gebhart/patrepeval huggingface dataset:
Realization of ultraviolet electroluminescence from ZnO homojunction with n-ZnO∕p-ZnO:As∕GaAs structure (2007)

ZnO homojunction light-emitting diode with n-ZnO∕p-ZnO:As∕GaAs structure is produced by metal organic chemical vapor deposition. The p-type ZnO:As film is obtained out of thermal diffusion of arsenic from GaAs substrate with subsequent thermal annealing at 550°C. The n-type layer is composed of unintentionally doped ZnO film. Desirable rectifying behavior is observed from the current-voltage curve of the ZnO p-n homojunction. Furthermore, two distinct electroluminescence bands centered at 3.2 and 2.5eV are obtained from the junction under forward bias at room temperature.
Lateral shearing common-path digital holographic microscopy based on a slightly trapezoid Sagnac interferometer (2017)

We propose a compact and easy-to-align lateral shearing common-path digital holographic microscopy, which is based on a slightly trapezoid Sagnac interferometer to create two laterally sheared beams and form off-axis geometry. In this interferometer, the two beams pass through a set of identical optical elements in opposite directions and have nearly the same optical path difference. Without any vibration isolation, the temporal stability of the setup is found to be around 0.011 rad. Compared with highly simple lateral shearing interferometer, the off-axis angle of the setup can be easily adjusted and quantitatively controlled, meanwhile the image quality is not degraded. The experiments for measuring the static and dynamic specimens are performed to demonstrate the capability and applicability.
A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method (2014)

Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications.
uvrD mutations enhance tandem repeat deletion in the Escherichia coli chromosome via SOS induction of the RecF recombination pathway (1997)

It has previously been shown that recombination between tandem repeats is not significantly affected by a recA mutation in Escherichia coli. Here, we describe the activation of a RecA-dependent recombination pathway in a hyper-recombination mutant. In order to analyse how tandem repeat deletion may proceed, we searched for mutants that affect this process. Three hyper-recombination clones were characterized and shown to be mutated in the uvrD gene. Two of the mutations were identified as opal mutations at codons 130 and 438. A uvrD::Tn5 mutation was used to investigate the mechanism of deletion formation in these mutants. The uvrD-mediated stimulation of deletion was abolished by a lexAind3 mutation or by inactivation of either the recA, recF, recQ or ruvA genes. We conclude that (i) this stimulation requires SOS induction and (ii) tandem repeat recombination in uvrD mutants occurs via the RecF pathway. In uvrD+ cells, constitutive expression of SOS genes is not sufficient to stimulate deletion formation. This suggests that the RecF recombination pathway activated by SOS induction is antagonized by the UvrD protein. Paradoxically, we observed that the overproduction of UvrD from a plasmid also stimulates tandem repeat deletion. However, this stimulation is RecA independent, as is deletion in a wild-type strain. We propose that the presence of an excess of the UvrD helicase favours replication slippage. This work suggests that the UvrD helicase controls a balance between different routes of tandem repeat deletion.
A Wortmannin−Cetuximab as a Double Drug (2009)

Double drugs are obtained when two pharmacologically active entities are covalently joined to improve potency. We conjugated the viridin Wm with a self-activating linkage to cetuximab and demonstrated the retention of immunoreactivity by the conjugate. Though cetuximab lacked a growth inhibitory activity against A549 cells, the Wm-cetuximab conjugate had an antiproliferative IC(50) of 155 nM in vitro. The chemistry of attaching a self-releasing Wm to clinically approved antibodies is general and, in selected instances, may yield antibody-based double drugs with improved efficacy.
Character and Caricature, Virtual and Real (2004)

Character, as personality, is formed through biology and culture. But the influence these forces have and the actual processes involved are not really known. Technology, as an important and always changing part of culture, offers us a window on the construction of character especially in that strange new place: cyberspace. The virtual world allows people to play with their character in ways that are very difficult “in real life.” This play reveals a great deal about what is biologically immutable and what isn’t after all. In particular gender, race, and embodiment in general are treated quite differently on-line then in the flesh. And character/caricature formation in the MUDS and MOOS and other cyber-places throws light on the processes of character, such as the roles of evocative technologies, the feedback loops of will and non-will (addiction), and the potentiality of fantasies actualized. In particular political participation on the internet reveals the limits of what real character an be manifested in a simulated environment. It seems cyborgian character is more plastic in some ways than most observers would have predicted; but character, as integrity, will still determine how far the role of caricature will go in supplanting character.
Optimizing Sample Handling for Urinary Proteomics (2008)

