gebhart/patrepeval huggingface dataset:
Nucleosides, Part LXIV, Base-Labile Protecting Groups for the Oligoribonucleotide Synthesis (2001)

New labile protecting groups for the anticipated synthesis of oligoribonucleotides were developed and introduced via their carbonochloridates 8 – 11 at the 5′-O position of thymidine (15) to form 16, 18, 21, and 24 in good yields (Schemes 2 and 3). Similarly, the 5′-O-diphenylphosphinoyl(dpp)-protected thymidine derivative 27 was synthesized with diphenylphosphinoyl chloride 14 as the reactive reagent. With the help of the model compounds 16, 18, 21, 24, and 27, the deprotection rates of these functions towards base treatment were recorded to evaluate their usefulness as temporary protecting groups in RNA assembly (Table). Finally, the relative stability of the 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) protecting group towards bases confirmed its use as a permanent blocking group in our npe/npeoc strategy.
Analysis of RAS gene mutations in acute myeloid leukemia by polymerase chain reaction and oligonucleotide probes. (1988)

In vitro DNA amplification followed by oligonucleotide dot blot analysis were used to study RAS gene mutations in acute myeloid leukemia (AML). Fifty-two presentation AML DNAs were screened for mutations in codons 12, 13, and 61 of NRAS and in codons 12 and 61 of KRAS and HRAS. Fourteen (27%) contained mutations--all in NRAS and predominantly in codon 12. The most common amino acid substitution identified was of glycine by aspartic acid at codon 12 (7/18), with a G----A transition being the most common base change (11/18). No particular correlation was observed between disease subtype and the incidence or type of NRAS mutation. In DNA samples from four patients, 2 NRAS mutations were found to coexist. NIH 3T3 focus-formation assays revealed that in each case the mutations were present in different NRAS alleles. We also report the absence of a mutated RAS gene in relapse DNAs of four patients in which a RAS oncogene had been detected at presentation. These observations suggest that RAS mutations arise as part of the evolution of neoplastic transformation.
Isolation and Proteomic Characterization of Human Parvulin-associating Preribosomal Ribonucleoprotein Complexes (2002)

Human parvulin (hParvulin; Par14/EPVH) belongs to the third family of peptidylprolyl cis-trans isomerases that exhibit an enzymatic activity of interconverting the cis-trans conformation of the prolyl peptide bond, and shows sequence similarity to the regulator enzyme for cell cycle transitions, human Pin1. However, the cellular function of hParvulin is entirely unknown. Here, we demonstrate that hParvulin associates with the preribosomal ribonucleoprotein (pre-rRNP) complexes, which contain preribosomal RNAs, at least 26 ribosomal proteins, and 26 trans-acting factors involved in rRNA processing and assembly at an early stage of ribosome biogenesis. Since an amino-terminal domain of hParvulin, which is proposed to be a putative DNA-binding domain, was alone sufficient to associate in principle with the pre-rRNP complexes, the association is probably through protein-RNA interaction. In addition, hParvulin co-precipitated at least 10 proteins not previously known to be involved in ribosome biogenesis. Coincidentally, most of these proteins are implicated in regulation of microtubule assembly or nucleolar reformation during the mitotic phase of the cell. Thus, these results, coupled with the preferential nuclear localization of hParvulin, suggest that hParvulin may be involved in ribosome biogenesis and/or nucleolar re-assembly of mammalian cells.
Comparison of the Endotracheal Tube and Laryngeal Mask in Airway Management by Paramedical Personnel (1992)

An evaluation of the laryngeal mask airway (LMA) as a means of airway support when used by paramedical personnel was performed. Forty medical and paramedical students attempted to intubate the tracheas of 40 healthy anesthetized adults with the LMA and a cuffed endotracheal tube (ETT). The number of attempts to achieve correct placement and the time taken to adequately ventilate the lungs were recorded for both devices. End-tidal carbon dioxide was detected significantly sooner after commencement of the intubation attempt using the LMA (mean 38.6 s) compared with the ETT (mean 88.3 s, P less than 0.0001). Ninety-four percent of the students successfully ventilated the lungs on their first attempt with the LMA, whereas only 69% intubated the trachea on their first attempt with the ETT (P less than 0.01). Five students were unable to intubate the trachea after three attempts with the ETT, but all positioned the LMA satisfactorily on their first try in a mean time of 40 s. We conclude that unskilled operators with minimal training can safely and successfully ventilate unconscious patients more rapidly using the LMA than the ETT. These results suggest the LMA should be available in all areas where resuscitation is performed.
Anti‐Inflammatory Effects of Extracts from a Bioenergy Crop, Switchgrass, in Cultured Adipocytes (2015)

