bluuebunny/crossref_metadata_2025 huggingface dataset:
Proof-of-concept: SCENTinel 1.1 rapidly discriminates COVID-19-related olfactory disorders
Authors: Hunter Stephanie R , Hannum Mackenzie E , Pellegrino Robert , O’Leary Maureen A , Rawson Nancy E , Reed Danielle R , Dalton Pamela H , Parma Valentina
Published: February 2023

It is estimated that 20%–67% of those with COVID-19 develop olfactory disorders, depending on the SARS-CoV-2 variant. However, there is an absence of quick, population-wide olfactory tests to screen for olfactory disorders. The purpose of this study was to provide a proof-of-concept that SCENTinel 1.1, a rapid, inexpensive, population-wide olfactory test, can discriminate between anosmia (total smell loss), hyposmia (reduced sense of smell), parosmia (distorted odor perception), and phantosmia (odor sensation without a source). Participants were mailed a SCENTinel 1.1 test, which measures odor detection, intensity, identification, and pleasantness, using one of 4 possible odors. Those who completed the test (N = 287) were divided into groups based on their self-reported olfactory function: quantitative olfactory disorder only (anosmia or hyposmia, N = 135), qualitative olfactory disorder only (parosmia and/or phantosmia; N = 86), and normosmia (normal sense of smell; N = 66). SCENTinel 1.1 accurately discriminates quantitative olfactory disorders, qualitative olfactory disorders, and normosmia groups. When olfactory disorders were assessed individually, SCENTinel 1.1 discriminates between hyposmia, parosmia, and anosmia. Participants with parosmia rated common odors less pleasant than those without parosmia. We provide proof-of-concept that SCENTinel 1.1, a rapid smell test, can discriminate quantitative and qualitative olfactory disorders, and is the only direct test to rapidly discriminate parosmia.
Application of machine learning methods to guide patient management by predicting the risk of malignancy of Bethesda III-V thyroid nodules
Authors: D’Andréa Grégoire , Gal Jocelyn , Mandine Loïc , Dassonville Olivier , Vandersteen Clair , Guevara Nicolas , Castillo Laurent , Poissonnet Gilles , Culié Dorian , Elaldi Roxane , Sarini Jérôme , Decotte Anne , Renaud Claire , Vergez Sébastien , Schiappa Renaud , Chamorey Emmanuel , Château Yann , Bozec Alexandre
Published: February 2023

Objective

Indeterminate thyroid nodules (ITN) are common and often lead to (sometimes unnecessary) diagnostic surgery. We aimed to evaluate the performance of two machine learning methods (ML), based on routinely available features to predict the risk of malignancy (RM) of ITN.

Design

Multi-centric diagnostic retrospective cohort study conducted between 2010 and 2020.

Methods

Adult patients who underwent surgery for at least one Bethesda III-V thyroid nodule (TN) with fully available medical records were included. Of the 7917 records reviewed, eligibility criteria were met in 1288 patients with 1335 TN. Patients were divided into training (940 TN) and validation cohort (395 TN). The diagnostic performance of a multivariate logistic regression model (LR) and its nomogram, and a random forest model (RF) in predicting the nature and RM of a TN were evaluated. All available clinical, biological, ultrasound, and cytological data of the patients were collected and used to construct the two algorithms.

Results

There were 253 (19%), 693 (52%), and 389 (29%) TN classified as Bethesda III, IV, and V, respectively, with an overall RM of 35%. Both cohorts were well-balanced for baseline characteristics. Both models were validated on the validation cohort, with performances in terms of specificity, sensitivity, positive predictive value, negative predictive value, and area under the receiver operating characteristic curve of 90%, 57.3%, 73.4%, 81.4%, 84% (CI95%: 78.5%-89.5%) for the LR model, and 87.6%, 54.7%, 68.1%, 80%, 82.6% (CI95%: 77.4%-87.9%) for the RF model, respectively.

Conclusions

Our ML models performed well in predicting the nature of Bethesda III-V TN. In addition, our freely available online nomogram helped to refine the RM, identifying low-risk TN that may benefit from surveillance in up to a third of ITN, and thus may reduce the number of unnecessary surgeries.
Trafficked Adult Males as (Un)Gendered Protection Seekers: Between Presumption of Invulnerability and Exclusion from Membership of a Particular Social Group
Authors: Magugliani Noemi
Published: February 2023

The United Nations High Commissioner for Refugees’ Guidelines on International Protection No 7: The Application of Article 1A(2) of the 1951 Convention and/or 1967 Protocol relating to the Status of Refugees to Victims of Trafficking and Persons at Risk of Being Trafficked recognize that, although not all trafficked persons fall within the scope of the 1951 Convention relating to the Status of Refugees, some could satisfy all elements of the refugee definition. Such a possibility is not least implicit in the 2000 Protocol to Prevent, Suppress and Punish Trafficking in Persons, Especially Women and Children, as well as in the 2005 Council of Europe Convention on Action against Trafficking in Human Beings. In order to obtain asylum, trafficked persons and their legal representatives tend to rely on the trafficked person being recognized as a member of a particular social group (PSG), and on establishing a well-founded fear of persecution on such a ground. While women trafficked for sexual exploitation have been recognized as members of a PSG in several jurisdictions, although not always in a consistent manner, the recognition of trafficked men as members of a PSG has proven to be more challenging. It is argued that the difficulties faced by adult men are attributable to the gender stereotyping operationalized by asylum decision-making bodies, which have consistently failed to recognize the gender dimension of trafficking with respect to men and boys, focusing almost entirely on women and girls as gendered subjects. In addition, the difficulties are also attributable to the nature of the exploitation to which most trafficked men are subjected, as forced labour and forced criminality are considered ‘lesser’ harms than sexual exploitation, and because violations of socio-economic rights as a ground for asylum are not yet fully recognized. This contribution explores the theoretical underpinnings of these two elements and their impact on the assessment of asylum claims brought by trafficked adult men, using the United Kingdom as a case study.
Usefulness of EUCAST rapid antibiotic susceptibility breakpoints and screening cut-off values directly from blood cultures for the inference of β-lactam resistance mechanisms in Enterobacterales
Authors: Cerrudo V , Cortés-Cuevas J L , García-Fernández S , Morosini M I , Cantón R , Sánchez-Díaz A M
Published: February 2023

