Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets

<p>Abstract</p> <p>Background</p> <p>Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as <it>16S rRNA</it>, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets.</p> <p>Methods</p> <p>Pairwise alignment techniques are used here to calculate genetic distances between sequence pairs. These methods are pleasingly parallel and have been shown to more accurately reflect accurate genetic distances in highly variable regions of <it>rRNA </it>genes than do traditional multiple sequence alignment (MSA) approaches. By utilizing Needleman-Wunsch (NW) pairwise alignment in conjunction with novel implementations of interpolative multidimensional scaling (MDS), we have developed an effective method for visualizing massive biosequence data sets and quickly identifying potential gene clusters.</p> <p>Results</p> <p>This study demonstrates the use of interpolative MDS to obtain clustering results that are qualitatively similar to those obtained through full MDS, but with substantial cost savings. In particular, the wall clock time required to cluster a set of 100,000 sequences has been reduced from seven hours to less than one hour through the use of interpolative MDS.</p> <p>Conclusions</p> <p>Although work remains to be done in selecting the optimal training set size for interpolative MDS, substantial computational cost savings will allow us to cluster much larger sequence sets in the future.</p

Singular Cucker-Smale Dynamics

The existing state of the art for singular models of flocking is overviewed, starting from microscopic model of Cucker and Smale with singular communication weight, through its mesoscopic mean-filed limit, up to the corresponding macroscopic regime. For the microscopic Cucker-Smale (CS) model, the collision-avoidance phenomenon is discussed, also in the presence of bonding forces and the decentralized control. For the kinetic mean-field model, the existence of global-in-time measure-valued solutions, with a special emphasis on a weak atomic uniqueness of solutions is sketched. Ultimately, for the macroscopic singular model, the summary of the existence results for the Euler-type alignment system is provided, including existence of strong solutions on one-dimensional torus, and the extension of this result to higher dimensions upon restriction on the smallness of initial data. Additionally, the pressureless Navier-Stokes-type system corresponding to particular choice of alignment kernel is presented, and compared - analytically and numerically - to the porous medium equation

Prospective study of oncologic outcomes after laparoscopic modified complete mesocolic excision for non-metastatic right colon cancer (PIONEER study): study protocol of a multicentre single-arm trial

Abstract Background The introduction of complete mesocolic excision (CME) with central vascular ligation (CVL) for right-sided colon cancer has improved the oncologic outcomes. Recently, we have introduced a modified CME (mCME) procedure that keeps the same principles as the originally described CME but with a more tailored approach. Some retrospective studies have reported the favourable oncologic outcomes of laparoscopic mCME for right-sided colon cancer; however, no prospective multicentre study has yet been conducted. Methods This study is a multi-institutional, prospective, single-arm study evaluating the oncologic outcomes of laparoscopic mCME for adenocarcinoma arising from the right side of the colon. A total of 250 patients will be recruited from five tertiary referral centres in South Korea. The primary outcome of this study is 3-year disease-free survival. Secondary outcome measures include 3-year overall survival, incidence of surgical complications, completeness of mCME, and distribution of metastatic lymph nodes. The quality of laparoscopic mCME will be assessed on the basis of photographs of the surgical specimen and the operation field after the completion of lymph node dissection. Discussion This is a prospective multicentre study to evaluate the oncologic outcomes of laparoscopic mCME for right-sided colon cancer. To the best of our knowledge, this will be the first study to prospectively and objectively assess the quality of laparoscopic mCME. The results will provide more evidence about oncologic outcomes with respect to the quality of laparoscopic mCME in right-sided colon cancer. Trial registration ClinicalTrials.gov ID: NCT03992599 (June 20, 2019). The posted information will be updated as needed to reflect protocol amendments and study progress

Heterotic Models from Vector Bundles on Toric Calabi-Yau Manifolds

We systematically approach the construction of heterotic E_8 X E_8 Calabi-Yau models, based on compact Calabi-Yau three-folds arising from toric geometry and vector bundles on these manifolds. We focus on a simple class of 101 such three-folds with smooth ambient spaces, on which we perform an exhaustive scan and find all positive monad bundles with SU(N), N=3,4,5 structure groups, subject to the heterotic anomaly cancellation constraint. We find that anomaly-free positive monads exist on only 11 of these toric three-folds with a total number of bundles of about 2000. Only 21 of these models, all of them on three-folds realizable as hypersurfaces in products of projective spaces, allow for three families of quarks and leptons. We also perform a preliminary scan over the much larger class of semi-positive monads which leads to about 44000 bundles with 280 of them satisfying the three-family constraint. These 280 models provide a starting point for heterotic model building based on toric three-folds.Comment: 41 pages, 5 figures. A table modified and a table adde

