gebhart/patrepeval huggingface dataset:
Arabidopsis bZIP Protein HY5 Directly Interacts with Light-Responsive Promoters in Mediating Light Control of Gene Expression (1998)

The Arabidopsis HY5 gene has been defined genetically as a positive regulator of photomorphogenesis and recently has been shown to encode a basic leucine zipper type of transcription factor. Here, we report that HY5 is constitutively nuclear localized and is involved in light regulation of transcriptional activity of the promoters containing the G-box, a well-characterized light-responsive element (LRE). In vitro DNA binding studies suggested that HY5 can bind specifically to the G-box DNA sequences but not to any of the other LREs present in the light-responsive promoters examined. High-irradiance light activation of two synthetic promoters containing either the consensus G-box alone or the G-box combined with the GATA motif (another LRE) and the native Arabidopsis ribulose bisphosphate carboxylase small subunit gene RBCS-1A promoter, which has an essential copy of the G-box, was significantly compromised in the hy5 mutant. The hy5 mutation's effect on the high-irradiance light activation of gene expression was observed in both photosynthetic and nonphotosynthetic tissues. Furthermore, the characteristic phytochrome-mediated red light- and far-red light-reversible low-fluence induction of the G-box-containing promoters was diminished specifically in hy5 plants. These results suggest that HY5 may interact directly with the G-box in the promoters of light-inducible genes to mediate light-controlled transcriptional activity.
The <i>apeE</i> Gene of <i>Salmonella typhimurium</i> Encodes an Outer Membrane Esterase Not Present in <i>Escherichia coli</i> (1998)

Salmonella typhimurium apeR mutations lead to overproduction of an outer membrane-associated N-acetyl phenylalanine beta-naphthyl ester-cleaving esterase that is encoded by the apeE gene (P. Collin-Osdoby and C. G. Miller, Mol. Gen. Genet. 243:674-680, 1994). This paper reports the cloning and nucleotide sequencing of the S. typhimurium apeE gene as well as some properties of the esterase that it encodes. The predicted product of apeE is a 69.9-kDa protein which is processed to a 67-kDa species by removal of a signal peptide. The predicted amino acid sequence of ApeE indicates that it is a member of the GDSL family of serine esterases/lipases. It is most similar to a lipase excreted by the entomopathogenic bacterium Photorhabdus luminescens. The Salmonella esterase catalyzes the hydrolysis of a variety of fatty acid naphthyl esters and of C6 to C16 fatty acid p-nitrophenyl esters but will not hydrolyze peptide bonds. A rapid diagnostic test reported to be useful in distinguishing Salmonella spp. from related organisms makes use of the ability of Salmonella to hydrolyze the chromogenic ester substrate methyl umbelliferyl caprylate. We report that the apeE gene product is the enzyme in Salmonella uniquely responsible for the hydrolysis of this substrate. Southern blot analysis indicates that Escherichia coli K-12 does not contain a close analog of apeE, and it appears that the apeE gene is contained in a region of DNA present in Salmonella but not in E. coli.
P4F-4 Feasibility of Two-Dimensional Quantitative Sonoelastographic Imaging (2007)

In this paper, a two-dimensional (2D) quantitative sonoelastographic technique for estimating local shear wave speeds from slowly propagating shear wave interference patterns (termed crawling waves) is presented. Homogeneous tissue- mimicking phantom results demonstrate the ability of quantitative sonoelastographic imaging to accurately reconstruct the true underlying shear wave speed distribution as verified using mechanical measurements. From heterogeneous phantoms containing a 5 or 10 mm stiff inclusion, results indicate that increasing the estimator kernel size increases the transition zone length about boundaries. Contrast-to-noise ratio (CNR) values from quantitative sonoelastograms obtained in heterogeneous phantoms reveal that the 2D quantitative sonoelastographic imaging technique outperforms the one-dimensional (ID) precursor in terms of image noise minimization and contrast enhancement. Experimental results from an embedded porcine liver specimen with an induced radiofrequency ablation (RFA) lesion validate 2D quantitative sonoelastographic imaging in tissue. Overall, 2D quantitative sonoelastography was shown to be a promising new imaging method to characterizing the shear wave speed distribution in elastic materials.
Time-varying Sea Surfaces from 3D Dual-sensor Streamer Data (2012)

that resolution is compromised leading to misinterpretation and mislocation of events. Realistic time-varying sea surfaces can be modeled based on Pierson-Moskowitz sea surface spectrum and Hasselmann’s directivity correction. Imaged sea surfaces are obtained by applying an imaging technique that is based on decomposed wavefields from dual sensor streamers. The speed and direction of the moving sea surface are obtained by performing spectral analysis on the imaged sea surface. A first imaged sea surface result from 3D field data acquired offshore Brazil is shown.
Deletion of heart‐type cytochrome <i>c</i> oxidase subunit 7a1 impairs skeletal muscle angiogenesis and oxidative phosphorylation (2012)

