bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR
Authors: Foo Aidan , Cerdeira Louise , Hughes Grant L. , Heinz Eva 
Published: August 2022

AbstractBackgroundOngoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value of these initially host-focused sequencing projects.MethodsTo analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (MicrobialINsightsUsingUnmappedReads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly availableAedes aegyptigenomic datasets, consisting of 62 samples with a broad range of sequencing depths.ResultsWe demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs.ConclusionsOur metagenomics workflow, MINUUR, was applied to a range ofAedes aegyptigenomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub (https://github.com/aidanfoo96/MINUUR) and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.
Single-cell phylogenies reveal deviations from clock-like, neutral evolution in cancer and healthy tissues
Authors: Borgsmüller Nico , Valecha Monica , Kuipers Jack , Beerenwinkel Niko , Posada David 
Published: August 2022

AbstractHow tumors evolve affects cancer progression, therapy response, and relapse. However, whether tumor evolution is driven primarily by selectively advantageous or neutral mutations remains under debate. Resolving this controversy has so far been limited by the use of bulk sequencing data. Here, we leverage the high resolution of single-cell DNA sequencing (scDNA-seq) to test for clock-like, neutral evolution. Under neutrality, different cell lineages evolve at a similar rate, accumulating mutations according to a molecular clock. We developed and benchmarked a test of the somatic clock based on single-cell phylogenies and applied it to 22 scDNA-seq datasets. We rejected the clock in 10/13 cancer and 5/9 healthy datasets. The clock rejection in seven cancer datasets could be related to known driver mutations. Our findings demonstrate the power of scDNA-seq for studying somatic evolution and suggest that some cancer and healthy cell populations are driven by selection while others seem to evolve under neutrality.
Mathematical model of the fast phase of the chlorophyll fluorescence induction curve
Authors: Lavrentyev V.M. 
Published: August 2022

AbstractIn natural conditions, plants are affected by various adverse environmental factors that can disrupt the photosynthetic apparatus, which can reduce the productivity of plants and ultimately reduce their yield. Measurement of the chlorophyll fluorescence induction (CFI) curve is a simple, non-destructive, inexpensive, and fast tool that can be used to analyze photosynthetic reactions and plant conditions. Mathematical modeling of the chlorophyll fluorescence induction curve is important not only for understanding the complex processes of photosynthesis but also can have practical applications in predicting ways to increase plant productivity. Currently, there are a sufficient number of models of varying complexity and detail that describe the processes of photosynthesis, however, no final agreement has been reached. A new model of reactions occurring in the process of the fast phase of the CFI curve, i.e. in the process of electron transport in the electron transport chain (ETC), is presented here. In the ETC model, it is considered as a system of elements in which electrons are sequentially transferred from one element of the system to another, according to the properties of the elements themselves and the connections between them. In addition, the mathematical model is based on the idea of dividing the entire flow of electrons, which moves through the ETC, into a sequence of individual flows. The proposed mathematical model differs in that each stage of electron transfer along the ETC is described separately and sequentially with the help of connection functions. This makes it possible to write the equations for the real OJIP curve and, as a result of their solution, to obtain the parameters of the entire electron transfer process.
On a mathematical connection between single-elimination sports tournaments and evolutionary trees
Authors: King Matthew C. , Rosenberg Noah A. 
Published: August 2022

AbstractHow many ways are there to arrange the sequence of games in a single-elimination sports tournament? We consider the connection between this enumeration problem and the enumeration of “labeled histories,” or sequences of asynchronous branching events, in mathematical phylogenetics. The possibility of playing multiple games simultaneously in different arenas suggests an extension of the enumeration of labeled histories to scenarios in which multiple branching events occur simultaneously. We provide a recursive result enumerating game sequences and labeled histories in which simultaneity is allowed. For a March Madness basketball tournament of 68 labeled teams, the number of possible sequences of games is ~ 1.91 × 1078if arbitrarily many arenas are available, but only ~ 3.60 × 1068if all games must be played sequentially on the same arena.
Can a short math video enhance the brain’s mathematical networks?
Authors: Amalric Marie , Roveyaz Pauline , Dehaene Stanislas 
Published: August 2022

