gebhart/patrepeval huggingface dataset:
High frequency of additional gene mutations in acute myeloid leukemia with <i>MLL</i> partial tandem duplication: <i>DNMT3A</i> mutation is associated with poor prognosis (2015)

The mutational profiles of acute myeloid leukemia (AML) with partial tandem duplication of mixed-lineage leukemia gene (MLL-PTD) have not been comprehensively studied. We studied 19 gene mutations for 98 patients with MLL-PTD AML to determine the mutation frequency and clinical correlations. MLL-PTD was screened by reverse-transcriptase PCR and confirmed by real-time quantitative PCR. The mutational analyses were performed with PCR-based assays followed by direct sequencing. Gene mutations of signaling pathways occurred in 63.3% of patients, with FLT3-ITD (44.9%) and FLT3-TKD (13.3%) being the most frequent. 66% of patients had gene mutations involving epigenetic regulation, and DNMT3A (32.7%), IDH2 (18.4%), TET2 (18.4%), and IDH1 (10.2%) mutations were most common. Genes of transcription pathways and tumor suppressors accounted for 23.5% and 10.2% of patients. RUNX1 mutation occurred in 23.5% of patients, while none had NPM1 or double CEBPA mutation. 90.8% of MLL-PTD AML patients had at least one additional gene mutation. Of 55 MLL-PTD AML patients who received standard chemotherapy, age older than 50 years and DNMT3A mutation were associated with inferior outcome. In conclusion, gene mutations involving DNA methylation and activated signaling pathway were common co-existed gene mutations. DNMT3A mutation was a poor prognostic factor in MLL-PTD AML.
Regulatory effects of the fruit extract of Lycium chinense and its active compound, betaine, on muscle differentiation and mitochondrial biogenesis in C2C12 cells (2019)

Our study was conducted to investigate the effects of the fruits of Lycium chinense Mill. (Lycii Fructus, LF) and its bioactive compound, betaine, on muscle differentiation and mitochondrial biogenesis in C2C12 cells. LF extract and betaine was analyzed by high-performance liquid chromatography (HPLC). The expression of myosin heavy chain (MyHC) and peroxisome proliferator-activated receptor gamma coactivator1-alpha (PGC-1α), sirtuin-1(Sirt-1), nuclear respiratory factor-1 (NRF-1), transcription factor A, mitochondrial (TFAM) and the phosphorylation of AMP-activated protein kinase (AMPK) and acetyl-CoA carboxylase (ACC), were determined in cellular or mitochondrial levels by quantitative polymerase chain reaction (qPCR) or Western blot, respectively. The glucose levels and total ATP contents were measured by the glucose consumption in a culture medium, cellular glucose uptake and ATP assays. LF extract at 4 mg/ml and betaine at 2 and 5 mM significantly increased the expression of MyHC in C2C12 myotubes, compared with non-treated cells. LF extract and betaine significantly increased the expression of PGC-1α, Sirt-1, NRF-1 and TFAM mRNA and protein in the myotubes, as well as phosphorylation of AMPK and ACC. Furthermore, LF extract and betaine significantly increased the mitochondrial protein contents, as the TFAM and NRF-1 expressions were increased. LF extract and betaine also significantly increased the glucose uptake and ATP contents in the myotubes. The LF extract contained 3.18% betaine was quantitated by HPLC. LF extract and betaine enhanced muscle differentiation and energy metabolism through the up-regulation of mitochondrial biogenesis-regulating factors, suggesting that LF extract and betaine can help to prevent the dysfunction of skeletal muscle.
Amperometric Biosensor for D-Lactate Assay (2008)

A carbon paste electrode biosensor for D-lactic acid analysis in biological samples was developed. D-lactate cytochrome c oxidoreductase from baker’s yeast (EC 1.1.2.4) was used as biorecognition element of the electrode in combination with phenazine methosulphate (PMS)–Reinecke’s salt precipitate as mediator. The enzyme was bound on paste due to Enzacryl using glutardialdehyde. The electrode response to D-lactate addition was linear in the concentration range of 0.015–100 mM. Limit of detection was equal to 56 μM when signal vs. noise criterium (S/N=3) is considered. Specificity for only D-lactate was proven. Relative standard deviation of 6.6 % for 12 mM D-lactate was found. The biosensor exerts long-term stability and also good stability during repeated measuring cycles. The electrode has a good potential for use in practical samples.
Universal approximation using feedforward networks with non-sigmoid hidden layer activation functions (1989)

