Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular mechanisms for the regulation of histone mRNA stem-loop–binding protein by phosphorylation

Significance As DNA is replicated during cell division, it must be packaged by histones. To match the level of available histones to DNA replication, histone mRNA expression is controlled by a 3′-end stem-loop structure unique to replication-dependent histone mRNAs. In Drosophila, this regulation is mediated by histone mRNA stem-loop–binding protein (dSLBP), which has minimal tertiary structure when not bound to RNA. We show here that phosphorylation of dSLBP dramatically increases binding affinity for stem-loop RNA. The phosphorylated C-terminal tail of dSLBP does not contact RNA. Instead, increased negative charge on the C-terminal tail and stabilization of structural elements by a phosphorylation site within the RNA-binding domain promote more compact conformations that should reduce the entropic barrier to binding histone mRNA. Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop–binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.
Noble gases and strontium isotopes in the unique meteorite Divnoe

Abstract— We present an isotope study of noble gases in Divnoe, an anomalous meteorite, and also Rb-Sr and K-Ar dating of this meteorite. The relatively young Rb-Sr age obtained (3.39 Ga) seems doubtful and, most probably, results from weathering or contamination. The ancient K-Ar age (4.67+0.20–0.40), together with clear excess of 129Xe, allows the suggestion of very early formation of the Divnoe meteorite. Concentrations and isotope ratios of noble gases in Divnoe are: 17.9 ≤ 3He ≤ 29.0 × 10−8; 20Ne = 6.22 × 10−8; 2.44 ≤ 36Ar ≤ 5.10 × 10−8; 130Xe = 41.3 × 10−12 cm3/g; 0.079 ≤ 3He/4He ≤ 0.193; 20Ne/22Ne = 0.860; 21Ne/22Ne = 0.927; 3.47 ≤ 40Ar/36Ar ≤ 9.47; 2.22 ≤ 36Ar/38Ar ≤ 3.27; 129Xe/132Xe = 1.09. The exposure age calculated from cosmogenic 3He, 21Ne, and 38Ar is 17.9 ± 0.9 Ma. On the basis of the isotope data for the noble gases and O, and abundances of K, Rb, and Sr, an attempt was made to estimate the relationship of Divnoe to other meteorite types. The O-isotope characteristics of Divnoe are clearly distinct from those of ordinary chondrites, acapulcoites/lodranites, and SNC meteorites (Petaev et al., 1994, Clayton, 1993). In plots of 136Xe vs.129Xe/130Xe, the Divnoe data fall outside of the data fields for carbonaceous and enstatite chondrites. The light noble gas data, especially the 40Ar/38Ar ratio, and the 40Ar, 38Ar, 3He, and 4He contents of Divnoe differ significantly from those of all meteorite types except diogenites. The K, Rb, and Sr abundances in Divnoe are substantially lower than in most other meteorites. In the concentrations of these elements, as well as in the REE pattern, the Divnoe meteorite is similar only to diogenites. Divnoe probably should be treated as a restite remaining after partial melting of the chondritic mantle of a parent asteroid body.
An Improved Admissible Heuristic for Learning Optimal Bayesian Networks

Recently two search algorithms, A* and breadth-first branch and bound (BFBnB), were developed based on a simple admissible heuristic for learning Bayesian network structures that optimize a scoring function. The heuristic represents a relaxation of the learning problem such that each variable chooses optimal parents independently. As a result, the heuristic may contain many directed cycles and result in a loose bound. This paper introduces an improved admissible heuristic that tries to avoid directed cycles within small groups of variables. A sparse representation is also introduced to store only the unique optimal parent choices. Empirical results show that the new techniques significantly improved the efficiency and scalability of A* and BFBnB on most of datasets tested in this paper.
Multi-target Tracking Using on-line Viterbi Optimisation and Stochastic Modelling

To study and compare the safety of intersection, traffic scientists today typically manually monitor the intersection during several days and count how often certain events such as evasive manoeuvres occur. This is a laboursome and costly procedure. The aim of this thesis is to provide tools that can reduce the amount of manual labour required by using automated video analytics. Two methods for creating for such tools are presented. The first method is a probabilistic background foreground segmentation that for each block of pixels calculate the probability that this block currently views the static background or some moving foreground object. This is done by deriving the probability distribution of the normalised cross correlation in the background and the foreground case respectively. The background distribution depends on the amount of structure in the block. The second method is a multi-target tracker that uses the probabilistic background foreground segmentation to produce the trajectories of all objects in the scene. It operates online but with a few seconds delay in order to incorporate information from both past and future frames when deciding on the current state. This means that the output is guaranteed to be consistent, i.e. no jumping between different hypothesis, and the respect constrains placed on the system such as "objects may not occupy the same space at the same time" or "objects may only appear at the border of the image". The methods have been tested both on synthetic and numerous sets of real data by implementing applications such as people counting, loitering detection and traffic surveillance. The applications have been shown to perform very well as long as the scene studied is not too large. (Less)
Glacier winds in the Rongbuk Valley, north of Mount Everest: 1. Meteorological modeling with remote sensing data

