gebhart/patrepeval huggingface dataset:
Angelo Celli and research on the prevention of malaria in Italy a century ago (2012)

The parasite responsible for severe malaria (Plasmodium falciparum) has recently been demonstrated to have been transmitted to humans from gorillas, a finding that substantiates an earlier hypothesis that malaria spread from monkeys to early neolithic peasants at the dawn of land cultivation. The first written records of seasonal and/ or intermittent fevers – which arewidely assumed to be malaria – are found in Sumerian, Babylonian, Assyrian, Chinese, Egyptian and Indian texts. In the fifth century BCE, these fevers became widespread in ancient Greece, prompting Hippocrates to investigate them and to attempt a detailed description. He tried to understand the relationship between the timing and frequency of intermittent fevers and the swelling of the spleen, as well as their relationship to where patients lived, identifying swampy areas as particularly inhospitable. These intermittent fevers affected the inhabitants of wetlands in and around ancient Rome, a situation most probably aggravated by population flows from North Africa around the time of the Punic wars. Some classical civilizations – for example, the Etruscans – channeled water flows and drained marshes, although this may have been primarily for land reclamation. In 1717, the Italian physician Giovanni Lancisi described factors associated with intermittent fevers and postulated that mosquitoes might have a role in transmitting them. Lancisi gave the word malaria its present medical meaning. The word began to be adopted in Italian and English medical texts in the eighteenth century, the word itself reflecting the popular belief that malaria was caused by stagnant air (‘mal’aria’) rising from swampy areas.
Effect of temperature on copper indium selenization (1997)

The reaction kinetics of copper indium diselenide formation is studied by measuring species composition as a function of time at 250°C and 325°C in a tubular chemical vapor deposition reactor. This extends our previous modeling and experimental study at 400°C. The initial copper–indium alloy is analyzed at the reaction temperatures using high-temperature X-ray diffraction measurements. This modifies the understanding of the chemistry of the copper indium growth kinetics and a new set of model equations is presented. The specific reaction rate constants and activation energies for the chemical reactions are obtained, enabling one to calculate the holding time for the reaction. © 1997 John Wiley & Sons, Ltd.
Deposition of Platinum Clusters on Surface-Modified Tobacco Mosaic Virus (2006)

Nanoscaled Pt conductors were prepared from genetically engineered Tobacco mosaic virus (TMV) templates through Pt cluster deposition on the outer surface of the TMV. Pt clusters were synthesized and deposited on the engineered TMV with surface-exposed cysteine via the in situ mineralization of hexachloroplatinate anions. This deposition was driven by the specific binding between thiols and the solid metal clusters. In addition, Pt-thiolate adducts are suggested to form on the engineered TMV in aqueous solutions that work as nucleation sites for the formation of the Pt clusters. The specific binding between Pt clusters and the engineered TMV template was investigated using UV/vis spectrophotometry and quartz crystal microbalance (QCM) analysis. The electric conductance of Pt-deposited TMV was greater than that of the uncoated TMV virion particles. This result suggests the application of metal cluster-deposited engineered TMV in future electrical devices such as rapid response sensors.
Mechanistic insights into high mobility group box-1 (HMGb1)-induced Toll-like receptor 4 (TLR4) dimer formation (2018)

Supplemental data for this article can be accessed here.High mobility group box-1 (HMGb1), an endogenous danger-associated molecular pattern protein (DAMP) whose extracellular release has been associated with sterile injury and various inflammatory diseases and conditions, has been shown to be a valuable clinical drug target. Elucidation of the specific interactions with the HMGb1 receptor, Toll-like receptor 4 (TLR4) and adaptor protein myeloid differentiation factor-2 (MD-2), will lead to more precisely targeted therapeutics. We sought to examine detailed interactions and dynamics of the HMGb1 A-box and B-box fragments, as well as the intact protein using <i>in silico</i> protein-protein docking (ZDOCK, ZRANK) and molecular dynamics (Schrödinger Desmond, New York, NY). Mutagenesis and SPR-binding studies allowed us to draw further conclusions regarding the details of the HMGb1-TLR4-MD2 interaction and shed light on the reasons for the opposing biological activities of HMGb1 A-box and B-box fragments. From our findings, we hypothesize that disulfide A-box fragment binds as an anchor toward the TLR4-MD-2 but does not facilitate the TLR4 dimer formation, thereby competing with the HMGb1-binding site and preventing HMGb1-induced signaling and downstream inflammation, whereas the pro-inflammatory B-box fragment retains the MD-2 active conformation and binds to both TLR4 proteins in the complex to aid TLR4 dimer formation, which activates the intracellular signaling for downstream inflammatory pathways and cytokine release. Communicated by Ramaswamy H. Sarma.
Polymeric delivery systems for nucleic acid therapeutics: Approaching the clinic (2021)

