Miracle-dz/UniFAR-FTUs huggingface dataset:
Bitrophic interactions shape biodiversity in space

Ecologists and conservation biologists often study particular trophic groups in isolation, which precludes an explicit assessment of the impact of multitrophic interactions on community structure and dynamics. Network ecology helps to fill this gap by focusing on species interactions, but it often ignores spatial processes. Here, we are taking a step forward in the integration of metacommunity and network approaches by studying a model of bitrophic interactions in a spatial context. We quantify the effect of bitrophic interactions on the diversity of plants and their animal interactors, and we show their complex dependence on the structure of the interaction network, the strength of interactions, and the dispersal rate. We then develop a method to parameterize our model with real-world networks and apply it to 54 datasets describing three types of interactions: pollination, fungal association, and insect herbivory. In all three network types, bitrophic interactions generally lead to an increase of plant and animal spatial heterogeneity by decreasing local species richness while increasing β-diversity.
Adding type parameterization to the Java language

Although the Java programming language has achieved widespread acceptance, one feature that seems sorely missed is the ability to use type parameters (as in Ada generics, C++ templates, and ML polymorphic functions or data types) to allow a general concept to be instantiated to one or more specific types. In this paper, we propose parameterized classes and interfaces in which the type parameter may be constrained to either implement a given interface or extend a given class. This design allows the body of a parameterized class to refer to methods on objects of the parameter type, without introducing any new type relations into the language. We show that these Java extensions may be implemented by expanding parameterized classes at class load time, without any extension or modification to existing Java bytecode, verifier or bytecode interpreter.
Mechanisms of Shared Attention for a Humanoid Robot

This paper outlines a proposal for constructing mechanisms of shared attention for a humanoid robot through a series of example tasks. Shared attention, the ability to selectively attend to objects that are mutually interesting, is vital for learning from another individual. The platform that we will use in designing this system is the upper-torso humanoid robot called Cog which is currently under construction at the MIT Artificial Intelligence Lab. We present a description of our approach, an outline of the work in progress, and a summary of the work completed so far.
Computer Simulation of Polymer Chains in Confinement

Properties of macromolecules confined in a narrow slit, pore or capillary are important due to of their practical importance. Theoretical treatment of such systems is also interesting because the introduction of confinement has an impact on most properties of polymer chains and it gained a longstanding attention. In order to determine the properties of such systems coarse-grained models of confined polymers were designed where macromolecules were represented by united atoms. Lattice approximation was also often introduced. Different macromolecular architectures were studied: linear, cyclic and star-branched chains. Computer simulation techniques (the variants of the Monet Carlo method like the Metropolis algorithm and the Replica Exchange method as well as Molecular Dynamics and Brownian Dynamics methods) applied for studies of such models were reviewed and evaluated. The structure of the polymer film and the dynamic properties were mainly presented and discussed. The influence of the width of the slit, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that a moderate confinement stabilizes folded chains while a strong confinement does not.
Experimental study of the behavioural mechanisms underlying self-organization in human crowds

In animal societies as well as in human crowds, many observed collective behaviours result from self-organized processes based on local interactions among individuals. However, models of crowd dynamics are still lacking a systematic individual-level experimental verification, and the local mechanisms underlying the formation of collective patterns are not yet known in detail. We have conducted a set of well-controlled experiments with pedestrians performing simple avoidance tasks in order to determine the laws ruling their behaviour during interactions. The analysis of the large trajectory dataset was used to compute a behavioural map that describes the average change of the direction and speed of a pedestrian for various interaction distances and angles. The experimental results reveal features of the decision process when pedestrians choose the side on which they evade, and show a side preference that is amplified by mutual interactions. The predictions of a binary interaction model based on the above findings were then compared with bidirectional flows of people recorded in a crowded street. Simulations generate two asymmetric lanes with opposite directions of motion, in quantitative agreement with our empirical observations. The knowledge of pedestrian behavioural laws is an important step ahead in the understanding of the underlying dynamics of crowd behaviour and allows for reliable predictions of collective pedestrian movements under natural conditions.
Manipulation of music for melody matching

Many types of user would find it valuable to search collectionsof music via queries representing music fragments, but suchsearching requires a reliable technique for identifying whether aprovided fragment occurs within a piece of music. The problem ofmatching fragments to music is made difficult by the psychology ofmusic perception, because literal matching may have litile relationto perceived melodic similarity, and by the interactions betweenthe multiple parts of typical pieces of music. In this paper weanalyse the propeties of music, music perception, and musicdatabase users, and use the analysis to propose alternativetechniques for extracting monophonic melodies from polyphonicmusic; we believe that such melodies can subsequently be used formatching of queries to data. We report on experiments with musiclisteners, which rank our proposed techniques for extractingmelodies.
A Novel Approach to Build a Gated Integrator for HighResolution Energy Spectroscopy Systems

