bluuebunny/crossref_metadata_2025 huggingface dataset:
‘My eyes are my ears’: Deaf people appropriating AIDS education messages in Uganda
Authors: Murangira Ambrose
Published: September 2022

The Ugandan effort to provide AIDS education for the entire population raised questions about how to reach people with disabilities. Based on semi-structured interviews and participant observation with Deaf people in Kampala, this study examined how communication technologies are used in general by Deaf people, and what is specific to communicating about HIV and AIDS. It found that communication technologies, whose purpose is to mediate information, are themselves mediated by social relations. Two contrasts are apparent: between types of technology and types of relationships. The ‘old’ technologies – broadcast and print – often depend on mediation by hearing people, who create the messages and explain audio information to Deaf associates. The ‘new’ digital technologies in the form of smartphones allow Deaf people to communicate directly with one another and facilitate new forms of Deaf sociality, both online and in person. They convey information about AIDS prevention directly, obviating the need to discuss sex with family members of the parental generation, which is culturally sensitive. Smartphones are highly appreciated by Deaf people but the costs of obtaining and using them exclude many.
First population estimates of two Critically Endangered frogs from an isolated forest plateau in Madagascar
Authors: Barata Izabela M. , Razafindraibe Jary H. , Ravelojaona Rojo Nadrianina , Ralovarisoa Etienne , Mullin Katherine E. , Hudson Michael A. , Dawson Jeff
Published: September 2022

In the largely deforested areas of Madagascar, small forest fragments remain as last refuges for amphibian diversity. Isolated populations of the Critically EndangeredAnodonthyla vallaniandAnilany helenaepersist in the fragmented forest of Ambohitantely but little information is available to inform their management and any conservation interventions. We generated estimates of population size and occupancy for both species in the largest fragment of Ambohitantely Special Reserve using acoustic survey data collected from 84 sites along 12 transects in December 2018. We used a single-season occupancy model to estimate detection and occupancy and a Royal–Nichols model to estimate abundance and population size.Anilany helenaeandA. vallanihad high occupancy rates (80 and 93%, respectively) whereas their detection rates differed (34 and 55%, respectively). Abundance and occupancy were best explained by vegetation structure whereas detection was influenced by time of survey and rainfall. For our sampled sites the estimated population sizes of males were 855 forA. vallani, with an estimated density of 52 individuals/ha, and 388 forA. helenae, with an estimated population density of 23 individuals/ha. Given their relatively low densities, small population sizes and restricted ranges, any further habitat loss could have drastic consequences for these populations. Our results provide guidance for future species-focused studies, and can inform conservation management at the local scale. Our work will help to improve species monitoring in Madagascar and elsewhere, especially for range-restricted non-charismatic amphibians.
Gender differences in psychosocial function and self-reported health status in late-diagnosed autistic adults: results from the FACE-ASD national cohort
Authors: Dubreucq Julien , Coutelle Romain , Lajnef Mohamed , Godin Ophélia , Amestoy Anouck , Atzori Paola , Baleyte Jean-Marc , Bonnot Olivier , Bouvard Manuel , Coulon Nathalie , Da Fonseca David , Demily Caroline , Delorme Richard , Fabrowski Marine , Givaudan Marion , Gollier-Briant Fanny , Guenolé Fabian , Humeau Elise , Leignier Sylvain , Lejuste Florian , Levy Charlotte , Rabot Juliette , Schröder Carmen M. , Valette Marie ,   the FACE-ASD (FondaMental Advanced Centers of Expertise for Autism Spectrum Disorder) Groups, Leboyer Marion , Speranza Mario
Published: September 2022

Background

While adult outcome in autism spectrum disorder (ASD) is generally measured using socially valued roles, it could also be understood in terms of aspects related to health status – an approach that could inform on potential gender differences.

Methods

We investigated gender differences in two aspects of outcome related to health-status, i.e. general functioning and self-perceived health status, and co-occurring health conditions in a large multi-center sample of autistic adults. Three hundred and eighty-three participants were consecutively recruited from the FondaMental Advanced Centers of Expertise for ASD cohort (a French network of seven expert centers) between 2013 and 2020. Evaluation included a medical interview, standardized scales for autism diagnosis, clinical and functional outcomes, self-perceived health status and verbal ability. Psychosocial function was measured using the Global Assessment of Functioning scale.

Results

While autistic women in this study were more likely than men to have socially valued roles, female gender was associated with poorer physical and mental health (e.g. a 7-fold risk for having three or more co-occurring physical health conditions) and a poorer self-perceived health status. Psychosocial function was negatively associated with depression and impairment in social communication. Half of the sample had multiple co-occurring health conditions but more than 70% reported that their visit at the Expert Center was their first contact with mental health services.

Conclusions

To improve objective and subjective aspects of health outcome, gender differences and a wide range of co-occurring health conditions should be taken into account when designing healthcare provision for autistic adults.
Internet use and psychological wellbeing among older adults in England: a difference-in-differences analysis over the COVID-19 pandemic
Authors: Kung Claryn S. J. , Steptoe Andrew
Published: September 2022

Background

Longitudinal evidence on how Internet use affects the psychological wellbeing of older adults has been mixed. As policymakers invest in efforts to reduce the digital divide, it is important to have robust evidence on whether encouraging Internet use among older adults is beneficial, or potentially detrimental, to their wellbeing.

