bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reversible Inhibition of Chlamydia trachomatis Infection in Epithelial Cells Due to Stimulation of P2X
4
Receptors
Authors: Pettengill Matthew A. , Marques-da-Silva Camila , Avila Maria Luisa , d'Arc dos Santos Oliveira Suellen , Lam Verissa W. , Ollawa Ikechukwu , Abdul Sater Ali A. , Coutinho-Silva Robson , Häcker Georg , Ojcius David M. 
Published: September 2012

ABSTRACT

Bacterial infections of the mucosal epithelium are a major cause of human disease. The prolonged presence of microbial pathogens stimulates inflammation of the local tissues, which leads to changes in the molecular composition of the extracellular milieu. A well-characterized molecule that is released to the extracellular milieu by stressed or infected cells is extracellular ATP and its ecto-enzymatic degradation products, which function as signaling molecules through ligation of purinergic receptors. There has been little information, however, on the effects of the extracellular metabolites on bacterial growth in inflamed tissues. Millimolar concentrations of ATP have been previously shown to inhibit irreversibly bacterial infection through ligation of P2X
7
receptors. We show here that the proinflammatory mediator, ATP, is released from
Chlamydia trachomatis
-infected epithelial cells. Moreover, further stimulation of the infected cells with micromolar extracellular ADP or ATP significantly impairs the growth of the bacteria, with a profile characteristic of the involvement of P2X
4
receptors. A specific role for P2X
4
was confirmed using cells overexpressing P2X
4
. The chlamydiae remain viable and return to normal growth kinetics after removal of the extracellular stimulus, similar to responses previously described for persistence of chlamydial infection.
Dectin-1 Is Not Required for Controlling Candida albicans Colonization of the Gastrointestinal Tract
Authors: Vautier Simon , Drummond Rebecca A. , Redelinghuys Pierre , Murray Graeme I. , MacCallum Donna M. , Brown Gordon D. 
Published: September 2012

ABSTRACT

Candida albicans
is normally found as a commensal microbe, commonly colonizing the gastrointestinal tract in humans. However, this fungus can also cause mucosal and systemic infections once immune function is compromised. Dectin-1 is an innate pattern recognition receptor essential for the control of fungal infections in both mice and humans; however, its role in the control of
C. albicans
colonization of the gastrointestinal tract has not been defined. Here, we demonstrate that in mice dectin-1 is essential for the control of gastrointestinal invasion during systemic infection, with dectin-1 deficiency associating with impaired fungal clearance and dysregulated cytokine production. Surprisingly, however, following oral infection, dectin-1 was not required for the control of mucosal colonization of the gastrointestinal tract, in terms of either fungal burdens or cytokine response. Thus, in mice, dectin-1 is essential for controlling systemic infection with
C. albicans
but appears to be redundant for the control of gastrointestinal colonization.
Efficient cooperative backup with decentralized trust management
Authors: Tran Nguyen , Chiang Frank , Li Jinyang 
Published: September 2012

Existing backup systems are unsatisfactory: commercial backup services are reliable but expensive while peer-to-peer systems are cheap but offer limited assurance of data reliability. This article introduces Friendstore, a system that provides inexpensive and reliable backup by giving users the choice to store backup data only on nodes they trust (typically those owned by friends and colleagues). Because it is built on trusted nodes, Friendstore is not burdened by the complexity required to cope with potentially malicious participants. Friendstore only needs to detect and repair accidental data loss and to ensure balanced storage exchange. The disadvantage of using only trusted nodes is that Friendstore cannot achieve perfect storage utilization.
Friendstore is designed for a heterogeneous environment where nodes have very different access link speeds and available disk spaces. To ensure long-term data reliability, a node with limited upload bandwidth refrains from storing more data than its calculated maintainable capacity. A high bandwidth node might be limited by its available disk space. We introduce a simple coding scheme, called XOR(1,2), which doubles a node's ability to store backup information in the same amount of disk space at the cost of doubling the amount of data transferred during restore. Analysis and simulations using long-term node activity traces show that a node can reliably back up tens of gigabytes of data even with low upload bandwidth.
Climatology-Calibrated Precipitation Analysis at Fine Scales: Statistical Adjustment of Stage IV toward CPC Gauge-Based Analysis
Authors: Hou Dingchen , charles Mike , Luo Yan , Toth Zoltan , Zhu Yuejian , Krzysztofowicz Roman , Lin Ying , Xie Pingping , Seo Dong-Jun , Pena Malaquias , Cui Bo 
Published: September 2012