Oxidative metabolism is needed for sustained skeletal muscle function. A key component of such metabolism is cytochrome c oxidase, the 13-subunit terminal complex of the mitochondrial electron transport chain. We used mice null for one of the two isoforms of Cox subunit 7a, heart/skeletal muscle-specific Cox7a1, to examine the cellular and functional responses of muscle adaptation in response to mitochondrial dysfunction. Specifically we determined if deletion of Cox7a1 would (1) limit exercise capacity, and (2) alter genes responsible for skeletal muscle capillarity and mitochondrial biogenesis. Sixteen male mice (Cox7a1 null mice, n = 8, and littermate controls, n = 8) performed incremental and run-to-exhaustion treadmill tests. The hindlimb muscles for both groups were analysed. The results indicated that capillary indices were reduced (by 30.7–44.9%) in the Cox7a1 null mice relative to controls. In addition, resting ATP levels and Cox specific activity were significantly reduced (>60%) in both glycolytic and oxidative muscle fibre types despite an increase in a major regulator of mitochondrial biogenesis, PGC-1β. These changes in the skeletal muscle resulted in exercise intolerance for the Cox7a1 null mice. Thus, our data indicate that deletion of the Cox7a1 isoform results in reduced muscle bioenergetics and hindlimb capillarity, helping to explain the observed impairment of muscle structure and function.
CMOS micromachined cantilever-in-cantilever devices with magnetic actuation (1996)

A novel magnetically actuated cantilever microactuator which produces a large angular deflection is described. The device is a nested cantilever structure for improved sensitivity, and is fabricated entirely using a standard CMOS process. The cantilever deflects bidirectionally, and has a static deflection of more than 2.5/spl deg/. It has a response time of 25 μs and at resonance has a deflection of more than 25/spl deg/.
WUSCHEL triggers innate antiviral immunity in plant stem cells (2020)

Stem cells in plants constantly supply daughter cells to form new organs and are expected to safeguard the integrity of the cells from biological invasion. Here, we show how stem cells of the <i>Arabidopsis</i> shoot apical meristem and their nascent daughter cells suppress infection by cucumber mosaic virus (CMV). The stem cell regulator WUSCHEL responds to CMV infection and represses virus accumulation in the meristem central and peripheral zones. WUSCHEL inhibits viral protein synthesis by repressing the expression of plant <i>S</i>-adenosyl-l-methionine-dependent methyltransferases, which are involved in ribosomal RNA processing and ribosome stability. Our results reveal a conserved strategy in plants to protect stem cells against viral intrusion and provide a molecular basis for WUSCHEL-mediated broad-spectrum innate antiviral immunity in plants.
Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6α branch (2016)

The membrane-bound transcription factor ATF6α plays a cytoprotective role in the unfolded protein response (UPR), required for cells to survive ER stress. Activation of ATF6α promotes cell survival in cancer models. We used cell-based screens to discover and develop Ceapins, a class of pyrazole amides, that block ATF6α signaling in response to ER stress. Ceapins sensitize cells to ER stress without impacting viability of unstressed cells. Ceapins are highly specific inhibitors of ATF6α signaling, not affecting signaling through the other branches of the UPR, or proteolytic processing of its close homolog ATF6β or SREBP (a cholesterol-regulated transcription factor), both activated by the same proteases. Ceapins are first-in-class inhibitors that can be used to explore both the mechanism of activation of ATF6α and its role in pathological settings. The discovery of Ceapins now enables pharmacological modulation all three UPR branches either singly or in combination.
Design and structural optimization of topological interlocking assemblies (2019)