Methods

We observe depressive symptoms and loneliness of adults aged 50 + in the nationally representative English Longitudinal Study of Ageing, from before (2018/19) to during the coronavirus disease 2019 (COVID-19) pandemic (June/July and November/December 2020). Our quasi-experimental difference-in-differences strategy compares within-individual wellbeing changes between older adults who desired to use the Internet more but experienced barriers including lack of skills, access, and equipment, with regular Internet users who did not desire to use the Internet more. To reduce selection bias, we match both groups on demographic and socioeconomic characteristics that are predictive of Internet use. We assume that in the absence of COVID-19 – a period of increased reliance on the Internet – the wellbeing trajectories of both groups would have followed a common trend.

Results

Compared with matched controls (N= 2983), participants reporting barriers to Internet use (N= 802) experienced a greater increase in the likelihood of depressive symptoms from before to during the pandemic, but not worse loneliness levels. This effect was stronger for women, those aged above 65 years, and those from lower-income households.

Conclusions

Besides enabling access to digital services, efforts to ensure older adults continue to be engaged members of an increasingly digital society could deliver returns in terms of a buffer against psychological distress.
WHO ARE WE TEACHING AND WHY ARE WE TEACHING THEM? THOUGHTS ON MUSICAL DIVERSITY IN UNIVERSITY COMPOSITION TEACHING
Authors: Godfrey John
Published: September 2022

Musical composition has traditionally been taught with the assumption that students share musical backgrounds and have similar aims. In today's highly diverse musical world, however, composition students are exposed to a multiplicity of musical languages. They develop their personal creative styles from an internal conceptual ‘melting pot’ and must also develop compositional methodologies for a potentially large array of disparate usages. This article argues that the teaching of composition should recognise both the rich global diversity of musics and the plethora of uses to which compositional techniques might be applied, and that such teaching might most productively be focused on imparting a broad selection of technical concepts from many musics, coupled with an interrogation of the underlying purposes of techniques taught. All musics must be treated as equally worthy of study and students’ embodied experiences respected. Curricula need to be designed with such a catholic view in mind, encouraging students to embrace the growing profusion of genres, techniques and resources available and develop a flexible, broadly informed and resourceful outlook.
Against free energy, for direct perception
Authors: Stoffregen Thomas A. , Heath Robert
Published: September 2022

We question the free energy principle (FEP) as it is used in contemporary physics. If the FEP is incorrect in physics, then it cannot ground the authors' arguments. We also question the assumption that perception requires inference. We argue that perception (including perception of social affordances) can be direct, in which case inference is not required.
What realism about agents requires
Authors: Sprevak Mark
Published: September 2022

Bruineberg et al. argue that the formal notion of a Markov blanket fails to provide a single principled boundary between an agent and its environment. I argue that one should not expect a general theory of agenthood to provide a single boundary; and the reliance on auxiliary assumptions is neither arbitrary nor reason to suspect instrumentalism.
What's special about space?
Authors: Parr Thomas
Published: September 2022

This commentary suggests that, although Markov blankets may have different interpretations in different systems, these distinctions rest not upon the type of blanket, but upon the model that determines the blanket. As an example, the conditions for a model in which the Markov blanket may be interpretable as a physical (spatial) boundary are considered.
The emperor has no blanket!
Authors: Raja Vicente , Baggs Edward , Chemero Anthony , Anderson Michael L.
Published: September 2022

While we applaud Bruineberg et al.'s analysis of the differences between Markov blankets and Friston blankets, we think it is not carried out to its ultimate consequences. There are reasons to think that, once Friston blankets are accepted as a theoretical construct, they do not do the work proponents of free energy principle (FEP) attribute to them. The emperor is indeed naked.
Does the metaphysical dog wag its formal tail? The free-energy principle and philosophical debates about life, mind, and matter
Authors: Wiese Wanja
Published: September 2022

According to Bruineberg and colleagues, philosophical arguments on life, mind, and matter that are based on the free-energy principle (FEP) (1) essentially draw on the Markov blanket construct and (2) tend to assume that strong metaphysical claims can be justified on the basis of metaphysically innocuous formal assumptions provided by FEP. I argue against both (1) and (2).
A continuity of Markov blanket interpretations under the free-energy principle
Authors: Seth Anil , Korbak Tomasz , Tschantz Alexander
Published: September 2022

Bruineberg and colleagues helpfully distinguish between instrumental and ontological interpretations of Markov blankets, exposing the dangers of using the former to make claims about the latter. However, proposing a sharp distinction neglects the value of recognising a continuum spanning from instrumental to ontological. This value extends to the related distinction between “being” and “having” a model.
RESOURCE ENDOWMENTS, AGENCY PROBLEMS, AND MONETARY OUTCOMES IN TWO COLONIAL AMERICAN MINTS, 1600-1700
Authors: Knodell Jane E. , Vizcarra Catalina M.
Published: September 2022

This paper examines the role that resource endowments played in the performance of two New World coinages. Massachusetts Bay and the Viceroyalty of Peru provide a useful study in contrasts, having markedly different institutions and resource endowments. Both colonies originally emphasised the provision of «good» money, that is, the provision of a uniform coin (in weight and fineness) and of a sensible mix of large and small denomination coins that would support the domestic economy. Their outcomes, however, differed. We suggest that in Potosi, the sheer volume of the resource endowment (silver) incentivised fraud and the neglect of the provision of fractionary coinage in the viceroyalty. In contrast, in Massachusetts Bay, the scarcity of the resource produced incentives better aligned with the production of «good» money. The northern colony produced a trustworthy coinage that provided small denomination coins for the domestic market.
Introduction to the Special Issue: Pluriversal relationality
Authors: Trownsell Tamara , Behera Navnita Chadha , Shani Giorgio
Published: September 2022

