Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the structure and functioning of polar pelagic ecosystems to predict the impacts of change

The determinants of the structure, functioning and resilience of pelagic ecosystems across most of the polar regions are not well known. Improved understanding is essential for assessing the value of biodiversity and predicting the effects of change (including in biodiversity) on these ecosystems and the services they maintain. Here we focus on the trophic interactions that underpin ecosystem structure, developing comparative analyses of how polar pelagic food webs vary in relation to the environment. We highlight that there is not a singular, generic Arctic or Antarctic pelagic food web, and, although there are characteristic pathways of energy flow dominated by a small number of species, alternative routes are important for maintaining energy transfer and resilience. These more complex routes cannot, however, provide the same rate of energy flow to highest trophic-level species. Food-web structure may be similar in different regions, but the individual species that dominate mid-trophic levels vary across polar regions. The characteristics (traits) of these species are also different and these differences influence a range of food-web processes. Low functional redundancy at key trophic levels makes these ecosystems particularly sensitive to change. To develop models for projecting responses of polar ecosystems to future environmental change, we propose a conceptual framework that links the life histories of pelagic species and the structure of polar food webs.
Validation of Macroscopic Forming Simulations of a Unidirectional Pre-Impregnated Material through Optical Measurements

Presenting interesting aspects such as a high strength-to-weight ratio, Carbon Fibre Reinforced Plastic components are frequently used in the aerospace industry. The forming step, which conforms the reinforcement to a specific geometry, is a sensitive phase of the manufacturing process. In order to detect the occurrence of defects prior to any trial, forming methods are often simulated via finite element software. The presented work will detail the simulation validation of a double curved helicopter frame forming out of a unidirectional carbon fibre pre-impregnated material (M21E, Hexcel®). The finite element model was based on an explicit approach at a macroscopic level and developed via the commercially available software Visual-Crash PAM (ESI®) [1]. The validation was carried out on six different preforms. Measurements of the top layers were performed by an enhanced version of a 4D measuring system, originally developed for non-woven fabric [2], able to make reproducible photographic and height measurements (Fig. 1). Experimental results were then compared to simulated ones. Due to material specificities, the photo quality reached for non-crimp fabrics could not be achieved [2]. After hardware and software modifications, measurements and analyses were eventually successfully completed. The validation of the simulation reached an accuracy of 1° to 3° depending on the geometrical features of the preform (Fig. 2).
Preparation of a high-quality PZT thick film with performance comparable to those of bulk materials for applications in MEMS

High-quality lead zirconate titanate (PZT) thick films have been prepared on silicon substrates by combining PZT–Si bonding and wet-etching technology. The bulk PZT wafer was first bonded to the silicon substrate using a 2 µm thick intermediate layer of epoxy resin with a bonding strength higher than 10 MPa. Then the bulk PZT was thinned by a wet-etching method. The thickness of the final PZT films depends on the etching time. The PZT thick films after being polished showed a surface roughness of about 20 nm (RMS), which can satisfy most of the requirements in MEMS. The prepared PZT thick films show a dielectric constant as high as 2400 below 100 kHz, remnant polarization of 13 µC cm−2, piezoelectric constant d31 of about −280 pm V−1 and Young's modulus of about 63 GPa. The measured electromechanical properties of the PZT thick films were comparable to those of the corresponding bulk ceramics. This approach makes it possible to obtain high-quality PZT films because it separates the PZT wafer fabrication from the target substrate and consequently allows integration of the PZT thick films onto many kinds of substrates. Finally, a self-sensing bulk PZT thick film actuator was fabricated as an example of a basic PZT–Si diaphragm structure that can be used in piezoelectric micropumps, and its sensing and actuating performances were also demonstrated.
Reducing Feedback Delay of Software Development Tools via Continuous Analysis

