Sampling and Inference for Beta Neutral-to-the-Left Models of Sparse Networks

Empirical evidence suggests that heavy-tailed degree distributions occurring in many real networks are well-approximated by power laws with exponents $\eta$ that may take values either less than and greater than two. Models based on various forms of exchangeability are able to capture power laws with $\eta < 2$, and admit tractable inference algorithms; we draw on previous results to show that $\eta > 2$ cannot be generated by the forms of exchangeability used in existing random graph models. Preferential attachment models generate power law exponents greater than two, but have been of limited use as statistical models due to the inherent difficulty of performing inference in non-exchangeable models. Motivated by this gap, we design and implement inference algorithms for a recently proposed class of models that generates $\eta$ of all possible values. We show that although they are not exchangeable, these models have probabilistic structure amenable to inference. Our methods make a large class of previously intractable models useful for statistical inference.Comment: Accepted for publication in the proceedings of Conference on Uncertainty in Artificial Intelligence (UAI) 201

Frustration Propagation in Tubular Foldable Mechanisms

Shell mechanisms are patterned surface-like structures with compliant deformation modes that allow them to change shape drastically. Examples include many origami and kirigami tessellations as well as other periodic truss mechanisms. The deployment paths of a shell mechanism are greatly constrained by the inextensibility of the constitutive material locally, and by the compatibility requirements of surface geometry globally. With notable exceptions (e.g., Miura-ori), the deployment of a shell mechanism often couples in-plane stretching and out-of-plane bending. Here, we investigate the repercussions of this kinematic coupling in the presence of geometric confinement, specifically in tubular states. We demonstrate that the confinement in the hoop direction leads to a frustration that propagates axially as if by buckling. We fully characterize this phenomenon in terms of amplitude, wavelength, and mode shape, in the asymptotic regime where the size of the unit cell of the mechanism~$r$ is small compared to the typical radius of curvature~$\rho$. In particular, we conclude that the amplitude and wavelength of the frustration are of order $\sqrt{r/\rho}$ and that the mode shape is an elastica solution. Derivations are carried out for a particular pyramidal truss mechanism. Findings are supported by numerical solutions of the exact kinematics.Comment: 7 figures, added figures and references, corrected typo

Organophosphate Toxicity Presenting with Cholinergic Crisis, Intermediate Syndrome and Delayed Polyneuropathy in Succession: a Rare Presentation

Background: Organophosphate (OP) self poisoning is a major health hazard in a predominantly agrarian country like India. Acute cholinergic crisis and intermediate syndrome are well recognized manifestations of OP toxicity, delayed polyneuropathy being an unusual clinical event.Case Report: We describe a 30-year-old male with suicidal chlorpyrifos poisoning who presented with cholinergic crisis; developed intermediate syndrome subsequently and ultimately three weeks later landed up with OP induced delayed polyneuropathy (OPIDPN).Conclusion: This reported case emphasizes on the importance of strict vigilance and follow up in patients with OP toxicity in order to recognise and appropriately treat chronic toxicities like OPIDPN

Many-Body Corrections to Charged-Current Neutrino Absorption Rates in Nuclear Matter

Including nucleon--nucleon correlations due to both Fermi statistics and nuclear forces, we have developed a general formalism for calculating the charged--current neutrino--nucleon absorption rates in nuclear matter. We find that at one half nuclear density many--body effects alone suppress the rates by a factor of two and that the suppression factors increase to $\sim$5 at $4\times10^{14}$ g cm$^{-3}$. The associated increase in the neutrino--matter mean--free--paths parallels that found for neutral--current interactions and opens up interesting possibilities in the context of the delayed supernova mechanism and protoneutron star cooling.Comment: 11 pages, APS REVTeX format, 1 PostScript figure, uuencoded compressed, and tarred, submitted to Physical Review Letter

Synthesis and biological evaluation of arylated novobiocin analogs as Hsp90 inhibitors

Novobiocin analogs lacking labile glycosidic ether have been designed, synthesized and evaluated for Hsp90 inhibitory activity. Replacement of the synthetically complex noviose sugar with simple aromatic side chains produced analogs that maintain moderate cytotoxic activity against MCF7 and SkBR3 breast cancer cell-lines. Rationale for the preparation of des-noviose novobiocin analogs in addition to their synthesis and biological evaluation are presented herein

Well-Sampled Far-Infrared Spectral Energy Distributions of z ~ 2 Galaxies: Evidence for Scaled up Cool Galaxies

We present an analysis of the far-infrared (FIR) spectral energy distributions (SEDs) of two massive K-selected galaxies at z = 2.122 and z = 2.024 detected at 24um, 70um, 160um by Spitzer, 250um, 350um, 500um by BLAST, and 870um by APEX. The large wavelength range of these observations and the availability of spectroscopic redshifts allow us to unambiguously identify the peak of the redshifted thermal emission from dust at ~ 300um. The SEDs of both galaxies are reasonably well fit by synthetic templates of local galaxies with L_IR ~ 10^{11} L_{sun} -- 10^{12} L_{sun} yet both galaxies have L_{IR} ~ 10^{13} L_{sun}. This suggests that these galaxies are not high redshift analogues of the Hyper-LIRGs/ULIRGs used in local templates, but are instead "scaled up" versions of local ULIRGs/LIRGs. For both galaxies the star formation rate determined from the best-fit FIR SEDs (SFR(L_{IR})) agrees with the SFR determined from the dust corrected H-alpha luminosity (SFR(H-alpha)) to within a factor of ~ 2; however, when the SFR of these galaxies is estimated using only the observed 24um flux and the standard luminosity-dependent template method (SFR(24um)), it systematically overestimates the SFR by as much as a factor of 6. A larger sample of 24 K-selected galaxies at z ~ 2.3 drawn from the Kriek et al. (2008) GNIRS sample shows the same trend between SFR(24um) and SFR(H-alpha). Using that sample we show that SFR(24um) and SFR(H-alpha) are in better agreement when SFR(24um) is estimated using the log average of local templates rather than selecting a single luminosity-dependent template, because this incorporates lower luminosity templates. The better agreement between SFRs from lower luminosity templates suggests that the FIR SEDs of the BLAST-detected galaxies may be typical for massive galaxies at z ~ 2, and that the majority are scaled up versions of lower luminosity local galaxies.Comment: 8 pages, 3 figures, revised version, accepted by Ap

