gebhart/patrepeval huggingface dataset:
Circulating micro‐RNA expression profiles in early stage nonsmall cell lung cancer (2011)

Circulating micro-RNA (miR) profiles have been proposed as promising diagnostic and prognostic biomarkers for cancer, including lung cancer. We have developed methods to accurately and reproducibly measure micro-RNA levels in serum and plasma. Here, we study paired serum and plasma samples from 220 patients with early stage nonsmall cell lung cancer (NSCLC) and 220 matched controls. We use qRT-PCR to measure the circulating levels of 30 different miRs that have previously been reported to be differently expressed in lung cancer tissue. Duplicate RNA extractions were performed for 10% of all samples, and micro-RNA measurements were highly correlated among those duplicates. This demonstrates high reproducibility of our assay. The expressions of miR-146b, miR-221, let-7a, miR-155, miR-17-5p, miR-27a and miR-106a were significantly reduced in the serum of NSCLC cases, while miR-29c was significantly increased. No significant differences were observed in plasma of patients compared with controls. Overall, expression levels in serum did not correlate well with levels in plasma. In secondary analyses, reduced plasma expression of let-7b was modestly associated with worse cancer-specific mortality in all patients, and reduced serum expression of miR-223 was modestly associated with cancer-specific mortality in stage IA/B patients. MiR profiles also showed considerable differences comparing African American and European Americans. In summary, we found significant differences in miR expression when comparing cases and controls and find evidence that expression of let-7b is associated with prognosis in NSCLC.
Nonalcoholic Fatty Liver Disease: Pathologic Patterns and Biopsy Evaluation in Clinical Research (2012)

Nonalcoholic fatty liver disease (NAFLD) results in histologically complex specific and nonspecific injury patterns. In clinical research of NAFLD, the liver biopsy evaluation provides a wealth of information on the architectural arrangement and severity of a variety of histologic changes, including steatosis, inflammation, cellular injury, and fibrosis. This information is summarized as an overall diagnostic category, such steatosis or steatohepatitis and the severity of the injury can be graded and staged. Histopathologic disease classification in NAFLD is related to but separate from evaluation of individual histologic lesions. The patient population under study may affect the prevalence of histologic findings and in particular, pediatric patients with NAFLD may show a higher prevalence of zone 1 steatosis and periportal fibrosis as compared with adult populations. For the purposes of clinical research, it is important to provide the pathologist with biopsies that are adequate to classify the disease process as well as to grade and stage the changes. A current understanding of NAFLD pathologic classification, as well as nuances of grading and staging, is presented in this review.
Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers (1991)

Polymorphisms in genomic fingerprints generated by arbitrarily primed PCR (AP-PCR) can distinguish between slightly divergent strains of any organism. Single oligodeoxyribonucleotide (oligo) primers have been used to generate such fingerprints, with the same primer being present at the 5' end of both strands for every PCR product. We used three arbitrary oligos, individually and in pairs, to generate six different genomic fingerprints of the same mouse genomic DNAs. Fewer than half of the products in genomic fingerprints generated using the oligos in pairs were the same as those produced by AP-PCR using one of the three oligos alone. Thus, a few oligos could be used in a very large number of single and pairwise combinations, each producing a distinct AP-PCR fingerprint with the potential to identify new polymorphisms. For example, 50 oligos can be used in a matrix of pairwise combinations to produce 2,500 fingerprints, in which at least half the data can be expected to be unique to each pair. We demonstrate this principle by using two oligos, alone and together, to generate three sets of fingerprints and map thirteen polymorphisms in the C57BL/6J x DBA/2J set of recombinant inbred mice.
Arabidopsis FAD2 Gene Encodes the Enzyme That Is Essential for Polyunsaturated Lipid Synthesis (1994)

John Okuley, Jonathan Lightner, Kenneth Feldmann, Narendra Yadav, Ellen Lark, John Browse, Arabidopsis FAD2 Gene Encodes the Enzyme That Is Essential for Polyunsaturated Lipid Synthesis, The Plant Cell, Vol. 6, No. 1 (Jan., 1994), pp. 147-158
Modeling and simulation of the heat transfer in a thermal battery (2006)

