bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using causal methods to map symptoms to brain circuits in neurodevelopment disorders: moving from identifying correlates to developing treatments
Authors: Cohen Alexander Li 
Published: March 2022

AbstractA wide variety of model systems and experimental techniques can provide insight into the structure and function of the human brain in typical development and in neurodevelopmental disorders. Unfortunately, this work, whether based on manipulation of animal models or observational and correlational methods in humans, has a high attrition rate in translating scientific discovery into practicable treatments and therapies for neurodevelopmental disorders.With new computational and neuromodulatory approaches to interrogating brain networks, opportunities exist for “bedside-to bedside-translation” with a potentially shorter path to therapeutic options. Specifically, methods like lesion network mapping can identify brain networks involved in the generation of complex symptomatology, both from acute onset lesion-related symptoms and from focal developmental anomalies. Traditional neuroimaging can examine the generalizability of these findings to idiopathic populations, while non-invasive neuromodulation techniques such as transcranial magnetic stimulation provide the ability to do targeted activation or inhibition of these specific brain regions and networks. In parallel, real-time functional MRI neurofeedback also allow for endogenous neuromodulation of specific targets that may be out of reach for transcranial exogenous methods.Discovery of novel neuroanatomical circuits for transdiagnostic symptoms and neuroimaging-based endophenotypes may now be feasible for neurodevelopmental disorders using data from cohorts with focal brain anomalies. These novel circuits, after validation in large-scale highly characterized research cohorts and tested prospectively using noninvasive neuromodulation and neurofeedback techniques, may represent a new pathway for symptom-based targeted therapy.
Correspondence of uroflowmetry and voiding diary in evaluation of voiding volume in children with lower urinary tract dysfunction
Authors: Özçift Burak 
Published: March 2022

Abstract
Background
Objective assessment of voided volumes in children with lower urinary tract dysfunction is important. This study aimed to compare and evaluate voided volumes obtained from a 48-h voiding diary and uroflowmetry in children with lower urinary tract dysfunction.

Methods
In this retrospective cohort study, voided volumes obtained by 48-h voiding diary and contemporaneous uroflowmetry were compared in terms of age, sex, and the three most common subtypes of lower urinary tract dysfunction (monosymptomatic nocturnal enuresis, overactive bladder, and dysfunctional voiding) in children. Patients were stratified according to voided volume differences between uroflowmetry and 48-h voiding diary.

Results
A total of 242 children were included in the study. Maximum and average voided volumes in uroflowmetry were higher than those in 48-h voiding diaries in the entire population (P < 0.001). While there was a significant difference between maximum voided volume in the two methods when evaluating patients with overactive bladder and dysfunctional voiding, there was no significant difference in those with monosymptomatic nocturnal enuresis (P = 0.001, P = 0.030, P = 0.206, respectively). A significant difference was observed between the three subtypes of lower urinary tract dysfunction in voided volumes (P < 0.001). When maximum and average voided volumes were compared for age subgroups, there was no significant difference in maximum and mean voided volumes only in voiding diary measurements (P > 0.05). When the two methods were compared, there was a difference in maximum and average voided volumes of more than 30% of the estimated bladder capacity in 94 (38.9%) and 86 (34.3%) children, respectively.

Conclusions
Uroflowmetry and a 48-h voiding diary should not be used interchangeably when evaluating children with lower urinary tract dysfunction. The results of uroflowmetry measurements should be used to support the diagnosis of underlying lower urinary tract dysfunction.
Comment on Environmental quality standards for diclofenac derived under the European Water Framework Directive: 1. Aquatic organisms (Leverett et al. in Environmental Sciences Europe 2021; 33: 133)
Authors: Maack Gerd , Äystö Lauri , Carere Mario , Clausen Henning , James Alice , Junghans Marion , Junttila Ville , Hollender Juliane , Marinov Dimitar , Stroomberg Gerard , Triebskorn Rita , Verbruggen Eric , Lettieri Teresa 
Published: March 2022

