gebhart/patrepeval huggingface dataset:
Functional Brain Networks Develop from a “Local to Distributed” Organization (2009)

The mature human brain is organized into a collection of specialized functional networks that flexibly interact to support various cognitive functions. Studies of development often attempt to identify the organizing principles that guide the maturation of these functional networks. In this report, we combine resting state functional connectivity MRI (rs-fcMRI), graph analysis, community detection, and spring-embedding visualization techniques to analyze four separate networks defined in earlier studies. As we have previously reported, we find, across development, a trend toward 'segregation' (a general decrease in correlation strength) between regions close in anatomical space and 'integration' (an increased correlation strength) between selected regions distant in space. The generalization of these earlier trends across multiple networks suggests that this is a general developmental principle for changes in functional connectivity that would extend to large-scale graph theoretic analyses of large-scale brain networks. Communities in children are predominantly arranged by anatomical proximity, while communities in adults predominantly reflect functional relationships, as defined from adult fMRI studies. In sum, over development, the organization of multiple functional networks shifts from a local anatomical emphasis in children to a more "distributed" architecture in young adults. We argue that this "local to distributed" developmental characterization has important implications for understanding the development of neural systems underlying cognition. Further, graph metrics (e.g., clustering coefficients and average path lengths) are similar in child and adult graphs, with both showing "small-world"-like properties, while community detection by modularity optimization reveals stable communities within the graphs that are clearly different between young children and young adults. These observations suggest that early school age children and adults both have relatively efficient systems that may solve similar information processing problems in divergent ways.
Identification and Characterization of Large Plasmids in Rhizobium meliloti using Agarose Gel Electrophoresis (1979)

Summary: The use of a modified procedure for the isolation of covalently closed circular DNA of high molecular weight, followed by agarose gel electrophoresis of the crude extracts, provides a simple screening method for detecting plasmids with molecular weights of more than 250× 106 from Agrobacterium tumefaciens, Pseudomonas putida and Rhizobium species. This method was used for a survey of plasmids in 25 symbiotically effective strains of Rhizobium meliloti from various geographical origins. Of these, 22 strains were found to carry at least one large plasmid. By electron microscopy and measurement of electrophoretic mobility in gels, the molecular weights of most of the plasmids were estimated to range from 90×106 to 200×106.
Bacteremia among Children Admitted to a Rural Hospital in Kenya (2005)

Community-acquired bacteremia is a major cause of death among children at a rural sub-Saharan district hospital, a finding that highlights the need for prevention and for overcoming the political and financial barriers to widespread use of existing vaccines for bacterial diseases.
Nematode Infection Triggers the de Novo Formation of Unloading Phloem That Allows Macromolecular Trafficking of Green Fluorescent Protein into Syncytia (2005)

Syncytial feeding complexes induced by the cyst nematode Heterodera schachtii represent strong metabolic sinks for photoassimilates. These newly formed structures were described to be symplastically isolated from the surrounding root tissue and their mechanism of carbohydrate import has repeatedly been under investigation. Here, we present analyses of the symplastic connectivity between the root phloem and these syncytia in nematode-infected Arabidopsis (Arabidopsis thaliana) plants expressing the gene of the green fluorescent protein (GFP) or of different GFP fusions under the control of the companion cell (CC)-specific AtSUC2 promoter. In the same plants, phloem differentiation during syncytium formation was monitored using cell-specific antibodies for CCs or sieve elements (SEs). Our results demonstrate that free, CC-derived GFP moved freely from the phloem into the syncytial domain. No or only marginal cell-to-cell passage of GFP was observed into other root cells adjacent to these syncytia. In contrast, membrane-anchored GFP variants as well as soluble GFP fusions with increased molecular masses were restricted to the SE-CC complex. The presented data also show that nematode infection triggers the de novo formation of phloem containing an approximately 3-fold excess of SEs over CCs. This newly formed phloem exhibits typical properties of unloading phloem previously described in other sink tissues. Our results reveal the existence of a symplastic pathway between phloem CCs and nematode-induced syncytia. The plasmodesmata responsible for this symplastic connectivity allow the cell-to-cell movement of macromolecules up to 30 kD and are likely to represent the major or exclusive path for the supply of assimilates from the phloem into the syncytial complex.
5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II (1997)

We have investigated the role of the RNA Polymerase II (Pol II) carboxy-terminal domain (CTD) in mRNA 5' capping. Transcripts made in vivo by Pol II with a truncated CTD had a lower proportion of capped 5' ends than those made by Pol II with a full-length CTD. In addition, the enzymes responsible for cap synthesis, RNA guanylyltransferase, and RNA (guanine-7)-methyltransferase bound directly to the phosphorylated, but not to the nonphosphorylated, form of the CTD in vitro. These results suggest that: (1) Pol II-specific capping of nascent transcripts in vivo is enhanced by recruitment of the capping enzymes to the CTD and (2) capping is co-ordinated with CTD phosphorylation.
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential (2012)

