gebhart/patrepeval huggingface dataset:
Isolation of amplified and overexpressed DNA sequences from adriamycin-resistant human breast cancer cells. (1987)

An MCF-7 human breast cancer cell line was selected which was 200-fold more resistant to Adriamycin than the wild type cell line. This Adriamycin-resistant (AdrR) cell line exhibited a multidrug-resistant phenotype and was cross-resistant to a wide range of antineoplastic agents including Vinca alkaloids, anthracyclines, and epipodophyllotoxins. Cytogenetic analysis of the AdrR cell line showed the presence of homogeneously staining regions on several chromosomes which were not present in the parental cell line. Using the technique of in-gel renaturation, DNA sequences which were amplified 50- to 100-fold in the AdrR cell line and which covered a total of over 140 kilobases were isolated. In addition, AdrR cells were found to contain amplified and overexpressed sequences which were homologous to hamster P-glycoprotein gene sequences. A hamster cDNA P-glycoprotein gene probe was used to screen a lambda gt10 cDNA library made from human AdrR cell line mRNA and human cDNA sequences homologous to the P-glycoprotein gene were isolated. Hybridization studies with the cloned human cDNA (pADR1) showed that the AdrR MCF-7 cell line contained a 60-fold amplification of this DNA sequence and that polyadenylated mRNA from the AdrR cell line contained a 4.8-kilobase transcript which was overexpressed 45-fold. There was a direct correlation between DNA and RNA copy number of this sequence and level of resistance among several MCF-7 Adriamycin-resistant cell lines. In situ hybridization studies demonstrated that the human P-glycoprotein gene sequence was found on chromosome 7q21.1 in normal human lymphocytes and that amplified DNA sequences isolated from the AdrR MCF-7 cells by the in-gel hybridization technique were linked to the human P-glycoprotein sequences in the homogeneously staining regions in the AdrR cells.
Conformationally Restricted Aza‐BODIPY: Highly Fluorescent, Stable Near‐Infrared Absorbing Dyes (2006)

Novel NIR fluorescent, conformational restricted aza-dipyrromethene boron difluoride (aza-BODIPY) dyes were prepared by an efficient process. Such conformational restricted aza-BODIPY dyes possess intense absorption, strong fluorescence, high chemical and photostability. Additionally, the sharp fluorescence of non-amine containing aza-BODIPY dyes is insensitive to solvent polarity.
FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis (2007)

In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.
Prognostic Utility of a Gene-Expression Signature in Untreated Node-Negative Breast Cancer (2005)

Purpose: Gene expression profiling has the potential to lead to a more accurate prognostic classification of breast cancer patients. Recently, a set of 70 genes had been identified that allowed risk classification of node-negative patients. We analysed the prognostic utility of a subset of these genes and compared it with established prognostic factors in a collective of 150 untreated node-negative breast cancer patients. Methods: cRNA of 150 untreated node-negative breast cancer patients was hybridized on the Affymetrix HG-U133A array and probe sets corresponding to the set of 70 genes were identified. A good and poor prognosis profile was generated for the expression of 52 genes. The prognostic utility of this gene-expression signature was then compared with established prognostic factors (i.e. histological grade, tumor size and steroid hormone receptor status). The prognostic utility for disease-free survival (DFS) was evaluated using univariate and multivariate statistical analyses. Results: 33 (22%) of the tumors were assigned to the good and 117 (78%) to the poor prognosis group based on the gene-expression signature. This led to a sensitivity of 93% with a specificity of 26%. 5-year DFS was 94% in the good and 78% in the poor prognosis group, respectively. However, this difference diminished with longer follow-up (p=0.167). Of the prognostic factors analysed, only histological grade was associated with DFS (p<0,0005). Conclusion: histological grade had a higher prognostic utility than the gene-expression signature in our cohort of untreated node-negative breast cancer patients.
Analysis of organ-enriched microRNAs in plasma as an approach to development of Universal Screening Test: feasibility study (2013)

