Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.

The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit.

Acrolein Increases the Pulmonary Tumorigenic Activity of the Tobacco-Specific Nitrosamine 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK).

Tobacco smoke is a complex mixture of more than 7000 chemicals, of which many are toxic and/or carcinogenic. Many hazard assessments of tobacco have focused on individual chemical exposures without consideration of how the chemicals may interact with one another. Two chemicals, the human carcinogen 4-methylnitrosamino-1-(3-pyridyl)-1-butanone (NNK) and a possible human carcinogen, acrolein, were hypothesized to interact with one another, possibly owing to the additive effects of DNA adduct formation or influence on the repair of mutagenic DNA adducts. To test our hypothesis that coexposure to NNK and acrolein is more carcinogenic than either chemical alone, A/J mice were exposed to NNK (i.p., 0, 2.5, or 7.5 µmol in saline) in the presence or absence of inhaled acrolein (15 ppmV). While the single 3 h exposure to acrolein alone did not induce lung adenomas, it significantly enhanced NNK's lung carcinogenicity. In addition, mice receiving both NNK and acrolein had more adenomas with dysplasia or progression than those receiving only NNK, suggesting that acrolein may also increase the severity of NNK-induced lung adenomas. To test the hypothesis that the interaction was due to effects on DNA adduct formation and repair, NNK- and acrolein pulmonary DNA adduct levels were assessed. There was no consistent effect of the coexposure on NNK-derived DNA adducts, and acrolein DNA adducts were not elevated above endogenous levels. This study supports the hypothesis that tobacco smoke chemicals combine to contribute to the carcinogenic potency of tobacco smoke, and the mechanism of interaction cannot be explained by alterations of DNA adduct levels.

Coexposure to Inhaled Aldehydes or Carbon Dioxide Enhances the Carcinogenic Properties of the Tobacco-Specific Nitrosamine 4-Methylnitrosamino-1-(3-pyridyl)-1-butanone in the A/J Mouse Lung.

Tobacco smoke is a complex mixture of chemicals, many of which are toxic and carcinogenic. Hazard assessments of tobacco smoke exposure have predominantly focused on either single chemical exposures or the more complex mixtures of tobacco smoke or its fractions. There are fewer studies exploring interactions between specific tobacco smoke chemicals. Aldehydes such as formaldehyde and acetaldehyde were hypothesized to enhance the carcinogenic properties of the human carcinogen, 4-methylnitrosamino-1-(3-pyridyl)-1-butanone (NNK) through a variety of mechanisms. This hypothesis was tested in the established NNK-induced A/J mouse lung tumor model. A/J mice were exposed to NNK (intraperitoneal injection, 0, 2.5, or 7.5 µmol in saline) in the presence or absence of acetaldehyde (0 or 360 ppmv) or formaldehyde (0 or 17 ppmv) for 3 h in a nose-only inhalation chamber, and lung tumors were counted 16 weeks later. Neither aldehyde by itself induced lung tumors. However, mice receiving both NNK and acetaldehyde or formaldehyde had more adenomas with dysplasia or progression than those receiving only NNK, suggesting that aldehydes may increase the severity of NNK-induced lung adenomas. The aldehyde coexposure did not affect the levels of NNK-derived DNA adduct levels. Similar studies tested the ability of a 3 h nose-only carbon dioxide (0, 5, 10, or 15%) coexposure to influence lung adenoma formation by NNK. While carbon dioxide alone was not carcinogenic, it significantly increased the number of NNK-derived lung adenomas without affecting NNK-derived DNA damage. These studies indicate that the chemicals in tobacco smoke work together to form a potent lung carcinogenic mixture.

Snapshots of human anatomy, locomotion, and behavior from Late Pleistocene footprints at Engare Sero, Tanzania.

Fossil hominin footprints preserve data on a remarkably short time scale compared to most other fossil evidence, offering snapshots of organisms in their immediate ecological and behavioral contexts. Here, we report on our excavations and analyses of more than 400 Late Pleistocene human footprints from Engare Sero, Tanzania. The site represents the largest assemblage of footprints currently known from the human fossil record in Africa. Speed estimates show that the trackways reflect both walking and running behaviors. Estimates of group composition suggest that these footprints were made by a mixed-sex and mixed-age group, but one that consisted of mostly adult females. One group of similarly-oriented trackways was attributed to 14 adult females who walked together at the same pace, with only two adult males and one juvenile accompanying them. In the context of modern ethnographic data, we suggest that these trackways may capture a unique snapshot of cooperative and sexually divided foraging behavior in Late Pleistocene humans.