During software development, the sooner a developer learns how code changes affect program analysis results, the more helpful that analysis is. Manually invoking an analysis may interrupt the developer's workflow or cause a delay before the developer learns the implications of the change. A better approach is continuous analysis tools that always provide up-to-date results. We present Codebase Replication, a technique that eases the implementation of continuous analysis tools by converting an existing offline analysis into an IDE-integrated, continuous tool with two desirable properties: isolation and currency. Codebase Replication creates and keeps in sync a copy of the developer's codebase. The analysis runs on the copy codebase without disturbing the developer and without being disturbed by the developer's changes. We developed Solstice, an open-source, publicly-available Eclipse plug-in that implements Codebase Replication. Solstice has less than 2.5 milliseconds overhead for most common developer actions. We used Solstice to implement four Eclipse-integrated continuous analysis tools based on the offline versions of FindBugs, PMD, data race detection, and unit testing. Each conversion required on average 710 LoC and 20 hours of implementation effort. Case studies indicate that Solstice-based continuous analysis tools are intuitive and easy-to-use.
Highly sensitive current sensor based on an optical microfiber loop resonator incorporating low index polymer

A highly sensitive current sensor based on an optical microfiber loop resonator (MLR) incorporating low index polymer is proposed and experimentally demonstrated. The microfiber with a waist diameter of 1 μm is wrapped around the nicrhrome wire with low index polymer coating and the optical MLR is realized. The use of the microfiber and low index polymer with high thermal property can effectively improve the current sensitivity of the proposed MLR-based sensing probe to be 437.9 pm/A2, which is ~10 times higher than the previous result.
Tied-Mixture Language Modeling in Continuous Space

This paper presents a new perspective to the language modeling problem by moving the word representations and modeling into the continuous space. In a previous work we introduced Gaussian-Mixture Language Model (GMLM) and presented some initial experiments. Here, we propose Tied-Mixture Language Model (TMLM), which does not have the model parameter estimation problems that GMLM has. TMLM provides a great deal of parameter tying across words, hence achieves robust parameter estimation. As such, TMLM can estimate the probability of any word that has as few as two occurrences in the training data. The speech recognition experiments with the TMLM show improvement over the word trigram model.
The first WIMPy halos

Dark matter direct and indirect detection signals depend crucially on the dark matter distribution. While the formation of large scale structure is independent of the nature of the cold dark matter (CDM), the fate of inhomogeneities on subgalactic scales, and hence the present day CDM distribution on these scales, depends on the microphysics of the CDM particles. We study the density contrast of weakly interacting massive particles (WIMPs) on subgalactic scales. We calculate the damping of the primordial power spectrum due to collisional damping and free streaming of WIMPy CDM and show that free streaming leads to a CDM power spectrum with a sharp cut-off at about . We also calculate the transfer function for the growth of the inhomogeneities in the linear regime, taking into account the suppression in the growth of the CDM density contrast after matter–radiation equality due to baryons and show that our analytic results are in good agreement with numerical calculations. Combining the transfer function with the damping of the primordial fluctuations we produce a WMAP normalized primordial CDM power spectrum, which can serve as an input for high resolution CDM simulations. We find that the smallest inhomogeneities typically have comoving radius of about 1 pc and enter the non-linear regime at a red-shift of 60 ± 20. We study the effect of scale dependence of the primordial power spectrum on these numbers and also use the spherical collapse model to make simple estimates of the properties of the first generation of WIMP halos to form. We find that the very first WIMPy halos may have a significant impact on indirect dark matter searches.
Vibrational and electronic properties of the proton transfer fluorophore 2-(5'-amino-2'-hydroxyphenyl)benzothiazole

This paper presents the theoretical and experimental study regarding the optical and structural properties of 2-(5'-amino-2'-hydroxyphenyl)benzothiazole. In order to investigate the potential application of this dye in organic light-emitting diodes, a photophysical characterization in film, solution and solid state was performed. Aditionally, Raman and infrared spectroscopies were also applied. The experimental results were compared with theoretical calculations achieved by Gaussian09 software.
Waveform generation in the weakly electric fish Gymnotus coropinae (Hoedeman): the electric organ and the electric organ discharge

