gebhart/patrepeval huggingface dataset:
Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike (2017)

The extraordinary genetic diversity of the HIV-1 envelope spike [Env; trimeric (gp160)<sub>3</sub>, cleaved to (gp120/gp41)<sub>3</sub>] poses challenges for vaccine development. Envs of different clinical isolates exhibit different sensitivities to antibody-mediated neutralization. Envs of difficult-to-neutralize viruses are thought to be more stable and conformationally homogeneous trimers than those of easy-to-neutralize viruses, thereby providing more effective concealment of conserved, functionally critical sites. In this study we have characterized the antigenic properties of an Env derived from one of the most neutralization-resistant HIV-1 isolates, CH120.6. Sequence variation at neutralizing epitopes does not fully account for its exceptional resistance to antibodies. The full-length, membrane-bound CH120.6 Env is indeed stable and conformationally homogeneous. Its antigenicity correlates closely with its neutralization sensitivity, and major changes in antigenicity upon CD4 engagement appear to be restricted to the coreceptor site. The CH120.6 gp140 trimer, the soluble and uncleaved ectodomain of (gp160)<sub>3</sub>, retains many antigenic properties of the intact Env, consistent with a conformation close to that of Env spikes on a virion, whereas its monomeric gp120 exposes many nonneutralizing or strain-specific epitopes. Thus, trimer organization and stability are important determinants not only for occluding many epitopes but also for conferring resistance to neutralization by all but a small set of antibodies. Env preparations derived from neutralization-resistant viruses may induce irrelevant antibody responses less frequently than do other Envs and may be excellent templates for developing soluble immunogens.
Realisierung einer Hierarchie aus Sprachnetzwerken (1990)

In this paper, the first realization of the so-called «semantic memory» is discussed. This new storage organization which was proposed by W. Hilberg can be used for a minimum-redundancy text-coding. After the description of the storage principle simulation methods of a semantic memory by means of hierarchical structured «language-networks», are presented. Then the design of a hardware prototype is surveyed
Effect of different irrigation management strategies on growth and yield of soybean. (2009)

In field experiment at Faisalabad, Pakistan conducted during August, 2005, the effect of different irrigation management strategies on growth and yield of soybean was investigated. The experiment comprised of eight irrigation practices of viz; rainfed, one irrigation at vegetative growth stage, one irrigation at flowering, one irrigation at pod formation, two irrigations at vegetative growth stage and at flowering, two irrigations at vegetative growth stage and at pod formation, two irrigations at flowering and at pod formation and three irrigations at vegetative growth stage, at flowering and at pod formation. Number of plants m, number of pods per plant, number of seeds per pod and seed yield was significantly higher when crop was irrigated with three irrigations at vegetative growth stage, at flowering and at pod formation.
Experimental design for stable genetic manipulation in mammalian cell lines: lentivirus and alternatives (2014)

The use of third-generation lentiviral vectors is now commonplace in most areas of basic biology. These systems provide a fast, efficient means for modulating gene expression, but experimental design needs to be carefully considered to minimize potential artefacts arising from off-target effects and other confounding factors. This review offers a starting point for those new to lentiviral-based vector systems, addressing the main issues involved with the use of lentiviral systems in vitro and outlines considerations which should be taken into account during experimental design. Factors such as selecting an appropriate system and controls, and practical titration of viral transduction are important considerations for experimental design. We also briefly describe some of the more recent advances in genome editing technology. TALENs and CRISPRs offer an alternative to lentivirus, providing endogenous gene editing with reduced off-target effects often at the expense of efficiency.
Double average parallel steady‐state free precession imaging: Optimized eddy current and transient oscillation compensation (2005)

Balanced steady-state free precession (SSFP) imaging is sensitive to off-resonance effects, which can lead to considerable artifacts during a transient phase following magnetization preparation or steady-state interruption. In addition, nonlinear k-space encoding is required if contrast-relevant k-space regions need to be acquired at specific delays following magnetization preparation or for transient artifact reduction in cardiac-gated k-space segmented CINE imaging. Such trajectories are problematic for balanced SSFP imaging due to nonconstant eddy current effects and resulting disruption of the steady state. In this work, a novel acquisition strategy for balanced SSFP imaging is presented that utilizes scan time reduction by parallel imaging for optimized "double average" eddy current compensation and artifact reduction during the transient phase following steady-state storage and magnetization preparation. Double average parallel SSFP imaging was applied to k-space segmented CINE SSFP tagging as well as nongated centrically encoded SSFP imaging. Phantom and human studies exhibit substantial reduction in steady-state storage and eddy current artifacts while maintaining spatial resolution, signal-to-noise ratio, and similar total scan time of a standard SSFP acquisition. The proposed technique can easily be extended to other acquisition schemes that would benefit from nonlinear reordering schemes and/or rely on interruption of the balanced SSFP steady state.
Mode of action of (R)-9-[4-hydroxy-2-(hydroxymethyl)butyl]guanine against herpesviruses (1995)

