Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes

Sex chromosomes have evolved independently many times across eukaryotes. Despite a considerable body of literature on the evolution of sex chromosomes, the causes and consequences of variation in the formation, degeneration, and turnover of sex chromosomes remain poorly understood. Comparative approaches in groups with sexual system variation can be valuable for understanding these questions. Plants are well-suited to such comparative studies, with many lineages containing relatively recent origins of dioecy and sex chromosomes as well as hermaphroditic close relatives. Rumex is a diverse genus of flowering plants harboring significant sexual system variation, including hermaphroditic and dioecious clades with XY sex chromosomes. Previous disagreement in the phylogenetic relationships among key species have rendered the history of sex chromosome evolution uncertain. Resolving this history is important to the development of Rumex as a system for the comparative study of sex chromosome evolution. Here, we leverage new transcriptome assemblies from 11 species representing the major clades in the genus, along with a whole-genome assembly generated for a pivotal hermaphroditic species, to further resolve the phylogeny and history of sex chromosome evolution in Rumex. Using phylogenomic approaches, we find evidence for two independent origins of sex chromosomes and introgression from unsampled taxa in the genus. Comparative genomics reveals massive chromosomal rearrangements in a dioecious species, with evidence for a complex origin of the sex chromosomes through multiple chromosomal fusions. However, we see no evidence of elevated rates of fusion on the sex chromosome in comparison with autosomes, providing no support for an adaptive hypothesis for the sex chromosome expansion. Overall, our results highlight the dynamic nature of sex chromosome systems in Rumex and illustrate the utility of the genus as a model for the comparative study of sex chromosome evolution.
Singer Identity Representation Learning Using Self-Supervised Techniques

Significant strides have been made in creating voice identity representations using speech data. However, the same level of progress has not been achieved for singing voices. To bridge this gap, we suggest a framework for training singer identity encoders to extract representations suitable for various singing-related tasks, such as singing voice similarity and synthesis. We explore different self-supervised learning techniques on a large collection of isolated vocal tracks and apply data augmentations during training to ensure that the representations are invariant to pitch and content variations. We evaluate the quality of the resulting representations on singer similarity and identification tasks across multiple datasets, with a particular emphasis on out-of-domain generalization. Our proposed framework produces high-quality embeddings that outperform both speaker verification and wav2vec 2.0 pre-trained baselines on singing voice while operating at 44.1 kHz. We release our code and trained models to facilitate further research on singing voice and related areas.
Weakly Supervised Multi-Pitch Estimation Using Cross-Version Alignment

Multi-pitch estimation (MPE), the task of detecting active pitches within a polyphonic music recording, has garnered signiﬁcant research interest in recent years. Most state-of-the-art approaches for MPE are based on deep networks trained using pitch annotations as targets. The success of current methods is therefore limited by the difﬁculty of obtaining large amounts of accurate annotations. In this paper, we propose a novel technique for learning MPE without any pitch annotations at all. Our approach exploits multiple recorded versions of a musical piece as surrogate targets. Given one version of a piece as input, we train a network to minimize the distance between its output and time–frequency representations of other versions of that piece. Since all versions are based on the same musical score, we hypothesize that the learned output corresponds to pitch estimates. To further ensure that this hypothesis holds, we incorporate domain knowledge about overtones and noise levels into the network. Overall, our method re-places strong pitch annotations with weaker and easier-to-obtain cross-version targets. In our experiments, we show that our proposed approach yields viable multi-pitch estimates and outperforms two baselines.
Spatiotemporal Variations in Hydroclimate across the Mediterranean Andes (30°–37°S) since the Early Twentieth Century

AbstractIn the Mediterranean Andes region (MA; 30°–37°S), the main rivers are largely fed by melting snowpack and provide freshwater to around 10 million people on both sides of the Andes Mountains. Water resources in the MA are under pressure because of the extensive development of industrial agriculture and mining activities. This pressure is increasing as the region faces one of its worst recorded droughts. Previous studies have pointed to El Nino–Southern Oscillation (ENSO) as the main climatic force impacting the MA. However, the role of decadal and multidecadal climate variability, their spatial patterns, and the recurrence of long-term droughts remains poorly studied. In an attempt to better understand these factors, spatial and temporal patterns of hydroclimatic variability are analyzed using an extensive database of streamflow, precipitation, and snowpack covering the period between 1910 and 2011. These analyses are based on the combination of correlation, principal components, and kernel estimat.
Investigating Sources of Elevated Lead in Drinking Water

x List of Abbreviations and Symbols Used . xi Acknowledgements . xii Chapter 1: Introduction . 1 1.1 Research Objectives . 3 1.2 Organization of Thesis . 3 Chapter 2: Background . 5 2.1 Principles of Corrosion . 5 2.2 Sources of Lead . 9 Chapter 3: Lead Monitoring Program . 19 3.
How Control and Transparency for Users Could Improve Artist Fairness in Music Recommender Systems

