Hybrid hidden Markov models and artificial neural networks for handwritten music recognition in mensural notation

In this paper, we present a hybrid approach using hidden Markov models (HMM) and artificial neural networks to deal with the task of handwritten Music Recognition in mensural notation. Previous works have shown that the task can be addressed with Gaussian density HMMs that can be trained and used in an end-to-end manner, that is, without prior segmentation of the symbols. However, the results achieved using that approach are not sufficiently accurate to be useful in practice. In this work, we hybridize HMMs with deep multilayer perceptrons (MLPs), which lead to remarkable improvements in optical symbol modeling. Moreover, this hybrid architecture maintains important advantages of HMMs such as the ability to properly model variable-length symbol sequences through segmentation-free training, and the simplicity and robustness of combining optical models with N-gram language models, which provide statistical a priori information about regularities in musical symbol concatenation observed in the training data. The results obtained with the proposed hybrid MLP-HMM approach outperform previous works by a wide margin, achieving symbol-level error rates around 26%, as compared with about 40% reported in previous works

End-to-End Page-Level Assessment of Handwritten Text Recognition

The evaluation of Handwritten Text Recognition (HTR) systems has traditionally used metrics based on the edit distance between HTR and ground truth (GT) transcripts, at both the character and word levels. This is very adequate when the experimental protocol assumes that both GT and HTR text lines are the same, which allows edit distances to be independently computed to each given line. Driven by recent advances in pattern recognition, HTR systems increasingly face the end-to-end page-level transcription of a document, where the precision of locating the different text lines and their corresponding reading order (RO) play a key role. In such a case, the standard metrics do not take into account the inconsistencies that might appear. In this paper, the problem of evaluating HTR systems at the page level is introduced in detail. We analyse the convenience of using a two-fold evaluation, where the transcription accuracy and the RO goodness are considered separately. Different alternatives are proposed, analysed and empirically compared both through partially simulated and through real, full end-to-end experiments. Results support the validity of the proposed two-fold evaluation approach. An important conclusion is that such an evaluation can be adequately achieved by just two simple and well-known metrics: the Word Error Rate (WER), that takes transcription sequentiality into account, and the here re-formulated Bag of Words Word Error Rate (bWER), that ignores order. While the latter directly and very accurately assess intrinsic word recognition errors, the difference between both metrics (ΔWER) gracefully correlates with the Normalised Spearman’s Foot Rule Distance (NSFD), a metric which explicitly measures RO errors associated with layout analysis flaws. To arrive to these conclusions, we have introduced another metric called Hungarian Word Word Rate (hWER), based on a here proposed regularised version of the Hungarian Algorithm. This metric is shown to be always almost identical to bWER and both bWER and hWER are also almost identical to WER whenever HTR transcripts and GT references are guarantee to be in the same RO.This paper is part of the I+D+i projects: PID2020-118447RA-I00 (MultiScore) and PID2020-116813RB-I00a (SimancasSearch), funded by MCIN/AEI/10.13039/501100011033. The first author research was developed in part with the Valencian Graduate School and Research Network of Artificial Intelligence (valgrAI, co-funded by Generalitat Valenciana and the European Union). The second author is supported by a María Zambrano grant from the Spanish Ministerio de Universidades and the European Union NextGenerationEU/PRTR. The third author is supported by grant ACIF/2021/356 from the “Programa I+D+i de la Generalitat Valenciana”

Effect of the feeding system on the fatty acid composition, expression of the Δ9-desaturase, Peroxisome Proliferator-Activated Receptor Alpha, Gamma, and Sterol Regulatory Element Binding Protein 1 genes in the semitendinous muscle of light lambs of the Rasa Aragonesa breed

