Miracle-dz/UniFAR-FTUs huggingface dataset:
Deerpox Virus Encodes an Inhibitor of Apoptosis That Regulates Bak and Bax

ABSTRACT Poxviruses encode numerous proteins that inhibit apoptosis, a form of cell death critical to the elimination of virally infected cells. Sequencing of the deerpox virus genome revealed DPV022, a protein that lacks obvious homology to cellular members of the Bcl-2 family but shares limited regions of amino acid identity with two unique poxviral inhibitors of apoptosis, M11L and F1L. Given the limited homology, we sought to determine whether DPV022 could inhibit apoptosis. Here we show that DPV022 localized to the mitochondria, where it inhibited apoptosis. We used a Saccharomyces cerevisiae model system to demonstrate that in the absence of all other Bcl-2 family proteins, DPV022 interacted directly with Bak and Bax. We confirmed the ability of DPV022 to interact with Bak and Bax by immunoprecipitation and showed that DPV022 prevented apoptosis induced by Bak and Bax overexpression. Moreover, we showed that DPV022 blocked apoptosis even when all the endogenous mammalian antiapoptotic proteins were neutralized by a combination of selective BH3 ligands. During virus infection, DPV022 interacted with endogenous Bak and Bax and prevented the conformational activation of both of them. Thus, we have characterized a novel poxviral inhibitor of apoptosis with intriguing amino acid differences from the well-studied proteins M11L and F1L.
Investigation of the c-Si/Al2O3 Interface for Silicon Surface Passivation

The role of the SiO2 interface for Al2O3 passivation layers on p-type Silicon is investigated. Thin (0.6-6.0 nm) SiO2 layers were prepared by means of HF etch and thermal oxidation on c-Si wafers prior to the Atomic Layer Deposition (ALD) of Al2O3. Subsequently, the Al2O3 layer was deposited and annealed and the films were characterized using Microwave Detected Photoconductivity (MDP), Fourier Transform InfraRed (FTIR) and Capacitance-Voltage (C(V)) measurements. The best passivation effect was found for a 2.0 nm SiO2 interface. Thicker interfaces reduce the effective minority carrier lifetime due to the formation of positive charges in the dielectric. C(V) hysteresis curves show that the charge density in Al2O3 is not stable but a function of the applied bias voltage and thickness of the SiO2 interface. The change in charge density could be described by trapping of electrons from Si into Al2O3 with SiO2 acting as a tunnel barrier. Since trapped electrons are part of the negative charges in Al2O3, a thin SiO2 interface is required to realize the high field effect passivation of Al2O3
Biomass and mass balance isotope content of mussel seep populations

iv Chapter 1: Introduction to the Hydrocarbon Seep System of the Northern Gulf of Mexico . 1 1.1 In the Context of Deep Trophic Systems . 1 1.2 Consequences to Stable Isotope Composition . 1 1.3 Underlying Geological Processes as a Source of Variation. 2 1.4 Upper-slope Seep Foundation Species Bathymodiolus childressi . 3 1.5 State of Knowledge of the Two Sites Sampled in This Study . 6 1.6 Sampling Design . 7 1.7 Stable Isotopes . 7 1.8 Three Isotopes, Three Values, One Source . 12 1.9 Objectives . 12 Chapter 2: Site-Specific Incorporation of Methane-Derived Respiratory Carbon in the Shells of the Seep Mussel Bathymodiolus childressi. 13 2.
Quantifying the Effects of Removing Permissions from Android Applications

With the growing popularity of Android smart phones, it is increasingly important to ensure the security of sensitive user information. A recent study found that approximately 26% of Android applications in Google Play can access personal data, such as contacts and email, and 42 percent, GPS location data [6]. While Android is known for giving the user control, it falls short when it comes to enabling and disabling the permissions on applications. Currently, the user is given the option to either give the application every permission it desires or not install it. While researchers have proposed approaches for allowing users to modify the permissions granted to applications, it is unclear how removing permissions would affect the behavior of current applications. At present, developers expect all requested permissions to be granted. In this paper, we take the first step to quantify the impact of enabling users to statically remove permissions on Android applications post-installation. We developed Pyandrazzi, a system for evaluating the effect of removing individual permissions from applications. Using Pyandrazzi, we evaluated how removing seven common permissions affect a set of randomly selected applications that request them. We found that approximately 5.8% of the 700 applications we tested crash after a permission is removed and investigated how the lack of certain permissions are handled more gracefully than others. Our results will help users make more informed decisions when removing permissions and help developers make their applications more robust to permission revocation.
Using Student Achievement Data to Support Instructional Decision Making

