gebhart/patrepeval huggingface dataset:
Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics (2009)

The difficulty of analyzing higher order RNA structure, especially for folding intermediates and for RNAs whose functions require domains that are conformationally flexible, emphasizes the need for new approaches for modeling RNA tertiary structure accurately. Here, we report a concise approach that makes use of facile RNA structure probing experiments that are then interpreted using a computational algorithm, carefully tailored to optimize both the resolution and refinement speed for the resulting structures, without requiring user intervention. The RNA secondary structure is first established using SHAPE chemistry. We then use a sequence-directed cleavage agent, which can be placed arbitrarily in many helical motifs, to obtain high quality inter-residue distances. We interpret this in-solution chemical information using a fast, coarse grained, discrete molecular dynamics engine in which each RNA nucleotide is represented by pseudoatoms for the phosphate, ribose, and nucleobase groups. By this approach, we refine base paired positions in yeast tRNA(Asp) to 4 A rmsd without any preexisting information or assumptions about secondary or tertiary structures. This blended experimental and computational approach has the potential to yield native-like models for the diverse universe of functionally important RNAs whose structures cannot be characterized by conventional structural methods.
Obstacle-avoiding rectilinear Steiner tree construction (2008)

In todaypsilas VLSI designs, there can be many blockages in a routing region. The obstacle-avoiding rectilinear Steiner minimum tree (OARSMT) problem has become an important problem in the physical design stage of VLSI circuits. This problem has attracted a lot of attentions in research and several approaches have been proposed to solve this problem effectively. In this paper, we will present a heuristic maze routing based approach to solve this OARSMT problem. It is commonly believed that maze routing based approaches can only handle small scale problems and there is a lack of an effective multi-terminal variant to handle multi-pin nets in practice. We will show in this paper that maze routing based approaches can also handle large scale OARSMT problems effectively. Our approach is based on the searching process as in maze routing and can handle multi-pin nets very well in both solution quality, running time and memory space usage. We have compared our results with those of the previous works and can show that we can out-perform the best previous results on this problem [15] by giving an OARSMT with 2.01% less wire length on average and can make a 27.04% improvement in wire length in comparison with a lower bound of the optimal solution on average, while the running times are all very short and comparable to those in [15]. Besides, due to the flexibility of maze routing, we can handle different kinds of obstacles with different convex or concave rectilinear shapes directly without a need to partition each blockage into a set of rectangular sub-blockages, which will increase the size of the problem.
Wearable sensor system for wireless state-of-health determination in cattle (2004)

Wearable systems for human and animal state-of-health determination share many design requirements. This paper discusses the design of a remote health monitoring system for cattle that hosts a suite of sensors and communicates wirelessly with a base station via Bluetooth telemetry.
Cranial base strategies for resection of craniopharyngioma in children (2005)

The optimal treatment of craniopharyngioma in children remains a challenge. The use of complete excision to minimize recurrence continues to be controversial because of the risk of postoperative morbidity and death. Advances in skull base approaches, modern microsurgical techniques, neuroimaging, and hormone replacement therapy, however, have allowed safe gross- or near-total resection in the majority of cases. Total removal of these tumors, if possible, offers the best chance of cure for the patient. Although craniopharyngiomas are not strictly tumors of skull base origin, their intimate relationship with the neurovascular structures of this region often requires a skull base approach to maximize the surgical corridor and facilitate adequate microsurgical resection. In this review, the authors focus on commonly used skull base approaches for the surgical management of craniopharyngioma. They discuss the relative indications, advantages, disadvantages, and complications associated with each approach. Illustrative cases and intraoperative videos are presented.
Real-time H.263+ frame rate control for low bit rate VBR video (2003)

H.263+ is an emerging video compression standard for the low bit rate visual communication. Most H.263+ rate control algorithms, e.g. the one used in the test model of the near-term (TMN), focus on macroblock level bit allocation and low latency by assuming a constant frame rate video encoding sent through a constant bit rate (CBR) channel. These algorithms cannot handle the fluctuation of the channel bandwidth well so that the transmitted video quality is degraded seriously. In this work, we propose a new H.263+ rate control scheme which supports the variable bit rate (VBR) channel through the frame rate adjustment. In particular, a fast realization of encoding frame rate control based on motion information within a sliding window is developed to efficiently determine the tradeoff between spatial and temporal qualities. Experimental results are provided to demonstrate the superior performance of the proposed scheme.
<scp>msari</scp> : Multiple sequence alignments for statistical detection of RNA secondary structure (2004)

