gebhart/patrepeval huggingface dataset:
34 Heat Shock Factor (1992)

OVERVIEW The transcriptional activation of genes encoding the heat shock proteins is mediated by the binding of heat shock factor (HSF) to specific DNA sequence elements (heat shock elements [HSEs]). The canonical HSE is a continuous array of three, alternately oriented nGAAn units. However, the number of repeating pentanucleotide units in an HSE can vary, and the unusual multimeric nature of HSF allows it to bind efficiently HSEs of different lengths. HSF activity is regulated by heat shock at the level of both DNA binding and transcriptional activation. The binding activity of HSF is dependent on its multimeric state, whereas transcriptional activity correlates with its heat-shock-induced phosphorylation. Complementary DNAs for yeast and Drosophila HSF have been cloned. Although heat shock proteins exhibit strong sequence conservation among many species, the sequences of Drosophila and yeast HSF are divergent, except in regions important for DNA binding and multimerization. In uninduced cells, heat shock promoters are organized in nuclease-hypersensitive chromatin structures. These hypersensitive sites apparently possess bound transcription factor IID (TFIID) and a transcriptionally engaged but arrested RNA polymerase molecule. The heat shock promoter is thus primed or potentiated for activity in the absence of heat shock. Binding of HSF upon heat induction leads to increased transcription by unknown mechanisms, possibly involving both the release of the arrested RNA polymerase and the recruitment of additional polymerase molecules to the promoter itself. INTRODUCTION The heat shock gene regulatory circuit has several features that make it an attractive model for investigating the activation of transcription.
Ordered micellar and inverse micellar lyotropic phases (2010)

In this article we review the ordered micellar and inverse micellar lyotropic liquid-crystalline phases that can be formed by amphiphilic molecules such as lipids and surfactants. We focus first on the self-assembly of amphiphiles into aggregates, and then consider the interfacial curvature and the role of curvature elasticity and packing constraints in determining the allowed structures. We then review the range of ordered micellar and inverse micellar phases that have so far been observed in a variety of surfactant and lipid systems. Finally, we describe certain characteristic properties, such as the epitaxy between phases, and the self-diffusion and electrical conductivity within such ordered micellar phases.
Ras Uses the Novel Tumor Suppressor RASSF1 as an Effector to Mediate Apoptosis (2000)

Although activated Ras proteins are usually associated with driving growth and transformation, they may also induce senescence, apoptosis, and terminal differentiation. The subversion of these anti-neoplastic effects during Ras-dependent tumor development may be as important as the acquisition of the pro-neoplastic effects. None of the currently identified potential Ras effector proteins can satisfactorily explain the apoptotic action of Ras. Consequently, we have sought to identify novel Ras effectors that may be responsible for apoptosis induction. By examining the EST data base, we identified a potential Ras association domain in the tumor suppressor RASSF1. We now show that RASSF1 binds Ras in a GTP-dependent manner, both in vivo and directly in vitro. Moreover, activated Ras enhances and dominant negative Ras inhibits the cell death induced by transient transfection of RASSF1 into 293-T cells. This cell death appears to be apoptotic in nature, as RASSF1-transfected 293-T cells exhibit membrane blebbing and can be rescued by the addition of a caspase inhibitor. Thus, the RASSF1 tumor suppressor may serve as a novel Ras effector that mediates the apoptotic effects of oncogenic Ras.
Miniaturized Water‐Jet Ultrasound Indentation System for Quantitative Assessment of Articular Cartilage Degeneration: A Validation Study (2020)

