gebhart/patrepeval huggingface dataset:
The ability of <i>Pseudomonas aeruginosa</i> to adopt a Small Colony Variant (SCV) phenotype is conserved, and not restricted to clinical isolates (2021)

ABSTRACT A subpopulation of Small Colony Variants (SCVs) is a frequently observed feature of Pseudomonas aeruginosa isolated from cystic fibrosis (CF) lungs biofilms. SCVs have almost exclusively been reported from infected hosts, essentially CF individuals or, by extension, from laboratory cultivation of strains originated from infected hosts. We previously reported the identification of P. aeruginosa SCVs emerging from a non-clinical strain and displaying features shared with clinical SCVs. In the present work, we investigated the ability of 22 P. aeruginosa isolates from various environmental origins to, under laboratory culture conditions, spontaneously adopt a SCV-like smaller alternative morphotype distinguishable from the ancestral parent strain. Unexpectedly, we found that all the P. aeruginosa strains tested have the ability to adopt a SCV morphotype, regardless of their origin. Based on the phenotypes already described for SCVs, the SCV-like morphotypes obtained were clustered in two groups displaying various phenotypic profiles, including one characteristic of already described SCVs. We conclude that the ability to switch to a SCV phenotype is a conserved feature in Pseudomonas aeruginosa . IMPORTANCE P. aeruginosa is an opportunistic pathogen that thrives in many environments. It is significant public health concern, notably because it is the most prevalent pathogen found in the lungs of people with cystic fibrosis (CF). In infected hosts, its persistence is believed to be related to the emergence of an alternative small colony variant (SCV) phenotype. By reporting the distribution of P. aeruginosa SCVs in various non-clinical environments, this work contributes to understanding a conserved adaptation mechanism used by P. aeruginosa to rapidly adapt in all environments. Counteraction of this strategy could prevent P. aeruginosa persistent infection in the future.
Decreased levels of autoantibodies against apolipoprotein B-100 antigens are associated with cardiovascular disease in systemic lupus erythematosus (2015)

Increased production of autoantibodies is a characteristic feature of systemic lupus erythematosus (SLE) and there is evidence that several of these autoantibodies may contribute to increased cardiovascular disease (CVD) in SLE. Autoantibodies against the apolipoprotein (apo) B-100 peptides p45 and p210 have been associated with a lower CVD risk in non-SLE cohorts. The aim of the present study was to investigate how SLE affects the occurrence of these potentially protective autoantibodies. The study cohort consisted of 434 SLE patients and 322 age- and sex-matched population controls. Antibodies against native and malondialdehyde (MDA)-modified p45 and p210 were measured by enzyme-linked immunosorbent assay (ELISA). SLE patients had significantly lower levels of p210 immunoglobulin (Ig)G and p45 IgM (both the native and malondialdehyde (MDA)-modified forms). SLE patients with manifest CVD (myocardial infarction, ischaemic cerebrovascular disease or peripheral vascular disease) had lower levels p210 IgG and p45 IgM than SLE patients without CVD. Decreased levels of these autoantibodies were also observed in SLE patients with permanent organ damage, as assessed by the Systemic Lupus International Collaborating Clinics/American College of Rheumatology (ACR) Damage Index (SDI). The present findings show that patients with SLE, a condition generally characterized by abundance of autoantibodies of multiple specificities, have reduced levels of antibodies against the apo B-100 antigens p45 and p210 and that the levels of these antibodies are reduced further in SLE patients with CVD. These observations suggest the possibility that an impaired antibody-mediated removal of damaged LDL particles may contribute to the development of vascular complications and organ damage in SLE.
Application of the DoE Concept for Peptide API Process Development at Bachem (2015)

ICH guideline Q11 [1] describes approaches to developing process and drug substance understanding. In a traditional approach, set points and operating ranges for process parameters are defined, and the drug substance control strategy is typically based on demonstration of process reproducibility and testing to meet established acceptance criteria. In an enhanced approach, risk management and more extensive scientific knowledge are used to select process parameters and unit operations that impact critical quality attributes (CQAs) for evaluation in further studies to establish design space(s) and control strategies applicable over lifecycle of the drug substance [1].
A deletion in the <scp><i>wapB</i></scp> promoter in many serotypes of <i>Pseudomonas aeruginosa</i> accounts for the lack of a terminal glucose residue in the core oligosaccharide and resistance to killing by <scp>R</scp>3‐pyocin (2013)