Both relationality and separateness are aspects of our everyday lives. How we engage these phenomena hinges on the particular existential assumptions that we take for granted. Within the discipline of International Relations (IR), both relationality and separateness have informed how global politics is studied and practiced. How states and their relations are conceived has, for instance, varied by the distinct degrees of privilege given to separation and interconnection: from notions of completely autonomous units like billiard balls to always emergent phenomena co-constituted through relations. The plurality of trajectories that inform this Special Issue illustrate how much broader the spectrum of relational engagement can be when we are cognisant of the impact of these existential assumptions on forms of life, knowing, and knowledge production in International Relations. By highlighting a spectrum of relational engagement, we raise important questions about the way the various knowledge frames in IR are acknowledged, legitimised, limited, and reproduced.
String diagram rewrite theory II: Rewriting with symmetric monoidal structure
Authors: Bonchi Filippo , Gadducci Fabio , Kissinger Aleks , Sobocinski Pawel , Zanasi Fabio
Published: September 2022

Symmetric monoidal theories (SMTs) generalise algebraic theories in a way that make them suitable to express resource-sensitive systems, in which variables cannot be copied or discarded at will. In SMTs, traditional tree-like terms are replaced by string diagrams, topological entities that can be intuitively thought of as diagrams of wires and boxes. Recently, string diagrams have become increasingly popular as a graphical syntax to reason about computational models across diverse fields, including programming language semantics, circuit theory, quantum mechanics, linguistics, and control theory. In applications, it is often convenient to implement the equations appearing in SMTs as rewriting rules. This poses the challenge of extending the traditional theory of term rewriting, which has been developed for algebraic theories, to string diagrams. In this paper, we develop a mathematical theory of string diagram rewriting for SMTs. Our approach exploits the correspondence between string diagram rewriting and double pushout (DPO) rewriting of certain graphs, introduced in the first paper of this series. Such a correspondence is only sound when the SMT includes a Frobenius algebra structure. In the present work, we show how an analogous correspondence may be established for arbitrary SMTs, once an appropriate notion of DPO rewriting (which we call convex) is identified. As proof of concept, we use our approach to show termination of two SMTs of interest: Frobenius semi-algebras and bialgebras.
Nutritional management of postoperative chylothorax in children with CHD
Authors: Fogg Kristi L. , Trauth Amiee , Horsley Megan , Vichayavilas Piyagarnt , Winder Melissa , Bailly David K. , Gordon Erin E.
Published: September 2022

Introduction:

Chylothorax after congenital cardiac surgery is associated with increased risk of malnutrition. Nutritional management following chylothorax diagnosis varies across sites and patient populations, and a standardised approach has not been disseminated. The aim of this review article is to provide contemporary recommendations related to nutritional management of chylothorax to minimise risk of malnutrition.

Methods:

The management guidelines were developed by consensus across four dietitians, one nurse practitioner, and two physicians with a cumulative 52 years of experience caring for children with CHD. A PubMed database search for relevant literature included the terms chylothorax, paediatric, postoperative, CHD, chylothorax management, growth failure, and malnutrition.

Results:

Fat-modified diets and nil per os therapies for all paediatric patients (<18 years of age) following cardiac surgery are highlighted in this review. Specific emphasis on strategies for treatment, duration of therapies, optimisation of nutrition including nutrition-focused lab monitoring, and supplementation strategies are provided.

Conclusions:

Our deliverable is a clinically useful guide for the nutritional management of chylothorax following paediatric cardiac surgery.
Receptivity to Instructional Feedback
Authors: Lipnevich Anastasiya A. , Lopera-Oquendo Carolina
Published: September 2022

Abstract: The purpose of this study was to report validity evidence for the instrument intended to measure receptivity to instructional feedback in a sample of secondary school students from Singapore ( N = 314). We tested a nested hierarchy of hypotheses for addressing the cross-group (i.e., gender) invariance and compared means on the receptivity to feedback subscales between gender groups. We also examined whether receptivity to feedback predicted student grades. The four-factor hypothesized model comprising experiential attitudes, instrumental attitudes, cognitive engagement, and behavioral engagement with feedback had a good model fit. Multi-group confirmatory factor analysis supported configural, metric, partial scalar, partial strict as well as variance and covariance invariance across gender groups. After controlling for gender, cognitive engagement, and experiential attitudes predicted increments in grades, suggesting evidence for discriminant validity among the receptivity factors as well as their relevance for the prediction of meaningful educational outcomes.
Satellites Can Accurately Take Earth’s Temperature
Authors: Dzombak Rebecca
Published: September 2022

Satellite-based measurements of land surface temperature may prove to be an essential pairing with near-surface air temperatures to understand global warming and cooling trends.
MESSENGER Reveals a More Dynamic Mercury Surface
Authors: Rehnberg Morgan
Published: September 2022

Image pairs indicate that 99% of the planet’s surface could be altered in the next 25 million years.
The Role of the North Atlantic Oscillation for Projections of Winter Mean Precipitation in Europe
Authors: McKenna C. M. , Maycock A. C.
Published: September 2022

