gebhart/patrepeval huggingface dataset:
Nisin M: a Bioengineered Nisin A Variant That Retains Full Induction Capacity but Has Significantly Reduced Antimicrobial Activity (2020)

Nisin A is a potent antimicrobial with potential as an alternative to traditional antibiotics, and a number of genetically modified variants have been created that target clinically relevant pathogens. In addition to antimicrobial activity, nisin autoregulates its own production via a signal transduction pathway, a property that has been exploited in a protein expression system termed the nisin-controlled gene expression (NICE) system. Although NICE has become one of the most popular protein expression systems, one drawback is that the inducer peptide, nisin A, also has inhibitory activity. It has already been demonstrated that the N-terminal region of nisin A contributes to antimicrobial activity and signal transduction properties; therefore, we conducted bioengineering of nisin at positions Pro9 and Gly10 within ring B to produce a bank of variants that could potentially be used as alternative induction peptides. One variant, designated nisin M, has threonines at positions 9 and 10 and retains induction capacity comparable to that of wild-type nisin A, while most of the antimicrobial activity is abolished. Further analysis confirmed that nisin M produces a mix of peptides as a result of different degrees of dehydration of the two threonines. We show that nisin M exhibits potential as a more suitable alternative to nisin A for the expression of proteins that may be difficult to express or for production of proteins in strains that are sensitive to wild-type nisin. Moreover, it may address the increasing demand by industry for optimization of peptide fermentations to increase yields or production rates.<b>IMPORTANCE</b> This study describes the generation of a nisin variant with superior characteristics for use in the NICE protein expression system. The variant, termed nisin M, retains an induction capacity comparable to that of wild-type nisin A but exhibits significantly reduced antimicrobial activity and can therefore be used at concentrations that are normally toxic to the expression host.
On the model of computation (2022)

opinion On the model of computation: point Author: William Dally NVIDIA, Incline Village, NV NVIDIA, Incline Village, NVView Profile Authors Info & Claims Communications of the ACMVolume 65Issue 9September 2022 pp 30–32https://doi.org/10.1145/3548783Published:19 August 2022Publication History 0citation6,034DownloadsMetricsTotal Citations0Total Downloads6,034Last 12 Months6,034Last 6 weeks63 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Specific neural substrate linking respiration to locomotion (2011)

When animals move, respiration increases to adapt for increased energy demands; the underlying mechanisms are still not understood. We investigated the neural substrates underlying the respiratory changes in relation to movement in lampreys. We showed that respiration increases following stimulation of the mesencephalic locomotor region (MLR) in an in vitro isolated preparation, an effect that persists in the absence of the spinal cord and caudal brainstem. By using electrophysiological and anatomical techniques, including whole-cell patch recordings, we identified a subset of neurons located in the dorsal MLR that send direct inputs to neurons in the respiratory generator. In semi-intact preparations, blockade of this region with 6-cyano-7-nitroquinoxaline-2,3-dione and (2R)-amino-5-phosphonovaleric acid greatly reduced the respiratory increases without affecting the locomotor movements. These results show that neurons in the respiratory generator receive direct glutamatergic connections from the MLR and that a subpopulation of MLR neurons plays a key role in the respiratory changes linked to movement.
RaceTrack (2005)

Bugs due to data races in multithreaded programs often exhibit non-deterministic symptoms and are notoriously difficult to find. This paper describes RaceTrack, a dynamic race detection tool that tracks the actions of a program and reports a warning whenever a suspicious pattern of activity has been observed. RaceTrack uses a novel hybrid detection algorithm and employs an adaptive approach that automatically directs more effort to areas that are more suspicious, thus providing more accurate warnings for much less over-head. A post-processing step correlates warnings and ranks code segments based on how strongly they are implicated in potential data races. We implemented RaceTrack inside the virtual machine of Microsoft's Common Language Runtime (product version v1.1.4322) and monitored several major, real-world applications directly out-of-the-box,without any modification. Adaptive tracking resulted in a slowdown ratio of about 3x on memory-intensive programs and typically much less than 2x on other programs,and a memory ratio of typically less than 1.2x. Several serious data race bugs were revealed, some previously unknown.
Low-temperature ordered states of dysprosium, terbium, and holmium aluminum garnets (1981)

The low-temperature ordered states of dysprosium, terbium, and holmium aluminum garnets have been investigated by the Luttinger-Tisza method, taking rigorously into account the dipole-dipole interaction. It is found that for each of these cases, in the absence of an external magnetic field, the lowest-energy configuration corresponds to antiferromagnetic ordering with three pairs of sublattices, in agreement with neutron scattering experiments. In the presence of external field along the [001] direction, the lowest-energy configuration turns out to be that of ferromagnetic chains in the $x$ and $y$ directions, with the nearest ferromagnetic chains pointing in the opposite directions, the same as that proposed by Landau and Keen. When the external magnetic field is along the [110] direction, there are two configurations which correspond to lowest energy; the individual chains are ferromagnetic but not all ferromagnetic chains are parallel, there being chains which point in opposite directions.
Compact hybrid defected ground plane (2004)

