Miracle-dz/UniFAR-FTUs huggingface dataset:
The structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90

Tetratricopeptide (TPR) domains are known protein interaction domains. We show that the TPR domain of FKBP8 selectively binds Hsp90, and interactions upstream of the conserved MEEVD motif are critical for tight binding. In contrast FKBP8 failed to bind intact Hsp70. The PPIase domain was not essential for the interaction with Hsp90 and binding was completely encompassed by the TPR domain alone. The conformation adopted by Hsp90 peptides, containing the conserved MEEVD motif, in the crystal structure were similar to that seen for the TPR domains of CHIP, AIP and Tah1. The carboxylate clamp interactions with bound Hsp90 peptide were a critical component of the interaction and mutation of Lys 307, involved in the carboxylate clamp, completely disrupted the interaction with Hsp90. FKBP8 binding to Hsp90 did not substantially influence its ATPase activity.
Image and video retargeting using Graph Cuts

Graph Cuts theory has been widely applied in the fields of network flow analysis, computer vision, computer graphics, and so on. In this paper, we use an approach of Graph Cuts to realize image and video retargeting. We regard image retargeting as a problem of energy minimization, so we construct a residual and directed graph based on the gradient of pixel value to find the cut path with minimal energy. Using pre-flow push algorithm and breadth-first search (BFS) algorithm, we obtain a labeled graph which is saturated. According to the labeled graph, we can find the minimal cut path, which is removed to reduce one row or column of image. On the basis of image retargeting, we retarget a video by taking the relevance of frames in temporal into account. We consider the inserted energy due to new edges created by previously non adjacent pixels that become neighbors after the cut removing. Experiments show that our method is satisfactory in image and video retargeting in visual effect.
Source number estimation in reverberant conditions via full-band weighted, adaptive fuzzy c-means clustering

We introduce a novel approach for source number estimation through an adaptive fuzzy c-means clustering. Spatial feature vectors are extracted from microphone observations, weighted for reliability and then clustered in a full-band manner using an adaptive variation on the fuzzy c-means. A number of quality measures are combined to produce a weighted sum which is used to find the optimal number of clusters at each iteration of the clustering algorithm. Experimental evaluations using real-world recordings from a reverberant room (RT60 = 390 ms) demonstrated encouraging performance in both even- and under-determined conditions.
A Persona is Not A Person : Designing Dialogs With ECAs After Wizard of Oz Simulations

After an enthusiastic effort towards developing increasingly refined systems, research on Embodied Conversational Agents (ECAs) is experiencing a stage of critical reflection on the role this new form of interaction may play in real applications. Question issues concern which are the domains in which ECAs may be of demonstrated utility, how the aspect and the behaviour of the agent which best suit a particular domain may be selected, which agent’s features affect its effectiveness, and many more. To answer these questions, several evaluation studies have been performed, with different aims and methods (see [25] for a review of the most recent of them). These studies were focused, initially, on analysis of individual images, with a comparison between 2D and 3D agents, evaluation of the ‘convincingness’ of emotional expressions [4] and similars. More recently, evaluation employed dynamic images in which global aspects of the agent performance were compared with those of other media (text, speech or human video: [5, 18]). The object of evaluation (a specific expression, the agent, the message or the interaction in its entirety) varies across these studies, as well as the evaluation criteria applied. As even the meaning of ‘usability’ is not yet clear for this interaction style, a large variety of terms has been employed to denote the aspects to investigate: naturalness, engagement, satisfaction, effectiveness, pleasantness, usefulness, attractiveness, and the most popular of them, ‘believability’. The importance of these studies in orienting research efforts towards aspects to develop with particular care is unquestionable. However, this kind of studies does not yet provide clear suggestions on which conversational style is appropriate for ECAs, in every application domain. In addition, very little is known about how real users will behave when interacting with animated characters and how much they will empathize with them [20]. In the large majority of the available studies, the object of evaluation is a monolog, not a dialog: as a consequence, the user attitude is mainly observational, passive. Therefore, these studies do not contribute to defining which interaction models with an ECA should be implemented in every application context. For instance, which type of initiative is preferable (system-driven or user-driven? ), which forms of empathy should be simulated in the agent, which expressions should be recognized in the user and, more in general, how the desired level of communication and engagement between agent and user may be established.
PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search

Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challenging task to identify weak motifs, since either a large amount of memory or execution time is required by current exact algorithms. A new exact algorithm, PairMotif, is proposed for planted (l, d) motif search (PMS) in this paper. To effectively reduce both candidate motifs and scanned l-mers, multiple pairs of l-mers with relatively large distances are selected from input sequences to restrict the search space. Comparisons with several recently proposed algorithms show that PairMotif requires less storage space and runs faster on most PMS instances. Particularly, among the algorithms compared, only PairMotif can solve the weak instance (27, 9) within 10 hours. Moreover, the performance of PairMotif is stable over the sequence length, which allows it to identify motifs in longer sequences. For the real biological data, experimental results demonstrate the validity of the proposed algorithm.
Internet of Things Security based on Devices Architecture

The Internet of Things, also called The Internet of Objects, refers to a wireless network between objects; usually the network will be wireless and self-configuring, such as household appliances. Secures IOT end-to-end, which means authenticating device communications, protecting code and applications, and securing devices from threats. Emergence accompanied the IoT technology, or when using of this technology and its deployment, an increase in security and privacy violation, so must take caution when used , and also paid to further research in this technology which that bothered a lot, including confidentiality, authenticity, and integrity. In this paper we will present the security and privacy when using the Internet of Things technology, depending on the architecture of the devices, and will be focusing on how security building in the devices, and protection requirements, by studying the architecture layer and IoT security infrastructure.
Development of pick-to-light communication middleware

Pick-to-light has been applied in logistics to support goods picking. Usually, the equipment supplier provides the goods application to the users. But with the development of the user business, the system will be required to be adjusted to meet the needs of the new goods pick work flow, especially to support multi ways of goods picking. This paper studied the low level communication between pick-to-light and monitor workstation, and developed a set of middleware to meet the pick-to-light picking system modification. The middleware is developed with Java language, and can be reused freely. With the middleware, the programmer can develop the pick system according to the adjustment of goods pick work flow. It is very convenient for logistics enterprises and education organizations to construct the goods picking system based on pick-to-light.
Intraorganizational communication with intranets

Intranets have been used to unify geographically dispersed work forces. They have been used to empower employees around the world (especially telecommuters and salespeople on the road) through a communication tool supporting collaboration, interaction, and real-time sharing of corporate information across functional boundaries and organizational levels. This form of distributed information infrastructure may even enable some corporate managers to redefine their computing strategies and organizational control to better address competitive business environments. Most studies of intranet performance have been conceptual or anecdotal; none has sought to collect empirical data from intranet implementers and synthesize their experience in order to guide other organizations to plan, control, implement, and evaluate intranets. That’s why I participated in “Intranet Impact and Effectiveness,” a study of the 500 largest organizations in Hong Kong, targeting five goals: investigate the reasons for intranet adoption; explore the extent intranets support intraorganizational communications; identify the problems and benefits associated with intranet implementation; evaluate the effect of organization size on intranet use; and analyze the effect of intranets on overall organizational performance, team collaboration, and business process reengineering (see the sidebar “How the Study Was Done”). Intranet adoption and diffusion. In today’s dynamic business environment, decisions about adopting technological innovations are influenced by the expectation that they will streamline a business process and improve overall organizational performance. In particular, organizations facing keen market competition have compelling incentives to evaluate innovative technologies to help them maintain or enhance their competitiveness. Intranet The technical performance and business contribution of intranet applications has proved to many organizations worldwide that intranet technology is a costeffective and efficient approach to supporting corporate distributed computing strategies [3]. Increasingly, all kinds of organizations are taking advantage of intranets to disseminate corporate documents, forms, news, policies, phone directories, product specifications, and pricing information. In addition to using the technology to integrate individual, group, departmental, and corporate communications, business managers are exploring intranets to enhance their organizations’ business strategies.
Hawkes process as a model of social interactions: a view on video dynamics

We study by computer simulation the ‘Hawkes process’ that was proposed in a recent paper by Crane and Sornette (2008 Proc. Natl Acad. Sci. USA 105 15649) as a plausible model for the dynamics of YouTube video viewing numbers. We test the claims made there that robust identification is possible for classes of dynamic response following activity bursts. Our simulated time series for the Hawkes process indeed fall into the different categories predicted by Crane and Sornette. However, the Hawkes process gives a much narrower spread of decay exponents than the YouTube data, suggesting limits to the universality of the Hawkes-based analysis.
Plan Execution Motivation in Multi-agent Systems

