bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochar Modulates Wheat Root Metabolome and Rhizosphere Microbiome in a Feedstock-dependent Manner
Authors: Yang Hanyue , Kerner Patricia , Liang Xi , Struhs Ethan , Mirkouei Amin , You Yaqi 
Published: July 2024

AbstractBackgroundBiochar is a multifunctional soil conditioner capable of enhancing soil health and plant productivity, but the underlying mechanisms remain elusive. Here we tackled this question using wheat as a model plant and through the lens of the rhizosphere, a vital soil-plant interface continuum. We systematically examined the effects of four types of biochar (corn stover, cattle manure, pine sawdust, or wheat straw) applied at two rates (0.25% or 2.5%, w/w).ResultsEmploying untargeted metabolomics and 16S rRNA gene sequencing, we revealed both common and unique modulating effects of the tested biochar treatments on wheat root metabolites and rhizosphere microbiome structure and functioning. Biochar modulated numerous metabolic pathways in wheat roots, where amino acid metabolism was the most common one, leading to cascade effects on the dynamics of a wide range of secondary metabolites, including many plant signaling molecules (e.g., flavonoid compounds, brassinosteroids) that are known to be involved in plant-microbe interactions. All biochar treatments increased rhizosphere microbial diversity, altered community composition, enhanced microbial interactions, and resulted in functional changes. Increased Burkholderiales (denitrifying bacteria) abundance and decreased Thermoplasmata (archaeal methanogens) abundance could explain biochar’s widely reported effects on nitrous oxide and methane mitigation, respectively. Biochar enhanced positive correlations among microbes and network complexity, particularly modularity, suggesting local adaptation through mutualism and/or synergism and the formation of modules of functionally interrelated taxa. A large number of diverse keystone taxa from both dominant and non-dominant phyla emerged after biochar treatments, including those known to be involved in methane, nitrogen, and sulfur cycling. Besides common alterations, treatment-specific alterations also occurred, and biochar type (i.e., feedstock choice) exerted greater influence than application rate. Wheat biochar applied at a 0.25% rate showed the strongest and distinct modulating effects, resulting in orchestrated changes in both root metabolites and rhizosphere microbiome, especially those relevant to plant-microbe interactions and likely beneficial to the host plant (e.g., upregulated biosynthesis of zeatin and down-regulated limonene degradation).ConclusionsOur work contributes to a mechanistic understanding of how biochar modulates the soil-plant continuum and provides new insights into the potential of top-down rhizosphere microbiome engineering through biochar-based reprogramming of root-microbe interactions.
Lipoprotein(a) is Associated with Increased Low-Density Plaque Volume
Authors: Fisher Rebecca , Nurmohamed Nick , Fisher Edward A. , Aquino Melissa , Earls James P. , Min James K. , Gurevitz Chen , Malick Waqas A. , Peters M. Robert , Goonewardena Sascha N. , Rosenson Robert S. 
Published: July 2024

