Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene variants in ZGRF1 implicated for a rare sensory reflex epilepsy

Hot water epilepsy (HWE) is a rare sensory reflex epilepsy syndrome where seizures are precipitated by a stimulus of contact with hot water. While there is genetic basis to its etiology, identity of specific genes underlying this relatively uncommon disorder has remained unknown. Here, we present our studies aimed at identifying a causative gene in a four-generation family (Family 227) with several of its members affected with the disorder, from the southern parts of India. We conducted whole exome-based sequencing, and examined the HWE genetic locus previously known to map to 4q24-q28 (HWE2, MIM: 613340) in the family and identified a sequence variant, c.1805C>T (p.Thr602Ile) in ZGRF1 co-segregating with the disorder. Complete transcript structure of ZGRF1 was examined in 288 HWE patients and five missense variants, Arg326Gln, Glu660Gly, Arg1862*, Phe1940Leu and Asp1984Gly, present exclusively or almost exclusively in the patients were found. Functional correlates of the six variants identified were examined in cultured mammalian cells. We observed spindle pole defects during cell division and partially disrupted localization of UPF1, a protein involved in cell cycle regulation, at spindles. Our observations provide insights into the genetic basis of HWE and suggest involvement of unanticipated molecular mechanisms underlying this neurobehavioral phenotype.
Analysis of real time compression algorithm for local speech syllable signals in English pronunciation

Abstract When the current algorithm is used to compress the signal, it will cause serious distortion of the signal. In this paper, a real-time compression algorithm for local speech syllable signals in English pronunciation based on variational Bayesian method is proposed. Firstly, the sparse base of the syllable signal is selected, and the signal observation matrix is established. BP algorithm and OMP algorithm are combined, and the syllable signal is reconstructed by sparse matrix of syllable signal. On this basis, the prior and posteriori functions of syllable signal are used to calculate the variational parameters of syllable signals, so that the real-time compression algorithm of syllable signals in local speech is realized. Experimental results show that the proposed algorithm can guarantee the quality of the signal.
Limits and constraints on mechanisms of cell-cycle regulation imposed by cell sizehomeostasis measurements

High-throughput imaging has led to an explosion of observations regarding cell-size homeostasis across the kingdoms of life. Among bacteria, “adder” behavior in which a constant size appears to be added during each cell cycle is ubiquitous, while various eukaryotes show other size-homeostasis behaviors. Since interactions between cell-cycle progression and growth ultimately determine size-homeostasis behaviors, we developed a general model of cell proliferation to: 1) discover how the requirement of cell-size homeostasis limits mechanisms of cell-cycle control; 2) predict how features of cell-cycle control translate into size-homeostasis measurements. Our analyses revealed plausible cell-cycle control scenarios that nevertheless fail to regulate cell size, conditions that generate apparent adder behavior without underlying adder mechanisms, cell-cycle features that play unintuitive roles in causing deviations from adder, and distinguishing predictions for extended size-homeostasis statistics according to the underlying control mechanism. The model thus provides holistic insight into the mechanistic implications of cell-size homeostasis measurements.
Missense Pathogenic variants in KIF4A Affect Dental Morphogenesis Resulting in X-linked Taurodontism, Microdontia and Dens-Invaginatus

The etiology of dental anomalies is multifactorial; and genetic and environmental factors that affect the dental lamina have been implicated. We investigated two families of European ancestry in which males were affected by taurodontism, microdontia and dens invaginatus. In both families, males were related to each other via unaffected females. A linkage analysis was conducted in a New Zealand family, followed by exome sequencing and focused analysis of the X-chromosome. In a US family, exome sequencing of the X-chromosome was followed by Sanger sequencing to conduct segregation analyses. We identified two independent missense variants in KIF4A that segregate in affected males and female carriers. The variant in a New Zealand family (p.Asp371His) predicts the substitution of a residue in the motor domain of the protein while the one in a US family (p.Arg771Lys) predicts the substitution of a residue in the domain that interacts with Protein Regulator of Cytokinesis 1 (PRC1). We demonstrated that the gene is expressed in the developing tooth bud during development, and that the p.Arg771Lys variant influences cell migration in an in vitro assay. These data implicate missense variations in KIF4A in a pathogenic mechanism that causes taurodontism, microdontia and dens invaginatus phenotypes.
Criticality as a Determinant of Integrated Information Φ in Human Brain Networks