[1] Persistent glacier winds blowing from noon to midnight in summer are present in the Rongbuk Valley, north of Mount Everest, with a maximum speed of 10 m s−1 and a vertical thickness as high as 1 km. These glacier winds may bring upper level atmosphere ozone to the surface, having a significant impact on the atmospheric environment. Such phenomena may be typical of the Tibetan Plateau, where most high mountains are covered by snow or glacier ice throughout the year. The Advanced Regional Prediction Model was used to simulate the down-valley flows, using realistic topography but neglecting synoptic winds. The modeling results agree well with the observations obtained in June 2002, revealing that the glacier winds are thermal flows primarily driven by the along-valley temperature gradient between the colder air over the glacier surface and the warmer air over surface areas covered by rock debris, which maintains air advection along the Rongbuk Valley. Downslope winds over the glacier slopes, especially from the western valley side, and the West Rongbuk Glacier, were forced by their inertia farther down into the valley and would intensify the glacier winds. The narrowing of the Rongbuk Valley could also speed up the glacier winds. Sensitivity tests showed that the detailed distribution of the Rongbuk Glacier, delineated by data from the Enhanced Thematic Mapper Plus on Landsat 7, plays an important role in glacier winds development. The glacier winds could be much weaker in winter when the area is completely snow covered.
Motion-based easy initialization of online foreground segmentation

Online foreground segmentation usually requires to be initialized in order to specify the segmentation model. In real environments, re-initialization is also often required because of unexpected events that can break the segmentation process (e.g. unintentional movements of the camera). Traditional approaches for the initialization can not deal with common cases conveniently, especially in the situations that the segmentation process is frequently broken (e.g. network meeting with laptop). In this paper we propose a method that enables online segmentation to be initialized easily. The core of our approach is a novel motion segmentation method, that is, the Segmentation from Small Motion (SfSM), which can accurately extract the foreground object based on its slight motion between two frames. To initialize the segmentation process, we first use SfSM to segment a series of frames, and then select the one with the highest confidence as the initialization frame. Unexpected events can be handled easily by detecting changes in the background, and then re-initialize the segmentation model in the changed scene. Experiments demonstrate that our method can effectively deal with common cases in a convenient way.
Detection of a subglacial lake in Glacier de Tête Rousse (Mont Blanc area, France)

Abstract The processes that form intraglacial lakes are poorly understood because of the difficulty in detecting and assessing such hidden lakes. Extensive geophysical surveys were performed between 2007 and 2010 in order to reassess the risk of an outburst flood from Glacier de Tete Rousse, French Alps, where outburst flooding from an intraglacial lake caused 175 fatalities in 1892. Our geophysical survey combined ground-penetrating radar measurements and nuclear magnetic resonance imaging. We found a subglacial water-filled reservoir with a volume of 55 000 m3. Artesian outpourings occurred when the subglacial cavity was reached by two borehole drillings, indicating that the hydrostatic water pressure exceeded the ice pressure at the bottom of the cavity. On the basis of these geophysical and glaciological findings, we warned the public authorities in July 2010 of the risk facing the 3000 inhabitants downstream of the glacier. The subglacial reservoir was drained artificially. This example demonstrates how geophysical surveys can be used to detect this type of hazard when it is suspected, in particular when no hydraulic outlet from the snout exists. Numerous ice temperature measurements have shown that the tongue of this glacier is cold-based. This thermal regime could explain the accumulation of water in this glacier.
Vascular Flora of the University of Central Oklahoma Selman Living Laboratory, Woodward, County, Oklahoma

The vascular flora of the University of Central Oklahoma Selman Living Laboratory (SLL) was surveyed from 1999 to 2003. The SLL is a 129.5 ha biological field station located in the Cimarron Gypsum Hills in Woodward County, Oklahoma. We identified 229 species in 61 families. The three families with the largest numbers of species were the Asteraceae (48), Poaceae (45), and Fabaceae (14). Two hundred eight species (91%) are native, and 156 (68%) are perennial. Fifty-six species were identified that previously had not been reported for Woodward County. Flowering/fruiting dates and habitat types for each species also are provided. Two species are classified as obligate gypsophiles. Seven riparian or floodplain species are characteristic of alkaline or saline habitats. General descriptions of the plant communities are provided. © 2003 Oklahoma Academy of Science
Quantitative theory of telomere length regulation and cellular senescence

