Miracle-dz/UniFAR-FTUs huggingface dataset:
Control of the Type 3 Secretion System in Vibrio harveyi by Quorum Sensing through Repression of ExsA

ABSTRACT The type 3 secretion system (T3SS) genes of Vibrio harveyi are activated at low cell density and repressed at high cell density by quorum sensing (QS). Repression requires LuxR, the master transcriptional regulator of QS-controlled genes. Here, we determine the mechanism underlying the LuxR repression of the T3SS system. Using a fluorescence-based cell sorting approach, we isolated V. harveyi mutants that are unable to express T3SS genes at low cell density and identified two mutations in the V. harveyi exsBA operon. While LuxR directly represses the expression of exsBA, complementation and epistasis analyses reveal that it is the repression of exsA expression, but not exsB expression, that is responsible for the QS-mediated repression of T3SS genes at high cell density. The present work further defines the genes in the V. harveyi QS regulon and elucidates a mechanism demonstrating how multiple regulators can be linked in series to direct the expression of QS target genes specifically at low or high cell density.
An automatic modulation classificationtechnique foraeronautical communications

The L-band Digital Aeronautical Communication System Type-1 (L-DACS1) has been considered as the potential standard for future aeronautical communications. As an important technique for L-DACS1, Automatic Modulation Classification (AMC) can recognize and demodulate the dynamically allocated signal in the system. However, due to the interference of Distance Measure Equipment (DME), performance degradation is encountered by the existing approaches in L-DACS1. In this paper, channel estimation and equalization from L-DACS1 pilot symbols were carried out to reduce the influence of channel especially the noise, which lead to an improved classification method for L-DACS1. It is shown through simulations that the method proposed in this paper outperforms the existing algorithm which is based on the sixth-order cumulates in terms of classification accuracy and complexity for L-DACS1 in aeronautical fading channels.
Prevalence and Predictors of Change in Adult-Child Primary Caregivers

Family caregiving research is increasingly contextual and dynamic, but few studies have examined prevalence and predictors of change in primary caregivers, those with the most frequent contact with healthcare professionals. We identified prevalence and predictors of 2-year change in primary adult-child caregivers. Data pooled from the 1992–2000 waves of the Health and Retirement Study (HRS) represent 1,068 parent-level care occasions and 3,616 child-level occasions. There is considerable 2-year stability in primary adult-child caregivers. Parents are more prone to experience a change in adult-child primary caregivers if they live by themselves and if they have more sons and daughters. As far as the adult children are concerned, daughters and children living closer to parents are more likely to remain primary caregivers. Results suggest that change in primary caregivers is more strongly associated with available alternatives and gender norms than burden and competing obligations.
Time under tension decreased with blood flow–restricted exercise

Objectives: Exercise to failure results in similar muscle protein synthesis responses, independent of intensity. However, low‐intensity exercise likely requires more time under tension and those with injuries may be incapable of sustaining the mechanical stress to reach failure. Design: The purpose was to determine whether elastic knee wraps (KW) provide a stimulus to decrease time under tension and overall volume of work while maintaining a similar level of metabolic stress. Methods: Thirteen healthy subjects participated in a randomized crossover study consisting of three trials. The first determined 1 repetition maximum (1RM) on the bilateral leg extension. Subjects were then assigned to a blood flow restriction (BFR) or control (CON) group. After trial 2, subjects crossed over to the opposite trial. KW were placed around the thigh of each leg during BFR. Leg extensions were completed at 30% 1RM until failure. Whole blood lactate (WBL) was taken pre‐, post‐, and 3 and 5 min postexercise. Heart rate (HR) was measured before, following the first and second sets, and 3 and 5 min postexercise. Results: This study found KW provide a BFR stimulus allowing failure to occur sooner with similar metabolic stress postreperfusion. There were no differences in HR at any time point. Conclusions: These results may benefit populations that cannot sustain the mechanical stress of high‐intensity exercise or low‐intensity exercise that requires a longer sustained time under tension.
Letter to the Editor: Electric Vehicle Demand Model for Load Flow Studies

Abstract This article introduces a specific and simple model for electric vehicles suitable for load flow studies. The electric vehicles demand system is modeled as a PQ bus with stochastic characteristics based on the concept of the queuing theory. All appropriate variables of stochastic PQ buses are given with closed formulas as a function of charging time. A specific manufacturer model of electric vehicles is used as study case.
The poison–antidote stability system of the broad‐host‐range Thiobacillus ferrooxidans plasmid pTF‐FC2

