gebhart/patrepeval huggingface dataset:
Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking. (1997)

Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme.
Antibodies: Key to a Robust Lateral Flow Immunoassay (2008)

Lateral flow immunoassays are well established as a valuable tool in medical, veterinary, food, agricultural, environmental, and industrial diagnostics. While in many instances they are used as a rapid screening tool and backed up bymore complex and time-consuming assays, they may also be used in some applications as the primary method of choice. As a consequence, these assays need to be constructed as robustly as any other diagnostic tests. While the physical components of the lateral flow test strip, construction techniques, and buffers and surfactants play amajor role in optimizing the test, at the very heart of these processes are the antibodies themselves. If the antibodies are not meticulously selected for their ability to recognize the target antigen(s) in this format, no amount of optimization will be able to overcome this inherent defect. Often, assay developersmay spend great deal of time struggling to ‘‘tweak’’ the assay to fit their specifications, but come away with an assay that just borders on having the right sensitivity and generally not very robust from a manufacturing standpoint. Instead, if they would spend more time in the creation and selection of optimized antibodies at the front end of the development process, it would make the rest of the development relatively easy. Lateral flow immunoassays are particularly demanding in terms of the affinity required in the interactions between antibodies and antigens. Consider a typical lateral flow strip with antibody immobilized on a test zone of 0.5–1.0 mm wide. Antigen flowing up the strip has a flow rate in the range of 0.66–0.16 mm per second depending on the flow rate of the nitrocellulose membrane selected (most often specified by the manufacturer as the time required to traverse 4 cm of the membrane and it ranges from 60 to 240 seconds [1]). Antigen thus spends between 1 and 6 seconds in the zone where it can interact with the immobilized antibody. The speed is actually much faster at the initiation of the flow, since flow rates decrease proportionately to the square of
Use of large bandwidth-duration binary phase shift keying signals in target delay Doppler measurements (1991)

Some classes of signals exhibiting a good delay-Doppler power resolution (ambiguity function) in active radar/sonar cases, and particularly in the case of true Doppler effect (compression ambiguity function), are discussed. Large WT BPSK signals are presented, which are the most performant in this sense, and are compared with more classical signals. A further improvement is given by amplitude modulation. Some examples are given of target parameters measurements achieved by using these signals, and especially by using the differential range and Doppler measurements. Some simulations are presented, and also some real underwater acoustic target measurements.
Adhesive enabling technology for directly plating copper onto glass/ceramic substrates (2014)

This study showcases that metal oxide adhesion promoters (MOAP) can function as strong adhesive layers between plated Cu and glass/ceramic. In this new approach a 10-200 nm thick metal oxide layer is deposited by a modified sol gel process followed by sintering. This enables reliable electroless and electrolytic metallization of glass or ceramic substrates. With the new approach, Cu can be plated on a variety of glass types. Substrate roughness appears to have only limited impact. The new approach also can be extended to ceramics such as Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and BaTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> . Cu film of over 50 μm thickness can be deposited without delamination. Adhesion of 15 μm thick Cu layers as measured by 90° peel strength tests can achieve well above 5 N/cm. The plated layer stands up well to solder reflow shock (260°C) and HAST without significant loss of adhesion. Good coverage of the MOAP layer and excellent copper adhesion inside the via holes of patterned substrates have been also demonstrated. There is no indication of blockages of holes with diameters >20 μm by the process.
Nanophase Iron Phosphate, Iron Arsenate, Iron Vanadate, and Iron Molybdate Minerals Synthesized within the Protein Cage of Ferritin (2005)

Nanoparticles of iron phosphate, iron arsenate, iron molybdate, and iron vanadate were synthesized within the 8 nm interior of ferritin. The synthesis involved reacting Fe(II) with ferritin in a buffered solution at pH 7.4 in the presence of phosphate, arsenate, vanadate, or molybdate. O2 was used as the oxidant to deposit the Fe(III) mineral inside ferritin. The rate of iron incorporation into ferritin was stimulated when oxo-anions were present. The simultaneous deposition of both iron and the oxo-anion was confirmed by elemental analysis and energy-dispersive X-ray analysis. The ferritin samples containing iron and one of the oxo-anions possessed different UV/vis spectra depending on the anion used during mineral formation. TEM analysis showed mineral cores with approximately 8 nm mineral particles consistent with the formation of mineral phases inside ferritin.
INSECT CONTROL WITH GROWTH REGULATORS INTERFERING WITH THE ENDOCRINE SYSTEM (1982)

