Miracle-dz/UniFAR-FTUs huggingface dataset:
Posttranscriptional Regulation of Glutamine Synthetase in the Filamentous Cyanobacterium Anabaena sp. PCC 7120: Differential Expression between Vegetative Cells and Heterocysts

ABSTRACT Genes homologous to those implicated in glutamine synthetase (GS) regulation by protein-protein interaction in the cyanobacterium Synechocystis sp. strain PCC 6803 are conserved in several cyanobacterial sequenced genomes. We investigated this GS regulatory mechanism in Anabaena sp. strain PCC 7120. In this strain the system operates with only one GS inactivation factor (inactivation factor 7A [IF7A]), encoded by open reading frame (ORF) asl2329 (gifA). Following addition of ammonium, expression of gifA is derepressed, leading to the synthesis of IF7A, and consequently, GS is inactivated. Upon ammonium removal, the GS activity returns to the initial level and IF7A becomes undetectable. The global nitrogen control protein NtcA binds to the gifA promoter. Constitutive high expression levels of gifA were found in an Anabaena ntcA mutant (CSE2), indicating a repressor role for NtcA. In vitro studies demonstrate that Anabaena GS is not inactivated by Synechocystis IFs (IF7 and IF17), indicating the specificity of the system. We constructed an Anabaena strain expressing a second inactivating factor, containing the amino-terminal part of IF17 from Synechocystis fused to IF7A. GS inactivation in this strain is more effective than that in the wild type (WT) and resembles that observed in Synechocystis. Finally we found differential expression of the IF system between heterocysts and vegetative cells of Anabaena.
Hippuristanol Reduces the Viability of Primary Effusion Lymphoma Cells both in Vitro and in Vivo

Primary effusion lymphoma (PEL) caused by Kaposi’s sarcoma-associated herpesvirus (also known as human herpesvirus-8) shows serious lymphomatous effusion in body cavities. PEL is difficult to treat and there is no standard treatment strategy. Hippuristanol is extracted from Okinawan coral Isis hippuris, and inhibits translational initiation by blocking eukaryotic initiation factor 4A, an ATP-dependent RNA helicase, binding to mRNA. Recently, there has been much interest in targeting translation initiation as an anticancer therapy. Here, we show that treatment of PEL cell lines with hippuristanol resulted in cell cycle arrest at G1 phase, and induced caspases activation and apoptosis. Hippuristanol also reduced the expression of cyclin D2, CDK2, CDK4, CDK6 and prosurvival XIAP and Mcl-1 proteins. Activation of activator protein-1, signal transducers and activators of transcription protein 3 and Akt pathways plays a critical role in the survival and growth of PEL cells. Hippuristanol suppressed the activities of these three pathways by inhibiting the expression of JunB, JunD, c-Fos, signal transducers and activators of transcription protein 3 and Akt proteins. In a xenograft mouse model that showed ascites and diffused organ invasion of PEL cells, treatment with hippuristanol significantly inhibited the growth and invasion of PEL cells compared with untreated mice. The results of the in vitro and in vivo experiments underline the potential usefulness of hippuristanol in the treatment of PEL.
On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data

We consider the problem of inferring fold changes in gene expression from cDNA microarray data. Standard procedures focus on the ratio of measured fluorescent intensities at each spot on the microarray, but to do so is to ignore the fact that the variation of such ratios is not constant. Estimates of gene expression changes are derived within a simple hierarchical model that accounts for measurement error and fluctuations in absolute gene expression levels. Significant gene expression changes are identified by deriving the posterior odds of change within a similar model. The methods are tested via simulation and are applied to a panel of Escherichia coli microarrays.
Geochemistry and Mixing Drive the Spatial Distribution of Free-Living Archaea and Bacteria in Yellowstone Lake

Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1–0.8, 0.8–3.0, and 3.0–20 μm) were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV). Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water) to 25:1 (vent water). Microbial population structures (both Bacteria and Archaea) were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 and V2 regions of 16S rRNA genes. Non-metric multidimensional scaling (NMDS) analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon), DOC (dissolved organic carbon), SO42-, O2 and metals were likely the major drivers for microbial population structures, however, mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (> 3 μm) and contained higher predicted operational taxonomic unit richness and microbial diversities (genus level) than free-living ones (<0.8 μm). Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.
Strategies for Optimizing Water-Exchange Rates of Lanthanide-Based Contrast Agents for Magnetic Resonance Imaging

