Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis

Caenorhabditis elegans is a model organism in biology, yet despite the tremendous information generated from genetic, genomic and functional analyses, C. elegans has rarely been used to address questions in ecological genetics. Here, we analyse genetic variation for chemosensory behaviour, an ecologically important trait that is also genetically well characterized, at both the phenotypic and molecular levels within three species of the genus Caenorhabditis. We show that the G‐protein ODR‐3 plays an important role in chemosensory avoidance behaviour and identify orthologues of odr‐3 in C. briggsae and C. remanei. Both quantitative genetic analysis of chemosensory behaviour and molecular population genetic analysis of odr‐3 show that there is little genetic variation among a worldwide collection of isolates of the primarily selfing C. elegans, whereas there is substantially more variation within a single population of the outcrossing C. remanei. Although there are a large number of substitutions at silent sites within odr‐3 among the three species, molecular evolution at the protein level is extremely conserved, suggesting that odr‐3 plays an important role in cell signalling during chemosensation and/or neuronal cilia development in C. remanei and in C. briggsae as it does in C. elegans. Our results suggest that C. remanei may be a more suitable subject for ecological and evolutionary genetic studies than C. elegans.
Cell Cycle Proteins Exhibit Altered Expression Patterns in Lentiviral-Associated Encephalitis

Cell cycle proteins regulate processes as diverse as cell division and cell death. Recently their role in neuronal death has been reported in several models of neurodegeneration. We have reported previously that two key regulators of the cell cycle, the retinoblastoma susceptibility gene product (pRb) and transcription factor E2F1, exhibit altered immunostaining patterns in simian immunodeficiency virus encephalitis (SIVE). Here we show that E2F1 and the inactivated, hyperphosphorylated form of pRb (ppRb) also exhibit altered immunostaining patterns in human immunodeficiency virus encephalitis (HIVE). Quantification of E2F1 and ppRb staining by immunofluorescent confocal microscopy confirms a significant increase in E2F1 and ppRb in both HIVE and the simian model. This increase in E2F1 and ppRb staining correlates with an increase in the presence of activated macrophages, suggesting a link between changes in cell cycle proteins and the presence of activated macrophages. Changes in ppRb and E2F1 staining in SIVE also correlate with alterations in E2F/DNA binding complexes present in the nuclear and cytoplasmic fractions from both midfrontal cortex and basal ganglia. These findings suggest that changes in cell cycle proteins occur in both HIVE and the simian model and that these changes have functional implications for gene expression in neural cells under encephalitic conditions mediated by macrophage activation or infiltration.
A Complex Ergovaline Gene Cluster in Epichloë Endophytes of Grasses

ABSTRACT Clavicipitaceous fungal endophytes of the genera Epichloë and Neotyphodium form symbioses with grasses of the subfamily Pooideae, in which they can synthesize an array of bioprotective alkaloids. Some strains produce the ergopeptine alkaloid ergovaline, which is implicated in livestock toxicoses caused by ingestion of endophyte-infected grasses. Cloning and analysis of a nonribosomal peptide synthetase (NRPS) gene from Neotyphodium lolii revealed a putative gene cluster for ergovaline biosynthesis containing a single-module NRPS gene, lpsB, and other genes orthologous to genes in the ergopeptine gene cluster of Claviceps purpurea and the clavine cluster of Aspergillus fumigatus. Despite conservation of gene sequence, gene order is substantially different between the N. lolii, C. purpurea, and A. fumigatus ergot alkaloid gene clusters. Southern analysis indicated that the N. lolii cluster was linked with previously identified ergovaline biosynthetic genes dmaW and lpsA. The ergovaline genes are closely associated with transposon relics, including retrotransposons and autonomous and nonautonomous DNA transposons. All genes in the cluster were highly expressed in planta, but expression was very low or undetectable in mycelia from axenic culture. This work provides a genetic foundation for elucidating biochemical steps in the ergovaline pathway, the ecological role of individual ergot alkaloid compounds, and the regulation of their synthesis in planta.
Self-Organization in High-Density Bacterial Colonies: Efficient Crowd Control

