Miracle-dz/UniFAR-FTUs huggingface dataset:
Breeding-Season Sympatry Facilitates Genetic Exchange Among Allopatric Wintering Populations of Northern Pintails in Japan and California

Abstract. The global redistribution of pathogens, such as highly pathogenic avian influenza, has renewed interest in the connectivity of continental populations of birds. Populations of the Northern Pintail (Anas acuta) wintering in Japan and California are considered separate from a management perspective. We used data from band recoveries and population genetics to assess the degree of biological independence of these wintering populations. Distributions of recoveries in Russia of Northern Pintails originally banded during winter in North America overlapped with distributions of Northern Pintails banded during winter in Japan. Thus these allopatric wintering populations are partially sympatric during the breeding season. The primary areas of overlap were along the Chukotka and Kamchatka peninsulas in Russia. Furthermore, band recoveries demonstrated dispersal of individuals between wintering populations both from North America to Japan and vice versa. Genetic analyses of samples from both wintering populations showed little evidence of population differentiation. The combination of banding and genetic markers demonstrates that these two continental populations are linked by low levels of dispersal as well as likely interbreeding in eastern Russia. Although the levels of dispersal are inconsequential for population dynamics, the combination of dispersal and interbreeding represents a viable pathway for exchange of genes, diseases, and/or parasites.
In vivo base editing restores sensory transduction and transiently improves auditory function in a mouse model of recessive deafness

Base editing in postnatal mice repairs a recessive hearing loss mutation, rescues sensory transduction, and transiently restores auditory function. At the base of deafness Mutations in the transmembrane channel-like 1 (TMC1) gene can cause hereditary hearing loss. Current treatments do not target the cause of the disease, focusing mainly on sound amplification. Here, Yeh et al. used base editing methods to treat a mouse model of genetic deafness caused by a point mutation in Tmc1. The authors included a cytosine base editor into a dual–adeno-associated virus (AAV) system and injected it into the inner ear of the animals with hearing loss. The treatment reversed the mutation, improved sensory transduction, and partially restored hearing in mice. These results suggest that base editing might be effective for rescuing recessive genetic hearing loss. Most genetic diseases arise from recessive point mutations that require correction, rather than disruption, of the pathogenic allele to benefit patients. Base editing has the potential to directly repair point mutations and provide therapeutic restoration of gene function. Mutations of transmembrane channel-like 1 gene (TMC1) can cause dominant or recessive deafness. We developed a base editing strategy to treat Baringo mice, which carry a recessive, loss-of-function point mutation (c.A545G; resulting in the substitution p.Y182C) in Tmc1 that causes deafness. Tmc1 encodes a protein that forms mechanosensitive ion channels in sensory hair cells of the inner ear and is required for normal auditory function. We found that sensory hair cells of Baringo mice have a complete loss of auditory sensory transduction. To repair the mutation, we tested several optimized cytosine base editors (CBEmax variants) and guide RNAs in Baringo mouse embryonic fibroblasts. We packaged the most promising CBE, derived from an activation-induced cytidine deaminase (AID), into dual adeno-associated viruses (AAVs) using a split-intein delivery system. The dual AID-CBEmax AAVs were injected into the inner ears of Baringo mice at postnatal day 1. Injected mice showed up to 51% reversion of the Tmc1 c.A545G point mutation to wild-type sequence (c.A545A) in Tmc1 transcripts. Repair of Tmc1 in vivo restored inner hair cell sensory transduction and hair cell morphology and transiently rescued low-frequency hearing 4 weeks after injection. These findings provide a foundation for a potential one-time treatment for recessive hearing loss and support further development of base editing to correct pathogenic point mutations.
Association of apolipoprotein E (RFLP) polymorphism with myopia

BACKGROUND: Myopia or nearsightedness is a spherical error of refraction, whereby the images are focused in front of retina. Eye, being an organ rich in activated oxygen species, requires a high level of antioxidants to protect the unsaturated fatty acids. Apolipoprotein E (APOE) is one of the proteins that is produced by Muller cells within the retina and is also endowed with antioxidant properties. Genetic polymorphism of APO E is controlled by three common alleles e3, e2 and e4 and rare e1, e4v at the APOE structural gene locus. Different isoforms of APO E differ in their antioxidant properties, and the e4 allele has lesser ability to combat oxidative stress. AIMS: Myopia being a disease influenced by oxidative stress, the present study was undertaken to find association of myopia with APO E polymorphism. MATERIALS AND METHODS: A total of 187 myopic cases and 192 controls were genotyped for apolipoprotein E polymorphism. RESULTS: In both controls and myopic cases, E3/3 genotype was found to be the most frequent one. There was an increase in E3/4 genotype frequency among male probands, high myopia cases and probands with early age at onset, suggesting that the E3/4 genotype might confer risk for myopia development. CONCLUSION: This association with E3/4 genotype might predispose susceptible individuals to develop high myopia and early onset myopia.
Extensive In Silico Analysis of the Functional and Structural Consequences of SNPs in Human ARX Gene

