bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whiteboard: a framework for the programmatic visualization of complex biological analyses
Authors: Sundström Görel , Zamani Neda , Grabherr Manfred G. , Mauceli Evan 
Published: February 2015

Abstract
Summary: Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets.
Availability and implementation: the C++ source code, coding samples and documentation are freely available under the Lesser General Public License from http://whiteboard-class.sourceforge.net/.
Contact: emauceli@parabasegenomics.com.
Factors affecting the availability of walleye pollock to acoustic and bottom trawl survey gear
Authors: Kotwicki Stan , Horne John K. , Punt André E. , Ianelli James N. 
Published: February 2015

Abstract
Abundances of semi-pelagic fish are often estimated using acoustic or bottom trawl surveys, both of which sample only a fraction of the water column. Acoustic instruments are effective at sampling the majority of the water column, but they have a near-surface blind zone and a near-bottom acoustic dead zone (ADZ), where fish remain undetected. Bottom trawls are effective near the seabed, but miss fish that are located above the effective fishing height of the trawl. Quantification of the extent of overlap between these gears is needed, particularly in cases where environmental factors play a role. We developed logistic regression models to predict the availability (qa) of walleye pollock (Gadus chalcogrammus) to both acoustic and bottom trawl gears using factors shown to affect qa (depth, light intensity, fish length) and introducing additional factors (tidal currents, surface and bottom temperature, sediment size). Results build on earlier studies and quantify the uncertainty associated with the estimation of the ADZ correction using Bayesian methods. Our findings indicate that on average during the day, walleye pollock are more available to the bottom trawl than to the acoustics. Availability to both gears depends mostly on bottom depth, light conditions, and fish size, and to a lesser extent sediment size. Availability to the acoustic gear is also related on surface temperature. Variability in availability to both gears also depends on environmental factors.
Spending-Biased Legislators: Discipline Through Disagreement
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Authors: Piguillem Facundo , Riboni Alessandro 
Published: February 2015

Abstract
We study legislators who have a present bias for spending: they want to increase current spending and procrastinate spending cuts. We show that disagreement in legislatures can lead to policy persistence that attenuates the temptation to overspend. Depending on the environment, legislators’ decisions to be fiscally responsible may either complement or substitute other legislators’ decisions. When legislators have low discount factors, their actions are strategic complements. Thus, changes of the political environment that induce fiscal responsibility are desirable as they generate a positive responsibility multiplier and reduce spending. However, when the discount factor is high, the same changes induce some legislators to free ride on others’ responsibility which may lead to higher spending.
Functional Evolution of Phosphatidylethanolamine Binding Proteins in Soybean and Arabidopsis
Authors: Wang Zheng , Zhou Zhengkui , Liu Yunfeng , Liu Tengfei , Li Qing , Ji Yuanyuan , Li Congcong , Fang Chao , Wang Min , Wu Mian , Shen Yanting , Tang Tian , Ma Jianxin , Tian Zhixi 
Published: February 2015

AbstractGene duplication provides resources for novel gene functions. Identification of the amino acids responsible for functional conservation and divergence of duplicated genes will strengthen our understanding of their evolutionary course. Here, we conducted a systemic functional investigation of phosphatidylethanolamine binding proteins (PEBPs) in soybean (Glycine max) and Arabidopsis thaliana. Our results demonstrated that after the ancestral duplication, the lineage of the common ancestor of the FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) subfamilies functionally diverged from the MOTHER OF FT AND TFL1 (MFT) subfamily to activate flowering and repress flowering, respectively. They also underwent further specialization after subsequent duplications. Although the functional divergence increased with duplication age, we observed rapid functional divergence for a few pairs of young duplicates in soybean. Association analysis between amino acids and functional variations identified critical amino acid residues that led to functional differences in PEBP members. Using transgenic analysis, we validated a subset of these differences. We report clear experimental evidence for the functional evolution of the PEBPs in the MFT, FT, and TFL1 subfamilies, which predate the origin of angiosperms. Our results highlight the role of amino acid divergence in driving evolutionary novelty after duplication.
An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania
Authors: Ramsey David S. L. , MacDonald Anna J. , Quasim Sumaiya , Barclay Candida , Sarre Stephen D. 
Published: February 2015

Summary

Polymerase chain reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR‐based tests are prone to contamination in sampling and the laboratory.

