gebhart/patrepeval huggingface dataset:
An Updated Overview on Wnt Signaling Pathways (2010)

Growth factor signaling is required for cellular differentiation, tissue morphogenesis, and tissue homeostasis. Misregulation of intracellular signal transduction can lead to developmental defects during embryogenesis or particular diseases in the adult. One family of growth factors important for these aspects is given by the Wnt proteins. In particular, Wnts have important functions in stem cell biology, cardiac development and differentiation, angiogenesis, cardiac hypertrophy, cardiac failure, and aging. Knowledge of growth factor signaling during differentiation will allow for improvement of targeted differentiation of embryonic or adult stem cells toward functional cardiomyocytes or for understanding the basis of diseases. Our major aim here is to provide a state of the art review summarizing our present knowledge of the intracellular Wnt-mediated signaling network. In particular, we provide evidence that the subdivision into canonical and noncanonical Wnt signaling pathways solely based on the identity of Wnt ligands or Frizzled receptors is not appropriate anymore. We thereby deliver a solid base for further upcoming articles of a review series focusing on the role of Wnt proteins on different aspects of cardiovascular development and dysfunction.
Overexpression of annexin a1 induced by terephthalic acid calculi in rat bladder cancer (2007)

Prolonged cell proliferation in response to irritation by bladder calculi can evoke malignant transformation of the urothelium. However, the molecular mechanisms responsible for calculi-associated bladder carcinogenesis are unknown. We compared the protein expression pattern of rat bladder transitional cell carcinomas (TCCs) induced by terephthalic acid with that of normal bladder tissues using 2-DE. Comparative analysis of the respective spot patterns on 2-DE showed 146 spots that were markedly changed in TCC samples. Subsequently, 56 of the variant protein spots were identified by MALDI-TOF MS. Among them, overexpression of annexin a1 (ANNA1) in rat TCCs was confirmed by Western blotting and real-time RT-PCR analysis. Immunohistochemical staining revealed that ANNA1, usually a cytoplasmic protein in normal urothelium, was translocated to the nucleus in rat bladder cancer cells. In contrast to the animal studies, examination of human clinical specimens showed that ANNA1 expression was reduced in TCC compared to normal urothelium. The expression of ANNA1 was inversely related to the level of differentiation of TCC. Our data suggest that overexpression of ANNA1 is involved in bladder carcinogenesis induced by bladder calculi and that translocation of the protein may be partly responsible for the effect. ANNA1 may serve as a new marker of differentiation for the histopathological grading of human TCC.
Beam instability in 980-nm power lasers: experiment and analysis (1994)

A theoretical analysis of beam instability (steering), commonly observed in high power ridge waveguide laser diodes is presented. A physical model of multiple interfering lateral modes is proposed and implemented in a two-dimensional self-consistent numerical code. It is shown that the dynamic evolution of the effective waveguide and the coherent lasing of emergent multiple lateral modes of the waveguide under high injection could lead to beam steering and knees in the fiber coupled L-I characteristics. The theory of simultaneous lasing and interaction between several lateral modes is found to be consistent with the observed back-plane radiation image.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid Detection of vanA and vanB Genes Directly from Clinical Specimens and Enrichment Broths by Real-Time Multiplex PCR Assay (2003)

A real-time PCR assay previously developed for use on the Roche LightCycler platform was investigated as an alternative to culture for the direct detection of vancomycin-resistant enterococci (VRE) in clinical specimens. PCR primers and fluorescence resonance energy transfer hybridization probes specific for the vanA and vanB genes were combined in a multiplex real-time PCR assay performed directly with fecal material obtained by rectal swabbing and with enrichment broth samples. DNA was prepared from the rectal swabs and enrichment broths with a commercially available DNA preparation column designed specifically for use with fecal specimens. One hundred eighty duplicate rectal swabs were obtained from 42 patients who were previously found to be positive for VRE and who were being monitored for carriage of VRE. Direct and enrichment broth cultures were performed with one swab, while PCR was performed with the other swab as well as any corresponding presumptive positive enrichment broth. In total, 100 specimens from 30 patients remained positive for VRE by at least one method. The multiplex real-time PCR was positive for 88 enrichment broths of rectal swabs from 27 patients but for only 45 rectal swabs from 15 patients. Direct culture was positive for VRE for only 43 specimens from 11 patients, while enrichment broth culture was positive for VRE for 75 specimens from 22 patients. Inhibition studies for the multiplex real-time PCR assay, performed by spiking the DNA extracts from 50 negative rectal swabs and the corresponding enrichment broths with between 1 and 10 CFU of a VanB Enterococcus faecium strain, detected inhibition rates of 55.1 and 10%, respectively. PCR performed directly with enrichment broths was found to be significantly more sensitive than enrichment broth culture (P < 0.025). Negative samples were identified significantly earlier by PCR than by culture alone.
Phenazine redox cycling enhances anaerobic survival in Pseudomonas aeruginosa by facilitating generation of ATP and a proton‐motive force (2014)

