Miracle-dz/UniFAR-FTUs huggingface dataset:
The serotonin transporter gene is a substrate for age and stress dependent epigenetic regulation in rhesus macaque brain: Potential roles in genetic selection and Gene × Environment interactions

Abstract In humans, it has been demonstrated that the serotonin transporter linked polymorphic region (5-HTTLPR) genotype moderates risk in the face of adversity. One mechanism by which stress could interact with genotype is via epigenetic modifications. We wanted to examine whether stress interacted with genotype to predict binding of a histone 3 protein trimethylated at lysine 3 (H3K4me3) that marks active promoters. The brains (N = 61) of male rhesus macaques that had been reared in the presence or absence of stress were archived and the hippocampusi dissected. Chromatin immunoprecipitation was performed with an antibody against H3K4me3 followed by sequencing on a SolexaG2A. The effects of age, genotype (5-HTTLPR long/long vs. short), and stress exposure (peer-reared vs. mother-reared) on levels of H3K4me3 binding were determined. We found effects of age and stress exposure. There was a decline in H3K4me3 from preadolescence to postadolescence and lower levels in peer-reared monkeys and no effects of genotype. When we controlled for age, however, we found that there were effects of 5-HTTLPR genotype and rearing condition on H3K4me3 binding. In a larger sample, we observed that cerebrospinal fluid 5-hydroxyindoleacetic acid levels were subject to interactive effects among age, rearing history, and genotype. Genes containing both genetic selection and epigenetic regulation may be particularly important in stress adaptation and development. We find evidence for selection at the solute carrier family C6 member 4 gene and observe epigenetic reorganization according to genotype, stress, and age. These data suggest that developmental stage may moderate effects of stress and serotonin transporter genotype in the emergence of alternative adaptation strategies and in the vulnerability to developmental or psychiatric disorders.
Characterization of the activation of latent TGF-beta by co-cultures of endothelial cells and pericytes or smooth muscle cells: a self- regulating system

The conversion of latent transforming growth factor beta (LTGF-beta) to the active species, transforming growth factor beta (TGF-beta), has been characterized in heterotypic cultures of bovine aortic endothelial (BAE) cells and bovine smooth muscle cells (SMCs). The formation of TGF- beta in co-cultures of BAE cells and SMCs was documented by a specific radioreceptor competition assay, while medium from homotypic cultures of BAE cells or SMCs contained no active TGF-beta as determined by this assay. The concentration of TGF-beta in the conditioned medium of heterotypic co-cultures was estimated to be 400-1,200 pg/ml using the inhibition of BAE cell migration as an assay. Northern blotting of poly A+ RNA extracted from both homotypic and heterotypic cultures of BAE cells and SMCs revealed that BAE cells produced both TGF-beta 1 and TGF- beta 2, while SMCs produced primarily TGF-beta 1. No change in the expression of these two forms of TGF-beta was apparent after 24 h in heterotypic cultures. Time course studies on the appearance of TGF-beta indicated that most of the active TGF-beta was generated within the first 12 h after the establishment of co-cultures. The generation of TGF-beta in co-cultures stimulated the production of the protease inhibitor plasminogen activator inhibitor-1 (PAI-1). The inclusion of neutralizing antibodies to TGF-beta in the co-culture medium blocked the observed increase in PAI-1 levels. The increased expression of PAI- 1 subsequent to TGF-beta formation blocked the activation of the protease required for conversion of LTGF-beta to TGF-beta as the inclusion of neutralizing antibodies to PAI-1 in the co-culture medium resulted in prolonged production of TGF-beta. This effect was lost upon removal of the PAI-1 antibodies. Thus, the activation of LTGF-beta appears to be a self-regulating system.
Random Di usion Models for Animal MovementP