AbstractBACKGROUNDLipoprotein(a) [Lp(a)] is an inherited risk factor for cardiovascular disease that is accompanied by a more severe coronary artery disease (CAD) phenotype and a higher risk for events. The objective of this study is to clarify the association between Lp(a) and coronary plaque characteristics in asymptomatic patients.METHODS373 consecutive asymptomatic patients were evaluated for primary prevention of CAD. Artificial intelligence quantitative coronary CTA (AI-QCT) was used to investigate the relationship between Lp(a) and coronary plaque characteristics. Multivariable linear regression adjusted for CAD risk factors (age, sex, race, diabetes, smoking), statin use, and body mass index were used to analyze associations between the Lp(a) (by quintile), high sensitivity C-reactive protein (hsCRP), coronary artery calcium (CAC) score, and AI-QCT findings. AI-QCT findings were defined as low-density non-calcified plaque volume (LD-NCPV).RESULTSThe mean age was 56.2±8.9 years, 71.6% were male, and 54.2% were taking statin therapy. Median LDL-C was 103(72,136)mg/dL, median Lp(a) was 31(11, 89)nmol/L, median Lp(a) corrected LDL-C was 101(64, 131)mg/dL. Median hsCRP levels were 0.8(0.4, 1.8)mg/L. Median CAC levels were 6.0(0.0,110.0). There was no association between Lp(a) concentrations and CAC(P=0.281). After adjustment for CAD risk factors, every quintile of Lp(a) increase was associated with a 0.4% increase in LD-NCPV(P=0.039). The inclusion of hsCRP to the models had no significant effect on LD-NCPV.CONCLUSIONSHigher Lp(a) concentrations in asymptomatic patients are significantly associated with increased low-density non-calcified plaque volume.Clinical PerspectiveLp(a) is a risk marker for early-onset coronary heart disease events. Early detection of vulnerable patients is critical to mitigating this risk that may be inadequately captured by the coronary artery calcium score. Low-density non-calcified plaque quantification by coronary computerized tomography is an approach that may be more suitable to assess risk in patients with high Lp(a) levels.
Determinants of glycemic control among persons living with type 2 diabetes mellitus attending a district hospital in Ghana
Authors: ADJEI ALEXANDER , BRIGHTSON KENNEDY TETTEY COFFIE , MENSAH MICHAEL MATEY , OSEI JEMIMA , DRAH MOSES , NARH CLEMENT TETTEH , ASARE KWABENA , ANTO FRANCIS 
Published: July 2024

Background Diabetes mellitus is a growing public health emergency with prevalence in sub-Sahara Africa expected to experience the highest increase by 2045. The cornerstone of diabetes management is glycemic control, a complex process with different contributing factors. This study determines the level of glycemic control and the associated individual factors among type 2 diabetes mellitus (T2DM) patients. Methods A cross-sectional descriptive study was conducted at the Shai-Osudoku District Hospital from October to December 2022. A structured questionnaire was used to collect data on socio-demographic characteristics, lifestyle modifications, co-morbidities, adherence to medication and diet regimens and duration of diabetes. Anthropometric and glycated hemoglobin (HbA1c) measurements were taken. Chi-squared and multivariate logistic regression analyses were carried out to determine factors associated with glycemic control at 95% confidence levels. Results A total of 227 patients participated in this study. The majority of the participants were females (77.97%) and the mean (+SD) age was 60.76 + 12.12 years. Good glycemic control (HbA1c < 7%) among the participants was 38.77% (n=88) and the median HbA1c was 7.5% (IQR: 6.5% to 9.4%). Significant factors associated with good glycemic control were eating healthy meals (AOR: 4.78, 95% CI: 1.65, 13.88: p=0.004), oral hypoglycemic agents alone (AOR: 15.71, 95% CI: 1.90, 129.44: p=0.010) and those with previously good glycemic control (AOR: 4.27, 95% CI: 2.16, 8.43: <0.001). Conclusion This study showed low levels of good glycemic control among T2DM patients at the primary care level in Ghana. Healthy eating, oral hypoglycemic agents and those with previously normal HbA1c were associated with glycemic control.
Shared and unique 3D genomic features of substance use disorders across multiple cell types
Authors: Trang Khanh B. , Chesi Alessandra , Toikumo Sylvanus , Pippin James A. , Pahl Matthew C. , O’Brien Joan M. , Amundadottir Laufey T. , Brown Kevin M. , Yang Wenli , Welles Jaclyn , Santoleri Dominic , Titchenell Paul M. , Seale Patrick , Zemel Babette S. , Wagley Yadav , Hankenson Kurt D. , Kaestner Klaus H. , Anderson Stewart A. , Kayser Matthew S. , Wells Andrew D. , Kranzler Henry R. , Kember Rachel L. , Grant Struan F.A. 
Published: July 2024

