gebhart/patrepeval huggingface dataset:
Knockdown screening of chromatin binding and regulatory proteins in zebrafish identified Suz12b as a regulator of tfpia and an antithrombotic drug target (2021)

Tissue factor pathway inhibitor (TFPI) is an anticoagulant protein that inhibits factor VIIa and Xa in the coagulation cascade. It has been shown that forkhead box P3 protein is a TFPI transcriptional repressor. However, there are no studies on chromatin remodeling that control TFPI expression. We hypothesized that the genome-wide knockdowns of the chromatin binding and regulatory proteins (CBRPs) in zebrafish could identify novel tfpia gene regulators. As an initial step, we selected 69 CBRP genes from the list of zebrafish thrombocyte-expressed genes. We then performed a 3-gene piggyback knockdown screen of these 69 genes, followed by quantification of tfpia mRNA levels. The results revealed that knockdown of brd7, ing2, ing3, ing4, and suz12b increased tfpia mRNA levels. The simultaneous knockdown of these 5 genes also increased tfpia mRNA levels. We also performed individual gene and simultaneous 5-gene knockdowns on the 5 genes in zebrafish larvae. We found that after laser injury, it took a longer time for the formation of the thrombus to occlude the caudal vessel compared to the control larvae. We then treated the larvae and adults with a chemical UNC6852 known to proteolytically degrade polycomb repressor complex 2, where SUZ12 is a member, and observed prolongation of time to occlude (TTO) the caudal vein after laser injury and increased tfpia mRNA levels in larvae and adults, respectively. In summary, our results have identified novel epigenetic regulators for tfpia and exploited this information to discover a drug that enhances tfpia mRNA levels and prolongation of TTO. This discovery provides the basis for testing whether UNC6852 could be used as an antithrombotic drug. This approach could be used to study the regulation of other plasma proteins, including coagulant and anticoagulant factors.
Structural heterogeneity of carbohydrate modifications affects serospecificity of <i>Campylobacter</i> flagellins (2002)

Flagellin from Campylobacter coli VC167 is post-translationally modified at > or = 16 amino acid residues with pseudaminic acid and three related derivatives. The predominant modification was 5,7-diacetamido-3,5,7,9 - tetradeoxy - l - glycero - l - manno - nonulosonic acid (pseudaminic acid, Pse5Ac7Ac), a modification that has been described previously on flagellin from Campylobacter jejuni 81-176. VC167 lacked two modi-fications present in 81-176 and instead had two unique modifications of masses 431 and 432 Da. Flagellins from both C. jejuni 81-176 and C. coli VC167 were also modified with an acetamidino form of pseudaminic acid (PseAm), but tandem mass spectrometry indicated that the structure of PseAm differed in the two strains. Synthesis of PseAm in C. coli VC167 requires a minimum of six ptm genes. In contrast, PseAm is synthesized in C. jejuni 81-176 via an alternative pathway using the product of the pseA gene. Mutation of the ptm genes in C. coli VC167 can be detected by changes in apparent Mr of flagellin in SDS-PAGE gels, changes in isoelectric focusing (IEF) patterns and loss of immunoreactivity with antiserum LAH2. These changes corresponded to loss of both 315 Da and 431 Da modifications from flagellin. Complementation of the VC167 ptm mutants with the 81-176 pseA gene in trans resulted in flagellins containing both 315 and 431 Da modifications, but these flagellins remained unreactive in LAH2 antibody, suggesting that the unique form of PseAm encoded by the ptm genes contributes to the serospecificity of the flagellar filament.
Automotive Multichip Modules (2009)

This chapter contains sections titled: Introduction Historical Powertrain Electronics Packaging Strategy Automotive Environmental Conditions Design Options Test Development for Motorola QFP [15.5] EMC Testing [15.7] Cost Analysis Summary This chapter contains sections titled: Acknowledgments References Appendix A15: Laminate MicroInterconnect (LMI) ]]>
Direct measurement of the electrogenic activity of o-type cytochrome oxidase from Escherichia coli reconstituted into planar lipid bilayers. (1985)

