Building a potential wetland restoration indicator for the contiguous United States

Wetlands provide key functions in the landscape from improving water quality, to regulating flows, to providing wildlife habitat. Over half of the wetlands in the contiguous United States (CONUS) have been converted to agricultural and urban land uses. However, over the last several decades, research has shown the benefits of wetlands to hydrologic, chemical, biological processes, spurring the creation of government programs and private initiatives to restore wetlands. Initiatives tend to focus on individual wetland creation, yet the greatest benefits are achieved when strategic restoration planning occurs across a watershed or multiple watersheds. For watershed-level wetland restoration planning to occur, informative data layers on potential wetland areas are needed. We created an indicator of potential wetland areas (PWA), using nationally available datasets to identify characteristics that could support wetland ecosystems, including: poorly drained soils and low-relief landscape positions as indicated by a derived topographic data layer. We compared our PWA with the National Wetlands Inventory (NWI) from 11 states throughout the CONUS to evaluate their alignment. The state-level percentage of NWI-designated wetlands directly overlapping the PWA ranged from 39 to 95%. When we included NWI that was immediately adjacent to the overlapping NWI, our range of correspondence to NWI ranged from 60 to 99%. Wetland restoration is more likely on certain landscapes (e.g., agriculture) than others due to the lack of substantive infrastructure and the potential for the restoration of hydrology; therefore, we combined the National Land Cover Dataset (NLCD) with the PWA to identify potentially restorable wetlands on agricultural land (PRW-Ag). The PRW-Ag identified a total of over 46 million ha with the potential to support wetlands. The largest concentrations of PRW-Ag occurred in the glaciated corn belt of the upper Mississippi River from Ohio to the Dakotas and in the Mississippi Alluvial Valley. The PRW-Ag layer could assist land managers in identifying sites that may qualify for enrollment in conservation programs, where planners can coordinate restoration efforts, or where decision makers can target resources to optimize the services provided across a watershed or multiple watersheds.     

Study of parameters in focus simulation functions of virtual slide

As a special function of Virtual Slide (VS) for thick specimens like cytology slides, multilayer (Z-stack) simulated focus and focus fusion were introduced. From the standpoint of surgical pathologist, the optimum parameters for multilayer focus simulation were examined. First, minimal thickness of the layer was checked by measuring thickness of small cells counting the number of the layers that come into focus. Then the optimal number of layers to scan, total thickness, was tried. Small-sized cell nuclei showed around 2 μm or less thickness. As minimal thickness of one layer for focus simulation, less than 2 μm is required. Papillary cell mass of urothelial carcinoma, aspiration cytology specimen of breast or thyroid, and uterine cervical smear showed different optimal thickness. Cells piling up more than 4 to 5 layer are difficult to make close up observation. Total 15 (to 30) μm thick scan was enough for most specimens. The "focus fusion" image is single layer image synthesized from multiple layer images. Several layer thicknesses were examined, and there was negligible difference between the focus fusion image synthesized from 0.25 and 1 μm thick layers. In the focus fusion image synthesized from 3 μm thick layers, some cells not to come into focus. The "focus fusion" seems to contain all the cells in one plane, and easy for screening. To emphasize the existence of myoepithelial cells in fibroadenoma of breast, or to clarify the 3-dimensional tissue structure, multilayer image was better. From our results, 10 layers with 1.5 μm thick each provide sufficient information in most specimens.     

Micro-organisms isolated from cadaveric samples of allograft musculoskeletal tissue

Allograft musculoskeletal tissue is commonly used in orthopaedic surgical procedures. Cadaveric donors of musculoskeletal tissue supply multiple allografts such as tendons, ligaments and bone. The microbiology laboratory of the South Eastern Area Laboratory Services (SEALS, Australia) has cultured cadaveric allograft musculoskeletal tissue samples for bacterial and fungal isolates since 2006. This study will retrospectively review the micro-organisms isolated over a 6-year period, 2006–2011. Swab and tissue samples were received for bioburden testing and were inoculated onto agar and/or broth culture media. Growth was obtained from 25.1 % of cadaveric allograft musculoskeletal tissue samples received. The predominant organisms isolated were coagulase-negative staphylococci and coliforms, with the heaviest bioburden recovered from the hemipelvis. The rate of bacterial and fungal isolates from cadaveric allograft musculoskeletal tissue samples is higher than that from living donors. The type of organism isolated may influence the suitability of the allograft for transplant.     

