Miracle-dz/UniFAR-FTUs huggingface dataset:
Using natural language processing and the gene ontology to populate a structured pathway database

Reading literature is one of the most time consuming tasks a busy scientist has to contend with. As the volume of literature continues to grow there is a need to sort through this information in a more efficient manner. Mapping the pathways of genes and proteins of interest is one goal that requires frequent reference to the literature. Pathway databases can help here and scientists currently have a choice between buying access to externally curated pathway databases or building their own in house. However such databases are either expensive to license or slow to populate manually. Building upon easily available, open-source tools we have developed a pipeline to automate the collection, structuring and storage of gene and protein interaction data from the literature. As a team of both biologists and computer scientists we integrated our natural language processing (NLP) software with the gene ontology (GO) to collect and translate unstructured text data into structured interaction data. For NLP we used a machine learning approach with a rule induction program, RAPIER (http://www. cs. utexas. edu/users/mUrapier. html). RAPIER was modified to learn rules from tagged documents, and then it was trained on a corpus tagged by expert curators. The resulting rules were used to extract information from a test corpus automatically. Extracted genes and proteins were mapped onto Locuslink, and extracted interactions were mapped onto GO. Once information was structured in this way it was stored in a pathway database and this formal structure allowed us to perform advanced data mining and visualization.
Approximate sequence alignment

iv Chapter 1: Introduction . 1 1.1 Motivation . 1 1.2 Problem Definition . 2 1.3 Common Approach . 3 1.4 Related Work . 4 1.5 Thesis Organization . 6 Chapter 2: Suffix Tree And Wavelet Tree . 7 2.1 Suffix Trees . 7 2.2 Wavelet Trees . 9 Chapter 3: A General Framework And A New Technique . 12 3.1 A General Framework . 12 3.2 A New Technique . 14 Chapter 4: Implementation . 17 4.1 Incorporating count filtering . 17 4.2 Filtering based on frequency distance . 20 4.3 Improving the verification . 22 Chapter 5: Experimental Analyses . 23 5.1 Experimental Setup . 23 5.2 Platform . 23 5.3 Source Code . 23 5.4 Experimentation . 23 5.5 Effect of position restricted alignment . 24 5.6 Effect of count filtering . 25 5.7 Effect of using hash table . 26 5.8 Effect of frequency distance filtering . 26 References . 29 Vita . 31
Mortality, kidney disease and cardiac procedures following acute coronary syndrome.

BACKGROUND Cardiac interventions are underutilized in patients with chronic kidney disease (CKD) following acute coronary syndrome (ACS) partly due to nephrotoxicity concerns. METHODS We analyzed outcomes of 4631 subjects with ACS enrolled in the Blockade of the Glycoprotein IIb/IIIa Receptor to Avoid Vascular Occlusion trial, including time to death, time to reduced renal function (50% reduction in estimated glomerular filtration rate (eGFR) or development of end-stage renal disease (ESRD)) and percent change in eGFR from baseline. RESULTS Subjects with a lower baseline eGFR were more likely to be older, female and have diabetes, hypertension, congestive heart failure or peripheral vascular disease (all P < 0.0001); they were less likely to be taking aspirin > or = 162 mg or to have undergone a percutaneous coronary intervention (PCI) prior to enrollment (P < 0.0001). As eGFR declined, the proportion of subjects experiencing death versus reduced eGFR or ESRD qualitatively increased. In adjusted analyses, every 10 ml/min/1.73 m(2) decrease in eGFR < or = 90 was associated with a 15% increased hazard of death (HR 1.15, P = 0.01). In adjusted analyses of predictors of percent change in eGFR, catheterization (cath) with or without PCI compared to medical therapy during follow-up was not associated with significant differences in long-term eGFR (P = 0.09). CONCLUSIONS Among CKD subjects in this study, the risk of death greatly outweighed the risk of reduced eGFR or development of ESRD following ACS and the occurrence of cath +/- PCI was not associated with significant differences in long-term renal function. The presence of CKD should not preclude potentially beneficial interventions and research should focus on reducing the high cardiovascular burden in this population.
Partitioning graphs to speed up point-to-point shortest path computations

