A regularization-patching dual quaternion optimization method for solving the hand-eye calibration problem

The hand-eye calibration problem is an important application problem in robot research. Based on the 2-norm of dual quaternion vectors, we propose a new dual quaternion optimization method for the hand-eye calibration problem. The dual quaternion optimization problem is decomposed to two quaternion optimization subproblems. The first quaternion optimization subproblem governs the rotation of the robot hand. It can be solved efficiently by the eigenvalue decomposition or singular value decomposition. If the optimal value of the first quaternion optimization subproblem is zero, then the system is rotationwise noiseless, i.e., there exists a ``perfect'' robot hand motion which meets all the testing poses rotationwise exactly. In this case, we apply the regularization technique for solving the second subproblem to minimize the distance of the translation. Otherwise we apply the patching technique to solve the second quaternion optimization subproblem. Then solving the second quaternion optimization subproblem turns out to be solving a quadratically constrained quadratic program. In this way, we give a complete description for the solution set of hand-eye calibration problems. This is new in the hand-eye calibration literature. The numerical results are also presented to show the efficiency of the proposed method

Spatial and temporal colonization dynamics of segmented filamentous bacteria is influenced by gender, age and experimental infection with Helicobacter hepaticus in Swiss Webster mice

In this study, we examined colonization dynamics of segmented filamentous bacteria (SFB) in intestine of Swiss Webster (SW) mice infected with Helicobacter hepaticus (Hh). At 8 weeks post-inoculation with Hh (WPI), cecal and colonic SFB levels in the control males were significantly lower compared to those at 16 WPI. Hh infection in both genders did not alter SFB levels in the jejunum and ileum, but increased SFB levels in the cecum and colon of males compared to the controls (P < 0.05) at 8 WPI. At 16 WPI, the Hh-infected females contained lower levels of SFB in the jejunum, cecum and colon compared to the female controls. Irrespective of gender, aging and Hh infection, the Il-17A mRNA levels decreased from the small intestine to the cecum and then to the colon, whereas the Foxp3 mRNA levels were comparable in these intestinal regions. There were significant differences in Il-17A mRNA levels in the ileum (P < 0.05, R2 = 0.31), with females having greater Il-17A mRNA levels than males, and higher SFB colonization levels related to more Il-17A mRNA. These results indicate that aging and gender play an important role in colonization dynamics of intestinal SFB and ileal SFB-associated Th17 response.United States. National Institutes of Health (P30-ES002109)United States. National Institutes of Health (R01OD11141)United States. National Institutes of Health (R01-CA067529

Correction to: The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomic

After publication of this supplement article [1], it is requested the grant ID in the Funding section should be corrected from NSF grant IIS-7811367 to NSF grant IIS-1902617. Therefore, the correct ‘Funding’ section in this article should read: This article has not received sponsorship for publication. We thank the National Science Foundation (NSF grant IIS-1902617) and the Data Science and Informatics Core for Cancer Research (CPRIT grant RP170668) for the financial support of ICIBM 2019, as well as the support from Cancer Prevention and Research Institute of Texas (RP180734)

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics

The goal of this editorial is to summarize the 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) conference that took place on June 9–11, 2019 in The Ohio State University, Columbus, OH, and to provide an introductory summary of the seven articles presented in this supplement issue. ICIBM 2019 hosted four keynote speakers, four eminent scholar speakers, five tutorials and workshops, twelve concurrent sessions and a poster session, totaling 23 posters, spanning state-of-the-art developments in bioinformatics, genomics, next-generation sequencing (NGS) analysis, scientific databases, cancer and medical genomics, and computational drug discovery. A total of 105 original manuscripts were submitted to ICIBM 2019, and after careful review, seven were selected for this supplement issue. These articles cover methods and applications for functional annotations of miRNA targeting, clonal evolution of bacterial cells, gene co-expression networks that describe a given phenotype, functional binding site analysis of RNA-binding proteins, normalization of genome architecture mapping data, sample predictions based on multiple NGS data types, and prediction of an individual’s genetic admixture given exonic single nucleotide polymorphisms data

Helicobacter hepaticus cytolethal distending toxin promotes intestinal carcinogenesis in 129Rag2‐deficient mice

Multiple pathogenic Gram-negative bacteria produce the cytolethal distending toxin (CDT) with activity of DNase I; CDT can induce DNA double-strand breaks (DSBs), G2/M cell cycle arrest, and apoptosis in cultured mammalian cells. However, the link of CDT to in vivo tumorigenesis is not fully understood. In this study, 129/SvEv Rag2−/−mice were gavaged with wild-type Helicobacter hepatics 3B1(Hh) and its isogenic cdtB mutant HhcdtBm7, followed by infection for 10 and 20 weeks (WPI). HhCDT deficiency did not affect cecal colonization levels of HhcdtBm7, but attenuated severity of cecal pathology in HhcdtBm7-infected mice. Of importance, preneoplasic dysplasia was progressed to cancer from 10 to 20 WPI in the Hh-infected mice but not in the HhcdtBm7-infected mice. In addition, the loss of HhCDT significantly dampened transcriptional upregulation of cecal Tnfα and Il-6, but elevated Il-10 mRNA levels when compared to Hh at 10 WPI. Furthermore, the presence of HhCDT increased numbers of lower bowel intestinal γH2AX-positive epithelial cells (a marker of DSBs) at both 10 and 20 WPI and augmented phospho-Stat3 foci[superscript +] intestinal crypts (activation of Stat3) at 20 WPI. Our findings suggest that CDT promoted Hh carcinogenesis by enhancing DSBs and activation of the Tnfα/Il-6-Stat3 signaling pathway.National Institutes of Health (U.S.) (Grant R01-OD01141)National Institutes of Health (U.S.) (Grant T32-OD010978)National Institutes of Health (U.S.) (Grant P01 CA28842

