Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Processes and Hub Genes of Acropora Palmata in Response to Thermal Stress And Bleaching

ABSTRACT Yuan, J.; Liu, L. ; Zhang, Y. ; Shen, C. , and Lin, S. , 2019. Molecular processes and hub genes of Acropora palmata in response to thermal stress and bleaching. Journal of Coastal Research, 35(1), 26–32. Coconut Creek (Florida), ISSN 0749-0208. Among many environmental factors, high temperature is the main factor that causes coral bleaching. Thus, analyses of the bleaching mechanism and important genes involved in coral responses to thermal stress and bleaching are important. This study explored the gene expression profiling data (GSE16151) from the Gene Expression Omnibus database by using bioinformatics analysis to study the molecular processes and hub genes involved in the thermal stress and bleaching responses of the coral Acropora palmata. The results suggest that thermal stress down-regulated the snoRNP genes, which led to a reduction of some ribosomal proteins, and then decreased biosynthesis, resulting in disruption of a series of biological processes such as the glyoxylate cycle and vitamin metabolic processes. Moreover, the coral cytoskeleton showed breakdown because the CCT7 gene was down-regulated and because of insufficient adenosine triphosphate production caused by the thermal stress. All these responses will destroy the P53 pathway and initiate apoptosis and ultimately necrosis. In addition, 107 differentially expressed genes were detected between the normal and bleached corals, indicating that snoRNPs, CCT7, RPL37, and RPS27A may be the hub genes responsible for thermal stress and bleaching responses. These genes can be used as new biomarkers to help solve the problem of coral bleaching.
The RWTH Phrase-based Statistical Machine Translation System

We give an overview of the RWTH phrase-based statistical machine translation system that was used in the evaluation campaign of the International Workshop on Spoken Language Translation 2005. We use a two pass approach. In the first pass, we generate a list of the N best translation candidates. The second pass consists of rescoring and reranking this N -best list. We will give a description of the search algorithm as well as the models that are used in each pass. We participated in the supplied data tracks for manual transcriptions for the following translation directions: Arabic-English, Chinese-English, English-Chinese and Japanese-English. For Japanese-English, we also participated in the C-Star track. In addition, we performed translations of automatic speech recognition output for ChineseEnglish and Japanese-English. For both language pairs, we translated the single-best ASR hypotheses. Additionally, we translated Chinese ASR lattices.
NUMERICAL MODELING OF THE DAEDALIA PLANUM LAVA FLOWS, MARS

Mars has been a target of scientific research for decades as its surface records a varied geologic history including the largest shield volcanoes in the solar system (Rossi and van Gasselt, 2010). The evidence of volcanism, from the shield volcanoes and the lava flows that extend for hundreds of kilometers, garnered the interest of many scientists to determine why the volcanism on the planet is at a scale much larger than on Earth (Zimbelman, 1998). Many previous studies compared terrestrial and Martian flows using empirical relationships to determine values for parameters such as eruption rate and viscosity (Zimbelman, 1998; Hiesinger et al., 2007). These terrestrial based empirical relationships have not been verified as being applicable to planetary flows (Crisp & Baloga, 1990). This study seeks to examine this issue by duplicating the flows using numerical modeling with the FLOWGO thermorheologic model of Harris and Rowland (2001) and comparing the generated eruption rate and viscosity values. For modeling of this study, the majority of model parameters were based on data taken from the terrestrial Piton de la Fournaise volcano except for values directly measured from the Mars flows such as flow dimensions and path slope. Dimensions of flows were measured from Mars Reconnaissance Orbiter’s Context Camera (CTX) images of the study region in Daedalia Planum, Mars. Slope and flow thickness required the use of elevation data from the Mars Orbiter Laser Altimeter (MOLA) instrument. Using these parameters, a set of three different models were generated that reproduced the flows in the Daedalia Planum within 10% of their measured length. The results of this study were comparable to the eruption rates and viscosity values of previous studies. This study has shown that Martian lava flows can be modeled using terrestrial flow parameter values with results comparable to prior solely empirical studies.
Real-time image analysis using wavelets: the "a trous" algorithm on MIMD architectures

