bluuebunny/crossref_metadata_2025 huggingface dataset:
Limitations introduced by a low participation rate of SARS-CoV-2 seroprevalence data
Authors: Pluss Olivia , Campbell Harlan , Pezzi Laura , Morales Ivonne , Roell Yannik , Quandelacy Talia M , Arora Rahul Krishan , Boucher Emily , Lamb Molly M , Chu May , Bärnighausen Till , Jaenisch Thomas
Published: September 2022

Background

There has been a large influx of COVID-19 seroprevalence studies, but comparability between the seroprevalence estimates has been an issue because of heterogeneities in testing platforms and study methodology. One potential source of heterogeneity is the response or participation rate.

Methods

We conducted a review of participation rates (PR) in SARS-CoV-2 seroprevalence studies collected by SeroTracker and examined their effect on the validity of study conclusions. PR was calculated as the count of participants for whom the investigators had collected a valid sample, divided by the number of people invited to participate in the study. A multivariable beta generalized linear model with logit link was fitted to determine if the PR of international household and community-based seroprevalence studies was associated with the factors of interest, from 1 December 2019 to 10 March 2021.

Results

We identified 90 papers based on screening and were able to calculate the PR for 35 out of 90 papers (39%), with a median PR of 70% and an interquartile range of 40.92; 61% of the studies did not report PR.

Conclusions

Many SARS-CoV-2 seroprevalence studies do not report PR. It is unclear what the median PR rate would be had a larger portion not had limitations in reporting. Low participation rates indicate limited representativeness of results. Non-probabilistic sampling frames were associated with higher participation rates but may be less representative. Standardized definitions of participation rate and data reporting necessary for the PR calculations are essential for understanding the representativeness of seroprevalence estimates in the population of interest.
“I don't like to be seen by a male provider”: health workers’ strike, economic, and sociocultural reasons for home birth in settings with free maternal healthcare in Nigeria
Authors: Ajayi Anthony Idowu , Ahinkorah Bright Opoku , Seidu Abdul-Aziz
Published: September 2022

Background

Ending maternal mortality has been a significant global health priority for decades. Many sub-Saharan African countries introduced user fee removal policies to attain this goal and ensure universal access to health facility delivery. However, many women in Nigeria continue to deliver at home. We examined the reasons for home birth in settings with free maternal healthcare in Southwestern and North Central Nigeria.

Methods

We adopted a fully mixed, sequential, equal-status design. For the quantitative study, we drew data from 211 women who reported giving birth at home from a survey of 1227 women of reproductive age who gave birth in the 5 y before the survey. The qualitative study involved six focus group discussions and 68 in-depth interviews. Data generated through the interviews were coded and subjected to inductive thematic analysis, while descriptive statistics were used to analyse the quantitative data.

Results

Women faced several barriers that limited their use of skilled birth attendants. These barriers operate at multiple levels and could be grouped as economic, sociocultural and health facility–related factors. Despite the user fee removal policy, lack of transportation, birth unpreparedness and lack of money pushed women to give birth at home. Also, sociocultural reasons such as hospital delivery not being deemed necessary in the community, women not wanting to be seen by male health workers, husbands not motivated and husbands’ disapproval hindered the use of health facilities for childbirth.

Conclusions

This study has demonstrated that free healthcare does not guarantee universal access to healthcare. Interventions, especially in the Nasarawa state of Nigeria, should focus on the education of mothers on the importance of health facility–based delivery and birth preparedness.
Efficient DNA/RNA extraction from tarsal plates by SK mill, a freeze-crush apparatus
Authors: Oku Hiroaki , Watanabe Akihide , Tokuda Yuichi , Nakayama Tomomichi , Tashiro Kei , Sotozono Chie , Nakano Masakazu
Published: September 2022

The tarsal plate is an eyelid tissue that maintains lid structure from inside the upper/lower eyelids, and it surrounds the meibomian glands and supports their unique secretion mechanism. Sebaceous carcinoma, a malignant eyelid tumour, can sometimes develop from the meibomian glands and is usually excised together with the tarsal plate during surgery, so the tarsal plate serves as a control research tissue. However, since the plate is thick, hard and heterogeneous with few cells, obtaining enough genomic DNA and/or total RNA is often difficult. Therefore, we attempted to establish an efficient protocol to obtain DNA and RNA simultaneously by comparing the combinations of homogenization (mortar/pestle, pellet pestle or SK mill) and purification (organic solvent or spin column) methods using rabbit tarsal plates. Based on the yield, quality and hands-on time, the SK mill and spin column was found to be the most efficient combination. We then applied the established protocol to extract DNA/RNA from six human tarsal-plate samples and succeeded in generating high-quality exome and transcriptome datasets via a next-generation sequencer with sufficient coverage and meibomian gland-specific expression of representative genes, respectively. Our new findings will provide ideal reference data for future genetic and gene-expression studies of sebaceous carcinoma.
Beyond Resistance, Beyond Assimilation: Reimagining Citizenship through Poetry
Authors: Azad Abdul Kalam , Nadkarni Divya , Bunders-Aelen Joske G F
Published: September 2022