Prenatal stress enhances NNK-induced lung tumors in A/J mice.

Children born to women who experience stress during pregnancy have an increased risk of cancer in later life, but no previous animal studies have tested such a link. We questioned whether prenatal stress (PS) in A/J mice affected the development of lung tumors after postnatal response to tobacco-specific nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Timed-bred A/J mice were randomly assigned on gestation day 12.5 to PS by restraint for 5 consecutive days or control (no restraint). Adult offspring of control and stressed pregnancies were all treated with three NNK injections (50 mg/kg every other day) and euthanized 16 weeks later to examine their lungs. Compared with controls, PS dams exhibited significantly increased levels of plasma corticosterone, increased adrenal weights and decreased fetus weights without fetal loss. Prenatally stressed litters had a significantly higher neonatal death rate within first week of life, and surviving male and female offspring developed lung epithelial proliferations with increase multiplicity, increased area and aggressive morphology. PS also induced more advanced atypical adenomatous hyperplasia lesions. We found no difference in lung NNK-derived methyl DNA adducts, but PS did significantly enhance CD3+ T cell and Foxp3+ T cell tumor infiltration. PS significantly increases multiplicity, area of NNK-induced lung tumors and advanced morphology. PS did not affect production of NNK-derived methyl DNA adducts but did increase lymphocytic infiltration of lung tumors. To our knowledge, this is the first animal model of PS with evaluation of cancer development in offspring.

Scythes, sickles and other blades: defining the diversity of pectoral fin morphotypes in Pachycormiformes.

The traditional terminology of 'scythe' or 'sickle' shaped is observed to be flawed as an effective descriptor for pectoral fin shape in pachycormids. The diversity of pachycormid pectoral fin shapes is assessed across the 14 recognised genera that preserve complete pectoral fins, and improved terms are defined to more effectively describe their form, supported by anatomical observation and aspect ratio analysis of individual fins, and corroborated by landmark analysis. Three clear and distinct pectoral fin structural morphotypes emerge (falceform, gladiform, falcataform), reflecting a diversity of pachycormid lifestyles throughout the Mesozoic, from agile pursuit predator to slow-cruising suspension feeder.

Inhaled Furan Selectively Damages Club Cells in Lungs of A/J Mice.

Furan, a possible human carcinogen, is a product of incomplete combustion and is present in cigarette smoke, engine exhaust, and processed food. Oral administration induces liver toxicity and carcinogenesis in F344 rats and B6C3F1 mice. To assess possible adverse effects from inhalation, A/J mice were nose-only exposed for 3 hours to furan (0, 30, 75, 150, 300, or 600 ppmv) and euthanized after 24 hours, 48 hours, or 1 week. Histopathology evaluation revealed bronchiolar club cell necrosis (diffuse, marked) with airway denudation following exposure to 300 and 600 ppmv furan with evidence of club cell regeneration and partial repair after 1 week. Initial signs of hepatotoxicity were observed in the 150 ppmv furan-exposed group. Acute necrosis and mineralization were observed in livers at 24 and 48 hours with hepatocyte regeneration by 1-week postexposure in mice exposed to 300 and 600 ppmv furan; the 300 ppmv exposed group had multifocal mineralization that evoked a mild granulomatous response. Measurement of urinary furan metabolites confirmed that the mice metabolized furan to the toxic intermediate, cis-2-butene-1,4-dial. These observations indicate that inhaled furan is toxic to lungs with club cells as the target as well as liver.

Hip extensor mechanics and the evolution of walking and climbing capabilities in humans, apes, and fossil hominins.

The evolutionary emergence of humans' remarkably economical walking gait remains a focus of research and debate, but experimentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental measurements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal-terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by the relative length and orientation of the ischium. Ape pelves permit greater extensor moments at the hip, enhancing climbing capability, but limit their range of hip extension, resulting in a crouched gait. Human pelves reduce hip extensor moments but permit a greater degree of hip extension, which greatly improves walking economy (i.e., distance traveled/energy consumed). Applying these results to fossil pelves suggests that early hominins differed from both humans and extant apes in having an economical walking gait without sacrificing climbing capability. Ardipithecus was capable of nearly human-like hip extension during bipedal walking, but retained the capacity for powerful, ape-like hip extension during vertical climbing. Hip extension capability was essentially human-like in Australopithecus afarensis and Australopithecus africanus, suggesting an economical walking gait but reduced mechanical advantage for powered hip extension during climbing.

