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Review of "Publishing Scholarly Editing: Archives, Computing, and Experience" by Christopher Ohge
No full textPaper 14: Is the Use of a Postoperative Hip Orthosis Beneficial Following Routine Arthroscopy of the Hip? A Retrospective Cohort Study
No full textA grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Objectives:
Treatment of intra- and extra-articular pathologies of the hip via arthroscopy continues to gain popularity. To date, the impact of routinely bracing patients postoperatively on patient reported outcome measures (PROMs) and re-operation rate has not been elucidated. The purpose of this study is to determine if there is a difference in PROMs and re-operation rate for patients who were braced versus those who were not braced following routine hip arthroscopy.
Methods:
This was a retrospective review of 193 patients who underwent hip arthroscopy from 2018 to 2021 by two orthopedic surgeons at a single institution. 101 patients prior to July 1, 2019 were immobilized in a hip orthosis following hip arthroscopy whereas 92 patients after July 1, 2019 were not. Baseline patient reported outcomes in the form of visual analog pain scale (VAS), modified Harris Hip Score (M-HHS), single assessment numeric evaluation (SANE) hip scores, VR-12 physical score, VR-12 mental score were obtained for all patients in both cohorts and postoperatively repeated at two weeks, four weeks, three months, six months, one year, and two years. Additionally, results were stratified by gender to assess gender-based difference. The groups were then compared to evaluate for a difference in PROMs over time. T-tests or Wilcoxon ranked-sum were utilized to compare these groups depending on normality of the data. Comparisons of categorical demographics such as age and gender between bracing groups were assessed using chi-squared tests. Re-operation rate was compared between the two groups using the Fischer Exact Test. Statistical significance was set at p<0.05 for all analyses.
Results:
After analyzing a cohort of patients who were braced and a cohort who were not braced postoperatively, no significant difference (p>.05) in PROMs at two weeks, four weeks, three months, one year or two years was detected for VAS, mHHS, SANE, VR-12 Physical and VR-12 Mental. No significant difference in reoperation rate was detected for the braced vs the non-braced cohort (p=.105). Demographics were not significantly different regarding gender distribution (p=0.418) and age (p=0.087) between groups.
Conclusions:
The findings above suggest the use of an orthosis after routine hip arthroscopy does not improve patient reported outcomes or alter the reoperation rate. Postoperative bracing increases perioperative cost and by foregoing routine bracing, patients may avoid associated morbidity that can come with wearing a brace for a prolonged period of time. The results of this project will help to guide clinical decision making as it pertains to whether to use a postoperative hip orthosis following routine hip arthroscopy
Enhanced Constitutive Theories for Classical Thermoviscoelastic Polymeric Fluids
No full textThis thesis presents ordered rate nonlinear constitutive theories for thermoviscoelastic fluids based on classical continuum mechanics (CCM). We refer to these fluids as classical thermoviscoelastic polymeric fluids. The conservation and balance laws of CCM constitute the core of the mathematical model. Constitutive theories for the Cauchy stress tensor are derived using the conjugate pair in the entropy inequality, additional desired physics, and the representation theorem. The constitutive theories for the Cauchy stress tensor consider convected time derivatives of Green’s strain tensor or Almansi strain tensor up to order n and the convected time derivatives of the Cauchy stress tensor up to order m. The resulting constitutive theories of order (m,n) are based on integrity and are valid for dilute as well as dense polymeric, compressible, and incompressible fluids with variable material coefficients. It is shown that Maxwell, Oldroyd-B, and Giesekus constitutive models can be described by a single constitutive theory. It is well established that the currently used Maxwell and Oldroyd-B models predict zero normal stress perpendicular to the flow direction. It is shown that this deficiency is a consequence of not retaining certain generators and invariants from the integrity (complete basis) in the constitutive theory and can be corrected by including additional generators and invariants in the constitutive theory. Similar improvements are also suggested for the Giesekus constitutive model. Model problem studies are presented for BVPs consisting of fully developed flow between parallel plates and lid driven cavities utilizing the new constitutive theories for Maxwell, Oldroyd-B, and Giesekus fluids. Results are comparedwith those obtained from currently used constitutive theories for the three polymeric fluids
A broadband thermal emission spectrum of the ultra-hot Jupiter WASP-18b
