Publications by authors named "A.K. Jain"

This study evaluated a dual management approach to enhance plant-growth by improving soil fertility, reducing pathogenic stress using PGPR that affect phosphorus-transporter (pht) genes. Among 213 maize rhizobacterial isolates, 40 demonstrated the ability to solubilize tri-calcium phosphate, potassium, zinc, and silicon, showing various PGP traits. Nine of these isolates exhibited significant antagonistic activity against the plant pathogens Colletotrichum chlorophyti and Xanthomonas axonopodis.

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Measuring the linear polarization signal in extreme-ultraviolet (EUV) spectral lines, produced by the Hanle effect, offers a promising technique for studying magnetic fields in the solar corona. The required signal-to-noise ratio for detecting the Hanle polarization signals is on the order of 10 (off-limb) to 10 (disk center). Measuring such low signals in the photon starved observations demands highly efficient instruments.

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  • This study investigates the clinical and MRI characteristics of children with autoimmune GFAP astrocytopathy, revealing limited data compared to what is known in adults.
  • Researchers analyzed cases of 15 children from various clinical centers, finding common symptoms like acute encephalitis and meningitis, and specific MRI patterns in all cases.
  • The findings suggest that GFAP antibodies lead to distinct clinical and imaging features, emphasizing the need for testing in pediatric patients with similar symptoms, especially those with brainstem involvement.
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Background: Despite the high incidence of spine trauma globally, traumatic spinal cord injury (tSCI) during pregnancy is considered a rare medical emergency. The literature on acute management of these patients is sparse compared with that of mothers with preexisting tSCI. This systematic review aims to evaluate management strategies for tSCI during pregnancy in improving neurologic, obstetric, and neonatal outcomes.

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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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  • Autologous anti-CD19 CAR T cells are becoming standard treatment for relapsed/refractory large B-cell lymphoma, but serious side effects like cytokine release syndrome (CRS) and neurotoxicity (ICANS) pose risks, often requiring ICU care.
  • In a study involving 925 patients in France, high rates of CRS (84.1%) and ICANS (40.5%) were observed, with significant proportions experiencing severe forms of these conditions.
  • Two prognostic scoring systems (CRS-PSS and ICANS-PSS) were developed to identify patients at higher risk for severe CRS and ICANS based on specific clinical factors, and these scores were validated in other patient groups treated with similar therapies.
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Objective: Glioblastoma multiforme (GBM), particularly the isocitrate dehydrogenase (IDH)-wildtype type, represents a significant clinical challenge due to its aggressive nature and poor prognosis. Despite advancements in medical imaging and its modalities, survival rates have not improved significantly, demanding innovative treatment planning and outcome prediction approaches.

Methods: This study utilizes a support vector machine (SVM) classifier using radiomics features to predict the overall survival (OS) of GBM, IDH-wildtype patients to short (<12 months) and long (≥12 months) survivors.

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Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy.

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  • - The study analyzed how different types of donors affect outcomes of hematopoietic cell transplantation (HCT) in patients with myelofibrosis, finding that the use of haploidentical donors rose significantly from 3% in 2013 to 19% in 2019.
  • - Among 1,032 patients with chronic-phase myelofibrosis, matched sibling donor HCTs showed better overall survival in the first three months compared to haploidentical and matched unrelated donor HCTs, with notably lower rates of graft failure.
  • - While matched sibling donors had superior early outcomes, there were no significant differences in long-term survival or disease-free survival among the different donor types, suggesting hap
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  • The study focuses on creating a deep learning digital pathology tool for accurately detecting, segmenting, and classifying nuclei in cancer tissues, addressing challenges in quantifying nuclear morphology in histologic images.
  • This tool was trained on nucleus annotations to analyze H&E-stained slides from various cancer cohorts (BRCA, LUAD, PRAD), revealing significant differences in nuclear features like shape and size linked to genomic instability and cancer prognosis.
  • Results highlighted that certain nuclear characteristics, particularly in fibroblasts, were associated with patient survival outcomes and gene expression related to tumor biology, paving the way for better understanding of cancer biomarkers.
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The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.

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Background: Primary percutaneous coronary intervention (pPCI) has improved clinical outcomes in patients with ST-segment-elevation myocardial infarction. However, as many as 50% of patients still have suboptimal myocardial reperfusion and experience extensive myocardial necrosis. The PiCSO-AMI-I trial (Pressure-Controlled Intermittent Coronary Sinus Occlusion-Acute Myocardial Infarction-I) evaluated whether PiCSO therapy can further reduce myocardial infarct size (IS) in patients undergoing pPCI.

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Developing an effective mRNA therapeutic often requires maximizing protein output per delivered mRNA molecule. We previously found that coding sequence (CDS) design can substantially affect protein output, with mRNA variants containing more optimal codons and higher secondary structure yielding the highest protein outputs due to their slow rates of mRNA decay. Here, we demonstrate that CDS-dependent differences in translation initiation and elongation rates lead to differences in translation- and deadenylation-dependent mRNA decay rates, thus explaining the effect of CDS on mRNA half-life.

