Miracle-dz/UniFAR-FTUs huggingface dataset:
Audio-to-score singing transcription based on a CRNN-HSMM hybrid model

This paper describes an automatic singing transcription (AST) method that estimates a human-readable musical score of a sung melody from an input music signal. Because of the considerable pitch and temporal variation of a singing voice, a naive cascading approach that estimates an F0 contour and quantizes it with estimated tatum times cannot avoid many pitch and rhythm errors. To solve this problem, we formulate a unified generative model of a music signal that consists of a semi-Markov language model representing the generative process of latent musical notes conditioned on musical keys and an acoustic model based on a convolutional recurrent neural network (CRNN) representing the generative process of an observed music signal from the notes. The resulting CRNN-HSMM hybrid model enables us to estimate the most-likely musical notes from a music signal with the Viterbi algorithm, while leveraging both the grammatical knowledge about musical notes and the expressive power of the CRNN. The experimental results showed that the proposed method outperformed the conventional state-of-the-art method and the integration of the musical language model with the acoustic model has a positive effect on the AST performance.
Beneficial Potential of Banha-Sasim-Tang for Stress-Sensitive Functional Dyspepsia via Modulation of Ghrelin: A Randomized Controlled Trial

Background: Functional dyspepsia (FD) is a highly complex pathophysiologic disease, which shows low recovery and high relapse rates. Therefore, a growing number of clinicians and patients are looking for alternative herbal medicine. Banha-Sasim-Tang (BST) is an herbal prescription for treating a wide range of dyspepsia in traditional Korean medicine (TKM). Aim of the study: This study aimed to evaluate the efficacy of BST on FD in patients with psychological stress-related symptoms and to investigate the involvement of ghrelin. This study is registered at https://cris.nih. go.kr/with the identification number KCT 0002811. Materials and methods: A total of 31 participants with FD who met the Rome IV criteria and the psychological stress-related pattern were enrolled in a double-blind, randomized, and controlled study. Participants were randomly assigned to the BST group (10 g twice daily for 4 weeks) or placebo group. The primary endpoint was a change in the Nepean Dyspepsia Index–Korean (NDI-K) score. The secondary endpoints were changes in the Visual Analog Scale (VAS) scores and plasma ghrelin level. Results: All participants completed the study (n = 15 for BST, n = 16 for placebo). BST decreased NDI-K scores compared with placebo, but the difference was not statistically significant (37.40 ± 27.40 vs 22.50 ± 23.85, p = 0.12). VAS scores and plasma total ghrelin levels were significantly improved in patients who were treated with BST (3.19 ± 1.60 vs 1.38 ± 2.85, p = 0.03 for VAS and 105.69 ± 287.89 vs -142.31 ± 314.32, p = 0.03 for total ghrelin). No BST-related adverse effects were observed during the trial. Conclusion: Our results indicate the clinical potential of BST for FD patients and are the first study to show the modulation of plasma ghrelin as one of its corresponding mechanisms. Clinical Trial Registration: https://cris.nih. go.kr/, identifier KCT 0002811.
The Impact of Locomotor Speed on the Human Metatarsophalangeal Joint Kinematics

This paper aims to further our previous study to investigate the effect of speed on the human metatarsophalangeal (MP) joint kinematics during running on level ground. The 3D motion of the foot segments was captured by a twelve-camera motion analysis system, and the ground reaction forces and moments were recorded by using a six-force plate array. The relative movement between the tarsometatarsi (hindfoot) and phalanges (forefoot) segments were recorded to obtain the 3D orientation and position of the functional axis (FA) of the MP joint. The results show that the FA locates about an average of 19% foot length (FL) anterior to the anatomical axis (AA) across all running speeds, and is also 4.8% FL inferior to the AA during normal and fast run. Similar to walking, the functional axis is more oblique than the anatomical axis with a more anterior–inferior orientation across all the running speeds. This suggests that representing MP joint with the AA may mislead the calculation of joint moment/power and muscle moment arms in both running and walking gait. Compared with previous study, we found that walking and running speeds have statistically significant effects on the position of the FA. The functional axis moves frontward to a more anterior position when the speed increases during walking and running. It transfers upward in the superior direction with increasing speed of walking, but moves more toward the inferior position when the velocity increased further to running. Also, the orientation of FA in sagittal plane became more oblique toward the vertical direction as the speed increased. This may help in moderating the muscular effort, increase the muscle EMA and improve the locomotor performance. These results would contribute to understanding the in vivo biomechanical function of the MP joint and also the foot propulsion during human locomotion.
Effects of Porcine Immature Oocyte Vitrification on Actin Microfilament Distribution and Chromatin Integrity During Early Embryo Development in vitro

