bluuebunny/crossref_metadata_2025 huggingface dataset:
The Politics of Aesthetic Preference in Participatory Music
Authors: Lemmon Eric
Published: February 2022

Bringing together an array of interdisciplinary subjects, this article seeks to proffer a theory of political aesthetic preference emergent within participatory musical works. Beginning with an overview of imitation in music and then recapping the critical work advanced by Kofi Agawu and Jean-Jacques Nattiez on musical semiology, this article first delves into how musical signs are interpreted and propagated within participatory settings. Subsequently, using Jürgen Habermas’s influential theory on the public sphere as well as the critical revisions to said theory proposed by Nancy Fraser and Michael Warner, participatory musics are conceptualised as constituting the formal space of a public in which the aesthetic direction of a participatory music work is negotiated among participants. Based on an analysis of Luke Dahl, Jorge Herrera and Carr Wilkerson’s multi-user instrument and participatory work TweetDreams, this article discusses the ways in which participant inputs and choices impact the poietic process of the work due to the clear rules that are set up within its interactive and algorithmic protocols for sonification. It concludes by pointing towards other recent research on participatory works, where the framing of participatory musics as a political–aesthetic space leads to broader questions about audience power and how the latter is negotiated and shared, then poses questions for future research on the audience’s choice in refusal and dissensus.
National electronic primary health care database in monitoring performance of primary care in Kyrgyzstan
Authors: Laatikainen Tiina , Inglin Laura , Chonmurunov Ilyas , Stambekov Bakhtiar , Altymycheva Aliina , Farrington Jill L.
Published: February 2022

Aim:

The aim of this study was to assess the feasibility of the national electronic primary health care (PHC) database in Kyrgyzstan in producing information on the disease burden of the patient population and on the processes and quality of care of noncommunicable diseases (NCDs) in PHC.

Background:

Strengthening of the PHC is essential for low- and middle-income countries (LMICs) to tackle the increasing burden of NCDs. Capacity building and quality improvement require timely data on processes and quality of care.

Methods:

A data extraction was carried out covering four PHC clinics in Bishkek in 2019 to pilot the use of the national data for quality assessment purposes. The data included patient-level information on all appointments in the clinics during the year 2018 and consisted of data of altogether 48 564 patients. Evaluation indicators of the WHO Package of Essential NCD Interventions framework were used to assess the process and outcome indicators of patients with hypertension or diabetes.

Findings:

The extracted data enabled the identification of different patient populations and analyses of various process and outcome indicators. The legibility of data was good and the structured database enabled easy data extraction and variable formation on patient level. As an example of process and outcome indicators of those with hypertension, the blood pressure was measured at least on two occasions of 90% of women and 89% of men, and blood pressure control was achieved among 61% of women and 53% of men with hypertension. This study showed that a rather basic system gathering nationally patient-level data to an electronic database can serve as an excellent information source for national authorities. Investments should be made to develop electronic health records and national databases also in LMICs.
Analyzing Data of a Multilab Replication Project With Individual Participant Data Meta-Analysis
Authors: van Aert Robbie C. M.
Published: February 2022

Abstract. Multilab replication projects such as Registered Replication Reports (RRR) and Many Labs projects are used to replicate an effect in different labs. Data of these projects are usually analyzed using conventional meta-analysis methods. This is certainly not the best approach because it does not make optimal use of the available data as a summary rather than participant data are analyzed. I propose to analyze data of multilab replication projects with individual participant data (IPD) meta-analysis where the participant data are analyzed directly. The prominent advantages of IPD meta-analysis are that it generally has larger statistical power to detect moderator effects and allows drawing conclusions at the participant and lab level. However, a disadvantage is that IPD meta-analysis is more complex than conventional meta-analysis. In this tutorial, I illustrate IPD meta-analysis using the RRR by McCarthy and colleagues, and I provide R code and recommendations to facilitate researchers to apply these methods.
The Arctic Ocean in CMIP6 Models: Biases and Projected Changes in Temperature and Salinity
Authors: Khosravi Narges , Wang Qiang , Koldunov Nikolay , Hinrichs Claudia , Semmler Tido , Danilov Sergey , Jung Thomas
Published: February 2022

We examine the historical evolution and projected changes in the hydrography of the deep basin of the Arctic Ocean in 23 climate models participating in the Coupled Model Intercomparison Project Phase 6 (CMIP6). The comparison between historical simulations and observational climatology shows that the simulated Atlantic Water (AW) layer is too deep and thick in the majority of models, including the multi‐model mean (MMM). Moreover, the halocline is too fresh in the MMM. Overall our findings indicate that there is no obvious improvement in the representation of the Arctic hydrography in CMIP6 compared to CMIP5. The climate change projections reveal that the sub‐Arctic seas are outstanding warming hotspots, causing a strong warming trend in the Arctic AW layer. The MMM temperature increase averaged over the upper 700 m at the end of the 21st century is about 40% and 60% higher in the Arctic Ocean than the global mean in the SSP245 and SSP585 scenarios, respectively. Salinity in the upper few hundred meters is projected to decrease in the Arctic deep basin in the MMM. However, the spread in projected salinity changes is large and the tendency toward stronger halocline in the MMM is not simulated by all the models. The identified biases and projection uncertainties call for a concerted effort for major improvements of coupled climate models.
Electrochemical Properties of Peat Particulate Organic Matter on a Global Scale: Relation to Peat Chemistry and Degree of Decomposition
Authors: Teickner Henning , Gao Chuanyu , Knorr Klaus‐Holger
Published: February 2022