Background

Reducing the turnaround time for reporting antimicrobial susceptibility testing (AST) results is important for adjusting empirical treatments and may impact clinical outcomes of septic patients, particularly in settings with high antimicrobial resistance. Disc diffusion could be useful for inferring β-lactam resistance mechanisms.

Objectives

To evaluate the usefulness of EUCAST rapid AST (RAST) disc diffusion breakpoints for the screening of resistance mechanisms (sRAST) and interpretive reading of resistance phenotypes to infer ESBL and carbapenemases production in Enterobacterales.

Methods

Blood cultures were artificially spiked with Enterobacterales clinical isolates with well-characterized β-lactam resistance mechanisms (n = 93), WT phenotypes (n = 26) and ATCC strains (n = 8). AST was performed by disc diffusion directly from blood cultures and inhibition zones were manually measured at 4, 6 and 8 h. To infer the presence of resistance mechanisms, EUCAST RAST breakpoints and screening cut-off values (sRAST) combined with the double-disc synergy test (DDS) for ESBLs or aztreonam susceptibility for carbapenemases detection were used.

Results

DDS together with sRAST detected all ESBL producers as early as at 4 h incubation. Cefotaxime was the antibiotic with the highest discriminatory power. The suspicion of carbapenemase production by sRAST at 8 h was possible in 73% of Klebsiella pneumoniae and in 100% of Escherichia coli carbapenemase-producing isolates. Phenotypic analysis improves the detection of some low hydrolytic carbapenemases (OXA-48 or KPC-3 mutants).

Conclusions

Early detection of β-lactam resistance mechanisms directly from positive blood cultures was possible using sRAST together with the interpretive reading of antibiotic resistance phenotypes. Some carbapenemase types such as OXA-48 might be difficult to infer. Screening-positive isolates should be confirmed using an alternative technique.
Molecular diagnostics for genotypic detection of antibiotic resistance: current landscape and future directions
Authors: Banerjee Ritu , Patel Robin
Published: February 2023

Antimicrobial resistance (AMR) among bacteria is an escalating public health emergency that has worsened during the COVID-19 pandemic. When making antibiotic treatment decisions, clinicians rely heavily on determination of antibiotic susceptibility or resistance by the microbiology laboratory, but conventional methods often take several days to identify AMR. There are now several commercially available molecular methods that detect antibiotic resistance genes within hours rather than days. While these methods have limitations, they offer promise for optimizing treatment and patient outcomes, and reducing further emergence of AMR. This review provides an overview of commercially available genotypic assays that detect individual resistance genes and/or resistance-associated mutations in a variety of specimen types and discusses how clinical outcomes studies may be used to demonstrate clinical utility of such diagnostics.
A robust scenario analysis approach to water recycling quantitative microbial risk assessment
Authors: Jones Christopher H , Wylie Varsha , Ford Hannah , Fawell John , Holmer Melanie , Bell Katherine
Published: February 2023

Aims

The growing need to access recycled water as a source for drinking water supply necessitates management of perceived risks. This study aimed to use quantitative microbial risk analysis (QMRA) to evaluate microbiological risks of indirect water recycling.

Methods and Results

Scenario analyses of risk probabilities of pathogen infection were conducted to investigate four key quantitative microbial risk assessment model assumptions: treatment process failure, drinking water consumption events per day, inclusion or exclusion of an engineered storage buffer, and treatment process redundancy. Results demonstrated that the proposed water recycling scheme could meet WHO pathogen risk guidelines of ∼10−3 annual risk of infection under 18 simulated scenarios.
Using artificial intelligence in medical school admissions screening to decrease inter- and intra-observer variability
Authors: Keir Graham , Hu Willie , Filippi Christopher G , Ellenbogen Lisa , Woldenberg Rona
Published: February 2023

Objectives

Inter- and intra-observer variability is a concern for medical school admissions. Artificial intelligence (AI) may present an opportunity to apply a fair standard to all applicants systematically and yet maintain sensitivity to nuances that have been a part of traditional screening methods.

Material and Methods

Data from 5 years of medical school applications were retrospectively accrued and analyzed. The applicants (m = 22 258 applicants) were split 60%–20%–20% into a training set (m = 13 354), validation set (m = 4452), and test set (m = 4452). An AI model was trained and evaluated with the ground truth being whether a given applicant was invited for an interview. In addition, a “real-world” evaluation was conducted simultaneously within an admissions cycle to observe how it would perform if utilized.

