bluuebunny/crossref_metadata_2025_split huggingface dataset:
Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework
Authors: He Wenchuang , Xiang Kunli , Chen Caijin , Wang Jie , Wu Zhiqiang 
Published: January 2023

Abstract
Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.
Integrated mRNA sequence optimization using deep learning
Authors: Gong Haoran , Wen Jianguo , Luo Ruihan , Feng Yuzhou , Guo JingJing , Fu Hongguang , Zhou Xiaobo 
Published: January 2023

Abstract
The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5′ untranslated region (UTR) and 3′UTR generation. In ORF optimization, BiLSTM-CRF (bidirectional long-short-term memory with conditional random field) is employed to determine the codon for each amino acid. In UTR generation, RNA-Bart (bidirectional auto-regressive transformer) is proposed to output the corresponding UTR. The results show that the optimized sequences of exogenous genes acquired the pattern of human endogenous gene sequence. In experimental validation, the mRNA sequence optimized by our method, compared with conventional method, shows higher protein expression. To the best of our knowledge, this is the first study by introducing deep-learning methods to integrated mRNA sequence optimization, and these results may contribute to the development of mRNA therapeutics.
Executive protocol designed for new review study called: systematic review and artificial intelligence network meta-analysis (RAIN) with the first application for COVID-19
Authors: Salari Nader , Shohaimi Shamarina , Kiaei Aliakbar , Hosseinian-Far Amin , Mansouri Kamran , Ahmadi Arash , Mohammadi Masoud 
Published: January 2023

Abstract

Artificial intelligence (AI) as a suite of technologies can complement systematic review and meta-analysis studies and answer questions that cannot be typically answered using traditional review protocols and reporting methods. The purpose of this protocol is to introduce a new protocol to complete systematic review and meta-analysis studies.

In this work, systematic review, meta-analysis, and meta-analysis network based on selected AI technique, and for P &lt; 0.05 are followed, with a view to responding to questions and challenges that the global population is facing in light of the COVID-19 pandemic.

Finally, it is expected that conducting reviews by following the proposed protocol can provide suitable answers to some of the research questions raised due to COVID-19.
Haemorrhage of human foetal cortex associated with SARS-CoV-2 infection
Authors: Massimo Marco , Barelli Carlotta , Moreno Catalina , Collesi Chiara , Holloway Rebecca K , Crespo Berta , Zentilin Lorena , Williams Anna , Miron Veronique E , Giacca Mauro , Long Katherine R 
Published: January 2023

AbstractMaternal viral infection and immune response are known to increase the risk of altered development of the foetal brain. Given the ongoing global pandemic of coronavirus disease 2019 (COVID-19), investigating the impact of SARS-CoV-2 on foetal brain health is of critical importance. Here, we report the presence of SARS-CoV-2 in first and second trimester foetal brain tissue in association with cortical haemorrhages. SARS-CoV-2 spike protein was sparsely detected within progenitors and neurons of the cortex itself, but was abundant in the choroid plexus of haemorrhagic samples. SARS-CoV-2 was also sparsely detected in placenta, amnion and umbilical cord tissues. Cortical haemorrhages were linked to a reduction in blood vessel integrity and an increase in immune cell infiltration into the foetal brain. Our findings indicate that SARS-CoV-2 infection may affect the foetal brain during early gestation and highlight the need for further study of its impact on subsequent neurological development.
Prospective study and validation of early warning marker discovery based on integrating multi-omics analysis in severe burn patients with sepsis
Authors: Huang Jiamin , Chen Yi , Guo Zaiwen , Yu Yanzhen , Zhang Yi , Li Pingsong , Shi Lei , Lv Guozhong , Sun Bingwei 
Published: January 2023

Abstract

Background
Early detection, timely diagnosis and rapid response are essential for case management and precautions of burn-associated sepsis. However, studies on indicators for early warning and intervention have rarely been conducted. This study was performed to better understand the pathophysiological changes and targets for prevention of severe burn injuries.

Methods
We conducted a multi-center, prospective multi-omics study, including genomics, microRNAomics, proteomics and single-cell transcriptomics, in 60 patients with severe burn injuries. A mouse model of severe burn injuries was also constructed to verify the early warning ability and therapeutic effects of potential markers.

