gebhart/patrepeval huggingface dataset:
A Single Active Site Mutation in the Pikromycin Thioesterase Generates a More Effective Macrocyclization Catalyst (2017)

Macrolactonization of natural product analogs presents a significant challenge to both biosynthetic assembly and synthetic chemistry. In the preceding paper , we identified a thioesterase (TE) domain catalytic bottleneck processing unnatural substrates in the pikromycin (Pik) system, preventing the formation of epimerized macrolactones. Here, we perform molecular dynamics simulations showing the epimerized hexaketide was accommodated within the Pik TE active site; however, intrinsic conformational preferences of the substrate resulted in predominately unproductive conformations, in agreement with the observed hydrolysis. Accordingly, we engineered the stereoselective Pik TE to yield a variant (TE<sub>S148C</sub>) with improved reaction kinetics and gain-of-function processing of an unnatural, epimerized hexaketide. Quantum mechanical comparison of model TE<sub>S148C</sub> and TE<sub>WT</sub> reaction coordinate diagrams revealed a change in mechanism from a stepwise addition-elimination (TE<sub>WT</sub>) to a lower energy concerted acyl substitution (TE<sub>S148C</sub>), accounting for the gain-of-function and improved reaction kinetics. Finally, we introduced the S148C mutation into a polyketide synthase module (PikAIII-TE) to impart increased substrate flexibility, enabling the production of diastereomeric macrolactones.
Predictive factors for regression of gastric MALT lymphoma after anti- <i>Helicobacter pylori</i> treatment (2001)

In H pylori positive patients with localised gastric MALT lymphoma, carefully evaluated and treated without any lymph node involvement assessed by endoscopic ultrasonography, complete remission of lymphoma was reached in 79% of cases.
Monoterpenes as Drug Shuttles:  Cytotoxic (6-Aminomethylnicotinate)dichloridoplatinum(II) Complexes with Potential To Overcome Cisplatin Resistance (2007)

(6-Aminomethylnicotinate)dichloridoplatinum(II) complexes 4 esterified with terpene alcohols were tested on a panel of five human tumor cell lines. While they were accumulated in all cell lines more readily than cisplatin (CDDP), their cytotoxicities were tumor-specific and structure-dependent. Cell lines known to feature elevated levels of antiapoptotic, ion-channel-affecting proteins or otherwise impaired caspase-9 activation responded better to 4 than to CDDP, e.g., the HL-60 leukemia to the fenchyl and bornyl derivatives 4a,b at an IC90 < or = 10 microM. The (-)-menthyl complex 4g was far better accumulated and more efficacious in CDDP-resistant 1411HP male germ cell tumor cells than in the congenerous CDDP-sensitive H12.1 cell line. 4g also broke the CDDP resistance of 518A2 melanoma cells. Cell decay in each case was apoptotic as to TUNEL and Annexin V fluorescence assays. Some complexes 4 seem to positively modulate the permeability of the cell membrane and of blocked mitochondrial anion channels.
Vacuum tool for handling microobjects with a NanoRobot (2002)

One of the basic tasks a robot has to perform is to manipulate objects. For macroscopic applications mechanical grippers usually grasp the workpiece. Because of the different scaling of gravity and adhesion such tools are no more suitable in micro manipulation. A better strategy is to use adhesion forces or vacuum. Therefore, after a brief introduction to adhesion phenomenons this paper focuses on the investigation of a vacuum gripping tool consisting of a glass pipette and a computer controlled vacuum supply. Special emphasis is laid on the optimization of the tool's parameters in order to improve its pick and place capability. The tool has been integrated into the ETHZ NanoRobot and tested on dedicated benchmark test. It was possible to grip 100 /spl mu/m sized diamond crystals and deposit them at arbitrary positions. Also emergency routines that allow to reliably get rid of sticking particles are presented. Finally the new setup of the multi-tool NanoRobot containing both the vacuum pipette and a microfabricated gripper is presented. It enables handling of micro-parts with more flexibility by working hand in hand.
Acoustic microscopy of interior planes (1979)

