Parallel Online Time Warping for Real-Time Audio-to-Score Alignment in Multi-core Systems

[EN] The Audio-to-Score framework consists of two separate stages: pre- processing and alignment. The alignment is commonly solved through offline Dynamic Time Warping (DTW), which is a method to find the path over the distortion matrix with the minimum cost to determine the relation between the performance and the musical score times. In this work we propose a par- allel online DTW solution based on a client-server architecture. The current version of the application has been implemented for multi-core architectures (x86, x64 and ARM), thus covering either powerful systems or mobile devices. An extensive experimentation has been conducted in order to validate the software. The experiments also show that our framework allows to achieve a good score alignment within the real-time window by using parallel computing techniques.This work has been partially supported by Spanish Ministry of Science and Innovation and FEDER under Projects TEC2012-38142-C04-01, TEC2012-38142-C04-03, TEC2012-38142-C04-04, TEC2015-67387-C4-1-R, TEC2015-67387-C4-3-R, TEC2015-67387-C4-4-R, the European Union FEDER (CAPAP-H5 network TIN2014-53522-REDT), and the Generalitat Valenciana under Grant PROMETEOII/2014/003.Alonso-Jordá, P.; Cortina, R.; Rodríguez-Serrano, F.; Vera-Candeas, P.; Alonso-González, M.; Ranilla, J. (2017). Parallel Online Time Warping for Real-Time Audio-to-Score Alignment in Multi-core Systems. The Journal of Supercomputing. 73(1):126-138. https://doi.org/10.1007/s11227-016-1647-5S126138731Joder C, Essid S, Richard G (2011) A conditional random field framework for robust and scalable audio-to-score matching. 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In: 16th International Society for music information retrieval conference, pp 742–748Rodríguez-Serrano FJ, Menéndez-Canal J, Vidal A, Cañadas-Quesada FJ, Cortina R (2015) A DTW based score following method for score-informed sound source separation. In: Proceedings of the 12th sound and music computing conference 2015 (SMC-15), Ireland, pp 491–496Carabias-Ortí JJ, Rodríguez-Serrano FJ, Vera-Candeas P, Cañadas-Quesada FJ, Ruíz-Reyes N (2013) Constrained non-negative sparse coding using learnt instrument templates for realtime music transcription. Eng Appl Artif Intell 26(7):1671–1680Raphael C (2006) Aligning music audio with symbolic scores using a hybrid graphical model. Mach Learn 65:389–409Schreck-Ensemble (2001–2004) ComParser 1.42. http://home.hku.nl/~pieter.suurmond/SOFT/CMP/doc/cmp.html . Accessed Sept 2015Itakura F (1975) Minimum prediction residual principle applied to speech recognition. 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Real-time Soundprism

