gebhart/patrepeval huggingface dataset:
Improved Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro and with Clinical Specimens (2020)

On 31 December 2019, the World Health Organization was informed of a cluster of cases of pneumonia of unknown etiology in Wuhan, China. Subsequent investigations identified a novel coronavirus, now named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from the affected patients. Highly sensitive and specific laboratory diagnostics are important for controlling the rapidly evolving SARS-CoV-2-associated coronavirus disease 2019 (COVID-19) epidemic. In this study, we developed and compared the performance of three novel real-time reverse transcription-PCR (RT-PCR) assays targeting the RNA-dependent RNA polymerase (RdRp)/helicase (Hel), spike (S), and nucleocapsid (N) genes of SARS-CoV-2 with that of the reported RdRp-P2 assay, which is used in >30 European laboratories. Among the three novel assays, the COVID-19-RdRp/Hel assay had the lowest limit of detection <i>in vitro</i> (1.8 50% tissue culture infective doses [TCID<sub>50</sub>]/ml with genomic RNA and 11.2 RNA copies/reaction with <i>in vitro</i> RNA transcripts). Among 273 specimens from 15 patients with laboratory-confirmed COVID-19 in Hong Kong, 77 (28.2%) were positive by both the COVID-19-RdRp/Hel and RdRp-P2 assays. The COVID-19-RdRp/Hel assay was positive for an additional 42 RdRp-P2-negative specimens (119/273 [43.6%] versus 77/273 [28.2%]; <i>P</i> < 0.001), including 29/120 (24.2%) respiratory tract specimens and 13/153 (8.5%) non-respiratory tract specimens. The mean viral load of these specimens was 3.21 × 10<sup>4</sup> RNA copies/ml (range, 2.21 × 10<sup>2</sup> to 4.71 × 10<sup>5</sup> RNA copies/ml). The COVID-19-RdRp/Hel assay did not cross-react with other human-pathogenic coronaviruses and respiratory pathogens in cell culture and clinical specimens, whereas the RdRp-P2 assay cross-reacted with SARS-CoV in cell culture. The highly sensitive and specific COVID-19-RdRp/Hel assay may help to improve the laboratory diagnosis of COVID-19.
Parkinson-related parkin reduces α-Synuclein phosphorylation in a gene transfer model (2010)

These data suggest that parkin reduces α-Synuclein levels and alters the balance between phosphatase and kinase activities that affect the levels of phosphorylated α-Synuclein. These results indicate novel mechanisms for parkin protection against α-Synuclein-induced toxicity in PD.
Brain Mitochondrial Function After Ischemia and Hypoxia (1973)

Respiratory function of rabbit brain mitochondria was well maintained after 37 minutes of severe systemic, normotensive hypoxemia. Respiratory control ratios and some state 3 rates were above normal, suggesting "tighter" coupling and lack of respiratory inhibition at cerebral venous oxygen tensions as low as 8 mm Hg and arterial oxygen tensions as low as 11 mm Hg. These findings agree with those of MacMillan and Siesjo, who found no change in the energy charge or nicotinamide adenine nucleotide dehydrogenase: nicotinamide adenine dinucleotide ratio after profound hypoxemia. Conventional concepts of brain tissue oxygenation are challenged by these findings. In addition, evidence supports the experiments of Eklof and Siesjo which show that cerebral venous oxygen tensions are inaccurate in defining tissue oxygenation at low perfusion pressures. Brain mitochondria were "loosely" coupled and inhibited under hypotensive and hypoxemic conditions.
Development of high-yield influenza A virus vaccine viruses (2015)

Vaccination is one of the most cost-effective ways to prevent infection. Influenza vaccines propagated in cultured cells are approved for use in humans, but their yields are often suboptimal. Here, we screened A/Puerto Rico/8/34 (PR8) virus mutant libraries to develop vaccine backbones (defined here as the six viral RNA segments not encoding haemagglutinin and neuraminidase) that support high yield in cell culture. We also tested mutations in the coding and regulatory regions of the virus, and chimeric haemagglutinin and neuraminidase genes. A combination of high-yield mutations from these screens led to a PR8 backbone that improved the titres of H1N1, H3N2, H5N1 and H7N9 vaccine viruses in African green monkey kidney and Madin-Darby canine kidney cells. This PR8 backbone also improves titres in embryonated chicken eggs, a common propagation system for influenza viruses. This PR8 vaccine backbone thus represents an advance in seasonal and pandemic influenza vaccine development.
Antibody-Targeted Nanoparticles for Cancer Therapy (2011)