Integrated information theory (IIT) postulates that consciousness arises from the cause-effect structure of a system but the optimal network conditions for this structure have not been elucidated. In the study, we test the hypothesis that network criticality, a dynamically balanced state between a large variation of functional network configurations and a large constraint of structural network configurations, is a necessary condition for the emergence of a cause-effect structure that results in a large Φ, a surrogate of integrated information. We also hypothesized that if the brain deviates from criticality, the cause-effect structure is obscured and Φ diminishes. We tested these hypotheses with a large-scale brain network model and high-density electroencephalography (EEG) acquired during various levels of human consciousness during general anesthesia. In the modeling study, maximal criticality coincided with maximal Φ. The constraint of the structural network on the functional network is maximized in the maximal criticality. The EEG study demonstrated an explicit relationship between Φ, criticality, and level of consciousness. Functional brain network significantly correlated with structural brain network only in conscious states. The results support the hypothesis that network criticality maximizes Φ.
Social factors, not anthropogenic noise or artificial light, influence onset of dawn singing in a common songbird

ABSTRACT With worldwide increases in artificial light and anthropogenic noise, understanding how these pollutants influence animals allows us to better mitigate potential negative effects. Both light and noise affect the timing of daily activities, including the onset of dawn song in birds, yet the influence of these pollutants compared with social factors that also influence song onset remains unknown. We investigated the onset of dawn song, testing hypotheses aimed at understanding the influences of light and noise pollution as well as male competition, pairing status, and breeding stage on timing of dawn singing by male House Wrens (Troglodytes aedon). Overall, models with social factors fit song onset data better than models with abiotic factors of noise and sky glow, and the highest ranking model included nesting stage, number of male neighbors, and temperature. Males began singing earlier when they were building nests and when mates were fertile than during later nesting stages. Males also sang earlier as the number of male neighbors increased. The timing of dawn song by male House Wrens appeared unaffected by day-to-day variation in light and noise pollution, with social factors having larger effects on the onset of daily behavior in this species.
Comparative Analysis of Models for Student Performance with Data Mining Tools

: In modern time the analysis of student performance is very challenging task for every educational institutions. The main reason behind that rapid growth of population and increasing number of schools and colleges claiming that they can give their students quality education and provide the best environment for quality learning and many other aspects through which they can increase the performance capabilities in each and every student. There are different researcher have worked in the field of analysis of student performance, but they have not achieved satisfactory result. In this research work, we have used various data mining techniques for analyzing of student performance using WEKA , Rapid Miner, Tanagra and Orange data mining tools in case of both Portuguese and Mathematics Dataset . Random forest gives best accuracy as 93.52% in Weka data mining tool while 73.65% of accuracy in Tanagra data mining tool in binary and multiclass problem respectively with Portuguese data set. Similarly, in case of Mathematics dataset, Radom forest achieved 92.40% of accuracy in Weka data mining tool while 74.43% of accuracy in Orange data mining tool with binary and multiclass problem respectively. Finally, Random forest is robust model for classification of student performance.
Comparative in vitro antimicrobial effect of Sarcocephalus latifolius (Sm.) E. A. Bruce leaves and roots on foodborne pathogens

