Miracle-dz/UniFAR-FTUs huggingface dataset:
New GFAP splice isoform (GFAPμ) differentially expressed in glioma translates into 21 kDa N-terminal GFAP protein

The glial fibrillary acidic protein (GFAP) is a type III intermediate filament (IF) protein that is highly expressed in astrocytes, neural stem cells, and in gliomas. Gliomas are a heterogeneous group of primary brain tumors that arise from glia cells or neural stem cells and rely on accurate diagnosis for prognosis and treatment strategies. GFAP is differentially expressed between glioma subtypes and therefore often used as a diagnostic marker. However, GFAP is highly regulated by the process of alternative splicing; many different isoforms have been identified. Differential expression of GFAP isoforms between glioma subtypes suggests that GFAP isoform-specific analyses could benefit diagnostics. In this study we report on the differential expression of a new GFAP isoform between glioma subtypes, GFAPμ. A short GFAP transcript resulting from GFAP exon 2 skipping was detected by RNA sequencing of human glioma. We show that GFAPμ mRNA is expressed in healthy brain tissue, glioma cell lines, and primary glioma cells and that it translates into a ~21 kDa GFAP protein. 21 kDa GFAP protein was detected in the IF protein fraction isolated from human spinal cord as well. We further show that induced GFAPμ expression disrupts the GFAP IF network. The characterization of this new GFAP isoform adds on to the numerous previously identified GFAP splice isoforms. It emphasizes the importance of studying the contribution of IF splice variants to specialized functions of the IF network and to glioma diagnostics. Summary statement RNA sequencing data of glioma patient material reveals the differential expression of a short GFAP splice isoform, GFAPμ, between glioma subtypes. GFAPμ translates into a 21 kDa N-terminal GFAP protein which can disrupt the GFAP intermediate filament network.
User Scheduling and Antenna Topology in Dense Massive MIMO Networks: An Experimental Study

A massive MIMO network can serve ten’s of users simultaneously. However, in dense scenarios the users are potentially closely-spaced, potentially resulting in substantial inter-user interference. Scheduling can overcome this by selecting the users that lead to the highest combined spectral efficiency. As scheduling comes with a significant pilot overhead, an alternative strategy could minimize user correlation by distributing the antenna elements in space. In this paper, we propose a comprehensive system study including antenna topology and distribution, user scheduling and pilot overhead reduction. Our user scheduling and pilot reduction algorithms are evaluated using system level simulations relying on indoor line-of-sight channel measurements from a 64 antenna base station at 2.61GHz. To have a thorough evaluation of the proposed algorithm, we consider four different antenna topologies, including co-located and distributed placement of the base station arrays. Our evaluation shows that in a conference room with 64 densely deployed users, our proposed low complexity algorithm can improve the spectral efficiency by at least 14% compared to random user selection with the best antenna distribution strategy. Finally, our results show that by relying on channel hardening, we reduce the pilot overhead by 3.2 $\times$ .
Genomic signatures of neurodegeneration and the evolution of mammalian brain.

Due to the complex adaptive costs and benefits of large brains and large neocortical volume, mammalian species exhibit huge variation in brain size. However, the precise nature of the genomic changes accounting for these variations remains poorly understood. Using genome-wide comparative analysis of gene family size of more than 39 fully sequenced mammalian species, I studied whether changes in the number of copies of genes involved in distinct cellular and developmental functions has contributed to shaping the morphological, physiological and metabolic machinery supporting brain evolution in mammalians. My results reveal an overrepresentation of gene families displaying a positive association between GFS and level of encephalization. This bias occurs most prominently in families associated with specific biological functions, such as cell-cell signalling, chemotaxis and immune system. Moreover, I find that most gene family size variations associated with increased brain size are mostly explained by the link between neocortex ratio and gene family size variations. The results in this study suggest that variations in gene family size underlie morphological adaptations during brain evolution in mammalian lineages. Lastly, using comparative transcriptomics analysis across different human tissue types with cellular longevities ranging from 120 days to over 70 years, I set out to identify the molecular signature of long term post-mitotic cell maintenance. I found that genes down regulated in Alzheimer’s and Parkinson’s disease are significantly enriched in genes whose expression levels are associated with increased post-mitotic cellular longevity (PMCL). This holds true also for genes down regulated in Hutchinson-Gilford progeria-derived fibroblasts. The work here presented suggest that PMCL-associated genes are part of a generalized machinery of post-mitotic maintenance and functional stability in both neural and non-neural that becomes compromised in two specific neurodegenerative conditions and supports the notion of a common molecular repertoire for cell maintenance differentially engaged in different cell types with differing survival requirements.
Notes on identity, new synonymy and larva of Ivalia Jacoby (Coleoptera: Chrysomelidae) with description of a new species

