gebhart/patrepeval huggingface dataset:
Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia (2021)

Acute myeloid and lymphoid leukemias often harbor chromosomal translocations involving the KMT2A gene, encoding the KMT2A lysine methyltransferase (also known as mixed-lineage leukemia-1), and produce in-frame fusions of KMT2A to other chromatin-regulatory proteins. Here we map fusion-specific targets across the genome for diverse KMT2A oncofusion proteins in cell lines and patient samples. By modifying CUT&Tag chromatin profiling for full automation, we identify common and tumor-subtype-specific sites of aberrant chromatin regulation induced by KMT2A oncofusion proteins. A subset of KMT2A oncofusion-binding sites are marked by bivalent (H3K4me3 and H3K27me3) chromatin signatures, and single-cell CUT&Tag profiling reveals that these sites display cell-to-cell heterogeneity suggestive of lineage plasticity. In addition, we find that aberrant enrichment of H3K4me3 in gene bodies is sensitive to Menin inhibitors, demonstrating the utility of automated chromatin profiling for identifying therapeutic vulnerabilities. Thus, integration of automated and single-cell CUT&Tag can uncover epigenomic heterogeneity within patient samples and predict sensitivity to therapeutic agents.
The role of emerging technologies in the diagnosis and staging of neoplastic diseases (1992)

The revolution in cell and molecular biology presents an unprecedented opportunity to develop an understanding of neoplastic diseases. The emerging technologies resulting from this revolution also present an opportunity to make the diagnosis and staging of neoplastic diseases more accurate. Unfortunately, the integration of these technologies into current clinical practice is not a simple task. The problems associated with the clinical applications of these technologies include standardization and simplification of the technologies so that they can be established in nonresearch institutions, selection of those technologies which provide clinically meaningful information, and finally, the implementation of large-scale clinical trials which will permit multivariate statistical analyses to determine if performance of the new studies actually add to a physician's ability to diagnose and stage cancer patients. In the future, the staging of patients with neoplastic diseases will include anatomic studies together with morphologic and biologic studies of the tumor cells. Data derived from these studies will be used to assess each patient's risk status regarding the likelihood of local and distant metastases being present. These highly accurate estimates of risk status will lead to an improvement in our ability to make individualized recommendations for therapy. Cancer 1992; 69:1520-1526.
A modified Girard derivatizing reagent for universal profiling and trace analysis of aldehydes and ketones by electrospray ionization tandem mass spectrometry (2007)

4-Hydrazino-N,N,N-trimethyl-4-oxobutanaminium iodide (HTMOB) is a modified Girard derivatizing reagent synthesized to improve the sensitivity of analysis of aldehydes and ketones with electrospray ionization tandem mass spectrometry. Compared with Girard T reagent the measured signal intensity increase is between 3.3 times (succinylacetone) and 7.0 times (17-hydroxyprogesterone). HTMOB is a universal profiling reagent for aldehydes and ketones. A neutral loss of 59 Da scan detects all aldehydes and ketones from acetone to corticosteroids. Applications described include the profiling of ketones, ketoacids and ketodiacids in the urine of children with ketosis and the profiling of long-chain aldehydes incorporated in plasma plasmalogens.
RNA polymerase II subunit composition, stoichiometry, and phosphorylation. (1990)

RNA polymerase II subunit composition, stoichiometry, and phosphorylation were investigated in Saccharomyces cerevisiae by attaching an epitope coding sequence to a well-characterized RNA polymerase II subunit gene (RPB3) and by immunoprecipitating the product of this gene with its associated polypeptides. The immunopurified enzyme catalyzed alpha-amanitin-sensitive RNA synthesis in vitro. The 10 polypeptides that immunoprecipitated were identical in size and number to those previously described for RNA polymerase II purified by conventional column chromatography. The relative stoichiometry of the subunits was deduced from knowledge of the sequence of the subunits and from the extent of labeling with [35S]methionine. Immunoprecipitation from 32P-labeled cell extracts revealed that three of the subunits, RPB1, RPB2, and RPB6, are phosphorylated in vivo. Phosphorylated and unphosphorylated forms of RPB1 could be distinguished; approximately half of the RNA polymerase II molecules contained a phosphorylated RPB1 subunit. These results more precisely define the subunit composition and phosphorylation of a eucaryotic RNA polymerase II enzyme.
Potential of acetic acid to restore methane production in anaerobic reactors critically intoxicated by ammonia as evidenced by metabolic and microbial monitoring (2023)

