bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-Reported Sensory Decline in Older Adults Is Longitudinally Associated With Both Modality-General and Modality-Specific Factors
Authors: O’ Dowd Alan , Hirst Rebecca J , Setti Annalisa , Kenny Rose Anne , Newell Fiona N
Published: November 2022

Background and Objectives

Self-reported sensory data provide important insight into an individual’s perception of sensory ability. It remains unclear what factors predict longitudinal change in self-reported sensory ability across multiple modalities during healthy aging. This study examined these associations in a cohort of older adults for vision, hearing, taste, and smell.

Research Design and Methods

Data on self-report sensory ability were drawn from 5,065 participants of The Irish Longitudinal Study on Ageing (mean age at baseline = 61.6, SD = 9.5, range 32–93 years; 59% female; resident in the Republic of Ireland) across 6 waves of data collection (2009–2021). Covariates included demographics, lifestyle factors, and measures of sensory, physical, mental, and cognitive health. Independent discrete survival analyses were performed for each sensory modality.

Results

A transition to self-reported fair/poor hearing was most prevalent (21% of the sample), followed by fair/poor vision (19%), smell (11%), and taste (6%). Participants who self-reported fair/poor function in one sensory modality were likely to report fair/poor ability in another sensory modality, although not for all pairings. Only self-rated fair/poor health was associated with increased odds of self-reported fair/poor ability across all sensory modalities. Age was associated with increased odds of self-reported fair/poor hearing, smell, and taste, as was current smoker status (vision, smell, and taste). Several other sensory (e.g., eye disease, hearing aid use) and nonsensory covariates (e.g., education, depression) were associated with the odds of self-reported fair/poor ability in one or two sensory modalities only.

Discussion and Implications

Over time, older adults perceive associations in fair/poor ability for multiple sensory modalities, albeit somewhat inconsistently. Both modality-general and modality-specific factors are associated with a transition from normal to fair/poor sensory ability. These results suggest the need for more routine testing of multiple senses with increasing age.
Developing-country status at the WTO: the divergent strategies of Brazil, India and China
Authors: Schöfer Till , Weinhardt Clara
Published: November 2022

The global power shift towards Brazil, India, China and other non-western powers has led to pressures to adjust international institutions to new economic realities. Most power shift theories assume that established powers defend their institutional privileges, while emerging powers challenge them. Conversely, in this article we reverse this assumption by shedding light on ‘privileges’ of the weak: many international institutions have established special rights for disadvantaged regime members. We ask what strategies emerging powers adopt as they come under pressure to give up these rights commonly reserved for regime members with developing country status. We present a novel conceptualization of four ideal-typical strategies that combine elements of resistance and accommodation. Empirically, we examine the strategies that Brazil, India and China (BICs) have adopted in the World Trade Organization. We find that no uniform approach exists across the BICs: while India fiercely resists giving up its status as a developing country and the flexibilities it comes with, Brazil adopts a pragmatic approach that largely accommodates established powers' demands to give up special rights reserved for developing countries. China pursues a mixed strategy of selective accommodation and resistance. These findings contribute to recent debates on global power shifts by illustrating how material incentives and status considerations shape the adaptation of international institutions as privileges for the weak are re-negotiated.
State Apologies and International Law
Authors: Gibney Mark
Published: November 2022

This article explores whether transnational state apologies—apologies from one state to another, but invariably apologies from “strong” states to “weak” ones—have any real meaning under international law. Without the force of law, states could continue to pursue the same or similar policies to those things for which they now apologize. One of the more remarkable aspects of transnational state apologies is the way in which they challenge the dominant “territorial” interpretation of international law. Through these apologies, states are committing themselves to protect not only their own citizens, but foreign nationals as well. Moreover, these principles are reflected in things like the Responsibility to Protect (R2P) initiative as well as the Arms Trade Treaty. On the other hand, there is also evidence of a fissure between (apologetic) words, on the one hand, and international law and state practice, most notably the law on state responsibility as well as the legal apartheid now institutionalized in both the United States and in Europe—the two largest purveyors of state apologies.
De-identified data quality assessment approaches by data vendors who license data to healthcare and life sciences researchers
Authors: Erwin Johnson C , Colquhoun Daniel , Ruppar Daniel A , Vetter Sascha
Published: November 2022

Objective

To gain insights into how data vendor companies (DVs), an important source of de-identified/anonymized licensed patient-related data (D/ALD) used in clinical informatics research in life sciences and the pharmaceutical industry, characterize, conduct, and communicate data quality assessments to researcher purchasers of D/ALD.

Materials and Methods

A qualitative study with interviews of DVs executives and decision-makers in data quality assessments (n = 12) and content analysis of interviews transcripts.

Results

Data quality, from the perspective of DVs, is characterized by how it is defined, validated, and processed. DVs identify data quality as the main contributor to successful collaborations with life sciences/pharmaceutical research partners. Data quality feedback from clients provides the basis for DVs reviews and inspections of quality processes. DVs value customer interactions, view collaboration, shared common goals, mutual expertise, and communication related to data quality as success factors.