Results
Through genomic analysis, we identified seven important susceptibility genes (DNAH11, LAMA2, ABCA2, ZFAND4, CEP290, MUC20 and ENTPD1) in patients with severe burn injuries complicated with sepsis. Through plasma miRNAomics studies, we identified four miRNAs (hsa-miR-16-5p, hsa-miR-185-5p, hsa-miR-451a and hsa-miR-423-5p) that may serve as early warning markers of burn-associated sepsis. A proteomic study indicated the changes in abundance of major proteins at different time points after severe burn injury and revealed the candidate early warning markers S100A8 and SERPINA10. In addition, the proteomic analysis indicated that neutrophils play an important role in the pathogenesis of severe burn injuries, as also supported by findings from single-cell transcriptome sequencing of neutrophils. Through further studies on severely burned mice, we determined that S100A8 is also a potential early therapeutic target for severe burn injuries, beyond being an early warning indicator.

Conclusions
Our multi-omics study identified seven susceptibility genes, four miRNAs and two proteins as early warning markers for severe burn-associated sepsis. In severe burn-associated sepsis, the protein S100A8 has both warning and therapeutic effects.
Updating the Adherence–Response for Oral Emtricitabine/Tenofovir Disoproxil Fumarate for Human Immunodeficiency Virus Pre-Exposure Prophylaxis Among Cisgender Women
Authors: Anderson Peter L , Marzinke Mark A , Glidden David V 
Published: January 2023

Abstract
Using intraerythrocytic tenofovir-diphosphate data from the emtricitabine/tenofovir disoproxil fumarate arms of HIV Prevention Trials Network (HPTN) 083 (men) and HPTN 084 (women), approximately 99% efficacy was achieved at a lower adherence threshold in HPTN 083 (≥2 doses/week) compared with HPTN 084 (daily), suggesting higher adherence is necessary for women vs men.
Accelerating Human Immunodeficiency Virus Self-Testing in the United States: A Call to Action
Authors: Ma Stephany , MacGowan Robin J , Mermin Jonathan H , Owen S Michele , Manabe Yukari C 
Published: January 2023

Abstract
Human immunodeficiency virus (HIV) self-testing has emerged as a tool to increase the proportion of people to know their status. Since the first HIV self-test was approved in 2012 by the US Food and Drug Administration (FDA), global access to HIV self-tests has been bolstered by public-private partnerships to ensure equitable access in low- and middle-income countries. However, no company has applied for FDA clearance in a decade. We highlight the potential benefits to reclassifying HIV self-tests from class III to class II.
Development of an LC-MRM-MS-Based Candidate Reference Measurement Procedure for Standardization of Serum Apolipoprotein (a) Tests
Authors: Ruhaak L Renee , Romijn Fred P H T M , Begcevic Brkovic Ilijana , Kuklenyik Zsusanna , Dittrich Julia , Ceglarek Uta , Hoofnagle Andrew N , Althaus Harald , Angles-Cano Eduardo , Coassin Stefan , Delatour Vincent , Deprez Liesbet , Dikaios Ioannis , Kostner Gerhard M , Kronenberg Florian , Lyle Alicia , Prinzing Urban , Vesper Hubert W , Cobbaert Christa M 
Published: January 2023

