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Background: Treat-all strategies improved patient outcomes, despite higher rates of loss to follow-up compared to the pre-treat era. Patients in Ethiopia experienced a higher rate of LTFU during the treat-all strategy period; however, studies did not identify contributing factors in comparison with previous strategies. This study aimed to assess the incidence and predictors of loss to follow-up before and after the start of the treat-all strategy among adults on anti-retroviral therapy in public health facilities in Hawassa City, Ethiopia. Methods: An institution-based retrospective follow-up study was conducted among 1190 randomly selected adults on antiretroviral therapy in public health facilities in Hawassa City. Using the Open Data Kit (ODK), data were collected from medical records and exported to Stata version 16 and R 4.2.1 for analysis. A Grays test and cumulative incidence curve were used to compare the cumulative incidence function of loss to follow-up. Bivariable and multivariable competing risk regression were fitted to identify predictors of LTFU and variables with a p-value <0.05 were considered significant. Results: The cumulative incidence of lost-to-follow-up was 4.92(3.84,6.3) and 8.67(7.26,10.3) per 100 person-years (PY) in pre-treat all and treat all cohorts, respectively. The cumulative incidence of mortality was 5.86(4.67,7.35) and 3(2.26,4.12) per 100 PY in pre-treat and treat all cohorts, respectively. Fair/poor adherence (aSHR:5.17; (95% CI 1.97, 13.51), underweight (aSHR:2.13; 95% CI: 1.15–3.93) and WHO stage III/IV (aSHR:2.69; 95% CI: 1.27, 5.71) were predictors of loss up in pre—treat all, whereas fair/poor adherence (aSHR = 2.07; 95% CI: 1.18, 3.68), underweight (aSHR:1.71; 95% CI: 1.13, 2.56), and CD4 cell >350 cell/m3 (aSHR: 1.67; 95% CI: 1.05, 2.65) predicts of loss up in treat all cohorts. Conclusion: This study demonstrated that the incidence of loss to follow-up was considerably higher in the treat-all period as compared to the pre-treat-all era. Poor medication compliance, underweight, and a CD4 level >350 cells/m3 contributed to the higher rate of LTFU in the treat-all strategy. Targeted interventions, such as nutritional support and strengthening medication adherence counseling, should be implemented to maintain treatment retention and reduce antiretroviral therapy dropout rates. [ABSTRACT FROM AUTHOR]

Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values—indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus. [ABSTRACT FROM AUTHOR]

The population-level case-fatality rate (CFR) associated with COVID-19 varies substantially, both across countries at any given time and within countries over time. We analyze the contribution of two key determinants of the variation in the observed CFR: the age-structure of diagnosed infection cases and age-specific case-fatality rates. We use data on diagnosed COVID-19 cases and death counts attributable to COVID-19 by age for China, Germany, Italy, South Korea, Spain, the United States, and New York City. We calculate the CFR for each population at the latest data point and also for Italy, Germany, Spain, and New York City over time. We use demographic decomposition to break the difference between CFRs into unique contributions arising from the age-structure of confirmed cases and the age-specific case-fatality. In late June 2020, CFRs varied from 2.2% in South Korea to 14.0% in Italy. The age-structure of detected cases often explains more than two-thirds of cross-country variation in the CFR. In Italy, the CFR increased from 4.2% to 14.0% between March 9 and June 30, 2020, and more than 90% of the change was due to increasing age-specific case-fatality rates. The importance of the age-structure of confirmed cases likely reflects several factors, including different testing regimes and differences in transmission trajectories; while increasing age-specific case-fatality rates in Italy could indicate other factors, such as the worsening health outcomes of those infected with COVID-19. Our findings lend support to recommendations for data to be disaggregated by age, and potentially other variables, to facilitate a better understanding of population-level differences in CFRs. They also show the need for well-designed seroprevalence studies to ascertain the extent to which differences in testing regimes drive differences in the age-structure of detected cases. [ABSTRACT FROM AUTHOR]