Methane production in peatlands is controlled by the availability of electron acceptors for microbial respiration, including peat dissolved organic matter (DOM) and particulate organic matter (POM). Despite the much larger mass of POM in peat, knowledge on the ranges of its electron transfer capacities—electron accepting capacity (EAC), and electron donating capacity (EDC)—is scarce in comparison to DOM and humic and fulvic acids. Moreover, it is unclear how peat POM chemistry and decomposition relate to its EAC and EDC. To address these knowledge gaps, we compiled peat samples with varying carbon contents from mid to high latitude peatlands and analyzed their EACPOM and EDCPOM, element ratios, decomposition indicators, and relative amounts of molecular structures as derived from mid infrared spectra. Peat EACPOM and EDCPOM are smaller (per gram carbon) than EAC and EDC of DOM and terrestrial and aquatic humic and fulvic acids and are highly variable within and between sites. Both are small in highly decomposed peat, unless it has larger amounts of quinones and phenols. Element ratio‐based models failed to predict EACPOM and EDCPOM, while mid infrared spectra‐based models can predict peat EACPOM to a large extent, but not EDCPOM. We suggest a conceptual model that describes how vegetation chemistry and decomposition control polymeric phenol and quinone contents as drivers of peat EDCPOM and EACPOM. The conceptual model implies that we need mechanistic models or spatially resolved measurements to understand the variability in peat EDCPOM and EACPOM and thus its role in controlling methane formation.
Wind Profile in the Wave Boundary Layer and Its Application in a Coupled Atmosphere‐Wave Model
Authors: Wu Lichuan , Qiao Fangli
Published: February 2022

Current models cannot capture well the impacts of wind waves on the atmospheric boundary layer. Here, we proposed a new turbulence closure model to estimate the wind stress in the wave boundary layer from viscous stress, shear‐induced turbulent stress, wind‐sea induced stress, and swell‐induced upward stress separately. The misalignment between the wind stress and wind is also considered in the model. Single‐column simulations indicate that (a) the swell‐induced upward momentum flux increases the surface wind and changes the wind direction, (b) the misalignment between the upward momentum flux and wind has a more significant impact on the wind profile than that from the downward momentum flux, and (c) the impact of swell‐induced upward momentum flux decreases with atmospheric convection. The proposed closure scheme was implemented into an atmosphere‐wave coupled model. A month‐long simulation over the ocean off California shows that the surface wind can be altered up to 5% by ocean surface gravity waves.
Comparison of MLT Momentum Fluxes Over the Andes at Four Different Latitudinal Sectors Using Multistatic Radar Configurations
Authors: Conte J. Federico , Chau Jorge L. , Liu Alan , Qiao Zishun , Fritts David C. , Hormaechea José L. , Salvador Jacobo O. , Milla Marco A.
Published: February 2022

The middle atmosphere over South America, particularly above the Andes mountain range, is known as one of the most dynamically active regions in the world. Previous studies have investigated wave dynamics at mesosphere and lower thermosphere (MLT) altitudes within this region, but only a handful of them have made use of continuous measurements provided by specular meteor radars (SMRs). Furthermore, it was only until recently that MLT horizontal wind gradients were estimated for the first time using Spread Spectrum Interferometric Multistatic meteor radar Observing Network (SIMONe) Argentina, a multistatic SMR network located in southern Patagonia. By observing larger amounts of meteors from different viewing angles, multistatic SMRs allow, among others, for more reliable momentum flux estimates. In this work, we explore and compare the summer and winter MLT momentum flux dynamics at low and middle latitude sectors over the Andes mountain range. We also investigate the intermittency of the total momentum flux over these sectors. For this purpose, we analyze measurements provided by four multistatic SMR networks: SIMONe Peru (12°S), CONDOR (30°S), SIMONe Argentina (49°S) and MMARIA‐SAAMER (54°S). We find that the momentum flux dynamics can change considerably over distances of only a few hundred km (e.g., southern Argentina). On the other hand, the contributions of large momentum fluxes to the total flux can be similar between regions separated by thousands of km (e.g., between Peru and southern Argentina).
Remote Sensing of Tundra Ecosystems Using High Spectral Resolution Reflectance: Opportunities and Challenges
Authors: Nelson Peter R. , Maguire Andrew J. , Pierrat Zoe , Orcutt Erica L. , Yang Dedi , Serbin Shawn , Frost Gerald V. , Macander Matthew J. , Magney Troy S. , Thompson David R. , Wang Jonathan A. , Oberbauer Steven F. , Zesati Sergio Vargas , Davidson Scott J. , Epstein Howard E. , Unger Steven , Campbell Petya K. E. , Carmon Nimrod , Velez‐Reyes Miguel , Huemmrich K. Fred
Published: February 2022

