Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Identification of Mycorrhizae of Cymbidium kanran (Orchidaceae) on Jeju Island, Korea

Abstract A fungal internal transcribed spacer region was used to identify the mycorrhizae of Cymbidium kanran. The family Russulaceae was found to be the most frequently occurring group in both root and soil samples. In phylogenetic analyses, the majority of the Russulaceae clones were clustered with Russula brevipes and R. cyanoxantha. Therefore, C. kanran may form symbiotic relationships with the genus Russula.
Effects of diffuse radiation on canopy gas exchange processes in a forest ecosystem

[1] Forest ecosystems across the globe show an increase in ecosystem carbon uptake efficiency under conditions with high fraction of diffuse radiation. Here, we combine eddy covariance flux measurements at a deciduous temperate forest in central Germany with canopy-scale modeling using the biophysical multilayer model CANVEG to investigate the impact of diffuse radiation on various canopy gas exchange processes and to elucidate the underlying mechanisms. Increasing diffuse radiation enhances canopy photosynthesis by redistributing the solar radiation load from light saturated sunlit leaves to nonsaturated shade leaves. Interactions with atmospheric vapor pressure deficit and reduced leaf respiration are only of minor importance to canopy photosynthesis. The response strength of carbon uptake to diffuse radiation depends on canopy characteristics such as leaf area index and leaf optical properties. Our model computations shows that both canopy photosynthesis and transpiration increase initially with diffuse fraction, but decrease after an optimum at a diffuse fraction of 0.45 due to reduction in global radiation. The initial increase in canopy photosynthesis exceeds the increase in transpiration, leading to a rise in water-use-efficiency. Our model predicts an increase in carbon isotope discrimination with water-use-efficiency resulting from differences in the leaf-to-air vapor pressure gradient and atmospheric vapor pressure deficit. This finding is in contrast to those predicted with simple big-leaf models that do not explicitly calculate leaf energy balance. At an annual scale, we estimate a decrease in annual carbon uptake for a potential increase in diffuse fraction, since diffuse fraction was beyond the optimum for 61% of the data.
Assessing optimal assignment under uncertainty: An interval-based algorithm

We consider the problem of multi-robot task-allocation when robots have to deal with uncertain utility estimates. Typically an allocation is performed to maximize expected utility; we consider a means for measuring the robustness of a given optimal allocation when robots have some measure of the uncertainty (e.g. a probability distribution, or moments of such distributions). We introduce the interval Hungarian algorithm, a new algorithm that extends the classic Kuhn—Munkres Hungarian algorithm to compute the maximum interval of deviation, for each entry in the assignment matrix, which will retain the same optimal assignment. The algorithm has a worst-case time complexity of O(n 4); we also introduce a parallel variant with O(n 3) running time, which is able to exploit the concurrent computing capabilities of distributed multi-robot systems. This provides an efficient measurement of the tolerance of the allocation to the uncertainties and dynamics, for both a specific interval and a set of interrelated intervals. We conduct experiments both in simulation and with physical robots to validate the approach and to gain insight into the effect of location uncertainty on allocations for multi-robot multi-target navigation tasks.
Fuzzy-enabled failure behaviour analysis for dependability assessment of networked systems

Dependability assessment of networked component-based systems requires fine-grained modelling of the failure behaviour and propagation aspects of individual components. We have recently introduced a formalism called FI4FA, enabling the analysis of I4 (incompletion, inconsistency, interference and impermanence) failures as well as the analysis of the corresponding mitigations.
Mechanisms of Barrier Layer Formation and Erosion from In Situ Observations in the Bay of Bengal

