bluuebunny/crossref_metadata_2025 huggingface dataset:
Multilevel analysis to identify the factors associated with caesarean section in Bangladesh: evidence from a nationally representative survey
Authors: Ahmed Md Sabbir , Islam Mansura , Jahan Ishrat , Shaon Imran Faisal
Published: January 2022

Background

Caesarean delivery has a significant role in reducing maternal and child death. However, unnecessary utilization has adverse health effects. This study aimed to assess the prevalence and associated factors of caesarean delivery in Bangladesh.

Methods

Data from the latest Bangladesh Multiple Indicator Cluster Survey (MICS, 2019) was used in this study. Since MICS data are hierarchical in nature, multilevel modelling was used.

Results

The prevalence of caesarean section (CS) was 67.4% among Bangladeshi women. Multilevel analysis suggests the age of the women, household wealth status, utilization of antenatal care (ANC) , delivery at a health facility and division were significantly associated with CS. Women who delivered in a private health facility had the highest odds for CS (odds ratio [OR] 10.35 [95% confidence interval {CI} 8.55 to 12.54]). Women 30–34 y of age had a 36% higher likelihood of CS compared with women 15–19 y of age (OR 1.36 [95% CI 1.03 to 1.79]). The odds of CS positively increased with household wealth status. Women who had at least one ANC visit had a 1.7 times higher possibility of CS (OR 1.70 [95% CI 1.26 to 2.30]).

Conclusions

Policy guidelines on caesarean deliveries are urgently needed in Bangladesh to avoid unnecessary caesarean deliveries and protect mothers from the consequences.
Relationship of TonB-dependent receptors with susceptibility to cefiderocol in clinical isolates of Pseudomonas aeruginosa
Authors: Gupta Aanchal , Landman David , Quale John
Published: January 2022

Objectives

Cefiderocol maintains activity against most MDR Gram-negative pathogens including Pseudomonas aeruginosa. In laboratory-derived isolates, down-regulation of TonB-dependent siderophore receptors have been implicated in resistance to cefiderocol.

Methods

In this report, the expression of seven TonB-dependent siderophore receptors was examined in 10 clinical isolates with cefiderocol MICs ranging from ≤0.03–8 mg/L. In addition, genetic sequences of the siderophore receptors were analysed to identify potentially disruptive mutations.

Results

There was no clear association between expression of the receptors with cefiderocol susceptibility, including the receptors piuA/piuD and pirA previously implicated in cefiderocol uptake. In addition, there were no disabling mutations identified in the receptors. Acquired β-lactamase activity also could not explain the range in cefiderocol susceptibility.

Conclusions

The aetiology of reduced susceptibility to cefiderocol in clinical isolates of P. aeruginosa remains an enigma and worthy of further investigation.
The feasibility and generalizability of assessing the appropriateness of antimicrobial prescribing in hospitals: a review of the Australian National Antimicrobial Prescribing Survey
Authors: James Rodney , Nakamachi Yoshiko , Morris Andrew , So Miranda , Ponnampalavanar Sasheela Sri La Sri , Chuki Pem , Loong Ly Sia , Lai Pauline Siew Mei , Chen Caroline , Ingram Robyn , Rajkhowa Arjun , Buising Kirsty , Thursky Karin
Published: January 2022

The National Antimicrobial Prescribing Survey (NAPS) is a web-based qualitative auditing platform that provides a standardized and validated tool to assist hospitals in assessing the appropriateness of antimicrobial prescribing practices. Since its release in 2013, the NAPS has been adopted by all hospital types within Australia, including public and private facilities, and supports them in meeting the national standards for accreditation. Hospitals can generate real-time reports to assist with local antimicrobial stewardship (AMS) activities and interventions. De-identified aggregate data from the NAPS are also submitted to the Antimicrobial Use and Resistance in Australia surveillance system, for national reporting purposes, and to strengthen national AMS strategies. With the successful implementation of the programme within Australia, the NAPS has now been adopted by countries with both well-resourced and resource-limited healthcare systems. We provide here a narrative review describing the experience of users utilizing the NAPS programme in Canada, Malaysia and Bhutan. We highlight the key barriers and facilitators to implementation and demonstrate that the NAPS methodology is feasible, generalizable and translatable to various settings and able to assist in initiatives to optimize the use of antimicrobials.
Bupivacaine Metabolite Can Interfere with Norfentanyl Measurement by LC–MS/MS
Authors: Mahowald Grace , Khaliq Tahira , Basu Sankha , Griggs David , Siegel Molly , Leffert Lisa , Bernstein Sarah , Flood James G , Uljon Sacha
Published: January 2022

Background

Liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) is the gold standard for the measurement of fentanyl and norfentanyl (NF) in urine and is favored over immunoassays due to its superior specificity. NF is the principal metabolite of fentanyl found in the urine and is typically present in higher abundance than fentanyl. Thus, the sensitivity and specificity of LC–MS/MS relies largely on the ability to identify and quantitate NF.

