gebhart/patrepeval huggingface dataset:
Re: The Androgen Receptor Regulates a Druggable Translational Regulon in Advanced Prostate Cancer (2019)

No AccessJournal of UrologyUrological Survey1 Mar 2020Re: The Androgen Receptor Regulates a Druggable Translational Regulon in Advanced Prostate Cancer Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000679.01AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: The Androgen Receptor Regulates a Druggable Translational Regulon in Advanced Prostate Cancer." The Journal of Urology, 203(3), p. 466 Suggested Reading : Androgen receptor targeted treatments of prostate cancer: 35 years of progress with antiandrogens. J Urol 2018; 200: 956. Link, Google Scholar : Blood based detection of androgen receptor splice variants in patients with advanced prostate cancer. J Urol 2016; 196: 1606. Link, Google Scholar © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue 3March 2020Page: 466-466 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement Loading ...
Massive MIMO Beam Management in Sub-6 GHz 5G NR (2022)

Beam codebooks are a new feature of massive multiple-input multiple-output (M-MIMO) in 5G new radio (NR). Codebooks comprised of beamforming vectors are used to transmit reference signals and obtain limited channel state information (CSI) from receivers via the codeword index. This enables large arrays that cannot otherwise obtain sufficient CSI. The performance, however, is limited by the codebook design. In this paper, we show that machine learning can be used to train site-specific codebooks for initial access. We design a neural network based on an autoencoder architecture that uses a beamspace observation in combination with RF environment characteristics to improve the synchronization signal (SS) burst codebook. We test our algorithm using a flexible dataset of channels generated from QuaDRiGa. The results show that our model outperforms the industry standard (DFT beams) and approaches the optimal performance (perfect CSI and singular value decomposition (SVD)-based beamforming), using only a few bits of feedback.
Low-Voltage Electrostatic Actuation With Inherent Position Feedback (2012)

Electrostatic actuation in microelectromechanical systems (MEMS) often requires generation and control of high-voltage drive signals for sufficient force. Voltages in excess of a few volts require specialized circuit technologies and often cannot be implemented monolithically with other functions, such as precision sense amplifiers. This paper presents a circuit for enabling high-voltage actuation with low-voltage electronics by utilizing passive amplification provided by the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> factor of an electrical <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RLC</i> resonator. The resonator is formed with the capacitive MEMS actuator connected in series to an inductor. Experimental results demonstrating voltage amplification by over an order of magnitude are presented. As a further benefit, the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RLC</i> circuit provides continuous position feedback in the form of position-dependent resonance frequency which is detected electronically. Inverse position dependence of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> factor also extends stable range of parallel-plate actuators over that achieved with constant-voltage drive.
Solid waste digestors: process performance and practice for municipal solid waste digestion (2001)

The most common types of anaerobic digesters for solid wastes have been compared based on biological and technical performance and reliability. Batch systems have the most simple designs and are the least expensive solid waste digesters. They have high potential for application in developing countries. Two-stage systems are the most complex and most expensive systems. Their greatest advantage lies in the equalisation of the organic loading rate in the first stage, allowing a more constant feeding rate of the methanogenic second stage. Two-stage systems with biomass accumulation devices in the second stage display a larger resistance toward toxicants and inhibiting substances such as ammonia. However, the large majority of industrial applications use one-stage systems and these are evenly split between "dry" systems (wastes are digested as received) and "wet" systems (wastes are slurried to about 12% total solids). Regarding biological performance, this study compares the different digester systems in terms of organic loading rates and biogas yields considering differences in input waste composition. As a whole, "dry" designs have proven reliable due to their higher biomass concentration, controlled feeding and spatial niches. Moreover, from a technical viewpoint the "dry" systems are more robust and flexible than "wet' systems.
Head and neck cancer N-glycome traits are cell line and HPV status–dependent (2022)

