bluuebunny/crossref_metadata_2025 huggingface dataset:
Rice husk and charred husk amendments increase porewater and plant Si but water management determines grain As and Cd concentration
Authors: Linam Franklin , Limmer Matt A. , Tappero Ryan , Seyfferth Angelia L.
Published: March 2022

Purpose

Rice is a staple crop worldwide and a silicon (Si) hyperaccumulator with Si levels reaching 5–10% of its mass; this can result in desilication and Si-deficiency if plant residues are not managed correctly. Rice is also uniquely subject to arsenic (As) and cadmium (Cd) contamination depending on soil conditions. Our goal is to quantify the effects of rice husk (a Si-rich milling byproduct) amendments and different water management strategies on rice uptake of Si, As, and Cd.

Methods

We employed 4 husk amendment treatments: Control (no husk), Husk (untreated husk), Biochar (husk pyrolyzed at 450 °C), and CharSil (husk combusted at > 1000 °C). Each of these amendments was studied under nonflooded, alternate wetting and drying (AWD), and flooded water management in a pot study. Porewater chemistry and mature plant elemental composition were measured.

Results

Husk and Biochar treatments, along with flooding, increased porewater and plant Si. Vegetative tissue As decreased with increasing porewater Si, but grain As and plant Cd were primarily controlled by water management. Grain As and Cd were inversely correlated and are simultaneously minimized in a redox potential (Eh) range of 225–275 mV in the studied soil. Ferrihydrite in root iron plaque decreased As translocation from porewater to grain, but amendments were not able to increase plaque ferrihydrite content.

Conclusion

We conclude moderate husk amendment rates (i.e., 4 years’ worth) with minimal pretreatment strongly increases rice Si content but may not be sufficient to decrease grain As in low Si and As soil.
The structure of production technologies with ratio inputs and outputs
Authors: Olesen Ole Bent , Petersen Niels Christian , Podinovski Victor V.
Published: March 2022

Applications of efficiency and productivity analysis in which some inputs and outputs are given in the form of percentages, averages and other types of ratio measures are sufficiently common in the literature. In two recent papers, the authors developed the variable and constant returns-to-scale technologies with both volume and ratio types of inputs and outputs, referred to as the R-VRS and R-CRS technologies. These technologies are generally nonconvex and have a complex structure. In this paper we explore this in detail. We show that the R-VRS technology can be stated as the union of a finite number of specially constructed standard VRS technologies. Similarly, the R-CRS technology in which all ratio inputs and outputs are of the fixed type, which are typically used to represent environmental and quality factors, can be stated as the union of a finite number of partial polyhedral cones. We show that these results have important theoretical, including conceptual, implications.
Active inference models do not contradict folk psychology
Authors: Smith Ryan , Ramstead Maxwell J. D. , Kiefer Alex
Published: March 2022

Active inference offers a unified theory of perception, learning, and decision-making at computational and neural levels of description. In this article, we address the worry that active inference may be in tension with the belief–desire–intention (BDI) model within folk psychology because it does not include terms for desires (or other conative constructs) at the mathematical level of description. To resolve this concern, we first provide a brief review of the historical progression from predictive coding to active inference, enabling us to distinguish between active inference formulations of motor control (which need not have desires under folk psychology) and active inference formulations of decision processes (which do have desires within folk psychology). We then show that, despite a superficial tension when viewed at the mathematical level of description, the active inference formalism contains terms that are readily identifiable as encoding both the objects of desire and the strength of desire at the psychological level of description. We demonstrate this with simple simulations of an active inference agent motivated to leave a dark room for different reasons. Despite their consistency, we further show how active inference may increase the granularity of folk-psychological descriptions by highlighting distinctions between drives to seek information versus reward—and how it may also offer more precise, quantitative folk-psychological predictions. Finally, we consider how the implicitly conative components of active inference may have partial analogues (i.e., “as if” desires) in other systems describable by the broader free energy principle to which it conforms.
Motor representation in acting together
Authors: Sinigaglia Corrado , Butterfill Stephen A.
Published: March 2022

People walk, build, paint and otherwise act together with a purpose in myriad ways. What is the relation between the actions people perform in acting together with a purpose and the outcome, or outcomes, to which their actions are directed? We argue that fully characterising this relation will require appeal not only to intention, knowledge and other familiar philosophical paraphernalia but also to another kind of representation involved in preparing and executing actions, namely motor representation. If we are right, motor representation plays a central role in the story of acting together.
Adults with tetralogy of Fallot show specific features of cerebral small vessel disease: the BACH San Donato study
Authors: Melazzini Luca , Savoldi Filippo , Chessa Massimo , Vitali Paolo , Zanardo Moreno , Bertoldo Enrico Giuseppe , Fiolo Valentina , Griffanti Ludovica , Carminati Mario , Frigiola Alessandro , Giamberti Alessandro , Secchi Francesco , Callus Edward , Codari Marina , Sardanelli Francesco
Published: March 2022

