bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life cycle greenhouse gas emissions of ethanol produced via fermentation of sugars derived from shrub willow (Salix ssp.) hot water extraction in the Northeast United States
Authors: Therasme Obste , Volk Timothy A. , Eisenbies Mark H. , Amidon Thomas E. , Fortier Marie-Odile 
Published: March 2021

Abstract
Background
The amount of carbon dioxide in the atmosphere has been on the rise for more than a century. Bioenergy crops are seen by the Intergovernmental Panel on Climate Change as an essential part of the solution to addressing climate change. To understand the potential impact of shrub willow (Salix spp.) crop in the northeast United States, effective and transparent life cycle assessment of these systems needs to occur.

Results
Here we show, ethanol produced from the fermentation of sugars from hot water extract of willow grown on cropland can sequester 0.012 ± 0.003 kg CO2eq MJ−1 for a supply system incorporating summer harvest and storage. Despite decreases in soil organic carbon when willow is instead grown on grassland, the produced fuel still can provide significant climate benefits compared to gasoline.

Conclusions
Shrub willow converted to ethanol can be a carbon negative source of transportation fuel when the electricity and heat required for the conversion process are generated from renewable biomass. The sequestration of carbon in the belowground portion of the plants is essential for the negative GHG balance for cropland and low GHG emissions in grassland.
Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host–pathogen interactions in the muscle stage
Authors: Hu Xiaoxiang , Liu Xiaolei , Li Chen , Zhang Yulu , Li Chengyao , Li Yanfeng , Chen Yingxi , Guo Heng , Bai Xue , Liu Mingyuan 
Published: March 2021

Abstract
Background
Parasites of the genus Trichinella are the pathogenic agents of trichinellosis, which is a widespread and severe foodborne parasitic disease. Trichinella spiralis resides primarily in mammalian skeletal muscle cells. After invading the cells of the host organism, T. spiralis must elude or invalidate the host’s innate and adaptive immune responses to survive. It is necessary to characterize the pathogenesis of trichinellosis to help to prevent the occurrence and further progression of this disease. The aims of this study were to elucidate the mechanisms of nurse cell formation, pathogenesis and immune evasion of T. spiralis, to provide valuable information for further research investigating the basic cell biology of Trichinella-infected muscle cells and the interaction between T. spiralis and its host.

Methods
We performed transcriptome profiling by RNA sequencing to identify global changes at 1, 3, 7, 10 and 15 days post-infection (dpi) in gene expression in the diaphragm after the parasite entered and persisted within the murine myocytes; the mice were infected by intravenous injection of newborn larvae. Gene expression analysis was based on the alignment results. Differentially expressed genes (DEGs) were identified based on their expression levels in various samples, and functional annotation and enrichment analysis were performed.

Results
The most extensive and dynamic gene expression responses in host diaphragms were observed during early infection (1 dpi). The number of DEGs and genes annotated in the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases decreased significantly in the infected mice compared to the uninfected mice at 3 and 7 dpi, suddenly increased sharply at 10 dpi, and then decreased to a lower level at 15 dpi, similar to that observed at 3 and 7 dpi. The massive initial reaction of the murine muscle cells to Trichinella infection steadied in the later stages of infection, with little additional changes detected for the remaining duration of the studied process. Although there were hundreds of DEGs at each time point, only 11 genes were consistently up- or downregulated at all 5 time points.

Conclusions
The gene expression patterns identified in this study can be employed to characterize the coordinated response of T. spiralis-infected myocytes in a time-resolved manner. This comprehensive dataset presents a distinct and sensitive picture of the interaction between host and parasite during intracellular infection, which can help to elucidate how pathogens evade host defenses and coordinate the biological functions of host cells to survive in the mammalian environment.

