Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of arbuscular mycorrhizal colonization on whole‐plant respiration and thermal acclimation of tropical tree seedlings

Abstract Symbiotic arbuscular mycorrhizal fungi (AMF) are ubiquitous in tropical forests. AMF play a role in the forest carbon cycle because they can increase nutrient acquisition and biomass of host plants, but also incur a carbon cost to the plant. Through their interactions with their host plants they have the potential to affect how plants respond to environmental perturbation such as global warming. Our objective was to experimentally determine how plant respiration rates and responses to warmer environment are affected by AMF colonization in seedlings of five tropical tree species at the whole plant level. We evaluated the interaction between AMF colonization and temperature on plant respiration against four possible outcomes; acclimation does or does not occur regardless of AMF, or AMF can increase or decrease respiratory acclimation. Seedlings were inoculated with AMF spores or sterilized inoculum and grown at ambient or elevated nighttime temperature. We measured whole plant and belowground respiration rates, as well as plant growth and biomass allocation. There was an overall increase in whole plant, root, and shoot respiration rate with AMF colonization, whereas temperature acclimation varied among species, showing support for three of the four possible responses. The influence of AMF colonization on growth and allocation also varied among plant species. This study shows that the effect of AMF colonization on acclimation differs among plant species. Given the cosmopolitan nature of AMF and the importance of plant acclimation for predicting climate feedbacks a better understanding of the patterns and mechanisms of acclimation is essential for improving predictions of how climate warming may influence vegetation feedbacks.
PITCH PROCESSING IN MUSIC AND SPEECH

INTRODUCTION A highly-debated question is to what extent music and language share processing components. Beyond syntax and temporal structure processing, one studied aspect is pitchprocessing in a given domain and across domains (e.g., [1]). Pitch processing is crucial in music. For example, in Western tonal music, it is a form-bearing dimension (next to temporal structures). Pitch processing is also crucial in speech, notably for discriminating questions and statements, as well as for communicating emotional expressions. This is valid for non-tone intonation languages (e.g., English, French) and tone languages (e.g., Mandarin, Thai, Vietnamese). However, for tone languages, pitch processing is even more crucial as pitch information is used for communicating word meaning. Tone languages comprise 70% of the world’s languages and are spoken by more than 50% of the world’s population. In these languages, tone variations (comprising predominantly fundamental frequency (F0) height and contour parameters) at the syllabic level have the same effect on word meaning as do vowel and consonant variations in non-tone languages. For example, the syllable /ma/ combined with different tones (e.g., tones describing contours of rather constant level, rising dipping or falling patterns in Mandarin) represents different lexical items. Interestingly, music and language differ in the size of the pitch differences that are relevant for each of the systems (speech intonation versus musical structures). For speech intonation of non-tonal languages, F0 variations, in particular those indicating statements and questions, are typically coarse (up to more than 12 semitones1 for the pitch rise of the final word in a question; e.g., [2]). For music (as in most research, we are referring here mostly to the Western tonal system), however, the pitch variations are typically more fine-grained (1 or 2 semitones; see [3]). In tone languages, the range of F0 variations can be as small as in music of the Western tonal system or larger depending on the tones and the tone languages. The present paper proposes an overview of research that investigates pitch processing by considering cognitive processes (related to context, learning, memory and/or knowledge) for both music and language material. While extensive research has focussed on pitch processing in musical material as well as the influence of musical expertise (e.g., comparing musicians and nonmusicians), research investigating pitch processing in tone language material for either musicians, nonmusicians or tone language speakers (or both), provides complementary information about underlying mechanisms. Furthermore, investigating deficits (such as in amusia) provides further insights into the potential domain-specificity or domaingenerality of pitch processing mechanisms.
Co–option of male courtship signals from aggressive display in bowerbirds

The pre–existing trait hypothesis suggests that females evolve a mating preference for an already existing male trait. This hypothesis poses a simple resolution to Darwin's long–standing question of how elaborate, male display traits evolve. The frequently observed convergence of aggressive and courtship displays across a wide array of species provides the only current support for this hypothesis. Here we provide much more detailed supporting evidence from bowerbird skrraa calls used in aggression and courtship. Consistent with the pre–existing trait hypothesis we show that (i) putatively co–opted skrraa calls used in courtship and aggression are homologous, (ii) skrraa calls were used in aggression in bowerbirds before being used in courtship, (iii) historically, intense, aggressive–like courtship calls were present near the time of co-option, and (iv) bower types contemporaneous with co–option emphasize design features that provide females protection from the adverse effects of intense courtship displays. These results, plus evidence for a female preference for males with intense aggressive–like courtship skrraa calls, suggest that aggressive skrraa calls have been co–opted for use in male courtship display.
Symmetries in the physics of strongly correlated electronic systems

