Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of Serum Response Factor (SRF) with the Elk-1 B Box Inhibits RhoA-Actin Signaling to SRF and Potentiates Transcriptional Activation by Elk-1

ABSTRACT Serum response factor (SRF) is a transcription factor which regulates many immediate-early genes. Rho GTPases regulate SRF activity through changes in actin dynamics, but some SRF target genes, such as c-fos, are insensitive to this pathway. At the c-fos promoter, SRF recruits members of the ternary complex factor (TCF) family of Ets domain proteins through interactions with the TCF B-box region. Analysis of c-fos promoter mutations demonstrates that the TCF and ATF/AP1 sites adjoining the SRF binding site inhibit activation of the promoter by RhoA-actin signaling. The presence of the TCF binding site is sufficient for inhibition, and experiments with an altered-specificity Elk-1 derivative demonstrate that inhibition can be mediated by the Elk-1 TCF. Using Elk-1 fusion proteins that can bind DNA autonomously, we show that inhibition of RhoA-actin signaling requires physical interaction between the Elk-1 B box and SRF. These results account for the insensitivity of c-fos to RhoA-actin signaling. Interaction of the B box with SRF also potentiates transcriptional activation by the Elk-1 C-terminal activation domain. Combinatorial interactions between SRF and TCF proteins are thus likely to play an important role in determining the relative sensitivity of SRF target genes to Ras- and Rho-controlled signal transduction pathways.
Community Discovery in Dynamic Networks

Several research studies have shown that complex networks modeling real-world phenomena are characterized by striking properties: (i) they are organized according to community structure, and (ii) their structure evolves with time. Many researchers have worked on methods that can efficiently unveil substructures in complex networks, giving birth to the field of community discovery. A novel and fascinating problem started capturing researcher interest recently: the identification of evolving communities. Dynamic networks can be used to model the evolution of a system: nodes and edges are mutable, and their presence, or absence, deeply impacts the community structure that composes them. This survey aims to present the distinctive features and challenges of dynamic community discovery and propose a classification of published approaches. As a “user manual,” this work organizes state-of-the-art methodologies into a taxonomy, based on their rationale, and their specific instantiation. Given a definition of network dynamics, desired community characteristics, and analytical needs, this survey will support researchers to identify the set of approaches that best fit their needs. The proposed classification could also help researchers choose in which direction to orient their future research.
Elevated [CO2] and forest vegetation: more a water issue than a carbon issue?

Studies of responses of forest vegetation to steadily increasing atmospheric concentrations of CO2 have focussed strongly on the potential of trees to absorb extra carbon; the effects of elevated [CO2] on plant–soil water relations via decreased stomatal conductance and increased ambient temperature have received less attention, but may be significant in the long term at the ecosystem level. CO2 augmentation experiments with young trees demonstrate small increases in aboveground carbon content, but these increases tend to diminish as trees get older. By contrast, several experiments suggest continued decreases in transpiration and increased soil water content under these conditions. In tropical forests, the major cause of increases in aboveground biomass observed in the recent past is not necessarily elevated [CO2]. Undoubtedly, the potential of monitoring trees in forest dynamics plots to deduce CO2-specific alterations in forest structure and standing biomass will unfold in the decades to come. The comprehensive understanding of responses of forest vegetation to elevated [CO2] in the Anthropocene will depend upon the inclusion of detailed measurements of soil water pools and water fluxes through the soil–plant–atmosphere continuum in future tree CO2 augmentation experiments and forest dynamics plot studies.
Do Substance Abuse Patients with More Psychopathology Receive More Treatment?

The association between psychopathology at treatment entry and the amount of treatment services received was evaluated in 104 alcohol-dependent and 100 cocaine-dependent male veterans treated for 1 month in either a day hospital or inpatient program. Measures of psychopathology included the Addiction Severity Index psychiatric composite score, the presence or absence of an antisocial personality disorder diagnosis, and the total number of additional lifetime or current psychiatric diagnoses. Patients with higher admission Addiction Severity Index psychiatric composite scores received more medical, alcohol, family/social, and psychiatric services. There was also preliminary evidence that patients who received more treatment showed greater improvement 7 months after admission. The relationships between the other measures of psychopathology and treatment services filed to achieve overall statistical significance, although significant relationships were found in several individual areas.
Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library

