Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species.

The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.

Towards Implementation of OMOP in a German University Hospital Consortium.

BACKGROUND: In 2015, the German Federal Ministry of Education and Research initiated a large data integration and data sharing research initiative to improve the reuse of data from patient care and translational research. The Observational Medical Outcomes Partnership (OMOP) common data model and the Observational Health Data Sciences and Informatics (OHDSI) tools could be used as a core element in this initiative for harmonizing the terminologies used as well as facilitating the federation of research analyses across institutions. OBJECTIVE: To realize an OMOP/OHDSI-based pilot implementation within a consortium of eight German university hospitals, evaluate the applicability to support data harmonization and sharing among them, and identify potential enhancement requirements. METHODS: The vocabularies and terminological mapping required for importing the fact data were prepared, and the process for importing the data from the source files was designed. For eight German university hospitals, a virtual machine preconfigured with the OMOP database and the OHDSI tools as well as the jobs to import the data and conduct the analysis was provided. Last, a federated/distributed query to test the approach was executed. RESULTS: While the mapping of ICD-10 German Modification succeeded with a rate of 98.8% of all terms for diagnoses, the procedures could not be mapped and hence an extension to the OMOP standard terminologies had to be made.Overall, the data of 3 million inpatients with approximately 26 million conditions, 21 million procedures, and 23 million observations have been imported.A federated query to identify a cohort of colorectal cancer patients was successfully executed and yielded 16,701 patient cases visualized in a Sunburst plot. CONCLUSION: OMOP/OHDSI is a viable open source solution for data integration in a German research consortium. Once the terminology problems can be solved, researchers can build on an active community for further development.

Secure Secondary Use of Clinical Data with Cloud-based NLP Services. Towards a Highly Scalable Research Infrastructure.

OBJECTIVES: The secondary use of clinical data provides large opportunities for clinical and translational research as well as quality assurance projects. For such purposes, it is necessary to provide a flexible and scalable infrastructure that is compliant with privacy requirements. The major goals of the cloud4health project are to define such an architecture, to implement a technical prototype that fulfills these requirements and to evaluate it with three use cases. METHODS: The architecture provides components for multiple data provider sites such as hospitals to extract free text as well as structured data from local sources and de-identify such data for further anonymous or pseudonymous processing. Free text documentation is analyzed and transformed into structured information by text-mining services, which are provided within a cloud-computing environment. Thus, newly gained annotations can be integrated along with the already available structured data items and the resulting data sets can be uploaded to a central study portal for further analysis. RESULTS: Based on the architecture design, a prototype has been implemented and is under evaluation in three clinical use cases. Data from several hundred patients provided by a University Hospital and a private hospital chain have already been processed. CONCLUSIONS: Cloud4health has shown how existing components for secondary use of structured data can be complemented with text-mining in a privacy compliant manner. The cloud-computing paradigm allows a flexible and dynamically adaptable service provision that facilitates the adoption of services by data providers without own investments in respective hardware resources and software tools.

Desmoid tumour (aggressive fibromatosis) of the colon mimics malignancy on dual time-point 18F-FDG PET/CT imaging.

A 58-year-old female who presented with a lower gastrointestinal bleed was referred for an (18)F-fluorodeoxyglucose (FDG) positron emission tomography (PET)/CT after a colonoscopy revealed a submucosal mass in the ascending colon. The PET/CT confirmed the presence of an FDG-avid mass in the ascending colon with no other FDG-avid abnormalities. Dual time-point imaging was performed and showed a significant increase in FDG uptake in the mass, which raised strong suspicion of a colon malignancy. Although an initial biopsy of the mass did not show evidence of neoplasia, a decision was made to proceed with a right hemicolectomy based on high clinical and imaging suspicion of malignancy. Histological evaluation of the hemicolectomy revealed a benign colon desmoid tumour.

Quantitative Photoacoustic Image Reconstruction using Fluence Dependent Chromophores.

In biomedical photoacoustic imaging the images are proportional to the absorbed optical energy density, and not the optical absorption, which makes it difficult to obtain a quantitatively accurate image showing the concentration of a particular absorbing chromophore from photoacoustic measurements alone. Here it is shown that the spatially varying concentration of a chromophore whose absorption becomes zero above a threshold light fluence can be estimated from photoacoustic images obtained at increasing illumination strengths. This technique provides an alternative to model-based multiwavelength approaches to quantitative photoacoustic imaging, and a new approach to photoacoustic molecular and functional imaging.

In vivo high-resolution 3D photoacoustic imaging of superficial vascular anatomy.