Abstract BACKGROUND Biogas and biomethane production from the on-farm anaerobic digestion (AD) of animal manure and agri-food wastes could play a key role in transforming Europe’s energy system by mitigating its dependence on fossil fuels and tackling the climate crisis. Although ammonia is essential for microbial growth, it inhibits the AD process if present in high concentrations, especially under its free form, thus leading to economic losses. In this study, which includes both metabolic and microbial monitoring, we tested a strategy to restore substrate conversion to methane in AD reactors facing free ammonia critical intoxication. RESULTS The AD process of three mesophilic semi-continuous 100L reactors critically intoxicated by free ammonia (&gt; 3.5 g_N L_slurry − 1 ; interrupted hydrolysis and methanogenesis) was restored by applying a strategy that included pH correction using acetic acid, washing out total ammonia with water, re-inoculation with active microbial flora and the progressive re-introduction of sugar beet pulp, a complex organic substrate. After five weeks, two intoxicated reactors restarted the production of CH 4 from the pulp hydrolysis and via hydrogenotrophic methanogenesis. The acetoclastic methanogenesis remained inhibited, probably due to the transient dominance in the slurry of a strictly methylothrophic methanogen of the archaeal genus Candidatus Methanoplasma, to the detriment of a versatile methanogen belonging to the Methanosarcina genus. Concomitantly, the third intoxicated reactor, in which the Methanosarcina members remained permanently dominant, faced transient hydrolysis inhibition but produced CH 4 from restored acetoclastic methanogenesis. After eight weeks, the AD process was functional in all formerly intoxicated reactors with a pulp to CH 4 conversion ratio of 0.41 ± 0.10 L N _CH 4 g_VS − 1 , analogous to the pulp biochemical methane potential (0.38 ± 0.03 L N _CH 4 g_VS − 1 ). CONCLUSIONS Despite a particularly extreme free ammonia intoxication, the proposed process recovery strategy allowed the hydrolysis and methane production to be restored in three intoxicated reactors within eight weeks, a period during which reinitiating the feedstock supply appeared to be crucial to sustain the process. The initial introduction of acetic acid allowed substantial CH 4 production during the recovery period and could enable the agronomic valorization of the effluents produced by full-scale reactors recovering from ammonia intoxication.
A reactive wet spinning approach to polypyrrole fibres (2011)

Electrically conducting, robust fibres comprised of both an alginate (Alg) biopolymer and a polypyrrole (PPy) component have been produced using reactive wet-spinning. Using this approach polypyrrole–biopolymer fibres were also produced with single-walled carbon nanotubes (CNTs), added to provide additional strength and conductivity. SEM images of the PPy–Alg composite fibres clearly show the tubular multifilament form of the alginate fibre impregnated with PPy nanoparticles. The fibres produced containing CNTs show a 78% increase in ultimate stress and 25% increase in elongation to break compared to PPy–alginate fibre. Young's modulus obtained for the PPy–Alg–CNT fibres showed a 30% increase compared to the PPy–alginate fibre. The fibres produced were electrochemically active and capable of electromechanical actuation with a strain of 0.7% produced at a scan rate of 100 mV s−1 of the potential.
Power flow control on 345 kV lines with the 200 MVA convertible static compensator (2005)

A 200 MVA, 345 kV system control FACTS device, consisting of two 100 MVA converters, two 100 MVA high voltage series transformers inserted in 345 kV transmission lines and a 200 MVA shunt transformer, was tested and utilized on a 345 kV network. This device, namely convertible static compensator (CSC), has four basic configurations: static synchronous compensator (STATCOM), static synchronous series compensator (SSSC), unified power flow controller (UPFC), and interline power flow controller (IPFC). The testing confirmed the device capability to operate in multiple configurations and its ability to control and regulate the power flows on two 345 kV transmission lines. The CSC test results confirmed its capability to regulate the substation bus voltage and line power flows under steady-state and dynamic conditions. The CSC flexibility allows to utilize it during normal as well as various emergency system conditions.
Voriconazole potentiates warfarin‐induced prothrombin time prolongation (2003)

