Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long‐standing questions about the evolution of biodiversity largely unexplored. Here, we used whole‐genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single‐nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high‐quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.
ERF9 of Poncirus trifoliata (L.) Raf. undergoes feedback regulation by ethylene and modulates cold tolerance via regulating a glutathione S‐transferase U17 gene

Summary Plant ethylene‐responsive factors (ERFs) play essential roles in cold stress response, but the molecular mechanisms underlying this process remain poorly understood. In this study, we characterized PtrERF9 from trifoliate orange (Poncirus trifoliata (L.) Raf. ), a cold‐hardy plant. PtrERF9 was up‐regulated by cold in an ethylene‐dependent manner. Overexpression of PtrERF9 conferred prominently enhanced freezing tolerance, which was drastically impaired when PtrERF9 was knocked down by virus‐induced gene silencing. Global transcriptome profiling indicated that silencing of PtrERF9 resulted in substantial transcriptional reprogramming of stress‐responsive genes involved in different biological processes. PtrERF9 was further verified to directly and specifically bind with the promoters of glutathione S‐transferase U17 (PtrGSTU17) and ACC synthase1 (PtrACS1). Consistently, PtrERF9‐overexpressing plants had higher levels of PtrGSTU17 transcript and GST activity, but accumulated less ROS, whereas the silenced plants showed the opposite changes. Meanwhile, knockdown of PtrERF9 decreased PtrACS1 expression, ACS activity and ACC content. However, overexpression of PtrERF9 in lemon, a cold‐sensitive species, caused negligible alterations of ethylene biosynthesis, which was attributed to perturbed interaction between PtrERF9, along with lemon homologue ClERF9, and the promoter of lemon ACS1 gene (ClACS1) due to mutation of the cis‐acting element. Taken together, these results indicate that PtrERF9 acts downstream of ethylene signalling and functions positively in cold tolerance via modulation of ROS homeostasis by regulating PtrGSTU17. In addition, PtrERF9 regulates ethylene biosynthesis by activating PtrACS1 gene, forming a feedback regulation loop to reinforce the transcriptional regulation of its target genes, which may contribute to the elite cold tolerance of Poncirus trifoliata.
Concurrent lacrimal gland melanocytoma and ocular melanocytosis in a dog

A 9-y-5-mo-old, spayed female, mixed-breed dog with buphthalmia and elevated intraocular pressure in the left eye, consistent with glaucoma, was evaluated. Black-pigmented, slightly elevated tissue with irregular margins was noted on the dorsolateral aspect of the left globe. Ultrasonography detected a mass, later identified as lacrimal gland, adjacent to the globe and the thickened uvea. The surgically removed lacrimal gland was effaced by dense sheets of melanin-laden cells. Within the enucleated globe, numerous melanin-laden cells infiltrated and expanded the rostral two-thirds thickness of the cornea, the entire anterior uvea (iris and ciliary body), and a rostral portion of the choroid. Melanin-laden cells in the left lacrimal gland and globe showed no nuclear atypia or mitotic figures, and reacted to anti-S100 and anti–melan A antibodies by immunohistochemistry. Our final diagnosis was concurrent lacrimal gland melanocytoma and ocular melanocytosis. The trabecular meshwork of the eye was obliterated by melanin-laden cells, which was the likely cause of glaucoma in this patient. To our knowledge, melanocytoma affecting the lacrimal gland has not been reported previously in a non-human mammalian species. Veterinary clinicians are encouraged to include melanocytoma in the differential list when examining an enlarged lacrimal gland.
The Effect of Body Position and the Reliability of Upper Limb Arterial Occlusion Pressure Using a Handheld Doppler Ultrasound for Blood Flow Restriction Training

