gebhart/patrepeval huggingface dataset:
Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq (2015)

Single-cell sequencing, which is used to detect clinically important tumor subpopulations, is necessary for understanding tumor heterogeneity. Here, we analyzed transcriptomic data obtained from 34 single cells from human lung adenocarcinoma (LADC) patient-derived xenografts (PDXs). To focus on the intrinsic transcriptomic signatures of these tumors, we filtered out genes that displayed extensive expression changes following xenografting and cell culture. Then, we performed clustering analysis using co-regulated gene modules rather than individual genes to minimize read drop-out errors associated with single-cell sequencing. This combined approach revealed two distinct intra-tumoral subgroups that were primarily distinguished by the gene module G64. The G64 module was predominantly composed of cell-cycle genes. E2F1 was found to be the transcription factor that most likely mediates the expression of the G64 module in single LADC cells. Interestingly, the G64 module also indicated inter-tumoral heterogeneity based on its association with patient survival and other clinical variables such as smoking status and tumor stage. Taken together, these results demonstrate the feasibility of single-cell RNA sequencing and the strength of our analytical pipeline for the identification of tumor subpopulations.
Etoposide pharmacology. (1992)

Etoposide, a podophyllotoxin derivative, has demonstrated antitumor efficacy in a number of human malignancies, including lymphomas, germinal tumors, and lung cancer (especially small cell). Etoposide's antineoplastic activity is achieved through DNA strand breakage, which likely results from the formation of a complex involving drug, DNA, and the DNA unwinding enzyme, topoisomerase II. The drug's steady state volume of distribution ranges from 5 to 17 L/m2, and it is highly bound to plasma protein with an average free plasma fraction of 6%. A number of etoposide metabolites have been confirmed or postulated. Several cell lines have been shown to acquire resistance to etoposide through membrane transport changes. Considerable intrapatient variability exists in pharmacokinetic parameters following intravenous (IV) and oral dosing. Approximately 30% to 40% of unchanged IV drug is excreted in the urine, whereas biliary excretion appears a minor route of drug elimination. The bioavailability of oral etoposide averages 50%, although wide variability exists both among and within different patients. Bioavailability decreases as the dose of oral etoposide is increased. Several recent studies have attempted to correlate etoposide plasma concentrations with toxicity (primarily myelosuppression) in hopes of using this information to optimize drug dosing.
Cellular basis of regulation of expression of idiotype. II. Immunity to anti-MOPC-460 idiotype antibodies increases the level of anti-trinitrophenyl antibodies bearing 460 idiotypes. (1979)

The antibody response of BALB/c mice to trinitrophenyl (TNP)-levan or TNP-Nocardia water-soluble mitogen (NWSM) includes a small but significant fraction of antibodies which share idiotypes (Id) with the dinitrophenyl (DNP)- and TNP-binding myeloma protein MOPC-460. Active immunization of BALB/c mice with MOPC-460 or passive administration of anti-460-Id antibodies suppresses the 460-Id+ component of the anti-TNP response. By contrast, active immunization of BALB/c with anti-460-Id antibodies or passive administration of BALB/c anti-[anti-460-Id] antibodies leads to an enhanced 460-Id+ component in the anti-TNP antibodies produced in response to TNP-levan or TNP-NWSM. This enhanced 460-Id+ response appears to be a result of the elimination of suppressor T lymphocytes specific for the 460-Id as T lymphocytes from such mice are unable to suppress the in vitro 460-Id+ response to TNP-NWSM whereas normal T cells are suppressive. These results indicate that suppressor cells specific for 460-Id normally regulate the activation of precursors of cells capable of secreting 460-Id+ anti-TNP antibodies.
Orphan receptor tyrosine kinase ROR2 as a potential therapeutic target for osteosarcoma (2009)