Obesity is a low‐grade inflammatory condition that is associated with several metabolic diseases such as diabetes and cardiovascular disorders. Moreover, bioactive compounds from food and botanicals have been shown to reduce inflammation. However, anti‐inflammatory roles of switchgrass, a bioenergy crop is currently unexplored. Hence, we hypothesize that bioactives from switchgrass may have potential benefits on obesity‐related inflammation by reducing proinflammatory adipokines. Bioactives were isolated from chopped switchgrass using ethanol. To test our hypothesis, 3T3L1 preadipocytes were pretreated with the crude ethanol extracts or extracts fractionated into different organic solvents, followed by lipopolysaccharide (LPS) to determine if the extracts reduced LPS‐induced inflammation. Interestingly, some of these extracts reduced significantly and in a dose‐dependent manner, secretion of Monocyte Chemotractant Protein‐1 (MCP‐1) and Interleukin‐6 (IL‐6) from 3T3‐L1 cells. Furthermore, using MTT assays, some extracts significantly reduced cell viability while others did not. In summary, these findings demonstrate that switchgrass‐derived bioactives reduce adipocyte inflammation and provide the first evidence for an added value of switchgrass in obesity‐related inflammation. Additional studies are needed to characterize the specific phytochemicals responsible for the reduction in inflammation and their mechanism of action. In conclusion, bioenergy crops such as switchgrass are economically viable sources of anti‐inflammatory dietary supplements.
Primary and Secondary Prevention of Ventricular Arrhythmias in Dilated Cardiomyopathy Nonsustained, Sustained, and Incessant (2009)

The occurrence of ventricular arrhythmias in patients with idiopathic dilated cardiomyopathy (DCM) who are treated with an implantable cardioverter-defibrillator (ICD) for primary or secondary prevention is not fully understood. In this nonrandomized, two-centre, observational study we analyzed the occurrence of ventricular arrhythmias in a total of 105 DCM patients (age, 53 +/- 13 years) treated with an ICD. Fifty-one patients with a left ventricular ejection fraction <or= 35% did not have prior sustained ventricular arrhythmias (primary prevention). The secondary prevention group consisted of 54 patients with documented sustained ventricular tachycardia (n = 25) or aborted sudden cardiac death (n = 29). During 32 +/- 7 months follow-up the number of patients with appropriate defibrillator therapies (n = 51) was comparable between the two groups (HR 0.79, 95% CI 0.454 to 1.361, P = 0.389). Importantly, less primary prevention patients experienced appropriate ICD shocks for any arrhythmic event (HR 0.35, 95% CI 0.186 to 0.777, P = 0.008), as well as appropriate ICD shocks for ventricular fibrillation (HR 0.31, 95% CI 0.167 to 0.737, P = 0.006). In contrast, antitachycardia pacing was more often observed in the primary prevention group (HR 2.75, 95% CI 1.031 to 6.238, P = 0.043). Two primary prevention and 6 secondary prevention patients received multiple ICD therapies in consequence of incessant ventricular tachycardia. The characteristics of ventricular arrhythmias in patients with DCM who are treated with an ICD for primary or secondary prevention vary according to the underlying indication. Therefore, different device programming according to the patient's history might improve ventricular tachyarrhythmia management.
Absorption Properties and Spectroscopic Studies of Dilute Sulfur Dioxide in Aqueous Glycerol Solutions (2012)