In this paper we analyze a particular model of control among intelligent agents, that of non-absolute control. Non-absolute control involves a "supervisor" agent that issues orders to a group of "subordinate" agents. An example might be an Internet user who issues a query to a group of software agents on remote hosts, or a human agent on Earth directing the activities of Mars-based semi-autonomous vehicles. The members of the subordinate group are assumed to be self-motivated, and individually rational (i.e., they are basically willing to carry out the supervisor's request if properly compensated). This assumption gives rise to the need for a reward policy that would motivate each agent to contribute to the group activity. In this paper we introduce such a policy under certain simplifying assumptions.
MicroRNA-34a suppresses the breast cancer stem cell-like characteristics by downregulating Notch1 pathway

MicroRNAs play pivotal roles in cancer stem cell regulation. Previous studies have shown that microRNA‐34a (miR‐34a) is downregulated in human breast cancer. However, it is unknown whether and how miR‐34a regulates breast cancer stem cells. Notch signaling is one of the most important pathways in stem cell maintenance and function. In this study, we verified that miR‐34a directly and functionally targeted Notch1 in MCF‐7 cells. We reported that miR‐34a negatively regulated cell proliferation, migration, and invasion and breast cancer stem cell propagation by downregulating Notch1. The expression of miR‐34a was negatively correlated with tumor stages, metastasis, and Notch1 expression in breast cancer tissues. Furthermore, overexpression of miR‐34a increased chemosensitivity of breast cancer cells to paclitaxel (PTX) by downregulating the Notch1 pathway. Mammosphere formation and expression of the stemness factor ALDH1 were also reduced in the cells treated with miR‐34a and PTX compared to those treated with PTX alone. Taken together, our results indicate that miR‐34a inhibited breast cancer stemness and increased the chemosensitivity to PTX partially by downregulating the Notch1 pathway, suggesting that miR‐34a/Notch1 play an important role in regulating breast cancer stem cells. Thus miR‐34a is a potential target for prevention and therapy of breast cancer.
Magician simulator — A realistic simulator for heterogeneous teams of autonomous robots

We report on the development of a new simulation environment for use in Multi-Robot Learning, Swarm Robotics, Robot Teaming, Human Factors and Operator Training. The simulator provides a realistic environment for examining methods for localization and navigation, sensor analysis, object identification and tracking, as well as strategy development, interface refinement and operator training (based on various degrees of heterogeneity, robot teaming, and connectivity). The simulation additionally incorporates real-time human-robot interaction and allows hybrid operation with a mix of simulated and real robots and sensor inputs.
Enhancing Real-Time Applications by Means of Multi-tier Cloud Federations

The evolution of Cloud Computing beyond the frontier of a single datacenter is justified as a mean to enhance various system architecture aspects like: cost, geo-locality, energy efficiency and structural properties. Orchestration of different cloud providers in order to ensure better Quality of Service (QoS) is refered to as Multi-Cloud. One such multi-cloud federation model is Community Clouds, a federation concept in which various micro-clouds are owned by different communities of individuals contributing cloud resources. Community Clouds provide high locality to services towards the user by bringing the Cloud in the edges of the network, and in some cases as an integral part of the access network. Another such type of multicloud federation is Structured Cloud Federation for Internet Service Providers and Telephony Providers, composed of geo distributed micro-clouds placed on the edges of the network and a centralized datacenter cloud on the core network. Services deployed in the micro-clouds have augmented locality, while services on the datacenter cloud enhanced performance. In this work we identify how these approaches to multi-cloud, through the ability to deploy services close to the final user, can be exploited to enhance existing real-time streaming applications. Furthermore a novel multi-cloud overlay algorithm is introduced that provides both latency and backbone traffic optimization for latency critical existing and novel services (concretely focusing on stream computation, live streaming).
Large non-Gaussianity from non-local inflation

We study the possibility of obtaining large non-Gaussian signatures in the cosmic microwave background in a general class of single-field non-local hilltop inflation models. We estimate the non-linearity parameter fNL which characterizes non-Gaussianity in such models and show that large non-Gaussianity is possible. For the recently proposed p-adic inflation model we find that fNL∼120 when the string coupling is order unity. We show that large non-Gaussianity is also possible in a toy model with an action similar to those which arise in string field theory.
Synthesis of lumped-distributed cascades with lossy transmission lines

