A Similarity Measure for GPU Kernel Subgraph Matching

Accelerator architectures specialize in executing SIMD (single instruction, multiple data) in lockstep. Because the majority of CUDA applications are parallelized loops, control flow information can provide an in-depth characterization of a kernel. CUDAflow is a tool that statically separates CUDA binaries into basic block regions and dynamically measures instruction and basic block frequencies. CUDAflow captures this information in a control flow graph (CFG) and performs subgraph matching across various kernel's CFGs to gain insights to an application's resource requirements, based on the shape and traversal of the graph, instruction operations executed and registers allocated, among other information. The utility of CUDAflow is demonstrated with SHOC and Rodinia application case studies on a variety of GPU architectures, revealing novel thread divergence characteristics that facilitates end users, autotuners and compilers in generating high performing code

Geometric control of myogenic cell fate.

This work combines expertise in stem cell biology and bioengineering to define the system for geometric control of proliferation and differentiation of myogenic progenitor cells. We have created an artificial niche of myogenic progenitor cells, namely, modified extracellular matrix (ECM) substrates with spatially embedded growth or differentiation factors (GF, DF) that predictably direct muscle cell fate in a geometric pattern. Embedded GF and DF signal progenitor cells from specifically defined areas on the ECM successfully competed against culture media for myogenic cell fate determination at a clearly defined boundary. Differentiation of myoblasts into myotubes is induced in growth-promoting medium, myotube formation is delayed in differentiation-promoting medium, and myogenic cells, at different stages of proliferation and differentiation, can be induced to coexist adjacently in identical culture media. This method can be used to identify molecular interactions between cells in different stages of myogenic differentiation, which are likely to be important determinants of tissue repair. The designed ECM niches can be further developed into a vehicle for transplantation of myogenic progenitor cells maintaining their regenerative potential. Additionally, this work may also serve as a general model to engineer synthetic cellular niches to harness the regenerative potential of organ stem cells

Human germ cell tumours: expression of γ-glutamyl transpeptidase and sensitivity to cisplatin

Previous studies have shown that the enzyme γ-glutamyl transpeptidase (GGT) is essential for the nephrotoxicity of cisplatin. This study was designed to determine whether GGT activity is necessary for the therapeutic effect of the drug. The relationship between GGT expression and clinical response to platinum-based chemotherapy was examined in 41 human germ cell tumours. Sections of formalin-fixed, paraffin-embedded tumours were immunohistochemically stained with an antibody directed against human GGT. There was no expression of GGT in any of the 17 seminomas or four dysgerminomas; whereas, 12/12 ovarian yolk sac tumours and 4/4 embryonal carcinomas of the testis were GGT-positive. In stage I tumours fewer tumour cells expressed GGT than in later stage tumours. In four germ cell tumours of mixed histology, the seminomatous and dysgerminoma areas were GGT-negative while the areas of the tumour with yolk sac or embryonal histology contained GGT-positive tumour cells. The patients with seminomas or dysgerminomas who were treated with cisplatin-based chemotherapy, all had a complete response despite the absence of GGT expression in these tumours. Fifteen of the 16 patients with yolk sac or embryonal carcinomas received cisplatin-based chemotherapy following surgery. Twelve had a complete response, while three failed to respond to platinum-based therapy. There was no correlation between the level of GGT-expression and response to therapy in this group. Three of the four patients with tumours of mixed histology were treated with cisplatin-based therapy, and had a complete response. Therefore, expression of GGT is not necessary for the therapeutic effect of cisplatin in germ cell tumours. The results from this study suggest that systemic inhibition of GGT would inhibit the nephrotoxic side-effect of cisplatin without interfering with its activity towards germ cell tumours. © 1999 Cancer Research Campaig

Mass-independent fractionation of oxygen isotopes during thermal decomposition of divalent metal carbonates: Crystallographic influence, potential mechanism and cosmochemical significance

