gebhart/patrepeval huggingface dataset:
Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster (2017)

Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in <i>Drosophila melanogaster</i>, expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. <i>Cis</i>-element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in <i>Drosophila melanogaster</i> undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the <i>RpII215</i><sup><i>C4</i></sup> mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for <i>Drosophila melanogaster</i> and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate.
Coding Algorithms in JPEG2000 (2004)

In this chapter, we have dealt with the fractional bit plane coding (EBCOT) and the MQ-coder for implementation of the adaptive binary arithmetic coding scheme proposed in JPEG2000 standard. We have described the terminologies and their underlying concepts behind these algorithms. The EBCOT has three passes and four coding operations. We have discussed in great detail the concepts behind these coding operations and how they are used in each coding pass in order to encode the bit-planes of the DWT coefficients. We have taken an example and have shown how to generate the context and data information by the EBCOT algorithm. This context and data pair is then used by the MQ-coder to generate compressed code words. We have described the flowcharts for all the modules in both the EBCOT and the MQ-coder algorithms and their implementation issues. We have discussed the Tier-2 encoding scheme using the tag tree coding mechanism. We have discussed the basic definitions for the tag tree with an example and have shown how the two dimensional integer arrays can be mapped into a tag tree. This tag tree encoding is basis for the encoding the code-block and layer information in the compressed file header. We have compressed a small component of size 80 x 60 and generated the code-block information and have displayed the results as an example. We have also shown the different progression orders achievable by the JPEG2000 standard in order to influence different areas applications. In summary, we have detailed the entropy encoding (Tier-1 and Tier-2 encoding) in this chapter.
Nanocolumnar Germanium Thin Films as a High-Rate Sodium-Ion Battery Anode Material (2013)

Both nanocolumnar and dense germanium thin films, synthesized by evaporative deposition, were tested as a potential anode material for sodium-ion batteries. The reversible capacity of the nanocolumnar films was found to be 430 mAh/g, which is higher than the theoretical capacity of 369 mAh/g. The nanocolumnar films retained 88% of their initial capacity after 100 cycles at C/5, whereas the dense films began to deteriorate after ∼15 cycles. Additionally, the nanocolumnar films were stable at charge/discharge rates up to 27C (10 A/g). The diffusion coefficient for sodium in germanium was estimated, from impedance analysis of the dense films, to be ∼10–13 cm2 s–1. Modeling of diffusion in the sodium- germanium system predicts that sodium diffusion in the near-surface layers of the material is significantly faster than in the bulk. These results show that small feature sizes are critical for rapid, reversible electrochemical sodiation of germanium.
A Hybird Optimization Approach for 2D-3D Registrationbased Fusion of Ultrasound and X-Ray (2013)

For transcatheter-based minimally invasive procedures in structural heart disease ultrasound and Xray are the two main imaging modalities. A live fusion of both real-time modalities could benefit the clinical workflow by combining the excellent instrument imaging of Xray with soft tissue imaging of ultrasound. A recent approach to fuse X-ray fluoroscopy with trans-esophageal echo (TEE) registers the ultrasound probe to X-ray images by a 2D-3D registration. We enhance the capture range of the current registration by first applying an evolutionary multi-resolution optimization before improving the accuracy with a local optimization. The capture range was increased up to 40 mm (single X-ray image per registration). Our final registration error is in the range of 4.3 mm (3D error) and 2.7 mm (projected error).
ChemInform Abstract: 5‐HT2 Antagonists: A Concept for the Treatment of Schizophrenia (1997)

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.
Behavioral and neural decomposition of skull-induced death awareness (2020)

Abstract Death awareness influences multiple aspects of human lives, but its psychological constructs and underlying brain mechanisms remain unclear. We address these by measuring behavioral and brain responses to images of human skulls. We show that skulls relative to control stimuli delay responses to life-related words but speed responses to death-related words. Skulls compared to the control stimuli induce early deactivations in the posterior ventral temporal cortex followed by activations in the posterior and anterior ventral temporal cortices. The early and late neural modulations by perceived skulls respectively predict skull-induced changes of behavioral responses to life- and death-related words and the early neural modulation further predicts death anxiety. Our findings decompose skull-induced death awareness into two-stage neural processes of a lifeless state of a former life. One sentence summary Behavioral and brain imaging findings decompose skull-induced death awareness into two-stage neural processes of a lifeless state of a former life.
Energy-efficient channel alignment of DWDM silicon photonic transceivers (2018)

