gebhart/patrepeval huggingface dataset:
Enabling High-Throughput Discovery of the RNA Transcription Landscape Using a Directional RNA Workflow and a Combinatorial Multiplexing Approach (2014)

Massively parallel next generation cDNA sequencing (RNA-Seq), has allowed many advances in the characterization and quantification of transcriptomes. In addition to enabling the detection of non-canonical transcription start sites and termination sites, alternative splice isoforms, transcript mutations and edits can be identified. Additionally, the ability to obtain information on the originating strand is useful for many reasons including for example: identification of antisense transcripts, determination of the transcribed strand of noncoding RNAs, and determination of expression levels of coding or noncoding overlapping transcripts. Overall, the ability to determine the originating strand can substantially enhance the value of a RNA-seq experiment. However, standard methods for sequencing RNA do not provide information on the DNA strand from which the RNA strand was transcribed, and methods for strand-specific library preparation can be inefficient and time-consuming. Our objective was to address this challenge by developing a streamlined, low input method for Directional RNA-Sequencing that highly retains strand orientation information while maintaining even coverage of transcript expression. This method is based on second strand labeling and excision after adaptor ligation; allowing differential tagging of the first strand cDNA ends. We have also extended the utility of this method by developing additional adaptor and primer reagents, including a dual barcoding approach that allows for multiplexing up to 96 samples. As a result, we have enabled highly multiplexed, strand-specific mRNA sequencing, as well as whole transcriptome sequencing (Total RNA-seq) from ribosomal-depleted samples, enabling the discovery of a much broader picture of expression dynamics including discovery of antisense transcripts. This work presents a streamlined, fast solution for complete RNA sequencing, with high quality data that illustrates the complexity and diversity of the RNA transcription landscape.
Changes of Enzymes Involved in Prostaglandin Metabolism and Prostaglandin Binding Proteins in Rat Brain During Development and Aging (1985)

In the developing rat brain, the enzymatic formation of prostaglandin D2 from prostaglandin H2 increased 60-fold from day 12 of gestation to birth. The activity still rose gradually to the highest level (90 nmol/min/g wet tissue) at day 7 after birth. The activities of prostaglandin E2 and F2 alpha synthetases in rat brain were highest at gestational age 19 days (30 nmol/min/g wet tissue), respectively. The specific activity of NADP-dependent 15-hydroxy-prostaglandin D2 dehydrogenase in rat brain was highest at the earliest gestational age we examined (day 12 of gestation). The specific bindings of prostaglandin D2 and E2 to the crude mitochondrial fraction of rat brain were observed from day 16 of gestation and increased to day 7 after birth. Although the activities of the enzymes responsible for prostaglandin metabolism were unchanged postmaturationally, the maximal concentrations of the binding sites on the synaptic membrane for both prostaglandins D2 and E2 decreased with constant affinity to less than one-sixth with age from 1 week to 24 months after birth. These results indicate that prostaglandins may play important roles during maturation and aging in rat brain.
Li-air batteries having ether-based electrolytes (2023)

A lithium-air battery includes a cathode including a porous active carbon material, a separator, an anode including lithium, and an electrolyte including a lithium salt and polyalkylene glycol ether, where the porous active carbon material is free of a metal-based catalyst.
Ultrafast line-broadening of the surface plasmon in Au-colloids embedded in a dielectric sol-gel matrix (1996)

The optical absorption of a bulk metal is spread over a wide spectral range. In contrast, colloids consisting of the same metal show narrow absorption resonances [1]. This spectral compression of the oscillator strength is due to enhanced optical coupling to the surface plasmon modes of spherical metal particles. E.g., the transmission spectrum of a gold-film does not show clear plasmon resonances, whereas the visible absorption spectra of gold-colloids embedded in dielectric matrices are dominated by the surface plasmon resonance lying at slightly lower energy than the onset of single-particle interband transitions.
Design probes study on user perceptions of a smart glasses concept (2015)

