bluuebunny/crossref_metadata_2025 huggingface dataset:
Inferring the intergalactic medium neutral fraction at z ∼ 6–8 with low-luminosity Lyman break galaxies
Authors: Bolan Patricia , Lemaux Brian C , Mason Charlotte , Bradač Maruša , Treu Tommaso , Strait Victoria , Pelliccia Debora , Pentericci Laura , Malkan Matthew
Published: October 2022

We present a Bayesian inference on the neutral hydrogen fraction of the intergalactic medium (IGM), $\overline{x}_{\small HI}$, at z ∼ 6–8 using the properties of Lyman break galaxies (LBGs) during the epoch of reionization. We use large samples of LBG candidates at 5.5 ≤ z ≤ 8.2 with spectroscopy from Keck/DEIMOS and Keck/MOSFIRE. For each galaxy, we incorporate either the Lyman-α (Lyα) equivalent width (EW) for detections or the EW limit spectrum for non-detections to parametrize the EW distribution at various ultraviolet brightnesses for a given redshift. Using our reference sample of galaxy candidates from the ionized universe at z ∼ 6.0, we are able to infer $\overline{x}_{\small HI}$ at two redshifts: z ∼ 6.7 and z ∼ 7.6. This work includes intrinsically faint, gravitationally lensed galaxies at z ∼ 6.0 in order to constrain the intrinsic faint-end Lyα EW distribution and provide a comparable population of galaxies to counterparts in our sample that are at higher redshift. The inclusion of faint galaxy candidates, in addition to a more sophisticated modelling framework, allows us to better isolate effects of the interstellar medium and circumgalactic medium on the observed Lyα distribution from those of the IGM. We infer an upper limit of $\overline{x}_{\small HI}$ ≤ 0.25 (0.44) at z = 6.7 ± 0.2 and a neutral fraction of $\overline{x}_{\small HI}$ = $0.83^{+0.08}_{-0.11}$ (0.83$^{+0.11}_{-0.21}$) at z = 7.6 ± 0.6, both within 68 per cent (95 per cent) uncertainty, results that favour a moderately late and fairly rapid reionization.
Constraining the interiors of asteroids through close encounters
Authors: Dinsmore Jack T , de Wit Julien
Published: October 2022

Knowledge of the interior density distribution of an asteroid can reveal its composition and constrain its evolutionary history. However, most asteroid observational techniques are not sensitive to interior properties. We investigate the interior constraints accessible through monitoring variations in angular velocity during a close encounter. We derive the equations of motion for a rigid asteroid’s orientation and angular velocity to arbitrary order and use them to generate synthetic angular velocity data for a representative asteroid on a close Earth encounter. We develop a toolkit AIME (Asteroid Interior Mapping from Encounters) which reconstructs asteroid density distribution from these data, and we perform injection-retrieval tests on these synthetic data to assess AIME’s accuracy and precision. We also perform a sensitivity analysis to asteroid parameters (e.g. asteroid shape and orbital elements), observational setup (e.g. measurement precision and cadence), and the mapping models used. We find that high precision in rotational period estimates (≲0.27 s) is necessary for each cadence, and that low perigees (≲ 18 Earth radii) are necessary to resolve large-scale density non-uniformities with uncertainties of $\sim 0.1{{\ \rm per\ cent}}$ of the local density under some models.
Low-density star cluster formation: discovery of a young faint fuzzy on the outskirts of the low-mass spiral galaxy NGC 247
Authors: Romanowsky Aaron J , Larsen Søren S , Villaume Alexa , Carlin Jeffrey L , Janz Joachim , Sand David J , Strader Jay , Brodie Jean P , Chakrabarti Sukanya , Cheng Chloe M , Crnojević Denija , Forbes Duncan A , Garling Christopher T , Hargis Jonathan R , Karunakaran Ananthan , Martín-Navarro Ignacio , Olsen Knut A G , Rider Nicole , Salimkumar Bitha , Santhanakrishnan Vakini , Spekkens Kristine , Tang Yimeng , van Dokkum Pieter G , Willman Beth
Published: October 2022

The classical globular clusters found in all galaxy types have half-light radii of rh ∼ 2–4 pc, which have been tied to formation in the dense cores of giant molecular clouds. Some old star clusters have larger sizes, and it is unclear if these represent a fundamentally different mode of low-density star cluster formation. We report the discovery of a rare, young ‘faint fuzzy’ star cluster, NGC 247-SC1, on the outskirts of the low-mass spiral galaxy NGC 247 in the nearby Sculptor group, and measure its radial velocity using Keck spectroscopy. We use Hubble Space Telescope imaging to measure the cluster half-light radius of rh ≃ 12 pc and a luminosity of LV ≃ 4 × 105L⊙. We produce a colour–magnitude diagram of cluster stars and compare to theoretical isochrones, finding an age of ≃300 Myr, a metallicity of [Z/H] ∼ −0.6 and an inferred mass of M⋆ ≃ 9 × 104M⊙. The narrow width of blue-loop star magnitudes implies an age spread of ≲50 Myr, while no old red-giant branch stars are found, so SC1 is consistent with hosting a single stellar population, modulo several unexplained bright ‘red straggler’ stars. SC1 appears to be surrounded by tidal debris, at the end of an ∼2 kpc long stellar filament that also hosts two low-mass, low-density clusters of a similar age. We explore a link between the formation of these unusual clusters and an external perturbation of their host galaxy, illuminating a possible channel by which some clusters are born with large sizes.
Interlopers speak out: studying the dark universe using small-scale lensing anisotropies
Authors: Dhanasingham Birendra , Cyr-Racine Francis-Yan , Peter Annika H G , Benson Andrew , Gilman Daniel
Published: October 2022

