Publications by authors named "Shepherd S"

Amide bond formation is fundamental in nature and is widely used in the synthesis of pharmaceuticals and other valuable products. Current methods for amide synthesis are often step and atom inefficient, requiring the use of protecting groups, deleterious reagents and organic solvents that create significant waste. The development of cleaner and more efficient catalytic methods for amide synthesis remains an urgent unmet need.

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Using joint genomic-transcriptomic analysis of 243 samples, we reveal recurrent patterns of nongenetic evolution in ccRCC not exclusively governed by genetic factors, including T-cell depletion, tumor T-cell receptor coevolution, potential cGAS-STING repression, and increased cell proliferation. These patterns can aid clinical management and guide novel treatment approaches.

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While the key aspects of genetic evolution and their clinical implications in clear cell renal-cell carcinoma (ccRCC) are well-documented, how genetic features co-evolve with the phenotype and tumor microenvironment (TME) remains elusive. Here, through joint genomic-transcriptomic analysis of 243 samples from 79 patients recruited to the TRACERx Renal study, we identify pervasive non-genetic intratumor heterogeneity, with over 40% not attributable to genetic alterations. By integrating tumor transcriptomes and phylogenetic structures, we observe convergent evolution to specific phenotypic traits, including cell proliferation, metabolic reprogramming and overexpression of putative cGAS-STING repressors amid high aneuploidy.

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Lipid nanoparticles (LNPs) are the most advanced delivery system currently available for RNA therapeutics. Their development has accelerated since the success of Patisiran, the first siRNA-LNP therapeutic, and the mRNA vaccines that emerged during the COVID-19 pandemic. Designing LNPs with specific targeting, high potency, and minimal side effects is crucial for their successful clinical use.

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Despite the numerous advantages demonstrated by microfluidic mixing for RNA-loaded lipid nanoparticle (RNA-LNP) production over bulk methods, such as precise size control, homogeneous distributions, higher encapsulation efficiencies, and improved reproducibility, their translation from research to commercial manufacturing remains elusive. A persistent challenge hindering the adoption of microfluidics for LNP production is the fouling of device surfaces during prolonged operation, which significantly diminishes performance and reliability. The complexity of LNP constituents, including lipids, cholesterol, RNA, and solvent mixtures, makes it difficult to find a single coating that can prevent fouling.

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The proteasome is considered an excellent drug target for many infectious diseases as well as cancer. Challenges with robust and safe supply of proteasomes from infectious agents, lack of structural information, and complex pharmacology due to multiple active sites have hampered progress in the infectious disease space. We recombinantly expressed the proteasome of the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease, and demonstrate pharmacological equivalence to the native T.

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DNA has shown great biocompatibility, programmable mechanical properties, and precise structural addressability at the nanometer scale, rendering it a material for constructing versatile nanorobots for biomedical applications. Here, we present the design principle, synthesis, and characterization of a DNA nanorobotic hand, called DNA NanoGripper, that contains a palm and four bendable fingers as inspired by naturally evolved human hands, bird claws, and bacteriophages. Each NanoGripper finger consists of three phalanges connected by three rotatable joints that are bendable in response to the binding of other entities.

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Optimising the timing of food intake relative to exercise may maximise the effectiveness of free-living exercise programmes on improvements in glycaemic control and cardio-metabolic health. This study aimed to assess the feasibility of a free-living, walking-based exercise programme and determine whether undertaking each exercise session before or after breakfast would most benefit longer-term metabolic health. Thirty-four people living with obesity (43±12 y, BMI 35.

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VHL disease is an inherited and autosomal dominant disorder affecting 1 in 36,0000 individuals worldwide. It is caused by von Hippel-Lindau (VHL) gene mutations and can affect both genders and all ethnic backgrounds (Nordstrom-O'Brien et al., 2009; Maher, 2004).

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Purpose: Ultrasmall silver sulfide nanoparticles (AgS-NP) have been identified as promising contrast agents for a number of modalities and in particular for dual-energy mammography. These AgS-NP have demonstrated marked advantages over clinically available agents with the ability to generate higher contrast with high biocompatibility. However, current synthesis methods for inorganic nanoparticles are low-throughput and highly time-intensive, limiting the possibility of large animal studies or eventual clinical use of this potential imaging agent.

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Acute malnutrition (AM) causes large loss of life and disability in children in Africa. Researchers are testing innovative approaches to increase efficiency of treatment programs. This paper presents results of a cost-effectiveness analysis of one such program in the Democratic Republic of the Congo (DRC) based on a secondary analysis of a randomized controlled trial Optimizing Treatment for Acute Malnutrition (OptiMA), conducted in DRC in 2018-20.

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Background: The mandible provides valuable insights into its biological identity. However, the existence of several terminologies for mandibular measurements and inconsistent language can lead to misinterpretation, confusion, and miscommunication.

Highlight: A standardised set of anatomical points, planes, and measurements would assist with these issues and ensure reproducibility and comparability.

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We report the design, development, and characterization of a miniaturized version of the photonic resonator absorption microscope (PRAM Mini), whose cost, size, and functionality are compatible with point-of-care (POC) diagnostic assay applications. Compared to previously reported versions of the PRAM instrument, the PRAM Mini components are integrated within an optical framework comprised of an acrylic breadboard and plastic alignment fixtures. The instrument incorporates a Raspberry Pi microprocessor and Bluetooth communication circuit board for wireless control and data connection to a linked smartphone.