While many studies have explored the growth of Pseudomonas aeruginosa, comparatively few have focused on its survival. Previously, we reported that endogenous phenazines support the anaerobic survival of P. aeruginosa, yet the physiological mechanism underpinning survival was unknown. Here, we demonstrate that phenazine redox cycling enables P. aeruginosa to oxidize glucose and pyruvate into acetate, which promotes survival by coupling acetate and ATP synthesis through the activity of acetate kinase. By measuring intracellular NAD(H) and ATP concentrations, we show that survival is correlated with ATP synthesis, which is tightly coupled to redox homeostasis during pyruvate fermentation but not during arginine fermentation. We also show that ATP hydrolysis is required to generate a proton-motive force using the ATP synthase complex during fermentation. Together, our results suggest that phenazines enable maintenance of the proton-motive force by promoting redox homeostasis and ATP synthesis. This work demonstrates the more general principle that extracellular redox-active molecules, such as phenazines, can broaden the metabolic versatility of microorganisms by facilitating energy generation.
First EBV vaccine trial in humans using recombinant vaccinia virus expressing the major membrane antigen. (1995)

In the absence of a truly representative animal model, the question of whether EBV-related diseases can be prevented by a vaccine has been studied for the first time in humans. A live recombinant virus based on the licensed vaccinia strain Tien Tan, expressing under the 11K vaccinia promoter the major EBV membrane antigen BNLF-1 MA (gp 220-340), was constructed and tested in three different human populations: EBV-positive and vaccinia-virus-exposed adults; EBV-positive, non-vaccinia-virus-exposed juveniles; and EBV and vaccinia virus-naive infants. No significant titre variations for EBV were observed in the adults, but EBV-neutralising titres increased in the vaccinated juveniles, while antibodies to VCA of EBV remained unchanged. All nine vaccinated infants developed antibodies to MA (membrane antigen) with neutralising properties in vitro; three of these infants were infected by EBV via natural routes over a period of 16 months after vaccination and all ten unvaccinated control infants became infected. It has been shown for the first time that protection against and/or delay of EBV infection by the natural route is possible in humans and that live vaccinia vectors can be used and are efficacious.
Surface nitridation of Li-rich layered Li(Li0.17Ni0.25Mn0.58)O2 oxide as cathode material for lithium-ion battery (2012)

A Li-rich layered Li(Li0.17Ni0.25Mn0.58)O2 oxide is prepared by a combination of co-precipitation and solid-state reaction. The surface nitridation is introduced into a Li-rich layered Li(Li0.17Ni0.25Mn0.58)O2 for the first time via heating at 400 °C in the ammonia atmosphere. The microstructure and morphology of the two samples are characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). It is demonstrated that the nitrogen exists with a trace amount in the surface layer of the Li-rich layered Li(Li0.17Ni0.25Mn0.58)O2 oxide after the nitridation treatment. Electrochemical performances of the electrodes are measured by galvanostatic charge–discharge tests, cyclic voltammetry and electrochemical impedance spectroscopy (EIS). As expected, the discharge capacity, high-rate capability and cycle stability of the nitrided sample are improved dramatically as compared with the as-prepared sample, which is further confirmed by the high electrocatalytic activity and accelerated lithium diffusion process. Apparently, the existence of nitrogen in the surface layer is responsible for the improvement of the reaction kinetics and electrochemical performance of the nitrided sample.
Synthesis and Reactivity of the Aquation Product of the Antitumor Complex trans-[RuIIICl4(indazole)2]− (2008)