The application of a photoacoustic imaging instrument based upon a Fabry-Perot polymer film ultrasound sensor to imaging the superficial vasculature is described. This approach provides a backward mode-sensing configuration that has the potential to overcome the limitations of current piezoelectric based detection systems used in superficial photoacoustic imaging. The system has been evaluated by obtaining non-invasive images of the vasculature in human and mouse skin as well as mouse models of human colorectal tumours. These studies showed that the system can provide high-resolution 3D images of vascular structures to depths of up to 5 mm. It is considered that this type of instrument may find a role in the clinical assessment of conditions characterized by changes in the vasculature such as skin tumours and superficial soft tissue damage due to burns, wounds or ulceration. It may also find application in the characterization of small animal cancer models where it is important to follow the tumour vasculature over time in order to study its development and/or response to therapy.

Up-regulation of hypertonicity-activated myo-inositol transporter SMIT1 by the cell volume-sensitive protein kinase SGK1.

Mechanisms of regulatory cell volume increase following cell shrinkage include accumulation of organic osmolytes such as betaine, taurine, sorbitol, glycerophosphorylcholine (GPC) and myo-inositol. Myo-inositol is taken up by the sodium-myo-inositol-transporter SMIT1 (SLC5A3) expressed in a wide variety of cell types. Hypertonicity induces the transcription of the SMIT1 gene upon binding of the transcription factor tonicity enhancer binding protein (TonEBP) to tonicity responsive enhancers (TonE) in the SMIT1 promoter region. However, little is known about post-translational regulation of the carrier protein. In this study we show that SMIT1 is modulated by the serum- and glucocorticoid-inducible kinase SGK1, a protein genomically up-regulated by hypertonicity. As demonstrated by two-electrode voltage-clamp in the Xenopus oocyte expression system, SMIT1-mediated myo-inositol-induced currents are up-regulated by coexpression of wild type SGK1 and constitutively active (S422D)SGK1 but not by inactive (K127N)SGK1. The increase in SMIT1 activity is due to an elevated cell surface expression of the carrier while its kinetic properties remain unaffected. According to the decay of SMIT1 activity in the presence of brefeldin A, SGK1 stabilizes the SMIT1 protein in the plasma membrane. The SGK isoforms SGK2, SGK3 and the closely related protein kinase B (PKB) are similarly capable of activating SMIT1 activity. SMIT1-mediated currents are decreased by coexpression of the ubiquitin-ligase Nedd4-2, an effect counteracted by additional coexpression of SGK1. In conclusion, the present observations disclose SGK isoforms and protein kinase B as novel regulators of SMIT1 activity.

Regulation of the epithelial calcium channel TRPV6 by the serum and glucocorticoid-inducible kinase isoforms SGK1 and SGK3.

Epithelial calcium (re)absorption is mediated by TRPV5 and TRPV6 channels. TRPV5 is modulated by the SGK1 kinase, a process requiring the PDZ-domain containing scaffold protein NHERF2. The present study explored whether TRPV6 is similarly regulated by SGKs and the scaffold proteins NHERF1/2. In Xenopus oocytes, SGKs activate TRPV6 by increasing its plasma membrane abundance. Deletion of the putative PDZ binding motif on TRPV6 did not abolish channel activation by SGKs. Furthermore, coexpression of neither NHERF1 nor NHERF2 affected TRPV6 or potentiated the SGKs stimulating effect. The present observations disclose a novel TRPV6 regulatory mechanism which presumably participates in calcium homeostasis.

Four consecutive renal transplantations in a patient with adenine phosphoribosyltransferase deficiency.

We report a patient with complete adenine phosphoribosyltransferase deficiency and urolithiasis, in whom 4 consecutive cadaveric renal transplantations were performed; 2,8-dihydroxyadenine crystal nephropathy recurred within weeks in the first and second graft when the patient was not treated with allopurinol immediately after transplantation. In the third graft, recurrence of disease could be prevented by immediate allopurinol treatment. This graft was lost due to chronic allograft nephropathy without significant crystal deposition. After a fourth transplantation, again without initial allopurinol, the disease recurred following an initial vascular rejection. Addition of allopurinol significantly improved renal function of the 2nd and 4th graft. This case indicates that outcome of renal transplantation in patients with adenine phosphoribosyltransferase deficiency critically depends on immediate postoperative pharmacotherapy with allopurinol, which is able to prevent 2,8-dihydroxyadenine nephropathy in the graft. Furthermore, rapid recurrence of disease without allopurinol seems to be triggered by delayed graft function and acute rejection.

Re-evaluation of differential phase contrast (DPC) in a scanning laser microscope using a split detector as an alternative to differential interference contrast (DIC) optics.

