gebhart/patrepeval huggingface dataset:
Dysregulated miRNA biogenesis downstream of cellular stress and ALS-causing mutations: a new mechanism for ALS (2020)

Abstract Interest in RNA dysfunction in amyotrophic lateral sclerosis (ALS) recently aroused upon discovering causative mutations in RNA‐binding protein genes. Here, we show that extensive down‐regulation of miRNA levels is a common molecular denominator for multiple forms of human ALS. We further demonstrate that pathogenic ALS‐causing mutations are sufficient to inhibit miRNA biogenesis at the Dicing step. Abnormalities of the stress response are involved in the pathogenesis of neurodegeneration, including ALS. Accordingly, we describe a novel mechanism for modulating microRNA biogenesis under stress, involving stress granule formation and re‐organization of DICER and AGO2 protein interactions with their partners. In line with this observation, enhancing DICER activity by a small molecule, enoxacin, is beneficial for neuromuscular function in two independent ALS mouse models. Characterizing miRNA biogenesis downstream of the stress response ties seemingly disparate pathways in neurodegeneration and further suggests that DICER and miRNAs affect neuronal integrity and are possible therapeutic targets.
Passive Targeting of Solid Tumors: Pathophysiological Principles and Physicochemical Aspects of Delivery Systems (2006)

The chaotic blood flow in tumor vasculature and the heterogeneous vascular permeability of tumor blood vessels are among the key barriers controlling passive delivery of macromolecular and particulate delivery systems into the interstitium of solid tumors. Already compromised by abnormal hydrostatic pressure gradients, compressive mechanical forces generated by tumor cell proliferation cause intratumoral vessels to compress and collapse, thus creating further barriers for passive targeting. Liposomes are perhaps the best studied vehicles in cancer drug delivery, capable of either increasing the drug concentration in solid tumors and/or limiting drug exposure to critical target sites such as bone marrow and myocardium. Long-circulating liposomes have the capability to deliver between 3 and 10 times more drug to solid tumors compared with the administered drug in its free form. Nanoparticles assembled from synthetic polymers have also received much attention in cancer drug delivery. Polymer-based drug delivery systems favorably alter the pharmacokinetics and biodistribution of conjugated drugs and accumulate in tumor interstitium following extravasation.
Topology Optimization Using a Hybrid Cellular Automaton Method With Local Control Rules (2006)

The hybrid cellular automaton (HCA) algorithm is a methodology developed to simulate the process of structural adaptation in bones. This methodology incorporates a distributed control loop within a structure in which ideally localized sensor cells activate local processes of the formation and resorption of material. With a proper control strategy, this process drives the overall structure to an optimal configuration. The controllers developed in this investigation include two-position, proportional, integral and derivative strategies. The HCA algorithm combines elements of the cellular automaton (CA) paradigm with finite element analysis (FEA). This methodology has proved to be computationally efficient to solve topology optimization problems. The resulting optimal structures are free of numerical instabilities such as the checkerboarding effect. This investigation presents the main features of the HCA algorithm and the influence of different parameters applied during the iterative optimization process.
Multimedia Transcoding in Mobile and Wireless Networks (2009)

"This book is designed to provide readers with relevant theoretical frameworks and latest technical and institutional solutions for transcoding multimedia in mobile and wireless networks" - Provided by publisher
Serious liver damage caused by butylphthalide soft capsule (2018)

A 78-year-old female patient with acute cerebral infarction received butylphtha-lide soft capsules 0.2 mg thrice daily. One week later, she experienced fatigue and anorexia. Two weeks later, she presented with yellowish skin and sclera. Laboratory tests revealed the following levels: aminotransferase (ALT) 1 574 U/L, aspartate aminotransferase (AST) 1 135 U/L, direct bilirubin (DBil) 58.8 μmol/L, indirect bilirubin (IBil) 62.0 μmol/L. Liver damage was diagnosed and considered to be related to butylphthalide soft capsules, and then the medication was discontinued. The patient was given IV infusions of reduced glutathione 1.8 mg, Shuganning injection (舒肝宁注射液)10 ml, polyene phosphorylcholine 232.5 mg and magnesium isoglycyrrhizinate 150 mg once daily. On day 4 after symptomatic treatment, she had an ALT level of 840 U/L, an AST level of 640 U/L, a DBil level of 50.1 μmol/L, an IBil level of 57.1 μmol/L. On day 17, the yellowish skin and sclera significantly improved, the diet returned to normal and physical strength recovered, the results of reexaminination showed ALT 64 U/L, AST 41 U/L, DBil 13.9 μmol/L, IBil 18.6 μmol/L.


