bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving early obesity leads to a cardiometabolic profile within normal ranges at 23 years old in a two-decade prospective follow-up study
Authors: Correa-Burrows Paulina , Rogan José , Blanco Estela , East Patricia , Lozoff Betsy , Gahagan Sheila , Burrows Raquel 
Published: September 2021

AbstractObesity is the most important predisposing factor for cardiovascular disease and type-2 diabetes. We explored the relationship between the age at onset of obesity and selected cardiometabolic parameters in young adults. Longitudinal study of n = 1,039 participants (48% males) in their early twenties. BMI was measured at birth, 1–5–10–12–14–16–23 years. BMI trajectories were interpolated. Five groups were identified: never obese (never-OB); early childhood obesity transitioning to non-obesity before adolescence (former-OB); obesity starting in preadolescence transitioning to non-obesity as adolescents (transient-OB); obesity from adolescence into early adulthood (recent-onset-OB); participants who were obese in early childhood and remained obese into adulthood (persistent-OB). Waist circumference (WC), blood pressure, lipids, glucose, and insulin were measured at 23 years. HOMA-IR and the Metabolic Syndrome Risk Z-Score were estimated. In the sample, 47% were obese during at least one time-point. Mean obesity duration was 20.7 years, 8.5 years, 6.2 years, and 3.3 years in persistent-OBs, recent-onset-OBs, former-OBs, and transient-OBs, respectively. The cardiometabolic profile was more adverse in recent-onset-OBs (12%) and persistent-OBs (15%) compared to never-OB participants (53%). Although former-OBs (15%) and transient-OBs (4%) had higher WC values than never-OBs, no differences were seen in other biomarkers. Both persistent and recent-onset obesity led to a cardiometabolic profile of risk in early adulthood, as suggested by values of WC, HOMA-IR, and hs-CRP above normal limits and HDL-chol values below normal limits. Participants who had obesity in early childhood or preadolescence but transitioned to a non-obesity status had a cardiometabolic profile similar to participants who were never obese and within normal limits. Obesity leads to risky values in a number of cardiometabolic biomarkers in young adulthood independent of age at obesity onset. Likewise, overcoming obesity during the pediatric age leads to a cardiometabolic profile within normal ranges at 23 years of age.
Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation
Authors: Hegre Siv Anita , Samdal Helle , Klima Antonin , Stovner Endre B. , Nørsett Kristin G. , Liabakk Nina Beate , Olsen Lene Christin , Chawla Konika , Aas Per Arne , Sætrom Pål 
Published: September 2021

AbstractProper regulation of the cell cycle is necessary for normal growth and development of all organisms. Conversely, altered cell cycle regulation often underlies proliferative diseases such as cancer. Long non-coding RNAs (lncRNAs) are recognized as important regulators of gene expression and are often found dysregulated in diseases, including cancers. However, identifying lncRNAs with cell cycle functions is challenging due to their often low and cell-type specific expression. We present a highly effective method that analyses changes in promoter activity, transcription, and RNA levels for identifying genes enriched for cell cycle functions. Specifically, by combining RNA sequencing with ChIP sequencing through the cell cycle of synchronized human keratinocytes, we identified 1009 genes with cell cycle-dependent expression and correlated changes in RNA polymerase II occupancy or promoter activity as measured by histone 3 lysine 4 trimethylation (H3K4me3). These genes were highly enriched for genes with known cell cycle functions and included 57 lncRNAs. We selected four of these lncRNAs—SNHG26, EMSLR, ZFAS1, and EPB41L4A-AS1—for further experimental validation and found that knockdown of each of the four lncRNAs affected cell cycle phase distributions and reduced proliferation in multiple cell lines. These results show that many genes with cell cycle functions have concomitant cell-cycle dependent changes in promoter activity, transcription, and RNA levels and support that our multi-omics method is well suited for identifying lncRNAs involved in the cell cycle.
Avoidance of different durations, colours and intensities of artificial light by adult seabirds
Authors: Syposz Martyna , Padget Oliver , Willis Jay , Van Doren Benjamin M. , Gillies Natasha , Fayet Annette L. , Wood Matt J. , Alejo Aarón , Guilford Tim 
Published: September 2021

