bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parameter estimation using data assimilation in an atmospheric general circulation model: From a perfect toward the real world
Authors: Schirber Sebastian , Klocke Daniel , Pincus Robert , Quaas Johannes , Anderson Jeffrey L. 
Published: November 2012

Key Points
Objective parameter estimation using Ensemble Kalman Filter techniques
Cumulus‐convection scheme of an atmospheric general circulation model
Applying numerical weather prediction techniques to a climate model
Forecast performance assessment of a kinematic and a magnetohydrodynamic solar wind model
Authors: Norquist Donald C. 
Published: November 2012

AbstractPerformance evaluation of operational models guides forecasters on use of their products, focuses model developers in making improvements, and informs other modelers considering use of the output for forcing data. Two operational solar wind models, the Enlil magnetohydrodynamic model, and the Wang‐Sheeley‐Arge kinematic model, were executed daily in 2007–2011 from solar photosphere magnetograms compiled from the Global Oscillation Network Group telescope system. The original (uncorrected) magnetic field specification and a zero point‐corrected (ZPC) version were used as inner boundary conditions (IBCs) in separate 7 day forecast executions. Forecasts of solar wind radial speed (Vsw) and interplanetary magnetic field (IMF) polarity were compared with observations from the Advanced Composition Explorer satellite. Forecast verification metrics were computed by forecast day, year, and uncorrected or corrected IBCs. High speed events (HSEs) and IMF polarity changes (IPCs) predicted and observed were compared. Neither model exhibited a significant systematic error except in 2009, when both failed to represent the slow solar wind. Using the ZPC initial conditions resulted in smaller forecast‐observation differences in the years with greater Vsw variance. This was due to in part to reduced variance in the Vsw predictions from the ZPC IBCs. Differences were nil or worse in the other years. The time‐varying component of the forecast‐observation differences was smallest at forecast days 3 to 5, followed by a sharp rise. Impact of ZPCs on IMF polarity predictions was small. HSE prediction performance depended on detection algorithm used. Both models under predicted the number of forecast periods having IPCs.
The plasma membrane transporter SLC5A8 suppresses tumour progression through depletion of survivin without involving its transport function
Authors: Coothankandaswamy Veena , Elangovan Selvakumar , Singh Nagendra , Prasad Puttur D. , Thangaraju Muthusamy , Ganapathy Vadivel 
Published: November 2012

SLC5A8 (solute carrier gene family 5A, member 8) is a sodium-coupled transporter for monocarboxylates. Among its substrates are the HDAC (histone deacetylase) inhibitors butyrate, propionate and pyruvate. Expression of SLC5A8 is silenced in cancers via DNA methylation, and ectopic expression of SLC5A8 in cancer cells induces apoptosis in the presence of its substrates that are HDAC inhibitors. In the present study we show that ectopic expression of SLC5A8 in cancer cells translocates the anti-apoptotic protein survivin to the plasma membrane through protein–protein interaction resulting in depletion of nuclear survivin and also decreases cellular levels of survivin through inhibition of transcription. These SLC5A8-induced changes in the location and levels of survivin result in cell-cycle arrest, disruption of the chromosome passenger complex involved in mitosis, induction of apoptosis and enhancement in chemosensitivity. These effects are seen independently of the transport function of SLC5A8 and histone acetylation status of the cell; in the presence of pyruvate, a SLC5A8 substrate and also an HDAC inhibitor, these effects are amplified. Ectopic expression of SLC5A8 in the breast cancer cell line MB231 inhibits the ability of cells to form colonies in vitro and to form tumours in mouse xenografts in vivo. The suppression of survivin transcription occurs independently of HDAC inhibition, and the underlying mechanism is associated with decreased phosphorylation of STAT3 (signal transducer and activator of transcription 3). The observed effects are specific for survivin with no apparent changes in expression of other inhibitor-of-apoptosis proteins. The present study unravels a novel, hitherto unrecognized, mechanism for the tumour-suppressive role of a plasma membrane transporter independent of its transport function.
A Pilot Study of Interpersonal Psychotherapy for Alcohol-Dependent Women with Co-Occurring Major Depression
Authors: Gamble Stephanie A. , Talbot Nancy L. , Cashman-Brown Sarah M. , He Hua , Poleshuck Ellen L. , Connors Gerard J. , Conner Kenneth R. 
Published: November 2012

