gebhart/patrepeval huggingface dataset:
Riboswitches: Discovery of Drugs That Target Bacterial Gene-Regulatory RNAs (2011)

Riboswitches are messenger RNA (mRNA) domains that regulate gene function in response to the intracellular concentration of a variety of metabolites and second messengers. They control essential genes in many pathogenic bacteria, thus representing an inviting new class of biomolecular target for the development of antibiotics and chemical-biological tools. In this Account, we briefly review the discovery of riboswitches in the first years of the 21st century and their ensuing characterization over the past decade. We then discuss the progress achieved so far in using riboswitches as a focus for drug discovery, considering both the value of past serendipity and the particular challenges that confront current researchers. Five mechanisms of gene regulation have been determined for riboswitches. Most bacterial riboswitches modulate either transcription termination or translation initiation in response to ligand binding. All known examples of eukaryotic riboswitches, and some bacterial riboswitches, control gene expression by alternative splicing. The glmS riboswitch, which is widespread in Gram-positive bacteria, is a catalytic RNA activated by ligand binding: its self-cleavage destabilizes the mRNA of which it is part. Finally, one example of a trans-acting riboswitch is known. Three-dimensional structures have been determined for representatives of 13 structurally distinct riboswitch classes, providing atomic-level insight into their mechanisms of ligand recognition. While cellular and viral RNAs have attracted widespread interest as potential drug targets, riboswitches show special promise due to the diversity of small-molecule recognition strategies that are on display in their ligand-binding pockets. Moreover, riboswitches have evolved to recognize small-molecule ligands, which is unique among known structured RNA domains. Structural and biochemical advances in the study of riboswitches provide an impetus for the development of methods for the discovery of novel riboswitch activators and inhibitors. Recent rational drug design efforts focused on select riboswitch classes have yielded a small number of candidate antibiotic compounds, including one active in a mouse model of Staphylococcus aureus infection. The development of high-throughput methods suitable for riboswitch-specific drug discovery is ongoing. A fragment-based screening approach employing equilibrium dialysis that may be generically useful has demonstrated early success. Riboswitch-mediated gene regulation is widely employed by bacteria; however, only the thiamine pyrophosphate-responsive riboswitch has thus far been found in eukaryotes. Thus, riboswitches are particularly attractive as targets for antibacterials. Indeed, antimicrobials with previously unknown mechanisms have been found to function by binding riboswitches and causing aberrant gene expression.
A SoC design for broadband wireless ad-hoc network node (2010)

During the past decade, wireless Ad-hoc network have been more and more popular in both military and civil areas, which due to its distinguishing characteristics as following: strongly network constructing, highly mobility, rapidly transmission. A SoC design for broad band wireless ad-hoc network node is proposed in this paper. In details, the system architecture design is given as well as the hardware design for customized IP core and the specific device driver. At the same time, a kind of data exchange technology which makes use of Network Bridge is designed to support the connection between Ethernet and ad-hoc network. The results of the hardware simulation and experiment show that the SoC system operates normally and has a good performance index.
The peptide-encoding CEP1 gene modulates lateral root and nodule numbers in Medicago truncatula (2013)

The role of MtCEP1, a member of the CEP (C-terminally encoded peptide) signaling peptide family, was examined in Medicago truncatula root development. MtCEP1 was expressed in root tips, vascular tissue, and young lateral organs, and was up-regulated by low nitrogen levels and, independently, by elevated CO2. Overexpressing MtCEP1 or applying MtCEP1 peptide to roots elicited developmental phenotypes: inhibition of lateral root formation, enhancement of nodulation, and the induction of periodic circumferential root swellings, which arose from cortical, epidermal, and pericycle cell divisions and featured an additional cortical cell layer. MtCEP peptide addition to other legume species induced similar phenotypes. The enhancement of nodulation by MtCEP1 is partially tolerant to high nitrate, which normally strongly suppresses nodulation. These nodules develop faster, are larger, and fix more nitrogen in the absence and presence of inhibiting nitrate levels. At 25mM nitrate, nodules formed on pre-existing swelling sites induced by MtCEP1 overexpression. RNA interference-mediated silencing of several MtCEP genes revealed a negative correlation between transcript levels of MtCEP1 and MtCEP2 with the number of lateral roots. MtCEP1 peptide-dependent phenotypes were abolished or attenuated by altering or deleting key residues in its 15 amino acid domain. RNA-Seq analysis revealed that 89 and 116 genes were significantly up- and down-regulated, respectively, by MtCEP1 overexpression, including transcription factors WRKY, bZIP, ERF, and MYB, homologues of LOB29, SUPERROOT2, and BABY BOOM. Taken together, the data suggest that the MtCEP1 peptide modulates lateral root and nodule development in M. truncatula.
Crucial Role of Endogenous Interleukin-10 Production in Myocardial Ischemia/Reperfusion Injury (2000)