Entanglements affect marine mammal species around the globe, and for some, those impacts are great enough to cause population declines. This study aimed to document rates and causes of entanglement and trends in local haulout abundance for Steller and California sea lions on the north coast of Washington from 2010–2018. We conducted small boat surveys to count sea lions and document entangled individuals. Rates of entanglement and entangling material occurrence were compared with records of stranded individuals on the Washington and Oregon coast and with packing bands recorded during beach debris surveys. The rate of entanglement for California sea lions was 2.13%, almost entirely composed of adult males, with a peak rate during June and July potentially due to some entangled individuals not migrating to their breeding grounds. For Steller sea lions, the rate of entanglement was 0.41%, composed of 77% adults (32.4% male, 63.3% female), 17.1% juveniles, 5.9% unknown age, and no pups. Steller sea lions exhibited a 7.9% ± 3.2 rate of increase in abundance at the study haulouts, which was similar to that seen in California sea lions (7.8% ± 4.2); both increases were greater than the population growth rates observed range-wide despite high rates of entanglement. Most entanglements for both species were classified as packing bands, followed by entanglement scars. Salmon flashers were also prevalent and only occurred from June–September during the local ocean salmon troll fishery. Packing band occurrence in beach debris surveys correlated with packing band entanglements observed on haulouts. However, no packing band entanglements were observed in the stranding record and the rate of stranded animals exhibiting evidence of entanglement was lower than expected, indicating that entanglement survival is higher than previously assumed. Future studies tracking individual entanglement outcomes are needed to develop effective, targeted management strategies. [ABSTRACT FROM AUTHOR]

Research on the songbird zebra finch (Taeniopygia guttata) has advanced our behavioral, hormonal, neuronal, and genetic understanding of vocal learning. However, little is known about the impact of typical experimental manipulations on the welfare of these birds. Here we explore whether the undirected singing rate can be used as an indicator of welfare. We tested this idea by performing a post hoc analysis of singing behavior in isolated male zebra finches subjected to interactive white noise, to surgery, or to tethering. We find that the latter two experimental manipulations transiently but reliably decreased singing rates. By contraposition, we infer that a high-sustained singing rate is suggestive of successful coping or improved welfare in these experiments. Our analysis across more than 300 days of song data suggests that a singing rate above a threshold of several hundred song motifs per day implies an absence of an acute stressor or a successful coping with stress. Because singing rate can be measured in a completely automatic fashion, its observation can help to reduce experimenter bias in welfare monitoring. Because singing rate measurements are non-invasive, we expect this study to contribute to the refinement of the current welfare monitoring tools in zebra finches. [ABSTRACT FROM AUTHOR]

We analyzed COVID-19 data through May 6th, 2020 using a partially observed Markov process. Our method uses a hybrid deterministic and stochastic formalism that allows for time variable transmission rates and detection probabilities. The model was fit using iterated particle filtering to case count and death count time series from 55 countries. We found evidence for a shrinking epidemic in 30 of the 55 examined countries. Of those 30 countries, 27 have significant evidence for subcritical transmission rates, although the decline in new cases is relatively slow compared to the initial growth rates. Generally, the transmission rates in Europe were lower than in the Americas and Asia. This suggests that global scale social distancing efforts to slow the spread of COVID-19 are effective although they need to be strengthened in many regions and maintained in others to avoid further resurgence of COVID-19. The slow decline also suggests alternative strategies to control the virus are needed before social distancing efforts are partially relaxed. [ABSTRACT FROM AUTHOR]

Temporary pacemakers (TPMs) are usually inserted in an emergency situation. However, there are few reports available regarding which route of access is best or what the most preferred approach is currently in tertiary hospitals. This study aimed to compare procedure times, complication rates, and indications for temporary pacing between the transjugular and transfemoral approaches to TPM placement. We analyzed consecutive patients who underwent TPM placement. Indications; procedure times; and rates of complications including localized infection, any bleeding, and pacing wire repositioning rates were analyzed. A total of 732 patients (361 treated via the transjugular approach and 371 treated via the transfemoral approach) were included. Complete atrioventricular block was the most common cause of TPM placement in both groups, but sick sinus syndrome was especially common in the transjugular approach group. Separately, procedure time was significantly shorter in the transjugular approach group (9.0 ± 8.0 minutes vs. 11.9 ± 9.7 minutes; P < 0.001). Overall complication rates were not significantly different between the two groups, and longer duration of temporary pacing was a risk factor for repositioning. The risk of reposition was significantly increased when the temporary pacing was continued more than 5 days and 3 days in the transjugular approach group and the transfemoral approach group, respectively. The transjugular approach should be considered if the TPM is required for more than 3 days. [ABSTRACT FROM AUTHOR]

