gebhart/patrepeval huggingface dataset:
5′ Exon replacement and repair by spliceosome-mediated RNA <i>trans</i>-splicing (2003)

Spliceosome-mediated RNA trans-splicing (SMaRT) has been used previously to reprogram mutant endogenous CFTR and factor VIII mRNAs in human epithelial cell and tissue models and knockout mice, respectively. Those studies used 3' exon replacement (3'ER); a process in which the distal portion of RNA is reprogrammed. Here, we also show that the 5' end of mRNA can be completely rewritten by 5'ER. For proof-of-concept, and to test whether 5'ER could generate functional CFTR, we generated a mutant minigene target containing CFTR exons 10-24 (deltaF508) and a mini-intron 10, and a pretrans-splicing molecule (targeted to intron 10) containing CFTR exons 1-10 (+F508), and tested these two constructs in 293T cells for anion efflux transport. Cells cotransfected with target and PTM showed a consistent increase in anion efflux, but there was no response in control cells that received PTM or target alone. Using a LacZ reporter system to accurately quantify trans-splicing efficiency, we tested several unique PTM designs. These studies provided two important findings as follows: (1) efficient trans-splicing can be achieved by binding the PTM to different locations in the target, and (2) relatively few changes in PTM design can have a profound impact on trans-splicing activity. Tethering the PTM close to the target 3' splice site (as opposed to the donor site) and inserting an intron in the PTM coding resulted in a 65-fold enhancement of LacZ activity. These studies demonstrate that (1) SMaRT can be used to reprogram the 5' end of mRNA, and (2) efficiency can be improved substantially.
A Consolidated and Continuous Synthesis of Ciprofloxacin from a Vinylogous Cyclopropyl Amide (2019)

Ciprofloxacin is a broad-spectrum antibiotic that is recognized as one of the World Health Organization's Essential Medicines. It is particularly effective in the treatment of Gram-negative bacterial infections associated with urinary, respiratory, and gastrointestinal tract infections. A streamlined and high yielding continuous synthesis of ciprofloxacin has been developed, which employs a chemoselective C-acylation step that precludes the need for intermediate isolations, extractions, or purifications. The end-to-end process has a residence time of 4.7 min with a 15.8 g/h throughput at laboratory scale and an overall isolated yield of 83%.
Variations in TcdB Activity and the Hypervirulence of Emerging Strains of Clostridium difficile (2010)

Hypervirulent strains of Clostridium difficile have emerged over the past decade, increasing the morbidity and mortality of patients infected by this opportunistic pathogen. Recent work suggested the major C. difficile virulence factor, TcdB, from hypervirulent strains (TcdB(HV)) was more cytotoxic in vitro than TcdB from historical strains (TcdB(HIST)). The current study investigated the in vivo impact of altered TcdB tropism, and the underlying mechanism responsible for the differences in activity between the two forms of this toxin. A combination of protein sequence analyses, in vivo studies using a Danio rerio model system, and cell entry combined with fluorescence assays were used to define the critical differences between TcdB(HV) and TcdB(HIST). Sequence analysis found that TcdB was the most variable protein expressed from the pathogenicity locus of C. difficile. In line with these sequence differences, the in vivo effects of TcdB(HV) were found to be substantially broader and more pronounced than those caused by TcdB(HIST). The increased toxicity of TcdB(HV) was related to the toxin's ability to enter cells more rapidly and at an earlier stage in endocytosis than TcdB(HIST). The underlying biochemical mechanism for more rapid cell entry was identified in experiments demonstrating that TcdB(HV) undergoes acid-induced conformational changes at a pH much higher than that of TcdB(HIST). Such pH-related conformational changes are known to be the inciting step in membrane insertion and translocation for TcdB. These data provide insight into a critical change in TcdB activity that contributes to the emerging hypervirulence of C. difficile.
Optimized GPU implementation of learning-based non-rigid multi-modal registration (2008)

