gebhart/patrepeval huggingface dataset:
Sequence comparison of new prokaryotic and mitochondrial members of the polypeptide chain release factor family predicts a five-domain model for release factor structure (1992)

We have recently reported the cloning and sequencing of the gene for the mitochondrial release factor mRF-1. mRF-1 displays high sequence similarity to the bacterial release factors RF-1 and RF-2. A database search for proteins resembling these three factors revealed high similarities to two amino acid sequences deduced from unassigned genomic reading frames in Escherichia coli and Bacillus subtilis. The amino acid sequence derived from the Bacillus reading frame is 47% identical to E.coli and Salmonella typhimurium RF-2, strongly suggesting that it represents B.subtilis RF-2. Our comparison suggests that the expression of the B.subtilis gene is, like that of the E.coli and S. typhimurium RF-2 genes, autoregulated by a stop codon dependent +1 frameshift. A comparison of prokaryotic and mitochondrial release factor sequences, including the putative B.subtilis RF-2, leads us to propose a five-domain model for release factor structure. Possible functions of the various domains are discussed.
Phase Behavior and Hydration of Silk Fibroin (2004)

The osmotic stress method was applied to study the thermodynamics of supramolecular self-assembly phenomena in crystallizable segments of Bombyx mori silkworm silk fibroin. By controlling compositions and phases of silk fibroin solution, the method provided a means for the direct investigation of microscopic and thermodynamic details of these intermolecular interactions in aqueous media. It is apparent that as osmotic pressure increases, silk fibroin molecules are crowded together to form silk I structure and then with further increase in osmotic pressure become an antiparallel beta-sheet structure, silk II. A partial ternary phase diagram of water-silk fibroin-LiBr was constructed based on the results. The results provide quantitative evidence that the silk I structure must contain water of hydration. The enhanced control over structure and phase behavior using osmotic stress, as embodied in the phase diagram, could potentially be utilized to design a new route for water-based wet spinning of regenerated silk fibroin.
Beyond 2D for Brain-Computer interfaces: Two 3D extensions of the P300-Speller (2014)

This paper, investigates the use of a 3D setting for Brain-Computer Interface (BCI) by implementing the 3D interface for the P300-Speller device. The 3D configurations were implemented using two different approaches which are called Natural 3D and Parallel 2D. The theoretical analyses concerning these two approaches are provided considering the modifications in speed, accuracy, and capacity. The experimental results on subjects who tested the 3D interfaces are then provided to validate the theoretical analyses.
Origin of repulsive force and structure/dynamics of interfacial water in OEG–protein interactions: a molecular simulation study (2008)

Molecular simulations were performed to investigate the origin of the strong repulsive force acting on a protein as the protein approaches an oligo (ethylene glycol) self-assembled monolayer (OEG-SAM) surface. Since the repulsive force is mainly generated from water molecules, the force from the water molecules near the surface was calculated layer by layer to further identify the molecular origin of the repulsive force. Results show that the strong repulsive force acting on the protein near the OEG-SAM surface is dominantly generated by the interfacial water molecules located between the OEG-SAM surface and lysozyme. A hydroxyl-terminated SAM (OH-SAM) surface was used for comparison. No significant repulsive force was observed from the water molecules between the protein and OH-SAM surface. Further studies show that the dipole distribution of the interfacial water molecules is significantly affected by the OEG-SAM surface, as opposed to the negligible impact from the OH-SAM surface. The interfacial water molecules above the OEG-SAM surface stay longer and reorient more slowly than those above the OH-SAM surface. These results from this work support the hypothesis that the OEG-SAM surface interacts strongly with interfacial water molecules and creates a stable hydration layer that prevents proteins from adsorbing to the surface.
ATRP under Biologically Relevant Conditions: Grafting from a Protein (2011)