Aquation of the investigational anticancer drug trans-[Ru(III)Cl4(Hind)2](-) (1, KP1019) results in the formation of mer,trans-[Ru(III)Cl3(Hind)2(H2O)] (2), which was isolated in high yield (85%) and characterized by spectroscopic methods and X-ray crystallography. Dissolution of 2 in acetone, led to its dimerization into [Ru(III)2(mu-Cl)2Cl4(Hind)4] x 2 (Me)2CO (3) in 79% yield, with release of two water molecules. Complex 2 reacts readily with nucleophilic organic molecules, viz., methanol or dimethyl sulfide, at room temperature by replacement of the aqua ligand to give mer,trans-[Ru(III)Cl3(Hind)2(MeOH)] (4) and mer,trans-[Ru(III)Cl3(Hind)2(Me2S)] (5) in 58 and 64% yield, respectively. By reaction of 2 with DMSO at room temperature or dimethyl sulfide at elevated temperatures trans,trans,trans-[Ru(II)Cl2(Hind)2(Me2S)2] (6) and trans,trans,trans-[Ru(II)Cl2(Hind)2(S-DMSO)2] (7) were prepared in 64 and 75% yield, respectively. Dissolution of 2 in acetonitrile or benzonitrile gave rise to mer,trans-[Ru(III)Cl3(Hind)(HNC(Me)ind)] (8a), mer,trans-[Ru(III)Cl3(Hind)(HNC(Ph)ind)] (8b), and trans,trans-[Ru(III)Cl2(HNC(Me)ind)2]Cl (9) in 67, 50, and 23% yield, respectively, upon metal-assisted iminoacylation of indazole, which is unprecedented for ruthenium(III). Furthermore, complex 2 reacts with the DNA-model bases 9-methyladenine (9-meade) and N6,N6-dimethyladenine (6-me2ade) to yield mer,trans-[Ru(III)Cl3(Hind)2(9-meade)] (10) and mer,trans-[Ru(III)Cl3(Hind)2(6-me2ade)] (11) with the purine bases bound to the Ru(III) center via N7 and N3, respectively. Complex 11 represents the first ruthenium complex in which the coordination of the purine ligand N6,N6-dimethyladenine occurs via N3. In addition, the polymer [Na(EtOAc)2Ru(III)(mu-Cl)4(Hind)2]n (12) was crystallized from ethyl acetate/diethyl ether solutions of Na[trans-Ru(III)Cl4(Hind)2] x 1.5 H2O (1a). The reported complexes were characterized by elemental analysis, IR and UV-vis spectroscopy, ESI mass spectrometry, cyclic voltammetry, and X-ray crystallography. Electrochemical investigations give insight into the mechanistic details of the solvolytic behavior of complex 2. The lability of the aqua ligand in 2 suggests that this complex is a potential active species responsible for the high antitumor activity of trans-[Ru(III)Cl4(Hind)2](-).
MugShots (2015)

We explore creating objects for expressive communication in the workspace. As an initial step, we created MugShots, a coffee mug with a wireless OLED display that switches between public and private social interaction modes. Targeted for the workplace, MugShots is an intimate communication device in the personal office space, yet alternates to become a social catalyst to trigger conversation when brought to public areas. We present a prototype of MugShots along with a 21-person study, providing initial discussions and insight on designing objects for communication.
Efficacy of bioadhesive patches in the treatment of recurrent aphthous stomatitis (1996)

This study evaluated the efficacy of bioadhesive hydrogel patches, made of a pharmaceutical grade cellulose derivative, in the control of pain and as an aid to healing of aphthous ulceration. Patients kept a twice daily ulcer diary to record their pain level on a visual analogue scale. The sensitivity of the test ulcer was assessed by a challenge with pure orange juice as a stimulant before and after application of the patch by the patient. A significant reduction in stimulated pain was recorded following application of the patches to the ulcers (P < 0.01). The patches were found to adhere longer to large ulcers in the early stages of ulceration, when they achieved their maximum protective and pain-attenuating effects. The ulcer size was recorded daily by the patient and patients claimed a reduction in healing time following patch therapy.
Photoassisted dry etching of GaN (1996)

Photoassisted etching of GaN in HCl by a 193 nm ArF excimer laser is reported. A directed stream of HCl etchant with background pressure of ∼5×10−4 Torr, sample temperature between 200 and 400 °C and 1400 mJ/cm2 laser fluence combined to produce etching. Smooth etch features and distinct sidewalls were observed. For the HCl/GaN system, photoassisted etching occurred only when both HCl and laser energy were present.
Radiation‐induced crystallinity changes in linear polyethylene: Influence of aging (1983)

