gebhart/patrepeval huggingface dataset:
Aspergilli and lignocellulosics: Enzymology and biotechnological applications (1994)

Aspergilli are versatile ascomycetes that are able to transform at a rapid rate a wide spectrum of lignin-related aromatic compounds. While it is clear that these fungi can degrade phenolic and polysaccharide components from lignocellulosic material, the status regarding degradation of high-molecular mass lignins is controversial. This review compiles data from the literature as well as that from the authors' laboratory with the aim of clarifying this point. The main body of evidence points towards the inability of aspergilli alone to degrade lignin free of low-molecular mass contaminants. Nevertheless, the ability of this genus to efficiently degrade hemicelluloses makes it an essential participant in the complex microbial system necessary for wood decay under natural conditions. Aspergilli are known to overproduce high levels of hemicellulolytic enzymes. Out of the large array of these enzymes that act in concert to degrade lignocellulosic material, only endoxylanases of aspergilli are described in so far as these are the main activities required for enzyme-aided bleaching. The biochemical features of the endoxylanases from Aspergillus niger are briefly described as these serve to illustrate how a complex family of isozymes is necessary to deal with the structural and chemical heterogeneity of xylans. Emphasis is placed on the biotechnological applications of lignocellulosic materials transformed by aspergilli. The key application areas are biopulping and biobleaching where a reduction in the use of environmentally harmful chemicals traditionally used in the pulp and paper industry is envisaged. Waste water treatment represents another vast application area where aspergilli have been shown to be effective not only in colour removal but also in the bioconversion of potentially noxious substances into useful bioproducts.
Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function (2007)

Glucocorticoid-induced TNF receptor ligand (GITRL), a recently identified member of the TNF family, binds to its receptor GITR on both effector and regulatory T cells and generates positive costimulatory signals implicated in a wide range of T cell functions. Structural analysis reveals that the human GITRL (hGITRL) ectodomain self-assembles into an atypical expanded homotrimer with sparse monomer-monomer interfaces. Consistent with the small intersubunit interfaces, hGITRL exhibits a relatively weak tendency to trimerize in solution and displays a monomer-trimer equilibrium not reported for other TNF family members. This unique assembly behavior has direct implications for hGITRL-GITR signaling, because enforced trimerization of soluble hGITRL ectodomain results in an approximately 100-fold increase in its receptor binding affinity and also in enhanced costimulatory activity. The apparent reduction in affinity that is the consequence of this dynamic equilibrium may represent a mechanism to realize the biologically optimal level of signaling through the hGITRL-GITR pathway, as opposed to the maximal achievable level.
Nonintrusive estimation of expected throughput for IEEE 802.11 devices (2014)

Knowing the available throughput of the IEEE 802.11 link is highly beneficial. One use case of such information is the selection of an Access Point (AP) that will provide highest throughput. In this paper, we present a scheme for non-intrusive estimation of expected throughput of an 802.11 device. The proposed scheme does not require any aid from the infrastructure (e.g., AP) and does not create any additional traffic overhead (e.g., probe traffic). Our scheme relies on passive sniffing of the ongoing traffic for short duration (typically less than a second). Via sniffing, we obtain necessary parameters for throughput estimation, such as the collision probability. We have implemented our scheme in Linux system and Android smartphone. Experimental evaluation shows that our scheme accurately estimates expected throughput in various experiment settings.
The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA (1985)

The RF IV form of M13 DNA was synthesized enzymatically in vitro, using the viral (+)strand as template, to contain phosphorothioate-modified internucleotidic linkages of the Rp configuration on the 5' side of every base of a particular type in the newly-synthesized (-)strand. Twenty nine restriction enzymes were then tested for their reactions with the appropriate modified DNA types having a phosphorothioate linkage placed exactly at the cleavage site(s) of these enzymes in the (-)strand. Eleven of the seventeen restriction enzymes tested that had recognition sequences of five bases or more could be used to convert the phosphorothioate DNA entirely into the nicked form, either by simply allowing the reaction to go to completion with excess enzyme (Ava I, Ava II, Ban II, Hind II, Nci I, Pst I or Pvu I) or by stopping the reaction at the appropriate time before the nicked DNA is linearized (Bam HI, Bgl I, Eco RI or Hind III). Only modification of the exact cleavage site in the (-)strand could block linearization by the first class of enzymes. The results presented imply that the restriction enzyme-directed nicking of phosphorothioate M13 DNA occurs exclusively in the (+)strand.
The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites (2005)