Interrogation of the urinary proteome for clinically useful biomarkers of disease will require normalization of methods for protein extraction and sample handling. Variations in collection methods and other procedures may introduce significant discrepancies in qualitative and quantitative measurements. Here we demonstrate that the method of protein extraction, length of handling at room temperature, and repetitive freeze-thaw cycles do not seem to alter the urinary proteome at either the protein or peptide level in a manner that degrades information obtainable by mass spectrometry.
Role of FOXC1 in regulation of basal-like/triple-negative breast cancer (2009)

11016 Background: Class identification studies have proposed 3 prognostically relevant molecular subtypes of breast cancer: luminal, HER2 and basal-like. The latter is associated with poor prognosis but its molecular basis is not clear. We hypothesized a direct correlation between FOXC1 expression and basal-like breast cancer. Methods: Expression of FOXC1, CK5, CK14, EGFR, c-Kit, αB-crystallin, ITGB4 and FOXC2 in basal-like breast cancer was examined using publicly available microarray datasets. A molecular signature of 40 genes sharing co-ordinate up or down regulation with FOXC1 was identified on one microarray (49 patients) and validated on 5 other microarrays (1,232 patients). The clinical significance of FOXC1 gene expression and the FOXC1 gene signature was evaluated using censored survival data. FOXC1 protein expression was assessed by immunohistochemistry (IHC) of a 96-sample breast cancer tissue microarray. Normal breast epithelial, luminal and basal breast cancer cells transfected with FOXC1 vectors were evaluated for cell proliferation, migration and invasion. Results: FOXC1 was found to be consistently and exclusively upregulated in basal-like triple negative breast cancer and was associated with poor overall survival (p&lt;0.0001). The FOXC1 gene signature accurately predicted the basal-like phenotype. IHC analysis of FOXC1 protein expression in human breast cancers confirmed its potential to be used as a clinical biomarker of basal-like breast cancer. Normal breast epithelial cells and luminal breast cancer cells with low or no FOXC1 expression underwent epithelial-to-mesenchymal transition and displayed increased cellular proliferation, migration, invasion, and expression of basal cell markers when FOXC1 was overexpressed. In contrast, knockdown of FOXC1 by shRNA in basal-like breast cancer cells conferred luminal phenotype. Breast cancer progression-linked signaling pathways like NF-κB and p38MAPK were significantly stimulated in basal-like breast cancer as well as by in vitro FOXC1 overexpression. Conclusions: FOXC1 is a dominant determinant of the basal-like phenotype of breast cancer. We propose FOXC1 to be the single best molecular marker of and a potential therapeutic target for basal-like / triple negative breast cancer. No significant financial relationships to disclose.
Novel conical microstructures created in silicon with femtosecond laser pulses (1998)

Summary form only given. Silicon wafers are mounted inside a vacuum chamber backfilled with gas and then irradiated with 800-nm pulses from a regeneratively amplified Ti:sapphire laser. Following laser treatment, the samples are removed from the chamber and analyzed with a scanning electron microscope (SEM).
Building an Effective Corpus By Using Acoustic Space Visualization (COSMOS) Method (2006)

This paper proposes the technique of building an effective corpus with lower cost by using the method of visualizing multiple HMM acoustic models into a 2D space ("COSMOS" method: comprehensive space map of objective signal, previously acoustic space map of sound) method. In an experiment of this paper, adapted acoustic models of 533 male speakers are made with a small quantity of voice samples (10 words) per speaker. Then a plotted map (called COSMOS map) featuring a total of 533 male speakers is generated utilizing the COSMOS method. A corpus was built by selecting 200 male speakers located only in the periphery of the distribution in the COSMOS map and by collecting voice samples (165 words) per speaker. The acoustic model trained from the corpus showed higher performance than the one trained from other corpus built with 200 male speakers selected randomly in the COSMOS map or all of 533 male speakers in the COSMOS map.
Derivatives containing both coumarin and benzimidazole potently induce caspase-dependent apoptosis of cancer cells through inhibition of PI3K-AKT-mTOR signaling (2015)

Coumarins are a large family of compounds derived from a wide range of plants, fungi, and bacteria, and coumarin derivatives can have extremely variable structures and consequently diverse biological properties including antitumor activity. Compounds that bear a benzimidazole moiety are known to possess antitumor activity and a variety of other biological activities. High-throughput screening of a compound library identified a coumarin-containing and a benzimidazole-containing compound [#32, 7-(diethylamino)-3-(1-methyl-1H-benzimidazol-2-yl)-2H-chromen-2-one] that has potent anticancer activity. Evaluation of 17 additional analogs further identified three compounds with anticancer activity in 14 different human cancer cell lines. Fluorescence-activated cell sorting and western blotting analyses suggested that these compounds can induce caspase-dependent apoptosis. Real-time reverse transcriptase PCR analyses of 26 cancer-related genes revealed that seven genes (NPPB, ATF3, DDIT4, CDH10, TSPAN14, TXNIP, and AXL) were significantly upregulated and nine genes (PAGE4, LRP8, SNCAIP, IGFBP5, SLCO2A1, CLDN2, ESRRG, D2HGDH, and PDGFRA) were significantly downregulated. The most upregulated gene is natriuretic peptide precursor B (NPPB) or brain natriuretic peptide, which is increased by 7-, 27-, and 197-fold at 12, 24, and 48 h, respectively. The second most upregulated gene is ATF3, which is increased by 23-fold at the 48 h timepoint. PAGE4 and IGFBP5 are the two most downregulated genes, with a 17-fold reduction in both genes. The expression of several genes (DDIT4, PDGFRA, LRP8, IGFBP5) and western blotting data on key signaling proteins indicate that compound #32 significantly inhibits the PI3K-AKT-mTOR pathway, an intracellular signaling pathway critical in cell proliferation and apoptosis.
Cell enlargement: One possible mechanism underlying cellular senescence (1989)

