Publications by authors named "Ajay Jain"

Light sheet microscopy and preparative clearing methods that improve light penetration in 3D tissues have revolutionized imaging in biomedical research. Here we present ADAPT-3D, a streamlined 3-step approach to turn tissues optically transparent while preserving tissue architecture with the versatility to handle diverse tissue sizes and types across species. Unlike extensive lipid removal utilized by existing protocols, ADAPT-3D only partially removes lipids to preserve cell membranes, yet the non-toxic aqueous refractive indexing solution still rapidly turns tissues transparent while preserving the fluorescence of endogenous and antibody conjugated fluorophores.

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Bioinformatic methodologies play a crucial role in the assessment of gut microbiota, offering advanced tools for analyzing complex microbial communities. These methodologies involve high-throughput sequencing technologies, such as 16S rRNA gene sequencing and metagenomics, which generate vast amounts of data on microbial diversity and functional potential, as well as whole-genome sequencing, which, while being more costly, has a more expansive potential. Bioinformatics tools and algorithms process these data to identify microbial taxa and quantify and elucidate their roles within the microbiome.

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Optical coherence tomography (OCT) imaging enables high resolution visualization of sub-surface tissue microstructures. However, OCT image analysis using deep learning is hampered by limited diverse training data to meet performance requirements and high inference latency for real-time applications. To address these challenges, we developed Octascope, a lightweight domain-specific convolutional neural network (CNN) - based model designed for OCT image analysis.

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Hepatoblastoma (HB) is a rare but highly malignant tumor that commonly arises in utero. The mainstay treatment is surgical resection, with adjuvant treatment options including chemotherapy, hepatic artery chemoembolization, and liver transplantation. Yttrium-90 (Y90) transarterial radioembolization (TARE Y90) is a developing treatment option that utilizes radioactive beads delivered specifically to blood vessels supplying the tumor.

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Multidrug resistance-associated protein 1 (MRP1) is an ATP-dependent transmembrane efflux pump that confers drug resistance. MRP1 is overexpressed in pancreatic ductal adenocarcinoma (PDAC) and other malignancies. However, its diagnostic value in cancer has not been explored.

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Purpose: This study evaluates the current state of andrology practice worldwide, identifies challenges faced by clinicians, and explores training, certification, and research opportunities. It also seeks to redefine the qualifications necessary to be recognized as an andrologist and to propose areas for standardization and improvement.

Materials And Methods: A global, cross-sectional survey was conducted using a 48-question online questionnaire designed by international experts.

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Background: Early discharge after primary percutaneous coronary intervention can increase the efficiency of health care, enabling cost savings. Dedicated virtual follow-up pathways can provide remote diagnostic information to aid earlier discharge, optimize care and reduce unplanned readmissions.

Objectives: The aims of this study were: 1) to review the long-term (1-year) safety of early hospital discharge (<48 hours) after ST-segment elevation myocardial infarction; 2) to assess the effect of virtual follow-up on medication adherence and ability to up-titrate secondary prevention medication; and 3) to determine the cost-effectiveness of a virtual follow-up pathway after early discharge.

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Background: The Society of Pediatric Liver Transplantation (SPLIT) has undergone tremendous growth with > 45 sites contributing data focusing on improving outcomes in pediatric liver transplantation (LT). We report and compare outcomes from the SPLIT Registry.

Methods: Patients < 18 years with first-time LT only enrolled into the SPLIT Registry between 2011 and 2023 were included.

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Background: It remains unclear whether there is a difference in overall survival (OS) benefit between (m)FOLFIRINOX and gemcitabine-nab-paclitaxel as preoperative regimens for localised pancreatic adenocarcinoma. This study aimed to investigate the outcome of patients with resected localised pancreatic adenocarcinoma following (m)FOLFIRINOX versus gemcitabine-nab-paclitaxel.

Methods: International multicentre retrospective study (16 centres, 8 countries, 3 continents), including consecutive patients after pancreatic resection for localised pancreatic adenocarcinoma following 2-6 months preoperative (m)FOLFIRINOX or gemcitabine-nab-paclitaxel (2010-2018).

