gebhart/patrepeval huggingface dataset:
A cis-acting element in the major immediate-early (IE) promoter of human cytomegalovirus is required for negative regulation by IE2 (1991)

The major immediate-early promoter (MIEP) of human cytomegalovirus (CMV) contains a number of different enhancer elements in both repetitive and nonrepetitive sequences that influence the level of downstream transcription. This report describes a cis-acting element in the MIEP that responds to negative regulation by the IE2 gene product. Deletion analysis demonstrated that the cis-acting repressor element is located between the TATA box and the transcription initiation site from -13 to -1. The DNA sequence of the repressor element is 5'-CGTTTAGTGAACC-3'. The sequence is found in both the human and simian CMV MIEPs but not the murine CMV MIEP or in several other enhancer-containing promoters. The repressor element was isolated in a DNA fragment from -13 to +3 and was found to be functional in either orientation. It could be transferred to a heterologous enhancer-containing promoter and was functional when placed between the TATA box and the transcription initiation site. The element did not function when placed downstream of the transcription initiation site. Therefore, the cis-acting repressor element is position dependent. The role of the repressor element and the IE2 gene product in human CMV productive or latent infection is discussed.
Biologic activities of antibodies to the neutral-polysaccharide component of the Pseudomonas aeruginosa lipopolysaccharide are blocked by O side chains and mucoid exopolysaccharide (alginate) (1995)

Virulent strains of Pseudomonas aeruginosa are either of a nonmucoid, lipopolysaccharide (LPS)-smooth or mucoid, LPS-rough phenotype, and immunity to these different variants is efficiently mediated by antibodies specific to O antigens or mucoid exopolysaccharide (also called alginate), respectively. In addition to O side chains and core polysaccharide components, the LPS of P. aeruginosa also contains neutral-polysaccharide components that express antigenic determinants common to many clinical isolates. We evaluated antibodies specific to neutral polysaccharides for the ability to mediate opsonic killing and protective immunity. Antibodies to these antigens mediated opsonic killing of poorly virulent nonmucoid LPS-rough isolates but not of isogenic strains with either a LPS-smooth or a mucoid phenotype. Antibodies to neutral-polysaccharide antigens also failed to protect neutropenic mice from challenge with modest doses of LPS-smooth P. aeruginosa strains (< 10(3) CFU per mouse), whereas O-antigen-specific antibodies were highly protective. Antibodies to neutral polysaccharides deposited significantly (P = 0.002) more C3 onto LPS-rough strains than did antibodies to O side chains, but this situation was reversed when isogenic LPS-smooth strains were tested. Given that protective immunity against P. aeruginosa must be directed against either nonmucoid LPS-smooth strains or mucoid LPS-rough strains, it appears that antibodies specific to neutral-polysaccharide antigens do not protect against P. aeruginosa infection. Lack of protection is likely due to the ability of both O side chains and mucoid exopolysaccharide (alginate) to interfere with the opsonic killing activity of neutral-polysaccharide-specific antibodies.
Detection of forgery in paintings using supervised learning (2009)

This paper examines whether machine learning and image analysis tools can be used to assist art experts in the authentication of unknown or disputed paintings. Recent work on this topic has presented some promising initial results. Our reexamination of some of these recently successful experiments shows that variations in image clarity in the experimental datasets were correlated with authenticity, and may have acted as a confounding factor, artificially improving the results. To determine the extent of this factor's influence on previous results, we provide a new ¿ground truth¿ data set in which originals and copies are known and image acquisition conditions are uniform. Multiple previously-successful methods are found ineffective on this new confounding-factor-free dataset, but we demonstrate that supervised machine learning on features derived from hidden-Markov-tree-modeling of the paintings' wavelet coefficients has the potential to distinguish copies from originals in the new dataset.
CONJUGATIVE TRANSPOSITION (1995)

