Miracle-dz/UniFAR-FTUs huggingface dataset:
00 8 v 1 3 0 A pr 2 00 5 Fragmentation and Evolution of Molecular Clouds . I : Algorithm and First Results

We present a series of simulations of the fragmentation of a molecular cloud, leading to the formation of a cluster of protostellar cores. We use Gaussian initial conditions with a power spectrum P (k) ∝ k −2 , assume an isothermal equation of state, and neglect turbulence and magnetic fields. The purpose of these simulations is to address a specific numerical problem called artificial fragmentation, that plagues simulations of cloud fragmentation with the Smoothed Particle Hydrodynamics algorithm (SPH). We argue that this is a serious problem that needs to be addressed, and that the only reasonable and practical way to address it is to use a relatively new technique called particle splitting. We performed three simulations, in which we allow N gen = 0, 1, and 2 levels of particle splitting. All simulations start up with 64 3 SPH particles, but their effective resolutions correspond to 64 3 , 128 3 , and 256 3 particles, respectively. The third simulation has a much higher resolution than most previous SPH simulations of cloud fragmentation, and is the first simulation of this kind to properly resolve the Jeans mass throughout the entire system, at all times, thus preventing artificial fragmentation. The high resolution of our simulations results in the formation of a large number of protostellar cores, nearly 3000 for the largest simulation. This greatly exceeds the typical number of cores (∼ 60) formed in previous simulations, and enabled us to discover various processes that affect the growth of the cores and the evolution of the cluster. The evolution of the cloud follows four distinct phases, or regimes. Initially, during the growth regime, the cloud evolves into a network of intersecting filaments. After roughly one dynamical time, core formation starts inside the dense gaseous fragments located at the intersection of the filaments, and to a lesser extent inside the filaments themselves, and the cloud enters the collapse regime. During this regime about 50% of the gas, essentially the gas that started up in overdense regions, is converted into cores. Competitive accretion is the main process that controls the mass evolution of cores, but we discovered that this process occurs locally, within each dense fragment. During the following accretion regime, most of the remaining gas does not form new cores, but rather accretes onto the existing cores. Eventually each gaseous fragment has turned into a subcluster of cores, and these subclusters later merge …
Lattice Modeling of Early-Age Behavior of Structural Concrete

The susceptibility of structural concrete to early-age cracking depends on material composition, methods of processing, structural boundary conditions, and a variety of environmental factors. Computational modeling offers a means for identifying primary factors and strategies for reducing cracking potential. Herein, lattice models are shown to be adept at simulating the thermal-hygral-mechanical phenomena that influence early-age cracking. In particular, this paper presents a lattice-based approach that utilizes a model of cementitious materials hydration to control the development of concrete properties, including stiffness, strength, and creep resistance. The approach is validated and used to simulate early-age cracking in concrete bridge decks. Structural configuration plays a key role in determining the magnitude and distribution of stresses caused by volume instabilities of the concrete material. Under restrained conditions, both thermal and hygral effects are found to be primary contributors to cracking potential.
Multinets, resonance varieties, and pencils of plane curves

We show that a line arrangement in the complex projective plane supports a nontrivial resonance variety if and only if it is the underlying arrangement of a ‘multinet’, a multi-arrangement with a partition into three or more equinumerous classes which have equal multiplicities at each inter-class intersection point, and satisfy a connectivity condition. We also prove that this combinatorial structure is equivalent to the existence of a pencil of plane curves, also satisfying a connectivity condition, whose singular fibers include at least three products of lines, which comprise the arrangement. We derive numerical conditions which impose restrictions on the number of classes, and the line and point multiplicities that can appear in multinets, and allow us to detect whether the associated pencils yield nonlinear fiberings of the complement.
Routing using potentials: a dynamic traffic-aware routing algorithm

We present a routing paradigm called PBR that utilizes steepest gradient search methods to route data packets. More specifically, the PBR paradigm assigns scalar potentials to network elements and forwards packets in the direction of maximum positive force. We show that the family of PBR schemes are loop free and that the standard shortest path routing algorithms are a special case of the PBR paradigm. We then show how to design a potential function that accounts for traffic conditions at a node. The resulting routing algorithm routes around congested areas while preserving the key desirable properties of IP routing mechanisms including hop-by-hop routing, local route computations and statistical multiplexing. Our simulations using the ns simulator indicate that the traffic aware routing algorithm shows significant improvements in end-to-end delay and jitter when compared to standard shortest path routing algorithms. The simulations also indicate that our algorithm does not incur too much control overheads and is fairly stable even when traffic conditions are dynamic.
Specific Death Symptoms and Organic Lesions of Blood Clam Tegillarca granosa in Acute Copper, Zinc, Lead and Cadmium Exposures

