bluuebunny/crossref_metadata_2025 huggingface dataset:
NATURAL RADIONUCLIDES IN SOIL AND ROOT VEGETABLES IN MALAYSIA: TRANSFER FACTORS AND DOSE ESTIMATES
Authors: Al Mutairi Abdul Majeed Muidh , Kabir Norlaili A
Published: September 2019

Tapioca and sweet potato are the fourth and fifth most consumed crops in Malaysia. The activity concentrations of natural radionuclides in these vegetables were assessed from two regions in Malaysia (Kedah and Penang) along with soil samples using gamma ray spectroscopy. The transfer factors of 226Ra, 232Th and 40K from soil to vegetables were calculated, and a dose assessment was performed. The activity concentrations of 226Ra, 232Th and 40K in soil samples did not show a significant variation with the regions investigated, and the average values obtained, in Bq/kg, (±SD) were as follows: 80 ± 41, 56 ± 12, 516 ± 119, respectively. The respective average activity concentrations in vegetables were as follows, in Bq/kg: (±SD) 2.0 ± 0.5, 6 ± 2, 153 ± 49. The corresponding transfer factors were calculated to be 0.03, 0.11 and 0.31 for 226Ra, 232Th and 40K, respectively. The average annual effective doses due to the exposure from soil and ingestion of vegetables were found to lie within the worldwide ranges.
High occurrence of transportation and logistics occupations among vascular dementia patients: an observational study
Authors: van Loenhoud A.C. , de Boer C. , Wols K. , Pijnenburg Y.A. , Lemstra A.W. , Bouwman F.H. , Prins N.D. , Scheltens P. , Ossenkoppele R. , van der Flier W.M.
Published: September 2019

Background

Growing evidence suggests a role of occupation in the emergence and manifestation of dementia. Occupations are often defined by complexity level, although working environments and activities differ in several other important ways. We aimed to capture the multi-faceted nature of occupation through its measurement as a qualitative (instead of a quantitative) variable and explored its relationship with different types of dementia.

Methods

We collected occupational information of 2,121 dementia patients with various suspected etiologies from the Amsterdam Dementia Cohort (age: 67±8, 57% male, MMSE: 21±5). Our final sample included individuals with Alzheimer’s disease (AD) dementia (n=1,467), frontotemporal dementia (n=281), vascular dementia (n=98), Lewy Body disease (n=174) and progressive supranuclear palsy/corticobasal degeneration (n=101). Within the AD group, we used neuropsychological data to further characterize patients by clinical phenotypes. All participants were categorized into one of 11 occupational classes, across which we evaluated the distribution of dementia (sub)types with Chi2 analyses. We gained further insight into occupation-dementia relationships through post-hoc logistic regressions that included various demographic and health characteristics as explanatory variables.

Results

There were significant differences in the distribution of dementia types across occupation groups (Chi2=85.87, p<.001). Vascular dementia was relatively common in the Transportation/Logistics sector, and higher vascular risk factors partly explained this relationship. Alzheimer’s disease occurred less in Transportation/Logistics and more in Health Care/Welfare occupations, which related to a higher/lower percentage of males. We found no relationships between occupational classes and clinical phenotypes of AD (Chi2=53.65, n.s.).

Conclusions

Relationships between occupation and dementia seem to exist beyond complexity level, which offers new opportunities for disease prevention and improvement of occupational health policy.
Node abnormality predicts seizure outcome and relates to long-term relapse after epilepsy surgery
Authors: Sinha Nishant , Wang Yujiang , da Silva Nádia Moreira , Miserocchi Anna , McEvoy Andrew W. , de Tisi Jane , Vos Sjoerd B. , Winston Gavin P. , Duncan John S. , Taylor Peter Neal
Published: September 2019

Objective

We assessed pre-operative structural brain networks and clinical characteristics of patients with drug resistant temporal lobe epilepsy (TLE) to identify correlates of post-surgical seizure outcome at 1 year and seizure relapses up to 5 years.

Methods

We retrospectively examined data from 51 TLE patients who underwent anterior temporal lobe resection (ATLR) and 29 healthy controls. For each patient, using the pre-operative structural, diffusion, and post-operative structural MRI, we generated two networks: ‘pre-surgery’ network and ‘surgically-spared’ network. The pre-surgery network is the whole-brain network before surgery and the surgically-spared network is a subnetwork of the pre-surgery network which is expected to remain unaffected by surgery and hence present post-operatively. Standardising these networks with respect to controls, we determined the number of abnormal nodes before surgery and expected to remain after surgery. We incorporated these 2 abnormality measures and 13 commonly acquired clinical data from each patient in a robust machine learning framework to estimate patient-specific chances of seizures persisting after surgery.

Results

Patients with more abnormal nodes had lower chance of seizure freedom at 1 year and even if seizure free at 1 year, were more likely to relapse within five years. In the surgically-spared networks of poor outcome patients, the number of abnormal nodes was greater and their locations more widespread than in good outcome patients. We achieved 0.84 ± 0.06 AUC and 0.89 ± 0.09 specificity in detecting unsuccessful seizure outcomes at 1-year. Moreover, the model-predicted likelihood of seizure relapse was significantly correlated with the grade of surgical outcome at year-one and associated with relapses up-to five years post-surgery.

