gebhart/patrepeval huggingface dataset:
Combined Computational–Experimental Approach to Explore the Molecular Mechanism of SaCas9 with a Broadened DNA Targeting Range (2019)

Despite accelerating development of CRISPR technology, there remains high demand for further interrogation of its fundamental biology. This is particularly fascinating as new improved CRISPR tools were artificially engineered to harbor beneficial features but often lack mechanistic explanation. SaCas9, a minimal Cas9 ideal for in vivo applications, suffers from long protospacer adjacent motif (PAM), which prompted effort on mutant KKH SaCas9 with relaxed PAM requirement. Leveraging structure-based molecular dynamics simulation, free-energy perturbation, and targeted experimentation, we developed a workflow for probing SaCas9 and a series of its variants, revealing intriguing dynamics of PAM recognition and the molecular mechanism of KKH mutations. Furthermore, we deployed this approach to design and validate new mutant SaCas9, SaCas9-NR and SaCas9-RL, with enhanced targeting range distinctive from the KKH mutant and improved activity in mammalian cells. Overall, our approach provides a dynamic understanding of SaCas9 PAM recognition and a new gateway to enlighten rationally designed Cas9 variants harboring novel properties.
Occurrence of l-menthyl-.BETA.-D-glucoside and methyl palmitate in rhizoma of japanese peppermint. (1978)

Our previous reports have described the isolation and identification of several minor constituents in the essential oil' obtained by steam distillation of a Japanese peppermint, SHUBI, as well as in the methanol extract of the fresh leaves.6) Nakayama et al.,') have
Carbon Distribution Near Interface between Base and Cladding Steels in Austenite Stainless Clad Steel Sheet (1989)

The distribution of carbon in austenite stainless clad steel sheets which consist of austenite stainless steel (SUS304L) as a cladding steel and 0.01%C steel as a base steel was investigated by means of a computer aided electron probe micro analysis, chemical analysis and emission spectrophotometry. A peak of carbon content near the interface between base steel and cladding steel was observed after hot-rolling and after annealing subsequent to hot-and cold-rolling. A coarse grain region was observed in base steel near the interface. These results were compared to the results calculated by diffusion equations where the carbon diffusion through the interface was considered by a chemical potential gradient of carbon. The calculated results showed the existence of the carbon peak in cladding steel near the interface and a carbon decrease in base steel near the interface, and agreed with results observed. By the comparison between results calculated and observed, the calculation method was confirmed to be applicable to predicting carbon distribution in an austenite stainless clad steel sheet.
Endovascular interventions in the management of acute extremity trauma: a narrative review (2021)

Minimally invasive endovascular interventions including stenting and embolization have been widely adopted for the treatment of emergent and traumatic thoracoabdominal injuries. In recent years, these techniques have been utilized in the setting of extremity vascular trauma with promising outcomes. By allowing for the rapid diagnosis and subsequent treatment of penetrating or blunt vascular extremity trauma, these techniques can help to minimize blood loss, reduce operative complications, and potentially prevent limb amputation. Here, we present a narrative review of the ever-increasing role of minimally invasive interventions in the management of extremity trauma and compare its use and outcomes to open surgical repair. A special focus is placed on diagnostic imaging modalities in trauma and the role of interventional radiologists in the work-up and treatment of extremity trauma. We discuss diagnostic imaging modalities that aid in the triaging of extremity trauma, such as Doppler sonography, CT angiography, and catheter-based angiography. We present an overview on the literature related to endovascular interventions such as embolotherapy and stent grafting as well as the technical challenges associated with each technique. Finally, we present our own cases on the workup and endovascular treatment of extremity trauma, including CT angiography, particulate and coil embolization, and stent graft placement.
Symbiont-Mediated Cytoplasmic Incompatibility: What have we Learned in 50 Years? (2020)

