Bedrock channel response to tetonic, climatic and eustatic forcings

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2001.Includes bibliographical references.The response of bedrock channels to external forcings is investigated in this thesis. The approach is to test and constrain a theoretical model for bedrock-channel incision based on shear stress using field data. The primary study area is a series of 21 small, coastal drainage basins in northern California, USA with known, varying rates and history of rock uplift. The initial application of a simple form of the model to the stream profiles suggests that (1) the channels are eroding at rates approximately equal to uplift rates (i.e. steady-state fluvial incision), and (2) erosion processes are proportionally more effective in the high-uplift-rate zone, with factors in addition to channel gradient responding to tectonic forcing. These results lead to the rest of the study, in which some of the assumptions of the simple model are rejected in order to explain the second observation. A more sophisticated model that includes both a stochastic distribution of floods and a threshold shear stress to initiate bedrock erosion predicts that a greater part of the distribution of flood events will exceed the threshold in steeper channels. Therefore, higher-gradient channels have proportionally higher erosion rates, as is observed in the high-uplift-rate streams of the California field site. The shear-stress model is tested and constrained through a detailed, field-based analysis of topography, lithology, stream morphology and regional hydrology to isolate those factors that respond to tectonics. The stochastic model is able to incorporate the observed variation in stream discharge due to orographic enhancement of precipitation by high topography associated with high uplift rates.(cont.) This increase in discharge appears to play a second-order role in setting the erosional effectiveness of the high-uplift zone. Other factors, including channel width, lithologic resistance and sediment flux, do not appear to vary in an important way with uplift rate, although this conclusion is based on analyses that have some limitations. The importance of thresholds is underscored by a direct calculation of critical shear stress during a rare bedrock-incision event in a low-erosion-rate creek in New York state (= 100-200 Pa). This event, the only one that caused significant bedrock plucking at the site in an -40-year period, is consistent with a low erosion rate, with few events that exceed the threshold. In contrast, similar 'z values are exceeded during high-frequency flood events in the steep, rapidly eroding California streams. Inclusion of an erosion threshold accounts for the observed relationship between channel gradient and rock-uplift rate in the California site. In summary, by using field examples, the shear-stress bedrock-incision model with a stochastic distribution of flood events and an erosion threshold is demonstrated to be an effective and powerful tool for exploring relationships amongst climatic, tectonic and surficial processes. In the final section of this thesis, a numerical modeling study couples the shear-stress model for onshore fluvial incision with a simple rule for offshore wave-based erosion of bedrock to explore the response of uplifting streams to eustatic fluctuations ...by Noah P. Snyder.Ph.D

Identifying wildlife reservoirs of neglected taeniid tapeworms : non-invasive diagnosis of endemic Taenia serialis infection in a wild primate population

Despite the global distribution and public health consequences of Taenia tapeworms, the life cycles of taeniids infecting wildlife hosts remain largely undescribed. The larval stage of Taenia serialis commonly parasitizes rodents and lagomorphs, but has been reported in a wide range of hosts that includes geladas (Theropithecus gelada), primates endemic to Ethiopia. Geladas exhibit protuberant larval cysts indicative of advanced T. serialis infection that are associated with high mortality. However, non-protuberant larvae can develop in deep tissue or the abdominal cavity, leading to underestimates of prevalence based solely on observable cysts. We adapted a non-invasive monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) to detect circulating Taenia spp. antigen in dried gelada urine. Analysis revealed that this assay was highly accurate in detecting Taenia antigen, with 98.4% specificity, 98.5% sensitivity, and an area under the curve of 0.99. We used this assay to investigate the prevalence of T. serialis infection in a wild gelada population, finding that infection is substantially more widespread than the occurrence of visible T. serialis cysts (16.4% tested positive at least once, while only 6% of the same population exhibited cysts). We examined whether age or sex predicted T. serialis infection as indicated by external cysts and antigen presence. Contrary to the female-bias observed in many Taenia-host systems, we found no significant sex bias in either cyst presence or antigen presence. Age, on the other hand, predicted cyst presence (older individuals were more likely to show cysts) but not antigen presence. We interpret this finding to indicate that T. serialis may infect individuals early in life but only result in visible disease later in life. This is the first application of an antigen ELISA to the study of larval Taenia infection in wildlife, opening the doors to the identification and description of infection dynamics in reservoir populations

