bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution and Dispersal in the Piping Plover
Authors: Haig Susan M. , Oring Lewis W. 
Published: October 2019

Abstract
Individually marked Piping Plovers (Charadrius melodus) were studied from 1981-1987 in Manitoba and Minnesota relative to dispersal patterns of age and sex classes. Unlike monogamous passerines, males returned to former breeding sites only slightly more often than females. Dispersal distances did not differ between the sexes. Across North America, 24-69% of adults exhibited breeding-site fidelity, a variability equivalent to that among species of migratory shorebirds. Distribution of Piping Plover habitat across the species range accounts for some of this variability: birds used local sites if they were available, rather than disperse long distances. Similar to most migratory shorebirds, few (1.6-23%) Piping Plover chicks returned to natal sites to breed. No difference was found in return patterns between first-year males and females, nor in distances either sex dispersed from natal sites. First-year birds were found in the vicinity of their natal sites when habitat was available. During winter, birds from the Northern Great Plains and Great Lakes were seen primarily in mixed population flocks on the Gulf of Mexico. Piping Plovers from Atlantic coast breeding areas wintered further south on the Atlantic.
Seed Handling Ability, Bill Structure, and the Cost of Specialization for Crossbills
Authors: Benkman Craig W. 
Published: October 2019

Abstract
Crossbills (Loxia) are specialized to extract and handle seeds from conifer cones. I evaluated the ability of crossbills to handle nonconifer seeds by comparing seed handling efficiencies with other cardueline finches. For all seed sizes, crossbills required seed encounter rates or seed abundances 2-3 times greater than other species to meet their daily energy requirements. Consequently, crossbills may suffer high mortality during conifer cone failures. Crossbills are inefficient at meeting their energy demands on nonconifer seeds because of their narrow mandibles, lowered horny palate, and large body size. The narrow mandibles enable crossbills to efficiently extract seeds from conifer cones and the lowered palate enables them to handle small seeds rapidly. Crossbills have evolved larger bills, and associated musculature and body mass, to provide the power necessary to separate cone scales. Some of the increase in body mass, however, may counterbalance the large bills to improve predator evasion.
3D genome organisation in Drosophila
Authors: Moretti Charlotte , Stévant Isabelle , Ghavi-Helm Yad 
Published: October 2019

AbstractEver since Thomas Hunt Morgan’s discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However, these domains might be formed through a slightly different mechanism than in vertebrates due to the presence of a large and potentially redundant set of insulator proteins and the minor role of dCTCF in TAD boundary formation. Here, we review the different levels of chromatin organisation in Drosophila and discuss mechanisms and factors that might be involved in TAD formation. The dynamics of TADs and enhancer–promoter interactions in the context of transcription are covered in the light of currently conflicting results. Finally, we illustrate the value of polymer modelling approaches to infer the principles governing the three-dimensional organisation of the Drosophila genome.
NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
Authors: Jiménez-Sánchez Daniel , Ariz Mikel , Morgado José Mário , Cortés-Domínguez Iván , Ortiz-de-Solórzano Carlos 
Published: October 2019

Abstract

Motivation
Recent advances in multiplex immunostaining and multispectral cytometry have opened the door to simultaneously visualizing an unprecedented number of biomarkers both in liquid and solid samples. Properly unmixing fluorescent emissions is a challenging task, which normally requires the characterization of the individual fluorochromes from control samples. As the number of fluorochromes increases, the cost in time and use of reagents becomes prohibitively high. Here, we present a fully unsupervised blind spectral unmixing method for the separation of fluorescent emissions in highly mixed spectral data, without the need for control samples. To this end, we extend an existing method based on non-negative Matrix Factorization, and introduce several critical improvements: initialization based on the theoretical spectra, automated selection of ‘sparse’ data and use of a re-initialized multilayer optimizer.

Results
Our algorithm is exhaustively tested using synthetic data to study its robustness against different levels of colocalization, signal to noise ratio, spectral resolution and the effect of errors in the initialization of the algorithm. Then, we compare the performance of our method to that of traditional spectral unmixing algorithms using novel multispectral flow and image cytometry systems. In all cases, we show that our blind unmixing algorithm performs robust unmixing of highly spatially and spectrally mixed data with an unprecedently low computational cost. In summary, we present the first use of a blind unmixing method in multispectral flow and image cytometry, opening the door to the widespread use of our method to efficiently pre-process multiplex immunostaining samples without the need of experimental controls.

Availability and implementation
https://github.com/djimenezsanchez/Blind_Unmixing_NMF_RI/ contains the source code and all datasets used in this manuscript.

