Miracle-dz/UniFAR-FTUs huggingface dataset:
SMBFT: A Modified Fuzzy c-Means Algorithm for Superpixel Generation

Most traditional superpixel segmentation methods used binary logic to generate superpixels for natural images. When these methods are used for images with significantly fuzzy characteristics, the boundary pixels sometimes cannot be correctly classified. In order to solve this problem, this paper proposes a Superpixel Method Based on Fuzzy Theory (SMBFT), which uses fuzzy theory as a guide and traditional fuzzy c-means clustering algorithm as a baseline. This method can make full use of the advantage of the fuzzy clustering algorithm in dealing with the images with the fuzzy characteristics. Boundary pixels which have higher uncertainties can be correctly classified with maximum probability. The superpixel has homogeneous pixels. Meanwhile, the paper also uses the surrounding neighborhood pixels to constrain the spatial information, which effectively alleviates the negative effects of noise. The paper tests on the images from Berkeley database and brain MR images from the Brain web. In addition, this paper proposes a comprehensive criterion to measure the weights of two kinds of criterions in choosing superpixel methods for color images. An evaluation criterion for medical image data sets employs the internal entropy of superpixels which is inspired by the concept of entropy in the information theory. The experimental results show that this method has superiorities than traditional methods both on natural images and medical images.
Association mapping for general combining ability with yield, plant height and ear height using F1 population in maize

General combining ability (GCA) is an important index for inbred lines breeding of maize. To identify the genetic loci of GCA and associated agronomic traits, an association analysis with 195 SSRs was made in phenotypic traits of 240 F1 derived from 120 elite inbred lines containing current breeding resources of maize crossed with 2 testers (Zheng58 and Chang7-2) in two places in 2018. All of the 20 association loci detected for grain yield (GY), plant height (PH), ear height (EH) and GCA for the three traits in two places could explain a phenotypic variation range of 7.31%-9.29%. Among the 20 association loci, 9 (7.31%-9.04%) were associated with GY, 4 (7.22%-8.91%) were related to GCA of GY, 1 (7.56%) was associated with PH, and 3 (7.53%-8.96%) were related to EH. In addition, 3 loci (9.14%-9.29%) were associated with GCA of PH whereas no locus was identified for GCA of EH. In the comparison of the association loci detected in Baoding and Handan, interestingly, one locus (7.69% and 8.11%) was identified in both environments and one locus (7.52% and 7.82%) was identified for yield and GCA of yield. Therefore, the identification of GY-, PH-, EH- and GCA-related association loci could not only provide references for high yield breeding of maize, but also help us comprehend the relationships among GY, agricultural traits and GCA.
RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams

Abstract Publishing, discussing, envisioning, modeling, designing and experimentally determining RNA three-dimensional (3D) structures involve preparation of two-dimensional (2D) drawings that depict critical functional features of the subject molecules, such as noncanonical base pairs and protein contacts. Here, we describe RiboDraw, new software for crafting these drawings. We illustrate the features of RiboDraw by applying it to several RNAs, including the Escherichia coli tRNA-Phe, the P4–P6 domain of Tetrahymena ribozyme, a −1 ribosomal frameshift stimulation element from beet western yellows virus and the 5′ untranslated region of SARS-CoV-2. We show secondary structure diagrams of the 23S and 16S subunits of the E. coli ribosome that reflect noncanonical base pairs, ribosomal proteins and structural motifs, and that convey the relative positions of these critical features in 3D space. This software is a MATLAB package freely available at https://github.com/DasLab/RiboDraw.
Prognostic value of serological markers of hepatitis B virus infection in squamous cell cervical cancer