The Institute of Education Sciences (IES) publishes practice guides in education to bring the best available evidence and expertise to bear on the types of challenges that cannot currently be addressed by a single intervention or program. Authors of practice guides seldom conduct the types of systematic literature searches that are the backbone of a meta-analysis, although they take advantage of such work when it is already published. Instead, authors use their expertise to identify the most important research with respect to their recommendations and conduct a search of recent publications to ensure that the research supporting the recommendations is up-to-date. Unique to IES-sponsored practice guides is that they are subjected to rigorous external peer review through the same office that is responsible for independent reviews of other IES publications. A critical task for peer reviewers of a practice guide is to determine whether the evidence cited in support of particular recommendations is up-to-date and that studies of similar or better quality that point in a different direction have not been ignored. Because practice guides depend on the expertise of their authors and their group decision making, the content of a practice guide is not and should not be viewed as a set of recommendations that in every case depends on and flows inevitably from scientific research. The goal of this practice guide is to formulate specific and coherent evidence-based recommendations for use by educators and education administrators to create the organizational conditions necessary to make decisions using student achievement data in classrooms, schools, and districts. The guide provides practical, clear information on critical topics related to data-based decision making and is based on the best available evidence as judged by the panel. Recommendations presented in this guide should not be construed to imply that no further research is warranted on the effectiveness of particular strategies for data-based decision making. Disclaimer The opinions and positions expressed in this practice guide are the authors' and do not necessarily represent the opinions and positions of the Institute of Education Sciences or the U.S. Department of Education. This practice guide should be reviewed and applied according to the specific needs of the educators and education agency using it, and with the full realization that it represents the judgments of the review panel regarding what constitutes sensible practice, based on the research available at the time of publication. This practice guide should be used …
Complex Services and According Business Models -- Design and Evaluation of an Analysis Framework in the Field of Telemedicine

Successful business models in the field of complex services are rare and often not profitable so far. In this design science research paper, we build and evaluate an analysis framework for such business models using the exemplary field of telemedicine. The framework is a morphological box. Its dimensions are derived from existing literature. In a second iteration and after applying it to 16 services, it is refined. The resulting artifact reveals three types of typical business model: enablers, supporters and patient-centered innovators. Besides the identification of these types, the framework allows service providers for the delimitation of own business models to others, for assessing competitors and consequently for the informed design of features leading to competitive advantages. The framework's structure allows for the elicitation of white spots -- so far not existing patterns -- for future business models and facilitates the provider's strategic positioning within the market and potential future adaptations.
Interference mitigation using transmitter filters in CDMA systems

We consider the use of transmitter filters as pre-equalizers at the base station to mitigate the interference in code division multiple access (CDMA) systems over multipath fading channels. It is shown that the transmitter filters can mitigate the. interference and thereby the capacity can be improved. The minimum variance distortionless response (MVDR) beamforming technique in antenna arrays is utilized to find the coefficients of the interference mitigation (IM) transmitter filters. To design the IM transmitter filters, we assume that the channel information is available.
Energy balance‐related behaviours associated with overweight and obesity in preschool children: a systematic review of prospective studies

The current review aimed to systematically identify dietary, physical activity and sedentary behaviours in preschool children (4–6 years of age) that are prospectively related to overweight or obesity later in childhood. Prospective studies published between January 1990 and June 2010 were selected from searches in PubMed, EMBASE, PsycINFO, CINAHL and Cochrane Library. Studies examining the prospective association between at least one relevant behaviour measured during preschool period (children aged 4–6 years at baseline) in relation to at least one anthropometric measurement at follow‐up (age <18 years) were included. Harvest plots were used to summarize the results and draw conclusions from the evidence.
Effects of Experimental Choices and Analysis Noise on Surveys of the “Rare Biosphere”

ABSTRACT When planning a survey of 16S rRNA genes from a complex environment, investigators face many choices including which primers to use and how to taxonomically classify sequences. In this study, we explored how these choices affected a survey of microbial diversity in a sample taken from the aerobic basin of the activated sludge of a North Carolina wastewater treatment plant. We performed pyrosequencing reactions on PCR products generated from primers targeting the V1-V2, V6, and V6-V7 variable regions of the 16S rRNA gene. We compared these sequences to 16S rRNA gene sequences found in a whole-genome shotgun pyrosequencing run performed on the same sample. We found that sequences generated from primers targeting the V1-V2 variable region had the best match to the whole-genome shotgun reaction across a range of taxonomic classifications from phylum to family. Pronounced differences between primer sets, however, occurred in the “rare biosphere” involving taxa that we observed in fewer than 11 sequences. We also examined the results of analysis strategies comparing a classification scheme using a nearest-neighbor approach to directly classifying sequences with a naïve Bayesian algorithm. Again, we observed pronounced differences between these analysis schemes in infrequently observed taxa. We conclude that if a study is meant to probe the rare biosphere, both the experimental conditions and analysis choices will have a profound impact on the observed results.
Two Algorithms for Inducing Causal Models from Data