Conclusion

Data quality evaluation practices are important. However, no uniform DVs industry standards for data quality assessment were identified. DVs describe their orientation to data quality evaluation as a direct result of not only the complex nature of data sources, but also of techniques, processes, and approaches used to construct data sets. Because real-world data (RWD), eg, patient data from electronic medical records, is used for real-world evidence (RWE) generation, the use of D/ALD will expand and require refinement. The focus on (and rigor in) data quality assessment (particularly in research necessary to make regulatory decisions) will require more structure, standards, and collaboration between DVs, life sciences/pharmaceutical, informaticists, and RWD/RWE policy-making stakeholders.
Challenging assumptions about burial ground biodiversity using flying beetles as indicators in urban areas
Authors: Cathcart-James Margaret , Foster Chris , Pickles Brian J
Published: November 2022

Biodiversity is fundamental to the provision of ecosystem services that benefit urban communities, yet one type of green space is largely overlooked in ecological research and local governance: urban burial grounds. Their longevity, profound importance to society, and ubiquitous nature, provide unique opportunities for urban biodiversity. However, there has been little scientific exploration of their potentials. To quantify biodiversity in urban burial grounds, a low impact methodology for the capture of flying beetles was developed and deployed at 20 sites in southern England. To the authors’ knowledge this work represents the largest sampling of burial grounds in a single study. We used Generalized linear Mixed Models to examine the influence of weather, local demographic variables, urban landscape and burial ground vegetation management on the abundance of flying beetles. We found significant variability in beetle assemblages over time and between burial grounds. Burial ground age was not significantly associated with flying beetle abundance, challenging long-standing assumptions about older burial grounds being more valuable for biodiversity. Increasing area of domestic gardens and hedgerows in the surrounding urban landscape was positively associated with beetle abundance, whereas the most significant negative association was with burial ground size. Additionally, management of burial grounds significantly influenced beetle abundance: more stringent regimes typically resulted in lower abundance, but sites with horticultural landscaping or biodiversity-focused regimes exhibited higher abundances.
Formation and thermodynamic evolution of plasmoids in active region jets
Authors: Mulay Sargam M , Tripathi Durgesh , Mason Helen , Del Zanna Giulio , Archontis Vasilis
Published: November 2022

We have carried out a comprehensive study of the temperature structure of plasmoids, which successively occurred in recurrent active region jets. The multithermal plasmoids were seen to be travelling along the multithreaded spire as well as at the footpoint region in the EUV/UV images recorded by the Atmospheric Imaging Assembly (AIA). The differential emission measure (DEM) analysis was performed using EUV AIA images, and the high-temperature part of the DEM was constrained by combining X-ray images from the X-ray telescope (XRT/Hinode). We observed a systematic rise and fall in brightness, electron number densities and the peak temperatures of the spire plasmoid during its propagation along the jet. The plasmoids at the footpoint (FPs) (1.0–2.5 MK) and plasmoids at the spire (SPs) (1.0–2.24 MK) were found to have similar peak temperatures, whereas the FPs have higher DEM weighted temperatures (2.2–5.7 MK) than the SPs (1.3–3.0 MK). A lower limit to the electron number densities of plasmoids – SPs (FPs) were obtained that ranged between 3.4–6.1 × 108 (3.3–5.9 × 108) cm−3 whereas for the spire, it ranged from 2.6–3.2 × 108 cm−3. Our analysis shows that the emission of these plasmoids starts close to the base of the jet(s), where we believe that a strong current interface is formed. This suggests that the blobs are plasmoids induced by a tearing-mode instability.
Diffstar: a fully parametric physical model for galaxy assembly history
Authors: Alarcon Alex , Hearin Andrew P , Becker Matthew R , Chaves-Montero Jonás
Published: November 2022

We present Diffstar , a smooth parametric model for the in situ star formation history (SFH) of galaxies. The Diffstar model is distinct from traditional SFH models because it is parametrized directly in terms of basic features of galaxy formation physics. Diffstar includes ingredients for: the halo mass assembly history; the accretion of gas into the dark matter halo; the fraction of gas that is eventually transformed into stars, ϵms; the time-scale over which this transformation occurs, τcons; and the possibility that some galaxies will experience a quenching event at time tq, and may subsequently experience rejuvenated star formation. We show that our model is sufficiently flexible to describe the average stellar mass histories of galaxies in both the IllustrisTNG (TNG) and UniverseMachine (UM) simulations with an accuracy of ∼0.1 dex across most of cosmic time. We use Diffstar to compare TNG to UM in common physical terms, finding that: (i) star formation in UM is less efficient and burstier relative to TNG; (ii) UM galaxies have longer gas consumption time-scales, relative to TNG; (iii) rejuvenated star formation is ubiquitous in UM, whereas quenched TNG galaxies rarely experience sustained rejuvenation; and (iv) in both simulations, the distributions of ϵms, τcons, and tq share a common characteristic dependence upon halo mass, and present significant correlations with halo assembly history. We conclude with a discussion of how Diffstar can be used in future applications to fit the SEDs of individual observed galaxies, as well as in forward-modelling applications that populate cosmological simulations with synthetic galaxies.
Opacity calculations in four to nine times ionized Pr, Nd, and Pm atoms for the spectral analysis of kilonovae
Authors: Carvajal Gallego H , Deprince J , Berengut J C , Palmeri P , Quinet P
Published: November 2022

