bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole-body voxel-based internal dosimetry using deep learning
Authors: Akhavanallaf Azadeh , Shiri Iscaac , Arabi Hossein , Zaidi Habib
Published: September 2020

Purpose

In the era of precision medicine, patient-specific dose calculation using Monte Carlo (MC) simulations is deemed the gold standard technique for risk-benefit analysis of radiation hazards and correlation with patient outcome. Hence, we propose a novel method to perform whole-body personalized organ-level dosimetry taking into account the heterogeneity of activity distribution, non-uniformity of surrounding medium, and patient-specific anatomy using deep learning algorithms.

Methods

We extended the voxel-scale MIRD approach from single S-value kernel to specific S-value kernels corresponding to patient-specific anatomy to construct 3D dose maps using hybrid emission/transmission image sets. In this context, we employed a Deep Neural Network (DNN) to predict the distribution of deposited energy, representing specific S-values, from a single source in the center of a 3D kernel composed of human body geometry. The training dataset consists of density maps obtained from CT images and the reference voxelwise S-values generated using Monte Carlo simulations. Accordingly, specific S-value kernels are inferred from the trained model and whole-body dose maps constructed in a manner analogous to the voxel-based MIRD formalism, i.e., convolving specific voxel S-values with the activity map. The dose map predicted using the DNN was compared with the reference generated using MC simulations and two MIRD-based methods, including Single and Multiple S-Values (SSV and MSV) and Olinda/EXM software package.

Results

The predicted specific voxel S-value kernels exhibited good agreement with the MC-based kernels serving as reference with a mean relative absolute error (MRAE) of 4.5 ± 1.8 (%). Bland and Altman analysis showed the lowest dose bias (2.6%) and smallest variance (CI: − 6.6, + 1.3) for DNN. The MRAE of estimated absorbed dose between DNN, MSV, and SSV with respect to the MC simulation reference were 2.6%, 3%, and 49%, respectively. In organ-level dosimetry, the MRAE between the proposed method and MSV, SSV, and Olinda/EXM were 5.1%, 21.8%, and 23.5%, respectively.

Conclusion

The proposed DNN-based WB internal dosimetry exhibited comparable performance to the direct Monte Carlo approach while overcoming the limitations of conventional dosimetry techniques in nuclear medicine.
Mixing characterization in different helically coiled configurations by laser-induced fluorescence
Authors: Kováts P. , Velten C. , Mansour M. , Thévenin D. , Zähringer K.
Published: September 2020

Flow Mixing of two miscible liquids has been characterized experimentally in three different helically coiled reactor configurations of two different lengths in the laminar flow regime at Re = 50…1000. A straight helical coil, a coiled flow inverter, and a new coiled flow reverser have been built, each in a 3-turn and a 6-turn configuration. Laser-induced fluorescence of resorufin has been used to visualize and quantify mixing in cross-sections throughout the reactors. A mixing coefficient is derived from the fluorescence images to allow for a quantitative measure and comparison of the six configurations. It becomes obvious from these experimental results, that an early flow redirection in the helical configuration is beneficial to mixing. The 3-turn reactors achieve nearly the same mixing coefficients as the 6-turn reactors with the double length. This can be explained by the stabilizing effect of the Dean vortices in the helix, which develop during the first two turns. After that, the liquid is trapped inside the vortices and further mixing is inhibited. Accordingly, the coiled flow inverter and coiled flow reverser configurations lead to much higher mixing coefficients than the straight helical coil. The results of these measurements are now used for validation of numerical simulations, which reproduce the geometrical and flow conditions of the experiments. Some exemplary results of these calculations are also shown in this article.

Graphic abstract

Mass fractions of tracer fluid at Re = 500 in the six examined helix configurations.
Competitive balance when winning breeds winners
Authors: Clark Derek J. , Nilssen Tore
Published: September 2020

In contest settings, heterogeneity between contestants generally leads to low effort provision, and many instruments have been suggested to restore competitive balance. We suggest that heterogeneity may evolve depending upon the outcome of previous contests. Restoring competitive balance in this setting is challenging, and we consider the choice faced by a principal who can distribute a prize fund over two consecutive all-pay auction contests. Contestants are heterogeneous in the sense that one of them has a head start in the first contest. The winner of contest one gains the stage prize and a net head start in contest two; the size of this net head start also varies between players. The head start of the early leader can be increased, neutralized or overturned. The principal aims to maximize total effort. We show how the potential head start that the initial underdog can gain is critical in determining expected efforts. When this parameter is small, the principal can do no better than running a single contest. When the initial underdog can catch up and surpass the first-contest favourite, there is scope to do better. Indeed, it is possible to completely neutralize the initial heterogeneity and capture all of the surplus from the players, inciting a level of expected effort equal to the prize value. Competitive balance is achieved by a judicious division of the prize budget.
Second primary malignancies of eye and ocular adnexa after a first primary elsewhere in the body
Authors: Alfaar Ahmad Samir , Saad Anas M. , KhalafAllah Mahmoud Tawfik , Elsherif Omneya Ezzat , Osman Moataz Hamed , Strauß Olaf
Published: September 2020

Purpose

The eye and its adnexal structures can give rise to first or consecutive primary malignancies or to encounter metastasis. Our aim was to define the characteristics of the second primary neoplasms affecting the eye and its adnexa and find the risk modifying factors for them after malignancies elsewhere in the body.

