John P. Klein
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View article: Combination Prostatic Artery Embolization Prior to Water-Jet Ablation (Aquablation) for Benign Prostatic Hypertrophy: A Propensity Score Analysis
Combination Prostatic Artery Embolization Prior to Water-Jet Ablation (Aquablation) for Benign Prostatic Hypertrophy: A Propensity Score Analysis Open
Objectives: To compare post-operative bleeding measures in patients who underwent prostatic artery embolization (PAE) prior to water-jet ablation (aquablation) vs. water-jet ablation alone. Methods: A retrospective review identified 145 pa…
View article: Legitimate ground-truth-free metrics for deep uncertainty classification scoring
Legitimate ground-truth-free metrics for deep uncertainty classification scoring Open
Despite the increasing demand for safer machine learning practices, the use of Uncertainty Quantification (UQ) methods in production remains limited. This limitation is exacerbated by the challenge of validating UQ methods in absence of UQ…
View article: Next-generation cell line selection methodology leveraging data lakes, natural language generation and advanced data analytics
Next-generation cell line selection methodology leveraging data lakes, natural language generation and advanced data analytics Open
Cell line development is an essential stage in biopharmaceutical development that often lies on the critical path. Failure to fully characterise the lead clone during initial screening can lead to lengthy project delays during scale-up, wh…
View article: Architecting complex, long-lived scientific software
Architecting complex, long-lived scientific software Open
Thanks also to all the participants in the workshops for their time and energy, and to Mary Popeck for her help in the second workshop. NR would also like to thank Peter Braam of Braam Research LLC for suggesting the SEI approach to him in…
View article: Architecting Complex, Long-Lived Scientific Software
Architecting Complex, Long-Lived Scientific Software Open
Software is a critical aspect of large-scale science, providing essential capabilities for making scientific discoveries. Large-scale scientific projects are vast in scope, with lifespans measured in decades and costs exceeding hundreds of…
View article: Supplemental Table 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 1. Multivariate analysis of late relapse, transplant-related mortality, overall survival after HCT for each disease (AML, ALL, CML, MDS)
View article: Supplemental Table 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 1. Multivariate analysis of late relapse, transplant-related mortality, overall survival after HCT for each disease (AML, ALL, CML, MDS)
View article: Data from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Data from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Purpose: Malignancy relapse remains a major obstacle for successful allogeneic hematopoietic cell transplantation (HCT). Chronic graft-versus-host disease (cGVHD) is associated with fewer relapses. However, when studying effects of cGVHD o…
View article: Supplemental Table 3 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 3 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 3. Multivariate analysis showing impact of cGVHD characteristics on treatment related mortality, disease free survival and overall survival in patients with CML who developed cGVHD
View article: Supplemental Figure 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Figure 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Figure 1. Cumulative incidence of cGVHD, relapse and death in patients with AML, ALL, CML, MDS
View article: Data from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Data from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Purpose: Malignancy relapse remains a major obstacle for successful allogeneic hematopoietic cell transplantation (HCT). Chronic graft-versus-host disease (cGVHD) is associated with fewer relapses. However, when studying effects of cGVHD o…
View article: Supplemental Figure 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Figure 1 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Figure 1. Cumulative incidence of cGVHD, relapse and death in patients with AML, ALL, CML, MDS
View article: Supplemental Table 4 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 4 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 4. Multivariate analysis showing impact of cGVHD characteristics on treatment related mortality, disease free survival, overall survival in patients with AML, ALL, MDS who developed cGVHD
View article: Supplemental Table 3 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 3 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 3. Multivariate analysis showing impact of cGVHD characteristics on treatment related mortality, disease free survival and overall survival in patients with CML who developed cGVHD
View article: Supplemental Table 2 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 2 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 2. Multivariate analysis showing impact of cGVHD characteristics in CML patients on relapse
View article: Supplemental Table 2 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 2 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 2. Multivariate analysis showing impact of cGVHD characteristics in CML patients on relapse
