bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled acceleration of GeV electron beams in an all-optical plasma waveguide
Authors: Oubrerie Kosta , Leblanc Adrien , Kononenko Olena , Lahaye Ronan , Andriyash Igor A. , Gautier Julien , Goddet Jean-Philippe , Martelli Lorenzo , Tafzi Amar , Ta Phuoc Kim , Smartsev Slava , Thaury Cédric 
Published: June 2022

AbstractLaser-plasma accelerators (LPAs) produce electric fields of the order of 100 GV m−1, more than 1000 times larger than those produced by radio-frequency accelerators. These uniquely strong fields make LPAs a promising path to generate electron beams beyond the TeV, an important goal in high-energy physics. Yet, large electric fields are of little benefit if they are not maintained over a long distance. It is therefore of the utmost importance to guide the ultra-intense laser pulse that drives the accelerator. Reaching very high energies is equally useless if the properties of the electron beam change completely from shot to shot, due to the intrinsic lack of stability of the injection process. State-of-the-art laser-plasma accelerators can already address guiding and control challenges separately by tweaking the plasma structures. However, the production of beams that are simultaneously high quality and high energy has yet to be demonstrated. This paper presents a novel experiment, coupling laser-plasma waveguides and controlled injection techniques, facilitating the reliable and efficient acceleration of high-quality electron beams up to 1.1 GeV, from a 50 TW-class laser.
Up and down the spectrum: upconversion nanocrystal and semiconductor material fused into a single nanocomposite
Authors: Gorris Hans H. , Farka Zdeněk 
Published: June 2022

AbstractA nanocomposite consisting of a cubic EuSe semiconductor material grown on a hexagonal upconversion nanoparticle has overcome the crystal lattice mismatch that typically prevents the epitaxial growth of such heterogeneous nanocrystals. Eu3+ at the interface layer shows its characteristic red emission band both under UV excitation light due to energy transfer from the semiconductor and under NIR excitation light due to energy transfer after photon-upconversion. Data storage and security applications are suggested for this new nanocomposite.
Application of positron emission tomography in psychiatry—methodological developments and future directions
Authors: Cervenka Simon , Frick Andreas , Bodén Robert , Lubberink Mark 
Published: June 2022

AbstractMental disorders represent an increasing source of disability and high costs for societies globally. Molecular imaging techniques such as positron emission tomography (PET) represent powerful tools with the potential to advance knowledge regarding disease mechanisms, allowing the development of new treatment approaches. Thus far, most PET research on pathophysiology in psychiatric disorders has focused on the monoaminergic neurotransmission systems, and although a series of discoveries have been made, the results have not led to any material changes in clinical practice. We outline areas of methodological development that can address some of the important obstacles to fruitful progress. First, we point towards new radioligands and targets that can lead to the identification of processes upstream, or parallel to disturbances in monoaminergic systems. Second, we describe the development of new methods of PET data quantification and PET systems that may facilitate research in psychiatric populations. Third, we review the application of multimodal imaging that can link molecular imaging data to other aspects of brain function, thus deepening our understanding of disease processes. Fourth, we highlight the need to develop imaging study protocols to include longitudinal and interventional paradigms, as well as frameworks to assess dimensional symptoms such that the field can move beyond cross-sectional studies within current diagnostic boundaries. Particular effort should be paid to include also the most severely ill patients. Finally, we discuss the importance of harmonizing data collection and promoting data sharing to reach the desired sample sizes needed to fully capture the phenotype of psychiatric conditions.
Reconsidering the role of patriarchy in upholding female genital modifications: analysis of contemporary and pre-industrial societies
Authors: Gruenbaum Ellen , Earp Brian D. , Shweder Richard A. 
Published: June 2022