The comb laser-driven microring-based dense wavelength division multiplexing silicon photonics is a promising candidate for next-generation optical interconnects. However, existing solutions for exploring the power-performance trade-off of such systems have been restricted to a limited design space, resulting from the unnecessary constraints of using an identical spacing for laser comb lines and microring channels, and of utilizing consecutive laser comb lines for data transmission. We propose an energy-efficient channel alignment scheme that aligns the microring channels to a subset of laser comb lines that are non-uniformly distributed in the free spectrum range of the microrings. Based on a well-established process variation model, our simulations show that the proposed scheme significantly reduces the microring tuning power in the presence of denser comb lines. The power saved from microring tuning can improve the overall system energy efficiency despite some power wasted in unused laser comb lines. We further conducted a case study for design space exploration using the proposed channel alignment scheme, seeking the most energy-efficient configuration in order to achieve a target aggregated data rate.
Differential Solute Gas Response in Ionic-Liquid-Based QCM Arrays: Elucidating Design Factors Responsible for Discriminative Explosive Gas Sensing (2011)

An eight-sensor array coupling a chemoselective room-temperature ionic liquid (RTIL) with quartz crystal microbalance (QCM) transduction is presented in this work in order to demonstrate the power of this approach in differentiating closely related analytes in sensory devices. The underlying mechanism behind the specific sensory response was explored by (i) studying mass loading and viscoelasticity effects of the sensing layers, predominantly through variation in damping impedance, the combination of which determines the sensitivity; (ii) creation of a solvation model based on Abraham's solvation descriptors which reveals the fact that polarizability and lipophilicity are the main factors influencing the dissolution of gas analytes into the RTILs; and (iii) determination of enthalpy and entropy values for the studied interactions and comparison via a simulation model, which is also effective for pattern discrimination, in order to establish a foundation for the analytical scientist as well as inspiration for synthetic pathways and innovative research into next-generation sensory approaches. The reported sensors displayed an excellent sensitivity with detection limit of <0.2%, fast response and recovery, and a workable temperature range of 27-55 °C and even higher. Linear discriminant analysis (LDA) showed a discrimination accuracy of 86-92% for nitromethane and 1-ethyl-2-nitrobenzene, 71% for different mixtures of nitromethane, and 100% for these analytes when thermodynamic parameters were used as input data. We envisage applications to detecting other nitroaromatics and security-related gas targets, and high-temperature or real-time situations where manual access is restricted, opening up new horizons in chemical sensing.
The Influence of an Electrolyte on Impedance Characteristics in n ‐ GaP Electrodes (1985)

Impedance of electrodes was measured by using a microcomputer‐aided measuring system. Mott‐Schottky plots were quite dispersive. Large frequency dispersion was ascribed to the interface state which was assumed to be formed as a result of corrosion. Charging and discharging of the interface states by ions in the electrolyte were determined by charge transfer at the electrode‐electrolyte interface and diffusion in the electrolyte, which could be characterized by charge‐transfer resistance and diffusion impedance . became predominant at low ionic concentration. It is pointed out that the influence of an electrolyte must be taken into consideration in interpreting the impedance data of some kinds of semiconductor electrodes.
Weyl points and line nodes in 3D photonic crystals (2013)

We present theoretical discoveries of frequency-isolated Weyl points and line nodes, 3D linear point- and line-degeneracies, in gyroid photonic crystals. The associated surface states exhibit topological-protection and flat bands realizable from microwave to optical frequencies.
Stack based module generator for analog MOS circuits (2002)

This paper describes a novel method for analog circuit partitioning and MOS transistor stacking. The method is based on a new algorithm dealing with analog specific constraints and on a set of heuristics for stack generation using a pattern database and transistor size trimming. Experimental results show the effectiveness of the method that is described.
High Power Density Silicon Combustion Systems for Micro Gas Turbine Engines (2003)

As part of an effort to develop a microscale gas turbine engine for power generation and micropropulsion applications, this paper presents the design, fabrication, experimental testing, and modeling of the combustion system. Two radial inflow combustor designs were examined; a single-zone arrangement and a primary and dilution-zone configuration. Both combustors were micromachined from silicon using deep reactive ion etching (DRIE) and aligned fusion wafer bonding. Hydrogen-air and hydrocarbon-air combustion were stabilized in both devices, each with chamber volumes of 191mm3. Exit gas temperatures as high as 1800 K and power densities in excess of 1100MW/m3 were achieved. For the same equivalence ratio and overall efficiency, the dual-zone combustor reached power densities nearly double that of the single-zone design. Because diagnostics in microscale devices are often highly intrusive, numerical simulations were used to gain insight into the fluid and combustion physics. Unlike large-scale combustors, the performance of the microcombustors was found to be more severely limited by heat transfer and chemical kinetics constraints. Important design trades are identified and recommendations for microcombustor design are presented.
ChemInform Abstract: A Novel Fluorescent Monomer for the Selective Detection of Phenols and Anilines. (1999)

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.
Projected Dose Optimization of Amino- and Hydroxypyrrolidine Purine PI3Kδ Immunomodulators (2021)

