bluuebunny/crossref_metadata_2025 huggingface dataset:
Streamlined data-gathering techniques to estimate the price and affordability of healthy and unhealthy diets under different pricing scenarios
Authors: Zorbas Christina , Lee Amanda , Peeters Anna , Lewis Meron , Landrigan Timothy , Backholer Kathryn
Published: July 2020

Objective:

To determine the reliability of streamlined data-gathering techniques for examining the price and affordability of a healthy (recommended) and unhealthy (current) diet. We additionally estimated the price and affordability of diets across socio-economic areas and quantified the influence of different pricing scenarios.

Design:

Following the Healthy Diets Australian Standardised Affordability and Pricing (ASAP) protocol, we compared a cross-sectional sample of food and beverage pricing data collected using online data and phone calls (lower-resource streamlined techniques) with data collected in-store from the same retailers.

Setting:

Food and beverage prices were collected from major supermarkets, fast food and alcohol retailers in eight conveniently sampled areas in Victoria, Australia (n72 stores), stratified by area-level deprivation and remoteness.

Participants:

This study did not involve human participants.

Results:

The biweekly price of a healthy diet was on average 21 % cheaper ($596) than an unhealthy diet ($721) for a four-person family using the streamlined techniques, which was comparable with estimates using in-store data (healthy: $594, unhealthy: $731). The diet price differential did not vary considerably across geographical areas (range: 18–23 %). Both diets were estimated to be unaffordable for families living on indicative low disposable household incomes and below the poverty line. The inclusion of generic brands notably reduced the prices of healthy and unhealthy diets (≥20 %), rendering both affordable against indicative low disposable household incomes. Inclusion of discounted prices marginally reduced diet prices (3 %).

Conclusions:

Streamlined data-gathering techniques are a reliable method for regular, flexible and widespread monitoring of the price and affordability of population diets in areas where supermarkets have an online presence.
Trade Impacts of Fossil Fuel Subsidies
Authors: Moerenhout Tom
Published: July 2020

This article introduces the various trade impacts of fossil fuel subsidies. There are large direct and pass-through trade impacts. Direct trade impacts are found when producer subsidies affect the markets for crude energy products such as crude oil, natural gas, and coal. Direct trade impacts are also found when consumer subsidies decrease the input costs of various industries, whether they refine crude products into energy carriers (e.g. gasoline, electricity) or they use energy products to produce non-energy products (e.g. iron and steel, plastics). Pass-through trade impacts are found when upstream fossil fuel subsidies lead to a lower-cost product that is then used in downstream production processes. We find that markets for fossil fuels, refined energy products and energy-intensive products are enormous. In 2018, crude fossil fuel exports were worth at least US$1.3 trillion, petroleum product exports at least US$800 billion, and exports of energy-intensive goods at least US$1.3 trillion. Their trade volume and export value, as well as their competition density highlight that fossil fuel subsidies have a direct impact on who wins and who loses in terms of market share.
Submerged for Some? Government Visibility, Race, and American Political Trust
Authors: Rosenthal Aaron
Published: July 2020

Scholarship concerning American government visibility has focused on the state’s growing submergence, yet these accounts contrast with racial and ethnic politics research focusing on the American state’s conspicuousness in the lives of people of color. Attending to this disconnect, I ask how government visibility varies across racial groups. Combining interviews and quantitative analysis within a policy feedback framework, I argue that five public policy trends have created a racial split in the American state’s visibility. For whites, submerged state policies have grown alongside the rising visibility of racialized poverty policies and taxation. As a result, whites are less aware of how government benefits them and more aware of how government uses tax dollars to fund programs perceived as solely benefitting racial others. For people of color, the decline of civil rights legislation has contrasted with criminal legal policies that have made the criminal legal system a uniquely visible manifestation of government in their lives. To demonstrate the political importance of this racial divide, I uncover a racial heterogeneity in people’s political trust attachments, wherein white trust is connected to welfare attitudes, while trust among people of color is associated with feelings about the police.
Institutions, the social capital structure, and multilevel marketing companies
Authors: Lofthouse Jordan K. , Storr Virgil Henry
Published: July 2020

In multilevel marketing companies (MLMs), member-distributors earn income from selling products and recruiting new members. Successful MLMs require a social capital structure where members can access and mobilize both strong and weak social ties. Utah has a disproportionate share of MLM companies located in the state and a disproportionate number of MLM participants. We argue that Utah's dominant religious institutions have led to the emergence of a social capital structure, making MLMs particularly viable. Utah is the most religiously homogeneous state; roughly half its population identifies as members of the Church of Jesus Christ of Latter-day Saints (LDS Church). The LDS Church's institutions foster a social capital structure where (almost all) members have access to and can leverage social capital in all its forms. LDS institutions encourage members to make meaningful social connections characterized by trust and reciprocity with other church members in local neighborhoods and across the world.
Fitting multi-population mortality models to socio-economic groups
Authors: Wen Jie , Cairns Andrew J.G. , Kleinow Torsten
Published: July 2020