AbstractAccording to the World Health Organization (WHO), customary female genital modification practices common in parts of Africa, South and Southeast Asia, and the Middle East are inherently patriarchal: they reflect deep-rooted inequality between the sexes characterized by male dominance and constitute an extreme form of discrimination against women. However, scholars have noted that while many societies have genital modification rites only for boys, with no equivalent rite for girls, the inverse does not hold. Rather, almost all societies that practice ritual female genital modification also practice ritual male genital modification, often for comparable reasons on children of similar ages, with the female rites led by women and the male rites led by men. In contrast, then, to the situation for boys in various cultures, girls are not singled out for genital modification on account of their sex or gender; nor do the social meanings of the female rites necessarily reflect a lower status. In some cases, the women’s rite serves to promote female within-sex bonding and network building—as the men’s rite typically does for males—thereby counterbalancing gendered asymmetries in political power and weakening male dominance in certain spheres. In such cases, and to that extent, the female rites can be described as counter-patriarchal. Selective efforts to discourage female genital modifications may thus inadvertently undermine women-centered communal networks while leaving male bonding rites intact. Scholars and activists should not rely on misleading generalizations from the WHO about the relationship between genital cutting and the social positioning of women as compared to men. To illustrate the complexity of this relationship, we compare patterns of practice across contemporary societies while also highlighting anthropological data regarding pre-industrial societies. Regarding the latter, we find no association between the presence of a female initiation rite and a key aspect of patriarchy as it is classically understood, namely, social endorsement of a gendered double-standard regarding premarital sexual activity. We situate this finding within the broader literature and discuss potential implications.
Cas9-induced large deletions and small indels are controlled in a convergent fashion
Authors: Kosicki Michael , Allen Felicity , Steward Frances , Tomberg Kärt , Pan Yangyang , Bradley Allan 
Published: June 2022

AbstractRepair of Cas9-induced double-stranded breaks results primarily in formation of small insertions and deletions (indels), but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a library of clonal NGS-validated mouse embryonic stem cells deficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection gene Nbn and the microhomology-mediated end joining gene Polq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation.
An index of access to essential infrastructure to identify where physical distancing is impossible
Authors: Günther Isabel , Harttgen Kenneth , Seiler Johannes , Utzinger Jürg 
Published: June 2022

AbstractTo identify areas at highest risk of infectious disease transmission in Africa, we develop a physical distancing index (PDI) based on the share of households without access to private toilets, water, space, transportation, and communication technology and weight it with population density. Our results highlight that in addition to improving health systems, countries across Africa, especially in the western part of Africa, need to address the lack of essential domestic infrastructure. Missing infrastructure prevents societies from limiting the spread of communicable diseases by undermining the effectiveness of governmental regulations on physical distancing. We also provide high-resolution risk maps that show which regions are most limited in protecting themselves. We find considerable spatial heterogeneity of the PDI within countries and show that it is highly correlated with detected COVID-19 cases. Governments could pay specific attention to these areas to target limited resources more precisely to prevent disease transmission.
Automated detection and segmentation of non-small cell lung cancer computed tomography images
Authors: Primakov Sergey P. , Ibrahim Abdalla , van Timmeren Janita E. , Wu Guangyao , Keek Simon A. , Beuque Manon , Granzier Renée W. Y. , Lavrova Elizaveta , Scrivener Madeleine , Sanduleanu Sebastian , Kayan Esma , Halilaj Iva , Lenaers Anouk , Wu Jianlin , Monshouwer René , Geets Xavier , Gietema Hester A. , Hendriks Lizza E. L. , Morin Olivier , Jochems Arthur , Woodruff Henry C. , Lambin Philippe 
Published: June 2022

AbstractDetection and segmentation of abnormalities on medical images is highly important for patient management including diagnosis, radiotherapy, response evaluation, as well as for quantitative image research. We present a fully automated pipeline for the detection and volumetric segmentation of non-small cell lung cancer (NSCLC) developed and validated on 1328 thoracic CT scans from 8 institutions. Along with quantitative performance detailed by image slice thickness, tumor size, image interpretation difficulty, and tumor location, we report an in-silico prospective clinical trial, where we show that the proposed method is faster and more reproducible compared to the experts. Moreover, we demonstrate that on average, radiologists & radiation oncologists preferred automatic segmentations in 56% of the cases. Additionally, we evaluate the prognostic power of the automatic contours by applying RECIST criteria and measuring the tumor volumes. Segmentations by our method stratified patients into low and high survival groups with higher significance compared to those methods based on manual contours.
Tropical volcanism enhanced the East Asian summer monsoon during the last millennium
Authors: Liu Fei , Gao Chaochao , Chai Jing , Robock Alan , Wang Bin , Li Jinbao , Zhang Xu , Huang Gang , Dong Wenjie 
Published: June 2022