We present a highly accurate method for identifying genes with conserved RNA secondary structure by searching multiple sequence alignments of a large set of candidate orthologs for correlated arrangements of reverse-complementary regions. This approach is growing increasingly feasible as the genomes of ever more organisms are sequenced. A program called msari implements this method and is significantly more accurate than existing methods in the context of automatically generated alignments, making it particularly applicable to high-throughput scans. In our tests, it discerned clustalw-generated multiple sequence alignments of signal recognition particle or RNaseP orthologs from controls with 89.1% sensitivity at 97.5% specificity and with 74.4% sensitivity with no false positives in 494 controls. We used msari to conduct a comprehensive scan for secondary structure in mRNAs of coding genes, and we found many genes with known mRNA secondary structure and compelling evidence for secondary structure in other genes. msari uses a method for coping with sequence redundancy that is likely to have applications in a large set of other comparison-based search methods. The program is available for download from http://theory.csail.mit.edu/MSARi.
Inhibition of biofouling by marine microorganisms and their metabolites (2006)

Development of microbial biofilms and the recruitment of propagules on the surfaces of man-made structures in the marine environment cause serious problems for the navies and for marine industries around the world. Current antifouling technology is based on the application of toxic substances that can be harmful to the natural environment. For this reason and the global ban of tributyl tin (TBT), there is a need for the development of "environmentally-friendly" antifoulants. Marine microbes are promising potential sources of non-toxic or less-toxic antifouling compounds as they can produce substances that inhibit not only the attachment and/or growth of microorganisms but also the settlement of invertebrate larvae and macroalgal spores. However, so far only few antilarval settlement compounds have been isolated and identified from bacteria. In this review knowledge about antifouling compounds produced by marine bacteria and diatoms are summarised and evaluated and future research directions are highlighted.
Developmental Validation of a Real-Time Quantitative PCR Assay for Automated Quantification of Human DNA (2003)

Our laboratory has developed an automated real-time quantitative PCR assay for detecting human DNA. The assay utilizes an in-house, custom-designed TaqMan-MGB sequence-specific probe (CFS-HumRT) and the ABD 7900HT SDS platform. Developmental validation has followed TWGDAM (1) guidelines and demonstrates that the assay is primate specific, is highly sensitive, yields consistent results, and works with human DNA extracted from a variety of body fluid stains. When operating within the dynamic range of the system using high-quality DNA samples. the technique yields similar quantification results to our current QuantiBlot assay with the added benefit of time saving through automation. Furthermore, the QPCR assay identifies how much amplifiable DNA is in a sample and thus has the potential to predict PCR success in downstream applications such as STR analysis.
The effect of chemically coated nanofiber reinforcement on biopolymer based nanocomposites (2007)

The aim of this work was to explore how various surface treatments would change the dispersion component of surface energy and acid-base character of hemp nanofibers, using inverse gas chromatography (IGC), and to investigate the effect of the incorporation of these modified nanofibers into a biopolymer matrix on the properties of their nano-composites. Bio-nanocomposite materials were prepared from poly (lactic acid) (PLA) and polyhydroxybutyrate (PHB) as the matrix, and the cellulose nanofibers extracted from hemp fiber by chemo-mechanical treatments. Cellulose fibrils have a high density of –OH groups on the surface, which have a tendency to form hydrogen bonds with adjacent fibrils, reducing interaction with the surrounding matrix. It is necessary to reduce the entanglement of the fibrils and improve their dispersion in the matrix by surface modification of fibers without deteriorating their reinforcing capability. The IGC results indicated that styrene maleic anhydride coated and ethylene-acrylic acid coated fibers improved their potential to interact with both acidic and basic resins. From transmission electron microscopy (TEM), it was shown that the nanofibers were partially dispersed in the polymer matrix. The mechanical properties of the nanocomposites were lower than those predicted by theoretical calculations for both nanofiber-reinforced biopolymers.
Frequency-Time Characteristics of Air-Borne Signals from Laser Welds (1994)

The acoustic emissions from laser lap welds in stainless steel sheet were recorded and analyzed. The acoustic signals emanating from the weld were sensed with an instrument microphone and analyzed using short‐time Fourier spectra to characterize their time‐frequency distributions. It was determined that the acoustic spectrum of good‐quality, full‐penetration welds could be differentiated from the spectra of poor‐quality welds, defined as either partial‐penetration welds or welds having a gap between the sheets being joined. A novel, relatively simple classifier based on total energy in the frequency band from 1 to 2 kHz correctly discriminated full penetration from partial penetration over 90% of the time on average. Partial‐penetration welds had less energy in this range than did full‐penetration welds. A slightly more sophisticated approach incorporating time‐averaging was found to be capable of predicting penetration with reliability approaching 100% for some welds but much less in some anomalous cases. The performance of this relatively simple classification algorithm was shown to be comparable to that found in previous work using neural network‐based classifiers. A classifier based on total signal energy was shown in preliminary trials to be capable of recognizing gapped lap welds from nongapped lap welds.
ChemInform Abstract: Non‐Degenerate Exchange of 1,2‐Dialkyl Groups in Naphthalenium Cations (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Chemotaxis of 3T3 and SV3T3 cells to fibronectin is mediated through the cell-attachment site in fibronectin and a fibronectin cell surface receptor. (1987)

