bluuebunny/crossref_metadata_2025_split huggingface dataset:
An automated approach to identifying search terms for systematic reviews using keyword co‐occurrence networks
Authors: Grames Eliza M. , Stillman Andrew N. , Tingley Morgan W. , Elphick Chris S. 
Published: July 2019

Abstract

Systematic review, meta‐analysis and other forms of evidence synthesis are critical to strengthen the evidence base concerning conservation issues and to answer ecological and evolutionary questions. Synthesis lags behind the pace of scientific publishing, however, due to time and resource costs which partial automation of evidence synthesis tasks could reduce. Additionally, current methods of retrieving evidence for synthesis are susceptible to bias towards studies with which researchers are familiar. In fields that lack standardized terminology encoded in an ontology, including ecology and evolution, research teams can unintentionally exclude articles from the review by omitting synonymous phrases in their search terms.

To combat these problems, we developed a quick, objective, reproducible method for generating search strategies that uses text mining and keyword co‐occurrence networks to identify the most important terms for a review. The method reduces bias in search strategy development because it does not rely on a predetermined set of articles and can improve search recall by identifying synonymous terms that research teams might otherwise omit.

When tested against the search strategies used in published environmental systematic reviews, our method performs as well as the published searches and retrieves gold‐standard hits that replicated versions of the original searches do not. Because the method is quasi‐automated, the amount of time required to develop a search strategy, conduct searches, and assemble results is reduced from approximately 17–34 hr to under 2 hr.

To facilitate use of the method for environmental evidence synthesis, we implemented the method in the R package litsearchr, which also contains a suite of functions to improve efficiency of systematic reviews by automatically deduplicating and assembling results from separate databases.
Overcoming the challenge of small effective sample sizes in home‐range estimation
Authors: Fleming Christen H. , Noonan Michael J. , Medici Emilia Patricia , Calabrese Justin M. 
Published: July 2019

AbstractTechnological advances have steadily increased the detail of animal tracking datasets, yet fundamental data limitations exist for many species that cause substantial biases in home‐range estimation. Specifically, the effective sample size of a range estimate is proportional to the number of observed range crossings, not the number of sampled locations. Currently, the most accurate home‐range estimators condition on an autocorrelation model, for which the standard estimation frame‐works are based on likelihood functions, even though these methods are known to underestimate variance—and therefore ranging area—when effective sample sizes are small.Residual maximum likelihood (REML) is a widely used method for reducing bias in maximum‐likelihood (ML) variance estimation at small sample sizes. Unfortunately, we find that REML is too unstable for practical application to continuous‐time movement models. When the effective sample sizeNis decreased toN ≤ (10), which is common in tracking applications, REML undergoes a sudden divergence in variance estimation. To avoid this issue, while retaining REML’s first‐order bias correction, we derive a family of estimators that leverage REML to make a perturbative correction to ML. We also derive AIC values for REML and our estimators, including cases where model structures differ, which is not generally understood to be possible.Using both simulated data and GPS data from lowland tapir (Tapirus terrestris), we show how our perturbative estimators are more accurate than traditional ML and REML methods. Specifically, when(5) home‐range crossings are observed, REML is unreliable by orders of magnitude, ML home ranges are ~30% underestimated, and our perturbative estimators yield home ranges that are only ~10% underestimated. A parametric bootstrap can then reduce the ML and perturbative home‐range underestimation to ~10% and ~3%, respectively.Home‐range estimation is one of the primary reasons for collecting animal tracking data, and small effective sample sizes are a more common problem than is currently realized. The methods introduced here allow for more accurate movement‐model and home‐range estimation at small effective sample sizes, and thus fill an important role for animal movement analysis. Given REML’s widespread use, our methods may also be useful in other contexts where effective sample sizes are small.
Neutrophil activation in septic acute kidney injury: A post hoc analysis of the FINNAKI study
Authors: Törnblom Sanna , Nisula Sara , Vaara Suvi T. , Poukkanen Meri , Andersson Sture , Pettilä Ville , Pesonen Eero 
Published: July 2019

