bluuebunny/crossref_metadata_2025 huggingface dataset:
3D Automatic Segmentation of Aortic Computed Tomography Angiography Combining Multi-View 2D Convolutional Neural Networks
Authors: Fantazzini Alice , Esposito Mario , Finotello Alice , Auricchio Ferdinando , Pane Bianca , Basso Curzio , Spinella Giovanni , Conti Michele
Published: August 2020

Purpose

The quantitative analysis of contrast-enhanced Computed Tomography Angiography (CTA) is essential to assess aortic anatomy, identify pathologies, and perform preoperative planning in vascular surgery. To overcome the limitations given by manual and semi-automatic segmentation tools, we apply a deep learning-based pipeline to automatically segment the CTA scans of the aortic lumen, from the ascending aorta to the iliac arteries, accounting for 3D spatial coherence.

Methods

A first convolutional neural network (CNN) is used to coarsely segment and locate the aorta in the whole sub-sampled CTA volume, then three single-view CNNs are used to effectively segment the aortic lumen from axial, sagittal, and coronal planes under higher resolution. Finally, the predictions of the three orthogonal networks are integrated to obtain a segmentation with spatial coherence.

Results

The coarse segmentation performed to identify the aortic lumen achieved a Dice coefficient (DSC) of 0.92 ± 0.01. Single-view axial, sagittal, and coronal CNNs provided a DSC of 0.92 ± 0.02, 0.92 ± 0.04, and 0.91 ± 0.02, respectively. Multi-view integration provided a DSC of 0.93 ± 0.02 and an average surface distance of 0.80 ± 0.26 mm on a test set of 10 CTA scans. The generation of the ground truth dataset took about 150 h and the overall training process took 18 h. In prediction phase, the adopted pipeline takes around 25 ± 1 s to get the final segmentation.

Conclusion

The achieved results show that the proposed pipeline can effectively localize and segment the aortic lumen in subjects with aneurysm.
Interdependencies in Mothers’ and Daughters’ Work-Family Life Course Trajectories: Similar but Different?
Authors: Vidal Sergi , Lersch Philipp M. , Jacob Marita , Hank Karsten
Published: August 2020

Women’s life courses underwent substantial changes in the family and work domains in the second half of the twentieth century. The associated fundamental changes in opportunity structures and values challenged the importance of families of origin for individual life courses, but two research strands suggest enduring within-family reproduction of women’s family behavior and work outcomes. We revisit this issue by studying two complementary types of intergenerational associations in women’s combined work-family trajectories. On the one hand, we examine similarities across mothers’ and daughters’ work-family trajectories to address the direct within-family reproduction of female life courses (intergenerational persistence). On the other hand, we examine systematic associations between work-family trajectories that are typical in each generation to address intergenerational interdependencies beyond direct reproduction that account for individual and societal constrains and opportunities that each generation faced (intergenerational correspondence). We use a within-dyad approach to sequence analysis and examine combined work-family trajectories between ages 18 and 35 of two generations of women, born in 1930–1949 and in 1958–1981, within the same family drawn from the German Socio-Economic Panel. Overall, we find evidence of small but nontrivial persistence in work-family trajectories across generations that is partly attributed to within-family mechanisms of reproduction. In addition, we find correspondence across typical trajectory patterns of each generation, without daughters necessarily resembling their mothers’ trajectories. The strength of the intergenerational associations varies by social background. Our research improves and broadens our understanding of the reproduction of female life courses across generations.
FORTA(Fit-fOR-The-Aged)-based medication optimization: retrospective analysis of experiences from an unconventional outpatient service
Authors: Rieg Sophia , Wehling Martin
Published: August 2020

Purpose

To address potentially harmful polypharmacy in multimorbid older patients. Secondary to assess FORTA (Fit-fOR-The-Aged) utility in ambulatory patients.

Methods

Consecutive patients attending a novel ambulatory service for gerontopharmacology were included in this retrospective analysis. Baseline data, diagnoses, previous drug treatment and recommended changes in medication were analysed and the change of the FORTA score (sum of over- and undertreatment errors) calculated.

Results

The analysis of 182 cases revealed a high number of recommended medication alterations per case (9.81; 95% CI 9.13–10.50). The FORTA score was significantly reduced from 4.24 ± 2.30 to 0.80 ± 1.08 (P < 0.00001), as were under- and overtreatment errors if analysed separately.

Conclusions

The large number of recommendations given in this special outpatient service points to a profound unmet medical need for improving medications in older patients. The FORTA approach was found to be useful to reduce both over- and undertreatment in multimorbid older patients.
Social-Computation-Supporting Kinds
Authors: Strohmaier David
Published: August 2020

Social kinds are heterogeneous. As a consequence of this diversity, some authors have sought to identify and analyse different kinds of social kinds. One distinct kind of social kinds, however, has not yet received sufficient attention. I propose that there exists a class of social-computation-supporting kinds, or SCS-kinds for short. These SCS-kinds are united by the function of enabling computations implemented by social groups. Examples of such SCS-kinds arereimbursement form,US dollar bill,chair of the board. I will analyse SCS-kinds, contrast my analysis with theories of institutional kinds, and discuss the benefits of investigating SCS-kinds.
Introduction: a global history of the Irish Revolution
Authors: Delaney Enda , McGarry Fearghal
Published: August 2020

