Miracle-dz/UniFAR-FTUs huggingface dataset:
Cvt9/Gsa9 Functions in Sequestering Selective Cytosolic Cargo Destined for the Vacuole

Three overlapping pathways mediate the transport of cytoplasmic material to the vacuole in Saccharomyces cerevisiae. The cytoplasm to vacuole targeting (Cvt) pathway transports the vacuolar hydrolase, aminopeptidase I (API), whereas pexophagy mediates the delivery of excess peroxisomes for degradation. Both the Cvt and pexophagy pathways are selective processes that specifically recognize their cargo. In contrast, macroautophagy nonselectively transports bulk cytosol to the vacuole for recycling. Most of the import machinery characterized thus far is required for all three modes of transport. However, unique features of each pathway dictate the requirement for additional components that differentiate these pathways from one another, including at the step of specific cargo selection. We have identified Cvt9 and its Pichia pastoris counterpart Gsa9. In S. cerevisiae, Cvt9 is required for the selective delivery of precursor API (prAPI) to the vacuole by the Cvt pathway and the targeted degradation of peroxisomes by pexophagy. In P. pastoris, Gsa9 is required for glucose-induced pexophagy. Significantly, neither Cvt9 nor Gsa9 is required for starvation-induced nonselective transport of bulk cytoplasmic cargo by macroautophagy. The deletion of CVT9 destabilizes the binding of prAPI to the membrane and analysis of a cvt9 temperature-sensitive mutant supports a direct role of Cvt9 in transport vesicle formation. Cvt9 oligomers peripherally associate with a novel, perivacuolar membrane compartment and interact with Apg1, a Ser/Thr kinase essential for both the Cvt pathway and autophagy. In P. pastoris Gsa9 is recruited to concentrated regions on the vacuole membrane that contact peroxisomes in the process of being engulfed by pexophagy. These biochemical and morphological results demonstrate that Cvt9 and the P. pastoris homologue Gsa9 may function at the step of selective cargo sequestration.
Ja n 20 03 Bicontinuous surfaces in self-assembling amphiphilic systems

Amphiphiles are molecules which have both hydrophilic and hydrophobic parts. In waterand/or oil-like solvent, they self-assemble into extended sheet-like structures due to the hydrophobic effect. The free energy of an amphiphilic system can be written as a functional of its interfacial geometry, and phase diagrams can be calculated by comparing the free energies following from different geometries. Here we focus on bicontinuous structures, where one highly convoluted interface spans the whole sample and thereby divides it into two separate labyrinths. The main models for surfaces of this class are triply periodic minimal surfaces, their constant mean curvature and parallel surface companions, and random surfaces. We discuss the geometrical properties of each of these types of surfaces and how they translate into the experimentally observed phase behavior of amphiphilic systems. 1 Surfaces in self-assembling amphiphilic systems The subject of this article is the theoretical description of amphiphilic systems, which are one example of soft condensed matter. Soft matter is material that has a typical energy scale of kBT ≈ 4 × 10J , where kB is the Boltzmann constant and T ≈ 300K is room temperature. For such material, perturbations arising from the thermally activated movement of its molecular components are sufficient to induce configurational changes, and entropy is at least equally important as energy in determining its material properties. The understanding of the underlying mechanisms is essential for the application of many technologies in everyday life, including colloidal dispersions (paints, inks, food, creams,
A Tool for Modeling Strategy and Aligned Portfolio Selection

A company depends on the definition and implementation of a set of projects aligned with the vision established by its senior management to accomplish its strategies. To this set of projects is given the name of portfolio. This paper implements a collaborative tool to support the construction and selection of a project portfolio aligned with the corporate strategy. The tool is capable of modeling the strategy through the construction of a strategy map and also to select a good portfolio applying this map in a multi-criteria algorithm. The tool was applied in three small companies to validate its capabilities.
No Feasible Monotone Interpolation for Cut-free Gentzen Type Propositional Calculus with Permutation Inference

The feasible monotone interpolation method has been one of the main tools to prove the exponential lowerbounds for relatively weak propositional systems. In [2], we introduced a simple combinatorial reasoning system, GCNF+permutation, as a candidate for an automatizable, though powerful, propositional calculus. We show that the monotone interpolation method is not applicable to prove the superpolynomial lower bounds for GCNF+permutation. At the same time, we show that Cutting Planes, Hilbert's Nullstellensatz and the polynomial calculus do not p-simulate GCNF+permutation. keywords: automated theorem proving, proof complexity, Craig's interpolation theorem, proof theory
Performance comparison of multicast-encouraging Explicit Rate Adjustment and packet-pair layered multicast