We compare results for 12 multi-population mortality models fitted to 10 distinct socio-economic groups in England, subdivided using the Index of Multiple Deprivation. Using the Bayes Information Criterion to compare models, we find that a special case of the common age effect (CAE) model fits best in a variety of situations, achieving the best balance between goodness of fit and parsimony. We provide a detailed discussion of key models to highlight which features are important. Group-specific period effects are found to be more important than group-specific age effects, and non-parametric age effects deliver significantly better results than parametric (e.g. linear) age effects. We also find that the addition of cohort effects is beneficial in some cases but not all. The preferred CAE model has the additional benefit of being coherent in the sense of Hyndman et al. ((2013) Demography50(1), 261–283); some of the other models considered are not.
Supported cognitive-behavioural therapy self-help versus treatment-as-usual for depressed informal caregivers of stroke survivors (CEDArS): feasibility randomised controlled trial
Authors: Farrand Paul , Woodford Joanne , Coumoundouros Chelsea , Svedin Frida
Published: July 2020

Demands placed on informal caregivers can result in an increased likelihood of experiencing common mental health difficulties that may affect their ability to undertake the caring role. Currently, however, few evidence-based interventions have been specifically developed for informal caregivers and available interventions are difficult to access. The Improving Access to Psychological Therapies (IAPT) programme aims to improve access to evidence-based psychological therapies for all groups and may therefore present an opportunity to meet informal caregiver needs. Located within the MRC Complex Intervention Framework, a Phase II feasibility randomised controlled trial (RCT) examines key methodological, procedural and clinical uncertainties associated with running a definitive Phase III RCT of an adapted written cognitive behavioural therapy (CBT) self-help intervention for informal caregivers of stroke survivors. Recruitment was low despite different recruitment strategies being adopted, highlighting significant challenges moving towards a Phase III RCT until resolved. Difficulties with study recruitment may reflect wider challenges engaging informal caregivers in psychological interventions and may have implications for IAPT services seeking to improve access for this group. Further attempts to develop a successful recruitment protocol to progress to a Phase III RCT examining effectiveness of the adapted CBT self-help intervention should be encouraged.

Key learning aims

After reading this article, readers should be able to:

(1)

Consider key feasibility issues with regard to recruitment and attrition when running a randomised controlled trial of an adapted written cognitive behavioural therapy (CBT) self-help intervention for informal caregivers of stroke survivors.

(2)

Understand potential barriers experienced by an informal caregiving population to accessing psychological interventions.

(3)

Appreciate implications for clinical practice to enhance access to IAPT services and low-intensity CBT working with an informal caregiver population.
Higher maternal weight is related to poorer fetal autonomic function
Authors: Christifano D. N. , Taylor M. K. , Carlson S. E. , Colombo J. , Gustafson K. M.
Published: July 2020

Maternal obesity is an established risk factor for poor infant neurodevelopmental outcomes; however, the link between maternal weight and fetal development in utero is unknown. We investigated whether maternal obesity negatively influences fetal autonomic nervous system (ANS) development. Fetal heart rate variability (HRV) is an index of the ANS that is associated with neurodevelopmental outcomes in the infant. Maternal–fetal magnetocardiograms were recorded using a fetal biomagnetometer at 36 weeks (n = 46). Fetal HRV was represented by the standard deviation of sinus beat-to-beat intervals (SDNN). Maternal weight was measured at enrollment (12–20 weeks) and 36 weeks. The relationships between fetal HRV and maternal weight at both time points were modeled using adjusted ordinary least squares regression models. Higher maternal weight at enrollment and 36 weeks were associated with lower fetal HRV, an indicator of poorer ANS development. Further study is needed to better understand how maternal obesity influences fetal autonomic development and long-term neurodevelopmental outcomes.
One Flood Is Not Enough: Pool‐Riffle Self‐Maintenance Under Time‐Varying Flows and Nonequilibrium Multifractional Sediment Transport
Authors: Vahidi Elham , Rodríguez José F. , Bayne Eddie , Saco Patricia M.
Published: July 2020