Turnover of o-type cytochrome oxidase purified from Escherichia coli and reconstituted into proteoliposomes leads to the generation of a transmembrane electrical potential (interior negative) by means of vectorial electron flow. In the experiments reported here, purified oxidase is reconstituted in planar lipid bilayers formed at the tip of patch pipets, and open-circuit membrane potentials generated by electron transfer are measured directly. Potentials of up to 4 mV (substrate side positive) are generated in the presence of reduced phenazine methosulfate or ubiquinol-1, and with both substrates, electrogenic activity is inhibited by cyanide. Furthermore, the membrane potential generated during oxidase turnover is inhibited progressively with applied voltages (substrate side positive), decreasing almost to zero at an applied voltage of 150 mV.
Molecular biological observations in gastric cancer. (1996)

Alterations in the structure and function of oncogenes and tumor suppressor genes, as well as genetic instability at several other genetic foci may be responsible for stomach carcinogenesis. The particular combination of multiple gene changes found in gastric cancer differs depending on the two histological types, strongly indicating that different genetic pathways exist for well differentiated or intestinal type and poorly differentiated or diffuse type gastric cancers. In general, genetic instability, telomerase activity, CD44 abnormal transcripts, and p53 mutation, all of which are common events of two types of gastric cancer, may be involved mainly in the early stage of stomach carcinogenesis, whereas activation of oncogenes and overexpression of the epidermal growth factor-related growth factor system may chiefly confer progression on gastric cancer. A new strategy of molecular diagnosis of gastrointestinal cancer, which has been implemented as a routine service in the Hiroshima University Clinical Laboratory, may provide new opportunities for early cancer diagnosis and more accurate evaluation of prognosis or grade of malignancy.
Darts-Conformer: Towards Efficient Gradient-Based Neural Architecture Search For End-to-End ASR (2021)

Neural architecture search (NAS) has been successfully applied to tasks like image classification and language modeling for finding efficient high-performance network architectures. In ASR field especially end-to-end ASR, the related research is still in its infancy. In this work, we focus on applying NAS on the most popular manually designed model: Conformer, and then propose an efficient ASR model searching method that benefits from the natural advantage of differentiable architecture search (Darts) in reducing computational overheads. We fuse Darts mutator and Conformer blocks to form a complete search space, within which a modified architecture called Darts-Conformer cell is found automatically. The entire searching process on AISHELL-1 dataset costs only 0.7 GPU days. Replacing the Conformer encoder by stacking searched cell, we get an end-to-end ASR model (named as Darts-Conformner) that outperforms the Conformer baseline by 4.7\% on the open-source AISHELL-1 dataset. Besides, we verify the transferability of the architecture searched on a small dataset to a larger 2k-hour dataset. To the best of our knowledge, this is the first successful attempt to apply gradient-based architecture search in the attention-based encoder-decoder ASR model.
The myth of the non-coordinating anion (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe myth of the non-coordinating anionMichael R. Rosenthal Cite this: J. Chem. Educ. 1973, 50, 5, 331Publication Date (Print):May 1, 1973Publication History Received3 August 2009Published online1 May 1973Published inissue 1 May 1973https://doi.org/10.1021/ed050p331RIGHTS & PERMISSIONSArticle Views2282Altmetric-Citations447LEARN 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 (4 MB) Get e-Alerts Get e-Alerts
Nucleophilic Dearomatization of Chloromethyl Naphthalene Derivatives via η<sup>3</sup>-Benzylpalladium Intermediates: A New Strategy for Catalytic Dearomatization (2011)

Palladium-catalyzed nucleophilic dearomatization of chloromethyl naphthalene derivatives to produce ortho- or para-substituted carbocycles in satisfactory to excellent yields has been developed. The unprecedented dearomatization reactions proceeded smoothly under mild conditions via η(3)-benzylpalladium intermediates.
Intraband relaxation time in quantum-well lasers (1989)

