Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial and photochemical reactivity of fluorescent dissolved organic matter in a coastal upwelling system

We observed significant changes in the dissolved oxygen content and the fluorescence of humic substances and dissolved aromatic amino acids after 24 h light and dark incubations in the coastal upwelling system of the Riía de Vigo under a wide variety of meteorologic and oceanographic conditions. Respiration rates were inversely correlated with the net production of humic fluorescence in the dark at a net rate of −0.027 ± 0.003 µg equivalents of quinine sulphate per µmol of O2, suggesting that marine humics are a by‐product of the bacterial respiration of dissolved organic matter (DOM). On the contrary, humic fluorescence consumption in the light minus dark incubations was positively correlated with the net production in the dark, indicating a rapid photodegradation of recently produced marine humic substances. Parallel incubation experiments demonstrated that daily photodegradation rates and residual humic fluorescence levels followed a seasonal pattern characterized by a marked autumn maximum. Finally, a significant linear correlation between the gross primary production (Pg) and the net production of aromatic amino acids fluorescence in the light pointed to the rapid consumption of dissolved protein‐like materials at a net average rate of −1.4 ± 0.2 ppb equivalents of tryptophan per day, which accumulates in the water column only when Pg exceeds 80 ± 20 µmol kg−1 d−1.
Automatic Detection and Correction for Chinese Misspelled Words Using Phonological and Orthographic Similarities

How to detect and correct misspelled words in documents is a very important issue for Mandarin and Japanese. This paper uses phonological similarity and orthographic similarity co-occurrence to train linear regression model. Using ACL-SIGHAN 2013 Bake-off Dataset, experimental results indicate that the detection F-score, error location F-score of our proposed method for Subtask 1 is 0.70 and 0.43 respectively, and the correction accuracy of the proposed method for Subtask 1 is 0.39.
Low Fetal Weight is Directly Caused by Sequestration of Parasites and Indirectly by IL-17 and IL-10 Imbalance in the Placenta of Pregnant Mice with Malaria

The sequestration of infected erythrocytes in the placenta can activate the syncytiotrophoblast to release cytokines that affect the micro-environment and influence the delivery of nutrients and oxygen to fetus. The high level of IL-10 has been reported in the intervillous space and could prevent the pathological effects. There is still no data of Th17 involvement in the pathogenesis of placental malaria. This study was conducted to reveal the influence of placental IL-17 and IL-10 levels on fetal weights in malaria placenta. Seventeen pregnant BALB/C mice were divided into control (8 pregnant mice) and treatment group (9 pregnant mice infected by Plasmodium berghei). Placental specimens stained with hematoxylin and eosin were examined to determine the level of cytoadherence by counting the infected erythrocytes in the intervillous space of placenta. Levels of IL-17 and IL-10 in the placenta were measured using ELISA. All fetuses were weighed by analytical balance. Statistical analysis using Structural Equation Modeling showed that cytoadherence caused an increased level of placental IL-17 and a decreased level of placental IL-10. Cytoadherence also caused low fetal weight. The increased level of placental IL-17 caused low fetal weight, and interestingly low fetal weight was caused by a decrease of placental IL-10. It can be concluded that low fetal weight in placental malaria is directly caused by sequestration of the parasites and indirectly by the local imbalance of IL-17 and IL-10 levels.
Inferring network structure from interventional time-course experiments

Graphical models are widely used to study biological networks. Interventions on network nodes are an important feature of many experimental designs for the study of biological networks. In this paper, we put forward a causal variant of dynamic Bayesian networks (DBNs) for the purpose of modeling time-course data with interventions. The models inherit the simplicity and computational efficiency of DBNs but allow interventional data to be integrated into network inference. We show empirical results, on both simulated and experimental data, that demonstrate the need to appropriately handle interventions when interventions form part of the design.
Nested loops revisited

Four variants of parallel index nested loop algorithms are compared with the parallel hybrid hash algorithm. The conclusions of experiments both with an analytic model and with an implementation in the Gamma parallel database system are that overall, parallel hybrid hash is the method of choice, but there are cases where nested loops with index wins big enough that systems could profit from implementing both algorithms. The experiments show further that among the nested loop algorithms, one of them, subset nested loops with sorting, clearly dominates. <<ETX>>
Structure Function Analysis of an ADP-ribosyltransferase Type III Effector and Its RNA-binding Target in Plant Immunity*

