bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using multiple imputation to estimate missing data in meta‐regression
Authors: Ellington E. Hance , Bastille‐Rousseau Guillaume , Austin Cayla , Landolt Kristen N. , Pond Bruce A. , Rees Erin E. , Robar Nicholas , Murray Dennis L. 
Published: December 2014

Summary

There is a growing need for scientific synthesis in ecology and evolution. In many cases, meta‐analytic techniques can be used to complement such synthesis. However, missing data are a serious problem for any synthetic efforts and can compromise the integrity of meta‐analyses in these and other disciplines. Currently, the prevalence of missing data in meta‐analytic data sets in ecology and the efficacy of different remedies for this problem have not been adequately quantified.

We generated meta‐analytic data sets based on literature reviews of experimental and observational data and found that missing data were prevalent in meta‐analytic ecological data sets. We then tested the performance of complete case removal (a widely used method when data are missing) and multiple imputation (an alternative method for data recovery) and assessed model bias, precision and multimodel rankings under a variety of simulated conditions using published meta‐regression data sets.

We found that complete case removal led to biased and imprecise coefficient estimates and yielded poorly specified models. In contrast, multiple imputation provided unbiased parameter estimates with only a small loss in precision. The performance of multiple imputation, however, was dependent on the type of data missing. It performed best when missing values were weighting variables, but performance was mixed when missing values were predictor variables. Multiple imputation performed poorly when imputing raw data which were then used to calculate effect size and the weighting variable.

We conclude that complete case removal should not be used in meta‐regression and that multiple imputation has the potential to be an indispensable tool for meta‐regression in ecology and evolution. However, we recommend that users assess the performance of multiple imputation by simulating missing data on a subset of their data before implementing it to recover actual missing data.
Decomposing phylodiversity
Authors: Marcon Eric , Hérault Bruno 
Published: December 2014

Summary

Measuring functional or phylogenetic diversity is the object of an active literature. The main issues to address are relating measures to a clear conceptual framework, allowing unavoidable estimation‐bias correction and decomposing diversity along spatial scales.

We provide a general mathematical framework to decompose measures of species‐neutral, phylogenetic or functional diversity into α and β components. We first unify the definitions of phylogenetic and functional entropy and diversity as a generalization of HCDT entropy and Hill numbers when an ultrametric tree is considered. We then derive the decomposition of diversity. We propose a bias correction of the estimates allowing meaningful computation from real, often undersampled communities. Entropy can be transformed into true diversity, that is an effective number of species or communities.

Estimators of α‐ and β‐entropy, phylogenetic and functional entropy are provided.

Proper definition and estimation of diversity is the first step towards better understanding its underlying ecological and evolutionary mechanisms.
Liver surgery in the multidisciplinary management of gastrointestinal stromal tumour
Authors: Cananzi Ferdinando C. M. , Belgaumkar Ajay , Lorenzi Bruno , Mudan Satvinder 
Published: December 2014

AbstractBackgroundAfter the introduction of tyrosine kinase inhibitors (TKIs), the role of surgical resection in treating liver metastasis from gastrointestinal stromal tumour (GIST) is unclear. In this study, we evaluated the outcome of patients treated with TKIs followed by surgery for metastatic GIST.MethodsEleven patients who underwent liver resection after downsizing TKIs therapy for metastatic GIST from 2006 until 2010 were reviewed.ResultsOne and 2‐year overall survival (OS) rates were 80.8% and 70.7%. All patients with an initially resectable tumour were still alive without recurrence. Patients operated on clinical response had a better outcome (1‐year and 2‐year OS rate of 100%) than those operated on disease progression (1‐year and 2‐year OS rates of 60% and 40%; P = 0.043). No deaths were observed among patients who achieved an R0 resection (R0 versus R1/R2, P = 0.001).ConclusionR0 resection and clinical response to TKI are predictors of survival. Surgical resection should be performed as soon as feasible in responder patients. In poor responders, surgery may not add any survival benefit, except in localized progressive disease. In resectable metastatic liver disease, preoperative TKIs or upfront surgery followed by adjuvant therapy could be considered. Larger studies are needed to determine the optimum approach in patients with metastatic GIST.
Measures of precision for dissimilarity‐based multivariate analysis of ecological communities
Authors: Anderson Marti J. , Santana‐Garcon Julia 
Published: December 2014