Life expectancy in adults with congenital heart disease (ACHD) has increased. As these patients grow older, they experience aging-related diseases more than their healthy peers. To better characterize this field, we launched the multi-disciplinary BACH (Brain Aging in Congenital Heart disease) San Donato study, that aimed at investigating signs of brain injury in ACHD. Twenty-three adults with repaired tetralogy of Fallot and 23 age- and sex-matched healthy controls were prospectively recruited and underwent brain magnetic resonance imaging. White matter hyperintensities (WMHs) were segmented using a machine-learning approach and automatically split into periventricular and deep. Cerebral microbleeds were manually counted. A subset of 14 patients were also assessed with an extensive neuropsychological battery. Age was 41.78 ± 10.33 years (mean ± standard deviation) for patients and 41.48 ± 10.28 years for controls (p = 0.921). Albeit not significantly, total brain (p = 0.282) and brain tissue volumes (p = 0.539 for cerebrospinal fluid, p = 0.661 for grey matter, p = 0.793 for white matter) were lower in ACHD, while total volume (p = 0.283) and sub-classes of WMHs (p = 0.386 for periventricular WMHs and p = 0.138 for deep WMHs) were higher in ACHD than in controls. Deep WMHs were associated with poorer performance at the frontal assessment battery (r = -0.650, p = 0.012). Also, patients had a much larger number of microbleeds than controls (median and interquartile range 5 [3–11] and 0 [0–0] respectively; p < 0.001). In this study, adults with tetralogy of Fallot showed specific signs of brain injury, with some clinical implications. Eventually, accurate characterization of brain health using neuroimaging and neuropsychological data would aid in the identification of ACHD patients at risk of cognitive deterioration.
The benefit of vaccination against COVID-19 outweighs the potential risk of myocarditis and pericarditis
Authors: Klamer T. A. , Linschoten M. , Asselbergs F. W.
Published: March 2022

Vaccines against coronavirus 2019 disease (COVID-19) have shown to be greatly effective in preventing viral spread, serious illness and death from this infectious disease and are therefore critical for the management of the COVID-19 pandemic. However, the listing of myocarditis and pericarditis as possible rare side effects of the messenger RNA (mRNA) vaccines against COVID-19 by regulatory agencies has sparked discussion on the vaccines’ safety. The most important published cohort studies to date demonstrat that myocarditis is a very rare side effect after COVID-19 mRNA vaccination, with an incidence of approximately 1–4 cases per 100,000 vaccinated persons. Young males (16–29 years) appear to be at highest risk, predominantly after receiving the second dose. The disease course is self-limiting in a vast majority of cases: 95% of patients show a rapid resolution of symptoms and normalisation of cardiac biomarkers, electro- and echocardiographic findings within days. Importantly, the available data suggest that the incidence rate of myocarditis in the context of COVID-19 is much greater than the risk of this side effect following vaccination. We conclude that the benefit of vaccination against COVID-19 outweighs the potential risk of myocarditis and pericarditis in both adolescents and adults. Prospective follow-up of patients who have developed these complications after vaccination is required to assess long-term outcomes.
Recommendations for Determining the Validity of Consumer Wearables and Smartphones for the Estimation of Energy Expenditure: Expert Statement and Checklist of the INTERLIVE Network
Authors: Argent Rob , Hetherington-Rauth Megan , Stang Julie , Tarp Jakob , Ortega Francisco B. , Molina-Garcia Pablo , Schumann Moritz , Bloch Wilhelm , Cheng Sulin , Grøntved Anders , Brønd Jan Christian , Ekelund Ulf , Sardinha Luis B. , Caulfield Brian
Published: March 2022

Background

Consumer wearables and smartphone devices commonly offer an estimate of energy expenditure (EE) to assist in the objective monitoring of physical activity to the general population. Alongside consumers, healthcare professionals and researchers are seeking to utilise these devices for the monitoring of training and improving human health. However, the methods of validation and reporting of EE estimation in these devices lacks rigour, negatively impacting on the ability to make comparisons between devices and provide transparent accuracy.

Objectives

The Towards Intelligent Health and Well-Being Network of Physical Activity Assessment (INTERLIVE) is a joint European initiative of six universities and one industrial partner. The network was founded in 2019 and strives towards developing best-practice recommendations for evaluating the validity of consumer wearables and smartphones. This expert statement presents a best-practice validation protocol for consumer wearables and smartphones in the estimation of EE.

Methods

The recommendations were developed through (1) a systematic literature review; (2) an unstructured review of the wider literature discussing the potential factors that may introduce bias during validation studies; and (3) evidence-informed expert opinions from members of the INTERLIVE network.

Results

The systematic literature review process identified 1645 potential articles, of which 62 were deemed eligible for the final dataset. Based on these studies and the wider literature search, a validation framework is proposed encompassing six key domains for validation: the target population, criterion measure, index measure, testing conditions, data processing and the statistical analysis.

Conclusions

The INTERLIVE network recommends that the proposed protocol, and checklists provided, are used to standardise the testing and reporting of the validation of any consumer wearable or smartphone device to estimate EE. This in turn will maximise the potential utility of these technologies for clinicians, researchers, consumers, and manufacturers/developers, while ensuring transparency, comparability, and replicability in validation.