Strongly correlated electron systems require the development of new theoretical schemes in order to describe their unusual and unexpected properties. The usual perturbation schemes are inadequate and new concepts must be introduced. In our scheme of calculations, the Composite Operator Method, is possible to recover, through a self-consistent calculation, a series of fundamental symmetries by choosing a suitable Hilbert space.
Understanding Cluster Gas Evolution and Fine-Scale Cosmic Microwave Background Anisotropy with Deep Sunyaev-Zeldovich Effect Surveys

We investigate the impact of gas evolution on the expected yields from deep Sunyaev-Zeldovich (SZ) effect surveys, as well as on the expected SZ effect contribution to fine-scale anisotropy in the cosmic microwave background (CMB). The approximate yields from SZ effect surveys are remarkably insensitive to gas evolution, even though the observable properties of the resulting clusters can be markedly different. The CMB angular power spectrum at high multipoles (l ≳ 2000, ≲ 5′) due to the SZ effect from clusters is quite sensitive to gas evolution. We show that moderate-resolution (≤ 1′) SZ effect imaging of clusters found in deep SZ effect surveys should allow a good understanding of gas evolution in galaxy clusters, independent of the details of the nature of the gas evolution. Such an understanding will be necessary before precise cosmological constraints can be set from yields of large cluster surveys.
Bayesian model determination for quantitative traitlociJaya

A reversible jump Markov chain Monte Carlo (MCMC) algorithm is illustrated to infer the number of quantitative trait loci (QTL) a ecting a phenotypic trait, their chromosomal locations, and their e ects. A multi-loci model is t to quantitative trait and molecular marker data, with the trait response modeled as a linear function of the additive and dominance e ects of the unknown QTL genotypes. The number of QTL is unknown and must be estimated as well. Inference summaries for the number of loci, their locations and e ects are obtained from the corresponding marginal posterior densities obtained by integrating the likelihood using reversible jump MCMC, rather than by optimizing the joint likelihood surface. Using simulated data and owering time data from Brassica napus we observe that the choice of prior distribution plays an important role in inference. This prior distribution greatly in uences how well the chain mixes as well as the posterior distribution of the number of loci. However, the posterior mode of the number of loci is not a ected by the choice of its prior. Further, neither the choice of prior nor the starting value for the number of loci a ect the estimated chromosomal locations and their e ects.
Adam - A DVE Simulator

During the past 25 years, a large amount of distributed virtual environment (DVE) systems has been proposed. Each was built to support a single scenario. This not only makes it impossible to rank these various DVEs, it also obscures the effect of each of the algorithms used in those systems. This makes it very hard to select the algorithms for a new scenario unless this scenario is a fairly exact copy of one of the previous sample-scenarios. To overcome this situation, we have created a modular simulator-based DVE testbed named Adam with the ability to plug in different scenarios as well as different algorithms. The testbed also contains a large set of measuring tools to compare and rank the effect of each algorithm and to allow finding optimal parameters for those algorithms. Our testbed currently supports two scenarios and several of the most common consistency algorithms found in the literature. We can compare the solutions on an objective scale and confirm that optimistic consistency typically outperforms loose consistency. Chapter
Search-As-You-Type in Forms : Leveraging the Usability and the Functionality of Search Paradigm in Relational Databases

Querying, or searching, is one of the most important issues in relational databases. There are many search paradigms, such as Structured Query Language (SQL), keyword search, and form search, a.k. a. Query-By-Example (QBE). Among them, QBE is a good trade-off between usability and functionality. However, existing QBE systems are often inconvenient for users to compose high-quality queries quickly. In this PhD workshop paper we investigate the problem of improving the usability of form-based interfaces by enabling them to (1) response a query in real time and (2) tolerate the misplacing of keywords among input boxes. We give the research challenges for achieving high performance and scalability, and introduce two of our prototype systems.
Mechanisms Underlying Atriopeptin‐Induced Increases in Hematocrit and Vascular Permeation in Rats

