Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth of Lactic Acid Bacteria: Infuence of Protocooperation, Bacteriophage Infection, and Prebiotic Carbohydrates

Lactic acid bacteria are a vital part of the fermented food industry and are the subject of much interest and research. Industry is especially interested in using modern molecular approaches to maintain and improve selected strains; several industrial uses could be improved by closer investigation, namely the protocooperation of S. thermophilus and L. bulgaricus, the role of CRISPRs in phage resistance, and the utilization of prebiotic carbohydrates. Questions such as what genes and pathways are shared during milk fermentation between S. thermophilus and L. bulgaricus, when and what genes are active during bacteriophage infection, and how and where does prebiotic carbohydrate utilization occur can be answered. By using microarrays, complete snapshot of gene expression during each of these conditions are generated and detailed expression profiles can be produced. By devising a screening system, the distribution of the phenotype of GOS fermentation over a wide array of lactic acid bacteria from explored. Once this phenotypic distribution is generated, selected strains that are able to utilize GOS can be studied in detail to determine the mechanics of GOS fermentation. Answering these questions will add to the understanding of what factors are involved in successful fermentation and eventually be able to improve strain selection methods. iii Acknowledgements I would like to acknowledge the great contributions of my committee members and teachers, as well as my fellow lab members, for all their help and support during my graduate education and the fulfilling of my degree. I would like to acknowledge the USDA and the University of Nebraska for providing funding for my research. I would like to thank my advisor, Dr. Hutkins, for his unwavering support and enthusiasm throughout my time here. My special thanks to Jae Kim for his patience and expertise in answering the many questions I asked, and for training me to do microarrays. I would also like to acknowledge the complete support of my family: my parents, Jana and Charles Goin, and my grandparents, Erma and Orville Gobber and Lorane Goin, who never once doubted me and always at least tried to understand what my research was about. iv Preface This thesis is comprised of three chapters and a conclusion section. The first chapter is a literature review on the influence of protocooperation and bacteriophage infection in Streptococcus thermophilus, and the fermentation of prebiotic carbohydrate by lactic acid bacteria. The second chapter describes our completed S. thermophilus transcriptome project in …
Multivalued dependencies for XML

The wide use of XML has necessitated the XML document semantically richer. The integrity constraints play an important role in relational world. And the integrity constraints for XML have been widely investigated over the past few years. There are a few researches on multivalued dependencies for XML (XMVDs) and most of them are based on paths. In this paper, we propose a novel approach for defining XMVDs in XML Schema. We introduce “participant” to organize the involved information items that are divided into three groups called determinant, dependency and codependency in our extension. Two existing components, selector and field, are used to locate the information items, which uses restricted XPath as path description language. In particular, we extend the semantics of the field component to support a set (list) of nodes and node with complex type. Related issues are discussed, such as comparing element nodes with complex type.
Widespread changes in dendritic and axonal morphology in Mecp2‐mutant mouse models of rett syndrome: Evidence for disruption of neuronal networks

Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the X‐linked gene MECP2. Girls with RTT show dramatic changes in brain function, but relatively few studies have explored the structure of neural circuits. Examining two mouse models of RTT (Mecp2B and Mecp2J), we previously documented changes in brain anatomy. Herein, we use confocal microscopy to study the effects of MeCP2 deficiency on the morphology of dendrites and axons in the fascia dentata (FD), CA1 area of hippocampus, and motor cortex following Lucifer yellow microinjection or carbocyanine dye tracing. At 3 weeks of age, most (33 of 41) morphological parameters were significantly altered in Mecp2B mice; fewer (23 of 39) were abnormal in Mecp2J mice. There were striking changes in the density and size of the dendritic spines and density and orientation of axons. In Mecp2B mice, dendritic spine density was decreased in the FD (∼11%), CA1 (14–22%), and motor cortex (∼16%). A decreased spine head size (∼9%) and an increased spine neck length (∼12%) were found in Mecp2B FD. In addition, axons in the motor cortex were disorganized. In Mecp2J mice, spine density was significantly decreased in CA1 (14–26%). In both models, dendritic swelling and elongated spine necks were seen in all areas studied. Marked variation in the type and extent of changes was noted in dendrites of adjacent neurons. Electron microscopy confirmed abnormalities in dendrites and axons and showed abnormal mitochondria. Our findings document widespread abnormalities of dendrites and axons that recapitulate those seen in RTT. J. Comp. Neurol. 514:240–258, 2009. © 2009 Wiley‐Liss, Inc.
Handling Resource Use Oscillation in Open Multi-Agent Systems

