gebhart/patrepeval huggingface dataset:
Circular ribosomal DNA plasmids transform Tetrahymena thermophila by homologous recombination with endogenous macronuclear ribosomal DNA. (1988)

We transformed the ciliate Tetrahymena thermophila by microinjection of circular plasmids containing the ribosomal RNA gene (rDNA). In the somatic macronucleus of Tetrahymena, the rDNA is in the form of linear palindromic molecules. The rDNA molecules from the C3 strain have a replication advantage over rDNA from both B strain and the C3 rDNA mutant rmm1. We constructed two circular plasmids carrying replication origin sequences from C3 rDNA and a point mutation (Pmr) in the 17S rRNA gene that confers resistance to the antibiotic paromomycin. One plasmid contained a single complete copy of the rRNA gene and its flanking sequences, while the other had an additional rDNA origin of replication. In all B or rmm1 Tetrahymena cell lines transformed with the plasmids, rDNA sequences from the plasmid were found in palindromic rDNA molecules. In one transformant line, a small amount of the plasmid was also retained in a form with the original circular restriction map. Our results show that the plasmids underwent homologous recombination with one arm of the endogenous rDNA to give heteropalindromic rDNA, or with both arms of the palindrome to form homopalindromic rDNA. The resulting recombinant molecules were able to replace the recipient's original rDNA completely, providing strong evidence that C3 rDNA sequences in the donor DNAs confer a replication advantage over recipient rDNA. Thus microinjection of circular plasmids provides a method for replacement of an endogenous gene or gene fragment with exogenous sequences.
CGM1a antigen of neutrophils, a receptor of gonococcal opacity proteins (1996)

Neisseria gonorrhoeae (GC) or Escherichia coli expressing phase-variable opacity (Opa) protein (Opa+ GC or Opa+ E. coli) adhere to human neutrophils and stimulate phagocytosis, whereas their counterparts not expressing Opa protein (Opa- GC or Opa- E. coli) do not. Opa+ GC or E. coli do not adhere to human lymphocytes and promyelocytic cell lines such as HL-60 cells. The adherence of Opa+ GC to the neutrophils can be enhanced dramatically if the neutrophils are preactivated. These data suggest that the components binding the Opa+ bacteria might exist in the granules. CGM1a antigen, a transmembrane protein of the carcinoembryonic antigen family, is exclusively expressed in the granulocytic lineage. The predicted molecular weight of CGM1a is approximately 30 kDa. We observed specific binding of OpaI+ E. coli to a 30-kDa band of polymorphonuclear leukocytes lysates. To prove the hypothesis that the 30-kDa CGM1a antigen from neutrophils was the receptor of Opa+ bacteria, we showed that a HeLa cell line expressing human CGM1a antigen (HeLa-CGM1a) bound Opa+ E. coli and subsequently engulfed the bacteria. Monoclonal antibodies (COL-1) against CGM1 blocked the interaction between Opa+ E. coli and HeLa-CGM1a. These results demonstrate that HeLa cells when expressing the CGM1a antigens bind and internalize OpaI+ bacteria.
The speleotourist experience: approaches to show cave operations in Australia and China (2016)

This article provides a comparative study of commercial cave tourism in Australia and China, focussing on themethods of site interpretation and presentation used by selected show caves. The key point of contrast betweenthe commercial speleotourist experiences offered in Australia and China is in the relative priority given to siteconservation and framing the cave as a spectacle for the enjoyment of visitors. The discussion draws on theauthors field research, visiting show caves as tourists to consider the significance of developments in ecotourismand geotourism for show cave management in Australia and China.
Defining structural requirements for neuropeptide Y receptors using truncated and conformationally restricted analogs (1993)