Early infantile epileptic encephalopathy 1 (EIEE1) is a rare but devastating neurologic disorder that displays concomitant cognitive and motor impairment, and is often presented in the first months of life with severe intellectual disability. The objective of this study is to classify the most deleterious nsSNPs in ARX gene that may cause EIEE1 disease. Despite the reported association of ARX gene mutations with vulnerability to several neurologic condition, there is lack of in silico analysis on the functional and structural impacts of single nucleotide polymorphisms (SNPs) of the ARX at protein level. Therefore, the pathogenic nsSNPs in the human ARX obtained from NCBI were analyzed for their functional and structural impact using bioinformatics tools like SIFT, Polyphen, PROVEAN, I-Mutant, and MUPro. The effects of the mutations on tertiary structure of the human ARX protein were predicted using RaptorX and visualized by UCSF Chimera while STRING was used to investigate its protein–protein interaction. Our extensive in silico analysis revealed 11 mutations that will significantly alter the structure of human ARX protein; that may disturb the domain which will affect the function of the protein. Extensive in silico analysis of the functional and structural consequences of SNPs in human ARX gene revealed 11 mutations (L535Q, R528S, R380L, V374D, L343Q, T333N, T333S, R332H, R330H, G34R and L33P) that may cause EIEE1.Therefore, can be used as diagnostic markers for EIEE1.
Keyword Extraction using Term-Domain Interdependence for Dictation of Radio News

In this paper, we propose keyword extraction method for dictation of radio news which consists of several domains. In our method, newspaper articles which are automatically classified into suitable domains are used in order to calculate feature vectors. The feature vectors shows term-domain interdependence and are used for selecting a suitable domain of each part of radio news.
Influence of supplemental Schisandra chinensis powder on growth performance, serum cholesterol, and meat quality of broilers

Abstract We assessed the effects of broiler diets (n = 45 birds/treatment) with Schisandra chinensis powder on growth performance, serum cholesterol, and meat quality over a 35-d feeding period. Dietary treatments included 0%; 0.05% antibiotics; and 0.5%, 1%, and 2% S. chinensis powder. No significant differences were found in growth performance, crude ash, carcass weight and ratio or spleen weights, high-density lipoprotein (HDL) cholesterol, and b* (yellowness) values among treatments. Moisture, crude protein, and crude fat contents in chicken thigh meat differed among all treatments. Compared to other treatments, increasing S. chinensis levels induced lowering of the liver and abdominal fat weights, total cholesterol and low-density lipoprotein (LDL)-cholesterol levels or pH, Thiobarbituric acid reactive substances (TBARSs), and L* (lightness) values. Total phenol, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, and a* (redness) values were increased by treatments with increasing levels of S. chinensis. Diets with 1% or 2% S. chinensis lead to a greater decrease in serum cholesterol and improvements in the physical–chemical properties and meat color stability of broilers.
Uncoupling of DNA Replication and Centrosome Duplication Cycles Is a Primary Cause of Haploid Instability in Mammalian Somatic Cells

Mammalian haploid somatic cells are unstable and prone to diploidize, but the cause of haploid instability remains largely unknown. Previously, we found that mammalian haploid somatic cells suffer chronic centrosome loss stemming from the uncoupling of DNA replication and centrosome duplication cycles. However, the lack of methodology to restore the coupling between DNA replication and centrosome duplication has precluded us from investigating the potential contribution of the haploidy-linked centrosome loss to haploid instability. In this study, we developed an experimental method that allows the re-coupling of DNA and centrosome cycles through the chronic extension of the G1/S phase without compromising cell proliferation using thymidine treatment/release cycles. Chronic extension of G1/S restored normal mitotic centrosome number and mitotic control, substantially improving the stability of the haploid state in HAP1 cells. Stabilization of the haploid state was compromised when cdk2 was inhibited during the extended G1/S, or when early G1 was chronically extended instead of G1/S, showing that the coupling of DNA and centrosome cycles rather than a general extension of the cell cycle is required for haploid stability. Our data indicate the chronic centriole loss arising from the uncoupling of centrosome and DNA cycles as a direct cause of genome instability in haploid somatic cells, and also demonstrate the feasibility of modulation of haploid stability through artificial coordination between DNA and centrosome cycles in mammalian somatic cells.
Towards Automatic Thesaurus Construction and Enrichment.