Trial Registration

PROSPERO ID: CRD42021223508.
Pleuro-pulmonary ultrasound in the diagnosis and follow-up of lung infections in children with cancer: a pilot study
Authors: Meli Mariaclaudia , La Spina Milena , Lo Nigro Luca , Trobia Gian Luca , Russo Giovanna , Di Cataldo Andrea
Published: March 2022

Purpose

Febrile neutropenia and lung infections are common and potential fatal complications of pediatric cancer patients during chemotherapy. Lung ultrasound (LUS) has a good accuracy in the diagnosis of pneumonia in childhood, but there is no data concerning its use in the diagnosis and follow-up of pulmonary infection in children with cancer. The goal of this pilot study is to verify the feasibility of lung ultrasonography for the diagnosis and follow up of pneumonia in children and adolescents with cancer.

Material and methods

This is a prospective observational case–control monocentric study conducted in the Pediatric Hematology and Oncology Department of University Hospital of Catania in patients aged < 18 years with cancer. Attending Physician used ultrasonography to detect pneumonia in cancer children with fever. As control group, cancer patients with no infection suspicion were also tested. LUS results were compared to chest X-ray (CXR) and/or chest CT scan, when these imaging techniques were performed, according to clinical indication.

Results

Thirty-eight patients were studied. All underwent LUS, 16 underwent CXR, 3 chest CT. Statistical analysis showed LUS specificity of 93% (95% CI 84–100%), and sensitivity of 100%; CXR, instead, showed a specificity of 83% (95% CI 62–100%) and a sensitivity of 50% (95% CI 1–99%).

Conclusion

This study shows for the first time that LUS allows physicians to diagnose pneumonia in children and young adults with cancer, with high specificity and sensitivity.
T4F3: temperature for fused filament fabrication
Authors: Zhang Jie , Van Hooreweder Brecht , Ferraris Eleonora
Published: March 2022

Temperature fields and their variations in printed parts are the basis for understanding the physical process of fused filament fabrication (FFF). However, reliable temperature data are still rather limited to date. This article presents a three-dimensional transient-state model to simulate the temporal and spatial temperature variations in FFF printed parts. Model variables range from geometry dimensions and (dynamic) material properties to process parameters, covering all important physical phenomena, including conduction anisotropy and radiant heat transfer. The validation of the model is performed against six sets of experimental temperature data obtained with different geometries, machines, materials, processes, temperature measuring methods, etc. Insights in the thermal process are also reported. For example, the heat penetration depth in printing with poly(lactic acid) is limited to 3 mm, and the Biot number intimately characterises the reheating peaks in temporal profiles. This model shows the potential to become a standardised tool to study the thermal characteristics of FFF printed parts. It is made openly available on website https://iiw.kuleuven.be/onderzoek/aml/technologyoffer.

Graphic abstract
From Business Ethics to Business Education: Peter-Hans Kolvenbach’s Contribution
Authors: Lozano Josep M.
Published: March 2022

This essay begins with a look at the contribution made by Business Ethics and by Corporate Social Responsibility (CSR) to Business Education, and how the first two have moved to the last over time. Yet their contributions also reveal limitations that need to be taken into account in the debate on the training provided by Business Schools. This debate cannot be confined to speaking of disciplines and their cross-cutting natures but rather needs to focus directly on the kind of personal profile fostered among business students. In the context of this debate on the future of Business Schools, the essay stresses the relevance of Peter-Hans Kolvenbach’s framework. He proposed an educational ideal based upon educating competent, conscious, compassionate, and committed people. This ideal took shape in the form of an educational paradigm integrating four dimensions: professional (utilitas), ethical-social (iustitia), humanist (humanitas) and spiritual (fides). The essay not only shows how each of these dimensions is in tune with some of the present proposals for renewing Business Education but also how Kolvenbach's more holistic approach can help to further integrate and spotlight the blind spots of each of them.
Parteiungen im Totalitarismus: Christenheiten und Ideologien im „Dritten Reich“
Authors: Auffarth Christoph
Published: March 2022

Totalitären Regimen wird nachgesagt, dass eine einzige Partei die Herrschaft an sich reißt und nun als einzige Partei alle anderen Gruppen und Institutionen unterwandert. Die Ideologie der Partei wird Staatsziel und verdrängt alle eigenständigen Organisationen und Weltbilder, besonders auch Religion und religiöse Institutionen. Dieser Artikel zeigt auf, dass sich ein solches Konzept des Totalitarismus (und davon abgeleitet der „Politischen Religion“) nicht auf den Nationalsozialismus in Deutschland anwenden lässt, indem verschiedene Parteiungen bei führenden Nationalsozialisten unterschieden werden.

