Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker ...selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.
The North Atlantic right whale (Eubalaena glacialis) is considered the most endangered large whale species as a result of historic whaling, modern ship collisions, and fishing entanglements. To ...monitor the distribution and movement patterns of the right whales within Stellwagen Bank National Marine Sanctuary (SBNMS), a critical feeding area at the mouth of the Massachusetts Bay, passive acoustic techniques were used. Passive acoustic recordings were made at between 7 and 9 locations throughout the SBNMS from January to May 2006, July to December 2006, and January to February 2007 (366 days). Recordings were made using Automated Recording Units (ARUs), produced by Cornell University, recording at frequencies between 0 and 1000 hertz. Right whale up-calls, a type of vocalization, are the dominant call type occurring within the study area. An automated detection program (Urazghildiiev and Clark 2006) detected over 22,522 up-calls in 89,280 hours of data. Up-calls were present throughout the sanctuary for 11 out of the 13 months, and were present throughout the 24 hour cycle, with a pronounced peak in activity in the late evening. These results show that right whales use the sanctuary to a greater extent than previously thought, particularly during the winter months. The Right Whale Sightings Advisory System (RWSAS) includes visual sightings of right whales from a variety of platforms. During the 366 recording days the RWSAS had 33 sightings of 311 right whales that could have fallen within the acoustic range (8 nautical miles radius) of the ARUs. Sightings from the RWSAS did not account for all the acoustic2behavior present throughout the sanctuary. These results suggest that passive acoustics is an effective tool for monitoring right whale activity and distribution, and can significantly augment management efficacy during months when other techniques are severely limited. The present results will help to direct further management decisions towards reducing ship-whale collisions and fishing entanglements with the right whales.
http://deepblue.lib.umich.edu/bitstream/2027.42/58601/1/SMussoline_Thesis.pdf
Basic Income Van Parijs, Philippe; Vanderborght, Yannick
2017, 2017-03-20
eBook
Providing a basic income to everyone, rich or poor, active or inactive, was advocated by Paine, Mill, and Galbraith but the idea was never taken seriously. Today, with the welfare state creaking, it ...is one of the world's most widely debated proposals. Philippe Van Parijs and Yannick Vanderborght present a comprehensive defense of this radical idea.
Lignin is a heteropolymer that is thought to form in the cell wall by combinatorial radical coupling of monolignols. Here, we present a simulation model of in vitro lignin polymerization, based on ...the combinatorial coupling theory, which allows us to predict the reaction conditions controlling the primary structure of lignin polymers. Our model predicts two controlling factors for the β-O-4 content of syringyl-guaiacyl lignins: the supply rate of monolignols and the relative amount of supplied sinapyl alcohol monomers. We have analyzed the in silico degradability of the resulting lignin polymers by cutting the resulting lignin polymers at β-O-4 bonds. These are cleaved in analytical methods used to study lignin composition, namely thioacidolysis and derivatization followed by reductive cleavage, under pulping conditions, and in some lignocellulosic biomass pretreatments.
Defining the appropriate scale over which to conduct a study in the marine environment is critical to achieving appropriate scientific, management, mitigation and conservation objectives. This paper ...focuses on applications of passive acoustic technologies over a range of spatial and temporal scales. It is divided into sections dealing with archival and real-time passive acoustic sensor applications. Each section assesses the principles behind using the respective technology and provides recent examples of research and management applications for marine mammals and fish. The section on archival sensors highlights the need for continued development of automated acoustic detectors to assess large data sets. Case studies are presented of detectors developed for determining seasonal occurrence and distribution of haddock sounds and humpback whale vocalizations. Also presented are studies of other applications using archival sensors: tracking singing humpback whales in Brazil, using vocalizations to assess the reproductive strategies of Arctic bearded seals and assessing regional variability in call patterns for North Atlantic right whales. The section on real-time passive acoustic sensors focuses on real-time buoys and towed arrays. Case studies presented include a real-time buoy system used for monitoring endangered North Atlantic right whales and a stationary autonomous array providing real-time access to Antarctic acoustic data. The value of using towed arrays for real-time applications is also assessed, and a case study is provided on the use of towed arrays to improve abundance estimates of North Pacific cetaceans and to better understand vocalization behaviors.
Passive acoustic tracking provides an unobtrusive method of studying the movement of sound-producing animals in the marine environment where traditional tracking methods may be costly or infeasible. ...We used passive acoustic tracking to characterize the fine-scale movements of singing humpback whales (Megaptera novaeangliae) on a northwest Atlantic feeding ground. Male humpback whales produce complex songs, a phenomenon that is well documented in tropical regions during the winter breeding season, but also occurs at higher latitudes during other times of year. Acoustic recordings were made throughout 2009 using an array of autonomous recording units deployed in the Stellwagen Bank National Marine Sanctuary. Song was recorded during spring and fall, and individual singing whales were localized and tracked throughout the array using a correlation sum estimation method on the time-synchronized recordings. Tracks were constructed for forty-three song sessions, revealing a high level of variation in movement patterns in both the spring and fall seasons, ranging from slow meandering to faster directional movement. Tracks were 30 min to 8 h in duration, and singers traveled distances ranging from 0.9 to 20.1 km. Mean swimming speed was 2.06 km/h (SD 0.95). Patterns and rates of movement indicated that most singers were actively swimming. In one case, two singers were tracked simultaneously, revealing a potential acoustic interaction. Our results provide a first description of the movements of singers on a northwest Atlantic feeding ground, and demonstrate the utility of passive acoustic tracking for studying the fine-scale movements of cetaceans within the behavioral context of their calls. These methods have further applications for conservation and management purposes, particularly by enhancing our ability to estimate cetacean densities using passive acoustic monitoring.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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