gebhart/patrepeval huggingface dataset:
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability (2005)

The chicken avidin gene belongs to an extended gene family encoding seven avidin-related genes (AVRs), of which only avidin is expressed in the chicken. The sequences of AVR4 and AVR5 are identical and the common protein (AVR4) has been expressed both in insect and bacterial systems. The recombinant proteins are similarly hyperthermostable and bind biotin with similarly high affinities. AVR4 was crystallized in the apo and biotin-complexed forms and their structures were determined at high resolution. Its tertiary and quaternary structures are very similar to those of avidin and streptavidin. Its biotin-binding site shows only a few alterations compared with those of avidin and streptavidin, which account for the observed differences in binding affinities. The increased hyperthermostability can be attributed to the conformation of the critical L3,4 loop and the extensive network of 1-3 inter-monomeric interactions. The loop contains a tandem Pro-Gly sequence and an Asp-Arg ion pair that collectively induce rigidity, thus maintaining its closed and ordered conformation in both the apo and biotin-complexed forms. In addition, Tyr115 is present on the AVR4 1-3 monomer-monomer interface, which is absent in avidin and streptavidin. The interface tyrosine generates inter-monomeric interactions, i.e. a tyrosine-tyrosine pi-pi interaction and a hydrogen bond with Lys92. The resultant network of interactions confers a larger 1-3 dimer-dimer contact surface on AVR4, which correlates nicely with its higher thermostability compared with avidin and streptavidin. Several of the proposed thermostability-determining factors were found to play a role in strengthening the tertiary and quaternary integrity of AVR4.
Identification and Characterization of the Major Phosphorylation Sites of the B-type Natriuretic Peptide Receptor (1998)

C-type natriuretic peptide (CNP) is a newly discovered factor that stimulates vasorelaxation and inhibits cell proliferation. Natriuretic peptide receptor-B (NPR-B) is the primary signaling molecule for CNP. Recently, the guanylyl cyclase activity of NPR-B was shown to correlate with its phosphorylation state, and it was suggested that receptor dephosphorylation is a mechanism of desensitization. We now report the identification and characterization of the major NPR-B phosphorylation sites. Mutagenesis and comigration studies using synthetic phosphopeptides were employed to identify five residues (Ser-513, Thr-516, Ser-518, Ser-523, and Ser-526) within the kinase homology domain that are phosphorylated when NPR-B is expressed in human 293 cells. Mutation of any of these residues to alanine reduced the receptor's phosphorylation state and CNP-dependent guanylyl cyclase activity. The reductions were not explained by decreases in receptor protein level as indicated by immunoblot analysis and determinations of cyclase activity in the absence of CNP or in the presence of detergent. Elimination of all of the phosphorylation sites resulted in a completely dephosphorylated receptor whose CNP-dependent cyclase activity was decreased by >90%. However, unlike NPR-A, the dephosphorylated receptor was not completely unresponsive to hormone. Finally, two additional residues (Gly-521 and Ser-522) were identified that when mutated to alanine reduced the overall phosphorylation state and hormone responsiveness of the receptor without abolishing the phosphorylation of a specific site. These data indicate that phosphorylation of the kinase homology domain is a critical event in the regulation of NPR-B.
Near-Field Scanning Tomography (2006)

A new tomography method that uses data of the electromagnetic scanning along the plane interface of a 3D inhomogeneous half-space in dependence on a parameter of the received signal that determines the effective depth of its formation is proposed. The retrieval of the 3D structure of media parameters is based on the solution of the 3D integral equations of the convolution kind with respect to lateral co-ordinates. Possibilities of the application of this approach to media diagnostics using known methods of the near-field sounding in various frequency ranges are considered
Clinicopathologic correlations of cranial magnetic resonance imaging of periventricular white matter (1990)

We studied clinical, imaging, and autopsy data on 7 patients who underwent magnetic resonance imaging (MRI) during life. Small periventricular zones of increased T2 signal corresponded to a periventricular cap consisting of subependymal glial accumulations, with some loss of the ependymal lining, and a surrounding pale-staining area of finely textured myelin and axons with an altered glial pattern. The fine-fiber zone is identifiable anatomically as the subcallosal fasciculus. This histologic pattern of subependymal glial accumulations and fine fibers is normal and is often associated with fibrotic small blood vessels. More extensive subcortical MRI changes corresponded, in 1 case, to multiple sclerosis, and in another to subcortical arteriosclerotic encephalopathy (Binswanger's disease) with widespread fiber loss and lacunar changes. Wallerian degeneration secondary to infarction occurred in some areas of MRI abnormality.
Self-Assembled TiO<sub>2</sub>–Graphene Hybrid Nanostructures for Enhanced Li-Ion Insertion (2009)