Methods

We analyzed urine specimens from women who had received bupivacaine and fentanyl for epidural analgesia during labor. We analyzed the contents of the epidural bag itself and purified bupivacaine metabolite N-desbutyl bupivacaine [or N-(2,6-dimethylphenyl)piperidine-2-carboxamide (NDB)] by LC–MS/MS.

Results

NDB interferes with the LC–MS/MS assay for NF. NDB passes through the Q1 mass selection filter because it is isobaric with the NF precursor ion (233 m/z). Further, it shares product ions with NF (84 m/z and 150 m/z), used as quantifier and qualifier ions, respectively, in our urine NF detection method. Baseline resolution of NDB and NF using these quantifier and qualifier ions could not be achieved. A unique product ion of NF (177 m/z) was useful for distinguishing NDB from NF.

Conclusion

Bupivacaine is a commonly used drug. Recognition of this interference by laboratories is critical for preventing the misidentification of NF, which can have profound effects on patient care.
Effect of health information technology (HIT)-based discharge transition interventions on patient readmissions and emergency room visits: a systematic review
Authors: Abraham Joanna , Meng Alicia , Tripathy Sanjna , Kitsiou Spyros , Kannampallil Thomas
Published: January 2022

Objective

To systematically synthesize and appraise the evidence on the effectiveness of health information technology (HIT)-based discharge care transition interventions (CTIs) on readmissions and emergency room visits.

Materials and Methods

We conducted a systematic search on multiple databases (MEDLINE, CINAHL, EMBASE, and CENTRAL) on June 29, 2020, targeting readmissions and emergency room visits. Prospective studies evaluating HIT-based CTIs published as original research articles in English language peer-reviewed journals were eligible for inclusion. Outcomes were pooled for narrative analysis.

Results

Eleven studies were included for review. Most studies (n = 6) were non-RCTs. Several studies (n = 9) assessed bridging interventions comprised of at least 1 pre- and 1 post-discharge component. The narrative analysis found improvements in patient experience and perceptions of discharge care.

Discussion

Given the statistical and clinical heterogeneity among studies, we could not ascertain the cumulative effect of CTIs on clinical outcomes. Nevertheless, we found gaps in current research and its implications for future work, including the need for a HIT-based care transition model for guiding theory-driven design and evaluation of HIT-based discharge CTIs.

Conclusions

We appraised and aggregated empirical evidence on the cumulative effectiveness of HIT-based interventions to support discharge transitions from hospital to home, and we highlighted the implications for evidence-based practice and informatics research.
Into the matrix: current methods for mitochondrial translation studies
Authors: Apostolopoulos Antonios , Iwasaki Shintaro
Published: January 2022

In addition to the cytoplasmic translation system, eukaryotic cells house additional protein synthesis machinery in mitochondria. The importance of this in organello translation is exemplified by clinical pathologies associated with mutations in mitochondrial translation factors. Although a detailed understanding of mitochondrial translation has long been awaited, quantitative, comprehensive and spatiotemporal measurements have posed analytic challenges. The recent development of novel approaches for studying mitochondrial protein synthesis has overcome these issues and expands our understanding of the unique translation system. Here, we review the current technologies for the investigation of mitochondrial translation and the insights provided by their application.
‘Beautiful, plain objects like [SKF] ball bearings’: The Enigma of Aestheticizing Anonymity in ‘Machine Art’ and Modernist Logotypes
Authors: Shales Ezra
Published: January 2022

The SKF ball bearing on display in the 1934 ‘Machine Art’ exhibition in the Museum of Modern Art is an icon referenced throughout visual culture studies but this article recognizes its materiality, identifying the corporate logotype and other branded markings that complicate its identity as anonymous or, in the words of museum curator Philip Johnson, as ‘plain’. SKF, Svenska Kullagerfabriken (The Swedish ball bearing factory), had a fully developed global advertising campaign that made it a more established brand name than MoMA, and pioneered the contemporary mode of speaking and thinking in logotypes—by 1934, Johnson’s claim notwithstanding, no one could ‘see’ an SKF ball bearing without seeing the company’s logo. Scholarly commentary has adhered to MoMA’s description as if the bearing were anonymous and not visibly branded. This essay describes the history of the SKF logotype and situates it as both pioneering and part of a complex corporate culture and aspect of brand standardization that intersected with globalization in unexpected ways. To delve into the commercial context and production of ball bearings is to unravel the contradictions inherent in identifying design as national or global, and the modernist idealization of anonymous industrial form as an aesthetic ideal.
Nitric Oxide Fumigation for Control of Ham Mite, Tyrophagus putrescentiae (Sarcoptiformes: Acaridae)
Authors: Yang Xiangbing , Liu Yong-Biao , Singh Rippy , Phillips Thomas W
Published: January 2022

