A POS-based preordering approach for English-to-Arabic statistical machine translation

In this work, we present a POS-based preordering approach that tackles both long- and short-distance reordering phenomena. Syntactic unlexicalized reordering rules are automatically extracted from a parallel corpus using only word alignment and a source-side language tagging. The reordering rules are used in a deterministic manner; this prevents the decoding speed from being bottlenecked in the reordering procedure. A new approach for both rule filtering and rule application is used to ensure a fast and efficient reordering. The tests performed on the IWSLT2016 English-to-Arabic evaluation benchmark show a noticeable increase in the overall Blue Score for our system over the baseline PSMT system

Establishment of secondary MEFs and secondary iPSCs.

<p>(A) Morphology of secondary MEFs. Scale bar, 10 μm. (B and C) Numbers of secondary iPSC colonies. (D) Morphology of secondary iPSC colonies. Scale bar, 50 μm. (E) Morphology of secondary iPSC cell lines. Scale bar, 10 μm. (F and G) Comparison of endogenous expressions of the four reprogramming factors, transgenes, and ESC-specific genes between primary and secondary iPSCs.</p

Evaluation of established mouse iPSC lines.

<p>(A) Contribution of iPSCs to mouse embryonic development. Embryos were analyzed by fluorescence microscopy at E13.5. (B) Coat color of adult chimeras at 7 weeks old. (C) Contribution of iPSCs to mouse testes. (D) EGFP-positive sperm and spermatids. Scale bar, 5 μm.</p

Reprogramming of mouse somatic cells and establishment of iPSCs.

<p>(A) Construction of PB vectors used in this study. (B) Timeline for the establishment of iPSC lines. (C) Morphology of donor MEFs. Scale bar, 50 μm. (D and E) Numbers of primary iPSC colonies. (F) Morphology of primary iPSC colonies. Scale bar, 50 μm. (G) Morphology of iPSC cell lines. Scale bar, 50 μm. (H and I) Endogenous expression levels of the four reprogramming factors, transgenes, and ESC-specific genes in MEFs and iPSCs.</p

Establishment of rat iPSCs and production of rat iPSC–derived sperm in mouse–rat interspecific chimeras.

<p>(A) Morphology of REFs. Scale bar, 50 μm. (B) Morphology of rat iPSC primary colonies. Scale bar, 50 μm. (C) Morphology of rat iPSCs. Scale bar, 50 μm. (D) Endogenous expression levels of the four reprogramming factors, transgenes, and ESC-specific genes in REFs and rat iPSCs. (E) Coat color of adult rat–mouse interspecific chimeras at 8 weeks of age. (F) Contribution of rat iPSCs to mouse testes. (G) Rat sperm in EGFP-positive seminiferous tubules of mouse–rat interspecific chimeras. Scale bar, 5 μm. (H) A rat offspring produced by ICSI and a wild-type rat offspring. (I) Genomic PCR of rat offspring.</p

A Comprehensive System for Generation and Evaluation of Induced Pluripotent Stem Cells Using piggyBac Transposition

<div><p>The most stringent criterion for evaluating pluripotency is generation of chimeric animals with germline transmission ability. Because the quality of induced pluripotent stem cell (iPSC) lines is heterogeneous, an easy and accurate system to evaluate these abilities would be useful. In this study, we describe a simple but comprehensive system for generating and evaluating iPSCs by single transfection of multiple piggyBac (PB) plasmid vectors encoding Tet-inducible polycistronic reprogramming factors, a pluripotent-cell–specific reporter, a constitutively active reporter, and a sperm-specific reporter. Using this system, we reprogrammed 129 and NOD mouse embryonic fibroblasts into iPSCs, and then evaluated the molecular and functional properties of the resultant iPSCs by quantitative RT-PCR analysis and chimera formation assays. The iPSCs contributed extensively to chimeras, as indicated by the constitutively active TagRFP reporter, and also differentiated into sperm, as indicated by the late-spermatogenesis–specific Acr (acrosin)-EGFP reporter. Next, we established secondary MEFs from E13.5 chimeric embryos and efficiently generated secondary iPSCs by simple addition of doxycycline. Finally, we applied this system to establishment and evaluation of rat iPSCs and production of rat sperm in mouse–rat interspecific chimeras. By monitoring the fluorescence of Acr-EGFP reporter, we could easily detect seminiferous tubules containing rat iPSC–derived spermatids and sperm. And, we succeeded to obtain viable offspring by intracytoplasmic sperm injection (ICSI) using these haploid male germ cells. We propose that this system will enable robust strategies for induction and evaluation of iPSCs, not only in rodents but also in other mammals. Such strategies will be especially valuable in non-rodent species, in which verification of germline transmission by mating is inefficient and time-consuming.</p></div

Changes of HPC surface marker expression in human iPS cell-derived hepatic progenitor-like colonies.