A gated integrator (GI) is to solve the ballistic deficit problem by integrating the signal until all the charge is collected from the detector. With the development of radioactive ion beam physics, heavy-charged particles like carbon ions have been applied to the treatment of deep-seated inoperable tumors in the therapy terminal of the Heavy ion Research Facility in Lanzhou (HIRFL) located at the Institute of Modern Physics (IMP), Chinese Academy of Sciences (CAS). An accurate low current measurement circuit was developed to control the beam current at 1pA range. The circuit consisted of a low current high sensitivity I/V converter and GI in an energy spectroscopy. This paper will show a new switch configuration made by transmission gates circuit which is used to prevent leakage current and at the same time used as a novel technique to compensate a charge injection in the reset switch.
Web & Grid Technologies in Bioinformatics , Computational and Systems Biology : A Review

The acquisition of biological data, ranging from molecular characterization and simulations (e.g. protein folding dynamics), to systems biology endeavors (e.g. whole organ simulations) all the way up to ecological observations (e.g. as to ascertain climate change’s impact on the biota) is growing at unprecedented speed. The use of computational and networking resources is thus unavoidable. As the datasets become bigger and the acquisition technology more refined, the biologist is empowered to ask deeper and more complex questions. These, in turn, drive a runoff effect where large research consortia emerge that span beyond organizations and national boundaries. Thus the need for reliable, robust, certified, curated, accessible, secure and timely data processing and management becomes entrenched within, and crucial to, 21 st century biology. Furthermore, the proliferation of biotechnologies and advances in biological sciences has produced a strong drive for new informatics solutions, both at the basic science and technological levels. The previously unknown situation of dealing with, on one hand, (potentially) exabytes of data, much of which is noisy, has large experimental errors or theoretical uncertainties associated with it, or on the other hand, large quantities of data that require automated computationally intense analysis and processing, have produced important innovations in web and grid technology. In this paper we present a trace of these technological changes in Web and Grid technology, including details of emerging infrastructures, standards, languages and tools, as they apply to bioinformatics, computational biology and systems biology. A major focus of this technological review is to collate up-to-date information regarding the design and implementation of various bioinformatics Webs, Grids, Web-based grids or Grid-based webs in terms of their infrastructure, standards, protocols, services, applications and other tools. This review, besides surveying the current state-of-the-art, will also provide a road map for future research and open questions.
Imaging , Diagnosis , Prognosis Digital Transcript Profile Analysis with aRNA-LongSAGE Validates FERMT 1 As a Potential Novel Prognostic Marker for Colon Cancer

Purpose: To use gene transcript profiling to identify cancer-associated gene expression. Experimental Design: Methods included (i) marker discovery using laser capture microdissection (LCM)-assisted specimen preparation and antisense RNA-long serial analysis of gene expression (aRNALongSAGE) on matched colon cancer and uninvolved colon tissue specimens (n 1⁄4 5). Candidate tumorassociated genes were selected by combining the LongSAGE libraries reported herein with our previous colon cancer LCM-microarray transcript profiling data; (ii) marker selection and validation by quantitative real-time PCR (n1⁄4 15) and immunohistochemistry (n1⁄4 31); and (iii) independent validation onmultiple tissue microarray (n 1⁄4 203). Results: Among 30 upregulated and 73 downregulated genes, upregulation of fermitin familymember 1 (FERMT1), adenosylhomocysteinase (AHCY), secernin 1 (SCRN1), and SAC3 domain-containing protein 1 (SAC3D1) expression and downregulation of IgJ andMALL expression in colon cancer were confirmed by quantitative PCR. FERMT1 and AHCY protein expression was also upregulated in colon cancer compared with uninvolved colon mucosa, and FERMT1 expression showed upregulation in colon adenoma. Patients with moderate/strong tumor FERMT1 protein expression (n 1⁄4 122) showed significantly poorer overall survival (OS; P1⁄4 0.011) and disease-free survival (DFS; P1⁄4 0.005) than patients with negative/weak tumor FERMT1 protein expression (n 1⁄4 81). Multivariate Cox regression analysis showed that FERMT1 protein expression was also an independent prognostic factor for OS (P1⁄4 0.018) and DFS (P1⁄4 0.009). In addition, upregulated FERMT1 protein expression appeared to have some specificity among alimentary tract tumors. Conclusions: FERMT1 is a novel prognostic factor for colon carcinoma. Clin Cancer Res; 17(9);
On Reduced-Complexity Soft-Output Detection of Continuous Phase Modulations

