Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathologic Prion Protein Infects Cells by Lipid-Raft Dependent Macropinocytosis

Transmissible spongiform encephalopathies, including variant-Creutzfeldt-Jakob disease (vCJD) in humans and bovine spongiform encephalopathies in cattle, are fatal neurodegenerative disorders characterized by protein misfolding of the host cellular prion protein (PrPC) to the infectious scrapie form (PrPSc). However, the mechanism that exogenous PrPSc infects cells and where pathologic conversion of PrPC to the PrPSc form occurs remains uncertain. Here we report that similar to the mechanism of HIV-1 TAT-mediated peptide transduction, processed mature, full length PrP contains a conserved N-terminal cationic domain that stimulates cellular uptake by lipid raft-dependent, macropinocytosis. Inhibition of macropinocytosis by three independent means prevented cellular uptake of recombinant PrP; however, it did not affect recombinant PrP cell surface association. In addition, fusion of the cationic N-terminal PrP domain to a Cre recombinase reporter protein was sufficient to promote both cellular uptake and escape from the macropinosomes into the cytoplasm. Inhibition of macropinocytosis was sufficient to prevent conversion of PrPC to the pathologic PrPSc form in N2a cells exposed to strain RML PrPSc infected brain homogenates, suggesting that a critical determinant of PrPC conversion occurs following macropinocytotic internalization and not through mere membrane association. Taken together, these observations provide a cellular mechanism that exogenous pathological PrPSc infects cells by lipid raft dependent, macropinocytosis.
Isolates: Serializability Enforcement for Concurrent ML

There has been much recent interest in exploring higher-level concurrency control abstractions such as software transactional memory (STM) to alleviate the complexity of reasoning about interactions among concurrent threads of control. Isolation and atomicity are the two critical properties provided by an STM that guarantee serializability of concurrent actions. Isolation ensures that transactions execute without interference from effects performed by other transactions, and atomicity guarantees that intermediate effects performed by a transaction are not seen by other concurrently executing transactions. While these properties have been primarily designed with shared memory in mind, there has been recent work (4; 5) that explores how atomicity could be leveraged to increase the expressivity of message-passing abstractions such as the first-class synchronous events found in Concurrent ML (CML) (14). Notably, these proposals do not enforce isolation of concurrently executing events, and thus cannot be used to enforce transactional execution of CML programs. In this paper, we consider the introduction of a new event combinator that addresses this significant limitation. An isolate is a combinator that allows a complex event to execute in isolation with other concurrently executing events (including other isolates). By doing so, it enables the integration of a true transactional semantics into a CML-style concurrency model, facilitating reasoning about CML programs in terms of serializable event orderings. Incorporating isolation into CML poses a number of challenging problems, however, whose solutions form the focus of this paper.
End-to-end consensus using end-to-end channels

End-to-end consensus ensures delivery of the same value to the application layer running in distributed processes. Deliveries that have not been acknowledged by the application before a failure are delivered again. End-to-end primitives are important for applications that need to enforce persistency. We present an algorithm that solves the end-to-end consensus problem. Our approach is to build end-to-end consensus using a new type of communication channels, end-to-end channels
An Investigation of the Effects of Different Types of Activities during Pauses in a Segmented Instructional Animation

Since the complex and transient information in instructional animations requires more cognitive resources, the segmenting principle has been proposed to reduce cognitive overload by providing smaller chunks with pauses between segments. This study examined the effects of different types of activities during pauses in a segmented animation. Four groups were asked to do different tasks in system-controlled pauses after each segment of an instructional animation: passive pauses (i.e., no-reflection vs. reflection), and active pauses (i.e., free-recall vs. short-answer). The results showed that active pause with free-recall group outperformed the two passive pause groups on both recall and transfer tests. However, no significant differences in mental effort for the instruction or the tests were found. The findings of this study provide valuable implications for effective ways of using pauses between segments in instructional animations. Keyword Segmenting principle, Instructional animation, Pauses in segments, Active pauses
Bayesian Modelling of Community-Based Multidimensional Trust in Participatory Sensing under Data Sparsity

We propose a new Bayesian model for reliable aggregation of crowdsourced estimates of real-valued quantities in participatory sensing applications. Existing approaches focus on probabilistic modelling of user's reliability as the key to accurate aggregation. However, these are either limited to estimating discrete quantities, or require a significant number of reports from each user to accurately model their reliability. To mitigate these issues, we adopt a community-based approach, which reduces the data required to reliably aggregate real-valued estimates, by leveraging correlations between the reporting behaviour of users belonging to different communities. As a result, our method is up to 16:6% more accurate than existing state-of-the-art methods and is up to 49% more effective under data sparsity when used to estimate Wi-Fi hotspot locations in a real-world crowdsourcing application.
Strong ferroelectric polarization of CH3NH3GeI3 with high-absorption and mobility transport anisotropy: theoretical study