Key words: 
Drug-induced liver injury; Butylphthalide soft capsules
Mechanism of HIV-1 Neutralization by Antibodies Targeting a Membrane-Proximal Region of gp41 (2013)

Induction of broadly neutralizing antibodies (bNAbs) is an important goal for HIV-1 vaccine development. Two autoreactive bNAbs, 2F5 and 4E10, recognize a conserved region on the HIV-1 envelope glycoprotein gp41 adjacent to the viral membrane known as the membrane-proximal external region (MPER). They block viral infection by targeting a fusion-intermediate conformation of gp41, assisted by an additional interaction with the viral membrane. Another MPER-specific antibody, 10E8, has recently been reported to neutralize HIV-1 with potency and breadth much greater than those of 2F5 or 4E10, but it appeared not to bind phospholipids and might target the untriggered envelope spikes, raising the hope that the MPER could be harnessed for vaccine design without major immunological concerns. Here, we show by three independent approaches that 10E8 indeed binds lipid bilayers through two hydrophobic residues in its CDR H3 (third heavy-chain complementarity-determining region). Its weak affinity for membranes in general and preference for cholesterol-rich membranes may account for its great neutralization potency, as it is less likely than other MPER-specific antibodies to bind cellular membranes nonspecifically. 10E8 binds with high affinity to a construct mimicking the fusion intermediate of gp41 but fails to recognize the envelope trimers representing the untriggered conformation. Moreover, we can improve the potency of 4E10 without affecting its binding to gp41 by a modification of its lipid-interacting CDR H3. These results reveal a general mechanism of HIV-1 neutralization by MPER-specific antibodies that involves interactions with viral lipids.
Fowl Cholera: Comparison of Serologic and Immunogenic Responses of Chickens and Turkeys (1965)

ens and ducks. I. Principles and technique of the test. J. Inf. Dis. 87: 13-23 (1950). 6. Kinjo, T., and R. A. Bankowski. Variations of complement fixation antigens prepared from the ornithosis agent and Herellealike bacteria with immune serums. Avian Diseases, In press, 1965. 7. Page, L. A., and R. A. Bankowski. Factors affecting the production and detection of ornithosis antibodies in infected turkeys. Am. J. Vet. Res. 21:971-978 (1960). 8. Rice, C. E. Atypical behaviour of certain avian antisera in complement fixation tests. Can. J. Comp. Med., 11:236-245 (1947). 9. Shimizu, Y., and R. A. Bankowski. The nature of serological reactions with the complement fixation test for ornithosis in avian serums. Proc. U.S. Livestock Sanitary Association, 542-551 (1961). 10. Shimizu, Y., and R. A. Bankowski. The nature of the cross reactions between a bacterium of the genus Herellea and the ornithosis virus in complement fixation. Am. J. Vet. Res. 24:1283-1290 (1963). 11. Shimizu, Y., and R. A. Bankowski. The characteristics of a bacterium used in complement fixation tests for orni,thosis. Avian Diseases 7:331-341 (1963). 12. Wolfe, M., L. Kornfeld, and F. S. Markham. Simplified indirect complement-fixation test applied to Newcastle disease immune avian serum. Proc. Soc. Exptl. Biol. Med. 70:490-494 (1949).
A method of improving the resolution and accuracy of rotary encoders using a code compensation technique (1992)

A method of improving the resolution and accuracy of incremental type rotary encoders using a phase encoding and code compensation system is described. Applying this system to an optical incremental encoder whose scale pitch is 1/3600 rotation, results in a resolution of up to 1/920000 rotation, and better than +or-1/300000 rotation (+or-0.0012 degrees ) precision is obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Novel InP-based phased-array wavelength demultiplexer using a generalized MMI-MZI configuration (1995)