Pseudomonas aeruginosa is an opportunistic human pathogen producing a variety of virulence factors. One of them is lipopolysaccharide, consisting of endotoxic lipid A and long-chain O-antigen polysaccharide, which are connected together through a short linker region, called core oligosaccharide. Chemical structures of the core oligosaccharide are well conserved, with one exception, in that certain strains of P. aeruginosa add a terminal glucose residue (Glc(IV) ) to core by a transferase reaction, due to the activity of a glucosyltransferase, WapB. Here, we investigated the regulation of wapB expression. Our results showed that while the majority of analysed genomes of P. aeruginosa contain wapB, many of these have a conserved identical 5-nucleotide deletion in the upstream region that inactivated the promoter. This deletion is within the -10 hexamer that is recognized by a principle sigma factor (RpoD, or σ70) as proven by data from an electromobility shift assay. These results provide the molecular basis of why LPS core of many P. aeruginosa strains is lacking Glc(IV) . In addition, we show that absence of Glc(IV) due to an inactive wapB promoter confers resistance to killing by R3-pyocin, a phage tail-like bacteriocin of P. aeruginosa.
Dynamic Holographic Optical Tweezers: Transforming Mesoscopic Matter with Light (2003)

Holographic optical tweezers use forces exerted by computergenerated holograms to capture, move, sort, and transform objects ranging in size from tens of nanometers to hundreds of micrometers. Holographic optical tweezers can be arranged in arbitrary three-dimensional configurations. Each trap in an array can be imbued with unique properties, such as the ability to exert controlled torques as well as forces, by appropriately engineering the beams’ wave fronts. This presentation introduces holographic optical trapping as a new technique, and highlights two applications: sorting mesoscopic objects with arrays of optical traps (optical fractionation) and driving microelectromechanical systems (MEMS) with arrays of optical vortices.
Evaluation of Hofmeister Effects on the Kinetic Stability of Proteins (2005)

Dissolved salts are known to affect properties of proteins in solution including solubility and melting temperature, and the effects of dissolved salts can be ranked qualitatively by the Hofmeister series. We seek a quantitative model to predict the effects of salts in the Hofmeister series on the deactivation kinetics of enzymes. Such a model would allow for a better prediction of useful biocatalyst lifetimes or an improved estimation of protein-based pharmaceutical shelf life. Here we consider a number of salt properties that are proposed indicators of Hofmeister effects in the literature as a means for predicting salt effects on the deactivation of horse liver alcohol dehydrogenase (HL-ADH), alpha-chymotrypsin, and monomeric red fluorescent protein (mRFP). We find that surface tension increments are not accurate predictors of salt effects but find a common trend between observed deactivation constants and B-viscosity coefficients of the Jones-Dole equation, which are indicative of ion hydration. This trend suggests that deactivation constants (log k(d,obs)) vary linearly with chaotropic B-viscosity coefficients but are relatively unchanged in kosmotropic solutions. The invariance with kosmotropic B-viscosity coefficients suggests the existence of a minimum deactivation constant for proteins. Differential scanning calorimetry is used to measure protein melting temperatures and thermodynamic parameters, which are used to calculate the intrinsic irreversible deactivation constant. We find that either the protein unfolding rate or the rate of intrinsic irreversible deactivation can control the observed deactivation rates.
Classification margin for improved class-based speech recognition performance (2012)

This paper investigates class-based speech recognition, and more precisely the impact of the selection of the training samples for each class on the final speech recognition performance. Increasing the number of recognition classes should lead to more specific models, and thus to better recognition performance, providing the trained model parameters are reliable. However, when the number of classes increases, the amount of training data for each class gets smaller, and may lead to unreliable parameters. The experiments described in the paper show that taking into account a classification margin tolerance helps associating more training data to each class, and improves the overall speech recognition performance.
The US Navy Coupled Ocean-Wave Prediction System (2014)