Intraband relaxation time, which causes spectral broadening of optical gain and spontaneous emission spectra, is estimated theoretically for quantum-well lasers. Carrier-carrier and carrier-longitudinal-optical (LO) phonon scattering mechanisms are considered, and it is shown that hole-hole, electron-hole, and hole-LO phonon scattering are dominant in spectral broadening. Intraband relaxation time determined by all of these mechanisms increases slightly with the decrease of well width. The dependence of intraband relaxation time on temperature, carrier density, and energy of electron and hole is also shown. Spectral line shape is discussed as an extension of the above calculation, and an approximated formula is given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Are all granzymes cytotoxic <i>in vivo</i> ? (2013)

Abstract Granzymes are serine proteases mainly found in cytotoxic lymphocytes. The most-studied member of this group is granzyme B, which is a potent cytotoxin that has set the paradigm that all granzymes are cyototoxic. In the last 5 years, this paradigm has become controversial. On one hand, there is a plethora of sometimes contradictory publications showing mainly caspase-independent cytotoxic effects of granzyme A and the so-called orphan granzymes in vitro. On the other hand, there are increasing numbers of reports of granzymes failing to induce cell death in vitro unless very high (potentially supra-physiological) concentrations are used. Furthermore, experiments with granzyme A or granzyme M knock-out mice reveal little or no deficit in their cytotoxic lymphocytes' killing ability ex vivo, but indicate impairment in the inflammatory response. These findings of non-cytotoxic effects of granzymes challenge dogma, and thus require alternative or additional explanations to be developed of the role of granzymes in defeating pathogens. Here we review evidence for granzyme cytotoxicity, give an overview of their non-cytotoxic functions, and suggest technical improvements for future investigations.
Reducing Uncertainty of Reserves Estimates Using Inversion of Time-Lapse Logging Data (2006)

Abstract The estimation of hydrocarbon reserves heavily depends on the accuracy of resistivity data and the reliability of their interpretation. To optimize data information extraction from acquired modern array resistivity logs, integrated inversion- based interpretation techniques are required. However, the direct application of an inversion method may provide an incorrect equivalent solution, resulting in erroneous hydrocarbon estimates. To solve the equivalency problem, we have developed a new method that reconstructs the formation model in steps using inversion of time-lapse Logging-While-Drilling (LWD) and Wireline (WL) measurements. The main steps are: Estimate resistivities of invaded and uncontaminated zones using LWD data focusing or inversion.Re-estimate resistivity of the invaded zone using WL logs, array data focusing or inversion.Estimate depth of invasion using WL data inversion and the results of the steps above.Re-estimate the model parameters using WL data inversion and the results of the steps above.Estimate parameters of a complex invasion radial profile using WL data inversion. To establish the effectiveness of the method, we tested it on a synthetic example that was constructed using LWD and WL logs acquired in a well from the South China Sea. This field data was also used for our case study. The conclusion is that the suggested method provides a framework for effective integration of time-lapse logging measurements to increase accuracy of formation evaluation.
Ultrastructural Studies of Diffuse Axonal Injury in Humans (1994)