As streaming services have become a main channel for music consumption, they significantly impact various stakeholders: users, artists who provide music, and other professionals working in the music industry. Therefore, it is essential to consider all stakeholders’ goals and values when developing and evaluating the music recommender systems integrated into these services. One vital goal is treating artists fairly, thereby giving them a fair chance to have their music recommended and listened to, and subsequently building a fan base. Such artist fairness is often assumed to have a trade-off with user goals such as satisfaction. Using insights from two studies, this work shows the opposite: some goals from different stakeholders are complementary. Our first study, in which we interview music artists, demonstrates that they often see increased transparency and control for users as a means to also improve artist fairness. We expand with a second study asking other music industry professionals about these topics using a questionnaire. Its results indicate that transparency towards users is highly valued and should be increased.
The Montreal Cognitive Assessment: Normative Data from a Large, Population-Based Sample of Healthy Adults in China

Background: The Montreal Cognitive Assessment (MoCA) is a valuable tool for detecting cognitive impairment, but its accuracy is significantly influenced by demographic and socio-cultural factors. Consequently, the development of appropriate normative values becomes particularly crucial in ensuring its reliable use and interpretation. Objective: Generate MoCA normative values based on demographics for healthy chinese adults. Methods: The assessment conducted in this study utilizes the MoCA scale, specifically employing the Mandarin-8.1 version (Chinese Mandarin version). Based on the geographical distribution of administrative regions in mainland china, this study recruited a total of 3,097 healthy individuals aged over 20 years. Drawing on insights from prior normative studies, we performed multiple linear regression analysis, incorporating age, gender, and education level as predictor variables, to examine their associations with the total score and sub-cognitive domains of MoCA. Subsequently, we established normative values and cut-off values stratified by age and education level. Results: The participants in this study (n=3,097) exhibit a balanced gender distribution, with an average age of 54.46 years (SD 14.38) and an average education period of 9.49 years (SD 4.61). The study population demonstrates an average MoCA score of 23.25 points (SD 4.82). The findings from the multiple linear regression analysis indicate that the total score of MoCA is influenced by age and education level, collectively accounting for 46.8% of the total variance. Higher age and lower education level are correlated with lower MoCA total scores. Conclusion: This study offers normative MoCA values specific to the Chinese population. Furthermore, the research findings indicate that a score of 26 may not represent the most optimal cut-off value. When assessing MoCA scores, it is imperative to comprehensively account for the participants' age and educational background.
Lost in Space: Preference and Performance of Parnassius smintheus Feeding on Sedum lanceolatum and Rhodiola integrifolia

ABSTRACT. A variety of factors affect how much certain plants are eaten by herbivorous insects. In the eastern foothills of the Rocky Mountains of Alberta, Canada, Parnassius smintheus larvae have been described as virtually monophagous on Sedum lanceolatum, however a second host plant Rhodiola integrifolia is found in the region. We explore the differences in herbivory, larval performance, and oviposition between host plants. We also surveyed host plant abundance in the field to determine the amount of feeding damage on both species. In the lab, we found that there was no preference for feeding on S. lanceolatum versus R. integrifolia. The growth and survival of P. smintheus larvae also was not affected by the host plant. In the field we found much lower rates of herbivory on R. integrifolia than S. lanceolatum. We conclude that there are differences in herbivory observed in the field because P. smintheus larvae encounter R. integrifolia much less than S. lanceolatum. Possible mechanisms include the two host plants occurring in different microhabitats, P. smintheus females not ovipositing near R. integrifolia, or P. smintheus larvae not being able to detect R. integrifolia from a distance.
Effects of Mining and Hydropower on Metals in Surface Waters : Case: Nam Ngum