Objective: The current study aimed to investigate the prognostic value of serological markers of hepatitis B virus (HBV) infection in squamous cell cervical cancer. Methods: Squamous cell cervical cancer patients treated by concurrent chemoradiotherapy from January 2013 to December 2015 at Yunnan Cancer Hospital were retrospectively reviewed. Results: Of a total of 277 patients, 12 (4.33%), 93 (33.57%), 2 (0.72%), 25 (9.02%), and 36 patients (13.00%) were seropositive for hepatitis B surface antigen (HBsAg), anti-hepatitis B surface antibodies (anti-HBs), hepatitis B envelope antigen (HBeAg), anti-hepatitis B envelope antibodies (anti-HBe), and anti-hepatitis B core antibodies (anti-HBc), respectively. No patients experienced more than mild hepatic adverse events during treatment. The five-year overall survival (OS) rates for patients with anti-HBs positive or negative status were 85.8% and 66.2% (p = 0.039), respectively. No statistically significant difference in the five-year OS rates was observed in HBsAg positive and negative, HBeAg positive and negative, anti-HBe positive and negative, anti-HBc positive and negative patients. The multivariable analysis revealed that anti-HBs positivity was an independent favorable prognostic factor for OS (HR= 0.279; 95%CI: 0.083-0.936; p = 0.039) in patients younger than 50 years. Conclusions: The presence of anti-HBs predicts a superior OS for squamous cell cervical cancer patients aged younger than 50 years.
Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera

Abstract Within the family Geminiviridae, the emergence of new species results from their high mutation and recombination rates. In this study, we report the variability and evolution of digitaria streak virus (DSV), a mastrevirus isolated in 1986 from the grass Digitaria setigera in an island of the Vanuatu archipelago. Viral DNA of DSV samples was amplified from D. setigera specimens, derived from the naturally infected original plant, which were propagated in different laboratories in France and Italy for more than 20 years. From the consensus sequences, the nucleotide substitution rate was estimated for the period between a sample and the original sequence published in 1987, as well as for the period between samples. In addition, the intra-host genetic complexity and diversity of 8 DSV populations with a total of 165 sequenced haplotypes was characterized. The evolutionary rate of DSV was estimated to be between 1.13 × 10−4 and 9.87 × 10−4 substitutions/site/year, within the ranges observed in other single-stranded DNA viruses and RNA viruses. Bioinformatic analyses revealed high variability and heterogeneity in DSV populations, which confirmed that mutant spectra are continuously generated and are organized as quasispecies. The analysis of polymorphisms revealed nucleotide substitution biases in viral genomes towards deamination and oxidation of single-stranded DNA. The differences in variability in each of the genomic regions reflected a dynamic and modular evolution in the mutant spectra that was not reflected in the consensus sequences. Strikingly, the most variable region of the DSV genome, encoding the movement protein, showed rapid fixation of the mutations in the consensus sequence and a concomitant dN/dS ratio of 6.130, which suggests strong positive selection in this region. Phylogenetic analyses revealed a possible divergence in three genetic lineages from the original Vanuatu DSV isolate.
Characterization of the complete chloroplast genome of Scrophularia cephalantha endemic to Korea

Abstract Scrophularia species are highly valued and widely used traditional medicinal plants in East Asia. In this article, the complete chloroplast genome of Scrophularia cephalantha, a species endemic to South Korea, is reported for the first time. The genome is 153,016 bp long, and it is composed of a pair of 25,485 bp inverted repeats (IRs), separated by a large single copy (LSC) region of 84,124 bp, and a small single copy (SSC) region of 17,922 bp. There are 133 predicted genes in the genome, comprising 88 protein-coding genes, 37 tRNAs, and 8 rRNAs, with an overall GC content of 38%. Phylogenetic analysis based on the chloroplast genome data showed that S. cephalantha is a sister species to S. buergeriana and S. ningpoensis. The data provide useful molecular information for phylogenetic and evolutionary studies of the genus Scrophularia and its related species.
Diagnosis of Typical Apple Diseases: A Deep Learning Method Based on Multi-Scale Dense Classification Network

