gebhart/patrepeval huggingface dataset:
Construction of Long Chromosomal Deletion Mutants of Escherichia coli and Minimization of the Genome (2008)

Genetic information consists of protein- and RNA-coding genes that exist in a range of sizes and noncoding cis- and trans-acting sequence elements. The use of long chromosomal deletion mutations is a powerful method for identifying essential genetic information through experimental reduction of the genome to its minimal gene set. Taking advantage of recent technical advances, we constructed sequence-specific long deletion mutations of the Escherichia coli chromosome. In a recent report (1), we described a set of E. coli medium-scale deletions (MDs) and large-scale deletions (LDs). Several LD mutations were combined to generate an engineered strain lacking approximately 30% of the parental chromosome. We then constructed another set of deletion mutations, MDs and small-scale deletions (SDs), and identified additional essential genetic regions using complementation analysis. To delete the remaining essential chromosomal regions, we developed an Flp recombinase target (FRT)-based system of site-specific recombination to move chromosomal regions onto mini-F plasmids in vivo. In this report, we describe the details of the construction of several of these types of large chromosomal deletion mutants.
Mesothelin, a possible target for immunotherapy, is expressed in primary AML cells (2007)

Primary AML cells express mesothelin but SS1(dsFv)PE38 is not active in killing these cells. Other approaches that utilize mesothelin as a target might be more effective and should be tested against AML cells.
Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system (2013)

A simple and robust method for targeted mutagenesis in zebrafish has long been sought. Previous methods generate monoallelic mutations in the germ line of F0 animals, usually delaying homozygosity for the mutation to the F2 generation. Generation of robust biallelic mutations in the F0 would allow for phenotypic analysis directly in injected animals. Recently the type II prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system has been adapted to serve as a targeted genome mutagenesis tool. Here we report an improved CRISPR/Cas system in zebrafish with custom guide RNAs and a zebrafish codon-optimized Cas9 protein that efficiently targeted a reporter transgene Tg(-5.1mnx1:egfp) and four endogenous loci (tyr, golden, mitfa, and ddx19). Mutagenesis rates reached 75-99%, indicating that most cells contained biallelic mutations. Recessive null-like phenotypes were observed in four of the five targeting cases, supporting high rates of biallelic gene disruption. We also observed efficient germ-line transmission of the Cas9-induced mutations. Finally, five genomic loci can be targeted simultaneously, resulting in multiple loss-of-function phenotypes in the same injected fish. This CRISPR/Cas9 system represents a highly effective and scalable gene knockout method in zebrafish and has the potential for applications in other model organisms.
A phase III randomized, doúble-blind, multiinstitutional trial of vaccinia melanoma oncolysate-active specific immunotherapy for patients with stage II melanoma (1995)

In this first interim analysis, active specific immunotherapy with VMO vs. V showed no difference in the disease free interval or overall survival. Subset analyses likewise showed no significant differences in outcome but the data suggest a potential difference in immunoreactivity between male and female patients with melanoma that awaits further follow up and may merit further investigation.
An α-syntrophin-dependent pool of AQP4 in astroglial end-feet confers bidirectional water flow between blood and brain (2003)

The water channel AQP4 is concentrated in perivascular and subpial membrane domains of brain astrocytes. These membranes form the interface between the neuropil and extracerebral liquid spaces. AQP4 is anchored at these membranes by its carboxyl terminus to alpha-syntrophin, an adapter protein associated with dystrophin. To test functions of the perivascular AQP4 pool, we studied mice homozygous for targeted disruption of the gene encoding alpha-syntrophin (alpha-Syn(-/-)). These animals show a marked loss of AQP4 from perivascular and subpial membranes but no decrease in other membrane domains, as judged by quantitative immunogold electron microscopy. In the basal state, perivascular and subpial astroglial end-feet were swollen in brains of alpha-Syn(-/-) mice compared to WT mice, suggesting reduced clearance of water generated by brain metabolism. When stressed by transient cerebral ischemia, brain edema was attenuated in alpha-Syn(-/-) mice, indicative of reduced water influx. Surprisingly, AQP4 was strongly reduced but alpha-syntrophin was retained in perivascular astroglial end-feet in WT mice examined 23 h after transient cerebral ischemia. Thus alpha-syntrophin-dependent anchoring of AQP4 is sensitive to ischemia, and loss of AQP4 from this site may retard the dissipation of postischemic brain edema. These studies identify a specific, syntrophin-dependent AQP4 pool that is expressed at distinct membrane domains and which mediates bidirectional transport of water across the brain-blood interface. The anchoring of AQP4 to alpha-syntrophin may be a target for treatment of brain edema, but therapeutic manipulations of AQP4 must consider the bidirectional water flux through this molecule.
Real-Time SLAM Relocalisation (2007)

