bluuebunny/crossref_metadata_2025 huggingface dataset:
BondGraphs.jl: composable energy-based modelling in systems biology
Authors: Forrest Joshua , Rajagopal Vijay , Stumpf Michael P H , Pan Michael
Published: September 2023

BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely used in engineering and has recently been shown to be a powerful approach for modelling biology. Models are mutable, hierarchical, multiscale, and multiphysics, and BondGraphs.jl is compatible with the Julia modelling ecosystem.

Availability and implementation

BondGraphs.jl is freely available under the MIT license. Source code and documentation can be found at https://github.com/jedforrest/BondGraphs.jl.
BQsupports: systematic assessment of the support and novelty of new biomedical associations
Authors: Fernández-Torras Adrià , Locatelli Martina , Bertoni Martino , Aloy Patrick
Published: September 2023

Motivation

Living a Big Data era in Biomedicine, there is an unmet need to systematically assess experimental observations in the context of available information. This assessment would offer a means for a comprehensive and robust validation of biomedical data results and provide an initial estimate of the potential novelty of the findings.

Results

Here we present BQsupports, a web-based tool built upon the Bioteque biomedical descriptors that systematically analyzes and quantifies the current support to a given set of observations. The tool relies on over 1000 distinct types of biomedical descriptors, covering over 11 different biological and chemical entities, including genes, cell lines, diseases, and small molecules. By exploring hundreds of descriptors, BQsupports provide support scores for each observation across a wide variety of biomedical contexts. These scores are then aggregated to summarize the biomedical support of the assessed dataset as a whole. Finally, the BQsupports also suggests predictive features of the given dataset, which can be exploited in downstream machine learning applications.

Availability and implementation

The web application and underlying data are available online (https://bqsupports.irbbarcelona.org).
In vitro callus induction and evaluation of antioxidant activity of Rhinacanthus nasutus (L.) Kurz
Authors: Yaowachai Wipa , Luecha Prathan , Taratima Worasitikulya
Published: September 2023

Rhinacanthus nasutus (L.) Kurz is used in Thai traditional medicine for the treatment of skin diseases, ringworm, and eczema. This research studied the effects of cytokinin and auxins on callus induction and evaluated antioxidant activity of R. nasutus. Nodes, young, and mature leaf explants were cultured on MS medium containing 0, 1, 2, 3, and 4 mg/l kinetin (6-furfurylaminopurine) and 0, 1 mg/l 1-naphthaleneacetic acid (NAA), indole-3-acetic acid (IAA), and 2,4-dichlorophenoxyacetic acid (2,4-D) for 6 weeks to induce callus. Calli derived from nodes, young and mature leaves, and other plant parts were ultrasonically extracted with methanol to determine total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity by ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picrylhtdrazyl (DPPH), and 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) assays. Nodal explants on MS medium containing 1 mg/l kinetin combined with 1 mg/l 2,4-D were most efficient in callus production with the average fresh and dry weight per explant of 2.29 ± 0.14 and 0.18 ± 0.01 g, respectively. Addition of kinetin combined with NAA or 2,4-D had a positive effect on callus induction from young and mature leaf explants. The leaf extract showed the highest TPC, TFC, FRAP, and IC50 of DPPH and ABTS assays (ca 113 mg GAE/g extract, 45 mg QE/g extract, 121 mg TE/g extract, 53 µg/ml and 14 µg/ml, respectively), followed by callus derived from nodes. Overall, phenolic content was higher than flavonoid content. A strong positive correlation was found between FRAP assay, TPC (r = 0.973), and TFC (r = 0.798), indicating that phenolic and flavonoid compounds are responsible for antioxidant activity of R. nasutus.
Myelin oligodendrocyte glycoprotein antibody and N-methyl-d-aspartate receptor antibody overlapping syndrome: insights from the recent case reports
Authors: Du Bing-Qing , Lai Qi-Lun , Li Er-Chuang , Cai Meng-Ting , Fang Gao-Li , Shen Chun-Hong , Zhang Yin-Xi , Ding Mei-Ping
Published: September 2023

The overlapping of two or more types of neural autoantibodies in one patient has increasingly been documented in recent years. The coexistence of myelin oligodendrocyte glycoprotein (MOG) and N-methyl-d-aspartate receptor (NMDAR) antibodies is most common, which leads to a unique condition known as the MOG antibody and NMDAR antibody overlapping syndrome (MNOS). Here, we have reviewed the pathogenesis, clinical manifestations, paraclinical features, and treatment of MNOS. Forty-nine patients with MNOS were included in this study. They were young males with a median onset age of 23 years. No tumors were observed in the patients, and 24 of them reported prodromal symptoms. The most common clinical presentations were psychiatric symptoms (35/49) and seizures (25/49). Abnormalities on magnetic resonance imaging involved the brainstem (11/49), cerebellum (9/49), and parietal lobe (9/49). Most patients mostly responded to immunotherapy and had a good long-term prognosis. However, the overall recurrence rate of MNOS was higher than that of mono antibody-positive diseases. The existence of concurrent NMDAR antibodies should be suspected in patients with MOG antibody-associated disease having psychiatric symptoms, seizures, movement disorders, or autonomic dysfunction. Similarly, serum MOG antibody testing should be performed when patients with anti-NMDAR encephalitis present with atypical clinical manifestations, such as visual impairment and limb weakness, and neuroradiological findings, such as optic nerve, spinal cord, or infratentorial involvement or meningeal enhancement. Early detection of the syndrome and prompt treatment can be beneficial for these patients, and maintenance immunosuppressive therapy is recommended due to the high overall recurrence rate of the syndrome.
Heterogeneity in RAG1 and RAG2 deficiency: 35 cases from a single-centre
Authors: Karaatmaca Betul , Cagdas Deniz , Esenboga Saliha , Erman Baran , Tan Cagman , Turul Ozgur Tuba , Boztug Kaan , van der Burg Mirjam , Sanal Ozden , Tezcan Ilhan
Published: September 2023

