Miracle-dz/UniFAR-FTUs huggingface dataset:
Protease Activity, Secretion, Cell Entry, Cytotoxicity, and Cellular Targets of Secreted Autotransporter Toxin of Uropathogenic Escherichia coli

ABSTRACT The secreted autotransporter toxin (Sat), found predominantly in uropathogenic Escherichia coli, is a member of the SPATE (serine protease autotransporters of Enterobacteriaceae) family and, as such, has serine protease activity and causes cytopathic effects on various cell types. To assess the contribution of the serine protease active site to the mechanism of action of Sat, mutations were made in the first (S256I), in the second (S258A), or in both (S256I/S258A) serine residues within the active site motif. Mutations in the first or both serines reduced protease activity to background levels (P < 0.001); a single mutation in the second serine reduced activity by 60% compared to wild type (P < 0.001). After reversion of the S256I mutation to wild type (I256S), we confirmed S256 as the catalytically active serine. None of these mutations affected secretion of the mature passenger domain or release into the supernatant. The S256I mutation, however, abrogated the cytotoxicity of Sat on human bladder (UM-UC-3) and kidney (HEK 293) epithelial cells, characterized by rounding and elongation, respectively, and a high level of cell detachment. Moreover, S256 is essential for Sat to mediate cytoskeletal contraction and actin loss in host cells as well as to degrade specific membrane/cytoskeletal (fodrin and leukocyte function-associated molecule 1) and nuclear [microtubule-associated proteins, LIM domain-only protein 7, Rap GTPase-activating protein, poly(ADP-ribose) polymerase] proteins in vitro. Lastly, Sat was internalized by host cells and localized to the cytoskeletal fraction where membrane/cytoskeletal target proteins reside.
Thermal Damping in Cavitating Nozzle Flows

Recent investigations of bubbly cavitating nozzle flows by Wang and Brennen (1998) and by Delale et al. (2001), where various damping effects are lumped together in an adhoc manner, have shown flow instabilities that lead to flashing flow solutions. Here, we investigate the stabilizing effect of thermal damping on these instabilities. For this reason we consider the energy equation within the bubble, assumed to be composed of vapor and gas, in the uniform pressure approximation (similar to that given by Nigmatulin et al., 1981 and by Prosperetti, 1991). The partial vapor pressure is fixed by the vapor saturation pressure corresponding to the interface temperature, which is evaluated by the Plesset-Zwick$^5$ formula assuming the thin boundary layer approximation within the liquid. Consequently, the partial gas pressure is evaluated by its relation to the heat flux through the interface in the uniform pressure approximation. The model is then coupled to the steady-state cavitating nozzle flow equations employed by Wang and Brennen and by Delale et al., replacing the previously assumed polytropic law for the partial gas pressure. The instabilities arising from the use of the polytropic law for the gas pressure in steady cavitating nozzle flows are seen to be stabilized by thermal damping with or without the occurrence of bubbly shock waves.
O-Sulfonation of Serine and Threonine

Protein sulfonation on serine and threonine residues is described for the first time. This post-translational modification is shown to occur in proteins isolated from organisms representing a broad span of eukaryote evolution, including the invertebrate mollusk Lymnaea stagnalis, the unicellular malaria parasite Plasmodium falciparum, and humans. Detection and structural characterization of this novel post-translational modification was carried out using liquid chromatography coupled to electrospray tandem mass spectrometry on proteins including a neuronal intermediate filament and a myosin light chain from the snail, a cathepsin-C-like enzyme from the parasite, and the cytoplasmic domain of the human orphan receptor tyrosine kinase Ror-2. These findings suggest that sulfonation of serine and threonine may be involved in multiple functions including protein assembly and signal transduction.
Late Cenozoic tectonic development of the intramontane Alai Valley, (Pamir‐Tien Shan region, central Asia): An example of intracontinental deformation due to the Indo‐Eurasia collision

The Pamir indentor of the northwestern Himalayan syntaxis is a first‐order feature demonstrating partly the northward extent of deformation due to the Cenozoic Indo‐Eurasia collision. The Alai Valley of Kyrgyzstan at the northern end of the indentor is a strategically positioned, E‐W trending intramontane basin that constrains the timing and extent of crustal deformation in this area of the collision zone. To quantify the convergence accommodated across the Alai Valley during the Late Cenozoic, we collected structural and stratigraphic field data, reviewed existing Soviet literature, and analyzed migrated seismic reflection profiles to construct and restore two regional sections crosscutting the basin. Our study suggests that the development, progressive closure, and conversion of this formerly marine basin into a terrestrial intramontane basin result from two main deformation events: (1) Distributed north‐south contraction took place during the late Oligocene–early Miocene, accommodated one third to half of the total shortening and was followed by the formation of a regional erosion surface; and (2) N‐S shortening resumed in the mid‐Miocene and continues today. During this second episode the thrust front migrated southward, localized along the Trans Alai ranges, and failed to reactivate earlier Neogene structures. Horizontal shortening of about 35% across the Alai Valley implies relatively low strain rates and displacement rates of about 4.18–4.69 × 10−16 s−1 and 0.66–0.78 mm yr−1, respectively, for the last 25 Myr. Our study confirms other regional observations indicating that contractional deformation occurred far in the interior of the Asian continent as early as the late Oligocene.
Human Immunodeficiency Virus ( HIV )-Induced Neurotoxicity : Roles for the NMDA Receptor Subtypes 2 A and 2 B and the Calcium-Activated Protease Calpain by a CSF-derived HIV-1 Strain

