378 research outputs found
Corrigendum: A Novel Phage PD-6A3, and Its Endolysin Ply6A3, With Extended Lytic Activity Against Acinetobacter baumannii
With widespread abuse of antibiotics, bacterial resistance has increasingly become a serious threat. Acinetobacter baumannii has emerged as one of the most important hospital-acquired pathogens worldwide. Bacteriophages (also called âphagesâ) could be used as a potential alternative therapy to meet the challenges posed by such pathogens. Endolysins from phages have also been attracting increasing interest as potential antimicrobial agents. Here, we isolated 14 phages against A. baumannii, determined the lytic spectrum of each phage, and selected one with a relatively broad host range, named vB_AbaP_PD-6A3 (PD-6A3 for short), for its biological characteristics. We over-expressed and purified the endolysin (Ply6A3) from this phage and tested its biological characteristics. The PD-6A3 is a novel phage, which can kill 32.4% (179/552) of clinical multidrug resistant A. baumannii (MDRAB) isolates. Interestingly, in vitro, this endolysin could not only inhibit A. baumannii, but also that of other strains, such as Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA). We found that lethal A. baumannii sepsis mice could be effectively rescued in vivo by phage PD-6A3 and endolysin Ply6A3 intraperitoneal injection. These characteristics reveal the promising potential of phage PD-6A3 and endolysin Ply6A3 as attractive candidates for the control of A. baumannii-associated nosocomial infections.</p
Transcriptome analysis of orange-spotted grouper (Epinephelus coioides) spleen in response to Singapore grouper iridovirus
<p>Abstract</p> <p>Background</p> <p>Orange-spotted grouper (<it>Epinephelus coioides</it>) is an economically important marine fish cultured in China and Southeast Asian countries. The emergence of infectious viral diseases, including iridovirus and betanodavirus, have severely affected food products based on this species, causing heavy economic losses. Limited available information on the genomics of <it>E. coioides </it>has hampered the understanding of the molecular mechanisms that underlie host-virus interactions. In this study, we used a 454 pyrosequencing method to investigate differentially-expressed genes in the spleen of the <it>E. coioides </it>infected with Singapore grouper iridovirus (SGIV).</p> <p>Results</p> <p>Using 454 pyrosequencing, we obtained abundant high-quality ESTs from two spleen-complementary DNA libraries which were constructed from SGIV-infected (V) and PBS-injected fish (used as a control: C). A total of 407,027 and 421,141 ESTs were produced in control and SGIV infected libraries, respectively. Among the assembled ESTs, 9,616 (C) and 10,426 (V) ESTs were successfully matched against known genes in the NCBI non-redundant (nr) database with a cut-off E-value above 10<sup>-5</sup>. Gene ontology (GO) analysis indicated that "cell part", "cellular process" and "binding" represented the largest category. Among the 25 clusters of orthologous group (COG) categories, the cluster for "translation, ribosomal structure and biogenesis" represented the largest group in the control (185 ESTs) and infected (172 ESTs) libraries. Further KEGG analysis revealed that pathways, including cellular metabolism and intracellular immune signaling, existed in the control and infected libraries. Comparative expression analysis indicated that certain genes associated with mitogen-activated protein kinase (MAPK), chemokine, toll-like receptor and RIG-I signaling pathway were alternated in response to SGIV infection. Moreover, changes in the pattern of gene expression were validated by qRT-PCR, including cytokines, cytokine receptors, and transcription factors, apoptosis-associated genes, and interferon related genes.</p> <p>Conclusion</p> <p>This study provided abundant ESTs that could contribute greatly to disclosing novel genes in marine fish. Furthermore, the alterations of predicted gene expression patterns reflected possible responses of these fish to the virus infection. Taken together, our data not only provided new information for identification of novel genes from marine vertebrates, but also shed new light on the understanding of defense mechanisms of marine fish to viral pathogens.</p
Multidifferential study of identified charged hadron distributions in -tagged jets in proton-proton collisions at 13 TeV
Jet fragmentation functions are measured for the first time in proton-proton
collisions for charged pions, kaons, and protons within jets recoiling against
a boson. The charged-hadron distributions are studied longitudinally and
transversely to the jet direction for jets with transverse momentum 20 GeV and in the pseudorapidity range . The
data sample was collected with the LHCb experiment at a center-of-mass energy
of 13 TeV, corresponding to an integrated luminosity of 1.64 fb. Triple
differential distributions as a function of the hadron longitudinal momentum
fraction, hadron transverse momentum, and jet transverse momentum are also
measured for the first time. This helps constrain transverse-momentum-dependent