The ham mite, Tyrophagus putrescentiae (Schrank) (Sarcoptiformes: Acaridae), is a common pest infesting several stored products, particularly the aged hams. In this study, we reported the efficacy of nitric oxide (NO) fumigation, a recently discovered fumigation treatment under the ultra-low oxygen environment, at various concentrations and time under the laboratory conditions at 25°C against different mite stages on both dietary media and ham meat. Our results showed that NO fumigation was effective against all mite stages and 100% control was achieved. Generally, the egg was the most tolerant stage and required 48-, 24-, 16-, and 8-h treatments to achieve 100% mortality at 0.5, 1, 1.5, and 2% NO concentration on dietary media, respectively. Tyrophagus putrescentiae mobile immatures and adult stages were less tolerant, and 100% mortality was achieved after 16-, 8-, 8-, and 4-h treatment at 0.5, 1, 1.5, and 2% NO, respectively. The median lethal concentration (LC50) of NO on egg was 0.86, 0.68, and 0.32% for 8-, 16-, and 24-h treatments. In addition, a confirmatory test was conducted on ham meat at 0.5 and 1.0% of NO and similar efficacy was found. Complete control of egg was achieved after 48- and 24-h treatment at 0.5 and 1.0% of NO, respectively, and larvae and adult mites were 100% controlled after 16 and 8 h at 0.5 and 1.0% of NO, respectively. Our results demonstrated that NO fumigation was effective against T. putrescentiae and can be a potential alternative treatment to methyl bromide for cured-ham pest control.
Court Decisions in the Republic of Korea on Japan's Accountability for Sexual Slavery of the Comfort Women
Authors: Nam Seunghyun
Published: January 2022

On January and April of 2021, two contradictory decisions on the comfort women issue were ruled by two courts in the Republic of Korea (ROK), stirring much controversy on the various legal issues concerning the comfort women. In the January decision, the court held Japan accountable for the acts committed against the comfort women and denied Japan’s immunity in the courts of the ROK because these atrocities constitute crimes against humanity when Japan illegally occupied Korea. On the other hand, the April decision, which was a case for another group of comfort women victims, dismissed the suit by ruling that Japan was rather immune on this issue in ROK courts because state immunity is considered to be part of customary international law. The court specifically referred to the Jurisdictional Immunities case before the International Court of Justice which found that violations of jus cogens as a substantive norm could not trump over procedural matters such as state immunity. As the April case has been appealed by the victims, this article aims to examine the historical background of the issue of comfort women and the main legal issues of these domestic decisions. The first issue concerns whether Japan is immune in ROK courts for even alleged violations of jus cogens, and the second issue is whether the individual claims of the comfort women are still valid today or whether they have been, as a matter of law, extinguished or waived through the 1965 Claims Agreement and the 2015 Agreement signed by both the ROK and Japan.
Robust schedules for tardiness optimization in job shop with interval uncertainty
Authors: Díaz Hernán , Palacios Juan José , Díaz Irene , Vela Camino R , González-Rodríguez Inés
Published: January 2022

This paper addresses a variant of the job shop scheduling problem with total tardiness minimization where task durations and due dates are uncertain. This uncertainty is modelled with intervals. Different ranking methods for intervals are considered and embedded into a genetic algorithm. A new robustness measure is proposed to compare the different ranking methods and assess their capacity to predict ‘expected delays’ of jobs. Experimental results show that dealing with uncertainty during the optimization process yields more robust solutions. A sensitivity analysis also shows that the robustness of the solutions given by the solving method increases when the uncertainty grows.
A new copyright law in the UAE
Authors: Al-Sharieh Saleh
Published: January 2022

The Federal Decree-Law No. 38 of 2021 on Copyright and Related Rights, published in the Official Gazette, Issue No. 712, on 26 September 2021

On 2 January 2022, the Federal Decree-Law No. 38 of 2021 on Copyright and Related Rights (‘Federal Decree-Law No. 38’), repealing the Federal Law No. 7 of 2002 on Copyrights and Related Rights (‘repealed law’), came into force in the United Arab Emirates. It seeks to facilitate the transition into the knowledge economy and implement the Marrakesh Treaty to Facilitate Access to Published Works for Persons Who Are Blind, Visually Impaired, or Otherwise Print Disabled (‘Marrakesh Treaty’).
Host Plant-Based Artificial Diets Enhance Development, Survival and Fecundity of the Edible Long-Horned Grasshopper Ruspolia differens (Orthoptera: Tettigoniidae)
Authors: Leonard Alfonce , Egonyu James P , Tanga Chrysantus M , Kyamanywa Samuel , Ekesi Sunday , Khamis Fathiya M , Subramanian Sevgan
Published: January 2022