Neuronal damage in human immunodeficiency virus type 1 (HIV-1) infection in the brain is thought to occur at least in part through NMDA receptor (NMDAR) excitation initiated by soluble neurotoxins from HIV-infected brain macrophages. Furthermore, brain regions enriched in NMDAR-2A (NR2A) and NMDAR-2B (NR2B) subunits, such as the hippocampus, are particularly vulnerable. Using cultured rat hippocampal cells and HIV-1-infected human monocyte-derived macrophages (HIV/MDM), we examined the role of NR2A and NR2B in HIV/MDM-induced hippocampal neuronal death. We used the primary HIV-1 strain Jago derived from the CSF of an individual with HIV-associated dementia and that robustly replicates in MDM. We found the following: (1) hippocampal neuronal susceptibility to HIV/MDM excitotoxins varies according to the developmental expression patterns of NR2A and NR2B; (2) NMDAR activation by HIV/MDM results in neuronal calpain activation, which results in neuronal death; and (3) selective antagonists of homomeric NR2B/NR2Band heteromeric NR2A/NR2B-containing NMDARs, as well as an inhibitor of calpain activity, afford neuroprotection against HIV/MDM. These studies establish a clear link between macrophage HIV infection, neuronal NR2A and NR2B activation, and calpain-mediated hippocampal neuronal death. They further suggest a dominant role for NR2A and NR2B in determining neuronal susceptibility in HIV-infected brain. Antagonists of NR2A and NR2B subunits as well as inhibitors of calpain activation offer attractive neuroprotective approaches against HIV in both developing and mature brain.
Performance enhancement of SSC sound source localization for indoor environment

The steered response power-phase transform algorithm (SRP-PHAT) has been widely utilized for robust sound source localization for indoor environment. Searching space clustering algorithm (SSC) is the improved version of SRP-PHAT, in which the computational complexity could be greatly reduced via the space division and clustering. However, SSC has to frequently perform the space division and clustering when the positions of microphone arrays are changed, which will induce additional computational complexity. In this paper, we proposed a coarse-to-fine region contraction SSC (CFRC-SSC) method to reduce the computational complexity of SSC for the sound source localization algorithm. The coarse level SSC with limited computational complexity will contract the whole searching space to several candidate spaces with limited size, which will reduce the searching volume for fine level SSC without omitting the actual sound source localization. Simulation results demonstrate that the proposed CFRC-SSC show a lower computational complexity in terms of SRP function evaluation times and space clustering calculation times compared to SSC.
For 2-D lattice spin systemsWeak Mixing Implies Strong Mixing

We prove that for nite range discrete spin systems on the two dimensional lattice Z 2 , the (weak) mixing condition which follows, for instance, from the Dobrushin-Shlosman uniqueness condition for the Gibbs state implies a stronger mixing property of the Gibbs state, similar to the Dobrushin-Shlosman complete analiticity condition, but restricted to all squares in the lattice, or, more generally, to all sets multiple of a large enough square. The key observation leading to the proof is that a change in the boundary conditions cannot propagate either in the bulk, because of the weak mixing condition, or along the boundary because it is one dimensional. As a consequence we obtain for ferro-magnetic Ising-type systems proofs that several nice properties hold arbitrarily close to the critical temperature; these properties include the existence of a convergent cluster expansion and uniform boundedness of the logarithmic Sobolev constant and rapid convergence to equilibrium of the associated Glauber dynamics on nice subsets of Z 2 , including the full lattice.
Optimization of Convex Functions with Random Pursuit

