Miracle-dz/UniFAR-FTUs huggingface dataset:
A newly identified gene cluster in Aspergillus nidulans comprises five novel genes localized in the alc region that are controlled both by the specific transactivator AlcR and the general carbon‐catabolite repressor CreA

Ethanol‐utilization in Aspergillus nidulans is mediated by alcohol dehydrogenase I and aldehyde dehydrogenase encoded by alcA and aldA, respectively. Both genes are under the transcriptional control of the specific activator AlcR and the general carbon catabolite repressor CreA. The alcR and alcA genes are closely linked in chromosome VII; aldA is located in chromosome VIII. We have identified five other transcripts that are expressed from the same genomic region as alcA and alcR. They are inducible by the gratuitous inducer ethyl methyl ketone (EMK), and are carbon catabolite repressed. The corresponding genes, designated alcMalcSalcOalcP, and alcU, are differentially regulated by the specific transcriptional activator AlcR, and they are not all under the direct control by the CreA repressor. Some of the inducible transcripts are very abundant in the cell, whereas others are poorly expressed. Two sets of genes, alcM/alcS and alcR/alcO, are divergently transcribed and probably share a common cis‐acting region, whereas alcP and alcU are individually transcribed from the same strand as alcA and alcR, and have their own promoters. The significance of the alc gene clustering is discussed. At least four of the five novel alc genes in the cluster are not essential for ethanol metabolism.
Evaluation of the Glutamine 27 Glutamic Acid Polymorphism in the Adrenoceptor β2 Surface Gene on Obesity and Metabolic Phenotypes in Taiwan

Background The single-nucleotide polymorphism (SNP), rs1042714 or glutamine 27 glutamic acid (Gln27Glu), in the adrenoceptor β2 surface (ADRB2) gene has previously been examined for association with obesity with inconclusive results. The objective of this study was to determine whether the ADRB2 rs1042714 SNP could influence obesity and obesity-related metabolic traits in a Taiwanese population. Methods The ADRB2 rs1042714 SNP and obesity-related metabolic traits including blood pressure, total cholesterol, triglyceride, fasting glucose, waist circumference, and body mass index (BMI) were examined in 967 individuals with general health examinations. Results Our data revealed that the ADRB2 rs1042714 SNP exhibited a significant association with obesity among the subjects (P = 0.021). Furthermore, the carriers of the GG genotype had a significantly higher BMI than those with the CC genotype (26.0 ± 5.6 vs 24.3 ± 3.8 kg/m2; P = 0.009) and those with the CG genotype (26.0 ± 5.6 vs 23.6 ± 3.3 kg/m2; P = 0.001). We also found a nominal association with systolic blood pressure (P = 0.058) and triglyceride (P = 0.055) levels in the ADRB2 rs1042714 SNP. Conclusions Our study indicates that the ADRB2 rs1042714 SNP may contribute to the risk of obesity and predict obesity-related metabolic traits such as BMI, triglyceride, and systolic blood pressure in Taiwanese subjects.
Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture

ABSTRACT Perirectal surveillance cultures and a stool culture grew Aeromonas species from three patients over a 6-week period and were without epidemiological links. Detection of the bla KPC-2 gene in one isolate prompted inclusion of non-Enterobacteriaceae in our surveillance culture workup. Whole-genome sequencing confirmed that the isolates were unrelated and provided data for Aeromonas reference genomes.
Surface roughness effects on seebeck coefficient in silicon ultra thin films

Surface roughness effects play a crucial role in determining the performance of a device with dimensionality in the sub-50nm scale. In this work we theoretically investigate surface roughness effects on Seebeck coefficient of ultrathin silicon film using non equilibrium Green's function technique. To systematically study surface roughness effects, thickness of the film is varied periodically with square wave profile characterized by two parameters: amplitude(A0) and wavelength(λ). The results show that Seebeck coefficient increases with increasing roughness amplitude and frequency(1/λ). It is found that current which flows through the device, due to temperature gradient, is reduced due to surface roughness. It is interesting to note that, though the current decreases, the voltage required to nullify this current increases. Due to this increase in voltage Seebeck coefficient increases.
Tracer Kinetic Modeling of the 5-HT1AReceptor Ligand [carbonyl-11C]WAY-100635 for PET