Disease has always been one of the main reasons for the decline of apple quality and yield, which directly harms the development of agricultural economy. Therefore, precise diagnosis of apple diseases and correct decision making are important measures to reduce agricultural losses and promote economic growth. In this paper, a novel Multi-scale Dense classification network is adopted to realize the diagnosis of 11 types of images, including healthy and diseased apple fruits and leaves. The diagnosis of different kinds of diseases and the same disease with different grades was accomplished. First of all, to solve the problem of insufficient images of anthracnose and ring rot, Cycle-GAN algorithm was applied to achieve dataset expansion on the basis of traditional image augmentation methods. Cycle-GAN learned the image characteristics of healthy apples and diseased apples to generate anthracnose and ring rot lesions on the surface of healthy apple fruits. The diseased apple images generated by Cycle-GAN were added to the training set, which improved the diagnosis performance compared with other traditional image augmentation methods. Subsequently, DenseNet and Multi-scale connection were adopted to establish two kinds of models, Multi-scale Dense Inception-V4 and Multi-scale Dense Inception-Resnet-V2, which facilitated the reuse of image features of the bottom layers in the classification neural networks. Both models accomplished the diagnosis of 11 different types of images. The classification accuracy was 94.31 and 94.74%, respectively, which exceeded DenseNet-121 network and reached the state-of-the-art level.
Resolving Indigenous village occupations and social history across the long century of European permanent settlement in Northeastern North America: The Mohawk River Valley ~1450-1635 CE

The timeframe of Indigenous settlements in Northeast North America in the 15th-17th centuries CE has until very recently been largely described in terms of European material culture and history. An independent chronology was usually absent. Radiocarbon dating has recently begun to change this conventional model radically. The challenge, if an alternative, independent timeframe and history is to be created, is to articulate a high-resolution chronology appropriate and comparable with the lived histories of the Indigenous village settlements of the period. Improving substantially on previous initial work, we report here high-resolution defined chronologies for the three most extensively excavated and iconic ancestral Kanienʼkehá꞉ka (Mohawk) village sites in New York (Smith-Pagerie, Klock and Garoga), and a fourth early historic Indigenous site, Brigg’s Run, and re-assess the wider chronology of the Mohawk River Valley in the mid-15th to earlier 17th centuries. This new chronology confirms initial suggestions from radiocarbon that a wholesale reappraisal of past assumptions is necessary, since our dates conflict completely with past dates and the previously presumed temporal order of these three iconic sites. In turn, a wider reassessment of northeastern North American early history and re-interpretation of Atlantic connectivities in the later 15th through early 17th centuries is required. Our new closely defined date ranges are achieved employing detailed archival analysis of excavation records to establish the contextual history for radiocarbon-dated samples from each site, tree-ring defined short time series from wood charcoal samples fitted against the radiocarbon calibration curve (‘wiggle-matching’), and Bayesian chronological modelling for each of the individual sites integrating all available prior knowledge and radiocarbon dating probabilities. We define (our preferred model) most likely (68.3% highest posterior density) village occupation ranges for Smith-Pagerie of ~1478–1498, Klock of ~1499–1521, Garoga of ~1550–1582, and Brigg’s Run of ~1619–1632.
Effect of 1,25-Dihydroxyvitamin D3 on Stem Cells from Human Apical Papilla: Adhesion, Spreading, Proliferation, and Osteogenic Differentiation

Currently, it still remains a difficult problem to treat apical insufficiency of young permanent teeth resulted from pulp necrosis or periapical periodontitis. Previous studies have demonstrated that the treatment of revascularization using stem cells from apical papilla (SCAPs) results in increased root length and thickness of traumatized immature teeth and necrotic pulp. In this study, we investigated the role of 1,25-dihydroxyvitamin D3 in regulating the adhesion, spreading, proliferation, and osteogenic differentiation of SCAP, laying the foundation for subsequent clinical drug development. The immature tooth samples were collected in clinical treatment. SCAPs with stable passage ability were isolated and cultured. The multidifferentiation potential was determined by directed induction culture, while the stem cell characteristics were identified by flow cytometry. There were three groups: group A—SCAPs general culture group; group B—SCAPs osteogenesis induction culture group; and group C—SCAPs osteogenesis induction culture+1,25-dihydroxyvitamin D3 group, and the groups were compared statistically. The proliferation of SCAPs in each groups was detected through CCK-8 assay. RT-qPCR was used to detect the transcription levels of Runx2, ALP, Col I, and OCN of SCAPs in each groups. Results exhibited that the isolated SCAPs had multidifferentiation potential and stem cell characteristics. After 24 h culturing, cells in group C spread better than those in groups A and B. The proliferation activity of SCAPs factored by CCK-8 ranked as group C > group B > group A, while the transcription levels of Runx2, ALP, Col I, and OCN leveled as group C > group B > group A. These results suggested that 1,25-dihydroxyvitamin D3 can significantly promote the adhesion, spreading, and proliferation of SACPs and improve the osteogenic differentiation of SCAPs by means of regulating upward the transcription level of osteogenic differentiation marker.
Complete mitochondrial genomes of representatives of two endemic sculpin families (Perciformes: Cottoidei) from Baikal – the world’s largest and deepest lake

