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An electric field propagating along a non-planar path can acquire geometric phases. Previously, geometric phases have been linked to spin redirection and independently to spatial mode transformation, resulting in the rotation of polarisation and intensity profiles, respectively. We investigate the non-planar propagation of scalar and vector light fields and demonstrate that polarisation and intensity profiles rotate by the same angle. The geometric phase acquired is proportional to j = ℓ + σ, where ℓ is the topological charge and σ is the helicity. Radial and azimuthally polarised beams with j = 0 are eigenmodes of the system and are not affected by the geometric path. The effects considered here are relevant for systems relying on photonic spin Hall effects, polarisation and vector microscopy, as well as topological optics in communication systems.

Background & Aims: Interactions between mucosal cell types, environmental stressors, and intestinal microbiota contribute to pathogenesis in inflammatory bowel disease (IBD). Here, we applied metaproteomics of the mucosalâluminal interface to study the disease-related biology of the human colonic mucosa. Methods: We recruited a discovery cohort of 51 IBD and non-IBD subjects endoscopically sampled by mucosal lavage at 6 colonic regions, and a validation cohort of 38 no-IBD subjects. Metaproteome data sets were produced for each sample and analyzed for association with colonic site and disease state using a suite of bioinformatic approaches. Localization of select proteins was determined by immunoblot analysis and immunohistochemistry of human endoscopic biopsy samples. Results: Co-occurrence analysis of the discovery cohort metaproteome showed that proteins at the mucosal surface clustered into modules with evidence of differential functional specialization (eg, iron regulation, microbial defense) and cellular origin (eg, epithelial or hemopoietic). These modules, validated in an independent cohort, were differentially associated spatially along the gastrointestinal tract, and 7 modules were associated selectively with non-IBD, ulcerative colitis, and/or Crohnâs disease states. In addition, the detailed composition of certain modules was altered in disease vs healthy states. We confirmed the predicted spatial and disease-associated localization of 28 proteins representing 4 different disease-related modules by immunoblot and immunohistochemistry visualization, with evidence for their distribution as millimeter-scale microgeographic mosaic. Conclusions: These findings suggest that the mucosal surface is a microgeographic mosaic of functional networks reflecting the local mucosal ecology, whose compositional differences in disease and healthy samples may provide a unique readout of physiologic and pathologic mucosal states. Keywords: Inflammatory Bowel Disease, Mucosal, Networks, Ecology, Metaproteomics

Abnormalities of the intestinal microbiota are implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC), two spectra of inflammatory bowel disease (IBD). However, the high complexity and low inter-individual overlap of intestinal microbial composition are formidable barriers to identifying microbial taxa representing this dysbiosis. These difficulties might be overcome by an ecologic analytic strategy to identify modules of interacting bacteria (rather than individual bacteria) as quantitative reproducible features of microbial composition in normal and IBD mucosa. We sequenced 16S ribosomal RNA genes from 179 endoscopic lavage samples from different intestinal regions in 64 subjects (32 controls, 16 CD and 16 UC patients in clinical remission). CD and UC patients showed a reduction in phylogenetic diversity and shifts in microbial composition, comparable to previous studies using conventional mucosal biopsies. Analysis of weighted co-occurrence network revealed 5 microbial modules. These modules were unprecedented, as they were detectable in all individuals, and their composition and abundance was recapitulated in an independent, biopsy-based mucosal dataset 2 modules were associated with healthy, CD, or UC disease states. Imputed metagenome analysis indicated that these modules displayed distinct metabolic functionality, specifically the enrichment of oxidative response and glycan metabolism pathways relevant to host-pathogen interaction in the disease-associated modules. The highly preserved microbial modules accurately classified IBD status of individual patients during disease quiescence, suggesting that microbial dysbiosis in IBD may be an underlying disorder independent of disease activity. Microbial modules thus provide an integrative view of microbial ecology relevant to IBD.