The interaction of sediment supply and hydrographs can affect, on a mesoscale, geomorphic features like pools and riffles, which are fundamental units of many gravel bed rivers. In the past decades, different hypotheses have been developed to characterize the hydrodynamics of pool‐riffle sequences; however, most of the previous studies considered equilibrium or near‐equilibrium sediment transport conditions. Here we investigate the stability of pools and riffles during a sequence of different hydrographs representative of a natural flow regime, without satisfying the equilibrium sediment transport condition. In the current study, the effects of bed geometry, sediment sorting and hydrograph duration, are explained and quantified. The results show that under nonequilibrium conditions, the reversal episodes are not always competent enough for complete self‐maintenance during a single flood. However, width variations and grain sorting effects prevented the pools to be completely filled up with the upstream sediment supply. Hydrograph duration had a significant role in the riffle bed geometry. Even though a single flood (irrespective of the magnitude) was not competent enough to restore the pool‐riffle feature, a sequence of floods progressively improved conditions for self‐maintenance. These findings can bring more insight into flow management strategies, in terms of the importance of multiple sequential floods for restoring rivers with high sediment supply.
The Delicacy of Arches
Authors: Morton Mary
Published: July 2020

Living in Geologic Time: How long will Utah’s arches grace the red rock desert?
Bayesian Poroelastic Aquifer Characterization From InSAR Surface Deformation Data. Part I: Maximum A Posteriori Estimate
Authors: Alghamdi Amal , Hesse Marc A. , Chen Jingyi , Ghattas Omar
Published: July 2020

Characterizing the properties of groundwater aquifers is essential for predicting aquifer response and managing groundwater resources. In this work, we develop a high‐dimensional scalable Bayesian inversion framework governed by a three‐dimensional quasi‐static linear poroelastic model to characterize lateral permeability variations in groundwater aquifers. We determine the maximum a posteriori (MAP) point of the posterior permeability distribution from centimeter‐level surface deformation measurements obtained from Interferometric Synthetic Aperture Radar (InSAR). The scalability of our method to high parameter dimension is achieved through the use of adjoint‐based derivatives, inexact Newton methods to determine the MAP point, and a Matérn class sparse prior precision operator. Together, these guarantee that the MAP point is found at a cost, measured in number of forward/adjoint poroelasticity solves, that is independent of the parameter dimension. We apply our methodology to a test case for a municipal well in Mesquite, Nevada, in which InSAR and GPS surface deformation data are available. We solve problems with up to320,824state variable degrees of freedom (DOFs) and16,896parameter DOFs. A consistent treatment of noise level is employed so that the aquifer characterization result does not depend on the pixel spacing of surface deformation data. Our results show that the use of InSAR data significantly improves characterization of lateral aquifer heterogeneity, and the InSAR‐based aquifer characterization recovers complex lateral displacement trends observed by independent daily GPS measurements.
The mevalonate pathway is an actionable vulnerability of t(4;14)-positive multiple myeloma
Authors: Longo Joseph , Smirnov Petr , Li Zhihua , Branchard Emily , van Leeuwen Jenna E. , Licht Jonathan D. , Haibe-Kains Benjamin , Andrews David W. , Keats Jonathan J. , Pugh Trevor J. , Trudel Suzanne , Penn Linda Z.
Published: July 2020

Multiple myeloma (MM) is a plasma cell malignancy that is often driven by chromosomal translocations. In particular, patients with t(4;14)-positive disease have worse prognosis compared to other MM subtypes. Herein, we demonstrated that t(4;14)-positive cells are highly dependent on the mevalonate (MVA) pathway for survival. Moreover, we showed that this metabolic vulnerability is immediately actionable, as inhibiting the MVA pathway with a statin preferentially induced apoptosis in t(4;14)-positive cells. In response to statin treatment, t(4;14)-positive cells activated the integrated stress response (ISR), which was augmented by co-treatment with bortezomib, a proteasome inhibitor. We identified that t(4;14)-positive cells depend on the MVA pathway for the synthesis of geranylgeranyl pyrophosphate (GGPP), as exogenous GGPP fully rescued statin-induced ISR activation and apoptosis. Inhibiting protein geranylgeranylation similarly induced the ISR in t(4;14)-positive cells, suggesting that this subtype of MM depends on GGPP, at least in part, for protein geranylgeranylation. Notably, fluvastatin treatment synergized with bortezomib to induce apoptosis in t(4;14)-positive cells and potentiated the anti-tumor activity of bortezomib in vivo. Our data implicate the t(4;14) translocation as a biomarker of statin sensitivity and warrant further clinical evaluation of a statin in combination with bortezomib for the treatment of t(4;14)-positive disease.
Giant photothermoelectric effect in silicon nanoribbon photodetectors
Authors: Dai Wei , Liu Weikang , Yang Jian , Xu Chao , Alabastri Alessandro , Liu Chang , Nordlander Peter , Guan Zhiqiang , Xu Hongxing
Published: July 2020

