bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ground‐truthing of a fish‐based environmental DNA metabarcoding method for assessing the quality of lakes
Authors: Li Jianlong , Hatton‐Ellis Tristan W. , Lawson Handley Lori‐Jayne , Kimbell Helen S. , Benucci Marco , Peirson Graeme , Hänfling Bernd 
Published: February 2019

Abstract

Accurate, cost‐effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive. Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non‐invasive method, which can provide semi‐quantitative information about fish communities in large lakes.

This study further investigated the potential of fish‐based eDNA metabarcoding as a tool for lake assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well‐described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA).

eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. Firstly, 24 species were detected, with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman's r = 0.74, df = 109, p < 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five‐level classification scale (‘DAFOR’). Lastly, four ecological fish communities were characterized using eDNA data which agree with the predefined lake types according to environmental characteristics.

Synthesis and applications. There are some limitations when using conventional captured‐based methods for surveying species richness and relative abundance, such as morphological identification bias, difficulties in recording small‐bodied, rare and/or elusive species and destructive impacts on the environment. This study provides further evidence that environmental DNA metabarcoding outperforms other captured‐based survey techniques in a wide range of lake types for community‐level analysis whether in species detection, relative abundance estimate using the standard five‐level classification scale or characterization ecological fish communities. Therefore, the fish‐based environmental DNA metabarcoding, a non‐invasive genetic method, has great potential as an assessment tool for lake quality under the European Water Framework Directive.
The mechanisms affecting seedling establishment in restored savanna understories are seasonally dependent
Authors: Sorenson Quinn M. , Damschen Ellen I. 
Published: February 2019

AbstractAgricultural land is being increasingly abandoned on a global scale, with over 200 million hectares recovering from agricultural use. Plant community regeneration differs greatly in structure and composition after agricultural impacts, yet the mechanisms underpinning these dramatic changes are poorly understood. It is critical to determine the relative importance of abiotic and biotic factors that limit plant establishment and success during the recovery process. In particular, below‐ground competition for resources in soils affected by former agricultural uses may play an important role in limiting plant establishment. Yet, below‐ground competition is generally studied less than above‐ground, especially in the context of land‐use history.We compare plant establishment with and without below‐ground competition in the context of a large‐scale experiment manipulating land‐use histories (i.e. with and without a history of agriculture) and restoration of historical vegetation structure (i.e. thinned and unthinned canopy trees) and determine how life stage and the local environment (e.g. soil water holding capacity, vegetation cover) influence this relationship.For three of our four target species, below‐ground competition strongly limited establishment success, but did not interact with land‐use history and canopy thinning directly. Instead, land‐use history and canopy thinning interacted to affect establishment during germination and survival in spring, while below‐ground competition limited growth during the summer. The strength of below‐ground competition was affected by local resources, but the directionality of this relationship depended on agricultural history and canopy thinning.Synthesis and applications. Because adding seeds increased establishment in all cases, we recommend confronting land‐use legacies by overcoming dispersal limitation with seed additions (even in degraded sites) and ensuring that below‐ground structures are managed during restoration, especially in summer. In addition, managers should consider how the relationship between local resources and below‐ground competition at individual sites might depend on land‐use history or canopy thinning.
Impacts of honeybee density on crop yield: A meta‐analysis
Authors: Rollin Orianne , Garibaldi Lucas A. 
Published: February 2019

Abstract

There is increasing recognition that pollination deficits are limiting crop yields world‐wide. However, management strategies for optimal insect pollination are still unclear for most crops. Current management focuses on providing high densities of honeybees, but recommended densities are highly variable, even within single crops and cultivars.

We performed an extensive literature search to record honeybee densities (colony density and/or flower visitation rates) and crop productivity (fruit set, seed set, fruit weight and/or yield). Effect sizes were represented as the difference in crop productivity between the two most extreme levels of honeybee densities.

Out of 795 reviewed studies, only 22 analysed the effect of at least two levels of honeybee densities on crop productivity (reporting 60 resulting effect sizes in total). Moreover, few recommendations for crop pollination management are based on results from controlled experimental designs, and with comparable methodology.

We found that both colony density and visitation rates increased all the productivity variables. However, effects were nonlinear for visitation rates, suggesting that there is an optimum (mean of 8–10 visits per flower) beyond which more honeybees are not beneficial (and can even be detrimental) for crop productivity.

Effect sizes for visitation rates were greater than that for colony densities, suggesting that visitation rates are a more direct measure of the pollination process. Data on the relation between colony density and visitation rates are lacking. Interestingly, effect sizes for visitation rates were greater for crops with separate sexes than those with hermaphroditic flowers; therefore, the benefits of honeybee pollination vary according to the crop biology.