Observing the environment in the vast regions of Earth through remote sensing platforms provides the tools to measure ecological dynamics. The Arctic tundra biome, one of the largest inaccessible terrestrial biomes on Earth, requires remote sensing across multiple spatial and temporal scales, from towers to satellites, particularly those equipped for imaging spectroscopy (IS). We describe a rationale for using IS derived from advances in our understanding of Arctic tundra vegetation communities and their interaction with the environment. To best leverage ongoing and forthcoming IS resources, including National Aeronautics and Space Administration’s Surface Biology and Geology mission, we identify a series of opportunities and challenges based on intrinsic spectral dimensionality analysis and a review of current data and literature that illustrates the unique attributes of the Arctic tundra biome. These opportunities and challenges include thematic vegetation mapping, complicated by low‐stature plants and very fine‐scale surface composition heterogeneity; development of scalable algorithms for retrieval of canopy and leaf traits; nuanced variation in vegetation growth and composition that complicates detection of long‐term trends; and rapid phenological changes across brief growing seasons that may go undetected due to low revisit frequency or be obscured by snow cover and clouds. We recommend improvements to future field campaigns and satellite missions, advocating for research that combines multi‐scale spectroscopy, from lab studies to satellites that enable frequent and continuous long‐term monitoring, to inform statistical and biophysical approaches to model vegetation dynamics.
The Occurrence of Large Floods in the United States in the Modern Hydroclimate Regime: Seasonality, Trends, and Large‐Scale Climate Associations
Authors: Collins M. J. , Hodgkins G. A. , Archfield S. A. , Hirsch R. M.
Published: February 2022

Many studies investigate river floods by analyzing annual maximum series that record the largest flow of each year, including many within‐bank events inconsequential for human communities. Fewer focus on larger floods, especially at the continental scale. Using 473 streamgages across the conterminous United States with near‐natural flow from 1966 to 2015, we characterized the seasonality, occurrence, and climatic associations of the 10 largest and 2 largest floods at each site. These are often overbank events that have ecosystem functions and pose risks to humans. We grouped sites into 14 clusters corresponding to climatic and physiographic regions and characterized their flood seasonality at a monthly resolution using a probabilistic method. We then evaluated annual occurrence regionally and nationally, and seasonal occurrence regionally, by complementing a traditional approach to trend analyses with a novel method based on expected occurrence. Relationships between flood occurrence and climate indices were also investigated. Large floods have strong seasonality in some regions, but in areas with numerous flood‐generating mechanisms, seasonality is more complex. There is little evidence nationally that large riverine floods are more or less frequent than expected in recent years and only two regions show significant trends in annual counts; few show seasonal trends. We found some regional relationships between flood counts and climate indices, annually and seasonally; nationally the Pacific North American pattern is related to annual counts of the 2 largest floods. Large‐flood occurrence was generally stable across the United States in the last five decades; this may or may not continue with projected warming.
Demystifying a Family-Based Epilepsy Adherence Problem-Solving Intervention: Exploring Adherence Barriers and Solutions
Authors: Williford Desireé N. , Guilfoyle Shanna M. , Modi Avani C.
Published: February 2022

Objective:

Barriers to medication adherence are common in pediatric epilepsy and associated with nonadherence, suboptimal seizure outcomes, and quality of life. A manualized, family-tailored education and problem-solving adherence intervention to address adherence barriers was tested in a randomized controlled trial in young children (2–12 years) with epilepsy. Study aims were to identify the adherence barriers and solutions chosen by families during intervention.

Method:

Participants with demonstrated suboptimal adherence were randomized to either education attention control or treatment. In this exploratory, secondary analysis, treatment group data were examined, including adherence barriers and solutions discussed during face-to-face problem-solving sessions and telephone follow-ups. Treatment data were independently coded utilizing codebook thematic analysis.

Results:

Twenty-seven children were randomized to treatment ( M = 7.5 ± 2.9; 59.1% female). Across sessions, coding revealed 10 adherence barriers: Overall Forgetting (38–57%), Change of Routine (14–24%), Competing Activities (5–19%), Opposition (0–9%), Transition of Responsibility (0–5%), Running Out of Medication (0–10%), Forgetting During Travel (0–10%), Medication Not a Priority (0–5%), Medication Taste (0–5%), and Pill Swallowing (0–5%). Eight solution types were chosen and implemented by families: Environmental Cuing (29–50%), Multi-Pronged solutions (0–24%), Positive Reinforcement (14–23%), Backup Doses (0–14%), Refill Tracking (0–10%), Caregiver Modeling of Adherence Behavior (0–5%), Pill Swallowing Intervention (0–5%), and Other (0–5%). A ninth solution type, Caregiver Reminders, was often incorporated into Multi-Pronged solutions.

Conclusions:

Results highlight key adherence barriers identified by families of children with epilepsy and solutions implemented to address them. These data provide guidance to health care teams on how to successfully address adherence barriers in clinical settings.