The photothermoelectric (PTE) effect enables efficient harvesting of the energy of photogenerated hot carriers and is a promising choice for high-efficiency photoelectric energy conversion and photodetection. Recently, the PTE effect was reported in low-dimensional nanomaterials, suggesting the possibility of optimizing their energy conversion efficiency. Unfortunately, the PTE effect becomes extremely inefficient in low-dimensional nanomaterials, owing to intrinsic disadvantages, such as low optical absorption and immature fabrication methods. In this study, a giant PTE effect was observed in lightly doped p-type silicon nanoribbons caused by photogenerated hot carriers. The open-circuit photovoltage responsivity of the device was 3-4 orders of magnitude higher than those of previously reported PTE devices. The measured photovoltage responses fit very well with the proposed photothermoelectric multiphysics models. This research proposes an application of the PTE effect and a possible method for utilizing hot carriers in semiconductors to significantly improve their photoelectric conversion efficiency.
Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation
Authors: Reyes Carolina , Hodgskiss Logan H , Kerou Melina , Pribasnig Thomas , Abby Sophie S , Bayer Barbara , Kraemer Stephan M , Schleper Christa
Published: July 2020

Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.
Author Correction: Identification of novel genetic variants predisposing to familial oral squamous cell carcinomas
Authors: Huang Yaping , Zhao Jizhi , Mao Guogen , Lee Grace Sanghee , Zhang Jia , Bi Lijun , Gu Liya , Chang Zhijie , Valentino Joseph , Li Guo-Min
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Prediction of breeding values for group-recorded traits including genomic information and an individually recorded correlated trait
Authors: Ma Xiang , Christensen Ole F. , Gao Hongding , Huang Ruihua , Nielsen Bjarne , Madsen Per , Jensen Just , Ostersen Tage , Li Pinghua , Shirali Mahmoud , Su Guosheng
Published: July 2020

Records on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.
Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks
Authors: Uttam Shikhar , Stern Andrew M. , Sevinsky Christopher J. , Furman Samantha , Pullara Filippo , Spagnolo Daniel , Nguyen Luong , Gough Albert , Ginty Fiona , Lansing Taylor D. , Chakra Chennubhotla S.
Published: July 2020

An unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial information in primary tumors that can be exploited to optimize prognostics, diagnostics and therapeutic strategies for precision medicine. Here, we develop a transformational spatial analytics computational and systems biology platform (SpAn) that predicts clinical outcomes and captures emergent spatial biology that can potentially inform therapeutic strategies. We apply SpAn to primary tumor tissue samples from a cohort of 432 chemo-naïve colorectal cancer (CRC) patients iteratively labeled with a highly multiplexed (hyperplexed) panel of 55 fluorescently tagged antibodies. We show that SpAn predicts the 5-year risk of CRC recurrence with a mean AUROC of 88.5% (SE of 0.1%), significantly better than current state-of-the-art methods. Additionally, SpAn infers the emergent network biology of tumor microenvironment spatial domains revealing a spatially-mediated role of CRC consensus molecular subtype features with the potential to inform precision medicine.
Avoiding dynastic, assortative mating, and population stratification biases in Mendelian randomization through within-family analyses
Authors: Brumpton Ben , Sanderson Eleanor , Heilbron Karl , Hartwig Fernando Pires , Harrison Sean , Vie Gunnhild Åberge , Cho Yoonsu , Howe Laura D. , Hughes Amanda , Boomsma Dorret I. , Havdahl Alexandra , Hopper John , Neale Michael , Nivard Michel G. , Pedersen Nancy L. , Reynolds Chandra A. , Tucker-Drob Elliot M. , Grotzinger Andrew , Howe Laurence , Morris Tim , Li Shuai ,   The Within-family Consortium, Brumpton Ben , Sanderson Eleanor , Heilbron Karl , Hartwig Fernando Pires , Harrison Sean , Vie Gunnhild Åberge , Cho Yoonsu , Howe Laura D. , Hughes Amanda , Boomsma Dorret I. , Havdahl Alexandra , Hopper John , Neale Michael , Nivard Michel G. , Pedersen Nancy L. , Reynolds Chandra A. , Tucker-Drob Elliot M. , Grotzinger Andrew , Howe Laurence , Morris Tim , Li Shuai , Auton Adam , Windmeijer Frank , Chen Wei-Min , Bjørngaard Johan Håkon , Hveem Kristian , Willer Cristen , Evans David M. , Kaprio Jaakko , Smith George Davey , Åsvold Bjørn Olav , Hemani Gibran , Davies Neil M. ,   The 23andMe Research Team, Heilbron Karl , Auton Adam , Auton Adam , Windmeijer Frank , Chen Wei-Min , Bjørngaard Johan Håkon , Hveem Kristian , Willer Cristen , Evans David M. , Kaprio Jaakko , Davey Smith George , Åsvold Bjørn Olav , Hemani Gibran , Davies Neil M.
Published: July 2020

