gebhart/patrepeval huggingface dataset:
The HtrA/DegP family protease MamE is a bifunctional protein with roles in magnetosome protein localization and magnetite biomineralization (2011)

Magnetotactic bacteria contain nanometre-sized, membrane-bound organelles, called magnetosomes, which are tasked with the biomineralization of small crystals of the iron oxide magnetite allowing the organism to use geomagnetic field lines for navigation. A key player in this process is the HtrA/DegP family protease MamE. In its absence, Magnetospirillum magneticum str AMB-1 is able to form magnetosome membranes but not magnetite crystals, a defect previously linked to the mislocalization of magnetosome proteins. In this work we use a directed genetic approach to find that MamE, and another predicted magnetosome-associated protease, MamO, likely function as proteases in vivo. However, as opposed to the complete loss of mamE where no biomineralization is observed, the protease-deficient variant of this protein still supports the initiation and formation of small, 20 nm-sized crystals of magnetite, too small to hold a permanent magnetic dipole moment. This analysis also reveals that MamE is a bifunctional protein with a protease-independent role in magnetosome protein localization and a protease-dependent role in maturation of small magnetite crystals. Together, these results imply the existence of a previously unrecognized 'checkpoint' in biomineralization where MamE moderates the completion of magnetite formation and thus committal to magneto-aerotaxis as the organism's dominant mode of navigating the environment.
Nano-Mechanical Oscillator and Basic Dynamics: Part I (2021)

Abstract This discussion introduces the student to the reality, in quantum technology, that analysis of any problem necessarily begins with the Hamiltonian representing the system. The quantum Hamiltonian represents the total energy of the system, the sum of kinetic energy plus potential energy, written in canonical coordinates and conjugate momenta, and where these variables become time independent quantum operators. The nature of the potential energy for the nano-vibrator, following Hooke’s law, serves to localize the particle. The relevance of the nano-vibrator Hamiltonian—sometimes called the harmonic oscillator Hamiltonian—is perhaps one of the most important Hamiltonians in quantum systems. Not only can it be extended to cover things like phonons in solids, vibrations in molecules, and the behavior of bosons, but it is also the basis for leading to the concept of a photon, the quantum radiation field, and the quantum vacuum. This chapter provides the basic introduction for vibration of a particle or a nano-rod and looks at the wave-like behavior that emerges from the solution to the time independent Schrödinger equation. When we include the time evolution, we can observe dynamical behavior and begin to examine the meaning of quantum measurement.
Self-Regulating PTC Heating Systems: A New Approach for Electric Heating Appliances (1972)

Self-regulating ceramic heating systems that operate without conventional thermostatic controls are now being designed into heated appliances. The result is longer life, lower cost, and more streamlined appliance packaging. The development appropriately comes at a time when end of life safety is receiving increased attention, cost reductions in heater-thermostat systems are producing diminishing returns, and the volume of heated portable appliances for personal care and food warming is growing rapidly. The Semiconducting barium titanate heaters undergo a crystalline phase change and resultant resistivity increase in the vicinity of the ferro-electric curie temperature. This characteristic provides high initial power at which point the sharply increasing heater resistance reduces power to the required steady-state level. Positive temperature coefficient (PTC) barium titanate has been used since the 1950's for low voltage sensors, but was only made available for appliance heaters by the recent development of line voltage materials for a different segment of industry-color television. One third of all color sets now use 120-V PTC degaussing elements. The paper discusses the complex thermal design considerations involved in the development of a PTC heater for 10-200 W appliances and reviews the application of a PTC heater to a food warmer.
Regulation of the prolyl hydroxylase domain protein 2 (<i>phd2</i>/<i>egln-1</i>) gene: identification of a functional hypoxia-responsive element (2005)

