gebhart/patrepeval huggingface dataset:
Seed‐based systematic discovery of specific transcription factor target genes (2008)

Reliable prediction of specific transcription factor target genes is a major challenge in systems biology and functional genomics. Current sequence-based methods yield many false predictions, due to the short and degenerated DNA-binding motifs. Here, we describe a new systematic genome-wide approach, the seed-distribution-distance method, that searches large-scale genome-wide expression data for genes that are similarly expressed as known targets. This method is used to identify genes that are likely targets, allowing sequence-based methods to focus on a subset of genes, giving rise to fewer false-positive predictions. We show by cross-validation that this method is robust in recovering specific target genes. Furthermore, this method identifies genes with typical functions and binding motifs of the seed. The method is illustrated by predicting novel targets of the transcription factor nuclear factor kappaB (NF-kappaB). Among the new targets is optineurin, which plays a key role in the pathogenesis of acquired blindness caused by adult-onset primary open-angle glaucoma. We show experimentally that the optineurin gene and other predicted genes are targets of NF-kappaB. Thus, our data provide a missing link in the signalling of NF-kappaB and the damping function of optineurin in signalling feedback of NF-kappaB. We present a robust and reliable method to enhance the genome-wide prediction of specific transcription factor target genes that exploits the vast amount of expression information available in public databases today.
Anatase Mesoporous TiO2 Nanofibers with High Surface Area for Solid‐State Dye‐Sensitized Solar Cells (2010)

Abstract Mesoporous nanofibers (NFs) with a high surface area of 112 m 2 /g have been prepared by electrospinning technique. The structures of mesoporous NFs and regular NFs are characterized and compared through scanning electron microscope (SEM), transmission electron microscopy (TEM), X‐ray diffraction (XRD) and selected area electron diffraction (SAED) studies. Using mesoporous TiO 2 NFs as the photoelectrode, solid‐state dye‐sensitized solar cells (SDSCs) have been fabricated employing D131 as the sensitizer and P3HT as the hole transporting material to yield an energy conversion efficiency ( η ) of 1.82%. A J sc of 3.979 mA cm −2 is obtained for mesoporous NF‐based devices, which is 3‐fold higher than that (0.973 mA cm −2 ) for regular NF‐based devices fabricated under the same condition ( η = 0.42%). Incident photon‐to‐current conversion efficiency (IPCE) and dye‐desorption test demonstrate that the increase in J sc is mainly due to greatly improved dye adsorption for mesoporous NFs as compared to that for regular NFs. In addition, intensity modulated photocurrent spectroscopy (IMPS) and intensity modulated photovoltage spectroscopy (IMVS) measurements indicate that the mesopores on NF surface have very minor effects on charge transport and collection. Initial aging test proves good stability of the fabricated devices, which indicates the promise of mesoporous NFs as photoelectrode for low‐cost SDSCs.
Nitrogen‐Doped Nanoporous Graphenic Carbon: An Efficient Conducting Support for O2 Cathode (2016)

Abstract Herein, we synthesize a nanoporous N‐doped graphenic carbon with high surface area and a higher graphenization/graphitic degree by further developing the metallothermic reduction of gaseous CO 2 by adding N 2 into the gas flow. The N‐doped nanoporous carbon is composed of both a highly porous graphenic and non‐graphitic matrix and homogeneously dispersed ordered graphitic nanodomains, which constitute a very unique composite carbon structure. The resulting N‐doped graphenic carbon exhibits much more favorable reactivity as a carbon conducting support in the O 2 cathode of Li‐O 2 batteries, increasing the specific capacity of the GC electrode from 5300 to 9600 mAh g −1 . The N‐doped carbon also exhibits lower overpotentials during initial cycling for the charging process as well as an enhanced cycling performance compared to the undoped carbon. These results demonstrate that N‐doping has a strong correlation with the enhanced performance of O 2 cathode of Li‐O 2 batteries.
A Novel Process for Etching Modulated Profiles (2009)

