bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of point spread function higher moments error on weak gravitational lensing – II. A comprehensive study
Authors: Zhang Tianqing , Almoubayyed Husni , Mandelbaum Rachel , Meyers Joshua E , Jarvis Mike , Kannawadi Arun , Schmitz Morgan A , Guinot Axel ,   The LSST Dark Energy Science Collaboration
Published: November 2022

Weak lensing is one of the most powerful probes for dark matter and dark energy science, although it faces increasing challenges in controlling systematic uncertainties as the statistical errors become smaller. The point spread function (PSF) needs to be precisely modeled to avoid systematic error on the weak lensing measurements. The weak lensing biases induced by errors in the PSF model second moments, i.e. its size and shape, are well-studied. However, Zhang et al. showed that errors in the higher moments of the PSF may also be a significant source of systematics for upcoming weak lensing surveys. Therefore, this work comprehensively investigate the modelling quality of PSF moments from the 3rd to 6th order, and propagate the PSFEx higher moments modelling error in the HSC survey data set to the weak lensing shear–shear correlation functions and their cosmological analyses. The overall multiplicative shear bias associated with errors in PSF higher moments can cause an ∼0.1σ shift on the cosmological parameters for LSST Y10, while the associated additive biases can induce 1σ uncertainties in cosmology parameter inference for LSST Y10, if not accounted. We compare the PSFEx model with PSF in Full FOV, and find similar performance in modelling the PSF higher moments. We conclude that PSF higher moment errors of the future PSF models should be reduced from those in current methods, otherwise needed to be explicitly modeled in the weak lensing analysis.
Searching for the extra-tidal stars of globular clusters using high-dimensional analysis and a core particle spray code
Authors: Grondin Steffani M , Webb Jeremy J , Leigh Nathan W C , Speagle(沈佳士) Joshua S , Khalifeh Reem J
Published: November 2022

Three-body interactions can eject stars from the core of a globular cluster, causing them to enter the Galactic halo as extra-tidal stars. While finding extra-tidal stars is imperative for understanding cluster evolution, connecting isolated extra-tidal field stars back to their birth cluster is extremely difficult. In this work, we present a new methodology consisting of high-dimensional data analysis and a particle spray code to identify extra-tidal stars of any Galactic globular cluster using M3 as a case study. Using the t-Stochastic Neighbour Embedding and Uniform Manifold Approximation and Projection machine learning dimensionality reduction algorithms, we first identify a set of 103 extra-tidal candidates in the APOGEE DR17 data catalogue with chemical abundances similar to M3 stars. To confirm each candidate’s extra-tidal nature, we introduce corespray – a new python-based three-body particle spray code that simulates extra-tidal stars for any Galactic globular cluster. Using Gaia EDR3 proper motions and APOGEE DR17 radial velocities, we apply multivariate Gaussian modelling and an extreme deconvolution to identify the extra-tidal candidates that are more likely to be associated with a distribution of corespray-simulated M3 extra-tidal stars than the field. Through these methods, we identify 10 new high-probability extra-tidal stars produced via three-body interactions in M3. We also explore whether any of our extra-tidal candidates are consistent with being ejected from M3 through different dynamical processes. Future applications of corespray will yield better understandings of core dynamics, star formation histories, and binary fractions in globular clusters.
The white dwarf binary pathways survey - IX. Three long period white dwarf plus subgiant binaries
Authors: Parsons S G , Hernandez M S , Toloza O , Zorotovic M , Schreiber M R , Gänsicke B T , Lagos F , Raddi R , Rebassa-Mansergas A , Ren J J , Koester D
Published: November 2022

Virtually all binaries consisting of a white dwarf with a non-degenerate companion can be classified as either close post-interaction systems (with orbital periods of a few days or less), or wide systems (with periods longer than decades), in which both components have effectively evolved as single stars. Binaries with periods between these two extremes can help constrain common envelope efficiency, or highlight alternative pathways towards the creation of compact binaries. To date such binaries have remained mostly elusive. Here we present three white dwarfs in binaries with evolved subgiant stars with orbital periods of 41, 52, and 461 d. Using Hubble Space Telescope spectroscopy we find that all three systems contain low mass white dwarfs (≤0.4 M⊙). One system, TYC 8394−1331−1, is the inner binary of a hierarchical triple, where the white dwarf plus subgiant binary is orbited by a more distant companion star. These binaries were likely formed from a phase of stable but non-conservative mass transfer, as opposed to common envelope evolution. All three systems will undergo a common envelope phase in the future, but the two shorter period systems are expected to merge during this event, while the longest period system is likely to survive and create a close binary with two low mass white dwarfs.
Markhor-derived Introgression of a Genomic Region EncompassingPAPSS2Confers High-altitude Adaptability in Tibetan Goats
Authors: Li Chao , Wu Yujiang , Chen Bingchun , Cai Yudong , Guo Jiazhong , Leonard Alexander S , Kalds Peter , Zhou Shiwei , Zhang Jingchen , Zhou Ping , Gan Shangqu , Jia Ting , Pu Tianchun , Suo Langda , Li Yan , Zhang Ke , Li Lan , Purevdorj Myagmarsuren , Wang Xihong , Li Ming , Wang Yu , Liu Yao , Huang Shuhong , Sonstegard Tad , Wang Ming-Shan , Kemp Stephen , Pausch Hubert , Chen Yulin , Han Jian-Lin , Jiang Yu , Wang Xiaolong
Published: November 2022

Understanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high > 3000 m above sea level and low < 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3′-phosphoadenosine 5′-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10−25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.
Asian Corn Borer (Ostrinia furnacalis) Infestation Increases Fusarium verticillioides Infection and Fumonisin Contamination in Maize and Reduces the Yield
Authors: Li Qincheng , Shi Jie , Huang Chaolong , Guo Jingfei , He Kanglai , Wang Zhenying
Published: November 2022

Field trials based on manual infestation of the Asian corn borer (ACB) (Ostrinia furnacalis [Guenée]) and Fusarium verticillioides (Nirenberg) atomization were conducted on four maize hybrids to investigate the relationship between ACB infestation and F. verticillioides infection, yield loss, and fumonisin contamination in maize. Analysis of fumonisins B1 and B2 was carried out using an LC-MS/MS system. In this study, manual ACB infestation significantly promoted F. verticillioides infection (both symptomatic and symptomless) and grain fumonisin levels. Ear rot incidence and severity, symptomless kernel infection, and fumonisin contamination were significantly correlated to each other and to ACB damage severity. Manual ACB infestation increased fumonisin levels from 580 to 4,418 µg/kg in 2018; 6,059 to 10,681 µg/kg in 2019 spring-sown maize (2019A); and 2,042 to 5,060 µg/kg in 2019 summer-sown maize (2019B), with the threshold of the European Union (EU) being 4,000 µg/kg. The threshold was exceeded in spring of 2019 in untreated controls. Regarding yield, significant negative correlation between ACB damage and ear weight was observed in three seasons. These results indicated that ACB infestation can lead to severe quality degradation and yield loss of maize. Kernel fumonisin levels may exceed the concentration threshold of the EU in certain conditions, threatening the health of livestock and humans. Measures should be taken to reduce ACB infestation to ensure food and feed security.
Survivals following discontinuation of PD-1 inhibitor treatment in advanced melanoma patients
Authors: Kartolo Adi , Tong Justin , Yeung Cynthia , Kuksis Markus , Hopman Wilma , Baetz Tara
Published: November 2022

The aim of this study was to evaluate overall survival post-treatment discontinuation survival (OSPTD) in advanced melanoma patients started on immunotherapy. This retrospective study included all unresectable advanced or metastatic melanoma patients who had permanent treatment discontinuation after receiving at least one cycle of palliative-intent programmed death-1 ± cytotoxic T-lymphocyte associated protein-4 inhibitor treatment from 2014 to 2019. Indications of permanent treatment discontinuation included treatment completion, toxicity or progression. OSPTD was defined as a time of permanent treatment discontinuation to the time of death. Our study (N = 96) had 27, 12 and 57 patients who discontinued PD-1 inhibitor treatment due to treatment completion, toxicity and progression, respectively. Median treatment durations received for the treatment completion, toxicity and progression groups were 24, 6 and 3 months, respectively. As expected those patients who had disease progression on immunotherapy had very poor survival compared to those that completed treatment or stopped due to toxicity. A multivariable Cox model excluding the patients who progressed indicated no significant OSPTD differences between the toxicity and treatment completion group (HR, 0.894; 95% CI, 0.232–3.449; P = 0.871) who received single or dual immunotherapy. Our real-world study highlighted similar, durable survival at PD-1 inhibitor discontinuation due to either toxicity or treatment completion, despite longer treatment duration received in the completion group than toxicity group. Patients with progression on PD-1 inhibitor treatment have very poor survival. Our findings must be interpreted with caution due to its retrospective nature and small sample size.
Materials and Methods for Recruiting Systematically Marginalized Youth and Families for Weight-Management Intervention Trials
Authors: Hardin Heather K. , Bender Anna E. , Killion Cheryl M. , Moore Shirley M.
Published: November 2022