This review covers the biosynthesis of aliphatic and aromatic polyketides as well as mixed polyketide/NRPS metabolites, and discusses the molecular genetics and enzymology of the proteins responsible for their formation.
A coherent distributed file cache with directory write-behind (1994)

Extensive caching is a key feature of the Echo distributed file system. Echo client machines maintain coherent caches of file and directory data and properties, with write-behind (delayed write-back) of all cached information. Echo specifies ordering constraints on this write-behind, enabling applications to store and maintain consistent data structures in the file system even when crashes or network faults prevent some writes from being completed. In this paper we describe the Echo cache's coherence and ordering semantics, show how they can improve the performance and consistency of applications, explain how they are implemented. We also discuss the general problem of reliably notifying applications and users when write-behind is lost; we addressed this problem as part of the Echo design, but did not find a fully satisfactory solution.
Selective Hydrogen Production from Methanol with a Defined Iron Pincer Catalyst under Mild Conditions (2013)

Molecularly well-defined iron pincer complexes promote the aqueous-phase reforming of methanol to carbon dioxide and hydrogen, which is of interest in the context of a methanol and hydrogen economy. For the first time, the use of earth-abundant iron complexes under mild conditions for efficient hydrogen generation from alcohols is demonstrated.
Clinically defined vascular depression (1997)

The symptoms of vascular depression are consistent with lesions that may damage striato-pallido-thalamo-cortical pathways and other areas. The concept of vascular depression can provide the impetus for investigations of prevention and treatment of cerebrovascular disease and for studies of the course of vascular depression and selection of antidepressants.
Predicting spontaneous termination of atrial fibrillation using the surface ECG (2006)

By recognizing and characterizing conditions under which atrial fibrillation (AF) is likely to terminate spontaneously or be sustained, improved treatment of sustained AF may result and unnecessary treatment of self-terminating AF avoided. Time-frequency measures that characterize AF, such as fibrillatory frequency, amplitude, and waveform shape (exponential decay), are extracted from the residual ECG following QRST cancellation. Three complexity measures are also studied, characterizing the degree of organization of atrial activity. All measures are analysed using a training set, consisting of 20 recordings of AF with known termination properties, and a test set of 30 recordings. Spontaneous termination was best predicted by a low and stable fibrillatory frequency and a low exponential decay. Using these predictors, 90% of the test set was correctly classified into terminating and sustained AF. Neither fibrillation amplitude nor the complexity measures differed significantly between the two sets.
Role of the Parasympathetic System in Airway Obstruction Due to Emphysema (1984)

To study the relative contributions of parasympathetic and sympathetic mechanisms in airway obstruction in patients with emphysema, we gave supramaximal doses of anticholinergic and adrenergic agents in sequence and in combination. Serial doses of one agent were administered to achieve a plateau of bronchodilatation; after that the other agent was administered. The plateau achieved with the anticholinergic agent (atropine methonitrate) was significantly higher than that achieved with the adrenergic agent (salbutamol). When the adrenergic agent was given first, additional bronchodilatation was achieved with subsequent use of the anticholinergic agent. When the anticholinergic agent was given first, no additional bronchodilatation was achieved with subsequent administration of the adrenergic agent. When both agents were given simultaneously, the degree of bronchodilatation was virtually identical to that obtained with the anticholinergic agent alone. Tests sensitive to small-airway and large-airway function and lung volumes gave essentially the same results. Thus, all achievable bronchodilatation was obtained with the anticholinergic agent alone. These results suggest that the two classes of agents produce bronchodilatation through a common cholinergic pathway in emphysema, and support the concept that parasympathetic activity is the dominant reversible component of airway obstruction in this disease.
Omega-3 Fatty Acids and Inflammatory Processes (2010)