The 'a trous' algorithm represents a discrete approach to the classical continuous wavelet transform. Similar to the fast wavelet transform the input signal is analyzed by using the coefficients of a properly chosen low-pass filter, but in contradistinction to the latter there follows no concluding decimation step. Examples of practical applications can be found in the field of cosmology for studying the formation of large scale structures of the Universe. In this paper we develop parallel algorithms on different MIMD architectures for the 2D 'a trous' decomposition. We implement the algorithm on several distributed memory architectures using the PVM paradigm and on a SGI POWERChallenge using a parallel version of the C programming language. Finally we investigate experimental results obtained on both of them.
Macroeconomic Stability or Cycles? The Role of the Wage‐Price Spiral

type="main"> We formulate a small and stylised dynamic macroeconomic model, and study how different specifications of the supply side affect the model's dynamic properties. The wage-price equilibrium-correction model (ECM) and the Phillips curve model (PCM) that both can be used to represent the supply side of a New Keynesian macro model, are synthesised in a generalised model of the wage-price spiral. We show that the choice of ECM or PCM has implications for the long-run stability of the macro model, without need of a NAIRU. We also find that the range of theoretically admissible dynamics is wide. For example, both the ECM and PCM may display endogenous cyclical fluctuations in inflation and unemployment, showing that even simple structures can give rise to complex dynamics. In practice that may entail that forecasting the effects of shocks and policy changes is difficult even in the best of circumstances.
Frequent Patterns Minning of Stock Data Using Hybrid Clustering Association Algorithm

Patterns and classification of stock or inventory data is very important for business support and decision making. Timely identification of newly emerging trends is also needed in business process. Sales patterns from inventory data indicate market trends and can be used in forecasting which has great potential for decision making, strategic planning and market competition. The objectives in this research are to get better decision making for improving sale, services and quality as to identify the reasons of dead stock, slow-moving, and fast-moving products which is useful mechanism for business support, investment and surveillance. In this paper we proposed an algorithm for mining patterns of huge stock data to predict factors affecting the sale of products. In the first phase, we divide the stock data in three different clusters on the basis of product categories and sold quantities i.e. Dead-Stock (DS), Slow-Moving (SM) and Fast-Moving (FM) using K-means algorithm. In the second phase we have proposed Most Frequent Pattern (MFP) algorithm to find frequencies of property values of the corresponding items. MFP provides frequent patterns of item attributes in each category of products and also gives sales trend in a compact form. The experimental result shows that the proposed hybrid k-mean plus MFP algorithm can generate more useful pattern from large stock data.
Modeling Per-Flow Throughput and Capturing Starvation in CSMA Multi-Hop Wireless Networks

—Multi-hop wireless networks employing random access protocols have been shown to incur large discrepancies in the throughputs achieved by the ﬂows sharing the network. Indeed, ﬂow throughputs can span orders of magnitude from near starvation to many times greater than the mean. In this paper, we address the foundations of this disparity. We show that the fundamental cause is not merely differences in the number of contending neighbors, but a generic coordination problem of CSMA-based random access in a multi-hop environment. We develop a new analytical model that incorporates this lack of coordination, identiﬁes dominating and starving ﬂows and accurately predicts per-ﬂow throughput in a large-scale network. We then propose metrics that quantify throughput imbalances due to the MAC protocol operation. Our model and metrics provide a deeper understanding of the behavior of CSMA protocols in arbitrary topologies and can aid the design of effective protocol solutions to the starvation problem.
Development of fragility curves for retrofitted multi-column bridge bent subjected to near fault lti