Rates of overweight and obesity are problematic among systematically marginalized youth; however, these youth and their families are a hard-to-reach research population. The purpose of our study was to identify facilitators and barriers for recruiting systematically marginalized families in youth weight-management intervention research. This study built upon existing evidence through involvement of youth, parents, community agency workers, and school nurses, and an exploration of both recruitment materials and processes. Seven focus groups were conducted with 48 participants from 4 stakeholder groups (youth, parents, school nurses, and community agency workers). A codebook approach to thematic analysis was used to identify key facilitator and barrier themes related to recruitment materials and processes across the stakeholder groups. Ecological systems theory was applied to contextualize the facilitators and barriers identified. Participants reported the need to actively recruit youth in the study through engaging, fun recruitment materials and processes. Participants reported greater interest in recruitment at community-based events, as compared to recruitment through health care providers, underscoring the depth of distrust that this sample group has for the health care system. Recommendations for recruitment materials and processes for weight-management intervention research with systematically marginalized families are proposed.
Socioeconomic status does not change decision-making in the treatment of distal radius fractures at a level 1 trauma center
Authors: Verlinsky Luke , Ulmer Clinton J. , Griffin Leah P. , Brady Christina I. , Rose Ryan A.
Published: November 2022

Objectives:

To compare operative rates, total hospital charges, and length of stay between different socioeconomic cohorts in treating distal radius fractures (DRFs).

Design:

A retrospective cohort study.

Setting:

Large public level 1 trauma center.

Patients:

A retrospective search of all trauma activations over a 7-year period (2013–2020) yielded 816 adult patients diagnosed with DRF. Patients were separated into cohorts of socioeconomic status based on 2010 US Census data and insurance status.

Intervention:

DRFs were treated either nonoperatively using closed reduction and splinting or operatively using open reduction and internal fixation, closed reduction percutaneous pinning, or external fixator application.

Main Outcome Measurements:

Operative rates of DRF, total hospital charges, and length of stay.

Results:

Patients who were uninsured or in the low-income socioeconomic cohort had no significant difference in operative rates, total hospital costs, or length of stay when compared with their respective insured or standard income groups. Younger patients and those with OTA/AO type C, bilateral, or open DRFs were more likely to undergo operative intervention.

Conclusions:

This study demonstrates that low socioeconomic status based on annual household income and insurance status was not associated with differences in operative rates on DRFs, length of stay, or total hospital charges. These results suggest that outcome disparities between groups may be caused by postoperative differences rather than treatment decision-making. Although this study investigates access to surgical care at a publicly funded level 1 trauma center, disparities may still exist in other models of care.

Level of Evidence:

Prognostic Level III.
Activating de novo monoallelic variants causing inborn errors of immunity in two unrelated children born of HIV-seroconcordant couples
Authors: Lugo Reyes Saul O. , Solórzano Suárez Andrea , Scheffler Mendoza Selma C. , Xóchihua Díaz Luis , González Serrano M. Edith , López Herrera Gabriela , Medina-Torres Edgar Alejandro , Cruz Ugalde Claudia I. , Olguín-Calderón Diana , Berrón Ruiz Laura , Espinosa-Padilla Sara E. , Yamazaki-Nakashimada Marco Antonio , Murata Chiharu
Published: November 2022

Introduction:

Around 20% of all inborn errors of immunity (IEI) are autosomal dominant or monoallelic, either by haploinsufficiency, negative dominance, or gain of function (GOF). GOF phenotypes usually include autoinflammation, autoimmunity, lymphoproliferation, allergies, and some infections.

Case series:

We describe the cases of two unrelated patients born of HIV-seroconcordant parents. Both patients are HIV-negative but carry de novo GOF missense variants that resulted in inflammatory lymphoproliferative IEI diseases: signal transducer and activator of transcription 3 (STAT3)-GOF and phosphatidylinositol 3-kinase, catalytic delta (PIK3CD)-GOF. Both variants were found through whole-exome sequencing and confirmed by Sanger.

An 11-year-old male with recurrent sinopulmonary infections, dysmorphism, growth delay, bronchiectasis, and mild mental retardation, as well as lymphopenia, thrombocytopenia, and high immunoglobulin M. Both his parents were known to be HIV-positive under anti-retroviral treatment. HIV infection was repeatedly ruled out in the patient, whom through whole-exome sequencing was found to have a heterozygous missense variant in exon 24 of PIK3CD, a hotspot transition, and the most reported variant in PIK3CD-GOF patients.

