Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning

The recent surge of coronavirus disease 2019 (COVID-19) hospitalizations severely challenges healthcare systems around the globe and has increased the demand for reliable tests predictive of disease severity and mortality. Using multiplexed targeted mass spectrometry assays on a robust triple quadrupole MS setup which is available in many clinical laboratories, we determined the precise concentrations of hundreds of proteins and metabolites in plasma from hospitalized COVID-19 patients. We observed a clear distinction between COVID-19 patients and controls and, strikingly, a significant difference between survivors and nonsurvivors. With increasing length of hospitalization, the survivors’ samples showed a trend toward normal concentrations, indicating a potential sensitive readout of treatment success. Building a machine learning multi-omic model that considers the concentrations of 10 proteins and five metabolites, we could predict patient survival with 92% accuracy (area under the receiver operating characteristic curve: 0.97) on the day of hospitalization. Hence, our standardized assays represent a unique opportunity for the early stratification of hospitalized COVID-19 patients.     

Effect of Tooth Removal on Recaptures of Raccoons

Abstract: Researchers have extensively used mark—recapture techniques to obtain information on demographic parameters of wildlife populations. However, researchers have recognized that a number of factors can influence capture probabilities of wildlife species, which in turn can bias mark—recapture estimates of demographic parameters. Tooth extraction, which is a commonly used technique in studies of mesopredator species to obtain precise age estimates and to monitor the use of vaccine baits, is an aspect of animal handling that clearly might affect the recapture probability of individuals. However, the effect that tooth removal has on the individual recapture probabilities of wildlife species is unknown. During 2005, we trapped and marked 91 raccoons (Procyon lotor) in northern Indiana, USA, as part of a mark—recapture study designed specifically to determine if tooth extractions have an effect on recapture probabilities of individuals. We performed tooth extractions on 50% of the raccoons at the time of capture, and we attempted to balance tooth extractions with respect to sex and age of raccoons. We used logistic regression to model the effects of sex, age, and tooth removal on recapture probabilities, and we used Mann—Whitney U-tests to examine the effect of tooth removal on the number of times we recaptured individuals. The probability of recapture differed between sexes but did not differ as a function of tooth removal or among age classes. In addition, we failed to detect any difference in the mean number of times that we recaptured raccoons between the tooth removed and non—tooth-removed groups. Our results suggest that managers can use tooth extractions as an effective management tool without biasing population estimates or compromising other management objectives.     

Crop processing of <Emphasis Type="Italic">Olea europaea</Emphasis> L.: an experimental approach for the interpretation of archaeobotanical olive remains

Archaeobotanical research, ethnographic observations and laboratory experiments are put together to create model sequences of olive processing, which are developed, presented and explored as an aid for the interpretation of rich archaeobotanical assemblages of Olea. We conclude that the remains of different processing stages are reasonably distinctive in the archaeobotanical record and assist in the identification of different types of olive remains, such as fragmented olive stones, the inner kernels, and fruit flesh     

Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis

A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS-PAGE to be a plasma protein concentration of about 10 mg/ml in 3% (w/v) Triton X-114. 2DE of proteins obtained by CPE of 400 μl of human plasma revealed about 200 spots constituting a spot pattern very different from the pattern of total plasma. The CPE procedure only had a limited contribution to the technical variation. Identification of about 60 spots, representing only 22 proteins, revealed that several proteins in the obtained subfraction were present in more isoforms or modifications. Among these were apolipoproteins (A-1, D, E, L1, and M), haptoglobin-related protein, phosphatidylcholine-sterol acyltransferase, serum amyloid A, and serum paraoxonase/arylesterase 1, which are proteins of a hydrophobic nature, as in plasma they relate to lipoprotein particles. Thus, Triton X-114-based CPE is a simple plasma prefractionation tool, attractive for detailed 2DE studies of hydrophobic plasma proteins and their isoforms or modifications.     