NASA image taken May 9, 2006, from the International Space Station, showing the outgoing tidal current and complex wave patterns near Punta Perihuete
Thermal Detectors for High Resolution Spectroscopy (1987)

Thermal calorimeters operating in the millikelvin temperature range are capable of detecting single particle or photon interactions with deposited energy thresholds as low as a few electron volts. Small monolithic devices can be made using integrated circuit fabrication techniques and should have resolutions near 1 eV. Relatively crude test devices have already achieved resolutions for soft X-rays that are several times better than the best solid state detectors. It also may be possible to construct kilogram-scale detectors with thresholds less than 1000 eV. High resolution calorimeters have obvious applications in many types of spectroscopy, while the large-volume detectors would be useful for neutrino measurements and other rare interactions and decays. The truly unique characteristic of these large calorimeters as particle detectors is their sensitivity to non-ionizing interactions, and it has been proposed to use them to search for certain dark matter candidates and other exotic particles.
Comparison of trimethylgallium and triethylgallium for the growth of GaN (1997)

GaN films grown by low-pressure metalorganic chemical vapor deposition using trimethylgallium and triethylgallium as gallium precursors are compared. The films were characterized by x-ray diffraction, Hall effect, photoluminescence, secondary ion mass spectroscopy, and etch pit density measurements. GaN layers grown using triethylgallium exhibited superior electrical and optical properties and a lower carbon impurity concentration.
Biomonitoring of prenatal analgesic intake and correlation with infantile anti-aeroallergens IgE (2016)

An association between prenatal acetaminophen or ibuprofen intake and an increased risk of asthma and increased IgE level in children is discussed in various epidemiological studies. Although the molecular mechanistic link is still unknown, the question whether or not acetaminophen and/or ibuprofen are safe pain medications during pregnancy arose. In this study, we associate maternal acetaminophen and ibuprofen intake during pregnancy and breastfeeding to infantile asthma phenotypes and elevated IgE level. Therefore, we analysed questionnaires from a local mother-child cohort and monitored drug intake by LC-MS biomonitoring in urine. No association was found between drug intake and any analysed health outcome using questionnaire data. For the information obtained from biomonitoring, no association was found for ibuprofen and acetaminophen intakes during breastfeeding. However, an association between prenatal acetaminophen intake and increased infantile IgEs related to aeroallergens was statistically detected, but not for asthma phenotypes.
Alteration at the ultramafic‐hosted Logatchev hydrothermal field: Constraints from trace element and Sr‐O isotope data (2012)

Serpentinized peridotite and gabbronorite represent the host rocks to the active, ultramafic‐hosted Logatchev hydrothermal field at the Mid‐Atlantic Ridge. We use trace element, δ 18 O and 87 Sr/ 86 Sr data from bulk rock samples and mineral separates in order to constrain the controls on the geochemical budget within the Logatchev hydrothermal system. The trace element data of serpentinized peridotite show strong compositional variations indicating a range of processes. Some peridotites experienced geochemical modifications associated with melt‐rock interaction processes prior to serpentinization, which resulted in positive correlations of increasing high field strength element (HFSE) concentrations and light rare earth element (LREE) contents. Other serpentinites and lizardite mineral separates are enriched in LREE, lacking a correlation with HFSE due to interaction with high‐temperature, black‐smoker type fluids. The enrichment of serpentinites and lizardite separates in trace elements, as well as locally developed negative Ce‐anomalies, indicate that interaction with low‐T ambient seawater is another important process in the Logatchev hydrothermal system. Hence, mixing of high‐T hydrothermal fluids during serpentinization and/or re‐equilibration of O‐isotope signatures during subsequent low‐T alteration is required to explain the trace element and δ 18 O temperature constraints. Highly radiogenic 87 Sr/ 86 Sr signatures of serpentinite and lizardite separates provide additional evidence for interaction with seawater‐derived fluids. Sparse talc alteration at the Logatchev site are most likely caused by Si‐metasomatism of serpentinite associated with the emplacement of shallow gabbro intrusion(s) generating localized hydrothermal circulation. In summary the geochemistry of serpentinites from the Logatchev site document subsurface processes and the evolution of a seafloor ultramafic hydrothermal system.
Selective Bond Cleavage in RAFT Agents Promoted by Low‐Energy Electron Attachment (2021)