The members of the Miya community in Assam, India have been facing an exacerbated threat of statelessness. Among the emancipatory grassroots organizations that have emerged to defend the rights of the Miya community, is an aesthetic resistance movement, now recognized as the ‘Miya Poetry’ movement. The bulk of the movement’s work since its emergence in 2016 has been to call attention to the discriminations and human rights violations faced by the Miya people in citizenship contestation processes. Miya poetry has, on the one hand, received wide acceptance as a poetry of protest and resistance in artistic, academic, and liberal media circles, while on the other, its contributors have been frequently criminalized or questioned by the state for their political views. In this article, we argue that Miya poetry should be looked at beyond the frames of resistance and protest in order to understand its social work as a human-rights movement. These poems have the affective capacity to build resilience, to facilitate complex understandings of difference, and to reimagine equality, democratic values, and freedom from forced assimilation as integral to the idea of citizenship. We used innovative methods to form our data corpus, combining life history interviews with analyses of selected poems. We deployed thematic analysis to report our results. The findings will be useful not only for the poets and artists of different genres who seek to defend human rights, but more broadly for global human-rights practices that wish to actuate a deeper reflective engagement with art-based activisms.
Analysis of the Antennal Transcriptome and Identification of Tissue-specific Expression of Olfactory-related Genes in Micromelalopha troglodyta (Lepidoptera: Notodontidae)
Authors: Zhang Yu , Feng Kai , Mei Ruolan , Li Wei , Tang Fang
Published: September 2022

Micromelalopha troglodyta (Graeser) has been one of the most serious pests on poplars in China. We used Illumina HiSeq 2000 sequencing to construct an antennal transcriptome and identify olfactory-related genes. In total, 142 transcripts were identified, including 74 odorant receptors (ORs), 32 odorant-binding proteins (OBPs), 13 chemosensory proteins (CSPs), 20 ionotropic receptors (IRs), and 3 sensory neuron membrane proteins (SNMPs). The genetic relationships were obtained by the phylogenetic tree, and the tissue-specific expression of important olfactory-related genes was determined by quantitative real-time PCR (qRT–PCR). The results showed that most of these genes are abundantly expressed in the antennae and head. In most insects, olfaction plays a key role in foraging, host localization, and searching for mates. Our research lays the foundation for future research on the molecular mechanism of the olfactory system in M. troglodyta. In addition, this study provides a theoretical basis for exploring the relationship between M. troglodyta and their host plants, and for the biological control of M. troglodyta using olfactory receptor as targets.
Prevalence of Pediculosis Among Primary School-Aged Students in Iran: an Updated Comprehensive Systematic Review and Meta-Analysis
Authors: Akbari Morteza , Sheikhi Soraya , Rafinejad Javad , Akbari Mohammad Reza , Pakzad Iraj , Abdi Fatemeh , Pakzad Reza , Aivazi Ali Ashraf
Published: September 2022

In this study, a systematic investigation was performed to estimate the prevalence of head lice infestation, and to determine the factors affecting the prevalence of heterogeneity among primary school-aged children in Iran. A comprehensive search was fulfilled in international databases, including MEDLINE, Scopus, Web of Science, and Embase, to identify the articles on the prevalence of pediculosis. So, all the cross-sectional epidemiological studies evaluating the prevalence of pediculosis were covered without any restrictions. A random-effects model was used to assess the pooled prevalence. A meta-regression method was applied to determine the factors affecting the heterogeneity among the studied population. An analysis was performed on 67 studies with a total sample size of 358,053. The total pooled estimate for the prevalence of pediculosis in boys and girls was 7.52% (95% CI: 6.15–9.03), 1.99% (95% CI: 1.25–2.89), and 8.97% (95% CI: 721–10.91), respectively. The highest and lowest pooled prevalence was in Hormozgan (southern Iran) (29.21%; 95% CI: 8.89–55.34) and Isfahan (Central Iran) (0.69%; 95% CI: 0.59–0.80), respectively. Based on the results of the univariate meta-regression, gender and father’s job showed a significant direct association with the prevalence of pediculosis, but the sample size had significant inverse relations with the prevalence of pediculosis. This study demonstrated that pediculosis is a common public health problem affecting school-aged children with a relatively high prevalence in Iran, especially among girls.
The Effect of Different Heavy Metals on the Development of Lucilia sericata (Diptera: Calliphoridae)
Authors: Kökdener Meltem , Gündüz Nevran Eylem Akman , Zeybekoğlu Ünal , Aykut Umut , Yılmaz Ahmet Fazıl
Published: September 2022