Genus Ivalia Jacoby is characterized morphologically, and Amphimeloides Jacoby syn. nov. and Taizonia Chen syn. nov. are junior synonyms with it. Several Ivalia species are figured, including Ivalia bella (Chen) comb. nov., I. dorsalis (Jacoby) comb. nov., and I. viridipennis Jacoby. A new species of Ivalia from the Nilgiri Hills in south India, I. korakundah sp. nov., is described and illustrated, including the larvae. Larvae were associated with adults by sequencing a fragment of the mitochondrial gene cytochrome oxidase I. Larval morphology is discussed and compared with that of other flea beetles.
Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus

Lineages of the cyanobacteria Prochlorococcus marinus have diverged into two genetically distinct ‘ecotypes,’ high-light adapted (HL) and low-light adapted (LL), which thrive under different environmental conditions. This type of niche differentiation in prokaryotes is often accompanied by genetic and genomic divergence. Differential selection pressure associated with ecotype divergence can be analyzed using models of codon evolution. However, some characteristics of the Prochlorococcus genome violate underlying assumptions of these models. For example, high levels of recombination between bacterial strains are known to cause false positives for codon models. Therefore, it is important that statistical methods for detecting recombination be reliable. In Chapter 2, I evaluate a set of recombination detection methods under four different scenarios related to functional divergence: 1) varying tree shape, 2) positive selection, 3) non-stationary evolution, and 4) varying levels of recombination and divergence.
Implementing Theory of Mind on a Robot Using Dynamic Epistemic Logic

Previous research has claimed dynamic epistemic logic (DEL) to be a suitable formalism for representing essential aspects of a Theory of Mind (ToM) for an autonomous agent. This includes the ability of the formalism to represent the reasoning involved in false-belief tasks of arbitrary order, and hence for autonomous agents based on the formalism to become able to pass such tests. This paper provides evidence for the claims by documenting the implementation of a DEL-based reasoning system on a humanoid robot. Our implementation allows the robot to perform cognitive perspective-taking, in particular to reason about the first- and higher-order beliefs of other agents. We demonstrate how this allows the robot to pass a quite general class of false-belief tasks involving human agents. Additionally, as is briefly illustrated, it allows the robot to proactively provide human agents with relevant information in situations where a system without ToM-abilities would fail. The symbolic grounding problem of turning robotic sensor input into logical action descriptions in DEL is achieved via a perception system based on deep neural networks.
Delete- and Ordering-Relaxation Heuristics for HTN Planning

In HTN planning, the hierarchy has a wide impact on solutions. First, there is (usually) no state-based goal given, the objective is given via the hierarchy. Second, it enforces actions to be in a plan. Third, planners are not allowed to add actions apart from those introduced via decomposition, i.e. via the hierarchy. However, no heuristic considers the interplay of hierarchy and actions in the plan exactly (without relaxation) because this makes heuristic calculation NP-hard even under delete relaxation. We introduce the problem class of delete- and ordering-free HTN planning as basis for novel HTN heuristics and show that its plan existence problem is still NP-complete. We then introduce heuristics based on the new class using an integer programming model to solve it.
Neural Tensor Model for Learning Multi-Aspect Factors in Recommender Systems