AbstractEcological studies require key decisions regarding the appropriate size and number of sampling units. No methods currently exist to measure precision for multivariate assemblage data when dissimilarity‐based analyses are intended to follow. Here, we propose a pseudo multivariate dissimilarity‐based standard error (MultSE) as a useful quantity for assessing sample‐size adequacy in studies of ecological communities. Based on sums of squared dissimilarities, MultSE measures variability in the position of the centroid in the space of a chosen dissimilarity measure under repeated sampling for a given sample size. We describe a novel double resampling method to quantify uncertainty in MultSE values with increasing sample size. For more complex designs, values of MultSE can be calculated from the pseudo residual mean square of a permanova model, with the double resampling done within appropriate cells in the design. R code functions for implementing these techniques, along with ecological examples, are provided.
Intrafollicular treatment with prostaglandins PGE2 and PGF2α inhibits the formation of luteinised unruptured follicles and restores normal ovulation in mares treated with flunixin‐meglumine
Authors: Martínez‐Boví R. , Cuervo‐Arango J. 
Published: December 2014

SummaryReasons for performing studyHaemorrhagic anovulatory follicle is the most common pathological anovulatory condition in the mare, but its cause remains unknown. An experimental model to induce luteinised unruptured follicles (LUF) with flunixin‐meglumine (FM) has been developed. Luteinised unruptured follicles share similar morphological and hormonal characteristics with haemorrhagic anovulatory follicles.ObjectivesTo test the effect of intrafollicular administration of prostaglandins PGE2 and PGF2α during the periovulatory period on ovulation and pregnancy in FM‐treated mares.Study designIn vivo experiment in a crossover design.MethodsFive mares were followed during 2 oestrous cycles each. All mares were given FM at 1.7 mg/kg bwt i.v. every 12 h from Hour 0 (Hour 0 = human chorionic gonadotrophin treatment) to Hour 36. In treatment cycles (n = 5), at Hour 32 the preovulatory follicle was punctured and 0.5 ml of a solution containing 500 μg of PGE2 and 125 μg of PGF2α was deposited within the follicle. In control cycles, water for injection was administered into the follicle at the same time. In 3 control and 3 treatment cycles, mares were also inseminated at Hour 24. Diagnosis of ovulation/LUF formation and pregnancy was performed by ultrasound examination between Hours 36 and 72 and 14 days after ovulation/LUF formation, respectively.ResultsDuring the treatment cycles, all mares ovulated normally (100% ovulation rate) 36–48 h after human chorionic gonadotrophin, while in 4 of 5 control cycles the mares developed an LUF (80%, P<0.05). All 3 inseminated mares became pregnant in the treatment cycles, but not in the control cycles.ConclusionsIntrafollicular treatment with PGE2 and PGF2α overcame the anovulatory effect of FM. This sheds new insights into the knowledge on the possible therapeutic options for ovulatory failure in the mare.
Melioidosis in a patient on monoclonal antibody therapy for psoriatic arthritis
Authors: Commons R. J. , Grivas R. , Currie B. J. 
Published: December 2014

AbstractMelioidosis is caused by the environmental bacterium Burkholderia pseudomallei and can present with severe sepsis. Predisposing risk factors are present in 80% of cases. Monoclonal antibodies are increasingly prescribed for varied medical conditions. This report describes the first known case of melioidosis in a patient whose only risk factor for disease is treatment with a monoclonal antibody. Prescribers of monoclonal antibodies and other immunosuppressants should ensure that their patients are aware of the potential risk of melioidosis prior to travel and the precautions that should be taken.
The human microbiome: opportunities and challenges for clinical care
Authors: Rogers G. B. 
Published: December 2014