Computing the shortest paths in graphs is a fundamental problem with numerous applications. The rapid growth of network in size and complexity has made it necessary to decrease the execution time of the shortest path algorithm. We develop an effective graph partition method to retrieve Balanced Traversing Distance partitions and constitute a hierarchical graph model based on the decomposed network for accelerating the path queries. We then propose a new heuristic hierarchical routing algorithm that can significantly reduce the search space by pruning unpromising subgraph branches. We evaluate our approach experimentally under different network partition schemes to show the gain in performance.
Genetic Variation of Ecophysiological Responses to CO 2 in Picea glauca Seedlings

To investigate genetic variation in the response of white spruce (Picea glauca (Moench) Voss) to CO2 eleva- tions, one-year-old seedlings of 11 provenances from Ontario were grown at 360, 530 and 700 � mol mol -1 CO2 concentra- tions. After 60 days of treatment, CO2 assimilation rate (A) at growth (CO2) was 32% and 74% higher in the 530 and 700 �mol mol -1 CO2 treatment, respectively, than in 360 �mol mol -1 (CO2). After 90 days, A under 530 and 700 �mol mol -1 (CO2) was 141% and 223% greater, respectively, than under 360 �mol mol -1 (CO2). When measured at a common (CO2) (360 �mol mol -1 ), however, A under 530 and 700 �mol mol -1 (CO2) treatment was 39% and 53% lower than in the 360 � mol mol -1 (CO2) treatment, respectively, after 60 days of treatment, and 22 and 35% less, respectively, after 90 days. The CO2 elevations also significantly suppressed Vcamx, Jmax and TPU after 60 days and 90 days of treatment. The (CO2) eleva- tions significantly reduced Stomatal conductance and transpiration after 60 days of treatment, but not after 90 days. gs was 28% and 35% lower under 530 and 700 � mol mol -1 (CO2), respectively, than under 360 � mol mol -1 (CO2) after 60 days of treatment. E was 23 and 33% lower under 530 and 700 �mol mol -1 , respectively, than under 360 �mol mol -1 (CO2). Pho- tosynthetic water use efficiency (WUE) was 80% and 157% higher after 60 days of treatment and 145% and 196% higher after 90 days, respectively, under 530 and 700 � mol mol -1 (CO2) than under 360 � mol mol -1 (CO2). There were no signifi- cant between-provenance differences in any of the above responses; nevertheless, the ecophysiological performance of seedlings was closely correlated with the temperature and precipitation regimes of the seed origin. In addition, provenance significantly affected seedling total biomass, shoot mass, shoot/root ratio and height growth.
Inhibition of Cell Proliferation by an Anti-EGFR Aptamer

Aptamers continue to receive interest as potential therapeutic agents for the treatment of diseases, including cancer. In order to determine whether aptamers might eventually prove to be as useful as other clinical biopolymers, such as antibodies, we selected aptamers against an important clinical target, human epidermal growth factor receptor (hEGFR). The initial selection yielded only a single clone that could bind to hEGFR, but further mutation and optimization yielded a family of tight-binding aptamers. One of the selected aptamers, E07, bound tightly to the wild-type receptor (Kd = 2.4 nM). This aptamer can compete with EGF for binding, binds to a novel epitope on EGFR, and also binds a deletion mutant, EGFRvIII, that is commonly found in breast and lung cancers, and especially in grade IV glioblastoma multiforme, a cancer which has for the most part proved unresponsive to current therapies. The aptamer binds to cells expressing EGFR, blocks receptor autophosphorylation, and prevents proliferation of tumor cells in three-dimensional matrices. In short, the aptamer is a promising candidate for further development as an anti-tumor therapeutic. In addition, Aptamer E07 is readily internalized into EGFR-expressing cells, raising the possibility that it might be used to escort other anti-tumor or contrast agents.
MULTIVARIATE ANALYSIS OF LAND USER CHANGE: OHIO TURNPIKE INTERCHANGES