Thermal batteries are primary disposable systems specially designed to develop a high energy density in during a short period. Differently from the classical electrochemical systems, the electrolyte of such batteries is solid at room temperature, which make them inert until they are heated to high temperatures (around 500ºC), when the electrolyte melts and begins to exhibit enough ionic mobility to establish electric current. The present work was devoted to developing a transient model of the heat generation and propagation within a second generation thermal battery, aiming the creation of a tool suitable for the research and development of such systems. The commercial CFD software Phoenics® was used and, through a typical finite volume approach, the related 2-D transport equations were solved, giving the time-dependent temperature profiles. The results show that the temperature of pseudo equilibrium state of these studied batteries are in accordance with the temperature related in the literature, and the fusion of electrolytes is a process virtually instantaneous when compared with the time to reach that state, allowing in this way to advance that the generation of electrical current occurs immediately after the termites actuation.
Induced Immunity to Plant Disease (1982)

Journal Article Induced Immunity to Plant Disease Get access Joseph Kuć Joseph Kuć Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 32, Issue 11, December 1982, Pages 854–860, https://doi.org/10.2307/1309008 Published: 01 December 1982 Article history Accepted: 18 June 1982 Published: 01 December 1982
Lethal Effects of Heat and Use of Localized Heat Treatment for Control of Bed Bug Infestations (2009)

Bed bugs, Cimex lectularius L., hide in cracks and crevices in furniture and are difficult to control. The bed bug thermal death kinetics were examined to develop a heat treatment method to eliminate bed bug infestations in room contents. High temperatures caused temporary immobilization (knockdown) of bed bugs even with exposures that did not have lethal effects. Exposure of bed bug adults to 39 degrees C for 240 min caused no mortality; however, as temperatures increased from 41 to 49 degrees C, exposure times that caused 100% mortality decreased. The temperature difference to provide a 10-fold change in the mortality was estimated at 4 degrees C, and the estimated activation energy (EA) was between 484 and 488.3 kJ/mol. This demonstrates that bed bugs are not more resistant or susceptible to changes in temperature than other tested insects and that the temperatures needed to kill bed bugs are relatively low. In room treatment tests, heat treatment times varied from 2 to 7 h with complete mortality of exposed bed bugs within the treatment envelope created by surrounding the treated furniture with polystyrene sheathing boards. Containment and circulation of heat around the treated material were crucial factors in an efficient heat treatment for bed bug control. The room floor material greatly affected containment of the heat. The tested method for limited heat treatment of furniture and other room contents required equipment costing less than US$400 and provided opportunity for residual pesticide application around the room with minimal disruption in use of treated room.
Assessment of local structural disorders of the bladder wall in partial bladder outlet obstruction using polarized light imaging (2014)

Partial bladder outlet obstruction causes prominent morphological changes in the bladder wall, which leads to bladder dysfunction. In this paper, we demonstrate that polarized light imaging can be used to identify the location of obstruction induced structural changes that other imaging modalities fail to detect. We induced 2-week and 6-week partial outlet obstruction in rats, harvested obstructed bladders, then measured their retardances while distended to high pressures and compared them to controls. Our results show that the retardance of the central part of the ventral side (above the ureters) closer to the urethra can be used as a potential metric of the distending bladder obstruction.
Identification of a series of potent telomerase inhibitors using a time-resolved fluorescence-based assay (1998)

A high-throughput, nonradioactive telomerase assay using a europium-labeled oligonucleotide probe and time-resolved fluorescence has been developed to detect PCR-amplified telomerase products. The use of a thermally activated TAQ polymerase, rather than a wax barrier, to implement a PCR hot-start facilitated the use of laboratory automation equipment. Results obtained with this high-throughput protocol correlate well with those obtained with the TRAP protocol. Screening a set of 125,000 compounds from the Berlex library, we identified a set of isothiazolone-containing telomerase inhibitors. The most potent of these inhibitors have submicromolar IC50 values and may be reacting with a telomerase thiol. These compounds may be useful tools to evaluate the effects of telomerase in cancer cells. Drug Dev. Res. 43:109–116, 1998. © 1998 Wiley-Liss, Inc.
Random pharmacokinetic profiles of EC-MPS in children with autoimmune disease (2010)

