-
Frontiers in Cellular and Infection... 2024To investigate the structure, composition, and functions of the gut microbiota in elderly patients with hyperlipidemia.
OBJECTIVE
To investigate the structure, composition, and functions of the gut microbiota in elderly patients with hyperlipidemia.
METHODS
Sixteen older patients diagnosed with hyperlipidemia (M group) and 10 healthy, age-matched normal volunteers (N group) were included. These groups were further subdivided by sex into the male normal (NM, n = 5), female normal (NF, n = 5), male hyperlipidemia (MM, n = 8), and female hyperlipidemia (MF, n = 8) subgroups. Stool samples were collected for high-throughput sequencing of 16S rRNA genes. Blood samples were collected for clinical biochemical index testing.
RESULTS
Alpha- and beta-diversity analyses revealed that the structure and composition of the gut microbiota were significantly different between the M and N groups. The relative abundances of , , , , and were significantly decreased, while those of , , and were significantly higher in the M group. There were also significant sex-related differences in microbial structure between the NM and NF groups, and between the MM and MF groups. Through functional prediction with PICRUSt 2, we observed distinct between-group variations in metabolic pathways associated with the gut microbiota and their impact on the functionality of the nervous system. Pearson's correlation coefficient was used as a distance metric to build co-abundance networks. A hypergeometric test was used to detect taxonomies with significant enrichment in specific clusters. We speculated that modules with and as the core microbes play an important ecological role in the intestinal microbiota of the M group. The relative intestinal abundances of and in the M group were positively correlated with serum triglyceride and low-density lipoprotein levels, while the relative abundance of was negatively correlated with the serum lipoprotein a level.
Topics: Humans; Gastrointestinal Microbiome; Male; Female; Aged; Hyperlipidemias; RNA, Ribosomal, 16S; Feces; Bacteria; High-Throughput Nucleotide Sequencing; Middle Aged; Aged, 80 and over
PubMed: 38812752
DOI: 10.3389/fcimb.2024.1333145 -
PloS One 2024A powerful way to predict how ecological communities will respond to future climate change is to test how they have responded to the climate of the past. We used climate...
A powerful way to predict how ecological communities will respond to future climate change is to test how they have responded to the climate of the past. We used climate oscillations including the Pacific Decadal Oscillation (PDO), North Pacific Gyre Oscillation, and El Niño Southern Oscillation (ENSO) and variation in upwelling, air temperature, and sea temperatures to test the sensitivity of nearshore rocky intertidal communities to climate variability. Prior research shows that multiple ecological processes of key taxa (growth, recruitment, and physiology) were sensitive to environmental variation during this time frame. We also investigated the effect of the concurrent sea star wasting disease outbreak in 2013-2014. We surveyed nearly 150 taxa from 11 rocky intertidal sites in Oregon and northern California annually for up to 14-years (2006-2020) to test if community structure (i.e., the abundance of functional groups) and diversity were sensitive to past environmental variation. We found little to no evidence that these communities were sensitive to annual variation in any of the environmental measures, and that each metric was associated with < 8.6% of yearly variation in community structure. Only the years elapsed since the outbreak of sea star wasting disease had a substantial effect on community structure, but in the mid-zone only where spatially dominant mussels are a main prey of the keystone predator sea star, Pisaster ochraceus. We conclude that the established sensitivity of multiple ecological processes to annual fluctuations in climate has not yet scaled up to influence community structure. Hence, the rocky intertidal system along this coastline appears resistant to the range of oceanic climate fluctuations that occurred during the study. However, given ongoing intensification of climate change and increasing frequencies of extreme events, future responses to climate change seem likely.
Topics: Climate Change; Animals; Ecosystem; Oregon; Oceans and Seas; California; Temperature; Starfish; Biodiversity; El Nino-Southern Oscillation; Pacific Ocean
PubMed: 38809830
DOI: 10.1371/journal.pone.0297697 -
Heliyon May 2024Groundwater is the fundamental component of the hydrological system that acts as a major factor in comprehensions of the physical processes in both the land surface and...