Abstract A novel hybrid defected ground structure (DGS), which interleaves a photonic bandgap structure (PBGS), is investigated theoretically as well as experimentally. It yields distinct multiple passbands and stopbands. The novel structure can be used either a compact diplexer or a dual stopband filter. With Chebyshev distributions on the interleaved PBGS, the passband and stopband performances improve significantly. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 44: 266–270, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20607
Delamination Growth Under Cyclic Loading at Elevated Temperature in Thermoplastic Composites (1989)

The cyclic Mode I delamination growth characteristics of unidirectional carbon/polyetheretherketone (PEEK) composites at ambient and elevated temperatures was studied. At room temperature, crack growth rate was found to increase as a function of cycles, a common characteristic for such materials under load-controlled conditions. In contrast, at elevated temperature 93°C (200°F), early delamination growth was characterized by decreasing growth rate (stable growth). With continued cycling, there was a breakdown of the process zone (craze-plastic zone) leading to rapid crack propagation. Increased temperature and lower rates of deformation tend to enhance ductility in PEEK-based thermoplastic composites through fibril formation resulting from the breakup of crystalline lamellae. This ductility tends to stabilize the crack front, most likely through craze formation ahead of the crack tip, resulting in an anomalous decrease in growth rate with increasing cycles. This behavior is termed as slow crack growth (SCG). The process zone (craze-plastic zone) eventually gives way to crack growth after a critical crack-tip opening displacement is reached. The crack growth process is associated with less ductility, even at elevated temperature 93°C (200°F). When crack growth occurs without any attendant process zone ahead of the crack, as in the case of the specimens tested at room temperature, less ductility is evident. These fracture surfaces display evidence of interlamellar failure. As a result of ductility and the active role of the process zone at elevated temperature, neither the strain energy release rate, G, nor the stress intensity factor, K, were found to be appropriate parameters to characterize the earlier part of delamination growth at elevated temperature. Instead, the process zone (craze-plastic zone) growth at elevated temperature was shown to be best described by a relaxation controlled growth model.
Vision guided lane transition (2002)

Many systems have been created which can keep an autonomous vehicle within a driving lane, but little experimental work has been reported that describes methods to transition a vehicle between lanes. Three techniques to accomplish lane transition using the ALVINN lane keeping system are reported here. The most basic involves intelligently switching between two trained ALVINN networks. The other techniques use active control of virtual camera views to move the vehicle into the destination lane.
Emerging role of relaxin in renal and cardiovascular function (2004)

Although traditionally associated with reproductive processes, relaxin is emerging as an important player in renal and cardiovascular function. Much of our recently acquired understanding of relaxin in this new context has arisen from studies of maternal renal and cardiovascular adaptations to pregnancy in rats where the hormone is turning out to be an important mediator. First, we highlight the influence of relaxin on renal hemodynamics and glomerular filtration rate, as well as on other peripheral circulations. Second, we discuss the effect of relaxin on both the steady and pulsatile systemic arterial load, as well as on the heart, in particular, coronary blood flow. Third, we consider the impact of the hormone on cultured endothelial and vascular smooth muscle cells. Fourth, we address the interaction of relaxin with renal and cardiac disease, as well as its role in angiogenesis. Finally, in Perspectives, we point out several key research questions in need of investigation that relate to a potential autocrine/paracrine role of relaxin in renal and cardiovascular tissues. Furthermore, on the basis of its potent vasodilatory and matrix-degrading attributes, we speculate about the therapeutic potential of relaxin in renal and cardiovascular diseases.
Mechanisms of antimicrobial resistance in Gram-negative bacilli (2015)

The burden of multidrug resistance in Gram-negative bacilli (GNB) now represents a daily issue for the management of antimicrobial therapy in intensive care unit (ICU) patients. In Enterobacteriaceae, the dramatic increase in the rates of resistance to third-generation cephalosporins mainly results from the spread of plasmid-borne extended-spectrum beta-lactamase (ESBL), especially those belonging to the CTX-M family. The efficacy of beta-lactam/beta-lactamase inhibitor associations for severe infections due to ESBL-producing Enterobacteriaceae has not been adequately evaluated in critically ill patients, and carbapenems still stands as the first-line choice in this situation. However, carbapenemase-producing strains have emerged worldwide over the past decade. VIM- and NDM-type metallo-beta-lactamases, OXA-48 and KPC appear as the most successful enzymes and may threaten the efficacy of carbapenems in the near future. ESBL- and carbapenemase-encoding plasmids frequently bear resistance determinants for other antimicrobial classes, including aminoglycosides (aminoglycoside-modifying enzymes or 16S rRNA methylases) and fluoroquinolones (Qnr, AAC(6')-Ib-cr or efflux pumps), a key feature that fosters the spread of multidrug resistance in Enterobacteriaceae. In non-fermenting GNB such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, multidrug resistance may emerge following the sole occurrence of sequential chromosomal mutations, which may lead to the overproduction of intrinsic beta-lactamases, hyper-expression of efflux pumps, target modifications and permeability alterations. P. aeruginosa and A. baumannii also have the ability to acquire mobile genetic elements encoding resistance determinants, including carbapenemases. Available options for the treatment of ICU-acquired infections due to carbapenem-resistant GNB are currently scarce, and recent reports emphasizing the spread of colistin resistance in environments with high volume of polymyxins use elicit major concern.
Characterization of a fibre optic swept laser source at 1 μm for optical coherence tomography imaging systems (2011)