Background Co-occurring major depression is prevalent among alcohol-dependent women and is a risk factor for poor treatment outcomes. This uncontrolled pilot study tested the feasibility, acceptability, and initial effects of interpersonal psychotherapy (IPT) for women with co-occurring alcohol dependence and major depression (AD-MD) in an outpatient community addiction treatment program. Methods Fourteen female patients with concurrent diagnoses of alcohol dependence and major depression participated. Assessments were conducted at baseline, midtreatment (8 and 16 weeks), posttreatment (24 weeks), and follow-up (32 weeks). Results Participants attended a mode of 8 out of 8 possible sessions of IPT in addition to their routine addiction care, and reported high treatment satisfaction on the Client Satisfaction Questionnaire-8. Women's drinking behavior, depressive symptoms, and interpersonal functioning improved significantly over the treatment period and were sustained at follow-up. Conclusions These preliminary findings suggest that IPT is a feasible, highly acceptable adjunctive behavioral intervention for AD-MD women.
Infections Acquired by Adults Who Receive Extracorporeal Membrane Oxygenation Risk Factors and Outcome
Authors: Aubron Cecile , Cheng Allen C. , Pilcher David , Leong Tim , Magrin Geoff , Cooper D. Jamie , Scheinkestel Carlos , Pellegrino Vince 
Published: November 2012

Objectives.To analyze infectious complications that occur in patients who receive extracorporeal membrane oxygenation (ECMO), associated risk factors, and consequences on patient outcome.Design.Retrospective observational survey from 2005 through 2011.Participants and Setting.Patients who required ECMO in an Australian referral center.Methods.Cases of bloodstream infection (BSI), catheter-associated urinary tract infection (CAUTI), and ventilator-associated pneumonia (YAP) that occurred in patients who received ECMO were analyzed.Results.A total of 146 ECMO procedures were performed for more than 48 hours in 139 patients, and 36 patients had a total of 46 infections (30.1 infectious episodes per 1,000 days of ECMO). They included 24 cases of BSI, 6 of them secondary to VAP; 23 cases of VAP; and 5 cases of CAUTI. The most frequent pathogens were Enterobacteriaceae (found in 16 of 46 cases), and Candida was the most common cause of BSI (in 9 of 24 cases). The Sequential Organ Failure Assessment score before ECMO initiation and the number of days of support were independenuy associated with a risk of BSI, with odds ratios of 1.23 (95% confidence interval [CI], 1.03-1.47; P = .019) and 1.08(95% CI, 1.03-1.19]; P = .006), respectively. Infected patients did not have a significantly higher mortality compared with uninfected patients (41.7% vs 32%; P = .315), but intensive care unit length of stay (16 days [interquartile range, 8-26 days] vs 11 days [IQR, 4-19 days]; P = .012) and hospital length of stay (33.5 days [interquartile range, 15.5-55.5] vs 24 days [interquartile range, 9-42 days]; P = .029) were longer.Conclusion.The probability of infection increased with the duration of support and the severity of illness before initiation of ECMO. Infections affected length of stay but did not have an impact on mortality.
Defining Relatedness in Studies of Transmission of Antimicrobial-Resistant Organisms Variability in Definitions across Studies and Impact of Different Approaches on Study Conclusions
Authors: Greenblatt Rachel M. , Han Jennifer H. , Nachamkin Irving , Tolomeo Pam , Lautenbach Ebbing 
Published: November 2012