Cytoplasmic incompatibility (CI) is the most common symbiont-induced reproductive manipulation. Specifically, symbiont-induced sperm modifications cause catastrophic mitotic defects in the fertilized embryo and ensuing lethality in crosses between symbiotic males and either aposymbiotic females or females harboring a different symbiont strain. However, if the female carries the same symbiont strain, then embryos develop properly, which imparts a relative fitness benefit to symbiont-transmitting mothers. Thus, CI drives maternally transmitted bacteria to high frequencies in arthropod species worldwide. In the past two decades, CI has experienced a boom in interest due in part to its (i) deployment in successful, worldwide efforts to reduce the spread of mosquito-borne diseases, (ii) causation by bacteriophage genes, cifA and cifB, that modify animal reproductive processes, and (iii) important impacts on incipient speciation. This review serves as a gateway to experimental, conceptual, and quantitative themes of CI and outlines significant gaps in our understanding of CI&amp;rsquo;s mechanism that are ripe for investigation from a diversity of subdisciplines in the life sciences.
Radiofrequency ablation for T1a tumors in a solitary kidney: promising intermediate oncologic and renal function outcomes. (2008)

Radiofrequency ablation is an attractive alternative for the management of patients with T1a renal cortical tumors in a solitary kidney. Renal function appears to be adequately maintained with promising oncologic outcomes at 2.5 years.
Intramolecular electron transfer in laccases (2011)

Rate constants and activation parameters have been determined for the internal electron transfer from type 1 (T1) to type 3 (T3) copper ions in laccase from both the fungus Trametes hirsuta and the lacquer tree Rhus vernicifera, using the pulse radiolysis method. The rate constant at 298 K and the enthalpy and entropy of activation were 25 ± 1 s(-1), 39.7 ± 5.0 kJ·mol(-1) and -87 ± 9 J·mol(-1) ·K(-1) for the fungal enzyme and 1.1 ± 0.1 s(-1), 9.8 ± 0.2 kJ·mol(-1) and -211 ± 3 J·mol(-1) ·K(-1) for the tree enzyme. The initial reduction of the T1 site by pulse radiolytically produced radicals was direct in the case of T. hirsuta laccase, but occured indirectly via a disulfide radical in R. vernicifera. The equilibrium constant that characterizes the electron transfer from T1 to T3 copper ions was 0.4 for T. hirsuta laccase and 1.5 for R. vernicifera laccase, leading to full reduction of the T1 site occurring at 2.9 ± 0.2 electron equivalents for T. hirsuta and 4 electron equivalents for R. vernicifera laccase. These results were compared with each other and with those for the same process in other multicopper oxidases, ascorbate oxidase and Streptomyces coelicolor laccase, using available structural information and electron transfer theory.
Research on credibility evaluation for radio frequency guided Hardware-In-the-Loop Simulation system (2017)

To ensure the effectiveness of the RF(Radio Frequency) guided HILS(Hardware-In-the-Loop Simulation) system, the credibility evaluation was necessary. At present, most of the methods were applied in the case of the simulation system input being consistent with the real system input, which is difficult to achieve in some subsystem of the RF guided HILS system. In this paper, the relative complete system reliability evaluation index system was established. Subsystems were classified, for different categories of subsystem, corresponding reliability assessment methods were studied. In particular, reliability evaluation methods based on performance level were put forward, when certain subsystems cannot be evaluated by consistency analysis methods. A simple example was given to show the evaluation process.
Joint US/Japanese program of full-size building tests for base seismic isolation (1990)

Shimizu Corporation of Japan and Argonne National Laboratory of the USA initiated a joint research program on base seismic isolation. The program is centered on testing and analyzing isolation systems in a full-size building and to obtain data on relative response between isolated and nonisolated structures under earthquake conditions. The test facility consists of two identical full-size three-story buildings built side by side, located at Tohoku University in Sendai, Japan. Since April 1989, after the installation of bearings, over 20 earthquake data have been recorded at Sendai test facility. This paper describes the test facility, isolation bearings, observed earthquake records, and responses of isolated and nonisolated buildings under earthquake loads. 3 refs., 15 figs.
Polyamidoamine Nanoparticles for the Oral Administration of Antimalarial Drugs (2018)