In recent years, nanoparticulate-mediated drug delivery research has examined a full spectrum of nanoparticles that can be used in diagnostic and therapeutic cancer applications. A key aspect of this technology is in the potential to specifically target the nanoparticles to diseased cells using a range of molecules, in particular antibodies. Antibody-nanoparticle conjugates have the potential to elicit effective targeting and release of therapeutic targets at the disease site, while minimizing off-target side effects caused by dosing of normal tissues. This article provides an overview of various antibody-conjugated nanoparticle strategies, focusing on the rationale of cell-surface receptors targeted and their potential clinical application.
Percutaneous aspiration of brain tumor cysts via the Ommaya reservoir system (1991)

We performed percutaneous aspiration of 21 brain tumor cysts in 20 patients using the Ommaya reservoir system. Ages ranged from 3 to 70 years, median 48. Sixteen were primary tumors (12 anaplastic glioma, 2 craniopharyngioma, 1 oligodendroglioma, 1 brainstem glioma) and 4 were metastatic. Fourteen had the CT appearance of a true cyst and 7 a pseudocyst. We placed 18 catheters through twist drill holes via CT stereotactic guidance and 3 through burr holes via CT guidance and effectively aspirated 3 to 50 ml cyst fluid from 1 to 18 times in each patient. Postaspiration CT showed complete or significant reduction in cyst size in all patients in whom it was performed (18 after initial aspiration and 9 after subsequent aspirations). Asymptomatic intracyst hemorrhage occurred in 2 patients after cyst wall biopsy and catheter placement. There have been no other complications at follow-up of 4 to 114 weeks. In our experience, tumor cyst aspiration by the Ommaya reservoir system is as effective as percutaneous needle aspiration, but after catheter placement aspiration can be performed with minimal technical skill, avoiding repeated CT guidance required for needle aspiration of recurrent deep-seated cysts.
Postexposure Protection of Guinea Pigs against a Lethal Ebola Virus Challenge Is Conferred by RNA Interference (2006)

Further development of this technology has the potential to yield effective treatments for EBOV HF as well as for diseases caused by other agents that are considered to be biological threats.
Treatment of a retinal dystrophy, fundus albipunctatus, with oral 9-cis- -carotene (2009)

BACKGROUND Fundus albipunctatus is a retinal dystrophy caused by a mutation in the gene encoding 11-cis-retinol dehydrogenase which delays the recovery of rod photoreceptor cells from light stimulation leading to night blindness. A recent study of a mouse model of fundus albipunctatus treated with 9-cis-retinal showed an improvement in visual function and structure. METHODS Seven patients with fundus albipunctatus were given a daily food supplement of four capsules containing high-dose 9-cis-beta-carotene for 90 days. The subjects were tested before and after treatment by visual field and electroretinogram in both eyes. This non-randomised prospective phase I study was registered at http://www.clinicaltrials.gov (NCT00478530). RESULTS All patients showed significant improvements in peripheral visual field (mean deviation improved from -4.77+/-2.0 to -3.28+/-2.28, p=0.009, t test) and a highly significant improvement in rod recovery rates measured electroretinographically (maximal scotopic b-wave amplitude responses, improved from 197+/-49 muV to 292+/-48 muV, p<0.001, t test). No complications or side effects were observed. CONCLUSION Oral treatment with 9-cis-beta-carotene led to reversal of a human retinal dystrophy. This potential therapy is readily available and should be evaluated in retinal dystrophies of similar mechanisms such as various types of retinitis pigmentosa.
Low-threshold electrically pumped vertical-cavity surface-emitting microlasers (1989)