No full textClose-in giant exoplanets with temperatures greater than 2,000 K (‘ultra-hot Jupiters’) have been the subject of extensive efforts to determine their atmospheric properties using thermal emission measurements from the Hubble Space Telescope (HST) and Spitzer Space Telescope1–3. However, previous studies have yielded inconsistent results because the small sizes of the spectral features and the limited information content of the data resulted in high sensitivity to the varying assumptions made in the treatment of instrument systematics and the atmospheric retrieval analysis3–12. Here we present a dayside thermal emission spectrum of the ultra-hot Jupiter WASP-18b obtained with the NIRISS13 instrument on the JWST. The data span 0.85 to 2.85 μm in wavelength at an average resolving power of 400 and exhibit minimal systematics. The spectrum shows three water emission features (at >6σ confidence) and evidence for optical opacity, possibly attributable to H−, TiO and VO (combined significance of 3.8σ). Models that fit the data require a thermal inversion, molecular dissociation as predicted by chemical equilibrium, a solar heavy-element abundance (‘metallicity’, M/H=1.03+1.11−0.51 times solar) and a carbon-to-oxygen (C/O) ratio less than unity. The data also yield a dayside brightness temperature map, which shows a peak in temperature near the substellar point that decreases steeply and symmetrically with longitude towards the terminators
De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica
No full textWe announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated “Haplotype 1”) is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome
Bio-inspired Reinforcement Learning & Predictive Flight Controllers for Unmanned Aerial Systems
No full textRecent advancements in computer technologies have dramatically increased the onboard processing power of autonomous aircraft as well as the performance of autopilot systems. The combination of exponential growth in applications of autonomous aircraft and computationally potent avionic systems provides opportunities and demand for adaptive, learning, and cognitive flight controller methods. This work investigates two flight controller methods: model predictive control (MPC) and reinforcement learning (RL) for fixed-wing UASs.In addition to the adaptivity of flight controllers, the transferability of controllers between aircraft in the same class is highly desirable. Therefore, using and adapting a flight controller between different aircraft can save overhead costs, time, and effort. This work uniquely presents a method to develop model-agnostic RL-based flight controllers capable of controlling aircraft platforms in the same class/category but different dynamic models (e.g., fixed-wing twin-boom pusher UASs weighing less than 12 lbs (5.4 kg)). The proposed method uses dynamic randomization of aircraft stability and control derivatives to develop the training environment and incorporate the memory functions into the policy using a recurrent neural network (RNN). Flying autonomous aircraft in constraint spaces (e.g., metropolitan areas, etc.) can result in a phase shift in the control signal and undesirable and sustained oscillations. Therefore, a unified RL-based longitudinal control policy is also developed to mitigate the oscillation issues due to coupling between outer (guidance) and inner loop control blocks. In addition, the dynamic model of aircraft is improved using the cross-entropy method (CEM) algorithm. CEM is a derivative-free optimization algorithm that supports process parallelization and can learn from actual flight test data to improve the fidelity of the dynamic model of aircraft. The MPC is formulated as a receding horizon control problem for the linearized aircraft model with a set of control constraints which is solved using the Sequential Quadratic Programming (SQP) optimization method. Uniquely, the stability of the MPC closed-loop system (GNC) is analyzed through Lyapunov theory, assessed by 1000 Monte Carlo numerical simulations. All the developed flight controllers were uniquely verified and validated (V&V) in actual flight tests and compared with two base flight controllers (commercial-off-the-shelf and LQR) explicitly designed for the testbed platforms. Two UAS platforms with different dynamics and weather conditions from low to medium wind intensities were chosen to evaluate proposed methods for practically viable flight controllers. MPC flight controllers' sensitivity to pertinent design parameters, such as controller update rate and the prediction horizon, were evaluated through flight tests.Finally, the controllers' performance, stability, and resilience to the partial failure of the control surfaces were investigated and documented
Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain
No full textProtonation of key histidine residues has been long implicated in the acid-mediated cellular action of the diphtheria toxin translocation (T-) domain, responsible for the delivery of the catalytic domain into the cell. Here, we use a combination of computational (constant-pH Molecular Dynamics simulations) and experimental (NMR, circular dichroism, and fluorescence spectroscopy along with the X-ray crystallography) approaches to characterize the initial stages of conformational change happening in solution in the wild-type T-domain and in the H223Q/H257Q double mutant. This replacement suppresses the acid-induced transition, resulting in the retention of a more stable protein structure in solutions at pH 5.5 and, consequently, in reduced membrane-disrupting activity. Here, for the first time, we report the pKa values of the histidine residues of the T-domain, measured by NMR-monitored pH titrations. Most peaks in the histidine side chain spectral region are titrated with pKas ranging from 6.2 to 6.8. However, the two most up-field peaks display little change down to pH 6, which is a limiting pH for this protein in solution at concentrations required for NMR. These peaks are absent in the double mutant, suggesting they belong to H223 and H257. The constant-pH simulations indicate that for the T-domain in solution, the pKa values for histidine residues range from 3.0 to 6.5, with those most difficult to protonate being H251 and H257. Taken together, our experimental and computational data demonstrate that previously suggested cooperative protonation of all six histidines in the T-domain does not occur
Evolution of five environmentally responsive gene families in a pine‐feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae
No full textA central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine‐specialized lineage evolved from angiosperm‐feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high‐quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under‐sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized
Biophysical and biochemical characterization of TolC as a potential target for efflux pump inhibition
No full textAntibiotic resistance is a major global threat to public health faced by healthcare services. Currently, about 1.27 million deaths are attributable to antibiotic-resistant infections globally. Global deaths attributable to antibiotic resistance have been predicted to increase to about 10 million by 2050 with an estimated global economic burden of about 100 million dollars. Overexpression of efflux pumps has been reported to be directly correlated with antibiotic resistance of different bacterial pathogens. The AcrAB-TolC system which belongs to the resistance-nodulation-division (RND) superfamily of efflux pumps, exclusively found in Gram-negative bacteria, is the best-characterized efflux pump in E. coli. Deletion of the gene that encodes TolC, the outer membrane component of the AcrAB-TolC efflux pump has been reported to significantly decreased bacterial resistance to many antibiotics. However, there is a limited understanding of the mechanism of TolC biogenesis due to its unique structure. This dissertation reports a systemic biophysical and biochemical characterization of TolC. We have developed a very easy-to-use, highly efficient method for the high-yield production of TolC from inclusion bodies. Also, we have used various biophysical techniques to systematically characterize the effect of various detergent properties on the folding of TolC. We have also used some in vitro and in vivo assays to show that the biogenesis of TolC involves the formation of folded periplasmic intermediates. We believe that the works reported in this dissertation will open the door to the design and development of TolC-assembly-pathway-targeted efflux pump inhibitors
“How does it feel with my teeth in your heart?”: Medea’s Persistent Mode of Maternal Agency Through Literary Eras
No full textAcross classics, authors have presented the mythologies of mothers who fail to conform to traditional modes of maternity and femininity. Mothers like Jocasta and Alcmene attempt to kill their children by “exposing” them and abandoning them in the wilderness. Oedipus’ mother Jocasta pins his ankles together and leaves him on Cithaeron because an oracle warned that he would one day kill his father Laius. Alcmene, fearful of Hera’s wrath, abandoned Heracles in the woods. Although neither Oedipus nor Heracles died from their mother’s exposure, both stories demonstrate the presence of infanticide in classical mythology. Escalating this, the mother of King Pentheus of Thebes, Agave is driven insane by Dionysus and tears her son limb from limb and carried his head back to Thebes on a stake. Each of these mothers transgresses outside of accepted mode of maternity and femininity. Each of them betrayed the accepted traditions of the home and family. But their stories mostly remain underexplored by authors outside of classics. Perhaps this is because they were unsuccessful in their passive attempted infanticide in both Jocasta and Alcmene’s case, or because Agave was possessed by a god and driven to murder her adult son, their stories do not hold the same power that an active and decisive mother does. Thus, there is one classical mother that continues to captivate authors, scholars, and audiences across centuries, genres, and geographies. Medea