Paleoenvironment, paleoecology, and evolution of Maniraptoran "dinosaurs"

Maniraptora is a taxonomic group that includes the well-known primitive bird, Archaeopteryx , that is thought to have had limited power of flight, the small, four-winged, feathered glider, Microraptor and the terrestrial runner Bambiraptor . All are herein considered important links in the origin of flight and a subsequent transition to terrestriality in some forms. In cladistic classifications, dromaeosaurid "dinosaurs" were only considered terrestrial cursors. The discovery of a gliding stage within the dromaeosaurs, a group purportedly closest to birds, confounds the currently suggested biologic framework. Any evolutionary framework lacking predictability for origin of flight scenarios must be fundamentally flawed. Paleoclimate was a significant factor for evolution of birds and birdlike dinosaurs during the Mesozoic. It is characterized by faunal and floral changes reflecting climatic change. For instance, the first known birds such as Archaeopteryx were arboreal and evolved during a warm period in the Late Jurassic. The Solnhofen quarries that produced Archaeopteryx have a windblown faunal and floral component from a forested area indicating a typical Jurassic forest with large trees. During the Early Cretaceous, the Jehol Biota climate was warm and forested providing a suitable arboreal habitat for Microraptor . The cooling trend at end of the Cretaceous opened up the environment making it difficult for poor fliers or gliders as forested areas became less dense. Terrestrial forms and birds with full flight capabilities could survive best in these new environments. Furthermore, birds with specialized manus claws for tree climbing were common in the Early Cretaceous and are so far unknown in the Late Cretaceous. This indicates a change in the avian community with fliers developing an increased ability to take off from flat surfaces. Dromaeosaurs survived well after their initial radiation during the Jehol Biota. Only terrestrial forms, such as Bambiraptor , have been found during the Late Cretaceous. Birds of modern aspect probably replaced the primitive dromaeosaurs, Microraptor and its kin, since they were more efficient fliers. A majority of cladistic analyses show Microraptor as the plesiomorphic sister group to the more terrestrial dromaeosaurs. The geologically younger Bambiraptor provides examples of the morphological changes necessary for the transition to ground dwelling and how this transition was accomplishe

Topical decolonization does not eradicate the skin microbiota of community-dwelling or hospitalized adults

Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial communities and levels of richness and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n = 8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach-water baths), and ICU patients (n = 7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before and again after decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the community-dwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus decreased significantly over time (P = 0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to those for the enrollment sampling (from enrollment to final sampling, P = 0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota

Prevalence of qacA/B genes and mupirocin resistance among methicillin-resistant Staphylococcus aureus (MRSA) isolates in the setting of chlorhexidine bathing without mupirocin

OBJECTIVE: We aimed to determine the frequency of qacA/B chlorhexidine tolerance genes and high-level mupirocin resistance among MRSA isolates before and after the introduction of a chlorhexidine (CHG) daily bathing intervention in a surgical intensive care unit (SICU). DESIGN: Retrospective cohort study (2005–2012) SETTING: A large tertiary-care center PATIENTS: Patients admitted to SICU who had MRSA surveillance cultures of the anterior nares METHODS: A random sample of banked MRSA anterior nares isolates recovered during (2005) and after (2006–2012) implementation of a daily CHG bathing protocol was examined for qacA/B genes and high-level mupirocin resistance. Staphylococcal cassette chromosome mec (SCCmec) typing was also performed. RESULTS: Of the 504 randomly selected isolates (63 per year), 36 (7.1%) were qacA/B positive ( + ) and 35 (6.9%) were mupirocin resistant. Of these, 184 (36.5%) isolates were SCCmec type IV. There was a significant trend for increasing qacA/B (P= .02; highest prevalence, 16.9% in 2009 and 2010) and SCCmec type IV (P< .001; highest prevalence, 52.4% in 2012) during the study period. qacA/B( + ) MRSA isolates were more likely to be mupirocin resistant (9 of 36 [25%] qacA/B( + ) vs 26 of 468 [5.6%] qacA/B(−); P= .003). CONCLUSIONS: A long-term, daily CHG bathing protocol was associated with a change in the frequency of qacA/B genes in MRSA isolates recovered from the anterior nares over an 8-year period. This change in the frequency of qacA/B genes is most likely due to patients in those years being exposed in prior admissions. Future studies need to further evaluate the implications of universal CHG daily bathing on MRSA qacA/B genes among hospitalized patients

No evidence that elevated CO\u3csub\u3e2\u3c/sub\u3e gives tropical lianas an advantage over tropical trees

Recent studies indicate that lianas are increasing in size and abundance relative to trees in neotropical forests. As a result, forest dynamics and carbon balance may be altered through liana‐induced suppression of tree growth and increases in tree mortality. Increasing atmospheric CO2 is hypothesized to be responsible for the increase in neotropical lianas, yet no study has directly compared the relative response of tropical lianas and trees to elevated CO2. We explicitly tested whether tropical lianas had a larger response to elevated CO2 than co‐occurring tropical trees and whether seasonal drought alters the response of either growth form. In two experiments conducted in central Panama, one spanning both wet and dry seasons and one restricted to the dry season, we grew liana (n = 12) and tree (n = 10) species in open‐top growth chambers maintained at ambient or twice‐ambient CO2 levels. Seedlings of eight individuals (four lianas, four trees) were grown in the ground in each chamber for at least 3 months during each season. We found that both liana and tree seedlings had a significant and positive response to elevated CO2 (in biomass, leaf area, leaf mass per area, and photosynthesis), but that the relative response to elevated CO2 for all variables was not significantly greater for lianas than trees regardless of the season. The lack of differences in the relative response between growth forms does not support the hypothesis that elevated CO2 is responsible for increasing liana size and abundance across the neotropics