During the Bay of Bengal (BoB) Boundary Layer Experiment (BoBBLE) in the southern BoB, time series of microstructure measurements were obtained at 8°N, 89°E from 4 to 14 July 2016. These observations captured events of barrier layer (BL) erosion and reformation. Initially, a three-layer structure was observed: a fresh surface mixed layer (ML) of thickness 10–20 m; a BL below of 30–40-m thickness with similar temperature but higher salinity; and a high salinity core layer, associated with the Summer Monsoon Current. Each of these three layers was in relative motion to the others, leading to regions of high shear at the interfaces. However, the destabilizing influence of the shear regions was not enough to overcome the haline stratification, and the three-layer structure was preserved. A salinity budget using in situ observations suggested that during the BL erosion, differential advection brought high salinity surface waters (34.5 psu) with weak stratification to the time series location and replaced the three-layer structure with a deep ML (~60 m). The resulting weakened stratification at the time series location then allowed atmospheric wind forcing to penetrate deeper. The turbulent kinetic energy dissipation rate and eddy diffusivity showed elevated values above 10−7 W kg−1 and 10−4 m2 s−1, respectively, in the upper 60 m. Later, the surface salinity decreased again (33.8 psu) through differential horizontal advection, stratification became stronger and elevated mixing rates were confined to the upper 20 m, and the BL reformed. A 1D model experiment suggested that in the study region, differential advection of temperature–salinity characteristics is essential for the maintenance of BL and to the extent to which mixing penetrates the water column.
Agents as Empirical Macroeconomists: Thomas J. Sargent's Contribution to Economics

Thomas J. Sargent has fundamentally changed and, in the words of Art Rolnick, who interviewed him in 2010, “irrevocably transformed” the field of macroeconomics—whether as sole author, as co-author with collaborators, as an author influenced by others, or as a teacher of the profession, influencing others. This paper is about his contribution to our field. The Nobel Memorial prize to Thomas J. Sargent and Christopher A. Sims has been awarded for the “empirical research on cause and effect in the macroeconomy” or, more broadly, for macroeconometrics. One often likes to distinguish between theorists, on the one hand, and empiricists and econometricians, on the other. Thomas J. Sargent holds a unique position in between. A key theme in a large part of his work has been to put the agents in his model on equal footing with the econometrician who is observing data from the model (i.e., to assume that agents are themselves empirical macroeconomists or macroeconometricians). In this paper, I use this theme to examine his work and his contributions to the study of economics.
On the Exploitation of the Redundant Energy in UW-OFDM: LMMSE Versus Sphere Detection

Unique word orthogonal frequency division multiplexing (UW-OFDM) inherently introduces a complex number Reed Solomon (RS) code. Originally, the code generator matrix of systematic coded UW-OFDM had been designed rather intuitively by minimizing the mean redundant energy. In this work we justify this approach by applying a cost function that incorporates the overall transceiver chain including a linear minimum mean square error (LMMSE) data estimator. In addition to the LMMSE estimator we investigate a nonlinear sphere detection (SD) receiver for both systematic and nonsystematic coded UW-OFDM. We study and interpret the estimators' performance and their diverse ability to exploit the redundant energy.
Optimal Dynamic Load Balance in Distributed Systems for Client Server Assignment

Internet is a network of several distributed systems that consists of clients and servers communicating with each other directly or indirectly. In order to improve the performance of such a system, client-server assignment plays an important role. Achieving optimal client-server assignment in internet distributed systems is a great challenge. It is dependent on various factors and can be achieved by various means. Our approach is mainly dependent on two important factors, 1) Total Message length and 2) Available servers in a system and size of the channels through a server. In our approach we propose an algorithm that is based on dynamic method, to obtain an approximately optimal solution for the client-server assignment problem. Our simulation results indicate that the proposed algorithm outperforms other client server assignment algorithms in terms of optimal value and running time. Keywords— Distributed systems, client-server systems, load balancing, communication load, optimization, dynamic method.
Evaluation of the skin sensitizing potency of chemicals by using the existing methods and considerations of relevance for elicitation