Monocular SLAM has the potential to turn inexpensive cameras into powerful pose sensors for applications such as robotics and augmented reality. However, current implementations lack the robustness required to be useful outside laboratory conditions: blur, sudden motion and occlusion all cause tracking to fail and corrupt the map. Here we present a system which automatically detects and recovers from tracking failure while preserving map integrity. By extending recent advances in keypoint recognition the system can quickly resume tracking - i.e. within a single frame time of 33 ms - using any of the features previously stored in the map. Extensive tests show that the system can reliably generate maps for long sequences even in the presence of frequent tracking failure.
Baffled circular loudspeaker array with broadband high directivity (2010)

Super-directional loudspeaker arrays can be used to achieve high directivity in a limited low-frequency range. As opposed to microphone arrays, the distance between the loudspeakers has to be relatively large, resulting in aliasing starting at relatively low frequencies. On the other hand, mounting a loudspeaker on a rigid baffle (e.g., a rigid cylinder or sphere) increases its directivity with frequency. Using super-directional array techniques at low frequencies and leveraging loudspeakers' increased directivity at high frequencies enables achieving high directivity both at low and high frequencies. The design of baffled circular loudspeaker arrays and an improved beamforming procedure for achieving high directivity in a broad frequency range is described.
N.m.r. studies of drug-receptor interactions as an aid to drug design (1984)

The importance of the relation between the structure of drugs and their biological activity has been recognised for almost 300 years (Locke, 1690). With the development of the idea of the receptor at the beginning of this century, the conceptual framework for modern structure-activity analysis was established. Over the ensuing years increasingly sophisticated studies of the relationships between chemical structure, conformation and physicochemical properties on the one hand and biological activity on the other, have made major contributions to the design of new and effective drugs, although for most systems the receptor remained simply an idea.
3D Origami-based multifunction-integrated immunodevice: low-cost and multiplexed sandwich chemiluminescence immunoassay on microfluidic paper-based analytical device (2012)

A novel 3D microfluidic paper-based immunodevice, integrated with blood plasma separation from whole blood samples, automation of rinse steps, and multiplexed CL detections, was developed for the first time based on the principle of origami (denoted as origami-based device). This 3D origami-based device, comprised of one test pad surrounded by four folding tabs, could be patterned and fabricated by wax-printing on paper in bulk. In this work, a sandwich-type chemiluminescence (CL) immunoassay was introduced into this 3D origami-based immunodevice, which could separate the operational procedures into several steps including (i) folding pads above/below and (ii) addition of reagent/buffer under a specific sequence. The CL behavior, blood plasma separation, washing protocol, and incubation time were investigated in this work. The developed 3D origami-based CL immunodevice, combined with a typical luminuol-H(2)O(2) CL system and catalyzed by Ag nanoparticles, showed excellent analytical performance for the simultaneous detection of four tumor markers. The whole blood samples were assayed and the results obtained were in agreement with the reference values from the parallel single-analyte test. This paper-based microfluidic origami CL detection system provides a new strategy for a low-cost, sensitive, simultaneous multiplex immunoassay and point-of-care diagnostics.
Analysis of the 11p13 Wilms' Tumor Suppressor Gene (WTI) in Ovarian Tumors (1993)