Synthesis and applications. Current practices for crop pollination assume that more honeybees are always better for crop yield, even if the effect of this management on crop production still unclear. In contrast, our analyses suggest that there is an optimum for honeybee densities. Despite the importance of honeybees and pollinator‐dependent crops world‐wide, there is a lack of studies designed for finding such an optimal level of crop pollination. Our analyses further suggest that visitation rates could be used as a proxy to guide management recommendations such as colony density and spatial arrangement.
Metabolic syndrome and time to pregnancy: a retrospective study of nulliparous women
Authors: Grieger JA , Grzeskowiak LE , Smithers LG , Bianco‐Miotto T , Leemaqz SY , Andraweera P , Poston L , McCowan LM , Kenny LC , Myers J , Walker JJ , Norman RJ , Dekker GA , Roberts CT 
Published: February 2019

ObjectiveTo determine: (1) the association between metabolic syndrome (MetS), time to pregnancy (TTP), and infertility; (2) associations between individual and an increasing number of MetS components, TTP, and infertility; and (3) whether these relationships differ by body mass index (BMI < 30 kg/m2 versus BMI ≥ 30 kg/m2).DesignRetrospective cohort study.SettingMultiple centres (in Australia, Ireland, New Zealand, and the UK).PopulationFive thousand five hundred and nineteen low‐risk nulliparous pregnant women.MethodsData on retrospectively reported TTP (number of months to conceive) and a blood sample to assess metabolic health were collected between 14 and 16 weeks of gestation. MetS was defined according to the International Diabetes Federation criteria. Accelerated failure time models with log‐normal distribution were conducted to estimate time ratios (TRs) and 95% CIs. Differences in MetS on infertility (TTP > 12 months) were compared using a generalised linear model (Poisson distribution) with robust variance estimates (relative risks, RRs; 95% CIs). All analyses (entire cohort and split by BMI) were controlled for a range of maternal and paternal confounding factors.Main outcome measuresTime to pregnancy and infertility.ResultsOf the 5519 women included, 12.4% (n = 684) had MetS. Compared with women without MetS, women with MetS had a longer TTP (adjusted TR 1.30; 95% CI 1.15–1.46), which was similar in women who were obese and in women who were not obese. Marginal estimates for median TTP in women with MetS versus without MetS was 3.1 months (3.0–3.3 months) versus 4.1 months (3.6–4.5 months), respectively. Women with MetS were at a 62% greater risk for infertility and were at a greater risk for infertility whether they were obese (adjusted RR 1.62; 95% CI 1.15–2.29) or not (adjusted RR 1.73; 95% CI 1.33–2.23). Reduced high‐density lipoprotein cholesterol (HDL‐C) and raised triglycerides (TGs) were the main individual components associated with risk for infertility.ConclusionMetabolic syndrome is associated with longer TTP and infertility, independent of obesity. Additional studies, before pregnancy, are required to support our findings and to determine the applicability of which combinations of metabolic abnormalities pose the greatest risk to delayed fertility, or whether individual components are amenable to modification.Tweetable abstractMetabolic syndrome is associated with longer time to pregnancy and infertility, independent of obesity.
The Status of Forensic Anthropology in Europe and South Africa: Results of the 2016 FASE Questionnaire on Forensic Anthropology
Authors: Obertová Zuzana , Adalian Pascal , Baccino Eric , Cunha Eugenia , De Boer Hans H. , Fracasso Tony , Kranioti Elena , Lefévre Philippe , Lynnerup Niels , Petaros Anja , Ross Ann , Steyn Maryna , Cattaneo Cristina 
Published: February 2019

AbstractOne of the goals of the Forensic Anthropology Society of Europe (FASE) is to map the existing education and practice opportunities in the field of forensic anthropology in order to support the development of the discipline and to optimize the training courses provided by the Society. To address this goal, an online questionnaire was sent to European and South African practitioners of forensic anthropology and related disciplines in 2016. The results of the questionnaire showed that the status and roles of forensic anthropologists vary depending on the national legal systems, education, and employment status of the practitioners. Despite the fact that the expertise of forensic anthropologists has been increasingly requested in a variety of investigations and the spectrum of tasks has become broader, including identification of living persons, specialized education in forensic anthropology is still restricted to a few graduate and postgraduate programs in European countries and to annual FASE courses.
Natural language processing to identify ureteric stones in radiology reports
Authors: Li Andrew Yu , Elliot Nikki 
Published: February 2019

