Miracle-dz/UniFAR-FTUs huggingface dataset:
Different Transcriptional Response to Xanthomonas citri subsp. citri between Kumquat and Sweet Orange with Contrasting Canker Tolerance

Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating biotic stresses affecting the citrus industry. Meiwa kumquat (Fortunella crassifolia) is canker-resistant, while Newhall navel orange (Citrus sinensis Osbeck) is canker-sensitive. To understand the molecular mechanisms underlying the differences in responses to Xcc, transcriptomic profiles of these two genotypes following Xcc attack were compared by using the Affymetrix citrus genome GeneChip. A total of 794 and 1324 differentially expressed genes (DEGs) were identified as canker-responsive genes in Meiwa and Newhall, respectively. Of these, 230 genes were expressed in common between both genotypes, while 564 and 1094 genes were only significantly expressed in either Meiwa or Newhall. Gene ontology (GO) annotation and Singular Enrichment Analysis (SEA) of the DEGs showed that genes related to the cell wall and polysaccharide metabolism were induced for basic defense in both Meiwa and Newhall, such as chitinase, glucanase and thaumatin-like protein. Moreover, apart from inducing basic defense, Meiwa showed specially upregulated expression of several genes involved in the response to biotic stimulus, defense response, and cation binding as comparing with Newhall. And in Newhall, abundant photosynthesis-related genes were significantly down-regulated, which may be in order to ensure the basic defense. This study revealed different molecular responses to canker disease in Meiwa and Newhall, affording insight into the response to canker and providing valuable information for the identification of potential genes for engineering canker tolerance in the future.
Detection of Acoustic Landmarks with High Resolution for Speech Processing

Earlier Investigations have shown that speech processing to incorporate certain acoustic characteristics of clear speech in conversational speech can improve its intelligibility under adverse listening conditions. This processing needs detection of acoustic landmarks, the important regions in speech containing cues for phoneme identification. This paper presents a method for landmark detection in which energy and centroid frequency variations in a number of frequency bands are used to detect the landmarks, followed by a wavelet based decomposition for improving the time localization of the landmarks. The method was able to detect 98.1 % of release bursts in VCV syllables with a temporal resolution of 3 ms, and 86 % of stop consonant landmarks in sentence material with 20 ms resolution.
A Dynamically Focusing Cochlear Implant Strategy Can Improve Vowel Identification in Noise

Objectives: The standard, monopolar (MP) electrode configuration used in commercially available cochlear implants (CI) creates a broad electrical field, which can lead to unwanted channel interactions. Use of more focused configurations, such as tripolar and phased array, has led to mixed results for improving speech understanding. The purpose of the present study was to assess the efficacy of a physiologically inspired configuration called dynamic focusing, using focused tripolar stimulation at low levels and less focused stimulation at high levels. Dynamic focusing may better mimic cochlear excitation patterns in normal acoustic hearing, while reducing the current levels necessary to achieve sufficient loudness at high levels. Design: Twenty postlingually deafened adult CI users participated in the study. Speech perception was assessed in quiet and in a four-talker babble background noise. Speech stimuli were closed-set spondees in noise, and medial vowels at 50 and 60 dB SPL in quiet and in noise. The signal to noise ratio was adjusted individually such that performance was between 40 and 60% correct with the MP strategy. Subjects were fitted with three experimental strategies matched for pulse duration, pulse rate, filter settings, and loudness on a channel-by-channel basis. The strategies included 14 channels programmed in MP, fixed partial tripolar (&sgr; = 0.8), and dynamic partial tripolar (&sgr; at 0.8 at threshold and 0.5 at the most comfortable level). Fifteen minutes of listening experience was provided with each strategy before testing. Sound quality ratings were also obtained. Results: Speech perception performance for vowel identification in quiet at 50 and 60 dB SPL and for spondees in noise was similar for the three tested strategies. However, performance on vowel identification in noise was significantly better for listeners using the dynamic focusing strategy. Sound quality ratings were similar for the three strategies. Some subjects obtained more benefit than others, with some individual differences explained by the relation between loudness growth and the rate of change from focused to broader stimulation. Conclusions: These initial results suggest that further exploration of dynamic focusing is warranted. Specifically, optimizing such strategies on an individual basis may lead to improvements in speech perception for more adult listeners and improve how CIs are tailored. Some listeners may also need a longer period of time to acclimate to a new program.
Macrothrombocytopenia and dense granule deficiency associated with FLI1 variants: ultrastructural and pathogenic features