[EN] This paper presents a parallel real-time sound source separation system for decomposing an audio signal captured with a single microphone in so many audio signals as the number of instruments that are really playing. This approach is usually known as Soundprism. The application scenario of the system is for a concert hall in which users, instead of listening to the mixed audio, want to receive the audio of just an instrument, focusing on a particular performance. The challenge is even greater since we are interested in a real-time system on handheld devices, i.e., devices characterized by both low power consumption and mobility. The results presented show that it is possible to obtain real-time results in the tested scenarios using an ARM processor aided by a GPU, when this one is present.This work has been supported by the "Ministerio de Economia y Competitividad" of Spain and FEDER under projects TEC2015-67387-C4-{1,2,3}-R.Muñoz-Montoro, AJ.; Ranilla, J.; Vera-Candeas, P.; Combarro, EF.; Alonso-Jordá, P. (2019). Real-time Soundprism. The Journal of Supercomputing. 75(3):1594-1609. https://doi.org/10.1007/s11227-018-2703-0S15941609753Alonso P, Cortina R, Rodríguez-Serrano FJ, Vera-Candeas P, Alonso-González M, Ranilla J (2017) Parallel online time warping for real-time audio-to-score alignment in multi-core systems. J Supercomput 73:126. https://doi.org/10.1007/s11227-016-1647-5Carabias-Orti JJ, Cobos M, Vera-Candeas P, Rodríguez-Serrano FJ (2013) Nonnegative signal factorization with learnt instrument models for sound source separation in close-microphone recordings. EURASIP J Adv Signal Process 2013:184. https://doi.org/10.1186/1687-6180-2013-184Carabias-Orti JJ, Rodriguez-Serrano FJ, Vera-Candeas P, Canadas-Quesada FJ, Ruiz-Reyes N (2015) An audio to score alignment framework using spectral factorization and dynamic time warping. In: 16th International Society for Music Information Retrieval Conference, pp 742–748Díaz-Gracia N, Cocaña-Fernández A, Alonso-González M, Martínez-Zaldívar FJ, Cortina R, García-Mollá VM, Alonso P, Ranilla J (2014) NNMFPACK: a versatile approach to an NNMF parallel library. In: Proceedings of the 2014 International Conference on Computational and Mathematical Methods in Science and Engineering, pp 456–465Díaz-Gracia N, Cocaña-Fernández A, Alonso-González M, Martínez-Zaldívar FJ, Cortina R, García-Mollá VM, Vidal AM (2015) Improving NNMFPACK with heterogeneous and efficient kernels for $$\beta$$ β -divergence metrics. J Supercomput 71:1846–1856. https://doi.org/10.1007/s11227-014-1363-yDriedger J, Grohganz H, Prätzlich T, Ewert S, Müller M (2013) Score-informed audio decomposition and applications. In: Proceedings of the 21st ACM International Conference on Multimedia, pp 541–544Duan Z, Pardo B (2011) Soundprism: an online system for score-informed source separation of music audio. IEEE J Sel Top Signal Process 5(6):1205–1215Duong NQ, Vincent E, Gribonval R (2010) Under-determined reverberant audio source separation using a full-rank spatial covariance model. IEEE Trans Audio Speech 18(7):1830–1840. https://doi.org/10.1109/TASL.2010.2050716Ewert S, Müller M (2011) Estimating note intensities in music recordings. In: Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, pp 385–388Ewert S, Pardo B, Mueller M, Plumbley MD (2014) Score-informed source separation for musical audio recordings: an overview. 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In: ISMIR. https://doi.org/10.1136/bmj.324.7341.827Marxer R, Janer J, Bonada J (2012) Low-latency instrument separation in polyphonic audio using timbre models. In: International Conference on Latent Variable Analysis and Signal Separation, pp 314–321Miron M, Carabias-Orti JJ, Janer J (2015) Improving score-informed source separation for classical music through note refinement. In: ISMIR, pp 448–454Ozerov A, Févotte C (2010) Multichannel nonnegative matrix factorization in convolutive mixtures for audio source separation. IEEE Trans Audio Speech Lang Process 18:550–563. https://doi.org/10.1109/TASL.2009.2031510Ozerov A, Vincent E, Bimbot F (2012) A general flexible framework for the handling of prior information in audio source separation. IEEE Trans Audio Speech Lang Process 20:1118–1133. https://doi.org/10.1109/TASL.2011.2172425Pätynen J, Pulkki V, Lokki T (2008) Anechoic recording system for symphony orchestra. 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Addressing Recruitment Challenges in the Engage-HU Trial in Young Children with Sickle Cell Disease