Colonies of bacterial cells can display complex collective dynamics, frequently culminating in the formation of biofilms and other ordered super-structures. Recent studies suggest that to cope with local environmental challenges, bacterial cells can actively seek out small chambers or cavities and assemble there, engaging in quorum sensing behavior. By using a novel microfluidic device, we showed that within chambers of distinct shapes and sizes allowing continuous cell escape, bacterial colonies can gradually self-organize. The directions of orientation of cells, their growth, and collective motion are mutually correlated and dictated by the chamber walls and locations of chamber exits. The ultimate highly organized steady state is conducive to a more-organized escape of cells from the chambers and increased access of nutrients into and evacuation of waste out of the colonies. Using a computational model, we suggest that the lengths of the cells might be optimized to maximize self-organization while minimizing the potential for stampede-like exit blockage. The self-organization described here may be crucial for the early stage of the organization of high-density bacterial colonies populating small, physically confined growth niches. It suggests that this phenomenon can play a critical role in bacterial biofilm initiation and development of other complex multicellular bacterial super-structures, including those implicated in infectious diseases.
The Genetics of Domestication of the Azuki Bean (Vigna angularis)

Genetic differences between azuki bean (Vigna angularis var. angularis) and its presumed wild ancestor (V. angularis var. nipponensis) were resolved into QTL for traits associated with adaptation to their respective distinct habits. A genetic linkage map constructed using progenies from a cross between Japanese cultivated and wild azuki beans covers 92.8% of the standard azuki bean linkage map. A reciprocal translocation between cultivated and wild azuki bean parents was identified on the basis of the linkage map having a pseudolinkage group and clustering of seed productivity-related QTL with large effect near the presumed breakpoints. In total, 162 QTL were identified for 46 domestication-related traits. Domestication of azuki bean has involved a trade-off between seed number and seed size: fewer but longer pods and fewer but larger seeds on plants with shorter stature in cultivated azuki bean being at the expense of overall seed yield. Genes found related to germination and flowering time in cultivated azuki bean may confer a selective advantage to the hybrid derivatives under some ecological conditions and may explain why azuki bean has evolved as a crop complex in Japan.
Cytoplasmic Fungal Lipases Release Fungicides from Ultra-Deformable Vesicular Drug Carriers

The Transfersome® is a lipid vesicle that contains membrane softeners, such as Tween 80, to make it ultra-deformable. This feature makes the Transfersome® an efficient carrier for delivery of therapeutic drugs across the skin barrier. It was reported that TDT 067 (a topical formulation of 15 mg/ml terbinafine in Transfersome® vesicles) has a much more potent antifungal activity in vitro compared with conventional terbinafine, which is a water-insoluble fungicide. Here we use ultra-structural studies and live imaging in a model fungus to describe the underlying mode of action. We show that terbinafine causes local collapse of the fungal endoplasmic reticulum, which was more efficient when terbinafine was delivered in Transfersome® vesicles (TFVs). When applied in liquid culture, fluorescently labeled TFVs rapidly entered the fungal cells (T1/2∼2 min). Entry was F-actin- and ATP-independent, indicating that it is a passive process. Ultra-structural studies showed that passage through the cell wall involves significant deformation of the vesicles, and depends on a high concentration of the surfactant Tween 80 in their membrane. Surprisingly, the TFVs collapsed into lipid droplets after entry into the cell and the terbinafine was released from their interior. With time, the lipid bodies were metabolized in an ATP-dependent fashion, suggesting that cytosolic lipases attack and degrade intruding TFVs. Indeed, the specific monoacylglycerol lipase inhibitor URB602 prevented Transfersome® degradation and neutralized the cytotoxic effect of Transfersome®-delivered terbinafine. These data suggest that (a) Transfersomes deliver the lipophilic fungicide Terbinafine to the fungal cell wall, (b) the membrane softener Tween 80 allows the passage of the Transfersomes into the fungal cell, and (c) fungal lipases digest the invading Transfersome® vesicles thereby releasing their cytotoxic content. As this mode of action of Transfersomes is independent of the drug cargo, these results demonstrate the potential of Transfersomes in the treatment of all fungal diseases.
The Effect of Perception of Organizational Support, Organizational Culture and Servant Leadership on Employee Performance at the Office of the Regional Development Planning Agency (BAPPEDA) of the Mentawai Islands Regency

