bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolite Changes Signal Genetic Regulatory Mechanisms for Robust Cell Behavior
Authors: Lee Sang Jun , Trostel Andrei , Adhya Sankar 
Published: January 2014

ABSTRACT

Exploiting mechanisms of utilizing the sugar
d
-galactose in
Escherichia coli
as a model system, we explored the consequences of accumulation of critical intermediates of the
d
-galactose metabolic pathways by monitoring cell growth, metabolites, and transcript profiles. These studies revealed both metabolic network changes far from the
d
-galactose pathway and changes in the global gene regulatory network. The concentration change of a critical intermediate disturbs the equilibrium state, generating a ripple effect through several metabolic pathways that ends up signaling up- or downregulation of specific sets of genes in a programmed manner to cope with the imbalance. Such long-range effects on metabolites and genetic regulatory mechanisms not only may be a common feature in bacteria but very likely operate during cellular development and differentiation in higher organisms as well as in disease cells, like cancer cells.

IMPORTANCE
Metabolite accumulation can create adverse intracellular conditions that are relieved by compensatory immediate changes of metabolite pools and later changes of transcript levels. It has been known that gene expression is normally regulated by added catabolic substrates (induction) or anabolic end products (repression). It is becoming apparent now that change in the concentration of metabolic intermediates also plays a critical role in genetic regulatory networks for metabolic homeostasis. Our study provides new insight into how metabolite pool changes transduce signals to global gene regulatory networks.
Microbial Sulfur Cycle in Two Hydrothermal Chimneys on the Southwest Indian Ridge
Authors: Cao Huiluo , Wang Yong , Lee On On , Zeng Xiang , Shao Zongze , Qian Pei-Yuan 
Published: January 2014

ABSTRACT

Sulfur is an important element in sustaining microbial communities present in hydrothermal vents. Sulfur oxidation has been extensively studied due to its importance in chemosynthetic pathways in hydrothermal fields; however, less is known about sulfate reduction. Here, the metagenomes of hydrothermal chimneys located on the ultraslow-spreading Southwest Indian Ridge (SWIR) were pyrosequenced to elucidate the associated microbial sulfur cycle. A taxonomic summary of known genes revealed a few dominant bacteria that participated in the microbial sulfur cycle, particularly sulfate-reducing
Deltaproteobacteria
. The metagenomes studied contained highly abundant genes related to sulfur oxidation and reduction. Several carbon metabolic pathways, in particular the Calvin-Benson-Bassham pathway and the reductive tricarboxylic acid cycles for CO
2
fixation, were identified in sulfur-oxidizing autotrophic bacteria. In contrast, highly abundant genes related to the oxidation of short-chain alkanes were grouped with sulfate-reducing bacteria, suggesting an important role for short-chain alkanes in the sulfur cycle. Furthermore, sulfur-oxidizing bacteria were associated with enrichment for genes involved in the denitrification pathway, while sulfate-reducing bacteria displayed enrichment for genes responsible for hydrogen utilization. In conclusion, this study provides insights regarding major microbial metabolic activities that are driven by the sulfur cycle in low-temperature hydrothermal chimneys present on an ultraslow midocean ridge.

IMPORTANCE
There have been limited studies on chimney sulfides located at ultraslow-spreading ridges. The analysis of metagenomes of hydrothermal chimneys on the ultraslow-spreading Southwest Indian Ridge suggests the presence of a microbial sulfur cycle. The sulfur cycle should be centralized within a microbial community that displays enrichment for sulfur metabolism-related genes. The present study elucidated a significant role of the microbial sulfur cycle in sustaining an entire microbial community in low-temperature hydrothermal chimneys on an ultraslow spreading midocean ridge, which has characteristics distinct from those of other types of hydrothermal fields.
Identification of a Membrane-Bound Transcriptional Regulator That Links Chitin and Natural Competence in Vibrio cholerae
Authors: Dalia Ankur B. , Lazinski David W. , Camilli Andrew 
Published: January 2014