Non-rigid multi-modal volume registration is computationally intensive due to its high-dimensional parameter space, where common CPU computation times are several minutes. Medical imaging applications using registration, however, demand ever faster implementations for several purposes: matching the data acquisition speed, providing smooth user interaction and steering for quality control, and performing population registration involving multiple datasets. Current GPUs offer an opportunity to boost the registration speed through high computational power at low cost. In our previous work, we have presented a GPU implementation of a non-rigid multi-modal volume registration that was 6 - 8 times faster than a software implementation. In this paper, we extend this work by describing how new features of the DX10-compatible GPUs and additional optimization strategies can be employed to further improve the algorithm performance. We have compared our optimized version with the previous version on the same GPU, and have observed a speedup factor of 3.6. Compared with the software implementation, we achieve a speedup factor of up to 44.
Exploitation of bacterial<i>N</i>-linked glycosylation to develop a novel recombinant glycoconjugate vaccine against<i>Francisella tularensis</i> (2013)

Glycoconjugate-based vaccines have proved to be effective at producing long-lasting protection against numerous pathogens. Here, we describe the application of bacterial protein glycan coupling technology (PGCT) to generate a novel recombinant glycoconjugate vaccine. We demonstrate the conjugation of the Francisella tularensis O-antigen to the Pseudomonas aeruginosa carrier protein exotoxin A using the Campylobacter jejuni PglB oligosaccharyltransferase. The resultant recombinant F. tularensis glycoconjugate vaccine is expressed in Escherichia coli where yields of 3 mg l(-1) of culture were routinely produced in a single-step purification process. Vaccination of BALB/c mice with the purified glycoconjugate boosted IgG levels and significantly increased the time to death upon subsequent challenge with F. tularensis subsp. holarctica. PGCT allows different polysaccharide and protein combinations to be produced recombinantly and could be easily applicable for the production of diverse glycoconjugate vaccines.
Decreased microRNA‐126 expression in psoriatic CD4<sup>+</sup> T cells promotes T‐helper 17 cell differentiation and the formation of dermatitis in imiquimod‐induced psoriasis‐like mice (2021)

Psoriasis is a chronic inflammatory skin disease with multiple genetic backgrounds, whose etiology and pathogenesis are still unclear. Complex T-cell immune imbalance has been demonstrated to play an important role in pathogenesis of psoriasis. This study reported that microRNA-126 (miR-126) expression was decreased in CD4<sup>+</sup> T cells of both psoriasis patients and psoriasis-like mouse models and its expression was negatively correlated with the Psoriasis Area and Severity Index (PASI) score of psoriasis patients. Conditional Mir126 knockout in mouse CD4<sup>+</sup> T cells can obviously aggravate the psoriasis-like dermatitis and promote T-helper (Th)1 and Th17 cells' infiltration in spleen of imiquimod (IMQ)-induced psoriasis-like mouse model. In addition, the mRNA expression of Il17a and Il17f were significantly increased in mouse naïve CD4<sup>+</sup> T cells with Mir126 knockout after stimulating with CD3 and CD28. Compared with naïve CD4<sup>+</sup> T cells, the expression of Mir126 was decreased in Th17 cells, and Mir126 knockout notably promoted the differentiation of naïve CD4<sup>+</sup> T cells to Th17 cells as well as the mRNA expression of Il17a, Il17f, Rorc, and Il23R. Our results revealed that decreased miR-126 in psoriatic CD4<sup>+</sup> T cells might accelerate the formation of skin lesions through promoting the differentiation of Th17 cells, thus suggesting a potential intervention target for psoriasis.
Characteristics of Different Nucleic Acid Staining Dyes for DNA Fragment Sizing by Flow Cytometry (1999)

An efficient and reliable double-stranded DNA (dsDNA) staining protocol for DNA fragment sizing by flow cytometry is presented. The protocol employs 0.8 microM of PicoGreen to label a wide range of DNA concentrations (0.5 ng/mL to 10,000 ng/mL) without regard to the solution dye/bp ratios and without initial quantification of the DNA analyte concentration. Using a combination of spectrofluorometry and flow cytometry experiments, we found that PicoGreen exhibited better overall performance than all the tested dsDNA binding dyes, such as TOTO-1. Fluorometric titration revealed that typical DNA staining protocols designed on the basis of the dye/bp ratio were highly dependent upon the DNA concentration for optimal results. PicoGreen was the least sensitive to the solution dye/bp ratio and was highly fluorescent in the presence of dsDNA. Using this new protocol, accurate histograms of HindIII digested lambda DNA were demonstrated for DNA concentrations ranging from 5 to 2000 ng/mL, and for dye/bp ratios from 106:1 to 1:4 at 0.8 microM of PicoGreen. The new one-step protocol is broadly applicable to any sensitive, laser-induced fluorescence method for detection of nucleic acids.
Size and stability of a naturally occurring virus inhibitor (1984)