Report on the May-June 2002 Englebright Lake deep coring campaign

This report describes the May-June 2002 Englebright Lake coring project. Englebright Lake is a 14-km-long reservoir on the Yuba River of northern California, impounded by Englebright Dam, which was completed in 1940. The sediments were cored to assess the current conditions in the reservoir as part of the California Bay-Delta Authority’s Upper Yuba River Studies Program. Sediment was collected using both hydraulic-piston and rotational coring equipment mounted on a floating drilling platform. Thirty boreholes were attempted at 7 sites spaced along the longitudinal axis of the reservoir. Complete sedimentary sections were recovered from 20 boreholes at 6 sites. In total, 335 m of sediment was cored, with 86% average recovery. The core sections (each up to 1.5 m long) were processed using a standard set of laboratory techniques, including geophysical logging of physical properties, splitting, visual descriptions, digital photography, and initial subsampling. This report presents the results of these analyses in a series of stratigraphic columns. Using the observed stratigraphy as a guide, several series of subsamples were collected for various sedimentologic, geochemical, and geochronological analyses. The results of laboratory analyses of most of these subsamples will be presented in future reports and articles

Sediment grain-size and loss-on-ignition analyses from 2002 Englebright Lake coring and sampling campaigns

This report presents sedimentologic data from three 2002 sampling campaigns conducted in Englebright Lake on the Yuba River in northern California. This work was done to assess the properties of the material deposited in the reservoir between completion of Englebright Dam in 1940 and 2002, as part of the Upper Yuba River Studies Program. Included are the results of grain-size-distribution and loss-on-ignition analyses for 561 samples, as well as an error analysis based on replicate pairs of subsamples

Cyclotomic integers, fusion categories, and subfactors

Dimensions of objects in fusion categories are cyclotomic integers, hence number theoretic results have implications in the study of fusion categories and finite depth subfactors. We give two such applications. The first application is determining a complete list of numbers in the interval (2, 76/33) which can occur as the Frobenius-Perron dimension of an object in a fusion category. The smallest number on this list is realized in a new fusion category which is constructed in the appendix written by V. Ostrik, while the others are all realized by known examples. The second application proves that in any family of graphs obtained by adding a 2-valent tree to a fixed graph, either only finitely many graphs are principal graphs of subfactors or the family consists of the A_n or D_n Dynkin diagrams. This result is effective, and we apply it to several families arising in the classification of subfactors of index less then 5.Comment: 47 pages, with an appendix by Victor Ostri

Quantum subgroups of the Haagerup fusion categories

We answer three related questions concerning the Haagerup subfactor and its even parts, the Haagerup fusion categories. Namely we find all simple module categories over each of the Haagerup fusion categories (in other words, we find the `"quantum subgroups" in the sense of Ocneanu), we find all subfactors whose principal even part is one of the Haagerup fusion categories, and we compute the Brauer-Picard groupoid of Morita equivalences of the Haagerup fusion categories. In addition to the two even parts of the Haagerup subfactor, there is exactly one more fusion category which is Morita equivalent to each of them. This third fusion category has six simple objects and the same fusion rules as one of the even parts of the Haagerup subfactor, but has not previously appeared in the literature. We also find the full lattice of intermediate subfactors for every subfactor whose even part is one of these three fusion categories, and we discuss how our results generalize to Izumi subfactors.Comment: Final version. 40 pages, many figure

Sociality predicts individual variation in the immunity of free-ranging rhesus macaques

This work was supported by CONICYT-Chilean scholarship [number 72190290], NIH grant [number R01AG060931] to N.S-M., L.J.N.B. and J.P.H., NIH grant [number R00AG051764] to N.S-M., NIH grant [number MH118203] to L.J.N.B.. and M.L.P, and NSF grant [number 1800558] to J.P.H. and Susan Anton. The CPRC is supported by the National Institutes of Health. An Animal and Biological Material Resource Center Grant [P40OD012217] was awarded to UPR from the Office of Research Infrastructure Programs (ORIP), and a Research Facilities Construction Grant [C06OD026690] was awarded for the renovation of CPRC facilities after Hurricane Maria.Social integration and social status can substantially affect an individual's health and survival. One route through which this occurs is by altering immune function, which can be highly sensitive to changes in the social environment. However, we currently have limited understanding of how sociality influences markers of immunity in naturalistic populations where social dynamics can be fully realized. To address this gap, we asked if social integration and social status in free-ranging rhesus macaques (Macaca mulatta) predict anatomical and physiological markers of immunity. We used data on agonistic interactions to determine social status, and social network analysis of grooming interactions to generate measures of individual variation in social integration. As measures of immunity, we included the size of two of the major organs involved in the immune response, the spleen and liver, and counts of three types of blood cells (red blood cells, platelets, and white blood cells). Controlling for body mass and age, we found that neither social status nor social integration predicted the size of anatomical markers of immunity. However, individuals that were more socially connected, i.e., with more grooming partners, had lower numbers of white blood cells than their socially isolated counterparts, indicating lower levels of inflammation with increasing levels of integration. These results build upon and extend our knowledge of the relationship between sociality and the immune system in humans and captive animals to free-ranging primates, demonstrating generalizability of the beneficial role of social integration on health.Publisher PDFPeer reviewe