New atomic data for radiative transitions in Pr V–X, Nd V–X, and Pm V–X were determined by means of large-scale calculations involving three independent theoretical methods, i.e. the pseudo-relativistic Hartree–Fock method including core-polarization corrections (HFR+CPOL), the multiconfiguration Dirac–Hartree–Fock (MCDHF) method, and the configuration interaction many-body perturbation theory (CI + MBPT) implemented in the ambit program. This multiplatform approach allowed us to estimate the reliability of the results obtained and to extract a large amount of energy levels, wavelengths, transition probabilities, and oscillator strengths for the determination of opacities required for the analysis of the spectra emitted in the early phases of kilonovae following neutron star mergers, i.e. for typical conditions corresponding to temperatures T > 20 000 K, a density ρ  = 10−10 g cm−3, and a time after the merger t  = 0.1 d. Our radiative parameters were compared in detail with the few experimental data published so far and their impact on the calculated opacities, in terms of atomic computation strategy, was also examined.
Multiple gas phases in supernova remnant IC 443: mapping shocked H2 with VLT/KMOS
Authors: Deng Yunwei , Zhang Zhi-Yu , Zhou Ping , Wang Junzhi , Fang Min , Lin Lingrui , Bian Fuyan , Chen Zhiwei , Shi Yong , Chen Guoyin , Li Hui
Published: November 2022

Supernovae and their remnants provide energetic feedback to the ambient interstellar medium (ISM), which is often distributed in multiple gas phases. Among them, warm molecular hydrogen (H2) often dominates the cooling of the shocked molecular ISM, which has been observed with the H2 emission lines at near-infrared wavelengths. Such studies, however, were either limited in narrow filter imaging or sparsely sampled mid-infrared spectroscopic observations with relatively poor angular resolutions. Here we present near-infrared (H and K bands) spectroscopic mosaic observations towards the A, B, C, and G regions of the supernova remnant (SNR) IC 443, with the K-band Multi-Object Spectrograph (KMOS) onboard the Very Large Telescope (VLT). We detected 20 rotational–vibrational transitions of H2, one H line (Brγ), and two [Fe ii] lines, which dominate broad-band images at both H and K bands. The spatial distribution of H2 lines at all regions is clumpy on scales from ∼0.1 down to ∼0.008 pc. The fitted excitation temperature of H2 is between 1500 and 2500 K, indicating warm shocked gas in these regions. The multigas phase comparison shows stratified shock structures in all regions, which explains the coexistence of multiple types of shocks in the same regions. Lastly, we verify the candidates of young stellar objects previously identified in these regions with our spectroscopic data, and find none of them are associated with young stars. This sets challenges to the previously proposed scenario of triggered star formation by SNR shocks in IC 443.
Precise near-infrared photometry, accounting for precipitable water vapour at SPECULOOS Southern Observatory
Authors: Pedersen Peter P , Murray C A , Queloz D , Gillon M , Demory B O , Triaud A H M J , de Wit J , Delrez L , Dransfield G , Ducrot E , Garcia L J , Gómez Maqueo Chew Y , Günther M N , Jehin E , McCormac J , Niraula P , Pozuelos F J , Rackham B V , Schanche N , Sebastian D , Thompson S J , Timmermans M , Wells R
Published: November 2022

The variability induced by precipitable water vapour (PWV) can heavily affect the accuracy of time-series photometric measurements gathered from the ground, especially in the near-infrared. We present here a novel method of modelling and mitigating this variability, as well as open-sourcing the developed tool – Umbrella. In this study, we evaluate the extent to which the photometry in three common bandpasses (r′, i′, z′), and SPECULOOS’ primary bandpass (I + z′), are photometrically affected by PWV variability. In this selection of bandpasses, the I + z′ bandpass was found to be most sensitive to PWV variability, followed by z′, i′, and r′. The correction was evaluated on global light curves of nearby late M- and L-type stars observed by SPECULOOS’ Southern Observatory (SSO) with the I + z′ bandpass, using PWV measurements from the LHATPRO and local temperature/humidity sensors. A median reduction in RMS of 1.1 per cent was observed for variability shorter than the expected transit duration for SSO’s targets. On timescales longer than the expected transit duration, where long-term variability may be induced, a median reduction in RMS of 53.8 per cent was observed for the same method of correction.
Analgesic Efficacy of Quadratus Lumborum Block in Patients Undergoing Nephrectomy: A Systematic Review and Meta-Analysis
Authors: Wang Jinxu , Chu Tiantian , Sun Rao , Xu Aijun
Published: November 2022

Objective

To evaluate the analgesic efficacy of quadratus lumborum block (QLB) in adults undergoing nephrectomy.

Design

Systematic review and meta-analysis.

Patients

Adult patients (≥18 years of age) received nephrectomy under general anesthesia.

Methods

We searched PubMed, Embase, the Cochrane Library, and Web of Science on January 10, 2022, including randomized controlled trials that evaluated the analgesic efficacy of QLB for patients undergoing nephrectomy.

