bluuebunny/crossref_metadata_2025 huggingface dataset:
BannMI deciphers potential n-to-1 information transduction in signaling pathways to unravel message of intrinsic apoptosis
Authors: Schmidt Bettina , Sers Christine , Klein Nadja
Published: November 2023

Motivation

Cell fate decisions, such as apoptosis or proliferation, are communicated via signaling pathways. The pathways are heavily intertwined and often consist of sequential interaction of proteins (kinases). Information integration takes place on the protein level via n-to-1 interactions. A state-of-the-art procedure to quantify information flow (edges) between signaling proteins (nodes) is network inference. However, edge weight calculation typically refers to 1-to-1 interactions only and relies on mean protein phosphorylation levels instead of single cell distributions. Information theoretic measures such as the mutual information (MI) have the potential to overcome these shortcomings but are still rarely used.

Results

This work proposes a Bayesian nearest neighbor-based MI estimator (BannMI) to quantify n-to-1 kinase dependency in signaling pathways. BannMI outperforms the state-of-the-art MI estimator on protein-like data in terms of mean squared error and Pearson correlation. Using BannMI, we analyze apoptotic signaling in phosphoproteomic cancerous and noncancerous breast cell line data. Our work provides evidence for cooperative signaling of several kinases in programmed cell death and identifies a potential key role of the mitogen-activated protein kinase p38.

Availability and implementation

Source code and applications are available at: https://github.com/zuiop11/nn_info and can be downloaded via Pip as Python package: nn-info.
Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics
Authors: Eren Kazım Kıvanç , Çınar Esra , Karakurt Hamza U , Özgür Arzucan
Published: November 2023

Motivation

Technical errors in sequencing or bioinformatics steps and difficulties in alignment at some genomic sites result in false positive (FP) variants. Filtering based on quality metrics is a common method for detecting FP variants, but setting thresholds to reduce FP rates may reduce the number of true positive variants by overlooking the more complex relationships between features. The goal of this study is to develop a machine learning-based model for identifying FPs that integrates quality metrics with genomic features and with the feature interpretability property to provide insights into model results.

Results

We propose a random forest-based model that utilizes genomic features to improve identification of FPs. Further examination of the features shows that the newly introduced features have an important impact on the prediction of variants misclassified by VEF, GATK-CNN, and GARFIELD, recently introduced FP detection systems. We applied cost-sensitive training to avoid errors in misclassification of true variants and developed a model that provides a robust mechanism against misclassification of true variants while increasing the prediction rate of FP variants. This model can be easily re-trained when factors such as experimental protocols might alter the FP distribution. In addition, it has an interpretability mechanism that allows users to understand the impact of features on the model’s predictions.

Availability and implementation

The software implementation can be found at https://github.com/ideateknoloji/FPDetect.
ROCCO: a robust method for detection of open chromatin via convex optimization
Authors: Hamilton Nolan H , Furey Terrence S
Published: November 2023

Motivation

Analysis of open chromatin regions across multiple samples from two or more distinct conditions can determine altered gene regulatory patterns associated with biological phenotypes and complex traits. The ATAC-seq assay allows for tractable genome-wide open chromatin profiling of large numbers of samples. Stable, broadly applicable genomic annotations of open chromatin regions are not available. Thus, most studies first identify open regions using peak calling methods for each sample independently. These are then heuristically combined to obtain a consensus peak set. Reconciling sample-specific peak results post hoc from larger cohorts is particularly challenging, and informative spatial features specific to open chromatin signals are not leveraged effectively.

Results

We propose a novel method, ROCCO, that determines consensus open chromatin regions across multiple samples simultaneously. ROCCO employs robust summary statistics and solves a constrained optimization problem formulated to account for both enrichment and spatial dependence of open chromatin signal data. We show this formulation admits attractive theoretical and conceptual properties as well as superior empirical performance compared to current methodology.

