Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees

Abstract Among the methods currently available for inferring species trees from gene trees, the GLASS method of Mossel and Roch (2010), the Shallowest Divergence (SD) method of Maddison and Knowles (2006), the STEAC method of Liu et al. (2009), and a related method that we call Minimum Average Coalescence (MAC) are computationally efficient and provide branch length estimates. Further, GLASS and STEAC have been shown to be consistent estimators of tree topology under a multispecies coalescent model. However, divergence time estimates obtained with these methods are all systematically biased under the model because the pairwise interspecific gene divergence times on which they rely must be more ancient than the species divergence time. Jewett and Rosenberg (2012) derived an expression for the bias of GLASS and used it to propose an improved method that they termed iGLASS. Here, we derive the biases of SD, STEAC, and MAC, and we propose improved analogues of these methods that we call iSD, iSTEAC, and iMAC. We conduct simulations to compare the performance of these methods with their original counterparts and with GLASS and iGLASS, finding that each of them decreases the bias and mean squared error of pairwise divergence time estimates. The new methods can therefore contribute to improvements in the estimation of species trees from information on gene trees.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98441/1/cmb%2E2012%2E0042.pd

Mollusks in the Northeastern Chukchi Sea

Infaunal and epifaunal mollusks of the northeastern Chukchi Sea were sampled and 139 molluscan taxa were identified. The pattern of spatial distribution of molluscan species was determined by cluster analysis, which resulted in six infaunal and five epifaunal station groups. Species characterizing various faunal groups are defined. Stepwise multiple discriminant analysis was applied to correlate benthic biological associations with environmental variables. Delineation of infaunal groups was mainly due to percentage of sand and bottom salinity, while epifaunal groups were separated by percent gravel and bottom temperature. An increase in abundance and biomass of infaunal mollusks occurred adjacent to and north and northwest of an identified bottom front between the Bering Shelf and Resident Chukchi Water and Alaska Coastal Water. Epifaunal molluscan abundance and biomass were highest near the coast. Mollusks, especially smaller species and the juvenile stages of larger species, represent a food resource for bottom-feeding predators in the study area.Key words: Chukchi Sea, mollusk, benthic, infauna, epifauna, bottom front, bottom-feeding predators, cluster analysis, discriminant analysisOn a fait un échantillonnage des mollusques de l'endofaune et de l'épifaune du nord-est de la mer des Tchouktches et on a identifié 139 taxons de mollusques. On a déterminé le schéma de répartition géographique des espèces de mollusques au moyen d'une analyse typologique, qui a donné six groupes de stations dans l'endofaune et cinq dans l'épifaune. On définit des espèces caractéristiques des divers groupes fauniques. On a appliqué une analyse discriminante multiple séquentielle pour corréler les associations biologiques du benthos aux variables de l'environnement. La délimitation des groupes de l'endofaune était due en grande partie au taux de sable et de salinité au fond, tandis que les groupes de l'épifaune étaient répartis en fonction du taux de gravier et de température au fond. Une augmentation dans la quantité et la biomasse des mollusques de l'endofaune apparaissait près du nord et du nord-ouest d'un front de fond compris entre le plateau continental, les eaux non brassées de la mer des Tchouktches et les eaux côtières de l'Alaska. C'est près de la côte qu'on retrouvait l'abondance et la biomasse maximales des mollusques de l'épifaune. Les mollusques, surtout ceux des petites espèces et ceux des grandes espèces qui étaient au stade juvénile, représentaient une source alimentaire pour les prédateurs benthiques vivant dans la zone d'étude.Mots clés : mer des Tchouktches, mollusque, benthique, enfofaune, épifaune, front au fond, prédateurs benthiques, analyse typologique, analyse discriminant