The present findings provide the first direct evidence that endogenous IL-10 inhibits the production of tumor necrosis factor-alpha and NO and serves to protect the ischemic and reperfused myocardium through the suppression of neutrophil recruitment.
Nuclear-mitotic apparatus protein: a structuralprotein interface between the nucleoskeleton and RNA splicing. (1994)

Vertebrate splicing factors are localized to discrete domains within the nuclei of somatic cells. The mechanism whereby such nuclear domains, identified as speckles by immunofluorescence microscopy, are generated is unclear. Recent studies suggest that the spatial order within the nucleus is maintained by nuclear matrix factors. Here we show that a protein in the nuclear matrix and mitotic apparatus [nuclear-mitotic apparatus protein, NuMA; Lydersen, B. & Pettijohn, D. (1980) Cell 22, 489-499] colocalizes with splicing factors in interphase nuclei and is associated with small nuclear ribonucleoproteins in a complex immunoprecipitated from HeLa extract with small nuclear ribonucleoprotein antibodies. Moreover, NuMA associates with splicing complexes that are reconstituted in vitro using wild-type pre-mRNA, but not with nonspecific RNA. Cumulatively, these observations suggest a function of NuMA or NuMA-like proteins in interphase cells in providing a bridge between RNA processing and the nucleoskeleton.
Cough-generated aerosols of Pseudomonas aeruginosa and other Gram-negative bacteria from patients with cystic fibrosis (2009)

During coughing, patients with CF produce viable aerosols of P aeruginosa and other Gram-negative bacteria of respirable size range, suggesting the potential for airborne transmission.
Twenty-five–year follow-up among survivors of childhood acute lymphoblastic leukemia: a report from the Childhood Cancer Survivor Study (2008)

Survivors of childhood acute lymphoblastic leukemia (ALL) are at risk for late effects of cancer therapy. Five-year ALL survivors (< 21 years at diagnosis; n = 5760 eligible, 4151 participants), diagnosed from 1970 to 1986 were compared with the general population and a sibling cohort (n = 3899). Cumulative mortality of 5760 5-year survivors was 13% at 25 years from diagnosis. Recurrent ALL (n = 483) and second neoplasms (SNs; n = 89) were the major causes of death. Among 185 survivors, 199 SNs occurred, 53% in the CNS. Survivors reported more multiple chronic medical conditions (CMCs; odds ratio [OR], 2.8; 95% CI, 2.4-3.2) and severe or life-threatening CMCs (OR, 3.6; 95% CI, 3.0-4.5) than siblings. Cumulative incidence of severe CMCs, including death, 25 years from diagnosis was 21.3% (95% CI, 18.2-24.4; 23.3% [95% CI, 19.4-27.2] and 13.4% [95% CI, 8.4-18.4] for irradiated and nonirradiated survivors, respectively). Survivors reported more adverse general and mental health, functional impairment, and activity limitations compared with siblings (P < .001). Rates of marriage, college graduation, employment, and health insurance were all lower compared with sibling controls (P < .001). Long-term survivors of childhood ALL exhibit excess mortality and morbidity. Survivors who received radiation therapy as part of their treatment or had a leukemia relapse are at greatest risk for adverse outcomes.
Nanoparticle-mediated catalase delivery protects human neurons from oxidative stress (2013)