Results

The algorithm had an accuracy of 95% on the training set, 88% on the validation set, and 88% on the test set. The area under the curve of the test set was 0.93. The SHapely Additive exPlanations (SHAP) values demonstrated that the model utilizes features in a concordant manner with current admissions rubrics. By using a combined human and AI evaluation process, the accuracy of the process was demonstrated to be 96% on the “real-world” evaluation with a negative predictive value of 0.97.

Discussion and Conclusion

These results demonstrate the feasibility of an AI approach applied to medical school admissions screening decision-making. Model explainability and supplemental analyses help ensure that the model makes decisions as intended.
The super-enhancer repertoire in porcine liver
Authors: Zhang Yi , Zhang Jinbi , Wang Caixia , Dai Hongjian , Du Xing , Li Qifa , Pan Zengxiang
Published: February 2023

The transcriptional initiation of genes is inextricably bound with the functions of cis-regulatory sequences. The pig is one of the most important livestock species and an ideal animal model for biomedical studies. At the same time, the liver is a critical organ with diverse and complex metabolic functions. Here, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with high-throughput sequencing to profile the chromatin landscape of histone H3 lysine 27 acetylation (H3K27ac), histone H3 lysine 4 monomethylation (H3K4me1), and CCAAT enhancer-binding protein β (C-EBPβ) in the 70-d-old porcine liver, compared the different profiles among the three markers and their associated stitched-enhancers by stitching and sorting the peaks within 12.5 kb (Pott and Lieb, 2015) and generated the porcine liver-specific super-enhancers (SEs) by the combination of three markers. Compared to typical enhancers (TEs) and other stitched-enhancers, liver-specific SEs showed a higher density of cis-motifs and SNPs, which may recruit more tissue-specific vital TFs. The expression profiles in fetal and 70-d-old pigs proved that a large proportion of SE-associated genes were up-regulated and were more related to hepatic metabolisms and detoxification pathways. Our results illustrated the difference and connection among promoter and enhancer markers, identified the features of liver SEs and their associated genes, and provided novel insight into cis-element identification, function, and liver transcriptional regulation.
Inner nuclear membrane proteins Lem2 and Bqt4 interact with different lipid synthesis enzymes in fission yeast
Authors: Hirano Yasuhiro , Kinugasa Yasuha , Kubota Yoshino , Obuse Chikashi , Haraguchi Tokuko , Hiraoka Yasushi
Published: February 2023

The nuclear envelope (NE) is a double-membrane structure consisting of inner and outer membranes that spatially separate the nucleus from the cytoplasm, and its function is critical for cellular functions such as genome maintenance. In the fission yeast, Schizosaccharomyces pombe, the inner nuclear membrane proteins, Lem2 and Bqt4, play pivotal roles in maintaining the NE structure. We previously found that the double deletion of lem2+ and bqt4+ causes a synthetic lethal defect associated with severe NE rupture, and overexpression of Elo2, a solo very-long-chain fatty acid elongase, suppresses this defect by restoring the NE. However, the molecular basis of this restoration remains elusive. To address this, we identified Lem2- and Bqt4-binding proteins via immunoprecipitation and mass spectrometry in this study. Forty-five and 23 proteins were identified as Lem2- and Bqt4-binding proteins, respectively. Although these binding proteins partially overlapped, Lem2 and Bqt4 interacted with different types of lipid metabolic enzymes: Cho2, Ole1 and Erg11 for Lem2 and Cwh43 for Bqt4. These enzymes are known to be involved in various lipid synthesis processes, suggesting that Lem2 and Bqt4 may contribute to the regulation of lipid synthesis by binding to these enzymes.
Three Layers of Uncertainty
Authors: Aydogan Ilke , Berger Loïc , Bosetti Valentina , Liu Ning
Published: February 2023

We explore decision-making under uncertainty using a framework that decomposes uncertainty into three distinct layers: (1) risk, which entails inherent randomness within a given probability model; (2) model ambiguity, which entails uncertainty about the probability model to be used; and (3) model misspecification, which entails uncertainty about the presence of the correct probability model among the set of models considered. Using a new experimental design, we isolate and measure attitudes toward each layer separately. We conduct our experiment on three different subject pools and document the existence of a behavioral distinction between the three layers. In addition to providing new insights into the underlying processes behind ambiguity aversion, we provide the first empirical evidence of the role of model misspecification in decision-making under uncertainty.
The Role of Age at Migration in Socio-Cultural Integration: Testing Mediating Mechanisms among Recent Refugees
Authors: Klok Jolien , van der Linden Meta
Published: February 2023

Although age (at migration) is an important factor to influence the socio-cultural integration process of refugees, we know fairly little about exactly how ageing does so. We consider intergroup contact and identification as member of the host city as socio-cultural integration and take the case of recent refugees in the Netherlands to propose and test two mechanisms; language comprehension and health. Using data from 764 recent refugees from the Bridge survey we employ structural equation modelling to test these mechanisms simultaneously for the two measures of socio-cultural integration. Language comprehension mediates the relationship between age and intergroup contact, while health mediates between age and identification. We conclude that a more careful consideration of age in integration literature is necessary, as up till now it has too often been used as a proxy for an array of (social) phenomena. The findings add to better understanding older refugees’ challenges in socio-cultural integration.
Satisfaction with current hormone therapy and goals of additional gender-affirming care in transgender adults
Authors: Siira Meron , Getahun Darios , Silverberg Michael J , Tangpricha Vin , Goodman Michael , Yeung Howa
Published: February 2023

Background

Many transgender persons seek hormone therapy to reduce gender dysphoria and improve quality of life, but little is known about patient satisfaction with current gender-affirming hormone therapy.