Background: HopU1 ADP-ribosylates GRP7, suppressing plant immunity. Results: The HopU1 structure has two novel loops required for GRP7 recognition, and HopU1 ribosylates GRP7 at an arginine in position 49 disrupting its function. Conclusion: HopU1 targets a conserved arginine in GRP7, disabling its ability to bind immunity-related RNA. Significance: The mechanistic details of how HopU1 recognizes its substrate reveal how HopU1 contributes to pathogenesis. The Pseudomonas syringae type III effector HopU1 is a mono-ADP-ribosyltransferase that is injected into plant cells by the type III protein secretion system. Inside the plant cell it suppresses immunity by modifying RNA-binding proteins including the glycine-rich RNA-binding protein GRP7. The crystal structure of HopU1 at 2.7-Å resolution reveals two unique protruding loops, L1 and L4, not found in other mono-ADP-ribosyltransferases. Site-directed mutagenesis demonstrates that these loops are essential for substrate recognition and enzymatic activity. HopU1 ADP-ribosylates the conserved arginine 49 of GRP7, and this reduces the ability of GRP7 to bind RNA in vitro. In vivo, expression of GRP7 with Arg-49 replaced with lysine does not complement the reduced immune responses of the Arabidopsis thaliana grp7-1 mutant demonstrating the importance of this residue for GRP7 function. These data provide mechanistic details how HopU1 recognizes this novel type of substrate and highlights the role of GRP7 in plant immunity.
Synthesis of FPGA Implementations from Loop Algorithms

We consider the problem of automatically mapping computation-intensive loop nests onto FPGA hardware. The regular cell array structure of these chips reflects the parallelism in regular loop-like computations. Furthermore, the flexibility of FPGAs allows the cost-effective implementation of reconfigurable high performance processor arrays. So far, there exists no continuous design flow that allows automated generation of FPGA configuration data from a loop nest specified in a high level language. Here, we present a methodology for automatic generation of synthesizable VHDL code specifying a processor array and optimized for FPGA implementation.
Light-like noncommutativity and duality from open strings/branes

In this paper we perform some non-trivial tests for the recently obtained open membrane/D-brane metrics and `generalized' noncommutativity parameters using Dp/NS5/M5-branes which have been deformed by light-like fields. The results obtained give further evidence that these open membrane/D-brane metrics and `generalized' noncommutativity parameters are correct. Further, we use the open brane data and supergravity duals to obtain more information about non-gravitational theories with light-like noncommutativity, or `generalized' light-like noncommutativity. In particular, we investigate various duality relations (strong coupling limits). In the light-like case we also comment on the relation between open membrane data (open membrane metric etc.) in six dimensions and open string data in five dimensions. Finally, we investigate the strong coupling limit (high energy limit) of five dimensional NCYM with Θ12 = Θ34. In particular, we find that this NCYM theory can be UV completed by a DLCQ compactification of M-theory.
Two‐stage instrumental variable methods for estimating the causal odds ratio: Analysis of bias

We present closed‐form expressions of asymptotic bias for the causal odds ratio from two estimation approaches of instrumental variable logistic regression: (i) the two‐stage predictor substitution (2SPS) method and (ii) the two‐stage residual inclusion (2SRI) approach. Under the 2SPS approach, the first stage model yields the predicted value of treatment as a function of an instrument and covariates, and in the second stage model for the outcome, this predicted value replaces the observed value of treatment as a covariate. Under the 2SRI approach, the first stage is the same, but the residual term of the first stage regression is included in the second stage regression, retaining the observed treatment as a covariate. Our bias assessment is for a different context from that of Terza (J. Health Econ. 2008; 27(3):531–543), who focused on the causal odds ratio conditional on the unmeasured confounder, whereas we focus on the causal odds ratio among compliers under the principal stratification framework. Our closed‐form bias results show that the 2SPS logistic regression generates asymptotically biased estimates of this causal odds ratio when there is no unmeasured confounding and that this bias increases with increasing unmeasured confounding. The 2SRI logistic regression is asymptotically unbiased when there is no unmeasured confounding, but when there is unmeasured confounding, there is bias and it increases with increasing unmeasured confounding. The closed‐form bias results provide guidance for using these IV logistic regression methods. Our simulation results are consistent with our closed‐form analytic results under different combinations of parameter settings. Copyright © 2011 John Wiley & Sons, Ltd.
Constellation and Interleaver Design for BICM

In this paper, we propose a new BICM design which considers hierarchical (nonequally spaced) constellations, a bit-level multiplexer, and multiple interleavers. It is shown that this new scheme outperform previous BICM designs because it exploits the temporal structure of the coded sequence. An analytical bound on the bit error rate (BER) of the proposed BICM scheme in terms of the constellation parameters and the multiplexing is developed for Nakagami-m fading channels. This bound is used to design a BICM transceiver with improved BER performance. Numerical results show that the gains compared to conventional BICM designs depend on the fading parameter and reach 2 dB for a target BER of 10^-7 and m=5.
Prediction of electromagnetic forces and vibrations in SRMs operating at steady state and transient speeds