Background: The precise calculation of arterial occlusive pressure is essential to accurately prescribe individualized pressures during blood flow restriction training. Arterial occlusion pressure in the lower limb varies significantly between different body positions while similar reports for the upper limb are lacking. Hypothesis: Body position has a significant effect in upper limb arterial occlusive pressure. Using cuffs with manual pump and a handheld Doppler ultrasound can be a reliable method to determine upper limb arterial blood flow restriction. Study Design: A randomized repeated measures design. Level of Evidence: Level 3. Methods: Forty-two healthy participants (age mean ± SD = 28.1 ± 7.7 years) completed measurements in supine, seated, and standing position by 3 blinded raters. A cuff with a manual pump and a handheld acoustic ultrasound were used. The Wilcoxon signed-rank test with Bonferroni correction was used to analyze differences between body positions. A within-subject coefficient of variation and an intraclass correlation coefficient (ICC) test were used to calculate reproducibility and reliability, respectively. Results: A significantly higher upper limb arterial occlusive pressure was found in seated compared with supine position (P < 0.031) and in supine compared with standing position (P < 0.031) in all raters. An ICC of 0.894 (95% CI = 0.824-0.939, P < 0.001) was found in supine, 0.973 (95% CI = 0.955-0.985, P < 0.001) in seated, and 0.984 (95% CI = 0.973-0.991, P < 0.001) in standing position. ICC for test-retest reliability was found 0.90 (95% CI = 0.814-0.946, P < 0.001), 0.873 (95% CI = 0.762-0.93, P < 0.001), and 0.858 (95% CI = 0.737-0.923, P < 0.001) in the supine, seated, and standing position, respectively. Conclusion: Upper limb arterial occlusive pressure was significantly dependent on body position. The method showed excellent interrater reliability and repeatability between different days. Clinical Relevance: Prescription of individualized pressures during blood flow restriction training requires measurement of upper limb arterial occlusive pressure in the appropriate position. The use of occlusion cuffs with a manual pump and a handheld Doppler ultrasound showed excellent reliability; however, the increased measurement error compared with the differences in arterial occlusive pressure between certain positions should be carefully considered for the clinical application of the method. Strength of Recommendations Taxonomy (SORT): B.
The association between the dietary pattern in abdominal obesity based on visceral fat index and dyslipidaemia in the Henan Rural Cohort Study

Abstract The present study aimed to explore the association between dietary patterns in abdominal obesity obtained by reduced-rank regression (RRR) with visceral fat index (VFI) as a dependent variable and dyslipidemia in rural adults in Henan, China. A total of 29538 people aged 18–79 were selected from the Henan Rural Cohort Study. RRR analysis was used to identify dietary patterns; logistic regression analysis and restricted cubic spline regression models were applied to analyze the association between dietary patterns in abdominal obesity and dyslipidemia. VFI was used as a mediator to estimate the mediation effect. The dietary pattern in abdominal obesity was characterized by high carbohydrate and red meat intake and low consumption of fresh fruits, vegetables, milk, etc. After full adjustment, the highest quartile of dietary pattern scores was significantly associated with an increased risk of dyslipidemia (OR: 1·33, 95 % CI 1·23–1·44, P trend < 0·001), there was a non-linear dose–response relationship between them (P overall-association < 0·001, P non-lin-association = 0·022). The result was similar in dose-response between the dietary pattern scores and VFI. The indirect effect partially mediated by VFI was significant (OR: 1·07, 95 % CI 1·06–1·08). VIF explained approximately 53·3 % of odds of dyslipidemia related to the dietary pattern. Abdominal obesity dietary pattern scores positively affected VFI and dyslipidemia; there was a dose-response in both relationships. Dyslipidemia progression increased with higher abdominal obesity dietary pattern scores. In addition, VFI played a partial mediating role in relationship between abdominal obesity dietary pattern and dyslipidemia.
Impact of Resting Heart Rate on Cardiovascular Mortality According to Serum Albumin Levels in a 24-year Follow-up Study on a General Japanese Population: NIPPON DATA80

Background Elevated resting heart rate (RHR) is associated with an increased risk of cardiovascular disease (CVD) and all-cause mortality. However, the findings of cohort studies differed. Thus, the impact of RHR on CVD mortality might be different according to the background of the population. Therefore, we examined the relationship of RHR and CVD mortality according to serum albumin (ALB) levels in a Japanese general population. Methods In total, 8,363 individuals without a history of CVD were followed for 24.0 years. The participants were divided into four groups according to the quartiles of RHR (Q1–Q4), and they were further classified into the high and low ALB groups based on a median value of 44 g/L. We estimated the multivariable-adjusted hazard ratios (HRs) of CVD mortality in each RHR group based on ALB levels, and the interaction between RHR and ALB groups on CVD mortality was evaluated. Results We found no significant association between RHR and CVD mortality. However, the Q4 of RHR was significantly associated with an increased risk for CVD mortality (HR 1.27; 95% confidence interval [CI], 1.02–1.57) in participants with a low ALB level. Meanwhile, the Q4 of RHR was significantly correlated with a decreased risk for CVD morality in those with a high ALB level (HR 0.61; 95% CI, 0.47–0.79) after adjusting for covariates. A significant interaction between RHR and ALB for CVD mortality was shown (P < 0.001). Conclusion The impact of RHR on CVD mortality differed according to ALB levels in a general Japanese population.
Electromyography in Congenital Zika Syndrome