A 6-year-old male with autoimmune hemolytic anemia, lymphoproliferation, short stature, and intractable diarrhea. Both his parents were found to be HIV-positive. HIV was repeatedly ruled out in the patient by ELISA and viral load. He was found to have a heterozygous missense/splice variant in exon 22 of STAT3, a hotspot transition, and the most reported variant in STAT3-GOF patients.

Discussion:

The AID/APOBEC3 A-H family of proteins are cytidine deaminases that induce G>A hypermutation in both the invading viral DNA and the host genome, which results in stop codons inside the endogenized retroviral sequence. Both variants found in our patients are G to A transitions. Retroviral infection might thus have resulted in host genome instability, and our patients’ rare congenital diseases are the unfortunate consequence of somatic hypermutation in one of their parents’ gametes.
Fish can infer relations between colour cues in a non-social learning task
Authors: La Loggia Océane , Rüfenacht Angélique , Taborsky Barbara
Published: November 2022

Transitive inference (TI) describes the ability to infer relationships between stimuli that have never been seen together before. Social cichlids can use TI in a social setting where observers assess dominance status after witnessing contests between different dyads of conspecifics. If cognitive processes are domain-general, animals should use abilities evolved in a social context also in a non-social context. Therefore, if TI is domain-general in fish, social fish should also be able to use TI in non-social tasks. Here we tested whether the cooperatively breeding cichlidNeolamprologus pulchercan infer transitive relationships between artificial stimuli in a non-social context. We used an associative learning paradigm where the fish received a food reward when correctly solving a colour discrimination task. Eleven of 12 subjects chose the predicted outcome for TI in the first test trial and five subjects performed with 100% accuracy in six successive test trials. We found no evidence that the fish solved the TI task by value transfer. Our findings show that fish also use TI in non-social tasks with artificial stimuli, thus generalizing past results reported in a social context and hinting toward a domain-general cognitive mechanism.
‘The correct name for the breadfruit’: on interdisciplinarity and the artist Sydney Parkinson's contested contributions to the botanical sciences
Authors: Fielding Russell
Published: November 2022

Breadfruit is a tropical fruit-bearing tree native to Oceania and a staple food in the diets of many Pacific Islander communities. During the so-called Age of Discovery, several European voyages returned from the Pacific with descriptions of the region's flora, including breadfruit. Since that time, scientists have sometimes struggled to agree upon an adequate acknowledgement of those early descriptions in modern botany and taxonomy. This paper considers one such struggle: the centuries-long disagreement among botanists regarding the value of the botanical descriptions and illustrations of breadfruit, as well as the proposed scientific name for the species attributed to Sydney Parkinson, a young artist who sailed with Cook aboard HMS
Endeavour
during the late eighteenth century. While Parkinson's descriptions were thorough, it is suggested here that his contributions were neglected by later scientists, due mainly to his status as an artist and to an approach that today we would call
interdisciplinary
. This outcome can be viewed as indicative of the tension between the arts and the sciences that remains to this day and, I suggest, continues to hamper our understanding of the natural world.
Using conditional Generative Adversarial Networks (GAN) to generatede novosynthetic cell nuclei for training machine learning-based image segmentation
Authors: Cosacak Mehmet Ilyas , Kizil Caghan
Published: November 2022

Generating masks on training data for augmenting machine learning is one of the challenges as it is time-consuming when performed manually. While variable random images can be generated by Generative Adversarial Networks, an image-to-image translation is needed to generate both images and ground truth data. To generate cells and their corresponding masks, we used a new approach to prepare the training data by adding masks on 4 different channels preventing any overlapping between masks on the same channel at an exactly 2-pixel distance. We used GAN to generate nuclei from only two images (415 and 435 nuclei) and tested different GANs with alternating activation functions and kernel sizes. Here, we provide the proof-of-principle application of GAN for image-to-image translation for cell nuclei and tested variable parameters such as kernel and filter sizes and alternating activation functions, which played important roles in GAN learning with small datasets. This approach will decrease the time required to generate versatile training datasets for various cell types and shapes with their corresponding masks for augmenting machine learning-based image segmentation.
Personalized Deep Learning based Source Imaging Framework Improves the Imaging of Epileptic Sources from MEG Interictal Spikes
Authors: Sun Rui , Zhang Wenbo , Bagić Anto , He Bin
Published: November 2022

