Miracle-dz/UniFAR-FTUs huggingface dataset:
The Pax9/Wnt pathway regulates secondary palate formation in mice

Clefts of the palate and/or lip arise in about 1/700 human live births and are caused by multiple genetic and environmental factors. Studies of mouse knockout models of cleft palate have improved our understanding of the molecular control of palatogenesis. While it is known that Pax9 regulates palatogenesis through Bmp, Fgf and Shh signaling, there is still much to learn about its precise relationship with other pathways. Here we show that alterations of Wnt expression and decreased Wnt activity in Pax9-/- palatal shelves are a result of Pax9’s ability to directly bind and repress the promoters of Dkk1 and Dkk2, proteins that antagonize Wnt signaling. The delivery of small-molecule Dkk inhibitors (Wnt agonists) into the tail-veins of pregnant Pax9+/- mice from E10.5 to E14.5 restored Wnt signaling, promoted cell proliferation, bone formation and restored the fusion of palatal shelves in Pax9-/- embryos. In contrast, other organ defects in Pax9 mutants were not corrected. These data uncover a unique molecular relationship between Pax9 and Wnt genes in palatogenesis and offer a new approach for treating cleft palates in humans. Summary Statement These studies demonstrate that the Pax9/Wnt genes regulate murine palatogenesis. This unique molecular relationship is proven by the correction of cleft defects in Pax9-deficient mice through Wnt agonist therapies.
Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana (Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes

The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
Marine Vibrionaceae as a reservoir for bioprospecting and ecology studies

(01/11/2017) Marine Vibrionaceae as a reservoir for bioprospecting and ecology studies The exploration of biodiversity (“bioprospecting”) provides mankind with an immense pool of novel organisms, molecules and information, which can be exploited for the development of innovative biotechnological processes and new ways to treat diseases. In the past decades, the marine environment emerged as an untapped source of biodiversity, and this study investigated the marine bacterial family Vibrionaceae (“vibrios”) for its potential as reservoir of novel biodiversity and of species relevant for the ecology of the marine environment. The characterization of a novel species, Vibrio galatheae, contributed to the understanding of the phylogeny and diversity of Vibrionaceae, while the use of growth conditions mimicking the niche of isolation showed that substrates that are abundant in the marine environment significantly influence the metabolism of vibrios. Indeed, during a screening of approximately three hundred strains, the number of vibrios capable to inhibit the growth of a fish pathogen was nearly doubled when isolates were grown on chitin, the most abundant polymer in the marine environment, as compared to when they were grown on mannose or glucose. This observation led to investigate at the transcriptome level the effects of chitin on the two vibrios Vibrio coralliilyticus and Photobacterium galatheae. It was shown that the dynamics of chitin colonization and utilization in these two species are similar to those reported for the well-characterized chitin colonizer Vibrio cholerae. Bacteria reach chitinous surfaces by chemotaxis before adhering to it and completing their chitin degradation/utilization program. The complementation of this information with the metabolomic profiles of the strains suggested a possible role of secondary metabolites in chitin colonization, although further work is required to elucidate whether they are produced to antagonize competitors or to communicate with other colonizers and/or a potential host. In conclusion, this PhD study adds to the knowledge of Vibrionaceae as an untapped reservoir of biodiversity and important players in the ecology of the marine environment. Studying microbial eco-physiology is important not only for the development of ecological models, but also as foundation for bioprospecting studies, where this knowledge may be used, for example, to elicit silent biosynthetic gene clusters during natural product discovery.
Hindbrain and Spinal Cord Contributions to the Cutaneous Sensory Innervation of the Larval Zebrafish Pectoral Fin

Vertebrate forelimbs contain arrays of sensory neuron fibers that transmit signals from the skin to the nervous system. We used the genetic toolkit and optical clarity of the larval zebrafish to conduct a live imaging study of the sensory neurons innervating the pectoral fin skin. Sensory neurons in both the hindbrain and the spinal cord innervate the fin, with most cells located in the hindbrain. The hindbrain somas are located in rhombomere seven/eight, laterally and dorsally displaced from the pectoral fin motor pool. The spinal cord somas are located in the most anterior part of the cord, aligned with myomere four. Single cell reconstructions were used to map afferent processes and compare the distributions of processes to soma locations. Reconstructions indicate that this sensory system breaks from the canonical somatotopic organization of sensory systems by lacking a clear organization with reference to fin region. Arborizations from a single cell branch widely over the skin, innervating the axial skin, lateral fin surface, and medial fin surface. The extensive branching over the fin and the surrounding axial surface suggests that these fin sensory neurons report on general conditions of the fin area rather than providing fine location specificity, as has been demonstrated in other vertebrate limbs. With neuron reconstructions that span the full primary afferent arborization from the soma to the peripheral cutaneous innervation, this neuroanatomical study describes a system of primary sensory neurons and lays the groundwork for future functional studies.
Combination of Isoflurane and Propofol as General Anesthesia During Orthopedic Surgery of Perioperative Cerebral Hypoperfusion Rats to Avoid Cognitive Impairment