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Article Synopsis
  • Early diagnosis of oral squamous cell carcinoma can help people get better treatment and live longer.
  • The study tested a new technique using Optical Coherence Tomography Angiography (OCTA) to check blood vessels in the mouth.
  • Results showed that this method can reliably measure different aspects of blood vessels, which may help doctors detect problems early.
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Background: In the context of an outbreak of HIV among people who inject drugs in Glasgow, Scotland, identified in 2015, our objectives were to: (1) develop epidemiological methods to estimate HIV incidence using data linkage, and (2) examine temporal changes in HIV incidence to inform public health responses.

Methods: This was a retrospective cohort study involving data linkage of laboratory HIV testing data to identify individuals with a history of drug use. Person-years (PY) and Poisson regression were used to estimate incidence by time period (pre-outbreak: 2000-2010 and 2011-2013; early outbreak: 2014-2016; ongoing outbreak: 2017-2019).

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Systemic delivery of messenger RNA (mRNA) for tissue-specific targeting using lipid nanoparticles (LNPs) holds great therapeutic potential. Nevertheless, how the structural characteristics of ionizable lipids (lipidoids) impact their capability to target cells and organs remains unclear. Here we engineered a class of siloxane-based ionizable lipids with varying structures and formulated siloxane-incorporated LNPs (SiLNPs) to control in vivo mRNA delivery to the liver, lung and spleen in mice.

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Muscle cells become stronger by expanding myofibrils, the chains of sarcomeres that produce contraction. Here we investigate how Mylpf (Myosin Light Chain Phosphorylatable Fast) abundance impacts myofibril assembly in fast-twitch muscle. The two zebrafish Mylpf genes ( and ) are exclusively expressed in fast-twitch muscle.

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Article Synopsis
  • To track global progress in reducing HIV incidence, a reliable evaluation method is essential since usual HIV diagnosis dates can misrepresent when the infection actually occurred.
  • A Bayesian statistical model was developed to more accurately estimate the proportions of recent and incident HIV infections in Scotland from 2015 to 2019 by incorporating various testing results and surveillance data.
  • The model found that 43.9% of diagnoses were incident infections and 21.6% were recent, particularly high among people who inject drugs, demonstrating the model's potential to enhance understanding of HIV transmission dynamics amidst data limitations.
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Background: In the treatment of acute malnutrition (AM), non-response is considered a treatment failure for not meeting recovery criteria within a therapeutic window of 12-16 weeks, but this category of children is misunderstood. As current research emphasizes ways to simplify and optimize treatment protocols, non-response emerges as a new issue to enhance program efficiency.

Methods: A prospective cohort study was conducted from 2019 to 2020 at two health centres in Mirriah, Niger among children aged 6-59 months with uncomplicated AM treated under the Optimising treatment for Acute MAlnutrition (OptiMA) protocol.

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Glucocorticoid receptor (GR) overexpression has been linked to increased tumour aggressiveness and treatment resistance. GR antagonists have been shown to enhance treatment effectiveness. Emerging research has investigated mifepristone, a GR antagonist, as an anticancer agent with limited research in the context of oral cancer.

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Article Synopsis
  • - This paper presents an advanced biosensing instrument that enhances the previously developed photonic resonator absorption microscope (PRAM) by adding features like autofocus and digital tracking of gold nanoparticle (AuNP) movement during biomolecular assays.
  • - The automated PRAM can capture wide panoramic images (“tiling”) and record dynamic sequences ("movies") to visualize and quantify the attachment and detachment of AuNPs on a photonic crystal surface.
  • - The instrument is demonstrated in two assays for detecting protein biomarkers, achieving a sensitivity of detecting microRNA-375 at extremely low concentrations (1 aM) in a quick and enzyme-free process, highlighting its potential for use in point-of-care diagnostics and studying biomolecular interactions at the single
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Highly diastereoselective self-assembly reactions give both enantiomers (Λ and Δ) of anti-parallel triple-stranded bimetallic Co(ii) and Co(iii) cationic helices, without the need for resolution; the first such reaction for Co. The complexes are water soluble and stable, even in the case of Co(ii). Studies in a range of cancer and healthy cell lines indicate high activity and selectivity, and substantial differences between enantiomers.

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Article Synopsis
  • Precision medicine relies on understanding genetic variants that cause disease and their effects, exemplified by the von Hippel-Lindau (VHL) gene involved in tumor suppression.
  • VHL mutations are linked to specific types of tumors, like clear cell renal cell carcinoma, necessitating refined methods to assess their consequences.
  • Researchers developed a technique to analyze nearly all single-nucleotide variants in VHL, leading to the identification of key pathogenic variants and enhancing the ability to classify these genetic changes in clinical settings.
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Background: Early detection of hearing loss and subsequent intervention leads to better speech, language and educational outcomes giving way to improved social economic prospects in adult life. This can be achieved through establishing newborn and infant hearing screening programs.

Objective: To determine the prevalence of hearing loss in newborns and infants in Nairobi, Kenya.

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