<p>Abstract</p> <p>Background</p> <p>Conjugated linoleic acids (CLAs) are receiving increasing attention because of their beneficial effects on human health, with milk and meat products derived from ruminants as important sources of CLA in the human diet. <it>SCD </it>gene is responsible for some of the variation in CLA concentration in adipose tissues, and <it>PPARγ</it>, <it>PPARα </it>and <it>SREBP1 </it>genes are regulator of <it>SCD </it>gene. The aim of this work was to evaluate the effect of the feeding system on fatty acid composition, CLA content and relative gene expression of Δ⁹-desaturase (<it>SCD</it>), Peroxisome Proliferator-Activated Receptor Gamma (<it>PPARγ</it>), Peroxisome Proliferator-Activated Receptor Alpha, <it>(PPARα) </it>and Sterol Regulatory Element Binding Protein <it>(SREBP1) </it>in Rasa Aragonesa light lambs in semitendinous muscle. Forty-four single-born male lambs were used to evaluate the effect of the feeding system, varying on an intensity gradient according to the use of concentrates: 1. grazing alfalfa, 2. grazing alfalfa with a supplement for lambs, 3. indoor lambs with grazing ewes and 4. drylot.</p> <p>Results</p> <p>Both grazing systems resulted in a higher concentration of vaccenic acid (VA), CLA, CLA/VA acid ratio, and a lower oleic content, oleic acid (C18:1)/stearic acid (C18:0) ratio, PUFA n-6/n-3 ratio and <it>SCD </it>expression compared to other diets. In addition feeding system affected the fatty acid composition and <it>SCD </it>expression, possibly due to CLA concentration or the PUFA n-6/n-3 ratio. Both expression of the <it>SCD </it>gene and the feeding system were important factors affecting CLA concentration in the animal's semitendinous muscle. <it>PPARγ, PPARα </it>and <it>SREBP1 </it>expression seemed to be unaffected by the feeding system. Although no significant results were found, <it>PPARγ, PPARα </it>and <it>SREBP1 </it>showed similar expression pattern as <it>SCD</it>. Moreover, the correlation results between <it>SCD </it>expression and <it>PPARγ </it>(p < 0.01), as well as <it>SREBP1 </it>(p < 0.01) expression, may suggest that these genes were affecting <it>SCD </it>expression in a different way.</p> <p>Conclusions</p> <p>The data indicated that the feeding system is the main factor affecting the fatty acid composition and <it>SCD </it>gene expression, which is also affected by CLA and possibly by n-6/n-3 PUFAs.</p

Estudio de la influencia de la inclusión de diferentes niveles de vitamina E en la dieta de corderos de raza Rasa aragonesa en la expresión de genes en yeyuno mediante la metodología de gen candidato

En el presente trabajo se ha estudiado la interacción gen-alimentación en corderos de raza Rasa Aragonesa de peso ternasco, a partir de tejido intestinal (yeyuno) de estos animales. Se estudió la expresión diferencial de genes implicados en la captación, transporte y eliminación de α-tocoferol (SCARB1, ABCA1, NPC1L, LPL, TTPA, APOE, CYP4F2), así como de genes que codifican factores de regulación de los mismos (PDKZ1, PPARG, PPARA, SREBP1 and CEBPB), en 58 animales agrupados según los diferentes días de finalización con concentrado suplementado con vitamina E, así como en 8 de ellos alimentados con alfalfa. La Reacción en Cadena de la Polimerasa cuantitativa a tiempo real (RT-qPCR) ha sido la técnica elegida para este análisis de expresión diferencial. Previamente se estudió la expresión tisular específica de cada gen mediante PCR convencional en: músculo Longissimus dorsi; grasa subcutánea; hígado, e intestino delgado (duodeno, íleon y yeyuno). En yeyuno han amplificado todos los genes excepto PDKZ1, que no amplificó en ninguna muestra, y TTPA que sólo amplificó en 25 muestras. El gen más estable bajo los distintos tratamientos fue el gen candidato APOE, seguido del gen de referencia (GR), RPL19 y la normalización se realizó frente a este último. En cuanto a la expresión de los genes candidatos, se obtuvo que LPL y SCARB1 podrían estar regulados mediante un mecanismo de retroalimentación negativa del α-tocoferol. Dichos genes muestran una regulación de la expresión génica mediada por α-tocoferol, que produce un incremento de su expresión cuando se suplementa vitamina E durante pocos días, y una disminución de la expresión al incrementar los días de suplementación. La menor expresión génica fue encontrada en los animales que pastaban alfalfa (rica en carotenos y vitamina E), lo que sugiere que la disminución en la expresión de dichos genes en estos animales podría estar mediada por los carotenos

Handwritten Music Recognition for Mensural notation with convolutional recurrent neural networks

[EN] Optical Music Recognition is the technology that allows computers to read music notation, which is also referred to as Handwritten Music Recognition when it is applied over handwritten notation. This technology aims at efficiently transcribing written music into a representation that can be further processed by a computer. This is of special interest to transcribe the large amount of music written in early notations, such as the Mensural notation, since they represent largely unexplored heritage for the musicological community. Traditional approaches to this problem are based on complex strategies with many explicit rules that only work for one particular type of manuscript. Machine learning approaches offer the promise of generalizable solutions, based on learning from just labelled examples. However, previous research has not achieved sufficiently acceptable results for handwritten Mensural notation. In this work we propose the use of deep neural networks, namely convolutional recurrent neural networks, which have proved effective in other similar domains such as handwritten text recognition. Our experimental results achieve, for the first time, recognition results that can be considered effective for transcribing handwritten Mensural notation, decreasing the symbol-level error rate of previous approaches from 25.7% to 7.0%. (C) 2019 Elsevier B.V. All rights reserved.First author thanks the support from the Spanish Ministry "HISPAMUS" project (TIN2017-86576-R), partially funded by the EU. The other authors were supported by the European Union's H2020 grant "Recognition and Enrichment of Archival Documents" (Ref. 674943), by the BBVA Foundacion through the 2017-2018 and 2018-2019 Digital Humanities research grants "Carabela" and "HistWeather - Dos Siglos de Datos Cilmaticos", and by EU JPICH project "HOME - History Of Medieval Europe"(Spanish PEICTI Ref. PCI2018-093122).Calvo-Zaragoza, J.; Toselli, AH.; Vidal, E. (2019). Handwritten Music Recognition for Mensural notation with convolutional recurrent neural networks. Pattern Recognition Letters. 128:115-121. https://doi.org/10.1016/j.patrec.2019.08.021S11512112