Isothermal gas–liquid equilibrium (GLE) data were reported at 298.15 K and 123.15 kPa for the absorption of dilute SO2 in aqueous glycerol solutions, in which SO2 partial pressures are calculated in the range of (0 to 140) Pa. The GLE data were obtained with uncertainties within ±0.02 K for temperatures, ± 0.133 kPa for total pressures, ± 3.5% for SO2 concentration in the gas phase, and ±5% for SO2 concentration in the liquid phase. The measurements showed that the solubility of dilute SO2 in the system of glycerol (1) + water (2) increases with the increasing glycerol concentrations in the whole composition, and the solubility of SO2 in the system of glycerol (1) + water (2) presents an extreme minimum of 60.1 mg·L–1 at the mass fraction of w1 = 1.00 when SO2 in the gas phase is designed at ySO2 = 5 × 10–4. In addition, UV, FTIR (Fourier transform infrared), 1H NMR, and fluorescence spectra in the absorption processes of SO2 in the system of glycerol (1) + water (2) were investigated to present important absorption mechanism. Based on the spectral results obtained, the possibility of intermolecular hydrogen bond formation by hydroxyl oxygen atoms in the glycerol molecule with hydrogen atom in the H2O molecule and S···O interaction formation by hydroxyl oxygen atom in the glycerol molecule with sulfur atom in the SO2 molecule are discussed.
Automatic Tuning of Stochastic Gradient Descent with Bayesian\n Optimisation (2020)

Many machine learning models require a training procedure based on running\nstochastic gradient descent. A key element for the efficiency of those\nalgorithms is the choice of the learning rate schedule. While finding good\nlearning rates schedules using Bayesian optimisation has been tackled by\nseveral authors, adapting it dynamically in a data-driven way is an open\nquestion. This is of high practical importance to users that need to train a\nsingle, expensive model. To tackle this problem, we introduce an original\nprobabilistic model for traces of optimisers, based on latent Gaussian\nprocesses and an auto-/regressive formulation, that flexibly adjusts to abrupt\nchanges of behaviours induced by new learning rate values. As illustrated, this\nmodel is well-suited to tackle a set of problems: first, for the on-line\nadaptation of the learning rate for a cold-started run; then, for tuning the\nschedule for a set of similar tasks (in a classical BO setup), as well as\nwarm-starting it for a new task.\n
Detecting Pyronin Y labeled RNA transcripts in live cell microenvironments by phasor-FLIM analysis (2013)

Pyronin Y is an environment-sensitive probe which labels all double-stranded RNA in live cells. Methods to determine which RNA species Pyronin Y may be labeling are limited due to the lack of studies aimed at determining whether this probe has different spectroscopic properties when bound to specific transcripts. A major issue is that transcripts are difficult to isolate and study individually. We detected transcripts directly in their biological environment allowing us to identify RNA species on the basis of their location in the cell. We show that the phasor approach to lifetime analysis has the sensitivity to determine at least six different RNA species in live fibroblast cells. The detected lifetime differences were consistent among cells. To our knowledge this is the first application of a spectroscopic technique aimed at identifying Pyronin Y labeled RNA subtypes in living cells.
A multi-scale PDMS fabrication strategy to bridge the size mismatch between integrated circuits and microfluidics (2014)

In recent years there has been great progress harnessing the small-feature size and programmability of integrated circuits (ICs) for biological applications, by building microfluidics directly on top of ICs. However, a major hurdle to the further development of this technology is the inherent size-mismatch between ICs (~mm) and microfluidic chips (~cm). Increasing the area of the ICs to match the size of the microfluidic chip, as has often been done in previous studies, leads to a waste of valuable space on the IC and an increase in fabrication cost (>100×). To address this challenge, we have developed a three dimensional PDMS chip that can straddle multiple length scales of hybrid IC/microfluidic chips. This approach allows millimeter-scale ICs, with no post-processing, to be integrated into a centimeter-sized PDMS chip. To fabricate this PDMS chip we use a combination of soft-lithography and laser micromachining. Soft lithography was used to define micrometer-scale fluid channels directly on the surface of the IC, allowing fluid to be controlled with high accuracy and brought into close proximity to sensors for highly sensitive measurements. Laser micromachining was used to create ~50 μm vias to connect these molded PDMS channels to a larger PDMS chip, which can connect multiple ICs and house fluid connections to the outside world. To demonstrate the utility of this approach, we built and demonstrated an in-flow magnetic cytometer that consisted of a 5 × 5 cm(2) microfluidic chip that incorporated a commercial 565 × 1145 μm(2) IC with a GMR sensing circuit. We additionally demonstrated the modularity of this approach by building a chip that incorporated two of these GMR chips connected in series.
Dielectric properties of sol-gel derived barium-strontium titanate (Ba/sub 0.4/Sr/sub 0.6/TiO/sub 3/) thin film (2002)