Strongly lensed systems are powerful probes of the distribution of dark matter on small scales. In this paper, we show that line-of-sight haloes between the source and the observers give rise to a distinct anisotropic signature in the two-point function of the effective lensing deflection field. We show in particular that the non-linear coupling between line-of-sight haloes and the main lens plane imprints a characteristic quadrupole moment on this two-point function whose amplitude reflects the abundance of such haloes within the strongly lensed field. We discuss how, by taking ratios of different multipole moments, such observables could be made robust under the mass-sheet transform. We also demonstrate that future extremely large telescopes have the ability to detect the quadrupole moment due to this unique anisotropic signature under ideal conditions. Our approach opens the door to statistically distinguish the effect of line-of-sight haloes from that of the main-lens substructure on lensed images, hence allowing one to probe dark matter physics in a new way.
GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals
Authors: Liu Xiaonan , Tian Dongmei , Li Cuiping , Tang Bixia , Wang Zhonghuang , Zhang Rongqin , Pan Yitong , Wang Yi , Zou Dong , Zhang Zhang , Song Shuhui
Published: October 2022

GWAS Atlas (https://ngdc.cncb.ac.cn/gwas/) is a manually curated resource of genome-wide genotype-to-phenotype associations for a wide range of species. Here, we present an updated implementation of GWAS Atlas by curating and incorporating more high-quality associations, with significant improvements and advances over the previous version. Specifically, the current release of GWAS Atlas incorporates a total of 278,109 curated genotype-to-phenotype associations for 1,444 different traits across 15 species (10 plants and 5 animals) from 830 publications and 3,432 studies. A collection of 6,084 lead SNPs of 439 traits and 486 experiment-validated causal variants of 157 traits are newly added. Moreover, 1,056 trait ontology terms are newly defined, resulting in 1,172 and 431 terms for Plant Phenotype and Trait Ontology and Animal Phenotype and Trait Ontology, respectively. Additionally, it is equipped with four online analysis tools and a submission platform, allowing users to perform data analysis and data submission. Collectively, as a core resource in the National Genomics Data Center, GWAS Atlas provides valuable genotype-to-phenotype associations for a diversity of species and thus plays an important role in agronomic trait study and molecular breeding.
The clinical and molecular characteristics of progressive hypothalamic/optic pathway pilocytic astrocytoma
Authors: Li Xiaoyu , Moreira Daniel C , Bag Asim K , Qaddoumi Ibrahim , Acharya Sahaja , Chiang Jason
Published: October 2022

Background

Unresectable hypothalamic/optic pathway pilocytic astrocytoma (PA) often progresses despite multiple therapies. Identifying clinical and molecular characteristics of progressive tumors may aid in prognostication and treatment.

Methods

We collected 72 unresectable, non-neurofibromatosis type 1-associated hypothalamic/optic pathway PA to identify clinical and biologic factors associated with tumor progression. Tumors that progressed after therapy, metastasized, or resulted in death were categorized into Cohort B; those that did not meet these criteria were categorized into Cohort A. DNA methylation and transcriptome analyses were performed on treatment-naïve tumors, and the findings were validated by immunohistochemistry (IHC).

Results

The median follow-up of the entire cohort was 12.3 years. Cohort B was associated with male sex (M:F = 2.6:1), younger age at diagnosis (median 3.2 years vs 6.7 years, P = .005), and high incidence of KIAA1549-BRAF fusion (81.5% vs 38.5%, P = .0032). Cohort B demonstrated decreased CpG methylation and increased RNA expression in mitochondrial genes and genes downstream of E2F and NKX2.3. Transcriptome analysis identified transcription factor TBX3 and protein kinase PIM1 as common downstream targets of E2F and NKX2.3. IHC confirmed increased expression of TBX3 and PIM1 in Cohort B tumors. Gene enrichment analysis identified enrichment of MYC targets and MAPK, PI3K/AKT/mTOR, and p53 pathways, as well as pathways related to mitochondrial function.

Conclusions

We identified risk factors associated with progressive PA. Our results support the model in which the p53-PIM1-MYC axis and TBX3 act alongside MAPK and PI3K/AKT/mTOR pathways to promote tumor progression, highlighting potential new targets for combination therapy and refining disease prognostication.
“They Just Assume That We’re All Going to Do the Wrong Thing With It. It’s Just Not True”: Stakeholder Perspectives About Peripherally Inserted Central Catheters in People Who Inject Drugs
Authors: Morales Yoelkys , Smyth Emma , Zubiago Julia , Bearnot Benjamin , Wurcel Alysse G
Published: October 2022

Background

In the absence of adequate harm reduction opportunities, people who inject drugs (PWID) are at increased risk for serious infections. Infectious diseases guidelines recommend extended periods of intravenous antibiotic treatment through peripherally inserted central catheters (PICCs), but PWID are often deemed unsuitable for this treatment. We conducted semi-structured interviews and focus groups to understand the perspectives and opinions of patients and clinicians on the use of PICCs for PWID.