The HIFs (hypoxia-inducible factors) are a family of heterodimeric transcription factors essential for the adaptation of cells to reduced oxygen supply. Three human PHDs (prolyl hydroxylase domain proteins, PHD1–PHD3) initiate oxygen-dependent degradation of HIF-α-subunits in normoxia. RNA interference directed against PHD2, but not PHD1 or PHD3, is sufficient to stabilize HIF-1α in normoxia. Therefore PHD2 is regarded as the main cellular oxygen sensor. PHD2 itself is up-regulated by hypoxia and may thus limit hypoxic signalling. By sequence analysis, we predicted a promoter approx. 3.5 kb 5′ of the translation start codon and a second promoter located in a CpG island immediately upstream of the coding sequence. A consensus HIF-1-binding site that is conserved in the murine phd2 gene was detected in the CpG island. By electrophoretic mobility-shift assay, we demonstrated binding of HIF-1 to the putative HIF-1-binding site. In luciferase reporter vectors, the isolated upstream promoter was inactive in all cell lines tested unless 200 bp were deleted at the 3′-end. The downstream promoter was active and induced by hypoxia. In reporter vectors containing both promoter sequences, luciferase activity was equal to vectors containing only the downstream promoter. In cells transfected with a vector containing both promoters, a single luciferase transcript was detectable. This transcript had the same length as transcripts from a vector containing the downstream promoter only. We conclude that the phd2 gene is transcribed exclusively from the downstream promoter that contains a functional hypoxia-responsive, cis-regulatory element. Our results establish that PHD2 is a direct HIF target gene.
Role of Insulin Receptor Substrates and Protein Kinase C-ζ in Vascular Permeability Factor/Vascular Endothelial Growth Factor Expression in Pancreatic Cancer Cells (2004)

Vascular permeability factor/vascular endothelial growth factor (VPF/VEGF), the critical molecule in tumor angiogenesis, is regulated by different stimuli, such as hypoxia and oncogenes, and also by growth factors. Previously we have shown that in AsPC-1 pancreatic adenocarcinoma cells, insulin-like growth factor receptor (IGF-IR) regulates VPF/VEGF expression. Insulin receptor substrate-1 and -2 (IRS-1 and IRS-2), two major downstream molecules of IGF-1R, are known to be important in the genesis of diabetes. In this study, we have defined a new role of IRS in angiogenesis. Both of the IRS proteins modulate VPF/VEGF expression in pancreatic cancer cells by different mechanistic pathways. The Sp1-dependent VPF/VEGF transcription is regulated mainly by IRS-2. Protein kinase C-zeta (PKC-zeta) plays a central role in VPF/VEGF expression and acts as a switching element. Furthermore, we have also demonstrated that the phosphatidylinositol 3-kinase pathway, but not the Ras pathway, is a downstream event of IRS proteins for VPF/VEGF expression in AsPC-1 cells. Interestingly, like renal cancer cells, in AsPC-1 cells PKC-zeta leads to direct Sp1-dependent VPF/VEGF transcription; in addition, it also promotes a negative feedback loop to IRS-2 that decreases the association of IRS-2/IGF-1R and IRS-2/p85. Taken together, our results show that in AsPC-1 pancreatic carcinoma cells, Sp1-dependent VPF/VEGF transcription is controlled by IGF-1R signaling through IRS-2 proteins and modulated by a negative feedback loop of PKC-zeta to IRS-2. Our data also suggest that IRS proteins, which are known to play crucial roles in IGF-1R signaling, are also important mediators for tumor angiogenesis.
NOTE ON A CLASS OF SOLUTIONS OF THE NAVIER-STOKES EQUATIONS REPRESENTING STEADY ROTATIONALLY-SYMMETRIC FLOW (1951)

This note describes one- and two-parameter families of solutions of steady rotationally-symmetric viscous flow. The solutions are such that the Navier-Stokes equations reduce to ordinary differential equations in a single position variable. The one-parameter family represents flow which is rigid-body rotation at infinity and over a plane through the origin; the solution given by von Kármán in 1921 is one member of this family. The two-parameter family represents flow which is rigid body rotation over each of two planes at a finite distance apart. The case of large Reynolds number is particularly interesting, since the two bounding planes are then separated by a region of rigid-body rotation and translation in which viscous effects are negligible.
Liver fibrosis (2008)

Liver damage leads to an inflammatory response and to the activation and proliferation of mesenchymal cell populations within the liver which remodel the extracellular matrix as part of an orchestrated wound-healing response. Chronic damage results in a progressive accumulation of scarring proteins (fibrosis) that, with increasing severity, alters tissue structure and function, leading to cirrhosis and liver failure. Efforts to modulate the fibrogenesis process have focused on understanding the biology of the heterogeneous liver fibroblast populations. The fibroblasts are derived from sources within and out with the liver. Fibroblasts expressing alpha-smooth muscle actin (myofibroblasts) may be derived from the transdifferentiation of quiescent hepatic stellate cells. Other fibroblasts emerge from the portal tracts within the liver. At least a proportion of these cells in diseased liver originate from the bone marrow. In addition, fibrogenic fibroblasts may also be generated through liver epithelial (hepatocyte and biliary epithelial cell)-mesenchymal transition. Whatever their origin, it is clear that fibrogenic fibroblast activity is sensitive to (and may be active in) the cytokine and chemokine profiles of liver-resident leucocytes such as macrophages. They may also be a component driving the regeneration of tissue. Understanding the complex intercellular interactions regulating liver fibrogenesis is of increasing importance in view of predicted increases in chronic liver disease and the current paucity of effective therapies.
High-level adaptive program optimization with ADAPT (2001)

