Constructing liberal and conservative supertrees and exact solutions for reduced consensus problems

This thesis studies two different approaches to extracting information from collections of phylogenetic trees: supertrees and reduced consensus. Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to date, but most of these are not designed with any specific properties in mind. Recently, Cotton and Wilkinson proposed extensions of the majority-rule consensus tree method to the supertree setting that inherit many of the appealing properties of the former. We study a variant of one of Cotton and Wilkinson\u27s methods, called majority-rule (+) supertrees. After proving that a key underlying problem for constructing majority-rule (+) supertrees is NP-hard, we develop a polynomial-size exact integer linear programming formulation of the problem. We then present a data reduction heuristic that identifies smaller subproblems that can be solved independently. While this technique is not guaranteed to produce optimal solutions, it can achieve substantial problem-size reduction. Finally, we report on a computational study of our approach on various real data sets, including the 121-taxon, 7-tree Seabirds data set of Kennedy and Page. The results indicate that our exact method is computationally feasible for moderately large inputs. For larger inputs, our data reduction heuristic makes it feasible to tackle problems that are well beyond the range of the basic integer programming approach. Comparisons between the results obtained by our heuristic and exact solutions indicate that the heuristic produces good answers. Our results also suggest that the majority-rule (+) approach, in both its basic form and with data reduction, yields biologically meaningful phylogenies. Generalizations of the strict and loose consensus methods to the supertree setting, recently introduced by McMorris and Wilkinson, are studied. The supertrees these methods produce are conservative in the sense that they only preserve information (in the form of splits) that is supported by at least one the input trees and that is not contradicted by any of the input trees. Alternative, equivalent, formulations of these supertrees are developed. These are used to prove the NP-completeness of the underlying optimization problems and to give exact integer linear programming solutions. For larger data sets, a divide and conquer approach is adopted, based on the structural properties of these supertrees. Experiments show that it is feasible to solve problems with several hundred taxa and several hundred trees in a reasonable amount of time. A rogue taxon in a collection of phylogenetic trees is one whose position varies drastically from tree to tree. The presence of such taxa can greatly reduce the resolution of the consensus tree (e.g., the majority-rule or strict consensus) for a collection. The reduced consensus approach aims to identify rogue taxa and to produce more informative consensus trees. Given a collection of phylogenetic trees over the same leaf set, the goal is to find a set of taxa whose removal maximizes the number of internal edges in the consensus tree of the collection. This problem is proven to be NP-hard for strict and majority-rule consensus. We describe exact integer linear programming formulations for computing reduced strict, majority and loose consensus trees. In experimental tests, our exact solutions show significant improvement over heuristic methods on several problem instances

Extraction methods for multidirectional driving point accelerance and transfer point accelerance matrices

To experimentally determine the multidirectional driving point and transfer accelerance matrices is a difficult task that has remained unsolved for 30 years. These matrices relate both linear and rotational degrees of freedom in three dimensions. The direct measurement of dynamic moments and rotational accelerations is very difficult. Little work exists on the subject and none includes so many DOF\u27s. Besides, it is assumed that any test attachment is rigid and none used angular accelerometers to measure the angular acceleration;Various errors in substructure testing are studied. The study reveals that the interface DOF deficiency error is the most catastrophic and sophisticated error. None of interfacial DOF\u27s can be neglected. The bias error can be corrected easily. The noise error appears to be most severe in the low frequency range. The exciter rocking motion leads to incorrect bare vehicle transmissibility matrix and incorrect global transmissibility matrix. The driving point difference error increases quickly as the distance between the impact and measurement points increases;The DOF deficiency error has several sources. It comes from the difference between the inverse from a complete interface model and the inverse of a reduced interface model. It also comes from the deletion of cross coupling terms between the neglected motions and remaining forces, the neglected forces and the remaining motions, and the neglected forces and the neglected motions;A number of numerical-experimental hybrid measurement methods are proposed and evaluated for finding the multidirectional driving point and transfer point accelerance matrices in both 2D and 3D. These methods are tested for their robustness under conditions of noisy data. A 2D implementation, called a T-bar, and a 3D implementation, called a C-bar, of an elastic test attachment structure, called Instrument Cluster , are developed. Accelerometers are embedded in the Instrument Cluster . The finite element model is an integral part of the experimental testing process. The FE FRF\u27s of the Instrument Cluster are used together with the experimental FRF\u27s of the combined structure. A new rotational accelerometer is used to obtain better rotational acceleration than two closely spaced linear accelerometers. Experimental results show this method is both feasible and promising