Implications for Impact Statement

This study reduces gaps between research and practice by highlighting family-identified medication adherence barriers and solutions successfully implemented over time by families of young children with epilepsy.
Insulin-like growth factor I mitigates post-traumatic stress by inhibiting AMP-kinase in orexin neurons
Authors: Fernández de Sevilla M. Estrella , Pignatelli Jaime , Zegarra-Valdivia Jonathan A. , Mendez Pablo , Nuñez Angel , Torres Alemán Ignacio
Published: February 2022

Maladaptive coping behaviors are probably involved in post-traumatic stress disorders (PTSD), but underlying mechanisms are incompletely understood. We now report that mice lacking functional insulin-like growth factor I (IGF-I) receptors in orexin neurons of the lateral hypothalamus (Firoc mice) are unresponsive to the anxiolytic actions of IGF-I and develop PTSD-like behavior that is ameliorated by inhibition of orexin neurons. Conversely, systemic IGF-I treatment ameliorated PTSD-like behavior in a wild-type mouse model of PTSD (PTSD mice). Further, systemic IGF-I modified the GABA/Glutamate synaptic structure in orexin neurons of naïve wild-type mice by increasing the dephosphorylation of GABA(B) receptor subunit through inhibition of AMP-kinase (AMPK). Significantly, pharmacological inhibition of AMPK mimicked IGF-I, normalizing fear behavior in PTSD mice. Thus, we suggest that IGF-I enables coping behaviors by balancing E/I input onto orexin neurons in a context-dependent manner. These observations provide a novel therapeutic approach to PTSD through modulation of AMPK.
Association of vision impairment and blindness with socioeconomic status in adults 50 years and older from Alto Amazonas, Peru
Authors: Nesemann John M. , Morocho-Alburqueque Noelia , Quincho-Lopez Alvaro , Muñoz Marleny , Liliana-Talero Sandra , Harding-Esch Emma M. , Saboyá-Díaz Martha Idalí , Honorio-Morales Harvy A. , Durand Salomón , Carey-Angeles Cristiam A. , Klausner Jeffrey D. , Lescano Andres G. , Keenan Jeremy D.
Published: February 2022

Objective

To determine the relationship between socioeconomic status (SES) and visual impairment (VI) or blindness in the rural Peruvian Amazon, hypothesizing that higher SES would have a protective effect on the odds of VI or blindness.

Methods

In this cross-sectional study of 16 rural communities in the Peruvian Amazon, consenting adults aged ≥ 50 years were recruited from ~30 randomly selected households per village. Each household was administered a questionnaire and had a SES score constructed using principal components analysis. Blindness and VI were determined using a ministry of health 3-meter visual acuity card.

Results

Overall, 207 adults aged ≥ 50 were eligible; 146 (70.5%) completed visual acuity screening and answered the questionnaire. Of those 146 participants who completed presenting visual acuity screening, 57 (39.0%, 95% CI 30.2–47.1) were classified as visually impaired and 6 (4.1%, 95% CI 0.9–7.3) as blind. Belonging to the highest SES tercile had a protective effect on VI or blindness (OR 0.29, 95% CI 0.09 to 0.91, p = 0.034), with a linear trend across decreasing levels of SES (p = 0.019). This observed effect remained significant regardless of how SES groups were assigned.

Conclusion

Belonging to a higher SES group resulted in a lower odds of VI or blindness compared to those in the lowest SES group. The observation of a dose response provides confidence in the observed association, but causality remains unclear. Blindness prevention programs could maximize impact by designing activities that specifically target people with lower SES.
Impact of cessation of regular cataract surgery during the COVID pandemic on the rates of posterior capsular rupture and post-operative cystoid macular oedema
Authors: Theodoraki Korina , Naderi Khayam , Lam Chun Fung Jeffrey , Tan Jit Kai , Jameel Ashmal , Lai Lily , Garcia Luis Onrubia , Low Sancy , Bhogal Mani , Robbie Scott , O’Brart David
Published: February 2022

Background/objectives

During the COVID-19, elective cataract surgery (CS) was significantly curtailed. We investigated whether consequent reduction of micro-surgical skills practice might lead to higher operative complications.

Methods

Single-centre, electronic note review of consecutive patients undergoing CS during three periods: 1st February 2019 to 13th January 2020 (P1) prior to pandemic; 3rd June 2020 to 11th January 2021 after 1st lockdown (P2); and 25th January to 30th July 2021 (P3) after/during second lockdown.

Results

2276 operations occurred during P1, 999 during P2, 846 during P3. During P1, posterior capsular rupture (PCR) rate was 1.67%, similar to P2 (1.30%, p = 0.54), but lower than P3 (3.55%, p = 0.002). There was no difference in PCR risk percentage scores between routine and PCR cases during P1 (1.90% vs 2.03%, p = 0.83), P2 (2% vs 2.18%, p = 0.18), or P3 (1.87% vs. 2.71%, p = 0.08). During P2 and P3, there was a higher rate of cystoid macular oedema (CMO) compared with P1 (4.9% and 6.86% vs. 1.93%, p = 0.0001), with no differences in proportion of diabetics or cases with CMO in combination with PCR. There was no difference in surgeons grade experiencing PCR.