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Antibiotic exposure during immunotherapy (IO) has been shown to negatively affect clinical outcomes in various cancer types. The aim of this study was to evaluate whether antibiotic exposure in patients with high-risk early-stage HER2-negative breast cancer (BC) undergoing treatment with neoadjuvant pembrolizumab impacted residual cancer burden (RCB) and pathologic complete response (pCR) in the pembrolizumab-4 arm of the ISPY-2 clinical trial. Patients received pembrolizumab for four cycles concurrently with weekly paclitaxel for 12 weeks, followed by four cycles of doxorubicin plus cyclophosphamide every 2 or 3 weeks.

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  • The study focuses on the preparation and analysis of three non-heme iron complexes (1, 2, and 3) using different N donor ligands, revealing unique structural characteristics and electrochemical behavior.
  • Complex 1 exhibited significant electrocatalytic activity in the oxygen reduction reaction (ORR), while complexes 2 and 3 showed minimal activity, highlighting the essential role of the oxime ligand in ORR.
  • Kinetic studies and chemical ORR experiments demonstrated how variations in ligand scaffolds affect the performance of these iron complexes, emphasizing the importance of the ligand's structure for effective catalysis.
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Background: This study investigated the association of intra-abdominal adhesions with the risk of peritoneal dialysis (PD) catheter complications.

Methods: Individuals undergoing laparoscopic PD catheter insertion were prospectively enrolled from eight centers in Canada and the United States. Patients were grouped based on the presence of adhesions observed during catheter insertion.

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Resting-state (rs) fMRI has been shown to be useful for preoperative mapping of functional areas in patients with brain tumors and epilepsy. However, its lack of standardization limits its widespread use and hinders multicenter collaboration. The American Society of Functional Neuroradiology, American Society of Pediatric Neuroradiology, and the American Society of Neuroradiology Functional and Diffusion MR Imaging Study Group recommend specific rs-fMRI acquisition approaches and preprocessing steps that will further support rs-fMRI for future clinical use.

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  • Long-read sequencing technology is enhancing the detection of genetic variants in complex regions of the genome and facilitating quicker genetic diagnoses in clinical settings.
  • Newer third-generation sequencing platforms, such as those from PacBio and Oxford Nanopore, are rapidly advancing, but traditional variant calling methods struggle with increased data complexity.
  • The developed local haplotype approximation method improves variant calling accuracy and allows DeepVariant to work effectively across various long-read sequencing platforms.
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Unlike many other hematologic malignancies, Richter syndrome (RS), an aggressive B cell lymphoma originating from indolent chronic lymphocytic leukemia, is responsive to PD-1 blockade. To discover the determinants of response, we analyze single-cell transcriptome data generated from 17 bone marrow samples longitudinally collected from 6 patients with RS. Response is associated with intermediate exhausted CD8 effector/effector memory T cells marked by high expression of the transcription factor ZNF683, determined to be evolving from stem-like memory cells and divergent from terminally exhausted cells.

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  • Salivary gland cancers (SGCs) are rare and aggressive, often lacking effective treatments when they spread, prompting a phase 2 trial of nivolumab and ipilimumab in 64 metastatic SGC patients.
  • Results showed some success in "other SGCs" cohort (16% response) but limited efficacy in adenoid cystic carcinoma (6% response), with notable adverse events occurring in 38% of patients.
  • Genetic and immune cell analyses indicated that responding tumors had active T cell responses and certain neoantigens, suggesting a potential path for treatment in non-ACC SGCs like salivary duct carcinomas.
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Belzutifan (Welireg, Merck & Co., Inc., Rahway, NJ, USA) is an oral, potent inhibitor of hypoxia-inducible factor 2α, approved for the treatment of certain patients with von Hippel-Lindau (VHL) disease-associated renal cell carcinoma (RCC), central nervous system hemangioblastomas, and pancreatic neuroendocrine tumors.

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Aberrantly expressed onco-mucin 16 (MUC16) and its post-cleavage generated surface tethered carboxy-terminal (MUC16-Cter) domain are strongly associated with poor prognosis and lethality of pancreatic (PC) and non-small cell lung cancer (NSCLC). To date, most anti-MUC16 antibodies are directed towards the extracellular domain of MUC16 (CA125), which is usually cleaved and shed in the circulation hence obscuring antibody accessibility to the cancer cells. Herein, we establish the utility of targeting a post-cleavage generated, surface-tethered oncogenic MUC16 carboxy-terminal (MUC16-Cter) domain by using a novel chimeric antibody in human IgG1 format, ch5E6, whose epitope expression directly correlates with disease severity in both cancers.

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Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population.

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