Climate models generally project an increase in the winter North Atlantic Oscillation (NAO) index under a future high‐emissions scenario, alongside an increase in winter precipitation in northern Europe and a decrease in southern Europe. The extent to which future forced NAO trends are important for European winter precipitation trends and their uncertainty remains unclear. We show using the Multimodel Large Ensemble Archive that the NAO plays a small role in northern European mean winter precipitation projections for 2080–2099. Conversely, half of the model uncertainty in southern European mean winter precipitation projections is potentially reducible through improved understanding of the NAO projections. Extreme positive NAO winters increase in frequency in most models as a consequence of mean NAO changes. These extremes also have more severe future precipitation impacts, largely because of mean precipitation changes. This has implications for future resilience to extreme positive NAO winters, which frequently have severe societal impacts.
Direct Evidence for Auroral Kilometric Radiation Propagation Into Radiation Belts Based on Arase Spacecraft and Van Allen Probe B
Authors: Deng Zhoukun , Xiao Fuliang , Zhou Qinghua , Zhang Sai , Liu Si , Yang Qiwu , Tang Jiawen , Kumamoto Atsushi , Miyoshi Yoshizumi , Nakamura Yosuke , Tsuchiya Fuminori , Kasahara Yoshiya , Shinohara Iku , Nakamura Satoko
Published: September 2022

Recent studies have shown that auroral kilometric radiation (AKR) can propagate from the polar source cavity into the equatorial radiation belt but there is no direct evidence yet. By examining 19‐month data from Arase satellite and Van Allen Probes, we report a unique event that distinct AKR emissions are observed simultaneously at high and low latitudes, with the peak wave spectra in the frequency 300–400 kHz. Using the three‐dimensional ray tracing method, we simulate the AKR ray paths at three typical frequencies (220, 350, and 550 kHz), and show that more ray paths for 350 kHz can propagate downward through the locations of Arase satellite and Van Allen Probe B than those for other two frequencies. This result can successfully explain the observation and provides a direct evidence that AKR can propagate to low latitude radiation belt under suitable conditions.
Reply to Comment by Stauning on “The PC Index Variations During 23/24 Solar Cycles: Relation to Solar Wind Parameters and Magnetic Disturbances”
Authors: Troshichev O. A. , Dolgacheva S. A. , Stepanov N. A. , Sormakov D. A.
Published: September 2022

The polar cap magnetic activity index (PC) was approved by IAGA as an index characterizing the solar wind energy input into the magnetosphere. Relation of the PC index to solar wind parameters and solar activity during 23/24 solar cycles has been studied in paper (Troshichev et al., 2021, https://doi.org/10.1029/2020JA028491). The paper was commented by Dr. Stauning, who states that results obtained in the study are based on erroneous data presented on web site http://pcindex.org. According to Dr. Stauning, the following invalidities served as a reason for this assertion: incorrect determination of quiet daily curve (QDC), taken as reference level for counting the PC index value, and incorrect QDC amplitudes, incorrect yearly average values of PC index (and EKL field), incorrect methods of the analysis. In our answer we argue the correctness of our analysis and resulted conclusions.
A Decomposition of the Atmospheric and Surface Contributions to the Outgoing Longwave Radiation
Authors: Huang Han , Huang Yi
Published: September 2022

The outgoing longwave radiation (OLR), which consists of the thermal radiation from both the atmosphere and surface, is of critical importance to the Earth radiation energy budget. To understand the global OLR distribution, it is important to quantify the varying atmospheric and surface contributions. In this work, we present such a quantification using radiative transfer computations based on global reanalysis atmospheric data. By dissecting the OLR simulated following the radiative transfer equation, we quantitatively measure the layer‐wise atmospheric contributions to OLR and compare it to the surface contribution in different spectral bands. One focus of this study is on the OLR in the far‐infrared (FIR), for which new satellites are expected to provide unprecedented measurements. We find that around 45% of the global mean OLR is radiated in the FIR and in polar regions the FIR contribution can increase to 60%. Our vertical decomposition of OLR discloses that although the atmospheric contribution generally surpasses the surface contribution, the enhanced FIR contribution in the polar regions mainly results from a relatively stronger surface (as opposed to atmospheric) contribution. This is allowed by the opening of the atmospheric window in the FIR in these extremely dry regions. Our analysis also reveals that the tropopause layer makes a minimum contribution to the OLR, which may be a unique spectroscopic feature of the Earth atmosphere. Clouds are found to reduce the atmospheric contribution in the FIR while enhancing it in the mid‐infrared.
Remote Sensing of Groundwater: Current Capabilities and Future Directions
Authors: Adams Kyra H. , Reager John T. , Rosen Paul , Wiese David N. , Farr Tom G. , Rao Shanti , Haines Bruce J. , Argus Donald F. , Liu Zhen , Smith Ryan , Famiglietti James S. , Rodell Matthew
Published: September 2022