AbstractLeverett et al. commented on the Environmental quality standard (EQS) for diclofenac derived under the European Water Framework Directive (Leverett et al. Environ Sci Eur 33: 133, 2021 https://doi.org/10.1186/s12302-021-00574-z). They postulated that the derived EQS value for diclofenac is not conducted according to the EQS Technical Guidance but rather using data of poor quality and relevance. Consequently, the authors suggested to use their alternative derived value instead. It is to be noted that the process for the EQS derivation for diclofenac is still ongoing and not finalized, and that as a consequence, any critical analysis is very premature. In general, within the current European Commission process, EQS value proposals are derived by expert groups led by the Joint Research Centre. In the specific case for diclofenac, Leverett and co-authors have also been actively involved as experts. This response to Leverett et al. (Environ Sci Eur 33:133, 2021) aims to clarify the reasoning-behind the proposal from a scientific point of view.
Phylogenetic relationships and evolutionary patterns of the genus Psammolestes Bergroth, 1911 (Hemiptera: Reduviidae: Triatominae)
Authors: Hernández Carolina , Alvarado Mateo , Salgado-Roa Fabian C. , Ballesteros Nathalia , Rueda-M Nicol , Oliveira Jader , Alevi Kaio Cesar Chaboli , da Rosa Joao Aristeu , Urbano Plutarco , Salazar Camilo , Ramírez Juan David 
Published: March 2022

Abstract
Background
The evolutionary history of biodiversity in South America has been poorly studied in the seasonal dry tropical forest (SDTF). Species diversification in this ecosystem may have a twofold explanation. First, intermittent connections in the middle and late Pleistocene promoted species dispersal and/or genetic connectivity between lineages isolated in disjunct patches of forest. Second, allopatric speciation proceeded immediately after the formation and colonization of the SDTF in the Neogene. Here we studied the diversification of Psammolestes, a genus endemic of the SDTF and naturally infected with Trypanosoma cruzi (agent of Chagas disease), using a combination of phylogenetic, population genetics and niche model methods, and evaluated the reliability of the three morphospecies currently recognized.

Results
Our multilocus analyses recovered P. coreodes and P. tertius in a monophyletic clade sister to P. arthuri. Species delimitation tests recovered these lineages as different species despite the shared genetic variation observed between P. coreodes and P. tertius in five genes. Also, genetic variation of the genus clustered in three groups that were consistent with the three morphospecies. Our demographic model predicted a scenario of divergence in absence of gene flow, suggesting that mixed haplotypes may be the result of shared ancestral variation since the divergence of the subtropical-temperate species P. coreodes and P. tertius. In contrast, the tropical species P. arthuri was highly differentiated from the other two in all tests of genetic structure, and consistently, the Monmonier’s algorithm identified a clear geographical barrier that separates this species from P. coreodes and P. tertius.

Conclusions
We found three genetically structured lineages within Psammolestes that diverged in absence of gene flow in the late Miocene. This result supports a scenario of species formation driven by geographical isolation rather than by divergence in the face of gene flow associated with climatic oscillations in the Pleistocene. Also, we identified the Amazon basin as a climatic barrier that separates tropical from subtropical-temperate species, thus promoting allopatric speciation after long range dispersion. Finally, each species of Psammolestes occupies different climatic niches suggesting that niche conservatism is not crucial for species differentiation. These findings influence the current vector surveillance programs of Chagas disease in the region.
The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge
Authors: Witkop Erin M. , Proestou Dina A. , Gomez-Chiarri Marta 
Published: March 2022

Abstract
Background
Apoptosis plays important roles in a variety of functions, including immunity and response to environmental stress. The Inhibitor of Apoptosis (IAP) gene family of apoptosis regulators is expanded in molluscs, including eastern, Crassostrea virginica, and Pacific, Crassostrea gigas, oysters. The functional importance of IAP expansion in apoptosis and immunity in oysters remains unknown.