Abstract
Two widely used precipitation analyses are the Climate Prediction Center (CPC) unified global daily gauge analysis and Stage IV analysis based on quantitative precipitation estimate with multisensor observations. The former is based on gauge records with a uniform quality control across the entire domain and thus bears more confidence, but provides only 24-h accumulation at ⅛° resolution. The Stage IV dataset, on the other hand, has higher spatial and temporal resolution, but is subject to different methods of quality control and adjustments by different River Forecasting Centers. This article describes a methodology used to generate a new dataset by adjusting the Stage IV 6-h accumulations based on available joint samples of the two analyses to take advantage of both datasets. A simple linear regression model is applied to the archived historical Stage IV and the CPC datasets after the former is aggregated to the CPC grid and daily accumulation. The aggregated Stage IV analysis is then adjusted based on this linear model and then downscaled back to its original resolution. The new dataset, named Climatology-Calibrated Precipitation Analysis (CCPA), retains the spatial and temporal patterns of the Stage IV analysis while having its long-term average and climate probability distribution closer to that of the CPC analysis. The limitation of the methodology at some locations is mainly associated with heavy to extreme precipitation events, which the Stage IV dataset tends to underestimate. CCPA cannot effectively correct this because of the linear regression model and the relative scarcity of heavy precipitation in the training data sample.
Observed Evolution of Northward-Propagating Intraseasonal Variation over the Western Pacific: A Case Study in Boreal Early Summer
Authors: Katsumata Masaki , Yamada Hiroyuki , Kubota Hisayuki , Moteki Qoosaku , Shirooka Ryuichi 
Published: September 2012

Abstract
This report describes the in situ observed evolution of the atmospheric profile during an event of the boreal summer intraseasonal variation (BSISV) in the tropical western Pacific Ocean. The convectively active region of the BSISV proceeded northward over the sounding and radar network. Over the array, the situation changed from a convectively inactive period to an active period. Inspection of the sounding data revealed the gradual moistening of the lower troposphere during the convectively inactive period. The sounding-derived heat and moisture budget analyses indicated that both the convective- and large-scale processes caused moistening of the lower and middle troposphere where the radar echo tops were observed most frequently. This study is the first to identify such a “preconditioning” process for the BSISV in the western Pacific using detailed in situ observational data. During the preconditioning, an increase in CAPE was observed, as in previous studies of the MJO. An increase of moisture in the boundary layer was responsible for the increase of CAPE. The large-scale horizontal convergence in the boundary layer may be a key factor to moisten the boundary layer through the convective-scale processes, as well as through the large-scale processes to moisten the lower and middle troposphere.
Impact of a Warm Ocean Eddy’s Circulation on Hurricane-Induced Sea Surface Cooling with Implications for Hurricane Intensity
Authors: Yablonsky Richard M. , Ginis Isaac 
Published: September 2012

Abstract
Upper oceanic heat content (OHC) in advance of a hurricane is generally superior to prestorm sea surface temperature (SST) for indicating favorable regions for hurricane intensification and maintenance. OHC is important because a hurricane’s surface winds mix the upper ocean and entrain cooler water into the oceanic mixed layer from below, subsequently cooling the sea surface in the region providing heat energy to the storm. For a given initial SST, increased OHC typically decreases the wind-induced sea surface cooling, and a warm ocean eddy (WCR) has a higher OHC than its surroundings, so conditions typically become more favorable for a hurricane to intensify when the storm’s core encounters a WCR. When considering hurricane intensity, however, one often-neglected aspect of a WCR is its anticyclonic circulation. This circulation may impact the location and magnitude of the hurricane-induced sea surface cooling. Using an ocean model, either prescribed hurricane wind stress or wind stress obtained via coupling to a hurricane model is applied to an initial ocean condition in which the SST is homogeneous, but a WCR is embedded in an otherwise horizontally homogeneous subsurface density field. Based on model experiments, when a WCR is located to the right of the storm track (in the Northern Hemisphere), the interaction of the WCR’s circulation with the hurricane-induced cold wake can cause increased sea surface cooling under the storm core and decreased storm intensity relative to the scenario where no WCR is present at all. Therefore, the presence of a WCR in advance of a hurricane sometimes creates a less favorable condition for hurricane intensification.
Cognitive Mapping in Persons Newly Diagnosed With Type 2 Diabetes
Authors: Hughes Lynne C. , Keith Susan E. , Byars Allyn , Wiginton Kristin L. 
Published: September 2012

