bluuebunny/crossref_metadata_2025 huggingface dataset:
A Weakness for the Maasai
Authors: Lekan Thomas M.
Published: January 2020

This chapter examines the ground-level debates over pastoral land rights that lay outside the aerial camera’s frame in Serengeti Shall Not Die. When the British gazetted Serengeti National Park in 1951, Tanganyika’s colonial government had guaranteed the Maasai rights of occupancy because they did not traditionally hunt and were deemed part of the natural landscape. Yet a prolonged drought brought increasing numbers of Maasai into the parklands in search of better-watered highland grazing, causing conflict with park officials. Such movements, coupled with scientific and administrative misunderstanding of transhumance and savanna resilience, led the British to propose excising the Ngorongoro region from the park to accommodate local land use. The Grzimeks and a “green network” of international allies asserted that cattle herding and wildlife conservation were incompatible due to livestock’s overgrazing. They buttressed this ecological claim with fears of racial degeneration, claiming that there were no more “true-blooded” Maasai left in the Serengeti. The Grzimeks’ advocacy helped to transform a colonial debate about “native” rights into an international scandal. The green network had discredited British imperialism yet inherited many of its paternalist assumptions about traditional African land use and modernist development.
An Honest Broker for the Animals
Authors: Lekan Thomas M.
Published: January 2020

This chapter examines how Bernhard Grzimek relaunched his quest to save the Serengeti in the wake of his son Michael’s death and the shift toward African self-rule under the leadership of Tanganyika’s new prime minister Julius Nyerere in 1960–1961. Unlike his compatriots in the IUCN who feared black-majority rule, Grzimek saw decolonization as a time of opportunity. He convinced Nyerere that expanding the country’s national park system would catalyze socioeconomic development through tourism, technical assistance, and direct aid. Working alongside John Owen, the director of Tanganyikan National Parks, Grzimek developed a para-diplomatic style of advocacy that promoted package tours and solicited donations on television and secured bilateral aid outside official state protocols. Such efforts created a strange alliance between nature conservationists hoping to curtail rural development and African modernizers hoping to promote it. These varied interests came together at Arusha in September 1961 at a landmark UNESCO-sponsored symposium where Nyerere pledged to protect Tanganyika’s wildlife inheritance so long as Europeans made good on their promises.
Who Cares for Africa’s Game?
Authors: Lekan Thomas M.
Published: January 2020

This chapter examines Bernhard Grzimek’s increasing inability to broker conservation politics in Tanzania during the 1960s as the country moved toward self-reliance and the Africanization of the wildlife sector. Grzimek found it difficult to make wildlife pay for themselves due to logistical problems of West German game-cropping projects, insufficient donations for expanding and maintaining Tanganyika’s national park system, and competition with Kenya for East Africa’s share of the wildlife tourism market. Such failures shaped and were shaped by Tanzania’s shift toward socialist development and Eastern Bloc partnerships that further jeopardized a tourism industry catering to foreign desires. Friction between Western conservationists and agricultural minister Derek Bryceson over Tanzania’s conservation priorities alienated Nyerere and other African observers, who resented international conservationists meddling in “national” heritage. The Africanization of the national park leadership in the early 1970s signaled that the fate of the Serengeti’s wild animals lay in Nyerere’s hands—not Grzimek’s.
Epilogue
Authors: Lekan Thomas M.
Published: January 2020

Six decades after the Grzimeks first arrived in the Serengeti, their quest still shapes the way that tourists, scientists, park staff, and Tanzanians are invited to understand the park’s origins and its significance for global conservation, as this short ethnographic moment at the Serengeti Visitor Center in Seronera reveals. A better exhibit script, one more attuned to a Tanzanian national context, would dispense with the white “charismatic megascientist” theme and focus squarely on the hopes and aspirations of political modernizers and customary land users in the early 1960s. Without a retooling of public outreach, the goal of integrated conservation and development in the Serengeti that is attuned to local priorities cannot be achieved.
Embarking: The Pittsburgh Survey, Workers’ Compensation, and the First Blush of Fame
Authors: Aronson Amy
Published: January 2020

In 1907, Crystal Eastman began a temporary job investigating industrial accidents with the Pittsburgh Survey, a comprehensive study of urban industrial life organized by Paul Kellogg and Edward Devine, financed by the newly formed Russell Sage Foundation. The project involved established leaders, such as Florence Kelley and John R. Commons, as well as young visual artists, including Lewis Hine and Joseph Stella, and brought a new generation of educated women into professional work in social welfare. Eastman’s study, later published as Work Accidents and the Law (1910), resulted in her appointment by Governor Charles Evans Hughes to chair New York’s new commission on employer liability in 1909. There, she proposed to overhaul common law standards, shifting to a no-fault distribution of risk and loss shared by workers, businesses, and consumers. The resulting legislation failed a constitutional challenge in 1911 but laid the groundwork for successful workers’ compensation laws in New York State and elsewhere.
Passages: Feminism, Journalism, and the Transatlantic Twenties
Authors: Aronson Amy
Published: January 2020

