Causal networks for climate model evaluation and constrained projections

Global climate models are central tools for understanding past and future climate change. The assessment of model skill, in turn, can benefit from modern data science approaches. Here we apply causal discovery algorithms to sea level pressure data from a large set of climate model simulations and, as a proxy for observations, meteorological reanalyses. We demonstrate how the resulting causal networks (fingerprints) offer an objective pathway for process-oriented model evaluation. Models with fingerprints closer to observations better reproduce important precipitation patterns over highly populated areas such as the Indian subcontinent, Africa, East Asia, Europe and North America. We further identify expected model interdependencies due to shared development backgrounds. Finally, our network metrics provide stronger relationships for constraining precipitation projections under climate change as compared to traditional evaluation metrics for storm tracks or precipitation itself. Such emergent relationships highlight the potential of causal networks to constrain longstanding uncertainties in climate change projections. Algorithms to assess causal relationships in data sets have seen increasing applications in climate science in recent years. Here, the authors show that these techniques can help to systematically evaluate the performance of climate models and, as a result, to constrain uncertainties in future climate change projections

Renovation of Nitrogenous Wastewater Via Land Application

Removal of inorganic and organic nitrogen from wastewater prior to recharge of ground and surface waters can be accomplished by judicious land application. This study focused attention upon the feasibility of using sprinkler irrigation as the wastewater delivery system with coastal bermudagrass (Cynodon dactylon L.,var. coastal) pasture as the wastewater sink. One site was located on a Sawyer soil near El Dorado, while the other was located on a Savannah soil near Malvern. This report is limited to the renovation of surface waters. Results revealed that nitrogen concentration in runoff water from rainfall was substantially less than nitrogen concentration of the wastewater applied to the soil and similar to background levels. Such results support the consideration of land application as a viable wastewater disposal method

A helicoidal transfer matrix model for inhomogeneous DNA melting

An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.Comment: v3: Matlab toolbox included with source file; article unchanged, 12 pages, 11 figures, RevTe

An Investigation of the Host Specificity of the Brown-headed Cowbird

We attempted to determine the factors associated with the lack of parasitism of the Common Grackle (Quiscalus quiscula) by the Brown-headed Cowbird (Molothrus ater). We investigated the breeding phenology of the two species, the responses of colonial- and noncolonial-nesting grackles to female cowbird models, the frequency of artificial egg rejection by grackles, incubation success of cowbird eggs transferred into grackle nests, and the survival rates of cowbirds cross-fostered into grackle nests. By the time cowbirds began egg-laying at our study sites, 88.5 % of all grackle nests were beyond the point of successful parasitism. Grackles responded much more aggressively toward female cowbird models than to Fox Sparrow (Passerella iliaca) models. Grackles rejected artificial cowbirds eggs more frequently during the prelay stage of the nesting cycle (13 rejections at 32 nests) compared to later stages. However, the rejection frequency during the later stages of nesting (lay and incubation) was virtually the same as in Rothstein\u27s original study (1975) (12.4 % vs. 11.3 %). A total of 14 cowbird eggs and nestlings were cross-fostered into grackle nests. Data were collected on six cowbird nestlings, none of which survived to fledging. Five of the nestlings died after two days, and the sixth nestling survived five days despite having two grackle nestmates that were each a day older. Grackle nestlings weighed more than twice as much as cowbird nestlings at hatching (5.4 ± 0.91 g vs. 2.5 ± 0.72 g), and had significantly greater gape widths and culmen lengths for the first two days after hatching. The lack of survival of cowbird nestlings in grackle nests may be partially due to this size asymmetry. However, one cowbird nestling died after two days despite having no grackle nestmates to compete with, thus suggesting the possibility of some behavioral incompatibility. This was unexpected as it is generally believed that nestling passerines have similar dietary requirements, with the exception of those species that feed their young primarily seeds or fruit. Of the eight eggs that did not hatch, four appeared to be the result of ineffective incubation. These clutches contained between four and six eggs total, whereas the clutches in which cowbird eggs hatched contained a total of three eggs or fewer. These data support the host incubation hypothesis for egg removal by female cowbirds. If Brown-headed Cowbirds preferred larger hosts in the past (as indicated by the fact that all but one of the species that regularly eject cowbird eggs are larger than the cowbird), then it may have been advantageous for a female cowbird to remove at least one host egg to ensure more effective incubation of her own smaller egg. Mourning Doves (Zenaida macroura) like Common Grackles exhibit a high rate of parasitic egg rejection behavior (31.2 %) for an accepter species. Despite Rothstein’s (1975a) conclusion that no geographic variation in egg rejection behavior exists, we found Mourning Doves in central Illinois rejected artific ial cowbird eggs at nearly twice the rate (58.6 %, x2 = 3.7, df = 1, p \u3c 0.06) of those in Rothstein’s trials. The reason for the lack of geographic variation in Rothstein\u27s trials may be the result of small sample sizes

