gebhart/patrepeval huggingface dataset:
BMP-9 signals via ALK1 and inhibits bFGF-induced endothelial cell proliferation and VEGF-stimulated angiogenesis (2007)

Genetic studies in mice and humans have shown that the transforming growth factor-beta (TGF-beta) type-I receptor activin receptor-like kinase 1 (ALK1) and its co-receptor endoglin play an important role in vascular development and angiogenesis. Here, we demonstrate that ALK1 is a signalling receptor for bone morphogenetic protein-9 (BMP-9) in endothelial cells (ECs). BMP-9 bound with high affinity to ALK1 and endoglin, and weakly to the type-I receptor ALK2 and to the BMP type-II receptor (BMPR-II) and activin type-II receptor (ActR-II) in transfected COS cells. Binding of BMP-9 to ALK2 was greatly facilitated when BMPR-II or ActR-II were co-expressed. Whereas BMP-9 predominantly bound to ALK1 and BMPR-II in ECs, it bound to ALK2 and BMPR-II in myoblasts. In addition, we observed binding of BMP-9 to ALK1 and endoglin in glioblastoma cells. BMP-9 activated Smad1 and/or Smad5, and induced ID1 protein and endoglin mRNA expression in ECs. Furthermore, BMP-9 was found to inhibit basic fibroblast growth factor (bFGF)-stimulated proliferation and migration of bovine aortic ECs (BAECs) and to block vascular endothelial growth factor (VEGF)-induced angiogenesis. Taken together, these results suggest that BMP-9 is a physiological ALK1 ligand that plays an important role in the regulation of angiogenesis.
Physiological and Psychological Fatigue in Extreme Conditions: Overtraining and Elite Athletes (2010)

This article will review relevant mechanisms and markers associated with overtraining syndrome (OTS), and discuss signs and symptoms, differential diagnosis, and current assessment tools for fatigue within the context of overtraining. The findings are drawn from original research and review articles referenced by PubMed and ScienceDirect databases. Sources were selected for their contributions to the current knowledge of biological, psychological, and molecular mechanisms. Data were reviewed for relevance to OTS and then evaluated against criteria that included significant OTS outcomes and findings. Information was systematically analyzed to identify patterns, dependencies, connections, and causal factors. Comparative analysis was confounded by inconsistent metrics, terminology, and variable methodology; potential biomarkers, treatment and prevention approaches, and future research directions are identified. Diagnosing OTS is difficult because underlying cause(s) are unknown; one must exclude other factors that degrade performance and mood status. Many studies are confounded by inadequate experimental designs, poor measures of performance, and different methods for characterizing OTS. OTS is complex because the demands of excessive training in combination with other biologic, psychological, and social stressors are difficult to quantify. However, changes in mood are always noted. Interrelations among dietary patterns; social, psychological and physiological profiles; and the neuroendocrine, immune, and central nervous systems are complex and not adequately elucidated.
Free-space entangled quantum carpets (2017)

The Talbot effect in quantum physics is known to produce intricate patterns in the probability distribution of a particle, known as ``quantum carpets,'' corresponding to the revival and replication of the initial wave function. Recently, it was shown that one can encode a $D$-level qudit in such a way that the Talbot effect can be used to process the $D$-dimensional quantum information [Far\'{\i}as et al., Phys. Rev. A 91, 062328 (2015)]. Here we introduce a scheme to produce free-propagating ``entangled quantum carpets'' with pairs of photons produced by spontaneous parametric down-conversion. First we introduce an optical device that can be used to synthesize arbitrary superposition states of Talbot qudits. Sending spatially entangled photon pairs through a pair of these devices produces an entangled pair of qudits. As an application, we show how the Talbot effect can be used to test a $D$-dimensional Bell inequality. Numerical simulations show that violation of the Bell inequality depends strongly on the amount of spatial correlation in the initial two-photon state. We briefly discuss how our optical scheme might be adapted to matter wave experiments.
Range sensing by projecting multi-slits with random cuts (2003)