An zwei Prozessen in der konsolidierten Herrschaft des Nationalsozialismus des Jahres 1937 wird deutlich, dass sowohl in den Kirchen als auch in der NSDAP Parteiungen konkurrierten, die ein ganz unterschiedliches Verhältnis zur herrschenden Ideologie bzw. zur Religion hatten: Das Schulgesetz forderte explizit gläubige Lehrer und behielt den Religionsunterricht bei, gegen den Vorstoß einer Parteiung innerhalb der Partei, den Nationalsozialismus als einziges „Bekenntnis“ zu erklären. Die päpstliche Enzyklika des gleichen Jahres richtet sich gegen eine Parteiung innerhalb des NS, die sie als „neuheidnisch“ im Gegensatz zum katholischen Christentum sieht, nicht aber gegen den Nationalsozialismus insgesamt.
From society to cells and back again: new opportunities for discovery at the biosocial interface
Authors: McDade Thomas W. , Harris Kathleen Mullan
Published: March 2022

A new generation of community- and population-based research is combining measures of social context, experience, and behavior with direct measures of physiology, gene sequence and function, and health. Studies drawing on models and methods from the social and biological sciences have the potential to illuminate the multilevel mechanisms through which experience becomes biology, and to move past decontextualized and reductionistic approaches to human development, behavior, and health. In this perspective we highlight challenges and opportunities at the biosocial interface, and briefly discuss COVID-19 as a case study demonstrating the importance of linking across levels of analysis.
On Blow-Up of Solutions to a Weakly Dissipative Two-Component Camassa–Holm System
Authors: Han Xuanxuan , Wang Tingting , Lu Yibin
Published: March 2022

In this paper, we consider a weakly dissipative two-component Camassa–Holm system. We demonstrate a simple sufficient condition on initial date to guarantee blow-up of solutions in finite time and guarantee the solutions exist globally in time. The results improve considerable the previous results.
Digital self-harm: an examination of the current literature with recommendations for future research
Authors: Soengkoeng Rinjani , Moustafa Ahmed A.
Published: March 2022

Digital self-harm (DSH) is a relatively new form of virtual self-harm that occurs mostly in young people, and has been defined as both the act of cyberbullying oneself (Fictitious Online Victimisation; FOV), and engaging with online spaces in a way that is detrimental to one’s psychological wellbeing. In our overview of DSH we aim to provide an understanding of this little-known subject by offering a clarification of extant terms, summarising current findings, and presenting recommendations for future research. The prevalence of DSH in teenagers appears to approach that of physical self-harm, and the behaviour is more common amongst young people who are ostracised and/or victimised by their peers. The motivations for DSH are heterogeneous, but there is evidence that, like physical self-harm, it may be a means of affect regulation. However, more research is required to untangle the different forms of DSH and gain a sense of their occurrence in different populations and age groups, their varying causes, their relationship to physical self-harm, and the means by which they should be measured.
Integrating the Anthropocene in Legal Education: Considerations for Asia
Authors: Liljeblad Jonathan
Published: March 2022

The scale and urgency of the consequences of the Anthropocene for human civilization call for comprehensive responses from human societies. As leaders in law, law schools have a role in helping their respective societies respond to the impacts of the Anthropocene. The present analysis discusses potential approaches to help law schools in Asia integrate the Anthropocene into their legal education curricula. Drawing upon existing legal education literature regarding issues of content, teaching tools, curriculum placement, and subject status as a law topic, the analysis explores the potential issues facing law schools in the adoption of the Anthropocene as a component of learning. The analysis then addresses the particular contextual sociocultural, economic, and political circumstances likely to challenge the integration of the Anthropocene into Asian law schools. The conclusion finishes with directions for future research.
Under the Influence of Commercial Values: Neoliberalized Business-Consumer Relations in the Swedish Certification Market, 1988–2018
Authors: Arnberg Klara , Gustavsson Martin , Tamm Hallström Kristina
Published: March 2022

Since the 1990s, a new model for market control organized through tripartite standards regimes (TSR), has expanded globally and affected most market exchanges through standard-setting, accreditation, and certification. This article investigates business-consumer relations under this regime, with a specific focus on the functions of accreditation and certification. In our case study of Sweden, a new picture of consumer protection under late capitalism evolves. Seeing it as a form of neoliberalization, the article uncovers a transition between two regimes of control; from one built on a potential conflict between consumer and business interests, to one based on the assumption that business interests are beneficial for all parties. Although business interest was formulated as pleasing the consumer—or the “customer”—by both certification firms and the Swedish Accreditation Authority, in practice consumer interest as something worth protecting was made abstract in the era of the TSR.
Jet impingement on the underside of a superhydrophobic surface
Authors: de la Cruz Roberto M. , Mäkiharju Simo A.
Published: March 2022