Recombination activating genes (RAG)1 and RAG2 deficiency leads to combined T/B-cell deficiency with varying clinical presentations. This study aimed to define the clinical/laboratory spectrum of RAG1 and RAG2 deficiency. We retrospectively reviewed the clinical/laboratory data of 35 patients, grouped them as severe combined immunodeficiency (SCID), Omenn syndrome (OS), and delayed-onset combined immunodeficiency (CID) and reported nine novel mutations. The male/female ratio was 23/12. Median age of clinical manifestations was 1 months (mo) (0.5–2), 2 mo (1.25–5), and 14 mo (3.63–27), age at diagnosis was 4 mo (3–6), 4.5 mo (2.5–9.75), and 27 mo (14.5–70) in SCID (n = 25; 71.4%), OS (n = 5; 14.3%), and CID (n = 5; 14.3%) patients, respectively. Common clinical manifestations were recurrent sinopulmonary infections 82.9%, oral moniliasis 62.9%, diarrhea 51.4%, and eczema/dermatitis 42.9%. Autoimmune features were present in 31.4% of the patients; 80% were in CID patients. Lymphopenia was present in 92% of SCID, 80% of OS, and 80% of CID patients. All SCID and CID patients had low T (CD3, CD4, and CD8), low B, and increased NK cell numbers. Twenty-eight patients underwent hematopoietic stem cell transplantation (HSCT), whereas seven patients died before HSCT. Median age at HSCT was 7 mo (4–13.5). Survival differed in groups; maximum in SCID patients who had an HLA-matched family donor, minimum in OS. Totally 19 (54.3%) patients survived. Early molecular genetic studies will give both individualized therapy options, and a survival advantage because of timely diagnosis and treatment. Further improvement in therapeutic outcomes will be possible if clinicians gain time for HSCT.
The Impact of Preventive Treatment for Multidrug- and Rifampin-Resistant Tuberculosis Exceeds Trial-Based Estimates
Authors: Kasaie Parastu , Pennington Jeff , Gupta Amita , Dowdy David W , Kendall Emily A
Published: September 2023

Background

Several clinical trials of tuberculosis preventive treatment (TPT) for household contacts of patients with multidrug- or rifampin-resistant tuberculosis (MDR/RR-TB) are nearing completion. The potential benefits of delivering TPT to MDR/RR-TB contacts extend beyond the outcomes that clinical trials can measure.

Methods

We developed an agent-based, household-structured TB and MDR/RR-TB transmission model, calibrated to an illustrative setting in India. We simulated contact investigation in households of patients with MDR/RR-TB, comparing an MDR/RR-TPT regimen (assuming 6-month duration, 70% efficacy) and associated active case finding against alternatives of contact investigation without TPT or no household intervention. We simulated the TB and MDR/RR-TB incidence averted relative to placebo over 2 years, as measurable by a typical trial, as well as the incidence averted over a longer time horizon, in the broader population, and relative to no contact investigation.

Results

Observing TPT and placebo recipients for 2 years as in a typical trial, MDR/RR-TPT was measured to prevent 72% (interquartile range, 45%–100%) of incident MDR/RR-TB among recipients; the median number needed to treat (NNT) to prevent 1 MDR/RR-TB case was 73, compared to placebo. This NNT decreased to 54 with 13–18 years of observation, to 27 when downstream transmission effects were also considered, and to 12 when the effects of active TB screening were included by comparing to a no-household-contact-intervention scenario.

Conclusions

If forthcoming trial results demonstrate efficacy, the long-term population impact of TPT for MDR/RR-TB—including the large effect of increased active TB detection among MDR/RR-TB contacts—could be much greater than suggested by trial outcomes alone.
Management Practices and Quality of Care: Evidence from the Private Health Care Sector in Tanzania
Authors: Powell-Jackson Timothy , King Jessica J C , Makungu Christina , Quaife Matthew , Goodman Catherine
Published: September 2023

We measure the adoption of management practices in over 220 private for-profit and non-profit health facilities in 64 districts across Tanzania and link these data to process quality-of-care metrics, assessed using undercover standardised patients and clinical observations. We find that better managed health facilities are more likely to provide correct treatment in accordance with national treatment guidelines, adhere to a checklist of essential questions and examinations, and comply with infection prevention and control practices. Moving from the 10th to the 90th percentile in the management practice score is associated with a 48% increase in correct treatment. We then leverage a large-scale field experiment of an internationally recognised management support intervention in which health facilities are assessed against comprehensive standards, given an individually tailored quality improvement plan and supported through training and mentoring visits. We find zero to small effects on management scores, suggesting that improving management practices in this setting may be challenging.
The Welfare Effects of Greenbelt Policy: Evidence from England
Authors: Koster Hans R A
Published: September 2023

