The Complex Pathway towards Farm-Level Sustainable Intensification: An Exploratory Network Analysis of Stakeholders’ Knowledge and Perception

peer-reviewedFarm-level sustainable intensification of agriculture (SIA) has become an important concept to ensuring food security while minimising negative externalities. However, progress towards its achievement is often constrained by the different perceptions and goals of various stakeholders that affect farm management decisions. This study examines farm-level SIA as a dynamic system with interactive components that are determined by the interests of the stakeholders involved. A systems thinking approach was used to identify and describe the pathways towards farm-level SIA across the three main pillars of sustainability. An explanatory network analysis of fuzzy cognitive maps (FCMs) that were collectively created by representative groups of farmers, farm advisors and policy makers was performed. The study shows that SIA is a complex dynamic system, affected by cognitive beliefs and particular knowledge within stakeholder groups. The study concludes that, although farm-level SIA is a complex process, common goals can be identified in collective decision making

New ADS Functionality for the Curator

In this paper we provide an update concerning the operations of the NASA Astrophysics Data System (ADS), its services and user interface, and the content currently indexed in its database. As the primary information system used by researchers in Astronomy, the ADS aims to provide a comprehensive index of all scholarly resources appearing in the literature. With the current effort in our community to support data and software citations, we discuss what steps the ADS is taking to provide the needed infrastructure in collaboration with publishers and data providers. A new API provides access to the ADS search interface, metrics, and libraries allowing users to programmatically automate discovery and curation tasks. The new ADS interface supports a greater integration of content and services with a variety of partners, including ORCID claiming, indexing of SIMBAD objects, and article graphics from a variety of publishers. Finally, we highlight how librarians can facilitate the ingest of gray literature that they curate into our system.Comment: Submitted to the Proceedings of Library and Information Services in Astronomy VIII, Strasbourg, Franc

Design of a Professional Practice Simulator for Educating and Motivating First-Year Engineering Students

Increasingly, first-year engineering curricula incorporate design projects. However, the faculty and staff effort and physical resources required for the number of students enrolled can be daunting and affect the quality of instruction. To reduce these costs, ensure a high quality educational experience, and reduce variability in student outcomes that occur with individual design projects, we developed a simulation of engineering professional practice, NephroTex, in which teams of students are guided through multiple design-build-test cycles by a mentor in a virtual internship. Here we report on the design process for the virtual internship and results of testing with first-year engineering students at a large, public university. Our results demonstrate that the novel virtual internship successfully educated and motivated first-year-engineering students. Importantly, the virtual environment captures rich discourse that can be used to assess the process of student learning with tools from existing learning theory

Identifying fine-scale archaeological features using KH-9 HEXAGON mapping and panoramic camera images : evidence from Liangzhu Ancient City

Historical fine-scale information of archaeological landscapes is crucial in archaeological investigations. However, documenting such information using satellite sensor data prior to 2000 remains a daunting challenge. Images from the declassified archives of KH-9 HEXAGON (KH-9) cameras, including the panoramic camera system (PCS) and mapping camera system (MCS), offer fine-scale information about archaeological sites. However, noise, contrast distortion and the availability of only a single panchromatic band can limit their potential, particularly for identifying features in subtropical climates within heterogeneous landscape types. This paper focuses on developing a novel multifaceted analytical framework with two components: image pre-processing and feature identification. The image pre-processing component is divided into two steps. First, a trained stationary wavelet transform (SWT) based on the normalized sill (NS) is developed to not only de-noises the image, but also preserve its original image characteristics. Then, the contrast of the de-noised images is optimized by the multi-resolution Top-hat (MTH) using multi-scale information. In the feature identification component, the MCS image is analysed using spatial colour composite write function memory (SCCWFM) and spatial novelty detection (SND). An ultra-fine spatial three-dimensional colour composite (UFSTCC) image and ultra-fine spatial digital surface model (UFSDSM) are produced to aid interpretation of the KH-9 PCS images. The proposed processing pipelines were tested on KH-9 MCS and PCS images of the World Heritage site at Liangzhu Ancient City (LAC) in China, which is characterized by a subtropical climate and a heterogeneous landscape types. The proposed pre-processing pipeline improved considerably the appearance of these images across the LAC landscape while maintaining the original image information. The developed digital analytical approaches for KH-9 PCS and MCS images facilitated straightforward identification of archaeological features in the LAC. The proposed framework has the potential to increase exploitation of the available KH-9 images in archaeological applications