ABSTRACT

Vibrio cholerae
is naturally competent when grown on chitin. It is known that expression of the major regulator of competence, TfoX, is controlled by chitin; however, the molecular mechanisms underlying this requirement for chitin have remained unclear. In the present study, we identify and characterize a membrane-bound transcriptional regulator that positively regulates the small RNA (sRNA) TfoR, which posttranscriptionally enhances
tfoX
translation. We show that this regulation of the
tfoR
promoter is direct by performing electrophoretic mobility shift assays and by heterologous expression of this system in
Escherichia coli
. This transcriptional regulator was recently identified independently and was named “TfoS” (S. Yamamoto et al., Mol. Microbiol., in press, doi:10.1111/mmi.12462). Using a constitutively active form of TfoS, we demonstrate that the activity of this regulator is sufficient to promote competence in
V. cholerae
in the absence of chitin. Also, TfoS contains a large periplasmic domain, which we hypothesized interacts with chitin to regulate TfoS activity. In the heterologous host
E. coli
, we demonstrate that chitin oligosaccharides are sufficient to activate TfoS activity at the
tfoR
promoter. Collectively, these data characterize TfoS as a novel chitin-sensing transcriptional regulator that represents the direct link between chitin and natural competence in
V. cholerae
.

IMPORTANCE
Naturally competent bacteria can take up exogenous DNA from the environment and integrate it into their genome by homologous recombination. This ability to take up exogenous DNA is shared by diverse bacterial species and serves as a mechanism to acquire new genes to enhance the fitness of the organism. Several members of the family
Vibrionaceae
become naturally competent when grown on chitin; however, a molecular understanding of how chitin activates competence is lacking. Here, we identify a novel membrane-bound transcriptional regulator that is required for natural transformation in the human pathogen
Vibrio cholerae
. We demonstrate that this regulator senses chitin oligosaccharides to activate the competence cascade, thus, uncovering the molecular link between chitin and natural competence in this
Vibrio
species.
Frequent users of US emergency departments: characteristics and opportunities for intervention
Authors: Vinton Deborah T , Capp Roberta , Rooks Sean P , Abbott Jean T , Ginde Adit A 
Published: January 2014

ObjectiveTo compare the characteristics of US adults by frequency of emergency department (ED) utilisation, specifically the prevalence of chronic diseases and outpatient primary care and mental health utilisation.MethodsWe analysed 157 818 adult participants of the 2004–2009 US National Health Interview Survey, an annual nationally representative sample. We defined ED utilisation during the past 12 months as non-users (0 ED visits), infrequent users (1–3 visits), frequent users (4–9 visits) and super-frequent users (≥10 visits). We compared demographic data, socioeconomic status, chronic diseases and access to care between these ED utilisation groups using multivariable logistic regression.ResultsOverall, super-frequent use was reported by 0.4% of US adults, frequent use by 2% and infrequent ED use by 19%. Patients reporting ≥4 ED visits were more likely to have Medicaid insurance (OR 1.57; 95% CI 1.34 to 1.85 vs private); fair or poor self-reported health (OR 2.98; 95% CI 2.57 to 3.46 vs excellent–very good); and chronic diseases such as coronary artery disease (OR 1.61; 95% CI 1.40 to 1.86), stroke (OR 1.58; 95% CI 1.36 to 1.83) or asthma (OR 1.64; 95% CI 1.46 to 1.85). While patients reporting the ED as their usual source of sick care were more likely to have ≥4 ED visits (OR 7.09; 95% CI 5.61 to 8.95 vs outpatient clinic as source), ≥10 outpatient visits in the past 12 months was also associated with frequent ED use (OR 11.4; 95% CI 9.09 to 14.2 vs no outpatient visits).ConclusionsFrequent ED users had a large burden of chronic diseases that also required high outpatient resources. Interventions designed to divert frequent ED users should focus on chronic disease management and access to outpatient services, particularly for Medicaid beneficiaries and other high risk subpopulations.
Paramedic rapid sequence intubation in patients with non-traumatic coma
Authors: Bernard S A , Smith K , Porter R , Jones C , Gailey A , Cresswell B , Cudini D , Hill S , Moore B , St Clair T 
Published: January 2014