Out of a field of many thousands of analogs of the insect juvenile hormones (JHA), only a few have found practical utility in the control of a variety of insect species. Their mode of action and the lack of foliar stability in all but the most recently discovered juvenoids have so far precluded their use against pests of field crops. A possible more efficacious mode of action is present in anti‐juvenile hormone agents (AJH), which can induce premature metamorphosis, but of which none of the present prototypes has yet been developed into a cost effective control agent. These AJH prototypes represent a number of very different action mechanisms and degrees of selectivity for different insect taxa. In an even more contemporary approach, the interference with neurohormonal pathways presents significant perspectives for insect control. RÉSUMÉ Lutte contre les insectes avec des regulateurs de croissance interferant avec le systeme endocrine Parmi les milliers d'analogues d'hormones juvéniles d'insectes (JHA), seuls quelques uns ont présenté une valeur pratique dans la lutte contre certaines espèces d'insectes. Leur mode d'action et la perte de stabilité foliaire générale, mème chez les juvénoïdes les plus récemment découverts, ont jusqu à présent contrarié leur utilisation contre les ravageurs des cultures. Un mode d'action peut‐être plus efficace existe avec les agents anti hormone juvénile (AJH), qui peuvent induire une métamorphose prématurée, mais aucun des prototypes actuels n'a encore été produit comme agent de lutte réellement rentable. Ces prototypes AJH présentent une gamme de mécanismes d'action différents et de degrés de sélectivité pour les différents taxons d'insectes. Selon une approche encore plus récente. l'interférence aves les voies neuroendocrines présente des espoirs intéressants pour la lutte contre les insectes.
A second protease of foot-and-mouth disease virus (1986)

Foot-and-mouth disease virus (FMDV) genes are expressed as a polyprotein which is rapidly processed into the four primary cleavage products L, P1, P2, and P3. In secondary cleavage reactions, these are further processed into the mature proteins. The FMDV L protein is located at the N terminus of the polyprotein and is the first gene product released from the nascent polyprotein. For analysis of its biological function, the L gene was mutated by site-directed mutagenesis of cloned cDNA. In vitro translation of in vitro transcripts of these DNAs and expression studies in Escherichia coli showed that the L mutants affect the processing of the viral polyprotein. The mutants isolated were partially or totally defective in processing the polyprotein at the L/P1 junction. These mutants could, however, be processed in the presence of the wild-type L protein. Furthermore, an antiserum directed against the L protein inhibited processing at the L/P1 cleavage site, so that the release of the L protein from the polyprotein was blocked. These data reveal that the L gene product represents a viral protease which catalyzes its own release from the nascent polyprotein.
<i>The</i>5ESS<i>Switching System</i>: Operational Software (1985)

The operational software of the 5ESS™ switching system has been designed to meet specific objectives for capacity, functionality, and reliability. It has also been designed to accommodate changing technology, changing system applications, and an ever-increasing feature application set. Structured programming techniques, high-level languages, and modular design techniques have been used to obtain these objectives. Specifically, the operational software architecture is organized as a set of functional software components utilizing the advantages of a generalized operating system and database manager to achieve a high degree of hardware independence. A primary cause for hardware churning is the introduction of new peripheral units in support of new feature applications. The peripheral control software shields the majority of the operational software from these changes. Standardized and locally well-defined interfaces to the operations support systems provide information to the customer for the administration and maintenance of the switching system.
Bone regeneration with resorbable polymeric membranes. III. Effect of poly(L‐lactide) membrane pore size on the bone healing process in large defects (1996)