Methods

We have queried the Surveillance, Epidemiology and End-Results “SEER”-9 program of the National Cancer Institute for the malignancies of the eye and its adnexa that occurred between 1973 and 2015. The malignancies were ordered chronologically according to their incidence: first or second primary malignancies. The tumors were classified according to ICD-O-3 classification. Standardized incidence ratios (SIR) and survival probabilities were calculated for subgroups.

Results

Among 3,578,950 cancer patients, 1203 experienced a second malignancies of the eye and its adnexa. The first malignancy was diagnosed between 50 and 69 years of age in 58.94% of them. The eyelid showed 280 events, while 50 in lacrimal gland, 181 in the orbit, 21 in the overlapping lesions, 15 in optic nerve, 148 in the conjunctiva, 9 in the cornea, 6 in the Retina, 379 in the choroid, and 93 in the ciliary body. The SIR of a second malignancy after a prior non-Hodgkin lymphoma was 2.42, and in case of previous skin carcinomas it was 3.02, melanoma of skin, and 2.13 and 1.58 in oral cavity/pharynx malignancies. The second ocular and adnexal neoplasms increased steadily over the 5-year periods on contrary to first primary neoplasms. The survival of patients affected with first ocular and adnexal neoplasms was significantly higher than those with second ocular and adnexal neoplasms. On the other side, second primary ocular and adnexal tumors showed a better survival than second primary malignancies elsewhere.

Conclusions

The epidemiological differences between first and second ocular and adnexal primaries suggest different underlying mechanisms. Careful ocular examination should be integrated in the long-term follow-up plan of cancer patients. Special attention should be given to patients with non-Hodgkin’s lymphoma and melanoma as first primary.
Increasing trend in Japan Sea Throughflow transport
Authors: Kida Shinichiro , Takayama Katsumi , Sasaki Yoshi N. , Matsuura Hiromi , Hirose Naoki
Published: September 2020

A long-term increasing trend in the transport of the Japan Sea Throughflow is observed from sea-level differences across the Tsushima Strait. Tidal gauge observations show sea level at Hakata, Japan, increasing at a higher rate than that at Busan, Korea. Numerical modeling results suggest that this increasing trend is forced by a northward shift in the Kuroshio axis. As the Kuroshio axis moves northward, sea level along the southern coast of Japan increases. The signal then propagates anticyclonically along the coast as topographic Rossby waves and Kelvin waves, raising sea level and, thus, increasing transport through the Tsushima Strait.
Exploring Personalised Autonomous Vehicles to Influence User Trust
Authors: Sun Xu , Li Jingpeng , Tang Pinyan , Zhou Siyuan , Peng Xiangjun , Li Hao Nan , Wang Qingfeng
Published: September 2020

Trust is a major determinant of acceptance of an autonomous vehicle (AV), and a lack of appropriate trust could prevent drivers and society in general from taking advantage of such technology. This paper makes a new attempt to explore the effects of personalised AVs as a novel approach to the cognitive underpinnings of drivers’ trust in AVs. The personalised AV system is able to identify the driving behaviours of users and thus adapt the driving style of the AV accordingly. A prototype of a personalised AV was designed and evaluated in a lab-based experimental study of 36 human drivers, which investigated the impact of the personalised AV on user trust when compared with manual human driving and non-personalised AVs. The findings show that a personalised AV appears to be significantly more reliable through accepting and understanding each driver’s behaviour, which could thereby increase a user’s willingness to trust the system. Furthermore, a personalised AV brings a sense of familiarity by making the system more recognisable and easier for users to estimate the quality of the automated system. Personalisation parameters were also explored and discussed to support the design of AV systems to be more socially acceptable and trustworthy.
Agile methodology of well pad development
Authors: Abramov Aleksandr
Published: September 2020

Placing of wells in clusters with unequal number of thereof is an emerging concept of well pad development which still requires scrutiny even from a theoretical standpoint. The concept has its potential in improving economic efficiency of one of the most capital intensive processes in upstream sector of petroleum industry—the well pad drilling. To advocate and strengthen this profitability enhancing potential, this work integrates clustering of unequal number of wells into modern project management methodologies (agile project management), which has not been done before. It is shown that such symbiosis, which is called here the adaptive well pad development (or agile methodology of well pad development), has twofold benefit consisting of (1) managing of and accounting for uncertainties of real projects and (2) further improving economic performance of development projects in comparison with standalone well pad configurations with unequal number of wells. To exemplify these advantages, detailed simulations of well pad drilling projects were performed with equal and unequal number of wells in clusters. The simulation model accounting for more than 40 parameters and individual features of wells shows that combination of unequal well clustering configurations with adaptation of well pad designs to updates in project parameters results in significant improvements to the net present value (NPV). For three drilling scenarios studied in this work, the NPV increments ranged from 8 to 36%. Additionally, it was found that groupings with unequal number of wells consistently outperform groupings with equal number of wells in uncertain conditions, and NPV improvements from 10 to 20% have been obtained. These findings enrich understanding of the vast space of clustering schemes with unequal number of wells and demonstrate how these well pad configurations can be applied to use ever-changing environment to one's advantage. On basis of this computational study, it is now valid to assert with high degree of certainty and confidence that industrial deployment of clustering with unequal number of wells in combination with proper organizational measures results in boost to the NPV of well pad development projects at the level of several to tens of percent.
Healthcare Students on Placements: a Cyclical Quality Method for Satisfaction Assessments
Authors: Boutillier Camille , Jeanrenaud Luc , Gilles Jean-Luc , Bouche Laurence , Cotting Jocelyne Quillet
Published: September 2020