Here, we use an experimental case–control approach to estimate the sensitivity and specificity of a sequential PCR‐based wildlife detection test used to identify incursions of red foxes into Tasmania from predator faeces (scats).

Our results show that the sensitivity of the fox test is high (∼94%) for the PCR‐based test on its own, but this decreases to ∼84% when combined with the DNA sequencing step. In contrast, the specificity increases from ∼96% in the PCR‐only test to ˜99·6% after inclusion of the DNA sequencing step.

The intense public scrutiny of the fox eradication programme in Tasmania has undoubtedly influenced the application of a sequential PCR test that maximizes specificity at the expense of sensitivity and so increases the risk that scats containing fox DNA would not be detected. This could lead to the establishment of foxes in Tasmania as a consequence.

Synthesis and applications. Importantly, the estimation of the sensitivity and specificity of sequential tests enables decisions about the risk associated with mistaken identification (i.e. false negatives vs. false positives) to be quantified for decision‐makers. The cost of false‐negative errors should be balanced against the costs of false‐positive errors, which could include the expenditure incurred in the application of unnecessary management actions were foxes not in fact present. Understanding the risks and costs associated with both false‐negative and false‐positive errors is therefore a key component to the decision‐making process for the management of the Tasmanian fox incursion.
Understanding Cross‐Country Differences in Valuation Ratios: A Variance Decomposition Approach
Authors: Chue Timothy K. 
Published: February 2015

AbstractWe use a variance decomposition approach to examine why aggregate valuation ratios differ across countries. In a cross section of 22 developed countries from 1980 to 2009, we find that 50 percent of all cross‐country differences in the aggregate price‐to‐book ratio (P/B) can be explained by cross‐country differences in expected future five‐year profitability. In the second half of our sample period, this percentage exceeds that of the first half, rising to almost 64 percent. Although international differences in accounting standards and conventions may have made earnings from different countries more difficult to compare relative to dividends, we find that it is still cross‐country differences in expected future profitability, rather than dividend growth rates, that are more closely related to international differences in valuation ratios. Even among 25 emerging markets, we find that expected future profitability at the five‐year horizon can account for 29 percent of all cross‐country P/B variations. Our results show that international investors are able to identify substantial cross‐country differences in future‐earnings prospects and incorporate them into stock market valuations.
Hemostatic resuscitation in postpartum hemorrhage – a supplement to surgery
Authors: Ekelund Kim , Hanke Gabriele , Stensballe Jakob , Wikkelsøe Anne , Albrechtsen Charlotte Krebs , Afshari Arash 
Published: February 2015

AbstractBackgroundPostpartum hemorrhage is a potentially life‐threatening albeit preventable condition that persists as a leading cause of maternal death. Identification of safe and cost‐effective hemostatic treatment options remains crucial as a supplement to surgery and uterotonic agents.ObjectiveThis review summarizes the background, current evidence and recommendations with regard to the role of fibrinogen, tranexamic acid, prothrombin complex concentrate, desmopressin, and recombinant factor VIIa in the treatment of patients with postpartum hemorrhage. The benefits and evidence behind traditional standard laboratory tests and viscoelastic hemostatic assays, i.e. thromboelastography TEG® and thromboelastometry ROTEM®, are discussed. In addition we assess and elaborate on the current paradigm and evidence for transfusion of these patients.Data sourcesPublications between 1994 and 2014 were identified from PubMed, EMBASE, Cochrane Library databases, and ClinicalTrial.gov.ResultsViscoelastic hemostatic assays were found to provide a real‐time continuum of coagulation and fibrinolysis when introduced as a supplement in transfusion management of postpartum hemorrhage. Fibrinogen should be considered when hypofibrinogenemia is identified. Early administration of 1–2 g tranexamic acid is recommended, followed by an additional dose in cases of ongoing bleeding. Uncontrolled hemorrhage requires early balanced transfusion.ConclusionDespite the lack of conclusive evidence for optimal hemostatic resuscitation in postpartum hemorrhage, the use of viscoelastic hemostatic assays, fibrinogen, tranexamic acid and balanced transfusion therapy may prove to be potentially pivotal in the treatment of postpartum hemorrhage.
Problematic Internet use is associated with substance use in young adolescents
Authors: Rücker Jeanine , Akre Christina , Berchtold André , Suris Joan‐Carles 
Published: February 2015

