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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Introgressions of novel diseases resistance genes from Miscanthus into energycane

Sugarcane (Saccharum) is among the world’s leading bioenergy crops. However, modern sugarcane cultivars are derived from a relatively small set of founder genotypes, which has contributed to cultivar susceptibility to diseases. Miscanthus is a close relative of sugarcane that is genetically diverse and a potential source of genes for improving sugarcane. We found that Miscanthus is a source of resistance to four major diseases of sugarcane and we crossed these disease-resistance genes into a predominantly sugarcane genetic background (BC1 generation). Additionally, we found that Miscanthus could also confer genes for chilling-tolerant photosynthesis to sugarcane, which would be highly advantageous for production of energycane in subtropical environments, like the southern coastal plain of the US. Using advanced modeling techniques, we found that standard marker-assisted selection could be effective for breeding resistance conferred by a small number of genes each with large effect (i.e. vertical resistance), but to breed for many genes each of small effect (i.e. horizontal resistance), genomic selection would be the better strategy. Lastly, we learned that Miscanthus can be induced to flower sooner by giving the plants short days (long nights) but that the ideal day length for a given accession depends on its adaptation to its latitude of origin, with tropical accessions requiring shorter days to flower than accessions from high latitudes. This information will facilitate plant breeders’ ability to make crosses between Miscanthus and sugarcane, and enable greater use of Miscanthus as a genetic resource to improve sugarcane.

09 BIOMASS FUELS↗
DOE OSTI2016

Vesicular Disease in 9-Week-Old Pigs Experimentally Infected with Senecavirus A

Senecavirus A has been infrequently associated with vesicular disease in swine since 1988. However, clinical disease has not been reproduced after experimental infection with this virus. Here we report vesicular disease in 9-week-old pigs after Sencavirus A infection by the intranasal route under experimental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.

Mathematics and Computing↗
DOE OSTI2024

Evaluation of partial volume correction and analysis of longitudinal [ 18 F]GTP1 tau PET imaging in Alzheimer's disease using linear mixed-effects models

Purpose: We evaluated the impact of partial volume correction (PVC) methods on the quantification of longitudinal [ 18 F]GTP1 tau positron-emission tomography (PET) in Alzheimer's disease and the suitability of describing the tau pathology burden temporal trajectories using linear mixed-effects models (LMEM). Methods: We applied van Cittert iterative deconvolution (VC), 2-compartment, and 3-compartment, and the geometric transfer matrix plus region-based voxelwise methods to data acquired in an Alzheimer's disease natural history study over 18 months at a single imaging site. We determined the optimal PVC method by comparing the standardized uptake value ratio change (%ΔSUVR) between diagnostic and tau burden–level groups and the longitudinal repeatability derived from the LMEM. The performance of LMEM analysis for calculating %ΔSUVR was evaluated in a natural history study and in a multisite clinical trial of semorinemab in prodromal to mild Alzheimer's disease by comparing results to traditional per-visit estimates. Results: The VC, 2-compartment, and 3-compartment PVC methods had similar performance, whereas region-based voxelwise overcorrected regions with a higher tau burden. The lowest within-subject variability and acceptable group separation scores were observed without PVC. The LMEM-derived %ΔSUVR values were similar to the per-visit estimates with lower variability. Conclusion: The results indicate that the tested PVC methods do not offer a clear advantage or improvement over non-PVC images for the quantification of longitudinal [ 18 F]GTP1 PET data. LMEM offers a robust framework for the longitudinal tau PET quantification with low longitudinal test–retest variability. Clinical trial registration: NCT02640092 and NCT03289143.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen–host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Envisioning urban environments resilient to vector-borne diseases: a protocol to study dengue in Vietnam