AbstractBackgroundMedical results generated by European CE Marking for In Vitro Diagnostic or in-house tests should be traceable to higher order reference measurement systems (RMS), such as International Federation of Clinical Chemistry and Laboratory Medicine (IFCC)-endorsed reference measurement procedures (RMPs) and reference materials. Currently, serum apolipoprotein (a) [apo(a)] is recognized as a novel risk factor for cardiovascular risk assessment and patient management. The former RMS for serum apo(a) is no longer available; consequently, an International System of Units (SI)-traceable, ideally multiplexed, and sustainable RMS for apo(a) is needed.MethodsA mass spectrometry (MS)-based candidate RMP (cRMP) for apo(a) was developed using quantitative bottom-up proteomics targeting 3 proteotypic peptides. The method was provisionally validated according to ISO 15193 using a single human serum based calibrator traceable to the former WHO-IFCC RMS.ResultsThe quantitation of serum apo(a) was by design independent of its size polymorphism, was linear from 3.8 to 456 nmol/L, and had a lower limit of quantitation for apo(a) of 3.8 nmol/L using peptide LFLEPTQADIALLK. Interpeptide agreement showed Pearson Rs of 0.987 and 0.984 for peptides GISSTVTGR and TPENYPNAGLTR, and method comparison indicated good correspondence (slopes 0.977, 1.033, and 1.085 for LFLEPTQADIALLK, GISSTVTGR, and TPENYPNAGLTR). Average within-laboratory imprecision of the cRMP was 8.9%, 11.9%, and 12.8% for the 3 peptides.ConclusionsA robust, antibody-independent, MS-based cRMP was developed as higher order RMP and an essential part of the apo(a) traceability chain and future RMS. The cRMP fulfils predefined analytical performance specifications, making it a promising RMP candidate in an SI-traceable MS-based RMS for apo(a).
High-Density Lipoprotein Lipidomics in Chronic Kidney Disease
Authors: Lidgard Benjamin , Hoofnagle Andrew N , Zelnick Leila R , de Boer Ian H , Fretts Amanda M , Kestenbaum Bryan R , Lemaitre Rozenn N , Robinson-Cohen Cassianne , Bansal Nisha 
Published: January 2023

AbstractBackgroundPatients with chronic kidney disease (CKD) have dysfunctional high-density lipoprotein (HDL) particles as compared with the general population. Understanding the lipid composition of HDL may provide mechanistic insight. We tested associations of estimated glomerular filtration rate (eGFR) and albuminuria with relative HDL abundance of ceramides, sphingomyelins, and phosphatidylcholines in participants with CKD.MethodsWe studied 490 participants with CKD from the Seattle Kidney Study. HDL was isolated from plasma; targeted lipidomics was used to quantify the relative abundance of ceramides, sphingomyelins, and phosphatidylcholines per 10 µg of total HDL protein. We evaluated the associations of eGFR and albuminuria with levels of individual lipids and lipid classes (including 7 ceramides, 6 sphingomyelins, and 24 phosphatidylcholines) using multivariable linear regression, controlling for multiple comparisons via the false discovery rate.ResultsThe mean (SD) eGFR was 45 (24) mL/min/1.73 m2; the median (IQR[interquartile range]) albuminuria was 108 (16, 686) mg/g (12.2 [1.8, 77.6] mg/mmol) urine creatinine. After adjusting for demographics, past medical history, laboratory values, and medication use, eGFR was not associated with higher relative abundance of any class of lipids or individual lipids. Greater albuminuria was significantly associated with a higher relative abundance of total ceramides and moderate–long R-chain sphingomyelins, ceramides 22:0 and 24:1, hexosylceramide 16:0, sphingomyelin 16:0, and phosphatidylcholines 29:0, 30:1, and 38:2; the strongest association was for hexosylceramide 16:0 (increase per doubling of urine albumin to creatinine ratio 0.022 (95% CI, 0.012–0.032).ConclusionsGreater albuminuria was significantly associated with specific alterations in the lipid composition of HDL in participants with CKD.
Association of central obesity with unique cardiac remodelling in young adults born small for gestational age
Authors: Bernardino Gabriel , Sepúlveda-Martínez Álvaro , Rodríguez-López Mérida , Prat-González Susanna , Pajuelo Carolina , Perea Rosario J , Caralt Maria T , Crovetto Francesca , González Ballester Miguel A , Sitges Marta , Bijnens Bart , Crispi Fàtima 
Published: January 2023

Abstract

Aims
Being born small for gestational age (SGA, 10% of all births) is associated with increased risk of cardiovascular mortality in adulthood together with lower exercise tolerance, but mechanistic pathways are unclear. Central obesity is known to worsen cardiovascular outcomes, but it is uncertain how it affects the heart in adults born SGA. We aimed to assess whether central obesity makes young adults born SGA more susceptible to cardiac remodelling and dysfunction.