View article: Supplemental Table 4 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia
Supplemental Table 4 from Impact of Chronic Graft-versus-Host Disease on Late Relapse and Survival on 7,489 Patients after Myeloablative Allogeneic Hematopoietic Cell Transplantation for Leukemia Open
Supplemental Table 4. Multivariate analysis showing impact of cGVHD characteristics on treatment related mortality, disease free survival, overall survival in patients with AML, ALL, MDS who developed cGVHD
View article: Model-Driven Engineering: Automatic Code Generation and Beyond
Model-Driven Engineering: Automatic Code Generation and Beyond Open
Increasing consideration of model-driven engineering (MDE) tools for software development efforts means that acquisition executives must more often deal with the following challenge: Vendors claim that by using MDE tools, they can generate…
View article: Self-mentoring: a new deep learning pipeline to train a self-supervised U-net for few-shot learning of bio-artificial capsule segmentation
Self-mentoring: a new deep learning pipeline to train a self-supervised U-net for few-shot learning of bio-artificial capsule segmentation Open
Background: Accurate segmentation of microscopic structures such as bio-artificial capsules in microscopy imaging is a prerequisite to the computer-aided understanding of important biomechanical phenomenons. State-of-the-art segmentation p…
View article: 5 costly online casino mistakes to avoid
5 costly online casino mistakes to avoid Open
The rules have changed since the arrival of smartphones, for example, it is possible to play with smaller stakes in the best online casino and have fun without suffering significant losses. This is what many people do: they play different …
View article: State space partitioning based on constrained spectral clustering for block particle filtering
State space partitioning based on constrained spectral clustering for block particle filtering Open
The particle filter (PF) is a powerful inference tool widely used to estimate the filtering distribution in non-linear and/or non-Gaussian problems. To overcome the curse of dimensionality of PF, the block PF (BPF) inserts a blocking step …
View article: SODA: Self-organizing data augmentation in deep neural networks -- Application to biomedical image segmentation tasks
SODA: Self-organizing data augmentation in deep neural networks -- Application to biomedical image segmentation tasks Open
In practice, data augmentation is assigned a predefined budget in terms of newly created samples per epoch. When using several types of data augmentation, the budget is usually uniformly distributed over the set of augmentations but one ca…
View article: Backpack:a Backpropagable Adversarial Embedding Scheme
Backpack:a Backpropagable Adversarial Embedding Scheme Open
A min max protocol offers a general method to automatically optimize steganographic algorithm against a wide class of steganalytic detectors. The quality of the resulting steganograhic algorithm depends on the ability to find an "adversari…
View article: Bayesian Transformation Models for Multivariate Survival Data: Bayesian transformation models
Bayesian Transformation Models for Multivariate Survival Data: Bayesian transformation models Open
In this paper we propose a general class of gamma frailty transformation models for multivariate survival data. The transformation class includes the commonly used proportional hazards and proportional odds models. The proposed class also …
View article: A Survey on the Interplay between Software Engineering and Systems Engineering during SoS Architecting
A Survey on the Interplay between Software Engineering and Systems Engineering during SoS Architecting Open
Background: The Systems Engineering and Software Engineering disciplines are highly intertwined in most modern Systems of Systems (SoS), and particularly so in industries such as defense, transportation, energy and health care. However, th…
View article: Comparing Outcomes with Bone Marrow or Peripheral Blood Stem Cells as Graft Source for Matched Sibling Transplants in Severe Aplastic Anemia across Different Economic Regions
Comparing Outcomes with Bone Marrow or Peripheral Blood Stem Cells as Graft Source for Matched Sibling Transplants in Severe Aplastic Anemia across Different Economic Regions Open
Bone marrow (BM) is the preferred graft source for hematopoietic stem cell transplantation (HSCT) in severe aplastic anemia (SAA) compared to mobilized peripheral blood stem cells (PBSC). We hypothesized that this recommendation may not ap…
View article: A Survey on the Interplay between Software Engineering and Systems Engineering during SoS Architecting - replication package
A Survey on the Interplay between Software Engineering and Systems Engineering during SoS Architecting - replication package Open
Replication package of the paper A Survey on the Interplay between Software Engineering and Systems Engineering during SoS Architecting. Paper accepted on the Empirical Software Engineering and Measurement Conference (ESEM), 2020.
View article: System-of-Systems Viewpoint for System Architecture Documentation
System-of-Systems Viewpoint for System Architecture Documentation Open
Context: The systems comprising a system of systems (SoS) are inde- pendently acquired, operated, and managed. Frequently, the architecture documentation of these existing systems addresses only a stand-alone perspective, and must be augme…