To further elucidate the minimum bioactive conformation of neuropeptide Y (NPY), a series of truncated and conformationally constrained analogues has been prepared. The synthesis and purification of these peptides was achieved using routine laboratory strategies and techniques. Parent molecules consisted of the native NPY N-terminal 1-4 and C-terminal 25-36 segments, having the residue 5-24 core replaced by either a single flexible omega-aminoalkanoic acid, or a more rigid Pro-Gly or Pro-DAla sequence which was expected to constrain a putative turn, and allow the N- and C-termini to align. Cross-linking between residues 2 and 27 through lactamization using side-chain length and chirality suggested by computer simulations, resulted in cyclo-(2/27)-des-AA7-24[Glu2,Gly6,DDpr27]NPY that exhibited very high affinity (Ki = 0.3 versus 0.3 nM for NPY) for the Y2 receptor using SK-N-BE2 human neuroblastoma cells, yet very low affinity for the Y1 receptor using SK-N-MC human neuroblastoma cells (Ki = 130 versus 2.0 nM for NPY). The added constraint resulting from bridging in this analogue as well as in others suggested that the combination of the deletion of residues 5-24 and the introduction of an internal ring produced exclusive selectivity for the Y2 receptor with little or no loss of affinity. The tolerance of structural recognition was further demonstrated as a second ring was introduced which was expected to constrain the amphiphilic alpha-helix, resulting in the full Y2 agonist dicyclo (2/27,28/32)-des-AA7-24 [Glu2,32,DAla6,DDpr27,Lys28]NPY. Improvement of Y1 binding activity was achieved only by including more residues (des-AA10-17) in the central PP-fold region, while allowing limited flexibility of the termini. Although the length of the bridge seemed to have little effect on binding potency, changes in the location of and chirality at the bridgehead resulted in analogues with different binding affinities. Combination of optimum structural modifications resulted in cyclo-(7/21)-des-AA10-18[Cys7,21]NPY, an analogue shortened by 25% but retaining comparable binding properties to that of native NPY at Y1 and Y2 receptor types (Ki = 5.1 and 1.3 nM, respectively).
TERT promoter mutations and telomerase reactivation in urothelial cancer (2015)

Reactivation of telomerase, the chromosome end-replicating enzyme, drives human cell immortality and cancer. Point mutations in the telomerase reverse transcriptase (TERT) gene promoter occur at high frequency in multiple cancers, including urothelial cancer (UC), but their effect on telomerase function has been unclear. In a study of 23 human UC cell lines, we show that these promoter mutations correlate with higher levels of TERT messenger RNA (mRNA), TERT protein, telomerase enzymatic activity, and telomere length. Although previous studies found no relation between TERT promoter mutations and UC patient outcome, we find that elevated TERT mRNA expression strongly correlates with reduced disease-specific survival in two independent UC patient cohorts (n = 35; n = 87). These results suggest that high telomerase activity may be a better marker of aggressive UC tumors than TERT promoter mutations alone.
Multiple Myeloma (2001)

Multiple myeloma (MM) is a malignancy of the plasma cell characterized by migration and localization to the bone marrow where cells then disseminate and facilitate the formation of bone lesions. Unfortunately, while treatment of this disease is effective in palliating the disease, and even prolonging survival, this disease is generally regarded as incurable. Understanding the basic biology of myeloma cells will ultimately lead to more effective treatments by developing target based therapy. In Section I, Dr. Bergsagel discusses the molecular pathogenesis of MM and shares insights regarding specific chromosomal translocations and their role in the genesis and progression of MM. New information regarding FGFR3 as an oncogene as well as how activating mutations may contribute to disease evolution and may be an important target for novel therapeutics of MM is presented. In Section II, Dr. Anderson elaborates on novel therapeutic approaches to MM also targeting fundamental genetic abnormalities in MM cells. Both preclinical and clinical studies of novel agents including PS-341 and IMiDs are highlighted. In Section III, Dr. Harousseau discusses the role of autologous stem cell transplant in MM. He highlights clinical trials addressing the question of conditioning regimens and the impact of tandem transplants. He also addresses the role of allogeneic BMT and the use of attenuated dose conditioning regimens (so called mini-allogeneic transplants) in the treatment of MM. In Section IV, Dr. Dalton provides an overview of the current state of myeloma therapy and summarizes the different and exciting approaches being undertaken to cure this disease.
Deep sequencing to reveal new variants in pooled DNA samples (2009)