Background: Perioperative cerebral hypoperfusion (CH) is common, although the underlying mechanism of cognitive impairment that results due to perioperative cerebral hypoperfusion remains to be determined. Isoflurane anesthesia induces neuronal injury via endoplasmic reticulum (ER) stress, whereas a sub-anesthetic dose of propofol improves postoperative cognitive function. However, the effects of the combination of isoflurane plus propofol, which is a common aesthetic combination administered to patients, on ER stress and cognition remain unknown. Methods: We sought to determine the effects of isoflurane plus propofol on ER stress and cognitive function in rats insulted by cerebral hypoperfusion. Ligation of the bilateral common carotid arteries (CCA) was adopted to develop the cerebral hypoperfusion rat model. A second surgery, open reduction and internal fixation (ORIF), requiring general anesthesia, was performed 30 days later so that the effects of anesthetics on the cognitive function of CH rats could be assessed. Rats received isoflurane alone (1.9%), propofol alone (40 mg·kg−1·h−1) or a combination of isoflurane and propofol (1% and 20 mg·kg−1·h−1 or 1.4% and 10 mg·kg−1·h−1). Behavioral studies (contextual fear conditioning [FC] test), histological analyses (Nissl staining) and biochemical analyses (western blotting of the harvested rat brain tissues) were employed. Results: Hippocampus-dependent memory of rats in group IP1 (1% isoflurane plus 20 mg·kg−1·h−1 propofol) was not impaired, and expression level of γ-aminobutyric acid A type receptor α1 subunit, a key cognition-related protein, remained normal. ER stress alleviator, binding immunoglobulin protein, increased extremely while ER stress transcription factor, C/EBP homologous protein, showed no statistical difference compared with the control group. Numbers of surviving neurons confirmed the substantial neuronal damage caused by propofol or isoflurane alone. Conclusions: These data suggest that ER stress contributes to the underlying mechanism of cognitive impairment and that the combination of isoflurane and propofol did not aggravate cognitive impairment and ER stress in aging rats with CH that were further subjected to ORIF surgery.
Theoretical and in silico Analyses Reveal MYC as a Dynamic Network Biomarker in Colon and Rectal Cancer

In this article, we make a theoretical and in silico study for uncovering and evaluating biomarkers in colon and rectal cancer (CRC) by the dynamic network biomarker (DNB) theory. We propose a strategy to employ the theoretical concept of UICC TNM classification in CRC. To reveal the critical transition of CRC, the DNB algorithm was implemented to analyze the genome-wide dynamic network through temporal gene expression data. The relationship between gene sets and clinical features was evaluated by weighted gene co-expression network analysis. The results show that MYC was significantly associated with tumor amplification, tumor immune cells, and survival times. The candidate tumor suppressor genes were ZBTB16, MAL, LIFR, and SLIT2. Protein–protein interaction (PPI) analysis shows that these candidate tumor suppressor genes were significant in immune cells. Data from the Human Protein Atlas showed that a high expression of these candidate tumor suppressor genes was associated with favorable prognosis in TNM stages I–IV. In conclusion, this work provides significant and novel information regarding the TNM stage, cause, and consequences of elevated MYC expression in CRC. MYC expression levels had significant negative correlations with tumor suppressor genes and immune cells.
A Comparative Study of the Gut Microbiota Associated With Immunoglobulin a Nephropathy and Membranous Nephropathy