Conclusion

Node abnormality offers a personalised non-invasive marker, that can be combined with clinical data, to better estimate the chances of seizure freedom at 1 year, and subsequent relapse up to 5 years after ATLR.
Comparison of bibliographic data sources: Implications for the robustness of university rankings
Authors: Huang Chun-Kai (Karl) , Neylon Cameron , Brookes-Kenworthy Chloe , Hosking Richard , Montgomery Lucy , Wilson Katie , Ozaygen Alkim
Published: September 2019

Universities are increasingly evaluated, both internally and externally on the basis of their outputs. Often these are converted to simple, and frequently contested, rankings based on quantitative analysis of those outputs. These rankings can have substantial implications for student and staff recruitment, research income and perceived prestige of a university. Both internal and external analyses usually rely on a single data source to define the set of outputs assigned to a specific university. Although some differences between such databases are documented, few studies have explored them at the institutional scale and examined the implications of these differences for the metrics and rankings that are derived from them. We address this gap by performing detailed bibliographic comparisons between three key databases: Web of Science (WoS), Scopus and, the recently relaunched Microsoft Academic (MSA). We analyse the differences between outputs with DOIs identified from each source for a sample of 155 universities and supplement this with a detailed manual analysis of the differences for fifteen universities. We find significant differences between the sources at the university level. Sources differ in the publication year of specific objects, the completeness of metadata, as well as in their coverage of disciplines, outlets, and publication type. We construct two simple rankings based on citation counts and open access status of the outputs for these universities and show dramatic changes in position based on the choice of bibliographic data sources. Those universities that experience the largest changes are frequently those from non-English speaking countries and those that are outside the top positions in international university rankings. Overall MSA has greater coverage than Scopus or WoS, but has less complete affiliation metadata. We suggest that robust evaluation measures need to consider the effect of choice of data sources and recommend an approach where data from multiple sources is integrated to provide a more robust dataset.
The Meta-Position of Phe4 in Leu-enkephalin Regulates Potency, Selectivity, Functional Activity, and Signaling Bias at the Delta and Mu Opioid Receptors
Authors: Cassell Robert J. , Sharma Krishna K. , Su Hongyu , Cummins Benjamin R. , Cui Haoyue , Mores Kendall L. , Blaine Arryn T. , Altman Ryan A. , van Rijn Richard M.
Published: September 2019

As tool compounds to study cardiac ischemia, the endogenous δ-opioid receptors (δOR) agonist Leu5-enkephalin and the more metabolically stable synthetic peptide [D-Ala2, D-Leu5]-enkephalin are frequently employed. However, both peptides have similar pharmacological profiles that restrict detailed investigation of the cellular mechanism of the δOR’s protective role during ischemic events. Thus, a need remains for δOR peptides with improved selectivity and unique signaling properties for investigating the specific roles for δOR signaling in cardiac ischemia. To this end, we explored substitution at the Phe4 position of Leu5-enkephalin for its ability to modulate receptor function and selectivity. Peptides were assessed for their affinity to bind to δORs and μ-opioid receptors (μORs) and potency to inhibit cAMP signaling and to recruit β-arrestin 2. Additionally, peptide stability was measured in rat plasma. Substitution of the meta-position of Phe4 of Leu5-enkephalin provided high-affinity ligands with varying levels of selectivity and bias at both the δOR and μOR and improved peptide stability, while substitution with picoline derivatives produced lower-affinity ligands with G protein biases at both receptors. Overall, these favorable substitutions at the meta-position of Phe4 may be combined with other modifications to Leu5-enkephalin to deliver improved agonists with finely tuned potency, selectivity, bias and drug-like properties.

Abstract Figure

TOC FIGURE
Development of a hybrid Bayesian network model for predicting acute fish toxicity using multiple lines of evidence
Authors: Moe S. Jannicke , Madsen Anders L. , Connors Kristin A. , Rawlings Jane M. , Belanger Scott E. , Landis Wayne G. , Wolf Raoul , Lillicrap Adam D.
Published: September 2019

A Bayesian network was developed for predicting the acute toxicity intervals of chemical substances to fish, based on information on fish embryo toxicity (FET) in combination with other information. This model can support the use of FET data in a Weight-of-Evidence (WOE) approach for replacing the use of juvenile fish. The BN predicted correct toxicity intervals for 69%-80% of the tested substances. The model was most sensitive to components quantified by toxicity data, and least sensitive to components quantified by expert knowledge. The model is publicly available through a web interface. Further development of this model should include additional lines of evidence, refinement of the discretisation, and training with a larger dataset for weighting of the lines of evidence. A refined version of this model can be a useful tool for predicting acute fish toxicity, and a contribution to more quantitative WOE approaches for ecotoxicology and environmental assessment more generally.