Few physical or chemical processes defy well-established laws of mass-dependent isotopic fractionation. A surprising example, discovered two decades ago, is that thermal decomposition of calcium and magnesium carbonate minerals (conducted in vacuo, to minimise back-reaction and isotopic exchange) causes the oxygen triple-isotope compositions of the resulting solid oxide and CO2 to fit on parallel mass-dependent fractionation lines in ln(1 + δ17O) versus ln(1 + δ18O) space, with anomalous depletion of 17O in the solid and equivalent enrichment of 17O in the CO2. By investigating the thermal decomposition of other natural divalent metal carbonates and one synthetic example, under similar conditions, we find that the unusual isotope effect occurs in all cases and that the magnitude of the anomaly (Δ′17O) seems to depend on the room temperature crystallographic structure of the carbonate. A lower cation coordination number (as associated with smaller cation radius) correlates with a Δ′17O value closer to zero. Local symmetry considerations may therefore be influential. Relative to a reference fractionation line of slope 0.524 and passing through VSMOW, solid oxides produced by thermal decomposition of orthorhombic carbonates were characterised by Δ′17O = −0.367 ± 0.004‰ (standard error). The comparable figure from rhombohedral examples was −0.317 ± 0.010‰, whereas from the sole monoclinic (synthesised) specimen it was −0.219 ± 0.011‰. The numerical values are, to some extent, dependent on details of the experimental procedure. We discuss potential origins of the isotopic anomaly, including the possibility of hyperfine coupling between 17O nuclei and unpaired electrons of transient radicals (the ‘magnetic isotope effect’). A new mechanism based on the latter process is proposed. The associated transition state is compatible with that suggested by recent quantum chemical and kinetic studies of the thermal decompositions of calcite and magnesite. An earlier suggestion based on the magnetic isotope effect is shown to be incompatible with the generation of a 17O anomaly, regardless of the identity of the carbonate. We cannot exclude the possibility that a Fermi resonance between states leading to dissociation may additionally affect the magnitude of Δ′17O in some cases. Our findings have cosmochemical implications, with thermal processing of carbonates providing a potential mechanism for the mass-independent fractionation of oxygen isotopes in protoplanetary systems

Machine Learning Predictions Electronic Couplings for Charge Transport Calculations of P3HT

The purpose of this work is to lower the computational cost of predicting charge mobilities in organic semiconductors, which will benefit the screening of candidates for inexpensive solar power generation. We characterize efforts to minimize the number of expensive quantum chemical calculations we perform by training machines to predict electronic couplings between monomers of poly-(3-hexylthiophene). We test five machine learning techniques and identify random forests as the most accurate, information-dense, and easy-to-implement approach for this problem, achieving mean-absolute-error of 0.02 [× 1.6 × 10−19 J], R2 = 0.986, predicting electronic couplings 390 times faster than quantum chemical calculations, and informing zero-field hole mobilities within 5% of prior work. We discuss strategies for identifying small effective training sets. In sum, we demonstrate an example problem where machine learning techniques provide an effective reduction in computational costs while helping to understand underlying structure–property relationships in a materials system with broad applicability

Sperm death and dumping in Drosophila

Mating with more than one male is the norm for females of many species. In addition to generating competition between the ejaculates of different males, multiple mating may allow females to bias sperm use. In Drosophila melanogaster, the last male to inseminate a female sires approximately 80% of subsequent progeny. Both sperm displacement, where resident sperm are removed from storage by the incoming ejaculate of the copulating male, and sperm incapacitation, where incoming seminal fluids supposedly interfere with resident sperm, have been implicated in this pattern of sperm use. But the idea of incapacitation is problematic because there are no known mechanisms by which an individual could damage rival sperm and not their own. Females also influence the process of sperm use, but exactly how is unclear. Here we show that seminal fluids do not kill rival sperm and that any 'incapacitation' is probably due to sperm ageing during sperm storage. We also show that females release stored sperm from the reproductive tract (sperm dumping) after copulation with a second male and that this requires neither incoming sperm nor seminal fluids. Instead, males may cause stored sperm to be dumped or females may differentially eject sperm from the previous mating