A novel type of wavelength demultiplexer is presented based on a generalized multimode interference/Mach Zehnder interferometer (MMI-MZI) configuration. This device combines the potential of low loss and high uniformity of the output channels with a small device size. Feasibility of the novel concept is demonstrated experimentally for a 4-channel demultiplexer with 4 nm channel spacing. Dimensions are 2800*106 mu m, which is the smallest device size reported so far
Fractionation of Oligonucleotides of Yeast Soluble Ribonucleic Acids by Countercurrent Distribution<sup>*</sup> (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFractionation of Oligonucleotides of Yeast Soluble Ribonucleic Acids by Countercurrent Distribution*B. P. Doctor and G. J. McCormickCite this: Biochemistry 1965, 4, 1, 49–54Publication Date (Print):January 1, 1965Publication History Published online1 May 2002Published inissue 1 January 1965https://pubs.acs.org/doi/10.1021/bi00877a009https://doi.org/10.1021/bi00877a009research-articleACS PublicationsRequest reuse permissionsArticle Views23Altmetric-Citations4LEARN 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-Alertsclose Get e-Alerts
Ubiquitous Autofragmentation of Fluorescent Proteins Creates Abundant Defective Ribosomal Products (DRiPs) for Immunosurveillance (2015)

Green fluorescent protein (GFP) and other fluorescent proteins are essential tools for biological research. When fused to peptides or proteins as a reporter, GFP enables localization and quantitation of gene products in otherwise unmanipulated live cells or organisms. We previously reported that a sizable fraction of nascent GFP is post-translationally converted into a 20-kDa Triton X-100-insoluble proteasome substrate (Qian, S. B., Princiotta, M. F., Bennink, J. R., and Yewdell, J. W. (2006) J. Biol. Chem. 281, 392-400; Dolan, B. P., Li, L., Veltri, C. A., Ireland, C. M., Bennink, J. R., and Yewdell, J. W. (2011) J. Immunol. 186, 2065-2072). Here, we show that a similarly sized fragment is generated by all GFP and red fluorescent protein family members we examined. We demonstrate that fragmentation is a by-product of GFP chromophore rearrangement. A non-rearranging GFP mutant fails to fragment and generates diminished levels of K(b)-SIINFEKL complexes when SIINFEKL is genetically fused to either the C- or N-terminal domains of GFP fusion proteins. Instructively, another fragmenting GFP mutant that cannot create the functional chromophore but still generates fragments also demonstrates diminished K(b)-SIINFEKL generation. However, the mutant and wild-type fragments differ fundamentally in that wild-type fragments are rapidly liberated from the intact molecule and degraded quickly, accounting for increased K(b)-SIINFEKL generation. In the fragmenting mutant, the fragments are generated slowly and remain associated, likely in a native conformation based on their original structural description (Barondeau, D. P., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D. (2006) J. Am. Chem. Soc. 128, 4685-4693). The wild-type GFP fragments represent the first biochemically defined natural defective ribosomal products to contribute peptides for immunosurveillance, enabling quantitation of peptide generation efficiency from this source of defective ribosomal products. More broadly, given the wide use of fluorescent proteins, their ubiquitous and abundant fragmentation must be considered when interpreting experiments using these extremely useful probes.
A combined Reed-Solomon encoder and syndrome generator with small hardware complexity (2003)

In most applications of a Reed-Solomon codec (coder/decoder) data are either being transmitted or being received where either the encoder or the decoder is active, while the other is idle. The idea presented is to show how the encoder can be transformed such that its implementation can make use of existing decoder circuitry, requiring only little additional hardware dedicated to the encoder. In CMOS design examples which were studied the encoder hardware savings amounted to more than 90%. The architecture can easily be programmed for different error correction powers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Engineered Distant Homolog of Pseudomonas syringae TTSS Effector From Physcomitrella patens Can Act as a Bacterial Virulence Factor (2018)