How might the history of Ireland's revolution be reassessed if viewed within a transnational, comparative or global framework? Drawing attention to recent writing on the subject, this introduction considers the conceptual and historiographical issues at stake in reframing the history of the Irish Revolution, as well as considering potential limitations to these approaches. We assess what topics in particular lend themselves to a fresh perspective focusing on Irish nationalism, while also indicating areas where there is considerable scope for new lines of inquiry. In this era of intensive commemoration of the events that unfolded between 1912 and 1923, this special issue serves to remind us that the history of the revolution should not be confined to the island of Ireland. We argue that thinking transnationally and comparatively can promote a more inclusive and diverse global history of Irish Revolution.
Violence against women in the Irish Civil War, 1922–3: gender-based harm in global perspective
Authors: Clark Gemma
Published: August 2020

Since the 1990s, in the wake of the wars and ethnic cleansing in the former Yugoslavia, violence against women in wartime has become a matter of international concern. This article, on gender-based violence (G.B.V.) during the Irish Civil War, draws on research from scholars and activists around the globe, and newly accessible archival sources, to highlight the relatively humane treatment of women in Ireland – even during the bitter final stages of the Irish Revolution, c.1912–23. Records of the Irish Free State's Compensation (Personal Injuries) Committee show that women suffered some serious and traumatising interpersonal violence during 1922–3 – often on account of their gender (as guardians of the domestic space). Women's interactions with the Civil War were thus distinctive from men's because of the prevalence in Ireland of forms of aggression and intimidation, including crimes against property, which transgressed public/private boundaries. However, I argue that it did not serve the strategy nor ideology of either warring side to denigrate women en masse. The genocidal aims underlying conflict-related G.B.V. elsewhere in the world were absent in Ireland, where gendered power structures, shored up by Catholic authority, remained largely unshaken by the revolution – despite the great efforts of many radical females. Revolutionary Ireland was not a safe place for many Irishwomen (nor indeed for some men); however, for pro- and anti-Treaty forces, maintaining propriety militated against the need for sexual violence as warfare.
How Much is One American Worth? How Competition Affects Trade Preferences
Authors: MUTZ DIANA C. , LEE AMBER HYE-YON
Published: August 2020

When forming opinions, mass publics may implicitly or explicitly value some people’s well-being more than others. Here we examine how two forms of this phenomenon—ethnocentric valuation and moral exclusion—affect attitudes toward international trade. We hypothesize that attitudes toward competition and believing that trade is a competition moderate the extent of ethnocentric valuation and moral exclusion; although all citizens value their co-nationals’ livelihoods systematically more than those of people in trading partner countries, greater ethnocentric valuation and moral exclusion occur when trade is seen as a competition and when individuals hold more positive attitudes toward competition.

Using two survey experiments conducted on representative samples of both Americans and Canadians, we examine how differential valuation of in-country and out-country job gains and losses influences trade policy preferences. We test a series of hypotheses using multiple variables tied to competitive attitudes across two countries that differ in their attitudes toward competition.
Repellent activity of Tanacetum parthenium (L.) and Tanacetum vulgare (L.) essential oils against Leptinotarsa decemlineata (Say)
Authors: Lazarević Jelica , Kostić Igor , Milanović Slobodan , Šešlija Jovanović Darka , Krnjajić Slobodan , Ćalić Dušica , Stanković Slađan , Kostić Miroslav
Published: August 2020

The Colorado potato beetle, Leptinotarsa decemlineata (Say), is one of the most destructive pest species to have developed resistance to most chemical insecticides. We determined the composition and evaluated the potential of Tanacetum parthenium L. and Tanacetum vulgare L. (Asteraceae family) essential oil (EO) application as an alternative eco-friendly control strategy against L. decemlineata. We assessed the antifeedant activity for L. decemlineata larvae and adults by estimating the damage to potato leaves treated with three concentrations of EOs dissolved in ethanol (0.125, 0.25 and 0.5%). Results showed that T. parthenium EO was more effective against larvae, and T. vulgare was more effective against adults. In an olfactometer assay, the time required to choose an untreated leaf disc did not depend on the Tanacetum species, or life stage examined. However, the concentration of EO exhibited a significant effect on the behaviour of both developmental stages. At higher EO concentrations, both third instar larvae and adults require less time to choose an untreated leaf disc. Additionally, T. parthenium EO provoked more rapid movement away from the treated leaf disc than T. vulgare, especially at the highest concentration. Successful modification of L. decemlineata behaviour by the two Tanacetum oils suggests that they possess the potential for use in potato protection.
There is a simplicity bias when generalising from ambiguous data
Authors: Durvasula Karthik , Liter Adam
Published: August 2020

How exactly do learners generalise in the face of ambiguous data? While there has been a substantial amount of research studying the biases that learners employ, there has been very little work on what sorts of biases are employed in the face of data that is ambiguous between phonological generalisations with different degrees of complexity. In this article, we present the results from three artificial language learning experiments that suggest that, at least for phonotactic sequence patterns, learners are able to keep track of multiple generalisations related to the same segmental co-occurrences; however, the generalisations they learn are only the simplest ones consistent with the data.
Notational equivalence in tonal geometry
Authors: Oakden Chris
Published: August 2020