Methods and results
A perinatal cohort from a tertiary university hospital in Spain of young adults (30–40 years) randomly selected, 80 born SGA (birth weight below 10th centile) and 75 with normal birth weight (controls) was recruited. We studied the associations between SGA and central obesity (measured via the hip-to-waist ratio and used as a continuous variable) and cardiac regional structure and function, assessed by cardiac magnetic resonance using statistical shape analysis. Both SGA and waist-to-hip were highly associated to cardiac shape (F = 3.94, P &lt; 0.001; F = 5.18, P &lt; 0.001 respectively) with a statistically significant interaction (F = 2.29, P = 0.02). While controls tend to increase left ventricular end-diastolic volumes, mass and stroke volume with increasing waist-to-hip ratio, young adults born SGA showed a unique response with inability to increase cardiac dimensions or mass resulting in reduced stroke volume and exercise capacity.

Conclusion
SGA young adults show a unique cardiac adaptation to central obesity. These results support considering SGA as a risk factor that may benefit from preventive strategies to reduce cardiometabolic risk.
The interaction of forced expiratory volume in 1 s and N-terminal pro-B-type natriuretic peptide with outcomes after transcatheter aortic valve replacement
Authors: Crestanello Juan A , Greason Kevin L , Mathew Jessey , Eleid Mackram F , Nkomo Vuyisile T , Rihal Charanjit S , Bagameri Gabor , Holmes David R , Pislaru Sorin V , Sandhu Gurpreet S , Lee Alexander T , King Katherine S , Alkhouli Mohamad 
Published: January 2023

Abstract

OBJECTIVES
Low forced expiratory volume in 1 s (FEV1) and elevated N-terminal pro-B-type natriuretic peptide (NT-Pro-BNP) have been individually associated with poor outcomes after transcatheter aortic valve replacement (TAVR). We hypothesized a combination of the 2 would provide prognostic indication after TAVR.

METHODS
We categorized 871 patients who received TAVR from 2008 to 2018 into 4 groups according to baseline FEV1 (&lt;60% or ≥60% predicted) and NT-Pro-BNP (&lt;1601 or ≥1601 pg/ml): group A (n = 312, high FEV1, low NT-Pro-BNP), group B (n = 275, high FEV1, high NT-Pro-BNP), group C (n = 123 low FEV1, low NT-Pro-BNP) and group D (n = 161, low FEV1, high NT-Pro-BNP). The primary end point was survival at 1 and 5 years.

RESULTS
Patients in group A had more severe aortic stenosis and achieved the best long-term survival at 1 [93% (95% CI: 90–96)] and 5 [45.3% (95% CI: 35.4–58)] years. Low FEV1 and high NT-Pro-BNP (group D) patients had more severe symptoms, higher Society of Thoracic Surgeons predicted risk of operative mortality, lower ejection fraction and aortic valve gradient at baseline. Patients in group D had the worst survival at 1 [76% (95% CI: 69–83)] and 5 years [13.1% (95% CI: 7–25)], hazard ratio compared to group A: 2.29 (95% CI: 1.6–3.2, P &lt; 0.001) with 25.7% of patients in New York Heart Association class III–IV. Patients in groups B and C had intermediate outcomes.

CONCLUSIONS
The combination of FEV1 and NT-Pro-BNP stratifies patients into 4 groups with distinct risk profiles and clinical outcomes. Patients with low FEV1 and high NT-Pro-BNP have increased comorbidities, poor functional outcomes and decreased long-term survival after TAVR.
Dyskeratosis Congenita Links Telomere Attrition to &#x2028;Age-Related Systemic Energetics
Authors: James Emma Naomi , Sagi-Kiss Virag , Bennett Mark , Mycielska Maria Elzbieta , Karen-Ng Lee Peng , Roberts Terry , Matta Sheila , Dokal Inderjeet , Bundy Jacob Guy , Parkinson Eric Kenneth 
Published: January 2023

