gebhart/patrepeval huggingface dataset:
Preliminary experiments for ARDRA validation on flora associated with intestinal mucosa (2001)

The human intestinal tract harbours a complex microbial ecosystem which plays a key role in nutrition and health. Although this microbiota has been studied in great detail by culture techniques, microscopic counts on human faeces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Almost all studies used faecal samples, and there is little data on bacteriology of mucosa-associated bacteria of the intestinal tract. We examined the procedure to extract DNA from intestinal tissue in sufficient quantity and quality for PCR amplification. Intestinal mucosa from germ-free and conventional rats was studied. Intestinal samples were washed to remove nonadherent bacteria, and the mucosa scraped off with a sterile scalpel. Microorganisms and cells were lysed by three enzymatic treatments for total community genomic DNA isolation. Released DNA was purified by spin-column and tissue had to be stored for 24 h in a reduced transport media for PCR amplification. Universal and bacterial oligonucleotides complementary to conserved regions in the 16S rDNA of 180 organisms were evaluated, before being used for PCR amplification. All these primers contain mismatches with some organisms which may influence PCR amplification. The 16S rDNA PCR with universal primers hybridises with a mitochondrial gene of rat, producing a 550 bp fragment which contaminates 16S rDNA fragments. Fifteen cycles of amplifications were performed to preserve the biodiversity of the sample. Theoretical 16S rDNA fragments with universal primers were calculated by a restriction fragment length analysis termed ARDRA (amplified rDNA restriction analysis). Three enzymes were used: HaeIII, RsaI and TaqI. Clustering was performed after separate restriction analysis with these enzymes. An example of this method was carried out after PCR amplification of the 16S rDNA fragment of five strains isolated from a jejunal sample by microbiology techniques. Further investigations on a larger number of strains will permit us to validate more precisely this method.
Supplementary Table S3 from Integrative Analysis of Pleomorphic Dermal Sarcomas Reveals Fibroblastic Differentiation and Susceptibility to Immunotherapy (2023)

&lt;p&gt;Quality measurements of exome sequencing&lt;/p&gt;
Effects of cell phone radiofrequency exposure on the human cytochrome P450 reductase (2012)

Accelerated and widespread of cell phones has increased the human exposure to radiofrequency electromagnetic fields (EMFs) and raises serious concerns about the biological and health-related effects of RF radiation. The present study aimed at the effect of cell phone RF (1.9 GHz) emitted by Universal Mobile Telecommunication System (UMTS), the third generation (3G) of cell phones on structure and function of human cytochrome P450 reductase. The ability of the cytochrome P450 reducatese to transfer the electron was measured by an exogenous electron acceptor cytochrome C with UV-vis spectrophotometer. Structural changes were studied by fluorescence spectroscopy, dynamic light scattering, Circular dichroism and capillary electrophoresis (Zeta potential). The results indicated that UMTS-like onehour RF exposure at 1 W/kg SAR slightly altered electron transfer ability and structure of cytochrome P450 reductases.
Minimizing Energy Consumption and Peak Power of Series Elastic Actuators: a Convex Optimization Framework for Elastic Element Design (2018)