Models of animal movement are necessary both as unambiguous descriptions of particular movement patterns and as starting points for the interpretation of observations on location. Radio-tracking, with frequent sampling so that successive observations are dependent, is an important special case to which only a single narrow class of models has been applied. The standard approach uses a bivariate Ornstein-Uhlenbeck diiusion process, for which the stationary distribution is always normal, limiting its exibility for modelling stationary home range or territorial behaviour. I describe a new class of random diiusion models for animal movement, exible enough to incorporate many realistic features, but simple enough to be estimated statistically and to be interpreted behaviourally. The models incorporate a nite number of diierent behavioural or physiological states for an animal, and a set of diiusion rules describing the movement of the animal while in particular states. Mathematically, the models are diiusions in nite random temporal environments. The class of models generalises the standard Ornstein-Uhlenbeck model (which can be though of as the 1-state case), and can represent features such as multimodal and asymmetric home ranges and utilization distributions. I give a range of examples of particular models within this class, including an application to the modelling of the movements of wood mice, for which radio-tracking can give information on behaviour, as well as location.
Entry prepared for the Internet Encyclopaedia of Ecological Economics

1. Introduction Agent-based modelling (ABM) is the computational study of social agents as evolving systems of autonomous interacting agents. ABM is a tool for the study of social systems from the complex adaptive system perspective. From this perspective, the researcher is interested in how macro phenomena are emerging from micro level behaviour among a heterogeneous set of interacting agents (Holland, 1992). By using ABM as computational laboratories, one may test in a systematic way different hypotheses related to attributes of the agents, their behavioural rules, and the types of interactions, and their effect on macro level stylized facts of the system. Since the early 1990s ABM has increasingly been used in most of the social sciences. I shall focus on the applications of ABM related to ecological economics (Janssen, 2002, 2005; Janssen and Ostrom, 2005). ABM of ecological economic systems can be defined as systems that are populated with heterogeneous population of agents, who determine their interactions with other agents and with their environment, on the basis of internalized social norms and mental models, internal behavioural rules and cognitive abilities, formal and informal institutional rules that affect how agents interact, individual and social learning, etc.
Group A Streptococci Bind to Mucin and Human Pharyngeal Cells through Sialic Acid-Containing Receptors

ABSTRACT The first step in the colonization of group A streptococci (Streptococcus pyogenes) is adherence to pharyngeal epithelial cells. Prior to adherence to their target tissue, the first barrier that the streptococci encounter is the mucous layer of the respiratory tract. The present study was undertaken to characterize the interaction between mucin, the major glycoprotein component of mucus, and streptococci. We report here that S. pyogenes is able to bind to bovine submaxillary mucin in solid-phase microtiter plate assays. Western blots probed with 125I-labeled mucin and a panel of monoclonal antibodies revealed that the streptococcal M protein is one of two cell wall-associated proteins responsible for this binding. The binding was further localized to the N-terminal portion of the M molecule. Further analysis revealed that the M protein binds to the sialic acid moieties on mucin, and this interaction seems to be based on M-protein conformation rather than specific amino acid sequences. We found that sialic acid also plays a critical role in the adherence of an M6 streptococcal strain to the Detroit 562 human pharyngeal cell line and have identified α2-6-linked sialic acid as an important sialylated linkage for M-protein recognition. Western blot analysis of extracted pharyngeal cell membrane proteins identified three potential sialic acid-containing receptors for the M protein. The results are the first to show that sialic acid not only is involved in the binding of the streptococci to mucin but also plays an important role in adherence of group A streptococci to the pharyngeal cell surface.
Improving the scalability of a multi-core web server

Improving the performance and scalability of Web servers enhances user experiences and reduces the costs of providing Web-based services. The advent of Multi-core technology motivates new studies to understand how efficiently Web servers utilize such hardware. This paper presents a detailed performance study of a Web server application deployed on a modern 2 socket, 4-cores per socket server. Our study show that default, "out-of-the-box" Web server configurations can cause the system to scale poorly with increasing core counts. We study two different types of workloads, namely a workload that imposes intense TCP/IP related OS activity and the SPECweb2009 Support workload, which incurs more application-level processing. We observe that the scaling behaviour is markedly different for these two types of workloads, mainly due to the difference in the performance characteristics of static and dynamic requests. The results of our experiments reveal that with workload-specific Web server configuration strategies a modern Multi-core server can be utilized up to 80% while still serving requests without significant queuing delays; utilizations beyond 90% are also possible, while still serving requests with acceptable response times.
Reflecting on the challenges of choosing and using a grounded theory approach.