Blood clam, Tegillarca granosa, habit in near-shore muddy sediments facing increasing danger of heavy metal contamination. In order to assess the acute toxicity of heavy metals on T. granosa, short term lethal concentration (LC50) of copper (Cu), zinc (Zn), lead (Pb), and cadmium (Cd) were determined, symptoms of death and organic lesions were illustrated. With relative high LC50 values obtained, T. granosa showed great heavy metal tolerance indicates adaptations to habitat environment. T. granosa died in acute Cd exposure showed specific death symptom with foot extended outside of the tightly closed shells. In this study, different metals led to different organic lesions. Dark red erosive and inflamed gills were observed for T. granosa exposed to acute Cu and Pb, respectively. Inflamed gonad and foot, and contracted mantle were observed for Cd and Zn exposure trials, respectively. The results of this study may provide knowledge to assist in heavy metal pollution bio-monitoring and quick diagnosis of massive death incidence.
Complex evolution of orthologous and paralogous decarboxylase genes

The decarboxylases are involved in neurotransmitter synthesis in animals, and in pathways of secondary metabolism in plants. Different decarboxylase proteins are characterized for their different substrate specificities, but are encoded by homologous genes. We study, within a maximum‐likelihood framework, the evolutionary relationships among dopa decarboxylase (Ddc), histidine decarboxylase (Hdc) and α‐methyldopa hypersensitive (amd) in animals, and tryptophan decarboxylase (Wdc) and tyrosine decarboxylase (Ydc) in plants. The evolutionary rates are heterogeneous. There are differences between paralogous genes in the same lineages: 4.13 × 10−10 nucleotide substitutions per site per year in mammalian Ddc vs. 1.95 in Hdc; between orthologous genes in different lineages, 7.62 in dipteran Ddc vs. 4.13 in mammalian Ddc; and very large temporal variations in some lineages, from 3.7 up to 54.9 in the Drosophila Ddc lineage. Our results are inconsistent with the molecular clock hypothesis.
Efficient MATLAB Computations with Sparse and Factored Tensors

In this paper, the term tensor refers simply to a multidimensional or $N$-way array, and we consider how specially structured tensors allow for efficient storage and computation. First, we study sparse tensors, which have the property that the vast majority of the elements are zero. We propose storing sparse tensors using coordinate format and describe the computational efficiency of this scheme for various mathematical operations, including those typical to tensor decomposition algorithms. Second, we study factored tensors, which have the property that they can be assembled from more basic components. We consider two specific types: A Tucker tensor can be expressed as the product of a core tensor (which itself may be dense, sparse, or factored) and a matrix along each mode, and a Kruskal tensor can be expressed as the sum of rank-1 tensors. We are interested in the case where the storage of the components is less than the storage of the full tensor, and we demonstrate that many elementary operations can be computed using only the components. All of the efficiencies described in this paper are implemented in the Tensor Toolbox for MATLAB.
Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA

The DNA polymerases involved in DNA replication achieve high processivity of nucleotide incorporation by forming a complex with processivity factors. A model system for replicative DNA polymerases, the bacteriophage T7 DNA polymerase (gp5), encoded by gene 5, forms a tight, 1∶1 complex with Escherichia coli thioredoxin. By a mechanism that is not fully understood, thioredoxin acts as a processivity factor and converts gp5 from a distributive polymerase into a highly processive one. We use a single-molecule imaging approach to visualize the interaction of fluorescently labeled T7 DNA polymerase with double-stranded DNA. We have observed T7 gp5, both with and without thioredoxin, binding nonspecifically to double-stranded DNA and diffusing along the duplex. The gp5/thioredoxin complex remains tightly bound to the DNA while diffusing, whereas gp5 without thioredoxin undergoes frequent dissociation from and rebinding to the DNA. These observations suggest that thioredoxin increases the processivity of T7 DNA polymerase by suppressing microscopic hopping on and off the DNA and keeping the complex tightly bound to the duplex.
The Systemic Theory of Living Systems and Relevance to CAM

The Systemic Theory of Living Systems is being published in several parts in eCAM. The theory is axiomatic. It originates from the phenomenological idea that physiological health is based on three factors: integrity of its structure or organization, O, functional organic energy reserve, E, and level of active biological intelligence, I. From the theory is derived a treatment strategy called Systemic Medicine (SM). This is based on identifying and prescribing phytomedicines and/or other medications that strengthen each factor. Energy-stimulating phytomedicines increase available energy and decrease total entropy of an open biological system by providing negative entropy. The same occurs with phytomedicines that act as biological intelligence modulators. They should be used as the first line of treatment in all ailments, since all pathologies, by definition, imply a higher than normal organic entropy. SM postulates that the state of health, H, of an individual, is effectively equal to the product of the strength of each factor H = O × E × I. SM observes that when all three factors are brought back to ideal levels, patients' conditions begin the recovery to normal health.
Strain‐dependent regulation of neurotransmission and actin‐remodelling proteins in the mouse hippocampus