The Challenge The convergence of ubiquitous electronic communications such as the Internet, electronic agents acting as proxies for human consumers, and web/grid service standards such as XML are rapidly ushering in a world where hordes of software agents, acting for humans, can rapidly select among multitudes of competing providers offering almost every imaginable service. This is inherently an " open " world, a marketplace where the agents operate as peers, neither designed nor operated under central control. Such a world offers the potential for unprecedented speed and efficiency in getting work done. In such open peer-to-peer systems we face, however, the potential of highly dysfunctional dynamics emerging as the result of many locally reasonable agent decisions [1]. Such " emergent dysfunctions " can take many forms, ranging from inefficient resource allocation [2] to chaotic inventory fluctuations [3] [4] to non-convergent collective decision processes [5]. This problem is exacerbated by the fact that agent societies operate in a realm whose communication and computational costs and capabilities are radically different from those in human society, leading to collective behaviors with which we may have little previous experience. It has been argued, for example, that the 1987 stock crash was due in part to the action of computer-based " program traders " that were able to execute trade decisions at unprecedented speed and volume, leading to unprecedented stock market volatility [6]. Let us focus on one specific example of emergent dysfunctional behavior: resource use oscillation in request-based resource sharing. Imagine that we have a collection of consumer agents faced with a range of competing providers for a given resource (e.g. a piece of information such as a weather report, a sensor or effector, a communication link, a storage or computational capability, or some kind of data analysis). Typically, though not exclusively, the utility offered by a resource is inversely related to how many consumers are using it. Each agent strives to select the resource with the highest utility (e.g. response time or quality), and resources are allocated first-come first-served to those who request them. This is a peer-to-peer mechanism: there is no one 'in charge'. This kind of resource allocation is widely used in settings that include fixed-price markets, internet routing, and so on. It is simple to implement, makes minimal bandwidth requirements, and-in the absence of delays in resource status information – allows consumers to quickly converge to a near optimal distribution …
A Fixed-Parameter Tractable Algorithm for Correlation Clustering with l Clusters

Given a graph G=(V,E) with real positive edge weights, where each edge (u, v) is labeled either + or – depending on whether u and v have been deemed to be similar or dissimilar, the problem of correlation clustering with l clusters is to partition the vertices of G into at most l clusters to minimize the total weight of + edges between clusters and – edges within clusters. This problem for general graphs is APX-complete. A fixed-parameter tractable (FPT) algorithm is presented, where the parameter k is defined as the maximum, over all blocks B of the graph, of the number of vertices that must be removed from B to obtain a forest.
Genetic Polymorphisms of Estrogen Receptors α and β and the Risk of Developing Prostate Cancer

