gebhart/patrepeval huggingface dataset:
Simulation of transmission electron microscope images of biological specimens (2011)

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated.
Cloning and sequencing of the beta-lactamase I gene of Bacillus cereus 5/B and its expression in Bacillus subtilis (1985)

The beta-lactamases of Bacillus cereus have attracted interest because they are secreted efficiently, because multiple enzymes are frequently present, and because their regulation has unusual features. beta-Lactamase I of strain 5/B is produced constitutively at a high level, and the exoenzyme appears to be several thousand daltons larger than the corresponding product of strain 569/H. We have cloned the gene for 5/B beta-lactamase I in Escherichia coli and B. subtilis and have sequenced the structural portion and the regulatory regions. The 5/B enzyme is produced at a low level in E. coli RR1(pRWY200) and remains cellbound. In B. subtilis it is formed in large amounts, and over 90% of it is released into the medium. There is a large degree of homology between the promoter and leader peptide regions of the 5/B and 569/H genes; both utilize UUG as the translation initiation codon (P. S. F. Mézes, R. W. Blacher, and J. O. Lampen, (J. Biol. Chem. 260:1218-1223, 1985). Although there are significant differences in the peptide segment where processing would be expected to occur, the NH2 terminus of the major 5/B product from B. subtilis BD170(pRWY215) is His-44, which is the same as the NH2 terminus of the major 569/H product from B. subtilis BD170(pRWM5).
Deposition and clinical efficacy of terbutaline sulphate from Turbuhaler, a new multi-dose powder inhaler (1989)

A radioaerosol technique has been developed in order to assess deposition patterns from a new metered dose powder inhaler (Turbuhaler, Astra Pharmaceuticals). The radionuclide Tc99m dissolved in chloroform was added to a spheronised formulation of micronised terbutaline sulphate and the chloroform was allowed to evaporate. Turbuhaler subsequently delivered 0.5 mg of treated drug per metered dose. In vitro tests with a multistage liquid impinger showed that the fractionation of the drug dose between different particle size bands was similar to the fractionation of radioactivity. In a group of ten asthmatic patients, a mean 14.2% (SEM 2.1) of the drug dose was deposited in the lungs, with 71.6% (3.0) of the dose in the oropharynx. Of the remainder, 13.7% (2.1) was deposited on the mouthpiece, and 0.5% (0.2) recovered from exhaled air. The radiolabel was present in both central and peripheral zones of the lungs. All patients bronchodilated; forced expiratory volume in one second (FEV1) increased from 1.40 (0.24) l to 1.77 (0.24) l (p less than 0.01) 20 min after inhalation. These results suggest that both the distribution of drug and the clinical effect of terbutaline sulphate delivered from Turbuhaler are similar to those from a pressurised metered dose inhaler (MDI).
Electromagnetic interference shielding of cellulose triacetate/multiwalled carbon nanotube composite films (2011)

Abstract Cellulose triacetate (CTA) and multiwalled carbon nanotube (MWNT) composite films were prepared by dispersing different weight percentages of MWNTs into a CTA solution. These composite blends were characterized by UV–vis spectroscopy (UV), and their surface mophology, thermal stability, and amended crystallinity were determined by atomic force microscopy (AFM), thermogravimetric analysis (TGA), and X‐ray diffraction (XRD), respectively. Measurements of the complex impedance of the composite samples were made in the form of films. Sheets prepared from conventional techniques were used to study microwave absorption in the microwave range of 2–12 GHz, and the effects of sample thickness on microwave absorption were investigated. The experimental results show that the electrical conductivity of composites increases with the increase in MWNT loading without a percolation threshold. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Robust Multiclass Signaling Overload Control (2006)

We propose multi-class signaling overload control algorithms, for telecommunication switches, that are robust against different input traffic patterns and system upgrades. In order to appropriately measure the system load when several classes of signaling traffic are present, we first introduce the concept of equivalent system load measure that converts the multiple system measures associated with different classes of traffic into a single measure with respect to a pre-defined base class. We use this measure to develop three multi-class overload detection and measurement algorithms. Next, we develop a new algorithm for partitioning the allowable equivalent system load across multiple traffic classes, using a strict priority scheme. Using simulations of call flows from mobile telecommunications standards, we compare different multi-class overload algorithms under a variety of overload conditions. Our simulation results indicate that our algorithm that measures system load using a combination of request acceptance rate and processor occupancy provides highly reactive and robust overload control. Last, for the purpose of making the overload control algorithms more robust, we propose a measurement-based simple regression technique to dynamically estimate key system parameters. We find that estimates derived in this manner converge rapidly to their true values.
What This Book Is All About (1985)

