bluuebunny/crossref_metadata_2025 huggingface dataset:
Constraining optimum swimming strategies in plesiosaurs: The effect of amplitude ratio on tandem pitching foils
Authors: Pourfarzan Ali , Wong Jaime G.
Published: April 2022

Identical tandem flippers of plesiosaurs, which are unique among all animals, have been a source of debate regarding the role of hind flippers in their locomotion. Here, inspired by the kinematics of plesiosaur flippers, the effect of the amplitude ratio on the propulsive performance of in-line tandem pitching foils is investigated through a series of particle image velocimetry experiments. Three leader-to-follower amplitude ratios are considered for the foils pitching over a range of 0–2π phase difference. For the first time, it is shown that the amplitude ratio can significantly affect the performance of the hind foil at spacing larger than one chord length. It is found that the thrust generation of the hind foil at the optimum phase difference augments by 130% when it is pitching at the twice angular amplitude of the upstream foil. Although the total performance of the rear-biased and equal amplitude models reaches similar values, thrust production of the hind foil in the equal amplitude model increases only by 23%. By contrast, the performance of the forward-biased model decreases drastically for all phase differences due to the destructive wake–foil interaction of the hind foil. Studying the instantaneous wake–foil interactions, it is found that high thrust generation is associated with the formation of a vortex pair on the suction side of the hind foil, which causes stronger trailing edge vortices to shed with a greater total wake spacing. Finally, through scaling analysis, high-thrust configurations of tandem models are ranked based on the total efficiency of the system.
Using gene expression programming to discover macroscopic governing equations hidden in the data of molecular simulations
Authors: Xing Haoyun , Zhang Jun , Ma Wenjun , Wen Dongsheng
Published: April 2022

The unprecedented amount of data and the advancement of machine learning methods are driving the rapid development of data-driven modeling in the community of fluid mechanics. In this work, a data-driven strategy is developed by the combination of the direct simulation Monte Carlo (DSMC) method and the gene expression programming (GEP) method. DSMC is a molecular simulation method without any assumed macroscopic governing equations a priori and is employed to generate data of flow fields, while the enhanced GEP method is leveraged to discover governing equations. We first validate our idea using two benchmarks, such as the Burgers equation and Sine–Gordon equation. Then, we apply the strategy to discover governing equations hidden in the complex fluid dynamics. Our results demonstrate that in the continuum regime, the discovered equations are consistent with the traditional ones with linear constitutive relations, while in the non-continuum regime such as shock wave, the discovered equation comprises of high-order constitutive relations, which are similar to those in the Burnett equation but with modified coefficients. Compared to the Navier–Stokes–Fourier equations and the Burnett equation, the prediction of the viscous stress and heat flux in the shock wave via the presented data-driven model has the best match to the DSMC data. It is promising to extend the proposed data-driven strategy to more complex problems and discover hidden governing equations which may be unknown so far.
Ligament Advanced Reinforcement System (LARS) synthetic graft for PCL reconstruction: systematic review and meta-analysis
Authors: Migliorini Filippo , Pintore Andrea , Vecchio Gianluca , Oliva Francesco , Hildebrand Frank , Maffulli Nicola
Published: April 2022

Introduction

Several strategies are available for posterior cruciate ligament (PCL) reconstruction.

Source of data

Recently published literature in PubMed, Google Scholar and Embase databases.

Areas of agreement

The Ligament Advanced Reinforcement System (LARS) is a scaffold type artificial ligament, which has been widely used for ligament reconstruction of the knee.

Areas of controversy

Current evidence on the reliability and feasibility of LARS for primary isolated PCL reconstruction is limited.

Growing points

The primary outcome of interest of the present work was to investigate the outcomes of PCL reconstruction using the LARS. The secondary outcome of interest was to compare the LARS versus four-strand hamstring tendon (4SHT) autograft for PCL reconstruction.

Areas timely for developing research

LARS for primary isolated PCL reconstruction seems to be effective and safe, with results comparable to the 4SHT autograft.
Disorganization of language and working memory systems in frontal versus temporal lobe epilepsy
Authors: Caciagli Lorenzo , Paquola Casey , He Xiaosong , Vollmar Christian , Centeno Maria , Wandschneider Britta , Braun Urs , Trimmel Karin , Vos Sjoerd B , Sidhu Meneka K , Thompson Pamela J , Baxendale Sallie , Winston Gavin P , Duncan John S , Bassett Dani S , Koepp Matthias J , Bernhardt Boris C
Published: April 2022