This review describes recent advances in strategies for tuning the water-exchange rates of contrast agents for magnetic resonance imaging (MRI). Water-exchange rates play a critical role in determining the efficiency of contrast agents; consequently, optimization of water-exchange rates, among other parameters, is necessary to achieve high efficiencies. This need has resulted in extensive research efforts to modulate water-exchange rates by chemically altering the coordination environments of the metal complexes that function as contrast agents. The focus of this review is coordination-chemistry-based strategies used to tune the water-exchange rates of lanthanide(III)-based contrast agents for MRI. Emphasis will be given to results published in the 21st century, as well as implications of these strategies on the design of contrast agents.
Mixing COP and OOP

We describe and justify thirteen technical properties that a component system must possess to work with object-oriented programming languages (such as Java, C++, or C#). Our components are designed for large-scale, modular construction of programs with static checking of program compositions. Jiazzi, our enhancement of Java, implements the technical properties that we describe. We use Jiazzi components in our examples, but only to make the discussion more concrete. Readers interested in the details of the Jiazzi component system should refer to our technical paper in OOPSLA '01 [8]. P1. Language support: Components should be described with a specific language construct. P2. Core language integration: Components should contain, import and export instances of constructs in the core language. As object-oriented software systems increase in size and complexity , components are becoming central to the design process, and they deserve language support. Otherwise, the lack of an explicit language construct for components places a substantial burden on programmers who implement components, and it obscures the pro-grammer's intent to the compiler and other programmers. Furthermore, components should be integrated with the core language , as opposed to working around the language with various compositional design patterns [6]. In class-based languages, the primary core language construct is the class, and large-scale elements of reuse are class libraries and frameworks. Jiazzi's units [5] are explicit language constructs that describe components. There are two types of units: atoms, which are built from Java classes, and compounds, which are built from other units. Both atoms and compounds import and export Java classes. P3. Coarse-grained connections: Connections between imports and exports should be able to connect many classes at once. Connections between components should be coarse-grained, because components represent large-scale software entities. Components should import, export, and connect together groups of classes, since management of individual imported and exported classes does not scale with larger designs. In Jiazzi, groups of classes are imported together, exported together, and connected together when units are linked; we call these groups of classes packages to emphasize their similarity to packages in standard Java. P4. Hierarchical composition: A component should be com-posable into a larger, encapsulated component. P5. Component instantiation: A component should be instantiated for each use. P6. External linking: A component's external class dependencies should be resolved by the user of the component. Composition of components to form larger, compound components enables the incremental construction of software. Outside a compound component, …
On the Dispersions of the Gel’fand–Pinsker Channel and Dirty Paper Coding

This paper studies the second-order coding rates for memoryless channels with a state sequence known non-causally at the encoder. In the case of finite alphabets, an achievability result is obtained using constant-composition random coding, and by using a small fraction of the block to transmit the empirical distribution of the state sequence. For error probabilities less than 0.5, it is shown that the second-order rate improves on an existing one based on independent and identically distributed random coding. In the Gaussian case (dirty paper coding) with an almost-sure power constraint, an achievability result is obtained using random coding over the surface of a sphere, and using a small fraction of the block to transmit a quantized description of the state power. It is shown that the second-order asymptotics are identical to the single-user Gaussian channel of the same input power without a state.
Challenging the Roles of NSP3 and Untranslated Regions in Rotavirus mRNA Translation

Rotavirus NSP3 is a translational surrogate of the PABP-poly(A) complex for rotavirus mRNAs. To further explore the effects of NSP3 and untranslated regions (UTRs) on rotavirus mRNAs translation, we used a quantitative in vivo assay with simultaneous cytoplasmic NSP3 expression (wild-type or deletion mutant) and electroporated rotavirus-like and standard synthetic mRNAs. This assay shows that the last four GACC nucleotides of viral mRNA are essential for efficient translation and that both the NSP3 eIF4G- and RNA-binding domains are required. We also show efficient translation of rotavirus-like mRNAs even with a 5’UTR as short as 5 nucleotides, while more than eleven nucleotides are required for the 3’UTR. Despite the weak requirement for a long 5’UTR, a good AUG environment remains a requirement for rotavirus mRNAs translation.
Dead variable analysis for multi-threaded heap manipulating programs

Dead variable reduction is a well-known optimization used to reduce state space. In this paper we present two novel reductions for explicit-state code model checking. These reductions are designed to efficiently handle multi-threaded heap-manipulating programs. We implemented the reductions in Java PathFinder and demonstrated their efficiency by verification of several non-trivial programs. We also formally show correctness of the approach.
Proximity Cluster Trees