Water patch topology and momentum loss resulting from a jet impacting on the underside of a flat plate with varied hydrophobicity were studied. The jet's Reynolds and Froude numbers ranged from 3700 to 31 000, and from 1 to 23, respectively. Hence effects of gravity were expected to be non-negligible, and data suggest that this is the case for hydrophobic surfaces. The interplay of gravity, surface tension, inertia and viscosity resulted in two distinct behaviours. On hydrophilic surfaces, water spread uniformly. Friction reduced momentum, and led to accumulation at the edges of the patch until gravity overcame surface tension and produced droplets. On hydrophobic surfaces, two rims formed, enclosing a thin laminar film. The patch shape was mostly determined by the balance of kinetic and surface energy. Dewetting occurred in most cases when the two rims merged, but for a narrow parameter, range water detached soon after impact and formed a type of skewed water bell. The transition in detachment topology was predicted reasonably by a simple model considering whether an attached or detached rim minimizes energy. Due to promotion of dewetting by gravity, the water patch area decreased compared to that reported in previous studies, which considered jet impingement on vertical surfaces and tops of horizontal surfaces. Owing to the application that motivated this study, the streamwise force on the plate was also measured. On hydrophobic surfaces the reduction in force correlated with the reduction in water patch area. Water patch area and momentum loss were both found to scale best with the contact-angle-modified Weber number.
Quantitative effects of environmental variation on stomatal anatomy and gas exchange in a grass model
Authors: Nunes Tiago D. G. , Slawinska Magdalena W. , Lindner Heike , Raissig Michael T.
Published: March 2022

Stomata are cellular pores on the leaf epidermis that allow plants to regulate carbon assimilation and water loss. Stomata integrate environmental signals to regulate pore apertures and adapt gas exchange to fluctuating conditions. Here, we quantified intraspecific plasticity of stomatal gas exchange and anatomy in response to seasonal variation in Brachypodium distachyon. Over the course of 2 years, we (a) used infrared gas analysis to assess light response kinetics of 120 Bd21-3 wild-type individuals in an environmentally fluctuating greenhouse and (b) microscopically determined the seasonal variability of stomatal anatomy in a subset of these plants. We observed systemic environmental effects on gas exchange measurements and remarkable intraspecific plasticity of stomatal anatomical traits. To reliably link anatomical variation to gas exchange, we adjusted anatomical gsmax calculations for grass stomatal morphology. We propose that systemic effects and variability in stomatal anatomy should be accounted for in long-term gas exchange studies.
Staying Egalitarian and the Origins of Agriculture in the Middle East
Authors: Hodder Ian
Published: March 2022

This article uses results from the recent excavations at Çatalhöyük in Turkey to propose that continuous tensions between egalitarian and hierarchical impulses were dealt with in two principal ways during the Neolithic of the Middle East. A tendency towards overall balance and community (termed molar) is seen as in tension with more particulate and molecular tendencies, with both being brought into play in order to combat inequalities. It is also suggested that tendencies towards more molecular systems increased over time, at different rates and in different ways in different places, partly as a response to constraints associated with more molar articulations. Finally, it is proposed that a shift to molecular autonomy was associated with agricultural intensification. Staying egalitarian can be seen as an active process that contributed to the Neolithic transformations.
The processing of bilingual (switched) compound verbs: Competition of words from different categories for lexical selection
Authors: Purmohammad Mehdi , Vorwerg Constanze , Abutalebi Jubin
Published: March 2022

This paper investigates the production of Persian–English bilingual compound verbs (BCVs) of the type [VERB+VERB]. In this type of code-switched structure, a lexical verb from the donor language English is combined with a light verb from the native language Persian. We tested the hypothesis that in Persian–English BCVs English verbs occupy the nominal slots of monolingual Persian complex predicates of the type [NOMINAL+VERB]. Two methodologies were used. A conversational-corpus analysis confirmed our predictions that Persian–English BCVs have translation-equivalent Persian compound verbs, that the English verbs denote the same action as the nominal constituents of those monolingual constructions, and that the support verbs tend to correspond in both types of compound verbs. A bilingual picture-word interference experiment provided evidence suggesting that English verbs interfere with the production of the nominal constituents of complex Persian verbs in Persian-bilingual speakers. We conclude that words from different word categories can compete for lexical access.
Hydrological Intensification Will Increase the Complexity of Water Resource Management
Authors: Ficklin Darren L. , Null Sarah E. , Abatzoglou John T. , Novick Kimberly A. , Myers Daniel T.
Published: March 2022

Global warming intensifies the hydrological cycle by altering the rate of water fluxes to and from the terrestrial surface, resulting in an increase in extreme precipitation events and longer dry spells. Prior hydrological intensification work has largely focused on precipitation without joint consideration of evaporative demand changes and how plants respond to these changes. Informed by state‐of‐the‐art climate models, we examine projected changes in hydrological intensification and its role in complicating water resources management using a framework that accounts for precipitation surplus and evaporative demand. Using a metric that combines the difference between daily precipitation and daily evaporative demand (surplus events) and consecutive days when evaporative demand exceeds precipitation (deficit time), we show that, globally, surplus events will become larger (+11.5% and +18.5% for moderate and high emission scenarios, respectively) and the duration between them longer (+5.1%; +9.6%) by the end of the century, with the largest changes in the northern latitudes. The intra‐annual occurrence of these extremes will stress existing water management infrastructure in major river basins, where over one third of years during 2070–2100 under a moderate emissions scenario will be hydrologically intense (large intra‐annual increases in surplus intensity and deficit time), tripling that of the historical baseline. Larger increases in hydrologically intense years are found in basins with large reservoir capacity (e.g., Amazon, Congo, and Danube River Basins), which have significant populations, irrigate considerable farmland, and support threatened and endangered aquatic species. Incorporating flexibility into water resource infrastructure and management will be paramount with continued hydrological intensification.
Boulder Dislodgement During Coastal Storms and Tsunamis: Insights From a New Ensemble Model
Authors: Weiss Robert , Irish Jennifer , Goodman Tchernov Beverly
Published: March 2022

