Heterogeneous Computing on Mixed Unstructured Grids with PyFR

PyFR is an open-source high-order accurate computational fluid dynamics solver for mixed unstructured grids that can target a range of hardware platforms from a single codebase. In this paper we demonstrate the ability of PyFR to perform high-order accurate unsteady simulations of flow on mixed unstructured grids using heterogeneous multi-node hardware. Specifically, after benchmarking single-node performance for various platforms, PyFR v0.2.2 is used to undertake simulations of unsteady flow over a circular cylinder at Reynolds number 3 900 using a mixed unstructured grid of prismatic and tetrahedral elements on a desktop workstation containing an Intel Xeon E5-2697 v2 CPU, an NVIDIA Tesla K40c GPU, and an AMD FirePro W9100 GPU. Both the performance and accuracy of PyFR are assessed. PyFR v0.2.2 is freely available under a 3-Clause New Style BSD license (see www.pyfr.org).Comment: 21 pages, 9 figures, 6 table

A class of Poisson-Nijenhuis structures on a tangent bundle

Equipping the tangent bundle TQ of a manifold with a symplectic form coming from a regular Lagrangian L, we explore how to obtain a Poisson-Nijenhuis structure from a given type (1,1) tensor field J on Q. It is argued that the complete lift of J is not the natural candidate for a Nijenhuis tensor on TQ, but plays a crucial role in the construction of a different tensor R, which appears to be the pullback under the Legendre transform of the lift of J to co-tangent manifold of Q. We show how this tangent bundle view brings new insights and is capable also of producing all important results which are known from previous studies on the cotangent bundle, in the case that Q is equipped with a Riemannian metric. The present approach further paves the way for future generalizations.Comment: 22 page

Relationship between emergency presentation, systemic inflammatory response, and cancer-specific survival in patients undergoing potentially curative surgery for colon cancer

Background Emergency presentation is recognized to be associated with poorer cancer-specific survival following curative resection for colorectal cancer. The present study examined the hypothesis that an enhanced systemic inflammatory response, prior to surgery, might explain the impact of emergency presentation on survival. Methods In all, 188 patients undergoing potentially curative resection for colorectal cancer were studied. Of these, 55 (29%) presented as emergencies. The systemic inflammatory response was assessed using the Glasgow Prognostic Score (mGPS), which is the combination of an elevated C-reactive protein (>10 mg/L) and hypoalbuminemia (<35 g/L). Results In the emergency group, tumor stage was greater (P < 0.01), more patients received adjuvant therapy (P < 0.01) more patients had an elevated mGPS (P < 0.01), and more patients died of their disease (P < 0.05). The minimum follow-up was 12 months; the median follow-up of the survivors was 48 months. Emergency presentation was associated with poorer 3-year cancer-specific survival in those patients aged 65 to 74 years (P < 0.01), in both males and females (P < 0.05), in the deprived (P < 0.01), in patients with tumor-node-metastasis (TNM) stage II disease (P < 0.01), in those who received no adjuvant therapy (P < 0.01), and in the mGPS 0 and 1 groups (P < 0.05) groups. On multivariate survival analysis of patients undergoing potentially curative surgery for TNM stage II colon cancer, emergency presentation (P < 0.05) and mGPS (P < 0.05) were independently associated with cancer-specific survival. Conclusions These results suggest that emergency presentation and the presence of systemic inflammatory response prior to surgery are linked and account for poorer cancer-specific survival in patients undergoing potentially curative surgery for colon cancer. Both emergency presentation and an elevated mGPS should be taken into account when assessing the likely outcome of these patients

TDP2 promotes repair of topoisomerase I-mediated DNA damage in the absence of TDP1

