Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds

The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin’s finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.
Advances in Random Fiber Lasers and Their Sensing Application

Compared with conventional laser, random laser (RL) has no resonant cavity, reducing the requirement of cavity design. In recent years, the random fiber laser (RFL), a novel kind of RL, has made great progress in theories and experiments. The RFL has a simpler structure, a more flexible design, and higher reliability. It has valuable applications for earth sciences, biological life sciences, and national defense security, due to these unique properties. This paper reviews the development of RFLs in the last decade, including their configurations based on various optical fibers and their output properties, especially the method of control. Moreover, we also introduce their applications in the optical fiber sensing system, which is a very important and practical orientation to study. Finally, this paper presents the prospects of RFLs.
Post-Translational S-Nitrosylation of Proteins in Regulating Cardiac Oxidative Stress

Like other post-translational modifications (PTMs) of proteins, S-nitrosylation has been considered a key regulatory mechanism of multiple cellular functions in many physiological and disease conditions. Emerging evidence has demonstrated that S-nitrosylation plays a crucial role in regulating redox homeostasis in the stressed heart, leading to discoveries in the mechanisms underlying the pathogenesis of heart diseases and cardiac protection. In this review, we summarize recent studies in understanding the molecular and biological basis of S-nitrosylation, including the formation, spatiotemporal specificity, homeostatic regulation, and association with cellular redox status. We also outline the currently available methods that have been applied to detect S-nitrosylation. Additionally, we synopsize the up-to-date studies of S-nitrosylation in various cardiac diseases in humans and animal models, and we discuss its therapeutic potential in cardiac protection. These pieces of information would bring new insights into understanding the role of S-nitrosylation in cardiac pathogenesis and provide novel avenues for developing novel therapeutic strategies for heart diseases.
Neural priming of adipose-derived stem cells by cell-imprinted substrates*

Cell-imprinting technology is a novel method for directing stem cell fate using substrates molded from target cells. Here, we fabricated and studied cell-imprinted substrates for neural priming in human adipose-derived stem cells in the absence of chemical cues. We molded polydimethylsiloxane silicone substrates on fixed differentiated neural progenitor cells (ReNcellTM VM). The ReNcellTM cell line consists of immortalized human neural progenitor cells that are capable to differentiate into neural cells. The fabricated cell-imprinted silicone substrates represent the geometrical micro- and nanotopology of the target cell morphology. During the molding procedure, no transfer of cellular proteins was detectable. In the first test with undifferentiated ReNcellTM VM cells, the cell-imprinted substrates could accelerate neural differentiation. With adipose-derived stem cells cultivated on the imprinted substrates, we observed modifications of cell morphology, shifting from spread to elongated shape. Both immunofluorescence and quantitative gene expression analysis showed upregulation of neural stem cell and early neuronal markers. Our study, for the first time, demonstrated the effectiveness of cell-imprinted substrates for neural priming of adipose-derived stem cells for regenerative medicine applications.
Identification and Characterization of “Candidatus Rickettsia Thierseensis”, a Novel Spotted Fever Group Rickettsia Species Detected in Austria

Rickettsia spp. are the second most common pathogens detected in Ixodes ricinus ticks in Austria after Borrelia burgdorferi sensu lato. Species belonging to the spotted fever group (SFG) are the causative agents for tick-borne rickettsiosis across the world. So far, only four SFG Rickettsia spp. were detected in Austria, namely R. helvetica, R. raoultii, R. monacensis and R. slovaca. Here, we describe the identification of a new SFG Rickettsia species detected in an I. ricinus tick. Sequencing of various rickettsial genes revealed a nucleotide sequence similarity of 99.6%, 98.5%, 97.3% and 98.5% to the gltA, ompA, ompB, and sca4 genes, respectively, of known and validated species. Additionally, sequencing of the htrA gene and 23S-5S intergenic spacer region also only showed 99.6% and 99.2%, respectively, similarity to known species. Therefore, and in accordance with current criteria for Rickettsia species discrimination, we hereby describe a new species of the SFG with putative pathogenic potential. We propose the name “Candidatus Rickettsia thierseensis” based on the village Thiersee in the Austrian province of Tyrol, where the carrying tick was found.
Long-term evaluation of autologous lamellar corneal grafts for the treatment of deep corneal ulcer in four dogs: a case report

Autologous lamellar corneal grafts were performed on four dogs with two deep corneal ulcers and two corneal perforations to achieve better visual and aesthetic outcomes. The donor corneal graft was harvested from the relatively normal corneal region of the affected eye and used to cover the corneal defect. At the two-year follow-up examination, ultrasound biomicroscopy was performed to confirm the thickness and endothelial continuity of the transplanted grafts and donor site of the cornea. The evaluations revealed that the dogs had healed without incident and that their vision had been maintained. Furthermore, the owners were satisfied with the aesthetic outcomes in all cases. Our findings show that autologous lamellar corneal grafts are useful and effective in treating canine corneal ulcers and perforations.
Vitamin D and Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD): An Update