Wild swarms of the long-horned grasshoppers Ruspolia differens (Serville) which are widely harvested for consumption and sale in Africa are seasonal and unsustainable, hence the need for innovative ways of artificially producing the insects. We investigated the development, survival, and reproduction of R. differens in the laboratory on diets mixed with host plants [Digitaria gayana Kunth, Cynodon dactylon (L.) and Megathyrsus maximus Jacq (Poales: Poaceae); Ageratum conyzoides L. (Asterales: Asteraceae)] identified from guts of their wild conspecifics with a view to developing a suitable diet for artificial mass rearing of the edible insect. A standard diet comprising ground black soldier fly, Hermetia illucens L. (Diptera: Startiomyidae) larvae, soybean flour, maize flour, vitamin premix, and ground bones was tested for rearing R. differens as a control against the same ingredients incorporated with individual powders of the different host plants. Whereas R. differens developed more slowly in the diet mixed with D. gayana than in the control diet; its development was faster in the diet mixed with C. dactylon. Mortalities of R. differens in host plant-based diets were 42.5–52.5%, far lower than in the control diet with 71% mortality. The insects raised on the diet mixed with M. maximus laid approximately twice more eggs compared to R. differens fecundities from the rest of the diets. However, inclusion of host plants in the diets had no detectable influence on R. differens adult weight and longevity. These findings support inclusion of specific host plants in artificial diets used for mass rearing of R. differens to enhance its survival, development, and fecundity.
Identification of a Subset of Stage I Colorectal Cancer Patients With High Recurrence Risk
Authors: Lee Lik Hang , Davis Lindy , Ylagan Lourdes , Omilian Angela R , Attwood Kristopher , Firat Canan , Shia Jinru , Paty Philip B , Cance William G
Published: January 2022

Background

A challenge in early-stage colorectal cancer (CRC) is identifying biomarkers that predict an increased risk for recurrence. A potential clinically adaptable biomarker is focal adhesion kinase (FAK), a tyrosine kinase that promotes invasion and metastasis.

Methods

An initial, single-institution, 298-patient cohort with all stages of CRC and long-term follow-up was assessed for FAK with tissue microarrays using immunohistochemistry. FAK expression was scored and dichotomized into high and low. Subsequently, a validation cohort of 517 early-stage CRCs from a separate institution was evaluated. All statistical tests were 2-sided.

Results

FAK overexpression did not correlate with any known histologic feature and was an early event in CRC, increasing from normal colon to stage I, and stage I to II, but not different at higher stages. High FAK was associated with decreased 10-year recurrence-free survival (RFS) among stage I patients (70.2% for high FAK vs 94.1% for low, P = .02), but not among higher stages in the initial cohort. The same finding was seen in the validation cohort (73.1% for high FAK vs 93.1% for low, P = .004). Multivariable survival analysis for stage I patients showed only two statistically significant factors predicting RFS: FAK (hazard ratio = 5.27, 95% confidence interval = 1.81 to 15.33, P = .002) and perineural invasion (hazard ratio = 7.38, 95% confidence interval = 1.01 to 53.96, P = .049). FAK was the only statistically significant factor in multivariable analysis across RFS, overall, and disease-specific survivals.

Conclusions

High FAK expression identified a subset of stage I CRC patients with high incidence of recurrence and reduced survival, suggesting that FAK has important prognostic value. These patients would immediately benefit from more rigorous surveillance protocols for recurrent disease.
Gynaecomastia-like change of a female breast with tri-layer ductal epithelium as described in the male breast
Authors: Fink Teagan , Deb Siddhartha , Chakrabarti Anannya
Published: January 2022

A 31-year-old female presented with asymmetrical fullness in the right breast and was found to have a large span of fibrocystic change and nodular glandular tissue on magnetic resonance imaging. Breast malignancy could not be excluded, and thus excisional biopsy was performed. Histopathology revealed a rare finding of gynaecomastia-like histopathological changes of a female breast. Gynaecomastia is traditionally a clinical condition affecting the male breast and characterized by ductal hyperplasia, periductal fibrosis and oedema of the tissue. We describe the first finding of gynaecomastia-like change with a tri-layer ductal epithelium in a female breast, as previously described in the male breast.
Imprints of the cosmic void evolution on the baryon processes inside galaxy haloes
Authors: Rodríguez Medrano Agustín M , Paz Dante J , Stasyszyn Federico A , Ruiz Andrés N
Published: January 2022