Highlights

A Bayesian network (BN) was developed to predict the toxicity of chemicals to fish

The BN uses fish embryo toxicity data in a quantitative weight-of-evidence approach

The BN integrates physical, chemical and toxicological properties of chemicals

Correct toxicity intervals were predicted for 69-80% of test cases

The BN is publicly available for demonstration and testing through a web interface
Nutritional signals rapidly activate oligodendrocyte differentiation in the adult hypothalamic median eminence
Authors: Kohnke Sara , Lam Brian , Buller Sophie , Zhao Chao , Nuzzaci Danae , Tadross John , Holmqvist Staffan , Ridley Katherine , Hathaway Hannah , Macklin Wendy , Yeo Giles SH , Franklin Robin JM , Rowitch David H , Blouet Clemence
Published: September 2019

The mediobasal hypothalamus (arcuate nucleus - ARC - and median eminence - ME -) controls energy balance, growth and fertility through its ability to integrate neuronal, nutritional and hormonal signals and coordinate the behavioural, neuroendocrine and metabolic responses required for these functions. While our understanding of the neural circuits downstream from ARC neurons is rapidly progressing, little is known about the function of other cell types. Here we describe an unexpected role for oligodendrocytes (OL) of the ME in monitoring nutritional signals. We show that refeeding following an overnight fast rapidly activates oligodendrocyte differentiation and the production of new OL in the ME specifically. No changes in myelination were measured in this time-frame. However, refeeding changed the expression of OL-derived extracellular matrix proteins decorin and tenascin-R, with consistent changes in the density of local perineuronal nets. Last, we show that OLs use mTORC1 signalling, a pathway required for OL differentiation, to survey energy and protein availability, specifically in the ME. We conclude that new oligodendrocytes formed in the ME in response to nutritional signals control the access of circulating metabolic cues to ARC interoceptive neurons.
Temporary pond loss as a result of pasture abandonment: exploring the social-ecological drivers and consequences on amphibians
Authors: Erős Nándor , Malos Cristian , Horváth Csaba , Hartel Tibor
Published: September 2019

Amphibian conservation in farming landscapes should address two challenges. First, to understand the relationship between landuse and amphibian habitat quality and second, to understand and support of the capacity of the local communities to continue those farming practices which supports amphibian friendly habitats. While the first challenge is addressed by several studies, there is virtually no study addressing the socio-economic drivers of landuse change. The major aim of this study to fill this knowledge gap by (i) documenting the temporary pond loss in 10 years in a traditionally managed pasture as a result of land abandonment and (ii) exploring the socio-economic and environmental drivers of abandonment. The results show a dramatic increase of scrub cover in the study area as a result of land abandonment. The formation of temporary ponds was negatively influenced by the increase of scrub cover in the vicinity of ponds. There were no differences between the amphibian species assemblages nor the species richness between the lost- and persisting ponds. The social component of the research highlights possible maladaptive paths in pasture management reinforced by the village depopulation, wrong interpretation of nature protection law by officials, scrub encroachment caused decrease in pasture quality and the demotivation of locals to restart traditional grazing. Conservation efforts in traditional farming landscapes facing land abandonment should (i) target the maximization of the quality of the remaining ponds for amphibians and (ii) should support reviving traditional farming practices within the local community.
A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production
Authors: Fouladiha Hamideh , Marashi Sayed-Amir , Torkashvand Fatemeh , Mahboudi Fereidoun , Lewis Nathan E. , Vaziri Behrouz
Published: September 2019

Chinese hamster ovary (CHO) cells are the main workhorse in the biopharmaceutical industry for the production of recombinant proteins, such as monoclonal antibodies. To date, a variety of metabolic engineering approaches have been used to improve the productivity of CHO cells. While genetic manipulations are potentially laborious in mammalian cells, rational design of CHO cell culture medium or efficient fed-batch strategies are more popular approaches for bioprocess optimization. In this study, a genome-scale metabolic network model of CHO cells was used to design feeding strategies for CHO cells to improve monoclonal antibody (mAb) production. A number of metabolites, including threonine and arachidonate, were suggested by the model to be added into cell culture medium. The designed composition has been experimentally validated, and then optimized, using design of experiment methods. About a two-fold increase in the total mAb expression has been observed using this strategy. Our approach can be used in similar bioprocess optimization problems, in order to suggest new ways of increasing production in different cell factories.
Eco-ethology and trait distribution of two congeneric species – different strategies for the plague pestAcanthoplus discoidalisand the long-leggedA. longipes(Orthoptera: Tettigoniidae)
Authors: Conti Erminia , Costa Giovanni , Mulder Christian
Published: September 2019