Congenital macrothrombocytopenia is a family of rare diseases, of which a significant fraction remains to be genetically characterized. To analyze cases of unexplained thrombocytopenia, 27 individuals from a patient cohort of the Bleeding and Thrombosis Exploration Center of the University Hospital of Marseille were recruited for a high-throughput gene sequencing study. This strategy led to the identification of two novel FLI1 variants (c.1010G>A and c.1033A>G) responsible for macrothrombocytopenia. The FLI1 variant carriers’ platelets exhibited a defect in aggregation induced by low-dose adenosine diphosphate (ADP), collagen and thrombin receptor-activating peptide (TRAP), a defect in adenosine triphosphate (ATP) secretion, a reduced mepacrine uptake and release and a reduced CD63 expression upon TRAP stimulation. Precise ultrastructural analysis of platelet content was performed using transmission electron microscopy and focused ion beam scanning electron microscopy. Remarkably, dense granules were nearly absent in the carriers’ platelets, presumably due to a biogenesis defect. Additionally, 25–29% of the platelets displayed giant α-granules, while a smaller proportion displayed vacuoles (7–9%) and autophagosome-like structures (0–3%). In vitro study of megakaryocytes derived from circulating CD34+ cells of the carriers revealed a maturation defect and reduced proplatelet formation potential. The study of the FLI1 variants revealed a significant reduction in protein nuclear accumulation and transcriptional activity properties. Intraplatelet flow cytometry efficiently detected the biomarker MYH10 in FLI1 variant carriers. Overall, this study provides new insights into the phenotype, pathophysiology and diagnosis of FLI1 variant-associated thrombocytopenia.
Sound event recognition in smart environments

A rich research was reported lately on sound event recognition (SER), a particular case of audio signal classification (ASC), which in turn is part of the more general research field of auditory scene analysis (ASA). The classification of sound events in a given environment is generally more precise with fewer classes and with better knowledge of sound events expected to occur in each class. Various techniques were described in the literature which allow good performance when sound events are strictly repeating. In an effort to develop an application that in the end recognize all sound events in a given context, this work describes an application of the SER in smart environments that aims at recognizing cough sounds. Such techniques cannot rely on the strict repeatability of sound events. They must move towards recognition of sound events that are rather similar to any one of a set of established models. The main working modes we examined were to model cough as non-speech utterances and to search for a match against a database of established models.
Virtual assistive companions for older adults: qualitative field study and design implications

This paper presents a qualitative study conducted to explore perceptions, attitudes and expectations for a virtual assistive companion designed to supplement human caregiving and facilitate an improved quality of life and long-term health benefits for older adults. The study was conducted adopting a human-centred approach; employing focus groups and individual interviews with older adults, professional caregivers and psychologists specialized in the aging process. Results indicated that users were in favour of a virtual companion and highlighted its potential to assist the accomplishment of daily activities and make more efficient use of human care services. Humanlike communication and behaviour were desirable whereas mixed opinions were expressed about humanlike appearance. The ramifications of the study are discussed in the form of design implications for the development of a virtual assistive companion that possesses the appropriate "social skills" to establish and maintain comfortable and acceptable long-term interaction and offers "useful" support to older adults.
Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York

This study examined the effect of dissolved organic matter (DOM) on ectoenzymatic activity, bacterial growth and community structure in the Hudson River. Our main approach was to mix bacterial communities and water from various locations in the Hudson River and its tributaries, and then to monitor bacterial activity and community structure determined by fluorescence in situ hybridization with oligonucleotide probes. The locations differed significantly in DOM composition and concentrations, ectoenzyme activity and bacterial community structure. We found that water source and, to a lesser extent, source of the inoculum significantly affected nearly all aspects of bacterial activity and community structure. A common inoculum grown in different waters often led to as much as a 2-fold difference in enzyme activities. When 2 different bacterial communities were inoculated in the same water, community structure and the activity of some ectoenzymes remained different after several days. Other data also pointed to a dependence of ectoenzyme activity on community structure. Activity of several ectoenzymes covaried with the relative abundances of the 4 bacterial groups we examined (alpha-, beta- and gamma-proteobacteria, and Cytophaga-like bacteria); the highest correlation was between beta-proteobacteria and phosphatase activity. In multi-variate regression analyses, community structure explained a significant amount of the variation in rates of all ectoenzymes except 2 proteases. The abundance of Cytophaga-like bacteria was the dominant variable in the regression models for the activity of 3 ectoenzymes. These data suggest that DOM can affect the relative abundance of the major heterotrophic bacterial groups, and that the relative abundance of these groups could have an impact on DOM hydrolysis.
Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode

1. A major goal of DNA barcoding is to identify species in local floras and ecological communities. With the consensus of a two‐locus DNA barcode (rbcL+matK) by the Consortium for the Barcode of Life (CBOL) Plant Working Group (2009), barcoding efforts have begun to focus on building the barcode library for land plants.
Master of research intership report Global Illumination and Image Appearance

In Computer Graphics, light plays an important role in the appearance of a scene. Choosing a different light configuration can lead to many different aesthetics for the final image. Lighting design is even more complex when using sophisticated global illumination rendering methods. In this report, we present a new approach to automatically design a lighting configuration according to the lighting goal specified by the user. The lighting goal is expressed as a set of target parameters. These target parameters are used to set up an objective function such that, when the function is minimized, the aesthetics of the image rendered using these optimal light parameters meet the requirements set by the user. Our results show that this method can be used to automatically design a lighting configuration that will give to the final image a classic photographic aesthetics, such as high-key or low-key aesthetics.
Explorer Predicting Target Language CCG Supertags Improves Neural Machine Translation

Neural machine translation (NMT) models are able to partially learn syntactic information from sequential lexical information. Still, some complex syntactic phenomena such as prepositional phrase attachment are poorly modeled. This work aims to answer two questions: 1) Does explicitly modeling target language syntax help NMT? 2) Is tight integration of words and syntax better than multitask training? We introduce syntactic information in the form of CCG supertags in the decoder, by interleaving the target supertags with the word sequence. Our results on WMT data show that explicitly modeling targetsyntax improves machine translation quality for German→English, a high-resource pair, and for Romanian→English, a lowresource pair and also several syntactic phenomena including prepositional phrase attachment. Furthermore, a tight coupling of words and syntax improves translation quality more than multitask training. By combining target-syntax with adding source-side dependency labels in the embedding layer, we obtain a total improvement of 0.9 BLEU for German→English and 1.2 BLEU for Romanian→English.
Raman spectroscopy for the discrimination of cancerous and normal skin

Abstract: Various studies have shown promising results in using Raman spectroscopy (RS) for the detection of skin cancers. In-vivo evaluations showed similar results to those found by trained dermatologists using dermoscopy, the current clinical practice for skin cancer diagnosis. However, dermoscopy is highly subjective which would make an objective, non-invasive diagnostic method useful. Although successful results were achieved, RS is barely applied in clinical routine yet. This review summarizes studies of Raman spectroscopy for skin cancer diagnosis ex vivo and in vivo. The latter has special demands that often lead to a tradeoff between applicability and classification performance. The necessary steps are explained for instrumentation design, handling, data analysis and clinical testing on groups with a sufficient amount of subjects in order to promote the application of RS in a routine clinical setting. A number of methods are summarized which attempt to overcome the ongoing challenge of reducing large background signals. Modifications of RS by combination with other diagnostic methods are summarized that can give a new perspective to future developments in RS.
Experimental investigation of surface charge accumulation behaviors on PTFE insulator under DC and impulse voltage in vacuum

Surface charge accumulated on insulators plays an important role in flashover process in vacuum, which has not yet been fully understood. In this paper, charging behaviors on insulator surface were experimentally examined under negative DC and impulse voltage. For the case of DC voltage, two charging stages were observed, i.e., the area near cathode was at first negatively charged under lower voltage (stage I) and then followed by a positively charged cathode-anode surface (stage II). Surface charging at stage I is considered to be caused by Schottky injection of homo-charges from electrode into sample surface layer. While at stage II secondary electron emission (SEE) process is responsible to the positively charged anode-cathode surface. However, charging at stage I is quite sensitive to pre-stress process, as well as the electrode-insulator interface conditions. The ongoing injection of electrons from cathode can lead to gradually decreasing in surface charge accumulation as the voltage duration increases. For the case of impulse voltage, Schottky injection of homo-charges has little influence on surface charging as the time is too short for charge injection and migration in surface layer. The SEE process will govern surface charging due to its extremely fast establishment process. A good linear relationship is obtained between saturated surface charge density and applied voltage, which is generally consistent with the numerical calculation result based on secondary electron emission avalanche theory. At last, it is confirmed that the ionization of desorbed gas from insulator surface and subsequent neutralization of electrons with positive surface charge is the main cause to eliminate surface charge in flashover.
Delayed Retention of New Word-Forms Is Better in Children than Adults Regardless of Language Ability: A Factorial Two-Way Study

