Multi-beam miniaturized volumetric scanning microscopy with a single 1-dimensional actuation

Miniaturized optical imaging systems often use a 2-dimensional (2-D) actuator such as a piezoelectric tube or microelectromechanical system actuator for the acquisition of 2-D and higher dimensional images over an areal field of view (FOV). Piezoelectric tubes are the most compact, but usually produce impractical sub-millimetre FOVs and are difficult to fabricate at scale, leading to high costs. Planar piezoelectric bending actuators ('benders') are substantially lower cost and capable of much larger actuations, albeit 1-dimensional (1-D) and traditionally inadequate for 2-D steering tasks. We present a piezoelectric bender imaging system that exploits mechanical motion coupling to produce multi-millimetre scale 2-D scan coverage. Leveraging optical coherence tomography with a long coherence length laser, we further extend the FOV using three depth-multiplexed imaging beams from optical fibres resonating in synchronicity across the width of the bender. Each fibre had a FOV of ~2.1 x 1.5 mm, contributing to a stitched field of ~2.1 x 2.9 mm with a beam resolution of 12.6 um full-width at half-maximum. Imaging of biological samples including stomach tissue, an ant and cell spheroids was performed. This multi-fold improvement in imaging coverage and cost-effectiveness promises to accelerate the advent of piezoelectric scanning in compact devices such as endoscopes for biomedicine, and headsets for augmented/virtual reality and neuroscience

Detection of genetic and epigenetic DNA markers in urine for the early detection of primary and recurrent hepatocellular carcinoma

Poster presented at American Association of the Study of Liver Diseases (AASLD) meeting in San Francisco California. Objective: Develop a urine test using a panel of select genetic and epigenetic markers for the early detection of primary and recurrent HCC. Introduction: Hepatocellular carcinoma (HCC) or liver cancer is an aggressive disease and one of the fastest growing cancers by incidence in the United States. Early detection is the key for effective treatment of HCC as the 5-year survival rate is 26% in early stage HCC as compared to only 2% when found after spreading to distant organs. The current marker, alpha-feto protein (AFP) and its fucosylated glycoform, L3, are of limited value with only 40-60% sensitivity.https://jdc.jefferson.edu/gastrohepposters/1000/thumbnail.jp

The influence of age and gender on skin-associated microbial communities in urban and rural human populations

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One (10): e0141842, doi:10.1371/journal.pone.0141842.Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.This work was supported by a grant from Johnson & Johnson (China)

The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine

Antibody-mediated immunity plays a key role in protection against SARS-CoV-2. We characterized B-cell-derived anti-SARS-CoV-2 RBD antibody repertoires from vaccinated and infected individuals and elucidate the mechanism of action of broadly neutralizing antibodies and dissect antibodies at the epitope level. The breadth and clonality of anti-RBD B cell response varies among individuals. The majority of neutralizing antibody clones lose or exhibit reduced activities against Beta, Delta, and Omicron variants. Nevertheless, a portion of anti-RBD antibody clones that develops after a primary series or booster dose of COVID-19 vaccination exhibit broad neutralization against emerging Omicron BA.2, BA.4, BA.5, BQ.1.1, XBB.1.5 and XBB.1.16 variants. These broadly neutralizing antibodies share genetic features including a conserved usage of the IGHV3-53 and 3–9 genes and recognize three clustered epitopes of the RBD, including epitopes that partially overlap the classically defined set identified early in the pandemic. The Fab-RBD crystal and Fab-Spike complex structures corroborate the epitope grouping of antibodies and reveal the detailed binding mode of broadly neutralizing antibodies. Structure-guided mutagenesis improves binding and neutralization potency of antibody with Omicron variants via a single amino-substitution. Together, these results provide an immunological basis for partial protection against severe COVID-19 by the ancestral strain-based vaccine and indicate guidance for next generation monoclonal antibody development and vaccine design

AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome

<p>Abstract</p> <p>Background</p> <p>To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance.</p> <p>Results</p> <p>Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA.</p> <p>Conclusions</p> <p>AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.</p

Thermoelectric effects in a double quantum dot system weakly coupled to ferromagnetic leads

Thermoelectric effects through a serial double quantum dot system weakly coupled to ferromagnetic leads are analyzed. Formal expressions of electrical conductance, thermal conductance, and thermal coefficient are obtained by means of Hubbard operators. The results show that although the thermopower is independent of the polarization of the leads, the figure of merit is reduced by an increase of polarization. The influences of temperature and interdot tunneling on the figure of merit are also investigated, and it is observed that increase of the interdot tunneling strength results in reduction of the figure of merit. The effect of temperature on the thermal conductance is also analyzed.Comment: 13 pages, 4 figure