Peter J. Shaw
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View article: Upper and Lower Respiratory Tract Compartmentalization in Pediatric Stem Cell Transplantation
Upper and Lower Respiratory Tract Compartmentalization in Pediatric Stem Cell Transplantation Open
Rationale Lung injury after hematopoietic stem cell transplantation (HCT) occurs due to infection, chemotherapy toxicity, and alloreactive inflammation. Analyses of bronchoalveolar lavage (BAL) fluid have revealed dominant pathobiologic si…
View article: Cytomegalovirus prophylaxis with letermovir in pediatric (birth to <18 years of age) hematopoietic cell transplant recipients: pharmacokinetics, efficacy, and safety results of a Phase 2b study
Cytomegalovirus prophylaxis with letermovir in pediatric (birth to <18 years of age) hematopoietic cell transplant recipients: pharmacokinetics, efficacy, and safety results of a Phase 2b study Open
Letermovir, a cytomegalovirus (CMV) terminase complex inhibitor, was first approved for prophylaxis of CMV infection and disease in adult CMV-seropositive allogeneic hematopoietic cell transplant (HCT) recipients (R+). This study evaluated…
View article: Integrating pulmonary and systemic transcriptomes to characterize lung injury after pediatric hematopoietic stem cell transplant
Integrating pulmonary and systemic transcriptomes to characterize lung injury after pediatric hematopoietic stem cell transplant Open
Hematopoietic stem cell transplantation (HCT) is a potentially life-saving therapy but can lead to lung injury due to chemoradiation toxicity, infection, and immune dysregulationWe previously showed that bronchoalveolar lavage (BAL) transc…
View article: Integrating Pulmonary and Systemic Transcriptomic Profiles to Characterize Lung Injury after Pediatric Hematopoietic Stem Cell Transplant
Integrating Pulmonary and Systemic Transcriptomic Profiles to Characterize Lung Injury after Pediatric Hematopoietic Stem Cell Transplant Open
Hematopoietic stem cell transplantation (HCT) is potentially curative for numerous malignant and non-malignant diseases but can lead to lung injury due to chemoradiation toxicity, infection, and immune dysregulation. Bronchoalveolar lavage…
View article: Compassionate access to virus-specific T cells for adoptive immunotherapy over 15 years
Compassionate access to virus-specific T cells for adoptive immunotherapy over 15 years Open
View article: Association of busulfan exposure and outcomes after HCT for patients with an inborn error of immunity
Association of busulfan exposure and outcomes after HCT for patients with an inborn error of immunity Open
Allogeneic hematopoietic cell transplantation (HCT) is a potentially curative treatment strategy for patients with inborn errors of immunities (IEIs). The objective of this study was to assess the optimal busulfan exposure before allogenei…
View article: The impact of age and renal function on the pharmacokinetics and protein binding characteristics of fludarabine in paediatric and adult patients undergoing allogeneic haematopoietic stem cell transplantation conditioning
The impact of age and renal function on the pharmacokinetics and protein binding characteristics of fludarabine in paediatric and adult patients undergoing allogeneic haematopoietic stem cell transplantation conditioning Open
View article: Compassionate access to virus-specific T cells for adoptive immunotherapy over 15 years
Compassionate access to virus-specific T cells for adoptive immunotherapy over 15 years Open
Adoptive T-cell immunotherapy holds great promise for the treatment of viral complications in immunocompromised patients resistant to standard anti-viral strategies. We present a retrospective analysis of 75 patients from 15 hospitals acro…
View article: Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation
Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation Open
View article: BAGEL: Bootstrapping Agents by Guiding Exploration with Language
BAGEL: Bootstrapping Agents by Guiding Exploration with Language Open
Following natural language instructions by executing actions in digital environments (e.g. web-browsers and REST APIs) is a challenging task for language model (LM) agents. Unfortunately, LM agents often fail to generalize to new environme…
View article: Helping or Herding? Reward Model Ensembles Mitigate but do not Eliminate Reward Hacking
Helping or Herding? Reward Model Ensembles Mitigate but do not Eliminate Reward Hacking Open
Reward models play a key role in aligning language model applications towards human preferences. However, this setup creates an incentive for the language model to exploit errors in the reward model to achieve high estimated reward, a phen…
View article: Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients
Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients Open
Lung injury is a major determinant of survival after pediatric hematopoietic cell transplantation (HCT). A deeper understanding of the relationship between pulmonary microbes, immunity, and the lung epithelium is needed to improve outcomes…
View article: Upper and/or Lower Respiratory Tract Infection Caused by Human Metapneumovirus After Allogeneic Hematopoietic Stem Cell Transplantation
Upper and/or Lower Respiratory Tract Infection Caused by Human Metapneumovirus After Allogeneic Hematopoietic Stem Cell Transplantation Open
Background Human metapneumovirus (hMPV) epidemiology, clinical characteristics and risk factors for poor outcome after allogeneic stem cell transplantation (allo-HCT) remain a poorly investigated area. Methods This retrospective multicente…
View article: minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data
minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data Open
Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments…
View article: Supplementary Information and Figures 1-3 from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
Supplementary Information and Figures 1-3 from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection Open
Supplementary Information and Figures 1-3 from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
View article: Data from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
Data from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection Open