A method is described for acquiring range data by projecting a single pattern of multiple slits. To obtain three-dimensional data by projecting a single pattern, certain codes for identifying each slit must be contained in the pattern. In addition, if the characteristics of the code embedded in the pattern are not affected by the change of relations between a position of a camera and that of a pattern projector, arbitrariness in positions of both the camera and the projector can be allowed. Random dots are used to identify each slit. The random dots are given as randomly distributed cuts on each slit. Thus, each slit is divided into many small line segments, and, using these segments as features, stereo matching is carried out to obtain three-dimensional data. Using adjacent relations among slit segments, segment pairs, whose adjacent segments also correspond to each other, are extracted and considered to be correct matches. From the resultant matches, the correspondence is propagated by utilizing the adjacency relationships to get an entire range image.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CD137 activation abrogates granulocyte-macrophage colony-stimulating factor-mediated anti-apoptosis in neutrophils (2000)

CD137 (ILA / 4-1BB) is a member of the TNF / NGF receptor family, and has previously been suggested to be involved in T cell activation and differentiation. Here, we demonstrate that blood neutrophils from control individuals and patients with cystic fibrosis express CD137 mRNA and surface protein. In contrast, lung neutrophils derived from patients with cystic fibrosis did not express detectable CD137 levels. Such CD137-deficient neutrophils could also be generated from normal neutrophils by TNF-alpha stimulation in vitro. TNF-alpha was found to be highly expressed in epithelial cells from cystic fibrosis but not normal lungs, suggesting that TNF-alpha might account for reduced neutrophil CD137 levels under inflammatory conditions in vivo. To investigate whether CD137 is involved in the regulation of apoptosis, neutrophils were activated with functional anti-CD137 antibody in the presence or absence of different neutrophil survival factors in vitro. Activation of CD137 abrogated GM-CSF-mediated anti-apoptosis in normal but not in CD137-deficient neutrophils. Moreover, G-CSF- and IFN-gamma-mediated neutrophil anti-apoptosis was not affected by anti-CD137 antibody treatment. In conclusion, these data suggest that CD137 activation may limit GM-CSF-mediated anti-apoptosis of neutrophils. The absence of this anti-inflammatory mechanism in inflammatory responses might be associated with massive neutrophil accumulation and consequent tissue damage.
A scalable mark-sweep garbage collector on large-scale shared-memory machines (1997)

This work describes implementation of a mark-sweep garbage collector (GC) for shared-memory machines and reports its performance. It is a simple ''parallel'' collector in which all processors cooperatively traverse objects in the global shared heap. The collector stops the application program during a collection and assumes a uniform access cost to all locations in the shared heap. Implementation is based on the Boehm-Demers-Weiser conservative GC (Boehm GC). Experiments have been done on Ultra Enterprise 10000 (Ultra Sparc processor 250 MHz, 64 processors). We wrote two applications, BH (an N-body problem solver) and CKY (a context free grammar parser) in a parallel extension to C++.Through the experiments, We observe that load balancing is the key to achieving scalability. A naive collector without load redistribution hardly exhibits speed-up (at most fourfold speed-up on 64 processors). Performance can be improved by dynamic load balancing, which exchanges objects to be scanned between processors, but we still observe that straightforward implementation severely limits performance. First, large objects become a source of significant load imbalance, because the unit of load redistribution is a single object. Performance is improved by splitting a large object into small pieces before pushing it onto the mark stack. Next, processors spend a significant amount of time uselessly because of serializing method for termination detection using a shared counter. This problem suddenly appeared on more than 32 processors. By implementing non-serializing method for termination detection, the idle time is eliminated and performance is improved. With all these careful implementation, we achieved average speed-up of 28.0 in BH and 28.6 in CKY on 64 processors.
Assignment of Free and Disulfide-Bonded Cysteine Residues in Testis Angiotensin-Converting Enzyme:  Functional Implications (1996)