It has been recently demonstrated that the acoustic microscope can be used to image planes relatively deep beneath the surface with a lateral resolution of approximately one acoustic wavelength. In order to minimize the aberration effects caused by refraction at the liquid-solid interface, liquid gallium is substituted for water as the coupling liquid, and mode conversion to shear waves within the solid is exploited. The imaging properties of this system are discussed from a geometrical viewpoint and some experimental results are presented.
Suppression of HER-2 via siRNA interference promotes apoptosis and decreases metastatic potential of SKOV-3 human ovarian carcinoma cells (2012)

The aberrant expression of human epidermal growth factor receptor-2 (HER-2) has been detected in ovarian cancer. However, the role of HER-2 in the development of ovarian cancer has not been sufficiently elucidated. The objective of this study was to determine the role of HER-2 in the apoptosis and metastasis of SKOV-3 ovarian cancer cells. SKOV-3 cells were transfected with three double‑stranded small interfering RNA (siRNA) molecules that target HER-2. Various sequences were synthesized by T7 transcription in vitro to select the most effective HER-2‑silencing siRNA. SKOV-3 cells were examined for growth inhibition using the MTT proliferation assay and apoptosis was assessed using flow cytometry and TUNEL assay. The Matrigel basement memebrane matrix was used to assess invasion and chemotactic mobility, as a model of tumor cell metastasis. Western blot analysis was used to detect the expression of matrix metallopeptidase-9 (MMP-9), E-cadherin, N-cadherin and vimentin. siRNA interference in HER-2 resulted in decreased cell proliferation and invasion and increased apoptosis. Western blot analysis demonstrated a marked increase in E-cadherin and MMP-9 and a reduction in N-cadherin and vimentin protein levels in the SKOV-3 cells. The suppression of HER-2 expression resulted in apoptosis and the inhibition of metastasis of SKOV-3 cells. Therefore, the overexpression of the HER-2 gene can enhance the metastatic potential of SKOV-3 cells by increasing the protein levels of MMP-9. Epithelial-mesenchymal transition may be involved in the HER-2 siRNA-induced invasion and migration of SKOV-3 cells. Taken together, these results suggest that HER-2 functions as an oncogene and may thus be an attractive therapeutic target in SKOV-3 ovarian cancer cells.
The Catalytic Properties of Hybrid Rubisco Comprising Tobacco Small and Sunflower Large Subunits Mirror the Kinetically Equivalent Source Rubiscos and Can Support Tobacco Growth (2007)

Plastomic replacement of the tobacco (Nicotiana tabacum) Rubisco large subunit gene (rbcL) with that from sunflower (Helianthus annuus; rbcL(S)) produced tobacco(Rst) transformants that produced a hybrid Rubisco consisting of sunflower large and tobacco small subunits (L(s)S(t)). The tobacco(Rst) plants required CO(2) (0.5% v/v) supplementation to grow autotrophically from seed despite the substrate saturated carboxylation rate, K(m), for CO(2) and CO(2)/O(2) selectivity of the L(s)S(t) enzyme mirroring the kinetically equivalent tobacco and sunflower Rubiscos. Consequently, at the onset of exponential growth when the source strength and leaf L(s)S(t) content were sufficient, tobacco(Rst) plants grew to maturity without CO(2) supplementation. When grown under a high pCO(2), the tobacco(Rst) seedlings grew slower than tobacco and exhibited unique growth phenotypes: Juvenile plants formed clusters of 10 to 20 structurally simple oblanceolate leaves, developed multiple apical meristems, and the mature leaves displayed marginal curling and dimpling. Depending on developmental stage, the L(s)S(t) content in tobacco(Rst) leaves was 4- to 7-fold less than tobacco, and gas exchange coupled with chlorophyll fluorescence showed that at 2 mbar pCO(2) and growth illumination CO(2) assimilation in mature tobacco(Rst) leaves remained limited by Rubisco activity and its rate (approximately 11 micromol m(-2) s(-1)) was half that of tobacco controls. (35)S-methionine labeling showed the stability of assembled L(s)S(t) was similar to tobacco Rubisco and measurements of light transient CO(2) assimilation rates showed L(s)S(t) was adequately regulated by tobacco Rubisco activase. We conclude limitations to tobacco(Rst) growth primarily stem from reduced rbcL(S) mRNA levels and the translation and/or assembly of sunflower large with the tobacco small subunits that restricted L(s)S(t) synthesis.
Regulation of Differentiation of Tracheal Epithelial Cells by Retinoids (1985)

