Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Sample Detection in Polyphonic Music

The term ‘sampling’ refers to the usage of snippets or loops from existing songs or sample libraries in new songs, mashups, or other music productions. The ability to automatically detect sampling in music is, for instance, beneﬁ-cial for studies tracking artist inﬂuences geographically and temporally. We present a method based on Non-negative Matrix Factorization (NMF) and Dynamic Time Warping (DTW) for the automatic detection of a sample in a pool of songs. The method comprises of two processing steps: ﬁrst, the DTW alignment path between NMF activations of a song and query sample is computed. Second, features are extracted from this path and used to train a Random Forest classiﬁer to detect the presence of the sample. The method is able to identify samples that are pitch shifted and/or time stretched with approximately 63% F-measure. We evaluate this method against a new publicly available dataset of real-world sample and song pairs.
Early genetic aberrations in patients with sporadic colorectal cancer

Chromosome instability (CIN) is widely observed in both sporadic and hereditary colorectal cancer (CRC). Defects in APC and WNT signaling are primarily associated with CIN in hereditary CRC, but the genetic causes for CIN in sporadic CRC remain elusive. Using high‐density SNP array and exome data from The Cancer Genome Atlas (TCGA), we characterized loss of heterozygosity (LOH) and copy number variation (CNV) in the peripheral blood, normal colon, and corresponding tumor tissue in 15 CRC patients with proficient mismatch repair (MMR) and 24 CRC patients with deficient MMR. We found a high frequency of 18q LOH in tumors and arm‐specific enrichment of genetic aberrations on 18q in the normal colon (primarily copy neutral LOH) and blood (primarily copy gain). These aberrations were specific to the sporadic, pMMR CRC. Though in tumor samples genetic aberrations were observed for genes commonly mutated in hereditary CRC (eg, APC, CTNNB1, SMAD4, BRAF), none of them showed LOH or CNV in the normal colon or blood. DCC located on 18q21.1 topped the list of genes with genetic aberrations in the tumor. In an independent cohort of 13 patients subjected to Whole Genome Sequencing (WGS), we found LOH and CNV on 18q in adenomatous polyp and tumor tissues. Our data suggests that patients with sporadic CRC may have genetic aberrations preferentially enriched on 18q in their blood, normal colon epithelium, and non‐malignant polyp lesions that may prove useful as a clinical marker for sporadic CRC detection and risk assessment.
Developmental history and application of CRISPR in human disease

Genome‐editing tools are programmable artificial nucleases, mainly including zinc‐finger nucleases, transcription activator‐like effector nucleases and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome‐editing tools make it possible to generate site‐specific DNA double‐strand breaks (DSBs) in the genome. DSBs will then be repaired by either error‐prone nonhomologous end joining or high‐fidelity homologous recombination mechanisms. Through these two different mechanisms, endogenous genes can be knocked out or precisely repaired/modified. Rapid developments in genome‐editing tools, especially CRISPR, have revolutionized human disease models generation, for example, various zebrafish, mouse, rat, pig, monkey and human cell lines have been constructed. Here, we review the developmental history of CRISPR and its application in studies of human diseases. In addition, we also briefly discussed the therapeutic application of CRISPR in the near future.
Integrated miRNA and mRNA Expression Profiling in Inflamed Colon of Patients with Ulcerative Colitis

Background Ulcerative colitis (UC) is associated with differential colonic expression of genes involved in immune response (e.g. IL8) and barrier integrity (e.g. cadherins). MicroRNAs (miRNAs) are regulators of gene expression and are involved in various immune-related diseases. In this study, we investigated (1) if miRNA expression in UC mucosa is altered and (2) if any of these changes correlate with mucosal mRNA expression. Integration of mRNA and miRNA expression profiling may allow the identification of functional links between dysregulated miRNAs and their target mRNA. Methodology Colonic mucosal biopsies were obtained from 17 UC (10 active and 7 inactive) patients and 10 normal controls. Total RNA was used to analyze miRNA and mRNA expression via Affymetrix miRNA 2.0 and Affymetrix Human Gene 1.0ST arrays, respectively. Both miRNA and gene expression profiles were integrated by correlation analysis to identify dysregulated miRNAs with their corresponding predicted target mRNA. Microarray data were validated with qRT-PCR. Regulation of IL8 and CDH11 expression by hsa-miR-200c-3p was determined by luciferase reporter assays. Results When comparing active UC patients vs. controls, 51 miRNAs and 1543 gene probe sets gave significantly different signals. In contrast, in inactive UC vs. controls, no significant miRNA expression differences were found while 155 gene probe sets had significantly different signals. We then identified potential target genes of the significantly dysregulated miRNAs and genes in active UC vs. controls and found a highly significant inverse correlation between hsa-miR-200c-3p and IL8, an inflammatory marker, and between hsa-miR-200c-3p and CDH11, a gene related to intestinal epithelial barrier function. We could demonstrate that hsa-miR-200c-3p directly regulates IL8 and CDH11 expression. Conclusion Differential expression of immune- and barrier-related genes in inflamed UC mucosa may be influenced by altered expression of miRNAs. Integrated analysis of miRNA and mRNA expression profiles revealed hsa-miR-200c-3p for use of miRNA mimics as therapeutics.
Conducting Biobehavioral Research in Patients With Advanced Cancer: Recruitment Challenges and Solutions