An Investigation of the Host Specificity of the Brown-headed Cowbird

We attempted to determine the factors associated with the lack of parasitism of the Common Grackle (Quiscalus quiscula) by the Brown-headed Cowbird (Molothrus ater). We investigated the breeding phenology of the two species, the responses of colonial- and noncolonial-nesting grackles to female cowbird models, the frequency of artificial egg rejection by grackles, incubation success of cowbird eggs transferred into grackle nests, and the survival rates of cowbirds cross-fostered into grackle nests. By the time cowbirds began egg-laying at our study sites, 88.5 % of all grackle nests were beyond the point of successful parasitism. Grackles responded much more aggressively toward female cowbird models than to Fox Sparrow (Passerella iliaca) models. Grackles rejected artificial cowbirds eggs more frequently during the prelay stage of the nesting cycle (13 rejections at 32 nests) compared to later stages. However, the rejection frequency during the later stages of nesting (lay and incubation) was virtually the same as in Rothstein\u27s original study (1975) (12.4 % vs. 11.3 %). A total of 14 cowbird eggs and nestlings were cross-fostered into grackle nests. Data were collected on six cowbird nestlings, none of which survived to fledging. Five of the nestlings died after two days, and the sixth nestling survived five days despite having two grackle nestmates that were each a day older. Grackle nestlings weighed more than twice as much as cowbird nestlings at hatching (5.4 ± 0.91 g vs. 2.5 ± 0.72 g), and had significantly greater gape widths and culmen lengths for the first two days after hatching. The lack of survival of cowbird nestlings in grackle nests may be partially due to this size asymmetry. However, one cowbird nestling died after two days despite having no grackle nestmates to compete with, thus suggesting the possibility of some behavioral incompatibility. This was unexpected as it is generally believed that nestling passerines have similar dietary requirements, with the exception of those species that feed their young primarily seeds or fruit. Of the eight eggs that did not hatch, four appeared to be the result of ineffective incubation. These clutches contained between four and six eggs total, whereas the clutches in which cowbird eggs hatched contained a total of three eggs or fewer. These data support the host incubation hypothesis for egg removal by female cowbirds. If Brown-headed Cowbirds preferred larger hosts in the past (as indicated by the fact that all but one of the species that regularly eject cowbird eggs are larger than the cowbird), then it may have been advantageous for a female cowbird to remove at least one host egg to ensure more effective incubation of her own smaller egg. Mourning Doves (Zenaida macroura) like Common Grackles exhibit a high rate of parasitic egg rejection behavior (31.2 %) for an accepter species. Despite Rothstein’s (1975a) conclusion that no geographic variation in egg rejection behavior exists, we found Mourning Doves in central Illinois rejected artific ial cowbird eggs at nearly twice the rate (58.6 %, x2 = 3.7, df = 1, p \u3c 0.06) of those in Rothstein’s trials. The reason for the lack of geographic variation in Rothstein\u27s trials may be the result of small sample sizes

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast). Results: In all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable. Conclusions: Most of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70% to 95% of total phosphoproteins, but only 40% to 60% of total p-sites

Rejection of Cowbird Eggs by Mourning Doves: A Manifestation of Nest Usurpation? Brian D. Peer and Eric K. Bollinger

This article was printed in The Auk, Volume 115, No.4 (1998)

EXPLANATIONS FOR THE INFREQUENT COWBIRD PARASITISM ON COMMON GRACKLES

We determined the factors responsible for the lack of parasitism on Common Grackles (Quiscalus quiscula) by Brown-headed Cowbirds (Molothrus ater). We found no evidence of parasitism on the 401 grackle nests we monitored in east-central Illinois. By the time cowbirds began laying eggs, 88.5% of all grackle nests were beyond the point of successful parasitism. Grackles rejected cowbird eggs more frequently during the prelaying stage of the nesting cycle (38.2%) compared to later stages (12.3%). Thirty-three cowbird eggs and nestlings were cross-fostered into grackle nests. Data were collected on 15 cowbird nestlings, of which three fledged. The cross-fostered cowbird eggs that did not hatch appeared to have been incubated ineffectively. These eggs were in clutches that contained four to six eggs, whereas the cowbird eggs that hatched were in clutches of three eggs or less. Grackles also responded more aggressively toward female cowbird models than to Fox Sparrow (Passerella iliaca) models in five of seven response categories. Cowbirds avoid parasitizing grackles even though the opportunity existed. Nest abandonment and infestation of grackle nests with ectoparasitic mites may decrease the suitability of grackles as hosts; however the primary reason for the infrequent cowbird parasitism on grackles appears to be past rejection behavior. Grackles likely rejected cowbird eggs at a higher frequency in the past and as a consequence grackles were avoided by cowbirds. Rejection apparently decreased in the absence of parasitism due to the high degree of intraclutch egg variability exhibited by grackles whiwhich would increase the chances of them mistakenly rejecting their own discordant eggs