In this paper, differential phase imaging (DPC) with transmitted light is implemented by adding a suitable detection system to a standard commercially available scanning confocal microscope. DPC, a long-established method in scanning optical microscopy, depends on detecting the intensity difference between opposite halves or quadrants of a split photodiode detector placed in an aperture plane. Here, DPC is compared with scanned differential interference contrast (DIC) using a variety of biological specimens and objective lenses of high numerical aperture. While DPC and DIC images are generally similar, DPC seems to have a greater depth of field. DPC has several advantages over DIC. These include low cost (no polarizing or strain-free optics are required), absence of a double scanning spot, electronically variable direction of shading and the ability to image specimens in plastic dishes where birefringence prevents the use of DIC. DPC is also here found to need 20 times less laser power at the specimen than DIC.

Photothermal determination of optical coefficients of tissue phantoms using an optical fibre probe.

The absorption and reduced scattering coefficients of turbid tissue phantoms have been determined from photothermal measurements made using an optical fibre probe. The thermal sensor was a thin polymer film positioned at the end of a multimode optical fibre. The film was illuminated by the output of a continuous-wave diode laser and formed the cavity of a low-finesse Fabry-Perot interferometer. Low energy laser pulses, launched into the fibre and passed through the film, produced an abrupt temperature rise in the target tissue, which was placed in contact with the film. The subsequent conduction of heat into the film caused a change in its optical thickness and hence the reflected intensity. The absorption and reduced scattering coefficients of gelatine tissue phantoms of known optical properties were determined from the measurements using a numerical model of photothermal signal generation and maximum a posteriori estimation. The determined optical coefficients were in good agreement with the known values. The results showed that the probe can be used for the determination of optical coefficients provided the thermal coefficients of the target tissue are known with low uncertainty.

Extrahepatic synthesis of complement proteins in inflammation.

The demonstration of local complement protein synthesis leads to speculation as to the biological significance of this phenomenon. A narrative review is provided to illuminate several queries. It is difficult to establish a causal role for the locally produced complement because participation of systemic complement cannot be excluded. It is also difficult to discern whether local complement synthesis is a beneficial response to an inflammatory event or whether it promotes tissue damage. Finally, it remains to be seen if the roles of local and systemic complement differ in these respects. Extrahepatic expression of complement components of the activation pathways may provide a rapid response to microbial invasion. Once produced and activated, these proteins evoke a phlogistic response composed of cells and soluble mediators of inflammation. Many cells, not only synthesize complement proteins, but can also be stimulated via their complement receptors. This positive feedback may enhance local immune defense, especially in organs isolated from plasma components. In addition, local environmental factors in different organs may differentially regulate complement synthesis. These factors may include pro-inflammatory molecules and non-immune effectors, such as tissue ischemia/reoxygenation and drugs. Local complement dysregulation due to inhibition of activity of a complement regulatory component was shown to cause disease and restoration of the capacity to regulate the complement pathway restored health. Extrahepatic complement synthesis may also modulate local cellular responses, as to decrease detrimental damage of the inflammatory reaction. The demonstration that complement proteins play a significant role in the clearance of apoptotic cells suggests that local synthesis and activation of complement may contribute not only to tissue damage but also to tissue repair.

Prediction of mortality and timing of referral for lung transplantation in cystic fibrosis patients.

Lung transplantation (Tx) is an optional treatment for cystic fibrosis (CF) patients with end-stage lung disease. The decision to place a patient on the Tx waiting list is frequently complex, difficult, and controversial. This study evaluated the current criteria for lung Tx and assessed additional parameters that may identify CF patients at high risk of death. Data were extracted from the medical records of 392 CF patients. Forty of these patients had a forced expiratory volume in 1 s (FEV(1)) less than 30% predicted, and nine of these 40 patients were transplanted. A comparison was performed between the survival of those transplanted (n = 9) and those not transplanted (n = 31), by means of Kaplan-Meier survival curves. The influence on survival of age, gender, nutritional status, sputum aspergillus, diabetes mellitus, recurrent hemoptysis, oxygen use, and the decline rate of FEV(1), were investigated by means of univariate and multivariate analyses. The rate of decline of FEV(1) was evaluated employing the linear regression model. CF patients with a FEV(1)< 30% and who did not receive a lung transplant had survived longer than CF patients who did receive a lung transplant (median survival 7.33 vs. 3.49 yr, 5-yr survival 73% vs. 29%). Two factors--rate of decline in FEV(1) values and age < 15 yr--were found to influence the mortality rate, while the other parameters examined did not. Our results indicate that the current criterion of FEV(1)< 30% predicted, alone is not sufficiently sensitive to predict the mortality rate in CF patients and time of referral for Tx, as many of these patients survive for long periods of time. Additional criteria to FEV(1)< 30%, should include rapidly declining FEV(1) values and age < 15 yr.

Transillumination of the palm for venipuncture in infants.