Until today, mobile computing has been very much confined to conventional computing form factors, i.e. laptops, tablets and smartphones, which have achieved de facto design standards in outlook and shape. However, wearable devices are emerging, and especially glasses are an appealing form factor for future devices. Currently, although companies such as Google have productized a solution, little user research and design exploration has been published on either the user preferences or the technology. We set ourselves to explore the design directions for smart glasses with user research grounded use cases and design alternatives. We describe our user research utilizing a smart glasses design probe in an experience sampling method study (n=12), and present a focus group based study (n=14) providing results on perceptions on alternative industrial designs for smart glasses.
Thermally Stable Self‐assembling Open‐Frameworks: Isostructural Cs+ and (CH3)4N+ Iron Germanium Sulfides (1996)

Abstract Here we report on investigations that have revealed for the first time that the Cs + ion templates the same metal germanium sulfide open‐framework as (CH 3 ) 4 N + (TMA + ), and that metal complexing agents enhance crystal size by at least two orders of magnitude. The synthesis, structures and thermal properties of Cs 2 FeGe 4 S 10 ·× H 2 O and TMA 2 FeGe 4 S 10 are also described. Both have 3D zinc blende‐type open‐framework structures. These materials have the same connectivity as TMA 2 MnGe 4 S 10 . The tetrahedral sites in the lattice are alternately substituted by pseudo‐tetrahedral Fe 2+ and adamantanoid Ge 4 S 10 4‐ building blocks, covalently linked together by Fe(μ‐S)Ge bridge bonds, to give a tetragonal unit cell. The charge‐balance of the anionic framework [Fe‐Ge 4 S 10 ] 2‐ is maintained by either Cs + or TMA + ions in the cavity spaces. Synthesis of these materials demonstrates an interesting example of a self‐assembly process in which a 3D framework is built from molecular precursors. Water adsorption‐desorption cycling from room temperature to 200 °C reveals framework flexibility between larger and smaller tetragonal unit cell 14 isotypes. The compound TMA 2 FeGe 4 S 10 is stable in nitrogen at 350 °C and under vacuum at 450 °C. The corresponding temperatures for Cs 2 FeGe 4 S 10 are 530 °C and 630°C; it is stable on cooling to room temperature under vacuum, and after subsequent exposure to air. Six hundred thirty degrees celsius is the highest recorded temperature at which the integrity of a non‐oxide framework has been maintained. The framework stability and flexibility of “all‐inorganic” Cs 2 FeGe 4 S 10 provides an encouraging example for researchers interested in developing sulfide‐based framework materials with practical applications.
Plenary lecture 2: &#x201C;Nanoscale field-effect transistors for flexible displays&#x201D; (2009)

Nanoscale field-effect transistors are of interest not only for ultra-scale integrated circuits, but also for next-generation active-matrix flat-panel displays. High-resolution flat-panel displays are typically composed of several million individual picture elements (pixels), and in active-matrix displays each pixel contains one or more field-effect transistors that precisely control the pixel brightness during the frame time. For large-area displays on glass substrates, the transistors must be manufactured without the use of high process temperatures, so hydrogenated amorphous silicon or laser-crystallized polycrystalline silicon are often utilized as the semiconductor. If the trend towards increased display resolution, higher frame rates, and greater color fidelity is to continue, field-effect transistors with improved high-frequency performance that can be manufactured on glass substrates will be required. In addition, for the realization of flexible and rollable active-matrix displays, the transistor manufacturing process must be compatible with heat-sensitive polymeric substrates. Finally, the true potential of active-matrix displays will be realized by integrating low-voltage, high-efficiency organic light-emitting diodes with low-voltage, high-frequency nanoscale field-effect transistors on flexible, transparent polymeric substrates.
Oxygen-Exchange Properties of MoO3: An in situ Raman Spectroscopy Study (1994)