Helicobacter hepaticus Cholesterol-α-glucosyltransferase is Essential for Establishing Colonization in Male A/JCr Mice

Background Helicobacter pylori cholesterol-α-glucosyltransferase (cgt) is essential for survival of H. pylori in mice. Enterohepatic H. hepaticus, the cause of colonic and hepatocellular carcinoma in susceptible mouse strains, contains an ortholog of the H. pylori cgt. However, the role of cgt in the pathogenesis of H. hepaticus has not been investigated. Materials and Methods Two cgt-deficient isogenic mutants of wild-type H. hepaticus (WT) 3B1 were generated and used to inoculate male A/JCr mice. Cecal and hepatic colonization levels of the mutants and WT 3B1 as well as select inflammation-associated cytokines were measured by qPCR at 4 months postinoculation. Results Both mutants were undetectable in the cecum of any inoculated mice (10 per mutant) but were detected in two livers (one for each mutant); by contrast, 9 and 7 of 10 mice inoculated with WT 3B1 were qPCR positive in the ceca and livers, respectively. The mice inoculated with the mutants developed significantly less severe hepatic inflammation (p < .05) and also produced significantly lower hepatic mRNA levels of proinflammatory cytokines Ifn-γ (p < .01) and Tnf-α (p ≤ .02) as well as anti-inflammatory factors Il10 and Foxp3 compared with the WT 3B1-inoculated mice. Additionally, the WT 3B1-inoculated mice developed significantly higher Th1-associated IgG2a (p < .0001) and Th2-associated IgG1 responses (p < .0001) to H. hepaticus infection than mice dosed with isogenic cgt mutants. Conclusion Our data indicate that the cholesterol-α-glucosyltransferase is required for establishing colonization of the intestine and liver and therefore plays a critical role in the pathogenesis of H. hepaticus.National Institutes of Health (U.S.) (Grant R010D011141)National Institutes of Health (U.S.) (Grant 01CA026731)National Institutes of Health (U.S.) (Grant R01AT004326)National Institutes of Health (U.S.) (Grant P30-ES002109

Innovating Computational Biology and Intelligent Medicine: ICIBM 2019 Special Issue

The International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Intelligent Biology and Medicine (ICIBM), which was established in 2012. The ICIBM 2019 was held from 9 to 11 June 2019 in Columbus, Ohio, USA. Out of the 105 original research manuscripts submitted to the conference, 18 were selected for publication in a Special Issue in Genes. The topics of the selected manuscripts cover a wide range of current topics in biomedical research including cancer informatics, transcriptomic, computational algorithms, visualization and tools, deep learning, and microbiome research. In this editorial, we briefly introduce each of the manuscripts and discuss their contribution to the advance of science and technology

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics

In this editorial, we briefly summarized the International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019) that was held on June 9-11, 2019 at Columbus, Ohio, USA. We further introduced the 19 research articles included in this supplement issue, covering four major areas, namely computational method development, genomics analysis, network-based analysis and biomarker prediction. The selected papers perform cutting edge computational research applied to a broad range of human diseases such as cancer, neural degenerative and chronic inflammatory disease. They also proposed solutions for fundamental medical genomics problems range from basic data processing and quality control to functional interpretation, biomarker and drug prediction, and database releasing

PCPL: Predicate-Correlation Perception Learning for Unbiased Scene Graph Generation

Today, scene graph generation(SGG) task is largely limited in realistic scenarios, mainly due to the extremely long-tailed bias of predicate annotation distribution. Thus, tackling the class imbalance trouble of SGG is critical and challenging. In this paper, we first discover that when predicate labels have strong correlation with each other, prevalent re-balancing strategies(e.g., re-sampling and re-weighting) will give rise to either over-fitting the tail data(e.g., bench sitting on sidewalk rather than on), or still suffering the adverse effect from the original uneven distribution(e.g., aggregating varied parked on/standing on/sitting on into on). We argue the principal reason is that re-balancing strategies are sensitive to the frequencies of predicates yet blind to their relatedness, which may play a more important role to promote the learning of predicate features. Therefore, we propose a novel Predicate-Correlation Perception Learning(PCPL for short) scheme to adaptively seek out appropriate loss weights by directly perceiving and utilizing the correlation among predicate classes. Moreover, our PCPL framework is further equipped with a graph encoder module to better extract context features. Extensive experiments on the benchmark VG150 dataset show that the proposed PCPL performs markedly better on tail classes while well-preserving the performance on head ones, which significantly outperforms previous state-of-the-art methods.Comment: To be appeared on ACMMM 202

Research Progress of Electrically Controlled Reconfigurable Polarization Manipulation Using Metasurface

Metasurfaces are two-dimensional artificial structures with numerous subwavelength elements arranged periodically or aperiodically. They have demonstrated their exceptional capabilities in electromagnetic wave polarization manipulation, opening new avenues for manipulating electromagnetic waves. Metasurfaces exhibiting electrically controlled reconfigurable polarization manipulation have garnered widespread research interest. These unique metasurfaces can dynamically adjust the polarization state of electromagnetic waves through real-time modification of their structure or material properties via electrical signals. This article provides a comprehensive overview of the development of metasurfaces exhibiting electrically controlled reconfigurable polarization manipulation and explores the technological advancements of metasurfaces with different transmission characteristics in the microwave region in detail. Furthermore, it delves into and anticipates the future development of this technology