Background: Sickle cell disease (SCD) is a genetic disorder that causes significant medical and neurologic morbidity in children. Hydroxyurea (HU) is the primary medication used to prevent these complications. National Heart, Lung, and Blood Institute (NHLBI) guidelines recommend offering HU to children as young as 9 months of age with SCD (HbSS or HbSB0 thalassemia) using a shared decision-making approach. Although HU has proven efficacious it remains underutilized and caregivers report that they are not always actively involved in the decision to initiate this therapy. Reasons for limited HU uptake likely include lack of clinician knowledge and training and negative caregiver perceptions. Thus, we developed the Engage-HU trial as a novel approach to address HU utilization barriers. A critical consideration for this trial was that SCD primarily affects individuals of African and Hispanic/Latino descent. In these minority populations, intervention trials are sometimes terminated early because of recruitment difficulties related to mistrust of research, caregiver burden, and transportation issues. As such, the Engage-HU trial design included best-practice strategies for recruiting people of color in research. This study describes these strategies, the initial recruitment plan, preliminary recruitment outcomes and strategies, and our procedural adaptations. Study Design and Methods: Engage-HU is a randomized control trial (NCT03442114) to assess how clinicians can engage caregivers in a shared discussion that considers their values and preferences and includes evidence that supports HU. Engage-HU compares two dissemination methods for clinicians to facilitate shared decision-making with caregivers of young children with SCD: 1) the American Society of Hematology Pocket Guide, and 2) the HU Shared-Decision Making (H-SDM) Toolkit. The study aims to recruit 174 caregivers and evaluate the effectiveness of the dissemination methods on patient-centered outcomes (caregiver confidence in decision-making and perceptions of experiencing shared decision-making) as well as HU uptake and child health outcomes. Eligible children are aged 0 to 5 years, candidates for HU, and their caregiver has not made a decision about HU in the past 3 months. The trial is being conducted at 9 sites in the United States and uses a stepped-wedge design. Data will be analyzed based on the intent-to-treat principle. All participants will remain in the arm of the study to which they were randomized, regardless of whether or not they receive the assigned dissemination method. The primary endpoints are caregiver decisional uncertainty and caregiver perception of shared decision-making measured using validated tools. Data will be analyzed using a linear mixed effects regression model with a robust variance estimator and maximum likelihood estimation with observations clustered within site. The Engage-HU trial includes adaptations to increase recruitment such as tailored messaging, a relational recruitment approach, streamlined data collection, and a Stakeholder Advisory Committee. However, even with these adaptations, the first 6-months of the trial yielded lower than anticipated recruitment. Rather than terminate the trial or accept low enrollment, the research team implemented a series of recruitment strategies to address barriers including helping to improve research coordinator knowledge of the study purpose and adjusting no-show and follow-up procedures (e.g., calls to families after missed appointments and reminder calls before appointments). Site clinicians and clinic staff were provided with additional training so they could give more context about Engage-HU to caregivers and the study principal investigator led monthly "all coordinator" calls to provide support by sharing updates and experiences about successful recruitment. Implementation of these strategies resulted in triple the number of enrollments over the next 7-months compared to the previous 6-months (Table 1). Our goal in sharing this information is to provide lessons learned that can be implemented in future trials with the systematically underserved SCD population. It is also anticipated that methods described here may also inform clinical approaches to better engage caregivers of young children around critical clinical conversations, such as initiating medications like HU. Disclosures King: Magenta Therapeutics: Membership on an entity's Board of Directors or advisory committees; Bioline: Consultancy; RiverVest: Consultancy; Novimmune: Research Funding; Celgene: Consultancy; Tioma Therapuetics: Consultancy; Amphivena Therapeutics: Research Funding; WUGEN: Current equity holder in private company; Cell Works: Consultancy; Incyte: Consultancy. Smith-Whitley:Prime: Other: Education material; Celgene: Membership on an entity's Board of Directors or advisory committees; Global Blood Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees. Neumayr:Emmaus: Consultancy; Bayer: Consultancy; CTD Holdings: Consultancy; Pfizer: Consultancy; ApoPharma: Consultancy, Membership on an entity's Board of Directors or advisory committees; Micelle: Other: Site principal investigator; GBT: Other: Site principal investigator; PCORI: Other: site principal investigator; Novartis: Other: co-investigator; Bluebird Bio: Other: co-investigator; Sangamo Therapeutics: Other; Silarus: Other; Celgene: Other; La Jolla Pharmaceuticals: Other; Forma: Other; Imara: Other; National Heart, Lung, and Blood Institute: Other; Health Resources and Services Administration: Other; Centers for Disease Control and Prevention: Other; Seattle Children's Research: Other. Yates:Novartis: Research Funding. Thompson:Novartis: Consultancy, Honoraria, Research Funding; CRISPR/Vertex: Research Funding; BMS: Consultancy, Research Funding; Baxalta: Research Funding; Biomarin: Research Funding; bluebird bio, Inc.: Consultancy, Research Funding. </jats:sec