Methods

We approached patients and clinicians (doctors, nurses, PICC nurses, social workers, and case workers) involved in patient care at Tufts Medical Center (Boston, Massachusetts) between August 2019 and April 2020 for semi-structured interviews and focus groups.

Results

Eleven of 14 (79%) patients agreed to participate in an in-depth interview, and 5 role-specific clinician focus groups (1 group consisting of infectious diseases, internal medicine, and addiction psychiatry doctors, 2 separate groups of floor nurses, 1 group of PICC nurses, and 1 group of social workers) were completed. Emergent themes included the overall agreement that PICCs improve healthcare, patients’ feelings that their stage of recovery from addiction was not taken into consideration, and clinicians’ anecdotal negative experiences driving decisions on PICCs.

Conclusions

When analyzed together, the experiences of PWID and clinicians shed light on ways the healthcare system can improve the quality of care for PWID hospitalized for infections. Further research is needed to develop a system of person-centered care for PWID that meets the specific needs of patients and improves the relationship between them and the healthcare system.
Comparison of Rhinovirus A–, B–, and C–Associated Respiratory Tract Illness Severity Based on the 5′-Untranslated Region Among Children Younger Than 5 Years
Authors: Sayama Akiko , Okamoto Michiko , Tamaki Raita , Saito-Obata Mariko , Saito Mayuko , Kamigaki Taro , Sayama Yusuke , Lirio Irene , Manalo Joanna Ina G , Tallo Veronica L , Lupisan Socorro P , Oshitani Hitoshi
Published: October 2022

Background

Rhinoviruses (RVs) are among the most frequently detected viruses from hospitalized children with severe acute respiratory infections, being classified into RV-A, RV-B, and RV-C (4 clades: C, GAC1, GAC2, and A2). This study aimed to compare the clinical characteristics and respiratory tract illness severity between the RV species and RV-C clades in children in primary care and hospital settings in rural communities in the Philippines.

Methods

Clinical samples and information of children <5 years old in the Philippines were collected from 2014 to 2016. The samples were tested by reverse-transcription polymerase chain reaction (RT-PCR) targeting the 5′-untranslated region. PCR-positive samples were sequenced, and RV species were identified by phylogenetic analysis.

Results

Overall, 3680 respiratory tract illness episodes in 1688 cohort children were documented; 713 of those were RV positive and identified as RV-A (n = 271), RV-B (n = 47), and RV-C (n = 395: C [n = 76], GAG1 [n = 172], GAG2 [n = 8], A2 [n = 138], and unidentified [n = 1]). Severe illnesses, low oxygen saturation, cough, and wheezing were more common in patients with RV-C, especially with GAC1, than in those with RV-A or RV-B. Furthermore, severe illness was significantly more common in RV-C (GAC1)–positive cases than in RV-A–positive cases (odds ratio, 2.61 [95% CI, 1.17–4.13]).

Conclusions

Children infected with RV-C had more severe illnesses than children infected with RV-A and RV-B. Moreover, emerging clades of RV-C were associated with increased severity.
Effectiveness of Influenza Vaccination of Pregnant Women for Prevention of Maternal and Early Infant Influenza-Associated Hospitalizations in South Africa: A Prospective Test-Negative Study
Authors: Nunes Marta C , Walaza Sibongile , Meiring Susan , Zar Heather J , Reubenson Gary , McMorrow Meredith , Tempia Stefano , Rossi Liza , Itzikowitz Raphaela , Bishop Kate , Mathunjwa Azwifarwi , Wise Amy , Treurnicht Florette K , Hellferscee Orienka , Laubscher Matt , Serafin Natali , Cutland Clare L , Madhi Shabir A , Cohen Cheryl
Published: October 2022

Background

Influenza vaccination during pregnancy reduces influenza-associated illness in the women and their infants, but effectiveness estimates against influenza-associated hospitalization are limited and lacking from settings with high human immunodeficiency virus (HIV) infection prevalence. We assessed the effect of maternal vaccination in HIV-uninfected women and women with HIV in preventing influenza-associated hospitalizations in infants and the women.

Methods

During 2015–2018, influenza vaccination campaigns targeting pregnant women were augmented at selected antenatal clinics; these were coupled with prospective hospital-based surveillance for acute respiratory or febrile illness in infants aged <6 months and cardiorespiratory illness among pregnant or postpartum women. Vaccine effectiveness (VE) was assessed using a test-negative case-control study.

Results

Overall, 71 influenza-positive and 371 influenza-negative infants were included in the analysis; mothers of 26.8% of influenza-positive infants were vaccinated during pregnancy compared with 35.6% of influenza-negative infants, corresponding to an adjusted VE (aVE) of 29.0% (95% confidence interval [CI], −33.6% to 62.3%). When limited to vaccine-matched strains, aVE was 65.2% (95% CI, 11.7%–86.3%). For maternal hospitalizations, 56 influenza-positive and 345 influenza-negative women were included in the analysis, with 28.6% of influenza-positive women being vaccinated compared with 38.3% of influenza-negatives, for an aVE of 46.9% (95% CI, −2.8% to 72.5%). Analysis restricted to HIV-uninfected women resulted in 82.8% (95% CI, 40.7%–95.0%) aVE. No significant aVE (−32.5% [95% CI, −208.7% to 43.1%]) was detected among women with HIV.