We used anionic sulfate surfactants to assist the stabilization of graphene in aqueous solutions and facilitate the self-assembly of in situ grown nanocrystalline TiO2, rutile and anatase, with graphene. These nanostructured TiO2-graphene hybrid materials were used for investigation of Li-ion insertion properties. The hybrid materials showed significantly enhanced Li-ion insertion/extraction in TiO2. The specific capacity was more than doubled at high charge rates, as compared with the pure TiO2 phase. The improved capacity at high charge-discharge rate may be attributed to increased electrode conductivity in the presence of a percolated graphene network embedded into the metal oxide electrodes.
[Chinese total diet study in 2000--the dietary mercuric intakes]. (2006)

The result shows that the total mercuric intakes in Chinese people are safe.
Status and Needs of In-Situ Real-time Process Particle Detection (1989)

Particle defects play a major role in yield losses in semiconductor device fabrication. It is generally acknowledged that about 50 percent of all yield losses are due to particles. Processing of devices with 0.35 to 0.5 μm minimum feature sizes will exacerbate the effects of particles due to the large relative abundance of submicron particles. The cleanroom is no longer the major particle contributor because current state-of-the-art cleanrooms have less than 10 particles (&lt;0.5 μm) per cubic foot. Particles in processing equipment now play the dominant role in wafer contamination. An analysis of the status and needs of particle detection techniques for semiconductor processing equipment and processes clearly shows that they are inadequate to meet the requirements of the next generation of devices. Detection limits must be improved both in terms of particle diameter and in the number of particles on a wafer. An experimental laser particle counter was fabricated and used to show that such a detector would be extremely useful for in-vacuum realtime particle detection. Experimental studies on wafer surface measurements show that current wafer surface scanning techniques cannot provide the level of detection needed for future devices. Ideas for a new generation of particle detection equipment are presented.
RNA Transport in Dendrites: A<i>cis</i>-Acting Targeting Element Is Contained within Neuronal BC1 RNA (1997)

In nerve cells, a select group of RNAs has been localized to dendritic domains. Here we have examined dendritic RNA transport in sympathetic neurons in primary culture, using a microinjection protocol with neuronal BC1 RNA and with BC1-derived sequence segments. After cytoplasmic microinjection, full-length BC1 RNA was selectively transported to dendrites; in contrast, control RNAs such as nuclear RNAs and random-sequence irrelevant RNAs remained restricted to cytoplasmic areas proximal to the injection sites. Chimeric RNAs were constructed that contained the full-length BC1 sequence inserted upstream or downstream of the coding regions of nondendritic mRNAs. After microinjection, such chimeric RNAs were specifically targeted to dendrites; microinjected corresponding nonchimeric mRNAs were not. Dendritic transport of BC1 RNA was rapid: the average dendritic delivery rate within the first hour after microinjection was 242 +/- 25 microm/hr. Whereas a 5'-BC1 segment of 62 nucleotides was transported to dendrites to extents and at levels similar to full-length BC1 RNA, a 3'-BC1 segment of 60 nucleotides did not exit injected somata to any significant degree. A cis-acting dendritic targeting element is thus contained in the 5' part of neuronal BC1 RNA. These results demonstrate that mechanisms exist in neurons for fast and specific transport of selected RNAs to dendrites.
Tunable GPON Receivers Enable Phased Migration to 1Gb/s per Subscriber (2009)

We demonstrate a tunable receiver with -30dBm sensitivity at 10−10 BER on any of seven 100GHz spaced channels, and propose deployment strategies for low-cost migration to up to 1Gb/s per subscriber downstream Wavelength-Agile PON.
Synovial Stem Cells Are Regionally Specified According to Local Microenvironments After Implantation for Cartilage Regeneration (2006)