Osteoarthritis is a common joint disease affecting a large population especially the elderly where cartilage degeneration is one of its hallmark symptoms. There is a need to develop new devices and instruments for the early detection and treatment of cartilage degeneration. In this study, we describe the development of a miniaturized water‐jet ultrasound indentation probe for this purpose. To evaluate the system, we applied it to characterize the degeneration of articular cartilage with the measurement of its morphologic, acoustic, and mechanical properties, using the enzymatic digestions of cartilage as a model of OA. Fifty cartilage samples were tested with 10 of them used for the reproducibility study and the other 40 for collagenase and trypsin digestions. Thickness, integrated reflection coefficient (IRC), effective stiffness, and energy dissipation ratio (EDR) were used to quantify the change of articular cartilage before and after degeneration. The measurement reproducibility as represented by the standardized coefficient of variation (SCV) was 2.6%, 10.2%, 11.5%, and 12.8% for thickness, IRC, stiffness, and EDR, respectively. A significant change of IRC, stiffness, and EDR was detected after degeneration by the designed probe ( p < 0.05). There was also a significant difference of IRC, stiffness, and EDR between trypsin and collagenase digestions ( p < 0.001). In conclusion, a miniaturized water‐jet ultrasound indentation probe has been designed, which has been successfully used to detect and differentiate cartilage degeneration simulated by enzymatic digestions. This probe, with future development, can be potentially suitable for quantitative assessment of cartilage degeneration with an arthroscopic operation.
Three-dimensional imaging of xenograft tumors using optical computed and emission tomography (2006)

The physical basis and preliminary applications of optical computed tomography (optical-CT) and optical emission computed tomography (optical-ECT) are introduced, as new techniques with potential to provide unique 3D information on a variety of aspects of tumor structure and function. A particular focus here is imaging tumor micro-vasculature, and the spatial distribution of viable tumor cells, although the techniques have the potential for much wider application. The principle attractiveness of optical-CT and optical-ECT are that high resolution (<20 microm) and high contrast co-registered 3D images of structure and function can be acquired for relatively large intact samples. The unique combination of high contrast and resolution offers advantages over micro-CT and micro-MRI, and the lack of requirement for sectioning offers advantages over confocal microscopy, conventional microscopy, and histological sectioning techniques. Optical-CT/ECT are implemented using in-house custom apparatus and a commercial dissecting microscope capable of both transmission and fluorescence imaging. Basic studies to characterize imaging performance are presented. Negligible geometrical distortion and accurate reconstruction of relative attenuation coefficients was observed. Optical-CT and optical-ECT are investigated here by application to high resolution imaging of HCT116 xenograft tumors, about 1 cc in dimension, which were transfected with constitutive red fluorescent protein (RFP). Tumor microvasculature was stained in vivo by tail vein injection of either passive absorbing dyes or active fluorescent markers (FITC conjugated lectin). Prior to imaging, the tumors were removed (ex vivo) and optically cleared in a key process to make the samples amenable to light transmission. The cleared tumors were imaged in three modes (i) optical-CT to image the 3D distribution of microvasculature as indicated by absorbing dye, (ii) optical-ECT using the FITC excitation and emission filter set, to determine microvasculature as indicated by lectin-endothelial binding, and (iii) optical-ECT using the DSRed2 filter set to determine the 3D distribution of viable tumor as indicated by RFP emission. A clear correlation was observed between the independent vasculature imaging modes (i) and (ii) and postimaging histological sections, providing substantial validation of the optical-CT and optical-ECT techniques. Strong correlation was also observed between the RFP imaging of mode iii, and modes i and ii, supporting the intuitive conclusion that well-perfused regions contain significant viable tumor. In summary, optical-CT and optical-ECT, when combined with new optical clearing techniques, represent powerful new imaging modalities with potential for providing unique information on the structure and function of tumors.
A novel AFM/STM/SEM system (1994)

An atomic force/scanning tunneling (AFM/STM) microscope intended for operation inside a scanning electron microscope (SEM) is described. This AFM/STM/SEM system enables us to image a sample conventionally by SEM as well as to investigate the local surface topography by AFM or STM. This device incorporates a new method for monitoring AFM cantilever deflection that utilizes the focused electron beam of the SEM.
Estudio de las características geológicas y genéticas de los afloramientos de Fluorita de la Felguerina (Campo de Caso-Oviedo). (1975)

Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.
Kinetic methods that are independent of the rate of reaction. (1983)

Kinetic methods for the quantification of substrates offer a number of advantages over equilibrium methods, such as speed and economy. However, in their most commonly practiced form they are liable to error from various sources in addition to those ordinarily encountered in equilibrium methods, owing to variations in enzymic activity between test and standard assays. In certain circumstances the differences in enzymic activity may be such as to completely invalidate the method. Such difficulties may, however, be avoided if three or more measurements are made during the reaction of the sample and are evaluated by one of five means. In each case data from the early course of the reaction are used to predict the total change in sensor signal at infinite time, from which the concentration of the substrate may be calculated as for an equilibrium method.
Analysis of temperature effects on the protein accumulation of the FT–FD module using newly generated Arabidopsis transgenic plants (2023)

Arabidopsis flowering is dependent on interactions between a component of the florigens FLOWERING LOCUS T (FT) and the basic leucine zipper (bZIP) transcription factor FD. These proteins form a complex that activates the genes required for flowering competence and integrates environmental cues, such as photoperiod and temperature. However, it remains largely unknown how FT and FD are regulated at the protein level. To address this, we created <i>FT</i> transgenic plants that express the N-terminal FLAG-tagged FT fusion protein under the control of its own promoter in <i>ft</i> mutant backgrounds. <i>FT</i> transgenic plants complemented the delayed flowering of the <i>ft</i> mutant and exhibited similar <i>FT</i> expression patterns to wild-type Col-0 plants in response to changes in photoperiod and temperature. Similarly, we generated <i>FD</i> transgenic plants in <i>fd</i> mutant backgrounds that express the N-terminal MYC-tagged FD fusion protein under the <i>FD</i> promoter, rescuing the late flowering phenotypes in the <i>fd</i> mutant. Using these transgenic plants, we investigated how temperature regulates the expression of FT and FD proteins. Temperature-dependent changes in FT and FD protein levels are primarily regulated at the transcript level, but protein-level temperature effects have also been observed to some extent. In addition, our examination of the expression patterns of FT and FD in different tissues revealed that similar to the spatial expression pattern of <i>FT</i>, <i>FD</i> mRNA was expressed in both the leaf and shoot apex, but FD protein was only detected in the apex, suggesting a regulatory mechanism that restricts FD protein expression in the leaf during the vegetative growth phase. These transgenic plants provided a valuable platform for investigating the role of the FT-FD module in flowering time regulation.
Fast and Reliable Restoration Method of Virtual Resources on OpenStack (2015)

We propose a fast and reliable restoration method of virtual resources on OpenStack when physical servers or virtual machines are down. Many providers have recently started cloud services, and the use of OpenStack, which is open source IaaS software, is increasing. When physical servers are down, there is a fail-over method using the high-availability cluster software such as Pacemaker to restore virtual resources. However, it takes a long time to restore all virtual resources. There is also a method for monitoring each virtual machine by using Ping or other methods and restoring a virtual machine when it is down. However, data may be destroyed due to the double mounts of virtual machines depending on the timing of failures because restoration methods of failed physical servers and virtual machines are independent. Therefore, we propose a fast and reliable restoration method with a uniform way for plural types virtual resources. In our method, Pacemaker only detects a physical server failure and notifies a failure to a virtual resource arrangement scheduler, then a virtual resource arrangement scheduler determines multiple physical servers to restore virtual resources and calls OpenStack APIs to rebuild. The virtual resource arrangement scheduler also detects virtual machine failures by using a Libvirt monitoring module and restores virtual machines without data loss by handling Pacemaker and Libvirt notifications uniformly. We implemented the proposed method and showed its effectiveness regarding fast restoration through performance measurements.
Designing IEEE 1149.1 compatible boundary-scan logic into an ASIC using Texas Instrument's Scope architecture (2002)