A novel process for spot repair of damaged anodized aluminum panels is described. The process is based on etching the aluminum oxide layer using special fixtures that provide controlled, gradual transitions of the etched profile, enabling the fabrication of "borderline"-free repaired regions. The process does not require the application of etching masks. The profile of the etched region is solely controlled by the geometry of the specially developed etching fixture. Excellent agreement has been noted between experimental results and transport controlled models that predict the etching profile.
The Effect of Thermal Aging on the Thermal Conductivity of Plasma Sprayed and EB-PVD Thermal Barrier Coatings (1996)

Thermal barrier coatings (TBCs) applied to the hot gas components of turbine engines lead to enhanced fuel efficiency and component reliability. Understanding the mechanisms which control the thermal transport behavior of the TBCs is of primary importance. Electron beam-physical vapor deposition (EB-PVD) and air plasma spraying (APS) are the two most commonly used coating techniques. These techniques produce coatings with unique microstructures which control their performance and stability. The density of the APS coatings was controlled by varying the spray parameters. The low density APS yttria-partially stabilized zirconia (yttria-PSZ) coatings yielded a thermal conductivity that is lower than both the high density APS coatings and the EB-PVD coatings. The thermal aging of both fully and partially stabilized zirconia are compared. The thermal conductivity of the coatings permanently increases upon exposure to high temperatures. These increases are attributed to microstructural changes within the coatings. This increase in thermal conductivity can be modeled using a relationship which depends on both the temperature and time of exposure. Although the EB-PVD coatings are less susceptible to thermal aging effects, results suggest that they typically have a higher thermal conductivity than APS coatings before thermal aging. The increases in thermal conductivity due to thermal aging for plasma sprayed partially stabilized zirconia have been found to be less than for plasma sprayed fully stabilized zirconia coatings.
Architektur des Ablaufkontrollsystems ActMan (1993)

Das Ablaufkontrollsystem ActMan realisiert den Kontroll- und Datenfluß in geregelten arbeitsteiligen Anwendungssystemen. In diesem Kapitel wird die Architektur des Ablaufkontrollsystems in ihren einzelnen Teilkomponenten beschrieben, während im anschließenden Kapitel ausgewählte Implementierungsaspekte bei der Realisierung von ActMan aufgezeigt werden. Zunächst wird die Stellung des Ablaufkontrollsystems im Verhältnis zu den zu integrierenden Anwendungssystemen erläutert (Abschnitt 7.1). Anhand der dabei eingeführten Zusatzebene lassen sich die systemtechnischen Anforderungen an das Ablaufkontrollsystem konkretisieren und grundsätzliche Entwurfsentscheidungen aufzeigen. Auf der Basis der getroffenen Entwurfsentscheidungen wird anschließend die softwaretechnische Rahmenarchitektur des Ablaufkontrollsystems ActMan eingeführt (Abschnitt 7.2). Die Rahmenarchitektur schafft einen Überblick über die zu realisierenden Softwarekomponenten und somit über den restlichen Teil des vorliegenden Kapitels.
All-Optical Low-Power 2R Regeneration of 10-Gb/s NRZ Signals Using a III-V on SOI Microdisk Laser (2013)

We demonstrate an all-optical low-power 2R regenerator of 10-Gb/s non-return-to-zero data based on a 10- μm-diameter electrically pumped microdisk laser, which is heterogeneously integrated onto the silicon-on-insulator platform and processed in a CMOS pilot line. The scheme results in BER improvement 8and works for submilliwatt-level input signals. The laser operates in the continuous-wave regime, and it is single mode at room temperature and consumes 6 mW of electrical power. Its regeneration capability is investigated in simulations and experimentally demonstrated.
Glossary extraction and utilization in the information search and delivery system for IBM Technical Support (2004)

In this paper we describe the practical aspects of extracting and using a glossary for a selected technical domain. We first describe the existing glossary extraction process, as applied to general corpora, and examine its shortcomings in the technical support domain. Then we propose a number of enhancements to it, including focusing the glossary on a selected domain context, providing support for multidomain glossaries, and importing domain-specific dictionaries. We apply our focused-glossary approach to the IBM Technical Support corpus and incorporate resulting glossaries within the information search and delivery system used by IBM Technical Support. We demonstrate the effectiveness of our approach by evaluating the quality of keywords and terms extracted from sample documents with the help of these glossaries.
Recent Insights on the Medicinal Chemistry of Sickle Cell Disease (2011)