Hierarchical spatial data structures provide a means for organizing data for efficient processing. Most spatial data structures are optimized for performing queries, such as intersection and containment testing, on large data sets. Set-up time and complexity of these structures can limit their value for small data sets, an often overlooked yet important category in geometric processing. We present a new hierarchical spatial data structure, dubbed a proximity cluster tree, which is particularly effective on small data sets. Proximity cluster trees are simple to implement, require minimal construction overhead, and are structured for fast distance-based queries. Proximity cluster trees were tested on randomly generated sets of 2D Bézier curves and on a text-rendering application requiring minimum-distance queries to 2D glyph outlines. Although proximity cluster trees were tailored for small data sets, empirical tests show that they also perform well on large data sets.
Intelligent control of an experimental articulated leg for a galloping machine

Intelligent controllers are being used with increasing effectiveness on complex systems. This work verifies the effectiveness of fuzzy control, an intelligent method, on a single, articulated-leg that was designed to be used on a high-speed galloping quadruped. Intelligent methods are compared to other control methods in simulation and on the OSU DASH (Dynamic Articulated Structure for High-performance) leg. It is shown that the intelligent controllers outperform non-learning methods. Using fuzzy control, the OSU DASH leg performs stable hopping on a treadmill moving at 2.0 m/s.
Slicing Up Global Value Chains

In this paper, we "slice up the global value chain" using a decomposition technique that has recently become feasible due to the development of the World Input-Output Database. We trace the value added by all labor and capital that is directly and indirectly needed for the production of final manufacturing goods. The production systems of these goods are highly prone to international fragmentation as many stages can be undertaken in any country with little variation in quality. We seek to establish a series of facts concerning the global fragmentation of production that can serve as a starting point for future analysis. We describe four major trends. First, international fragmentation, as measured by the foreign value-added content of production, has rapidly increased since the early 1990s. Second, in most global value chains there is a strong shift towards value being added by capital and high-skilled labor, and away from less-skilled labor. Third, within global value chains, advanced nations increasingly specialize in activities carried out by high-skilled workers. Fourth, emerging economies surprisingly specialize in capital-intensive activities.
To Visualize the Coupling among Modules

There are levels of coupling and cohesion between classes in object oriented systems as well as between modules. Low module coupling is one of the quantifying the module coupling. The degree of coupling is a measure of the software quality. So far, several studies have been done on quantifying the module coupling and relating the results to effective software design process, in this article, we propose new some coupling such as import call coupling, import scalar coupling, import stamp coupling, import tramp coupling, export call coupling, export scalar coupling, export tramp coupling, and export stamp coupling and try to develop a software system for visualization of the module coupling. Module coupling visualization can help programmers to see bottlenecks in their design and re-engineer it for improvement
Driver fatigue monitoring system based on eye state analysis

Driver fatigue has been one of the major causes of accidents all over the world. This paper presents a real-time fatigue monitoring system which exploits driver's eye to detect fatigue. The approach uses Viola-Jones Face Cascade of classifiers for the detection of Driver's Face. The eye region is estimated heuristically with respect to the width and height of the detected face. The run length of the distribution of the pixel intensities quantised into bins are used as features and are extracted from the eye region on a frame by frame basis. The feature is well able to discriminate the different states of the driver's eye like open, nearly closed and closed. A Support Vector Machine (SVM) is finally integrated within the system to classify the facial appearance as either fatigued or otherwise. The overall system achieved an accuracy of 93.5%.
TWO-STAGE MODEL SELECTION WITH PARAMETERS WEIGHTED HIDDEN MARKOV MODELS AND LIKELIHOOD RATIO FOR PART-OF-SPEECH TAGGING

In many natural language processing applications two or more models usually have to be involved for accuracy. But it is difficult for minor models, such as "backoff" taggers in part-of-speech tagging, to cooperate smoothly with the ma- jor probabilistic model. We introduce a two-stage approach for model selection between hidden Markov models and other minor models. In the first stage, the major model is extended to give a set of candidates for model selection. Param- eters weighted hidden Markov model is presented using weighted ratio to create the candidate set. In the second stage, heuristic rules and features are used as evaluation functions to give extra scores to candidates in the set. Such scores are calculated using a diagnostic likelihood ratio test based on sensitivity and speci- ficity criteria. The selection procedure can be fulfilled using swarm optimization technique. Experiment results on public tagging data sets show the applicability of the proposed approach.
Hermite Polynomial Characterization of Heartbeats with Graphics Processing Units

In this paper we address the massive parallelization of the characterization of heartbeats by means of Graphics Processors. Heart- beats are represented with Hermite polynomials due to the compactness and robustness of this representation. Both the o-line and on-line char- acterization of QRS complexes are covered, thus, assessing the capabili- ties of Graphics Processors for these tasks. The results yield that o-line processing with a GPU can be computed 200 faster than a standard CPU, while on-line processing can be 100 faster.
Simulating natural disasters — A complex systems framework