Boulders are excellent candidate deposits to study coastal inundation events by storms and tsunamis due to their significant preservation potential. However, it is difficult to infer how and what forcing dislodged the boulder. We present a new model that enables ensemble and Monte‐Carlo‐type simulations to study the sensitivity of boulder, the fluid flow, and environmental parameters. Our examples show that boulder transport is complex and nonlinear, and to acknowledge the uncertainties of the boulder's preexisting transport conditions, a range of velocities and environmental parameters should be used to quantify the flow that caused boulder dislodgement.
Topographic Stabilization of Ocean Rings
Authors: Gulliver L. T. , Radko T.
Published: March 2022

Coherent large‐scale vortices in the open ocean can retain their structure and properties for periods as long as several years. However, the patterns of potential vorticity in such vortices suggest that they are baroclinically unstable and therefore should rapidly disintegrate. This study proposes a plausible explanation of the longevity of large‐scale ocean rings based on bottom roughness, which restricts flow in the lower layer and thereby stabilizes the eddy. We perform a series of simulations in which topography is represented by the observationally derived Goff‐Jordan spectrum. We demonstrate that topography stabilizes coherent vortices and dramatically prolongs their lifespan. In contrast, the same vortices in the flat‐bottom model exhibit strong instability and fragmentation on the timescale of weeks. A critical depth variance exists that allows vortices to remain stable and circularly symmetric indefinitely. Our investigation underscores the essential role played by topography in the dynamics of large‐ and meso‐scale flows.
Rapid Watershed Delineation Using an Automatic Outlet Relocation Algorithm
Authors: Xie Jiaxin , Liu Xiaomang , Bai Peng , Liu Changming
Published: March 2022

Delineating the boundaries of numerous watersheds is essential for hydrological analysis in the big data era. Various techniques, such as ArcGIS, have been developed to delineate watershed boundaries. However, existing techniques suffer from two laborious manual processes: (a) Determine flow accumulation thresholds through trial and error to derive digital stream networks; (b) Manually relocate watershed outlets to the correct stream networks. Here, we proposed an automatic outlet relocation (AOR) algorithm for rapid watershed delineation without manual processing. The AOR algorithm relocates outlets to correct stream networks by analyzing flow accumulation gradients along the flow directions. An experiment using the AOR algorithm in 1,398 watersheds across the contiguous United States showed that 94.1% of the watersheds were correctly delineated, compared to 81.3% accuracy of the ArcGIS relocation algorithm (Snap Pour Point). In addition, the AOR algorithm took 58 min to delineate the 1,398 watersheds on a 90 m‐resolution flow direction, while the ArcGIS algorithm required 586 min to perform the same task. Thus, the AOR algorithm offers an opportunity to automatically delineate a large number of watersheds for hydrological simulations in the big data era. Software with a graphical user interface for the AOR algorithm is freely available on GitHub (https://github.com/xiejx5/watershed_delineation).
Untargeted metabolic analysis in dried blood spots reveals metabolic signature in 22q11.2 deletion syndrome
Authors: Korteling Dorinde , Boks Marco P. , Fiksinski Ania M. , van Hoek Ilja N. , Vorstman Jacob A. S. , Verhoeven-Duif Nanda M. , Jans Judith J. M. , Zinkstok Janneke R.
Published: March 2022

The 22q11.2 deletion syndrome (22q11.2DS) is characterized by a well-defined microdeletion and is associated with increased risk of neurodevelopmental phenotypes including autism spectrum disorders (ASD) and intellectual impairment. The typically deleted region in 22q11.2DS contains multiple genes with the potential of altering metabolism. Deficits in metabolic processes during early brain development may help explain the increased prevalence of neurodevelopmental phenotypes seen in 22q11.2DS. However, relatively little is known about the metabolic impact of the 22q11.2 deletion, while such insight may lead to increased understanding of the etiology. We performed untargeted metabolic analysis in a large sample of dried blood spots derived from 49 22q11.2DS patients and 87 controls, to identify a metabolic signature for 22q11.2DS. We also examined trait-specific metabolomic patterns within 22q11.2DS patients, focusing on intelligence (intelligence quotient, IQ) and ASD. We used the Boruta algorithm to select metabolites distinguishing patients from controls, patients with ASD from patients without, and patients with an IQ score in the lowest range from patients with an IQ score in the highest range. The relevance of the selected metabolites was visualized with principal component score plots, after which random forest analysis and logistic regression were used to measure predictive performance of the selected metabolites. Analysis yielded a distinct metabolic signature for 22q11.2DS as compared to controls, and trait-specific (IQ and ASD) metabolomic patterns within 22q11.2DS patients. The metabolic characteristics of 22q11.2DS provide insights in biological mechanisms underlying the neurodevelopmental phenotype and may ultimately aid in identifying novel therapeutic targets for patients with developmental disorders.
Identification of a novel MAGT1 mutation supports a diagnosis of XMEN disease
Authors: Watson Christopher M. , Nadat Fatima , Ahmed Sammiya , Crinnion Laura A. , O’Riordan Sean , Carter Clive , Savic Sinisa
Published: March 2022