This study focuses on developing fragility-based seismic vulnerability assessment techniques for seismically retrofitted multi-column bridge bent. Fragility curves are developed using Probabilistic Seismic Demand Model (PSDM) to assess the relative performance of different retrofit methods under near fault ground motions. Two different retrofit techniques namely CFRP jacketing and ECC jacketing are used in this study. The distinctive and catastrophic features of near fault ground motions place serious demand on structures located in the near field region of an earthquake and require special attention. In order to investigate the near fault ground motions effects, a total of 20 near fault ground motions are utilized to evaluate the likelihood of exceeding the seismic capacity of the retrofitted bridge bent. Results obtained from this study indicate that the properties of retrofitting materials have a significant effect on the damage probability of the retrofitted bridge bents. The findings can serve as a guide to express the impact of retrofit on the bridge bent vulnerability.
A Novel Serine Protease Secreted by Medicinal Maggots Enhances Plasminogen Activator-Induced Fibrinolysis

Maggots of the blowfly Lucilia sericata are used for the treatment of chronic wounds. As haemostatic processes play an important role in wound healing, this study focused on the effects of maggot secretions on coagulation and fibrinolysis. The results showed that maggot secretions enhance plasminogen activator-induced formation of plasmin and fibrinolysis in a dose- and time-dependent manner. By contrast, coagulation was not affected by secretions. Biochemical studies indicated that a novel serine protease within secretions, designated Sericase, cleaved plasminogen to several fragments. Recombinant Sericase degraded plasminogen leading amongst others to the formation of the mini-plasminogen like fragment Val454-plasminogen. In addition, the presence of a non-proteolytic cofactor in secretions was discovered, which plays a role in the enhancement of plasminogen activator-induced fibrinolysis by Sericase. We conclude from our in vitro studies that the novel serine protease Sericase, with the aid of a non-proteolytic cofactor, enhances plasminogen activator-induced fibrinolysis.
Graph Decomposition Using Self-organizing Trees

In this paper, we present a new approach for graph decomposition using topological and hierarchical partitioning of data. Our method called GD-SOM-Tree (Graph Decomposition using Self-Organizing Trees) is based on self-organizing models. The benefit of this novel approach is to represent and visualize hierarchical relations which replace the original graph with a summary and gives a good understanding of the underlying problem.
Dynamic Critical-Path Scheduling: An Effective Technique for Allocating Task Graphs to Multiprocessors

In this paper, we propose a static scheduling algorithm for allocating task graphs to fully connected multiprocessors. We discuss six recently reported scheduling algorithms and show that they possess one drawback or the other which can lead to poor performance. The proposed algorithm, which is called the Dynamic Critical-Path (DCP) scheduling algorithm, is different from the previously proposed algorithms in a number of ways. First, it determines the critical path of the task graph and selects the next node to be scheduled in a dynamic fashion. Second, it rearranges the schedule on each processor dynamically in the sense that the positions of the nodes in the partial schedules are not fixed until all nodes have been considered. Third, it selects a suitable processor for a node by looking ahead the potential start times of the remaining nodes on that processor, and schedules relatively less important nodes to the processors already in use. A global as well as a pair-wise comparison is carried out for all seven algorithms under various scheduling conditions. The DCP algorithm outperforms the previous algorithms by a considerable margin. Despite having a number of new features, the DCP algorithm has admissible time complexity, is economical in terms of the number of processors used and is suitable for a wide range of graph structures.
Motion planning with sequential convex optimization and convex collision checking

We present a new optimization-based approach for robotic motion planning among obstacles. Like CHOMP (Covariant Hamiltonian Optimization for Motion Planning), our algorithm can be used to find collision-free trajectories from naïve, straight-line initializations that might be in collision. At the core of our approach are (a) a sequential convex optimization procedure, which penalizes collisions with a hinge loss and increases the penalty coefficients in an outer loop as necessary, and (b) an efficient formulation of the no-collisions constraint that directly considers continuous-time safety Our algorithm is implemented in a software package called TrajOpt. We report results from a series of experiments comparing TrajOpt with CHOMP and randomized planners from OMPL, with regard to planning time and path quality. We consider motion planning for 7 DOF robot arms, 18 DOF full-body robots, statically stable walking motion for the 34 DOF Atlas humanoid robot, and physical experiments with the 18 DOF PR2. We also apply TrajOpt to plan curvature-constrained steerable needle trajectories in the SE(3) configuration space and multiple non-intersecting curved channels within 3D-printed implants for intracavitary brachytherapy. Details, videos, and source code are freely available at: http://rll.berkeley. edu/trajopt/ijrr.
Regulation of progesterone receptor A and B expression in human preterm, term, and postterm placental villi