We recently described a virus inhibitor (contact-blocking virus inhibitor) which was produced spontaneously by untransformed human and murine cells in tissue culture (S. Baron and L. McKerlie , Infect. Immun . 32:449-453, 1981). This contact-blocking virus inhibitor was characterized by broad antiviral activity, high potency, and reversible inhibition of viral attachment. Unlike interferon, the antiviral activity of the contact-blocking virus inhibitor is not species specific. An inhibitor with similar properties can also be demonstrated in many body fluids and surface secretions. We report here studies on the stability of the antiviral species which indicate that it is resistant to denaturation by heat (100 degrees C), acid (pH 2), and alkali (pH 12). The antiviral activity against all viruses tested resides in a low-molecular-weight molecule. The range of characteristics so far determined for the contact-blocking virus inhibitor distinguishes it from other virus inhibitors reported in the literature.
On the Base Current Components in SOI Symmetric Lateral Bipolar Transistors (2016)

The base current components in semiconductor on insulator symmetric lateral bipolar transistors are examined in detail to yield insight into the underlying device physics. For Si-OI devices, the base current component due to recombination in the quasineutral base is negligible, the component due to injection into the emitter has a weaker than 1/N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</sub> dependence because of the effect of heavy doping. The component due to recombination in the emitter-base diode space-charge region is associated with the fabrication process, and could be reduced to a negligible level with process optimization. For SiGe-OI devices, the effect of heavy doping appears to be less than for Si-OI devices. The result is higher maximum current gain for SiGe-OI devices than for comparably doped Si-OI devices.
Inverse-Ordered Fabrication of Free-Standing CNT Sheets for Supercapacitor (2015)

Free-standing thin carbon nanotube (CNT) sheets are challenging to handle and control for device fabrication. In this paper, we report on the inverse-ordered fabrication method from thick CNT sheets to thin free-standing CNT sheets. As proof of the concept, thin CNT sheets for a supercapacitor were fabricated from 200 thick layers. The results show that the thin CNT sheet was electrochemically stable and had enhanced capacitive performance. The smaller the number of layers is, the larger the specific capacitances we have (from 10.10 F g–1 to 51.37 F g–1). Energy and power density were increased from 0.50 to 2.57 Wh kg–1 and from 0.33 to 2.31 kWkg–1, respectively. This simple and scalable inverse-ordered method is capable to fabricate CNT sheets in various forms, allowing fast trials on various applications.
Off-axis pumping of air clad photonic crystal fiber lasers and amplifiers (2011)

We investigate a new, free space, off-axis pumping method for pumping PCF lasers and amplifiers. Experiments show that the lasing performance is improved compared to standard on-axis pumping, while maintaining all other advantages.
The Role of Surface Oxygen in the Growth of Large Single-Crystal Graphene on Copper (2013)

Oxygen Control of Graphene Growth The growth of graphene on copper surfaces through the decomposition of hydrocarbons such as methane can result in a wide variety of crystal domain sizes and morphologies. Hao et al. (p. 720 , published online 24 October; see the cover) found that the presence of surface oxygen could limit the number of nucleation sites and allowed centimeter-scale domains to grow through a diffusion-limited mechanism. The electrical conductivity of the graphene was comparable to that of exfoliated graphene.
Improving Anomaly Detection with a Self-Supervised Task Based on Generative Adversarial Network (2022)

Existing anomaly detection models show success in detecting abnormal images with generative adversarial networks on the insufficient annotation of anomalous samples. However, existing models cannot accurately identify the anomaly samples which are close to the normal samples. We assume that the main reason is that these methods ignore the diversity of patterns in normal samples. To alleviate the above issue, this paper proposes a novel anomaly detection framework based on generative adversarial network, called ADe-GAN. More concretely, we construct a self-supervised learning task to fully explore the pattern information and latent representations of input images. In model inferring stage, we design a new abnormality score approach by jointly considering the pattern information and reconstruction errors to improve the performance of anomaly detection. Extensive experiments show that the ADe-GAN outperforms the state-of-the-art methods over several real-world datasets.
TERNARY INTERCALATION COMPOUND OF GRAPHITE WITH ALUMINUM FLUORIDE AND FLUORINE (1981)