Several neurodegenerative diseases and brain injury involve reactive oxygen species and implicate oxidative stress in disease mechanisms. Hydrogen peroxide (H2O2) formation due to mitochondrial superoxide leakage perpetuates oxidative stress in neuronal injury. Catalase, an H2O2-degrading enzyme, thus remains an important antioxidant therapy target. However, catalase therapy is restricted by its labile nature and inadequate delivery. Here, a nanotechnology approach was evaluated using catalase-loaded, poly(lactic co-glycolic acid) nanoparticles (NPs) in human neuronal protection against oxidative damage. This study showed highly efficient catalase encapsulation capable of retaining ~99% enzymatic activity. NPs released catalase rapidly, and antioxidant activity was sustained for over a month. NP uptake in human neurons was rapid and nontoxic. Although human neurons were highly sensitive to H2O2, NP-mediated catalase delivery successfully protected cultured neurons from H2O2-induced oxidative stress. Catalase-loaded NPs significantly reduced H2O2-induced protein oxidation, DNA damage, mitochondrial membrane transition pore opening and loss of cell membrane integrity and restored neuronal morphology, neurite network and microtubule-associated protein-2 levels. Further, catalase-loaded NPs improved neuronal recovery from H2O2 pre-exposure better than free catalase, suggesting possible applications in ameliorating stroke-relevant oxidative stress. Brain targeting of catalase-loaded NPs may find wide therapeutic applications for oxidative stress-associated acute and chronic neurodegenerative disorders.
Features Recognition from Piping and Instrumentation Diagrams in Image Format Using a Deep Learning Network (2019)

A piping and instrumentation diagram (P&ID) is a key drawing widely used in the energy industry. In a digital P&ID, all included objects are classified and made amenable to computerized data management. However, despite being widespread, a large number of P&IDs in the image format still in use throughout the process (plant design, procurement, construction, and commissioning) are hampered by difficulties associated with contractual relationships and software systems. In this study, we propose a method that uses deep learning techniques to recognize and extract important information from the objects in the image-format P&IDs. We define the training data structure required for developing a deep learning model for the P&ID recognition. The proposed method consists of preprocessing and recognition stages. In the preprocessing stage, diagram alignment, outer border removal, and title box removal are performed. In the recognition stage, symbols, characters, lines, and tables are detected. The objects for recognition are symbols, characters, lines, and tables in P&ID drawings. A new deep learning model for symbol detection is defined using AlexNet. We also employ the connectionist text proposal network (CTPN) for character detection, and traditional image processing techniques for P&ID line and table detection. In the experiments where two test P&IDs were recognized according to the proposed method, recognition accuracies for symbol, characters, and lines were found to be 91.6%, 83.1%, and 90.6% on average, respectively.
Low-voltage, high extinction ratio carrier-depletion Mach-Zehnder silicon optical modulator (2011)

As a result of the low modulation efficiency of carrier-depletion Mach-Zehnder silicon optical modulator, it always needs a high voltage around 6 V, which is very difficult to supply in an integrated high-speed CMOS chip. We demonstrate a carrier-depletion Mach-Zehnder silicon optical modulator which works at a low voltage. Its coplanar waveguide electrode is carefully designed to make sure the electrical wave loss along the device is low. The device operates well at a data rate of 12.5 Gb/s, whose phase-shifter length is 2 mm. Voltages with the swinging amplitudes being 1 V and 2 V are applied to the device with the reverse bias voltages of 0.5 V and 0.8 V. The extinction ratios are 7.67 and 12.79 dB respectively.
Three Amino Acid Changes in Avian Coronavirus Spike Protein Allow Binding to Kidney Tissue (2019)