Estrogen may be involved in the development of prostate cancer. The association between genetic polymorphisms of estrogen receptors α (ESR1) and β (ESR2) and prostate cancer risk was examined in a nested case-control study in Washington County, Maryland. Incident prostate cancer cases (n = 269) were matched to one or two controls (n = 440) by age, sex, race, and date of blood donation. Associations between estrogen receptor genotypes or dietary intake and the development of prostate cancer were examined in conditional logistic regression models. Results from this study showed that six single base-pair polymorphisms (SNPs) of ESR1 (rs1801132, rs2077647, rs746432, rs2273206, rs851982, rs2228480) and four SNPs of ESR2 (rs4986938, rs928554, rs8018687, rs number not available for ESR2 5696 bp 3′ of STP A>G) were not significantly associated with prostate cancer risk, either by allelic or genotypic frequencies. However, an interactive association with BMI was observed in the relationship between prostate cancer risk and genotypes of ESR2 38 bp 3′ of STP G>A (rs4986938) (p = 0.031). An interaction between intake level of phytoestrogen and genotypes of ESR1 Ex1-192G>C (rs746432) and between intake level of phytoestrogen and genotypes of ESR1 Ex8+229G>A (rs2228480) and risk of prostate cancer was observed (p = 0.0009 and p = 0.044, respectively). In conclusion, selected genetic polymorphisms of ESR1 and ESR2, overall, were not associated with prostate cancer risk. However, a variation in risk by BMI and phytoestrogen intake was implicated.
An ACO-based Scheduling Strategy on Load Balancing in Cloud Computing Environment

Overload balance of cloud data centers is a matter of great concern. Live migration of virtual machines presents an effective method to realize load balancing and to optimize resources utilization. With the rapidly increasing scale of cloud data centers, traditional centralized migration strategy begins to show lack of scalability and reliability. In this paper, we propose a novel distributed VM migration strategy based on a metaheuristic algorithm called Ant Colony Optimization. In our ACO-VMM Strategy, local migration agent autonomously monitors the resource utilization and launches the migration. At monitoring stage, it takes both the previous and current system condition into account to avoid unnecessary migrations. Besides, it adopts two different traversing strategies for ants in order to find the near-optimal mapping relationship between virtual machines (VMs) and physical machines (PMs). Experimental results show that ACO-VMM outperforms the existing migration strategies by achieving load balance of whole system, as well as reducing the number of migrations and maintaining the required performance levels.
Serious Fun: Cartooning for Privacy Protection

This paper presents our solution to the 2013 MediaEval Visual Privacy Task [3]. We apply cartoon-like eects to captured video such that identities of persons are protected while behavioural information and hence system intelligibility are maintained. We present our processing pipeline which includes additional protection steps such as re-colouring or additional blurring and discuss early evaluation results.
An XMM-Newton Observation of the Luminous Seyfert 1 Galaxy Markarian 509

We present the spectral analysis of an early XMM-Newton observation of the luminous Seyfert 1 galaxy Mrk 509. We find the hard (2-10 keV) continuum slope, including reflection, to be somewhat flatter (Γ = 1.75) than that of a typical broad-line Seyfert 1 galaxy. The most obvious feature in the hard X-ray spectrum is a narrow emission line near 6.4 keV with an equivalent width of ~50 eV. The energy and strength of this line is consistent with fluorescence from "neutral" iron in the molecular torus, and we note the emerging ubiquity of this feature in XMM-Newton and Chandra observations of Seyfert 1 galaxies over a wide luminosity range. We also find evidence for a second emission line at 6.7-6.9 keV, which we attempt to model by reflection from a highly ionized disk. A "soft excess," evident as an upward curvature in the continuum flux below ~1.5 keV, cannot be explained solely by enhanced reflection from the ionized disk. The RGS spectrum shows only weak discrete emission and absorption features in the soft X-ray spectrum, supporting our conclusion that the soft excess emission in Mrk 509 represents the high-energy portion of optically thick, thermal emission from the inner accretion disk.
A Dialectic of Social Justice: Finding Synergy between Life and Work through Reflection and Dialogue

Educational administration scholars have long argued that reflective practice and meaningful critical dialogue are important aspects of thoughtful leadership. This article explores the efficacy and utility of these two activities in relation to learning about and enacting leadership for social justice. The article centers on the reflective narratives of two leadership-for-social-justice scholars. It considers how their discrete experiences and ongoing dialogue contributed to their development, and it reveals the complexities and deficiencies that they continue to reconcile. The article concludes with a discussion of the value of engaging in these activities. It is written with established and emerging scholars in mind, who are seeking to understand what social justice means and who are striving to situate themselves as active members of a scholarly community.
Gene microarray analyses for potential biomarkers of single and recurrent venous thromboembolism