Radical polymerization with reversible addition-fragmentation chain transfer (RAFT polymerization) has been successfully applied to generate polymers of well-defined architecture. For RAFT polymerization a source of radicals is required. Recent work has demonstrated that for minimal side-reactions and high spatio-temporal control these should be formed directly from the RAFT agent or macroRAFT agent (usually carbonothiosulfanyl compounds) thermally, photochemically or by electrochemical reduction. In this work, we investigated low-energy electron attachment to a common RAFT agent (cyanomethyl benzodithioate), and, for comparison, a simple carbonothioylsulfanyl compound (dimethyl trithiocarbonate, DMTTC) in the gas phase by means of mass spectrometry as well as quantum chemical calculations. We observe for both compounds that specific cleavage of the C-S bond is induced upon low-energy electron attachment at electron energies close to zero eV. This applies even in the case of a poor homolytic leaving group (<sup>.</sup> CH<sub>3</sub> in DMTTC). All other dissociation reactions found at higher electron energies are much less abundant. The present results show a high control of the chemical reactions induced by electron attachment.
The Effect of the Mammalian Neuropeptide, Gastrin-Releasing Peptide (GRP), on Gastrointestinal and Pancreatic Hormone Secretion in Man (1983)

Gastrin-releasing peptide, a newly isolated mammalian peptide similar in its structure and actions to the amphibian peptide, bombesin, has recently been localized to nerves in the brain, gut and pancreas. The present study investigates its effects on gut and pancreatic peptides in man. Intravenous infusion of 0.7 and 2.9 pmol min-1 kg-1 produced significant elevation of plasma gastrin, cholecystokinin-like immunoreactivity and neurotensin. It was found also to potentiate glucose-dependent insulin secretion. Its specific location in nerve fibres in the proximal gut and pancreas and its selective effect on gastroenteropancreatic peptides may favour its role as a physiological regulatory neuropeptide.
B cell antigen receptor signal strength and peripheral B cell development are regulated by a 9-<i>O</i>-acetyl sialic acid esterase (2008)

We show that the enzymatic acetylation and deacetylation of a cell surface carbohydrate controls B cell development, signaling, and immunological tolerance. Mice with a mutation in sialate:O-acetyl esterase, an enzyme that specifically removes acetyl moieties from the 9-OH position of alpha2-6-linked sialic acid, exhibit enhanced B cell receptor (BCR) activation, defects in peripheral B cell development, and spontaneously develop antichromatin autoantibodies and glomerular immune complex deposits. The 9-O-acetylation state of sialic acid regulates the function of CD22, a Siglec that functions in vivo as an inhibitor of BCR signaling. These results describe a novel catalytic regulator of B cell signaling and underscore the crucial role of inhibitory signaling in the maintenance of immunological tolerance in the B lineage.
Microbubble signal classification using NSSA-based filtering methods (2017)

Microbubbles (MBs) are capable of binding specifically to molecular markers on the vascular endothelium to enable sensitive detection of early stage disease. Traditional microbubble imaging techniques rely on the nonlinearity of microbubble signal to differentiate it from surrounding tissue. However, the presence of harmonic energy among echogenic tissue interfaces can limit the effectiveness of these methods in enhancing microbubble contrast. In many cases, it is challenging to achieve any quantitative separation between static tissue signal and bound MB signal (Fig. 1B). In this study, we use normalized singular spectrum area (NSSA) to differentiate between static tissue signal, bound MB signal, and free MB signal in a mouse hindlimb tumor.
Minimizing Power Loss in Air-Cored Coils for TET Heart Pump Systems (2011)