This study investigates the impacts of three different heavy metals at different concentrations on some life-history traits of Lucilia sericata (Meigen 1826) (Diptera: Calliphoridae). First-instar larvae of L. sericata were reared on a diet containing four concentrations (0.25, 0.50, 1, and 2 µg/g) of the heavy metals (cadmium, zinc copper). The parameters measured were larval and pupal mortality, larval length, adult, pupal, and larval weight, and development time. Larval and pupal survival decreased as heavy metal concentrations increased. Pupal weight was significantly different among heavy metals andc oncentrations, but the adult weight was not significantly different among heavy metals and concentrations. The larval length was significantly different among concentrations and heavy metals. This study reveals that the presence of heavy metal in carrion or the carrion environment should be inconsidered when estimating the time of colonization in forensic investigations.
Cancer risks by sex and variant type in PTEN hamartoma tumor syndrome
Authors: Hendricks Linda A J , Hoogerbrugge Nicoline , Mensenkamp Arjen R , Brunet Joan , Lleuger-Pujol Roser , Høberg-Vetti Hildegunn , Tveit Haavind Marianne , Innella Giovanni , Turchetti Daniela , Aretz Stefan , Spier Isabel , Tischkowitz Marc , Jahn Arne , Links Thera P , Olderode-Berends Maran J W , Blatnik Ana , Leter Edward M , Evans D Gareth , Woodward Emma R , Steinke-Lange Verena , Anastasiadou Violetta C , Colas Chrystelle , Villy Marie-Charlotte , Benusiglio Patrick R , Gerasimenko Anna , Barili Valeria , Branchaud Maud , Houdayer Claude , Tesi Bianca , Yazicioglu M Omer , van der Post Rachel S , Schuurs-Hoeijmakers Janneke H M ,   PTEN Study Group, van Hest Liselotte P , Adank Muriel A , Duijkers Floor , Nielsen Maartje , Verbeek Katja C J , van Ierland Yvette , Giltay Jacques C , Vos Janet R , Vos Janet R
Published: September 2022

Background

PTEN Hamartoma Tumor Syndrome (PHTS) is a rare syndrome with a broad phenotypic spectrum, including increased risks of breast (BC, 67%-78% at age 60 years), endometrial (EC, 19%-28%), and thyroid cancer (TC, 6%-38%). Current risks are likely overestimated due to ascertainment bias. We aimed to provide more accurate and personalized cancer risks.

Methods

This was a European, adult PHTS cohort study with data from medical files, registries, and/or questionnaires. Cancer risks and hazard ratios were assessed with Kaplan-Meier and Cox regression analyses, and standardized incidence ratios were calculated. Bias correction consisted of excluding cancer index cases and incident case analyses.

Results

A total of 455 patients were included, including 50.5% index cases, 372 with prospective follow-up (median 6 years, interquartile range = 3-10 years), and 159 of 281 females and 39 of 174 males with cancer. By age 60 years, PHTS-related cancer risk was higher in females (68.4% to 86.3%) than males (16.4% to 20.8%). Female BC risks ranged from 54.3% (95% confidence interval [CI] = 43.0% to 66.4%) to 75.8% (95% CI = 60.7% to 88.4%), with two- to threefold increased risks for PTEN truncating and approximately twofold for phosphatase domain variants. EC risks ranged from 6.4% (95% CI = 2.1% to 18.6%) to 22.1% (95% CI = 11.6% to 39.6%) and TC risks from 8.9% (95% CI = 5.1% to 15.3%) to 20.5% (95% CI = 11.3% to 35.4%). Colorectal cancer, renal cancer, and melanoma risks were each less than 10.0%.

Conclusions

Females have a different BC risk depending on their PTEN germline variant. PHTS patients are predominantly at risk of BC (females), EC, and TC. This should be the main focus of surveillance. These lower, more unbiased and personalized risks provide guidance for optimized cancer risk management.
The effect of social approval on perceptions following social media message sharing applied to fake news
Authors: Walther Joseph B , Lew Zijian , Edwards America L , Quick Justice
Published: September 2022

A field experiment examined social approval in the form of Twitter “Likes” on individuals’ perceptions after retweeting a fictitious news story about a politician. The study incorporated research about feedback effects on self-perception online, partisan bias, and negativity principles. Participants read or retweeted a (verifiably false) news story via social media, and researchers appended systematic increments of Likes to the retweets. A baseline hypothesis test found no effect on perceptions due to retweeting versus simply reading a news story. Results supported a predicted three-way interaction effect between positive versus negative news story, political congruence with participants’ political party identification, and the reception of 0–22 Likes on perceptions of the politician. More Likes magnified negative perceptions of politicians, from fictitious news, when news stories were negative and focused on politicians from one’s opposite political party.
Caregiver Expressed Emotion in Families of Youth With Spina Bifida: Demographic, Medical, and Family Correlates
Authors: Stiles-Shields Colleen , Kritikos Tessa K , Winning Adrien M , Starnes Meredith , Holmbeck Grayson N
Published: September 2022

Objective

Caregiver expressed emotion (EE), an interview-based measure of emotional valence within an interpersonal relationship, is associated with psychosocial outcomes across multiple conditions. Guided by a model implicating a bidirectional role of “Chronic Family Stress” in the unfolding of EE in family environments, the current study examined demographic, medical, and family-level variables in association with EE in caregivers of children with spina bifida (SB).

Methods

Data were combined from 2 distinct studies of families with a child with SB, resulting in a sample of 174 (ages 8–17). Linear regressions examined the family stressors and child variables in association with maternal and paternal warmth and criticism, as coded from EE interviews.

Results

Higher levels of family stress were associated with paternal criticism (p = .03), while having non-Hispanic White children was associated with both maternal and paternal criticism (ps < .005). Having children younger in age (ps < .01) and without a shunt (ps < .01) was associated with higher warmth.