Atom transfer radical polymerization (ATRP) methods were developed in water-based media, to grow polymers from proteins under biologically relevant conditions. These conditions gave good control over the resulting polymers, while still preserving the protein's native structure. Several reaction parameters, such as ligand structure, halide species, and initiation mode were optimized in water and PBS buffer to yield well-defined polymers grown from bovine serum albumin (BSA), functionalized with cleavable ATRP initiators (I). The CuCl complex with ligand 2,2'-bipyridyne (bpy) provides the best conditions for the polymerization of oligo(ethylene oxide) methacrylate (OEOMA) in water at 30 °C under normal ATRP conditions (I/CuCl/CuCl<sub>2</sub>/bpy = 1/1/9/22), while the CuBr/bpy complex gave better performance in PBS. Activators generated by electron transfer (AGET) ATRP gave well-controlled polymerization of OEOMA at 30 °C with the ligand tris(2-pyridylmethyl)amine (TPMA), (I/CuBr<sub>2</sub>/TPMA = 1/10/11). The AGET ATRP reactions required slow feeding of a very small amount of ascorbic acid into the aqueous reaction medium or buffer. The reaction conditions developed were used to create a smart, thermoresponsive, protein-polymer hybrid.
One-step labelling of oligonucleotides with fluoresceine during automated synthesis (1990)

One-step labelling of oligonucleotides with fluoresceine during automated synthesis Get access F. Suhubert, F. Suhubert Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Ahlert, K. Ahlert Search for other works by this author on: Oxford Academic PubMed Google Scholar D. Cech, D. Cech 1Department of Chemistry, humboldt UniversityInvalidenstrasse 42, Berlin 1040, GDR, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Rosenthal A. Rosenthal 2MRC Molecular Genetics UnitHills Road, Cambridge CB2 2QH, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 11, 11 June 1990, Page 3427, https://doi.org/10.1093/nar/18.11.3427 Published: 11 June 1990 Article history Received: 30 March 1990 Published: 11 June 1990
Role of progenitor endothelial cells in cardiovascular disease and upcoming therapies (2007)

The field of cell-based transplantation has expanded considerably and is poised to become an established cardiovascular therapy in the near future. In this review, we will focus on endothelial progenitor cells (EPCs), which are immature cells capable of differentiating into mature endothelial cells. EPCs share many surface marker antigens such as CD34, AC133, Flk-1, etc. with hematopoietic stem cells (HSCs) and the major source of EPCs as well as HSCs is the bone marrow (BM). BM-derived EPCs are mobilized into peripheral blood and recruited to the foci of pathophysiological neovascularization and reendothelialization, thereby contributing to vascular regeneration. Severe EPC dysfunction is an indicator of poor prognosis and severe endothelial dysfunction. Indeed, number of circulating EPCs and their migratory activity are reduced in patients with diabetes, coronary artery disease (CAD), or subjects with multiple coronary risk factors. Effective neovascularization induced by EPC transplantation for hindlimb, myocardial, and cerebral ischemia has been demonstrated in many preclinical studies, and early clinical trials of EPC transplantation in chronic and acute CAD indicate safety and feasibility of myocardial cell-based therapies. For therapeutic reendothelialization in patients undergoing percutaneous coronary intervention, CD34 antibody-coated stents have been used clinically to capture circulating EPCs at the injury sites and enhance reendothelialization and safety of stents. Further development in cell processing technology for efficient isolation, expansion, mobilization, recruitment, and transplantation of EPCs into target tissues are underway and expected to be tested in clinical trials in the near future.
Homophilic PECAM-1(CD31) interactions prevent endothelial cell apoptosis but do not support cell spreading or migration (1999)

PECAM-1 (CD31) is a highly abundant cell surface glycoprotein expressed on haemopoietic and endothelial cells. As well as mediating homophilic (PECAM-1/PECAM-1) adhesion, PECAM-1 can also bind the integrin alphavbeta3. Both PECAM-1 and alphavbeta3 have been shown to have roles in regulating angiogenesis, endothelial tube formation and in the case of alphavbeta3, endothelial cell apoptosis. In this study we show that despite being expressed at equivalent levels, endothelial alphavbeta3 is not a ligand for PECAM-1. Rather, PECAM-1 supports homophilic binding on HUVEC with similar characteristics to those we have previously reported for leukocytes and becomes tyrosine phosphorylated after homophilic PECAM-1 and integrin/fibronectin engagement. Immunoprecipitation studies show that in addition to SHP-2, tyrosine phosphorylated PECAM-1 can interact with at least four other phosphoproteins in pervanadate stimulated HUVEC. While PECAM-1/PECAM-1 interactions support robust endothelial cell adhesion, they do not support cell spreading or migration. In addition PECAM-1 homophilic adhesion rescues HUVEC from serum deprivation-induced apoptosis. Taken together our results indicate that PECAM-1 homophilic interactions play an important role in interendothelial cell adhesion, survival and signalling.
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 (2020)