Individual mouse strains differ significantly in terms of behaviour, cognitive function and long‐term potentiation. Hippocampal gene expression profiling of eight different mouse strains points towards strain‐specific regulation of genes involved in neuronal information storage. Protein expression with regard to strain‐ dependent expression of structures related to neuronal information storage has not been investigated yet. Herein, a proteomic approach based on two‐dimensional gel electrophoresis coupled with mass spectrometry (MALDI‐TOF/TOF) has been chosen to address this question by determining strain‐dependent expression of proteins involved in neurotransmission and activity‐induced actin remodelling in hippocampal tissue of five mouse strains. Of 31 spots representing 16 different gene products analysed and quantified, N‐ethylmaleimide‐sensitive fusion protein, N‐ethylmaleimide‐sensitive factor attachment protein‐α, actin‐like protein 3, profilin and cofilin were expressed in a strain‐dependent manner. By treating protein expression as a phenotype, we have shown significant genetic variation in brain protein expression. Further experiments in this direction may provide an indication of the genetic elements that contribute to the phenotypic differences between the selected strains through the expressional level of the translated protein. In view of this, we propose that proteomic analysis enabling to concomitantly survey the expression of a large number of proteins could serve as a valuable tool for genetic and physiological studies of central nervous system function.
Study of combined effects of zero copy and pre-processing on Input/Output performance of multimedia on demand streaming server

The growing broadband internet connectivity has made services like Media on Demand (MoD) and News on Demand (NoD) a huge business. Media servers play an important role and critical part of providing real time MoD services. The major challenges are the handling of multimedia files and their real time streaming, which require fast processing as well as transmission of multimedia by the server. One of the important features of media server design is Input/Output (I/O) performance of multimedia files to network. This performance also affects the overall delay in case of end-to-end QoS. In this paper, we have proposed an idea to improve the I/O performance by enhancing zero copy methodology with pre-processed multimedia. Our proposed idea's implementation results present five times reduction of total transmission and processing time delay in comparison to without zero copying and pre-processing in media server. Moreover, there is a 15% reduction in CPU usage of the multimedia server.
A Split Cache Hierarchy for Enabling Data-Oriented Optimizations

Today's caches tightly couple data with metadata (Address Tags) at the cache line granularity. The co-location of data and its identifying metadata means that they require multiple approaches to locate data (associative way searches and level-by-level searches), evict data (coherent writebacks buffers and associative level-by-level searches) and keep data coherent (directory indirections and associative level-by-level searches). This results in complex implementations with many corner cases, increased latency and energy, and limited flexibility for data optimizations. We propose splitting the metadata and data into two separate structures: a metadata hierarchy and a data hierarchy. Themetadata hierarchy tracks the location of the data in the data hierarchy. This allows us to easily apply many differentoptimizations to the data hierarchy, including smart data placement, dynamic coherence, and direct accesses. The new split cache hierarchy, Direct-to-Master (D2M), provides a unified mechanism for cache searching, eviction, and coherence, that eliminates level-by-level data movement and searches, associative cache address tags comparisons andabout 90% of the indirections through a central directory. Optimizations such as moving LLC slices to the near-side ofthe network and private/shared data classification can easily be built on top off D2M to further improve its efficiency. Thisapproach delivers a 54% improvement in cache hierarchy EDP vs. a mobile processor and 40% vs. a server processor, reducesnetwork traffic by an average of 70%, reduces the L1 miss latency by 30% and is especially effective for workloads with high cache pressure.
Striated flagellar roots: isolation and partial characterization of a calcium-modulated contractile organelle