Transmitted primarily by Aedes aegypti (Ae. aegypti) and Aedes albopictus (Ae. albopictus), arboviral diseases pose a major global public health threat. Dengue, chikungunya, and zika are increasingly prevalent in Southeast Asia. Among other arboviruses, dengue and zika are becoming more common in Central and South America. Given human encroachment into previously uninhabited, often deforested areas, to provide new housing in regions of population expansion, conceptualizing built urban environments in a novel way is urgently needed to safeguard against the growing climate change-driven threat of vector-borne diseases. By understanding the spread from a One Health perspective, enhanced control and prevention can be achieved. This is particularly important considering that climate change is likely to significantly impact the persistence of ponded water where mosquitoes breed due to increasing temperature and shifting rainfall patterns with regard to magnitude, duration, frequency, and season. Models can incorporate aquatic mosquito stages and adult spatial dynamics when habitats are heterogeneously available, thereby including dispersal and susceptible-exposed-infected-recovered (SEIR) epidemiology. Coupled with human population distribution (density, locations), atmospheric conditions (air temperature, precipitation), and hydrological conditions (soil moisture distribution, ponding persistence in topographic depressions), modeling has improved predictive ability for infection rates. However, it has not informed interventional approaches from an urban environment perspective which considers the role of ponds/lakes that support green spaces, the density of population that enables rapid spread of disease, and varying micro-habitats for various mosquito stages under climate change. Here, for an example of dengue in Vietnam, a preventive and predictive approach to design resilient urban environments is proposed, which uses data from rapidly expanding metropolitan communities to learn continually. This protocol deploys computational approaches including simulation and machine learning/artificial intelligence, underpinned by surveillance and medical data for validation and adaptive learning. Its application may best inform urban planning in low-middle income countries in tropical zones where arboviral pathogens are prevalent.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Tools and Apps to Enhance Situational Awareness for Global Disease Surveillance</strong

Situational awareness is important for both early warning and early detection of a disease outbreak. We will describe a suite of tools developed at Los Alamos National Laboratory that provide actionable information and knowledge for enhanced situational awareness during an unfolding event. The BRD is a searchable database, a one stop shop for disease surveillance resources and can be used for validating information received about disease outbreaks. Furthermore, the BaRD is a searchable database that catalogs and classifies epidemiological model-specific information to allow facile selection. The SWAP is an app to provide a context for a rapidly unfolding event through graphical visualization.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Heat-Related Mortality Projections for Cardiovascular and Respiratory Disease Under the Changing Climate in Beijing, China

Because heat-related health effects tend to become more serious at higher temperatures, there is an urgent need to determine the mortality projection of specific heat-sensitive diseases to provide more detailed information regarding the variation of the sensitivity of such diseases. In this study, the specific mortality of cardiovascular and respiratory disease in Beijing was initially projected under five different global-scale General Circulation Models (GCMs) and two Representative Concentration Pathways scenarios (RCPs) in the 2020s, 2050s, and 2080s compared to the 1980s. Multi-model ensembles indicated cardiovascular mortality could increase by an average percentage of 18.4 percent, 47.8 percent, and 69.0 percent in the 2020s, 2050s, and 2080s under RCP 4.5, respectively, and by 16.6 percent, 73.8 percent and 134 percent in different decades respectively, under RCP 8.5 compared to the baseline range. The same increasing pattern was also observed in respiratory mortality. The heat-related deaths under the RCP 8.5 scenario were found to reach a higher number and to increase more rapidly during the 21st century compared to the RCP4.5 scenario, especially in the 2050s and the 2080s. The projection results show potential trends in cause-specific mortality in the context of climate change, and provide support for public health interventions tailored to specific climate-related future health risks.

health↗
NASA NTRS2021

Climate Predicts Geographic and Temporal Variation in Mosquito-Borne Disease Dynamics on Two Continents

Climate drives population dynamics through multiple mechanisms, which can lead to seemingly context-dependent effects of climate on natural populations. For climate-sensitive diseases such as dengue, chikungunya, and Zika, climate appears to have opposing effects in different contexts. Here we show that a model, parameterized with laboratory measured climate-driven mosquito physiology, captures three key epidemic characteristics across ecologically and culturally distinct settings in Ecuador and Kenya: the number, timing, and duration of outbreaks. The model generates a range of disease dynamics consistent with observed Aedes aegypti abundances and laboratory-confirmed arboviral incidence with variable accuracy (28–85% for vectors, 44–88%for incidence). The model predicted vector dynamics better in sites with a smaller proportion of young children in the population, lower mean temperature, and homes with piped water and made of cement. Models with limited calibration that robustly capture climate-virus relationships can help guide intervention efforts and climate change disease projections.