Recommender systems often involve multi-aspect factors. For example, when shopping for shoes online, consumers usually look through their images, ratings, and product's reviews before making their decisions. To learn multi-aspect factors, many context-aware models have been developed based on tensor factorizations. However, existing models assume multilinear structures in the tensor data, thus failing to capture nonlinear feature interactions. To fill this gap, we propose a novel nonlinear tensor machine, which combines deep neural networks and tensor algebra to capture nonlinear interactions among multi-aspect factors. We further consider adversarial learning to assist the training of our model. Extensive experiments demonstrate the effectiveness of the proposed model.
Long survival of “living fossils” with low taxonomic diversities in an evolving food web

Abstract Living fossils are taxonomic groups surviving for a long time without any remarkable morphological change. Most of them retain low taxonomic diversities. Although some of them have survived in refuges to avoid predators and competitors, not all living fossils live in refuges. The survival of these groups, therefore, should be discussed in the context of biological interaction. I carried out computer simulations of a model food web system, in which each species feeds on others according to its feeding preference. The system evolves via evolution of species. In the simulation, some clades, like “living fossils,” survived for a long time with low species diversities. Such clades consisted of species with low evolutionary rates, which result in high predation pressure and intraclade competition for food. Nevertheless, the clades sustainably utilize prey clades and are consequently provided with sufficient food. In addition, because of the low species diversities of the clades, predators of the clades soon become extinct through lack of food. This study strongly suggests that in an evolving food web system, the low evolutionary rates of living fossils allow the long survival of those groups with low taxonomic diversities.
Woody Shrubs as a Barrier to Invasion by Cogongrass (Imperata cylindrica)

Abstract Cogongrass invades forests through rhizomatous growth and wind-dispersed seeds. Increased density and abundance of woody vegetation along forest edges may strengthen biotic resistance to invasion by creating a vegetative barrier to dispersal, growth, or establishment of cogongrass. We evaluated differences in dispersal of cogongrass spikelets experimentally released from road edges into tallgrass-dominated and shrub-encroached longleaf pine forests (Pinus palustris). Average maximum dispersal distances were greater in the pine–tallgrass forest (17.3 m) compared to the pine–shrub forest association (9.4 m). Spikelets were more likely to be intercepted by vegetation in pine–shrub forests compared to pine–tallgrass forests. Results suggest that dense woody vegetation along forest edges will slow spread from wind-dispersed cogongrass seeds. Nomenclature: Bluestem grasses, Andropogon spp. , Schizachyrium spp. ; cogongrass, Imperata cylindrica (L.) Beauv. ; longleaf pine, Pinus palustris Mill Interpretative Summary: It has been suggested that dense woody vegetation along forest edges may form a barrier to invasive species either through effects on microhabitat or effects on seed dispersal. This study evaluated use of dense woody vegetation along forest edges as a barrier to seed dispersal into forest interiors. In this study, more cogongrass spikelets dispersed farther into open longleaf pine forests with a tallgrass understory compared to longleaf pine forests with dense shrubby understories. Reduced wind speed and increased vegetative interception of spikelet in the shrub-encroached forests may have prevented greater dispersal into these forests. However, a few spikelets released into open or shrubby forests dispersed farther than could be measured. These results suggest that managers seeking to control cogongrass may benefit by maintaining dense woody edges along forests and prioritizing management techniques that prevent spread of or treat cogongrass growing near less densely wooded habitats. These results also suggest that although dense woody vegetation may slow spread of cogongrass into forest interiors, such vegetation is unlikely to completely prevent invasion. Therefore, managers will need to implement additional control techniques in order to protect these forested areas from invasion.
Physicochemical properties of soy protein isolates-acacia gum conjugates.