Compile-time optimization is often limited by a lack of target machine and input data set knowledge. Without this information, compilers may be forced to make conservative assumptions to preserve correctness and to avoid performance degradation. In order to cope with this lack of information at compile-time, adaptive and dynamic systems can be used to perform optimization at runtime when complete knowledge of input and machine parameters is available. This paper presents a compiler-supported high-level adaptive optimization system. Users describe, in a domain specific language, optimizations performed by stand-alone optimization tools and backend compiler flags, as well as heuristics for applying these optimizations dynamically at runtime. The ADAPT compiler reads these descriptions and generates application-specific runtime systems to apply the heuristics. To facilitate the usage of existing tools and compilers, overheads are minimized by decoupling optimization from execution. Our system, ADAPT, supports a range of paradigms proposed recently, including dynamic compilation, parameterization and runtime sampling. We demonstrate our system by applying several optimization techniques to a suite of benchmarks on two target machines. ADAPT is shown to consistently outperform statically generated executables, improving performance by as much as 70%.
Kinematic Strategies for Upper Arm–Forearm Coordination in Three Dimensions (2000)

This study addressed the question of how the three-dimensional (3-D) control strategy for the upper arm depends on what the forearm is doing. Subjects were instructed to point a laser-attached in line with the upper arm-toward various visual targets, such that two-dimensional (2-D) pointing directions of the upper arm were held constant across different tasks. For each such task, subjects maintained one of several static upper arm-forearm configurations, i. e., each with a set elbow angle and forearm orientation. Upper arm, forearm, and eye orientations were measured with the use of 3-D search coils. The results confirmed that Donders' law (a behavioral restriction of 3-D orientation vectors to a 2-D "surface") does not hold across all pointing tasks, i.e., for a given pointing target, upper arm torsion varied widely. However, for any one static elbow configuration, torsional variance was considerably reduced and was independent of previous arm position, resulting in a thin, Donders-like surface of orientation vectors. More importantly, the shape of this surface (which describes upper arm torsion as a function of its 2-D pointing direction) depended on both elbow angle and forearm orientation. For pointing with the arm fully extended or with the elbow flexed in the horizontal plane, a Listing's-law-like strategy was observed, minimizing shoulder rotations to and from center at the cost of position-dependent tilts in the forearm. In contrast, when the arm was bent in the vertical plane, the surface of best fit showed a Fick-like twist that increased continuously as a function of static elbow flexion, thereby reducing position-dependent tilts of the forearm with respect to gravity. In each case, the torsional variance from these surfaces remained constant, suggesting that Donders' law was obeyed equally well for each task condition. Further experiments established that these kinematic rules were independent of gaze direction and eye orientation, suggesting that Donders' law of the arm does not coordinate with Listing's law for the eye. These results revive the idea that Donders' law is an important governing principle for the control of arm movements but also suggest that its various forms may only be limited manifestations of a more general set of context-dependent kinematic rules. We propose that these rules are implemented by neural velocity commands arising as a function of initial arm orientation and desired pointing direction, calculated such that the torsional orientation of the upper arm is implicitly coordinated with desired forearm posture.
Radial Symmetry Detection and Shape Characterization with the Multiscale Area Projection Transform (2012)

Abstract We present a novel method to characterize 3D surfaces through the computation of a function called (multiscale) area projection transform, measuring the likelihood of points in the 3D space to be center of radial symmetry at selected scales (radii). The function is derived through a simple geometric framework based on parallel surfaces and can be easily computed on triangulated meshes. It measures locally the area of the surface well approximated by a sphere of radius R centered in the point and can be normalized in order to obtain a scale invariant radial symmetry enhancement transform. This transform can therefore be used to detect and characterize salient regions like approximately spherical and approximately cylindrical surface parts and, being robust against holes and missing parts, it is suitable for real world applications e.g. anatomical features detection. Furthermore, its histograms can be effectively used to build a global shape descriptor that provides very good results in shape retrieval experiments.
Associations of dietary calcium intake and calcium supplementation with myocardial infarction and stroke risk and overall cardiovascular mortality in the Heidelberg cohort of the European Prospective Investigation into Cancer and Nutrition study (EPIC-Heidelberg) (2012)

Increasing calcium intake from diet might not confer significant cardiovascular benefits, while calcium supplements, which might raise MI risk, should be taken with caution.
Differential Susceptibility of RAE-1 Isoforms to Mouse Cytomegalovirus (2009)