Sarcocephalus latifolius (Sm.) E. A. Bruce is a plant used traditionally to treat a wide range of infectious diseases, including foodborne ones. This study aimed to compare its roots and leaves extract antibacterial effects in vitro. Thus, these organs were collected, dried and powdered for the extractions and phytochemical screening. Four extracts (water, ethyl-acetate, methanol and ethanol) were tested on ten references strains (RS) and nine non references strains of Staphylococcus isolated from meat strains (MS) using disk method. Minimal inhibitory (MIC) and bactericidal concentrations (MBC) were determined respectively by macrodilution method and by solid culture medium. The results showed that the MS seem more susceptible than RS. The lowest activity was shown by roots hydro-ethanolic extract on Micrococcus luteus, whereas the highest was obtained with leaves ethanolic extract on Staphylococcus cohini. The MIC ranges from 0.312 to 25 mg/ml for the MS and from 6.25 to 12.50 mg/ml for the RS. About MBC, they vary from 12.50 to 50 mg/ml for all susceptible tested microorganisms. S. latifolius extracts have an inhibitory effect on both strains such as Staphylococcus xylosus, Escherichia coli O157, Staphylococcus sciuri, Staphylococcus aureus, M. luteus, Candida albicans, S. cohinii, Proteus mirabilis and bactericidal effect on the three last ones. These results support the traditional use of S. latifolius in infectious diseases control; furthermore, its leaves seem more effective than the roots. These findings may serve as a starting point for the development of a new drug for the control of this kind of diseases and could sustain the species use. Key words: Pathogens, medicinal plant, Sarcocephalus latifolius, phytochemical screening, metabolites.
Exfoliated near infrared fluorescent CaCuSi4O10 nanosheets with ultra-high photostability and brightness for biological imaging

Imaging of complex (biological) samples in the near infrared (nIR) range of the spectrum is beneficial due to reduced light scattering, absorption, phototoxicity and autofluorescence. However, there are only few near infrared fluorescent materials known and suitable for biomedical applications. Here, we exfoliate the layered pigment CaCuSi4O10 (known as Egyptian Blue, EB) via facile tip sonication into nanosheets (EB-NS) with ultra-high nIR fluorescence stability and brightness. The size of EB-NS can be tailored by tip sonication to diameters < 20 nm and heights down to 1 nm. EB-NS fluoresce at 910 nm and the total fluorescence intensity scales with the number of Cu2+ ions that serve as luminescent centers. Furthermore, EB-NS display no bleaching and ultra-high brightness compared to other nIR fluorophores. The versatility of EB-NS is demonstrated by in vivo single-particle tracking and microrheology measurements in developing Drosophila embryos. Additionally, we show that EB-NS can be uptaken by plants and remotely detected in a low cost stand-off detection setup despite strong plant background fluorescence. In summary, EB-NS are a highly versatile, bright, photostable and biocompatible nIR fluorescent material that has the potential for a wide range of bioimaging applications both in animal and plant systems.
The complete mitochondrial genome of the critically endangered Lesser Antillean iguana (Iguana delicatissima; Squamata: Iguanidae)

Abstract The Lesser Antillean iguana, Iguana delicatissima Laurenti 1768, is one of the most endangered vertebrate taxa in the West Indies. This species faces significant threats, including introgressive hybridization with the introduced congener Iguana iguana. We deploy a combination of off-target sequence capture obtained from Illumina® reads and targeted Sanger reads to assemble the mitochondrial genome of I. delicatissima. The mitogenome is 16,616 bp in length and is comprised of 13 protein-coding genes, two ribosomal subunits (rRNAs), 22 transfer RNAs, and a control region. Gene order is identical to that of congener I. iguana and other closely related taxa, absent of any tandem repeat regions. We show the phylogenetic utility of the mitogenome with a maximum-likelihood analysis, which yields a topology concordant with previous studies of iguanine taxa. We are hopeful that this genomic resource will be useful in further informing applied conservation and management for this critically endangered species.
Broiler intestine DMT1 gene expression and bone characteristics, as affected by in ovo injection of different forms of manganese