Aim

To examine patient satisfaction with current gender-affirming hormone therapy and patients’ goals of additional hormone therapy.

Methods

Transgender adults in the validated multicenter STRONG cohort (Study of Transition, Outcomes, and Gender) were asked to complete a cross-sectional survey about current and planned hormone therapy and the effects that they experienced or hoped to gain. The proportion of respondents reporting overall satisfaction with hormone therapy were compared with χ2 or Fisher exact test. Cochran-Mantel-Haenszel analysis was used to compare the covariates of interest while controlling for age at the time of survey completion.

Outcomes

Patient satisfaction across hormone therapies, each measured with a 5-point scale, was averaged and dichotomized.

Results

Out of 2136 eligible transgender adults, 696 (33%) completed the survey: 350 transfeminine (TF) and 346 transmasculine (TM) respondents. Most participants (80%) were satisfied or very satisfied with their current hormone therapies. TF participants and older participants were less likely to report being satisfied with their current hormone therapies than TM participants and younger participants, respectively. However, TM and TF categories were not associated with patient satisfaction after controlling for age at the time of survey completion. More TF persons planned to take additional treatment. The most frequent goals for additional hormone therapy for TF persons included breast size growth, feminine body fat distribution, and facial feature softening; for TM persons, goals included diminishing dysphoria, greater muscle mass, and masculine body fat distribution.

Clinical Implications

Multidisciplinary care beyond provision of hormone therapy—such as involvement of surgical, dermatologic, reproductive health, mental health, and/or gender expression care—may be important to help achieve unmet gender-affirming care goals.

Strengths and Limitations

This study had a modest response rate and included only respondents with private insurance, limiting generalizability.

Conclusion

Understanding patient satisfaction and goals of care will assist shared decision making and counseling in patient-centered gender-affirming therapy.
Elevated [CO2] negatively impacts C4 photosynthesis under heat and water stress without penalizing biomass
Authors: Al-Salman Yazen , Ghannoum Oula , Cano Francisco Javier
Published: February 2023

Elevated [CO2] (eCO2) and water stress reduce leaf stomatal conductance (gs), which may affect leaf thermoregulation during heat waves (heat stress). Two sorghum lines, with different leaf width were grown in a glasshouse at a mean day temperature of 30 °C, under different [CO2] and watering levels, and subjected to heat stress (43 °C) for 6 d at the start of the reproductive stage. We measured leaf photosynthetic and stomatal responses to light transients before harvesting the plants. Photosynthesis at growth conditions (Agrowth) and biomass accumulation were enhanced by eCO2 under control conditions. Heat stress increased gs, especially in wider leaves, and reduced the time constant of stomatal opening (kopen) at ambient [CO2] but not eCO2. However, heat stress reduced photosynthesis under water stress and eCO2 due to increased leaf temperature and reduced evaporative cooling. eCO2 prevented the reduction of biomass under both water and heat stress, possibly due to improved plant and soil water status as a result of reduced gs. Our results suggest that the response of the C4 crop sorghum to future climate conditions depends on the trade-off between low gs needed for high water use efficiency and drought tolerance, and the high gs needed for improved thermoregulation and heat tolerance under an eCO2 future.
Evaluation of loop-mediated isothermal amplification assay for visual detection ofAcinetobacter baumanniidirectly from soil and water sample from Mangalore
Authors: Nayak Srajana , Do Carmo Lobo Nia , Anupama Karanth Padyana , Nayak Ashwath , Akshay Sadanand Dangari , Maiti Biswajit
Published: February 2023

Acinetobacter baumannii is a well-known nosocomial pathogen that commonly inhabits soil and water and has been implicated in numerous hospital-acquired infections. The existing methods for detecting A. baumannii have several drawbacks, such as being time-consuming, expensive, labor-intensive, and unable to distinguish between closely related Acinetobacter species. Thus, it is important to have a simple, rapid, sensitive, and specific method for its detection. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay using hydroxynaphthol blue dye to visualize A. baumannii by targeting its pgaD gene. The LAMP assay was performed using a simple dry bath and was shown to be specific and highly sensitive, as it could detect up to 10 pg/μl of A. baumannii DNA. Further, the optimized assay was used to detect A. baumannii in soil and water samples by culture-medium enrichment. Out of 27 samples tested, 14 (51.85%) samples were positive for A. baumannii through LAMP assay, while only 5 (18.51%) samples were found to be positive through conventional methods. Thus, the LAMP assay has been found to be a simple, rapid, sensitive, and specific method that can be used as a point-of-care diagnostic tool for detecting A. baumannii.
Normal functions and maximal order types
Authors: Freund Anton , Manca Davide
Published: February 2023