Electromagnetic source imaging (ESI) has been widely used to image brain activities for research and clinical applications from MEG and EEG. It is a challenging task due to the ill-posedness of the problem and the complexity of modeling the underlying brain dynamics. Deep learning has gained attention in the ESI field for its ability to model complex distributions and has successfully demonstrated improved imaging performance for ESI. In this work, we investigated the capability of imaging epileptic sources from MEG interictal spikes using deep learning-based source imaging framework (DeepSIF). A generic DeepSIF model was first trained with a generic head model using a template MRI. A fine-tuning procedure was proposed to introduce personalized head model information into the neural network for a personalized DeepSIF model. Two models were evaluated and compared in extensive computer simulations. The MEG-DeepSIF approach was further rigorously validated for imaging epileptogenic regions from interictal spike recordings in focal epilepsy patients. We demonstrated that DeepSIF can be successfully applied to MEG recordings and the additional fine-tuning step for personalized DeepSIF can alleviate the impact of head model variations and further improve the performance significantly. In a cohort of 29 drug-resistant focal epilepsy patients, the personalized DeepSIF model provided a sublobar concordance of 93%, sublobar sensitivity of 77% and specificity of 99%, respectively. When compared to the seizure-onset-zone defined by intracranial recordings, the localization error is 15.78 ± 5.54 mm; and when compared with resection volume in seizure free patients, the spatial dispersion is 8.19 ± 8.14 mm. DeepSIF enables an accurate and robust imaging of spatiotemporal brain dynamics from MEG recordings, suggesting its unique value to neuroscience research and clinical applications.
Towards One Health surveillance of antibiotic resistance, use and residues of antibiotics in France: characterisation and mapping of existing programmes in humans, animals, food and the environment
Authors: Collineau L. , Bourély C. , Rousset L. , Berger-Carbonne A. , Ploy MC. , Pulcini C. , Colomb-Cotinat M.
Published: November 2022

International organizations are calling for One Health approaches to tackle antibiotic resistance (ABR). In France, the diversity of surveillance programmes makes it difficult to get an overview of the current surveillance system and its level of integration. This study aimed to map and characterise all French surveillance programmes for ABR, antibiotic use (ABU) and antibiotic residues in humans, animals, food and the environment, to identify integration points, gaps and overlaps.

A literature review and interviews with 36 programme coordinators were conducted to identify and characterise programmes using a standardized grid (28 variables). Forty-eight programmes were included. They targeted the human (n=35), animal (n=12), food (n=3) and/or the environment (n=1); 35 programmes focused on ABR, 14 on ABU and two on antibiotic residues. Two programmes were cross-sectoral. Among the 35 ABR programmes, 23 collected bacterial isolates. Bacteria most targeted wereEscherichia coli(n=17 programmes),Klebsiella pneumoniae(n=13), andStaphylococcus aureus(n=12). ESBL-producingE. coliwas monitored by the majority of ABR programmes in humans, animals and food, and is a good candidate for integrated data analysis. ABU indicators were highly variable. Areas poorly covered were the environmental sector, overseas territories, ABR colonisation in humans and ABU in companion animals.

The French surveillance system appears rich and extensive, but with gaps and only few integration points. We believe this mapping will be of high interest to policy makers and surveillance stakeholders, and that our methodology may inspire other countries willing to progress towards One Health surveillance of ABR.
Establishing Internationally Accepted Conceptual and Operational Definitions of Social Prescribing Through Expert Consensus: A Delphi Study
Authors: Muhl Caitlin , Mulligan Kate , Bayoumi Imaan , Ashcroft Rachelle , Godfrey Christina
Published: November 2022

Introduction

With the social prescribing movement gaining traction globally, there is a need for an agreed definition of social prescribing. There are two types of definitions – conceptual and operational, meaning agreement on both types of definitions is needed.

Objective

The aim of this study was to establish internationally accepted conceptual and operational definitions of social prescribing.

Design

A three-round Delphi study was conducted.

Methods

Consensus was defineda priorias ≥80% agreement. In Round 1, participants were asked to list key elements that are essential to the conceptual definition of social prescribing and to provide corresponding statements that operationalize each of the key elements. In Round 2, participants were asked to rate their agreement with items from the first round for inclusion in the conceptual and/or operational definitions of social prescribing. Based on the findings from this round, the conceptual and operational definitions of social prescribing were developed, including long and short versions of the conceptual definition. In Round 3, participants were asked to rate their agreement with the conceptual and operational definitions of social prescribing.

Participants

This study involved an international, multidisciplinary panel of experts. The expert panel (n=48) represented 26 different countries across five continents, numerous expert groups, and a variety of years of experience with social prescribing, with the average being 5 years (range = 1-20 years).

Results

After three rounds, internationally accepted conceptual and operational definitions of social prescribing were established. The definitions were transformed into the Common Understanding of Social Prescribing (CUSP) conceptual framework.

Conclusion

This foundational work offers a common thread – a shared sense of what social prescribing is, which may be woven into social prescribing research, policy, and practice to foster common understanding of this concept.