We compare low-complexity schemes for soft-output detection of continuous phase modulations (CPMs). In particular, we address the problem of minimizing the complexity of the front end filters and that of the trellis exploited by the detection algorithm, with the aim of assuring a negligible performance degradation with respect to the optimal full-complexity receiver. We show that the approach providing the simplest front end is that based on the CPM decomposition proposed by Moqvist and Aulin. On the other hand, we prove that the most convenient solution in terms of trellis complexity is provided by the CPM decomposition proposed by Mengali and Morelli, possibly combined with suitable techniques for reduced trellis search.
Tractable Meta-Reasoning in Propositional Logics of Belief

Finding adequate semantic models of deductive reasoning is a difficult problem, if deductions are to be performed efficiently and in a semantically appropriate way. The model of reasoning provided by possible-worlds semantics has been found deficient both for computational and intuitive reasons. Existing semantic approaches that were proposed as alternatives to possible-worlds semantics either suffer from computational intractability or do not allow agents to have meta-beliefs. This work, based on relevance logic, proposes a model of belief where an agent can hold met a-beliefs and reason about them and other world knowledge efficiently. It is also shown how the model can be extended to include positive introspection without losing efficiency.
Prevention of Damage Due to Alkali-Aggregate Reaction (AAR) in Concrete Construction—Canadian Approach

This paper outlines the philosophy behind the 1994 revision of the Canadian Standards Association guidelines for preventing the risk of damage due to alkali-aggregate reaction (AAR) in new construction. Aggregates may be selected based on documented previous field performance, petrographic examination, or satisfactory performance in a sequence of accelerated and long-term expansion tests. If the aggregate is deemed not deleteriously reactive by one of these methods, it may be used in concrete with no further precautions. Potentially alkali-silica reactive aggregates may be considered for use in concrete provided appropriate preventive measures are taken to reduce the risk of damaging expansion. Recommended measures are: (1) limiting the total alkali content of the concrete (from portland cement and other sources) and (2) the use of supplementary cementing materials (SCMs), such as fly ash or slag. Minimum replacement levels are given for fly ash (20 to 30% depending on composition) and slag (50%). If these SCMs are to be used at lower replacement levels or at high concrete alkali levels, concrete-prism testing is required to assure the efficacy of the reduced amount of SCM in controlling expansion with the proposed aggregate. As yet, there is no specific guidance for using silica fume with reactive aggregates. Advice regarding alkali-carbonate reactive aggregates is restricted to selective quarrying and beneficiation to exclude the reactive material.
Can LSI help reconstructing requirements traceability in design and test?

Managing traceability data is an important aspect of the software development process. In this paper, we investigate to what extent latent semantic indexing (LSI), an information retrieval technique, can help recovering the information needed for automatically reconstructing traceability during the development process. We experimented with two different link selection strategies and applied LSI in multiple case studies varying in size and context. We discuss the results of a small lab study, a larger case study and a large industrial case study
Micromachined Si-well scintillator pixel detectors

In this thesis a new design is presented for the position-sensitive detection of radiation with sub-millimeter spatial resolution. It consists of a matrix of scintillation crystals encapsulated in well-type silicon sensors. The wells can be realised by means of deep reactive ion etching of a silicon wafer. Scintillation crystal material can be deposited into the wells, e.g. by evaporation techniques or as a powder with a binder. The light created on the absorption of a radiation quantum in the scintillator material is confined by the vertical silicon sidewalls, reflected at the top and collected at a photodiode at the bottom of the well. The signal generated by this silicon photodiode is proportional to the energy deposited by the radiation quantum in the scintillation material. The development of this new detector, the "micromachined Si-well scintillator pixel detector" is not yet completed. However, its principle and its elaborate processing based on three different technologies, i.e. the integrated circuits technology, the silicon micromachining and the scintillator research, have been extensively studied. The first prototypes of well sensor have been successfully tested for the detection of gamma rays, alpha particles and thermal neutrons, demonstrating the feasibility of such a device.
On Exponential Synchronization of Kuramoto Oscillators

In this technical note we study the problem of exponential synchronization for one of the most popular models of coupled phase oscillators, the Kuramoto model. We consider the special case of finite oscillators with distinct, bounded natural frequencies. Our first result derives a lower bound on the coupling gain which is necessary for the onset of synchronization. This bound improves the one derived by Jadbabaie . We then calculate a lower bound on the coupling gain that is sufficient to guarantee oscillator synchronization and derive further sufficient conditions to ensure exponential synchronization of the angular frequencies of all oscillators to the mean natural frequency of the group. We also characterize the coupling gain that is sufficient for the oscillator phase differences to approach any desired compact set in finite time.
Neural Machine Translation with Extended Context

We investigate the use of extended context in attention-based neural machine translation. We base our experiments on translated movie subtitles and discuss the effect of increasing the segments beyond single translation units. We study the use of extended source language context as well as bilingual context extensions. The models learn to distinguish between information from different segments and are surprisingly robust with respect to translation quality. In this pilot study, we observe interesting cross-sentential attention patterns that improve textual coherence in translation at least in some selected cases.
Intercomparison of tropical tropospheric humidity in GCMs with AMSU‐B water vapor data

