gebhart/patrepeval huggingface dataset:
Resolution of the reaction sequence during the reduction of O2 by cytochrome oxidase. (1993)

Time-resolved resonance Raman spectroscopy has been used to study the reduction of dioxygen by the mitochondrial enzyme, cytochrome oxidase. In agreement with earlier reports, Fe(2+)-O2 and Fe(3+)-OH- are detected in the initial and final stages of the reaction, respectively. Two additional intermediates, a peroxy [Fe(3+)-O(-)-O-(H)] and a ferryl (Fe4+ = O), occur transiently. The peroxy species shows an oxygen-isotope-sensitive mode at 358 cm-1 that is assigned as the nu(Fe(3+)-O-) stretching vibration. Our kinetic analysis indicates that the peroxy species we detect occurs upon proton uptake from bulk solution; whether this species bridges to Cu(B) remains uncertain. For the ferryl, nu(Fe(4+) = O) is at 790 cm-1. In our time-resolved spectra, the 358 cm-1 mode appears prior to the 790 cm-1 vibration. By using kinetic parameters deduced from the time-resolved Raman work and from a variety of time-resolved optical studies from other laboratories, we have assigned rate constants to several steps in the linear reaction sequence proposed by G. T. Babcock and M. Wikström [(1992) Nature (London) 356, 301-309]. Simulations of this kinetic scheme provide insight into the temporal behavior of key intermediates in the O2 reduction process. A striking aspect of the reaction time course is that rapid O2-binding and trapping chemistry is followed by a progressive slowing down of succeeding steps in the process, which allows the various transient species to build up to concentrations sufficient for their detection by our time-resolved techniques. Our analysis indicates that this behavior reflects a mechanism in which conditions that allow efficient dioxygen bond cleavage are not inherent to the active site but are only established as the reaction proceeds. This catalytic strategy provides an effective means by which to couple the free energy available in late intermediates in the reduction reaction to the proton-pumping function of the enzyme.
Robust Immunity and Heterologous Protection against Influenza in Mice Elicited by a Novel Recombinant NP-M2e Fusion Protein Expressed in E. coli (2012)

The NM2e fusion protein expressed in E. coli was highly immunogenic in mice. Immunization with NM2e formulated with aluminum hydroxide gel protected mice against a lethal dose of a heterologous influenza virus. Vaccination with recombinant NM2e fusion protein is a promising strategy for the development of a universal influenza vaccine.
Single-stranded DNA-binding proteins (SSBs) -- sources and applications in molecular biology. (2005)

Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination, and repair in bacteria, archaea and eukarya. The SSBs share a common core ssDNA-binding domain with a conserved OB (oligonucleotide/oligosaccharide binding) fold. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. In recent years, there has been an increasing interest in SSBs because they are useful for molecular biology methods and for analytical purposes. In this review, we concentrate on recent advances in the discovery of new sources of SSBs as well as certain aspects of their applications in analytical sciences.
New type of matching layer for air-coupled ultrasonic transducers (2002)

This paper presents a new concept in the design of an impedance matching structure for air coupled ultrasonic transducers. A reflective layer structure is inserted between the transducer and propagation medium with a small air space. Adjusting the air space and the reflectivity of the inserted structure causes the transducer impedance to match with the impedance of the propagation medium. Two such structures were investigated as a reflector: a polymer thin film and a thick plate with many holes. Wave impedance theory was applied to these reflecting structures, and the impedance of a thin film layer at the incident surface was calculated using boundary conditions. Impedance of holed plate is calculated in a similar fashion. It was found that the calculated impedance of these structures approximately matched the impedance of the PZT air transducer (40 KHz). The acoustic pressure output was maximized by adjusting the position of the matching structure. A theoretical gain of up to 10 dB in the acoustic pressure was predicted under ideal circumstances, and the experimental observations showed a gain of 9.5 dB in the acoustic pressure for a 12 microm polyethylene film placed at a distance of approximately 0.1 mm from the transducer's surface. The increase was 9.8 dB for a polyvinylidene fluoride (PVDF) film and 9.7 dB for a 1.5 mm printed circuit board with many holes at a distance of approximately 25 microm from the transducer's surface.
Cost-effective wavelength selectable light sourceusingDFB fibre laser array (2000)