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

<p>Abstract</p> <p>Background</p> <p>Genome-wide computational analysis of alternative splicing (AS) in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. <it>Chlamydomonas</it>, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in <it>Chlamydomonas reinhardtii </it>using its recently completed genome sequence and all available ESTs and cDNAs.</p> <p>Results</p> <p>Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at <url>http://combi.cs.colostate.edu/as/chlamy</url>.</p> <p>Conclusions</p> <p>The extent of AS in <it>Chlamydomonas </it>that we observed is much smaller than observed in land plants, but is much higher than in simple unicellular heterotrophic eukaryotes. The percentage of different alternative splicing events is similar to flowering plants. Prevalence of constitutive and alternative splicing in <it>Chlamydomonas</it>, together with its simplicity, many available public resources, and well developed genetic and molecular tools for this organism make it an excellent model system to elucidate the mechanisms involved in regulated splicing in photosynthetic eukaryotes.</p

Metabolic engineering of Arabidopsis for butanetriol production using bacterial genes

Includes bibliographical references (pages 119-120).1,2,4-butanetriol (butanetriol) is a useful precursor for the synthesis of the energetic material butanetriol trinitrate and several pharmaceutical compounds. Bacterial synthesis of butanetriol from xylose or arabinose takes place in a pathway that requires four enzymes. To produce butanetriol in plants by expressing bacterial enzymes, we cloned native bacterial or codon optimized synthetic genes under different promoters into a binary vector and stably transformed Arabidopsis plants. Transgenic lines expressing introduced genes were analyzed for the production of butanetriol using gas chromatography coupled to mass spectrometry (GC-MS). Soil-grown transgenic plants expressing these genes produced up to 20 µg/g of butanetriol. To test if an exogenous supply of pentose sugar precursors would enhance the butanetriol level, transgenic plants were grown in a medium supplemented with either xylose or arabinose and the amount of butanetriol was quantified. Plants expressing synthetic genes in the arabinose pathway showed up to a forty-fold increase in butanetriol levels after arabinose was added to the medium. Transgenic plants expressing either bacterial or synthetic xylose pathways, or the arabinose pathway showed toxicity symptoms when xylose or arabinose was added to the medium, suggesting that a by-product in the pathway or butanetriol affected plant growth. Furthermore, the metabolite profile of plants expressing arabinose and xylose pathways was altered. Our results demonstrate that bacterial pathways that produce butanetriol can be engineered into plants to produce this chemical. This proof-of-concept study for phytoproduction of butanetriol paves the way to further manipulate metabolic pathways in plants to enhance the level of butanetriol production.Published with support from the Colorado State University Libraries Open Access Research and Scholarship Fund

Anaerobic microbial community response to methanogenic inhibitors 2‐bromoethanesulfonate and propynoic acid

Methanogenic inhibitors are often used to study methanogenesis in complex microbial communities or inhibit methanogens in the gastrointestinal tract of livestock. However, the resulting structural and functional changes in archaeal and bacterial communities are poorly understood. We characterized microbial community structure and activity in mesocosms seeded with cow dung and municipal wastewater treatment plant anaerobic digester sludge after exposure to two methanogenic inhibitors, 2‐bromoethanesulfonate (BES) and propynoic acid (PA). Methane production was reduced by 89% (0.5 mmol/L BES), 100% (10 mmol/LBES), 24% (0.1 mmol/LPA), and 95% (10 mmol/LPA). Using modified primers targeting the methyl‐coenzyme M reductase (mcrA) gene, changes in mcrA gene expression were found to correspond with changes in methane production and the relative activity of methanogens. Methanogenic activity was determined by the relative abundance of methanogen 16S rRNA cDNA as a percentage of the total community 16S rRNA cDNA. Overall, methanogenic activity was lower when mesocosms were exposed to higher concentrations of both inhibitors, and aceticlastic methanogens were inhibited to a greater extent than hydrogenotrophic methanogens. Syntrophic bacterial activity, measured by 16S rRNA cDNA, was also reduced following exposure to both inhibitors, but the overall structure of the active bacterial community was not significantly affected.This manuscript reports a comprehensive approach to characterizing the effects of commonly used methanogenesis inhibitors on an anaerobic microbial community. We use mock and environmental communities and target two genes using DNA‐ and RNA‐based methods. Results from Illumina sequencing of the 16S rRNA gene, 16S rRNA cDNA, mcrA gene, and mcrA transcript cDNA highlight shifts in both methanogenic archaeal activity and syntrophic bacterial activity.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134127/1/mbo3349.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134127/2/mbo3349_am.pd