After the vote was won, Crystal Eastman hoped to transform successful but single-issue suffragism into a class- and race-conscious, transnationally minded feminism. She ran afoul of Alice Paul, unquestioned leader of the National Woman’s Party, who wanted another targeted single-issue campaign. By 1923, Eastman, Paul, and the organization agreed on the Equal Rights Amendment (ERA) as their new “great demand.” In its all-encompassing simplicity, the ERA solved the problem of how a single-issue campaign could seek redress for the huge and complicated problem of gender inequality. Unfortunately, the idea splintered coalitions in the wider women’s movement, alienating the party from a whole network of once-compatible Progressive groups. Eastman, now living in her husband’s native London with their children, worked as a journalist, covering this debate. By 1926, little progress had been made, and she welcomed a fresh tack. She began working with Paul to campaign for equal rights provisions in international treaties.
Coming Home
Authors: Aronson Amy
Published: January 2020

By 1927, Crystal Eastman had been living as the freelance journalist she never wanted to be, pitching article after article to conservative or capricious editors. She had recently covered the momentous International Woman Suffrage Alliance congress in Paris, but was generally exhausted from childcare and homemaking, frustrated by declining health, and almost always behind in her bills. She longed to return to home. Paul Kellogg advised patient planning and supplied a prescient idea for new line of work, but she returned to New York quite hastily, with only a short speaking engagement planned. Three weeks later, Walter died of a cerebral hemorrhage. Deep in mourning, Eastman began a temporary job organizing a celebration for The Nation. Her colleagues noticed she was fighting a tremendous battle. In fact, she was mortally ill. Her kidneys, damaged long ago by scarlet fever, were now giving out. Ten months later, she passed away.
Energy conditions in arbitrary dimensions
Authors: Maeda Hideki , Martínez Cristián
Published: January 2020

Energy conditions for matter fields are comprehensively investigated in arbitrary $n(\ge 3)$ dimensions without specifying future and past directions locally. We classify an energy–momentum tensor into $n$-dimensional counterparts of the Hawking–Ellis types I to IV, where type III is defined by a more useful form than those adopted by Hawking and Ellis and other authors to identify the type-III energy–momentum tensor in a given spacetime. We also provide necessary and sufficient conditions for types I and II as inequalities for the orthonormal components of the energy–momentum tensor in a canonical form and show that types III and IV violate all the standard energy conditions. Lastly, we study energy conditions for a set of physically motivated matter fields.
Low-density granulocytes and monocytes as biomarkers of cardiovascular risk in systemic lupus erythematosus
Authors: López Patricia , Rodríguez-Carrio Javier , Martínez-Zapico Aleida , Pérez-Álvarez Ángel I , Suárez-Díaz Silvia , Mozo Lourdes , Benavente Lorena , Caminal-Montero Luis , Suárez Ana
Published: January 2020

Objective

The aim was to evaluate the most relevant cell populations involved in vascular homeostasis as potential biomarkers of SLE-related cardiovascular disease (CVD).

Methods

Low-density granulocytes (LDGs), monocyte subsets, endothelial progenitor cells, angiogenic T (Tang) cells, CD4+CD28null and Th1/Th17 lymphocytes and serum cytokine levels were quantified in 109 SLE patients and 33 controls in relationship to the presence of subclinical carotid atheromatosis or cardiovascular disease. A second cohort including 31 recent-onset SLE patients was also included.

Results

Raised monocyte and LDG counts, particularly those LDGs negative for CD16/CD14 expression (nLDGs), in addition to the ratios of monocytes and nLDGs to high-density lipoprotein-cholesterol (HDLc) molecules (MHR and nLHR, respectively), were present in SLE patients with traditional risk factors or subclinical atheromatosis but not in those who were CV-free, thus revealing their value in the identification of patients at risk of CVD, even at the onset of disease. Accordingly, nLDGs were correlated positively with carotid intima–media thickness (cIMT) and with inflammatory markers (CRP and IL-6). A bias towards more differentiated monocyte subsets, related to increased IFN-α and IL-17 serum levels, was also observed in patients. Intermediate monocytes were especially expanded, but independently of their involvement in CVD. Finally, CD4+CD28null, Th17 and Th1 lymphocytes were increased, with CD4+CD28null and Th17 cells being associated with cIMT, whereas endothelial progenitor and Tang cell levels were reduced in all SLE patients.