High trait variability among insects reflects a combination of intra- and inter-phenotype variations. Our aim was to assess if the trait distribution of body measurements can be more significantly influenced by sex (intraspecific variance) or by species (interspecific variance). To achieve this, we collected in Namibia tettigoniids belonging to two congeneric species of armoured ground crickets:Acanthoplus discoidalis(a significant pest in African croplands) and the long-leggedAcanthoplus longipes. We measured in the field the total body length, the maximal pronotal width and length, and the femur and tibia lengths of the hind legs in 106 adults. We also derived the body mass from length and width values of the sampled specimens. No significant differences emerged in the two species by sex. A discriminant analysis clearly shows that at species level the locomotory traits as captured by tibia and femur lengths and the size traits as captured by body and pronotal lengths account for 99% of the total variance and clearly separate this pest from its congeneric species. In essence, it is not primarily the body size that differentiates the two species, but rather the pronotum and hind leg larger sizes ofA. longipes. Different eco-ethological requirements, like the peculiarity of the calling song and the movements within the vegetation (and the consequently needed energy), independently force these functional traits.
KIT ligand protects against both light-induced and genetic photoreceptor degeneration
Authors: Li Huirong , Lian Lili , Liu Bo , Chen Yu , Yang Jinglei , Jian Shuhui , Zhou Jiajia , Xu Ying , Ma Xiaoyin , Qu Jia , Hou Ling
Published: September 2019

Photoreceptor cell degeneration is a major cause of blindness and a considerable health burden during aging but effective therapeutic or preventive strategies have not so far become commercially available. Here we show in mouse models that signaling through the tyrosine kinase receptor KIT protects photoreceptor cells against both light-induced and inherited retinal degeneration. Upon light damage, photoreceptor cells upregulate Kit ligand (KITL) and activate KIT signaling, which in turn induces nuclear accumulation of the transcription factor NRF2 and stimulates the expression of the antioxidant geneHmox1. Conversely, a viableKitmutation promotes light-induced photoreceptor damage, which is reversed by experimental expression ofHmox1. Furthermore, overexpression of KITL from a viral AAV8 vector prevents photoreceptor cell death and partially restores retinal function after light damage or in genetic models of human retinitis pigmentosa. Hence, application of KITL may provide a novel therapeutic avenue for prevention or treatment of retinal degenerative diseases.
Bayesian analysis of GWAS summary data reveals differential signatures of natural selection across human complex traits and functional genomic categories
Authors: Zeng Jian , Xue Angli , Jiang Longda , Lloyd-Jones Luke R , Wu Yang , Wang Huanwei , Zheng Zhili , Yengo Loic , Kemper Kathryn E , Goddard Michael E , Wray Naomi R , Visscher Peter M , Yang Jian
Published: September 2019

Understanding how natural selection has shaped the genetic architecture of complex traits and diseases is of importance in medical and evolutionary genetics. Bayesian methods have been developed using individual-level data to estimate multiple features of genetic architecture, including signatures of natural selection. Here, we present an enhanced method (SBayesS) that only requires GWAS summary statistics and incorporates functional genomic annotations. We analysed GWAS data with large sample sizes for 155 complex traits and detected pervasive signatures of negative selection with diverse estimates of SNP-based heritability and polygenicity. Projecting these estimates onto a map of genetic architecture obtained from evolutionary simulations revealed relatively strong natural selection on genetic variants associated with cardiorespiratory and cognitive traits and relatively small number of mutational targets for diseases. Averaging across traits, the joint distribution of SNP effect size and MAF varied across functional genomic regions (likely to be a consequence of natural selection), with enrichment in both the number of associated variants and the magnitude of effect sizes in regions such as transcriptional start sites, coding regions and 5’- and 3’-UTRs.
Derivation of endometrial gland organoids from term post-partum placenta
Authors: Marinić Mirna , Lynch Vincent J.
Published: September 2019

A major limitation of recently developed methods for the generation of endometrial gland organoids is their reliance on decidua isolated from endometrial biopsies or elective termination of pregnancies. Here we report the successful establishment of endometrial gland organoids from decidua isolated from term placental membranes, as well as the identification of potential survival factors for the co-culture of gland organoids and endometrial stromal fibroblasts. These modifications facilitate the generation of patient-specific endometrial gland organoids with known pregnancy outcomes, such as term vs. preterm birth.
Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination
Authors: Toren Dmitri , Kulaga Anton , Jethva Mineshbhai , Rubin Eitan , Snezhkina Anastasia V , Kudryavtseva Anna V , Nowicki Dmitry , Tacutu Robi , Moskalev Alexey A , Fraifeld Vadim E
Published: September 2019

One important question in aging research is how differences in genomics and transcriptomics determine the maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in non-model organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking-based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that of other long- and short-lived mammals. Gray whales are among the top 1% longest-lived mammals. Despite the extreme environment, or maybe due to a remarkable adaptation to its habitat (intermittent hypoxia, Arctic water, and high pressure), gray whales reach at least the age of 77 years. In this work, we show that long-lived mammals share common gene expression patterns between themselves, including high expression of DNA maintenance and repair, ubiquitination, apoptosis, and immune responses. Additionally, the level of expression for gray whale orthologs of pro- and anti-longevity genes found in model organisms is in support of their alleged role and direction in lifespan determination. Remarkably, among highly expressed pro-longevity genes many are stress-related, reflecting an adaptation to extreme environmental conditions. The conducted analysis suggests that the gray whale potentially possesses high resistance to cancer and stress, at least in part ensuring its longevity. This new transcriptome assembly also provides important resources to support the efforts of maintaining the endangered population of gray whales.
Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining
Authors: Suárez Gabriel A. , Dugan Kyle R. , Renda Brian A. , Leonard Sean P. , Gangavarapu Lakshmi S. , Barrick Jeffrey E.
Published: September 2019

