Miracle-dz/UniFAR-FTUs huggingface dataset:
Trophic Controls on Stage Transformations of a Toxic Ambush‐Predator Dinoflagellate 1

ABSTRACT. The toxic dinoflagellate, Pfiesteria piscicida, was recently implicated as the causative agent for about 50% of the major fish kills occurring over a three‐year period in the Albemarle‐Pamlico Estuarine System of the southeastern USA. Transformations between life‐history stages of this dinoflagellate are controlled by the availability of fresh fish secretions or fish tissues, and secondarily influenced by the availability of alternate prey including bacteria, algae, microfauna, and mammalian tissues. Toxic zoospores of P. piscicida subdue fish by excreting lethal neurotoxins that narcotize the prey, disrupt its osmoregulatory system, and attack its nervous system. While prey are dying, the zoospores feed upon bits of fish tissue and complete the sexual phase of the dinoflagellate life cycle. Other stages in the complex life cycle of P. piscidia include cryptic forms of filose, rhizopodial, and lobose amoebae that can form within minutes from toxic zoospores, gametes, or planozygotes. These cryptic amoebae feed upon fish carcasses and other prey and, thus far, have proven less vulnerable to microbial predators than flagellated life‐history stages. Lobose amoebae that develop from toxic zoospores and planozygotes during colder periods have also shown ambush behavior toward live fish. In the presence of abundant flagellated algal prey, amoeboid stages produce nontoxic zoospores that can become toxic and form gametes when they detect what is presumed to be a threshold level of a stimulatory substance(s) derived from live fish. The diverse amoeboid stages of this fish “ambush‐predator” and at least one other Pfiesteria‐like species are ubiquitous and abundant in brackish waters along the western Atlantic and Gulf Coasts, indicating a need to re‐evaluate the role of dinoflagellates in the microbial food webs of turbid nutrient‐enriched estuaries.
Simple Cache Partitioning for Networked Workloads

Modern datacenters often run a mix of latency-sensitive and throughput-oriented workloads, which are consolidated onto the same physical machines to improve resource utilization. Performance isolation under these conditions is an important component in satisfying service level objectives (SLOs). This paper examines cache partitioning as a mechanism to meet latency targets. Cache partitioning has been studied extensively in prior work; however, its effectiveness is not well understood for modern datacenter applications that enjoy recent improvements in low-latency networking, such as stack bypass and faster underlying technologies (e.g., DPDK, InfiniBand). These applications have tight tail latency SLOs of tens to hundreds of microseconds. We find that cache partitioning is effective in achieving performance isolation among diverse workload mixes for such environments, without requiring complex configurations or online controllers. On our modern multi-core server using Intel Cache Allocation Technology, we show that cache partitioning can protect the performance of latency-sensitive networked applications from local resource contention. Our code is publicly available on Github.
The Relative Importance of Strength and Balance in Chair Rise by Functionally Impaired Older Individuals

OBJECTIVE: The ability to stand independently and safely from the seated position is essential for independent function. This investigation determined the relative contributions of measures of lower extremity strength and measures of balance control in explaining the performance characteristics of sitting‐to‐standing. Variables analyzed included those related to success of the activity (e.g., time to rise, lowest chair height) and to biomechanical characteristics of performance (e.g., how fast specific body segments moved).
A Stimulating Experience

The purpose of this study was to examine the views of international Science Olympiad participants on the benefits of the competition and the factors that affected their career aspirations. We also investigated how students’ choice of competition category varied with respect to gender. The sample included 273 International Sustainable World Energy, Engineering, and Environment Project (I-SWEEEP) participants from 39 countries. Mixed-methods were used to analyze the data. Descriptive statistics and t-statistics were provided to answer the first question. As a means of addressing the second question, a chi-square test was utilized to examine how participants’ category selection differed by gender. Qualitative analysis was used to reveal the types of benefits students reaped from participation in the I-SWEEEP. Results indicated that students were most affected by their teachers, parents, and personal interests. Although the relationship between gender and competition category was not statistically significant, there nevertheless emerged a pattern showing that girls preferred environmental science projects (45.5%) to engineering projects (24.4%). Qualitative analyses revealed six themes as benefits that students gained from participation in the I-SWEEEP. The relationship among the fundamental themes was also examined and revealed important findings. The results have educational implications for helping students accomplish to be science, technology, engineering, and mathematics (STEM) professionals in the future.
Religiously friendly democracy: Framing political and religious identities in Catholic and Muslim societies