Objective. The progesterone receptor (PR)‐A/B ratio in the myometrium is reported to be closely related to labor onset. This might represent a potential target for therapeutic interventions for postterm and preterm deliveries, though the mechanisms currently remain unknown. The aim of this study was to investigate the regulation mechanism of PR‐A and B expression in human preterm, term, and postterm placental villi. Design. Experimental study. Setting. People's Hospital of Jiangsu Province, China. Population. Singleton women of preterm (PRNIL, not in labor, n = 10), term (TNIL, not in labor, n = 10; TIL, in labor, n = 10), and postterm (PONIL, not in labor, n = 10) cesarean deliveries. Methods. The PR‐A/PR‐B mRNA and protein ratios were analyzed using real‐time reverse transcription‐polymerase chain reaction and western blots in villi from preterm, term, postterm groups. PONIL and PRNIL villi were incubated with prostaglandin F2α (PG) and indomethacin for 72 hours, respectively, and the PR‐A/PR‐B mRNA and protein ratios and p38 signaling pathway were explored. Results. The PR‐A/PR‐B ratio was highest in TIL, followed by PRNIL, PONIL and TNIL. Indomethacin significantly up‐regulated PR‐B expression, thereby decreasing the PR‐A/PR‐B ratio (p < 0.05). Meanwhile, PG reduced the expression of PR‐B and increased PR‐A, leading to a significant increase in the PR‐A/PR‐B ratio (p < 0.05). We also determined that the PR‐A/PR‐B ratio was mediated through the activation of p38 mitogen‐activated protein kinase. Conclusion. These results demonstrate that the PR‐A/PR‐B ratio plays a key role in the mechanisms regulating preterm, term, and postterm deliveries.
Age-related slowing of response selection and production in a visual choice reaction time task

Aging is associated with delayed processing in choice reaction time (CRT) tasks, but the processing stages most impacted by aging have not been clearly identified. Here, we analyzed CRT latencies in a computerized serial visual feature-conjunction task. Participants responded to a target letter (probability 40%) by pressing one mouse button, and responded to distractor letters differing either in color, shape, or both features from the target (probabilities 20% each) by pressing the other mouse button. Stimuli were presented randomly to the left and right visual fields and stimulus onset asynchronies (SOAs) were adaptively reduced following correct responses using a staircase procedure. In Experiment 1, we tested 1466 participants who ranged in age from 18 to 65 years. CRT latencies increased significantly with age (r = 0.47, 2.80 ms/year). Central processing time (CPT), isolated by subtracting simple reaction times (SRT) (obtained in a companion experiment performed on the same day) from CRT latencies, accounted for more than 80% of age-related CRT slowing, with most of the remaining increase in latency due to slowed motor responses. Participants were faster and more accurate when the stimulus location was spatially compatible with the mouse button used for responding, and this effect increased slightly with age. Participants took longer to respond to distractors with target color or shape than to distractors with no target features. However, the additional time needed to discriminate the more target-like distractors did not increase with age. In Experiment 2, we replicated the findings of Experiment 1 in a second population of 178 participants (ages 18–82 years). CRT latencies did not differ significantly in the two experiments, and similar effects of age, distractor similarity, and stimulus-response spatial compatibility were found. The results suggest that the age-related slowing in visual CRT latencies is largely due to delays in response selection and production.
Temporal Data Mining in Dynamic Feature Spaces