Vertical-cavity electrically driven lasers with three GaInAs quantum wells and diameters of several μm exhibit roomtemperature pulsed current thresholds as low as 1·3mA with 958 nm output wavelength.
DNA demethylation (1999)

Cytosine 5′ methylation of CpG dinucleotides within and around genes exerts a major influence on transcription in many plants and animals (1–3). DNA methylation can be causal for transcriptional silencing (4–5) and targets the machinery necessary to assemble specialized chromatin enriched in deacetylated histones (6–8). Once established in somatic cells, CpG methylation patterns within the genome are very stable and provide an attractive mechanism for segregating a large fraction of stably repressed chromatin (9–11). In contrast, DNA methylation is remarkably dynamic during early mammalian development and in certain tumor cells (12, 13). Alterations in the methylation status of the entire genome (14, 15), individual chromosomes (16), and specific genes (17–20) are essential for normal development (21, 22) and can promote tumorigenesis (23, 24). Understanding how these important transitions might be regulated requires the biochemical definition of the enzymatic processes that both methylate and demethylate the genome.
Notch2: a second mammalian Notch gene (1992)

Notch is a cell surface receptor that mediates a wide variety of cellular interactions that specify cell fate during Drosophila development. Recently, homologs of Drosophila Notch have been isolated from Xenopus, human and rat, and the expression patterns of these vertebrate proteins suggest that they may be functionally analogous to their Drosophila counterpart. We have now identified a second rat gene that exhibits substantial nucleic and amino acid sequence identity to Drosophila Notch. This gene, designated Notch2, encodes a protein that contains all the structural motifs characteristic of a Notch protein. Thus, mammals differ from Drosophila in having more than one Notch gene. Northern and in situ hybridisation analyses in the developing and adult rat identify distinct spatial and temporal patterns of expression for Notch1 and Notch2, indicating that these genes are not redundant. These results suggest that the great diversity of cell-fate decisions regulated by Notch in Drosophila may be further expanded in vertebrates by the activation of distinct Notch proteins.
Identification of a Genetic Signature of Activated Signal Transducer and Activator of Transcription 3 in Human Tumors (2005)

Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that is activated in diverse human tumors and may play a direct role in malignant transformation. However, the full complement of target genes that STAT3 regulates to promote oncogenesis is not known. We created a system to express a constitutively active form of STAT3, STAT3-C, in mouse fibroblasts and used it to identify STAT3 targets. We showed that a subset of these targets, which include transcription factors regulating cell growth, survival, and differentiation, are coexpressed in a range of human tumors. Using immunohistochemical staining of tissue microarrays, we showed that these targets are enriched in breast and prostate tumors harboring activated STAT3. Finally, we showed that STAT3 is required for the expression of these genes in a breast cancer cell line. Taken together, these results identify a cohort of STAT3 targets that may mediate its role in oncogenesis.
Observation of Periodic Fine Structure in Reflectance from Biological Tissue: A New Technique for Measuring Nuclear Size Distribution (1998)

We report observation of a fine structure component in backscattered light from mucosal tissue which is periodic in wavelength. This structure is ordinarily masked by a diffusive background. We have identified the origin of this component as being due to light which is Mie scattered by surface epithelial cell nuclei. By analyzing the amplitude and frequency of the fine structure, the density and size distribution of these nuclei can be extracted. These quantities are important indicators of neoplastic precancerous changes in biological tissue.
Herpes simplex virus mRNA species mapping in EcoRI fragment I (1982)

We described the detailed characterization and high-resolution mapping of nine herpes simplex virus type 1 mRNAs encoded in EcoRI fragment I. Four of these mRNAs are partially colinear and encode the same sized polypeptide in vitro. Nucleotide sequence analysis of the DNA around the 5' ends of these mRNAs suggested that the larger may encode a small (ca. 100-dalton) polypeptide not resolvable by in vitro translation.
MESOSCOPIC SUPERCONDUCTOR SEMICONDUCTOR HETEROSTRUCTURES (1994)