[Carbonyl-11C]WAY-100635 is a promising PET radioligand for the 5-HT1A receptor, having demonstrated more favorable characteristics for in vivo imaging than the previously available [O-methyl-11C]WAY-100635. The current study evaluates different tracer kinetic modelling strategies for the quantification of 5-HT1A receptor binding in human brain. Mathematical modelling of the carbonyl-labeled radiotracer is investigated using compartmental structures, including both plasma input and reference tissue approaches. Furthermore, the application of basis function methods allows for the investigation of parametric imaging, providing functional maps of both delivery and binding of the radioligand. Parameter estimates of binding from normal volunteers indicate a low intra- versus a high intersubject variability. It is concluded that a simplified reference tissue approach may be used to quantify 5-HT1A binding either in terms of ROI data or as parametric images.
Ion microprobe analysis—a review of geological applications

Abstract In ion microprobe analysis the specimen is bombarded with a focussed ion beam a few µm in diameter and the secondary ions produced are accelerated into the entrance slit of a mass spectrometer. An outline of the salient features of the instrument is given here, together with an account of the methods used for quantitative elemental and isotopic analysis. The major part of this paper consists of a comprehensive account of the geological applications of ion microprobe analysis. These include elemental analysis, especially for trace elements (down to sub-ppm levels in many cases) and light elements (H-F) which are beyond the scope of the electron microprobe. The other main area of geological interest is isotopic analysis, where the ion microprobe has the advantage over conventional mass spectrometry of being capable of in situ analysis of selected points on polished sections, obviating the need for laborious specimen preparation, and enabling spatially-resolved data to be obtained, with a resolution of a few µm. The ion microprobe has been especially successful in U-Pb zircon dating and the study of isotope anomalies in meteorites. Other significant applications include diffusion and stable isotope studies.
Analytical model to study the impact of ferroelectric materials SBT/PZT on elliptical gate all around junctionless transistor

In the present work, the impact of Negative Capacitance (NC) effect of ferroelectric materials has been studied on Elliptical Gate All Around Junctionless Transistors by incorporating these materials as gate insulator. Landau Devonshire theory and parabolic potential approximation has been used to develop an analytical model to obtain various electrical parameters like surface potential, gate capacitance, subthreshold slope etc. The effect of varying aspect ratio (AR) has been incorporated in the model by obtaining effective radius depending on lengths of major and minor axes. Using the developed model a comparative analysis has been done for devices with two different ferroelectric materials, PZT and SBT, to investigate the feasibility of these materials for integration into future CMOS technology. It has been observed that for different aspect ratios, the device exhibits gain > 1 which also leads to point subthreshold swing value as low as 9mV/dec for SBT and 11mV/dec for PZT for a small range of applied bias, thereby, signifying suitability of such devices for sub-60mV/dec, low power applications.
Toward translating Indonesian spoken utterances to/from other languages

This paper outlines the National Institute of Information and Communications Technology / Advanced Telecommunications Research Institute International (NICT/ATR) research activities in developing a spoken language translation system, specially for translating Indonesian spoken utterances into/from Japanese or English. Since the NICT/ATR Japanese-English speech translation system is an established one and has been widely known for many years, our focus here is only on the additional components that are related to the Indonesian spoken language technology. This includes the development of an Indonesian large vocabulary continuous speech recognizer, Indonesian-Japanese and Indonesian-English machine translators, and an Indonesian speech synthesizer. Each of these component technologies was developed by using corpus-based speech and language processing approaches. Currently, all these components have been successfully incorporated into the mobile terminal of the NICT/ATR multilingual speech translation system.
Identification, Characterization, and Expression Levels of Putative Adhesive Proteins From the Tube-Dwelling Polychaete Sabellaria alveolata