Coadministration of voriconazole and warfarin potentiates warfarin-induced prothrombin time prolongation. Regular monitoring of prothrombin time is recommended if these drugs are coadministered, with appropriate adjustment of the dose of warfarin.
Immunosuppressive activity of a purified spleen extract (lymphocytic chalone?) is not due to polyamines spermine and spermidine. (1979)

Spermine, spermidine and a purified spleen extract (PSE) have been compared in vivo in these three tests: hemolytic plaque forming capacity in sensitized mice, delayed hypersensitivity reaction and 3H-thymidine incorporation into various tissue cells. The results obtained demonstrated that the immunosuppressive activity of PSE cannot be attributed to those polyamines. Ion exchange analysis of PSE before and after acid hydrolysis confirmed the absence of free and/or bound polyamines in the studied extract.
Friedreich’s ataxia: iron chelators that target the mitochondrion as a therapeutic strategy? (2003)

Friedreich's ataxia (FA) is a severe inherited spinocerebellar ataxia that primarily affects the nervous system and heart leading to early confinement in a wheelchair and death. The gene defective in FA, FRDA, encodes a mitochondrial protein known as frataxin. A triplet repeat expansion within intron 1 of the FRDA gene results in a marked decrease in frataxin expression. Over the last 5 years it has become clear that this results in mitochondrial iron accumulation that generates oxidative stress and results in damage to critical biological molecules. Drugs that reduce oxidative stress have a limited effect on the progression and pathology of the disease, probably because these agents cannot remove the iron accumulation. In this review, the potential of iron chelators, namely the 2-pyridylcarboxaldehyde isonicotinoyl hydrazone (PCIH) analogues, as agents to remove mitochondrial iron deposits is discussed. These ligands have been specifically designed to enter and target mitochondrial iron pools, which is a property lacking in desferrioxamine, the only chelator in widespread clinical use. This latter drug may not have any beneficial effect in FA patients, probably because of its hydrophilicity that prevents mitochondrial access. Indeed, standard chelation regimens will probably not work in FA, as these patients do not exhibit gross iron-loading. Considering that there is no effective treatment for FA, it is essential that the therapeutic potential of iron chelators that target mitochondrial iron pools is assessed experimentally.
Chemical Composition of Antigen 60 from Mycobacterium bovis BCG (1986)

Antigen 60 (A60), the main thermostable immunogen of tuberculin and PPD, has been purified from Mycobacterium bovis BCG cytoplasm, and identified by crossed immunoelectrophoresis with anti-BCG polyclonal antiserum. Two A60 fractions, free lipids and lipid-conjugated compounds, have been recognized. The free lipids represented about 30% (dry weight), and consisted essentially of C16-C18 fatty acids, and of phosphatidyl-inositol-mannosides. Lipoconjugates, upon DEAE-cellulose chromatography and gel filtration, yielded two main fractions of neutral and polar components. Chromatography of delipidated and deproteinized A60 on Sephadex G-100 yielded: a high molecular weight fraction (Al, 18%, a lipoglucan of congruent to 10(6)), and a low molecular weight fraction (B, 10%, a lipopeptidoglycan of congruent to 10(4)) containing mannose, glucose, and small amounts of arabinose. The polysaccharide moieties of fractions Al and B were submitted to acetylation, methylation, and acid hydrolysis, and the structure of the hydrolysed polymer was deduced by combined gas chromatography/mass spectrometry analysis. The results indicated a branched structure involving 1,4-, 1,6-, and 1,4,6-linked D-gluco- or D-manno-pyranosyl residues. Glucan- and peptidoglycan-bound fatty acids were identified as saturated (C16-C18) and monounsaturated linear acids (C12-C18). Immunodiffusion on agarose gel indicated that delipidation and proteolysis did not suppress the ability of A60 to yield immunoprecipitates with anti-A60 antiserum. The high polymer fractions obtained by chromatography on DEAE cellulose and Sephadex G-100 were also reactive. It is concluded that A60 is made of free lipids and of lipopeptidoglycans of high molecular weights (10(6)-10(7)) endowed with immunogenic properties.
Non-Proteinuric Diabetic Nephropathy (2015)