The Lausanne University Hospital (CHUV, Switzerland) is a university hospital with more than 11,000 employees who perform clinical, research and teaching roles. It was ranked in March 2019 among the ten best hospitals in the world according to the magazine Newsweek. The education scheme of the CHUV includes the practical training of more than 1700 young people, in particular from the University of Applied Sciences and Arts of Western Switzerland (HES-SO). This research and development, carried out in collaboration with the University of Teacher Education of State of Vaud (UTE Vaud), has enabled the creation and implementation of a cyclical method for evaluating the satisfaction of HES-SO healthcare students at CHUV. The method created and tested—the Cycle of Construction and Quality Control for Satisfaction Evaluations (CCQCSE)—comprises nine stages: Issues, Analysis, Design, Items, Information, Collection, Processing, Feedback and Adjustment. It was designed with the help of a multidisciplinary team of healthcare professionals (CHUV) and experts in education sciences (UTE Vaud) as part of a master’s thesis (Kaeser 2018) directed by our research team. A 4-month pilot phase allowed more than 250 placement students’ satisfaction levels to be collected with respect to ten aspects of the practical training scheme, and provided diagnostic feedback. Identifying strengths and areas for improvement has significantly helped with the development of a quality policy for student training at the institution. CCQCSE is now considered as a robust method in line with the quality measures already in place at CHUV. In particular, it encouraged those responsible for the practical training to reflect on their mentoring practices. Beyond the context of CHUV and the mentoring of healthcare students on placements, the CCQCSE model could be transferred to other sectors in which training placements are offered, opening up new avenues of collaborative research.
The 1994 Piedmont flood: an archetype of extreme precipitation events in Northern Italy
Authors: Grazzini F. , Fragkoulidis G. , Pavan V. , Antolini G.
Published: September 2020

Extreme precipitation events (EPEs) are meteorological phenomena of major concern for the densely populated regions of northern and central Italy. Although statistically rare, they tend to be recurrent in autumn and share common characteristics in the large-scale dynamical evolution responsible for their generation. Past studies on EPEs have reported, as the main triggering factor, a meridionally elongated upper-level trough embedded in an incoming Rossby wave packet. In this respect, we show how the meteorological conditions leading to the devastating 1994 Piedmont flood represent a typical flow evolution for this type of extreme events. Exploiting the systematic classification of EPEs recently published by the authors and taking advantage of a new observational dataset, this article revisits the role of the large-scale flow on this and similar cases of past EPEs.
Editorial
Authors: Barrett Steve
Published: September 2020

Garbage collection isn't a glamorous application, but there are several projects and demonstrations under way that aim to showcase the use of hydrogen and fuel cell powered garbage (or waste or refuse) collection trucks.
Toward a standardized procedure for charcoal analysis
Authors: Tsakiridou Margarita , Cunningham Laura , Hardiman Mark
Published: September 2020

Sedimentary charcoal records are used for understanding fire as an earth system process; however, no standardized laboratory methodology exists. Varying sample volumes and chemical treatments (i.e., type of chemical for length of time) are used for the deflocculation and extraction of charcoal from sediment samples. Here, we present the first systematic assessment of the effect of commonly used chemicals on charcoal area and number of fragments. In modern charcoal the area of fragments was significantly different depending on the chemical treatment. We subsequently applied H2O2 (33%), NaClO (12.5%), and HNO3 (50%) to a late-glacial–early Holocene paleorecord and tested different sample volumes. The effects of the treatments were consistent between modern and fossil experiments, which demonstrates the validity of applying results from the modern experiment to the fossil records. Based on our experiments we suggest (1) H2O2 33%, especially for highly organic sediments; (2) avoidance of high concentrations of NaClO for prolonged periods of time, and of HNO3; and (3) samples of 1 cm3 provided typically consistent profiles. Our results indicate that charcoal properties can be influenced by treatment type and sample volume, thus emphasizing the need for a common protocol to enable reliable multi-study comparisons or composite fire histories.
Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set
Authors: Murchie Tyler J. , Kuch Melanie , Duggan Ana T. , Ledger Marissa L. , Roche Kévin , Klunk Jennifer , Karpinski Emil , Hackenberger Dirk , Sadoway Tara , MacPhee Ross , Froese Duane , Poinar Hendrik
Published: September 2020