Poly(l-lactide) membranes of various pore sizes: microporous, medium pore size (10–20 μm), and large pore size (20–200 μm) were implanted in 15 mature New Zealand female rabbits to cover a 10-mm diaphyseal defect created in the radius. Five rabbits were implanted with each membrane. No internal fixation was used, as it was assumed that the intact ulna splints the radius adequately. Postoperative radiographs revealed the formation of hematoma within the bone defect. At the 2nd week after surgery, the hematoma was resorbed and the formation of new bone was noted radiologically either at the ends of the bone fragments or as osteophytes on the proximal and distal edges of the membrane. At 4 weeks, the newly formed bone was growing centripetally from the fragment ends. The bone regeneration took place in the majority of the cases under investigation, regardless of the pore size of the polymeric membranes used. There were, however, some differences in the intensity of the bone regeneration process. Although at 2 weeks after surgery bone formation was seen radiographically in all animals, at 6 months five rabbits of five, four rabbits of five, and three rabbits of five implanted respectively with microporous membrane, medium pore-size membrane, and large pore-size membrane showed complete regeneration of bone within the defects. It is suggested that the primary function of the membrane used to cover bone defects is to preserve the osteogenic components present in the space under the membrane from escaping and support the growth of cells within the “medullary cavity” formed by the tubular implant. © 1996 John Wiley & Sons, Inc.
Axonal Transport, Amyloid Precursor Protein, Kinesin-1, and the Processing Apparatus: Revisited (2005)

The sequential enzymatic actions of beta-APP cleaving enzyme 1 (BACE1), presenilins (PS), and other proteins of the gamma-secretase complex liberate beta-amyloid (Abeta) peptides from larger integral membrane proteins, termed beta-amyloid precursor proteins (APPs). Relatively little is known about the normal function(s) of APP or the neuronal compartment(s) in which APP undergoes proteolytic processing. Recent studies have been interpreted as consistent with the idea that APP serves as a kinesin-1 cargo receptor and that PS and BACE1 are associated with the APP-resident membranous cargos that undergo rapid axonal transport. In this report, derived from a collaboration among several independent laboratories, we examined the potential associations of APP and kinesin-1 using glutathione S-transferase pull-down and coimmunoprecipitation assays. In addition, we assessed the trafficking of membrane proteins in the sciatic nerves of transgenic mice with heterozygous or homozygous deletions of APP. In contrast to previous reports, we were unable to find evidence for direct interactions between APP and kinesin-1. Furthermore, the transport of kinesin-1 and tyrosine kinase receptors, previously reported to require APP, was unchanged in axons of APP-deficient mice. Finally, we show that two components of the APP proteolytic machinery, i.e., PS1 and BACE1, are not cotransported with APP in the sciatic nerves of mice. These findings suggest that the hypothesis that APP serves as a kinesin-1 receptor and that the proteolytic processing machinery responsible for generating Abeta is transported in the same vesicular compartment in axons of peripheral nerves requires revision.
Personal Projection (2004)

This paper introduces the technology and applications of personal projectors: small and inexpensive video projection devices intended for use in battery-powered hand-held or wearable products. A prototype constructed in our research group, based on an array of semiconductor lasers, is then discussed.
A Novel Class of High-Performance Perfluorocyclobutane-Containing Polymers for Second-Order Nonlinear Optics (2000)

A series of novel second-order nonlinear opitcal (NLO) thermoset polymers containing silicon-perfluorocyclobutane (PFCB) has been developed. The synthesis was accomplished using the cross-linking reaction between the di(trifluorovinylether)-containing NLO chromophores and the tris(trifluorovinylether) monomer in a solid state at 180−250 °C. The preliminary results have indicated these polymers to possess excellent processability, low optical loss, and a combination of the highly desirable thermal, nonlinear optical, and mechanical properties.
Protein misfolding, amyotrophic lateral sclerosis and guanabenz: protocol for a phase II RCT with futility design (ProMISe trial) (2017)

The study protocol was approved by the Ethics Committee of IRCCS 'Carlo Besta Foundation' of Milan (Eudract no. 2014-005367-32 Pre-results) based on the Helsinki declaration.
Combustion efficiency of flares. Report for October 1980-February 1984 (1985)

The paper gives results of a study to provide data on industrial flare emissions. (Emissions of incompletely burned hydrocarbons from industrial flares may contribute to air pollution. Available data on flare emissions are sparse, and methods to sample operating flares are unavailable.) Tests were conducted on 3-, 6-, and 12-in.-diameter flare heads. Propane was used as the flare fuel, diluted with nitrogen to control the heating value. The following results were obtained: (1) soot (from smoky flares) accounts for <0.5% of the unburned hydrocarbon emissions; (2) the size of the flare head did not influence hydrocarbon combustion efficiency; and (3) the stability of the flare flame influenced combustion efficiency, with unstable flames tending to promote inefficient combustion. A relationship between gas heating value and exit velocity was developed to denote the region of flame instability.
Putting Fear in Its Place: Remapping of Hippocampal Place Cells during Fear Conditioning (2004)