Groundwater is the fundamental component of the hydrological system that acts as a major factor in comprehensions of the physical processes in both the land surface and the atmosphere. Determining groundwater, which directly affects the agricultural productivity of semi-arid mountainous regions, is crucial. Mountain ecosystems, once abundant with flowing water, now face immense pressure from a changing climate, evident in the drying of springs and the diminishing flow of groundwater. Ensuring a steady flow of water, fair access to it, and responsible use are the cornerstones of a secure future for mountain communities. This study aims to assess the groundwater potential zones using remote sensing and a geospatial approach in the Mustang Valley's rural municipalities (Thasang and Gharapjhong). Nine factors were assigned to assess the groundwater potential map: slope, drainage density, lineament density, geology, soil, land use/land cover, rainfall, aspect, and soil moisture. The Bayesian weights of evidence model was used to delineate the groundwater potential zone. The study categorized groundwater potential across the region, creating five zones: very high, high, moderate, low, and very low. These zones covered 0.6 %, 12.4 %, 51.2 %, 35.5 %, and 0.3 % of the study area. The accuracy of the groundwater potential map was assessed by comparing its predictions with the actual locations of springs, using the area under the curve metric. The receiver operating characteristics curve analysis yielded an area under the curve of 0.7226, indicating a 72.26 % accuracy in predicting the presence of groundwater. The findings of this paper contribute to a better understanding of groundwater potential zones, which can support policymakers and planners for hydrological, meteorological, and crop planning applications in this climatically vulnerable region.
PubMed: 38807886
DOI: 10.1016/j.heliyon.2024.e31281 -
Heliyon May 2024The pathogenesis of diabetes and its microvascular complications are intimately associated with renin angiotensin system dysregulation. Evidence suggests the angiotensin...
BACKGROUND
The pathogenesis of diabetes and its microvascular complications are intimately associated with renin angiotensin system dysregulation. Evidence suggests the angiotensin converting enzyme 2 (ACE2)/angiotensin 1-7 (Ang 1-7)/Mas receptor (MasR) axis regulates metabolic imbalances, inflammatory responses, reduces oxidative stress, and sustains microvascular integrity, thereby strengthening defences against diabetic conditions. This study aims to conduct a comprehensive analysis of the ACE2/Ang 1-7/MasR axis in diabetes and its microvascular complications over the past two decades, focusing on key contributors, research hotspots, and thematic trends.
METHODS
This cross-sectional bibliometric analysis of 349 English-language publications was performed using HistCite, VOSviewer, CiteSpace, and Bibliometrix R for visualization and metric analysis. Primary analytical metrics included publication count and keyword trend dynamics.
RESULTS
The United States, contributing 105 articles, emerged as the most productive country, with the University of Florida leading institutions with 18 publications. Benter IF was the most prolific author with 14 publications, and was the leading journal with 13 articles. A total of 151 of the 527 author's keywords with two or more occurrences clustered into four major clusters: diabetic microvascular pathogenesis, metabolic systems, type 2 diabetes, and coronavirus infections. Keywords such as "SARS", "ACE2", "coronavirus", "receptor" and "infection" displayed the strongest citation bursts. The thematic evolution in this field expanded from focusing on the renin angiotensin system (2002-2009) to incorporating ACE2 and diabetes metabolism (2010-2016). The latter period (2017-2023) witnessed a significant surge in diabetes research, reflecting the impact of COVID-19 and associated conditions such as diabetic retinopathy and cardiomyopathy.
CONCLUSIONS
This scientometric study offers a detailed analysis of the ACE2/Ang 1-7/MasR axis in diabetes and its microvascular complications, providing valuable insights for future research directions.