AbstractIntroductionNatural language processing (NLP) is an emerging tool which has the ability to automate data extraction from large volumes of unstructured text. One of the main described uses of NLP in radiology is cohort building for epidemiological studies. This study aims to assess the accuracy of NLP in identifying a group of patients positive for ureteric stones on Computed Tomography – Kidneys, Ureter, Bladder (CT KUB) reports.MethodsRetrospective review of all CT KUB reports in a single calendar year. A locally available NLP tool was used to automatically classify the reports based on positivity for ureteric stones. This was validated by manual review and refined to maximize the accuracy of stone detection.ResultsA total of 1874 CT KUB reports were identified. Manual classification of ureteric stone positivity was 36% compared with 27% using NLP. The accuracy of NLP was 85% with a sensitivity of 66% and specificity of 95%. Incorrect classification was due to misspellings, variable syntax, terminology, pluralization and the inability to exclude clinical request details from the search algorithm.ConclusionsOur NLP tool demonstrated high specificity but low sensitivity at identifying CT KUB reports that are positive for ureteric stones. This was attributable to the lack of feature extraction tools tailored for analysing radiology text, incompleteness of the medical lexicon database and heterogeneity of unstructured reports. Improvements in these areas will help improve data extraction accuracy.
I can see clearly now: Reinterpreting statistical significance
Authors: Dushoff Jonathan , Kain Morgan P. , Bolker Benjamin M. 
Published: February 2019

Abstract

Null hypothesis significance testing (NHST) remains popular despite decades of concern about misuse and misinterpretation. There are many recent suggestions for mitigating problems arising from NHST, including calls for abandoning NHST in favour of Bayesian or information‐theoretic approaches. We believe that NHST will continue to be widely used, and can be most usefully interpreted as a guide to whether a certain effect can be seen clearly in a particular context (e.g. whether we can clearly see that a correlation or between‐group difference is positive or negative).

We believe that much misinterpretation of NHST is due to language: significance testing has little to do with other meanings of the word ‘significance’. We therefore suggest that researchers describe the conclusions of null‐hypothesis tests in terms of statistical ‘clarity’ rather than ‘significance’. We illustrate our point by rewriting common misinterpretations of the meaning of statistical tests found in the literature using the language of ‘clarity’.

The meaning of statistical tests become easier to interpret and explain when viewed through the lens of ‘statistical clarity’.

Our suggestion is mild, but practical: this simple semantic change could enhance clarity in statistical communication.
Epigenetic age is a cell‐intrinsic property in transplanted human hematopoietic cells
Authors: Søraas Arne , Matsuyama Mieko , de Lima Marcos , Wald David , Buechner Jochen , Gedde‐Dahl Tobias , Søraas Camilla Lund , Chen Brian , Ferrucci Luigi , Dahl John Arne , Horvath Steve , Matsuyama Shigemi 
Published: February 2019

AbstractThe age of tissues and cells can be accurately estimated by DNA methylation analysis. The multitissue DNA methylation (DNAm) age predictor combines the DNAm levels of 353 CpG dinucleotides to arrive at an age estimate referred to as DNAm age. Recent studies based on short‐term observations showed that the DNAm age of reconstituted blood following allogeneic hematopoietic stem cell transplantation (HSCT) reflects the age of the donor. However, it is not known whether the DNAm age of donor blood remains independent of the recipient's age over the long term. Importantly, long‐term studies including child recipients have the potential to clearly reveal whether DNAm age is cell‐intrinsic or whether it is modulated by extracellular cues in vivo. Here, we address this question by analyzing blood methylation data from HSCT donor and recipient pairs who greatly differed in chronological age (age differences between 1 and 49 years). We found that the DNAm age of the reconstituted blood was not influenced by the recipient's age, even 17 years after HSCT, in individuals without relapse of their hematologic disorder. However, the DNAm age of recipients with relapse of leukemia was unstable. These data are consistent with our previous findings concerning the abnormal DNAm age of cancer cells, and it can potentially be exploited to monitor the health of HSCT recipients. Our data demonstrate that transplanted human hematopoietic stem cells have an intrinsic DNAm age that is unaffected by the environment in a recipient of a different age.
Medication adherence in first episode psychosis: the role of pre‐onset subthreshold symptoms
Authors: Daneault J.‐G. , Maraj A. , Lepage M. , Malla A. , Schmitz N. , Iyer S. N. , Joober R. , Shah J. L. 
Published: February 2019