We previously demonstrated that synovium-derived MSCs had greater in vitro chondrogenic ability than other mesenchymal tissues, suggesting a superior cell source for cartilage regeneration. Here, we transplanted undifferentiated synovium-derived MSCs into a full-thickness articular cartilage defect of adult rabbits and defined the cellular events to elucidate the mechanisms that govern multilineage differentiation of MSCs. Full-thickness osteochondral defects were created in the knee; the defects were filled with 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate-labeled MSCs and covered with periosteum. After 4 weeks, although the cell density decreased, transplanted MSCs produced a great amount of cartilage matrix extensively. The periosteum became thinner, and chondroprogenitors in the periosteum produced a small amount of cartilage matrix. In the deeper zone, transplanted MSCs progressed to the hypertrophic chondrocyte-like cells. In the deep zone, some transplanted cells differentiated into bone cells and were replaced with host cells thereafter. In the next phase, the border between bone and cartilage moved upwards. In addition, integrations between native cartilage and regenerated tissue were improved. Chondrocyte-like cells derived from the transplanted MSCs still remained at least after 24 weeks. Histological scores of the MSC group improved continuously and were always better than those of two other control groups. Immunohistological analyses and transmission electron microscopy confirmed that the MSCs produced abundant cartilage matrix. We demonstrated that transplanted synovium-derived MSCs were altered over a time course according to the microenvironments. Our results will advance MSC-based therapeutic strategies for cartilage injury and provide the clues for the mechanisms that govern multilineage differentiation of MSCs.
Comparison of Transcription-Mediated Amplification and PCR Assay Results for Various Genital Specimen Types for Detection of <i>Mycoplasma genitalium</i> (2006)

Mycoplasma genitalium is now recognized as a possible cause of several idiopathic sexually transmitted disease (STD) syndromes. However, due to the difficulty of culture of this fastidious bacterium, nucleic acid amplification tests (NAATs) are necessary for its detection in patient specimens. In the current study we compared a newly developed research-only transcription-mediated amplification (TMA) assay (Gen-Probe Incorporated) to our in-house DNA-based PCR assay for detection of M. genitalium. The relative performance characteristics of these two NAATs were assessed with genital specimens from 284 women and 352 men reporting to an STD clinic in Seattle, WA. Among the women, M. genitalium was detected by the TMA and PCR assays in 36 (13%) and 39 (14%) vaginal swab specimens, respectively (kappa = 0.923); 26 (9%) and 23 (8%) cervical swab specimens, respectively (kappa = 0.843); and 25 (9%) and 28 (10%) urine specimens, respectively (kappa = 0.687). Among the M. genitalium-positive women, the relative sensitivities of detection for the TMA and PCR assays were 84% and 91%, respectively, for vaginal swab specimens; 60% and 53%, respectively, for cervical swab specimens; and 58% and 65%, respectively, for urine specimens. By using an infected patient (a woman positive at any site by TMA assay and at any site by PCR) as a proxy for a "gold standard," the specificities of detection were >99.5% for both the TMA and the PCR assays. Among the men, M. genitalium was detected in 24 urine specimens (6.8%) by the TMA assay, 26 (7.4%) urine specimens by PCR assay, and 32 urine specimens (9%) by either test (kappa = 0.791). We conclude that the M. genitalium TMA and PCR assays are highly specific and that vaginal swab specimens are the most sensitive specimen type for the detection of M. genitalium in women.
2'3'-Carbonates in the synthesis of uridine 5'-deoxy and 2',5'-dideoxy derivatives (1976)

Detritylation of 2',3'-O-carbonyl-5'-O-trityluridine (Ia) with ethereal hydrogen chloride affords 2',3'-O-carbonyluridine (Ib; 83%) which is converted by mesylation to the 5'-mesylcarbonate Ic (75%). Reaction of compound, Ic with tetrabutylammonium bromide in DMF affords the 5'-bromo carbonate Id (77%) which is reduced with tributyltin hydride to the 5'-deoxyuridine 2',3'-cyclic carbonate Ie (70%). When heated with imidazole, compound Ie affords the 2,2'-anhydro derivative IIa (76%) which is converted to the 2'-chloro derivative IIIa (88%) on heating with HC1/DMF. The tributyltin hydride reduction of compound IIIa gives 2',5'-dideoxyuridine (IIIb; 68%). When heated with NaHCO3 in DMF, the 5'-bromo carbonate Id affords the anhydro bromo derivative IIb (50%) which is converted to the 2',5'-dichloro derivative IIIc (86%) on heating with HC1/DMF. The tributyltin hydride reduction of compound IIIc affords the 2',5'-dideoxy derivative IIIb (59%). Alkaline hydrolysis of the 2,2'-anhydro derivative IIa affords the arabinosyl derivative IVa which is converted to the diacetyl derivative IVb (34%) by acetylation. When refluxed in water, the 2',3'-cyclic carbonates Ib, Id, and Ie are hydrolysed to the parent nucleosides, namely, uridine (Va; 81%), 5'-bromo-5'-deoxyuridine (Vb; 78%), and 5'-deoxyuridine (Vc; 83%). Hydrolysis of carbonates Ib and Ie is accompanied by the formation of the 2,2'-anhydro derivatives IIc (10%) and IIa (5%) as by-products.
Cannabis and its cannabinoids analysis by gas chromatography–mass spectrometry with Cold EI (2021)