In situ Raman spectroscopy was used to investigate the oxygen-exchange properties of MoO3 and the role of bulk defects during redox processes. A change of the absorption coefficients between MoO3 and molybdenum suboxides as evidenced by a change in color from pale yellow to gray blue may contribute to a general decrease in Raman intensities. An alteration of the Raman scattering tenser of MoO3-x, is indicated by additional Raman bands and by changes in signal intensity ratios compared to stoichiometric MoO3. This different scattering tenser may also contribute to the lower Raman efficiency of Mo suboxides. Furthermore, besides temperature-induced broadening and signal shifts, Raman spectra of MoO3 seem to be sensitive to the crystallite size due to sintering and crystal growth. Calcination in O-18(2) after evacuation at 393 K (sufficient to remove physically adsorbed H2O and CO2 from the surface) does not result in any detectable spectral changes due to O-18 exchange. On the other hand, after evacuation at 648 K leading to a higher degree of reduction, calcination in O-18(2) gives rise to bands due to an O-18 incorporation into MoO3. Therefore, the intensity ratio of the O-18-related bands relative to those of the O-18-free stoichiometric oxide may correlate with the initial bulk defect concentration in oxygen-deficient MoO3. The long time required for the O-16 reexchange of MoO3 when fully reoxidized in O-18(2), constitutes a proof of the essential role played by defects in the anion vacancy conductor MoO3 during the exchange process. H2O present in the gas phase has no detectable influence on the O-16 reexchange in MoO3.
An Organometallic Protein Kinase Inhibitor Pharmacologically Activates p53 and Induces Apoptosis in Human Melanoma Cells (2007)

Unlike other tumors, melanomas harbor wild-type (WT) p53 but exhibit impaired p53-dependent apoptosis. The mechanisms for the impaired p53 activation are poorly understood but may be linked to the high expression of the p53 suppressor Mdm2, which is found in >50% of melanoma lesions. Here, we describe an organometallic glycogen synthase kinase 3beta (GSK3beta) inhibitor (DW1/2) as a potent activator of p53 and inducer of cell death in otherwise highly chemoresistant melanoma cells. Using RNA interference and pharmacologic approaches, we show that p53 is required for the cytotoxic effects of this organometallic inhibitor. The DW1/2 compound was barely able to induce cell death in melanoma cells with p53 mutations, further confirming the requirement for p53-WT in the cytotoxic effects of the GSK3beta inhibition. Mechanistic analysis of the p53-dependent cell death indicated an apoptotic mechanism involving depolarization of mitochondrial membrane potential, caspase cleavage, and elevated NOXA expression. The effect of p53 was not simply due to passive up-regulation of protein expression as adenoviral-mediated overexpression of p53 was not able to induce cell death. Treatment of melanoma cells with DW1/2 was instead found to decrease levels of Mdm2 and Mdm4. The importance of Mdm2 down-regulation in DW1/2-induced apoptosis was confirmed by treating the p53-WT cells with the p53/Mdm2 antagonist Nutlin-3. Taken together, our data provide a new strategy for the pharmacologic activation of p53 in melanoma, which may be a viable approach for overcoming apoptotic resistance in melanoma and offer new hope for rational melanoma therapy.
Successful Treatment of Patients with von Willebrand Disease using a High-Purity Double-Virus Inactivated Factor VIII/von Willebrand Factor Concentrate (Immunate®) (2002)

Fourteen patients with different types of von Willebrand disease (vWD) having acute bleeds or elective surgery were treated with Immunate(sound recording copyright sign), a double-virus inactivated factor VIII/von Willebrand factor (FVIII/vWF) concentrate. The concentrate was applied as a bolus or via continuous infusion. FVIII activity (FVIIIc), vWF antigen (vWF:Ag), ristocetin cofactor activity (vWF:RCo), collagen binding activity (vWF:CB), activated partial thromboplastin time (aPTT), and von Willebrand multimers (vW-multimers) were monitored for 48 hours. Pharmacokinetic analyses were performed. The clinical efficacy was rated excellent or good. Bleeding complications occurred in 3 patients due to an additional FXIII deficiency in one patient, to a surgically induced bleed in another patient, and a rather short substitution period in the third patient. There were no serious adverse experiences. One patient showed a phlebitic reaction at the site of venous access after more than 100 hours of continuous infusion, requiring a change to application via bolus.
The efficacy of fluticasone furoate administered in the morning or evening is comparable in patients with persistent asthma (2016)

AM and PM doses of once-daily FF 100 μg produced comparable improvements in lung function relative to placebo.
A Dual-Polarization Silicon-Photonic Coherent Transmitter Supporting 552 Gb/s/wavelength (2020)