Conclusions

Family stressors, absence of the negative impacts of systemic racism, shunt status, and age appear to be associated with the expression of EE in caregivers of a child with SB. Findings highlight multiple assessment considerations, including assessing EE when children are younger to engage caregivers with children with SB when they are more likely to be expressing more warmth. Pinpointing factors associated with caregiver EE in SB will help to better identify families at risk for high levels of criticism and also aid in the development of targeted prevention and intervention programs.
Dysregulation of Long Noncoding RNANEAT1/miR-199a-5/BiP Axis in Patients with Diabetic Neuropathy
Authors: Hassani Seyedeh Sara , Karamali Negin , Rajabinejad Misagh , Ashjari Donya , Afshar Hezarkhani Leila , Gorgin Karaji Ali , Salari Farhad , Rezaiemanesh Alireza
Published: September 2022

Objective

Diabetic neuropathy (DN) is a type of nerve damage and the most common complication of diabetes. Regarding the association between endoplasmic reticulum (ER) stress with the pathogenesis of neuropathy, this study aims to examine binding immunoglobulin protein (BiP) gene expression and long noncoding RNA nuclear enriched abundant transcript 1 (NEAT1), miR-199a-5 as its regulator in the peripheral blood of DN patients compared to diabetic patients without neuropathy.

Methods

Peripheral blood samples were obtained from DN (n = 20) patients and diabetic patients without neuropathy (non-DN) (n = 20). After RNA extraction from peripheral blood mononuclear cells, reverse transcription-quantitative polymerase chain reaction was performed to evaluate RNA expression.

Results

The results showed that the expression level of NEAT1 and BiP genes in the DN group increased significantly compared to the non-DN group. Also, the expression level of miR-199a-5p in the DN group was significantly downregulated.

Conclusion

As a result, the axis of NEAT1, miR-199a-5p, and BiP may have a role in the DN pathogenesis.
Natural history of pulmonary coccidioidomycosis: Further examination of the VA-Armed Forces Database
Authors: Shemuel Joseph , Bays Derek J , Thompson George R , Reef Susan , Snyder Linda , Freifeld Alana J , Huppert Milt , Salkin David , Wilson Machelle D , Galgiani John N
Published: September 2022

There are still many limitations related to the understanding of the natural history of differing forms of coccidioidomycosis (CM), including characterizing the spectrum of pulmonary disease. The historical Veterans Administration-Armed Forces database, recorded primarily before the advent of antifungal therapy, presents an opportunity to characterize the natural history of pulmonary CM. We performed a retrospective cohort study of 342 armed forces service members who were diagnosed with pulmonary CM at VA facilities between 1955 to 1958, followed through 1966, who did not receive antifungal therapy. Patients were grouped by predominant pulmonary finding on chest radiographs. The all-cause mortality was low for all patients (4.6%). Cavities had a median size of 3-3.9 cm (IQR: 2-2.9–4-4.9 cm), with heterogeneous wall thickness and no fluid level, while nodules had a median size of 1-1.19 cm (Interquartile range [IQR] 1-1.9–2-2.9 cm) and sharp borders. The majority of cavities were chronic (85.6%), and just under half were found incidentally. Median complement fixation titers in both the nodular and cavitary groups were negative, with higher titers in the cavitary group overall.

This retrospective cohort study of non-disseminated coccidioidomycosis, the largest to date, sheds light on the natural history, serologic markers, and radiologic characteristics of this understudied disease. These findings have implications for the evaluation and management of CM.
The light-curve intrinsic variability in 47 Kepler contact binary stars
Authors: Debski B
Published: September 2022

This work studies the significance of light-curve intrinsic variability in the numerical modelling of contact binaries. Using synthetic light curves, we show that the starspot-based intrinsic variability increases the apparent mass ratio by $\Delta q=5{{\ \rm per\ cent}}$. For systems with orbital period P > 0.3 d, the effects of intrinsic variability averaged over a long time are compensated by Kepler-mission-like phase smearing. Further, we analyse 47 totally eclipsing Kepler mission contact binaries. We find a sharp cut-off of the intrinsic variability at P = 0.45 d. With light-curve numerical modelling and observational relations, we derive the physical parameters of 47 systems. At least 53 per cent of binaries have a possible third companion. 21 binaries show the O’Connell effect in the averaged phase curve. 19 of them have a primary maximum lower than the secondary, suggesting a stationary dark region on the trailing side. Using the P = 0.45 d cut-off, we propose a new approach to the period–colour relation. The only parameter correlating with the magnitude of the intrinsic variability is the apparent effective temperature ratio. We conclude that, instead of describing the system parameters, the A/W subtype division should be applicable only to the light curves, as a tentative phenomenon.
Deep near-infrared survey towards the W40 and Serpens South region in the Aquila Rift: A comprehensive catalogue of young stellar objects
Authors: Sun Jia , Gutermuth Robert A , Wang Hongchi , Zhang Miaomiao , Zhang Shuinai , Ma Yuehui , Du Xinyu , Long Min
Published: September 2022