Transformations of well partial orders induce functions on the ordinals, via the notion of maximal order type. In most examples from the literature, these functions are not normal, in marked contrast with the central role that normal functions play in ordinal analysis and related work from computability theory. The present paper aims to explain this phenomenon. In order to do so, we investigate a rich class of order transformations that are known as $\textsf {WPO}$-dilators. According to a first main result of this paper, $\textsf {WPO}$-dilators induce normal functions when they satisfy a rather restrictive condition, which we call strong normality. Moreover, the reverse implication holds as well, for reasonably well-behaved $\textsf {WPO}$-dilators. Strong normality also allows us to explain another phenomenon: by previous work of Freund, Rathjen and Weiermann, a uniform Kruskal theorem for $\textsf {WPO}$-dilators is as strong as $\varPi ^1_1$-comprehension, while the corresponding result for normal dilators on linear orders is equivalent to the much weaker principle of $\varPi ^1_1$-induction. As our second main result, we show that $\varPi ^1_1$-induction is equivalent to the uniform Kruskal theorem for $\textsf {WPO}$-dilators that are strongly normal.
ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions – XV. Steady accretion from global collapse to core feeding in massive hub-filament system SDC335
Authors: Xu Feng-Wei , Wang Ke , Liu Tie , Goldsmith Paul F , Zhang Qizhou , Juvela Mika , Liu Hong-Li , Qin Sheng-Li , Li Guang-Xing , Tej Anandmayee , Garay Guido , Bronfman Leonardo , Li Shanghuo , Wu Yue-Fang , Gómez Gilberto C , Vázquez-Semadeni Enrique , Tatematsu Ken’ichi , Ren Zhiyuan , Zhang Yong , Toth L Viktor , Liu Xunchuan , Yue Nannan , Zhang Siju , Baug Tapas , Issac Namitha , Stutz Amelia M , Liu Meizhu , Fuller Gary A , Tang Mengyao , Zhang Chao , Dewangan Lokesh , Lee Chang Won , Zhou Jianwen , Xie Jinjin , Jiao Wenyu , Wang Chao , Liu Rong , Luo Qiuyi , Soam Archana , Eswaraiah Chakali
Published: February 2023

We present ALMA Band-3/7 observations towards ‘the Heart’ of a massive hub-filament system (HFS) SDC335, to investigate its fragmentation and accretion. At a resolution of ∼0.03 pc, 3 mm continuum emission resolves two massive dense cores MM1 and MM2, with $383(^{\scriptscriptstyle +234}_{\scriptscriptstyle -120})$ M⊙ (10–24 % mass of ‘the Heart’) and $74(^{\scriptscriptstyle +47}_{\scriptscriptstyle -24})$ M⊙, respectively. With a resolution down to 0.01 pc, 0.87 mm continuum emission shows MM1 further fragments into six condensations and multi-transition lines of H2CS provide temperature estimation. The relation between separation and mass of condensations at a scale of 0.01 pc favors turbulent Jeans fragmentation where the turbulence seems to be scale-free rather than scale-dependent. We use the H13CO+ J = 1 − 0 emission line to resolve the complex gas motion inside ‘the Heart’ in position-position-velocity space. We identify four major gas streams connected to large-scale filaments, inheriting the anti-clockwise spiral pattern. Along these streams, gas feeds the central massive core MM1. Assuming an inclination angle of 45(± 15)° and a H13CO+ abundance of 5(± 3) × 10−11, the total mass infall rate is estimated to be 2.40(± 0.78) × 10−3 M⊙ yr−1, numerically consistent with the accretion rates derived from the clump-scale spherical infall model and the core-scale outflows. The consistency suggests a continuous, near steady-state, and efficient accretion from global collapse, therefore ensuring core feeding. Our comprehensive study of SDC335 showcases the detailed gas kinematics in a prototypical massive infalling clump, and calls for further systematic and statistical studies in a large sample.
ATOMS: ALMA three-millimetre observations of massive star-forming regions – XIV. Properties of resolved ultra-compact H iiregions
Authors: Zhang C , Zhu Feng-Yao , Liu Tie , Ren Z-Y , Liu H-L , Wang Ke , Wu J-W , Zhang Y , Zhou J-W , Tatematsu K , Garay Guido , Tej Anandmayee , Li Shanghuo , Xu W F , Lee Chang Won , Bronfman Leonardo , Soam Archana , Li D
Published: February 2023

Hydrogen radio recombination lines (RRLs) are one of the major diagnostics of the physical properties of H ii regions. We use RRL H40α, He40α, and 3 mm continuum emission to investigate the properties of a large sample of resolved UC H ii regions identified in the ATOMS survey. In total, we identify 94 UC H ii regions from H40α emission. The basic parameters for these UC H ii regions, such as electron density, emission measure, electron temperature, ionic abundance ratio (n$_{\rm He^+}$/n$_{\rm H^+}$), and line width are derived. The median electron density and the median n$_{\rm He^+}$/n$_{\rm H^+}$ ratio of these UC H ii regions derived from RRLs are ∼9000 cm−3 and 0.11, respectively. Within UC H ii regions, the n$_{\rm He^+}$/n$_{\rm H^+}$ ratios derived from the intensity ratio of the He40α and H40α lines seems to be higher in the boundary region than in the centre. The H40α line width is mainly broadened by thermal motion and microturbulence. The electron temperature of these UC H ii regions has a median value of ∼6700 K, and its dependence on galactocentric distance is weak.
Search for the Epoch of Reionization with HERA: upper limits on the closure phase delay power spectrum
Authors: Keller Pascal M , Nikolic Bojan , Thyagarajan Nithyanandan , Carilli Chris L , Bernardi Gianni , Charles Ntsikelelo , Bester Landman , Smirnov Oleg M , Kern Nicholas S , Dillon Joshua S , Hazelton Bryna J , Morales Miguel F , Jacobs Daniel C , Parsons Aaron R , Abdurashidova Zara , Adams Tyrone , Aguirre James E , Alexander Paul , Ali Zaki S , Baartman Rushelle , Balfour Yanga , Beardsley Adam P , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Bull Philip , Burba Jacob , Carey Steven , Cheng Carina , DeBoer David R , Acedo Eloy de Lera , Dexter Matt , Eksteen Nico , Ely John , Ewall-Wice Aaron , Fagnoni Nicolas , Fritz Randall , Furlanetto Steven R , Gale-Sides Kingsley , Glendenning Brian , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Halday Ziyaad , Hewitt Jacqueline N , Hickish Jack , Julius Austin , Kariseb MacCalvin , Kerrigan Joshua , Kittiwisit Piyanat , Kohn Saul A , Kolopanis Matthew , Lanman Adam , Plante Paul La , Liu Adrian , Loots Anita , Ma Yin-Zhe , MacMahon David Harold Edward , Malan Lourence , Malgas Cresshim , Malgas Keith , Marero Bradley , Martinot Zachary E , Mesinger Andrei , Molewa Mathakane , Mosiane Tshegofalang , Murray Steven G , Neben Abraham R , Nuwegeld Hans , Pascua Robert , Patra Nipanjana , Pieterse Samantha , Pober Jonathan C , Razavi-Ghods Nima , Robnett James , Rosie Kathryn , Santos Mario G , Sims Peter , Smith Craig , Swarts Hilton , Van Wyngaarden Pieter , Williams Peter K G , Zheng Haoxuan
Published: February 2023

