An image dataset of cleared, x-rayed, and fossil leaves vetted to plant family for human and machine learning.

Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning.

Leafcutter bee nests and pupae from the Rancho La Brea Tar Pits of Southern California: implications for understanding the paleoenvironment of the Late Pleistocene.

The Rancho La Brea Tar Pits is the world's richest and most important Late Pleistocene fossil locality and best renowned for numerous fossil mammals and birds excavated over the past century. Less researched are insects, even though these specimens frequently serve as the most valuable paleoenvironemental indicators due to their narrow climate restrictions and life cycles. Our goal was to examine fossil material that included insect-plant associations, and thus an even higher potential for significant paleoenviromental data. Micro-CT scans of two exceptionally preserved leafcutter bee nest cells from the Rancho La Brea Tar Pits in Los Angeles, California reveal intact pupae dated between ∼23,000-40,000 radiocarbon years BP. Here identified as best matched to Megachile (Litomegachile) gentilis Cresson (Hymenoptera: Megachilidae) based on environmental niche models as well as morphometrics, the nest cells (LACMRLP 388E) document rare preservation and life-stage. The result of complex plant-insect interactions, they offer new insights into the environment of the Late Pleistocene in southern California. The remarkable preservation of the nest cells suggests they were assembled and nested in the ground where they were excavated. The four different types of dicotyledonous leaves used to construct the cells were likely collected in close proximity to the nest and infer a wooded or riparian habitat with sufficient pollen sources for larval provisions. LACMRLP 388E is the first record of fossil Megachile Latreille cells with pupae. Consequently, it provides a pre-modern age location for a Nearctic group, whose phylogenetic relationships and biogeographic history remain poorly understood. Megachile gentilis appears to respond to climate change as it has expanded its distribution across elevation gradients over time as estimated by habitat suitability comparisons between low and high elevations; it currently inhabits mesic habitats which occurred at a lower elevation during the Last Glacial Maximum ∼21,000 years ago. Nevertheless, the broad ecological niche of M. gentilis appears to have remained stable.

Sojourn time and lead time projection in lung cancer screening.

OBJECTIVES: We investigate screening sensitivity, transition probability and sojourn time in lung cancer screening for male heavy smokers using the Mayo Lung Project data. We also estimate the lead time distribution, its property, and the projected effect of taking regular chest X-rays for lung cancer detection. METHODS: We apply the statistical method developed by Wu et al. [1] using the Mayo Lung Project (MLP) data, to make Bayesian inference for the screening test sensitivity, the age-dependent transition probability from disease-free to preclinical state, and the sojourn time distribution, for male heavy smokers in a periodic screening program. We then apply the statistical method developed by Wu et al. [2] using the Bayesian posterior samples from the MLP data to make inference for the lead time, the time of diagnosis advanced by screening for male heavy smokers. The lead time is distributed as a mixture of a point mass at zero and a piecewise continuous distribution, which corresponds to the probability of no-early-detection, and the probability distribution of the early diagnosis time. We present estimates of these two measures for male heavy smokers by simulations. RESULTS: The posterior sensitivity is almost symmetric, with posterior mean 0.89, and posterior median 0.91; the 95% highest posterior density (HPD) interval is (0.72, 0.98). The posterior mean sojourn time is 2.24 years, with a posterior median of 2.20 years for male heavy smokers. The 95% HPD interval for the mean sojourn time is (1.57, 3.35) years. The age-dependent transition probability is not a monotone function of age; it has a single maximum at age 68. The mean lead time increases as the screening time interval decreases. The standard error of the lead time also increases as the screening time interval decreases. CONCLUSION: Although the mean sojourn time for male heavy smokers is longer than expected, the predictive estimation of the lead time is much shorter. This may provide policy makers important information on the effectiveness of the chest X-rays and sputum cytology in lung cancer early detection.

A projection of benefits due to fecal occult blood test for colorectal cancer.

OBJECTIVES: A prospective study to estimate benefits due to fecal occult blood tests for colorectal cancer are carried out for both males and females, under different screening frequencies. METHODS: We apply the statistical method developed by Wu et al. (2007) [1] using the Minnesota colorectal cancer study group data, to make Bayesian inference for the lead time, the time of diagnosis advanced by screening for both male and female participants in a periodic screening program. The lead time is distributed as a mixture of a point mass at zero and a piecewise continuous distribution. The two parts of the mixture correspond to two aspects of the screening: the probability of no benefit, or the percentage of interval cases; and the probability distribution of the early diagnosis time. We present estimates of these two measures for males and females by simulation studies using the Minnesota study group data. We also provide the mean, mode, variance, and density curve of the program's lead time by gender. This may provide policy makers important information on the effectiveness of the FOBT screening in colorectal cancer early detection. RESULTS: The mean lead time increases as the screening time interval decreases for both males and females. The standard error of the lead time also increases as the screening time interval decreases for both genders. Females seem get more benefit than males, in that females usually have a longer lead time than males if both take the test at the same time interval and the lead time mode for females is greater than that of males in the same screening time interval. CONCLUSION: According to the predictive estimation of the lead time distribution, to guarantee a 90% chance of early detection, it seems necessary for the males to take the fecal occult blood test every 9 months, while the females can take it annually.

Estimating key parameters in FOBT screening for colorectal cancer.