A cost-effective wavelength selectable light source comprising a distributed feedback (DFB) fibre laser array is proposed. A large number of wavelengths can be selected via optical space switches using only one shared pump laser. The structure is a good candidate for use as a wavelength selectable backup transmitter for wavelength division multiplexed (WDM) systems.
Diastolic Blood Pressure in Patients With Tibia Fractures Under Anaesthesia: Implications for the Diagnosis of Compartment Syndrome (2007)

There is a predictable response of DBP in patients with tibia fractures treated with intramedullary (IM) nailing under general anesthesia. The preoperative DBP is a good indicator of the postoperative DBP, and the intraoperative DBP is significantly lower (average 18 mm Hg; P < 0.05). The surgeon should recognize that intraoperative DeltaP may be lower than DeltaP once the patient is awakened in deciding whether to perform a fasciotomy or awaken the patient and perform serial examinations and or compartment pressure measurements. Intraoperative DeltaP may be spuriously low compared with that after the patient is awakened.
Hive: operating system fault containment for shared-memory multiprocessors (1997)

Reliability and scalability are major concerns when designing general-purpose operating systems for large-scale shared-memory multiprocessors. This dissertation describes Hive, an operating system with a novel kernel architecture that addresses these issues. Hive is structured as an internal distributed system of independent kernels called cells. This architecture improves reliability because a hardware or software error damages only one cell rather than the whole system. The architecture improves scalability because few kernel resources are shared by processes running on different cells. The Hive prototype is a complete implementation of UNIX SVR4 and is targeted to run on the Stanford FLASH multiprocessor. The research described in the dissertation makes three primary contributions: (1) it demonstrates that distributed system mechanisms can be used to provide fault containment inside a shared-memory multiprocessor; (2) it provides a specification for a set of hardware features, imple...
Polymers with Very Low Polydispersities from Atom Transfer Radical Polymerization (1996)

A radical polymerization process that yields well-defined polymers normally obtained only through anionic polymerizations is reported. Atom transfer radical polymerizations of styrene were conducted with several solubilizing ligands for the copper(I) halides: 4,4'-di-tert-butyl, 4,4'-di-n-heptyl, and 4,4'-di-(5-nonyl)-2,2'-dipyridyl. The resulting polymerizations have all of the characteristics of a living polymerization and displayed linear semilogarithmic kinetic plots, a linear correlation between the number-average molecular weight and the monomer conversion, and low polydispersities (ratio of the weight-average to number-average molecular weights of 1.04 to 1.05). Similar results were obtained for the polymerization of acrylates.
Irritable bowel syndrome immune hypothesis: the role of lymphocytes and mast cells (2010)

The heterogeneity of diagnostic criteria and experimentation methods could account for some of the differences in the results found in the selected research. There are indications that give reason to believe these patients have "low-grade intestinal inflammation", and the increase in T-lymphocytes and mast cells has been associated with disorders found in IBS such as the communication between the intestine and the nervous system, the increase in intestinal permeability and changes in the microbiota.
Driving intention recognition and behaviour prediction based on a double-layer hidden Markov model (2012)

We propose a model structure with a double-layer hidden Markov model (HMM) to recognise driving intention and predict driving behaviour. The upper-layer multi-dimensional discrete HMM (MDHMM) in the double-layer HMM represents driving intention in a combined working case, constructed according to the driving behaviours in certain single working cases in the lower-layer multi-dimensional Gaussian HMM (MGHMM). The driving behaviours are recognised by manoeuvring the signals of the driver and vehicle state information, and the recognised results are sent to the upper-layer HMM to recognise driving intentions. Also, driving behaviours in the near future are predicted using the likelihood-maximum method. A real-time driving simulator test on the combined working cases showed that the double-layer HMM can recognise driving intention and predict driving behaviour accurately and efficiently. As a result, the model provides the basis for pre-warning and intervention of danger and improving comfort performance.
The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme (1995)