: EC-MPS has a different PK profile from MMF. The data suggest that patients on EC-MPS must undergo a complete PK profile to assess adequate exposure. The 6-hour concentration provides an estimate of the exposure and should be targeted between 3-4 mg/L.
Emission in the deep vacuum ultraviolet from a plasma formed by incandescently heating hydrogen gas with trace amounts of potassium carbonate (2003)

A hydrogen plasma with intense extreme ultraviolet and visible emission was generated from low pressure hydrogen gas (0.1–1 mbar) in contact with a hot tungsten filament only when the filament heated a titanium dissociator coated with K2CO3 above 750°C. The electric field strength from the filament was about 1 V cm−1, two orders of magnitude lower than the starting voltages measured for gas glow discharges. The emission of the Hα and Hβ transitions as well as the Lα and Lβ transitions were recorded and analysed. The plasma seemed to be far from thermal equilibrium, and no conventional mechanism was found to explain the formation of a hydrogen plasma by incandescently heating hydrogen gas in the presence of trace amounts of K2CO3. The temporal behaviour of the plasma was recorded via hydrogen Balmer alpha line emission when all power into the cell was terminated and an excessive afterglow duration (2 s) was observed. The plasma was found to be dependent on the chemistry of atomic hydrogen with potassium since no plasma formed with Na2CO3 replacing K2CO3 and the time constant of the emission following the removal of all of the power to the cell matched that of the cooling of the filament and the resulting shift from atomic to molecular hydrogen. Our results indicate that a novel chemical power source is present and that it forms the energetic hydrogen plasma that is a potential new light source.
Description of Two NewABCB11Mutations Responsible for Type 2 Benign Recurrent Intrahepatic Cholestasis in a French-Canadian Family (2011)

Benign recurrent intrahepatic cholestasis is a rare clinical entity that is caused by mutations in the canalicular transport genes. The present report describes two individuals from the same family whose symptoms were typical of the clinical characteristics of type 2 benign recurrent intrahepatic cholestasis. Sequencing of the ABCB11 gene revealed two previously unreported mutations that predict the absence of expression of the protein. The clinical presentation of the current cases are discussed, as are the differential diagnosis and genetic characteristics of the hereditary cholestatic disorders, overemphasizing the possibility of making a definite genetic diagnosis.
Carbon Dioxide Protects the Perinatal Brain From Hypoxic-Ischemic Damage: An Experimental Study in the Immature Rat (1995)

The results indicate that in an immature rat model normocapnic cerebral hypoxia-ischemia is associated with less severe brain damage than in hypocapnic hypoxia-ischemia and that mild hypercapnia is more protective than normocapnia. The findings in an experimental model merit further animal investigations as well as a clinical reappraisal of the ventilatory management of sick newborn human infants.
Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries (2007)

The FightAIDS@Home distributed computing project uses AutoDock for an initial virtual screen of HIV protease structures against a broad range of 1771 ligands including both known protease inhibitors and a diverse library of other ligands. The volume of results allows novel large-scale analyses of binding energy "profiles" for HIV structures. Beyond identifying potential lead compounds, these characterizations provide methods for choosing representative wild-type and mutant protein structures from the larger set. From the binding energy profiles of the PDB structures, a principal component analysis based analysis identifies seven "spanning" proteases. A complementary analysis finds that the wild-type protease structure 2BPZ best captures the central tendency of the protease set. Using a comparison of known protease inhibitors against the diverse ligand set yields an AutoDock binding energy "significance" threshold of -7.0 kcal/mol between significant, strongly binding ligands and other weak/nonspecific binding energies. This threshold captures nearly 98% of known inhibitor interactions while rejecting more than 95% of suspected noninhibitor interactions. These methods should be of general use in virtual screening projects and will be used to improve further FightAIDS@Home experiments.
Interferon in Oncological Practice: Review of Interferon Biology, Clinical Applications, and Toxicities (2001)

a better understanding of IFN biology, indications, side effect profiles, and toxicity management will aid in optimizing its use in the treatment of patients with cancer.
Mammalian topoisomerase II inhibitory activity of 1-cyclopropyl-6,8-difluoro-1,4-dihydro-7-(2,6-dimethyl-4-pyridinyl)-4-oxo-3-quinolinecarboxylic acid and related derivatives (1993)