ABSTRACTRecent genome-wide association studies (GWAS) have revealed shared genetic components among alcohol, opioid, tobacco and cannabis use disorders. However, the extent of the underlying shared causal variants and effector genes, along with their cellular context, remain unclear. We leveraged our existing 3D genomic datasets comprising high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq and RNA-seq across >50 diverse human cell types to focus on genomic regions that coincide with GWAS loci. Using stratified LD regression, we determined the proportion of genome-wide SNP heritability attributable to the features assayed across our cell types by integrating recent GWAS summary statistics for the relevant traits: alcohol use disorder (AUD), tobacco use disorder (TUD), opioid use disorder (OUD) and cannabis use disorder (CanUD). Statistically significant enrichments (P<0.05) were observed in 14 specific cell types, with heritability reaching 9.2-fold for iPSC-derived cortical neurons and neural progenitors, confirming that they are crucial cell types for further functional exploration. Additionally, several pancreatic cell types, notably pancreatic beta cells, showed enrichment for TUD, with heritability enrichments up to 4.8-fold, suggesting genomic overlap with metabolic processes. Further investigation revealed significant positive genetic correlations between T2D with both TUD and CanUD (FDR<0.05) and a significant negative genetic correlation with AUD. Interestingly, after partitioning the heritability for each cell type’s cis-regulatory elements, the correlation between T2D and TUD for pancreatic beta cells was greater (r=0.2) than the global genetic correlation value. Our study provides new genomic insights into substance use disorders and implicates cell types where functional follow-up studies could reveal causal variant-gene mechanisms underpinning these disorders.
Exploring measures to increase detection of malaria cases through reactive case detection in a Southern Province of Zambia-like Setup: A modelling study
Authors: Chiziba Chilochibi , Silal Sheetal 
Published: July 2024

IntroductionIn Zambia, malaria prevalence varies spatially, posing challenges for intervention strategies. Asymptomatic and clinical carriers not accessing healthcare further complicate efforts, necessitating reactive case detection (RCD) to target undetected infections. However, operational hurdles, such as resource shortages and logistical complexities—including shortages of community health workers (CHWs), difficulties reaching residents, and limitations in malaria rapid diagnostic tests (RDTs)—hinder RCD’s effectiveness. Identifying effective improvement measures given circumstances that may lead to deficient intervention outcomes may improve the situation.MethodsA mathematical model of malaria transmission conforming to Zambia’s low transmission areas defined as areas with an incidence of fewer than 200 malaria cases per 1,000 population per year was developed to simulate RCD using parameters and data from published articles. We explored the impact of literature-identified challenges on RCD performance in malaria detection and potential strategies to enhance detection rates. The examined factors and improvement measures included increasing CHWs, adjusting reaction time, RDT sensitivity, and implementing focal mass drug administration (fMDA).ResultsSimulation findings suggest that a shortage of CHWs and limited availability of RDTs have the highest negative impact on RCD compared to other challenges. In scenarios where CHWs or RDT availability for RCD were reduced by 50%, annual malaria cases were predicted to increase by approximately 17%. Only the incorporation of fMDA as an improvement measure succeeded in countering the situation. Increasing CHWs to offset RCD inefficiencies caused by limited RDT sensitivity or difficulties in finding individuals resulted in fewer cases than improving reaction time or increasing the screening radius.ConclusionsParticipation of CHWs is voluntary and primarily motivated by informal incentives, often provided by donors. Finding sustainable means to ensure the sufficient availability of CHWs may guarantee continued RCD contributions towards maintaining stable malaria prevalence and elimination. More research is required to explore the application of RCD in archetypical transmission areas suitable for RCD as improvement measures to the identified challenges hindering RCD. Furthermore, archetype-based targeting of interventions, including RCD, may also be explored to inform the optimisation of intervention resource allocation to overcome the widening gap in malaria funding.
Racism and health and wellbeing among children and youth - an updated systematic review and meta-analysis
Authors: Priest Naomi , Lim Chiao Kee , Doery Kate , Lawrence Jourdyn A. , Zoumboulis Georgia , King Gabriella , Lamisa Dewan , He Fan , Wijesuriya Rushani , Mateo Camila M. , Chong Shiau , Truong Mandy , Perry Ryan , King Paula Toko , Paki Natalie Paki , Joseph Corey , Pagram Dot , Lekamge Roshini Balasooriya , Mikolajczak Gosia , Darnett Emily , Trenerry Brigid , Jha Shloka , Masunga Joan Gakii , Paradies Yin , Kelly Yvonne , Karlsen Saffron , Guo Shuaijun 
Published: July 2024