BackgroundInflammation, reflected by high plasma interleukin‐6 concentration, is associated with acute kidney injury (AKI) in septic patients. Neutrophil activation has pathophysiological significance in experimental septic AKI. We hypothesized that neutrophil activation is associated with AKI in critically ill sepsis patients.MethodsWe measured plasma (n = 182) and urine (n = 118) activin A (a rapidly released cytosolic neutrophil protein), interleukin‐8 (a chemotactic factor for neutrophils), myeloperoxidase (a neutrophil biomarker released in tissues), and interleukin‐6 on intensive care unit admission (plasma and urine) and 24 hours later (plasma) in sepsis patients manifesting their first organ dysfunction between 24 hours preceding admission and the second calendar day in intensive care unit. AKI was defined by the Kidney Disease: Improving Global Outcomes criteria.ResultsPlasma admission interleukin‐8 (240 [60‐971] vs 50 [19‐164] pg/mL, P < .001) and activin A (845 [554‐1895] vs 469 [285‐862] pg/mL, P < .001) were but myeloperoxidase (169 [111‐300] vs 144 [88‐215] ng/mL, P = .059) was not higher among patients with AKI compared with those without. Urine admission interleukin‐8 (50.4 [19.8‐145.3] vs 9.5 [2.7‐28.7] ng/mL, P < .001) and myeloperoxidase (7.7 [1.5‐12.6] vs 1.9 [0.4‐6.9] ng/mL, P < .001) were but activin A (9.7 [1.4‐42.6] vs 4.0 [0.0‐33.0] ng/mL, P = .064) was not higher in AKI than non‐AKI patients. Urine myeloperoxidase correlated with urine interleukin‐8 (R = .627, P < .001) but not with plasma myeloperoxidase (R = .131, P = .158).ConclusionInterleukin‐8 in plasma and urine was associated with septic AKI. Elevated plasma activin A indicates intravascular neutrophil activation in septic AKI. Concomitant plasma and urine myeloperoxidase measurements suggest neutrophil accumulation into injured kidneys.
Meta‐analysis of natural, unnatural and cause‐specific mortality rates following discharge from in‐patient psychiatric facilities
Authors: Swaraj S. , Wang M. , Chung D. , Curtis J. , Firth J. , Ramanuj P. P. , Sara G. , Large M. 
Published: July 2019

BackgroundPeople discharged from in‐patient psychiatric facilities have highly elevated rates of suicide, and there is increasing concern about natural mortality among the seriously mentally ill.MethodA meta‐analysis of English‐language, peer‐reviewed longitudinal studies of mortality among patients discharged from in‐patient psychiatric facilities was conducted using papers published in MEDLINE, PsycINFO or EMBASE (from 1 January 1960 to 1 April 2018) located using the terms ((suicid*).ti AND (hospital OR discharg* OR inpatient OR in‐patient OR admit*)).ab and ((mortality OR outcome* OR death*) AND (psych* OR mental*)).ti AND (admit* OR admis* OR hospital* OR inpatient* OR in‐patient* OR discharg*).ab. Pooled mortality rates for aggregated natural and unnatural causes, and the specific causes of suicide, accident, homicide, vascular, neoplastic, respiratory, gastrointestinal, infectious and metabolic death were calculated using a random‐effects meta‐analytic model. Between‐study heterogeneity was investigated using subgroup analysis and metaregression.ResultsThe pooled natural death rate of 1128 per 100 000 person‐years exceeded the pooled unnatural deaths of 479 per 100 000 person‐year among studies with varying periods of follow‐up. Natural deaths significantly exceeded unnatural deaths among studies with a mean follow‐up of longer than 2 years, and vascular deaths exceeded suicide deaths among studies with mean period of follow‐up of 5 years or longer.ConclusionSuicide may be the largest single cause of death in the short term after discharge from in‐patient psychiatric facilities but vascular disease is the major cause of mortality in the medium‐ and long‐term.
Poor management in protected areas is associated with lowered tropical mammal diversity
Authors: Oberosler V. , Tenan S. , Zipkin E. F. , Rovero F. 
Published: July 2019