AbstractMany teaching websites, such as the Khan Academy, propose vivid videos illustrating a mathematical concept. Using fMRI, we asked whether watching such a video suffices to rapidly change the brain networks for mathematical knowledge. We capitalized on the finding that, when judging the truth of short spoken statements, distinct semantic regions activate depending on whether the statements bear on mathematical knowledge or on other domains of semantic knowledge. Here, participants answered such questions before and after watching a lively five-minute video which taught them the rudiments of a new domain. During the video, a distinct math-responsive network, comprising anterior intraparietal and inferior temporal nodes, showed inter-subject synchrony when viewing mathematics course rather than control courses in biology or law. However, this experience led to minimal subsequent changes in the activity of those domain-specific areas when answering questions on the same topics a few minutes later. All taught facts, whether mathematical or not, led to domain-general repetition enhancement, particularly prominent in the cuneus, posterior cingulate and posterior parietal cortices. We conclude that short videos do not suffice to induce a meaningful lasting change in the brain’s math-responsive network, but merely engage domain-general regions possibly involved in episodic short-term memory.Significance StatementTeaching mathematical concepts is difficult. To facilitate the comprehension and appeal of mathematics, several teaching websites provide vivid videos illustrating math concepts. Here, however, we show that merely watching such videos fails to improve the brain networks for mathematics. During the video itself, these networks are transiently engaged – but a few minutes later, when we ask questions about the taught concepts, performance is only minimally improved, and the participants engage generic regions thought to be involved in short-memory and language, rather than the targeted math-responsive regions. Brief video watching is therefore insufficient as a pedagogical device, probably because it misses ingredients such as teacher-pupil interactions, explicit teaching, active engagement, retrieval practice, repetition, and sleep.
Sequential roles for red blood cell binding proteins enable phased commitment to invasion for malaria parasites
Authors: Hart Melissa N. , Mohring Franziska , Donvito Sophia M. , Thomas James A. , Muller-Sienerth Nicole , Wright Gavin J. , Knuepfer Ellen , Saibil Helen R. , Moon Robert W. 
Published: August 2022

SummaryInvasion of red blood cells (RBCs) by Plasmodium merozoites is critical to their continued survival within the host. Two major protein families, the Duffy binding-like proteins (DBPs/EBAs) and the reticulocyte binding like proteins (RBLs/RHs) have been studied extensively in P. falciparum and are hypothesized to have overlapping, but critical roles just prior to host cell entry. The zoonotic malaria parasite, P. knowlesi, has larger invasive merozoites and contains a smaller, less redundant, DBP and RBL repertoire than P. falciparum. One DBP (DBPα) and one RBL, normocyte binding protein Xa (NBPXa) are essential for invasion of human RBCs. Taking advantage of the unique biological features of P. knowlesi and iterative CRISPR-Cas9 genome editing, we determine the precise order of key invasion milestones and demonstrate distinct roles for each family. These distinct roles support a mechanism for phased commitment to invasion and can be targeted synergistically with invasion inhibitory antibodies.
A Genetic Variant of Fatty Acid Amide Hydrolase (FAAH) Exacerbates Hormone-Mediated Orexigenic Feeding in Mice
Authors: Balsevich Georgia , Petrie Gavin N , Heinz Daniel E , Singh Arashdeep , Aukema Robert J , Hunker Avery C , Vecchiarelli Haley A , Yau Hiulan , Sticht Martin , Thompson Roger J , Lee Francis S , Zweifel Larry S , Chelikani Prasanth K , Gassen Nils C , Hill Matthew N 
Published: August 2022

AbstractFatty acid amide hydrolase (FAAH) degrades the endocannabinoid anandamide. A polymorphism in FAAH (FAAH C385A) reduces FAAH expression, increases anandamide levels, and increases the risk of obesity. Nevertheless, some studies have found no association between FAAH C385A and obesity. We investigated whether the environmental context governs the impact of FAAH C385A on metabolic outcomes. Using a C385A knock-in mouse model, we found that under basal conditions, there was no effect of the FAAH C385A polymorphism on body weight or composition. By contrast, FAAH A/A mice are more susceptible to glucocorticoid-induced hyperphagia, weight gain, and activation of hypothalamic AMPK. AMPK inhibition occluded the amplified hyperphagic response to glucocorticoids in FAAH A/A mice. FAAH knockdown exclusively in AgRP neurons mimicked the exaggerated feeding response of FAAH A/A mice to glucocorticoids. FAAH A/A mice likewise presented exaggerated orexigenic responses to ghrelin, while FAAH knockdown in AgRP neurons blunted leptin anorectic responses. Together, the FAAH A/A genotype amplifies orexigenic responses and decreases anorexigenic responses, providing a putative mechanism explaining the diverging human findings.
Inhibitory inputs from hippocampal CA1 to retrosplenial agranular cortex gate social behavior
Authors: Shi Yuhan , Yan Jingjing , Xu Xiaohong , Qiu Zilong 
Published: August 2022