Diabetic nephropathy patients traditionally show significant macroalbuminuria prior to the development of renal impairment. However, this clinical paradigm has recently been questioned. Epidemiological surveys confirm that chronic kidney disease (CKD) diagnosed by a low glomerular filtration rate (GFR) is more common in diabetic patients than in the non-diabetic population but a low number of patients had levels of proteinuria above that which traditionally defines overt diabetic nephropathy (>500 mg/g). The large number of patients with low levels of proteinuria suggests that the traditional clinical paradigm of overt diabetic nephropathy is changing since it does not seem to be the underlying renal lesion in most of diabetic subjects with CKD.
Improvements to an Optical Magneto-Mechanical Device (2017)

An Optical Magneto-Mechanical Device (OMMD) is used to measure the deflection of a rotating magnetic shape memory alloy in a magnetic field. It consists of a camera that rotates with a sample inside an electromagnet. Software analyzes the images and produces deflection data. Modifications have been made to increase reliability, convenience, and reparability. The OMMD was moved from a temporary to a permanent setup, which alleviates the need to install the OMMD on another piece of characterization equipment. This lowers the downtime of other vital equipment, reduces setup time, and negates the danger of moving sensitive equipment and samples. We replaced in-house electronic hardware with standard third-party equipment, which is both more robust and much easier to repair. Control programs were adapted to the new hardware and given more flexibility.
Differential effects of dietary saturated and trans-fatty acids on expression of genes associated with insulin sensitivity in rat adipose tissue (2005)

The effects of SFAs on the aforementioned genes except PPARgamma could be extrapolated towards decreased insulin sensitivity, while only the alteration in the mRNA levels of PPARgamma and resistin could be associated with insulin resistance in TFA-fed rats. These findings suggest that dietary SFAs and TFAs alter the expression of different genes associated with insulin sensitivity in adipose tissue.
Distribution of the EP3 prostaglandin E2 receptor subtype in the rat brain: Relationship to sites of interleukin-1-induced cellular responsiveness (2000)

The activation of neurosecretory neurons that express corticotropin-releasing hormone (CRH) in response to increased circulating levels of interleukin-1beta (IL-1beta) depends on prostaglandin E(2) (PGE(2)) acting locally within the brain parenchyma. To identify potential central targets for PGE(2) relevant to pituitary-adrenal control, the distribution of mRNA encoding the PGE(2) receptor subtype EP3 (EP3R) was analyzed in rat brain. Hybridization histochemistry revealed prominent labeling of cells in discrete portions of the olfactory system, iso- and hippocampal cortices, and subcortical telencephalic structures in the septal region and amygdala. Labeling over the midline, intralaminar, and anterior thalamic groups was particularly prominent. EP3R expression was enriched in the median preoptic nucleus and adjoining aspects of the medial preoptic area (MPO) implicated in thermoregulatory/febrile responses and sleep induction. EP3R-expressing cells were also prominent in brainstem cell groups involved in nociceptive information processing/modulation (periaqueductal gray, locus coeruleus (LC), parabrachial nucleus (PB), caudal raphé nuclei), arousal and wakefulness (LC, midbrain raphé and tuberomammillary nuclei); and in conveying interoceptive input, including systemic IL-1 signals, to the endocrine hypothalamus (nucleus of the solitary tract (NTS) and rostral ventrolateral medulla [VLM]). Combined hybridization histochemical detection of EP3R mRNA with immunolocalization of IL-1beta-induced Fos protein expression identified cytokine-sensitive, EP3R-positive cells in the medial NTS, rostral VLM, and, to a lesser extent, aspects of the MPO. These findings are consistent with the view that increased circulating IL-1 may stimulate central neural mechanisms, including hypothalamic CRH neurons, through an EP3R-dependent mechanism involving PGE(2)-mediated activation of cells in the caudal medulla and/or preoptic region.
Distributed garbage collection for large-scale mobile actor systems (2006)