AbstractThere is a growing appreciation of the importance of the human microbiome to our normal physiology. This complex microbial ecosystem plays a range of roles, including influencing the development and function of our immune systems, providing essential nutrients, regulating metabolism and protecting us from opportunistic infections. Our increasing understanding of these processes is due, to a large extent, to the development of high‐throughput sequencing technologies, providing for the first time a means by which complex microbial dynamics can be detailed. There is also a growing recognition that disruption of commensal microbiota, a phenomenon known as dysbiosis, is associated with several common disorders, including inflammatory bowel disease, type 2 diabetes and oncogenesis. Further, where innate immunity fails to protect us, the microbial communities that colonise the external surfaces of our bodies represent a ready source of infection. This review discusses the mechanisms that govern our interaction with our resident microbiota, both in health and disease, the technological advances that allow us to gain insight into these relationships, and the way in which our growing understanding can inform clinical practice.
Effects of viewing 9/11 footage on distress andIslamophobia: a temporally expanded approach
Authors: Choma Becky L. , Charlesford Jaysan J. , Dalling Leah , Smith Kirsty 
Published: December 2014

AbstractWe investigated whether viewing September 11 footage affected peoples’ perceived distress spanning past, present, and anticipated future. Participants (n= 174) were randomly assigned to a 9/11, fear, or neutral condition and completed measures of temporal perceived distress, distress of future terrorism, Islamophobia, and restriction of civil liberties attitudes. Participants in the neutral and fear conditions perceived their 9/11‐related distress as declining over time. Those in the 9/11 condition perceived their distress as higher at present and declining from present (vs. past ratings). Those viewing 9/11 (vs. neutral or fear) footage reported greater future terrorism distress, more prejudice, and greater restriction of civil liberties. These differences were explained by higher 9/11‐related distress ratings for past 5 years, present, and future.
The Influence of Sexual Orientation and Sexual Role on Male Grooming-Related Injuries and Infections
Authors: Gaither Thomas W. , Truesdale Matthew , Harris Catherine R. , Alwaal Amjad , Shindel Alan W. , Allen Isabel E. , Breyer Benjamin N. 
Published: December 2014

ABSTRACT

Aim
Pubic hair grooming is a common practice in the United States and coincides with prevalence of grooming-related injuries. Men who have sex with men (MSM) groom more frequently than men who have sex with women (MSW). We aim to characterize the influence of sexual orientation and sexual role on grooming behavior, injuries, and infections in men in the United States.

Methods
We conducted a nationally representative survey of noninstitutionalized adults aged 18–65 residing in the United States. We examined the prevalence and risk factors of injuries and infections that occur as a result of personal grooming.

Results
Of the 4,062 men who completed the survey, 3,176 (78.2%) report having sex with only women (MSW), 198 (4.9%) report sex with men (MSM), and 688 (16.9%) report not being sexually active. MSM are more likely to groom (42.5% vs. 29.0%, P &lt; 0.001) and groom more around the anus, scrotum, and penile shaft compared with MSW. MSM receptive partners groom more often (50.9% vs. 26.9%, P = 0.005) and groom more for sex (85.3% vs. 51.9%, P &lt; 0.001) compared with MSM insertive partners. MSM report more injuries to the anus (7.0% vs. 1.0%, P &lt; 0.001), more grooming-related infections (7.0% vs. 1.0%, P &lt; 0.001) and abscesses (8.8% vs. 2.5%, P = 0.010), as well as lifetime sexually transmitted infections (STIs) (1.65 vs. 1.45, P = 0.038) compared with MSW. More receptive partners report grooming at the time of their STI infection (52.2% vs. 14.3%, P &lt; 0.001) compared with insertive partners.

Conclusions
Sexual orientation, and in particular sexual role, may influence male grooming behavior and impact grooming-related injuries and infections. Anogenital grooming may put one at risk for an STI. Healthcare providers should be aware of different grooming practices in order to better educate safe depilatory practices (i.e., the use of electric razors for anogenital grooming) in patients of all sexual orientations.
Elevation of 8‐hydroxy‐2′‐deoxyguanosine in the cerebrospinal fluid of three patients with superficial siderosis
Authors: Ozaki Kokoro , Sanjo Nobuo , Ishikawa Kinya , Higashi Miwa , Hattori Takaaki , Tanuma Naoyuki , Miyata Rie , Hayashi Masaharu , Yokota Takanori , Okawa Atsushi , Mizusawa Hidehiro 
Published: December 2014