I measure the economic effects of greenbelts that prohibit new construction beyond a predefined urban fringe and therefore act as urban growth boundaries. I focus on England, where 13% of the land is designated as greenbelt land. I provide reduced-form evidence and estimate a quantitative equilibrium model that includes amenities, housing supply, a traffic congestion externality, agglomeration forces, productivity and household location choices. Greenbelt policy generates positive amenity effects, but also strongly reduces housing supply. I find that greenbelts increase welfare because amenity effects are sufficiently strong. At the same time, however, greenbelts decrease housing affordability by limiting housing supply.
Acquired risk factors and incident atrial fibrillation according to age and genetic predisposition
Authors: Wang Ningjian , Yu Yuefeng , Sun Ying , Zhang Haojie , Wang Yuying , Chen Chi , Tan Xiao , Wang Bin , Lu Yingli
Published: September 2023

Background and Aims

Atrial fibrillation (AF) is the most common sustained arrhythmia in adults. Investigations of risk factor profiles for AF according to age and genetic risk groups are essential to promote individualized strategies for the prevention and control of AF.

Methods

A total of 409 661 participants (mean age, 56 years; 46% men) free of AF at baseline and with complete information about risk factors were included from the UK Biobank cohort. The hazard ratios and population-attributable risk (PAR) percentages of incident AF associated with 23 risk factors were examined, including 3 social factors, 7 health behaviours, 6 cardiometabolic factors, 6 clinical comorbidities, and the genetic risk score (GRS), across 3 age groups (40–49, 50–59, and 60–69 years) and 3 genetic risk groups (low, moderate, and high GRS).

Results

After a follow-up of 5 027 587 person-years, 23 847 participants developed AF. Most cardiometabolic factors and clinical comorbidities showed a significant interaction with age, whereby the associations were generally strengthened in younger groups (Pinteraction < .002). However, only low LDL cholesterol, renal dysfunction, and cardiovascular disease showed a significant interaction with genetic risk, and the associations with these factors were stronger in lower genetic risk groups (Pinteraction < .002). Cardiometabolic factors consistently accounted for the largest number of incident AF cases across all age groups (PAR: 36.2%–38.9%) and genetic risk groups (34.0%–41.9%), with hypertension and overweight/obesity being the two leading modifiable factors. Health behaviours (PAR: 11.5% vs. 8.7%) and genetic risk factors (19.1% vs. 14.3%) contributed to more AF cases in the 40–49 years group than in the 60–69 years group, while the contribution of clinical comorbidities remained relatively stable across different age groups. The AF risk attributable to overall cardiometabolic factors (PAR: 41.9% in the low genetic risk group and 34.0% in the high genetic risk group) and clinical comorbidities (24.7% and 15.9%) decreased with increasing genetic risk. The impact of social factors on AF was relatively low across the groups by age and genetic risk.

Conclusions

This study provided comprehensive information about age- and genetic predisposition-related risk factor profiles for AF in a cohort of UK adults. Prioritizing risk factors according to age and genetic risk stratifications may help to achieve precise and efficient prevention of AF.
Clinical course of hypertrophic cardiomyopathy patients implanted with a transvenous or subcutaneous defibrillator
Authors: Francia Pietro , Ziacchi Matteo , Adduci Carmen , Ammendola Ernesto , Pieragnoli Paolo , De Filippo Paolo , Rapacciuolo Antonio , Rella Valeria , Migliore Federico , Viani Stefano , Musumeci Maria Beatrice , Biagini Elena , Lovecchio Mariolina , Baldini Rossella , Falasconi Giulio , Autore Camillo , Biffi Mauro , Cecchi Franco
Published: September 2023

Aims

The implantable cardioverter-defibrillator (ICD) is a life-saving therapy in patients with hypertrophic cardiomyopathy (HCM) at risk of sudden cardiac death. Implantable cardioverter-defibrillator complications are of concern. The subcutaneous ICD (S-ICD) does not use transvenous leads and is expected to reduce complications. However, it does not provide bradycardia and anti-tachycardia pacing (ATP). The aim of this study was to compare appropriate and inappropriate ICD interventions, complications, disease-related adverse events and mortality between HCM patients implanted with a S- or transvenous (TV)-ICD.

Methods and results

Consecutive HCM patients implanted with a S- (n = 216) or TV-ICD (n = 211) were enrolled. Propensity-adjusted cumulative Kaplan–Meier curves and multivariate Cox proportional hazard ratios were used to compare 5-year event-free survival and the risk of events. The S-ICD patients had lower 5-year risk of appropriate (HR: 0.32; 95%CI: 0.15–0.65; P = 0.002) and inappropriate (HR: 0.44; 95%CI: 0.20–0.95; P = 0.038) ICD interventions, driven by a high incidence of ATP therapy in the TV-ICD group. The S- and TV-ICD patients experienced similar 5-year rate of device-related complications, albeit the risk of major lead-related complications was lower in S-ICD patients (HR: 0.17; 95%CI: 0.038–0.79; P = 0.023). The TV- and S-ICD patients displayed similar risk of disease-related complications (HR: 0.64; 95%CI: 0.27–1.52; P = 0.309) and mortality (HR: 0.74; 95%CI: 0.29–1.87; P = 0.521).

