bluuebunny/crossref_metadata_2025_split huggingface dataset:
An environmental justice fictional case study for engaging non-majors in human biology
Authors: Peters John Jacob 
Published: March 2024

ABSTRACT

The impacts of climate change are and will continue to be far-reaching, and environmental justice communities are disproportionately impacted due to environmental racism and related forms of oppression. Vision and Change in Undergraduate Biology Education encourages that the connection between science and society be explicitly taught in science classrooms. Here, I describe a fictional case study where students decide how to allocate a budget at a non-profit organization tasked with mitigating environmental issues in a town that contains environmental justice communities. Students are each assigned a role in the community and must reach a consensus on their budget in small groups before the whole class votes on a consensus budget. Afterward, students perform a metacognitive activity that encourages them to reflect on the human health impacts of their decisions and how their role impacted their decision-making process. Quantitative and qualitative feedback from students shows that by the end of the course, students appreciate the importance of science literacy in understanding global issues and that they are able to connect environmental justice to their lives and coursework. This case study helps fill an unmet need in climate change education by allowing students to practice empathy in topics related to climate change and environmental justice.
Plasminogen activator urokinase interacts with the fusion protein and antagonizes the growth of Peste des petits ruminants virus
Authors: Wu Junhuang , Yang Wenping , Li Lingxia , Wu Jingyan , He Jijun , Ru Yi , Ren Jingjing , Wang Yong , Zheng Haixue , Shang Youjun , Li Dan 
Published: March 2024

ABSTRACT

Peste des petits ruminants is an acute and highly contagious disease caused by the Peste des petits ruminants virus (PPRV). Host proteins play a crucial role in viral replication. However, the effect of fusion (F) protein-interacting partners on PPRV infection is poorly understood. In this study, we found that the expression of goat plasminogen activator urokinase (PLAU) gradually decreased in a time- and dose-dependent manner in PPRV-infected goat alveolar macrophages (GAMs). Goat PLAU was subsequently identified using co-immunoprecipitation and confocal microscopy as an F protein binding partner. The overexpression of goat PLAU inhibited PPRV growth and replication, whereas silencing goat PLAU promoted viral growth and replication. Additionally, we confirmed that goat PLAU interacted with a virus-induced signaling adapter (VISA) to antagonize F-mediated VISA degradation, increasing the production of type I interferon. We also found that goat PLAU reduced the inhibition of PPRV replication in VISA-knockdown GAMs. Our results show that the host protein PLAU inhibits the growth and replication of PPRV by VISA-triggering RIG-I-like receptors and provides insight into the host protein that antagonizes PPRV immunosuppression.

IMPORTANCE
The role of host proteins that interact with Peste des petits ruminants virus (PPRV) fusion (F) protein in PPRV replication is poorly understood. This study confirmed that goat plasminogen activator urokinase (PLAU) interacts with the PPRV F protein. We further discovered that goat PLAU inhibited PPRV replication by enhancing virus-induced signaling adapter (VISA) expression and reducing the ability of the F protein to degrade VISA. These findings offer insights into host resistance to viral invasion and suggest new strategies and directions for developing PPR vaccines.
Discovery and characterization of novel DNA viruses in
Apis mellifera
: expanding the honey bee virome through metagenomic analysis
Authors: Kadlečková Dominika , Saláková Martina , Erban Tomáš , Tachezy Ruth 
Published: March 2024