We study assemblies of convex rigid blocks regularly arranged to approximate a given freeform surface. Our designs rely solely on the geometric arrangement of blocks to form a stable assembly, neither requiring explicit connectors or complex joints, nor relying on friction between blocks. The convexity of the blocks simplifies fabrication, as they can be easily cut from different materials such as stone, wood, or foam. However, designing stable assemblies is challenging, since adjacent pairs of blocks are restricted in their relative motion only in the direction orthogonal to a single common planar interface surface. We show that despite this weak interaction, structurally stable, and in some cases, globally interlocking assemblies can be found for a variety of freeform designs. Our optimization algorithm is based on a theoretical link between static equilibrium conditions and a geometric, global interlocking property of the assembly---that an assembly is globally interlocking if and only if the equilibrium conditions are satisfied for arbitrary external forces and torques. Inspired by this connection, we define a measure of stability that spans from single-load equilibrium to global interlocking, motivated by tilt analysis experiments used in structural engineering. We use this measure to optimize the geometry of blocks to achieve a static equilibrium for a maximal cone of directions, as opposed to considering only self-load scenarios with a single gravity direction. In the limit, this optimization can achieve globally interlocking structures. We show how different geometric patterns give rise to a variety of design options and validate our results with physical prototypes.
Inhibition of the <i>in vitro</i> formation of irreversibly sickled cells by cepharanthine (1983)

A method was developed to prepare irreversibly sickled cells (ISC) in vitro under a physiological condition. By exposing sickle red cells to repeated deoxygenation-reoxygenation cycles for 15 h at 37 degrees C, 20-30% of the red cells formed ISC. These cells were separated from biconcave-shaped cells by a gradient density centrifugation. The percentage of the formation of ISC was determined spectrophotometrically after cells were haemolysed. Cepharanthine, a bisbenzylisoquinoline alkaloid, was found to inhibit this in vitro formation of irreversibly sickled cells by 50% at 15 microns. This concentration was much lower than that required to inhibit the in vitro sickling.
Laser diode-pumped visible upconversion fiber laser (1993)

We report a civ room-temperature upconversion fiber laser oscillation at 521 and 635 nm. The fiber was pumped simultaneously by two single spatial mode laser diodes, one at 833 nm, the other at either 985 or 1016nm. The laser medium, supplied by Le Verre Fluore, is a fluoride glass fiber doped with 2000 ppm Pr3+ and 4000 ppm Yb3+. The active ion for laser oscillation is Pr3+ The high lying states of the Pr3+ ion are excited by the sequential absorption of two photons. (See Fig. 1.) The intermediate state in the upconversion process, 1G4, may be populated either by ground state absorption or by energy transfer from a nearby excited Yb3+ ion.
증예(症例) : 응급 대장 내시경 술로 해결한 S자 결장 염전 (2006)

S자 결장 염전은 급성 복통을 호소하는 장폐색의 흔한 원인으로 수술적 치료와 비술술적 치료가 있다. 응급 수술적 절제술은 술 후 사망률과 이환률이 높아서 혈액검사와 임상소견상 괴저의 소견이 의심되지 않으며, 수술적 치료 전 내시경적 복원술로 복원을 시도한 후 , 재발을 방지하기 위한 예정 수술을 시행하는 것이 권장된다. 이에 본 저자들은 수술 전 대장내시경으로써 S자 결장염전을 복원한 후 예정 수술로써 성공적으로 치료된 예가 있어서 문헌 고찰과 함께 보고하는 바이다.
CEO Compensation and Earnings Sensitivity: A Perspective from CEO Duality (2018)

The design of chief-executive-officer (CEO) compensation influences a CEOâ€™s decisions and the degree to which the company in question values foreign and domestic earnings. This study explores how CEO compensation structure influences foreign and domestic earnings. This study investigates 1, 393 listed and over-the-counter companies from 2001 to 2004. The results show that when a CEO also serves as the chairperson of the board of directors, the design of CEO compensation does not assign high weighting to foreign earnings. By contrast, when a CEO is not the chairperson of the board of directors, the design of CEO compensation assigns significantly high weighting to foreign earnings. This research is one of the few studies that explore the influence of a CEO who also serves as the chairperson of the board of directors on CEO compensation composition. The findings reveal that agency problems due to a CEO also serving as the chairperson of the board of directors may influence the importance of foreign earnings in relation to CEO compensation. This study substantially contributes to the fields of corporate governance and earnings management
Thermal Etching of 6H–SiC Substrate Surface (2003)

