Algorithms for Computing Wiener Indices of Acyclic and Unicyclic Graphs

Let $G=(V(G),E(G))$ be a molecular graph, where $V(G)$ and $E(G)$ are the sets of vertices (atoms) and edges (bonds). A topological index of a molecular graph is a numerical quantity which helps to predict the chemical/physical properties of the molecules. The Wiener, Wiener polarity and the terminal Wiener indices are the distance based topological indices. In this paper, we described a linear time algorithm {\bf(LTA)} that computes the Wiener index for acyclic graphs and extended this algorithm for unicyclic graphs. The same algorithms are modified to compute the terminal Wiener index and the Wiener polarity index. All these algorithms compute the indices in time $O(n)$

Inhibiting IL-1 signaling pathways to inhibit catabolic processes in disc degeneration

Intervertebral disc degeneration is characterized by an imbalance between catabolic and anabolic signaling, with an increase in catabolic cytokines particularly IL-1β, a key regulator of IVD degeneration. This study aimed to investigate intracellular signaling pathways activated by IL-1β, and GDF-5 in the degenerate IVD to identify potential new therapeutic targets. Human NP cells were cultured in alginate beads to regain in vivo phenotype prior to stimulation with IL-1β or GDF-5 for 30 min, a proteasome profiler array was initially utilized to screen activation status of 46 signaling proteins. Immunoflourescence was used to investigate activation of the NFκB pathway. Cell-based ELISAs were then deployed to confirm results for ERK1/2, p38 MAPK, c-jun, and IκB signaling. IHC was utilized to investigate native activation status within human IVD tissue between grades of degeneration. Finally, cells were stimulated with IL-1β in the absence or presence of p38 MAPK, c-jun, JNK, and NFκB inhibitors to investigate effects on MMP3, MMP13, IL-1β, IL-6, and IL-8 mRNA expression. This study demonstrated three key signaling pathways which were differentially activated by IL-1β but not GDF-5; namely p38 MAPK, c-jun, and NFκB. While ERK 1/2 was activated by both GDF-5 and IL-1. Immunohistochemistry demonstrated p38 MAPK, c-jun, and NFκB were activated during human IVD degeneration and inhibition of these pathways reduced or abrogated the catabolic effects of IL-1β, with inhibition of NFκB signaling demonstrating most widespread inhibition of IL-1β catabolic effect

novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/

A Google Earth-based surveillance system for schistosomiasis japonica implemented in the lower reaches of the Yangtze River, China

<p>Abstract</p> <p>Background</p> <p>Due to the success of the national schistosomiasis control programme in China, transmission has been sufficiently reduced in many areas to severely limit identification of areas at risk by conventional snail surveys only. In this study, we imported Google Earth technology and a Global Positioning System (GPS) into the monitoring system for schistosomiasis surveillance of the banks of the Yangtze River in Jiangsu Province, China.</p> <p>Methods</p> <p>A total of 45 sites were selected and the risk was assessed monthly by water exposure of sentinel mice at these sites from May to September in 2009 and 2010. The results were assembled and broadcast via the Google Earth platform.</p> <p>Results</p> <p>The intensity of schistosomiasis transmission showed peaks of risk in June and September of 2009, while there was only one small peak in June in 2010 as the number of detected positive transmission sites dropped dramatically that year thanks to improved mollusciciding. River ports were found to be areas of particular risk, but ferry terminals and other centres of river-related activities were also problematic.</p> <p>Conclusions</p> <p>The results confirm that the surveillance system can be rapidly updated and easily maintained, which proves the Google Earth approach to be a user-friendly, inexpensive warning system for schistosomiasis risk.</p

Aluminium-induced inhibition of root elongation in Arabidopsis is mediated by ethylene and auxin