We previously demonstrated an inverse relationship between the G1 volume of human diploid fibroblast-like (HDFL) cells obtained from foreskin tissue and clonal replicative potential. On the basis of these results, we suggested that one process underlying in vitro senescence is a progressive increase in the mean cell volume of successive progeny within clonal lineages. We now report that the size of HDFL cells, as well as of chick embryo fibroblasts, can be increased in the virtual absence of cell division by culturing at low density and at low serum concentration (0.1-1.0%). Consequent to an increase in cell size, the replicative potential of the cells is reduced to the level of later-passage cells of similar size. By clonal analysis, the populations of enlarged cells contain up to three times as many nondividing cells as do controls. In the enlarged populations, the proportion of cells producing attenuated clones (four or fewer progeny) increases by about 30%, whereas the proportion of cells yielding greater than 32 cells declines by a similar percentage. These observations lead us to propose that replicative potential may be limited by cell size, which in turn may be regulated by a kinetic relationship between cellular growth and cell division cycles.
A 0.65V 1.2mW 2.4GHz/400MHz dual-mode phase modulator for mobile healthcare applications (2014)

A 0.65V 2.4GHz/400MHz digital-intensive phase modulator is implemented in 65nm CMOS. In ultra-low voltage design, the two-point modulator suffers a lot from the DCO nonlinearity. In this work, we employ a 2.4GHz semidigital fractional-N PLL with an FIR filter embedded 1-bit high-pass modulation to overcome the nonlinearity problem in the conventional two-point modulator. The 400MHz modulator performs an FIR-embedded OQPSK modulation to reduce the spectral regrowth in high frequencies. For compact area and low voltage design, an inverter based phase interpolator with a harmonic filtering technique is designed after generating multiphase signals directly from the 2.4GHz output. The 1Mb/s GFSK 2.4GHz and the 10Mb/s OQPSK 400MHz modulators consume 0.94mW and 1.2mW and achieve the EVM values of 5.7% and 6.4% respectively.
P2X7 Deficiency Attenuates Renal Injury in Experimental Glomerulonephritis (2009)

The P2X7 receptor is a ligand-gated cation channel that is normally expressed by a variety of immune cells, including macrophages and lymphocytes. Because it leads to membrane blebbing, release of IL-1beta, and cell death by apoptosis or necrosis, it is a potential therapeutic target for a variety of inflammatory diseases. Although the P2X7 receptor is usually not detectable in normal renal tissue, we previously reported increased expression of both mRNA and protein in mesangial cells and macrophages infiltrating the glomeruli in animal models of antibody-mediated glomerulonephritis. In this study, we used P2X7-knockout mice in the same experimental model of glomerulonephritis and found that P2X7 deficiency was significantly renoprotective compared with wild-type controls, evidenced by better renal function, a striking reduction in proteinuria, and decreased histologic glomerular injury. In addition, the selective P2X7 antagonist A-438079 prevented the development of antibody-mediated glomerulonephritis in rats. These results support a proinflammatory role for P2X7 in immune-mediated renal injury and suggest that the P2X7 receptor is a potential therapeutic target.
Probabilistic checking of proofs (1998)

We give a new characterization of NP: the class NP contains exactly those languages L for which membership proofs (a proof that an input x is in L ) can be verified probabilistically in polynomial time using logarithmic number of random bits and by reading sublogarithmic number of bits from the proof. We discuss implications of this characterization; specifically, we show that approximating Clique and Independent Set, even in a very weak sense, is NP-hard.
Cavity Optomechanics: Back-Action at the Mesoscale (2008)

The coupling of optical and mechanical degrees of freedom is the underlying principle of many techniques to measure mechanical displacement, from macroscale gravitational wave detectors to microscale cantilevers used in scanning probe microscopy. Recent experiments have reached a regime where the back-action of photons caused by radiation pressure can influence the optomechanical dynamics, giving rise to a host of long-anticipated phenomena. Here we review these developments and discuss the opportunities for innovative technology as well as for fundamental science.
The Chemistry and Technology of Rubber-Bound and Related Novel Antioxidants (1972)