A summary is given of recent results on carrier transport in mesoscopic conductors with superconducting electrodes. Three-dimensional transport in the diffusive limit is studied with crystalline silicon membranes sandwiched between two niobium electrodes or between one electrode superconducting and one normal. At low temperatures, inelastic scattering is negligible in the intermediate silicon layer. At finite voltages the distribution of electrons over the energies in the silicon is found to be strongly nonthermal, with details depending on the interplay between Andreev scattering and elastic scattering at the interfaces. At small voltages, well below the gap-voltage, transport is phase-coherent. A supercurrent is found if both electrodes are superconducting, provided the membrane is thin enough. If only one electrode is superconducting or for thick membranes an enhanced conductance is observed, which decreases with increasing voltage and magnetic field. Two-dimensional transport and the ballistic regime are being studied by using InAs- and GaAs-based heterostructures. Various interesting theoretical predictions have been made and some novel phenomena have been discovered experimentally. Interesting new phenomena have also been found in mesoscopic normal metals with superconducting electrodes.
One‐Step Fast Synthesis of Li 4 Ti 5 O 12 Particles Using an Atmospheric Pressure Plasma Jet (2013)

A one‐step process to fabricate crystalline Li 4 Ti 5 O 12 ( LTO ) particles directly from solution using an atmospheric pressure plasma jet ( APPJ ) is reported. This process uses Ti and Li ions‐containing salt solutions as the precursor, which is ultrasonically nebulized and then transported to the downstream of the APPJ using a carrier gas. With an extremely short contact time (&lt;0.1 s) between the precursor droplets and the plasma jet, crystalline LTO can be fabricated in one step without additional rinse and postannealing steps. The LTO particle size can be effectively controlled using a preheater, the precursor solution composition and concentration, and the carrier gas flow rate. By properly adjusting the operating condition, particles of diameters from 100 nm to few μm with various morphologies can be obtained. When used as an electrode material, the resulting LTO powders fabricated under selected conditions show specific capacities over 100 mAh/g even at 50 C rate.
Probabilistic Multicast: Generalizing the Multicast Paradigm to Improve Scalability (2005)

The article considers the multicast-to-some generalization of the traditional multicast paradigm. In this form of communication, a multicast group is still associated with each multicast message. It is, however, only necessary for any randomly determined subset of the multicast group to receive a multicast message. This subset is not defined a priori nor is it necessarily the same from one multicast to the next for the same group. It explores the use of this probabilistic multicast communication paradigm to address scalability issues in the response collection application which arises in some distributed computing applications. It also shows how this form of multicast can be used to reduce the discarding of responses to the multicast message due to buffer overflow at the multicast source. >
Visual outcomes and patient satisfaction with a rotational asymmetric refractive intraocular lens for emmetropic presbyopia (2015)

Dr. Schallhorn is a consultant to Abbott Medical Optics. No other author has a financial or proprietary interest in any material or method mentioned.
A simple synthesis of dienones via isomerization of alkynones effected by palladium catalysts (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA simple synthesis of dienones via isomerization of alkynones effected by palladium catalystsBarry M. Trost and Thomas. SchmidtCite this: J. Am. Chem. Soc. 1988, 110, 7, 2301–2303Publication Date (Print):March 1, 1988Publication History Published online1 May 2002Published inissue 1 March 1988https://doi.org/10.1021/ja00215a051RIGHTS & PERMISSIONSArticle Views1461Altmetric-Citations132LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (394 KB) Get e-Alerts Get e-Alerts
Vascular cells respond differentially to transforming growth factors beta 1 and beta 2 in vitro. (1991)