An in vitro culture system of rabbit tracheal epithelial cells has been developed to study the regulation of differentiation of the respiratory epithelium on the molecular level. At high density in the absence of retinoids these cells become squamous, stratify, and ultimately form cross-linked envelopes. Several factors influence this terminal differentiation: high Ca2+ concentrations and serum factors promote, whereas retinoids and medium conditioned by fibroblasts inhibit this process. Terminal squamous cell differentiation is accompanied by several biochemical changes: the synthesis of proteoglycans is dramatically reduced and the expression of keratin intermediate filaments is altered. Besides the eight major keratins expressed in undifferentiated cells, terminally differentiated cells also express a 48 kDa keratin. The expression of this keratin correlates well with squamous cell differentiation and appears to be under the control of retinoic acid. The level at which these biochemical changes are regulated has yet to be established. Specific retinol- and retinoic acid-binding proteins have been identified in these cells; the correlation between binding and biological activity of retinoids in this system is in agreement with a role for these binding proteins in mediating the action of these agents.
Dimethylzirconocene-catalyzed polymerization of alkylsilanes (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDimethylzirconocene-catalyzed polymerization of alkylsilanesWilliam H. Campbell, Terrence K. Hilty, and Lori YurgaCite this: Organometallics 1989, 8, 11, 2615–2618Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://doi.org/10.1021/om00113a016RIGHTS & PERMISSIONSArticle Views195Altmetric-Citations41LEARN 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 InReddit PDF (548 KB) Get e-Alerts Get e-Alerts
A New Method for Synchronous Generator Core Quality Evaluation (2004)

A new technique for detecting the presence and severity of inter-laminar short circuits as well as estimating the status of core compression (or looseness) in laminated magnetic cores of synchronous generators, with a single test equipment is demonstrated in this paper. The core loss measurement obtained from a flux injection probe that injects flux (of varying amplitude, frequency, and wave-shape) into two nominally adjacent teeth over a localized region, is used as an indicator for detecting and distinguishing the two fault conditions. An injection probe system was developed and tested, in the laboratory, using stacks of full size generator laminations with various induced fault conditions. The injection probe was shown to detect the presence of shorted laminations at the bottom of the slot and to gauge the degree of core compression or looseness. In addition, a unique differential probe was developed and tested to demonstrate the capability of detecting as few as five shorted laminations.
Fault-tolerant BIBD networks (2003)

The use of multiple buses can improve both the fault tolerance and performance of local area computer networks. Existing schemes either depend on active components for full connectivity or can experience decreased performance as many hosts attempt to access one bus. An architecture class based on balanced incomplete block designs (BIBDs) is proposed to address these problems. A BIBD architecture uses redundant communication channels and exhibits degradable performance as faults occur. The performability of such networks is evaluated, where evaluation is based on stochastic activity network models. The results obtained are provided for comparison of BIBD network performability with that of conventional multibus networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Space-Time Block Coding-Based Beamforming for Beam Squint Compensation (2018)