IntroductionPre-hospital intubation by paramedics is widely used in comatose patients prior to transportation to hospital, but the optimal technique for intubation is uncertain. One approach is paramedic rapid sequence intubation (RSI), which may improve outcomes in adult patients with traumatic brain injury. However, many patients present to emergency medical services with coma of non-traumatic cause and the role of paramedic RSI in these patients remains uncertain.MethodsThe electronic Victorian Ambulance Clinical Information System was searched for the term ‘suxamethonium’ between 2008 and 2011. We reviewed the patient care records and included patients with suspected non-traumatic coma who were treated and transported by road-based paramedics. Demographics, intubation conditions, vital signs (before and after drug administration) and complications were recorded. Younger patients (<60 years) were compared with older patients.ResultsThere were 1152 paramedic RSI attempts of which 551 were for non-traumatic coma. The success rate for intubation was 97.5%. There was a significant drop in blood pressure in younger patients (<60 years) with the mean systolic blood pressure decreasing by 16 mm Hg (95% CI 11 to 21). In older patients, the systolic blood pressure also decreased significantly by 20 mm Hg (95% CI 17 to 24). Four patients suffered brief cardiac arrest during pre-hospital care, all of whom were successfully resuscitated and transported to hospital.ConclusionsParamedic RSI in patients with non-traumatic coma has a high procedural success rate. Further studies are required to determine whether this procedure improves outcomes.
PCAT-1, a Long Noncoding RNA, Regulates BRCA2 and Controls Homologous Recombination in Cancer
Authors: Prensner John R. , Chen Wei , Iyer Matthew K. , Cao Qi , Ma Teng , Han Sumin , Sahu Anirban , Malik Rohit , Wilder-Romans Kari , Navone Nora , Logothetis Christopher J. , Araujo John C. , Pisters Louis L. , Tewari Ashutosh K. , Canman Christine E. , Knudsen Karen E. , Kitabayashi Naoki , Rubin Mark A. , Demichelis Francesca , Lawrence Theodore S. , Chinnaiyan Arul M. , Feng Felix Y. 
Published: January 2014

Abstract
Impairment of double-stranded DNA break (DSB) repair is essential to many cancers. However, although mutations in DSB repair proteins are common in hereditary cancers, mechanisms of impaired DSB repair in sporadic cancers remain incompletely understood. Here, we describe the first role for a long noncoding RNA (lncRNA) in DSB repair in prostate cancer. We identify PCAT-1, a prostate cancer outlier lncRNA, which regulates cell response to genotoxic stress. PCAT-1 expression produces a functional deficiency in homologous recombination through its repression of the BRCA2 tumor suppressor, which, in turn, imparts a high sensitivity to small-molecule inhibitors of PARP1. These effects reflected a posttranscriptional repression of the BRCA2 3′UTR by PCAT-1. Our observations thus offer a novel mechanism of “BRCAness” in sporadic cancers. Cancer Res; 74(6); 1651–60. ©2014 AACR.
Large-Eddy Simulations of Convective Boundary Layers over Flat and Urbanlike Surfaces
Authors: Park Seung-Bu , Baik Jong-Jin 
Published: January 2014

Abstract
The effects of urbanlike surfaces with a block array on the dry convective boundary layer (CBL) are numerically investigated using the parallelized large-eddy simulation model. Five cases representing a free CBL, a sheared CBL, and a strongly sheared CBL over flat surfaces, a sheared CBL over a block array, and a sheared CBL over a modeled canopy layer are simulated and compared. In the sheared CBL over a block array, mixed-layer flow is decelerated because of increased surface shear and horizontal convective rolls appear in the mixed layer. In contrast, convection cells and intermediate structures between cells and rolls occur in the free and sheared CBLs over flat surfaces, respectively. Horizontal convective rolls and the traces of block-induced turbulent eddies are detected in the spectral density fields of vertical velocity and in the vertical profiles of vertical velocity skewness in the sheared CBL over a block array. The decelerated mixed-layer flow in the sheared CBL over a block array leads to stronger wind shear in the entrainment zone than in the other cases, resulting in streamwise alternating updrafts and downdrafts there. While the contributions to vertical turbulent heat flux by rising cool air and sinking cool air are dominant in the free CBL, the contributions to vertical turbulent heat flux by sinking warm air and rising warm air increase as the wind shear in the entrainment zone increases. Because of enhanced turbulence activity and wavelike motions in the entrainment zone, the magnitude of entrainment heat flux in the CBL over a block array is larger than that in the other cases.
The Role of the Mean State of Arctic Sea Ice on Near-Surface Temperature Trends
Authors: van der Linden E. C. , Bintanja R. , Hazeleger W. , Katsman C. A. 
Published: January 2014