by Michael Daniel Driessen This research project explores the relationship between faith and nation, and the institutional entanglements of religion, state and democracy in Catholic and Muslim societies. It is specifically animated by the following research question: What are the effects of bringing religion into the public sphere in new democracies, especially those whose theological values are considered to be hostile to democratic precepts? My analysis presents a theory for modeling the dynamics which are created when states allow hostile religions more access to the political and public spheres during moments of democratization (or lesser forms of political liberalization) by a) allowing religious political parties to contest elections and b) biasing religion-state arrangements in favor of religion. Drawing from more than eighteen months of field research in Italy and Algeria, I test the mechanisms of my theory through in-depth case studies in both a Catholic and Islamic setting and then use cross-national data on religion-state arrangements by Grim and Finke (2006) and Fox (2008) to statistically explore the theory‟s wider explanatory weight.
Tsc2 Null Murine Neuroepithelial Cells Are a Model for Human Tuber Giant Cells, and Show Activation of an mTOR Pathway

Cortical tubers are developmental brain malformations in the tuberous sclerosis complex (TSC) that cause epilepsy and autism in TSC patients whose pathogenesis is uncertain. Tsc2 null murine neuroepithelial progenitor (NEP) cells display persistent growth when growth factors are withdrawn, express GFAP at high levels, and have reduced expression of a set of early neuronal lineage markers. Tsc2 null NEP cells exhibit aberrant differentiation into giant cells that express both beta III-tubulin and GFAP and that are morphologically similar to giant cells in human tubers. Tsc2 null giant cells and tuber giant cells have similar transcriptional profiles. Tsc2 null NEP cells express high levels of phosphorylated S6kinase, S6, Stat3, and 4E-BP-1, which is reversed by treatment with rapamycin, an inhibitor of mTOR. We conclude that giant cells in human tubers likely result from a complete loss of TSC2 expression and activation of an mTOR pathway during cortical development.
Motivational State Influences the Content of Hippocampal Sequences

Hippocampal sharp wave-ripple (SWR) associated sequence activity, commonly referred to as replay, has generally been thought of as mediating the transfer of recent experience into the neocortex. However, a number of recent studies have shown that the content of sequences is not limited to recent experience. To investigate whether internally generated stimuli, such as appetitive motivational states, affect the content of SWR-associated spiking activity, we recorded from ensembles of CA1 place cells while rats were performing a motivational shift task on a simple T-maze. Rats were food restricted or water restricted on alternating days and trained to make a left turn for food and right turn for water. We found that SWR-associated spiking activity recorded prior to task performance was correlated with motivational state and overall behavioural choices, suggesting that it also mediates retrieval of past behavioural episodes to facilitate planning for motivationally relevant outcomes.
DETECTION OF SHALLOWLY BURIED LANDMINES FROM GROUND PENETRATING RADAR SIGNALS

A method for detecting shallowly buried landmines using sequential GPR data is presented. After removing dominant coherent component of ground surface reflection from GPR data, three kinds of target features related to wave correlation, energy ratio, and signal arrival times are extracted. Since the detection problem treated here is reduced to a binary hypothesis test, an approach based on a likelihood ratio test is employed as a detection algorithm. In order to check the detection performance, the Monte Carlo simulation is carried out for data generated by the two-dimensional finite difference time domain (FDTD) method. The results given in the form of ROC curves show that good performance is obtained in spite of simple three-dimensional feature vector.
User Interactive MPEG-4 Compatible Facial Animation System

This paper describes different processes and their interactions needed to generate a virtual environment inhabited by a clone representing real people and virtual autonomous actors. It requires communication between a cloned face (or avatar) and virtual face. This needs the cloning and mimicking aspects to reconstruct the 3D model and movements of the real face. The autonomous virtual face is able to respond and interact through facial expressions and speech. Several main processing are necessary to reach this goal. The processing of the input data is crucial since it represents the only interaction of the user with the virtual world and autonomous actor. We have implemented the processing of the two basic media used in a dialog, which are speech and facial expressions. We also discuss about the implementation of the emotionally autonomous actor. Finally we give a description of the real-time facial animation system. The whole system is based on the MPEG-4 definition of FAP, visemes and expressions.
Examining the Treatment Validation Consultation Model

