bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heart Rate Variability During Mindful Breathing Meditation
Authors: Natarajan Aravind 
Published: August 2022

AbstractIn this article, we discuss Heart Rate Variability (HRV) measured during mindful breathing meditation. We provide a pedagogical computation of 2 commonly used HRV metrics, i.e. the root mean square of successive differences (RMSSD) and the standard deviation of RR intervals (SDRR), in terms of Fourier components. It is shown that the RMSSD preferentially weights higher frequency Fourier modes, making it unsuitable as a biosignal for mindful breathing meditation which encourages slow breathing. We propose a new metric called the autonomic balance index (ABI) which uses Respiratory Sinus Arrhythmia to quantify the fraction of HRV contributed by the parasympathetic nervous system. We apply this metric to HRV data collected during two different meditation techniques, and show that the ABI is significantly elevated during mindful breathing, making it a good signal for biofeedback during meditation sessions.
Fadrozole-mediated sex reversal in the embryonic chicken gonad involves a PAX2 positive undifferentiated supporting cell state
Authors: Estermann Martin A. , Smith Craig A. 
Published: August 2022

AbstractGonadal sex differentiation among vertebrates involves divergent fates of a common groups of progenitor cells present in both presumptive ovaries and testes. The first cell type to differentiate gives rise to pre-Sertoli cells in the testis, and pre-follicular cells in the ovary. These cells derive form a common lineage of so-called “supporting cells”. In birds and other egg-laying vertebrates, locally synthesised estrogen has a central role in ovarian development and influence the fate of these supporting cells. Manipulation of estrogen levels during embryonic development induces gonadal sex reversal, providing an experimental setting to evaluate the process of gonadal sex differentiation. Recently, we identified PAX2 as a novel marker of the undifferentiated supporting cell lineage in the chicken embryo, expressed in both sexes prior to overt gonadal sex differentiation. PAX2 expression is downregulated at the onset of gonadal sex differentiation in both males and females. The analysis of this undifferentiated supporting cell marker, together with Sertoli (male) and pre-granulosa (female) will enhance our understanding of supporting cell differentiation. Here we characterized the supporting cells differentiation process and identified undifferentiated supporting cells in estrogen-mediated sex reversal experiments. Female embryos treated with the aromatase inhibitor fadrozole developed ovotestis, containing pre-granulosa cells, Sertoli cells and PAX2 positive undifferentiated supporting cells. In contrast, male embryos treated with 17β-estradiol showed no PAX2+ undifferentiated gonadal supporting cells. Fadrozole time-course as well as multiple dose analysis suggests that supporting cell transdifferentiation involves a dedifferentiation event into a PAX2+ undifferentiated supporting cell state, followed by a redifferentiation towards the opposite sex lineage.
Warm blood meal increases digestion rate and milk protein production to maximize reproductive output for the tsetse fly, Glossina morsitans
Authors: Benoit Joshua B. , Lahondère Chloé , Attardo Geoffrey M. , Michalkova Veronika , Oyen Kennan , Xiao Yanyu , Aksoy Serap 
Published: August 2022

AbstractThe ingestion of blood represents a significant pressure that immediately increases water, oxidative, and thermal stress, but provides a significant nutrient source to generate resources necessary for the development of progeny. Thermal stress has been assumed to solely be a negative byproduct that has to be alleviated to prevent stress. Here, we examined if the short thermal bouts incurred during a warm blood meal are beneficial to reproduction. To do so, we examined the duration of pregnancy and milk gland protein expression in the tsetse fly, Glossina morsitans, that consumed a warm or cool blood meal. We noted that an optimal temperature for blood ingestion yielded a reduction in the duration of pregnancy. This decline in the duration of pregnancy is due to increased rate of blood digestion when consuming warm blood. This increased digestion likely provided more energy that leads to increased expression of transcript for milk-associated proteins. The shorter duration of pregnancy is predicted to yield an increase in population growth compared to those that consume cool or above host temperatures. These studies provide evidence that consumption of a warm blood meal is likely beneficial for specific aspects of vector biology.
HiCAT: A tool for automatic annotation of centromere structure
Authors: Gao Shenghan , Yang Xiaofei , Zhao Xixi , Wang Bo , Ye Kai 
Published: August 2022

