Flexible STEM with Simultaneous Phase and Depth Contrast

Recent advances in scanning transmission electron microscopy (STEM) have rekindled interest in multi-channel detectors and prompted the exploration of unconventional scan patterns. These emerging needs are not yet addressed by standard commercial hardware. The system described here incorporates a flexible scan generator that enables exploration of low-acceleration scan patterns, while data are recorded by a scalable eight-channel array of nonmultiplexed analog-to-digital converters. System integration with SerialEM provides a flexible route for automated acquisition protocols including tomography. Using a solid-state quadrant detector with additional annular rings, we explore the generation and detection of various STEM contrast modes. Through-focus bright-field scans relate to phase contrast, similarly to wide-field TEM. More strikingly, comparing images acquired from different off-axis detector elements reveals lateral shifts dependent on defocus. Compensation of this parallax effect leads to decomposition of integrated differential phase contrast (iDPC) to separable contributions relating to projected electric potential and to defocus. Thus, a single scan provides both a computationally refocused phase contrast image and a second image in which the signed intensity, bright or dark, represents the degree of defocus.

Experimental investigation of the wave-induced motion of and force distribution along a flexible stem

The work presents an experimental investigation into the motion of and hydrodynamic forces along a single flexible stem in regular waves. The experiment covers a large range in relevant non-dimensional parameters: the drag-to-stiffness ratio $CaL\in [0.003,3.8]$, the inertia-to-stiffness ratio $CaL/KC\in [4\times 10^{-5},14.8]$, the Keulegan–Carpenter number $KC\in [3.8,145]$ and the Reynolds number $Re\in [230,2900]$. The two first parameters relate to the response of the stem in waves and thus account for material properties, while the two last parameters are relevant for hydrodynamic forces on the stem. The displacement of the stem was captured with a digital video camera and the displacement along the stem was captured for every 2.5 mm at 25 Hz. This unique laboratory data set allowed for the following analyses: (i) Determination of the relevant non-dimensional parameter to predict the stem motion and shape. (ii) A direct comparison between the measured force for mimics of two lengths (0.15 m and 0.30 m) illustrating the force reduction potential for flexible mimics. (iii) Direct evaluation of the average force coefficients $C_{D}$ (drag) and $C_{M}$ (inertia) for the flexible stems. (iv) The distributed external hydrodynamic loading and the internal shear forces were estimated from the laboratory experiments. The distribution of the shear force helped to understand the breakage mechanisms of flexible stems. (v) A linkage between phase lags and internal shear forces was suggested. The data set is considered valuable as validation material for numerical models of stem motion in waves.

Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertoires

MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative-miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low grade glioma patient samples indicate that the alternative-miR-9 plays a distinct role in preventing tumor progression. To generalize our model, we provide evidence that distortion of pri-miRNA stems correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.

Understanding form and function of the stem in early flattened echinoderms (pleurocystitids) using a microstructural approach

Pleurocystitid rhombiferans are among the most unusual echinoderms whose mode of life has been long debated. These echinoderms are usually interpreted as vagile epibenthic echinoderms, moving over the sea bottom by means of a flexible stem. Although their life habits and posture are reasonably well understood, the mechanisms that control the movement of stem are highly controversial. Specifically, it is unknown whether the stem flexibility was under the control of muscles or ligamentary mutable collagenous tissues (MCTs). Here, we reconstruct palaeoanatomy of the two Ordovician pleurocystitid rhombiferans (PleurocystitesandAmecystis) based on stereom microstructure. We show that the articular facets of columnals in pleurocystitid rhombiferans are composed of fine labyrinthic stereom. Comparison with modern echinoderms suggests that this type of stereom was associated with muscles implying that their stem was a muscular locomotory organ supporting an active mode of life.

Development of a Colonoscope Sheath Device for Colonoscopy

Endoscopy is a minimally invasive procedure using instruments that pass through the body for diagnostic purposes and minimizes the risks associated with open surgery. Colonoscopy can viewed as an endoscopic procedure of the colon. Colonoscopy may cause extreme discomfort to the patient and also carries the risks of perforating the lining of the colon, splenic ruptures, or bleeding. The technology is an endoscope that has an exoskeleton structure of controllable stiffness and a highly flexible stem. The device saves the patient from the pain caused by the shaft of a colonoscope when it is guided from the anus to the end of the sigmoid colon. The stiffenable sheath guides the shaft of the colonoscope up to the end of the sigmoid colon to avoid looping the shaft of the colonoscope. A prototype of the device was built and tested to validate its effectiveness. In order to further improve the performance of the device, skilled endoscopists tested and validated the device using a colonoscopy training model. The colonoscopy training model is comprised of a configurable rubber colon, a human torso, a display, and sensing part. It measures the forces caused by the distal tip and the shaft of the colonoscope and the pressure to open up the lumen. The force sensors at the rubber colon constraints measure the forces, and the real-time display panel will show the results to the colonoscopist and record the data for analysis. The endoscopy sheath device improves the process of endoscopy by reducing the mechanical trauma and loops caused by the shaft of the endoscope. With the guide provided by the colonoscope sheath, the forces to the constraints of a colon are significantly decreased in the sigmoid colon. The colonoscope sheath helps to reduce the force to constraints of the colon and isolates the direct contact between the shaft of a colonoscope and a colon wall up to the end of the sigmoid colon. For the complicated shape of the colon, the endoscopy sheath also solved possible looping problems. The colonoscope training model effectively measures the forces and makes it possible to validate the effectiveness of the endoscopy sheath.