One goal of synthetic biology is to improve the efficiency and predictability of living cells by removing extraneous genes from their genomes. We demonstrate improved methods for engineering the genome of the metabolically versatile and naturally transformable bacterium Acinetobacter baylyi ADP1 and apply them to a genome streamlining project. In Golden Transformation, linear DNA fragments constructed by Golden Gate Assembly are directly added to cells to create targeted deletions, edits, or additions to the chromosome. We tested the dispensability of 55 regions of the ADP1 chromosome using Golden Transformation. The 19 successful multiple-gene deletions ranged in size from 21 to 183 kilobases and collectively accounted for 24.6% of its genome. Deletion success could only be partially predicted on the basis of a single-gene knockout strain collection and a new Tn-Seq experiment. We further show that ADP1’s native CRISPR/Cas locus is active and can be retargeted using Golden Transformation. We reprogrammed it to create a CRISPR-Lock, which validates that a gene has been successfully removed from the chromosome and prevents it from being reacquired. These methods can be used together to implement combinatorial routes to further genome streamlining and for more rapid and assured metabolic engineering of this versatile chassis organism.
Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Authors: Samuels Tamsin J. , Järvelin Aino I. , Ish-Horowicz David , Davis Ilan
Published: September 2019

The numerous neurons and glia that form the brain originate from tightly controlled growth and division of neural stem cells, regulated systemically by known extrinsic signals. However, the intrinsic mechanisms that control the characteristic proliferation rates of individual neural stem cells are unknown. Here, we show that the size and division rates of Drosophila neural stem cells (neuroblasts) are controlled by the highly conserved RNA binding protein Imp (IGF2BP), via one of its top binding targets in the brain, myc mRNA. We show that Imp stabilises myc mRNA leading to increased Myc protein levels, larger neuroblasts, and faster division rates. Declining Imp levels throughout development limit myc mRNA stability to restrain neuroblast growth and division, while heterogeneous Imp expression correlates with myc mRNA stability between individual neuroblasts in the brain. We propose that Imp-dependent regulation of myc mRNA stability fine-tunes individual neural stem cell proliferation rates.

Abstract Figure
Life history genomic regions explain differences in Atlantic salmon marine diet specialization
Authors: Aykanat Tutku , Rasmussen Martin , Ozerov Mikhail , Niemelä Eero , Paulin Lars , Vähä Juha-Pekka , Hindar Kjetil , Wennevik Vidar , Pedersen Torstein , Svenning Martin-A. , Primmer Craig R.
Published: September 2019

Animals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction.

We aimed to test the hypothesis that heritable resource acquisition variation that co-varies with efficiency along the ontogeny would influence maturation timing of individuals.

To test this hypothesis, we utilized Atlantic salmon as a model which exhibit a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as the stomach fullness and composition) of individuals with different ages, and linked it genomic regions (haploblocks) that were previously identified to be associated with age-at-maturity.

Consistent with the hypothesis, we demonstrated that one of the life history genomic regions tested (six6) was indeed associated with age-dependent differences in stomach fullness. Prey composition was marginally linked to both genomic regions (six6andvgll3). We further showed Atlantic salmon switched to the so-called “feast and famine” strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often.

These results suggest genetic variation underlying resource utilization variation may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food-web structures.
Architecture of the Mto1/2 microtubule nucleation complex
Authors: Thakur Harish C. , Lynch Eric M. , Borek Weronika E. , Bao Xun X. , Ashraf Sanju , Zou Juan , Rappsilber Juri , Cook Atlanta G. , Sawin Kenneth E.
Published: September 2019

Proteins that contain a Centrosomin Motif 1 (CM1) domain are key regulators ofγ-tubulin complex-dependent microtubule nucleation, but how they are organized in higher-order structures is largely unknown. Mto1[bonsai], a truncated functional version of theSchizosaccharomyces pombeCM1 protein Mto1, interacts with Mto2 to form an Mto1/2[bonsai] complexin vivo. Here we show that recombinant Mto1/2[bonsai] forms higher-order multimersin vitroand that Mto2 alone can also multimerize. We demonstrate that Mto2 multimerization involves two separate homodimerization domains, the near N-terminal domain (NND) and the twin-cysteine domain (TCD). The TCD crystal structure reveals a stable homodimer with a novel dimerization interface. While the NND homodimer is intrinsically less stable, using crosslinking mass spectrometry we show that within Mto1/2[bonsai] complexes, it can be reinforced by additional cooperative interactions involving both Mto2 and Mto1[bonsai]. We propose a model for Mto1/2[bonsai] complex architecture that is supported by functional analysis of mutantsin vivo.
Leiomyosarcoma with osteoclast‐like (LMS‐OGC) giant cells the breast: A report of a rare case
Authors: Xu Zhonghai , Gu Junjun , Zhang Shan , Zhang Zhanjiao , Fang Wei
Published: September 2019

