Uncovering morphoproteomic relationships using probabilistic graphical models and resource description framework knowledgebases

Title from PDF of title page (University of Missouri--Columbia, viewed on July 29, 2013).The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Dissertation advisor: Dr. Chi-Ren ShyuIncludes bibliographical references.Vita.Ph. D. University of Missouri-Columbia 2012."July 2012"The heterogeneity of individual patient responses to conventional drug therapies is one of the central problems in personalized medicine and has great impact on clinical outcomes. To address this problem a new field of morphoproteomics was recently introduced. Morphoproteomics is a new method aimed at comprehensive analysis of protein circuitries in diseased cells to design effective drug therapies for individual patient cases. However, due to the overwhelming amount of molecular information that needs to be processed, successful adoption of morphoproteomics will greatly depend on availability of a comprehensive computerized knowledgebase and intelligent retrieval technologies. We have, therefore, initiated new research with the overall goal to develop informatics methods to support morphoproteomic studies. We integrate evidence and information extracted from Whole Slide Imaging (WSI) and Immunohistochemistry (IHC) as well as from a semantic “mashup” of publicly available knowledge sources to provide pathologists a comprehensive picture of morphoproteomic mechanisms. This dissertation introduces novel methods for improving IHC antibody/antigen test selection as well as uncovering morphoproteomic relationships using probabilistic graphical models and Resource Description Framework (RDF) graphs of biomedical knowledgebases. Our methods have great potential to bring a broad impact in to pathology and personalize medicine as well as to be extended to more general systems biology domain.Includes bibliographical reference

ConvFormer: Parameter Reduction in Transformer Models for 3D Human Pose Estimation by Leveraging Dynamic Multi-Headed Convolutional Attention

Recently, fully-transformer architectures have replaced the defacto convolutional architecture for the 3D human pose estimation task. In this paper we propose \textbf{\textit{ConvFormer}}, a novel convolutional transformer that leverages a new \textbf{\textit{dynamic multi-headed convolutional self-attention}} mechanism for monocular 3D human pose estimation. We designed a spatial and temporal convolutional transformer to comprehensively model human joint relations within individual frames and globally across the motion sequence. Moreover, we introduce a novel notion of \textbf{\textit{temporal joints profile}} for our temporal ConvFormer that fuses complete temporal information immediately for a local neighborhood of joint features. We have quantitatively and qualitatively validated our method on three common benchmark datasets: Human3.6M, MPI-INF-3DHP, and HumanEva. Extensive experiments have been conducted to identify the optimal hyper-parameter set. These experiments demonstrated that we achieved a \textbf{significant parameter reduction relative to prior transformer models} while attaining State-of-the-Art (SOTA) or near SOTA on all three datasets. Additionally, we achieved SOTA for Protocol III on H36M for both GT and CPN detection inputs. Finally, we obtained SOTA on all three metrics for the MPI-INF-3DHP dataset and for all three subjects on HumanEva under Protocol II

Near-Surface Seismic Measurements in Gravel Pit, Over Highway Tunnel and Underground Tubes with Ground Truth Information as an Open Data Set

In this article, we describe in detail three seismic measurement campaigns based on refraction methods that we conducted at different sites in Bavaria, Germany. The measured data is published as an open data set. The particularity of this data set lies in its available ground truth information about each measurement site. Acquiring seismic data from sites with ground truth information is important for validation of seismic inversion algorithms. Since near-surface seismic field data with ground truth information is rather limited, we anticipate this data set to be a valuable contribution to the research community. For the measurements, three sites have been selected: (1) a gravel pit with a ground water layer, (2) a site above a highway tunnel and (3) a surface over underground tubes. The measurements have been conducted using line arrays of geophones, the Geode Seismograph from Geometrics Inc. and hammer strikes as seismic source. To obtain inversion results a travel time tomography based on first-arrivals within the software SeisImager is used. The inversion results show that we are able to image the ground water layer in the gravel pit, the highway tunnel and partly features of underground tubes. Furthermore, the results coincide with available ground truth information about the measurement sites. This paper summarizes the measurement campaigns and the respective data sets obtained through these campaigns. The data have been published by the authors as an open data set under the license CC BY 4.0 on figshare to make it available to the research community for validation of seismic data processing and inversion techniques