Despite significant advances in cancer treatment and symptom management interventions over the last decade, patients continue to struggle with cancer-related symptoms. Adequate baseline and longitudinal data are crucial for designing interventions to improve patient quality of life and reduce symptom burden; however, recruitment of patients with advanced cancer in longitudinal research is difficult. Our purpose is to describe challenges and solutions to recruitment of patients with advanced cancer in two biobehavioral research studies examining cancer-related symptoms. Study 1: Symptom data and peripheral blood for markers of inflammation were collected from newly diagnosed patients receiving chemotherapy on the first day of therapy and every 3–4 weeks for up to 6 months. Study 2: Symptom data, blood, and skin biopsies were collected from cancer patients taking epidermal growth factor receptor inhibitors at specific time points over 4 months. Screening and recruitment results for both studies are summarized. Timing informed consent with baseline data collection prior to treatment initiation was a significant recruitment challenge for both the studies. Possible solutions include tailoring recruitment to fit clinic needs, increasing research staff availability during clinic hours, and adding recruitment sites. Identifying solutions to these challenges will permit the conduct of studies that may lead to identification of factors contributing to variability in symptoms and development of tailored patient interventions for patients with advanced cancer.
Improvement of the Melting Reaction in Sintering Process by the Fine Part Selective Granulation of Clayish Iron Ores

Synopsis In order to clarify the melting reaction of iron ores with limestone fines, the melt formation process was directly observed. Single particle firing tests and small packed bed firing tests were carried out for evaluating the sintering performance of sinter mix pseudo-particles. It was made clear from the direct observation of melt formation that the melting behavior of solid phases formed from primary melt is important to improve the coalescence of sinter mix pseudo-particles. The iron ores containing quartzite ("quartz-rich iron ore") are easier in forming the melt than the ores containing much clay minerals ("clayish iron ore"). The pseudo-particle using fine clayish iron ores as the adhering part was strong both before and after firing. The results of a small packed bed sintering test showed that segregation of limestone in sinter mix is effective in forming the melt. The increase in limestone concentration of quartz-rich iron are fines which are adhering to a coarse nucleus particle is the most effective for coalescing pseudo-particles and for making a desirable pore network during sintering. On the basis of these results, the "fine part selective granulation method of clayish iron ores" was newly proposed to improve the sintering performance of iron ores.
Biochemical basis for the age-related sensitivity of broilers to aflatoxin B1

Abstract In this study, we investigated the mechanism underlying age-related susceptibility in broilers to aflatoxin B1 (AFB1). The results showed that AFB1 induced significant changes in serum alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transferase (GGT) activity & liver superoxide dismutase (SOD), malonaldehyde (MDA), glutathione peroxidase (GSH-Px) and glutathione S-transferase (GST) activity at day 7, 21 and 42 relative to control group. However, AFB1-induced changes in serum biochemical parameters and liver antioxidant activities become less severe with increasing age of broilers. Particularly, liver cytosolic GST activity increases with the age of broilers, crucial for the detoxification of AFB1. The mRNA expression level of Cytochrome P450 (CYP) enzymes was significantly higher at day 7, and decreases at day 21 and 42. While, the mRNA expression level of liver GSTA3, GSTA4 and EPHX1 increases with age of broilers. Maximum AFB1 residues level was detected at day 42 relative to day 7 and 21. While, AFM1 residues level increases (p < 0.05) from day 7 to 21, but decreases (p > 0.05) at day 42. Most importantly, our data confirmed the efficient AFB1-bioactivation by CYP enzymes and deficient detoxification of GST enzymes at younger age (∼7-day old) compared to older age. In summary, the age-related changes particularly in phase-I and phase-II enzymes mainly responsible for AFB1 bioactivation and detoxification may be partially accountable for the increased susceptibility of younger broilers (∼7-day old) compared to older broilers.
Faecal calprotectin detects subclinical bowel inflammation and may predict treatment response in spondyloarthritis

