Optimizing Memory Efficiency for Convolution Kernels on Kepler GPUs

Convolution is a fundamental operation in many applications, such as computer vision, natural language processing, image processing, etc. Recent successes of convolutional neural networks in various deep learning applications put even higher demand on fast convolution. The high computation throughput and memory bandwidth of graphics processing units (GPUs) make GPUs a natural choice for accelerating convolution operations. However, maximally exploiting the available memory bandwidth of GPUs for convolution is a challenging task. This paper introduces a general model to address the mismatch between the memory bank width of GPUs and computation data width of threads. Based on this model, we develop two convolution kernels, one for the general case and the other for a special case with one input channel. By carefully optimizing memory access patterns and computation patterns, we design a communication-optimized kernel for the special case and a communication-reduced kernel for the general case. Experimental data based on implementations on Kepler GPUs show that our kernels achieve 5.16X and 35.5% average performance improvement over the latest cuDNN library, for the special case and the general case, respectively

Effector Caspase Dcp-1 and IAP Protein Bruce Regulate Starvation-Induced Autophagy during Drosophila Melanogaster Oogenesis

A complex relationship exists between autophagy and apoptosis, but the regulatory mechanisms underlying their interactions are largely unknown. We conducted a systematic study of Drosophila melanogaster cell death–related genes to determine their requirement in the regulation of starvation-induced autophagy. We discovered that six cell death genes—death caspase-1 (Dcp-1), hid, Bruce, Buffy, debcl, and p53—as well as Ras–Raf–mitogen activated protein kinase signaling pathway components had a role in autophagy regulation in D. melanogaster cultured cells. During D. melanogaster oogenesis, we found that autophagy is induced at two nutrient status checkpoints: germarium and mid-oogenesis. At these two stages, the effector caspase Dcp-1 and the inhibitor of apoptosis protein Bruce function to regulate both autophagy and starvation-induced cell death. Mutations in Atg1 and Atg7 resulted in reduced DNA fragmentation in degenerating midstage egg chambers but did not appear to affect nuclear condensation, which indicates that autophagy contributes in part to cell death in the ovary. Our study provides new insights into the molecular mechanisms that coordinately regulate autophagic and apoptotic events in vivo.Canadian Institutes of Health (MOP-78882); National Institutes of Health (R01 GM60574); Summer Undergraduate Research Fellowship program at Boston University; National Science Foundation (0450339

Complexity in surfaces of densest packings for families of polyhedra

Packings of hard polyhedra have been studied for centuries due to their mathematical aesthetic and more recently for their applications in fields such as nanoscience, granular and colloidal matter, and biology. In all these fields, particle shape is important for structure and properties, especially upon crowding. Here, we explore packing as a function of shape. By combining simulations and analytic calculations, we study three 2-parameter families of hard polyhedra and report an extensive and systematic analysis of the densest packings of more than 55,000 convex shapes. The three families have the symmetries of triangle groups (icosahedral, octahedral, tetrahedral) and interpolate between various symmetric solids (Platonic, Archimedean, Catalan). We find that optimal (maximum) packing density surfaces that reveal unexpected richness and complexity, containing as many as 130 different structures within a single family. Our results demonstrate the utility of thinking of shape not as a static property of an object in the context of packings, but rather as but one point in a higher dimensional shape space whose neighbors in that space may have identical or markedly different packings. Finally, we present and interpret our packing results in a consistent and generally applicable way by proposing a method to distinguish regions of packings and classify types of transitions between them.Comment: 16 pages, 8 figure

Becomeageneticcounselor.org: A Website to Facilitate Recruitment of African- Americans and Latinos into the Genetic Counseling Profession

This article describes the development of the website “Become a Genetic Counselor”. The website is created to facilitate the recruitment of underrepresented minorities (URM’s) into the genetic counseling profession, specifically African- Americans and Latinos. URM’s have been found to make decisions about future career paths earlier than Caucasians, as early as middle school or high school. Thus “Become a Genetic Counselor” is targeted to African-American and Latino students ranging from middle-school age through college age. URM’s have fewer family and social influences who know about genetic counseling, have fewer role models in the healthcare industries, and are more likely to have financial barriers to higher education. “Become a Genetic Counselor” is designed to be a comprehensive resource to address the barriers to entering into the genetic counseling profession encountered by URM’s. The website defines genetic counselors and genetic counseling, describes the work that genetic counselors do and the settings that they work in, provides detailed information about how to prepare for entering into a genetic counseling graduate program and how to finance the education, and introduces role models in the field, in the form of autobiographical interviews

EXTH-08. REPLACEMENT OF MICROGLIA BY BRAIN-ENGRAFTED MACROPHAGES PREVENTS MEMORY DEFICITS AFTER THERAPEUTIC WHOLE-BRAIN IRRADIATION

Abstract Microglia have a distinct origin compared to blood circulating myeloid cells. Under normal physiological conditions, microglia are maintained by self-renewal, independent of hematopoietic progenitors. Following genetic or pharmacologic depletion, newborn microglia derive from the local residual pool and quickly repopulate the entire brain. The depletion of brain resident microglia during therapeutic whole-brain irradiation fully prevents irradiation-induced synaptic loss and recognition memory deficits but the mechanisms driving these protective effects are unknown. Here, we demonstrate that after CSF-1R inhibitor-mediated microglia depletion and therapeutic whole-brain irradiation, circulating monocytes engraft into the brain and replace the microglia pool. These monocyte-derived brain-engrafted macrophages have reduced phagocytic activity compared to microglia from irradiated brains, but similar to locally repopulated microglia without brain irradiation. Transcriptome comparisons reveal that brain-engrafted macrophages have both monocyte and embryonic microglia signatures. These results suggest that monocyte-derived brain-engrafted macrophages represent a novel therapeutic avenue for the treatment of brain radiotherapy-induced cognitive deficits