Lead iodide perovskite has long been considered to be promising for photovoltaic applications due to the high power conversion efficiency. However, the toxicity and instability of lead iodide perovskite limit its widespread use. Recently, germanium iodide perovskite CH3NH3GeI3 has attracted much attention due to the lead-free and high distorted structure. In this study, we exhibited a detailed theoretical investigation to predict total ferroelectric polarization of about 13.8 μC cm−2 and disentangle the contributions of MA cation (MA = CH3NH3), the center charge of MA cation and Ge2+ ion relative to the inorganic framework. Based on the electronic structure, optical absorption as well as carrier mobility of the system are further calculated, which exhibit strong anisotropy along the same direction. Further regulating atomic structure to strengthen or weaken the polarization, variable optical absorption spectra and hence tunable efficiencies are obtained. By analyzing the electronic structure with applied increased polarization, we conclude that polarization driven optical absorption can be attributed to an increased p–p orbital transition from I to Ge. In the case of CH3NH3GeI3, we discuss the relationship between ferroelectricity and photovoltaic performance, reveal the potential of utilizing polar material for higher solar conversion, and speculate that it is a general rule to raise the efficiency by enhancing the polarization.
High-order total variation minimization for interior tomography

Recently, an accurate solution to the interior problem was proposed based on the total variation (TV) minimization, assuming that a region of interest (ROI) is piecewise constant. In this paper, we generalize that assumption to allow a piecewise polynomial ROI, introduce the high-order TV (HOT), and prove that an ROI can be accurately reconstructed from projection data associated with x-rays through the ROI via the HOT minimization if the ROI is piecewise polynomial. Then, we verify our theoretical results in numerical simulation.
Inferring developer expertise through defect analysis

Fixing defects is an essential software development activity. For commercial software vendors, the time to repair defects in deployed business-critical software products or applications is a key quality metric for sustained customer satisfaction. In this paper, we report on the analysis of about 1,500 defect records from an IBM middle-ware product collected over a five-year period. The analysis includes a characterization of each repaired defect by topic and a ranking of developers by inferred expertise on each topic. We find clear evidence that defect resolution time is strongly influenced by a specific developer and his/her expertise in the defect's topic. To validate our approach, we conducted interviews with the product's manager who provided us with his own ranking of developer expertise for comparison. We argue that our automated developer expertise ranking can be beneficial in the planning of a software project and is applicable beyond software support in the other phases of the software lifecycle.
Develop Human Safety Mechanism for Human-Symbiotic Mobile Manipulators: Compliant Hybrid Joints

Today, robots are expected to provide various services directly to humans in environments, this situation has led to the idea of teams consisting of humans and robots working cooperatively on the same task. Various names for this type of human–robot cooperation system have emerged including human-friendly robots, personal robots, assistant robots and symbiotic robots. These robots will continue to be employed also in the 21st century to cope with the increase in the elderly and handicapped, the decrease in the birth rate and working population and will be introduced into non-industrial areas such as homes and offices to make a rich and comfortable life. Such robots as home-use robots, assistance robots, and service robots, should deal with diverse tasks (Fujie, Tani, and Hirano 1994; Kawamura and Iskarous 1994). One of the specific situations in the non-industrial areas is that the robots coexist and help humans in their life environments. The robots, therefore, must be with the capability of human-robot coexistence. They can be called “humansymbiotic robots” (HSRs). There are various problems to be solved to develop the HSRs. Working and moving among humans requires special concerns on the safety issues, the safety of human in view of an unexpected collision should be assured. A HSR should weight not significantly more than a human, but mechanical compliance of the surface and joints is also a necessity. In the past two decades, many researchers have studied to reduce in advance the unexpected collision accidents between an industrial robot and a human operator by isolating robots in work cells that automatically shut down if a person enters; visuals (signs, flashing lights), and audio devices would indicate conditions by the operation and vision/sound alarms, and so on. Because these accident precautions approaches are difficult to assure human safety in human-robot environments in which an interaction between the person and the robot is presupposed, we have to consider other ways to deal with human-robot collisions and such contacts can take place anywhere on the body of the robot. Therefore, the HSR should be constructed on the basis of a new philosophy from that of past robots. Lim and Tanie (2000) proposed the HSR must be constructed for
Cell shifting aware of wirelength and overlap