Sedimentary ancient DNA (sedaDNA) has been established as a viable biomolecular proxy for tracking taxon presence through time in a local environment, even in the total absence of surviving tissues. SedaDNA is thought to survive through mineral binding, facilitating long-term biomolecular preservation, but also challenging DNA isolation. Two common limitations in sedaDNA extraction are the carryover of other substances that inhibit enzymatic reactions, and the loss of authentic sedaDNA when attempting to reduce inhibitor co-elution. Here, we present a sedaDNA extraction procedure paired with targeted enrichment intended to maximize DNA recovery. Our procedure exhibits a 7.7–19.3x increase in on-target plant and animal sedaDNA compared to a commercial soil extraction kit, and a 1.2–59.9x increase compared to a metabarcoding approach. To illustrate the effectiveness of our cold spin extraction and PalaeoChip capture enrichment approach, we present results for the diachronic presence of plants and animals from Yukon permafrost samples dating to the Pleistocene-Holocene transition, and discuss new potential evidence for the late survival (~9700 years ago) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike region of Yukon, Canada. This enrichment approach translates to a more taxonomically diverse dataset and improved on-target sequencing.
PEOPLING OF OCEANIA: CLARIFYING AN INITIAL SETTLEMENT HORIZON IN THE MARIANA ISLANDS AT 1500 BC
Authors: Carson Mike T
Published: September 2020

Radiocarbon (14C) has been instrumental in clarifying how people came to inhabit the expanse of Pacific Oceania, now supporting an “incremental growth model” that shows a number of long-distance sea-crossing migrations over the last few millennia. A crucial step in this narrative involved the initial settlement of the remote-distance Oceanic region, in the case of the Mariana Islands around 1500 BC. The Marianas case can be demonstrated through delineation of stratigraphic layers, dating of individual points or features within those layers, redundant dating of samples in secure contexts, localized and taxon-specific corrections for marine samples, and cross-constraining dating of superimposed layer sequences. Based on the technical and methodological lessons from the Marianas example, the further steps of the incremental growth model will continue to be refined across Pacific Oceania. Many of these issues may be relevant for broader research of ancient settlement horizons in other regions.
Cytogenomic results following high-chance non-invasive prenatal testing: a UK national audit
Authors: Togneri Fiona S. , Allen Stephanie K. , Mann Kathy , Holgado Elaine , Morgan Sian
Published: September 2020

Objective

Non-invasive prenatal testing (NIPT) is increasingly being adopted as a screening test in the UK and is currently accessed through certain National Health Service healthcare systems or by private provision. This audit aims to describe reasons for and results of cytogenomic investigations carried out within UK genetic laboratories following an NIPT result indicating increased chance of cytogenomic abnormality (‘high-chance NIPT result’).

Method

A questionnaire was sent out to 24 genetics laboratories in the UK and completed by 18/24 (75%).

Results

Data were returned representing 1831 singleton pregnancies. A total of 1329 (73%) invasive samples were taken following NIPT results showing a high chance of trisomy 21; this was confirmed in 1305 (98%) of these by invasive sampling. Trisomy 21 was confirmed in >99% of patients who also had high-screen risk results or abnormal scan findings. Amongst invasive samples taken due to NIPT results indicating a high chance of trisomy 18, 84% yielded a compatible result, and this number dropped to 49% for trisomy 13 and 51% for sex chromosomes.

Conclusion

In the UK, the majority of patients having invasive sampling for high-chance NIPT results are doing so following an NIPT result indicating an increased chance of common trisomies (92%). In this population, NIPT performs particularly well for trisomy 21, but less well for other indications.
ARE YOU SERIOUS? ANALYSING EXAGGERATION IN RICHARD AYRES'SNO. 37B
Authors: Coenen-Rowe Lewis
Published: September 2020

Exaggeration as a deliberate aesthetic device has seen increased popularity with composers working in the western art music tradition in the last few decades. Their music promotes a feeling of excessiveness as an intentional compositional effect, worthy of being taken seriously. This would seem to encourage the development of analytical techniques for understanding how it works, but almost by definition exaggeration tends to be resistant to analysis, its transgressive, anti-rational character appearing incompatible with the systematic approaches associated with this discipline. This article analyses the forms of exaggeration employed in Richard Ayres's orchestral pieceNo. 37b(2006) and the techniques used to achieve them, developing a framework for how we might attempt to analyse exaggeration in a manner that is rigorous but sensitive to the nature of musical exaggeration. The article finishes by making the case for how exaggeration can be interpreted as sincere as well as ironic and why deliberate exaggeration has become an appropriate and attractive device for composers in the last few decades
Philip Venables and Ted Huffman, Denis & Katya, London, Southbank Centre, Purcell Room, 13–14 March 2020
Authors: Haggett George K.
Published: September 2020