Trade-offs between sociality and gastrointestinal parasite infection in the context of a natural disaster

This work was supported by ANID-Chilean scholarship [number 72190290], the National Institutes of Health Grants [R01AG060931] to N.S-M., L.J.N.B. and J.P.H., [R00AG051764] to N.S-M, [R01MH118203] to M.L.P., M.J.M, L.J.N.B. and N.S-M., [R01MH096875] to M.L.P., L.J.N.B. and M.J.M., [U01MH121260] to N.S-M., M.L.P. and M.J.M., a European Research Council Consolidator Grant to L.J.N.B. [Friend Origins - 864461].Parasites and infectious diseases constitute important challenges particularly for group-living animals. Social contact and shared space can both increase parasite transmission risk, while individual differences in social capital can help prevent infections. For example, high social status individuals and those with more or stronger affiliative partnerships may have better immunity and, thus, lower parasitic burden. To test for health trade-offs in the costs and benefits of sociality, we quantified how parasitic load varied with an individual's social status, as well as with their affiliative relationships with weakly and strongly bonded partners, in a free-ranging population of rhesus macaques, Macaca mulatta. We found that high status was associated with a lower risk of protozoa infection at older ages compared to younger and low-status animals. Social resources can also be protective against infection under environmentally challenging situations, such as natural disasters. Using cross-sectional data, we additionally examined the impact of a major hurricane on the sociality - parasite relationship in this system and found that the hurricane influenced the prevalence of specific parasites independent of sociality. Overall, our study adds to the growing evidence for social status as a strong predictor of infection risk and highlights how extreme environmental events could shape vulnerability and resistance to infection.Peer reviewe

Social connections predict brain structure in a multidimensional free-ranging primate society

Reproduction and survival in most primate species reflects management of both competitive and cooperative relationships. Here, we investigated the links between neuroanatomy and sociality in free-ranging rhesus macaques. In adults, the number of social partners predicted the volume of the mid–superior temporal sulcus and ventral-dysgranular insula, implicated in social decision-making and empathy, respectively. We found no link between brain structure and other key social variables such as social status or indirect connectedness in adults, nor between maternal social networks or status and dependent infant brain structure. Our findings demonstrate that the size of specific brain structures varies with the number of direct affiliative social connections and suggest that this relationship may arise during development. These results reinforce proposed links between social network size, biological success, and the expansion of specific brain circuits

Canvass: a crowd-sourced, natural-product screening library for exploring biological space