Aluminium (Al) is phytotoxic when solubilized into Al3+ in acidic soils. One of the earliest and distinct symptoms of Al3+ toxicity is inhibition of root elongation. To decipher the mechanism by which Al3+ inhibits root elongation, the role of ethylene and auxin in Al3+-induced inhibition of root elongation in Arabidopsis thaliana was investigated using the wild type and mutants defective in ethylene signalling (etr1-3 and ein2-1) and auxin polar transport (aux1-7 and pin2). Exposure of wild-type Arabidopsis to AlCl3 led to a marked inhibition of root elongation, and elicited a rapid ethylene evolution and enhanced activity of the ethylene reporter EBS:GUS in root apices. Root elongation in etr1-3 and ein2-1 mutants was less inhibited by Al3+ than that in wild-type plants. Ethylene synthesis inhibitors, Co2+ and aminoethoxyvinylglycine (AVG), and an antagonist of ethylene perception (Ag+) abolished the Al3+-induced inhibition of root elongation. There was less inhibition of root elongation by Al3+ in aux1-7 and pin2 mutants than in the wild type. The auxin polar transport inhibitor, naphthylphthalamic acid (NPA), substantially alleviated the Al3+-induced inhibition of root elongation. The Al3+ and ethylene synthesis precursor aminocyclopropane carboxylic acid (ACC) increased auxin reporter DR5:GUS activity in roots. The Al3+-induced increase in DR5:GUS activity was reduced by AVG, while the Al3+-induced increase in EBS:GUS activity was not altered by NPA. Al3+ and ACC increased transcripts of AUX1 and PIN2, and this effect was no longer observed in the presence of AVG and Co2+. These findings indicate that Al3+-induced ethylene production is likely to act as a signal to alter auxin distribution in roots by disrupting AUX1- and PIN2-mediated auxin polar transport, leading to arrest of root elongation

A thermodynamically consistent quasi-particle model without temperature-dependent infinity of the vacuum zero point energy

In this paper, an improved quasi-particle model is presented. Unlike the previous approach of establishing quasi-particle model, we introduce a classical background field (it is allowed to depend on the temperature) to deal with the infinity of thermal vacuum energy which exists in previous quasi-particle models. After taking into account the effect of this classical background field, the partition function of quasi-particle system can be made well-defined. Based on this and following the standard ensemble theory, we construct a thermodynamically consistent quasi-particle model without the need of any reformulation of statistical mechanics or thermodynamical consistency relation. As an application of our model, we employ it to the case of (2+1) flavor QGP at zero chemical potential and finite temperature and obtain a good fit to the recent lattice simulation results of S. Borsanyi $et$ $al$. A comparison of the result of our model with early calculations using other models is also presented. It is shown that our method is general and can be generalized to the case where the effective mass depends not only on the temperature but also on the chemical potential.Comment: 7 pages, 4 figure

MMS Study of the Structure of Ionâ Scale Flux Ropes in the Earth’s Crossâ Tail Current Sheet

This study analyzes 25 ionâ scale flux ropes in the Magnetospheric Multiscale (MMS) observations to determine their structures. The high temporal and spatial resolution MMS measurements enable the application of multispacecraft techniques to ionâ scale flux ropes. Flux ropes are identified as quasiâ oneâ dimensional (quasiâ 1â D) when they retain the features of reconnecting current sheets; that is, the magnetic field gradient is predominantly northward or southward, and quasiâ 2â D when they exhibit circular cross sections; that is, the magnetic field gradients in the plane transverse to the flux rope axis are comparable. The analysis shows that the quasiâ 2â D events have larger core fields and smaller pressure variations than the quasiâ 1â D events. These two types of flux ropes could be the result of different processes, including magnetic reconnection with different dawnâ dusk magnetic field components, temporal transformation of flattened structure to circular, or interactions with external environments.Plain Language SummaryMagnetic flux ropes are fundamental magnetic structures in space plasma physics and are commonly seen in the universe, such as, astrophysical jets, coronal mass ejections, and planetary magnetospheres. Flux ropes are important in mass and energy transport across plasma and magnetic boundaries, and they are found in a wide range of spatial sizes, from several tens of kilometers, that is, ionâ scale flux ropes, to tens of millions of kilometers, that is, coronal mass ejections, in the solar system. The ionâ scale flux ropes can be formed during magnetic reconnection and are hypothesized to energize electrons and influence the reconnection rate. Previous examinations of the structure of ionâ scale flux ropes were greatly limited by measurement resolution. The unprecedented Magnetospheric Multiscale (MMS) mission high temporal and spatial resolution measurements provide a unique opportunity to investigate flux rope structures. By employing multispacecraft techniques, this study has provided new insights into the magnetic field variations and dimensionality of ionâ scale flux ropes in the Earth’s magnetotail. The results are consistent with the evolution of ionâ scale flux ropes from initially flattened current sheetâ like flux ropes near the time of formation into lower energy state with circular cross section predicted by theory and termed as the â Taylorâ state.Key PointsIonâ scale flux ropes are observed to have either flattened or circular cross sections using MDD and GS reconstructionAnalysis of 25 flux ropes show that circular crossâ section flux ropes have stronger core field and smaller thermal pressures than flattened flux ropesThe two types of flux ropes may be the results of reconnection, temporal evolution, or interactions with external environmentPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150544/1/grl59049.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150544/2/grl59049_am.pd