AbstractSignificant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres are annotated in a semi-manual way. Here, we propose HiCAT, a generalizable automatic centromere annotation tool, based on hierarchical tandem repeat mining and maximization of tandem repeat coverage to facilitate decoding of centromere architecture. We applied HiCAT to human CHM13-T2T and gapless Arabidopsis thaliana genomes. Our results not only were generally consistent with previous inferences but also greatly improved annotation continuity and revealed additional fine structures, demonstrating HiCAT’s performance and general applicability.
The glycolipid GlcCer is recruited into the viral envelope to promote phenuivirus binding to host cells
Authors: Uckeley Zina M. , Mazelier Magalie , Lüchtenborg Christian , Winter Sophie L. , Schad Paulina , Chlanda Petr , Brügger Britta , Lozach Pierre-Yves 
Published: August 2022

AbstractVirus–receptor interactions largely contribute to the tropism and outcome of an infection. Here, we found that the glycolipid glucosylceramide (GlcCer) is a major component of Uukuniemi phenuivirus and allows viral binding to host cells. A lipidomic analysis with mass spectrometry revealed the lipidome of UUKV particles and indicated that GlcCer was enriched in both infected cells and viral particles. In addition, the infectivity of UUKV depended on the conversion of ceramide (Cer) into GlcCer in the Golgi network of producer cells. In contrast, depletion of GlcCer in virions profoundly impaired the attachment of UUKV and other related viruses to target cells. Furthermore, competing GlcCer ligands prevented virus binding to various cell types. Altogether, our results demonstrate that glycolipids are essential structural determinants of the virions necessary for virus attachment to host cells and have strong implications for future work on the identification of virus receptors.
Chemical compositions of essential oils, antimicrobial effect and antioxidant activity studies of Hyoscyamus niger L. from Turkey
Authors: İnci Şule , Sancar Pelin Yilmaz , Demirpolat Azize , Kirbag Sevda , Civelek Semsettin 
Published: August 2022

ABSTRACTIn this study, essential oil components of the Hyoscyamus niger L. plant and their antimicrobial and antioxidant properties were determined. The essential oils were obtained separately from both the aerial parts and seeds of the plant using the hydrodistillation method. Antimicrobial activity was determined using the disk diffusion method. Total antioxidant level (TAS), total oxidant level (TOS), and 2.2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity were detected for the antioxidant activity of the plant. The main essential oil components of the above-ground parts Hyoscyamus niger were determined as major components the phytol 52.09%, hexahydrofarnesyl acetone 19.66 %. H. niger seeds were hydrodistilled separately, obtaining yields of 0.7% (v w-1) of yellow oils. In the essential oils of H. niger seeds, forty-one components were identified representing 99.0% of the oils. According to the results of the analysis hexahydrofarnesyl acetone 46.36%, hexanal 9.05% as major components. It was determined that the methanol extracts of the above-ground H. niger inhibited the growth of pathogenic microorganisms at different rates (13-32 mm). TAS value of methanol extracts of H. niger was calculated as 3.7705 mmol, while the TOS value was calculated as 6.9403 μmol. It was determined that the scavenging effects of the DPPH radical increase, depend on increasing concentrations.
A resource for the comparison and integration of heterogeneous microbiome networks
Authors: Hu Zhenjun , Kishore Dileep , Wang Yan , Birzu Gabriel , DeLisi Charles , Korolev Kirill , Segrè Daniel 
Published: August 2022

AbstractNaturally occurring microbial communities often comprise thousands of taxa involved in complex networks of interactions. These interactions can be mediated by several mechanisms, including the competition for resources, the exchange of signals and nutrients, cell-cell contact and antibiotic warfare. In addition to direct measurements and computational predictions of interactions, abundant data on microbial co-occurrence associations can be inferred from correlations of taxa across samples, which can be estimated from metagenomic, and amplicon datasets. The analysis and interpretation of interaction and correlation networks are limited by the challenge of comparing across different datasets, due to heterogeneity of the data itself and to the lack of a platform to facilitate such comparisons. Here, we introduce the Microbial Interaction Network Database (MIND) - a web-based platform for the integrative analysis of different types of microbial networks, freely available athttp://microbialnet.org/. In addition to containing a growing body of curated data, including amplicon-based co-occurrence networks, genome-scale model-derived networks, metabolic influence networks and horizontal gene transfer networks, MIND allows users to upload and analyze newly generated networks using a JSON format and standard NCBI taxonomy. The platform provides convenient functions to compare and query multiple networks simultaneously, and to visualize and export networks and datasets. Through some illustrative examples, we demonstrate how the platform might facilitate discoveries and help generate new hypotheses on host-associated and environmentally important microbial ecosystems through the power of knowledge integration.
circAβ RNA drives the formation and deposition of β-amyloid plaques in the sporadic Alzheimer’s disease
Authors: Mo Dingding 
Published: August 2022