<i>Pseudomonas syringae</i> pv. <i>phaseolicola</i> is the causative agent of halo blight in common bean (<i>Phaseolus vulgaris</i>). Similar to other pathogenic gram-negative bacteria, it secrets a set of type III effectors into host cells to subvert defense mechanisms. HopQ1 (for Hrp outer protein Q) is one of these type III effectors contributing to virulence of bacteria. Upon delivery into a plant cell, HopQ1 undergoes phosphorylation, binds host 14-3-3 proteins and suppresses defense-related signaling. Some plants however, evolved systems to recognize HopQ1 and respond to its presence and thus to prevent infection. HopQ1 shows homology to Nucleoside Hydrolases (NHs), but it contains a modified calcium binding motif not found in the canonical enzymes. CLuster ANalysis of Sequences (CLANS) revealed that HopQ1 and alike proteins make a distinct group of putative NHs located distantly from the classical enzymes. The HopQ1 - like protein (HLP) group comprises sequences from plant pathogenic bacteria, fungi, and lower plants. Our data suggest that the evolution of HopQ1 homologs in bacteria, fungi, and algae was independent. The location of moss HopQ1 homologs inside the fungal clade indicates a possibility of horizontal gene transfer (HGT) between those taxa. We identified a HLP in the moss <i>Physcomitrella patens</i>. Our experiments show that this protein (referred to as PpHLP) extended by a TTSS signal of HopQ1 promoted <i>P. syringae</i> growth in bean and was recognized by <i>Nicotiana benthamiana</i> immune system. Thus, despite the low sequence similarity to HopQ1 the engineered PpHLP acted as a bacterial virulence factor and displayed similar to HopQ1 virulence properties.
Synthesis and Biological Evaluation of Paclitaxel Analogs (2001)

The complex natural product paclitaxel (Taxol®), first isolated from Taxus brevifolia, is a member of a large family of taxane diterpenoids. Paclitaxel is extensively used for the treatment of solid tumors, particularly those of the breasts and ovaries. In order to obtain additional information about the mechanism of action of paclitaxel and the environment of the paclitaxel-binding site, several fluorescent analogs of paclitaxel were synthesized, and their biological activities have been evaluated. For the investigation of possible synergistic effects, concurrent modifications on selected positions have been performed and their biological evaluation were studied.
Generating Visible Spectrum Images from Thermal Infrared (2018)

Transformation of thermal infrared (TIR) images into visual, i.e. perceptually realistic color (RGB) images, is a challenging problem. TIR cameras have the ability to see in scenarios where vision is severely impaired, for example in total darkness or fog, and they are commonly used, e.g., for surveillance and automotive applications. However, interpretation of TIR images is difficult, especially for untrained operators. Enhancing the TIR image display by transforming it into a plausible, visual, perceptually realistic RGB image presumably facilitates interpretation. Existing grayscale to RGB, so called, colorization methods cannot be applied to TIR images directly since those methods only estimate the chrominance and not the luminance. In the absence of conventional colorization methods, we propose two fully automatic TIR to visual color image transformation methods, a two-step and an integrated approach, based on Convolutional Neural Networks. The methods require neither pre- nor postprocessing, do not require any user input, and are robust to image pair misalignments. We show that the methods do indeed produce perceptually realistic results on publicly available data, which is assessed both qualitatively and quantitatively.
Identifying Entity Properties from Text with Zero-shot Learning (2019)

We propose a method for identifying a set of entity properties from text. Identifying entity properties is similar to a relation extraction task that can be cast as a classification of sentences. Normally, this task can be achieved by distant supervised learning by automatically preparing training sentences for each property; however, it is impractical to prepare training sentences for every property. Therefore, we describe a zero-shot learning problem for this task and propose a neural network-based model that does not rely on a complete training set comprising training sentences for every property. To achieve this, we utilize embeddings of properties obtained from a knowledge graph embedding using different components of a knowledge graph structure. The embeddings of properties are combined with the model to enable identification of properties with no available training sentences. By using our newly constructed dataset as well as an existing dataset, experiments revealed that our model achieved a better performance for properties with no training sentences, relative to baseline results, even comparable to that achieved for properties with training sentences.
Comparison of ultra-widefield fluorescein angiography with the Heidelberg Spectralis&reg; noncontact ultra-widefield module versus the Optos&reg; Optomap&reg; (2013)

