Livelihood gains and ecological costs of NTFP dependence: assessing the roles of dependence, ecological knowledge and market structure in three contrasting human and ecological settings in south India

Non-timber forest products (NTFPs) constitute the single largest determinant of livelihoods for scores of forest fringe communities and poor people in the tropics. In India over 50 million people are believed to be directly dependent upon NTFPs for their subsistence. However, such human dependence on NTFPs for livelihood gains (win) has most frequently been at a certain ecological cost (lose). If livelihoods are to be maintained, the existing ‘win-lose’ settings have to be steered to a ‘win-win’ mode, otherwise, there could be severe erosion of the biological resources and loss of livelihoods (‘lose-lose’). Examining the dependence of forest fringe communities on NTFPs at three sites in south India with contrasting human and ecological settings, three key factors (extent of dependence on NTFPs, indigenous ecological knowledge and market organization) are likely to constrain reaching the win-win situation. How these factors shape the ecological cost of harvesting NTFPs at the three sites is examined. Within the parameter space of these factors, it is possible to predict outcomes and associations that will conform to win-win or win-lose situations. Empirical data derived from the three study sites demonstrate the causality of the observed associations. The key for long-term livelihood gains lies in reducing the ecological cost. Certain interventions and recommendations that could optimize the balance between livelihood gains and ecological cost are proposed

The Real Symplectic Groups in Quantum Mechanics and Optics

text of abstract (We present a utilitarian review of the family of matrix groups $Sp(2n,\Re)$, in a form suited to various applications both in optics and quantum mechanics. We contrast these groups and their geometry with the much more familiar Euclidean and unitary geometries. Both the properties of finite group elements and of the Lie algebra are studied, and special attention is paid to the so-called unitary metaplectic representation of $Sp(2n,\Re)$. Global decomposition theorems, interesting subgroups and their generators are described. Turning to $n$-mode quantum systems, we define and study their variance matrices in general states, the implications of the Heisenberg uncertainty principles, and develop a U(n)-invariant squeezing criterion. The particular properties of Wigner distributions and Gaussian pure state wavefunctions under $Sp(2n,\Re)$ action are delineated.)Comment: Review article 43 pages, revtex, no figures, replaced because somefonts were giving problem in autometic ps generatio

Statistical tests for large tree-structured data

We develop a general statistical framework for the analysis and inference of large tree-structured data, with a focus on developing asymptotic goodness-of-fit tests. We first propose a consistent statistical model for binary trees, from which we develop a class of invariant tests. Using the model for binary trees, we then construct tests for general trees by using the distributional properties of the Continuum Random Tree, which arises as the invariant limit for a broad class of models for tree-structured data based on conditioned Galton–Watson processes. The test statistics for the goodness-of-fit tests are simple to compute and are asymptotically distributed as χ2 and F random variables. We illustrate our methods on an important application of detecting tumour heterogeneity in brain cancer. We use a novel approach with tree-based representations of magnetic resonance images and employ the developed tests to ascertain tumor heterogeneity between two groups of patients

A study of arteriovenous crossing patterns in branch retinal vein occlusion

Introduction: Branch retinal vein occlusion (BRVO) almost always occurs at an arteriovenous crossing, where the artery and vein share a common adventitial sheath. Aim: The study was designed to evaluate the anatomic position of the crossing vessels at the site of occlusion in a case of BRVO. Materials and Methods: A cross sectional descriptive study was conducted among 20 BRVO patients attending Ophthalmology outpatient department of a tertiary care hospital during the period of September 2013 to August 2014. A semi structured questionnaire was used to evaluate the sociodemographic characters and co-morbidity among the patients. The fundus of the patients were examined with 90D lens under slit lamp and the fundus photographs were taken. Results: Twenty patients were considered in the study. Eleven were male and nine were female patients. Mean age of the male group was 50.09±4.94 years. Mean age of the female group was 49.33±3.77 years. In all, there were 21 eyes with branch retinal vein occlusion. Out of which 11 were left eyes, eight were right eyes and one patient was having occlusion in both the eyes. In BRVO cases, among 17(80.9%) eyes, the artery was anterior to the vein and in the remaining 4(19.1%) eyes the vein was anterior to the artery. No statistically significant difference was observed regarding the position of artery and vein in BRVO and control eyes (p=0.9). The superiotemporal occlusions were more in number 13 (61.9%) as compared to inferiotemporal occlusions in 8 (38.1%) eyes. Amajority 17(85%) of patients were hypertensive. Conclusion: In the present study the incidence of artery anterior to the vein was higher compare to vein anterior to the artery, the knowledge of which is useful to understand the patho-physiology and management of BRV