SUMMARY This article deals with the electric organ and its discharge in Gymnotus coropinae, a representative species of one of the three main clades of the genus. Three regions with bilateral symmetry are described: (1) subopercular (medial and lateral columns of complex shaped electrocytes); (2) abdominal (medial and lateral columns of cuboidal and fusiform electrocytes); and (3) main [four columns, one dorso-lateral (containing fusiform electrocytes) and three medial (containing cuboidal electrocytes)]. Subopercular electrocytes are all caudally innervated whereas two of the medial subopercular ones are also rostrally innervated. Fusiform electrocytes are medially innervated at the abdominal portion, and at their rostral and caudal poles at the main portion. Cuboidal electrocytes are always caudally innervated. The subopercular portion generates a slow head-negative wave (V1r) followed by a head-positive spike (V3r). The abdominal and main portions generate a fast tetra-phasic complex (V2345ct). Since subopercular components prevail in the near field and the rest in the far field, time coincidence of V3r with V2 leads to different waveforms depending on the position of the receiver. This confirms the splitting hypothesis of communication and exploration channels based on the different timing, frequency band and reach of the regional waveforms. The following hypothesis is compatible with the observed anatomo-functional organization: V1r corresponds to the rostral activation of medial subopercular electrocytes and V3r to the caudal activation of all subopercular electrocytes; V2, and part of V3ct, corresponds to the successive activation of the rostral and caudal poles of dorso-lateral fusiform electrocytes; and V345ct is initiated in the caudal face of cuboidal electrocytes by synaptic activation (V3ct) and it is completed (V45ct) by the successive activation of rostral and caudal faces by the action currents evoked in the opposite face.
Adapting K-Nearest Neighbor for Tag Recommendation in Folksonomies

Folksonomies, otherwise known as Collaborative Tagging Systems, enable Internet users to share, annotate and search for online resources with user selected labels called tags. Tag recommendation, the suggestion of an ordered set of tags during the annotation process, reduces the user effort from a keyboard entry to a mouse click. By simplifying the annotation process tagging is promoted, noise in the data is reduced through the elimination of discrepancies that result in redundant tags, and ambiguous tags may be avoided. Tag recommenders can suggest tags that maximize utility, offer tags the user may not have previously considered or steer users toward adopting a core vocabulary. In sum, tag recommendation promotes a denser dataset that is useful in its own right or can be exploited by a myriad of data mining techniques for additional functionality. While there exists a long history of recommendation algorithms, the data structure of a Folksonomy is distinct from those found in traditional recommendation problems. We first explore two data reduction techniques, p-core processing and Hebbian deflation, then demonstrate how to adapt K-Nearest Neighbor for use with Folksonomies by incorporating user, resource and tag information into the algorithm. We further investigate multiple techniques for user modeling required to compute the similarity among users. Additionally we demonstrate that tag boosting, the promoting of tags previously applied by a user to a resource, improves the coverage and accuracy of K-Nearest Neighbor. These techniques are evaluated through extensive experimentation using data collected from two real Collaborative Tagging Web sites. Finally the modified K-Nearest Neighbor algorithm is compared with alternative techniques based on popularity and link analysis. We find that K-Nearest Neighbor modified for use with Folksonomies generates excellent recommendations, scales well with large datasets, and is applicable to both narrow and broadly focused Folksonomies.
Associational Resistance and Associational Susceptibility: Having Right or Wrong Neighbors

Specific plant associations may decrease (associational resistance, AR) or increase (associational susceptibility, AS) the likelihood of detection by, and/or vulnerability to, herbivores. We discuss presumed mechanisms leading to AR and AS, suggest others, and conduct meta-analyses on plant and herbivore traits affecting AR and AS, and the effects of habitat. Specific plant associations determine the likelihood of detection and/or vulnerability of focal plants to herbivores. AS is more likely with insects and AR more likely with mammals. Unpalatable neighbors increase the likelihood of AR. An herbivore's feeding guild, diet breadth, and habitat type do not influence the likelihood of AR or AS. The effectiveness of AR in reducing herbivore abundance is independent of whether neighboring plants are within a plot of focal crops or along the edge of a plot. AR and AS may be applicable to associations among herbivores, and may be appropriately studied from a landscape perspective.
The Cosmic Evolution Survey (COSMOS): A Large-Scale Structure at z = 0.73 and the Relation of Galaxy Morphologies to Local Environment