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Light sheet microscopy and preparative clearing methods that improve light penetration in 3D tissues have revolutionized imaging in biomedical research. While most clearing methods focus on removing molecules that scatter light, the methods generally involve immersing tissues in solutions that minimize refraction of light to enhance detection of fluorescent signal deeper into tissues. Here, we developed a new tissue preparative method called ADAPT-3D with broad applicability across species and tissue types.

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Background: Lower socioeconomic status (SES) has been associated with increased mortality from coronary heart disease. This excess risk, relative to affluent patients, may be due to a combination of more adverse cardiovascular-risk factors, inequalities in access to cardiac investigations, longer waiting times for cardiac revascularisation and lower use of secondary prevention drugs. We sought to investigate whether socio-economic status influenced long-term all-cause mortality after PCI in a large metropolitan city (London), which serves a population of 11 million people with a mixed social background over a 10-year period.

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The Indian Society of Gastroenterology has developed an evidence-based practice guideline for the management of caustic ingestion-related gastrointestinal (GI) injuries. A modified Delphi process was used to arrive at this consensus containing 41 statements. These statements were generated after two rounds of electronic voting, one round of physical meeting, and extensive review of the available literature.

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  • Coronary computed tomography angiography (CCTA) was evaluated as an alternative to intravascular imaging techniques for assessing plaque pathology in patients with chronic coronary syndrome.
  • The study involved 70 patients and compared CCTA with near-infrared spectroscopy-intravascular ultrasound (NIRS-IVUS) to analyze atheroma burden and composition, focusing on the accuracy of detecting lipid-rich plaques.
  • Results showed that CCTA had limitations in accurately measuring plaque dimensions and composition, leading to potential issues in planning for coronary interventions.
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  • Thoracic and abdominal aortic aneurysms have different genetic and clinical characteristics, which can be better understood using single-cell RNA sequencing rather than traditional bulk RNA methods that average gene expression across all cells.* -
  • Analysis of single-cell datasets identified three distinct populations of smooth muscle cells (SMCs) in aortic tissues, with a significantly higher proportion of a unique SMC group in TAA compared to AAA.* -
  • Certain genes linked to extracellular matrix organization and insulin-like growth factor transport were found to be upregulated in TAA SMCs, suggesting these may play a role in the development of TAAs; further studies are needed to explore these pathways.*
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Background: Coronary angioplasty and stent insertion is a first line treatment for patients with coronary artery disease, however it is complicated in the long-term by in-stent restenosis (ISR) in a proportion of patients with an associated morbidity. Despite this, currently there are no effective treatments available for the prevention of ISR. Repeat percutaneous revascularisation carries increased risks of major adverse cardiovascular events and a higher incidence of stent failure.

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  • Cross-docking involves predicting how new small-molecule ligands will bind to a protein when these ligands are different from the known binding partners, which is a more complex task than re-docking the original ligands.
  • The updated PINC benchmark uses temporal segregation to evaluate cross-docking accuracy, including predictions for 846 future ligands across ten protein targets and an extension for 128 macrocyclic ligands based on data from previously known non-macrocyclic ligands.
  • Overall, using methods like Surflex-Dock and ForceGen, the study achieved impressive success rates, with 68% accuracy for the best poses and 92% for any correct poses, outperforming alternative methods like AutoDock Vina and
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  • - The study aimed to evaluate the effectiveness of short (<120 days) versus long (>180 days) antiviral prophylaxis for preventing cytomegalovirus (CMV) disease in pediatric liver transplant recipients by analyzing data from the Society of Pediatric Liver Transplantation registry between 2015 and 2019.
  • - Among the 199 enrolled participants, shorter prophylaxis resulted in higher occurrences of CMV DNAemia (26.8% vs. 13.8%) and CMV syndrome (18.8% vs. 6.9%) compared to longer prophylaxis, while end-organ disease rates were similar between the two groups.
  • - Long prophylaxis was associated with a significantly higher incidence of neutropenia (55
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  • Hepatic ischemia-reperfusion injury (IRI) occurs when blood flow returns to previously deprived liver tissues, causing significant cellular damage that may lead to liver dysfunction or failure.
  • While restoring blood flow is critical for healing, the process can paradoxically cause additional harm through a complex series of events.
  • The review discusses various laboratory models for studying hepatic IRI mechanisms, including animal models (like mice and pigs), cell lines, and machine perfusion setups.
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Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) is common in children. We hypothesized environmental toxins could drive progression to metabolic dysfunction-associated steatohepatitis (MASH), and assayed serum toxins and metabolites in children with histologically characterized MASLD/MASH.