Leiomyosarcoma with osteoclast‐like giant cells (LMS‐OGC) has seldom been reported clinically. LMS‐OGC of the breast is extremely rare according to the literature. Here, we report a case of LMS‐OGC leiomyosarcoma with osteoclast‐like giant cells of the breast. A 51‐year‐old female patient presented with a breast mass which was treated surgically and the pathological examination of the tumor indicated LMS‐OGC. Microscopically, the tumor was composed of spindle cells arranged in bundles or spokes with giant tumor cells and mitosis. Eosinophilic cytoplasm and morphologically benign osteoclast‐like cells were mixed together. Immunohistochemistry examination revealed SMA and desmin were positive with a Ki‐67 proliferation index of 40%. However, CK (AE1/AE3), E‐cadherin, ER, PR, CD34, S‐100 and CD10 were negatively expressed in the tumor tissue. LMS‐OGC is a soft tissue malignant tumor which develops extremely rarely in the breast. It should be differentiated and diagnosed according to the history, histological characteristics and immunohistochemical staining.
Tree aboveground biomass and species richness of the mature tropical forests of Darien, Panama, and their role in global climate change mitigation and biodiversity conservation
Authors: Mateo‐Vega Javier , Arroyo‐Mora J. Pablo , Potvin Catherine
Published: September 2019

The remote forests of the Darien region in eastern Panama are among the last remnants of relatively undisturbed forest habitat in the Central American isthmus. Despite decades of efforts by the government, nongovernmental organizations, and civil society, including Indigenous peoples, to protect the region's natural heritage, it remains under significant threat due to widespread illegal logging. Now, the Panamanian government is considering the mechanism, Reducing Emissions from Deforestation and Forest Degradation (REDD+), as another option to limit forest loss. Central to the proper functioning of REDD+ is the need to reduce uncertainties in estimates of aboveground biomass (AGB). These estimates are used to establish realistic reference levels against which additional contributions to reducing carbon dioxide emissions from the loss and degradation of forests can be financially compensated. Also, highly desirable to REDD+ is the achievement of biodiversity cobenefits. REDD+ investments will likely be directed primarily to areas where the potential to simultaneously mitigate climate change and conserve biodiversity is highest. Here, we present the results of a field‐based forest carbon inventorying method tested in Darien's mature forests with the participation of Embera and Wounaan Indigenous peoples. We also explore whether variations in field‐based estimates of AGB across mature forests, in both undisturbed and disturbed areas, are detectable through free and readily‐available remote sensing data sources. Furthermore, we examine and compare AGB and tree species richness in Darien with other well‐studied forest sites across the tropics. Our findings reveal that Darien's forests play a crucial role globally and regionally in storing carbon and housing biodiversity, and support the imperative need to protect these forests in a culturally appropriate manner with the region's Indigenous peoples.
Relationships between coarse woody debris habitat quality and forest maturity attributes
Authors: van Galen Laura G. , Jordan Gregory J. , Baker Susan C.
Published: September 2019

Coarse woody debris (CWD) is an important contributor to forest biodiversity because it provides essential habitat for saproxylic (dead wood‐dependent) species. However, CWD is frequently overlooked in forest management and restoration decisions around the world. We have therefore developed an index of CWD habitat quality that integrates four important characteristics of saproxylic habitat. We apply this index to wet eucalypt forests in Tasmania, Australia. The relationships between the CWD index and standing forest structural and floristic maturity metrics were weak (R2< .09), highlighting the necessity to explicitly factor CWD habitat into conservation planning. A hump‐shaped relationship between current CWD habitat quality and variables linked to future quality (standing tree basal area and the number of old‐growth eucalypts) implies that stands with medium current quality provide better potential future habitat than stands with high current quality. CWD habitat quality was lower in previously harvested stands. We present a web app that calculates CWD habitat quality scores from raw field measurements. Our approach can be applied in conservation assessments to determine habitat availability for biodiversity, and to quantify the impacts of management actions and restoration activities.
The on‐ground feasibility of a waterless barrier to stop the spread of invasive cane toads in Western Australia
Authors: Gregg Emily A. , Tingley Reid , Phillips Benjamin L.
Published: September 2019