The technique of cell shifting has the advantage of linearly smoothing the overlap in placement. In the shifting process we should preserve the integrity of the original placement as much as possible and do less damage to the relative locations of the cells. The current cell shifting methods only locally or globally smooth the density without considering the relation between the local and the global density. Furthermore, the cells generally are treated as points with area during cell shifting. In this paper we present a new cell shifting technique called CSAWO to smooth the density distribution. CSAWO obtains the shifting distance while considering the local and the global density distribution simultaneously. The density and wire length are taken into consideration while shifting the cells. We also separate the standard cells and the macro blocks crossing multi-bin, and give the cell shifting distance by summing the shifting vector of the discrete module so as to get a more smooth speed. CSAWO has been embedded into the global placement process of CPlace, experimental result shows that the average runtime and HPWL have reduced 78% and 7% respectively comparing to DPlace[9].
Semi-supervised learning for facial expression recognition

Automatic classification by machines is one of the basic tasks required in any pattern recognition and human computer interaction applications. In this paper, we discuss training probabilistic classifiers with labeled and unlabeled data. We provide an analysis which shows under what conditions unlabeled data can be used in learning to improve classification performance. We discuss the implications of this analysis to a specific type of probabilistic classifiers, Bayesian networks, and propose a structure learning algorithm that can utilize unlabeled data to improve classification. Finally, we show how the resulting algorithms are successfully employed in a facial expression recognition application.
Catalytic Activity of cGMP-Dependent Protein Kinase Type I in Intact Cells Is Independent of N-Terminal Autophosphorylation

Although cGMP-dependent protein kinase type I (cGKI) is an important mediator of cGMP signaling and upcoming drug target, its in vivo-biochemistry is not well understood. Many studies showed that purified cGKI autophosphorylates multiple sites at its N-terminus. Autophosphorylation might be involved in kinase activation, but it is unclear whether this happens also in intact cells. To study cGKI autophosphorylation in vitro and in vivo, we have generated phospho-specific antisera against major in vitro-autophosphorylation sites of the cGKI isoforms, cGKIα and cGKIβ. These antisera detected specifically and with high sensitivity phospho-cGKIα (Thr58), phospho-cGKIα (Thr84), or phospho-cGKIβ (Thr56/Ser63/Ser79). Using these antisera, we show that ATP-induced autophosphorylation of cGKI in purified preparations and cell extracts did neither require nor induce an enzyme conformation capable of substrate heterophosphorylation; it was even inhibited by pre-incubation with cGMP. Interestingly, phospho-cGKI species were not detectable in intact murine cells and tissues, both under basal conditions and after induction of cGKI catalytic activity. We conclude that N-terminal phosphorylation, although readily induced in vitro, is not required for the catalytic activity of cGKIα and cGKIβ in vivo. These results will also inform screening strategies to identify novel cGKI modulators.
Strategies for Sustainability: Institutional and Organisational Challenges

Sustainable Development (SD) is a global role model that claims to function as a general orientation for shaping societal processes, i.e. , local, regional, national and international development. This is in line with the Brundtland and justice-oriented understanding of the term. It is understood as a role model and sometimes also interpreted as a regulative ideal. However, it does not state how exactly “sustainable” societies will or should look. It does not give us a step-by-step pattern to follow, but something like a frame of what ought to be done in order to transform today’s societies, including their economies. [. ]
Dimensions: why do we need a new data handling architecture for sensor networks?

An important class of networked systems is emerging that involve very large numbers of small, low-power, wireless devices. These systems offer the ability to sense the environment densely, offering unprecedented opportunities for many scientific disciplines to observe the physical world. In this paper, we argue that a data handling architecture for these devices should incorporate their extreme resource constraints - energy, storage and processing - and spatio-temporal interpretation of the physical world in the design, cost model, and metrics of evaluation. We describe DIMENSIONS, a system that provides a unified view of data handling in sensor networks, incorporating long-term storage, multi-resolution data access and spatio-temporal pattern mining.
Personalized medicine for cystic fibrosis: Establishing human model systems

With over 1,500 identifiable mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that result in distinct functional and phenotypical abnormalities, it is virtually impossible to perform randomized clinical trials to identify the best therapeutics for all patients. Therefore, a personalized medicine approach is essential. The only way to realistically accomplish this is through the development of improved in vitro human model systems. The lack of a readily available and infinite supply of human CFTR‐expressing airway epithelial cells is a key bottleneck. We propose that a concerted two‐pronged approach is necessary for patient‐specific cystic fibrosis research to continue to prosper and realize its potential: (1) more effective culture and differentiation conditions for growing primary human airway and nasal epithelial cells and (2) the development of collective protocols for efficiently differentiating disease‐ and patient‐specific induced pluripotent stem cells (iPSC) into pure populations of adult epithelial cells. Ultimately, we need a personalized human model system for cystic fibrosis with the capacity for uncomplicated bankability, widespread availability, and universal applicability for patient‐specific disease modeling, novel pharmacotherapy investigation and screening, and readily executable genetic modification. Pediatr Pulmonol. 2015; 50:S14–S23. © 2015 Wiley Periodicals, Inc.
IIR Volterra Filtering with Application to Bilinear Systems