The response of porous hydroxyapatite to contiguous tissue infection.

Two patients are presented in whom severe clinical infection developed in tissue adjacent to and contiguous with previously implanted blocks of porous hydroxyapatite. Both infections resolved with appropriate antibiotics, debridement, and drainage of infected tissues. Hydroxyapatite blocks were left in situ. This unusually favorable response of an alloplast to infection is attributable to the abundant vascular supply of this porous implant. Although reliable dogma can hardly be concluded from two clinical examples, these experiences suggest that once ingrown, porous hydroxyapatite does not behave in a fashion that is typical of foreign bodies in the midst of infection. For the first time, clinical evidence has been offered to support the experimental data that vascularized hydroxyapatite has the ability to resist infection.     

Classifying tissue samples from measurements on cells with within-class tissue sample heterogeneity

We consider here the problem of classifying a macro-level object based on measurements of embedded (micro-level) observations within each object, for example, classifying a patient based on measurements on a collection of a random number of their cells. Classification problems with this hierarchical, nested structure have not received the same statistical understanding as the general classification problem. Some heuristic approaches have been developed and a few authors have proposed formal statistical models. We focus on the problem where heterogeneity exists between the macro-level objects within a class. We propose a model-based statistical methodology that models the log-odds of the macro-level object belonging to a class using a latent-class variable model to account for this heterogeneity. The latent classes are estimated by clustering the macro-level object density estimates. We apply this method to the detection of patients with cervical neoplasia based on quantitative cytology measurements on cells in a Papanicolaou smear. Quantitative cytology is much cheaper and potentially can take less time than the current standard of care. The results show that the automated quantitative cytology using the proposed method is roughly equivalent to clinical cytopathology and shows significant improvement over a statistical model that does not account for the heterogeneity of the data.     

Rapid radiometric detection of mycobacterial growth from smear-positive tissue samples from pigs

Rapid demonstration of mycobacteria in slaughter pigs is important for medical, epidemiological and economic reasons. The Bactec radiometric system detected more mycobacteria in less time than conventional culture on solid medium.     

Rapid radiometric detection of mycobacterial growth from smear-positive tissue samples from pigs

Rapid demonstration of mycobacteria in slaughter pigs is important for medical, epidemiological and economic reasons. The Bactec radiometric system detected more mycobacteria in less time than conventional culture on solid medium.     

Targeted protein pullout from human tissue samples using competitive elution

One commonly used strategy to gain information on the proteins in a cell is to isolate the proteins of interest by specific binders, often antibodies. Not only the specificity of the capturing antibodies but also the washing and elution conditions are crucial to avoid false-positive protein identifications. Eluting the target protein from the matrix, while avoiding the release of unrelated background proteins, should both provide more correct information on the target protein and its interaction partners, and minimize the effort to perform downstream analyses through the reduced number of eluted proteins. In this study, a novel approach for selective protein pullout is presented. Monospecific antibodies were used to selectively pullout target proteins from a complex biosample. Subsequently, the target proteins were competitively eluted from the affinity media with the recombinant antigen. To deplete the antigen from the eluted sample, IMAC spin columns were utilized to bind the N-terminal His-tag of the antigens. The competitive elution method was applied both to a model system, and for the extraction of a native human target protein. In the model system the recombinant target protein BBC7 was spiked into a protein extract of human liver, whereas an endogenously expressed target protein, cTAGE5, was extracted from the liver extract directly. SDS-PAGE analysis and mass spectrometry confirmed affinity isolation of expected target proteins. More selective elution was obtained using the competitive procedure as compared to elution at low pH. Competitive elution has thus been shown to offer an effective approach for wide-scale pullout experiments where proteins and their interaction partners are to be studied.     

Efficient stem cell isolation from under vacuum preserved tissue samples

Different approaches for the isolation of stem/progenitor cells have been reported, including stem cell selection in stringent culture conditions. We evaluated the possibility of isolating human progenitor cells from surgical specimens preserved by under vacuum sealing and cooling, a clinical practice approached by several hospitals as alternative to formalin. Renal tissue samples (n = 20) maintained under vacuum from 6 to 48 h at 4°C were used to isolate human renal CD133⁺ progenitor cells. We obtained CD133⁺ progenitors from unsorted cells derived from disaggregated tissues from each sample. Phenotypic characterization as well as in vitro and in vivo differentiation of the obtained CD133⁺ lines showed results comparable with sorted CD133⁺ cells obtained from fresh tissue. These results indicate that the process of sealing under vacuum and cooling appears as a suitable tissue treatment to isolate hypoxia resistant cells, such as human stem/progenitor cells, and that this procedure can be exploited to render the extraction of stem cells from human samples more practical and feasible.     