Radio interferometers aiming to measure the power spectrum of the redshifted 21 cm line during the Epoch of Reionization (EoR) need to achieve an unprecedented dynamic range to separate the weak signal from overwhelming foreground emissions. Calibration inaccuracies can compromise the sensitivity of these measurements to the effect that a detection of the EoR is precluded. An alternative to standard analysis techniques makes use of the closure phase, which allows one to bypass antenna-based direction-independent calibration. Similarly to standard approaches, we use a delay spectrum technique to search for the EoR signal. Using 94 nights of data observed with Phase I of the Hydrogen Epoch of Reionization Array (HERA), we place approximate constraints on the 21 cm power spectrum at z = 7.7. We find at 95 per cent confidence that the 21 cm EoR brightness temperature is ≤(372)2 ‘pseudo’ mK2 at 1.14 ‘pseudo’ h Mpc−1, where the ‘pseudo’ emphasizes that these limits are to be interpreted as approximations to the actual distance scales and brightness temperatures. Using a fiducial EoR model, we demonstrate the feasibility of detecting the EoR with the full array. Compared to standard methods, the closure phase processing is relatively simple, thereby providing an important independent check on results derived using visibility intensities, or related.
Planetary nurseries: vortices formed at smooth viscosity transition
Authors: Regály Zs , Kadam K , Tarczay-Nehéz D
Published: February 2023

Excitation of Rossby wave instability and development of a large-scale vortex at the outer dead zone edge of protoplanetary discs is one of the leading theories that explains horseshoe-like brightness distribution in transition discs. Formation of such vortices requires a relatively sharp viscosity transition. Detailed modelling, however, indicates that viscosity transitions at the outer edge of the dead zone is relatively smooth. In this study, we present 2D global, non-isothermal, gas–dust coupled hydrodynamic simulations to investigate the possibility of vortex excitation at smooth viscosity transitions. Our models are based on a recently postulated scenario, wherein the recombination of charged particles on the surface of dust grains results in reduced ionization fraction and, in turn, the turbulence due to magnetorotational instability. Thus, the α-parameter for the disc viscosity depends on the local dust-to-gas mass ratio. We found that the smooth viscosity transitions at the outer edge of the dead zone can become Rossby unstable and form vortices. A single large-scale vortex develops if the dust content of the disc is well coupled to the gas; however, multiple small-scale vortices ensue for the case of less coupled dust. As both type of vortices are trapped at the dead zone outer edge, they provide sufficient time for dust growth. The solid content collected by the vortices can exceed several hundred Earth masses, while the dust-to-gas density ratio within often exceeds unity. Thus, such vortices function as planetary nurseries within the disc, providing ideal sites for formation of planetesimals and eventually planetary systems.
Three-dimensional core-collapse supernovae with complex magnetic structures – II. Rotational instabilities and multimessenger signatures
Authors: Bugli M , Guilet J , Foglizzo T , Obergaulinger M
Published: February 2023

The gravitational collapse of rapidly rotating massive stars can lead to the onset of the low T/|W| instability within the central proto-neutron star (PNS), which leaves strong signatures in both the gravitational wave (GW) and neutrino emission. Strong large-scale magnetic fields are usually invoked to explain outstanding stellar explosions of rapidly rotating progenitors, but their impact on the growth of such instability has not yet been cleared. We analyse a series of three-dimensional magnetohydrodynamic models to characterize the effects of different magnetic configurations on the development of the low T/|W| and the related multimessenger features. In the absence of magnetic fields, we observe the growth on dynamical time-scales of the low T/|W|, associated with a strong burst of GW and a correlated modulation of the neutrino emission. However, models with a strong magnetic field show a quenching of the low T/|W|, due to a flattening of the rotation profile in the first ∼100 ms after shock formation caused by the magnetic transport of angular momentum. The associated GW emission is weakened by an order of magnitude, exhibits a broader spectral shape, and has no dominant feature associated with the PNS large-scale oscillation modes. Neutrino luminosities are damped along the equatorial plane due to a more oblate PNS, and the only clear modulation in the signal is due to Standing Accretion Shock Instability activity. Finally, magnetized models produce lower luminosities for νe than for $\bar{\nu }_e$, which is connected to a higher concentration of neutron-rich material in the PNS surroundings.
Exploring the role of composition and mass loading on the properties of hadronic jets
Authors: Kantzas D , Markoff S , Lucchini M , Ceccobello C , Chatterjee K
Published: February 2023