Finite Element Modelling and Damage Detection of Seam Weld

© Springer Nature Singapore Pte Ltd 2020. Seam welds are widely used in assembled structures for connecting components. However, the dynamic effects of a seam weld are often difficult to characterise in numerical models for several reasons: (1) it is often not wise to build a fine mesh on the seam line which will add considerable computational cost for a structure with many welds, (2) the mechanical properties of weld materials are not well known; (3) sometimes some geometric information about welds is not known beforehand. In this work, the finite element model of a welding connection part is developed by employing CSEAM element in NASTRAN and its feasibility for representing a seam weld is investigated. Based on this result, a damage detection method by updating the properties of the built CSEAM elements is also proposed for welding quality assurance. The damage takes the form of a gap in the weld which causes a sharp change of model strain energy at the edges of the gap for certain vibration modes. Specifically, the model strain energy shape is used as the objective function. A Kriging model is introduced for efficiency and simulation of a T-shaped welded plate structure to demonstrate the effectiveness of this method

The Kuroshio Extension : a leading mechanism for the seasonal sea-level variability along the west coast of Japan

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Ocean Dynamics 60 (2010): 667-672, doi:10.1007/s10236-009-0239-9.Sea level changes coherently along the two coasts of Japan on the seasonal time scale. AVISO satellite altimetry data and OFES (OGCM for the Earth Simulator) results indicate that the variation propagates clockwise from Japan's east coast through the Tsushima Strait into the Japan/East Sea (JES) and then northward along the west coast. In this study, we hypothesize and test numerically that the sea level variability along the west coast of Japan is remotely forced by the Kuroshio Extension (KE) off the east coast. Topographic Rossby waves and boundary Kelvin waves facilitate the connection. Our 3-d POM model when forced by observed wind stress reproduces well the seasonal changes in the vicinity of JES. Two additional experiments were conducted to examine the relative roles of remote forcing and local forcing. The sea level variability inside the JES was dramatically reduced when the Tsushima Strait is blocked in one experiment. The removal of the local forcing, in another experiment, has little effect on the JES variability. Both experiments support our hypothesis that the open-ocean forcing, possibly through the KE variability, is the leading forcing mechanism for sea level change along the west coast of Japan.This work was conducted when Chao Ma was a visiting graduate student at WHOI. His visit has been supported by China Scholarship Council and WHOI Academics Office. This study has been supported by WHOI’s Coastal Ocean Institute, the National Basic Research Program of China 2005CB422303 and 2007CB481804), the International Science and Technology Cooperation Program of China (2006DFB21250), the Natural Science Foundation of China (40706006) , and the Ministry of Education’s 111 Project (B07036). Lin was supported by the Program for New Century Excellent Talents in University (NECT-07-0781)

Quiver Structure of Heterotic Moduli

We analyse the vector bundle moduli arising from generic heterotic compactifications from the point of view of quiver representations. Phenomena such as stability walls, crossing between chambers of supersymmetry, splitting of non-Abelian bundles and dynamic generation of D-terms are succinctly encoded into finite quivers. By studying the Poincar\'e polynomial of the quiver moduli space using the Reineke formula, we can learn about such useful concepts as Donaldson-Thomas invariants, instanton transitions and supersymmetry breaking.Comment: 38 pages, 5 figures, 1 tabl

Density of states, Potts zeros, and Fisher zeros of the Q-state Potts model for continuous Q

The Q-state Potts model can be extended to noninteger and even complex Q in the FK representation. In the FK representation the partition function,Z(Q,a), is a polynomial in Q and v=a-1(a=e^-T) and the coefficients of this polynomial,Phi(b,c), are the number of graphs on the lattice consisting of b bonds and c connected clusters. We introduce the random-cluster transfer matrix to compute Phi exactly on finite square lattices. Given the FK representation of the partition function we begin by studying the critical Potts model Z_{CP}=Z(Q,a_c), where a_c=1+sqrt{Q}. We find a set of zeros in the complex w=sqrt{Q} plane that map to the Beraha numbers for real positive Q. We also identify tilde{Q}_c(L), the value of Q for a lattice of width L above which the locus of zeros in the complex p=v/sqrt{Q} plane lies on the unit circle. We find that 1/tilde{Q}_c->0 as 1/L->0. We then study zeros of the AF Potts model in the complex Q plane and determine Q_c(a), the largest value of Q for a fixed value of a below which there is AF order. We find excellent agreement with Q_c=(1-a)(a+3). We also investigate the locus of zeros of the FM Potts model in the complex Q plane and confirm that Q_c=(a-1)^2. We show that the edge singularity in the complex Q plane approaches Q_c as Q_c(L)~Q_c+AL^-y_q, and determine the scaling exponent y_q. Finally, by finite size scaling of the Fisher zeros near the AF critical point we determine the thermal exponent y_t as a function of Q in the range 2<Q<3. We find that y_t is a smooth function of Q and is well fit by y_t=(1+Au+Bu^2)/(C+Du) where u=u(Q). For Q=3 we find y_t~0.6; however if we include lattices up to L=12 we find y_t~0.50.Comment: to appear in Physical Review