Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational methods for the alignment and score-informed transcription of piano music

This thesis is concerned with computational methods for alignment and score-informed transcription of piano music. Firstly, several methods are proposed to improve the alignment robustness and accuracy when various versions of one piece of music show complex differences with respect to acoustic conditions or musical interpretation. Secondly, score to performance alignment is applied to enable score-informed transcription. Although music alignment methods have considerably improved in accuracy in recent years, the task remains challenging. The research in this thesis aims to improve the robustness for some cases where there are substantial differences between versions and state-of-the-art methods may fail in identifying a correct alignment. This thesis first exploits the availability of multiple versions of the piece to be aligned. By processing these jointly, the alignment process can be stabilised by exploiting additional examples of how a section might be interpreted or which acoustic conditions may arise. Two methods are proposed, progressive alignment and profile HMM, both adapted from the multiple biological sequence alignment task. Experiments demonstrate that these methods can indeed improve the alignment accuracy and robustness over comparable pairwise methods. Secondly, this thesis presents a score to performance alignment method that can improve the robustness in cases where some musical voices, such as the melody, are played asynchronously to others – a stylistic device used in musical expression. The asynchronies between the melody and the accompaniment are handled by treating the voices as separate timelines in a multi-dimensional variant of dynamic time warping (DTW). The method measurably improves the alignment accuracy for pieces with asynchronous voices and preserves the accuracy otherwise. Once an accurate alignment between a score and an audio recording is available, the score information can be exploited as prior knowledge in automatic music transcription (AMT), for scenarios where score is available, such as music tutoring. Score-informed dictionary learning is used to learn the spectral pattern of each pitch that describes the energy distribution of the associated notes in the recording. More precisely, the dictionary learning process in non-negative matrix factorization (NMF) is constrained using the aligned score. This way, by adapting the dictionary to a given recording, the proposed method improves the accuracy over the state-of-the-art.
Toward Intelligent Physical Design: Deep Learning and GPU Acceleration

Deep learning (DL) has achieved tremendous success in computer vision, natural language processing and gaming. Would DL help push physical design toward a more intelligent paradigm to meet the post-Moore era design automation challenges? We will discuss several supervised deep learning models and our works applying these models in physical design and related EDA domains. In addition to supervised learning, we will also illustrate that reinforcement learning and unsupervised learning with deep learning can be applied to design automation tasks. Furthermore, we will show the potential of GPU accelerated physical design with an example of placement engines implemented with deep learning frameworks such as TensorFlow and PyTorch. With deep learning and GPU accelerated algorithms, we could make physical design more intelligent.
High-revenue Online Provisioning for Virtual Clusters in Multi-tenant Cloud Data Center Network

The rapid development of cloud computing and high requirements of operators requires strong support from the underlying Data Center Networks. Therefore, the effectiveness of using resources in the data center networks becomes a point of concern for operators and material for research. In this paper, we discuss the online virtual-cluster provision problem for multiple tenants with an aim to decide when and where the virtual cluster should be placed in a data center network. Our objective is maximizing the total revenue for the data center networks under the constraints. In order to solve this problem, this paper divides it into two parts: online multi-tenancy scheduling and virtual cluster placement. The first part aims to determine the scheduling orders for the multiple tenants, and the second part aims to determine the locations of virtual machines. We first approach the problem by using the variational inequality model and discuss the existence of the optimal solution. After that, we prove that provisioning virtual clusters for a multi-tenant data center network that maximizes revenue is NP-hard. Due to the complexity of this problem, an efficient heuristic algorithm OMS (Online Multi-tenancy Scheduling) is proposed to solve the online multi-tenancy scheduling problem. We further explore the virtual cluster placement problem based on the OMS and propose a novel algorithm during the virtual machine placement. We evaluate our algorithms through a series of simulations, and the simulations results demonstrate that OMS can significantly increase the efficiency and total revenue for the data centers.
PSION+: Combining Logical Topology and Physical Layout Optimization for Wavelength-Routed ONoCs

Optical networks-on-chip (ONoCs) are a promising solution for high-performance multicore integration with better latency and bandwidth than traditional electrical NoCs. Wavelength-routed ONoCs (WRONoCs) offer yet additional performance guarantees. However, WRONoC design presents new EDA challenges which have not yet been fully addressed. So far, most topology analysis is abstract, i.e., overlooks layout concerns, while for layout the tools available perform place and route (P&R) but no topology optimization. Thus, a need arises for a novel optimization method combining both aspects of WRONoC design. In this article, such a method, PSION+, is laid out. This new procedure uses a linear programming model to optimize a WRONoC physical layout template to optimality. This template-based optimization scheme is a new idea in this area that seeks to minimize problem complexity while keeping design flexibility. A simple layout template format is introduced and explored. Finally, multiple model reduction techniques to reduce solver run-time are also presented and tested. When compared to the state-of-the-art design procedure, results show a decrease in maximum optical insertion loss of 41%.
The Play Your Process Method for Business Process-Based Digital Game Design