K.M. Hornik, M. Stinchcombe, and H. White (Univ. of California at San Diego, Dept. of Economics Discussion Paper, June 1988; to appear in Neural Networks) showed that multilayer feedforward networks with as few as one hidden layer, no squashing at the output layer, and arbitrary sigmoid activation function at the hidden layer are universal approximators: they are capable of arbitrarily accurate approximation to arbitrary mappings, provided sufficiently many hidden units are available. The present authors obtain identical conclusions but do not require the hidden-unit activation to be sigmoid. Instead, it can be a rather general nonlinear function. Thus, multilayer feedforward networks possess universal approximation capabilities by virtue of the presence of intermediate layers with sufficiently many parallel processors; the properties of the intermediate-layer activation function are not so crucial. In particular, sigmoid activation functions are not necessary for universal approximation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A comparative study of neural network models for lexical intent classification (2015)

Domain and intent classification are critical pre-processing steps for many speech understanding and dialog systems, as it allows for certain types of utterances to be routed to particular subsystems. In previous work, we explored many types of neural network (NN) architectures — some feedforward and some recurrent — for lexical intent classification and found that they improved upon more traditional statistical baselines. In this paper we carry out a more comprehensive comparison of NN models including the recently proposed gated recurrent unit network, for two domain/intent classification tasks. Furthermore, whereas the previous work was confined to relatively small and controlled datasets, we now include experiments based on a large set obtained from the Cortana personal assistant application. We compare feedforward, recurrent, and gated — such as LSTM and GRU — networks against each other. On both the ATIS intent task and the much larger Cortana domain classification tasks, gated networks outperform recurrent models, which in turn outperform feedforward networks. Also, we compared standard word vector models against a representation which encodes words as sets of character n-grams to mitigate the out-of-vocabulary problem. We find that in nearly all cases, the standard word vectors outperform character-based word representations. Best results are obtained by linearly combining scores from NN models with log likelihood ratios obtained from N-gram language models.
Analysis of oil content of groundnuts by nuclear magnetic resonance spectrometry (1985)

Abstract One hundred groundnut germplasm accessions were analysed for their oil content by the standard Soxhlet extraction procedure using petroleum ether: the results were compared using functional analysis with those obtained with a commercial nuclear magnetic resonance (n.m.r.) spectrometer. On another 78 experimental samples, oil content was first obtained using the n.m.r. method and the Soxhlet values were predicted using the above functional relationship. On the 78 samples the predicted values were highly correlated (r=0.972) with those obtained by Soxhlet extraction. The n.m.r. method is rapid, easy, acurate and non‐destructive.
Fast, Exact Model Selection and Permutation Testing for l2-Regularized Logistic Regression (2012)

Regularized logistic regression is a standard classification method used in statistics and machine learning. Unlike regularized least squares problems such as ridge regression, the parameter estimates cannot be computed in closed-form and instead must be estimated using an iterative technique. This paper addresses the computational problem of regularized logistic regression that is commonly encountered in model selection and classifier statistical significance testing, in which a large number of related logistic regression problems must be solved for. Our proposed approach solves the problems simultaneously through an iterative technique, which also garners computational efficiencies by leveraging the redundancies across the related problems. We demonstrate analytically that our method provides a substantial complexity reduction, which is further validated by our results on real-world datasets. 1
Ethinyl estradiol acutely attenuates abnormal coronary vasomotor responses to acetylcholine in postmenopausal women. (1994)