Fibronectin (FN) is a multidomain extracellular matrix protein that induces attachment and chemotactic migration of fibroblastic cells. In this study we analyzed the molecular determinants involved in the FN-induced chemotactic migration of normal and SV40-transformed 3T3 cells. Two different monoclonal antibodies to the cell-binding site of FN blocked chemotaxis to a 140-kD FN fragment (Ca 140) containing the cell-binding domain. A monoclonal antibody to a determinant distant from the cell-binding site did not affect chemotaxis. A synthetic tetrapeptide, RGDS, which represents the major cell-attachment sequence, was able to compete with FN and the Ca 140 fragment in chemotaxis assays, but this peptide itself had no significant chemotactic activity. A larger peptide encompassing this sequence, GRGDSP, was chemotactic, while the peptide GRGESP, where a glutamic acid residue was substituted for aspartic acid, was inactive. Chemotactic migration could be prevented in a dose-dependent manner by a rabbit polyclonal antiserum to a 140-kD cell surface FN receptor. This antibody was more effective on normal than on transformed 3T3 cells. Neither the anti-FN receptor antiserum nor a monoclonal antibody to the cell-binding site of FN blocked migration induced by another potent chemoattractant, platelet-derived growth factor. These data indicate that FN-induced chemotaxis of 3T3 and SV3T3 cells is mediated via the RGDS cell-attachment site of FN and the 140-kD cell surface FN receptor. The interaction is specific and can be altered by transformation.
Detailed behavioral analysis of water maze acquisition under systemic NMDA or muscarinic antagonism: Nonspatial pretraining eliminates spatial learning deficits. (1996)

A detailed behavioral analysis of water-maze acquisition showed that the N-methyl-D-aspartate (NMDA) antagonist NPC17742 and the muscarinic antagonist scopolamine caused sensorimotor disturbances in behaviors required for maze performances and that these correlated with acquisition impairments in both hidden and visible platform versions of the maze in male rats. Behavioral disturbances included thigmotaxic swimming, swimming over and deflecting off the platform, abnormal swim behavior, and hyperactivity. Rats familiar with the behavioral strategies involved in the task performed normally under NPC17742 or scopolamine. The results indicated that drug-induced sensorimotor disturbances contributed to poor acquisition scores in naive rats. NMDA or muscarinic activity may contribute to but do not appear to be essential for spatial learning in the water maze.
Efficient Synthesis of Chiral <i>ansa</i>-Metallocenes by Amine Elimination. Synthesis, Structure, and Reactivity of <i>rac</i>-(EBI)Zr(NMe<sub>2</sub>)<sub>2</sub> (1996)

The amine elimination reaction of Zr(NMe2)4 (2) and (EBI)H2 (1,2-bis(3-indenyl)ethane, 3) in toluene at 100 °C affords pure rac-(EBI)Zr(NMe2)2 (rac-4, EBI = ethylene-1,2-bis(1-indenyl)) in 68% isolated yield. This reaction proceeds via the rapidly formed mono-indenyl intermediate (η5-C9H6CH2CH2C9H7)Zr(NMe2)3 (6) which undergoes reversible intermolecular amine elimination with a second equivalent of 2 to give the binuclear species (μ-η5,η5-EBI){Zr(NMe2)3}2 (5, rac and meso isomers) or reversible intramolecular amine elimination to give either rac-4 or meso-4. The kinetic metallocene product is a 1/1 mixture of rac-4 and meso-4, the thermodynamic product is rac-4, and the meso-4 to rac-4 isomerization is catalyzed by the NMe2H co-product. The rac-4/meso-4 product ratio can be controlled by adjusting the rate of NMe2H removal from the reaction vessel and the steady state concentration of amine in the reaction mixture. The molecular structure of rac-4 has been determined by X-ray crystallography. rac-4 is converted to rac-(EBI)ZrCl2 (rac-1) in high yield by reaction with NMe2H·HCl (92% isolated) or Me3SiCl (quantitative). The syntheses of 2, rac-4, and rac-1 can be combined in a “one pot” synthesis of rac-1 from ZrCl4 in 68% overall yield. Alkylation of rac-4 with AlMe3 affords rac-(EBI)ZrMe2 (rac-7) in 90% isolated yield. rac-4 can be used directly as a catalyst precursor for the isospecific polymerization of propylene.
Variations in the Atmospheric Radiocarbon Concentration over the Past 1300 Years (1960)