Availability and implementation

Source code, documentation, and usage demos for ROCCO are available on GitHub at: https://github.com/nolan-h-hamilton/ROCCO. ROCCO can also be installed as a stand-alone binary utility using pip/PyPI.
An accurate spectrophotometric method for chitosan quantification
Authors: González-Davis Oscar , Betanzo Itandehui , Vazquez-Duhalt Rafael
Published: November 2023

Chitosan is a biopolymer obtained from chitin, one of the most abundant biopolymers in nature. Numerous applications of chitosan are well known in the biomedical, environmental, and industrial fields, and the potential applications are considerable. This work reports a new spectrophotometric method to determine chitosan concentration accurately. The method is based on the deamination of chitosan by nitrite in acidic conditions, followed by a carbohydrate determination by the anthrone reagent.
Liraglutide, a GLP-1 agonist, as a new adjunct treatment in Hailey–Hailey disease: a case report
Authors: Barry Rory , Murray Gregg , Hellen Rebecca , Ní Raghallaigh Síona
Published: November 2023

Hailey–Hailey disease (HHD) is a rare, heritable blistering disorder with a predilection for intertriginous areas, and is caused by mutations in the ATP2C1 gene. We present a case of a 60-year-old woman who has had poorly controlled HHD for 45 years, despite various treatments. Her HHD has become very well controlled since commencing liraglutide, for newly diagnosed type 2 diabetes, with loss of HHD disease control on discontinuation.
High-frequency transcranial alternating current stimulation matching individual frequency of somatosensory evoked high-frequency oscillations can modulate the somatosensory system through thalamocortical pathway
Authors: Cruciani Alessandro , Pellegrino Giovanni , Todisco Antonio , Motolese Francesco , Sferruzzi Marco , Norata Davide , Santoro Francesca , Musumeci Gabriella , Rossi Mariagrazia , Pilato Fabio , Di Lazzaro Vincenzo , Capone Fioravante
Published: November 2023

tACS (transcranial alternating current stimulation) is a technique for modulating brain activity through electrical current. Its effects depend on cortical entrainment, which is most effective when transcranial alternating current stimulation matches the brain’s natural rhythm. High-frequency oscillations produced by external stimuli are useful for studying the somatosensory pathway. Our study aims to explore transcranial alternating current stimulation’s impact on the somatosensory system when synchronized with individual high-frequency oscillation frequencies. We conducted a randomized, sham-controlled study with 14 healthy participants. The study had three phases: Individualized transcranial alternating current stimulation (matching the individual’s high-frequency oscillation rhythm), Standard transcranial alternating current stimulation (600 Hz), and sham stimulation. We measured early and late HFO components after median nerve electrical stimulation at three time points: before (T0), immediately after (T1), and 10 min after transcranial alternating current stimulation (T2). Compared to Sham and Standard stimulation Individualized transcranial alternating current stimulation significantly enhanced high-frequency oscillations, especially the early component, immediately after stimulation and for at least 15 min. No other effects were observed for other high-frequency oscillation measures. In summary, our study provides initial evidence that transcranial alternating current stimulation synchronized with an individual’s high-frequency oscillation frequency can precisely and time-specifically modulate thalamocortical activity. These insights may pave the way for innovative, personalized neuromodulation methods for the somatosensory system.
Treatment Failure in a UK Malaria Patient Harboring Genetically Variant Plasmodium falciparum From Uganda With Reduced In Vitro Susceptibility to Artemisinin and Lumefantrine
Authors: van Schalkwyk Donelly A , Pratt Sade , Nolder Debbie , Stewart Lindsay B , Liddy Helen , Muwanguzi-Karugaba Julian , Beshir Khalid B , Britten Dawn , Victory Emma , Rogers Claire , Millard James , Brown Michael , Nabarro Laura E , Taylor Andrew , Young Bernadette C , Chiodini Peter L , Sutherland Colin J
Published: November 2023

Background

Recent cases of clinical failure in malaria patients in the United Kingdom (UK) treated with artemether-lumefantrine have implications for malaria chemotherapy worldwide.