The structural and electrical properties of sol-gel derived barium-strontium-titanate (Ba/sub 0.4/Sr/sub 0.6/TiO/sub 3/) thin films have been investigated. The as-fired films are found to be amorphous, and the films crystallize to cubic phase only after a post deposition annealing at 700/spl deg/C for one hour in air. The measured room temperature dielectric constant (/spl epsi/') of the film was about 320. The dielectric constant did not show any significant frequency dependence up to 100 kHz. The temperature dependence of dielectric constant exhibited a diffused a ferroelectric to paraelectric phase transition at -60/spl deg/C. The room temperature dielectric constant and magnitude of the dielectric peak at the Curie point is found to be dependent on the thickness of the film. The obtained dielectric data on sol-gel barium strontium titanate thin films on platinized silicon substrates has been analyzed in the light of a barrier layer model.
Microstrip Antenna Efficiency and Surface Wave Loss (2021)

The efficiency components of a rectangular microstrip antenna (MSA) have been traditionally computed using the cavity model. The MSA cavity model does not include surface wave losses, but has been extended to include them. MSA surface wave losses have been assumed to be TM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> mode on a shorted dielectric slab, which have no lower cutoff frequency. Here we examine this assumption using full-wave simulation. The nonradiative losses appear inconsistent with the generation of a pure TM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> mode.
Advances in mesenchymal stem cell biology (2004)

Purpose of review: Mesenchymal stem cells (MSCs) have been studied for their potential application to the repair of mesenchymal and nonmesenchymal tissues such as nerve. This review highlights some of the recent advances in the expansion and identification of MSCs and we discuss a new, emerging logic: the trophic effects of MSCs on tissue repair. Recent findings: Recent studies have shown that MSCs mediate trophic effects, which may have a significant impact on tissue repair unrelated to the direct differentiation of MSCs into specific phenotypes. Other studies have also expanded our knowledge on cell surface markers for MSCs, and a novel culture technique has been developed for MSC expansion. These recent developments may have a profound impact on the application of MSCs to tissue repair. Summary: The idea that MSCs have potential to promote tissue repair by direct differentiation, cell replacement therapy, is widely known, while the concept that MSCs can affect tissue repair via a trophic effect (providing a reparative milieu) is new and expands the possibilities for using MSCs to regenerate or repair tissues. The expanded use and characterization of MSC markers may have a profound impact on the isolation or purification of MSCs from different tissues or may be used as release criteria for MSCs used in clinical applications. In addition, recent modifications in MSC culture conditions may allow for greater expansion of cells for different clinical applications.
The Intrinsic Estimator for Age‐Period‐Cohort Analysis: What It Is and How to Use It (2008)

A new approach to the statistical estimation of age‐period‐cohort (APC) accounting models, called the intrinsic estimator (IE), recently has been developed. This article (1) further describes the IE algebraically, geometrically, and verbally, (2) reviews properties of the IE as a statistical estimator, (3) provides model validation evidence for the IE both from an empirical example and from a simulation exercise, (4) relates the coefficients of the IE to those of conventional constrained APC models using formal definitions of statistical estimability, hypothesis testing, and empirical applications that directly address a criticism that often has been lodged at general‐purpose methods of APC analysis, and (5) introduces computer software for application of the IE that interested users can readily access. The authors conclude that the IE holds the potential for applications not only to APC analysis but also to similar problems of structural underidentification in sociology.
Inside Cover: Direct Transformation of Molecular Dinitrogen into Ammonia Catalyzed by Cobalt Dinitrogen Complexes Bearing Anionic PNP Pincer Ligands (Angew. Chem. Int. Ed. 46/2016) (2016)

Cobalt complexes bearing an anionic PNP-type pincer ligand are effective catalysts for the reduction of molecular dinitrogen into ammonia under mild reaction conditions, as shown by K. Yoshizawa, Y. Nishibayashi, and co-workers in their Communication on page 14291 ff. These findings provide valuable insight for the development of nitrogen fixation systems based on transition-metal dinitrogen complexes as catalysts.
Use of a Cationic Emulsion of Latanoprost to Treat Glaucoma Patients with Ocular Surface Disease: A Preclinical Review (2023)