Cognitive impairment is a common comorbidity of epilepsy and adversely impacts people with both frontal lobe (FLE) and temporal lobe (TLE) epilepsy. While its neural substrates have been investigated extensively in TLE, functional imaging studies in FLE are scarce. In this study, we profiled the neural processes underlying cognitive impairment in FLE and directly compared FLE and TLE to establish commonalities and differences. We investigated 172 adult participants (56 with FLE, 64 with TLE and 52 controls) using neuropsychological tests and four functional MRI tasks probing expressive language (verbal fluency, verb generation) and working memory (verbal and visuo-spatial). Patient groups were comparable in disease duration and anti-seizure medication load. We devised a multiscale approach to map brain activation and deactivation during cognition and track reorganization in FLE and TLE. Voxel-based analyses were complemented with profiling of task effects across established motifs of functional brain organization: (i) canonical resting-state functional systems; and (ii) the principal functional connectivity gradient, which encodes a continuous transition of regional connectivity profiles, anchoring lower-level sensory and transmodal brain areas at the opposite ends of a spectrum. We show that cognitive impairment in FLE is associated with reduced activation across attentional and executive systems, as well as reduced deactivation of the default mode system, indicative of a large-scale disorganization of task-related recruitment. The imaging signatures of dysfunction in FLE are broadly similar to those in TLE, but some patterns are syndrome-specific: altered default-mode deactivation is more prominent in FLE, while impaired recruitment of posterior language areas during a task with semantic demands is more marked in TLE. Functional abnormalities in FLE and TLE appear overall modulated by disease load. On balance, our study elucidates neural processes underlying language and working memory impairment in FLE, identifies shared and syndrome-specific alterations in the two most common focal epilepsies and sheds light on system behaviour that may be amenable to future remediation strategies.
Multimodality Deep Phenotyping Methods to Assess Mechanisms of Poor Right Ventricular–Pulmonary Artery Coupling
Authors: Raza Farhan , Kozitza Callyn , Lechuga Chris , Seiter Daniel , Corrado Philip , Merchant Mohammed , Dharmavaram Naga , Korcarz Claudia , Eldridge Marlowe , Francois Christopher , Wieben Oliver , Chesler Naomi
Published: April 2022

Deep phenotyping of pulmonary hypertension (PH) with multimodal diagnostic exercise interventions can lead to early focused therapeutic interventions. Herein, we report methods to simultaneously assess pulmonary impedance, differential biventricular myocardial strain, and right ventricular:pulmonary arterial (RV:PA) uncoupling during exercise, which we pilot in subjects with suspected PH. As proof-of-concept, we show that four subjects with different diagnoses [pulmonary arterial hypertension (PAH); chronic thromboembolic disease (CTEPH); PH due to heart failure with preserved ejection fraction (PH-HFpEF); and noncardiac dyspnea (NCD)] have distinct patterns of response to exercise. RV:PA coupling assessment with exercise was highest-to-lowest in this order: PAH > CTEPH > PH-HFpEF > NCD. Input impedance (Z0) with exercise was highest in precapillary PH (PAH, CTEPH), followed by PH-HFpEF and NCD. Characteristic impedance (ZC) tended to decline with exercise, except for the PH-HFpEF subject (initial Zc increase at moderate workload with subsequent decrease at higher workload with augmentation in cardiac output). Differential myocardial strain was normal in PAH, CTEPH, and NCD subjects and lower in the PH-HFpEF subject in the interventricular septum. The combination of these metrics allowed novel insights into mechanisms of RV:PA uncoupling. For example, while the PH-HFpEF subject had hemodynamics comparable to the NCD subject at rest, with exercise coupling dropped precipitously, which can be attributed (by decreased myocardial strain of interventricular septum) to poor support from the left ventricle (LV). We conclude that this deep phenotyping approach may distinguish afterload sensitive vs. LV-dependent mechanisms of RV:PA uncoupling in PH, which may lead to novel therapeutically relevant insights.
In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus
Authors: de Lima Leonardo G. , Ruiz-Ruano Francisco J.
Published: April 2022

