gebhart/patrepeval huggingface dataset:
Epidemiology of Human Immunodeficiency Virus in the United States (2007)

The human immunodeficiency virus (HIV) epidemic emerged in the early 1980s with HIV infection as a highly lethal disease among men who have sex with men and among frequent recipients of blood product transfusions. Advances in the treatment of HIV infection have resulted in a fundamental shift in its epidemiology, to a potentially chronic and manageable condition. However, challenges in the prevention of this infection remain. In particular, increasing evidence suggests that transmission of drug-resistant virus is becoming more common and that the epidemic is having a profound impact on morbidity and mortality in ethnic and racial minority subgroups in the United States. New population-based data collection systems designed to describe trends in behaviors associated with HIV transmission and better methods for measuring the true incidence of transmission will better elucidate the characteristics of HIV infection in the United States and inform future public health policies.
Modeling Multiple Species of Nicotine and Deschloroepibatidine Interacting with α4β2 Nicotinic Acetylcholine Receptor:  From Microscopic Binding to Phenomenological Binding Affinity (2005)

A variety of molecular modeling, molecular docking, and first-principles electronic structure calculations were performed to study how the alpha4beta2 nicotinic acetylcholine receptor (nAChR) binds with different species of two typical agonists, (S)-(-)-nicotine and (R)-(-)-deschloroepibatidine, each of which is distinguished by different free bases and protonation states. On the basis of these results, predictions were made regarding the corresponding microscopic binding free energies. Hydrogen-bonding and cation-pi interactions between the receptor and the respective ligands were found to be the dominant factors differentiating the binding strengths of different microscopic binding species. The calculated results and analyses demonstrate that, for each agonist, all the species are interchangeable and can quickly achieve a thermodynamic equilibrium in solution and at the nAChR binding site. This allows quantitation of the equilibrium concentration distributions of the free ligand species and the corresponding microscopic ligand-receptor binding species, their pH dependence, and their contributions to the phenomenological binding affinity. The predicted equilibrium concentration distributions, pK(a) values, absolute phenomenological binding affinities, and their pH dependence are all in good agreement with available experimental data, suggesting that the computational strategy from the microscopic binding species and affinities to the phenomenological binding affinity is reliable for studying alpha4beta2 nAChR-ligand binding. This should provide valuable information for future rational design of drugs targeting nAChRs. The general strategy of the "from-microscopic-to-phenomenological" approach for studying interactions of alpha4beta2 nAChRs with (S)-(-)-nicotine and (R)-(-)-deschloroepibatidine may also be useful in studying other types of ligand-protein interactions involving multiple molecular species of a ligand and in associated rational drug design.
<title>New interferometric profiler for smooth and rough surfaces</title> (1993)

A new method of optical, non-contact profiling of rough surfaces is described that utilizes interferometric techniques as well as digital signal processing algorithms to produce fast, accurate, repeatable 3-D surface profile measurements. When combined with more traditional phase-shifting measurement techniques, this produces an instrument capable of profiling surfaces with rms roughness, Rq, ranging from 1 angstrom to 20 micrometers , and measurement of steps up to 100 micrometers . Sample data are discussed and a comparison with other surface profiling techniques is presented.
The proteolytic enzymes of the K-1 strain of Streptomyces griseus obtained from a commercial preparation (Pronase). Specificity and immobilization of aminopeptidase. (1975)

