gebhart/patrepeval huggingface dataset:
Transient expression of green fluorescent protein in various plastid types following microprojectile bombardment (1998)

Summary The green fluorescent protein gene ( gfp ) is a widely used reporter in both animals and plants. Fusions between the plastid rrn promoter or the Escherichia coli trc promoter and the gfp coding region have been delivered to chloroplasts using gold or tungsten microprojectiles, and fluorescence from GFP was visible in individual tobacco chloroplasts and in the abnormally large chloroplasts of the arc 6 mutant of Arabidopsis thaliana 2–4 days after bombardment. The fusion of the gfp coding region to the bacterial trc promoter demonstrated that a bacterial promoter is active in chloroplasts in vivo . GFP was also detectable in amyloplasts of potato tubers and in chromoplasts of marigold petals, carrot roots and pepper fruits 4 days after bombardment. This demonstrates that GFP can be used as a reporter for transient gene expression in chloroplasts and in non‐photosynthetic plastids in a range of higher plants.
Linkage analysis and long QT syndrome. Using genetics to study cardiovascular disease. (1992)

The identification of the chromosomal location of the long QT locus is the first step in defining the specific mutations that cause this disease.
Diagnosis and treatment of acne. (2004)

Acne can cause significant embarrassment and anxiety in affected patients. It is important for family physicians to educate patients about available treatment options and their expected outcomes. Topical retinoids, benzoyl peroxide, sulfacetamide, and azelaic acid are effective in patients with mild or moderate comedones. Topical erythromycin or clindamycin can be added in patients with mild to moderate inflammatory acne or mixed acne. A six-month course of oral erythromycin, doxycycline, tetracycline, or minocycline can be used in patients with moderate to severe inflammatory acne. A low-androgen oral contraceptive pill is effective in women with moderate to severe acne. Isotretinoin is reserved for use in the treatment of the most severe or refractory cases of inflammatory acne. Because of its poor side effect profile and teratogenicity, isotretinoin (Accutane) must by prescribed by a physician who is a registered member of the manufacturer's System to Manage Accutane-Related Teratogenicity program.
Immune complex–mediated antigen presentation induces tumor immunity (2002)

Antigen uptake receptors on dendritic cells (DCs) provide efficient entry for the initiation of antigen-specific adaptive immunity. Here we show that targeting of antigen to Fc receptors on DCs accomplishes combined activation of Th1 CD4 and CD8 effector responses in vivo, namely delayed-type hypersensitivity and tumor immunity. Tumor immunity specific for ovalbumin-expressing tumors was provided by immunization with wild-type but not FcγRγ–/– DCs loaded with ovalbumin-containing immune complexes. Tumor protection was eliminated when immune complex–loaded DCs lacked β2 microglobulin, TAP, or MHC class II, demonstrating that Fc receptor–targeted antigenic uptake led to both MHC class I– and class II–restricted responses, which together are required for effector tumor immunity. Thus the cross-presentation pathway accessed by antigens acquired endocytically through Fc receptors links humoral and cellular immunity. These data suggest that administration of antitumor antibodies may enhance tumor-specific T cell responses in vivo and provide the rationale for Fc receptor targeting in vaccine development.
MetaSim—A Sequencing Simulator for Genomics and Metagenomics (2008)

MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.
Interaction of cations with phosphate uptake by Saccharomyces cerevisiae. Effects of surface potential (1979)

The effect of bivalent cations on phosphate uptake by Saccharomyces cerevisiae was investigated. Phosphate uptake via the Na+-dependent transport system at pH 7.2 is stimulated by bivalent cations. The apparent affinity of phosphate for the transport mechanism is increased, but the apparent affinity for Na+ is decreased. Uptake of phosphate via the Na+-independent transport system is accompanied by a net proton influx of 2H+ and an efflux of 1 K+ for each phosphate ion taken up. At pH 4.5 phosphate uptake via the Na+-independent system is stimulated by bivalent cations, whereas at pH 7.2 uptake is inhibited. The effect of bivalent cations on phosphate uptake can be ascribed to a decrease in the surface potential.
Transmission of chronic spongiform encephalopathy with kuru plaques from humans to small rodents (1979)

