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Final report on CCQM-K125: elements in infant formula
Merrick, J,Saxby, D,Dutra, E S,Sena, R C,Araú,jo, T O,Almeida, M D,Yang, L,Pihillagawa, I G,Mester, Z,Sandoval, S,Wei, C,Castillo, M E D,Oster, C,Fisicaro, P,Rienitz, O,Pape, C,Schulz, U,Jä BUREAU INTERNATIONAL DES POIDS ET MESURES 2017 METROLOGIA -BERLIN- Vol.54 No.1
Sanderson, Michael J.,Copetti, Dario,Bú,rquez, Alberto,Bustamante, Enriquena,Charboneau, Joseph L. M.,Eguiarte, Luis E.,Kumar, Sudhir,Lee, Hyun Oh,Lee, Junki,McMahon, Michelle,Steele, Kelly,Wing Botanical Society of America, Inc. (Columbus) * Bu 2015 American journal of botany Vol. No.
<P>• <I>Premise of the study:</I> Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.</P><P>• <I>Methods:</I> Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).</P><P>• <I>Key results:</I> The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid <I>ndh</I> genes. This loss supports a statistically strong association across seed plants between the loss of <I>ndh</I> genes and the loss of the IR. Many nonplastid copies of plastid <I>ndh</I> genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear <I>pgr5</I>, which functions in a partially redundant pathway, was intact.</P><P>• <I>Conclusions:</I> The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid <I>ndh</I> gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.</P>
Sugawa, Fumihiro,Araú,zo-Bravo, Marcos J,Yoon, Juyong,Kim, Kee-Pyo,Aramaki, Shinya,Wu, Guangming,Stehling, Martin,Psathaki, Olympia E,Hü,bner, Karin,Schö,ler, Hans R BlackWell Publishing Ltd 2015 The EMBO journal Vol.34 No.8
<P>Primordial germ cells (PGCs) develop only into sperm and oocytes <I>in vivo</I>. The molecular mechanisms underlying human PGC specification are poorly understood due to inaccessibility of cell materials and lack of <I>in vitro</I> models for tracking the earliest stages of germ cell development. Here, we describe a defined and stepwise differentiation system for inducing pre-migratory PGC-like cells (PGCLCs) from human pluripotent stem cells (PSCs). In response to cytokines, PSCs differentiate first into a heterogeneous mesoderm-like cell population and then into PGCLCs, which exhibit minimal PRDM14 expression. PGC specification in humans is similar to the murine process, with the sequential activation of mesodermal and PGC genes, and the suppression of neural induction and of <I>de novo</I> DNA methylation, suggesting that human PGC formation is induced via epigenesis, the process of germ cell specification via inductive signals from surrounding somatic cells. This study demonstrates that PGC commitment in humans shares key features with that of the mouse, but also highlights key differences, including transcriptional regulation during the early stage of human PGC development (3–6 weeks). A more comprehensive understanding of human germ cell development may lead to methodology for successfully generating PSC-derived gametes for reproductive medicine.</P>
BACH: Grand challenge on breast cancer histology images
Aresta, Guilherme,Araú,jo, Teresa,Kwok, Scotty,Chennamsetty, Sai Saketh,Safwan, Mohammed,Alex, Varghese,Marami, Bahram,Prastawa, Marcel,Chan, Monica,Donovan, Michael,Fernandez, Gerardo,Zeineh, J Elsevier 2019 Medical image analysis Vol.56 No.-
<P><B>Abstract</B></P> <P>Breast cancer is the most common invasive cancer in women, affecting more than 10% of women worldwide. Microscopic analysis of a biopsy remains one of the most important methods to diagnose the type of breast cancer. This requires specialized analysis by pathologists, in a task that i) is highly time- and cost-consuming and ii) often leads to nonconsensual results. The relevance and potential of automatic classification algorithms using hematoxylin-eosin stained histopathological images has already been demonstrated, but the reported results are still sub-optimal for clinical use. With the goal of advancing the state-of-the-art in automatic classification, the Grand Challenge on BreAst Cancer Histology images (BACH) was organized in conjunction with the 15th International Conference on Image Analysis and Recognition (ICIAR 2018). BACH aimed at the classification and localization of clinically relevant histopathological classes in microscopy and whole-slide images from a large annotated dataset, specifically compiled and made publicly available for the challenge. Following a positive response from the scientific community, a total of 64 submissions, out of 677 registrations, effectively entered the competition. The submitted algorithms improved the state-of-the-art in automatic classification of breast cancer with microscopy images to an accuracy of 87%. Convolutional neuronal networks were the most successful methodology in the BACH challenge. Detailed analysis of the collective results allowed the identification of remaining challenges in the field and recommendations for future developments. The BACH dataset remains publicly available as to promote further improvements to the field of automatic classification in digital pathology.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The BACH challenge was organized to push forward methods for automatic classification of breast cancer biopsies using clinical hematoxylin-eosin stained histopathological images. </LI> <LI> A large public dataset, composed of 400 microscopy images and 30 whole-slide images, was specifically compiled for the BACH challenge. </LI> <LI> A total of 64 methods were submitted, out of 677 registration, and a detailed comparative analysis was carried out for the methods with higher accuracy scores. </LI> <LI> Several submitted algorithms performed better than the state-of-the-art in terms of accuracy (top score of 87%). </LI> <LI> Convolutional neural networks dominated the submissions, and was the method of choice in the algorithm that won the challenge. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Terá,n Hilares, Ruly,dos Santos, Jú,lio Cé,sar,Ahmed, Muhammad Ajaz,Jeon, Seok Hwan,da Silva, Silvio Silvé,rio,Han, Jong-In Elsevier 2016 Bioresource technology Vol.214 No.-
