A datalogger to identify vocalizing dolphins

Author Posting. © Acoustical Society of America, 1991. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 90 (1991): 1668-1671, doi:10.1121/1.401908.A datalogger was developed to identify vocalizing dolphins within socially interacting captive groups. Every 50 ms the logger stores data on the level and frequency of detected sound. Dataloggers are temporarily attached to dolphins by suction cups for data collection sessions lasting up to 45 min. Later, computer analysis of data from the dataloggers reveals which dolphin produced each vocalization recorded during the session. Results from use of dataloggers with two captive bottlenose dolphins (Tursiops truncatus) at the New England Aquarium in Boston, MA are presented. The possible use of dataloggers with wild dolphins is discussed.This work was supported by ONR Grant No. N00014-87-K-0236

Clinical features of COVID-19 and SARS epidemics. A literature review

SARS-CoV-2, responsible for the current pandemic, is a novel strain of the Coronaviridae family, which has infected humans as a result of the leap to a new species. It causes an atypical pneumonia similar to that caused by SARS-CoV in 2003. SARS-CoV-2 has currently infected more than 9,200,000 people and caused almost 480,000 deaths worldwide. Although SARS-CoV-2 and SARS-CoV have similar phylogenetic and pathogenetic characteristics, they show important differences in clinical manifestations. We have reviewed the recent literature comparing the characteristics of the two epidemics and highlight their peculiar aspects. An analysis of all signs and symptoms of 3,365 SARS patients and 23,280 COVID-19 patients as well as of the comorbidities has been carried out. A total of 17 and 75 studies regarding patients with SARS and COVID-19, respectively, were included in the analysis. The analysis revealed an overlap of some symptoms between the two infections. Unlike SARS patients, COVID-19 patients have developed respiratory, neurological and gastrointestinal symptoms, and, in a limited number of subjects, symptoms involving organs such as skin and subcutaneous tissue, kidneys, cardiovascular system, liver and eyes. This analysis was conducted in order to direct towards an early identification of the infection, a suitable diagnostic procedure and the adoption of appropriate containment measures

AAV-CRISPR Persistence in the Eye of the Beholder

Despite advances in genome editing technologies based on the adeno-associated virus (AAV)-CRISPR system, there are still concerns about the long-term persistence of recombinant AAV vectors in several organs (liver, muscle, eye) possibly leading to cytotoxicity or genotoxicity related to off-target effects. Indeed, there are still unanswered questions about long-lasting in vivo AAV persistence as a linear or circular DNA that is not targeted by epigenetic silencing in many tissues. In 2017, Kim et al.1 reported an editing approach based on AAV-CjCas9 to downregulate Vegfa or the hypoxia-inducible transcription factor Hif1a in mice displaying age-related macular degeneration (AMD)-related pathological choroidal neovascularization (CNV) induced by laser treatment. Although partial knockdown of either Vegfa or Hif1a provided benefits and reduced the area of CNV, local opsin dysfunction near the Vegfa-edited cells of murine retinal pigment epithelium (RPE) was observed. Conversely, no cone dysfunction was reported upon Hif1a partial knockdown. Lastly, no genome-wide off-target indels, evaluated 6 weeks after intravitreal injection of AAV-CjCas9 vector, were scored, indicating that prolonged expression of AAV-CjCas9 in vivo did not aggravate the genotoxic risk associated with the CjCas9 nuclease. In this issue of Molecular Therapy, the authors now report a long-term (14 months) safety study on C57BL/6J mice intravitreally injected with AAV-CjCas9 vectors targeting Vegfa or Hif1a genes.2 The findings continue to show that the AAV-CRISPR system in the eyes is long lasting, effective, and safe