1-Cyclopropyl-6,8-difluoro-1,4-dihydro-7-(2,6-dimethyl-4-pyridinyl)-4-ox o-3-quinolinecarboxylic acid (1), a previously reported potent inhibitor of bacterial DNA gyrase, was found to be interactive with mammalian topoisomerase II (topo II). In a DNA-cleavage assay using topo II isolated from HeLa cells, 1 exhibited an EC50 value of 7.6 microM (VP-16; EC50 = 0.81 microM). A series of analogues modified at the 1-, 2-, 3-, 5-, and 7-positions of 1 were subsequently made and assessed for topo II inhibition. Compound 1 was considerably more potent than derivatives where the 1-substituent was alkyl, aryl, or H, or when N-c-C3H5 was replaced with S. The descarboxyl (i.e., 3-H) analogue had potency comparable to that of 1; when both these compounds were substituted at the 2-position with methyl or phenyl, an interesting relationship between activity and the conformation of the carboxyl group emerged. Upon replacement of the 5-H of 1 with NH2 or F, sustained potency was seen. No enhancement of activity was evident upon replacing the 7-substituent of 1 with other pyridinyl groups, 4-methyl-1-piperazinyl, or pyrrolidinyl groups; however, the 7-(4-hydroxyphenyl) analogue (CP-115,953) was 6-fold more potent than 1. The topo II inhibitory properties of 1 translated to modest in vitro cytotoxicity and in vivo activity versus P388.
Laminin targeting of a peripheral nerve-highlighting peptide enables degenerated nerve visualization (2016)

Target-blind activity-based screening of molecular libraries is often used to develop first-generation compounds, but subsequent target identification is rate-limiting to developing improved agents with higher specific affinity and lower off-target binding. A fluorescently labeled nerve-binding peptide, NP41, selected by phage display, highlights peripheral nerves in vivo. Nerve highlighting has the potential to improve surgical outcomes by facilitating intraoperative nerve identification, reducing accidental nerve transection, and facilitating repair of damaged nerves. To enable screening of molecular target-specific molecules for higher nerve contrast and to identify potential toxicities, NP41's binding target was sought. Laminin-421 and -211 were identified by proximity-based labeling using singlet oxygen and by an adapted version of TRICEPS-based ligand-receptor capture to identify glycoprotein receptors via ligand cross-linking. In proximity labeling, photooxidation of a ligand-conjugated singlet oxygen generator is coupled to chemical labeling of locally oxidized residues. Photooxidation of methylene blue-NP41-bound nerves, followed by biotin hydrazide labeling and purification, resulted in light-induced enrichment of laminin subunits α4 and α2, nidogen 1, and decorin (FDR-adjusted <i>P</i> value < 10<sup>-7</sup>) and minor enrichment of laminin-γ1 and collagens I and VI. Glycoprotein receptor capture also identified laminin-α4 and -γ1. Laminins colocalized with NP41 within nerve sheath, particularly perineurium, where laminin-421 is predominant. Binding assays with phage expressing NP41 confirmed binding to purified laminin-421, laminin-211, and laminin-α4. Affinity for these extracellular matrix proteins explains the striking ability of NP41 to highlight degenerated nerve "ghosts" months posttransection that are invisible to the unaided eye but retain hollow laminin-rich tubular structures.
Geldanamycin and its analogue 17-allylamino-17-demethoxygeldanamycin lowers Bcr-Abl levels and induces apoptosis and differentiation of Bcr-Abl-positive human leukemic blasts. (2001)