The approvals of idelalisib and duvelisib have validated PI3Kδ inhibitors for the treatment for hematological malignancies driven by the PI3K/AKT pathway. Our program led to the identification of structurally distinct heterocycloalkyl purine inhibitors with excellent isoform and kinome selectivity; however, they had high projected human doses. Improved ligand contacts gave potency enhancements, while replacement of metabolic liabilities led to extended half-lives in preclinical species, affording PI3Kδ inhibitors with low once-daily predicted human doses. Treatment of C57BL/6-Foxp3-GDL reporter mice with 30 and 100 mg/kg/day of <b>3c</b> (MSD-496486311) led to a 70% reduction in Foxp3-expressing regulatory T cells as observed through bioluminescence imaging with luciferin, consistent with the role of PI3K/AKT signaling in Treg cell proliferation. As a model for allergic rhinitis and asthma, treatment of ovalbumin-challenged Brown Norway rats with 0.3 to 30 mg/kg/day of <b>3c</b> gave a dose-dependent reduction in pulmonary bronchoalveolar lavage inflammation eosinophil cell count.
Single-Degree-of-Freedom Rigidly Foldable Origami Flashers (2015)

We present the design for a family of deployable structures based on the origami flasher that are rigidly foldable, i.e., foldable with revolute joints at the hinges and planar rigid faces, and that exhibit a single degree of freedom in their motion. These structures may be used to realize highly compact deployable mechanisms.
Figure S5 from Distinguishing Tumor from Associated Fibrosis to Increase Diagnostic Biopsy Yield with Polarization-Sensitive Optical Coherence Tomography (2023)

Figure S5 from Distinguishing Tumor from Associated Fibrosis to Increase Diagnostic Biopsy Yield with Polarization-Sensitive Optical Coherence Tomography
Neural Network Models for Usage Based Remaining Life Computation (2006)

In engine structural life computations, it is common practice to assign a life of certain number of start-stop cycles based on a standard flight or mission. This is done during design through detailed calculations of stresses and temperatures for a standard flight, and the use of material property and failure models. The limitation of the design phase stress and temperature calculations is that they cannot take into account actual operating temperatures and stresses. This limitation results in either very conservative life estimates and subsequent wastage of good components, or in catastrophic damage because of highly aggressive operational conditions which were not accounted for in design. In order to improve significantly the accuracy of the life prediction, the component temperatures and stresses need to be computed for actual operating conditions. However, thermal and stress models are very detailed and complex, and it could take on the order of a few hours to complete a stress and temperature simulation of critical components for a flight. The objective of this work is to develop dynamic neural network models, that would enable us to compute the stresses and temperatures at critical locations, in orders of magnitude less computation time than required by more detailed thermal and stress models. This work expands on the work done previously [1] where a linear system identification approach was developed. The current paper describes the development of a neural network model and the temperature results achieved in comparison with the original models for Honeywell turbine and compressor components. Given certain inputs such as engine speed and gas temperatures for the flight, the models compute the component critical location temperatures for the same flight in a very small fraction of time it would take the original thermal model to compute.
Subthalamic nucleus stimulation in patients with a prior pallidotomy (2002)

Physicians who perform STN surgery in patients with prior pallidotomy should be aware of the electrophysiological differences between the STN that had undergone pallidotomy and the one that had not, to avoid prolonging recording time to search for the typical STN. The implications of these findings for the current models of information processing in the basal ganglia are discussed.
ChemInform Abstract: Positional Flexibility: Syntheses and Characterization of Six Uranium Chalcogenides Related to the 2H Hexagonal Perovskite Family. (2015)

Abstract Ba 4 USe 6 (I), Ba 3 FeUSe 6 (II), Ba 3 MnUSe 6 (III), Ba 3 MnUS 6 (IV), Ba 3.3 Rb 0.7 US 6 (V), and Ba 3.2 K 0.8 US 6 (VI) are prepared by solid state reaction of stoichiometric amounts of the elements and CsCl, RbCl, and KCl acting as a flux (C‐coated evacuated silica tubes, 1173 K, 4 d; cooling to 673 K at a rate of 2.5 K/h).
Human Omental Microvascular Endothelial and Mesothelial Cells: Characterization of Two Distinct Mesodermally Derived Epithelial Cells (1997)