We consider unconstrained randomized optimization of convex objective functions. We analyze the Random Pursuit algorithm, which iteratively computes an approximate solution to the optimization problem by repeated optimization over a randomly chosen one-dimensional subspace. This randomized method only uses zeroth-order information about the objective function and does not need any problem-specific parametrization. We prove convergence and give convergence rates for smooth objectives assuming that the one-dimensional optimization can be solved exactly or approximately by an oracle. A convenient property of Random Pursuit is its invariance under strictly monotone transformations of the objective function. It thus enjoys identical convergence behavior on a wider function class. To support the theoretical results we present extensive numerical performance results of Random Pursuit, two gradient-free algorithms recently proposed by Nesterov, and a classical adaptive step-size random search scheme. We also present an accelerated heuristic version of the Random Pursuit algorithm which significantly improves standard Random Pursuit on all numerical benchmark problems. A general comparison of the experimental results reveals that (i) standard Random Pursuit is effective on strongly convex functions with moderate condition number, and (ii) the accelerated scheme is comparable to Nesterov's fast gradient method and outperforms adaptive step-size strategies. The appendix contains additional supporting online material.
The strong equivalence principle from a gravitational gauge structure

Gravitational self-interactions are assumed to be determined by the covariant derivative acting on the Riemann–Christoffel field strength. Once imposed on a metric theory, this Yang–Mills gauge constraint extends the equality of gravitational mass and inertial mass to compact bodies with non-negligible gravitational binding energy. Applied to generalized Brans–Dicke theories, it singles out Einstein's tensor theory and Nordström scalar theory for gravity but also suggests a way to implement a minimal violation of the strong equivalence principle.
Management accounting systems change and departmental performance: the influence of managerial information and task uncertainty

Despite the proliferation of new management accounting techniques amidst pressures of organizational and global change, the issue of changes in firm-wide management accounting and control systems (MACSs) has largely been ignored in the research literature. This study explores the indirect effect of MACSs change on departmental performance for a cross-sectional sample of 232 medium-sized Singaporean firms. It is hypothesized that MACSs change affects performance but not directly. Instead, this relationship is mediated by managerial-relevant information that is impacted by MACSs change, which in turn, enhances performance. Task uncertainty is expected to moderate the intervening linkages; specifically, the latter are anticipated to strengthen under conditions of more task variability and task difficulty and thus, augment the indirect effect of MACSs change on performance. The results offer support for the positive indirect effect of improving departmental performance from more managerial-relevant information, triggered by MACSs change. Although not large, the indirect effect is strengthened when task variability and task difficulty are high. Overall, the findings are consistent with the stated purposes of management accounting that are embedded in normative definitions, and which are relied upon to motivate the framework for analysis.
Teams in Organizations

This article offers a typology of team types found in organizations and reports the results of two surveys sent to U.S. organizations asking about the prevalence, duties, composition, and structure of groups and teams in practice. One sample was randomly selected from the entire population of U.S. organizations; the second sample consisted of organizations known or believed to use teams. Nearly half (48%) of the respondents in the random sample indicated that their organization used some type of team, and ongoing project teams were reported most frequently. Teams were more prevalent in organizations with multiple departments, multiple divisions, higher sales, and more employees. Interpersonal conflict was the best predictor of perceived team effectiveness, but several structural and composition characteristics of the team were related to conflict and/or effectiveness as well. Organizations that reported using teams generally did not support them in terms of team-level performance feedback or compensation practices.
Human tracking using ceiling pyroelectric infrared sensors

This paper presents a novel human tracking scheme by using pyroelectric infrared sensors. The scheme includes the visibility modulation of each sensor detector, the layout of the system, the localization and tracking algorithms. The results from the 3D simulations using Webots and Matlab together validate our scheme, and comparisons with other related schemes are made as well. Simulations show that the proposed approach achieves higher tracking accuracy than those of other schemes.
Agent based control of Virtual Power Plants

The transition of traditional power systems into the flexible smart grids is under way. This paper presents a new interesting concept where Microgrids and other production or consumption units form a Virtual Power Plant. The main goal is to present the advantages of using agents for Virtual Power Plant control. More specifically this paper through examples and case studies presents how the local intelligence and the social ability of the agents may provide solutions in the optimal and effective control of a Virtual Power Plant.
A Development Platform for Wireless Sensor Networks with Biomedical Applications

Wireless sensor network (WSN) is a technology that will become an integral part of everyday life. It has countless potential applications in ubiquitous and pervasive computing, including those in biomedical technology and healthcare industry. As the number and variety of wireless sensor device types increase, a middleware layer capable of linking various implementations into a single programming abstraction will be needed. This paper aims to build a platform that allows users to develop WSN applications with ease, and is robust enough to support complex system development. A flexible platform based on Java and JADE (Java Agent Based Development) is proposed to handle sensor network integration and application development. Design methodology is carefully presented. A prototype implementation is described, and illustrated by an application in the healthcare domain. We believe that this work would help bridging the gaps existed among WSN researchers, application developers, and users, and is significant in realizing the full potential of WSN.
Software Engineering for Self-Adaptive Systems: A Research Road Map (Draft Version) ⁄