We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We provide a case study for the application of the methods to the problem of identifying and extracting arguments about anthropomorphism during a critical period in the development of comparative psychology. We show how a combination of classification systems and mixed-membership models trained over large digital libraries can inform resource discovery in this domain. Through a novel approach of “drill-down” topic modeling—simultaneously reducing both the size of the corpus and the unit of analysis—we are able to reduce a large collection of fulltext volumes to a much smaller set of pages within six focal volumes containing arguments of interest to historians and philosophers of comparative psychology. The volumes identified in this way did not appear among the first ten results of the keyword search in the HathiTrust digital library and the pages bear the kind of “close reading” needed to generate original interpretations that is the heart of scholarly work in the humanities. Zooming back out, we provide a way to place the books onto a map of science originally constructed from very different data and for different purposes. The multilevel approach advances understanding of the intellectual and societal contexts in which writings are interpreted.
Pre-harvest foliar spray of micronutrients and growth regulators on yield attributes of litchi (Litchi chinensis Sonn.) ‘Purbi’

The present research work was carried out under Horticulture Garden, Department of Horticulture (Fruit & Fruit Tech.), Bihar Agricultural College, Sabour to examine the response of pre-harvest foliar application of micronutrients and growth regulators on yield attributes of litchi (Litchi chinensis Sonn.) 'Purbi'. The results indicate that the micronutrients and plant growth regulators had beneficial effect on flowering, fruiting, fruit retention and fruit yield. The maximum fruit set (48.64%), fruit retention (25.36%) and number of fruits tree(-1) (4982) were recorded with application of NAA (20 ppm) in comparison to control. A minimum fruit drop (74.64%) and fruit cracking (7.96%) was also obtained with application of NAA (20 ppm) while the maximum fruit drop (82.94%) and fruit cracking (13.92%) was recorded under control. The highest fruit yield tree(-1) was recorded with application of NAA (20 ppm) (102.98 kg) followed by 2,4-D (10 ppm) whereas it was recorded minimum in control (56.96 kg). The length, width, volume and weight of fruits were significantly influenced by the application of different micronutrient and growth regulators with maximum fruit length (4.29 cm), width (3.7 cm), volume (18.86 cc) and weight (20.67 g) in the pre-harvest application of NAA (20 ppm), which was statistically at par with foliar spray of 2,4-D (10 ppm), ZnSO(4) (0.50%) and borax (0.75%). However, minimum fruit length (3.36 cm), width (3.62 cm), volume (14.52 cc) and weight (15.76 g) were recorded under control. Therefore, from the experiment, it can be said that the foliar spray of micronutrients and growth regulators were very useful to enhance the yield of litchi orchard significantly.
Comparative life cycle assessment and life cycle costing of four disposal scenarios for used polyethylene terephthalate bottles in Mauritius

The annual rise in population growth coupled with the flourishing tourism industry in Mauritius has lead to a considerable increase in the amount of solid waste generated. In parallel, the disposal of non-biodegradable wastes, especially plastic packaging and plastic bottles, has also shown a steady rise. Improper disposal of used polyethylene terephthalate (PET) bottles constitutes an eyesore to the environmental landscape and is a threat to the flourishing tourism industry. It is of utmost importance, therefore, to determine a suitable disposal method for used PET bottles which is not only environmentally efficient but is also cost effective. This study investigated the environmental impacts and the cost effectiveness of four selected disposal alternatives for used PET bottles in Mauritius. The four disposal routes investigated were: 100% landfilling; 75% incineration with energy recovery and 25% landfilling; 40% flake production (partial recycling) and 60% landfilling; and 75% flake production and 25% landfilling. Environmental impacts of the disposal alternatives were determined using ISO standardized life cycle assessment (LCA) and with the support of SimaPro 7.1 software. Cost effectiveness was determined using life cycle costing (LCC). Collected data were entered into a constructed Excel-based model to calculate the different cost categories, Net present values, damage costs and payback periods. LCA and LCC results indicated that 75% flake production and 25% landfilling was the most environmentally efficient and cost-effective disposal route for used PET bottles in Mauritius.
A Search for Submillisecond Pulsations in Unidentified FIRST and NVSS Radio Sources

We have searched 92 unidentified sources from the Faint Images of the Radio Sky at Twenty Centimeters (FIRST) and NRAO VLA Sky Survey (NVSS) 1400 MHz radio survey catalogs for radio pulsations at 610 MHz. The selected radio sources are bright, have no identification with extragalactic objects, are pointlike, and are more than 5% linearly polarized. Our search was sensitive to submillisecond pulsations from pulsars with dispersion measures less than ∼500 pc cm-3 in the absence of scattering. We have detected no pulsations from these sources and consider possible effects that might prevent detection. We conclude that, as a population, these sources are unlikely to be pulsars.
Heuristic minimization of multiple-valued relations