Aberrant interactions between the host and the intestinal bacteria are thought to contribute to the pathogenesis of many digestive diseases. However, studying the complex ecosystem at the human mucosal-luminal interface (MLI) is challenging and requires an integrative systems biology approach. Therefore, we developed a novel method integrating lavage sampling of the human mucosal surface, high-throughput proteomics, and a unique suite of bioinformatic and statistical analyses. Shotgun proteomic analysis of secreted proteins recovered from the MLI confirmed the presence of both human and bacterial components. To profile the MLI metaproteome, we collected 205 mucosal lavage samples from 38 healthy subjects, and subjected them to high-throughput proteomics. The spectral data were subjected to a rigorous data processing pipeline to optimize suitability for quantitation and analysis, and then were evaluated using a set of biostatistical tools. Compared to the mucosal transcriptome, the MLI metaproteome was enriched for extracellular proteins involved in response to stimulus and immune system processes. Analysis of the metaproteome revealed significant individual-related as well as anatomic region-related (biogeographic) features. Quantitative shotgun proteomics established the identity and confirmed the biogeographic association of 49 proteins (including 3 functional protein networks) demarcating the proximal and distal colon. This robust and integrated proteomic approach is thus effective for identifying functional features of the human mucosal ecosystem, and a fresh understanding of the basic biology and disease processes at the MLI.

Abstract Background The purpose of this study was to determine whether some of the clinical features of fibromyalgia (FM) that patients would like to see improved aggregate into definable clusters. Methods Seven hundred and eighty-eight patients with clinically confirmed FM and baseline pain ≥40 mm on a 100 mm visual analogue scale ranked 5 FM clinical features that the subjects would most like to see improved after treatment (one for each priority quintile) from a list of 20 developed during focus groups. For each subject, clinical features were transformed into vectors with rankings assigned values 1-5 (lowest to highest ranking). Logistic analysis was used to create a distance matrix and hierarchical cluster analysis was applied to identify cluster structure. The frequency of cluster selection was determined, and cluster importance was ranked using cluster scores derived from rankings of the clinical features. Multidimensional scaling was used to visualize and conceptualize cluster relationships. Results Six clinical features clusters were identified and named based on their key characteristics. In order of selection frequency, the clusters were Pain (90%; 4 clinical features), Fatigue (89%; 4 clinical features), Domestic (42%; 4 clinical features), Impairment (29%; 3 functions), Affective (21%; 3 clinical features), and Social (9%; 2 functional). The "Pain Cluster" was ranked of greatest importance by 54% of subjects, followed by Fatigue, which was given the highest ranking by 28% of subjects. Multidimensional scaling mapped these clusters to two dimensions: Status (bounded by Physical and Emotional domains), and Setting (bounded by Individual and Group interactions). Conclusion Common clinical features of FM could be grouped into 6 clusters (Pain, Fatigue, Domestic, Impairment, Affective, and Social) based on patient perception of relevance to treatment. Furthermore, these 6 clusters could be charted in the 2 dimensions of Status and Setting, thus providing a unique perspective for interpretation of FM symptomatology.

Abstract Background It has been postulated that atypical and melancholic depression subtypes exist in depressed fibromyalgia (FM) patients, yet no study has empirically tested this hypothesis. The purpose of this study is to determine whether major depressive disorder (MDD) with atypical features and MDD with melancholic features occurs in a FM sample and to describe their demographic, clinical and diagnostic characteristics. Methods An observational cohort study using a descriptive cross-sectional design recruited a convenience sample of 76 outpatients with FM from an academic Rheumatology clinic and a community mental health practice. Diagnoses of FM were confirmed using the 1990 ACR classification guidelines. Diagnoses of MDD and diagnostic subtypes were determined using the DSM-IV-TR criteria. Clinical characteristics were measured using the Fibromyalgia Impact Questionnaire, Structured Interview Guide for the Hamilton Depression Rating Scale with Atypical Depression Supplement and other standardized instruments. Odds ratios were computed on subtype-specific diagnostic criteria. Correlations assessed associations between subtype diagnoses and diagnostic criteria. Results Of the 76 subjects with FM, 11.8% (n = 9) were euthymic, 52.6% (n = 40) met diagnostic criteria for MDD with atypical features and 35.6% (n = 27) for MDD with melancholic features. Groups did not differ on demographic characteristics except for gender (p = 0.01). The non-depressed and atypical groups trended toward having a longer duration of FM symptoms (18.05 yrs. ± 12.83; 20.36 yrs. ± 15.07) compared to the melancholic group (14.11 yrs. ± 8.82; p = 0.09). The two depressed groups experienced greater severity on all clinical features compared to the non-depressed group. The atypical group did not differ clinically from the melancholic group except the latter experienced greater depression severity (p = 0.001). The atypical group demonstrated the highest prevalence and correlations with atypical-specific diagnostic criteria: (e.g., weight gain/ increased appetite: OR = 3.5, p = 0.02), as did the melancholic group for melancholic-specific criteria: (e.g., anhedonia: OR = 20, p < 0.001). Conclusion Depressed fibromyalgia patients commonly experience both atypical and melancholic depressive features; however, in this study, atypical depression was 1.5 times more common than melancholic depression. This finding may have significant research and clinical implications.