Background Nonword repetition, the ability to retain and repeat unfamiliar sequences of phonemes is usually impaired in children with specific language impairment (SLI), but it is unclear whether this explains slow language learning. Traditional nonword repetition tests involve a single presentation of nonwords for immediate repetition. Here we considered whether rate of learning of novel phonological sequences was impaired when the same items were presented repeatedly. Methodology/Principal Findings Three complex nonwords were each presented for repetition five times in two sessions (A and B) separated by one hour. We studied both adults and children from (i) families with a child with SLI and (ii) families whose children did not have SLI. This gave a 2×2 design with familial SLI as one factor, and age (up to or above 18 years) as the other. Overall, participants from families with SLI were poorer at nonword repetition than their peers from typical-language families, and there was a trend for children with SLI to show less within-session learning than typically developing children. However, between-session retention, measured as the difference between the last trial from session 1 and the first trial of session 2, showed a significant age effect, η2 = . 139, p = . 004, regardless of family SLI status. Adult participants showed a decrease in score from the last trial of session A to the first trial of session B, whereas children maintained their level of performance, regardless of whether or not they had SLI. Conclusions/Significance Poor nonword repetition in SLI appears to reflect inadequate encoding of phonological information, rather than problems retaining encoded information. Furthermore, the nonword learning task is consistent with the notion of a sensitive period in language learning: Children show better retention over a delay for new phonological sequences than adults, regardless of overall level of language ability.
A New Re-Ranking Method Using Enhanced Pseudo-Relevance Feedback for Content-Based Medical Image Retrieval

We propose a novel re-ranking method for content-based medical image retrieval based on the idea of pseudo-relevance feedback (PRF). Since the highest ranked images in original retrieval results are not always relevant, a naive PRF based re-ranking approach is not capable of producing a satisfactory result. We employ a two-step approach to address this issue. In step 1, a Pearson's correlation coefficient based similarity update method is used to re-rank the high ranked images. In step 2, after estimating a relevance probability for each of the highest ranked images, a fuzzy SVM ensemble based approach is adopted to re-rank the images. The experiments demonstrate that the proposed method outperforms two other re-ranking methods.
Exploiting Semantics for Analyzing and Verifying Business Rules in Web Services Composition and Contracting

Web services composition process needs business rules to regulate the behavior of the partner services. However, designing these rules is time-consuming and error-prone, especially under the condition that current standards barely provide any abstract and high-level guidance. In this spirit, rule analysis and verification for services composition is urgently required to augment its reliability and usability. In this paper, we choose a variant of Description Logics, called ALCO(Q*), as the underlying logic, and provide a formal mapping to transform ECA rules, so that the semantics in the original ECA rules can be captured and are computationally traceable. To this end, we further investigate some important properties for business rules, namely, redundancy, termination and conflict, and propose several sound and complete algorithms to resolve them.
Data Envelopment Analysis for Technological, Environmental andEconomic Analysis of Motorway Underpasses

Underpasses play an important role in ensuring permeability of line traffic structures (motorways, expressways) for feral species. There are many studies, articles and methodological guidebooks available describing proper design principles for technical parameters of underpasses and their placement within the terrain. Width, height and length are the main technical parameters affecting wildlife migration. Wildlife behaviour and their requirements for the mentioned technical parameters of underpasses also have been examined in depth. In practically all cases, underpass functionality grows with increasing width and height. Of course, this also results in greater construction costs. The objective should therefore be to find a balanced compromise enabling “sufficient” functionality while maintaining “reasonable” costs. Data envelopment analysis (DEA) provides a way to identify “good” solutions in the sense of “sufficient” underpass functionality with “reasonable” total costs. Underpass functionality calculations were based on a methodology for calculating migration potentials (Žak and Florian, 2013). Total costs were established according to actual construction work prices in the Czech Republic, including prices for preparations, design, construction, maintenance, and demolition. The results indicate that DEA can be used to find “good” solutions and can be of assistance in particular when planning measures to ensure motorways are permeable to wildlife.
IsoBase: a database of functionally related proteins across PPI networks

We describe IsoBase, a database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo Sapiens. Nearly all existing algorithms for orthology detection are based on sequence comparison. Although these have been successful in orthology prediction to some extent, we seek to go beyond these methods by the integration of sequence data and protein–protein interaction (PPI) networks to help in identifying true functionally related proteins. With that motivation, we introduce IsoBase, the first publicly available ortholog database that focuses on functionally related proteins. The groupings were computed using the IsoRankN algorithm that uses spectral methods to combine sequence and PPI data and produce clusters of functionally related proteins. These clusters compare favorably with those from existing approaches: proteins within an IsoBase cluster are more likely to share similar Gene Ontology (GO) annotation. A total of 48 120 proteins were clustered into 12 693 functionally related groups. The IsoBase database may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword. The database is freely available for download at http://isobase.csail. mit.edu/.