bluuebunny/crossref_metadata_2025_split huggingface dataset:
FleQ DNA Binding Consensus Sequence Revealed by Studies of FleQ-Dependent Regulation of Biofilm Gene Expression in Pseudomonas aeruginosa
Authors: Baraquet Claudine , Harwood Caroline S. 
Published: October 2015

ABSTRACT

The transcription factor FleQ from
Pseudomonas aeruginosa
derepresses expression of genes involved in biofilm formation when intracellular levels of the second messenger cyclic diguanosine monophosphate (c-di-GMP) are high. FleQ also activates transcription of flagellar genes, and the expression of these genes is highest at low intracellular c-di-GMP. FleQ thus plays a central role in mediating the transition between planktonic and biofilm lifestyles of
P. aeruginosa
. Previous work showed that FleQ controls expression of the
pel
operon for Pel exopolysaccharide biosynthesis by converting from a repressor to an activator upon binding c-di-GMP. To explore the activity of FleQ further, we carried out DNase I footprinting at three additional biofilm gene promoters, those of
psl
,
cdrAB
, and PA2440. The expression of
cdrAB
, encoding a cell surface adhesin, was sufficiently responsive to FleQ to allow us to carry out
in vivo
promoter assays. The results showed that, similarly to our observations with the
pel
operon, FleQ switches from a repressor to an activator of
cdrAB
gene expression in response to c-di-GMP. From the footprinting data, we identified a FleQ DNA binding consensus sequence. A search for this conserved sequence in bacterial genome sequences led to the identification of FleQ binding sites in the promoters of the
siaABCD
operon, important for cell aggregation, and the
bdlA
gene, important for biofilm dispersal, in
P. aeruginosa
. We also identified FleQ binding sites upstream of
lapA
-like adhesin genes in other
Pseudomonas
species.

IMPORTANCE
The transcription factor FleQ is widely distributed in
Pseudomonas
species. In all species examined, it is a master regulator of flagellar gene expression. It also regulates diverse genes involved in biofilm formation in
P. aeruginosa
when intracellular levels of the second messenger c-di-GMP are high. Unlike flagellar genes, biofilm-associated genes are not always easy to recognize in genome sequences. Here, we identified a consensus DNA binding sequence for FleQ. This allowed us to survey
Pseudomonas
strains and find new genes that are likely regulated by FleQ and possibly involved in biofilm formation.
Multi-component dark matter in the light of new AMS-02 data
Authors: Lai Chang , Huang Da , Geng Chao-Qiang 
Published: October 2015

We study the possible positron/electron excesses within the multi-component leptonically decaying dark matter (DM) scenario by fitting the most recent AMS-02 data on the positron fraction and total [Formula: see text] flux. We show that both the single- and two-component DM models are able to fit the two AMS-02 datasets. However, the single-component DM model favors the [Formula: see text] energy cutoff from the DM decay less than 1 TeV through the [Formula: see text]-channel, which is already well constrained by the diffuse [Formula: see text]-ray spectrum measured by Fermi-LAT. For the two-component case with closing the [Formula: see text]-mode for the heavy DM particle, we find that the new AMS-02 data allows the heavy DM cutoff larger than 1 TeV, providing a good description of the high-energy behavior of the total [Formula: see text] flux and satisfying the diffuse [Formula: see text]-ray constraint.
Multi-component dark matter
Authors: Geng Chao-Qiang , Huang Da , Lai Chang 
Published: October 2015

We review the multi-component decaying dark matter (DM) scenario to explain the possible cosmic ray excesses in the positron fraction, the positron and electron respective fluxes, and the total [Formula: see text] flux observed by AMS-02. We show that the two-component DM model can fit the AMS-02 datasets. In particular, we demonstrate that the heavier DM component with its mass around 1 TeV dominantly decaying through the [Formula: see text] and [Formula: see text]-channels describes the high-energy behavior of the total [Formula: see text] flux data above 500 GeV, while the lighter one of O(100) GeV mainly through the [Formula: see text]-channel explains the substructure around 100 GeV.
Smith Woodward's ideas on fish classification
Authors: Forey Peter L. 
Published: October 2015