ObjectiveThe experience of pre‐onset subthreshold psychotic symptoms (STPS, signifying a clinical high‐risk state) in first episode psychosis (FEP) predicts poorer outcomes during treatment, possibly through differential adherence to medication. We explored whether adherence differs between FEP patients with and without pre‐onset STPS.MethodsAntipsychotic medication adherence was compared in 263 STPS+ and 158 STPS− subjects in a specialized early intervention program for FEP. Data were gathered from a larger observational study conducted between 2003 and 2016. STPS status, sociodemographic, and baseline clinical variables were tested as predictors of non‐adherence using univariate and multivariate logistic regressions. Time to onset of non‐adherence was analyzed using Kaplan–Meier curves. The same predictors were tested as predictors of time to onset of non‐adherence using Cox regression models.ResultsMedication non‐adherence was higher in STPS+ participants (78.9% vs. 68.9%). STPS status (OR 1.709), substance use disorder (OR 1.767), and milder positive symptoms (OR 0.972) were significant baseline predictors of non‐adherence. Substance use disorder (HR 1.410), milder positive symptoms (HR 0.990), and lack of contact between the clinical team and relatives (HR 1.356) were significant baseline predictors of time to non‐adherence.ConclusionFEP patients who experience pre‐onset STPS are more likely to be non‐adherent to antipsychotic medication over 2 years of intervention. FEP programs should routinely evaluate pre‐onset symptomatology to deliver more personalized treatments, with emphasis on engaging both patients and family members from the beginning of care.
Hallucinations in patients with borderline personality disorder: characteristics, severity, and relationship with schizotypy and loneliness
Authors: Slotema C. W. , Bayrak H. , Linszen M. M. J. , Deen M. , Sommer I. E. C. 
Published: February 2019

ObjectiveIn patients with borderline personality disorder (BPD), data are lacking on characteristics and severity of hallucinations in modalities other than the auditory (verbal) type. The same applies to relationships between hallucinations and the severity of depression, anxiety, schizotypy, and loneliness.MethodsIn 60 female patients withBPD(37 also with hallucinations), this cross‐sectional study explored characteristics and severity of (i) hallucinations and (ii) schizotypal features, (iii) severity of depression and anxiety, and (iv) loneliness, and the relationships between hallucinations and the other characteristics.ResultsIn patients with hallucinations, 80% experienced hallucinations in more than one modality; in the different modalities, the characteristics of the hallucinations were similar. The criteria for loneliness were fulfilled in 81% and 48% of patients with and without hallucinations. Compared to patients withBPDwithout hallucinations, the presence of hallucinations was associated with higher scores for depression, anxiety, loneliness, and schizotypy. Furthermore, the severity of hallucinations showed a positive correlation with the severity of loneliness and schizotypy.ConclusionPatients withBPDexperienced hallucinations with characteristics similar to the more frequently studied auditory (verbal) hallucinations. Higher scores for schizotypy and loneliness indicate that patients with hallucinations had more characteristics of cluster A personality disorders.
Cocaine'omics: Genome‐wide and transcriptome‐wide analyses provide biological insight into cocaine use and dependence
Authors: Huggett Spencer B. , Stallings Michael C. 
Published: February 2019

AbstractWe investigated the genetic and molecular architecture of cocaine dependence (CD) and cocaine use by integrating genome‐/transcriptome‐wide analyses. To prioritize candidates for follow‐up investigation, we also sought to translate gene expression findings across species. Using data from the largest genome‐wide association study (GWAS) of CD to date (n = 3176, 74% with CD), we assessed genomic heritability, gene‐based associations, and tissue enrichment. We detected a significant single‐nucleotide polymorphism heritability of 28% for CD and identified three genes (two loci) underlying this predisposition: the C1qL2 (complement component C1 q like 2), KCTD20 (potassium channel tetramerization domain containing 20), and STK38 (serine/threonine kinase 38) genes. Tissue enrichment analyses indicated robust enrichment in numerous brain regions, including the hippocampus. We used postmortem human hippocampal RNA‐sequencing data from previous study (n = 15, seven chronic cocaine users) to follow up genome‐wide results and to identify differentially expressed genes/transcripts and gene networks underlying cocaine use. Cross‐species analyses utilized hippocampal gene expression from a mouse model of cocaine use. Differentially expressed genes/transcripts in humans were enriched for the genes nominally associated with CD via GWAS (P < 0.05) and for differentially expressed genes in the hippocampus of cocaine‐exposed mice. We identified KCTD20 as a central component of a hippocampal gene network strongly associated with human cocaine use, and this gene network was conserved in the mouse hippocampus. We outline a framework to map and translate genome‐wide findings onto tissue‐specific gene expression, which provided biological insight into cocaine use/dependence.
Housing Squats as “Educational Sites of Resistance”: The Process of Movement Social Base Formation in the Struggle for the House
Authors: Caciagli Carlotta 
Published: February 2019

AbstractThis paper aims to contribute to the scholarly work on the internal dynamics of contemporary housing movements. In particular, it explores the spatial strategies through which squat inhabitants change the configuration of the squat to turn an abandoned building into a house for multiple families. The main argument is that these strategies, requiring horizontal participation and solidarity, catalyse the transformation of a sum of people dispossessed of the house into a collective, political subject. Therefore, the author proposes to analyse housing squats as “educational sites of resistance”. The findings come from the author's participant observation of Rome's housing movement organisation Coordinamento Cittadino di Lotta per la casa. In addition to providing empirical knowledge, the paper aims to offer inputs for investigating to what extent the process of politicisation is shaped by the space and what constitute the peculiarities of a so‐recomposed collective subject.