An unusual case of spongiform encephalopathy was transmitted directly from a human to rats and mice. After serial passages, incubation periods were shortened to about six months in rats and four months in mice. Clinical symptoms were similar in rats and mice, including ruffled fur, arched back, bradykinesia, and hind limb paralysis. Pathologically, a spongy state, proliferation of astrocytes, and neuronal changes were observed. Electron microscopic observation of the parietal cortex of rats and mice disclosed many membrane-bound vacuoles in the neuropil, predominantly in dendrites. In the pons of mice, intramyelinic vacuoles and accumulation of extracellular fluid were prominent. The clinicopathological symptoms of the affected animals resembled those in other experimental spongiform encephalopathies, especially scrapie.
Excess Quantum Noise Fluctuations in Unstable-resonator Lasers (1996)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Yuh-Jen Cheng, Paul Mussche, Geoff Fanning, and A. E. Siegman, "Excess Quantum Noise Fluctuations in Unstable-resonator Lasers," Optics & Photonics News 7(12), 16-17 (1996) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Gastric Cancer Associated with Gastritis Cystica Profunda in Patients without Previous Gastric Surgery (2010)

Gastritis cystica profunda (GCP) is an uncommom hyperplastic lesion, which is located within the submucosa. GCP may occur several years after previous gastric surgery. In some reported cases, it was a premalignant condition and may lead to carcinoma of the stomach. We report a case of a 54-year-old man with epigastric pain and dyspepsia. He had undergone peritoneal dialysis for end stage renal disease about 13 years prior. An Upper gastrointestinal endoscopy showed elevated lesion at the gastric antrum, looking like an advanced gastric cancer or gastrointestinal stromal tumor. Endoscopic biopsy results were tubular adenoma with low-grade dysplasia. When followed up 9 months later, the lesion had increased in size and symptoms remained. We therefore performed a subtotal gastrectomy. The final biopsy was adenocarcinoma arising in GCP. (J Korean Surg Soc 2010;79:S26-30)
A 14-ns 14-Mb CMOS DRAM with 300-mW active power (1992)

A 4-Mb high-speed DRAM (HSDRAM) has been developed and fabricated by using 0.7- mu m L/sub eff/ CMOS technology with PMOS arrays inside n-type wells and p-type substrate plate trench cells. The 13.18-mm*6.38-mm chip, organized as either 512 K word*8 b or 1 M word*4 b, achieves a nominal random-access time of 14 ns and a nominal column-access time of 7 ns, with a 3.6-V V/sub cc/ and provision of address multiplexing. The high level of performance is achieved by using a short-signal-path architecture with center bonding pads and a pulsed sensing scheme with a limited bit-line swing. A fast word-line boosting scheme and a two-stage word-line delay monitor provide fast word-line transition and detection. A new data output circuit, which interfaces a 3.6-V V/sub cc/ to a 5-V bus with an NMOS-only driver, also contributes to the fast access speed by means of a preconditioning scheme and boosting scheme. Limiting the bit-line voltage swing for bit-line sensing results in a low power dissipation of 300 mW for a 60-ns cycle time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
<title>Quantitative Materials Evaluation And Inspection With The Image Analysing Computer</title> (1972)

Many important quality tests on materials and components are made by visual assessment. Operators use microscopes to make visual assessments to describe, for example, the non-metallic inclusion content of steel or the grain size in a variety of materials. Human inspectors frequently have to watch miles of fast moving strips of paper, steel, cloth and other materials to spot and record visible defects. Also, Exr example, electron micrographs are examined to determine particle size distributions and radiographs are inspected visually to evaluate porosity.
The open agent architecture: A framework for building distributed software systems (1999)