This paper employs a computational framework to demonstrate that two competing feature-geometric models of tonal representation are notationally equivalent. A model-theoretic analysis of these structures using a low-complexity logic yields two main results. First, the current study demonstrates that the models do not differ in their empirical coverage of assimilatory tone-sandhi processes in Chinese dialects, contrary to previous claims. Second, the models are shown to be bi-interpretable (using a more restrictive definition of bi-interpretability than earlier studies), thus providing a formally rigorous demonstration that the differences between the structures of the models are superficial, rather than substantive. The computational characterisation pursued here is well suited to questions of notational equivalence, because it allows for a principled comparison of the empirical coverage and structural content of two models using a single formalism.
Monte Carlo estimation of the probability of causal contacts between communicating civilizations
Authors: Lares M. , Funes J. G. , Gramajo L.
Published: August 2020

In this work we address the problem of estimating the probabilities of causal contacts between civilizations in the Galaxy. We make no assumptions regarding the origin and evolution of intelligent life. We simply assume a network of causally connected nodes. These nodes refer somehow to intelligent agents with the capacity of receiving and emitting electromagnetic signals. Here we present a three-parametric statistical Monte Carlo model of the network in a simplified sketch of the Galaxy. Our goal, using Monte Carlo simulations, is to explore the parameter space and analyse the probabilities of causal contacts. We find that the odds to make a contact over decades of monitoring are low for most models, except for those of a galaxy densely populated with long-standing civilizations. We also find that the probability of causal contacts increases with the lifetime of civilizations more significantly than with the number of active civilizations. We show that the maximum probability of making a contact occurs when a civilization discovers the required communication technology.
Analyzing Internal Variability and Forced Response of Subdaily and Daily Extreme Precipitation Over Europe
Authors: Wood R. R. , Ludwig R.
Published: August 2020

At regional to local scales internal variability is expected to be a dominant source of uncertainty in analyzing precipitation extremes and mean precipitation even far into the 21st century. A debated topic is whether a faster increase in subdaily precipitation extremes can be expected. Here we analyzed seasonal maximum precipitation in various time steps (3 hr, days, and 5 days) from a high‐resolution 50‐member large‐ensemble (CRCM5‐LE) and compared them to changes in mean precipitation over Europe. Our results show that the magnitude of change in extreme precipitation varies for season and duration. Subdaily extremes increase at higher rates than daily extremes and show higher scaling with temperature. Northern Europe shows widespread scaling above Clausius‐Clapeyron of subdaily extremes in all seasons and for daily extremes in winter/spring. Scaling above Clausius‐Clapeyron is also visible over Eastern Europe in winter/spring. For most regions and seasons the forced response emerges from the internal variability by midcentury.
Deriving the Magnetopause Position from the Soft X‐Ray Image by Using the Tangent Fitting Approach
Authors: Sun Tianran , Wang Chi , Connor Hyunju K. , Jorgensen Anders M. , Sembay Steven
Published: August 2020

Imaging is one of the essential techniques to observe astronomical structures. While analyzing the observed images, it is a challenge in many scientific fields to reconstruct the 3‐D structures from 2‐D image(s). This report discusses this challenge in the context of reconstructing the structure of the Earth's magnetosphere from the X‐ray image and presents a new technique. Specifically, it finds the optimum match of tangent directions derived from the X‐ray image and the parameterized magnetopause function. We name this approach as the tangent fitting approach (TFA). TFA is further validated based on the magnetohydrodynamic (MHD) simulations of the X‐ray images with different viewing geometries. TFA enables the reconstruction of the large‐scale magnetopause from a single X‐ray image, applicable to time‐dependent situations such as cases during magnetic storms. It is also noted that TFA has a potential broader application to remote sensing data, for instance, energetic neutral atom (ENA) observations. Lastly, this new approach is compared with other magnetopause reconstruction approaches.
Retraction Note: p62 improves AD-like pathology by increasing autophagy
Authors: Caccamo A. , Ferreira E. , Branca C. , Oddo S.
Published: August 2020

The Editor-in-Chief and publisher have retracted this article.
Targeted therapy for hepatocellular carcinoma
Authors: Huang Ao , Yang Xin-Rong , Chung Wen-Yuan , Dennison Ashley R. , Zhou Jian
Published: August 2020

The last 3 years have seen the emergence of promising targeted therapies for the treatment of hepatocellular carcinoma (HCC). Sorafenib has been the mainstay of treatment for a decade and newer modalities were ineffective and did not confer any increased therapeutic benefit until the introduction of lenvatinib which was approved based on its non-inferiority to sorafenib. The subsequent success of regorafenib in HCC patients who progress on sorafenib treatment heralded a new era of second-line treatment and was quickly followed by ramucirumab, cabozantinib, and the most influential, immune checkpoint inhibitors (ICIs). Over the same period combination therapies, including anti-angiogenesis agents with ICIs, dual ICIs and targeted agents in conjunction with surgery or other loco-regional therapies, have been extensively investigated and have shown promise and provided the basis for exciting clinical trials. Work continues to develop additional novel therapeutic agents which could potentially augment the presently available options and understand the underlying mechanisms responsible for drug resistance, with the goal of improving the survival of patients with HCC.
A critical synthesis of the role of the pharmacist in oral healthcare and management of medication-related osteonecrosis of the jaw
Authors: Sturrock A. , Preshaw P. M. , Hayes C. , Wilkes S.
Published: August 2020

Objective

To consolidate extant published evidence in relation to the potential of integrating oral healthcare for patients at risk of developing medication-related osteonecrosis of the jaw (MRONJ).