STRENGTHS AND LIMITATIONS OF THIS STUDY

Strengths of this study include the consensus method that was chosen, the diversity and size of the expert panel, and the fact that consensus was defineda priorias ≥80% agreement

Limitations of this study include the fact that only those who could speak, read, and write English were eligible to participate in this study, the attrition of the expert panel, and the fact that the expert panel did not reach 100% agreement on the definitions
A new chapter of the Japanese beetle invasion saga: predicting suitability from long-infested areas to inform surveillance strategies in Europe
Authors: Borner Leyli , Martinetti Davide , Poggi Sylvain
Published: November 2022

The Japanese beetle (Popillia japonica) is a polyphagous pest that spreads rapidly and is estimated to cost more than 460 M$/year in damage and control in the USA alone. This study provides risk maps to inform surveillance strategies in Continental Europe, following the beetle’s introduction and successive spread in the last decade. We developed a species distribution model using a machine-learning algorithm, considering factors relevant to the beetle’s biology, climate, land use and human-related variables. This analysis was performed using presence-only data from native and invaded ranges (Japan, North America, Azores archipelago - Portugal). We gathered more than 30 000 presence data from citizen science platforms and standardized surveys, and generated pseudo-absences using the target-group method. We used the environmental structure of data to randomly sample pseudo-absences, and evaluate model performanceviaa block cross-validation strategy. Our results show that climate, in particular seasonal trends, and human-related variables, are major drivers of the Japanese beetle distribution at the global scale. Risk maps show that Central Europe can be considered as suitable, whereas Southern and Northern European countries are at lower risk. The region currently occupied is among the most suitable according to our predictions, and represents less than 1% of the highest suitable area in Europe. A major cluster of high suitability areas is located near the currently infested zone, whereas others are scattered across the continent. This highlights the importance of designing surveillance strategies considering both active insect dispersal and the possibility of hitchhiking to reach distant areas.
An adaptive interaction between cell type and metabolism drives ploidy evolution in a wild yeast
Authors: Crandall Johnathan G. , Fisher Kaitlin J. , Sato Trey K. , Hittinger Chris Todd
Published: November 2022

Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here we report an unusual recurrent ploidy reduction in replicate populations of the budding yeastSaccharomyces eubayanusexperimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.
Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination
Authors: Namias Alice , Sahlin Kristoffer , Makoundou Patrick , Bonnici Iago , Sicard Mathieu , Belkhir Khalid , Weill Mylène
Published: November 2022

This study developed a new bioinformatics pipeline to acquire all the different copies of multi-copy gene families based on Oxford Nanopore Technologies sequencing of PCR products. We used this pipeline to acquire the sequences of highly similar copies of thecidAandcidBgenes present in the genomes ofWolbachia pipientis(wPip) bacteria infecting the cells ofCulex pipiensmosquitoes. The approach is based on read mapping, SNP calling and haplotyping, using our already wide existing reference database for thecidgenes obtained by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants (or haplotypes). In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the pipeline through a combination of analyses of simulated reads and of gene sequence acquisitions through cloning and Sanger sequencing. For genes of which the haplotype cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants.
Wolverine density distribution reflects past persecution and current management in Scandinavia
Authors: Moqanaki Ehsan , Milleret Cyril , Dupont Pierre , Brøseth Henrik , Bischof Richard
Published: November 2022

After centuries of intense persecution, several large carnivore species in Europe and North America have experienced a rebound. Today’s spatial configuration of large carnivore populations has likely arisen from the interplay between their ecological traits and current environmental conditions, but also from their history of persecution and protection. Yet, due to the challenge of studying population-level phenomena, we are rarely able to disentangle and quantify the influence of past and present factors driving the spatial distribution and density of these controversial species. Using spatial capture-recapture models and a data set of 742 genetically identified wolverinesGulo gulocollected over ½ million km2across their entire range in Norway and Sweden, we identify landscape-level factors explaining the current population density of wolverines in the Scandinavian Peninsula. Distance from the relic range along the Swedish-Norwegian border, where the wolverine population survived a long history of persecution, remains a key determinant of wolverine density today. However, regional differences in management and environmental conditions also played an important role in shaping spatial patterns in present-day wolverine density. Specifically, we found evidence of slower recolonization in areas that had set lower wolverine population goals in terms of the desired number of annual reproductions. Management of transboundary large carnivore populations at biologically relevant scales may be inhibited by administrative fragmentation. Yet, as our study shows, population-level monitoring is an achievable prerequisite for a comprehensive understanding of the distribution and density of large carnivores across an increasingly anthropogenic landscape.
The repertoire of copy number alteration signatures in human cancer
Authors: Tao Ziyu , Wang Shixiang , Wu Chenxu , Wu Tao , Zhao Xiangyu , Ning Wei , Wang Guangshuai , Wang Jinyu , Chen Jing , Diao Kaixuan , Chen Fuxiang , Liu Xue-Song
Published: November 2022