Cosmic voids provide a unique environment to study galaxy formation and evolution. In this paper, we analyse a set of hydrodynamic zoom-in simulations of voids, to analyse in detail their inner structures. These voids were identified in a cosmological simulation and classified according to their surrounding dynamics at very large scales: whether they are in expansion or contraction at their outskirts. We study how these environments and the dynamics of voids impact the baryonic processes inside haloes and their mechanisms of formation and evolution. We find an underabundance of processed gas within the voids that can be associated with the lack of massive haloes. By studying the dynamical phase-space diagram of haloes and the halo-particle correlation function, we find that haloes inside of contracting voids are slightly affected by the presence of bigger structures, in comparison to haloes in the inner regions of expanding voids. This fact is consistent when you see dark matter or gas particles. We show that the halo assembly depends on the void dynamical state: haloes in expanding voids assemble slowly than those in contracting voids and in the general universe. This difference in the assembly impacts the baryonic evolution of haloes. Overall the redshift range analysed that haloes in voids have less baryon content than haloes in the general universe and particularly at z = 0 less stellar content. Our results suggest that the large-scale void environment modulate the baryonic process occurring inside haloes according to the void dynamical state.
Dark Energy Survey Year 3 results: marginalization over redshift distribution uncertainties using ranking of discrete realizations
Authors: Cordero Juan P , Harrison Ian , Rollins Richard P , Bernstein G M , Bridle S L , Alarcon A , Alves O , Amon A , Andrade-Oliveira F , Camacho H , Campos A , Choi A , DeRose J , Dodelson S , Eckert K , Eifler T F , Everett S , Fang X , Friedrich O , Gruen D , Gruendl R A , Hartley W G , Huff E M , Krause E , Kuropatkin N , MacCrann N , McCullough J , Myles J , Pandey S , Raveri M , Rosenfeld R , Rykoff E S , Sánchez C , Sánchez J , Sevilla-Noarbe I , Sheldon E , Troxel M , Wechsler R , Yanny B , Yin B , Zhang Y , Aguena M , Allam S , Bertin E , Brooks D , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Castander F J , Cawthon R , Costanzi M , da Costa L , da Silva Pereira M E , De Vicente J , Diehl H T , Dietrich J , Doel P , Elvin-Poole J , Ferrero I , Flaugher B , Fosalba P , Frieman J , Garcia-Bellido J , Gerdes D , Gschwend J , Gutierrez G , Hinton S , Hollowood D L , Honscheid K , Hoyle B , James D , Kuehn K , Lahav O , Maia M A G , March M , Menanteau F , Miquel R , Morgan R , Muir J , Palmese A , Paz-Chinchon F , Pieres A , Plazas Malagón A , Sánchez E , Scarpine V , Serrano S , Smith M , Soares-Santos M , Suchyta E , Swanson M , Tarle G , Thomas D , To C , Varga T N ,   (DES Collaboration)
Published: January 2022

Cosmological information from weak lensing surveys is maximized by sorting source galaxies into tomographic redshift subsamples. Any uncertainties on these redshift distributions must be correctly propagated into the cosmological results. We present hyperrank, a new method for marginalizing over redshift distribution uncertainties, using discrete samples from the space of all possible redshift distributions, improving over simple parametrized models. In hyperrank, the set of proposed redshift distributions is ranked according to a small (between one and four) number of summary values, which are then sampled, along with other nuisance parameters and cosmological parameters in the Monte Carlo chain used for inference. This approach can be regarded as a general method for marginalizing over discrete realizations of data vector variation with nuisance parameters, which can consequently be sampled separately from the main parameters of interest, allowing for increased computational efficiency. We focus on the case of weak lensing cosmic shear analyses and demonstrate our method using simulations made for the Dark Energy Survey (DES). We show that the method can correctly and efficiently marginalize over a wide range of models for the redshift distribution uncertainty. Finally, we compare hyperrank to the common mean-shifting method of marginalizing over redshift uncertainty, validating that this simpler model is sufficient for use in the DES Year 3 cosmology results presented in companion papers.
Machine-learning prediction for mean motion resonance behaviour – The planar case
Authors: Li Xin , Li Jian , Xia Zhihong Jeff , Georgakarakos Nikolaos
Published: January 2022

Most recently, machine learning has been used to study the dynamics of integrable Hamiltonian systems and the chaotic 3-body problem. In this work, we consider an intermediate case of regular motion in a non-integrable system: the behaviour of objects in the 2:3 mean motion resonance with Neptune. We show that, given initial data from a short 6250 yr numerical integration, the best-trained artificial neural network (ANN) can predict the trajectories of the 2:3 resonators over the subsequent 18 750 yr evolution, covering a full libration cycle over the combined time period. By comparing our ANN’s prediction of the resonant angle to the outcome of numerical integrations, the former can predict the resonant angle with an accuracy as small as of a few degrees only, while it has the advantage of considerably saving computational time. More specifically, the trained ANN can effectively measure the resonant amplitudes of the 2:3 resonators, and thus provides a fast approach that can identify the resonant candidates. This may be helpful in classifying a huge population of KBOs to be discovered in future surveys.
Detectability of the gravitational redshift effect from the asymmetric galaxy clustering
Authors: Saga Shohei , Taruya Atsushi , Rasera Yann , Breton Michel-Andrès
Published: January 2022

It has been recently recognized that the observational relativistic effects, mainly arising from the light propagation in an inhomogeneous universe, induce the dipole asymmetry in the cross-correlation function of galaxies. In particular, the dipole asymmetry at small scales is shown to be dominated by the gravitational redshift effects. In this paper, we exploit a simple analytical description for the dipole asymmetry in the cross-correlation function valid at quasi-linear regime. In contrast to the previous model, a new prescription involves only 1D integrals, providing a faster way to reproduce the results obtained by Saga et al. Using the analytical model, we discuss the detectability of the dipole signal induced by the gravitational redshift effect from upcoming galaxy surveys. The gravitational redshift effect at small scales enhances the signal-to-noise ratio (S/N) of the dipole, and in most of the cases considered, the S/N is found to reach a maximum at z ≈ 0.5. We show that current and future surveys such as DESI and SKA provide an idealistic data set, giving a large S/N of 10–20. Two potential systematics arising from off-centred galaxies are also discussed (transverse Doppler effect and diminution of the gravitational redshift effect), and their impacts are found to be mitigated by a partial cancellation between two competitive effects. Thus, the detection of the dipole signal at small scales is directly linked to the gravitational redshift effect, and should provide an alternative route to test gravity.
Automatic algorithm to obtain v sin i values via Fourier transform in the BeSOS database
Authors: Solar Martín , Arcos Catalina , Curé Michel , Levenhagen Ronaldo S , Araya Ignacio
Published: January 2022