A new nonlinear filtering technique by means of infinite impulse response (IIR) Volterra functionals is developed. It yields the projection onto the closed class of finite Volterra series with separable kernels of arbitrary degree k. Such an optimal estimator is finitely realizable as a bilinear system with parameters that are computable off line. Moreover, if the original system model is itself bilinear, this computation is finitely recursive through higher moments of degree 2 k. Two simple illustrating examples are developed: (i) estimation of the covariance of the internal white noise driving a linear system and (ii) filtering of a non-Gaussian linear system (driven by a Poisson process). The robustness with respect to the observation noise distribution is finally examined.
Deep and narrow binary content-addressable memories using FPGA-based BRAMs

Binary Content Addressable Memories (BCAMs) are massively parallel search engines capable of searching the entire memory space in a single clock cycle. BCAMs are used in a wide range of applications, such as memory management, networks, data compression, DSP, and databases. Due to the increasing amount of processed information, modern BCAM applications demand a deep searching space. However, traditional BCAM approaches in FPGAs suffer from storage inefficiency. In this paper, a novel and efficient technique for constructing deep and narrow BCAMs out of standard SRAM blocks in FPGAs is proposed. This technique is most efficient for deep and narrow CAMs since the BRAM consumption is exponential to pattern width. Using Altera's Stratix V device, traditional methods achieve up to 64K-entry BCAM while the proposed technique achieves up to 4M entries. For the 64K-entry test-case, traditional methods consume 43 times more ALMs and achieves only one-third of the Fmax. A fully parameterized Verilog implementation is available1. This implementation has been extensively tested using Altera's tools.
On the propagation of non stationary pressure waves in stellar interiors

An analysis of the propagation of non stationary waves in the adiabatic region of stellar interior is presented. An equation of motion with an effective potential is derived, similar to the Zerilli equation known in the propagation of gravitational waves. The Huyghens principle is violated in this case and the energy diffusion outward null cones is expected. Numerical calculations demonstrate that the diffusion is weak for the case of standard Solar model; thus no significant effect corresponding to quasinormal modes can be expected. The likely reason for the absence of stronger features is the restriction of our analysis to adiabatic regions only, where the breakdown of the Huyghens principle is insignificant.
Variable-Rate Two-Phase Collaborative Communication Protocols for Wireless Networks

The performance of two-phase collaborative communication protocols is studied for wireless networks. All the communication nodes in the cluster are assumed to share the same channel and transmit or receive collaboratively in a quasi-static Rayleigh flat-fading environment. In addition to small-scale fading, the effect of large-scale path loss is also considered. Based on a decode-and-forward approach, we consider various variable-rate two-phase protocols that can achieve full diversity order and analyze the effect of node geometry on their performance in terms of the outage probability of mutual information. For the single-relay node case, it is shown that if the collaborator node is close to the source node, a protocol based on space-time coding (STC) can achieve good diversity gain. Otherwise, a protocol based on receiver diversity performs better. These protocols are also compared with one based on fixed-rate repetition coding and their performance tradeoffs with node geometry are studied. The second part deals with multiple relays. It is known that with N relays an asymptotic diversity order of N+1 is achievable with STC-based protocols in the two-phase framework. However, in the framework of collaborative STC, those relay nodes which fail to decode remain silent (this event is referred to as a node erasure). We show that this node erasure has the potential to considerably reduce the diversity order and point out the importance of designing the STC to be robust against such node erasure
A Systems View of a Neuromorphic VLSI Echolocation System

Echolocating bats have long demonstrated the potential for air-coupled sonar to guide agile navigation through complex 3D environments. While air-coupled sonar has been extensively used in mobile ground robotics and a considerable amount of the bat's auditory system has been studied, little work has been done to understand how the neural circuitry of the bat can integrate echoes into a coherent, behaving system. This paper addresses the unique characteristics of bat echolocation and how they impact the design of a neuromorphic VLSI-based echolocation system. By constructing a system to solve bat-specific sensorimotor tasks the authors have encountered a number of interesting issues and questions that commonly face neuromorphic VLSI designers. Successes, problematic issues, and future directions are discussed