Introduction: Congenital Zika virus syndrome is a distinct pattern of birth defects in fetuses infected by the Zika virus. It presents a broad clinical spectrum that includes occurrences of microcephaly, hypertonia, dysphagia, hyperexcitability, seizures, and arthrogryposis. Imaging findings show neuronal migration disorders. Methodology: Case reports have suggested that arthrogryposis has a neurogenic cause. We analyzed needle electromyography and nerve conduction examinations on 77 patients aged 2–24 months presenting highly probable congenital Zika virus syndrome, with or without arthrogryposis. Results: All those with arthrogryposis presented with chronic muscle denervation in the electromyography examination. Similarly, children with single or reversible joint abnormalities at birth showed the same findings. Denervation in the paravertebral musculature was found in all of the children with diaphragmatic paralysis or thoracic deformities. Conclusions: We propose that congenital contractures associated with congenital Zika virus syndrome are caused by the malformation of upper and lower motor neurons during embryogenesis.
Alteration in Cellular Signaling and Metabolic Reprogramming during Viral Infection

Cellular activities are finely regulated by numerous signaling pathways to support specific functions of complex life processes. Viruses are obligate intracellular parasites. ABSTRACT Cellular activities are finely regulated by numerous signaling pathways to support specific functions of complex life processes. Viruses are obligate intracellular parasites. Each step of viral replication is ultimately governed by the interaction of a virus with its host cells. Because of the demands of viral replication, the nutritional needs of virus-infected cells differ from those of uninfected cells. To improve their chances of survival and replication, viruses have evolved to commandeer cellular processes, including cell metabolism, augmenting these processes to support their needs. This article summarizes recent findings regarding virus-induced alterations to major cellular metabolic pathways focusing on how viruses modulate various signaling cascades to induce these changes. We begin with a general introduction describing the role played by signaling pathways in cellular metabolism. We then discuss how different viruses target these signaling pathways to reprogram host metabolism to favor the viral needs. We highlight the gaps in understanding metabolism-related virus-host interactions and discuss how studying these changes will enhance our understanding of fundamental processes involved in metabolic regulation. Finally, we discuss the potential to harness these processes to combat viral diseases, as well as other diseases, including metabolic disorders and cancers.
Serum Amino Acids Patterns and 4-Year Sarcopenia Risk in Community-Dwelling Chinese Older Adults

Introduction: Dietary protein intake and serum amino acids (AAs) are factors controlling the rate of muscle protein synthesis and catabolism. This study examined the association between serum AAs patterns and incident sarcopenia in community-dwelling older adults. Methods: Chinese older adults in Hong Kong aged ≥65 years attended a health check at baseline and 4-year follow-up. At baseline, fasting blood was collected to measure 17 serum AAs. Serum AAs patterns were identified using principal component analysis. Dietary protein intake was assessed using a validated food frequency questionnaire. A composite score was computed by summing the principal component score and sex-standardized protein intake. Six composite scores representing each AAs pattern were available for each participant. Sarcopenia was defined using the updated version of the Asian Working Group for Sarcopenia. Crude and adjusted multiple logistic regressions were performed to examine the associations between each of the 6 composite scores and sarcopenia over 4 years. Results are presented as odds ratio (OR) and 95% confidence interval (CI). To address multiple testing, a Bonferroni correction was applied using a corrected significance level of p < 0.008 (α 0.05/6 patterns). Results: Data of 2,610 participants (mean age 71.6 years, 45.4% men) were available. In men, serum AAs patterns characterized by high branched-chain AAs (BCAAs) (OR 0.77, 95% CI 0.69–0.87, p < 0.001) and tyrosine, tryptophan, and phenylalanine (OR 0.79, 95% CI 0.71–0.89, p < 0.001) were significantly associated with a lower risk of sarcopenia over 4-year follow-up. After adjusting for confounders, the associations were no longer significant. In women, serum AAs patterns characterized by glutamine, glutamic acid, and methionine (OR 1.28, 95% CI 1.11–1.47, p = 0.001) and arginine, taurine, and serine (OR 1.20, 95% CI 1.06–1.35, p = 0.003) were associated with a higher risk of sarcopenia. After adjusting for confounders, serum AAs pattern characterized by high BCAAs (adjusted OR 1.52, 95% CI 1.25–1.86, p < 0.001) and arginine, taurine, and serine (adjusted OR 1.30, 95% CI 1.09–1.56, p = 0.004) were significantly associated with a higher risk of sarcopenia. No association between other AAs patterns with incident sarcopenia was found. Conclusions: In community-dwelling Chinese older adults, serum AAs patterns characterized by high BCAAs and nonessential AAs (arginine, taurine, and serine) were associated with a higher risk of sarcopenia in women. Findings may allow identifying new targets for interventions.
Investigation of Residual Bearing Capacity of Inclined Sections of Damaged Reinforced Concrete Beams