Satellite DNAs (SatDNA) are ubiquitously present in eukaryotic genomes and have been recently associated with several biological roles. Understanding the evolution and significance of SatDNA requires an extensive comparison across multiple phylogenetic depths. We combined the RepeatExplorer pipeline and cytogenetic approaches to conduct a comprehensive identification and analysis of the satellitome in 37 species from the genus Drosophila. We identified 188 SatDNA-like families, 112 of them being characterized for the first time. Repeat analysis within a phylogenetic framework has revealed the deeply divergent nature of SatDNA sequences in the Drosophila genus. The SatDNA content varied from 0.54% of the D. arizonae genome to 38.8% of the D. albomicans genome, with the SatDNA content often following a phylogenetic signal. Monomer size and guanine–cytosine-content also showed extreme variation ranging 2–570 bp and 9.1–71.4%, respectively. SatDNA families are shared among closely related species, consistent with the SatDNA library hypothesis. However, we uncovered the emergence of species-specific SatDNA families through amplification of unique or low abundant sequences in a lineage. Finally, we found that genome sizes of the Sophophora subgenus are positively correlated with transposable element content, whereas genome size in the Drosophila subgenus is positively correlated with SatDNA. This finding indicates genome size could be driven by different categories of repetitive elements in each subgenus. Altogether, we conducted the most comprehensive satellitome analysis in Drosophila from a phylogenetic perspective and generated the largest catalog of SatDNA sequences to date, enabling future discoveries in SatDNA evolution and Drosophila genome architecture.
Long-Term Impact of Hurricane Sandy Exposure on Positive and Negative Affect: The Role of Perceived Social Support
Authors: Wolters Bram , Kok Almar , Huisman Martijn , Cartwright Francine , Pruchno Rachel
Published: April 2022

Objectives

Natural disasters can have devastating, long-lasting effects on the mental health of older adults. However, few studies have examined associations among disaster exposure and positive and negative affect, and no longitudinal studies have investigated the extent to which predisaster perceived social support affects these associations. These analyses examine the associations among predisaster perceived social support, disaster exposure, and positive and negative affect experienced by community-dwelling older adults 4 years after Hurricane Sandy, controlling for predisaster affect.

Methods

Self-reported data collected before and after Hurricane Sandy from participants (aged 50–74 years) in the ORANJ BOWL panel (N = 2,442) were analyzed using linear regression models.

Results

Higher levels of peritraumatic stress experienced during Hurricane Sandy and greater hardship experienced after the storm were associated with more negative affect 4 years following the disaster. Higher perceived social support at baseline was related to more positive affect and less negative affect both before and after the hurricane. Social support did not moderate the effect of hurricane exposure on either positive or negative affect.

Discussion

Findings suggest that psychological effects may persist years after natural disasters and that more effective interventions may be needed during and after a disaster. While social support is critical to positive and negative affect in general, its buffering effects when disaster strikes may be limited.
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae
Authors: Wang Ziwei , Rouard Mathieu , Biswas Manosh Kumar , Droc Gaetan , Cui Dongli , Roux Nicolas , Baurens Franc-Christophe , Ge Xue-Jun , Schwarzacher Trude , Heslop-Harrison Pat (J S) , Liu Qing
Published: April 2022

Background

Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales.

Findings

Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11.

Conclusions

The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET
Authors: Jamadar Sharna D , Liang Emma X , Zhong Shenjun , Ward Phillip G D , Carey Alexandra , McIntyre Richard , Chen Zhaolin , Egan Gary F
Published: April 2022

Background

“Functional” [18F]-fluorodeoxyglucose positron emission tomography (FDG-fPET) is a new approach for measuring glucose uptake in the human brain. The goal of FDG-fPET is to maintain a constant plasma supply of radioactive FDG in order to track, with high temporal resolution, the dynamic uptake of glucose during neuronal activity that occurs in response to a task or at rest. FDG-fPET has most often been applied in simultaneous BOLD-fMRI/FDG-fPET (blood oxygenation level–dependent functional MRI fluorodeoxyglucose functional positron emission tomography) imaging. BOLD-fMRI/FDG-fPET provides the capability to image the 2 primary sources of energetic dynamics in the brain, the cerebrovascular haemodynamic response and cerebral glucose uptake.

Findings

In this Data Note, we describe an open access dataset, Monash DaCRA fPET-fMRI, which contrasts 3 radiotracer administration protocols for FDG-fPET: bolus, constant infusion, and hybrid bolus/infusion. Participants (n = 5 in each group) were randomly assigned to each radiotracer administration protocol and underwent simultaneous BOLD-fMRI/FDG-fPET scanning while viewing a flickering checkerboard. The bolus group received the full FDG dose in a standard bolus administration, the infusion group received the full FDG dose as a slow infusion over the duration of the scan, and the bolus-infusion group received 50% of the FDG dose as bolus and 50% as constant infusion. We validate the dataset by contrasting plasma radioactivity, grey matter mean uptake, and task-related activity in the visual cortex.

