 nm period.
Effect of Halothane Anesthesia on the Human Cortical Visual Evoked Response (1980)

The visual evoked response (VER) was monitored in eight women intraoperatively during anesthesia with halothane in oxygen administered via endotracheal tube. Control measurements were made prior to anesthetic induction in these unpremedicated patients. The latency of the positive peak designated P1 increased progressively from a mean of 113 +/- 10 (SD) msec in the awake state to the following values at indicated end-tidal halothane concentrations: 123 +/- 10 msec at 0.75 per cent; 130 +/- 9 msec at 0.90 per cent; 134 +/- 9 msec at 1.13 per cent. The differences among mean latency values at these anesthetic concentrations were insufficient to conclude that VER latency would be a useful monitor of anesthetic depth. However, significant effects were seen at clinical levels of halothane anesthesia, and the prolongation caused by anesthesia must be considered when using VERs to monitor central nervous system function during neurosurgery.
Effect of L-alpha-glyceryl-phosphorylcholine on amnesia caused by scopolamine. (1991)

The present study was carried out to test the effects of L-alpha-glycerylphosphorylcholine (L-alpha-GFC) on memory impairment induced by scopolamine in man. Thirty-two healthy young volunteers were randomly allocated to four different groups. They were given a ten day pretreatment with either L-alpha-GFC or placebo, p.o., and on the eleventh day either scopolamine or placebo, i.m. Before and 0.5, 1, 2, 3, and 6 h after injection the subjects were given attention and mnemonic tests. The findings of this study indicate that the drug is able to antagonize impairment of attention and memory induced by scopolamine.
Isodityrosine Cross-Linking Mediates Insolubilization of Cell Walls in Chlamydomonas (1993)

Sabine Waffenschmidt, Jeffrey P. Woessner, Karin Beer, Ursula W. Goodenough, Isodityrosine Cross-Linking Mediates Insolubilization of Cell Walls in Chlamydomonas, The Plant Cell, Vol. 5, No. 7 (Jul., 1993), pp. 809-820
An analysis of sequencing surgeries with durations that follow the lognormal, gamma, or normal distribution (2012)

The smallest-variance-first-rule (SV) is generally accepted as the optimal policy for sequencing two surgeries, although it has been proven formally only for several restricted cases. We extend prior work, studying three distributions as models of surgery duration (the lognormal, gamma, and normal) and including overtime in a total-cost objective function comprising surgeon-and patient-waiting-, operating-room-idle-, and staff overtimes. We specify expected waiting and idle time as functions of the parameters of surgery duration to identify the best rule to sequence two surgeries. We compare the relative values of expected waiting and idle times numerically with that of expected overtime. Results recommend that the SV rule be used to minimize total expected cost of waiting, idle and overtime. We find that gamma and normal distributions with the same mean and variance as the lognormal give nearly the same expected waiting and idle times, observing that the lognormal in combination with either the gamma or normal gives a similar result. We extend to the three-surgery case, showing that sequencing the first surgery is most important. We demonstrate how our results can be applied by using them as a basis for a heuristic that assigns surgeries to multiple operating rooms and then sequences them.
Identifying model metal hyperaccumulating plants: germplasm analysis of 20 Brassicaceae accessions from a wide geographical area (2003)

• Here we report on the first phase of a funded programme to select a wild relative of Arabidopsis thaliana for use in large-scale genomic strategies, including forward and reverse genetic screens for the identification of genes involved in metal hyperaccumulation. • Twenty accessions of metal accumulating species of the Brassicaceae collected from Austria, France, Turkey and the USA during spring-summer 2001 were evaluated. • The criteria established for selection were: hyperaccumulation of metal (Ni, Zn); compact growth habit; reasonable time to flowering; production of ≥ 1000 seeds per plant; self-fertility; a compact diploid genome; high sequence identity with A. thaliana; and ≥ 0.1% transformation efficiency with easy selection. As part of this selection process we also report, for the first time, the stable genetic transformation of various hyperaccumulator species with both the green fluorescence protein (GFP) and the bar selectable marker. • We conclude that metal hyperaccumulation ability, self-fertility, seed set, transformation efficiency and a diploid genome were the most important selection criteria. Based on an overall assessment of the performance of all 20 accessions, Thlaspi caerulescens Félix de Pallières showed the most promise as a model hyperaccumulator.
Stacking faults and twins in gallium phosphide layers grown on silicon (2002)