Tritium labeling of potential lipophilic myelin probes

Two potential lipophilic myelin imaging agents (1,1,2,2‐tetrafluoro‐1,2‐diphenylethane and 1‐fluoroadamantane) were tritium labeled. The most effective method employed the microwave discharge activation of tritium gas technique and resulted in specific activities of 177 mCi/mmol for 1,1,2,2‐tetrafluoro‐1,2‐diphenylethane and 593 mCi/mmol for 1‐fluoroadamantane. Using this tritiation method significant amounts of tritium‐for‐fluorine substitution was also observed in the labeling of 1‐fluoroadamatane, resulting in nearly equivalent amounts of tritiated adamantane and fluoroadamantane.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90398/1/2580210110_ftp.pd

Increased Lysis of Stem Cells but Not Their Differentiated Cells by Natural Killer Cells; De-Differentiation or Reprogramming Activates NK Cells

The aims of this study are to demonstrate the increased lysis of stem cells but not their differentiated counterparts by the NK cells and to determine whether disturbance in cell differentiation is a cause for increased sensitivity to NK cell mediated cytotoxicity. Increased cytotoxicity and augmented secretion of IFN-γ were both observed when PBMCs or NK cells were co-incubated with primary UCLA oral squamous carcinoma stem cells (UCLA-OSCSCs) when compared to differentiated UCLA oral squamous carcinoma cells (UCLA-OSCCs). In addition, human embryonic stem cells (hESCs) were also lysed greatly by the NK cells. Moreover, NK cells were found to lyse human Mesenchymal Stem Cells (hMSCs), human dental pulp stem cells (hDPSCs) and human induced pluripotent stem cells (hiPSCs) significantly more than their differentiated counterparts or parental lines from which they were derived. It was also found that inhibition of differentiation or reversion of cells to a less-differentiated phenotype by blocking NFκB or targeted knock down of COX2 in monocytes significantly augmented NK cell cytotoxicity and secretion of IFN-γ. Taken together, these results suggest that stem cells are significant targets of the NK cell cytotoxicity. However, to support differentiation of a subset of tumor or healthy untransformed primary stem cells, NK cells may be required to lyse a number of stem cells and/or those which are either defective or incapable of full differentiation in order to lose their cytotoxic function and gain the ability to secrete cytokines (split anergy). Therefore, patients with cancer may benefit from repeated allogeneic NK cell transplantation for specific elimination of cancer stem cells

The Canadian Neuromuscular Disease Registry 2010-2019: A Decade of Facilitating Clinical Research Througha Nationwide, Pan-NeuromuscularDisease Registry

We report the recruitment activities and outcomes of a multi-disease neuromuscular patient registry in Canada. The Canadian Neuromuscular Disease Registry (CNDR) registers individuals across Canada with a confirmed diagnosis of a neuromuscular disease. Diagnosis and contact information are collected across all diseases and detailed prospective data is collected for 5 specific diseases: Amyotrophic Lateral Sclerosis (ALS), Duchenne Muscular Dystrophy (DMD), Myotonic Dystrophy (DM), Limb Girdle Muscular Dystrophy (LGMD), and Spinal Muscular Atrophy (SMA). Since 2010, the CNDR has registered 4306 patients (1154 pediatric and 3148 adult) with 91 different neuromuscular diagnoses and has facilitated 125 projects (73 academic, 3 not-for-profit, 3 government, and 46 commercial) using registry data. In conclusion, the CNDR is an effective and productive pan-neuromuscular registry that has successfully facilitated a substantial number of studies over the past 10 years

The 21Na(p,gamma)22Mg Reaction and Oxygen-Neon Novae

The 21Na(p,gamma)22Mg reaction is expected to play an important role in the nucleosynthesis of 22Na in Oxygen-Neon novae. The decay of 22Na leads to the emission of a characteristic 1.275 MeV gamma-ray line. This report provides the first direct measurement of the rate of this reaction using a radioactive 21Na beam, and discusses its astrophysical implications. The energy of the important state was measured to be E$_{c.m.}$= 205.7 $\pm$ 0.5 keV with a resonance strength $\omega\gamma = 1.03\pm0.16_{stat}\pm0.14_{sys}$ meV.Comment: Accepted for publication in Physical Review Letter