Miracle-dz/UniFAR-FTUs huggingface dataset:
1 The Nicrophorus vespilloides genome and methylome , a beetle with complex social behavior 1 2

20. CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. Abstract 22 Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of 23 genomes available for comparison spanning multiple independent lineages. For example, complex social 24 behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are 25 Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa 26 that also vary in their levels of sociality. Here we present information on the genome of the subsocial beetle 27 Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social 28 behavior. We used this genome to address two questions. First, does life history predict overlap in gene 29 models more strongly than phylogenetic groupings? Second, like other insects with highly developed social 30 behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found the overlap in gene 31 models was similar between N. vespilloides and all other insect groups regardless of life history. Unlike 32 previous studies of beetles, we found strong evidence of DNA methylation, which allows this species to be 33 used to address questions about the potential role of methylation in social behavior. The addition of this 34 genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of 35 sociality.
OBSERVING THE ROOTS OF SOLAR CORONAL HEATING—IN THE CHROMOSPHERE

The Sun's corona is millions of degrees hotter than its 5000 K photosphere. This heating enigma is typically addressed by invoking the deposition at coronal heights of nonthermal energy generated by the interplay between convection and magnetic field near the photosphere. However, it remains unclear how and where coronal heating occurs and how the corona is filled with hot plasma. We show that energy deposition at coronal heights cannot be the only source of coronal heating by revealing a significant coronal mass supply mechanism that is driven from below, in the chromosphere. We quantify the asymmetry of spectral lines observed with Hinode and SOHO and identify faint but ubiquitous upflows with velocities that are similar (50–100 km s−1) across a wide range of magnetic field configurations and for temperatures from 100,000 to several million degrees. These upflows are spatiotemporally correlated with and have similar upward velocities as recently discovered, cool (10,000 K) chromospheric jets or (type II) spicules. We find these upflows to be pervasive and universal. Order of magnitude estimates constrained by conservation of mass and observed emission measures indicate that the mass supplied by these spicules can play a significant role in supplying the corona with hot plasma. The properties of these events are incompatible with coronal loop models that include only nanoflares at coronal heights. Our results suggest that a significant part of the heating and energizing of the corona occurs at chromospheric heights, in association with chromospheric jets.
Design of Decentralized Fuzzy Logic Load Frequency Controller

This paper presents a novel approach for designing a decentralized controller for load frequency control of interconnected power areas. The proposed fuzzy logic load frequency controller (FLFC) has been designed to improve the dynamic performance of the frequency and tie line power under a sudden load change in the power areas. The effect of generation rate constraint (GRC) for both areas has been considered in the controller design. The proposed FLFC consists of two internal fuzzy logic controllers namely, the PD- like fuzzy logic controller and the PI-like fuzzy logic controller. The FLFC has been co-coordinated with the conventional integral controller. Time-domain simulations using MATALB/SIMULINK program has been performed to demonstrate the effectiveness of the proposed FLFC. The simulation results show that the proposed FLFC can provide good damping and reduce the overshoot even in the presence of the GRC.
Small-Space Dictionary Matching Dissertation Proposal

The dictionary matching problem seeks all location in a given text that match any of the patterns in a given dictionary. Efficient algorithms for dictionary matching scan the text once, searching for all patterns simultaneously. There are many scenarios in which storage capacity is limited or the data sets are exceedingly large. The added constraint of performing efficient dictionary matching using little or no extra space is a challenging and practical problem. This project focuses on the problem of performing dictionary matching in one and two dimensions within small space. In one-dimension, the theoretical ideas for performing dictionary matching in small space have mostly been developed. The major challenge is in the algorithmic engineering of combining the succinct data structures with an algorithm for the generalized suffix tree. In two-dimensions, we will develop new algorithms to perform dictionary matching in small space and linear time.
Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal

The structure of human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The sequence [5′-AGGG(TTAGGG)3] has been used as a model for telomere DNA in both NMR and X-ray crystallographic studies, the results of which show dramatically different structures. In Na+ solution, NMR revealed an antiparallel G-quadruplex structure that featured both diagonal and lateral TTA loops. Crystallographic studies in the presence of K+ revealed a flattened, propeller-shaped structure featuring a parallel-stranded G-quadruplex with symmetrical external TTA loops. We report the results of biophysical experiments in solution and computational studies that are inconsistent with the reported crystal structure, indicating that a different structure exists in K+ solutions. Sedimentation coefficients were determined experimentally in both Na+ and K+ solutions and were compared with values calculated using bead models for the reported NMR and crystal structures. Although the solution NMR structure accurately predicted the observed S-value in Na+ solution, the crystal structure predicted an S-value that differed dramatically from that experimentally observed in K+ solution. The environments of loop adenines were probed by quantitative fluorescence studies using strategic and systematic single-substitutions of 2-aminopurine for adenine bases. Both fluorescence intensity and quenching experiments in K+ yielded results at odds with quantitative predictions from the reported crystal structure. Circular dichroism and fluorescence quenching studies in the presence of the crowding agent polyethylene glycol showed dramatic changes in the quadruplex structure in K+ solutions, but not in Na+ solutions, suggesting that the crystal environment may have selected for a particular conformational form. Molecular dynamics simulations were performed to yield model structures for the K+ quadruplex form that are consistent with our biophysical results and with previously reported chemical modification studies. These models suggest that the biologically relevant structure of the human telomere quadruplex in K+ solution is not the one determined in the published crystalline state.
Green cloud VM migration: Power use analysis

To migrate virtual machines requires not only time but also energy. If pursuing a follow-the-renewables computing paradigm, migrating virtual machines between data centres on the basis of clean energy availability, understanding not only the time requirements of migration but also its energy consumption is key. Existing research has paid little attention to the energy required to perform virtual machine migrations however. In this paper we present the results of an experimental study focused on the power and energy consumption of various workloads throughout the migration process. We also discuss challenges encountered during the study restricting our ability to migrate certain types of workloads. Based on our analysis we draw conclusions about the types of workloads suitable for migration and the manner in which each can be most effectively migrated.
On compiling embedded languages in LISP

In INTERLISP we find a number of embedded languages such as the iterative statement and the pattern match facility in the CLISP package, the editor and makefile languages and so forth. We will in this paper concentrate on the problem of extending the LISP language and discuss a method to compile such extensions. We propose the language to be implemented through an interpreter (written in LISP) and that compilation of statements in such an embedded language is done through partial evaluation. The interpreter is partially evaluated with respect to the actual statements, and an object program in LISP is obtained. This LISP code can further be compiled to machine code by the standard LISP compiler. We have implemented the iterative statement and a CLISP-like pattern matcher and used a program manipulation system to generate object programs in LISP. Comparisons will be made with the corresponding INTERLISP implementations, which use special purpose compilers in order to generate the LISP code.
Brundan-Kazhdan-Lusztig and super duality conjectures

We formulate a general super duality conjecture on connections between parabolic categories O of modules over Lie superalgebras and Lie algebras of type A, based on a Fock space formalism of their Kazhdan-Lusztig theories which was initiated by Brundan. We show that the Brundan-Kazhdan-Lusztig (BKL) polynomials for Lie superalgebra gl(m|n) in our parabolic setup can be identified with the usual parabolic Kazhdan-Lusztig polynomials. We establish some special cases of the BKL conjecture on the parabolic category O of gl(m|n)-modules and additional results which support the BKL conjecture and super duality conjecture.
Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions

Changes in intermolecular interactions (differential interactions) may influence the progression of cancer. Specific genes and their regulatory networks may be more closely associated with cancer when taking their transcriptional and post-transcriptional levels and dynamic and static interactions into account simultaneously. In this paper, a differential interaction analysis was performed to detect lung adenocarcinoma-related genes. Furthermore, a miRNA-TF (transcription factor) synergistic regulation network was constructed to identify three kinds of co-regulated motifs, namely, triplet, crosstalk and joint. Not only were the known cancer-related miRNAs and TFs (let-7, miR-15a, miR-17, TP53, ETS1, and so on) were detected in the motifs, but also the miR-15, let-7 and miR-17 families showed a tendency to regulate the triplet, crosstalk and joint motifs, respectively. Moreover, several biological functions (i.e., cell cycle, signaling pathways and hemopoiesis) associated with the three motifs were found to be frequently targeted by the drugs for lung adenocarcinoma. Specifically, the two 4-node motifs (crosstalk and joint) based on co-expression and interaction had a closer relationship to lung adenocarcinoma, and so further research was performed on them. A 10-gene biomarker (UBC, SRC, SP1, MYC, STAT3, JUN, NR3C1, RB1, GRB2 and MAPK1) was selected from the joint motif, and a survival analysis indicated its significant association with survival. Among the ten genes, JUN, NR3C1 and GRB2 are our newly detected candidate lung adenocarcinoma-related genes. The genes, regulators and regulatory motifs detected in this work will provide potential drug targets and new strategies for individual therapy.
The glucose transporter (GLUT-4) and vesicle-associated membrane protein-2 (VAMP-2) are segregated from recycling endosomes in insulin- sensitive cells

Insulin stimulates glucose transport in adipocytes by translocation of the glucose transporter (GLUT-4) from an intracellular site to the cell surface. We have characterized different synaptobrevin/vesicle- associated membrane protein (VAMP) homologues in adipocytes and studied their intracellular distribution with respect to GLUT-4. VAMP-1, VAMP- 2, and cellubrevin cDNAs were isolated from a 3T3-L1 adipocyte expression library. VAMP-2 and cellubrevin were: (a) the most abundant isoforms in adipocytes, (b) detectable in all insulin responsive tissues, (c) translocated to the cell surface in response to insulin, and (d) found in immunoadsorbed GLUT-4 vesicles. To further define their intracellular distribution, 3T3-L1 adipocytes were incubated with a transferrin/HRP conjugate (Tf/HRP) and endosomes ablated following addition of DAB and H2O2. While this resulted in ablation of > 90% of the transferrin receptor (TfR) and cellubrevin found in intracellular membranes, 60% of GLUT-4 and 90% of VAMP-2 was not ablated. Immuno-EM on intracellular vesicles from adipocytes revealed that VAMP-2 was colocalized with GLUT-4, whereas only partial colocalization was observed between GLUT-4 and cellubrevin. These studies show that two different v-SNAREs, cellubrevin and VAMP-2, are partially segregated in different intracellular compartments in adipocytes, implying that they may define separate classes of secretory vesicles in these cells. We conclude that a proportion of GLUT-4 is found in recycling endosomes in nonstimulated adipocytes together with cellubrevin and the transferrin receptor. In addition, GLUT-4 and VAMP-2 are selectively enriched in a postendocytic compartment. Further study is required to elucidate the function of this latter compartment in insulin-responsive cells.
Sparse Representations and Low-Rank Tensor Approximation

We discuss a technique that allows blind recovery of signals or blind identification of mixtures in instances where such recovery or identification were previously thought to be impossible: (i) closely located or highly correlated sources in antenna array processing, (ii) highly correlated spreading codes in CDMA radio communication, (iii) nearly dependent spectra in fluorescent spectroscopy. This has important implications -- in the case of antenna array processing, it allows for joint localization and extraction of multiple sources from the measurement of a noisy mixture recorded on multiple sensors in an entirely deterministic manner. In the case of CDMA, it allows the possibility of having a number of users larger than the spreading gain. In the case of fluorescent spectroscopy, it allows for detection of nearly identical chemical constituents. The proposed technique involves the solution of a bounded coherence low-rank multilinear approximation problem. We show that bounded coherence allows us to establish existence and uniqueness of the recovered solution.
A System Architecture for Parallel Corpus-based Grammar Learning

