Prosody and Intonation in Formosan Languages

The Formosan languages are the languages of the Aboriginal peoples of Taiwan. These languages are part of the Austronesian language family, and represent all but one primary branch of this family of 1,200+ languages. The Formosan languages are endangered, some critically so. While these languages have seen attention in the literature for their syntactic and phonological systems, little work has been done on their prosodic structure or intonation. This dissertation analyzes the prosodic structure and intonational phonology of Mantauran Rukai, Budai Rukai, Tsou, Kanakanavu, Hla’alua, Sandimen Paiwan, Piuma Paiwan, Kavalan, Amis, Bunun, Tgdaya Seediq, Truku Seediq, and Pazeh, based on original fieldwork. In addition, archival materials are incorporated into analyses of Tsou, Truku Seediq, Tgdaya Seediq, and Puyuma. This study finds that the Formosan languages show rich tonal phonologies in their intonational systems, and have complex interactions between stress assignment and morphology. Some examples include the following: Mantauran Rukai, previously described as an initial-stress language, actually has a complex stress assignment system with an alternation between first- and third-syllable stress, which as a system is unique in descriptions of stress assignment in the world’s languages. Hla’alua (Saaroa), previously described as having free variation between antepenultimate and penultimate stress, actually has an accent system in which some lexical items are consistently produced without an accented syllable, while others are. Hla’alua also has a rich tonal phonology assigned at two higher levels of the prosodic hierarchy. Kavalan has a unique rule that causes spreading tones to shift to the opposite domain edge when a certain number of tonal elements are aligned to the same boundary. Elements of the intonational phonology in Amis and Kavalan include glottal stops in addition to tonal elements. Bunun has distinct pitch accent melodies for words vs. clitics. In addition to the unique features found in individual Formosan languages, this dissertation’s comparative study finds at least two geographic areas within Taiwan in which features of prosody and intonation cluster. One is southwestern Taiwan, including Tsou, Kanakanavu, Hla’alua, and Rukai, which share features including a lack of glide-vowel contrasts and variability of initial H vs. L elements in certain prosodic domains. The other is eastern Taiwan, including Amis, Kavalan, and Puyuma, which share features including suppression of non-IP-final pitch accents, alternations between ultimate and pre-ultimate F0 peaks across intonational contours, and interactions between glottal stop epenthesis and intonational phonology

Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research

Author Posting. © Acoustical Society of America, 2015. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 138 (2015); 3742, doi:10.1121/1.4937607.Analytical and numerical scatteringmodels with accompanying digital representations are used increasingly to predict acoustic backscatter by fish and zooplankton in research and ecosystem monitoring applications. Ten such models were applied to targets with simple geometric shapes and parameterized (e.g., size and material properties) to represent biological organisms such as zooplankton and fish, and their predictions of acoustic backscatter were compared to those from exact or approximate analytical models, i.e., benchmarks. These comparisons were made for a sphere, spherical shell, prolate spheroid, and finite cylinder, each with homogeneous composition. For each shape, four target boundary conditions were considered: rigid-fixed, pressure-release, gas-filled, and weakly scattering. Target strength (dB re 1 m2) was calculated as a function of insonifying frequency (f = 12 to 400 kHz) and angle of incidence (θ = 0° to 90°). In general, the numerical models (i.e., boundary- and finite-element) matched the benchmarks over the full range of simulation parameters. While inherent errors associated with the approximate analytical models were illustrated, so were the advantages as they are computationally efficient and in certain cases, outperformed the numerical models under conditions where the numerical models did not convergeThis work was supported by the NOAA Fisheries Advanced Sampling Technologies Working Group, the Office of Naval Research, and the National Oceanic Partnership Program. Josiah S. Renfree

Genome editing reveals a role for OCT4 in human embryogenesis.

Despite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR-Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using these refined methods, we efficiently and specifically targeted the gene encoding OCT4 (POU5F1) in diploid human zygotes and found that blastocyst development was compromised. Transcriptomics analysis revealed that, in POU5F1-null cells, gene expression was downregulated not only for extra-embryonic trophectoderm genes, such as CDX2, but also for regulators of the pluripotent epiblast, including NANOG. By contrast, Pou5f1-null mouse embryos maintained the expression of orthologous genes, and blastocyst development was established, but maintenance was compromised. We conclude that CRISPR-Cas9-mediated genome editing is a powerful method for investigating gene function in the context of human development.DW was supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre Programme. NK was supported by the University of Oxford Clarendon Fund. AB was supported by a British Heart Foundation PhD Studentship (FS/11/77/39327). LV was supported by core grant funding from the Wellcome Trust and Medical Research Council (PSAG028). J-SK was supported by the Institute for Basic Science (IBS-R021-D1). Work in the KKN and JMAT labs was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust (FC001120 and FC001193)

Vision, challenges and opportunities for a Plant Cell Atlas

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.</jats:p

Adult Intracranial Myxoid Mesenchymal Tumor with EWSR1-ATF1 Gene Fusion.

BACKGROUND: Intracranial myxoid mesenchymal tumors (IMMTs) carrying an EWSR1-CREB gene family fusion are extremely rare and have only been identified in 10 previous reports. All but one has been found in children or young adults. Although there appear to be similarities to a myxoid variant of angiomatoid fibrous histiocytoma (AFH), clear histologic differences exist that appear to distinguish IMMTs as a distinct and novel entity. Previous reports have lacked detailed long-term follow-up and recommendations regarding treatment approach. CASE DESCRIPTION: This case describes a 48-year-old woman who presented with a left intraventricular mass that was identified on histology as an IMMT with an EWSR1-ATF1 gene fusion. After initial resection, the tumor demonstrated local recurrence. Repeat resection was performed followed by immediate demonstration of local and distant tumor recurrence. Histologic analysis of the tumor demonstrated a myxoid mesenchymal tumor distinct from AFH. Fractionated stereotactic radiation therapy was administered after the second resection, and tumor control was achieved at 1 year. CONCLUSIONS: Intracranial myxoid mesenchymal tumor is a novel and rare entity that has been previously identified in only 10 cases. This case is particularly remarkable because it is only the second IMMT case to occur in a middle-aged adult and shares striking similarities in clinical presentation to the previously reported case. Given the aggressive recurrence seen with the presented case, we recommend the treatment plan to be surgical resection followed by adjuvant radiation therapy

Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research

The article of record as published may be found at https://doi.org/10.1121/1.4937607Analytical and numerical scatteringmodels with accompanying digital representations are used increasingly to predict acoustic backscatter by fish and zooplankton in research and ecosystem monitoring applications. Ten such models were applied to targets with simple geometric shapes and parameterized (e.g., size and material properties) to represent biological organisms such as zooplankton and fish, and their predictions of acoustic backscatter were compared to those from exact or approximate analytical models, i.e., benchmarks. These comparisons were made for a sphere, spherical shell, prolate spheroid, and finite cylinder, each with homogeneous composition. For each shape, four target boundary conditions were considered: rigid-fixed, pressure-release, gas-filled, and weakly scattering. Target strength (dB re 1 m2) was calculated as a function of insonifying frequency (f = 12 to 400 kHz) and angle of incidence (θ = 0° to 90°). In general, the numerical models (i.e., boundary- and finite-element) matched the benchmarks over the full range of simulation parameters. While inherent errors associated with the approximate analytical models were illustrated, so were the advantages as they are computationally efficient and in certain cases, outperformed the numerical models under conditions where the numerical models did not convergeThis work was supported by the NOAA Fisheries Advanced Sampling Technologies Working Group, the Office of Naval Research, and the National Oceanic Partnership Program. Josiah S. Renfree