A design that was described and simulated behaviorally in Verilog, and synthesized and optimized using Synopsys, is discussed., IEEE 1149.1-compatible (Scope) logic was added to the optimized design and Mentor gate-level simulations were performed. The performance and area impact on the chip of the Scope logic is examined and synthesis is used to minimize it.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Investigation on the Dispersion Relation of a 3D LC-based Metamaterial with an Omnidirectional Left-Handed Frequency Band (2006)

A novel three-dimensional LC-based metamaterial topology is presented. Using a balanced unit cell an omnidirectional left-handed frequency band is shown to exist by algebraic calculation. Two interleaved unit cells, each rotated by 90deg, support polarization-independent omnidirectional left-handed wave propagation
"Senecio Inaequidens" (Asteraceae) y otras tres especies ruderales o arvenses interesantes en La Rioja (2001)

Se presentan tres nuevas citas para el catalogo floristico de La Rioja, que corresponden a las especies ruderales o arvenses Senecio inaequidens, Lavatera cretica (Malvaceae) y Lobulaa-ia rnaritirna (Cruciferae). Tambien se amplia el area de distribucion regional de Abutilon theophrasti (Malvaceae). Se discuten algunas caracteristicas agronomicas y ecologicas de 5. inaequidens.

Palabras clave: Plantas vasculares, flora, malas hierbas, La Rioja, Espana.
Futbolcularda Hazırlık Dönemi Antrenmanlarının Bazı Motorik Parametreler Üzerine Etkisi (2019)

Bu calismanin amaci duzenli olarak uygulanan hazirlik donemi futbol antrenmanlarinin futbolcularin fiziksel ve temel bazi motorik ozelliklerinde meydana gelen degisikliklerin incelenmesidir. Arastirmaya Etimesgut Belediye Spor U19 takiminda oynayan 18-19 yas araliginda toplam 20 gonullu genc erkek amator futbolcu katilmistir. Futbolculara 8 hafta boyunca, haftada 5 gun ve gunde 90 dakika futbol antrenmanlari uygulanmistir. Sporcularin performansla ilgili motorik ve fiziksel ozelliklerini belirlemek amaciyla hazirlik donemi oncesi ve duzenli olarak uygulanan futbol antrenmanlari sonunda sporcularin yas, boy uzunlugu ve vucut agirligi belirlenerek vucut kutle indeksleri hesaplanmis ayrica Cooper, dikey sicrama, esneklik, 30 metre surat, 30 saniye mekik ve 30 saniye sinav testleri uygulanmistir. Arastirma kapsaminda elde edilen verilerin degerlendirilmesinde SPSS 16.0 istatistik paket programi kullanilmistir. Sporcularin normal dagilim gosterdigi degiskenlerde on test ve son test degerlerinin karsilastirilmalari bagimsiz gruplarda paired simple t testi ile normal dagilim gostermeyen degiskenlerde ise Non-Parametrik Wilcoxon Signed Ranks testi ile belirlenmistir. Arastirma bulgularina gore 8 hafta suren futbol antrenmanlarinin neticesinde sporcularin aerobik guc, anaerobik guc, dikey sicrama, esneklik, 30 saniye mekik ve 30 saniye sinav degerlerinde istatistiksel olarak anlamli artis gorulurken (p<0,05), vucut kutle indeksi ve 30 metre surat degerlerimde anlamli azalmalar tespit edilmistir (p<0,05). Sonuc olarak, hazirlik donemi antrenmanlarinin futbolcularin fiziksel ve motorik parametrelerini gelistirici etkisinin oldugunu ve sporcularin ihtiyaclari dogrultusunda uygulanan futbol antrenmanlarinin sportif performansi olumlu yonde etkileyebilecegi soylenebilir.
Selective ground-fault protection using an adaptive algorithm model in neutral ungrounded power systems (2002)

The selective ground-fault protection is greatly valued for the safe and reliable operation of power systems. In order to eliminate the effect of zero-sequence current transformer's phase character on selective ground-fault protection devices, this paper proposes a new adaptive principle of selective ground-fault protection, and gives an algorithm model of action criterion based on the half-wave Fourier algorithm. The simulation results show that this criterion will possess very good selectivity to ground faults.
A Novel Concept of Short-Flux Path Switched Reluctance Motor for Electrical Vehicles (2015)