Thesaurus construction with minimum human efforts often relies on automatic methods to discover terms and their relations. Hence, the quality of a thesaurus heavily depends on the chosen methodologies for: (i) building its content (terminology extraction task) and (ii) designing its structure (semantic similarity task). The performance of the existing methods on automatic thesaurus construction is still less accurate than the handcrafted ones of which is important to highlight the drawbacks to let new strategies build more accurate thesauri models. In this paper, we will provide a systematic analysis of existing methods for both tasks and discuss their feasibility based on an Italian Cybersecurity corpus. In particular, we will provide a detailed analysis on how the semantic relationships network of a thesaurus can be automatically built, and investigate the ways to enrich the terminological scope of a thesaurus by taking into account the information contained in external domain-oriented semantic sets.
Automatic Matching of Paintings and Descriptions in Art-Historic Archives using Multimodal Analysis

Cultural heritage data plays a pivotal role in the understanding of human history and culture. A wealth of information is buried in art-historic archives which can be extracted via digitization and analysis. This information can facilitate search and browsing, help art historians to track the provenance of artworks and enable wider semantic text exploration for digital cultural resources. However, this information is contained in images of artworks, as well as textual descriptions or annotations accompanied with the images. During the digitization of such resources, the valuable associations between the images and texts are frequently lost. In this project description, we propose an approach to retrieve the associations between images and texts for artworks from art-historic archives. To this end, we use machine learning to generate text descriptions for the extracted images on the one hand, and to detect descriptive phrases and titles of images from the text on the other hand. Finally, we use embeddings to align both, the descriptions and the images.
The Role of Library Councils in Canadian Higher Education: An Exploratory Study

Scholarship exploring the makeup, function, and efficacy of collegial governance structures within the context of Canadian higher education is limited and primarily focused on the board or the senate. This paper expands that scholarship by focusing on the governance structures of the university library. The objective of this study was to determine the extent of library councils in Canadian universities and to examine their composition, role, and function as evidenced in their governing documents. Using Karl Mannheim’s document method to analyze the terms of reference of 23 library councils, findings reveal that, overwhelmingly, library councils function as information-sharing and discussion forums rather than decision-making bodies. The paper concludes with a review of progressive language and governance practice as gathered from the document analysis.
Effect of urea fertilization on ectomycorrhizae of 20-year-old Tsuga heterophylla

Granular urea (46% N) was applied at rates of 224 and 448 kg N/ha to 4 × 4 m plots within at 20-year-old stand composed almost exclusively of western hemlock (Tsugaheterophylla (Raf.) Sarg. ), located in the Mount Seymour Demonstration Forest, North Vancouver, British Columbia. Changes in the abundance of 10 mycorrhizal types (Cenococcumgeophilum Fr., Lactariusscrobiculatus (Fr.) Fr. , Myceliumradicisatrovirens Melin, Thelephoraterrestris Fr. , three Russula morphotypes, two unidentified basidiomycetes, and a mantleless morphotype resembling E-strain) were assessed using random soil cores taken at 0, 1, 3, 6, and 11 months after fertilization. On both treated and control plots, total number of fine roots and number of basidiomycetous mycorrhizae remained constant, while C. geophilum mycorrhizae decreased slightly and those lacking mantles increased. The observed changes were independent of fertilizer levels and the shifts in pH brought about by urea hydrolysis.
Preparation and characterization of 5‐fluorouracil‐loaded poly(ϵ‐caprolactone) microspheres for drug administration

Microspheres of 5‐fluorouracil‐loaded poly(ϵ‐caprolactone) (PCL) were prepared by spray‐drying procedure. The degradation characteristics and 5‐fluorouracil release in vitro as well as in vivo were investigated. The average molecular weight, weight loss, crystallinity, and morphology of microspheres were determined using GPC, DSC, and SEM, at different times during the in vitro degradation process. The size distribution of the microspheres indicated that most of the particles were smaller than 3 µm. A 30% weight loss as well as an increase of crystallinity were observed on day 330 of incubation. The percentage of entrapment efficiency of 5‐FU was 49% (44 µg of drug/mg of microspheres). The in vitro total release of 5‐FU took place in 8 days. Determination of plasma 5‐FU concentration in vivo using s.c. injection of 5‐FU‐loaded microspheres in Wistar rats by HPLC with analysis of data using a non‐compartmental model showed drug in plasma 18 days after administration with a maximum drug concentration of 1.5 µg/ml at 96 h. Pharmacokineticallly, a significant increase of AUC and MRT of 5‐FU with regard to the administration of the drug in solution. Scanning electron microscopy and histological studies indicated that the microspheres were surrounded by connective tissue and inflammatory processes were not evident. As a result of these characteristics, the 5‐FU‐loaded PCL microspheres could be used for drug delivery. Drug Dev Res 63:41–53, 2004. © 2004 Wiley‐Liss, Inc.
Strain‐specific progression of α‐amanitin—treated mouse embryos beyond the two‐cell stage