AIM: To assess the efficacy of transillumination of the palm of the hand in establishing venous access in small infants. METHODS: One hundred infants aged 2 to 36 months were considered for venipuncture under transillumination following failure to find an accessible vein or a failed venipuncture attempt. RESULTS: In 40 of the 100 infants, a vein was visible with transillumination. In 22 of these children, previous attempts to achieve a venous line failed (mean number of failed venipunctures 2.11 +/- 0.6) and in 18 infants, no vein could be identified. Using transillumination, venous access was established with just one venipuncture in 39 of the 40 patients. CONCLUSIONS: Transillumination of the palm can aid in establishing venous access in infants. This can be easily carried out using a common otoscope.

Cellular localization of complement C3 and C4 transcripts in intestinal specimens from patients with Crohn's disease.

It has been suggested that the increase in C3 and C4 levels in jejunal perfusates of patients with Crohn's disease (CD) results from local intestinal synthesis of complement. The present study evaluated the expression of these complement genes in inflamed tissues from patients with CD. Surgically resected specimens from patients with CD and control tissue obtained from subjects with adenocarcinoma of the colon were evaluated for C3 and C4 gene expression by the use of 35S-labelled anti-sense RNA probes. All tissue samples, diseased and normal tissue, expressed C4 mRNA throughout in the intestinal epithelium. C3 mRNA was not detected in epithelial cells in histologically normal tissue, but in diseased specimens there was a focal distribution of C3 mRNA in epithelial cells of the crypts, but not in villous epithelium. Focal C3 gene expression correlated with crypt abscess formation and the presence of polymorphonuclear leucocytes in the lumen of the crypts. In addition, C3 mRNA was also found in macrophages of the submucosa. These macrophages were CD68+, fusiform with faint cytoplasm and morphologically different from the large rounded lamina propria macrophages, which do not express C3 mRNA. Multinucleated giant cells did not express either C3 or C4 genes. In addition to its presence in intestinal epithelium, C4 mRNA was also expressed in mast cells, which however did not express C3 mRNA. These observations identify cells in the intestinal wall expressing complement genes and support the hypothesis that there is local regulated production of complement in the intestine of patients with CD, and subsequent complement activation may contribute to the inflammatory process.

Local complement genes expression in the mammary gland: effect of gestation and inflammation.

Complement components in breast milk may enhance the local immune response in the gut of infants. In this study, we investigated the expression of complement genes in the mammary gland and attempted to determine possible regulatory mechanisms. We have studied the expression of C3, C4, factor B, and HLA-DRalpha mRNA by in situ hybridization in gestational mammary gland specimens and compared these findings to those in breast tissue affected with an inflammatory process, lactating adenoma or idiopathic gynecomastia. In normal resting breast, only C4 mRNA was noted in some ductal epithelium. In gestational mammary gland, there was a diffuse expression of C4, C3, and factor B mRNA in the epithelial cells of the acini. A similar pattern of complement gene expression was found in localized areas of an infectious inflammatory process. In addition, in the inflammatory specimens, there was also expression of C3 mRNA in infiltrating macrophages (CD 68 positive cells). In gynecomastia, C4 mRNA was noted in ductal epithelium, and there was a marked increased expression of C3 mRNA in the proliferating epithelium of the lactating adenoma. HLA-DRalpha was observed only in macrophages involved in the inflammatory response. Our findings, which reflect the hormonal and inflammatory events in vivo, provide new insights as to in situ complement gene expression.

Near-infrared optical properties of ex vivo human uterus determined by the Monte Carlo inversion technique.

The optical properties, absorption (mua) and reduced scattering coefficient (mu's), of ex vivo human myometrium and leiomyoma (fibroid) have been determined by the Monte Carlo inversion technique over the wavelength range 600-1000 nm. This region is currently of interest for new, minimal-access, surgical laser procedures such as photodynamic therapy (PDT) for abnormalities of the uterus, and interstitial laser photocoagulation (ILP) for the thermal ablation of fibroids. In the region 630-675 nm (corresponding to PDT), the optical coefficients of myometrium are mua = 0.041+/-0.012 mm(-1) and mu's = 1.37+/-0.19 mm(-1). For the wavelength range 800-1000 nm (associated with infrared lasers for ILP), the optical coefficients of fibroid were found to be mua = 0.020+/-0.003 mm(-1) and mu's = 0.56+/-0.03 mm(-1). Overall, the optical properties of fibroid were found to be lower than myometrium, and this was attributed to the differences in both anatomy and vascularity. The results show that PDT for ablation of the uterine endometrium is most unlikely to affect any tissues beyond the myometrium, and that the region around 800 nm is the most effective for ablation of fibroids using ILP as the penetration depth of light is greatest at this wavelength.