Conclusions

In P3 following 9 months of curtailed elective CS, PCR rates were increased across all surgeon grades, occurring in cases with similar risk percentage scores. CMO rates were increased during COVID and not related to proportion of diabetics or increased PCR rates. The reduction in elective CS during the pandemic was associated with more complications, perhaps due to attenuation of microsurgical skills.
ACE2 binding is an ancestral and evolvable trait of sarbecoviruses
Authors: Starr Tyler N. , Zepeda Samantha K. , Walls Alexandra C. , Greaney Allison J. , Alkhovsky Sergey , Veesler David , Bloom Jesse D.
Published: February 2022

Two different sarbecoviruses have caused major human outbreaks in the past two decades1,2. Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the spike receptor-binding domain2–6. However, binding to ACE2 orthologues of humans, bats and other species has been observed only sporadically among the broader diversity of bat sarbecoviruses7–11. Here we use high-throughput assays12 to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades. Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2. Moreover, ACE2 binding is highly evolvable—for many sarbecovirus receptor-binding domains, there are single amino-acid mutations that enable binding to new ACE2 orthologues. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. Our results point to the deep ancestral origin and evolutionary plasticity of ACE2 binding, broadening the range of sarbecoviruses that should be considered to have spillover potential.
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles
Authors: Hautakangas Heidi , Winsvold Bendik S. , Ruotsalainen Sanni E. , Bjornsdottir Gyda , Harder Aster V. E. , Kogelman Lisette J. A. , Thomas Laurent F. , Noordam Raymond , Benner Christian , Gormley Padhraig , Artto Ville , Banasik Karina , Bjornsdottir Anna , Boomsma Dorret I. , Brumpton Ben M. , Burgdorf Kristoffer Sølvsten , Buring Julie E. , Chalmer Mona Ameri , de Boer Irene , Dichgans Martin , Erikstrup Christian , Färkkilä Markus , Garbrielsen Maiken Elvestad , Ghanbari Mohsen , Hagen Knut , Häppölä Paavo , Hottenga Jouke-Jan , Hrafnsdottir Maria G. , Hveem Kristian , Johnsen Marianne Bakke , Kähönen Mika , Kristoffersen Espen S. , Kurth Tobias , Lehtimäki Terho , Lighart Lannie , Magnusson Sigurdur H. , Malik Rainer , Pedersen Ole Birger , Pelzer Nadine , Penninx Brenda W. J. H. , Ran Caroline , Ridker Paul M. , Rosendaal Frits R. , Sigurdardottir Gudrun R. , Skogholt Anne Heidi , Sveinsson Olafur A. , Thorgeirsson Thorgeir E. , Ullum Henrik , Vijfhuizen Lisanne S. , Widén Elisabeth , van Dijk Ko Willems ,   International Headache Genetics Consortium, de Boer Irene , van den Maagdenberg Arn M. J. M. ,   HUNT All-in Headache,   Danish Blood Donor Study Genomic Cohort, Aromaa Arpo , Belin Andrea Carmine , Freilinger Tobias , Ikram M. Arfan , Järvelin Marjo-Riitta , Raitakari Olli T. , Terwindt Gisela M. , Kallela Mikko , Wessman Maija , Olesen Jes , Chasman Daniel I. , Nyholt Dale R. , Stefánsson Hreinn , Stefansson Kari , van den Maagdenberg Arn M. J. M. , Hansen Thomas Folkmann , Ripatti Samuli , Zwart John-Anker , Palotie Aarno , Pirinen Matti
Published: February 2022

Migraine affects over a billion individuals worldwide but its genetic underpinning remains largely unknown. Here, we performed a genome-wide association study of 102,084 migraine cases and 771,257 controls and identified 123 loci, of which 86 are previously unknown. These loci provide an opportunity to evaluate shared and distinct genetic components in the two main migraine subtypes: migraine with aura and migraine without aura. Stratification of the risk loci using 29,679 cases with subtype information indicated three risk variants that seem specific for migraine with aura (in HMOX2, CACNA1A and MPPED2), two that seem specific for migraine without aura (near SPINK2 and near FECH) and nine that increase susceptibility for migraine regardless of subtype. The new risk loci include genes encoding recent migraine-specific drug targets, namely calcitonin gene-related peptide (CALCA/CALCB) and serotonin 1F receptor (HTR1F). Overall, genomic annotations among migraine-associated variants were enriched in both vascular and central nervous system tissue/cell types, supporting unequivocally that neurovascular mechanisms underlie migraine pathophysiology.
Establishment of reference standards for multifaceted mosaic variant analysis
Authors: Ha Yoo-Jin , Oh Myung Joon , Kim Junhan , Kim Jisoo , Kang Seungseok , Minna John D. , Kim Hyun Seok , Kim Sangwoo
Published: February 2022

Detection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of ultra-deep sequenced WES data based on reference standards generated by cell line mixtures, providing a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition such as in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference data will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements.
The involvement of cyclotides in mutual interactions of violets and the two-spotted spider mite
Authors: Slazak Blazej , Jędrzejska Aleksandra , Badyra Bogna , Sybilska Anna , Lewandowski Mariusz , Kozak Marcin , Kapusta Małgorzata , Shariatgorji Reza , Nilsson Anna , Andrén Per E. , Göransson Ulf , Kiełkiewicz Małgorzata
Published: February 2022