Conclusions

Influenza vaccination during pregnancy prevented influenza-associated hospitalizations among young infants when infected with vaccine strains and among HIV-uninfected women.
Effector XopQ-induced stromule formation inNicotiana benthamianadepends on ETI signaling components ADR1 and NRG1
Authors: Prautsch Jennifer , Erickson Jessica Lee , Özyürek Sedef , Gormanns Rahel , Franke Lars , Lu Yang , Marx Jolina , Niemeyer Frederik , Parker Jane E , Stuttmann Johannes , Schattat Martin Hartmut
Published: October 2022

In Nicotiana benthamiana, the expression of the Xanthomonas effector XANTHOMONAS OUTER PROTEIN Q (XopQ) triggers RECOGNITION OF XOPQ1 (ROQ1)-dependent effector-triggered immunity (ETI) responses accompanied by the accumulation of plastids around the nucleus and the formation of stromules. Both plastid clustering and stromules were proposed to contribute to ETI-related hypersensitive cell death and thereby to plant immunity. Whether these reactions are directly connected to ETI signaling events has not been tested. Here, we utilized transient expression experiments to determine whether XopQ-triggered plastid reactions are a result of XopQ perception by the immune receptor ROQ1 or a consequence of XopQ virulence activity. We found that N. benthamiana mutants lacking ROQ1, ENHANCED DISEASE SUSCEPTIBILITY 1, or the helper NUCLEOTIDE-BINDING LEUCINE-RICH REPEAT IMMUNE RECEPTORS (NLRs) N-REQUIRED GENE 1 (NRG1) and ACTIVATED DISEASE RESISTANCE GENE 1 (ADR1), fail to elicit XopQ-dependent host cell death and stromule formation. Mutants lacking only NRG1 lost XopQ-dependent cell death but retained some stromule induction that was abolished in the nrg1_adr1 double mutant. This analysis aligns XopQ-triggered stromules with the ETI signaling cascade but not to host programmed cell death. Furthermore, data reveal that XopQ-triggered plastid clustering is not strictly linked to stromule formation during ETI. Our data suggest that stromule formation, in contrast to chloroplast perinuclear dynamics, is an integral part of the N. benthamiana ETI response and that both NRG1 and ADR1 hNLRs play a role in this ETI response.
Endophilin A2 protects against renal fibrosis by targeting TGF‐β/Smad signaling
Authors: Mai Xiaoyi , Shang Jinyan , Chen Qiuyuan , Gu Shijie , Hong Yu , Zhou Jiaguo , Zhang Minzhou
Published: October 2022

Renal fibrosis underlies all forms of end‐stage kidney disease. Endophilin A2 (EndoA2) plays a role in nephrotic syndrome; however, its effect on renal fibrosis remains unknown. Here, we demonstrate that EndoA2 protects against kidney interstitial fibrosis via the transforming growth factor‐β (TGF‐β)/Smad signaling pathway. Mouse kidneys with fibrosis or kidney biopsy specimens from patients with fibrotic nephropathy had lower levels of EndoA2 protein expression than that in kidneys without fibrosis. In vivo overexpression of EndoA2 with the endophilin A2 transgene (EndoA2Tg) notably prevented renal fibrosis, decreased the protein expression of profibrotic molecules, suppressed tubular injury, and reduced apoptotic tubular cells in the obstructed kidney cortex of mice with unilateral ureteral obstruction (UUO). In vivo and in vitro overexpression of EndoA2 markedly inhibited UUO‐ or TGF‐β1‐induced phosphorylation of Smad2/3 and tubular epithelial cells dedifferentiation. Furthermore, EndoA2 was co‐immunoprecipitated with the type II TGF‐β receptor (TβRII), thus inhibiting the binding of the type I TGF‐β receptor (TβRI) to TβRII. These findings indicate that EndoA2 mitigates renal fibrosis, at least partially, via modulating the TGF‐β/Smad signaling. Targeting EndoA2 may be a new potential therapeutic strategy for treatment of renal fibrosis.
Intravesical instillation of platelet-rich plasma for treatment of interstitial cystitis/bladder pain syndrome: A pilot study
Authors: El Hefnawy Ahmed S. , Hasan Mohamed Attya Ahmed , El Sawy Esam , Abdel-Razik Mohamed , El-Tabey Nasr
Published: October 2022

Objective

The aim of this study was to evaluate the feasibility of intravesical instillation of platelet-rich plasma (PRP) to treat interstitial cystitis/bladder pain syndrome (IC/BPS).

Materials and methods

Twenty PRP samples were tested in vitro for stability after exposure to urine samples with different pH. A pilot study involving 21 female patients with IC/BPS was conducted, and 6 weekly doses of autologous PRP (50 mL) were administered. Patients were followed up at the 2nd, 4th, 8th, and 12th weeks after terminating instillation. The primary endpoint was the visual analog scale (VAS) for pain, and the secondary endpoints included the IC symptom index, IC problem index of the O'Leary-Sant questionnaire and global response assessment, urine culture, and uroflowmetry. Success was defined as a reduction in VAS by 30% or more compared with basal level, and adverse events were recorded.