The Technical Committee of Classification and Labelling dealing with harmonized classification of substances and classification criteria under Directive 67/548/EEC on behalf of the European Commission nominated an expert group on skin sensitization in order to investigate further the possibility for potency consideration of skin sensitizers for future development of the classification criteria. All substances and preparations should be classified on the basis of their intrinsic properties and should be labelled accordingly with the rules set up in the Directive 67/548/EEC. The classification should be the same under their full life cycle and in the case that there is no harmonized classification the substance or preparation should be self‐classified by the manufacturer in accordance with the same criteria. The Directive does not apply to certain preparations in the finished state, such as medical products, cosmetics, food and feeding stuffs, which are subject to specific community legislation. The main questions that are answered in this report are whether it would be possible to give detailed guidance on how to grade allergen potency based on the existing methods, whether such grading could be translated into practical thresholds and whether these could be set for both induction and elicitation. Examples are given for substances falling into various potency groups for skin sensitization relating to results from the local lymph node assay, the guinea pig maximization test, the Buehler method and human experience.
Bayesian prediction of RNA translation from ribosome profiling

Abstract Ribosome profiling via high-throughput sequencing (ribo-seq) is a promising new technique for characterizing the occupancy of ribosomes on messenger RNA (mRNA) at base-pair resolution. The ribosome is responsible for translating mRNA into proteins, so information about its occupancy offers a detailed view of ribosome density and position which could be used to discover new translated open reading frames (ORFs), among other things. In this work, we propose Rp-Bp, an unsupervised Bayesian approach to predict translated ORFs from ribosome profiles. We use state-of-the-art Markov chain Monte Carlo techniques to estimate posterior distributions of the likelihood of translation of each ORF. Hence, an important feature of Rp-Bp is its ability to incorporate and propagate uncertainty in the prediction process. A second novel contribution is automatic Bayesian selection of read lengths and ribosome P-site offsets (BPPS). We empirically demonstrate that our read length selection technique modestly improves sensitivity by identifying more canonical and non-canonical ORFs. Proteomics- and quantitative translation initiation sequencing-based validation verifies the high quality of all of the predictions. Experimental comparison shows that Rp-Bp results in more peptide identifications and proteomics-validated ORF predictions compared to another recent tool for translation prediction.
Significant lateral dip changes may have limited the scale of the 2015 Mw 7.8 Gorkha earthquake

The 2015 Mw 7.8 Gorkha earthquake has drawn interest due to its complex fault geometry. Both geodetic and geologic studies have focused on the dip variations. In this study we invert the coseismic geodetic data for the 2‐D dip variations of the earthquake. The best fit model confirms that the dip varies with depth, and suggests that there is a significant lateral dip anomaly along strike. The depth‐dependent dip variation suggests that the earthquake ruptured a ramp‐flat fault. The shallow ramp may have prevented the rupture breaking through the surface. In addition, a lateral large‐dip anomaly is found in the northeastern corner of the slip area, which supports the previous findings of inferred interseismic fault coupling, coseismic high‐frequency radiations, and the aftershock mechanisms. This lateral dip anomaly is likely associated with local tearing within the Indian slab. It may have blocked the east‐southeastward rupture propagations of the Gorkha earthquake, implying important controls on the earthquake scale and the spatial limits of ruptures.
Environmental constraints on life histories in Antarctic ecosystems: tempos, timings and predictability

Knowledge of Antarctic biotas and environments has increased dramatically in recent years. There has also been a rapid increase in the use of novel technologies. Despite this, some fundamental aspects of environmental control that structure physiological, ecological and life‐history traits in Antarctic organisms have received little attention. Possibly the most important of these is the timing and availability of resources, and the way in which this dictates the tempo or pace of life. The clearest view of this effect comes from comparisons of species living in different habitats. Here, we (i) show that the timing and extent of resource availability, from nutrients to colonisable space, differ across Antarctic marine, intertidal and terrestrial habitats, and (ii) illustrate that these differences affect the rate at which organisms function. Consequently, there are many dramatic biological differences between organisms that live as little as 10 m apart, but have gaping voids between them ecologically.
Implication of cAMP during porcine sperm capacitation and protein tyrosine phosphorylation