Climate-change ecology↗
DOE OSTI2017

A Universal Biosensor for Infectious Disease

With increased travel and globalization, the spread of new diseases has become a threat to global health—and global security. Whether in a rural village or an urban medical clinic, healthcare workers need diagnostics that provide answers then and there, for any disease, in order to effectively treat individual patients or widespread outbreaks. That’s why Harshini Mukundan and her team at Los Alamos National Laboratory are working to develop a universal biosensor. “If we are able to mimic the body’s immune recognition in the laboratory, we could have a universal strategy for the early diagnosis of all infections,” said Mukundan. Our immune system recognizes pathogens, regardless of their origin, by identifying discrete signatures in the human host. Mukundan's team is working to imitate this ability in the laboratory, which could lead to a simple solution to diagnose all diseases and improve lives across the world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

MeWRKY20 and its interacting and activating autophagy-related protein 8 (MeATG8) regulate plant disease resistance in cassava

Highlights: • A systematic genome-wide of MeATGs is performed. • MeWRKY20 physically interacts with MeATG8a/8f/8h. • MeWRKY20 activates the transcription of MeATG8a. • MeATG8s and MeWRKY20 regulate defense response in cassava. As a highly conserved mechanism, autophagy is responsible for the transport of cytoplasmic constituents in the vacuoles or lysosomes. Moreover, autophagy is essential for plant development and various stress responses. In this study, 34 MeATGs were systematically identified in cassava, and their transcripts were commonly regulated by Xanthomonas axonopodis pv manihotis (Xam). Through transient expression in Nicotiana benthamiana, the subcellular locations of 4 MeATG8s were revealed. Notably, MeWRKY20 was identified as physical interacting protein of MeATG8a/8f/8h and upstream transcriptional activator of MeATG8a. Through virus-induced gene silencing (VIGS) in cassava, we found that MeATG8-silenced and MeWRKY20-silenced plants resulted in disease sensitive, with less callose depositions and lower autophagic activity. This study may facilitate our understanding of the upstream MeWRKY20 and underlying target as well as interacting proteins of MeATG8s in immune response. Taken together, MeWRKY20 and MeATG8a/8f/8h are essential for disease resistance against bacterial blight by forming various transcriptional modules and interacting complex in cassava.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Disease Diagnostics Research at Los Alamos National Laboratory

Human evolution and persistent diseases have existed side-by-side. A recent concern is the re-emergence of tuberculosis, one of the oldest and most challenging diseases known to man. Effective diagnosis can save lives and prevent its spread. This talk will cover how our immune system discriminates between itself and foreign entities and how a new laboratory and nature inspired strategy can detect tuberculosis equally well in human and animal populations. The approach is being extended to other applications such as the identification of strep throat and respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Modifications to Nano- and Microstructural Quality and the Effects on Mechanical Integrity in Paget's Disease of Bone