In plasmid pTF‐FC2, three small open reading frames (ORFs) are situated between the repB (primase) gene and the repA (helicase) gene of its IncQ‐type replicon. Disruption of each of the three ORFs followed by tests for plasmid stability and host cell growth indicated that the ORFs encoded a poison–antidote plasmid stability system. The three genes were named pasA, pasB and pasC (plasmid addiction system), in which PasA is the antidote, PasB the toxin and PasC a protein that appears to enhance the ability of the antidote to neutralize the toxin. Disruption of the pasA gene resulted in two different spontaneous deletions, which inactivated the stability system but did not alter the host range or plasmid copy number. This indicated that the three small ORFs were not involved in plasmid replication. When placed behind a tac promoter, induction of pasB was found to be highly lethal to host cells, which suggests that the Pas system acts by killing plasmid‐free host cells rather than by retarding the growth of plasmid‐free segregants, as occurs in the ParD system of R1. In spite of this, the presence of the Pas poison–antidote system resulted in a relatively modest threefold stabilization of the pTF‐FC2 host replicon and a similar increase in the stabilization of an unstable heterologous R1 plasmid replicon. The Pas system is a poison–antidote plasmid stability module, which appears to have become integrated within the pTF‐FC2 replicon module.
Gene Mapping in Isolated Populations: New Roles for Old Friends?

Population isolates are increasingly being used in attempts to map genes underlying complex diseases. To further explore the utility of isolates for this purpose, we explore linkage disequilibrium patterns in polymorphisms from two regions (VWF and NF1) in three isolated populations from Finland. At the NF1 locus, the Finnish populations have greater pairwise disequilibrium than populations from Africa, Asia, or northern Europe. However, populations from ‘New Finland’ and ‘Old Finland’ do not differ in their disequilibrium levels at either the NF1 or the VWF locus. In addition, disequilibrium patterns and haplotype diversity do not differ between a sample from the Åland Islands, Finland, and a collection of outbred Centre d’Etude du Polymorphisme Humain families. These results show that linkage disequilibrium patterns sometimes differ among populations with different histories and founding dates, but some putative isolated populations may not significantly differ from larger admixed populations. We discuss factors that should be considered when using isolated populations in gene-mapping studies.
A nano-actuator via cavity-enhanced optical dipole force

In this paper, we demonstrate a nano-actuator using a silicon-based monolithic cavity nano-opto-mechanical system. The nano-actuator is constructed by a special designed nano-scale silicon suspended cantilever which is efficiently driven by the optical gradient force. In experiment, the actuator obtains a tuning range up to 52 nm. The optical power consumption is reduced to 0.04 mW/nm, which is much smaller than typical value of 3mW/nm in optomechanical systems.
A plaque reduction test for dengue virus neutralizing antibodies.

A technique for performing a plaque reduction test for dengue virus neutralizing antibody is described. Experiments designed to test the accuracy of the antibody measurement are presented and analysed by the method for a parallel line graded response assay. Statistical analysis indicates a high degree of accuracy, and the relative merits of this type of test for dengue neutralizing antibody are discussed.
Effect of Amiloride and Spironolactone on Renal Tubular Function, Ambulatory Blood Pressure, and Pulse Wave Velocity in Healthy Participants in a Double-Blinded, Randomized, Placebo-Controlled, Crossover Trial

We wanted to test the hypothesis that treatment with amiloride or spironolactone reduced ambulatory (ABP) and central blood pressure (CBP) and that tubular transport via ENaCγ and AQP2 was increased after furosemide treatment. During baseline conditions, there were no differences in ABP, CBP, renal tubular function, or plasma concentrations of vasoactive hormones. After furosemide treatment, an increase in CBP, CH2o, FENa, FEK, u-AQP2/min, u-ENaCγ/min, PRC, p-Ang II, and p-Aldo was observed. The increases in water and sodium absorption via AQP2 and ENaC after furosemide treatment most likely are compensatory phenomena to antagonize water and sodium depletion.
The effects of pregnancy spacing on infant and child mortality in Matlab, Bangladesh: How they vary by the type of pregnancy outcome that began the interval

Using high-quality longitudinal data on 125,720 singleton live births in Matlab, Bangladesh, we assessed the effects of duration of intervals between pregnancy outcomes on infant and child mortality and how these effects vary over subperiods of infancy and childhood and by the type of outcome that began the interval. Controlling for other correlates of infant and child mortality, we find that shorter intervals are associated with higher mortality. Interval effects are greater if the interval began with a live birth than with another pregnancy outcome. In the first week of the child's life, the effects of short intervals are greater if the sibling born at the beginning of the interval died; after the first month, the effects are greater if that sibling was still alive. Many relationships found are consistent with the maternal depletion hypothesis, and some with sibling competition. Some appear to be due to correlated risks among births to the same mother.
Movement demands of elite rugby league players during Australian National Rugby League and European Super League matches.