Conclusion

Hypertrophic cardiomyopathy patients implanted with a S-ICD had lower 5-year risk of appropriate and inappropriate ICD therapies as well as of major lead-related complications as compared to those implanted with a TV-ICD. Long-term comparative follow-up studies will clarify whether the lower incidence of major lead-related complications will translate into a morbidity or survival benefit.
Digest: Ecological and life-history drivers of avian skull evolution
Authors: Tanda Madeleine , Deal Ethan
Published: September 2023

What are the factors that drive the patterns and evolutionary rates of morphological characteristics? To answer this question, Hunt et al. explore shape variation and rates of change in modern avian skulls using morphometric measurements and phylogenetic analyses. They find that habitat density and migration have the strongest influences on avian skull variation and that denser habitats, longer migratory distances, and precocial developmental modes are all associated with faster rates of morphological evolution.
Novel ribotype/sequence type associations and diverse CRISPR-Cas systems in environmental Clostridioides difficile strains from northern Iraq
Authors: Rashid Srwa J , Nale Janet Y , Millard Andrew D , Clokie Martha R J
Published: September 2023

The environment is a natural reservoir of Clostridioides difficile, and here, we aimed to isolate the pathogen from seven locations in northern Iraq. Four of the sites yielded thirty-one isolates (ten from soils, twenty-one from sediments), which together represent ribotypes (RTs) 001 (five), 010 (five), 011 (two), 035 (two), 091 (eight), and 604 (nine). Twenty-five of the isolates (∼81%) are non-toxigenic, while six (∼19%) encode the toxin A and B genes. The genomes of eleven selected isolates represent six sequence types (STs): ST-3 (two), ST-15 (one), ST-107 (five), ST-137 (one), ST-177 (one), and ST-181 (one). Five novel RT/ST associations: RT011/ST-137, RT035/ST-107, RT091/ST-107, RT604/ST-177, and RT604/ST-181 were identified, and the first three are linked to RTs previously uncharacterized by multilocus sequence typing (MLST). Nine of the genomes belong to Clade 1, and two are closely related to the cryptic C-I clade. Diverse multiple prophages and CRISPR-Cas systems (class 1 subtype I-B1 and class 2 type V CRISPR-Cas systems) with spacers identical to other C. difficile phages and plasmids were detected in the genomes. Our data show the broader diversity that exists within environmental C. difficile strains from a much less studied location and their potential role in the evolution and emergence of new strains.
Association Between the Appendicular Extracellular-to-Intracellular Water Ratio and All-Cause Mortality: A 10-Year Longitudinal Study
Authors: Iwasaka Chiharu , Yamada Yosuke , Nishida Yuichiro , Hara Megumi , Yasukata Jun , Miyoshi Nobuyuki , Shimanoe Chisato , Nanri Hinako , Furukawa Takuma , Koga Kayoko , Horita Mikako , Higaki Yasuki , Tanaka Keitaro
Published: September 2023

The appendicular extracellular-to-intracellular water ratio (A-E/I) is a potential marker of skeletal muscle quality, reflecting the balance of water distribution between the extracellular and intracellular compartments of the appendicular limb regions. A-E/I has been increasingly used in recent studies; however, its association with adverse outcomes remains unclear. This study investigated the potential association between A-E/I and all-cause mortality. A prospective cohort study of 8 015 middle-aged and older adults (comprised of 4 755 women, aged 45–74 years) residing in a Japanese community was conducted. The baseline assessment was performed between 2010 and 2012, and the follow-up period lasted until July 2022. A-E/I and skeletal muscle mass were measured using segmental bioelectrical impedance spectroscopy. Handgrip strength (HGS) was measured using a Smedley-type dynamometer. Lifestyle, medical history, and physical activity were assessed by questionnaire and accelerometer. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) for each quartile (Q) of A-E/I were estimated using the multivariable Cox regression model. During a 10.5-year median follow-up, the mortality rates were 8.9 and 3.6 per 1 000 person-years for men (292 deaths) and women (174 deaths), respectively. A-E/I quartiles were positively associated with all-cause mortality in both sexes (men: Q1, HR: 1.0 [95% CI: reference], Q4, HR: 1.8 [1.1–2.9], ptrend < .05; women, Q4, HR: 2.2 [1.3–3.8], ptrend < .01). This association remained significant after further adjustment for skeletal muscle mass and HGS (ptrend < .05). Our findings suggest that A-E/I serves as an early predictive marker for mortality in middle-aged and older Japanese adults.
Residential Segregation, Perceived Neighborhood Environment, and All-Cause Mortality Among Community-Dwelling Older Chinese Americans
Authors: Jiang Yanping , Zhu Yuyang , Tang Fengyan , Chung Tammy , Wu Bei
Published: September 2023

Objectives

Residential segregation profoundly affects mental and physical health. However, impacts of residential segregation and other neighborhood characteristics on health among older Asian Americans are not fully understood. This study aimed to close this gap by examining effects of residential segregation, perceived neighborhood cohesion, and neighborhood disorder on all-cause mortality among older Chinese immigrants, as well as testing whether the association between residential segregation and mortality would be mediated by perceived neighborhood cohesion and neighborhood disorder.

Methods

Data were drawn from a subsample of 3,094 older Chinese Americans aged 60 and older (mean age = 72.8 years) from the Population Study of Chinese Elderly in Chicago. Residential segregation was derived using 2010–2014 American Community Survey data. Participants completed surveys on perceived neighborhood cohesion and neighborhood disorder between 2011 and 2013. All-cause mortality was tracked until December 2021.