Serious games have been understood as a useful tool to engage, educate and train individuals in many areas. They are also suitable for the business processes management area where it is expected that business-process-based digital games can bring together players (process actors) to better understand and learn organizational business processes. This paper presents a game design method for the development of serious games which aims to provide business process understanding to players, as well as to allow them to reflect on process challenges and difficulties. The design of serious business process games requires game designers to have business process modeling skills and instructions on how to represent business process elements in the game context. This research was conducted using the Design Science Research Methodology, and addresses the challenge of providing a method for the design of serious business process games. The method receives business process models as input and comprises steps to (i) map business process elements into game design elements, game design and development, and (ii) evaluate games with game designers, process actors, and game players. In order to validate the method, a set of games was built and evaluated with players. The designed games were evaluated as to adequate quality, although fun and entertainment can still be improved, and players´ understanding regarding process increase after games are played
Analysis of the Localization of Fluorescent PpROP1 and PpROP-GEF4 Fusion Proteins in Moss Protonemata Based on Genomic “Knock-In” and Estradiol-Titratable Expression

Tip growth of pollen tubes, root hairs, and apical cells of moss protonemata is controlled by ROP (Rho of plants) GTPases, which were shown to accumulate at the apical plasma membrane of these cells. However, most ROP localization patterns reported in the literature are based on fluorescent protein tagging and need to be interpreted with caution, as ROP fusion proteins were generally overexpressed at undefined levels, in many cases without assessing effects on tip growth. ROP-GEFs, important regulators of ROP activity, were also described to accumulate at the apical plasma membrane during tip growth. However, to date only the localization of fluorescent ROP-GEF fusion proteins strongly overexpressed using highly active promoters have been investigated. Here, the intracellular distributions of fluorescent PpROP1 and PpROP-GEF4 fusion proteins expressed at essentially endogenous levels in apical cells of Physcomitrella patens “knock-in” protonemata were analyzed. Whereas PpROP-GEF4 was found to associate with a small apical plasma membrane domain, PpROP1 expression was below the detection limit. Estradiol-titratable expression of a fluorescent PpROP1 fusion protein at the lowest detectable level, at which plant development was only marginally affected, was therefore employed to show that PpROP1 also accumulates at the apical plasma membrane, although within a substantially larger domain. Interestingly, RNA-Seq data indicated that the majority of all genes active in protonemata are expressed at lower levels than PpROP1, suggesting that estradiol-titratable expression may represent an important alternative to “knock-in” based analysis of the intracellular distribution of fluorescent fusion proteins in protonemal cells.
Lactobacillus plantarum KLDS1.0318 Ameliorates Impaired Intestinal Immunity and Metabolic Disorders in Cyclophosphamide-Treated Mice

Cyclophosphamide (CTX), a clinically important antineoplastic drug, also leads to some side effects such as nausea, vomiting and diarrhea in the consumer. In this study, Lactobacillus plantarum (L. plantarum) KLDS1.0318 preserved in our laboratory was orally administered to CTX-treated mice to explore its potential effects to attenuate the toxic effects of CTX-induced by modulating intestinal immune response, promoting intestinal integrity and improving metabolic profile. BALB/c mice were randomly divided into six groups including normal control group (NC; non-CTX with sterile saline), model control group (MC; CTX-treated with sterile saline), CTX-treated with L. plantarum KLDS1.0318 (10 mL/kg) groups with three different doses (KLDS1.0318-L, 5 × 107 CFU/mL; KLDS1.0318-M, 5 × 108 CFU/mL; KLDS1.0318-H, 5 × 109 CFU/mL), and CTX-treated with levamisole hydrochloride (40 mg/kg) as a positive control (PC) group. After receiving the bacterium for 20 days, samples of small intestine and colonic contents were collected for different analyses. The results revealed that the levels of cytokines secreted by Th1 cells (IL-2, IFN-γ, and TNF-α) and Th2 cells (IL-4, IL-6, and IL-10) in probiotic treatment groups were significantly higher than those in the MC group. Histopathological results showed that L. plantarum KLDS1.0318 favorably recovered CTX-induced abnormal intestinal morphology by improving the villus height and crypt depth as well as quantity of goblet cells and mucins production. Compared to CTX alone-treated group, the production of short-chain fatty acids (SCFAs) were significantly increased and the levels of pH and ammonia were decreased significantly with high dose L. plantarum KLDS1.0318 supplementation. Compared with mice in CTX alone-treated group, mice in three groups of KLDS1.0318 had increased Bifidobacterium and Lactobacillus and decreased Escherichia and Enterococcus in their cecal content. The present findings suggested that L. plantarum KLDS1.0318 could be of significant advantage to mitigate the harmful effects of CTX and improve the intestinal health in mice.
STEM/Non-STEM Divide Structures Undergraduate Beliefs About Gender and Talent in Academia