Use of Maximum Likelihood-Mixed Models to select stable reference genes: a case of heat stress response in sheep

<p>Abstract</p> <p>Background</p> <p>Reference genes with stable expression are required to normalize expression differences of target genes in qPCR experiments. Several procedures and companion software have been proposed to find the most stable genes. Model based procedures are attractive because they provide a solid statistical framework. NormFinder, a widely used software, uses a model based method. The pairwise comparison procedure implemented in GeNorm is a simpler procedure but one of the most extensively used. In the present work a statistical approach based in Maximum Likelihood estimation under mixed models was tested and compared with NormFinder and geNorm softwares. Sixteen candidate genes were tested in whole blood samples from control and heat stressed sheep.</p> <p>Results</p> <p>A model including gene and treatment as fixed effects, sample (animal), gene by treatment, gene by sample and treatment by sample interactions as random effects with heteroskedastic residual variance in gene by treatment levels was selected using goodness of fit and predictive ability criteria among a variety of models. Mean Square Error obtained under the selected model was used as indicator of gene expression stability. Genes top and bottom ranked by the three approaches were similar; however, notable differences for the best pair of genes selected for each method and the remaining genes of the rankings were shown. Differences among the expression values of normalized targets for each statistical approach were also found.</p> <p>Conclusions</p> <p>Optimal statistical properties of Maximum Likelihood estimation joined to mixed model flexibility allow for more accurate estimation of expression stability of genes under many different situations. Accurate selection of reference genes has a direct impact over the normalized expression values of a given target gene. This may be critical when the aim of the study is to compare expression rate differences among samples under different environmental conditions, tissues, cell types or genotypes. To select reference genes not only statistical but also functional and biological criteria should be considered. Under the method here proposed <it>SDHA/MDH1 </it>have arisen as the best set of reference genes to be used in qPCR assays to study heat shock in ovine blood samples.</p

Development of a SNP parentage assignment panel in some North-Eastern Spanish meat sheep breeds

Aim of study: To validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, and develop a cost effective genotyping system to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment.Area of study: SpainMaterial and methods: Nine sheep breeds were sampled: Rasa Aragonesa (n=38), Navarra (n=39), Ansotana (n=41), Xisqueta (n=41), Churra Tensina (n=38), Maellana (39), Roya Bilbilitana (n=24), Ojinegra (n=36) and Cartera (n=39), and these animals were genotyped with the Illumina OvineSNP50 BeadChip array. Genotypes were extracted from the sets of 249 SNPs and 163 SNPs for parentage assignment designed in France and North America, respectively. Validation of a selected cost-effective genotyping panel of 158 SNPs from the French panel were performed by Kompetitive allele specific PCR (KASP). Additionally, some functional SNPs (n=15) were also genotyped.Main results: The set of 249 SNPs for parentage assignment showed better diversity, probability of identity, and exclusion probabilities than the set of 163 SNPs. The average minor allele frequency for the set of 249, 163 and 158 SNPs were 0.41 + 0.01, 0.39 + 0.01 and 0.42 + 0.01, respectively. The parentage assignment rate was highly dependent to the percentage of putative sires genotyped.Research highlights: The described method is a cost-effective genotyping system combining the genotyping of SNPs for the parentage assignment with some functional SNPs, which was successfully used in some Spanish meat sheep breeds

Influence of the temperature and the genotype of the HSP90AA1 gene over sperm chromatin stability in Manchega rams

