Recommendations for repositories and scientific gateways from a neuroscience perspective

Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular needs. INCF (International Neuroinformatics Coordinating Facility) has developed a set of recommendations and associated criteria for choosing or setting up and running a repository or scientific gateway, intended for the neuroscience community, with a FAIR neuroscience perspective. These recommendations have neurosciences as their primary use case but are often general. Considering the perspectives of researchers and providers of repositories as well as scientific gateways, the recommendations harmonize and complement existing work on criteria for repositories and best practices. The recommendations cover a range of important areas including accessibility, licensing, community responsibility and technical and financial sustainability of a service.Comment: 10 pages, submitted to Scientific Dat

Compton scattering beyond the impulse approximation

We treat the non-relativistic Compton scattering process in which an incoming photon scatters from an N-electron many-body state to yield an outgoing photon and a recoil electron, without invoking the commonly used frameworks of either the impulse approximation (IA) or the independent particle model (IPM). An expression for the associated triple differential scattering cross section is obtained in terms of Dyson orbitals, which give the overlap amplitudes between the N-electron initial state and the (N-1) electron singly ionized quantum states of the target. We show how in the high energy transfer regime, one can recover from our general formalism the standard IA based formula for the cross section which involves the ground state electron momentum density (EMD) of the initial state. Our formalism will permit the analysis and interpretation of electronic transitions in correlated electron systems via inelastic x-ray scattering (IXS) spectroscopy beyond the constraints of the IA and the IPM.Comment: 7 pages, 1 figur

A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body

Cancer-associated fibroblasts are positively correlated with metastatic potential of human gastric cancers

<p>Abstract</p> <p>Background</p> <p>The prognosis of gastric cancer patients is difficult to predict because of defects in establishing the surgical-pathological features. Cancer-associated fibroblasts (CAFs) have been found to play prominent role in promoting tumor growth, invasion and metastasis. Thus raises the hypothesis that the extent of CAFs prevalence may help to establish the prognosis of gastric cancer patients.</p> <p>Methods</p> <p>Immunochemistry and realtime-PCR experiments were carried out to compare the expression of proteins which are specific markers of CAFs or secreted by CAFs in the tumor and normal tissue specimens. The extent of CAFs' prevalence was graded according to immunochemical staining, and correlation was further analyzed between CAFs' prevalence and other tumor characteristics which may influence the prognosis of gastric cancer patients.</p> <p>Results</p> <p>Nearly 80 percent of normal gastric tissues were negative or weak positive for CAFs staining, while more than 60 percent of gastric cancer tissues were moderate or strong positive for CAFs staining. Realtime-PCR results also showed significant elevated expression of FAP, SDF-1 and TGF-β1 in gastric cancer tissues compared to normal gastric tissues. Further analysis showed that CAFs' prevalence was correlated with tumor size, depth of the tumor, lymph node metastasis, liver metastasis or peritoneum metastasis.</p> <p>Conclusions</p> <p>Reactive cancer associated fibroblasts (CAFs) were frequently accumulated in gastric cancer tissues, and the prevalence of CAFs was correlated with tumor size, depth of the tumor and tumor metastasis, thus give some supports for establishing the prognosis of the gastric cancer patients.</p

Research into the Development of the RHODOS Multi-threaded Microkernel

An important factor contributing to an operating systems&apos; performance is the design and efficiency of the kernel code. This is especially true for microkernel based operating systems where the microkernel and kernel provides support for system servers. RHODOS is a microkernel based distributed operating system designed as a testbed for the study of the numerous research topics available in this area. The current version of RHODOS uses a single threaded microkernel, which fulfilled our requirements of providing a stable platform. A significant drawback of a single threaded architecture is the difficulty with which paging can be implemented. This report details the current state of the RHODOS single threaded microkernel and provides justification for the implementation of a multi threaded microkernel. *This work was partly supported by Australian Research Council under Grants A48831034 and A49232429, and the Deakin University Research Grant 0504010151. RHODOS September 8, 1994 ii INDE..