Compared to rigid actuators, Series Elastic Actuators (SEAs) offer a potential reduction of motor energy consumption and peak power, though these benefits are highly dependent on the design of the torque-elongation profile of the elastic element. In the case of linear springs, natural dynamics is a traditional method for this design, but it has two major limitations: arbitrary load trajectories are difficult or impossible to analyze and it does not consider actuator constraints. Parametric optimization is also a popular design method that addresses these limitations, but solutions are only optimal within the space of the parameters. To overcome these limitations, we propose a non-parametric convex optimization program for the design of the nonlinear elastic element that minimizes energy consumption and peak power for an arbitrary periodic reference trajectory. To obtain convexity, we introduce a convex approximation to the expression of peak power; energy consumption is shown to be convex without approximation. The combination of peak power and energy consumption in the cost function leads to a multiobjective convex optimization framework that comprises the main contribution of this paper. As a case study, we recover the elongation-torque profile of a cubic spring, given its natural oscillation as the reference load. We then design nonlinear SEAs for an ankle prosthesis that minimize energy consumption and peak power for different trajectories and extend the range of achievable tasks when subject to actuator constraints.
New Strategies for Organic Catalysis:  The First Highly Enantioselective Organocatalytic Diels−Alder Reaction (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNew Strategies for Organic Catalysis: The First Highly Enantioselective Organocatalytic Diels−Alder ReactionKateri A. Ahrendt, Christopher J. Borths, and David W. C. MacMillanView Author Information Department of Chemistry, University of California Berkeley, California 94720 Cite this: J. Am. Chem. Soc. 2000, 122, 17, 4243–4244Publication Date (Web):April 15, 2000Publication History Received7 January 2000Published online15 April 2000Published inissue 1 May 2000https://pubs.acs.org/doi/10.1021/ja000092shttps://doi.org/10.1021/ja000092srapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views57345Altmetric-Citations1453LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Catalysts,Cyclization,Ions,Stereoselectivity Get e-Alerts
CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective (2019)

Filamentous fungi play an important role in human health and industrial/agricultural production. With the increasing number of full genomes available for fungal species, the study of filamentous fungi has brought about a wider range of genetic manipulation opportunities. However, the utilization of traditional methods to study fungi is time consuming and laborious. Recent rapid progress and wide application of a versatile genome editing technology, i.e., the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-related nuclease 9) system, has revolutionized biological research and has many innovative applications in a wide range of fields showing great promise in research and application of filamentous fungi. In this review, we introduce the CRISPR/Cas9 genome editing technology focusing on its application in research of filamentous fungi and we discuss the general considerations of genome editing using CRISPR/Cas9 system illustrating vector construction, multiple editing strategies, technical consideration of different sizes of homology arms on genome editing efficiency, off-target effects, and different transformation methodologies. In addition, we discuss the challenges encountered using CRISPR/Cas9 technology and give the perspectives of future applications of CRISPR/Cas9 technology for basic research and practical application of filamentous fungi.
Implantation of Combined Telemetric ECG and Blood Pressure Transmitters to Determine Spontaneous Baroreflex Sensitivity in Conscious Mice (2021)

Blood pressure (BP) and heart rate (HR) are both controlled by the autonomic nervous system (ANS) and are closely intertwined due to reflex mechanisms. The baroreflex is a key homeostatic mechanism to counteract acute, short-term changes in arterial BP and to maintain BP in a relatively narrow physiological range. BP is sensed by baroreceptors located in the aortic arch and carotid sinus. When BP changes, signals are transmitted to the central nervous system and are then communicated to the parasympathetic and sympathetic branches of the autonomic nervous system to adjust HR. A rise in BP causes a reflex decrease in HR, a drop in BP causes a reflex increase in HR. Baroreflex sensitivity (BRS) is the quantitative relationship between changes in arterial BP and corresponding changes in HR. Cardiovascular diseases are often associated with impaired baroreflex function. In various studies reduced BRS has been reported in e.g., heart failure, myocardial infarction, or coronary artery disease. Determination of BRS requires information from both BP and HR, which can be recorded simultaneously using telemetric devices. The surgical procedure is described beginning with the insertion of the pressure sensor into the left carotid artery and positioning of its tip in the aortic arch to monitor arterial pressure followed by the subcutaneous placement of the transmitter and ECG electrodes. We also describe postoperative intensive care and analgesic management. After a two-week period of post-surgery recovery long-term ECG and BP recordings are performed in conscious and unrestrained mice. Finally, we include examples of high-quality recordings and the analysis of spontaneous baroreceptor sensitivity using the sequence method.
Electron Transfer Reactions between Gels and Quinones (1997)