Osteosarcoma is the most prevalent bone malignant tumor in children and adolescents, and displays heterogeneous histology and high propensity for distant metastasis. Although adjuvant chemotherapy remarkably improved treatment outcome over the past few decades, prognosis for osteosarcoma patients with pulmonary metastasis is still unsatisfactory. To identify novel therapeutic targets for osteosarcoma, we investigated the gene expression profile of osteosarcomas by cDNA microarray analysis and found transactivation of receptor tyrosine kinase-like orphan receptor 2 (ROR2) expression in the majority of osteosarcoma samples. Treatment of osteosarcoma cell lines with siRNA against ROR2 significantly inhibited cell proliferation and migration. We also identified wingless-type MMTV integration site family, member 5B (WNT5B) as a putative ROR2 ligand and that the physiological interaction of WNT5B and ROR2 could enhance cell migration, indicating the possible roles of ROR2 and WNT5B in the metastatic property of osteosarcoma cells. Taken together, our findings revealed that the WNT5B/ROR2 signaling pathway is a promising therapeutic target for osteosarcoma.
Local ablation vs. resection for the treatment of hepatocellular carcinoma (2006)

We read with great interest and enthusiasm the AASLD practice guidelines, “Management of Hepatocellular Carcinoma” where the current status of surveillance for hepatocellular carcinoma (HCC) as well as diagnosis, staging, and treatment of patients with HCC was comprehensively reviewed.1 Specific evidence supporting recommendations were provided and areas requiring active research noted. In the treatment section regarding percutaneous ablation, we concurred this is the best treatment option for patients with early stage HCC who are not suitable for resection or transplantation. Nevertheless, the statement that there are no randomized controlled trials (RCT) comparing local ablation to resection may be somewhat misleading and thus needs clarification. In Taiwan where chronic viral hepatitis and HCC are endemic,2 we have conducted a prospective study to compare tumor recurrence and survival among patients with small HCC after surgical resection or percutaneous ethanol injection therapy.3 In this study, a total of 76 eligible patients were randomly assigned to two groups based on treatment. By using Cox regression model and Kaplan-Meier survival analysis, our results showed no statistical significance for tumor recurrence and a similar survival benefit between the two treatment groups. Although the number of patients in this study is relatively small, our observations clearly imply that percutaneous ethanol injection therapy appears to be as safe and effective as surgical resection, and both treatments can be considered first-line therapeutic options for small HCC. With these encouraging results, further larger prospective randomized controlled studies are awaited to compare other local ablation modalities (radiofrequency, microwave, laser or cryotherapy) with surgical resection for the treatment of small HCC. Jia-Horng Kao* , Ding-Shinn Chen*, * Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan, Graduate Institute of Clinical Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan, Hepatitis Research Center, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
TIG and Plasma Welding: Process Techniques, Recommended Practices and Applications (1990)

Process fundamentals Applying the TIG process Mechanised Orbital tube welding Tube to template welding Micro-TIG welding Hot wire TIG welding Narrow gap TIG welding Process fundamentals: Applying the plasma process The future.
Inhibition of the aquaporin 3 water channel increases the sensitivity of prostate cancer cells to cryotherapy (2009)

Aquaporins (AQPs) are intrinsic membrane proteins that facilitate selective water and small solute movement across the plasma membrane. In this study, we investigate the role of inhibiting AQPs in sensitising prostate cancer cells to cryotherapy. PC-3 and DU145 prostate cancer cells were cooled to 0, -5 and -10 degrees C. The expression of AQP3 in response to freezing was determined using real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. Aquaporins were inhibited using mercuric chloride (HgCl(2)) and small interfering RNA (siRNA) duplex, and cell survival was assessed using a colorimetric assay. There was a significant increase in AQP3 expression in response to freezing. Cells treated with AQP3 siRNA were more sensitive to cryoinjury compared with control cells (P<0.001). Inhibition of the AQPs by HgCl(2) also increased the sensitivity of both cell lines to cryoinjury and there was a complete loss of cell viability at -10 degrees C (P<0.01). In conclusion, we have shown that AQP3 is involved directly in cryoinjury. Inhibition of AQP3 increases the sensitivity of prostate cancer cells to freezing. This strategy may be exploited in the clinic to improve the efficacy of prostate cryotherapy.
Binding of Anti‐HIV Drugs to Human Serum Albumin (2004)