Second messengers are involved in sperm fertilizing potential, as both motility and the acrosome reaction are influenced by cAMP. Moreover, the activity of cyclic nucleotides is implicated in the appearance of tyrosine phosphorylated sperm proteins, which is associated with capacitation in the mammalian spermatozoa. Nevertheless, the involvement of the cAMP/protein kinase A (PK‐A) pathway during pig sperm capacitation may be different from that observed in other mammals. The objective of the present study was to clarify the cAMP/PK‐A pathway during the capacitation of porcine spermatozoa and to evaluate this impact on the p32 sperm tyrosine phosphoprotein appearance. The presence of p32 was assessed after incubating fresh pig sperm with IBMX/db‐cAMP, H‐89, a PK‐A inhibitor or bistyrphostin, a tyrosine kinase inhibitor, in capacitating (CM) or non‐capacitating conditions (NCM) by immunoblotting SDS‐extracted and separated sperm proteins using an anti‐phosphotyrosine antibody. When pig spermatozoa were incubated in CM supplemented with H‐89 (50 μM) or bistyrphostin (1.2 μM), capacitation decreased significantly (P < 0.001). The p32 sperm tyrosine phosphoprotein, previously shown to be associated with capacitation of porcine sperm though not necessarily an end point of this phenomenon, was not modulated by IBMX/db‐cAMP (100 μM/1 mM), H‐89 (50 μM) nor bistyrphostin (1.2 μM). Our results indicate, therefore, that pig sperm are regulated somewhat differently than as described for other mammals, because although the cAMP/PK‐A and tyrosine kinase pathways are involved in capacitation, they do not influence the appearance of p32. Mol. Reprod. Dev. 69: 428–435, 2004. © 2004 Wiley‐Liss, Inc.
Generating Pseudotransactions for Improving Sparse Matrix Factorization

Recent research on Recommender Systems, specifically Collaborative Filtering, has focussed on Matrix Factorization (MF) methods, which have been shown to provide good solutions to the cold start problem. However, typically the same settings are used for Matrix factorization regardless of the density of the matrix. In our experiments, we found that for MF, Root Mean Square Error (RMSE) for recommendations increases (i.e. performance drops) for sparse matrices. We propose a Two Stage MF approach so MF is run twice over the whole matrix; the first stage uses MF to generate a small percentage of pseudotransactions that are added to the original matrix to increase its density, and the second stage re-runs MF over this denser matrix to predict the user-item transactions in the testing set. We show using data from Movielens that such methods can improve on the performance of MF for sparse martrices.
Variability and Changes of the Growing Season Length and Frost Days Number in Russian sub-Arctic

Observational data from the Russian sub-Arctic stations are used to investigate long-term variability of the growing season length (GSL) and the number of frost days (FD) in 1949-2013. Consistent with the global warming pattern we find a trend-like increase (decrease) of GSL (FD) which is evident since early 1970 th of the last century. These trendlike changes are best pronounced at Western stations (i.e. in European Russia and western Siberia) and they are essentially smaller to the East. Although we find some significant links to regional teleconnections (such as Scandinavian, East Atlantic and West Pacific teleconnections), in general our results imply rather weak impact of large scale atmospheric dynamics on interannual variability of GSL and FD. Further analysis of correlations between GSL and FD on the one side and snow cover on the other side revealed generally stronger links to snow cover compared to teleconnections. However, revealed links to regional atmospheric teleconnections and snow cover are significantly impacted by the linear trends. In general, our results imply that compared to large scale atmospheric dynamics impacting interannual variability, snow cover (being a result of wintertime synoptic activity) plays a more important role in decadal-interdecadal variations of GSL and FD in Russian sub-Arctic, which may have some value regarding predictability of the summer climate in the region.
Atlas based liver segmentation using nonrigid registration with a B-spline transformation model