Research and popular debate on female underrepresentation in academia has focused on STEM fields. But recent work has offered a unifying explanation for gender representation across the STEM/non-STEM divide. This proposed explanation, called the field-specific ability beliefs (FAB) hypothesis, postulates that, in combination with pervasive stereotypes that link men but not women with intellectual talent, academics perpetuate female underrepresentation by transmitting to students in earlier stages of education their beliefs about how much intellectual talent is required for success in each academic field. This theory was supported by a nationwide survey of U.S. academics that showed both STEM and non-STEM fields with fewer women are also the fields that academics believe require more brilliance. We test this top-down schema with a nationwide survey of U.S. undergraduates, assessing the extent to which undergraduate beliefs about talent in academia mirror those of academics. We find no evidence that academics transmit their beliefs to undergraduates. We also use a second survey “identical to the first but with each field's gender ratio provided as added information” to explicitly test the relationship between undergraduate beliefs about gender and talent in academia. The results for this second survey suggest that the extent to which undergraduates rate brilliance as essential to success in an academic field is highly sensitive to this added information for non-STEM fields, but not STEM fields. Overall, our study offers evidence that, contrary to FAB hypothesis, the STEM/non-STEM divide principally shapes undergraduate beliefs about both gender and talent in academia.
A Novel RNF139 Mutation in Hemangioblastomas: Case Report

Hemangioblastomas (HBs) are classified as grade I tumors with uncertain origin according to the World Health Organization's classification system. HBs are characterized by rich mesenchymal cells and abundant capillaries. It has been shown that tumorigenesis of HBs depends on mutational inactivation of Von Hippel-Lindau (VHL) tumor suppressor gene. Therefore, the majority of patients will undergo VHL single gene test, and sequencing scheme is rarely used in clinic. In this study, we described a girl and her father successively found to have HBs within half a year. The results of next-generation sequencing (NGS) and Sanger sequencing analysis showed that both of them carried heterozygous mutation of RNF139 p.Q650R. This mutation was interpreted as Pathogenic variation based on the American College of Medical Genetics and Genomics (ACMG) guideline. Sanger sequencing was performed with other family members. No mutation on rs118184842 locus of RNF139 gene was found in the samples from the girl's mother, uncle and aunt. This report supports that the novel mutation of RNF139 p.Q650R probably serve as a key role in HBs progression.
Postreperfusion Blood Pressure Variability After Endovascular Thrombectomy Affects Outcomes in Acute Ischemic Stroke Patients With Poor Collateral Circulation

Background and Purpose: We evaluated the effect of 24 h blood pressure variability (BPV) on clinical outcomes in acute ischemic stroke patients with successful recanalization after endovascular recanalization therapy (ERT). Methods: Patients with anterior circulation occlusion were evaluated if they underwent ERT based on multiphase computed tomography angiography and achieved successful recanalization (≥thrombolysis in cerebral ischemia 2b). Collateral degrees were dichotomized based on the pial arterial filling score, with a score of 0–3 defined as a poor collateral status. BPV parameters include mean, standard deviation, coefficient of variation, and variation independent of the mean (VIM) for systolic blood pressure (SBP), diastolic blood pressure (DBP), mean blood pressure, and pulse rate (PR). These parameters were measured for 24 h after ERT and were analyzed according to occlusion sites and stroke mechanisms. Associations of BPV parameters with clinical outcomes were investigated with stratification based on the baseline collateral status. Results: BPV was significantly different according to the occlusion sites and stroke mechanisms, and higher BPV was observed in patients with internal carotid artery occlusion or cardioembolic occlusion. After adjustment for confounders, most BPV parameters remained significant to predict functional outcomes at 3 months in patients with poor collateral circulation. However, no significant association was found between BPV parameters and clinical outcomes in patients with good collateral circulation. Conclusion: Postreperfusion BP management by decreasing BPV may have influence on improving clinical outcome in cases of poor collateral circulation among patients achieving successful recanalization after ERT.
Computational Studies on the Potency and Selectivity of PUGNAc Derivatives Against GH3, GH20, and GH84 β-N-acetyl-D-hexosaminidases

