bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating Climatological Bias Errors for the Global Precipitation Climatology Project (GPCP)
Authors: Adler Robert F. , Gu Guojun , Huffman George J. 
Published: September 2011

AbstractA procedure is described to estimate bias errors for mean precipitation by using multiple estimates from different algorithms, satellite sources, and merged products. The Global Precipitation Climatology Project (GPCP) monthly product is used as a base precipitation estimate, with other input products included when they are within ±50% of the GPCP estimates on a zonal-mean basis (ocean and land separately). The standard deviation σ of the included products is then taken to be the estimated systematic, or bias, error. The results allow one to examine monthly climatologies and the annual climatology, producing maps of estimated bias errors, zonal-mean errors, and estimated errors over large areas such as ocean and land for both the tropics and the globe. For ocean areas, where there is the largest question as to absolute magnitude of precipitation, the analysis shows spatial variations in the estimated bias errors, indicating areas where one should have more or less confidence in the mean precipitation estimates. In the tropics, relative bias error estimates (σ/μ, where μ is the mean precipitation) over the eastern Pacific Ocean are as large as 20%, as compared with 10%–15% in the western Pacific part of the ITCZ. An examination of latitudinal differences over ocean clearly shows an increase in estimated bias error at higher latitudes, reaching up to 50%. Over land, the error estimates also locate regions of potential problems in the tropics and larger cold-season errors at high latitudes that are due to snow. An empirical technique to area average the gridded errors (σ) is described that allows one to make error estimates for arbitrary areas and for the tropics and the globe (land and ocean separately, and combined). Over the tropics this calculation leads to a relative error estimate for tropical land and ocean combined of 7%, which is considered to be an upper bound because of the lack of sign-of-the-error canceling when integrating over different areas with a different number of input products. For the globe the calculated relative error estimate from this study is about 9%, which is also probably a slight overestimate. These tropical and global estimated bias errors provide one estimate of the current state of knowledge of the planet’s mean precipitation.
Present Wave Climate in the Bay of Biscay: Spatiotemporal Variability and Trends from 1958 to 2001
Authors: Charles Elodie , Idier Déborah , Thiébot Jérôme , Le Cozannet Gonéri , Pedreros Rodrigo , Ardhuin Fabrice , Planton Serge 
Published: September 2011

AbstractClimate change impacts on wave conditions can increase the risk of offshore and coastal hazards. The present paper investigates wave climate multidecadal trends and interannual variability in the Bay of Biscay during the past decades (1958–2001). Wave fields are computed with a wave modeling system based on the WAVEWATCH III code and forced by 40-yr European Centre for Medium-Range Weather Forecasts Re-Analysis (ERA-40) wind fields. It provides both an extended spatiotemporal domain and a refined spatial resolution over the Bay of Biscay. The validation of the wave model is based on 11 buoys, allowing for the use of computed wave fields in the analysis of mean and extreme wave height trends and variability. Wave height, period, and direction are examined for a large array of wave conditions (by seasons, high percentiles of wave heights, different periods). Several trends for recent periods are identified, notably an increase of summer significant wave height, a southerly shift of autumn extreme wave direction, and a northerly shift of spring extreme wave direction. Wave fields exhibit high interannual variability, with a normalized standard deviation of seasonal wave height greater than 15% in wintertime. The relationship with Northern Hemisphere teleconnection patterns is investigated at regional scale, especially along the coast. It highlights a strong correlation between local wave conditions and the North Atlantic Oscillation and the east Atlantic pattern indices. This relationship is further investigated at the local scale with a new method based on bivariate diagrams, allowing the identification of the type of waves (swell, storm, intermediate waves) impacted. These results are discussed in terms of comparison with previous studies and coastal risk implications.
Guiding the interactive exploration of metabolic pathway interconnections
Authors: Jusufi Ilir , Klukas Christian , Kerren Andreas , Schreiber Falk 
Published: September 2011