AbstractThere is increasing evidence for impacts of light pollution on the physiology and behaviour of wild animals. Nocturnally active Procellariiform seabirds are often found grounded in areas polluted by light and struggle to take to the air again without human intervention. Hence, understanding their responses to different wavelengths and intensities of light is urgently needed to inform mitigation measures. Here, we demonstrate how different light characteristics can affect the nocturnal flight of Manx shearwatersPuffinus puffinusby experimentally introducing lights at a colony subject to low levels of light pollution due to passing ships and coastal developments. The density of birds in flight above the colony was measured using a thermal imaging camera. We compared number of flying shearwaters under dark conditions and in response to an artificially introduced light, and observed fewer birds in flight during ‘light-on’ periods, suggesting that adult shearwaters were repelled by the light. This effect was stronger with higher light intensity, increasing duration of ‘light-on’ periods and with green and blue compared to red light. Thus, we recommend lower light intensity, red colour, and shorter duration of ‘light-on’ periods as mitigation measures to reduce the effects of light at breeding colonies and in their vicinity.
Identification of early and intermediate biomarkers for ARDS mortality by multi-omic approaches
Authors: Liao S. Y. , Casanova N. G. , Bime C. , Camp S. M. , Lynn H. , Garcia Joe G. N. 
Published: September 2021

AbstractThe lack of successful clinical trials in acute respiratory distress syndrome (ARDS) has highlighted the unmet need for biomarkers predicting ARDS mortality and for novel therapeutics to reduce ARDS mortality. We utilized a systems biology multi-“omics” approach to identify predictive biomarkers for ARDS mortality. Integrating analyses were designed to differentiate ARDS non-survivors and survivors (568 subjects, 27% overall 28-day mortality) using datasets derived from multiple ‘omics’ studies in a multi-institution ARDS cohort (54% European descent, 40% African descent). ‘Omics’ data was available for each subject and included genome-wide association studies (GWAS, n = 297), RNA sequencing (n = 93), DNA methylation data (n = 61), and selective proteomic network analysis (n = 240). Integration of available “omic” data identified a 9-gene set (TNPO1, NUP214, HDAC1, HNRNPA1, GATAD2A, FOSB, DDX17, PHF20, CREBBP) that differentiated ARDS survivors/non-survivors, results that were validated utilizing a longitudinal transcription dataset. Pathway analysis identified TP53-, HDAC1-, TGF-β-, and IL-6-signaling pathways to be associated with ARDS mortality. Predictive biomarker discovery identified transcription levels of the 9-gene set (AUC-0.83) and Day 7 angiopoietin 2 protein levels as potential candidate predictors of ARDS mortality (AUC-0.70). These results underscore the value of utilizing integrated “multi-omics” approaches in underpowered datasets from racially diverse ARDS subjects.
A new qualitative RT-PCR assay detecting SARS-CoV-2
Authors: Favaro Marco , Mattina Walter , Pistoia Enrico Salvatore , Gaziano Roberta , Di Francesco Paolo , Middleton Simon , D’Angelo Silvia , Altarozzi Tullio , Fontana Carla 
Published: September 2021