Diffuse axonal injury (DAI) is observed commonly in traumatically brain injured humans. However, traditional histologic methods have proven of limited use in identifying reactive axonal change early (< 12 h) in the posttraumatic course. Recently, we have reported, in both humans and animals, that antibodies targeting neurofilament subunits are useful in the light microscopic recognition of early reactive change. In the present study, we extend our previous efforts in humans by analyzing the progression of traumatic brain injury (TBI)-induced axonal change at the ultrastructural level. This effort was initiated to follow the subcellular progression of reactive axonal change in humans and to determine whether this progression parallels that described in animals. Two commercially prepared antibodies were used to recognize reactive axonal change in patients surviving from 6 to 88 h. The NR4 antibody was used to target the light neurofilament subunit (NF-L), and the SMI32 antibody was used to target the heavy neurofilament subunit (NF-H). Plastic-embedded tissue sections were screened for evidence of reactive axonal change, and once identified, this reactive change was analyzed at the ultrastructural level. At 6 h survival, focally enlarged, immunoreactive axons with axolemmal infolding or disordered neurofilaments were seen within fields of axons exhibiting no apparent abnormality. By 12 h, some axons exhibited continued neurofilamentous misalignment, pronounced immunoreactivity, vacuolization, and, occasionally, disconnection. At later stages, specifically 30 and 60 h survival, further accumulation of neurofilaments and organelles had led to the further expansion of the axis cylinder, and clearly disconnected reactive swellings were recognized. These contained a dense core of disordered immunoreactive neurofilaments partially encompassed by a cap of less densely aggregated organelles. At 88 h, the reactive axons were larger and elongated, consistent with the continued delivery of organelles by axoplasmic transport. At the later time points, considerable heterogeneity was observed, with focally enlarged disconnected axons being observed in relation to axons showing less advanced reactive change. Our findings suggest that neurofilamentous disruption is a pivotal event in axonal injury.
Fabrication of two-dimensional arrays of nanometer-size clusters with the atomic force microscope (1995)

An atomic force microscope tip is used as a vector positioner to manipulate nanometer-size preformed Au clusters deposited on atomically smooth substrates. Using this technique, two-dimensional cluster nanostructures can be assembled at room temperature.
A Flow-Through Cell Electroporation Device for Rapidly and Efficiently Transfecting Massive Amounts of Cells in vitro and ex vivo (2016)

Continuous cell electroporation is an appealing non-viral approach for genetically transfecting a large number of cells. Yet the traditional macro-scale devices suffer from the unsatisfactory transfection efficiency and/or cell viability due to their high voltage, while the emerging microfluidic electroporation devices is still limited by their low cell processing speed. Here we present a flow-through cell electroporation device integrating large-sized flow tube and small-spaced distributed needle electrode array. Relatively large flow tube enables high flow rate, simple flow characterization and low shear force, while well-organized needle array electrodes produce an even-distributed electric field with low voltage. Thus the difficulties for seeking the fine balance between high flow rate and low electroporation voltage were steered clear. Efficient in vitro electrotransfection of plasmid DNA was demonstrated in several hard-to-transfect cell lines. Furthermore, we also explored ex vivo electroporated mouse erythrocyte as the carrier of RNA. The strong ability of RNA loading and short exposure time of freshly isolated cells jointly ensured a high yield of valid carrier erythrocytes, which further successfully delivered RNA into targeted tissue. Both in vitro and ex vivo electrotransfection could be accomplished at high cell processing speed (20 million cells per minute) which remarkably outperforms previous devices.
Vibration detection by observation of speckle patterns (2014)

When laser light illuminates a rough surface it is scattered into a speckle pattern that is strongly dependent on the surface geometry. Here, we show that it is possible to sense surface vibrations by measuring signal variations from a single pixel detector that collects a small portion of the scattered light. By carefully tuning the probing laser beam size and the detector’s aperture it was possible to record a good quality signal in the acoustic band. This approach eliminates the need for an interferometer and thus opens the door to the possibility of detecting vibrations at distances of few hundreds of meters.
The determination of glass transition temperatures by differential thermal analysis (1960)

Differential thermal analysis has been applied to the study of glass transitions in polymers; DTA can detect the discontinuous changes in specific heat which are associated with such transitions. The apparatus used must have considerably greater sensitivity than that required for measuring transitions involving latent heats. Amplification of the differential-thermocouple e.m.f. permits detection of temperature changes of 0.01°C. An aluminum block furnace having the high stability necessary for this amplification has been constructed. The DTA glass temperatures are comparable to those obtained by other methods, and the precision of the determinations is usually better than 1–2°C. This technique appears to be superior to others in convenience and speed. Wide variations in particle size and heating rate have no significant effect on the measured transition temperature. The glass temperature of polyacrylonitrile has been the subject of disagreement. Differential thermal analysis has shown that it rises from 56°C. for a sample of molecular weight 1500 to 80°C. for samples of molecular weight greater than 75,000.
A network-based localized mobility solution for Distributed Mobility Management (2011)