Electron transfer reactions of quinone derivatives (QDs) with poly(4-vinylpyridine) gels in organic solvents were studied by means of ESR spectroscopy. Formation of radical anions from the QDs and cations from polymeric base was established. The QD2- anions resulting from disproportionation of the QD•- radical anions produce additional cross-links in the gel, causing it to collapse. Sulfhydryl compounds complexed with the gel prevent formation of the ESR signals when the QDs are supplied into the solvent surrounding the gel under oxygen-free conditions. Oxidation of the sulfhydryl compound adsorbed onto the gel results in its desorption, enabling the gel to react with the QD, producing ESR signals. Gels modified with the sulfhydryl compounds collapse in response to the supply of oxygen into their liquid environment.
Aqueous Medium Radical Addition to Ketimines with a Phenolic Hydroxyl Group (2004)

Intermolecular alkyl radical addition to ketimines having 2-phenolic hydroxyl group proceeded effectively in aqueous media, providing the novel method for construction of all-substituted sp3-hybridized carbon center.
Multiple turbo codes for deep-space communications (1995)

In this article, we introduce multiple turbo codes and a suitable decoder structure derived from an approximation to the maximum a posteriori probability (MAP) decision rule, which is substantially difierent from the decoder for two-code-based encoders. We analyze the efiect of interleaver choice on the weight distribution of the code, and we describe simulation results on the improved performance of these new codes.
CLOVE (2016)

Multi-tenant datacenters predominantly use equal-cost multipath (ECMP) routing to distribute traffic over multiple network paths. However, ECMP static hashing causes unequal load-balancing and collisions, leading to low throughput and high latencies. Recently proposed alternatives for load-balancing perform better, but are impractical as they require either changing the tenant VM network stacks (e.g., MPTCP) or replacing all the network switches (e.g., CONGA).
Using agents and autonomic computing to build next generation seamless mobility services (2007)

Next generation networks seek to integrate wide-area and local-area wireless and wired systems in order to provide seamless services to the end user, providing freedom of movement between metropolitan/enterprise and indoor/outdoor coverage while maintaining continuity of applications experience. Seamless Mobility, and its vision of seamless service delivery, requires significant changes to existing wired and wireless network management systems. Seamless Mobility is an experiential architecture, predicated on providing mechanisms that enable a user to accomplish his or her tasks without regard to technology. This talk will describe a novel autonomic architecture that uses a variety of different types of agents to synthesize knowledge about the environment, the context of users and their service and resource needs, and the capabilities and constraints placed on the network at any given time.
Performance-Robustness Tradeoffs in Adversarially Robust Control and Estimation (2023)

While $\mathcal{H}_\infty$ methods can introduce robustness against worst-case perturbations, their nominal performance under conventional stochastic disturbances is often drastically reduced. Though this fundamental tradeoff between nominal performance and robustness is known to exist, it is not well-characterized in quantitative terms. Toward addressing this issue, we borrow the increasingly ubiquitous notion of adversarial training from machine learning to construct a class of controllers which are optimized for disturbances consisting of mixed stochastic and worst-case components. We find that this problem admits a linear time invariant optimal controller that has a form closely related to suboptimal $\mathcal{H}_\infty$ solutions. We then provide a quantitative performance-robustness tradeoff analysis in two analytically tractable cases: state feedback control, and state estimation. In these special cases, we demonstrate that the severity of the tradeoff depends in an interpretable manner upon system-theoretic properties such as the spectrum of the controllability gramian, the spectrum of the observability gramian, and the stability of the system. This provides practitioners with general guidance for determining how much robustness to incorporate based on a priori system knowledge. We empirically validate our results by comparing the performance of our controller against standard baselines, and plotting tradeoff curves.
AF6q21, a Novel Partner of the MLL Gene in t(6; 11)(q21; q23), Defines a Forkhead Transcriptional Factor Subfamily (1997)