In normal somatic cells, telomere length shortens with each cell replication. This progressive shortening is associated with cellular senescence and apoptosis. Germ cells, stem cells, and the majority of cancer cells express telomerase, an enzyme that extends telomere length and, when expressed at sufficient levels, can immortalize or extend the life span of a cell line. It is believed that telomeres switch between two states: capped and uncapped. The telomere state determines its accessibility to telomerase and also the onset of senescence. One hypothesis is that the t loop, a large lariat-like structure, represents the capped state. In this paper we model a telomere state on the basis of the biophysics of t-loop formation, allowing us to develop a single mathematical model that accounts for two processes: telomere length regulation for telomerase positive cells and cellular senescence in somatic cells. The model predicts the steady-state length distribution for telomerase positive cells, describes the time evolution of telomere length, and computes the life span of a cell line on the basis of the levels of TRF2 and telomerase expression. The model reproduces a wide range of experimental behavior and fits data from immortal cell lines (HeLa S3 and 293T) and somatic cells (human diploid fibroblasts) well. We conclude that the t loop as the capped state is a quantitatively reasonable model of telomere length regulation and cellular senescence.
A performance counter architecture for computing accurate CPI components

A common way of representing processor performance is to use Cycles per Instruction (CPI) `stacks' which break performance into a baseline CPI plus a number of individual miss event CPI components. CPI stacks can be very helpful in gaining insight into the behavior of an application on a given microprocessor; consequently, they are widely used by software application developers and computer architects. However, computing CPI stacks on superscalar out-of-order processors is challenging because of various overlaps among execution and miss events (cache misses, TLB misses, and branch mispredictions). This paper shows that meaningful and accurate CPI stacks can be computed for superscalar out-of-order processors. Using interval analysis, a novel method for analyzing out-of-order processor performance, we gain understanding into the performance impact of the various miss events. Based on this understanding, we propose a novel way of architecting hardware performance counters for building accurate CPI stacks. The additional hardware for implementing these counters is limited and comparable to existing hardware performance counter architectures while being significantly more accurate than previous approaches.
Monitoring city subsidence by D-InSAR in Tianjin area

D-InSAR technique has been widely adopted to monitor land subsidence caused by withdrawal of water, oil, gas, and other minerals. Though many cities in China have seriously suffered from land subsidence caused by ground water over-extracting, few of them have enough money to do the leveling control of the subsidence. Compared with leveling and GPS surveying, D-InSAR is more cost-efficient and precise. As Tianjin city has scores of ERS-1/2 SAR data, thousands of valuable leveling data, smooth topography and severe subsidence, it is an ideal place to test and analyze D-lnSAR technique. However, D-InSAR is liable to be contaminated by atmosphere delay, temporal decorrelation and baseline errors. As these errors cannot be removed by SAR data processing, some auxiliary data such as leveling data and DEM data have been introduced into D-InSAR data processing. Therefore, This work accurately analyzes the features of atmosphere delay and temporal decorrelation with the auxiliary data in Tianjin urban area. The results demonstrate that D-InSAR can detect subsidence within three months. Further actions will be undertaken to improve the D-InSAR subsidence monitoring system, such as using Envisat data, gathering GPS zenith delay data to eliminate the atmosphere delay, and so on. The ultimate interest of our research is to establish a robust, cost efficient city subsidence monitoring system by using D-InSAR technique and other measurement.
A Weighted Distance Similarity Model to Improve the Accuracy of Collaborative Recommender System

Collaborative filtering is one of the most widely used methods to provide product recommendation in online stores. The key component of the method is to find similar users or items by using user-item matrix so that products can be recommended based on the similarities. However, traditional collaborative filtering approaches compute the similarity between a target user and the other user without considering a target item. More specifically, they give an equal weight to each of the items which are rated by both users. However, we think that the similarity between the target item and each of the co-rated items is a very important factor when we calculate the similarity between two users. Therefore, in this paper we propose a new similarity function that takes similarities between a target item and each of the co-rated items and the proportion of common ratings into account. Experimental results from Movie Lens dataset show that the method improves accuracy of recommender system significantly.
Hardware Diagnosis as Program Debugging

Horn clauses provide a useful framework for writing executable structural representations for digital circuits. This paper discusses how these representations can be used to diagnose faulty circuits using algorithmic program debugging techniques developed by Shapiro. The sound theoretical basis of these techniques is one of the major advantages of this approach. This framework also provides a new perspective on some of the hardware diagnosis techniques suggested in the literature.
A regressor-free adaptive impedance controller for robot manipulators without Slotine and Li's modification: theory and experiments