Purpose The purpose of this study was to determine the issues and perceptions of persons newly diagnosed (within last 3 months) with type 2 diabetes. Methods In this qualitative study, 16 adults newly diagnosed with type 2 diabetes were recruited, who completed a demographic, lifestyle, and diabetes management questionnaire and then were interviewed using cognitive mapping. Participants were asked to write words or phrases that came to mind when thinking about living with diabetes. From these words, common concepts were identified, grouped into clusters, and reduced into categories. Associations were sought between demographics and categories. Results A total of 260 Post-It notes were written, from which 123 concepts were identified and grouped into 24 clusters. The most frequent concept was eat, and the 3 most frequent clusters were food, negative emotions, and diabetes and its complications. The 9 categories, in order of frequency, were as follows: (1) need to (self-management), (2) concerns, (3) “I’m sick”, (4) emotional distress, (5) loss, (6) the no’s (limitations), (7) fears and complications, (8) have to (medical management), and (9) coping. Persons with a college education and a later interview date since diagnosis were associated with the concepts in the need to and have to categories. Concepts in the I’m sick category were associated with lower income and Hispanic ethnicity. Conclusions Diabetes educators should consider this holistic representation of the issues and perceptions reflected in the common concepts, clusters, and categories expressed by persons newly diagnosed with diabetes.
Communicating advanced cancer patients’ symptoms via the Internet: A pooled analysis of two randomized trials examining caregiver preparedness, physical burden, and negative mood
Authors: Chih Ming-Yuan , DuBenske Lori L , Hawkins Robert P , Brown Roger L , Dinauer Susan K , Cleary James F , Gustafson David H 
Published: September 2012

Background: Using available communication technologies, clinicians may offer timely support to family caregivers in managing symptoms in patients with advanced cancer at home. Aim: To assess the effects of an online symptom reporting system on caregiver preparedness, physical burden, and negative mood. Design: A pooled analysis of two randomized trials (NCT00214162 and NCT00365963) was conducted to compare caregiver outcomes at 6 and 12 months after intervention between two randomized, unblinded groups using General Linear Mixed Modeling. Caregivers in one group (Comprehensive Health Enhancement Support System-Only) were given access to an interactive cancer communication system, the Comprehensive Health Enhancement Support System. Those in the other group (Comprehensive Health Enhancement Support System + Clinician Report) received access to Comprehensive Health Enhancement Support System plus an online symptom reporting system called the Clinician Report. Clinicians of patients in the Comprehensive Health Enhancement Support System + Clinician Report group received e-mail alerts notifying them when a symptom distress was reported over a predetermined threshold. Setting/participants: Dyads ( n = 235) of advanced-stage lung, breast, and prostate cancer patients and their adult caregivers were recruited at five outpatient oncology clinics in the United States. Results: Caregivers in the Comprehensive Health Enhancement Support System + Clinician Report group reported less negative mood than those in the Comprehensive Health Enhancement Support System-Only group at both 6 months ( p = 0.009) and 12 months ( p = 0.004). Groups were not significantly different on caregiver preparedness or physical burden at either time point. Conclusions: This study provides new evidence that by using an online symptom reporting system, caregivers may experience less emotional distress due to the Clinician Report’s timely communication of caregiving needs in symptom management to clinicians.
Theorizing Scarcity
Authors: Panayotakis Costas 
Published: September 2012