Vitrification is mainly used to cryopreserve female gametes. This technique allows maintaining cell viability, functionality, and developmental potential at low temperatures into liquid nitrogen at −196°C. For this, the addition of cryoprotectant agents, which are substances that provide cell protection during cooling and warming, is required. However, they have been reported to be toxic, reducing oocyte viability, maturation, fertilization, and embryo development, possibly by altering cell cytoskeleton structure and chromatin. Previous studies have evaluated the effects of vitrification in the germinal vesicle, metaphase II oocytes, zygotes, and blastocysts, but the knowledge of its impact on their further embryo development is limited. Other studies have evaluated the role of actin microfilaments and chromatin, based on the fertilization and embryo development rates obtained, but not the direct evaluation of these structures in embryos produced from vitrified immature oocytes. Therefore, this study was designed to evaluate how the vitrification of porcine immature oocytes affects early embryo development by the evaluation of actin microfilament distribution and chromatin integrity. Results demonstrate that the damage generated by the vitrification of immature oocytes affects viability, maturation, and the distribution of actin microfilaments and chromatin integrity, observed in early embryos. Therefore, it is suggested that vitrification could affect oocyte repair mechanisms in those structures, being one of the mechanisms that explain the low embryo development rates after vitrification.
Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective

Antibiotics are freqeuently used in the livestock sector in low- and middle-income countries for treatment, prophylaxis, and growth promotion. However, there is limited information into the zoonotic prevalence and dissemination patterns of antimicrobial resistance (AMR) within these environments. In this study we used pig farming in Thailand as a model to explore AMR; 156 pig farms were included, comprising of small-sized (<50 sows) and medium-sized (≥100 sows) farms, where bacterial isolates were selectively cultured from animal rectal and human fecal samples. Bacterial isolates were subjected to antimicrobial susceptibility testing (AST), and whole-genome sequencing. Our results indicate extensive zoonotic sharing of antibiotic resistance genes (ARGs) by horizontal gene transfer. Resistance to multiple antibiotics was observed with higher prevalence in medium-scale farms. Zoonotic transmission of colistin resistance in small-scale farms had a dissemination gradient from pigs to handlers to non-livestock contacts. We highly recommend reducing the antimicrobial use in animals’ feeds and medications, especially the last resort drug colistin.
Application of the Mirror Technique for Three-Dimensional Electron Microscopy of Neurochemically Identified GABA-ergic Dendrites

In the nervous system synaptic input arrives chiefly on dendrites and their type and distribution have been assumed pivotal in signal integration. We have developed an immunohistochemistry (IH)-correlated electron microscopy (EM) method – the “mirror” technique – by which synaptic input to entire dendrites of neurochemically identified interneurons (INs) can be mapped due preserving high-fidelity tissue ultrastructure. Hence, this approach allows quantitative assessment of morphometric parameters of synaptic inputs along the whole length of dendrites originating from the parent soma. The method exploits the fact that adjoining sections have truncated or cut cell bodies which appear on the common surfaces in a mirror fashion. In one of the sections the histochemical marker of the GABAergic subtype, calbindin was revealed in cell bodies whereas in the other section the remaining part of the very same cell bodies were subjected to serial section EM to trace and reconstruct the synaptology of entire dendrites. Here, we provide exemplary data on the synaptic coverage of two dendrites belonging to the same calbindin-D28K immunopositive IN and determine the spatial distribution of asymmetric and symmetric synapses, surface area and volume of the presynaptic boutons, morphometric parameters of synaptic vesicles, and area extent of the active zones.
AMPA-Type Glutamate Receptors Associated With Vascular Smooth Muscle Cell Subpopulations in Atherosclerosis and Vascular Injury