Abstract Ternary intercalation compound of graphite with AlF3 and F2, CxF(AlF3)y was prepared under fluorine atmosphere at temperatures of 20–400 °C. Typical 1st stage compound has a composition of C6F(AlF3)0.15 with repeat distance 9.40 Å. Rapid progress in the reaction led to the formation of graphite fluoride, (C2F)n.
Monitoring of Epstein-Barr Virus DNA Load in Peripheral Blood by Quantitative Competitive PCR (1999)

A competitive quantitative PCR (Q-PCR) assay combined with simple silica-based DNA extraction was developed for monitoring of Epstein-Barr virus (EBV) DNA load in unfractionated peripheral blood. The Q-PCR is based on competitive coamplification of a highly conserved 213-bp region of the EBNA-1 open reading frame with an internal standard (IS), added in a known concentration. The IS has the same amplicon length and base composition as the wild-type (WT) EBNA-1 amplicon but differs in 23 internally randomized bases. Competitive coamplification yields two PCR products that are quantified by enzyme immunoassay or by electrochemiluminescence detection, with probes specific for the 23 differing internal nucleotides. The Q-PCR has a sensitivity of 10 copies of either WT or IS plasmid DNA. The Q-PCR was validated by quantification of known amounts of plasmid containing the WT EBNA-1 target. Furthermore, we determined EBV genome copy numbers in different cell lines. For EBV quantification in clinical samples, DNA was isolated from lysed whole blood by silica-affinity purification. Forty-six percent of healthy donor peripheral blood samples were positive by Q-PCR. In most of these samples, viral load was less than 2,000 EBV copies/ml of blood. In peripheral blood samples from two AIDS-related non-Hodgkin's lymphoma patients, elevated EBV loads (up to 120,000 copies/ml) were observed, which decreased upon therapy. In Burkitt's lymphoma patients, up to 4,592,000 EBV genome copies/ml of blood were detected. In conclusion, the EBNA-1-based Q-PCR assay provides a reproducible, accurate, and easy method for studying the relationship between EBV load and clinical parameters.
Fundamental studies in the conversion of coals to fuels of increased hydrogen content. Volume 1. The chemistry and mechanisms of coal conversion to clean fuel. Interim report, June 1979-December 1980 (1981)

Coal conversions were examined at a variety of conditions. Reaction products were characterized by numerous techniques to give insight into the compositional changes occurring at short times, the influence of coal and solvent composition and the extent of solvent-coal interactions. Coal dissolution in high boiling solvents was investigated in parallel studies using pure model compounds and high boiling coal-derived liquids. Procedures were developed to separate coal-derived liquids into distillate and nondistillable fractions and to effect further separation on a preparative scale into different chemical classes. Liquid chromatography was used extensively to characterize the solvents and relate their composition to coal conversion.
Preexisting human antibodies neutralize recently emerged H7N9 influenza strains (2015)

The emergence and seasonal persistence of pathogenic H7N9 influenza viruses in China have raised concerns about the pandemic potential of this strain, which, if realized, would have a substantial effect on global health and economies. H7N9 viruses are able to bind to human sialic acid receptors and are also able to develop resistance to neuraminidase inhibitors without a loss in fitness. It is not clear whether prior exposure to circulating human influenza viruses or influenza vaccination confers immunity to H7N9 strains. Here, we demonstrate that 3 of 83 H3 HA-reactive monoclonal antibodies generated by individuals that had previously undergone influenza A virus vaccination were able to neutralize H7N9 viruses and protect mice against homologous challenge. The H7N9-neutralizing antibodies bound to the HA stalk domain but exhibited a difference in their breadth of reactivity to different H7 influenza subtypes. Mapping viral escape mutations suggested that these antibodies bind at least two different epitopes on the stalk region. Together, these results indicate that these broadly neutralizing antibodies may contribute to the development of therapies against H7N9 strains and may also be effective against pathogenic H7 strains that emerge in the future.
Characterization of WSi x Films Deposited by Reacting  WF 6 with a Mixture of SiH2Cl2 and Si2 H 6 (1992)