Be stars are found to rotate close to their critical rotation and therefore they are considered an important laboratory for the study of stellar rotation. In this context, we obtain the projected rotational velocity of a sample of classical Be southern stars in the BeSOS database via Fourier transforms in an automated way for several absorption lines at different epochs. A Gaussian profile is fitted to eight observed photospheric He i lines in order to select automatically from the profile the spectral signal given by areas under the curve of 95.45, 98.75, and 99.83 per cent, to obtain vsin i via the Fourier transform technique. The values obtained are in global agreement with the literature. Analysing only one line is not enough to set the vsin i value: depending on the line, the value in most cases is underestimated with respect to λ4471. When gravity-darkening effects are included, apparent values increase by ∼10 per cent. The resolution of the instrument Pontificia Universidad Catolica High Echelle Resolution Optical Spectrograph (PUCHEROS) used for BeSOS spectra ($R \sim 17\, 000$) constrains the theoretical lower bound possible to vsin i ∼ 100  km s−1. The procedure has limitations, using a linear limb-darkening function with ε = 0.6 for classical Be stars rotating close to the break-up velocity without gravity-darkening corrections, which cannot be negligible. Previous works measure vsin i values using just one spectral line and here we demonstrate that with more lines the results can vary. This could be due to the photospheric distribution of atomic transitions in classical Be stars.
Stellar response after stripping as a model for common-envelope outcomes
Authors: Vigna-Gómez Alejandro , Wassink Michelle , Klencki Jakub , Istrate Alina , Nelemans Gijs , Mandel Ilya
Published: January 2022

Binary neutron stars have been observed as millisecond pulsars, gravitational-wave sources, and as the progenitors of short gamma-ray bursts and kilonovae. Massive stellar binaries that evolve into merging double neutron stars are believed to experience a common-envelope episode. During this episode, the envelope of a giant star engulfs the whole binary. The energy transferred from the orbit to the envelope by drag forces or from other energy sources can eject the envelope from the binary system, leading to a stripped short-period binary. In this paper, we use one-dimensional single stellar evolution to explore the final stages of the common-envelope phase in progenitors of neutron star binaries. We consider an instantaneously stripped donor star as a proxy for the common-envelope phase and study the star’s subsequent radial evolution. We determine a range of stripping boundaries that allow the star to avoid significant rapid re-expansion and that thus represent plausible boundaries for the termination of the common-envelope episode. We find that these boundaries lie above the maximum compression point, a commonly used location of the core/envelope boundary. We conclude that stars may retain fractions of a solar mass of hydrogen-rich material even after the common-envelope episode. If we consider orbital energy as the only energy source available, all of our models would overfill their Roche lobe after ejecting the envelope, whose binding energy includes gravitational, thermal, radiation, and recombination energy terms.
Surface tension of cosmic voids as a possible source for dark energy
Authors: Yusofi E , Khanpour M , Khanpour B , Ramzanpour M A , Mohsenzadeh M
Published: January 2022

The cosmological constant is estimated by considering the surface tension of supervoids in a void-dominated cosmic fluid by which we can get a possible source of dark energy. Looking at voids as bubbles, we define the concept of surface tension which is shown to have an almost constant value for supervoids that are enclosed by superclusters. The surface tensions of voids are computed by dimensional method for galaxies and superclusters with different values for each group. At large scale which vast voids are dominant the positive cosmological constants obtained of order (≃ +10−52 m−2), which are very close to those given by Planck.
Placing Ancient DNA Sequences into Reference Phylogenies
Authors: Martiniano Rui , De Sanctis Bianca , Hallast Pille , Durbin Richard
Published: January 2022

Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.
A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA
Authors: Krieger Madeline C , Dutcher H Auguste , Ashford Andrew J , Raghavan Rahul
Published: January 2022

Small RNAs (sRNAs) are important gene regulators in bacteria, but it is unclear how new sRNAs originate and become part of regulatory networks that coordinate bacterial response to environmental stimuli. Using a covariance modeling-based approach, we analyzed the presence of hundreds of sRNAs in more than a thousand genomes across Enterobacterales, a bacterial order with a confluence of factors that allows robust genome-scale sRNA analyses: several well-studied organisms with fairly conserved genome structures, an established phylogeny, and substantial nucleotide diversity within a narrow evolutionary space. We discovered that a majority of sRNAs arose recently, and uncovered protein-coding genes as a potential source from which new sRNAs arise. A detailed investigation of the emergence of OxyS, a peroxide-responding sRNA, revealed that it evolved from a fragment of a peroxidase messenger RNA. Importantly, although it replaced the ancestral peroxidase, OxyS continues to be part of the ancestral peroxide-response regulon, indicating that an sRNA that arises from a protein-coding gene would inherently be part of the parental protein’s regulatory network. This new insight provides a fresh framework for understanding sRNA origin and regulatory integration in bacteria.
Exosomes released from Sertoli cells contribute to the survival of Leydig cells through CCL20 in rats
Authors: Ma Yi , Zhou Yan , Zou Sha-Sha , Sun Yun , Chen Xiang-Feng
Published: January 2022