Methods

A critical synthesis and consolidation of five publications was undertaken. As a mechanism of situating the extant work within the context of primary healthcare provision, the Rainbow Model of Integrated Care was applied as a theoretical lens through which the conceptual findings could be collectively applied to practice.

Results

The critical synthesis revealed a thematic emergence relating to both formative and normative integration. The most salient of these were the identification of limited shared clinical records, and disconnection of oral healthcare provision from patients’ general medical care. The three levels of the Rainbow Model of Integrated Care reflected a series of issues for address.

Conclusion

In the context of collaborative, multi-disciplinary working for patients at risk of development of MRONJ, pharmacists are a professional group which this research reveals to be an underutilised resource. Reduction of oral health inequality at all levels of patient care is a key priority and this research highlights areas for address in relation to requirements for interprofessional education, optimal communication and policies reflective and facilitative of these.
Digestive symptoms of COVID-19 and expression of ACE2 in digestive tract organs
Authors: Xu Jiabin , Chu Mei , Zhong Fan , Tan Xinghua , Tang Guofang , Mai Jianbo , Lai Niangmei , Guan Chenyu , Liang Yujie , Liao Guiqing
Published: August 2020

SARS-CoV-2 has resulted in numerous cases of Coronavirus Disease 2019 (COVID-19) worldwide. In addition to fever and respiratory symptoms, digestive symptoms also are observed in some patients with COVID-19. Angiotensin-converting enzyme 2 (ACE2) was reported to be the receptor for SARS-CoV-2. The aim of this study was to comprehensively investigate the digestive symptoms that occur in COVID-19 patients, and the potential pathogenic route of the SARS-CoV-2 infection in digestive tract organs (from the oral cavity to the gastrointestinal tract). We investigated the digestive symptoms of 48 patients with COVID-19 and explored ACE2 expression in digestive tract and lung cancers, based on a series of bulk and single-cell RNA sequencing data obtained from public databases. We found that 25% (12/48) of the patients with COVID-19 suffered from digestive symptoms, among which pharyngalgia (7/48) was the most common manifestation, followed by diarrhea (3/48), anorexia (3/48), and nausea (1/48). The bulk tissue RNA sequencing analysis indicated that digestive tract organs had higher ACE2 expression levels compared to the lung, and the expression of ACE2 in the lung increased with age. Single-cell RNA-Seq results showed that the ACE2-positive-cell ratio in digestive tract organs was significantly higher compared to the lung. ACE2 expression was higher in tumor cells compared to normal control (NC) tissues. While in gastric tissues, ACE2 expression gradually increased from chronic gastritis to metaplasia, to early cancer. Our data might provide a theoretical basis for screening the SARS-CoV-2 susceptible population and for the clinical classification of treatment of patients with COVID-19.
Improving the accuracy of medical diagnosis with causal machine learning
Authors: Richens Jonathan G. , Lee Ciarán M. , Johri Saurabh
Published: August 2020

Machine learning promises to revolutionize clinical decision making and diagnosis. In medical diagnosis a doctor aims to explain a patient’s symptoms by determining the diseases causing them. However, existing machine learning approaches to diagnosis are purely associative, identifying diseases that are strongly correlated with a patients symptoms. We show that this inability to disentangle correlation from causation can result in sub-optimal or dangerous diagnoses. To overcome this, we reformulate diagnosis as a counterfactual inference task and derive counterfactual diagnostic algorithms. We compare our counterfactual algorithms to the standard associative algorithm and 44 doctors using a test set of clinical vignettes. While the associative algorithm achieves an accuracy placing in the top 48% of doctors in our cohort, our counterfactual algorithm places in the top 25% of doctors, achieving expert clinical accuracy. Our results show that causal reasoning is a vital missing ingredient for applying machine learning to medical diagnosis.
Energy storing bricks for stationary PEDOT supercapacitors
Authors: Wang Hongmin , Diao Yifan , Lu Yang , Yang Haoru , Zhou Qingjun , Chrulski Kenneth , D’Arcy Julio M.
Published: August 2020

Fired brick is a universal building material, produced by thousand-year-old technology, that throughout history has seldom served any other purpose. Here, we develop a scalable, cost-effective and versatile chemical synthesis using a fired brick to control oxidative radical polymerization and deposition of a nanofibrillar coating of the conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT). A fired brick’s open microstructure, mechanical robustness and ~8 wt% α-Fe2O3 content afford an ideal substrate for developing electrochemical PEDOT electrodes and stationary supercapacitors that readily stack into modules. Five-minute epoxy serves as a waterproof case enabling the operation of our supercapacitors while submerged underwater and a gel electrolyte extends cycling stability to 10,000 cycles with ~90% capacitance retention.
Giant voltage-controlled modulation of spin Hall nano-oscillator damping
Authors: Fulara Himanshu , Zahedinejad Mohammad , Khymyn Roman , Dvornik Mykola , Fukami Shunsuke , Kanai Shun , Ohno Hideo , Åkerman Johan
Published: August 2020