Abstract In this study, five new mitogenomes from four endemic Lake Baikal sculpins were determined: Cottocomephorus grewingkii (Dybowski, 1874) (GB#MW732165), Cottocomephorus inermis (Yakovlev, 1890) (GB#MW732163), and Paracottus knerii (Dybowski, 1874) (GB#MW732164) (Family Cottocomephoridae – Bighead sculpins), and from two specimens of Procottus major Taliev, 1949 (GB##MW732166, MW732167) from Family Abyssocottidae (Deep-water sculpins). Together with recently published mitogenomes of Baikal Oilfishes (Sandel et al. 2017), the first mitogenome-based phylogenetic tree for all three endemic Baikal sculpin families is presented. Complete mitogenome phylogeny supports the monophyletic origin of the lake Baikal sculpins species flock, but does not support the monophyly of the family Cottocomephoridae (Bighead sculpins).
The Effect and Safety of 5-HT1F Receptor Agonist Lasmiditan on Migraine: A Systematic Review and Meta-Analysis

Background Migraine has a great impact on public health. Current acute therapies do not satisfy all migraineurs. The novel serotonin 5-HT1F receptor agonist appears more promising for aborting migraine attacks. Objective To evaluate the clinical efficacy and safety of lasmiditan in treating acute migraine attacks. Methods The literature search was performed in PubMed, Embase, and the Cochrane Central Register of Controlled Trials for randomized controlled trials (RCTs) which assessed the effect and safety of lasmiditan on migraine. The risk of bias was assessed using the Cochrane Collaboration's risk of bias tool. Results were extracted and pooled as risk ratios (RRs) with a fixed or random-effects model. Results Based on the four included RCTs, pooled estimates showed that lasmiditan with the 50 mg, 100 mg, and 200 mg doses was superior to placebo at 2 h after the first dose in terms of pain freedom, absence of migraine-associated symptoms, headache relief, no/mild disability, and global impression of change (very much/much better) (RRs ranged from 1.13 to 1.96), except for nausea-free and vomiting-free. Both lasmiditan 100 mg and 200 mg resulted in significantly fewer patients using rescue medication (100 mg: RR = 0.75, 95% CI (0.61, 0.92), P = 0.007; 200 mg: RR = 0.81, 95% CI (0.66, 0.99), P = 0.04) at 2-24 h postdose, compared with placebo. Safety data showed that the proportion of patients reporting at least one treatment-emergent adverse event (TEAE) and the incidence of most common TEAEs such as dizziness, paresthesia, fatigue, somnolence, and nausea was higher in the lasmiditan groups (50 mg, 100 mg, and 200 mg), compared with placebo. There was no significant difference between lasmiditan and placebo in terms of cardiovascular-related TEAEs (RR = 2.75, 95% CI (0.81, 9.37), P = 0.11). Compared with lasmiditan 100 mg, lasmiditan 200 mg was more effective in pain freedom at 2 h after the first dose (RR = 0.83, 95% CI (0.74, 0.94), P = 0.004) but associated with a higher risk of reporting at least one TEAE (RR = 0.88, 95% CI (0.81, 0.96), P = 0.006). Conclusions Lasmiditan with the 50 mg, 100 mg, and 200 mg doses are effective and safe in acute migraine treatment. Lasmiditan 200 mg is more effective than lasmiditan 100 mg in pain freedom, while lasmiditan 100 mg is better tolerated in the short-term follow-up. Further larger sample-size RCTs are required to verify the applicability and tolerability in the long term.
Heading towards a dead end: The role of DND1 in germ line differentiation of human iPSCs