Thermal etching was investigated as one of the methods of obtaining atomically flat surfaces of SiC substrates. The formation of a graphite layer on substrate surface was suppressed by reducing the C/Si ratio in the vapor phase. Although (1120) substrates etched in argon atmosphere had round pits on their surface, such pits were not observed and an atomically flat surface with an RMS roughness of approximately 0.3 nm was obtained in nitrogen atmosphere even at the high etching rate of 250 µm/h. The substrates with higher nitrogen concentrations had both higher surface flatness and higher etching rate. The thermal etching method was found to be an effective technique for obtaining the flat surface of SiC substrates that is suitable for crystal growth and/or device fabrication. The etching mechanisms of (0001) and (1120) surfaces were compared, and the result was discussed by taking into consideration the bond configuration on the surface.
Clinical Spectrum of Spontaneous Pneumomediastinum in Children (2004)

Spontaneous pneumomediastinum (SPM) is a rare condition in children and probably underdiagnosed in pediatric patients visiting the pediatric emergent unit complaining of acute chest pain, dyspnea or neck discomfort. To evaluate the clinical features of SPM in children, we retrospectively analyzed 19 patients under the age of 18 with a diagnosis of SPM at the Changhua Christian Hospital from June 1994 to June 2003. The diagnosis of SPM was made on frontal chest radiography, including the cervical region. Lateral views were useful if there was a doubt in the diagnosis. In our series. SPM was most commonly associated with infections (42%) followed by asthma (21%) and idiopathic factor (21%). In addition, the most common clinical symptom was chest pain (58%) followed by dyspnea (53%), and the most common specific physical finding was subcutaneous emphysema (79%) followed by Hamman’s sign (21%). All of our cases admitted to the hospital, but six patients (32%) required intensive care treatment due to severe respiratory distress. The mean hospital length of stay for all cases was 4.5±2.6 days (±SD) with a range of 2 to 11 days. All patients had complete or nearly complete resolution of findings on chest radiography before discharge. No recurrence was found in our cases in the past 10 years. In conclusion, SPM is a rare condition but benign in itself in children. If pediatric patients, especially with a history of respiratory infectious disorder or asthma exacerbation, suffer from chest pain, dyspnea or neck discomfort in pediatric emergent unit, the diagnosis of SPM should be considered and chest radiography should be performed. WE recommend children with SPM may require short hospitalization for observation and management of possible complication associated with respiratory compromise, such as accompanying pneumothorax.
Scintigraphic comparison of budesonide deposition from two dry powder inhalers (2000)

Chlorofluorocarbons (CFCs), used in metered dose inhalers (MDIs), have been identified as being deleterious to the environment leading to a ban on their production. Dry powder inhalers (DPIs) are a widely used alternative to MDIs. One disadvantage of DPIs is that in vivo lung deposition can be influenced by the patient's inspiratory flow rate. The ASTA Medica multi-dose dry powder inhaler (AM-MDPI) has been designed to offer low resistance on inhalation, so that asthmatic patients can achieve inhaled flow rates of approximately 90 L x min(-1). The aim of the study was to evaluate the in vivo deposition of budesonide from the AM-MDPI at different flow rates and to compare this with delivery from a Turbuhaler DPI at a high flow rate. The study was a scintigraphic, randomized, crossover study in which 13 healthy volunteers inhaled a single 200 microg dose of radiolabelled budesonide on four separate occasions with a minimum 44-h washout period between dosings. At the lowest flow rate of 54 L x min(-1), comparable to that for the Turbuhaler (58 L x min(-1)), a similar percentage of the metered dose was delivered to the lung (AM-MDPI median 19.9%; Turbuhaler median 21.4%). At high flow rate (peak inspiratory flow rate 99 L x min(-1)) the AM-MDPI delivered significantly more drug to the lung (median 32.1% of metered dose) than at 65 L x min(-1) or 54 L x min(-1) (median 25.0% and 19.9% of metered dose, respectively), thus demonstrating flow rate dependence. The pattern of regional lung deposition from the AM-MDPI was similar for all three inhalation manoeuvres. It was concluded that the ASTA Medica multi-dose dry powder inhaler achieves at least as much deposition of budesonide in the lungs as a Turbuhaler when used at similar inspiratory flow rates.
A system for efficient neural stimulation with energy recovery (2003)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2004.
Pyridinylquinazolines Selectively Inhibit Human Methionine Aminopeptidase-1 in Cells (2013)