β-N-acetyl-D-hexosaminidases have attracted significant attention due to their crucial role in diverse physiological functions including antibacterial synergists, pathogen defense, virus infection, lysosomal storage, and protein glycosylation. In particular, the GH3 β-N-acetyl-D-hexosaminidase of V. cholerae (VcNagZ), human GH20 β-N-acetyl-D-hexosaminidase B (HsHexB), and human GH84 β-N-acetyl-D-hexosaminidase (hOGA) are three important representative glycosidases. These have been found to be implicated in β-lactam resistance (VcNagZ), lysosomal storage disorders (HsHexB) and Alzheimer's disease (hOGA). Considering the profound effects of these three enzymes, many small molecule inhibitors with good potency and selectivity have been reported to regulate the corresponding physiological functions. In this paper, the best-known inhibitors PUGNAc and two of its derivatives (N-valeryl-PUGNAc and EtBuPUG) were selected as model compounds and docked into the active pockets of VcNagZ, HsHexB, and hOGA, respectively. Subsequently, molecular dynamics simulations of the nine systems were performed to systematically compare their binding modes from active pocket architecture and individual interactions. Furthermore, the binding free energy and free energy decomposition are calculated using the MM/GBSA methods to predict the binding affinities of enzyme-inhibitor systems and to quantitatively analyze the contribution of each residue. The results show that PUGNAc is deeply-buried in the active pockets of all three enzymes, which indicates its potency (but not selectivity) against VcNagZ, HsHexB, and hOGA. However, EtBuPUG, bearing branched 2-isobutamido, adopted strained conformations and was only located in the active pocket of VcNagZ. It has completely moved out of the pocket of HsHexB and lacks interactions with HsHexB. This indicates why the selectivity of EtBuPUG to VcNagZ/HsHexB is the largest, reaching 968-fold. In addition, the contributions of the catalytic residue Asp253 (VcNagZ), Asp254 (VcNagZ), Asp175 (hOGA), and Asp354 (HsHexB) are important to distinguish the activity and selectivity of these inhibitors. The results of this study provide a helpful structural guideline to promote the development of novel and selective inhibitors against specific β-N-acetyl-D-hexosaminidases.
Coronal Loop Seismology Using Standing Kink Oscillations With a Lookup Table

The transverse structure of coronal loops plays a key role in the physics but the small transverse scales can be difficult to observe directly. For wider loops the density profile may be estimated by forward modelling of the transverse intensity profile. The transverse density profile may also be estimated seismologically using kink oscillations in coronal loops. The strong damping of kink oscillations is attributed to resonant absorption and the damping profile contains information about the transverse structure of the loop. However, the analytical descriptions for damping by resonant absorption presently only describe the behaviour for thin inhomogeneous layers. Previous numerical studies have demonstrated that this thin boundary approximation produces poor estimates of the damping behaviour in loops with wider inhomogeneous layers. Both the seismological and forward modelling approaches suggest loops have a range of layer widths and so there is a need for a description of the damping behaviour that accurately describes such loops. We perform a parametric study of the damping of standing kink oscillations by resonant absorption for a wide range of inhomogeneous layer widths and density contrast ratios, with a focus on the values most relevant to observational cases. We describe the damping profile produced by our numerical simulations without prior assumption of its shape and compile our results into a lookup table which may be used to produce accurate seismological estimates for kink oscillation observations.
Mitochondrial DNA Damage Does Not Determine C. elegans Lifespan

The mitochondrial free radical theory of aging (mFRTA) proposes that accumulation of oxidative damage to macromolecules in mitochondria is a causative mechanism for aging. Accumulation of mitochondrial DNA (mtDNA) damage may be of particular interest in this context. While there is evidence for age-dependent accumulation of mtDNA damage, there have been only a limited number of investigations into mtDNA damage as a determinant of longevity. This lack of quantitative data regarding mtDNA damage is predominantly due to a lack of reliable assays to measure mtDNA damage. Here, we report adaptation of a quantitative real-time polymerase chain reaction (qRT-PCR) assay for the detection of sequence-specific mtDNA damage in C. elegans and apply this method to investigate the role of mtDNA damage in the aging of nematodes. We compare damage levels in old and young animals and also between wild-type animals and long-lived mutant strains or strains with modifications in ROS detoxification or production rates. We confirm an age-dependent increase in mtDNA damage levels in C. elegans but found that there is no simple relationship between mtDNA damage and lifespan. MtDNA damage levels were high in some mutants with long lifespan (and vice versa). We next investigated mtDNA damage, lifespan and healthspan effects in nematode subjected to exogenously elevated damage (UV- or γ-radiation induced). We, again, observed a complex relationship between damage and lifespan in such animals. Despite causing a significant elevation in mtDNA damage, γ-radiation did not shorten the lifespan of nematodes at any of the doses tested. When mtDNA damage levels were elevated significantly using UV-radiation, nematodes did suffer from shorter lifespan at the higher end of exposure tested. However, surprisingly, we also found hormetic lifespan and healthspan benefits in nematodes treated with intermediate doses of UV-radiation, despite the fact that mtDNA damage in these animals was also significantly elevated. Our results suggest that within a wide physiological range, the level of mtDNA damage does not control lifespan in C. elegans.