Estimates from Mendelian randomization studies of unrelated individuals can be biased due to uncontrolled confounding from familial effects. Here we describe methods for within-family Mendelian randomization analyses and use simulation studies to show that family-based analyses can reduce such biases. We illustrate empirically how familial effects can affect estimates using data from 61,008 siblings from the Nord-Trøndelag Health Study and UK Biobank and replicated our findings using 222,368 siblings from 23andMe. Both Mendelian randomization estimates using unrelated individuals and within family methods reproduced established effects of lower BMI reducing risk of diabetes and high blood pressure. However, while Mendelian randomization estimates from samples of unrelated individuals suggested that taller height and lower BMI increase educational attainment, these effects were strongly attenuated in within-family Mendelian randomization analyses. Our findings indicate the necessity of controlling for population structure and familial effects in Mendelian randomization studies.
Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing
Authors: Sadegh Sepideh , Matschinske Julian , Blumenthal David B. , Galindez Gihanna , Kacprowski Tim , List Markus , Nasirigerdeh Reza , Oubounyt Mhaned , Pichlmair Andreas , Rose Tim Daniel , Salgado-Albarrán Marisol , Späth Julian , Stukalov Alexey , Wenke Nina K. , Yuan Kevin , Pauling Josch K. , Baumbach Jan
Published: July 2020

Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. Various studies exist about the molecular mechanisms of viral infection. However, such information is spread across many publications and it is very time-consuming to integrate, and exploit. We develop CoVex, an interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drug candidates. Thus, CoVex is a resource to understand molecular mechanisms of pathogenicity and to prioritize candidate therapeutics. We investigate recent hypotheses on a systems biology level to explore mechanistic virus life cycle drivers, and to extract drug repurposing candidates. CoVex renders COVID-19 drug research systems-medicine-ready by giving the scientific community direct access to network medicine algorithms. It is available at https://exbio.wzw.tum.de/covex/.
Atmospheric transport is a major pathway of microplastics to remote regions
Authors: Evangeliou N. , Grythe H. , Klimont Z. , Heyes C. , Eckhardt S. , Lopez-Aparicio S. , Stohl A.
Published: July 2020

In recent years, marine, freshwater and terrestrial pollution with microplastics has been discussed extensively, whereas atmospheric microplastic transport has been largely overlooked. Here, we present global simulations of atmospheric transport of microplastic particles produced by road traffic (TWPs – tire wear particles and BWPs – brake wear particles), a major source that can be quantified relatively well. We find a high transport efficiencies of these particles to remote regions. About 34% of the emitted coarse TWPs and 30% of the emitted coarse BWPs (100 kt yr−1 and 40 kt yr−1 respectively) were deposited in the World Ocean. These amounts are of similar magnitude as the total estimated direct and riverine transport of TWPs and fibres to the ocean (64 kt yr−1). We suggest that the Arctic may be a particularly sensitive receptor region, where the light-absorbing properties of TWPs and BWPs may also cause accelerated warming and melting of the cryosphere.
Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming
Authors: Zheng Zhen-Zhen , Zheng Li-Wei , Xu Min Nina , Tan Ehui , Hutchins David A. , Deng Wenchao , Zhang Yao , Shi Dalin , Dai Minhan , Kao Shuh-Ji
Published: July 2020

In the context of continuously increasing anthropogenic nitrogen inputs, knowledge of how ammonia oxidation (AO) in the ocean responds to warming is crucial to predicting future changes in marine nitrogen biogeochemistry. Here, we show divergent thermal response patterns for marine AO across a wide onshore/offshore trophic gradient. We find ammonia oxidizer community and ambient substrate co-regulate optimum temperatures (Topt), generating distinct thermal response patterns with Topt varying from ≤14 °C to ≥34 °C. Substrate addition elevates Topt when ambient substrate is unsaturated. The thermal sensitivity of kinetic parameters allows us to predict responses of both AO rate and Topt at varying substrate and temperature below the critical temperature. A warming ocean promotes nearshore AO, while suppressing offshore AO. Our findings reconcile field inconsistencies of temperature effects on AO, suggesting that predictive biogeochemical models need to include such differential warming mechanisms on this key nitrogen cycle process.
Transplacental transmission of SARS-CoV-2 infection
Authors: Vivanti Alexandre J. , Vauloup-Fellous Christelle , Prevot Sophie , Zupan Veronique , Suffee Cecile , Do Cao Jeremy , Benachi Alexandra , De Luca Daniele
Published: July 2020

