Miracle-dz/UniFAR-FTUs huggingface dataset:
The Origins of Human Cancer : Molecular Mechanisms of Carcinogenesis and Their Implications for Cancer Prevention and Treatmentâ€ ” Twenty-seventh G

EpidemiolÃ3gica! studies provide evidence that environmental factors (external agents such as chemicals, radiation, and viruses) play a major role in the causation of the majority of human tumors. This is a highly optimistic message, since it implies that cancer is largely a preventable disease. To meet this challenge we must, however, understand the mech anisms of cancer causation at the cellular and molecular levels and, in a parallel effort, develop new laboratory methods that can be used to identify specific causative agents in humans. The approach must be comprehensive since it is likely that human cancers are due to complex interactions between multiple factors, including the combined actions of chemical and viral agents. This paper reviews recent studies from our laboratory and studies by other investigators related to these themes. A major principle in studies on mechanisms of carcinogenesis is that the process proceeds through multiple discernible stages, including ini tiation, promotion, and progression. It is likely that the transition between these stages is driven by different environmental and endogenous factors and involves different biochemical mechanisms and genetic elements. Several types of chemicals initiate the carcinogenic process by yielding highly reactive species that bind covalenti) to cellular DNA. Our group has elucidated the details of this process with two groups of compounds, aromatic amines and polycyclic aromatic hydrocarbons, emphasizing how these agents distort the conformation of DNA and its functions during DNA replication and transcription. The implications of these findings with respect to oncogene activation, DNA amplification, gene transposi tion, and chromosome translocations are discussed. Our studies on tumor promotion have concentrated on the mechanisms of action of the potent tumor promoter 12-O-tetradecanoylphorbol-l 3-acetate. Studies from sev eral laboratories indicate that this agent and related compounds produce their effects by activating a specific cellular enzyme, protein kinase C (PKC). This produces a cascade of events which include alterations in the function of membrane-associated ion channels and receptors, altera tions in gene expression and, ultimately, changes in cellular differentiation and proliferation. Recent studies on the isolation and stable overexpression of a cloned DNA sequence that encodes PKC are described. The results obtained provide direct evidence that PKC plays a critical role in growth control. The possible role of PKC, and other mediators of signal transduction pathways, in the origin of certain human cancers is also discussed. Finally, this paper discusses how insights into molecular mechanisms of carcinogenesis provide new approaches to the detection of specific causes of human cancer, using an approach termed "molecular cancer epidemiology," and also new strategies for cancer prevention and treat
Increasing System Availability with Local Recovery Based on Fault Localization

Due to the fact that software systems cannot be tested exhaustively, software systems must cope with residual defects at run-time. Local recovery is an approach for recovering from errors, in which only the defective parts of the system are recovered while the other parts are kept operational. To be efficient, local recovery must be aware of which component is at fault. In this paper, we combine a fault localization technique (spectrum-based fault localization, SFL) with local recovery techniques to achieve fully autonomous fault detection, isolation, and recovery. A framework is used for decomposing the system into separate units that can be recovered in isolation, while SFL is used for monitoring the activities of these units and diagnose the faulty one whenever an error is detected. We have applied our approach to MPlayer, a large open-source software. We have observed that SFL can increase the system availability by 23.4% on average.
Incorporating Action into Diagnostic Problem Solving (An Abridged Report)

Reasoning about action and change is integral to the diagnosis, testing and repair of many artifacts, and yet there is no formal account of diagnostic problem solving which incorporates a theory of action and change. In this abridged report, we provide a situation calculus framework for diagnostic problem solving. Using this framework, we present results towards a characterization of diagnosis for behaviorally static systems whose state can be affected by events which occur in the world, and which require world-altering actions to achieve tests and repairs. Diagnosis is defined more broadly in terms of what happened in addition to the traditional conjccture of what is wrong. Observations of events and actions in the world are used to diagnose some system malfunctions. By developing our characterization in terms of the situation calculus, we are able to contribute towards a formal characterization and semantics for this broader notion of diagnosis, testing and repair, in addition to dealing formally with issues such as the frame problem.
A human centromere protein, CENP-B, has a DNA binding domain containing four potential alpha helices at the NH2 terminus, which is separable from dimerizing activity