The shelter of the tube-dwelling polychaete Sabellaria alveolata is composed of mineral particles assembled with spots of a proteinaceous cement. The adhesive proteins constituting the cement were identified on the basis of their sequence similarity with proteins of a phylogenetically related species, Phragmatopoma californica. Two positively charged proteins, Sa-1 and Sa-2, share common features: they both have a mass of 22 kDa; are rich in glycine, tyrosine and basic residues; and show repeated peptide motifs. The consensus repeat of Sa-1 is KGAYGAKGLGYGNKAGYGAYG (occurring 6–8 times), while Sa-2 displays the consensus heptapeptide VHKAAWG (5 times) and undecapeptide VHKAAGYGGYG (8 times). Two variants of a serine-rich protein, Sa-3A (22 kDa) and Sa-3B (21 kDa), were also identified. Their serine residues account for 75 mol% and are probably phosphorylated, meaning that Sa-3 is very acidic and negatively charged. Moreover, tyrosine residues of all adhesive proteins are presumably modified into DOPA. Although protein sequences are not well-conserved between S. alveolata and P. californica, their main characteristics (including amino acid composition, post-translational modifications, repeated patterns, isoelectric point, and mass) are shared by both species. This suggests that these features are more important for their function than the primary structure of the proteins. The mRNA abundance for each protein was estimated by quantitative real-time PCR, revealing relative expression levels of about 5, 11, 1.5, and 1 for Sa-1, -2, -3A, and -3B, respectively. These levels could be indicative of charge neutralization phenomena or could reflect their function (interface vs. bulk) in the cement.
Regulation of Anti-Müllerian Hormone Production in the Cow: A Multiscale Study at Endocrine, Ovarian, Follicular, and Granulosa Cell Levels1

Anti-Müllerian hormone (AMH) is an endocrine marker that can help predict superovulatory responses to treatments administered to cows for embryo production. However, the optimal time of the estrous cycle at which a blood test should be performed for a highly reliable prognosis has not yet been established. Moreover, little is known about the regulation of AMH production. To answer these questions, a study was designed to investigate the regulation of AMH production in cows selected for their high or low ovulatory responses to superovulation. At the granulosa cell level, AMH production was inhibited by follicle-stimulating hormone but enhanced by bone morphogenetic proteins. At the follicular level, the expression of AMH within the follicle was dependent on the stage of follicular development. At the ovarian level, the size of the pool of small antral growing follicles determined ovarian AMH production. At the endocrine level, AMH followed a specific dynamic profile during the estrous cycle, which occurred independently of the follicular waves of terminal follicular development. Cows selected for their high or low responses to superovulation did not differ in the regulation of AMH production, but cows with higher responses had higher plasma AMH concentrations throughout the cycle. The optimal period of the estrous cycle at which to measure AMH concentrations with the aim of selecting the best cows for embryo production was found to be at estrus and after Day 12 of the cycle. Based on this multiscale study, we propose a model that integrates the different regulatory levels of AMH production.
Efficient insertional mutagenesis in lactococci and other gram-positive bacteria

In lactococci, the study of chromosomal genes and their regulation is limited by the lack of an efficient transposon mutagenesis system. We associated the insertion sequence ISS1 with the thermosensitive replicon pG+ host to generate a mutagenic tool that can be used even in poorly transformable strains. ISS1 transposition is random in different lactococcal strains as well as in Enterococcus faecalis and Streptococcus thermophilus. High-frequency random insertion (of about 1%) obtained with this system in Lactococcus lactis allows efficient mutagenesis, with typically one insertion per cell. After ISS1 replicative transposition, the chromosome contains duplicated ISS1 sequences flanking pG+ host. This structure allows cloning of the interrupted gene. In addition, efficient excision of the plasmid leaves a single ISS1 copy at the mutated site, thus generating a stable mutant strain with no foreign markers. Mutants obtained by this transposition system are food grade and can thus be used in fermentation processes.
Scaling relations of star-forming regions: from kpc-sized clumps to H ii regions