The present study addresses the effect of heat stress on males' reproduction ability. For that, we have evaluated the sperm DNA fragmentation (DFI) by SCSA of ejaculates incubated at 37°C during 0, 24 and 48 hours after its collection, as a way to mimic the temperature circumstances to which spermatozoa will be subject to in the ewe uterus. The effects of temperature and temperature-humidity index (THI) from day 60 prior collection to the date of semen collection on DFI were examined. To better understand the causes determining the sensitivity of spermatozoa to heat, this study was conducted in 60 males with alternative genotypes for the SNP G/C-660 of the HSP90AA1 promoter, which encode for the Hsp90α protein. The Hsp90α protein predominates in the brain and testis, and its role in spermatogenesis has been described in several species. Ridge regression analyses showed that days 29 to 35 and 7 to 14 before sperm collection (bsc) were the most critical regarding the effect of heat stress over DFI values. Mixed model analyses revealed that DFI increases over a threshold of 30°C for maximum temperature and 22 for THI at days 29 to 35 and 7 to 14 bsc only in animals carrying the GG-660 genotype. The period 29-35 bsc coincide with the meiosis I process for which the effect of the Hsp90α has been described in mice. The period 7-14 bsc may correspond with later stages of the meiosis II and early stages of epididymal maturation in which the replacement of histones by protamines occurs. Because of GG-660 genotype has been associated to lower levels of HSP90AA1 expression, suboptimal amounts of HSP90AA1 mRNA in GG-660 animals under heat stress conditions make spermatozoa DNA more susceptible to be fragmented. Thus, selecting against the GG-660 genotype could decrease the DNA fragmentation and spermatozoa thermal susceptibility in the heat season, and its putative subsequent fertility gains.This work was supported by RTA2009-00098-00-00 INIA project (Subprograma de Investigación Fundamental orientada a los Recursos y Tecnologías Agrarias).Peer Reviewe

Changes in HSP gene and protein expression in natural scrapie with brain damage

Heat shock proteins (Hsp) perform cytoprotective functions such as apoptosis regulation and inflammatory response control. These proteins can also be secreted to the extracellular medium, acting as inflammatory mediators, and their chaperone activity permits correct folding of proteins and avoids the aggregation of anomalous isoforms. Several studies have proposed the implication of Hsp in prion diseases. We analysed the gene expression and protein distribution of different members of the Hsp27, Hsp70, and Hsp90 families in the central nervous system of sheep naturally infected with scrapie. Different expression profiles were observed in the areas analysed. Whereas changes in transcript levels were not observed in the cerebellum or medulla oblongata, a significant decrease in HSP27 and HSP90 was detected in the prefrontal cortex. In contrast, HSP73 was over-expressed in diencephalons of scrapie animals. Western blotting did not reveal significant differences in Hsp90 and Hsp70 protein expression between scrapie and control animals. Expression rates identified by real-time RT-PCR and western blotting were compared with the extent of classical scrapie lesions using stepwise regression. Changes in Hsp gene and protein expression were associated with prion protein deposition, gliosis and spongiosis rather than with apoptosis. Finally, immunohistochemistry revealed intense Hsp70 and Hsp90 immunolabelling in Purkinje cells of scrapie sheep. In contrast, controls displayed little or no staining in these cells. The observed differences in gene expression and protein distribution suggest that the heat shock proteins analysed play a role in the natural form of the disease

Posidonia oceanica restoration, a relevant strategy after boat anchoring degradation?

Trabajo presentado al 7th Mediterranean Symposium on Marine Vegetation, celebrado en Génova (Italia), los días 19 y 20 de septiembre de 2022.The anchoring of large pleasure boats constitutes one of the main threats in shallow marine habitats and particularly for seagrass beds. In the Mediterranean, this activity has seen constant development during the last decades, causing major physical disturbances in Posidonia oceanica meadows and associated ecosystem services, notably in terms of climate change mitigation (i.e. carbon fixation and sequestration capacities). In this context, the aims of the present study are to estimate the impact of these anchoring activities on P. oceanica meadows in a particularly highlyfrequented area (Sant’Amanza gulf, SE Corsica Island) and to set up a strategy to restore this major carbon sink. Since the last decade, time-series of marine habitat maps revealed an important regression of P. oceanica meadows, with a loss of 72.9 ha, corresponding to 11% of the meadow surface and 9% decline in the total carbon fixation and sequestration performed each year. Moreover, in the most impacted part of the bay (Balistra bay), a loss of 16.6 ha (28%) has been recorded between 2011 and 2022. Following recent enforcement of anchoring regulation, prohibiting the anchoring of large units (greater than 24 m), and the lockdown linked to the COVID-19 pandemic, anchorages in the seagrass reduced by 92%, between 2018 and 2022. Natural recovery was observed at the edge of the meadow (plagiotropic rhizomes) but this growth is slow and the areas to recover are large. As a result, a transplant experiment, from cuttings harvested from the adjacent meadows, was initiated in the spring 2021. Four restoration techniques are being tested in the some pilot sites and the development of these transplants will be monitored and compared to the natural recovery.This research has been co-financed by INTERREG program (GIREPAM), Collectivity of Corsica Corse (PADDUC-CHANGE), SETEC Foundation, Environment Office of Corsica and the French Office of Biodiversity (RenforC program)