EE attenuates abnormal coronary vasomotor responses to acetylcholine in postmenopausal women. EE also decreases basal coronary vasomotor tone as manifested by increased coronary flow, decreased resistance, and increased epicardial cross-sectional area. These acute effects of estrogen on coronary vasoreactivity may explain, in part, the cardioprotective effects of estrogen in postmenopausal women.
Building, modifying and using component generators (1993)

The tools used to generate implementations from component descriptions are called component generators. The protocol considered supports call processing by controlling the set-up and take-down of connections carrying telephone calls. The exercises discussed investigate the use of component generators in the construction of the protocol handler and related components. The component descriptions and generic architectures developed in these exercises are built by composing reusable components and applying generative tools. The component generators use information obtained from the component descriptions to instantiate the generic architecture. In addition to providing a perspective on the approach to component generation, related work in knowledge-based software engineering is presented. These exercises are generalized, outlining a process for developing software which takes advantage of component generator technology and supports several forms of component composition. >
Advanced glycation end products biphasically modulate bone resorption in osteoclast-like cells (2015)

Advanced glycation end products (AGEs) disturb bone remodeling during aging, and this process is accelerated in diabetes. However, their role in modulation of osteoclast-induced bone resorption is controversial, with some studies indicating that AGEs enhance bone resorption and others showing the opposite effect. We determined whether AGEs present at different stages of osteoclast differentiation affect bone resorption differently. Based on increased levels of tartrate-resistant acid phosphatase (TRAP) and cathepsin K (CTSK), we identified day 4 of induction as the dividing time of cell fusion stage and mature stage in RAW264.7 cell-derived osteoclast-like cells (OCLs). AGE-modified BSA (50-400 μg/ml) or control BSA (100 μg/ml) was then added at the beginning of each stage. Results showed that the presence of AGEs at the cell fusion stage reduced pit numbers, resorption area, and CTSK expression. Moreover, expression of receptor activator of nuclear factor-κB (RANK) as well as the number of TRAP-positive cells, nuclei per OCL, actin rings, and podosomes also decreased. However, the presence of AGEs at the mature stage enlarged the resorption area markedly and increased pit numbers slightly. Intriguingly, only the number of nuclei per OCL and podosomes increased. These data indicate that AGEs biphasically modulate bone resorption activity of OCLs in a differentiation stage-dependent manner. AGEs at the cell fusion stage reduce bone resorption dramatically, mainly via suppression of RANK expression in osteoclast precursors, whereas AGEs at the mature stage enhance bone resorption slightly, most likely by increasing the number of podosomes in mature OCLs.
Molecular Recognition of a RNA:DNA Hybrid Structure (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMolecular Recognition of a RNA:DNA Hybrid StructureJinsong Ren, Xiaogang Qu, Nanibhushan Dattagupta, and Jonathan B. ChairesView Author Information Department of Biochemistry University of Mississippi Medical Center 2500 North State Street, Jackson, Mississippi 39216-4505 Applied Gene Technologies, Inc. 6190 Cornerstone Court East, Suite 101 San Diego, California 92121 Cite this: J. Am. Chem. Soc. 2001, 123, 27, 6742–6743Publication Date (Web):June 15, 2001Publication History Received8 February 2001Revised29 May 2001Published online15 June 2001Published inissue 1 July 2001https://doi.org/10.1021/ja015649yCopyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views876Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (39 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Assays,Chemical structure,Genetics,Molecular structure,Peptides and proteins Get e-Alerts
Easy Preparation of Bioactive Peptides from the Novel <i>N</i>α-Trifluoroethyl Amino Acids (2000)

Abstract N α-Trifluoroethyl amino acids have been prepared for the first time and unexpectedly found to behave as conventionally N-protected amino acids. Novel unnatural peptides are easily prepared in high yields without racemization. The observed chemistry results from steric factors as well as from the acidity of the CF3CH2NH group, according to comparative experiments. Of ten dipeptides that were tested for antitumor activity, CF3CH2–l-Tyr–l-Ile–OtBu was the most active.
The leukemogenic action of phorbol. (1970)

The unesterified, water-soluble compound phorbol, which does not act as a promoting agent for skin carcinogenesis when applied topically (although phorbol esters extracted from croton seed oil display pronounced activity), was tested in female SWR mice for promoting action by the systemic route, in the hope of overcoming a suspected solubility barrier in the skin. The results were negative.