This paper describes an architecture for exploiting implicit information about the grammar of the languages included in a parallel corpus. By initially applying statistical word alignment and defining an appropriate representation format for cross-linguistic structural correspondence, this implicit information can feed a system for bootstrapping grammars. The proposed architecture will be underlying in the new PTOLEMAIOS project.
Development of on package indicator sensor for real-time monitoring of meat quality

Aim: The aim was to develop an indicator sensor for real-time monitoring of meat quality and to compare the response of indicator sensor with meat quality parameters at ambient temperature. Materials and Methods: Indicator sensor was prepared using bromophenol blue (1% w/v) as indicator solution and filter paper as indicator carrier. Indicator sensor was fabricated by coating indicator solution onto carrier by centrifugation. To observe the response of indicator sensor buffalo meat was packed in polystyrene foam trays covered with PVC film and indicator sensor was attached to the inner side of packaging film. The pattern of color change in indicator sensor was monitored and compared with meat quality parameters viz. total volatile basic nitrogen, D-glucose, standard plate count and tyrosine value to correlate ability of indicator sensor for its suitability to predict the meat quality and storage life. Results: The indicator sensor changed its color from yellow to blue starting from margins during the storage period of 24 h at ambient temperature and this correlated well with changes in meat quality parameters. Conclusions: The indicator sensor can be used for real-time monitoring of meat quality as the color of indicator sensor changed from yellow to blue starting from margins when meat deteriorates with advancement of the storage period. Thus by observing the color of indicator sensor quality of meat and shelf life can be predicted.
Automatic Web Page Classification

To facilitate user browsing of Web, some websites such as Yahoo! (http://dir.yahoo.com) and Open Directory Project (http://dmoz.org) manually maintain a hierarchical structure. While manual classification of web pages provides high accuracy, it is very expensive. To automatically include new emerging pages into these hierarchies, web page classification becomes a hot research topic in web information retrieval.
Understanding Environmental Influences on Movements and Depth Distributions of Tunas and Billfishes Can Significantly Improve Population Assessments

The vulnerability of the highly mobile tunas (family Scombridae) and billfishes (fami- lies Istiophoridae and Xiphiidae) to various fishing gears and detection by aerial surveys is influenced by their depth distributions, travel speeds, residency times, and aggregation. As a result, understand- ing the effects of the physical environment on fish behavior is critical for robust population assess- ments. Numerous studies have attempted to understand the movements and habitat requirements of tunas and billfishes by correlating catch statistics with environmental conditions averaged over time and space. Such correlations do not necessarily elucidate the requisite relationships because the data are not gathered simultaneously, and because error terms are often too broad to demonstrate meaning- ful relationships. More important, using catch statistics to determine the effects of environmental conditions on catch statistics can never prove causation and result in tautology, unless independent measures of fish abundance are available. The situation is not necessarily improved when catch statis- tics are correlated with satellite-derived sea surface temperature data. Tunas and billfish fish do not always live at the surface and, more importantly, regularly move through vertical thermal gradients (1°C m -1 ) that are orders of magnitude steeper than horizontal gradients ( 1°C km -1 ). Sea surface temperature gradients per se are, therefore, unlikely to influence horizontal movements or aggrega- tion. Direct observations of tuna and billfish behaviors (collected via acoustic telemetry or electronic data-recording tags) can, however, be readily combined with information on their physiologically- based environmental tolerances, forage abundance, and appropriate oceanographic data. The result- ing models can correct both traditional catch-per-unit effort data and aerial survey data for differences in gear vulnerability, and thus significantly improve population assessments.
Eleganolone, a Diterpene from the French Marine Alga Bifurcaria bifurcata Inhibits Growth of the Human Pathogens Trypanosoma brucei and Plasmodium falciparum