Graphical Abstract
Genetic diversity analysis of Dermacentor nuttalli within Inner Mongolia, China
Authors: Gui Zheng , Wu Lin , Cai Hao , Mu Lan , Yu Jing-Feng , Fu Shao-Yin , Si Xiao-Yan 
Published: March 2021

AbstractBackgroundTicks (Arthropoda, Ixodida), after mosquitoes, are the second most prevalent vector of infectious diseases. They are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. However, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous Region of China, surprisingly, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied.MethodsWe characterized the haplotype distribution ofDermacentor nuttalliin four main pastoral areas of the Inner Mongolia Autonomous Region, by sampling 109 individuals (recovered from sheep) in April–August 2019. The 16S rRNA gene, cytochrome c oxidase subunit I (COI), and the internal transcribed spacer 2 region (ITS2) were amplified and sequenced from extracted DNA.ResultsTwenty-six haplotypes were identified using 16S rRNA sequences, 57 haplotypes were identified with COI sequences, and 75 haplotypes were identified with ITS2 sequences. Among the three genes, total haplotype diversity was greater than 0.7, while total nucleotide diversity was greater than 0.06. Neutrality tests revealed a significantly negative Tajima’s D result, while Fu's Fs was not significantly positive. Fixation index values (FST) indicated that the degree of genetic differentiation among some sampled populations was small, while for others it was moderate. Analysis of molecular variance (AMOVA) revealed that the variation within populations was greater than that among populations. The mismatch analysis ofD. nuttalliexhibited double peaks.ConclusionThe genetic diversity ofD. nuttallipopulations in our region can likely adapt to different geographical environments, thereby leading to genetic diversity, and creating genetic differentiation among different populations. However, genetic differentiation is cryptic and does not form a pedigree geographical structure.Graphical Abstract
The reproducibility of measuring maximum abdominal aortic aneurysm diameter from ultrasound images
Authors: Matthews Evan O. , Pinchbeck Jenna , Elmore Kylie , Jones Rhondda E. , Moxon Joseph V. , Golledge Jonathan 
Published: March 2021

Abstract
Background
Accurate repeat assessment of the diameter of an abdominal aortic aneurysm (AAA) is important. This study investigated the reproducibility of different methods of measuring AAA diameter from ultrasound images.

Methods
Fifty AAA patients were assessed by ultrasound. Maximum AAA diameter was measured independently by three trained observers on two separate occasions using a standardised protocol. Five diameters were measured from each scan, three in the anterior–posterior (AP) and two in the transverse (TV) plane, including inner-to-inner (ITI), outer-to-outer (OTO) and leading edge-to-leading edge (LETLE). Intra- and inter-observer reproducibility were reported as reproducibility coefficients. Statistical comparison of methods was performed using linear mixed effects models.

Results
Intra-observer reproducibility coefficients (AP LETLE 2.2 mm; AP ITI 2.4 mm; AP OTO 2.6 mm) were smaller than inter-observer reproducibility coefficients (AP LETLE 4.6 mm: AP ITI 4.5; and AP OTO 4.8 mm). There was no statistically significant difference in intra-observer reproducibility of three types of measurements performed in the AP plane. Measurements obtained in the TV plane had statistically significant worse intra-observer reproducibility than those performed in the AP plane.

Conclusions
This study suggests that the comparison of maximum AAA diameter between repeat images is most reproducibly performed by a single trained observer measuring diameters in the AP plane.
Diagnostic accuracy of lung ultrasound for SARS-CoV-2: a retrospective cohort study
Authors: Brenner Daniel S. , Liu Gigi Y. , Omron Rodney , Tang Olive , Garibaldi Brian T. , Fong Tiffany C. 
Published: March 2021

Abstract
Background
As medical infrastructures are strained by SARS-CoV-2, rapid and accurate screening tools are essential. In portions of the world, reverse transcription polymerase chain reaction (RT-PCR) testing remains slow and in limited supply, and computed tomography is expensive, inefficient, and involves exposure to ionizing radiation. Multiple studies evaluating the efficiency of lung point-of-care ultrasound (POCUS) have been published recently, but include relatively small cohorts and often focus on characteristics associated with severe illness rather than screening efficacy. This study utilizes a retrospective cohort to evaluate the test characteristics (sensitivity, specificity, likelihood ratios, predictive values) of lung POCUS in the diagnosis of SARS-CoV-2, and to determine lung score cutoffs that maximize performance for use as a screening tool.