L-21 ScaI ribozyme is a linear form of the self-splicing intron from the precursor of the Tetrahymena thermophila LSU intron. The time scales for tertiary folding of L-21 ScaI were investigated in two ways after bringing it from a partially denatured state at 60 degrees C and 1 mM Mg2+ to a renatured state of 15 degrees C and 10 mM Mg2+. First, formation of a catalytically active structure was monitored by measuring the kinetics of the reaction: p*CUCUA3 + G<==>p*CUCU + GA3. This reaction mimics the first step of splicing. After 1 min of folding time, the catalytic rate is roughly 10% of the rate attained after 8 h of folding. This indicates that much of the structure refolds quickly. Also, at least two time scales of folding are observed, separated by a lag time of about 30 min. To define the regions folding on various time scales, all the guanosines of L-21 ScaI were probed with kethoxal at 15 degrees C while folding was in progress. Based on folding time scales, the guanosines can be placed into at least four classes. These are guanosines that (1) are already protected at 60 degrees C in 1 mM Mg2+ or which fold immediately, (2) fold during the lag time, (3) continue to fold after 1 h, and (4) never fold. These results give insight into the folding pathway of a group I ribozyme at nucleotide resolution. This provides useful information on the regions whose foldings are important for catalytic function of the ribozyme. The method may also provide a general way to suggest regions of an RNA that may interact with each other to form tertiary structure.
Role of intrastructural/intermolecular help in immunization with peptide-phospholipid complexes (1991)

The design of effective subunit vaccines requires the inclusion of both B and T cell epitopes. The best mechanism for including both types of epitopes within an Ag is dependent upon how the Ag is processed by the APC for presentation to a responsive Th cell. If it is more efficient to process a single molecule for both helper and primary epitopes, than covalent linkage of B cells and T cell epitopes for intramolecular presentation of help would be recommended. If however, separate peptides containing either B or Th cell epitopes could be included within a single complex for the elicitation of intermolecular/intrastructural help, more antigenically diverse structures could be designed. This paper reports that it is possible to generate intermolecular/intrastructural help within an antigenic peptide-phospholipid (PL) complex. These peptide-PL complexes use well defined epitopes from Plasmodium falciparum as Ag. In addition to generating intrastructural help, we have shown that the Ir to these peptide-PL complexes is controlled by Ir genes and is similar to the Ir to the circumsporozoite protein of this pathogen.
MPEG-2 compliant trick play over a digital interface (2003)

With the introduction of disc-based digital video recorders, consumers expect similar trick play modes to those found on analog tape-based systems. When the digital video recorder plays back over a digital interface it must produce trick play streams that comply with the format for the normal play streams. In this paper we propose a low complexity algorithm to generate trick play streams compliant with the MPEG-2 standard.
Biodegradable Polymer Composite Grafts Promote the Survival and Differentiation of Retinal Progenitor Cells (2005)

Retinal progenitor cells (RPCs) are multipotent central nervous system precursors that give rise to all of the cell types of the retina during development. Several groups have reported that mammalian RPCs can be isolated and expanded in culture and can differentiate into retinal neurons upon grafting to the mature, diseased eye. However, cell delivery and survival remain formidable obstacles to application of RPCs in a clinical setting. Because biodegradable polymer/progenitor constructs have been shown to be capable of tissue generation in other compartments, we evaluated the survival, migration, and differentiation of RPCs delivered on PLLA/PLGA polymer substrates to the mouse subretinal space and compared these results to conventional injections of RPCs. Polymer composite grafts resulted in a near 10-fold increase in the number of surviving cells after 4 weeks, with a 16-fold increase in cell delivery. Grafted RPCs migrated into the host retina and expressed the mature markers neurofilament-200, glial fibrillary acidic protein, protein kinase C-alpha, recoverin, and rhodopsin. We conclude that biodegradable polymer/progenitor cell composite grafts provide an effective means of increasing progenitor cell survival and overall yield when transplanting to sites within the central nervous system such as the retina.
Generation of Enantiomerically Enriched Lithium Indenides by Means of (–)‐Sparteine: Structure, Stereoselective Substitution, and Solvent Effects (1995)