Human omental microvascular endothelial (HOME) and mesothelial (MESO) cells share many phenotypic properties, but can be characterized from one another based upon a comprehensive panel of endothelial and mesothelial markers. Traditional cell markers such as von-Willebrand factor, DiI-Ac-LDL, and Ulex europaeus I lectin are not sufficient to distinguish between HOME and MESO cells. Furthermore, immunoreactivity to a panel of endothelial cell-specific monoclonal antibodies, including representatives from the known clusters of differentiation (CD), indicate that some of these antigens are coexpressed in HOME and MESO cells. In distinguishing between the two cell types, HOME and not MESO cells express E-selectin, E/P-selectin, P-selectin (CD62), Le-y, and VLA-6 (CDw49f*). Moreover, HOME cells and not MESO cells form tube-like structures when cultured on Matrigel. MESO cells differ from HOME cells based upon (1) the expression of cytokeratins; (2) their rapid proliferation in response to platelet-derived growth factor; and (3) a change from an epitheliod to fibroblast-like morphology in response to tumor necrosis factor and epidermal growth factor. Both HOME and MESO cells express tissue plasminogen activator and plasminogen activator inhibitor, but urokinase activity is only expressed by MESO cells. As there is no one universal endothelial or mesothelial cell marker that can specifically confirm the identity of these cells, it appears necessary to employ a comprehensive panel of cell markers to rule out the possibility of misidentifying a cell culture.
Diastereoselective Addition of Allylzinc Bromide to Imines Derived from (R)-Phenylglycine Amide (2001)

The highly diastereoselective addition of allylzinc bromide to imines derived from (R)-phenylglycine amide is reported. Homoallylamines with high enantiomeric purity are obtained from the adducts in three steps on removal of the chiral auxiliary by means of a nonreductive protocol. Removal of the auxiliary by hydrogenation leads to the saturated amines, also in high enantiomeric purity.
Integration of opinion mining service flow with anonymous information (2012)

Nowadays, we are exposed to lots of digital data. You cannot imagine how many data is creating even now in the world. However, we cannot know and find which and where is the data really what we needed. Moreover, we cannot trust whether someone is telling the truth or not on the web. So, our study is giving you the service flow how to choose data wisely. And, in our study, we include anonymous information for increasing data correction.
Comparative study of optical and scintillation properties of Ce:YAGG, Ce:GAGG and Ce:LuAGG transparent ceramics (2016)

We investigated photoluminescence (PL) and scintillation properties of 0.8 mol % Ce-doped (Y, Gd, Lu)3Al2Ga3O12 (Ce:YAGG, Ce:GAGG and Ce:LuAGG) transparent ceramics, which were fabricated by the vacuum sintering method. The obtained samples showed a strong and broad PL emission in the wavelength range from 470 to 600 nm owing to 5d–4f transitions of Ce3+. The PL and scintillation decay curves consisted of two or three exponential components, and the primary components ranged around 35–43 ns. Besides, the scintillation spectra excited by X-rays showed similar features with those in PL. In the X-ray induced afterglow measurements, the Ce:LuAGG sample exhibited the weakest afterglow intensity. The pulse height spectra of these samples showed clear photoabsorption peaks. Among those samples, Ce:LuAGG sample showed the highest scintillation light yield of 18,700 ph/MeV.
Structure of RagB, a major immunodominant outer‐membrane surface receptor antigen of Porphyromonas gingivalis (2015)

Porphyromonas gingivalis is the main causative agent of periodontitis. It deregulates the inflammatory and innate host immune responses through virulence factors, which include the immunodominant outer-membrane surface receptor antigens A (PgRagA) and B (PgRagB), co-transcribed from the rag pathogenicity island. The former is predicted to be a Ton-dependent porin-type translocator but the targets of this translocation and the molecular function of PgRagB are unknown. Phenomenologically, PgRagB has been linked with epithelial cell invasion and virulence according to murine models. It also acts as a Toll-like receptor agonist and promotes multiple mediators of inflammation. Hence, PgRagB is a candidate for the development of a periodontitis vaccine, which would be facilitated by the knowledge of its atomic structure. Here, we crystallized and solved the structure of 54-kDa PgRagB, which revealed a single domain centered on a curved helical scaffold. It consists of four tetratrico peptide repeats (TPR1-4), each arranged as two helices connected by a linker, plus two extra downstream capping helices. The concave surface bears four large intertwined irregular inserts (A-D), which contribute to an overall compact moiety. Overall, PgRagB shows substantial structural similarity with Bacteroides thetaiotaomicron SusD and Tannerella forsythia NanU, which are, respectively, engaged in binding and uptake of malto-oligosaccharide/starch and sialic acid. This suggests a similar sugar-binding function for PgRagB for uptake by the cognate PgRagA translocator, and, consistently, three potential monosaccharide-binding sites were tentatively assigned on the molecular surface.
Reply to B. Meunier’s Letter to the Editor Re: Brewer G. J.; Nutrients 2015, 7, 10053–10064 (2016)

In a letter to the editor, Meunier [1] apparently attempts to discredit the copper-2 hypothesis for causation of the Alzheimer's disease (AD) epidemic in developed countries proposed by myself in a review in this journal [2].[...].