Objective.Comparison of studies evaluating patient-to-patient transmission of organisms is difficult, given the lack of standardized criteria. We used fluoroquinolone-resistantEscherichia coli(FQREC) as a model to characterize variability in definitions of relatedness across studies and to evaluate the resultant impact on study conclusions.Design.Narrative review and cohort study.Methods.The narrative review compared relatedness criteria across studies of FQREC. Additionally, an existing database was used to compare relatedness of isolates on the basis of molecular criteria alone versus molecular plus clinical criteria with different temporal cutoffs (hospitalization overlap of ≥1 day or allowance for nonoverlap of hospitalization dates of ≤7 days or ≤30 days).Results.Forty-six articles met narrative review inclusion criteria. Sixteen studies exclusively utilized molecular criteria to define relatedness. Thirty studies included molecular and clinical criteria. Of these, 6 included temporal data (ie, time period of isolate identification), 10 included patient location, and 14 included proximity and temporal criteria. For the database analysis, 353 patients were colonized with FQREC. There were 2 main clusters containing 48 and 17 related isolates within 49 pulsed-field gel electrophoresis types. Among the clusters, 18.4% of isolates were related by molecular criteria. Incorporating clinical criteria, fewer isolates were considered related: 5.7% of isolates using 30-day criteria, 3.1% using 7-day criteria, and 1.4% using 1-day overlap.Conclusions.There is considerable variability in definitions of relatedness of FQREC. Utilizing molecular criteria alone to define relatedness overestimates transmission compared with definitions including clinical criteria. Standard definitions of relatedness in studies of antimicrobial-resistant organisms are needed.
An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data
Authors: Kocak Mehmet , Olusegun George E. , Pyne Saumyadipta , Pounds Stanley 
Published: November 2012

AbstractMotivation: There is a substantial body of works in the biology literature that seeks to characterize the cyclic behavior of genes during cell division. Gene expression microarrays made it possible to measure the expression profiles of thousands of genes simultaneously in time-course experiments to assess changes in the expression levels of genes over time. In this context, the commonly used procedures for testing include the permutation test by de Lichtenberg et al. and the Fisher’s G-test, both of which are designed to evaluate periodicity against noise. However, it is possible that a gene of interest may have expression that is neither cyclic nor just noise. Thus, there is a need for a new test for periodicity that can identify cyclic patterns against not only noise but also other non-cyclic patterns such as linear, quadratic or higher order polynomial patterns.Results: To address this weakness, we have introduced an empirical Bayes approach to test for periodicity and compare its performance in terms of sensitivity and specificity with that of the permutation test and Fisher’s G-test through extensive simulations and by application to a set of time-course experiments on the Schizosaccharomyces pombe cell-cycle gene expression. We use ‘conserved’ and ‘cycling’ genes by Lu et al. to assess the sensitivity and CESR genes by Chenet al. to assess the specificity of our new empirical Bayes method.Availability and implementation: The SAS Macro for our empirical Bayes test for periodicity is included in the supplementary materials along with a sample run of the MACRO program.Contact: mkocak1@uthsc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
High-throughput microbial population genomics using the Cortex variation assembler
Authors: Iqbal Zamin , Turner Isaac , McVean Gil 
Published: November 2012

Abstract
Summary: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads.
Availability: http://cortexassembler.sourceforge.net (GPLv3 license).
Contact: zam@well.ox.ac.uk, mcvean@well.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Non-redundant compendium of human ncRNA genes in GeneCards
Authors: Belinky Frida , Bahir Iris , Stelzer Gil , Zimmerman Shahar , Rosen Naomi , Nativ Noam , Dalah Irina , Iny Stein Tsippi , Rappaport Noa , Mituyama Toutai , Safran Marilyn , Lancet Doron 
Published: November 2012