Conjugative transposons are important determinants of antibiotic resistance, especially in gram-positive bacteria. They are remarkably promiscuous and can conjugate between bacteria belonging to different species and genera. Transposon-promoted conjugation may be similar to F plasmid-promoted conjugation, as it appears that only one strand of the transposon DNA is transferred from donor to recipient. The recent determination of the entire nucleotide sequence of Tn916 allowed us to make specific predictions about the possible function of different open reading frames and the position of a (hypothetical) origin of transfer. The mechanism of recombination during conjugative transposition differs from that of other transposons, as shown by the absence of a duplication of the target sequence upon integration. The current model for recombination postulates that staggered double-stranded cleavages occur at each end of the transposon. One DNA strand is cut six bases from the end of the transposon, and the other strand is cut immediately adjacent to the end. The ends of the excised transposon are then ligated to form a circular intermediate with a six-base heteroduplex. Staggered cleavages of the circular intermediate and the target DNA allow the transposon to insert into the target, where it is flanked by heteroduplex regions that are resolved by replication. All hosts examined contain preferential target sites: these are not specific sequences but apparently consist of bent DNA. The site-specific recombinases encoded by conjugative transposons belong to the integrase family. Like phage lambda integrase, the integrase of Tn916 has two DNA-binding domains that recognize different sequences, one within the ends of the element and one that includes target DNA. The affinity of Tn916 integrase for target sites correlates with the frequency of integration into a particular site. The similarity between conjugative transposons and phage lambda is striking and suggests that both use the same mechanism of recombination. In lambda, however, recombining sites must be homologous. Homology may be necessary because of branch migration, which is thought to occur during recombination. In conjugative transposition, the recombining sites are nearly always different, and therefore branch migration probably does not occur. This review presents a speculative model for the alignment of the ends of Tn916 during excision that was adapted from one recently proposed for lambda.
Wet mammals shake at tuned frequencies to dry (2012)

In cold wet weather, mammals face hypothermia if they cannot dry themselves. By rapidly oscillating their bodies, through a process similar to shivering, furry mammals can dry themselves within seconds. We use high-speed videography and fur particle tracking to characterize the shakes of 33 animals (16 animals species and five dog breeds), ranging over four orders of magnitude in mass from mice to bears. We here report the power law relationship between shaking frequency f and body mass M to be f ∼ M(-0.22), which is close to our prediction of f ∼ M(-0.19) based upon the balance of centrifugal and capillary forces. We also observe a novel role for loose mammalian dermal tissue: by whipping around the body, it increases the speed of drops leaving the animal and the ensuing dryness relative to tight dermal tissue.
Diffraction properties of stratified volume holographic optical elements (1992)

We present a unified treatment of the diffraction properties of stratified volume holographic optical elements (SVHOE’s). We show that the relative phasing of the diffraction orders as they propagate from layer to layer gives rise to a unique notched diffraction response of the +1 order (for the case of Bragg incidence) as a function of the normalized buffer-layer thickness, the grating spatial frequency, and the readout wavelength. For certain combinations of these parameters Bragg diffraction behavior characteristic of volume holographic optical elements (VHOE’s) is observed, whereas for other combinations pure Raman–Nath behavior periodically recurs. By using these same relative-phasing arguments, the principal features of the periodic angular sensitivity of the +1 and −1 orders can be predicted. In addition to examining the fundamental aspects of SVHOE diffraction behavior, we discuss several possible applications, including optical array generation, spatial frequency filtering, and wavelength notch filtering. With the use of the SVHOE concept, holographic materials with otherwise exemplary characteristics that are currently available only in thin-film form can be used in structures designed either to access unique SVHOE diffraction properties or to emulate conventional VHOE’s.
Ends-out, or replacement, gene targeting in Drosophila (2003)

