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1,313
result(s) for
"Parrish, M"
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Local, expressive, quantum-number-preserving VQE ansätze for fermionic systems
We propose VQE circuit fabrics with advantageous properties for the simulation of strongly correlated ground and excited states of molecules and materials under the Jordan–Wigner mapping that can be implemented linearly locally and preserve all relevant quantum numbers: the number of spin up ( α ) and down ( β ) electrons and the total spin squared. We demonstrate that our entangler circuits are expressive already at low depth and parameter count, appear to become universal, and may be trainable without having to cross regions of vanishing gradient, when the number of parameters becomes sufficiently large and when these parameters are suitably initialized. One particularly appealing construction achieves this with just orbital rotations and pair exchange gates. We derive optimal four-term parameter shift rules for and provide explicit decompositions of our quantum number preserving gates and perform numerical demonstrations on highly correlated molecules on up to 20 qubits.
Journal Article
The photochemical ring-opening of 1,3-cyclohexadiene imaged by ultrafast electron diffraction
The ultrafast photoinduced ring-opening of 1,3-cyclohexadiene constitutes a textbook example of electrocyclic reactions in organic chemistry and a model for photobiological reactions in vitamin D synthesis. Although the relaxation from the photoexcited electronic state during the ring-opening has been investigated in numerous studies, the accompanying changes in atomic distance have not been resolved. Here we present a direct and unambiguous observation of the ring-opening reaction path on the femtosecond timescale and subångström length scale using megaelectronvolt ultrafast electron diffraction. We followed the carbon–carbon bond dissociation and the structural opening of the 1,3-cyclohexadiene ring by the direct measurement of time-dependent changes in the distribution of interatomic distances. We observed a substantial acceleration of the ring-opening motion after internal conversion to the ground state due to a steepening of the electronic potential gradient towards the product minima. The ring-opening motion transforms into rotation of the terminal ethylene groups in the photoproduct 1,3,5-hexatriene on the subpicosecond timescale.
The photochemical electrocyclic ring-opening of 1,3-cyclohexadiene is a textbook organic chemistry reaction. Now, using ultrafast electron diffraction its reaction pathway has been resolved on the level of atomic distances and on its natural femtosecond timescale. Furthermore, coherent isomerization dynamics of the photoproduct 1,3,5-hexatriene were observed.
Journal Article
Potent antibody-mediated neutralization limits bacteriophage treatment of a pulmonary Mycobacterium abscessus infection
post
An 81-year-old immunocompetent patient with bronchiectasis and refractory
Mycobacterium abscessus
lung disease was treated for 6 months with a three-phage cocktail active against the strain. In this case study of phage to lower infectious burden, intravenous administration was safe and reduced the
M. abscessus
sputum load tenfold within one month. However, after two months,
M. abscessus
counts increased as the patient mounted a robust IgM- and IgG-mediated neutralizing antibody response to the phages, which was associated with limited therapeutic efficacy.
Initial promise of a bacteriophage therapy for a persistent bacterial infection in an immunocompetent patient was curtailed in conjunction with a rise in phage-specific neutralizing antibodies.
Journal Article
Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction
Simultaneous observation of nuclear and electronic motion is crucial for a complete understanding of molecular dynamics in excited electronic states. It is challenging for a single experiment to independently follow both electronic and nuclear dynamics at the same time. Here we show that ultrafast electron diffraction can be used to simultaneously record both electronic and nuclear dynamics in isolated pyridine molecules, naturally disentangling the two components. Electronic state changes (S₁→S₀ internal conversion) were reflected by a strong transient signal in small-angle inelastic scattering, and nuclear structural changes (ring puckering) were monitored by large-angle elastic diffraction. Supported by ab initio nonadiabatic molecular dynamics and diffraction simulations, our experiment provides a clear view of the interplay between electronic and nuclear dynamics of the photoexcited pyridine molecule.
Journal Article
Differential gene expression in peripheral leukocytes of pre-weaned Holstein heifer calves with respiratory disease
Bovine respiratory disease (BRD) is a leading cause of calf morbidity and mortality, and prevalence remains high despite current management practices. Differential gene expression (DGE) provides detailed insight into individual immune responses and can illuminate enriched pathways and biomarkers that contribute to disease susceptibility and outcomes. The aims of this study were to investigate differences in peripheral leukocyte gene expression in Holstein preweaned heifer calves 1) with and without BRD, and 2) across weeks of age. Calves were enrolled for this short-term longitudinal study on two commercial dairies in Washington State. Calves were assessed every two weeks throughout the pre-weaning period using clinical respiratory scoring (CRS) and thoracic ultrasonography (TUS), and blood samples were collected. Calves were selected that were either healthy (n = 10) or had BRD diagnosed by CRS (n = 7), TUS (n = 6), or both (n = 6) in weeks 5 or 7 of life). Three consecutive time point samples were analyzed for each BRD calf consisting of PRE, ONSET, and POST samples. Nineteen genes of interest were selected based on previous gene expression studies in cattle: ALOX15 , BPI , CATHL6 , CXCL8 , DHX58 , GZMB , HPGD , IFNG , IL17D , IL1R2 , ISG15 , LCN2 , LIF , MX1 , OAS2 , PGLYRP1 , S100A8 , SELP , and TNF . Comparisons were made between age and disease time point matched BRD and healthy calves as well as between calf weeks of age. No DGE was observed between diseased and healthy calves; however, DGE was observed between calf weeks of age regardless of disease state. Developmental differences in leukocyte gene expression, phenotype, and functionality make pre-weaned calves immunologically distinct from mature cattle, and early life shifts in calf leukocyte populations likely contribute to the age-related gene expression differences we observed. Age overshadows disease impacts to influence gene expression in young calves, and immune development progresses upon a common trajectory regardless of disease during the preweaning period.