A Grounded Qualitative Analysis of the Effect of a Focus Group on Design Process in a Virtual Internship

A key component associated with the development of an entrepreneurial mindset is the ability to understand customerneeds and consider this when developing a product. This study sought to understand whether the inclusion of a customerfocus group as part of a virtual internship created any differences in the design processes of sophomore engineeringstudents (114 students). The Nephrotex virtual internship requires that students design a dialysis membrane by optimizinga selection of four components: membrane polymer, polymerization process, processing surfactant, and carbon nanotubepercentage. We found that sophomores who engaged in a focus group during the virtual internship Nephrotex showed(statistically) equal focus on cost versus technical measures of design performance during the focus group. Despite this,design cost was lower in the section that participated in a focus group, with no decrease in product quality. This indicatesthat customer voice may be an important factor in decreasing product cost. We also found that sophomore studentsprioritized their interviewing of customers within the focus group towards end users, such as the patient and nephrologist.Qualitative analysis of sophomore responses demonstrated that they found utility in the focus group (30% of participants)but did not necessarily believe that the customers had useful knowledge of the relevant design attributes (17% ofparticipants). Such realizations may have contributed to the equivalent quality and decreased costs associated with thedesigns of sophomores who participated in a focus group

Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network.

BACKGROUND: Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored. METHODS: We took a hypothesis-driven approach using available genome-wide datasets to identify genetic variants regulating gene expression in the TNF superfamily cytokine signalling network and the association of these variants with autoimmune and autoinflammatory disease. Using paired gene expression and genetic data, we identified genetic variants associated with gene expression, expression quantitative trait loci (eQTLs), in four peripheral blood cell subsets. We then examined whether eQTLs were dependent on gene expression level or the presence of active enhancer chromatin marks. Using these eQTLs as genetic markers of the TNF superfamily signalling network, we performed targeted gene set association analysis in eight autoimmune and autoinflammatory disease genome-wide association studies. RESULTS: Comparison of TNF superfamily network gene expression and regulatory variants across four leucocyte subsets revealed patterns that differed between cell types. eQTLs for genes in this network were not dependent on absolute gene expression levels and were not enriched for chromatin marks of active enhancers. By examining autoimmune disease risk variants among our eQTLs, we found that risk alleles can be associated with either increased or decreased expression of co-stimulatory TNF superfamily cytokines, receptors or downstream signalling molecules. Gene set disease association analysis revealed that eQTLs for genes in the TNF superfamily pathway were associated with six of the eight autoimmune and autoinflammatory diseases examined, demonstrating associations beyond single genome-wide significant hits. CONCLUSIONS: This systematic analysis of the influence of regulatory genetic variants in the TNF superfamily network reveals widespread and diverse roles for these cytokines in susceptibility to a number of immune-mediated diseases.The Intramural Research Program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and the National Library of Medicine of the US National Institutes of Health (Intramural Research Program) , Wellcome Trust (080327/Z/06/Z, 087007/Z/08/Z, 094227/Z/10/Z, Clinical PhD Programme, 079895, 076113 and 085475) , Medical Research Council (G0400929) , National Institute for Health Research , National Institutes of Health (Oxford-Cambridge Scholars Program) , Istanbul University Research Fund and UK Behcet’s Syndrome Society.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13073-016-0329-