This paper deals with the design of a novel Switched Reluctance Motor (SRM) with short flux path for electrical vehicles. Design consists of the segmented water cooled stator with the toroidal winding and the rotor with salient poles also in a form of segments. The SRM dimensions have been calculated on the base of input requirements. The static and dynamic parameters of SRM are obtained from simulation models based on Finite element method and torque, power versus speed characteristics are presented.
Millimeter-Wave InP Image Line Self-Mixing Gunn Oscillator (1981)

Indium Phosphide Gunn Diodes have been used to develop self -mixing oscillators in the 60-GHz region using dielectric image line techniques. Experiments have been performed to measure conversion characteristics and minimum detectable signal. Applications are suggested based on minimum detectable signal for systems requiring small size and low cost.
Dual role of a single multienzyme complex in the oxidative decarboxylation of pyruvate and branched-chain 2-oxo acids in <i>Bacillus subtilis</i> (1983)

The pyruvate dehydrogenase and branched-chain 2-oxo acid dehydrogenase activities of Bacillus subtilis were found to co-purify as a single multienzyme complex. Mutants of B. subtilis with defects in the pyruvate decarboxylase (E1) and dihydrolipoamide dehydrogenase (E3) components of the pyruvate dehydrogenase complex were correspondingly affected in branched-chain 2-oxo acid dehydrogenase complex activity. Selective inhibition of the E1 or lipoate acetyltransferase (E2) components in vitro led to parallel losses in pyruvate dehydrogenase and branched-chain 2-oxo acid dehydrogenase complex activity. The pyruvate dehydrogenase and branched-chain 2-oxo acid dehydrogenase complexes of B. subtilis at the very least share many structural components, and are probably one and the same. The E3 component appeared to be identical for the pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and branched-chain 2-oxo acid dehydrogenase complexes in this organism and to be the product of a single structural gene. Long-chain branched fatty acids are thought to be essential for maintaining membrane fluidity in B. subtilis, and it was observed that the ace (pyruvate dehydrogenase complex) mutant 61142 was unable rapidly to take up acetoacetate, unlike the wild-type, indicative of a defect in membrane permeability. A single pyruvate dehydrogenase and branched-chain 2-oxo acid dehydrogenase complex can be seen as an economical means of supplying two different sets of essential metabolites.
Outside-in Software Development: A Practical Approach to Building Successful Stakeholder-based Products (2007)

thinking complements any approach your teams may be taking to the actual implementation of software, but it changes how you measure success. A successful team does a lot of learning and not much speculation.-Tom PoppendieckBuild Software That Delivers Maximum Business Value to Every Key StakeholderImagine your ideal development project. It will deliver exactly what your clients need. It will achieve broad, rapid, enthusiastic adoption. And it will be designed and built by a productive, high-morale team of expert software professionals. Using this book's breakthrough outside-in approach to software development, your next project can be that ideal project.In Outside-in Software Development, two of IBM's most respected software leaders, Carl Kessler and John Sweitzer, show you how to identify the stakeholders who'll determine your project's real value, shape every decision around their real needs, and deliver software that achieves broad, rapid, enthusiastic adoption.The authors present an end-to-end framework and practical implementation techniques any development team can quickly benefit from, regardless of project type or scope. Using their proven approach, you can improve the effectiveness of every client conversation, define priorities with greater visibility and clarity, and make sure all your code delivers maximum business value.Coverage includes Understanding your stakeholders and the organizational and business context they operate in Clarifying the short- and long-term stakeholder goals your project will satisfy More effectively mapping project expectations to outcomes Building more consumable software: systems that are easier to deploy, use, and support Continuously enhancing alignment with stakeholder goals Helping stakeholders manage ongoing change long after you've delivered your product Mastering the leadership techniques needed to drive development