Results
Lung POCUS examinations had sensitivity 86%, specificity 71.6%, NPV 81.7%, and PPV 77.7%. The Lung Ultrasound Score had an area under the curve of 0.84 (95% CI 0.78, 0.90). When including only complete examinations visualizing 12 lung fields, lung POCUS had sensitivity 90.9% and specificity 75.6%, with NPV 87.2% and PPV 82.0% and an area under the curve of 0.89 (95% CI 0.83, 0.96). Lung POCUS was less accurate in patients with a history of interstitial lung disease, severe emphysema, and heart failure.

Conclusions
When applied in the appropriate patient population, lung POCUS is an inexpensive and reliable tool for rapid screening and diagnosis of SARS-CoV-2 in symptomatic patients with influenza-like illness. Adoption of lung POCUS screening for SARS-CoV-2 may identify patients who do not require additional testing and reduce the need for RT-PCR testing in resource-limited environments and during surge periods.
A COVID-19 pregnant patient with thrombotic thrombocytopenic purpura: a case report
Authors: Aminimoghaddam Soheila , Afrooz Narjes , Nasiri Setare , Motaghi Nejad Ozra , Mahmoudzadeh Fatemeh 
Published: March 2021

Abstract
Background
Pregnancy seems to increase the risk of thrombotic thrombocytopenic purpura (TTP) relapses and make the TTP more severe in any of the pregnancy trimesters, or even during the postpartum period.

Case presentation
This study highlights details of treating a COVID-19 pregnant patient who survived. This 21-year addicted White woman was admitted at her 29th week and delivered a stillbirth. She was transferred to another hospital after showing signs of TTP, which was caused by a viral infection.

Conclusion
This viral infection caused fever and dyspnea, and the patient was tested positive for COVID-19 infection. A chest computed tomography scan showed diffuse multiple bilateral consolidations and interlobar septal thickening. She stayed at the Intensive Care Unit for 20 days and treated with plasmapheresis. As far as we know, this is the first report of a TTP pregnant patient with COVID-19 infection.
Hemophagocytic lymphohistiocytosis and myelodysplastic syndrome: a case report and review of the literature
Authors: Sun Y. , Blieden C. , Merritt B. Y. , Sosa R. , Rivero Gustavo 
Published: March 2021

Abstract
Background
Hemophagocytic lymphohistiocytosis (HLH) is characterized by hyperinflammation and life-threatening cytopenias. Survival is poor, and management is pivotal on rapid identification of the disease. HLH is associated with hematologic malignancies, however correlation with myelodysplastic syndromes (MDS) is exceedingly unusual. Although minimizing overwhelming hyperinflammation by treating hemophagocytosis are central for HLH outcome, there is urgent necessity to identify potential initiating mechanisms that could assist in therapy design.

Case description
Here, we describe an elderly African American patient who developed rapid onset of cytopenias and coagulopathy associated with hepatic and bone marrow hemophagocytosis. We analyze four additional similar cases to isolate clinical, laboratory and cytogenetic findings expected in patients exhibiting concurrent HLH and MDS. HLH linked with MDS retains common HLH features associated with systemic hyperinflammation such as fever, hypotension, hepatosplenomegaly, hyperferritinemia, coagulopathy and rapidly evolving cytopenias. Typical MDS chromosomic abnormality such as trisomy 8 was frequently observed in our studied cases.

Conclusion
Our case describes difficulties while managing HLH in MDS patients. Diagnosis should be based on identifying HLH appropriate criteria and if possible karyotypic abnormalities normally observed in MDS.
METTL3-mediated m6A modification regulates cell cycle progression of dental pulp stem cells
Authors: Luo Haiyun , Liu Wenjing , Zhang Yanli , Yang Yeqing , Jiang Xiao , Wu Shiqing , Shao Longquan 
Published: March 2021

Abstract
Background
Dental pulp stem cells (DPSCs) are a promising cell source in endodontic regeneration and tissue engineering with limited self-renewal and pluripotency capacity. N6-methyladenosine (m6A) is the most prevalent, reversible internal modification in RNAs associated with stem cell fate determination. In this study, we aim to explore the biological effect of m6A methylation in DPSCs.