We present the properties of eight star-forming regions, or ‘clumps,’ in three galaxies at z ∼ 1.3 from the WiggleZ Dark Energy Survey, which are resolved with the OH Suppressing InfraRed Imaging Spectrograph (OSIRIS) integral field spectrograph. Within turbulent discs, σ ∼ 90 km s^−1, clumps are measured with average sizes of 1.5 kpc and average Jeans masses of 4.2 × 10^9 M_⊙, in total accounting for 40–60 per cent of the stellar mass of the discs. These findings lend observational support to models that predict larger clumps will form as a result of higher disc velocity dispersions driven-up by cosmological gas accretion. As a consequence of the changes in global environment, it may be predicted that star-forming regions at high redshift should not resemble star-forming regions locally. Yet despite the increased sizes and dispersions, clumps and H_II regions are found to follow tight scaling relations over the range z = 0–2 for Hα size, velocity dispersion, luminosity and mass when comparing >2000 H_II regions locally and 30 clumps at z > 1 (σ ∝ r^(0.42 ±0.03), L_(Hα) ∝ r^(2.72 ±0.04), L_(Hα) ∝ σ^(4.18 ±0.21) and L_Hα ∝ M_Jeans^(1.24±0.05) ). We discuss these results in the context of the existing simulations of clump formation and evolution, with an emphasis on the processes that drive-up the turbulent motions in the interstellar medium. Our results indicate that while the turbulence of discs may have important implications for the size and luminosity of regions which form within them, the same processes govern their formation from high redshift to the current epoch.
Improvement of portal flow and hepatic microcirculatory tissue flow with N-acetylcysteine in dogs with obstructive jaundice produced by bile duct ligation.

OBJECTIVE To find out if N-acetylcysteine (NAC) would improve hepatic circulation in dogs with obstructive jaundice. DESIGN Open laboratory study. SETTING University hospitals, Japan and France. MATERIALS 14 male beagle dogs and 10 male Wistar rats. INTERVENTIONS Obstructive jaundice was produced by ligation of the common bile duct (CBD) for 7 days in both dogs and rats. Either 5% dextrose (control group, n = 7) or NAC (NAC group, n = 7) was given to dogs. Sinusoidal endothelial cells were obtained from rats after ligation by elutriation, and varying amounts of NAC were given. MAIN OUTCOME MEASURES The volumes of portal blood flow and hepatic microcirculatory tissue flow were reduced after ligation of the CBD, but those increased after NAC had been given to dogs with obstructive jaundice. NAC increased the concentrations of plasma cyclic 3',5'-guanosine monophosphate (cGMP). It also increased concentrations of serum and hepatic-reduced glutathione, and hepatic adenosine triphosphate (ATP) in cholestatic dogs, and secretion of cGMP from sinusoidal endothelial cells from rats with obstructive jaundice. CONCLUSION These results suggest that NAC given intravenously effectively improves hepatic circulation and hepatic function in dogs with obstructive jaundice.
Land use scenario simulation based on multi-agent system

Rapid industrialization and urbanization of China have deepened the conflicts of the land supply and demand. In this transition period, there occur many changes to the land utilization. Central and local governments should make prompt effective and scientific planning and control of land use to satisfy requirements of economic and social development. Taking Xinbei district of Changzhou city as the study case, based on the Multi-Agent System (MAS) and GIS technology, this paper set different land use scenarios according to development strategies and characteristics of the study area, and made quantitative analysis of land use scenarios to demonstrate the mainline of land use scenarios. Based on the above analysis, constructed scenario simulation model, analyzed simulation result, put forward feedback information of the scenario simulation model, for the references of land use planning's decision.
Statistical Analysis of Exceptional Events: The Italian Regulatory Experience

In the analysis of reliability performance of distribution utilities, as well as in continuity of supply regulation, criteria are needed for separating normal operation data from exceptional events. In recent years a number of statistical methodologies has been proposed for this purpose. We present here the new methodology that was adopted by the Italian regulatory authority at the beginning of 2008. The decision is supported by a statistical analysis of the number of faults on the medium voltage (MV) and low voltage (LV) networks, for each six-hour time interval in a three year time span, for different provinces and distribution companies. The new methodology is employed in the reward and penalty mechanisms that regulate the SAIDI, SAIFI, and MAIFI indicators and, with some original provisions, also in the Guaranteed Standard on maximum restoration times.
Bulk acoustic wave filters for GPS with extreme stopband attenuation