HL-60/Bcr-Abl cells, with ectopic expression of p185 Bcr-Abl tyrosine kinase (TK), and K562 cells, with endogenous expression of p210 Bcr-Abl TK, display a high degree of resistance against antileukemic drug-induced apoptosis (G. Fang et al., Blood, 96: 2246-2256, 2000). Present studies demonstrate that treatment with ansamycin antibiotic geldanamycin (GA), or its less toxic analogue 17-allylamino-17-demethoxygeldanamycin (17-AAG), induces cytosolic accumulation of cytochrome c and cleavage and activities of caspase-9 and caspase-3, triggering apoptosis of HL-60/Bcr-Abl and K562 cells. GA or 17-AAG down-regulated intracellular Bcr-Abl and c-Raf protein levels, as well as reduced Akt kinase activity. Similar to Raf-1, v-Src, and Her-2-neu, Bcr-Abl TK has chaperone association with heat shock protein 90 (Hsp90). By binding and inhibiting Hsp90, GA or 17-AAG treatment shifted the binding of Bcr-Abl from Hsp90 to Hsp70 and induced the proteasomal degradation of Bcr-Abl, because cotreatment with proteasome inhibitor PSC341 reduced both GA (or 17-AAG)-mediated down-regulation of Bcr-Abl levels and inhibited apoptosis of HL-60/Bcr-Abl and K562 cells. These data establish the in vitro activity of GA and 17-AAG against Bcr-Abl-positive leukemic cells and support the in vivo investigation of 17-AAG against Bcr-Abl-positive leukemias.
Nucleotide sequence of murine purine nucleoside phosphorylase cDNA (1991)

Journal Article Nucleotide sequence of murine purine nucleoside phosphorylase cDNA Get access Jack P. Jenuth, Jack P. Jenuth Department of Medical Biochemistry, University of Calgary3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Floyd F. Snyder, Floyd F. Snyder * Department of Medical Biochemistry, University of Calgary3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar John L. Portis John L. Portis Department of Medical Biochemistry, University of Calgary3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 7, 11 April 1991, Page 1708, https://doi.org/10.1093/nar/19.7.1708 Published: 11 April 1991 Article history Received: 21 February 1991 Published: 11 April 1991
Automated Aeroponics System Using IoT for Smart Farming (2017)

In recent years, the Internet of Things (IoT) has received much attention in the areas of industry and academia. Currently, IoT technologies are being applied in many fields and is changing lives in many areas such as smart homes, smart cities, smart grids, autonomous cars, and the industrial internet. Howbeit, traditional agriculture is still waiting for many changes to occur in networking technology especially in IoT. Many researchers and engineers are working towards applying IoT technology to traditional agricultural methods. Aeroponics farming is an efficient and effective process for growing plants without using soil. When we apply IoT technology to an aeroponics system, it is expected that there will be many improvements such as decreasing water usage, increasing plant yield, minimizing rate of growth and reducing the workforce. In this paper, we designed and implemented a new automatic aeroponics system using IoT devices. Our system is comprised of three main components: a mobile application, service platform and IoT devices with sensors. The mobile application provides the user a graphical user interface to monitor and adjust the aeroponics system. The service platform is a middleware system that provides information for the mobile application to store the gathered information from IoT devices using sensors within the aeroponics system. The IoT device uses sensors within the aeroponics system to control each pump and access data. Our work is a new application in the agricultural industry and is expected to be a promising application that will help the farmer with increasing productivity in farming and reducing carbon footprint.
High-dose methotrexate and/or leucovorin rescue for the treatment of children with lymphoblastic malignancies: do we really know why, when and how? (2005)

Methotrexate (MTX) remains a mainstay in the treatment of children with hematological malignancies. The availability of an antidote/rescue agent, leucovorin (LV) has allowed escalation of MTX doses to achieve enormous plasma concentrations, compared with plasma folate. However, a recent review of more than 40 trials for children with ALL concluded that the addition of high dose MTX (HDMTX) in many different doses and schedules did not improve CNS therapy and made only minor improvements in systemic therapy for children with ALL [11]. Some assessment suggested that by HDMTX benefits only limited amount of children with ALL. Recent treatment schedules vary markedly in terms of timing, dosing and scheduling of MTX and/or leukovorin, which may leave us uncertain with ideas such as "how should we best use HDMTX and LV?" or "why are we still using such by industry recommended doses of MTX?" The answer of how best to incorporate HDMTX and/or LV into ALL treatment plans is still not known and further clinical and pharmacological studies dealing with still controversial systemic MTX issue are actual even now, after more than 5 decades of clinical experiences with the MTX in pediatric oncology.