AbstractExtreme East Asian summer monsoon (EASM) rainfall frequently induces floods that threaten millions of people, and has been generally attributed to internal climate variability. In contrast to the hydrological weakening theory of volcanic eruptions, here we present convergent empirical and modeling evidence for significant intensification of EASM rainfall in response to strong tropical volcanic eruptions. Our multi-proxy analyses show a significantly increased EASM in the first summer after tropical eruptions from 1470 AD to the present, and the more frequent occurrence of El Niños in the first boreal winter after eruptions is necessary for the enhanced EASM. Model simulation ensembles show that a volcano-induced El Niño and the associated stronger than non-volcanic El Niño warm pool air-sea interaction intensify EASM precipitation, overwhelming volcanic-induced moisture deficiency. This work sheds light on the intertwined relationship between external forcing and internal climate variability and potential flood disasters resulting from tropical volcanic eruptions.
A longitudinal multi-scanner multimodal human neuroimaging dataset
Authors: Hawco Colin , Dickie Erin W. , Herman Gabrielle , Turner Jessica A. , Argyelan Miklos , Malhotra Anil K. , Buchanan Robert W. , Voineskos Aristotle N. 
Published: June 2022

AbstractHuman neuroimaging has led to an overwhelming amount of research into brain function in healthy and clinical populations. However, a better appreciation of the limitations of small sample studies has led to an increased number of multi-site, multi-scanner protocols to understand human brain function. As part of a multi-site project examining social cognition in schizophrenia, a group of “travelling human phantoms” had structural T1, diffusion, and resting-state functional MRIs obtained annually at each of three sites. Scan protocols were carefully harmonized across sites prior to the study. Due to scanner upgrades at each site (all sites acquired PRISMA MRIs during the study) and one participant being replaced, the end result was 30 MRI scans across 4 people, 6 MRIs, and 4 years. This dataset includes multiple neuroimaging modalities and repeated scans across six MRIs. It can be used to evaluate differences across scanners, consistency of pipeline outputs, or test multi-scanner harmonization approaches.
Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features
Authors: Sayah Anousheh , Bencheqroun Camelia , Bhuvaneshwar Krithika , Belouali Anas , Bakas Spyridon , Sako Chiharu , Davatzikos Christos , Alaoui Adil , Madhavan Subha , Gusev Yuriy 
Published: June 2022

AbstractMalignancy of the brain and CNS is unfortunately a common diagnosis. A large subset of these lesions tends to be high grade tumors which portend poor prognoses and low survival rates, and are estimated to be the tenth leading cause of death worldwide. The complex nature of the brain tissue environment in which these lesions arise offers a rich opportunity for translational research. Magnetic Resonance Imaging (MRI) can provide a comprehensive view of the abnormal regions in the brain, therefore, its applications in the translational brain cancer research is considered essential for the diagnosis and monitoring of disease. Recent years has seen rapid growth in the field of radiogenomics, especially in cancer, and scientists have been able to successfully integrate the quantitative data extracted from medical images (also known as radiomics) with genomics to answer new and clinically relevant questions. In this paper, we took raw MRI scans from the REMBRANDT data collection from public domain, and performed volumetric segmentation to identify subregions of the brain. Radiomic features were then extracted to represent the MRIs in a quantitative yet summarized format. This resulting dataset now enables further biomedical and integrative data analysis, and is being made public via the NeuroImaging Tools & Resources Collaboratory (NITRC) repository (https://www.nitrc.org/projects/rembrandt_brain/).
Genotypic and tissue-specific variation of Populus nigra transcriptome profiles in response to drought
Authors: Eckert Christian , Wildhagen Henning , Paulo Maria João , Scalabrin Simone , Ballauff Johannes , Schnabel Sabine K. , Vendramin Vera , Keurentjes Joost J. B. , Bogeat-Triboulot Marie-Béatrice , Taylor Gail , Polle Andrea 
Published: June 2022

AbstractClimate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis.
Rough backs: taxonomic value of epicuticular sculpturing in the genus Milnesium Doyère, 1840 (Tardigrada: Apochela)
Authors: Morek Witold , Wałach Karol , Michalczyk Łukasz 
Published: June 2022