We evaluated massive parallel sequencing and long-range PCR (LRP) for rare variant detection and allele frequency estimation in pooled DNA samples. Exons 2 to 16 of the MUTYH gene were analyzed in breast cancer patients with Illumina's (Solexa) technology. From a pool of 287 genomic DNA samples we generated a single LRP product, while the same LRP was performed on 88 individual samples and the resulting products then pooled. Concentrations of constituent samples were measured with fluorimetry for genomic DNA and high-resolution melting curve analysis (HR-MCA) for LRP products. Illumina sequencing results were compared to Sanger sequencing data of individual samples. Correlation between allele frequencies detected by both methods was poor in the first pool, presumably because the genomic samples amplified unequally in the LRP, due to DNA quality variability. In contrast, allele frequencies correlated well in the second pool, in which all expected alleles at a frequency of 1% and higher were reliably detected, plus the majority of singletons (0.6% allele frequency). We describe custom bioinformatics and statistics to optimize detection of rare variants and to estimate required sequencing depth. Our results provide directions for designing high-throughput analyses of candidate genes.
Glucose uptake in human and animal muscle cells in culture (1990)

Human muscle cells were grown in culture from satellite cells present in muscle biopsies and fusion-competent clones were identified. Hexose uptake was studied in fused myotubes of human muscle cells in culture and compared with hexose uptake in myotubes of the rat L6 and mouse C2C12 muscle cell lines. Uptake of 2-deoxyglucose was saturable and showed an apparent Km of about 1.5 mM in myotubes of all three cell types. The Vmax of uptake was about 6000 pmol/(min.mg protein) in human cells, 4000 pmol/(min.mg protein) in mouse C2C12 muscle cells, and 500 pmol/(min.mg protein) in L6 cells. Hexose uptake was inhibited approximately 90% by cytochalasin B in human, rat, and mouse muscle cell cultures. Insulin stimulated 2-deoxyglucose uptake in all three cultures. The hormone also stimulated transport of 3-O-methylglucose. The sensitivity to insulin was higher in human and C2C12 mouse myotubes (half-maximal stimulation observed at 3.5 X 10(-9) M) than in rat L6 myotubes (half-maximal stimulation observed at 2.5 X 10(-8) M). However, insulin (10(-6) M) stimulated hexose uptake to a larger extent (2.37-fold) in L6 than in either human (1.58-fold) or mouse (1.39-fold) myotubes. It is concluded that human muscle cells grown in culture display carrier-mediated glucose uptake, with qualitatively similar characteristics to those of other muscle cells, and that insulin stimulates hexose uptake in human cells. These cultures will be instrumental in the study of human insulin resistance and in investigations on the mechanism of action of antidiabetic drugs.
Nonmuscle Contractile Proteins: The Role of Actin and Myosin in Cell Motility and Shape Determination (1977)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Differential analysis of DNA microarray gene expression data (2003)

Here, we review briefly the sources of experimental and biological variance that affect the interpretation of high-dimensional DNA microarray experiments. We discuss methods using a regularized t-test based on a Bayesian statistical framework that allow the identification of differentially regulated genes with a higher level of confidence than a simple t-test when only a few experimental replicates are available. We also describe a computational method for calculating the global false-positive and false-negative levels inherent in a DNA microarray data set. This method provides a probability of differential expression for each gene based on experiment-wide false-positive and -negative levels driven by experimental error and biological variance.
Consistent placement of macro-blocks using floorplanning and standard-cell placement (2002)

While a number of recent works address large-scale standard-cell placement, they typically assume that all macros are fixed. Floorplanning techniques are very good at handling macros, but do not scale to hundreds of thousands of placeable objects. Therefore we combine floorplanning techniques with placement techniques in a design flow that solves the more general placement problem. Our work shows how to place macros consistently with large numbers of small standard cells. Our techniques can also be used to guide circuit designers who prefer to place macros by hand.
HLA-binding regions of HIV-1 proteins. I. Detection of seven HLA binding regions in the HIV-1 Nef protein (1991)