Human testicular angiotensin-converting enzyme (tACE) is an extracellular protein that contains seven cysteine residues. The cysteines occur in a sequential distribution that is precisely mimicked in the tACE from rabbit and mouse, and in both domains of all known species of somatic ACE. One of the cysteines in human tACE, Cys496, is present in the reduced form as shown by labeling it with 5-[[2-(iodoacetyl)amino]ethylamino]naphthalene-1-sulfonic acid, isolating the fluorescent peptide from enzymatic digests by HPLC, and analyzing its sequence by matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). Thiol reagents have no significant effect on the activity of tACE, indicating that this Cys is not involved in catalysis. The other six cysteines exist as three disulfides. Mass spectral analysis of cyanogen bromide peptides has established that the cystine connectivities follow a nearest-neighbor, aabbcc, pattern i.e., Cys152-Cys158, Cys352-Cys370, and Cys538-Cys550, in which the disulfides form three small loops of five, 17, and 11 residues, respectively. Although these disulfide loops constitute less than 5% of the total sequence of the protein, they contribute to the overall structural stabilization of tACE.
A Facile Synthesis of Homologous 4,4′-Dialkanoic Acid Substituted 2,2′-Bipyridines (2002)

A convenient three-step synthesis has been developed to prepare a series of homologous 4,4′-dialkanoic acid substituted 2,2′-bipyridines from 4,4′-dimethyl-2,2′-bipyridine.
A New Selective Agent for Eukaryotic Cloning Vectors (1980)

An aminoglycoside antibiotic, G418, has been shown to be an inhibitor of many pro- and eukaryotes at concentrations from 1-300 microgram/ml. A bacterial R-plasmid determinant that phosphorylates and inactivates antibiotic G418 can be introduced into yeast by transformation and expresses resistance to G418. It is suggested that this combination of antibiotic and dominant resistance mechanism may be useful in recombinant DNA studies as a cloning selection in eukaryotes.
Proteins are potent biomarkers to detect colon cancer progression (2014)

Colon cancer is the most common type of cancer and major cause of death worldwide. The detection of colon cancer is difficult in early stages. However, the secretory proteins have been used as ideal biomarker for the detection of colon cancer progress in cancer patients. Serum/tissue protein expression could help general practitioners to identify colon cancer at earlier stages. By this way, we use the biomarkers to evaluate the anticancer drugs and their response to therapy in cancer models. Recently, the biomarker discovery is important in cancer biology and disease management. Also, many measurable specific molecular components have been studied in colon cancer therapeutics. The biomolecules are mainly DNA, RNA, metabolites, enzymes, mRNA, aptamers and proteins. Thus, in this review we demonstrate the important protein biomarker in colon cancer development and molecular identification of protein biomarker discovery.
A Novel Quasi-Resonant Snubber-Assisted ZCS-PWM DC-DC Converter with High Frequency Link (2007)

In this paper, a novel type of auxiliary switched capacitor assisted edge resonant soft switching PWM resonant DC-DC Converter with two simple auxiliary commutation lossless inductor snubbers. The operation principle of this converter is described using the switching mode equivalent circuits. This newly developed multi resonant DC-DC Converter can regulate its dc output AC power under a principle of constant frequency edge-resonant soft switching commutation by asymmetrical PWM duty cycle control scheme. The high frequency power regulation and actual power characteristics of the proposed soft switching PWM resonant DC-DC Converter are evaluated and discussed. The operating performances of the newly proposed soft switching inverter are represented based on simulation a results from an application point of view.
CTLA-4: a moving target in immunotherapy (2017)

CD28 and CTLA-4 are members of a family of immunoglobulin-related receptors that are responsible for various aspects of T-cell immune regulation. The family includes CD28, CTLA-4, and ICOS as well as other proteins, including PD-1, BTLA, and TIGIT. These receptors have both stimulatory (CD28, ICOS) and inhibitory roles (CTLA-4, PD-1, <i>BTLA</i>, and TIGIT) in T-cell function. Increasingly, these pathways are targeted as part of immune modulatory strategies to treat cancers, referred to generically as immune checkpoint blockade, and conversely to treat autoimmunity and CTLA-4 deficiency. Here, we focus on the biology of the CD28/CTLA-4 pathway as a framework for understanding the impacts of therapeutic manipulation of this pathway.
Single nucleotide polymorphisms in the human interleukin-1B gene affect transcription according to haplotype context (2006)

