bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toxoplasma gondii Infection of Alzheimer's Disease Mice Reduces Brain Amyloid Density Globally and Regionally
Authors: Yanes Katherine J O , Guanzon Nathanial A , Azevedo Ricardo , Wheeler Damian G , Gandhi Sunil P , Lodoen Melissa B 
Published: September 2024

Abstract

Background
Toxoplasma gondii infection of Alzheimer's disease model mice decreases amyloid β plaques. We aimed to determine if there is a brain regional difference in amyloid β reduction in the brains of T. gondii-infected compared to control mice.

Method
Three-month-old 5xFAD (AD model) mice were injected with T. gondii or with phosphate-buffered saline as a control. Intact brains were harvested at 6 weeks postinfection, optically cleared using iDISCO+, and brain-wide amyloid burden was visualized using volumetric light-sheet imaging. Amyloid signal was quantified across each brain and computationally mapped to the Allen Institute Brain Reference Atlas to determine amyloid density in each region.

Results
A brain-wide analysis of amyloid in control and T. gondii-infected 5xFAD mice revealed that T. gondii infection decreased amyloid burden in the brain globally as well as in the cortex and hippocampus, and many daughter regions. Daughter regions that showed reduced amyloid burden included the prelimbic cortex, visual cortex, and retrosplenial cortex. The olfactory tubercle, a region known to have increased monocytes following T. gondii infection, also showed reduced amyloid after infection.

Conclusions
T. gondii infection of AD mice reduces amyloid burden in a brain region-specific manner that overlaps with known regions of T. gondii infection and peripheral immune cell infiltration.
Chronic Oral Inoculation of Porphyromonas gingivalis and Treponema denticola Induce Different Brain Pathologies in a Mouse Model of Alzheimer Disease
Authors: Ciccotosto Giuseppe D , Mohammed Ali I , Paolini Rita , Bijlsma Elly , Toulson Su , Holden James , Reynolds Eric C , Dashper Stuart G , Butler Catherine A 
Published: September 2024

Abstract
Periodontitis is a chronic inflammatory disease driven by dysbiosis in subgingival microbial communities leading to increased abundance of a limited number of pathobionts, including Porphyromonas gingivalis and Treponema denticola. Oral health, particularly periodontitis, is a modifiable risk factor for Alzheimer disease (AD) pathogenesis, with components of both these bacteria identified in postmortem brains of persons with AD. Repeated oral inoculation of mice with P. gingivalis results in brain infiltration of bacterial products, increased inflammation, and induction of AD-like biomarkers. P. gingivalis displays synergistic virulence with T. denticola during periodontitis. The aim of the current study was to determine the ability of P. gingivalis and T. denticola, grown in physiologically relevant conditions, individually and in combination, to induce AD-like pathology following chronic oral inoculation of female mice over 12 weeks. P. gingivalis alone significantly increased all 7 brain pathologies examined: neuronal damage, activation of astrocytes and microglia, expression of inflammatory cytokines interleukin 1β (IL-1β) and interleukin 6 and production of amyloid-β plaques and hyperphosphorylated tau, in the hippocampus, cortex and midbrain, compared to control mice. T. denticola alone significantly increased neuronal damage, activation of astrocytes and microglia, and expression of IL-1β, in the hippocampus, cortex and midbrain, compared to control mice. Coinoculation of P. gingivalis with T. denticola significantly increased activation of astrocytes and microglia in the hippocampus, cortex and midbrain, and increased production of hyperphosphorylated tau and IL-1β in the hippocampus only. The host brain response elicited by oral coinoculation was less than that elicited by each bacterium, suggesting coinoculation was less pathogenic.
Retrospective Analysis of Blood Biomarkers of Neurological Injury in Human Cases of Viral Infection and Bacterial Sepsis
Authors: Bartlett Maggie L , Goux Heather , Johnson Linwood , Schully Kevin L , Gregory Melissa , Brandsma Joost , Chenoweth Josh G , Clark Danielle V , Rivera Luis Felipe , Lezcano-Coba Carlos , Vittor Amy Y , Hayes Ronald , Galué Josefrancisco , Carrera Jean-Paul , Smith Darci R 
Published: September 2024

Abstract

Background
Blood biomarkers of neurological injury could provide a rapid diagnosis of central nervous system injury caused by infections. A Food and Drug Administration (FDA)-approved assay for mild traumatic brain injury (TBI) measures glial fibrillary acidic protein (GFAP) and ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), which signal astrocyte and neuronal injury, respectively. Here, we assessed the applicability of this biomarker assay for determining infection-induced brain injury.