We recently described the purification of two aminopeptidases from Streptomyces griseus (Vosbeck, K.D., Chow, K.-F., and Awad, W.M., Jr. (1973) J. Biol. Chem. 248, 6329-6034). An analysis of the amino acid composition reveals very little differences in the two proteins. Each protein has alanine as the NH2-terminal residue. The aminopeptidases were treated separately with acetic anhydride; as noted in the past, the presence of glycerol is required to achieve excellent yields of acetylated active derivatives (Siegel, S., and Awad, W.M., Jr. (1973 J. Biol. Chem. 248, 3233-3240). However, in the present case much higher concentrations of glycerol (50%) are needed during acetylation to obtain derivatives with completely reacted NH2-terminal residues. The epsilon-amino groups were not completely acetylated. In contrast to the native enzymes, the acetylated derivatives show an affinity for DEAE-cellulose, a property consonant with the changes in net charge. The kinetic constants for each enzyme against L-leucine-p-nitroanilide do not change significantly after acetylation. The specificities of the two aminopeptidases were examined extensively on a semiquantitative basis. The activities are not restricted by the length of substrate chains. Each enzyme shows a preference for hydrophobic residues at the ultimate and penultimate positions. Charge residues are released a slower rates. No prolidase activity is demonstrable even at high enzyme to substrate ratios; however, NH2-terminal proline residues are released readily. D-Amino acid residues at the ultimate or penultimate position substantially reduce the rate of hydrolysis; D-leucyl-D-leucine is not hydrolyzed...
High-resolution ultrasonic thermometer for radiation dosimetry (2008)

This paper describes recent developments in the area of high-precision ultrasonic thermometry with the potential to provide on-site direct determination of radiation doses administered for cancer treatment. Conventional calorimeters used for this purpose measure radiation-induced heating in a water phantom at one point in space by means of immersed thermistors and are subject to various thermal disturbances due to Ohmic heating and interactions of the radiation with the sensor probes. By contrast, the method described here is based on a high-resolution ultrasonic system that determines the change of the speed of sound due to small temperature changes in an acoustic propagation path in the radiation-heated water, thereby avoiding such undesired thermal effects. The thermometer is able to measure tens of microkelvin changes in the water temperature averaged over the acoustic path of about 60 cm at room temperature, with root-mean-squared noise of about 5 microK. Both incandescent and ionizing radiation heating data are presented for analog and digital implementations of a laboratory prototype. This application of the ultrasonic technique opens up possibilities for a new approach to performing therapy-level radiation dosimetry for medical clinics and standards laboratories.
Basic Antenna and Propagation Theory (2010)

This chapter contains sections titled: Introduction Characteristics of Electromagnetic Waves Interaction between Two Waves Polarization Characteristics of an Antenna Propagation References
Action of Sodium Chlorite on Cellulose and Cellulose Derivatives (1970)

Oxidation of cellulose, O-methyl cellulose, and partially carboxymethylated cellulose with sodium chlorite has been investigated for different concentrations, pH values, reaction times, temperatures, and natures of the substrate. It was found that decom position of sodium chlorite in presence and absence of cellulose showed the same trend. However, change in the chlorite content was nearly the same at pH 4, whereas in pres ence of cellulöse it was higher at pH 6 and 8. The oxidized cellulose showed a decrease in the D.P., a slight increase in the copper number, and an increase in the carboxyl content, depending on the reaction conditions. Oxidation of O-methyl cellulose and partially carboxymethylated cellulose is accompanied by depolymerisation, an increase in the carboxyl content, and a slight decrease in the D.S. of the former and a decrease in the carboxyl content of the latter. The oxidation of cellulose derivatives seems to be independent of the number of free hydroxyl groups, particularly in the acidic medium. A mechanism for the oxidation of cellulose with sodium chlorite is also suggested.
A visual approach to multimedia querying and presentation (1997)

Multimedia data has become readily available from a variety of resources, such as the Web, to users (ranging from naive to sophisticated) who need to select and to present the data in a way that is meaningful to their particular applications. Delaunay"" is our framework for querying and presenting multimedia data stored in distributed data repositories, including the Web. It is unique in combining user-defined layouts with ad hoc querying capabilities, thereby enabling users to tailor, in a simple way, the layout of virtual documents composed of retrieved mdimedia objects. In this paper, we focus on the object-oriented data models, on the declarative query languages, and on how the results of the queries to disparate resources are integrated to form coherent user-defined documents.
MRI‐guided vascular access with an active visualization needle (2011)