Results

The mean ± SD of VAS was significantly reduced compared with basal level (4.4 ± 2.6 vs. 8.8 ± 1.1, respectively, p = 0.001). Meanwhile, 80% of cases were considered successful, with a 50.1% reduction in the mean score compared with the basal level. The mean ± SD of IC symptom index and IC problem index significantly improved compared with the basal level. Global response assessment was markedly, moderately, and slightly improved in 2 (10%), 10 (50%), and 5 (25%) patients, respectively, and showed no change in 3 (15%). Three patients had positive urine cultures at follow-up, but 1 withdrew after 2 sessions because of a lack of efficacy.

Conclusions

Repeated intravesical instillation of PRP could be considered an effective and safe approach for treating IC/BPS.
Lung Cancer Screening Knowledge, Attitudes and Practice Patterns Among Primary and Pulmonary Care Clinicians
Authors: Carter-Bawa Lisa , Walsh Leah E. , Schofield Elizabeth , Williamson Timothy J. , Hamann Heidi A. , Ostroff Jamie S.
Published: October 2022

Background

Lung cancer screening has the potential to identify lung cancer at an early stage when more treatment options exist. However, discussions with and referrals of screening-eligible patients remain unacceptably low. We need to better understand clinician knowledge, attitudes, and practice patterns to identify strategies to improve lung cancer screening uptake. Prior studies have focused on understanding these factors from physicians only. Nevertheless, many patients receive primary care from nurse practitioners and physician assistants where prevention and early detection conversations are most likely to occur. Therefore, we must engage the full range of clinicians treating screening-eligible patients.

Objectives

To describe attitudes, beliefs and referral practice patterns, lung cancer screening knowledge, and concordance with lung cancer screening guidelines among nurse practitioners, physicians, and physician assistants in the U.S.

Methods

Descriptive, cross-sectional study using survey methodology with clinical vignettes to examine clinician factors and concordance with U.S. Preventive Services Task Force (USPSTF) Lung Cancer Screening Guidelines.

Results

Participants scored low on attitudes toward shared decision-making, high on the importance of shared decision-making in lung cancer screening, and low on barriers to lung cancer screening referral. In addition, midrange scores on empathy toward patients with smoking history were noted. Lung cancer screening knowledge was low regardless of clinician specialty; the most endorsed response when presented with a hypothetical patient was to refer for lung cancer screening using a chest X-ray.

Discussion

Findings demonstrate that most clinicians are nonconcordant with USPSTF guidelines, erroneously believing a chest X-ray is appropriate for lung cancer screening. Clinicians must follow evidence-based practice guidelines, highlighting the need for targeted continuing education about lung cancer screening for clinicians who treat screening-eligible patients.
Critical Incident Reports Related to Ventilator Use: Analysis of the Japan Quality Council National Database
Authors: Akiyama Naomi , Kajiwara Shihoko , Tamaki Takahiro , Shiroiwa Takeru
Published: October 2022

Objective

This study aimed to assess the factors associated with medical device incidents.

Methods

In this mixed-methods study, we used incident reporting data from the Japan Council for Quality Health Care. Of the 232 medical device–related reports that were downloaded, 34 (14.7%) were ventilator-associated incidents. Data related to patients, situations, and incidents were collected and coded.

Results

The frequencies of ventilator-associated accidents were 20 (58.8%) during the daytime and 14 (41.2%) during the night/early morning. Ventilator-associated accidents occurred more frequently in the hospital room (n = 22 [64.7%]) than in the intensive care unit (n = 4 [11.8%]). Problems with ventilators occurred in only 4 cases (11.8%); in most cases, medical professionals experienced difficulty with the use or management of ventilators (n = 30 [88.2%]), and 50% of them were due to misuse/misapplication of ventilators (n = 17 [50.0%]). Ventilator-associated accidents were caused by an entanglement of complex factors—hardware, software, environment, liveware, and liveware-liveware interaction. Communication and alarm-related errors were reported to be related, as were intuitiveness or complicated specifications of the device.

Conclusions

Our study revealed that ventilator-associated accidents were caused by an entanglement of complex factors and were related to inadequate communication among caregivers and families. Moreover, alarms were overlooked owing to inattentiveness. Mistakes were generally caused by a lack of experience, insufficient training, or outright negligence. To reduce the occurrence of ventilator-associated accidents, hospital administrators should develop protocols for employment of new devices. Medical devices should be developed from the perspective of human engineering, which could be one of the systems approaches.
Ranavirus infection-induced avoidance behaviour in wood frog juveniles: do amphibians socially distance?
Authors: Le Sage E. H. , Diamond M. , Crespi E. J.
Published: October 2022

Hosts may limit exposure to pathogens through changes in behaviour, such as avoiding infected individuals or contaminated areas. Here, we tested for a behavioural response to ranavirus infection in juvenile wood frogs (
Rana sylvatica
) because the majority of dispersal between populations occurs during this life stage. We hypothesized that if infections are transmissible and detectable at this life stage, then susceptibles would display avoidance behaviours when introduced to an infected conspecific. Despite no apparent signs of infection, we observed a greater distance between susceptible–infected pairs, compared to pairs of either two infected or two susceptible animals. Further, distances between susceptible–infected pairs were positively related to the infection intensity of the focal exposed frog, suggesting the cue to avoid infected conspecifics may become more detectable with more intense infections. Although we did not quantify whether the transmission was affected by their distancing, our findings suggest that juvenile frogs have the potential to reduce terrestrial transmission of ranaviruses through avoidance behaviours.
A retrospective assessment of COVID-19 model performance in the USA
Authors: Colonna Kyle J. , Nane Gabriela F. , Choma Ernani F. , Cooke Roger M. , Evans John S.
Published: October 2022