Salt-Enhanced Reproductive Development of Suaeda salsa L. Coincided With Ion Transporter Gene Upregulation in Flowers and Increased Pollen K+ Content

Halophytes are adapted to saline environments and demonstrate optimal reproductive growth under high salinity. To gain insight into the salt tolerance mechanism and effects of salinity in the halophyte Suaeda salsa, the number of flowers and seeds, seed size, anther development, ion content, and flower transcript profiles, as well as the relative expression levels of genes involved in ion transport, were analyzed in S. salsa plants treated with 0 or 200 mM NaCl. The seed size, flower number, seed number per leaf axil, and anther fertility were all significantly increased by 200 mM NaCl treatment. The Na+ and Cl− contents in the leaves, stems, and pollen of NaCl-treated plants were all markedly higher, and the K+ content in the leaves and stems was significantly lower, than those in untreated control plants. By contrast, the K+ content in pollen grains did not decrease, but rather increased, upon NaCl treatment. Genes related to Na+, K+ and, Cl− transport, such as SOS1, KEA, AKT1, NHX1, and CHX, showed increased expression in the flowers of NaCl-treated plants. These results suggest that ionic homeostasis in reproductive organs, especially in pollen grains under salt-treated conditions, involves increased expression of ion transport-related genes

LAMOST observations in the Kepler field. Analysis of the stellar parameters measured with the LASP based on the low-resolution spectra

All of the 14 subfields of the Kepler field have been observed at least once with the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST, Xinglong Observatory, China) during the 2012-2014 observation seasons. There are 88,628 reduced spectra with SNR$_g$ (signal-to-noise ratio in g band) $\geq$ 6 after the first round (2012-2014) of observations for the LAMOST-Kepler project (LK-project). By adopting the upgraded version of the LAMOST Stellar Parameter pipeline (LASP), we have determined the atmospheric parameters ($T_{\rm eff}$ , $\log g$, and $\rm [Fe/H]$) and heliocentric radial velocity $v_{\rm rad}$ for 51,406 stars with 61,226 spectra. Compared with atmospheric parameters derived from both high-resolution spectroscopy and asteroseismology method for common stars in Huber et al. (2014), an external calibration of LASP atmospheric parameters was made, leading to the determination of external errors for the giants and dwarfs, respectively. Multiple spectroscopic observations for the same objects of the LK-project were used to estimate the internal uncertainties of the atmospheric parameters as a function of SNR$_g$ with the unbiased estimation method. The LASP atmospheric parameters were calibrated based on both the external and internal uncertainties for the giants and dwarfs, respectively. A general statistical analysis of the stellar parameters leads to discovery of 106 candidate metal-poor stars, 9 candidate very metal-poor stars, and 18 candidate high-velocity stars. Fitting formulae were obtained segmentally for both the calibrated atmospheric parameters of the LK-project and the KIC parameters with the common stars. The calibrated atmospheric parameters and radial velocities of the LK-project will be useful for studying stars in the Kepler field.Comment: 53 pages, 21 figures, 5 tables, Accepted for publication by ApJ

Nanoarchitectonic Engineering of Thermal-Responsive Magnetic Nanorobot Collectives for Intracranial Aneurysm Therapy