Fusion genes implicating the MLL gene have been recently demonstrated in various 11q23 chromosomal abnormalities in human hematopoietic malignancies. We analyzed a t(6;11)(q21;q23) translocation detected in a secondary acute myeloblastic leukemia. This translocation results in fusion of the MLL gene on 11q23 to a previously unknown gene on chromosome 6 that differs from the previously reported MLL partner gene AF6q. The novel gene, named AF6q21, encodes a forkhead (FH) protein with strong similarities to the two FH family members whose genes are already known to be involved in chromosomal translocations of human malignancies, AFX and FKHR. Strikingly, in these translocations the breakpoints are located at the same position within the FH domains. Therefore, AF6q21, AFX, and FKHR could define a new FH subfamily particularly involved in human malignancies.
Multiple-Input Describing Functions and Nonlinear System Design (1968)

The practicing control engineer should find the book valuable as a complete reference work in the subject area. If his background in mathematics is not sufficient to enable him to follow the theoretical development of ~ h a ~ t e rc.o1mfort- ably, he can omit that chapter and will still find a complete presentation in every chapter except Chapters Seven and Eight, based on the physically motivated concept of harmonic analysis of the nonlinearity output. Chapter Seven, which includes random processes at the nonlinearity input, requires a statistical approach. But this too reduces to a rather simple matter in the very important class of problems involving static single-valued nonlinearities. Chapter Eight treats transient responses by related forms of quasi-linearization which are developed completely within that chapter. Thus it is hoped that every control engineer will find the principal ideas presented in a manner which is meaningful and appealing to him.
First Results of the Superconducting ECR Ion Source Venus with 28 GHz (2005)

VENUS (Versatile ECR ion source for NUclear Science) is a next generation superconducting ECR ion source, designed to produce high current, high charge state ions for the 88‐Inch Cyclotron at the Lawrence Berkeley National Laboratory. VENUS also serves as the prototype ion source for the RIA (Rare Isotope Accelerator) front end. The magnetic confinement configuration consists of three superconducting axial coils and six superconducting radial coils in a sextupole configuration. The nominal design fields of the axial magnets are 4T at injection and 3T at extraction; the nominal radial design field strength at the plasma chamber wall is 2T, making VENUS the world most powerful ECR plasma confinement structure. From the beginning, VENUS has been designed for optimum operation at 28 GHz with high power (10 kW).In 2003 the VENUS ECR ion source was commissioned at 18 GHz, while preparations for 28 GHz operation were being conducted. During this commissioning phase with 18 GHz, tests with various gases and metals have been performed with up to 2000 W RF power. At the initial commissioning tests at 18 GHz, 1100 eμA of O6+, 160 eμA of Xe20+, 160 eμA of Bi25+ and 100 eμA of Bi30+ and 11 eμA of Bi41+ were produced.In May 2004 the 28 GHz microwave power has been coupled into the VENUS ECR ion source. At initial operation more than 320 eμA of Xe20+ (twice the amount extracted at 18 GHz), 240 eμA of Bi24+ and Bi25+, and 245 eμA of Bi29+ were extracted. The paper briefly describes the design of the VENUS source, the 28 GHz microwave system and its beam analyzing system. First results at 28 GHz including emittance measurements are presented.
Nichtinvasive Bestimmung des pulmonalarteriellen Verschlussdrucks bei Patienten mit Pulmonalhypertonie mittels 4D MR-Phasenkontrastbildgebung (2013)

Problemstellung: Der mittels Rechtsherzkatheter (RHK) bestimmte pulmonalarterielle Verschlussdruck (PAWP) schätzt den linksatriellen Druck ab und ist für Klassifikation und Therapie von Patienten mit Pulmonalhypertonie (PH) von großer klinischer Relevanz, da aufgrund seines Wertes zwischen prä- und postkapillärer PH unterschieden wird. Ziel dieser explorativen Studie von PatientInnen mit PH war die Abschätzung des PAWP, aus den mittels Magnetresonanz-Phasenkontrastbildgebung (MRPCI) gemessenen Blutflussmustern im linken Vorhof.
Full Day Kindergarten in Nevada: A Health Impact Assessment (2015)