Methods
We measured serum levels of GFAP and UCH-L1 retrospectively in serum samples from 3 study populations: (1) human cases infected with Venezuelan equine encephalitis virus (VEEV) and Madariaga virus (MADV) (n = 73), (2) human sepsis patients who were severely ill or diagnosed with encephalitis (n = 66), and (3) sepsis cases that were subsequently evaluated for cognitive impairment (n = 64).

Results
In the virus infection group, we found elevated GFAP for VEEV (P = .014) and MADV (P = .011) infections, which correlated with seizures (P = .006). In the bacterial sepsis group, GFAP was elevated in cases diagnosed with encephalitis (P = .0007) and correlated with headaches (P = .0002). In the bacterial sepsis cases with a later cognitive assessment, elevated GFAP (P = .0057) at study enrollment was associated with cognitive impairment 6 months later with a positive prognostic capacity of 79% (95% confidence interval, 66%–95%; P = .0068).

Conclusions
GFAP and UCH-L1 levels measured using an FDA-approved assay for TBI may indicate brain injury resulting from viral or bacterial infections and could predict the development of neurological sequelae.
COVID-19 mRNA Vaccines Induce Robust Levels of IgG but Limited Amounts of IgA Within the Oronasopharynx of Young Children
Authors: Tang Ying , Boribong Brittany P , Swank Zoe N , Demokritou Melina , Luban Maria A F , Fasano Alessio , Du Michelle , Wolf Rebecca L , Griffiths Joseph , Shultz John , Borberg Ella , Chalise Sujata , Gonzalez Wanda I , Walt David R , Yonker Lael M , Horwitz Bruce H 
Published: September 2024

Abstract

Background
Understanding antibody responses to SARS-CoV-2 vaccination is crucial for refining COVID-19 immunization strategies. Generation of mucosal immune responses, including mucosal IgA, could be of potential benefit to vaccine efficacy; however, limited evidence exists regarding the production of mucosal antibodies following the administration of current mRNA vaccines to young children.

Methods
We measured the levels of antibodies against SARS-CoV-2 from a cohort of children under 5 years of age (n = 24) undergoing SARS-CoV-2 mRNA vaccination (serially collected, matched serum and saliva samples) or in a convenience sample of children under 5 years of age presenting to pediatric emergency department (nasal swabs, n = 103). Furthermore, we assessed salivary and nasal samples for the ability to induce SARS-CoV-2 spike-mediated neutrophil extracellular traps (NET) formation.

Results
Longitudinal analysis of post-vaccine responses in saliva revealed the induction of SARS-CoV-2–specific IgG but not IgA. Similarly, SARS-CoV-2–specific IgA was only observed in nasal samples obtained from previously infected children with or without vaccination, but not in vaccinated children without a history of infection. In addition, oronasopharyngeal samples obtained from children with prior infection were able to trigger enhanced spike-mediated NET formation, and IgA played a key role in driving this process.

Conclusions
Despite the induction of specific IgG in the oronasal mucosa, current intramuscular vaccines have limited ability to generate mucosal IgA in young children. These results confirm the independence of mucosal IgA responses from systemic humoral responses following mRNA vaccination and suggest potential future vaccination strategies for enhancing mucosal protection in this young age group.
Effect of NH4Cl supplementation on growth, photosynthesis, and triacylglycerol content in Chlamydomonas reinhardtii under mixotrophic cultivation
Authors: Sittisaree Wattanapong , Yokthongwattana Kittisak , Aonbangkhen Chanat , Yingchutrakul Yodying , Krobthong Sucheewin 
Published: September 2024

Abstract

Aim
Ammonium chloride (NH4Cl) is one of the nitrogen sources for microalgal cultivation. An excessive amounts of NH4Cl are toxic for microalgae. However, combining mixotrophic conditions and excessive quantities of NH4Cl positively affects microalgal biomass and lipid production. In this study, we investigated the impact of NH4Cl on the growth, biomass, and triglyceride (TAG) content of the green microalga Chlamydomonas reinhardtii especially under mixotrophic conditions.