This article critically examines the neoclassical approach to scarcity as well as critiques of neoclassical economics that focus either on the formation of people’s wants (the demand side of scarcity) or on the production and distribution of the goods needed to satisfy these wants (the supply side). I argue that critiques of the neoclassical approach are right to emphasize the relationship between the determinants of scarcity and the economic system as a whole but are less convincing when they project the possibility of overcoming neoclassical scarcity altogether. JEL Codes: A10, P10, Z13
Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii
Authors: Mastrobuoni Guido , Irgang Susann , Pietzke Matthias , Aßmus Heike E , Wenzel Markus , Schulze Waltraud X , Kempa Stefan 
Published: September 2012

Abstract

Background
The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a photosynthetic organism for the first time and we established a method to study proteome dynamics in the green alga Chlamydomonas reinhardtii, an emerging model system for plant biology. In addition, we combined the analysis of protein synthesis with metabolic profiling to study the dynamic changes of metabolism and proteome turnover under salt stress conditions.

Results
To study de novo protein synthesis an arginine auxotroph Chlamydomonas strain was cultivated in presence of stable isotope-labeled arginine for 24 hours. From the time course experiment in 3 salt concentrations we could identify more than 2500 proteins and their H/L ratio in at least one experimental condition; for 998 protiens at least 3 ratio counts were detected in the 24 h time point (0 mM NaCl). After fractionation we could identify 3115 proteins and for 1765 of them we determined their de novo synthesis rate. Consistently with previous findings we showed that RuBisCO is among the most prominent proteins in the cell; and similar abundance and turnover for the small and large RuBisCO subunit could be calculated. The D1 protein was identified among proteins with a high synthesis rates. A global median half-life of 45 h was calculated for Chlamydomonas proteins under the chosen conditions.

Conclusion
To investigate the temporal co-regulation of the proteome and metabolome, we applied salt stress to Chlamydomonas and studied the time dependent regulation of protein expression and changes in the metabolome. The main metabolic response to salt stress was observed within the amino acid metabolism. In particular, proline was up-regulated manifold and according to that an increased carbon flow within the proline biosynthetic pathway could be measured. In parallel the analysis of abundance and de novo synthesis of the corresponding enzymes revealed that metabolic rearrangements precede adjustments of protein abundance.
An efficient RNA interference screening strategy for gene functional analysis
Authors: Chang Chih-Hung , Wang Hsiang-Iu , Lu Hsiang-Chia , Chen Cheng-En , Chen Hong-Hwa , Yeh Hsin-Hung , Tang Chuan Yi 
Published: September 2012

Abstract

Background
RNA interference (RNAi) is commonly applied in genome-scale gene functional screens. However, a one-on-one RNAi analysis that targets each gene is cost-ineffective and laborious. Previous studies have indicated that siRNAs can also affect RNAs that are near-perfectly complementary, and this phenomenon has been termed an off-target effect. This phenomenon implies that it is possible to silence several genes simultaneously with a carefully designed siRNA.

Results
We propose a strategy that is combined with a heuristic algorithm to design suitable siRNAs that can target multiple genes and a group testing method that would reduce the number of required RNAi experiments in a large-scale RNAi analysis. To verify the efficacy of our strategy, we used the Orchid expressed sequence tag data as a case study to screen the putative transcription factors that are involved in plant disease responses. According to our computation, 94 qualified siRNAs were sufficient to examine all of the predicated 229 transcription factors. In addition, among the 94 computer-designed siRNAs, an siRNA that targets both TF15 (a previously identified transcription factor that is involved in the plant disease-response pathway) and TF21 was introduced into orchids. The experimental results showed that this siRNA can simultaneously silence TF15 and TF21, and application of our strategy successfully confirmed that TF15 is involved in plant defense responses. Interestingly, our second-round analysis, which used an siRNA specific to TF21, indicated that TF21 is a previously unidentified transcription factor that is related to plant defense responses.