PURPOSE This study compared the movement demands of players competing in matches from the elite Australian and European rugby league competitions. METHODS Global positioning system devices were used to measure 192 performances of forwards, adjustables, and outside backs during National Rugby League (NRL; n = 88) and European Super League (SL; n = 104) matches. Total and relative distances covered overall and at low (0-3.5 m/s), moderate (3.6-5 m/s), and high (>5 m/s) speeds were measured alongside changes in movement variables across the early, middle, and late phases of the season. RESULTS The relative distance covered in SL matches (95.8 ± 18.6 m/min) was significantly greater (P < .05) than in NRL matches (90.2 ± 8.3 m/min). Relative low-speed activity (70.3 ± 4.9 m/min vs 75.5 ± 18.9 m/min) and moderate-speed running (12.5 ± 3.3 m m/min vs 14.2 ± 3.8 m/min) were highest (P < .05) in the SL matches, and relative high-speed distance was greater (P < .05) during NRL matches (7.8 ± 2.1 m/min vs 6.1 ± 1.7 m/min). CONCLUSIONS NRL players have better maintenance of high-speed running between the first and second halves of matches and perform less low- and moderate-speed activity, indicating that the NRL provides a higher standard of rugby league competition than the SL.
HARVESTING AND PROCESSING OF MICROALGAE BIOMASS FRACTIONS FOR BIODIESEL PRODUCTION (A REVIEW)

There has been a recent resurgent interest in microalgae as an oil producer for biofuel applications. An adequate supply of nutrients and carbon dioxide enables algae to successfully transform light energy of the sun into energy - rich chemical compounds through photosynthesis. A strain with high lipids, successfully grown and harvested, could provide oil for most of our process by volume, which would then provide the most profitable output. Significant advances have also been made in upstream processing to generate cellular biomass and oil. However, the process of extracting and purifying of oil from algae continues to prove a significant challenge in producing both microalgae bioproducts and biofuel, as the oil extraction from algae is relatively energy-intensive and expensive. The aim of this review is to focus on different harvesting and extraction processes of algae for biodiesel production reported within the last decade.
Resistance to Neutralization by Antibodies Targeting the Coiled Coil of Fusion-active Envelope Is a Common Feature of Retroviruses*

The human T-cell leukemia virus transmembrane glycoprotein (TM) is a typical class 1 membrane fusion protein and a subunit of the viral envelope glycoprotein complex. Following activation, the TM undergoes conformational transitions from a native nonfusogenic state to a fusion-active pre-hairpin intermediate that subsequently resolves to a compact trimer-of-hairpins or six-helix bundle. Disruption of these structural transitions inhibits membrane fusion and viral entry and validates TM as an anti-viral and vaccine target. To investigate the immunological properties of fusion-active TM, we have generated a panel of monoclonal antibodies that recognize the coiled-coil domain of the pre-hairpin intermediate. Antibody reactivity is highly sensitive to the conformation of the coiled coil as binding is dramatically reduced or lost on denatured antigen. Moreover, a unique group of antibodies are 100-1000-fold more reactive with the coiled coil than the trimer-of-hairpins form of TM. The antibodies recognize virally expressed envelope, and significantly, some selectively bind to envelope only under conditions that promote membrane fusion. Most importantly, many of the antibodies potently block six-helix bundle formation in vitro. Nevertheless, viral envelope was remarkably resistant to neutralization by antibodies directed to the coiled coil. The data imply that the coiled coil of viral envelope is poorly exposed to antibody during membrane fusion. We suggest that resistance to neutralization by antibodies directed to fusion-associated structures is a common property of retroviral TM and perhaps of other viral class I fusion proteins. These observations have significant implications for vaccine design.
JAMIE: joint analysis of multiple ChIP-chip experiments

MOTIVATION Chromatin immunoprecipitation followed by genome tiling array hybridization (ChIP-chip) is a powerful approach to identify transcription factor binding sites (TFBSs) in target genomes. When multiple related ChIP-chip datasets are available, analyzing them jointly allows one to borrow information across datasets to improve peak detection. This is particularly useful for analyzing noisy datasets. RESULTS We propose a hierarchical mixture model and develop an R package JAMIE to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for sharing information across experiments. Real data tests illustrate the advantage of JAMIE over a strategy that analyzes individual datasets separately. AVAILABILITY JAMIE is freely available from http://www.biostat. jhsph.edu/~hji/jamie
Comparative osteology of the plethodontid salamander genus Aneides