Non-alcoholic fatty liver disease (NAFLD) is the first cause of chronic liver disease worldwide; it ranges from simple steatosis to steatohepatitis (NASH) and, potentially, cirrhosis and hepatocarcinoma. NAFLD is also an independent risk factor for type 2 diabetes, cardiovascular diseases, and mortality. As it is largely associated with insulin resistance and related disorders, NAFLD has been recently re-named as Metabolic dysfunction-Associated Fatty Liver Disease (MAFLD). At present, there are no approved pharmacological treatments for this condition. Vitamin D is a molecule with extensive anti-fibrotic, anti-inflammatory, and insulin-sensitizing properties, which have been proven also in hepatic cells and is involved in immune-metabolic pathways within the gut–adipose tissue–liver axis. Epidemiological data support a relationship hypovitaminosis D and the presence of NAFLD and steatohepatitis (NASH); however, results from vitamin D supplementation trials on liver outcomes are controversial. This narrative review provides an overview of the latest evidence on pathophysiological pathways connecting vitamin D to NAFLD, with emphasis on the effects of vitamin D treatment in MAFLD by a nonsystematic literature review of PubMed published clinical trials. This article conforms to the Scale for Assessment of Narrative Review Articles (SANRA) guidelines. Evidence so far available supports the hypothesis of potential benefits of vitamin D supplementation in selected populations of NAFLD patients, as those with shorter disease duration and mild to moderate liver damage.
Characterisation of the reversible formate dehydrogenases of Shewanella

The reversible action of tungsten or molybdenum-containing formate dehydrogenase (FDH) enzymes in reducing CO2 to formate has been proposed for storing renewably produced electricity with concomitant CO2 sequestration. Previous attempts have highlighted the unfeasibility of using purified enzyme systems for biotechnological purposes. In response the possibility of using the exoelectrogenic bacteria Shewanella oneidensis in association with a cathode to drive intracellular CO2 reduction is proposed. Since the native FDH enzymes of S.oneidensis have not been previously studied, this work concerns their characterisation and directionality to inform both on native physiology and possible future biotechnological applications. This thesis demonstrates that the native FDH enzymes of S.oneidensis are capable of CO2 reductase activity. Both forward (Km 39 μM) and reverse (Km 1.43 mM) directions of FDH catalysis in whole cell cultures are maximal when cultured in the presence of W. When grown under such conditions, two FDH isoforms (Fdh1αβγ and Fdh2αβγ) contribute to these activities, with protein purification confirming Fdh2αβγ as a tungstoenzyme. CO2 reductase activity in S.oneidensis cultures could be driven by a cathode in simple three electrode electrochemical experiments without exogenous mediators with high coloumbic efficiency, representing an interesting paradigm for future inexpensive microbial electrosynthetic study.
Graphene Oxide-Coated Gold Nanorods: Synthesis and Applications

The application of gold nanorods (AuNRs) and graphene oxide (GO) has been widely studied due to their unique properties. Although each material has its own challenges, their combination produces an exceptional material for many applications such as sensor, therapeutics, and many others. This review covers the progress made so far in the synthesis and application of GO-coated AuNRs (GO–AuNRs). Initially, it highlights different methods of synthesizing AuNRs and GO followed by two approaches (ex situ and in situ approaches) of coating AuNRs with GO. In addition, the properties of GO–AuNRs composite such as biocompatibility, photothermal profiling, and their various applications, which include photothermal therapy, theranostic, sensor, and other applications of GO–AuNRs are also discussed. The review concludes with challenges associated with GO–AuNRs and future perspectives.
The Stimulation of Neurogenesis Improves the Cognitive Status of Aging Rats Subjected to Gestational and Perinatal Deficiency of B9–12 Vitamins