This study of interchanges along the Ohio Turnpike over an eighteen-year period suggests that age, by itself, will not be a significant predictor of interchange development. Certain interchanges have experienced rapid transformation since the opening of the turnpike. The development observed at these interchanges can best be explained by the proximity of these interchanges to large and small urban centers, by the growth rates of the nearest large and small urban centers, by the existence of extensive public facilities in the interchange community, and by the amount of traffic on the turnpike and on the roads that intersect the turnpike. Urban variables (growth rates, distances, and population sizes) do not significantly add to the explanation of variations in the amount of commercial highway property. Instead, land acreage devoted to restaurants, motels, and gas stations is significantly dependent upon traffic variables and public policy variables. /DOT/
Runtime support for adaptive power capping on heterogeneous SoCs

Power capping is a fundamental method for reducing the energy consumption of a wide range of modern computing environments, ranging from mobile embedded systems to datacentres. Unfortunately, maximising performance and system efficiency under static power caps remains challenging, while maximising performance under dynamic power caps has been largely unexplored. We present an adaptive power capping method that reduces the power consumption and maximizes the performance of heterogeneous SoCs for mobile and server platforms. Our technique combines power capping with coordinated DVFS, data partitioning and core allocations on a heterogeneous SoC with ARM processors and FPGA resources. We design our framework as a run-time system based on OpenMP and OpenCL to utilise the heterogeneous resources. We evaluate it through five data-parallel benchmarks on the Xilinx SoC which allows fully voltage and frequency control. Our experiments show a significant performance boost of 30% under dynamic power caps with concurrent execution on ARM and FPGA, compared to a naive separate approach.
Clock-Less Design Methodology For Digital System Design

As design systems have grown in complexity and clock speeds are constantly increasing, several limitations to the conceptual framework of synchronous design have begun to be noticed. Some notable problems due to higher performance demand are difficulty in global distribution of clock, clock skew, high power dissipation, interfacing difficulties and traversing the chip"s longest wire in one clock cycle. It is therefore not a surprise that the area of asynchronous circuits and systems, which generally do not suffer from these problems are gaining importance. Here we take into account new research concept which improves digital system implementations, which is basically asynchronous digital design. Asynchronous systems can be realized using clock-less chip implementation techniques which avoids the clock. This system gives importance to the arrival of data and sequence, only when required, thus reducing power consumption, EMI etc. The proposed methodology ensures the validity of the data by taking care of glitches, delays and hazards. The design of a new methodology for asynchronous system development is discussed in this paper.
Gyroscopic measurements of the rower's oar pitch angle

In this paper we present an instrumentation system which integrates inertial motion sensing and mobile computing technologies to acquire sensory information during on-water rowing. The use of miniaturized piezoelectric gyros is proposed and tested to sense the oar rotation. By time-integrating the gyro output signal, the pitch angle, namely the angle the blade is away from perpendicular to the water surface, can be monitored during the stroke cycle. Timing information about the different phases of the stroke cycle, and the patterns of oar pitch motion during the stroke cycle are presented, in connection with the performance of single sculling trials, in conditions of both slow and fast rowing. The validity of our approach is then discussed, with regard to either the gyro metrological specifications or the idiosyncrasies of the difficult environment where rowing is carried out and gyro measurements are taken.
Curbing Power or Progress? Governing with an Opposition Veto

Veto institutions are often dominated by government opponents with rival electoral and policy interests (e.g. \divided government"). I investigate the tradeoff between policy control and policy blockade when both the government and the veto party may cater to opposing special interests. The value of an opposition veto depends on whether electoral accountability can discipline bad type politicians. When this is not the case, a veto is beneficial only if the government's special interests are expected to be harmful. In contrast, when bad types care about (re-)election, a veto always increases expected welfare, providing a new rationale for the frequent occurrence of "divided government". Without policy rivalry, an opposition veto fares even better.
Cell Cycle-Dependent Regulation of Saccharomyces cerevisiae Donor Preference during Mating-Type Switching by SBF (Swi4/Swi6) and Fkh1