Current strategies for the mass administration of antimalarial drugs demand oral formulations to target the asexual <i>Plasmodium</i> stages in the peripheral bloodstream, whereas recommendations for future interventions stress the importance of also targeting the transmission stages of the parasite as it passes between humans and mosquitoes. Orally administered polyamidoamine (PAA) nanoparticles conjugated to chloroquine reached the blood circulation and cured <i>Plasmodium yoelii</i>-infected mice, slightly improving the activity of the free drug and inducing in the animals immunity against malaria. Liquid chromatography with tandem mass spectrometry analysis of affinity chromatography-purified PAA ligands suggested a high adhesiveness of PAAs to <i>Plasmodium falciparum</i> proteins, which might be the mechanism responsible for the preferential binding of PAAs to <i>Plasmodium</i>-infected erythrocytes vs. non-infected red blood cells. The weak antimalarial activity of some PAAs was found to operate through inhibition of parasite invasion, whereas the observed polymer intake by macrophages indicated a potential of PAAs for the treatment of certain coinfections such as <i>Plasmodium</i> and <i>Leishmania</i>. When fluorescein-labeled PAAs were fed to females of the malaria mosquito vectors <i>Anopheles atroparvus</i> and <i>Anopheles gambiae</i>, persistent fluorescence was observed in the midgut and in other insect's tissues. These results present PAAs as a versatile platform for the encapsulation of orally administered antimalarial drugs and for direct administration of antimalarials to mosquitoes, targeting mosquito stages of <i>Plasmodium</i>.
Inhibition of hematopoiesis by competitive binding of transcription factor PU.1. (1994)

Transcription factors have been shown to play a role as "master switch" factors in the programming of hematopoietic cell commitment and differentiation. PU.1 is a hematopoietic-specific member of the Ets family of transcription factors. In human bone marrow CD34-enriched progenitor cells, PU.1 expression was upregulated during the early phases of granulocytic/monocytic differentiation, preceding expression of its target genes encoding CD11b and the macrophage-colony-stimulating factor receptor, whereas PU.1 was expressed at stable levels throughout erythroid differentiation. To study PU.1 function, we synthesized double-stranded phosphorothioate oligonucleotides containing a characterized PU.1 site and demonstrated their ability to specifically compete for PU.1 DNA binding. When added to CD34+ cells in vitro, wild-type PU.1-binding oligonucleotides significantly blocked hematopoietic colony formation, whereas mutated PU.1 oligonucleotides which no longer bind PU.1 had no specific inhibitory effect. These results demonstrate that PU.1 is developmentally upregulated during normal human myelopoiesis and that the function of PU.1 is critical for the development of in vitro hematopoiesis.
A Neuroprotective Function of NSF1 Sustains Autophagy and Lysosomal Trafficking inDrosophila (2014)

A common feature of many neurodegenerative diseases is the accumulation of toxic proteins that disrupt vital cellular functions. Degradative pathways such as autophagy play an important protective role in breaking down misfolded and long-lived proteins. Neurons are particularly vulnerable to defects in these pathways, but many of the details regarding the link between autophagy and neurodegeneration remain unclear. We previously found that temperature-sensitive paralytic mutants in Drosophila are enriched for those exhibiting age-dependent neurodegeneration. Here we show that one of these mutants, comatose (comt), in addition to locomotor defects, displays shortened lifespan and progressive neurodegeneration, including loss of dopaminerigic (DA) neurons. comt encodes N-ethyl-maleimide sensitive fusion protein (NSF1), which has a well-documented role in synaptic transmission. However, the neurodegenerative phenotypes we observe in comt mutants do not appear to depend on defects in synaptic transmission, but rather from their inability to sustain autophagy under stress, due at least in part to a defect in trafficking of lysosomal proteases such as cathepsin-L. Conversely, overexpression of NSF1 rescues α-synuclein-induced toxicity of DA neurons in a model of Parkinson's disease. Our results demonstrate a neuroprotective role for NSF1 that involves mediation of fusion events crucial for degradative pathways such as autophagy, providing greater understanding of cellular dysfunctions common to several neurodegenerative diseases.
Expedient Deep-Water Propellant Anchor Mooring System. (1975)