Peregrine Falcon Survey, West Greenland, 1972

... The main purpose of the 1972 survey was to study a sample area of West Greenland to supply baseline data about peregrine falcons from which future surveys could determine the status and trends of this bird in Greenland. The main part of the study had as its goals: 1) to determine the density, distribution, and reproductive success of nesting peregrines in a sample area; 2) to band all peregrine nestlings found; 3) to determine prey species of the peregrine; 4) to make interspecific observations of peregrines and gyrfalcons; 5) to make detailed observations from a blind of a sample peregrine falcon eyrie; 6) to conduct a small-bird census in the area of the sample eyrie; 7) to make a photographic record in colour slides and movies of the investigations. ... Eight peregrine falcon eyries and 3 gyrfalcon eyries were found in the survey area. In all, 18 nestlings were found in the 8 peregrine eyries. Of the 8 eyries, 1 had no young, but showed signs of occupancy ... and was defended by an aggressive pair of falcons. Of the other 7 eyries where we found hatched young, 1 had 4 young, 4 had 3 young, and 2 had 1 young bird each. Of the total of 18 nestling peregrines, 13 were banded and 5 were fully-fledged, on the wing, and unable to be caught for banding. Of the peregrine nestlings banded, 9 were males and 4 were females. The number of nestlings (18) in the 8 peregrine eyries gave a production rate of 2.25 per eyrie, or 2.57 if an average is taken of the 7 eyries actually producing young. At 1 eyrie a young falcon was found dead (the eyrie with 4 young). We know that at least 8 of the remaining 17 young fledged successfully, but we are uncertain about the success of the others and cannot therefore make a definite statement on fledging ratio. We estimate, however, that the fledging rate of the peregrines in our survey area was at least 2.00 per producing eyrie. The maximum dimensions of our irregularly-shaped survey area were 39 x 34 miles (63 x 55 km). The estimated area of the survey was about 800 sq. mi. (2,072 sq. km), or about 700 sq. mi. (1,800 sq. km) when the surface area of fiords and lakes is excluded. The nesting density of the active, young-producing peregrine eyries (7) was about 1 pair per 100 sq. mi. (260 sq. km). ... At the 3 gyrfalcon (Falco rusticolus) eyries we found 8 nestlings or fully-fledged young, of which we were able to band 3. Peregrines and gyrfalcons (and a rare white-tailed sea eagle, Haliaetus albicilla) are the only avian predators nesting in southern West Greenland, although ravens (Corvus corax) competed for some nesting cliff sites. We collected remains of prey species and pellets at each falcon eyrie. Addled eggs (2) from 2 peregrine eyries were collected for pesticide analysis. Eggshell fragments for thickness determination were gathered at 5 peregrine eyries. ... Peregrine falcons in West Greenland appear to be in a healthy state as evidenced by a high nesting density (1/100 sq. mi.) and a high production rate (2.25/eyrie), especially in light of the unusually severe conditions in West Greenland during the winter and late spring of 1971-72. We found little interspecific competition for prey species between peregrines and gyrfalcons. The gyrfalcon is already nesting in West Greenland before the peregrines arrive from their winter migration to the south. The gyrfalcons could therefore be expected to be aggressive in defence of their nesting cliffs and thereby occupy optimal cliffs. Despite this, all the peregrines we studied occupied high, sheer, and quite optimal nesting cliffs. Gyrfalcons seemed to prefer a nesting site lower down on a cliff face than peregrines, and both falcons preferred high, sheer cliffs with a southern exposure. Ravens were relegated to lower, less desirable (more accessible) cliffs for nesting. We await pesticide analysis of the peregrine falcon eggs and prey species collected, as well as eggshell thickness determination. Before these facts are determined we can say nothing definite about the status of peregrines in Greenland. Nesting density and production, however, suggest that the status of the peregrine is better in Greenland than in other areas of the north. ..

Evaluation of the Vitek MS matrix-assisted laser desorption ionization–time of flight mass spectrometry system for identification of clinically relevant filamentous fungi

Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n = 2] and Aspergillus calidoustus [n = 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare

Optimizing identification of clinically relevant gram-positive organisms by use of the bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including “heavy” (H) and “light” (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or “score.” We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS

SARS-CoV-2 E gene variant alters analytical sensitivity characteristics of viral detection using a commercial reverse transcription-PCR assay

Diagnostic assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for patient management, infection prevention, and the public health response for coronavirus disease 2019 (COVID-19). The efficacy and reliability of these assays are of paramount importance in both tracking and controlling the spread of the virus. Real-time reverse transcription-PCR (RT-PCR) assays rely on a fixed genetic sequence for primer and probe binding. Mutations can potentially alter the accuracy of these assays and lead to unpredictable analytical performance characteristics and false-negative results. Here, we identify a G-to-U transversion (nucleotide 26372) in the SARS-CoV-2 E gene in three specimens with reduced viral detection efficiency using a widely available commercial assay. Further analysis of the public GISAID repository led to the identification of 18 additional genomes with this mutation, which reflect five independent mutational events. This work supports the use of dual-target assays to reduce the number of false-negative PCR results

Outcrop conservation : Promoting accessibility, inclusivity, and reproducibility through digital preservation

We thank Georgina Heldreich for providing useful comments on an early draft of the manuscript. We gratefully acknowledge the detailed and constructive reviews by Kim Senger and two anonymous reviewers, all of which greatly improved the manuscript.Peer reviewedPublisher PD