We questioned the significance of haplotype structure in gene regulation by testing whether individual single nucleotide polymorphisms (SNPs) within a gene promoter region [interleukin-1-beta (IL1B)] might affect promoter function and, if so, whether function was dependent on haplotype context. We sequenced genomic DNA from 25 individuals of diverse ethnicity, focusing on exons and upstream flanking regions of genes of the cluster. We identified four IL1B promoter region SNPs that were active in transient transfection reporter gene assays. To substantiate allelic differences found in reporter gene assays, we also examined nuclear protein binding to promoter sequence oligonucleotides containing different alleles of the SNPs. The effect of individual SNPs on reporter gene transcription varied according to which alleles of the three other SNPs were present in the promoter construct. The SNP patterns that influenced function reflected common haplotypes that occur in the population, suggesting functionally significant interactions between SNPs according to haplotype context. Of the haplotypes that include the four functional IL1B promoter SNPs (-3737, -1464, -511, -31), the four haplotypes that showed different contextual effects on SNP function accounted for >98% of the estimated haplotypes in Caucasian and African-American populations. This finding underlines the importance of understanding the haplotype structure of populations used for genetic studies and may be especially important in the functional analysis of genetic variation across gene regulatory regions.
Modulation of Alzheimer-Like Synaptic and Cholinergic Deficits in Transgenic Mice by Human Apolipoprotein E Depends on Isoform , Aging, and Overexpression of Amyloid β Peptides But Not on Plaque Formation (2002)

The most frequent human apolipoprotein (apo) E isoforms, E3 and E4, differentially affect Alzheimer's disease (AD) risk (E4 > E3) and age of onset (E4 < E3). Compared with apoE3, apoE4 promotes the cerebral deposition of amyloid beta (Abeta) peptides, which are derived from the amyloid precursor protein (APP) and play a central role in AD. However, it is uncertain whether Abeta deposition into plaques is the main mechanism by which apoE isoforms affect AD. We analyzed murine apoE-deficient transgenic mice expressing in their brains human APP (hAPP) and Abeta together with apoE3 or apoE4. Because cognitive decline in AD correlates better with decreases in synaptophysin-immunoreactive presynaptic terminals, choline acetyltransferase (ChAT) activity, and ChAT-positive fibers than with plaque load, we compared these parameters in hAPP/apoE3 and hAPP/apoE4 mice and singly transgenic controls at 6-7, 12-15, and 19-24 months of age. Brain aging in the context of high levels of nondeposited human Abeta resulted in progressive synaptic/cholinergic deficits. ApoE3 delayed the synaptic deficits until old age, whereas apoE4 was not protective at any of the ages analyzed. Old hAPP/apoE4 mice had more plaques than old hAPP/apoE3 mice, but synaptic/cholinergic deficits preceded plaque formation in hAPP/apoE4 mice. Moreover, despite their different plaque loads, old hAPP/apoE4 and hAPP/apoE3 mice had comparable synaptic/cholinergic deficits, and these deficits were found not only in the hippocampus but also in the neocortex, which in most mice contained no plaques. Thus, apoE3, but not apoE4, delays age- and Abeta-dependent synaptic deficits through a plaque-independent mechanism. This difference could contribute to the differential effects of apoE isoforms on the risk and onset of AD.
The clash of paradigms: Australian literary theory after liberalism (2008)

This essay argues that contemporary Australian literary theory, like most varieties of contemporary critical theory, is losing whatever relevance it once had, not because ‘theory’ has lost intellectual force, but because the contexts in which it operated have radically changed. A ‘crisis in liberalism’ and the rise of neo-liberalism and the new conservatism, I argue, requires a reassessment of the project of critical theory. This is especially crucial in the case of Australian literary criticism, given that Australian literary liberalism is historically complicit with a wider white patrician liberalism that has recently begun to contest itself in response to the new conservative politics of race.
Wnt signaling: is the party in the nucleus? (2006)