T he Open Agent Architecture (OAA), developed and used for several years at SRI International, makes it possible for software services to be provided through the cooperative e orts of distributed collections of autonomous agents.Communication and cooperation between agents are brokered by one or more facilitators, which are responsible for matching requests, from users and agents, with descriptions of the capabilities of other agents.T hus it is not generally required that a user or agent know the identities, locations, or number of other agents involved in satisfying a request.OAA is structured so as to minimize the e ort involved in creating new agents and ''wrapping'' legacy applications, written in various languages and operating on various platforms ; to encourage the reuse of existing agents ; and to allow for dynamism and exibility in the makeup of agent communities.Distinguishing features of OAA as compared with related work include extreme exibility in using facilitator-based delegation of complex goals, triggers, and data management requests ; agent-based provision of multimodal user interfaces ; and built-in support for including the user as a privileged member of the agent community.T his article explains the structure and elements of agent-based systems constructed using OAA.T he characteristics and use of each major component of OAA infrastructure are described, including the agent library, the Interagent Communication Language, capabilities declarations, service requests, facilitation, management of data repositories, and autonomous monitoring using triggers.T o provide technical context, we describe the motivations for OAA's design, and situate its features within the realm of alternative software paradigms.A summary is given of OAA-based systems built to date, and brief descriptions are given of several of these.The evolution of models for the design and construction of software systems is being driven forward by several closely interrelated trends : adoption of a networked computing model is leading to a greatly d The increased reliance on distributed sites for both data and processing
Safety and efficacy of nivolumab in the treatment of cancers: A meta‐analysis of 27 prospective clinical trials (2016)

Immune checkpoint inhibition therapy has benefited people and shown powerful anti-tumor activity during the past several years. Nivolumab, a fully human IgG4 monoclonal antibody against PD-1, is a widely studied immune checkpoint inhibitor for the treatment of cancers. To assess the safety and efficacy of nivolumab, 27 clinical trials on nivolumab were analyzed. Results showed that the summary risks of all grade adverse effects (AEs) and grade ≥3 AEs were 0.65 and 0.12. The rate of nivolumab-related death was 0.25%. The most common any grade AEs were fatigue (25.1%), rush (13.0%), pruritus (12.5%), diarrhea (12.1%), nausea (11.8%) and asthenia (10.4%). The most common grade ≥3 AEs were hypophosphatemia (only 2.3%) and lymphopenia (only 2.1%). The pooled objective response rate (ORR), 6-month progression-free survival (PFS) rate and 1-year overall survival (OS) rate were 0.26, 0.40 and 0.52, respectively. The odds ratio of ORR between PD-L1 positive and negative was 2.34 (95% CI 1.77-3.10, p < 0.0001). The odds ratios of ORR, 6-month PFS rate and 1-year OS rate between nivolumab and chemotherapeutics were 2.77 (95% CI 1.69-4.56, p < 0.0001), 1.97 (95% CI 1.02-3.81, p = 0.04) and 1.87 (95% CI 1.46-2.40, p <0.0001), respectively. In conclusion, nivolumab has durable outcomes with tolerable AEs and drug-related deaths in cancer patients. Nivolumab monotherapy has better treatment response compared with chemotherapy, whereas chemotherapeutics have significantly higher risk of adverse effects than nivolumab.
Oxygen saturation and breathing patterns in infancy. 2: Preterm infants at discharge from special care. (1991)

Overnight 12 hour tape recordings of arterial oxygen saturation (SaO2, pulse oximeter in the beat to beat mode), breathing movements, and airflow were made on 66 preterm infants (median gestational age 34 weeks, range 25-36) who had reached term (37 weeks) and were ready for discharge from the special care baby unit. No infant was given additional inspired oxygen during the study. The median baseline SaO2 was 99.4% (range 88.9-100%). Eight infants had baseline SaO2 values below 97%, the lowest value observed in a study on full term infants. All but one infant had short-lived falls in SaO2 to less than or equal to 80% (desaturations), which were more frequent (5.4 compared with 0.9/hour) and longer (mean duration 1.5 compared with 1.2 seconds) than in full term infants. There was no evidence that gestational age at birth influenced the frequency or duration of desaturations among the preterm infants. The frequency of relatively prolonged episodes of desaturation (SaO2 less than or equal to 80% for greater than or equal to 4 seconds), however, decreased significantly with increasing gestational age (0.5, 0.4, 0.2, and 0.1 episodes/hour in infants at less than or equal to 32, 33-34, 35, and 36 weeks' gestational age, respectively). Analysis of the respiratory patterns associated with such episodes showed that 5% occurred despite both continued breathing movements and continuous airflow. Five infants had outlying recordings: three had baseline SaO2 values of less than 95% (88.9, 92.7, and 93.8%), and two had many prolonged desaturations (14 and 92/hour; median for total group 0.2, 95th centile 2.3). None of these five infants had been considered clinically to have dis order of oxygenation. Although these data are insufficient to provide information about outcome, we conclude that reference data on arterial oxygenation in preterm infants are important to enable the identification of otherwise unrecognized hypoxaemia.
Mild traumatic brain injury: a risk factor for neurodegeneration (2010)