Multicast-encouraging explicit rate adjustment (MeERA) and packet-pair receiver-driven cumulative layer multicast (PLM) are two of the recently proposed receiver-driven layered multicast congestion control protocols. Both have used explicit rate adjustment techniques in detecting and controlling congestion. Both have also been evaluated by their authors and claim a few advances. However, there is no known study that evaluates these protocols in comparison. In this work, we evaluate both of them in comparison using criteria such as responsiveness, the efficiency of network utilization, fairness, TCP-friendliness, fast convergence, coordination of receivers behind the same bottleneck link, and feasibility in terms of implementation. Performance evaluation is done using a network simulator (ns2).
The 68 kDa subunit of mammalian cleavage factor I interacts with the U7 small nuclear ribonucleoprotein and participates in 3′-end processing of animal histone mRNAs

Metazoan replication-dependent histone pre-mRNAs undergo a unique 3′-cleavage reaction which does not result in mRNA polyadenylation. Although the cleavage site is defined by histone-specific factors (hairpin binding protein, a 100-kDa zinc-finger protein and the U7 snRNP), a large complex consisting of cleavage/polyadenylation specificity factor, two subunits of cleavage stimulation factor and symplekin acts as the effector of RNA cleavage. Here, we report that yet another protein involved in cleavage/polyadenylation, mammalian cleavage factor I 68-kDa subunit (CF Im68), participates in histone RNA 3′-end processing. CF Im68 was found in a highly purified U7 snRNP preparation. Its interaction with the U7 snRNP depends on the N-terminus of the U7 snRNP protein Lsm11, known to be important for histone RNA processing. In vivo, both depletion and overexpression of CF Im68 cause significant decreases in processing efficiency. In vitro 3′-end processing is slightly stimulated by the addition of low amounts of CF Im68, but inhibited by high amounts or by anti-CF Im68 antibody. Finally, immunoprecipitation of CF Im68 results in a strong enrichment of histone pre-mRNAs. In contrast, the small CF Im subunit, CF Im25, does not appear to be involved in histone RNA processing.
Biological Extremity Reconstruction after Sarcoma Resection: Past, Present, and Future

In sarcoma surgery besides a wide local resection, limb salvage became more and more important. Reconstruction of bone and soft tissue defects after sarcoma resection poses a major challenge for surgeons. Nowadays a broad range of reconstructive methods exist to deal with bony defects. Among these are prostheses, bone autografts, or bone allografts. Furthermore a variety of plastic reconstructive techniques exist that allow soft tissue reconstruction or coverage after sarcoma resection. Here we discuss the historical highlights, the present role, and possible future options for biological reconstruction.
Data Structures for Big Data

The present day world dealing with big data (expanding very fast in 4Vs: Volume, Varity, Velocity and Veracity) needs New advanced kind of logical and physical storage structures, New advanced kind of heterogeneous data structures, New mathematical theories and New models for processing giant big data in 4Vs. In the literature, there is no appropriate data structure for big data, no appropriate network topology for big data, no appropriate distributed system for big data. The existing data structures, network topologies and type of distributed system are not sufficiently rich to deal with big data. The existing network topologies like tree topology or bus/ring/star/mesh/hybrid topologies seem to be weak topologies for big data processing. For a success, there is no other way but to develop ‘new data structures’, ‘new type of distributed systems’ having a very fast and tremendous extent of mutual compatibility and mutual understanding with the new data structures, ‘new type of network topologies’ to support the new distributed system, and of course ‘new mathematical/logical theory’ models. Needless to mention that the next important issue is how to integrate all these ‘new’ to make ultimately a single and simple scalable system to the laymen users. With these views in mind, Biswas [11, 12, 15] introduced a new special type of fundamental data structure ‘atrain’ exclusively for heterogeneous big data (where, the data structure ‘train’ is exclusively for homogeneous big data) and then introduced a new distributed system called by ‘Atrain Distributed System’ (ADS) which can process big data of any 4V of any momentum. The rich merit of ADS [15] is due to its layout architecture making it infinitely scalable both in breadth (horizontally) and depth (vertically). The ‘Atrain Distributed System’ (ADS) could be unitier or multitier having a single unique Pilot Computer (PC) and several Distributed Computers (DCs) connected by new
International Conference on Information Fusion ( FUSION ) Distrbuted Data Association for Multi-Target Tracking in Sensor Networks

Associating sensor measurements with target tracks is a fundamental and challenging problem in multi-target tracking. The problem is even more challenging in the context of sensor networks, since association is coupled across the network, yet centralized data processing is in general infeasible due to power and bandwidth limitations. Hence efficient, distributed solutions are needed. We propose techniques based on graphical models to efficiently solve such data association problems in sensor networks. Our approach takes advantage of the sparsity inherent in the problem structure resulting from the fact that each target can be observed by only a small number of sensors and makes use of efficient message-passing algorithms for graphical models to infer the maximum a posteriori association configuration. We illustrate our approach for several typical scenarios in multitarget tracking. Our approach scales well with the number of sensor nodes in the network, and it is well-suited for distributed implementation. Distributed inference is realized by a messagepassing algorithm which requires iterative, parallel exchange of information among neighboring nodes on the graph. So as to address trade-offs between inference performance and communication costs, we also propose a communication-sensitive form of message-passing that is capable of achieving near-optimal performance using far less communication. We demonstrate the effectiveness of our approach with experiments on simulated data.
An Unsolvable Problem of Elementary Number Theory