AbstractThe world is facing an exceptional pandemic caused by SARS-CoV-2. To allow the diagnosis of COVID-19 infections, several assays based on the real-time PCR technique have been proposed. The requests for diagnosis are such that it was immediately clear that the choice of the most suitable method for each microbiology laboratory had to be based, on the one hand, on the availability of materials, and on the other hand, on the personnel and training priorities for this activity. Unfortunately, due to high demand, the shortage of commercial diagnostic kits has also become a major problem. To overcome these critical issues, we have developed a new qualitative RT-PCR probe. Our system detects three genes—RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N)—and uses the β-actin gene as an endogenous internal control. The results from our assay are in complete agreement with the results obtained using a commercially available kit, except for two samples that did not pass the endogenous internal control. The coincidence rate was 0.96. The LoD of our assay was 140 cp/reaction for N and 14 cp/reaction for RdRp and E. Our kit was designed to be open, either for the nucleic acid extraction step or for the RT-PCR assay, and to be carried out on several instruments. Therefore, it is free from the industrial production logics of closed systems, and conversely, it is hypothetically available for distribution in large quantities to any microbiological laboratory. The kit is currently distributed worldwide (called MOLgen-COVID-19; Adaltis). A new version of the kit for detecting the S gene is also available.
Analysis of a gene family for PDF-like peptides from Arabidopsis
Authors: Omidvar Reza , Vosseler Nadine , Abbas Amjad , Gutmann Birgit , Grünwald-Gruber Clemens , Altmann Friedrich , Siddique Shahid , Bohlmann Holger 
Published: September 2021

Abstract Plant defensins are small, basic peptides that have a characteristic three-dimensional folding pattern which is stabilized by four disulfide bridges. We show here that Arabidopsis contains in addition to the proper plant defensins a group of 9 plant defensin-like (PdfL) genes. They are all expressed at low levels while GUS fusions of the promoters showed expression in most tissues with only minor differences. We produced two of the encoded peptides in E. coli and tested the antimicrobial activity in vitro. Both were highly active against fungi but had lower activity against bacteria. At higher concentrations hyperbranching and swollen tips, which are indicative of antimicrobial activity, were induced in Fusarium graminearum by both peptides. Overexpression lines for most PdfL genes were produced using the 35S CaMV promoter to study their possible in planta function. With the exception of PdfL4.1 these lines had enhanced resistance against F. oxysporum. All PDFL peptides were also transiently expressed in Nicotiana benthamiana leaves with agroinfiltration using the pPZP3425 vector. In case of PDFL1.4 this resulted in complete death of the infiltrated tissues after 7 days. All other PDFLs resulted only in various degrees of small necrotic lesions. In conclusion, our results show that at least some of the PdfL genes could function in plant resistance.
High levels of osteoprotegerin are associated with coronary artery calcification in patients suspected of a chronic coronary syndrome
Authors: Dekker Mirthe , Waissi Farahnaz , Silvis Max J. M. , Bennekom Joelle V. , Schoneveld Arjan H. , de Winter Robbert J. , Isgum Ivana , Lessmann Nikolas , Velthuis Birgitta K. , Pasterkamp Gerard , Mosterd Arend , Timmers Leo , de Kleijn Dominique P. V. 
Published: September 2021

AbstractPlasma osteoprotegerin (OPG) and vascular smooth muscle cell (VSMC) derived extracellular vesicles (EVs) are important regulators in the process of vascular calcification (VC). In population studies, high levels of OPG are associated with events. In animal studies, however, high OPG levels result in reduction of VC. VSMC-derived EVs are assumed to be responsible for OPG transport and VC but this role has not been studied. For this, we investigated the association between OPG in plasma and circulating EVs with coronary artery calcium (CAC) as surrogate for VC in symptomatic patients. We retrospectively assessed 742 patients undergoing myocardial perfusion imaging (MPI). CAC scores were determined on the MPI-CT images using a previously developed automated algorithm. Levels of OPG were quantified in plasma and two EV-subpopulations (LDL and TEX), using an electrochemiluminescence immunoassay. Circulating levels of OPG were independently associated with CAC scores in plasma; OR 1.39 (95% CI 1.17–1.65), and both EV populations; EV-LDL; OR 1.51 (95% CI 1.27–1.80) and EV-TEX; OR 1.21 (95% CI 1.02–1.42). High levels of OPG in plasma were independently associated with CAC scores in this symptomatic patient cohort. High levels of EV-derived OPG showed the same positive association with CAC scores, suggesting that EV-derived OPG mirrors the same pathophysiological process as plasma OPG.
The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids
Authors: Nielsen Tue Kjærgaard , Horemans Benjamin , Lood Cédric , T’Syen Jeroen , van Noort Vera , Lavigne Rob , Ellegaard-Jensen Lea , Hylling Ole , Aamand Jens , Springael Dirk , Hansen Lars Hestbjerg 
Published: September 2021

AbstractAminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its recalcitrant transformation product, 2,6-dichlorobenzamide (BAM), as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, requiring additional treatment in drinking water treatment plants or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. We present the complete genome of MSH1, which was determined independently in two institutes at Aarhus University and KU Leuven. Divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism, pBAM1 and pBAM2, the genome of MSH1 contained two megaplasmids and three smaller plasmids. The MSH1 substrain from KU Leuven showed a reduced genome lacking a megaplasmid and three smaller plasmids and was designated substrain MK1, whereas the Aarhus variant with all plasmids was designated substrain DK1. A plasmid stability experiment indicate that substrain DK1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Finally, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.
Quantitative assessment of sensitizing potency using a dose–response adaptation of GARDskin
Authors: Gradin Robin , Forreryd Andy , Mattson Ulrika , Jerre Anders , Johansson Henrik 
Published: September 2021

AbstractHundreds of chemicals have been identified as skin sensitizers. These are chemicals that possess the ability to induce hypersensitivity reactions in humans, giving rise to a condition termed allergic contact dermatitis. The capacity to limit hazardous exposure to such chemicals depends upon the ability to accurately identify and characterize their skin sensitizing potency. This has traditionally been accomplished using animal models, but their widespread use offers challenges from both an ethical and a scientific perspective. Comprehensive efforts have been made by the scientific community to develop new approach methodologies (NAMs) capable of replacing in vivo assays, which have successfully yielded several methods that can identify skin sensitizers. However, there is still a lack of new approaches that can effectively measure skin sensitizing potency. We present a novel methodology for quantitative assessment of skin sensitizing potency, which is founded on the already established protocols of the GARDskin assay. This approach analyses dose–response relationships in the GARDskin assay to identify chemical-specific concentrations that are sufficient to induce a positive response in the assay. We here compare results for 22 skin sensitizers analyzed using this method with both human and LLNA potency reference data and show that the results correlate strongly and significantly with both metrics (rLLNA = 0.81, p = 9.1 × 10–5; rHuman = 0.74, p = 1.5 × 10–3). In conclusion, the results suggest that the proposed GARDskin dose–response methodology provides a novel non-animal approach for quantitative potency assessment, which could represent an important step towards reducing the need for in vivo experiments.
Agro-productivity amidst environmental degradation and energy usage in Nigeria
Authors: Adeleye Bosede Ngozi , Daramola Praise , Onabote Ademola , Osabohien Romanus 
Published: September 2021

AbstractThis study revisits the 2030 United Nations Sustainable Development Goal (SDG) 2 which aims to “end hunger, achieve food security, improve nutrition and promote sustainable agriculture” by highlighting the impact of environmental degradation (proxied by carbon emissions) and non-renewable energy on agro-productivity in Nigeria. Using annual time series data from 1980 to 2018, the study engages the Johansen cointegration and impulse response functions (IRFs) techniques within the vector autoregressive (VAR) framework. Evidence reveals that carbon emissions significantly reduce agro-productivity by 0.23% while non-renewable energy boosts agro-productivity by 5.38%, on average, ceteris paribus. Other results reveal that domestic credit, rural population and arable land exert asymmetric effects. These outcomes are consistent and align with a priori expectations. Policy recommendations are discussed.
A novel lncRNA–protein interaction prediction method based on deep forest with cascade forest structure
Authors: Tian Xiongfei , Shen Ling , Wang Zhenwu , Zhou Liqian , Peng Lihong 
Published: September 2021