Globally, groundwater represents a critical natural resource that is affected by changes in natural supply and renewal, as well as by increasing human demand and consumption. However, despite its critical role, groundwater is difficult to accurately quantify as it is beneath the Earth surface. Here, we review several state‐of‐the‐art remote sensing techniques useful for local‐ to global‐scale groundwater monitoring and assessment, including proxies for groundwater extraction. These include inferring changes in subsurface water from mass changes using gravitational measurements, and analyzing changes in the Earth surface height using Interferometric Synthetic Aperture Radar, Light Detection and Ranging, Airborne Electromagnetic Systems, and satellite altimetry. Remote sensing information is often used in tandem with ground‐based observations such as hydraulic head in wells, Global Navigational Satellite System monitoring, and numerical modeling to complement the space‐based approaches. In the future, fusing different remote sensing techniques capable of operating in various environments will yield additional insight on the state and rate of use for groundwater across the globe.
Multiplexed electrospraying of water in cone-jet mode using a UV-embossed pyramidal micronozzle film
Authors: Jeong Ji-hun , Park Kwangseok , Kim Hyoungsoo , Park Inyong , Choi Jinyoung , Lee Seung S.
Published: September 2022

The electrospraying of water in the cone-jet mode is difficult in practical applications owing to its low throughput and the electrical discharge caused by the high surface tension of water. A film with multiple dielectric micronozzles is essential for multiplexed electrospraying of water in cone-jet mode without electrical discharge. Thus, a pyramidal micronozzle film with five nozzles was fabricated using the UV-embossing process. The pyramidal micronozzle film consisted of pyramidal micronozzles, a micropillar array, and an in-plane extractor, which were proposed to minimize wetting and concentrate the electric field to the water meniscus at the tip of the pyramidal micronozzle. The electrospraying of water using a single pyramidal micronozzle was visualized by a high-speed camera at a flow rate of 0.15–0.50 ml/h with voltages of 0.0–2.3 kV, −1.6 kV, and −4.0 kV at the water, guide ring, and collector, respectively. Three distinct modes, the dripping, spindle, and cone-jet modes, were observed and distinguished according to the motion of the water meniscus at the nozzle tip. The steady Taylor cone and jet were observed in a voltage range of 1.3–2.0 kV in water, particularly in cone-jet mode. Multiplexed electrospraying of water in cone-jet mode at a flow rate of 1.5 ml/h was performed using a pyramidal micronozzle film, demonstrating the potential for a high-throughput electrospraying system.
DNA methylation as a potential mediator of the association between prenatal tobacco and alcohol exposure and child neurodevelopment in a South African birth cohort
Authors: Abrishamcar Sarina , Chen Junyu , Feil Dakotah , Kilanowski Anna , Koen Nastassja , Vanker Aneesa , Wedderburn Catherine J. , Donald Kirsten A. , Zar Heather J. , Stein Dan J. , Hüls Anke
Published: September 2022

Prenatal tobacco exposure (PTE) and prenatal alcohol exposure (PAE) have been associated with an increased risk of delayed neurodevelopment in children as well as differential newborn DNA methylation (DNAm). However, the biological mechanisms connecting PTE and PAE, DNAm, and neurodevelopment are largely unknown. Here we aim to determine whether differential DNAm mediates the association between PTE and PAE and neurodevelopment at 6 (N = 112) and 24 months (N = 184) in children from the South African Drakenstein Child Health Study. PTE and PAE were assessed antenatally using urine cotinine measurements and the ASSIST questionnaire, respectively. Cord blood DNAm was measured using the EPIC and 450 K BeadChips. Neurodevelopment (cognitive, language, motor, adaptive behavior, socioemotional) was measured using the Bayley Scales of Infant and Toddler Development, Third Edition. We constructed methylation risk scores (MRS) for PTE and PAE and conducted causal mediation analysis (CMA) with these MRS as mediators. Next, we conducted a high-dimensional mediation analysis to identify individual CpG sites as potential mediators, followed by a CMA to estimate the average causal mediation effects (ACME) and total effect (TE). PTE and PAE were associated with neurodevelopment at 6 but not at 24 months. PTE MRS reached a prediction accuracy (R2) of 0.23 but did not significantly mediate the association between PTE and neurodevelopment. PAE MRS was not predictive of PAE (R2 = 0.006). For PTE, 31 CpG sites and eight CpG sites were identified as significant mediators (ACME and TEP < 0.05) for the cognitive and motor domains at 6 months, respectively. For PAE, 16 CpG sites and 1 CpG site were significant mediators for the motor and adaptive behavior domains at 6 months, respectively. Several of the associated genes, includingMAD1L1, CAMTA1, andALDH1A2have been implicated in neurodevelopmental delay, suggesting that differential DNAm may partly explain the biological mechanisms underlying the relationship between PTE and PAE and child neurodevelopment.
Nonsense-mediated mRNA decay inhibition synergizes with MDM2 inhibition to suppress TP53 wild-type cancer cells in p53 isoform-dependent manner
Authors: Li Ying , Wu Meng , Zhang Lili , Wan Li , Li Hexin , Zhang Lanxin , Sun Gaoyuan , Huang Wei , Zhang Junhua , Su Fei , Tang Min , Xiao Fei
Published: September 2022