Transforming growth factor beta 1 (TGF-beta 1) and beta 2 (TGF-beta 2) are equipotent in many cell systems studies thus far. Recent data, however, show different effects elicited by these two growth factors in specific biologic systems. This investigation compares the effects of TGF-beta 1 and TGF-beta 2 bovine aortic endothelial cells (BAECs), rat epididymal fat pad microvascular endothelium (RFCs), and bovine aortic smooth muscle cells (BASCs). In two-dimensional cultures, proliferation of BAECs, BASMCs, and RFCs were all inhibited by TGF-beta 1, while in response to TGF-beta 2, BASMCs were fully inhibited, RFCs were modestly inhibited, and BAECs were unaffected. Bovine aortic endothelial cell migration was significantly inhibited by TGF-beta 1, but only slightly inhibited by TGF-beta 2. In contrast, BASMC migration was enhanced by TGF-beta 1 and was not affected by TGF-beta 2. In three-dimensional cultures, RFCs were stimulated to undergo in vitro angiogenesis in response to TGF-beta 1 and TGF-beta 2 at 10-fold higher concentrations. Three distinct receptor assays demonstrated the presence of type I and type II TGF-beta 1 cell-surface-binding proteins on BAECs, BASMCs, and RFCs. Labeled TGF-beta 1 was competed off completely with 100-fold molar excess unlabeled TGF-beta 1, but only partially with equivalent excess unlabeled TGF-beta 2. Furthermore the ratios of type I to type II TGF-beta receptors in these three vascular cell types vary from 1:1 in BAECs to 1.5:1 in RFCs to 3:1 in BASMCs and can be correlated with the differences noted in cellular responses to TGF-beta 1 and TGF-beta 2 in proliferation, migration, and in vitro angiogenic assays. These findings support the hypothesis that there are different responses to the TGF-beta s, depending on the cell type and experimental conditions as well as the TGF-beta concentration and isoform used.
Percutaneous sequential bacillus Calmette-Guèrin and mitomycin C for panurothelial carcinomatosis. (2005)

A 59 year old male presented with a 4 month history of lower urinary tract symptoms. Exhaustive urological investigations revealed papillary tumors and carcinoma in situ extending from the prostatic urethra, throughout the bladder, up both ureters and into the renal pelves. Tumors were resected where possible and then bacillus Calmette-Guèrin (BCG) and mitomycin C (MMC) were infused sequentially through bilateral nephrostomy tubes for a total of six BCG and three MMC instillations. Follow up 1 month post treatment demonstrated a complete response which persisted for 2 years. Then there appeared a solitary papillomatous recurrence in the bladder which was successfully resected. Side effects were the occasional fever and BCG induced granulomatous prostatitis which slowly resolved. In conclusion, sequential BCG/MMC instillations were effective treatment for widespread panurothelial carcinomatosis.
Electronic dispersion compensation by signal predistortion using digital Processing and a dual-drive Mach-Zehnder Modulator (2005)

We propose and investigate a novel electronic dispersion compensation technique, in which signal precompensation is achieved using a dual-drive Mach-Zehnder modulator, driven by adaptive nonlinear digital filters. The results demonstrate effective compensation of over 13600 ps/nm, equivalent to 800 km of standard single-mode fiber, at 10 Gb/s.
O‐linked N‐acetylglucosamine levels in cerebellar neurons respond reciprocally to pertubations of phosphorylation (1999)

The novel intracellular carbohydrate O-linked N-acetylglucosamine (O-GlcNAc) is present on proteins ranging from those of viruses to those of humans and include cytosolic, nuclear and plasma-membrane proteins. In this report we have examined the effect of manipulation of phosphorylation on the levels of O-GlcNAc in cerebellar neurons from early postnatal mice. Our results indicate a reciprocal response of O-GlcNAc levels to phosphorylation. Activation of protein kinase A or C, for example, results in reduced levels of O-GlcNAc specifically in the fraction of cytoskeletal and cytoskeleton-associated proteins, while inhibition of the same kinases results in increased levels of O-GlcNAc. These data are in keeping with a reciprocal action of O-GlcNAc with respect to phosphorylation and suggest that this modification may have a role in signal transduction.
Zur Reaktivität von C =N-Doppelbindungssystemen, VI Reaktionen mit Sulfonamiden und Sulfamiden / The Reactivity of the C=N-Double Bond System, VI Reactions with Sulfonamides and Sulfamides (1975)

Benzenesulfonic amide reacts with N-methylene-tert-butylamine and acetic anhydride in boiling benzene to give 5-tert-butyl-1,3-benzenesulfonyl-perhydro-1,3,5-triazine. Sulfamide, and benzylidene aniline, and acetic anhydride (1:1:1) yield N-benzylidene sulfamide, or (1:2:2) N,N′-bis-benzylidene sulfamide.