Long chain fatty acids influence inflammation through a variety of mechanisms; many of these are mediated by, or at least associated with, changes in fatty acid composition of cell membranes. Changes in these compositions can modify membrane fluidity, cell signaling leading to altered gene expression, and the pattern of lipid mediator production. Cell involved in the inflammatory response are typically rich in the n-6 fatty acid arachidonic acid, but the contents of arachidonic acid and of the n-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) can be altered through oral administration of EPA and DHA. Eicosanoids produced from arachidonic acid have roles in inflammation. EPA also gives rise to eicosanoids and these often have differing properties from those of arachidonic acid-derived eicosanoids. EPA and DHA give rise to newly discovered resolvins which are anti-inflammatory and inflammation resolving. Increased membrane content of EPA and DHA (and decreased arachidonic acid content) results in a changed pattern of production of eicosanoids and resolvins. Changing the fatty acid composition of cells involved in the inflammatory response also affects production of peptide mediators of inflammation (adhesion molecules, cytokines etc.). Thus, the fatty acid composition of cells involved in the inflammatory response influences their function; the contents of arachidonic acid, EPA and DHA appear to be especially important. The anti-inflammatory effects of marine n-3 PUFAs suggest that they may be useful as therapeutic agents in disorders with an inflammatory component.
A Quest for Systematic Constitutive Formulations for General Field and Wave Systems Based on the Volterra Differential Operators (2000)

A systematic formulation of constitutive relations for general field systems is explored, which takes into account the main material features. These are dispersion, inhomogeneity, which can be present in linear and nonlinear systems. There are two main difficulties associated with existing representations: Dispersion is usually referred to in the spectral domain, while inhomogeneity is obviously a spatiotemporal phenomenon; moreover, the existing representations involve spatiotemporally dependent integrals, and those suggest non-local interaction which raises relativistic causality issues. The present approach introduces new representations in terms of Volterra differential operators, which obviate these difficulties within the domain of their validity, allowing for spatiotemporal representation of both dispersion and inhomogeneity, in linear and nonlinear systems. Minkowski's methodology for representation of material properties in the presence of moving media is re-examined in view of the new constituti...
The development of imatinib as a therapeutic agent for chronic myeloid leukemia (2004)

Imatinib has revolutionized drug therapy of chronic myeloid leukemia (CML). Preclinical studies were promising but the results of clinical trials by far exceeded expectations. Responses in chronic phase are unprecedented, with rates of complete cytogenetic response (CCR) of more than 40% in patients after failure of interferon-alpha (IFN) and more than 80% in newly diagnosed patients, a level of efficacy that led to regulatory approval in record time. While most of these responses are stable, resistance to treatment after an initial response is common in more advanced phases of the disease. Mutations in the kinase domain (KD) of BCR-ABL that impair imatinib binding have been identified as the leading cause of resistance. Patients with CCR who achieve a profound reduction of BCR-ABL mRNA have a very low risk of disease progression. However, residual disease usually remains detectable with reverse transcription-polymerase chain reaction (RT-PCR), indicating that disease eradication may pose a significant challenge. The mechanisms underlying the persistence of minimal residual disease are unknown. In this manuscript, we review the preclinical and clinical development of imatinib for the therapy of CML, resistance and strategies that may help to eliminate resistant or residual leukemia.
Video prediction block structure and the emerging high efficiency video coding standard (2012)