Mu L. , Zhao H. , Zhao M. , Cui Ch., Liu L. (2011): Physicochemical properties of soy protein isolatesacacia gum conjugates . Czech J. Food Sci., 29: 129–136. Protein-polysaccharide conjugates were generally prepared by dry-heating. However, it was time-consuming and the sample gained was inhomogeneous. A faster way of preparing protein-polysaccharide conjugates is needed. Accordingly, soy protein isolates (SPI)-Acacia gum (GA) conjugates prepared by the wet-heating method were studied in the present work. Physicochemical properties of SPI-GA conjugates were also determined. The results showed that the wet-heating method could improve the rate of the graft reaction of protein and polysaccharide. The solubility of SPI-GA conjugates was significantly ( P < 0.05) higher than that of unreacted SPI-GA mixtures and SPI at the same pH values. The emulsion activity index (EAI) of the grafted SPI increased remarkably. Moreover, a significant ( P < 0.05) improvement on the emulsifying stability index (ESI) was observed and emulsions with a smaller droplet size were obtained. No visible flocculation during extended storage (30 days) was observed. The time course of the development of the graft reaction of SPI with GA was also shown by SDS-PAGE.
Learning Regional Attention Convolutional Neural Network for Motion Intention Recognition Based on EEG Data

Recent deep learning-based Brain-Computer Interface (BCI) decoding algorithms mainly focus on spatial-temporal features, while failing to explicitly explore spectral information which is one of the most important cues for BCI. In this paper, we propose a novel regional attention convolutional neural network (RACNN) to take full advantage of spectral-spatial-temporal features for EEG motion intention recognition. Time-frequency based analysis is adopted to reveal spectral-temporal features in terms of neural oscillations of primary sensorimotor. The basic idea of RACNN is to identify the activated area of the primary sensorimotor adaptively. The RACNN aggregates a varied number of spectral-temporal features produced by a backbone convolutional neural network into a compact fixed-length representation. Inspired by the neuroscience findings that functional asymmetry of the cerebral hemisphere, we propose a region biased loss to encourage high attention weights for the most critical regions. Extensive evaluations on two benchmark datasets and real-world BCI dataset show that our approach significantly outperforms previous methods.
Bone Regeneration Capability of 3D Printed Ceramic Scaffolds

In this study, we evaluated the bone regenerative capability of a customizable hydroxyapatite (HA) and tricalcium phosphate (TCP) scaffold using a digital light processing (DLP)-type 3D printing system. Twelve healthy adult male beagle dogs were the study subjects. A total of 48 defects were created, with two defects on each side of the mandible in all the dogs. The defect sites in the negative control group (sixteen defects) were left untreated (the NS group), whereas those in the positive control group (sixteen defects) were filled with a particle-type substitute (the PS group). The defect sites in the experimental groups (sixteen defects) were filled with a 3D printed substitute (the 3DS group). Six dogs each were exterminated after healing periods of 4 and 8 weeks. Radiological and histomorphometrical evaluations were then performed. None of the groups showed any specific problems. In radiological evaluation, there was a significant difference in the amount of new bone formation after 4 weeks (p < 0.05) between the PS and 3DS groups. For both of the evaluations, the difference in the total amount of bone after 8 weeks was statistically significant (p < 0.05). There was no statistically significant difference in new bone between the PS and 3DS groups in both evaluations after 8 weeks (p > 0.05). The proposed HA/TCP scaffold without polymers, obtained using the DLP-type 3D printing system, can be applied for bone regeneration. The 3D printing of a HA/TCP scaffold without polymers can be used for fabricating customized bone grafting substitutes.
Prediction of Extent of Corrosion using Electrical Resistivity

Corrosion of concrete structures has been one of the major causes of structural failure. The progress of corrosion cannot be visually assessed until a crack or a delamination appears. Early detection of the corrosion could help limit the location and the extent of necessary repairs or replacement, as well as reduce the cost associated with rehabilitation work. The corrosion process can be tracked using several electrochemical techniques. Most commonly the half-cell potential measurement technique is used for this purpose. Through this paper, an extensive literature review is made in relationship between electrical resistivity and rate of corrosion. This paper also reviews and assesses research concerning the influential parameters such as method of measuring rate of corrosion, effect of curing condition , diameter of rebar and cover on measuring electrical resistivity of concrete. Moreover, concrete resistivity concept, application, and combined use of the four point Wenner concrete resistivity method and the half-cell potential method are introduced. Keywords— Electrical resistivity, Rate of corrosion
Mutations at therug4locus alter the carbon and nitrogen metabolism of pea plants through an effect on sucrose synthase