The NKG2D receptor is one of the most potent activating natural killer cell receptors involved in antiviral responses. The mouse NKG2D ligands MULT-1, RAE-1, and H60 are regulated by murine cytomegalovirus (MCMV) proteins m145, m152, and m155, respectively. In addition, the m138 protein interferes with the expression of both MULT-1 and H60. We show here that one of five RAE-1 isoforms, RAE-1delta, is resistant to downregulation by MCMV and that this escape has functional importance in vivo. Although m152 retained newly synthesized RAE-1delta and RAE-1gamma in the endoplasmic reticulum, no viral regulator was able to affect the mature RAE-1delta form which remains expressed on the surfaces of infected cells. This differential susceptibility to downregulation by MCMV is not a consequence of faster maturation of RAE-1delta compared to RAE-1gamma but rather an intrinsic property of the mature surface-resident protein. This difference can be attributed to the absence of a PLWY motif from RAE-1delta. Altogether, these findings provide evidence for a novel mechanism of host escape from viral immunoevasion of NKG2D-dependent control.
Guaranteed bounds on the performance cost of a fast real-time suboptimal constrained MPC controller (2004)

A fundamental limitation on the implementation of constrained model predictive control (MPC) is the excessive computational time required to evaluate the constrained controls at each sample interval. Prior results show that premature termination of algorithms which solve the quadratic programming (QP) subproblem associated with the computation of the MPC controller at each sampling interval, can be used to decrease the necessary CPU time, with favorable results, but there is no guarantee on the performance of such ad hoc methods. In this paper, a new supervisory algorithm is introduced in order to guarantee bounds on the performance of any non-feasible algorithm, which on solving the QP subproblem is terminated before convergence has occurred. This supervisory algorithm allows for real-time control of a large class of systems using a suboptimal constrained MPC controller with guaranteed bounds on its performance. An example is included to illustrate how this method performs under the limitations of real-time control.
Embryonic Stem Cells (2005)

Stem cells, which have a great capacity for self-renewal and can differentiate into at least one committed cell type, exist in embryonic and adult organisms of many phyla. Although stem cells of various types from mice and other lower organisms have been studied for many years, it was not until the derivation of stem cell lines from human embryos in 1998 (1,2) that the idea of stem cell-based therapies became widespread for the treatment of a range of disorders from Alzheimer’s disease to type I diabetes. Efforts to generate insulin-producing islet cells from murine and human embryonic stem (ES) cells followed the establishment of these ES cell lines. In this review we will discuss the derivation procedures and growth characteristics of ES cell lines from these two species and the status of research to promote their differentiation into cells of the endocrine pancreas lineage.
Oxetanes. IX. Structural and Solvent Effects in the Reaction of γ-Bromoalcohols with Base<sup>1,2</sup> (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxetanes. IX. Structural and Solvent Effects in the Reaction of γ-Bromoalcohols with Base1,2SCOTT SEARLES Jr., RICHARD G. NICKERSON, and WILLIAM K. WITSIEPECite this: J. Org. Chem. 1959, 24, 12, 1839–1844Publication Date (Print):December 1, 1959Publication History Published online1 May 2002Published inissue 1 December 1959https://pubs.acs.org/doi/10.1021/jo01094a001https://doi.org/10.1021/jo01094a001research-articleACS PublicationsRequest reuse permissionsArticle Views609Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Organic Nonvolatile Memory Devices Based on Ferroelectricity (2009)

A memory functionality is a prerequisite for many applications of electronic devices. Organic nonvolatile memory devices based on ferroelectricity are a promising approach toward the development of a low-cost memory technology. In this Review Article we discuss the latest developments in this area with a focus on three of the most important device concepts: ferroelectric capacitors, field-effect transistors, and diodes. Integration of these devices into larger memory arrays is also discussed.
[Three cases of Stenotrophomonas maltophilia pneumonia]. (2003)

We encountered 3 cases of pneumonia caused by Stenotrophomonas maltophilia between January and June 2001. S. maltophilia is resistant to broad-spectrum antibiotics including carbapenem. Reported studies indicate that excessive use of broad-spectrum antibiotics may induce resistance in this organism. However, our data showed that there was no clear correlation between the amounts of carbapenems used in our hospital and the isolation of the organism. If broad-spectrum antibiotics are ineffective or even actually worsen a case of pneumonia, S. maltophilia may be the sole causative organism, and a potent double- (or triple-) combination therapy consisting of minocyclin and one or two other potent antimicrobial agents should be considered.