While most people agree that medical care and healthy behaviors impact health, the environmental and social determinants of health are equally, if not more, important. For example, the environment around us and how our communities are built can impact injury, safety, and physical activity. Ultimately, decisions made in sectors usually considered outside of health, such as transportation and planning, can have important intended and unintended impacts on health. Education, too, is connected to health (Marmot &amp; Wilkinson, 2006). This HIA assesses how modifying access to full-day kindergarten (FDK) in Nevada could potentially impact health.
Periodontal Microsurgery – A Review (2014)

Over the past decade, the field of periodontics has seen increasing surgical refinement of many procedures. Consistent successful periodontal treatment procedures demand clinical expertise that challenges the technical skills of periodontists to the limit of and beyond the range of visual acuity. Periodontal microsurgery is the refinement of basic surgical techniques made possible by the improved visual acuity gained with the use of surgical microscope. The effect of periodontal microsurgery may include more predictable therapeutic results, less invasive procedure with reduced patient discomfort, more rapid healing, improved cosmetic results and greater patient acceptance.
High-pressure phases ofMg2Sifrom first principles (2016)

First-principles calculations are presented to resolve the possible pressure-dependent phases of ${\mathrm{Mg}}_{2}\mathrm{Si}$. Although previous reports show that ${\mathrm{Mg}}_{2}\mathrm{Si}$ is characterized by the cubic antifluorite $Fm\overline{3}m$ structure at low pressures, the situation at higher pressures is less clear with many contradicting results. Here we utilize several methods to examine the stability, electron, phonon, and transport properties of this material as a function of pressure and temperature. We find that ${\mathrm{Mg}}_{2}\mathrm{Si}$ is thermodynamically stable at low and high pressures. Between 6 and 24 GPa, ${\mathrm{Mg}}_{2}\mathrm{Si}$ can transform into ${\mathrm{Mg}}_{9}{\mathrm{Si}}_{5}$, a defected compound, and vice versa, without energy cost. Perhaps this result is related to the aforementioned inconsistency in the structures reported for ${\mathrm{Mg}}_{2}\mathrm{Si}$ within this pressure range. Focusing solely on ${\mathrm{Mg}}_{2}\mathrm{Si}$, we find a new monoclinic $C2/m$ structure of ${\mathrm{Mg}}_{2}\mathrm{Si}$, which is stable at high pressures within thermodynamical considerations. The calculated electrical conductivity and Seebeck coefficient taking into account results from the electronic structure calculations help us understand better how transport can be affected in this material by modulating pressure and temperature.
Rapid indicators for monitoring the health of Chlamydomonas nivalis biomass during preservation (2021)

Abstract Microalgae are photosynthetic microorganisms that have increasingly attracted interest in the last decade due to their potential for industrial applications. One crucial aspect for the industrial-scale valorisation of algae biomass concerns the quality control during its preservation before being treated to obtain the end-product. Monitoring biomass quality is essential and can be potentially accomplished with the aid of specific biochemical indicators called biomarkers. In this context, the main aim of this work was to identify potential indicators of microalgae biomass viability that could be used as markers of its quality during storage/preservation for commercial operations. The health status of a suspension of Chlamydomonas nivalis was assessed at 4 ºC and 25 ºC during 10 days of storage. The use of the pulse-amplitude-modulation technique, based on chlorophyll fluorescence, was a valuable indicator of the culture viability. The measurement of DNA and of chlorophyll in the supernatant, indicative of cell lysis, also provided satisfactory results; in the case of the DNA, the limit of detection was 3.9 µg DNA·mL −1 . The effect of different concentrations of a well-known and cheap preservative, acetic acid, was also evaluated at 4 ºC. This work identified three suitable biomarkers to be used as rapid indicators of the quality of the microalgal suspension prior to its reception for biorefinery activities.