Author(s) Title Number of Pages Date Marko Kallio Effects of Mining and Hydropower on Metals in Surface Waters Case: Nam Ngum 75 pages + 10 pages of Appendices 11 April 2014 Degree Bachelor of Science Degree Programme Environmental Engineering Specialisation option Water Management Instructor(s) Juha Sarkkula, Supervisor Kaj Lindedahl, Senior Lecturer Nam Ngum, a river in Lao PDR, is experiencing rapid development of hydropower and mining. Hydropower dams may influence the water quality via sediment trapping and hydrology changes. They also create barriers for migration of aquatic animals. Mining, on the other hand, has potential severely impair water quality in their surroundings. Nam Ngum River Basin is located north of Vientiane. The watershed contains tropical and sub-tropical areas of distinct dry and wet seasons. The watershed is divided in mountainous Upper Nam Ngum (The area upstream from the dam Nam Ngum 1) and relatively flat Lower Nam Ngum in Vientiane Plains. Mining operations are largely located in the upper part of the watershed, with only a few mines located in the lower part. Mining operations usually impact surrounding water bodies. Acid Mine Drainage brings water of low pH and high metal content into streams. Runoff from the mining sites has high concentration of suspended solids. Because of the affiliation of metals to adhere to solid particles (instead of being in a soluble form) in the water column, sediment transport becomes a major factor in the distribution of mine related pollution of waters. Polluted sediments get transported into reservoirs where they may leach out into solution in anoxic, low pH conditions. Where water quality data is available (mostly in the Lower Nam Ngum), no sign of mining related pollution could be traced. The major mining sites are far upstream and beyond several reservoirs that trap contaminants. In the Nam Ngum, mining pollution seems to be therefore concentrated in the area where water quality data is not currently available. A water quality sampling programme is suggested which addresses the gaps of sampling network in the Nam Ngum. A set of 7 new networks, 10 existing ones and cooperation with mining and hydropower companies would create a monitoring network for efficient management of the water resource for all stakeholders. With recent developments in water quality monitoring and industrial development, Nam Ngum may have the potential to become a benchmark watershed of water resource management in south-east Asia.
Thermal properties of directionally oriented polymer fibrous materials as a function of fibre arrangement at mesoscopic level

Thermal properties of directionally oriented fibrous materials have been investigated in this research with the purpose of considering the influence of fibre arrangement at mesoscopic level. The range of various distributions of fibres in the fibrous materials was obtained by applying different twist intensity during spinning of cotton fibres. From various twisted cotton yarns the knitted fabrics were produced under controlled conditions, so as to obtain as similar as possible constructions. This made possible to obtain the heterogeneity of the porous fibrous structures coming from the mesoscopic level. Thermal conductivity and heat transfer coefficient of the materials were investigated. The results obtained indicate the arrangement of fibres (or their compactness, orientation and migration), which, in turn, was determined by twist intensity (mesoscopic scale), as the key factor influencing thermal properties. Yarn compactness and fibre migration, determined by lateral forces imposed by the twist inserted in yarn, affected variations in structural parameters of the knitted fabrics, and thus influenced their thermal properties. Fibre orientation manifested itself in surface geometry of the yarn was also proved to have a considerable influence on heat transfer properties.
Analysis of Ribonucleotide 5 ’-Triphosphate Analogs as Potential Inhibitors of Zika Virus 1 RNA-dependent RNA Polymerase Using Non-Radioactive Polymerase Assays 2 3

23 Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the 24 Americas and has been linked to the development of microcephaly and to a dramatically 25 increased number of Guillain-Barre Syndrome cases. Currently, no vaccine or therapeutic 26 options exist for the prevention or treatment of ZIKV infections. In this report, we have 27 expressed, purified and characterized full-length NS5 and the polymerase domain (NS5pol) of 28 ZIKV RNA-dependent RNA polymerase. Using purified NS5, we have developed an in vitro 29 non-radioactive primer extension assay employing a fluorescently labeled primer-template pair. 30 Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this 31 assay. Our results show that Mn is required for enzymatic activity while Mg is not. We found 32 that ZIKV NS5 can utilize ssDNA as a template or a primer, but not dsDNA, to synthesize RNA. 33 The assay was used to compare the efficiency of incorporation of analog 5’-triphosphates by the 34 ZIKV polymerase and to calculate their discrimination versus natural ribonucleotide 35 triphosphates (rNTPs). The IC50 values for analog rNTPs were determined in an alternative non36 radioactive coupled-enzyme assay. We determined that, in general, 2’-C-methyl and 2’-C37 ethynyl substituted analog 5’-triphosphates were efficiently incorporated by the ZIKV 38 polymerase and were also efficient chain terminators. Derivatives of these molecules may serve 39 as potential antiviral compounds to be developed to combat ZIKV infection. This report provides 40 the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase 41 assays in the identification of potential ZIKV inhibitors. 42 43 on Jauary 4, 2017 by U N IV O F C O LO R A D O httpaac.asm . rg/ D ow nladed fom
mi-Replacing ground corn with incremental amounts of liquid molasses does not change milk enterolactone but decreases production in dairy cows fed flaxseed meal