We report the development of a swept wavelength laser at 1 micron based on a linear cavity fibre configuration with an intra-cavity half symmetrical confocal Fabry-Perot tunable filter and a semiconductor optical amplifier as a gain medium. The performances of the source in terms of parameters like: sweep repetition rate (1-20 kHz), center wavelength (1065 nm), wavelength scanning range (max. 50nm), instantaneous line-width (&lt;0.1nm) and a boosted output power of around 40 mW are demonstrated. The new source tested on an OCT system is exhibiting sufficient linearity in wave-number (k-space) at 1 kHz repetition rate; therefore no k-trigger, or wavelength rescaling process was needed.
A New Paradigm For Diversity In Engineering (2020)

social psychologist with 8 years of experience as a faculty member teaching and researching the processes involved in changing stereotypes and prejudice, as well as 6 years of experience as an administrator in the Diversity Resource Office directing projects, writing grants, and developing forums based upon theory and research for creating effective diversity tools and best practices.
A Conserved Three-nucleotide Core Motif Defines Musashi RNA Binding Specificity (2014)

Musashi (MSI) family proteins control cell proliferation and differentiation in many biological systems. They are overexpressed in tumors of several origins, and their expression level correlates with poor prognosis. MSI proteins control gene expression by binding RNA and regulating its translation. They contain two RNA recognition motif (RRM) domains, which recognize a defined sequence element. The relative contribution of each nucleotide to the binding affinity and specificity is unknown. We analyzed the binding specificity of three MSI family RRM domains using a quantitative fluorescence anisotropy assay. We found that the core element driving recognition is the sequence UAG. Nucleotides outside of this motif have a limited contribution to binding free energy. For mouse MSI1, recognition is determined by the first of the two RRM domains. The second RRM adds affinity but does not contribute to binding specificity. In contrast, the recognition element for Drosophila MSI is more extensive than the mouse homolog, suggesting functional divergence. The short nature of the binding determinant suggests that protein-RNA affinity alone is insufficient to drive target selection by MSI family proteins.
The properties of manganese-zinc ferrites and the physical processes governing them (1957)

The paper outlines some of the electrical and physical properties of manganese-zinc ferrites and the mechanisms by which they occur. Initial permeability is shown to depend on stoichiometry, granular structure and composition, while the temperature coefficient of permeability is shown to be controllable by the addition of small amounts of trivalent metallic impurities. The influence of composition and manufacturing conditions on the losses, Curie point and induction is examined, and a note on the high-frequency properties is included.
Synthesis of 2,2-Disubstituted Azaindolines by Intramolecular Cyclization in Acidic Media (2011)

International audience
Reduced Heart Rate Recovery Is Associated with Poorer Cognitive Function in Older Adults with Cardiovascular Disease (2012)

Cardiovascular disease (CVD) in older adults has been associated with varying degrees of cognitive dysfunction. Several mechanisms may explain this association, including impaired cardiovascular reactivity to autonomic nervous system (ANS) signaling. Reduced heart rate recovery following a stress test may be considered an indication of impaired ANS function (i.e., reduced parasympathetic activity). Participants were 47 older adults (53-83 years) who underwent a treadmill stress test and were administered a comprehensive neuropsychological battery upon entry to phase II cardiac rehabilitation. Reduced parasympathetic activity was associated with impaired cognitive performance on a measure of global cognitive function and on tasks of speeded executive function and confrontation naming. These relationships suggest that changes in autonomic function may be mechanistically related to the impaired cognitive function prevalent in CVD patients.
Lipid Dynamics in Diisobutylene-Maleic Acid (DIBMA) Lipid Particles in Presence of Sensory Rhodopsin II (2021)

