Miracle-dz/UniFAR-FTUs huggingface dataset:
Building an Adaptive Operating System for Predictability and Efficiency

We address the system-level challenge of supporting a dynamically changing, complex mix of simultaneously running applications with diverse requirements including responsiveness, throughput, and performance guarantees. In our approach, called Adaptive Resource Centric Computing (ARCC), the OS distributes resources to QoS domains called cells, which are explicitly parallel lightweight containers with guaranteed, user-level access to resources. The resource allocations are dynamically adjusted whenever applications change state or the mix of applications changes. This paper gives explicit details about our implementation of ARCC on Tessellation OS, an experimental platform for resource management on multicore-based computers. We discuss the implementation of cells, user-level scheduling, and resource allocation policies. Our running example is a realistic video conferencing scenario that incorporates parallelism, QoS guarantees, and dynamic optimization with two-level scheduling. Our system reduces reserved CPU bandwidth to 69.95% of that of a static allocation, while still meeting performance and QoS targets.
Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity.
Processing Moving kNN Queries Using Influential Neighbor Sets

The moving k nearest neighbor query, which computes one's k nearest neighbor set and maintains it while at move, is gaining importance due to the prevalent use of smart mobile devices such as smart phones. Safe region is a popular technique in processing the moving k nearest neighbor query. It is a region where the movement of the query object does not cause the current k nearest neighbor set to change. Processing a moving k nearest neighbor query is a continuing process of checking the validity of the safe region and recomputing it if invalidated. The size of the safe region largely decides the frequency of safe region recomputation and hence query processing efficiency. Existing moving k nearest neighbor algorithms lack efficiency due to either computing small safe regions and have to recompute frequently or computing large safe regions (i.e., an order-k Voronoi cell) with a high cost. In this paper, we take a third approach. Instead of safe regions, we use a small set of safe guarding objects. We prove that, as long as the the current k nearest neighbors are closer to the query object than the safe guarding objects, the current k nearest neighbors stay valid and no recomputation is required. This way, we avoid the high cost of safe region recomputation. We also prove that, the region defined by the safe guarding objects is the largest possible safe region. This means that the recomputation frequency of our method is also minimized. We conduct extensive experiments comparing our method with the state-of-the-art method on both real and synthetic data sets. The results confirm the superiority of our method.
Impact of Atlantic multidecadal oscillations on India/Sahel rainfall and Atlantic hurricanes

Prominent multidecadal fluctuations of India summer rainfall, Sahel summer rainfall, and Atlantic Hurricane activity have been observed during the 20th century. Understanding their mechanism(s) will have enormous social and economic implications. We first use statistical analyses to show that these climate phenomena are coherently linked. Next, we use the GFDL CM2.1 climate model to show that the multidecadal variability in the Atlantic ocean can cause the observed multidecadal variations of India summer rainfall, Sahel summer rainfall and Atlantic Hurricane activity (as inferred from vertical wind shear changes). These results suggest that to interpret recent climate change we cannot ignore the important role of Atlantic multidecadal variability.
Revisiting the silence of Asian immigrant students: The negotiation of Korean immigrant students' identities in science classrooms