The results obtained in the present study, along with the data reported by us and others previously, are encouraging and lay the ground for further investigation of the described approach for UST development.
Light‐Induced Formation of G‐Quadruplex DNA Secondary Structures (2005)

A little light release: Temporarily blocked (“caged”) dG nucleosides that can be incorporated into oligodeoxynucleotides are presented (see figure). Their hydrogen-bond-recognition site is inaccessible in the inactive form; this prevents, for example, the formation of secondary structures. Light can trigger the release of the unmodified oligonucleotide and thus induce correct folding. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2005/z500198_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Influenza B Virus NS1-Truncated Mutants: Live-Attenuated Vaccine Approach (2008)

Type B influenza viruses can cause substantial morbidity and mortality in the population, and vaccination remains by far the best means of protection against infections with these viruses. Here, we report the construction of mutant influenza B viruses for potential use as improved live-virus vaccine candidates. Employing reverse genetics, we altered the NS1 gene, which encodes a type I interferon (IFN) antagonist. The resulting NS1 mutant viruses induced IFN and, as a consequence, were found to be attenuated in vitro and in vivo. The absence of pathogenicity of the NS1 mutants in both BALB/c and C57BL/6 PKR(-/-) mice was confirmed. We also provide evidence that influenza B virus NS1 mutants induce a self-adjuvanted immune response and confer effective protection against challenge with both homologous and heterologous B virus strains in mice.
Continuous Assessment of the Cerebral Vasomotor Reactivity in Head Injury (1997)

Computer analysis of slow waves in ABP and ICP is able to provide a continuous index of cerebrovascular reactivity to changes in arterial pressure, which is of prognostic significance.
Electrospray Ionization Mass Spectrometry of Recombinantly Engineered Antibody Fragments (1994)

Mass spectrometry has been used to confirm the correct protein expression of Fab and F(ab')2 fragments of the humanized anti-p185HER2 antibody huMAb4D5. These data demonstrate that electrospray ionization mass spectrometry can be used routinely to measure the masses of purified proteins as large as 100 kDa, with an accuracy of < or = 0.02%. This level of accuracy is helpful in demonstrating the faithful translation and proper posttranslational modification of these proteins. Accurate and reliable mass assignments by electrospray ionization mass spectrometry are achieved by calibrating with protein mass standards, optimizing resolution, and using methods to improve sample purity. On-line reversed-phase high-performance liquid chromatography/mass spectrometry has been employed to improve sample purity and thereby increase sensitivity. Disulfide reduction to yield the component subunits provides additional confirmation of the correct amino acid sequence with greater absolute mass accuracy. A volatile reducing agent such as tributylphosphine provides a convenient method to generate subunits for mass measurement while requiring little or no further sample purification.
Distribution, Data, Deployment: Software Architecture Convergence in Big Data Systems (2014)

Big data applications are pushing the limits of software engineering on multiple horizons. Successful solutions span the design of the data, distribution, and deployment architectures. The body of software architecture knowledge must evolve to capture this advanced design knowledge for big data systems. This article is a first step on this path. Our research is proceeding in two complementary directions. First, we're expanding our collection of architecture tactics and encoding them in an environment that supports navigation between quality attributes and tactics, making crosscutting concerns for design choices explicit. Second, we're linking tactics to design solutions based on specific big data technologies, enabling architects to rapidly relate a particular technology's capabilities to a specific set of tactics.
Phase-matched periodic electric-field-induced second-harmonic generation in optical fibers (1989)