Ends-in and ends-out refer to the two arrangements of donor DNA that can be used for gene targeting. Both have been used for targeted mutagenesis, but require donors of differing design. Ends-out targeting is more frequently used in mice and yeast because it gives a straightforward route to replace or delete a target locus. Although ends-in targeting has been successful in Drosophila, an attempt at ends-out targeting failed. To test whether ends-out targeting could be used in Drosophila, we applied two strategies for ends-out gene replacement at the endogenous yellow (y) locus in Drosophila. First, a mutant allele was rescued by replacement with an 8-kb y(+) DNA fragment at a rate of approximately 1/800 gametes. Second, a wild-type gene was disrupted by the insertion of a marker gene in exon 1 at a rate of approximately 1/380 gametes. The I-SceI endonuclease component alone is not sufficient for targeting: the FLP recombinase is also needed to generate the extrachromosomal donor. When both components are used we find that ends-out targeting can be approximately as efficient as ends-in targeting, and is likely to be generally useful for Drosophila gene targeting.
Microfluidic fabrication of smart microgels from macromolecular precursors (2010)

Stimuli-responsive polymer microgels can be produced with exquisite control using droplet microfluidics; however, in existing methods, the droplet templating is strongly coupled to the material synthesis, because droplet solidification usually occurs through rapid polymerization immediately after the microfluidic droplet formation. This circumstance limits independent control of the material properties and the morphology of the resultant microgel particles. To overcome this limitation, we produce sensitive polymer microgels from pre-fabricated precursor polymers. We use microfluidic devices to emulsify semidilute solutions of crosslinkable poly(N-isopropylacrylamide) and solidify the drops via polymer-analogous gelation. This approach separates the polymer synthesis from the particle gelation and allows each to be controlled independently, thus enabling us to form monodisperse, thermo-responsive microgel particles with well-controlled composition and functionality. In addition, the microfluidic templating allows us to form complex particle morphologies such as hollow gel shells, anisotropic microgels, or multi-layered microgel capsules.
Solvation Energies of Amino Acid Side Chains and Backbone in a Family of Host−Guest Pentapeptides (1996)

Octanol-to-water solvation free energies of acetyl amino amides (Ac-X-amides) [Fauchère, J.L., & Pliska, V. (1983) Eur. J. Med. Chem. --Chim. Ther. 18,369] form the basis for computational comparisons of protein stabilities by means of the atomic solvation parameter formalism of Eisenberg and McLachlan [(1986) Nature 319, 199]. In order to explore this approach for more complex systems, we have determined by octanol-to-water partitioning the solvation energies of (1) the guest (X) side chains in the host-guest pentapeptides AcWL-X-LL, (2) the carboxy terminus of the pentapeptides, and (3) the peptide bonds of the homologous series of peptides AcWLm (m = 1-6). Solvation parameters were derived from the solvation energies using estimates of the solvent-accessible surface areas (ASA) obtained from hard-sphere Monte Carlo simulations. The measurements lead to a side chain solvation-energy scale for the pentapeptides and suggest the need for modifying the Asp, Glu, and Cys values of the "Fauchère-Pliska" solvation-energy scale fro the Ac-X-amides. We find that the unfavorable solvation energy of nonpolar residues can be calculated accurately by a solvation parameter of 22.8 +/- 0.8 cal/mol/A2, which agrees satisfactorily with the AC-X-amide data and thereby validates the Monte Carlo ASA results. Unlike the Ac-X-amide data, the apparent solvation energies of the uncharged polar residues are also largely unfavorable. This unexpected finding probably results, primarily, from differences in conformation and hydrogen bonding in octanol and buffer but may also be due to the additional flaking peptide bonds of the pentapeptides. The atomic solvation parameter (ASP) for the peptide bond is comparable to the ASP of the charged carboxy terminus which is an order of magnitude larger than the ASP of the uncharged polar side chains of the Ac-X-amides. The very large peptide bond ASP, -96 +/- 6 cal/mol/A2, profoundly affects the results of computational comparisons of protein stability which use ASPs derived from octanol-water partitioning data.
Evidence for two distinct activation states available to B lymphocytes. (1984)