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious coronavirus disease 2019 (COVID-19) epidemic. Here, we present cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B<sup>0</sup>AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 angstroms at the ACE2-RBD interface. The ACE2-B<sup>0</sup>AT1 complex is assembled as a dimer of heterodimers, with the collectrin-like domain of ACE2 mediating homodimerization. The RBD is recognized by the extracellular peptidase domain of ACE2 mainly through polar residues. These findings provide important insights into the molecular basis for coronavirus recognition and infection.
Paroxysmal Atrial Fibrillation Triggered By A Monomorphic Ventricular Couplet In A Patient With Acute Coronary Syndrome (2012)

Atrial fibrillation is a common arrhythmia in patients suffering from acute myocardial infarction, however its pathophysiological mechanisms are not fully understood. We describe the unusual case of a 76-year old woman admitted for non-ST-segment elevation myocardial infarction, who developed multiple episodes of paroxysmal atrial fibrillation triggered by monomorphic ventricular couplets. Beta-blocking and amiodarone therapy resulted efficacious in preventing arrhythmic recurrences. We then discuss the possible arrhythmogenic mechanisms, with special emphasis on the unique electrophysiological, hemodynamic, cellular and anatomical milieu created by acute myocardial ischemia.
Internal Combustion Engine in Theory and Practice (1985)

This revised edition of Taylor's classic work on the internal-combustion engine incorporates changes and additions in engine design and control that have been brought on by the world petroleum crisis, the subsequent emphasis on fuel economy, and the legal restraints on air pollution. The fundamentals and the topical organization, however, remain the same. The analytic rather than merely descriptive treatment of actual engine cycles, the exhaustive studies of air capacity, heat flow, friction, and the effects of cylinder size, and the emphasis on application have been preserved. These are the basic qualities that have made Taylor's work indispensable to more than one generation of engineers and designers of internal-combustion engines, as well as to teachers and graduate students in the fields of power, internal-combustion engineering, and general machine design.
Platelet-derived growth factor-A and its receptor are expressed in separate, but adjacent cell layers of the mouse embryo (1992)

The localized developmental expression of murine platelet-derived growth factor A (PDGF-A) was compared to that of its receptor (Pdgfra). Our in situ hybridization study included germ layers of primitive streak embryos, early axial structures (dermatome, myotome, sclerotome, floor plate), the skin and some of its derivatives (hair and mammary gland), the developing forelimb, the branchial arches and various sense organs (otic vesicle, olfactory epithelium and the eye). We report that PDGF-A and Pdgfra are expressed in separate, but adjacent cell layers in these structures and that in most, the ligand is expressed in the epithelium, whereas the receptor in the mesenchyme. This localization corresponds to classical experimental evidence for developmental interactions across cell layers. We suggest that the spatio-temporal regulation of PDGF-A and Pdgfra, and other related systems, represents one model for the spatial regulation of receptor-ligand interactions.
Alleviation of jet lag by melatonin: preliminary results of controlled double blind trial. (1986)

Alleviation of jet lag by melatonin: preliminary results of controlled double blind trial Jet lag is an ill defined phenomenon resulting from rapid flight across several time zones.'It is considered to be due to desynchronisation of circadian rhythms, such as the sleep-wake cycle, with local time and to lack of sleep.' A means of rapidly resynchronising body rhythms to local time would benefit people who suffer badly from jet lag.Various remedies for alleviating jet lag have been proposed: manipulation of dietary intake and, more recently, appropriate exposure to'bright light have been used, though both are time consuming.2 3We previously suggested that melatonin, a methoxyindole secreted by the pineal gland, might be simpler and more effective in treating jet lag.4In view of its resynchronising properties in animals,5 its ability to transduce light-dark information, its hypnotic effects in man, and its low toxicity we examined whether it helped people adapt to new time zones.
Combinatorial Sequencing-by-Hybridization: Analysis of the NF1 Gene (2006)