Results

A total of 12 randomized controlled trials (N = 821 patients) were included in the study. Compared with the non-block, single-shot QLB reduced postoperative opioid consumption (mean difference [MD], −8.37 mg intravenous morphine equivalent; 95% confidence interval [CI], −12.19 to −4.54 mg) and pain scores at 2 hours, 6 hours, 12 hours, and 24 hours at rest and during movement after nephrectomy. Single-shot QLB also prolonged the time to first analgesic request (MD, 6.44 hours; 95% CI, 2.23 to 10.65 hours), shortened the length of hospital stay (MD, −0.32 day; 95% CI, −0.55 to −0.09 day), and decreased the incidence of postoperative nausea and vomiting (risk ratio, 0.48; 95% CI, 0.36 to 0.65). Compared with continuous epidural anesthesia, repeated QLB could provide comparable postoperative analgesic benefits.

Conclusions

Single-shot QLB provided a statistically significant but clinically small improvement in postoperative analgesia and recovery for patients undergoing nephrectomy. The QLB would be beneficial as part of multimodal analgesia. Future research might need to determine which approach of QLB is superior for postoperative analgesia after nephrectomy.
Graph zeta functions and Wilson loops in a Kazakov–Migdal model
Authors: Matsuura So , Ohta Kazutoshi
Published: November 2022

In this paper, we consider an extended Kazakov–Migdal model defined on an arbitrary graph. The partition function of the model, which is expressed as the summation of all Wilson loops on the graph, turns out to be represented by the Bartholdi zeta function weighted by unitary matrices on the edges of the graph. The partition function on the cycle graph at finite N is expressed by the generating function of the generalized Catalan numbers. The partition function on an arbitrary graph can be exactly evaluated at large N, which is expressed as an infinite product of a kind of deformed Ihara zeta function. The non-zero-area Wilson loops do not contribute to the leading part of the 1/N expansion of the free energy but to the next leading. The semi-circle distribution of the eigenvalues of the scalar fields is still an exact solution of the model at large N on an arbitrary regular graph, but it reflects only zero-area Wilson loops.
The effect of corn silage hybrid and inclusion on performance of finishing steers and silage hybrid effects on digestibility and performance of growing steers
Authors: Hilscher F Henry , Bittner Curt J , Gramkow Jana L , Jolly-Breithaupt Melissa L , Norman Mitch M , Wilson Hannah C , Watson Andrea K , MacDonald James C , Anderson John N , Erickson Galen E
Published: November 2022

Three experiments evaluated the effects of three corn silage hybrids, inclusion, and nutrient digestibility in growing and finishing diets. The three hybrids tested included a control (CON), a hybrid containing a brown midrib (bm3) trait (BM3), and an experimental bm3 hybrid with the soft endosperm trait (BM3-SOFT). Experiment 1 utilized 360 crossbred steers (body weight [BW] = 334; SD = 25 kg) to evaluate inclusion of silage in a finishing diet at (15% or 45% of diet dry matter [DM]) and silage hybrid (CON, BM3, or BM3-SOFT). Experiment 2 and 3 utilized 216 crossbred steers (BW = 324; SD = 10 kg) and six ruminally fistulated steers (BW = 274; SD = 27 kg), respectively, to evaluate effects of either CON, BM3, or BM3-SOFT silage hybrids on performance and nutrient digestibility in growing diets. In Exp. 1, there was a silage inclusion × hybrid interaction for average daily gain (ADG) and gain-to-feed ratio (G:F). All treatments with 15% silage had greater (P ≤ 0.04) ADG and G:F compared with 45% silage. Cattle fed BM3-SOFT had greater ADG and G:F than cattle fed CON or BM3 when silage was included at 15% of the diet. When silage was fed at 45% of the diet DM, ADG did not differ between cattle fed either bm3 hybrid. Cattle fed BM3 had the greatest G:F (P < 0.01), with no difference between BM3-SOFT and CON. At 15% silage inclusion, hot carcass weight (HCW) was greater (P < 0.01) for cattle fed BM3-SOFT compared with cattle fed CON and BM3 but did not differ between cattle fed BM3 and CON. At 45% silage inclusion, steers fed either bm3 hybrid did not differ in HCW but were both heavier (P < 0.01) compared with cattle fed CON. In Exp. 2, ending BW, dry matter intake (DMI), and ADG were greater (P < 0.01) for steers fed either bm3 hybrid compared to steers fed the CON, but not different between steers fed the bm3 hybrids. There were no differences (P = 0.26) in G:F between the silage hybrids. In Exp. 3, steers fed either bm3 had greater (P < 0.01) neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility than steers fed the CON. Ruminal pH was lower (P < 0.01), and total volatile fatty acid (VFA) concentration was greater (P < 0.01) for steers fed bm3 hybrids compared to steers fed CON. Feeding silage with the bm3 trait improved fiber digestibility, which increased DMI and subsequent ADG in high-forage growing diets. Feeding corn silage with the bm3 trait improved performance compared to non-bm3 corn silage when included above typical roughage concentration.
Effects of Swaddling During Bottle Feeding in Preterm Infants
Authors: Smith Allison P. , Sweeney Jane K. , Ross Erin Sundseth , Blackburn Susan
Published: November 2022

Background:

Preterm infants have immature oral feeding skills, affecting length of hospital stay and long-term feeding outcomes. Swaddling has positive effects on pain and stress responses, state regulation, and physiological stability in preterm infants in the neonatal intensive care unit (NICU). Swaddling during bottle feeding may support preterm infant behavioral organization and oral feeding skills. Swaddling is used inconsistently during feeding in the NICU and has not been critically examined for effects on bottle feeding performance in preterm infants.