Although some research has been conducted on vibrations in switched reluctance motors, the response during transients, which may occur during sudden load changes or braking, has not received much investigation. In this paper, a simulation model to predict the transient vibration of SRMs is developed. The vibration prediction model is built based on the detailed normal force vs. phase current and rotor position lookup table using finite element calculations. The model is then verified by a running motor test, which shows acceptable accuracy. The results reveal that there are abundant harmonics of transient force during transients, and thus resonance may be excited. This model allows the possibility of improved design of SRMs from a vibration and acoustic noise, point of view.
Power-Aware Computing with Dynamic Knobs

We present PowerDial, a system for dynamically adapting application behavior to execute successfully in the face of load and power fluctuations. PowerDial transforms static configuration parameters into dynamic knobs that the PowerDial control system can manipulate to dynamically trade off the accuracy of the computation in return for reductions in the computational resources that the application requires to produce its results. These reductions translate into power savings. Our experimental results show that PowerDial can enable our benchmark applications to execute responsively in the face of power caps (imposed, for example, in response to cooling system failures) that would otherwise significantly impair the delivered performance. They also show that PowerDial can reduce the number of machines required to meet peak load, in our experiments enabling up to a 75% reduction in direct power and capital costs.
Epstein-Barr Virus Association with Peptic Ulcer Disease

Background. Helicobacter pylori (HP) infection and nonsteroidal anti-inflammatory drugs (NSAID) use are considered the main risk to develop peptic ulcer disease (PUD). However, PUD also occurs in the absence of HP infection and/or NSAID use. Recently, we have found evidence that Epstein-Barr virus (EBV) reactivation increases the risk to develop premalignant and malignant gastric lesions. Objective. To study a possible association between EBV and PUD. Methods. Antibodies against an EBV reactivation antigen, HP, and the HP virulence factor CagA were measured in sera from 207 Mexican subjects, controls (healthy individuals, n = 129), and PUD patients (n = 78, 58 duodenal and 20 gastric ulcers). Statistical associations were estimated. Results. Duodenal PUD was significantly associated with high anti-EBV IgG titers (p = 0.022, OR = 2.5), while anti-EBV IgA was positively associated with gastric PUD (p = 0.002, OR = 10.1). Conclusions. Our study suggests that EBV reactivation in gastric and duodenal epithelium increases the risk to develop PUD.
Mach bands in the lateral eye of Limulus

Patterns of optic nerve activity were computed for stationary step patterns of illumination from theoretical models of lateral inhibiton based on revised Hartlin-Ratliff equations. The computed response patterns contain well-defined Mach bands which match closely in amplitude and shape those recorded from single optic nerve fibers of the Limulus lateral eye. Theory and experiment show that the amplitude of the Mach bands is reduced by in inhibitory nonlinearity, the width of the Mach bands is approximately equal to the lateral dimension of the inhibitory field, but the shapes of the Mach bands are poor indices of the precise configuration of the inhibitory field. Theorems are proved establishing the equivalence of Mach-band patterns for models of different dimensions and a uniqueness condition for solutions of the piecewise linear model.
A High-Throughput Maximum a posteriori Probability Detector

This paper presents a maximum a posteriori probability (MAP) detector, based on a forward-only algorithm that can achieve high throughputs. The MAP algorithm is optimal in terms of bit error rate (BER) performance and, with Turbo decoding, can approach performance close to the channel capacity limit. The proposed detector utilizes a deep-pipelined architecture implemented in skew-tolerant domino and experimentally measured results verify the detector can achieve throughputs greater than 750 MHz while consuming 2.4 W. The detector is implemented in a 0.13mum CMOS technology and has a die area of 9.9 mm2.
Incremental Type Checking in OCL Compilers

In software engineering, modeling tools have become widely accepted to increase application reliability and decrease development time. The UML and the OCL became industry standards and are supported by many Computer-Aided Software Engineering tools. The increasing number of modeled functionalities results in complex models that need more and more textual constraints to express the hidden restrictions applying to the systems. The usual scenario of model development is to create an initial model of the system, and then fine-tune it with simple modifications. During development, rebuilding all the constraints is unnecessary when only a few changes have been applied. In this paper, we present an algorithm that handles changes incrementally on expression level, thus required rebuilds are kept to a minimum. The background and implementation framework for the discussed compiler is the Visual Modeling and Transformation System, but the algorithm is general enough to support any tree-based compiler integrated into an IDE.
Lymphoid dendritic cells are potent stimulators of the primary mixed leukocyte reaction in mice.