Conclusion

The present study highlights the potential use of MHR and nLHR as valuable biomarkers of CVD risk in SLE patients, even at diagnosis. The increased amounts of nLDGs, monocytes, Th17 and senescent-CD28null subsets, coupled with reduced pro-angiogenic endothelial progenitor cells and Tang cells, could underlie the development of atheromatosis in SLE.
Properties and abundance of overlapping genes in viruses
Authors: Schlub Timothy E , Holmes Edward C
Published: January 2020

Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering <10 nt, and 84 per cent are <50 nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families.
Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
Authors: Lassalle Florent , Beale Mathew A , Bharucha Tehmina , Williams Charlotte A , Williams Rachel J , Cudini Juliana , Goldstein Richard , Haque Tanzina , Depledge Daniel P , Breuer Judith
Published: January 2020

Herpes Simplex Virus type 1 (HSV-1) chronically infects over 70 per cent of the global population. Clinical manifestations are largely restricted to recurrent epidermal vesicles. However, HSV-1 also leads to encephalitis, the infection of the brain parenchyma, with high associated rates of mortality and morbidity. In this study, we performed target enrichment followed by direct sequencing of HSV-1 genomes, using target enrichment methods on the cerebrospinal fluid (CSF) of clinical encephalitis patients and from skin swabs of epidermal vesicles on non-encephalopathic patients. Phylogenetic analysis revealed high inter-host diversity and little population structure. In contrast, samples from different lesions in the same patient clustered with similar patterns of allelic variants. Comparison of consensus genome sequences shows HSV-1 has been freely recombining, except for distinct islands of linkage disequilibrium (LD). This suggests functional constraints prevent recombination between certain genes, notably those encoding pairs of interacting proteins. Distinct LD patterns characterised subsets of viruses recovered from CSF and skin lesions, which may reflect different evolutionary constraints in different body compartments. Functions of genes under differential constraint related to immunity or tropism and provide new hypotheses on tissue-specific mechanisms of viral infection and latency.
Resilience: nitrogen limitation, mycorrhiza and long-term palaeoecological plant–nutrient dynamics
Authors: Bonsall Michael B. , Froyd Cynthia A. , Jeffers Elizabeth S.
Published: January 2020

Ecosystem dynamics are driven by both biotic and abiotic processes, and perturbations can push ecosystems into novel dynamical regimes. Plant–plant, plant–soil and mycorrhizal associations all affect plant ecosystem dynamics; however, the direction and magnitude of these effects vary by context and their contribution to ecosystem resilience over long time periods remains unknown. Here, using a mathematical framework, we investigate the effects of plant feedbacks and mycorrhiza on plant–nutrient interactions. We show evidence for strong nutrient controlled feedbacks, moderation by mycorrhiza and influence on ecological resilience. We use this model to investigate the resilience of a longitudinal palaeoecological birch–
δ
15
N interaction to plant–soil feedbacks and mycorrhizal associations. The birch–
δ
15
N system demonstrated high levels of resilience. Mycorrhiza were predicted to increase resilience by supporting plant–nitrogen uptake and immobilizing excess nitrogen; in contrast, long-term enrichment in available nitrogen by plant–soil feedbacks is expected to decrease ecological resilience.
Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996
Authors: Infante-Domínguez Carmen , de la Haba Rafael R. , Corral Paulina , Sanchez-Porro Cristina , Arahal David R. , Ventosa Antonio
Published: January 2020

A comparative taxonomic study of

Halorubrum distributum

,

Halorubrum terrestre

,

Halorubrum arcis

and

Halorubrum litoreum

was carried out using different approaches, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), phylogenomic analysis based on the comparison of the core genome, orthologous average nucleotide identity (OrthoANI), Genome-to-Genome Distance Calculator (GGDC), synteny plots and polar lipid profile (PLP). The MLSA study, using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB′, and the phylogenomic analysis based on 1347 core translated gene sequences obtained from their genomes showed that

Halorubrum distributum

JCM 9100T,

Halorubrum terrestre

JCM 10247T,

Halorubrum arcis

JCM 13916T and

Halorubrum litoreum

JCM 13561T formed a robust cluster, clearly separated from the rest of species of the genus

Halorubrum

. The OrthoANI and digital DDH values, calculated by the GGDC, showed percentages among Hrr. distributum JCM 9100T, Hrr. terrestre JCM 10247T, Hrr. arcis JCM 13916T and Hrr. litoreum JCM 13561T that ranged from 98.1 to 97.5 %, and 84.0 to 78.0 %, respectively, while these values among those strains and the type strains of their most related species of

Halorubrum

were equal or lower than 90.8 and 41.2 %, respectively. Moreover, degree of synteny across the four genomes was very high, especially between the genomes of

Halorubrum litoreum

JCM 13561T and

Halorubrum arcis

JCM 13916T. In addition, the PLP is quite similar among the four strains studied, showing a common pattern typical of the neutrophilic species of the genus

Halorubrum

. Overall, these data show that Hrr. distributum, Hrr. terrestre, Hrr. arcis and Hrr. litoreum constitute a single species. Thus, the latter three should be considered as later, heterotypic synonyms of Hrr. distributum based on the rules for priority of names. We propose an emended description of Hrr. distributum, including the features of Hrr. terrestre, Hrr. arcis and Hrr. litoreum.
Dictyobacter vulcani sp. nov., belonging to the class Ktedonobacteria, isolated from soil of the Mt Zao volcano
Authors: Zheng Yu , Wang Chiung-mei , Sakai Yasuteru , Abe Keietsu , Yokota Akira , Yabe Shuhei
Published: January 2020