Copy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and SNP array. The 14 signatures of CNA have been extracted from 2778 pan-cancer analysis of whole genomes (PCAWG) WGS samples, and further validated with 10851 the cancer genome atlas (TCGA) SNP array dataset. Novel patterns of CNA have been revealed through this study. The activities of some CNA signatures consistently predict cancer patients’ prognosis. This study provides a repertoire for understanding the signatures of CNA in cancer, with potential implications for cancer prognosis, evolution, and etiology.
CRitical Assessment of genomic COntamination detection at several Taxonomic ranks (CRACOT)
Authors: Cornet Luc , Lupo Valérian , Declerck Stéphane , Baurain Denis
Published: November 2022

Background

Genome contamination is a well-known issue in (meta)genomics. Although it has received a lot of attention, with an increasing number of detection tools made available over the years, no comparison between these tools exists in the literature.

Results

Here, we report the benchmarking of six of the most popular tools using a simulated framework. Our simulations were conducted on six different taxonomic ranks, from phylum to species. The analysis of the estimated contamination levels indicates that the precision of the tools is not good, often due to large overdetection but also underdetection, especially at the genus and species ranks. Furthermore, our results show that only redundant contamination is accurately estimated.

Conclusion

Our results indicate that using a combination of tools, including Kraken2, is necessary to estimate the contamination level accurately. We also provide a freely available contamination simulation framework, CRACOT, which may be useful for estimating the accuracy of future algorithms.
Taxonomic vs genomic fungi: contrasting evolutionary loss of protistan genomic heritage and emergence of fungal novelties
Authors: Merényi Zsolt , Krizsán Krisztina , Sahu Neha , Liu Xiao-Bin , Bálint Balázs , Stajich Jason , Spatafora Joseph W. , Nagy László G.
Published: November 2022

Fungi are among the most ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. However, despite intense interest in their origins, major genomic trends characterising the evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here, we reconstructed gene family evolution across 123 genomes of fungi and relatives and show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and highly episodic innovation via gene duplication. We find that the gene content of early-diverging fungi is protist-like in many respects, owing to the conservation of protist genes in early fungi. While gene loss has been constant and gradual during early fungal evolution, our reconstructions show that gene innovation showed two peaks. Gene groups with the largest contribution to genomic change included extracellular proteins, transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal evolution. Taken together, this work provided a highly resolved genome-wide catalogue of gene family changes across fungal evolution. This suggests that the genome of pre-fungal ancestors may have been transformed into the archetypal fungal genome by a combination of gradual gene loss, turnover and two large duplication events rather than by abrupt changes, and consequently, that the taxonomically defined fungal kingdom does not represent a genomically uniform assemblage of extant species characterized by diagnostic synapomorphies.
An open-access EEG dataset for speech decoding: Exploring the role of articulation and coarticulation
Authors: Moreira João Pedro Carvalho , Carvalho Vinícius Rezende , Mendes Eduardo Mazoni Andrade Marçal , Fallah Ariah , Sejnowski Terrence J. , Lainscsek Claudia , Comstock Lindy
Published: November 2022

Electroencephalography (EEG) holds promise for brain-computer interface (BCI) devices as a non-invasive measure of neural activity. With increased attention to EEG-based BCI systems, publicly available datasets that can represent the complex tasks required for naturalistic speech decoding are necessary to establish a common standard of performance within the BCI community. Effective solutions must overcome various kinds of noise in the EEG signal and remain reliable across sessions and subjects without overfitting to a specific dataset or task. We present two validated datasets (N=8 and N=16) for classification at the phoneme and word level and by the articulatory properties of phonemes. EEG signals were recorded from 64 channels while subjects listened to and repeated six consonants and five vowels. Individual phonemes were combined in different phonetic environments to produce coarticulated variation in forty consonant-vowel pairs, twenty real words, and twenty pseudowords. Phoneme pairs and words were presented during a control condition and during transcranial magnetic stimulation targeted to inhibit or augment the EEG signal associated with specific articulatory processes.
Legionella pneumophilamodulates host cytoskeleton by an effector of transglutaminase activity
Authors: Liu Yan , Liu Yao , Luo Zhao-Qing
Published: November 2022