A deficiency in B-vitamins is known to lead to persistent developmental defects in various organs during early life. The nervous system is particularly affected with functional retardation in infants and young adults. In addition, even if in some cases no damage appears evident in the beginning of life, correlations have been shown between B-vitamin metabolism and neurodegenerative diseases. However, despite the usual treatment based on B-vitamin injections, the neurological outcomes remain poorly rescued in the majority of cases, compared with physiological functions. In this study, we explored whether a neonatal stimulation of neurogenesis could compensate atrophy of specific brain areas such as the hippocampus, in the case of B-vitamin deficiency. Using a physiological mild transient hypoxia within the first 24 h after birth, rat-pups, submitted or not to neonatal B-vitamin deficiency, were followed until 330-days-of-age for their cognitive capacities and their hippocampus status. Our results showed a gender effect since females were more affected than males by the deficiency, showing a persistent low body weight and poor cognitive performance to exit a maze. Nevertheless, the neonatal stimulation of neurogenesis with hypoxia rescued the maze performance during adulthood without modifying physiological markers, such as body weight and circulating homocysteine. Our findings were reinforced by an increase of several markers at 330-days-of-age in hypoxic animals, such as Ammon’s Horn 1hippocampus (CA1) thickness and the expression of key actors of synaptic dynamic, such as the NMDA-receptor-1 (NMDAR1) and the post-synaptic-density-95 (PSD-95). We have not focused our conclusion on the neonatal hypoxia as a putative treatment, but we have discussed that, in the case of neurologic retardation associated with a reduced B-vitamin status, stimulation of the latent neurogenesis in infants could ameliorate their quality of life during their lifespan.
Centre of Pressure Estimation during Walking Using Only Inertial-Measurement Units and End-To-End Statistical Modelling

Estimation of the centre of pressure (COP) is an important part of the gait analysis, for example, when evaluating the functional capacity of individuals affected by motor impairment. Inertial measurement units (IMUs) and force sensors are commonly used to measure gait characteristic of healthy and impaired subjects. We present a methodology for estimating the COP solely from raw gyroscope, accelerometer, and magnetometer data from IMUs using statistical modelling. We demonstrate the viability of the method using an example of two models: a linear model and a non-linear Long-Short-Term Memory (LSTM) neural network model. Models were trained on the COP ground truth data measured using an instrumented treadmill and achieved the average intra-subject root mean square (RMS) error between estimated and ground truth COP of 12.3 mm and the average inter-subject RMS error of 23.7 mm which is comparable or better than similar studies so far. We show that the calibration procedure in the instrumented treadmill can be as short as a couple of minutes without the decrease in our model performance. We also show that the magnetic component of the recorded IMU signal, which is most sensitive to environmental changes, can be safely dropped without a significant decrease in model performance. Finally, we show that the number of IMUs can be reduced to five without deterioration in the model performance.
To reduce the average age of autism diagnosis, screen preschoolers in primary care

The American Academy of Pediatrics recommends autism spectrum disorder screening at the 18- and 24-month well-child visits. However, despite widespread toddler screening, many children are not diagnosed until school age, and delayed diagnosis is more common among low-income and minority children. Offering autism spectrum disorder screening at preschool well-child checks might reduce disparities and lower the overall age of diagnosis and service initiation. However, screening tools that span the preschool ages and are tailored for primary care are needed. Lay abstract Pediatric primary care providers check for autism signs, usually using a standard checklist, at 18- and 24-month well-child visits. When the checklist shows possible autism, children should be referred for additional treatment and evaluation with an autism specialist. However, many children with autism spectrum disorder are not detected as toddlers. Low-income and minority children are particularly likely to have a late autism spectrum disorder diagnosis. Checking for autism at preschool-aged well-child visits might be one way to identify autism spectrum disorder earlier, especially for low-income and minority children.
Ortho-Functionalized Dibenzhydryl Substituents in α-Diimine Pd Catalyzed Ethylene Polymerization and Copolymerization

Sterically bulky diarylmethyl-based ligands have received increasing attention in the field of late-transition-metal catalyzed olefin polymerization. Ortho-substituents may have a significant impact on the performance of diarylmethyl-based α-diimine Pd catalysts. In this contribution, a series of α-diimine Pd catalysts bearing ortho-methoxyl/hydroxyl functionalized dibenzhydryl units were prepared, characterized, and investigated in ethylene polymerization and copolymerization with methyl acrylate (MA). The catalytic performances were improved by introducing more ortho-substituents. The catalysts exhibited good thermal stabilities at high temperatures, producing branched polyethylenes. The catalysts bearing hydroxyl groups possessing intramolecular H-bonding, resulted in slightly higher incorporation ratios of MA unit when compared with the catalysts bearing methoxyl groups.
Heterotrimeric G-Protein Signalers and RGSs in Aspergillus fumigatus

The heterotrimeric G-protein (G-protein) signaling pathway is one of the most important signaling pathways that transmit external signals into the inside of the cell, triggering appropriate biological responses. The external signals are sensed by various G-protein-coupled receptors (GPCRs) and transmitted into G-proteins consisting of the α, β, and γ subunits. Regulators of G-protein signaling (RGSs) are the key controllers of G-protein signaling pathways. GPCRs, G-proteins, and RGSs are the primary upstream components of the G-protein signaling pathway, and they are highly conserved in most filamentous fungi, playing diverse roles in biological processes. Recent studies characterized the G-protein signaling components in the opportunistic pathogenic fungus Aspergillus fumigatus. In this review, we have summarized the characteristics and functions of GPCRs, G-proteins, and RGSs, and their regulatory roles in governing fungal growth, asexual development, germination, stress tolerance, and virulence in A. fumigatus.
Improved Long-term Survival with Contralateral Mastectomy in Young Women