ABSTRACT

To date, many viruses have been discovered to infect honey bees. In this study, we used high-throughput sequencing to expand the known virome of the honey bee,
Apis mellifera
, by identifying several novel DNA viruses. While the majority of previously identified bee viruses are RNA, our study reveals nine new genomes from the
Parvoviridae
family, tentatively named Bee densoviruses 1 to 9. In addition, we characterized a large DNA virus, Apis mellifera filamentous-like virus (AmFLV), which shares limited protein identities with the known Apis mellifera filamentous virus. The complete sequence of AmFLV, obtained by a combination of laboratory techniques and bioinformatics, spans 152,678 bp. Linear dsDNA genome encodes for 112 proteins, of which 49 are annotated. Another large virus we discovered is Apis mellifera nudivirus, which belongs to a group of
Alphanudivirus
. The virus has a length of 129,467 bp and a circular dsDNA genome, and has 106 protein encoding genes. The virus contains most of the core genes of the family
Nudiviridae
. This research demonstrates the effectiveness of viral binning in identifying viruses in honey bee virology, showcasing its initial application in this field.

IMPORTANCE
Honey bees contribute significantly to food security by providing pollination services. Understanding the virome of honey bees is crucial for the health and conservation of bee populations and also for the stability of the ecosystems and economies for which they are indispensable. This study unveils previously unknown DNA viruses in the honey bee virome, expanding our knowledge of potential threats to bee health. The use of the viral binning approach we employed in this study offers a promising method to uncovering and understanding the vast viral diversity in these essential pollinators.
Argonaute and Dicer are essential for communication between
Trichoderma atroviride
and fungal hosts during mycoparasitism
Authors: Enriquez-Felix Eli Efrain , Pérez-Salazar Camilo , Rico-Ruiz José Guillermo , Calheiros de Carvalho Ana , Cruz-Morales Pablo , Villalobos-Escobedo José Manuel , Herrera-Estrella Alfredo 
Published: March 2024

ABSTRACT

Trichoderma
species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism,
Trichoderma
spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host’s cell wall. Here, we explored the participation of the
Trichoderma atroviride
RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the
T. atroviride
-RNAi when interacting with
Alternaria alternata, Rhizoctonia solani
AG2
,
and
R. solani
AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the
Trichoderma
-host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition (
het
) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in
T. atroviride
dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established.

IMPORTANCE

There is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing
Trichoderma
species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by
Trichoderma
species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of
Trichoderma
species, there are still unsolved questions related to how
Trichoderma
regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by
Trichoderma atroviride
.
Integrated bacterial transcriptome and host metabolome analysis reveals insights into “
Candidatus
Liberibacter asiaticus” population dynamics in the fruit pith of three citrus cultivars with different tolerance
Authors: Li Yun , Ma Ruifeng , Gao Chenying , Li Ziyi , Zheng Yongqin , Fang Fang , Wang Cheng , Li Guohua , Du Xiaozhen , Xu Changbao , Xu Meirong , Liu Rui , Deng Xiaoling , Zheng Zheng 
Published: March 2024

ABSTRACT

“
Candidatus
Liberibacter asiaticus” (CLas), the causal agent of citrus Huanglongbing (HLB), is able to multiply to a high abundance in citrus fruit pith. However, little is known about the biological processes and phytochemical substances that are vital for CLas colonization and growth in fruit pith. In this study, CLas-infected fruit pith of three citrus cultivars (“Shatangju” mandarin, “Guanxi” pomelo, and “Shatian” pomelo) exhibiting different tolerance to CLas were collected and used for dual RNA-Seq and untargeted metabolome analysis. Comparative transcriptome analysis found that the activation of the CLas noncyclic TCA pathway and pathogenic-related effectors could contribute to the colonization and growth of CLas in fruit pith. The pre-established Type 2 prophage in the CLas genome and the induction of its CRISPR/
cas
system could enhance the phage resistance of CLas and, in turn, facilitate CLas population growth in fruit pith. CLas infection caused the accumulation of amino acids that were correlated with tolerance to CLas. The accumulation of most sugars and organic acids in CLas-infected fruit pith, which could be due to the phloem blockage caused by CLas infection, was thought to be beneficial for CLas growth in localized phloem tissue. The higher levels of flavonoids and terpenoids in the fruit pith of CLas-tolerant cultivars, particularly those known for their antimicrobial properties, could hinder the growth of CLas. This study advances our understanding of CLas multiplication in fruit pith and offers novel insight into metabolites that could be responsible for tolerance to CLas or essential to CLas population growth.

