Correlating High-dimensional longitudinal microbial features with time-varying outcomes with FLORAL.

Correlating time-dependent patient characteristics and matched microbiome samples can be helpful to identify biomarkers in longitudinal microbiome studies. Existing approaches typically repeat a pre-specified modeling approach for all taxonomic features, followed by a multiple testing adjustment step for false discovery rate (FDR) control. In this work, we develop an alternative strategy of using log-ratio penalized generalized estimating equations, which directly models the longitudinal patient characteristic of interest as the outcome variable and treats microbial features as high-dimensional compositional covariates.

Olfactory bulb microglia activation mediates neuronal pyroptosis in ozone-exposed mice with olfactory and cognitive dysfunction.

In recent years, there has been a notable increase in the concentration of air pollutants in the troposphere, especially ozone. However, limited research has gone beyond examining histopathological alterations in the olfactory bulb (OB) to explore the effects of ozone exposure on olfactory and cognitive functions. In our study, we exposed nine-month-old C57BL/6 mice to ozone at a concentration of 1.

Scalable log-ratio lasso regression for enhanced microbial feature selection with FLORAL.

Identifying predictive biomarkers of patient outcomes from high-throughput microbiome data is of high interest, while existing computational methods do not satisfactorily account for complex survival endpoints, longitudinal samples, and taxa-specific sequencing biases. We present FLORAL, an open-source tool to perform scalable log-ratio lasso regression and microbial feature selection for continuous, binary, time-to-event, and competing risk outcomes, with compatibility for longitudinal microbiome data as time-dependent covariates. The proposed method adapts the augmented Lagrangian algorithm for a zero-sum constraint optimization problem while enabling a two-stage screening process for enhanced false-positive control.

Deciphering the roles of nitrogen source in sharping synchronous metabolic pathways of linear alkylbenzene sulfonate and nitrogen in a membrane biofilm for treating greywater.

Nitrogen (N) source is an important factor affecting biological wastewater treatment. Although the oxygen-based membrane biofilm showed excellent greywater treatment performance, how N source impacts the synchronous removal of organics and N is still unclear. In this work, how N species (urea, nitrate and ammonia) affect synchronous metabolic pathways of organics and N were evaluated during greywater treatment in the membrane biofilm.

Walnut shell oil-bath torrefaction coupled with fast pyrolysis: Effect of torrefaction heating modes.

Lignocellulosic biomass, renewable with short growth cycle and diverse sources, can be substituted fossil fuel. However, low effective hydrogen-to-carbon ratio (H/C) limits its applications. Torrefaction and co-pyrolysis with high H/C feedstocks are promising technology.

Assessment of pathogenicity and functional characterization of gene mutations in diabetic patients.

Background: Adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 (APPL1) plays a crucial role in regulating insulin signaling and glucose metabolism. Mutations in the gene have been associated with the development of maturity-onset diabetes of the young type 14 (MODY14). Currently, only two mutations [c.

Advances in epileptic network findings of hypothalamic hamartomas.

Hypothalamic hamartomas (HHs) are congenital developmental malformations located in the hypothalamus. They are associated with a characteristic clinical manifestation known as gelastic seizures (GS). However, the traditional understanding of HHs has been limited, resulting in insufficient treatment options and high recurrence rates of seizures after surgery.

Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease.

Microbial transformation of bile acids affects intestinal immune homoeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease.

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia.

Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations.

High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients.

Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity.

Enhanced Feature Selection for Microbiome Data using FLORAL: Scalable Log-ratio Lasso Regression.

Identifying predictive biomarkers of patient outcomes from high-throughput microbiome data is of high interest, while existing computational methods do not satisfactorily account for complex survival endpoints, longitudinal samples, and taxa-specific sequencing biases. We present FLORAL (https://vdblab.github.

Effect of multidisciplinary health education based on lifestyle medicine on menopausal syndrome and lifestyle behaviors of menopausal women: A clinical controlled study.

Background: Menopausal women may experience menopausal syndrome and long-term effects caused by low estrogen levels, such as senile dementia and osteoporosis in the elderly. Most menopausal women may have misconceptions about menopause and low use of pharmacological interventions. These misconceptions may damage the quality of life and miss the critical period for preventing senile diseases.

Effect of different plant communities on NO in an urban road greenbelt in Nanjing, China.

As an important part of urban ecosystems, plants can reduce NO concentrations in the air. However, there is little evidence of the effects of different plant communities on NO concentrations in street-scale green spaces. We used a multifunctional lifting environmental detector to investigate the impact of environmental factors and small plant communities on NO concentrations in street green spaces during the summer and winter in Nanjing, China.