Glycosylation is the most common post-translational modification of proteins, and glycosylation changes at cell surfaces are frequently associated with malignant epithelia including head and neck squamous cell carcinoma (HNSCC). In HNSCC, 5-year survival remains poor, averaging around 50% globally: this is partly related to late diagnosis. Specific protein glycosylation signatures on malignant keratinocytes have promise as diagnostic and prognostic biomarkers and as therapeutic targets. Nevertheless, HNSCC-specific glycome is to date largely unknown. Herein, we tested six established HNSCC cell lines to capture the qualitative and semi-quantitative N-glycome using porous graphitized carbon liquid chromatography coupled to electrospray ionisation tandem mass spectrometry. Oligomannose-type N-glycans were the predominant features in all HNSCC cell lines analysed (57.5-70%). The levels of sialylated N-glycans showed considerable cell line-dependent differences ranging from 24 to 35%. Importantly, α2-6 linked sialylated N-glycans were dominant across most HNSCC cell lines except in SCC-9 cells where similar levels of α2-6 and α2-3 sialylated N-glycans were observed. Furthermore, we found that HPV-positive cell lines contained higher levels of phosphorylated oligomannose N-glycans, which hint towards an upregulation of lysosomal pathways. Almost all fucose-type N-glycans carried core-fucose residues with just minor levels (< 4%) of Lewis-type fucosylation identified. We also observed paucimannose-type N-glycans (2-5.5%), though in low levels. Finally, we identified oligomannose N-glycans carrying core-fucose residues and confirmed their structure by tandem mass spectrometry. This first systematic mapping of the N-glycome revealed diverse and specific glycosylation features in HNSCC, paving the way for further studies aimed at assessing their possible diagnostic relevance.
Tumor-Associated Enzyme-Activatable Spherical Nucleic Acids (2022)

Maximizing the tissue-targeting efficiency of nanomaterials while also protecting them from rapid clearance from the bloodstream and limiting their immunogenicity remains a central problem in the field of systemic-administered nanomedicine. Herein, we introduce a generalizable strategy to simultaneously increase tumor accumulation, prolong blood circulation, and limit nonspecific immune activation of nanomaterials <i>via</i> peptide-based, tumor-responsive, "sheddable" coatings. Spherical nucleic acids (SNAs) were designed and synthesized to contain an exterior coating composed of zwitterionic polypeptides with recognition sequences for tumor-associated proteases. In the presence of matrix metalloproteinases (MMPs), the polypetide coating is rapidly cleaved, leading to increased cellular uptake of these SNAs, relative to SNAs containing nonsheddable shells. Moreover, the zwitterionic nature of the polypeptide shell shields the SNAs from immune system recognition, which extends their blood circulation time and improves tumor accumulation and <i>in vivo</i> cellular uptake relative to control SNAs with no protective coating. Taken together, these results indicate that this strategy is a viable method for increasing nanoparticle tumor accumulation and can have utility for the systemic delivery of oligonucleotides and nanomaterials to target cells <i>in vivo</i> with low immunogenicity.
High-Resolution Electrometer with Micromechanical Variable Capacitor (2002)

We have designed, fabricated, and operated an electrometer with a noise-equivalent resolution of 535 electrons rms (86 aC). The electrometer incorporates a silicon resonator that acts as a variable capacitor and is fabricated using a new self-assembly process that demonstrates for the first time the integration of lownoise, low-leakage JFETs with SOI structures. The resolution of the measurements made with the electrometer thus far has been limited to 9500 electrons (1.5 fC) because of a large quiescent charge on the input, generated by JFET gate current. At 1.5 fC, the MEMS electrometer charge resolution is an order of magnitude better than those quoted for the best commercial instruments. Improvements that should lead to higher resolution are proposed.
Breaking the Third Wall: Implementing 3D-Printing Techniques to Expand the Complexity and Abilities of Multi-Organ-on-a-Chip Devices (2021)

The understanding that systemic context and tissue crosstalk are essential keys for bridging the gap between in vitro models and in vivo conditions led to a growing effort in the last decade to develop advanced multi-organ-on-a-chip devices. However, many of the proposed devices have failed to implement the means to allow for conditions tailored to each organ individually, a crucial aspect in cell functionality. Here, we present two 3D-print-based fabrication methods for a generic multi-organ-on-a-chip device: One with a PDMS microfluidic core unit and one based on 3D-printed units. The device was designed for culturing different tissues in separate compartments by integrating individual pairs of inlets and outlets, thus enabling tissue-specific perfusion rates that facilitate the generation of individual tissue-adapted perfusion profiles. The device allowed tissue crosstalk using microchannel configuration and permeable membranes used as barriers between individual cell culture compartments. Computational fluid dynamics (CFD) simulation confirmed the capability to generate significant differences in shear stress between the two individual culture compartments, each with a selective shear force. In addition, we provide preliminary findings that indicate the feasibility for biological compatibility for cell culture and long-term incubation in 3D-printed wells. Finally, we offer a cost-effective, accessible protocol enabling the design and fabrication of advanced multi-organ-on-a-chip devices.
The Oxidant-Scavenging Abilities in the Oral Cavity May Be Regulated by a Collaboration among Antioxidants in Saliva, Microorganisms, Blood Cells and Polyphenols: A Chemiluminescence-Based Study (2013)