ABSTRACT Saccharomyces mating-type switching occurs through a double-strand break-initiated gene conversion event at MAT, using one of two donors located distantly on the same chromosome, HMLα and HMRa. MATa cells preferentially choose HMLα, a decision that depends on the recombination enhancer (RE) that controls recombination along the left arm of chromosome III. We previously showed that an fhk1Δ mutation reduces HMLα usage in MATa cells, but not to the level seen when RE is deleted. We now report that donor preference also depends on binding of the Swi4/Swi6 (SBF) transcription factors to an evolutionarily conserved SCB site within RE. As at other SCB-containing promoters, SBF binds to RE in the G1 phase. Surprisingly, Fkh1 binds to RE only in G2, which contrasts with its cell cycle-independent binding to its other target promoters. SBF and Fkh1 define two independent RE activation pathways, as deletion of both Fkh1 and SCB results in nearly complete loss of HML usage in MATa cells. These transcription factors create an epigenetic modification of RE in a fashion that apparently does not involve transcription. In addition, the putative helicase Chl1, previously involved in donor preference, functions in the SBF pathway.
Switching between formations for multiple mobile robots via synchronous controller

This paper proposes a new synchronous control law to perform multiple mobile robots trajectory tracking while maintaining time-varying formations. Each robot is controlled to track its desired trajectory while synchronizing its motion with the two nearby robots to maintain the desired time-varying formation. The dynamic model of the wheeled mobile robot (WMR) is derived, so as, it can be divided into a translational and rotational model, in order to control each model separately. Then, a synchronous controller for each robot's translation is proposed to guarantee the asymptotic stability of both position and synchronization errors. Also, an orientation controller is proposed to ensure that the robot is always oriented towards its desired position. The simulation results verify the effectiveness of the proposed synchronous controller in the formation control tasks.
JVN-TDT Entity Linking Systems at TAC-KBP2012

We present two methods for entity linking in two of our systems submitted to TAC/KBP 2012. The first one, namely Method 1, learns coherence among co/occurrence entities re/ ferred to within a text by exploiting Wikipe/ dia’s link structure and the second one, namely Method 2, combines some heuristics with a statistical model for entity linking. Method 1 exploits two features to train a classifier and exploits coreference relations among co/ occurring mentions. Method 2 is a hybrid me/ thod containing two phases. The first phase is a rule/based phase that filters candidates and, if possible, it disambiguates mentions with high reliability. The second phase employs a statis/ tical model to rank the candidates of each re/ maining mention and choose the one with the highest ranking as the right referent of that mention. Experiments are conducted to eva/ luate two methods on two datasets – TAC/ KBP2011 and TAC/KBP2012 datasets.
Providing efficient, scalable and privacy preserved verification mechanism in remote attestation

Numerous applications are running in a distributed environment in today's large networked world. Corporations really need a mechanism to monitor their own application(s) running on remote devices. One such mechanism by Trusted Computing Group (TCG) called remote attestation that can monitor and verify trustworthiness of remote applications. In this regard, many solutions have been provided on how to monitor remote applications. However, It becomes quite challenging task, when applications are running on millions of devices and it becomes necessary for the corporates to verify all of the applications. In this paper we have provided an efficient, scalable and privacy preserved mechanism to tackle the scalability of all these kinds of verifications. Machine learning algorithms are incorporated as Hadoop/MapReduce functions on the public cloud. The rest of low CPU intensive and privacy preserved verifications are performed on the private cloud.
Separation of Interleaved Web Sessions with Heuristic Search

We describe a heuristic search-based method for interleaved HTTP (Web) session reconstruction building upon first order Markov models. An interleaved session is generated by a user who is concurrently browsing the same web site in two or more web sessions (browser tabs or windows). In order to assure data quality for subsequent phases in analyzing user's browsing behavior, such sessions need to be separated in advance. We propose a separating process based on best-first search and trained first order Markov chains. We develop a testing method based on various measures of reconstructed sessions similarity to original ones. We evaluate the developed method on two real world click stream data sources: a web shop and a university student records information system. Preliminary results show that the proposed method performs well.
Role of Relative and Absolute Performance Evaluations in Intergroup Competition