Conclusions

The Monash DaCRA fPET-fMRI dataset provides significant reuse value for researchers interested in the comparison of signal dynamics in fPET, and its relationship with fMRI task-evoked activity.
scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues
Authors: Bai Yulong , Qin Yidi , Fan Zhenjiang , Morrison Robert M , Nam KyongNyon , Zarour Hassane M , Koldamova Radosveta , Padiath Quasar Saleem , Kim Soyeon , Park Hyun Jung
Published: April 2022

Background

Alternative polyadenylation (APA) causes shortening or lengthening of the 3ʹ-untranslated region (3ʹ-UTR) of genes (APA genes) in diverse cellular processes such as cell proliferation and differentiation. To identify cell-type–specific APA genes in scRNA-Seq data, current bioinformatic methods have several limitations. First, they assume certain read coverage shapes in the scRNA-Seq data, which can be violated in multiple APA genes. Second, their identification is limited between 2 cell types and not directly applicable to the data of multiple cell types. Third, they do not control undesired source of variance, which potentially introduces noise to the cell-type–specific identification of APA genes.

Findings

We developed a combination of a computational change-point algorithm and a statistical model, single-cell Multi-group identification of APA (scMAPA). To avoid the assumptions on the read coverage shape, scMAPA formulates a change-point problem after transforming the 3ʹ biased scRNA-Seq data to represent the full-length 3ʹ-UTR signal. To identify cell-type–specific APA genes while adjusting for undesired source of variation, scMAPA models APA isoforms in consideration of the cell types and the undesired source. In our novel simulation data and data from human peripheral blood mononuclear cells, scMAPA outperforms existing methods in sensitivity, robustness, and stability. In mouse brain data consisting of multiple cell types sampled from multiple regions, scMAPA identifies cell-type–specific APA genes, elucidating novel roles of APA for dividing immune cells and differentiated neuron cells and in multiple brain disorders.

Conclusions

scMAPA elucidates the cell-type–specific function of APA events and sheds novel insights into the functional roles of APA events in complex tissues.
Deep learning inversion of Rayleigh-wave dispersion curves with geological constraints for near-surface investigations
Authors: Chen Xinhua , Xia Jianghai , Pang Jingyin , Zhou Changjiang , Mi Binbin
Published: April 2022

With the emergence of massive seismic data sets, surface wave methods using deep learning (DL) can effectively obtain shear wave velocity (Vs) structure for non-invasive near-surface investigations. Previous studies on DL inversion for deep geophysical investigation have a reference model to generate the training data set, while near-surface investigations have no model. Therefore, we systematically give a set of training data set generation processes. In the process, we use both prior information and the observed data to constrain the data set so that the DL inversion model can learn the local geological characteristics of the survey area. Because the space of inverted Vs models is constrained and thus narrowed, the inversion non-uniqueness can be reduced. Furthermore, the mean squared error, which is commonly used as loss function, may cause a poor fitting accuracy of phase velocities at high frequencies in near-surface applications. To make the fitting accuracy evenly in all frequency bands, we modify the loss function into a weighted mean squared relative error. We designed a convolutional neural network (CNN) to directly invert fundamental-mode Rayleigh-wave phase velocity for 1-D Vs models. To verify the feasibility and reliability of the proposed algorithm, we tested and compared it with the Levenberg–Marquardt (L-M) inversion and neighbourhood algorithm (NA) using field data from the Lawrence experiment (USA) and the Wuwei experiment (China). In both experiments, the inverted Vs models by CNN are consistent with the borehole information and are similar to that from existing methods after fine tuning of model parameters. The average root mean squares errors (RMSEs) of the CNN, NA and L-M methods are also similar, except in the Lawrence experiment, the RMSE of CNN is 17.33 m s−1 lower than previous studies using the L-M method. Moreover, the comparison of different loss functions for the Wuwei experiment indicates that the modified loss function can achieve higher accuracy than the traditional one. The proposed CNN is therefore ideally suited for rapid, repeated near-surface subsurface imaging and monitoring under similar geological settings.
Pre-processing data to reduce biases: full matching incorporating an instrumental variable in population-based studies
Authors: Cerna-Turoff Ilan , Maurer Katherine , Baiocchi Michael
Published: April 2022

Background

Epidemiologists are often concerned with unobserved biases that produce confounding in population-based studies. We introduce a new design approach—‘full matching incorporating an instrumental variable (IV)’ or ‘Full-IV Matching’—and illustrate its utility in reducing observed and unobserved biases to increase inference accuracy. Our motivating example is tailored to a central question in humanitarian emergencies—the difference in sexual violence risk by displacement setting.