SUMMARY Slotine and Li's modification is a well-known, simple, and elegant approach for robot adaptive control to avoid the feedback of joint accelerations. This paper presents a simple strategy to implement a regressor-free adaptive impedance controller without using Slotine and Li's modification. In the new strategy, the joint acceleration vector and the dynamics of robot are assumed to be unavailable. Their effects are covered by using the function approximation technique so that there is no need for the joint acceleration feedback. The closed-loop stability and boundedness of internal signals are justified by the Lyapunov-like technique. Experimental results for a two-dimensional (2D) robot are presented to show the effectiveness of the proposed strategy.
Resting Microglial Cells Are Highly Dynamic Surveillants of Brain Parenchyma in Vivo

Microglial cells represent the immune system of the mammalian brain and therefore are critically involved in various injuries and diseases. Little is known about their role in the healthy brain and their immediate reaction to brain damage. By using in vivo two-photon imaging in neocortex, we found that microglial cells are highly active in their presumed resting state, continually surveying their microenvironment with extremely motile processes and protrusions. Furthermore, blood-brain barrier disruption provoked immediate and focal activation of microglia, switching their behavior from patroling to shielding of the injured site. Microglia thus are busy and vigilant housekeepers in the adult brain.
An Overview of the Nigel Text Generation Grammar

Research on the text generation task has led to creation of a large systemic grammar of English, Nigel, which is embedded in a computer program. The grammar and the systemic framework have been extended by addition of a semantic stratum. The grammar generates sentences and other units under several kinds of experimental control.This paper describes augmentations of various precedents in the systemic framework. The emphasis is on developments which control the text to fulfill a purpose, and on characteristics which make Nigel relatively easy to embed in a larger experimental program.
Dynamic Policy Based Replication on the Grid

In this paper we present a new grid replication concept based on dynamic policies, that we aim as a concept to address the problem of large scale dynamic grid data repositories and a long lived data cycle. Based on the current tools and concepts available in nowadays grid solution landscape, we introduce the concept of dynamic policy based replication on grids. We also present a basic architecture based on Globus components that we aim to develop as a next step of this work.
Blind MIMO communication based on Subspace Estimation

A new method is proposed for blindly estimating the top singular modes in a reciprocal MIMO (Multiple Input Multiple Output) channel, while at the same time using these modes for multi-stream communication without the need for training data. The uplink and downlink parties obtain the relevant singular modes from the received data blocks as the eigenvectors/eigenvalues of the spatial empirical correlation matrices. The only requirement is that the separate data streams are statistically uncorrelated. The approach relies on a key and simple “need to know” observation about MIMO transmission : In order both to transmit and receive, one party needs only the singular values and one set of singular vectors, say the left set, while the other party needs only the corresponding right set of singular vectors in addition to the singular values; no party needs both sets of vectors, and other aspects of H are irrelevant to both parties. Advantages of this blind approach include no need for higher order statistic based estimation and convergence in one iteration. EDICS: 1-MAPP MULTICHANNEL SIGNAL PROCESSING APPLICATIONS 1-ACOM Antenna arrays and multichannel processing for communications
Silencing of the hydra serine protease inhibitor Kazal1 gene mimics the human SPINK1 pancreatic phenotype

In hydra, the endodermal epithelial cells carry out the digestive function together with the gland cells that produce zymogens and express the evolutionarily conserved gene Kazal1. To assess the hydra Kazal1 function, we silenced gene expression through double-stranded RNA feeding. A progressive Kazal1 silencing affected homeostatic conditions as evidenced by the low budding rate and the induced animal death. Concomitantly, a dramatic disorganization followed by a massive death of gland cells was observed, whereas the cytoplasm of digestive cells became highly vacuolated. The presence of mitochondria and late endosomes within those vacuoles assigned them as autophagosomes. The enhanced Kazal1 expression in regenerating tips was strongly diminished in Kazal1(–) hydra, and the amputation stress led to an immediate disorganization of the gland cells, vacuolization of the digestive cells and death after prolonged silencing. This first cellular phenotype resulting from a gene knock-down in cnidarians suggests that the Kazal1 serine-protease-inhibitor activity is required to prevent excessive autophagy in intact hydra and to exert a cytoprotective function to survive the amputation stress. Interestingly, these functions parallel the pancreatic autophagy phenotype observed upon mutation within the Kazal domain of the SPINK1 and SPINK3 genes in human and mice, respectively.
Self-Organizing Dynamic Fractional Frequency Reuse in OFDMA Systems

We describe an algorithm for sub-carrier and power allocation that achieves out-of-cell interference avoidance through dynamic fractional frequency reuse (FFR) in downlink of cellular systems based on orthogonal frequency division multiple access (OFDMA). The focus in on the constant-bit-rate (CBR) traffic type flows (e.g., VoIP). Our approach is based on the continuous "selfish" optimization of resource allocation by each sector. No a priori frequency planning and/or inter-cell coordination is required. We show, both analytically (on a simple illustrative example) and by simulations (of a more realistic system), that the algorithm leads the system to "self-organize" into efficient frequency reuse patterns.