Incrementally Computing Minimal Unsatisfiable Cores of QBFs via a Clause Group Solver API

We consider the incremental computation of minimal unsatisfiable cores (MUCs) of QBFs. To this end, we equipped our incremental QBF solver DepQBF with a novel API to allow for incremental solving based on clause groups. A clause group is a set of clauses which is incrementally added to or removed from a previously solved QBF. Our implementation of the novel API is related to incremental SAT solving based on selector variables and assumptions. However, the API entirely hides selector variables and assumptions from the user, which facilitates the integration of DepQBF in other tools. We present implementation details and, for the first time, report on experiments related to the computation of MUCs of QBFs using DepQBF's novel clause group API.Comment: (fixed typo), camera-ready version, 6-page tool paper, to appear in proceedings of SAT 2015, LNCS, Springe

Network Defence Using Attacker-Defender Interaction Modelling

Network security is still lacking an efficient system which selects a response action based on observed security events and which is capable of running autonomously. The main reason for this is the lack of an effective defence strategy. In this Ph.D., we endeavour to create such a defence strategy. We propose to model the interaction between an attacker and a defender to comprehend how the attacker’s goals affect his actions and use the model as a basis for a more refined network defence strategy. We formulate the research questions that need to be answered and we discuss, how the answers to these questions relate to the proposed solution. This research is at the initial phase and will contribute to a Ph.D. thesis in four years

Attenuation of Zinc Finger Nuclease Toxicity by Small-Molecule Regulation of Protein Levels

Zinc finger nucleases (ZFNs) have been used successfully to create genome-specific double-strand breaks and thereby stimulate gene targeting by several thousand fold. ZFNs are chimeric proteins composed of a specific DNA-binding domain linked to a non-specific DNA-cleavage domain. By changing key residues in the recognition helix of the specific DNA-binding domain, one can alter the ZFN binding specificity and thereby change the sequence to which a ZFN pair is being targeted. For these and other reasons, ZFNs are being pursued as reagents for genome modification, including use in gene therapy. In order for ZFNs to reach their full potential, it is important to attenuate the cytotoxic effects currently associated with many ZFNs. Here, we evaluate two potential strategies for reducing toxicity by regulating protein levels. Both strategies involve creating ZFNs with shortened half-lives and then regulating protein level with small molecules. First, we destabilize ZFNs by linking a ubiquitin moiety to the N-terminus and regulate ZFN levels using a proteasome inhibitor. Second, we destabilize ZFNs by linking a modified destabilizing FKBP12 domain to the N-terminus and regulate ZFN levels by using a small molecule that blocks the destabilization effect of the N-terminal domain. We show that by regulating protein levels, we can maintain high rates of ZFN-mediated gene targeting while reducing ZFN toxicity

The biological origin of linguistic diversity

In contrast with animal communication systems, diversity is characteristic of almost every aspect of human language. Languages variously employ tones, clicks, or manual signs to signal differences in meaning; some languages lack the noun-verb distinction (e.g., Straits Salish), whereas others have a proliferation of fine-grained syntactic categories (e.g., Tzeltal); and some languages do without morphology (e.g., Mandarin), while others pack a whole sentence into a single word (e.g., Cayuga). A challenge for evolutionary biology is to reconcile the diversity of languages with the high degree of biological uniformity of their speakers. Here, we model processes of language change and geographical dispersion and find a consistent pressure for flexible learning, irrespective of the language being spoken. This pressure arises because flexible learners can best cope with the observed high rates of linguistic change associated with divergent cultural evolution following human migration. Thus, rather than genetic adaptations for specific aspects of language, such as recursion, the coevolution of genes and fast-changing linguistic structure provides the biological basis for linguistic diversity. Only biological adaptations for flexible learning combined with cultural evolution can explain how each child has the potential to learn any human language