Methods

We conducted a series of 1000 Monte Carlo simulations generated from a population-based survey after the 2010 Haitian earthquake and included earthquake damage severity as an IV and the unmeasured variable of ‘social capital’. We compared standardized mean differences (SMDs) for covariates after different designs to understand potential biases. Mean risk differences (RDs) were used to assess each design’s accuracy in estimating the oracle of the simulated data set.

Results

Naive analysis and pair matching equivalently performed. Full matching reduced imbalances between exposed and comparison groups across covariates, except for the unobserved covariate of ‘social capital’. Pair and full matching overstated differences in sexual violence risk when displaced to a camp vs a community [pair: RD = 0.13, 95% simulation interval (SI) 0.09–0.16; full: RD = 0.11, 95% SI 0.08–0.14). Full-IV Matching reduced imbalances across observed covariates and importantly ‘social capital’. The estimated risk difference (RD = 0.07, 95% SI 0.03–0.11) was closest to the oracle (RD = 0.06, 95% SI 0.4–0.8).

Conclusion

Full-IV Matching is a novel approach that is promising for increasing inference accuracy when unmeasured sources of bias likely exist.
Exploring the “Military Time”: Historical Timing, Civil–Military Relations, and the Military Revolution in Russia and Japan
Authors: Kadercan Burak
Published: April 2022

What is the relationship between civil–military relations and the emergence as well as diffusion of military innovations? More precisely, how do civil–military relations affect a state's capacity for adopting military innovations? While both topics, military innovations and civil–military relations, have individually attracted considerable scholarly attention, very few studies deal with them in tandem. This study builds on the existing research on the relationship between “historical timing,” civil–military relations, and the diffusion of military reforms and advances an analytical framework that treats “time” as an explanatory dynamic, using the reception of the “military revolution” on Russia and Japan as exploratory cases. In both cases, historical timing played crucial roles in defining the “balance of [political] power” between the rulers and the existing military establishment, which then led to diverging paths in terms of adopting and internalizing the military reforms associated with the aforementioned revolution.
Inwardness: Comparative Religious Philosophy in Modern Egypt
Authors: El Shakry Omnia
Published: April 2022

This article centers the Islamic philosopher ʿUthman Amin in order to explore the intellectual exchange between Muslim and Christian scholars in twentieth-century Egypt. Specifically, I look at inwardness, intellectual dialogue, and interreligious friendships in a field that has traditionally been dominated by scholarship on the relationship between Islam and politics or Islam and the law. I elucidate Amin’s philosophy of inwardness and its attendant virtues of seclusion, spiritual contemplation, and the jihad of the self—paying particular attention to reading as an illuminative embodied practice—through the lens of an Islamic discursive tradition. How might we understand the concept of an Islamic discursive tradition, as a philosophy of reasoned and embodied religion, within the context of such interreligious encounters? Amin, I argue, was engaged in an experimentum mentis in which inwardness provided an angle of lucidity from which Islam and Christianity could gaze upon one another. In so doing, I demonstrate the heuristic value of theorizations of tradition by Alasdair MacIntyre and Talal Asad to studies of interreligious encounter and scholarly exchange.
Prognostic Factors for In-Hospital Mortality of Geriatric Burns From the US National Inpatient Sample 2016 to 2018
Authors: Yi Yangtian , Vrouwe Sebastian Q , Gottlieb Lawrence J , Rubin Daniel S
Published: April 2022

Older adults with an acute burn experience a high frequency of in-hospital mortality. However, traditional burn mortality prediction models are less accurate for older adults likely because they do not account for geriatric specific factors, such as frailty. This study aims to investigate the impact of frailty on in-hospital mortality in older adult burn patients. Patients ≥50 years of age with an acute burn diagnosis in the National Inpatient Sample (2016–2018) were included in the cohort. Three multivariable logistic regression models to predict in-hospital mortality were generated and compared. The models were 1) age and percent total body surface area, 2) age, percent total body surface area and the Elixhauser Comorbidity Index, and 3) age, percent total body surface area, and Hospital Frailty Risk Score. A total of 60,515 weighted discharges were included in the cohort. In-hospital mortality increased with age, as 3.3% of 50- to 64-year-olds, 5.3% of 65- to 74-year-olds, 6.6% of 75- to 84-year-olds, and 9.9% of ≥85-year-olds died during the acute burn admission (P < .001). The multivariable model that included Hospital Frailty Risk Score had a higher area under the receiver operating characteristics curve than the model with age and percent total body surface area (0.84 vs 0.79; P < .001) and the model with Elixhauser Comorbidity Index (0.84 vs 0.83; P = .013). Frailty improved prediction of in-hospital mortality for older adult acute burn patients and burn specialists should consider implementing a frailty instrument to evaluate older adults with an acute burn injury.
Analyses of Bloodmeal Hosts and Prevalence of Rickettsia parkeri in the Gulf Coast Tick Amblyomma maculatum (Acari: Ixodidae) From a Reconstructed Piedmont Prairie Ecosystem, North Carolina
Authors: Johnson Connie R , Ponnusamy Loganathan , Richards Allen L , Apperson Charles S
Published: April 2022