Estrogen metabolism in the human lung: impact of tumorigenesis, smoke, sex and race/ethnicity.

Previous data from this group demonstrate that the murine lung metabolizes estrogen. Production of the putative carcinogen 4-hydroxyestrogen (4-OHE) is elevated within the lungs of female vs. male mice and accelerated by tobacco smoke. The goal of this study was to determine if the human lung metabolizes estrogen and evaluate the impact of tumor formation, smoke, sex and race/ethnicity on metabolism. Urine and lung tissue (normal, tumor) were obtained from 49 non-small cell lung cancer patients. Healthy postmenopausal Caucasian (n = 19) and Chinese (n = 20) American women (never-smokers) donated urine. Quantitative RT-PCR analyses indicate that multiple estrogen synthesis and metabolism genes are expressed in human bronchoalveolar cells. Estrogen and its metabolites were measured in lung tissue and urine using liquid chromatography/tandem mass spectrometry. Wilcoxon rank tests were used for statistical comparisons. E1, E2, E3 and estrogen metabolites 2-OHE1, 2-OHE2, 4-OHE1, 4-OHE2, 2-OME1 and 2-OME2 were detected at higher levels in tumor vs. adjacent normal tissue and in women vs. men (P < 0.05). The proportion of 4-OHEs was higher in tumors than in normal lung tissue (P < 0.05), and elevated in normal tissue from current- vs. never-smoking women (P = 0.006); similar trends were observed in urine. The proportion of 4-OHEs in the urine of postmenopausal Chinese American women was 1.8-fold higher than that of Caucasian women (P = 0.015). These data indicate that estrogen metabolites are present in the human lung. A shift towards 4-hydroxylation during lung tumorigenesis may contribute to the risk conferred by smoking, sex or race/ethnicity.

Dental microwear profilometry of African non-cercopithecoid catarrhines of the Early Miocene.

The Early Miocene of Kenya has yielded the remains of many important stem catarrhine species that provide a glimpse of the East African primate radiation at a time of major faunal turnover. These taxa have been subject to innumerable studies, yet there is still no consensus on their dietary niches. Here we report results of an analysis of dental microwear textures of non-cercopithecoid catarrhines from the Early Miocene of Kenya. Scanning confocal profilometry of all available molar specimens with undamaged occlusal surfaces revealed 82 individuals with unobscured antemortem microwear, representing Dendropithecus, Micropithecus, Limnopithecus, Proconsul, and Rangwapithecus. Scale-sensitive fractal analysis was used to generate microwear texture attributes for each individual, and the fossil taxa were compared with each other using conservative non-parametric statistical tests. This study revealed no discernible variation in microwear texture among the fossil taxa, which is consistent with results from a previous feature-based microwear study using smaller samples. Our results suggest that, despite their morphological differences, these taxa likely often consumed foods with similar abrasive and fracture properties. However, statistical analyses of microwear texture data indicate differences between the Miocene fossil sample and several extant anthropoid primate genera. This suggests that the African non-cercopithecoid catarrhines included in our study, despite variations in tooth form, had generalist diets that were not yet specialized to the degree of many modern taxa.

Remnants of an ancient forest provide ecological context for Early Miocene fossil apes.

The lineage of apes and humans (Hominoidea) evolved and radiated across Afro-Arabia in the early Neogene during a time of global climatic changes and ongoing tectonic processes that formed the East African Rift. These changes probably created highly variable environments and introduced selective pressures influencing the diversification of early apes. However, interpreting the connection between environmental dynamics and adaptive evolution is hampered by difficulties in locating taxa within specific ecological contexts: time-averaged or reworked deposits may not faithfully represent individual palaeohabitats. Here we present multiproxy evidence from Early Miocene deposits on Rusinga Island, Kenya, which directly ties the early ape Proconsul to a widespread, dense, multistoried, closed-canopy tropical seasonal forest set in a warm and relatively wet, local climate. These results underscore the importance of forested environments in the evolution of early apes.

What college students do not know: where are the gaps in sexual health knowledge?