This paper summarizes the SHELscape model ([1]), a complex systems framework developed for understanding economic transitions after natural disasters. The model is spatially defined with two agent categories (workers and owners) across two region types (rural and urban) producing two types of goods (food and a tradeable good). Seven behavioral modules define the setup of a low-income agrarian economy. A stylized calibrated system is subjected to a food production shock and changes of population, incomes, and consumption distributions are tracked. Coping mechanisms result in temporary consumption smoothing through savings; however, a large majority of the population still falls below the consumption poverty line. Two policy options, a cash transfer and a food transfer scheme, and their effects on the region are tested. Results show that income transfers result in higher income inequality while the food transfer scheme increases the rate of savings growth. The aim of this paper is to highlight how an agent-based framework can be used to study complex systems especially when data is weak and an immediate policy response is required.
Recursive LS filtering using block Householder transformations

A systolic block Householder transformation is proposed to implement the HT (Householder transformation) on a systolic array as well as to apply it to the RLS algorithm. Since the data are fetched in a block manner, vector operations are in general required for the vectorized array. The approach makes the HT suitable for VLSI implementation as well as applicable to real-time high-throughput applications of modern signal processing. <<ETX>>
The Role of Functions of Aggression in Associations Between Behavioral Inhibition and Activation and Mental Health Outcomes

ABSTRACT While the behavioral acitivation system (BAS) has been most consistently linked to externalizing behaviors, the behavioral inhibition system (BIS) has been more closely related to internalizing outcomes. Proactive and reactive aggression have demonstrated a similar pattern of association, with proactive aggression more closely linked to externalizing behavior and reactive aggression more consistently linked to internalizing symptoms. Despite theoretical links, few studies have examined associations between these constructs. Accordingly, the current study examined associations between the BAS and BIS and proactive and reactive aggression, and the role of proactive and reactive aggression in the link between the BAS and BIS and mental health outcomes. The BAS was associated with both proactive and reactive aggression, while the BIS was uniquely related to reactive aggression. Both proactive and reactive aggression appear to be playing a role in associations between the BAS and indicated mental health outcomes. Implications and future directions are discussed.
An Analysis of Provisioning and Allocation Policies for Infrastructure-as-a-Service Clouds

Today, many commercial and private cloud computing providers offer resources for leasing under the infrastructure as a service (IaaS) paradigm. Although an abundance of mechanisms already facilitate the lease and use of single infrastructure resources, to complete multi-job workloads IaaS users still need to select adequate provisioning and allocation policies to instantiate resources and map computational jobs to them. While such policies have been studied in the past, no experimental investigation in the context of clouds currently exists that considers them jointly. In this paper we present a comprehensive and empirical performance-cost analysis of provisioning and allocation policies in IaaS clouds. We first introduce a taxonomy of both types of policies, based on the type of information used in the decision process, and map to this taxonomy eight provisioning and four allocation policies. Then, we analyze the performance and cost of these policies through experimentation in three clouds, including Amazon EC2. We show that policies that dynamically provision and/or allocate resources can achieve better performance and cost. Finally, we also look at the interplay between provisioning and allocation, for which we show preliminary results.
Chair-based fidgeting and energy expenditure

Introduction Sedentariness is associated with chronic health conditions, impaired cognitive function and obesity. Work contributes significantly to sedentariness because many work tasks necessitate sitting. Few sustained solutions exist to reverse workplace sedentariness. Here, we evaluated a chair and an under-table device that were designed to promote fidgeting while seated. Our hypothesis was that an under-table leg-fidget bar and/or a fidget-promoting chair significantly increased energy expenditure. We compared these devices with chair-based exercise and walking. Materials and methods We measured energy expenditure and heart rate in 16 people while they sat and worked using a standard chair, an under-desk device that encourages leg fidgeting and a fidget-promoting chair. We compared outcomes with chair-based exercise and walking. Results Energy expenditure increased significantly while using either an under-table leg-fidget bar or a fidget-promoting chair, when compared to the standard office chair (standard chair, 76±31 kcal/hour; leg-fidget bar, 98±42 kcal/hour (p<0.001); fidget chair, 89±40 kcal/hour (p=0.03)). However, heart rate did not increase significantly in either case. Bouts of exercise performed while seated provided energetic and heart rate equivalency to walking at 2 mph. Conclusions Chairs and devices that promote fidgeting can increase energy expenditure by ∼20–30% but not increase heart rate. Dynamic sitting may be among a lexicon of options to help people move more while at work.