Host feeding patterns and the prevalence of infection with Rickettsia parkeri were determined for the primary vector, Amblyomma maculatum Koch as well as sympatric tick species A. americanum (Linnaeus) and Dermacentor variabilis (Say) collected from a reconstructed prairie in the Piedmont region of North Carolina during 2011 and 2012. The occurrence of R. parkeri among A. maculatum adults and nymphs was 36.9% (45/122) and 33.3% (2/6), respectively. Rickettsia parkeri was detected in a single male A. americanum 2.3% (1/43). A PCR-reverse line blot hybridization assay of a 12S rDNA fragment amplified from remnant larval and nymphal bloodmeals of host-seeking ticks was used to identify bloodmeal hosts. Of the tick samples tested, bloodmeal host identification was successful for 29.3% (12/41) of adult A. americanum and 39.2% (20/51) of adult D. variabilis. For A. maculatum, bloodmeal host identification was successful for 50% (61/122) of adults collected from vegetation and 100% (4/4) of nymphs removed from cotton rats (Sigmodon hispidus Say and Ord). The cotton rat was the most common bloodmeal host with 59.0% (36/61) identified for adult A. maculatum. No statistically significant association was observed, however, between bloodmeal host and pathogen prevalence for any tick species. While the cotton rat was an important bloodmeal host for A. maculatum nymphs, this vertebrate did not appear to be the primary source of R. parkeri infection for A. maculatum.
Blow Flies (Diptera: Calliphoridae) and the American Diet: Effects of Fat Content on Blow Fly Development
Authors: Noblesse A P , Meeds A W , Weidner L M
Published: April 2022

Forensic entomology is an important field of forensic science that utilizes insect evidence in criminal investigations. Blow flies (Diptera: Calliphoridae) are among the first colonizers of remains and are frequently used in determining the minimum postmortem interval (mPMI). Blow fly development is influenced by a variety of factors including temperature and feeding substrate. Unfortunately, dietary fat content remains an understudied factor in the development process, which is problematic given the high rates of obesity in the United States. To study the effects of fat content on blow flies we investigated survivorship, adult weight, and development time (overall and by sex) of Lucilia sericata (Meigen) and Phormia regina (Meigen) on ground beef with 10%, 20%, or 27% fat. As fat content increased, survivorship decreased across both species with significant impact to P. regina. While P. regina adults were generally larger than L. sericata across all fat levels, only L. sericata demonstrated a significant (P < 0.05) difference in weight by sex. Overall development times did not vary by fat content, excluding 27% for P. regina. Additionally, development times did not vary by sex for P. regina but did differ (P < 0.05) for L. sericata with females taking longer to develop. These findings provide insight into the effect of fat content on blow fly development, a factor that should be considered when estimating an mPMI. By understanding how fat levels affect the survivorship and development of the species studied here, we can begin improving the practice of insect evidence analysis in casework.
Evaluating the Efficacy of a New Alternating Pressure Air Mattress Aimed at Reducing Pressure Injuries During the Transport of Combat Casualties
Authors: Lavender Steven A , Kachlan Anas , Pennells Simon E , Spence David
Published: April 2022

Introduction

The development of pressure ulcers during aeromedical transport of combat casualties is an issue that continues to exist, especially during long transport flights. This study investigated the potential for a new intervention, an air-inflated insulating mattress pad (IMP) that has a pump system designed to alternate the pressurization of air cells under the patient, thus temporally shifting the pressure concentration locations.

Materials and Methods

In a repeated measures design study, 12 participants experienced the following four simulated transport conditions, each for 90 minutes: (1) The North Atlantic Treaty Organization (NATO) litter by itself (control condition), (2) the NATO litter covered with the standard mattress pad (Warrior Evacuation Pad), (3) the NATO litter covered with the air-inflated mattress (IMP), and (4) the NATO litter, covered with the standard mattress pad that was covered by the insulating mattress pad. Peak pressure readings were obtained every 15 seconds under the head, torso, pelvis, legs, and heels.