The sites and modes of action of several B cell mitogens and interleukins were examined. Cell cycle analyses of B cell responses to several polyclonal activators including LPS, DXS, LPS plus DXS, and anti-immunoglobulin were performed. Two different states of B cell activation distinguished by RNA content, DNA content, and cell size were observed. LPS promoted transitions throughout the cell cycle, whereas DXS primarily caused exit from G0. Synergy between LPS and DXS was observed in elicitation of exit from G0. Activation by anti-immunoglobulin was found to be influenced by the antibody dose and the cell density of culture. Interleukins could influence anti-IgM-induced responses by increasing G0 exit, and by increasing commitment to DNA synthesis. A model of B cell activation in which cells are stimulated to a stage with intermediate RNA levels (G1A) by polyclonal activators is suggested. Some interleukins appear to be involved in this process. At G1A, cells are receptive to signals delivered by interleukins or some polyclonal activators that drive them to late G1 and DNA synthesis. After cell division, cells re-enter G1A in which interleukins or mitogens are necessary for a continued response.
Site-specific integration mediated by a hybrid adenovirus/adeno-associated virus vector (1999)

Adenovirus (Ad) and adeno-associated virus (AAV) have attractive and complementary properties that can be exploited for gene transfer purposes. Ad vectors are probably the most efficient vehicles to deliver foreign genes both in vitro and in vivo. AAV exhibits the unique ability to establish latency by efficiently integrating at a specific locus of human chromosome 19 (AAVS1). Two viral elements are necessary for the integration at AAVS1: Rep68/78 and the inverted terminal repeats (AAV-ITRs). In this study, we report the development of two helper-dependent adenoviral (HD) vectors, one carrying the Rep78 gene, the other an AAV-ITR-flanked transgene. Although Rep proteins have been demonstrated to interfere with Ad replication, HD Rep78 vector was successfully amplified on serial passages in 293CRE4 cells with a yield of 50-100 transducing units per cell. DNA integration at the AAVS1 site also was demonstrated in hepatoma cells coinfected with the HD-expressing Rep78 and with the second HD vector carrying a transgene flanked by AAV-ITRs. The high transduction efficiency, large cloning capacity, and high titer of the HD, combined with the site-specific integration machinery provided by AAV-derived components, make the Ad/AAV hybrid viruses a promising vehicle for gene therapy.
Luminescent molecular logic gates: the two-input inhibit (INH) function (2000)

The Tb(III) complex 3, is the first example of a molecular logic gate corresponding to a two-input INHIBIT function, A ⁁ B′ where the ‘output’, a sharp, line-like, terbium emission, is only observed with two chemical inputs (i) the presence of protons and (ii) the absence of molecular oxygen.
PocketWeb (2012)

The high network latencies and limited battery life of mobile phones can make mobile web browsing a frustrating experience. In prior work, we proposed trading memory capacity for lower web access latency and a more convenient data transfer schedule from an energy perspective by prefetching slowly-changing data (search queries and results) nightly, when the phone is charging. However, most web content is intrinsically much more dynamic and may be updated multiple times a day, thus eliminating the effectiveness of periodic updates. This paper addresses the challenge of prefetching dynamic web content in a timely fashion, giving the user an instant web browsing experience but without aggravating the battery lifetime issue. We start by analyzing the web access traces of 8,000 users, and observe that mobile web browsing exhibits a strong spatiotemporal signature, which is different for every user. We propose to use a machine learning approach based on stochastic gradient boosting techniques to efficiently model this signature on a per user basis. The machine learning model is capable of accurately predicting future web accesses and prefetching the content in a timely manner. Our experimental evaluation with 48,000 models trained on real user datasets shows that we can accurately prefetch 60% of the URLs for about 80-90% of the users within 2 minutes before the request. The system prototype we built not only provides more than 80% lower web access time for more than 80% of the users, but it also achieves the same or lower radio energy dissipation by more than 50% for the majority of mobile users.
Small Scale Bio Fuel Cells for Long Duration Unattended Ground Sensor Applications. (2006)