OBJECTIVES: The association between screening sensitivity, transition probability, and individual's age in FOBT for colorectal cancer are explored, for both males and females. METHODS: We apply the statistical method developed by Wu et al. [1] using the Minnesota colorectal cancer study group data, to make Bayesian inference for the age-dependent screening test sensitivity, the age-dependent transition probability from disease-free to preclinical state, and the sojourn time distribution, for both male and female participants in a periodic screening program. This gives us more information on the effectiveness of the fecal occult blood test in colorectal cancer detection. RESULTS: The sensitivity appears to increase with age for both genders. However, the posterior mean sensitivity is not monotonic with age for males; it has a peak around age 74. The standard errors of the sensitivity are not monotone either; there is a minimum at age 69 for males and at age 78 for females. The age-dependent transition probability is not a monotone function of age; it has a single maximum at age 72 for males and a single maximum at age 75 for females. The age dependency seems more dramatic for females than for males. The posterior mean sojourn time is 4.08 years for males and 2.41 years for females, with a posterior median of 1.66 years for males and 1.88 years for females. The 95% highest posterior density (HPD) interval is (0.97, 20.28) for males and (1.15, 5.96) for females, which are very large ranges, especially for males. The reason might be that there were fewer men than women in the annual screening program. CONCLUSION: Reliable estimates of age-dependent sensitivity and transition probability are of great value to policy-makers regarding the initial age for colorectal cancer screening exams. We found that the mean sojourn time for males is much longer than that for females, which may imply that FOBT screening for colorectal cancer may be more effective for males than for females.

Pinus baileyi (section Pinus, Pinaceae) from the Paleogene of Idaho, USA.

Pinus baileyi from the Paleogene of Idaho was initially related to the bristlecone pine P. longaeva (subgen. Strobus, sect. Parrya, subsect. Balfourianae) from western North America. Unlike the centromucronate condition in P. longaeva, P. baileyi cones have raised umbos that are excentromucronate, i.e., the mucro positioned in the upper umbo field above the keel. Cone size and scale morphology shows that P. baileyi more closely resembles excentromucronate pines of subsects. Halepenses and Pinus sensu Gernandt et al. (2005, Taxon 54: 29-42), but is most similar to P. resinosa, P. kesiya, and P. massoniana of subsect. Pinus. Morphologically, P. baileyi resembles the fossil species P. princetonensis and P. arnoldii from the Eocene Princeton Chert, British Columbia, Canada. Pinus baileyi extends the western North American range of ovulate cones resembling subsect. Pinus from the middle Eocene of British Columbia, Canada and Washington, USA to the Oligocene of Idaho, USA. Pinus baileyi, and possibly P. princetonensis and P. arnoldii, indicates the presence of early populations of subsect. Pinus-type pines in the western cordillera of North America, raising the possibility that P. resinosa and P. tropicalis may have evolved from this group.

Estimating the cumulative risk of false positive cancer screenings.

BACKGROUND: When evaluating cancer screening it is important to estimate the cumulative risk of false positives from periodic screening. Because the data typically come from studies in which the number of screenings varies by subject, estimation must take into account dropouts. A previous approach to estimate the probability of at least one false positive in n screenings unrealistically assumed that the probability of dropout does not depend on prior false positives. METHOD: By redefining the random variables, we obviate the unrealistic dropout assumption. We also propose a relatively simple logistic regression and extend estimation to the expected number of false positives in n screenings. RESULTS: We illustrate our methodology using data from women ages 40 to 64 who received up to four annual breast cancer screenings in the Health Insurance Program of Greater New York study, which began in 1963. Covariates were age, time since previous screening, screening number, and whether or not a previous false positive occurred. Defining a false positive as an unnecessary biopsy, the only statistically significant covariate was whether or not a previous false positive occurred. Because the effect of screening number was not statistically significant, extrapolation beyond 4 screenings was reasonable. The estimated mean number of unnecessary biopsies in 10 years per woman screened is.11 with 95% confidence interval of (.10,.12). Defining a false positive as an unnecessary work-up, all the covariates were statistically significant and the estimated mean number of unnecessary work-ups in 4 years per woman screened is.34 with 95% confidence interval (.32,.36). CONCLUSION: Using data from multiple cancer screenings with dropouts, and allowing dropout to depend on previous history of false positives, we propose a logistic regression model to estimate both the probability of at least one false positive and the expected number of false positives associated with n cancer screenings. The methodology can be used for both informed decision making at the individual level, as well as planning of health services.

Using observational data to estimate an upper bound on the reduction in cancer mortality due to periodic screening.

BACKGROUND: Because randomized cancer screening trials are very expensive, observational cancer screening studies can play an important role in the early phases of screening evaluation. Periodic screening evaluation (PSE) is a methodology for estimating the reduction in population cancer mortality from data on subjects who receive regularly scheduled screens. Although PSE does not require assumptions about natural history of cancer it requires other assumptions, particularly progressive detection - the assumption that once a cancer is detected by a screening test, it will always be detected by the screening test. METHODS: We formulate a simple version of PSE and show that it leads to an upper bound on screening efficacy if the progressive detection assumption does not hold (and any effect of birth cohort is minimal) To determine if the upper bound is reasonable, for three randomized screening trials, we compared PSE estimates based only on screened subjects with PSE estimates based on all subjects. RESULTS: In the three randomized screening trials, PSE estimates based on screened subjects gave fairly close results to PSE estimates based on all subjects. CONCLUSION: PSE has promise for obtaining an upper bound on the reduction in population cancer mortality rates based on observational screening data. If the upper bound estimate is found to be small and any birth cohort effects are likely minimal, then a definitive randomized trial would not be warranted.