Approaches to investigate biological processes have been of strong interest in the past few years and are the focus of several research areas, especially Systems Biology. Biochemical networks as representations of processes are very important for a comprehensive understanding of living beings. Drawings of these networks are often visually overloaded and do not scale. A common solution to deal with this complexity is to divide the complete network, for example, the metabolism, into a large set of single pathways that are hierarchically structured. If those pathways are visualized, this strategy generates additional navigation and exploration problems as the user loses the context within the complete network. In this article, we present a general solution to this problem of visualizing interconnected pathways and discuss it in context of biochemical networks. Our new visualization approach supports the analyst in obtaining an overview to related pathways if they are working within a particular pathway of interest. By using glyphs, brushing, and topological information of the related pathways, our interactive visualization is able to intuitively guide the exploration and navigation process, and thus the analysis processes too. To deal with real data and current networks, our tool has been implemented as a plugin for the VANTED system.
Population distribution models: species distributions are better modeled using biologically relevant data partitions
Authors: Gonzalez Sergio C , Soto-Centeno J Angel , Reed David L 
Published: September 2011

Abstract

Background
Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions.

Results
Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit.

Conclusions
Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications.
Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis
Authors: Seal John B , Alverdy John C , Zaborina Olga , An Gary 
Published: September 2011

Abstract

Background
There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis.

Methodology/Principal Findings
An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed - i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data - i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design - i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses.

Conclusions/Significance
Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research.
Polarized expression of the membrane ASP protein derived from HIV-1 antisense transcription in T cells
Authors: Clerc Isabelle , Laverdure Sylvain , Torresilla Cynthia , Landry Sébastien , Borel Sophie , Vargas Amandine , Arpin-André Charlotte , Gay Bernard , Briant Laurence , Gross Antoine , Barbeau Benoît , Mesnard Jean-Michel 
Published: September 2011

Abstract

Background
Retroviral gene expression generally depends on a full-length transcript that initiates in the 5' LTR, which is either left unspliced or alternatively spliced. We and others have demonstrated the existence of antisense transcription initiating in the 3' LTR in human lymphotropic retroviruses, including HTLV-1, HTLV-2, and HIV-1. Such transcripts have been postulated to encode antisense proteins important for the establishment of viral infections. The antisense strand of the HIV-1 proviral DNA contains an ORF termed asp, coding for a highly hydrophobic protein. However, although anti-ASP antibodies have been described to be present in HIV-1-infected patients, its in vivo expression requires further support. The objective of this present study was to clearly demonstrate that ASP is effectively expressed in infected T cells and to provide a better characterization of its subcellular localization.

Results
We first investigated the subcellular localization of ASP by transfecting Jurkat T cells with vectors expressing ASP tagged with the Flag epitope to its N-terminus. Using immunofluorescence microscopy, we found that ASP localized to the plasma membrane in transfected Jurkat T cells, but with different staining patterns. In addition to an entire distribution to the plasma membrane, ASP showed an asymmetric localization and could also be detected in membrane connections between two cells. We then infected Jurkat T cells with NL4.3 virus coding for ASP tagged with the Flag epitope at its C-terminal end. By this approach, we were capable of showing that ASP is effectively expressed from the HIV-1 3' LTR in infected T cells, with an asymmetric localization of the viral protein at the plasma membrane.

Conclusion
These results demonstrate for the first time that ASP can be detected when expressed from full-length HIV-1 proviral DNA and that its localization is consistent with Jurkat T cells overexpressing ASP.
Duplex PCR assay for the detection of avian adeno virus and chicken anemia virus prevalent in Pakistan
Authors: Rehman Latif U , Sultan Bakht , Ali Ijaz , Bhatti Muhammad A , Khan Sana U , Zaman Khaliq U , Jahangiri Anila T , Khan Najib U , Iqbal Aqib , Bakht Jehan , Swati Zahoor A , Rehman Muti U 
Published: September 2011

AbstractAvian Adeno viruses and Chicken Anemia Viruses cause serious economic losses to the poultry industry of Pakistan each year. Timely and efficient diagnosis of the viruses is needed in order to practice prevention and control strategies. In the first part of this study, we investigated broilers, breeder and Layer stocks for morbidity and mortality rates due to AAV and CAV infections and any co-infections by examining signs and symptoms typical of their infestation or post mortem examination. In the second part of the study, we developed a duplex PCR assay for the detection of AAV and CAV which is capable to simultaneously detect both the viral types prevalent in Pakistan with high sensitivity and 100% specificity.
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer
Authors: Kaur Mandeep , MacPherson Cameron R , Schmeier Sebastian , Narasimhan Kothandaraman , Choolani Mahesh , Bajic Vladimir B 
Published: September 2011

Abstract

Background
Our study focuses on identifying potential biomarkers for diagnosis and early detection of ovarian cancer (OC) through the study of transcription regulation of genes affected by estrogen hormone.