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Performance Evaluation of Voice-Data Integrated Traffic in IEEE 802 . 11 and IEEE 802 . 16 e WLAN

With the advent of 4G mobile communication system the traffic of wired and wireless network becomes voice/videodata integrated service. In this paper traffic model of Markov Modulated Poisson Process (MMPP) is applied for bursty traffic of Wireless LAN (WLAN), especially in IEEE 802.11 WLAN, known as WiFi, and IEEE 802.16e WLAN is known as WiMAX. Traffic of both networks is heavily affected by the fading of wireless channel. The traffic parameters of IEEE 802.11 WLAN are evaluated using Giuseppe Bianchi state transition chain. The profile of probability of idle condition, the probability of one successful transmission and the probability of collision is shown against the number of users. The packet blocking probability and throughput of WLAN are observed varying packet arrival rate. In this paper, a mathematical model of VoIP traffic over wireless channel under IEEE 802.16e WLAN is also analyzed under Rayleigh and Nakagami-m fading cases with the help of MMPP and discrete time Markov chain (DTMC) model. Finally, mean delay of both wired and wireless LAN are compared. Key-Words: Voice-data integrated service, MMPP, DTMC, Rayleigh fading, Nakagami-m fading, VoIP.
Differential Effects of Mechanical and Biological Stimuli on Matrix Metalloproteinase Promoter Activation in the Thoracic Aorta

Background— The effect of multiple integrated stimuli on vascular wall expression of matrix metalloproteinases (MMPs) remains unknown. Accordingly, this study examined the influence of the vasoactive peptide angiotensin II (Ang II) on wall tension–induced promoter activation of MMP-2, MMP-9, and membrane type-1 MMP (MT1-MMP). Methods and Results— Thoracic aortic rings harvested from transgenic reporter mice containing the MMP-2, MMP-9, or MT1-MMP promoter sequence fused to a reporter gene were subjected to 3 hours of wall tension at 70, 85, or 100 mm Hg, with or without 100 nM Ang II. Total RNA was harvested from the aortic rings, and reporter gene transcripts were quantified by quantitative real-time polymerase chain reaction to measure MMP promoter activity. MT1-MMP promoter activity was increased at both 85 and 100 mm Hg, compared with baseline tension of 70 mm Hg, whereas treatment with Ang II stimulated MT1-MMP promoter activity to the same degree at all tension levels (P<0.05). Elevated tension and Ang II displayed a potential synergistic enhancement of MMP-2 promoter activation at 85 and 100 mm Hg, whereas the same stimuli caused a decrease in MMP-9 promoter activity (P<0.05) at 100 mm Hg. Conclusions— This study demonstrated that exposure to a relevant biological stimulus (Ang II) in the presence of elevated tension modulated MMP promoter activation. Furthermore, these data suggest that a mechanical-molecular set point exists for the induction of MMP promoter activation and that this set point can be adjusted up or down by a secondary biological stimulus. Together, these results may have significant clinical implications toward the regulation of hypertensive vascular remodeling.
Advances in Studies and Applications of Centroidal Voronoi Tessellations

Centroidal Voronoi tessellations (CVTs) have become a useful tool in many applications ranging from geometric modeling, image and data analysis, and numerical partial differential equations, to problems in physics, astrophysics, chemistry, and biology. In this paper, we briefly review the CVT concept and a few of its generalizations and well-known properties. We then present an overview of recent advances in both mathematical and computational studies and in practical applications of CVTs. Whenever possible, we point out some outstanding issues that still need investigating. AMS subject classifications: 5202, 52B55, 62H30, 6502, 65D30, 65U05, 65Y25, 68U05, 68U10
The temporal context of face perception : behavioural, electrophysiological and neuroimaging correlates