Neurofibromatosis type 1 (NF1), one of the most common autosomal dominant disorders, is caused by mutations in the NF1 gene. A variety of methods are currently used in clinical settings to define disease-causing mutations. We describe microarray-based combinatorial sequencing-by-hybridization (cSBH), which overcomes some disadvantages associated with other techniques. Sequence readout of 2 kb was achieved on a single slide, with detection of base substitutions, insertions and small deletions. In addition, cSBH analysis of the entire NF1 gene demonstrates reproducibility, efficiency and reduced time; therefore, representing an alternative to extensive DNA sequence characterization.
Layout and Thermal Analysis of PowerDevices Using a PC/XC (1990)

Thermal analysis during the design process is an essential step towards the achievement of high reliability in modern high density hybrid and integrated circuits. Thermal analysis is also essential for modern, high density PCBs. Traditionally, a solution of the thermal problem is obtained by either the method of finite differences or the method of finite elements. Both methods, however, require a fine 3‐D partition of the substrate, leading to large systems of linear equations the solution of which demands substantial computing power provided by number crunching machines and/or powerful computer work‐stations. The widespread use of personal computers, however, dictates the development of new approaches to the thermal problems so that a design engineer can solve them in reasonable time with a PC. A new treatment of steady‐state thermal analysis combined with a layout editor is proposed in this paper, which makes use of the analytical solution for the temperature distribution in a single‐layer substrate with heat sources on the surface, and having an isothermal bottom surface. In this way the mathematical complexity of the problem is dramatically reduced allowing the thermal analysis of Multi Chip Modules (M.C.M.s) and complex hybrid circuits with the use of a PC/XT or compatible.
High concentrations of N-acetylaspartylglutamate (NAAG) selectively activate NMDA receptors on mouse spinal cord neurons in cell culture (1986)

We examined the membrane action of the endogenous dipeptide and putative neurotransmitter N-acetylaspartylglutamate (NAAG) on the excitatory amino acid receptors of cultured mouse spinal cord neurons using electrophysiological methods. Responses to NAAG (1 microM-5 mM) were compared to those elicited by N-methyl-D-aspartate (1 microM-1 mM) and L-glutamate (0.5-500 microM). Under voltage clamp, concentration-response curves of agonist-evoked currents demonstrated that NAAG was much less potent than either L-glutamate or N-methyl-D-aspartate (NMDA), so that inward currents could be evoked only at NAAG concentrations above 300 microM. Analysis of the dipeptide by high-pressure liquid chromatography showed no evidence of contamination by excitatory amino acids, suggesting that NAAG has an intrinsic, although weak, neuroexcitatory action on spinal neurons. Previous studies have shown that activation of NMDA receptors produces a voltage-dependent response. The current-voltage relationship of responses evoked by NAAG was also voltage-dependent. The peptide-activated conductance decreased with hyperpolarization in the presence of extracellular Mg2+, such that little inward current could be evoked at a membrane potential of -80 mV. In addition, responses to NAAG were completely antagonized by 250 microM DL-2-amino-5-phosphonovaleric acid, a specific NMDA-receptor antagonist. Application of NAAG in Mg2+-free medium resulted in an inward current with a large increase in membrane current noise. The spectral density function of this current noise could be fitted with a single Lorentzian with a decay time constant near 5 msec and a calculated single-channel conductance of 50-60 pS.(ABSTRACT TRUNCATED AT 250 WORDS)
Effects of distraction and compression on proliferation of growth plate chondrocytes: A study in rabbits (1993)

An external fixation device was applied across the distal femoral physis in 30 rabbits, and distraction or compression was performed for 3–21 days; either no operation or a sham-operation was performed on the contralateral side. Proliferating cells were labeled with 5-bromo-2'-d?oxyuridine, a thymidine analogue, and subsequently localized in decalcified histologic sections using a specific monoclonal antibody.The height of the proliferative and hypertrophic zones was increased after distraction; additionally, fracture-separation through the hypertrophic zone or at the junction of the physis and metaphysis was seen in 13 of the 15 specimens. Labeled cells were encountered only in the proliferative zone in all specimens except after early distraction, where labeled chondrocytes were seen close to the separation gap in the hypertrophic zone, too. Distraction had no effect on the number of labeled cells. A reduction in the height of the proliferative and hypertrophic zones occurred after compression, and the number of proliferating chondrocytes decreased.
Narcolepsy: current treatment options and future approaches (2008)

