Quarkonium states in a complex-valued potential

We calculate quarkonium binding energies using a realistic complex-valued potential for both an isotropic and anisotropic quark-gluon plasma. We determine the disassociation temperatures of the ground and first excited states considering both the real and imaginary parts of the binding energy. We show that the effect of momentum-space anisotropy is smaller on the imaginary part of the binding energy than on the real part of the binding energy. In the case that one assumes an isotropic plasma, we find disassociation temperatures for the J/psi, Upsilon and chi_b of 1.6 T_c, 2.8 T_c, and 1.5 T_c, respectively. We find that a finite oblate momentum-space anisotropy increases the disassociation temperature for all states considered and results in a splitting of the p-wave states associated with the chi_b first excited state of bottomonium.Comment: 23 pages, 9 figures; v4: subtraction of V_infinity corrected to only subtract Re[V_infinity

Effects of Modification of Pain Protocol on Incidence of Post Operative Nausea and Vomiting.

BackgroundA Perioperative Surgical Home (PSH) care model applies a standardized multidisciplinary approach to patient care using evidence-based medicine to modify and improve protocols. Analysis of patient outcome measures, such as postoperative nausea and vomiting (PONV), allows for refinement of existing protocols to improve patient care. We aim to compare the incidence of PONV in patients who underwent primary total joint arthroplasty before and after modification of our PSH pain protocol.MethodsAll total joint replacement PSH (TJR-PSH) patients who underwent primary THA (n=149) or TKA (n=212) in the study period were included. The modified protocol added a single dose of intravenous (IV) ketorolac given in the operating room and oxycodone immediate release orally instead of IV Hydromorphone in the Post Anesthesia Care Unit (PACU). The outcomes were (1) incidence of PONV and (2) average pain score in the PACU. We also examined the effect of primary anesthetic (spinal vs. GA) on these outcomes. The groups were compared using chi-square tests of proportions.ResultsThe incidence of post-operative nausea in the PACU decreased significantly with the modified protocol (27.4% vs. 38.1%, p=0.0442). There was no difference in PONV based on choice of anesthetic or procedure. Average PACU pain scores did not differ significantly between the two protocols.ConclusionSimple modifications to TJR-PSH multimodal pain management protocol, with decrease in IV narcotic use, resulted in a lower incidence of postoperative nausea, without compromising average PACU pain scores. This report demonstrates the need for continuous monitoring of PSH pathways and implementation of revisions as needed

Mismeasured Mortality: Correcting Estimates of Wolf Poaching in the United States

Measuring rates and causes of mortalities is important in animal ecology and management. Observing the fates of known individuals is a common method of estimating life history variables, including mortality patterns. It has long been assumed that data lost when known animals disappear were unbiased. We test and reject this assumption under conditions common to most, if not all, studies using marked animals. We illustrate the bias for 4 endangered wolf populations in the United States by reanalyzing data and assumptions about the known and unknown fates of marked wolves to calculate the degree to which risks of different causes of death were mismeasured. We find that, when using traditional methods, the relative risk of mortality from legal killing measured as a proportion of all known fates was overestimated by 0.05–0.16 and the relative risk of poaching was underestimated by 0.17–0.44. We show that published government estimates are affected by these biases and, importantly, are underestimating the risk of poaching. The underestimates have obscured the magnitude of poaching as the major threat to endangered wolf populations. We offer methods to correct estimates of mortality risk for marked animals of any taxon and describe the conditions under which traditional methods produce more or less bias. We also show how correcting past and future estimates of mortality parameters can address uncertainty about wildlife populations and increase the predictability and sustainability of wildlife management interventions

FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

A Cold Nearby Cloud Inside the Local Bubble

The high-latitude Galactic H I cloud toward the extragalactic radio source 3C 225 is characterized by very narrow 21 cm emission and absorption indicative of a very low H I spin temperature of about 20 K. Through high-resolution optical spectroscopy, we report the detection of strong, very narrow Na I absorption corresponding to this cloud toward a number of nearby stars. Assuming that the turbulent H I and Na I motions are similar, we derive a cloud temperature of 20 (+6, -8) K (in complete agreement with the 21 cm results) and a line-of-sight turbulent velocity of 0.37+/-0.08 km/s from a comparison of the H I and Na I absorption linewidths. We also place a firm upper limit of 45 pc on the distance of the cloud, which situates it well inside the Local Bubble in this direction and makes it the nearest-known cold diffuse cloud discovered to date.Comment: 11 pages, 3 figures, accepted for publication in ApJ Letter

TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program

A function for binaural integration in auditory grouping and segregation in the inferior colliculus

Responses of neurons to binaural, harmonic complex stimuli in urethane-anesthetized guinea pig inferior colliculus (IC) are reported. To assess the binaural integration of harmonicity cues for sound segregation and grouping, responses were measured to harmonic complexes with different fundamental frequencies presented to each ear. Simultaneously gated harmonic stimuli with fundamental frequencies of 125 Hz and 145 Hz were presented to the left and right ears, respectively, and recordings made from 96 neurons with characteristic frequencies >2 kHz in the central nucleus of the IC. Of these units, 70 responded continuously throughout the stimulus and were excited by the stimulus at the contralateral ear. The stimulus at the ipsilateral ear excited (EE: 14%; 10/70), inhibited (EI: 33%; 23/70), or had no significant effect (EO: 53%; 37/70), defined by the effect on firing rate. The neurons phase locked to the temporal envelope at each ear to varying degrees depending on signal level. Many of the cells (predominantly EO) were dominated by the response to the contralateral stimulus. Another group (predominantly EI) synchronized to the contralateral stimulus and were suppressed by the ipsilateral stimulus in a phasic manner. A third group synchronized to the stimuli at both ears (predominantly EE). Finally, a group only responded when the waveform peaks from each ear coincided. We conclude that these groups of neurons represent different “streams” of information but exhibit modifications of the response rather than encoding a feature of the stimulus, like pitch