Abstract
Smith Woodward embarked on the production of a catalogue of fossil fishes half a century after Louis Agassiz began a similar exercise. These two palaeontological goliaths remain the only authorities who saw all relevant fossil fish material in all important collections. Between their works there was a substantial increase in the number of species recognized, reflecting the nineteenth-century passion for collecting, the rise of museums, as well as an acceptance that species change through time. Agassiz was working in pre-evolutionary days but Smith Woodward's view on fish diversity was strongly influenced by the theory of evolution and specifically the writings of Thomas Henry Huxley as well as those of Edward Drinker Cope and Ramsay Heatley Traquair and their ideas of grades of evolution. Many of Smith Woodward's generic and species descriptions survive today as his lasting legacy. Higher classification has changed considerably with new discoveries and differing methods of classification.
Tomato (Solanum lycopersicum) and root-knot nematodes (Meloidogyne spp.) – a century-old battle
Authors: Seid Awol , Fininsa Chemeda , Mekete Tesfamariam , Decraemer Wilfrida , Wesemael Wim M.L. 
Published: October 2015

The encounter betweenMeloidogynespecies and tomato is many centuries old.Meloidogynespecies are known to cause high levels of economic loss worldwide in a multitude of agricultural crops, including tomato. This review was initiated to provide an overview of the damage potential ofMeloidogynespp. on cultivars of tomato (Solanum lycopersicum), and to compile the different studies done on the management ofMeloidogynespp. on tomato with particular emphasis on theMiresistance gene. Numerous studies have been conducted to assess the damage potential of root-knot nematode on various tomato cultivars; its yield loss potential ranges from 25 to 100%. A range of management options from using synthetic nematicides to soilless cultures have been tried and are available for managingMeloidogynespp. Resistant commercial cultivars and rootstocks carrying theMigene have been used successfully to manageMeloidogyne incognita,M. javanicaandM. arenaria. However, virulent populations have been detected. Relying on a single root-knot nematode management strategy is an outdated concept and different management options should be used in an integrated management context by considering the whole system of disease management. In future management ofMeloidogynespecies, care must be taken in directly extrapolating the tolerance limit determined elsewhere, since it is affected by many factors such as the type of initial inoculum and physiological races ofMeloidogynespp., environmental conditions, types of cultivars and experimental approaches used.
The Arbitrary Definition of the Current Atlantic Major Hurricane Landfall Drought
Authors: Hart Robert E. , Chavas Daniel R. , Guishard Mark P. 
Published: October 2015

Abstract
A major hurricane [96+ knots (kt; 1 kt = 0.51 m s–1) of maximum sustained wind] has not made landfall in the United States since Wilma (2005). Recent elegant stochastic–statistical modeling estimates the return period of a 9-yr streak for this metric as 177 yr, suggesting extraordinary rarity, especially in the context of the length of the record (1851–2014). Current awareness of the drought is increased given that the 2015 hurricane season is expected to be suppressed from El Niño and the recent anniversaries of several noteworthy landfalls.
Yet, here we show that the significance or even existence of the current 9-yr drought is highly dependent on the metric used. Acknowledging that wind intensity estimates are binned every 5 kt and have approximate 10-kt uncertainty, we examine the same record using landfall thresholds of 95–105 kt. Using 105-kt landfall, 1993–2003 becomes a previously unreported yet more remarkable 11-yr drought and 1981–88 becomes an 8-yr drought. Further, landfall minimum sea level pressure is more reliably estimated than maximum sustained wind speed. For landfall intensities stronger than 960 hPa (a climatological threshold for 100 kt), the current drought disappears because of Irene (2011) and Sandy (2012). A coastline-independent yet nearby proximity metric is tested and reveals a nonexistent drought.
Accordingly, this study suggests the following: 1) Caution is advised when identifying a hurricane drought and its historical significance. 2) Using hurricane landfall statistics to infer a climate signal is fraught with issues (threshold, coastline, and potentially nonscientific contributions), regardless of intensity metric. 3) From a societal context, human and financial losses matter most, and Irene [2011; $8 billion (U.S. dollars)] and Sandy (2012; $88 billion) occurred during the current drought.
Effects of Climatological Model Biases on the Projection of Tropical Climate Change
Authors: Zhou Zhen-Qiang , Xie Shang-Ping 
Published: October 2015