In deep underground engineering, in a large spatial, high-stress environment, rapid excavation is likely to affect the loading rate of the fault structure and to cause stick-slip. In this study, an experiment was conducted to explore the stick-slip characteristics at different loading rates. A double-sided shear experiment and the digital speckle correlation method were used to analyze the evolution of the displacement field, the slip displacement, and the slip rate of the fault's stick-slip activity at different loading rates as well as their correlation with the loading rate. The loading rate, moment magnitude, and stress drop of the fault's stick-slip and their corresponding relationships were studied. The results show that the occurrence of stick-slip is inversely proportional to the loading rate. The evolution of the fault-slip displacement field at different loading rates is similar. At a given loading rate, the magnitude is positively correlated with the stress drop. The magnitude and stress drop are inversely related to the loading rate. [ABSTRACT FROM AUTHOR]

It is standard practice to model site-to-site variability of substitution rates by discretizing a continuous distribution into a small number, K, of equiprobable rate categories. We demonstrate that the variance of this discretized distribution has an upper bound determined solely by the choice of K and the mean of the distribution. This bound can introduce biases into statistical inference, especially when estimating parameters governing site-to-site variability of substitution rates. Applications to two large collections of sequence alignments demonstrate that this upper bound is often reached in analyses of real data. When parameter estimation is of primary interest, additional rate categories or more flexible modeling methods should be considered. [ABSTRACT FROM AUTHOR]

Biological nitrogen (N) fixation is an important process supporting primary production in ecosystems, especially in those where N availability is limiting growth, such as peatlands and boreal forests. In many peatlands, peat mosses (genus Sphagnum) are the prime ecosystem engineers, and like feather mosses in boreal forests, they are associated with a diverse community of diazotrophs (N2-fixing microorganisms) that live in and on their tissue. The large variation in N2 fixation rates reported in literature remains, however, to be explained. To assess the potential roles of habitat (including nutrient concentration) and species traits (in particular litter decomposability and photosynthetic capacity) on the variability in N2 fixation rates, we compared rates associated with various Sphagnum moss species in a bog, the surrounding forest and a fen in Sweden. We found appreciable variation in N2 fixation rates among moss species and habitats, and showed that both species and habitat conditions strongly influenced N2 fixation. We here show that higher decomposition rates, as explained by lower levels of decomposition-inhibiting compounds, and higher phosphorous (P) levels, are related with higher diazotrophic activity. Combining our findings with those of other studies, we propose a conceptual model in which both species-specific traits of mosses (as related to the trade-off between rapid photosynthesis and resistance to decomposition) and P availability, explain N2 fixation rates. This is expected to result in a tight coupling between P and N cycling in peatlands. [ABSTRACT FROM AUTHOR]

Tooth replacement rate is an important contributor to feeding ecology for polyphyodont animals. Dinosaurs exhibit a wide range of tooth replacement rates, mirroring their diverse craniofacial specializations, but little is known about broad-scale allometric or evolutionary patterns within the group. In the current broad but sparse dinosaurian sample, only three non-avian theropod tooth replacement rates have been estimated. We estimated tooth formation and replacement rates in three additional non-avian theropod dinosaurs, the derived latest Cretaceous abelisaurid Majungasaurus and the more generalized Late Jurassic Allosaurus and Ceratosaurus. We created the largest dental histological and CT dataset for any theropod dinosaur, sectioning and scanning over a dozen toothed elements of Majungasaurus and several additional elements from the other two genera. Using this large sample, we created models of tooth formation time that allow for theropod replacement rates to be estimated non-destructively. In contrast to previous results for theropods, we found high tooth replacement rates in all three genera, with Allosaurus and Ceratosaurus rates of ~100 days and 56 days for Majungasaurus. The latter rate is on par with those of derived herbivorous dinosaurs including some neosauropods, hadrosaurids, and ceratopsians. This elevated rate may be a response to high rates of tooth wear in Majungasaurus. Within Dinosauria, there is no relationship between body mass and tooth replacement rate and no trends in replacement rate over time. Rather, tooth replacement rate is clade-specific, with elevated rates in abelisaurids and diplodocoids and lower rates in coelurosaurs. [ABSTRACT FROM AUTHOR]