The alphoid DNA-CENP-B (centromere protein B) complex is the first sequence-specific DNA/protein complex detected in the centromeric region of human chromosomes. In the reaction, CENP-B recognizes a 17-bp sequence (CENP-B box) and assembles two alphoid DNA molecules into a complex, which is designated complex A (Muro, Y., H. Masumoto, K. Yoda, N. Nozaki, M. Ohashi, and T. Okazaki. 1992. J. Cell Biol. 116:585-596). Since CENP-B gene is conserved in mammalian species and CENP-B boxes are found also in mouse centromere satellite DNA (minor satellite), this sequence-specific DNA-protein interaction may be important for some kind of common centromere function. In this study we have characterized the structure of CENP-B and CENP-B-alphoid DNA complex. We have shown by chemical cross-linking that CENP-B formed a dimer, and have estimated by molecular weight determination the composition of complex A to be a CENP-B dimer and two molecules of alphoid DNA. The DNA binding domain has been delimited within the NH2-terminal 125-amino acid region containing four potential alpha-helices using truncated CENP-B made in Escherichia coli cells. We have shown that CENP-B had sites highly sensitive to proteases and that the DNA binding domain was separable from the dimerizing activity by the proteolytic cleavage at 20 kD from the COOH terminus of the molecule. Thus, CENP-B may organize a higher order structure in the centromere by juxtaposing two CENP-B boxes in the alphoid DNA repeat through both the DNA-protein and protein-protein interactions.
An 1×(2N+1) MMI Optical Splitters Based on SOI Rib Waveguide

We propose an 1times(2N+1) multimode interference (MMI) optical splitters based on silicon on insulator (SOI) rib waveguide in this paper. This paper introduces the technique of SOI waveguide and the advantages of the SOI waveguide, and then we describe the mathematic formulation based on beam propagation method (BPM). Some guided rules are also briefly derived and discussed. We also give a brief conclusion of our designed 1times(2N+1) MMI optical splitters based on SOI rib waveguide
When Acyclicity Is Not Enough: Limitations of the Causal Graph

Causal graphs are widely used in planning to capture the internal structure of planning instances. In the past, causal graphs have been exploited to generate hierarchical plans, to compute heuristics, and to identify classes of planning instances that are easy to solve. It is generally believed that planning is easier when the causal graph is acyclic. In this paper we show that this is not true in the worst case, proving that the problem of plan existence is PSPACE-complete even when the causal graph is acyclic. Since the variables of the planning instances in our reduction are propositional, this result applies to STRIPS planning with negative pre-conditions. Having established that planning is hard for acyclic causal graphs, we study a subclass of planning instances with acyclic causal graphs whose variables have strongly connected domain transition graphs. For this class, we show that plan existence is easy, but that bounded plan existence is hard, implying that optimal planning is significantly harder than satisficing planning for this class.
A new ant colony algorithm for multi-label classification with applications in bioinfomatics

The conventional classification task of data mining can be called single-label classification, since there is a single class attribute to be predicted. This paper addresses a more challenging version of the classification task, where there are two or more class attributes to be predicted. We propose a new ant colony algorithm for the multi-label classification task. The new algorithm, called MuLAM (Multi-Label Ant-Miner) is a major extension of Ant-Miner, the first ant colony algorithm for discovering classification rules. We report results comparing the performance of MuLAM with the performance of three other classification techniques, namely the very simple majority classifier, the original Ant-Miner algorithm and C5.0, a very popular rule induction algorithm. The experiments were performed using five bioinformatics datasets, involving the prediction of several kinds of protein function.
Generation of the AML1‐EVI‐1 fusion gene in the t(3;21)(q26;q22) causes blastic crisis in chronic myelocytic leukemia.

The t(3;21)(q26;q22) translocation, which is one of the consistent chromosomal abnormalities found in blastic crisis of chronic myelocytic leukemia (CML), is thought to play an important role in the leukemic progression of CML to an acute blastic crisis phase. The AML1 gene, which is located at the translocation breakpoint of the t(8;21)(q22;q22) translocation found in acute myelocytic leukemia, was also rearranged by the t(3;21)(q26;q22) translocation. Screening of a cDNA library of the t(3;21)‐carrying leukemic cell line cells (SKH1) resulted in the isolation of two potentially complete AML1‐EVI‐1 chimeric cDNAs of 6 kb. Two species of AML1‐EVI‐1 fusion transcripts of 8.2 and 7.0 kb were detected in SKH1 cells. These cells expressed the 180 kDa AML1‐EVI‐1 fusion protein containing an N‐terminal half of AML1 including a runt homology domain which is fused to the entire zinc finger EVI‐1 protein. The AML1‐EVI‐1 fusion transcript was consistent in all three cases of the t(3;21)‐carrying leukemia examined by RNA‐based PCR. These findings strongly suggest that the t(3;21) translocation results in the formation of a new class of chimeric transcription factor which could contribute to the leukemic progression of CML through interference with cell growth and differentiation.
Word-level traversal of finite state machines using algebraic geometry