In the analysis of large systems such as high-speed digital computing networks and circuits on an LSI or VLSI silicon chip, lossy lumped-distributed networks have been used to model their interconnections. A solution of the synthesis problem for these networks will aid in the design of these circuits. This paper establishes single-variable realizability conditions and synthesis procedures for the class of lossy lumped-distributed cascade networks which contain lossy transmission lines and are desctribed by a driving point impedance expession of the form Z_{0}=\frac{\sum_{i=0}^{n} a_{i}(s,z_{0})e^{(2i-n)}T_{0}\gamma (s)} {\sum_{i=0}^{n} b_{i}(s, z_{0})e^{(2i-n)}T_{0}\gamma (s)} where a_{i}(s, z_{0}), b_{i}(s, z_{0}) are two-variable, real polynomials in s and z_{0} , with z_{0} the characteristic impedance, \gamma (s) the progagation constant, and To the total "electrical length" characterizing each of the lossy lines. The cascade networks consist of commensurate, uniform and/or tapered, lossy (except distortionless [3], [4]) transmission lines interconnected by passive, lumped (lossless and/or lossy) two-ports and terminated in a passive load. This class includes general lines, leakage-free lines, RC -lines and acoustic filters. The results also apply to cascades with noncommensurate lines and to cascades of mixed transmission-line types.
Combination-sensitive neurons in the primary auditory cortex of the mustached bat

In the mustached bat, Pteronotus parnellii, neurons in the primary auditory cortex (AI) have been thought to respond primarily to single frequencies, as in other mammals. However, neurons in the Doppler- shifted constant-frequency (DSCF) area, a part of the mustached bat's AI that contains an overrepresentation of the prominent CF2 component of the biosonar signal, were found to show facilitative responses to combinations of different frequencies in the pulse and echo. The essential components for facilitation were the pulse FM1 and the echo CF2. The FM1-CF2 facilitation was sensitive to echo delays, indicating that DSCF neurons respond better to targets within particular ranges. On average, the longest discriminable echo delay, based on increased impulse counts due to facilitation, corresponded to a target range of 4.3 m, and the most discriminable delay corresponded to a target 3.6 m distant. Since mustached bats first show a behavioral response to a target at a distance of 3-4 m, DSCF neurons are suited to signal the presence of an insect within this behaviorally important range. DSCF neurons were broadly tuned to echo delay, with the average minimum discriminable echo delay corresponding to a target range of 1.9 m, and the delay tuning of the neurons followed (tracked) changes in pulse duration, indicating that facilitation occurs during much of the approach phase of insect pursuit when target characterization is presumably occurring. These results show that AI neurons in the mustached bat are specialized to respond to complex, behaviorally relevant stimuli during the search and approach phases of insect pursuit.
otal antioxidant activity in Parkinson's Disease

Parkinson’s disease (PD) is one of the major progressive neurological disorders, characterized by the loss of dopaminergic neurons in pars compacta of the substantia nigra. The causes for this is the interactions between external toxins (which arise from environmental, dietary and life style factors) and internal toxins arising from normal metabolism, genetic and epigenetic (mitochondria, membranes and proteins) components. Oxidative stress is one of the intermediary risk factors that could initiate and promote degeneration of neurons. Even though oxidative stress in brain is an important factor in the neuropathology of PD, yet the role of systemic oxidative stress is inconclusive. In the present study, we estimated the total antioxidant activity (AOA) and albumin levels in twenty PD patients who were on levodopa, and in age matched twenty-five normal con-trols. We observed a significant reduction in total antioxidant activity in PD patients with a mean value of 0.93 ± 0.17 mmol/l as compared to 1.06 ± 0.16 mmol/l in controls (P < 0.001). Albumin levels were also significantly reduced in PD patients, with a mean of 2.52 ± 0.29 g/dl as compared to 3.0 ± 0.54 g/dl in controls (P < 0.001). It could be concluded from our study that the diminution in total antioxidant activity could be due to the reduction of radical trapping capacity of naturally occurring antioxidant albumin, which in turn could be due to reduced dietary supplementation or defective absorption of amino acids. Supplemen-tation of multiple antioxidants may slow down the progression of the disease.
TIPExtop: An exploratory design tool for emergency planning

Emergency planning is an ongoing activity in which a multidisciplinary group of experts intermittently collaborate to define the most appropriate response to risks. One of the most important tasks of emergency planning is risk reduction. Such a task compiles the analysis of capabilities to face an emergency, the prioritizing of activities, and the definition of procedures and strategies. It is therefore a reflection process based on exchanging information between planners and exploring alternatives. Despite the exploration of alternatives is an especially relevant activity to design better plans, recent research on computer-mediated collaborative tools for planning do not usually offer support for this activity. Thus, with the purpose of supporting reflection during the development of risk reduction tasks, this paper presents an exploratory design tool that allow planners to assess the space of alternatives and the underlying information related those alternatives. This planning tool will help planners to examine and contextualize information, allowing them to define more suitable response strategies.