SARS-CoV-2 outbreak is the first pandemic of the century. SARS-CoV-2 infection is transmitted through droplets; other transmission routes are hypothesized but not confirmed. So far, it is unclear whether and how SARS-CoV-2 can be transmitted from the mother to the fetus. We demonstrate the transplacental transmission of SARS-CoV-2 in a neonate born to a mother infected in the last trimester and presenting with neurological compromise. The transmission is confirmed by comprehensive virological and pathological investigations. In detail, SARS-CoV-2 causes: (1) maternal viremia, (2) placental infection demonstrated by immunohistochemistry and very high viral load; placental inflammation, as shown by histological examination and immunohistochemistry, and (3) neonatal viremia following placental infection. The neonate is studied clinically, through imaging, and followed up. The neonate presented with neurological manifestations, similar to those described in adult patients.
Telomere-to-telomere assembly of a complete human X chromosome
Authors: Miga Karen H. , Koren Sergey , Rhie Arang , Vollger Mitchell R. , Gershman Ariel , Bzikadze Andrey , Brooks Shelise , Howe Edmund , Porubsky David , Logsdon Glennis A. , Schneider Valerie A. , Potapova Tamara , Wood Jonathan , Chow William , Armstrong Joel , Fredrickson Jeanne , Pak Evgenia , Tigyi Kristof , Kremitzki Milinn , Markovic Christopher , Maduro Valerie , Dutra Amalia , Bouffard Gerard G. , Chang Alexander M. , Hansen Nancy F. , Wilfert Amy B. , Thibaud-Nissen Françoise , Schmitt Anthony D. , Belton Jon-Matthew , Selvaraj Siddarth , Dennis Megan Y. , Soto Daniela C. , Sahasrabudhe Ruta , Kaya Gulhan , Quick Josh , Loman Nicholas J. , Holmes Nadine , Loose Matthew , Surti Urvashi , Risques Rosa ana , Graves Lindsay Tina A. , Fulton Robert , Hall Ira , Paten Benedict , Howe Kerstin , Timp Winston , Young Alice , Mullikin James C. , Pevzner Pavel A. , Gerton Jennifer L. , Sullivan Beth A. , Eichler Evan E. , Phillippy Adam M.
Published: July 2020

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.
High-resolution terrestrial climate, bioclimate and vegetation for the last 120,000 years
Authors: Beyer Robert M. , Krapp Mario , Manica Andrea
Published: July 2020

The variability of climate has profoundly impacted a wide range of macroecological processes in the Late Quaternary. Our understanding of these has greatly benefited from palaeoclimate simulations, however, high-quality reconstructions of ecologically relevant climatic variables have thus far been limited to a few selected time periods. Here, we present a 0.5° resolution bias-corrected dataset of global monthly temperature, precipitation, cloud cover, relative humidity and wind speed, 17 bioclimatic variables, annual net primary productivity, leaf area index and biomes, covering the last 120,000 years at a temporal resolution of 1,000–2,000 years. We combined medium-resolution HadCM3 climate simulations of the last 120,000 years with high-resolution HadAM3H simulations of the last 21,000 years, and modern-era instrumental data. This allows for the temporal variability of small-scale features whilst ensuring consistency with observed climate. Our data make it possible to perform continuous-time analyses at a high spatial resolution for a wide range of climatic and ecological applications - such as habitat and species distribution modelling, dispersal and extinction processes, biogeography and bioanthropology.
Diversity of a bacterial community associated with Cliona lobata Hancock and Gelliodes pumila (Lendenfeld, 1887) sponges on the South-East coast of India
Authors: Meenatchi Ramu , Brindangnanam Pownraj , Hassan Saqib , Rathna Kumarasamy , Kiran G. Seghal , Selvin Joseph
Published: July 2020

Marine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay suffered from pollution due to the dumping of untreated domestic sewage, effluents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial-abundant sponge species, such asGelliodes pumilaandCliona lobata, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3–V4 region-specific primers. In bothC. lobataandG. pumila,there was an overwhelming dominance (98 and 99%) of phylum Candidatus SaccharibacteriaandProteobacteria,respectively.The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique toG. pumilaandC. lobata, respectively; 15 shared OTUs).Alphaproteobacteriawas the most abundant class in both the sponge species. Unclassified species of phylum Candidatus SaccharibacteriafromC. lobataandChelotivorans compostifromG. pumilawere the most abundant bacterial species. The predominance ofAlphaproteobacteriaalso revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay. Studies on sponge microbiomes at various understudied geographical locations might be helpful in predicting the status of reef environments.
ADAD1 and ADAD2, testis-specific adenosine deaminase domain-containing proteins, are required for male fertility
Authors: Snyder Elizabeth , Chukrallah Lauren , Seltzer Kelly , Goodwin Leslie , Braun Robert E.
Published: July 2020