Oral history is experiencing something of a heyday in the public imagination. The past ten years have seen a proliferation of podcasts – Sarah Koenig's Serial, Brian Reed's S-Town, Jon Ronson's The Butterfly Effect – which revolve around the testimony of ordinary people. Many of their fictional counterparts, most overtly Archive 81, hinge around the very practice of documenting, archiving and interpreting oral histories. BBC radio's oral history The Century Speaks (1999) was broadcast to an audience of millions. In the same year, radio historian Susan Douglas presciently called for a return to orality: ‘a mode of communication reliant on storytelling, listening, and group memory’. Common to these cultural products is a desire to capture a zeitgeist in a peculiarly direct and interpersonal way: through the intimacy of hearing a witness's own voice, oral history media eludes writing and embraces the subjectivity of the spoken and unscripted. To listen to somebody's testimony is to foster a distinctive relationship with them and their past, to receive it in their words and in some sense relive it on their terms.
Adverse childhood experiences and household food insecurity among children aged 0–5 years in the USA
Authors: Baiden Philip , LaBrenz Catherine A , Thrasher Shawndaya , Asiedua-Baiden Gladys , Harerimana Boniface
Published: September 2020

Objective:

Although studies have examined the association between adverse childhood experiences (ACE) and health and mental health outcomes, few studies have investigated the association between ACE and household food insecurity among children aged 0–5 years in the USA. The objective of this study is to investigate the association between ACE and household food insecurity among children aged 0–5 years.

Design:

The data used in this study came from the 2016–2017 National Survey of Children’s Health. Data were analysed using multinomial logistic regression with household food insecurity as the outcome variable.

Setting:

United States.

Participants:

An analytic sample of 17 543 children aged 0–5 years (51·4% boys).

Results:

Of the 17 543 respondents, 83·7% experienced no childhood adversity. About one in twenty (4·8%) children experienced moderate-to-severe food insecurity. Controlling for other factors, children with one adverse childhood experience had 1·43 times the risk of mild food insecurity (95 % CI 1·25, 1·63) and 2·33 times the risk of moderate-to-severe food insecurity (95 % CI 1·84, 2·95). The risk of mild food insecurity among children with two or more ACE was 1·5 times higher (95 % CI 1·24, 1·81) and that of moderate-to-severe food insecurity was 3·96 times higher (95 % CI 3·01, 5·20), when compared with children with no childhood adversity.

Conclusion:

Given the critical period of development during the first few years of life, preventing ACE and food insecurity and early intervention in cases of adversity exposure is crucial to mitigate their negative impact on child development.
A systematic review of instruments measuring grief after perinatal loss and factors associated with grief reactions
Authors: Setubal M.S. , Bolibio R. , Jesus R.C. , Benute G.G. , Gibelli M.A. , Bertolassi N. , Barbosa T. , Gomes A. , Figueiredo F. , Ferreira R. , Francisco R. , Stein Bernardes L.
Published: September 2020

Objective

Expectant parents who live through perinatal loss experience intense grief, which is not always acknowledged or accepted. A screening tool to detect bereaved parents’ grief reactions can guide professionals, including perinatal palliative care teams, to provide follow-up for those in need. This review's goal is to identify and synthesize the international published literature on existent instruments specifically measuring the grieving process after any perinatal loss and to identify factors that could moderate grief reactions.

Method

Systematic review (PROSPERO # CRD42018092555) with critical synthesis. PUBMED, Cochrane, and PsycINFO databases were searched in English language articles using the keywords “perinatal” AND (“grief” OR “bereavement” OR mourning) AND (“scale” OR “questionnaire” OR “measure” OR “assessment”) up to May 2018. Eligibility criteria included every study using a measure to assess perinatal grief after all kinds of perinatal losses, including validations and translations to other languages and interventions designed to alleviate grief symptoms.

Results

A total of 67 papers met inclusion criteria. Seven instruments measuring perinatal grief published between 1984 and 2002 are described. The Perinatal Grief Scale (PGS) was used in 53 of the selected studies. Of those, 39 analyzed factors associated with grief reactions. Six articles used PGS scores to evaluate pre- and post-bereavement interventions. Studies in English language only might have limited the number of articles.

Significance of results

The PGS is the most used standardized measures to assess grief after perinatal loss. All parents living through any kind of perinatal loss should be screened.
The Anomalous 2019 Antarctic Ozone Hole in the GEOS Constituent Data Assimilation System With MLS Observations
Authors: Wargan Krzysztof , Weir Brad , Manney Gloria L. , Cohn Stephen E. , Livesey Nathaniel J.
Published: September 2020

A rare disturbance of the stratospheric Antarctic polar vortex in September 2019 led to a significantly higher than usual polar total ozone column. We use assimilation of ozone, HCl, and N2O data from the Microwave Limb Sounder with the Global Earth Observing System (GEOS) Constituent Data Assimilation System driven by reanalysis meteorology to study the evolution of the 2019 Antarctic polar ozone. We find that the maximum 2019 ozone hole area was near 10 × 106 km2, and as little as 20% of that in 2018 in mid‐September. However, the magnitude of vortex‐averaged chemical ozone depletion was not significantly different between the 2 years despite earlier chlorine deactivation in 2019. The assimilation results show that most of the differences between 2018 and 2019 Antarctic ozone resulted from two factors: (1) the geometry of the 2019 vortex, with ozone‐rich middle‐stratospheric air masses overlying the lower portion of the vortex and leading to a significant reduction of the total column, and (2) significantly reduced vortex volume. The anomalously small ozone hole of 2019 was comparable in size to the record breaking 2002 case and the mechanisms responsible were similar in the two cases. While the 2019 sudden stratospheric warming is classified as minor, its impact on ozone was very significant.
Assimilation of Sparse Continuous Near‐Earth Weather Measurements by NECTAR Model Morphing
Authors: Galkin I. A. , Reinisch B. W. , Vesnin A. M. , Bilitza D. , Fridman S. , Habarulema J. B. , Veliz O.
Published: September 2020