Abstract This study was conducted to compare the effects of in ovo injection of different sources of manganese (Mn) on Divalent Metal Transporter 1 (DMT1) gene expression in the small intestine of broilers embryo and hatchling, and its subsequent effects on bone development. A total of 480 fertile eggs (ROSS 308) on embryonic day 17 were divided into 6 treatments with 3 replicates of 20 fertile eggs per replicate. Treatments were included: non-injected (NC) and diluent-injected controls (PC), manganese sulphate (MnS), manganese-methionine (Mn-Met), nano manganese (NMn) and nano manganese-methionine (NMn-Met) groups. Results showed that in ovo injection of different sources of Mn could change the DMT1 mRNA level of intestinal cells (p < .05). DMT1 mRNA level was up-regulated significantly (p < .05) by both nano forms of Mn on embryonic day 18 (E18) and post-hatch day 1 (P1) in all intestinal segments. On post-hatch day 7 (P7), bone length was higher in NMn treatment (p < .05) and tibia ash were affected by NMn and NMn-Met groups (p < .05). On (E18), the percentage of fresh and dry tibia weights were affected by Mn-Met, while on P14, the same characteristics were affected by NMn and MnS treatments, respectively (p < .05). The percentage of Mn in the tibiae ash content significantly (p < .05) enhanced by nano forms of Mn. It is concluded that in ovo injection of nano forms of Mn, either NMn or NMn-Met can be considered as a new strategy to improve Mn absorption in broilers intestine. Highlights In ovo injection of nanoparticles led to positive effects on DMT1 mRNA level in different intestinal segment of broilers embryo and hatchling. In ovo injection of nanoparticles enhance the percentage of Mn in the tibiae ash content of broilers embryo and hatchling. In ovo injection of Mn sources improved bone development.
The critical role of mental imagery in human emotion: insights from Aphantasia

One proposed function of imagery is to make thoughts more emotionally evocative through sensory simulations. Here we report a novel test of this theory utilizing a special population with no visual imagery: Aphantasia. After using multi-method verification of aphantasia, we show that this condition, but not the general population, is associated with a flat-line physiological response to frightening written, but not perceptual scenarios, supporting imagery’s critical role in emotion.
Co-disposition of chitosan nanoparticles by multi types of hepatic cells and their subsequent biological elimination: the mechanism and kinetic studies at the cellular and animal levels

Background: The clearance of nanomaterials (NMs) from the liver is essential for clinical safety, and their hepatic clearance is primarily determined by the co-disposition process of various types of hepatic cells. Studies of this process and the subsequent clearance routes are urgently needed for organic NMs, which are used as drug carriers more commonly than the inorganic ones. Materials and methods: In this study, the co-disposition of chitosan-based nanoparticles (CsNps) by macrophages and hepatocytes at both the cellular and animal levels as well as their subsequent biological elimination were investigated. RAW264.7 and Hepa1-6 cells were used as models of Kupffer cells and hepatocytes, respectively. Results: The cellular studies showed that CsNps released from RAW264.7 cells could enter Hepa1-6 cells through both clathrin- and caveolin-mediated endocytosis. The transport from Kupffer cells to hepatocytes was also studied in mice, and it was observed that most CsNps localized to the hepatocytes after intravenous injection. Following the distribution in hepatocytes, the hepatobiliary–fecal excretion route was shown to be the primary elimination route for CsNps, besides the kidney–urinary excretion route. The elimination of CsNps in mice was a lengthy process, with a half time of about 2 months. Conclusion: The demonstration in this study of the transport of CsNps from macrophages to hepatocytes and the subsequent hepatobiliary–fecal excretion provides basic information for the future development and clinical application of NMs.
Evolutionary arms-races between host and parasitic RNA replicators in an artificial cell-like system