XMEN (X-linked immunodeficiency with magnesium defect) is caused by loss-of-function mutations in MAGT1 which is encoded on the X chromosome. The disorder is characterised by CD4 lymphopenia, severe chronic viral infections and defective T-lymphocyte activation. XMEN patients are susceptible to Epstein-Barr virus infections and persistently low levels of intracellular Mg2+. Here we describe a patient that presented with multiple recurrent infections and a subsequent diffuse B-cell lymphoma. Molecular genetic analysis by exome sequencing identified a novel hemizygous MAGT1 nonsense mutation c.1005T>A (NM_032121.5) p.(Cys335*), confirming a diagnosis of XMEN deficiency. Follow-up immunophenotyping was performed by antibody staining and flow cytometry; proliferation was determined by 3H-thymidine uptake after activation by PHA and anti-CD3. Cytotoxic natural killer cell activity was assessed with K562 target cells using the NKTESTTM assay. While lymphocyte populations were superficially intact, B cells were largely naive with a reduced memory cell compartment. Translated NKG2D was absent on both NK and T cells in the proband, and normally expressed in the carrier mother. In vitro NK cell activity was intact in both the proband and his mother. This report adds to the growing number of identified XMEN cases, raising awareness of a, still rare, X-linked immunodeficiency.
Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections
Authors: Chung Hattie , Merakou Christina , Schaefers Matthew M. , Flett Kelly B. , Martini Sarah , Lu Roger , Blumenthal Jennifer A. , Webster Shanice S. , Cross Ashley R. , Al Ahmar Roy , Halpin Erin , Anderson Michelle , Moore Nicholas S. , Snesrud Eric C. , Yu Hongwei D. , Goldberg Joanna B. , O’Toole George A. , McGann Patrick , Stam Jason A. , Hinkle Mary , McAdam Alexander J. , Kishony Roy , Priebe Gregory P.
Published: March 2022

Acute bacterial infections are often treated empirically, with the choice of antibiotic therapy updated during treatment. The effects of such rapid antibiotic switching on the evolution of antibiotic resistance in individual patients are poorly understood. Here we find that low-frequency antibiotic resistance mutations emerge, contract, and even go to extinction within days of changes in therapy. We analyzed Pseudomonas aeruginosa populations in sputum samples collected serially from 7 mechanically ventilated patients at the onset of respiratory infection. Combining short- and long-read sequencing and resistance phenotyping of 420 isolates revealed that while new infections are near-clonal, reflecting a recent colonization bottleneck, resistance mutations could emerge at low frequencies within days of therapy. We then measured the in vivo frequencies of select resistance mutations in intact sputum samples with resistance-targeted deep amplicon sequencing (RETRA-Seq), which revealed that rare resistance mutations not detected by clinically used culture-based methods can increase by nearly 40-fold over 5–12 days in response to antibiotic changes. Conversely, mutations conferring resistance to antibiotics not administered diminish and even go to extinction. Our results underscore how therapy choice shapes the dynamics of low-frequency resistance mutations at short time scales, and the findings provide a possibility for driving resistance mutations to extinction during early stages of infection by designing patient-specific antibiotic cycling strategies informed by deep genomic surveillance.
Co-translational assembly orchestrates competing biogenesis pathways
Authors: Seidel Maximilian , Becker Anja , Pereira Filipa , Landry Jonathan J. M. , de Azevedo Nayara Trevisan Doimo , Fusco Claudia M. , Kaindl Eva , Romanov Natalie , Baumbach Janina , Langer Julian D. , Schuman Erin M. , Patil Kiran Raosaheb , Hummer Gerhard , Benes Vladimir , Beck Martin
Published: March 2022

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.
Restoring and attributing ancient texts using deep neural networks
Authors: Assael Yannis , Sommerschield Thea , Shillingford Brendan , Bordbar Mahyar , Pavlopoulos John , Chatzipanagiotou Marita , Androutsopoulos Ion , Prag Jonathan , de Freitas Nando
Published: March 2022

Ancient history relies on disciplines such as epigraphy—the study of inscribed texts known as inscriptions—for evidence of the thought, language, society and history of past civilizations1. However, over the centuries, many inscriptions have been damaged to the point of illegibility, transported far from their original location and their date of writing is steeped in uncertainty. Here we present Ithaca, a deep neural network for the textual restoration, geographical attribution and chronological attribution of ancient Greek inscriptions. Ithaca is designed to assist and expand the historian’s workflow. The architecture of Ithaca focuses on collaboration, decision support and interpretability. While Ithaca alone achieves 62% accuracy when restoring damaged texts, the use of Ithaca by historians improved their accuracy from 25% to 72%, confirming the synergistic effect of this research tool. Ithaca can attribute inscriptions to their original location with an accuracy of 71% and can date them to less than 30 years of their ground-truth ranges, redating key texts of Classical Athens and contributing to topical debates in ancient history. This research shows how models such as Ithaca can unlock the cooperative potential between artificial intelligence and historians, transformationally impacting the way that we study and write about one of the most important periods in human history.
Integrated electronic skin (e-skin) for harvesting of TENG energy through push–pull ionic electrets and ion-ion hopping mechanism
Authors: Cheedarala Ravi Kumar , Song Jung Il
Published: March 2022