Supplementary information
Supplementary data are available at Bioinformatics online.
Historical, Ethical, and (Extra)legal Perspectives on Culpability in Accidental Species Introductions
Authors: Perry Gad , Curzer Howard , Farmer Michael , Gore Meredith L , Simberloff Daniel 
Published: October 2019

AbstractSome nonnative species benefit humans, but many become invasive, with high economic, cultural, and ecological costs. Although many introductions are considered accidental, inadvertent, or unintentional, this terminology often cannot be justified. Prevention policies have been proposed or implemented, and a diversity of proven control methods is available, but invasion problems grow, largely because feasible policy and management approaches are not implemented. The lack of action reflects willful myopia, a decision not to act because of negligence by policymakers, managers, and individuals. We explore the multidimensional ethical implications of this view and propose a continuum of ethical hazard. We relate the ethical dimensions to legal aspects of culpability and suggest a possible cutoff for legal liability. Finally, we identify four components of a desired policy response: It must ensure legal authority for action, base policy response on market forces, assure that more than simplistic economic considerations underpin decisions, and better engage the public.
Traversing the Wasteland: A Framework for Assessing Ecological Threats to Drylands
Authors: Hoover David L , Bestelmeyer Brandon , Grimm Nancy B , Huxman Travis E , Reed Sasha C , Sala Osvaldo , Seastedt Timothy R , Wilmer Hailey , Ferrenberg Scott 
Published: October 2019

Abstract
Drylands cover 41% of the Earth's terrestrial surface, play a critical role in global ecosystem function, and are home to over two billion people. Like other biomes, drylands face increasing pressure from global change, but many of these ecosystems are close to tipping points, which, if crossed, can lead to abrupt transitions and persistent degraded states. Their limited but variable precipitation, low soil fertility, and low productivity have given rise to a perception that drylands are wastelands, needing societal intervention to bring value to them. Negative perceptions of drylands synergistically combine with conflicting sociocultural values regarding what constitutes a threat to these ecosystems. In the present article, we propose a framework for assessing threats to dryland ecosystems and suggest we must also combat the negative perceptions of drylands in order to preserve the ecosystem services that they offer.
Conceptual Risk Framework: Integrating Ecological Risk of Introduced Species with Recipient Ecosystems
Authors: Probert Anna F , Ward Darren F , Beggs Jacqueline R , Lin Sheng-Lin , Stanley Margaret C 
Published: October 2019

AbstractGlobal changes are predicted to facilitate the introduction, establishment, and spread of species into new environments leading to potential negative impacts on local biodiversity. Evaluating the risk associated with introduced species with a high likelihood of arrival, or species that have already been introduced, is therefore increasingly important. In the present article, we outline an operational framework to provide a basis for assessing the ecological risk of introduced species in order to facilitate justifiable management decisions. The framework integrates information based on both the species and the (potential) recipient ecosystems, using existing tools to guide pest managers through the stepwise process. This enables the prediction of high-risk species and the identification of those ecosystems most vulnerable to invasion, and facilitates understanding of the potential mechanisms and magnitude of pest impacts. The framework can be applied to different invasion scenarios to evaluate the risks and impacts of species.
Machine learning in the estimation of causal effects: targeted minimum loss-based estimation and double/debiased machine learning
Authors: Díaz Iván 
Published: October 2019

Summary
In recent decades, the fields of statistical and machine learning have seen a revolution in the development of data-adaptive regression methods that have optimal performance under flexible, sometimes minimal, assumptions on the true regression functions. These developments have impacted all areas of applied and theoretical statistics and have allowed data analysts to avoid the biases incurred under the pervasive practice of parametric model misspecification. In this commentary, I discuss issues around the use of data-adaptive regression in estimation of causal inference parameters. To ground ideas, I focus on two estimation approaches with roots in semi-parametric estimation theory: targeted minimum loss-based estimation (TMLE; van der Laan and Rubin, 2006) and double/debiased machine learning (DML; Chernozhukov and others, 2018). This commentary is not comprehensive, the literature on these topics is rich, and there are many subtleties and developments which I do not address. These two frameworks represent only a small fraction of an increasingly large number of methods for causal inference using machine learning. To my knowledge, they are the only methods grounded in statistical semi-parametric theory that also allow unrestricted use of data-adaptive regression techniques.
Genetic variants in m6A modification genes are associated with colorectal cancer risk
Authors: Meng Yixuan , Li Shuwei , Gu Dongying , Xu Kaili , Du Mulong , Zhu Lingjun , Chu Haiyan , Zhang Zhengdong , Wu Yuan , Fu Zan , Wang Meilin 
Published: October 2019