Phase-matched electric-field-induced second-harmonic generation is demonstrated in single-mode germania-doped silica fibers. A periodic second-order nonlinearity is induced by a simple interdigitated electrode structure, which can be rotated to permit phase matching between all propagating modes. The most efficient mode interaction between HE11ω and HE112ω is achieved at 1.064 μm by using a Q-switched Nd+3:YAG laser. In principle, phase matching at any propagating wavelength is possible. This technique could be applied to planar as well as cylindrical waveguides and can be used with many non-χ(2) materials. The asymmetry in the applied electric field enhances the optical-field overlaps between modes of dissimilar orders, and this is also demonstrated. A conversion efficiency of 4.0 × 10−4% has been obtained in unoptimized devices. Device optimization is also discussed.
Predisposition to Cancer Caused by Genetic and Functional Defects of Mammalian Atad5 (2011)

ATAD5, the human ortholog of yeast Elg1, plays a role in PCNA deubiquitination. Since PCNA modification is important to regulate DNA damage bypass, ATAD5 may be important for suppression of genomic instability in mammals in vivo. To test this hypothesis, we generated heterozygous (Atad5(+/m)) mice that were haploinsuffficient for Atad5. Atad5(+/m) mice displayed high levels of genomic instability in vivo, and Atad5(+/m) mouse embryonic fibroblasts (MEFs) exhibited molecular defects in PCNA deubiquitination in response to DNA damage, as well as DNA damage hypersensitivity and high levels of genomic instability, apoptosis, and aneuploidy. Importantly, 90% of haploinsufficient Atad5(+/m) mice developed tumors, including sarcomas, carcinomas, and adenocarcinomas, between 11 and 20 months of age. High levels of genomic alterations were evident in tumors that arose in the Atad5(+/m) mice. Consistent with a role for Atad5 in suppressing tumorigenesis, we also identified somatic mutations of ATAD5 in 4.6% of sporadic human endometrial tumors, including two nonsense mutations that resulted in loss of proper ATAD5 function. Taken together, our findings indicate that loss-of-function mutations in mammalian Atad5 are sufficient to cause genomic instability and tumorigenesis.
Three‐in‐One Chromatography‐Free Purification, Tag Removal, and Site‐Specific Modification of Recombinant Fusion Proteins Using Sortase A and Elastin‐like Polypeptides (2013)

Sorting it out: Applied in tandem, elastin-like polypeptides (ELPs, see scheme) and the Sortase A (SrtA) transpeptidase provide a method for chromatography-free purification of recombinant proteins and optional, site-specific conjugation of the protein to a small molecule (yellow). This system provides an efficient mechanism for generating bioactive proteins at high yields and purities. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
PAMPs and DAMPs: signal 0s that spur autophagy and immunity (2012)

Pathogen-associated molecular pattern molecules (PAMPs) are derived from microorganisms and recognized by pattern recognition receptor (PRR)-bearing cells of the innate immune system as well as many epithelial cells. In contrast, damage-associated molecular pattern molecules (DAMPs) are cell-derived and initiate and perpetuate immunity in response to trauma, ischemia, and tissue damage, either in the absence or presence of pathogenic infection. Most PAMPs and DAMPs serve as so-called 'Signal 0s' that bind specific receptors [Toll-like receptors, NOD-like receptors, RIG-I-like receptors, AIM2-like receptors, and the receptor for advanced glycation end products (RAGE)] to promote autophagy. Autophagy, a conserved lysosomal degradation pathway, is a cell survival mechanism invoked in response to environmental and cellular stress. Autophagy is inferred to have been present in the last common eukaryotic ancestor and only to have been lost by some obligatory intracellular parasites. As such, autophagy represents a unifying biology, subserving survival and the earliest host defense strategies, predating apoptosis, within eukaryotes. Here, we review recent advances in our understanding of autophagic molecular mechanisms and functions in emergent immunity.
Variable β-catenin expression in colorectal cancers indicates tumor progression driven by the tumor environment (2001)