Research progress on pyrolysis of nitrogen-containing biomass for fuels, materials, and chemicals production.

Pyrolysis of nitrogen-containing biomass holds tremendous potential for producing varieties of high value-added products, alleviating energy depletion. Based on the research status about nitrogen-containing biomass pyrolysis, the effect of biomass feedstock composition on pyrolysis products is first introduced from the aspects of elemental analysis, proximate analysis, and biochemical composition. The properties of biomass with high and low nitrogen used in pyrolysis are briefly summarized.

CT-measured body composition radiomics predict lymph node metastasis in localized pancreatic ductal adenocarcinoma.

Background: To explored the value of CT-measured body composition radiomics in preoperative evaluation of lymph node metastasis (LNM) in localized pancreatic ductal adenocarcinoma (LPDAC).

Methods: We retrospectively collected patients with LPDAC who underwent surgical resection from January 2016 to June 2022. According to whether there was LNM after operation, the patients were divided into LNM group and non-LNM group in both male and female patients.

Co-torrefaction of corncob and waste cooking oil coupled with fast co-pyrolysis for bio-oil production.

Lignocellulosic biomass is a rich source of fixed renewable carbon and a promising alternative to fossil sources. However, low effective hydrogen to carbon ratio limits its applications. This work studied the influence of oil-bath co-torrefaction of corncob and waste cooking oil for co-pyrolysis.

pH-dependent microbial niches succession and antibiotic resistance genes distribution in an oxygen-based membrane biofilm reactor treating greywater.

System pH is found to crucially affect biofilm growth and microorganisms' activity in the biofilm-based wastewater treatment system. This study investigated the pH-dependent pollutants removal, microbial niches succession and antibiotic resistance genes (ARGs) accumulation in an oxygen-based membrane biofilm reactor treating greywater. Results indicated that neutral conditions achieved the highest biofilm concentration and living cells, which enabled the highest pollutants removal rates; multifarious functional groups in biofilm enabled pollutants adsorption, which favored its continuous bio-removal.

Conditioning Regimens are Associated with Distinct Patterns of Microbiota Injury in Allogeneic Hematopoietic Cell Transplantation.

Purpose: The gut microbiota is subject to multiple insults in allogeneic hematopoietic cell transplantation (allo-HCT) recipients. We hypothesized that preparative conditioning regimens contribute to microbiota perturbation in allo-HCT.

Experimental Design: This was a retrospective study that evaluated the relationship between conditioning regimens exposure in 1,188 allo-HCT recipients and the gut microbiome.

Preservation of the fecal microbiome is associated with reduced severity of graft-versus-host disease.

Following allogeneic hematopoietic cell transplantation (allo-HCT), the gastrointestinal (GI) tract is frequently affected by acute graft-versus-host disease (aGVHD), the pathophysiology of which is associated with a dysbiotic microbiome. Since microbial composition varies along the length of the GI tract, the authors hypothesized that microbiome features correlate with the pattern of organ involvement after allo-HCT. We evaluated 266 allo-HCT recipients from whom 1303 stool samples were profiled by 16S ribosomal gene sequencing.

MAIT and Vδ2 unconventional T cells are supported by a diverse intestinal microbiome and correlate with favorable patient outcome after allogeneic HCT.

Microbial diversity is associated with improved outcomes in recipients of allogeneic hematopoietic cell transplantation (allo-HCT), but the mechanism underlying this observation is unclear. In a cohort of 174 patients who underwent allo-HCT, we demonstrate that a diverse intestinal microbiome early after allo-HCT is associated with an increased number of innate-like mucosal-associated invariant T (MAIT) cells, which are in turn associated with improved overall survival and less acute graft-versus-host disease (aGVHD). Immune profiling of conventional and unconventional immune cell subsets revealed that the prevalence of Vδ2 cells, the major circulating subpopulation of γδ T cells, closely correlated with the frequency of MAIT cells and was associated with less aGVHD.

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.

Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics.

Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy.

Anti-CD19 chimeric antigen receptor (CAR) T cell therapy has led to unprecedented responses in patients with high-risk hematologic malignancies. However, up to 60% of patients still experience disease relapse and up to 80% of patients experience CAR-mediated toxicities, such as cytokine release syndrome or immune effector cell-associated neurotoxicity syndrome. We investigated the role of the intestinal microbiome on these outcomes in a multicenter study of patients with B cell lymphoma and leukemia.