Adaptation-related aftereffects (AEs) and repetition priming (PR) are two phenomena when recent experiences alter face perception. Although the behavioural reflections of AEs and PR are quite different, both phenomena share some similarities regarding their functional properties and neural correlates. As most of the previous studies focused on either one or the other phenomenon, little is known about the relationship between AEs and PR. The present studies attempted to fill this gap. Study I investigated face identity AEs and PR within the same stimulus repetition paradigm, keeping timing and task constant. Following face or Fourier phase randomized (noise) stimuli, participants classified test faces varying on a morph continuum between two famous identities. Study I showed that AEs and PR can be observed within the same paradigm and subjects, behaviourally and in event-related potentials (ERPs). Interestingly, we found identity-specific as well as category-specific ERP modulations. Study II further investigated the factors underlying face identity AEs in a similar paradigm. The results confirmed and extended the findings of Study I, e.g., there were again different ERP modulations by stimulus category and face identity. In Study III, AEs and image-specific PR were investigated in the perception of face gender using functional magnetic resonance imaging (fMRI). Study III suggested dissociations between 1) gender-specific AEs and image-specific PR in behaviour, 2) brain areas associated with AEs and PR, and 3) brain areas associated with gender-specific and categorical processes. In conclusion, the present studies showed that similarity between adaptor and test faces and ambiguity of the test face both determine whether AE or PR is observed, and suggested that exclusive mechanisms might underlie both phenomena. Our results also revealed that the processing of face identity or gender runs in parallel to object-category processing during the earlier processing stages.
Dynamic Grid Refinement for Fluid Simulations on Parallel Graphics Architectures

We present a physically-based fluid simulation with dynamic grid refinement on parallel SIMD graphics hardware. The irregular and dynamic structure of an adaptive grid requires sophisticated memory access patterns as well as a decomposition of the problem for parallel processing and the distribution of tasks to multiple threads. In this paper, we focus on the representation and management of the dynamic grid on the graphics device for an efficient parallelization of the advection step and the iterative solving of the Poisson equation. In order to achieve high performance, we utilize the hardware's capabilities like fast cache access and trilinear filtering. Furthermore, expensive data transfer between host and device is minimized to avoid a major bottleneck. We report results on the inherent overhead of the dynamic grid compared to an equivalent Cartesian grid. In addition, a visual simulation of smoke is presented with radiosity-based illumination and volume ray casting at interactive frame rates.
Effects of Simulated Climate Change on Plant Phenology and Nitrogen Mineralization in Alaskan Arctic Tundra

ABSTRACT This study was part of the International Tundra Experiment (ITEX) and examined the effects of increased winter snow depth and decreased growing season length on the phenology of four arctic plant species (Betula nana, Salix pulchra, Eriophorum vaginatum, and Vaccinium vitis-idaea) and seasonal nitrogen availability in arctic snowbed communities. Increased snow depth had a large effect on the temporal pattern of first date snow-free in spring, bud break, and flowering, but did not affect the rate of plant development. By contrast, snow depth had a large qualitative effect on N mineralization in deep snow zones, causing a shift in the timing and amount of N mineralized compared to ambient snow zones. Nitrogen mineralization in deep snow zones occurred mainly overwinter, whereas N mineralization in ambient snow zones occurred mainly in spring. Concentrations of soil dissolved organic nitrogen (DON) were approximately 5 times greater than concentrations of inorganic nitrogen (DIN) and did not vary significantly over the season. Projected increases in the depth and duration of snow cover in arctic plant communities will likely have minor effects on the rate of plant phenological development, but potentially large effects on patterns of N cycling.
Correlations Between Leptin Gene Polymorphisms 223 A/G, 1019 G/A, 492 G/C, 976 C/A, and Anthropometrical and Biochemical Parameters in Children With Obesity

AbstractThe aim of this study was to establish the manner in which the LEPR 223, 1019, 492, and 976 gene polymorphisms influence child obesity.We performed a prospective case-control study on 264 hospitalized children from Romania (Nutrichild study) whom we divided into 2 groups: Group I —143 controls and Group II—121 obese children.The 2 groups were evaluated regarding the anthropometry (MUAC, TST, H/L, hip, and abdominal circumference), paraclinical results (protein, leptin, adiponectin, TNF alfa, IL 6, IL 8, VEGF, protein, albumin) and LEPR 223, 1019, 492, and 976 gene polymorphisms. We noticed that the most frequent genotypes in obese children were AG+GG for LEPR 223 gene (P = 0.0001) and GA+AA for LEPR 1019 gene (P = 0.0001), whereas LEPR 492 and LEPR 976 gene polymorphisms did not correlate with obesity. MUAC, TST, H/L, leptin, and adiponectin were correlated with the GG genotype of the LEPR 223 gene, whereas the AG genotype correlated with TNF alpha and serum IL 8. Hip and abdominal perimeters were higher in LEPR 1019 AA genotype carriers, whereas TNF alpha and IL 6 correlated with the GG genotype of the same gene. Obesity did not correlate with protein serum levels.We observed that obesity is more frequent in children with LEPR 223 AG+GG and LEPR 1019 GA+AA genotypes. In obese children LEPR 223/492/1019 AG/GG/GA, GG/GG/GA and AA/GG/GA combined genotypes are more frequent.