Astrophysical jets are relativistic outflows that remain collimated for remarkably many orders of magnitude. Despite decades of research, the origin of cosmic rays (CRs) remains unclear, but jets launched by both supermassive black holes in the centre of galaxies and stellar-mass black holes harboured in X-ray binaries (BHXBs) are among the candidate sources for CR acceleration. When CRs accelerate in astrophysical jets, they initiate particle cascades that form γ-rays and neutrinos. In the so-called hadronic scenario, the population of accelerated CRs requires a significant amount of energy to properly explain the spectral constraints, similarly to a purely leptonic scenario. The amount of energy required often exceeds the Eddington limit or even the total energy available within the jets. The exact energy source for the accelerated protons is unclear, but due to energy conservation along the jets, it is believed to come from the jet itself via transfer of energy from the magnetic fields or kinetic energy from the outflow. To address this hadronic energy issue and to self-consistently evolve the energy flux along the flows, we explore a novel treatment for including hadronic content, in which instabilities along the jet/wind border play a critical role. We discuss the impact of the different jet compositions on the jet dynamics for a pair dominated and an electron-proton jet and, consequently, the emitted spectrum, accounting for both leptonic and hadronic processes. Finally, we discuss the implications of this mass-loading scenario to address the proton energy issue.
Simulating a full-sky high resolution Galactic synchrotron spectral index map using neural networks
Authors: Irfan Melis O
Published: February 2023

We present a model for the full-sky diffuse Galactic synchrotron spectral index with an appropriate level of spatial structure for a resolution of 56 arcmin (to match the resolution of the Haslam 408 MHz data). Observational data at 408 MHz and 23 GHz have been used to provide spectral indices at a resolution of 5 degrees. In this work, we make use of convolutional neural networks to provide a realistic proxy for the higher resolution information, in place of the genuine structure. Our deep learning algorithm has been trained using 14.4 arcmin observational data from the 1.4 GHz Parkes radio continuum survey. We compare synchrotron emission maps constructed by extrapolating the Haslam data using various spectral index maps, of different angular resolution, with the Global Sky Model. We add these foreground maps to a total emission model for a 21-cm intensity mapping experiment, then attempt to remove the foregrounds. The different models all display different spectral or spatial behaviour and so each provide a useful and different tool to the community for testing component separation techniques. We find that for an experiment operating using a cosine aperture taper beam with a primary full width at half maximum between 1.1 and 1.6 degrees, and the principal component analysis technique of foreground removal, there is a discernible difference between synchrotron spectral index models with a resolution larger than 5 degrees but that no greater resolution than 5 degrees is required.
Dwarf AGNs from variability for the origins of seeds (DAVOS): optical variability of broad-line dwarf AGNs from the zwicky transient facility
Authors: Wang Z Franklin , Burke Colin J , Liu Xin , Shen Yue
Published: February 2023

We study the optical variability of a sample of candidate low-mass (dwarf and Seyfert) active galactic nuclei (AGNs) using Zwicky Transient Facility g-band light curves. Our sample is compiled from broad-line AGNs in dwarf galaxies reported in the literature with single-epoch virial black hole (BH) masses in the range MBH ∼ 104–108 M⊙. We measure the characteristic ‘damping’ time-scale of the optical variability τDRW, beyond which the power spectral density flattens, of a final sample of 79 candidate low-mass AGNs with high-quality light curves. Our results provide further confirmation of the MBH–τDRW relation from previous work within 1σ agreement, adding 78 new low-mass AGNs to the relation. The agreement suggests that the virial BH mass estimates for these AGNs are generally reasonable. We expect that the optical light curve of an accreting intermediate-mass black hole (IMBH) to vary with a rest-frame damping time-scale of ∼tens of hours, which could enable detection and direct mass estimation of accreting IMBHs in wide-field time-domain imaging surveys with sufficient cadence like with the Vera C. Rubin Observatory.
Toxic inhalation of sodium metabisulphite by-products from a shipping container
Authors: Sack C , Reeb-Whitaker C K , Todorov D , Darby P S
Published: February 2023

Logistics workers who handle cargo containers are at risk of toxic inhalation injuries, although prevalence and severities of these injuries are not well characterized. We report on a previously healthy 37-year-old supervisor who was acutely exposed to sodium metabisulphite and its thermal degradation by-products during a routine inspection of a shipping container. The employee developed chemical pneumonitis with acute non-cardiogenic pulmonary oedema and subsequent severe reactive airway dysfunction syndrome.
Clinical Features, Treatment, and Outcome of Psittacosis Pneumonia: A Multicenter Study
Authors: Ni Yueyan , Zhong Huanhuan , Gu Yu , Liu Li , Zhang Qiang , Wang Li , Wan Bing , Chen Shi , Cao Min , Xu Jin , Chen Cheng , Chen Yanbin , Sun Siqing , Ji Lei , Sun Wenkui , Wang Cheng , Yang Jian , Lu Xin , Shi Bin , Feng Chunlai , Su Xin
Published: February 2023

Background

We aimed to describe psittacosis pneumonia and risk factors for developing severe pneumonia in this multicenter clinical study.