Infectious bronchitis virus (IBV) infects ciliated epithelial cells in the chicken respiratory tract. While some IBV strains replicate locally, others can disseminate to various organs, including the kidney. Here, we elucidate the determinants for kidney tropism by studying interactions between the receptor-binding domain (RBD) of the viral attachment protein spike from two IBV strains with different tropisms. Recombinantly produced RBDs from the nephropathogenic IBV strain QX and from the nonnephropathogenic strain M41 bound to the epithelial cells of the trachea. In contrast, only QX-RBD binds more extensively to cells of the digestive tract, urogenital tract, and kidneys. While removal of sialic acids from tissues prevented binding of all proteins to all tissues, binding of QX-RBD to trachea and kidney could not be blocked by preincubation with synthetic alpha-2,3-linked sialic acids. The lack of binding of QX-RBD to a previously identified IBV-M41 receptor was confirmed by enzyme-linked immunosorbent assay (ELISA), demonstrating that tissue binding of QX-RBD is dependent on a different sialylated glycan receptor. Using chimeric RBD proteins, we discovered that the region encompassing amino acids 99 to 159 of QX-RBD was required to establish kidney binding. In particular, QX-RBD amino acids 110 to 112 (KIP) were sufficient to render IBV-M41 with the ability to bind to kidney, while the reciprocal mutations in IBV-QX abolished kidney binding completely. Structural analysis of both RBDs suggests that the receptor-binding site for QX is located at a different location on the spike than that of M41.<b>IMPORTANCE</b> Infectious bronchitis virus is the causative agent of infectious bronchitis in chickens. Upon infection of chicken flocks, the poultry industry faces substantial economic losses by diminished egg quality and increased morbidity and mortality of infected animals. While all IBV strains infect the chicken respiratory tract via the ciliated epithelial layer of the trachea, some strains can also replicate in the kidneys, dividing IBV into the following two pathotypes: nonnephropathogenic (example, IBV-M41) and nephropathogenic viruses (including IBV-QX). Here, we set out to identify the determinants for the extended nephropathogenic tropism of IBV-QX. Our data reveal that each pathotype makes use of a different sialylated glycan ligand, with binding sites on opposite sides of the attachment protein. This knowledge should facilitate the design of antivirals to prevent coronavirus infections in the field.
Nonlinear Optical Communication Networks (1998)

Optical Fiber Propagation. Optical Amplifiers. Optical Transmission Systems. Soliton Optical Communications. Repeaterless Systems. Long Distance TDM Transmission. WDM Optically Amplified Systems. Transmission in All-Optical Networks. Appendices. Index.
Dynamic deformation of red blood cell in Dual-trap Optical Tweezers (2010)

Three-dimensional dynamic deformation of a red blood cell in a dual-trap optical tweezers is computed with the elastic membrane theory and is compared with the experimental results. When a soft particle is trapped by a laser beam, the particle is deformed depending on the radiation stress distribution whereas the stress distribution on the particle in turn depends on the deformation of its morphological shape. We compute the stress re-distribution on the deformed cell and its subsequent deformations recursively until a final equilibrium state solution is achieved. The experiment is done with the red blood cells in suspension swollen to spherical shape. The cell membrane elasticity coefficient is obtained by fitting the theoretical prediction with the experimental data. This approach allows us to evaluate up to 20% deformation of cell's shape.
Articular Cartilage: Injury Pathways and Treatment Options (2006)

Articular cartilage injury and degeneration is a frequent occurrence in synovial joints. Treatment of these articular cartilage lesions are a challenge because this tissue is incapable of quality repair and/or regeneration to its native state. Nonoperative treatments endeavor to control symptoms, and include anti-inflammatory medication, viscosupplementation, bracing, orthotics, and activity modification. Techniques to stimulate the intrinsic repair (fibrocartilage) process include drilling, abrasion, and microfracture of the subchondral bone. Currently, the clinical biologic approaches to treat cartilage defects include autologous chondrocyte implantation, periosteal transfer, and osteochondral autograft or allograft transplantation. Newer strategies employing tissue engineering being studied involve the use of combinations of progenitor cells, bioactive factors, and matrices, and the use of focal synthetic devices. Many new and innovative treatments are being explored in this exciting field. However, there is a paucity of prospective, randomized controlled clinical trials that have compared the various techniques, treatment options, indications and efficacy.
Redirecting T cells to hematological malignancies with bispecific antibodies (2017)