Purpose:

To examine the effects of swaddling on bottle feeding quality and efficiency in preterm infants.

Methods:

A convenience sample of 30 infants born before 34 weeks of gestation was selected in an urban level IV NICU. Using an experimental, randomized crossover design, each infant was swaddled for one feeding and unswaddled for one feeding. Feeding efficiency was measured by rate and volume consumed. Feeding quality was examined by the Early Feeding Skills Assessment and frequency of physiological changes. Data were analyzed using dependent t tests and Wilcoxon signed rank test.

Results:

When swaddled, participants demonstrated significantly better scores on all related subtests of the Early Feeding Skills Assessment (P ≤ .001). Infants demonstrated no difference in frequency of bradycardia or oxygen desaturations greater than 4 seconds. No significant differences were found in feeding efficiency outcomes.

Implications for Practice and Research:

Swaddling can be used in the NICU to improve bottle feeding quality in preterm infants. Future investigation is needed on long-term effects of swaddling during bottle feeding on feeding performance, weight gain, and length of stay.
Role of Pharmacogenomics in the Efficacy and Safety of Thiopurines in Inflammatory Bowel Disease
Authors: Gutiérrez-Valencia Marta , Leache Leire , Saiz Luis Carlos , Beloqui Juan J. , Barajas Miguel , Vicuña Miren , Erviti Juan
Published: November 2022

Background:

Thiopurines’ toxicity often leads to dose reduction or discontinuation. This systematic review aims to synthesize the evidence on the effect of genotype-based dosing of thiopurines on treatment efficacy and safety in inflammatory bowel disease (objective #1), and the association between genotype status and the efficacy and safety profile (objective #2).

Methods:

The Cochrane Library, MEDLINE, and EMBASE were searched in August 2021. A total of 80 studies (19,859 individuals) were included. Meta-analyses for mortality, different types of adverse events (AEs), withdrawal due to AE, change in disease activity and clinical remission were performed following mainly a fixed-effects model. PROSPERO registration: CRD42020148130.

Results:

Genotype-based dosing was associated to a significantly lower incidence of hematologic AEs (risk ratio=0.71; 95% CI: 0.56-0.90; I
2: 47%; 4 randomized controlled trials; moderate quality), which may be attributable to nudix hydrolase 15 (NUDT15) testing more than to thiopurine methyltransferase (TPMT) genotyping. No differences were found in other outcomes. Mutations in TPMT and NUDT15 genes were associated to a higher probability of serious AEs [odds ratio (OR) TPMT=4.98; OR NUDT15=11.44], hematologic AEs (OR TPMT=3.18), and serious hematologic AEs (OR TPMT=7.88; OR NUDT15=12.83). TPMT was also associated with a higher risk of withdrawals due to AEs (OR=3.38), and NUDT15 with gastrointestinal AEs (OR=2.04). Mutations in the ITPA gene did not lead to significant differences. Evidence of an association between other genes and clinical outcomes is still scarce.

Conclusions:

Mutations in TPMT and NUDT15 genes predispose patients to suffer thiopurine-induced toxicity, and genotype-guided treatment has been shown to contribute to the prevention of thiopurine-induced toxicity, especially in the case of NUDT15 in Asians.
John Edward Casida. 22 December 1929—30 June 2018
Authors: Hammock Bruce D. , Li Qing X.
Published: November 2022

John Edward Casida's research in pesticide toxicology led to more effective agricultural chemicals that are far safer for human and environmental health. He used pesticides as probes for his fundamental studies of metabolism and mode of action, resulting in great insight into biological chemistry and the underlying mechanisms of regulatory biology, ranging from voltage-gated sodium channels, through the ryanodine receptor and calcium regulation, the gamma-aminobutyric acid (GABA)-gated chloride channel, to the nicotinic acetylcholine receptors. These discoveries, among many others, have had a profound impact on pharmacology and toxicology. His research career started with the introduction of DDT into agricultural practice and continued to assist in the development of many pesticides that dominate the market today. John Casida trained multiple generations of toxicologists who obtained leading positions in government, industry and academics. He spent many of his formative years in Madison, Wisconsin, where he entered the University of Wisconsin, received his BS, MS and PhD and then joined the faculty to become a full professor six years later. He then moved to the Entomology Department at the University of California, Berkeley where he remained active in teaching and research until his death. He loved laboratory science and this, coupled with insatiable curiosity and a gift for finding the unexpected, led to papers from his laboratory sparkling with creativity. He similarly loved teaching at all levels and had just finished grading the final examination in his toxicology class at the time of his passing. John won numerous national and international awards and is widely viewed as the premiere pesticide toxicologist.
Acceleration waves and oscillating gas bubbles modelled by rational extended thermodynamics
Authors: Brini F. , Seccia L.
Published: November 2022

The study of acceleration waves for a rarefied polyatomic gas is carried out in planar, cylindrical and spherical geometry referring to the rational extended thermodynamics theory with 14 moments. The case of a rarefied monatomic gas is determined as a limit case, and the role of geometry and molecular degrees of freedom is investigated. In addition, the behaviour of an acceleration wave travelling inside an oscillating gas bubble is modelled by the 14-moment PDE system under adiabatic condition. We show that dissipation combined with hyperbolicity tends to inhibit shock formation, and that the dynamic pressure cannot be zero inside the oscillating bubble. This fact can produce observable effects even in the Navier–Stokes approximation, if the gas exhibits high bulk viscosity.
Light-induced swirling and locomotion
Authors: Maghsoodi Ameneh , Bhattacharya Kaushik
Published: November 2022