The Wnt signaling pathway controls cell proliferation and body patterning throughout development. A surprising number of cytoplasmic Wnt regulators (e.g., beta-catenin, Bcl-9/Lgs, APC, Axin) also appear, often transiently, in the nucleus. beta-Catenin is an integral component of E-cadherin complexes at intercellular adherens junctions, but also recruits chromatin remodeling complexes to activate transcription in the nucleus. The APC tumor suppressor is a part of the cytoplasmic beta-catenin destruction complex, yet also counteracts beta-catenin transactivation and histone H3K4 methylation at Wnt target genes. Furthermore, APC coordinates the cyclic exchange of Wnt coregulator complexes at the DNA. These opposing roles of APC and beta-catenin enable a rapid coordination of gene expression and cytoskeletal organization throughout the cell in response to signaling.
Toward Dietary Assessment via Mobile Phone Video Cameras. (2010)

Reliable dietary assessment is a challenging yet essential task for determining general health. Existing efforts are manual, require considerable effort, and are prone to underestimation and misrepresentation of food intake. We propose leveraging mobile phones to make this process faster, easier and automatic. Using mobile phones with built-in video cameras, individuals capture short videos of their meals; our software then automatically analyzes the videos to recognize dishes and estimate calories. Preliminary experiments on 20 typical dishes from a local cafeteria show promising results. Our approach complements existing dietary assessment methods to help individuals better manage their diet to prevent obesity and other diet-related diseases.
The AC-3 Multichannel Coder (1993)

This paper describes the operation of the AC-3 multichannel adaptive transform coder. Coding a multiplicity of channels as a single entity is more efficient that coding individual channels, permitting a lower net data rate. The major processing blocks of the AC-3 coder are presented and discussed, along with the underlying psychoacoustic principles. Strengths and limitations of the coding techniques are cited. I.
Cardiolipins Are Biomarkers of Mitochondria-Rich Thyroid Oncocytic Tumors (2016)

Oncocytic tumors are characterized by an excessive eosinophilic, granular cytoplasm due to aberrant accumulation of mitochondria. Mutations in mitochondrial DNA occur in oncocytic thyroid tumors, but there is no information about their lipid composition, which might reveal candidate theranostic molecules. Here, we used desorption electrospray ionization mass spectrometry (DESI-MS) to image and chemically characterize the lipid composition of oncocytic thyroid tumors, as compared with nononcocytic thyroid tumors and normal thyroid samples. We identified a novel molecular signature of oncocytic tumors characterized by an abnormally high abundance and chemical diversity of cardiolipins (CL), including many oxidized species. DESI-MS imaging and IHC experiments confirmed that the spatial distribution of CLs overlapped with regions of accumulation of mitochondria-rich oncocytic cells. Fluorescent imaging and mitochondrial isolation showed that both mitochondrial accumulation and alteration in CL composition of mitochondria occurred in oncocytic tumors cells, thus contributing the aberrant molecular signatures detected. A total of 219 molecular ions, including CLs, other glycerophospholipids, fatty acids, and metabolites, were found at increased or decreased abundance in oncocytic, nononcocytic, or normal thyroid tissues. Our findings suggest new candidate targets for clinical and therapeutic use against oncocytic tumors. Cancer Res; 76(22); 6588-97. ©2016 AACR.
Transcriptional Activation of APETALA1 by LEAFY (1999)

Plants produce new appendages reiteratively from groups of stem cells called shoot apical meristems. LEAFY (LFY) and APETALA1 (AP1) are pivotal for the switch to the reproductive phase, where instead of leaves the shoot apical meristem produces flowers. Use of steroid-inducible activation of LFY demonstrated that early expression of AP1 is a result of transcriptional induction by LFY. This AP1 induction is independent of protein synthesis and occurs specifically in the tissues and at the developmental stage in which floral fate is assumed. Later expression of AP1 appears to be only indirectly affected by LFY.
Adaptive workflow management—an integrated approach and system architecture (2000)

In this paper, we present an integrated approach and a three-tier System Architecture for Adaptive Workflow Management. An important feature of this Architecture, is the inclusion of a Planning component, not seen so far in most Workflow systems, which helps to integrate Planning and Adaptive Workflow Management. Another important feature of this Architecture, is that it has been developed primarily by synthesizing existing research in the Workflow area., instead of "reinventing the wheel"; this should render the Architecture easier to implement, since many of its theoretical underpinnings have already been thoroughly investigated by other researchers.