We recorded hippocampal place cells in two spatial environments: a training environment in which rats underwent fear conditioning and a neutral control environment. Fear conditioning caused many place cells to alter (or remap) their preferred firing locations in the training environment, whereas most cells remained stable in the control environment. This finding indicates that aversive reinforcement can induce place cell remapping even when the environment itself remains unchanged. Furthermore, contextual fear conditioning caused significantly more remapping of place cells than auditory fear conditioning, suggesting that place cell remapping was related to the rat's learned fear of the environment. These results suggest that one possible function of place cell remapping may be to generate new spatial representations of a single environment, which could help the animal to discriminate among different motivational contexts within that environment.
Clinical and roentgenographic evaluation of endoscopic suspension of the vesical neck for urinary incontinence. (1975)

Forty-four consecutive patients, without residual urine or infecttion, were operated upon for urinary stress incontinence by endoscopie suspension of the vesical neck. All patients had preoperative and post-operative lateral view cystograms which showed after operation substantial upward and forward elevation of the urethrovesical junction as measured by the posterior urethrovesical angle, the angle of urethral inclination, and elevation of the base of bladder. Despite a significant history of an urgency component to their incontinence in many patients, as well as 44 previous operations in 22 of the patients, a carefully performed cystometrogram and cholinergic sensitivity test were not helpful in detecting abnormalities of the detrusor muscle. Fourty-one patients were cured, and in three others, the condition was not cured, the failure group. The lateral view cystogram was the most diagnostic test in that two in the failure group did not show preoperatively the roentgenographic hallmark of stress urinary incontinence.
Amputations in patients attending a diabetic clinic in Addis Abeba, Ethiopia. (1995)

During 18 years, 1976 to 1994, 43(1.9%) of the 2,250 patients registered in the Diabetic Clinic at Yekatit 12 Hospital, Addis Abeba, Ethiopia (six patients) required an amputation at diagnosis or during the course of diabetes mellitus. Male to female ratios was 2:1; eight patients had Type 1 and 35 Type 2 diabetes. Diabetic peripheral neuropathy was the underlying condition in at least 21 of the 43 patients; only five cases of ischaemic gangrene were seen. Mean ge at amputation was 37.4 +/- 8.7 years in Type 1 patients and 58.6 +/- 12.1 in Type 2. Twenty-three of the 43 are now dead, 12 of the deaths having been due to sepsis in patients who refused an amputation in the face of progressing gangrene. Eleven of the 43 still attend regularly up to 11 years after an amputation. Most patients who needed below-knee amputations did not regain independence because of difficulty obtaining prostheses.
Whole-Genome Sequence Analysis of <i>Pseudomonas syringae</i> pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition (2005)

Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.
Intersections : a transdisciplinary approach to media, identity, and place (2002)

This paper examines Cabramatta as an intersection of many cultural flows and diverse experiences and argues for a transdisciplinary approach and a focus on place to adequately grasp and analyse the comlexity of media and social relations in culturally diverse contexts.
Video quality metric for temporal fluctuation measurement (2010)

Temporal fluctuation artifact is often observed in digitally compressed video. However, the fluctuation intensity cannot be correctly measured by the traditional image/video quality metric, e.g., the peak signal-to-noise ratio (PSNR), which only addresses on the quality of a single image. Although there are several metrics proposed for temporal fluctuation measurement, e.g., the <i>sum of squared differences (SSD)</i> and <i>motion compensated SSD (MCSSD)</i>, these first difference based algorithms may falsely treat a smoothly continuous change of pixels as the temporal fluctuation artifact. To overcome this problem, this contribution proposes a second difference based temporal metric, named the <i>motion estimated mean scaled absolute second difference (MEMSASD)</i> The performance of the MEMSASD is examined using a number of video sequences with varying degrees of temporal fluctuation, which are generated by an H.264/AVC compliant codec. Compared with existing metrics such as the PSNR, the SSD and the MCSSD, the results of the proposed metric better reflect the temporal fluctuation intensity.