ABSTRACTRetrosplenial cortex has been implicated in processing sensory information and spatial learning, with abnormal neural activity observed in association with psychedelics and in mouse and non-human primate models of autism spectrum disorders (ASD). The direct role of the retrosplenial cortex in regulating social behaviors remains unclear. This work reveals that the neural activity of retrosplenial agranular cortex (RSA), a subregion of retrosplenial cortex, is initially activated, then quickly suppressed upon social contact. The up-down phase of RSA neurons is crucial for normal social behaviors. PV-positive GABAergic neurons in the hippocampal CA1 region were found to send inhibitory projections to RSA. Blocking these CA1-RSA inhibitory inputs significantly impaired social behavior. Notably, enhancing the CA1-RSA inhibitory input could rescue social behavior defects in an ASD mouse model. This work suggests a neural mechanism for salience processing of social behavior and identifies a potential target for ASD intervention using neural modulation approaches.
Evaluating the effect of metabolic traits on oral and oropharyngeal cancer risk using Mendelian randomization
Authors: Gormley Mark , Dudding Tom , Thomas Steven J , Tyrrell Jessica , Ness Andrew R , Pring Miranda , Legge Danny , Smith George Davey , Richmond Rebecca C , Vincent Emma E , Bull Caroline 
Published: August 2022

AbstractA recent World Health Organization report states that at least 40% of all cancer cases may be preventable, with smoking, alcohol consumption and obesity identified as three of the most important modifiable lifestyle factors. Given the significant decline in smoking rates, particularly within developing countries, other potentially modifiable risk factors for head and neck cancer warrant investigation. Obesity and related metabolic disorders such as type 2 diabetes and hypertension have been associated with head and neck cancer risk in multiple observational studies. However, obesity has also been correlated with smoking, with bias, confounding or reverse causality possibly explaining these findings. To overcome the challenges of observational studies, we conducted two-sample Mendelian randomization (inverse variance weighted (IVW) method) using genetic variants which were robustly associated with obesity, T2D and hypertension in genome-wide association studies (GWAS). Outcome data was taken from the largest available GWAS of 6,034 oral and oropharyngeal cases, with 6,585 controls. We found limited evidence of a causal effect of genetically proxied body mass index (OR IVW = 0.89, 95%CI 0.72–1.09, p = 0.26 per 1 SD in BMI (4.81 kg/m2)) on oral and oropharyngeal cancer risk. Similarly, there was limited evidence for related traits including type 2 diabetes and hypertension. Smoking appears to act as a mediator in the relationship between obesity and head and neck cancer.
Phylodynamics of SARS-CoV-2 transmissions in France, Europe and the world during 2020
Authors: Coppée Romain , Blanquart François , Jary Aude , Leducq Valentin , Ferré Valentine Marie , Franco Yusti Anna Maria , Daniel Lena , Charpentier Charlotte , Lebourgeois Samuel , Zafilaza Karen , Calvez Vincent , Descamps Diane , Marcelin Anne-Geneviève , Visseaux Benoit , Bridier-Nahmias Antoine 
Published: August 2022

AbstractBackgroundAlthough France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of SARS-CoV-2 transmissions within France, Europe and worldwide remain only partially characterized during the first year of the pandemic.MethodsHere, we analyzed GISAID deposited sequences from January to December 2020 (n = 638,706 sequences). To tackle the huge number of sequences without the bias of analyzing a single sequence subset, we produced 100 independent and randomly selected sequence datasets and related phylogenetic trees for different geographic scales (worldwide, European countries and French administrative regions) and time periods (first and second half of 2020). We applied a maximum likelihood discrete trait phylogeographic method to date transmission events and to estimate the geographic spread of SARS-CoV-2 to, from and within France, Europe and worldwide.ResultsThe results unraveled two different patterns of inter- and intra-territory transmission events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental transmissions, for which France has played a pivotal role. SARS-CoV-2 transmissions with France were concentrated with North America and Europe (mainly Italy, Spain, United Kingdom, Belgium and Germany) during the first wave, and were limited to neighboring countries without strong intercontinental transmission during the second one. Regarding French administrative regions, the Paris area was the main source of transmissions during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon and Marseille area, the two other most densely populated cities in France.ConclusionBy enabling the inclusion of tens of thousands of viral sequences, this original phylogenetic strategy enabled us to robustly depict SARS-CoV-2 transmissions through France, Europe and worldwide in 2020.
Wide mismatches in the sequences of primers and probes for Monkeypox virus diagnostic assays
Authors: Wu Fuqing , Oghuan Jeremiah , Gitter Anna , Mena Kristina D. , Brown Eric L. 
Published: August 2022