In this letter, the beam squint problem, which causes significant variations in radiated beam gain over frequencies in a millimeter wave communication system, is investigated. A constant modulus beamformer design, which is formulated to maximize the expected average beam gain within the bandwidth with limited variation over frequencies within the bandwidth, is proposed. A semidefinite relaxation method is developed to solve the optimization problem under the constant modulus constraints. Depending on the eigenvalues of the optimal solution, either direct beamforming or transmit diversity-based beamforming is employed for data transmissions. Through numerical results, the proposed transmission scheme can compensate for beam squint effectively and improve system throughput. Overall, a transmission scheme for beam squint compensation in wideband wireless communication systems is provided.
AN ANALYSIS OF HYPERBOLE IN THE ALBUM "ONE THING AT A TIME" BY MORGAN WALLEN (2023)

Figurative language is a linguistic device that involves using words, phrases, or expressions beyond their literal or dictionary meanings. Figurative language is commonly used in song lyrics to enhance the depth, emotion, and impact of the song. The research aims to identify the use of hyperbole in the album "One Thing At A Time" by Morgan Wallen and to analyze the meaning of the hyperbole found in the songs. The data collection involves several steps, including listening to the songs, reading scripts, and categorizing hyperbolic expressions within the lyrics. The collected data was then analyzed descriptively using a qualitative method. The theory by Knickerbocker and Reninger (1963) was applied to identify the hyperbole in the song lyrics, and the theory by Leech (1981) was used to interpret the meaning. The results showed that there were ten data of hyperbole found in five songs by Morgan Wallen. The study highlighted the importance of the singer's use of hyperbole in the song, emphasizing how he can create powerful feelings and provide multiple levels of meaning that the listeners can relate to.
Glucose-Regulated Insulin Expression in Diabetic Rats (2001)

Retroviral vectors encoding glucose-responsive promoters driving furin expression may provide an amplified, glucose-regulated secretion of insulin. We constructed LhI*TFSN virus to encode a glucose-regulatable transforming growth factor alpha promoter controlling furin expression with a viral LTR promoter driving constitutive expression of furin-cleavable human proinsulin. Autologous BB rat vascular smooth muscle cells transduced with LhI*TFSN virus and cultured in 1.7 and 16.7 mM glucose secreted 50.7 +/- 3.2 and 136.0 +/- 11.0 microU (mean +/- SD) of insulin per 10(6) cells per day, respectively. After the onset of diabetes spontaneously diabetic congenic DR lyp/lyp BB rats received stomach implants containing 2 x 10(6) LhI*TFSN-transduced primary rat vascular smooth muscle cells. In eight treated rats there was a major reduction in insulin requirement to as low as 25% of pretreatment level for up to 3 months and one rat became insulin free without hypoglycemia. Intraperitoneal glucose tolerance tests (IPGTTs) in diabetic rats receiving control implants did not show the characteristic decline in blood glucose of normal rats after glucose administration. In contrast, diabetic rats receiving LhI*TFSN-transduced cells showed significant clearances of blood glucose. These data suggest clinically significant levels of glucose-regulated insulin delivery from implanted vascular smooth muscle cells transduced with LhI*TFSN vector.
Molecular biology and pathogenesis of Kaposi sarcoma-associated herpesvirus (2003)

Kaposi sarcoma (KS)-associated herpesvirus (KSHV) is the most recently discovered human oncogenic herpesvirus. The virus is associated with KS lesions and other human malignancies, including pleural effusion lymphomas and multicentric castleman's disease. The sequence of the viral genome demonstrated that it belongs to the gammaherpesvirus family similar to the Epstein-Barr virus, the only other known human herpesvirus associated with human cancers. Molecular studies have identified a number of viral genes involved in regulation of cell proliferation, gene regulation, chromatin remodeling and apoptosis. KSHV transforms human endothelial cells in vitro with low efficiency and expresses a repertoire of latent genes involved in the establishment of latency. One of these latent proteins, the latency-associated nuclear antigen (LANA) is required for episomal maintenance and tethers the viral genome to the host chromatin. LANA has now been shown to be a multifunctional protein involved in numerous cellular functions including binding to the retinoblastoma protein and p53, regulating cell proliferation and apoptosis.
Overlapped-shaking: A local authentication method for mobile applications (2014)