ABSTRACTBackgroundEvidence of racism’s health harms among children and youth is rapidly increasing, though attention to impacts on physical health and biomarker outcomes is more emergent. We performed a systematic review of recent publications to examine the association between racism and health among children and youth, with a meta-analysis of the specific relationships between racism and physical health and biomarkers.MethodsWe conducted a systematic literature search using four databases: Medline, PsycINFO, PubMed, and ERIC. Four inclusion criteria were used to identify eligible studies: (1) exposure was experiences of racism, (2) outcome was health and wellbeing, (3) quantitative methods were used to estimate the association between racism and health outcomes, and (4) the effect size of associations between racism and health and wellbeing was reported for participants aged 0-24 years. Correlation coefficients were used to report the pooled effect size for each outcome indicator.ResultsThere were 463 eligible studies included in the screening process, with 42 studies focusing on physical health or biomarker outcomes. Random-effects meta-analysis found minimal to moderate positive associations between racism and C-reactive protein, Interleukin 6, body mass index (BMI), obesity, systolic blood pressure, salivary cortisol, asthma, and somatic symptoms. There were marginal positive associations between racism and Tumour Necrosis Factor-α, cortisol collected via saliva, urine and hair, BMI-z score, and diastolic blood pressure, with imprecise estimates and wide confidence intervals.ConclusionsRacism is associated with negative physical health and biomarker outcomes that relate to multiple physiological systems and biological processes in childhood and adolescence. This has implications for health and wellbeing during childhood and adolescence and future chronic disease risk. Collective and structural changes to eliminate racism and create a healthy and equitable future for all children and youth are urgently required.HIGHLIGHTSRacism impacts foundations for optimal health and development for children, youth and their caregivers.Evidence shows racism is associated with inflammation, cortisol, weight status, blood pressure, asthma and somatic symptoms in children and youth.Future research needs to prioritise systemic racism and its impact on child and youth health.Collective and structural changes are urgently needed to eliminate racism.
Using the basic reproduction ratio to quantify transmission and identify data gaps for epizootic haemorrhagic disease virus
Authors: Gubbins Simon 
Published: July 2024

AbstractEpizootic haemorrhagic disease virus (EHDV) is an arbovirus transmitted byCulicoidesbiting midges that has recently emerged in Europe. Here, the basic reproduction ratio (R0) was used to quantify the transmission of EHDV and its dependence on temperature for cattle and deer. Using data from the published literature the parameters needed to calculateR0were estimated with Bayesian methods to incorporate uncertainty in the calculations. The Sobol method of sensitivity analysis was used to determine the parameters having the greatest influence onR0and, hence, to identify important data gaps. Depending on the strain the maximumR0for EHDV varied from 0.7 to 2.5 in cattle and 1.3 to 4.3 in deer. The maximumR0occurred at temperatures between 22 and 25 °C, while the lowest temperature at whichR0exceeded one was between 16 and 20 °C. The sensitivity analysis identified the threshold temperature for virus replication, the probability of transmission from host to vector and the vector to host ratio as the most important parameters influencingR0. Furthermore, there are only limited data on EHDV in European deer species and on transmission in wildlife and at the livestock/wildlife interface. These data gaps should be the focus of future research.
The role of stomatin-like protein (STOML) inPlasmodium falciparum
Authors: Verhoef Julie M.J. , Bekkering Ezra T. , Boshoven Cas , Hannon Megan , Proellochs Nicholas I. , Spruijt Cornelia G. , Kooij Taco W.A. 
Published: July 2024