Invasion and dissemination of well-differentiated carcinomas are often associated with loss of epithelial differentiation and gain of mesenchyme-like capabilities of the tumor cells at the invasive front. However, when comparing central areas of primary colorectal carcinomas and corresponding metastases, we again found the same differentiated epithelial growth patterns. These characteristic phenotypic changes were associated with distinct expression patterns of beta-catenin, the main oncogenic protein in colorectal carcinomas, and E-cadherin. Nuclear beta-catenin was found in dedifferentiated mesenchyme-like tumor cells at the invasive front, but strikingly, as in central areas of the primary tumors, was localized to the membrane and cytoplasm in polarized epithelial tumor cells in the metastases. This expression pattern was accompanied by changes in E-cadherin expression and proliferative activity. On the basis of these data, we postulate that an important driving force for progression of well-differentiated colorectal carcinomas is the specific environment, initiating two transient phenotypic transition processes by modulating intracellular beta-catenin distribution in tumor cells.
Identification of a p65 Peptide That Selectively Inhibits NF-κ B Activation Induced by Various Inflammatory Stimuli and Its Role in Down-regulation of NF-κB-mediated Gene Expression and Up-regulation of Apoptosis (2004)

Because of the critical role of the nuclear transcription factor NF-kappaB in inflammation, viral replication, carcinogenesis, antiapoptosis, invasion, and metastasis, specific inhibitors of this nuclear factor are being sought and tested as treatments. NF-kappaB activation is known to require p65 phosphorylation at serine residues 276, 529, and 536 before it undergoes nuclear translocation. Small protein domains, termed protein transduction domains (PTDs), which are able to penetrate cell membranes can be used to transport other proteins across the cell membrane. We have identified two peptides from the p65 subunit of NF-kappaB (P1 and P6 were from amino acid residues 271-282 and 525-537, respectively) that, when linked with a PTD derived from the third helix sequence of antennapedia, inhibited tumor necrosis factor (TNF)-induced NF-kappaB activation in vivo. Linkage to the PTD was not, however, required to suppress the binding of the p50-p65-heterodimer to the DNA in vitro. PTD-p65-P1 had no effect on TNF-induced AP-1 activation. PTD-p65-P1 suppressed NF-kappaB activation induced by lipopolysaccharide, interleukin-1, okadaic acid, phorbol 12-myristate 13-acetate, H(2)O(2), and cigarette smoke condensate as well as that induced by TNF. PTD-p65-P1 had no effect on TNF-induced inhibitory subunit of NF-kappaB(IkappaBalpha) phosphorylation, IkappaBalpha degradation, or IkappaBalpha kinase activation, but it blocked TNF-induced p65 phosphorylation and nuclear translocation. NF-kappaB-regulated reporter gene expression induced by TNF, TNF receptor 1, TNF receptor-associated death domain, TNF receptor-associated factor-2, NF-kappaB-inducing kinase, IkappaBalpha kinase, and p65 was also suppressed by these peptides. Suppression of NF-kappaB by PTD-p65-P1 enhanced the apoptosis induced by TNF and chemotherapeutic agents. Overall, our results demonstrate the identification of a p65 peptide that can selectively inhibit NF-kappaB activation induced by various inflammatory stimuli, down-regulate NF-kappaB-mediated gene expression, and up-regulate apoptosis.
High breakdown voltage AlGaN-GaN power-HEMT design and high current density switching behavior (2003)

AlGaN-GaN power high-electron mobility transistors (HEMTs) with 600-V breakdown voltage are fabricated and demonstrated as switching power devices for motor drive and power supply applications. The fabricated power HEMT realized the high breakdown voltage by optimized field plate technique and the low on-state resistance of 3.3 m/spl Omega/cm/sup 2/, which is 20 times lower than that or silicon MOSFETs, thanks to the high critical field of GaN material and the high mobility in 2DEG channel. The fabricated devices also demonstrated the high current density switching of 850 A/cm/sup 2/ turn-off. These results show that AlGaN-GaN power-HEMTs are one of the most promising candidates for future switching power device for power electronics applications.
A generalized depth estimation algorithm with a single image (1992)