<p>(<b>A</b>) After 12 days of culture with cytokines, CD13^highCD133⁺ cells were sorted onto GFP-MEFs. After 10–12 days, cells were trypsinized and stained with antibodies against CD13 and CD133. Expression of CD13 and CD133 was analyzed by flow cytometry. (<b>B–E</b>) Colony forming activity of CD13⁺CD133⁺, CD13⁺CD133⁻, CD13⁻CD133⁺, and CD13⁻CD133⁻ fractions of human iPS cell-derived HPCs. At every replating step, cells stained with antibodies against CD13 and CD133 were sorted onto new GFP-MEFs, and their colony-forming activity was analyzed. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067541#s3" target="_blank">Results</a> are represented as the mean colony count ± SD (duplicate samples). N.D. shows “not determined”.</p

An <i>In Vitro</i> Expansion System for Generation of Human iPS Cell-Derived Hepatic Progenitor-Like Cells Exhibiting a Bipotent Differentiation Potential

<div><p>Hepatoblasts, hepatic stem/progenitor cells in liver development, have a high proliferative potential and the ability to differentiate into both hepatocytes and cholangiocytes. In regenerative medicine and drug screening for the treatment of severe liver diseases, human induced pluripotent stem (iPS) cell-derived mature functional hepatocytes are considered to be a potentially good cell source. However, induction of proliferation of these cells is difficult <i>ex vivo</i>. To circumvent this problem, we generated hepatic progenitor-like cells from human iPS cells using serial cytokine treatments <i>in vitro</i>. Highly proliferative hepatic progenitor-like cells were purified by fluorescence-activated cell sorting using antibodies against CD13 and CD133 that are known cell surface markers of hepatic stem/progenitor cells in fetal and adult mouse livers. When the purified CD13^highCD133⁺ cells were cultured at a low density with feeder cells in the presence of suitable growth factors and signaling inhibitors (ALK inhibitor A-83-01 and ROCK inhibitor Y-27632), individual cells gave rise to relatively large colonies. These colonies consisted of two types of cells expressing hepatocytic marker genes (hepatocyte nuclear factor 4α and α-fetoprotein) and a cholangiocytic marker gene (cytokeratin 7), and continued to proliferate over long periods of time. In a spheroid formation assay, these cells were found to express genes required for mature liver function, such as cytochrome P450 enzymes, and secrete albumin. When these cells were cultured in a suitable extracellular matrix gel, they eventually formed a cholangiocytic cyst-like structure with epithelial polarity, suggesting that human iPS cell-derived hepatic progenitor-like cells have a bipotent differentiation ability. Collectively these data indicate that this novel procedure using an <i>in vitro</i> expansion system is useful for not only liver regeneration but also for the determination of molecular mechanisms that regulate liver development.</p></div

Isolation of HPCs from human iPS cell-derived hepatic lineage cells.

<p>(<b>A</b>) Expression of hepatic progenitor markers in undifferentiated human iPS cells and differentiated cells. After 12 days of culture with or without cytokines, cells were stained with antibodies against CD13 and CD133, and then analyzed by flow cytometry. Ratios of CD13^highCD133⁺ cells are shown. (<b>B</b>) Representative images of a colony derived from a single CD13^highCD133⁺ cell. Colonies were stained with antibodies against AFP and HNF4α. Nuclei were counterstained with DAPI. (<b>C</b>) Culture condition of the human iPS cell-derived hepatic progenitor colony assay. CD13^highCD133⁺ cells were sorted and cultured on MEFs in the presence or absence of A-83-01 (ALK inhibitor) and Y-27632 (ROCK inhibitor). <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067541#s3" target="_blank">Results</a> are represented as the mean colony count ± SD (triplicate samples). (<b>D</b>) CD13⁻CD133⁻, CD13 weakly single positive, CD13^mid single positive and CD13^highCD133⁺ cells were sorted onto MEFs. The cells were cultured in standard culture media in the presence of A-83-01 and Y-27632. Large colonies (containing more than 100 cells) derived from individual sorted cells were counted. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067541#s3" target="_blank">Results</a> are represented as the mean colony count ± SD (triplicate samples).</p

Expressions of hepatic functional genes in differentiated HPCs.

<p>The levels of mRNAs encoding phase 1 and 2 enzymes in human iPS cell-derived HPCs from the 3rd culture, and spheroids derived from human iPS cell-derived HPCs from the 3rd culture are shown as the fold values relative to the levels in uncultured human hepatocytes. Spheroid formation was induced by hanging drop culture in the presence or absence of OSM. The results are represented as the mean colony counts ± SD (spheroid culture, n = 6; HPCs, n = 3; uncultured human hepatocytes, n = 2).</p