The thermodynamically controlled equilibration of the configurationally labile diastereomeric lithium 1-alkylindenide/(–)-sparteine complexes in diethyl ether/hexane combined with the crystallization of the diastereomer shown (1; R = Me, nBu) results in a stereoselective addition of these complexes to carbonyl compounds with enantiofacial differentiation at the indenide moiety. In THF/hexane, however, the solvent displaces the chiral ligand and leads to complete racemization of the products.
Activation of mammalian Chk1 during DNA replication arrest (2001)

Checkpoints maintain order and fidelity in the cell cycle by blocking late-occurring events when earlier events are improperly executed. Here we describe evidence for the participation of Chk1 in an intra-S phase checkpoint in mammalian cells. We show that both Chk1 and Chk2 are phosphorylated and activated in a caffeine-sensitive signaling pathway during S phase, but only in response to replication blocks, not during normal S phase progression. Replication block-induced activation of Chk1 and Chk2 occurs normally in ataxia telangiectasia (AT) cells, which are deficient in the S phase response to ionizing radiation (IR). Resumption of synthesis after removal of replication blocks correlates with the inactivation of Chk1 but not Chk2. Using a selective small molecule inhibitor, cells lacking Chk1 function show a progressive change in the global pattern of replication origin firing in the absence of any DNA replication. Thus, Chk1 is apparently necessary for an intra-S phase checkpoint, ensuring that activation of late replication origins is blocked and arrested replication fork integrity is maintained when DNA synthesis is inhibited.
TSC-22 contributes to hematopoietic precursor cell proliferation and repopulation and is epigenetically silenced in large granular lymphocyte leukemia (2009)

Aberrant methylation of tumor suppressor genes can lead to their silencing in many cancers. TSC-22 is a gene silenced in several solid tumors, but its function and the mechanism(s) responsible for its silencing are largely unknown. Here we demonstrate that the TSC-22 promoter is methylated in primary mouse T or natural killer (NK) large granular lymphocyte (LGL) leukemia and this is associated with down-regulation or silencing of TSC-22 expression. The TSC-22 deregulation was reversed in vivo by a 5-aza-2'-deoxycytidine therapy of T or NK LGL leukemia, which significantly increased survival of the mice bearing this disease. Ectopic expression of TSC-22 in mouse leukemia or lymphoma cell lines resulted in delayed in vivo tumor formation. Targeted disruption of TSC-22 in wild-type mice enhanced proliferation and in vivo repopulation efficiency of hematopoietic precursor cells (HPCs). Collectively, our data suggest that TSC-22 normally contributes to the regulation of HPC function and is a putative tumor suppressor gene that is hypermethylated and silenced in T or NK LGL leukemia.
Ascertaining effects of nanoscale polymeric interfaces on competitive protein adsorption at the individual protein level (2016)