Abstract
The underlying mechanisms of plasma metabolite signatures of human aging and age-related diseases are not clear but telomere attrition and dysfunction are central to both. Dyskeratosis congenita (DC) is associated with mutations in the telomerase enzyme complex (TERT, TERC, and DKC1) and progressive telomere attrition. We analyzed the effect of telomere attrition on senescence-associated metabolites in fibroblast-conditioned media and DC patient plasma. Samples were analyzed by gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry. We showed extracellular citrate was repressed by canonical telomerase function in vitro and associated with DC leukocyte telomere attrition in vivo, leading to the hypothesis that altered citrate metabolism detects telomere dysfunction. However, elevated citrate and senescence factors only weakly distinguished DC patients from controls, whereas elevated levels of other tricarboxylic acid cycle (TCA) metabolites, lactate, and especially pyruvate distinguished them with high significance. The DC plasma signature most resembled that of patients with loss of function pyruvate dehydrogenase complex mutations and that of older subjects but significantly not those of type 2 diabetes, lactic acidosis, or elevated mitochondrial reactive oxygen species. Additionally, our data are consistent with further metabolism of citrate and lactate in the liver and kidneys. Citrate uptake in certain organs modulates age-related disease in mice and our data have similarities with age-related disease signatures in humans. Our results have implications for the role of telomere dysfunction in human aging in addition to its early diagnosis and the monitoring of anti-senescence therapeutics, especially those designed to improve telomere function.
Galyean appreciation club review: a holistic perspective of the societal relevance of beef production and its impacts on climate change
Authors: Tedeschi Luis O , Beauchemin Karen A 
Published: January 2023

Abstract
This article provides a science-based, data-driven perspective on the relevance of the beef herd in the U.S. to our society and greenhouse gas (GHG) contribution to climate change. Cattle operations are subject to criticism for their environmental burden, often based on incomplete information disseminated about their social, economic, nutritional, and ecological benefits and detriments. The 2019 data published by the U.S. Environmental Protection Agency reported that U.S. beef cattle emitted 22.6% of the total agricultural emissions, representing about 2.2% of the total anthropogenic emissions of CO2 equivalent (CO2e). Simulations from a computer model developed to address global energy and climate challenges, set to use extreme improvements in livestock and crop production systems, indicated a potential reduction in global CO2e emissions of 4.6% but without significant enhancement in the temperature change by 2030. There are many natural and anthropogenic sources of CH4 emissions. Contrary to the increased contribution of peatlands and water reservoirs to atmospheric CO2e, the steady decrease in the U.S. cattle population is estimated to have reduced its methane (CH4) emissions by about 30% from 1975 to 2021. This CH4 emission deacceleration of 2.46 Mt CO2e/yr2 might be even more significant than reported. Many opportunities exist to mitigate CH4 emissions of beef production, leading to a realistic prospect of a 5% to 15% reduction in the short term after considering the overlapping impacts of combined strategies. Reduction strategies include feeding synthetic chemicals that inactivate the methyl-coenzyme M reductase (the enzyme that catalyzes the last step of methanogenesis in the rumen), red seaweed or algae extracts, ionophore antibiotics, phytochemicals (e.g., condensed tannins and essential oils), and other nutritional manipulations. The proposed net-zero concept might not solve the global warming problem because it will only balance future anthropogenic GHG emissions with anthropogenic removals, leaving global warming on a standby state. Recommendations for consuming red meat products should consider human nutrition, health, and disease and remain independent of controversial evidence of causational relationships with perceived negative environmental impacts of beef production that are not based on scientific data.
To Like or Not to Like? An Experimental Study on Relational Closeness, Social Grooming, Reciprocity, and Emotions in Social Media Liking
Authors: Stsiampkouskaya Kseniya , Joinson Adam , Piwek Lukasz 
Published: January 2023

Abstract
We conducted a randomized-controlled experiment with 201 participants to investigate the effects of relationship closeness, emotions, and the receipt of Likes on reciprocal Liking behaviors. We found that individuals engaged in interchange-oriented social grooming by giving Likes to close friends regardless of whether they had received Likes from them before. However, when relationship closeness was low, participants mirrored their acquaintances’ behavior by reciprocating Likes for Likes. Additionally, high-arousal positive emotions mediated the effects of receiving Likes on the intention to Like other users’ content, but this result only held true when relational closeness was not accounted for in the model. Our study explains why people give Likes on social media and what factors shape their Liking intentions. The results of our study contribute to the existing knowledge of the social norm of reciprocity, social grooming, emotion regulation, relational closeness, and social media Liking.