An aerobic, Gram-stain-positive, mesophilic

Ktedonobacteria

strain, W12T, was isolated from soil of the Mt Zao volcano in Miyagi, Japan. Cells were filamentous, non-motile, and grew at 20–37 °C (optimally at 30 °C), at pH 5.0–7.0 (optimally at pH 6.0) and with <2 % (w/v) NaCl on 10-fold diluted Reasoner’s 2A (R2A) medium. Oval-shaped spores were formed on aerial mycelia. Strain W12T hydrolysed microcrystalline cellulose and xylan very weakly, and used d-glucose as its sole carbon source. The major menaquinone was MK-9, and the major cellular fatty acids were C16 : 1 2-OH, iso-C17 : 0, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and anteiso-C17 : 0. Cell-wall sugars were mannose and xylose, and cell-wall amino acids were d-glutamic acid, glycine, l-serine, d-alanine, l-alanine, β-alanine and l-ornithine. Polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. Strain W12T has a genome of 7.42 Mb with 49.7 mol% G+C content. Nine copies of 16S rRNA genes with a maximum dissimilarity of 1.02 % and 13 biosynthetic gene clusters mainly coding for peptide products were predicted in the genome. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that strain W12T represents a novel species in the genus

Dictyobacter

. The most closely related

Dictyobacter

type strain was

Dictyobacter alpinus

Uno16T, with 16S rRNA gene sequence similarity and genomic average nucleotide identity of 98.37 % and 80.00 %, respectively. Herein, we propose the name Dictyobacter vulcani sp. nov. for the type strain W12T (=NBRC 113551T=BCRC 81169T) in the bacterial class

Ktedonobacteria

.
Corynebacterium suranareeae sp. nov., a glutamate producing bacterium isolated from soil and its complete genome-based analysis
Authors: Nantapong Nawarat , Matsutani Minenosuke , Kanchanasin Pawina , Kataoka Naoya , Paisrisan Pawantree , Matsushita Kazunobu , Tanasupawat Somboon
Published: January 2020

Strain N24T was isolated from soil contaminated with starling’s feces collected from Roi-Et province, Thailand. Cells of N24T were Gram-stain-positive rods, aerobic and non-spore-forming. N24T was positive for catalase, urease, citrate utilization, nitrate reduction and Methyl Red (MR) test but negative for oxidase, casein, gelatin liquefaction, tyrosine, Voges–Proskauer (VP) reaction and starch hydrolysis. Meso-diaminopimelic acid, rhamnose, ribose, arabinose and galactose were detected in its whole-cell hydrolysates. The results of the 16S rRNA gene sequence analysis indicated that N24T represented a member of the genus

Corynebacterium

. N24T was closely related to

Corynebacterium glutamicum

ATCC 13032T, with 99.0 % 16S rRNA gene sequence similarity. According to results obtained using in silico DNA–DNA hybridization approaches, N24T showed highest DNA–DNA relatedness (27.6 %) and average nucleotide identity (84.1 %) to

Corynebacterium glutamicum

ATCC 13032T. The DNA G+C content of N24T was 51.8 mol% (genome based). The major cellular fatty acids of N24T were C16 : 0, and C18 : 1ω9c. N24T had the nine isoprenes unit, MK-9(H2) as the predominant menaquinone. The predominant polar lipids were phosphatidylglycerol, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were also present. According to the complete genome sequence data, strain N24T and

C. glutamicum

ATCC 13032T are close phylogenetic neighbours, but have different genome characteristics. On the basis of the results of the genotypic and genomic studies and phenotypic characteristics including chemotaxonomy, strain N24T should be classified as representing a novel species of the genus

Corynebacterium

, for which the name Corynebacterium suranareeae sp. nov. is proposed. The type strain is N24T (TBRC 5845T=NBRC 113465T).
Serratia vespertilionis (García-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981)
Authors: García-Fraile Paula , Spröer Cathrin , Chesneau Olivier , Criscuolo Alexis , Lang Elke , Clermont Dominique
Published: January 2020

A previous 16S rRNA gene sequence comparison had demonstrated that the type strains of

Serratia vespertilionis

and

Serratia ficaria

shared 99.5 % sequence similarity. Despite the 56.2 % homology by DNA–DNA hybridization previously found between these strains, the results of an in silico whole-genome sequence comparison and a new DNA–DNA hybridization study have clearly demonstrated that the genomes of the type strain of

S. vespertilionis

deposited in different Culture Collections (52T=CECT 8595T=DSM 28727T) and the type strain of

S. ficaria

(culture DSM 4569T), cannot support such a species differentiation. Tests for substrate utilization redone on the deposited cultures of these strains has also shown very few differences between the type strains of both species. Based on these results, and since the name