Abstract The coalescence of GaP islands, grown on Si(001), Si(111), Si(110) and Si(113) surfaces by chemical beam epitaxy, has been investigated by high-resolution transmission electron microscopy. Stacking faults and first-order twins are observed within islands before coalescence and result from stacking errors during growth on the smaller P-terminated {111} facets of GaP islands. Upon island coalescence, complex moire fringes are observed contiguous to highly faulted {111} planes within epitaxial layers grown on all four Si substrate orientations and are attributed to multiple twinning. Second-and third-order twins are also observed within (111) and (110) layers and their formation is attributed to successive twinning on differently inclined {111} facets. Amongst the four orientations, coalesced growths on the Si(111) surface are the most defective and this may be caused by a higher density of P-terminated {111} facets on islands grown on the Si(111) surface.
1.7-ps, microwave, integrated-circuit-compatible InAs/AlSb resonant tunneling diodes (1993)

Microwave integrated-circuit-compatible InAs/AlSb resonant tunneling diodes (RTDs) have been fabricated. The resulting devices have peak current densities of 3.3*10/sup 5/ A/cm/sup 2/ with peak-to-valley ratios of 3.3. Switching transition times of 1.7 ps are measured using electrooptic sampling techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
State of the Science: An Update on Renal Cell Carcinoma (2012)

Renal cell carcinomas (RCC) are emerging as a complex set of diseases that are having a major socioeconomic impact and showing a continued rise in incidence throughout the world. As the field of urologic oncology faces these trends, several major genomic and mechanistic discoveries are altering our core understanding of this multitude of cancers, including several new rare subtypes of renal cancers. In this review, these new findings are examined and placed in the context of the well-established association of clear cell RCC (ccRCC) with mutations in the von Hippel-Lindau (VHL) gene and resultant aberrant hypoxia inducible factor (HIF) signaling. The impact of novel ccRCC-associated genetic lesions on chromatin remodeling and epigenetic regulation is explored. The effects of VHL mutation on primary ciliary function, extracellular matrix homeostasis, and tumor metabolism are discussed. Studies of VHL proteostasis, with the goal of harnessing the proteostatic machinery to refunctionalize mutant VHL, are reviewed. Translational efforts using molecular tools to elucidate discriminating features of ccRCC tumors and develop improved prognostic and predictive algorithms are presented, and new therapeutics arising from the earliest molecular discoveries in ccRCC are summarized. By creating an integrated review of the key genomic and molecular biological disease characteristics of ccRCC and placing these data in the context of the evolving therapeutic landscape, we intend to facilitate interaction among basic, translational, and clinical researchers involved in the treatment of this devastating disease, and accelerate progress toward its ultimate eradication.
Direct Writing of Flexible Electronics through Room Temperature Liquid Metal Ink (2012)

The present method opens the way to directly and quickly writing flexible electronics which can be as simple as signing a name or drawing a picture on the paper. The unique merit of the GaIn(10)-based liquid metal ink lies in its low melting temperature, well controlled wettability, high electrical conductivity and good biocompability. The new electronics writing strategy and basic principle has generalized purpose and can be extended to more industrial areas, even daily life.
The Truth About Dirty Oil: Is CCS the Answer? (2010)

Does carbon capture and sequestration (CCS) make sense in the oil sands?
Preparation and thermal properties of bismaleimide blends based on hydroxyphenyl maleimide (2005)

Abstract N ‐(4‐hydroxyphenyl)maleimide was melt‐blended with the glycidyl ether of bisphenol‐A and various mole percentages of 4, 4′‐(diaminodiphenylsulfone) bismaleimide. The cure behaviour of the resins was evaluated by differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA). The blends showed distinct reductions in the onset of cure ( T o ) and peak exothermic ( T exo ) temperatures. The blends cured at low temperatures exhibited glass transition temperatures ( T g s) higher than the cure temperatures. The cured blends showed high moduli, glass transition temperatures in excess of 250 °C and good thermal stabilities up to 400 °C. Copyright © 2005 Society of Chemical Industry
A Link between FXYD3 (Mat-8)-mediated Na,K-ATPase Regulation and Differentiation of Caco-2 Intestinal Epithelial Cells (2008)