Methods and results
Under photoautotrophic conditions (without organic carbon supplementation), adding 25 mM NH4Cl had no significant effect on microalgal growth or TAG content. However, under mixotrophic condition (with acetate supplementation), NH4Cl interfered with microalgal growth while inducing TAG content. To explore these effects further, we conducted a two-step cultivation process and found that NH4Cl reduced microalgal growth, but induced total lipid and TAG content, especially after 4-day cultivation. The photosynthesis performances showed that NH4Cl completely inhibited oxygen evolution on day 4. However, NH4Cl slightly reduced the Fv/Fm ratio indicating that the NH4Cl supplementation directly affects microalgal photosynthesis. To investigate the TAG induction effect by NH4Cl, we compared the protein expression profiles of microalgae grown mixotrophically with and without 25 mM NH4Cl using a proteomics approach. This analysis identified 1782 proteins, with putative acetate uptake transporter GFY5 and acyl-coenzyme A oxidase being overexpressed in the NH4Cl-treated group.

Conclusion
These findings suggested that NH4Cl supplementation may stimulate acetate utilization and fatty acid synthesis pathways in microalgae cells. Our study indicated that NH4Cl supplementation can induce microalgal biomass and lipid production, particularly when combined with mixotrophic conditions.
Navigating electronic health record accuracy by examination of sex incongruent conditions
Authors: Cai Ling , DeBerardinis Ralph J , Zhan Xiaowei , Xiao Guanghua , Xie Yang 
Published: September 2024

Abstract

Objective
The increasing reliance on electronic health records (EHRs) for research and clinical care necessitates robust methods for assessing data quality and identifying inconsistencies. To address this need, we develop and apply the incongruence rate (IR) using sex-specific medical conditions. We also characterized participants with incongruent records to better understand the scope and nature of data discrepancies.

Materials and Methods
In this cross-sectional study, we used the All of Us Research Program’s latest version 7 (v7) EHR data to identify prevalent sex-specific conditions and evaluated the occurrence of incongruent cases, quantified as IR.

Results
Among the 92 597 males and 152 551 females with condition occurrence data available from All of Us and sex-conformed gender, we identified 167 prevalent sex-specific conditions. Among the 37 537 biological males and 95 499 biological females with these sex-specific conditions, we detected an overall IR of 0.86%. Attempt to include non-cisgender participants result in inflated overall IR. Additionally, a significant proportion of participants with incongruent conditions also presented with conditions congruent to their biological sex, indicating a mix of accurate and erroneous records. These incongruences were not geographically or temporally isolated, suggesting systematic issues in EHR data integrity.

Discussion
Our findings call attention to the existence of systemic data incongruences in sex-specific conditions and the need for robust validation checks. Extending IR evaluation to non-cisgender participants or non-sex-based conditions remain a challenge.

Conclusion
The sex condition-specific IR, when applied to adult populations, provides a valuable metric for data quality assessment in EHRs.
Acceptability, feasibility, and impact of the MyGut digital health platform in the monitoring and management of inflammatory bowel disease
Authors: Zhen Jamie , Simoneau Maude , Sharma Pooja , Germain Pascale , Watier-Levesque Pascale , Othman Abdulrahman , Marshall John K , Afif Waqqas , Narula Neeraj 
Published: September 2024

Abstract

Background
Digital health monitoring may help facilitate self-management strategies when caring for patients with inflammatory bowel disease (IBD).

Aims
This study investigated the feasibility of implementing the MyGut health application when caring for patients with IBD and evaluated whether its use improved health outcomes.

Methods
We conducted a prospective trial in 2 Canadian hospitals from 2020 to 2023. Patients with IBD were recruited from gastroenterology clinics, and the MyGut application was installed onto their mobile devices. Metrics such as acceptability, satisfaction, feasibility, quality-of-life scores (measured through the short IBD questionnaire [SIBDQ]), and resource utilization were collected throughout the 1-year follow-up period.

Results
Of the 84 patients enrolled, 58 patients (69%) continued to use the app until the study completion. At recruitment, all 84 patients (100%) were willing to use the MyGut application after a brief tutorial. There was a significant improvement in the SIBDQ scores after 1 year of MyGut use (mean = 56.0, SD 8.85 vs 52.0, SD 9.84) (P = .012). However, only 42.9% (21/49) of the patients were willing to continue using the application after 1 year, a significant decrease compared with the 71.4% (35/49) who were willing to continue after 2 months (P = .001). No differences were observed in the number of emergency room visits/hospitalizations (P = .78) before and after 1 year of MyGut use.