Abstract
Century-scale global near-surface temperature trends in response to rising greenhouse gas concentrations in climate models vary by almost a factor of 2, with greatest intermodel spread in the Arctic region where sea ice is a key climate component. Three factors contribute to the intermodel spread: 1) model formulation, 2) control climate state, and 3) internal climate variability. This study focuses on the influence of Arctic sea ice in the control climate on the intermodel spread in warming, using idealized 1% yr−1 CO2 increase simulations of 33 state-of-the-art global climate models, and combining sea ice–temperature relations on local to large spatial scales. On the Arctic mean scale, the spread in temperature trends is only weakly related to ice volume or area in the control climate, and is probably not dominated by internal variability. This suggests that other processes, such as ocean heat transport and meteorological conditions, play a more important role in the spread of long-term Arctic warming than control sea ice conditions. However, on a local scale, sea ice–warming relations show that in regions with more sea ice, models generally simulate more warming in winter and less warming in summer. The local winter warming is clearly related to control sea ice and universal among models, whereas summer sea ice–warming relations are more diverse, and are probably dominated by differences in model formulation. To obtain a more realistic representation of Arctic warming, it is recommended to simulate control sea ice conditions in climate models so that the spatial pattern is correct.
Impact of Variable Atmospheric and Oceanic Form Drag on Simulations of Arctic Sea Ice*
Authors: Tsamados Michel , Feltham Daniel L. , Schroeder David , Flocco Daniela , Farrell Sinead L. , Kurtz Nathan , Laxon Seymour W. , Bacon Sheldon 
Published: January 2014

Abstract
Over Arctic sea ice, pressure ridges and floe and melt pond edges all introduce discrete obstructions to the flow of air or water past the ice and are a source of form drag. In current climate models form drag is only accounted for by tuning the air–ice and ice–ocean drag coefficients, that is, by effectively altering the roughness length in a surface drag parameterization. The existing approach of the skin drag parameter tuning is poorly constrained by observations and fails to describe correctly the physics associated with the air–ice and ocean–ice drag. Here, the authors combine recent theoretical developments to deduce the total neutral form drag coefficients from properties of the ice cover such as ice concentration, vertical extent and area of the ridges, freeboard and floe draft, and the size of floes and melt ponds. The drag coefficients are incorporated into the Los Alamos Sea Ice Model (CICE) and show the influence of the new drag parameterization on the motion and state of the ice cover, with the most noticeable being a depletion of sea ice over the west boundary of the Arctic Ocean and over the Beaufort Sea. The new parameterization allows the drag coefficients to be coupled to the sea ice state and therefore to evolve spatially and temporally. It is found that the range of values predicted for the drag coefficients agree with the range of values measured in several regions of the Arctic. Finally, the implications of the new form drag formulation for the spinup or spindown of the Arctic Ocean are discussed.
Polar Lows over the Nordic Seas: Improved Representation in ERA-Interim Compared to ERA-40 and the Impact on Downscaled Simulations
Authors: Laffineur Thibaut , Claud Chantal , Chaboureau Jean-Pierre , Noer Gunnar 
Published: January 2014

Abstract
Polar lows are intense high-latitude mesocyclones that form during the cold season over open sea. Their relatively small-scale and short life span lead to a rather poor representation in model outputs and meteorological reanalyses. In this paper, the ability of the Interim European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-Interim) to represent polar lows over the Norwegian and Barents Sea is assessed, and a comparison with the 40-yr ECMWF Re-Analysis (ERA-40) is provided for three cold seasons (1999–2000 until 2001–02). A better representation in ERA-Interim is found, with 13 systems captured out of the 29 observed, against 6 in the case of ERA-40. Reasons for the lack of representation are identified. Unexpectedly, the representation of different polar low sizes does not appear to be linked to the resolution. Rather, it is the representation of synoptic conditions that appears to be essential. In a second part, a downscaling is conducted using the mesoscale model Méso-NH. For each observed polar low, a pair of simulations is performed: one initialized by ERA-Interim and the other one by ERA-40. An improvement is noted with 22 polar lows represented when ERA-Interim is used. Through a model-to-satellite approach, it is shown that even if polar lows are simulated, convective processes remain insufficiently represented. Wind speeds, which were underestimated in reanalyses, are nevertheless more realistic in the Méso-NH simulations. These results are supported by a spectral analysis of reanalyses and Méso-NH fields.
Dry Tropical Nights and Wet Extreme Heat in Beijing: Atypical Configurations between High Temperature and Humidity
Authors: Chen Ruidan , Lu Riyu 
Published: January 2014