Abstract Background This study explored the feasibility of using an Internet survey of people with fibromyalgia (FM), with a view to providing information on demographics, sources of information, symptoms, functionality, perceived aggravating factors, perceived triggering events, health care utilization, management strategies, and medication use. Methods A survey questionnaire was developed by the National Fibromyalgia Association (NFA) in conjunction with a task force of "experts in the field". The questionnaire underwent several rounds of testing to improve its face validity, content validity, clarity and readability before it was mounted on the internet. The questionnaire consisted of 121 items and is available online at the website of the National Fibromyalgia Association. Results The questionnaire was completed by 2,569 people. Most were from the United States, with at least one respondent from each of the 50 states. Respondents were predominantly middle-aged Caucasian females, most of whom had FM symptoms for ≥ 4 years. The most common problems were morning stiffness, fatigue, nonrestorative sleep, pain, concentration, and memory. Aggravating factors included: emotional distress, weather changes, insomnia, and strenuous activity. Respondents rated the most effective management modalities as rest, heat, pain medications, antidepressants, and hypnotics. The most commonly used medications were: acetaminophen, ibuprofen, naproxen, cyclobenzaprine, amitriptyline, and aspirin. The medications perceived to be the most effective were: hydrocodone preparations, aprazolam, oxycodone preparations, zolpidem, cyclobenzaprine, and clonazepam. Conclusion This survey provides a snap-shot of FM at the end of 2005, as reported by a self-selected population of people. This descriptive data has a heuristic function, in that it identifies several issues for further research, such as the prescribing habits of FM health care providers, the role of emotional precipitants, the impact of obesity, the significance of low back pain and the nature of FM related stiffness.

In the United States, extensive investments have been made to restore the ecological function and services of coastal marine habitats. Despite a growing body of science supporting coastal restoration, few studies have addressed the suite of societally enabling conditions that helped facilitate successful restoration and recovery efforts that occurred at meaningful ecological (i.e., ecosystem) scales, and where restoration efforts were sustained for longer (i.e., several years to decades) periods. Here, we examined three case studies involving large-scale and long-term restoration efforts including the seagrass restoration effort in Tampa Bay, Florida, the oyster restoration effort in the Chesapeake Bay in Maryland and Virginia, and the tidal marsh restoration effort in San Francisco Bay, California. The ecological systems and the specifics of the ecological restoration were not the focus of our study. Rather, we focused on the underlying social and political contexts of each case study and found common themes of the factors of restoration which appear to be important for maintaining support for large-scale restoration efforts. Four critical elements for sustaining public and/or political support for large-scale restoration include: (1) resources should be invested in building public support prior to significant investments into ecological restoration; (2) building political support provides a level of significance to the recovery planning efforts and creates motivation to set and achieve meaningful recovery goals; (3) recovery plans need to be science-based with clear, measurable goals that resonate with the public; and (4) the accountability of progress toward reaching goals needs to be communicated frequently and in a way that the general public comprehends. These conclusions may help other communities move away from repetitive, single, and seemingly unconnected restoration projects towards more large-scale, bigger impact, and coordinated restoration efforts., Competing Interests: Conflicts of Interest: The authors declare no conflict of interest.