S. ficaria

was validly published earlier,

S. vespertilionis

should be considered as a later heterotypic synonym of

S. ficaria

, in application of the priority rule. The type strain of the species

S. ficaria

is strain 4024T=DSM 4569T=NCTC 12148T=ATCC 33105T=CIP 79.23T=ICPB 4050T.
Halostella pelagica sp. nov. and Halostella litorea sp. nov., isolated from salted brown alga Laminaria
Authors: Han Dong , Cui Heng-Lin
Published: January 2020

Three rod-shaped halophilic archaeal strains, DL-M4T, LYG-109 and DLLS-108T, were isolated from the salted brown alga Laminaria produced in different marine areas of PR China. Cells of strains were motile, formed red-pigmented colonies on agar and lysed in distilled water. The three strains grew optimally with 2.6 M NaCl, with 0.05–0.3 M MgCl2, at 37 °C and at pH 7.0–7.5. The results of phylogenetic analyses based on the 16S rRNA and rpoB′ genes differentiated these strains into two clusters belonging to the genus

Halostella

, which currently contains

Halostella salina

CBA1114T and

Halostella limicola

LT12T. Strains DL-M4T and LYG-109 formed a single cluster separate from the current two members of

Halostella

(94.4–95.7 and 90.0–90.9 % similarities, respectively) while strain DLLS-108T had Hsl. salina CBA1114T as its nearest neighbour (97.7–97.8 and 95.9 % similarities, respectively) and was separated from Hsl. limicola LT12T (94.4–95.8 and 93.4 % similarities, respectively). These clusters represented two distinct novel species as indicated by phenotypic characteristics, polar lipid compositions and whole-genome comparisons. Diverse phenotypic characteristics, morphology and growth characteristics, nutrition and miscellaneous biochemical tests differentiate strains DL-M4T, LYG-109, DLLS-108T from Hsl. limicola LT12T and Hsl. salina CBA1114T. Strains DL-M4T and LYG-109 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three unidentified glycolipids, while strain DLLS-108T contained these polar lipids and two unidentified phospholipids. The major respiratory quinones detected in the three isolates were menaquinone MK-8 and MK-8(H2). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the isolated strains and the current two members of

Halostella

were found to be 79.3–86.6 (ANI) and 22.9–49.8 % (isDDH). All these results showed that the three isolates represent two novel species of the genus

Halostella

for which the names Halostella pelagica sp. nov. [type strain dl-M4T (=CGMCC 1.13603T=JCM 32954T)] and Halostella litorea sp. nov. [type strain DLLS-108T(=CGMCC 1.13610T=JCM 32955T)] are proposed.
Metastatic breast cancer patient perception of somatic tumor genomic testing
Authors: Adams Elizabeth J. , Asad Sarah , Reinbolt Raquel , Collier Katharine A. , Abdel-Rasoul Mahmoud , Gillespie Susan , Chen James L. , Cherian Mathew A. , Noonan Anne M. , Sardesai Sagar , VanDeusen Jeffrey , Wesolowski Robert , Williams Nicole , Shapiro Charles L. , Macrae Erin R. , Pilarski Robert , Toland Amanda E. , Senter Leigha , Ramaswamy Bhuvaneswari , Lee Clara N. , Lustberg Maryam B. , Stover Daniel G.
Published: January 2020

Purpose

To assess metastatic breast cancer (MBC) patient perceptions and comprehension of tumor genomic testing and to evaluate associations with psychological wellbeing.

Methods

In a prospective, single institution, single-arm trial, patients with MBC underwent next-generation sequencing at study entry, with sequencing results released at progression. Patients who completed surveys before undergoing sequencing were included in the study (n=58). We administered four validated psychosocial measures: Center for Epidemiologic Studies Depression Scale, Beck Anxiety Inventory, Trust in Physician Scale, and Communication and Attitudinal Self-Efficacy scale for Cancer. Genetic comprehension was assessed using 7-question objective and 6-question subjective measures. Longitudinal data were assessed using paired Wilcoxon signed rank and McNemar’s test of agreement.

Results

There were no significant differences between the beginning and end of study in depression, anxiety, physician trust, or self-efficacy (median time on study: 7.6 months). Depression and anxiety were positively associated with each other and both negatively associated with self-efficacy. Self-efficacy decreased from pre-to post-genomic testing (p=0.05). There was a wide range of objective genetics comprehension and comprehension was significantly lower in non-white patients (p=0.02) and patients with lower income (p=0.04). Patients expressed increased confidence in their ability to teach others about genetics at end of study.

Conclusions

This is the only study, to our knowledge, to longitudinally evaluate multiple psychological metrics in MBC as patients undergo tumor genomic testing. Among patients with MBC, depression and anxiety metrics were negatively correlated with patient self-efficacy. Patients undergoing somatic genomic testing had limited genomic knowledge, which varied by demographic groups.
Frequent Daytime Napping is Detrimental to Human Health: A phenotype-wide Mendelian Randomization Study
Authors: Chen Lanlan , Tian Aowen , Liu Zhipeng , Zhang Miaoran , Pan Xingchen , He Chang , Liu Wanqing , Chen Peng
Published: January 2020

Background

It remains controversial whether daytime napping is beneficial for human health.

