Effective monitoring of freshwater fish

Freshwater ecosystems constitute only a small fraction of the planet’s water resources, yet support much of its diversity, with freshwater fish accounting for more species than birds, mammals, amphibians, or reptiles. Fresh waters are, however, particularly vulnerable to anthropogenic impacts, including habitat loss, climate and land use change, nutrient enrichment, and biological invasions. This environmental degradation, combined with unprecedented rates of biodiversity change, highlights the importance of robust and replicable programmes to monitor freshwater fish assemblages. Such monitoring programmes can have diverse aims, including confirming the presence of a single species (e.g. early detection of alien species), tracking changes in the abundance of threatened species, or documenting long-term temporal changes in entire communities. Irrespective of their motivation, monitoring programmes are only fit for purpose if they have clearly articulated aims and collect data that can meet those aims. This review, therefore, highlights the importance of identifying the key aims in monitoring programmes, and outlines the different methods of sampling freshwater fish that can be used to meet these aims. We emphasise that investigators must address issues around sampling design, statistical power, species’ detectability, taxonomy, and ethics in their monitoring programmes. Additionally, programmes must ensure that high-quality monitoring data are properly curated and deposited in repositories that will endure. Through fostering improved practice in freshwater fish monitoring, this review aims to help programmes improve understanding of the processes that shape the Earth's freshwater ecosystems, and help protect these systems in face of rapid environmental change

Collagen Fiber Orientation and Dispersion in the Upper Cervix of Non-Pregnant and Pregnant Women.

The structural integrity of the cervix in pregnancy is necessary for carrying a pregnancy until term, and the organization of human cervical tissue collagen likely plays an important role in the tissue's structural function. Collagen fibers in the cervical extracellular matrix exhibit preferential directionality, and this collagen network ultrastructure is hypothesized to reorient and remodel during cervical softening and dilation at time of parturition. Within the cervix, the upper half is substantially loaded during pregnancy and is where the premature funneling starts to happen. To characterize the cervical collagen ultrastructure for the upper half of the human cervix, we imaged whole axial tissue slices from non-pregnant and pregnant women undergoing hysterectomy or cesarean hysterectomy respectively using optical coherence tomography (OCT) and implemented a pixel-wise fiber orientation tracking method to measure the distribution of fiber orientation. The collagen fiber orientation maps show that there are two radial zones and the preferential fiber direction is circumferential in a dominant outer radial zone. The OCT data also reveal that there are two anatomic regions with distinct fiber orientation and dispersion properties. These regions are labeled: Region 1-the posterior and anterior quadrants in the outer radial zone and Region 2-the left and right quadrants in the outer radial zone and all quadrants in the inner radial zone. When comparing samples from nulliparous vs multiparous women, no differences in these fiber properties were noted. Pregnant tissue samples exhibit an overall higher fiber dispersion and more heterogeneous fiber properties within the sample than non-pregnant tissue. Collectively, these OCT data suggest that collagen fiber dispersion and directionality may play a role in cervical remodeling during pregnancy, where distinct remodeling properties exist according to anatomical quadrant

The dominant fiber direction <i>θ</i> in the outer radial zone in four quadrants for all specimens imaged.

<p>Each circle represents the dominant fiber directions in one quadrant. Each line represents one cervical sample averaged across all 400 μm × 400 μm radial subregions, with the line color representing the standard deviation (SD) between the radial subregions. Red represents higher SD and blue represents lower SD. Posterior and anterior quadrants both have more uniform dominant directions among samples (lines having a narrower spread) and within a single specimen there is lower SD between the radial subregions (lines having a bluish color). Left and right quadrants have a wider spread of the dominant fiber direction between samples, and within an individual sample, fiber directions also change more dramatically along radial direction.</p

Media 2: Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography

Originally published in Biomedical Optics Express on 01 April 2015 (boe-6-4-1090

Patient demographics of specimens used for this study.

<p>Patient demographics of specimens used for this study.</p

Representative OCT <i>en face</i> images and overlaid fiber orientation maps of cervical slices with different inner zone widths.

<p>(A), (C), (E), and (G) are OCT <i>en face</i> images taken 245 μm beneath the cut surface and (B), (D), (F), and (H) are overlaid fiber orientation maps. (A), (C), and (E) were from non-pregnant patients with wide, narrow, and no inner zones. (G) was from a pregnant patient. The white line sketches the inner canal. The red contour delineates the inner radial zone according to local fiber orientation. The yellow bars in (B), (D), (F), and (H) show local dominant fiber orientation in each 400 × 400 μm sub-region. (A)-(B), (C)-(D), (E)-(F), and (G)-(H) are Speicemen 1, Speciemen 2, Speciemen 3, and Speciemen 13 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166709#pone.0166709.t001" target="_blank">Table 1</a> respectively.</p

The anatomical position of the cervix, sample preparation and terms.

<p>(A) The anatomical position of the uterus and the cervix produced from an MRI of a patient at 22 weeks of gestation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166709#pone.0166709.ref004" target="_blank">4</a>]. The proximal end of the cervix is the internal os and the distal end of the cervix is the external os. (B) Illustration of specimen preparation of the upper cervix. The cervix is cut perpendicular to the inner canal to obtain slices for experiments. The sliced cervix in (B) is oriented the same as shown in (A). The imaging direction is perpendicular to cutting direction, normal to cervical slices. (C) Illustration of four anatomical quadrants (A-anterior, P-posterior, L-left, and R-right), inner and outer radial zones, and 400μm × 400μm subregions used for fiber dispersion analysis.</p

SD of dominant direction <i>θ</i> (unit: rad) in different parity groups and pregnancy statuses.

<p>Results from each quadrant in the outer radial zone and some combinations are shown. NP groups do not have significant differences among themselves. Between NP groups and PG, the only significant difference is found between primiparous NP and PG when P/A quadrants are combined (<i>p</i> = 0.004). Unlike the analysis for <i>b</i>, nulliparous NP (<i>p</i> = 0.276) and multiparous NP (<i>p</i> = 0.143) do not have a significant difference with PG in the SD of <i>θ</i>. No significant difference is found in L/R quadrants.</p

A pixel-wise directionality map on an <i>en face</i> image parallel from and 245 μm beneath the cut surface (Specimen 1 in Table 1).

<p>(A) directionality map with locations of 400 μm × 400 μm subregions corresponding to 80 pixels × 80 pixels.; (B) OCT image within the white box in (A); (C) directionality map within the white box in (B). Pixels with no fiber information are coded in black. Each 400 μm × 400 μm subregion represents a location for the fiber orientation and dispersion analysis in the A (anterior), P (posterior), L (left), and R (right) quadrants. Along the radial direction, the boxes are divided into inner region (red) and outer region (green).</p

Representative fiber distributions found in the upper cervix and corresponding 2D von-Mises fits.

<p>The dominant direction <i>θ</i> is shown by dotted line. All four subregions are taken from the outer radial zone of the same NP sample (Specimen 5 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166709#pone.0166709.t001" target="_blank">Table 1</a>). A subregion with (A) a single family of fibers that have the most alignment (<i>b</i> = 0.820) and (B) highly dispersed fibers that are randomly oriented in the plane. A subregion with (C) two fiber families and (D) three fiber families. (Note: current distribution fitting methodology cannot distinguish the multiple fiber families.)</p