<P><B>Abstract</B></P> <P>Hydrodynamic cavitation (HC) was employed in order to improve the efficiency of alkaline pretreatment of sugarcane bagasse (SCB). Response surface methodology (RSM) was used to optimize pretreatment parameters: NaOH concentration (0.1–0.5M), solid/liquid ratio (S/L, 3–10%) and HC time (15–45min), in terms of glucan content, lignin removal and enzymatic digestibility. Under an optimal HC condition (0.48M of NaOH, 4.27% of S/L ratio and 44.48min), 52.1% of glucan content, 60.4% of lignin removal and 97.2% of enzymatic digestibility were achieved. Moreover, enzymatic hydrolysis of the pretreated SCB resulted in a yield 82% and 30% higher than the untreated and alkaline-treated controls, respectively. HC was found to be a potent and promising approach to pretreat lignocellulosic biomass.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Hydrodynamic cavitation (HC) was combined with an alkaline pretreatment. </LI> <LI> HC-assisted pretreatment was statistically optimized and experimentally verified. </LI> <LI> High enzymatic digestibility of 97.2% was achieved. </LI> <LI> The HC increased enzymatic digestibility by 30%. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Direct reprogramming of human neural stem cells by OCT4
Kim, Jeong Beom,Greber, Boris,Araú,zo-Bravo, Marcos J.,Meyer, Johann,Park, Kook In,Zaehres, Holm,Schö,ler, Hans R. Macmillan Publishers Limited. All rights reserved 2009 Nature Vol.461 No.7264
Induced pluripotent stem (iPS) cells have been generated from mouse and human somatic cells by ectopic expression of four transcription factors (OCT4 (also called POU5F1), SOX2, c-Myc and KLF4). We previously reported that Oct4 alone is sufficient to reprogram directly adult mouse neural stem cells to iPS cells. Here we report the generation of one-factor human iPS cells from human fetal neural stem cells (one-factor (1F) human NiPS cells) by ectopic expression of OCT4 alone. One-factor human NiPS cells resemble human embryonic stem cells in global gene expression profiles, epigenetic status, as well as pluripotency in vitro and in vivo. These findings demonstrate that the transcription factor OCT4 is sufficient to reprogram human neural stem cells to pluripotency. One-factor iPS cell generation will advance the field further towards understanding reprogramming and generating patient-specific pluripotent stem cells.
Kim, Jong Soo,Choi, Hyun Woo,Araú,zo-Bravo, Marcos J.,Schö,ler, Hans R.,Do, Jeong Tae The Company of Biologists Ltd. 2015 Journal of cell science Vol.128 No.1
<P>Direct reprogramming of somatic cells to pluripotent stem cells entails the obliteration of somatic cell memory and the reestablishment of epigenetic events. Induced pluripotent stem cells (iPSCs) have been created by reprogramming somatic cells through the transduction of reprogramming factors. During cell reprogramming, female somatic cells must overcome at least one more barrier than male somatic cells in order to enter a pluripotent state, as they must reactivate an inactive X chromosome (Xi). In this study, we investigated whether the sex of somatic cells affects reprogramming efficiency, differentiation potential and the post-transcriptional processing of <I>Xist</I> RNA after reprogramming. There were no differences between male and female iPSCs with respect to reprogramming efficiency or their differentiation potential <I>in vivo</I>. However, reactivating Xi took longer than reactivating pluripotency-related genes. We also found that direct reprogramming leads to gender-appropriate post-transcriptional reprogramming – like male embryonic stem cells (ESCs), male iPSCs expressed only the long <I>Xist</I> isoform, whereas female iPSCs, like female ESCs, expressed both the long and short isoforms.</P>
Kim, Jeong Beom,Lee, Hyunah,Araú,zo‐,Bravo, Marcos J,Hwang, Kyujin,Nam, Donggyu,Park, Myung Rae,Zaehres, Holm,Park, Kook In,Lee, Seok‐,Jin EMBO 2015 The EMBO journal Vol.34 No.23
<P>The generation of patient-specific oligodendrocyte progenitor cells (OPCs) holds great potential as an expandable cell source for cell replacement therapy as well as drug screening in spinal cord injury or demyelinating diseases. Here, we demonstrate that induced OPCs (iOPCs) can be directly derived from adult mouse fibroblasts by Oct4-mediated direct reprogramming, using anchorage-independent growth to ensure high purity. Homogeneous iOPCs exhibit typical small-bipolar morphology, maintain their self-renewal capacity and OPC marker expression for more than 31 passages, share high similarity in the global gene expression profile to wild-type OPCs, and give rise to mature oligodendrocytes and astrocytes in vitro and in vivo. Notably, transplanted iOPCs contribute to functional recovery in a spinal cord injury (SCI) model without tumor formation. This study provides a simple strategy to generate functional self-renewing iOPCs and yields insights for the in-depth study of demyelination and regenerative medicine.</P>