FXYD3 (Mat-8) proteins are regulators of Na,K-ATPase. In normal tissue, FXYD3 is mainly expressed in stomach and colon, but it is also overexpressed in cancer cells, suggesting a role in tumorogenesis. We show that FXYD3 silencing has no effect on cell proliferation but promotes cell apoptosis and prevents cell differentiation of human colon adenocarcinoma cells (Caco-2), which is reflected by a reduction in alkaline phosphatase and villin expression, a change in several other differentiation markers, and a decrease in transepithelial resistance. Inhibition of cell differentiation in FXYD3-deficient cells is accompanied by an increase in the apparent Na+ and K+ affinities of Na,K-ATPase, reflecting the absence of Na,K-pump regulation by FXYD3. In addition, we observe a decrease in the maximal Na,K-ATPase activity due to a decrease in its turnover number, which correlates with a change in Na,K-ATPase isozyme expression that is characteristic of cancer cells. Overall, our results suggest an important role of FXYD3 in cell differentiation of Caco-2 cells. One possibility is that FXYD3 silencing prevents proper regulation of Na,K-ATPase, which leads to perturbation of cellular Na+ and K+ homeostasis and changes in the expression of Na,K-ATPase isozymes, whose functional properties are incompatible with Caco-2 cell differentiation.
An efficient addressing scheme for shaping of multi-dimensional signal constellations using a lookup table (2002)

The paper describes a lookup table for the addressing of an optimally shaped constellation. The method is based on partitioning the subconstellations into shaping macro-shells of integer bit rate and increasing average energy. A lookup table is used to select a subset of the partitions in the cartesian product space. By devising appropriate partitioning/merging rules, the author obtains suboptimum schemes of very low addressing complexity and small performance degradation. The performance is computed using weight distribution of an optimally shaped constellation.
Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis (2008)

Pseudomonas aeruginosa is a ubiquitous bacterium that causes opportunistic infections in a range of host tissues and organs. Infections by P. aeruginosa are difficult to treat and hence there is interest in the development of effective therapeutics. One of the key mechanisms that P. aeruginosa uses to control the expression of many virulence factors is the N-acylated homoserine lactone (AHL) regulatory system. Hence, there is considerable interest in targeting this regulatory pathway to develop novel therapeutics for infection control. P. aeruginosa is the principal cause of microbial keratitis and of infections in cystic fibrosis (CF) sufferers, and AHL-dependent cell-to-cell signalling has been shown to be important for both infection types. However, keratitis tends to be an acute infection whereas infection of CF patients develops into a chronic, life-long infection. Thus, it is unclear whether AHL-regulated virulence plays the same role during these infections. This review presents a comparison of the role of AHL signalling in P. aeruginosa-mediated microbial keratitis and chronic lung infections of CF patients.
Fundamentals of stable continuum generation at high repetition rates (2000)

A continuum generated from highly nonlinear seed pulses (N/spl Gt/1) propagating in a medium with only self-phase modulation (SPM) or with SPM and anomalous dispersion is highly sensitive to the noise of the input pump pulse. The combination of SPM and normal dispersion improves the stability. However, more efficient spectral broadening schemes are desirable for generating a broad-band continuum at gigahertz rates. The adiabatic compression of weakly nonlinear pulses (N/spl sime/1) via the soliton effect efficiently generates a broad-band continuum that is robust against noise. Detailed characterization of continuum generation in several different fibers is reported.
Chulitna region, south-central Alaska (1987)

Abstract The Upper Chulitna region of Alaska is on the south flank of the centralAlaska Range on the southeast side of Denali National Park (Fig. 1). It was first recognized as an unusual entity by S. R. Capps, who mapped a belt of Triassic rocks (1919) during a reconnaissance of mineral deposits; he called the area the Upper Chulitna region. The Chulitna River forms a barrier to access, but once across the Chulitna the country is open and ranges from rolling, easily hikeable country to rugged and difficult. Some of the key sections of the Chulitna region are strikingly exposed in canyon walls, and flybys from either fixed- or rotary-wing aircraft provide excellent overviews of the geology (Figs. 2, 3).
Structure−Activity Relationships of Pregabalin and Analogues That Target the α<sub>2</sub>-δ Protein (2005)

Pregabalin exhibits robust activity in preclinical assays indicative of potential antiepileptic, anxiolytic, and antihyperalgesic clinical efficacy. It binds with high affinity to the alpha(2)-delta subunit of voltage-gated calcium channels and is a substrate of the system L neutral amino acid transporter. A series of pregabalin analogues were prepared and evaluated for their alpha(2)-delta binding affinity as demonstrated by their ability to inhibit binding of [(3)H]gabapentin to pig brain membranes and for their potency to inhibit the uptake of [(3)H]leucine into CHO cells, a measure of their ability to compete with the endogenous substrate at the system L transporter. Compounds were also assessed in vivo for their ability to promote anxiolytic, analgesic, and anticonvulsant actions. These studies suggest that distinct structure activity relationships exist for alpha(2)-delta binding and system L transport inhibition. However, both interactions appear to play an important role in the in vivo profile of these compounds.
Expression of the interferon‐induced MxA protein in viral encephalitis (2003)