IMPORTANCE

Citrus Huanglongbing (HLB, also called citrus greening disease) is a highly destructive disease currently threatening citrus production worldwide. HLB is caused by an unculturable bacterial pathogen, “
Candidatus
Liberibacter asiaticus” (CLas). However, the mechanism of CLas colonization and growth in citrus hosts is poorly understood. In this study, we utilized the fruit pith tissue, which was able to maintain the CLas at a high abundance, as the materials for dual RNA-Seq and untargeted metabolome analysis, aiming to reveal the biological processes and phytochemical substances that are vital for CLas colonization and growth. We provided a genome-wide CLas transcriptome landscape in the fruit pith of three citrus cultivars with different tolerance and identified the important genes/pathways that contribute to CLas colonization and growth in the fruit pith. Metabolome profiling identified the key metabolites, which were mainly affected by CLas infection and influenced the population dynamic of CLas in fruit pith.
Variation in the relationship between fasting glucose and HbA1c: implications for the diagnosis of diabetes in different age and ethnic groups
Authors: Ram Yashesvini , Xu Yongjin , Cheng Alan , Dunn Timothy , Ajjan Ramzi A 
Published: March 2024

IntroductionIdentify non-glycemic factors affecting the relationship between fasting plasma glucose (FPG) and glycated hemoglobin (HbA1c), in order to refine diabetes diagnostic criteria.Research design and methodsRelationship between FPG–HbA1c was assessed in 12 531 individuals from 2001 to 2018 US National Health and Nutrition Examination Survey. Using a recently described method, FPG and HbA1c were used to calculate apparent glycation ratio (AGR) of red blood cells for different subgroups based on age, race, and gender.ResultsAt an FPG of 7 mmol/L, black individuals had a higher HbA1c (p<0.001, mean: 50.2 mmol/mol, 95% CI (49.8 to 50.4)) compared with white individuals (47.4 mmol/mol (47.2 to 47.5)). This corresponds to NGSP (National Glycohemoglobin Standardization Program) units of 6.7% and 6.5% for black versus white individuals, respectively. Similarly, individuals under 21 years had lower HbA1c (p<0.001, 47.9 mmol/mol (47.7 to 48.1), 6.5%) compared with those over 50 years (48.3 mmol/mol (48.2 to 48.5), 6.6%). Differences were also observed between women (p<0.001, 49.2 mmol/mol (49.1 to 49.3), 6.7%) and men (47.0 mmol/mol (46.8 to 47.1), 6.5%). Of note, the difference in HbA1c at FPG of 7 mmol/L in black females over 50 and white males under 21 years was 5 mmol/mol (0.46%). AGR differences according to race (p<0.001), age (p<0.001), and gender (p<0.001) explained altered glucose–HbA1c relationship in the analyzed groups.ConclusionsFPG–HbA1c relationship is affected by non-glycemic factors leading to incorrect diagnosis of diabetes in some individuals and ethnic groups. Assessment of AGR helps understand individual-specific relationship between glucose levels and HbA1c, which has the potential to more accurately diagnose and manage diabetes.
Greater persistence and adherence to basal insulin therapy is associated with lower healthcare utilization and medical costs in patients with type 2 diabetes: a retrospective database analysis
Authors: Aroda Vanita R , Nielsen Nick , Mangla Kamal K , Multani Jasjit , Divino Victoria , Namvar Tarlan , Rajpura Jigar 
Published: March 2024