ABSTRACT Paget's disease of bone (PDB) is the second most common bone disease mostly developing after 50 years of age at one or more localized skeletal sites; it is associated with severely high bone turnover, bone enlargement, bowing/deformity, cracking, and pain. Here, to specifically address the origins of the deteriorated mechanical integrity, we use a cohort of control and PDB human biopsies to investigate multiscale architectural and compositional modifications to the bone structure (ie, bone quality) and relate these changes to mechanical property measurements to provide further insight into the clinical manifestations (ie, deformities and bowing) and fracture risk caused by PDB. Here, at the level of the collagen and mineral (ie, nanometer-length scale), we find a 19% lower mineral content and lower carbonate-to-phosphate ratio in PDB, which accounts for the 14% lower stiffness and 19% lower hardness promoting plastic deformation in pathological bone. At the microstructural scale, trabecular regions are known to become densified, whereas cortical bone loses its characteristic parallel-aligned osteonal pattern, which is replaced with a mosaic of lamellar and woven bone. Although we find this loss of anisotropic alignment produces a straighter crack path in mechanically-loaded PDB cases, cortical fracture toughness appears to be maintained due to increased plastic deformation. Clearly, the altered quality of the bone structure in PDB affects the mechanical integrity leading to complications such as bowing, deformities, and stable cracks called fissure fractures associated with this disease. Although the lower mineralization and loss of aligned Haversian structures do produce a lower modulus tissue, which is susceptible to deformities, our results indicate that the higher levels of plasticity may compensate for the lost microstructural features and maintain the resistance to crack growth. © 2014 American Society for Bone and Mineral Research

Zimmermann, Elizabeth A.↗
DOE OSTI2013

Endovascular Treatment of Diabetic Foot in a Selected Population of Patients with Below-the-Knee Disease: Is the Angiosome Model Effective?

Purpose. To evaluate the efficacy of percutaneous transluminal angioplasty (PTA) in a selected population of diabetic patients with below-the-knee (BTK) disease and to analyze the reliability of the angiosome model. Methods. We made a retrospective analysis of the results of PTA performed in 201 diabetic patients with BTK-only disease treated at our institute from January 2005 to December 2011. We evaluated the postoperative technical success, and at 1, 6, and 12 months' follow-up, we assessed the rates and values of partial and complete ulcer healing, restenosis, major and minor amputation, limb salvage, and percutaneous oximetry (TcPO{sub 2}) (Student's t test). We used the angiosome model to compare different clinicolaboratory outcomes in patients treated by direct revascularization (DR) from patients treated with indirect revascularization (IR) technique by Student's t test and the {chi}{sup 2} test. Results. At a mean {+-} standard deviation follow-up of 17.5 {+-} 12 months, we observed a mortality rate of 3.5 %, a major amputation rate of 9.4 %, and a limb salvage rate of 87 % with a statistically significant increase of TcPO{sub 2} values at follow-up compared to baseline (p < 0.05). In 34 patients, treatment was performed with the IR technique and in 167 by DR; in both groups, there was a statistically significant increase of TcPO{sub 2} values at follow-up compared to baseline (p < 0.05), without statistically significant differences in therapeutic efficacy. Conclusion. PTA of the BTK-only disease is a safe and effective option. The DR technique is the first treatment option; we believe, however, that IR is similarly effective, with good results over time.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Local Thermal Ablation with Continuous EGFR Tyrosine Kinase Inhibitors for EGFR-Mutant Non-small Cell Lung Cancers that Developed Extra-Central Nervous System (CNS) Oligoprogressive Disease

Background: Most epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) patients treated with tyrosine kinase inhibitors (TKIs) experience oligoprogressive disease. Local ablation for isolated resistant sites continued with the original EGFR-TKI showed good efficacy in these patients. We conducted this multicenter retrospective study to investigate the potential benefit of thermal ablation in NSCLC patients that developed extra-central nervous system (CNS) oligoprogressive disease during TKI treatment. Methods: A total of 71 EGFR-mutant patients treated with EGFR-TKIs were identified. Progression-free survival 1 (PFS1) was calculated from the initiation of TKI treatment to first progression. Patients with metastatic sites ≤ 3 in less than 3 extra-CNS organs suitable for local ablation therapy received either radiofrequency ablation or microwave ablation to these sites and continued on the original TKIs. PFS2 was defined from the first progression to second progression after ablation. Results: The median PFS1 for all patients was 11.8 months. Eighty extra-CNS oligoprogressive lesions in 71 patients were ablated. Thirty-six of 71 patients progressed after thermal ablation and 31 of whom died during the study period. The median PFS2 after thermal ablation was 10.0 months, and the median overall survival was 26.4 months. PFS1 and PFS2 were highly correlated with OS, whereas PFS1 was not correlated with PFS2. The numbers of oligoprogressive lesions were significantly and independently associated with PFS2. Conclusion: Local thermal ablation for the oligoprogressive lesions with continuous EGFR-TKI treatment is associated with additional 10 months of disease control and should be recommended in TKI acquired resistant-NSCLC patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Chinese social media analysis for disease surveillance