We have identified a large-scale structure at z ≃ 0.73 in the COSMOS field, coherently described by the distribution of galaxy photometric redshifts, an ACS weak-lensing convergence map, and the distribution of extended X-ray sources in a mosaic of XMM-Newton observations. The main peak seen in these maps corresponds to a rich cluster with TX = 3.51 keV and LX = (1.56 ± 0.04) × 1044 ergs s-1 (0.1-2.4 keV band). We estimate an X-ray mass within r500 corresponding to M500 ≃ 1.6 × 1014 M☉ and a total lensing mass (extrapolated by fitting a NFW profile) MNFW = (6 ± 3) × 1015 M☉. We use an automated morphological classification of all galaxies brighter than IAB = 24 over the structure area to measure the fraction of early-type objects as a function of local projected density Σ10, based on photometric redshifts derived from ground-based deep multiband photometry. We recover a robust morphology-density relation at this redshift, indicating, for comparable local densities, a smaller fraction of early-type galaxies than today. Interestingly, this difference is less strong at the highest densities and becomes more severe in intermediate environments. We also find, however, local "inversions" of the observed global relation, possibly driven by the large-scale environment. In particular, we find direct correspondence of a large concentration of disk galaxies to (the colder side of) a possible shock region detected in the X-ray temperature map and surface brightness distribution of the dominant cluster. We interpret this as potential evidence of shock-induced star formation in existing galaxy disks, during the ongoing merger between two subclusters. Our analysis reveals the value of combining various measures of the projected mass density to locate distant structures and their potential for elucidating the physical processes at work in the transformation of galaxy morphologies.
89Zr-anti-γH2AX-TAT but not 18F-FDG Allows Early Monitoring of Response to Chemotherapy in a Mouse Model of Pancreatic Ductal Adenocarcinoma

Purpose: Late-stage, unresectable pancreatic ductal adenocarcinoma (PDAC) is largely resistant to chemotherapy and consequently has a very poor 5-year survival rate of <5%. The ability to assess the efficacy of a treatment soon after its initiation would enable rapid switching to potentially more effective therapies if the current treatment is found to be futile. We have evaluated the ability of the PET imaging agent, 89Zr-anti-γH2AX-TAT, to monitor DNA damage in response to fluorouracil (5-FU), gemcitabine, or capecitabine treatment in a mouse model of pancreatic cancer. We have also compared the utility of this approach against the standard clinical PET radiotracer, 18F-FDG. Experimental Design: C57BL/6 mice bearing subcutaneous pancreatic cancer (KPC; B8484) allografts were treated with 5-FU, gemcitabine, or capecitabine. Therapeutic response was monitored by PET and ex vivo biodistribution experiments using either 89Zr-anti-γH2AX-TAT or 18F-FDG as imaging agents. To further examine the effect of therapeutic response upon uptake of these imaging agents, IHC analysis of harvested tumor allograft tissue was also performed. Results: Accumulation of 89Zr-anti-γH2AX-TAT in the tumors of mice that received chemotherapy was higher compared with vehicle-treated mice and was shown to be specifically mediated by γH2AX. In contrast, 18F-FDG did not provide useful indications of therapeutic response. Conclusions: 89Zr-anti-γH2AX-TAT has shown a superior ability to monitor early therapeutic responses to chemotherapy by PET imaging compared with 18F-FDG in an allograft model of PDAC in mice. Clin Cancer Res; 23(21); 6498–504. ©2017 AACR.
Pacific Asia Conference on Information Systems ( PACIS ) July 2008 AN ONTOLOGY-BASED DOCUMENT RECOMMENDATION SYSTEM : DESIGN , IMPLEMENTATION , AND EVALUATION