Active star-forming regions are excellent laboratories for studying the origins and evolution of young stellar object (YSO) clustering. The W40–Serpens South region is such a region, and we compile a large near- and mid-infrared catalogue of point sources in it, based on deep near-infrared observations of Canada-France-Hawaii Telescope (CFHT) in combination with Two Micron All Sky Survey (2MASS), UKIRT Infrared Deep Sky Survey (UKIDSS), and Spitzer catalogues. From this catalogue, we identify 832 YSOs, and classify 15, 135, 647, and 35 of them to be deeply embedded sources, Class I YSOs, Class II YSOs, and transition disc sources, respectively. In general, these YSOs are well correlated with the filamentary structures of molecular clouds, especially the deeply embedded sources and the Class I YSOs. The W40 central region is dominated by Class II YSOs, but in the Serpens South region, half of the YSOs are Class I. We further generate a minimum spanning tree (MST) for all the YSOs. Around the W40 cluster, there are eight prominent MST branches that may trace the vestigial molecular gas filaments that once fed gas to the central natal gas clump. Of the eight, only two now include detectable filamentary gas in Herschel data and corresponding Class I YSOs, while the other six are populated exclusively with Class II YSOs. Four MST branches overlap with the Serpens South main filament, and where they intersect, molecular gas ‘hubs’ and more Class I YSOs are found. Our results imply a mixture of YSO distributions composed of both primordial and somewhat evolved YSOs in this star-forming region.
Hierarchical structure of YSO clusters in the W40 and Serpens South region: group extraction and comparison with fractal clusters
Authors: Sun Jia , Gutermuth Robert A , Wang Hongchi , Zhang Shuinai , Long Min
Published: September 2022

Young stellar clusters are believed to inherit the spatial distribution like hierarchical structures of their natal molecular cloud during their formation. However, the change of the structures between the cloud and the young clusters is not well constrained observationally. We select the W40–Serpens South region (∼7 × 9 pc2) of the Aquila Rift as a testbed and investigate hierarchical properties of spatial distribution of young stellar objects (YSOs) in this region. We develop a minimum spanning tree (MST) based method to group stars into several levels by successively cutting down edges longer than an algorithmically determined critical value. A total of 832 YSOs are divided into 5 levels with 23 groups. For describing the hierarchical properties in a controlled way, we construct a set of synthetic source distributions at various fractal dimensions, and apply the same method to explore their group characters. By comparing the Q parameter and the surface density profiles of the observed and the synthetic data, we find that the YSO observation matches spatial patterns from multifractal dimensions. In the periphery region where the molecular clouds are more diffuse, the YSO structure is close to a fractal dimension of 2.0. While in the core regions, the fractal dimensions are close to 1.6 and 1.4 for the W40 and the Serpens South regions, respectively. Therefore, the YSOs may inherit the fractal pattern of the dense part of the molecular clouds, but such pattern dissipates slowly in several Myr.
Dissecting the microphysics behind the metallicity-dependence of massive stars radii
Authors: Xin Chengcheng , Renzo Mathieu , Metzger Brian D
Published: September 2022

Understanding the radii of massive stars throughout their evolution is important to answering numerous questions about stellar physics, from binary interactions on the main sequence to the pre-supernova radii. One important factor determining a star’s radius is the fraction of its mass in elements heavier than Helium (metallicity, Z). However, the metallicity enters stellar evolution through several distinct microphysical processes, and which dominates can change throughout stellar evolution and with the overall magnitude of Z. We perform a series of numerical experiments with 15 $\, \mathrm{M}_{\odot }$mesa models computed doubling separately the metallicity entering the radiative opacity, the equation of state, and the nuclear reaction network to isolate the impact of each on stellar radii. We explore separately models centred around two metallicity values: one near solar Z = 0.02 and another sub-solar Z ∼ 10−3, and consider several key epochs from the end of the main sequence to core carbon depletion. We find that the metallicity entering the opacity dominates at most epochs for the solar metallicity models, contributing to on average ∼60–90 per cent of the total change in stellar radius. Nuclear reactions have a larger impact (∼50–70 per cent) during most epochs in the subsolar Z models. The methodology introduced here can be employed more generally to propagate known microphysics errors into uncertainties on macrophysical observables including stellar radii.
The chemical enrichment in the early Universe as probed by JWST via direct metallicity measurements at z ∼ 8
Authors: Curti Mirko , D’Eugenio Francesco , Carniani Stefano , Maiolino Roberto , Sandles Lester , Witstok Joris , Baker William M , Bennett Jake S , Piotrowska Joanna M , Tacchella Sandro , Charlot Stephane , Nakajima Kimihiko , Maheson Gabriel , Mannucci Filippo , Amiri Amirnezam , Arribas Santiago , Belfiore Francesco , Bonaventura Nina R , Bunker Andrew J , Chevallard Jacopo , Cresci Giovanni , Curtis-Lake Emma , Hayden-Pawson Connor , Jones Gareth C , Kumari Nimisha , Laseter Isaac , Looser Tobias J , Marconi Alessandro , Maseda Michael V , Scholtz Jan , Smit Renske , Übler Hannah , Wallace Imaan E B
Published: September 2022