Reachability analysis is a tool for formal equivalence and model checking of sequential circuits. Conventional techniques are mostly bit-level, in that the reachable states, transition relations and property predicates are all represented using Boolean variables and functions. The problem suffers from exponential space and time complexities; therefore, some form of abstraction is desirable. This paper introduces a new concept of implicit state enumeration of finite state machines (FSMs) performed at the word-level. Using algebraic geometry, we show that the state-space of a sequential circuit can be encoded, canonically, as the zeros of a word-level polynomial F (S) over the Galois field F2k, where S = {s0, . , sk-1} is the word-level representation of a k-bit state register. Subsequently, concepts of elimination ideals and Grobner bases can be employed for FSM traversal. The paper describes the complete theory of word-level FSM traversal and demonstrates the feasibility of the approach with experiments over a set of sequential circuit benchmarks.
PASE: Synthesizing Existing Transport Strategies for Near-Optimal Data Center Transport

Several data center transport protocols have been proposed in recent years (e.g., DCTCP, PDQ, and pFabric). In this paper, we first identify the underlying strategies used by the existing data center transports, namely, in-network Prioritization (used in pFabric), Arbitration (used in PDQ), and Self-adjusting at Endpoints (PASE) (used in DCTCP). We show that these strategies are complimentary to each other, rather than substitutes, as they have different strengths and can address each other’s limitations. Unfortunately, prior data center transports use only one of these strategies. As a result, they either achieve near-optimal performance or deployment friendliness (i.e., require no changes to the data plane) but not both. Based on this insight, we design a data center transport protocol called PASE, which carefully synthesizes these strategies by assigning different transport responsibilities to each strategy. The key advantage of PASE over prior art is that it achieves both near-optimal performance as well as deployment friendliness. PASE does not require any changes in network switches (hardware or software); yet, it achieves comparable, or even better, performance than the state-of-the-art protocols (such as pFabric) that require changes to network elements. Our evaluation results show that the PASE performs well for a wide range of application workloads and network settings.
Image labeling by multiple segmentation

In this paper, we provide a method for image labeling by combining the local features and contextual cues in a multiple segmentation framework. Our main insight is to weight the classification results of each image region in different levels, which are obtained by a series of learned discriminative models based on bag of features. The contextual cues are implicitly embedded as feature selection in learning process. Multiple segmentation framework provides robust representation, allowing a wide variety of cues to contribute to the confidence in each semantic label. Our algorithm has been applied on the lotus hill institute(LHI) 15-class dataset and outperforms other state-of-the-art methods.
Radio Resource Management for Improving Energy Self-sufficiency of Green Mobile Networks

Three factors make power supply one of the most urgent and challenging issues for the future of mobile networks. First, the expected fast growth of mobile traffic raises doubts about the sustainability of mobile communications, that already account for 0.5% of the woldwide energy consumption. Second, power supply has become far the largest component of the operational costs of running a network. Third, the deployment of network infrastructures in emerging countries is strategic, but, in these countries, the power grid is not always reliable. Renewable energy sources can help to cope with these issues. However, one of their main drawbacks is the intermittent and difficult to predict energy generation profile. The feasibility of renewable power supply for base station (BS) powering depends then by the possibility to reduce the BS consumption and to adapt it to the amount of available energy. In this paper, we consider a cluster of BSs powered with photovoltaic (PV) panels and equipped with energy storage units. Resource on Demand (RoD) strategies are implemented to reduce the cluster energy consumption and to adapt it to energy availability. The results show that resource of demand can effectively be applied to make off-grid BS deployment feasible.
Taguchi robust design for the multi-response with consideration for the manufacturing tolerance used in high speed air blower motor

In mass production, manufacturing tolerances are unavoidably generated in the rotor between the core and the permanent magnet. Because back electromotive force (EMF) and cogging torque are influenced by manufacturing tolerances, it is necessary to improve the tolerances by changing specific factors. In this paper, a Taguchi robust design is conducted on an air blower motor that is used to circulate the air in the fuel cell stack. Because the Taguchi robust design cannot achieve a multi-response, a multi-response signal-to-noise (MRSN) ratio based on the Taguchi robust design is employed to consider the back EMF and cogging torque. Finally, an optimum shape is determined to select the combination of control factors in the robust design, and the back EMF and the cogging torque are improved.
Greedy based population seeding technique in Ant Colony Optimization algorithm

In this paper, a new population seeding technique has been introduced in ACO algorithm. The method used for seeding technique is Greedy method. Along with the proposed method, a meta-heuristic algorithm Ant Colony Optimization is explained along with its applications on various problems. A detailed explanation of how the problem can fit into ACO algorithm is given. A tabular column of how the ACO has been modified to solve the respective problem has been given out.
Patterns of integration of DNA microinjected into cultured mammalian cells: evidence for homologous recombination between injected plasmid DNA molecules