Human serum albumin (HSA), the most prominent protein in plasma, is best known for its exceptional ligand (i.e., drug) binding capacity. Here, values of the dissociation equilibrium constant (Kd)for the binding of HIV protease and reverse transcriptase inhibitors to HSA are reported. The binding of abacavir, atazanavir,didanosine, efavirenz, emtricitabine, lamivudine, nelfinavir,nevirapine, ritonavir, saquinavir, stavudine, zalcitabine, and zidovudine to the Sudlow site I (i.e., the warfarin cleft) located in the subdomain IIA involves the alteration of the HSA structure around Trp214 and induces intrinsic tryptophan fluorescence quenching. Accordingly, ibuprofen that primarily binds to the Sudlow site II located in the subdomain IIIA does not affect the HSA intrinsic tryptophan fluorescence and the binding of anti-HIV drugs to the Sudlow site 1. Accounting for the physiological concentration of HSA (= 7.0 x 10(-4) M), the average anti-HIV drug concentration in plasma (= 1.0 x 10(-4) M), and Kd values for the binding of anti-HIV drugs to HSA (ranging between 4.4 x 10(-5)M and 3.8 x 10(-4) M), it appears that the fraction of HIV protease and reverse transcriptase inhibitors bound to HSA ranges between 63% and 91%. This represents a significant drawback in the anti-HIV therapy and management, the anti-HIV drug concentration required to achieve 90% protease and reverse transcriptase inhibition in the presence of plasma proteins appears to be at least one order of magnitude higher than that required in their absence.
Round window membrane. Structure function and permeability: A review (1997)

The ultrastructure of the round window membrane of humans, monkeys, felines, and rodents discloses three basic layers: an outer epithelium, a middle core of connective tissue, and an inner epithelium. Interspecies variations are mainly in terms of thickness, being thinnest in rodents and thicker in humans. Morphologic evidence suggests that the layers of the round window participate in absorption and secretion of substances to and from the inner ear, and that the entire membrane could play a role in the defense system of the ear. Different substances, including antibiotics, local anesthetics, and tracers such as cationic ferritin, horseradish peroxidase, and 1 mu latex microspheres, are placed in the middle ear side traverse the membrane. Cationic ferritin and 1 micron microspheres placed in perilymph become incorporated by the inner epithelial cells of the membrane. Permeability is selective; factors include size, concentration, liposolubility, electrical charge, and thickness of the membrane. Passage of substances through the round window membrane is by different pathways, the nature of which is seemingly decided at the outer epithelium of the round window membrane.
Functional Analyses of the Transcription Factor Sp4 Reveal Properties Distinct from Sp1 and Sp3 (1995)

Sp4 is a human sequence-specific DNA binding protein with structural features similar to those described for the transcription factors Sp1 and Sp3. These three proteins contain two glutamine-rich regions and a highly conserved DNA binding domain composed of three zinc fingers. Consistently, Sp1, Sp3, and Sp4 do have the same DNA binding specificities. In this report, we have embarked on a detailed analysis of the transcriptional properties of Sp4 in direct comparison to Sp1 and Sp3. Cotransfection experiments into Drosophila SL2 cells lacking endogenous Sp factors demonstrate that Sp4 is an activator protein like Sp1. However, in contrast to Sp1, Sp4 is not able to act synergistically through adjacent binding sites. The transactivation function of Sp4 resides, like that of Sp1, in the N-terminal glutamine-rich region. Sp4 can function as a target for the Sp1 activation domains in a superactivation assay, suggesting that the activation domains of Sp1 and Sp4 are functionally related. Furthermore, we show that Sp4-mediated transcriptional activation can be repressed by Sp3. Taken together, our results demonstrate that the transcription factor Sp4 exhibits specific functional properties distinct from Sp1 and Sp3.
Ionic Strength Dependence of the Oxidation of Iodide and Ferrocyanide by Compound I of Horseradish Peroxidase (1978)