MxA protein accumulates cytoplasmically in response to interferon stimulation, and mediates resistance against several viruses. In order to test whether MxA may serve as a diagnostic tool for viral infections of the central nervous system (CNS), we performed MxA immunohistochemistry on biopsies and autopsies of 57 patients with neurological disorders of known viral and nonviral aetiology. MxA was detectable in all HIV patients with proven opportunistic viral encephalitis, in all patients suffering from isolated viral encephalitis, in one of three HIV patients with cerebral toxoplasmosis, and in one case of micronodular encephalitis. No MxA was detectable in HIV patients with isolated HIV encephalitis or HIV infection accompanied by an opportunistic nonviral disorder. We were unable to show MxA expression in a variety of nonviral inflammatory and noninflammatory disorders of the CNS. Several cases of Rasmussen's encephalitis and multiple sclerosis tested negative, arguing against their possible viral aetiology. Two-colour immunohistochemistry identified macrophages and activated microglia as MxA expressing cells. In all studied cases MxA expression was accompanied by a marked T-cell infiltrate. Therefore, the detection of MxA-protein is a sensitive adjuvant marker for those cases of viral encephalitis which are accompanied by pronounced lymphocytic infiltrates.
Evaluation of olibanum resin as microencapsulating agent for controlled drug delivery (2006)

Olibanum resin was evaluated as microencapsulating agent and to prepare resin-coated microcapsules. Resin-coated microcapsules of nifedipine were prepared by an industrially feasible emulsification-solvent evaporation method and the microcapsules were investigated. The resin-coated microcapsules are spherical, discrete, free-flowing and multinucleate monolithic type. Microencapsulation efficiency was in the range 98-105%. Nifedipine release from the resin-coated microcapsules was slow over 24 h and depended on core: coat ratio, wall thickness and size of the microcapsules. Drug release was by non-fickian diffusion mechanism. Good linear relationships were observed between wall thickness of the microcapsules and release rate and T50 values. Resin-coated microcapsules of nifedipine exhibited good controlled release characteristics and were found suitable for once a day oral controlled release products.
A structure for real-time Stenotype transcription (1970)

We have experimentally demonstrated the technical feasibility of on-line Stenotype transcription for System/360 using a compacted dictionary program and a search algorithm for content addressing variable-length dictionary arguments. Methods of reducing word errors from twenty-seven percent to approximately six percent are discussed. Retraining in Stenotype extensions as well as modifications of the dictionary organization algorithm permit this reduction in the word-error rate.
Effect of factor VIII on tissue factor-initiated spatial clot growth (2003)

Using time-lapse videomicroscopy, we studied the role of coagulation factor VIII (fVIII) in tissue factor-initiated spatial clot growth on fibroblast monolayers in a thin layer of non-stirred recalcified plasma from healthy donors or patients with severe Haemophilia A. Analysis of temporal evolution of light-scattering profiles from a growing clot revealed existence of two phases in the clot growth-initiation phase in a narrow (0.2 mm) zone adjacent to activator surface and elongation phase in plasma volume. While the initiation phase did not differ in normal and haemophilic plasmas, the rate of clot growth in the elongation phase in haemophilic plasma constituted only 30% of that in normal plasma. Supplementation of haemophilic plasma with 0.05 U/ml fVIII restored the normal clot growth rate (44.9 +/- 2.5 microm/min) at high but not at low fibroblast density. Our results indicate that the functioning of the intrinsic tenase complex is critical for normal spatial clot growth.
Deep transfer via second-order Markov logic (2009)

Standard inductive learning requires that training and test instances come from the same distribution. Transfer learning seeks to remove this restriction. In shallow transfer, test instances are from the same domain, but have a different distribution. In deep transfer, test instances are from a different domain entirely (i.e., described by different predicates). Humans routinely perform deep transfer, but few learning systems, if any, are capable of it. In this paper we propose an approach based on a form of second-order Markov logic. Our algorithm discovers structural regularities in the source domain in the form of Markov logic formulas with predicate variables, and instantiates these formulas with predicates from the target domain. Using this approach, we have successfully transferred learned knowledge among molecular biology, social network and Web domains. The discovered patterns include broadly useful properties of predicates, like symmetry and transitivity, and relations among predicates, such as various forms of homophily.