Organic extracts of 20 species of French seaweed have been screened against Trypanosoma brucei rhodesiense trypomastigotes, the parasite responsible for sleeping sickness. These extracts have previously shown potent antiprotozoal activities in vitro against Plasmodium falciparum and Leishmania donovani. The selectivity of the extracts was also evaluated by testing cytotoxicity on a mammalian L6 cell line. The ethyl acetate extract of the brown seaweed, Bifurcaria bifurcata, showed strong trypanocidal activity with a mild selectivity index (IC50 = 0.53 µg/mL; selectivity index (SI) = 11.6). Bio-guided fractionation led to the isolation of eleganolone, the main diterpenoid isolated from this species. Eleganolone contributes only mildly to the trypanocidal activity of the ethyl acetate extract (IC50 = 45.0 µM, SI = 4.0). However, a selective activity against P. falciparum erythrocytic stages in vitro has been highlighted (IC50 = 7.9 µM, SI = 21.6).
Academic Vocabulary: Explicit and Incidental Instruction for Students of Diverse Language Backgrounds

Abstract Vocabulary knowledge is a crucial element of reading comprehension. Academic vocabulary poses particular challenges for students and should be a focus of instruction, particularly for students from diverse language backgrounds. This study was part of a larger literacy in social studies intervention aimed at increasing students’ reading comprehension and engagement. A repeated measures multivariate analysis of variance indicated that although both emergent bilingual and English monolingual students improved on words that were explicitly taught, only English monolingual students improved in their knowledge of words that were incidentally taught. Qualitative observational notes indicated that teachers’ explicit vocabulary instruction included the use of graphic organizers, think–pair–share activities, and scaffolded discussions. Teachers taught word-learning strategies and developed word consciousness to different degrees. Findings could indicate that emergent bilingual students are less likely to benefit from incidental instruction of academic vocabulary words, which supports previous literature on the crucial role of explicit vocabulary instruction.
Genetics of Microstructure of the Corpus Callosum in Older Adults

The current study sought to examine the relative influence of genetic and environmental factors on corpus callosum (CC) microstructure in a community sample of older adult twins. Analyses were undertaken in 284 healthy older twins (66% female; 79 MZ and 63 DZ pairs) from the Older Australian Twins Study. The average age of the sample was 69.82 (SD = 4.76) years. Brain imaging scans were collected and DTI measures were estimated for the whole CC as well as its five subregions. Parcellation of the CC was performed using Analyze. In addition, white matter lesion (WMLs) burden was estimated. Heritability and genetic correlation analyses were undertaken using the SOLAR software package. Age, sex, scanner, handedness and blood pressure were considered as covariates. Heritability (h2) analysis for the DTI metrics of whole CC, indicated significant h2 for fractional anisotropy (FA) (h2 = 0.56; p = 2.89×10−10), mean diffusivity (MD) (h2 = 0.52; p = 0.30×10−6), radial diffusivity (RD) (h2 = 0.49; p = 0.2×10−6) and axial diffusivity (AD) (h2 = 0.37; p = 8.15×10−5). We also performed bivariate genetic correlation analyses between (i) whole CC DTI measures and (ii) whole CC DTI measures with total brain WML burden. Across the DTI measures for the whole CC, MD and RD shared 84% of the common genetic variance, followed by MD- AD (77%), FA - RD (52%), RD - AD (37%) and FA – MD (11%). For total WMLs, significant genetic correlations indicated that there was 19% shared common genetic variance with whole CC MD, followed by CC RD (17%), CC AD (16%) and CC FA (5%). Our findings suggest that the CC microstructure is under moderate genetic control. There was also evidence of shared genetic factors between the CC DTI measures. In contrast, there was less shared genetic variance between WMLs and the CC DTI metrics, suggesting fewer common genetic variants.