The physical association of HLA class I or H-2 molecules with 36 HIV-1 Nef synthetic peptides was studied using a direct peptide binding assay (PBA) in solid phase. To assess the functional significance of the PBA results, the Nef peptides were also tested for their ability to inhibit the lytic activity of human or murine CTL. The PBA results showed that seven partly overlapping regions of the Nef protein contained MHC binding peptides (4-18, 46-67, 73-94, 100-128, 126-155, 182-198, and 192-206). Five of these seven regions included all the already described epitopes recognized by CD8+ human CTL. The two other regions, 4-18 and 46-67, are not yet described as antigenic for human CD8+ cells but they are located in the N-terminal part of Nef that was previously described as being stimulator for rat or chimpanzee CD4+ cells. Altogether, it can be concluded that 1) In virtually 100% of the cases, the PBA is capable to detect known antigenic peptides recognized by CTL. 2) The PBA and the functional inhibition assay provide similar results, supporting the functional significance of PBA results. 3) The PBA is easy to handle on a large scale, using multiple peptide and several MHC molecules, so that it can be used as a routine method for prevision of possibly epitopic sequences. 4) Systematic studies of peptides issued from the whole sequence of a given protein allow to map polyepitopic areas that are probably the most interesting parts of proteins for a vaccine purpose.
Development of Neural Network Architectures for Self- Organizing Pattern Recognition and Robotics (1992)

During the second year of the DARPA ANNT Program contact, new neural network architectures were developed to carry out autonomous real-time preprocessing, segmentation, recognition, timing, and control of both spatial and temporal inputs. These architectures contribute to: (1) preprocessing of visual form and motion signals; (2) preprocessing of acoustic signals; (3) adaptive pattern recognition and categorization in an unsupervised learning context; (4) adaptive pattern recognition and prediction in a supervised learning context; (5) processing of temporal patterns using working memory networks, with applications to 3-D object recognition; (6) adaptive timing for task scheduling; (7) adaptive sensory-motor control using head-centered spatial representations of 3-D target position.
Electron Trapping in Dye/Polymer Blend Photovoltaic Cells (2000)

Charge separation and charge transport have been limiting factors in photovoltaic cells that utilize conjugated polymer blends. These authors have exploited the ability of a soluble perylene dye (see Figure) to form crystals within a polymer matrix to achieve a blend that enables good charge transfer and separation, due largely to the crystals' ability to act as electron traps.
Stereoselective Enzymatic Esterification of 3‐BenzoyIthio‐2‐methylpropanoic Acid (1992)

A key intermediate, S-(−)-3-benzoylthio-2-methylpropanoic acid (1) was made in high optical purity by the lipase-catalyzed stereoselective esterification of racemic 1 with methanol in an organic solvent system. Among various lipases evaluated, Amano P-30 lipase from Pseudomonas sp. efficiently catalyzed the esterification of 1 to yield R-(+) methyl ester and unreacted S-(−) 1. A reaction yield of 40 mol% and an optical purity of 97.2% were obtained for compound 1 at a substrate concentration of 0.1 m (22 mg/ml). Lipase P-30 was immobilized on Accurel polypropylene (PP) and the immobilized enzyme was reused (23 cycles) in the esterification reaction without loss of enzyme acitivity, productivity or optical purity. Among various solvents evaluated, toluene was found to be the most suitable organic solvent and methanol was the best alcohol for the esterification of racemic 1 by immobilized lipase. Substrate concentrations as high as 1.0 m were used in the esterification reaction. When the temperature was increased from 28° C to 60° C, the reaction time required for the esterification of 0.1 m substrate decreased from 16 h to 2 h. On increasing the methanol to substrate molar ratio from 1:1 to 4:1, the rate of esterification decreased. A lipase fermentation using Pseudomonas sp. ATCC 21 808 was developed. In the batch-fermentation process, 56 units/ml of extracellular lipase activity was obtained. A fed-batch process using soybean oil gave a significant increase in the lipase activity (126 units/ml). Crude lipase recovered from the filtrate by ethanol precipitation and immobilized on Accurel PP was also effective: S-(−) compound 1 was obtained in 35 mol% yield and 95% optical purity.
Functionalization of Carbon Nanotubes with a Metal-Containing Molecular Complex (2001)

Raw and oxidized carbon nanotubes have been reacted with Vaska's complex. It has been found that Ir coordinates to these nanotubes by two distinctive pathways. With raw nanotubes, the process is through a η2-coordination process. With oxidized nanotubes, the reaction occurs by coordination through the increased number of oxygen atoms, forming a hexacoordinate structure around the Ir atom. The reaction process significantly increases oxidized nanotube solubility in dimethylformamide.
Small‐molecule activators of TMEM16A, a calcium‐activated chloride channel, stimulate epithelial chloride secretion and intestinal contraction (2011)