The design of remotely activated, untethered devices without onboard power is a continuing challenge in soft robotics. This work describes a method of generating a whirling motion in pre-stressed photomechanical liquid crystal elastomer fibres using steady illumination that can be exploited for propulsion and mixing. Photomechanical liquid crystal elastomers (LCEs) can convert light directly into mechanical deformation, making them attractive candidates for soft actuators capable of remote and multi-mode actuation. We propose a three-dimensional multi-scale model of the nonlinear and non-local dynamics of fibres of photomechanical LCEs under illumination. We use the model to show that pre-stressed helix-like fibres immersed in a fluid can undergo a periodic whirling motion under steady illumination. We analyse the photo-driven spatio-temporal pattern and stability of the whirling deformation, and provide a parametric study. Unlike previous work on photo-driven periodic motion, this whirling motion does not exploit instabilities in the form of snap-through phenomena, or unilateral constraints as in rolling. More broadly, our work provides an unusual example of a physical system capable of periodic motion under steady stimulus that does not exploit instabilities. We finally show that such motion can be exploited in developing remote controlled bioinspired microswimmers and novel micromixers.
Scavenging in the realm of senses: smell and vision drive recruitment at carcasses in Neotropical ecosystems
Authors: Naves-Alegre Lara , Morales-Reyes Zebensui , Sánchez-Zapata José Antonio , Sebastián-González Esther , Ovaskainen Otso
Published: November 2022

Social information, acquired through the observation of other individuals, is especially relevant among species belonging to the same guild. The unpredictable and ephemeral nature of carrion implies that social mechanisms may be selected among scavenger species to facilitate carcass location and consumption. Here, we apply a survival-modelling strategy to data obtained through the placement and monitoring of carcasses in the field to analyse possible information transmission cascades within a Neotropical scavenger community. Our study highlights how the use of different senses (smell and sight) within this guild facilitates carcass location through the transmission of social information between species with different carrion foraging efficiencies. Vultures with a highly developed sense of smell play a key role in this process, as they are the first to arrive at the carcasses and their presence seems to serve as a visual cue for other species to locate the resource. Our study supports the local enhancement hypothesis within scavengers, whereby individuals locate carcasses by following foraging heterospecifics, also suggesting the importance of the sense of smell in the maintenance of the community structure.
Exceptional soft tissue preservation reveals a cnidarian affinity for a Cambrian phosphatic tubicolous enigma
Authors: Zhang Guangxu , Parry Luke A. , Vinther Jakob , Ma Xiaoya
Published: November 2022

Exoskeletal dwelling tubes are widespread among extant animals and early fossil assemblages. Exceptional fossils from the Cambrian reveal independent origins of tube dwelling by several clades including cnidarians, lophophorates, annelids, scalidophorans, panarthropods and ambulacrarians. However, most fossil tubes lack preservation of soft parts, making it difficult to understand their affinities and evolutionary significance.
Gangtoucunia aspera
(Wulongqing Formation, Cambrian Stage 4) was an annulated, gradually expanding phosphatic tube, with occasional attachments of multiple, smaller juveniles and has previously been interpreted as the dwelling tube of a ‘worm’ (e.g. a scalidophoran), lophophorate or problematicum. Here, we report the first soft tissues from
Gangtoucunia
that reveal a smooth body with circumoral tentacles and a blind, spacious gut that is partitioned by septa. This is consistent with cnidarian polyps and phylogenetic analysis resolves
Gangtoucunia
as a total group medusozoan. The tube of
Gangtoucunia
is phenotypically similar to problematic annulated tubular fossils (e.g.
Sphenothallus
,
Byronia
, hyolithelminths), which have been compared to both cnidarians and annelids, and are among the oldest assemblages of skeletal fossils. The cnidarian characters of
G. aspera
suggest that these early tubular taxa are best interpreted as cnidarians rather than sessile bilaterians in the absence of contrary soft tissue evidence.
SARS-CoV-2 antibody prevalence among industrial livestock operation workers and nearby community residents, North Carolina, USA, 2021-2022
Authors: Gigot Carolyn , Pisanic Nora , Kruczynski Kate , Rivera Magdielis Gregory , Spicer Kristoffer , Kurowski Kathleen M. , Randad Pranay , Koehler Kirsten , Clarke William A. , Holmes Phyla , Hall DJ , Hall Devon , Heaney Christopher D.
Published: November 2022