The management of narcolepsy is presently at a turning point. Three main avenues are considered in this review: 1) Two tendencies characterize the conventional treatment of narcolepsy. Modafinil has replaced methylphenidate and amphetamine as the first-line treatment of excessive daytime sleepiness (EDS) and sleep attacks, based on randomized, double blind, placebo-controlled clinical trials of modafinil, but on no direct comparison of modafinil versus traditional stimulants. For cataplexy, sleep paralysis, and hypnagogic hallucinations, new antidepressants tend to replace tricyclic antidepressants and selective serotonin reuptake inhibitors (SSRIs) in spite of a lack of randomized, double blind, placebo-controlled clinical trials of these compounds; 2) The conventional treatment of narcolepsy is now challenged by sodium oxybate, the sodium salt of gammahydroxybutyrate, based on a series of randomized, double-blind, placebo-controlled clinical trials and a long-term open label study. This treatment has a fairly good efficacy and is active on all symptoms of narcolepsy. Careful titration up to an adequate level is essential both to obtain positive results and avoid adverse effects; 3) A series of new treatments are currently being tested, either in animal models or in humans, They include novel stimulant and anticataplectic drugs, endocrine therapy, and, more attractively, totally new approaches based on the present state of knowledge of the pathophysiology of narcolepsy with cataplexy, hypocretine-based therapies, and immunotherapy.
Temperature dependence of polarized photoluminescence from nonpolar m-plane InGaN multiple quantum wells for blue laser diodes (2008)

Polarized photoluminescence (PL) spectra from nonpolar m-plane InGaN multiple quantum wells (MQWs) in blue laser diode wafers fabricated on m-plane GaN substrates were measured as a function of temperature. The polarization ratio (ρ) and the energy difference between the highest and the second highest valence bands estimated from the energy difference between PL peaks (ΔE) increased with increasing InN molar fraction x (or the estimated anisotropic compressive strain along the m-axis εyy) in the MQWs. The values of ρ at 300K and ΔE were 0.71 and 76meV for the case of 430nm PL peak (x=0.104, εyy=+0.75%) and 0.92 and 123meV for the case of 485nm PL peak (x=0.175, εyy=+1.26%). These results suggest that the preferred stripe direction is the c axis for nonpolar m-plane laser diodes in the region from violet to near green.
Interleukin-2-Dependent Mechanisms of Tolerance and Immunity In Vivo (2006)

IL-2 is a critical T cell growth factor in vitro, but predominantly mediates tolerance in vivo. IL-2 is mainly produced by CD4(+) Th cells, but the role of Th cell-derived IL-2 in vivo is controversial. We demonstrate that during immunity to a tumor/self-Ag, the predominant role of Th cell-derived IL-2 was to maintain IL-2Ralpha (CD25) on CD4(+) T regulatory cells (T(reg)), which resulted in their maintenance of the T(reg) cell lineage factor, Forkhead/winged helix transcription factor (Foxp3), and tolerance. However, in the absence of T(reg) cells, Th cell-derived IL-2 maintained effector T cells and caused autoimmunity. IL-2R signaling was indispensable for T(reg) cell homeostasis and efficient suppressor function in vivo, but, surprisingly, was not required for their generation, because IL-2(-/-) and CD25(-/-) mice both contained Foxp3(+) T cells in the periphery. IL-2R signaling was also important for CD8(+) T cell immunity, because CD25(-/-) tumor-reactive CD8(+) T cells failed to affect established tumors. Conversely, IL-2R signaling was not required for Th cell function. Lastly, administration of anti-IL-2 plus exogenous IL-15 to tumor-bearing mice enhanced the adoptive immunotherapy of cancer. Therefore, Th cell-derived IL-2 paradoxically controls both tolerance and immunity to a tumor/self-Ag in vivo.