Recently, it has become clear that head trauma can lead to a progressive neurodegeneration known as chronic traumatic encephalopathy. Although the medical literature also implicates head trauma as a risk factor for Alzheimer's disease, these findings are predominantly based on clinical diagnostic criteria that lack specificity. The dementia that follows head injuries or repetitive mild trauma may be caused by chronic traumatic encephalopathy, alone or in conjunction with other neurodegenerations (for example, Alzheimer's disease). Prospective longitudinal studies of head-injured individuals, with neuropathological verification, will not only improve understanding of head trauma as a risk factor for dementia but will also enhance treatment and prevention of a variety of neurodegenerative diseases.
High-performance and scalable on-chip digital Fourier transform spectroscopy (2018)

On-chip spectrometers have the potential to offer dramatic size, weight, and power advantages over conventional benchtop instruments for many applications such as spectroscopic sensing, optical network performance monitoring, hyperspectral imaging, and radio-frequency spectrum analysis. Existing on-chip spectrometer designs, however, are limited in spectral channel count and signal-to-noise ratio. Here we demonstrate a transformative on-chip digital Fourier transform spectrometer that acquires high-resolution spectra via time-domain modulation of a reconfigurable Mach-Zehnder interferometer. The device, fabricated and packaged using industry-standard silicon photonics technology, claims the multiplex advantage to dramatically boost the signal-to-noise ratio and unprecedented scalability capable of addressing exponentially increasing numbers of spectral channels. We further explore and implement machine learning regularization techniques to spectrum reconstruction. Using an 'elastic-D<sub>1</sub>' regularized regression method that we develop, we achieved significant noise suppression for both broad (>600 GHz) and narrow (<25 GHz) spectral features, as well as spectral resolution enhancement beyond the classical Rayleigh criterion.
Transmembrane Transport of Endo- and Xenobiotics by Mammalian ATP-Binding Cassette Multidrug Resistance Proteins (2006)

Multidrug Resistance Proteins (MRPs), together with the cystic fibrosis conductance regulator (CFTR/ABCC7) and the sulfonylurea receptors (SUR1/ABCC8 and SUR2/ABCC9) comprise the 13 members of the human "C" branch of the ATP binding cassette (ABC) superfamily. All C branch proteins share conserved structural features in their nucleotide binding domains (NBDs) that distinguish them from other ABC proteins. The MRPs can be further divided into two subfamilies "long" (MRP1, -2, -3, -6, and -7) and "short" (MRP4, -5, -8, -9, and -10). The short MRPs have a typical ABC transporter structure with two polytropic membrane spanning domains (MSDs) and two NBDs, while the long MRPs have an additional NH2-terminal MSD. In vitro, the MRPs can collectively confer resistance to natural product drugs and their conjugated metabolites, platinum compounds, folate antimetabolites, nucleoside and nucleotide analogs, arsenical and antimonial oxyanions, peptide-based agents, and, under certain circumstances, alkylating agents. The MRPs are also primary active transporters of other structurally diverse compounds, including glutathione, glucuronide, and sulfate conjugates of a large number of xeno- and endobiotics. In vivo, several MRPs are major contributors to the distribution and elimination of a wide range of both anticancer and non-anticancer drugs and metabolites. In this review, we describe what is known of the structure of the MRPs and the mechanisms by which they recognize and transport their diverse substrates. We also summarize knowledge of their possible physiological functions and evidence that they may be involved in the clinical drug resistance of various forms of cancer.
Evaluation of novel strategies to combat hepatitis B virus targetting wild-type and drug-resistant mutants in experimental models. (2001)