There is a need to improve outcomes for patients with recurrent and/or refractory hematological malignancies. Immunotherapy holds the promise to meet this need, because it does not rely on the cytotoxic mechanism of conventional therapies. Among different forms of immunotherapy, redirecting T cells to hematological malignancies with bispecific antibodies (BsAbs) is an attractive strategy. BsAbs are an "off-the-shelf" product that is easily scalable in contrast to adoptive T-cell therapies. Among these, the bispecific T-cell engager blinatumomab has emerged as the most successful BsAb to date. It consists of 2 single-chain variable fragments specific for CD19 present on B-cell malignancies and CD3 expressed on almost all T cells. Blinatumomab has shown potent antitumor activity as a single agent, particularly for acute lymphoblastic leukemia, resulting in its US Food and Drug Administration approval. However, although successful in inducing remissions, these are normally short-lived, with median response durations of <1 year. Nevertheless, the success of blinatumomab has reinvigorated the BsAb field, which is bustling with preclinical and clinical studies for not only B-cell-derived lymphoblastic leukemia and lymphoma but also acute myeloid leukemia and multiple myeloma. Here, we will review the successes and challenges of T-cell-targeted BsAbs for the immunotherapy of hematological malignancies with special focus on conducted clinical studies and strategies to improve their efficacy.
Construction and Behavior of Circularly Permuted and Telocentric Chromosomes in <i>Saccharomyces cerevisiae</i> (1986)

We developed techniques that allow us to construct novel variants of Saccharomyces cerevisiae chromosomes. These modified chromosomes have precisely determined structures. A metacentric derivative of chromosome III which lacks the telomere-associated X and Y' elements, which are found at the telomeres of most yeast chromosomes, behaves normally in both mitosis and meiosis. We made a circularly permuted telocentric version of yeast chromosome III whose closest telomere was 33 kilobases from the centromere. This telocentric chromosome was lost at a frequency of 1.6 X 10(-5) per cell compared with a frequency of 4.0 X 10(-6) for the natural metacentric version of chromosome III. An extremely telocentric chromosome whose closet telomere was only 3.5 kilobases from the centromere was lost at a frequency of 6.0 X 10(-5). The mitotic stability of telocentric chromosomes shows that the very high frequency of nondisjunction observed for short linear artificial chromosomes is not due to inadequate centromere-telomere separation.
Two and three-color fluorescence flow cytometric analysis of immunoidentified viable bacteria (2000)

With the appropriate filter sets of both Bryte-HS (Bio-Rad, Hercules, CA) and FACScan (Becton Dickinson, San Jose, CA) flow cytometers, the measurement of separated green (SYBR Green I), orange-red (propidium iodide), and far red (RPE-Cy5) fluorescence was possible, allowing the enumeration of viable immunodetected bacteria. The entire protocol is completed in less than 3 h, offering numerous possibilities for rapid and precise analyses in sanitary, industrial, and environmental microbiology.
IRF/Type I IFN signaling serves as a valuable therapeutic target in the pathogenesis of inflammatory bowel disease (2021)

Inflammatory bowel disease (IBD) is an autoimmune disease characterized by unresolved colitis and epithelial injury. Intestinal microbiota and its interaction with immune system are critical etiologic factors. In response to gut virome and bacteria derived nucleic acid, interferon regulatory factors (IRFs) are activated to promote the production of cytokines, including type I interferons (IFN-Is), to help maintain intestinal homeostasis under both physiological and pathophysiological conditions. However, derailed IRF/IFN-I pathway other-wisely contributes to the progression of IBD with distinct IRF member exerting differential regulatory effect. Here, we summarize the recent advances regarding the role of IRF/IFN-I pathway in the development of IBD. We emphasize that IFN-I is a double-edged sword in IBD pathogenesis, as IFN-Is are protective in acute colitis while becoming pro-inflammatory during the chronic recovery phase. Besides, the functional outcome of IRFs is diverse and complex, which hinges on the cell types affected and the presence of other immune mediators. All in all, IRF/IFN-I pathway serves as a versatile regulator in IBD pathogenesis and holds the potential for therapeutic interventions.