645 research outputs found
Multi-omics integration reveals molecular networks and regulators of psoriasis.
BackgroundPsoriasis is a complex multi-factorial disease, involving both genetic susceptibilities and environmental triggers. Genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS) have been carried out to identify genetic and epigenetic variants that are associated with psoriasis. However, these loci cannot fully explain the disease pathogenesis.MethodsTo achieve a comprehensive mechanistic understanding of psoriasis, we conducted a systems biology study, integrating multi-omics datasets including GWAS, EWAS, tissue-specific transcriptome, expression quantitative trait loci (eQTLs), gene networks, and biological pathways to identify the key genes, processes, and networks that are genetically and epigenetically associated with psoriasis risk.ResultsThis integrative genomics study identified both well-characterized (e.g., the IL17 pathway in both GWAS and EWAS) and novel biological processes (e.g., the branched chain amino acid catabolism process in GWAS and the platelet and coagulation pathway in EWAS) involved in psoriasis. Finally, by utilizing tissue-specific gene regulatory networks, we unraveled the interactions among the psoriasis-associated genes and pathways in a tissue-specific manner and detected potential key regulatory genes in the psoriasis networks.ConclusionsThe integration and convergence of multi-omics signals provide deeper and comprehensive insights into the biological mechanisms associated with psoriasis susceptibility
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Molecular genetic characterization of a pathogenicity-attenuated mutant of Pseudomonas syringae pathovar syringae
A pathogenicity locus of Pseudomonas syringae pv.
syringae identified by Tn5 mutagenesis was investigated.
The mutant strain PS9024 is attenuated for disease
expression in its host, Phaseolus vulgaris, but produces
the hypersensitive reaction (HR) in the nonhost, tobacco
(Nicotina tabacum). A cosmid clone carrying 16 kilobases
(kb) of contiguous genomic DNA partially complements this
mutant. Altered growth of the mutant in planta was also
partially restored. Marker exchange mutagenesis with Tn3-
HoHo1 at two other sites within this locus results in
mutants with attenuated and severely reduced
pathogenicity. The locus is complex and contains
repetitive DNA sequences. Northern analysis reveals that
this locus is expressed in planta, but is not expressed in
a rich growth medium, and the transcript is larger than 10
kb, suggesting that the locus is transcribed as a
polycistronic mRNA. Comparison of total cellular protein
profiles of R32 and PS9024 using SDS-PAGE analysis further
reveals that at least nine protein bands ranging from
approximately 100 kD or above in size are present in the
wild type strain R32, but absent from the mutant.
Additionally, a protein of approximately 45 kD is absent
from the mutant. The site of Tn5 insertion has been
partially sequenced. The initial search of the data banks
suggested a gene or genes related to the ornithine
biosynthetic pathway map to this locus. Further study
strongly suggest a gene that encodes a membranceassociated
protein and under the control of a promoter
identical to appA gene promoter maps at this site and it
is involved in the process of pathogenesis
Improving Neural Machine Translation by Multi-Knowledge Integration with Prompting
Improving neural machine translation (NMT) systems with prompting has
achieved significant progress in recent years. In this work, we focus on how to
integrate multi-knowledge, multiple types of knowledge, into NMT models to
enhance the performance with prompting. We propose a unified framework, which
can integrate effectively multiple types of knowledge including sentences,
terminologies/phrases and translation templates into NMT models. We utilize
multiple types of knowledge as prefix-prompts of input for the encoder and
decoder of NMT models to guide the translation process. The approach requires
no changes to the model architecture and effectively adapts to domain-specific
translation without retraining. The experiments on English-Chinese and
English-German translation demonstrate that our approach significantly
outperform strong baselines, achieving high translation quality and terminology
match accuracy.Comment: Camera-ready. Accepted by EMNLP 2023 Finding
Analysis of optical absorption in GaAs nanowire arrays
In this study, the influence of the geometric parameters on the optical absorption of gallium arsenide [GaAs] nanowire arrays [NWAs] has been systematically analyzed using finite-difference time-domain simulations. The calculations reveal that the optical absorption is sensitive to the geometric parameters such as diameter [D], length [L], and filling ratio [D/P], and more efficient light absorption can be obtained in GaAs NWAs than in thin films with the same thickness due to the combined effects of intrinsic antireflection and efficient excitation of resonant modes. Optimized geometric parameters are obtained as follows: D = 180 nm, L = 2 μm, and D/P = 0.5. Meanwhile, the simulation on the absorption of GaAs NWAs for oblique incidence has also been carried out. The underlying physics is discussed in this work
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