Abstract
Climate models suffer from long-standing biases, including the double intertropical convergence zone (ITCZ) problem and the excessive westward extension of the equatorial Pacific cold tongue. An atmospheric general circulation model is used to investigate how model biases in the mean state affect the projection of tropical climate change. The model is forced with a pattern of sea surface temperature (SST) increase derived from a coupled simulation of global warming but uses an SST climatology derived from either observations or a coupled historical simulation. The comparison of the experiments reveals that the climatological biases have important impacts on projected changes in the tropics. Specifically, during February–April when the climatological ITCZ displaces spuriously into the Southern Hemisphere, the model overestimates (underestimates) the projected rainfall increase in the warmer climate south (north) of the equator over the eastern Pacific. Furthermore, the global warming–induced Walker circulation slowdown is biased weak in the projection using coupled model climatology, suggesting that the projection of the reduced equatorial Pacific trade winds may also be underestimated. This is related to the bias that the climatological Walker circulation is too weak in the model, which is in turn due to a too-weak mean SST gradient in the zonal direction. The results highlight the importance of improving the climatological simulation for more reliable projections of regional climate change.
How Has Human-Induced Climate Change Affected California Drought Risk?
Authors: Cheng Linyin , Hoerling Martin , AghaKouchak Amir , Livneh Ben , Quan Xiao-Wei , Eischeid Jon 
Published: October 2015

Abstract
The current California drought has cast a heavy burden on statewide agriculture and water resources, further exacerbated by concurrent extreme high temperatures. Furthermore, industrial-era global radiative forcing brings into question the role of long-term climate change with regard to California drought. How has human-induced climate change affected California drought risk? Here, observations and model experimentation are applied to characterize this drought employing metrics that synthesize drought duration, cumulative precipitation deficit, and soil moisture depletion. The model simulations show that increases in radiative forcing since the late nineteenth century induce both increased annual precipitation and increased surface temperature over California, consistent with prior model studies and with observed long-term change. As a result, there is no material difference in the frequency of droughts defined using bivariate indicators of precipitation and near-surface (10 cm) soil moisture, because shallow soil moisture responds most sensitively to increased evaporation driven by warming, which compensates the increase in the precipitation. However, when using soil moisture within a deep root zone layer (1 m) as covariate, droughts become less frequent because deep soil moisture responds most sensitively to increased precipitation. The results illustrate the different land surface responses to anthropogenic forcing that are relevant for near-surface moisture exchange and for root zone moisture availability. The latter is especially relevant for agricultural impacts as the deep layer dictates moisture availability for plants, trees, and many crops. The results thus indicate that the net effect of climate change has made agricultural drought less likely and that the current severe impacts of drought on California’s agriculture have not been substantially caused by long-term climate changes.
Endometrial cancer: correlation of apparent diffusion coefficient (ADC) with tumor cellularity and tumor grade
Authors: Kishimoto Keiko , Tajima Shinya , Maeda Ichiro , Takagi Masayuki , Ueno Takahiko , Suzuki Nao , Nakajima Yasuo 
Published: October 2015

Background Diffusion-weighted imaging (DWI) and the apparent diffusion coefficient (ADC) are widely used for detecting uterine endometrial cancer. The relationships between ADC values and pathological features of endometrial cancer have not yet been established. Purpose To investigate whether ADC values of endometrial cancer vary according to histologic tumor cellularity and tumor grade. Material and Methods We retrospectively reviewed 30 pathologically confirmed endometrial cancers. All patients underwent conventional non-enhanced magnetic resonance imaging (MRI) and DWI procedures, and ADC values were calculated. Tumor cellularity was evaluated by counting cancer cells in three high-power ( × 400) fields. The correlation between ADC values and tumor cellularity was assessed using Pearson’s correlation coefficient test for statistical analysis. Results The mean ± standard deviation (SD) ADC value ( ×10−3 mm2/s) of endometrial cancer was 0.85 ± 0.22 (range, 0.55–1.71). The mean ± SD tumor cellularity was 528.36 ± 16.89 (range, 298.0–763.6). ADC values were significantly inversely correlated with tumor cellularity. No significant relationship was observed between ADC values and tumor grade (mean ADC values: G1, 0.88 ± 0.265 × 10−3 mm2/s; G2, 0.80 ± 0.178 × 10−3 mm2/s; G3, 0.81 ± 0.117 × 10−3 mm2/s). Conclusion There is a significant inverse relationship between ADC values and tumor cellularity in endometrial cancer. No significant differences in average ADC value were observed between G1, G2, and G3 tumors. However, the lower the tumor grade, the wider the SD.
Evaluation of guideline-adherent treatment in cluster headache
Authors: Lademann Victoria , Jansen Jan-Peter , Evers Stefan , Frese Achim 
Published: October 2015