Summary The biochemical and molecular basis of the wrinkled-seeded phenotype ofrug4mutants of pea (Pisum sativumL.) has been investigated. Mutant embryos have reduced starch contents and only 5% of the sucrose synthase activity of wild-type embryos during development. Activities of other enzymes involved in the conversion of sucrose to starch are unaffected. A gene encoding an isoform of sucrose synthase expressed in the embryo co-segregates with therug4locus, and one of the three mutant alleles has been show to carry a point mutation in this gene that converts a highly conserved arginine residue to a lysine residue. It is highly likely that the reduced starch content of the mutant embryo is a direct consequence of the loss of sucrose synthase activity. The mutations reduce the activity of sucrose synthase in the testa and the leaf by 50% or less, but activity inRhizobium-infected root nodules is reduced by 85%. Although the nodules of mutant plants contain metabolically active bacteroids, the N content and δ15N values of these plants in the field indicate that, unlike wild-type plants, they derive little of their N from N2 fixation viaRhizobium. Sucrose synthase thus appears to be essential for the supply of carbon for bacteroid metabolism and/or ammonia assimilation during nitrogen assimilation.
Extra-hematopoietic immunomodulatory role of the SCID-susceptibility gene DOCK-2 identified by stepwise maturation of human iPSCs into clonogenic mesodermal stromal progenitors

Stromal cells contribute to organ integrity as fibroblasts and to vascular stability as pericytes, in addition to their enigmatic niche function in many tissues. Their inherent immunomodulatory capacity attracted particular attention, initiating numerous clinical trials, particularly testing trophic regeneration and immunomodulation. Key stromal immune functions are still enigmatic. Here we show that dedicator of cytokinesis (DOCK-2) previously described for causing immune cell dysfunction plays a role in extra-hematopoietic immunity by regulating stromal/fibroblast immunomodulatory function. We used three independent strategies including iPSC-derived mesodermal stromal cell (MSC) lineage maturation, severe combined immunodeficiency (SCID) patient-derived cells and CRISPR/Cas9 knockout to support our findings. Human induced pluripotent stem cells (iPSCs) were generated from healthy bone marrow and umbilical cord blood-derived fibroblasts by Sendai virus-mediated transient expression of Yamanaka factors. After mesoderm induction, stromal differentiation was induced by platelet-derived growth factors under animal serum-free conditions. Under feeder-free defined conditions, iPSCs differentiated into expandable and cryo-preservable CD73+/CD105+/Tra-1-81− early iPS-MSCs lacking immunosuppressive potential. Successive maturation was required for reaching the canonical MSC phenotype and immunomodulatory competence over time, while maintaining clonogenicity, comparable to parental MSCs. Sequential RNAseq revealed acquisition of a spectrum of immune-related genes significantly expressed in mature iPS-MSCs and resembling parental MSC’s immune gene expression. The DOCK-2 gene attracted our attention because mutations can cause SCID. Interestingly, SCID patient-derived fibroblast lines harboring bi-allelic DOCK-2 mutations showed significantly reduced immunomodulatory capacity compared to non-mutated control fibroblasts. CRISPR/Cas9-mediated DOCK-2 knockout in healthy iPSCs resulted in iPS-MSCs that also displayed reduced immunomodulatory capacity, thus confirming a role of DOCK-2 in stromal immune function. At a mechanistic level, DOCK-2 deficiency resulted in disturbed subcellular localization of CDC42. This provides first evidence for an extra-hematopoietic immunomodulatory role of DOCK-2 in stromal cells, previously considered restricted to hampering immune cell migration/function resulting in SCID. We may speculate that some of the signs and symptoms of persisting immune disease after successful hematopoietic stem cell transplantation in SCID patients could at least in part be due to mutations, like DOCK-2−/−, permissive outside the hematopoietic immune system, as evidenced also by the increased virus infection susceptibility of DOCK-2 deficient fibroblasts.