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The associated publication reports proteogenomic analysis of human pancreatic ductal adenocarcinoma (PDAC), where we provided significantly mutated genes (SMGs)/biomarkers, cellular pathways, and cell types as potential therapeutic targets to improve stratification of patients with PDAC. This protocol describes the detailed methods for whole exome sequencing (WES) and RNA sequencing analyses of PDAC samples, including tissue processing for proteogenomic analysis, DNA and RNA extraction, experimental procedures for WES and RNA sequencing, and WES and RNA sequencing data analyses.

The associated publication reports proteogenomic analysis of human pancreatic ductal adenocarcinoma (PDAC), where we provided significantly mutated genes (SMGs)/biomarkers, cellular pathways, and cell types as potential therapeutic targets to improve stratification of patients with PDAC. This protocol describes the detailed methods for mass spectrometry-based proteomic analysis of PDAC samples, including sample preparation, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, and data analyses (peptide/protein identification and quantitation).

The associated publication reports proteogenomic analysis of human pancreatic ductal adenocarcinoma (PDAC), where we provided significantly mutated genes (SMGs)/biomarkers, cellular pathways, and cell types as potential therapeutic targets to improve stratification of patients with PDAC. This protocol describes the detailed methods for cell-based assays for potential prognostic biomarkers in PDAC, including cell culture, viral transduction, and cell-based assays.

The associated publication reports proteogenomic analysis of human pancreatic ductal adenocarcinoma (PDAC), where we provided significantly mutated genes (SMGs)/biomarkers, cellular pathways, and cell types as potential therapeutic targets to improve stratification of patients with PDAC. This protocol describes the detailed methods for assays for orthotopic PDAC mouse models, including mouse tumour tissue processing, ultrasound imaging, Masson-trichrome staining, and IHC analysis for immune cell markers.

The associated publication reports proteogenomic analysis of human pancreatic ductal adenocarcinoma (PDAC), where we provided significantly mutated genes (SMGs)/biomarkers, cellular pathways, and cell types as potential therapeutic targets to improve stratification of patients with PDAC. This protocol describes the detailed methods for bioinformatics analysis of PDAC subtypes, including tumour purity estimation, subtype prediction for tumour samples in previous cohorts, pathway enrichment analysis, kinase activity analysis, and pan-omics analysis.

We report a proteogenomic analysis of pancreatic ductal adenocarcinoma (PDAC). Mutation-phosphorylation correlations identified signaling pathways associated with somatic mutations in significantly mutated genes. Messenger RNA-protein abundance correlations revealed potential prognostic biomarkers correlated with patient survival. Integrated clustering of mRNA, protein and phosphorylation data identified six PDAC subtypes. Cellular pathways represented by mRNA and protein signatures, defining the subtypes and compositions of cell types in the subtypes, characterized them as classical progenitor (TS1), squamous (TS2-4), immunogenic progenitor (IS1) and exocrine-like (IS2) subtypes. Compared with the mRNA data, protein and phosphorylation data further classified the squamous subtypes into activated stroma-enriched (TS2), invasive (TS3) and invasive-proliferative (TS4) squamous subtypes. Orthotopic mouse PDAC models revealed a higher number of pro-tumorigenic immune cells in TS4, inhibiting T cell proliferation. Our proteogenomic analysis provides significantly mutated genes/biomarkers, cellular pathways and cell types as potential therapeutic targets to improve stratification of patients with PDAC.