Infusion of atriopeptin into humans and animals induces diuresis, natriuresis, hemodynamic changes, and an increase in arterial hematocrit. The objective of the present study was to elucidate the mechanism(s) responsible for the increase in hematocrit in rats given atriopeptin-24 (AP-24). Infusion of AP-24 for 30 minutes increased large vessel and total vascular hematocrits by 10-15percent; while decreasing microvascular hematocrits by 9-26percent; in numerous tissues. Regional vascular permeation by [131I] bovine serum albumin was markedly increased (2-5.6-fold) in many tissues, consistent with a 16percent; decrease in plasma volume. AP-24 infusion had no effect on extracellular fluid volume or the volume of circulating red cells. Vascular resistance was decreased and was associated with a significant increase in blood flow in many, but not all, tissues. In the atrium and in the small and large intestine the percentage decrease in microvascular hematocrit exceeded the increase in blood flow. These observations indicate that the increase in large vessel hematocrit induced by AP-24 infusion 1) is accompanied by a decrease in (microvascular) hematocrit in many tissues, 2) reflects an increase in overall (i.e., total vascular hematocrit), and 3) is the consequence of a decrease in plasma volume resulting from a marked increase in the rate of vascular permeation by plasma constituents in multiple tissues.
Factor Models for Recommending Given Names

We describe in this paper our contribution to the ECML PKDD Discovery Challenge 2013 (Oine Track). This years task was to predict the next given names a user of a name search engine interacts with. We model the user preferences with a sequential factor model that we optimize with respect to the Bayesian Personalized Ranking (BPR) Optimization Criterion. Therefore we complement the sequential factor model with prex smoothing in order to explicitly model syntactical similarity.
Anchors for Effectors: Subversion of Phosphoinositide Lipids by Legionella

The facultative intracellular pathogen Legionella pneumophila replicates in free-living amoebae and macrophages within a distinct compartment, the “Legionella-containing vacuole” (LCV). LCV formation involves phosphoinositide (PI) glycerolipids, which are key factors controlling vesicle trafficking pathways and membrane dynamics of eukaryotic cells. To govern the interactions with host cells, L. pneumophila employs the Icm/Dot type IV secretion system and more than 250 translocated “effector proteins” that presumably subvert host signaling and vesicle trafficking pathways. Some of the effector proteins anchor through distinct PIs to the cytosolic face of LCVs and promote the interaction with host vesicles and organelles, catalyze guanine nucleotide exchange of small GTPases, or bind to PI-metabolizing enzymes, such as OCRL1. The PI 5-phosphatase OCRL1 and its Dictyostelium homologue Dd5P4 restrict intracellular growth of L. pneumophila. Moreover, OCRL1/Dd5P4, PI 3-kinases (PI3Ks), and PI4KIIIβ regulate LCV formation and localization of the effector protein SidC, which selectively decorates the LCV membrane. SidC and its 20-kDa “P4C” fragment are robust and specific probes for phosphatidylinositol-4-phosphate, and SidC can be targeted to purify intact LCVs by immuno-magnetic separation. Taken together, bacterial PI-binding effectors as well as host PIs and PI-modulating enzymes play a pivotal role for intracellular replication of L. pneumophila, and the PI-binding effectors are valuable tools for the analysis of eukaryotic PI lipids.
VIP: Visualization of integrated proteomics data

The post-genomic era is characterized by the rapid data accumulation leading to unwieldy and large volumes of biological data. The proteomics results (large sets of identified proteins or peptides) that originate from several workflow steps, play an important role in the analysis of a proteomics experiment. As a result, the area of high-through-put proteomics created new visualization challenges in interpreting large-scale datasets. We present VIP, an interactive visualization tool for proteomics data, which integrates protein or peptide features emanating at every step of the proteomics analysis and combines them visually in synthetic maps. Our novel tool offers the flexibility to choose any desired features according to the analysis objectives, examine simultaneously more than one maps and interact with the visualization by querying and filtering the results. The synthetic maps visualization aims not only at summarizing proteomics experiments in a unified manner for both 2DE-MS and LC-MS based analyses, but also at providing a quick and combined overview of protein/peptide features, thus facilitating the data analysis and interpretation.
Synthetic Zinc Finger Proteins: The Advent of Targeted Gene Regulation and Genome Modification Technologies