The Civil Engineering Laboratory has investigated the best means for installing CEL 20K Propellant Anchor quickly, effectively, and efficiently in the seafloor. This anchor can achieve holding capacities of 20,000 pounds in water depths of 20,000 feet. Several concepts were examined for launching the anchor system and deploying the anchor and line. Also included were advanced concepts for laterally distant anchor deployment. Alternate components were identified, and candidate systems were synthesized and evaluated. A buoy-launchable, free-falling, bale-on-anchor system was selected as best satisfying the broadest range of foreseeable needs. Preliminary design information is given for this 'standard expedient mooring system package.' The system includes a feature for automatic length adjustment, stopping, and locking of the line at the anchor to provide a taut surface moor; this feature can be deleted to reduce cost. The package can be towed to a site or launched from a suitable carrier. A launching system is described that permits the proposed package to be launched from most surface vessels having an open cargo deck capable of accommodating the size and weight of the package; no ship-borne load-handling equipment is required. (Author)
Ocean current observation and spectrum analysis in central Chukchi Sea during the summer of 2008 (2013)

在 2008 的夏天期间，第三 CHINARE 北极远征在中央 Chukchi 海 Xuelong 碎冰船上船被执行。一个能沉入水中的绳索系统在车站 CN-01 被部署并且恢复(71 '
Analysis of Phase-Locked Timing Extraction Circuits for Pulse Code Transmission (1974)

An analysis is presented of the performance of phaselocked timing extraction circuits for baseband pulse code transmission. The phase error of the extracted timing wave is influenced by the properties of three essential stages in signal processing: prefiltering, nonlinear treatment, and narrow-band filtering. The analysis enables us to calculate quantitatively the quasi-static and the dynamic part of the phase error for arbitrary but specified types of signal processing. This is more than can be done with existing theory in the case of resonant-type timing extraction circuits. Examples are given for practical cases, and conditions for optimum performance are derived. Furthermore, the behavior of such phase-locked circuits in a chain of repeaters is investigated, and in particular, the propagation law for jitter. Byrne's model, as used for resonant-type timing extraction circuits, therefore is generalized. It is shown analytically and experimentally that by proper implementation of the timing extraction circuit, considerable improvement can be obtained as compared with resonant-type circuits.
Supplemental Figure 1 from Calcipotriol Targets LRP6 to Inhibit Wnt Signaling in Pancreatic Cancer (2023)

&lt;p&gt;Supplemental Figure 1. Calcipotriol does not inhibit Wnt signaling through VDR sequestration of β-catenin or induction of DKK1. (A) AsPC-1 cells were treated with 100 nM calcipotriol for 4 hours. Whole cell lysates were collected and immunoprecipitated with anti- β-catenin or isotype control antibodies followed by western blots for β-catenin, E-cadherin or VDR. (B) Western blot for DKK-1 and tubulin (loading control) and (C) BAR reporter activity for indicated conditions. AsPC-1 cells were transfected with control or DKK1 siRNA for 48 hours and treated with vehicle or 100 nM calcipotriol for an additional 24 hours. BAR was normalized to vehicle and siRNA control and is reported as mean {plus minus} SD, with one representative experiment of 3 biological repeats shown.&lt;/p&gt;
Reproducibility of segment lengths obtained from a low cost markerless camera system (2012)

info:eu-repo/semantics/published
Cognitive Style as a Basis for MIS and DSS Designs: Much ADO About Nothing? (1983)

It is commonly believed that the user's cognitive style should be considered in the design of Management Information Systems and Decision Support Systems. In contrast, an examination of the literature and a consideration of some of the broader issues involved in MIS and DSS design lead to the conclusions that: (1) the currently available literature on cognitive style is an unsatisfactory basis for deriving operational design guidelines, and (2) further cognitive style research is unlikely to provide a satisfactory body of knowledge from which to derive such guidelines. The article presents six specific bases for these two conclusions. From a manager's pespective, the outcome of the study is a suggestion: maintain a healthy skepticism if it is suggested that paper and pencil assessments of the user's cognitive style should be used as a basis for MIS or DSS designs. From a researcher's viewpoint, the study raises two questions: (1) If our research interest is MIS and DSS design, does it seem that further research in cognitive style is a wise allocation of our research resources? (2) If our research interest is cognitive style, does it seem that the use of cognitive style as a basis for MIS and DSS designs will become an important application area?
Regenerative braking algorithm for a hybrid electric vehicle with CVT ratio control (2006)