Plants employ different chemicals to protect themselves from herbivory. These defenses may be constitutive or triggered by stress. The chemicals can be toxic, act as repellents, phagosuppressants and/or phago-deterrents. The two-spotted spider mite (Tetranychus urticae) is a generalist arthropod herbivorous pest and its feeding causes extensive damage both to crops and wild plants. Cyclotides are cyclic peptides involved in host-plant defenses. A single Viola sp. can produce more than a hundred cyclotides with different biological activities and roles. The organ and tissue specific cyclotide patterns change over the seasons and/or with environment, but the role of biotic/abiotic stress in shaping them remains unclear. Here, we demonstrate the involvement of cyclotides in mutual interactions between violets and mites. We used immunohistochemistry and mass spectrometry imaging to show the ingested cyclotides in T. urticae and assess the Viola odorata response to mite feeding. Moreover, to assess how mites are affected by feeding on violets, acceptance and reproductive performance was compared between Viola uliginosa, V. odorata and Phaseolus vulgaris. We demonstrate that cyclotides had been taken in by mites feeding on the violets. The ingested peptides were found in contact with epithelial cells of the mite digestive system, in the fecal matter, feces, ovary and eggs. Mites preferred common bean plants (P. vulgaris) to any of the violet species; the latter affected their reproductive performance. The production of particular cyclotides in V. odorata (denoted by molecular weights: 2979, 3001, 3017, 3068, 3084, 3123) was activated by mite feeding and their levels were significantly elevated compared to the control after 5 and 21 days of infestation. Specific cyclotides may affect mites by being indigestible or through direct interaction with cells in the mite digestive tract and reproductive organs. A group of particular peptides in V. odorata appears to be involved in defense response against herbivores.
Maternal age and maternal environment affect egg composition, yolk testosterone, offspring growth and behaviour in laying hens
Authors: Widowski Tina M. , Cooley Leanne , Hendriksen Simone , Peixoto Mariana Roedel Lopez Vieira
Published: February 2022

Maternal effects have been reported to alter offspring phenotype in laying hens. In this study, we investigated the effects of maternal environment and maternal age on egg traits and offspring development and behaviour. For this, we ran two experiments. First (E1), commercial hybrid hens were reared either in aviary or barren brooding cages, then housed in aviary, conventional cages or furnished (enriched) cages, thus forming different maternal housing treatments. Hens from each treatment were inseminated at three ages, and measures of egg composition, yolk testosterone concentration and offspring’s development, anxiety and fearfulness were assessed. In experiment 2 (E2), maternal age effects on offspring's growth and behaviour were further investigated using fertile eggs from commercial breeder flocks at three different ages. Results from E1 showed that Old hens laid heavier eggs with less yolk testosterone and produced offspring with fewer indicators of anxiety and fearfulness. Maternal rearing and housing affected egg traits, offspring weight and behaviour, but not in a consistent way. Effects of maternal age were not replicated in E2, possibly due to differences in management or higher tolerance to maternal effects in commercial breeders. Overall, our research confirms that maternal age and maternal environment affects egg composition, with maternal age specifically affecting yolk testosterone concentration, which may mediate physical and behavioural effects in offspring.
Semantic segmentation of COVID-19 lesions with a multiscale dilated convolutional network
Authors: Zhang Jianxiong , Ding Xuefeng , Hu Dasha , Jiang Yuming
Published: February 2022

Automatic segmentation of infected lesions from computed tomography (CT) of COVID-19 patients is crucial for accurate diagnosis and follow-up assessment. The remaining challenges are the obvious scale difference between different types of COVID-19 lesions and the similarity between the lesions and normal tissues. This work aims to segment lesions of different scales and lesion boundaries correctly by utilizing multiscale and multilevel features. A novel multiscale dilated convolutional network (MSDC-Net) is proposed against the scale difference of lesions and the low contrast between lesions and normal tissues in CT images. In our MSDC-Net, we propose a multiscale feature capture block (MSFCB) to effectively capture multiscale features for better segmentation of lesions at different scales. Furthermore, a multilevel feature aggregate (MLFA) module is proposed to reduce the information loss in the downsampling process. Experiments on the publicly available COVID-19 CT Segmentation dataset demonstrate that the proposed MSDC-Net is superior to other existing methods in segmenting lesion boundaries and large, medium, and small lesions, and achieves the best results in Dice similarity coefficient, sensitivity and mean intersection-over-union (mIoU) scores of 82.4%, 81.1% and 78.2%, respectively. Compared with other methods, the proposed model has an average improvement of 10.6% and 11.8% on Dice and mIoU. Compared with the existing methods, our network achieves more accurate segmentation of lesions at various scales and lesion boundaries, which will facilitate further clinical analysis. In the future, we consider integrating the automatic detection and segmentation of COVID-19, and conduct research on the automatic diagnosis system of COVID-19.
Cyber-physical defense in the quantum Era
Authors: Barbeau Michel , Garcia-Alfaro Joaquin
Published: February 2022

Networked-Control Systems (NCSs), a type of cyber-physical systems, consist of tightly integrated computing, communication and control technologies. While being very flexible environments, they are vulnerable to computing and networking attacks. Recent NCSs hacking incidents had major impact. They call for more research on cyber-physical security. Fears about the use of quantum computing to break current cryptosystems make matters worse. While the quantum threat motivated the creation of new disciplines to handle the issue, such as post-quantum cryptography, other fields have overlooked the existence of quantum-enabled adversaries. This is the case of cyber-physical defense research, a distinct but complementary discipline to cyber-physical protection. Cyber-physical defense refers to the capability to detect and react in response to cyber-physical attacks. Concretely, it involves the integration of mechanisms to identify adverse events and prepare response plans, during and after incidents occur. In this paper, we assume that the eventually available quantum computer will provide an advantage to adversaries against defenders, unless they also adopt this technology. We envision the necessity for a paradigm shift, where an increase of adversarial resources because of quantum supremacy does not translate into a higher likelihood of disruptions. Consistently with current system design practices in other areas, such as the use of artificial intelligence for the reinforcement of attack detection tools, we outline a vision for next generation cyber-physical defense layers leveraging ideas from quantum computing and machine learning. Through an example, we show that defenders of NCSs can learn and improve their strategies to anticipate and recover from attacks.
Socio-semantic networks as mutualistic networks
Authors: St-Onge Jonathan , Renaud-Desjardins Louis , Mongeau Pierre , Saint-Charles Johanne
Published: February 2022