AbstractSuperficial siderosis is a progressive disorder of the central nervous system in which chronic intrathecal bleeding leads to hemosiderin deposition in the brain and spinal cord. Although it is hypothesized that oxidative stress caused by deposited iron contributes to the pathomechanism of superficial siderosis, there is a paucity of research supporting this hypothesis. We examined the cerebrospinal fluid of three patients with superficial siderosis for the oxidative stress marker 8‐hydroxy‐2′‐deoxyguanosine. The origin of bleeding was identified in two of the three patients, who subsequently underwent surgical treatment. We detected elevated 8‐hydroxy‐2′‐deoxyguanosine levels in the cerebrospinal fluid of all three patients that remained high in two patients, even after surgical treatment. Elevated 8‐hydroxy‐2′‐deoxyguanosine levels suggest that oxidative stress is involved in the pathomechanism of superficial siderosis.
BURSTING POLLEN is required to organize the pollen germination plaque and pollen tube tip in Arabidopsis thaliana
Authors: Hoedemaekers Karin , Derksen Jan , Hoogstrate Suzanne W. , Wolters‐Arts Mieke , Oh Sung‐Aeong , Twell David , Mariani Celestina , Rieu Ivo 
Published: December 2014

Summary

Pollen germination may occur via the so‐called germination pores or directly through the pollen wall at the site of contact with the stigma. In this study, we addressed what processes take place during pollen hydration (i.e. before tube emergence), in a species with extra‐poral pollen germination, Arabidopsis thaliana.

A T‐DNA mutant population was screened by segregation distortion analysis. Histological and electron microscopy techniques were applied to examine the wild‐type and mutant phenotypes.

Within 1 h of the start of pollen hydration, an intine‐like structure consisting of cellulose, callose and at least partly de‐esterified pectin was formed at the pollen wall. Subsequently, this ‘germination plaque’ gradually extended and opened up to provide passage for the cytoplasm into the emerging pollen tube. BURSTING POLLEN (BUP) was identified as a gene essential for the correct organization of this plaque and the tip of the pollen tube. BUP encodes a novel Golgi‐located glycosyltransferase related to the glycosyltransferase 4 (GT4) subfamily which is conserved throughout the plant kingdom.

Extra‐poral pollen germination involves the development of a germination plaque and BUP defines the correct plastic‐elastic properties of this plaque and the pollen tube tip by affecting pectin synthesis or delivery.
Leaf morphology of 40 evergreen and deciduous broadleaved subtropical tree species and relationships to functional ecophysiological traits
Authors: Kröber W. , Heklau H. , Bruelheide H. 
Published: December 2014

AbstractWe explored potential of morphological and anatomical leaf traits for predicting ecophysiological key functions in subtropical trees. We asked whether the ecophysiological parameters stomatal conductance and xylem cavitation vulnerability could be predicted from microscopy leaf traits. We investigated 21 deciduous and 19 evergreen subtropical tree species, using individuals of the same age and from the same environment in the Biodiversity‐Ecosystem Functioning experiment at Jiangxi (BEF‐China). Information‐theoretic linear model selection was used to identify the best combination of morphological and anatomical predictors for ecophysiological functions. Leaf anatomy and morphology strongly depended on leaf habit. Evergreen species tended to have thicker leaves, thicker spongy and palisade mesophyll, more palisade mesophyll layers and a thicker subepidermis. Over 50% of all evergreen species had leaves with multi‐layered palisade parenchyma, while only one deciduous species (Koelreuteria bipinnata) had this. Interactions with leaf habit were also included in best multi‐predictor models for stomatal conductance (gs) and xylem cavitation vulnerability. In addition, maximum gs was positively related to log ratio of palisade to spongy mesophyll thickness. Vapour pressure deficit (vpd) for maximum gs increased with the log ratio of palisade to spongy mesophyll thickness in species having leaves with papillae. In contrast, maximum specific hydraulic conductivity and xylem pressure at which 50% loss of maximum specific xylem hydraulic conductivity occurred (Ψ50) were best predicted by leaf habit and density of spongy parenchyma. Evergreen species had lower Ψ50 values and lower maximum xylem hydraulic conductivities. As hydraulic leaf and wood characteristics were reflected in structural leaf traits, there is high potential for identifying further linkages between morphological and anatomical leaf traits and ecophysiological responses.
Increasing substrate heterogeneity as a bet‐hedging strategy for restoring wetland vegetation
Authors: Doherty James M. , Zedler Joy B. 
Published: December 2014