With the recent development of biomaterials and biodevices with reduced dimensionality, it is critical to comprehend protein adhesion processes to nanoscale solid surfaces, especially those occurring in a competitive adsorption environment. Complex sequences of adhesion events in competitive adsorption involving multicomponent protein systems have been extensively investigated, but our understanding is still limited primarily to macroscopic adhesion onto chemically simple surfaces. We examine the competitive adsorption behavior from a binary protein mixture containing bovine serum albumin and fibrinogen at the single protein level. We subsequently evaluate a series of adsorption and displacement processes occurring on both the macroscopic homopolymer and nanoscopic diblock copolymer surfaces, while systematically varying the protein concentration and incubation time. We identify the similarities and dissimilarities in competitive protein adsorption behavior between the two polymeric surfaces, the former presenting chemical uniformity at macroscale versus the latter exhibiting periodic nanointerfaces of chemically alternating polymeric segments. We then present our novel experimental finding of a large increase in the nanointerface-engaged residence time of the initially bound proteins and further explain the origin of this phenomenon manifested on nanoscale diblock copolymer surfaces. The outcomes of this study may provide timely insight into nanoscale competitive protein adsorption that is much needed in designing bioimplant and tissue engineering materials. In addition, the fundamental understanding gained from this study can be beneficial for the development of highly miniaturized biodevices and biomaterials fabricated by using nanoscale polymeric materials and interfaces.
Immigration and Evangelism in the British Union of Seventh-day Adventists (2011)

Immigration and its influence upon host nations present many vexing questions with both positive and problematic consequences. This is applicable to the immigrants as well as the host population. It is a fitting subject for a detailed and objective analysis of how it has worked out in the British Isles and Ireland in the past fifty years. This period has seen a totally indigenous White church transformed into an almost wholly immigrant church. In the mid-1950s the British Union Conference membership was approximately 7,500 of which only a handful were non-indigenous. Incidentally, the worldwide membership of the church which also reached its one million mark in the mid-1950s was also largely composed of White members. The majority of these lived in the United States. Today, the Adventist Church worldwide and the British Church is mainly non-White. This development is a source of perplexity and joy to church leaders and members for a variety of reasons. Not the least of these is the lack of effective evangelism in the Western world. What follows relates to the situation of the church in the United Kingdom. The time provided to write this article did not allow for extended research. Nevertheless the following is factually relevant to the present time
Pt-coated InN nanorods for selective detection of hydrogen at room temperature (2005)

Single crystal InN nanorods were successfully grown on c-Al2O3 by hydride-metalorganic vapor phase epitaxy. The measured resistance of bare InN nanorods does not change upon exposure to hydrogen ambient. The addition of sputter-deposited clusters of Pt onto the surface of the InN nanorods, however, produced a significant change in the measured room temperature resistance. The measured resistance changed systematically by 0.5%–12% as the ambient hydrogen concentration in N2 was varied between 10 and 250 ppm after 15 min exposure time. Importantly, a relatively low power consumption of ∼0.3mW was measured under these conditions. There was no response at room temperature to O2, N2O, or NH3 exposures.
E-cadherin regulates cell growth by modulating proliferation-dependent β -catenin transcriptional activity (2001)

β-Catenin is essential for E-cadherin–mediated cell adhesion in epithelial cells, but it also forms nuclear complexes with high mobility group transcription factors. Using a mouse mammary epithelial cell system, we have shown previously that conversion of epithelial cells to a fibroblastoid phenotype (epithelial-mesenchymal transition) involves downregulation of E-cadherin and upregulation of β-catenin transcriptional activity. Here, we demonstrate that transient expression of exogenous E-cadherin in both epithelial and fibroblastoid cells arrested cell growth or caused apoptosis, depending on the cellular E-cadherin levels. By expressing E-cadherin subdomains, we show that the growth-suppressive effect of E-cadherin required the presence of its cytoplasmic β-catenin interaction domain and/or correlated strictly with the ability to negatively interfere with β-catenin transcriptional activity. Furthermore, coexpression of β-catenin or lymphoid enhancer binding factor-1 or T cell factor 3 with E-cadherin rescued β-catenin transcriptional activity and counteracted E-cadherin–mediated cell cycle arrest. Stable expression of E-cadherin in fibroblastoid cells decreased β-catenin activity and reduced cell growth. Since proliferating cells had a higher β-catenin activity than G1 phase–arrested or contact-inhibited cells, we conclude that β-catenin transcriptional activity is essential for cell proliferation and can be controlled by E-cadherin in a cell adhesion-independent manner.