In the ISO/IEC 14496-10 |ITU-T H.264 advanced video coding (AVC) standard, the prediction block sizes can be 16×16, 8×8 and 4×4 for Intra prediction; 16×16, 16×8, 8×16, 8×8, 8×4, 4×8 and 4×4 for Inter prediction. In the first HEVC test model (HM1.0), each 2N×2N Intra CU may consist of either one 2N×2N prediction unit (PU) or four N×N prediction units; while each 2N×2N Inter CU may consist of one 2N×2N PU, two 2N×N or N×2N PUs or four N×N PUs. Since then, some investigations have been made to the prediction block structure based on HM1.0, including the removal of N×N prediction partition mode for all coding units (CU) except the smallest CU, and the removal of 4×4 Inter prediction. Experimental results show that with both these simplifications, the encoder complexity can be greatly reduced at the minimum cost of coding efficiency. Therefore both of these two suggestions were adopted by the HEVC standard.
ANTHRACYCLINES - A REVIEW OF GENERAL AND SPECIAL TOXICITY STUDIES (1995)

Preclinical safety assessment data on doxorubicin (DOXO), epirubicin (EPI), idarubicin (IDA) and methoxymorpholinodoxorubicin (MORPHO), from mouse, rat and dog studies are reviewed. These data are put into perspective allowing for extrapolations across species, doses and dose regimens with recommendations for proper human use. The compounds were administered intravenously or intraperitoneally in studies ranging from single dose to multiple dose studies of different durations. The compounds were given once, daily, weekly or cyclically. In the cyclic administration studies, DOXO, EPI, and IDA were given for 3 consecutive days a week for 6 or 13 weeks; MORPHO was given for 3 consecutive days a week every three weeks for a total of 9 cycles. The duration of the cyclic studies was from 6-26 weeks. Daily dose studies lasted from 4-26 weeks. In the single dose studies the recovery ranged from 4 weeks to one year; in the multiple dose studies from 4 to 8 weeks. A few special studies were also considered. In all studies reviewed, 2 different types of toxicity were observed. These toxicities occur also in man. The first is the acute toxicity, which is the consequence of cytotoxicity and expresses the exaggerated pharmacological activity of the compounds. The target sites in all 3 species and in man include the hemolymphopoietic system (HLPS), the gastrointestinal (GI) tract, skin and testes; all renewing cell types. The second type of toxicity is the chronic progressive toxicity. This toxicity is the expression and result of sustained disruption of cytoplasmic homeostasis and occurs in non-renewing cell types. The target sites include the heart (both animals and man), kidneys (rodents) and peripheral nervous system (PNS) (rodents). From single administration animal data, chronicity, site and magnitude of toxicities can be predicted in man. Despite strong mitogenic stimuli in the rat, there is no evidence that there is a potential for hemolympho- or hepatocarcinogenicity with these compounds.
Multi-Scale Context Aggregation by Dilated Convolutions (2015)

State-of-the-art models for semantic segmentation are based on adaptations of convolutional networks that had originally been designed for image classification. However, dense prediction and image classification are structurally different. In this work, we develop a new convolutional network module that is specifically designed for dense prediction. The presented module uses dilated convolutions to systematically aggregate multi-scale contextual information without losing resolution. The architecture is based on the fact that dilated convolutions support exponential expansion of the receptive field without loss of resolution or coverage. We show that the presented context module increases the accuracy of state-of-the-art semantic segmentation systems. In addition, we examine the adaptation of image classification networks to dense prediction and show that simplifying the adapted network can increase accuracy.
The Nox1/4 Dual Inhibitor GKT137831 or Nox4 Knockdown Inhibits Angiotensin‐II‐Induced Adult Mouse Cardiac Fibroblast Proliferation and Migration. AT1 Physically Associates With Nox4 (2015)