Results

Residential segregation was associated with elevated all-cause mortality risk; this association, however, was no longer statistically significant after controlling for sociodemographic, behavioral, and health covariates. Perceived neighborhood cohesion, but not neighborhood disorder, was significantly associated with decreased mortality risks. There were no indirect effects of residential segregation on all-cause mortality through perceived neighborhood cohesion or neighborhood disorder. These effects were consistent across male and female participants.

Discussion

These results suggest the importance of neighborhood social environment, specifically perceptions of neighborhood cohesion, in influencing mortality risk among older Chinese immigrants. The findings also indicate the need to conduct further research to examine the health impact of residential segregation among this population.
The Relationship Between Cognitive Decline and All-Cause Mortality Is Modified by Living Alone and a Small Social Network: A Paradox of Isolation
Authors: Murayama Hiroshi , Sugiyama Mika , Inagaki Hiroki , Ura Chiaki , Miyamae Fumiko , Edahiro Ayako , Motokawa Keiko , Okamura Tsuyoshi , Awata Shuichi
Published: September 2023

Objectives

Although cognitive decline is a well-known mortality risk, it has not been adequately investigated, whether social relationships modify the relationship between cognitive decline and mortality. We examined the modifying effects of social relationships (household composition, social network [frequency of social contact with individuals outside the household], and social participation) on the association between cognitive decline and all-cause mortality in older Japanese people.

Methods

In 2015, a baseline questionnaire was distributed to all 132,005 independent community-dwelling individuals aged ≥65 years resident in Adachi Ward of the Tokyo Metropolitan area. The final sample analyzed comprised 74,872 participants (men: 44.9%; mean age: 73.7 ± 6.0 years). Cognitive decline was assessed using a self-administered dementia checklist that was validated using the Clinical Dementia Rating Scale.

Results

A Cox proportional hazard model with an average follow-up of 1,657 days revealed that cognitive decline was associated with higher mortality (hazard ratio [HR]: 1.37, 95% confidence interval [95% CI]: 1.25–1.50). We identified significant associations among household composition, social networks, and cognitive decline. Stratified analyses indicated that the cognitive decline–mortality association was stronger among participants with low contact frequency (HR = 1.60, 95% CI: 1.39–1.85) than high frequency (HR = 1.24, 95% CI: 1.11–1.39). Conversely, the association was weaker among individuals living alone (HR = 1.13, 95% CI: 0.90–1.40) than among cohabiting individuals (HR = 1.43, 95% CI: 1.29–1.57).

Conclusions

Although living alone and having a small social network represent an isolated status, their modifying effects were the opposite. These findings indicate that the isolation type should be considered when implementing support strategies for older adults with cognitive decline or dementia.
Corporate Governance
Authors: Mallin Christine A.
Published: September 2023

Corporate Governance is made up of four main parts. The first part looks at developments in corporate governance. The second part is concerned with owners and stakeholders. This includes an examination of family-owned firms, institutional investments, and socially responsible investment. The third part examines directors and the board structure. The fourth part is about international corporate governance; it reviews corporate governance in continental Europe, central and eastern Europe, the Asia-Pacific, South Africa, Egypt, India, and Brazil.
Poor oral health influences head and neck cancer patient survival: an International Head and Neck Cancer Epidemiology Consortium pooled analysis
Authors: Tasoulas Jason , Farquhar Douglas R , Sheth Siddharth , Hackman Trevor , Yarbrough Wendell G , Agala Chris B , Koric Alzina , Giraldi Luca , Fabianova Eleonora , Lissowska Jolanta , Świątkowska Beata , Vilensky Marta , Wünsch-Filho Victor , de Carvalho Marcos Brasilino , López Rossana Verónica Mendoza , Holcátová Ivana , Serraino Diego , Polesel Jerry , Canova Cristina , Richiardi Lorenzo , Zevallos Jose P , Ness Andy , Pring Miranda , Thomas Steve J , Dudding Tom , Lee Yuan-Chin Amy , Hashibe Mia , Boffetta Paolo , Olshan Andrew F , Divaris Kimon , Amelio Antonio L
Published: September 2023

Background

Poor oral health has been identified as a prognostic factor potentially affecting the survival of patients with head and neck squamous cell carcinoma. However, evidence to date supporting this association has emanated from studies based on single cohorts with small-to-modest sample sizes.

Methods

Pooled analysis of 2449 head and neck squamous cell carcinoma participants from 4 studies of the International Head and Neck Cancer Epidemiology Consortium included data on periodontal disease, tooth brushing frequency, mouthwash use, numbers of natural teeth, and dental visits over the 10 years prior to diagnosis. Multivariable generalized linear regression models were used and adjusted for age, sex, race, geographic region, tumor site, tumor-node-metastasis stage, treatment modality, education, and smoking to estimate risk ratios (RR) of associations between measures of oral health and overall survival.