Methods
m6A immunoprecipitation with deep sequencing (m6A RIP-seq) demonstrated the features of m6A modifications in DPSC transcriptome. Lentiviral vectors were constructed to knockdown or overexpress methyltransferase like 3 (METTL3). Cell morphology, viability, senescence, and apoptosis were analyzed by β-galactosidase, TUNEL staining, and flow cytometry. Bioinformatic analysis combing m6A RIP and shMETTL3 RNA-seq functionally enriched overlapped genes and screened target of METTL3. Cell cycle distributions were assayed by flow cytometry, and m6A RIP-qPCR was used to confirm METTL3-mediated m6A methylation.

Results
Here, m6A peak distribution, binding area, and motif in DPSCs were first revealed by m6A RIP-seq. We also found a relatively high expression level of METTL3 in immature DPSCs with superior regenerative potential and METTL3 knockdown induced cell apoptosis and senescence. A conjoint analysis of m6A RIP and RNA sequencing showed METTL3 depletion associated with cell cycle, mitosis, and alteration of METTL3 resulted in cell cycle arrest. Furthermore, the protein interaction network of differentially expressed genes identified Polo-like kinase 1 (PLK1), a critical cycle modulator, as the target of METTL3-mediated m6A methylation in DPSCs.

Conclusions
These results revealed m6A methylated hallmarks in DPSCs and a regulatory role of METTL3 in cell cycle control. Our study shed light on therapeutic approaches in vital pulp therapy and served new insight into stem cell-based tissue engineering.
Development of the new CPTSD diagnosis for ICD-11
Authors: Maercker Andreas 
Published: March 2021

Abstract
Background
The diagnosis of complex post-traumatic stress disorder (CPTSD) was proposed several decades ago by scientist-practitioners, almost parallel to the first description of the diagnosis of post-traumatic stress disorder (PTSD). In the previous International Classification of Diseases, version 10 (ICD-10) issued by the World Health Organization (WHO), this symptom constellation was termed ‘enduring personality change after catastrophic experience’. This diagnosis has not been clinically influential, nor has it been subjected to much research. Thus, in a multi-stage process of ICD-11 development, the diagnosis of CPTSD was developed.

Methods
This paper provides a review of the historical lines of development that led to the CPTSD diagnosis, as well as the results since the ICD-11 publication in 2018.

Results
The CPTSD diagnosis comprises the core symptoms of the – newly, narrowly defined – PTSD diagnosis, the three symptom groups of affective, relationship, and self-concept changes. The diagnosis is clinically easy to use in accordance with the WHO development goals for the ICD-11 and has shown good psychodiagnostic properties in various studies, including good discrimination from personality disorder with borderline pattern.

Conclusion
The scholarly use of the new diagnosis has resulted in an increasing number of published studies on this topic in the diagnostic and therapeutic fields.
An analysis of COVID-19 economic measures and attitudes: evidence from social media mining
Authors: Domalewska Dorota 
Published: March 2021

AbstractThis paper explores the public perception of economic measures implemented as a reaction to the COVID-19 pandemic in Poland in March–June 2020. A mixed-method approach was used to analyse big data coming from tweets and Facebook posts related to the mitigation measures to provide evidence for longitudinal trends, correlations, theme classification and perception. The online discussion oscillated around political and economic issues. The implementation of the anti-crisis measures triggered a barrage of criticism pointing out the shortcomings and ineffectiveness of the solutions. The revised relief legislation was accompanied by a wide-reaching informative campaign about the relief package, which decreased negative sentiment. The analysis also showed that with regard to online discussion about risk mitigation, social media users are more concerned about short-term economic and social effects rather than long-term effects of the pandemic. The findings have significant implications for the understanding of public sentiment related to the COVID-19 pandemic, economic attitudes and relief support implemented to fight the adverse effects of the pandemic.
The role of net ecosystem productivity and of inventories in climate change research: the need for “net ecosystem productivity with harvest”, NEPH
Authors: Schulze E. D. , Valentini R. , Bouriaud O. 
Published: March 2021

Abstract
Background
There is an urgent need for quantifying the terrestrial carbon sink in the context of global carbon emissions. However, neither the flux measurements, nor the national wood balances fulfil this purpose. In this discussion article we point at various shortcomings and necessary improvements of these approaches in order to achieve a true quantification of the carbon exchange of land surfaces.