We have examined the status of the Wilms' tumor suppressor gene (WT1), residing at chromosome 11 band p13, in a total of 40 cancers of the female reproductive tract. Northern blot analysis revealed that the WT1 gene is expressed in a large percentage of ovarian tumors (75%) analyzed. Single-strand conformation polymorphism analysis was performed on all the tumors in this study in an attempt to detect mutations within the WT1 gene. Only silent mutations were detected within intron 7 of WT1 using this method. Loss of heterozygosity studies were performed at the WT1 locus in several ovarian tumors and revealed that in the informative cases, heterozygosity was retained.
Coupling of Two Superconductors through a Ferromagnet: Evidence for aπJunction (2001)

We report measurements of the temperature dependence of the critical current, I(c), in Josephson junctions consisting of conventional superconducting banks of Nb and a weakly ferromagnetic interlayer of a CuxNi1-x alloy, with x around 0.5. With decreasing temperature I(c) generally increases, but for specific thicknesses of the ferromagnetic interlayer, a maximum is found followed by a strong decrease down to zero, after which I(c) rises again. Such a sharp cusp can be explained only by assuming that the junction changes from a 0-phase state at high temperatures to a pi phase state at low temperatures.
Genevestigator V3: A Reference Expression Database for the Meta‐Analysis of Transcriptomes (2008)

The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation.
Structure Determination of Biological Macromolecules in Solution Using Nuclear Magnetic Resonance Spectroscopy (2000)

A detailed understanding of the function of a biological macromolecule requires knowledge of its three-dimensional structure. Most atomic-resolution structures of biological macromolecules have been solved either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) in solution. This review surveys the method of NMR structure determination. First, a brief introduction to NMR and its basic concepts is presented. The main part of the article deals with the individual steps necessary for an NMR structure determination. At the end, the discussion turns to considerations on the influence of the molecular size of the macromolecules on the structure determination by NMR. New techniques are discussed that greatly enhance the possibilities of applying NMR to large molecular systems.
Conformational Studies of the O-specific Polysaccharide of Shigella flexneri 5a and of Four Related Synthetic Pentasaccharide Fragments Using NMR and Molecular Modeling (2003)

As part of a program for the development of synthetic vaccines against the pathogen Shigella flexneri, we used a combination of NMR and molecular modeling methods to study the conformations of the O-specific polysaccharide (O-SP) of S. flexneri 5a and of four related synthetic pentasaccharide fragments. The NMR study, based on the analysis of 1H and 13C chemical shifts, the evaluation of inter-residue distances, and the measurement of one- and three-bond heteronuclear coupling constants, showed that the conformation of one of the four pentasaccharides is similar to that of the native O-SP in solution. Interestingly, inhibition enzyme-linked immunosorbent assay demonstrated that a protective monoclonal antibody specific for S. flexneri 5a has a greater affinity for this pentasaccharide than for the others. We carried out a complete conformational search on the pentasaccharides using the CICADA algorithm interfaced with MM3 force field. We calculated Boltzmann-averaged inter-residue distances and 3JC,H coupling constants for the different conformational families and compared the results with NMR data for all pentasaccharides. Our experimental data are consistent with only one conformational family. We also used molecular modeling data to build models of the O-SP with the molecular builder program POLYS. The models that are in agreement with NMR data adopt right-handed 3-fold helical structures in which the branched glucosyl residue points outwards.
Direct Film Transfer (DFT) Technology for Kerf-Free Silicon Wafering (2008)

A new beam-induced large-area crystalline silicon PV wafering process with near zero kerf-loss has been developed. This paper introduces the Direct Film Transfer (DFT) process and describes its practical utilization to slice thin (50-150μm) PV wafers in high-volume manufacturing. The material characteristics such as lifetime, mechanical strength and TTV when monocrystalline silicon ingots are wafered using this new process are also summarized and show excellent results compared to traditional multi-wire slurry saw (MWSS) slicing methods.
Elimination of hypoxic protection by 5-thio-D-glucose in multicell spheroids. (1978)