Many methods have been developed for inducing cause from statistical data. Those employing linear regression have historically been discounted, due to their inability to distinguish true from spurious cause. We present a regression-based statistic that avoids this problem by separating direct and indirect influences. We use this statistic in two causal induction algorithms, each taking a different approach to constructing causal models. We demonstrate empirically the accuracy of these algorithms.
Network Morphism

We present a systematic study on how to morph a well-trained neural network to a new one so that its network function can be completely preserved. We define this as network morphism in this research. After morphing a parent network, the child network is expected to inherit the knowledge from its parent network and also has the potential to continue growing into a more powerful one with much shortened training time. The first requirement for this network morphism is its ability to handle diverse morphing types of networks, including changes of depth, width, kernel size, and even subnet. To meet this requirement, we first introduce the network morphism equations, and then develop novel morphing algorithms for all these morphing types for both classic and convolutional neural networks. The second requirement is its ability to deal with non-linearity in a network. We propose a family of parametric-activation functions to facilitate the morphing of any continuous nonlinear activation neurons. Experimental results on benchmark datasets and typical neural networks demonstrate the effectiveness of the proposed network morphism scheme.
A diary study of rendezvousing: implications for position-aware computing and communications for the general public

This paper presents a diary study of rendezvousing as performed by university students. The study suggests that endezvousing frequently does not occur exactly as planned, but this is not necessarily problematic. It also reveals that 'problem' rendezvous were attributed more frequently to modes of travel, over-running of previous activities and lack of information about other rendezvousers, than to lack of information about travel, or local geography. These, and other, findings have implications for the design of position-aware computing and communications for the general public.
User-level secure deletion on log-structured file systems

Deleting a file from a storage medium serves two purposes: it reclaims storage resources and ensures that any sensitive information contained in the file becomes inaccessible. When done for the latter purpose, it is critical that the file is securely deleted, meaning that its content does not persist on the storage medium after deletion. Secure deletion is the act of deleting data from a storage medium such that the data is afterwards irrecoverable from the storage medium. The time between deleting data and it becoming irrecoverable is called the deletion latency.
Urban change detection based on self-organizing feature map neural network

Change detection is a newly developed method for identifying land surface changes recorded in temporal remote sensing data. When traditional statistic classification algorithms are normally used in change detection for temporal multi-spectral remote sensing data, a singularity structure problem should occur if performing direct classification change detection approach, which is caused by different spectrum come from the same training area. In order to solve this problem a Self-Organizing Feature Map neural network is developed, which is based on the weight of samplings and data. The result indicates direct classification change detection is better than that of post classification comparison based on maximum likelihood classification algorithm.
Ballistic to Diffusive Crossover in III–V Nanowire Transistors

In this paper, the authors examine the crossover between ballistic and diffusive transport in III-V nanowire transistors. The authors find that at lower drain voltages the ballistic-to-diffusive crossover occurs at channel lengths of approximately 2.3 nm at room temperature. However, when increasing the drain voltage, the ballistic-to-diffusive crossover can be more than nine times as long at room temperature. As the temperature is decreased, a finding in initially the performance is not significantly improved. However, as the temperature approaches 100 K, the ballistic-to-diffusive crossover increases to longer channel lengths quite dramatically. When InAs, InSb, and InP nanowires are compared at room temperature, the InAs and InSb performance in a similar fashion each with ballistic regions in excess of 10 nm, but that InP has no significant ballistic regime. Finally, simulation of several 10-nm InAs trigate transistors and show that for dopants deeply buried in the source and drain the devices appear ballistic, but when dopants appear near the source-channel interface, significant reductions in performance occur
An Improvement of Handoff Latency by Virtual MAPs for HMIPv6

The Hierarchical Mobile IP have been introduced as the way of constructing efficient wireless networks. But, in case the HMIPv6 is applied to the actual networks, it has problems that the load unbalance and overload to the MAP might be brought out because of the difference between the theoretical structure and the structure of actual network. In this paper, the scheme adopting the virtual MAP to the HMIPv6 is proposed. This solves the problems mentioned above and reduces handover delay time. The virtual MAP is the one of the routers located between the MN and actual MAP. In order to approve the scheme, the handoff latency of the standard HMIPv6 and the proposed HMIPv6 with virtual MAP are analyzed, respectively. The analytical results show that the proposed scheme improves the handoff latency. Experiments are performed to evaluate the handoff latency in terms of the amount of transmission packets under various conditions. The simulation results show that the proposed scheme is more effective than the standard HMIPv6 scheme.
On adaptable middleware product lines