The abortive activity of topoisomerases can result in clastogenic and/or lethal DNA damage in which the topoisomerase is covalently linked to the 3'- or 5'-terminus of a DNA strand break. This type of DNA damage is implicated in chromosome translocations and neurological disease and underlies the clinical efficacy of an important class of anticancer topoisomerase 'poisons'. Tyrosyl DNA phosphodiesterase-1 protects cells from abortive topoisomerase I (Top1) activity by hydrolyzing the 3'-phosphotyrosyl bond that links Top1 to a DNA strand break and is currently the only known human enzyme that displays this activity in cells. Recently, we identified a second tyrosyl DNA phosphodiesterase (TDP2; aka TTRAP/EAPII) that possesses weak 3'-tyrosyl DNA phosphodiesterase (3'-TDP) activity, in vitro. Herein, we have examined whether TDP2 contributes to the repair of Top1-mediated DNA breaks by deleting Tdp1 and Tdp2 separately and together in murine and avian cells. We show that while deletion of Tdp1 in wild-type DT40 cells and mouse embryonic fibroblasts decreases DNA strand break repair rates and cellular survival in response to Top1-induced DNA damage, deletion of Tdp2 does not. However, deletion of both Tdp1 and Tdp2 reduces rates of DNA strand break repair and cell survival below that observed in Tdp1(-)(/)(-) cells, suggesting that Tdp2 contributes to cellular 3'-TDP activity in the absence of Tdp1. Consistent with this idea, over-expression of human TDP2 in Tdp1(-)(/)(-)/Tdp2(-)(/)(-)(/)(-) DT40 cells increases DNA strand break repair rates and cell survival above that observed in Tdp1(-)(/)(-) DT40 cells, suggesting that Tdp2 over-expression can partially complement the defect imposed by loss of Tdp1. Finally, mice lacking both Tdp1 and Tdp2 exhibit greater sensitivity to Top1 poisons than do mice lacking Tdp1 alone, further suggesting that Tdp2 contributes to the repair of Top1-mediated DNA damage in the absence of Tdp1. In contrast, we failed to detect a contribution for Tdp1 to repair Top2-mediated damage. Together, our data suggest that Tdp1 and Tdp2 fulfil overlapping roles following Top1-induced DNA damage, but not following Top2-induced DNA damage, in vivo

Synaptotagmin 5 regulates Ca2+-dependent Weibel-Palade body exocytosis in human endothelial cells.

Membrane protein insertion is an essential cellular process. The broad biophysical and topological range of membrane proteins necessitates multiple insertion pathways, which remain incompletely defined. Here, we have discovered a new membrane protein insertion pathway, identified the class of substrates it handles, explained why other known pathways do not work for these substrates and reconstituted the pathway using purified components