Sickle Cell Disease (SCD) is one of the most prevalent hematological diseases in the world. SCD is a genetic disease characterized by punctual mutation that basis on the exchange of glutamic acid to valine in a beta chain of hemoglobin. In deoxygenated state, the interaction among the beta chains leads to hemoglobin polymerization carrying out to deformation of cytoskeleton structure of red blood cells to a sickle shape. Currently, the treatment is performed with the antineoplasic drug hydroxyurea. This review summarizes current knowledge about possible targets and the approaches to discover new compounds to treat the SCD symptoms. Drug design based on therapeutical application and molecular modifications strategies will be discussed.
Supplementary Figure 1 from The Chemokine Receptor CXCR7 Is Highly Expressed in Human Glioma Cells and Mediates Antiapoptotic Effects (2023)

Supplementary Figure 1 from The Chemokine Receptor CXCR7 Is Highly Expressed in Human Glioma Cells and Mediates Antiapoptotic Effects
Microcalorimetric Determination of Thermodynamic Parameters for Ionophore−Siderophore Host−Guest Complex Formation (2000)

Thermodynamic parameters (delta H, delta S, and delta G) were determined by microcalorimetry in wet chloroform for host-guest assembly formation involving second-sphere complexation of the siderophore ferrioxamine B by crown ether (18-crown-6, cis-dicyclohexano-18-crown-6, benzo-18-crown-6) and cryptand (2.2.2 cryptand) hosts. Similar data were also collected for the same hosts with the pentylammonium ion guest, which corresponds to the pendant pentylamine side chain of ferroxamine B. Host-guest assembly formation constants (Ka) obtained from microcalorimetry agree with values obtained indirectly from chloroform/water extraction studies in those cases where comparable data are available. On the basis of a trend established by the pentylammonium guest, an enhanced stability relative to the crown ethers is observed for the assembly composed of ferrioxamine B and 2.2.2 cryptand that is due to entropic effects. Trends in delta H and delta S with changes in host and guest structure are discussed and attributed directly to host-guest complex formation, as solvation effects were determined to be insignificant (delta Cp = 0).
Cu2O-Based Electrochemical Biosensor for Non-Invasive and Portable Glucose Detection (2022)

Electrochemical voltammetric sensors are some of the most promising types of sensors for monitoring various physiological analytes due to their implementation as non-invasive and portable devices. Advantages in reduced analysis time, cost-effectiveness, selective sensing, and simple techniques with low-powered circuits distinguish voltammetric sensors from other methods. In this work, we developed a Cu<sub>2</sub>O-based non-enzymatic portable glucose sensor on a graphene paste printed on cellulose cloth. The electron transfer of Cu<sub>2</sub>O in a NaOH alkaline medium and sweat equivalent solution at very low potential (+0.35 V) enable its implementation as a low-powered portable glucose sensor. The redox mechanism of the electrodes with the analyte solution was confirmed through cyclic voltammetry, differential pulse voltammetry, and electrochemical impedance spectroscopy studies. The developed biocompatible, disposable, and reproducible sensors showed sensing performance in the range of 0.1 to 1 mM glucose, with a sensitivity of 1082.5 ± 4.7% µA mM<sup>-1</sup> cm<sup>-2</sup> on Cu<sub>2</sub>O coated glassy carbon electrode and 182.9 ± 8.83% µA mM<sup>-1</sup> cm<sup>-2</sup> on Cu<sub>2</sub>O coated graphene printed electrodes, making them a strong candidate for future portable, non-invasive glucose monitoring devices on biodegradable substrates. For portable applications we demonstrated the sensor on artificial sweat in 0.1 M NaOH solution, indicating the Cu<sub>2</sub>O nanocluster is selective to glucose from 0.0 to +0.6 V even in the presence of common interference such as urea and NaCl.
A radio system with multi-element antennas (2002)

