Assessing Environmental Governance of the Hudson River Valley: Application of an IPPEP Model

The process of obtaining effective implementation of environmental laws is a process of “environmental governance.” Law, including environmental law and other fields of law related to environmental law, is essential to frame, facilitate, and foster the major parties to correctly play their roles. This thesis has been articulated through a Model of Interactions of Parties in the Process of Environmental Protection (IPPEP Model), which has been developed by Professor Wang Xi of Shanghai Jiao Tong University, in the context of the People’s Republic of China. The IPPEP Model is a tool for observing and accessing environmental governance at work. It is being tested by regional studies in various locations, such as the United States, the State of New York, and in this IPPEP case study of New York’s Hudson River Valley. The IPPEP model being examined, however, has universal applicability. Use of this model can predict that environmental standards will fail to be observed when necessary “Third Parties” are weak or absent. A nation with a commitment to the “rule of law” will enact and apply necessary legal procedures to ensure that each party can take part in the system and perform their role effectively. Part I of this paper describes the IPPEP Model. Part II is a brief introduction to the history of Hudson River Valley. Part III introduces the major parties or players in the process of protecting Hudson River Valley. Part IV consists of five case studies applying the IPPEP Model in cases of Hudson River Valley conservation. Part V concludes the paper

Two-dimensional loosely and tightly bound solitons in optical lattices and inverted traps

We study the dynamics of nonlinear localized excitations (solitons) in two-dimensional (2D) Bose-Einstein condensates (BECs) with repulsive interactions, loaded into an optical lattice (OL), which is combined with an external parabolic potential. First, we demonstrate analytically that a broad (loosely bound, LB) soliton state, based on a 2D Bloch function near the edge of the Brillouin zone (BZ), has a negative effective mass (while the mass of a localized state is positive near the BZ center). The negative-mass soliton cannot be held by the usual trap, but it is safely confined by an inverted parabolic potential (anti-trap). Direct simulations demonstrate that the LB solitons (including the ones with intrinsic vorticity) are stable and can freely move on top of the OL. The frequency of elliptic motion of the LB-soliton's center in the anti-trapping potential is very close to the analytical prediction which treats the solition as a quasi-particle. In addition, the LB soliton of the vortex type features real rotation around its center. We also find an abrupt transition, which occurs with the increase of the number of atoms, from the negative-mass LB states to tightly bound (TB) solitons. An estimate demonstrates that, for the zero-vorticity states, the transition occurs when the number of atoms attains a critical number N=10^3, while for the vortex the transition takes place at N=5x10^3 atoms. The positive-mass LB states constructed near the BZ center (including vortices) can move freely too. The effects predicted for BECs also apply to optical spatial solitons in bulk photonic crystals.Comment: 17 pages, 12 figure

Dynamics of positive- and negative-mass solitons in optical lattices and inverted traps

We study the dynamics of one-dimensional solitons in the attractive and repulsive Bose-Einstein condensates (BECs) loaded into an optical lattice (OL), which is combined with an external parabolic potential. First, we demonstrate analytically that, in the repulsive BEC, where the soliton is of the gap type, its effective mass is \emph{negative}. This gives rise to a prediction for the experiment: such a soliton cannot be not held by the usual parabolic trap, but it can be captured (performing harmonic oscillations) by an anti-trapping inverted parabolic potential. We also study the motion of the soliton a in long system, concluding that, in the cases of both the positive and negative mass, it moves freely, provided that its amplitude is below a certain critical value; above it, the soliton's velocity decreases due to the interaction with the OL. At a late stage, the damped motion becomes chaotic. We also investigate the evolution of a two-soliton pulse in the attractive model. The pulse generates a persistent breather, if its amplitude is not too large; otherwise, fusion into a single fundamental soliton takes place. Collisions between two solitons captured in the parabolic trap or anti-trap are considered too. Depending on their amplitudes and phase difference, the solitons either perform stable oscillations, colliding indefinitely many times, or merge into a single soliton. Effects reported in this work for BECs can also be formulated for optical solitons in nonlinear photonic crystals. In particular, the capture of the negative-mass soliton in the anti-trap implies that a bright optical soliton in a self-defocusing medium with a periodic structure of the refractive index may be stable in an anti-waveguide.Comment: 22pages, 9 figures, submitted to Journal of Physics

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Vaccine strain affects seroconversion after influenza vaccination in COPD patients and healthy older people

Though clinical guidelines recommend influenza vaccination for chronic obstructive pulmonary disease (COPD) patients and other high-risk populations, it is unclear whether current vaccination strategies induce optimal antibody responses. This study aimed to identify key variables associated with strain-specific antibody responses in COPD patients and healthy older people. 76 COPD and 72 healthy participants were recruited from two Australian centres and inoculated with influenza vaccine. Serum strain-specific antibody titres were measured pre- and post-inoculation. Seroconversion rate was the primary endpoint. Antibody responses varied between vaccine strains. The highest rates of seroconversion were seen with novel strains (36–55%), with lesser responses to strains included in the vaccine in more than one consecutive year (27–33%). Vaccine responses were similar in COPD patients and healthy participants. Vaccine strain, hypertension and latitude were independent predictors of seroconversion. Our findings reassure that influenza vaccination is equally immunogenic in COPD patients and healthy older people; however, there is room for improvement. There may be a need to personalise the yearly influenza vaccine, including consideration of pre-existing antibody titres, in order to target gaps in individual antibody repertoires and improve protection