ABSTRACT The present article explores the utility and feasibility of treatment validation consultation (TVC). Although evidence exists for behavioral consultation, few findings have been reported for TVC. TVC is based on core components of behavioral consultation, but has several unique characteristics. In this article, TVC is situated within the behavioral consultation literature; one case study is used to demonstrate TVC’s utility and feasibility; and considerations for future TVC research are explored.
Injectivity Conditions of 2D and 3D Uniform Cubic B-Spline Functions

Uniform cubic B-spline functions have been used for mapping functions in various areas such as image warping and morphing, 3D deformation, and volume morphing. The injectivity (one-to-one property) of a mapping function is crucial to obtaining desirable results in these areas. This paper considers the injectivity conditions of 2D and 3D uniform cubic B-spline functions. We propose a geometric interpretation of the injectivity of a uniform cubic B-spline function, with which 2D and 3D cases can be handled in a similar way. Based on our geometric interpretation, we present sufficient conditions for injectivity which are represented in terms of control point displacements. These sufficient conditions can be easily tested and will be useful in guaranteeing the injectivity of mapping functions in application areas.
Gateway selection in multi-hop wireless networks

This thesis describes the implementation of MultiNAT, an application that attempts to provide the benefits of client multi-homing while requiring minimal client configuration, and the evaluation of a novel link-selection algorithm, called AvMet, that significantly outperforms earlier multi-homing methods. The main motivation behind MultiNAT is the growing popularity of cheap broadband Internet connections, which are still not reliable enough for important applications. The increasing prevalence of wireless networks, with their attendant unpredictability and high rates of loss, is further exacerbating the situation. Recent work has shown that multi-homing can increase both Internet performance as well as the end-to-end availability of Internet services. Most previous solutions have required complicated client configuration or have routed packets through dedicated overlay networks; MultiNAT attempts to provide a simpler solution. MultiNAT automatically forwards connection attempts over all local interfaces and uses the resulting connection establishment times along with link-selection metrics to select which interface to use. MultiNAT is able to sustain transfer speeds in excess of 4 megabytes per second, while imposing only an extra 150 microseconds of latency per packet. MultiNAT supports a variety of link-selection metrics, each with its own strengths and weaknesses. The MONET race-based scheme works well in wired networks, but is misled by the unpredictable nature of wireless losses. The ETT metric performs relatively well at finding high-throughput paths in multi-hop wireless networks, but can be incorrect when faced with heavy load. Unfortunately, neither of these metrics address end-to-end performance when packets traverse both wired and wireless networks. To fill this need, we propose AvMet, a link-selection scheme that tracks past connection history in order to improve current predictions. We evaluate AvMet on a variety of network configurations and find that AvMet is not misled by wireless losses. AvMet is able to outperform existing predictors in all network configurations and can improve end-to-end availability by up to half an order of magnitude. Thesis Supervisor: Hari Balakrishnan Title: Associate Professor
Differentiation of embryonic stem cells into hepatocytes: Biological functions and therapeutic application

Embryonic stem (ES) cells provide a unique source for tissue regeneration. We examined whether mouse ES cells can efficiently differentiate into transplantable hepatocytes. ES cells were implanted into mouse livers 24 hours after carbon tetrachloride intoxication; ES‐derived cells with several hepatocyte‐cell‐markers were generated. They were able to grow in vitro and showed morphology consistent with typical mature hepatocytes and expressed hepatocyte‐specific genes. After transplantation into the carbon tetrachloride‐injured mouse liver, ES‐derived green fluorescent protein‐positive cells were incorporated into liver tissue and rescued mice from hepatic injury. No teratoma formation was observed in the transplant recipients. In conclusion, ES cells can provide a valuable tool for studying the molecular basis for differentiation of hepatocytes and form the basis for cell therapies.
An Evolutionary Analysis of Antigen Processing and Presentation across Different Timescales Reveals Pervasive Selection