Several studies have shown that discourse and social relationships are intertwined and co-evolve. However, we lack theoretical models to explain the phenomenon. Inspired by recent work in ecology, we propose to model socio-semantic networks as an interaction between two intermingled data generating processes: a social community process and a document-based process. We consider the link between semantic and social ties as analogous to the interactions found in pollination networks whereby agents visit hidden topics in a similar way that insects visit specific plants for pollination. We use the ENRON socio-semantic email network to investigate if it exhibits properties that characterize mutualistic networks, namely moderate connectance, heterogeneous degree distribution, moderate modularity and high nestedness. To do so, we build a plant-pollinator matrix where “insect species” are communities detected via block modelling, “plant species” are latent topics detected with topic modelling, and the interaction between the two is the total number of visits a community makes to specific topics. Our results show that the ENRON socio-semantic interaction matrix respects the aforementioned criteria of mutualism paving the way for the development of a relevant framework to better understand the dynamic of human socio-semantic interactions.
Olfactory responses of Trissolcus mitsukurii to plants attacked by target and non-target stink bugs suggest low risk for biological control
Authors: Rondoni Gabriele , Chierici Elena , Giovannini Lucrezia , Sabbatini-Peverieri Giuseppino , Roversi Pio Federico , Conti Eric
Published: February 2022

In crop systems, successful management of invasive insect herbivores can be achieved through the introduction of exotic biocontrol agents, parasitoids or predators, having a coevolutionary history with the pest. To avert threats to local biodiversity, recent legislations require a risk assessment for the organism to be released. Evaluation of its ability to exploit, for host location, odours associated with target and non-target species is crucial for a better definition of its ecological host range. Using Y-tube olfactometer bioassays in a quarantine laboratory, we investigated the ability of the Asian egg parasitoid Trissolcus mitsukurii (Hymenoptera: Scelionidae) to exploit odours associated with the global invader Halyomorpha halys (Hemiptera: Pentatomidae) and with non-target stink bugs native to Southern Europe. We demonstrated that T. mitsukurii is attracted by plants exposed to feeding and egg deposition of the coevolved H. halys and the native Nezara viridula, while it is not attracted by physogastric (gravid) females or eggs alone. Remarkably, T. mitsukurii is repelled by plants bearing eggs of the beneficial Arma custos. Our results contribute to a more thorough and nuanced assessment of the potential non-target risks in the case of mass-release of parasitoids as part of a biological control programme for invasive stink bugs.
Magnetoencephalography detects phase-amplitude coupling in Parkinson’s disease
Authors: Tanaka Masataka , Yanagisawa Takufumi , Fukuma Ryohei , Tani Naoki , Oshino Satoru , Mihara Masahito , Hattori Noriaki , Kajiyama Yuta , Hashimoto Ryota , Ikeda Manabu , Mochizuki Hideki , Kishima Haruhiko
Published: February 2022

To characterize Parkinson’s disease, abnormal phase-amplitude coupling is assessed in the cortico-basal circuit using invasive recordings. It is unknown whether the same phenomenon might be found in regions other than the cortico-basal ganglia circuit. We hypothesized that using magnetoencephalography to assess phase-amplitude coupling in the whole brain can characterize Parkinson’s disease. We recorded resting-state magnetoencephalographic signals in patients with Parkinson’s disease and in healthy age- and sex-matched participants. We compared whole-brain signals from the two groups, evaluating the power spectra of 3 frequency bands (alpha, 8–12 Hz; beta, 13–25 Hz; gamma, 50–100 Hz) and the coupling between gamma amplitude and alpha or beta phases. Patients with Parkinson’s disease showed significant beta–gamma phase-amplitude coupling that was widely distributed in the sensorimotor, occipital, and temporal cortices; healthy participants showed such coupling only in parts of the somatosensory and temporal cortices. Moreover, beta- and gamma-band power differed significantly between participants in the two groups (P < 0.05). Finally, beta–gamma phase-amplitude coupling in the sensorimotor cortices correlated significantly with motor symptoms of Parkinson’s disease (P < 0.05); beta- and gamma-band power did not. We thus demonstrated that beta–gamma phase-amplitude coupling in the resting state characterizes Parkinson’s disease.
Diagnostic value of F-18 FDG PET/CT in fever or inflammation of unknown origin in a large single-center retrospective study
Authors: Weitzer Friedrich , Nazerani Hooshmand Tina , Pernthaler Birgit , Sorantin Erich , Aigner Reingard Maria
Published: February 2022