Industrial livestock operations (ILOs), particularly processing facilities, emerged as centers of coronavirus disease 2019 (COVID-19) outbreaks in spring 2020. Confirmed cases of COVID-19 underestimate true prevalence. To investigate prevalence of antibodies against SARS-CoV-2, we enrolled 279 participants in North Carolina from February 2021 to July 2022: 90 from households with at least one ILO worker (ILO), 97 from high-ILO intensity areas (ILO neighbors – ILON), and 92 from metropolitan areas (Metro). Participants provided a saliva swab we analyzed for SARS-CoV-2 IgG using a multiplex immunoassay. Prevalence of infection-induced IgG (positive for nucleocapsid and receptor binding domain) was higher among ILO (63%) compared to ILON (42.9%) and Metro (48.7%) participants (prevalence ratio [PR] =1.38; 95% confidence interval [CI]: 1.06, 1.80; ref. ILON and Metro combined). Prevalence of infection-induced IgG was also higher among ILO participants compared to an Atlanta healthcare worker cohort (PR=2.45, 95% CI: 1.8, 3.3) and a general population cohort in North Carolina (PRs 6.37-10.67). Infection-induced IgG prevalence increased over the study period. Participants reporting not masking in public in the past two weeks had higher infection-induced IgG prevalence (78.6%) compared to participants reporting masking (49.3%) (PR=1.59; 95% CI: 1.19, 2.13). Lower education, more people per bedroom, Hispanic/Latino ethnicity, and more contact with people outside the home were also associated with higher infection-induced IgG prevalence. Similar proportions of ILO (51.6%), ILON (48.4%), and Metro (55.4%) participants completed the COVID-19 primary vaccination series; median completion was more than four months later for ILO compared to ILON and Metro participants.

Importance

Few studies have measured COVID-19 seroprevalence in North Carolina, especially among rural, Black, and Hispanic/Latino communities that have been heavily affected. Antibody results show high rates of COVID-19 among industrial livestock operation workers and their household members. Antibody results add to evidence of health disparities in COVID-19 by socioeconomic status and ethnicity. Associations between masking and physical distancing with antibody results also add to evidence of the effectiveness of these prevention strategies. Delays in the timing of receipt of COVID-19 vaccination reinforce the importance of dismantling vaccination barriers, especially for industrial livestock operation workers and their household members.
Isolation of Extracellular Vesicles from human plasma samples: The importance of controls
Authors: Tsamchoe Migmar , Petrillo Stephanie , Metrakos Peter , Lazaris Anthoula
Published: November 2022

There are a number of methods for the isolation of extracellular vesicles (EV) which include the traditional ultracentrifugation to column-based kits available from different companies. Isolation of EVs from complex fluids, such as blood, has several challenges as the detection of low abundance molecules can easily be masked by more abundant proteins, when performing mass spectrometry. For this reason, several commercially available kits contain Thromboplastin D (TP-D) to promote clotting, thus removing clotting factors and abundant proteins resulting in increased detection of proteins. Our study demonstrates that plasma pretreated with Rabbit brain derived TP-D (the most common additive), generated a dynamic range of proteins compared to plasma alone, however, most of these proteins were contaminants introduced from the TP-D (99.1% purity). As an alternative, we tested recombinant TP and demonstrated that although it did not introduce any significant contaminants, we did not see any difference in the detection of proteins. Thus TP-D is not required, and any protein additives must be carefully screened.
Dual function of the O-antigen WaaL ligase ofAggregatibacter actinomycetemcomitans
Authors: Danforth David R. , Melloni Marcella , Thorpe Richard , Cohen Avi , Voogt Richard , Tristano Jake , Mintz Keith P.
Published: November 2022

Protein glycosylation is critical to the quaternary structure and collagen binding activity of the extracellular matrix protein adhesin A (EmaA) associated withAggregatibacter actinomycetemcomitans. The glycosylation of this large, trimeric autotransporter adhesin is postulated to be mediated by WaaL, an enzyme with the canonical function to ligate the O-polysaccharide (O-PS) antigen with a terminal sugar of the lipid A-core oligosaccharide of lipopolysaccharide (LPS). In this study, we have determined that theEscherichia coli waaLortholog (rflA) does not restore collagen binding of awaaLmutant strain ofA. actinomycetemcomitansbut does restore O-PS ligase activity following transformation of a plasmid expressingwaaL. Therefore, a heterologousE. coliexpression system was developed constituted of two independently replicating plasmids expressing eitherwaaLoremaAofA. actinomycetemcomitansto directly demonstrate the necessity of ligase activity for EmaA collagen binding. Proper expression of the protein encoded by each plasmid was characterized, and the individually transformed strains did not promote collagen binding. However, co-expression of the two plasmids resulted in a strain with a significant increase in collagen binding activity and a change in the biochemical properties of the protein. These results provide additional data supporting the novel hypothesis that the WaaL ligase ofA. actinomycetemcomitansshares a dual role as a ligase in LPS biosynthesis and is required for collagen binding activity of EmaA.

Importance

The human oral pathogenA. actinomycetemcomitansis a causative agent of periodontal and several systemic diseases. The organism expresses an adhesin, EmaA, important for the colonization of this pathobiont via collagen binding and biofilm formation. EmaA is suggested to be modified with sugars and the modification is mediated using the same enzymes involved in lipopolysaccharide (LPS) biosynthesis. In this study, evidence is presented which suggests that the WaaL ligase, the enzyme that ligates the O-polysaccharide (O-PS) antigen with a terminal sugar of the lipid A-core oligosaccharide of LPS, is required for the collagen binding activity of EmaA. This finding represents a new paradigm for the posttranslational modification of this type of autotransporter protein.
Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
Authors: Bond Marielle L. , Davis Eric S. , Quiroga Ivana Y. , Love Michael I. , Won Hyejung , Phanstiel Douglas H.
Published: November 2022