Results
Phylogenetic analysis of IAP genes in 10 molluscs identified lineage specific gene expansion in bivalve species. Greater IAP gene family expansion was observed in C. virginica than C. gigas (69 vs. 40), resulting mainly from tandem duplications. Functional domain analysis of oyster IAP proteins revealed 3 novel Baculoviral IAP Repeat (BIR) domain types and 14 domain architecture types across gene clusters, 4 of which are not present in model organisms. Phylogenetic analysis of bivalve IAPs suggests a complex history of domain loss and gain. Most IAP genes in oysters (76% of C. virginica and 82% of C. gigas), representing all domain architecture types, were expressed in response to immune challenge (Ostreid Herpesvirus OsHV-1, bacterial probionts Phaeobacter inhibens and Bacillus pumilus, several Vibrio spp., pathogenic Aliiroseovarius crassostreae, and protozoan parasite Perkinsus marinus). Patterns of IAP and apoptosis-related differential gene expression differed between the two oyster species, where C. virginica, in general, differentially expressed a unique set of IAP genes in each challenge, while C. gigas differentially expressed an overlapping set of IAP genes across challenges. Apoptosis gene expression patterns clustered mainly by resistance/susceptibility of the oyster host to immune challenge. Weighted Gene Correlation Network Analysis (WGCNA) revealed unique combinations of transcripts for 1 to 12 IAP domain architecture types, including novel types, were significantly co-expressed in response to immune challenge with transcripts in apoptosis-related pathways.

Conclusions
Unprecedented diversity characterized by novel BIR domains and protein domain architectures was observed in oyster IAPs. Complex patterns of gene expression of novel and conserved IAPs in response to a variety of ecologically-relevant immune challenges, combined with evidence of direct co-expression of IAP genes with apoptosis-related transcripts, suggests IAP expansion facilitates complex and nuanced regulation of apoptosis and other immune responses in oysters.
Improvement of prediction ability by integrating multi-omic datasets in barley
Authors: Wu Po-Ya , Stich Benjamin , Weisweiler Marius , Shrestha Asis , Erban Alexander , Westhoff Philipp , Inghelandt Delphine Van 
Published: March 2022

Abstract
Background
Genomic prediction (GP) based on single nucleotide polymorphisms (SNP) has become a broadly used tool to increase the gain of selection in plant breeding. However, using predictors that are biologically closer to the phenotypes such as transcriptome and metabolome may increase the prediction ability in GP. The objectives of this study were to (i) assess the prediction ability for three yield-related phenotypic traits using different omic datasets as single predictors compared to a SNP array, where these omic datasets included different types of sequence variants (full-SV, deleterious-dSV, and tolerant-tSV), different types of transcriptome (expression presence/absence variation-ePAV, gene expression-GE, and transcript expression-TE) sampled from two tissues, leaf and seedling, and metabolites (M); (ii) investigate the improvement in prediction ability when combining multiple omic datasets information to predict phenotypic variation in barley breeding programs; (iii) explore the predictive performance when using SV, GE, and ePAV from simulated 3’end mRNA sequencing of different lengths as predictors.

Results
The prediction ability from genomic best linear unbiased prediction (GBLUP) for the three traits using dSV information was higher than when using tSV, all SV information, or the SNP array. Any predictors from the transcriptome (GE, TE, as well as ePAV) and metabolome provided higher prediction abilities compared to the SNP array and SV on average across the three traits. In addition, some (di)-similarity existed between different omic datasets, and therefore provided complementary biological perspectives to phenotypic variation. Optimal combining the information of dSV, TE, ePAV, as well as metabolites into GP models could improve the prediction ability over that of the single predictors alone.

Conclusions
The use of integrated omic datasets in GP model is highly recommended. Furthermore, we evaluated a cost-effective approach generating 3’end mRNA sequencing with transcriptome data extracted from seedling without losing prediction ability in comparison to the full-length mRNA sequencing, paving the path for the use of such prediction methods in commercial breeding programs.
SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs
Authors: Garber Arkadiy I. , Armbruster Catherine R. , Lee Stella E. , Cooper Vaughn S. , Bomberger Jennifer M. , McAllister Sean M. 
Published: March 2022

AbstractBackgroundShotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encompass organisms spanning multiple domains of life, necessitating increasingly elaborate software for accurate taxonomic classification of assembled sequences.ResultsWhile many software tools for taxonomic classification exist, SprayNPray offers a quick and user-friendly, semi-automated approach, allowing users to separate contigs by taxonomy (and other metrics) of interest. Easy installation, usage, and intuitive output, which is amenable to visual inspection and/or further computational parsing, will reduce barriers for biologists beginning to analyze genomes and metagenomes. This approach can be used for broad-level overviews, preliminary analyses, or as a supplement to other taxonomic classification or binning software. SprayNPray profiles contigs using multiple metrics, including closest homologs from a user-specified reference database, gene density, read coverage, GC content, tetranucleotide frequency, and codon-usage bias.ConclusionsThe output from this software is designed to allow users to spot-check metagenome-assembled genomes, identify, and remove contigs from putative contaminants in isolate assemblies, identify bacteria in eukaryotic assemblies (and vice-versa), and identify possible horizontal gene transfer events.
A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution
Authors: Bailey Emma , Field Linda , Rawlings Christopher , King Rob , Mohareb Fady , Pak Keywan-Hassani , Hughes David , Williamson Martin , Ganko Eric , Buer Benjamin , Nauen Ralf 
Published: March 2022

Abstract
Background
Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs).

Methods and findings
In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species.

Conclusion and significance
This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.
Transcriptome analysis reveals key developmental and metabolic regulatory aspects of oil palm (Elaeis guineensis Jacq.) during zygotic embryo development
Authors: Zhang Anni , Jin Longfei , Yarra Rajesh , Cao Hongxing , Chen Ping , John Martin Jerome Jeyakumar 
Published: March 2022

Abstract
Background
Oil palm is the most efficient oil-producing crop in the world, and the yield of palm oil is associated with embryonic development. However, a comprehensive understanding of zygotic embryo development at the molecular level remains elusive. In order to address this issue, we report the transcriptomic analysis of zygotic embryo development in oil palm, specifically focusing on regulatory genes involved in important biological pathways.

Results
In this study, three cDNA libraries were prepared from embryos at S1 (early-stage), S2 (middle-stage), and S3 (late-stage). There were 16,367, 16,500, and 18,012 genes characterized at the S1, S2, and S3 stages of embryonic development, respectively. A total of 1522, 2698, and 142 genes were differentially expressed in S1 vs S2, S1 vs S3, and S2 vs S3, respectively. Using Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify key genes and pathways. In the hormone signaling pathway, genes related to auxin antagonize the output of cytokinin which regulates the development of embryo meristem. The genes related to abscisic acid negatively regulating the synthesis of gibberellin were strongly up-regulated in the mid-late stage of embryonic development. The results were reported the early synthesis and mid-late degradation of sucrose, as well as the activation of the continuous degradation pathway of temporary starch, providing the nutrients needed for differentiation of the embryonic cell. Moreover, the transcripts of genes involved in fatty acid synthesis were also abundantly accumulated in the zygotic embryos.

Conclusion
Taken together, our research provides a new perspective on the developmental and metabolic regulation of zygotic embryo development at the transcriptional level in oil palm.
“Phoenix in Flight”: an unique fruit morphology ensures wind dispersal of seeds of the phoenix tree (Firmiana simplex (L.) W. Wight)
Authors: Gan Shi-Rui , Guo Jun-Cheng , Zhang Yun-Xiao , Wang Xiao-Fan , Huang Lan-Jie 
Published: March 2022

Abstract
Background
Many seed plants produce winged diaspores that use wind to disperse their seeds. The morphology of these diaspores is directly related to the seed dispersal potential. The majority of winged diaspores have flat wings and only seeds; however, some angiosperms, such as Firmiana produce winged fruit with a different morphology, whose seed dispersal mechanisms are not yet fully understood. In this study, we observed the fruit development of F. simplex and determined the morphological characteristics of mature fruit and their effects on the flight performance of the fruit.

Results
We found that the pericarp of F. simplex dehisced early and continued to unfold and expand during fruit development until ripening, finally formed a spoon-shaped wing with multiple alternate seeds on each edge. The wing caused mature fruit to spin stably during descent to provide a low terminal velocity, which was correlated with the wing loading and the distribution of seeds on the pericarp. When the curvature distribution of the pericarp surface substantially changed, the aerodynamic characteristics of fruit during descent altered, resulting in the inability of the fruit to spin.

Conclusions
Our results suggest that the curved shape and alternate seed distribution are necessary for the winged diaspore of F. simplex to stabilize spinning during wind dispersal. These unique morphological characteristics are related to the early cracking of fruits during development, which may be an adaptation for the wind dispersal of seeds.