Results
The results are based on a set of 323 experimentally validated OC-associated genes compiled from several databases, and their subset controlled by estrogen. For these two gene sets we computationally determined transcription factors (TFs) that putatively regulate transcription initiation. We ranked these TFs based on the number of genes they are likely to control. In this way, we selected 17 top-ranked TFs as potential key regulators and thus possible biomarkers for a set of 323 OC-associated genes. For 77 estrogen controlled genes from this set we identified three unique TFs as potential biomarkers.

Conclusions
We introduced a new methodology to identify potential diagnostic biomarkers for OC. This report is the first bioinformatics study that explores multiple transcriptional regulators of OC-associated genes as potential diagnostic biomarkers in connection with estrogen responsiveness. We show that 64% of TF biomarkers identified in our study are validated based on real-time data from microarray expression studies. As an illustration, our method could identify CP2 that in combination with CA125 has been reported to be sensitive in diagnosing ovarian tumors.
The burden of malaria in post-emergency refugee sites: A retrospective study
Authors: Anderson Jamie , Doocy Shannon , Haskew Christopher , Spiegel Paul , Moss William J 
Published: September 2011

Abstract

Background
Almost two-thirds of refugees, internally displaced persons, returnees and other persons affected by humanitarian emergencies live in malaria endemic regions. Malaria remains a significant threat to the health of these populations.

Methods
Data on malaria incidence and mortality were analyzed from January 2006 to December 2009 from the United Nations High Commissioner for Refugees Health Information System database collected at sites in Burundi, Chad, Cameroon, Ethiopia, Kenya, Sudan, Tanzania, Thailand, and Uganda. Data from three countries during 2006 and 2007, and all nine countries from 2008 to 2009, were used to describe trends in malaria incidence and mortality. Monthly counts of malaria morbidity and mortality were aggregated into an annual country rate averaged over the study period.

Results
An average of 1.18 million refugees resided in 60 refugee sites within nine countries with at least 50 cases of malaria per 1000 refugees during the study period 2008-2009. The highest incidence of malaria was in refugee sites in Tanzania, where the annual incidence of malaria was 399 confirmed cases per 1,000 refugees and 728 confirmed cases per 1,000 refugee children younger than five years. Malaria incidence in children younger than five years of age, based on the sum of confirmed and suspected cases, declined substantially at sites in two countries between 2006 and 2009, but a slight increase was reported at sites within four of seven countries between 2008 and 2009. Annual malaria mortality rates were highest in sites in Sudan (0.9 deaths per 1,000 refugees), Uganda and Tanzania (0.7 deaths per 1000 refugees each). Malaria was the cause of 16% of deaths in refugee children younger than five years of age in all study sites.

Conclusions
These findings represent one of the most extensive reports on malaria among refugees in post-emergency sites. Despite declines in malaria incidence among refugees in several countries, malaria remains a significant cause of mortality among children younger than five years of age. Further progress in malaria control, both within and outside of post-emergency sites, is necessary to further reduce malaria incidence and mortality among refugees and achieve global goals in malaria control and elimination.
Awareness, attitudes and prevention of malaria in the cities of Douala and Yaoundé (Cameroon)
Authors: Ndo Cyrille , Menze-Djantio Benjamin , Antonio-Nkondjio Christophe 
Published: September 2011

Abstract

Background
There is little information on the social perception of malaria and the use of prevention methods in Cameroon. This study was designed to assess knowledge, attitude and management of malaria in households living in the cities of Douala and Yaoundé.

Results
Over 82% of people interviewed associated malaria transmission to mosquito bites. Methods used for malaria prevention were: environmental sanitation 1645 (76.1%), use of bed nets 1491 (69%), insecticide spray/coils 265 (12.3%) and netting of doors or windows 42 (1.9%). Bed net ownership was significantly high in Yaoundé (73.8%) (P < 0.0001), whereas the use of insecticide spray or coils was significantly important in Douala (16.3%) (P < 0.0001). Some of the problems experienced by families using ITN were the difficulty in finding chemicals for the retreatment of nets 702 (47%), insufficient financial means to buy new bed nets to replace old ones 366 (24.5%) or, to provide bed nets to everybody in the household 289 (19.4%) and the sensation of feeling excessive heat when sleeping under a bed net 74 (5%). The amount spent monthly by a household for vector control and malaria treatment was estimated at 2377 fcfa (3.6 euros) and 4562 fcfa (6.95 euros) respectively. These amounts were not significantly different between households of Douala and Yaoundé. Concerning management of malaria cases, 18.6% of people declare going to the hospital when suffering from malaria. The majority of people (81.4%) do self medication - they either buy drugs from the pharmacists, street sellers or they use plants to cure malaria.