A crucial problem for primitive replicators before the origin of life is the appearance of parasitic or selfish replicators, which destabilize molecular cooperation and prevent the development of complexity. To date, theoretical and experimental studies have indicated that spatial structures, such as cell-like compartments, support sustainable replication of primitive replicators even in the presence of parasites. However, it is still a mystery how these host and parasitic replicators can evolve when they undergo long-term co-replication. Here, we investigated the coevolutionary process between an artificial RNA replicator (host RNA) and spontaneously appearing parasitic replicator (parasitic RNA) in artificial cell-like compartments. We performed a long-term replication experiment and found that the population dynamics of the host and parasitic RNAs gradually changed and novel types of hosts and parasites continued to appear. Competitive replication assays confirmed that parasite-resistant evolution of the host RNA and counter-adaptive evolution of the parasitic RNA occurred one after another. These results demonstrated that evolutionary arms races occur in this simple molecular system and generate a continuously-evolving molecular ecosystem. This coevolutionary process between host and parasitic molecules might play an important role in the open-ended evolution and development of complexity for primitive self-replication systems.
Non-Targeted Metabolomics Reveals Patterns of Metabolic Changes during Poplar Seed Germination

Research Highlights: This study was the first to use metabolomics techniques to investigate seed germination in poplar, a model woody plant. Our results lay a foundation for uncovering changes in metabolite levels during woody plant seed germination and for understanding the underlying mechanism. Background and Objectives: Poplar is a model woody plant. Because poplar can be easily propagated asexually, the molecular mechanism of poplar seed germination has not been well studied. However, long-term asexual reproduction of poplar leads to seedlings with weak resistance, high vulnerability to degradation, and reduced growth potential. Materials and Methods: The non-targeted metabolomics technique was used to analyze changing trends in metabolite contents during the poplar seed germination process. Results: We found that the number of differential metabolites increased as seed germination progressed. Metabolic pathway analysis of differential metabolites revealed that galactose metabolism and alanine, aspartate, and glutamate metabolism were significantly enriched during all germination periods. MapMan-based visual analysis of metabolic pathways of differential metabolites indicated that glutamine, glutamic acid, phenylalanine, arginine, and asparagine contents increased with germination time, with most metabolites related to glucose metabolism following similar trends. Contents of most metabolites related to the tricarboxylic acid cycle exhibited a fluctuating pattern. Conclusions: This study has revealed the major changes taking place in primary metabolite contents during poplar seed germination and has laid the foundation for elucidation of the molecular mechanism of poplar seed germination.
Translation elongation factor 1A2 is encoded by one of four closely related eef1a genes and is dispensable for survival in zebrafish

Zebrafish are valuable model organisms for the study of human single-gene disorders: they are genetically manipulable, their development is well understood, and mutant lines with measurable, disease-appropriate phenotypic abnormalities can be used for high throughput drug screening approaches. However, gene duplication events in zebrafish can result in redundancy of gene function, masking loss of function phenotypes and thus confounding this approach to disease modelling. Furthermore, recent studies have yielded contrasting results depending on whether specific genes are targeted using genome editing to make mutant lines, or whether morpholinos are used (morphants). De novo missense mutations in the human gene EEF1A2, encoding a tissue-specific translation elongation factor, cause severe neurodevelopmental disorders; there is a real need for a model system in which to study these disorders and we wanted to explore the possibility of a zebrafish model. We identified four eef1a genes and examined their developmental and tissue-specific expression patterns: eef1a1l1 is first to be expressed whilst eef1a2 is only detected later during development. We then determined the effects of introducing null mutations into eEF1A2 in zebrafish using CRISPR/Cas9 gene editing, in order to compare the results with previously described morphants, and with the severe neurodegenerative lethal phenotype of eEF1A2-null mice. In contrast with both earlier analysis in zebrafish using morpholinos and with the mouse eEF1A2-null mice, disruption of the eef1a2 gene in zebrafish is compatible with normal lifespan. The resulting lines, however, may provide a valuable platform for studying the effects of expression of mutant human eEF1A2 mRNA.