Central nervous system immune interactome is a function of cancer lineage, tumor microenvironment, and STAT3 expression.

BACKGROUNDImmune cell profiling of primary and metastatic CNS tumors has been focused on the tumor, not the tumor microenvironment (TME), or has been analyzed via biopsies.METHODSEn bloc resections of gliomas (n = 10) and lung metastases (n = 10) were analyzed via tissue segmentation and high-dimension Opal 7-color multiplex imaging. Single-cell RNA analyses were used to infer immune cell functionality.RESULTSWithin gliomas, T cells were localized in the infiltrating edge and perivascular space of tumors, while residing mostly in the stroma of metastatic tumors. CD163+ macrophages were evident throughout the TME of metastatic tumors, whereas in gliomas, CD68+, CD11c+CD68+, and CD11c+CD68+CD163+ cell subtypes were commonly observed. In lung metastases, T cells interacted with CD163+ macrophages as dyads and clusters at the brain-tumor interface and within the tumor itself and as clusters within the necrotic core. In contrast, gliomas typically lacked dyad and cluster interactions, except for T cell CD68+ cell dyads within the tumor. Analysis of transcriptomic data in glioblastomas revealed that innate immune cells expressed both proinflammatory and immunosuppressive gene signatures.CONCLUSIONOur results show that immunosuppressive macrophages are abundant within the TME and that the immune cell interactome between cancer lineages is distinct. Further, these data provide information for evaluating the role of different immune cell populations in brain tumor growth and therapeutic responses.FUNDINGThis study was supported by the NIH (NS120547), a Developmental research project award (P50CA221747), ReMission Alliance, institutional funding from Northwestern University and the Lurie Comprehensive Cancer Center, and gifts from the Mosky family and Perry McKay. Performed in the Flow Cytometry & Cellular Imaging Core Facility at MD Anderson Cancer Center, this study received support in part from the NIH (CA016672) and the National Cancer Institute (NCI) Research Specialist award 1 (R50 CA243707). Additional support was provided by CCSG Bioinformatics Shared Resource 5 (P30 CA046592), a gift from Agilent Technologies, a Research Scholar Grant from the American Cancer Society (RSG-16-005-01), a Precision Health Investigator Award from University of Michigan (U-M) Precision Health, the NCI (R37-CA214955), startup institutional research funds from U-M, and a Biomedical Informatics & Data Science Training Grant (T32GM141746)

Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages

Pancreatic ductal adenocarcinoma (PDA) is accompanied by reprogramming of the local microenvironment, but changes at distal sites are poorly understood. We implanted biomaterial scaffolds, which act as an artificial premetastatic niche, into immunocompetent tumor-bearing and control mice, and identified a unique tumor-specific gene expression signature that includes high expression of C1qa, C1qb, Trem2, and Chil3 Single-cell RNA sequencing mapped these genes to two distinct macrophage populations in the scaffolds, one marked by elevated C1qa, C1qb, and Trem2, the other with high Chil3, Ly6c2 and Plac8 In mice, expression of these genes in the corresponding populations was elevated in tumor-associated macrophages compared with macrophages in the normal pancreas. We then analyzed single-cell RNA sequencing from patient samples, and determined expression of C1QA, C1QB, and TREM2 is elevated in human macrophages in primary tumors and liver metastases. Single-cell sequencing analysis of patient blood revealed a substantial enrichment of the same gene signature in monocytes. Taken together, our study identifies two distinct tumor-associated macrophage and monocyte populations that reflects systemic immune changes in pancreatic ductal adenocarcinoma patients

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 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

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