Gene therapy using nucleic acids has many clinical applications for the treatment of diseases with a genetic origin as well as for the development of innovative vaccine formulations. Since nucleic acids in their free form are rapidly degraded by nucleases present in extracellular matrices, have poor pharmacokinetics and hardly pass cellular membranes, carrier systems are required. Suitable carriers that protect the nucleic acid payload against enzymatic attack, prolong circulation time after systemic administration and assist in cellular binding and internalization are needed to develop nucleic acid based drug products. Viral vectors have been investigated and are also clinically used as delivery vehicles. However, some major drawbacks are associated with their use. Therefore there has been substantial attention on the use of non-viral carrier systems based on cationic lipids and polymers. This review focuses on the properties of polymer-based nucleic acid formulations, also referred as polyplexes. Different polymeric systems are summarized, and the cellular barriers polyplexes encounter and ways to tackle these are discussed. Finally attention is given to the clinical status of non-viral nucleic acid formulations.
Downlink capacity and coverage trade-offs in WCDMA with advanced antenna systems (2003)

Advanced antenna technologies are identified as one of the key techniques to improve the capacity and coverage of third generation WCDMA (FDD) systems. Advanced antennas can solve the capacity limitations in certain urban cells. Furthermore, they can also extend the coverage of large rural cells. The goal of this contribution is to highlight the downlink capacity and coverage gains and show the potential in capacity and coverage trade-offs for a WCDMA downlink provided by the use of advanced antenna systems installed at WCDMA base stations.
A study of voltage contrast image using Monte Carlo simulation (2007)

Using Monte Carlo simulation, we studied voltage contrast (VC) image caused by negative charging. In order to simulate the VC image, we have developed an electron scattering program based on a consideration of the spatial charge conduction model. Also we have established a cluster computing system of 60 CPUs to shorten the processing time. Using a Monte Carlo simulator, we succeeded in obtaining the simulated VC image. Comparison between simulated images and experimental images reveals that the simulated images are in good agreement with some experimental images.
A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans (2011)

Abstract Background Correct annotation of function is essential if one is to take full advantage of the vast amounts of genomic sequence data. The accuracy of sequence-based functional annotations is often variable, particularly if the sequence homology to a known function is low. Indeed recent work has shown that even proteins with very high sequence identity can have different folds and functions, and therefore caution is needed in assigning functions by sequence homology in the absence of experimental validation. Experimental methods are therefore needed to efficiently evaluate annotations in a way that complements current high throughput technologies. Here, we describe the use of nuclear magnetic resonance (NMR)-based ligand screening as a tool for testing functional assignments of putative enzymes that may be of variable reliability. Results The target genes for this study are putative enzymes from the methanogenic archaeon Methanosarcina acetivorans (MA) that have been selected after manual genome re-annotation and demonstrate detectable in vivo expression at the level of the transcriptome. The experimental approach begins with heterologous E. coli expression and purification of individual MA gene products. An NMR-based ligand screen of the purified protein then identifies possible substrates or products from a library of candidate compounds chosen from the putative pathway and other related pathways. These data are used to determine if the current sequence-based annotation is likely to be correct. For a number of case studies, additional experiments (such as in vivo genetic complementation) were performed to determine function so that the reliability of the NMR screen could be independently assessed. Conclusions In all examples studied, the NMR screen was indicative of whether the functional annotation was correct. Thus, the case studies described demonstrate that NMR-based ligand screening is an effective and rapid tool for confirming or negating the annotated gene function of putative enzymes. In particular, no protein-specific assay needs to be developed, which makes the approach broadly applicable for validating putative functions using an automated pipeline strategy.
Computational and Experimental Analysis of Direct CNG Injection and Mixture Formation in a Spark Ignition Research Engine (2010)