The restoration of the normal function of the tumour suppressors, such as p53, is an important strategy in tumour therapeutics. Nonsense-mediated mRNA decay (NMD) inhibition by NMD inhibitor (NMDi) upregulates functional p53 isoforms, p53β and p53γ, and activates the p53 pathway. XR-2, a novel mouse double minute 2 homolog (MDM2) inhibitor, can disrupt the interaction between p53 and MDM2, thus decreasing the MDM2-mediated degradation of p53 and increasing the p53 protein levels. However, the combined effects of these two agents have not been thoroughly explored. This study combined XR-2 and NMDi in four TP53 wild-types and four TP53-mutated cancer cell lines. The combination of these two agents achieved significant synergistic effects on TP53 wild-type cancer cell lines by transactivating p53 target genes, inducing apoptosis, cell-cycle arrest and DNA damage repair. The p53β isoform induced by NMDi enhances the transactivation ability of p53α induced by XR-2, which partially explains the mechanism of the synergistic effects of XR-2 and NMDi. This study identified a combination treatment of NMDi and XR-2 which could serve as a novel cancer therapeutic approach for MDM2-overexpressed TP53 wild-type cancers and delineated a future therapy based on the further reactivation of p53.
Genomic basis of insularity and ecological divergence in barn owls (Tyto alba) of the Canary Islands
Authors: Cumer Tristan , Machado Ana Paula , Siverio Felipe , Cherkaoui Sidi Imad , Roque Inês , Lourenço Rui , Charter Motti , Roulin Alexandre , Goudet Jérôme
Published: September 2022

Islands, and the particular organisms that populate them, have long fascinated biologists. Due to their isolation, islands offer unique opportunities to study the effect of neutral and adaptive mechanisms in determining genomic and phenotypical divergence. In the Canary Islands, an archipelago rich in endemics, the barn owl (Tyto alba), present in all the islands, is thought to have diverged into a subspecies (T. a. gracilirostris) on the eastern ones, Fuerteventura and Lanzarote. Taking advantage of 40 whole-genomes and modern population genomics tools, we provide the first look at the origin and genetic makeup of barn owls of this archipelago. We show that the Canaries hold diverse, long-standing and monophyletic populations with a neat distinction of gene pools from the different islands. Using a new method, less sensitive to structure than classical FST, to detect regions involved in local adaptation to insular environments, we identified a haplotype-like region likely under selection in all Canaries individuals and genes in this region suggest morphological adaptations to insularity. In the eastern islands, where the subspecies is present, genomic traces of selection pinpoint signs of adapted body proportions and blood pressure, consistent with the smaller size of this population living in a hot arid climate. In turn, genomic regions under selection in the western barn owls from Tenerife showed an enrichment in genes linked to hypoxia, a potential response to inhabiting a small island with a marked altitudinal gradient. Our results illustrate the interplay of neutral and adaptive forces in shaping divergence and early onset speciation.
Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data
Authors: Shiraishi Yuichi , Okada Ai , Chiba Kenichi , Kawachi Asuka , Omori Ikuko , Mateos Raúl Nicolás , Iida Naoko , Yamauchi Hirofumi , Kosaki Kenjiro , Yoshimi Akihide
Published: September 2022

Many disease-associated genomic variants disrupt gene function through abnormal splicing. With the advancement of genomic medicine, identifying disease-associated splicing associated variants has become more important than ever. Most bioinformatics approaches to detect splicing associated variants require both genome and transcriptomic data. However, there are not many datasets where both of them are available. In this study, we develop a methodology to detect genomic variants that cause splicing changes (more specifically, intron retention), using transcriptome sequencing data alone. After evaluating its sensitivity and precision, we apply it to 230,988 transcriptome sequencing data from the publicly available repository and identified 27,049 intron retention associated variants (IRAVs). In addition, by exploring positional relationships with variants registered in existing disease databases, we extract 3,000 putative disease-associated IRAVs, which range from cancer drivers to variants linked with autosomal recessive disorders. The in-silico screening framework demonstrates the possibility of near-automatically acquiring medical knowledge, making the most of massively accumulated publicly available sequencing data. Collections of IRAVs identified in this study are available through IRAVDB (https://iravdb.io/).
Experimental validation that human microbiome phages use alternative genetic coding
Authors: Peters Samantha L. , Borges Adair L. , Giannone Richard J. , Morowitz Michael J. , Banfield Jillian F. , Hettich Robert L.
Published: September 2022

Previous bioinformatic analyses of metagenomic data have indicated that bacteriophages can use genetic codes different from those of their host bacteria. In particular, reassignment of stop codon TAG to glutamine (a variation known as ‘genetic code 15’) has been predicted. Here, we use LC-MS/MS-based metaproteomics of human fecal samples to provide experimental evidence of the use of genetic code 15 in two crAss-like phages. Furthermore, the proteomic data from several phage structural proteins supports the reassignment of the TAG stop codon to glutamine late in the phage infection cycle. Thus, our work experimentally validates the expression of genetic code 15 in human microbiome phages.
SARS-CoV-2 infects adipose tissue in a fat depot- and viral lineage-dependent manner
Authors: Saccon Tatiana Dandolini , Mousovich-Neto Felippe , Ludwig Raissa Guimarães , Carregari Victor Corasolla , dos Anjos Souza Ana Beatriz , dos Passos Amanda Stephane Cruz , Martini Matheus Cavalheiro , Barbosa Priscilla Paschoal , de Souza Gabriela Fabiano , Muraro Stéfanie Primon , Forato Julia , Amorim Mariene Ribeiro , Marques Rafael Elias , Veras Flavio Protasio , Barreto Ester , Gonçalves Tiago Tomazini , Paiva Isadora Marques , Fazolini Narayana P. B. , Onodera Carolina Mie Kawagosi , Martins Junior Ronaldo Bragança , de Araújo Paulo Henrique Cavalcanti , Batah Sabrina Setembre , Viana Rosa Maria Mendes , de Melo Danilo Machado , Fabro Alexandre Todorovic , Arruda Eurico , Queiroz Cunha Fernando , Cunha Thiago Mattar , Pretti Marco Antônio M. , Smith Bradley Joseph , Marques-Souza Henrique , Knittel Thiago L. , Ruiz Gabriel Palermo , Profeta Gerson S. , Fontes-Cal Tereza Cristina Minto , Boroni Mariana , Vinolo Marco Aurélio Ramirez , Farias Alessandro S. , Moraes-Vieira Pedro Manoel M. , Bizzacchi Joyce Maria Annichino , Teesalu Tambet , Chaim Felipe David Mendonça , Cazzo Everton , Chaim Elinton Adami , Proença-Módena José Luiz , Martins-de-Souza Daniel , Osako Mariana Kiomy , Leiria Luiz Osório , Mori Marcelo A.
Published: September 2022