Dasatinib is a multitargeted kinase inhibitor that was recently approved for the treatment of chronic myelogenous leukemia and Philadelphia chromosome–positive acute lymphoblastic leukemia with resistance or intolerance to prior therapy. I…
View article: Data from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
Data from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection Open
Dasatinib is a multitargeted kinase inhibitor that was recently approved for the treatment of chronic myelogenous leukemia and Philadelphia chromosome–positive acute lymphoblastic leukemia with resistance or intolerance to prior therapy. I…
View article: Supplementary Information and Figures 1-3 from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
Supplementary Information and Figures 1-3 from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection Open
Supplementary Information and Figures 1-3 from Identification of Candidate Molecular Markers Predicting Sensitivity in Solid Tumors to Dasatinib: Rationale for Patient Selection
View article: Validation of a liquid chromatography‐tandem mass spectrometry method for simultaneous quantification of <i>N</i>,<i>N</i>‐dimethylacetamide and <i>N</i>‐monomethylacetamide in pediatric plasma
Validation of a liquid chromatography‐tandem mass spectrometry method for simultaneous quantification of <i>N</i>,<i>N</i>‐dimethylacetamide and <i>N</i>‐monomethylacetamide in pediatric plasma Open
N,N –dimethylacetamide is an excipient used in intravenous busulfan formulations, a drug used in hematopoietic stem cell transplantation conditioning. The aim of this study was to develop and validate a liquid chromatography‐tandem mass sp…
View article: Evaluation of treosulfan cumulative exposure in paediatric patients through population pharmacokinetics and dosing simulations
Evaluation of treosulfan cumulative exposure in paediatric patients through population pharmacokinetics and dosing simulations Open
Aim To investigate the pharmacokinetics (PK) of intravenous treosulfan in paediatric patients undergoing haematopoietic stem cell transplantation (HSCT) for a broad range of diseases and to explore the impact of different dosing regimens o…
View article: Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT
Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT Open
Patients with hypomorphic mutations in the RAG1 or RAG2 gene present with either Omenn syndrome or atypical combined immunodeficiency with a wide phenotypic range. Hematopoietic stem cell transplantation (HSCT) is potentially curative, but…
View article: Pix2Struct: Screenshot Parsing as Pretraining for Visual Language Understanding
Pix2Struct: Screenshot Parsing as Pretraining for Visual Language Understanding Open
Visually-situated language is ubiquitous -- sources range from textbooks with diagrams to web pages with images and tables, to mobile apps with buttons and forms. Perhaps due to this diversity, previous work has typically relied on domain-…
View article: Challenges associated with test dose pharmacokinetic predictions of high dose melphalan exposure in patients with multiple myeloma
Challenges associated with test dose pharmacokinetic predictions of high dose melphalan exposure in patients with multiple myeloma Open
Aim To evaluate the accuracy of melphalan test dose pharmacokinetic (PK) predictions of the subsequent high dose (HDM) area under the concentration-versus-time curve (AUC) and to identify sources of prediction error (PE). Methods A prospec…
View article: Generate-and-Retrieve: use your predictions to improve retrieval for semantic parsing
Generate-and-Retrieve: use your predictions to improve retrieval for semantic parsing Open
A common recent approach to semantic parsing augments sequence-to-sequence models by retrieving and appending a set of training samples, called exemplars. The effectiveness of this recipe is limited by the ability to retrieve informative e…
View article: Ibrutinib Treatment of Pediatric Chronic Graft-versus-Host Disease: Primary Results from the Phase 1/2 iMAGINE Study
Ibrutinib Treatment of Pediatric Chronic Graft-versus-Host Disease: Primary Results from the Phase 1/2 iMAGINE Study Open
Chronic graft-versus-host disease (cGVHD) is a potentially life-threatening complication of allogeneic hematopoietic stem cell transplantation. Clinical data surrounding cGVHD therapies in younger children are limited and critically needed…
View article: Polydopamine-Mediated Protein Adsorption Alters the Epigenetic Status and Differentiation of Primary Human Adipose-Derived Stem Cells (hASCs)
Polydopamine-Mediated Protein Adsorption Alters the Epigenetic Status and Differentiation of Primary Human Adipose-Derived Stem Cells (hASCs) Open
Polydopamine (PDA) is a biocompatible cell-adhesive polymer with versatile applications in biomedical devices. Previous studies have shown that PDA coating could improve cell adhesion and differentiation of human mesenchymal stem cells (hM…
View article: MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data
MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data Open
2. Abstract Here we present the R package - MinSNPs. This is designed to assemble resolution optimised sets of single nucleotide polymorphisms (SNPs) from alignments such as genome wide orthologous SNP matrices. We also demonstrate a pipel…
View article: Third-party CMV- and EBV-specific T-cells for first viral reactivation after allogeneic stem cell transplant
Third-party CMV- and EBV-specific T-cells for first viral reactivation after allogeneic stem cell transplant Open
Virus-specific T-cells (VSTs) from third-party donors mediate short- and long-term antiviral effects in allogeneic hematopoietic stem cell transplant (HSCT) recipients with relapsed or refractory viral infections. We investigated early adm…
View article: Measurable residual disease analysis in paediatric acute lymphoblastic leukaemia patients with ABL-class fusions
Measurable residual disease analysis in paediatric acute lymphoblastic leukaemia patients with ABL-class fusions Open
View article: Association between the magnitude of intravenous busulfan exposure and development of hepatic veno-occlusive disease in children and young adults undergoing myeloablative allogeneic hematopoietic cell transplantation
Association between the magnitude of intravenous busulfan exposure and development of hepatic veno-occlusive disease in children and young adults undergoing myeloablative allogeneic hematopoietic cell transplantation Open