Adenosine-to-inosine RNA editing, a fundamental RNA modification, is regulated by adenosine deaminase (AD) domain containing proteins. Within the testis, RNA editing is catalyzed by ADARB1 and is regulated in a cell-type dependent manner. This study examined the role of two testis-specific AD domain proteins, ADAD1 and ADAD2, on testis RNA editing and male germ cell differentiation. ADAD1, previously shown to localize to round spermatids, and ADAD2 had distinct localization patterns with ADAD2 expressed predominantly in mid- to late-pachytene spermatocytes suggesting a role for both in meiotic and post-meiotic germ cell RNA editing. AD domain analysis showed the AD domain of both ADADs was likely catalytically inactive, similar to known negative regulators of RNA editing. To assess the impact of Adad mutation on male germ cell RNA editing, CRISPR-induced alleles of each were generated in mouse. Mutation of either Adad resulted in complete male sterility with Adad1 mutants displaying severe teratospermia and Adad2 mutant germ cells unable to progress beyond round spermatid. However, mutation of neither Adad1 nor Adad2 impacted RNA editing efficiency or site selection. Taken together, these results demonstrate ADAD1 and ADAD2 are essential regulators of male germ cell differentiation with molecular functions unrelated to A-to-I RNA editing.
The social supergene dates back to the speciation time of two Solenopsis fire ant species
Authors: Cohen Pnina , Privman Eyal
Published: July 2020

Colony social organization of multiple Solenopsis fire ant species is determined by a supergene with two haplotypes SB and Sb, which are similar to X/Y sex chromosomes. The ancestral monogyne (single-queen) social form has been associated with homozygous SB/SB queens, while queens in colonies with the derived polygyne (multi-queen) social structure are heterozygous SB/Sb. By comparing 14 Solenopsis invicta genomes and the outgroup S. fugax, we dated the formation of the supergene to 1.1 (0.7–1.6) million years ago, much older than previous estimates, and close to the estimated time of speciation of the two socially polymorphic species S. invicta and S. richteri. We also used 12 S. invicta and S. richteri genomes to compare the evolutionary distances between these species and the distances between the social haplotypes, and found them to be similar. A phylogenetic analysis suggested that the monophyletic Sb clade is more closely related to S. richteri SB haplotypes than to S. invicta SB haplotypes. We conclude that the formation of the supergene occurred concomitantly with the process of speciation of the Solenopsis socially-polymorphic clade, and hypothesize that the Sb variant first arouse in one incipiently-speciating population and then introgressed into the other populations or species.
Kinome profiling of peripheral blood mononuclear cells collected prior to vaccination reveals biomarkers and potential mechanisms of vaccine unresponsiveness in pigs
Authors: Lipsit Sean W. L. , Wilkinson James , Scruten Erin , Facciuolo Antonio , Denomy Connor , Griebel Philip J. , Kusalik Anthony , Plastow Graham , Napper Scott
Published: July 2020

Inter-individual variance in host immune responses following vaccination can result in failure to develop protective immunity leaving individuals at risk for infection in addition to compromising herd immunity. While developing more efficacious vaccines is one strategy to mitigate this problem, predicting vaccine responsiveness prior to vaccination could inform which individuals require adjunct disease management strategies. To identify biomarkers of vaccine responsiveness, a cohort of pigs (n = 120) were vaccinated and pigs representing the high (n = 6; 90th percentile) and low (n = 6; 10th percentile) responders based on vaccine-specific antibody responses following vaccination were further analyzed. Kinase-mediated phosphorylation events within peripheral blood mononuclear cells collected prior to vaccination identified 53 differentially phosphorylated peptides when comparing low responders with high responders. Functional enrichment analysis revealed pro-inflammatory cytokine signaling pathways as dysregulated, and this was further substantiated by detection of higher (p < 0.01) concentrations of interferon-gamma in plasma of low responders compared to high responders prior to vaccination. In addition, low responder pigs with high plasma interferon-gamma showed lower (p < 0.01) birth weights than high responder pigs. These associations between vaccine responsiveness, cytokine signaling within peripheral immune cells, and body weight in pigs provide both evidence and insight into potential biomarkers for identifying low responders to vaccination.
GBA3: a polymorphic pseudogene in humans that experienced repeated gene loss during mammalian evolution
Authors: Lopes-Marques Monica , Serrano Catarina , Cardoso Ana R. , Salazar Renato , Seixas Susana , Amorim António , Azevedo Luisa , Prata Maria J.
Published: July 2020