Both oxidative stress and inflammation contribute to chronic hypertension-induced myocardial fibrosis and adverse cardiac remodeling. Here we investigated whether angiotensin (Ang)-II-induced fibroblast proliferation and migration are NADPH oxidase (Nox) 4/ROS and IL-18 dependent. Our results show that the potent induction of mouse cardiac fibroblast (CF) proliferation and migration by Ang-II is markedly attenuated by Nox4 knockdown and the Nox inhibitor DPI. Further, Nox4 knockdown and DPI pre-treatment attenuated Ang-II-induced IL-18, IL-18Rα and collagen expression, and MMP9 and LOX activation. While neutralization of IL-18 blunted Ang-II-induced CF proliferation and migration, knockdown of MMP9 attenuated CF migration. The antioxidant NAC and the cell-permeable SOD mimetics Tempol, MnTBAP, and MnTMPyP attenuated oxidative stress and inhibited CF proliferation and migration. The Nox1/Nox4 dual inhibitor GKT137831 also blunted Ang-II-induced H2 O2 production and CF proliferation and migration. Further, AT1 bound Nox4, and Ang-II enhanced their physical association. Notably, GKT137831 attenuated the AT1/Nox4 interaction. These results indicate that Ang-II induces CF proliferation and migration in part via Nox4/ROS-dependent IL-18 induction and MMP9 activation, and may involve AT1/Nox4 physical association. Thus, either (i) neutralizing IL-18, (ii) blocking AT1/Nox4 interaction or (iii) use of the Nox1/Nox4 inhibitor GKT137831 may have therapeutic potential in chronic hypertension-induced adverse cardiac remodeling.
From Pulsus to Pulseless (2006)

Computer simulations and nonlinear dynamics have provided invaluable tools for illuminating the underlying mechanisms of cardiac arrhythmias. Here, we review how this approach has led to major insights into the mechanisms of spatially discordant alternans, a key arrhythmogenic factor predisposing the heart to re-entry and lethal arrhythmias. During spatially discordant alternans, the action potential duration (APD) alternates out of phase in different regions of the heart, markedly enhancing dispersion of refractoriness so that ectopic beats have a high probability of inducing reentry. We show how, at the cellular level, instabilities in membrane voltage (ie, steep APD restitution slope) and intracellular Ca (Cai) cycling dynamics cause APD and the Cai transient to alternate and how the characteristics of alternans are affected by different "modes" of the bidirectional coupling between voltage and Cai. We illustrate how, at the tissue level, additional factors, such as conduction velocity restitution and ectopic beats, promote spatially discordant alternans. These insights have illuminated the mechanistic basis underlying the clinical association of cardiac alternans (eg, T wave alternans) with arrhythmia risk, which may lead to novel therapeutic approaches to avert sudden cardiac death.
Increased MAP kinase activity in Alzheimer's and Down syndrome but not in schizophrenia human brain (2004)

Abnormal phosphorylation of tau is a feature of Alzheimer's disease (AD), which develops prematurely in Down syndrome (DS) patients. Cognitive impairment is also recognized as a clinical characteristic of schizophrenia, which does not appear to be associated with tau-aggregate formation. Several kinases can phosphorylate tau in cell-free assays. Here we show increased activity of mitogen-activated protein kinases (MAPKs) (including ERK1/2, SAPKs and p38) in post mortem AD and DS brains, which could not be accounted for by expression changes. In contrast, glycogen synthase kinase-3 activity (GSK-3 alpha beta) was reduced significantly. Examination of tau in AD and DS using antibodies selective for MAPK phosphorylation sites showed increased immunoreactivity. In addition, phosphorylation of S(199), reportedly a selective substrate for cyclin-dependent kinase-5 (cdk5) or GSK-3 alpha beta was only observed in AD samples, which showed a concomitant increase in the expression of p25, the enhancing cofactor for cdk5 activity. However, in schizophrenia brain, MAPK-phosphorylated tau was unchanged compared to matched controls, despite similar expression levels to those in AD. The activities of the MAPKs and GSK-3 alpha beta were also unchanged. These data demonstrate that in AD and DS, enhanced MAPK activity, which has an established role in regulating neuronal plasticity and survival, can account for irregular tau phosphorylation, and that the molecular processes involved in these neurodegenerative disorders are distinct from those in schizophrenia. These data also question the significance of GSK-3 alpha beta, as much previous work carried out in vitro has placed this kinase as a favoured candidate for involvement in the pathological phosphorylation of tau.