Considering the amount of technology that goes into making them, modern electronic components are fantastic value. A 4017 CMOS decade-counter I.C. costs about as much as a single portion of raw steak, and a lettuce changes hands for the price of a 115 W power transistor. High technology comes cheap!
Rh‐Catalyzed Annulation of <i>ortho</i>‐C−H Bonds of 2‐Arylimidazoles with 1,4,2‐Dioxazol‐5‐ones toward 5‐Arylimidazo[1,2‐<i>c</i>]quinazolines (2017)

Abstract A Rh‐catalyzed unique and direct approach for constructing a series of 5‐arylimidazo[1,2‐ c ]quinazolines in moderate to excellent yields from simple and readily available 2‐arylimidazoles and 3‐phenyl‐1,4,2‐dioxazol‐5‐ones was described. This procedure proceeds with sequential ortho ‐C−H bond amidation and cyclization, which represents a facile and straightforward pathway to access such frameworks. magnified image
Mobile data management: challenges of wireless and offline data access (2002)

Applications require access to database servers for many purposes. Mobile users, those who use their computing devices away from a traditional local area network, require access to data even when central database servers are unavailable. iAnywhere Solutions provides a number of solutions that address the challenges of offline and wireless data access. The article discusses those challenges and presents solutions.
Quantifying aptamer–protein binding via thermofluorimetric analysis (2015)

Effective aptamer-based protein assays require coupling to a quantitative reporter of aptamer-protein binding. Typically, this involves a direct optical or electrochemical readout of DNA hybridization or an amplification step coupled to the readout. However, method development is often hampered by the multiplicity of aptamer-target binding mechanisms, which can interfere with the hybridization step. As a simpler and more generalizable readout of aptamer-protein binding, we report that thermofluorimetric analysis (TFA) can be used to quantitatively assay protein levels. Sub-nanomolar detection (0.74 nM) of platelet-derived growth factor (PDGF) with its corresponding aptamer is shown as a test case. In the presence of various DNA intercalating dyes, protein-bound aptamers exhibit a change in fluorescence intensity compared to the intercalated, unbound aptamer. This allows thermal resolution of bound and unbound aptamers using fluorescence melting analysis (-dF/dT curves). Remarkably, the homogeneous optical method allows subtraction of autofluorescence in human serum, giving PDGF detection limits of 1.8 and 10.7 nM in serum diluted 1:7 and 1:3, respectively. We have thus demonstrated that bound and unbound aptamers can be thermally resolved in a homogeneous format using a simple qPCR instrument-even in human serum. The simplicity of this approach provides an important step toward a robust, generalizable readout of aptamer-protein binding.
Noncompliance With Congestive Heart Failure Therapy in the Elderly (1994)

A large proportion of patients who begin digoxin therapy end CHF therapy or consume substantially less medication than expected in the first year of therapy. Such high rates of cessation could represent an important impediment to effective CHF therapy.
Bronchial Casts in Children: A Proposed Classification Based on Nine Cases and a Review of the Literature (1997)

Bronchial casts are characterized by the formation of obstructive airway plugs that may be large enough to fill the branching pattern of an entire lung. The condition is rare but can occur at any age. Casts may be secondary to underlying diseases such as asthma and cystic fibrosis, but there are often no predisposing factors. There is no accepted classification system for bronchial casts; but only a confusion of descriptive terms such as mucoid impaction, fibrinous bronchitis, and pseudomembranous bronchitis. Based on a review of nine well-documented cases and the available literature, we have separated bronchial casts into two well-defined groups: Type 1 (inflammatory), consisting of casts composed mainly of fibrin with a dense eosinophilic inflammatory infiltrate; and Type 2 (acellular), consisting of casts composed mainly of mucin with little or no cellular infiltrate and occurring only in children with congenital cyanotic heart disease. Acute mortality was high in both groups. Survivors of Type 1 casts seem to be well controlled with inhaled steroids. Optimal therapy for patients with Type 2 casts is not clear; the prognosis probably depends on underlying cardiac status. We hope that this simple classification will provide a framework for further study of this obscure condition.
Cities: an environmental history (2014)

List of Figures and Tables Acknowledgements Introduction Chapter 1: Trading Village to Global Megalopolis: The Origins and Expansion of Cities Chapter 2: Communities Responding to Disasters and Threats: Vulnerable and Resiliant Cities Chapter 3: Foods, Goods, Materials and Ornaments: The Metabolism of Cities Chapter 4: Smoke, Fumes, Dust and Smog: Changing the Atmosphere of Cities Chapter 5: Water from the Hills, the Ground, the Sea and the Roof: Towards Integrated Water Resource Management in Cities Chapter 6: Sanitation, Sewage and Mountains of Trash: Wastewater and Garbage in Cities Chapter 7: Urban Sounds and Smells: The Noisy, Aromatic City Chapter 8: Cities and a Dynamic Earth: Urban Changes to the Land Surface and Responses to Geophysical Hazards Chapter 9: Urban Greenspaces: The Tamed and Wild Nature in Cities Chapter 10: Urban Sustainability: Cities for Future Generations Final Thoughs Notes Bibliography Index
Aircraft Interrogation Scheduling with ASTRO-DABS (1974)