PubMed: 38807880
DOI: 10.1016/j.heliyon.2024.e31405 -
Journal of Medical Internet Research May 2024Clinical natural language processing (NLP) researchers need access to directly comparable evaluation results for applications such as text deidentification across a...
BACKGROUND
Clinical natural language processing (NLP) researchers need access to directly comparable evaluation results for applications such as text deidentification across a range of corpus types and the means to easily test new systems or corpora within the same framework. Current systems, reported metrics, and the personally identifiable information (PII) categories evaluated are not easily comparable.
OBJECTIVE
This study presents an open-source and extensible end-to-end framework for comparing clinical NLP system performance across corpora even when the annotation categories do not align.
METHODS
As a use case for this framework, we use 6 off-the-shelf text deidentification systems (ie, CliniDeID, deid from PhysioNet, MITRE Identity Scrubber Toolkit [MIST], NeuroNER, National Library of Medicine [NLM] Scrubber, and Philter) across 3 standard clinical text corpora for the task (2 of which are publicly available) and 1 private corpus (all in English), with annotation categories that are not directly analogous. The framework is built on shell scripts that can be extended to include new systems, corpora, and performance metrics. We present this open tool, multiple means for aligning PII categories during evaluation, and our initial timing and performance metric findings. Code for running this framework with all settings needed to run all pairs are available via Codeberg and GitHub.
RESULTS
From this case study, we found large differences in processing speed between systems. The fastest system (ie, MIST) processed an average of 24.57 (SD 26.23) notes per second, while the slowest (ie, CliniDeID) processed an average of 1.00 notes per second. No system uniformly outperformed the others at identifying PII across corpora and categories. Instead, a rich tapestry of performance trade-offs emerged for PII categories. CliniDeID and Philter prioritize recall over precision (with an average recall 6.9 and 11.2 points higher, respectively, for partially matching spans of text matching any PII category), while the other 4 systems consistently have higher precision (with MIST's precision scoring 20.2 points higher, NLM Scrubber scoring 4.4 points higher, NeuroNER scoring 7.2 points higher, and deid scoring 17.1 points higher). The macroaverage recall across corpora for identifying names, one of the more sensitive PII categories, included deid (48.8%) and MIST (66.9%) at the low end and NeuroNER (84.1%), NLM Scrubber (88.1%), and CliniDeID (95.9%) at the high end. A variety of metrics across categories and corpora are reported with a wider variety (eg, F-score) available via the tool.
CONCLUSIONS
NLP systems in general and deidentification systems and corpora in our use case tend to be evaluated in stand-alone research articles that only include a limited set of comparators. We hold that a single evaluation pipeline across multiple systems and corpora allows for more nuanced comparisons. Our open pipeline should reduce barriers to evaluation and system advancement.
Topics: Natural Language Processing; Humans
PubMed: 38805692
DOI: 10.2196/55676 -
BMJ Open Quality May 2024Clinical practice guidelines recommend screening for primary hyperaldosteronism (PH) in patients with resistant hypertension. However, screening rates are low in the...
Clinical practice guidelines recommend screening for primary hyperaldosteronism (PH) in patients with resistant hypertension. However, screening rates are low in the outpatient setting. We sought to increase screening rates for PH in patients with resistant hypertension in our Veterans Affairs (VA) outpatient resident physician clinic, with the goal of improving blood pressure control. Patients with possible resistant hypertension were identified through a VA Primary Care Almanac Metric query, with subsequent chart review for resistant hypertension criteria. Three sequential patient-directed cycles were implemented using rapid cycle improvement methodology during a weekly dedicated resident quality improvement half-day. In the first cycle, patients with resistant hypertension had preclinic PH screening labs ordered and were scheduled in the clinic for hypertension follow-up. In the second cycle, patients without screening labs completed were called to confirm medication adherence and counselled to screen for PH. In the third cycle, patients with positive screening labs were called to discuss mineralocorticoid receptor antagonist (MRA) initiation and possible endocrinology referral. Of 97 patients initially identified, 58 (60%) were found to have resistant hypertension while 39 had pseudoresistant hypertension from medication non-adherence. Of the 58 with resistant hypertension, 44 had not previously been screened for PH while 14 (24%) had already been screened or were already taking an MRA. Our screening rate for PH in resistant hypertension patients increased from 24% at the start of the project to 84% (37/44) after two cycles. Of the 37 tested, 24% (9/37) screened positive for PH, and 5 patients were started on MRAs. This resident-led quality improvement project demonstrated that a focused intervention process can improve PH identification and treatment.