Internet traffic has increased steeply in recent years, due in great part to social platforms and peer-to-peer networks. In addition, users' wireless access represents an ever-growing portion of such demand, thus posing a paradigm shift in the flow of Internet information, for which most deployed architectures are not prepared for.
Cyberattacks: Why, What, Who, and How (2009)

As computers, information systems, and networking have become increasingly ubiquitous, cybersecurity has become even more critical for the continuity of basic business operations. This article analyzes the challenges associated with cybersecurity, including attack patterns and trends.
Optimum Design of Linear Antenna Arrays Using a Hybrid MoM/GA Algorithm (2011)

Synthesis of arbitrarily shaped radiation patterns using linear antenna arrays has a significant importance in many applications. Many attempts based on analytical schemes are exerted for this purpose. However, these analytical methods are developed for specific problems, and usually synthesis of the radiation pattern is subject to only one restriction. On the other hand, optimization algorithms are utilized for more general problems. However, these algorithms require more computational time. In this letter, a new hybrid technique for synthesizing arbitrary-shaped radiation pattern using a linear array is developed. The algorithm is based on a combination between the method of moments (MoM) and the genetic algorithm (GA). The proposed algorithm is applied to synthesis of both symmetric and asymmetric radiation pattern distributions with minimum number of elements. Excellent agreement is obtained by comparison to other analytical and optimization techniques.
Suppression of CoSix Induced Leakage Current Using Novel Capping Process for Sub-0.10um node SRAM Cell Technology (2002)

We present a novel capping process for sub-0.10um node SRAM cell to suppress the Co silicide induced leakage current. The dimensions in the SRAM cell are scaled down to sub-0.10um. As a result, the CoSix induced leakage current increases as the sizes of the contact and the active area decrease due to the CoSix defects and the contact etch induced CoSix pitting. The double stacked layers on Co silicide successfully reduced the junction leakage current and widened the borderless contact etching process window by suppression of the CoSix defects and the Co silicide pittings.
Color-Weakness Compensation Using Riemann Normal Coordinates (2012)

We introduce normal coordinates in Riemann spaces as a tool to construct color-weak compensation methods. We use them to compute color stimuli for a color weak observers that result in the same color perception as the original image presented to a color normal observer in the sense that perceived color-differences are identical for both. The compensation is obtained through a color-difference-preserving map, i.e. an isometry between the 3D color spaces of a color-normal and any given color-weak observer. This approach uses discrimination threshold data and is free from approximation errors due to local linearization. The performance is evaluated with the help of semantic differential (SD) tests.
Producing Covalent Microarrays of Amine‐Conjugated DNA Probes on Various Functional Surfaces to Create Stable and Reliable Biosensors (2018)

Abstract Oligonucleotide‐based microarrays are ideal tools for genetic testing and diagnostics due to their stability, ease of synthesis, and high specificity for the target of interest. This study reports on the effectiveness of several coupling strategies to covalently attach single‐stranded nucleic acids to surfaces, focusing on the robustness of the attachment in various environmental conditions, such as pH and temperature. Various characteristics of DNA microarrays produced using amine‐conjugated DNA probes on five different functional surfaces, commonly used for immobilization of biomolecules, namely, epoxy, carboxyl, amine, aldehyde, and N ‐hydroxysuccinimide‐coated substrates, are investigated. Immobilization efficiency, changes in surface energy, as well as the stability of the conjugated DNA upon exposure to various environmental conditions are measured. Finally, in order to study the postimmobilization viability of the developed biosensors, microarrays of synthetic RNA cleaving probes (DNAzyme) are immobilized onto these surfaces and their functionality is evaluated through their ability to detect Escherichia coli at various temperatures. Results show that epoxy‐coated plastic surfaces are most ideal for the creation of DNA‐based biosensing chips. This study provides a guideline for producing oligonucleotide‐based microarrays on glass and plastic substrates and can be used for developing microarray‐based biosensors, suitable for long‐term storage.