In the ASTRO-DABS concept for surveillance and data link, aircraft are interrogated by one of three geostationary transmitter satellites, each covering 1/3 of the contiguous United States. Interrogation scheduling involves a roll call such that aircraft responses to receiving satellites do not overlap (garble). A simple approach is developed which utilizes range ordering of aircraft with respect to transmitter satellites, but is independent of receiver satellite locations and aircraft distribution. Bounds on roll-call duration are established, showing that interrogation of 80 000 aircraft requires between 4.0 and 6.4 seconds with the ASTRO-DABS transmission format. If aircraft distribution is regionally concentrated (i.e., clustered), the roll-call duration nears the lower bound, since fewer gaps between interrogations are needed to preclude garbling.
Application of mismatched filter theory to bandpass impulse response measurements (1993)

The Letter shows how a mismatched filter for the compression of a bandpass arbitrary length pseudorandom bit sequence (PRBS) may be generated. A comparison is made between the standard matched filter and the mismatched filter in terms of accuracy, dynamic range, noise gain, simplicity of implementation and flexibility to shape the probing pulse, when such filters are used for the determination of wideband bandpass impulse response measurements. This study was carried out in the context of mobile radio channel sounding.
The ras oncogene--an important regulatory element in lower eucaryotic organisms (1989)

The ras proto-oncogene in mammalian cells encodes a 21-kilodalton guanosine triphosphate (GTP)-binding protein. This gene is frequently activated in human cancer. As one approach toward understanding the mechanisms of cellular transformation by ras, the function of this gene in lower eucaryotic organisms has been studied. In the yeast Saccharomyces cerevisiae, the RAS gene products serve as essential function by regulating cyclic adenosine monophosphate metabolism. Stimulation of adenylyl cyclase is dependent not only on RAS protein complexed to GTP, but also on the CDC25 and IRA gene products, which appear to control the RAS GTP-guanosine diphosphate cycle. Although analysis of RAS biochemistry in S. cerevisiae has identified mechanisms central to RAS action, RAS regulation of adenylyl cyclase appears to be strictly limited to this particular organism. In Schizosaccharomyces pombe, Dictyostelium discoideum, and Drosophila melanogaster, ras-encoded proteins are not involved with regulation of adenylyl cyclase, similar to what is observed in mammalian cells. However, the ras gene product in these other lower eucaryotes is clearly required for appropriate responses to extracellular signals such as mating factors and chemoattractants and for normal growth and development of the organism. The identification of other GTP-binding proteins in S. cerevisiae with distinct yet essential functions underscores the fundamental importance of G-protein regulatory processes in normal cell physiology.
Friction and wear of plasma-deposited diamond films (1993)

Reciprocating sliding friction experiments in humid air and in dry nitrogen and unidirectional sliding friction experiments in ultrahigh vacuum were conducted with a natural diamond pin in contact with microwave-plasma-deposited diamond films. Diamond films with a surface roughness (R rms) ranging from 15 to 160 nm were produced by microwave-plasma-assisted chemical vapor deposition. In humid air and in dry nitrogen, abrasion occurred when the diamond pin made grooves in the surfaces of diamond films, and thus, the initial coefficients of friction increased with increasing initial surface roughness. The equilibrium coefficients of friction were independent of the initial surface roughness of the diamond films. In vacuum the friction for diamond films contacting a diamond pin arose primarily from adhesion between the sliding surfaces. In these cases, the initial and equilibrium coefficients of friction were independent of the initial surface roughness of the diamond films. The equilibrium coefficients of friction were 0.02–0.04 in humid air and in dry nitrogen, but 1.5–1.8 in vacuum. The wear factor of the diamond films depended on the initial surface roughness, regardless of environment; it increased with increasing initial surface roughness. The wear factors were considerably higher in vacuum than in humid air and in dry nitrogen.
Towards Agrobots: Trajectory Control of an Autonomous Tractor Using Type-2 Fuzzy Logic Controllers (2014)