Distributed actor garbage collection (GC) is a notoriously hard problem due to the nature of distributed actor systems---no common clock, no coherent global information, asynchronous and unordered message passing, autonomous behavior of actors, and counter-intuitive actor marking to identify live actors. Most existing distributed actor GC algorithms rely on First-In-First-Out (FIFO) communication, which constrains the actor model and is impractical with actor mobility; others depend on stop-the-world synchronization, which is intrusive and impractical for users' computations. Existing actor GC algorithms ignore actor mobility and resource access restrictions. Existing distributed passive object GC algorithms cannot be directly reused because of the different semantics of passive objects and actors. 
To overcome the problems that existing algorithms cannot solve, this thesis presents a practical actor GC mechanism for distributed mobile actor systems. Our approach starts formalizing garbage actors, and then we show two different but similar transformation methods that prove the equivalence of actor GC and passive object GC. Two actor marking algorithms are derived from the transformation methods---the back pointer algorithm and the N-color algorithm. The back pointer algorithm has linear time complexity of O(E + V) and extra space complexity of O(E + V), and the N-color algorithm has time complexity of O(Elg* M) and extra space complexity of O(M), given that E is the number of references, V, the number of actors, and M, the number of unblocked and root actors. The N-color algorithm only requires scanning the reference graph once while the back pointer algorithm requires scanning it twice. 
The thesis follows by describing our distributed mobile actor GC mechanism. It consists of (1) an asynchronous, non-FIFO reference listing based algorithm which supports hierarchical GC (local and global GC), (2) a new fault-tolerant, distributed snapshot-based algorithm which collects cyclic and acyclic garbage in a partial set of computing hosts, and (3) formal models and correctness proofs. Experimental results have confirmed that our approach is practical and scalable.
Wavelength-tunable polarization-independent demultiplexing in an all-fiber polarization diversity nonlinear optical-loop mirror (1998)

Summary form only given. Polarization-independent demultiplexing in the nonlinear optical-loop mirror has previously been achieved through the use of polarization-maintaining optical fiber (PMF) as the active nonlinear element in the loop or through the introduction of polarization diversity by the inclusion of a birefringent crystal in a loop with standard dispersion-shifted fiber. The high cost and limited availability of PMF places restrictions on its use, whereas, in the second case, the use of bulk optical components and the limited operating wavelength range make an all-fiber solution more favorable. In the loop mirror configuration used in this study the polarization diversity was obtained by splicing a short section of PMF into the loop instead of a birefringent crystal.
A study of the “david” reaction (1961)

Abstract Some of the variables influencing the David reaction have been studied. An improved method is described. Among the oestrogens studied only compounds with a 17β and a 16α, or 16β‐hydroxyl group gave a positive David reaction; the approximate relative chromogenicities were oestriol:100, 16‐epioestriol: 60, 6‐hydroxyoestriol: 16 and 2‐hydroxyoestriol: 7%. The presence of highly purified methylated and chromatographed urinary residues greatly diminished the David chromogenicity of oestriol. This decrease was linearly related to log concentration of urinary residue.
Clarity MCode (1995)

article Free Access Share on Clarity MCode: a retargetable intermediate representation for compilation Authors: Brian T. Lewis Sun Microsystems Laboratories, 2550 Garcia Avenue, MTV29-112, Mountain View, California and Alladin Enterprises, 203 Santa Margarita Avenue, Menlo Park, California Sun Microsystems Laboratories, 2550 Garcia Avenue, MTV29-112, Mountain View, California and Alladin Enterprises, 203 Santa Margarita Avenue, Menlo Park, CaliforniaView Profile , L. Peter Deutsch Sun Microsystems Laboratories, 2550 Garcia Avenue, MTV29-112, Mountain View, California and Alladin Enterprises, 203 Santa Margarita Avenue, Menlo Park, California Sun Microsystems Laboratories, 2550 Garcia Avenue, MTV29-112, Mountain View, California and Alladin Enterprises, 203 Santa Margarita Avenue, Menlo Park, CaliforniaView Profile , Theodore C. Goldstein Sun Microsystems Laboratories, 2550 Garcia Avenue, MTV29-112, Mountain View, California and Alladin Enterprises, 203 Santa Margarita Avenue, Menlo Park, California Sun Microsystems Laboratories, 2550 Garcia Avenue, MTV29-112, Mountain View, California and Alladin Enterprises, 203 Santa Margarita Avenue, Menlo Park, CaliforniaView Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 30Issue 3March 1993 pp 119–128https://doi.org/10.1145/202530.202542Online:01 March 1995Publication History 5citation332DownloadsMetricsTotal Citations5Total Downloads332Last 12 Months11Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF