bluuebunny/crossref_metadata_2025 huggingface dataset:
Prostaatspecifiek membraanantigeen radioligandtherapie met alfastralers, een review
Authors: Privé Bastiaan M. , van Gemert Willemijn A. M. , Nagarajah James , Mehra Niven , Gerritsen Winald R. , van Oort Inge M. , Gotthardt Martin , Heskamp Sandra , Janssen Marcel J. R.
Published: August 2020

Samenvatting

Prostaatspecifiek membraanantigeen (PSMA) radioligandtherapie is een veelbelovende experimentele behandeling voor gemetastaseerd prostaatcarcinoom. In de nog lopende fase III-studie wordt lutetium-177 (177Lu)-PSMA, een bètastraler, gebruikt. Er wordt momenteel echter ook op beperkte schaal geëxperimenteerd met alfastralers die zijn gekoppeld aan PSMA-liganden, met name actinium-225 (225Ac)-PSMA. In vergelijking met bètastralers leiden alfastralers tot moeizamer herstellende DNA-schade, waarmee ze mogelijk effectiever zijn en een betere immunologische respons geven. Daarnaast hebben alfastralers een veel geringer doordringend vermogen, wat een voordeel zou kunnen zijn bij patiënten met diffuse beenmergmetastasering en bij patiënten met micrometastasen. De bijwerkingen op de speekselklieren zijn echter waarschijnlijk wel ernstiger. Net als bij bèta-PSMA-therapie is alfa-PSMA-therapie vooralsnog experimenteel. Het effect van alfastralers is enkel onderzocht in retrospectieve series – er zijn nog geen prospectieve of vergelijkende studies verricht – waardoor de resultaten voorzichtig moeten worden geïnterpreteerd. De wereldwijde productie van 225Ac en andere alfastralers zou bovendien fors moeten worden opgeschaald om klinische studies en grootschalig gebruik mogelijk te maken. In deze review geven we een overzicht van de eerste klinische data omtrent alfa-PSMA-therapie.
CEEMDAN-IMFx-PCA-CICA: an improved single-channel blind source separation in multimedia environment for motion artifact reduction in ambulatory ECG
Authors: Xiong Fan , Chen Dongyi
Published: August 2020

Long-term monitoring of ECG via wearable monitoring systems has already been widely adopted to detect and prevent heart diseases. However, one of the main issues faced by wearable ECG monitoring systems is that motion artifacts significantly affect the systems' stability and reliability. Therefore, motion artifact reduction is a very challenging task in filtering and processing physiological signals. Based on the existing algorithms and ECG prior knowledge, in this paper, we propose an algorithm, CEEMDAN-IMFx-PCA-CICA, for motion artifact reduction in ambulatory ECG signals using single-channel blind source separation technique. Our algorithm first utilizes CEEMDAN to decompose the mixed signals into IMFs (intrinsic mode function) containing different source signal features, thereby forming new multi-dimensional signals. Using the correlation between IMFx (IMF component with the most ECG features) and each IMF, and PCA are then applied to reduce the dimension of each IMF. Finally, the blind separation of the source ECG signals is achieved by using CICA with IMFx as the constraint reference component. The results of our experiments indicate that our algorithm outperformed CEEMDAN-CICA, CEEMDAN-PCA-CICA, and improved CEEMDAN-PCA-CICA. Besides, the number of iterations of the CICA is significantly reduced; the separated source signal is better; the obtained result is stable. Furthermore, the separated ECG signal has a higher correlation with the source ECG signal and a lower RRMSE, especially in the case of high noise-to-signal ratios.
Shannon entropy in time-varying semantic networks of titles of scientific paper
Authors: Vale Cunha Marcelo do , Ribeiro Santos Carlos Cesar , Moret Marcelo Albano , de Barros Pereira Hernane Borges
Published: August 2020

Recent work has employed information theory in social and complex networks. Studies often discuss entropy in the degree distributions of a network. However, no specific work on entropy exists in clique networks. This work is an extension of a previous study that discussed this topic. We propose a method for calculating the entropy of a clique network and its minimum and maximum values in temporal semantic networks based on titles of scientific papers. In addition, the critical network of moments was extracted. We use the titles of scientific papers published in Nature and Science over ten-year period. The results show the diversity of vocabulary over time, based on the entropy values of vertices and edges. In each critical network, we discover the paths that connect important words and an interesting modular structure.
Exploring dynamic multilayer graphs for digital humanities
Authors: Bornhofen Stefan , Düring Marten
Published: August 2020

The paper presents Intergraph, a graph-based visual analytics technical demonstrator for the exploration and study of content in historical document collections. The designed prototype is motivated by a practical use case on a corpus of circa 15.000 digitized resources about European integration since 1945. The corpus allowed generating a dynamic multilayer network which represents different kinds of named entities appearing and co-appearing in the collections. To our knowledge, Intergraph is one of the first interactive tools to visualize dynamic multilayer graphs for collections of digitized historical sources. Graph visualization and interaction methods have been designed based on user requirements for content exploration by non-technical users without a strong background in network science, and to compensate for common flaws with the annotation of named entities. Users work with self-selected subsets of the overall data by interacting with a scene of small graphs which can be added, altered and compared. This allows an interest-driven navigation in the corpus and the discovery of the interconnections of its entities across time.
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets
Authors: Zhang Qiong , Liu Wei , Zhang Hong-Mei , Xie Gui-Yan , Miao Ya-Ru , Xia Mengxuan , Guo An-Yuan
Published: August 2020

Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF–target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of chromatin immunoprecipitation sequencing (ChIP-seq) provide great opportunities to discover the TF–target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7190 ChIP-seq samples of 659 TFs and high-confidence binding sites of 699 TFs) and epigenetic modification information to predict accurate TF–target regulations. hTFtarget offers the following functions for users to explore TF–target regulations: (1) browse or search general targets of a query TF across datasets; (2) browse TF–target regulations for a query TF in a specific dataset or tissue; (3) search potential TFs for a given target gene or non-coding RNA; (4) investigate co-association between TFs in cell lines; (5) explore potential co-regulations for given target genes or TFs; (6) predict candidate TF binding sites on given DNA sequences; (7) visualize ChIP-seq peaks for different TFs and conditions in a genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF–target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.
Disaster Response to a Mass Casualty Incident in a Hospital Fire by Regional Disaster Medical Assistance Team: Characteristics of Hospital Fire
Authors: Jang Jae Ho , Cho Jin-Seong , Lim Youg Su , Hyun Sung Youl , Woo Jae-Hyug , Choi Woo Sung , Choi Jae Yeon , Yang Hyuk Jun
Published: August 2020

Objective:

A disaster in the hospital is particularly serious and quite different from other ordinary disasters. This study aimed at analyzing the activity outcomes of a disaster medical assistance team (DMAT) for a fire disaster at the hospital.

Methods:

The data which was documented by a DMAT and emergent medical technicians of a fire department contained information about the patient’s characteristics, medical records, triage results, and the hospital which the patient was transferred from. Patients were categorized into four groups according to results of field triage using the simple triage and rapid treatment method.

Results:

DMAT arrived on the scene in 37 minutes. One hundred and thirty eight (138) patients were evacuated from the disaster scene. There were 25 patients (18.1%) in the Red group, 96 patients (69.6%) in the Yellow group, and 1 patient (0.7%) in the Green group. One patient died. There were 16 (11.6%) medical staff and hospital employees. The injury of the caregiver or the medical staff was more severe compared to the family protector.

Conclusions:

For an effective disaster-response system in hospital disasters, it is important to secure the safety of medical staff, to utilize available medical resources, to secure patients’ medical records, and to reorganize the DMAT dispatch system.
Tensile strength of glacial ice deduced from observations of the 2015 eastern Skaftá cauldron collapse, Vatnajökull ice cap, Iceland
Authors: Ultee Lizz , Meyer Colin , Minchew Brent
Published: August 2020

The representation of iceberg calving in numerical models is a key source of uncertainty in century-scale sea-level rise projections. Parameters central to model representations of calving, including the tensile strength of glacier ice, remain poorly constrained. Grain-size and sample-size dependence make it difficult to reconcile laboratory and in situ estimates of ice tensile strength. Further, assumptions of various numerical models obscure comparison of the ‘strength’ parameter with a physically observable value. Here, we address the problem of fracture during calving using an analogous natural laboratory: a viscoelastic analysis of observed surface deformation and associated stresses in the 2015 collapse of eastern Skaftá cauldron, Vatnajökull ice cap, Iceland. We find that the ice within the cauldron could have experienced instantaneous elastic stress on the order of several MPa. We observe surface crevasses at the cauldron edges and center, but find that large areas of ice remain intact despite high stress. Our findings suggest a tensile strength of glacier ice on the order of 1 MPa, consistent with laboratory estimates but exceeding previous glacier-specific estimates.
THE KUZNETS CURVE IN BRAZIL, 1850-2010
Authors: Gómez León María
Published: August 2020

Using social tables and modern household surveys, this article explores Brazil's income distribution from a historical perspective (1850-2010), examining its relationship with economic development and the factors driving inequality changes. It shows that Brazil's inequality was not always high, but rather followed a Kuznets curve, increasing from the early 20thcentury, reaching a high plateau between the 1970s and 1990s and declining thereafter. Notably, results highlight the importance of both economic and political factors for enabling the completion of the second Kuznets curve phase.
Learning from a case of right ventricular outflow tract stenting in tricuspid atresia with critical pulmonary stenosis
Authors: Awasthy Neeraj , Chimoriya Romila , Kumar Gaurav
Published: August 2020

Tricuspid valve atresia with severe pulmonary stenosis is one of the common cyanotic diseases in neonate. Child can succumb due to profound cyanosis and arterial hypoxaemia after closure of patent ductus arteriosus. Evolving procedure of right ventricular outflow tract stenting may be considered as a palliative procedure in such vulnerable group, destined for a later definitive management. The right ventricular outflow tract stenting is described essentially for tetralogy of Fallot physiology with a catheter course across tricuspid valve. We describe a case of successful right ventricular outflow tract stenting in a 5-day-old symptomatic neonate. We discuss the possible routes and the tips to facilitate right ventricular outflow tract stenting in such a case. This happens to be the first reported case description with successful stenting of neonate with tricuspid atresia with critical pulmonic stenosis.
Design activism: catalysing communities of practice
Authors: Mallo Daniel , Tardiveau Armelle , Parsons Rorie
Published: August 2020

Over the last decade, we have witnessed renewed interest in design as a socially engaged practice. Much of the debates around ‘social design’ point towards myriad approaches and disciplinary fields interwoven with grass-roots initiatives and social movements. Among these, design activism has gained traction as critical spatial practice that operates on the fringes of commercial and institutional spheres.

The temporal, spatial and experimental nature of design activism is well delineated in scholarship but its long-term effect on everyday urban environments remains elusive. Moreover, the influence of design activism on socio-spatial dynamics is indeed largely under researched. By mobilising social practice theory, this paper proposes a novel theorisation of design activism that sheds light on the social formations and collective practices catalysed through the activist impulse. This ontological shift embraces an understanding of the socio-material world through practice. Such characterisation of design activism underscores collective moments of integration of the constitutive elements of practice, encapsulated by Shove, Pantzar and Watson as ‘material, competence and meaning’.

The authors' own empirical research, funded by the Economic and Social Research Council (ESRC) in the UK, reveals design activism as necessarily intertwined with other everyday practices – gardening, celebrating, playing – that coalesce around a shared sense of citizenship. It also advances the role of design activism in forging communities of practice: mutually supportive and self-sustaining groups emerging out of the personal relations sustained and organised around a practice of place making.
Living with buildings, living with microbes: probiosis and architecture
Authors: Ramirez-Figueroa Carolina , Beckett Richard
Published: August 2020

In this paper we establish a dialogue with Living with Buildings to contextualise NOTBAD (Niches for Organic Territories in Bio-Augmented Design), a multidisciplinary research project at the intersection of architecture and microbiology, sited within a wider historical discourse connecting architecture and health. Living with Buildings (2018) was organised by the Wellcome Trust to trace the changing landscape of health and architecture, setting out to show how connections between the ways we feel and the places in which we spend our lives have historically evolved as our ideas about health and disease have changed. Taking our cue from the pieces at the exhibition, we discuss how the eighteenth century saw the emergence of an imaginary of cleanliness linked to miasma theory, locating bad smells and odours as the origin of disease and resulting in the adoption of rituals of purification in buildings. Treatments of plastering, coating and whitewashing popularised in the nineteenth century are testament to a shift from olfactory to visual codes of hygiene and to the ‘antibiotic turn’ in architecture.

We extend the historical analysis to suggest that architecture finds itself at a crossroads. Although there is a growing understanding of how much architecture influences our wellbeing, architectural thought still clings to the antibiotic turn. Following the tradition of exchange between architecture and medicine, we propose the notion of Probiotic Architecture as a way of framing the shifting understanding of health in architectural design, suggesting that the microorganisms that colonise humans (the human microbiome) and our built environment (the built environment microbiome) have the potential to influence our health and the resilience of our buildings. Against the backdrop of the design research project Niches for Organic Territories in Bio-Augmented Design (NOTBAD), we suggest the need to reverse notions that all microbes are bad, to and propose instead materials and prototypes that encourage benign microbial growth.
‘opened out […] like an oyster shell': the Roach bed Portland stone cladding of the Smithsons’ Economist Building
Authors: Wigzell Freya
Published: August 2020

Alison & Peter Smithson's Economist Building in London (1960–1964) has been much written about, but one of its most distinctive features – the Roach bed Portland stone cladding – has been relatively little discussed. Although there have been various retrospective explanations for the choice of this previously unused stone, whose surface is marked by cavities of now vanished shells, no direct evidence from the time fully accounts for the decision. Reliance upon inference, and upon retrospective statements, mean that no definitive explanation for the choice is now possible. Some new evidence from archives and interviews, and a re-examination of the contemporary concerns of the Smithsons, and of their artist friends Eduardo Paolozzi and Nigel Henderson, fellow members of the Independent Group during the 1950s, however, suggest a plausible, though speculative, interpretation. When considered in light of the Smithsons' and their friends' interests in pattern, in hidden orders, and in the problems of ‘human association’, the choice of Roach bed Portland stone seems less surprising. More than just ‘pretty’, as Peter Smithson was later to describe the material, it can be seen to connect with a fascination with underlying, non-human, systems of order, while at the same time providing a particularly expressive form of protection for human identity in the modern city.
Global mid-upper arm circumference cut-offs for adults: a call to action
Authors: Maalouf-Manasseh Zeina , Remancus Sandra , Milner Erin , Fenlason Lindy , Quick Timothy , Patsche Cecilie B , Bose Kaushik , Collins Steve , Ververs Mija , Walia Sonia , Escobar-Alegria Jessica , Chung Mei , Tang Alice M
Published: August 2020

Since 2009, mid-upper arm circumference (MUAC) has become an accepted measure for screening children for acute malnutrition and determining eligibility for services to manage acute malnutrition. Use of MUAC has increased the reach and enhanced the quality of community-based management of acute malnutrition services. Increasingly, MUAC is also used to assess nutritional status and eligibility for nutrition support among adolescents and adults, including pregnant and lactating women and HIV and TB clients. However, globally recognised cut-offs have not been established to classify malnutrition among adults using MUAC. Therefore, different countries and programmes use different MUAC cut-offs to determine eligibility for programme services. Patient monitoring guidelines provided by WHO for country adaptation to support the integrated management of adult illness do not include MUAC, in part because guidance does not exist about what MUAC cut-off should trigger further action.
Ultra-processed foods and early childhood caries in 0–3‐year‐olds enrolled at Primary Healthcare Centers in Southern Brazil
Authors: de Souza Maurício Santos , Vaz Juliana dos Santos , Martins-Silva Thais , Bomfim Rafael Aiello , Cascaes Andreia Morales
Published: August 2020

Objective:

To investigate the relationship between ultra-processed food consumption and early childhood caries.

Design:

Cross-sectional analysis of baseline data from a cluster randomised controlled study. Outcomes included the prevalence of children with non-cavitated and cavitated caries. The main exposure was the total daily consumption of ultra-processed foods (up to three times and four times or more), assessed through a FFQ. Potential confounders were socio-demographic characteristics of the child and caregiver/family, child breast-feeding, oral hygiene and use of dental services. Poisson regression using robust variance adjustment was used to estimate prevalence ratios (PR) and their respective 95 % CI.

Setting:

Primary Healthcare Centers in an urban area of Pelotas, Southern Brazil.

Participants:

Children aged 0–3 years (n 309).

Results:

Consumption of ultra-processed foods four times or more a day was found in 67·6 % of children; 24·4 and 12·0 % presented non-cavitated and cavitated caries, respectively. After adjustment, children who consumed ultra-processed foods four times or more a day were more likely to present both non-cavitated caries (PR 2·25, 95 % CI 1·19, 4·27, P = 0·013) and cavitated caries (PR 3·48, 95 % CI 1·18, 10·30, P = 0·024) compared with those who have consumed them up to three times a day.

Conclusions:

Consumption of ultra-processed foods is associated with early childhood caries. Interventions aiming at reducing ultra-processed food consumption should be implemented to improve children’s oral health.
The interstellar communication relay
Authors: McConnell Brian
Published: August 2020

The paper describes the architecture for a data repository and distribution system to be used in the case of a SETI detection event. This system is conceptually modelled after the Deep Space Network, although the hardware and infrastructure involved are different and substantially less expensive to operate. The system is designed to accommodate a large number of users from a variety of fields who wish to contribute to the analysis and comprehension effort that would follow the detection of an information-bearing signal.
Periodic printed semi-annular substrate loaded TM01–TE11 mode converter
Authors: Chittora Ashish , Yadav Swati Varun
Published: August 2020

A mode converter design using the concept of periodic substrates loading in a circular waveguide, to convert TM01 mode to TE11 mode is presented in this paper. The detailed design principle, simulation, and measurement results are included in this study. Simulation results show that the purity of output fundamental TE11 mode of the converter approaches 99.2% for an operating frequency of 3.2 GHz. The mode conversion efficiency is more than 90% over 3.07–3.25 GHz band and the relative bandwidth is 5.6% (180 MHz). The proposed TM01–TE11 mode converter has advantages, such as the compact, lightweight structure, high conversion efficiency, and proper bandwidth. The fabrication cost is relatively low and the structure is easy to fabricate. The power-handling capability is limited to 10 MW due to dielectric-based design. The compactness and portability of the system (e.g. Space applications, Accelerators, High Power Microwave) can be improved significantly using the proposed mode converter.
Gene expression and target-site mutations are associated with resistance to ALS inhibitors in annual sedge (Cyperus compressus) biotypes from Georgia
Authors: Yu Jialin , McCullough Patrick E. , McElroy J. Scott , Jespersen David , Shilling Donn G.
Published: August 2020

Annual sedge (Cyperus compressus L.) populations with resistance to halosulfuron were identified in turfgrass at two new locations in Georgia. Research was conducted to evaluate (1) resistance levels to two acetolactate synthase (ALS) inhibitors, (2) ALS enzyme susceptibility, (3) genetic differences associated with resistance, and (4) differential levels of ALS gene expression in these biotypes. In dose–response experiments, the biotypes were >160 times resistant to halosulfuron but only 12 times more resistant to imazaquin compared with a susceptible biotype. In vitro enzyme assays indicated that resistant (R) biotypes required 6.1-fold greater concentrations of imazaquin to reduce ALS activity 50% compared with the susceptible (S) biotype. Both R biotypes had a similar Pro-197-Ser amino acid substitution in the ALS gene that confers resistance to sulfonylureas. Compared with the S biotype, R biotypes had 4.4 times higher ALS gene expression than the S biotype. No differences in gene copy number were found between any biotypes for the ALS gene. Overall, ALS-resistant C. compressus selected by halosulfuron use in turfgrass may be exhibiting partial susceptibility to imazaquin but complete resistance to sulfonylureas. Differential levels of susceptibility to ALS inhibitors for these biotypes are associated with the Pro-197-Ser substitution and enhanced expression of the ALS gene.
The problem of Orobanche spp. and Phelipanche spp. and their management in Iran
Authors: Nosratti Iraj , Mobli Ahmadreza , Mohammadi Gholamreza , Yousefi Ali Reza , Sabeti Peyman , Chauhan Bhagirath S.
Published: August 2020

Broomrape species (Orobanche spp. and Phelipanche spp.) pose a tremendous threat to economically important crops in Iran; however, there is little information on the country’s major broomrape species, their distribution and host ranges, and the subsequent crop losses they cause. The literature from Iran describes Egyptian broomrape (Orobanche aegyptiaca Pers.), hemp broomrape (Orobanche ramosa L.), Phelipanche nana (Reut.) Beck, and Orobanche cumana Wallr. as the major species of broomrape infesting agricultural fields. Solanaceae crops are among the most susceptible crops to infestation by broomrape in the country, and farmers are either shifting production to crops with lesser value or abandoning crop production entirely. Among infested crops, tomato (Solanum lycopersicum L.) is the most susceptible and widely infested, resulting in annual crop yield reductions of up to 40%. Chick pea (Cicer arietinum L.) and canola (Brassica napus L.) are also highly susceptible to broomrape infestation. Current control methods (physical, agronomical, biological, and chemical) have not proven to be effective or economic. The microscopic size of broomrape seeds and the presence of a wide range of host plants (weeds and crops) have promoted the spread of broomrape to new areas of Iran. Hence, the familiarization of farmers with the biology of broomrape would be highly effective in finding suitable control measures and in preventing its further distribution.
Planning a Sustainable Future for Earth’s Oceans
Authors: Van Stavel Jordan , Karstensen Johannes , Hermes Juliet , Pearlman Jay
Published: August 2020

Ocean experts are engaged in a long-term effort to envision, develop, and implement best practices for meeting today’s needs while preserving ocean resources for future generations.
Bringing Satellite Observations Down to Earth
Authors: Goss Heather
Published: August 2020

This month’s issue of Eos shows how scientists can sometimes get a better look at something by stepping far—much, much farther—away.
What Configuration of the Atmospheric Circulation Drives Extreme Net and Total Moisture Transport Into the Arctic
Authors: Papritz L. , Dunn‐Sigouin E.
Published: August 2020

Previous work highlighted different configurations of the atmospheric circulation causing moisture transport into the Arctic and contributing to surface warming. Here, we clarify the configurations leading to extreme wintertime events of zonal‐mean net and total (sum of absolute values of poleward and equatorward) moisture transports by comparing feature‐based weather system diagnostics with zonal‐wavenumber decomposition of moisture transport in reanalysis data. Results show that extreme Arctic moisture transport events are attributable to individual weather systems, where cyclones favor net transport and blocks favor total transport. Zonal‐wavenumber decomposition reveals that net moisture transport is dominated by planetary scales (zonal‐wavenumbers k ≤ 3). Comparison between the two diagnostics suggests that blocks account for planetary scale contributions to net transport by interacting with cyclones rather than driving the transport themselves. Finally, net and total moisture transport events result in Arctic surface warming via different underlying processes related to cyclones and blocks, respectively.
Slab Rollback Orogeny Model: A Test of Concept
Authors: Dal Zilio Luca , Kissling Edi , Gerya Taras , van Dinther Ylona
Published: August 2020

Buoyancy forces associated with subducting lithosphere control the dynamics of convergent margins. In the postcollisional stage these forces are significantly reduced, yet mountain building and seismicity are ongoing, albeit at lower rates. We leverage advances of a newly developed seismo‐thermo‐mechanical modeling approach to simulate tectonic and seismicity processes in a self‐driven subduction and continental collision setting. We demonstrate that the rearrangement of forces due to slab breakoff, in the postcollisional stage, causes bending and rollback of the residual slab, suction forces, and mantle traction at the base of the upper plate, while stress coupling transfers to the shallow crust. Our results provide an explanation for the postcollisional evolution of the Central Alps, where the so‐called Slab Rollback Orogeny model explains the slow yet persistent upper plate advance, the height of the mountain range, and a seismicity pattern consistent with the different tectonic regimes throughout the orogen.
Spatial Footprints of Storm Surges Along the Global Coastlines
Authors: Enríquez Alejandra R. , Wahl Thomas , Marcos Marta , Haigh Ivan D.
Published: August 2020

We perform the first global analysis of the spatial footprints of storm surges, using observed and simulated storm surge data. Three different techniques are applied to quantify the spatial footprints: clustering analysis, percentage of co‐occurrence, and joint probability analysis. The capability of the simulated data to represent the observed storm surge footprints is demonstrated. Results lead to the identification of coastline stretches prone to be impacted simultaneously by the same storm surge events. The spatial footprint sizes differ around the globe, partially conditioned by the geography of the coastline, that is, more irregular coastlines consist of a larger number of different storm surge clusters with varying footprint sizes. For the northwestern Atlantic, spatial footprints of storm surges vary when specifically accounting for tropical cyclones, using storm track information in the storm surge simulations. Our results provide important new insights into the spatial footprints of storm surges at the global scale and will help to facilitate improvements in how coastal flood risk is identified, assessed, and managed, by taking these spatial features into account.
Nutrient Uptake in the Supraglacial Stream Network of an Antarctic Glacier
Authors: Bergstrom A. , Gooseff M. N. , Singley J. G. , Cohen M. J. , Welch K. A.
Published: August 2020

In polar regions, where many glaciers are cold based (frozen to their beds), biological communities on the glacier surface can modulate and transform nutrients, controlling downstream delivery. However, it remains unclear whether supraglacial streams are nutrient sinks or sources and the rates of nutrient processing. In order to test this, we conducted tracer injections in three supraglacial streams (62 to 123 m long) on Canada Glacier in the Taylor Valley, of the McMurdo Dry Valleys, Antarctica. We conducted a series of additions including nitrate (N), N + phosphate (P), N + P + glucose (C), and N + C. In two reaches, N‐only additions resulted in N uptake. The third reach showed net N release during the N‐only addition, but high N uptake in the N + P addition, indicating P‐limitation or N + P colimitation. Coinjecting C did not increase N‐uptake. Additionally, in these systems at low N concentrations the streams can be a net source of nitrogen. We confirmed these findings using laboratory‐based nutrient incubation experiments on sediment collected from stream channels on Canada Glacier and two other glaciers in the Taylor Valley. Together, these results suggest there is active biological processing of nutrients occurring in these supraglacial streams despite low sediment cover, high flow velocities, and cold temperatures, modifying the input signals to proglacial streams. As glaciers worldwide undergo rapid change, these findings further our understanding of how melt generated on glacier surfaces set the initial nutrient signature for subglacial and downstream environments.
A Machine‐Learning‐Based Model for Water Quality in Coastal Waters, Taking Dissolved Oxygen and Hypoxia in Chesapeake Bay as an Example
Authors: Yu Xin , Shen Jian , Du Jiabi
Published: August 2020

Hypoxia is a big concern in coastal waters as it affects ecosystem health, fishery yield, and marine water resources. Accurately modeling coastal hypoxia is still very challenging even with the most advanced numerical models. A data‐driven model for coastal water quality is proposed in this study and is applied to predict the temporal‐spatial variations of dissolved oxygen (DO) and hypoxic condition in Chesapeake Bay, the largest estuary in the United States with mean summer hypoxic zone extending about 150 km along its main axis. The proposed model has three major components including empirical orthogonal functions analysis, automatic selection of forcing transformation, and neural network training. It first uses empirical orthogonal functions to extract the principal components, then applies neural network to train models for the temporal variations of principal components, and finally reconstructs the three‐dimensional temporal‐spatial variations of the DO. Using the first 75% of the 32‐year (1985–2016) data set for training, the model shows good performance for the testing period (the remaining 25% data set). Selection of forcings for the first mode points to the dominant role of streamflow in controlling interannual variability of bay‐wide DO condition. Different from previous empirical models, the approach is able to simulate three‐dimensional variations of water quality variables and it does not use in situ measured water quality variables but only external forcings as model inputs. Even though the approach is used for the hypoxia problem in Chesapeake Bay, the methodology is readily applicable to other coastal systems that are systematically monitored.
Bowel inflammation in cancer patients: the microbiome, antibiotics and interleukin-9
Authors: Halama Niels
Published: August 2020

Microbiome composition can impact disease courses and also immunotherapy outcomes in solid tumours. It is still unclear how the microbiome might impact treatments in oncology, but also how modulation via antibiotics might interfere. Elegant work now identified interleukin-9 and dysbiosis as relevant factors, providing some answers for these questions.
LncRNA Hoxaas3 promotes lung fibroblast activation and fibrosis by targeting miR-450b-5p to regulate Runx1
Authors: Lin Shuang , Zhang Rui , Xu Lei , Ma Rui , Xu Liming , Zhu Linghua , Hu Jian , An Xiaoxia
Published: August 2020

Long noncoding RNAs (lncRNAs) participate in organ fibrosis and various pulmonary diseases, but its role in idiopathic pulmonary fibrosis (IPF) is not fully understood. In this study, we found lncRNA Hoxaas3 (Hoxaas3) was up-regulated in the mice model of BLM-induced PF and TGF-β1-induced fibrogenesis in lung fibroblasts (LF). Overexpression of Hoxaas3 promoted fibrogenesis, whereas Hoxaas3 inhibition attenuated lung fibrosis both in vitro and in vivo, through regulation of miR-450b-5p. Furthermore, miR-450b-5p inhibition stimulated fibrogenesis by regulating runt-related transcription factor 1 (Runx1), whereas up-regulation of miR-450b-5p alleviated fibrogenesis in LF. Mechanistically, our study showed that Hoxaas3 regulated lung fibroblast activation and fibrogenesis by acting as a competing endogenous RNA for miR-450b-5p: Hoxaas3 decreased the expression of miR-450b-5p to stimulate level and activity of Runx1 and induced fibrotic LF, whereas Runx1 inhibition alleviated the pro-fibrotic effect of Hoxaas3. In addition, Hoxaas3 was regulated by TGF-β1/Smad4 pathway as its transcriptional target. In conclusion, our study showed the role and mechanism of the TGF-β1/Smad4- Hoxaas3–miR-450b-5p–Runx1 axis for a better understanding of PF, demonstrated Hoxaas3 maybe a new diagnostic biomarker or potential therapeutic target for IPF.
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
Authors: Bentsen Mette , Goymann Philipp , Schultheis Hendrik , Klee Kathrin , Petrova Anastasiia , Wiegandt René , Fust Annika , Preussner Jens , Kuenne Carsten , Braun Thomas , Kim Johnny , Looso Mario
Published: August 2020

While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.
Fibroblast-enriched endoplasmic reticulum protein TXNDC5 promotes pulmonary fibrosis by augmenting TGFβ signaling through TGFBR1 stabilization
Authors: Lee Tzu-Han , Yeh Chih-Fan , Lee Ying-Tung , Shih Ying-Chun , Chen Yen-Ting , Hung Chen-Ting , You Ming-Yi , Wu Pei-Chen , Shentu Tzu-Pin , Huang Ru-Ting , Lin Yu-Shan , Wu Yueh-Feng , Lin Sung-Jan , Lu Frank-Leigh , Tsao Po-Nien , Lin Tzu-Hung , Lo Shen-Chuan , Tseng Yi-Shuan , Wu Wan-Lin , Chen Chiung-Nien , Wu Chau-Chung , Lin Shuei-Liong , Sperling Anne I. , Guzy Robert D. , Fang Yun , Yang Kai-Chien
Published: August 2020

Pulmonary fibrosis (PF) is a major public health problem with limited therapeutic options. There is a clear need to identify novel mediators of PF to develop effective therapeutics. Here we show that an ER protein disulfide isomerase, thioredoxin domain containing 5 (TXNDC5), is highly upregulated in the lung tissues from both patients with idiopathic pulmonary fibrosis and a mouse model of bleomycin (BLM)-induced PF. Global deletion of Txndc5 markedly reduces the extent of PF and preserves lung function in mice following BLM treatment. Mechanistic investigations demonstrate that TXNDC5 promotes fibrogenesis by enhancing TGFβ1 signaling through direct binding with and stabilization of TGFBR1 in lung fibroblasts. Moreover, TGFβ1 stimulation is shown to upregulate TXNDC5 via ER stress/ATF6-dependent transcriptional control in lung fibroblasts. Inducing fibroblast-specific deletion of Txndc5 mitigates the progression of BLM-induced PF and lung function deterioration. Targeting TXNDC5, therefore, could be a novel therapeutic approach against PF.
Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6
Authors: Schmidt Jan Marten , Bleichert Franziska
Published: August 2020

Eukaryotic DNA replication initiation relies on the origin recognition complex (ORC), a DNA-binding ATPase that loads the Mcm2–7 replicative helicase onto replication origins. Here, we report cryo-electron microscopy (cryo-EM) structures of DNA-bound Drosophila ORC with and without the co-loader Cdc6. These structures reveal that Orc1 and Orc4 constitute the primary DNA binding site in the ORC ring and cooperate with the winged-helix domains to stabilize DNA bending. A loop region near the catalytic Walker B motif of Orc1 directly contacts DNA, allosterically coupling DNA binding to ORC’s ATPase site. Correlating structural and biochemical data show that DNA sequence modulates DNA binding and remodeling by ORC, and that DNA bending promotes Mcm2–7 loading in vitro. Together, these findings explain the distinct DNA sequence-dependencies of metazoan and S. cerevisiae initiators in origin recognition and support a model in which DNA geometry and bendability contribute to Mcm2–7 loading site selection in metazoans.
Directed manipulation of membrane proteins by fluorescent magnetic nanoparticles
Authors: Li Jia Hui , Santos-Otte Paula , Au Braedyn , Rentsch Jakob , Block Stephan , Ewers Helge
Published: August 2020

The plasma membrane is the interface through which cells interact with their environment. Membrane proteins are embedded in the lipid bilayer of the plasma membrane and their function in this context is often linked to their specific location and dynamics within the membrane. However, few methods are available to manipulate membrane protein location at the single-molecule level. Here, we use fluorescent magnetic nanoparticles (FMNPs) to track membrane molecules and to control their movement. FMNPs allow single-particle tracking (SPT) at 10 nm and 5 ms spatiotemporal resolution, and using a magnetic needle, we pull membrane components laterally with femtonewton-range forces. In this way, we drag membrane proteins over the surface of living cells. Doing so, we detect barriers which we could localize to the submembrane actin cytoskeleton by super-resolution microscopy. We present here a versatile approach to probe membrane processes in live cells via the magnetic control of membrane protein motion.
Reconciling qualitative, abstract, and scalable modeling of biological networks
Authors: Paulevé Loïc , Kolčák Juri , Chatain Thomas , Haar Stefan
Published: August 2020