A radio hardware concept for indoor WLAN applications is described in which both the transmitter and the receiver use multi-element antennas. The system exploits the increased capacity of the multiple-input multiple-output (MIMO) indoor radio channel and it is designed especially for high data rates. A technique to measure the MIMO channel matrix is described. A weak pseudo-noise sequence out of a set of Gold codes is added to each transmitted signal from which the amplitude and phase of the carrier corresponding to that antenna is identified at each receive antenna. The data signals are reconstructed at the receiver in a weighted-signal combining network where IQ modulators steer the complex weights. Fully transparent transmission at high data rates is possible in this way.
ChemInform Abstract: Alkali Metal Reduction Potentials Measured in Chloroaluminate Ambient‐ Temperature Molten Salts. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: HLA and Cancer: 12th International Histocompatibility Workshop Study (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Structure-based stabilization of SOSIP Env enhances recombinant ectodomain durability and yield (2022)

ABSTRACT The envelope glycoprotein (Env) is the main focus of HIV-1 vaccine development due to its critical role in viral entry. Despite advances in protein engineering, many Env proteins remain recalcitrant to recombinant expression due to their inherent metastability, making biochemical and immunological experiments impractical or impossible. Here we report a novel proline-stabilization strategy to facilitate the production of prefusion Env trimers. This approach, termed “2P”, works synergistically with previously described SOSIP mutations and dramatically increases the yield of recombinantly expressed Env ectodomains without altering the antigenic or conformational properties of native Env. We determined that the 2P mutations function by enhancing the durability of the prefusion conformation and that this stabilization strategy is broadly applicable to evolutionarily and antigenically diverse Envs. These findings provide a new Env stabilization platform to facilitate biochemical research and expand the number of Env variants that can be developed as future HIV-1 vaccine candidates.
Center Approach to Accelerate Technology Commercialization (2016)

Introduction The Center for Electrochemical Engineering Research at Ohio University (CEER) is dedicated to electrochemical research and development, innovation, education, and economic growth [1]. The Center focuses on providing out of the box solutions to the problems encountered by chemical and electrochemical industries. The mission of the Center is to: (1) Develop solutions to global problems (sustainable food, energy, water, air) through an electrochemical approach; (2) Educate future generations of experts in electrochemistry and electrochemical technologies; (3) Be a resource to industry and government on policy issues where electrochemical technologies can provide solutions; (4) Disseminate scientific knowledge on electrochemistry and electrochemical technologies; and (5) Contribute to economic growth. CEER has implemented a novel approach to accelerate technology commercialization from the University. The approach involves technology marketing and commercialization in parallel with its development through a combination of state programs and Industry/University partnerships. Through this approach, challenges in market acceptance get identified early during the technology development roadmap. In this talk, the approach will be discussed under the context of the development of the electrolysis of coal for the production of high value products. References [1] Ohio University Center for Electrochemical Engineering Research, https://www.ohio.edu/engineering/ceer/index.cfm, (accessed 04/18/2016).
Cutting Edge: NANOG Activates Autophagy under Hypoxic Stress by Binding to BNIP3L Promoter (2017)

Hypoxia upregulates the core pluripotency factors NANOG, SOX2, and OCT4, associated with tumor aggressiveness and resistance to conventional anticancer treatments. We have previously reported that hypoxia-induced NANOG contributed in vitro to tumor cell resistance to autologous-specific CTL and in vivo to the in situ recruitment of immune-suppressive cells. In this study, we investigated the mechanisms underlying NANOG-mediated tumor cell resistance to specific lysis under hypoxia. We demonstrated the tumor-promoting effect of hypoxia on tumor initiation into immunodeficient mice using human non-small lung carcinoma cells. We next showed a link between NANOG and autophagy activation under hypoxia because inhibition of NANOG decreased autophagy in tumor cells. Chromatin immunoprecipitation and luciferase reporter assays revealed a direct binding of NANOG to a transcriptionally active site in a BNIP3L enhancer sequence. These data establish a new link between the pluripotency factor NANOG and autophagy involved in resistance to CTL under hypoxia.
Magnetic resonance imaging of the jugular foramen. (1985)