Abstract The discovery that C-nitrosoanilines react with olefins to give p -phenylenediamines has made possible the synthesis of powerful antioxidants from a wide range of naturally occurring and synthetic unsaturated compounds. Simple alkenes, vegetable oils, and factices may be converted to antidegradants whose behavior parallels that of commercially available materials. The reaction of 4-nitrosoanilines or 4-nitrosophenols with natural and synthetic rubber or latices gives rubber-bound antioxidants which are completely resistant to extraction by water or organic solvents. No major modification of technological processing or fabrication techniques is necessary, and the reaction takes place conveniently during vulcanization. Attachment of the protective group to the rubber molecule does not affect its antioxidant activity, but reduces its effectiveness when migration to the surface is required, e.g. , in protection against ozone. Although faster at elevated temperatures, the nitroso-olefin reaction will occur at room temperature, and this allows the preparation of chemically modified raw rubbers by carrying out the reaction in latex before coagulation and drying.
Engineering of a Novel Anti-CD40L Domain Antibody for Treatment of Autoimmune Diseases (2014)

CD40-CD40L interactions play a critical role in regulating immune responses. Blockade of CD40L by Abs, such as the anti-CD40L Ab 5c8, demonstrated positive clinical effects in patients with autoimmune diseases; however, incidents of thromboembolism (TE) precluded further development of these molecules. In this study, we examined the role of the Fc domain interaction with FcγRs in modulating platelet activation and potential for TE. Our results show that the interaction of the 5c8 wild-type IgG1 Fc domain with FcγRs is responsible for platelet activation, as measured by induction of PAC-1 and CD62P. A version of 5c8 with a mutated IgG1 tail was identified that showed minimal FcγR binding and platelet activation while maintaining full binding to CD40L. To address whether Fc effector function is required for immunosuppression, a potent Ab fragment, termed a "domain Ab" (dAb), against murine CD40L was identified and fused to a murine IgG1 Fc domain containing a D265A mutation that lacks Fc effector function. In vitro, this dAb-Fc demonstrated comparable potency to the benchmark mAb MR-1 in inhibiting B cell and dendritic cell activation. Furthermore, the anti-CD40L dAb-Fc exhibited a notable efficacy comparable to MR-1 in various preclinical models, such as keyhole limpet hemocyanin-induced Ab responses, alloantigen-induced T cell proliferation, "heart-to-ear" transplantation, and NZB × NZW F1 spontaneous lupus. Thus, our data show that immunosuppression and TE can be uncoupled and that a CD40L dAb with an inert Fc tail is expected to be efficacious for treating autoimmune diseases, with reduced risk for TE.
Inflammatory Cytokines Induce Production of CHI3L1 by Articular Chondrocytes (2005)

Elevated levels of CHI3L1 (chitinase-3-like protein 1) are associated with disorders exhibiting increased connective tissue turnover, such as rheumatoid arthritis, osteoarthritis, scleroderma, and cirrhosis of the liver. This secreted protein is not synthesized in young healthy cartilage, but is produced in cartilage from old donors or patients with osteoarthritis. The molecular processes governing the induction of CHI3L1 are currently unknown. To elucidate the molecular events involved in CHI3L1 synthesis, we investigated two models of articular chondrocytes: neonatal rat chondrocytes, which do not express CHI3L1, and human chondrocytes, which express CHI3L1 constitutively. In neonatal rat chondrocytes, the inflammatory cytokines tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 potently induced steady-state levels of CHI3L1 mRNA and protein secretion. Treatment of chondrocytes with TNF-alpha for as little as 1 h was sufficient for sustained induction up to 72 h afterward. Using inhibitors selective for the major signaling pathways implicated in mediating the effects of TNF-alpha and interleukin-1, only inhibition of NF-kappaB activation was effective in curtailing cytokine-induced expression, including after removal of the cytokine, indicating that induction and continued production of CHI3L1 are controlled mainly by this transcription factor. Inhibition of NF-kappaB signaling also abolished constitutive expression by human chondrocytes. Thus, induction and continued secretion of CHI3L1 in chondrocytes require sustained activation of NF-kappaB. Selective induction of CHI3L1 by cytokines acting through NF-kappaB coupled with the known restriction of the catabolic responses by CHI3L1 in response to these inflammatory cytokines represents a key regulatory feedback process in controlling connective tissue turnover.
Optical networking in the European ACTS Programme (1996)

Summary form only given. The ACTS Programme (advanced communications technologies and services) is the European Commission's major programme for supporting pre-competitive research and technological development in telecommunications, in the period 1995-1998.