Methionine aminopeptidases (MetAPs), which remove the initiator methionine from nascent peptides, are essential in all organisms. While MetAP2 has been demonstrated to be a therapeutic target for inhibiting angiogenesis in mammals, MetAP1 seems to be vital for cell proliferation. Our earlier efforts identified two structural classes of human MetAP1 (HsMetAP1)-selective inhibitors (1–4), but all of them failed to inhibit cellular HsMetAP1. Using Mn(II) or Zn(II) to activate HsMetAP1, we found that 1–4 could only effectively inhibit purified HsMetAP1 in the presence of physiologically unachievable concentrations of Co(II). In an effort to seek Co(II)-independent inhibitors, a novel structural class containing a 2-(pyridin-2-yl)quinazoline core has been discovered. Many compounds in this class potently and selectively inhibited HsMetAP1 without Co(II). Subsequently, we demonstrated that 11j, an auxiliary metal-dependent inhibitor, effectively inhibited HsMetAP1 in primary cells. This is the first report that an HsMetAP1-selective inhibitor is effective against its target in cells.
Identification of a domoic acid-producing<i>Pseudo-nitzschia</i>species (Bacillariophyceae) in the Dutch Wadden Sea with electron microscopy and molecular probes (1996)

Biological monitoring in the Dutch Wadden Sea between November 1993 and July 1994 revealed Pseudo-nitzschia-like pennate chain-forming diatom species with cell numbers ranging from 10^2 to 10^5 per litre. Cultured isolates and field samples were examined by electron microscopy, which revealed the majority to be Pseudo-nitzschia pungens. This species dominated over other diatoms in the phytoplankton population during November 1993 and at the end of June 1994. At the beginning of June 1994, P. fraldulenta was also present; occasionally, P. delicatissima was observed. One isolate showed the characteristic morphology of P. multiseries. Species-specific polyclonal antibodies and large-subunit (LSU) rRNA-targeted oligonucleotides for North American strains of P. multiseries and P. pungens applied to the European isolates, confirmed species designations based on electron microscopy. The isolate of P. multiseries from the Dutch Wadden Sea produced domoic acid; after 55 days of growth about 19 pg per cell was measured. This is the first report of a domoic acid-producing P. multiseries isolated from European coastal waters.
Vers une autonomie d’apprentissage des apprenants débutant en français langue étrangère (2009)

International audience
Some observations on seeding and stability of nc-Si solar cells (2005)

We describe a study on the critical seeding step for preparation of nanocrystalline silicon (nc-Si) p-i-n type solar cells by single-chamber RF-PECVD on native SnO/sub 2/ coated glass superstates. A novel seeding scheme using closed-chamber (CC) plasma has proved effective in eliminating the Si:H incubation layer and reduce optical loss without using ZnO coating. This seeding process does not accumulate a film. Rather, it modifies the surface region of a pre-deposited film. The efficacy of this approach is, however, hindered both by dopant cross-contamination and process sensitivity to the degree of substrate texture. This method is compared with conventional p-layer seeding using non-static plasma which, on ZnO-coated SnO/sub 2/, has resulted in 6.5% single cells with ZnO/AI back contact. Also compared is i-layer seeding. Our 'near-the-edge' nc-Si single junction cells show excellent stability under light and in the dark, without post-deposition oxidation. An 8.7% a-Si/nc-Si tandem solar cell (post light soaking) has been confirmed by NREL.
Effect of pre‐adsorbed proteins on attachment, proliferation, and function of endothelial cells (2002)

As certain proteins control cell adhesion, it has been hoped that cell transplantation and tissue engineering could be augmented by pre-adsorption of specific proteins to biological or synthetic surfaces. The questions that remain, however, are whether such proteins can affect cell production as well as adhesion, and if so, whether in a protein-specific manner. We examined the adhesion and the biochemical secretion of bovine aortic endothelial cells (BAEC) on tissue culture polystyrene (TCPS) discs coated with fibronectin (Fn), laminin (Ln), or gelatin. The three coating proteins nonspecifically promote sub-confluent and post-confluent endothelial cell production of total protein up to 2.5-fold of the reference value. Total soluble glycosaminoglycan (GAG) production slightly increased with the different coatings only at low cell density. In contrast, Ln and Fn, not gelatin, drastically enhanced post-confluent BAEC production of prostaglandin (PGI2). However, antibody-blockage of the alpha5 integrin, constituent of the Fn receptor in BAEC, appeared to inhibit the upregulation of PGI2 production observed on Fn-coated surfaces. The results indicate that the cell adhesion mediators used as coating agents dictate cell biological production as well as adhesion and proliferation.