Liver segmentation is an important step for the therapeutic decision making in liver surgery. However, manual segmentation is timeconsuming and tedious and so the need for accurate and robust automatic segmentation methods for clinical data arises. In this work an atlas in combination with nonrigid registration is used to segment the liver in actual clinical CT images. First, the atlas is built on twenty training images using nonrigid registration with a novel surface distance penalty. Next, this atlas is nonrigidly registered to ten test images. Currently, the user interaction is limited to the initialization of a rigid registration and to the definition of a region of interest for the nonrigid registration. Future work will focus on replacing the remaining user interaction with fully automatic procedures. Results are promising with an average overlap error of 10.4% and an average RMS distance of 5.0mm for the ten test images. Errors occur mainly at sites where the atlas is ill-defined such as the border between the heart and the liver.
Food Safety Attitudes in College Students: A Structural Equation Modeling Analysis of a Conceptual Model

College students are one of the most at-risk population groups for food poisoning, due to risky food safety behaviors. Using the Likert Scale, undergraduate students were asked to participate in a Food Safety Survey which was completed by 499 students ages 18–25. Data was analyzed using SPSS and AMOS statistical software. Four conceptual definitions regarding food safety were defined as: general food safety, bacterial food safety, produce food safety, and politics associated with food safety. Knowledge seems to be an important factor in shaping students attitudes regarding general and bacterial safety. Ethnicity plays a role in how people view the politics of food safety, and the safety of organic foods.
Low latitude ice cores record Pacific sea surface temperatures

Oxygen isotope variations in ice cores from Bolivia and Peru are highly correlated with sea surface temperatures (SSTs) across the equatorial Pacific Ocean, which are closely linked to ENSO variability. Circulation anomalies associated with this variability control moisture flux from the equatorial and tropical Atlantic Ocean and Amazon Basin to the ice core sites. Below average SSTs lead to higher accumulation rates and isotopically lighter snow; such conditions are also associated with lower atmospheric freezing levels. During warm events, opposite conditions prevail. Oxygen isotope variations in an ice core from the Himalayas also reflect SST variations in the equatorial Pacific Ocean, pointing to the prospect of reconstructing low latitude circulation anomalies from a network of ice cores in selected locations.
SIIPU*S: A Semantic Pattern Learning Algorithm

The efficacy of pattern-based question answering system is mostly determined by the size of the semantic pattern base and the expression capability of the semantic patterns. We find that the expression capabilities of semantic patterns are determined by their instantiation degrees. Hence, we propose an evaluation strategy named Semantic Identifiability Inverse Pattern Universality (SIIPU), using which we can estimate the instantiation degree of a pattern for a certain semantic requirement. Moreover, on the basis of SIIPU, we propose a semantic pattern learning algorithm named SIIPU*S. Using SIIPU*S we can extract the semantic patterns at the most appropriate instantiation level for a given semantic requirement from a training corpus. Preliminary results show the proposed method? s efficacy to extract patterns at different instantiation levels and their effects in analyzing questions.
Solution techniques for a crane sequencing problem

In the areas of power plant maintenance, shipyard and warehouse management, resources (items) assigned to locations need to be relocated. It is essential to develop efficient techniques for relocating items to new locations using a crane such that the sum of the cost of moving the items and the cost of loading/unloading the items is minimised. This problem is defined as the crane sequencing problem (CSP). Since the CSP determines the routes for a crane to relocate items, it is closely related to some variants of the travelling salesman problem. However, the CSP considers the capacities of locations and intermediate drops (i.e. preemptions) during a multiple period planning horizon. In this article, a mathematical model and hybrid ant systems are developed for the CSP. Computational experiments were conducted to evaluate the performances of the proposed techniques, and results show that the proposed heuristics are effective.