Abstract
Motivation: Non-coding RNA (ncRNA) genes are increasingly acknowledged for their importance in the human genome. However, there is no comprehensive non-redundant database for all such human genes.
Results: We leveraged the effective platform of GeneCards, the human gene compendium, together with the power of fRNAdb and additional primary sources, to judiciously unify all ncRNA gene entries obtainable from 15 different primary sources. Overlapping entries were clustered to unified locations based on an algorithm employing genomic coordinates. This allowed GeneCards’ gamut of relevant entries to rise ∼5-fold, resulting in ∼80 000 human non-redundant ncRNAs, belonging to 14 classes. Such ‘grand unification’ within a regularly updated data structure will assist future ncRNA research.
Availability and implementation: All of these non-coding RNAs are included among the ∼122 500 entries in GeneCards V3.09, along with pertinent annotation, automatically mined by its built-in pipeline from 100 data sources. This information is available at www.genecards.org.
Contact: Frida.Belinky@weizmann.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Authors: Miller Chase A. , Anthony Jon , Meyer Michelle M. , Marth Gabor 
Published: November 2012

Abstract
Motivation: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e.g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available.
Results: Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications.
Availability and implementation: Software is freely available online at http://chmille4.github.com/Scribl/ and is implemented in JavaScript with all modern browsers supported.
Contact: gabor.marth@bc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Inhaled Nitric Oxide Attenuates the Adverse Effects of Transfusing Stored Syngeneic Erythrocytes in Mice with Endothelial Dysfunction after Hemorrhagic Shock
Authors: Lei Chong , Yu Binglan , Shahid Mohd , Beloiartsev Arkadi , Bloch Kenneth D. , Zapol Warren M. 
Published: November 2012

Background
The authors investigated whether transfusion with stored erythrocytes would increase tissue injury, inflammation, oxidative stress, and mortality (adverse effects of transfusing stored erythrocytes) in a murine model of hemorrhagic shock. They tested whether the adverse effects associated with transfusing stored erythrocytes were exacerbated by endothelial dysfunction and ameliorated by inhaling nitric oxide.

Methods
The authors studied mice fed a high-fat diet (HFD-fed; to induce endothelial dysfunction) or a standard diet for 4-6 weeks. Mice were subjected to 90 min of hemorrhagic shock, followed by resuscitation with leukoreduced syngeneic erythrocytes stored less than 24 h (fresh erythrocytes) or stored for 2 weeks (stored erythrocytes).

Results
In standard-diet-fed mice at 2 h after resuscitation, transfusion with stored erythrocytes increased tissue injury more than transfusion with fresh erythrocytes. The adverse effects of transfusing stored erythrocytes were more marked in HFD-fed mice and associated with increased lactate levels and short-term mortality. Compared with fresh erythrocytes, resuscitation with stored erythrocytes was associated with a reduction in P50, increased plasma hemoglobin levels, and increased indices of inflammation and oxidative stress, effects that were exacerbated in HFD-fed mice. Inhaled nitric oxide reduced tissue injury, lactate levels, and indices of inflammation and oxidative stress and improved short-term survival in HFD-fed mice resuscitated with stored erythrocytes.

Conclusions
Resuscitation with stored erythrocytes adversely impacts outcome in mice with hemorrhagic shock, an effect that is exacerbated in mice with endothelial dysfunction. Inhaled nitric oxide reduces tissue injury and improves short-term survival in HFD-fed mice resuscitated with stored erythrocytes.
Guillain–Barré Syndrome After Influenza Vaccination in the United States, A Report From the CDC/FDA Vaccine Adverse Event Reporting System (1990–2009)
Authors: Souayah Nizar , Yacoub Hussam A. , Khan Hafiz M.R. , Farhad Khosro , Mehyar Lubna Shafiq , Maybodi Leila , Menkes Daniel L. , Qureshi Adnan I. 
Published: November 2012

Abstract

Objectives:
To determine the rate of Guillain–Barré syndrome (GBS) after administration of influenza vaccine in the United States and to provide further information about the characteristics and temporal profile of these incidents.