Here, it is reported that there are hundreds of thou- sands of deaths caused by seasonal flu all around the world every year. More other diseases such as chickenpox, malaria, etc. are also serious threats to people’s physical and mental health. There are 250,000–500,000 deaths every year around the world. Therefore proper techniques for disease surveillance are highly demanded. Recently, social media analysis is regarded as an efficient way to achieve this goal, which is feasible since growing number of people have been posting their health information on social media such as blogs, personal websites, etc. Previous work on social media analysis mainly focused on English materials but hardly considered Chinese materials, which hinders the application of such technique to Chinese peo- ple. In this paper, we proposed a new method of Chinese social media analysis for disease surveillance. More specifically, we compared different kinds of methods in the process of classification and then proposed a new way to process Chinese text data. The Chinese Sina micro-blog data collected from September to December 2013 are used to validate the effectiveness of the proposed method. The results show that a high classification precision of 87.49 % in average has been obtained. Comparing with the data from the authority, Chinese National Influenza Center, we can predict the outbreak time of flu 5 days earlier.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Computational Biorheology of Human Blood Flow in Health and Disease

Hematologic disorders arising from infectious diseases, hereditary factors and environmental influences can lead to, and can be influenced by, significant changes in the shape, mechanical and physical properties of red blood cells (RBCs), and the biorheology of blood flow. Hence, modeling of hematologic disorders should take into account the multiphase nature of blood flow, especially in arterioles and capillaries. We present here an overview of a general computational framework based on dissipative particle dynamics (DPD) which has broad applicability in cell biophysics with implications for diagnostics, therapeutics and drug efficacy assessments for a wide variety of human diseases. This computational approach, validated by independent experimental results, is capable of modeling the biorheology of whole blood and its individual components during blood flow so as to investigate cell mechanistic processes in health and disease. DPD is a Lagrangian method that can be derived from systematic coarse-graining of molecular dynamics but can scale efficiently up to arterioles and can also be used to model RBCs down to the spectrin level. We start from experimental measurements of a single RBC to extract the relevant biophysical parameters, using single-cell measurements involving such methods as optical tweezers, atomic force microscopy and micropipette aspiration, and cell-population experiments involving microfluidic devices. We then use these validated RBC models to predict the biorheological behavior of whole blood in healthy or pathological states, and compare the simulations with experimental results involving apparent viscosity and other relevant parameters. Finally, while the approach discussed here is sufficiently general to address a broad spectrum of hematologic disorders including certain types of cancer, this paper specifically deals with results obtained using this computational framework for blood flow in malaria and sickle cell anemia.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Radiation-Associated Pericardial Disease

Purpose of Review: This review highlights the literature related to pericardial injury following radiation for oncologic diseases. Recent Findings: Radiation-associated pericardial disease can have devastating consequences. Unfortunately, there is considerably less evidence regarding pericardial syndromes following thoracic radiation as compared to other cardiovascular outcomes. Pericardial complications of radiation may arise acutely or have an insidious onset several decades after treatment. Transthoracic echocardiography is the screening imaging modality of choice, while cardiac magnetic resonance imaging further characterizes the pericardium and guides treatment decision-making. Cardiac CT can be useful for assessing pericardial calcification. Ongoing efforts to lessen inadvertent cardiac injury are directed towards the revision of radiation techniques and protocols. Summary: As survival of mediastinal and thoracic malignancies continues to improve, radiation-associated pericardial disease is increasingly relevant. Though advances in radiation oncology demonstrate promise in curtailing cardiotoxicity, the long-term effects pertaining to pericardial complications remain to be seen.

62 RADIOLOGY AND NUCLEAR MEDICINE↗