OBJECTIVE: This study aimed to understand the gaps in college students' knowledge regarding sexual health information. PARTICIPANTS: A sample of 242 participants enrolled in an introductory college course participated in this study in the Fall 2009 semester. METHODS: Students participated in 1 of 2 brief interventions and wrote a response paper about their experience. The papers were analyzed using conventional content analysis for information that was new to participants by looking for key words that suggested learning took place. RESULTS: The findings indicated that the majority of participants learned new information. Most learning occurred regarding sexually transmitted infections (ie, types, symptoms, prevalence, treatment, testing) and correct condom use. There were also demographic differences regarding reported new information. CONCLUSIONS: Findings can be used to develop future sex education programs for college students by providing college educators with an understanding of where students lack knowledge of sexual health.

Structure of an engineered ß-lactamase maltose binding protein fusion protein: insights into heterotropic allosteric regulation.

Engineering novel allostery into existing proteins is a challenging endeavor to obtain novel sensors, therapeutic proteins, or modulate metabolic and cellular processes. The RG13 protein achieves such allostery by inserting a circularly permuted TEM-1 ß-lactamase gene into the maltose binding protein (MBP). RG13 is positively regulated by maltose yet is, serendipitously, inhibited by Zn(2+) at low µM concentration. To probe the structure and allostery of RG13, we crystallized RG13 in the presence of mM Zn(2+) concentration and determined its structure. The structure reveals that the MBP and TEM-1 domains are in close proximity connected via two linkers and a zinc ion bridging both domains. By bridging both TEM-1 and MBP, Zn(2+) acts to "twist tie" the linkers thereby partially dislodging a linker between the two domains from its original catalytically productive position in TEM-1. This linker 1 contains residues normally part of the TEM-1 active site including the critical ß3 and ß4 strands important for activity. Mutagenesis of residues comprising the crystallographically observed Zn(2+) site only slightly affected Zn(2+) inhibition 2- to 4-fold. Combined with previous mutagenesis results we therefore hypothesize the presence of two or more inter-domain mutually exclusive inhibitory Zn(2+) sites. Mutagenesis and molecular modeling of an intact TEM-1 domain near MBP within the RG13 framework indicated a close surface proximity of the two domains with maltose switching being critically dependent on MBP linker anchoring residues and linker length. Structural analysis indicated that the linker attachment sites on MBP are at a site that, upon maltose binding, harbors both the largest local Cα distance changes and displays surface curvature changes, from concave to relatively flat becoming thus less sterically intrusive. Maltose activation and zinc inhibition of RG13 are hypothesized to have opposite effects on productive relaxation of the TEM-1 ß3 linker region via steric and/or linker juxtapositioning mechanisms.

F.O.R.E.play: the utility of brief sexual health interventions among college students.

OBJECTIVES: The authors aimed to determine the most effective brief sexual health intervention for college students, while also evaluating students' preferences for learning about sexual health, in order to develop a university program. METHODS: A total of 302 students enrolled in an introductory college course participated and were randomly assigned to 1 of 3 brief interventions during a regularly scheduled class and completed pre- and postsurveys assessing knowledge, motivation to use condoms, and condom self-efficacy. RESULTS: Findings indicated that having an actual person in charge of the learning process resulted in higher knowledge gains and highlighted a student preference for discussion-based learning, viewing pictures of sexually transmitted infections, and hearing real-life experiences about the consequences of unsafe sex. CONCLUSIONS: These findings will be used to tailor a future intervention targeting college students for use with freshmen students at this university.

Endometrioma occurring in abdominal wall incisions after cesarean section.

OBJECTIVE: To investigate outcomes following incisional endometrioma after cesarean section and correlate the role of predisposing factors. STUDY DESIGN: Chart review of patients from a 7-year period noting surgical history, previous incisions, uterine exteriorization, and wound irrigation at cesarean section, preoperative and final endometrioma size, mass location, fascial involvement, and mesh placement. RESULTS: All 16 patients had cesarean section as their last surgery and 15 of 16 had transverse incisions. Patients averaged 29.2 years of age, had two prior surgeries with time to symptoms of 25.9 months. Endometriomas were primarily left of midline, extrafascial in 10 patients and intrafascial 3 patients, and involved fascia and muscle in 3 patients. Estimated and actual sizes were similar (p = 0.54) and not correlated with mesh placement (p = 0.21). No patient had concomitant pelvic endometriosis. CONCLUSION: Incisional endometriomas developing after cesarean section occur primarily on the left of transverse incisions. Endometrioma size estimates correlate well with surgical findings but not with the need for mesh placement.