Abstract not provided.
Rapid Analysis of Raman Image Data Using Two-Way Multivariate Curve Resolution (1998)

The application of standard two-way curve resolution methods is reported for analysis of three-way Raman image data. Two current curve resolution methods are described: principal factor multivariate curve resolution (PF-MCR), which uses principal factor analysis (PFA) combined with varimax rotation and alternating least-squares optimization (ALS), and orthogonal projection multivariate curve resolution (OP-MCR), which uses a Gram–Schmidt modified orthogonal projection approach (OPA) followed by ALS. The OP-MCR technique is shown to be an extremely rapid method of analysis producing results equivalent to those of PF-MCR in one-third to one-fourth the time. The results from MCR analysis using either method provide the number of chemical species present in the sample, the spectrum of each species for identification, and the concentration image for each species. The additional benefit of image noise reduction also results from the MCR techniques. A brief description of the theory is presented followed by analysis and comparison of results for two real Raman image data. A discussion is given addressing the rapid analysis aspects of OP-MCR and the relative merits and drawbacks of the technique in comparison to PF-MCR. The use of data subsampling is also discussed as a way of decreasing analysis time without loss in accuracy or performance.
Environmental and genetic factors associated with morphine response in the postoperative period (2006)

Age and prior use of psychotropic agents are associated with postoperative morphine dose requirements. Whether ABCB1 polymorphisms might predict morphine side effects remains to be determined.
Structure of Methylammonium Lead Iodide Within Mesoporous Titanium Dioxide: Active Material in High-Performance Perovskite Solar Cells (2013)

We report the structure of methylammonium lead(II) iodide perovskite in mesoporous TiO2, as used in high-performance solar cells. Pair distribution function analysis of X-ray scattering reveals a two component nanostructure: one component with medium range crystalline order (30 atom %) and another with only local structural coherence (70 atom %). The nanostructuring correlates with a blueshift of the absorption onset and increases the photoluminescence. Our findings underscore the importance of fully characterizing and controlling the structure for improved solar cell efficiency.
Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature (2006)

The molecular biology of metastatic potential in melanoma has been studied many times previously and changes in the expression of many genes have been linked to metastatic behaviour. What is lacking is a systematic characterization of the regulatory relationships between genes whose expression is related to metastatic potential. Such a characterization would produce a molecular taxonomy for melanoma which could feasibly be used to identify epigenetic mechanisms behind changes in metastatic behaviour. To achieve this we carried out three separate DNA microarray analyses on a total of 86 cultures of melanoma. Significantly, multiple testing correction revealed that previous reports describing correlations of gene expression with activating mutations in BRAF or NRAS were incorrect and that no gene expression patterns correlate with the mutation status of these MAPK pathway components. Instead, we identified three different sample cohorts (A, B and C) and found that these cohorts represent melanoma groups of differing metastatic potential. Cohorts A and B were susceptible to transforming growth factor-beta (TGFbeta)-mediated inhibition of proliferation and had low motility. Cohort C was resistant to TGFbeta and demonstrated high motility. Meta-analysis of the data against previous studies linking gene expression and phenotype confirmed that cohorts A and C represent transcription signatures of weakly and strongly metastatic melanomas, respectively. Gene expression co-regulation suggested that signalling via TGFbeta-type and Wnt/beta-catenin pathways underwent considerable change between cohorts. These results suggest a model for the transition from weakly to strongly metastatic melanomas in which TGFbeta-type signalling upregulates genes expressing vasculogenic/extracellular matrix remodelling factors and Wnt signal inhibitors, coinciding with a downregulation of genes downstream of Wnt signalling.