Abstract A previous paper described an unusual crystallinity effect observed in ultrahigh molecular weight linear polyethylene (UHMW PE) and conventional high density polyethylene (HDPE). It was discovered that upon exposure to high energy radiation, these polymers experience a significant increase in the degree of crystallinity. The present paper describes another equally unexpected and surprising phenomenon observed in irradiated UHMW PE and HDPE. It was accidentally found that the irradiated polyethylenes exhibit an aging effect; their heat of fusion and hence their degree of crystallinity increases monotonically with the aging time (since initial irradiation) at ambient conditions. Surprisingly, the aging process in irradiated polyethylenes was observed to persist even after 31 months. The magnitude of the aging effect is a strong function of the initial molecular weight of the unirradiated polymers and the irradiation dose. The aging phenomenon could not be accelerated by thermal annealing. The exact mechanisms causing the aging phenomenon remain rather elusive at the present time, but possible reasons are explored.
Dysregulation of the angiopoietin–Tie-2 axis in sepsis and ARDS (2013)

Dynamic changes in microvascular endothelial structure and function are pivotal in the acute inflammatory response, the body’s rapid, coordinated effort to localize, sequester, and eliminate microbial invaders at their portal of entry. To achieve this, the endothelium becomes leaky and inflamed, providing innate immune cells and humoral effector molecules access to the site of infection. During sepsis this locally adaptive response becomes manifest throughout the body, leading to dangerous host consequences. Increased leakiness in the pulmonary circulation contributes to acute respiratory distress syndrome (ARDS), a complication of sepsis associated with 40% mortality. Understanding the molecular governance of vascular leak and inflammation has major diagnostic, prognostic, and potentially therapeutic implications for this common and pernicious disease. This review summarizes results from cell-based experiments, animal models, and observational human studies; together, these studies suggest that an endothelial receptor called Tie2 and its ligands, called angiopoietins, form a signaling axis key to the vascular dyshomeostasis that underlies sepsis.
Mutation Master: Profiles of substitutions in hepatitis C virus RNA of the core, alternate reading frame, and NS2 coding regions (2002)

The RNA genome of the hepatitis C virus (HCV) undergoes rapid evolutionary change. Efforts to control this virus would benefit from the advent of facile methods to identify characteristic features of HCV RNA and proteins, and to condense the vast amount of mutational data into a readily interpretable form. Many HCV sequences are available in GenBank. To facilitate analysis, consensus sequences were constructed to eliminate the overrepresentation of certain genotypes, such as genotype 1, and a novel package of sequence analysis tools was developed. Mutation Master generates profiles of point mutations in a population of sequences and produces a set of visual displays and tables indicating the number, frequency, and character of substitutions. It can be used to analyze hundreds of sequences at a time. When applied to 255 HCV core protein sequences, Mutation Master identified variable domains and a series of mutations meriting further investigation. It flagged position 4, for example, where 90% or more of all sequences in genotypes 1, 2, 4, and 5, have N4, whereas those in genotypes 3, 6, 7, 8, 9, and 10 have L4. This pattern is noteworthy: L (hydrophobic) to N (polar) substitutions are generally rare, and genotypes 1, 2, 4, and 5 do not form a recognized super family of sequences. Thus, the L4N substitution probably arose independently several times. Moreover, not one member of genotypes 1, 2, 4, or 5 has L4 and not one member of genotypes 3, 6, 7, 8, 9, or 10 has N4. This nonoverlapping pattern suggests that coordinated changes at position 4 and a second site are required to yield a viable virus. The package generated a table of genotype-specific substitutions whose future analysis may help to identify interacting amino acids. Three substitutions were present in 100% of genotype 2 members and absent from all others: A68D, R74K, and R114H. Finally, this study revealed thatARFP, a novel protein encoded in an overlapping reading frame, is as conserved as conventional HCV proteins, a result supporting a role for ARFP in the viral life cycle. Whereas most conventional programs for phylogenetic analysis of sequences provide information about overall relatedness of genes or genomes, this program highlights and profiles point mutations. This is important because determinants of pathogenicity and drug susceptibility are likely to result from changes at only one or two key nucleotides or amino acid sites, and would not be detected by the type of pairwise comparisons that have usually been performed on HCV to date. This study is the first application of Mutation Master, which is now available upon request (http://tandem.biomath.mssm.edu/mutationmaster.html).
Attractive step-step interactions, tricriticality, and faceting in the orientational phase diagram of silicon surfaces between [113] and [114] (1995)