AIM To explore three different approaches to grounded theory and consider some of the possible philosophical assumptions underpinning them. BACKGROUND Grounded theory is a comprehensive yet complex methodology that offers a procedural structure that guides the researcher. However, divergent approaches to grounded theory present dilemmas for novice researchers seeking to choose a suitable research method. REVIEW METHODS This is a methodology paper. DATA SOURCES This is a reflexive paper that explores some of the challenges experienced by a PhD student when choosing and operationalising a grounded theory approach. DISCUSSION Before embarking on a study, novice grounded theory researchers should examine their research beliefs to assist them in selecting the most suitable approach. This requires an insight into the approaches' philosophical assumptions, such as those pertaining to ontology and epistemology. Researchers need to be clear about the philosophical assumptions underpinning their studies and the effects that different approaches will have on the research results. CONCLUSION This paper presents a personal account of the journey of a novice grounded theory researcher who chose a grounded theory approach and worked within its theoretical parameters. IMPLICATIONS FOR RESEARCH/PRACTICE Novice grounded theory researchers need to understand the different philosophical assumptions that influence the various grounded theory approaches, before choosing one particular approach.
Adaptive and Efficient Peer Selection in Peer-to-Peer Streaming Networks

Nowadays Peer-to-Peer technologies for content distribution such as file-sharing and streaming media delivery are quite popular with Internet users. For P2P streaming applications, an appropriate peer selection scheme is critical to reduce startup delay and to provide media delivery of high quality. In this work, we propose a novel peer selection scheme AEPS that is both efficient and adaptive to dynamic P2P network. The AEPS combines the advantages of round-trip time based (RTT-based) schemes and available bandwidth based (ABW-based) schemes, to perform efficient and accurate selection. Experiments under three distinct scenarios are realized to quantitatively compare the AEPS with other selection schemes. The experiment results exhibit that the AEPS is more accurate than RTT-based schemes and more efficient than ABW-based schemes, achieving impressive performance in general.
Adult Tetralogy of Fallot: Quantitative Assessment of Pulmonary Perfusion With Time-Resolved Three Dimensional Magnetic Resonance Angiography

Purpose:To determine the potential role of dynamic temporally resolved three dimensional (3D) contrast-enhanced magnetic resonance angiography (MRA) for quantitative evaluation of pulmonary perfusion in adult patients with surgically treated Tetralogy of Fallot (ToF). Materials and Methods:Institutional review board approval and written informed consent were obtained for this Health Insurance Portability and Accountability Act–compliant study. Thirty consecutive patients with surgically repaired ToF and 30 age-matched controls underwent breath-hold 3D time-resolved MRA (TR-MRA) and single-phase high-resolution 3D MRA of the thorax at 1.5 T. Two readers evaluated both datasets for image quality and findings. On TR-MRA datasets, regions-of-interest were placed over main pulmonary artery and lung fields obtaining signal intensity time curves. Using analytic software, time-to-peak (TTP), mean transit time (MTT), maximal signal intensity (MSI), maximum upslope of the curve (MUS), pulmonary blood volume (PBV), and pulmonary blood flow (PBF) were calculated. Pulmonary radionuclide scintigraphy was available for a subgroup of patients with ToF (n = 12). Results:For ToF patients with unilateral pulmonary artery (PA) stenosis, TTP, and MTT were significantly longer, and MSI, MUS, PBV, and PBF were significantly lower in the ipsilateral lung compared with control subjects (P < 0.001 for all). There was no significant difference in TTP, MTT, MSI, MUS, PBV, and PBF between ToF patients without postsurgical stenotic residua and control subjects (P > 0.05 for all), nor between the mentioned perfusion indices for the contralateral lung in ToF patients with unilateral PA stenosis and control subjects (P > 0.05 for all). In ToF, patient with unilateral PA stenosis, analysis of contralateral-to-ipsilateral lung perfusion ratios on radionuclide scintigraphy and TR-MRA revealed significant correlation (r = 0.96). Bland-Altman plot showed a mean difference of 2.2% between the measured ratios (limits of agreement; −7.6%–12.0%). Conclusion:Time-resolved 3D contrast-enhanced MRA has potential for noninvasive and quantitative assessment of altered patterns of pulmonary perfusion in adult ToF, and may be a reliable technique for evaluation of postsurgical residua in these patients.
Genetic diversity of Toxoplasma gondii in animals and humans