The genus Aneides is one of 26 genera of highly specialized lungless salamanders in the family Plethodontidae. Within the family, members of the genus have been considered specialized and advanced by virtue of their loss of the aquatic larval stage and their climbing and arboreal tendencies. This report is an attempt to present information concerning osteological variation within the species of Aneides, to make detailed osteological comparisons of the species, and to compare the genus with closely related genera. Of the five species of Aneides, three occur in far western North America: Aneides ferreus, Aneides flavipunctatus, and Aneides lugubris. Aneides hardii occurs at high elevations in south-central New Mexico, and Aneides aeneus is found in the Appalachian highlands of eastern United States. Recently a trend has developed in the direction of comparative osteological studies of salamanders. The study of the family Ambystomatidae by Tihen ( '58) , Baird's ('51) anatomical study of the plethodontid genus Pseudoeurycea, and the osteological approach used by Hansen and Tanner ('58) in studying several species of the plethodontid genus Bolitoglossa are examples of such work. No previous comparative studies have dealt with Aneides, however, and none have considered all of the species of a genus. Some information concerning the osteology of Aneides may be found in the published works of Wiedersheim (1877), Cope (1889), Dunn ('26), and Hilton ('45). These studies contain no information concerning inter-specific variation and it is apparent that lugubris was the species studied. Lowe ('50) utilized some osteological characters in delimiting the genus. His characters are also those used by Cope, Dunn, and Bishop ('43) and include: premaxillae fused, maxilla with posterior portion knife-edged and edentulous, and terminal phalanges Y-shaped. These have remained the major characters differentiating Aneides from its close plethodontid relatives Plethodm and Ensatina. In the following account each bone is described in detail for the genus Aneides and comparisons are made with the condition seen in the related genera Plethodon and Ensatina. A discussion of evolutionary relationships of the various species of Aneides and of the phylogenetic position of the genus within the family Plethodontidae has been prepared on the basis of the analysis presented here, and will be published elsewhere.
Theoretical approaches to e-book research

The adoption and continued use of innovations by societies, organisations and individuals has been a subject of research since before the 1930s. A variety of different theories have been developed to account for the different speeds at which innovations are adopted and the factors that affect the adoption process. This paper reviews theories of the adoption of innovations with particular reference to the recent phenomenon of the e-book as a cultural innovation that is having an impact on individuals, organizations and national policy makers. The paper will suggest which theories are most appropriate for the different levels at which the innovation is employed.
Kara1k: A Karaoke Dataset for Cover Song Identification and Singing Voice Analysis

We introduce Kara1k, a new musical dataset composed of 2,000 analyzed songs thanks to a partnership with a karaoke company. The dataset is divided into 1,000 cover songs provided by Recisio Karafun application1, and the corresponding 1,000 songs by the original artists. Kara1k is mainly dedicated toward cover song identification and singing voice analysis. For both tasks, it offers novel approaches, as each cover song is a studio-recorded song with the same arrangement as the original recording, but with different singers and musicians. Essentia, harmony-analyser, Marsyas, Vamp plugins and YAAFE have been used to extract audio features for each track in Kara1k. We provide metadata such as the title, genre, original artist, year, International Standard Recording Code and the ground truths for the singer's gender, backing vocals, duets and lyrics' language. Additionally, we provide the instrumental track and the pure singing voice track for each cover song. We showcase two use-case experiments for Kara1k. In the cover song identification task using the Dynamic Time Warping method, we provide a comparison of traditional and new features: chroma and MFCC features, chords and keys, and chroma and chord distances. We obtain 84-89% identification accuracy for three of the features, which justifies our focus on karaoke songs. In the supporting experiment on singer gender classification, we evaluate the difference in the performance in two conditions - a pure singing voice and the singing voice mixed with the background music. The Kara1k dataset is freely available under the KaraMIR project website2.
A High Affinity Binding Site for the Polypyrimidine Tract Binding Protein (PTB) Is Located in the 5'-Untranslated Region of the Rat Proteinase α1-Inhibitor 3 Variant I Gene

Abstract As a first step towards understanding the mechanism underlying the differential gene expression of the two variants of the rat proteinase-inhibitor α1-Inhibitor 3 (α1I3) corresponding genomic clones were isolated. The 100% similarity between the sequence of one genomic clone and that of the α1-I3 variant I cDNA strongly suggested that its 5′-sequence represented the upstream region of the corresponding gene. Several putative cis-regulatory elements were identified as well as a polypyrimidine tract located between the transcription start site of the α1-I3 variant I mRNA and the AUG codon. The polypyrimidine tract functions as a positive cis-element in a heterologous promoter. By electrophoretic mobility shift assays (EMSA) we have shown that a GST (glutathione S-transferase) fusion of the rat polypyrimidine tract binding protein (PTB) has a high affinity for the pyrimidine-rich sense strand but not for the complementary sequence of the 5′-untranslated region of the α1-I3 variant I gene.