Results

While both mattress pads significantly reduced the peak pressures relative to the litter-only condition, the new IMP with the alternating cell pressurizations, by itself or in combination with the standard mattress pad, further reduced the peak pressures under the regions with the localized highest pressures, namely the head, pelvis, and heels. Moreover, the IMP with alternating pressure introduced the most variability in the peak pressure readings, which reduces the peak pressure exposure periods for specific tissue locations.

Conclusions

The IMP with alternating cell pressurizations could further reduce the likelihood of pressure injuries during aeromedical transport of combat casualties.
Simple interpretation of the seemingly complicated X-ray spectral variation of NGC 5548
Authors: Midooka Takuya , Ebisawa Ken , Mizumoto Misaki , Sugawara Yasuharu
Published: April 2022

NGC 5548 is a very well-studied Seyfert 1 galaxy in broad wavelengths. Previous multiwavelength observation campaigns have indicated that its multiple absorbers are highly variable and complex. A previous study applied a two-zone partial covering model with different covering fractions to explain the complex X-ray spectral variation and reported a correlation between one of the covering fractions and the photon index of the power-law continuum. However, it is not straightforward to physically understand such a correlation. In this paper, we propose a model to avoid this unphysical situation; the central X-ray emission region is partially covered by clumpy absorbers composed of double layers. These ‘double partial coverings’ have precisely the same covering fraction. Based on our model, we have conducted an extensive spectral study using the data taken by XMM–Newton, Suzaku, and NuSTAR in the range of 0.3–78 keV for 16 yr. Consequently, we have found that the X-ray spectral variations are mainly explained by independent changes of the following three components; (1) the soft excess spectral component below ∼1 keV, (2) the cut-off power-law normalization, and (3) the partial covering fraction of the clumpy absorbers. In particular, spectral variations above ∼1 keV are mostly explained only by the changes of the partial covering fraction and the power-law normalization. In contrast, the photon index and all the other spectral parameters are not significantly variable.
Determining the aberrations in a nearly diffraction-limited spectrograph
Authors: Sánchez B , Watson A M , Cuevas S
Published: April 2022

We present a method to determine the static aberrations in a nearly diffraction-limited spectrograph introduced, for example, by alignment or manufacturing errors. We consider an instrument with two stages separated by a slit or image slicer located in the intermediate focal plane. In such a spectrograph, it is not trivial to distinguish aberrations in the first stage, before the slit, from those in the second, after the slit. However, our method achieves this. Measuring these aberrations separately opens the possibility of reducing them, by realignment or other means, and thereby improving the optical performance of the instrument. The method is based on fitting models to multiple images of a point source, with controlled displacements of the source perpendicular to the slit and controlled defocuses of the second stage or the detector. Fitting models to these images allows the determination of the aberrations in both stages. Our key discovery is that the displaced and defocused images provide additional information which allows us to break the ambiguity between the two stages. We present simulations that validate the performance of the method.
Molecular Phylogeny Reveals the Past Transoceanic Voyages of Drywood Termites (Isoptera, Kalotermitidae)
Authors: Buček Aleš , Wang Menglin , Šobotník Jan , Hellemans Simon , Sillam-Dussès David , Mizumoto Nobuaki , Stiblík Petr , Clitheroe Crystal , Lu Tomer , González Plaza Juan José , Mohagan Alma , Rafanomezantsoa Jean-Jacques , Fisher Brian , Engel Michael S. , Roisin Yves , Evans Theodore A. , Scheffrahn Rudolf , Bourguignon Thomas
Published: April 2022

Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ∼120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Ma (75–93 Ma 95% highest posterior density), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ∼40 disjunctions among biogeographic realms were dated at <50 Ma, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles
Authors: Clementel Damiano , Del Conte Alessio , Monzon Alexander Miguel , Camagni Giorgia F , Minervini Giovanni , Piovesan Damiano , Tosatto Silvio C E
Published: April 2022

Residue interaction networks (RINs) are used to represent residue contacts in protein structures. Thanks to the advances in network theory, RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present the new RING 3.0 version extending the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations (e.g. NMR or molecular dynamics ensembles) are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable. Contact evolution across models (or time) is displayed as a heatmap and can help in the discovery of correlating interaction patterns. The web server, together with an extensive help and tutorial, is available from URL: https://ring.biocomputingup.it/.
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins
Authors: Ilnitskiy Ivan S , Zharikova Anastasia A , Mironov Andrey A
Published: April 2022