MRI-guided access to central veins is feasible in our animal model. When image guidance is necessary for vascular access, performing this component under MRI will allow wholly MRI-guided catheterization procedures that do not require adjunctive imaging facilities such as x-ray or ultrasound. The active needle design showed enhanced visibility, as expected. These capabilities may permit more complex catheter-based cardiovascular interventional procedures enabled by enhanced image guidance.
Detecting changes in content and posting time distributions in social media (2013)

We address a problem of detecting changes in information posted to social media taking both content and posting time distributions into account. To this end, we introduce a generative model consisting of two components, one for a content distribution and the other for a timing distribution, approximating the shape of the parameter change by a series of step functions. We then propose an efficient algorithm to detect change points by maximizing the likelihood of generating the observed sequence data, which has time complexity almost proportional to the length of observed sequence (possible change points). We experimentally evaluate the method on synthetic data streams and demonstrate the importance of considering both distributions to improve the accuracy. We, further, apply our method to real scoring stream data extracted from a Japanese word-of-mouth communication site for cosmetics and show that it can detect change points and the detected parameter change patterns are interpretable through an in-depth investigation of actual reviews.
Anergic T Cells as Suppressor Cells in Vitro (1994)

T cell-mediated suppression is an established phenomenon, but its underlying mechanisms are obscure. An in vitro system was used to test the possibility that anergic T cells can act as specific suppressor cells. Anergic human T cells caused inhibition of antigen-specific and allospecific T cell proliferation. In order for the inhibition to occur, the anergic T cells had to be specific for the same antigen-presenting cells (APCs) as the T cells that were suppressed. The mechanism of this suppression appears to be competition for the APC surface and for locally produced interleukin-2.
A 25mA CMOS LDO with &#x2212;85dB PSRR at 2.5MHz (2013)

A CMOS low-dropout regulator (LDO) with high power-supply rejection ratio (PSRR) achieved by the proposed supply ripple feed-forward path is presented in this paper. The LDO is simple with two additional low-pass filters included. No extra power is consumed when comparing to the traditional design. The proposed LDO is implemented in 0.18-μ m CMOS technology. It occupies active area of 0.042 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . With the proposed embedded supply ripple feed-forward path, in the maximum loading of 25 mA, it achieves PSRR of -85 dB at 2.5 MHz and PSRR better than -55 dB when frequency is below 5 MHz with a 4.7-μF output capacitor. The measured quiescent current is 15 μA only. The overshoot and undershoot voltages are less than 40 mV when loading changes between 1 mA and 25 mA within 40 ns. The LDO achieves line and load regulations of 3 mV/V and 50 μV/mA, respectively.
A sensitive and specific method for measurement of multiple retinoids in human serum with UHPLC-MS/MS (2011)

Retinol (vitamin A) circulates at 1-4 μM concentration and is easily measured in serum. However, retinol is biologically inactive. Its metabolite, retinoic acid (RA), is believed to be responsible for biological effects of vitamin A, and hence the measurement of retinol concentrations is of limited value. A UHPLC-MS/MS method using isotope-labeled internal standards was developed and validated for quantitative analysis of endogenous RA isomers and metabolites. The method was used to measure retinoids in serum samples from 20 healthy men. In the fed state, the measured concentrations were 3.1 ± 0.2 nM for atRA, 0.1 ± 0.02 nM for 9-cisRA, 5.3 ± 1.3 nM for 13-cisRA, 0.4 ± 0.4 nM for 9,13-dicisRA, and 17.2 ± 6.8 nM for 4oxo-13-cisRA. The concentrations of the retinoids were not significantly different when measured after an overnight fast (3.0 ± 0.1 nM for atRA, 0.09 ± 0.01 nM for 9-cisRA, 3.9 ± 0.2 nM for 13-cisRA, 0.3 ± 0.1 nM for 9,13-dicisRA, and 11.9 ± 1.6 nM for 4oxo-13-cisRA). 11-cisRA and 4OH-RA were not detected in human serum. The high sensitivity of the MS/MS method combined with the UHPLC separation power allowed detection of endogenous 9-cisRA and 4oxo-atRA for the first time in human serum.
A “Clean” TEM (2010)