Topics: Humans; Hyperaldosteronism; Quality Improvement; Hypertension; Mass Screening; Female; Male; Middle Aged; Ambulatory Care Facilities; Aged; United States; Internship and Residency; United States Department of Veterans Affairs
PubMed: 38802267
DOI: 10.1136/bmjoq-2023-002611 -
Journal of Cellular and Molecular... May 2024Previous studies have found that ferroptosis plays an important role in a variety of neurological diseases. However, the precise role of ferroptosis in the multiple...
Previous studies have found that ferroptosis plays an important role in a variety of neurological diseases. However, the precise role of ferroptosis in the multiple sclerosis patients remains uncertain. We defined and validated a computational metric of ferroptosis levels. The ferroptosis scores were computed using the AUCell method, which reflects the enrichment scores of ferroptosis-related genes through gene ranking. The reliability of the ferroptosis score was assessed using various methods, involving cells induced to undergo ferroptosis by six different ferroptosis inducers. Through a comprehensive approach integrating snRNA-seq, spatial transcriptomics, and spatial proteomics data, we explored the role of ferroptosis in multiple sclerosis. Our findings revealed that among seven sampling regions of different white matter lesions, the edges of active lesions exhibited the highest ferroptosis score, which was associated with activation of the phagocyte system. Remyelination lesions exhibit the lowest ferroptosis score. In the cortex, ferroptosis score were elevated in neurons, relevant to a variety of neurodegenerative disease-related pathways. Spatial transcriptomics demonstrated a significant co-localization among ferroptosis score, neurodegeneration and microglia, which was verified by spatial proteomics. Furthermore, we established a diagnostic model of multiple sclerosis based on 24 ferroptosis-related genes in the peripheral blood. Ferroptosis might exhibits a dual role in the context of multiple sclerosis, relevant to both neuroimmunity and neurodegeneration, thereby presenting a promising and novel therapeutic target. Ferroptosis-related genes in the blood that could potentially serve as diagnostic and prognostic markers for multiple sclerosis.
Topics: Ferroptosis; Multiple Sclerosis; Humans; Proteomics; Transcriptome; Microglia; Gene Expression Profiling; Computational Biology; Neurons; Multiomics
PubMed: 38801304
DOI: 10.1111/jcmm.18396 -
Protein Science : a Publication of the... Jun 2024Thermal stability of proteins is a primary metric for evaluating their physical properties. Although researchers attempted to predict it using machine learning...
Thermal stability of proteins is a primary metric for evaluating their physical properties. Although researchers attempted to predict it using machine learning frameworks, their performance has been dependent on the quality and quantity of published data. This is due to the technical limitation that thermodynamic characterization of protein denaturation by fluorescence or calorimetry in a high-throughput manner has been challenging. Obtaining a melting curve that derives solely from the target protein requires laborious purification, making it far from practical to prepare a hundred or more samples in a single workflow. Here, we aimed to overcome this throughput limitation by leveraging the high protein secretion efficacy of Brevibacillus and consecutive treatment with plate-scale purification methodologies. By handling the entire process of expression, purification, and analysis on a per-plate basis, we enabled the direct observation of protein denaturation in 384 samples within 4 days. To demonstrate a practical application of the system, we conducted a comprehensive analysis of 186 single mutants of a single-chain variable fragment of nivolumab, harvesting the melting temperature (T) ranging from -9.3 up to +10.8°C compared to the wild-type sequence. Our findings will allow for data-driven stabilization in protein design and streamlining the rational approaches.