Title of Document: REVISITING THE SILENCE OF ASIAN IMMIGRANT STUDENTS: THE NEGOTIATION OF KOREAN IMMIGRANT STUDENTS’ IDENTITIES IN SCIENCE CLASSROOMS Minjung Ryu, Ph.D., 2012 Directed By: Assistant Professor, Ann Ryu Edwards, Department of Teaching and Learning, Policy and Leadership This dissertation is a study about Korean immigrant students’ identities, including academic identities related to science learning and identities along various social dimensions. I explore how Korean immigrant students participate in science classrooms and how they enact and negotiate their identities in their classroom discursive participation. My dissertation is motivated by the increasing attention in educational research to the intersectionality between science learning and various dimensions of identities (e.g., gender, race, ethnicity, social networks) and a dearth of such research addressing Asian immigrant students. Asian immigrant students are stereotyped as quiet and successful learners, particularly in science and mathematics classes, and their success is often explained by cultural differences. I confront this static and oversimplified notion of cultural differences and Asians’ academic success and examine the intersectionality between science learning and identities of Asian immigrant students, with the specific case of Korean immigrants. Drawing upon cultural historical and sociolinguistic perspectives of identity, I propose a theoretical framework that underscores multiple levels of contexts (macro level, meso level, personal, and micro level contexts) in understanding and analyzing students’ identities. Based on a year-long ethnographic study in two high school Advanced Placement Biology classes in a public high school, I present the meso level contexts of the focal school and biology classes, and in-depth analyses of three focal students. The findings illustrate: (1) how meso level contexts play a critical role in these students’ identities and science classroom participation, (2) how the meso level contexts are reinterpreted and have different meanings to different students depending on their personal contexts, and (3) how students negotiated their positions to achieve certain identity goals. I discuss the implications of the findings for the science education of racially, ethnically, and linguistically diverse students, particularly given the increasing number of immigrant students in U.S. classrooms, and for the education of Asian immigrant students. REVISITING THE SILENCE OF ASIAN IMMIGRANT STUDENTS: THE NEGOTIATION OF KOREAN IMMIGRANT STUDENTS’ IDENTITIES IN SCIENCE CLASSROOMS
The choice modelling approach to environmental valuation

The authors contributing to the book show that choice modelling offers considerable potential for the evaluation of environmental goods and services. Its flexibility to cope with a wide range of applications is well demonstrated. The technique also presents numerous challenges to practitioners. A number of these are addressed in the book. Informed and innovative, this book will prove indispensable to all scholars, researchers and practitioners in the areas of environmental studies and environmental economics.
Experimental demonstration of accelerated extinction in source-sink metapopulations

Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source-sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source-sink effects in laboratory populations of Daphnia magna. Time-to-extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed that source-sink configurations increased population variability (the coefficient of variation in abundance) and extinction hazard compared with homogeneous environments. These results suggest that where environments are spatially heterogeneous, accurate assessments of extinction risk will require understanding the exchange of organisms among population sources and sinks. Such heterogeneity may be the norm rather than the exception because of both the intrinsic heterogeneity naturally exhibited by ecosystems and increasing habitat fragmentation by human activity.
Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling

Accurate modelling of biological systems requires a deeper and more complete knowledge about the molecular components and their functional associations than we currently have. Traditionally, new knowledge on protein associations generated by experiments has played a central role in systems modelling, in contrast to generally less trusted bio-computational predictions. However, we will not achieve realistic modelling of complex molecular systems if the current experimental designs lead to biased screenings of real protein networks and leave large, functionally important areas poorly characterised. To assess the likelihood of this, we have built comprehensive network models of the yeast and human proteomes by using a meta-statistical integration of diverse computationally predicted protein association datasets. We have compared these predicted networks against combined experimental datasets from seven biological resources at different level of statistical significance. These eukaryotic predicted networks resemble all the topological and noise features of the experimentally inferred networks in both species, and we also show that this observation is not due to random behaviour. In addition, the topology of the predicted networks contains information on true protein associations, beyond the constitutive first order binary predictions. We also observe that most of the reliable predicted protein associations are experimentally uncharacterised in our models, constituting the hidden or “dark matter” of networks by analogy to astronomical systems. Some of this dark matter shows enrichment of particular functions and contains key functional elements of protein networks, such as hubs associated with important functional areas like the regulation of Ras protein signal transduction in human cells. Thus, characterising this large and functionally important dark matter, elusive to established experimental designs, may be crucial for modelling biological systems. In any case, these predictions provide a valuable guide to these experimentally elusive regions.
How To Withstand Mobile Virus Attacks

We initiate a study of distributed adversarial model of computation in which faults are non-stationary and can move through the network, analogous to a spread of a virus or a worm. We show how local computations (at each processor) and global computations can be made robust using a constant factor resilience and a polynomial factor redundancy in the computation.
Mechanical Strength and Viscoelastic Response of the Periodontal Ligament in Relation to Structure