Spin Hall nano-oscillators (SHNOs) are emerging spintronic devices for microwave signal generation and oscillator-based neuromorphic computing combining nano-scale footprint, fast and ultra-wide microwave frequency tunability, CMOS compatibility, and strong non-linear properties providing robust large-scale mutual synchronization in chains and two-dimensional arrays. While SHNOs can be tuned via magnetic fields and the drive current, neither approach is conducive to individual SHNO control in large arrays. Here, we demonstrate electrically gated W/CoFeB/MgO nano-constrictions in which the voltage-dependent perpendicular magnetic anisotropy tunes the frequency and, thanks to nano-constriction geometry, drastically modifies the spin-wave localization in the constriction region resulting in a giant 42% variation of the effective damping over four volts. As a consequence, the SHNO threshold current can be strongly tuned. Our demonstration adds key functionality to nano-constriction SHNOs and paves the way for energy-efficient control of individual oscillators in SHNO chains and arrays for neuromorphic computing.
A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome
Authors: Perumal Sampath , Koh Chu Shin , Jin Lingling , Buchwaldt Miles , Higgins Erin E. , Zheng Chunfang , Sankoff David , Robinson Stephen J. , Kagale Sateesh , Navabi Zahra-Katy , Tang Lily , Horner Kyla N. , He Zhesi , Bancroft Ian , Chalhoub Boulos , Sharpe Andrew G. , Parkin Isobel A. P.
Published: August 2020

It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseedBrassica nigra, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplicationBrassica-specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separatingB. nigrafrom its diploid relatives.
Schooling and Covid-19: lessons from recent research on EdTech
Authors: Fairlie Robert , Loyalka Prashant
Published: August 2020

The wide-scale global movement of school education to remote instruction due to Covid-19 is unprecedented. The use of educational technology (EdTech) offers an alternative to in-person learning and reinforces social distancing, but there is limited evidence on whether and how EdTech affects academic outcomes. Recently, we conducted two large-scale randomized experiments, involving ~10,000 primary school students in China and Russia, to evaluate the effectiveness of EdTech as a substitute for traditional schooling. In China, we examined whether EdTech improves academic outcomes relative to paper-and-pencil workbook exercises of identical content. We found that EdTech was a perfect substitute for traditional learning. In Russia, we further explored how much EdTech can substitute for traditional learning. We found that EdTech substitutes only to a limited extent. The findings from these large-scale trials indicate that we need to be careful about using EdTech as a full-scale substitute for the traditional instruction received by schoolchildren.
Combining expert and crowd-sourced training data to map urban form and functions for the continental US
Authors: Demuzere Matthias , Hankey Steve , Mills Gerald , Zhang Wenwen , Lu Tianjun , Bechtel Benjamin
Published: August 2020

Although continental urban areas are relatively small, they are major drivers of environmental change at local, regional and global scales. Moreover, they are especially vulnerable to these changes owing to the concentration of population and their exposure to a range of hydro-meteorological hazards, emphasizing the need for spatially detailed information on urbanized landscapes. These data need to be consistent in content and scale and provide a holistic description of urban layouts to address different user needs. Here, we map the continental United States into Local Climate Zone (LCZ) types at a 100 m spatial resolution using expert and crowd-sourced information. There are 10 urban LCZ types, each associated with a set of relevant variables such that the map represents a valuable database of urban properties. These data are benchmarked against continental-wide existing and novel geographic databases on urban form. We anticipate the dataset provided here will be useful for researchers and practitioners to assess how the configuration, size, and shape of cities impact the important human and environmental outcomes.
An annotated fluorescence image dataset for training nuclear segmentation methods
Authors: Kromp Florian , Bozsaky Eva , Rifatbegovic Fikret , Fischer Lukas , Ambros Magdalena , Berneder Maria , Weiss Tamara , Lazic Daria , Dörr Wolfgang , Hanbury Allan , Beiske Klaus , Ambros Peter F. , Ambros Inge M. , Taschner-Mandl Sabine
Published: August 2020

Fully-automated nuclear image segmentation is the prerequisite to ensure statistically significant, quantitative analyses of tissue preparations,applied in digital pathology or quantitative microscopy. The design of segmentation methods that work independently of the tissue type or preparation is complex, due to variations in nuclear morphology, staining intensity, cell density and nuclei aggregations. Machine learning-based segmentation methods can overcome these challenges, however high quality expert-annotated images are required for training. Currently, the limited number of annotated fluorescence image datasets publicly available do not cover a broad range of tissues and preparations. We present a comprehensive, annotated dataset including tightly aggregated nuclei of multiple tissues for the training of machine learning-based nuclear segmentation algorithms. The proposed dataset covers sample preparation methods frequently used in quantitative immunofluorescence microscopy. We demonstrate the heterogeneity of the dataset with respect to multiple parameters such as magnification, modality, signal-to-noise ratio and diagnosis. Based on a suggested split into training and test sets and additional single-nuclei expert annotations, machine learning-based image segmentation methods can be trained and evaluated.
Electronic and optical competence of TiO2/BiVO4 nanocomposites in the photocatalytic processes
Authors: Drisya K. T. , Solís-López M. , Ríos-Ramírez J. J. , Durán-Álvarez J. C. , Rousseau A. , Velumani S. , Asomoza R. , Kassiba A. , Jantrania A. , Castaneda H.
Published: August 2020