IRE1α–XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity

Tumours evade immune control by creating hostile microenvironments that perturb T cell metabolism and effector function 1?4 . However, it remains unclear how intra-tumoral T cells integrate and interpret metabolic stress signals. Here we report that ovarian cancer?an aggressive malignancy that is refractory to standard treatments and current immunotherapies 5?8 ?induces endoplasmic reticulum stress and activates the IRE1α?XBP1 arm of the unfolded protein response 9,10 in T cells to control their mitochondrial respiration and anti-tumour function. In T cells isolated from specimens collected from patients with ovarian cancer, upregulation of XBP1 was associated with decreased infiltration of T cells into tumours and with reduced IFNG mRNA expression. Malignant ascites fluid obtained from patients with ovarian cancer inhibited glucose uptake and caused N-linked protein glycosylation defects in T cells, which triggered IRE1α?XBP1 activation that suppressed mitochondrial activity and IFNγ production. Mechanistically, induction of XBP1 regulated the abundance of glutamine carriers and thus limited the influx of glutamine that is necessary to sustain mitochondrial respiration in T cells under glucose-deprived conditions. Restoring N-linked protein glycosylation, abrogating IRE1α?XBP1 activation or enforcing expression of glutamine transporters enhanced mitochondrial respiration in human T cells exposed to ovarian cancer ascites. XBP1-deficient T cells in the metastatic ovarian cancer milieu exhibited global transcriptional reprogramming and improved effector capacity. Accordingly, mice that bear ovarian cancer and lack XBP1 selectively in T cells demonstrate superior anti-tumour immunity, delayed malignant progression and increased overall survival. Controlling endoplasmic reticulum stress or targeting IRE1α?XBP1 signalling may help to restore the metabolic fitness and anti-tumour capacity of T cells in cancer hosts.Fil: Song, Minkyung. Weill Cornell Medicine; Estados UnidosFil: Sandoval, Tito A.. Weill Cornell Medicine; Estados UnidosFil: Chae, Chang-Suk. Weill Cornell Medicine; Estados UnidosFil: Chopra, Sahil. Weill Cornell Medicine; Estados UnidosFil: Tan, Chen. Weill Cornell Medicine; Estados UnidosFil: Rutkowski, Melanie R.. University of Virginia; Estados UnidosFil: Raundhal, Mahesh. Dana Farber Cancer Institute; Estados Unidos. Harvard Medical School; Estados UnidosFil: Chaurio, Ricardo A.. H. Lee Moffitt Cancer Center & Research Institute; Estados UnidosFil: Payne, Kyle K.. H. Lee Moffitt Cancer Center & Research Institute; Estados UnidosFil: Konrad, Csaba. Weill Cornell Medicine; Estados UnidosFil: Bettigole, Sarah E.. Quentis Therapeutics Inc.; Estados UnidosFil: Shin, Hee Rae. Quentis Therapeutics Inc.; Estados UnidosFil: Crowley, Michael J. P.. Weill Cornell Graduate School of Medical Sciences; Estados UnidosFil: Cerliani, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Kossenkov, Andrew V.. The Wistar Institute; Estados UnidosFil: Motorykin, Ievgen. Weill Cornell Medicine,; Estados UnidosFil: Zhang, Sheng. Weill Cornell Medicine,; Estados UnidosFil: Manfredi, Giovanni. Weill Cornell Medicine,; Estados UnidosFil: Zamarin, Dmitriy. Memorial Sloan Kettering Cancer Center; Estados UnidosFil: Holcomb, Kevin. Weill Cornell Medicine,; Estados UnidosFil: Rodriguez, Paulo C.. H. Lee Moffitt Cancer Center & Research Institute; Estados UnidosFil: Rabinovich, Gabriel Adrián. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Conejo Garcia, Jose R.. H. Lee Moffitt Cancer Center & Research Institute; Estados UnidosFil: Glimcher, Laurie H.. Dana Farber Cancer Institute; Estados Unidos. Harvard Medical School; Estados UnidosFil: Cubillos-Ruiz, Juan R.. Weill Graduate School Of Medical Sciences; Estados Unidos. Weill Graduate School Of Medical Sciences; Estados Unido

Durvalumab Plus Carboplatin/Paclitaxel Followed by Maintenance Durvalumab With or Without Olaparib as First-Line Treatment for Advanced Endometrial Cancer: The Phase III DUO-E Trial

PURPOSE Immunotherapy and chemotherapy combinations have shown activity in endometrial cancer, with greater benefit in mismatch repair (MMR)-deficient (dMMR) than MMR-proficient (pMMR) disease. Adding a poly(ADP-ribose) polymerase inhibitor may improve outcomes, especially in pMMR disease. METHODS This phase III, global, double-blind, placebo-controlled trial randomly assigned eligible patients with newly diagnosed advanced or recurrent endometrial cancer 1:1:1 to: carboplatin/paclitaxel plus durvalumab placebo followed by placebo maintenance (control arm); carboplatin/paclitaxel plus durvalumab followed by maintenance durvalumab plus olaparib placebo (durvalumab arm); or carboplatin/paclitaxel plus durvalumab followed by maintenance durvalumab plus olaparib (durvalumab + olaparib arm). The primary end points were progression-free survival (PFS) in the durvalumab arm versus control and the durvalumab + olaparib arm versus control. RESULTS Seven hundred eighteen patients were randomly assigned. In the intention-to-treat population, statistically significant PFS benefit was observed in the durvalumab (hazard ratio [HR], 0.71 [95% CI, 0.57 to 0.89]; P = .003) and durvalumab + olaparib arms (HR, 0.55 [95% CI, 0.43 to 0.69]; P < .0001) versus control. Prespecified, exploratory subgroup analyses showed PFS benefit in dMMR (HR [durvalumab v control], 0.42 [95% CI, 0.22 to 0.80]; HR [durvalumab + olaparib v control], 0.41 [95% CI, 0.21 to 0.75]) and pMMR subgroups (HR [durvalumab v control], 0.77 [95% CI, 0.60 to 0.97]; HR [durvalumab + olaparib v control] 0.57; [95% CI, 0.44 to 0.73]); and in PD-L1-positive subgroups (HR [durvalumab v control], 0.63 [95% CI, 0.48 to 0.83]; HR [durvalumab + olaparib v control], 0.42 [95% CI, 0.31 to 0.57]). Interim overall survival results (maturity approximately 28%) were supportive of the primary outcomes (durvalumab v control: HR, 0.77 [95% CI, 0.56 to 1.07]; P = .120; durvalumab + olaparib v control: HR, 0.59 [95% CI, 0.42 to 0.83]; P = .003). The safety profiles of the experimental arms were generally consistent with individual agents. CONCLUSION Carboplatin/paclitaxel plus durvalumab followed by maintenance durvalumab with or without olaparib demonstrated a statistically significant and clinically meaningful PFS benefit in patients with advanced or recurrent endometrial cancer