The mechanical strength of the periodontal ligament (PDL) was first measured as force required to extract a tooth from its socket using human specimens. Thereafter, tooth-PDL-bone preparations have extensively been used for measurement of the mechanical response of the PDL. In vitro treatments of such specimens with specific enzymes allowed one to investigate into the roles of the structural components in the mechanical support of the PDL. The viscoelastic responses of the PDL may be examined by analysis of the stress-relaxation. Video polarised microscopy suggested that the collagen molecules and fibrils in the stretched fibre bundles progressively align along the deformation direction during the relaxation. The stress-relaxation process of the PDL can be well expressed by a function with three exponential decay terms. Analysis after in vitro digestion of the collagen fibres by collagenase revealed that the collagen fibre components may play an important role in the long-term relaxation component of the stress-relaxation process of the PDL. The dynamic measurements of the viscoelastic properties of the PDL have recently suggested that the PDL can absorb more energy in compression than in shear and tension. These viscoelastic mechanisms of the PDL tissue could reduce the risk of injury to the PDL.
Entropy of the intracluster medium at high redshift

Recent observations of the entropy of the intracluster medium (ICM) at high redshift are not consistent with a redshift-independent entropy floor. To interpret these observations, we study models in which the entropy of ICM is enhanced at the epoch of cluster formation (zf), which then passively evolves as a result of radiative cooling until the epoch of observation (zo). We confirm that a z-independent entropy floor is incompatible with the observations. We find that models in which energy deposition into the ICM increases with redshift [scaling approximately as ∼M 0.6 (1 + z f) 2.2 ] are consistent with observations of low- and high-redshift clusters. Possible sources of such non-gravitational heating are briefly discussed.
Enabling Tissue-Scale Cardiac Simulations Using Heterogeneous Computing on Tianhe-2

We develop a simulator for 3D tissue of the human cardiac ventricle with a physiologically realistic cell model and deploy it on the supercomputer Tianhe-2. In order to attain the full performance of the heterogeneous CPU-Xeon Phi design, we use carefully optimized codes for both devices and combine them to obtain suitable load balancing. Using a large number of nodes, we are able to perform tissue-scale simulations of the electrical activity and calcium handling in millions of cells, at a level of detail that tracks the states of trillions of ryanodine receptors. We can thus simulate arrythmogenic spiral waves and other complex arrhythmogenic patterns which arise from calcium handling deficiencies in human cardiac ventricle tissue. Due to extensive code tuning and parallelization via OpenMP, MPI, and SCIF/COI, large scale simulations of 10 heartbeats can be performed in a matter of hours. Test results indicate excellent scalability, thus paving the way for detailed whole-heart simulations in future generations of leadership class supercomputers.
Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations

Synchronization between neuronal populations plays an important role in information transmission between brain areas. In particular, collective oscillations emerging from the synchronized activity of thousands of neurons can increase the functional connectivity between neural assemblies by coherently coordinating their phases. This synchrony of neuronal activity can take place within a cortical patch or between different cortical regions. While short-range interactions between neurons involve just a few milliseconds, communication through long-range projections between different regions could take up to tens of milliseconds. How these heterogeneous transmission delays affect communication between neuronal populations is not well known. To address this question, we have studied the dynamics of two bidirectionally delayed-coupled neuronal populations using conductance-based spiking models, examining how different synaptic delays give rise to in-phase/anti-phase transitions at particular frequencies within the gamma range, and how this behavior is related to the phase coherence between the two populations at different frequencies. We have used spectral analysis and information theory to quantify the information exchanged between the two networks. For different transmission delays between the two coupled populations, we analyze how the local field potential and multi-unit activity calculated from one population convey information in response to a set of external inputs applied to the other population. The results confirm that zero-lag synchronization maximizes information transmission, although out-of-phase synchronization allows for efficient communication provided the coupling delay, the phase lag between the populations, and the frequency of the oscillations are properly matched.
A Unified Approach to Distributed Concurrency Control