Mobile applications become increasingly popular currently. Both authentication and privacy are very important for mobile applications. A promising approach for local authentication is to match the acceleration sensor samples of the two candidate smart phones. However, the acceleration sensor on the smart phones sample at different rates and the starting phases are not aligned. This paper presents a new local authentication method for mobile applications called Overlapped-shaking. Overlapped-shaking is a background service for smart phones which can measure the similarities between two shaking patterns. We design a new acceleration samples matching method called SAM, which can handle the data in different sample rates and offset at the beginning. We implement a demonstration of Overlapped-shaking service on Android smart phones. Test results show that our approach works very well for acceleration-based smart phone authentications.
The principal components of natural images (1992)

A neural net was used to analyse samples of natural images and text. For the natural images, components resemble derivatives of Gaussian operators, similar to those found in visual cortex and inferred from psychophysics. While the results from natural images do not depend on scale, those from text images are highly scale dependent. Convolution of one of the text components with an original image shows that it is sensitive to inter-word gaps.
Mouse Models for Cardiac Conduction System Development (2003)

The mouse is the animal of choice for the study of molecular mechanisms involved in the regulation of cardiovascular morphogenesis and function. Recently, a series of genetically engineered mouse models have been reported (e.g. cGATA6/lacZ, MinK/lacZ knock-in/knock-out, engrailed2/lacZ, Cardiac troponin I/lacZ) that provide new and exciting information on the development of the atrioventricular conduction system (AVCS). On the basis of these and ongoing studies, concepts for the formation of the AVCS are continuously being adjusted. A proper understanding of the normal developmental mechanisms underlying the cardiac remodelling leading to the formation of the AVCS is imperative for the interpretation of cardiac abnormalities, including conduction disturbances, as observed in some genetically perturbed (knockout) mice. In this paper information on murine AVCS development will be integrated with published and unpublished results from studies in other vertebrates, including human and rabbit. We will illustrate that although many pieces of the puzzle still remain to be gathered, the outline of a very complex and critical event in cardiac morphogenesis is slowly emerging. Specifically, we will re-evaluate the concept of the 'primary ring' in the context of the new insights in the development of the AV junction as provided by the respective mouse models described above.
Novel apodization and pellicle optical models for accurate optical proximity correction modeling at 45 and <inline-formula><math altimg="none" display="inline" overflow="scroll"><mrow><mn>32</mn><mspace width="0.3em" /><mi>nm</mi></mrow></math></inline-formula> (2007)

An accurate optical model is the foundation of an accurate optical proximity correction (OPC) model, which has always been the key for successful implementation of model-based OPC. As critical dimension (CD) control requirements become severe at the 45- and 32-nm device generations, OPC model accuracy and hence optical model accuracy requirements become more stringent. In previous generations, certain optical effects could be safely ignored. For example, the transmission attenuation particularly at high spatial frequencies caused by lens apodization effects and organic pellicle films was ignored or not accurately modeled in conventional OPC simulators. These effects are now playing a more important role in OPC modeling as technology scales down. Our simulations indicate these effects can cause CD modeling errors of 5 nm or larger, at the 45-nm technology node and beyond. Therefore, they must be accurately modeled in OPC modeling. In our OPC modeling methodology, we propose two novel low-pass-filter models to capture the frequency-dependent transmission attenuation due to lens apodization and to pellicle films. These parameterized novel low-pass-filter models ensure that lens apodization and pellicle-film-induced transmission attenuation can be appropriately account for through regression during the experimental OPC model calibration stage in the case where no measured transmission data are available, thus enabling physics-centric OPC model building with considerably higher accuracy. We can then avoid overfitting the OPC model, which could cause instability in the OPC correction stage. The validity and efficiency of the proposed novel models are also verified using an industry-standard lithography simulator as well as an experimental OPC model calibration at the 45-nm technology node.