Tungsten silicide films produced by dichlorosilane reduction of tungsten hexafluoride have better step coverage and adhesion than films produced by the more common process of silane reduction. However, depositing uniform films with a silicon to tungsten ratio significantly higher than 2.6 has been difficult with the dichlorosilane process. In order to gain control of the silicon to tungsten ratio of the film a small amount of disilane can be added to the dichlorosilane and tungsten hexafluoride based chemical vapor deposition process. The silicon content of the resulting films is directly proportional to the disilane partial pressure. The films produced by this process have lower fluorine content and better adhesion than films produced by silane reduction. This implies a reduction in polycide open‐circuit failures, especially at design rules below 0.8 μm.
Properties and Biological Activities of Thioredoxins (2001)

The mammalian thioredoxins are a family of small (approximately 12 kDa) redox proteins that undergo NADPH-dependent reduction by thioredoxin reductase and in turn reduce oxidized cysteine groups on proteins. The two main thioredoxins are thioredoxin- 1, a cytosolic and nuclear form, and thioredoxin-2, a mitochondrial form. Thioredoxin-1 has been studied more. It performs many biological actions including the supply of reducing equivalents to thioredoxin peroxidases and ribonucleotide reductase, the regulation of transcription factor activity, and the regulation of enzyme activity by heterodimer formation. Thioredoxin-1 stimulates cell growth and is an inhibitor of apoptosis. Thioredoxins may play a role in a variety of human diseases including cancer. An increased level of thioredoxin-1 is found in many human tumors, where it is associated with aggressive tumor growth. Drugs are being developed that inhibit thioredoxin and that have antitumor activity.
Adhesive plasters. [Patent application; coatings for crucibles, control rods, etc] (1975)

Adhesive plaster compositions are provided by treating particles of Y/sub 2/O/sub 3/, Eu/sub 2/O/sub 3/, Gd/sub 2/O/sub 3/, or Nd/sub 2/O/sub 3/ with dilute acid solutions. The resulting compositions were found to harden spontaneously into rigid reticulated masses resembling plaster of Paris. Upon heating, the hardened material is decomposed into the oxide, yet retains the reticulated rigid structure. 1 table.
<title>Electron-beam microcolumn technology and applications</title> (1995)

A fully functional electron beam microcolumn, 3.5 mm in length, demonstrating a probe size of 10 nm and beam current >= 1 nA at 1 keV has been successfully developed. This paper presents its current status and future directions. Potential applications ranging from low cost scanning electron microscopy to arrays of such microcolumns for lithography, metrology, testing etc. will be discussed.
Quantum Dots Tailored with Poly(<i>p</i><i>ara-</i>phenylene vinylene) (2004)

In polymer−nanoparticle composites, uniform dispersion of the nanoparticles carries advantages over cases where nanoparticle aggregation dominates. Such dispersion has been particularly difficult to obtain in the case of composites prepared from nanoparticles and conjugated polymers. Here, we show that cadmium selenide nanocrystals, or quantum dots, can be integrated into thin films of poly(para-phenylene vinylene) (PPV) without aggregation. The two key departures from previous studies of quantum-dot/electronic polymer composites are (1) the synthesis of high-quality quantum dots directly in novel, functional ligands, thus eliminating the need for ligand exchange, and (2) polymerization chemistry that grafts PPV to the quantum dot surface. Solid-state photoluminescence spectra of composite materials prepared by these novel techniques reveal the critical importance of the quantum dot−polymer interface that will enable new investigations in nanoparticle-based light-emitting devices.
Apodization design for the focused forked grating coupler (2017)

The Forked Grating Coupler (FGC) is a novel silicon photonics device that can interface with Optical Vortex (OV) light beams. First generation FGC devices had long adiabatic feed tapers and flat-amplitude grating apodization functions. This resulted in an inconveniently large device with degraded OV mode fidelity. New designs have been developed with a focused forked gratings allowing size to be reduced significantly. In addition, a Hamming apodization improves vortex mode fidelity within the constraint of a short focal length.