Saliva has become a central research issue in oral physiology and pathology. Over the evolution, the oral cavity has evolved the antioxidants uric acid, ascorbate reduced glutathione, plasma-derived albumin and antioxidants polyphenols from nutrients that are delivered to the oral cavity. However, blood cells extravasated from injured capillaries in gingival pathologies, or following tooth brushing and use of tooth picks, may attenuate the toxic activities of H2O2 generated by oral streptococci and by oxidants generated by activated phagocytes. Employing a highly sensitive luminol-dependent chemiluminescence, the DPPH radical and XTT assays to quantify oxidant-scavenging abilities (OSA), we show that saliva can strongly decompose both oxygen and nitrogen species. However, lipophilic antioxidant polyphenols in plants, which are poorly soluble in water and therefore not fully available as effective antioxidants, can nevertheless be solubilized either by small amounts of ethanol, whole saliva or also by salivary albumin and mucin. Plant-derived polyphenols can also act in collaboration with whole saliva, human red blood cells, platelets, and also with catalase-positive microorganisms to decompose reactive oxygen species (ROS). Furthermore, polyphenols from nutrient can avidly adhere to mucosal surfaces, are retained there for long periods and may function as a "slow-release devises" capable of affecting the redox status in the oral cavity. The OSA of saliva is due to the sum result of low molecular weight antioxidants, albumin, polyphenols from nutrients, blood elements and microbial antioxidants. Taken together, saliva and its antioxidants are considered regulators of the redox status in the oral cavity under physiological and pathological conditions.
Seeing Temporal Modulation of Lights from Standard Cameras (2018)

In this paper, we propose a novel method for measuring the temporal modulation of lights by using off-the-shelf cameras. In particular, we show that the invisible flicker patterns of various lights such as fluorescent lights can be measured by a simple combination of an off-the-shelf camera and any moving object with specular reflection. Unlike the existing methods, we do not need high speed cameras nor specially designed coded exposure cameras. Based on the extracted flicker patterns of environment lights, we also propose an efficient method for deblurring motion blurs in images. The proposed method enables us to deblur images with better frequency characteristics, which are induced by the flicker patterns of environment lights. The real image experiments show the efficiency of the proposed method.
Pyrrolnitrin, Captan + Benomyl, and High CO2 Enhance Raspberry Shelf Life at 0 or 18C (1992)

The effects of preharvest applications of pyrrolnitrin (a biologically derived fungicide) on postharvest longevity of `Bristol' black raspberry (Rubus occidentals L.) and `Heritage' red raspberry [R. idaeus L. var. strigosus (Michx.) Maxim] were evaluated at two storage temperatures. Preharvest fungicide treatments were 200 mg pyrrolnitrin/liter, a standard fungicide treatment (captan + benomyl or iprodione) or a distilled water control applied 1 day before first harvest. Black raspberries were stored at 18 or 0 ± lC in air or 20% CO 2 . Red raspberries were stored at the same temperatures in air only. Pyrrolnitrin-treated berries often had less gray mold (Botrytis cinerea Pers. ex Fr.) in storage than the control but more than berries treated with the standard fungicides. Storage in a modified atmosphere of 20% CO 2 greatly improved postharvest quality of black raspberries at both storage temperatures by reducing gray mold development. The combination of standard fungicide or pyrrolnitrin, high CO 2 , and low temperature resulted in more than 2 weeks of storage with less than 5% disease on black raspberries; however, discoloration limited marketability after≈ 8 days under these conditions. Chemical names used: 3-chloro-4-(2'-nitro-3'-chlorophenyl) -pyrrole (pyrrolnitrin); N-trichloromethylthio-4-cyclohexene-l12-dicarboximide (captan); methyl 1-(butylcarbamoyl) -2-benzimidazolecarbamate) (benomyl); 3-(3,5 -dichlorophenyl) -N-(l-methylethyl -2,4-dioxo-l-imi-dazolidinecarboxamide (Rovral, iprodione).
Minimum and Maximum Entropy Distributions for Binary Systems with Known Means and Pairwise Correlations (2017)

Maximum entropy models are increasingly being used to describe the collective activity of neural populations with measured mean neural activities and pairwise correlations, but the full space of probability distributions consistent with these constraints has not been explored. We provide upper and lower bounds on the entropy for the <i>minimum</i> entropy distribution over arbitrarily large collections of binary units with any fixed set of mean values and pairwise correlations. We also construct specific low-entropy distributions for several relevant cases. Surprisingly, the minimum entropy solution has entropy scaling logarithmically with system size for any set of first- and second-order statistics consistent with arbitrarily large systems. We further demonstrate that some sets of these low-order statistics can only be realized by small systems. Our results show how only small amounts of randomness are needed to mimic low-order statistical properties of highly entropic distributions, and we discuss some applications for engineered and biological information transmission systems.
Effect of Fluosol-DA and hetastarch on local cerebral blood flow, cortical O2 availability and computerized EEG data during cerebral ischaemia* (1990)