Nanocomposites with different ratios of titanium dioxide and bismuth vanadate [TiO2]/[BiVO4] give rise to compatible electronic band structure alignment at their interfaces to ensure enhanced photoactivated charge transfer under visible light. The sol–gel method and suitable post-synthesis thermal treatments were used to synthesize different compositions with stabilized anatase phase of TiO2 and monoclinic scheelite polymorph BiVO4. Structural, electronic and optical characterizations were performed and the results were analysed as a function of the stoichiometry, in which both crystalline structures show a clear junction formation among their characteristic stacking planes. Photocatalytic and (photo) electrochemical responses of the nanocomposites were investigated and tested for the degradation of azo dyes (Acid Blue-113, AB-113) (~ 99%) under visible light radiation. The nanocomposite with a mass ratio of (1:10) shows the highest photocatalytic efficiency compared to the other compositions. HRTEM images showed marked regions in which both crystalline structures form a clear junction and their characteristic planes. However, the increase of BiVO4 content in the network overcomes the photocatalytic activity due to the decrease in the reduction potential of the photo-generated electrons with high recombination rates.
Sedimentary and geochemical characteristics of Triassic new type of polyhalite potassium resources in Northeast Sichuan and its genetic study
Authors: Zhong Jiaai , Zheng Mianping , Zhang Yongsheng , Tang Xueyuan , Zhang XueFei
Published: August 2020

Polyhalite has been discovered for years in the Triassic of the Sichuan Basin. However, it is difficult to exploit and utilize such polyhalite because of its deep burial depth and its coexistence with anhydrite or dolomite. Therefore, it has always been regarded as “dead ore”. Based on slice identification, X-powder diffraction, chemical analysis, REEs analysis and strontium isotope test on halite samples from the fourth and fifth member of Jialingjiang Formation to Leikoupo Formation of Wells ZK601 and ZK001 in Xuanhan area, Northeast Sichuan Basin, this paper discovers thick layers of granular polyhalite associated with halite and the polyhalite content accounts for 10–30%. These deep polyhalites can be obtained by water-soluble mining and utilized, so they are called “new type polyhalite potash deposits”. The deposit is deep buried at 3,000 m underground, and the thickness of a single layer can be more than 30 m. It is stable in regional distribution. The discovery of the “new type polyhalite potash deposits” has “activated” polyhalite, which has been considered as deep “dead ore” and has great significance for potash prospecting in China.
Establishment of an experimental model for MHC homo-to-hetero transplantation
Authors: Murata Tomoki , Wada Haruka , Otsuka Ryo , Sasaki Airi , Tsuji Hyuma , Itoh Mizuho , Eguchi Nanami , Kawai Tatsuo , Seino Ken-ichiro
Published: August 2020

Preventing rejection is a major challenge in transplantation medicine, even when using pluripotent stem cell-derived grafts. In iPS cell (iPSC)-based transplantation, to reduce the risk of rejection, it is thought to be optimal that preparing the cells from donors whose human leukocyte antigen-haplotype are homozygous. Generally, this approach is referred to as major histocompatibility complex (MHC) homo-to-hetero transplantation, which is MHC-matched but minor antigen-mismatched. To investigate the immune response in the MHC homo-to-hetero transplantation, we established a murine experimental system in which MHC-matched but minor antigen-mismatched tissue (skin) grafts were transplanted into MHC-heterozygous recipients. Unexpectedly, only minor antigen-mismatched grafts were rejected at the same time points as rejection of fully allogeneic grafts. A vigorous anti-donor type T cell response was detected in vitro and conventional immunosuppressants targeting T cell activation had limited effects on controlling rejection. However, anti-donor antibodies were not detected only in the minor antigen-mismatched transplantation. This murine transplantation model can be used to further analyze immunological subjects for MHC homo-to-hetero iPSC-based transplantation.
A new approach to separate hydrogen from carbon dioxide using graphdiyne-like membrane
Authors: Rezaee Parham , Naeij Hamid Reza
Published: August 2020

In order to separate a mixture of hydrogen ($$\text {H}_{2}$$

H
2

) and carbon dioxide ($$\text {CO}_{2}$$

CO
2

) gases, we have proposed a new approach employing the graphdiyne-like membrane (GDY-H) using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. GDY-H is constructed by removing one-third diacetylenic ($${{-}\text {C}{\equiv}\text {C}{-}\text {C}{\equiv}\text {C}{-}}$$

-
C
≡
C
-
C
≡
C
-

) bonds linkages and replacing with hydrogen atoms in graphdiyne structure. Our DFT calculations exhibit poor selectivity and good permeances for $$\text {H}_{2}$$

H
2

/$$\text {CO}_{2}$$

CO
2

gases passing through this membrane. To improve the performance of the GDY-H membrane for $$\text {H}_{2}$$

H
2

/$$\text {CO}_{2}$$

CO
2

separation, we have placed two layers of GDY-H adjacent to each other which the distance between them is 2 nm. Then, we have inserted 1,3,5-triaminobenzene between two layers. In this approach, the selectivity of $$\text {H}_{2}$$

H
2

/$$\text {CO}_{2}$$

CO
2

is increased from 5.65 to completely purified $$\text {H}_{2}$$

H
2

gas at 300 K. Furthermore, GDY-H membrane represents excellent permeance, about $$10^8$$