fragmentation functions. Differences in the shapes and magnitudes of the
measured distributions for the different hadron species provide insights into
the hadronization process for jets predominantly initiated by light quarks.Comment: All figures and tables, along with machine-readable versions and any
supplementary material and additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-013.html (LHCb
public pages
Study of the decay
The decay is studied
in proton-proton collisions at a center-of-mass energy of TeV
using data corresponding to an integrated luminosity of 5
collected by the LHCb experiment. In the system, the
state observed at the BaBar and Belle experiments is
resolved into two narrower states, and ,
whose masses and widths are measured to be where the first uncertainties are statistical and the second
systematic. The results are consistent with a previous LHCb measurement using a
prompt sample. Evidence of a new
state is found with a local significance of , whose mass and width
are measured to be and , respectively. In addition, evidence of a new decay mode
is found with a significance of
. The relative branching fraction of with respect to the
decay is measured to be , where the first
uncertainty is statistical, the second systematic and the third originates from
the branching fractions of charm hadron decays.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-028.html (LHCb
public pages
Measurement of the ratios of branching fractions and
The ratios of branching fractions
and are measured, assuming isospin symmetry, using a
sample of proton-proton collision data corresponding to 3.0 fb of
integrated luminosity recorded by the LHCb experiment during 2011 and 2012. The
tau lepton is identified in the decay mode
. The measured values are
and
, where the first uncertainty is
statistical and the second is systematic. The correlation between these
measurements is . Results are consistent with the current average
of these quantities and are at a combined 1.9 standard deviations from the
predictions based on lepton flavor universality in the Standard Model.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-039.html (LHCb
public pages
Dataflow Optimization through Exploring Single-Layer and Inter-Layer Data Reuse in Memory-Constrained Accelerators
Off-chip memory access has become the performance and energy bottleneck in memory-constrained neural network accelerators. To provide a solution for the energy efficient processing of various neural network models, this paper proposes a dataflow optimization method for modern neural networks by exploring the opportunity of single-layer and inter-layer data reuse to minimize the amount of off-chip memory access in memory-constrained accelerators. A mathematical analysis of three inter-layer data reuse methods is first presented. Then, a comprehensive exploration to determine the optimal data reuse strategy from single-layer and inter-layer data reuse approaches is proposed. The result shows that when compared to the existing single-layer-based exploration method, SmartShuttle, the proposed approach can achieve up to 20.5% and 32.5% of off-chip memory access reduction for ResNeXt-50 and DenseNet-121, respectively
Dataflow Optimization through Exploring Single-Layer and Inter-Layer Data Reuse in Memory-Constrained Accelerators
Off-chip memory access has become the performance and energy bottleneck in memory-constrained neural network accelerators. To provide a solution for the energy efficient processing of various neural network models, this paper proposes a dataflow optimization method for modern neural networks by exploring the opportunity of single-layer and inter-layer data reuse to minimize the amount of off-chip memory access in memory-constrained accelerators. A mathematical analysis of three inter-layer data reuse methods is first presented. Then, a comprehensive exploration to determine the optimal data reuse strategy from single-layer and inter-layer data reuse approaches is proposed. The result shows that when compared to the existing single-layer-based exploration method, SmartShuttle, the proposed approach can achieve up to 20.5% and 32.5% of off-chip memory access reduction for ResNeXt-50 and DenseNet-121, respectively
Scalable Hardware Efficient Architecture for Parallel FIR Filters with Symmetric Coefficients
Symmetric convolutions can be utilized for potential hardware resource reduction. However, they have not been realized in state-of-the-art transposed block FIR designs. Therefore, we explore the feasibility of symmetric convolution in transposed parallel FIRs and propose a scalable hardware efficient parallel architecture. The proposed design inserts delay elements after multipliers for temporal reuse of intermediate tap products. By doing this, the number of required multipliers can be reduced by half. As a result, we can achieve up to 3.2Ă and 1.64Ă area efficiency improvements over the modern transposed block method on reconfigurable and fixed designs, respectively. These results confirm the effectiveness of the proposed STB-FIR architecture for hardware-efficient, high-speed signal processing
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