We report the isolation of striated flagellar roots from the Prasinophycean green alga Tetraselmis striata using sedimentation in gradients of sucrose and flotation on gradients of colloidal silica. PAGE in the presence of 0.1% SDS demonstrates that striated flagellar roots are composed of a number of polypeptides, the most predominant one being a protein of 20,000 Mr. The 20,000 Mr protein band represents approximately 63% of the Coomassie Brilliant Blue staining of gels of isolated flagellar roots. Two-dimensional gel electrophoresis (isoelectric focusing and SDS PAGE) resolves the major 20,000 Mr flagellar root protein into two components of nearly identical Mr, but of differing isoelectric points (i.e., pl's of 4.9 and 4.8), which we have designated 20,000-Mr-alpha and 20,000-Mr-beta, respectively. Densitometric scans of two-dimensional gels of cell extracts indicate that the 20,000-Mr-alpha and -beta polypeptides vary, in their stoichiometry, between 2:1 and 1:1. This variability appears to be related to the state of contraction or extension of the striated flagellar roots at the time of cell lysis. Incubation of cells with 32PO4 followed by analysis of cell extracts by two-dimensional gel electrophoresis and autoradiography reveals that the more acidic 20,000- Mr-beta component is phosphorylated and the 20,000-Mr-alpha component contains no detectable label. These results suggest that the 20,000-Mr- alpha component is converted to the more acidic 20,000-Mr-beta form by phosphorylation. Both the 20,000-Mr-alpha and -beta flagellar root components exhibit a calcium-induced reduction in relative electrophoretic mobilities in two-dimensional alkaline urea gels. Antiserum raised in rabbits against the 20,000-Mr protein binds to both the 20,000-Mr-alpha and 20,000-Mr-beta forms of the flagellar root protein when analyzed by electrophoretic immunoblot techniques. Indirect immunofluorescence on vegetative or interphase cells demonstrate that the antibodies bind to two cyclindrical organelles located in the anterior region of the cell. Immunocytochemical investigations at ultrastructural resolution using this antiserum and a colloidal gold-conjugated antirabbit-IgG reveals immunospecific labeling of striated flagellar roots and their extensions. We conclude that striated flagellar roots are simple ion-sensitive contractile organelles composed predominantly of a 20,000 Mr calcium-binding phosphoprotein, and that this protein is largely responsible for the motile behavior of these organelles.
Limits on the provable consequences of one-way permutations

We present strong evidence that the implication, “if one-way permutations exist, then secure secret key agreement is possible”, is not provable by standard techniques. Since both sides of this implication are widely believed true in real life, to show that the implication is false requires a new model. We consider a world where all parties have access to a black box for a randomly selected permutation. Being totally random, this permutation will be strongly one-way in a provable, information-theoretic way. We show that, if P = N P, no protocol for secret key agreement is secure in such a setting. Thus, to prove that a secret key agreement protocol which uses a one-way permutation as a black box is secure is as hard as proving P ≠ N P. We also obtain, as a corollary, that there is an oracle relative to which the implication is false, i.e., there is a one-way permutation, yet secret-exchange is impossible. Thus, no technique which relativizes can prove that secret exchange can be based on any one-way permutation. Our results present a general framework for proving statements of the form, “Cryptographic application X is not likely possible based solely on complexity assumption Y. ”
Vhl deletion in renal epithelia causes HIF-1α-dependent, HIF-2α-independent angiogenesis and constitutive diuresis

One of the earliest requirements for the formation of a solid tumor is the establishment of an adequate blood supply. Clear cell renal cell carcinomas (ccRCC) are highly vascularized tumors in which the earliest genetic event is most commonly the biallelic inactivation of the VHL tumor suppressor gene, leading to constitutive activation of the HIF-1α and HIF-2α transcription factors, which are known angiogenic factors. However it remains unclear whether either or both HIF-1α or HIF-2α stabilization in normal renal epithelial cells are necessary or sufficient for alterations in blood vessel formation. We show that renal epithelium-specific deletion of Vhl in mice causes increased medullary vascularization and that this phenotype is completely rescued by Hif1a co-deletion, but not by co-deletion of Hif2a. A physiological consequence of changes in the blood vessels of the vasa recta in Vhl-deficient mice is a diabetes insipidus phenotype of excretion of large amounts of highly diluted urine. This constitutive diuresis is fully compensated by increased water consumption and mice do not show any signs of dehydration, renal failure or salt wasting and blood electrolyte levels remain unchanged. Co-deletion of Hif1a, but not Hif2a, with Vhl, fully restored kidney morphology and function, correlating with the rescue of the vasculature. We hypothesize that the increased medullary vasculature alters salt uptake from the renal interstitium, resulting in a disruption of the osmotic gradient and impaired urinary concentration. Taken together, our study characterizes a new mouse model for a form of diabetes insipidus and non-obstructive hydronephrosis and provides new insights into the physiological and pathophysiological effects of HIF-1α stabilization on the vasculature in the kidney.
Energy-Efficient Indexing For Information Dissemination In Wireless Systems

We consider the application of high volume information dissemination in broadcast based mobile environments. Since current mobile units accessing broadcast information have limited battery capacity, the problem of quick and energy-e cient access to data becomes particularly relevant as the number and sizes of information units increases. We propose several randomized and Hu man-encoding based indexing schemes that are sensitive to data popularity patterns to structure data transmission on the wireless medium, so that the average energy consumption of mobile units is minimized while trying to access desired data. We then propose an algorithm for PCS units to tune into desired data independent of the actual transmission scheme being used. We also empirically study the proposed schemes and propose di erent transmission modes for the base station to dynamically adapt to changes in the number of data les to be broadcasted, the available bandwidth and the accuracy of data popularity patterns.