“All microscopes cause contamination of the specimen under the electron beam,” said our instructor at the EELS school I was attending. “Ours doesn't!” I responded. This only caused him to repeat his assertion.
A java API for historical ciphers (2001)

This paper describes a project suitable for a software engineering or object-oriented design course. The project consists of asking students to design an application programming interface (API) for a particular range of applications. An API-design project has several features not always found in application-design projects: It forces students to focus carefully on the distinction between the programming and the user interfaces; it provides a good justification for studying existing APIs as model code; it provides a natural way to divide tasks between different groups of designers/programmers; and, the final product can be used as the basis for programming projects in other courses. In this case the particular project we describe is the design of an API for implementing Historical Cipher algorithms.
Pinpointing users with location estimation techniques and Wi‐Fi hotspot technology (2008)

Abstract Location awareness is becoming an important capability for mobile computing; however, it has not been possible until now to provide cheap pervasive positioning systems. Wide area coverage is most famously achieved by using global positioning systems (GPS). A constellation of low‐orbit satellites cover the earth's surface. Unfortunately GPS does not work indoors and has limited success in big cities because of the ‘urban canyon’ effect. PlaceLab is a research project that attempts to solve the ubiquity issues surrounding 802.11‐based location estimation. PlaceLab, like RADAR, uses a device's 802.11 interface; however, it does not require the area to be pre‐calibrated. It predicts location via the known positions of the access points detected by the device. Commonly used systems have a number of drawbacks, including cost, accuracy and the ability to work indoors. PlaceLab is a piece of open source software developed by Intel Research that can pinpoint a user within a Wi‐Fi network. We set out here to investigate whether PlaceLab can be used as a means of establishing a user's position. This type of investigation could, if successful, pave the way for the development of other location‐based applications. This report documents the efforts to answer the above question. PlaceLab was found to work, but only in ideal locations where factors such as the number of floors and the lack of available APs did not affect its use. It was concluded that these factors prevent the system from being effective as a means of establishing a user's position in most locations on campus. Copyright © 2008 John Wiley & Sons, Ltd.
RELATIONSHIP BETWEEN INTRACELLULAR GLUTATHIONE AND CYTOTOXICITY OF ALKYLATING AGENTS IN TWO HUMAN CANCER CELL LINES (1999)

Objective To investigate the relationship between the intracellular glutathione (GSH) and the cytotoxicity of two alkylating agents, nitrogen mustard and cisplatin, in the human leukemia (HL) 60 and gastric cancer (SGC) 7901 cell lines Methods The cytotoxicity of the alkylating agents was evaluated using the modified tetrazolium dye assay The total cellular content of glutathione was determined by the modified method of Tietze Results In the HL 60 cells, 50 μmol/L buthionine sulfoximine, a glutathione synthesis inhibitor, depleted the cellular glutathione by about 90% Such depletion greatly increased the cytotoxicity of nitrogen mustard, with the cell survival rate reducing from 70 0% to 40 0% A strong inverse correlation was identified between the nitrogen mustard cytotoxicity and the cellular glutathione levels modulated with buthionine sulfoximine ( r =0 98) However, the cytotoxicity of nitrogen mustard in the cells with 70% glutathione remaining was similar to that in the control cells with an intact glutathione pool In the SGC 7901 cells, significant enhancement of the cisplatin cytotoxicity was observed after the extensive glutathione depletion (by about 90%), and such effect was more pronounced in the hypoxic cells than in the aerobic cells (dose modifying factors, 2 62 vs 1 87) Conclusions The cellular glutathione plays an important role in the expression of the alkylating agent cytotoxicity in the HL 60 cells, and the aerobic or the hypoxic SGC 7901 cells
Evolution Analysis of Large-Scale Software Systems Using Design Structure Matrices and Design Rule Theory (2007)

Designers often seek modular architectures to better accommodate expected changes and to enable parallel development. However, we lack a formal theory and model of modularity and software evolution, which can be used for description, prediction, and prescription. According to Baldwin and Clark’s [1] theory, modular architectures add value to system designs by creating options to improve the system by substituting or experimenting on individual modules. In this paper, we evaluate their theory by looking at the design evolution of two software product platforms through the modeling lens of design structure matrices (DSMs) and design rule theory. Our analysis shows that DSM models and options theory can explain how real-world modularization activities in one case allowed for different rates of evolution in different software modules and in another case conferred distinct strategic advantages on a firm (by permitting substitution of an at-risk software module without substantial change to the rest of the system). The experiment supports our hypothesis that these formal models and theory can account for important aspects of software design evolution in large-scale systems. 1.
Strongly Coupled Plasmonic Modes on Macroscopic Areas via Template-Assisted Colloidal Self-Assembly (2014)

We present ensembles of surface-ordered nanoparticle arrangements, which are formed by template-assisted self-assembly of monodisperse, protein-coated gold nanoparticles in wrinkle templates. Centimeter-squared areas of highly regular, linear assemblies with tunable line width are fabricated and their extinction cross sections can be characterized by conventional UV/vis/NIR spectroscopy. Modeling based on electrodynamic simulations shows a clear signature of strong plasmonic coupling with an interparticle spacing of 1-2 nm. We find evidence for well-defined plasmonic modes of quasi-infinite chains, such as resonance splitting and multiple radiant modes. Beyond elementary simulations on the individual chain level, we introduce an advanced model, which considers the chain length distribution as well as disorder. The step toward macroscopic sample areas not only opens perspectives for a range of applications in sensing, plasmonic light harvesting, surface enhanced spectroscopy, and information technology but also eases the investigation of hybridization and metamaterial effects fundamentally.
DAS Acquisition In A Matured Field During 4D: A Challenging Initiative With Multiple Objectives (2015)

Abstract A complex carbonate oil reservoir off the coast of Qatar has been under production since 1997. The field development is based on horizontal oil producers, water injectors and the use of Electrical Submersible Pumps (ESP) as the artificial lift method. A full field 4D seismic data acquisition was undertaken in 2014 to support the future development phases. A Distributed Acoustic Sensing (DAS) acquisition was included in the 4D seismic program to capture a Vertical Seismic Profile and observe the fluid flow dynamics inside the well bore together with the reservoir inflow. The dynamics of gas fraction was imaged through a tuned operating sequence of the well. A digital movie was captured for each location in the wellbore from toe to pump intake. The first of its kind sonic data capture involved a DAS system using fiber optics. Thanks to a permanent fiber optic into the well, the simultaneous captures of DAS system reduce the incremental cost for the DAS information. Gas locking in the ESP is the major cause of down time and reduced ESP run life. The selected well is in an area with limited water drive. The high cost of replacing failed ESPs affects the economic limit of the well and thus reduces the recoverable oil. The applied operational sequence successfully observed intermittent ingestion of gassy fluids into the ESP intake. This provided key information to diagnose the root cause of gas-lock. The incident free operation has clearly imaged (filmed) the fluid dynamics of gas and liquids interacting with the ES pump intake. How detailed the challenges of preparing and conducting this operation were overcome is described. The operational field constraints cover safety, weather constraints, unmanned well platforms, the effects of streamer shooting and simultaneous production operations. On-shore details are described in relation to unusual job planning requirements including logistics and statutory requirements. The results show DAS images that identify the specific gas volumetric fraction of fluids all along the well and entering the pump intake. The acquisition program fully captured the development and movement of large gas bubbles towards the ESP and which subsequently develop into a gas-lock event. The sensing includes images from the drain toe, to ESP intake and onto the well head. The acquired data shows the root causes of operational difficulties particularly during an ESP restart. One can see the actual gas handling performance of the ESP system as the specific gas volume fraction at ESP intake evolves over time. The full sequence of this DAS advanced application has fully captured a gas lock event. This brings key information to improve ESP performance in a gassy environment from the completion design and operating points of view.