Objective

To examine the causal relationship between daytime napping and the risk for various human diseases.

Design

Phenotype-wide Mendelian randomization study.

Setting

Non-UK Biobank cohorts reported in published genome-wide association studies (GWAS) provided the outcome phenotypes in the discovery stage. The UK Biobank cohort provided the outcome phenotypes in the validation stage.

Participants

The UK Biobank GWAS included 361,194 European-ancestry residents in the UK. Non-UKBB GWAS included various numbers of participants.

Exposure

Self-reported daytime napping frequency.

Main outcome measure

A wide-spectrum of human health outcomes including obesity, major depressive disorder, and high cholesterol.

Methods

We examined the causal relationship between daytime napping frequency in the UK Biobank as exposure and a panel of 1,146 health outcomes reported in genome-wide association studies (GWAS), using a two-sample Mendelian randomization analysis. The significant findings were further validated in the UK Biobank health outcomes of 4,203 human traits and diseases. The causal effects were estimated using a fixed-effect inverse variance weighted model. MR-Egger intercept test was applied to detect horizontal pleiotropy, along with Cochran’s Q test to assess heterogeneity among the causal effects of IVs.

Findings

There were significant causal relationships between daytime napping frequency and a wide spectrum of human health outcomes. In particular, we validated that frequent daytime napping increased the risks of major depressive disorder, obesity and abnormal lipid profile.

Interpretation

The current study showed that frequent daytime napping mainly had adverse impacts on physical and mental health. Cautions should be taken for health recommendations on daytime napping. Further studies are necessary to precisely define the best daytime napping strategies.
Age differences in retrieval-related reinstatement reflect age-related dedifferentiation at encoding
Authors: Hill Paul F. , King Danielle R. , Rugg Michael D.
Published: January 2020

Age-related reductions in neural specificity have been linked to cognitive decline. We examined whether age differences in specificity of retrieval-related cortical reinstatement could be explained by analogous differences at encoding, and whether reinstatement was associated with memory performance in an age-dependent or age-independent manner. Young and older adults underwent fMRI as they encoded words paired with images of faces or scenes. During a subsequent scanned memory test participants judged whether test words were studied or unstudied and, for words judged studied, also made a source memory judgment about the associated image category. Using multi-voxel pattern analyses, we identified a robust age-related decline in scene reinstatement. This decline was fully explained by age differences in neural differentiation at encoding. These results suggest that, regardless of age, the specificity with which events are neurally processed at the time of encoding determines the fidelity of cortical reinstatement at retrieval.
Visual and oculomotor abilities predict professional baseball batting performance
Authors: Liu Sicong , Edmunds Frederick R. , Burris Kyle , Appelbaum Lawrence Gregory
Published: January 2020

Scientists and practitioners have long debated about the specific visual skills needed to excel at hitting a pitched baseball. This study aimed to advance the debate by evaluating the relationship between pre-season visual and oculomotor evaluations and pitch-by-pitch season performance data from professional baseball batters. Eye tracking, visual-motor, and optometric evaluations collected during spring training 2018 were obtained from 71 professional baseball players. Pitch-level data from Trackman 3D Doppler radar were obtained from these players during the subsequent season and used to generate batting propensity scores for swinging at pitches out of the strike zone (O-Swing), swinging at pitches in the strike zone (Z-Swing), and swinging at, but missing pitches in the strike zone (Z-Miss). Nested regression models were used to test which vision-related evaluation(s) could best predict the standardized plate discipline scores as well as the batters’ highest attained league levels during the season. Results indicated that visual evaluations relying on eye tracking (e.g., smooth pursuit accuracy and oculomotor processing speed) significantly predicted the highest attained league level and the propensity scores associated with O-Swing and Z-Swing, but not Z-Miss. These exploratory findings indicate that batters with superior visual and oculomotor abilities are generally more discerning at the plate. When combined with other known performance advantages in perceptual and cognitive abilities for elite athletes, these results provide a wholistic view of visual expertise in athletes.
TMSNP: a web server to predict pathogenesis of missense mutations in transmembrane region of membrane proteins
Authors: Garcia-Recio Adrián , Gómez-Tamayo José Carlos , Reina Iker , Campillo Mercedes , Cordomí Arnau , Olivella Mireia
Published: January 2020

The massive amount of data generated from genome sequencing have given rise to several mutation predictor tools although no mutation database or predictor tool have been developed specifically for the transmembrane region of membrane proteins.

We present TMSNP, a database that currently contains information from 2624 pathogenic and 195964 non-pathogenic reported mutations located on the TM region of membrane proteins. The computed conservation parameters and annotations on these mutations were used to train a machine-learning model that classifies TM mutations as pathogenic or non-pathogenic. The presented tool improves considerably the prediction power of commonly used mutation predictors and additionally represents the first mutation prediction tool specific for TM mutations.