Amphiphilic diisobutylene/maleic acid (DIBMA) copolymers extract lipid-encased membrane proteins from lipid bilayers in a detergent-free manner, yielding nanosized, discoidal DIBMA lipid particles (DIBMALPs). Depending on the DIBMA/lipid ratio, the size of DIBMALPs can be broadly varied which makes them suitable for the incorporation of proteins of different sizes. Here, we examine the influence of the DIBMALP sizes and the presence of protein on the dynamics of encased lipids. As shown by a set of biophysical methods, the stability of DIBMALPs remains unaffected at different DIBMA/lipid ratios. Coarse-grained molecular dynamics simulations confirm the formation of viable DIBMALPs with an overall size of up to 35 nm. Electron paramagnetic resonance spectroscopy of nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels reveals that the dynamics of enclosed lipids are not altered by the DIBMALP size. The presence of the membrane protein sensory rhodopsin II from <i>Natronomonas pharaonis</i> (<i>Np</i>SRII) results in a slight increase in the lipid dynamics compared to empty DIBMALPs. The light-induced photocycle shows full functionality of DIBMALPs-embedded <i>Np</i>SRII and a significant effect of the protein-to-lipid ratio during preparation on the <i>Np</i>SRII dynamics. This study indicates a possible expansion of the applicability of the DIBMALP technology on studies of membrane protein-protein interaction and oligomerization in a constraining environment.
CCDC 781681: Experimental Crystal Structure Determination (2011)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum (2015)

The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic that is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods, little is currently known about the information theoretic limit on the estimation accuracy as a function of sample size. Here, we show that using the SFS to estimate the size history of a population has a minimax error of at least O(1/log s), where s is the number of independent segregating sites used in the analysis. This rate is exponentially worse than known convergence rates for many classical estimation problems in statistics. Another surprising aspect of our theoretical bound is that it does not depend on the dimension of the SFS, which is related to the number of sampled individuals. This means that, for a fixed number s of segregating sites considered, using more individuals does not help to reduce the minimax error bound. Our result pertains to populations that have experienced a bottleneck, and we argue that it can be expected to apply to many populations in nature.
Survey on path and view planning for UAVs (2020)

In recent decades, unmanned aerial vehicles (UAVs) have developed rapidly and been widely applied in many domains, including photography, reconstruction, monitoring, and search and rescue. In such applications, one key issue is path and view planning, which tells UAVs exactly where to fly and how to search. With specific consideration for three popular UAV applications (scene reconstruction, environment exploration, and aerial cinematography), we present a survey that should assist researchers in positioning and evaluating their works in the context of existing solutions. /Conclusions It should also help newcomers and practitioners in related fields quickly gain an overview of the vast literature. In addition to the current research status, we analyze and elaborate on advantages, disadvantages, and potential explorative trends for each application domain.
Synthesis of the mitochondrial inner membrane in cultured Xenopus laevis oocytes. (1976)

The purpose of this study was to investigate the contribution of mitochondrial and cytoplasmic protein synthesis to the biogenesis of cytochrome oxidase (ferrocytochrome c:oxygen oxidoreductase EC 1.9.3.1) and rutamycin-sensitive adenosine triphosphatase (ATP phosphohydrolase EC 3.6.1.3) in cultured oocytes of the toad, Xenopus laevis. X. laevis cytochrome oxidase was purified over 23-fold with respect to specific activity and over 29-fold with respect to specific heme a content from oocyte submitochondrial particles. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate separated the enzyme into six subunits with molecular weights of 44,000, 33,000, 23,000, 17,000, 12,000 and 9,500. the synthesis of the three larger subunits is sensitive to chloramphenicol (an inhibitor of mitochondrial protein synthesis), indicating that these subunits are made on mitochondrial ribosomes; the synthesis of the three smaller subunits is sensitive to cycloheximide (an inhibitor of cytoplasmic protein synthesis) and therefore occurs on cytoplasmic ribosomes. X. laevis rutamycin-sensitive ATPase, purified over 19-fold from oocyte submitochondrial pparticles, consists of 10 subunits with molecular weights of 56,000, 53,000, 41,000, 32,000, 29,000, 24,000, 21,000, 17,500 (2), and 11,500 on sodium dodecyl sulfate-polyacrylamide gels. The 29,000, 21,000, and one of the 17,500-dalton polypeptides are synthesized in the presence of cycloheximide and are, therefore, products of mitochondrial protein synthesis; the synthesis of the remaining seven subunits occurs in the presence of chloramphenicol, indicating that these subunits are made on cytoplasmic ribosomes. The synthesis of protein by mitochondria in cultured oocytes appears to be dependent upon cytoplasmic protein synthesis. In the presence of cycloheximide, the mitoribosomal synthesis of the subunits of cytochrome oxidase and rutamycin-sensitive ATPase is detectable only after a prior inhibition of mitochondrial protein synthesis by chloramphenicol. Oocyte mitochondrial ribosomes synthesize at least nine polypeptides after chloramphenicol treatment, three of which are components of neither cytochrome oxidase nor rutamycin-sensitive ATPase.