AbstractNumerous protected areas (PAs) have been created worldwide to safeguard wildlife and other natural resources from anthropogenic threats such as habitat destruction and bushmeat hunting. However, conservation efforts in many tropical PAs are still inadequate, revealing deficiencies in management effectiveness. It is therefore important to quantify how different protection regimes impact wildlife within PAs. We investigated the differences between forest mammal communities in two ecologically comparable PAs in the Udzungwa Mountains (Tanzania) with contrasting management regimes. One is a well‐protected national park with efficient law enforcement; the other has suffered decades of inadequate protection, mainly resulting in high levels of illegal hunting. Using camera‐trapping data, we assessed the target communities in terms of species richness, functional composition (i.e. proportions of trophic guilds) and species‐specific occurrences, all while accounting for imperfect detection. We found striking differences between the two mammal communities: lower species richness, alteration in the trophic structure and reduced occurrence probabilities for most species in the forest with high disturbance. The difference in occurrence probability between the two PAs tended to be highest for larger‐bodied species. Our results show that strictly enforced legal protection is required to maintain diverse mammal communities in tropical forests under ever‐increasing anthropogenic threats. While PAs are the cornerstone of efforts to conserve tropical biodiversity, the future of biodiversity within them is closely tied to the effectiveness of enforcement.
Drivers affecting mammal community structure and functional diversity under varied conservation efforts in a tropical rainforest in Cameroon
Authors: Laméris D. W. , Tagg N. , Kuenbou J. K. , Sterck E. H. M. , Willie J. 
Published: July 2019

AbstractAs well as leading to a loss of biodiversity (i.e. species richness and abundance), human activities also affect ecosystem functioning. Documenting how the suite of ecological roles changes following disturbance provides a complementary source of information for conservation management. To this end, we measured mammal diversity in terms of community structure (i.e. abundance, composition and species richness) and functional diversity in three sites differing in conservation effort in a tropical rainforest in Cameroon. Results show that sites without primary or secondary conservation efforts had lower mammal abundances and an altered mammal composition but similar species richness compared to better‐protected areas. In terms of functional diversity, we found more variation of traits (i.e. FDis) in the site with primary conservation and higher abundances of functionally unique species (i.e. FOri) in sites with either primary or secondary conservation efforts. We found no overall difference in the abundance of specialist and generalist species between sites (i.e. FSpe). We identified several drivers affecting abundance, species richness and functional diversity of mammal communities, although there did not appear to be a common driver affecting all mammal diversity measures in a similar way. Our results suggest that, in addition to preserving mammal abundance and community composition, conservation efforts (both primary and secondary) are able to contribute to maintaining higher levels of functional diversity compared to areas devoid of conservation. We demonstrate that functional diversity metrics can provide valuable additional information about the status of mammal communities that can be used to better inform conservation management.
Accumbens neuroimmune signaling and dysregulation of astrocytic glutamate transport underlie conditioned nicotine‐seeking behavior
Authors: Namba Mark D. , Kupchik Yonatan M. , Spencer Sade M. , Garcia‐Keller Constanza , Goenaga Julianna G. , Powell Gregory L. , Vicino Ian A. , Hogue Ian B. , Gipson Cassandra D. 
Published: July 2019

AbstractNicotine self‐administration is associated with decreased expression of the glial glutamate transporter (GLT‐1) and the cystine‐glutamate exchange protein xCT within the nucleus accumbens core (NAcore). N‐acetylcysteine (NAC) has been shown to restore these proteins in a rodent model of drug addiction and relapse. However, the specific molecular mechanisms driving its inhibitory effects on cue‐induced nicotine reinstatement are unknown. Here, we confirm that extinction of nicotine‐seeking behavior is associated with impaired NAcore GLT‐1 function and expression and demonstrates that reinstatement of nicotine seeking rapidly enhances membrane fraction GLT‐1 expression. Extinction and cue‐induced reinstatement of nicotine seeking was also associated with increased tumor necrosis factor alpha (TNFα) and decreased glial fibrillary acidic protein (GFAP) expression in the NAcore. NAC treatment (100 mg/kg/day, i.p., for 5 d) inhibited cue‐induced nicotine seeking and suppressed AMPA to NMDA current ratios, suggesting that NAC reduces NAcore postsynaptic excitability. In separate experiments, rats received NAC and an antisense vivo‐morpholino to selectively suppress GLT‐1 expression in the NAcore during extinction and were subsequently tested for cue‐induced reinstatement of nicotine seeking. NAC treatment rescued NAcore GLT‐1 expression and attenuated cue‐induced nicotine seeking, which was blocked by GLT‐1 antisense. NAC also reduced TNFα expression in the NAcore. Viral manipulation of the NF‐κB pathway, which is downstream of TNFα, revealed that cue‐induced nicotine seeking is regulated by NF‐κB pathway signaling in the NAcore independent of GLT‐1 expression. Ultimately, these results are the first to show that immunomodulatory mechanisms may regulate known nicotine‐induced alterations in glutamatergic plasticity that mediate cue‐induced nicotine‐seeking behavior.
Effects of repetitive transcranial magnetic stimulation (rTMS) on craving and substance consumption in patients with substance dependence: a systematic review and meta‐analysis
Authors: Zhang Jack J. Q. , Fong Kenneth N. K. , Ouyang Rang‐ge , Siu Andrew M. H. , Kranz Georg S. 
Published: July 2019