Mouse embryos produced by the fertilization of eggs from (B6D2)F1 and CF‐1 mice differ in their ability to complete the second cell cycle in the presence of α‐amanitin. Essentially all embryos obtained from CF‐1 mothers arrest at the two‐cell stage when cultured from the late one‐cell stage in α‐amanitin at concentrations that prevent zygotic genome activation, while up to 15% of the embryos obtained from (B6D2)F1 mothers can progress to the three‐ to four‐cell stage. This occurs even at α‐amanitin concentrations that are fivefold greater than that required to prevent gene transcription. We propose that eggs of certain strains of mice may be endowed with greater supplies of macromolecules to support early development and that a percentage of these embryos can complete the second cell cycle in the absence of transcription. This difference may contribute to the strain‐dependent differences in development in vitro. © 1995 Wiley‐Liss, Inc.
naturaList: a package to classify occurrence records in levels of confidence in species identification

There is a big volume of occurrence records available in biodiversity databases, but researchers should guarantee its quality before use it in scientific studies. A problem that might compromise the quality of occurrence data is species misidentification. We address this issue by presenting naturaList, a R package designed to classify species occurrence data according to identification reliability. naturaList allows to classify species occurrences up to six levels of confidence in species identification, and to filter occurrence data accordingly. The highest level of confidence is assigned to records identified by a specialist, whose name must be provided by the user. The other five levels of confidence are derived from the occurrence data. We demonstrate naturaList functions using occurrences of Alsophila setosa, a tree fern species from Atlantic Forest, as example. We classified and filtered data in grid cells in order to maintain only the highest-level records in each cell. Then we selected only those records classified in the two highest levels of confidence. From 323 occurrences of Alsophila setosa displaying geographic coordinates, 69 (21%) were identified by a specialist. After filtering the highest-level records inside grid cells, 102 records remained. From these grid cell filtered data, 38 occurrences (37%) were classified into the highest confidence level. Three records were removed using an interactive map module, due to falling in sea sites or outside the native range size of the species. Since we selected only records classified in the two highest levels of confidence, the final dataset contained 94 occurrence records. naturaList guarantees the reproducibility of occurrence data processing and cleaning. Macroecologists, biogeographers and taxonomists might benefit from using naturaList package to evaluate the quality of species identification in occurrence data and by identify sites that need evaluation of taxonomic classification of species.
Detecting Manipulation in Regression Discontinuity Is Neither Always Necessary Nor Informative

The main attraction of Regression Discontinuity (RD) is local randomization around the cutoff. However, often the running variable (or just ''score'') is manipulated to ruin the local randomization. To detect manipulation, typically, the continuity at the cutoff of the score density function is tested. This paper shows via formal counter-examples that the score density continuity is neither necessary nor sufficient for RD identification. The score density continuity should not give a false sense of security when not rejected, and lack of it should not be taken as a reason to give up on the RD study hastily. Also, if the treatment cannot be implemented without manipulation of the score, then manipulation should be considered as part of the treatment effect. These findings suggest thinking more about the consequences of manipulation and the desired treatment effect, instead of mechanically applying score density continuity tests.
i-SATA: A MATLAB based toolbox to estimate current density generated by transcranial direct current stimulation in an individual brain

Objective. Transcranial Direct Current Stimulation (tDCS) is a technique where a weak current is passed through the electrodes placed on the scalp. The distribution of the electric current induced in the brain due to tDCS is provided by simulation toolbox like Realistic volumetric Approach based Simulator for Transcranial electric stimulation (ROAST). However, the procedure to estimate the total current density induced at the target and the intermediary region of the cortex is complex. The Systematic-Approach-for-tDCS-Analysis (SATA) was developed to overcome this problem. However, SATA is limited to standardized (MNI152) headspace only. Here we develop individual-SATA (i-SATA) to extend it to individual head. Approach. T1-weighted images of 15 subjects were taken from two Magnetic Resonance Imaging scanners of different strengths. Across the subjects, the montages were simulated in ROAST. i-SATA converts the ROAST output to Talairach space. The x, y and z coordinates of the anterior commissure (AC), posterior commissure (PC), and Mid-Sagittal (MS) points are necessary for the conversion. AC and PC are detected using the acpcdetect toolbox. We developed a method to determine the MS in the image and cross-verified its location manually using BrainSight®. Main results. Determination of points with i-SATA is fast and accurate. The i-SATA provided estimates of the current-density induced across an individual’s cortical lobes and gyri as tested on images from two different scanners. Significance. Researchers can use i-SATA for customizing tDCS-montages. With i-SATA it is also easier to compute the inter-individual variation in current-density across the target and intermediary regions of the brain. The software is publicly available.