The bacterial pathogenLegionella pneumophiladelivers more than 330 effector proteins into host cells through its Dot/Icm type IV secretion system (T4SS) to facilitate its intracellular replication. A number of these effectors modulate organelle trafficking pathways to create a membrane-bound niche called theLegionellacontaining vacuole (LCV). In this study, we found thatL. pneumophilainduces F-actin accumulation in host cell cortex by its Dot/Icm substrate RavJ (Lpg0944). RavJ harbors an C101H138D170motif associated with human tissue transglutaminases (TGs). We showed that RavJ catalyzes a covalent linkage between actin and the Motin family proteins Angiomotin (AMOT) and Angiomotin-like 1 (AMOTL1), proteins known to regulate tube formation and cell migration. Further study revealed that RavJ-induced crosslink between actin and AMOT occurs on its Gln354residue. Crosslink between actin and AMOT significantly reduces the binding between actin and its binding partner cofilin, suggesting that RavJ inhibits actin depolymerization. We also demonstrated that the metaeffector LegL1 directly interacts with RavJ to antagonize its transglutaminase activity, leading to reduced crosslink between actin and Motin proteins. Our results reveal a novel mechanism of modulating the host actin cytoskeleton byL. pneumophila.
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43
Authors: Lam Andy Y.W. , Tsuboyama Kotaro , Tadakuma Hisashi , Tomari Yukihide
Published: November 2022

Protein misfolding and aggregation are characteristic features of neurodegenerative diseases. While molecular chaperones are well-known suppressors of these aberrant events, we recently reported that highly disordered, hydrophilic and charged heat-resistant obscure (Hero) proteins may have similar effects. Specifically, Hero proteins can maintain the activity of other proteins from denaturing conditions in vitro, while their overexpression can suppress cellular aggregation and toxicity associated with aggregation-prone proteins. However, it is unclear how these protective effects are achieved. Here, we utilized single-molecule FRET to monitor the conformations of the aggregation-prone prion-like low complexity domain (LCD) of TAR DNA-binding protein 43 (TDP-43). While we observed high conformational heterogeneity in wild-type LCD, the ALS-associated mutation A315T promoted collapsed conformations. In contrast, an Hsp40 chaperone, DNAJA2, and a Hero protein, Hero11 stabilized extended states of the LCD, consistent with their ability to suppress the aggregation of TDP-43. Our results link single-molecule effects on conformation to macro effects on bulk aggregation, where a Hero protein, like a chaperone, can maintain the conformational integrity of a client protein to prevent its aggregation.
Learning to predict based on self- versus externally induced prediction violations: a direct comparison using a Bayesian inference modelling approach
Authors: Boonstra E.A. , Slagter H.A.
Published: November 2022

Predictive processing is quickly gaining ground as a theory of perception and attention. From this perspective the brain is cast as an organism’s predictive model of how its world works and will continue to work in the future. However, research on the brain’s predictive capacities remains beholden to traditional research practices in which participants are passively shown stimuli without their active involvement. The current study is an investigation into ways in which self-generated predictions may differ from externally induced predictions. Participants completed a volatile spatial attention task under both conditions on different days. We used the Hierarchical Gaussian Filter, an approximate Bayesian inference model, to determine subject-specific parameters of belief-updating and inferred volatility. We found preliminary evidence in support of self-generated predictions incurring a larger reaction time cost when violated compared to predictions induced by sensory cue, which translated to participants’ increased sensitivity to changes in environmental volatility. Our results suggest that internally generated predictions may be afforded more weight, but these results are complicated by session order and duration effects, as well as a lack of statistical power. We discuss the limitations of our study preventing us from replicating previous research, and ways to remedy these shortcomings in future studies.
Conscious perception and the role of the basal ganglia: preliminary findings from a deep brain stimulation study
Authors: Boonstra E.A. , Bais M.N. , van Schouwenburg M.R. , van den Munckhof P. , Smit D.J.A. , Denys D. , Slagter H.A.
Published: November 2022

Conscious perception is thought to depend on global amplification of sensory input. In recent years, the basal ganglia have been implicated in gating conscious access due to their consistent involvement in thalamocortical loops. However, much of the evidence implicating the basal ganglia in these processes in humans is correlational. The current study is a preliminary investigation in four patients to explore whether deep brain stimulation (DBS) in the basal ganglia might improve conscious perception. In our study, treatment-resistant obsessive-compulsive disorder (OCD) patients with a striatal DBS implant completed two canonical conscious perception tasks: emotion-induced blindness and backward masking. We found preliminary evidence in support of a role played by the basal ganglia in conscious perception at the behavioral level: patients performed better when stimulation was active, but we could not establish neural effects corresponding to these behavioral findings, possibly due to our small sample size. We discuss the potential implications and limitations of our study and delineate avenues for future research.