A high incidence of leukemias developed, however, both in the group receiving preliminary skin painting with 7,12-dimethylbenz(a)anthracene followed by phorbol injections and in the phorbol control group. The tumors were of lymphoid origin, mostly nonthymic. There were also many reticulum cell sarcomas in the phorbol-treated mice, but the incidence did not appear to be higher than in the control groups.

The potential value of phorbol as a chemical leukemogenic agent for the study of the mechanism of leukemogenesis is discussed.
When Clocks Go Bad: Neurobehavioural Consequences of Disrupted Circadian Timing (2008)

Progress in unravelling the cellular and molecular basis of mammalian circadian regulation over the past decade has provided us with new avenues through which we can explore central nervous system disease. Deteriorations in measurable circadian output parameters, such as sleep/wake deficits and dysregulation of circulating hormone levels, are common features of most central nervous system disorders. At the core of the mammalian circadian system is a complex of molecular oscillations within the hypothalamic suprachiasmatic nucleus. These oscillations are modifiable by afferent signals from the environment, and integrated signals are subsequently conveyed to remote central neural circuits where specific output rhythms are regulated. Mutations in circadian genes in mice can disturb both molecular oscillations and measurable output rhythms. Moreover, systematic analysis of these mutants indicates that they can express an array of abnormal behavioural phenotypes that are intermediate signatures of central nervous system disorders. Furthermore, the response of these mutants to psychoactive drugs suggests that clock genes can modify a number of the brain's critical neurotransmitter systems. This evidence has led to promising investigations into clock gene polymorphisms in psychiatric disease. Preliminary indications favour the systematic investigation of the contribution of circadian genes to central nervous system disease.
Pulling off the comeback: shrink, expand, neither, both? (2012)

Purpose In this paper, the authors aim to build a prescriptive framework to help managers in turning around their ailing organizations. Their framework focuses on the extent of contractionary and expansionary initiatives needed to rebuild long‐term competitive advantage. They make the case that managers engaging in a pro‐active and balanced approach to scaling down and growing their organizations can boost the success of their recovery efforts. Design/methodology/approach The authors build their framework based on academic research on corporate turnarounds, their scholarly work on corporate restructuring, and their combined experiences and observations in industry. Their framework proposes four possible outcomes of the turnaround process: comeback, adrift, running‐on‐empty, and collapse. They provide examples to describe each outcome. Findings The authors' framework suggests that the interaction between two restructuring actions – retrenchment and repositioning ‐ determines the outcome of corporate turnarounds. By overemphasizing downsizing, managers fail to jumpstart entrepreneurial growth that can propel the firm towards long‐term competitive advantage. Similarly, stresses arising from excessive growth programs can quickly drain firm resources. As such, all managers need to assess the alignment between downsizing efforts and growth‐oriented initiatives. By bringing awareness to the interdependency between retrenchment and repositioning, the authors' framework can guide managers in making necessary adjustments on the way to fixing their organization. Originality/value Retrenchment and repositioning represent the means available to managers attempting corporate turnaround. However, corporate turnarounds often fail due to an overemphasis on one phase of the restructuring process, at the expense of the other. This framework points to the delicate retrenchment‐repositioning required to achieve successful turnaround.
Clavines as Antitumor Agents; 2<sup>1,2,3</sup>. Natural 8-Hydroxymethyl-ergoline Type Clavines and their Derivatives (1986)