This research aims to determine and analyze the influence of Perception of Organizational Support, Organizational Culture and Servant Leadership on Employee Performance at the Office of the Regional Development Planning Agency (BAPPEDA) of the Mentawai Islands Regency. This research is exploratory research with quantitative method. Sampling technique with census, so sample size 84 employee. This research uses SPSS 16. This results of this research showed, perceptions of organizational support have positive and significant effect to employee performance, organizational culture have positive and significant effect to employee performance, and then servant leadership have positive and significant effect to employee performance. Keywords: Perceptions Of Organizational Support, Organizational Culture, Servant Leadership and Employee Performance. DOI : 10.7176/EJBM/11-6-11
One-Pass Authentication and Key Agreement Procedure in IP Multimedia Subsystem for UMTS

In IP Multimedia Subsystem (IMS) of UMTS, both packet-switch domain and IMS authentications are necessary for the IMS subscriber, so-called the two-pass authentication. However, the IMS authentication is carried out by IMS authentication and key agreement (IMS AKA). Since IMS AKA is based on 3GPP AKA that is used to Packet-switch domain authentication, almost all of the operations are the same. It is inefficient that almost all involved steps in the two-pass authentication are duplicated. Hence, Lin et al.'s proposed the one-pass authentication to increase efficiency of the IMS authentication. Unfortunately, in addition to some security problems, the one-pass authentication procedure only has unilateral authentication without capabilities of mutual authentication and key agreement. Therefore, this paper proposes an one-pass AKA procedure, which not only avoids the lacks of the one-pass authentication procedure but also does not lose the efficiency.
Amino Acid Compositions of 27 Food Fishes and Their Importance in Clinical Nutrition

Proteins and amino acids are important biomolecules which regulate key metabolic pathways and serve as precursors for synthesis of biologically important substances; moreover, amino acids are building blocks of proteins. Fish is an important dietary source of quality animal proteins and amino acids and play important role in human nutrition. In the present investigation, crude protein content and amino acid compositions of important food fishes from different habitats have been studied. Crude protein content was determined by Kjeldahl method and amino acid composition was analyzed by high performance liquid chromatography and information on 27 food fishes was generated. The analysis showed that the cold water species are rich in lysine and aspartic acid, marine fishes in leucine, small indigenous fishes in histidine, and the carps and catfishes in glutamic acid and glycine. The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs.
Separation length in high-enthalpy shock/boundary-layer interaction