Coastal ecosystems are under pressure from a vast array of anthropogenic stressors, including development and climate change, resulting in significant habitat losses globally Conservation policies are often implemented with the intent of reducing habitat loss. However, losses already incurred will require restoration if ecosystem functions and services are to be recovered. The United States has a long history of wetland loss and recognizes that averting loss requires a multi-pronged approach including mitigation for regulated activities and non-mitigation (voluntary herein) restoration. The 1989 "No Net Loss" (NNL) policy stated the Federal government's intent that losses of wetlands would be offset by at least as many gains of wetlands. However, coastal wetlands losses result from both regulated and non-regulated activities. We examined the effectiveness of Federally funded, voluntary restoration efforts in helping avert losses of coastal wetlands by assessing: (1) What are the current and past trends in coastal wetland change in the U.S.?; and (2) How much and where are voluntary restoration efforts occurring? First, we calculated palustrine and estuarine wetland change in U.S. coastal shoreline counties using data from NOAA's Coastal Change Analysis Program, which integrates both types of potential losses and gains. We then synthesized available data on Federally funded, voluntary restoration of coastal wetlands. We found that from 1996 to 2010, the U.S. lost 139,552 acres (~565 km 2 ) of estuarine wetlands (2.5% of 1996 area) and 336,922 acres (~1,363 km 2 ) of palustrine wetlands (1.4%). From 2006 to 2015, restoration of 145,442 acres (~589 km 2 ) of estuarine wetlands and 154,772 acres (~626 km 2 ) of palustrine wetlands occurred. Further, wetland losses and restoration were not always geographically aligned, resulting in local and regional "winners" and "losers." While these restoration efforts have been considerable, restoration and mitigation collectively have not been able to keep pace with wetland losses; thus, reversing this trend will likely require greater investment in coastal habitat conservation and restoration efforts. We further conclude that "area restored," the most prevalent metric used to assess progress, is inadequate, as it does not necessarily equate to restoration of functions. Assessing the effectiveness of wetland restoration not just in the U.S., but globally, will require allocation of sufficient funding for long-term monitoring of restored wetland functions, as well as implementation of standardized methods for monitoring data collection, synthesis, interpretation, and application., Competing Interests: Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

This report describes five cases of myocarditis in the common cuttlefish, Sepia officinalis. Both the systemic heart and the branchial hearts exhibited inflammatory lesions. Vibrio species were isolated from four of these cases.

New nephrons developed in goldfish, Carassius auratus, several weeks following hexachlorobutadiene-induced (HCBD) nephrotoxicity. Basophilic clusters of presumptive nephrogenic cells incorporated 5-bromo, 2'deoxyuridine (BrdU) one week after HCBD injection, indicating initiation of DNA synthesis. These clusters, like renal vesicles in the developing kidney, elongated, fused with collecting ducts and developed into immature nephrons during the next 2 weeks. Stereologic quantification showed the volume percent of the kidney occupied by the developing nephrons was greater in HCBD-treated fish 2, 3, 4, and 10 weeks after injection than in the control fish. The presence of large numbers of developing nephrons may provide a marker for renal injury in fish from contaminated waterways.

The cellular immune response of rainbow trout, Salmo gairdneri, to sheep erythrocytes was investigated. Both the primary and secondary responses were measured using the migration inhibition factor (MIF), antigen-binding (ABC), and plaque-forming cell (PFC) assays. These immune function assays provide measures of both T and B cell activity. The kinetics of these three responses at 16 degrees C were determined by sampling fish over an 18 day period for the primary response and a ten day period for the secondary response. The peak MIF response occurred two days after injection, while the primary peak PFC response was observed 14 days post-injection. Two ABC peaks were observed in the primary response, one at four days and one at ten days after injection. In the secondary response the peak ABC response was observed four days and the peak PFC response six days post-inoculation. The possible interrelationships of the various cell populations are discussed.

Necropsy examination of moribund or dead specimens is an essential step in diagnosing fish diseases. This article discusses basic anatomy and necropsy procedures. A large part of the article has been devoted to methods of procuring samples for laboratory analysis and histologic examination. To determine which findings are responsible for the mortalities, the entire case history and gross necropsy findings must be reviewed. Careful observations made during the necropsy examination provide valuable information immediately, as well as later on in the interpretation of laboratory data.

The effect of manipulating dietary levels of cortisol and metyrapone on peripheral concentrations of serum cortisol was examined in rainbow trout, Salmo gairdneri. Fish were fed 0, 10, 20, 30, 40 or 50 mg/kg body weight/day of metyrapone or cortisol for 7 days. All levels of cortisol tested increased peripheral levels of serum cortisol. Feeding a level of 30-40 mg/kg body weight/day of metyrapone depressed serum cortisol. We describe, herein, a noninvasive technique for suppression or stimulation of serum cortisol in rainbow trout.

Two cases of retinoblastoma in fish are described. The neoplasms occurred in a porkfish (Anisotremus virginicus, Linnaeus) and in a brown bullhead (Ictalurus nebulosus, Lesueur).