Conclusions
This study demonstrates that patients are willing to use digital health monitoring platforms and this may lead to improved quality of life. However, sustained efforts must be made to optimize its long-term feasibility.
Life table study of Rachiplusia nu (Lepidoptera: Noctuidae) on different food sources and artificial diet
Authors: Alves Juarez da S , Pasqualotto Larissa , Soares Vanessa N , Trombin de Souza Michele , Trombin de Souza Mireli , Rakes Matheus , Horikoshi Renato J , Miraldo Leonardo L , Ovejero Ramiro L F , Berger Geraldo U , Bernardi Daniel 
Published: September 2024

Abstract
Rachiplusia nu Guenée is a polyphagous species able to develop on several cultivated and non-cultivated host plants. However, basic life history information about this pest on hosts is scarce. In this study, R. nu larvae did not survive on leaves of non-Bt corn, wheat, Bt cotton that expresses proteins Cry1Ac+Cry2Ab2 or on Intacta2 Xtend soybean that expresses the Cry1A.105/Cry2Ab2/Cry1Ac proteins. Rachiplusia nu showed a viable egg-to-adult biological cycle (54%–66.3%) on non-Bt soybean, sunflower, canola, vetch, Persian clover, alfalfa, bean, and forage turnip hosts, similar to larvae raised on the artificial diet. In addition, R. nu was unable to complete larval development on non-Bt cotton, and only 45.2% of R. nu larvae reached the pupal stage when fed leaves of intacta RR2 PRO soybean that expresses the Cry1Ac protein. Larval and pupal mass of surviving insects on Cry1Ac soybean leaves were also lower (larval: 0.104 g; pupal: 0.099 g) in relation to other food sources (larval: 0.165–0.189 g; pupal: 0.173–0.192 g). The total fecundity of R. nu on Cry1Ac soybean leaves was ≈65% lower in relation to other food sources. This fact caused ≈60% the net reproductive rate (Ro) and intrinsic rate of increase (rm) when compared to other food sources. Our findings indicate that the Cry1Ac soybean negatively affects the biological parameters of R. nu. Non-Bt soybean, sunflower, canola, vetch, Persian clover, alfalfa, bean, and forage turnip are viable food sources for the survival and development of R. nu.
Simultaneous enumeration of yeast and bacterial cells in the context of industrial bioprocesses
Authors: Martins Carolina Teixeira , Jacobus Ana Paula , Conceição Renilson , Barbin Douglas Fernandes , Bolini Helena , Gombert Andreas Karoly 
Published: September 2024

Abstract

In scenarios where yeast and bacterial cells coexist, it is of interest to simultaneously quantify the concentrations of both cell types, since traditional methods used to determine these concentrations individually take more time and resources. Here, we compared different methods for quantifying the fuel ethanol Saccharomyces cerevisiae PE-2 yeast strain and cells from the probiotic Lactiplantibacillus plantarum strain in microbial suspensions. Individual suspensions were prepared, mixed in 1:1 or 100:1 yeast-to-bacteria ratios, covering the range typically encountered in sugarcane biorefineries, and analyzed using bright field microscopy, manual and automatic Spread-plate and Drop-plate counting, flow cytometry (at 1:1 and 100:1 ratios), and a Coulter Counter (at 1:1 and 100:1 ratios). We observed that for yeast cell counts in the mixture (1:1 and 100:1 ratios), flow cytometry, the Coulter Counter, and both Spread-plate options (manual and automatic CFU counting) yielded statistically similar results, while the Drop-plate and microscopy-based methods gave statistically different results. For bacterial cell quantification, the microscopy-based method, Drop-plate, and both Spread-plate plating options and flow cytometry (1:1 ratio) produced no significantly different results (p &gt; .05). In contrast, the Coulter Counter (1:1 ratio) and flow cytometry (100:1 ratio) presented results statistically different (p &lt; .05). Additionally, quantifying bacterial cells in a mixed suspension at a 100:1 ratio wasn't possible due to an overlap between yeast cell debris and bacterial cells. We conclude that each method has limitations, advantages, and disadvantages.