RF filters for GPS receivers inside phones require extreme stopband attenuation in order to protect the weak GPS signals from interference by the cellular phone bands and ISM bands. In contrast to RF filters for cellular phone bands which typically require a relative bandwidth up to 4.5% a GPS filter needs less than 0.5% relative bandwidth. The reduced bandwidth requirement can be traded in for low insertion loss and high stopband attenuation. The impact of this tradeoff on the design of the bulk acoustic wave (BAW) filters is discussed in this paper. The choice of the filter topology and acoustic layer stack forming the resonators as well as the spurious mode suppression need to be re-optimized under the new constraints. As a result of this optimization, a filter for GPS signals with a minimum insertion loss of 1.2 dB and a stopband attenuation of 50 dB is presented.
Modeling the potential effects of atrazine on aquatic communities in midwestern streams

The comprehensive aquatic systems model for atrazine (CASMATZ) estimates the potential toxic effects of atrazine on populations of aquatic plants and consumers in a generic lower‐order midwestern stream. The CASMATZ simulates the daily production of 20 periphyton and 6 aquatic vascular plant species. The modeled consumer community consists of 17 functionally defined species of zooplankton, benthic invertebrates, bacteria, and fish. Daily values of population biomass (grams of carbon per square meter) are calculated as nonlinear functions of population bioenergetics, physical–chemical environmental parameters, grazing/predator–prey interactions, and population‐specific direct and indirect responses to atrazine. The CASMATZ uses Monte Carlo methods to characterize the implications of phenotypic variability, environmental variability, and uncertainty associated with atrazine toxicity data in estimating the potential impacts of time‐varying atrazine exposures on population biomass and community structure. Comparisons of modeled biomass values for plants and consumers with published data indicate that the generic reference simulation realistically describes ecological production in lower‐order midwestern streams. Probabilistic assessments were conducted using the CASMATZ to evaluate potential modeled changes in plant community structure resulting from measured atrazine exposure profiles in 3 midwestern US streams representing watersheds highly vulnerable to runoff. Deviation in the median values of maximum 30‐d average Steinhaus similarity index ranged from 0.09% to 2.52% from the reference simulation. The CASMATZ could therefore be used for the purposes of risk assessment by comparison of site monitoring–based model output to a biologically relevant Steinhaus similarity index level of concern. Used as a generic screening technology or in site‐specific applications, the CASMATZ provides an effective, coherent, and transparent modeling framework for assessing ecological risks posed by pesticides in lower‐order streams. Environ Toxicol Chem 2013;32:2402–2411. © 2013 SETAC
Design of Meningococcal Factor H Binding Protein Mutant Vaccines That Do Not Bind Human Complement Factor H

ABSTRACT Meningococcal factor H binding protein (fHbp) is a human species-specific ligand for the complement regulator, factor H (fH). In recent studies, fHbp vaccines in which arginine at position 41 was replaced by serine (R41S) had impaired fH binding. The mutant vaccines elicited bactericidal responses in human fH transgenic mice superior to those elicited by control fHbp vaccines that bound human fH. Based on sequence similarity, fHbp has been classified into three variant groups. Here we report that although R41 is present in fHbp from variant groups 1 and 2, the R41S substitution eliminated fH binding only in variant group 1 proteins. To identify mutants in variant group 2 with impaired fH binding, we generated fHbp structural models and predicted 63 residues influencing fH binding. From these, we created 11 mutants with one or two amino acid substitutions in a variant group 2 protein and identified six that decreased fH binding. Three of these six mutants retained conformational epitopes recognized by all six anti-fHbp monoclonal antibodies (MAbs) tested and elicited serum complement-mediated bactericidal antibody titers in wild-type mice that were not significantly different from those obtained with the control vaccine. Thus, fHbp amino acid residues that affect human fH binding differ across variant groups. This result suggests that fHbp sequence variation induced by immune selection also affects fH binding motifs via coevolution. The three new fHbp mutants from variant group 2, which do not bind human fH, retained important epitopes for eliciting bactericidal antibodies and may be promising vaccine candidates.