Long-term Follow Up of Van Nes Rotationplasty for Proximal Focal Femoral Deficiency

Proximal focal femoral deficiency (PFFD) is a congenital anomaly that presents challenges for orthopaedic and prosthetic management. The Van Nes rotationplasty is one treatment in which the extremity is surgically rotated to utilize the ankle and foot as a functional knee joint in a prosthesis. The purpose of this study is to determine the long-term functional and quality of life (QOL) outcomes for individuals who have undergone rotationplasty surgery for congenital PFFD compared to age and gender matched controls

Long-term Follow up of Van Nes Rotationplasty for Congenital Proximal Focal Femoral Deficiency [Proceedings]

INTRODUCTIONProximal focal femoral deficiency (PFFD) is a congenital anomaly that presents challenges for orthopaedic and prosthetic management. The Van Nes rotationplasty is one treatment in which the extremity is surgically rotated to utilize the ankle and foot as a functional knee joint in a prosthesis. The purpose of this study is to determine the long-term functional and quality of life (QOL) outcomes for individuals who have undergone rotationplasty surgery for congenital PFFD compared to age and gender matched controls. METHODSThis prospective study had 12 prosthetic participants (PFFD Group: 8 M, 4F, age range 16-57 years) average 31.6±13.5 years and 12 control participants (Control Group: 8M, 4F) with an average age 32.6±14.1 years. Participants completed the following outcome questionnaires: SF-36, Revised-Faces Pain Scale, Harris Hip Score, Oswestry back pain score; and underwent lower extremity range of motion (ROM), hand held dynamometry, gait analysis, computerized dynamic posturography and Timed ‘Up& Go’ (TUG) testing. The PFFD Group also completed the Prosthetic Evaluation Questionnaire© (PEQ). The Wilcoxon Signed rank test was used to statistically compare each PFFD Group participant to the matched Control Group participant with values statistically significant at p\u3c 0.0123. RESULTSParticipants had rotationplasty performed at an average age of 6.5±3.9 years with follow up testing done 25.1±11.2 years later. All adult subjects were working full time in a variety of manual and office/desk jobs. No significant issues were seen for body image. Pain: The PFFD and Control Groups both reported similar low back pain with 6.8±9.7% and 7.0±13.0% disability respectively on the Oswestry back pain questionnaire. On the day of testing, only one PFFD participant reported mild low back pain on the Revised- Faces Pain Scale. The average Harris Hip Score for the PFFD Group was 92.7±9.2 out of 100, indicating excellent outcome. Two participants reported pain on their non-prosthetic hip. ROM: The PFFD Group showed significantly decreased hip flexion and ankle dorsiflexion, and increased ankle plantarflexion strength on the prosthetic side compared to the Control Group. The PFFD Group had significantly greater ankle abduction strength on their non-prosthetic side compared to the Control Group. Strength: The PFFD Group demonstrated significantly weaker hip flexion, hip abduction and ankle plantarflexion on the prosthetic side compared to the Control Group. TUG: The PFFD Group scored an average of 8.5±1.6 seconds on the TUG, demonstrating a low fall risk. The Control Group scored significantly lower with an average of 6.5 ±1.0 seconds. SF-36: There were no significant differences between the groups in overall health and well-being. PEQ©: The PFFD Group scored lower in areas of satisfaction, appearance, and sounds of the prosthesis. However, participants reported that others perceived them well and they did not see themselves as a social burden. Gait Analysis: Temporal-spatial gait parameters for the PFFD Group demonstrated significant decrease in cadence, stride time, opposite foot off, single support and walking speed compared to Control Group. Posturography: The PFFD Group showed significant decrease in symmetry in stance, as well as a decrease in end point and maximum excursion in limits of stability testing compared to the Control Group. DISCUSSION AND CONCLUSIONOverall, long-term follow up of teens and adults who underwent Van Nes rotationplasty showed that they maintained a high level of function, participation and QOL. They did present with significant differences in temporal spatial and posturography parameters compared to the Control Group