One-Sentence Summary
This study compares methods for simultaneously quantifying yeast and bacterial cells in a mixed sample, highlighting that in different cell proportions, some methods cannot quantify both cell types and present distinct advantages and limitations regarding time, cost, and precision.
Childhood Cancer-Connect: Identifying solutions to elevating the cancer experience for adolescents and young adults with cancer
Authors: Roth Michael E , Hawkins Douglas S , Merrill Janette K , Henderson Tara O 
Published: September 2024

Abstract
Adolescents and young adults with cancer (aged 15-39 years) experience unique challenges because of their developmental life stage, and many have limited access to support and resources. Childhood Cancer (CC)-Connect, the patient assistance component of the White House Cancer Moonshot Childhood Cancer–Data Integration for Research, Education, Care, and Clinical Trials initiative that aims to help childhood cancer families find the best care for their child, undertook a multipronged effort to identify key strategies for addressing the unique needs of adolescents and young adults with cancer. This article describes the 4 strategies that emerged to form a comprehensive framework for addressing the unmet needs of adolescents and young adults with cancer, which can improve outcomes and enhance the cancer care experience for this vulnerable population.
Alignment and comparison of directed networks via transition couplings of random walks
Authors: Yi Bongsoo , O’Connor Kevin , McGoff Kevin , Nobel Andrew B 
Published: September 2024

Abstract
We describe and study a transport-based procedure called network optimal transition coupling (NetOTC) for the comparison and alignment of two networks. The networks of interest may be directed or undirected, weighted or unweighted, and may have distinct vertex sets of different sizes. Given two networks and a cost function relating their vertices, NetOTC finds a transition coupling of their associated random walks having minimum expected cost. The minimizing cost quantifies the difference between the networks, while the optimal transport plan itself provides alignments of both the vertices and the edges of the two networks. Coupling of the full random walks, rather than their marginal distributions, ensures that NetOTC captures local and global information about the networks and preserves edges. NetOTC has no free parameters and does not rely on randomization. We investigate a number of theoretical properties of NetOTC and present experiments establishing its empirical performance.
Physical obstacles in the substrate cause maize root growth trajectories to switch from vertical to oblique
Authors: Yao Jiaojiao , Barés Jonathan , Dupuy Lionel X , Kolb Evelyne 
Published: September 2024

Abstract
Hard pans, soil compaction, soil aggregation, and stones create physical barriers that can affect the development of a root system. Roots are known to exploit paths of least resistance to avoid such obstacles, but the mechanism through which this is achieved is not well understood. Here, we used a combination of 3D-printed substrates with a high-throughput live-imaging platform to study the responses of maize roots to a range of physical barriers. Using image analysis algorithms, we determined the properties of growth trajectories and identified how the presence of rigid circular obstacles affects the ability of a primary root to maintain its vertical trajectory. The results showed that the types of growth responses were limited, with both vertical and oblique trajectories being found to be stable and influenced by the size of the obstacles. When obstacles were of intermediate sizes, trajectories were unstable and changed in nature through time. We formalized the conditions required for root trajectory to change from vertical to oblique, linking the angle at which the root detaches from the obstacle to the root curvature due to gravitropism. Exploitation of paths of least resistance by a root might therefore be constrained by the ability of the root to curve and respond to gravitropic signals.
A genomic journey across the past, present, and future of South American maize
Authors: Dominguez Pia Guadalupe , Freilij Damián , Lia Verónica Viviana 
Published: September 2024

Abstract
Maize (Zea mays ssp. mays) diverged from one of its wild relatives, the teosinte Zea mays ssp. parviglumis, in the lowlands of southwest Mexico ~9000 years ago. Following this divergence, maize rapidly expanded throughout the Americas becoming a staple food. This dispersal was accompanied by significant demographic and selective changes, leading to the development of numerous local varieties with a complex evolutionary history that remains incompletely understood. In recent years, genomic advances have challenged traditional models of maize domestication and spread to South America. At least three distinct genetic lineages associated with different migratory waves have been described: ancestral Andean, ancestral Lowland, and Pan-American. Additionally, the significant role of the teosinte Zea mays ssp. mexicana in the evolution of modern maize has been recently uncovered. Genomic studies have shed light on highland adaptation processes, revealing largely independent adaptation events in Meso and South America. As new evidence emerges, the regional complexity underlying maize diversity and the need for comprehensive, multiscale approaches have become evident. In the face of climate change and evolving agricultural landscapes, the conservation of native maize in South America is of growing interest, with genomics serving as an invaluable tool for identifying and preserving the genetic variability of locally adapted germplasm.