IntroductionWe aimed to assess persistence and adherence to basal insulin therapy, their association with all-cause healthcare resource utilization (HCRU) and direct medical costs, and predictors of persistence and adherence in adults with type 2 diabetes.Research design and methodsA retrospective cohort study was conducted with US adults with type 2 diabetes initiating basal insulin therapy between January 1, 2016, and December 31, 2018, using IQVIA PharMetrics Plus claims data. Persistence and adherence were assessed during 1 year post-initiation per previous definitions. Demographic/clinical characteristics were assessed during the 1 year pre-initiation. Inverse probability of treatment weighting (IPTW) was used to adjust for confounding variables. Post-IPTW, all-cause HCRU and direct medical costs were assessed during the first-year and second-year post-initiation by persistence and adherence status. Multivariable logistic regression was used to identify predictors of persistence and adherence.ResultsThe final sample comprised 64,953 patients; 56.8% demonstrated persistence and 41.9% demonstrated adherence. Patients demonstrating persistence and adherence were significantly less likely to have a hospitalization than patients demonstrating non-persistence or non-adherence, respectively. In the second-year post-initiation, total mean all-cause direct medical costs per patient were lower for patients demonstrating persistence and significantly lower for patients demonstrating adherence. Prior use of both oral and injectable antidiabetic medication predicted persistence and adherence compared with patients with only prior oral antidiabetic medication use (persistence OR, 1.50 (95% CI, 1.44 to 1.57); adherence OR, 1.48 (95% CI, 1.42 to 1.55)).ConclusionsPersistence and adherence to basal insulin was associated with fewer hospitalizations and lower direct medical costs.
Omentin associates with serum metabolite profiles indicating lower diabetes risk: KORA F4 Study
Authors: Ratter-Rieck Jacqueline M , Shi Mengya , Suhre Karsten , Prehn Cornelia , Adamski Jerzy , Rathmann Wolfgang , Thorand Barbara , Roden Michael , Peters Annette , Wang-Sattler Rui , Herder Christian 
Published: March 2024

IntroductionCirculating omentin levels have been positively associated with insulin sensitivity. Although a role for adiponectin in this relationship has been suggested, underlying mechanisms remain elusive. In order to reveal the relationship between omentin and systemic metabolism, this study aimed to investigate associations of serum concentrations of omentin and metabolites.Research design and methodsThis study is based on 1124 participants aged 61–82 years from the population-based KORA (Cooperative Health Research in the Region of Augsburg) F4 Study, for whom both serum omentin levels and metabolite concentration profiles were available. Associations were assessed with five multivariable regression models, which were stepwise adjusted for multiple potential confounders, including age, sex, body mass index, waist-to-hip ratio, lifestyle markers (physical activity, smoking behavior and alcohol consumption), serum adiponectin levels, high-density lipoprotein cholesterol, use of lipid-lowering or anti-inflammatory medication, history of myocardial infarction and stroke, homeostasis model assessment 2 of insulin resistance, diabetes status, and use of oral glucose-lowering medication and insulin.ResultsOmentin levels significantly associated with multiple metabolites including amino acids, acylcarnitines, and lipids (eg, sphingomyelins and phosphatidylcholines (PCs)). Positive associations for several PCs, such as diacyl (PC aa C32:1) and alkyl-alkyl (PC ae C32:2), were significant in models 1–4, whereas those with hydroxytetradecenoylcarnitine (C14:1-OH) were significant in all five models. Omentin concentrations were negatively associated with several metabolite ratios, such as the valine-to-PC ae C32:2 and the serine-to-PC ae C32:2 ratios in most models.ConclusionsOur results suggest that omentin may influence insulin sensitivity and diabetes risk by changing systemic lipid metabolism, but further mechanistic studies investigating effects of omentin on metabolism of insulin-sensitive tissues are needed.
Dynamic monitoring of circulating tumor DNA reveals outcomes and genomic alterations in patients with relapsed or refractory large B-cell lymphoma undergoing CAR T-cell therapy
Authors: Zou Hesong , Liu Wei , Wang Xiaojuan , Wang Yi , Wang Chunyang , Qiu Chen , Liu Huimin , Shan Dandan , Xie Ting , Huang Wenyang , Sui Weiwei , Yi Shuhua , An Gang , Xu Yan , Ma Tonghui , Wang Jianxiang , Qiu Lugui , Zou Dehui 
Published: March 2024