AbstractMimicking the natural heterogeneity of wetland substrates, e.g. by roughening surface soil or constructing hummocks, has been shown to facilitate wetland plant establishment. We asked if incorporating substrate heterogeneity could also help plants withstand variation in moisture levels. In a wetland with Carex stricta (tussock sedge) as the main restoration target, we manipulated substrates to create different soil moisture environments for planted C. stricta plugs. Our artificial mounds mimicked tussocks formed by C. stricta in natural meadows (circa 10–40 cm in height); we also varied mound compositions and created shallow depressions. Monitoring demonstrated variation in soil moisture among our treatments and natural differences in soil moisture between experimental blocks. Additionally, rainfall varied from severe drought in year 1 to extreme rainfall in year 2. Plug survival, flowering, cover, biomass, leaf length, and growth rate all varied with treatment, block, and/or year. Interactions among those factors were common. Planting plugs in shallow depressions exacerbated stress in a wet block during a wet year, causing low survival. Planting plugs in moisture‐retaining peat pots allowed them to survive and sustain growth even in a dry block during a dry year. We conclude that heterogeneous substrates can be used to hedge against environmental variability by widening the range of microsites available within a restoration site and thereby moderating stressful conditions in some areas.
Need for certification of household water treatment products: examples from Haiti
Authors: Murray Anna , Pierre‐Louis Jocelyne , Joseph Flaurine , Sylvain Ginelove , Patrick Molly , Lantagne Daniele 
Published: December 2014

AbstractObjectiveTo evaluate four household water treatment (HWT) products currently seeking approval for distribution in Haiti, through the application of a recently‐developed national HWT product certification process.MethodsFour chemical treatment products were evaluated against the certification process validation stage by verifying international product certifications confirming treatment efficacy and reviewing laboratory efficacy data against WHO HWT microbiological performance targets; and against the approval stage by confirming product composition, evaluating treated water chemical content against national and international drinking water quality guidelines and reviewing packaging for dosing ability and usage directions in Creole.ResultsNone of the four evaluated products fulfilled validation or approval stage requirements. None was certified by an international agency as efficacious for drinking water treatment, and none had data demonstrating its ability to meet WHO HWT performance targets. All product sample compositions differed from labelled composition by >20%, and no packaging included complete usage directions in Creole.ConclusionsProduct manufacturers provided information that was inapplicable, did not demonstrate product efficacy, and was insufficient to ensure safe product use. Capacity building is needed with country regulatory agencies to objectively evaluate HWT products. Products should be internationally assessed against WHO performance targets and also locally approved, considering language, culture and usability, to ensure effective HWT.
Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage
Authors: Gruber Ansgar , Rocap Gabrielle , Kroth Peter G. , Armbrust E. Virginia , Mock Thomas 
Published: December 2014

SummaryThe plastids of ecologically and economically important algae from phyla such as stramenopiles, dinoflagellates and cryptophytes were acquired via a secondary endosymbiosis and are surrounded by three or four membranes. Nuclear‐encoded plastid‐localized proteins contain N‐terminal bipartite targeting peptides with the conserved amino acid sequence motif ‘ASAFAP’. Here we identify the plastid proteomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum, using a customized prediction tool (ASAFind) that identifies nuclear‐encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved ‘ASAFAP’ motifs and transit peptides. We tested ASAFind against a large reference dataset of diatom proteins with experimentally confirmed subcellular localization and found that the tool accurately identified plastid‐localized proteins with both high sensitivity and high specificity. To identify nucleus‐encoded plastid proteins of T. pseudonana and P. tricornutum we generated optimized sets of gene models for both whole genomes, to increase the percentage of full‐length proteins compared with previous assembly model sets. ASAFind applied to these optimized sets revealed that about 8% of the proteins encoded in their nuclear genomes were predicted to be plastid localized and therefore represent the putative plastid proteomes of these algae.