Dendrite cells (DCs) are a new cell type initially identified in mouse lymphoid organs. Recently, DCs have been purified from mouse spleen. This paper demonstrates a functional role of DCs: they are potent stimulators of the primary mixed leukocytes reaction (MLR). As few as 300-1000 DCs doubled the proliferative activity of 5 X 10(6) allogeneic responder spleen cells, while 0.3-1.0 X 10(5) DCs induced a maximal stimulation of 30- to 80-fold. Between these extremes, the log of the MLR response increased linearly with the log of DC numbers. This dose-response assay was then used to compare the potency of purified DCs with that of other heterogeneous lymphoid populations, many of which gave dose-response curves with similar slopes. The potency of purified DCs as MLR stimulators was 100-300 times greater than that of unfractionated spleen cells. When spleen cells were fractionated by simple physical techniques, MLR-stimulating capacity in the subpopulations correlated closely with DC numbers. Removal of splenic B or T lymphocytes, by anti-immunoglobulin or anti-brain serum plus complement, did not reduce MLR-stimulating capacity. Finally, several populations, enriched in mononuclear phagocytes but lacking in DCs, stimulated weakly if at all. We conclude that DCs are a potent stimulating cell and are at least 100 times more effective than other major cell subclasses--i.e., B and T lymphocytes and macrophages.
Expanding social identity theory for research in media effects: Two international studies and a theoretical model.

In this paper we propose that Tajfel's (1979) social identity theory (SIT) and self-categorization theory (SCT, Turner, Brown & Tajfel, 1987) is a relevant and helpful theoretical groundwork to explain selective exposure to media content in general and to entertainment media in particular. It is hypothesized that gender and national identity have a significant effect on selective exposure to entertainment series when being salient. Two international quasi-experimental studies have been conducted, the first study in the U.S. and Germany (N = 419) and the second in Great Britain and Germany (N = 154). As expected, participants rated series that feature protagonists of their own sex higher with regard to entertainment and intention to watch than those that featured protagonists of the opposite sex. However, national identity did not have the effects expected. Participants from all three countries gave similar ratings to series produced in their home-country as those produced abroad. The use of SIT is discussed in terms of what processes of the theory are of particular importance to explain media related behavior and how to empirically apply the theory in media effects research to make it work. A two-process model of SIT in media effects research is suggested: the process of social comparison is amended with a much simpler process of searching for similarities.
Web Query Reformulation via Joint Modeling of Latent Topic Dependency and Term Context

An important way to improve users’ satisfaction in Web search is to assist them by issuing more effective queries. One such approach is query reformulation, which generates new queries according to the current query issued by users. A common procedure for conducting reformulation is to generate some candidate queries first, then a scoring method is employed to assess these candidates. Currently, most of the existing methods are context based. They rely heavily on the context relation of terms in the history queries and cannot detect and maintain the semantic consistency of queries. In this article, we propose a graphical model to score queries. The proposed model exploits a latent topic space, which is automatically derived from the query log, to detect semantic dependency of terms in a query and dependency among topics. Meanwhile, the graphical model also captures the term context in the history query by skip-bigram and n-gram language models. In addition, our model can be easily extended to consider users’ history search interests when we conduct query reformulation for different users. In the task of candidate query generation, we investigate a social tagging data resource—Delicious bookmark—to generate addition and substitution patterns that are employed as supplements to the patterns generated from query log data.
Critical Conversations: Tensions and Opportunities of the Dialogical Classroom

English teachers and educators of English teachers should work within rather than against the tensions present in their classrooms. For us, nothing could be more key. Until university teacher educators construct and enact classrooms that embrace the dialogical tensions and possibilities within those settings, new and veteran teachers in the profession will have few if any sustained experiences upon which to base their own dialogical classrooms. Moreover, to either deny that tensions exist or to struggle to eradicate them is to misunderstand the purpose and possibility of tension. Learners caught between stabilizing and destabilizing tensions enter a state of wobble, one that asks them to pay attention to the issues at hand and to author a response. The goal is not to remove oneself from that tension but instead to enter into a dialogue that, like the cables on a suspension bridge, uses tension for support and equilibrium.
Incorporating vertical results into search click models

In modern search engines, an increasing number of search result pages (SERPs) are federated from multiple specialized search engines (called verticals, such as Image or Video). As an effective approach to interpret users' click-through behavior as feedback information, most click models were designed to reduce the position bias and improve ranking performance of ordinary search results, which have homogeneous appearances. However, when vertical results are combined with ordinary ones, significant differences in presentation may lead to user behavior biases and thus failure of state-of-the-art click models. With the help of a popular commercial search engine in China, we collected a large scale log data set which contains behavior information on both vertical and ordinary results. We also performed eye-tracking analysis to study user's real-world examining behavior. According these analysis, we found that different result appearances may cause different behavior biases both for vertical results (local effect) and for the whole result lists (global effect). These biases include: examine bias for vertical results (especially those with multimedia components), trust bias for result lists with vertical results, and a higher probability of result revisitation for vertical results. Based on these findings, a novel click model considering these biases besides position bias was constructed to describe interaction with SERPs containing verticals. Experimental results show that the new Vertical-aware Click Model (VCM) is better at interpreting user click behavior on federated searches in terms of both log-likelihood and perplexity than existing models.