Direct injection (DI) of compressed natural gas (CNG) under high pressure conditions is a topic of great interest, owing to its potential for improving SI engine performance and fuel consumption. However, relevant technical difficulties have yet to be resolved in order to stabilize combustion process, especially for stratified engine operating conditions. The present paper is focused on experimental and numerical investigations of the jet formation and fuel-air mixing process in a research optical-access single-cylinder engine. The engine is based on the multi-cylinder engine under development within the European Community (EC) VII Framework Program (FP) InGAS Integrated Project, and features a centrally mounted poppet-valve injector on a pent-roof combustion chamber with a bowl in piston. Experimental investigations were made by means of the planar laser-induced fluorescence technique, and revealed a cycle-to-cycle jet shape variability. In particular, for specific cylinder pressure values at the start of injection, the jet can adhere to chamber walls for a relevant number of cycles, leading to an ‘umbrella-like’ shape. This can change the mixing capabilities of the combustion chamber and cause instabilities in the combustion process. The mentioned behaviour is strongly dependent not only on the injection and cylinder pressures, but also on important design parameters, such as needle cone angle and in-chamber injector protrusion. For this reason, in order to obtain a deep insight into the injected gas behaviour on an average cycle basis, the experimental investigation was supported by a numerical analysis. Simulations were carried out by an optimized variable-density finite-volume numerical model which was built within the Star-CD environment. A previously developed and validated ‘virtual injector’ model was implemented. The outcomes of the numerical model were compared to laser-induced fluorescence images, for both stratified- and homogeneous-charge engine operating conditions and a good agreement was obtained, substantiating the reliability of the applied computational model. Then, the effects of the injector protrusion in the combustion chamber and of injection timing were analyzed, and their impact on jet stability and mixture-formation process was analyzed.
Parametric imaging of Dynamic Vascular Patterns of Focal Liver Lesions in contrast-enhanced ultrasound (2009)

The differentiation between benign and malignant Focal Liver Lesions (FLL) plays an important role in diagnosis and therapeutic planning of liver diseases. This differentiation, based on characterization, relies on the observation of the Dynamic Vascular Patterns (DVP) of FLL with respect to surrounding healthy parenchyma, and may be observed during contrast-enhanced ultrasound imaging after a bolus injection. For instance, a hemangioma (i.e. a benign FLL) exhibits a hyper-enhanced signature over time, whereas a metastasis (i.e. a malignant FLL) usually presents hyper-enhanced foci during the arterial phase and becomes hypo-enhanced afterwards. The objective of this work was to develop a new parametric imaging technique, aimed at mapping the DVP signatures into a single image called DVP parametric image, conceived as a diagnostic aid tool for characterizing FLL types. The DVP parametric images were the object of a clinical assessment. The resulting sensitivity and specificity were 97% and 91%, respectively.
Real-time In Vitro Monitoring of Odorant Receptor Activation by an Odorant in the Vapor Phase (2019)

Olfactory perception begins with the interaction of odorants with odorant receptors (OR) expressed by olfactory sensory neurons (OSN). Odor recognition follows a combinatorial coding scheme, where one OR can be activated by a set of odorants and one odorant can activate a combination of ORs. Through such combinatorial coding, organisms can detect and discriminate between a myriad of volatile odor molecules. Thus, an odor at a given concentration can be described by an activation pattern of ORs, which is specific to each odor. In that sense, cracking the mechanisms that the brain uses to perceive odor requires the understanding odorant-OR interactions. This is why the olfaction community is committed to "de-orphanize" these receptors. Conventional in vitro systems used to identify odorant-OR interactions have utilized incubating cell media with odorant, which is distinct from the natural detection of odors via vapor odorants dissolution into nasal mucosa before interacting with ORs. Here, we describe a new method that allows for real-time monitoring of OR activation via vapor-phase odorants. Our method relies on measuring cAMP release by luminescence using the Glosensor assay. It bridges current gaps between in vivo and in vitro approaches and provides a basis for a biomimetic volatile chemical sensor.
Lift NIH restrictions on chimera research (2015)

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Anomaly Detection and Diagnosis Using Pre-Processing and Time-Delay Autoencoder (2021)

This paper proposes an anomaly detection algorithm for a factory automation system, which jointly performs data pre-processing and time-delay autoencoder (TDAE) with a hybrid loss function. The source data are pre-processed by digital filters before feeding into a TDAE for anomaly detection. The digital filters extract analog signals from a variety of frequency bands to facilitate identifying anomalies. The pre-processed data then takes time-delay reform to explore temporal relationship of data signals. In addition, two anomaly diagnosis algorithms, a statistical based method and an autoencoder based method, are presented. Numerical results show that time-delay reform can improve the anomaly detection accuracy compared to the conventional autoencoder. Data pre-processing can further improve the anomaly detection accuracy. Moreover, we confirm that our anomaly diagnosis algorithms outperform traditional method that does not perform data pre-processing and time-delay reform.
Identification of the intrinsic self-trapped hole center in KD2PO4 (1999)