Background Several treatment guidelines exist for cluster headache. However, it is not yet known how many cluster headache patients are treated according to these guidelines. Methods We enrolled 434 cluster headache patients with confirmed diagnosis referred to two tertiary pain centers. The history of treatment was registered and analyzed according to the treatment guidelines of the European Federation of Neurological Societies. Results Regarding acute attack treatment, 62.1% of the episodic and 71.0% of the chronic cluster headache patients were treated according to the guidelines. The efficacy rate was above 92% in both groups. Regarding prophylactic treatment, 31.3% of the episodic and 50.9% of the chronic cluster headache patients were treated according to the guidelines. The efficacy rate was 92.8% for episodic and 70.9% for chronic cluster headache. Conclusion The rate of guideline-adherent treatment in cluster headache is about 70% for acute treatment and about 35% for prophylactic treatment. The efficacy of this treatment is significantly higher than the efficacy of non-guideline-adherent treatment.
Prevalence of neuropathic pain in early multiple sclerosis
Authors: Heitmann Henrik , Biberacher Viola , Tiemann Laura , Buck Dorothea , Loleit Verena , Selter Rebecca C , Knier Benjamin , Tölle Thomas R , Mühlau Mark , Berthele Achim , Hemmer Bernhard , Ploner Markus 
Published: October 2015

Background: Pain is considered a frequent symptom in multiple sclerosis. Neuropathic pain is the type of pain most closely related to the pathology of multiple sclerosis and its prevalence estimates vary largely. Objective: We prospectively assessed the prevalence of neuropathic pain in patients with early multiple sclerosis and investigated the association of neuropathic pain with other clinical parameters. Methods: A total of 377 outpatients with multiple sclerosis at an early disease stage were included in this prospective study. Mean disease duration was 4.2 years, mean Expanded Disability Status Scale (EDSS) score was 1.6, 96.8% of patients were classified as having relapsing–remitting multiple sclerosis. Neuropathic pain was assessed using the PainDETECT questionnaire (PDQ). Depression, fatigue and cognition were assessed using the Beck Depression Inventory (BDI), the Fatigue Scale for Motor and Cognitive Functions (FSMC) and the Paced Auditory Serial Addition Test. Results: PDQ scores indicative of neuropathic pain were found in 4.2% of patients. Regression analysis revealed EDSS, BDI and FMSC scores as strongest predictors of PDQ scores. Conclusions: Neuropathic pain appears to be less frequent in early multiple sclerosis than expected and is significantly associated with disability, depression and fatigue. The assessment and therapy of pain in multiple sclerosis should thus take into account neuropsychiatric symptoms already at early disease stages.
Long-term remissions after FCR chemoimmunotherapy in previously untreated patients with CLL: updated results of the CLL8 trial
Authors: Fischer Kirsten , Bahlo Jasmin , Fink Anna Maria , Goede Valentin , Herling Carmen Diana , Cramer Paula , Langerbeins Petra , von Tresckow Julia , Engelke Anja , Maurer Christian , Kovacs Gabor , Herling Marco , Tausch Eugen , Kreuzer Karl-Anton , Eichhorst Barbara , Böttcher Sebastian , Seymour John F. , Ghia Paolo , Marlton Paula , Kneba Michael , Wendtner Clemens-Martin , Döhner Hartmut , Stilgenbauer Stephan , Hallek Michael 
Published: October 2015

Key Points
Long-term remissions after FCR chemoimmunotherapy in previously untreated patients with CLL. Updated results on safety and efficacy of the CLL8 trial.
Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Authors: Davies Nathaniel J. , Krusche Peter , Tauber Eran , Ott Sascha 
Published: October 2015

Abstract
Background
Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than non-functional sequences. Successful comparisons of distantly related species will thus yield highly important sequence elements likely to serve fundamental biological roles. RNA regulatory elements are less well understood than those in DNA. In this study we use the emerging model organism Nasonia vitripennis, a parasitic wasp, in a comparative analysis against 12 insect genomes to identify deeply conserved non-coding elements (CNEs) conserved in large groups of insects, with a focus on 5’ UTRs and promoter sequences.