The authors propose a heuristic procedure for the minimization problem of multiple-valued relations based on a paradigm of the more advanced two-level minimization techniques for regular functions. The goal of the procedure is to find a compatible representation with the minimum number of the product terms. The authors present some special properties associated with relations not found in functions. These properties must be carefully accounted for while implementing a procedure that is effective in achieving high quality results. The authors have implemented these algorithms in a program called GYOCRO, and provide experimental evidence of their effectiveness. <<ETX>>
Functional Characterization by Genetic Complementation of aroB-Encoded Dehydroquinate Synthase from Mycobacterium tuberculosis H37Rv and Its Heterologous Expression and Purification

ABSTRACT The recent recrudescence of Mycobacterium tuberculosis infection and the emergence of multidrug-resistant strains have created an urgent need for new therapeutics against tuberculosis. The enzymes of the shikimate pathway are attractive drug targets because this route is absent in mammals and, in M. tuberculosis, it is essential for pathogen viability. This pathway leads to the biosynthesis of aromatic compounds, including aromatic amino acids, and it is found in plants, fungi, bacteria, and apicomplexan parasites. The aroB-encoded enzyme dehydroquinate synthase is the second enzyme of this pathway, and it catalyzes the cyclization of 3-deoxy-d-arabino-heptulosonate-7-phosphate in 3-dehydroquinate. Here we describe the PCR amplification and cloning of the aroB gene and the overexpression and purification of its product, dehydroquinate synthase, to homogeneity. In order to probe where the recombinant dehydroquinate synthase was active, genetic complementation studies were performed. The Escherichia coli AB2847 mutant was used to demonstrate that the plasmid construction was able to repair the mutants, allowing them to grow in minimal medium devoid of aromatic compound supplementation. In addition, homogeneous recombinant M. tuberculosis dehydroquinate synthase was active in the absence of other enzymes, showing that it is homomeric. These results will support the structural studies with M. tuberculosis dehydroquinate synthase that are essential for the rational design of antimycobacterial agents.
Characterization of bedload discharge in bores and very unsteady flows in an ephemeral channel

Bedload flux under steady flow conditions is calculated by a multitude of available methods and equations. Yet, very little is known about the effect of very unsteady flows, such as flash floods and specifically bores, on bedload flux. The unpredictable nature of the floods together with many logistic difficulties and safety issues in monitoring explain this gap in knowledge. Global climate change may increase flood event occurrence, making their understanding even more crucial. The methodology of our study is based on automatically monitoring bedload flux (Reid slot samplers). Automation allowed high frequency monitoring of hydraulic parameters and bedload flux. Added novelty includes pipe and plate microphones for capturing acoustic signals of bedload sediments and 3-D velocimetry for characterizing turbulence. Alerting sensors and cellular data transmission enabled onsite presence upon bore arrival. Calibration between the acoustic indirect sensors and the direct slot samplers allows determination of bedload flux at a frequency of 1 Hz. Analyses of flood events indicate an increase in turbulent kinetic energy, instantaneous vertical velocities, shear stress and bedload flux during the rising limb within the first two minutes after bore arrival. This has implications for the likely destabilization of the channel bed and for bedload transport after passage of the bore and during subsequent, less unsteady flows.
MESSENGER Observations of Fast Plasma Flows in Mercury's Magnetotail

We present the first observation of fast plasma flows in Mercury's magnetotail. Mercury experiences substorm activity phenomenologically similar to Earth's; however, field‐of‐view limitations of the Fast Imaging Plasma Spectrometer (FIPS) prevent the instrument from detecting fast flows in the plasma sheet. Although FIPS measures incomplete plasma distributions, subsonic flows impart an asymmetry on the partial plasma distribution, even if the flow directions are outside the field of view. We combine FIPS observations from 387 intervals containing magnetic field dipolarizations to mitigate these instrument limitations. By taking advantage of variations in spacecraft pointing during these intervals, we construct composite plasma distributions from which mean flows are determined. We find that dipolarizations at Mercury are embedded within fast sunward flows with an averaged speed of ~300 km/s compared to a typical background flow of ~50 km/s.
An adaptive energy efficient MAC protocol for the medical body area network

Medical body area networks will employ both implantable and bodyworn devices to support a diverse range of applications with throughputs ranging from several bits per hour up to 10 Mbps. The challenge is to accommodate this range of applications within a single wireless network based on a suitably flexible and power efficient medium access control protocol. To this end, we present a Medical Medium Access Control (MedMAC) protocol for energy efficient and adaptable channel access in body area networks. The MedMAC incorporates a novel synchronisation mechanism and initial power efficiency simulations show that the MedMAC protocol outperforms the IEEE 802.15. 4 protocol for two classes of medical applications.
Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Therapeutic Vulnerabilities