Methods:
Data were acquired from the Vaccine Adverse Event Reporting System, supplemented by data from the Center for Biologics and Research under the Freedom of Information Act between 1990 and 2009.

Results:
There were 802 cases (mean age, 54.72 ± 18.4 years) of GBS reported after influenza vaccination in the United States between 1990 and 2009. Among the 802 vaccinated patients with available data, 624 (77.8%) developed GBS within 6 weeks and 78 (9.7%) after 6 weeks, whereas these data were unavailable for the remaining 100 patients (13%). The reporting rate of post–influenza vaccine GBS was within the range expected in the general population or approximately 0.46 cases per million vaccinations. A non-Gaussian distribution of GBS within the first 6 weeks post-vaccination was noted, given that the peak incidence occurred in the second week.

Conclusions:
The incidence of post–influenza vaccine GBS is similar to the incidence of idiopathic GBS in the general population. Although the nonnormal distribution of post-vaccination GBS suggests that some cases may be triggered by vaccination, the greater risk of complications from influenza virus infections makes vaccination the first-line strategy for infection prevention and support the current guidelines on vaccination.
Thermal Acclimation of the Symbiotic Alga Symbiodinium spp. Alleviates Photobleaching under Heat Stress
Authors: Takahashi Shunichi , Yoshioka-Nishimura Miho , Nanba Daisuke , Badger Murray R. 
Published: November 2012

Abstract
A moderate increase in seawater temperature causes coral bleaching, at least partially through photobleaching of the symbiotic algae Symbiodinium spp. Photobleaching of Symbiodinium spp. is primarily associated with the loss of light-harvesting proteins of photosystem II (PSII) and follows the inactivation of PSII under heat stress. Here, we examined the effect of increased growth temperature on the change in sensitivity of Symbiodinium spp. PSII inactivation and photobleaching under heat stress. When Symbiodinium spp. cells were grown at 25°C and 30°C, the thermal tolerance of PSII, measured by the thermal stability of the maximum quantum yield of PSII in darkness, was commonly enhanced in all six Symbiodinium spp. tested. In Symbiodinium sp. CCMP827, it took 6 h to acquire the maximum PSII thermal tolerance after transfer from 25°C to 30°C. The effect of increased growth temperature on the thermal tolerance of PSII was completely abolished by chloramphenicol, indicating that the acclimation mechanism of PSII is associated with the de novo synthesis of proteins. When CCMP827 cells were exposed to light at temperature ranging from 25°C to 35°C, the sensitivity of cells to both high temperature-induced photoinhibition and photobleaching was ameliorated by increased growth temperatures. These results demonstrate that thermal acclimation of Symbiodinium spp. helps to improve the thermal tolerance of PSII, resulting in reduced inactivation of PSII and algal photobleaching. These results suggest that whole-organism coral bleaching associated with algal photobleaching can be at least partially suppressed by the thermal acclimation of Symbiodinium spp. at higher growth temperatures.
Beam-induced oxidation of monomeric U(IV) species
Authors: Alessi Daniel S. , Uster Benjamin , Borca Camelia N. , Grolimund Daniel , Bernier-Latmani Rizlan 
Published: November 2012

UraniumLIII-edge X-ray absorption spectroscopy is often used to probe the oxidation state and coordination of uranium in environmental samples, and micrometre-sized beams can be used to spatially map the distribution of uranium relative to other elements. Here a variety of uranium-containing environmental samples are analyzed at both microbeam and larger beam sizes to determine whether reoxidation of U(IV) occurred. Monomeric U(IV), a recently discovered product of U(VI) reduction by microbes and certain iron-bearing minerals at uranium-contaminated field sites, was found to be reoxidized during microbeam (3 µm × 2 µm) analysis of biomass and sediments containing the species but not at larger beam sizes. Thus, care must be taken when using X-ray microprobes to analyze samples containing monomeric U(IV).