Provision of some autonomous functions to an agricultural vehicle would lighten the job of the operator but in doing so, the accuracy should not be lost to still obtain an optimal yield. Autonomous navigation of an agricultural vehicle involves the control of different dynamic subsystems, such as the yaw angle dynamics and the longitudinal speed dynamics. In this study, a proportional-integral-derivative controller is used to control the longitudinal velocity of the tractor. For the control of the yaw angle dynamics, a proportional-derivative controller works in parallel with a type-2 fuzzy neural network. In such an arrangement, the former ensures the stability of the related subsystem, while the latter learns the system dynamics and becomes the leading controller. In this way, instead of modeling the interactions between the subsystems prior to the design of a model-based control, we develop a control algorithm which learns the interactions online from the measured feedback error. In addition to the control of the stated subsystems, a kinematic controller is needed to correct the errors in both the x- and the y- axis for the trajectory tracking problem of the tractor. To demonstrate the real-time abilities of the proposed control scheme, an autonomous tractor is equipped with the use of reasonably priced sensors and actuators. Experimental results show the efficacy and the efficiency of the proposed learning algorithm.
<i>Brd2</i> disruption in mice causes severe obesity without Type 2 diabetes (2009)

Certain human subpopulations are metabolically healthy but obese, or metabolically obese but normal weight; such mutations uncouple obesity from glucose intolerance, revealing pathways implicated in Type 2 diabetes. Current searches for relevant genes consume significant effort. We have reported previously a novel double bromodomain protein called Brd2, which is a transcriptional co-activator/co-repressor with SWI/SNF (switch mating type/sucrose non-fermenting)-like functions that regulates chromatin. In the present study, we show that wholebody disruption of Brd2, an unusual MHC gene, causes lifelong severe obesity in mice with pancreatic islet expansion, hyperinsulinaemia, hepatosteatosis and elevated pro-inflammatory cytokines, but, surprisingly, enhanced glucose tolerance, elevated adiponectin, increased weight of brown adipose tissue, heat production and expression of mitochondrial uncoupling proteins in brown adipose tissue, reduced macrophage infiltration in white adipose tissue, and lowered blood glucose, leading to an improved metabolic profile and avoiding eventual Type 2 diabetes. Brd2 is highly expressed in pancreatic beta-cells, where it normally inhibits beta-cell mitosis and insulin transcription. In 3T3-L1 pre-adipocytes, Brd2 normally co-represses PPAR-gamma (peroxisome-proliferator-activated receptor-gamma) and inhibits adipogenesis. Brd2 knockdown protects 3T3-L1 adipocytes from TNF-alpha (tumour necrosis factor-alpha)-induced insulin resistance, thereby decoupling inflammation from insulin resistance. Thus hypomorphic Brd2 shifts energy balance toward storage without causing glucose intolerance and may provide a novel model for obese metabolically healthy humans.
Differential pressure sticking of drill string (1998)

Abstract The frictional forces acting on a drill string in a borehole can be large if the drill string is embedded in a pastelike filter cake formed at the borehole wall by the drilling fluid. In extreme conditions, the drill string can become stuck, leading to expensive delays in the drilling process. The hydraulic pressure within the wellbore is usually higher than the pore pressure within the rock. This excess pressure is responsible both for the growth of the filter cake, and for the normal force that can hold the drill string against the borehole wall. We obtain estimates of the normal and frictional forces acting on the drill string, based on an analysis of the pressure and concentration profile within the filter cake. The forces can be minimized by ensuring that the cake is highly compressible, so that the bulk of the pressure drop between the borehole and porous rock occurs across a thin boundary layer at the base of the cake. The forces acting on a sphere (rather than a cylindrical drill string) are also modeled, and are compared against experiment. The predicted fictional force is smaller than observed experimentally, but the predicted t 3/4 growth of the force with time t agrees with experiment.
High-level secretion of recombinant monomeric murine and human single-chain Fv antibodies from Drosophila S2 cells (2011)

Single-chain variable fragment (scFvs) antibodies are small polypeptides (∼26 kD) containing the heavy (V(H)) and light (V(L)) immunoglobulin domains of a parent antibody connected by a flexible linker. In addition to being frequently used in diagnostics and therapy for an increasing number of human diseases, scFvs are important tools for structural biology as crystallization chaperones. Although scFvs can be expressed in many different organisms, the expression level of an scFv strongly depends on its particular amino acid sequence. We report here a system allowing for easy and efficient cloning of (i) scFvs selected by phage display and (ii) individual heavy and light chain sequences from hybridoma cDNA into expression plasmids engineered for secretion of the recombinant fragment produced in Drosophila S2 cells. We validated the method by producing five scFvs derived from human and murine parent antibodies directed against various antigens. The production yields varied between 5 and 12 mg monomeric scFv per liter of supernatant, indicating a relative independence on the individual sequences. The recombinant scFvs bound their cognate antigen with high affinity, comparable with the parent antibodies. The suitability of the produced recombinant fragments for structural studies was demonstrated by crystallization and structure determination of one of the produced scFvs, derived from a broadly neutralizing antibody against the major glycoprotein E2 of the hepatitis C virus. Structural comparison with the Protein Data Bank revealed the typical spatial organization of V(H) and V(L) domains, further validating the here-reported expression system.