TMSNP is available athttp://lmc.uab.es/tmsnp/

Contact

mireia.olivella@esci.upf.edu
The role of maternal effects on offspring performance in familiar and novel environments
Authors: Vrtílek Milan , Chuard Pierre J. C. , Iglesias-Carrasco Maider , Jennions Michael D. , Head Megan L.
Published: January 2020

Maternal effects are an important evolutionary force that may either facilitate adaptation to a new environment or buffer against unfavourable conditions. The degree of variation in traits expressed by siblings from different mothers is frequently sensitive to environmental conditions. This could generate a Maternal-by-Environment interaction (M×E) that could inflate estimates of Genotype-by-Environment effects (G×E). We aimed to test for environment-specific maternal effects (M×E) using a paternal full-sib/half-sib breeding design in the seed beetleCallosobruchus maculatus,where we split and reared offspring from the same mother on two different bean host types – original and novel. Our quantitative genetic analysis indicated that maternal effects were very small on both host types for all the measured life-history traits. There was also little evidence that maternal oviposition preference for a particular host type predicted her offspring’s performance on that host. Further, additive genetic variance for most traits was relatively high on both hosts. While there was higher heritability for offspring reared in the novel host, there was no evidence for G×Es, and most cross-host genetic correlations were positive. This suggests that offspring from the same family ranked similarly for performance on both host types. Our results point to a genetic basis of host adaptation in the seed beetle, rather than maternal effects. Even so, we encourage researchers to test for potential M×Es because, due to a lack of testing, it remains unclear how often they arise.
Local translation in perisynaptic astrocytic processes is specific and regulated by fear conditioning
Authors: Mazaré Noémie , Oudart Marc , Moulard Julien , Cheung Giselle , Tortuyaux Romain , Mailly Philippe , Mazaud David , Bemelmans Alexis-Pierre , Boulay Anne-Cécile , Blugeon Corinne , Jourdren Laurent , Le Crom Stéphane , Rouach Nathalie , Cohen-Salmon Martine
Published: January 2020

Local translation is a conserved molecular mechanism conferring cells the ability to quickly respond to local stimuli. It not only permits cells with complex morphology to bypass somatic protein synthesis and transport, but also contributes locally to the establishment of molecular and functional polarity. In the brain, local translation has been extensively studied in neurons and has only been recently reported in astrocytes, whose fine processes contact both blood vessels and synapses. Yet the specificity and regulation of astrocyte local translation remain unknown. Here, we studied hippocampal perisynaptic astrocytic processes (PAPs) and show that they contain all the machinery for translation. Using our recently refined polysome immunoprecipitation technique, we then characterized the pool of polysomal mRNAs in PAPs, referred to as the PAPome, and compared it to the one found in the whole astrocyte. We found that the PAPome encoded an unexpected molecular repertoire, mostly composed of cytoplasmic proteins and of proteins involved in iron homeostasis, translation, cell cycle and cytoskeleton. Among them, ezrin (Ezr), ferritin heavy chain 1 (Fth1) and 60S acidic ribosomal protein1 (Rplp1) were enriched in PAPs compared to perivascular astrocytic processes, indicating that local translation differs at these two interfaces. Remarkably, PAPs were also enriched in transcripts coding for proteins involved in learning and memory, such as ferritin (Ftl1 and Fth1), G1/S-specific cyclin-D2 (Ccnd2), E3 ubiquitin-protein ligase (Mdm2), Receptor of activated protein C kinase 1 (Gnb2l1) and Elongation factor 1-alpha 1 (Eef1a1). To address their regulation in a physiological context, we assessed their local translation after fear conditioning. We found alterations in their density and/or distribution in astrocytes as well as a drop in their translation specifically in PAPs. In all, our results reveal an unexpected molecular repertoire of hippocampal PAPs, which is regulated by local translation during learning and memory processes.
Utilizing top-down hyperspectral imaging for monitoring genotype and growth conditions in maize
Authors: Tirado Sara B. , St Dennis Susan , Enders Tara A. , Springer Nathan M.
Published: January 2020

There is significant enthusiasm about the potential for hyperspectral imaging to document variation among plant species, genotypes or growing conditions. However, in many cases the application of hyperspectral imaging is performed in highly controlled situations that focus on a flat portion of a leaf or side-views of plants that would be difficult to obtain in field settings. We were interested in assessing the potential for applying hyperspectral imaging to document variation in genotypes or abiotic stresses in a fashion that could be implemented in field settings. Specifically, we focused on collecting top-down hyperspectral images of maize seedlings similar to a view that would be collected in a typical maize field. A top-down image of a maize seedling includes a view into the funnel-like whorl at the center of the plant with several leaves radiating outwards. There is substantial variability in the reflectance profile of different portions of this plant. To deal with the variability in reflectance profiles that arises from this morphology we implemented a method that divides the longest leaf into 10 segments from the center to the leaf tip. We show that using these segments provides improved ability to discriminate different genotypes or abiotic stress conditions (heat, cold or salinity stress) for maize seedlings. We also found substantial differences in the ability to successfully classify abiotic stress conditions among different inbred genotypes of maize. This provides an approach that can be implemented to help classify genotype and environmental variation for maize seedlings that could be implemented in field settings.