Results
We report the identification of 322 CNEs conserved across a broad range of insect orders. The identified regions are associated with regulatory and developmental genes, and contain short footprints revealing aspects of their likely function in translational regulation. The most ancient regions identified in our analysis were all found to overlap transcribed regions of genes, reflecting stronger conservation of translational regulatory elements than transcriptional elements. Further expanding sequence analyses to non-insect species we also report the discovery of, to our knowledge, the two oldest and most ubiquitous CNE’s yet described in the animal kingdom (700 MYA). These ancient conserved non-coding elements are associated with the two ribosomal stalk genes, RPLP1 and RPLP2, and were very likely functional in some of the earliest animals.

Conclusions
We report the identification of the most deeply conserved CNE’s found to date, and several other deeply conserved elements which are without exception, part of 5’ untranslated regions of transcripts, and occur in a number of key translational regulatory genes, highlighting translational regulation of translational regulators as a conserved feature of insect genomes.
On Browder’s convergence theorem and Halpern iteration process for G-nonexpansive mappings in Hilbert spaces endowed with graphs
Authors: Tiammee Jukrapong , Kaewkhao Attapol , Suantai Suthep 
Published: October 2015

AbstractIn this paper, we prove Browder’s convergence theorem for G-nonexpansive mappings in a Hilbert space with a directed graph. Moreover, we also prove strong convergence of the Halpern iteration process to a fixed point of G-nonexpansive mappings in a Hilbert space endowed with a directed graph. The main results obtained in this paper extend and generalize many well-known results in the literature.
Semiclassical orthogonal polynomial systems on nonuniform lattices, deformations of the Askey table, and analogues of isomonodromy
Authors: Witte N. S. 
Published: October 2015

AbstractA 𝔻-semiclassical weight is one which satisfies a particular linear, first-order homogeneous equation in a divided-difference operator 𝔻. It is known that the system of polynomials, orthogonal with respect to this weight, and the associated functions satisfy a linear, first-order homogeneous matrix equation in the divided-difference operator termed thespectral equation. Attached to the spectral equation is a structure which constitutes a number of relations such as those arising from compatibility with the three-term recurrence relation. Here this structure is elucidated in the general case of quadratic lattices. The simplest examples of the 𝔻-semiclassical orthogonal polynomial systems are precisely those in the Askey table of hypergeometric and basic hypergeometric orthogonal polynomials. However within the 𝔻-semiclassical class it is entirely natural to define a generalization of the Askey table weights which involve a deformation with respect to new deformation variables. We completely construct the analogous structures arising from such deformations and their relations with the other elements of the theory. As an example we treat the first nontrivial deformation of the Askey–Wilson orthogonal polynomial system defined by the q-quadratic divided-difference operator, the Askey–Wilson operator, and derive the coupled first-order divided-difference equations characterizing its evolution in the deformation variable. We show that this system is a member of a sequence of classical solutions to theq-Painlevé system.
A Review of Drying Processes in the Production of Pumpkin Powder
Authors: Roongruangsri Warawaran , Bronlund John E. 
Published: October 2015

Abstract
Pumpkin is widely used as a valuable food source and is gaining the attention of healthcare consumers. Dried powdering pumpkin is an alternative way to increase the consumption. For these reasons, a sound knowledge of the processes for drying and powdering of pumpkin is needed. Therefore, the present review summarizes data from the literature and points out promising areas for further research. This review focused mainly on various processes of dried pumpkin powder, including pre-treatment techniques which can influence the quality of dried product. Impacts of drying and storage methods on quality changes were also revealed in dried pumpkin powder such as the loss of color, changes in texture or an off-flavor and decreases in carotenoids or other nutrients. Moreover, this review also collected the basic information about characterization of pumpkin fruit and also chemical characteristics and nutritional values of pumpkin. Finally, the review pointed out areas for future research to further elucidate the best methods of dried pumpkin powdering for the local companies.