Middleware helps to manage the complexity and heterogeneity inherent in distributed systems. Traditional middleware has a monolithic architecture, which makes it difficult to adapt to special requirements such as those present in embedded applications. Middleware for small devices has to cope with a broad range of requirements as well as with the stringent resource constraints. In this paper we propose a family-based approach based on aspect-oriented programming (AOP) for the implementation of middleware product lines which are highly configurable and adaptable. Such an adaptable middleware is statically configured according to the requirements of the specific distributed application. Furthermore, the middleware is also capable of adapting to the dynamics of the distributed embedded system by dynamically reconfiguring itself during runtime. An efficient dynamic aspect weaver is needed for this kind of adaptability. We also discuss a family of dynamic weavers that complements our study of the family based middleware.
Towards Network Application Service Interface

With ever-growing applications of diverse requirements over Internet, traditional inclusion of all applications into the application layer becomes difficult and impractical. Open Network Application Service/Reference Model (ONAS/RM) proposed by SC-Netcom Lab suggests a service-oriented Network Application Service Interface (NASI) be explicitly defined to clearly set the boundary between real applications and network. In the development of NASI, we discovered that temporal domain may cause significant impacts over the way a system operates which is not a major concern of many other works, thus in this paper we derived a Temporal Multi-Aspect Model (TM-AM) explicitly incorporating temporal domain to better manipulate system behavior. Besides, having realized the limited flexibility provided by conventional static model, we designed NASI as a reconfigurable system, whose instance is dynamically generated according to the requirements imposed. The discussion on dynamic NASI instance generation is given in this paper.
Transforming UML static models into object-oriented code

The authors propose a reuse based rigorous method using UML and algebraic specifications. Our contribution is towards an embedding of the object oriented code generation within a rigorous process that facilitates reuse, evolution and maintenance of the software. In previous work we described the GSBL/sup OO/ language (L. Fevre and S. Clerici, 1999) to cope with the formalization of UML static models, and the SpReIm model for the definition of the structure of reusable components. Our current goal is to map design artifacts to object oriented code. We describe a rigorous process to forward engineer UML static models. The emphasis is given to the transformation of UML class diagrams into object oriented code. In particular, we describe how to transform OCL specifications into GSBL/sup 00/.
Trade and Productivity

We estimate the effect of international trade on average labour productivity across countries. Our empirical approach relies on a summary measure of trade that, we argue, is preferable to the one conventionally used on both theoretical and empirical grounds. In contrast to the marginally significant and non-robust effects of trade on productivity found previously, our estimates are highly significant and robust even when we include institutional quality and geographic factors in the empirical analysis. We also examine the channels through which trade and institutional quality affect average labour productivity. Our finding is that trade works through labour efficiency, while institutional quality works through physical and human capital accumulation. We conclude with an exploratory analysis of the role of trade policies for average labour productivity.
Space, time, and the use of language : an investigation of relationships

Does temporal language depend on spatial language? Many parallels between spatial and temporal expressions, and many examples of metaphorical processes, seem to prove this. But how are expressions such as before and after, in front and behind actually used in natural discourse - does their application reflect a conceptual dependency relation? The book addresses this question from an innovative perspective, drawing together earlier findings from various directions and supplementing them by empirical investigations.
Functional Toll-like receptor 4 mutations modulate the response to fibrinogen

Summary Fibrinogen has been implicated in atherosclerosis; in part by activating the lipopolysaccharide (LPS) receptor Toll-like receptor 4 (TLR4). The fibrinogen-TLR4 signalling pathway remains un-characterised. In human macrophages fibrinogen stimulated interleukin (IL)6 expression and ERK (extracellular signal-related kinase) phosphorylation. In HEK293-CD14-MD2 cells expressing TLR4, fibrinogen induced robust phosphorylation of ERK1, p38α and JNK and activated transcription factors NFκB, Elk-1 and AP-1 (activator protein-1). The net effect of this signaling pathway was a pro-inflammatory response characterised by IL6 and TNFα synthesis and increased IL8,matrix metalloproteinase (MMP)1, MMP9, and MCP-1 promoter activity. Two common TLR4 mutations, D299G and T399I, render the receptor LPS hyporesponsive. The effect of fibrinogen on polymorphic variant TLR4s was markedly different; enhancing activation of kinases, transcription factors, cytokine synthesis and promoter activity. This study indicates that fibrinogen activates TLR4, explaining how fibrinogen promotes inflammatory protein expression.