Prostaglandin analogue topical medications are one of the most effective therapeutic approaches for the chronic management of glaucoma and ocular hypertension, through the reduction of elevated intra ocular pressure (IOP). While many of the first generations of anti-glaucoma eye drops were preserved with benzalkonium chloride, their repeated use may induce chronic ocular surface toxicity that leads to ocular surface disease (OSD) signs and symptoms. As a result, soft-preservatives and preservative-free formulations have been developed with the goal to avoid the long-term iatrogenic toxicity of the preservative agents. In addition, it has been suggested that OSD and its associated inflammation may negatively impact the efficacy of the IOP-lowering medications, including treatment adherence and compliance. Hence, it may be particularly interesting that glaucoma medications can concomitantly protect and "heal" the ocular surface and its environment while lowering elevated IOP, for the greater benefit of glaucoma patients. The objective of the present review is to briefly present the preclinical data of the cationic oil-in-water emulsion of latanoprost (latanoprost-CE) to shed some light on its mechanisms of action. It overall supports the following hypothesis: the restoration of a healthy ocular surface environment and treatment of the OSD signs and symptoms will allow for an improved elevated IOP reduction and glaucoma management. This would be achieved with a once daily dosing regimen to preserve glaucoma patients' vision, ocular surface, and quality-of-life and wellness.
Embolization of Portal Vein Branches Induces Hepatocyte Replication in Swine: A Potential Step in Hepatic Gene Therapy (1999)

Substantial hepatocyte replication occurred 2-7 days after embolization of portal vein branches. Further research will help determine if this procedure can facilitate retroviral transduction in large animals. If successful, the low morbidity of this method may allow its use in humans for gene therapy.
Computational Imaging Technology for Nanolithography (2013)

The rapid advancement of modern electronic technology is founded on Moore’s Law, which stipulates an exponential increase in transistor densities, leading to more and more functionalities in an integrated circuit (IC). A critical challenge in IC manufacturing lies in the nanolithography process, where the circuit pattern on a wafer is imprinted through imaging a photomask. Because of the small feature size compared with the wavelength of the light source, image distortion is significant due to diffraction and other aberrations. Computational technology, together with the modeling of the imaging process, is now an essential process to design the source and mask patterns that can counteract the distortions and allow for the printing of small features.
Application of SIMULINK in Non-linear System Analysis (2008)

This paper proposes using the SIMULINK toolbox in Matlab to analyze and check the nonlinear control system.According to the non-linear system mathematical model,SIMULINK toolbox can be directly used to build simulation model and proceed with the simulation study.This method can flexibly change the system structure and parameters,making the non-linear system performance analysis very simple and convenient;the analysis of system response curve helps to point out the way of improving the performance function of non-linear control system.
Administration of deoxyribonucleosides or inhibition of their catabolism as a pharmacological approach for mitochondrial DNA depletion syndrome (2013)

Mitochondrial DNA (mtDNA) depletion syndrome (MDS) is characterized by a reduction in mtDNA copy number and consequent mitochondrial dysfunction in affected tissues. A subgroup of MDS is caused by mutations in genes that disrupt deoxyribonucleotide metabolism, which ultimately leads to limited availability of one or several deoxyribonucleoside triphosphates (dNTPs), and subsequent mtDNA depletion. Here, using in vitro experimental approaches (primary cell culture of deoxyguanosine kinase-deficient cells and thymidine-induced mtDNA depletion in culture as a model of mitochondrial neurogastrointestinal encephalomyopathy, MNGIE), we show that supplements of those deoxyribonucleosides (dNs) involved in each biochemical defect (deoxyguanosine or deoxycytidine, dCtd) prevents mtDNA copy number reduction. Similar effects can be obtained by specific inhibition of dN catabolism using tetrahydrouridine (THU; inhibitor of cytidine deaminase) or immucillin H (inhibitor of purine nucleoside phosphorylase). In addition, using an MNGIE animal model, we provide evidence that mitochondrial dNTP content can be modulated in vivo by systemic administration of dCtd or THU. In spite of the severity associated with diseases due to defects in mtDNA replication, there are currently no effective therapeutic options available. Only in the case of MNGIE, allogeneic hematopoietic stem cell transplantation has proven efficient as a long-term therapeutic strategy. We propose increasing cellular availability of the deficient dNTP precursor by direct administration of the dN or inhibition of its catabolism, as a potential treatment for mtDNA depletion syndrome caused by defects in dNTP metabolism.