Stable Isotopes (δD, δ13C, δ15N) Reveal Associations Among Geographic Location and Condition of Alaskan Northern Pintails

Abstract: Information on spring migration routes, geographic linkages among winter, spring, and breeding locations, and potential geographic effects on arrival body condition of northern pintails (Anas acuta) are currently unknown. Through a combination of stable-isotope measurements of tissues representing different periods of dietary integration and body composition analyses, we examined these linkages for pintails breeding in Alaska, USA. We collected 77 females at 4 locations upon spring arrival. We performed carbon (δ¹³C), nitrogen (δ¹⁵N), and hydrogen (δD) isotope measurements on flight feathers, breast feathers, and whole blood, and we conducted body composition analyses. Inference based on stable-isotope values in pintail tissues suggests that philopatry to Alaska was strong, as most of the collected females had stable-isotope values consistent with the boreal forest of Canada or western Alaska and most spring migrating females had whole-blood values indicating use of a food web in the boreal forest before collection. These patterns highlight the importance of the boreal forest for production and staging of pintails. Breast feather isotope values grown during prealternate molt were variable and covered the currently documented distribution of wintering pintails. Our results indicate associations among specific geographic areas, habitat use, and arrival condition of female pintails settling in Alaska. Females that wintered or staged in coastal habitat (as indicated by elevated δ¹³C values) arrived with less body fat compared to those that we inferred to have wintered or staged on inland freshwater habitat. Those females we inferred to use coastal areas appeared to rely more heavily on agricultural fields for nutrient acquisition (as indicated by elevated δ¹⁵N but low δ¹³C values). Our results provide the first link between low-condition females and inferred use of specific geographic areas before arrival. Conservation on wintering grounds should focus on restoration and protection of wetland complexes that provide adequate natural food resources in proximity to coastal systems that are heavily used by wintering pintails. Conservation efforts should also focus on the boreal forest, not only for pintail, but for other boreal-dependent species such as lesser scaup (Aythya affinis) (JOURNAL OF WILDLIFE MANAGEMENT 72(3):715–725; 2008)     

Changing land management of lowland wet grasslands of the UK: impacts on snipe abundance and habitat quality

Snipe Gallinago gallinago breeding on lowland wet grasslands in England have undergone widespread and dramatic declines in abundance and distribution since at least the 1970s. There are many potential drivers of the decline but reductions in habitat quality, driven by land management, are often proposed as a contributing factor in the historical declines of breeding waders. Breeding snipe are now restricted to a few key places such as nature reserves and environmentally sensitive areas where management for breeding waders is implemented. On average, populations have continued to decline, even in these key areas, though population trends vary from a decline of 98% to an increase of 61% between the early 1990s and 2006. We examined the relationship between regional variation in snipe population trends and soil conditions, other habitat features and land management. Snipe were more likely to persist in fields where the soil conditions were wet and soft. Fields are wetter and softer now than in the early 1990s and management influenced these conditions. Soil softness increased with decreasing grazing pressure and increasing surface flooding. Soil moisture increased with surface flooding and was higher in organic soils. Changes in field condition were consistent with decreases in grazing pressure and increases in surface flooding. In spite of habitat condition being altered in a way that should have been beneficial to snipe, the numbers have continued to decline. Thus, it is unlikely that the measures of habitat condition examined here have been the driver of the decline and other factors must be involved. Research efforts should now focus on alternative explanations of the decline, for example, changes in other key aspects of habitat quality such as prey abundance, or changes in snipe productivity or mortality.     

Mild Detritylation of Nucleic Acid Hydroxyl Groups by Warming Up

It is challenging to effectively deprotect hydroxyl groups of acid-or-base sensitive bio-macromolecules without causing even minor defects and compromising high quality of final products. We report here a mild detritylation strategy in mildly acidic buffers to remove the DMTr protection from the 5′-hydroxyl groups of synthetic nucleic acids. The DMTr-groups can be easily and effectively removed at pH 4.5 or 5.0 with slight warming up (40°C), offering virtually quantitative deprotection. This warming-up strategy is particularly useful for deprotection of the modified nucleic acids that are sensitive to the conventional acid deprotection. As a first step towards our long-term goal of synthesizing defect-free nucleic acids, our novel and simple strategy further increases the quality of synthetic nucleic acids.     

Intra-individual variation in body temperature and pectoral muscle size in nestling Alpine swifts Apus melba in response to an episode of inclement weather

The Alpine swift (Apus melba) forages on insects caught exclusively on the wing, implying that dependent nestlings face acute food shortage in periods of cold and rainy weather. Therefore, there should be strong selection on nestling swifts to evolve physiological strategies to cope with periods of undernutrition. We have investigated intra-individual changes in nestling pectoral muscle and body temperature in response to a 1-week period of inclement weather. The pectoral muscle is the largest reserves of proteins, and nestlings have to devote a large amount of energy in the maintenance of body temperature. The results show that nestling pectoral muscle size and body temperature were significantly reduced during the episode of inclement weather. Assuming that these physiological changes are adaptive, our study suggests that nestling swifts spare energy by a pronounced reduction (up to 18°C) in body temperature and use proteins from the pectoral muscle as a source of extra energy to survive prolonged periods of fasting.