The gene encoding the cytosolic β-glucosidase GBA3 shows pseudogenization due to a truncated allele (rs358231) that is polymorphic in humans. Since this enzyme is involved in the transformation of many plant β-glycosides, this particular case of gene loss may have been influenced by dietary adaptations during evolution. In humans, apart from the inactivating allele, we found that GBA3 accumulated additional damaging mutations, implying an extensive GBA3 loss. The allelic distribution of loss-of-function alleles revealed significant differences between human populations which can be partially related with their staple diet. The analysis of mammalian orthologs disclosed that GBA3 underwent at least nine pseudogenization events. Most events of pseudogenization occurred in carnivorous lineages, suggesting a possible link to a β-glycoside poor diet. However, GBA3 was also lost in omnivorous and herbivorous species, hinting that the physiological role of GBA3 is not fully understood and other unknown causes may underlie GBA3 pseudogenization. Such possibility relies upon a putative role in sialic acid biology, where GBA3 participates in a cellular network involving NEU2 and CMAH. Overall, our data shows that the recurrent loss of GBA3 in mammals is likely to represent an evolutionary endpoint of the relaxation of selective constraints triggered by diet-related factors.
Genomic imprinting analyses identify maternal effects as a cause of phenotypic variability in type 1 diabetes and rheumatoid arthritis
Authors: Blunk Inga , Thomsen Hauke , Reinsch Norbert , Mayer Manfred , Försti Asta , Sundquist Jan , Sundquist Kristina , Hemminki Kari
Published: July 2020

Imprinted genes, giving rise to parent-of-origin effects (POEs), have been hypothesised to affect type 1 diabetes (T1D) and rheumatoid arthritis (RA). However, maternal effects may also play a role. By using a mixed model that is able to simultaneously consider all kinds of POEs, the importance of POEs for the development of T1D and RA was investigated in a variance components analysis. The analysis was based on Swedish population-scale pedigree data. With P = 0.18 (T1D) and P = 0.26 (RA) imprinting variances were not significant. Explaining up to 19.00% (± 2.00%) and 15.00% (± 6.00%) of the phenotypic variance, the maternal environmental variance was significant for T1D (P = 1.60 × 10−24) and for RA (P = 0.02). For the first time, the existence of maternal genetic effects on RA was indicated, contributing up to 16.00% (± 3.00%) of the total variance. Environmental factors such as the social economic index, the number of offspring, birth year as well as their interactions with sex showed large effects.
Adaptive tuning of infrared emission using VO2 thin films
Authors: Larciprete M. C. , Centini M. , Paoloni S. , Fratoddi I. , Dereshgi S. A. , Tang K. , Wu J. , Aydin K.
Published: July 2020

Phase-transition materials provide exciting opportunities for controlling optical properties of photonic devices dynamically. Here, we systematically investigate the infrared emission from a thin film of vanadium dioxide (VO2). We experimentally demonstrate that such thin films are promising candidates to tune and control the thermal radiation of an underlying hot body with different emissivity features. In particular, we studied two different heat sources with completely different emissivity features, i.e. a black body-like and a mirror-like heated body. The infrared emission characteristics were investigated in the 3.5–5.1 μm spectral range using the infrared thermography technique which included heating the sample, and then cooling back. Experimental results were theoretically analyzed by modelling the VO2 film as a metamaterial for a temperature range close to its critical temperature. Our systematic study reveals that VO2 thin films with just one layer 80 nm thick has the potential to develop completely different dynamic tuning of infrared radiation, enabling both black-body emission suppression and as well as mirror emissivity boosting, in the same single layer device. Understanding the dynamics and effects of thermal tuning on infrared emission will benefit wide range of infrared technologies including thermal emitters, sensors, active IR filters and detectors.
Force–frequency relationship during fatiguing contractions of rat medial gastrocnemius muscle
Authors: MacDougall Keenan B. , Devrome Andrea N. , Kristensen Anders M. , MacIntosh Brian R.
Published: July 2020

The force–frequency relationship presents the amount of force a muscle can produce as a function of the frequency of activation. During repetitive muscular contractions, fatigue and potentiation may both impact the resultant contractile response. However, both the apparent fatigue observed, and the potential for activity-dependent potentiation can be affected by the frequency of activation. Thus, we wanted to explore the effects that repetitive stimulation had on the force–frequency relationship. The force–frequency relationship of the rat medial gastrocnemius muscle was investigated during consecutive bouts of increasing fatigue with 20 to 100 Hz stimulation. Force was measured prior to the fatiguing protocol, during each of three levels of fatigue, and after 30 min of recovery. Force at each frequency was quantified relative to the pre-fatigued 100 Hz contractions, as well as the percentage reduction of force from the pre-fatigued level at a given frequency. We observed less reduction in force at low frequencies compared to high frequencies, suggesting an interplay of fatigue and potentiation, in which potentiation can “protect” against fatigue in a frequency-dependent manner. The exact mechanism of fatigue is unknown, however the substantial reduction of force at high frequency suggests a role for reduced force per cross-bridge.