Many interesting real-world applications for temporal data mining are hindered by concept drift. One particular form of concept drift is characterized by changes to the underlying feature space. Seemingly little has been done in this area. This paper presents FAE, an incremental ensemble approach to mining data subject to such concept drift. Empirical results on large data streams demonstrate promise.
Role of Homodimerization of Human Cytomegalovirus DNA Polymerase Accessory Protein UL44 in Origin-Dependent DNA Replication in Cells

ABSTRACT The presumed processivity subunit of human cytomegalovirus (HCMV) DNA polymerase, UL44, forms homodimers. The dimerization of UL44 is important for binding to DNA in vitro; however, whether it is also important for DNA replication in a cellular context is unknown. Here we show that UL44 point mutants that are impaired for dimerization, but not for nuclear localization or interaction with the C terminus of the polymerase catalytic subunit, are not capable of supporting HCMV oriLyt-dependent DNA replication in cells. These data suggest that the disruption of UL44 homodimers could represent a novel anti-HCMV strategy.
A unified approach to the inverse kinematic solution for a redundant manipulator

SUMMARY For a kinematically redundant manipulator, some performance indices can be optimized while carrying out a given task. So far, the redundancy resolution has been solved at the joint angle level, the joint velocity level, or joint acceleration level depending on the performance indices. According to the resolution level, the solution is represented by high-order differential equations or superfluous number of equations. We propose a unified approach to the inverse kinematic solution which optimizes it at the joint velocity level regardless of the types of the performance indices. A unified approach to obtain an optimal joint velocity is derived by using the necessary condition for optimality so that the proposed method provides an optimal solution for any performance indices and tasks. The optimal solution becomes a set of the minimum number of first-order differential equations which requires a minimum search dimension.To show the validity of the approach, it is applied to a three-link planar manipulator for various types of performance indices.
Hydrophobic actuation of a DNA origami bilayer structure.

Amphiphilic compounds have a strong tendency to form aggregates in aqueous solutions. It is shown that such aggregation can be utilized to fold cholesterol-modified, single-layered DNA origami structures into sandwich-like bilayer structures, which hide the cholesterol modifications in their interior. The DNA bilayer structures unfold after addition of the surfactant Tween 80, and also in the presence of lipid bilayer membranes, with opening kinetics well described by stretched exponentials. It is also demonstrated that by combination with an appropriate lock and key mechanism, hydrophobic actuation of DNA sandwiches can be made conditional on the presence of an additional molecular input such as a specific DNA sequence.
Acute effects of soccer training on white blood cell count in elite female players.

PURPOSE To investigate the acute changes in leukocyte number and cortisol after a single bout of soccer training. METHODS Ten elite female national-team soccer players and 8 nonathletes participated in the study. The duration of the exercise was 2 h, and it was performed at an intensity of 75% of maximal heart rate (HRmax). Blood samples were taken before, immediately after, and 4 h after a soccer training session to determine total white blood cells; the subsets of neutrophils, lymphocytes, monocytes, eosinophils, and basophils; and cortisol. At the same time, blood samples were obtained from nonathletes who refrained from exercise. RESULTS Data analysis indicated a significant increase in total white blood cells in the athletes postexercise (P < .001). The leukocytosis was still evident after 4 h of recovery (78% higher than the preexercise values), and there was a significant difference between athletes and nonathletes (P < .001). This leukocytosis was primarily caused by neutrophilia-there were no significant differences in lymphocytes after the end of exercise or between the 2 groups (P > 0.05). In addition, there was a statistically significant difference in cortisol concentration between athletes and nonathletes after the exercise (P < .001). CONCLUSION These findings revealed that the single bout of soccer training at an intensity of 75% of HRmax induced leukocytosis without affecting the lymphocyte count in elite female athletes and probably the effectiveness of cellular components of adaptive immunity. Coaches should provide adequate time (>4 h) until the next exercise session.