Our data shows that P. acidipropionici has several of the desired features that are required to become a platform for the production of chemical commodities: multiple pathways for efficient feedstock utilization, ability to fix CO2, robustness, and efficient production of propionic acid, a potential precursor for valuable 3-carbon compounds.
Distribution of iduronate 2-sulphate residues in heparan sulphate. Evidence for an ordered polymeric structure (1991)

The structure of human skin fibroblast heparan sulphate has been examined by depolymerization with heparinase, which specifically cleaves highly sulphated disaccharides of structure GlcNSO3 (+/-6S)-alpha 1,4IdoA(2S) [N-sulphated glucosamine (6-sulphate)-alpha 1,4-iduronic acid 2-sulphate]. Heparan sulphate contained only a small proportion (approximately 10%) of linkages susceptible to this enzyme. The major products of depolymerization with heparinase were large oligosaccharides with an average molecular mass of 10 kDa (dp approximately 40, where dp is degree of polymerization; for disaccharides, dp = 2 etc.) as assessed by gel filtration on Sepharose CL-6B, compared with a molecular mass of 45 kDa (dp approximately 200) for the intact chains. The large heparinase-resistant oligosaccharides were highly susceptible to depolymerization with the enzyme heparitinase, which cleaves heparan sulphate in areas of low sulphation, where N-acetylated disaccharides [GlcNAc-alpha 1,4GlcA (N-acetylglucosaminyl-alpha 1,4-glucuronic acid)] are the predominant structural unit. Further analysis of the location of the heparinase cleavage sites indicated that they were predominantly found in a central position in GlcNSO3-alpha 1,4IdoA repeat sequences of average length four to seven disaccharides (dp 8-14). These results indicate that heparinase cleaves heparan sulphate in approximately four or five N-sulphated domains, each domain containing a cluster of two or three susceptible disaccharides; the domains are separated by long N-acetyl-rich sequences that are markedly deficient in sulphate groups. On the basis of these findings a model is proposed which depicts heparan sulphate as an ordered polymeric structure composed of an alternate arrangement of sulphate-rich and sulphate-poor regions. The sulphate-rich regions are likely to be flexible areas of the chain because of their high content of the conformationally versatile IdoA and IdoA(2S) residues. The model has important implications for the biosynthesis and functions of heparan sulphate.
Performance analysis of a LAN/WAN bridging architecture (2003)

A performance analysis of a virtual-circuit-based wide-area network (WAN) that performs local-area-network (LAN) bridging is presented. This type of WAN is suitable for LAN bridging because the conversion of functions between the LAN protocol and the WAN protocol can be simplified by assigning a virtual circuit to each bridge-to-bridge (edge-to-edge) connection. With this architecture, routing is performed efficiently and network resources are used on demand. Analytical approximations of bridge throughput packet delay and packet-loss rates are provided as a function of network and protocol parameters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interactive retrieval of targets for wide area surveillance (2010)

We address the problem of interactive search for a target of interest in surveillance imagery. Our solution consists of iteratively learning a distance metric for retrieval, based on user feedback. The approach employs (retrieval) rank based constraints and convex optimization to efficiently learn the distance metric. The algorithm uses both user labeled and unlabeled examples in the learning process. The method is fast enough for a new metric to be learned interactively for each target query. In order to reduce the burden on the user, a model-independent active learning method is used to select key examples, for response solicitation. This leads to a significant reduction in the number of user-interactions required for retrieving the target of interest. The proposed method is evaluated on challenging pedestrian and vehicle data sets, and compares favorably to the state of the art in target re-acquisition algorithms.
A Novel Diagnostic Tool for Selecting Patients With Mesenchymal-Type Colon Cancer Reveals Intratumor Subtype Heterogeneity (2016)

The CMS4 RT-qPCR test is a promising clinical tool for selecting individual patients for CMS4-subtype-targeted therapy.
Study of Low-Speed Pre-Ignition in Boosted Spark Ignition Engine (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper analyzes low-speed pre-ignition (LSPI), a sudden pre-ignition phenomenon that occurs in downsized boosted gasoline engines in low engine speed high-load operation regions.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This research visualized the in-cylinder state before the start of LSPI combustion and observed the behavior of particles, which are thought to be the ignition source. The research also analyzed pre-ignition by injecting deposit flakes and other combustible particulate substances into the combustion chamber. The analysis found that these particles require at least two combustion cycles to reach a glowing state that forms an ignition source. As a result, deposits peeling from combustion chamber walls were identified as a new mechanism causing pre-ignition.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Additionally, results also suggested that the well-known phenomenon in which the LSPI frequency rises in accordance with greater oil dilution may also be explained by an increase in deposit generation.&lt;/div&gt;&lt;/div&gt;
Photochemical and Thermal Reactions of Azido-oligopyridines: Diazepinones, a New Class of Metal-Complex Ligands (2000)

