Study of Fine-Grained, Irregular Parallel Applications on a Many-Core Processor

This dissertation demonstrates the possibility of obtaining strong speedups for a variety of parallel applications versus the best serial and parallel implementations on commodity platforms. These results were obtained using the PRAM-inspired Explicit Multi-Threading (XMT) many-core computing platform, which is designed to efficiently support execution of both serial and parallel code and switching between the two. Biconnectivity: For finding the biconnected components of a graph, we demonstrate speedups of 9x to 33x on XMT relative to the best serial algorithm using a relatively modest silicon budget. Further evidence suggests that speedups of 21x to 48x are possible. For graph connectivity, we demonstrate that XMT outperforms two contemporary NVIDIA GPUs of similar or greater silicon area. Prior studies of parallel biconnectivity algorithms achieved at most a 4x speedup, but we could not find biconnectivity code for GPUs to compare biconnectivity against them. Triconnectivity: We present a parallel solution to the problem of determining the triconnected components of an undirected graph. We obtain significant speedups on XMT over the only published optimal (linear-time) serial implementation of a triconnected components algorithm running on a modern CPU. To our knowledge, no other parallel implementation of a triconnected components algorithm has been published for any platform. Burrows-Wheeler compression: We present novel work-optimal parallel algorithms for Burrows-Wheeler compression and decompression of strings over a constant alphabet and their empirical evaluation. To validate these theoretical algorithms, we implement them on XMT and show speedups of up to 25x for compression, and 13x for decompression, versus bzip2, the de facto standard implementation of Burrows-Wheeler compression. Fast Fourier transform (FFT): Using FFT as an example, we examine the impact that adoption of some enabling technologies, including silicon photonics, would have on the performance of a many-core architecture. The results show that a single-chip many-core processor could potentially outperform a large high-performance computing cluster. Boosted decision trees: This chapter focuses on the hybrid memory architecture of the XMT computer platform, a key part of which is a flexible all-to-all interconnection network that connects processors to shared memory modules. First, to understand some recent advances in GPU memory architecture and how they relate to this hybrid memory architecture, we use microbenchmarks including list ranking. Then, we contrast the scalability of applications with that of routines. In particular, regardless of the scalability needs of full applications, some routines may involve smaller problem sizes, and in particular smaller levels of parallelism, perhaps even serial. To see how a hybrid memory architecture can benefit such applications, we simulate a computer with such an architecture and demonstrate the potential for a speedup of 3.3X over NVIDIA's most powerful GPU to date for XGBoost, an implementation of boosted decision trees, a timely machine learning approach. Boolean satisfiability (SAT): SAT is an important performance-hungry problem with applications in many problem domains. However, most work on parallelizing SAT solvers has focused on coarse-grained, mostly embarrassing parallelism. Here, we study fine-grained parallelism that can speed up existing sequential SAT solvers. We show the potential for speedups of up to 382X across a variety of problem instances. We hope that these results will stimulate future research

The relationship between tumour budding, tumour microenvironment and survival in patients with primary operable colorectal cancer

Background: Tumor budding is an independent prognostic factor in colorectal cancer (CRC) and has recently been well-defined by the International Tumour Budding Consensus Conference (ITBCC). Objective: The aim of the present study was to use the ITBCC budding evaluation method to examine the relationship between tumor budding, tumor factors, tumor microenvironment, and survival in patients with primary operable CRC. Methods: Hematoxylin and eosin-stained slides of 952 CRC patients diagnosed between 1997 and 2007 were evaluated for tumor budding according to the ITBCC criteria. The tumor microenvironment was evaluated using tumor stroma percentage (TSP) and Klintrup–Makinen (KM) grade to assess the tumor inflammatory cell infiltrate. Results: High budding (n = 268, 28%) was significantly associated with TNM stage (p < 0.001), competent mismatch repair (MMR; p < 0.05), venous invasion (p < 0.001), weak KM grade (p < 0.001), high TSP (p < 0.001), and reduced cancer-specific survival (CSS) (hazard ratio 8.68, 95% confidence interval 6.30–11.97; p < 0.001). Tumor budding effectively stratifies CSS stage T1 through to T4 (all p < 0.05) independent of associated factors. Conclusions: Tumor budding effectively stratifies patients’ survival in primary operable CRC independent of other phenotypic features. In particular, the combination of T stage and budding should form the basis of a new staging system for primary operable CRC. Tumor budding has been defined as a single tumor cell or small cluster of four or fewer tumor cells at the invasive front12,18 and should be considered a promising and strong prognostic factor in colorectal cancer (CRC).19 Widespread reporting of tumor budding has not progressed to routine clinical practice due to a lack of consensus on scoring methods. However, routine reporting is now advocated by using the approach outlined by the International Tumour Budding Consensus Conference (ITBCC), with recommendations for the assessment and reporting of tumor budding in CRC.6 The ITBCC recommends that tumor budding should be included in future CRC guidelines and protocols and should be considered, along with other clinicopathological factors, in a multidisciplinary setting. The recent dataset for histopathological reporting of CRC by the royal pathologist stated that they would reconsider reporting tumor budding when new data become available.4 The tumor microenvironment also plays an important role in CRC outcomes. Marked peritumoral inflammation has been associated with favorable outcome,3,14 while the presence of a high tumor stroma percentage (TSP) has been validated as a stage-independent marker of reduced survival in patients with primary operable CRC.7,8. Both contribute to the development of a tumor microenvironment score that can potentially supplement the current TNM staging system.9 The aim of this study was to assess the proposed method by ITBCC in clinical practice and investigate the relationship between tumor budding and tumor factors, tumor microenvironment, and survival in primary operable CRC

Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

SummaryTrans-acting siRNA form through a refined RNAi mechanism in plants. miRNA-guided cleavage triggers entry of precursor transcripts into an RNA-DEPENDENT RNA POLYMERASE6 pathway, and sets the register for phased tasiRNA formation by DICER-LIKE4. Here, we show that miR390-ARGONAUTE7 complexes function in distinct cleavage or noncleavage modes at two target sites in TAS3a transcripts. The AGO7 cleavage, but not the noncleavage, function could be provided by AGO1, the dominant miRNA-associated AGO, but only when AGO1 was guided to a modified target site through an alternate miRNA. AGO7 was highly selective for interaction with miR390, and miR390 in turn was excluded from association with AGO1 due entirely to an incompatible 5′ adenosine. Analysis of AGO1, AGO2, and AGO7 revealed a potent 5′ nucleotide discrimination function for some, although not all, ARGONAUTEs. miR390 and AGO7, therefore, evolved as a highly specific miRNA guide/effector protein pair to function at two distinct tasiRNA biogenesis steps

Expanded chemical diversity sampling through whole protein evolution

A directed evolution method has been developed that allows random substitution of a contiguous trinucleotide sequence for TAG throughout a target gene for use in conjunction with an expanded genetic code. Using TEM-1 β-lactamase and enhanced green fluorescent protein as targets, protein variants were identified whose functional phenotype was rescued in vivo when co-expressed with orthogonal tRNA–aminoacyl-tRNA synthase pairs that insert p-iodophenylalanine in response to UAG. Sequencing of the selected clones that retained the target protein function revealed that >90% of the variants contained in-frame TAG codons distributed throughout the target gene. Such an approach will allow broader sampling of new chemical diversity by proteins, so opening new avenues for studying biological systems and for adapting proteins for biotechnological applications. A common set of reagents allows the method to be used on different protein systems and in combination with an array of different unnatural amino acids, so helping to reveal the true potential for engineering proteins through expanded chemical diversity sampling

Form Drag and Mixing Due to Tidal Flow past a Sharp Point

Barotropic tidal currents flowing over rough topography may be slowed by two bottom boundary–related processes: tangential stress of the bottom boundary layer, which is generally well represented by a quadratic drag law, and normal stress from bottom pressure, known as form drag. Form drag is rarely estimated from oceanic observations because it is difficult to measure the bottom pressure over a large spatial domain. The “external” and “internal” components of the form drag are associated, respectively, with sea surface and isopycnals deformations. This study presents model and observational estimates of the components of drag for Three Tree Point, a sloping ridge projecting 1 km into Puget Sound, Washington. Internal form drag was integrated from repeat microstructure sections and exceeded the net drag due to bottom friction by a factor of 10–50 during maximum flood. In observations and numerical simulations, form drag was produced by a lee wave, as well as by horizontal flow separation in the model. The external form drag was not measured, but in numerical simulations was found to be comparable to the internal form drag. Form drag appears to be the primary mechanism for extracting energy from the barotropic tide. Turbulent buoyancy flux is strongest near the ridge in both observations and model results

Young children's research: children aged 4-8 years finding solutions at home and at school

Children's research capacities have become increasingly recognised by adults, yet children remain excluded from the academy, with reports of their research participation generally located in adults' agenda. Such practice restricts children's freedom to make choices in matters affecting them, underestimates children’s capabilities and denies children particular rights. The present paper reports on one aspect of a small-scale critical ethnographic study adopting a constructivist grounded approach to conceptualise ways in which children's naturalistic behaviours may be perceived as research. The study builds on multi-disciplinary theoretical perspectives, embracing 'new' sociology, psychology, economics, philosophy and early childhood education and care (ECEC). Research questions include: 'What is the nature of ECEC research?' and 'Do children’s enquiries count as research?' Initially, data were collected from the academy: professional researchers (n=14) confirmed 'finding solutions' as a research behaviour and indicated children aged 4-8 years, their practitioners and primary carers as 'theoretical sampling'. Consequently, multi-modal case studies were constructed with children (n=138) and their practitioners (n=17) in three ‘good’ schools, with selected children and their primary carers also participating at home. This paper reports on data emerging from children aged 4-8 years at school (n=17) and at home (n=5). Outcomes indicate that participating children found diverse solutions to diverse problems, some of which they set themselves. Some solutions engaged children in high order thinking, whilst others did not; selecting resources and trialing activities engaged children in 'finding solutions'. Conversely, when children's time, provocations and activities were directed by adults, the quality of their solutions was limited, they focused on pleasing adults and their motivation to propose solutions decreased. In this study, professional researchers recognised 'finding solutions' as research behaviour and children aged 4-8 years naturalistically presented with capacities for finding solutions; however, the children's encounters with adults affected the solutions they found