AbstractBackground and AimsRepetitive transcranial magnetic stimulation (rTMS) is increasingly used as an intervention for treating substance dependence. We aimed to assess evidence of the anti‐craving and consumption‐reducing effects of rTMS in patients with alcohol, nicotine and illicit drug dependence.MethodsA systematic review and meta‐analysis of 26 randomized controlled trials (RCTs) published from January 2000 to October 2018 that investigated the effects of rTMS on craving and substance consumption in patients with nicotine, alcohol and illicit drug dependence (n = 748). Craving, measured using self‐reported questionnaires or visual analog scale, and substance consumption, measured using self‐report substance intake or number of addiction relapse cases, were considered as primary and secondary outcomes, respectively. Substance type, study design and rTMS parameters were used as the independent factors in the meta‐regression.ResultsResults showed that excitatory rTMS of the left dorsolateral pre‐frontal cortex (DLPFC) significantly reduced craving [Hedges' g = −0.62; 95% confidence interval (CI) = −0.89 to −0.35; P < 0.0001], compared with sham stimulation. Moreover, meta‐regression revealed a significant positive association between the total number of stimulation pulses and effect size among studies using excitatory left DLPFC stimulation (P = 0.01). Effects of other rTMS protocols on craving were not significant. However, when examining substance consumption, excitatory rTMS of the left DLPFC and excitatory deep TMS (dTMS) of the bilateral DLPFC and insula revealed significant consumption‐reducing effects, compared with sham stimulation.ConclusionExcitatory repetitive transcranial magnetic stimulation of the dorsolateral pre‐frontal cortex appears to have an acute effect on reducing craving and substance consumption in patients with substance dependence. The anti‐craving effect may be associated with stimulation dose.
The collectivity of British alcohol consumption trends across different temporal processes: a quantile age–period–cohort analysis
Authors: Holmes John , Ally Abdallah K. , Meier Petra S. , Pryce Robert 
Published: July 2019

AbstractBackground and aimsUK alcohol consumption per capita has fallen by 18% since 2004, while the alcohol‐specific death rate has risen by 6%. Inconsistent consumption trends across the population may explain this. Drawing on the theory of the collectivity of drinking cultures and age–period–cohort analyses, we tested whether consumption trends are consistent across lighter and heavier drinkers for three temporal processes: (i) the life‐course, (ii) calendar time and (iii) successive birth cohorts.DesignSex‐specific quantile age–period–cohort regressions using repeat cross‐sectional survey data.SettingGreat Britain, 1984–2011.ParticipantsAdult (18+) drinkers responding to 17 waves of the General Lifestyle Survey (total n = 175 986).MeasurementsDependent variables: the 10th, 25th, 50th, 75th, 90th, 95th and 99th quantiles of the logged weekly alcohol consumption distribution (excluding abstainers). Independent variables: seven age groups (18–24, 25–34… 65–74, 75+ years), five time‐periods (1984–88… 2002–06, 2008–11) and 16 five‐year birth cohorts (1915–19… 1990–94). Additional control variables: ethnicity and UK country.FindingsWithin age, period and cohort trends, changes in consumption were not consistently in the same direction at different quantiles of the consumption distribution. When they were, the scale of change sometimes differed between quantiles. For example, between 1996‐2000 and 2008‐2011, consumption among women decreased by 18% [95% confidence interval (CI) = −32 to –2%] at the 10th quantile but increased by 11% (95% CI = 2–21%) at the median and by 28% (95% CI = 19–38%) at the 99th quantile, implying that consumption fell among lighter drinkers and rose among heavier drinkers. This type of polarized trend also occurred between 1984–88 and 1996–2000 for men and women. Age trends showed collectivity, but cohort trends showed a mixture of collectivity and polarization.ConclusionsCountervailing alcohol consumption and alcohol‐related harm trends in the United Kingdom may be explained by lighter and heavier drinkers having different period and cohort trends, as well as by the presence of cohort trends that mean consumption may rise in some age groups while falling in others.
Carious lesion management in children and adolescents by Australian dentists
Authors: Keys T , Burrow MF , Rajan S , Rompre P , Doméjean S , Muller‐Bolla M , Manton DJ 
Published: July 2019