Enabling MSI-Guided Laser Capture Microdissection

Introduction/Rationale: Coupling MALDI mass spectrometry imaging (MALDI-MSI) with Laser Capture Microdissection (LCM) allows for precise dissection of tissue regions based on molecular features [1]. Automated methods for alignment of the coordinate systems of the MSI and LCM platforms reduces errors associated with manual definition of ROI’s and increases throughput (a major bottleneck for LCM). Here we present the development of a method to transfer regions of interest from MALDI MSI images to an LCM platform, using consecutive tissue sections mounted on ITO conductive slides for MALDI MSI and on PEN-coated slides for LCM. Methods: The test system consists of a gelatin-embedded mouse liver. 12 µm slices were cut using a cryostat and two consecutive slices were mounted on ITO and PEN slides. The ITO slide was spray-coated with DHB (30mg/mL, MeOH 70%, water 30%, 0.2% TFA) and a MALDI image was acquired with an EP-MALDI source coupled to a Q-Exactive mass spectrometer. The MSI data was imported into MATLAB. The tissue mounted on the PEN slide was stained with hematoxylin and a high resolution optical image acquired using an Aperio Scanscope. The LCM instrument used was an Apotome 2 Axio Observer Z1 microscope equipped with a Palm Robomover LCM system (both Zeiss). Results: An image of an ion with a regular distribution on the tissue is used to align the MS image to the optical image of the hematoxylin-stained tissue section mounted on the PEN slide. The optical image of the PEN slide tissue section is imported in MATLAB and cropped to match the size of the MALDI image. An intensity-based co-registration algorithm is then used to align the MS image to the cropped optical image. The MS image is then rescaled to match to the original optical image. To obtain regions-of-interest to transfer to the LCM platform, the MSI data was TIC normalized and a k-means cluster analysis performed. The image of the cluster of interest was aligned to the PEN slide using the same transformations used for the whole MSI data, binarized and segmented to obtain the coordinates of the vertices of the cluster region. Vertex coordinates were expressed after setting the axes origin to a user-defined reference point on the slide. The coordinates of the origin in the Aperio reference system were then matched to the coordinates of the reference point in the Zeiss coordinate system and the same transformation applied. Coordinates were then formatted as an Element file readable by the LCM and exported as text files. Border coordinates were imported in the Zeiss PALMRobo software and regions of interest automatically dissected. Conclusions/Novelty: The presented method enables rapid transfer of coordinates from a MALDI image to an LCM instrument, increasing throughput and reducing errors due to freehand cutting. The method is applicable to consecutive tissue sections, and ROI’s can be defined either by MSI or via histopathological specification

Spin Echo Decay in a Stochastic Field Environment

We derive a general formalism with which it is possible to obtain the time dependence of the echo size for a spin in a stochastic field environment. Our model is based on ``strong collisions''. We examine in detail three cases where: (I) the local field is Ising-like, (II) the field distribution is continuous and has a finite second moment, and (III) the distribution is Lorentzian. The first two cases show a T2 minimum effect and are exponential in time cubed for short times. The last case can be approximated by a phenomenological stretched exponential.Comment: 11 pages + 3 postscript figure

Spectroscopy of 35^{35}P using the one-proton knockout reaction

The structure of $^{35}$P was studied with a one-proton knockout reaction at88~MeV/u from a $^{36}$S projectile beam at NSCL. The $\gamma$ rays from thedepopulation of excited states in $^{35}$P were detected with GRETINA, whilethe $^{35}$P nuclei were identified event-by-event in the focal plane of theS800 spectrograph. The level scheme of $^{35}$P was deduced up to 7.5 MeV using$\gamma-\gamma$ coincidences. The observed levels were attributed to protonremovals from the $sd$-shell and also from the deeply-bound $p\_{1/2}$ orbital.The orbital angular momentum of each state was derived from the comparisonbetween experimental and calculated shapes of individual ($\gamma$-gated)parallel momentum distributions. Despite the use of different reactions andtheir associate models, spectroscopic factors, $C^2S$, derived from the$^{36}$S $(-1p)$ knockout reaction agree with those obtained earlier from$^{36}$S($d$,\nuc{3}{He}) transfer, if a reduction factor $R\_s$, as deducedfrom inclusive one-nucleon removal cross sections, is applied to the knockout transitions.In addition to the expected proton-hole configurations, other states were observedwith individual cross sections of the order of 0.5~mb. Based on their shiftedparallel momentum distributions, their decay modes to negative parity states,their high excitation energy (around 4.7~MeV) and the fact that they were notobserved in the ($d$,\nuc{3}{He}) reaction, we propose that they may resultfrom a two-step mechanism or a nucleon-exchange reaction with subsequent neutronevaporation. Regardless of the mechanism, that could not yet be clarified, thesestates likely correspond to neutron core excitations in \nuc{35}{P}. Thisnewly-identified pathway, although weak, offers the possibility to selectivelypopulate certain intruder configurations that are otherwise hard to produceand identify.Comment: 5 figures, 1 table, accepted for publication in Physical Review

Relative influence of the adeno-associated virus (AAV) type 2 p5 element for recombinant AAV vector site-specific integration.

The p5 promoter region of the adeno-associated virus type 2 (AAV-2) rep gene has been described as essential for Rep-mediated site-specific integration (RMSSI) of plasmid sequences in human chromosome 19. We report here that insertion of a full-length or minimal p5 element between the viral inverted terminal repeats does not significantly increase RMSSI of a recombinant AAV (rAAV) vector after infection of growth-arrested or proliferating human cells. This result suggests that the p5 element may not improve RMSSI of rAAV vectors in vivo