Triple-negative breast cancer (TNBC) is characterized by the absence of expression of estrogen receptor, progesterone receptor, and HER-2. Thirty percent of patients recur after first-line treatment, and metastatic TNBC (mTNBC) has a poor prognosis with median survival of one year. Here, we present initial analyses of whole genome and transcriptome sequencing data from 14 prospective mTNBC. We have cataloged the collection of somatic genomic alterations in these advanced tumors, particularly those that may inform targeted therapies. Genes mutated in multiple tumors included TP53, LRP1B, HERC1, CDH5, RB1, and NF1. Notable genes involved in focal structural events were CTNNA1, PTEN, FBXW7, BRCA2, WT1, FGFR1, KRAS, HRAS, ARAF, BRAF, and PGCP. Homozygous deletion of CTNNA1 was detected in 2 of 6 African Americans. RNA sequencing revealed consistent overexpression of the FOXM1 gene when tumor gene expression was compared with nonmalignant breast samples. Using an outlier analysis of gene expression comparing one cancer with all the others, we detected expression patterns unique to each patient's tumor. Integrative DNA/RNA analysis provided evidence for deregulation of mutated genes, including the monoallelic expression of TP53 mutations. Finally, molecular alterations in several cancers supported targeted therapeutic intervention on clinical trials with known inhibitors, particularly for alterations in the RAS/RAF/MEK/ERK and PI3K/AKT/mTOR pathways. In conclusion, whole genome and transcriptome profiling of mTNBC have provided insights into somatic events occurring in this difficult to treat cancer. These genomic data have guided patients to investigational treatment trials and provide hypotheses for future trials in this irremediable cancer. Mol Cancer Ther; 12(1); 104–16. ©2012 AACR.
Martian Eolian Dust Probed by ChemCam

The ubiquitous eolian dust on Mars plays important roles in the current sedimentary and atmospheric processes of the planet. The ChemCam instrument retrieves a consistent eolian dust composition at the submillimeter scale from every first laser shot on Mars targets. Its composition presents significant differences with the Aeolis Palus soils and the Bagnold dunes as it contains lower CaO and higher SiO2. The dust FeO and TiO2 contents are also higher, probably associated with nanophase oxide components. The dust spectra show the presence of volatile elements (S and Cl), and the hydrogen content is similar to Bagnold sands but lower than Aeolis Palus soils. Consequently, the dust may be a contributor to the amorphous component of soils, but differences in composition indicate that the two materials are not equivalent.
TDP-43 Is Not a Common Cause of Sporadic Amyotrophic Lateral Sclerosis

Background TAR DNA binding protein, encoded by TARDBP, was shown to be a central component of ubiquitin-positive, tau-negative inclusions in frontotemporal lobar degeneration (FTLD-U) and amyotrophic lateral sclerosis (ALS). Recently, mutations in TARDBP have been linked to familial and sporadic ALS. Methodology/Principal Findings To further examine the frequency of mutations in TARDBP in sporadic ALS, 279 ALS cases and 806 neurologically normal control individuals of European descent were screened for sequence variants, copy number variants, genetic and haplotype association with disease. An additional 173 African samples from the Human Gene Diversity Panel were sequenced as this population had the highest likelihood of finding changes. No mutations were found in the ALS cases. Several genetic variants were identified in controls, which were considered as non-pathogenic changes. Furthermore, pathogenic structural variants were not observed in the cases and there was no genetic or haplotype association with disease status across the TARDBP locus. Conclusions Our data indicate that genetic variation in TARDBP is not a common cause of sporadic ALS in North American.
A Simple Retroelement Based Knock-Down System in Dictyostelium: Further Insights into RNA Interference Mechanisms

Characteristics of DIRS-1 Mediated Knock-Downs We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cassette containing the inverted terminal repeats and a fragment of a gene of interest was sufficient to activate the RNAi response, resulting in the generation of ~21 nt siRNAs, a reduction of mRNA and protein expression of the respective endogene. Surprisingly, no transitivity was observed on the endogene. This was in contrast to previous observations, where endogenous siRNAs caused spreading on an artificial transgene. Knock-down was successful on seven target genes that we examined. In three cases a phenotypic analysis proved the efficiency of the approach. One of the target genes was apparently essential because no knock-out could be obtained; the RNAi mediated knock-down, however, resulted in a very slow growing culture indicating a still viable reduction of gene expression. Advantages of the DIRS-1–RNAi System The knock-down system required a short DNA fragment (~400 bp) of the target gene as an initial trigger. Further siRNAs were generated by RdRPs since we have shown some siRNAs with a 5’-triphosphate group. Extrachromosomal vectors facilitate the procedure and allowed for molecular and phenotypic analysis within one week. The system provides an efficient and rapid method to reduce protein levels including those of essential genes.