3D chromatin structure has been shown to play a role in regulating gene transcription during biological transitions. While our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising 4 biological replicates and 6 billion reads per time point. Statistical analysis revealed 1,503 differential loops. Gained loops were enriched for AP-1 occupancy and correlated with increased expression of genes at their anchors. Lost loops were characterized by increases in expression of genes within the loop boundaries. Linear modeling revealed that changes in histone H3 K27 acetylation, chromatin accessibility, and JUN binding in between the loop anchors were as predictive of changes in loop strength as changes to CTCF and/or cohesin occupancy at loop anchors. Finally, we built linear models and found that incorporating the dynamics of enhancer acetylation and loop strength increased accuracy of gene expression predictions.
Computed tomography analysis of vulnerable carotid atherosclerotic plaque and relationship to clinical characteristics
Authors: Giannotti N. , McNulty J.P. , Foley S.J. , Barry M. , Crowe M. , Dolan E. , Harbison J. , Horgan G. , Kavanagh E. , O’Connell M , Marnane M. , Murphy S. , McDonnell C. , O’Donohoe M. , Williams D. , Kelly P.J.
Published: November 2022

Objective

The presence of atherosclerotic plaque components such as lipid rich necrotic core and intraplaque haemorrhage is associated with increased plaque vulnerability, and may be used to stratify the risk of future cerebrovascular events. Our aim was to investigate the relationship between selected carotid plaque components imaged with CTA, patient characteristics, and clinical outcomes.

Methods

Symptomatic patients underwent carotid CTA as part of the BIOVASC study. Images were analysed for plaque volume composition with a semi-automatic Hounsfield Unit (HU)-based algorithm. Plaque components were classified based on their attenuation values: lipids <61 HU, fibrous tissue 61-129 HU and calcium >131 HU. Parametric and non-parametric tests were performed to compare plaque measurements to clinical characteristics and outcomes.

Results

One-hundred and two symptomatic carotids were analysed (avg. age 69y, 54.9% Male, 29.4% severe stenosis). Mean plaque volume was 480±230 mm3, and the mean LRNC volume was 170±100 mm3. A difference in LRNC volume was identified between moderate and severe stenosis (190–150 mm3, p=0.012). Regression analysis showed that age and gender may predict increased plaque volume (p<0.001). A trend for reduced mean plaque LRNC was identified in patients receiving statins (130-210 mm3, p=0.08). Intra-reader reliability showed good agreement (0.62-0.78, p<0.001) between CTA plaque measurements.

Conclusions

In-vivo CTA plaque volume composition assessment is feasible with good intra-reader reliability. Our findings suggest that CTA-HU measurements may be used to provide improved mechanistic and diagnostic insights into atherosclerotic disease, and facilitate the quantification of selected plaque components whose presence may be associated with increased plaque vulnerability.

Key Points

Plaque CTA Hounsfield Unit (HU) measurement and segmentation techniques can provide improved mechanistic and diagnostic insights into atherosclerotic disease.

Plaque components characterisation using CTA HU measurements may help clinicians to identify patients presenting with high-risk vulnerable plaque.

CTA plaque volume composition assessment is feasible with good reliability observed between measurements taken at different time-points.
DNA-PKcs is required for cGAS/STING-dependent viral DNA sensing in human cells
Authors: Hristova Dayana , Oliveira Marisa , Wagner Emma , Melcher Alan , Harrington Kevin , Belot Alexandre , Ferguson Brian J
Published: November 2022

To mount an efficient interferon response to virus infection, intracellular pattern recognition receptors (PRRs) sense viral nucleic acids and activate anti-viral gene transcription. The mechanisms by which intracellular DNA and DNA viruses are sensed are relevant not only to antiviral innate immunity, but also to autoinflammation and anti-tumour immunity through initiation of sterile inflammation by self-DNA recognition. The PRRs that directly sense and respond to viral or damaged self-DNA function by signalling to activate interferon regulatory factor (IRF)-dependent type one interferon (IFN-I) transcription. We and others have previously defined DNA-dependent protein kinase (DNA-PK) as an essential component of the DNA-dependent antiviral innate immune system. Here, we show that DNA-PK is essential for STING-dependent IFN-I responses in human cells during stimulation with exogenous DNA and infection with DNA viruses.
Cell lineage predicts neural connectivity beyond cell type
Authors: Matelsky Jordan K. , Wester Brock , Kording Konrad P.
Published: November 2022

As an organism develops, a zygote becomes the body through repeated cell division. This process produces the mitotic family tree, and cells specialize into their ultimate phenotype through interaction with other cells but also through the history of divisions. Biologists often cluster cells in the body into “cell types,” using e.g. their morphologies and molecular makeup. While morphomolecular cell type carries information about phenotype and function, there may be unknown, missing information available in this family tree. Emerging methods are making these lineage trees progressively observable. Here, using the complete mitotic family tree and connectome of the nematodeC. eleganswe ask about the role of cell-types and their family tree. We can thus evaluate how well we can predict synaptic connection with only cell-type information versus with the family tree lineage. We show that neglecting lineage can produce misleading insights into the mechanisms underlying neural wiring: underlying lineage can confound the effect of cell type. These results suggest that the concept of cell-type needs to be re-thought in the context of this emerging knowledge about cell lineage.