Non‐linear Error Compensation Technique with Associative Restoration (NECTAR) is a novel approach to the assimilation of fragmentary sensor data to produce a global nowcast of the near‐Earth space weather. NECTAR restores missing information by iteratively transforming (“morphing”) an underlying global climatology model into agreement with currently available sensor data. The morphing procedure benefits from analysis of the inherent multiscale diurnal periodicity of the geosystems by processing 24‐hr time histories of the differences between measured and climate‐expected values at each sensor site. The 24‐hr deviation time series are used to compute and then globally interpolate the diurnal deviation harmonics. NECTAR therefore views the geosystem in terms of its periodic planetary‐scale basis to associate observed fragments of the activity with the grand‐scale weather processes of the matching variability scales. Such approach strengthens the restorative capability of the assimilation, specifically when only a limited number of observatories is available for the weather nowcast. Scenarios where the NECTAR concept works best are common in planetary‐scale near‐Earth weather applications, especially where sensor instrumentation is complex, expensive, and therefore scarce. To conduct the assimilation process, NECTAR employs a Hopfield feedback recurrent neural network commonly used in the associative memory architectures. Associative memories mimic human capability to restore full information from its initial fragments. When applied to the sparse spatial data, such a neural network becomes a nonlinear multiscale interpolator of missing information. Early tests of the NECTAR morphing reveal its enhanced capability to predict system dynamics over no‐data regions (spatial interpolation).
Retracted: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts
Authors: Jiang Shan , Zhou Daizhan , Wang Yin-Ying , Jia Peilin , Wan Chunling , Li Xingwang , He Guang , Cao Dongmei , Jiang Xiaoqian , Kendler Kenneth S. , Tsuang Ming , Mize Travis , Wu Jain-Shing , Lu Yimei , He Lin , Chen Jingchun , Zhao Zhongming , Chen Xiangning
Published: September 2020

Schizophrenia (SCZ) is a severe psychiatric disorder with a strong genetic component. High heritability of SCZ suggests a major role for transmitted genetic variants. Furthermore, SCZ is also associated with a marked reduction in fecundity, leading to the hypothesis that alleles with large effects on risk might often occur de novo. In this study, we conducted whole-genome sequencing for 23 families from two cohorts with unaffected siblings and parents. Two nonsense de novo mutations (DNMs) inGJC1andHIST1H2ADwere identified in SCZ patients. Ten genes (DPYSL2, NBPF1, SDK1, ZNF595, ZNF718, GCNT2, SNX9, AACS, KCNQ1, andMSI2) were found to carry more DNMs in SCZ patients than their unaffected siblings by burden test. Expression analyses indicated that these DNM implicated genes showed significantly higher expression in prefrontal cortex in prenatal stage. The DNM in theGJC1gene is highly likely a loss function mutation (pLI = 0.94), leading to the dysregulation of ion channel in the glutamatergic excitatory neurons. Analysis of rare variants in independent exome sequencing dataset indicates thatGJC1has significantly more rare variants in SCZ patients than in unaffected controls. Data from genome-wide association studies suggested that common variants in theGJC1gene may be associated with SCZ and SCZ-related traits. Genes co-expressed withGJC1are involved in SCZ, SCZ-associated pathways, and drug targets. These evidences suggest thatGJC1may be a risk gene for SCZ and its function may be involved in prenatal and early neurodevelopment, a vulnerable period for developmental disorders such as SCZ.
Sulforaphene inhibits esophageal cancer progression via suppressing SCD and CDH3 expression, and activating the GADD45B-MAP2K3-p38-p53 feedback loop
Authors: Han Sichong , Wang Yandong , Ma Jie , Wang Zhe , Wang Hui-Min David , Yuan Qipeng
Published: September 2020

Esophageal cancer is one of the most common cancer with limited therapeutic strategies, thus it is important to develop more effective strategies to against it. Sulforaphene (SFE), an isothiocyanate isolated from radish seeds, was proved to inhibit esophageal cancer progression in the current study. Flow cytometric analysis showed SFE induced cell apoptosis and cycle arrest in G2/M phase. Also, scrape motility and transwell assays presented SFE reduced esophageal cancer cell metastasis. Microarray results showed the influence of SFE on esophageal cancer cells was related with stearoyl-CoA desaturase (SCD), cadherin 3 (CDH3), mitogen-activated protein kinase kinase 3 (MAP2K3) and growth arrest and DNA damage inducible beta (GADD45B). SCD and CDH3 could promote esophageal cancer metastasis via activating the Wnt pathway, while the latter one was involved in a positive feedback loop, GADD45B-MAP2K3-p38-p53, to suppress esophageal cancer growth. GADD45B was known to be the target gene of p53, and we proved in this study, it could increase the phosphorylation level of MAP2K3 in esophageal cancer cells, activating p38 and p53 in turn. SFE treatment elevated MAP2K3 and GADD45B expression and further stimulated this feedback loop to better exert antitumor effect. In summary, these results demonstrated that SFE had the potential for developing as a chemotherapeutic agent because of its inhibitory effects on esophageal cancer metastasis and proliferation.
RGS12 is required for the maintenance of mitochondrial function during skeletal development
Authors: Yuan Gongsheng , Yang Shuting , Liu Min , Yang Shuying
Published: September 2020