Extensive amounts of data from next-generation sequencing and omics studies have led to the accumulation of information that provides insight into the evolutionary landscape of related proteins. Here, we present OrthoQuantum, a web server that allows for time-efficient analysis and visualization of phylogenetic profiles of any set of eukaryotic proteins. It is a simple-to-use tool capable of searching large input sets of proteins. Using data from open source databases of orthologous sequences in a wide range of taxonomic groups, it enables users to assess coupled evolutionary patterns and helps define lineage-specific innovations. The web interface allows to perform queries with gene names and UniProt identifiers in different phylogenetic clades and supplement presence with an additional BLAST search. The conservation patterns of proteins are coded as binary vectors, i.e., strings that encode the presence or absence of orthologous proteins in other genomes. These strings are used to calculate top-scoring correlation pairs needed for finding co-inherited proteins which are simultaneously present or simultaneously absent in specific lineages. Profiles are visualized in combination with phylogenetic trees in a JavaScript-based interface. The OrthoQuantum v1.0 web server is freely available at http://orthoq.bioinf.fbb.msu.ru along with documentation and tutorial.
Indole modulates cooperative protein–protein interactions in the flagellar motor
Authors: Gupta Rachit , Rhee Kathy Y , Beagle Sarah D , Chawla Ravi , Perdomo Nicolas , Lockless Steve W , Lele Pushkar P
Published: April 2022

Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum's direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
Men’s Rights Activism and Anti-Feminist Resistance in Turkey and Norway
Authors: Eslen-Ziya Hande , Bjørnholt Margunn
Published: April 2022

This article, by addressing the growing anti-feminist activism and mobilization and its consequences for gender equality and women’s rights, sheds light on anti-feminist resistance in Turkey and Norway. Using the concept of counter movement, we study men’s rights mobilization in Turkey and Norway, two countries with different histories and realities of women’s rights and gender equality. We first compare how the respective men’s rights movements emerged in response to, or parallel with, the advances of women’s movements. Investigating mass media and social media content from the most prominent contemporary men’s rights groups in each country provides a qualitative comparative analysis of men’s rights mobilization. Men’s rights groups in Turkey and Norway share many of the same concerns, but while men’s rights activists in Turkey challenge gender equality and defend the traditional family, in Norway, men’s rights activism is a masculinist co-optation of the gender equality discourse.
Low-Dose Cadmium Potentiates Metabolic Reprogramming Following Early-Life Respiratory Syncytial Virus Infection
Authors: Jarrell Zachery R , Smith Matthew Ryan , Kim Ki-Hye , Lee Youri , Hu Xin , He Xiaojia , Orr Michael , Chen Yan , Kang Sang-Moo , Jones Dean P , Go Young-Mi
Published: April 2022

Respiratory syncytial virus (RSV) infection causes serious pulmonary disease and death in high-risk infants and elderly. Cadmium (Cd) is a toxic environmental metal contaminant and constantly exposed to humans. Limited information is available on Cd toxicity after early-life respiratory virus infection. In this study, we examined the effects of low-dose Cd exposure following early-life RSV infection on lung metabolism and inflammation using mouse and fibroblast culture models. C57BL/6J mice at 8 days old were exposed to RSV 2 times with a 4-week interval. A subset of RSV-infected mice was subsequently treated with Cd at a low dose in drinking water (RSV infection at infant age [RSVinf]+Cd) for 16 weeks. The results of inflammatory marker analysis showed that the levels of cytokines and chemokines were substantially higher in RSVinf+Cd group than other groups, implying that low-dose Cd following early-life RSV infection enhanced lung inflammation. Moreover, histopathology data showed that inflammatory cells and thickening of the alveolar walls as a profibrotic signature were evident in RSVinf+Cd. The metabolomics data revealed that RSVinf+Cd-caused metabolic disruption in histamine and histidine, vitamin D and urea cycle, and pyrimidine pathway accompanying with mechanistic target of rapamycin complex-1 activation. Taken together, our study demonstrates for the first time that cumulative Cd exposure following early-life RSV infection has a significant impact on subsequent inflammation and lung metabolism. Thus, early-life respiratory infection may reprogram metabolism and potentiate Cd toxicity, enhance inflammation, and cause fibrosis later in life.
Ethical Challenges When Caring for African American Older Adults Requesting to Withdraw From Dialysis
Authors: Hain Debra J. , Haras Mary S.
Published: April 2022

The number of African American adults 65 years and older with end-stage kidney disease receiving maintenance hemodialysis is increasing. The high symptom burden (ie, pain, fatigue, depression) can make it challenging for many to continue dialysis, which can lead to request to withdraw from dialysis. This can present ethical challenges when someone has diminished decision-making capacity and no advance directives or family to assist with this complex decision. This article will provide a brief overview of ethical issues to consider when responding to an older adult's request to withdraw from a life-sustaining treatment such as dialysis. Suggestions for research to address the gaps in knowledge will be presented.