Visceral adiposity is a risk factor for severe COVID-19, and a link between adipose tissue infection and disease progression has been proposed. Here we demonstrate that SARS-CoV-2 infects human adipose tissue and undergoes productive infection in fat cells. However, susceptibility to infection and the cellular response depends on the anatomical origin of the cells and the viral lineage. Visceral fat cells express more ACE2 and are more susceptible to SARS-CoV-2 infection than their subcutaneous counterparts. SARS-CoV-2 infection leads to inhibition of lipolysis in subcutaneous fat cells, while in visceral fat cells, it results in higher expression of pro-inflammatory cytokines. Viral load and cellular response are attenuated when visceral fat cells are infected with the SARS-CoV-2 gamma variant. A similar degree of cell death occurs 4-days after SARS-CoV-2 infection, regardless of the cell origin or viral lineage. Hence, SARS-CoV-2 infects human fat cells, replicating and altering cell function and viability in a depot- and viral lineage-dependent fashion.
Eolian chronology reveals causal links between tectonics, climate, and erg generation
Authors: Vainer Shlomy , Matmon Ari , Ben Dor Yoav , Verrecchia Eric P. , Eckardt Frank ,   ASTER Team, Aumaître Georges , Bourlès Didier L. , Keddadouche Karim
Published: September 2022

Evaluating the impact and implications of eolian repositories that mark large-scale climatic transitions requires knowledge about the timing of their emplacement and the mechanisms responsible for their production, which remain highly uncertain. Here we apply numerical modeling of cosmogenic nuclide data, measured in the largest continuous terrestrial body of sand on Earth, to determine settings under which the sand was generated, by constraining the timing of sand introduction into the interior of southern Africa. Our findings reveal that major events of sand formation and accumulation in the Kalahari Basin occurred between ~2.2 and 1 Myr ago. The establishment of the Kalahari sand field corresponds to regional, continental, and global scale morphotectonic and climatic changes that contributed to the mass production and widespread dispersion of sand. These changes substantially altered existing habitats, thus constituting a crucial milestone for flora, fauna, and hominins in southern Africa during the Pleistocene.
Interferon regulatory factor 1 (IRF-1) promotes intestinal group 3 innate lymphoid responses during Citrobacter rodentium infection
Authors: Schmalzl Angelika , Leupold Tamara , Kreiss Lucas , Waldner Maximilian , Schürmann Sebastian , Neurath Markus F. , Becker Christoph , Wirtz Stefan
Published: September 2022

Group 3 innate lymphoid cells (ILC3s) are crucial mediators of immunity and epithelial barrier function during immune responses against extracellular bacteria. Here, we identify Interferon regulatory factor 1 (IRF-1), a transcription factor previously associated with type 1 immunity, as an essential regulator of intestinal ILC3 accumulation and effector cytokine production. We demonstrate that IRF-1 is upregulated in the context of infection with the enteropathogen Citrobacter rodentium and that its presence is central for anatomical containment and prevention of pathogen dissemination. We furthermore show that IRF-1 is required in order for intestinal ILC3s to produce large amounts of the protective effector cytokine IL-22 early in the course of infection. On a molecular level, our data indicate that IRF-1 controls ILC3 numbers and their activation by direct transcriptional regulation of the IL-12Rβ1 chain, thereby allowing ILCs to physiologically respond to IL-23 stimulation.
MYPT1-PP1β phosphatase negatively regulates both chromatin landscape and co-activator recruitment for beige adipogenesis
Authors: Takahashi Hiroki , Yang Ge , Yoneshiro Takeshi , Abe Yohei , Ito Ryo , Yang Chaoran , Nakazono Junna , Okamoto-Katsuyama Mayumi , Uchida Aoi , Arai Makoto , Jin Hitomi , Choi Hyunmi , Tumenjargal Myagmar , Xie Shiyu , Zhang Ji , Sagae Hina , Zhao Yanan , Yamaguchi Rei , Nomura Yu , Shimizu Yuichi , Yamada Kaito , Yasuda Satoshi , Kimura Hiroshi , Tanaka Toshiya , Wada Youichiro , Kodama Tatsuhiko , Aburatani Hiroyuki , Zhu Min-Sheng , Inagaki Takeshi , Osborne Timothy F. , Kawamura Takeshi , Ishihama Yasushi , Matsumura Yoshihiro , Sakai Juro
Published: September 2022