The effect of 5-thio-D-glucose on oxic and hypoxic V79-171 Chinese hamster cells was studied in vitro with single cells and multicell spheroids. At concentrations that were not toxic to oxic cells, this compound killed hypoxic cells with a D0 of 1 hr with a 5 mM concentration and more rapidly at 10 mM beginning 2 hr after incubation at 37 degrees. 5-Thio-D-glucose also sensitized hypoxic cells to radiation and protected oxic cells from radiation damage. Multicell spheroids irradiated after incubation with the compound demonstrated increased radiosensitivity, although the relative contribution of cytotoxicity and hypoxic cell sensitization could not be evaluated. Spheroid reoxygenation by decreased cell respiration was determined not to be a contributing factor, suggesting that the spheroid-sensitizing effect was due to drug effects on hypoxic cells. The dramatic increase in multicell spheroid radiosensitivity that resulted from treatment with 5-thio-D-glucose suggests that this compound may be used to increase the effectiveness of radiotherapy by eliminating hypoxic protection.
Optimized Synthesis of Hydrogen-Bond Surrogate Helices:  Surprising Effects of Microwave Heating on the Activity of Grubbs Catalysts (2006)

This manuscript discusses microwave-assisted solid-phase synthesis of hydrogen-bond surrogate based alpha-helices and analogues by ring-closing metathesis (RCM). Microwave-mediated RCM allows access to a greater variety of amino acid residues in the macrocycles in shorter reaction times and higher yields compared to conventional heating. Surprisingly, we discovered that the Grubbs II catalyst is highly active under the influence of microwaves but catalytically dead under oil-bath conditions for the metathesis of these peptide bisolefins. [reaction: see text]
Cardiotrophin-1 Stimulation of Cardiac Fibroblast Growth (2002)

Cardiotrophin-1 (CT-1), a member of the interleukin-6 superfamily, and endothelin-1 (ET-1) are potent hypertrophic factors in cardiomyocytes. Although CT-1 and ET-1 gene expression in the heart is upregulated in experimental heart failure, their role in the activation of the cardiac fibroblast is unknown. This study was designed to identify the presence and action of CT-1 and its receptor complex, glycoprotein130 (gp130) and leukemia inhibitory factor (LIF) receptor, on cardiac fibroblast growth in cultured adult canine cardiac fibroblasts. In addition, we investigated the interaction between CT-1/gp130/LIF receptor and ET-1/endothelin type A (ET(A)) receptor axis. Immunohistochemistry was performed using the indirect immunoperoxidase method, while we assessed the cell cycle of cardiac fibroblasts by flow cytometry, DNA synthesis by [(3)H]thymidine incorporation, and collagen synthesis by [(3)H]proline incorporation, respectively. CT-1 and gp130/LIF receptor were widely present in the cytoplasm of the cardiac fibroblasts. Exogenous CT-1 markedly stimulated [(3)H]thymidine and [(3)H]proline incorporations (P<0.01), with accumulation of cells in the S phase. Blockade of gp130 or LIF receptor inhibited basal growth as well as CT-1- or ET-1-stimulated cardiac fibroblast growth. The specific ET(A) receptor antagonist, BQ123, significantly inhibited CT-1-stimulated DNA synthesis. This study demonstrates that CT-1 and its receptors are present in cardiac fibroblasts. In addition, growth of these cells stimulated by endogenous and exogenous CT-1 requires gp130/LIF receptor as well as ET(A) receptor activation. We conclude that gp130/LIF receptor and ET(A) receptor activation are essential for cardiac fibroblast growth by CT-1 and that there is synergism with ET-1/ET(A) receptor axis.
Genotype Prevalence and Risk Factors for Severe Clinical Adenovirus Infection, United States 2004-2006 (2007)