Recent studies have shown that the kinetics of hepatitis B virus (HBV) clearance during antiviral therapy are slow, requiring long-term therapy to control viral replication. It has also been shown that emergence of resistant mutants is accelerated by high HBV replication and hepatocyte turnover, which are common features in patients with chronic HBV infection. It is therefore important to continue research on novel antiviral agents to design optimal combination strategies. The duck and woodchuck models of hepadnavirus infection are currently the best models for the investigation of the inhibitory effect of nucleoside analogues on wild-type and lamivudine-resistant mutants. Our studies revealed that these mutants have a decreased priming and elongation activity, and remain sensitive to novel nucleoside analogues. Tissue culture experiments with transient transfection of wild-type and mutant viruses also confirmed these data. Infection studies in primary hepatocytes and in animal models gave insight into the pathobiology of lamivudine-resistant mutants, as well as into the kinetics of wild-type virus clearance during antiviral therapy. Furthermore, it appears that novel strategies inducing a specific anti-HBV immune response by a DNA vaccine approach may induce viral clearance. Altogether, these results suggest that: (i) lamivudine-resistant mutants are likely to be cross-resistant to other L-cytidine analogues; (ii) antiviral therapy using a single reverse transcriptase (RT) inhibitor is likely to fail to eradicate viral covalently closed circular DNA; and (iii) new nucleoside analogues with unique mode of action (inhibition of priming or elongation of RT, or DNA polymerase activity) and activity against lamivudine-resistant strains are emerging. Combination of these new anti-HBV agents with DNA based immunization may prove useful to eradicate viral infection.
Mechanisms of resistance to drugs that inhibit DNA topoisomerases. (1991)

DNA topoisomerases are essential nuclear enzymes that are involved in DNA replication. Clinically useful antitumor drugs such as doxorubicin, daunorubicin (anthracyclines), etoposide, teniposide (epipodophyllotoxins), and amsacrine (an aminoacridine) interfere with the function of topoisomerase II and camptothecin and its analogs inhibit topoisomerase I. Some mammalian tumor cells that express resistance to drugs that interfere with topoisomerase I or topoisomerase II have alterations in their respective topoisomerases. In this paper, we review the functions of the topoisomerases, discuss aspects of their cellular regulation, ask how interference with topoisomerase function can lead to tumor cell death, discuss the biochemical features of tumor cells that are resistant to these anti-topoisomerase drugs, and, in the context of drug resistance, we raise questions about how these drugs exert their cytotoxicity.
Human Plasma Protein C (1979)

Protein C is a vitamin K-dependent protein, which exists in bovine plasma as a precursor of a serine protease. In this study, protein C was isolated to homogeneity from human plasma by barium citrate adsorption and elution, ammonium sulfate fractionation, DEAE-Sephadex chromatography, dextran sulfate agarose chromatography, and preparative polyacrylamide gel electrophoresis. Human protein C (M(r) = 62,000) contains 23% carbohydrate and is composed of a light chain (M(r) = 21,000) and a heavy chain (M(r) = 41,000) held together by a disulfide bond(s). The light chain has an amino-terminal sequence of Ala-Asn-Ser-Phe-Leu- and the heavy chain has an aminoterminal sequence of Asp-Pro-Glu-Asp-Gln. The residues that are identical to bovine protein C are underlined. Incubation of human protein C with human alpha-thrombin at an enzyme to substrate weight ratio of 1:50 resulted in the formation of activated protein C, an enzyme with serine amidase activity. In the activation reaction, the apparent molecular weight of the heavy chain decreased from 41,000 to 40,000 as determined by gel electrophoresis in the presence of sodium dodecyl sulfate. No apparent change in the molecular weight of the light chain was observed in the activation process. The heavy chain of human activated protein C also contains the active-site serine residue as evidenced by its ability to react with radiolabeled diisopropyl fluorophosphate. Human activated protein C markedly prolongs the kaolin-cephalin clotting time of human plasma, but not that of bovine plasma. The amidolytic and anticoagulant activities of human activated protein C were completely obviated by prior incubation of the enzyme with diisopropyl fluorophosphate. These results indicate that human protein C, like its bovine counterpart, exists in plasma as a zymogen and is converted to a serine protease by limited proteolysis with attendant anticoagulant activity.