AbstractAimThis study examined whether problematic Internet use was associated with substance use among young adolescents and assessed whether this association accounted for the use of tobacco, alcohol, cannabis and other drugs.MethodsUsing the Internet Addiction Test, we divided a representative sample of 3067 adolescents in Switzerland (mean age 14 years) into regular and problematic Internet users. We performed a bivariate analysis and two logistic regression models, to analyse substances separately and simultaneously, and developed a log‐linear model to define the associations between significant variables.ResultsProblematic Internet users were more likely to be female, to use substances, to come from nonintact families, to report poor emotional well‐being and to be below average students. The first model showed significant associations between problematic users and each substance, with adjusted odds ratios of 2.05 for tobacco, 1.72 for alcohol, 1.94 for cannabis and 2.73 for other drugs. Only smoking remained significant in the second model, with an adjusted odds ratio of 1.71.ConclusionProblematic Internet use is associated with other risky behaviours and may be an important early predictor of adolescent substance use. Therefore, it should be included in the psychosocial screening of adolescents.
Transplantation of ABO A2 kidneys into O recipients: do IgM anti‐A1 titers matter?
Authors: Tierney Joshua , Shaffer David 
Published: February 2015

AbstractBackgroundThe ABO blood subgroup A2 expresses lower levels of A antigen on the cell surface and is less immunogenic toward anti‐A immunoglobulin present in blood type O or B recipients. Previous studies have shown successful kidney transplantation from A2 donors into O or B recipients with low pre‐transplant anti‐A titers. Previous studies suggest good results with recipient IgG titers <1:8. Few studies have specifically evaluated the importance of anti‐A1 IgM titers on early outcomes following A2 to O or B kidney transplantation.MethodsWe performed a single center, retrospective review of all A2 to O living donor kidney transplants. All recipients had pre‐transplant anti‐A IgG titers <1:8. IgM titers were measured in all recipients and were reported but not used to determine eligibility for transplant.ResultsFrom 2001 to 2013, we performed seven consecutive A2 to O living donor kidney transplants. Early allograft dysfunction, acute rejection or thrombotic microangiopathy, occurred in four patients and were associated with high IgM titers despite low IgG titers.ConclusionsOur data show a high incidence of early acute rejection or thrombotic microangiopathy in A2 to O kidney transplants with high recipient anti‐A IgM titers despite low IgG titers. Steps to lower anti‐IgM pre‐transplant may reduce the risk of early allograft dysfunction in A2 to O or B kidney transplants. Attention should be paid to IgM titers in establishing individual center selection criteria for A2 to B kidney transplants under the new UNOS kidney allocation system.
Lung transplantation in chronic obstructive pulmonary disease: long‐term survival, freedom from bronchiolitis obliterans syndrome, and factors influencing outcome
Authors: Zeriouh Mohamed , Mohite Prashant N. , Sabashnikov Anton , Zych Bartlomiej , Patil Nikhil P. , Garcia‐Saez Diana , Koch Achim , Ghodsizad Ali , Weymann Alexander , Soresi Simona , Wittwer Thorsten , Choi Yeong‐Hoon , Wippermann Jens , Wahlers Thorsten , Popov Aron‐Frederik , Simon André R. 
Published: February 2015

AbstractObjectivesLung transplantation (LTx) remains the definitive treatment for end‐stage lung failure, whereas chronic obstructive pulmonary disease (COPD) represents one of the main diagnoses leading to the indication for a transplant. We sought to assess long‐term outcomes after LTx in patients diagnosed with COPD and analyze factors influencing outcome in this frequent patient cohort.MethodsBetween January 2007 and November 2013, a total of 88 LTx were performed in patients with COPD in our institution. Patients with emphysema associated with alpha1‐antitrypsin deficiency were excluded from this observation. The study design was a retrospective review of the prospectively collected data. A large number of pre‐, intra‐, and postoperative variables were analyzed including long‐term survival and freedom from bronchiolitis obliterans syndrome (BOS). Furthermore, impact of different variables on survival was analyzed.ResultsPreoperative donor data indicated a large proportion of marginal donors. While the overall cumulative survival after six yr was 57.4%, the results in terms of BOS‐free survival in long‐term follow‐up were 39.7% after six yr. Patients with COPD were also associated with a low incidence (2.3%) of the need for postoperative extracorporeal life support (ECLS).ConclusionsLong‐term results after LTx in patients with COPD are acceptable with excellent survival, freedom from BOS, and low use of ECLS postoperatively despite permanently increasing proportion of marginal organs used.
Prevalence and incidence of diabetes mellitus: a nationwide population‐based pharmaco‐epidemiological study in Sweden
Authors: Jansson S. P. O. , Fall K. , Brus O. , Magnuson A. , Wändell P. , Östgren C. J. , Rolandsson O. 
Published: February 2015