For both populations, we observed a statistically significant increasing trend of adenovirus type 21 detection over time. Among adenovirus isolates recovered from specimens from civilians, 50% were associated with hospitalization, 19.6% with a chronic disease condition, 11% with a bone marrow or solid organ transplantation, 7.4% with intensive care unit stay, and 4.2% with a cancer diagnosis. Multivariable risk factor modeling for adenovirus disease severity found that age <7 years (odds ratio [OR], 3.2; 95% confidence interval [CI], 1.4-7.4), chronic disease (OR, 3.6; 95% CI, 2.6-5.1), recent transplantation (OR, 2.7; 95% CI, 1.3-5.2), and adenovirus type 5 (OR, 2.7; 95% CI, 1.5-4.7) or type 21 infection (OR, 7.6; 95% CI, 2.6-22.3) increased the risk of severe disease.
Methionine synthase (MTR) 2756 (A → G) polymorphism, double heterozygosity methionine synthase 2756 AG/methionine synthase reductase (MTRR) 66 AG, and elevated homocysteinemia are three risk factors for having a child with Down syndrome (2003)

Contradictory findings have been recently published on the evaluation of genetic polymorphisms of methylenetetrahydrofolate reductase (MTHFR 677 C-->T) and methionine synthase reductase (MTRR 66 A-->G) as risk factors for having a child with Down syndrome (DS); however, the influence of polymorphisms of methionine synthase (MTR 2756 A-->G) and of MTHFR 1298 A-->C has never been evaluated. In this study, the risk of being a DS case or having a DS child (case mother) was studied by multiple logistic regression analysis of the independent and combined genotypes and of plasma homocysteine, folates, and vitamin B12 in 92 DS cases and 140 control subjects as well as in 63 case mothers and 72 age-matched control mothers from Sicily. (The MTHFR 677 T allele frequency was not different in DS cases and case mothers, compared to the respective control groups). After adjustment for age, total homocysteine (t-Hcys) and MTR 2756 AG/GG genotype were significant risk factors for having a DS child, with odds ratio (OR) of 6.7 (95% CI: 1.4-32.0, P = 0.016) and of 3.5 (95% CI: 1.2-10.9, P = 0.028), respectively. By comparison, MTR 2756 AG/GG genotype increased significantly the risk of being a DS case, with an OR of 3.8 (95% CI: 1.4-10.5, P = 0.009). The double heterozygosity MTR 2756 AG/MTRR 66 AG was the single combined genotype that was a significant risk factor for having a DS child, with an OR estimated at 5.0 (95% CI: 1.1-24.1), after adjustment for t-Hcys. In conclusion, our results provide evidences that homocysteine and MTR genetic polymorphism are two potent risk factors for mothers to have a DS child in Sicily.
Physical principles of membrane organization (1980)

Membranes are the most common cellular structures in both plants and animals. They are now recognized as being involved in almost all aspects of cellular activity ranging from motility and food entrapment in simple unicellular organisms, to energy transduction, immunorecognition, nerve conduction and biosynthesis in plants and higher organisms. This functional diversity is reflected in the wide variety of lipids and particularly of proteins that compose different membranes. An understanding of the physical principles that govern the molecular organization of membranes is essential for an understanding of their physiological roles since structure and function are much more interdependent in membranes than in, say, simple chemical reactions in solution. We must recognize, however, that the word ‘understanding’ means different things in different disciplines, and nowhere is this more apparent than in this multidisciplinary area where biology, chemistry and physics meet.
IsdG and IsdI, Heme-degrading Enzymes in the Cytoplasm of Staphylococcus aureus (2003)

Staphylococcus aureus requires iron for growth and utilizes heme as a source of iron during infection. Staphylococcal surface proteins capture hemoglobin, release heme from hemoglobin and transport this compound across the cell wall envelope and plasma membrane into the bacterial cytoplasm. Here we show that Staphylococcus aureus isdG and isdI encode cytoplasmic proteins with heme binding properties. IsdG and IsdI cleave the tetrapyrrol ring structure of heme in the presence of NADPH cytochrome P450 reductase, thereby releasing iron. Further, IsdI complements the heme utilization deficiency of a Corynebacterium ulcerans heme oxygenase mutant, demonstrating in vivo activity of this enzyme. Although Staphylococcus epidermidis, Listeria monocytogenes, and Bacillus anthracis encode homologues of IsdG and IsdI, these proteins are not found in other bacteria or mammals. Thus, it appears that bacterial pathogens evolved different strategies to retrieve iron from scavenged heme molecules and that staphylococcal IsdG and IsdI represent examples of bacterial heme-oxygenases.