Mitochondrial morphology and function are crucial for tissue homeostasis, such as for skeletal development, but the cellular and molecular mechanisms remain unclear. Here, we provide evidence that regulator of G-protein signaling 12 (RGS12) is present in the mitochondria of primary chondrocytes and cartilage tissues. Deletion of RGS12 in type II collagen-positive cells led to a significant decrease in mitochondrial number, membrane potential, and oxidative phosphorylation function. Mechanistically, RGS12 promoted the function of ATP5A as an enhancer of tyrosine phosphorylation. Mice with RGS12 deficiency in the chondrocyte lineage showed serious body retardation, decreased bone mass, and chondrocyte apoptosis due to the defective activity of ATP synthase. To our knowledge, this is the first report that RGS12 is required for maintaining the function of mitochondria, which may allow it to orchestrate responses to cellular homeostasis.
Woodland strawberry WRKY71 acts as a promoter of flowering via a transcriptional regulatory cascade
Authors: Lei Yingying , Sun Yiping , Wang Baotian , Yu Shuang , Dai Hongyan , Li He , Zhang Zhihong , Zhang Junxiang
Published: September 2020

The WRKY proteins are a large family of transcription factors that play important roles in stress responses and plant development. However, the roles of most WRKYs in strawberry are not well known. In this study, FvWRKY71 was isolated from the woodland strawberry ‘Ruegen’. FvWRKY71 was highly expressed in the shoot apex and red fruit. Subcellular localization analysis showed that FvWRKY71 was located in the nucleus. Transactivation analysis showed that FvWRKY71 presented transcriptional activation activity in yeast. Overexpression of FvWRKY71 in Arabidopsis and woodland strawberry revealed early flowering in the transgenic plants compared with the wild-type control. Gene expression analysis indicated that the transcript levels of the flowering time and development integrator genes AP1, LFY, FT, AGL42, FUL, FPF1, SEP1, SEP2, and SEP3 were increased in FvWRKY71-overexpressing Arabidopsis and strawberry plants compared with the wild-type controls, which may result in accelerated flowering in transgenic plants. Furthermore, FvWRKY71 was proven to directly bind to the W-boxes (TTGACT/C) of the FvFUL, FvSEP1, FvAGL42, FvLFY, and FvFPF1 promoters in vitro and in vivo. Taken together, our results reveal a transcriptional regulatory cascade of FvWRKY71 involved in promoting flowering in woodland strawberry.
The GAMYB-like gene SlMYB33 mediates flowering and pollen development in tomato
Authors: Zhang Yan , Zhang Bo , Yang Tongwen , Zhang Jie , Liu Bin , Zhan Xiangqiang , Liang Yan
Published: September 2020

GAMYBs are positive GA signaling factors that exhibit essential functions in reproductive development, particularly in anther and pollen development. However, there is no direct evidence of the regulation of any GAMYB in these biological processes in tomato (Solanum lycopersicum). Here, we identified a tomato GAMYB-like gene, SlMYB33, and characterized its specific roles. SlMYB33 is predominately expressed in the stamens and pistils. During flower development, high mRNA abundance of SlMYB33 is detected in both male and female organs, such as microspore mother cells, anthers, pollen grains, and ovules. Silencing of SlMYB33 leads to delayed flowering, aberrant pollen viability, and poor fertility in tomato. Histological analyses indicate that SlMYB33 exerts its function in pollen development in the mature stage. Further transcriptomic analyses imply that the knockdown of SlMYB33 significantly inhibits the expression of genes related to flowering in shoot apices, and alters the transcription of genes controlling sugar metabolism in anthers. Taken together, our study suggests that SlMYB33 regulates tomato flowering and pollen maturity, probably by modulating the expression of genes responsible for flowering and sugar metabolism, respectively.
The Phoebe genome sheds light on the evolution of magnoliids
Authors: Chen Shi-Pin , Sun Wei-Hong , Xiong Yuan-Fang , Jiang Yu-Ting , Liu Xue-Die , Liao Xing-Yu , Zhang Di-Yang , Jiang Shu-Zhen , Li Yu , Liu Bin , Ma Liang , Yu Xia , He Li , Liu Bao , Feng Jin-Lin , Feng Li-Zhen , Wang Zhi-Wen , Zou Shuang-Quan , Lan Si-Ren , Liu Zhong-Jian
Published: September 2020