Cause determination is challenging in fever or inflammation of unknown origin (FUO/IUO) despite today’s diagnostic modalities. We evaluated the value of F-18 FDG PET/CT in an unselected patient collective. This retrospective nonrandomized single-center study enrolled 300 male and female patients with FUO/IUO. PET/CT findings were compared with final clinical outcomes to determine the sensitivity, specificity, clinical significance, etiological distribution of final diagnoses, impact on treatment, role of white-blood cell count (WBC), and C-reactive protein (CRP). In 54.0% (162/300) PET/CT was the decisive exanimation for establishing the final diagnosis, in 13.3% (40/300) the findings were equivocal and indecisive, in 3.3% (10/300) PET/CT findings were false positive, while in 29.3% (88/300) a normal F-18 FDG pattern was present. Statistical analysis showed a sensitivity of 80.2% and a specificity of 89.8% for the contribution of PET/CT to the final diagnosis. CRP levels and WBC were not associated with PET/CT outcome. PET/CT let to new treatment in 24.0% (72/300), treatment change in 18.0% (54/300), no treatment change in 49.6% (149/300), and in 8.3% (25/300) no data was available. Our study demonstrates the utility of F-18 FDG PET/CT for source finding in FUO/IUO if other diagnostic tools fail.
Lavender oil as eco-friendly alternative to protect wood against termites without negative effect on wood properties
Authors: Šimůnková Kristýna , Hýsek Štěpán , Reinprecht Ladislav , Šobotník Jan , Lišková Tereza , Pánek Miloš
Published: February 2022

Timber suffers from various biological damages. Recent efforts aim on nature-friendly sustainable technologies of wood protection to replace classical synthetic agents having usually negative impact on many non-target organisms including man. This research investigated the biocidal effectiveness of lavender oil (LO) in protecting the Norway spruce (Picea abies) wood against the termites Reticulitermes flavipes and the brown-rot fungus Rhodonia placenta. Following, selected physical characteristics of spruce wood treated with LO were evaluated: colour changes, roughness, surface wetting with water and surface free energy (SFE). Experiments showed that LO increased the resistance of spruce wood to termites nearly to the level of its treatment with commercial biocide based on trivalent boron and quaternary ammonium salt. The additional hydrophobic treatment of wood ensured its full termite-resistance even after artificial weathering in Xenotest and leaching in water according to EN 84, respectively. It shows a high potential of LO to protect wood against termites. Adversely, the effectiveness of 5% LO against rot was not sufficient. The colour of the oil-treated wood was preserved, its roughness increased slightly, and wetting and SFE led to a positive change, improving the adhesion of potentially applied coatings or adhesives for exterior exposures.
Automated recognition of the cricket batting backlift technique in video footage using deep learning architectures
Authors: Moodley Tevin , van der Haar Dustin , Noorbhai Habib
Published: February 2022

There have been limited studies demonstrating the validation of batting techniques in cricket using machine learning. This study demonstrates how the batting backlift technique in cricket can be automatically recognised in video footage and compares the performance of popular deep learning architectures, namely, AlexNet, Inception V3, Inception Resnet V2, and Xception. A dataset is created containing the lateral and straight backlift classes and assessed according to standard machine learning metrics. The architectures had similar performance with one false positive in the lateral class and a precision score of 100%, along with a recall score of 95%, and an f1-score of 98% for each architecture, respectively. The AlexNet architecture performed the worst out of the four architectures as it incorrectly classified four images that were supposed to be in the straight class. The architecture that is best suited for the problem domain is the Xception architecture with a loss of 0.03 and 98.2.5% accuracy, thus demonstrating its capability in differentiating between lateral and straight backlifts. This study provides a way forward in the automatic recognition of player patterns and motion capture, making it less challenging for sports scientists, biomechanists and video analysts working in the field.
Detection of Mycobacterium tuberculosis complex DNA in oronasal swabs from infected African buffaloes (Syncerus caffer)
Authors: Clarke Charlene , Cooper David V. , Miller Michele A. , Goosen Wynand J.
Published: February 2022

Mycobacterium bovis (M. bovis), a member of the Mycobacterium tuberculosis complex (MTBC), is the causative agent of bovine TB (bTB) in animals. Spread occurs through inhalation or ingestion of bacilli transmitted from infected individuals. Early and accurate detection of infected African buffaloes shedding M. bovis is essential for interrupting transmission. In this pilot study, we determined if MTBC DNA could be detected in M. bovis infected buffalo oronasal secretions using a molecular transport media (PrimeStore MTM) with oronasal swabs and a rapid qPCR assay (Xpert MTB/RIF Ultra). Bovine TB test-positive buffaloes were culled, then tissue samples and oronasal swabs collected post-mortem for mycobacterial culture and Ultra testing, respectively. The Ultra detected MTBC DNA in 5/12 swabs from M. bovis culture-confirmed buffaloes. Oronasal swabs from M. bovis negative buffaloes (n = 20) were negative on Ultra, indicating the high specificity of this test. This study showed that MTM can successfully preserve MTBC DNA in oronasal swabs. The proportion of MTBC positive oronasal swabs was higher than expected and suggests that the Ultra may be an additional method for identifying infected buffaloes. Further studies are needed to confirm the utility of the Ultra assay with oronasal swabs as an assay to evaluate possible MTBC shedding in buffaloes.
Dark-induced vertical growth of chemobrionic architectures in silver-based precipitating chemical gardens
Authors: Busupalli Balanagulu , Patel Vipul Kirtikumar
Published: February 2022

The light sensitivity of many silver compounds has restricted the observation of silver-based chemical gardens.