Methods: Environmental chemicals, common in household items, perfluoroalkyl substances (PFAS), polybrominated flame retardants (polybrominated diphenyl ethers [PBDEs]), and metabolic profiles were assayed in children enrolled in the multicenter NASH Clinical Research Network Pediatric Database 2.

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  • - The study analyzed how calcific (Ca) burden affects the accuracy of coronary computed tomography angiography (CTA) in assessing plaque burden and composition, using near-infrared spectroscopy-intravascular ultrasound (NIRS-IVUS) as a comparison standard.
  • - Involving 64 patients and 186 vessels, results indicated that while Ca did not significantly alter correlations between NIRS-IVUS and CTA at the segment and lesion levels, it did affect their agreement at the cross-sectional level, specifically regarding lipid and Ca components.
  • - Ultimately, the presence of Ca burden influenced measurements and predictions of plaque volume and composition between NIRS-IVUS and CTA, highlighting the importance of considering coronary calcification in clinical evaluations.
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  • Total parenteral nutrition (TPN) is a lifesaving IV feeding method but can cause serious side effects like gut microbial changes and liver injury.
  • A study involving 31 piglets tested the effects of transferring fecal microbiota from healthy pigs to those on TPN, with various groups including a control, TPN alone, TPN with antibiotics, and TPN with fecal transplant.
  • The results showed that fecal microbiota transplant (FMT) helped prevent gut atrophy, liver injury, and harmful microbial changes seen in TPN, suggesting that gut microbes could be critical for developing new treatments.
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Pancreatic ductal adenocarcinoma (PDAC) is one of the most recalcitrant cancers due to its late diagnosis, poor therapeutic response, and highly heterogeneous microenvironment. Nanotechnology has the potential to overcome some of the challenges to improve diagnostics and tumor-specific drug delivery but they have not been plausibly viable in clinical settings. The review focuses on active targeting strategies to enhance pancreatic tumor-specific uptake for nanoparticles.

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  • Percutaneous renal biopsy is used to diagnose kidney cancer, but it faces challenges in accurately sampling tissues.
  • A new optical coherence tomography probe was developed to differentiate between tumor and normal tissues, improving biopsy guidance and accuracy.
  • Convolutional neural networks were utilized to enhance tissue recognition, achieving 99.1% accuracy in identifying carcinoma and distinguishing oncocytoma, ultimately improving diagnosis during biopsy procedures.
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  • Homozygosity for the rs893403-GG genotype is associated with a higher risk of kidney allograft rejection due to long-term T lymphocyte infiltration after ischemia-reperfusion injury.
  • The study analyzed the impact of the rs893403 genotype on kidney transplant histopathology by comparing biopsy results with genotyping and examining mRNA expression in ischemic donor kidneys.
  • Results show that recipients with the GG genotype had significantly higher tubulitis scores and increased expression of specific mRNAs and proteins associated with inflammation compared to those with AG genotypes, suggesting a link between this genotype and rejection mechanisms.
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  • The study investigates the impact of preoperative chemo(radio)therapy on patients with localized pancreatic adenocarcinoma, focusing on the rare occurrence of pathological complete response (pCR), where no cancer cells are found post-surgery.
  • Conducted in 19 centers across 8 countries with 1758 participants, the research shows that only 4.8% of patients achieved pCR, which is linked to better overall survival rates compared to those who did not achieve pCR.
  • Factors influencing the likelihood of pCR included the use of multiagent chemotherapy regimens other than the (m)FOLFIRINOX treatment, highlighting the need for tailored therapeutic approaches.
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