With the explosion of information, more and more people are embarrassed to manage information effectively. How to search and retrieve accurate information match to people’s requirements has been an important issue in information management research. Although search engine can solve this problem partly, the support of manage information is still limited. To use search engine, the users should input precise keywords by themselves first and this stage might cause much confusion to users. For that reason, we need a recommendation system that can catch users’ preferences to help users to obtain information more quickly and conveniently without copious process. In our research, a recommendation system is designed based on users’ profile. We use ontology technology to be the core of our recommendation system, because ontology can describe the concepts and relations of individual’s domain knowledge. Formal Concept Analysis (FCA) algorithm is one of the most popular methods to build ontology, and we apply it to construct our experimental system to recommend master theses to subjects. In order to evaluate our recommendation system, we developed a FCA-based system and another Scoring FCA-based system as treatments, and a Keyword-based system as a control group. We focus on both users’ satisfaction on information quality and system quality of our systems. The results show that users have higher information satisfaction on Scoring FCA-based system and FCA-based system than Keyword-based system. This study contributes to research and practice in information recommendation system.
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments

MOTIVATION The development of powerful automatic methods for the comparison of protein sequences has become increasingly important. Profile-to-profile comparisons allow for the use of broader information about protein families, resulting in more sensitive and accurate comparisons of distantly related sequences. A key part in the comparison of two profiles is the method for the calculation of scores for the position matches. A number of methods based on various theoretical considerations have been proposed. We implemented several previously reported scoring functions as well as our own functions, and compared them on the basis of their ability to produce accurate short ungapped alignments of a given length. RESULTS Our results suggest that the family of the probabilistic methods (log-odds based methods and prof_sim) may be the more appropriate choice for the generation of initial 'seeds' as the first step to produce local profile-profile alignments. The most effective scoring systems were the closely related modifications of functions previously implemented in the COMPASS and Picasso methods.
Web Service Discovery via Semantic Association Ranking and Hyperclique Pattern Discovery

Semantic Web technology is a promising first step for automated Web service discovery. Most current approaches for Web service discovery cater to semantic Web services, i.e., Web services that have associated semantic descriptions. It is unrealistic, however, to expect all new services to have associated semantic descriptions. Furthermore, the descriptions of the vast majority of already existing services do not have explicitly associated semantics. In this paper we present a novel approach for Web service discovery that combines semantic and statistical association metrics. Semantic metrics are based on the semantic aspects of relevant ontology. Statistical association metrics are based on the association aspects of Web services instances (their inputs and outputs). Specifically, our approach exploits semantic relationship ranking for establishing semantic relevance, and a hyperclique pattern discovery method for grouping Web service parameters into meaningful associations. These associations combined by the semantic relevance are then leveraged to discover and rank Web services
An Opposite Effect of the CDK Inhibitor, p18INK4c on Embryonic Stem Cells Compared with Tumor and Adult Stem Cells

Self-renewal is a feature common to both adult and embryonic stem (ES) cells, as well as tumor stem cells (TSCs). The cyclin-dependent kinase inhibitor, p18INK4c, is a known tumor suppressor that can inhibit self-renewal of tumor cells or adult stem cells. Here, we demonstrate an opposite effect of p18 on ES cells in comparison with teratoma cells. Our results unexpectedly showed that overexpression of p18 accelerated the growth of mouse ES cells and embryonic bodies (EB); on the contrary, inhibited the growth of late stage teratoma. Up-regulation of ES cell markers (i.e., Oct4, Nanog, Sox2, and Rex1) were detected in both ES and EB cells, while concomitant down-regulation of various differentiation markers was observed in EB cells. These results demonstrate that p18 has an opposite effect on ES cells as compared with tumor cells and adult stem cells. Mechanistically, expression of CDK4 was significantly increased with overexpression of p18 in ES cells, likely leading to a release of CDK2 from the inhibition by p21 and p27. As a result, self-renewal of ES cells was enhanced. Our current study suggests that targeting p18 in different cell types may yield different outcomes, thereby having implications for therapeutic manipulations of cell cycle machinery in stem cells.