Objective: Intestinal inflammation is frequent in patients with spondyloarthritis (SpA). Here, we test the validity of faecal calprotectin as a marker of intestinal inflammation in SpA patients and evaluate the response of adalimumab in patients with and without intestinal lesions. Method: Patients were included on the basis of active SpA with a Bath Ankylosing Spondylitis Disease Activity Index ≥ 4. After a 4 week non-steroidal anti-inflammatory drug washout period, patients were divided into two groups based on faecal calprotectin level (> 100 mg/kg, n = 15, and < 50 mg/kg, n = 15). Adalimumab 40 mg every other week was initiated. Patients with calprotectin >100 mg/kg received an additional 40 mg of adalimumab at baseline. Patients were followed with clinical examination at weeks 12, 20, and 52; magnetic resonance imaging (MRI) at weeks 0, 20, and 52; and endoscopy at weeks 0 and 20. Results: The groups were similar with regard to clinical disease activity measures at baseline. Faecal calprotectin above 100 mg/kg accurately identified patients with intestinal inflammation. Twelve of the 15 patients with elevated calprotectin had bowel lesions, compared to only one patient in the control group. On MRI, the group with elevated calprotectin had more inflammation in the sacroiliac joints. Finally, the group with intestinal inflammation had a better clinical response to adalimumab, as evaluated by the Ankylosing Spondylitis Disease Activity Score. Conclusion: Elevated faecal calprotectin accurately identified SpA patients with bowel inflammation and more inflammation on MRI. Elevated faecal calprotectin at baseline may predict a better treatment response.
Child and family characteristics moderate agreement between caregiver and clinician report of autism symptoms

Rates of autism spectrum disorder (ASD) and age at first diagnosis vary considerably across the United States and are moderated by children's sex, race, ethnicity, and availability of services. We additionally suggest that degree of caregiver–clinician agreement on ASD symptoms may play a role in ASD assessment. Since gold standard ASD assessment integrates caregiver‐reported developmental history with clinician observations, differential agreement between reporters across demographic groups may contribute to a host of detrimental outcomes. Here, we investigate whether caregiver–clinician agreement on ASD symptoms varies according to child and family characteristics. Comprehensive data from 2,759 families in the Simons Simplex Collection were analyzed. Linear models were created with caregiver reports predicting clinician reports, and moderating effects of child characteristics and family factors were examined. Poorer reporter correspondence was observed when children had higher IQ scores, stronger adaptive behavior, and more behavioral difficulties. Greater disagreement was also associated with African American racial status (for younger children), lower household income, and paternal social difficulties (for older children). Children's biological sex did not moderate caregiver–clinician agreement. Marked disagreement between caregivers and clinicians could lead to suboptimal or insufficient intervention services and negative experiences for families throughout development. Such families may also be less likely to qualify for research studies, and therefore be underrepresented in the ASD literature. Modified assessment procedures may be required to improve assessment accuracy and family experiences. Autism Res 2018, 11: 476–487. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
Effects of the NK1 antagonist, aprepitant, on response to oral and intranasal oxycodone in prescription opioid abusers

Pre‐clinical studies suggest that the neurokinin‐1 (NK1) receptor may modulate the response to opioids, with NK1 inactivation leading to decreased opioid reinforcement, tolerance and withdrawal. Aprepitant is a selective NK1 antagonist currently marketed for clinical use as an anti‐emetic. This 6‐week in‐patient study used a randomized, double‐blind, double‐dummy, within‐subject, crossover design. Subjects (n = 8; 6 male/2 female) were healthy, adult volunteers who provided subjective and objective evidence of current prescription opioid abuse (without physical dependence) and underwent careful medical and psychiatric screening. Fifteen experimental conditions, consisting of one aprepitant dose (0, 40 and 200 mg, p.o. given as a 2‐hour pre‐treatment) in combination with one oxycodone dose [placebo, oral (20 and 40 mg/70 kg) and intranasal (15 and 30 mg/70 kg)], were examined. Sessions were conducted at least 48‐hour apart and multi‐dimensional measures were collected repeatedly throughout the 6‐hour session duration. Oxycodone, by both routes of administration, produced significant dose‐related effects on the predicted measures (e.g. subjective measures of abuse liability, respiratory depression and miosis). Pre‐treatment with aprepitant (200 mg) significantly enhanced ratings of oxycodone subjective effects related to euphoria and liking and doubled the street value estimates for the highest test doses of oxycodone by both routes. Some objective measures (respiratory function, observer‐rated opioid agonist effects) were similarly enhanced by pre‐treatment with the highest dose of aprepitant. All dose combinations were safely tolerated. These findings are discussed in the context of the potential utility of NK1 antagonists in the treatment of opioid use disorders.
Physical activity, sedentary behaviour and energy balance in the preschool child: opportunities for early obesity prevention