A synchrotron x-ray scattering study is presented of the orientational phase diagram of Si surfaces misoriented by up to 6\ifmmode^\circ\else\textdegree\fi{} from the cubic [113] direction towards [001] and for temperatures between 300 and 1500 K. At the highest temperatures (above 1223 K), the surface is uniformly stepped. In this region, the intensity of near-specularly scattered x rays increases with decreasing temperature, suggesting a corresponding increase in the surface roughness. Specifically, the temperature dependence of the intensity of the near-specular diffuse scattering may be described as a power law versus reduced temperature: ${\mathit{I}}_{\mathit{D}}$\ensuremath{\sim}${\mathit{t}}_{\mathit{s}}^{\mathrm{\ensuremath{-}}\ensuremath{\lambda}}$, with \ensuremath{\lambda}=0.76\ifmmode\pm\else\textpm\fi{}0.2 (${\mathit{t}}_{\mathit{s}}$(\ensuremath{\theta})=[T-${\mathit{T}}_{\mathit{s}}$(\ensuremath{\theta})]/${\mathit{T}}_{\mathit{s}}$(\ensuremath{\theta}), where ${\mathit{T}}_{\mathit{s}}$(\ensuremath{\theta}) is spinodal temperature for surface misorientation \ensuremath{\theta}). Below ${\mathit{T}}_{\mathit{t}}$=1223\ifmmode\pm\else\textpm\fi{}40 K, there is a two-phase region in which (113) facets appear in coexistence with the stepped phase. We identify ${\mathit{T}}_{\mathit{t}}$ as a tricritical point. The misorientation angle at the phase boundary separating one- and two-phase regions may be also described as a power law versus reduced temperature: \ensuremath{\theta}=${\mathrm{\ensuremath{\theta}}}_{0}$${\mathit{t}}^{\mathrm{\ensuremath{\beta}}}$, with \ensuremath{\beta}=0.42\ifmmode\pm\else\textpm\fi{}0.10 [t=(${\mathit{T}}_{\mathit{t}}$-T)/${\mathit{T}}_{\mathit{t}}$]. The behavior of the intensity of the diffuse scattering above ${\mathit{T}}_{\mathit{t}}$ and of the phase boundary below ${\mathit{T}}_{\mathit{t}}$ can be understood qualitatively on the basis of a mean-field theory incorporating a direct attractive interaction between steps. However, the observed tricritical exponents are not given correctly. For temperatures between a triple point at ${\mathit{T}}_{3}$=1134\ifmmode\pm\else\textpm\fi{}40 and 300 K, coexistence between the (113) facet and the (114) facet is found.
Segmented Filamentous Bacteria Are Potent Stimuli of a Physiologically Normal State of the Murine Gut Mucosal Immune System (1999)

Segmented filamentous bacteria (SFB) are autochthonous bacteria inhabiting the intestinal tracts of many species, including humans. We studied the effect of SFB on the mucosal immune system by monoassociating formerly germfree C3H/HeN mice with SFB. At various time points during 190 days of colonization, fragment cultures of small intestine and Peyer's patches (PP) were analyzed for total immunoglobulin A (IgA) and SFB-specific IgA production. Also, phenotypic changes indicating germinal center reactions (GCRs) and the activation of CD4(+) T cells in PP were determined by using fluorescence-activated cell sorter analyses. A second group of SFB-monoassociated mice was colonized with a gram-negative commensal, Morganella morganii, to determine if the mucosal immune system was again stimulated and to evaluate the effect of prior colonization with SFB on the ability of M. morganii to translocate to the spleen and mesenteric lymph nodes. We found that SFB stimulated GCRs in PP from day 6 after monoassociation, that GCRs only gradually waned over the entire length of colonization, that natural IgA production was increased to levels 24 to 63% of that of conventionally reared mice, and that SFB-specific IgA was produced but accounted for less than 1.4% of total IgA. Also, the proportion of CD4(+), CD45RBlow T cells, indicative of activated cells, gradually increased in the PP to the level found in conventionally reared mice. Secondary colonization with M. morganii was able to stimulate GCRs anew, leading to a specific IgA antibody response. Previous stimulation of mucosal immunity by SFB did not prevent the translocation of M. morganii in the double-colonized mice. Our findings generally indicate that SFB are one of the single most potent microbial stimuli of the gut mucosal immune system.
msa: an R package for multiple sequence alignment (2015)

msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.