AbstractLong noncoding RNAs (lncRNAs) regulate many biological processes by interacting with corresponding RNA-binding proteins. The identification of lncRNA–protein Interactions (LPIs) is significantly important to well characterize the biological functions and mechanisms of lncRNAs. Existing computational methods have been effectively applied to LPI prediction. However, the majority of them were evaluated only on one LPI dataset, thereby resulting in prediction bias. More importantly, part of models did not discover possible LPIs for new lncRNAs (or proteins). In addition, the prediction performance remains limited. To solve with the above problems, in this study, we develop a Deep Forest-based LPI prediction method (LPIDF). First, five LPI datasets are obtained and the corresponding sequence information of lncRNAs and proteins are collected. Second, features of lncRNAs and proteins are constructed based on four-nucleotide composition and BioSeq2vec with encoder-decoder structure, respectively. Finally, a deep forest model with cascade forest structure is developed to find new LPIs. We compare LPIDF with four classical association prediction models based on three fivefold cross validations on lncRNAs, proteins, and LPIs. LPIDF obtains better average AUCs of 0.9012, 0.6937 and 0.9457, and the best average AUPRs of 0.9022, 0.6860, and 0.9382, respectively, for the three CVs, significantly outperforming other methods. The results show that the lncRNA FTX may interact with the protein P35637 and needs further validation.
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates
Authors: Zambrana Carme , Xenos Alexandros , Böttcher René , Malod-Dognin Noël , Pržulj Nataša 
Published: September 2021

AbstractThe COVID-19 pandemic is raging. It revealed the importance of rapid scientific advancement towards understanding and treating new diseases. To address this challenge, we adapt an explainable artificial intelligence algorithm for data fusion and utilize it on new omics data on viral–host interactions, human protein interactions, and drugs to better understand SARS-CoV-2 infection mechanisms and predict new drug–target interactions for COVID-19. We discover that in the human interactome, the human proteins targeted by SARS-CoV-2 proteins and the genes that are differentially expressed after the infection have common neighbors central in the interactome that may be key to the disease mechanisms. We uncover 185 new drug–target interactions targeting 49 of these key genes and suggest re-purposing of 149 FDA-approved drugs, including drugs targeting VEGF and nitric oxide signaling, whose pathways coincide with the observed COVID-19 symptoms. Our integrative methodology is universal and can enable insight into this and other serious diseases.
Agreement between commercially available ELISA and in-house Luminex SARS-CoV-2 antibody immunoassays
Authors: Santano Rebeca , Barrios Diana , Crispi Fàtima , Crovetto Francesca , Vidal Marta , Chi Jordi , Izquierdo Luis , Gratacós Eduard , Moncunill Gemma , Dobaño Carlota 
Published: September 2021

AbstractSerological diagnostic of the severe respiratory distress syndrome coronavirus 2 (SARS-CoV-2) is a valuable tool for the determination of immunity and surveillance of exposure to the virus. In the context of an ongoing pandemic, it is essential to externally validate widely used tests to assure correct diagnostics and epidemiological estimations. We evaluated the performance of the COVID-19 ELISA IgG and the COVID-19 ELISA IgM/A (Vircell, S.L.) against a highly specific and sensitive in-house Luminex immunoassay in a set of samples from pregnant women and cord blood. The agreement between both assays was moderate to high for IgG but low for IgM/A. Considering seropositivity by either IgG and/or IgM/A, the technical performance of the ELISA was highly imbalanced, with 96% sensitivity at the expense of 22% specificity. As for the clinical performance, the negative predictive value reached 87% while the positive predictive value was 51%. Our results stress the need for highly specific and sensitive assays and external validation of diagnostic tests with different sets of samples to avoid the clinical, epidemiological and personal disturbances derived from serological misdiagnosis.
Robust squeezed light against mode mismatch using a self imaging optical parametric oscillator
Authors: Roh Chan , Gwak Geunhee , Ra Young-Sik 
Published: September 2021

AbstractWe present squeezed light that is robust against spatial mode mismatch (beam displacement, tilt, and beam-size difference), which is generated from a self-imaging optical parametric oscillator below the threshold. We investigate the quantum properties of the generated light when the oscillator is detuned from the ideal self-imaging condition for stable operation. We find that the generated light is more robust to mode mismatch than single-mode squeezed light having the same squeezing level, and it even outperforms the single-mode infinitely squeezed light as the strength of mode mismatch increases.