The jugular foramen in normal volunteers was studied with 1.5 T magnetic resonance (MR) systems in 3-mm-thick head- and surface-coil images. Anatomic sections through cadaver heads were correlated with the MR images to identify the jugular bulb and the course of cranial nerves IX-XI. Sagittal images were more useful than coronal or axial to show the course of these nerves through the skull base. MR demonstrates the anatomic relations of the jugular foramen (except its osseous margins) such that its primary use in evaluating this region can be anticipated.
Endoplasmic reticulum quality control of asialoglycoprotein receptor H2a involves a determinant for retention and not retrieval (1997)

The human asialoglycoprotein receptor H2a subunit contains a charged pentapeptide, EGHRG, in its ectodomain that is the only sequence absent from the H2b alternatively spliced variant. H2b exits the endoplasmic reticulum (ER) even when singly expressed, whereas H2a gives rise to a cleaved soluble secreted ectodomain fragment; uncleaved membrane-bound H2a molecules are completely retained and degraded in the ER. We have inserted the H2a pentapeptide into the sequence of the H1 subunit (H1i5), which caused complete ER retention but, unexpectedly, no degradation. This suggests that the pentapeptide is a determinant for ER retention not colocalizing in H2a with the determinant for degradation. The state of sugar chain processing and the ER localization of H1i5, which was unchanged at 15 degrees C or after treatment with nocodazole, indicate ER retention and not retrieval from the cis-Golgi or the intermediate compartment. H1i5 folded similarly to H1, and both associated to calnexin. However, whereas H1 dissociated with a half time of 45 min, H1i5 remained bound to the chaperone for prolonged periods. The correct global folding of H2a and H1i5 and of other normal precursors and unassembled proteins and the true ER retention, and not exit and retrieval, suggest a difference in their quality control mechanism compared with that of misfolded proteins, which does involve retrieval. However, both pathways may involve calnexin.
Rethinking Class-Discrimination Based CNN Channel Pruning (2020)

Channel pruning has received ever-increasing focus on network compression. In particular, class-discrimination based channel pruning has made major headway, as it fits seamlessly with the classification objective of CNNs and provides good explainability. Prior works singly propose and evaluate their discriminant functions, while further study on the effectiveness of the adopted metrics is absent. To this end, we initiate the first study on the effectiveness of a broad range of discriminant functions on channel pruning. Conventional single-variate binary-class statistics like Student's T-Test are also included in our study via an intuitive generalization. The winning metric of our study has a greater ability to select informative channels over other state-of-the-art methods, which is substantiated by our qualitative and quantitative analysis. Moreover, we develop a FLOP-normalized sensitivity analysis scheme to automate the structural pruning procedure. On CIFAR-10, CIFAR-100, and ILSVRC-2012 datasets, our pruned models achieve higher accuracy with less inference cost compared to state-of-the-art results. For example, on ILSVRC-2012, our 44.3% FLOPs-pruned ResNet-50 has only a 0.3% top-1 accuracy drop, which significantly outperforms the state of the art.
Asset Modeling using Serverless Computing (2021)

Assets in the domain of Internet of Things (IoT) generate time-series data such as sensor readings and alerts. In addition, the assets have associated static data such as the make, model and other manufacturing information. The sensors in the asset components may have implicit relationships with each other, which are not interpretable without domain knowledge. Many problems exist which involve computation of relationships between sensors or subsystems in the asset components. Typically, the number of sensors in a real world asset may range anywhere from tens to thousands of sensors - and in this case, finding relationships between them becomes a highly computationally intensive task. In this paper, we study one such problem of anomaly detection in industrial data based on the functioning of the sensors and their interrelationships in both normal and abnormal conditions. We further demonstrate the issue of run-time and performance complexity in this problem, and present a speed-up strategy using Serverless Computing for parallelization, and demonstrate the usefulness of this method by comparing the speed-up achieved.