Socioeconomic conditions and number of pain sites in women

<p>Abstract</p> <p>Background</p> <p>Women in deprived socioeconomic situations run a high pain risk. Although number of pain sites (NPS) is considered highly relevant in pain assessment, little is known regarding the relationship between socioeconomic conditions and NPS.</p> <p>Methods</p> <p>The study population comprised 653 women; 160 recurrence-free long-term gynecological cancer survivors, and 493 women selected at random from the general population. Demographic characteristics and co-morbidity over the past 12 months were assessed. Socioeconomic conditions were measured by Socioeconomic Condition Index (SCI), comprising education, employment status, income, ability to pay bills, self-perceived health, and satisfaction with number of close friends. Main outcome measure NPS was recorded using a body outline diagram indicating where the respondents had experienced pain during the past week. Chi-square test and forward stepwise logistic regression were applied.</p> <p>Results and Conclusion</p> <p>There were only minor differences in SCI scores between women with 0, 1-2 or 3 NPS. Four or more NPS was associated with younger age, higher BMI and low SCI. After adjustment for age, BMI and co-morbidity, we found a strong association between low SCI scores and four or more NPS, indicating that there is a threshold in the NPS count for when socioeconomic determinants are associated to NPS in women.</p

Engaging Caregivers and Providers of Children With Sickle Cell Anemia in Shared Decision Making for Hydroxyurea: Protocol for a Multicenter Randomized Controlled Trial

BACKGROUND: Sickle cell anemia (SCA) is a genetic blood disorder that puts children at a risk of serious medical complications, early morbidity and mortality, and high health care utilization. Until recently, hydroxyurea was the only disease-modifying treatment for this life-threatening disease and has remained the only option for children younger than 5 years. Evidence-based guidelines recommend using a shared decision-making (SDM) approach for offering hydroxyurea to children with SCA (HbSS or HbS/β0 thalassemia) aged as early as 9 months. However, the uptake remains suboptimal, likely because caregivers lack information about hydroxyurea and have concerns about its safety and potential long-term side effects. Moreover, clinicians do not routinely receive training or tools, especially those that provide medical evidence and consider caregivers' preferences and values, to facilitate a shared discussion with caregivers. OBJECTIVE: The aim of this study is to understand how best to help parents of young children with sickle cell disease and their clinicians have a shared discussion about hydroxyurea (one that considers medical evidence and parent values and preferences). METHODS: We designed our study to compare the effectiveness of two methods for disseminating hydroxyurea guidelines to facilitate SDM: a clinician pocket guide (ie, usual care) and a clinician hydroxyurea SDM toolkit (H-SDM toolkit). Our primary outcomes are caregiver reports of decisional uncertainty and knowledge of hydroxyurea. The study also assesses the number of children (aged 0-5 years) who were offered and prescribed hydroxyurea and the resultant health outcomes. RESULTS: The Ethics Committee of the Cincinnati Children's Hospital Medical Center approved this study in November 2017. As of February 2021, we have enrolled 120 caregiver participants. CONCLUSIONS: The long-term objective of this study is to improve the quality of care for children with SCA. Using multicomponent dissemination methods developed in partnership with key stakeholders and designed to address barriers to high-quality care, caregivers of patients with SCA can make informed and shared decisions about their health. TRIAL REGISTRATION: ClinicalTrials.gov NCT03442114; https://clinicaltrials.gov/ct2/show/NCT03442114. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/27650

Signatures of Selection in Fusion Transcripts Resulting From Chromosomal Translocations in Human Cancer

BACKGROUND: The recurrence and non-random distribution of translocation breakpoints in human tumors are usually attributed to local sequence features present in the vicinity of the breakpoints. However, it has also been suggested that functional constraints might contribute to delimit the position of translocation breakpoints within the genes involved, but a quantitative analysis of such contribution has been lacking. METHODOLOGY: We have analyzed two well-known signatures of functional selection, such as reading-frame compatibility and non-random combinations of protein domains, on an extensive dataset of fusion proteins resulting from chromosomal translocations in cancer. CONCLUSIONS: Our data provide strong experimental support for the concept that the position of translocation breakpoints in the genome of cancer cells is determined, to a large extent, by the need to combine certain protein domains and to keep an intact reading frame in fusion transcripts. Additionally, the information that we have assembled affords a global view of the oncogenic mechanisms and domain architectures that are used by fusion proteins. This can be used to assess the functional impact of novel chromosomal translocations and to predict the position of breakpoints in the genes involved