Predicting biological systems’ behaviors requires taking into account many molecular and genetic elements for which limited information is available past a global knowledge of their pairwise interactions. Logical modeling, notably with Boolean Networks (BNs), is a well-established approach that enables reasoning on the qualitative dynamics of networks. Several dynamical interpretations of BNs have been proposed. The synchronous and (fully) asynchronous ones are the most prominent, where the value of either all or only one component can change at each step. Here we prove that, besides being costly to analyze, these usual interpretations can preclude the prediction of certain behaviors observed in quantitative systems. We introduce an execution paradigm, the Most Permissive Boolean Networks (MPBNs), which offers the formal guarantee not to miss any behavior achievable by a quantitative model following the same logic. Moreover, MPBNs significantly reduce the complexity of dynamical analysis, enabling to model genome-scale networks.
Time-resolved photoemission of infinitely periodic atomic arrangements: correlation-dressed excited states of solids
Authors: Kim Youngjae , Lee JaeDong
Published: August 2020

A theory of the time-resolved photoemission spectroscopy (TRPES) is developed, which enables to explore the real-time electron dynamics of infinitely periodic crystalline solids. In the strongly correlated electron systems NiO and CuO, the early-stage dynamics of the valence band edge are found to be sharply contrasted between those in the spectra of TRPES. This provides a new dynamical insight to the Zaanen–Sawatzky–Allen (ZSA) classification scheme of correlated insulators and makes us assert that NiO dynamically behaves like the Mott–Hubbard insulator (MHI) and CuO like the charge transfer insulator (CTI). In the two-dimensional carbon layer graphene, the real-time electron dynamics of quantum-phase-dressed excited states, i.e., due to the Berry phase and the pseudospin correlation, are investigated in an unprecedented way through the time-resolved angle-resolved photoemission spectroscopy (TR-ARPES). In particular, the dephasing dynamics of optically doped electrons and holes in the massless Dirac band, accompanying a field-induced gliding of the Dirac cone, are discovered.
Machine-learned metrics for predicting the likelihood of success in materials discovery
Authors: Kim Yoolhee , Kim Edward , Antono Erin , Meredig Bryce , Ling Julia
Published: August 2020

Materials discovery is often compared to the challenge of finding a needle in a haystack. While much work has focused on accurately predicting the properties of candidate materials with machine learning (ML), which amounts to evaluating whether a given candidate is a piece of straw or a needle, less attention has been paid to a critical question: are we searching in the right haystack? We refer to the haystack as the design space for a particular materials discovery problem (i.e., the set of possible candidate materials to synthesize), and thus frame this question as one of design space selection. In this paper, we introduce two metrics, the predicted fraction of improved candidates (PFIC), and the cumulative maximum likelihood of improvement (CMLI), which we demonstrate can identify discovery-rich and discovery-poor design spaces, respectively. A combined classification system, composed of the CMLI and PFIC metrics, is then used to identify optimal design spaces with high precision, and thus show the potential to significantly accelerate ML-driven materials discovery.
Author Correction: Prestin kinetics and corresponding frequency dependence augment during early development of the outer hair cell within the mouse organ of Corti
Authors: Bai Jun-Ping , Navaratnam Dhasakumar , Santos-Sacchi Joseph
Published: August 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Objective function estimation for solving optimization problems in gate-model quantum computers
Authors: Gyongyosi Laszlo
Published: August 2020

Quantum computers provide a valuable resource to solve computational problems. The maximization of the objective function of a computational problem is a crucial problem in gate-model quantum computers. The objective function estimation is a high-cost procedure that requires several rounds of quantum computations and measurements. Here, we define a method for objective function estimation of arbitrary computational problems in gate-model quantum computers. The proposed solution significantly reduces the costs of the objective function estimation and provides an optimized estimate of the state of the quantum computer for solving optimization problems.
Feasibility and safety of surgical microwave ablation for hepatocellular carcinoma in elderly patients: a single center analysis in Japan
Authors: Imamura Hajime , Takami Yuko , Ryu Tomoki , Wada Yoshiyuki , Sasaki Shin , Ureshino Hiroki , Saitsu Hideki
Published: August 2020

The feasibility and safety of microwave ablation in elderly hepatocellular carcinoma (HCC) patients remains unknown. The aim of this study was to evaluate the feasibility and safety of surgical microwave ablation for HCC in patients older than 80 years of age. This retrospective study enrolled consecutive 114 patients older than 80 years of age who underwent surgical microwave ablation for HCC between July 1994 and December 2017. We analyzed perioperative outcomes and long-term outcomes to clarify the prognostic factors. The 1-, 3-, 5-year overall survival and recurrence-free survival rates were 97.3%, 76.0%, 49.2% and 84.2%, 44.7%, and 32.5%, respectively. The overall major morbidity rates (Clavien–Dindo grade IIIA or above) were 2.6%. There were no cases of mortality. Multivariate analysis showed that hepatitis C virus antibody (HCV-Ab) positivity and the presence of multiple tumors were independent prognostic factors for long-term outcomes. The overall survival rate of patients with HCV-Ab negative and single tumor was better than that of other patients (p = 0.026). Surgical microwave ablation was feasible and safe for elderly patients with HCC. Elderly patients with HCV-Ab negative and single tumor would be expected to have better long-term outcomes after surgical microwave ablation.