Experiments were performed in the T5 Hypervelocity Shock Tunnel to investigate nonequilibrium real-gas effects on separation length using a double-wedge geometry and nitrogen test gas. Local external flow conditions were estimated by computing the inviscid nonequilibrium flow field. A new scaling parameter was developed to approximately account for wall temperature effects on separation length for a laminar nonreacting boundary layer and arbitrary viscosity law. A classification was introduced to divide mechanisms for real-gas effects into those acting internal and external to viscous regions of the flow. Internal mechanisms were further subdivided into those arising upstream and downstream of separation. Analysis based on the ideal dissociating gas model and a scaling law for separation length of a nonreacting boundary layer showed that external mechanisms due to dissociation may decrease separation length at low incidence but depend on the free-stream dissociation at high incidence. A limited numerical study of reacting boundary layers showed that internal mechanisms due to recombination occurring in the boundary layer upstream of separation cause a slight decrease in separation length relative to a nonreacting boundary layer with the same external conditions. Correlations were obtained of experimentally measured separation length using local external flow parameters computed for reacting flow, which scales out external mechanisms but not internal mechanisms. These showed the importance of the new scaling parameter in high-enthalpy flows, a linear relationship between separation length and reattachment pressure ratio, and a Reynolds-number effect for transitional interactions. A significant increase in scaled separation length was observed in the experimental data at high enthalpy. The increase was attributed to an internal mechanism arising from recombination in the free-shear layer downstream of separation, perhaps altering its velocity profile. This real-gas effect depends on the combined presence of free-stream dissociation and a cold wall.
A Measurement of the Angular Power Spectrum of the CMB Temperature Anisotropy from the 2003 Flight of BOOMERANG

We report on observations of the cosmic microwave background (CMB) obtained during the 2003 January flight of BOOMERANG. These results are derived from 195 hr of observation with four 145 GHz polarization-sensitive bolometer (PSB) pairs, identical in design to the four 143 GHz Planck High Frequency Instrument (HFI) polarized pixels. The data include 75 hr of observations distributed over 1.84% of the sky with an additional 120 hr concentrated on the central portion of the field, which represents 0.22% of the full sky. From these data we derive an estimate of the angular power spectrum of temperature fluctuations of the CMB in 24 bands over the multipole range 50 ≤ l ≤ 1500. A series of features, consistent with those expected from acoustic oscillations in the primordial photon-baryon fluid, are clearly evident in the power spectrum, as is the exponential damping of power on scales smaller than the photon mean free path at the epoch of last scattering (l ≳ 900). As a consistency check, the collaboration has performed two fully independent analyses of the time-ordered data, which are found to be in excellent agreement.
Changes in Community Structure of Resting State Functional Connectivity in Unipolar Depression

Major depression is a prevalent disorder that imposes a significant burden on society, yet objective laboratory-style tests to assist in diagnosis are lacking. We employed network-based analyses of “resting state” functional neuroimaging data to ascertain group differences in the endogenous cortical activity between healthy and depressed subjects. We additionally sought to use machine learning techniques to explore the ability of these network-based measures of resting state activity to provide diagnostic information for depression. Resting state fMRI data were acquired from twenty two depressed outpatients and twenty two healthy subjects matched for age and gender. These data were anatomically parcellated and functional connectivity matrices were then derived using the linear correlations between the BOLD signal fluctuations of all pairs of cortical and subcortical regions. We characterised the hierarchical organization of these matrices using network-based matrics, with an emphasis on their mid-scale “modularity” arrangement. Whilst whole brain measures of organization did not differ between groups, a significant rearrangement of their community structure was observed. Furthermore we were able to classify individuals with a high level of accuracy using a support vector machine, primarily through the use of a modularity-based metric known as the participation index. In conclusion, the application of machine learning techniques to features of resting state fMRI network activity shows promising potential to assist in the diagnosis of major depression, now suggesting the need for validation in independent data sets.
Auditory processing and phonological awareness skills of five-year-old children with and without musical experience.

PURPOSE To investigate the relations between musical experience, auditory processing and phonological awareness of groups of 5-year-old children with and without musical experience. METHODS Participants were 56 5-year-old subjects of both genders, 26 in the Study Group, consisting of children with musical experience, and 30 in the Control Group, consisting of children without musical experience. All participants were assessed with the Simplified Auditory Processing Assessment and Phonological Awareness Test and the data was statistically analyzed. RESULTS There was a statistically significant difference between the results of the sequential memory test for verbal and non-verbal sounds with four stimuli, phonological awareness tasks of rhyme recognition, phonemic synthesis and phonemic deletion. Analysis of multiple binary logistic regression showed that, with exception of the sequential verbal memory with four syllables, the observed difference in subjects' performance was associated with their musical experience. CONCLUSION Musical experience improves auditory and metalinguistic abilities of 5-year-old children.
Polynomial-time implication problems for unary inclusion dependencies