Results

Remaining natural teeth (10-19 teeth: RR = 0.81, 95% confidence interval [CI] = 0.69 to 0.95; ≥20 teeth: RR = 0.88, 95% CI = 0.78 to 0.99) and frequent dental visits (>5 visits: RR = 0.77, 95% CI = 0.66 to 0.91) were associated with better overall survival. The inverse association with natural teeth was most pronounced among patients with hypopharyngeal and/or laryngeal, and not otherwise specified head and neck squamous cell carcinoma. The association with dental visits was most pronounced among patients with oropharyngeal head and neck squamous cell carcinoma. Patient-reported gingival bleeding, tooth brushing, and report of ever use of mouthwash were not associated with overall survival.

Conclusions

Good oral health as defined by maintenance of the natural dentition and frequent dental visits appears to be associated with improved overall survival among head and neck squamous cell carcinoma patients.
New atomic data for C i Rydberg states compared with solar UV spectra
Authors: Storey P J , Dufresne R P , Del Zanna G
Published: September 2023

We use the Breit–Pauli R-matrix method to calculate accurate energies and radiative data for states in C i up to n = 30 and with l ≤ 3. We provide the full data set of decays to the five 2s2 2p2 ground configuration states 3P0,1,2, 1D2, and 1S0. This is the first complete set of data for transitions from n ≥ 5. We compare oscillator strengths and transition probabilities with the few previously calculated values for such transitions, finding generally good agreement (within 10 per cent) with the exception of values recently recommended by National Institute of Standards and Technology, where significant discrepancies are found. We then calculate spectral line intensities originating from the Rydberg states using typical chromospheric conditions and assuming local thermal equilibrium, and compare them with well-calibrated Solar and Heliospheric Observatory Solar Ultraviolet Measurements of Emitted Radiation ultraviolet (UV) spectra of the quiet Sun. The relative intensities of the Rydberg series are in excellent agreement with observation, which provides firm evidence for the identifications and blends of nearly 200 UV lines. Such comparison also resulted in a large number of new identifications of C i lines in the spectra. We also estimate optical depth effects and find that these can account for much of the absorption noted in the observations. The atomic data can be applied to model a wide range of solar and astrophysical observations.
Spectral analysis of the LMXB XTE J1810−189 with NICER data
Authors: Manca A , Sanna A , Marino A , Di Salvo T , Mazzola S M , Riggio A , Deiosso N , Cabras C , Burderi L
Published: September 2023

X-ray Timing Explorer J1810−189 is a low-mass X-ray binary transient system hosting a neutron star, which underwent a three-month-long outburst in 2020. In order to study its spectral evolution during this outburst, we analysed all the available observations performed by Neutron star Interior Composition Explorer, in the 1–10 keV energy band. First, we fitted the spectra with a thermal Comptonization model. Our analysis revealed the lack of a significant direct emission from a blackbody-like component, therefore we calculated the optical depth of the Comptonizing region, deriving an upper limit of 4.5, which suggests the presence of a moderately thick corona. We also attempted to fit the spectrum with an alternative model, i.e. a cold Comptonized emission from a disc and a direct thermal component from the neutron star, finding a similarly good fit. The source did not enter a full high luminosity/soft state throughout the outburst, with a photon index ranging from ∼1.7 to ∼2.2, and an average unabsorbed flux in the 1–10 keV band of ∼3.6 × 10−10 erg cm−2 s−1. We searched for the presence of Fe K-shell emission lines in the range ∼6.4–7 keV, significantly detecting a broad component only in a couple of observations. Finally, we conducted a time-resolved spectral analysis of the detected type-I X-ray burst, observed during the outburst, finding no evidence of a photospheric radius expansion. The type-I burst duration suggests a mix of H/He fuel.
The dynamical evolution of protoplanetary discs and planets in dense star clusters
Authors: Flammini Dotti Francesco , Capuzzo-Dolcetta R , Kouwenhoven M B N
Published: September 2023

Most stars are born in dense stellar environments, where the formation and early evolution of planetary systems may be significantly perturbed by encounters with neighbouring stars. To investigate the fate of circumstellar gas discs and planets around young stars dense stellar environments, we numerically evolve star–disc–planet systems. We use the N-body codes NBODY6++ GPU and SnIPES for the dynamical evolution of the stellar population, and the SPH-based code GaSPH for the dynamical evolution of protoplanetary discs. The secular evolution of a planetary system in a cluster differs from that of a field star. Most stellar encounters are tidal, adiabatic, and nearly-parabolic. The parameters that characterize the impact of an encounter include the orientation of the protoplanetary disc and planet relative to the orbit of the encountering star, and the orbital phase, and the semimajor axis of the planet. We investigate this dependence for close encounters (rp/a ≤ 100, where rp is the periastron distance of the encountering star and a is the semimajor axis of the planet). We also investigate distant perturbers (rp/a ≫ 100), which have a moderate effect on the dynamical evolution of the planet and the protoplanetary disc. We find that the evolution of protoplanetary discs in star clusters differs significantly from that of isolated systems. When interpreting the outcome of the planet formation process, it is thus important to consider their birth environments.
Photosynthesis under a red Sun: predicting the absorption characteristics of an extraterrestrial light-harvesting antenna
Authors: Duffy Christopher D P , Canchon Gregoire , Haworth Thomas J , Gillen Edward , Chitnavis Samir , Mullineaux Conrad W
Published: September 2023