The kinetics of the oxidation of iodide and ferrocyanide by compound I of horseradish peroxidase have been studied at 25°C as a function of ionic strength and pH. The ionic strength dependencies of the second‐order rate constants are tested with an extended form of the Debye‐Hückel equation for the activity coefficients of the reacting species. For the reaction of iodide with compound I it is shown that the pH variation of the rate constant at zero ionic strength is caused mainly by titrating a catalytically important acid group and not mainly by the varying charge of the protein. The ferrocyanide reaction rate with compound I does not correlate with enzyme net charge, at all pH values. The influence of electrostatic interactions on reaction rates is discussed.
Thermal Decomposition of Wheat Straw and Mallee Residue Under Pyrolysis Conditions<sup>†</sup> (2009)

The pyrolysis behavior of wheat straw and mallee residue and resulting gases, liquids, and chars were examined. The specific heat and thermal conductivity of both species were measured using computer-aided thermal analysis at heating rates of 10 and 100 °C/min to a temperature of 1000 °C. The sample decomposition was also measured by thermogravimetry. Gas chromatography detected evolved gases, and the bio-oils were characterized using GC-MS. Chars were examined using FTIR, proximate, and ultimate analysis. Both species initially displayed endothermic behavior, followed by rapid decomposition and fluctuating specific heat and thermal conductivity between 250 and 500 °C. Oxides of carbon were the primary gases evolved, with small amounts of hydrocarbons and hydrogen. The bio-oils predominantly contained oxygenated aromatics and organic acids, and the chars had high fixed carbon and low sulfur. In all instances approximately half of the product output was liquid. Straw produced 14% gas and 32% solid at 500 °C, whereas mallee produced 13% gas and 36% solid. At 1000 °C the proportions of solid decreased and gas increased. The efficiency of pyrolysis to 500 °C, assuming no losses, was around 96% for both species. At 1000 °C the efficiency decreased, with pyrolysis of mallee slightly more efficient than for straw.
Renal and vascular actions of equol in the rat (1997)

Equol is a modest natriuretic and vasorelaxant agent in the rat. Further studies are required in order to investigate the potential natriuretic and perhaps hypotensive actions of dietary equol precursors (daidzein).
C coding standards (2011)

The EMBOSS C coding standards are summarised below. Mostly they concern layout of the code, some well established principles of C programming, and tips for programming EMBOSS objects (C data structures) and functions. There are a few guidelines which you should try to follow when writing code for EMBOSS.
Micropipette aspiration of guinea pig megakaryocytes: absence of fragmentation and dependence on maturation stage. (1989)

Platelet release has been alternatively viewed as a fragmentation of platelet territories demarcated within the cytoplasm of mature megakaryocytes or as a later event involving segmentation of proplatelet pseudopodia extended from the cell. The mechanical constraints on platelet release were evaluated by measuring the resistance of guinea pig megakaryocytes to aspiration into micropipettes of similar diameter to the width of naturally forming proplatelet projections. Application of increasing negative pressure to the surface of the cells resulted in progressively longer extensions being drawn into the pipette until maximal extension lengths were reached. None of the passively aspirated cytoplasmic extensions fragmented off the cells even at the highest aspiration pressure under physiologic study conditions. The longest extensions were aspirated from megakaryocytes of the most advanced maturation stage, and a proportion of the mature cells yielded very long extensions over 50 mu and up to 150 mu in length. Surprisingly, the ease of aspiration did not correlate to cell size during any stage of maturation. The mechanical behavior of guinea pig megakaryocytes indicates a large availability of surface for extension in mature cells ideal for active proplatelet projection. The lack of mechanical fragility suggests that platelet release is a very late maturational event not yet initiated in the "mature" megakaryocytes available for study from marrow harvests.
<title>Ultrafast Gating Of Proximity Focused Microchannel-Plate Intensifiers</title> (1983)