Toxoplasma gondii is one of the most widespread parasites of domestic, wild, and companion animals, and it also commonly infects humans. Toxoplasma gondii has a complex life cycle. Sexual development occurs only in the cat gut, while asexual replication occurs in many vertebrate hosts. These features combine to create an unusual population structure. The vast majority of strains in North America and Europe fall into three recently derived, clonal lineages known as types I, II and III. Recent studies have revealed that South American strains are more genetically diverse and comprise distinct genotypes. These differences have been shaped by infrequent sexual recombination, population sweeps and biogeography. The majority of human infections that have been studied in North America and Europe are caused by type II strains, which are also common in agricultural animals from these regions. In contrast, several diverse genotypes of T. gondii are associated with severe infections in humans in South America. Defining the population structure of T. gondii from new regions has important implications for transmission, immunogenicity and pathogenesis.
Dynamic Multi-view, Multi-format, Multi-user Visualizations: For Future Cities

This paper introduces the concept of dynamic Multi-View, Multi-Format, Multi-User Visualizations. It also suggests aligning all visualization branches to a common problem, namely the design and implementation of future sustainable cities, such as Jakarta, Indonesia. While a lot of visualization research has extensively discussed the emotional, cognitive and coordinative benefits of visual representations, the application of such tools to solve grand societal problems has been neglected. We suggest focusing on Future Cities, since they require solutions and because the field seems to be ideal to align the various subgroups of visualization research. We derived this insight from about 1000 events in our physical value lab and our own software development - the Visual Manager and the Shuffler. The Visual Manager uses visual metaphors to illustrate risk assessment scenarios. The Shuffler is a framework to create coordinated multiple views. The innovative part of this framework is that different visual representations, complementary business logics and datasets can be distributed to different views, which calls for more transdisciplinary work in the design of dynamic multi-view, multi-format and multi-user software. This paper is relevant for researchers in all subgroups of visualization research - especially Knowledge Visualization and Information Visualization.
REVIEW OF DRESSING AND TRUING OPERATIONS FOR GRINDING WHEELS

Grinding is an operation applied in almost every type of manufacturing process. It aims to produce high surface finish and to maintain close tolerances in the manufactured product. To make the grinding operation more productive and efficient, dressing and truing operations are performed on the grinding wheels. Various techniques are available and are used for the same. Since many permutations and combinations exists among the factors like economics, efficiency, accuracy, complexity, etc. of the dressing process, so continuous efforts are made to develop or adopt a technique that gives the best result while fulfilling the maximum number of factors. This can be accomplished by comparing the present techniques on the same ground. With this aim, the unconventional techniques with in-process configuration were developed that have several advantages over their conventional counterparts.
Training Principals and Teachers for Mastery Learning.

The emphasis of the Denver Mastery Learning Program is on inservice. Project staff members train principals using methods and materials that the prin cipals will use later with their faculties. The training includes opportunities for them to discuss with project staff members any concerns or questions they may have and to brainstorm possible solutions. Topics for the inservice sessions are grouped under three headings: Planning for Mastery, Teaching for Mastery, and Managing a Mastery Learning Class room. The contributions of Benjamin Bloom, Lorin Anderson, James Block, and Madeline Hunter are re flected in the training. Two of the units are sequential, with each session applying the ideas presented in the previous sessions. Thus teachers are taken through a carefully planned systematic approach in how to plan a mastery unit and how to make it successful when they teach it. Each inservice session is conducted before or after school during a one-hour staff development meet ing. All sessions follow a similar format: the principal first discusses the main ideas with teachers and then has them participate in an application activity. These short, active sessions allow teachers to practice the ideas immediately so they can easily make the transfer to their own classrooms.
New frontiers for self research