Considerable attention has been focussed in recent years upon the validity of the radiocarbon dating method by papers whose authors have considered that one or other of the fundamental principles might either be in error or require serious modification (Crowe, 1958; Milojčić, 1957; Elsasser, Ney, and Winkler, 1957; Daniel, 1959). It has even been suggested that errors as great as 800 years might arise between datings on the same sample made in different laboratories (Crowe, 1958). In the light of such criticism, it is clearly of the utmost importance to investigate, and, if possible, justify the basic assumptions on which the validity of the method rests.
Global '90 cars: electronics-aided (1989)

The role that will be played by electronics in the automobiles of the 1990s is examined. Automatic traction control, active suspensions, and tire pressure control systems are among the features that will be available. Electronic throttle controls and fuzzy logic controls will be used for automatic transmissions and antilock braking systems. Car buyers' resistance to complex electronic readouts has sparked a trend back to analog dashboard instruments. However, although the readout is analog, the rest of the instrumentation is electronic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Advanced real time integrated processors (2003)

A powerful integrated processor architecture has been developed by Hughes Aircraft Company to meet sensor, sensor fusion, and mission processing requirements. The Hughes Modular Processor (HMP) is based on development for the Lockheed F-22 Advanced Tactical Fighter Common Integrated Processor (CIP), and rests on an extensive prior history of high-performance imbedded signal and data processors. The authors discuss the HMP integrated, open architecture. This architecture has been demonstrated in an integrated electronic warfare, communications, radar, electrooptical and mission processing application, as well as in stand-alone sensor/mission processing configurations. Single application HMP configurations such as mission computing and dedicated sensor processors can be derived. Key technology issues are addressed, and innovative solutions to the difficulties of modular systems are presented. Specific module designs incorporating advanced packaging technology are discussed with emphasis on functionality and performance. The overall support software environment is characterized, with particular emphasis on the Ada compilation system, the operating system, and application user software development system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis of Diamond by Direct Conversion of Graphite under Very High Pressure (2003)

Polycrystalline diamond was successively synthesized recently at very high pressure and temperature using a Kawai-type apparatus, which turned out to be extremely hard when compared with currently available sintered diamond products and natural single crystal diamonds. Here the author summarizes the results of experiments and reviews aspects of the synthesis of polycrystalline diamonds by the direct conversion of graphite. Some future perspectives and related unsolved problems are also discussed on the basis the results of our and other experimental studies on the synthesis of polycrystalline diamond.
Laser scanning tomography of localised nerve fibre layer defects (1998)

The majority of localised RNFL defects can be detected in reflectivity images from laser scanning tomograms. Localised RNFL defects may be differentiated according to surface topography into those with and those without a measurable surface depression. A small but deep RNFL defect is not necessarily associated with a scotoma in routine 6 degrees grid VF static perimetry.
Optical Characterization of Infrared Emitting Rare-Earth-Doped Fluoride Nanocrystals and Their Transparent Nanocomposites (2007)

Nanocrystalline LaF3:Nd and CaF2:Er with rare-earth concentrations ranging from 0.5 to 16.7 mol % and dispersible particle sizes less than 100 nm were synthesized by solvothermal synthesis. Optical absorption, emission, and quantum efficiency were measured for the nanocrystals. Dopant levels of 0.5 mol % rare earth exhibited the best emission characteristics, with maximum quantum efficiencies of 95 and 51% for LaF3:Nd and CaF2:Er, respectively. The nanopowders were suspended in PFCB (6F variant) polymer-in-toluene solutions to make transparent suspensions that could be cast to make transparent nanocomposites. Scattering analysis indicates that the excellent transmission can be attributed to nanocrystals dispersed in the composite at length scales less than 100 nm.
Gbb/Bmp signaling is essential for maintaining germline stem cells and for repressing<i>bam</i>transcription in the<i>Drosophila</i>testis (2004)

Stem cells are responsible for replacing damaged or dying cells in various adult tissues throughout a lifetime. They possess great potential for future regenerative medicine and gene therapy. However, the mechanisms governing stem cell regulation are poorly understood. Germline stem cells (GSCs) in the Drosophila testis have been shown to reside in niches, and thus these represent an excellent system for studying relationships between niches and stem cells. Here we show that Bmp signals from somatic cells are essential for maintaining GSCs in the Drosophila testis. Somatic cyst cells and hub cells express two Bmp molecules, Gbb and Dpp. Our genetic analysis indicates that gbb functions cooperatively with dpp to maintain male GSCs, although gbb alone is essential for GSC maintenance. Furthermore, mutant clonal analysis shows that Bmp signals directly act on GSCs and control their maintenance. In GSCs defective in Bmp signaling, expression of bam is upregulated, whereas forced bam expression in GSCs causes the GSCs to be lost. This study demonstrates that Bmp signals from the somatic cells maintain GSCs, at least in part, by repressing bam expression in the Drosophila testis. dpp signaling is known to be essential for maintaining GSCs in the Drosophila ovary. This study further suggests that both Drosophila male and female GSCs use Bmp signals to maintain GSCs.