Topics: Protein Stability; Thermodynamics; Protein Denaturation; High-Throughput Screening Assays; Brevibacillus
PubMed: 38801228
DOI: 10.1002/pro.5029 -
Computational and Structural... Dec 2024Accidents at work may force workers to face abrupt changes in their daily life: one of the most impactful accident cases consists of the worker remaining in a...
Accidents at work may force workers to face abrupt changes in their daily life: one of the most impactful accident cases consists of the worker remaining in a wheelchair. Return To Work (RTW) of wheelchair users in their working age is still challenging, encompassing the expertise of clinical and rehabilitation personnel and social workers to match the workers' residual capabilities with job requirements. This work describes a novel and prototypical knowledge-based Decision Support System (DSS) that matches workers' residual capabilities with job requirements, thus helping vocational therapists and clinical personnel in the RTW decision-making process for WUs. The DSS leverages expert knowledge in the form of ontologies to represent the International Classification of Functioning, Disability, and Health (ICF) and the Occupational Information Network (O*NET). These taxonomies enable both workers' health conditions and job requirements formalization, which are processed to assess the suitability of a job depending on a worker's condition. Consequently, the DSS suggests a list of jobs a wheelchair user can still perform, exploiting his/her residual abilities at their best. The manuscript describes the theoretical approach and technological foundations of such DSS, illustrating its development, its output metric, and application. The developed solution was tested with real wheelchair users' health conditions provided by the Italian National Institute for Insurance against Accidents at Work. The feasibility of an approach based on objective data was thus demonstrated, providing a novel point of view in the critical process of decision-making during RTW.
PubMed: 38800691
DOI: 10.1016/j.csbj.2024.05.013 -
Neurophotonics Sep 2024Motion artifacts in the signals recorded during optical fiber-based measurements can lead to misinterpretation of data. In this work, we address this problem during...
SIGNIFICANCE
Motion artifacts in the signals recorded during optical fiber-based measurements can lead to misinterpretation of data. In this work, we address this problem during rodent experiments and develop a motion artifacts correction (MAC) algorithm for single-fiber system (SFS) hemodynamics measurements from the brains of rodents.
AIM
(i) To distinguish the effect of motion artifacts in the SFS signals. (ii) Develop a MAC algorithm by combining information from the experiments and simulations and validate it.
APPROACH
Monte-Carlo (MC) simulations were performed across 450 to 790 nm to identify wavelengths where the reflectance is least sensitive to blood absorption-based changes. This wavelength region is then used to develop a quantitative metric to measure motion artifacts, termed the dissimilarity metric (DM). We used MC simulations to mimic artifacts seen during experiments. Further, we developed a mathematical model describing light intensity at various optical interfaces. Finally, an MAC algorithm was formulated and validated using simulation and experimental data.
RESULTS
We found that the 670 to 680 nm wavelength region is relatively less sensitive to blood absorption. The standard deviation of DM () can measure the relative magnitude of motion artifacts in the SFS signals. The artifacts cause rapid shifts in the reflectance data that can be modeled as transmission changes in the optical lightpath. The changes observed during the experiment were found to be in agreement to those obtained from MC simulations. The mathematical model developed to model transmission changes to represent motion artifacts was extended to an MAC algorithm. The MAC algorithm was validated using simulations and experimental data.
CONCLUSIONS
We distinguished motion artifacts from SFS signals during in vivo hemodynamic monitoring experiments. From simulation and experimental data, we showed that motion artifacts can be modeled as transmission changes. The developed MAC algorithm was shown to minimize artifactual variations in both simulation and experimental data.
PubMed: 38799809
DOI: 10.1117/1.NPh.11.S1.S11511