Protein kinase A promotes beige adipogenesis downstream from β-adrenergic receptor signaling by phosphorylating proteins, including histone H3 lysine 9 (H3K9) demethylase JMJD1A. To ensure homeostasis, this process needs to be reversible however, this step is not well understood. We show that myosin phosphatase target subunit 1- protein phosphatase 1β (MYPT1-PP1β) phosphatase activity is inhibited via PKA-dependent phosphorylation, which increases phosphorylated JMJD1A and beige adipogenesis. Mechanistically, MYPT1-PP1β depletion results in JMJD1A-mediated H3K9 demethylation and activation of the Ucp1 enhancer/promoter regions. Interestingly, MYPT1-PP1β also dephosphorylates myosin light chain which regulates actomyosin tension-mediated activation of YAP/TAZ which directly stimulates Ucp1 gene expression. Pre-adipocyte specific Mypt1 deficiency increases cold tolerance with higher Ucp1 levels in subcutaneous white adipose tissues compared to control mice, confirming this regulatory mechanism in vivo. Thus, we have uncovered regulatory cross-talk involved in beige adipogenesis that coordinates epigenetic regulation with direct activation of the mechano-sensitive YAP/TAZ transcriptional co-activators.
Multicolor ultralong phosphorescence from perovskite-like octahedral α-AlF3
Authors: Cao Peisheng , Zheng Haoyue , Wu Peng
Published: September 2022

Designing organic fluorescent and phosphorescent materials based on various core fluorophore has gained great attention, but it is unclear whether similar luminescent units exist for inorganic materials. Inspired by the BX6 octahedral structure of luminescent metal halide perovskites (MHP), here we propose that the BX6 octahedron may be a core structure for luminescent inorganic materials. In this regard, excitation-dependent color-tunable phosphorescence is discovered from α-AlF3 featuring AlF6 octahedron. Through further exploration of the BX6 unit by altering the dimension and changing the center metal (B) and ligand (X), luminescence from KAlF4, (NH4)3AlF6, AlCl3, Al(OH)3, Ga2O3, InCl3, and CdCl2 are also discovered. The phosphorescence of α-AlF3 can be ascribed to clusterization-triggered emission, i.e., weak through space interaction of the n electrons of F atoms bring close proximity in the AlF6 octahedra (inter/intra). These discoveries will deepen the understanding and contribute to further development of BX6 octahedron-based luminescent materials.
High PSQI score is associated with the development of dyskinesia in Parkinson’s disease
Authors: Tang Xiaohui , Yang Jingyun , Zhu Yining , Gong Haiyan , Sun Hui , Chen Fan , Guan Qiang , Yu Lijia , Wang Weijia , Zhang Zengping , Li Li , Ma Guozhao , Wang Xijin
Published: September 2022

Dyskinesia is one of the most disabling motor complications in Parkinson’s Disease (PD). Sleep is crucial to keep neural circuit homeostasis, and PD patients often suffer from sleep disturbance. However, few prospective studies have been conducted to investigate the association of sleep quality with dyskinesia in PD. The objective of the current study is to investigate the association between sleep quality and dyskinesia and build a prediction model for dyskinesia in PD. We prospectively followed a group of PD patients without dyskinesia at baseline for a maximum of 36 months. Univariable and multivariable Cox regression with stepwise variable selection was used to investigate risk factors for dyskinesia. The performance of the model was assessed by the time-dependent area under the receiver-operating characteristic curve (AUC). At the end of follow-up, 32.8% of patients developed dyskinesia. Patients with bad sleep quality had a significantly higher proportion of dyskinesia compared with those with good sleep quality (48.1% vs. 20.6%, p = 0.023). Multivariable Cox regression selected duration of PD, sleep quality, cognition, mood, and levodopa dose. Notably, high Pittsburgh sleep quality index (PSQI) score was independently associated with an increased risk of dyskinesia (HR = 2.96, 95% CI 1.05–8.35, p = 0.041). The model achieved a good discriminative ability, with the highest AUC being 0.83 at 35 months. Our results indicated that high PSQI score may increase the risk of developing dyskinesia in PD, implying that therapeutic intervention targeting improving sleep quality may be a promising approach to prevent or delay the development of dyskinesia in PD.
Influence of point-of-use dispensers on lead level assessment in drinking water of a lead pipe-free campus
Authors: Adhikari Saroj , Lin Yi-Pin , Ng Ding-Quan
Published: September 2022

Point-of-use (POU) dispensers, referring to those directly connected to the water supply lines, are widely used in public facilities such as schools and universities in Taiwan. These dispensers are equipped with filters that can remove contaminants, including heavy metals in drinking water. Assessment of water lead (Pb) levels rely heavily on sampling surveys that involve various sampling protocols. This study evaluated the effects of using first draw (FD), flush (FL) incorporating at least 20 s of flushing, and random daytime (RDT) sampling protocols on Pb level assessment in water samples collected from faucets and POU dispensers of a Pb pipe-free campus between March 2017 and July 2020. This was the first study to examine the influence of POU dispensers on different sampling protocols and their survey results. Pb levels in 19% of faucet and 11% of dispenser samples exceeded the Taiwan EPA standard of 10 μg/L. FL sampling produced the lowest Pb levels, followed by RDT and FD in the samples collected from faucets. Interestingly, all three sampling protocols exhibited similar Pb levels in samples collected from dispensers. Thus, any of the three sampling protocols can be employed to monitor Pb levels in water samples collected from dispensers.