Ecological divergence and medial cuneiform morphology in gorillas.

Gorillas are more closely related to each other than to any other extant primate and are all terrestrial knuckle-walkers, but taxa differ along a gradient of dietary strategies and the frequency of arboreality in their behavioral repertoire. In this study, we test the hypothesis that medial cuneiform morphology falls on a morphocline in gorillas that tracks function related to hallucial abduction ability and relative frequency of arboreality. This morphocline predicts that western gorillas, being the most arboreal, should display a medial cuneiform anatomy that reflects the greatest hallucial abduction ability, followed by grauer gorillas, and then by mountain gorillas. Using a three-dimensional methodology to measure angles between articular surfaces, relative articular and nonarticular areas, and the curvatures of the hallucial articular surface, the functional predictions are partially confirmed in separating western gorillas from both eastern gorillas. Western gorillas are characterized by a more medially oriented, proportionately larger, and more mediolaterally curved hallucial facet than are eastern gorillas. These characteristics follow the predictions for a more prehensile hallux in western gorillas relative to a more stable, plantigrade hallux in eastern gorillas. The characteristics that distinguish eastern gorilla taxa from one another appear unrelated to hallucial abduction ability or frequency of arboreality. In total, this reexamination of medial cuneiform morphology suggests differentiation between eastern and western gorillas due to a longstanding ecological divergence and more recent and possibly non-adaptive differences between eastern taxa.

Laetoli footprints preserve earliest direct evidence of human-like bipedal biomechanics.

BACKGROUND: Debates over the evolution of hominin bipedalism, a defining human characteristic, revolve around whether early bipeds walked more like humans, with energetically efficient extended hind limbs, or more like apes with flexed hind limbs. The 3.6 million year old hominin footprints at Laetoli, Tanzania represent the earliest direct evidence of hominin bipedalism. Determining the kinematics of Laetoli hominins will allow us to understand whether selection acted to decrease energy costs of bipedalism by 3.6 Ma. METHODOLOGY/PRINCIPAL FINDINGS: Using an experimental design, we show that the Laetoli hominins walked with weight transfer most similar to the economical extended limb bipedalism of humans. Humans walked through a sand trackway using both extended limb bipedalism, and more flexed limb bipedalism. Footprint morphology from extended limb trials matches weight distribution patterns found in the Laetoli footprints. CONCLUSIONS: These results provide us with the earliest direct evidence of kinematically human-like bipedalism currently known, and show that extended limb bipedalism evolved long before the appearance of the genus Homo. Since extended-limb bipedalism is more energetically economical than ape-like bipedalism, energy expenditure was likely an important selection pressure on hominin bipeds by 3.6 Ma.

Stratigraphic interpretation of the Kulu Formation (Early Miocene, Rusinga Island, Kenya) and its implications for primate evolution.

Early Miocene fossils from Rusinga Island, Kenya, provide some of the best evidence for catarrhine evolution and diversification, and, together with more than eighty-five other mammalian species, form an important comparative reference for understanding faunal succession in East Africa. While there is consensus over the stratigraphic position of most of Rusinga's volcaniclastic deposits, the lacustrine Kulu Formation has been placed in various parts of the geological sequence by different researchers. To resolve this discrepancy, we conducted detailed geological analyses which indicate that the Kulu Formation was formed in the Early Miocene during a period of volcanic inactivity and subsidence following the early, mainly explosive hyper-alkaline phase of the Kisingiri complex and prior to the final eruptions of nephelinitic lavas. The underlying Hiwegi and older formations were locally deformed and deeply eroded before sedimentation began in the Kulu basin, so that the Kulu sediments may be significantly younger than the 17.8 Ma Hiwegi Formation and not much older than the overlying Kiangata Agglomerata-Lunene Lava series, loosely dated to ca. 15 Ma. The overall similarities between Kulu and Hiwegi faunas imply long-term ecological stability in this region. Our stratigraphic interpretation suggests that the Kulu fauna is contemporaneous with faunas from West Turkana, implying that differences between these assemblages-particularly in the primate communities--reflect paleobiogeographic and/or paleocological differences. Finally, the position of the Kulu Formation restricts the time frame during which the substantial faunal turnover seen in the differences between the primate and mammalian communities of Rusinga and Maboko Islands could have occurred.