The activity, metabolism, and mode of action of (R)-9-[4-hydroxy-2-(hydroxymethyl)butyl]guanine (H2G) against herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) and varicella-zoster virus (VZV) were studied. Compared to acyclovir (ACV), H2G has superior activity against VZV (50% inhibitory concentration of 2.3 microM) and Epstein-Barr virus (50% inhibitory concentration of 0.9 microM), comparable activity against HSV-1, and weaker activity against HSV-2. The antiviral effect on HSV-1 showed persistence after removal of compound. H2G was metabolized to its mono-, di- and triphosphate derivatives in virus-infected cells, with H2G-triphosphate being the predominant product. Only small amounts of H2G-triphosphate were detected in uninfected cells (1 to 10 pmol/10(6) cells), whereas the level in HSV-1-infected cells reached 1,900 pmol/10(6) cells. H2G was a substrate for all three viral thymidine kinases and could also be phosphorylated by mitochondrial deoxyguanosine kinase. The intracellular half-life of H2G-triphosphate varied in uninfected (2.5 h) and infected (HSV-1, 14 h; VZV, 3.7 h) cells but was always longer than the half-life of ACV-triphosphate (1 to 2 h). H2G-triphosphate inhibited HSV-1, HSV-2, and VZV DNA polymerases competitively with dGTP (Ki of 2.8, 2.2, and 0.3 microM, respectively) but could not replace dGTP as a substrate in a polymerase assay. H2G was not an obligate chain terminator but would only support limited DNA chain extension. Only very small amounts of radioactivity, which were too low to be identified by high-performance liquid chromatography analysis of the digested DNA, could be detected in purified DNA from uninfected cells incubated with [3H]H2G. Thus, H2G acts as an anti-herpesvirus agent, particularly potent against VZV, by formation of high concentrations of relatively stable H2G-triphosphate, which is a potent inhibitor of the viral DNA polymerases.
Accurate frequency response determinations from discrete step response data (1987)

An approach is presented for quickly obtaining the complex frequency response of a system from sampled step-response data. Digital signal processing techniques are used extensively. An analysis of errors resulting from sampling, quantization, first differencing and record length is included.
Mobile Phone–based Infectious Disease Surveillance System, Sri Lanka (2010)

Because many infectious diseases are emerging in animals in low-income and middle-income countries, surveillance of animal health in these areas may be needed for forecasting disease risks to humans. We present an overview of a mobile phone-based frontline surveillance system developed and implemented in Sri Lanka. Field veterinarians reported animal health information by using mobile phones. Submissions increased steadily over 9 months, with ≈4,000 interactions between field veterinarians and reports on the animal population received by the system. Development of human resources and increased communication between local stakeholders (groups and persons whose actions are affected by emerging infectious diseases and animal health) were instrumental for successful implementation. The primary lesson learned was that mobile phone-based surveillance of animal populations is acceptable and feasible in lower-resource settings. However, any system implementation plan must consider the time needed to garner support for novel surveillance methods among users and stakeholders.
Magnesium-Doped Lithium Niobate For Higher Optical Power Applications (1985)

Compositions of lithium niobate containing 4.5 at.% or more MgO have the ability to transmit, without distortion, light 100 times as intense as undopecl compositions. Holographic diffraction measurements of photorefraction have demonstrated that the improved performance is due to a hundredfold increase in the photoconductivity, rather than to a decrease in the Glass current. The damage-resistant compositions are also distinguished by a thermal activation energy of 0.1 eV for the diffraction efficiency, an OH-stretch vibration at 2.83 Am, a lattice phonon absorption at 21.2 Am, an electron spin resonance signal for Fe impurities at 1500 G, and, after reduction by heating in a vacuum, an optical absorption band at 1.2 um. (The corresponding values for undopedl LiNbO3 are 0.5 eV, 2.87 um, 21.8 um, 790 G, and 0.5 um, respectively.) The high photoconductivity is thus related to a distinctive electronic environment for impurities in the damage-resistant crystals. The photoconductivity strongly affects the impedance and time constants of signal processing devices made of LiNbO3.
Better abstractions for secure server-side scripting (2008)

It is notoriously difficult to program a solid web application. Besides addressing web interactions, state maintenance, and whimsical user navigation behaviors, programmers must also avoid a minefield of security vulnerabilities. The problem is twofold. First, we lack a clear understanding of the new computation model underlying web applications. Second, we lack proper abstractions for hiding common and subtle coding details that are orthogonal to the business functionalities of specific web applications.
Central Nervous System Serotonin Function and Cardiovascular Responses to Stress (2001)