AbstractAimTo investigate the changes in prevalence and incidence of pharmacologically and non‐pharmacologically treated diabetes in Sweden during 2005 to 2013.MethodsWe obtained data on gender, date of birth and pharmacologically and non‐pharmacologically treated diabetes from national registers for all Swedish residents.ResultsDuring the study period a total of 240 871 new cases of pharmacologically treated diabetes was found. The age‐standardized incidence during the follow‐up was 4.34 and 3.16 per 1000 individuals in men and women, respectively. A decreasing time trend in incidence for men of 0.6% per year (0.994, 95% CI 0.989–0.999) and for women of 0.7% per year (0.993, 95% CI 0.986–0.999) was observed. The age‐standardized prevalence increased from 41.9 and 29.9 per 1000 in 2005/2006 to 50.8 and 34.6 in 2012/2013 in men and women, respectively. This corresponds to an annually increasing time trend for both men (1.024, 95% CI 1.022–1.027) and women (1.019, 95% CI 1.016–1.021). The total age‐standardized prevalence of pharmacologically and non‐pharmacologically treated diabetes (2012) was 46.9 per 1000 (55.6 for men and 38.8 for women). This corresponds to an annually increasing time trend (2010–2012) for both men (1.017, 95% CI 1.013–1.021) and women (1.012, 95% CI 1.008–1.016).ConclusionsThe prevalence of pharmacologically treated diabetes increased moderately during 8 years of follow‐up, while the incidence decreased modestly. This is in contrast to the results reported by most other studies. The total prevalence of diabetes (both pharmacologically and non‐pharmacologically treated) in Sweden is relatively low, from a global viewpoint.
Glomerular haemodynamic profile of patients with Type 1 diabetes compared with healthy control subjects
Authors: Škrtić M. , Lytvyn Y. , Yang G. K. , Yip P. , Lai V. , Silverman M. , Cherney D. Z. I. 
Published: February 2015

AbstractAimsTo evaluate the glomerular haemodynamic profile of patients with Type 1 diabetes with either renal hyperfiltration (GFR ≥ 135 ml/min/1.73 m2) or renal normofiltration (GFR 90–134 ml/min/1.73 m2) during euglycaemic and hyperglycaemic conditions, and to compare this profile with that of a similar group of healthy control subjects.MethodsGomez's equations were used to derive afferent and efferent arteriolar resistances, glomerular hydrostatic pressure and filtration pressure.ResultsAt baseline, during clamped euglycaemia, patients with Type 1 diabetes and hyperfiltration had lower mean ± sd afferent arteriolar resistance than both those with Type 1 diabetes and normofiltration (914 ± 494 vs. 2065 ± 597 dyne/s/cm5; P < 0.001) and healthy control subjects (1676 ± 707 dyne/s/cm5; p < 0.001). By contrast, efferent arteriolar resistance was similar in the three groups. Patients with Type 1 diabetes and hyperfiltration also had higher mean ± sd glomerular hydrostatic pressure than both healthy control subjects and patients with Type 1 diabetes and normofiltration (66 ± 6 vs. 60 ± 3 vs. 55 ± 3 mmHg; P < 0.05). Similar findings for afferent arteriolar resistance, efferent arteriolar resistance, glomerular hydrostatic pressure and filtration pressure were observed during clamped hyperglycaemia.ConclusionHyperfiltration in Type 1 diabetes is primarily driven by alterations in afferent arteriolar resistance rather than efferent arteriolar resistance. Renal protective therapies should focus on afferent renal arteriolar mechanisms through the use of pharmacological agents that target tubuloglomerular feedback, including sodium‐glucose cotransporter 2 inhibitors and incretins.
Community‐based peer support significantly improves metabolic control in people with Type 2 diabetes in Yaoundé, Cameroon
Authors: Assah F. K. , Atanga E. N. , Enoru S. , Sobngwi E. , Mbanya J. C. 
Published: February 2015