Objectives and Aims: Vascular smooth muscle cells (VSMCs) are key constituents of both normal arteries and atherosclerotic plaques. They have an ability to adapt to changes in the local environment by undergoing phenotypic modulation. An improved understanding of the mechanisms that regulate VSMC phenotypic changes may provide insights that suggest new therapeutic targets in treatment of cardiovascular disease (CVD). The amino-acid glutamate has been associated with CVD risk and VSMCs metabolism in experimental models, and glutamate receptors regulate VSMC biology and promote pulmonary vascular remodeling. However, glutamate-signaling in human atherosclerosis has not been explored. Methods and Results: We identified glutamate receptors and glutamate metabolism-related enzymes in VSMCs from human atherosclerotic lesions, as determined by single cell RNA sequencing and microarray analysis. Expression of the receptor subunits glutamate receptor, ionotropic, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic (AMPA)-type subunit 1 (GRIA1) and 2 (GRIA2) was restricted to cells of mesenchymal origin, primarily VSMCs, as confirmed by immunostaining. In a rat model of arterial injury and repair, changes of GRIA1 and GRIA2 mRNA level were most pronounced at time points associated with VSMC proliferation, migration, and phenotypic modulation. In vitro, human carotid artery SMCs expressed GRIA1, and selective AMPA-type receptor blocking inhibited expression of typical contractile markers and promoted pathways associated with VSMC phenotypic modulation. In our biobank of human carotid endarterectomies, low expression of AMPA-type receptor subunits was associated with higher content of inflammatory cells and a higher frequency of adverse clinical events such as stroke. Conclusion: AMPA-type glutamate receptors are expressed in VSMCs and are associated with phenotypic modulation. Patients suffering from adverse clinical events showed significantly lower mRNA level of GRIA1 and GRIA2 in their atherosclerotic lesions compared to asymptomatic patients. These results warrant further mapping of neurotransmitter signaling in the pathogenesis of human atherosclerosis.
Assessment of Suicide Risks During the First Week Immediately After Discharge From Psychiatric Inpatient Facility

Background: The suicide rate in first week after psychiatric discharge is alarmingly high. Although a risk assessment prior to discharge is standard praxis, it can be difficult to take into consideration the obstacles that patient will meet once discharged. A follow-up-visit during the first week after discharge is an opportunity to reevaluate whether a person may be at risk of suicide. Aim: To determine how many patients, of those who were assessed, were evaluated to be at elevated risk of suicide during the first week after psychiatric discharge and secondarily to identify predictors of this and predictors for receiving a follow-up visit during first week after discharge. Methods: All patients discharged between March 1st 2018 to January 17th 2019 were offered a home visit including a systematic risk assessment. Socio-demographics and clinical variables were obtained from medical records and logistic regression analyses were used to identify predictors of a higher suicide risk assessment as well as receiving a follow-up visit. Results: Information from 1905 discharges were included. Of these, 1,052 were seen in follow-up meetings. Risk assessments was conducted in a total of 567 discharge procedures, of which 28 (5%) had an elevated risk of suicide. A history of suicide attempt, suicide risk having been the reason for admission, a first diagnosis of a psychiatric disorder was associated with an elevated risk of suicide after discharge. Conclusion: Follow-up visits could serve as an important tool to identify people whose suicidal risk were overlooked at discharge or exposed to severe stressors after discharge.
Dietary Supplementation With Chlorogenic Acid Derived From Lonicera macranthoides Hand-Mazz Improves Meat Quality and Muscle Fiber Characteristics of Finishing Pigs via Enhancement of Antioxidant Capacity

Chlorogenic acid (CGA), one of the most abundant polyphenol compounds in nature, is regarded as a potential feed additive to promote animal health and enhance the meat products’ quality via its various biological properties. The current study aims: (1) to determine whether dietary CGA supplementation improves meat quality and muscle fiber characteristics, and (2) to ascertain whether the corresponding improvement is associated with enhancing the antioxidant capacity of the finishing pigs. Thirty-two (Large × White × Landrace) finishing pigs with an average initial body weight of 71.89 ± 0.92 kg were allotted to 4 groups, and each was fed diets supplemented with 0, 0.02, 0.04, or 0.08% (weight/weight) of CGA. The meat quality traits, muscle fiber characteristics, and the serum and muscle antioxidant capacity were assessed. Results suggested that, compared with the control group, dietary CGA supplementation at a level of 0.04% significantly decreased the b∗ value and distinctly increased the inosinic acid content of longissimus dorsi (LD) and biceps femoris (BF) muscles (P < 0.01). Moreover, dietary supplementation with 0.04% of CGA markedly improved the amino acid composition of LD and BF muscles, as well as augmented the mRNA abundance of Nrf-2, GPX-1, MyoD, MyoG, and oxidative muscle fiber (I and IIa) in LD muscle (P < 0.05). This result indicates that a diet supplemented with 0.04% of CGA promotes myogenesis and induces a transformation toward more oxidative muscle fibers in LD muscle, subsequently improving meat quality. Besides, dietary supplementation with 0.02% and 0.04% of CGA notably enhanced the serum GSH-PX level (P < 0.01). Considering all these effects are closely related to the alteration of antioxidant activities of the finishing pigs, the underlying metabolism is likely connected to the boosting of their antioxidant capacity induced by dietary CGA.
Statistical Properties of Musical Creativity: Roles of Hierarchy and Uncertainty in Statistical Learning