Conclusions
Our computational results showed that it is possible to screen all genes with fewer experiments than would be required for the traditional one-on-one RNAi screening. We also verified that our strategy is capable of identifying genes that are involved in a specific phenotype.
Omega 3 polyunsaturated fatty acid improves spatial learning and hippocampal Peroxisome Proliferator Activated Receptors (PPARα and PPARγ) gene expression in rats
Authors: Hajjar Toktam , Meng Goh Y , Rajion Mohamed A , Vidyadaran Sharmili , Othman Fauziah , Farjam Abdoreza S , Li Tan A , Ebrahimi Mahdi 
Published: September 2012

Abstract

Background
This study examined the effects of dietary polyunsaturated fatty acids (PUFA) as different n-6: n-3 ratios on spatial learning and gene expression of peroxisome- proliferator-activated receptors (PPARs) in the hippocampus of rats. Thirty male Sprague–Dawley rats were randomly allotted into 3 groups of ten animals each and received experimental diets with different n-6: n-3 PUFA ratios of either 65:1, 22:1 or 4.5:1. After 10 weeks, the spatial memory of the animals was assessed using the Morris Water Maze test. The expression of PPARα and PPARγ genes were determined using real-time PCR.

Results
Decreasing dietary n-6: n-3 PUFA ratios improved the cognitive performance of animals in the Morris water maze test along with the upregulation of PPARα and PPARγ gene expression. The animals with the lowest dietary n-6: n-3 PUFA ratio presented the highest spatial learning improvement and PPAR gene expression.

Conclusion
It can be concluded that modulation of n-6: n-3 PUFA ratios in the diet may lead to increased hippocampal PPAR gene expression and consequently improved spatial learning and memory in rats.
Arabidopsis mutant sk156 reveals complex regulation of SPL15 in a miR156-controlled gene network
Authors: Wei Shu , Gruber Margaret Y , Yu Bianyun , Gao Ming-Jun , Khachatourians George G , Hegedus Dwayne D , Parkin Isobel AP , Hannoufa Abdelali 
Published: September 2012

Abstract

Background
The Arabidopsis microRNA156 (miR156) regulates 11 members of the SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) family by base pairing to complementary target mRNAs. Each SPL gene further regulates a set of other genes; thus, miR156 controls numerous genes through a complex gene regulation network. Increased axillary branching occurs in transgenic Arabidopsis overexpressing miR156b, similar to that observed in loss-of-function max3 and max4 mutants with lesions in carotenoid cleavage dioxygenases. Arabidopsis miR156b was found to enhance carotenoid levels and reproductive shoot branching when expressed in Brassica napus, suggesting a link between miR156b expression and carotenoid metabolism. However, details of the miR156 regulatory network of SPL genes related to carotenoid metabolism are not known.

Results
In this study, an Arabidopsis T-DNA enhancer mutant, sk156, was identified due to its altered branching and trichome morphology and increased seed carotenoid levels compared to wild type (WT) ecovar Columbia. Enhanced miR156b expression due to the 35S enhancers present on the T-DNA insert was responsible for these phenotypes. Constitutive and leaf primodium-specific expression of a miR156-insensitive (mutated) SPL15 (SPL15m) largely restored WT seed carotenoid levels and plant morphology when expressed in sk156. The Arabidopsis native miR156-sensitive SPL15 (SPL15n) and SPL15m driven by a native SPL15 promoter did not restore the WT phenotype in sk156. Our findings suggest that SPL15 function is somewhat redundant with other SPL family members, which collectively affect plant phenotypes. Moreover, substantially decreased miR156b transcript levels in sk156 expressing SPL15m, together with the presence of multiple repeats of SPL-binding GTAC core sequence close to the miR156b transcription start site, suggested feedback regulation of miR156b expression by SPL15. This was supported by the demonstration of specific in vitro interaction between DNA-binding SBP domain of SPL15 and the proximal promoter sequence of miR156b.

Conclusions
Enhanced miR156b expression in sk156 leads to the mutant phenotype including carotenoid levels in the seed through suppression of SPL15 and other SPL target genes. Moreover, SPL15 has a regulatory role not only for downstream components, but also for its own upstream regulator miR156b.