AbstractRapid and accurate diagnosis of infections is fundamental to containment of disease. Several monkeypox virus (MPV) real-time diagnostic assays have been recommended by the CDC; however, the specificity of the primers and probes in these assays for the ongoing MPV outbreak has not been investigated. We analyzed the primer and probe sequences present in the CDC recommended monkeypox virus (MPV) generic real-time PCR assay by aligning those sequences against 1,730 MPV complete genomes reported in 2022 worldwide. Sequence mismatches were found in 99.08% and 97.46% of genomes for the MPV generic forward and reverse primers, respectively. Mismatch-corrected primers were synthetized and compared to the generic assay for MPV detection. Results showed that the two primer-template mismatches resulted in a ∼11-fold underestimation of initial template DNA in the reaction and 4-fold increase in the 95% LOD. We further evaluated the specificity of seven other real-time PCR assays used for MPV and orthopoxvirus (OPV) detection and identified two assays with the highest matching score (>99.6%) to the global MPV genome database in 2022. Genetic variations in the primer-probe regions across MPV genomes could indicate the temporal and spatial emergence pattern of monkeypox disease. Our results show that the current MPV real-time generic assay may not be optimal to accurately detect MPV, and the mismatch-corrected assay with full complementarity between primers and current MPV genomes could provide a more sensitive and accurate detection of MPV.
Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking
Authors: Rao Lu , Li Peijun , Liu Xinglei , Wang Qi , Son Alexander I. , Gennerich Arne , Liu Judy S. , Fu Xiaoqin 
Published: August 2022

SUMMARYMutations in the microtubule (MT)-binding protein doublecortin (DCX) or in the MT- based molecular motor dynein result in lissencephaly. However, a functional link between DCX and dynein has not been defined. Here, we demonstrate that DCX negatively regulates dynein-mediated retrograde transport by reducing dynein’s association with MTs and by disrupting the composition of the dynein motor complex. Previous work showed an increased binding of the adaptor protein C-Jun-amino-terminal kinase-interacting protein 3 (JIP3) to dynein in the absence of DCX. Using purified components, we demonstrate that JIP3 forms an active motor complex with dynein and its cofactor dynactin with two dyneins per complex. DCX competes with the binding of the second dynein, resulting in a velocity reduction of the complex. We conclude that DCX negatively regulates dynein-mediated retrograde transport through two critical interactions by regulating dynein binding to MTs and by regulating the association of JIP3 to the dynein motor complex.
The VGNC: Expanding Standardized Vertebrate Gene Nomenclature
Authors: Jones Tamsin E.M. , Yates Bethan , Braschi Bryony , Gray Kristian , Tweedie Susan , Seal Ruth L. , Bruford Elspeth A. 
Published: August 2022

AbstractThe Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HGNC (HUGO Gene Nomenclature Committee), to approve gene nomenclature in vertebrate species without an existing dedicated nomenclature committee. The VGNC aims to harmonize gene nomenclature across selected vertebrate species in line with human gene nomenclature, with orthologs assigned the same nomenclature where possible. This article presents an overview of the VGNC project and discussion of key findings resulting from this work to date. VGNC approved nomenclature is accessible at https://vertebrate.genenames.org, and is additionally displayed by the NCBI, Ensembl and UniProt databases.
Internal-led cyber frauds in Indian banks: an effective machine learning–based defense system to fraud detection, prioritization and prevention
Authors: Chhabra Roy Neha , Prabhakaran Sreeleakha 
Published: August 2022

PurposeThe study aims to overview the different types of internal-led cyber fraud that have gained mainstream attention in recent major-value fraud events involving prominent Indian banks. The authors attempted to identify and classify cyber frauds and its drivers and correlate them for optimal mitigation planning.Design/methodology/approachThe methodology opted for the identification and classification is through a detailed literature review and focus group discussion with risk and vigilance officers and cyber cell experts. The authors assessed the future of cyber fraud in the Indian banking business through the machine learning–based k-nearest neighbor (K-NN) approach and prioritized and predicted the future of cyber fraud. The predicted future revealing dominance of a few specific cyber frauds will help to get an appropriate fraud prevention model, using an associated parties centric (victim and offender) root-cause approach. The study uses correlation analysis and maps frauds with their respective drivers to determine the resource specific effective mitigation plan.FindingsFinally, the paper concludes with a conceptual framework for preventing internal-led cyber fraud within the scope of the study. A cyber fraud mitigation ecosystem will be helpful for policymakers and fraud investigation officers to create a more robust environment for banks through timely and quick detection of cyber frauds and prevention of them.Research limitations/implicationsAdditionally, the study supports the Reserve Bank of India and the Government of India's launched cyber security initiates and schemes which ensure protection for the banking ecosystem i.e. RBI direct scheme, integrated ombudsman scheme, cyber swachhta kendra (botnet cleaning and malware analysis centre), National Cyber Coordination Centre (NCCC) and Security Monitoring Centre (SMC).Practical implicationsStructured and effective internal-led plans for cyber fraud mitigation proposed in this study will conserve banks, employees, regulatory authorities, customers and economic resources, save bank authorities’ and policymakers’ time and money, and conserve resources. Additionally, this will enhance the reputation of the Indian banking industry and extend its lifespan.Originality/valueThe innovative insider-led cyber fraud mitigation approach quickly identifies cyber fraud, prioritizes it, identifies its prominent root causes, map frauds with respective root causes and then suggests strategies to ensure a cost-effective and time-saving bank ecosystem.