Abstract The article reports on the results of the numerical and the laboratory tests to determine the effect of concrete damages near support areas in compressed zone of the reinforced concrete beams on their residual bearing capacity of inclined sections. According to the experimental plan, 15 single-span freely supported experimental samples with dimensions of 100×200×1200 mm made with different artificial damages within the shear span aν (1d, 2d, and 3d) were tested. The numerical test of prototypes was performed in software complex LIRA-SAPR 2017. The results of laboratory and numerical experiments showed good convergence regarding the bearing capacity, however, the nature of the fracture in samples B11-B14 did not match. Empirical - conducting laboratory experiments on samples using modern methods of measurement; numerical modelling – using software complex LIRA-SAPR 2017; analysis and statistical processing of the obtained research results; comparison of the obtained results; abstraction; generalization; deduction; formulation of the main conclusions and recommendations. The analysis found that the bearing capacity decreases with increased area of damage and shear span. Conducting the calculations in software complex LIRA-SAPR allows to predict the work elements and determine the bearing capacity with good accuracy, but in comparison with the real data there still are some differences in the character of destruction.
Deep Learning Meets Private Talk: Conversational AI Can Predict Speaker Traits by Eavesdropping for Only 30 Seconds

Conversational AI such as smart speakers placed in home environments can accidentally activate and record people’s talk for a short time. What can such devices learn about people by listening in on ongoing conversations? Taking two commonly used speaker traits as an example, we present the results of an experiment that simulates Conversational AI eavesdropping on ongoing talk using transcriptions of naturalistic conversations in private settings. We show that a currently popular type of deep learning-based system can reliably predict if a speaker is “young”, “old”, “female” or “male” (age=99%, gender=82%) based on what they say in around 30 seconds. Our results exemplify how powerful current big data language models are when it comes to data-driven predictions of personal information based on how people talk, even when listening only for a short time. We conclude the experiment with a critical comment on the increasingly pervasive use of such user modeling technology to compute speaker traits, touching upon some potential ethical concerns, bias, and privacy issues.
Ultrasonographic Tissue Perfusion in Peri-implant Health and Disease

Color flow ultrasonography has played a crucial role in medicine for its ability to assess dynamic tissue perfusion and blood flow variations as an indicator of a pathologic condition. While this feature of ultrasound is routinely employed in various medical fields, its intraoral application for the assessment of tissue perfusion at diseased versus healthy dental implants has never been explored. We tested the hypothesis that quantified tissue perfusion of power Doppler ultrasonography correlates with the clinically assessed inflammation of dental implants. Specifically, we designed a discordant-matched case-control study in which patients with nonadjacent dental implants with different clinical diagnoses (healthy, peri-implant mucositis, or peri-implantitis) were scanned and analyzed with real-time ultrasonography. Forty-two posterior implants in 21 patients were included. Ultrasound scans were obtained at the implant regions of midbuccal, mesial/distal (averaged as interproximal), and transverse to compute the velocity- and power-weighted color pixel density from color velocity (CV) and color power (CP), respectively. Linear mixed effect models were then used to assess the relationship between the clinical diagnoses and ultrasound CV and CP. Overall, the results strongly suggested that ultrasound’s quantified CV and CP directly correlate with the clinical diagnosis of dental implants at health, peri-implant mucositis, and peri-implantitis. This study showed for the first time that ultrasound color flow can be applicable in the diagnosis of peri-implant disease and can act as a valuable tool for evaluating the degree of clinical inflammation at implant sites.
Shifts in biochemical and physiological responses by the inoculation of arbuscular mycorrhizal fungi in Triticum aestivum growing under drought conditions.

BACKGROUND A decrease in rainfall is one of the main constraints on wheat production, but the association of wheat with arbuscular mycorrhizal fungi (AMF) may be an alternative for crop production under drought conditions. Here, we used three wheat cultivars (Purple, Ilustre and Maxi Baer) inoculated with two AMF strains, one obtained from the hyperarid Atacama Desert (northern Chile; Fm) and the other obtained from southern Chile (Cc). Plants were maintained under two irrigation conditions (normal irrigation and drought), and the physiological behaviour and enzymatic and nonenzymatic antioxidant activities in the shoots were determined. In addition, the phenolic compounds were identified by HPLC-DAD-ESI-MS/MS and quantified. RESULTS AMF colonization produced higher levels of ΦPSII and photosynthetic pigments. High values of catalase in Purple-Cc, ascorbate peroxidase in Purple-Cc, glutathione reductase in Maxi-Cc, and superoxide dismutase in Purple-Cc, all under stress, were registered. Of the inoculated cultivars, Purple-Cc showed the highest flavonoid levels, while hydroxycinnamic acids were higher in Maxi-Fm without drought with apigenin and luteolin being the most abundant. High levels of phenols were present in the Ilustre-Fm plants without drought. Under normal irrigation, high levels of antioxidant activities were registered in the AMF treatments, whereas under stress conditions, in general, high values were observed under the Fm inoculation. CONCLUSION Our results showed that the greatest antioxidant activity and phenolic content occurred in wheat plants inoculated with AMF, indicating their influence on coping with water stress, which is of importance in vast areas where global climate change is resulting in diminished rainfall. This article is protected by copyright. All rights reserved.