Significance Statement

This study describes the importance of using spatial information for the analysis of hyperspectral images of maize seedling. The segmentation of maize seedling leaves provides improved resolution for using hyperspectral variation to document genotypic and environmental variation in maize.
BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs
Authors: Luhmann Nina , Holley Guillaume , Achtman Mark
Published: January 2020

BlastFrost is a highly efficient method for querying 100,000s of genome assemblies. It builds on Bifrost, a recently developed dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants. Here we describe the algorithms and implementation of BlastFrost. We also present two exemplar practical applications. In the first, we determined the presence of the individual genes within the SPI-2Salmonellapathogenicity island within a collection of 926 representative genomes in minutes. In the second application, we determined the existence of known single nucleotide polymorphisms associated with fluoroquinolone resistance in the genesgyrA, gyrBandparEamong 190, 209 Salmonella genomes. BlastFrost is available for download athttps://github.com/nluhmann/BlastFrost.
A bacterial symbiont protects honey bees from fungal disease
Authors: Miller Delaney L. , Smith Eric A. , Newton Irene L. G.
Published: January 2020

Fungi are the leading cause of insect disease, contributing to the decline of wild and managed populations1,2. For ecologically and economically critical species, such as the European honey bee (Apis mellifera), the presence and prevalence of fungal pathogens can have far reaching consequences, endangering other species and threatening food security3,4,5. Our ability to address fungal epidemics and opportunistic infections is currently hampered by the limited number of antifungal therapies6,7. Novel antifungal treatments are frequently of bacterial origin and produced by defensive symbionts (bacteria that associate with an animal/plant host and protect against natural enemies89. Here we examined the capacity of a honey bee-associated bacterium,Bombella apis, to suppress the growth of fungal pathogens and ultimately protect bee brood (larvae and pupae) from infection. Our results showed that strains ofB. apisinhibit the growth of two insect fungal pathogens,Beauveria bassianaandAspergillus flavus, in vitro. This phenotype was recapitulatedin vivo; bee brood supplemented withB. apiswere significantly less likely to be infected byA. flavus. Additionally, the presence ofB. apisreduced sporulation ofA. flavusin the few bees that were infected. Analyses of biosynthetic gene clusters acrossB. apisstrains suggest antifungal production via a Type I polyketide synthase. Secreted metabolites fromB. apisalone were sufficient to suppress fungal growth, supporting this hypothesis. Together, these data suggest thatB. apisprotects bee brood from fungal infection by the secretion of an antifungal metabolite. On the basis of this discovery, new antifungal treatments could be developed to mitigate honey bee colony losses, and, in the future, could address fungal epidemics in other species.
Recipient and donor characteristics govern the hierarchical structure of heterospecific pollen competition networks
Authors: Lanuza Jose B. , Bartomeus Ignasi , Ashman Tia Lynn , Rader Romina
Published: January 2020

Pollinator sharing can have negative consequences for plant fitness with the arrival of foreign pollen, yet responses are often variable among species. Plant traits and relatedness of donor and recipient species have been suggested to drive the variations in plant fitness, but how they shape the structure of pollen competition networks has been overlooked at the community level.

To understand the importance of traits and relatedness we conducted a controlled glasshouse experiment with an artificial co-flowering community. We performed 900 reciprocal crosses by experimentally transferring pollen among 10 species belonging to three different plant families.

We found a significant reduction in seed set for 67% of the crosses, driven largely by recipient traits and the interaction between recipient-donor traits under specific circumstances of trait-matching. These traits and their asymmetries among species led to a hierarchical (or transitive) structure of pollen competition with clear winners and losers depending on specific combination of traits.

A greater understanding of the importance of trait matching and asymmetries among donor and recipient plant species will facilitate knowledge of the mechanisms underlying foreign pollen impacts upon plant reproductive fitness. This will require a shift from pairwise to community level interactions.
Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D inDrosophilaneurons
Authors: Insolera Ryan , Lőrincz Péter , Wishnie Alec J , Juhász Gábor , Collins Catherine A
Published: January 2020

A healthy population of mitochondria, maintained by proper fission, fusion, and degradation, is critical for the long-term survival and function of neurons. Here, our discovery of mitophagy intermediates in fission-impairedDrosophilaneurons brings new perspective into the relationship between mitochondrial fission and mitophagy. Neurons lacking either the ataxia disease gene Vps13D or the dynamin related protein Drp1 contain enlarged mitochondria that are engaged with autophagy machinery and also lack matrix components due to rupture. Reporter assays combined with genetic studies imply that mitophagy both initiates and is completed in Drp1 impaired neurons, but fails to complete in Vps13D impaired neurons, which accumulate compromised mitochondria within stalled mito-phagophores. Our findings imply that in fission-defective neurons, mitophagy becomes induced, and that the lipid channel containing protein Vps13D has separable functions in mitochondrial fission and phagophore elongation.