Cannabis extracts and products were analyzed by gas chromatography-mass spectrometry (GC-MS) with Cold EI for their full content including terpenes, sesquiterpenes, sesquiterpinols, fatty acids, delta 9-tetrahydrocannabinol (THC), cannabidiol (CBD), other cannabinoids, hydrocarbons, sterols, diglycerides, triglycerides, and impurities. GC-MS with Cold EI is based on interfacing GC and MS with supersonic molecular beams (SMB) along with electron ionization of vibrationally cold sample compounds in the SMB in a fly-through ion source (hence the name Cold EI). GC-MS with Cold EI improves all the performance aspects of GC-MS, enables the analysis of Cannabinoids with OH groups without derivatization, while providing enhanced molecular ions for improved identification, and enables internal quantitation without calibration. We found over 50 cannabinoid compounds including a new one with a Cold EI mass spectrum very similar to delta 9-THC as well as relatively large cannabinoids with molecular weight above m/z = 400. Because the analysis was universal in full scan and not targeted, we found impurities such as bromo CBD and fluticasone propionate and could monitor the formation of oxidized CBD during decarboxylation. In addition, GC-MS with Cold EI enabled nontargeted full analysis of terpenes, sesquiterpenes, and sesquiterpinols in cannabis extracts with good internal quantitation. GC-MS with Cold EI further served with very good sensitivity for the concentration determination of delta 9-THC in CBD-related products. Finally, cannabis drugs such as EP-1 used in Israel for treatment of epilepsy and for children with autism spectrum disorder (ASD) were analyzed for their full cannabinoids content for learning on the entourage effect and for drug activity optimization.
Analysis of the role of the Shine-Dalgarno sequence and mRNA secondary structure on the efficiency of translational initiation in the Euglena gracilis chloroplast atpH mRNA (1994)

Chloroplast mRNAs in Euglena gracilis fall into two classes. One class has a Shine-Dalgarno sequence 5' to the AUG start codon while the other group of mRNAs does not have any conserved sequence elements near the start codon. The chloroplast mRNA encoding the atpH gene has been selected as an example of a message which has a Shine-Dalgarno sequence (GGAGUU) located in the initiation region. Mutations in the Shine-Dalgarno sequence result in 2-5-fold reductions in the efficiency of the message in initiation complex formation depending on the precise mutation. Secondary structure mapping of the initiation region of the atpH mRNA suggests that a number of mRNA conformations are present in an equilibrium mixture. Mutations in the Shine-Dalgarno sequence had little effect on the overall structure of the mRNA. Directed mutations which place the Shine-Dalgarno sequence into a region of higher secondary structure drastically reduce the activity of the message. The monocistronic form of the atpH mRNA has a 5'-untranslated leader region slightly over 70 nucleotides in length. Deletions in the leader suggest that a minimum length of 10 bases 5' to the start codon is important for activity in initiation. The presence of the full leader increased efficiency in initiation about 2-fold compared to messages with leaders 25-40 residues in length.
Measurement of adenine nucleotides in plasma (2003)