NCATS thanks Dingyin Tao for assistance with compound characterization. This research was supported by the Intramural Research Program of the National Center for Advancing Translational Sciences, National Institutes of Health (NIH). R.B.A. acknowledges support from NSF (CHE-1665145) and NIH (GM126221). M.K.B. acknowledges support from NIH (5R01GM110131). N.Z.B. thanks support from NIGMS, NIH (R01GM114061). J.K.C. acknowledges support from NSF (CHE-1665331). J.C. acknowledges support from the Fogarty International Center, NIH (TW009872). P.A.C. acknowledges support from the National Cancer Institute (NCI), NIH (R01 CA158275), and the NIH/National Institute of Aging (P01 AG012411). N.K.G. acknowledges support from NSF (CHE-1464898). B.C.G. thanks the support of NSF (RUI: 213569), the Camille and Henry Dreyfus Foundation, and the Arnold and Mabel Beckman Foundation. C.C.H. thanks the start-up funds from the Scripps Institution of Oceanography for support. J.N.J. acknowledges support from NIH (GM 063557, GM 084333). A.D.K. thanks the support from NCI, NIH (P01CA125066). D.G.I.K. acknowledges support from the National Center for Complementary and Integrative Health (1 R01 AT008088) and the Fogarty International Center, NIH (U01 TW00313), and gratefully acknowledges courtesies extended by the Government of Madagascar (Ministere des Eaux et Forets). O.K. thanks NIH (R01GM071779) for financial support. T.J.M. acknowledges support from NIH (GM116952). S.M. acknowledges support from NIH (DA045884-01, DA046487-01, AA026949-01), the Office of the Assistant Secretary of Defense for Health Affairs through the Peer Reviewed Medical Research Program (W81XWH-17-1-0256), and NCI, NIH, through a Cancer Center Support Grant (P30 CA008748). K.N.M. thanks the California Department of Food and Agriculture Pierce's Disease and Glassy Winged Sharpshooter Board for support. B.T.M. thanks Michael Mullowney for his contribution in the isolation, elucidation, and submission of the compounds in this work. P.N. acknowledges support from NIH (R01 GM111476). L.E.O. acknowledges support from NIH (R01-HL25854, R01-GM30859, R0-1-NS-12389). L.E.B., J.K.S., and J.A.P. thank the NIH (R35 GM-118173, R24 GM-111625) for research support. F.R. thanks the American Lebanese Syrian Associated Charities (ALSAC) for financial support. I.S. thanks the University of Oklahoma Startup funds for support. J.T.S. acknowledges support from ACS PRF (53767-ND1) and NSF (CHE-1414298), and thanks Drs. Kellan N. Lamb and Michael J. Di Maso for their synthetic contribution. B.S. acknowledges support from NIH (CA78747, CA106150, GM114353, GM115575). W.S. acknowledges support from NIGMS, NIH (R15GM116032, P30 GM103450), and thanks the University of Arkansas for startup funds and the Arkansas Biosciences Institute (ABI) for seed money. C.R.J.S. acknowledges support from NIH (R01GM121656). D.S.T. thanks the support of NIH (T32 CA062948-Gudas) and PhRMA Foundation to A.L.V., NIH (P41 GM076267) to D.S.T., and CCSG NIH (P30 CA008748) to C.B. Thompson. R.E.T. acknowledges support from NIGMS, NIH (GM129465). R.J.T. thanks the American Cancer Society (RSG-12-253-01-CDD) and NSF (CHE1361173) for support. D.A.V. thanks the Camille and Henry Dreyfus Foundation, the National Science Foundation (CHE-0353662, CHE-1005253, and CHE-1725142), the Beckman Foundation, the Sherman Fairchild Foundation, the John Stauffer Charitable Trust, and the Christian Scholars Foundation for support. J.W. acknowledges support from the American Cancer Society through the Research Scholar Grant (RSG-13-011-01-CDD). W.M.W.acknowledges support from NIGMS, NIH (GM119426), and NSF (CHE1755698). A.Z. acknowledges support from NSF (CHE-1463819). (Intramural Research Program of the National Center for Advancing Translational Sciences, National Institutes of Health (NIH); CHE-1665145 - NSF; CHE-1665331 - NSF; CHE-1464898 - NSF; RUI: 213569 - NSF; CHE-1414298 - NSF; CHE1361173 - NSF; CHE1755698 - NSF; CHE-1463819 - NSF; GM126221 - NIH; 5R01GM110131 - NIH; GM 063557 - NIH; GM 084333 - NIH; R01GM071779 - NIH; GM116952 - NIH; DA045884-01 - NIH; DA046487-01 - NIH; AA026949-01 - NIH; R01 GM111476 - NIH; R01-HL25854 - NIH; R01-GM30859 - NIH; R0-1-NS-12389 - NIH; R35 GM-118173 - NIH; R24 GM-111625 - NIH; CA78747 - NIH; CA106150 - NIH; GM114353 - NIH; GM115575 - NIH; R01GM121656 - NIH; T32 CA062948-Gudas - NIH; P41 GM076267 - NIH; R01GM114061 - NIGMS, NIH; R15GM116032 - NIGMS, NIH; P30 GM103450 - NIGMS, NIH; GM129465 - NIGMS, NIH; GM119426 - NIGMS, NIH; TW009872 - Fogarty International Center, NIH; U01 TW00313 - Fogarty International Center, NIH; R01 CA158275 - National Cancer Institute (NCI), NIH; P01 AG012411 - NIH/National Institute of Aging; Camille and Henry Dreyfus Foundation; Arnold and Mabel Beckman Foundation; Scripps Institution of Oceanography; P01CA125066 - NCI, NIH; 1 R01 AT008088 - National Center for Complementary and Integrative Health; W81XWH-17-1-0256 - Office of the Assistant Secretary of Defense for Health Affairs through the Peer Reviewed Medical Research Program; P30 CA008748 - NCI, NIH, through a Cancer Center Support Grant; California Department of Food and Agriculture Pierce's Disease and Glassy Winged Sharpshooter Board; American Lebanese Syrian Associated Charities (ALSAC); University of Oklahoma Startup funds; 53767-ND1 - ACS PRF; PhRMA Foundation; P30 CA008748 - CCSG NIH; RSG-12-253-01-CDD - American Cancer Society; RSG-13-011-01-CDD - American Cancer Society; CHE-0353662 - National Science Foundation; CHE-1005253 - National Science Foundation; CHE-1725142 - National Science Foundation; Beckman Foundation; Sherman Fairchild Foundation; John Stauffer Charitable Trust; Christian Scholars Foundation)Published versionSupporting documentatio