Venous thromboembolism is a major cause of morbidity and mortality with a high recurrence rate. The present study aimed to explore the molecular mechanisms and potential biomarkers of single venous thromboembolism (SVTE) and recurrent venous thromboembolism (RVTE). The microarray dataset GSE19151 was downloaded from Gene Expression Omnibus, which contained data from whole blood samples from 63 healthy controls, 32 SVTE and 38 RVTE patients. Differentially expressed genes (DEGs) in the SVTE and RVTE groups compared with those in the controls were identified using the t-test, followed by clustering analysis of DEGs and samples. Functional and pathway enrichment analyses were performed for DEGs in patients with RVTE and SVTE, as well as specific DEGs in patients with RVTE. The identified 42 DEGs in RVTE were mainly enriched in biological processes of cellular protein metabolism, gene expression and translational elongation as well as in pathways associated with ribosomes, Parkinson's disease and oxidative phosphorylation. In SVTE, 20 DEGs were identified, which were mainly involved in biological processes of biopolymer biosynthesis, translational elongation and cellular protein metabolism as well as pathways associated with ribosomes and cardiac muscle contraction. In RVTE, 22 specific DEGs were mainly involved in translational elongation, negative regulation of the force of heart contraction by chemical signals, cell proliferation, ribosomal pathways and protein export. The identified DEGs of SVTE, including COX7C and UQCRQ, may be potential biomarkers for SVTE, and the specific DEGs of RVTE, including ADRBK1, NDUFA5 and ATP5O, may be potential biomarkers for RVTE.
Oxidized Phospholipids Inhibit Phagocytosis and Impair Outcome in Gram-Negative Sepsis In Vivo1

Oxidized phospholipids that are generated during inflammation exert anti-inflammatory properties and prevent death during murine endotoxemia. Oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine (OxPAPC) inhibits the interaction of LPS with LPS-binding protein and CD14. In this study, we determined the functional properties of OxPAPC and potential interference with CD14 during abdominal sepsis caused by Escherichia coli. Administration of OxPAPC rendered mice highly susceptible to E. coli peritonitis, as indicated by an accelerated mortality and enhanced bacterial outgrowth and dissemination. CD14−/− mice also displayed increased mortality and bacterial outgrowth and OxPAPC did not further impair host defense in these animals. The mechanisms by which OxPAPC and CD14 deficiency impaired the immune response differed: whereas CD14−/− mice demonstrated a strongly reduced recruitment of phagocytes to the site of the infection, OxPAPC did not influence the influx of inflammatory cells but strongly diminished the phagocytosing capacity of neutrophils and macrophages by a CD14-independent mechanism. Furthermore, OxPAPC potently inhibited uptake of fluorospheres as well as receptor-mediated endocytosis and fluid-phase pinocytosis. These data suggest that oxidized phospholipids such as produced during inflammatory reactions may contribute to mortality during Gram-negative sepsis in vivo via impairment of the phagocytic properties of professional phagocytes.
An RF Carrier Bursting System Using Partial Quantization Noise Cancellation

This paper introduces a method for bandpass cancellation of the quantization noise occurring in high efficiency, envelope pulsed transmitter architectures-or carrier bursting. An equivalent complex baseband model of the proposed system, including the -modulator and cancellation signal generation, is developed. Analysis of the baseband model is performed, leading to analytical expressions of the power amplifier drain efficiency, assuming the use of an ideal class B power amplifier. These expressions are further used to study the impact of key system parameters, i.e. the compensation signal variance and clipping probability, on the class B power amplifier drain efficiency and signal-to-noise ratio. The paper concludes with simulations followed by practical measurements in order to validate the functionality of the method and to evaluate the performance-trend predictions made by the theoretical framework in terms of efficiency and spectral purity.
Multidimensional Interval-Data : Metrics and Factorial Analysis