Here, we discuss the feasibility of photosynthesis on Earth-like rocky planets in close orbit around ultracool red dwarf stars. Stars of this type have very limited emission in the photosynthetically active region of the spectrum (400–700 nm), suggesting that they may not be able to support oxygenic photosynthesis. However, photoautotrophs on Earth frequently exploit very dim environments with the aid of highly structured and extremely efficient antenna systems. Moreover, the anoxygenic photosynthetic bacteria, which do not need to oxidize water to source electrons, can exploit far-red and near-infrared light. Here, we apply a simple model of a photosynthetic antenna to a range of model stellar spectra, ranging from ultracool (2300 K) to Sun-like (5800 K). We assume that a photosynthetic organism will evolve an antenna that maximizes the rate of energy input while also minimizing fluctuations. The latter is the noise cancelling principle recently reported by Arp et al. Applied to the solar spectrum, this predicts optimal antenna configurations in agreement with the chlorophyll Soret absorption bands. Applied to cooler stars, the optimal antenna peaks become redder with decreasing stellar temperature, crossing to the typical wavelength ranges associated with anoxygenic photoautotrophs at ∼3300 K. Lastly, we compare the relative input power delivered by antennae of equivalent size around different stars and find that the predicted variation is within the same order of magnitude. We conclude that low-mass stars do not automatically present light-limiting conditions for photosynthesis, but they may select for anoxygenic organisms.
The integrated galaxy-wide stellar initial mass function over the radial acceleration range of early-type galaxies
Authors: Dabringhausen J , Kroupa P
Published: September 2023

The observed radial accelerations of 462 early-type galaxies (ETGs) at their half-mass radii are discussed. They are compared to the baryonic masses of the same galaxies, which are derived from theoretical expectations for their stellar populations and cover a range from $\approx 10^4 \, {\rm M}_{\odot }$ to $\approx 10^{11} \, {\rm M}_{\odot }$. Both quantities are plotted against each other, and it is tested whether they lie (within errors) along theoretical radial acceleration relations (RARs). We choose the Newtonian RAR and two Milgromian, or MONDian RARs. At low radial accelerations (corresponding to low masses), the Newtonian RAR fails without non-baryonic dark matter, but the two MONDian ones may work, provided moderate out-of-equilibrium dynamics in some of the low-mass ETGs. However all three RARs fail at high accelerations (corresponding to high masses) if all ETGs have formed their stellar populations with the canonical stellar initial mass function (IMF). A much better agreement with the observations can however be accomplished, if the theory of the integrated galaxy-wide stellar initial mass functions (IGIMFs) is used instead. This is because the IGIMF-theory predicts the formation of an overabundance of stellar remnants during the lifetime of the massive ETGs. Thus their baryonic masses today are higher than they would be if the ETGs had formed with a canonical IMF. Also the masses of the stellar-mass black holes should be rather high, which would mean that most of them probably formed when the massive ETGs were not as metal-enriched as they are today. The IGIMF-approach confirms downsizing.
Probing infrared dark clouds with class I methanol masers and thermal molecular emission using the Onsala 20 meter telescope
Authors: Shakhvorostova N N , Alakoz A V , Bayandina O S , Olofsson A O H , Val’tts I E
Published: September 2023

Infrared dark clouds (IRDCs) represent the earliest stage of high-mass star formation and host molecular cores at different states of activity from quiet state without any IR-signature of star formation to active state with IR-signatures and pronounced maser activity. Many IRDCs show indications of shocked gas associated with protostar outflows and can contain class I methanol masers (cIMMs). The aim of this study is to probe different types of cores in IRDCs with cIMMs and thermal molecular emission and to investigate the relationship between presence of cIMMs and physical conditions in IRDCs. For a sample of 37 molecular cores, using the 20-m Onsala radio telescope, we collected molecular line data at 44, 85, and 97 GHz for more than 15 species including CH3OH, CH3CCH, and CS. Kinetic temperature of the gas and molecular column densities were obtained. Methanol emission at 44 GHz was detected in 29 sources, with 4 sources are being new discoveries. None of the cores in quiescent state show emission at 44 GHz. Our results testify that cIMM emission is a reliable marker of advanced state of molecular cores. The higher detection rate for intermediate and IR-quiet sources suggests that cIMMs most readily trace the early stages of star formation characterized by moderate IR-signatures. We found that masers with higher flux densities tend to be associated with emission in the CH3CCH lines with higher integrated intensities. Sources undetected at 44 GHz have 4 times lower integrated intensities of CH3CCH and exhibit poorer molecular spectra than the most sources with cIMMs.
The stellar mass of the Gaia-Sausage/Enceladus accretion remnant
Authors: Lane James M M , Bovy Jo , Mackereth J Ted
Published: September 2023

The Gaia-Sausage/Enceladus (GS/E) structure is an accretion remnant that comprises a large fraction of the Milky Way’s stellar halo. We study GS/E using high-purity samples of kinematically selected stars from APOGEE DR16 and Gaia. Employing a novel framework to account for kinematic selection biases using distribution functions, we fit density profiles to these GS/E samples and measure their masses. We find that GS/E has a shallow density profile in the inner Galaxy, with a break between 15 and 25 kpc beyond which the profile steepens. We also find that GS/E is triaxial, with axis ratios 1:0.55:0.45 (nearly prolate), and the major axis is oriented about 80° from the Sun–Galactic centre line and 16° above the plane. We measure a stellar mass for GS/E of $1.45\, ^{+0.92}_{-0.51}\, \mathrm{(stat.)}\, ^{+0.13}_{-0.37} \mathrm{(sys.)}\ \times 10^{8}$ M⊙. Our mass estimate is lower than others in the literature, a finding we attribute to the excellent purity of the samples we work with. We also fit a density profile to the entire Milky Way stellar halo, finding a mass in the range of 6.7–8.4 × 108 M⊙, and implying that GS/E could make up as little as 15–25 per cent of the mass of the Milky Way stellar halo. Our lower stellar mass combined with standard stellar mass-to-halo mass relations implies that GS/E constituted a minor 1:8 mass-ratio merger at the time of its accretion.
Gas absorption towards the η Tel debris disc: winds or clouds?
Authors: Iglesias Daniela P , Panić Olja , Rebollido Isabel
Published: September 2023