Conspectus The understanding of gene regulation and the structure and function of the human genome increased dramatically at the end of the 20th century. Yet the technologies for manipulating the genome have been slower to develop. For instance, the field of gene therapy has been focused on correcting genetic diseases and augmenting tissue repair for more than 40 years. However, with the exception of a few very low efficiency approaches, conventional genetic engineering methods have only been able to add auxiliary genes to cells. This has been a substantial obstacle to the clinical success of gene therapies and has also led to severe unintended consequences in several cases. Therefore, technologies that facilitate the precise modification of cellular genomes have diverse and significant implications in many facets of research and are essential for translating the products of the Genomic Revolution into tangible benefits for medicine and biotechnology. To address this need, in the 1990s, we embarked on a mission to develop technologies for engineering protein–DNA interactions with the aim of creating custom tools capable of targeting any DNA sequence. Our goal has been to allow researchers to reach into genomes to specifically regulate, knock out, or replace any gene. To realize these goals, we initially focused on understanding and manipulating zinc finger proteins. In particular, we sought to create a simple and straightforward method that enables unspecialized laboratories to engineer custom DNA-modifying proteins using only defined modular components, a web-based utility, and standard recombinant DNA technology. Two significant challenges we faced were (i) the development of zinc finger domains that target sequences not recognized by naturally occurring zinc finger proteins and (ii) determining how individual zinc finger domains could be tethered together as polydactyl proteins to recognize unique locations within complex genomes. We and others have since used this modular assembly method to engineer artificial proteins and enzymes that activate, repress, or create defined changes to user-specified genes in human cells, plants, and other organisms. We have also engineered novel methods for externally controlling protein activity and delivery, as well as developed new strategies for the directed evolution of protein and enzyme function. This Account summarizes our work in these areas and highlights independent studies that have successfully used the modular assembly approach to create proteins with novel function. We also discuss emerging alternative methods for genomic targeting, including transcription activator-like effectors (TALEs) and CRISPR/Cas systems, and how they complement the synthetic zinc finger protein technology.
Geotagging Named Entities in News and Online Documents

News sources generate constant streams of text with many references to real world entities; understanding the content from such sources often requires effectively detecting the geographic foci of the entities. We study the problem of associating geography to named entities in online documents. More specifically, given a named entity and a page (or a set of pages) where the entity is mentioned, the problem being studied is how the geographic focus of the name can be resolved at a location granularity (e.g. city or country), assuming that the name has a geographic focus. We further study dispersion, and show that the dispersion of a name can be estimated with a good accuracy, allowing a geo-centre to be detected at an exact dispersion level. Two key features of our approach are: (i) minimal assumption is made on the structure of the mentions hence the approach can be applied to a diverse and heterogeneous set of web pages, and (ii) the approach is unsupervised, leveraging shallow English linguistic features and the large volume of location data in public domain. We evaluate our methods under different task settings and with different categories of named entities. Our evaluation reveals that the geo-centre of a name can be estimated with a good accuracy based on some simple statistics of the mentions, and that the accuracy of the estimation varies with the categories of the names.
Development and evaluation of Cooperative Adaptive Cruise Controllers

In this paper, we present a Cooperative Adaptive Cruise Control (CACC) system consists of several autonomous ground vehicles (AGVs). Using vehicle to vehicle communication, the designed cooperative controller could minimize inter vehicle spacing, meanwhile, guarantee the platoon's stability. We use mainly two algorithms to design our longitudinal controllers to the problem, a frequency domain approach and controller based on model predictive control. In order to validate the effectiveness of the proposed method, we conduct simulations on a simulated environment by coupling Matlab with Carsim. Simulation results show capabilities of all the designed controllers could make the vehicle follow a vehicle ahead of it at a desired safety distance.
Partial Highest Possible Edge Analysis for Interactive Image Accessibility

Relevance feedback is a technique that takes advantage of human-computer interaction to refine high level queries represented by low level features. Among RF schemes, the most popular technique is SVM based RF scheme. When SVM is used as a classifier in RF, there are two strategies. One strategy is to display the most positive images and use them as the training samples. The most-positive images are chosen as the ones farthest from the boundary on the positive side, plus those nearest from the boundary on the negative side if necessary. Another strategy is that most of SVM based RF scheme does not consider the unlabeled samples even though they are useful in constructing a good classifier. To overcome these drawbacks, in this paper we propose a biased maximum margin analysis (BMMA) and semi supervised BMMA (semiBMMA) for integrating the distinct properties of feedbacks and also to utilize the information of unlabeled samples. The BMMA differentiates positive from negative feedbacks, whereas semiBMMA takes into account the information of unlabeled samples by the introduction of Laplacian regularizer to BMMA. To validate the efficacy of the proposed approach, we test it on both synthesized data and real-world images. Promising results are achieved and this can significantly improve the performance of CBIR systems.
Spectrum leasing via selective cooperation in distributed cognitive radio networks

Cognitive radio (CR) has been widely recognized as a promising paradigm to achieve efficient use of the spectrum resource. While a lot of attention has been paid to the hierarchical access model of CR, the spectrum leasing model in which PUs can actively lease their spectrum to SUs for certain reward has not been studied thoroughly. In this paper, by assuming a PU is willing to lease its bandwidth for a fraction of time to SUs in exchange for selective cooperation, we propose a game model to describe the dynamic interaction between the PU and SUs. In our model, the PU plays a game with each of the potential SUs and selects the best one to cooperate with. We prove that there is always a unique Nash Equilibrium (NE) for each game. Moreover, we propose a simple distributed algorithm for practical implementation of the model. Simulation results verify that our approach can benefit both the PU and the SU in terms of utility and transmission rate.