Proximity-focused, microchannel-plate (MCP) image intensifiers have been used at Los Alamos for many years to allow single frame film and video exposure times in the range of 2.5 to 10 ns. There is now a program to reduce gating times to <1 ns. This paper reviews previous work and the problems in achieving good resolution with gating times of <1 ns. The key problems involve applying fast electrical gating signals to the tube elements. We present computer modeling studies of the combined tube, tube connection, and pulser system and show that low photocathode surface resistivity must be obtained to permit fast gating between the photocathode and the MCP input. We discuss ways of making low-resistivity S20 photocathodes, using gallium arsenide photocathodes, and various means of gating the tubes. A variety of pulser designs are being experimentally evaluated including spark gaps, avalanche transistors, Krytron tubes with sharpening gaps, step recovery diodes, and photoconductive elements (PCEs). The results of these studies are presented. Because of the high capacitances involved in most gating schemes, the tube connection geometry must be of low-impedance design, and our solution is presented. Finally, ways of testing these high-speed camera systems are discussed.
Seismic interpretation using global image segmentation (2003)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2003Seismic interpretation using global image segmentationAuthors: Dave HaleJeff EmanuelDave HaleLandmark Graphics and Jeff EmanuelLandmark Graphicshttps://doi.org/10.1190/1.1817860 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1817860FiguresReferencesRelatedDetailsCited ByInteractive Fault Extraction in 3-D Seismic Data Using the Hough Transform and Tracking VectorsIEEE Transactions on Computational Imaging, Vol. 3, No. 1Supervised learning to detect salt bodyPablo Guillen, German Larrazabal*, Gladys González, Dainis Boumber, and Ricardo Vilalta19 August 2015Salt delineation via interpreter-guided 3D seismic image segmentationAdam D. Halpert, Robert G. Clapp, and Biondo Biondi26 March 2014 | Interpretation, Vol. 2, No. 2Image segmentation for velocity model construction and updatingAdam D. Halpert, Robert G. Clapp, Jesse Lomask, and Biondo Biondi15 December 2008Fault identification using competitive learningMarcos Machado and Marcelo Gattass23 November 2007Application of image segmentation to tracking 3D salt boundariesGEOPHYSICS, Vol. 72, No. 4Seismic event tracking by global path optimizationMorgan P. Brown, Scott A. Morton, and Gary Whittle6 October 2006Application of Surface Topological Segmentation to Seismic ImagingMeshing for velocity modeling and ray tracing in complex velocity fieldsGEOPHYSICS, Vol. 71, No. 1 SEG Technical Program Expanded Abstracts 2003ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2003 Pages: 2452 publication data© 2003 Copyright © 2003 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 03 Jan 2005 CITATION INFORMATION Dave Hale and Jeff Emanuel, (2003), "Seismic interpretation using global image segmentation," SEG Technical Program Expanded Abstracts : 2410-2413. https://doi.org/10.1190/1.1817860 Plain-Language Summary PDF DownloadLoading ...
Learning to Generate Code Sketches. (2021)

Traditional generative models are limited to predicting sequences of terminal tokens. However, ambiguities in the generation task may lead to incorrect outputs. Towards addressing this, we introduce Grammformers, transformer-based grammar-guided models that learn (without explicit supervision) to generate sketches -- sequences of tokens with holes. Through reinforcement learning, Grammformers learn to introduce holes avoiding the generation of incorrect tokens where there is ambiguity in the target task. 
We train Grammformers for statement-level source code completion, i.e., the generation of code snippets given an ambiguous user intent, such as a partial code context. We evaluate Grammformers on code completion for C# and Python and show that it generates 10-50% more accurate sketches compared to traditional generative models and 37-50% longer sketches compared to sketch-generating baselines trained with similar techniques.
Cleavable surfactants (1995)

Abstract A brief review of cleavable surfactants, synthesized and characterized by the author and his co-workers, is presented. Two types of cleavable surfactants have been reported; each contains a labile functional group. Both single and double-chain first generation cleavable surfactants are cleaved to give nonsurfactant fragments: a water-insoluble organic compound and a water-soluble ionic compound. Single-chain second generation cleavable surfactants are cleaved to give another surfactant and a water-soluble organic compound; double-chain second generation surfactants are cleaved to give two single-chain surfactants. Cleavable surfactants allow the elimination of problems associated with the presence of aggregated surfactants after their beneficial use.