This study was designed to assess the effects of volume expansion with Fluosol-DA and hetastarch on local cerebral blood flow (CBF), cortical O2 availability (O2a) and computerized EEG power data during cerebral ischaemia in a primate stroke model. Focal cerebral ischaemia was produced in 20 anaesthetized Macaca monkeys by right unilateral middle cerebral artery (MCA) occlusion by the transorbital technique. Following occlusion of the right MCA, monkeys were randomized into one of the following treatment groups: Group A--Fluosol-DA 15 ml kg-1 i.v. + 40% O2; Group B--Fluosol-DA 15 ml kg-1 i.v. + 100% O2; Group C--hetastarch 30 ml kg-1 i.v. + 40% O2; Group D--hetastarch 30 ml kg-1 i.v. + 100% O2. In Group A, local CBF increased and EEG power data improved while O2a showed no change in the right MCA territory. In Group B, local CBF increased from 84% (P less than 0.001), O2a improved significantly, and EEG power data showed significant improvement in the right hemisphere. Cardiac output did not change during the Fluosol-DA infusions. In Groups C and D, local CBF increased significantly, O2a did not change, and EEG power data improved significantly in the right hemisphere. Cardiac output also increased significantly during the hetastarch infusions. These results show that Fluosol-DA and hetastarch improve local CBF and EEG power data in ischaemic brain. Only the Fluosol-DA + 100% O2 increased the O2a in the ischaemic brain. We conclude that the benefits with Fluosol-DA are due to its ability to increase O2 delivery to ischaemic brain.
Linked Scan (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Current advances in cell therapeutics: a biomacromolecules application perspective (2022)

Cell therapeutics promises to revolutionize the treatment of various secretory cell dysfunctions. Current and future advances in designing functional biomacromolecules will be critical to ensure that optimal delivery of therapeutic cells is achieved with desired biosafety and potency.
Absence of hydroxyurea‐induced mutational effects supports higher utilisation for the treatment of sickle cell anaemia (2021)

Hydroxyurea (hydroxycarbamide) is approved for treating both children and adults with sickle cell anaemia (SCA). Fetal haemoglobin (HbF) induction is the primary treatment response, along with improved anaemia, reduced haemolysis, myelosuppression and decreased endothelial inflammation. Hydroxyurea has proven clinical efficacy for SCA - treatment significantly reduces disease manifestations and prolongs survival. Despite these recognised benefits, long-standing concerns regarding the risks of mutagenic and potentially carcinogenic drug exposure have hampered efforts for broad hydroxyurea use in SCA, although these are based largely on outdated experimental models and treatment experiences with myeloproliferative neoplasms. Consequently, many patients with SCA are not receiving this highly effective disease-modifying therapy. In this review, we describe the concept of genotoxicity and its laboratory measurements, summarise hydroxyurea-associated data from both preclinical and clinical studies, and discuss carcinogenic potential. The genotoxicity results clearly demonstrate that hydroxyurea does not directly bind DNA and is not mutagenic. Rather, its genotoxic effects are limited to indirect clastogenicity occurring in select cell types, and only when high dose and time thresholds are exceeded. This absence of mutagenic activity is consistent with the observed lack of any compelling carcinogenic potential. Since hydroxyurea therapy for SCA carries minimal carcinogenic risks, the current drug labelling should be modified accordingly, and prescribing practices should be broadened to allow better access and increased utilisation of this highly effective drug.
Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.) (2016)

Cellulose is the primary determinant of mechanical strength in plant tissues. Late-season lodging is inversely related to the amount of cellulose in a unit length of the stem. Wheat is the most widely grown of all the crops globally, yet information on its CesA gene family is limited. We have identified 22 CesA genes from bread wheat, which include homoeologs from each of the three genomes, and named them as TaCesAXA, TaCesAXB or TaCesAXD, where X denotes the gene number and the last suffix stands for the respective genome. Sequence analyses of the CESA proteins from wheat and their orthologs from barley, maize, rice, and several dicot species (Arabidopsis, beet, cotton, poplar, potato, rose gum and soybean) revealed motifs unique to monocots (Poales) or dicots. Novel structural motifs CQIC and SVICEXWFA were identified, which distinguished the CESAs involved in the formation of primary and secondary cell wall (PCW and SCW) in all the species. We also identified several new motifs specific to monocots or dicots. The conserved motifs identified in this study possibly play functional roles specific to PCW or SCW formation. The new insights from this study advance our knowledge about the structure, function and evolution of the CesA family in plants in general and wheat in particular. This information will be useful in improving culm strength to reduce lodging or alter wall composition to improve biofuel production.