With an estimated 226,870 diagnoses and 39,510 deaths in 2012, breast cancer remains the most commonly occurring and second most lethal cancer among women in the United States (Howlader et al., 2011). Among those with breast cancer, patients aged less than 40 remain a particular challenge due, in part, to the inherent biologic aggressiveness of their tumors. Young women have tumors that are more likely to be high-grade histopathologically; have a higher mitotic rate with lymphovascular invasion (LVI); have more pathologic LNs; and are more likely to be hormone receptor (HR) negative/HER2 negative (“triple negative”; Colleoni et al., 2002; Carey et al., 2006; Anders et al., 2008, Kurian et al., 2009; Lund et al., 2009; Telli et al., 2011; Ademuyiwa et al., 2013; de la Rochefordiere et al., 2013). Moreover, the patients are more likely to be black, have a family history of breast cancer, and have less favorable outcomes (Adami et al.,
Design and Implementation of the Arithmetic Circuits testing using Accumulator based Built-in Self Test

: Current VLSI circuits, e.g., data path architectures or digital signal Processing chips frequently contain arithmetic modules such as accumulators, Arithmetic Logic Units (ALUs). The basic idea of ABIST is to utilize accumulators for built-in testing which is compression of the CUT responses or generation of test patterns and has been shown to result in low hardware overhead and low impact on the circuit speed. In this work an accumulator-based test pattern generation scheme that compares with the previously proposed schemes and it was proved that the test vectors generated by an accumulator whose inputs are driven by a constant pattern can have acceptable pseudorandom individuality, if the input pattern is appropriately selected. Weighted pseudorandom Built-In Self-Test (BIST) schemes have been utilized in order to drive down the number of vectors to achieve complete fault coverage in BIST applications. Impartial sets comprising three weights, namely 0, 1, and 0.5 can be successfully utilized for test pattern generation, because they result in both low testing time and less power consumption. In this work, the digital circuits such as s27 Bench mark and SISO are, accumulator based BIST. Finally, the synthesis results of these circuits are compared with normal BIST. It was found that the circuit as low delay using accumulator based BIST.
V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants

We present V.PhyloMaker, a freely available package for R designed to generate phylogenies for vascular plants. The mega‐tree implemented in V.PhyloMaker (i.e. GBOTB.extended.tre), which was derived from two recently published mega‐trees and includes 74 533 species and all families of extant vascular plants, is the largest dated phylogeny for vascular plants. V.PhyloMaker can generate phylogenies for very large species lists (the largest species list that we tested included 314 686 species). V.PhyloMaker generates phylogenies at a fast speed, much faster than other phylogeny‐generating packages. Our tests of V.PhyloMaker show that generating a phylogeny for 60 000 species requires less than six hours. V.PhyloMaker includes an approach to attach genera or species to their close relatives in a phylogeny. We provide a simple example in this paper to show how to use V.PhyloMaker to generate phylogenies.
Introduction to Skinner-Urban’s Work on the Iwasawa Main Conjecture for GL2

These notes are organized as follows. In Section 2 we formulate various Iwasawa main conjectures for modular forms. We also explain an old result of Ribet to illustrate the rough idea of the strategy behind the later proofs. In Sections 3 and 4 we introduce the notions of automorphic forms and Eisenstein series on the unitary group GU(2,2). Section 5 is devoted to explaining the Galois argument. Sections 6-9 give the tools used in the computation for the Fourier and Fourier-Jacobi coefficients of various Eisenstein series, which is a crucial ingredient in the argument. In Section 10 we give an example of a theorem of the author generalizing the Skinner-Urban work.
1.12 Mammalian Retina Development

Daniel Kerschensteiner, a John F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, MO, United States; b Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, United States; c Department of Biomedical Engineering, Washington University School of Medicine, Saint Louis, MO, United States; and d Hope Center for Neurological Disorders, Washington University School of Medicine, Saint Louis, MO, United States
Partial sleep deprivation on dietary energy intake in healthy population: a systematic review and meta-analysis

1Nephrology and Mineral Metabolism Department. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. Mexico City, Mexico. 2School of Medicine. Universidad Nacional Autónoma de México. Mexico City, Mexico. 3Molecular Biology Department. Instituto Nacional de Cardiología Ignacio Chávez. Mexico City, Mexico. 4Sleep Disorders Clinic. Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. Mexico City, Mexico