The development of highly durable, stretchable, and steady triboelectric nanogenerators (TENGs) is highly desirable to satisfy the tight requirement of energy demand. Here, we presented a novel integrated polymeric membrane that is designed by PEDOT: PSSa-naphthalene sulfonated polyimide (PPNSP)-EMI.BF4 Electronic skin (e-skin) for potential TENG applications. The proposed TENG e-skin is fabricated by an interconnected architecture with push–pull ionic electrets that can threshold the transfer of charges through an ion-hopping mechanism for the generation of a higher output voltage (Voc) and currents (Jsc) against an electronegative PTFE film. PPNSP was synthesized from the condensation of naphthalene-tetracarboxylic dianhydride, 2,2′-benzidine sulfonic acid, and 4,4′diaminodiphenyl ether through an addition copolymerization protocol, and PEDOT: PSSa was subsequently deposited using the dip-coating method. Porous networked PPNSP e-skin with continuous ion transport nano-channels is synthesized by introducing simple and strong molecular push–pull interactions via intrinsic ions. In addition, EMI.BF4 ionic liquid (IL) is doped inside the PPNSP skin to interexchange ions to enhance the potential window for higher output Voc and Iscs. In this article, we investigated the push–pull dynamic interactions between PPNSP-EMI.BF4 e-skin and PTFE and tolerable output performance. The novel PPNSP- EMI.BF4 e-skin TENG produced upto 49.1 V and 1.03 µA at 1 Hz, 74 V and 1.45 µA at 2 Hz, 122.3 V and 2.21 µA at 3 Hz and 171 V and 3.6 µA at 4 Hz, and 195 V and 4.43 µA at 5 Hz, respectively. The proposed novel TENG device was shown to be highly flexible, highly durable, commercially viable, and a prospective candidate to produce higher electrical charge outputs at various applied frequencies.
Normalization of clonal diversity in gene therapy studies using shape constrained splines
Authors: Del Core L. , Cesana D. , Gallina P. , Secanechia Y. N. Serina , Rudilosso L. , Montini E. , Wit E. C. , Calabria A. , Grzegorczyk M. A.
Published: March 2022

Viral vectors are used to insert genetic material into semirandom genomic positions of hematopoietic stem cells which, after reinfusion into patients, regenerate the entire hematopoietic system. Hematopoietic cells originating from genetically modified stem cells will harbor insertions in specific genomic positions called integration sites, which represent unique genetic marks of clonal identity. Therefore, the analysis of vector integration sites present in the genomic DNA of circulating cells allows to determine the number of clones in the blood ecosystem. Shannon diversity index is adopted to evaluate the heterogeneity of the transduced population of gene corrected cells. However, this measure can be affected by several technical variables such as the DNA amount used and the sequencing depth of the library analyzed and therefore the comparison across samples may be affected by these confounding factors. We developed an advanced spline-regression approach that leverages on confounding effects to provide a normalized entropy index. Our proposed method was first validated and compared with two state of the art approaches in a specifically designed in vitro assay. Subsequently our approach allowed to observe the expected impact of vector genotoxicity on entropy level decay in an in vivo model of hematopoietic stem cell gene therapy based on tumor prone mice.
Impact of urban structure on infectious disease spreading
Authors: Aguilar Javier , Bassolas Aleix , Ghoshal Gourab , Hazarie Surendra , Kirkley Alec , Mazzoli Mattia , Meloni Sandro , Mimar Sayat , Nicosia Vincenzo , Ramasco José J. , Sadilek Adam
Published: March 2022

The ongoing SARS-CoV-2 pandemic has been holding the world hostage for several years now. Mobility is key to viral spreading and its restriction is the main non-pharmaceutical interventions to fight the virus expansion. Previous works have shown a connection between the structural organization of cities and the movement patterns of their residents. This puts urban centers in the focus of epidemic surveillance and interventions. Here we show that the organization of urban flows has a tremendous impact on disease spreading and on the amenability of different mitigation strategies. By studying anonymous and aggregated intra-urban flows in a variety of cities in the United States and other countries, and a combination of empirical analysis and analytical methods, we demonstrate that the response of cities to epidemic spreading can be roughly classified in two major types according to the overall organization of those flows. Hierarchical cities, where flows are concentrated primarily between mobility hotspots, are particularly vulnerable to the rapid spread of epidemics. Nevertheless, mobility restrictions in such types of cities are very effective in mitigating the spread of a virus. Conversely, in sprawled cities which present many centers of activity, the spread of an epidemic is much slower, but the response to mobility restrictions is much weaker and less effective. Investing resources on early monitoring and prompt ad-hoc interventions in more vulnerable cities may prove helpful in containing and reducing the impact of future pandemics.