TMEM16A (ANO1) is a calcium-activated chloride channel (CaCC) expressed in secretory epithelia, smooth muscle, and other tissues. Cell-based functional screening of ∼110,000 compounds revealed compounds that activated TMEM16A CaCC conductance without increasing cytoplasmic Ca(2+). By patch-clamp, N-aroylaminothiazole "activators" (E(act)) strongly increased Cl(-) current at 0 Ca(2+), whereas tetrazolylbenzamide "potentiators" (F(act)) were not active at 0 Ca(2+) but reduced the EC(50) for Ca(2+)-dependent TMEM16A activation. Of 682 analogs tested, the most potent activator (E(act)) and potentiator (F(act)) produced large and more sustained CaCC Cl(-) currents than general agonists of Ca(2+) signaling, with EC(50) 3-6 μM and Cl(-) conductance comparable to that induced transiently by Ca(2+)-elevating purinergic agonists. Analogs of activators were identified that fully inhibited TMEM16A Cl(-) conductance, providing further evidence for direct TMEM16A binding. The TMEM16A activators increased CaCC conductance in human salivary and airway submucosal gland epithelial cells, and IL-4 treated bronchial cells, and stimulated submucosal gland secretion in human bronchi and smooth muscle contraction in mouse intestine. Small-molecule, TMEM16A-targeted activators may be useful for drug therapy of cystic fibrosis, dry mouth, and gastrointestinal hypomotility disorders, and for pharmacological dissection of TMEM16A function.
Use of a triaxial magnetometer for respiratory measurements (1991)

We describe a triaxial magnetometer (Tri-mag) system, which consists of a transmitter, four sensors, a processing unit, and a personal computer (PC). The Tri-mag processing unit outputs the position of each sensor relative to the transmitter in three orthogonal coordinates, and this information is communicated to the PC. First, we demonstrated that within a defined octant of a sphere in which the center is the transmitter, we can measure radial distances with an accuracy of +/- 1 mm over a range extending from 10 to 70 cm from the transmitter. Second, we recorded the three-dimensional movement of sensors on the anterior and posterior surfaces of the chest wall during maximum voluntary ventilation in four normal men; all sensors were placed in the midsagittal plane of the body. Anterior sensors were located on the sternum at the level of the third intercostal space and at 2 cm above the umbilicus, whereas posterior sensors were located on the posterior spine at the same vertical levels as the anterior sensors. In all subjects the following was found. 1) Both anterior sensors moved anterior and cephalad during inspiration. The anterior thoracic sensor showed greater vertical than anteroposterior (A-P) movement, whereas the anterior abdominal sensor showed greater A-P than vertical movement. 2) Inspiration was associated with spinal extension, whereas expiration was associated with spinal flexion. Third, we used Tri-mag information to 1) measure tidal volume (VT) over a range extending from 500 ml to inspiratory capacity and 2) measure the change in end-expiratory lung volume (EELV) over a range extending from FRC to FRC plus a minimum of 1.5 liters. Our results indicate that greater than 96% of the changes in VT and greater than 82% of the changes in EELV can be accounted for by changes in A-P, vertical, and lateral dimensions of the chest wall.
Ambiguities in Visual Tracking of Articulated Objects Using Two- and Three-Dimensional Models (2003)

Three-dimensional (3D) kinematic models are widely-used in video-based figure tracking. We show that these models can suffer from singularities when motion is directed along the viewing axis of a single camera. The single camera case is important because it arises in many interesting applications, such as motion capture from movie footage, video surveillance, and vision-based user-interfaces.We describe a novel two-dimensional scaled prismatic model (SPM) for figure registration. In contrast to 3D kinematic models, the SPM has fewer singularity problems and does not require detailed knowledge of the 3D kinematics. We fully characterize the singularities in the SPM and demonstrate tracking through singularities using synthetic and real examples.We demonstrate the application of our model to motion capture from movies. Fred Astaire is tracked in a clip from the film "Shall We Dance". We also present the use of monocular hand tracking in a 3D user-interface. These results demonstrate the benefits of the SPM in tracking with a single source of video.
No association between the dopamine D2 receptor gene and Korean alcoholism (1997)

Department of Neuropsychiatry, College of Medicine, Korea University, 126–1, 5-Ka, Anam-Dong, Sungbuk-Ku, Seoul 136–705, Korea