A depth estimation algorithm proposed by A.P. Pentland (1987) is generalized. In the proposed algorithm, the raw image data in the vicinity of the edge is used to estimate the depth from defocus. Since no differentiation operation on the image data is required before the optimization process, the method is less sensitive to the noise disturbance of measurements. Furthermore, the edge orientation that was critical in Pentland's approach will not be required in the case. This algorithm is then applied to synthetic images containing various amounts of noise to test its performance. Experimental results indicate that the depth estimation errors are kept within 5% of true values on the average when it is applied to real images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Particle sorting by a structured microfluidic ratchet device with tunable selectivity: theory and experiment (2012)

We theoretically predict and experimentally demonstrate that several different particle species can be separated from each other by means of a ratchet device, consisting of periodically arranged triangular (ratchet) shaped obstacles. We propose an explicit algorithm for suitably tailoring the externally applied, time-dependent voltage protocol so that one or several, arbitrarily selected particle species are forced to migrate oppositely to all the remaining species. As an example we present numerical simulations for a mixture of five species, labelled according to their increasing size, so that species 2 and 4 simultaneously move in one direction and species 1, 3, and 5 in the other. The selection of species to be separated from the others can be changed at any time by simply adapting the voltage protocol. This general theoretical concept to utilize one device for many different sorting tasks is experimentally confirmed for a mixture of three colloidal particle species.
Correlation between Ozone Resistance and Relative Chlorophyll Fluorescence or Relative Stomatal Conductance of Bedding Plants (2001)

Eight species of bedding plants were exposed to 400 ppb ozone (O3) for 4 h. On the basis of the resulting foliar injury, Madagascar periwinkle (Catharanthus roseus) and impatiens (Impatiens walleriana) were the most resistant to O3, and wax begonia (Begonia xsemperflorens-cultorum) was the most sensitive to O3. Clorophyll fluorescence (Fv/Fm) and stomatal conductance were measured before and after the O3 fumigation. There was a significant regression between, the degree of foliage injury by O3 and relative chlorophyll fluorescence (RCF, ratio of post-fumigation Fv/Fm: pre-fumigation Fv/Fm) or relative stomatal conductance (RSC, ratio of post-fumigation stomatal conductance: pre-fumigation stomatal conductance) (r=-0.84, P＜0.001 and r=0.64, P＜0.05 respectively). That is, species of tested bedding plants that had stronger O3 resistance generally had higher RCF and lower RSC values. It is suggested that RCF and RSC measurements could serve as indicators to screen plants for O3 resistance.
Optimization of linear double-stranded RNA for the production of multiple siRNAs targeting hepatitis C virus (2009)

RNA interference (RNAi)-based gene silencing possesses great therapeutic potential for inhibiting replication of human viruses such as hepatitis C virus (HCV). However, one of the putative limitations for its use as a therapy is the rapid emergence of escape variants. These contain deletions or mutations within the viral genome sequences complementary to the small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) being used for treatment. As a potential solution to this problem, we constructed an expression system for duplex RNAs harboring two siRNA units using convergent H1 and U6 Pol III promoters. Here, the length and orientation of the transcript, tandem siRNA (tsiRNA), were optimized to be processed by the intracellular ribonuclease Dicer into functional siRNAs targeting different sequences. Assessment in transfected cells indicates that the length of the tsiRNA duplex (40-42 base pairs) is more critical for both siRNA-producing capacity and gene silencing activity than the orientation of each siRNA unit. In Huh7 cells replicating full-length HCV RNA, expression of length-optimized tsiRNA inhibited viral protein levels as efficiently as a single 21-nucleotide siRNA-expression construct, without affecting miRNA maturation or induction of an interferon response. We verified that the anti-viral activity of tsiRNA was achieved by precise cleavage of two target sites. A distinct advantage of this strategy is that each side of the optimized linear duplex RNA could enter into the Dicer-mediated processing machinery, thus likely providing more equal and efficient production of multiple siRNAs required for reducing the chance of viral escape.