Abstract
The N6-methyladenosine (m6A) modification plays important regulatory roles in gene expression, cancer occurrence and metastasis. Herein, we aimed to explore the association between genetic variants in m6A modification genes and susceptibility to colorectal cancer. We used logistic regression models to investigate the associations between candidate single-nucleotide polymorphisms (SNPs) in 20 m6A modification genes and colorectal cancer risk. The false discovery rate (FDR) method was used for multiple comparisons. Dual luciferase assays and RNA m6A quantifications were applied to assess transcriptional activity and measure m6A levels, respectively. We found that SND1 rs118049207 was significantly associated with colorectal cancer risk in a Nanjing population (odds ratio (OR) = 1.69, 95% confidence interval (95% CI) = 1.31–2.18, P = 6.51 × 10−6). This finding was further replicated in an independent Beijing population (OR = 1.36, 95% CI = 1.04–1.79, P = 2.41 × 10−2) and in a combined analysis (OR = 1.52, 95% CI = 1.27–1.84, P = 8.75 × 10−6). Stratification and interaction analyses showed that SND1 rs118049207 multiplicatively interacted with the sex and drinking status of the patients to enhance their colorectal cancer risk (P = 1.56 × 10−3 and 1.41 × 10−2, respectively). Furthermore, rs118049207 served as an intronic enhancer on SND1 driven by DMRT3. SND1 mRNA expression was markedly increased in colorectal tumour tissues compared with adjacent normal tissues. The colorimetric m6A quantification strategy revealed that SND1 could alter m6A levels in colorectal cancer cell lines. Our findings indicated that genetic variants in m6A modification genes might be promising predictors of colorectal cancer risk.
Reinstatement of Event Details during Episodic Simulation in the Hippocampus
Authors: Thakral Preston P , Madore Kevin P , Addis Donna Rose , Schacter Daniel L 
Published: October 2019

Abstract
According to the constructive episodic simulation hypothesis, episodic simulation (i.e., imagining specific novel future episodes) draws on some of the same neurocognitive processes that support episodic memory (i.e., recalling specific past episodes). Episodic retrieval supports the ability to simulate future experiences by providing access to episodic details (e.g., the people and locations that comprise memories) that can be recombined in new ways. In the current functional neuroimaging study, we test this hypothesis by examining whether the hippocampus, a region implicated in the reinstatement of episodic information during memory, supports reinstatement of episodic information during simulation. Employing a multivoxel pattern similarity analysis, we interrogated the similarity between hippocampal neural patterns during memory and simulation at the level of individual event details. Our findings indicate that the hippocampus supports the reinstatement of detail-specific information from episodic memory during simulation, with the level of reinstatement contributing to the subjective experience of simulated details.
Cell atlas of the foetal human heart and implications for autoimmune-mediated congenital heart block
Authors: Suryawanshi Hemant , Clancy Robert , Morozov Pavel , Halushka Marc K , Buyon Jill P , Tuschl Thomas 
Published: October 2019

Abstract

Aims
Investigating human heart development and applying this to deviations resulting in disease is incomplete without molecular characterization of the cell types required for normal functioning. We investigated foetal human heart single-cell transcriptomes from mid-gestational healthy and anti-SSA/Ro associated congenital heart block (CHB) samples.

Methods and results
Three healthy foetal human hearts (19th to 22nd week of gestation) and one foetal heart affected by autoimmune-associated CHB (21st week of gestation) were subjected to enzymatic dissociation using the Langendorff preparation to obtain single-cell suspensions followed by 10× Genomics- and Illumina-based single-cell RNA-sequencing (scRNA-seq). In addition to the myocytes, fibroblasts, immune cells, and other minor cell types, previously uncharacterized diverse sub-populations of endothelial cells were identified in the human heart. Differential gene expression analysis revealed increased and heterogeneous interferon responses in varied cell types of the CHB heart compared with the healthy controls. In addition, we also identified matrisome transcripts enriched in CHB stromal cells that potentially contribute to extracellular matrix deposition and subsequent fibrosis.

Conclusion
These data provide an information-rich resource to further our understanding of human heart development, which, as illustrated by comparison to a heart exposed to a maternal autoimmune environment, can be leveraged to provide insight into the pathogenesis of disease.
Physician adherence to clinical guidelines in euthanasia and assisted suicide in the Netherlands: a qualitative study
Authors: Riley Sean R , Overbeek Anouk , van der Heide Agnes 
Published: October 2019

Abstract

Background
Euthanasia and assisted suicide laws in the Netherlands require physicians meet clinical guidelines when performing the practice to ensure death is peaceful and painless. Despite oversight by the regional review committees over each case, little research exists into the frequency of guideline deviation and the reasons for nonadherence.

Methods
Cases reported and reviewed between 2012 and 2017 that did not meet due medical care were analysed for thematic content. Semistructured interviews were conducted with 11 Dutch physicians on their experience with the clinical and pharmacological elements of euthanasia and assisted suicide, their interaction and comportment with the recommended guidelines, and reasons why guideline deviation might occur. Reported case reviews and interviews were used to obtain themes and subthemes to understand how and why deviations from clinical guidelines happened.