The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses.
Exploring Dimensions of Advocacy in Service: A Content Analysis Extending the Framework of Counselor Community Engagement Activities in Chi Sigma Iota Chapters

ABSTRACT Counselor Community Engagement (CCE) is a collaborative process whereby counselors and community members identify, plan, and execute strategies that promote wellness and human dignity within the community. Although Chi Sigma Iota (CSI) has an established framework for CCE inspired by Dr. Jane E. Myers (10 Key Considerations), no study has explored the use of this framework in practice. Using directive content analysis methodology, these researchers examined the 2013–2014 CSI Chapter CCE activities (n = 247), confirming the degree to which the 10 Key Considerations reflect CCE activities and refining the framework to support purposeful engagement and advocacy with individuals, groups, and communities. Implications for practice and suggestions for future research are provided.
Robust Multipoint Simultaneous Identical-by-Descent Mapping for Two Linked Loci

A challenging issue in genetic mapping of complex human diseases is localizing disease susceptibility genes when the genetic effects are small to moderate. There are greater complexities when multiple loci are linked to a chromosomal region. Liang et al. [Hum Hered 2001;51:64–78] proposed a robust multipoint method that can simultaneously estimate both the position of a trait locus and its effect on disease status by using affected sib pairs (ASPs). Based on the framework of generalized estimating equations (GEEs), the estimate and standard error of the position of a trait locus are robust to different genetic models. To utilize other relative pairs collected in pedigree data, Schaid et al. [Am J Hum Genet 2005;76:128–138] extended Liang’s method to various types of affected relative pairs (ARPs) by two approaches: unconstrained and constrained methods. However, the above methods are limited to situations in which only one trait locus exists on the chromosome of interest. The mean functions are no longer correctly specified when there are multiple causative loci linked to a chromosomal region. To overcome this, Biernacka et al. [Genet Epidemiol 2005;28:33–47] considered the multipoint methods for ASPs to allow for two linked disease genes. We further generalize the approach to cover other types of ARPs. To reflect realistic situations for complex human diseases, we set modest sizes of genetic effects in our simulation. Our results suggest that several hundred independent pedigrees are needed, and markers with high information, to provide reliable estimates of trait locus positions and their confidence intervals. Bootstrap resampling can correct the downward bias of the robust variance for location estimates. These methods are applied to a prostate cancer linkage study on chromosome 20 and compared with the results for the one-locus model [Am J Hum Genet 2005;76:128–138]. We have implemented the multipoint IBD mapping for one and two linked loci in our software GEEARP, which allows analyses for five general types of ARPs.
On relative observability of discrete-event systems

We identify a new observability concept, called relative observability, in supervisory control of discrete-event systems under partial observation. A fixed, ambient language is given, relative to which observability is tested. Relative observability is stronger than observability, but enjoys the important property that it is preserved under set union; hence there exists the supremal relatively observable sublanguage of a given language. Relative observability is weaker than normality, and thus yields, when combined with controllability, a generally larger controlled behavior; in particular, no constraint is imposed that only observable controllable events may be disabled. We present algorithms which compute the supremal relatively observable (and controllable) sublanguage of a given language, which is generally larger than the normal counterparts. We demonstrate the new observability concept and algorithms with a Guideway example.
Lifetime of OH masers at the tip of the asymptotic giant branch

Context. A large fraction of otherwise similar asymptotic giant branch stars (AGB) do not show OH maser emission. As shown recently, a restricted lifetime may give a natural explanation as to why only part of any sample emits maser emission at a given epoch. Aims. We wish to probe the lifetime of 1612 MHz OH masers in circumstellar shells of AGB stars. Methods. We reobserved a sample of OH/IR stars discovered more than 28 years ago to determine the number of stars that may have since lost their masers. Results. We redetected all 114 OH masers. The minimum lifetime inferred is 2800 years (1σ). This maser lifetime applies to AGB stars with strong mass loss leading to very red infrared colors. The velocities and mean flux density levels have not changed since their discovery. As the minimum lifetime is of the same order as the wind crossing time, strong variations in the mass-loss process affecting the excitation conditions on timescales of ≈3000 years or less are unlikely.