10
8

gas permeation unit (GPU), for $$\text {H}_{2}$$

H
2

molecule at temperatures above 20 K. The $$\text {H}_{2}$$

H
2

permeance is much higher than the value of the usual industrial limits. Moreover, our proposed approach shows a good balance between the selectivity and permeance parameters for the gas separation which is an essential factor for $$\text {H}_{2}$$

H
2

purification and $$\text {CO}_{2}$$

CO
2

capture processes in the industry.
Acoustic analysis of starting jets in an anechoic chamber: implications for volcano monitoring
Authors: Peña Fernández J. J. , Cigala V. , Kueppers U. , Sesterhenn J.
Published: August 2020

Explosive volcanic eruptions are associated with a plethora of geophysical signals. Among them, acoustic signals provide ample information about eruptive dynamics and are widely used for monitoring purposes. However, a mechanistic correlation of monitoring signals, underlying source processes and reasons for short-term variations is incomplete. Scaled laboratory experiments can mimic a wide range of explosive volcanic eruption conditions. Here, starting (non-steady) compressible gas jets are created using a shock tube in an anechoic chamber and their acoustic signature is recorded with a microphone array. Noise sources are mapped in time and frequency using wavelet analysis and their dependence from pressure ratio, non-dimensional mass supply and exit-to-throat area ratio is deciphered. We observed that the pressure ratio controls the establishment of supersonic conditions and their duration, and influences the interaction between shock, shear layer, and vortex ring. The non-dimensional mass supply affects the duration of the discharge, the maximum velocity of the flow, and the existence of a trailing jet. Lower values of exit-to-throat area ratio induce a faster decay of the acoustic fingerprint of the jet flow. The simplistic experiments presented here, and their acoustic analysis will serve as an essential starting point to infer source conditions prior to and during impulsive volcanic eruptions.
Transformation of the recalcitrant pesticide chlordecone by Desulfovibrio sp.86 with a switch from ring-opening dechlorination to reductive sulfidation activity
Authors: Della-Negra Oriane , Chaussonnerie Sébastien , Fonknechten Nuria , Barbance Agnès , Muselet Delphine , Martin Déborah E. , Fouteau Stéphanie , Fischer Cécile , Saaidi Pierre-Loïc , Le Paslier Denis
Published: August 2020

The insecticide chlordecone has been used in the French West Indies for decades, resulting in long term pollution, human health problems and social crisis. In addition to bacterial consortia and Citrobacter sp.86 previously described to transform chlordecone into three families of transformation products (A: hydrochlordecones, B: polychloroindenes and C: polychloroindenecarboxylic acids), another bacterium Desulfovibrio sp.86, showing the same abilities has been isolated and its genome was sequenced. Ring-opening dechlorination, leading to A, B and C families, was observed as previously described. Changing operating conditions in the presence of chlordecone gave rise to the formation of an unknown sulfur-containing transformation product instead of the aforementioned ones. Its structural elucidation enabled to conclude to a thiol derivative, which corresponds to an undocumented bacterial reductive sulfidation. Microbial experiments pointed out that the chlordecone thiol derivative was observed in anaerobiosis, and required the presence of an electron acceptor containing sulfur or hydrogen sulfide, in a confined atmosphere. It seems that this new reaction is also active on hydrochlordecones, as the 10-monohydrochlordecone A1 was transformed the same way. Moreover, the chlordecone thiol derivative called F1 was detected in several chlordecone contaminated mangrove bed sediments from Martinique Island, highlighting the environmental relevance of these results.
Phytoestrogen genistein hinders ovarian oxidative damage and apoptotic cell death-induced by ionizing radiation: co-operative role of ER-β, TGF-β, and FOXL-2
Authors: Haddad Yasmin Hamdy , Said Riham S. , Kamel Rehab , Morsy Engy M. El , El-Demerdash Ebtehal
Published: August 2020

Radiotherapy is a well-known cause of premature ovarian failure (POF). Therefore, we investigated the molecular influence of genistein (GEN) on the ovarian reserve of rats exposed to ϒ-radiation. Female Sprague Dawley rats were exposed to a 3.2 Gy γ-radiation to induce POF and/or treated with either GEN (5 mg/kg, i.p.) or Ethinyl estradiol (E2; 0.1 mg/kg, s.c.), once daily for 10 days. GEN was able to conserve primordial follicles stock and population of growing follicles accompanied with reduction in atretic follicles. GEN restored the circulating estradiol and anti-Müllerian hormone levels which were diminished after irradiation. GEN has potent antioxidant activity against radiation-mediated oxidative stress through upregulating endogenous glutathione levels and glutathione peroxidase activity. Mechanistically, GEN inhibited the intrinsic pathway of apoptosis by repressing Bax expression and augmenting Bcl-2 expression resulted in reduced Bax/Bcl-2 ratio with subsequent reduction in cytochrome c and caspase 3 expression. These promising effects of GEN are associated with improving granulosa cells proliferation. On the molecular basis, GEN reversed ovarian apoptosis through up-regulation of ER-β and FOXL-2 with downregulation of TGF-β expression, therefore inhibiting transition of primordial follicles to more growing follicles. GEN may constitute a novel therapeutic modality for safeguarding ovarian function of females’ cancer survivors.
The role of seagrass vegetation and local environmental conditions in shaping benthic bacterial and macroinvertebrate communities in a tropical coastal lagoon
Authors: Alsaffar Z. , Pearman J. K. , Cúrdia J. , Ellis J. , Calleja M. Ll. , Ruiz-Compean P. , Roth F. , Villalobos R. , Jones B. H. , Morán X. A. G. , Carvalho S.
Published: August 2020