A unified model for distributed concurrency control is presented, which enables the system to utilise the semantics of an application. We assume that concurrent accesses to data are made by transactions and that data objects are instances of abstract types. The semantics of an application is given to the system by the application programmer using a specification language. In this way any change in the requirements for concurrent access can be introduced and utilised with the minimum of effort made by the programmer. The model suggests a uniform approach to implementing atomic objects. We address both the problems of synchronising operations invoked by transactions on objects and the problem of synchronising transactions, so that their execution satisfies the correctness criterion of serialisability. We show that a wide range of protocols can be implemented using this model: existing concurrency control protocols for distributed environments can be obtained, as well as hybrid protocols that combine features of the former. By separating the scheduler module into two different modules which perform the local synchronisation of operations invoked on objects by transactions and the synchronisation of transactions, respectively, the problem of incompatibility of protocols is overcome and different protocols are permitted within the same application at the same time.
A dynamic hybrid scheduling algorithm with clients' departure for impatient clients in heterogeneous environments

The essence of efficient scheduling and data transmission techniques lies in providing the Web-applications with advanced data processing capabilities. In this paper we have efficiently combined the push and the pull scheduling to develop a new, practical, dynamic, hybrid scheduling strategy for heterogenous, asymmetric environments. The proposed algorithm dynamically computes the probabilities and the optimal cutoff-point to separate the push and the pull data sets. The data items are also assumed to be of variable lengths. While the push strategy uses the flat, round-robin scheduling, the pull items are determined by stretch-optimal (max-request min-service time) scheduling policy. In order to make the scheduling more practical, we have considered the impact of the impatience of the clients waiting to get the service of a particular data item. The effects of this impatience can lead to departure of specific client(s) from the system. Our proposed hybrid scheduling strategy takes care of these effects to capture a real portrayal of the system dynamics. These scenarios are modelled by suitable birth and death process to analyze the overall expected delay of the system. Subsequently, simulation results corroborate the average system performance and points out significant improvement over existing hybrid systems in terms of average waiting time spent by a client.
Information Seeking: An Organizational Dilemma

From the Publisher: How do people in organizations get the information they need to do their work, and what are the effects of their research - positive and negative - on their organizations? Indeed, says the author of this unique, provocative study, the forces that promote ignorance within organizations often outweigh the drive to obtain knowledge. Johnson explores both sides of the information-seeking dilemma, the reasons why people do and do not look for and get the information they need - and why the multi-billion-dollar technologies that have been developed to facilitate information gathering so often fail. Research-based, with a model to explain how information seeking works in organizations, Dr. Johnson's book is fascinating, essential reading not only for gatherers of information in all types of organizations, but for the purveyors, their technological support staffs.
What is the Cosmic-Ray Luminosity of Our Galaxy?

The total cosmic-ray luminosity of the Galaxy is an important constraint on models of cosmic-ray generation. The diffuse high-energy γ-ray and radio synchrotron emissions of the Milky Way are used to derive this luminosity. The result is almost 2 orders of magnitude larger than the standard estimate, based on the observed isotopic abundances of cosmic-ray nuclides. We discuss the plausible interpretation of this discrepancy and the possible origin of such a relatively large luminosity.
Expecting More in Relationships – Implications of Relational Entitlement

Abstract Sense of relational entitlement refers to what individuals’ believe they “should” expect from their romantic partner. When expectations are both unrealistic and not met by one’s partner, there is a potential for adverse consequences. Researchers surveyed 195 female participants between the ages 18-60. The study examined the influence of one’s sense of relational entitlement with varying conflict strategies. The findings revealed that extreme forms of one’s sense of relational entitlement was associated with conflict strategies like verbal aggression, and control & domination. Thus, one’s sense of relational entitlement appears to play a significant role in how individuals handle conflict.