AbstractMembers of theStomatin,Prohibitin,Flotillin andHflK/C (SPFH) protein family form large membrane anchored or spanning complexes and are involved in various functions in different organelles. The human malaria causing parasitePlasmodium falciparumharbors four SPFH proteins, including prohibitin 1 and 2, prohibitin-like protein (PHBL), and stomatin-like protein (STOML) which all localize to the parasite mitochondrion. In the murine model parasitePlasmodium berghei,STOMLhas been shown to be essential and to localize to puncta on mitochondrial branching points in oocyst stages. In this study, we investigate the function of STOML in the human malaria parasite,P. falciparum. We show that deletion ofSTOMLcauses a significant growth defect and slower asexual blood-stage (ABS) development, while sexual-stage development remains unaffected. Parasites lackingSTOMLwere not more sensitive to respiratory chain targeting drugs, rendering a function of STOML in respiratory chain assembly unlikely. Epitope tagging of endogenous STOML revealed a distinct punctate localization on branching points and endings of the ABS mitochondrial network. STOML resides in a large protein complex and pulldown experiments identified a zinc dependent metalloprotease, FtsH, as a likely interaction partner. The predicted AlphaFold structure of STOML shows high similarity with the bacterial HflK/C, which has been shown to form a large vault like structure around the bacterial FtsH hexamers. Combined, our results suggest that a similar STOML-FtsH complex localized to specific loci ofP. falciparummitochondria facilitate the parasite’s asexual blood-stage development.
Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission
Authors: Debray Reena , Dickson Carly C. , Webb Shasta E. , Archie Elizabeth A. , Tung Jenny 
Published: July 2024

SUMMARYIn humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmissionper se, is not well understood. Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners. We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms.
Multipath projection stereolithography (MPS) for 3D printing microfluidic devices
Authors: Geffert Zachary J. , Xiong Zheng , Grutzmacher Jenna , Wilderman Maximilian , Mohammadi Ali , Filip Alex , Li Zhen , Soman Pranav 
Published: July 2024

AbstractAlthough many lab-on-chip applications require inch-sized devices with microscale feature resolution, achieving this via current 3D printing methods remains challenging due to inherent tradeoffs between print resolution, design complexity, and build sizes. Inspired by microscopes that can switch objectives to achieve multiscale imaging, we report a new optical printer coined as Multipath Projection Stereolithography (MPS) specifically designed for printing microfluidic devices. MPS is designed to switch between high-resolution (1×mode, ∼10µm) and low-resolution (3× mode, ∼30µm) optical paths to generate centimeter sized constructs (3cm × 6cm) with a feature resolution of ∼10µm. Illumination and projection systems were designed, resin formulations were optimized, and slicing software was integrated with hardware with the goal of ease of use. Using a test-case of micromixers, we show user-defined CAD models can be directly input to an automated slicing software to define printing of low-resolution features via the 3× mode with embedded microscale fins via 1× mode. A new computational model, validated using experimental results, was used to simulate various fin designs and experiments were conducted to verify simulated mixing efficiencies. New 3D out-of-plane micromixer designs were simulated and tested. To show broad applications of MPS, multi-chambered chips and microfluidic devices with microtraps were also printed. Overall, MPS can be a new fabrication tool to rapidly print a range of lab-on-chip applications.
A Field-Deployable Arsenic Sensor IntegratingBacillus Megateriumwith CMOS Technology
Authors: Hu Chelsea Y. , McManus John , Aghlmand Fatemeh , Larsson Elin , Emami Azita , Murray Richard M. 
Published: July 2024

AbstractBacteria innately monitor their environment by dynamically regulating gene expression to respond to fluctuating conditions. Through synthetic biology, we can harness this natural capability to design cell-based sensors.Bacillus megaterium, a soil bacterium, stands out due to its remarkable heavy metal tolerance and sporulation ability, making it an ideal candidate for heavy metal detection with low transportation costs. However, challenges persist: the synthetic biology toolkit for this strain is underdeveloped and conventional whole-cell sensors necessitate specialized laboratory equipment to read the output. In our study, we genetically modifiedB. megateriumfor arsenic detection, establishing a detection threshold below the EPA recommendation of 10 ppb for drinking water in both vegetative cell form and spore form. Additionally, we integrated both engineeredB. megateriumliving cells and spores with CMOS chip for field-deployable arsenic detection. We show that the limit of detection of our integrated sensor is applicable in soil and air arsenic contamination testing. As a proof of concept, this work paves the way for deploying our sensor in resource-limited settings, ensuring real-time arsenic detection in challenging environments.Abstract Figure