Modeling suggests that excluding invasive cane toads from artificial water points (e.g., pastoral dams) along an arid coastal corridor in Western Australia would create a “waterless barrier” halting their spread. In this study, we explored one critical assumption of these models: that toads cannot persist in the corridor during the dry season without access to artificial water points. We explicitly tested this assumption by translocating and radio‐tracking 78 male cane toads in the proposed barrier region during the dry season. Telemetered toads moved substantial distances (maximum distance >2.5 km/night) and were adept at finding shelter. Nonetheless, toads experienced high water loss rates (1.89%/hr) and rapid mortality in both desert (mean ± SD = 43.6 hr ±1.4) and coastal (24.5 hr ±1.2) habitats. Survival analysis suggested that toads could survive a maximum of 5 days without access to surface water and would move a maximum of 5.35 km in this time. Our results confirm that artificial water points are a critical resource for toads in the proposed barrier region and provide further evidence that the waterless barrier could successfully halt toad expansion in Western Australia.
Of cowboys, fish, and pangolins: US trade in exotic leather
Authors: Heinrich Sarah , Ross Joshua V. , Cassey Phill
Published: September 2019

Illegal wildlife trade is a lucrative business, which is driving many species towards extinction. Pangolins (Manis spp.) and arapaimas (Arapaima spp.) are two CITES listed genera coveted in the leather fashion industry for their unique skin pattern. The US has contributed to the decline of pangolin species and was historically a large market for pangolin leather products. While the US trade in pangolin products has declined since 2000, we suspect that pangolin leather may now be substituted by arapaima products. Arapaima leather trade has increased significantly since the year 2011. We found a strong positive correlation between the US states trading in both arapaima and pangolin leather products. The US states that were most involved in this trade had a lower population density and were comparatively wealthier than others. Leather items of both arapaima and pangolin were found for sale on eBay, with 75% of incidents in breach of eBay policy, and potentially illegal. Pangolin leather products were also falsely advertised as arapaima products. We conclude that arapaima leather is increasingly used to satisfy the persisting demand for exotic leather, and further research is urgently needed to determine the effect of the trade on wild arapaima populations.
Patterns of genetic diversity in African forest elephants living in a human‐modified landscape in southwest Gabon
Authors: Johnson Mireille B. , Parker Lillian D. , Vanthomme Hadrien , Tchignoumba Landry , Deichmann Jessica L. , Maldonado Jesús E. , Korte Lisa , Alonso Alfonso
Published: September 2019

We investigated the patterns of genetic diversity and structure of African forest elephants in a human‐modified landscape in the Gamba complex of protected areas (GCPA), a tropical wilderness area along the southwest coast of Gabon. We collected 298 elephant fecal samples from four sites (Sette Cama, Gamba area, Vera Plains, and Mayonami), along approximately 80 km of coastline from north to south. We used microsatellites and mitochondrial DNA (mtDNA) to successfully genotype 295 of the 298 fecal samples, and identified 213 individuals. Using sex markers, we identified 84 males and 118 females; we could not determine the sex of the remaining 11 individuals. We also characterized the sex, group size, and social status of crop‐raiding elephants and did not find characteristics distinguishing them from nonraiders. Overall, our mtDNA and microsatellite markers revealed that elephants in the research area maintain high levels of genetic variation and low levels of subdivision. Gene flow appears to be mostly mediated by male dispersal away from natal herds. Our structure analysis revealed two highly admixed genetic clusters, attributable to high connectivity among the protected areas. However, forest areas within the GCPA have become increasingly fragmented by human‐induced habitat modification. We detected a pattern of isolation by distance, accentuated by the presence of the town of Gamba between Sette‐Cama and Mayonami. We found a high degree of connectivity among sampling locations within the GCPA. This supports the importance of establishing agricultural best practices to reduce habitat loss that may sever gene exchange and to maintain connectivity, as well as to avoid human–elephant conflict that can result in retaliatory killing of elephants in this area. This study emphasizes the importance of conducting baseline monitoring of demographic data, genetic diversity, and structure to enable future comparisons to assess the long‐term impact of human‐induced habitat fragmentation.
Risk of potential pesticide use to honeybee and bumblebee survival and distribution: A country‐wide analysis for The Netherlands
Authors: Yasrebi‐de Kom Izak A. R. , Biesmeijer Jacobus C. , Aguirre‐Gutiérrez Jesús
Published: September 2019

Aim

Bees play an important role in natural ecosystems and the world's food supply. In the past decades, bee abundance and diversity have declined globally. This has resulted in decreased pollination services for natural ecosystems and the agricultural sector at the field scale. One of the causes of the decline in bee abundance and diversity is the use of pesticides. Linking pesticide use, land use and bee presence could provide crucial insights into areas, and pesticides that pose a significant threat to the abundance and diversity of bees. Obtaining actual figures of farmer pesticide use is rarely possible. Therefore, we designed a method to study the effects of potential pesticide use on the survival and distribution of honeybees and bumblebees.

Location

The Netherlands.

Methods

A pesticide risk model was implemented incorporating a hazard quotient as the risk assessment. The number of allowed pesticide active ingredients per crop that could pose a risk to honeybees and bumblebees was linked to the Dutch crop parcel locations for 2015 and 2016. The potential pesticide risk maps were analysed using honeybee colony survival and bumblebee presence data.