Software’s ability to adapt at run-time to changing user needs, system intrusions or faults, changing operational environment, and resource variability has been proposed as a means to cope with the complexity of today’s softwareintensive systems. Such self-adaptive systems can conflgure and reconflgure themselves, augment their functionality, continually optimize themselves, protect themselves, and recover themselves, while keeping most of their complexity hidden from the user and administrator. In this paper, we present research road map for software engineering of selfadaptive systems focusing on four views, which we identify as essential: requirements, modelling, engineering, and assurances.
Semantics and pragmatics in the derivation of aspectual readings in Russian

Natural language expressions are generally underspecified and need specification of different kinds to get a contextually relevant interpretation. One instance of underspecification is the imperfective aspect in Russian, which gives rise to a considerable variety of readings. This poses certain problems for an account in purley semantic terms: What is the common denominator of all these interpretations? Is there a systematic way to derive the different readings? To answer these and related questions, this paper proposes a an account in more pragmatic terms based on a ‘selectional theory’ of aspect.
SVD Block Processing for Non-linear Image Noise Filtering

A new algorithm for noise filtering, based on non-linear processing of image in blocks, using singular value decomposition (SVD) is presented in this paper. Noise filtering is performed in the domain of singular values and singular vectors. A priori noise variance knowledge is not required, because singular value-based noise variance estimation is performed in the first phase of the procedure. The non-linear filtering is based on eliminating changes in singular values and singular vectors caused by additional Gaussian white noise. Processing of image in smaller blocks makes SYD-based procedure computationally feasible. Experimental results have demonstrated the validity of the approach.
Insect egg deposition induces defence responses in Pinus sylvestris: characterisation of the elicitor

SUMMARY Egg deposition by the phytophagous sawfly Diprion pini L. (Hymenoptera, Diprionidae) is known to induce locally and systemically the emission of volatiles in Scots pine (Pinus sylvestris L.) that attract the egg parasitoid Chrysonotomyia ruforum Krausse (Hymenoptera, Eulophidae). The egg parasitoids kill the eggs and thus prevent damage to the plant from feeding sawfly larvae. The elicitor inducing the pine's response is known to be located in the oviduct secretion which the female sawfly applies to the eggs when inserting them into a slit in the pine needle using the sclerotized ovipositor valves. In this study we have characterized the elicitor. The elicitor was still active when isolated from the oviduct and applied directly to slits made in the pine needles. However, as soon as the oviduct secretion was dissolved in Aqua dest. and stored for 3 h at room temperature or kept frozen at -80°C, its activity was lost. In contrast, oviduct secretion kept its eliciting activity, when dissolved in Ringer solution (pH 7.2) both after storage at room temperature and after freezing. The activity of the elicitor vanished after treatment of the oviduct secretion with proteinase K, which destroyed all proteins. This suggests that the elicitor in the oviduct secretion is a peptide or protein, or a component bound to these. SDS-PAGE revealed a similar, but not identical protein pattern from hemolymph and oviduct secretion. Hemolymph itself has no eliciting effect. The elicitor in the oviduct secretion is only active when transferred to slit pine needles, since its application on undamaged needles did not induce the emission of attractive volatiles.
UC Merced Proceedings of the Annual Meeting of the Cognitive Science Society Title Grounded Representations for Sensory-Motor Learning : A Linguistic Approach

We have empirically discovered that the space of human actions has a linguistic structure. This is a sensory-motor space consisting of the evolution of the joint angles of the human body in movement. The space of human activity has its own phonemes, morphemes, words (nouns, verbs, adjectives, adverbs), and sentences formed by syntax. This has a number of implications for the grounding problem and cognition in general. We present a Human Activity Language (HAL) for symbolic manipulation of visual and motor information. The embodiment of the language serves as the interface between visual perception and the motor subsystem. The visuo-motor language is defined using a linguistic approach. In phonology, we define basic atomic segments that are used to compose human activity. In morphology, we study how visuo-motor phonemes are combined to form strings representing human activity and to generate a higher-level morphological grammar. In syntax, we present a model for visuo-motor sentence construction where the subject corresponds to the active joints (noun) modified by a posture (adjective). A verbal phrase involves the representation of the human activity (verb) and timing coordination among different joints (adverb).
Fairness PEP solution for satellite TCP

Satellite communication is widely deployed because of its wide coverage. However, satellite links show very poor TCP performances because of its disadvantages such as very long round trip time, high packet loss rate and limited bandwidths. In this paper, we suggest the Performance Enhancing Proxy (PEP) solution applied with 3-segment splitting. On top of that, we also apply the Token Bucket Filter (TBF) algorithm into our PEP solution to improve TCP fairness. The performance analysis is performed in a real test-bed and proves that 3-segment splitting based PEP solution can improve TCP throughput over satellite environments. Furthermore, our TBF algorithm is effective for improving TCP fairness and ensuring TCP throughput.