Gap Junction Mediated Intercellular Metabolite Transfer in the Cochlea Is Compromised in Connexin30 Null Mice

Connexin26 (Cx26) and connexin30 (Cx30) are two major protein subunits that co-assemble to form gap junctions (GJs) in the cochlea. Mutations in either one of them are the major cause of non-syndromic prelingual deafness in humans. Because the mechanisms of cochlear pathogenesis caused by Cx mutations are unclear, we investigated effects of Cx30 null mutation on GJ-mediated ionic and metabolic coupling in the cochlea of mice. A novel flattened cochlear preparation was used to directly assess intercellular coupling in the sensory epithelium of the cochlea. Double-electrode patch clamp recordings revealed that the absence of Cx30 did not significantly change GJ conductance among the cochlear supporting cells. The preserved electrical coupling is consistent with immunolabeling data showing extensive Cx26 GJs in the cochlea of the mutant mice. In contrast, dye diffusion assays showed that the rate and extent of intercellular transfer of multiple fluorescent dyes (including a non-metabolizable D-glucose analogue, 2-NBDG) among cochlear supporting cells were severely reduced in Cx30 null mice. Since the sensory epithelium in the cochlea is an avascular organ, GJ-facilitated intercellular transfer of nutrient and signaling molecules may play essential roles in cellular homeostasis. To test this possibility, NBDG was used as a tracer to study the contribution of GJs in transporting glucose into the cochlear sensory epithelium when delivered systemically. NBDG uptake in cochlear supporting cells was significantly reduced in Cx30 null mice. The decrease was also observed with GJ blockers or glucose competition, supporting the specificity of our tests. These data indicate that GJs facilitate efficient uptake of glucose in the supporting cells. This study provides the first direct experimental evidence showing that the transfer of metabolically-important molecules in cochlear supporting cells is dependent on the normal function of GJs, thereby suggesting a novel pathogenesis process in the cochlea for Cx-mutation-linked deafness

Pentoxifylline associated to hypertonic saline solution attenuates inflammatory process and apoptosis after intestinal ischemia/reperfusion in rats

PURPOSE:To evaluate intestinal inflammatory and apoptotic processes after intestinal ischemia/reperfusion injury, modulated by pentoxifylline and hypertonic saline.METHODS:It was allocated into four groups (n=6), 24 male Wistar rats (200 to 250g) and submitted to intestinal ischemia for 40 min and reperfusion for 80 min: IR (did not receive any treatment); HS group (Hypertonic Saline, 4ml/kg-IV); PTX group (Pentoxifylline, 30mg/kg-IV); HS+PTX group (Hypertonic Saline and Pentoxifylline). All animals were heparinized (100U/kg). At the end of reperfusion, ileal fragments were removed and stained on hematoxylin-eosin and histochemical studies for COX-2, Bcl-2 and cleaved caspase-3.RESULTS:The values of sO2 were higher on treated groups at 40 minutes of reperfusion (p=0.0081) and 80 minutes of reperfusion (p=0.0072). Serum lactate values were lower on treated groups after 40 minutes of reperfusion (p=0.0003) and 80 minutes of reperfusion (p=0.0098). Morphologic tissue injuries showed higher grades on IR group versus other groups: HS (p=0.0006), PTX (p=0.0433) and HS+PTX (p=0.0040). The histochemical study showed lesser expression of COX-2 (p=0.0015) and Bcl-2 (p=0.0012) on HS+PTX group. A lower expression of cleaved caspase-3 was demonstrated in PTX (p=0.0090; PTXvsIR).CONCLUSION:The combined use of pentoxifylline and hypertonic saline offers best results on inflammatory and apoptotic inhibitory aspects after intestinal ischemia/reperfusion.São Paulo University Medical SchoolUSP Medical SchoolFederal University of São Paulo Medical SchoolUSP School of MedicineUSP School of Medicine Department of SurgeryUSP Medical School Department of SurgeryUNIFESP, Medical SchoolSciEL