Azido-oligopyridines were prepared, and their photochemical reactions resulted in diazepinones linked to pyridine moieties. The thermal reactions of azido-oligopyridines with triple bonds yielded 2H-azirines directly attached to oligopyridines.
Cytokine-activated human endothelial monolayers support enhanced neutrophil transmigration via a mechanism involving both endothelial-leukocyte adhesion molecule-1 and intercellular adhesion molecule-1 (1991)

rIL-1 beta treatment of cultured human endothelial cells (HEC) promotes polymorphonuclear leukocyte (PMN) adhesion and transmigration. Using in vitro quantitative monolayer adhesion and videomicroscopic transmigration assays, we have examined the contributions of endothelial-leukocyte adhesion molecule-1 (ELAM-1), intercellular adhesion molecule-1 (ICAM-1), and the leukocyte adhesion complex, CD11/CD18, to these processes. Maximal enhancement of PMN adhesion and transmigration were observed after 4 h of rIL-1 beta treatment, when surface expression of ELAM-1 had peaked and ICAM-1 was modestly increased. Blocking mAb directed to either ELAM-1 or ICAM-1 inhibited greater than 90% of the up-regulated PMN transmigration. Blocking mAb directed to either CD11a/CD18 (LFA-1, a ICAM-1 counter-receptor), CD11b/CD18 (Mo-1), or CD18 (common beta 2-integrin) also blocked greater than 90% of PMN transmigration. At later time points (24 or 48 h), ELAM-1 surface expression was markedly decreased, whereas ICAM-1 expression was increased over the 4-h level; PMN adhesion remained elevated (approximately 50 to 60% of 4 h level), but transmigration returned to levels seen with unactivated HEC. These data indicate that PMN interaction with at least two distinct HEC adhesion molecules is necessary for transendothelial migration and suggests that PMN adhesion and transmigration, although interrelated, are mechanistically distinct processes.
The biosynthesis of calendic acid, octadeca-(8E,10E, 12Z)-trienoic, acid, by developing marigold seeds: origins of (E,E,Z) and (Z,E,Z) conjugated triene acids in higher plants (1985)

Using an homogenate of marigold seeds, gathered 15 days after flower-drop, [1-14C] linoleic acid and [1-14C] oleic acid were incorporated into calendic acid with little randomisation of the label. [1-14C] Linolenic acid was not incorporated. Despite requiring 12,13-dehydrogenation to form linoleic acid, the putative precursor, oleic acid was better incorporated than administered linoleic acid. Stearic acid, requiring both 12,13- and 9,10-dehydrogenation, was a poor precursor. The results of a series of double-labelling experiments support and supplement these conclusions.[8,8,11,11,16,16,17,17-2H8]Octadec-9-enoic acid was synthesised and employed in a mass-spectral experiment to show that conversion into calendic acid involves loss of two deuterium and two hydrogen atoms (deuterium at C-16 and C-17 was introduced for loading purposes only, in order to increase the sensitivity of the experiment). Taken with [3H]-labelling work, the experiment indicates that during conversion of linoleic acid into calendic acid, there is no loss of the labelled hydrogens at C-9, -10, -12, or -13, but loss of hydrogen from each of C-8 and C-11.(9S)-Hydroxyoctadeca-(10E,l2Z)-dienoic acid (α-dimorphecolic acid) was isolated and converted into (R/S)-hydroxy- and -hydroperoxy-[9-3H]octadeca-(10E,l2Z)-dienoic acids. Neither labelled specimen was converted into calendic acid by marigold seed homogenate. Abstraction of a hydrogen atom from C-l 1 of linoleic acid is viewed as giving an (E)-allylic radical which, as in lipoxygenase reactions, can be trapped by oxygen at C-9, thus providing a source of α-dimorphecolic acid, a minor component of marigold seed oil. However, this hydroxyacid is apparently a terminus rather than an intermediate for calendic acid. Formation of the latter seems best accounted for by formal loss of a hydrogen atom from C-8 of the (E)-allylic radical. The general position relating to the formation of (E,E,Z) and (Z,E,Z)-trienes is summarised.
Physiological Patterns of Electrical Stimulation Can Induce Neuronal Gene Expression by Activating N-Type Calcium Channels (2001)