We analyse the chemical properties of three z∼ 8 galaxies behind the galaxy cluster SMACS J0723.3-7327, observed as part of the Early Release Observations programme of the James Webb Space Telescope. Exploiting [O iii]λ4363 auroral line detections in NIRSpec spectra, we robustly apply the direct Te  method for the very first time at such high redshift, measuring metallicities ranging from extremely metal poor (12 + log(O/H)≈ 7) to about one-third solar. We also discuss the excitation properties of these sources, and compare them with local strong-line metallicity calibrations. We find that none of the considered diagnostics match simultaneously the observed relations between metallicity and strong-line ratios for the three sources, implying that a proper re-assessment of the calibrations may be needed at these redshifts. On the mass–metallicity plane, the two galaxies at z ∼ 7.6 ($\rm log(M_*/M_{\odot }) = 8.1, 8.7$) have metallicities that are consistent with the extrapolation of the mass–metallicity relation at z∼2–3, while the least massive galaxy at z ∼ 8.5 ($\rm log(M_*/M_{\odot }) = 7.8$) shows instead a significantly lower metallicity. The three galaxies show different level of offset relative to the Fundamental Metallicity Relation, with two of them (at z∼ 7.6) being marginally consistent, while the z∼ 8.5 source deviating significantly, being probably far from the smooth equilibrium between gas flows, star formation, and metal enrichment in place at later epochs.
Non-universal stellar initial mass functions: large uncertainties in star formation rates at z ≈ 2–4 and other astrophysical probes
Authors: Ziegler Joshua J , Edwards Thomas D P , Suliga Anna M , Tamborra Irene , Horiuchi Shunsaku , Ando Shin’ichiro , Freese Katherine
Published: September 2022

We explore the assumption, widely used in many astrophysical calculations, that the stellar initial mass function (IMF) is universal across all galaxies. By considering both a canonical broken-power-law IMF and a non-universal IMF, we are able to compare the effect of different IMFs on multiple observables and derived quantities in astrophysics. Specifically, we consider a non-universal IMF that varies as a function of the local star formation rate, and explore the effects on the star formation rate density (SFRD), the extragalactic background light, the supernova (both core-collapse and thermonuclear) rates, and the diffuse supernova neutrino background. Our most interesting result is that our adopted varying IMF leads to much greater uncertainty on the SFRD at $z \approx 2-4$ than is usually assumed. Indeed, we find an SFRD (inferred using observed galaxy luminosity distributions) that is a factor of $\gtrsim 3$ lower than canonical results obtained using a universal IMF. Secondly, the non-universal IMF we explore implies a reduction in the supernova core-collapse rate of a factor of $\sim 2$, compared against a universal IMF. The other potential tracers are only slightly affected by changes to the properties of the IMF. We find that currently available data do not provide a clear preference for universal or non-universal IMF. However, improvements to measurements of the star formation rate and core-collapse supernova rate at redshifts $z \gtrsim 2$ may offer the best prospects for discernment.
Chemical abundances of the Typhon stellar stream
Authors: Ji Alexander P , Naidu Rohan P , Brauer Kaley , Ting Yuan-Sen , Simon Joshua D
Published: September 2022

We present the first high-resolution chemical abundances of seven stars in the recently discovered high-energy stream Typhon. Typhon stars have apocentres r ≳ 100 kpc, making this the first detailed chemical picture of the Milky Way’s very distant stellar halo. Though the sample size is limited, we find that Typhon’s chemical abundances are more like a dwarf galaxy than a globular cluster, showing a metallicity dispersion and no presence of multiple stellar populations. Typhon stars display enhanced α-element abundances and increasing r-process abundances with increasing metallicity. The high-α abundances suggest a short star formation duration for Typhon, but this is at odds with expectations for the distant Milky Way halo and the presence of delayed r-process enrichment. If the progenitor of Typhon is indeed a new dwarf galaxy, possible scenarios explaining this apparent contradiction include a dynamical interaction that increases Typhon’s orbital energy, a burst of enhanced late-time star formation that raises [α/Fe], and/or group pre-processing by another dwarf galaxy before infall into the Milky Way. Alternatively, Typhon could be the high-energy tail of a more massive disrupted dwarf galaxy that lost energy through dynamical friction. We cannot clearly identify a known low-energy progenitor of Typhon in the Milky Way, but 70 per cent of high-apocentre stars in cosmological simulations are from high-energy tails of large dwarf galaxies. Typhon’s surprising combination of kinematics and chemistry thus underscores the need to fully characterize the dynamical history and detailed abundances of known substructures before identifying the origin of new substructures.
Long-read single-molecule RNA structure sequencing using nanopore
Authors: Bizuayehu Teshome Tilahun , Labun Kornel , Jakubec Martin , Jefimov Kirill , Niazi Adnan Muhammad , Valen Eivind
Published: September 2022

RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
Translational enhancement by base editing of the Kozak sequence rescues haploinsufficiency
Authors: Ambrosini Chiara , Destefanis Eliana , Kheir Eyemen , Broso Francesca , Alessandrini Federica , Longhi Sara , Battisti Nicolò , Pesce Isabella , Dassi Erik , Petris Gianluca , Cereseto Anna , Quattrone Alessandro
Published: September 2022