We investigated the influence of seagrass canopies on the benthic biodiversity of bacteria and macroinvertebrates in a Red Sea tropical lagoon. Changes in abundance, number of taxa and assemblage structure were analyzed in response to seagrass densities (low, SLD; high, SHD; seagrasses with algae, SA), and compared with unvegetated sediments. Biological and environmental variables were examined in these four habitats (hereafter called treatments), both in the underlaying sediments and overlaying waters, at three randomly picked locations in March 2017. Differences between treatments were more apparent in the benthic habitat than in the overlaying waters. The presence of vegetation (more than its cover) and changes in sedimentary features (grain size and metals) at local scales influenced the observed biological patterns, particularly for macroinvertebrates. Of note, the highest percentage of exclusive macroinvertebrate taxa (18% of the gamma diversity) was observed in the SHD treatment peaking in the SA for bacteria. Benthic macroinvertebrates and bacteria shared a generally low number of taxa across treatments and locations; approximately, 25% of the gamma diversity was shared among all treatments and locations for macrofauna, dropping to 11% for bacteria. Given the low overlap in the species distribution across the lagoon, sustaining the connectivity among heterogeneous soft sediment habitats appears to be essential for maintaining regional biodiversity. This study addresses a current scientific gap related to the relative contributions of vegetated and unvegetated habitats to biodiversity in tropical regions.
A novel biomarker of MMP-cleaved prolargin is elevated in patients with psoriatic arthritis
Authors: Sinkeviciute Dovile , Skovlund Groen Solveig , Sun Shu , Manon-Jensen Tina , Aspberg Anders , Önnerfjord Patrik , Bay-Jensen Anne-Christine , Kristensen Salome , Holm Nielsen Signe
Published: August 2020

Psoriatic arthritis (PsA) is a chronic musculoskeletal inflammatory disease found in up to 30% of psoriasis patients. Prolargin—an extracellular matrix (ECM) protein present in cartilage and tendon—has been previously shown elevated in serum of patients with psoriasis. ECM protein fragments can reflect tissue turnover and pathological changes; thus, this study aimed to develop, validate and characterize a novel biomarker PROM targeting a matrix metalloproteinase (MMP)-cleaved prolargin neo-epitope, and to evaluate it as a biomarker for PsA. A competitive ELISA was developed with a monoclonal mouse antibody; dilution- and spiking-recovery, inter- and intra-variation, and accuracy were evaluated. Serum levels were evaluated in 55 healthy individuals and 111 patients diagnosed with PsA by the CASPAR criteria. Results indicated that the PROM assay was specific for the neo-epitope. Inter- and intra- assay variations were 11% and 4%, respectively. PROM was elevated (p = 0.0003) in patients with PsA (median: 0.24, IQR: 0.19–0.31) compared to healthy controls (0.18; 0.14–0.23) at baseline. AUROC for separation of healthy controls from PsA patients was 0.674 (95% CI 0.597–0.744, P < 0.001). In conclusion, MMP-cleaved prolargin can be quantified in serum by the PROM assay and has the potential to separate patients with PsA from healthy controls.
A novel strain of acetic acid bacteria Gluconobacter oxydans FBFS97 involved in riboflavin production
Authors: Noman Abeer Essam , Al-Barha Naif S. , Sharaf Abdul-Aziz M. , Al-Maqtari Qais Ali , Mohedein Amani , Mohammed Hammad Hamed Hammad , Chen Fusheng
Published: August 2020

A novel bacterial strain of acetic acid bacteria capable of producing riboflavin was isolated from the soil sample collected in Wuhan, China. The isolated strain was identified as Gluconobacter oxydans FBFS97 based on several phenotype characteristics, biochemicals tests, and 16S rRNA gene sequence conducted. Furthermore, the complete genome sequencing of the isolated strain has showed that it contains a complete operon for the biosynthesis of riboflavin. In order to obtain the maximum concentration of riboflavin production, Gluconobacter oxydans FBFS97 was optimized in shake flask cultures through response surface methodology employing Plackett–Burman design (PBD), and Central composite design (CCD). The results of the pre-experiments displayed that fructose and tryptone were found to be the most suitable sources of carbon and nitrogen for riboflavin production. Then, PBD was conducted for initial screening of eleven minerals (FeSO4, FeCl3, KH2PO4, K2HPO4, MgSO4, ZnSO4, NaCl, CaCl2, KCl, ZnCl2, and AlCl3.6H2O) for their significances on riboflavin production by Gluconobacter oxydans strain FBFS97. The most significant variables affecting on riboflavin production are K2HPO4 and CaCl2, the interaction affects and levels of these variables were optimized by CCD. After optimization of the medium compositions for riboflavin production were determined as follows: fructose 25 g/L, tryptone 12.5 g/L, K2HPO4 9 g/L, and CaCl2 0.06 g/L with maximum riboflavin production 23.24 mg/L.