Creativity is part of human nature and is commonly understood as a phenomenon whereby something original and worthwhile is formed. Owing to this ability, humans can produce innovative information that often facilitates growth in our society. Creativity also contributes to esthetic and artistic productions, such as music and art. However, the mechanism by which creativity emerges in the brain remains debatable. Recently, a growing body of evidence has suggested that statistical learning contributes to creativity. Statistical learning is an innate and implicit function of the human brain and is considered essential for brain development. Through statistical learning, humans can produce and comprehend structured information, such as music. It is thought that creativity is linked to acquired knowledge, but so-called “eureka” moments often occur unexpectedly under subconscious conditions, without the intention to use the acquired knowledge. Given that a creative moment is intrinsically implicit, we postulate that some types of creativity can be linked to implicit statistical knowledge in the brain. This article reviews neural and computational studies on how creativity emerges within the framework of statistical learning in the brain (i.e., statistical creativity). Here, we propose a hierarchical model of statistical learning: statistically chunking into a unit (hereafter and shallow statistical learning) and combining several units (hereafter and deep statistical learning). We suggest that deep statistical learning contributes dominantly to statistical creativity in music. Furthermore, the temporal dynamics of perceptual uncertainty can be another potential causal factor in statistical creativity. Considering that statistical learning is fundamental to brain development, we also discuss how typical versus atypical brain development modulates hierarchical statistical learning and statistical creativity. We believe that this review will shed light on the key roles of statistical learning in musical creativity and facilitate further investigation of how creativity emerges in the brain.
Low Intra-Individual Variation in Mean Platelet Volume Over Time in Systemic Lupus Erythematosus

Platelets have recently emerged as important immune modulators in systemic lupus erythematosus (SLE), in addition to their role in thrombosis and cardiovascular disease. However, studies investigating mean platelet volume (MPV) in SLE are often scarce, conflicting and cross-sectional. In this study, MPV was measured in clinical routine throughout a defined time-period to quantify both individual MPV fluctuations and investigate if such variations are associated with disease activity and clinical phenotypes of SLE. Of our 212 patients, 34 patients had only one MPV value reported with the remaining 178 patients having between 2 and 19 visits with recorded MPV values. The intra-individual MPV variation was low, with a median variation of 0.7 fL. This was further supported by the finding that 84% of patients stayed within their reference interval category (i.e., small, normal or large) over time. In our cohort, no correlation between disease activity and MPV neither cross-sectionally nor longitudinally was found. Mean platelet volume values were significantly smaller in SLE patients (mean 10.5 fL) compared to controls (mean 10.8 fL), p < 0.0001. Based on the reference interval, 2.4% (n = 5) of patients had large-sized platelets, 84.4% (n = 179) had normal-sized and 13.2% (n = 28) had small-sized. A larger proportion (85.7%) of patients with small-sized platelets met the anti-dsDNA criterion (ACR10b; p = 0.003) compared to patients with normal and large (57.6%) sized platelets. In conclusion, the intra-individual MPV variation was of low magnitude and fluctuations in disease activity did not have any significant impact on MPV longitudinally. This lack of variability in MPV over time indicates that measuring MPV at any time-point is sufficient. Further studies are warranted to evaluate MPV as a possible biomarker in SLE, as well as to determine the underlying mechanisms influencing platelet size in SLE.
Daily Rhythms of the Body and the Biological Clock

Earth’s rotation creates a cycle of day and night, which is observed as changes in light levels and temperature. During evolution, plants and animals adapted to these cycles, developing daily cycles of physical and behavioral processes that are driven by a central biological clock, also known as the circadian clock. Even in the absence of changes in light between day and night, the biological clock creates cycles called circadian rhythms. The nervous system transfers information about the external light level to the biological clock in the brain, which matches the clock’s cycle to the external environment. The biological clock prepares the body for environmental changes. The modern world has created disruptions in the circadian clock’s timing, because of electrical lighting, flights to other time zones, and work during the night. The study of chronobiology studies the mechanisms of the biological clock and the clock’s influence on human health.
Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks

Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.