Coronavirus disease 2019 (COVID-19) forecasts from over 100 models are readily available. However, little published information exists regarding the performance of their uncertainty estimates (i.e. probabilistic performance). To evaluate their probabilistic performance, we employ the classical model (CM), an established method typically used to validate expert opinion. In this analysis, we assess both the predictive and probabilistic performance of COVID-19 forecasting models during 2021. We also compare the performance of aggregated forecasts (i.e. ensembles) based on equal and CM performance-based weights to an established ensemble from the Centers for Disease Control and Prevention (CDC). Our analysis of forecasts of COVID-19 mortality from 22 individual models and three ensembles across 49 states indicates that—(i) good predictive performance does not imply good probabilistic performance, and vice versa; (ii) models often provide tight but inaccurate uncertainty estimates; (iii) most models perform worse than a naive baseline model; (iv) both the CDC and CM performance-weighted ensembles perform well; but (v) while the CDC ensemble was more informative, the CM ensemble was more statistically accurate across states. This study presents a worthwhile method for appropriately assessing the performance of probabilistic forecasts and can potentially improve both public health decision-making and COVID-19 modelling.
Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
Authors: Poterek Marya L. , Vogels Chantal B. F. , Grubaugh Nathan D. , Ebel Gregory D. , Alex Perkins T. , Cavany Sean M.
Published: October 2022

Though instances of arthropod-borne (arbo)virus co-infection have been documented clinically, the overall incidence of arbovirus co-infection and its drivers are not well understood. Now that dengue, Zika and chikungunya viruses are all in circulation across tropical and subtropical regions of the Americas, it is important to understand the environmental and biological conditions that make co-infections more likely to occur. To understand this, we developed a mathematical model of co-circulation of two arboviruses, with transmission parameters approximating dengue, Zika and/or chikungunya viruses, and co-infection possible in both humans and mosquitoes. We examined the influence of seasonal timing of arbovirus co-circulation on the extent of co-infection. By undertaking a sensitivity analysis of this model, we examined how biological factors interact with seasonality to determine arbovirus co-infection transmission and prevalence. We found that temporal synchrony of the co-infecting viruses and average temperature were the most influential drivers of co-infection incidence. Our model highlights the synergistic effect of co-transmission from mosquitoes, which leads to more than double the number of co-infections than would be expected in a scenario without co-transmission. Our results suggest that appreciable numbers of co-infections are unlikely to occur except in tropical climates when the viruses co-occur in time and space.
Social encounters produce different autonomic response between dominants and subordinates in crows
Authors: Takeda Kazuaki , Takahashi Nana , Izawa Ei-Ichi
Published: October 2022

Recent studies of behavioural physiology on animals have suggested the crucial role of peripherally physiological signals in eliciting arousal and emotion. Heart rate (HR) is one of the useful and critical signals to measure autonomic regulation as a physiological basis for arousal and emotion in response to biologically significant stimuli such as social encounter with conspecific individuals. However, our understanding of peripherally physiological response such as HRs and autonomic activities under social contexts of non-human animals is still limited, particularly in birds. Here, we examined the autonomic activity of behaving crows exposed to a dominant and a subordinate conspecific by using non-invasive electrocardiogram recording. We found different patterns of autonomic responses dependent on the relative dominance position: dominant crows encountering subordinates showed the elevation of sympathetic activity, whereas subordinates encountering dominants showed decreased HR with elevated parasympathetic activity. This is the first study in birds to report different autonomic responses dependent on relative dominance positions during dyadic social encounters. The present study advances our understanding of the role of the peripheral autonomic system, as an interactive system with the brain, in eliciting emotion/arousal associated with socially challenging environments from an evolutionary perspective.
Preying dangerously: black widow spider venom resistance in sympatric lizards
Authors: Thill Vicki L. , Moniz Haley A. , Teglas Mike B. , Wasley McKenzie J. , Feldman Chris R.
Published: October 2022

Lizards and spiders are natural adversaries, yet little is known of adaptations that lizards might possess for dealing with the venomous defences of spider prey. In the Western USA, two lizard species (
Elgaria multicarinata
and
Sceloporus occidentalis
) are sympatric with and predate western black widow spiders (
Latrodectus hesperus
). The consequences of black widow spider venom (BWSV) can be severe, and are well understood for mammals but unknown for reptiles. We evaluated potential resistance to BWSV in the lizards that consume black widows, and a potentially susceptible species (
Uta stansburiana
) known as prey of widows. We investigated BWSV effects on whole-animal performance (sprint) and muscle tissue at two venom doses compared with control injections. Sprint speed was not significantly decreased in
E. multicarinata
or
S. occidentalis
in any treatment, while
U. stansburiana
suffered significant performance reductions in response to BWSV. Furthermore,
E. multicarinata
showed minimal tissue damage and immune response, while
S. occidentalis
and
U. stansburiana
exhibited increased muscle damage and immune system infiltration in response to BWSV. Our data suggest predator–prey relationships between lizards and spiders are complex, possibly leading to physiological and molecular adaptations that allow some lizards to tolerate or overcome the dangerous defences of their arachnid prey.
Friend of a friend models of network growth
Authors: Levens Watson , Szorkovszky Alex , Sumpter David J. T.
Published: October 2022