Purpose: To compare ultra-widefield fluorescein angiography imaging using the Optos ® Optomap ® and the Heidelberg Spectralis ® noncontact ultra-widefield module. Methods: Five patients (ten eyes) underwent ultra-widefield fluorescein angiography using the Optos ® panoramic P200Tx imaging system and the noncontact ultra-widefield module in the Heidelberg Spectralis ® HRA+OCT system. The images were obtained as a single, nonsteered shot centered on the macula. The area of imaged retina was outlined and quantified using Adobe ® Photoshop ® C5 software. The total area and area within each of four visualized quadrants was calculated and compared between the two imaging modalities. Three masked reviewers also evaluated each quadrant per eye (40 total quadrants) to determine which modality imaged the retinal vasculature most peripherally. Results: Optos ® imaging captured a total retinal area averaging 151,362 pixels, ranging from 116,998 to 205,833 pixels, while the area captured using the Heidelberg Spectralis ® was 101,786 pixels, ranging from 73,424 to 116,319 ( P = 0.0002). The average area per individual quadrant imaged by Optos ® versus the Heidelberg Spectralis ® superiorly was 32,373 vs 32,789 pixels, respectively ( P = 0.91), inferiorly was 24,665 vs 26,117 pixels, respectively ( P = 0.71), temporally was 47,948 vs 20,645 pixels, respectively ( P = 0.0001), and nasally was 46,374 vs 22,234 pixels, respectively ( P = 0.0001). The Heidelberg Spectralis ® was able to image the superior and inferior retinal vasculature to a more distal point than was the Optos ® , in nine of ten eyes (18 of 20 quadrants). The Optos ® was able to image the nasal and temporal retinal vasculature to a more distal point than was the Heidelberg Spectralis ® , in ten of ten eyes (20 of 20 quadrants). Conclusion: The ultra-widefield fluorescein angiography obtained with the Optos ® and Heidelberg Spectralis ® ultra-widefield imaging systems are both excellent modalities that provide views of the peripheral retina. On a single nonsteered image, the Optos ® Optomap ® covered a significantly larger total retinal surface area, with greater image variability, than did the Heidelberg Spectralis ® ultra-widefield module. The Optos ® captured an appreciably wider view of the retina temporally and nasally, albeit with peripheral distortion, while the ultra-widefield Heidelberg Spectralis ® module was able to image the superior and inferior retinal vasculature more peripherally. The clinical significance of these findings as well as the area imaged on steered montaged images remains to be determined. Keywords: peripheral, retina, wide-angle, widefield, ultra-widefield
Isolation of the gene and hypothalamic cDNA for the common precursor of gonadotropin-releasing hormone and prolactin release-inhibiting factor in human and rat. (1986)

Cloned cDNAs encoding the precursor protein for gonadotropin-releasing hormone (Gn-RH) and prolactin release-inhibiting factor (PIF) were isolated from libraries derived from human and rat hypothalamic mRNA. Nucleotide sequence analyses predict precursor proteins of 92 amino acids for both species and show identity between the human placental and human hypothalamic precursor proteins. Whereas the Gn-RH peptide structure is completely conserved in human and rat, the PIF domain of the precursor displays 70% interspecies homology. Genomic analyses revealed the presence of a single Gn-RH-PIF gene in human and rat containing sequences corresponding to the cDNA distributed across four exons.
An Efficient Resource Allocation for TCP Services in IEEE 802.16 Wireless MANs (2007)

In IEEE 802.16 Wireless MANs supporting OFDMA- PHY, random access with CDMA-based mechanism is proposed to request bandwidth for uplink data. Collision, which increases the Round Trip Time (RTT), is not avoided due to random access during requesting bandwidth among subscriber stations (SSs). In this paper, we propose an efficient resource allocation for Transmission Control Protocol (TCP) services with resolving RTT increasing problem caused by the wireless access of the best effort service and enhancing network performance in IEEE 802.16 Wireless MANs supporting OFDMA-PHY. The proposed resource allocation estimates the uplink traffic of SS based on the downlink traffic to the SS and allocates the resource to the SS, which transmits uplink traffic with the allocated resource. Our simulation results show that the proposed scheme provides better performance.