Journal Article
Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease
Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microbiome. Fecal samples were collected from calves (n = 167) of different breeds (Holstein, Jersey, Jersey-cross and beef-cross) from 4–21 d of age. Daily clinical evaluations assessed health status. Calves with loose or watery feces were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to behavior. Calves with normal or semiformed feces and no clinical illness were classified as healthy (H). One hundred and three fecal samples were obtained from consistently healthy calves and 64 samples were from calves with diarrhea (n = 39 BS; n = 25 DS). The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Differences were identified by a linear-mixed effects model with a negative binomial error. DS and Jersey calves had a higher relative abundance of Streptococcus gallolyticus relative to H Holstein calves. In addition, DS calves had a lower relative abundance of Bifidobacterium longum and an enrichment of Escherichia coli . Species of the genus Lactobacillus , such as an unclassified Lactobacillus , Lactobacillus reuteri , and Lactobacillus salivarius were enriched in calves with GI disease. Moreover, we created a model to predict GI disease based on the fecal microbiome composition. The presence of Eggerthella lenta , Bifidobacterium longum , and Collinsella aerofaciens were associated with a healthy clinical outcome. Although lactobacilli are often associated with beneficial probiotic properties, the presence of E . coli and Lactobacillus species had the highest coefficients positively associated with GI disease prediction. Our results indicate that there are differences in the fecal microbiome of calves associated with GI disease severity and breed specificities.
Journal Article
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance
Mycobacterium abscessus
(MAB) is an emerging pathogen that leads to chronic lung infections. To date, the global population structure of non-cystic fibrosis (CF) MAB and evolutionary patterns of drug resistance emergence have not been investigated. Here we construct a global dataset of 1,279 MAB whole genomes from CF or non-CF patients. We utilize whole genome analysis to assess relatedness, phylogeography, and drug resistance evolution. MAB isolates from CF and non-CF hosts are interspersed throughout the phylogeny, such that the majority of dominant circulating clones include isolates from both populations, indicating that global spread of MAB clones is not sequestered to CF contexts. We identify a large clade of
M. abscessus
harboring the
erm
(41) T28C mutation, predicted to confer macrolide susceptibility in this otherwise macrolide-resistant species. Identification of multiple evolutionary events within this clade, consistent with regain of wild type, intrinsic macrolide resistance, underscores the critical importance of macrolides in MAB.
Mycobacterium abscessus is an emerging infection that usually affects patients with structural lung diseases such as cystic fibrosis (CF). Here, the authors use phylogenetic analyses to demonstrate close relationships between isolates from CF and non-CF patients and identify antibiotic resistance markers.
Journal Article
RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing
Alternative splicing affects the function of many cardiac proteins, including that of the sarcomeric protein titin. Wei Guo
et al
. now show that the gene
RBM20
, previously identified as mutated in some individuals with dilated cardiomyopathy, is a splicing factor that regulates the alternative splicing of the gene encoding titin and many other key cardiac genes.
Alternative splicing has a major role in cardiac adaptive responses, as exemplified by the isoform switch of the sarcomeric protein titin, which adjusts ventricular filling. By positional cloning using a previously characterized rat strain with altered titin mRNA splicing, we identified a loss-of-function mutation in the gene encoding RNA binding motif protein 20 (
Rbm20
) as the underlying cause of pathological titin isoform expression. The phenotype of Rbm20-deficient rats resembled the pathology seen in individuals with dilated cardiomyopathy caused by
RBM20
mutations. Deep sequencing of the human and rat cardiac transcriptome revealed an RBM20-dependent regulation of alternative splicing. In addition to titin (
TTN
), we identified a set of 30 genes with conserved splicing regulation between humans and rats. This network is enriched for genes that have previously been linked to cardiomyopathy, ion homeostasis and sarcomere biology. Our studies emphasize the key role of post-transcriptional regulation in cardiac function and provide mechanistic insights into the pathogenesis of human heart failure.
Journal Article
Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves
Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Therefore, effective strategies to manipulate the microbiome of dairy calves under commercial dairy operations are of great importance to improve animal health and reduce antimicrobial usage. The objective of this study was to develop a farm-specific FMT product and to investigate its effects on clinical outcomes and fecal microbial composition of dairy calves. The FMT product was derived from feces from healthy donors (5–24 days of age) raised in the same calf ranch facility as the FMT recipients. Healthy and diarrheic calves were randomly enrolled to a control (n = 115) or FMT (n = 112) treatment group (~36 g of processed fecal matter once daily for 3 days). Fecal samples were collected at enrollment and again 9 days later after the first FMT dose. Although the FMT product was rich in organisms typically known for their beneficial probiotic properties, the FMT therapy did not prevent or ameliorate GI disease in dairy calves. In fact, calves that received FMT were less likely to recover from GI disease, and more likely to die due to GI disease complications. Fecal microbial community analysis revealed an increase in the alpha-diversity in FMT calves; however, no major differences across treatment groups were observed in the beta-diversity analysis. Calves that received FMT had higher relative abundance of an uncultured organism of the genus Lactobacillus and Lactobacillus reuteri on day 10. Moreover, FMT calves had lower relative abundance of Clostridium nexile and Bacteroides vulgatus on day 10. Our results indicate the need to have an established protocol when developing FMT products, based on rigorous inclusion and exclusion criteria for the selection of FMT donors free of potential pathogens, no history of disease or antibiotic treatment.
Journal Article