Reciprocal communication between Sertoli and Leydig cells occurs in the testes; however, the detailed mechanisms involved are not completely understood. Exosomes can communicate within neighboring or distant cells to regulate cell function. Our aim was to determine whether exosomes released from Sertoli cells can regulate the survival of Leydig cells. We found that exosomes released from rat primary Sertoli cells could be internalized by Leydig cells in vitro, and promote the survival of Leydig cells, as assessed by optical density at 450 nm, compared to untreated control (mean ± SD: 0.95 ± 0.04 vs 0.79 ± 0.03, P < 0.05). When the exosomes were injected into the interstitial area of rat testis, they could also be internalized by Leydig cells in vivo. To investigate if exosomes released from Sertoli cells can reach Leydig cells in vivo, exosomes were injected into the efferent duct, from where they entered the interstitial space from seminiferous tubules, which indicated that they may cross the blood–testis barrier (BTB). Further in vitro studies found that exosomes released from Sertoli cells significantly increased CC-chemokine ligand 20 (Ccl20) mRNA (mean ± SD: 2.79 ± 0.08 vs 0.98 ± 0.04, P < 0.01) and protein (mean ± SD: 1.08 ± 0.06 vs 0.53 ± 0.05 ng/ml, P < 0.01) levels in Leydig cells, compared to the untreated Leydig cells. CCL20 promoted the phosphorylation of AKT (protein kinase B) in Leydig cells, compared to untreated control (mean ± SD: 0.074 ± 0.002 vs 0.051 ± 0.002, P < 0.01). In conclusion, our results demonstrated that exosomes released by Sertoli cells may cross the BTB and promote the survival of Leydig cells. The findings may add new evidence for Sertoli–Leydig cell communication.
Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel
Authors: Kolář Michal H , Nagy Gabor , Kunkel John , Vaiana Sara M , Bock Lars V , Grubmüller Helmut
Published: January 2022

The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.
Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds
Authors: Bose Tanaya , Fridkin Gil , Davidovich Chen , Krupkin Miri , Dinger Nikita , Falkovich Alla H , Peleg Yoav , Agmon Ilana , Bashan Anat , Yonath Ada
Published: January 2022

Although the mode of action of the ribosomes, the multi-component universal effective protein-synthesis organelles, has been thoroughly explored, their mere appearance remained elusive. Our earlier comparative structural studies suggested that a universal internal small RNA pocket-like segment called by us the protoribosome, which is still embedded in the contemporary ribosome, is a vestige of the primordial ribosome. Herein, after constructing such pockets, we show using the "fragment reaction" and its analyses by MALDI-TOF and LC–MS mass spectrometry techniques, that several protoribosome constructs are indeed capable of mediating peptide-bond formation. These findings present strong evidence supporting our hypothesis on origin of life and on ribosome's construction, thus suggesting that the protoribosome may be the missing link between the RNA dominated world and the contemporary nucleic acids/proteins life.
Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation
Authors: Simeone Ines , Rubolino Carmela , Noviello Teresa Maria Rosaria , Farinello Diego , Cerulo Luigi , Marzi Matteo Jacopo , Nicassio Francesco
Published: January 2022

It is currently unknown how many RNA transcripts are able to induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD). We developed TDMDfinder, a computational pipeline that identifies ‘high confidence’ TDMD interactions in the Human and Mouse transcriptomes by combining sequence alignment and feature selection approaches. Our predictions suggested that TDMD is widespread, with potentially every miRNA controlled by endogenous targets. We experimentally tested 37 TDMDfinder predictions, of which 17 showed TDMD effects as measured by RT-qPCR and small RNA sequencing, linking the miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families to novel endogenous TDMDs. In some cases, TDMD was found to affect different members of the same miRNA family selectively. Features like complementarity to the miRNA 3′ region, bulge size and hybridization energy appeared to be the main factors determining sensitivity. Computational analyses performed using the multiomic TCGA platform substantiated the involvement of many TDMD transcripts in human cancer and highlighted 36 highly significant interactions, suggesting TDMD as a new potential oncogenic mechanism. In conclusion, TDMDfinder provides the first inventory of bona fide human and mouse TDMDs. Available as a free webtool, TDMDfinder allows users to search for any TDMD interaction of interest by customizing its selection criteria.
NBS1-CtIP–mediated DNA end resection suppresses cGAS binding to micronuclei
Authors: Abdisalaam Salim , Mukherjee Shibani , Bhattacharya Souparno , Kumari Sharda , Sinha Debapriya , Ortega Janice , Li Guo-Min , Sadek Hesham A , Krishnan Sunil , Asaithamby Aroumougame
Published: January 2022