η Telescopii is an ∼23 Myr old A-type star surrounded by an edge-on debris disc hypothesized to harbour gas. Recent analysis of far- and near-ultraviolet spectroscopic observations of η Tel found absorption features at ∼−23 and ∼−18 km s−1 in several atomic lines, attributed to circumstellar and interstellar gas, respectively. In this work, we put the circumstellar origin of the gas to a test by analysing high-resolution optical spectroscopy of η Tel and of three other stars with a similar line of sight as η Tel: HD 181327, HD 180575, and ρ Tel. We found absorption features at ∼−23 and ∼−18 km s−1 in the Ca ii H&K lines, and at ∼−23 km s−1 in the Na i D1&D2 doublet in η Tel, in agreement with previous findings in the ultraviolet. However, we also found absorption features at ∼−23 km s−1 in the Ca ii K lines of the three other stars analysed. This strongly implies that the absorption lines previously attributed to circumstellar gas are more likely due to an interstellar cloud traversing the line of sight of η Tel instead.
Dense forests of microshots in bursts from FRB 20220912A
Authors: Hewitt Danté M , Hessels Jason W T , Ould-Boukattine Omar S , Chawla Pragya , Cognard Ismaël , Gopinath Akshatha , Guillemot Lucas , Huppenkothen Daniela , Nimmo Kenzie , Snelders Mark P
Published: September 2023

We report on exceptionally bright bursts (>400 Jy ms) detected from the repeating fast radio burst source FRB 20220912A using the Nançay radio telescope (NRT), as part of the ECLAT (Extragalactic Coherent Light from Astrophysical Transients) monitoring campaign. These bursts exhibit extremely luminous, broad-band, short-duration structures (∼16 μs), which we term ‘microshots’ and which can be especially well studied in the NRT data given the excellent signal-to-noise and dynamic range (32-bit samples). The estimated peak flux density of the brightest microshot is 450 Jy. We show that the microshots are clustered into dense ‘forests’ by modelling them as Weibull distributions and obtaining Weibull shape parameters of approximately 0.5. Our polarimetric analysis reveals that the bursts are nearly 100 per cent linearly polarized; have ≲10 per cent circular polarization fractions; a near-zero average rotation measure of 0.10(6) rad m−2; and varying polarization position angles over the burst duration. For one of the bursts, we analyse raw voltage data from simultaneous observations with the Westerbork RT-1 single 25-m dish. These data allow us to measure the scintillation bandwidth, 0.30(3) MHz, and to probe the bursts on (sub-)microsecond time-scales. Some important nuances related to dedispersion are also discussed. We propose that the emission mechanism for the broad-band microshots is potentially different from the emission mechanism of the broader burst components, which still show a residual drift of a few hundred MHz ms−1 after correcting for dispersion using the microshots. We discuss how the observed emission is phenomenologically analogous to different types of radio bursts from the Sun.
COVID-19 vaccine confidence, concerns, and uptake in children aged 5 and older in Calgary, Alberta: a longitudinal cohort study
Authors: Doucette Emily J , Ricketson Leah , Tarannum Tarannum , Alatorre Isabella , Gray Joslyn , Constantinescu Cora , Kuhn Susan , Dunn Jessica K E , Kellner James D
Published: September 2023

Objectives

Beginning early in the pandemic, there was a worldwide effort to develop effective vaccines against the SARS-CoV-2 virus. Before and after the approval and implementation of vaccines, there were concerns about their need as well as their safety and rapid development. We explored child demographic characteristics and parental concerns to identify factors associated with the decision to vaccinate.

Methods

A cohort of 1035 children from Calgary was assembled in 2020 to participate in 5 visits every 6 months for survey completion and blood sampling for SARS-CoV-2 antibodies. Visits 1 to 2 occurred before approval of vaccines for children; Visits 3 to 5 occurred after vaccine approval for different age groups. We described vaccine concerns and utilized logistic regression to examine factors associated with the decision to vaccinate in children ≥5 years of age.

Results

Children ≥12 years of age, of non-white or non-black ethnicity, and who had received previous influenza vaccines had higher odds of being vaccinated against SARS-CoV-2. Children with previous SARS-CoV-2 infection had lower odds of being vaccinated. The most common concerns in early 2021 were about vaccine safety. By summer 2022, the most common concern was a belief that vaccines were not necessary. Through the study 88% of children were vaccinated.

Conclusions

Age, ethnicity, previous infections, and vaccine attitudes were associated with parental decision to vaccinate against SARS-CoV-2. For children who remained unvaccinated, parents continued to have safety concerns and questioned the necessity of the vaccine. Complacency about the need for vaccination may be more challenging to address and overcome than concerns about safety alone.