Results
Violations of due medical care were found in 42 (0.07%) of reported cases. The regional review committees found physicians in violation of due medical care mostly for inadequate confirmation of coma-induction and deviations from recommended drug dosages. Physicians reported that they rarely deviated from the guidelines, with the most common reasons being concern for the patient’s family, concern over the drug efficacy, mistrust in the provided guidelines, or relying on the poor advice of pharmacists or hospital administrators.

Conclusions
Deviations from the guidelines and violations of due medical care are rare, but should nonetheless be monitored and prevented. A few areas for improvement include skills training for physicians, consistency between review committee rulings, and further clarity on dosage recommendations.
Dynamics of the microbial community during growth of the house dust mite Dermatophagoides farinae in culture
Authors: Klimov Pavel , Molva Vit , Nesvorna Marta , Pekar Stano , Shcherbachenko Elena , Erban Tomas , Hubert Jan 
Published: October 2019

ABSTRACTThe variation in house dust mite microbial communities is important because various microorganisms modulate the production of allergens by their mite hosts and/or contaminate immunotherapeutic extracts. Temporal changes in mite microbiomes and the mite culture environment occurring at different stages of mite culture development are particularly understudied in this system. Here, we analyzed the dynamics of microbial communities during the culture growth of Dermatophagoides farinae. Changes in microbiomes were related to three key variables: the mite population density, microbial microcosm respiration and concentration of guanine (the mite nitrogenous waste metabolite). Mite populations exhibited the following phases: exponential growth, plateau and exponential decline. The intracellular bacterium Cardinium and the yeast Saccharomyces cerevisiae prevailed in the internal mite microbiomes, and the bacterium Lactobacillus fermentum was prevalent in the mite diet. The reduction in the mite population size during the late phases of culture development was related to the changes in their microbial profiles: the intracellular bacterium Cardinium was replaced by Staphylococcus, Oceanobacillus and Virgibacillus, and S. cerevisiae was replaced by the antagonistic fungi Aspergillus penicillioides and Candida. Increases in the guanine content were positively correlated with increases in the Staphylococcus and A. penicillioides profiles in the culture environment. Our results show that the mite microbiome exhibits strong, dynamic alterations in its profiles across different mite culture growth stages.
A screening system using minimal media identifies a flavin-competing inhibitor of Porphyromonas gingivalis growth
Authors: Saiki Keitarou , Urano-Tashiro Yumiko , Konishi Kiyoshi , Takahashi Yukihiro 
Published: October 2019

ABSTRACT
Chronic periodontitis is caused by dysbiosis of human oral commensals and especially by increase in Porphyromonas gingivalis. Inhibitors of P. gingivalis growth are expected to serve as effective drugs for the periodontal therapy. In the present study, we isolated new growth inhibitors of P. gingivalis using minimal media for P. gingivalis. The minimal media included the previously reported Globulin–Albumin (GA) and the newly developed Lactalbumin-Ferric chloride (LF) and Globulin-Calcium chloride (GC); all supported growth of the wild-type strain of P. gingivalis but did not support the growth of a mutant defective for a type IX secretion system. GC contains CaCl2, indicating that P. gingivalis requires a calcium ion for growth. Using LF and GA, we screened about 100 000 compounds and identified 73 that strongly inhibited the growth of P. gingivalis. More than half of these candidates would not have been obtained if these minimal media had not been used in our screen. One of our candidate inhibitors was diphenyleneiodonium chloride (DPIC), which showed strong bactericidal activity against P. gingivalis. Excess amounts of flavin adenine dinucleotide or flavin mononucleotide suppressed the inhibitory activity of DPIC, suggesting that DPIC would be a novel potent growth inhibitor.
Is Aging Biology Ageist?
Authors: Cohen Alan A , Levasseur Mélanie , Raina Parminder , Fried Linda P , Fülöp Tamàs 
Published: October 2019

Abstract
The scientific questions we pursue are shaped by our cultural assumptions and biases, often in ways we are unaware. Here, we argue that modern biases against older adults (ageism) have unconsciously led aging biologists to assume that traits of older individuals are negative and those of younger individuals positive. We illustrate this bias with the example of how a medieval Chinese scholar might have approached the task of understanding aging biology. In particular, aging biologists have tended to emphasize functional declines during aging, rather than biological adaptation and population selection or composition processes; the reality is certainly that all these processes interact. Failure to make these distinctions could lead to interventions that improve superficial markers of aging while harming underlying health, particularly as the health priorities of older adults (autonomy, function, freedom from suffering, etc.) are often quite different from the goals of aging biologists (reducing disease, prolonging life). One approach to disentangling positive, negative, and neutral changes is to map trajectories of change across the life course of an individual (physiobiography). We emphasize that our goal is not to criticize our colleagues—we have been guilty too—but rather to help us all improve our science.