Results
We discuss the necessity of incorporating all lateral fluxes, but mainly the export of biomass by harvest, into the flux balance and to recognize feedbacks between management and fluxes to make flux measurements compatible with inventories. At the same time, we discuss the necessity that national reports of wood use need to fully recognize the use of wood for energy use. Both approaches of establishing an ecosystem carbon balance, fluxes and inventories, have shortcomings.

Conclusions
Including harvest and feedbacks by management appears to be the main requirement for the flux approach. A better quantification of wood use for bioenergy seems a real need for integrating the national wood balances into the global carbon cycle.
Proposed virulence-associated genes of Streptococcus suis isolates from the United States serve as predictors of pathogenicity
Authors: Estrada April A. , Gottschalk Marcelo , Rendahl Aaron , Rossow Stephanie , Marshall-Lund Lacey , Marthaler Douglas G. , Gebhart Connie J. 
Published: March 2021

AbstractBackgroundThere is limited information on the distribution of virulence-associated genes (VAGs) in U.S.Streptococcus suisisolates, resulting in little understanding of the pathogenic potential of these isolates. This lack also reduces our understanding of the epidemiology associated withS. suisin the United States and thus affects the efficiency of control and prevention strategies.In this study we applied whole genome sequencing (WGS)-based approaches for the characterization ofS. suisand identification of VAGs.ResultsOf 208 S. suisisolates classified as pathogenic, possibly opportunistic, and commensal pathotypes, the genotype based on the classical VAGs (epf,mrp, andslyencoding the extracellular protein factor, muramidase-release protein, and suilysin, respectively) was identified in 9% (epf+/mrp+/sly+) of the pathogenic pathotype. Using the chi-square test and LASSO regression model, the VAGsofs(encoding the serum opacity factor) andsrtF(encoding sortase F) were selected out of 71 published VAGs as having a significant association with pathotype, and both genes were found in 95% of the pathogenic pathotype. Theofs+/srtF+ genotype was also present in 74% of ‘pathogenic’ isolates from a separate validation set of isolates.Pan-genome clustering resulted in the differentiation of a group of isolates from five swine production companies into clusters corresponding to clonal complex (CC) and virulence-associated (VA) genotypes. The same CC-VA genotype patterns were identified in multiple production companies, suggesting a lack of association between production company, CC, or VA genotype.ConclusionsThe proposedofsandsrtFgenes were stronger predictors for differentiating pathogenic and commensalS. suisisolates compared to the classical VAGs in two sets of U.S. isolates. Pan-genome analysis in combination with metadata (serotype, ST/CC, VA genotype) was illustrated to be a valuable subtyping tool to describe the genetic diversity ofS. suis.
Dynamic connectedness between stock markets in the presence of the COVID-19 pandemic: does economic policy uncertainty matter?
Authors: Youssef Manel , Mokni Khaled , Ajmi Ahdi Noomen 
Published: March 2021

AbstractThis study investigates the dynamic connectedness between stock indices and the effect of economic policy uncertainty (EPU) in eight countries where COVID-19 was most widespread (China, Italy, France, Germany, Spain, Russia, the US, and the UK) by implementing the time-varying VAR (TVP-VAR) model for daily data over the period spanning from 01/01/2015 to 05/18/2020. Results showed that stock markets were highly connected during the entire period, but the dynamic spillovers reached unprecedented heights during the COVID-19 pandemic in the first quarter of 2020. Moreover, we found that the European stock markets (except Italy) transmitted more spillovers to all other stock markets than they received, primarily during the COVID-19 outbreak. Further analysis using a nonlinear framework showed that the dynamic connectedness was more pronounced for negative than for positive returns. Also, findings showed that the direction of the EPU effect on net connectedness changed during the pandemic onset, indicating that information spillovers from a given market may signal either good or bad news for other markets, depending on the prevailing economic situation. These results have important implications for individual investors, portfolio managers, policymakers, investment banks, and central banks.