Efficient stem cell isolation from under vacuum preserved tissue samples

Different approaches for the isolation of stem/progenitor cells have been reported, including stem cell selection in stringent culture conditions. We evaluated the possibility of isolating human progenitor cells from surgical specimens preserved by under vacuum sealing and cooling, a clinical practice approached by several hospitals as alternative to formalin. Renal tissue samples (n = 20) maintained under vacuum from 6 to 48 h at 4°C were used to isolate human renal CD133⁺ progenitor cells. We obtained CD133⁺ progenitors from unsorted cells derived from disaggregated tissues from each sample. Phenotypic characterization as well as in vitro and in vivo differentiation of the obtained CD133⁺ lines showed results comparable with sorted CD133⁺ cells obtained from fresh tissue. These results indicate that the process of sealing under vacuum and cooling appears as a suitable tissue treatment to isolate hypoxia resistant cells, such as human stem/progenitor cells, and that this procedure can be exploited to render the extraction of stem cells from human samples more practical and feasible.     

Collection of tissue and culture samples from the canine reproductive tract

Definitive diagnosis of reproductive tract infection or other disease often requires sampling of tissue, either for culture or histopathology. Indications, sample collection technique, possible side-effects and interpretation of results are reviewed. Pertinent facts include: (1) collection of uterine biopsy specimens via laparotomy was associated with higher yield of diagnostic samples and fewer side-effects than other less invasive techniques; (2) vaginal culture samples should be collected from the anterior vagina to minimize number of contaminants in the sample; (3) collection of culture samples from the anterior vagina during proestrus or estrus, in the presence of discharge originating in the uterus, was a non-invasive technique for assessment for uterine infection; (4) samples for bacterial culture from mucosal surfaces, including the vagina and penis, must be quantitated to allow interpretation, with moderate to heavy growth of any single aerobic bacterial organism relevant; (5) mycoplasma and ureaplasma are part of the normal flora of the genitourinary tract in dogs and bitches and, because most laboratories cannot give reliable quantitative results, interpretation of positive results often is difficult; (6) collection of prostatic tissue samples for cytology or culture was more likely to yield a correct diagnosis than submission of ejaculated prostatic fluid.     

Evaluation of metabolite extraction strategies from tissue samples using NMR metabolomics

Metabolomic analysis of tissue samples can be applied across multiple fields including medicine, toxicology, and environmental sciences. A thorough evaluation of several metabolite extraction procedures from tissues is therefore warranted. This has been achieved at two research laboratories using muscle and liver tissues from fish. Multiple replicates of homogenous tissues were extracted using the following solvent systems of varying polarities: perchloric acid, acetonitrile/water, methanol/water, and methanol/chloroform/water. Extraction of metabolites from ground wet tissue, ground dry tissue, and homogenized wet tissue was also compared. The hydrophilic metabolites were analyzed using 1-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectroscopy and projections of 2-dimensional J-resolved (p-JRES) NMR, and the spectra evaluated using principal components analysis. Yield, reproducibility, ease, and speed were the criteria for assessing the quality of an extraction protocol for metabolomics. Both laboratories observed that the yields of low molecular weight metabolites were similar among the solvent extractions; however, acetonitrile-based extractions provided poorer fractionation and extracted lipids and macromolecules into the polar solvent. Extraction using perchloric acid produced the greatest variation between replicates due to peak shifts in the spectra, while acetonitrile-based extraction produced highest reproducibility. Spectra from extraction of ground wet tissues generated more macromolecules and lower reproducibility compared with other tissue disruption methods. The p-JRES NMR approach reduced peak congestion and yielded flatter baselines, and subsequently separated the metabolic fingerprints of different samples more clearly than by 1D NMR. Overall, single organic solvent extractions are quick and easy and produce reasonable results. However, considering both yield and reproducibility of the hydrophilic metabolites as well as recovery of the hydrophobic metabolites, we conclude that the methanol/chloroform/water extraction is the preferred method. C. Y. Lin and H. Wu contributed equally.     