BackgroundOver 50% of patients with relapsed or refractory large B-cell lymphoma (r/r LBCL) receiving CD19-targeted chimeric antigen receptor (CAR19) T-cell therapy fail to achieve durable remission. Early identification of relapse or progression remains a significant challenge. In this study, we prospectively investigate the prognostic value of dynamic circulating tumor DNA (ctDNA) and track genetic evolution non-invasively, for the first time in an Asian population of r/r patients undergoing CAR19 T-cell therapy.MethodsLongitudinal plasma samples were prospectively collected both before lymphodepletion and at multiple timepoints after CAR19 T-cell infusion. ctDNA was detected using a capture-based next-generation sequencing which has been validated in untreated LBCL.ResultsThe study enrolled 23 patients with r/r LBCL and collected a total of 101 ctDNA samples. Higher pretreatment ctDNA levels were associated with inferior progression-free survival (PFS) (p=0.031) and overall survival (OS) (p=0.023). Patients with undetectable ctDNA negative (ctDNA–) at day 14 (D14) achieved an impressive 3-month complete response rate of 77.8% vs 22.2% (p=0.015) in patients with detectable ctDNA positive (ctDNA+), similar results observed for D28. CtDNA– at D28 predicted significantly longer 1-year PFS (90.9% vs 27.3%; p=0.004) and OS (90.9% vs 49.1%; p=0.003) compared with patients who remained ctDNA+. Notably, it is the first time to report that shorter ctDNA fragments (<170 base pairs) were significantly associated with poorer PFS (p=0.031 for D14; p=0.002 for D28) and OS (p=0.013 for D14; p=0.008 for D28) in patients with LBCL receiving CAR T-cell therapy. Multiple mutated genes exhibited an elevated prevalence among patients with progressive disease, includingTP53,IGLL5,PIM1,BTG1,CD79B,GNA13, andP2RY8. Notably, we observed a significant correlation betweenIGLL5mutation and inferior PFS (p=0.008) and OS (p=0.014).ConclusionsOur study highlights that dynamic ctDNA monitoring during CAR T-cell therapy can be a promising non-invasive method for early predicting treatment response and survival outcomes. Additionally, the ctDNA mutational profile provides novel insights into the mechanisms of tumor-intrinsic resistance to CAR19 T-cell therapy.
Exact wave solutions of new generalized Bogoyavlensky–Konopelchenko model in fluid mechanics
Authors: Seadawy Aly R. , Ali Asghar , Bekir Ahmet 
Published: March 2024

In this paper, we examine a novel generalized [Formula: see text]-dimensional Bogoyavlensky–Konopelchenko (gBK) model analytically via application of five mathematical methods, namely called Extended Simple Equation (ESE) method, Modified Extended Auxiliary equation mapping (MEAEM) method, [Formula: see text]-expansion method, [Formula: see text]-expansion method and modified F-expansion method, respectively, to obtain different types solitary wave solutions in the form of trigonometric, hyperbolic, rational and exponential functions as compared to solutions exist in [S. T. Chen and W. X. Ma, Math. China 13 (2018) 525; A. Sonia, A. Jamshad, S.-U. Rehman and A. Ali, Int. J. Appl. Comput. Math. 9 (2023)]. The research focuses on physical systems, physiology, mathematical applications, engineering fields, and the chemical processes of species in the porous nanoparticles, examining the impact of various parameters on the nonlinear model. The graphs of some solutions are plotted in the form of two-dimensional and three-dimensional by assigning the particular values to the paraments with the assistance of mathematica software which illustrated the physical behavior of the concern model. The derived solution has numerous applications in fluid dynamics and the interaction of Riemann waves and long waves.