We investigate the moral hazard problem in which a principal delegates multiple tasks to multiple workers. The principal imperfectly monitors their action choices by observing the public signals that are correlated with each other through a macro shock. He divides the workers into two groups and makes them compete with each other. We show that when the number of tasks is sufficiently large, relative performance evaluation between the groups accompanied by absolute performance evaluation results in eliminating unwanted equilibria. In this case, any approximate Nash equilibrium nearly induces the first-best allocation.
Proving theorems by pattern recognition I

Certain preliminary results on doing mathematics by machines (“mechanical mathematics”) were reported in an earlier paper [20]. The writer suggested developing inferential analysis as a branch of applied logic and as a sister discipline of numerical analysis. This analogy rests on the basic distinction of pure existence proofs, elegant procedures which in theory always terminate, and efficient procedures which are more complex to describe but can more feasibly be carried out in practice. In contrast with pure logic, the chief emphasis of inferential analysis is on the efficiency of algorithms, which is usually attained by paying a great deal more attention to the detailed structures of the problems and their solutions, to take advantage of possible systematic short cuts. The possibilities of much more elaborate calculations by machines provide an incentive to studying a group of rather minute questions which were formerly regarded as of small theoretical interest. When the range of actual human computation was narrow, there seemed little point in obtaining faster procedures which were still far beyond what was feasible. Furthermore, on account of the versatility of machines, it now appears that as more progress is made, strategies in the search for proofs, or what are often called heuristic methods, will also gradually become part of the subject matter of inferential analysis. An analogous situation in numerical analysis would be, for example, to make the machine choose to apply different tricks such as taking the Fourier transform to obtain a solution of some differential equation.
On the existence of stationary points for the Steiglitz-McBride algorithm

Most convergence results for adaptive identification algorithms have been developed in sufficient order settings, involving an unknown system with known degree. Reduced-order settings, in which the degree of the unknown system is underestimated, are more common, but more difficult to analyze. Deducing stationary points in these cases typically involves solving nonlinear equations, hence the sparseness of results for reduced-order cases. If we allow ourselves the tractable case in which the input to an identification experiment is white noise, we shall show that the Steiglitz-McBride method (1965) indeed admits a stationary point in reduced-order settings for which the resulting model is stable. Our interest in this study stems from a previous result, showing an attractive a priori bound on the mismodeling error at any such stationary point.
Synthesizing statecharts from multiple interrelated scenarios

In de£ning the behaviour of a system, requirement speci£cations make use of a number of scenarios that are interrelated in many ways. Current approaches, even though giving directions on how to translate them into statecharts, treat each scenario separately. In this paper we propose a method of synthesizing statecharts from multiple scenarios, with respect to the relationships among them. We describe a set of rules for the synthesis of statecharts from multiple scenarios, as a means to properly describe the requirements speci£cations of a system.
Regulation control of underactuated mechanical systems based on a new matching equation of port-controlled hamiltonian systems

We consider the control of Port-Controlled Hamiltonian (PCH) systems, which are a generalization of Euler-Lagrange Systems. A new matching equation for PCH systems is developed so that Interconnection Damping Assignment Passivity-Based Control (IDA-PBC) can be extended to the regulation of some underactuated PCH systems whose kinetic energy must be modified. A simple underactuated mechanical system (the inertial wheel pendulum) is used to demonstrate the effectiveness of the proposed method.
A Novel Seven Input Majority Gate in Quantum-dot Cellular Automata

A Quantum Cellular Automaton (QCA) is a nanotechnology which is an attractive alternative for transistor based technologies in the near future. A new seven input majority gate in quantum dot cellular automata is proposed in this paper. The basic elements in QCA are majority and inverter gates, therefore using a majority gate with more inputs in QCA circuit will cause reduction in cell count, latency and complexity. Furthermore, by using the proposed seven input majority gate we can design four inputs AND gate and OR gate in only two clock phases. By applying these kinds of gates QCA circuits could be simplified and optimized. In order to prove the functionality of the proposed device, QCADesigner tool and some physical proofs are utilized.