Coherent optical links improve spectral efficiency over their intensity-modulation direct-detect (IM-DD) counterparts using advanced modulation schemes such as quadrature phase shift keying (QPSK) and quadrature amplitude modulation (QAM), and by utilizing dual polarization (DP) of light. This increase in spectral efficiency also leads to stringent requirements for the link components. The transmitter (TX) must simultaneously achieve high bandwidth (BW), linearity, output swing, and reliability. In this article, we present a silicon-photonic Mach-Zehnder modulator-based optical TX on an Silicon-on-Insulator (SOI) process, and linear, high-swing SiGe drivers on 130-nm BiCMOS process. The output stage of the driver uses a voltage breakdown enhancement technique to ensure the reliability of the TX. A resistor-based capacitor splitting technique is introduced, and aided by other methods such as zero-peaking and degeneration, the targeted gain, BW, swing, and linearity for the driver are realized. The driver achieves a differential swing of 6 V peak-to-peak, a total harmonic distortion (THD) of 3.6%, and more than 40 GHz of electrical BW. Co-designed and co-packaged with the silicon-photonic modulators, the TX achieves 272 Gb/s/wavelength with DP-16 QAM at 6-V peak-to-peak driver swing and exceeds 0.5 Tb/s/wavelength data rates with DP-16 QAM at 2.4-V peak-to-peak driver swing. The low-cost, compact, and all-Si/SiGe design matches the required optical SNR performance of LiNbO3 modulators with III-V drivers at 34 Gbaud.
Genetic aberrations of c-myc and CCND1 in the development of invasive bladder cancer (2002)

Detrusor muscle invasive transitional cell carcinoma is associated with poor prognosis and is responsible for the majority of bladder cancer related deaths. Amplifications of c-myc and CCND1 are associated with detrusor-muscle-invasive transitional cell carcinoma, however, their precise role in driving disease progression is unclear. Fluorescence in situ hybridisation on archival tissue from 16 patients with primary diagnosis of > or = pT2 transitional cell carcinoma and 15 cases with primary pTa/pT1 disease subsequently progressing to detrusor-muscle-invasion was performed, in the latter group both pre and post muscle invasive events were studied. No patients presenting with >/=pT2 had amplification of c-myc, two out of 16 (12.5%) had CCND1 amplification. Of patients who developed > or = pT2, two out of 15 (13.3%) had amplification of c-myc, both in > or = pT2, five out of 15 (33.3%) had CCND1 amplification, two in pTa/pT1 tumours, three in > or = pT2 transitional cell carcinomas. In total, two out of 31 (6.5%) of patients' > or = pT2 TCCs were amplified for c-myc and six out of 31 (19%) were amplified for CCND1. Eighty-seven per cent (40 out of 46) of tumours were polysomic for chromosome 8 and 80% (37 out of 46) were polysomic for chromosome 11 and this reflected the high copy numbers of c-myc and CCND1 observed. In almost all cases an increase in c-myc/CCND1 copy number occurred prior to invasion and persisted in advanced disease. Amplification of CCND1 or alterations in c-myc/CCND1 early in bladder cancer may have clinical relevance in promoting and predicting progression to detrusor-muscle-invasive transitional cell carcinoma.
Novel antibody probes for the characterization of endosialin/TEM-1 (2016)

Endosialin (Tumor Endothelial Marker-1 (TEM-1), CD248) is primarily expressed on pericytes of tumor-associated microvasculature, tumor-associated stromal cells and directly on tumors of mesenchymal origin, including sarcoma and melanoma. While the function of endosialin/TEM-1 is incompletely understood, studies have suggested a role in supporting tumor growth and invasion thus making it an attractive therapeutic target. In an effort to further understand its role in cancer, we previously developed a humanized anti-endosialin/TEM-1 monoclonal antibody (mAb), called ontuxizumab (MORAb-004) for testing in preclinical and clinical studies. We herein report on the generation of an extensive panel of recombinant endosialin/TEM-1 protein extracellular domain (ECD) fragments and novel mAbs against ECD motifs. The domain-specific epitopes were mapped against ECD sub-domains to identify those that can detect distinct structural motifs and can be potentially formatted as probes suitable for diagnostic and functional studies. A number of mAbS were shown to cross-react with the murine and human protein, potentially allowing their use in human animal models and corresponding clinical trials. In addition, pairing of several mAbs supported their use in immunoassays that can detect soluble endosialin/TEM-1 (sEND) in the serum of healthy subjects and cancer patients.
HART, a heterogeneous architecture for real-time image processing (1992)