PEMBINAAN NARAPIDANA YANG MENGALAMI GANGGUAN JIWA DI DALAM LEMBAGA PEMASYARAKATAN

PEMBINAAN NARAPIDANA YANG MENGALAMI GANGGUAN JIWADI LEMBAGA PEMASYARAKATAN Agusriadi Dahlan Ali Suhaimi ABSTRAKLembaga Pemasyarakatan sebelumnya disebut Penjara adalah tempat orang-orang yang melakukan kriminalitas dan pelanggaran hukum lainnya agar mereka dapat menyadari kesalahannya dan mempertanggungjawabkan apa yang telah mereka perbuat. Hukuman yang mereka terima sebagai balasan yang setimpal terhadap perbuatan mereka, meskipun nilai-nilai kemanusiaan beserta hak asasinya kurang diperhatikan. Lembaga Pemasyarakatan merupakan tempat yang stressfull atau menekan yang dapat berpengaruh terhadap fisik dan kejiwaan (psikologi) seseorang ditambah kecemasan yang berlebihan sehingga muncul depresi yang mengakibatkan seseorang melakukan bunuh diri. Akibat stress melahirkan depresi dan depresi biasanya akan terjadi kegoncangan kejiwaan yang luar biasa yang dapat mengakibatkan seseorang menjadi tidak waras (gila). Undang-Undang No.12/1995 tentang Lembaga Pemasyarakatan maupun Peraturan Pemerintah No. 99 Tahun 2012 tentang Perubahan Kedua Atas Peraturan Pemerintah Nomor 32 Tahun 1999 tentang Syarat dan Tata Cara Pelaksanaan Hak Warga Binaan Pemasyarakatan tidak menjelaskan ketentuan terhadap narapidana yang gila di dalam lapas sebagaimana yang pernah terjadi di Lapas Kelas II-A Lambaro, Aceh Besar dan Rutan Klas I Tanjung Gusta, Medan. Selanjutnya yang bersangkutan dikirim ke Lapas Kelas Klass II-B Meulaboh tanggal 27 Januari 2014. Selama tujuh hari di Lapas Klass II-B Meulaboh Zabir bin Ilyas kemudian di titipkan di Rumah Sakit Jiwa Banda Aceh karena penyakitnya sudah mencapai stadium empat untuk mendapatkan perawatan dan penyembuhan kejiwaannya. Bagaimanakah pengaturan dan pembinaan terhadap narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan. Kemudian bagaimanakah kepastian hukum bagi narapidana yang sedang mengalami gangguan kejiwaan, dan bagaimana status hukum bagi narapidana yang sembuh dari gangguan kejiwaan. Penelitian dan pengkajian ini bertujuan untuk mengetahui pengaturan dan pembinaan terhadap narapidana yang mengalami gangguan kejiwaan dalam Lapas dan mengidentifikasi kepastian hukum bagi narapidana yang sedang mengalami gangguan kejiwaan serta mengetahui status hukum bagi narapidana yang sembuh dari gangguan kejiwaan.Metode yang digunakan adalah metode penelitian yuridis-normatif dengan menggunakan jenis penelitian deskriptis analisis dalam rangka untuk menemukan aturan hukum, prinsip-prinsip hukum, norma maupun doktrin-doktrin hukum dengan pendekatan undang-undang, kasus. Sumber data adalah data sekunder berupa bahan hukum primer, bahan hukum sekunder, dan bahan hukum tersier.Hasil penelitian menunjukkan bahwa Pengaturan tentang perawatan narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan di Indonesia belum diatur, baik dalam Undang-Undang Nomor 12 Tahun 1995 tentang Lembaga Pemasyarakatan maupun PP No. 99 Tahun 2012 tentang PP No. 99 Tahun 2012 tentang Perubahan Kedua Atas PP No.32 Tahun 1999 tentang Syarat dan Tata Cara Pelaksanaan Hak Warga Binaan Pemasyarakatan. Namun bila narapidana sakit atau gangguan kesehatan lainnya yang tidak termasuk gangguan kejiwaan ada aturan tentang perawatan medis. Adapun mengenai narapidana yang mengalami gangguan kejiwaan di Lembaga Pemasyarakatan di Indonesia hingga kini belum ada kepastian hukum karena kasus seperti ini sangat langka terjadi di Indonesia. Pihak otoritas hanya menggunakan hak diskresi yang dimilikinya untuk menyelesaikan kasus tersebut sebagaimana terjadi di Lapas Porong Surabaya. Tetapi di Aceh kasus ini baru pertama kali terjadi yang dialami Zabir bin Ilyas pada tahun 2014. Pimpinan Lapas memutuskan memasukkan Zabir bin Ilyas ke Rumah Sakit Jiwa Banda Aceh. Terkait status hukum narapidana yang sembuh dari gangguan kejiwaan masih tetap sebagai tersangka (ditahan). Tidak ada keringanan hukuman apalagi sampai dibebaskan sebelum masa hukuman habis dijalankan. Hingga kini tidak ada satupun aturan yang mengatur baik secara implisit maupun ekplisit yang mengatur tentang narapidana yang sembuh dari penyakit kejiwaan (gila).Disarankan kepada Pemerintah agar merevisi Undang-Undang Nomor 12 Tahun 1995 tentang Lembaga Pemasyarakatan dan memasukkan salah satu pasal yang mengatur mengenai narapidana yang mengalami gangguan kejiwaan di dalam Lembaga Pemasyarakatan. Agar terwujudnya kepastian hukum di Indonesia mengenai narapidana yang mengalami gangguan kejiwaan dalam lebaga pemasyarakatan untuk membuat regulasi legal baik berupa undang-undang khusus atau melalui Peraturan Pemerintah. Kemudian disarankan agar narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan dapat dibebaskan dan dikembalikan ke keluarganya atau dimasukkan ke rumah sakit jiwa hingga sembuh.Kata Kunci : Pembinaan, Narapidana, Gangguan Jiwa, Lembaga Pemasyarakatan.Banda Ace