AbstractThe phylum Tardigrada comprises ~ 1400 described species that inhabit a wide range of ecosystems throughout the globe. Tardigrades are generally considered taxonomically challenging due to a strongly limited number of taxonomically informative morphological traits and microscopic size. Of all tardigrade groups, the taxonomy of Milnesium Doyère, 1840 is particularly difficult because in comparison with most other eutardigrades, the genus lacks the taxonomically informative egg shell ornamentation and/or placoids in the muscle pharynx. Therefore, any new morphological traits that could be used in species delineation and identification are priceless. In this contribution, we review and evaluate taxonomic value of the dorsal cuticle morphology. Specifically, by means of experimental taxonomy, we demonstrate the first extreme case of ontogenetic variability in dorsal epicuticle sculpturing using a new species from Portugal, Milnesium decorumsp. nov. Furthermore, we verify the existence of dorsal gibbosities in Milnesium reticulatum Pilato, Binda, Lisi, 2002, the only species of the genus allegedly exhibiting these structures. Finally, we provide a diagnostic key to the Milnesium granulatum morphogroup.
A multicentre cross-sectional survey study on acute wound classification in the emergency department and its interobserver variability
Authors: van Gennip Lisanne , Haverkamp Frederike J. C. , Sir Özcan , Tan Edward C. T. H. 
Published: June 2022

AbstractAnnually, a vast number of patients visits the emergency department for acute wounds. Many wound classification systems exist, but often these were not originally designed for acute wounds. This study aimed to assess the most frequently used classifications for acute wounds in the Netherlands and the interobserver variability of the Gustilo Anderson wound classification (GAWC) and Red Cross wound classification (RCWC) in acute wounds. This multicentre cross-sectional survey study employed an online oral questionnaire. We contacted emergency physicians from eleven hospitals in the south-eastern part of the Netherlands and identified the currently applied classifications. Participants classified ten fictitious wounds by applying the GAWC and RCWC. Afterwards, they rated the user-friendliness of these classifications. We examined the interobserver variability of both classifications using a Fleiss’ kappa analysis, with a subdivision in RCWC grades and types representing wound severity and injured tissue structures. The study included twenty emergency physicians from eight hospitals. Fifty percent of the participants reported using a classification for acute wounds, mostly the GAWC. The interobserver variability of the GAWC (κ = 0.46; 95% CI 0.44–0.49) and RCWC grades (κ = 0.56; 95% CI 0.53–0.59) was moderate, and it was good for the RCWC types (κ = 0.69; 95% CI 0.66–0.73). Participants considered both classifications helpful for acute wound assessment when the emergency physician was less experienced, despite a moderate user-friendliness. The GAWC was only of additional value in wounds with fractures, whereas the RCWC’s additional value in acute wound assessment was independent of the presence of a fracture. Emergency physicians are reserved to use a classification for acute wound assessment. The interobserver variability of the GAWC and RCWC in acute wounds is promising, and both classifications are easy to apply. However, their user-friendliness is moderate. It is recommended to apply the GAWC to acute wounds with underlying fractures and the RCWC to major traumatic injuries. Awareness should be raised of existing wound classifications, specifically among less experienced healthcare professionals.
Radiomics-based machine learning models to distinguish between metastatic and healthy bone using lesion-center-based geometric regions of interest
Authors: Naseri Hossein , Skamene Sonia , Tolba Marwan , Faye Mame Daro , Ramia Paul , Khriguian Julia , Patrick Haley , Andrade Hernandez Aixa X. , David Marc , Kildea John 
Published: June 2022

AbstractRadiomics-based machine learning classifiers have shown potential for detecting bone metastases (BM) and for evaluating BM response to radiotherapy (RT). However, current radiomics models require large datasets of images with expert-segmented 3D regions of interest (ROIs). Full ROI segmentation is time consuming and oncologists often outline just RT treatment fields in clinical practice. This presents a challenge for real-world radiomics research. As such, a method that simplifies BM identification but does not compromise the power of radiomics is needed. The objective of this study was to investigate the feasibility of radiomics models for BM detection using lesion-center-based geometric ROIs. The planning-CT images of 170 patients with non-metastatic lung cancer and 189 patients with spinal BM were used. The point locations of 631 BM and 674 healthy bone (HB) regions were identified by experts. ROIs with various geometric shapes were centered and automatically delineated on the identified locations, and 107 radiomics features were extracted. Various feature selection methods and machine learning classifiers were evaluated. Our point-based radiomics pipeline was successful in differentiating BM from HB. Lesion-center-based segmentation approach greatly simplifies the process of preparing images for use in radiomics studies and avoids the bottleneck of full ROI segmentation.