A variety of single-gene human diseases are caused by haploinsufficiency, a genetic condition by which mutational inactivation of one allele leads to reduced protein levels and functional impairment. Translational enhancement of the spare allele could exert a therapeutic effect. Here we developed BOOST, a novel gene-editing approach to rescue haploinsufficiency loci by the change of specific single nucleotides in the Kozak sequence, which controls translation by regulating start codon recognition. We evaluated for translational strength 230 Kozak sequences of annotated human haploinsufficient genes and 4621 derived variants, which can be installed by base editing, by a high-throughput reporter assay. Of these variants, 149 increased the translation of 47 Kozak sequences, demonstrating that a substantial proportion of haploinsufficient genes are controlled by suboptimal Kozak sequences. Validation of 18 variants for 8 genes produced an average enhancement in an expression window compatible with the rescue of the genetic imbalance. Base editing of the NCF1 gene, whose monoallelic loss causes chronic granulomatous disease, resulted in the desired increase of NCF1 (p47phox) protein levels in a relevant cell model. We propose BOOST as a fine-tuned approach to modulate translation, applicable to the correction of dozens of haploinsufficient monogenic disorders independently of the causing mutation.
snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs
Authors: Bergeron Danny , Paraqindes Hermes , Fafard-Couture Étienne , Deschamps-Francoeur Gabrielle , Faucher-Giguère Laurence , Bouchard-Bourelle Philia , Abou Elela Sherif , Catez Frédéric , Marcel Virginie , Scott Michelle S
Published: September 2022

snoDB is an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources. In the second edition of this database (snoDB 2.0), we added an entirely new section on ribosomal RNA (rRNA) chemical modifications guided by snoRNAs with easy navigation between the different rRNA versions used in the literature and experimentally measured levels of modification. We also included new layers of information, including snoRNA motifs, secondary structure prediction, snoRNA–protein interactions, copy annotations and low structure bias expression data in a wide panel of tissues and cell lines to bolster functional probing of snoRNA biology. Version 2.0 features updated identifiers, more links to external resources and duplicate entry resolution. As a result, snoDB 2.0, which is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/, represents a one-stop shop for snoRNA features, rRNA modification targets, functional impact and potential regulators.
Nanopore tweezers measurements of RecQ conformational changes reveal the energy landscape of helicase motion
Authors: Craig Jonathan M , Mills Maria , Kim Hwanhee C , Huang Jesse R , Abell Sarah J , Mount Jonathan W , Gundlach Jens H , Neuman Keir C , Laszlo Andrew H
Published: September 2022

Helicases are essential for nearly all nucleic acid processes across the tree of life, yet detailed understanding of how they couple ATP hydrolysis to translocation and unwinding remains incomplete because their small (∼300 picometer), fast (∼1 ms) steps are difficult to resolve. Here, we use Nanopore Tweezers to observe single Escherichia coli RecQ helicases as they translocate on and unwind DNA at ultrahigh spatiotemporal resolution. Nanopore Tweezers simultaneously resolve individual steps of RecQ along the DNA and conformational changes of the helicase associated with stepping. Our data reveal the mechanochemical coupling between physical domain motions and chemical reactions that together produce directed motion of the helicase along DNA. Nanopore Tweezers measurements are performed under either assisting or opposing force applied directly on RecQ, shedding light on how RecQ responds to such forces in vivo. Determining the rates of translocation and physical conformational changes under a wide range of assisting and opposing forces reveals the underlying dynamic energy landscape that drives RecQ motion. We show that RecQ has a highly asymmetric energy landscape that enables RecQ to maintain velocity when encountering molecular roadblocks such as bound proteins and DNA secondary structures. This energy landscape also provides a mechanistic basis making RecQ an ‘active helicase,’ capable of unwinding dsDNA as fast as it translocates on ssDNA. Such an energy landscape may be a general strategy for molecular motors to maintain consistent velocity despite opposing loads or roadblocks.
PLK3 amplification and tumor immune microenvironment of metastatic tumors are linked to adjuvant treatment outcomes in uterine serous cancer
Authors: Jones Wendell , Tait David , Livasy Chad , Ganapathi Mahrukh , Ganapathi Ram
Published: September 2022

Uterine serous carcinoma (USC), an aggressive variant of endometrial cancer representing approximately 10% of endometrial cancer diagnoses, accounts for ∼39% of endometrial cancer-related deaths. We examined the role of genomic alterations in advanced-stage USC associated with outcome using paired primary-metastatic tumors (n = 29) treated with adjuvant platinum and taxane chemotherapy. Comparative genomic analysis of paired primary-metastatic patient tumors included whole exome sequencing and targeted gene expression. Both PLK3 amplification and the tumor immune microenvironment (TIME) in metastatic tumors were linked to time-to-recurrence (TTR) risk without any such association observed with primary tumors. TP53 loss was significantly more frequent in metastatic tumors of platinum-resistant versus platinum-sensitive patients and was also associated with increased recurrence and mortality risk. Increased levels of chr1 breakpoints in USC metastatic versus primary tumors co-occur with PLK3 amplification. PLK3 and the TIME are potential targets for improving outcomes in USC adjuvant therapy.
Systematic analysis of the underlying genomic architecture for transcriptional–translational coupling in prokaryotes
Authors: Bharti Richa , Siebert Daniel , Blombach Bastian , Grimm Dominik G
Published: September 2022