Statistical units described by interval-valued variables represent a special case of Symbolic Objects, where all descriptors are quantitative variables. In this context, the paper presents two different metrics in R for interval-valued data that are based on the definition of the Hausdorff distance in R. Hausdorff distance in R (for any p ≥ 1) is a L∞ norm between pairs of closed sets. However, when p > 1 the problem complexity leads towards the definition of L2 norms approximating as well as possible the Hausdorff distance. Given a set of n units described by p interval-valued variables, we compute and represent the distances over factorial planes that are defined by factorial analyses that are consistent with the two distance measure definitions.
Fingerprint image: pre- and post-processing

Automatic Fingerprint Identification Systems (AFIS) are widely used for personal identification due to uniqueness of fingerprints. Minutiae-based fingerprint matching techniques are normally used for fingerprint matching. Fingerprint matching results and their accuracy depends on presence of valid minutiae. In this paper, we present a new technique for fingerprint image post-processing. This post-processing is used to eliminate a large number of false extracted minutiae from skeletonised fingerprint images. We propose a windowing post-processing method that takes into account the neighbourhood of each minutia within defined window and check for minutia validation and invalidation. We also present a complete pre-processing system including new segmentation technique that is required to extract region of interest (ROI) accurately from a fingerprint image. The results are confirmed by visual inspections of validated minutiae of the FVC2004 reference fingerprint image database. Experimental results obtained by the proposed approach show efficient reduction of false minutiae.
New Sources of Development Finance: Funding the Millennium Development Goals

United Nations University T interaction between formal government legislation and policies with the ‘informal’ efforts and livelihoods of people is crucial to the understanding of development and to the design of policy to reduce poverty. The task of collating and interpreting the vast experience of attempts to link formal with informal sectors is incomplete. What lessons can be drawn from these experiences of successes as well as failures? How do they alter our conceptualizations of the formal and the informal? And, most importantly, what are the implications for policymakers addressing the challenge of development and poverty reduction?
A 3D Facial Expression Tracking Method Using Piecewise Deformations

We present a new fast method for 3D facial expression tracking based on piecewise non-rigid deformations. Our method takes as input a video-rate sequence of face meshes that record the shape and time- varying expressions of a human face, and deforms a source mesh to match each input mesh to output a new mesh sequence with the same connectivity that reflects the facial shape and expressional variations. In mesh matching, we automatically segment the source mesh and estimate a non-rigid transformation for each segment to approximate the input mesh closely. Piecewise non-rigid transformation significantly reduces computational complexity and improves tracking speed because it greatly decreases the unknowns to be estimated. Our method can also achieve desired tracking accuracy because segmentation can be adjusted automatically and flexibly to approximate arbitrary deformations on the input mesh. Experiments demonstrate the efficiency of our method.
Ultra-High-Throughput VLSI Architecture of H.265/HEVC CABAC Encoder for UHDTV Applications

Ultra high definition television (UHDTV) imposes extremely high throughput requirement on video encoders based on High Efficiency Video Coding (H.265/HEVC) and Advanced Video Coding (H.264/AVC) standards. Context-adaptive binary arithmetic coding (CABAC) is the entropy coding component of these standards. In very-large-scale integration implementation, CABAC has known difficulties in being effectively pipelined and parallelized, due to the critical bin-to-bin data dependencies in its algorithm. This paper addresses the throughput requirement of CABAC encoding for UHDTV applications. The proposed optimizations including prenormalization, hybrid path coverage and lookahead rLPS to reduce the critical path delay of binary arithmetic encoding (BAE) by exploiting the incompleteness of data dependencies in rLPS updating. Meanwhile, the number of bins BAE delivers per clock cycle is increased by the proposed bypass bin splitting technique. The context modeling and binarization components are also optimized. As a result, our CABAC encoder delivers an average of 4.37 bins per clock cycle. Its maximum clock frequency reaches 420 MHz when synthesized in 90 nm. The corresponding overall throughput is 1836 Mbin/s that is 62.5% higher than the state-of-the-art architecture.