Abstractβ-amyloid peptides (Aβ) play key causal role in Alzheimer’s disease (AD). However, the mechanisms of Aβ biogenesis in sporadic AD are still largely unknown. Moreover, current AD mouse models which overexpress mutated human APP and presenilin proteins can only mimic limited characteristics of familial AD. We recently discovered an alternative Aβ production pathway from Aβ175, an Aβ peptide containing polypeptide translated from circular circAβ-a RNA generated via backsplicing of the APP gene transcript. Here, wildtype human circAβ-a RNA was overexpressed in wildtype mouse frontal cortex. Results showed that circAβ-a overexpression drove intracellular Aβ accumulation and extensive depositions of neuronal Aβ plaques in mouse brain in vivo. This recapitulates the critical Aβ hallmarks of sporadic AD and represents a sporadic AD mouse model. In summary, the causal relationship between circAβ RNA overexpression and AD pathology was demonstrated. This novel AD mouse model will accelerate disease-modifying drug development of this detrimental neurodegenerative disease.
An Effective mRNA-LNP Vaccine Against the Lethal Plague Bacterium
Authors: Kon Edo , Levy Yinon , Elia Uri , Cohen Hila , Hazan-Halevy Inbal , Aftalion Moshe , Ezra Assaf , Bar-Haim Erez , Naidu Gonna Somu , Diesendruck Yael , Rotem Shahar , Ad-El Nitay , Goldsmith Meir , Mamroud Emanuelle , Peer Dan , Cohen Ofer 
Published: August 2022

AbstractPlague is a rapidly deteriorating contagious disease that has killed millions of people during the history of mankind and is caused by the gram-negative bacterium Yersinia pestis. Currently, the disease is treated effectively with antibiotics. However, in the case of an outbreak caused by a multiple-antibiotic-resistant strain, alternative countermeasures are required. Despite the many efforts to develop a safe vaccine against the disease, there is still no vaccine approved for use in western countries. mRNA Lipid Nanoparticle (mRNA-LNP) vaccines have been demonstrated during the Covid-19 pandemic to be a versatile, clinically relevant, and rapidly manufactured vaccine platform. However, harnessing this platform for bacterial pathogens remains a formidable challenge. Here, we describe the design of several mRNA-LNP vaccine versions against Y. pestis, based on the F1 capsular antigen. We demonstrate that mRNA-LNP vaccines encoding the F1 antigen with either no signal sequences or conjugated to human Fc, provide substantial cellular and humoral responses. Most importantly, these vaccine candidates fully protect animals against Y. pestis infection. The results of this study suggest that mRNA-LNPs can be effective as anti-bacterial vaccines, and further developed to combat other bacterial pathogens, which are urgently needed, given the looming threat of antibiotic resistance.One-Sentence SummaryA novel mRNA-LNP vaccine against Y. pestis, the etiological agent of plague and the first documented mRNA-LNP vaccine to protect against a lethal bacterial pathogen infection.
Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples
Authors: Wagner David M. , Birdsell Dawn N. , McDonough Ryelan F. , Nottingham Roxanne , Kocos Karisma , Celona Kimberly , Özsürekci Yasemin , Öhrman Caroline , Karlsson Linda , Myrtennäs Kerstin , Sjödin Andreas , Johansson Anders , Keim Paul S. , Forsman Mats , Sahl Jason W. 
Published: August 2022

AbstractFrancisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for F. tularensis that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze Francisella DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of F. tularensis and other diverse species in the family Francisellaceae. Probes that targeted genomic regions also present in non-Francisellaceae species were excluded, and probes specific to particular Francisella species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level Francisella DNA, including human clinical tularemia samples, environmental samples (i.e., animal tissue and air filters), and whole ticks/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of F. tularensis or other Francisella species in complex samples, identification of mixtures of different Francisella species in the same sample, analysis of gene content (e.g., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.
Analysis of Inbred Mouse strains’ High-Impact Genotype-phenotype Hypotheses (AIMHIGH) reveals novel disease-causing candidate genes
Authors: Yoo Boyoung , Nair Surag , Fang Zhuoqing , Arora Rushil , Wang Meiyue , Peltz Gary , Bejerano Gill 
Published: August 2022

AbstractInbred mouse strains reveal the molecular basis of mammalian traits and diseases, particularly recessive ones. We utilized mouse community curated resources to set up an automated screen to discover novel testable gene function hypotheses. Using 11,832 community contributed strain-differentiating experiments and trait presence/absence scoring, we searched for all experiments where strains can be split by their phenotypic values (e.g., high vs. low responders). Then, using 48 sequenced strains, we found one or more candidate gene for each experiment where homozygous high-impact variants (such as stopgain, frameshifts) segregate strains into these same binary grouping. Our approach rediscovered 212 known gene-phenotype relationships, almost always highlighting potentially novel causal variants, as well as thousands of gene function hypotheses. To help find the most exciting hypotheses, we improved the state of the art in machine learning driven literature-based discovery (LBD). Reading on our top 3 ranked candidate genes per experiment reveals 80% of rediscovered relationships, compared to 5% reading at random. We proposed 1,842 novel gene-phenotype testable hypotheses using our approach. We built a web portal at aimhigh.stanford.edu to allow researchers to view all our testable hypotheses in detail. Our open-source code can be rerun as more sequenced strains and phenotyping experiments become available.
Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits
Authors: Zhou Zhichao , St. John Emily , Anantharaman Karthik , Reysenbach Anna-Louise 
Published: August 2022

AbstractBackgroundWhen deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal vent deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018, and document their potential implications in biogeochemical cycles.ResultsOur dataset represents 3,635 metagenome-assembled genomes encompassing 511 novel genera, with 395 Bacteria and 116 Archaea, providing many targets for cultivation of novel archaeal and bacterial families. Notably, 52% (206) of the novel bacterial genera and 72% (84) of the novel archaeal genera were found at the deep-sea Brothers volcano, many of which were endemic to the volcano. We report some of the first examples of medium to high-quality MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur and hydrogen metabolic processes across all sites, and illustrates sulfur and nitrogen metabolic ‘handoffs’ in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment.ConclusionOur study of globally-distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.
The role and mechanism of NRF2 in endothelial cells and smooth muscle cells of pulmonary artery
Authors: Ning Shasha , Guo Xinyue , Zhu Yanan , Li Chenghui , Li Ruixue , Meng Yinan , Luo Weiwei , Lu Dezhang , Yin Yupeng 
Published: August 2022

AbstractPulmonary hypertension (PH) is a kind of fatal disease. There are no existing drugs that could reverse the diseas. NF-E2-related factor 2 (NRF2) is one of the most important moleculars in the range of cell protection. We examined the expression of NRF2 in PH models and explored the role of NRF2 in regulating abnormal phenotypes in pulmonary artery cells. We determined the expression level of NRF2 in lung tissues of PH model decreased significantly. We found that NRF2 was reduced in rat pulmonary artery endothelial cells (rPAEC) under hypoxia, while it was overexpressed in rat pulmonary artery smooth muscle cells (rPASMC) under hypoxia. Next, the results showed that knockdown NRF2 in rPAEC promoted endothelial-mesenchymal transformation and upregulated reactive oxygen species level. After the rPASMC was treated with siRNA or activator, we found that NRF2 could promote cell proliferation by regulating PDGFR/ERK1/2 and mTOR/P70S6K pathways, and accelerate cell migration by affecting MMP2/3/7. Therefore, the study suggests that the combination of NRF2 activators should be considered to eliminate the promoting effect of NRF2 activators on proliferation and migration of rPASMC.Summary statementHypoxia regulates NRF2 in PAECs and PASMCs differently. We found that NRF2 could promote cell proliferation by regulating PDGFR/ERK1/2 and mTOR/P70S6K pathways, and accelerate cell migration by affecting MMP2/3/7.