Unary inclusion dependencies are database constraints expressing subset relationships. The decidability of implication for these dependencies together with embedded implicational dependencies, such as functional dependencies, are investigated. As shown by Casanova et al., the unrestricted and finite implication problems are different for the class of functional and unary inclusion dependencies; also, for this class and for any fixed k, finite implication has no k-ary complete axiomatization. For both of these problems, complete axiomatizations and polynomial-time decision procedures are provided: linear time for unrestricted implication and cubic time for finite implication. It follows that functional and unary inclusion dependencies form a semantically natural class of first-order sentences with equality, which although not finitely controllable, is efficiently solvable and docile. Generalizing from these results, it is shown that the interaction between functionaland inclusion dependencies characterizes: (1) unrestricted implication of unary inclusion and all embedded implicational dependencies; (2) finite implication of unary inclusion and all full implicational dependencies; (3) finite implication of unary inclusion and all embedded tuple-generating dependencies. As a direct consequence of this analysis, most of the applications of dependency implication are extended, within polynomial-time, to database design problems involving unary inclusion dependencies. Such examples are tests for lossless joins and tests for complementarity of projective views. Finally, if one additionally requires that
Predictive Mortality Index for Community-Dwelling Elderly Koreans

Abstract There are very few predictive indexes for long-term mortality among community-dwelling elderly Asian individuals, despite its importance, given the rapid and continuous increase in this population. We aimed to develop 10-year predictive mortality indexes for community-dwelling elderly Korean men and women based on routinely collected clinical data. We used data from 2244 elderly individuals (older than 60 years of age) from the southwest Seoul Study, a prospective cohort study, for the development of a prognostic index. An independent longitudinal cohort of 679 elderly participants was selected from the Korean Genome Epidemiology Study in Ansan City for validation. During a 10-year follow-up, 393 participants (17.5%) from the development cohort died. Nine risk factors were identified and weighed in the Cox proportional regression model to create a point scoring system: age, male sex, smoking, diabetes, systolic blood pressure, triglyceride, total cholesterol, white blood cell count, and hemoglobin. In the development cohort, the 10-year mortality risk was 6.6%, 14.8%, 18.2%, and 38.4% among subjects with 1 to 4, 5 to 7, 8 to 9, and ≥10 points, respectively. In the validation cohort, the 10-year mortality risk was 5.2%, 12.0%, 16.0%, and 16.0% according to these categories. The C-statistic for the point system was 0.73 and 0.67 in the development and validation cohorts, respectively. The present study provides valuable information for prognosis among elderly Koreans and may guide individualized approaches for appropriate care in a rapidly aging society.
Wall crossing formula for = 4 dyons: a macroscopic derivation

We derive the wall crossing formula for the decay of a quarter BPS dyon into a pair of half-BPS dyons by analyzing the quantum dynamics of multi-centered black holes in = 4 supersymmetric string theories. Our analysis encompasses the cases where the final decay products are non-primitive dyons. The results are in agreement with the microscopic formula for the dyon spectrum in the special case of heterotic string theory on T6.
Diagrammatic reasoning and hypostatic abstraction in statistics education

Abstract Peirce's notions of diagrammatic reasoning and hypostatic abstraction are relevant to educational research in areas where diagrams and abstraction play an important role. In this paper, I analyze an example from statistics education in which diagrammatic reasoning created opportunities for hypostatic abstraction. For instance, where students initially characterized data points as being ‘spread out,’ they later said, ‘the spread is large. ’ This is a prototypical example of hypostatic abstraction — taking a predicate as a new object that can have predicates itself. More generally, the notion of diagrammatic reasoning proved helpful to identify the key learning processes involved in learning to reason about statistical concepts.