Stent-assisted coiling is a main treatment modality for intracranial aneurysms (IAs) in clinics, but critical challenges remain to be overcome, such as exogenous implant-induced stenosis and reliance on antiplatelet agents. Herein, we report an endovascular approach for IA therapy without stent grafting or microcatheter shaping, enabled by active delivery of thrombin (Th) to target aneurysms using innovative phase-change material (PCM)-coated magnetite-thrombin (Fe3O4-Th@PCM) FTP nanorobots. The nanorobots are controlled by an integrated actuation system of dynamic torque-force hybrid magnetic fields. With robust intravascular navigation guided by real-time ultrasound imaging, nanorobotic collectives can effectively accumulate and retain in model aneurysms constructed in vivo, followed by controlled release of the encapsulated Th for rapid occlusion of the aneurysm upon melting the protective PCM (thermally responsive in a tunable manner) through focused magnetic hyperthermia. Complete and stable aneurysm embolization was confirmed by postoperative examination and 2-week postembolization follow-up using digital subtraction angiography (DSA), contrast-enhanced ultrasound (CEUS) and histological analysis. The safety of the embolization therapy was assessed through biocompatibility evaluation and histopathology assays. Our strategy, seamlessly integrating secure drug packaging, agile magnetic actuation and clinical interventional imaging, avoids possible exogenous implant rejection, circumvents cumbersome microcatheter shaping, and offers a promising option for IA therapy

A prospective study of two-dimensional ultrasonography combined with shear wave elastography for pregnancy-related diastasis recti abdominis

ObjectivesTo compare the inter-rectus distance (IRD), rectus abdominis thickness (RAT), and stiffness in women during pregnancy and postpartum and identify the risk and protective factors affecting diastasis recti abdominis (DRA).Materials and methodsA total of 171 pregnant women who volunteered to participate in this study were recruited. Using an ultrasonographic diagnostic instrument with shear wave elastography function, IRD, RAT and the Young’s modulus of the rectus abdominis muscles were measured at 12 weeks, 37 weeks of pregnancy, and 6 weeks postpartum.ResultsThe IRD at 37 weeks was significantly higher than that at 12 weeks and then decreased at 6 weeks postpartum, but it was still higher than that at 12 weeks (p < 0.001). RAT and Young’s modulus decreased significantly at 37 weeks compared with those at 12 weeks and then recovered at 6 weeks postpartum, but they were lower than those at 12 weeks (p < 0.001). IRD at 12 weeks was significantly higher in multiparae than in primiparae (p < 0.001). Moreover, positive correlation between the RAT and Young’s modulus of rectus abdominis muscles at 12 and 37 weeks of gestation and 6 weeks postpartum (p < 0.001) was observed. Multiple linear regression analysis showed that the regression equation was significant (f = 24.856, p < 001).ConclusionOur study identified differences in IRD, thickness and stiffness of the rectus abdominis muscle between early and advanced pregnancy and the postpartum period. The risk and protective factors of DRA may guide pregnant women’s protection and treatment

Multi-year succession of cyanobacteria blooms in a highland reservoir with changing nutrient status, Guizhou Province, China

Over the last 22 years significant phytoplankton changes in Hongfeng lake reservoir have been observed with multiple years of harmful cyanobacteria blooms (cHABs). Fish farming and other anthropogenic activities from 1994-2001 triggered the harmful blooms. Nine years after the cessation of aquaculture, a conversion from problematic species (Microcystis spp, Aphanizomenon flos-aquae) to the less problematic species P. limnetica and other associated non-cyanobacteria taxa was recorded. Through this period of change, trophic factors (bottom-up) were re-examined, and correlations between cHABs and selected environmental variables were observed. Higher temperatures, nutrients (TN, TP) and available light significantly favored the development of Microcystis spp blooms. With declining nutrient loads, and a decline in TP relative to TN there was a competitive shift from Microcystis summer blooms to the growth of Pseudanabaena limnetica and other non-cyanobacteria. Pseudanabaena limnetica was favored over Microcystis spp when temperatures were <20°C and TP was <0.03 mg L-1. The apparent species succession to P. limnetica was enhanced by a competitive advantage under varied light conditions. Multiple environmental and biotic conditions (not always nutrients) were driving cHABs. Although only a selected number of environmental variables were examined, the CCA analysis supports observations that temperature and nutrients were associated with the species shift. The replacement of cHABs with the growth of less toxic cyanobacteria like P. limnetica, and other algae creates an interesting scenario (new community condition) for the removal of problematic taxa in reservoir systems. Diverting or controlling blooms will have direct implications on water quality and economic remediation initiatives in reservoir and lake management