Conclusion
The study revealed a high awareness of populations on malaria and ITNs. However some attitudes hindering the use of ITN or related to the management of clinical cases need further attention.
TECHNICAL NOTE—Procurement Strategies with Unreliable Suppliers
Authors: Federgruen Awi , Yang Nan 
Published: September 2011

We propose and analyze a general periodic-review model in which the firm has access to a set of potential suppliers, each with specific yield and price characteristics. Assuming that unsatisfied demand is backlogged, the firm incurs three types of costs: (i) procurement costs, (ii) inventory-carrying costs for units carried over from one period to the next, and (iii) backlogging costs. A procurement strategy requires the specification, in each period, of (i) the set of suppliers to be retained, (ii) their respective shares in this period's replenishments, as well as (iii) the traditional aggregate order placed (among the various suppliers). We show how the optimal procurement strategy can be obtained with an efficient algorithm. A base-stock policy is no longer optimal, but in each period there exists a maximum inventory level, such that orders are placed if and only if the starting inventory is below this threshold. In each period it is optimal to retain a given number of suppliers that are cheapest in terms of that period's effective cost rates, i.e., the expected cost per usable unit. The optimal number of suppliers to be retained in a given period depends on all current and future parameters and distributions, but this dependence can be aggregated into a single so-called benchmark cost measure. Under Normal yield and demand distributions, the suppliers' market shares are determined by a single aggregate score, itself the product of a simple reliability score and a cost score.
Biomarkers for Predicting Serious Cardiac Outcomes at 72 Hours in Patients Presenting Early after Chest Pain Onset with Symptoms of Acute Coronary Syndromes
Authors: Kavsak Peter A , Hill Stephen A , Bhanich Supapol Wendy , Devereaux Philip J , Worster Andrew 
Published: September 2011

Abstract

BACKGROUND
Most outcome studies of patients presenting early to the emergency department with potential acute coronary syndromes have focused on either the index diagnosis of myocardial infarction (MI) or a composite end point at a later time frame (30 days or 1 year). We investigated the performance of 9 biomarkers for an early serious outcome.

METHODS
Patients (n = 186) who presented to the emergency department within 6 h of chest pain onset had their presentation serum sample measured for the following analytes: creatine kinase, creatine kinase isoenzyme MB, enhanced AccuTnI troponin I (Beckman Coulter), high-sensitivity cardiac troponin T (hs-cTnT), ischemia-modified albumin, interleukin-6, investigation use only hs-cTnI (Beckman Coulter), N-terminal pro–B-type natriuretic peptide, and cardiac troponin I (Abbott AxSym). We followed patients until 72 h after presentation and determined whether they experienced the following serious cardiac outcomes: MI, heart failure, serious arrhythmia, refractory ischemic cardiac pain, or death. ROC curves were analyzed to determine the area under the ROC curve (AUC) and optimal cutoffs for the biomarkers.

RESULTS
The AUCs for the hs-cTnI assay (0.86; 95% CI, 0.76–0.96), the AccuTnI assay (0.86; 95% CI, 0.78–0.95), and the hs-cTnT assay (0.82; 95% CI, 0.71–0.94) assays were significantly higher than those for the other 6 assays (AUC values ≤0.71 for the rest of the biomarkers, P &lt; 0.05). The ROC curve–derived optimal cutoffs were ≥19 ng/L (diagnostic sensitivity, 80%; specificity, 88%), ≥0.018 μg/L (diagnostic sensitivity, 75%; specificity, 86%), and ≥32 ng/L (diagnostic sensitivity, 68%; specificity, 92%) for the hs-cTnI, AccuTnI, and hs-cTnT assays, respectively.

CONCLUSIONS
The optimal cutoffs for predicting serious cardiac outcomes in this low-risk population are different from the published 99th percentiles. Larger studies are required to verify these findings.