The goal of this study was to identify the most important variables affecting bioluminescent ATP, ADP and AMP measurements in plasma and to develop an assay that takes these variables into account. Blood samples were drawn from conscious dogs. A 'stop solution' containing EDTA was prepared, which greatly retarded plasma ATP degradation by chelating Mg(+2) and Ca(+2) that are co-factors for many ATPases. Stop solution and blood were mixed using a two-syringe withdrawal system. Samples were centrifuged twice in order to remove red blood cells, and ATP was measured in the supernatant using the firefly luciferase assay. Sample pH was adjusted to the optimal range (7.75-7.95) and Mg(2+) (necessary for the luciferase reaction) was added back to the sample within the luminometer 2 s prior to luciferase addition. Four assay tubes were prepared for each plasma sample, containing standard additions of 0-15 pmol added ATP, in order to quantify native plasma ATP content. In separate plasma/stop solution samples ADP + ATP was measured after converting ADP to ATP via the pyruvate kinase reaction, and AMP + ADP + ATP was measured after addition of both myokinase and pyruvate kinase. Addition of forskolin and isobutylmethylxanthine (IBMX) to the stop solution to inhibit platelets resulted in lower ATP concentrations. Measurement of ATP and haemoglobin from lysed erythrocytes revealed that haemolysis exerts a strong influence on plasma ATP concentration that must be taken into account.
Analysis of risk factors for the development of equine protozoal myeloencephalitis in horses (2000)

Development of EPM was associated with a number of management-related factors that can be altered to decrease the risk for the disease.
An algorithm to deal with incremental layout alteration (2002)

Incremental design alteration usually requires complete rework on the IC layout. An algorithm is proposed which tackles the problem in minimum time and creates the least perturbation to the original layout, preserving performance. The algorithm aims at automatic adjustment of layout due to minor change on logic design. As a result, the designer need not re-execute the whole placement process or manually correct the placement. Using dynamic variables to form the database, it is more efficient to implement the algorithm. Results and computation time of the algorithm are also found advantageous.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Specific Genomic Location within the <i>icm</i> / <i>dot</i> Pathogenesis Region of Different <i>Legionella</i> Species Encodes Functionally Similar but Nonhomologous Virulence Proteins (2004)

Legionella pneumophila, the major causative agent of Legionnaires' disease, is a facultative intracellular pathogen that grows within human macrophages and amoebae. Intracellular growth involves the formation of a replicative phagosome that requires the Icm/Dot type IV secretion system. Part of the icm/dot region in L. pneumophila contains the icmTSRQPO genes. The proteins encoded by the icmR and icmQ genes were shown to exhibit a chaperone-substrate relationship. Analysis of this region from other pathogenic Legionella species, i.e., L. micdadei and L. longbeachae, indicated that the overall organization of this region is highly conserved, but it was found to contain a favorable site for gene variation. In the place where the icmR gene was expected to be located, other open reading frames that are nonhomologous to each other or to any entry in the GenBank database were found (migAB in L. micdadei and ligB in L. longbeachae). Examination of these unique genes revealed an outstanding phenomenon; by use of interspecies complementation, the icmR, migB, and ligB gene products were found to be functionally similar. In addition, the function of these proteins was usually dependent on the presence of the corresponding IcmQ proteins. Moreover, each of these proteins (IcmR, LigB, and MigB) was found to interact with the corresponding IcmQ proteins, and the genes encoding these proteins were found to be regulated by CpxR. This study reveals new evidence of gene variation occurring in the same genomic location within the icm/dot locus in various Legionella species. The genes found at this site were shown to be similarly regulated and to encode species-specific, nonhomologous, but functionally similar proteins.
Rapid Production of Graphical User Interfaces (1990)

Abstract : There is a growing demand within the military for effective, flexible and configurable command and control workstations suiting the diversity of experience and working style that commanders bring to the decision making process. This need motivates development of real-time three-dimensional simulators at the Naval Postgraduate School. Our work concentrates on the graphical user interface and presents a study of information display, interface human factors, and underlying implementation efficiency considerations so as to enhance real time simulation systems with minimal degradation in performance. High quality interface software is costly in time and money, and it is essential for effective system performance. Our research culminated in the implementation of the NPS Panel Designer and ToolBox (NPSPD), an automated development environment that enables design, implementation, modification, and testing of customized graphical user interfaces. NPSPD includes automatic generation of compilable source code which can stand alone or be integrated quickly into a developer's application. NPSPD was developed using Silicon Graphics Inc. IRIS 4D/70GT and 4D/GTX workstations, relatively low cost systems which are commercially available. Methodology used and techniques developed provide a foundation applicable to any hardware capable of a windowing environment and graphics display.