The DND microRNA-mediated repression inhibitor 1 (DND1) is a conserved RNA binding protein (RBP) that plays important roles in survival and fate maintenance of primordial germ cells (PGCs) and in the development of the male germline in zebrafish and mice. Dead end was shown to be expressed in human pluripotent stem cells (PSCs), PGCs and spermatogonia, but little is known about its specific role concerning pluripotency and human germline development. Here we use CRISPR/Cas mediated knockout and PGC-like cell (PGCLC) differentiation in human iPSCs to determine if DND1 (1) plays a role in maintaining pluripotency and (2) in specification of PGCLCs. We generated several clonal lines carrying biallelic loss of function mutations and analysed their differentiation potential towards PGCLCs and their gene expression on RNA and protein levels via RNA sequencing and mass spectrometry. The generated knockout iPSCs showed no differences in pluripotency gene expression, proliferation, or trilineage differentiation potential, but yielded reduced numbers of PGCLCs as compared with their parental iPSCs. RNAseq analysis of mutated PGCLCs revealed that the overall gene expression remains like non-mutated PGCLCs. However, reduced expression of genes associated with PGC differentiation and maintenance (e.g., NANOS3, PRDM1) was observed. Together, we show that DND1 iPSCs maintain their pluripotency but exhibit a reduced differentiation to PGCLCs. This versatile model will allow further analysis of the specific mechanisms by which DND1 influences PGC differentiation and maintenance.
Assessment of Wettability and Contact Angle of Bonding Agent with Enamel Surface Etched by Five Commercially Available Etchants: An In Vitro Study

Background The quantity and quality of the etching pattern produced by acids play a significant role in the wettability and contact angle of the adhesive with the enamel surface in orthodontics. The better the etch pattern, the more the surface energy of the enamel, better the penetration of the adhesive, which ultimately results in better bond strength. The present study aimed to evaluate the contact angle of the bonding agent with the enamel surface etched by five commercially available etchants and check if any difference existed between the five. Materials and Methods Twenty-five human maxillary and mandibular central incisors and premolars extracted for orthodontic or dental purposes were used in this study as samples. The teeth were allocated into five groups based upon the etchant used to etch the enamel surface. After the samples were etched, a hard tissue microtome was used to create thin slices of the enamel surface. The samples were then exposed to bonding agent Ormco Enlight. The bonding agent was released in the form of droplets onto the enamel slices mounted on a contact angle goniometer. The contact angle values were tabulated, and statistical analysis using the one-way ANOVA test was carried out. Results The contact angle measurements of the etchant group, DPI, were the lowest, while D-tech has the highest contact angle values. However, statistical analysis revealed no statistically significant difference between the contact angle measurements of the five groups included in the study. Conclusion No statistically significant difference existed between the five etchant groups included in the study. However, commercially available etchant DPI showed lesser contact angle and thus better wettability in comparison to other groups. Further elemental analysis and surface analysis are required to validate these results.
Circulating Biomarkers for Cardiovascular Disease Risk Prediction in Patients With Cardiovascular Disease

Cardiovascular disease (CVD) is the leading cause of death globally. Risk assessment is crucial for identifying at-risk individuals who require immediate attention as well as to guide the intensity of medical therapy to reduce subsequent risk of CVD. In the past decade, many risk prediction models have been proposed to estimate the risk of developing CVD. However, in patients with a history of CVD, the current models that based on traditional risk factors provide limited power in predicting recurrent cardiovascular events. Several biomarkers from different pathophysiological pathways have been identified to predict cardiovascular events, and the incorporation of biomarkers into risk assessment may contribute to enhance risk stratification in secondary prevention. This review focuses on biomarkers related to cardiovascular and metabolic diseases, including B-type natriuretic peptide, high-sensitivity cardiac troponin I, adiponectin, adipocyte fatty acid-binding protein, heart-type fatty acid-binding protein, lipocalin-2, fibroblast growth factor 19 and 21, retinol-binding protein 4, plasminogen activator inhibitor-1, 25-hydroxyvitamin D, and proprotein convertase subtilisin/kexin type 9, and discusses the potential utility of these biomarkers in cardiovascular risk prediction among patients with CVD. Many of these biomarkers have shown promise in improving risk prediction of CVD. Further research is needed to assess the validity of biomarker and whether the strategy for incorporating biomarker into clinical practice may help to optimize decision-making and therapeutic management.