Transcriptional-translational coupling is accepted to be a fundamental mechanism of gene expression in prokaryotes and therefore has been analyzed in detail. However, the underlying genomic architecture of the expression machinery has not been well investigated so far. In this study, we established a bioinformatics pipeline to systematically investigated >1800 bacterial genomes for the abundance of transcriptional and translational associated genes clustered in distinct gene cassettes. We identified three highly frequent cassettes containing transcriptional and translational genes, i.e. rplk-nusG (gene cassette 1; in 553 genomes), rpoA-rplQ-rpsD-rpsK-rpsM (gene cassette 2; in 656 genomes) and nusA-infB (gene cassette 3; in 877 genomes). Interestingly, each of the three cassettes harbors a gene (nusG, rpsD and nusA) encoding a protein which links transcription and translation in bacteria. The analyses suggest an enrichment of these cassettes in pathogenic bacterial phyla with >70% for cassette 3 (i.e. Neisseria, Salmonella and Escherichia) and >50% for cassette 1 (i.e. Treponema, Prevotella, Leptospira and Fusobacterium) and cassette 2 (i.e. Helicobacter, Campylobacter, Treponema and Prevotella). These insights form the basis to analyze the transcriptional regulatory mechanisms orchestrating transcriptional–translational coupling and might open novel avenues for future biotechnological approaches.
Obesity and its association with mental health among Mexican children and adolescents: systematic review
Authors: Godina-Flores Naara L , Gutierrez-Gómez Yareni Yunuen , García-Botello Marcela , López-Cruz Lizet , Moreno-García Carlos Francisco , Aceves-Martins Magaly
Published: September 2022

Context

Obesity and mental health issues increasingly affect children and adolescents, but whether obesity is a risk factor for mental health issues is unclear.

Objective

To systematically review the association between obesity and mental health issues (ie, anxiety and/or depression) among Mexican children and adolescents.

Data sourcing, extraction, and synthesis

A literature search of 13 databases and 1 search engine was conducted. Population, exposure, comparison, outcomes, and study design data were extracted, analyzed, and narratively synthesized. The JBI critical appraisal tool was used to evaluate evidence quality.

Results

A total of 16 studies with 12 103 participants between 8 and 18 years old were included. Four studies focused on anxiety outcomes, 10 on depression, and 2 on both (ie, anxiety and depression). Evidence is unclear about the association of obesity with anxiety. However, most evidence shows that Mexican children and adolescents with overweight or obesity are more likely to have depression or report a higher number of depressive symptoms than normal-weight participants. Such likelihood is greater for females.

Conclusion

Health promotion interventions to treat or prevent obesity could also consider mental health outcomes.

Systematic Review Registration

PROSPERO registration no. CRD42019154132
Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia presenting as a solitary lung nodule: a rare histopathological diagnosis
Authors: Simon Natalie , Negmeldin Mostafa
Published: September 2022

We present a case of diffuse idiopathic pulmonary neuroendocrine cell hyperplasia (DIPNECH) in a 56-year-old woman, who presented to our emergency department with a 7-day history of exertional dyspnoea. Due to profound haemodynamic compromise, pulmonary embolism (PE) was suspected, and the patient underwent emergency thrombolysis on admission. A subsequent computerized tomography pulmonary angiogram revealed extensive bilateral PE. Incidentally, a 1.3 cm lesion within the right upper lobe, associated with pleural tethering, was identified. Positron emission tomography computerized tomography and, subsequently, histopathology revealed this lesion to be primary DIPNECH, a rare pre-invasive hyperplasia of neuroendocrine cells. While studies are scarce and cohort numbers are low, somatostatin analogues and protein kinase inhibitors have been proven to reduce symptoms and increase progression-free survival in DIPNECH, respectively.
An unusual ileocecal tumor
Authors: Inoue Takato , Inoue Naonori , Kawamura Takuji , Uno Koji
Published: September 2022

We report the case of diffuse large B-cell lymphoma (DLBCL) with a fistula from the ileum to the cecum. A 57-year-old male came to the hospital complaining of abdominal pain. He underwent an abdominal computed tomography with contrast, which showed full-thickness wall thickening at the ileocecal region. He underwent a lower gastrointestinal endoscopy. No tumor was found at the ileocecal valve, and macroscopic findings were normal. The scope was advanced to the cecum, an additional outpouching was found. The outpouching appeared to be an ileocecal fistula. The diagnosis was DLBCL.
Shortened chordae tendineae of the tricuspid valve with right ventricular dysfunction caused by acute myocarditis lead to cardiogenic shock during pericardial drainage: a case report
Authors: Higuchi Motoaki , Mitomi Kisato , Chiba Yoshiro
Published: September 2022

A 63-year-old woman was admitted to the hospital with general malaise and pericardial and thoracoabdominal effusions of unknown cause. After pericardial drainage for drug-resistant right heart failure, she developed right ventricular (RV) dysfunction and cardiogenic shock caused by severe tricuspid regurgitation (TR). Findings during emergency surgery included tricuspid valve (TV) junction failure caused by shortening of the chordae tendineae of the TV, which is an organic abnormality. Additionally, myocardial biopsy results revealed myocarditis. Although acute myocarditis developed with RV dysfunction, pericardial effusion suppressed venous return, which temporarily improved her pathological condition. However, RV dysfunction and severe TR were thought to have manifested after the venous return suppression was alleviated by pericardial drainage. Because venous return changes significantly after pericardial drainage, it is necessary to examine the need for drainage and re-evaluate the post-operative RV system.