Abstract
Generally, tropical nights [TN; minimum temperature (Tmin) ≥25°C] occur under wet air conditions, while extreme heat [EH; maximum temperature (Tmax) ≥35°C] occurs under dry air conditions. This can be explained by higher humidity favoring TN through reducing longwave radiation cooling, and lower humidity favoring EH through enhancing solar radiation at the surface. The present study focuses on the atypical phenomena of dry TN (30% of all TN days) and wet EH (20% of all EH days) in Beijing during July and August, 1979–2008. It was found that meteorological conditions, including large-scale circulations and specific humidity, exhibit a resemblance between typical (wet TN and dry EH) and atypical (dry TN and wet EH) cases. That is, the meteorological anomalies for dry TN are similar to those for dry EH, and the anomalies for wet EH are similar to those for wet TN. For instance, descending anomalies, which lead to lower humidity and are thus associated with dry EH, appear for more than 70% of dry TN cases. In addition, the persistence of high temperature from day to night, and from night to day, also contribute significantly to dry TN and wet EH, respectively. About 50% of dry TN days and about 70% of wet EH days are preceded by EH and TN, respectively. It can be concluded from these results that both meteorological conditions and temperature persistence contribute greatly to dry TN and wet EH.
Toward More Usable Electronic Voting
Authors: Campbell Bryan A. , Tossell Chad C. , Byrne Michael D. , Kortum Philip 
Published: January 2014

Objective: The goal of this research was to assess the usability of a voting system designed for smartphones. Background: Smartphones offer remote participation in elections through the use of pervasive technology. Voting on these devices could, among other benefits, increase voter participation while allowing voters to use familiar technology. However, the usability of these systems has not been assessed. Method: A mobile voting system optimized for use on a smartphone was designed and tested against traditional voting platforms for usability. Results: There were no reliable differences between the smartphone-based system and other voting methods in efficiency and perceived usability. More important, though, smartphone owners committed fewer errors on the mobile voting system than on the traditional voting systems. Conclusion: Even with the known limitations of small mobile platforms in both displays and controls, a carefully designed system can provide a usable voting method. Much of the concern about mobile voting is in the area of security; therefore, although these results are promising, security concerns and usability issues arising from mitigating them must be strongly considered. Application: The results of this experiment may help to inform current and future election and public policy officials about the benefits of allowing voters to vote with familiar hardware.
Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model
Authors: Gao Rui , Liu Yanxia , Gjesing Anette Prior , Hollensted Mette , Wan Xianzi , He Shuwen , Pedersen Oluf , Yi Xin , Wang Jun , Hansen Torben 
Published: January 2014

Abstract

Background
Monogenic diabetes is a genetic disease often caused by mutations in genes involved in beta-cell function. Correct sub-categorization of the disease is a prerequisite for appropriate treatment and genetic counseling. Target-region capture sequencing is a combination of genomic region enrichment and next generation sequencing which might be used as an efficient way to diagnose various genetic disorders. We aimed to develop a target-region capture sequencing platform to screen 117 selected candidate genes involved in metabolism for mutations and to evaluate its performance using monogenic diabetes as a study-model.

Results
The performance of the assay was evaluated in 70 patients carrying known disease causing mutations previously identified in HNF4A, GCK, HNF1A, HNF1B, INS, or KCNJ11. Target regions with a less than 20-fold sequencing depth were either introns or UTRs. When only considering translated regions, the coverage was 100% with a 50-fold minimum depth. Among the 70 analyzed samples, 63 small size single nucleotide polymorphisms and indels as well as 7 large deletions and duplications were identified as being the pathogenic variants. The mutations identified by the present technique were identical with those previously identified through Sanger sequencing and Multiplex Ligation-dependent Probe Amplification.

Conclusions
We hereby demonstrated that the established platform as an accurate and high-throughput gene testing method which might be useful in the clinical diagnosis of monogenic diabetes.