Prevalence of obesity in preschool children has increased dramatically in recent years. The preschool years (age 3–6 years) have been regarded as critical for the programming of energy balance, via the concept of early ‘adiposity rebound’. Children who undergo early adiposity rebound are at increased risk of later obesity. Recent evidence suggests that associations between timing of adiposity rebound and later obesity may not reflect programming, but might denote that ‘obesogenic’ growth trajectories are often established by the preschool period. Studies of objectively-measured physical activity and sedentary behaviour in preschool children show that levels of physical activity are typically low and sedentary behaviour high. The review of evidence presented here is supportive of the hypothesis that physical activity is protective against obesity in the preschool period, and that sedentary behaviour, particularly television viewing, is obesogenic. Definitive evidence on dose–response relationships between physical activity, sedentary behaviour and obesity remain unclear. Dose–response evidence could be obtained fairly readily by intervention and longitudinal observational studies that use accelerometry in preschool children. The generalisability of much of the evidence base is limited and there is a need for research on the influence of physical activity and sedentary behaviour in the preschool years in the aetiology of obesity in the developing world.
Beam focal spot position: The forgotten linac QA parameter. An EPID‐based phantomless method for routine Stereotactic linac QA

Abstract Modern day Stereotactic treatments require high geometric accuracy of the delivered treatment. To achieve the required accuracy the IGRT imaging isocenter needs to closely coincide with the treatment beam isocenter. An influence on this isocenter coincidence and on the spatial positioning of the beam itself is the alignment of the treatment beam focal spot with collimator rotation axis. The positioning of the focal spot is dependent on the linac beam steering and on the stability of the monitor chamber and beam steering servo system. As such, there is the potential for focal spot misalignment and this should be checked on a regular basis. Traditional methods for measuring focal spot position are either indirect, inaccurate, or time consuming and hence impractical for routine use. In this study a novel, phantomless method has been developed using the EPID (Electronic Portal Imaging Device) that utilizes the different heights of the MLC and jaws. The method has been performed on four linear accelerators and benchmarked against an alternate ion chamber‐based method. The method has been found to be reproducible to within ±0.012 mm (1 SD) and in agreement with the ion chamber‐based method to within 0.001 ± 0.015 mm (1 SD). The method could easily be incorporated into a departmental routine linac QA (Quality Assurance) program.
AN OVERVIEW OF MOISTURE DAMAGE PERFORMANCE TESTS ON ASPHALT MIXTURES

This paper presents a review of moisture damage performance tests on asphalt mixtures. The moisture damage remains to be a detriment to the durability of the Hot Mix Asphalt (HMA) pavement. Moisture damage can be defined in forms of adhesive failure between bitumen and aggregates and cohesive failure within bitumen. Aggregate mineralogy, bitumen characteristics and anti-stripping additive dominantly influence the performance of asphalt mixtures towards moisture damage alongside construction methods, climate and traffic loading. Various laboratory test methods have been developed to quantify the moisture damage performance of asphalt mixtures by resembles the action in the field, including qualitative test such as Boiling Water Test (ASTM D3625) and quantitative tests such as Modified Lottman Test (AASHTO T283). Both of these tests consist of two phases, which are conditioning and evaluation phase. This paper will review the effectiveness of the selected available tests based on various asphalt mixtures materials. Generally, this study indicates that asphalt mixtures consisted of limestone aggregates, modified bitumen and addition of anti-stripping additives will provide more resistant towards moisture damage.
Latent Transforming Growth Factor β Binding Protein 2 (LTBP2) as a Novel Biomarker for the Diagnosis and Prognosis of Pancreatic Carcinoma

Background Latent transforming growth factor β binding protein 2 (LTBP2) is proven to be associated with ECM and involved in the advancement of several kinds of cancer. The present study evaluated the diagnosis and prognosis of pancreatic carcinoma (PC) using LTBP2 as a biomarker. Material/Methods Protein levels of LTBP2 were evaluated in 111 pairs of pancreatic ductal adenocarcinoma (PDAC) tissues and adjacent nontumor tissues via immunohistochemistry. ELISA method was used to quantify the serum concentration of LTBP2. The subjects in this study included 141 PDAC patients, 20 patients with benign pancreatic disease, and 20 healthy volunteers. Results IHC results showed that LTBP2 levels were significantly elevated in the PDAC tissues as compared with the adjacent nontumor tissues (P<0.05). Sixty-one of the 111 (54.9%) PDAC tissues showed high expression of the protein. LTBP2 overexpression was significantly correlated with poor differentiation (P=0.018) and advanced TNM stage (P=0.036). Moreover, Kaplan-Meier analysis showed that high levels of LTBP2 predicted worse overall survival (P=0.001) and disease-free survival (P=0.001). Multivariate Cox regression analysis indicated that high expression of LTBP2 was an autonomous prognostic factor for poor overall and disease-free survival (P=0.001; P=0.002). Receiver operating characteristic (ROC) curve analyses of showed that LTBP-2 had an area under the curve (AUC) of 0.846 (95% confidence intervals: 0.757–0.934) and cut-off value of 19.12. Conclusions LTBP2 is a novel biomarker for the diagnosis of PC and may be a potential target for PDAC clinical therapy.