The cytostatic potentials of 16 clavines were determined in the L5178y mouse lymphoma cell system: three of them are natural 8-hydroxymethylergoline type alkaloids (elymoclavine, lysergol, dihydrolysergol-I) and 13 are semisynthetic derivatives (O-acyl-; 1-alkyl-; 1-alkyl-O-acyl-; 1,O-dialkyl-; masked aldehydes). It is shown that in contrast to these alkaloids some of their derivatives are potent cytostatic agents: 1-propylelymoclavine (ED50 cone.: 2.2 µM), 1-propylelymoclavine-O-butyrate (2.7 µM), 6-methyl-8β-(2′-oxo-cyclohexylidenemethyl)-ergoline-I (4.0 µM). O-Acyl derivatives without substitution at N-1 were almost inactive. The substitution of the hydrogen at N-1 of inactive clavines by an alkyl group with three carbon atoms led to very active compounds indicating that the nature of the substituent at N-1 is very important for cytostatic activity. Incorporation studies in the presence of 1-propylelymoclavine showed that this compound inhibits primarily DNA synthesis. Partial syntheses of new ergolines are described.
Human endogenous retrovirus K and cancer: Innocent bystander or tumorigenic accomplice? (2014)

Harbored as relics of ancient germline infections, human endogenous retroviruses (HERVs) now constitute up to 8% of our genome. A proportion of this sequence has been co-opted for molecular and cellular processes, beneficial to human physiology, such as the fusogenic activity of the envelope protein, a vital component of placentogenesis. However, the discovery of high levels of HERV-K mRNA and protein and even virions in a wide array of cancers has revealed that HERV-K may be playing a more sinister role-a role as an etiological agent in cancer itself. Whether the presence of this retroviral material is simply an epiphenomenon, or an actual causative factor, is a hotly debated topic. This review will summarize the current state of knowledge regarding HERV-K and cancer and attempt to outline the potential mechanisms by which HERV-K could be involved in the onset and promotion of carcinogenesis.
Network-Coding-Based Gateway Handover Scheme for Terabit Satellite Networks (2013)

This paper proposes the use of network coding in handover strategies applied in Smart Gateway Diversity (SGD) architectures, in order to mitigate information losses usually experienced by traditional handover techniques. The focus is actually about the benefit resulting from network coding application in terms of improved transmission robustness at the cost of reasonable satellite capacity waste.
Thrombospondin-1 Is a Plasmatic Marker of Peripheral Arterial Disease That Modulates Endothelial Progenitor Cell Angiogenic Properties (2010)

NCT00377897.).
Temperature and Growth Rate Effects on the <i>hok/sok</i> Killer Locus for Enhanced Plasmid Stability (1994)

The hok/sok locus, isolated from the multiple-resistance plasmid R1 of Escherichia coli, is very efficient at ensuring the stable maintenance of plasmids in Gram-negative systems by killing plasmid-free cells as they arise. To investigate independently the influence of temperature and growth rate on the effectiveness of hok/sok, continuous fermentations have been conducted with the pUC-based, IPTG-induced, beta-galactosidase expression vector pTKW106. At fixed temperature (37 degrees C), decreasing the dilution rate decreased plasmid stability, and at a fixed, low dilution rate (D = 0.15/h), decreasing the temperature resulted in an increase in plasmid stability. These trends are explained by the specific beta-galactosidase activity of each continuous fermentation: higher, specific, recombinant protein expression led to decreased plasmid stability (due to either segregational or structural instability, as determined by plasmid DNA isolation). A representative fed-batch medium produced more beta-galactosidase on a volumetric basis than M9C in the chemostat, and addition of the hok/sok locus increased segregational stability by 8-22-fold in continuous fermentations that lacked antibiotic selection pressure and in which beta-galactosidase was constantly expressed a 12% of total cell protein for 60 h (43-47 generations).
Molecular mechanisms and implications for infection of lipopolysaccharide variation in <i>Neisseria</i> (1995)

The lipopolysaccharides of the pathogenic Neisseria species are subject to structural variation owing to a combination of intrinsic changes in lipopolysaccharide (LPS) biosynthesis and external modification of the LPS molecule with sialic acid. This variation appears to control bacterial behaviour by altering their ability to interact with human cells and to evade host immune defences. This interconversion of LPS phenotypes, which is also observed during the natural infection, is probably due to environmental regulation of LPS biosynthesis superimposed on spontaneous changes in the DNA of distinct LPS loci. LPS variation may be a common strategy of mucosal pathogens to colonize and persist within the human host.