These findings suggest the 5HTTLPR polymorphism affects CNS serotonin function, and they are consistent with the general hypothesis that CNS serotonin function is involved in the regulation of potentially health-damaging biobehavioral characteristics. In particular, the l allele could contribute, through its association with increased cardiovascular reactivity to stress, to increased risk of cardiovascular disease.
Innovative dual function nc-SiOx:H layer leading to a &gt;16% efficient multi-junction thin-film silicon solar cell (2011)

We present our development of n-type nano-structured hydrogenated silicon oxide (nc-SiOx:H) as a dual-function layer in multi-junction solar cells. We optimized nc-SiOx:H and attained a conductivity suitable for a doped layer and optical property suitable for an inter-reflection layer. We tested the effectiveness of the dual-function nc-SiOx:H layer by replacing the normal n layer between the middle and the bottom cells in an a-Si:H/a-SiGe:H/nc-Si:H triple-junction structure. A significant gain in the middle cell current density of ∼1.0 mA/cm2 is achieved. We further optimized the component cells and the triple-junction structures and attained an initial active-area cell efficiency of 16.3%.
Event-join optimization in temporal relational databases (1989)

An Event-Join combines temporal join and outer-join properties into a single operation. It is mostly used to group temporal attributes of an entity into a single relation. In this paper, we motivate the need to support the efficient processing of event-joins, and introduce several optimization algorithms, both for a general data organization and for specialized organizations (sorted and append-only databases). For the append-only data-base we introduce a data structure that can improve the performance of event-joins as well as other queries. Finally, we evaluate the performance of the proposed algorithms.
The role(s) of lipophosphoglycan (LPG) in the establishment of <i>Leishmania major</i> infections in mammalian hosts (2003)

The abundant cell surface glycolipid lipophosphoglycan (LPG) was implicated in many steps of the Leishmania infectious cycle by biochemical tests. The presence of other abundant surface or secreted glycoconjugates sharing LPG domains, however, has led to uncertainty about the relative contribution of LPG in vivo. Here we used an Leishmania major lpg1- mutant, which lacks LPG alone and shows attenuated virulence, to dissect the role of LPG in the establishment of macrophage infections in vivo. lpg1- was highly susceptible to human complement, had lost the ability to inhibit phagolysosomal fusion transiently, and was oxidant sensitive. Studies of mouse mutants defective in relevant defense mechanisms confirmed the role of LPG in oxidant resistance but called into question the importance of transient inhibition of phagolysosomal fusion for Leishmania macrophage survival. Moreover, the limited lytic activity of mouse complement appears to be an ineffective pathogen defense mechanism in vitro and in vivo, unlike human hosts. In contrast, lpg1- parasites bound C3b and resisted low pH and proteases normally, entered macrophages efficiently and silently, and continued to inhibit host-signaling pathways. These studies illustrate the value of mechanistic approaches focusing on both parasite and host defense pathways in dissecting the specific biological roles of complex virulence factors such as LPG.
Priors for people tracking from small training sets (2005)

We advocate the use of scaled Gaussian process latent variable models (SGPLVM) to learn prior models of 3D human pose for 3D people tracking. The SGPLVM simultaneously optimizes a low-dimensional embedding of the high-dimensional pose data and a density function that both gives higher probability to points close to training data and provides a nonlinear probabilistic mapping from the low-dimensional latent space to the full-dimensional pose space. The SGPLVM is a natural choice when only small amounts of training data are available. We demonstrate our approach with two distinct motions, golfing and walking. We show that the SGPLVM sufficiently constrains the problem such that tracking can be accomplished with straightforward deterministic optimization.
A Radio Assay for the Study of Radio Frequency Tag Antenna Performance (2005)

In recent years, passive radio frequency (RF) tags that\ncommunicate using modulated backscatter radiation have shown great\npotential for use in inventory management, parcel and postal\ntracking, for use as remote sensors, and in a host of other Radio\nFrequency Identification (RFID) applications. However, for the\nwidespread use of these tags to become reality, much basic\nresearch is needed to reduce the cost, increase the range, and\nincrease the reliability of the RF tag. This research seeks to\nenhance the performance of passive RF tags by developing a series\nof tests, or radio assay, to measure the following: the\nperformance of RF tag antennas as a function of antenna material\nand manufacturing technique and the antenna performance when\nattached to various materials. The radio assay experiments are\ndesigned for RF tag antennas that operate in the far field of the\ntag reader and communicate using modulated backscatter radiation\nat 915 MHz. Three flexible, folded dipoles, printed on plastic\nsubstrates, were measured in the radio assay experiments. The\nresults of the experiments include the following: the antenna gain\npenalty (relative to a baseline antenna) for each antenna material\nand manufacturing technique, the antenna gain penalty (relative to\nthe free space antenna gain) due to material losses when the tag\nantenna is attached to an object, and the benefits (in terms of\nantenna gain) of tuning each tag antenna to the material to which\nit is attached. The results are presented in a form to aid RF\nengineers in the design of RF tag system link budgets.
Increased cadmium tolerance and accumulation by plants expressing bacterial arsenate reductase (2003)

• Cadmium (Cd) is a major environmental pollutant that poses a serious threat to natural ecosystems. However, most initial attempts to engineer phytoremediation of Cd have not succeeded in developing sufficient Cd tolerance for vigorous plant growth. • We found that the bacterial arsenate reductase gene (arsC) provided Cd(II) resistance to Escherichia coli. When ArsC is overexpressed in tobacco (Nicotiana tabacum) and Arabidopsis thaliana, both transgenic plant species showed significantly greater Cd tolerance than wild-type controls. • At 50, 75, and 100 µm concentrations of Cd (II), the ArsC expressing transgenic lines grew bigger with broader leaves and longer roots than wild-type controls, which were stunted, turned yellow, flowered early, and often died. At the various Cd(II) concentrations, ArsC transgenic plants attained f. wt 2-3-fold higher than the wild-type plants and had roots significantly longer than wild-type plants. These transgenic plants also contained 30-50% higher Cd concentrations than wild-type plants. • It is likely that the arsC gene directs Cd tolerance via the electrochemical reduction of Cd(II) to Cd(0).
Hetero-epitaxy of III-V compounds lattice-matched to InP by MOCVD for device applications (2009)

Device quality Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.49</sub> In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.51</sub> As/Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> As MHEMT structures have been grown by MOCVD on GaAs substrates, with 2-DEG mobility over 8700 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V-s and sheet carrier density at around 4 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> . A 150 nm T-gate transistor demonstrated unity current gain cutoff frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) and maximum oscillation frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ) of 279 and 231 GHz, respectively.
Role of the Accessory Gene Regulator <i>agr</i> in Community-Associated Methicillin-Resistant Staphylococcus aureus Pathogenesis (2011)

The molecular basis underlying the pathogenic success of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is not completely understood, but differential gene expression has been suggested to account at least in part for the high virulence of CA-MRSA strains. Here, we show that the agr gene regulatory system has a crucial role in the development of skin infections in the most prevalent CA-MRSA strain USA300. Importantly, our data indicate that this is due to discrepancies between the agr regulon of CA-MRSA and those of hospital-associated MRSA and laboratory strains. In particular, agr regulation in strain USA300 led to exceptionally strong expression of toxins and exoenzymes, upregulation of fibrinogen-binding proteins, increased capacity to bind fibrinogen, and increased expression of methicillin resistance genes. Our findings demonstrate that agr functionality is critical for CA-MRSA disease and indicate that an adaptation of the agr regulon contributed to the evolution of highly pathogenic CA-MRSA.
Influence of GaAs capping on the optical properties of InGaAs/GaAs surface quantum dots with 1.5 μm emission (1998)

Uncapped InGaAs quantum dots (surface quantum dots) on a GaAs substrate emit photoluminescence at a long wavelength of 1.53 μm at room temperature. When the surface dots are covered by a GaAs cap layer, the emission energy of the dots increases by 287 meV. This large energy shift is mainly caused by inducing compressive stress from the cap layer. In segregation on the surface led to greater photoluminescence intensity in the surface quantum dots even at room temperature due to the suppression of nonradiative surface recombination.
Predictive Cruise Control in Hybrid Electric Vehicles (2009)

Deceleration rates have considerable influence on the fuel economy of hybrid electric vehicles. Given the vehicle characteristics and actual/measured operating conditions, as well as upcoming route information, optimal velocity trajectories can be constructed that maximize energy recovery. To support the driver in tracking of the energy optimal velocity trajectory, automatic cruise control is an important driver aid. In practice, perfect tracking of the optimal velocity trajectory is often not possible. An Adaptive Cruise Control (ACC) system is employed to react to the actual traffic situation. The combination of optimal velocity trajectory construction and ACC is presented as Predictive Cruise Control (PCC).
Mining Social Media Streams to Improve Public Health Allergy Surveillance (2015)

Allergies are one of the most common chronic diseases worldwide. One in five Americans suffer from either allergy or asthma symptoms. With the prevalence of social media, people sharing experiences and opinions on personal health symptoms and concerns on social media are increasing. Mining those publicly available health related data potentially provides valuable healthcare insights. In this paper, we propose a real-time allergy surveillance system that first classifies tweets to identify those that mention actual allergy incidents using bag-of-words model and NaiveBayesMultinomial classifier and applies in-depth text and spatiotemporal analysis. Our experimental results show that the proposed system can detect predominant allergy types with high precision and that allergy-related tweet volume is highly correlated to the weather data (daily maximum temperature). We believe that this is the first study that examines a large-scale social media stream for in-depth analysis of allergy activities.