AbstractAimsTo examine the effectiveness of a community‐based multilevel peer support intervention in addition to usual diabetes care on improving glycaemic levels, blood pressure and lipids in patients with Type 2 diabetes in Yaoundé, Cameroon.MethodsA total of 96 subjects with poorly controlled Type 2 diabetes (intervention group) and 96 age‐ and sex‐matched controls were recruited and followed up over 6 months. The intervention subjects underwent a peer support intervention through peer‐led group meetings, personal encounters and telephone calls. Both intervention subjects and controls continued their usual clinical care. HbA1c, blood pressure, blood lipids and self‐care behaviours were measured at 0 and 6 months.ResultsThere was significant reduction in HbA1c in the intervention group [–33 mmol/mol (–3.0%)] compared with controls [–14 mmol/mol (–1.3%)]; P < 0.001. Peer support also led to significant reductions in fasting blood sugar (–0.83 g/l P < 0.001), cholesterol (–0.54 g/l P < 0.001), HDL (–0.09 g/l, P < 0.001), BMI (–2.71 kg/m² P < 0.001) and diastolic pressure (–6.77 mmHg, P < 0.001) over the 6‐month period. Also, diabetes self‐care behaviours in the intervention group improved significantly over the 6 months of peer support.ConclusionCommunity‐based peer support, in addition to usual care, significantly improved metabolic control in patients with uncontrolled Type 2 diabetes in Yaoundé, Cameroon. This could provide a model for optimizing diabetes care and control in other settings with limited healthcare and financial resources.
Major bleeding risk prediction using Chronic Kidney Disease Epidemiology Collaboration and Modification of Diet in Renal Disease equations in acute coronary syndrome
Authors: Flores‐Blanco Pedro J. , López‐Cuenca Ángel , Januzzi James L. , Marín Francisco , Sánchez‐Martínez Marianela , Quintana‐Giner Miriam , Romero‐Aniorte Ana I. , Valdés Mariano , Manzano‐Fernández Sergio 
Published: February 2015

AbstractBackgroundChronic Kidney Disease Epidemiology Collaboration (CKD‐EPI) equations estimate glomerular filtration rate more accurately than the Modification of Diet in Renal Disease (MDRD) Study equation. Our aim was to evaluate whether CKD‐EPI equations based on serum creatinine and/or cystatin C (CysC) predict risk for major bleeding (MB) more accurately than the MDRD Study equation in patients with non‐ST‐segment elevation acute coronary syndromes (ACS).Materials and methodsThree hundred and fifty consecutive subjects with non‐ST‐segment elevation ACS (68 ± 12 years, 70% male) were studied. Glomerular filtration rate was estimated using the CKD‐EPI and MDRD Study equations. The primary endpoint was the occurrence of MB during the follow‐up, which was defined according to the Bleeding Academic Research Consortium Definition criteria as bleeding types 3–5.ResultsDuring the median follow‐up of 589 days (interquartile range, 390–986), 27 patients had MB (0·04% events per person year). Patients with MB had worse kidney function parameters, regardless of the estimating equation used (P < 0·001). After multivariate Cox regression adjustment, both CysC‐based CKD‐EPI equations were independent predictors of MB (CKD‐EPIcreatinine‐cystatin C per mL/min/1·73 m2, HR = 0·973 (95%CI 0·955–0·991; P = 0·003) and CKD‐EPIcystatin C per mL/min/1·73 m2, HR = 0·976 (95%CI 0·976–0·992; P = 0·003), while the CKD‐EPIcreatinine and MDRD equations did not achieve statistical significance. Both CKD‐EPIcreatine‐cystatin C and CKD‐EPIcystatin C were associated with a significant improvement in MB risk reclassification.ConclusionsIn this cohort of non‐ST‐segment elevation ACS patients with relatively preserved renal function, both CysC‐based CKD‐EPI equations improved ability to predict risk for MB and were superior to other equations for this application.