Linking Type and Extent of Head Trauma to Cavum Septum Pellucidum in Older Adults With and Without Alzheimer Disease and Related Dementias

Background and objectives: Cavum septum pellucidum (CSP) is a common but nonspecific MRI finding in individuals with prior head trauma. The type and extent of head trauma related to CSP, CSP features specific to head trauma, and the impact of brain atrophy on CSP are unknown. We evaluated CSP cross-sectionally and longitudinally in healthy and clinically impaired older adults who underwent detailed lifetime head trauma characterization. Methods: This is an observational cohort study of University of California, San Francisco Memory and Aging Center participants (healthy controls [HCs], those with Alzheimer disease or related dementias [ADRDs], subset with traumatic encephalopathy syndrome [TES]). We characterized traumatic brain injury (TBI) and repetitive head impacts (RHI) through contact/collision sports. Study groups were no RHI/TBI, prior TBI only, prior RHI only, and prior RHI + TBI. We additionally looked within TBI (1, 2, or 3+) and RHI (1-4, 5-10, and 11+ years). All underwent baseline MRI, and 67% completed a second MRI (median follow-up = 5.4 years). CSP measures included grade (0-4) and length (millimeters). Groups were compared on likelihood of CSP (logistic regression, odds ratios [ORs]) and whether CSP length discriminated groups (area under the curve [AUC]). Results: Our sample included 266 participants (N = 160 HCs, N = 106 with ADRD or TES; age 66.8 ± 8.2 years, 45.3% female). Overall, 123 (49.8%) participants had no RHI/TBI, 52 (21.1%) had TBI only, 41 (16.6%) had RHI only, 31 (12.6%) had RHI + TBI, and 20 were classified as those with TES (7.5%). Compared with no RHI/TBI, RHI + TBI (OR 3.11 [1.23-7.88]) and TES (OR 11.6 [2.46-54.8]) had greater odds of CSP. Approximately 5-10 years (OR 2.96 [1.13-7.77]) and 11+ years of RHI (OR 3.14 [1.06-9.31]) had higher odds of CSP. CSP length modestly discriminated participants with 5-10 years (AUC 0.63 [0.51-0.75]) and 11+ years of prior RHI (AUC 0.69 [0.55-0.84]) from no RHI/TBI (cut point = 6 mm). Strongest effects were noted in analyses of American football participation. Longitudinally, CSP grade was unchanged in 165 (91.7%), and length was unchanged in 171 (95.5%) participants. Discussion: Among older adults with and without neurodegenerative disease, risk of CSP is driven more by duration (years) of RHI, especially American football, than number of TBI. CSP length (≥6 mm) is relatively specific to individuals who have had substantial prior RHI. Neurodegenerative disease and progressive atrophy do not clearly influence development or worsening of CSP

Bayesian estimation of incomplete data using conditionally specified priors

In this paper, a class of conjugate prior for estimating incomplete count data based on a broad class of conjugate prior distributions is presented. The new class of prior distributions arises from a conditional perspective, making use of the conditional specification methodology and can be considered as the generalisation of the form of prior distributions that have been used previously in the estimation of in- complete count data well. Finally, some examples of simulated and real data are given

Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome

Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell-type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knock-in mice carrying frequent RTT-associated mutations (encoding T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons. We found that most gene-expression changes were largely specific to each RTT-associated mutation and cell type. Lowly expressed cell-type-enriched genes were preferentially disrupted by MeCP2 mutations, with upregulated and downregulated genes reflecting distinct functional categories. Subcellular RNA analysis in MeCP2-mutant neurons further revealed reductions in the nascent transcription of long genes and uncovered widespread post-transcriptional compensation at the cellular level. Finally, we overcame X-linked cellular mosaicism in female RTT models and identified distinct gene-expression changes between neighboring wild-type and mutant neurons, providing contextual insights into RTT etiology that support personalized therapeutic interventions