Airborne S-Band SAR for forest biophysical retrieval in temperate mixed forests of the UK

Radar backscatter from forest canopies is related to forest cover, canopy structure and aboveground biomass (AGB). The S-band frequency (3.1–3.3 GHz) lies between the longer L-band (1–2 GHz) and the shorter C-band (5–6 GHz) and has been insufficiently studied for forest applications due to limited data availability. In anticipation of the British built NovaSAR-S satellite mission, this study evaluates the benefits of polarimetric S-band SAR for forest biophysical properties. To understand the scattering mechanisms in forest canopies at S-band the Michigan Microwave Canopy Scattering (MIMICS-I) radiative transfer model was used. S-band backscatter was found to have high sensitivity to the forest canopy characteristics across all polarisations and incidence angles. This sensitivity originates from ground/trunk interaction as the dominant scattering mechanism related to broadleaved species for co-polarised mode and specific incidence angles. The study was carried out in the temperate mixed forest at Savernake Forest and Wytham Woods in southern England, where airborne S-band SAR imagery and field data are available from the recent AirSAR campaign. Field data from the test sites revealed wide ranges of forest parameters, including average canopy height (6–23 m), diameter at breast-height (7–42 cm), basal area (0.2–56 m2/ha), stem density (20–350 trees/ha) and woody biomass density (31–520 t/ha). S-band backscatter-biomass relationships suggest increasing backscatter sensitivity to forest AGB with least error between 90.63 and 99.39 t/ha and coefficient of determination (r2) between 0.42 and 0.47 for the co-polarised channel at 0.25 ha resolution. The conclusion is that S-band SAR data such as from NovaSAR-S is suitable for monitoring forest aboveground biomass less than 100 t/ha at 25 m resolution in low to medium incidence angle rang

Measurement Report: Firework Impacts on Air Quality in Metro Manila, Philippines, during the 2019 New Year Revelry

Fireworks degrade air quality, reduce visibility, alter atmospheric chemistry, and cause short-term adverse health effects. However, there have not been any comprehensive physicochemical and optical measurements of fireworks and their associated impacts in a Southeast Asia megacity, where fireworks are a regular part of the culture. Size-resolved particulate matter (PM) measurements were made before, during, and after New Year 2019 at the Manila Observatory in Quezon City, Philippines, as part of the Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP2Ex). A high-spectral-resolution lidar (HSRL) recorded a substantial increase in backscattered signal associated with high aerosol loading ∼440 m above the surface during the peak of firework activities around 00:00 (local time). This was accompanied by PM2.5 concentrations peaking at 383.9 µg m−3. During the firework event, water-soluble ions and elements, which affect particle formation, growth, and fate, were mostly in the submicrometer diameter range. Total (\u3e0.056 µm) water-soluble bulk particle mass concentrations were enriched by 5.7 times during the fireworks relative to the background (i.e., average of before and after the firework). The water-soluble mass fraction of PM2.5 increased by 18.5 % above that of background values. This corresponded to increased volume fractions of inorganics which increased bulk particle hygroscopicity, kappa (κ), from 0.11 (background) to 0.18 (fireworks). Potassium and non-sea-salt (nss) SO42- role= presentation style= box-sizing: border-box; border-radius: 0px; display: inline; line-height: normal; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative; \u3e2−4 contributed the most (70.9 %) to the water-soluble mass, with their mass size distributions shifting from a smaller to a larger submicrometer mode during the firework event. On the other hand, mass size distributions for NO3- role= presentation style= box-sizing: border-box; border-radius: 0px; display: inline; line-height: normal; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative; \u3e−3, Cl−, and Mg2+ (21.1 % mass contribution) shifted from a supermicrometer mode to a submicrometer mode. Being both uninfluenced by secondary aerosol formation and constituents of firework materials, a subset of species were identified as the best firework tracer species (Cu, Ba, Sr, K+, Al, and Pb). Although these species (excluding K+) only contributed 2.1 % of the total mass concentration of water-soluble ions and elements, they exhibited the highest enrichments (6.1 to 65.2) during the fireworks. Surface microscopy analysis confirmed the presence of potassium/chloride-rich cubic particles along with capsule-shaped particles in firework samples. The results of this study highlight how firework emissions change the physicochemical and optical properties of water-soluble particles (e.g., mass size distribution, composition, hygroscopicity, and aerosol backscatter), which subsequently alters the background aerosol\u27s respirability, influence on surroundings, ability to uptake gases, and viability as cloud condensation nuclei (CCN)