Preface. About The Monograph Series. Part I: Overview. The New Frontier For Self Research, Herbert W. Marsh, Rhonda G. Craven, and Dennis M. Moinerney. Part II: Theoretical Issues. The Ontogeny Of Ability Self Concepts And Subjective Task Values. Jacquelynne S. Eccles. On The Relationships Between Explicit and Implicit Global Self-esteem and Personality, Jerry Suls and Zlatan Krizan. Self-efficacy and Self-concept Beliefs: Jointly Contributing To The Quality Of Human Life, Frank Pajares, and Dale H. Schunk. Do Self-beliefs Matter? Evidence From A Meta-analysis, Jeffrey C. Valentine and David L. Dubois. Self Theories In A Non-western Milieu: Ten Years of Research In The Arab Culture, Maher M. Abu Hilal. What Comes First? : A Reciprocal Effects Model of The Mutually Reinforcing Effects Of Academic Self-concept And Achievement, Herbert W. Marsh, and Rhonda G. Craven. Part III: Measurement Issues. Experiences With And Reflections On The Self-concept Construct Within An Historical Framework, William B. Michael and Joan J. Michael. Multiple Frames Of Reference: The Relation Among Academic Self-concept Interest And Academic Choices, Olaf Koller, Jurgen Baumert, and Ulrich Trautwein. Reconsidering The Measurement Of Student Self-concept: Use And Misuse, Alexander Seeshing Yeung. Self-esteem Success/pretensions: Assessing Pretensions/importance In Self-esteem, John Hattie and Richard Fletcher. Part IV: Applied Studies: Focus On Schooling. Self-concepts Of Indigenous And Non-indigenous Australian Students, Nola Purdle. Edifying Pathways To Walk The Dream: An Empirical Analysis of Indigenous Australian Students' Aspirations, Self-concepts, And Realities Rhonda G. Craven, and Herbert W. Marsh. Achievement-related Self-perceptions And The Reading Recovery Programme: A Longitudinal Study, James W. Chapman and William E. Tunmer. Factorial Structure And Comparison Between Obese And Non-obese Chinese Children's Physical Self-concept, K. T. Hau, R. Y. T. Sung, C. W. Yu, and P. W. C. Lau. Fear Of Failure In Students' Academic Lives: Exploring The Roles Of Self-handicapping And Defensive Pessimism, Andrew J. Martin. About The Editors. About The Contributors. Index.
Drosophila Mis12 Complex Acts as a Single Functional Unit Essential for Anaphase Chromosome Movement and a Robust Spindle Assembly Checkpoint

The kinetochore is a dynamic multiprotein complex assembled at the centromere in mitosis. Exactly how the structure of the kinetochore changes during mitosis and how its individual components contribute to chromosome segregation is largely unknown. Here we have focused on the contribution of the Mis12 complex to kinetochore assembly and function throughout mitosis in Drosophila. We show that despite the sequential kinetochore recruitment of Mis12 complex subunits Mis12 and Nsl1, the complex acts as a single functional unit. mis12 and nsl1 mutants show strikingly similar developmental and mitotic defects in which chromosomes are able to congress at metaphase, but their anaphase movement is strongly affected. While kinetochore association of Ndc80 absolutely depends on both Mis12 and Nsl1, BubR1 localization shows only partial dependency. In the presence of residual centromeric BubR1 the checkpoint still responds to microtubule depolymerization but is significantly weaker. These observations point to a complexity of the checkpoint response that may reflect subpopulations of BubR1 associated with residual kinetochore components, the core centromere, or elsewhere in the cell. Importantly our results indicate that core structural elements of the inner plate of the kinetochore have a greater contribution to faithful chromosome segregation in anaphase than in earlier stages of mitosis.