Methods

We collected the data of psittacosis pneumonia cases diagnosed with metagenomic next-generation sequencing (mNGS) assay from April 2018 to April 2022 in 15 tertiary hospitals in China.

Results

A total of 122 patients were enrolled; 50.0% had a definite history of bird exposure. In 81.2% of cases, onset happened in autumn or winter. The common symptoms were fever (99.2%), cough (63.1%), fatigue (52.5%), shortness of breath (50.0%), chills (37.7%), central nervous system symptoms (36.9%), myalgia (29.5%), and gastrointestinal tract symptoms (15.6%). Laboratory tests showed that >70% of cases had elevated C-reactive protein, procalcitonin, erythrocyte sedimentation rate, D-dimer, lactate dehydrogenase, and aspartate aminotransferase, and >50% had hyponatremia and hypoproteinemia. The most common imaging finding was consolidation (71.3%), and 42.6% of cases met the criteria for severe pneumonia. Age >65 years and male sex were the risk factors for severe pneumonia. The effective proportion of patients treated with tetracyclines was higher than that of fluoroquinolones (66/69 [95.7%] vs 18/58 [31.0%]; P < .001), and the median defervescence time was shorter. After medication adjustment when the diagnosis was clarified, 119 of 122 (97.5%) patients were finally cured and the other 3 (2.5%) died.

Conclusions

Psittacosis pneumonia has a high rate of severe disease. Proven diagnosis could be rapidly confirmed by mNGS. Tetracycline therapy had a rapid effect and a high cure rate.
Machines in the Hands of Capitalists: Power and Profit in Late Eighteenth-Century Cornish Copper Mines
Authors: O’Sullivan Mary
Published: February 2023

In the inaugural issue of Past and Present, Eric Hobsbawm cautioned historians against the assumption that a capitalist economy has an inherent tendency to cost-saving and technological innovation, emphasizing that ‘It has a bias only towards profit’. Inspired by Hobsbawm, this article shows how a history of profit can elucidate the economic and social history of machines. Beginning with miners’ protests at the stoppage of Boulton & Watt steam engines in Cornish copper mines in the late 1780s, it shows that these engines’ implications for the people who invested in, and worked, the mines were conditioned by a complex relationship between profit and power: mechanical power, which was crucial to the mining of copper and the costs of its production; imperial power, given fluctuating demand for copper from different parts of the British empire; and market power, since control over price setting on the British copper market was crucial for Cornish mining profits. Understanding what determined mines’ profits helps to account for capitalists’ decisions to stop their engines as well as copper miners’ protests at their actions. More generally, it suggests the potential of studying the economic and social history of new machines through the lens of profit.
Persulfidation of transcription factor MYB10 inhibits anthocyanin synthesis in red-skinned pear
Authors: Yao Gaifang , Gou Shasha , Zhong Tingying , Wei Shuwei , An Xin , Sun Hongye , Sun Chen , Hu Kangdi , Zhang Hua
Published: February 2023

Hydrogen sulfide (H2S) is a gaseous signaling molecule that delays color change during fruit ripening. Whether H2S affects anthocyanin biosynthesis in red-skinned pears (Pyrus L.) remains unclear. Here, we found that H2S substantially inhibits anthocyanin accumulation in red-skinned pears and the expression of several genes encoding transcription factors is affected in response to H2S signaling. For example, PyMYB10 and PyMYB73 were down-regulated, whereas PyMYB114 and PyMYB6 were up-regulated. Bioinformatics analysis showed that PyMYB73 and PyMYB6, each containing an EAR motif, may negatively regulate anthocyanin accumulation. Transient expression analysis showed that PyMYB73 substantially promotes anthocyanin biosynthesis by co-transforming with PyMYB10/PyMYB114 + PybHLH3; however, PyMYB6 inhibited anthocyanin biosynthesis in strawberry (Fragaria vesca) receptacles and pear fruits, and PyMYB73 interacted with PyMYB10 and PyMYB6 but not PyMYB114 or PybHLH3. Further investigation showed that Cys194 and Cys218 of PyMYB10 were modified by persulfidation and that PyMYB10Cys218Ala substantially increased anthocyanin accumulation by a transient transformation system. Co-transformation of PyMYB10Cys218Ala + PyMYB73/PyMYB6 also promoted anthocyanin accumulation in pear fruits. Yeast two-hybrid assays showed that the mutation of PyMYB10 did not affect the interaction between PyMYB10 and PyMYB73, but it inhibited interaction with PyMYB6. Moreover, H2S weakened the interaction between PyMYB10 and PyMYB73 but enhanced the interaction with PyMYB6. Thus, we provided a model in which PyMYB10 undergoes persulfidation at Cys218, enhancing the interaction with PyMYB6 and reducing the interaction with PyMYB73. These subsequently results in lower expression of the anthocyanin biosynthesis-related genes Pyrus dihydroflavonol 4-reductase (PyDFR), Pyrus anthocyanidin synthase (PyANS), Pyrus UDP-glucose: flavonoid 3-glucosyl transferase (PyUFGT) and Pyrus glutathione S-transferase (PyGST), thereby inhibiting anthocyanin accumulation in red-skinned pears. Our findings provided a molecular mechanism for H2S-mediated anthocyanin biosynthesis in red-skinned pears.