We make use of microwave measurements of the tropical free tropospheric relative humidity (FTH) to evaluate the extent to which the water vapor distribution in four general circulation models is faithful to reality. The comparison is performed in the tropics by sorting the FTH in dynamical regimes defined upon the 500 hPa vertical velocity. Because microwave radiation penetrates non‐rainy and warm clouds, we are able to estimate the FTH over most of the dynamical regimes that characterize the tropics. The comparisons reveal that two models simulate a free troposphere drier than observed (<10%), while the others agree with the observations. Despite some differences, the level of agreement is good enough to lend confidence in the representation of atmospheric moistening processes. A climate change scenario, tested on two models, shows a tendency to maintain the FTH to an almost fixed value be it an ascending or a subsiding regime.
Thermal Conductivity of a Nano-Structured Material

In this paper, the phonon Boltzmann equation is solved numerically to study the phonon thermal conductivity of nano-structured thin films opened a nano-hole in a host material. We focused on effects of hole size on the reduction of thermal conductivity. The simulation shows that the temperature profiles in nano-structures are very different from those in conventional bulk materials, due to ballistic phonon transport at nanoscale. The conventional heat conduction equations cannot be applied to solve the heat transfer in solids at nanoscale. The effective thermal conductivity of nano-structures are calculated from temperature gradient. We predict the thermal conductivity dependence on the size of a nano-hole. At constant thin film thickness the larger the hole size, the smaller is the thermal conductivity of two-dimensional nano-structured thin film. The results of this study can be used to the development of thermal management of heat conduction by using artificial physical property.
Improved impedance matrix compression (IMC) technique for efficient wavelet‐based method of moments solution of scattering problems

The iterative impedance matrix compression (IMC) method iteratively constructs and solves a reduced version of the method of moments (MoM) impedance matrix based on analysis of the error in fulfilling the original matrix equation. Hence, it is possible that some of the selected basis functions, while dominant in the analyzed error, will have very little weight in the solution itself. Here, we propose a backward elimination step, which is aimed at discarding these superfluous basis functions. To demonstrate this idea, we use the scattering problem of a TMz plane wave by a conducting cylinder of square cross‐section. The resultant compression ratio is in good agreement with the theoretical limit of the compression ratio obtained a posteriori, based on the exact MoM solution. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 40: 275–280, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11351
Ovule morphogenesis in Ranunculaceae and its systematic significance.

BACKGROUND AND AIMS Ranunculaceae has a prominent phylogenetic position in Ranunculales which appears at the base of eudicots. The aims of the present paper are to reveal the features of ovule morphogenesis in different taxa and gain a better understanding of the systematics of Ranunculaceae. METHODS Flowers of 17 species from three subfamilies, nine tribes and 16 genera of Ranunculaceae, at successive developmental stages, were collected in the wild and studied with a scanning electron microscope. KEY RESULTS The integuments in the unitegmic ovules in Helleborus, Ranunculus and Oxygraphis, as well as the inner integuments in the bitegmic genera, initiate annularly and eventually become cup-shaped. However, the integuments in the unitegmic ovules in Anemone and Clematis, as well as the outer integuments in the bitegmic genera, arise semi-annularly and eventually become hood-shaped. Different kinds of appendages appear on the ovules during development. In Coptis of subfamily Coptidoideae, a wrap-shaped appendage arises outside the ovule and envelopes the ovule entirely. In the genera of subfamily Thalictroideae and tribe Anemoneae of subfamily Ranunculoideae, appendages appear on the placenta, the funicle or both. In tribe Helleboreae of subfamily Ranunculoideae, an alary appendage is initiated where the integument and the funicle join and becomes hood-shaped. CONCLUSIONS Ovule morphogenesis characteristics are significant in classification at the levels of subfamilies and tribes. The initiation patterns of the integuments and the development of appendages show diversity in Ranunculaceae. The present observations suggest that the bitegmic, hood-shaped outer integument and endostomic micropyle are primitive while the unitegmic, cupular-shaped outer integument and bistomic micropyle are derivative.
Risk, Cognitive Control, and Adolescence. Challenging the Dual Systems Model

According to the dual systems model, adolescence is a period of imbalance between cognitive and motivational systems that results in increased tendency towards risk. In the study, we investigated the effects of rewards on risk-taking and cognitive control in 90 adolescents (13-16) and 96 adults (1835). Our results challenge the assumptions of the model as we observed that rewards lead adolescents to more conservative decisions in one of the risk tasks used in the study. We also observed that in cognitive control tasks, rewards influenced reaction latencies, but not the efficiency of control processes.