There have been considerable interest in the coordination chemistry of metal complexes with pyrazole and their derivatives owing to diverse coordination modes and relevance to a biological-active metal center with imidazole-like ligands.1–8 Recently, we studied metal complexes with a multidentate ligand, N,N,N¢,N¢-tetrakis(3,5-dimethyl-1-pyrazolyl)methyl-1,4phenylenediamine (tpmp), having the 1,4-phenylenediamine moiety, and isolated a dinuclear cobalt complex from a reaction of cobalt(II) chloride and tpmp consisting of two tetrahedral cobalt(II) atoms with two pyrazolato-nitrogen atoms of tpmp and two chloride atoms.6 In this study, we tried to extend this work to reactions with other metal salts, such as cobalt(II) acetate and nickel(II) acetate. We found totally different products with 3,5-dimethyl-1-pyrazolyl)methanolato (dmpm–), as shown in Fig. 1, [M4(dmpm)4(O2CCH3)4]·2CH3CN (M = Ni and Co). Here, we report on the crystal structures of these complexes. The ligand tpmp was synthesized by a method described in the literature.8 [Ni4(dmpm)4(O2CCH3)4]·2CH3CN To a solution of tpmp (54 mg, 0.1 mmol) in 10 cm3 of acetonitrile was added 25 mg (0.1 mmol) of nickel(II) acetate tetrahydrate. The reaction mixture was stirred overnight at room temperature. The resulting cleargreen solution was left for several days to yield green crystals. These crystals were collected, washed by acetonitrile, and dried under a vacuum. Yield, 35 mg. Anal. Found: C, 41.42; H, 5.27; N, 13.49%. Calcd for C36H54N10Ni4O12: C, 41.04; H, 5.17; N, Tetranuclear Nickel(II) and Cobalt(II) Complexes with 3,5-Dimethyl-1pyrazolylmethanolato and Acetato Bridges Having a Cubane Core

In a PET detector using pixelated scintillator, a 511 keV annihilation photon incident on a pixel might deposit part of its energy and could be almost simultaneously detected in several adjacent pixels. These inter-crystal scattered events are typically considered invalid events in PET if their energies are not within the energy window. The purpose of this study is to develop a new position decoder circuit (PDC) capable of multiplexing a number of channels and recovering the inter-crystal scattered events to improve the sensitivity of the PET detector consisting of Geiger-mode avalanche photodiode (GAPD) arrays. The PET detector module consisted of a 4 × 4 array of LYSO crystals and a 4 × 4 array of 3 × 3 mm2 GAPDs. The output signals from 2 detector modules were transmitted to the PDC which amplified the signals, selected the two fastest amplified signals among 32 signals and output their digital addresses and analog pulses. The PDC outputs were fed into a data acquisition system and arrival time, energy and address of the outputs were estimated and stored in list mode format. The recovery of inter-crystal scattered events was carried out by using the energy and time criteria in post-processing. The average energy resolution of a detector module at 511 keV was 17.1 ± 1.1% and 17.8 ± 1.3% before and after the recovery of inter-crystal scattered events, respectively. The increase in photopeak counts ranged from 5.3% to 26.7% depending on the pixel and source positions. The results of this study show that the new PDC design is useful to increase the sensitivity of PET detector through the recovery of inter-crystal scattered events while maintaining its high channel reduction ratio.

Hydra is a flexible wireless network testbed being developed at UT Austin. Our focus is networks that support multiple wireless hops and where the network, especially the MAC, takes advantage of sophisticated PHY techniques, such as OFDM and MIMO. We argue that for this domain simulation alone is not adequate and that working prototypes are needed to validate algorithms and protocols. Hydra nodes consist of a flexible RF front-end and a general purpose machine with a software based MAC and PHY. Using the frameworks of the Click modular router and GNU radio and coding in C++ makes it relatively easy to implement working prototypes of cross-layer designs that require custom MACs and PHYs. We present the architecture and implementation of Hydra, as well as a preliminary cross-layer design experiment for a rate-adaptive MAC. These early results show Hydra is a capable prototyping tool for wireless network research.

We investigate how to improve link quality without degrading data rate by exploiting tradeoffs between diversity and spatial multiplexing gains in multi-input multi-output ad-hoc networks. When the set of input rates for a MIMO network is given, we propose that maximizing the minimum diversity gain among the links provides a reasonable solution to optimize the overall link error probability when there is a reasonably high signal to noise ratio. We verify the performance using simulation based on a modified ns2.