Background: Firearm-related death rates and years of potential life lost (YPLL) vary widely between population subgroups and states. However, changes or inflections in temporal trends within subgroups and states are not fully documented. We assessed temporal patterns and inflections in the rates of firearm deaths and %YPLL due to firearms for overall and by sex, age, race/ethnicity, intent, and states in the United States between 1999 and 2016. Methods: We extracted age-adjusted firearm mortality and YPLL rates per 100,000, and %YPLL from 1999 to 2016 by using the WONDER (Wide-ranging Online Data for Epidemiologic Research) database. We used Joinpoint Regression to assess temporal trends, the inflection points, and annual percentage change (APC) from 1999 to 2016. Results: National firearm mortality rates were 10.3 and 11.8 per 100,000 in 1999 and 2016, with two distinct segments; a plateau until 2014 followed by an increase of APC = 7.2% (95% CI 3.1, 11.4). YPLL rates were from 304.7 and 338.2 in 1999 and 2016 with a steady APC increase in %YPLL of 0.65% (95% CI 0.43, 0.87) from 1999 to an inflection point in 2014, followed by a larger APC in %YPLL of 5.1% (95% CI 0.1, 10.4). The upward trend in firearm mortality and YPLL rates starting in 2014 was observed in subgroups of male, non-Hispanic blacks, Hispanic whites and for firearm assaults. The inflection points for firearm mortality and YPLL rates also varied across states. Conclusions: Within the United States, firearm mortality rates and YPLL remained constant between 1999 and 2014 and has been increasing subsequently. There was, however, an increase in firearm mortality rates in several subgroups and individual states earlier than 2014. [ABSTRACT FROM AUTHOR]

Entrainment is a ubiquitous property not only of interacting non-linear dynamical systems but also of human movements. In the study reported here, two premises of entrainment theory were investigated in a tapping task conducted in both interpersonal (i.e. between individuals) and intrapersonal (i.e. between effectors) conditions. Hypothesis 1 was that interacting oscillatory systems should demonstrate synchronisation, which was predicted to emerge as in-phase tapping behaviour in both inter- and intrapersonal conditions. Support for Hypothesis 1 was observed in the in-phase synchronisation of tapping in both individual bimanual trials and uni-manual and bimanual tapping in dyads. By contrast, Hypothesis 2 was that the oscillatory system with the faster initial rate would decelerate, whereas the one with the slower initial rate would accelerate, as manifest in increased self-paced tapping rates amongst participants with initially slower rates and decreased rates amongst ones who initially tapped at faster rates. However, that pattern predicted in Hypothesis 2 was not observed; on the contrary, all participants increased their tapping rates in interpersonal conditions, which occurred significantly amongst participants with the lowest preferred tapping rates. Such an outcome indicates a novel aspect of synchronised movement in humans that warrants further investigation. [ABSTRACT FROM AUTHOR]

Surgical microscopes are vital tools for ophthalmic surgeons. The recent development of an integrated OCT system for the first time allows to look at tissue features below the surface. Hence, these systems can drastically improve the quality and reduce the risk of surgical interventions. However, current commercial OCT-enhanced ophthalmic surgical microscopes provide only one additional cross sectional view to the standard microscope image and feature a low update rate. To present volumetric data at a high update rate, much faster OCT systems than the ones applied in today’s surgical microscopes need to be developed. We demonstrate live volumetric retinal OCT imaging, which may provide a sufficiently large volume size (330x330x595 Voxel) and high update frequency (24.2 Hz) such that the surgeon may even purely rely on the OCT for certain surgical maneuvers. It represents a major technological step towards the possible application of OCT-only surgical microscopes in the future which would be much more compact thus enabling many additional minimal invasive applications. We show that multi-MHz A-scan rates are essential for such a device. Additionally, advanced phase-based OCT techniques require 3D OCT volumes to be detected with a stable optical phase. These techniques can provide additional functional information of the retina. Up to now, classical OCT was to slow for this, so our system can pave the way to holographic OCT with a traditional confocal flying spot approach. For the first time, we present point scanning volumetric OCT imaging of the posterior eye with up to 191.2 Hz volume rate. We show that this volume rate is high enough to enable a sufficiently stable optical phase to a level, where remaining phase errors can be corrected. Applying advanced post processing concepts for numerical refocusing or computational adaptive optics should be possible in future with such a system. [ABSTRACT FROM AUTHOR]