Lauraceae includes the genusPhoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome ofPhoebe bourneiNanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated inP. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, includingAGL12-like genes that may be related to the regulation ofP. bourneiroots andFIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis.SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. FourATMYB46-and threePtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks inP. bournei. Overall, theP. bourneireference genome provides insight into the origin, evolution, and diversification ofPhoebeand other magnoliids.
American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations
Authors: Karpinski Emil , Hackenberger Dirk , Zazula Grant , Widga Chris , Duggan Ana T. , Golding G. Brian , Kuch Melanie , Klunk Jennifer , Jass Christopher N. , Groves Pam , Druckenmiller Patrick , Schubert Blaine W. , Arroyo-Cabrales Joaquin , Simpson William F. , Hoganson John W. , Fisher Daniel C. , Ho Simon Y. W. , MacPhee Ross D. E. , Poinar Hendrik N.
Published: September 2020

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.
Astrocyte-mediated switch in spike timing-dependent plasticity during hippocampal development
Authors: Falcón-Moya Rafael , Pérez-Rodríguez Mikel , Prius-Mengual José , Andrade-Talavera Yuniesky , Arroyo-García Luis E. , Pérez-Artés Rocío , Mateos-Aparicio Pedro , Guerra-Gomes Sónia , Oliveira João Filipe , Flores Gonzalo , Rodríguez-Moreno Antonio
Published: September 2020

Presynaptic spike timing-dependent long-term depression (t-LTD) at hippocampal CA3-CA1 synapses is evident until the 3rd postnatal week in mice, disappearing during the 4th week. At more mature stages, we found that the protocol that induced t-LTD induced t-LTP. We characterized this form of t-LTP and the mechanisms involved in its induction, as well as that driving this switch from t-LTD to t-LTP. We found that this t-LTP is expressed presynaptically at CA3-CA1 synapses, as witnessed by coefficient of variation, number of failures, paired-pulse ratio and miniature responses analysis. Additionally, this form of presynaptic t-LTP does not require NMDARs but the activation of mGluRs and the entry of Ca2+ into the postsynaptic neuron through L-type voltage-dependent Ca2+ channels and the release of Ca2+ from intracellular stores. Nitric oxide is also required as a messenger from the postsynaptic neuron. Crucially, the release of adenosine and glutamate by astrocytes is required for t-LTP induction and for the switch from t-LTD to t-LTP. Thus, we have discovered a developmental switch of synaptic transmission from t-LTD to t-LTP at hippocampal CA3-CA1 synapses in which astrocytes play a central role and revealed a form of presynaptic LTP and the rules for its induction.
Dual roles of neutrophils in metastatic colonization are governed by the host NK cell status
Authors: Li Peishan , Lu Ming , Shi Jiayuan , Hua Li , Gong Zheng , Li Qing , Shultz Leonard D. , Ren Guangwen
Published: September 2020

The role of neutrophils in solid tumor metastasis remains largely controversial. In preclinical models of solid tumors, both pro-metastatic and anti-metastatic effects of neutrophils have been reported. In this study, using mouse models of breast cancer, we demonstrate that the metastasis-modulating effects of neutrophils are dictated by the status of host natural killer (NK) cells. In NK cell-deficient mice, granulocyte colony-stimulating factor-expanded neutrophils show an inhibitory effect on the metastatic colonization of breast tumor cells in the lung. In contrast, in NK cell-competent mice, neutrophils facilitate metastatic colonization in the same tumor models. In an ex vivo neutrophil-NK cell-tumor cell tri-cell co-culture system, neutrophils are shown to potentially suppress the tumoricidal activity of NK cells, while neutrophils themselves are tumoricidal. Intriguingly, these two modulatory effects by neutrophils are both mediated by reactive oxygen species. Collectively, the absence or presence of NK cells, governs the net tumor-modulatory effects of neutrophils.
Dearomative 1,4-difunctionalization of naphthalenes via palladium-catalyzed tandem Heck/Suzuki coupling reaction
Authors: Zhou Bo , Wang Hongliang , Cao Zhong-Yan , Zhu Jia-Wen , Liang Ren-Xiao , Hong Xin , Jia Yi-Xia
Published: September 2020

Dearomative functionalization reactions represent an important strategy for the synthesis of valuable three-dimensional molecules from simple planar aromatics. Naphthalene is a challenging arene towards transition-metal-catalyzed dearomative difunctionalization reactions. Reported herein is an application of naphthalene as a masked conjugated diene in a palladium-catalyzed dearomative 1,4-diarylation or 1,4-vinylarylation reaction via tandem Heck/Suzuki sequence. Three types of 1,4-dihydronaphthalene-based spirocyclic compounds are achieved in excellent regio- and diastereoselectivities. Key to this transformation is the inhibition of a few competitive side reactions, including intramolecular naphthalenyl C-H arylation, intermolecular Suzuki cross-coupling, dearomative 1,2-difunctionalization, and dearomative reductive-Heck reaction. Density functional theory (DFT) calculations imply that the facile exergonic dearomative insertion of a naphthalene double bond disrupts the sequence of direct Suzuki coupling, leading to the tandem Heck/Suzuki coupling reaction. The observed regioselectivity towards 1,4-difunctionalization is due to the steric repulsions between the introduced aryl group and the spiro-scaffold in 1,2-difunctionalization.