We investigated the effects of replacing ground corn (GRC) with incremental amounts of liquid molasses (LM) on milk enterolactone concentration, antioxidant enzymes activity in plasma, production, milk fatty acid (FA) profile, and nutrient utilization in Jersey cows fed flaxseed meal and low-starch diets. Sixteen multiparous organically certified Jersey cows averaging (mean ± standard deviation) 101 ± 45 d in milk, 462 ± 38 kg of body weight, and 19.8 ± 3.90 kg/d of milk in the beginning of the study were randomly assigned to treatment sequences in a replicated 4 × 4 Latin square design, with 14 d for diet adaptation and 7 d for data and sample collection. Diets were fed as total mixed rations consisting (dry matter basis) of 52% grass-legume bale-age, 8% grass hay, 8.5% soyhulls, 2.5% roasted soybean, 15% flaxseed meal, and 2% minerals-vitamins premix. The GRC-to-LM dietary ratios (dry matter basis) were 12:0, 8:4, 4:8, and 0:12. Orthogonal polynomials were used to test linear, quadratic, and cubic effects using the MIXED procedure of SAS (SAS Institute Inc., Cary, NC). The milk concentration of enterolac-tone tended to respond cubically, thus suggesting that replacing GRC with LM did not affect this lignan in milk. The plasma activities of the antioxidant enzymes glutathione peroxidase and catalase did not differ, but superoxide dismutase activity tended to respond cubi-cally with feeding increasing amounts of LM. Dry matter intake and yields of milk and milk fat, true protein, and lactose decreased linearly with substituting GRC for LM. Whereas the concentrations of milk fat and milk true protein did not differ across treatments, milk lactose content decreased linearly. Feeding incremental levels of LM reduced linearly the milk concentration of urea N and the amount of N excreted in urine, and tended to decrease linearly the concentration of plasma urea N. Apparent total-tract digestibilities of dry matter, organic matter, and neutral and acid detergent fiber did not differ across treatments, whereas digestibility of crude protein decreased linearly. Digestibility of starch responded linearly and quadratically, but the actual differences between treatments were too small to be biologically significant. Milk FA profile was substantially changed most notably by linear increases in cis -9, trans -11 18:2, cis -9, cis -12, cis -15 18:3, Σ odd-chain FA, and the trans -11-to- trans -10 ratio, and linear decreases in cis -9 18:1 and cis -9, cis -12 18:2 when replacing GRC by incremental amounts of LM.
Lighting up cancer aggressiveness: targeting the urokinase plasminogen activator receptor for intraoperative optical imaging

With a 5-year recurrence rate of 30-78%, urothelial cell carcinoma (UCC) rates amongst the highest of all solid malignancies. Consequently, after transurethral resection patients are subjugated to life-long endoscopic surveillance. A multimodal near-infrared (NIR) fluorescence based imaging strategy can improve diagnosis, resection, and surveillance, hence increasing quality of life. Methods & Results: Per immunohistochemistry, UCCs show prominent uPAR expression at the tumor-stroma interface and EpCAM on epithelial cells. uPAR and EpCAM are expressed by 6/7 and 4/7 UCC cell lines, respectively. In vitro, MNPR-101-IRDye800CW has a picomolar affinity for domain 2-3 of uPAR. In vivo fluorescence imaging with MNPR-101-IRDye800CW, specifically delineates both subcutaneous and orthotopic human UM-UC-3luc2 tumors with TBRs reaching as high as 6.8, differing significantly from the isotype controls Infliximab-IRDye800CW and Ritux - imab-IRDye800CW ( p < 0.0001). Photoacoustic 3D in depth imaging confirms the homogenous distribution of MNPR-101-IRDye800CW through the tumor. Conclusion: MNPR-101-IRDye800CW is suitable for multimodal imaging of UCC, awaiting clinical translation.
Digital Commons @ University of Digital Commons @ University of South Florida South Florida

Obesity is a major risk factor for osteoarthritis (OA). There is evidence that diabetes also increases risk. Our hypothesis is that A1C is a predictor of OA severity. The aim is to investigate the association between A1C, BMI, and knee and hip OA severity. This is a cross-sectional study within the Veterans Health Administration (VHA) database containing 818 patients with diagnosed diabetes. Patients at one VHA facility with recorded diabetes in fiscal year 2020 were identified. A1C and BMI data was obtained from the electronic health record. Chart reviews were performed to collect data on imaging reports of weight-bearing joints in order to assign an OA severity level. The exposure was BMI and A1C. The outcome was the presence and/or severity of OA in the record. Participants who used nicotine and/or were missing an A1C in the past 12 months, as well as those without weight-bearing imaging, were excluded. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated as a function of A1C and BMI with logistic regression analysis. 220 participants (white, non-Hispanic/Latino males, aged 55-64 years) with weight-bearing imaging were included. Participants with OA did not have a significantly different BMI or A1C than participants without OA. There was no association between BMI and OA severity (OR: 1.00, 95% CI: 0.94-1.07). There was a non-statistically significant inverse association between A1C and OA severity (OR: 0.92, 95% CI: 0.77-1.11). In diabetic patients, BMI does not seem to be predictive of OA severity, whereas better glucose control (lower A1C) is associated with increasing severity of OA, although this was not statistically significant. This is supported by literature that shows the pro-inflammatory nature of insulin and means that tight control of A1C could negatively impact OA. Future research should focus on treating patients with T2DM and OA with exercise and other therapies aimed at improving insulin resistance.
Contesting Community The Limits And Potential Of Local Organizing

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