A regenerative braking algorithm is proposed for a hybrid electric vehicle with a continuously variable transmission (CVT) to make the maximum use of the regenerative braking energy. In the regenerative braking algorithm, the regenerative torque is determined by considering the motor capacity, battery state of charge (SOC), and vehicle velocity. The regenerative braking force is calculated from the brake control unit by comparing the demanded brake torque and the motor torque available. The wheel pressure is reduced by the amount of the regenerative braking force and is supplied from the hydraulic brake module. In addition, the CVT speed ratio control algorithm is suggested during braking for optimal motor operation. The optimal operation line is proposed to operate the motor in the most efficient region while keeping the motor speed as low as possible by considering engine noise and friction. It is found from the experiments that the regenerative braking algorithm with CVT ratio control offers an improved battery SOC, which provides increased recuperation energy by 8 per cent for the federal urban driving schedule compared with that of the conventional CVT ratio control.
Die zwei Kulturen (2004)

Wenn Medienpraktiker und Medienwissenschaftler über Theorie reden, macht sich Unverständnis, oftmals auch nur ein Klima der Ignoranz breit. Die Frage: ,Worüber reden die überhaupt?‘ scheint in der Luft zu hängen, wenn die einen über die anderen reden. Forschungsbefunde der Wissenschaftler halten die Praktiker meist für irrelevant; umgekehrt werden aktuelle Probleme des praktischen Journalismus in der Welt der Medienwissenschaft nur ausnahmsweise (vor allem, wenn damit Forschungsgelder zu akquirieren sind) aufgegriffen.
Sound recordings from the 2007 emergence of Brood XIII cicada (2007)

Level calibrated recordings of the Brood XIII 17-year periodic cicadas were made in June, 2007 in River Forest, Illinois. Brood XIII consists of three separate species: Magicicada cassini, M. septendecim, and the more rare M. septendecula. Power spectrum analysis of a 2 min segment of the recording shows a 5.95 kHz resonance with Q≊6, indicative of cassini, and a 5 dB lower resonance at 1.35 kHz with a Q≊13.5, indicative of septendecim. Since other researchers have estimated that the power of septendecim is 20 dB below that of cassini, the high level of the septendecim song suggests that 30 times more septendecim than cassini were singing. Computation of the sound pressure level shows a 2–5 dB variation with a period of 7.5 s, indicative of synchronized chorus singing of cassini.
Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection and analysis of IgG non-responders (2020)

Patients with severe COVID-19 both seroconvert earlier and develop higher concentrations of SARS-CoV-2-specific IgG than patients with mild symptoms. Of those patients who not develop detectable IgG antibodies, all have detectable virus-neutralizing antibodies, suggesting immunity. Our results showing that not all COVID-19 patients develop detectable IgG using two validated commercial clinical methods, even over time, are vital for the interpretation of COVID-19 seroprevalence surveys.
Radiosurgery for Unruptured Intervention-Naïve Pediatric Brain Arteriovenous Malformations (2019)

Treatment of unruptured, intervention-naïve AVMs in the pediatric population with SRS carries an approximately 2% annual risk of morbidity and mortality, which appears to plateau after 10 yr. The poorly described natural history of pediatric AVMs renders any comparison of SRS vs conservative management imperfect.
ProteoMod: A new tool to quantitate protein post‐translational modifications (2004)

Post-translational modifications (PTMs) are known to regulate biological processes by controlling protein function. The effect of a PTM on protein function depends critically on the position and the number of modifications. While there are convenient methods available to qualitatively examine modifications like phosphorylation, glycosylation, acetylation and methylation, methods available for their quantitative assessment are cumbersome. We have developed a new tool that allows quantitation of the number of phosphorylation events in proteins with ease. The "ProteoMod" tool depends on shifts in the isoelectric points of proteins upon post-translational change. The extent of shift exhibited upon phosphorylation is algorithmically converted into the number of phosphorylations conferred. The validity of ProteoMod was confirmed by examining proteins with previously known number of phosphorylations. The list of proteins examined included HSP27, HSP70 and tumor suppressor p53. The approach can also be applied to estimate modifications like acetylation, methylation and sialylation in proteins. We analyzed shifts in isoelectric points due to sialylation events in N-glycoproteins. Using influenza hemagglutinin we show that shifts in isoelectric points correlate with intracellular distribution of this model membrane protein. In addition to extending the application of two dimensional gel electrophoresis to quantitate modifications, our study also highlights its potential use in cell biology.