The intrinsic “self-trapped” hole center in KD2PO4 crystals has been identified using electron paramagnetic resonance and electron-nuclear double resonance. These defects, labeled [D2PO4]o centers, can be formed at 77 K by irradiating with either 60 kV x rays or the fourth harmonic (266 nm) of a pulsed Nd:YAG laser. The hole is equally shared by two adjacent oxygen ions, and hyperfine interactions with one phosphorus and two equivalent deuterons are observed. The sample used in this investigation was approximately 80% deuterated, thus both [D2PO4]o and [HDPO4]o centers were detected, with the former being dominant. These intrinsic self-trapped hole centers are of interest because of their potential role in the transient optical absorption produced in KD2PO4 crystals at room temperature by intense 266 nm laser pulses.
Extending accurate spectral induced polarization measurements into the kHz range: modelling and removal of errors from interactions between the parasitic capacitive coupling and the sample holder (2019)

SUMMARY Spectral induced polarization (SIP), describing the measurement of the frequency domain electrical impedance magnitude and phase of porous materials, has been widely used to characterize subsurface hydrological/biogeochemical properties and processes. SIP data collected at frequencies higher than 100 Hz are expected to describe the polarization of small particles providing insights into the physicochemical properties of clays, nanoparticles and microorganisms. However, the phase measurements at these high frequencies are often contaminated by errors due to the parasitic capacitive coupling of the SIP instrument, especially for lower conductivity samples. We developed a model showing the measured phase is the sum of the true sample phase and an error term ωCinZx, where ω is the angular frequency; Cin is the instrument input capacitance and Zx is a measurable impedance function related to the sample holder properties and the reference resistor. Based on this model, a new phase correction method is proposed that results in highly accurate SIP data up to 20 kHz as well as the determination of Cin. We tested the correction method using electric circuits, NaCl fluids and three unconsolidated samples (sand, sand-clay and sand-pyrite mixtures). The corrected phase for the circuit and NaCl fluid experiments showed excellent agreement with the theoretical phase response across the studied frequency range (errors &amp;lt;1 mrad). For unconsolidated samples, removal of errors results in phase spectra more consistent with expected polarization mechanisms, as based on phase peaks recorded for small pyrite and clay particles at high frequencies. These phase peaks could not be identified in the uncorrected data. Our approach can substantially enhance the value of the SIP method for the characterization of fine-grained sediments and rocks.
SCOREing in Retinal Venous Occlusive Disease (2009)

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Analysis of the plant growth‐promoting properties encoded by the genome of the rhizobacterium P seudomonas putida   BIRD ‐1 (2012)

Pseudomonas putida BIRD-1 is a plant growth-promoting rhizobacterium whose genome size is 5.7 Mbp. It adheres to plant roots and colonizes the rhizosphere to high cell densities even in soils with low moisture. This property is linked to its ability to synthesize trehalose, since a mutant deficient in the synthesis of trehalose exhibited less tolerance to desiccation than the parental strain. The genome of BIRD-1 encodes a wide range of proteins that help it to deal with reactive oxygen stress generated in the plant rhizosphere. BIRD-1 plant growth-promoting rhizobacteria properties derive from its ability to enhance phosphorous and iron solubilization and to produce phytohormones. BIRD-1 is capable of solubilizing insoluble inorganic phosphate forms through acid production. The genome of BIRD-1 encodes at least five phosphatases related to phosphorous solubilization, one of them being a phytase that facilitates the utilization of phytic acid, the main storage form of phosphorous in plants. Pyoverdine is the siderophore produced by this strain, a mutant that in the FvpD siderophore synthase failed to grow on medium without supplementary iron, but the mutant was as competitive as the parental strain in soils because it captures the siderophores produced by other microbes. BIRD-1 overproduces indole-3-acetic acid through convergent pathways.
Wireless Network Coding with Local Network Views: Coded Layer Scheduling (2011)

One of the fundamental challenges in the design of distributed wireless networks is the large dynamic range of network state. Since continuous tracking of global network state at all nodes is practically impossible, nodes can only acquire limited local views of the whole network to design their transmission strategies. In this paper, we study multi-layer wireless networks and assume that each node has only a limited knowledge, namely 1-local view, where each S-D pair has enough information to perform optimally when other pairs do not interfere, along with connectivity information for rest of the network. We investigate the information-theoretic limits of communication with such limited knowledge at the nodes. We develop a novel transmission strategy, namely Coded Layer Scheduling, that solely relies on 1-local view at the nodes and incorporates three different techniques: (1) per layer interference avoidance, (2) repetition coding to allow overhearing of the interference, and (3) network coding to allow interference neutralization. We show that our proposed scheme can provide a significant throughput gain compared with the conventional interference avoidance strategies. Furthermore, we show that our strategy maximizes the achievable normalized sum-rate for some classes of networks, hence, characterizing the normalized sum-capacity of those networks with 1-local view.