Results

Non‐significant negative effects of potential pesticide risk on honeybee colony survival and bumblebee presence were found. A significant negative effect of greenhouses was identified for both honeybees and bumblebees. The most important factors in the models predicting honeybee colony survival and bumblebee presence were urban land areas and natural grasslands, respectively, both showing a positive effect.

Main conclusions

Here, the first attempt to estimate and map pesticide risk to bees in the Netherlands in a country‐wide manner is presented. The results could provide crucial high‐resolution insights for bee conservation action and facilitate the increase of pollination services in natural ecosystems and the agricultural sector on a local and country‐wide scale.
Caveat consumptor notitia museo: Let the museum data user beware
Authors: Nekola Jeffrey C. , Hutchins Benjamin T. , Schofield Alison , Najev Briante , Perez Kathryn E.
Published: September 2019

Issue

Lot accession information from natural history collections represents a potentially vital source of large datasets to test biodiversity, biogeography and macroecology hypotheses. But does such information provide an accurate portrayal of the natural world? We review the many types of bias and error intrinsic to museum collection data and consider how these factors may affect their ability to accurately test ecological hypotheses.

Evidence

We considered all Texas land snail collections from the two major repositories in the state and compared them with an ecological sample drawn across the same landscape. We found that museum collection localities were biased in favour of regions with higher human population densities and iconic destinations. They also tended to be made during attractive temporal windows. Small, uncharismatic taxa tended to be under‐collected while larger, charismatic species were over‐collected. As a result, for most species it was impossible to use museum lot frequency to accurately predict frequency and abundance in an ecological sample. Species misidentification rate was approximately 20%, while 4% of lots represented more than one species. Errors were spread across the entire shell size spectrum and were present in 75% of taxonomic families. Contingency table analysis documented significant dependence of both misidentification and mixed lot rates upon shell size and family richness.

Conclusion

Researchers should limit their use of museum record data to situations where their inherent biases and errors are irrelevant, rectifiable or explicitly considered. At the same time museums should begin incorporating expert specimen verification into their digitization programs.
Environmental factors explain the spatial mismatches between species richness and phylogenetic diversity of terrestrial mammals
Authors: Barreto Elisa , Graham Catherine H. , Rangel Thiago F.
Published: September 2019

Aim

Explore the spatial variation of the relationships between species richness (SR), phylogenetic diversity (PD) and environmental factors to infer the possible mechanisms underlying patterns of diversity in different regions of the globe.

Location

Global.

Time period

Present day.

Major taxa studied

Terrestrial mammals.

Methods

We used a hexagonal grid to map SR and PD of mammals and four environmental factors (temperature, productivity, elevation and climate‐change velocity since the Last Glacial Maximum). We related those variables through direct and indirect pathways using a novel combination of path analysis and geographically weighted regression to account for spatial non‐stationarity of path coefficients.

Results

Species richness, PD and environmental factors relate differently across the geographical space, with most relationships varying in both magnitude and direction. Species richness is associated with lower PD in much of the tropics and in the Americas, which reflects the tropical origin and the recent diversification of some mammalian clades in these regions. Environmental effects on PD are predominantly mediated by their effects on SR. But once richness is controlled for, the relationships between environmental factors and PD (i.e. PDSR) highlight environmentally driven changes in species composition. Environmental–PDSR relationships suggest that the relative importance of different mechanisms driving biodiversity shifts spatially. Across most of the globe, temperature and productivity are the strongest predictors of richness, whereas PDSR is best predicted by temperature.

Main conclusions

Richness explains most spatial variation in PD, but both dimensions of biodiversity respond differently to environmental conditions across the globe, as indicated by the spatial mismatches in the relationships between environmental factors and these two types of diversity. We show that accounting for spatial non‐stationarity and environmental effects on PD while controlling for richness uncovers a more complex scenario of drivers of biodiversity than previously observed.
Blood donor–recipient sex mismatch: outcomes impacted?
Authors: Tran Minh‐Ha
Published: September 2019

Background and objectives

A number of recent publications have questioned whether female donor transfusions (particularly of red cells) or donor–recipient sex mismatch are associated with increased risk for mortality. A systematic review was conducted to further explore this concern.

Materials and methods

A literature search was performed to identify original studies linking red‐blood‐cell transfusion donor or recipient gender to mortality risk. Exclusion criteria included (1) absence of a focus on gender mismatch and mortality outcomes, (2) nonclinical studies, (3) non‐English language studies.

Results

The initial search strategy yielded 136 results and 8 studies met all selection criteria. An additional 2 studies were found by supplemental search. Six of the ten studies reported increased mortality risk with sex mismatch, while four reported no increase in mortality. Study end‐points varied, thus limiting generalizability. Conflicting evidence was noted in regard to female donor sex, sex mismatch, directionality of risk, age of donors and recipients, and transfusion burden.

Conclusion

Additional studies are needed to resolve this issue. As the majority of studies relied upon a ‘big data’ approach, there is concern for subtle confounding.