We examined the fate of DNA microinjected into nuclei of cultured mammalian cells. The sequence composition and the physical form of the vector carrying the selectable gene affected the efficiency of DNA-mediated transformation. Introduction of sequences near the simian virus 40 origin of DNA replication or in the long terminal repeat of avian sarcoma provirus into a recombinant plasmid containing the herpes simplex virus thymidine kinase gene. (pBR322/HSV-tk) enhanced the frequency of transformation of LMtk- and RAT-2tk- cells to the TK+ phenotype 20- to 40-fold. In cells receiving injections of only a few plasmid DNA molecules, the transformation frequency was 40-fold higher after injection of linear molecules than after injection of supercoiled molecules. By controlling the number of gene copies injected into a recipient cell, we could obtain transformants containing a single copy or as many as 50 to 100 copies of the selectable gene. Multiple copies of the transforming gene were not scattered throughout the host genome but were integrated as a concatemer at one or a very few sites in the host chromosome. Independent transformants contained the donated genes in different chromosomes. The orientation of the gene copies within the concatemer was not random; rather, the copies were organized as tandem head-to-tail arrays. By analyzing transformants obtained by coinjecting two vectors which were identical except that in one a portion of the vector was inverted, we were able to conclude that the head-to-tail concatemers were generated predominantly by homologous recombination. Surprisingly, these head-to-tail concatemers were found in transformants obtained by injecting either supercoiled or linear plasmid DNA. Even though we demonstrated that cultured mammalian cells contain the enzymes for ligating two DNA molecules very efficiently irrespective of the sequences or topology at their ends, we found that even linear plasmid DNA was recruited into the concatemer by homologous recombination.
Cytokine patterns in fibromyalgia and their correlation with clinical manifestations.

OBJECTIVE To examine the possible role of the soluble factor in fibromyalgia (FM) by studying the correlation of cytokine levels with the patients' clinical and psychiatric profile. METHODS Eighty FM patients underwent clinical and psychiatric evaluations, and plasma levels of cytokines (IL-1, IL-6, IL-8, IL-10, TNF-alpha), aspecific markers of inflammation, rheumatoid factor (RF), anti-extractable nuclear antigen (ENA) antibodies, and anti-nuclear factor (FAN) were measured. RESULTS Higher levels of IL-10, IL-8 and TNF-alpha were found in FM patients than in controls. Significant correlations between the biochemical parameters and clinical data were found. CONCLUSION The higher levels of cytokines found in FM patients suggest the presence of an inflammatory response system (IRS) and highlight a parallel between the clinical symptoms and biochemical data. They support the hypothesis that cytokines may play a role in the clinical features of fibromyalgia. In addition, the similar cytokine patterns found in FM patients with different psychiatric profiles suggests that IRS impairment may play a specific role in the disease.
Structure and mechanical behavior of Big Area Additive Manufacturing (BAAM) materials

Purpose This paper aims to investigate the deposited structure and mechanical performance of printed materials obtained during initial development of the Big Area Additive Manufacturing (BAAM) system at Oak Ridge National Laboratory. Issues unique to large-scale polymer deposition are identified and presented to reduce the learning curve for the development of similar systems. Design/methodology/approach Although the BAAM’s individual extruded bead is 10-20× larger (∼9 mm) than the typical small-scale systems, the overall characteristics of the deposited material are very similar. This study relates the structure of BAAM materials to the material composition, deposition parameters and resulting mechanical performance. Findings Materials investigated during initial trials are suitable for stiffness-limited applications. The strength of printed materials can be significantly reduced by voids and imperfect fusion between layers. Deposited material was found to have voids between adjacent beads and micro-porosity within a given bead. Failure generally occurs at interfaces between adjacent beads and successive layers, indicating imperfect contact area and polymer fusion. Practical implications The incorporation of second-phase reinforcement in printed materials can significantly improve stiffness but can result in notable anisotropy that needs to be accounted for in the design of BAAM-printed structures. Originality/value This initial evaluation of BAAM-deposited structures and mechanical performance will guide the current research effort for improving interlaminar strength and process control.
YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) provides high-quality curated genomic, genetic, and molecular information on the genes and their products of the budding yeast Saccharomyces cerevisiae. To accommodate the increasingly complex, diverse needs of researchers for searching and comparing data, SGD has implemented InterMine (http://www.InterMine.org), an open source data warehouse system with a sophisticated querying interface, to create YeastMine (http://yeastmine.yeastgenome.org). YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types. YeastMine offers multiple scenarios in which it can be used such as a powerful search interface, a discovery tool, a curation aid and also a complex database presentation format. Database URL: http://yeastmine.yeastgenome. org