One of the best-known models in network science is preferential attachment. In this model, the probability of attaching to a node depends on the degree of
all
nodes in the population, and thus depends on global information. In many biological, physical and social systems, however, interactions between individuals depend only on local information. Here, we investigate a truly local model of network formation—based on the idea of a friend of a friend—with the following rule: individuals choose one node at random and link to it with probability
p
, then they choose a neighbour of that node and link with probability
q
. Our model produces power-laws with empirical exponents ranging from 1.5 upwards and clustering coefficients ranging from 0 up to 0.5 (consistent with many real networks). For small
p
and
q
= 1, the model produces super-hub networks, and we prove that for
p
= 0 and
q
= 1, the proportion of non-hubs tends to 1 as the network grows. We show that power-law degree distributions, small world clustering and super-hub networks are all outcomes of this, more general, yet conceptually simple model.
Sampling biases obscure the early diversification of the largest living vertebrate group
Authors: Henderson Struan , Dunne Emma M. , Giles Sam
Published: October 2022

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet spatio-temporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends, reconstruct local richness and apply richness estimation techniques to a recently assembled occurrence database for Palaeozoic ray-finned fishes. We identify substantial fossil record biases, such as geographical bias in sampling centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the occurrence distributions, reflecting historical biases in sampling and taxonomic practices, to the extent that evenness has an overriding effect on diversity estimates. Other than a genuine rise in diversity in the Tournaisian following the end-Devonian mass extinction, diversity estimates for Palaeozoic actinopterygians appear to lack biological signal, are heavily biased and are highly dependent on sampling. Increased sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends.
Phenology in the deep sea: seasonal and tidal feeding rhythms in a keystone octocoral
Authors: Girard Fanny , Litvin Steven Y. , Sherman Alana , McGill Paul , Gannon Amanda , Lovera Christopher , DeVogelaere Andrew , Burton Erica , Graves Dale , Schnittger Aaron , Barry Jim
Published: October 2022

Biological rhythms are widely known in terrestrial and marine systems, where the behaviour or function of organisms may be tuned to environmental variation over periods from minutes to seasons or longer. Although well characterized in coastal environments, phenology remains poorly understood in the deep sea. Here we characterized intra-annual dynamics of feeding activity for the deep-sea octocoral
Paragorgia arborea
. Hourly changes in polyp activity were quantified using a time-lapse camera deployed for a year on Sur Ridge (1230 m depth; Northeast Pacific). The relationship between feeding and environmental variables, including surface primary production, temperature, acoustic backscatter, current speed and direction, was evaluated. Feeding activity was highly seasonal, with a dormancy period identified between January and early April, reflecting seasonal changes in food availability as suggested by primary production and acoustic backscatter data. Moreover, feeding varied with tides, which likely affected food delivery through cyclic oscillation in current speed and direction. This study provides the first evidence of behavioural rhythms in a coral species at depth greater than 1 km. Information on the feeding biology of this cosmopolitan deep-sea octocoral will contribute to a better understanding of how future environmental change may affect deep-sea coral communities and the ecosystem services they provide.
Pseudomonas fitomaticsae sp. nov., isolated at Marimurtra Botanical Garden in Blanes, Catalonia, Spain
Authors: Atanasov Kostadin Evgeniev , Galbis David Miñana , Cornadó Deborah , Serpico Annabel , Sánchez Guiomar , Bosch Montserrat , Ferrer Albert , Altabella Teresa
Published: October 2022

In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81T. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase- and oxidase-positive. The optimal growth temperature of strain FIT81T is 28 °C, although it can grow within a temperature range of 4–32 °C. The pH growth tolerance ranges between pH 5 and 10, and it tolerates 4% (w/v) NaCl. A 16S rRNA phylogenetic analysis positioned strain FIT81T within the genus

Pseudomonas

, and multilocus sequence analysis revealed that

Pseudomonas gozinkensis

IzPS32dT,

Pseudomonas glycinae

MS586T,

Pseudomonas allokribbensis

IzPS23T, 'Pseudomonas kribbensis' 46–2 and

Pseudomonas koreensis

PS9-14T are the top five most closely related species, which were selected for further genome-to-genome comparisons, as well as for physiological and chemotaxonomic characterization. The genome size of strain FIT81T is 6 492 796 base-pairs long, with 60.6 mol% of G+C content. Average nucleotide identity and digital DNA–DNA hybridization analyses yielded values of 93.6 and 56.1%, respectively, when the FIT81T genome was compared to that of the closest type strain

P. gozinkensis

IzPS32dT. Taken together, the obtained genomic, physiologic and chemotaxonomic data indicate that strain FIT81T is different from its closest relative species, which lead us to suggest that it is a novel species to be included in the list of type strains with the name Pseudomonas fitomaticsae sp. nov. (FIT81T=CECT 30374T=DSM 112699T).
Niabella agricola sp. nov., isolated from paddy soil
Authors: Lin Shih-Yao , Tsai Chia-Fang , Hameed Asif , Lee Tzung-Han , Young Chiu-Chung
Published: October 2022