Accuracy and perceptions of virtual microscopy compared with glass slide microscopy in cervical cytology

A. Evered and N. Dudding Accuracy and perceptions of virtual microscopy compared with glass slide microscopy in cervical cytology Objective: To evaluate virtual microscopy in terms of diagnostic performance and acceptability among practising cytologists. Methods: Twenty‐four experienced cytologists were recruited to examine 20 SurePath® cervical cytology slides by virtual microscopy. Diagnostic accuracy was compared with glass slide microscopy using an unbiased crossover experimental design. Responses were allocated a score of one for a correct identification of normal or abnormal (borderline/atypical changes in squamous or glandular cells or worse) and a score of zero for an incorrect response (a normal slide reported as abnormal or vice versa). Perceptions of virtual microscopy were assessed by questionnaire analysis. Results: Participants yielded a total of 285 responses for the virtual slide set and 300 for the glass slide set. The approximate time to screen a virtual slide was 18 minutes, compared with 8 minutes or less for a glass slide. Overall there was no significant difference between virtual microscopy and glass slide microscopy in terms of diagnostic accuracy (P = 0.22). Virtual microscopy under‐performed when images were captured over a narrow focal range (P = 0.01). Diagnostic accuracy of virtual microscopy equalled that of glass slide microscopy when participants were able to focus through the full thickness of the slide images (P = 0.07). The most common difficulties experienced by participants with virtual microscopy were freezing of the computer screen during image download, slow response of the computer during slide movement and, in some instances, ‘fuzzy’ images. Cytologists have a strong preference for glass slides over virtual microscopy despite the overall equal diagnostic performance of the two viewing modalities. Conclusions: Diagnostic accuracy of virtual microscopy can equal that of glass slide microscopy. However, without good computer network connections, wide focal range and software that permits effortless navigation across virtual slides, cytologists are unlikely to be convinced of the utility of this technology for cytology screening and diagnosis.     

Evaluation of a hydrogel-fiber composite for ACL tissue engineering

The anterior cruciate ligament (ACL) is necessary for normal knee stability and movement. Unfortunately the ACL is also the most frequently injured ligament of the knee with severe disruptions requiring surgical intervention. In response to this, tissue engineering has emerged as an option for ACL replacement and repair. In this study we present a novel hydrogel-fibrous scaffold as a potential option for ACL replacement. The scaffold was composed of PLLA fibers, in a previously evaluated braid-twist structure, combined with a polyethylene glycol diacrylate (PEGDA) hydrogel to improve viscoelastic properties. Both hydrogel concentration (10%, 15%, and 20%) and amount of hydrogel (soaking the fibrous scaffold in hydrogel solution or encasing the scaffold in a block of hydrogel) were evaluated. It was found that the braid-twist scaffold had a greater porosity and larger number of pores above 100 μm than braided scaffolds with the same braiding angle. After testing for their effects on swelling, fiber degradation, and protein release, as well as viscoelastic and tensile testing (when combined with fibrous scaffolds), it was found that the composite scaffold soaked in 10% hydrogel had the best chemical release and mechanical properties. The optimized structure behaved similarly to natural ligament in tension with the addition of the hydrogel decreasing the ultimate tensile stress (UTS), but the UTS was still comparable to natural ACL. In addition, cellular studies showed that the hydrogel-PLLA fiber composite supported fibroblast growth.     

Purification of mitochondrial DNA from total cellular DNA of small tissue samples

A method is presented for the isolation of highly purified mitochondrial (mt)DNA from a crude DNA extract, making use of the different mobilities of covalently closed circular mtDNA vs. endonuclease-digested nuclear DNA in agarose gels. The preparation is virtually free of any contaminating linear DNA, as judged from its electron microscopic appearance, and can be used for further procedures such as polymerase chain reaction (PCR). Since isolation of mitochondria is not a prerequisite for this method, it can be applied to tissue samples in the mg range. In principle, the method can be applied to every eukaryotic species, provided a molecular hybridization probe is available which permits the position of mtDNA to be located in an agarose gel. This probe can be a cDNA, a DNA fragment generated by PCR, or mtDNA itself, if only the approximate size of the genome is known.