The pathogenesis of immunoglobulin A nephropathy (IgAN) and membranous nephropathy (MN) is characterized by immune dysregulation, which is related to gut dysbiosis. The aim of the study was to compare the gut microbiota of patients with IgAN and MN vs. healthy controls. We used 16S rDNA amplicon sequencing to investigate the bacterial communities of 44 patients with kidney biopsy-proven IgAN, 40 patients with kidney biopsy-proven MN, and 30 matched healthy controls (HC). The abundance of Escherichia-Shigella and Defluviitaleaceae_incertae_sedis were significantly higher in IgAN than in HC, whereas lower abundances were observed for Roseburia, Lachnospiraceae_unclassified, Clostridium_sensu_stricto_1, and Fusobacterium. Furthermore, the abundance of Escherichia-Shigella, Peptostreptococcaceae_incertae_sedis, Streptococcus, and Enterobacteriaceae_unclassified increased, while that of Lachnospira, Lachnospiraceae_unclassified, Clostridium_sensu_stricto_1, and Veillonella decreased in MN. The abundance of Megasphaera and Bilophila was higher, whereas that of Megamonas, Veillonella, Klebsiella, and Streptococcus was lower in patients with IgAN than in those with MN. Analysis of the correlations showed that in the IgAN group, Prevotella was positively correlated, while Klebsiella, Citrobacter, and Fusobacterium were negatively correlated with the level of serum albumin. Positive correlation also existed between Bilophila and Crescents in the Oxford classification of IgAN. In the MN group, negative correlation was observed between Escherichia-Shigella and proteinuria, Bacteroides and Klebsiella showed positive correlation with the MN stage. Patients with IgAN and MN exhibited gut microbial signatures distinct from healthy controls. Our study suggests the potential of gut microbiota as specific biomarker and contributor in the pathogenesis of IgAN and MN.
Passive acoustic monitoring as a law enforcement tool for Afrotropical rainforests

Hunting for wild meat is pervasive in Afrotropical forests and often the primary threat to large-bodied mammals even within protected areas, the effectiveness of which (at reducing hunting) is correlated with law enforcement efforts, especially anti-poaching patrols. However, although tropical protected areas are critically underfunded and law enforcement accounts for a substantial proportion of their budgets, few have mechanisms in place to evaluate and adaptively adjust anti-poaching strategies based on robust field evidence.
Ownership Structure and the Risk: Analysis of Indian Firms

Abstract Considering the positive relationship between ownership and firm performance in the corporate finance literature, the paper aims to investigate the effect of ownership structure on the risk associated with the firm. Portfolio theories state that an investment with a high return is expected to be associated with high risk; so, it can be argued that ownership should have a positive relation with risk too. However, another explanation is that since large shareholders, such as promoters and financial institutions, have a significant stake in firms, in developing countries like India they will avoid excess risk taking, and so there should be a negative relationship between ownership and risk associated with firms. Analysing Nifty-500 companies for the period of 2006/07–2015/16, the study has found that Indian blockholders are in general risk-averse. Results also suggest that profitability and growth opportunities have negative effects on risk, which again establishes the positive association between ownership structure and profitability.
Optimal Scheduling of Residential Electricity Demand Based on the Power Management of Hybrid Energy Resources

Abstract The present study sought to address the scheduling of the grid-connected hybrid energy resources under uncertainty of renewable sources, and load in the residential sector. After introducing hybrid resources, scheduling model was implemented through a power management algorithm in an attempt to optimize resource cost, emissions, and energy not supplied (ENS). The stated problem consists of two decision-making layers with different weight coefficients based on the prioritization of each objective function. The proposed algorithm is selected for energy optimal management based on technical constraints of the dispatchable and non-dispatchable resources, uncertainty parameters and day ahead real time pricing (RTP). Furthermore, the impact of demand response programs (DRP) on the given algorithm was investigated using load shedding and load shifting techniques. Finally, the results obtained led to the optimization of the functions in all decision-making layers with different modes of operation.
Hedges in Russian EAP writing: A corpus-based study of research papers in management

Abstract The fact that English has become a lingua franca of academic communication has led to increased attention to teaching English for academic purposes (EAP) at the academia. Academic discourse markers, such as hedges, have been an important topic in academic writing research whose prime aim is helping non-Anglophone researchers to present their research findings in English for international publication. This study investigates the use of the most frequent hedging devices in a corpus of 58 works written by Russian university students and compares it to a corpus of articles published in peer-reviewed journals in business and management. The analysis of learner corpus data has provided evidence of how Russian ELF speakers use the language, showing significant differences between the use of hedges by the students and professional writers. The research has also highlighted a number of challenges which non-native learners face when writing academic texts. The study may contribute to a higher level of L2 academic writing in ELF contexts and have implications for creating EAP courses, research of second language acquisition and writing pedagogy.
A Novel and Compact Circularly Polarized Antenna for 5G Wireless Local Area Network Application