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative, orange-coloured bacterium (designated strain CC-SYL272T) isolated from paddy soil. Cells were observed to be strictly aerobic, non-motile and non-spore-forming rods, exhibiting positive catalase and oxidase. Strain CC-SYL272T was found to grow optimally at 20–40 °C, pH 6.0–8.0 and NaCl 0–2 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CC-SYL272T belongs to the genus

Niabella

, family

Chitinophagaceae

, and is most closely related to

Niabella pedocola

(97.8 %) followed by

Niabella drilacis

(97.2 %) and established a distinct taxonomic lineage associated with these species. The highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-SYL272T
versus Niabella species (69.1–83.5 %, n=8). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-SYL272T against

N. pedocola

was 27.3 %. The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The major polyamines were putrescine and sym-homospermidine. The dominating cellular fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and C16 : 1
 ω6c/C16 : 1
 ω7c. The draft genome (6.25 Mb) of strain CC-SYL272T spanned three contigs having 47.1 mol% DNA G+C content, 5087 protein-encoding genes, 10 rRNA genes and 44 tRNA genes. The genome harboured genes involved in the depolymerization of both animal and plant polysaccharides. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH and the phylogenomic placement, strain CC-SYL272T is considered to represent a novel species of the genus

Niabella

, affiliated to the family

Chitinophagaceae

, for which the name Niabella agricola sp. nov. is proposed. The type strain is CC-SYL272T (=BCRC 81319T=JCM 34758T).
Evaluation of eleven commercially available PCR kits for the detection of Monkeypox virus DNA
Authors: Michel Janine , Targosz Angelina , Rinner Thomas , Bourquain Daniel , Brinkmann Annika , Sacks Jilian A. , Schaade Lars , Nitsche Andreas
Published: October 2022

Prior to the international spread of Monkeypox in May 2022, PCR kits for the detection of Orthopoxviruses, and specifically for monkeypox virus, were rarely available. Here we describe the evaluation of eleven recently-developed commercially available PCR kits for the detection of Monkeypox virus DNA.
Chronic activation of dopaminergic neurons via bioluminescence-optogenetics provides neuroprotection in a rodent model of Parkinson’s disease
Authors: Shiu Fu Hung , Skelton Henry , Berglund Ken , Fernandez Alejandra M. , Gutekunst Claire-Anne N. , Robinson Elizabeth R. , Wang Zuhui , Gross Robert E.
Published: October 2022

Previous studies in human patients and rodent models of Parkinson’s disease (PD) have established neuroprotection of dopaminergic (DA) neurons in substantia nigra pars compacta (SNC) by physical exercise, but the precise origin of this neuroprotective effect has yet to be elucidated. In this study, we tested a hypothesis that enhanced activity of DA neurons in SNC results in neuroprotection using the unilateral 6-hydroxydopamine (6-OHDA) injection model in mice. To increase activity of DA neurons chronically and specifically, we injected an adeno-associated viral vector carrying a step-function luminopsin (SFL) – a fusion protein of light-emittingGaussialuciferase and light-sensing step-function channelrhodopsin 2 – into SNC ipsilateral to 6-OHDA using the pan-neuronal human synapsin I promoter or the Cre-lox system in transgenic mice expressing the recombinase under control of the tyrosine hydroxylase (TH) promoter. Upon application of SFL substrate, coelenterazine (CTZ), the luciferase moiety of luminopsin emits bioluminescence which in turn activate the opsin moiety. Daily injection of CTZ for 4 weeks ameliorated a stereotypical behavior, namely ipsiversive rotations, induced by unilateral 6-OHDA. In addition, postmortem immunohistochemistry against TH revealed less severe neurodegeneration of DA neurons compared to vehicle-injected control animals. Furthermore, when mice were pretreated with ANA-12, a selective antagonist for tropomyosin receptor kinase B (TrkB), the behavioral improvement and neuroprotective effect were diminished. These results suggest that increased neuronal activity of DA neurons provides neuroprotection against 6-OHDA injury and alleviates its symptoms through the brain-derived neurotrophic factor-TrkB pathway.
Infection of primary nasal epithelial cells differentiates among lethal and seasonal human coronaviruses
Authors: Otter Clayton J. , Fausto Alejandra , Tan Li Hui , Cohen Noam A. , Weiss Susan R.
Published: October 2022

The nasal epithelium is the initial entry portal and primary barrier to infection by all human coronaviruses (HCoVs). We utilize primary nasal epithelial cells grown at air-liquid interface, which recapitulate the heterogeneous cellular population as well as mucociliary clearance functions of thein vivonasal epithelium, to compare lethal (SARS-CoV-2 and MERS-CoV) and seasonal (HCoV-NL63 and HCoV-229E) HCoVs. All four HCoVs replicate productively in nasal cultures but diverge significantly in terms of cytotoxicity induced following infection, as the seasonal HCoVs as well as SARS-CoV-2 cause cellular cytotoxicity as well as epithelial barrier disruption, while MERS-CoV does not. Treatment of nasal cultures with type 2 cytokine IL-13 to mimic asthmatic airways differentially impacts HCoV replication, enhancing MERS-CoV replication but reducing that of SARS-CoV-2 and HCoV-NL63. This study highlights diversity among HCoVs during infection of the nasal epithelium, which is likely to influence downstream infection outcomes such as disease severity and transmissibility.