Today, real-time image processing hardware primarily takes the form of a high speed front end accelerator, targetted toward iconic and intermediate level algorithmic tasks. Examples of contemporary commercial systems are: Datacube, Maxtor and, Data Translation (for PC); Microsystem Mainboard, and Analogic (for VME). These are supported by a range of software environments, such as Visilog or Semper, which permit pre-defined library routines to be executed in a user friendly environment. In some cases, the hardware supports complex operations ranging from morphological operators to stereo vision algorithms. Whilst addressing a required market niche and pushing image processing into real applications, these products are inherently limited by the host machine's processing power and the interconnection topology adopted within the hardware itself. The authors describe a new architecture which is designed to address these problems and evolve to match the requirements of dynamic scene analysis and understanding.
Gene expression profiling of whole blood in ipilimumab-treated patients for identification of potential biomarkers of immune-related gastrointestinal adverse events (2013)

Gene expression profiling of peripheral blood, sampled before or early in the course of treatment with ipilimumab, resulted in the identification of a set of potential biomarkers that were associated with occurrence of GI irAEs. However, because of the low sensitivity of these biomarkers, they cannot be used alone to predict which patients will develop GI irAEs. Further investigation of these biomarkers in a larger patient cohort is warranted.
Effect of second pass in 2-sided FSW of high-strength structural steel (2014)

Peer reviewed
Noise-Resilient DNN: Tolerating Noise in PCM-Based AI Accelerators via Noise-Aware Training (2021)

Phase change memory (PCM)-based “Analog-AI” accelerators are gaining importance for inference in edge applications due to the energy efficiency offered by in-memory computing. Nevertheless, noise sources inherent to PCM devices cause inaccuracies in the deep neural network (DNN) weight values. Such inaccuracies can lead to severe degradation in model accuracy. To address this, we propose two techniques to improve noise resiliency of DNNs: 1) drift regularization (DR) and 2) multiplicative noise training (MNT). We evaluate convolutional networks trained on image classification and recurrent neural networks trained on language modeling and show that our techniques improve model accuracy by up to 12% over one month.
Directed Regio- and Stereoselective Nickel-Catalyzed Addition of Alkyl Grignard Reagents to Allylic Ethers (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirected Regio- and Stereoselective Nickel-Catalyzed Addition of Alkyl Grignard Reagents to Allylic EthersMary T. Didiuk, James P. Morken, and Amir H. HoveydaCite this: J. Am. Chem. Soc. 1995, 117, 27, 7273–7274Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/ja00132a039https://doi.org/10.1021/ja00132a039research-articleACS PublicationsRequest reuse permissionsArticle Views985Altmetric-Citations71LEARN 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 InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Optimization of naringenin and p ‐coumaric acid hydroxylation using the native E. coli hydroxylase complex, HpaBC (2015)

Flavonoids are a growing class of bioactive natural products with distinct and interesting bioactivity both in vitro and in vivo. The extraction of flavonoids from plant sources is limited by their low natural abundance and commonly results in a mixture of products that are difficult to separate. However, due to recent advances, the microbial production of plant natural products has developed as a promising alternative for flavonoid production. Through optimization of media, induction temperature, induction point, and substrate delay time, we demonstrate the highest conversion of naringenin to eriodictyol (62.7 ± 2.7 mg/L) to date, using the native E. coli hydroxylase complex, HpaBC. We also show the first evidence of in vivo HpaBC activity towards the monohydroxylated flavan-3-ol afzelechin with catechin product titers of 34.7 ± 1.5 mg/L. This work confirms the wide applicability of HpaBC towards realizing efficient de novo production of various orthohydroxylated flavonoids and flavonoid derived products in E. coli.