Cyclic guanosine monophosphate–adenosine monophosphate synthase (cGAS) is activated in cells with defective DNA damage repair and signaling (DDR) factors, but a direct role for DDR factors in regulating cGAS activation in response to micronuclear DNA is still poorly understood. Here, we provide novel evidence that Nijmegen breakage syndrome 1 (NBS1) protein, a well-studied DNA double-strand break (DSB) sensor—in coordination with Ataxia Telangiectasia Mutated (ATM), a protein kinase, and Carboxy-terminal binding protein 1 interacting protein (CtIP), a DNA end resection factor—functions as an upstream regulator that prevents cGAS from binding micronuclear DNA. When NBS1 binds to micronuclear DNA via its fork-head–associated domain, it recruits CtIP and ATM via its N- and C-terminal domains, respectively. Subsequently, ATM stabilizes NBS1’s interaction with micronuclear DNA, and CtIP converts DSB ends into single-strand DNA ends; these two key events prevent cGAS from binding micronuclear DNA. Additionally, by using a cGAS tripartite system, we show that cells lacking NBS1 not only recruit cGAS to a major fraction of micronuclear DNA but also activate cGAS in response to these micronuclear DNA. Collectively, our results underscore how NBS1 and its binding partners prevent cGAS from binding micronuclear DNA, in addition to their classical functions in DDR signaling.
The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7
Authors: Maldotti Mara , Lauria Andrea , Anselmi Francesca , Molineris Ivan , Tamburrini Annalaura , Meng Guohua , Polignano Isabelle Laurence , Scrivano Mirko Giuseppe , Campestre Fabiola , Simon Lisa Marie , Rapelli Stefania , Morandi Edoardo , Incarnato Danny , Oliviero Salvatore
Published: January 2022

The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.
Surgical and anatomic factors predict development of leptomeningeal disease in patients with melanoma brain metastases
Authors: Lowe Stephen R , Wang Christopher P , Brisco Amanda , Whiting Junmin , Arrington John , Ahmed Kamran , Yu Michael , Robinson Timothy , Oliver Daniel , Etame Arnold , Tran Nam , Beer Furlan Andre , Sahebjam Solmaz , Mokhtari Sepideh , Piña Yolanda , Macaulay Robert , Forsyth Peter , Vogelbaum Michael A , Liu James K C
Published: January 2022

Background

Leptomeningeal disease (LMD) is a devastating complication of systemic malignancy, of which there is an unclear etiology. The aim of this study is to determine if surgical or anatomic factors can predict LMD in patients with metastatic melanoma.

Methods

A retrospective chart review was performed of 1162 patients treated at single institution for melanoma brain metastases (MBM). Patients with fewer than 3 months follow-up or lacking appropriate imaging were excluded. Demographic information, surgical, and anatomic data were collected.

Results

Eight hundred and twenty-seven patients were included in the final review. On multivariate analysis for the entire cohort, female gender, dural-based and intraventricular metastasis, and tumor bordering CSF spaces were associated with increased risk of LMD. Surgical resection was not significant for risk of LMD. On multivariate analysis of patients who have undergone surgical resection of a metastatic tumor, dural-based and intraventricular metastasis, ventricular entry during surgery, and metastasis in the infratentorial space were associated with increased risk of LMD. On multivariate analysis of patients who did not undergo surgery, chemotherapy after initial diagnosis and metastasis bordering CSF spaces were associated with increased risk of LMD.

Conclusion

In a single-institution cohort of MBM, we found that surgical resection alone did not result in an increased risk of LMD. Anatomical factors such as dural-based and intraventricular metastasis were significant for developing LMD, as well as entry into a CSF space during surgical resection. These data suggest a strong correlation between anatomic location and tumor cell seeding in relation to the development of LMD.
Weldable and closed-loop recyclable monolithic dynamic covalent polymer aerogels
Authors: Zhang Xinhai , Zhao Jun , Liu Kai , Li Guangfeng , Zhao Dong , Zhang Zhaoming , Wan Junjun , Yang Xue , Bai Ruixue , Wang Yongming , Zhang Wei , Yan Xuzhou
Published: January 2022

Owing to their low density, high porosity and unique micro-nanostructures, aerogels are attractive for application in various fields; however, they suffer from shrinkage and/or cracking during preparation, mechanical brittleness, low production efficiency and non-degradation. Herein, we introduce the concept of dynamic covalent polymer chemistry to produce a new class of aerogels—referred to as DCPAs. The resulting lightweight DCPAs have the potential to be prepared on a large scale and feature high porosity (90.7%–91.3%), large degrees of compression (80% strain) and bending (diametral deflection of 30 mm) without any cracks, as well as considerable tensile properties (an elongation with a break at 32.7%). In addition, the DCPAs showcase the emergent characteristics of weldability, repairability, degradability and closed-loop recyclability that are highly desirable for providing versatile material platforms, though hardly achieved by traditional aerogels. Taking advantage of their robust porous structures, we demonstrate the potential of DCPAs for applications in thermal insulation and emulsion separation. These findings reveal that the dynamic covalent bond strategy would be generalized for the production of a new generation of aerogels with customized features for functioning in the field of intelligent and sustainable materials.