Abstract The research paper presents a novel and compact circularly polarized (CP) antenna for a 5G wireless local area network (WLAN) application. It consists of a circular patch and a coaxial probe feed radiator. Circular polarization (CP) is attained by symmetric semi-circular slits of radius r1 at three edges of a circular path with 90° in direction, and the other semicircular slit is of different radius r2. To improve the impedance bandwidth and axial ratio, the radius of the fourth semicircular slit on circular patch antenna is varied. The design is verified by fabricating a compact antenna of 0. 65λ0 × 0. 65λ0 × 0. 01λ0. The measured 10 dB impedance bandwidth is 3.9 % (5.36–5.56 GHz), 3-dB axial ratio bandwidth is 1.1 % (5.43–5.49 GHz) and gain of 6.6 dBi at resonant frequency of 5.37 GHz is obtained. The authors also describe two-dimensional radiation patterns of azimuth and elevation plane surface current distribution of the CP patch, VSWR < 2. The proposed CP antenna is suitable for the 5G WLAN application. The proposed design is compared with various techniques in literature and tabulated. The measured results are also discussed and they are in good agreement with simulated results.
The Role of Antibodies in the Pathogenesis of Multiple Sclerosis

The presence of persistent intrathecal oligoclonal immunoglobulin G (IgG) bands (OCBs) and lesional IgG deposition are seminal features of multiple sclerosis (MS) disease pathology. Despite extensive investigations, the role of antibodies, the products of mature CD19+ B cells, in disease development is still controversial and under significant debate. Recent success of B cell depletion therapies has revealed that CD20+ B cells contribute to MS pathogenesis via both antigen-presentation and T-cell-regulation. However, the limited efficacy of CD20+ B cell depletion therapies for the treatment of progressive MS indicates that additional mechanisms are involved. In this review, we present findings suggesting a potential pathological role for increased intrathecal IgGs, the relation of circulating antibodies to intrathecal IgGs, and the selective elevation of IgG1 and IgG3 subclasses in MS. We propose a working hypothesis that circulating B cells and antibodies contribute significantly to intrathecal IgGs, thereby exerting primary and pathogenic effects in MS development. Increased levels of IgG1 and IgG3 antibodies induce potent antibody-mediated cytotoxicity to central nervous system (CNS) cells and/or reduce the threshold required for antigen-driven antibody clustering leading to optimal activation of immune responses. Direct proof of the pathogenic roles of antibodies in MS may provide opportunities for novel blood biomarker identification as well as strategies for the development of effective therapeutic interventions.
Impact of the Hydrogel Amendment and the Dry Period Duration on the Green Roof Retention Capacity

Abstract Climate changes as well as the urbanisation and economic development influence the characteristics of the stormwater runoff in the cities. The sealing of drainage basin surface leads to an increase of the runoff intensity, thereby decreasing the rainwater infiltration. This situation can lead to the risk of flooding in urban areas. Therefore, especially in great cities there is a need for application of such solutions that will support the operation of the sewage systems. The examples of such solutions are, among others, the green roofs. The paper presents the results of investigation of the water retention capacity of 4 green roof models containing following growing media: (1) the typical green roof substrate without any amendments, (2) the substrate with addition of about 1 % by weight of hydrogel (the cross-linked potassium polyacrylate), (3) the substrate containing about 0.25 % by weight of hydrogel, (4) the substrate with addition of expanded clay and perlite. The models were not vegetated in order to investigate only the water retention capacity of drainage elements and substrates. The water retention capacity of green roof models was investigated in the laboratory conditions with use of artificial precipitations simulated after diverse antecedent dry weather periods (ADWP) amounting to: 1, 2, 5, 7, and 12 days. The intensities of artificial precipitations were relatively high and ranged from 1.14 to 1.27 mm/min, whereas their durations ranged from 7.75 to 12.56 min. These values of intensities and durations corresponded to the design rainfall intensities calculated using Blaszczyk’s equation for annual rain depth equal to 600 mm and the return periods ranged from 5 to 15 years. The obtained results indicate that the water retention capacity of green roof models, expressed as the volumes (or depths) of rainwater retained within their structures, increases with an increase of ADWP. Results indicate that the relation between ADWP and the amount of water retained in the layers of green roofs in the case of relatively short antecedent dry weather periods provided for the analysis (from 1 to 7 days) may be approximately linear. The results of the one-way ANOVA indicate that in the case of all models there is a statistically significant difference between the values of retention depth for specified ADWP (p < 0.001). During more than half of simulated precipitations, especially in the case of longer ADWPs lasting 5, 7, and 12 days the best water retention capacity had Model 3, with substrate containing about 0.25 % by weight of hydrogel. On the other hand, the results show that the weakest retention capacity had Model 2 (with substrate containing 1 % by weight of hydrogel). In the case of longer ADWPs (lasting 7 and 12 days) relatively weak water retention capacity had Model 4 (with substrate containing the addition of expanded clay and perlite). It can be concluded that too large amount of hydrogel added to the substrate can have an unfavourable impact on the water retention capacity of green roofs.