Activity-dependent neuronal gene expression is thought to require activation of L-type calcium channels, a view based primarily on studies in which chronic potassium (K(+)) depolarization was used to mimic neuronal activity. However, N-type calcium channels are primarily inactivated during chronic depolarization, and their potential contribution to gene expression induced by physiological patterns of stimulation has not been defined. In the present study, electrical stimulation of dissociated primary sensory neurons at 5 Hz, or treatment with elevated K(+), produced a large increase in the percentage of neurons that express tyrosine hydroxylase (TH) mRNA and protein. However, blockade of L-type channels, which completely inhibited K(+)-induced expression, had no effect on TH expression induced by patterned stimulation. Conversely, blockade of N-type channels completely inhibited TH induction by patterned stimulation, whereas K(+)-induced expression was unaffected. Similar results were obtained for depolarization-induced expression of the immediate early genes Nurr1 and Nur77. In addition, TH induction by patterned stimulation was significantly reduced by inhibitors of PKA and PKC but was unaffected by inhibition of the mitogen-activated protein kinase (MAPK) pathway. On the other hand, K(+)-induced TH expression was significantly reduced by inhibition of the MAPK pathway but was unaffected by inhibitors of PKA or PKC. These results demonstrate that N-type calcium channels can directly link phasic membrane depolarization to gene expression, challenging the view that activation of L-type channels is required for nuclear responses to physiological patterns of activity. Moreover, our data show that phasic and chronic depolarizing stimuli act through distinct mechanisms to induce neuronal gene expression.
Nitric oxide and endothelin secretion by brain microvessel endothelial cells: Regulation by cyclic nucleotides (1993)

Endothelin (ET)-1 was originally characterized as a potent vasoconstrictor peptide secreted by vascular endothelial cells. It possesses a wide range of biological activities within the cardiovascular system and in other organs, including the brain. Also secreted by endothelial cells, nitric oxide (NO), has recently been identified as a relaxing factor, as well as a pleiotropic mediator, second messenger, immune defence molecule, and neurotransmitter. Most of the data concerning the secretion of these two agents in vitro has been collected from studies on macrovascular endothelial cells. Given the remarkable heterogeneity of endothelia in terms of morphology and function, we have analyzed the ability of brain microvessel endothelial cells in vitro to release ET-1 and NO, which, at the level of the blood-brain barrier, have perivascular astrocytes as potential targets. The present study was performed with immortalized rat brain microvessel endothelial cells, which display in culture a non transformed phenotype. Our data demonstrate that: (1) these cells release NO when induced by IFN gamma and TNF alpha, (2) they constitutively secrete ET-1, and (3) cAMP potentiates the cytokine-induced NO release and exerts a biphasic regulation on ET-1 secretion: micromolar concentrations of 8-Br-cAMP inhibit and higher doses stimulate ET-1 secretion. This stimulation is blocked by EGTA and the calmodulin antagonist W7, but not by protein kinase C inhibitors, suggesting the involvement of the calmodulin branch of the calcium messenger system. These results suggest that cerebral microvessel endothelial cells may participate in vivo to the regulation of glial activity in the brain through the release of NO and ET-1.
Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor (2013)

Misfolding and associated loss of function are common problems in constructing fusion RNA complexes due to changes in energy landscape and the nearest-neighbor principle. Here we report the incorporation and application of the pRNA-3WJ motif of the phi29 DNA packaging motor into fusion RNA with controllable and predictable folding. The motif included three discontinuous ∼18 nucleotide (nt) fragments, displayed a distinct low folding energy (Shu D et al., Nature Nanotechnology, 2011, 6:658-667), and folded spontaneously into a leading core that enabled the correct folding of other functionalities fused to the RNA complex. Three individual fragments dispersed at any location within the sequence allowed the other RNA functional modules to fold into their original structures with authentic functions, as tested by Hepatitis B virus ribozyme, siRNA, and aptamers for malachite green (MG), spinach, and streptavidin (STV). Only nine complementary nucleotides were present for any two of the three ∼18-nt fragments, but the three 9 bp branches were so powerful that they disrupted other double strands with more than 15 bp within the fusion RNA. This system enabled the production of fusion complexes harboring multiple RNA functionalities with correct folding for potential applications in biotechnology, nanomedicine and nanotechnology. We also applied this system to investigate the principles governing the folding of RNA in vivo and in vitro. Temporal production of RNA sequences during in vivo transcription caused RNA to fold into different conformations that could not be predicted with routine principles derived from in vitro studies.
Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (1988)

Probabilistic Reasoning in Intelligent Systems is a complete and accessible account of the theoretical foundations and computational methods that underlie plausible reasoning under uncertainty. The author provides a coherent explication of probability as a language for reasoning with partial belief and offers a unifying perspective on other AI approaches to uncertainty, such as the Dempster-Shafer formalism, truth maintenance systems, and nonmonotonic logic. The author distinguishes syntactic and semantic approaches to uncertainty--and offers techniques, based on belief networks, that provid