Transcutaneous energy transfer (TET) has been shown to provide an effective means of supplying power to implantable devices by avoiding the risk of infection associated with wires passing through the skin. However, it is important to manage the heat generated by the TET systems and avoid the potential of thermal tissue damage. This paper introduces a new optimization procedure to minimize the amount of power dissipated in the power transfer coils of an implantable TET heart pump system. By analyzing the overall circuit impedance it is possible to observe that a zero voltage switched TET system may dissipate different amounts of power in the power transfer coils while delivering the same amount of power. In this study an objective function was developed to determine the best configuration of resonant capacitors for any particular set of TET coils in order to minimize power loss. A set of TET coils was characterized by their self inductance, operating coupling range and their equivalent series resistance profile. When delivering 15 W over a coupling range of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> =0.1 to 0.55 (corresponding to a separation of up to 25 mm), the optimal configuration improves heating performance and provides frequency stability over the extended range of coupling variation. When compared to a traditional tuning configuration tuned to a nominal resonant frequency.
A nonstoichiometric structural model to characterize changes in the nickel hydroxide electrode during cycling (2003)

Experimental capacities and mass changes are recorded using an electrochemical quartz crystal microbalance during the first 9 charge and discharge cycles of nickel hydroxide thin films cycled in 3.0 weight percent (wt%) potassium hydroxide electrolyte. For the first time, the film capacities have been corrected for the oxygen evolution side reaction, and the data used as input into the point defect-containing structural model to track the changes that occur during short-term cycling. Variations in capacity and mass during formation and charge/discharge cycling are related to changes in the point defect parameters, thus providing a structural origin for the unique experimental variations observed here and often reported in the literature, but previously unexplained. Proton-, potassium-, and water-content vary in the active material during charge/discharge cycling. The observed capacity loss, or ''capacity fade'', is explained by incomplete incorporation of potassium ions in (or near) the nickel vacancy during charge, as additional protons are then allowed to occupy the vacant lattice site. The increase in water content during reduction parallels the expansion of the electrode that is well known during cycling. This result confirms the origin of the swelling phenomenon as being caused by water incorporation. The model and methodology developed in this paper can be used to correlate electrochemical signatures with material chemical structure.
Graphical dictionaries and the memorable space of graphical passwords (2004)

In commonplace textual password schemes, users choose passwords that are easy to recall. Since memorable&#13;\npasswords typically exhibit patterns, they are exploitable by brute-force password crackers using attack dictionaries. This leads us to ask what classes of graphical passwords users find memorable. We postulate one such class supported by a collection of cognitive studies on visual recall, which can be characterized as mirror symmetric (reflective) passwords. We assume that an attacker would put this class in an attack dictionary for graphical passwords and propose&#13;\nhow an attacker might order such a dictionary. We extend the existing analysis of graphical passwords by analyzing the size of the mirror symmetric password space relative to the full password space of the graphical password scheme of Jermyn et al. (1999), and show it to be exponentially smaller (assuming appropriate axes of reflection). This reduction in size can be compensated for by longer passwords: the size of the space of mirror symmetric passwords of length about L + 5 exceeds that of the full password space for corresponding length L &amp;lt;= 14 on a 5x5 grid. This work could be used to help in formulating password rules for graphical password users and in creating proactive graphical password checkers.
Vaccines against ‘the other’<i>Ebolavirus</i>species (2016)

The Ebolavirus genus includes five member species, all of which pose a threat to global public health. These viruses cause fatal hemorrhagic fever in humans and nonhuman primates, and are considered category A pathogens due to the risk of their use as a bioweapon. The potential for an outbreak, either as a result of a natural emergence, deliberate release, or imported case underscores the need for protective vaccines. Recent progress in advancing vaccines for use against the strain of Zaire ebolavirus (EBOV) responsible for the West African Ebola outbreak offers reasons for optimism against EBOV, and demonstrates that protection against other Ebolavirus species is achievable.
Synthesis and Antiviral Activity of Acyclic Derivatives of 5‐Ethyl‐2′‐Deoxyuridine (1986)

Abstract Four acyclic pyrimidine derivatives of 5‐ethyl‐2′‐deoxyuridine (1) (EDU) have been synthesized and tested for their activities against vesicular stomatitis virus, vaccinia virus and various strains of herpes simplex virus type 1 (HSV‐1) and herpes simplex virus type 2 (HSV‐2) in primary rabbit kidney (PRK) cell cultures. The acyclic nucleoside analogues of EDU exhibited no activity against any of the viruses tested.