AbstractBackgroundThe management of carious lesions in children and adolescents can have lifelong implications for the patient. The aim of this study was to assess the decision‐making process of dentists when managing carious lesions in children and adolescents.MethodsApproximately, 11 000 dentists listed as members of the Australian Dental Association Inc. (ADA) and Australian and New Zealand Society of Paediatric Dentistry (ANZSPD) were emailed a link in April 2017 to a 19‐question survey delivered by SurveyMonkey™.ResultsIn this study, 887 responses were received. In ‘enamel‐limited’ carious lesions, dentists intervened most frequently in primary tooth approximal (365, 41.1%), followed by permanent tooth occlusal (295, 33.3%) and approximal (244, 27.5%), and primary tooth occlusal (203, 22.9%) surface carious lesions. Age, university of graduation, practicing state, decade of graduation and frequency of treatment of children between 6 and 15 years were significant demographic factors influencing the restorative threshold.ConclusionsAustralian dentists reported significant variation in their management of approximal and occlusal carious lesions in both primary and permanent teeth. A substantial proportion of respondents would intervene surgically on non‐cavitated enamel‐limited lesions.
Extreme colour variation in the larvae of the executioner clownfrog, Dendropsophus carnifex (Anura: Hylidae), living in nearby ponds of different light exposure and duration
Authors: Pintanel Pol , Salinas‐Ivanenko Sofia , Gutiérrez‐Pesquera Luis Miguel , Almeida‐Reinoso Freddy , Merino‐Viteri Andrés , Tejedo Miguel 
Published: July 2019

AbstractHere, we describe the extreme plasticity in colour variation in the tadpole of the executioner clownfrog, Dendropsophus carnifex (Anura: Hylidae), found across nearby ponds in Mindo (Ecuador). Tadpole coloration was compared between individuals from four distinct ponds revealing two explicit colour schemes, a pale phenotype which is commonly described for this species and a bright phenotype which, to our knowledge, has not been described before. In addition, the bright phenotype revealed reversibility to the pale phenotype in laboratory conditions. We discuss the functionality and driving factors for these contrasting colour phenotypes including the potential role of distinct ecological conditions.Abstract in Spanish is available with online material.
Assembly patterns of tree seedling communities in a human‐dominated Tropical landscape
Authors: Menezes Tatiane G. C. , Melo Felipe P. L. 
Published: July 2019

AbstractUnderstanding how different components of species diversity of regenerating areas respond to both time of abandonment and landscape metrics may offer crucial information for both theoretical and practical purposes. Using 15 regeneration areas (from 4 to 30 years) and nine areas of mature forest, we assessed how tree seedling assemblage responds to time of abandonment and forest cover in terms of species diversity and taxonomic composition. We found that species diversity of seedlings responded positively to time of abandonment, but was not influence by forest cover. Diversity of rare and common species (0D and 1D, respectively) but not dominant species (2D) increased with time of abandonment, reaching reference values very quickly (ca. 20 years). However, species composition seemed to respond to both ageing of forest stand and landscape structure represented by forest cover. Our findings reinforce that in human‐dominated landscapes, local processes related to recovery with time should be more important for plant community assembly than landscape structure, leading to a number of possibilities for multiple successional pathways.Abstract in Portuguese is available with online material.