Methods

Parasites were isolated from an index case of confirmed Plasmodium falciparum treatment failure after standard treatment, and from comparable travel-acquired UK malaria cases. Drug susceptibility in vitro and genotypes at 6 resistance-associated loci were determined for all parasite isolates and compared with clinical outcomes for each parasite donor.

Results

A traveler, who returned to the UK from Uganda in 2022 with Plasmodium falciparum malaria, twice failed treatment with full courses of artemether-lumefantrine. Parasites from the patient exhibited significantly reduced susceptibility to artemisinin (ring-stage survival, 17.3% [95% confidence interval {CI}, 13.6%–21.1%]; P < .0001) and lumefantrine (effective concentration preventing 50% of growth = 259.4 nM [95% CI, 130.6–388.2 nM]; P = .001). Parasite genotyping identified an allele of pfk13 encoding both the A675V variant in the Pfk13 propeller domain and a novel L145V nonpropeller variant. In vitro susceptibility testing of 6 other P. falciparum lines of Ugandan origin identified reduced susceptibility to artemisinin and lumefantrine in 1 additional line, also from a 2022 treatment failure case. These parasites did not harbor a pfk13 propeller domain variant but rather the novel nonpropeller variant T349I. Variant alleles of pfubp1, pfap2mu, and pfcoronin were also identified among the 7 parasite lines.

Conclusions

We confirm, in a documented case of artemether-lumefantrine treatment failure imported from Uganda, the presence of pfk13 mutations encoding L145V and A675V. Parasites with reduced susceptibility to both artemisinin and lumefantrine may be emerging in Uganda.
Transcatheter aortic valve replacement using the two-step inflation technique and the kissing-balloon technique for a patient with a protruding stent in the left main coronary artery: a case report
Authors: Ohi Takuma , Watanabe Naoki , Takagi Kensuke , Morishima Itsuro
Published: November 2023

Background

When performing transcatheter aortic valve replacement (TAVR) for a patient with a protruding stent in the coronary arteries, there is a risk of stent deformation and coronary occlusion. However, safe and optimal methods have not been established.

Case summary

An 87-year-old woman with a protruding stent in the left main coronary artery (LMCA) underwent TAVR. The two-step inflation and kissing-balloon techniques were performed to optimize the transcatheter heart valve (THV) and to avoid LMCA stent deformation. The THV was implemented with minimal aortic regurgitation and no deformation of the stent in the LMCA.

Discussion

This was the first case report of TAVR, performed in a patient with a protruding stent in the coronary arteries, using the kissing-balloon technique and the two-step inflation technique. The combination of these two techniques was the optimal method for THV implantation without stent deformation in coronary arteries.
Maintaining or increasing cardiorespiratory fitness is associated with reduced hospital admission rate
Authors: Griffin Frida , Ekblom-Bak Elin , Arvidsson Daniel , Paulsson Sofia , Börjesson Mats
Published: November 2023

Aims

The aim of this study was to investigate the association between change in cardiorespiratory fitness (CRF) and cardiovascular disease (CVD)-related and all-cause hospital admission and explore if the association varies dependently on prior admission, baseline CRF, sex, and age.

Methods and results

A total of 91 140 adult participants (41.5% women) with two examinations from occupational health profile assessments between 1986 and 2019 were included (mean of 3.2 years between examinations). Cardiorespiratory fitness was assessed as maximal oxygen consumption and estimated through a submaximal cycle test. Cardiorespiratory fitness change was defined as annual percentage change in relative CRF (mL/min/kg) and further divided into ‘decliners’ (≤1%), ‘maintainers’ (−1% to 1%), and ‘increasers’ (>1%). Hospital admissions were followed over a mean of 7 years. Natural cubic splines and Cox proportional hazards model were applied. Additionally, prevented fraction for the population was calculated. Increase in CRF was associated with a lower risk of CVD [hazard ratio (HR) = 0.99] and all-cause hospital admission (HR = 0.99), after multilevel adjustment for confounders and change in smoking, diet, and stress. Compared with a decline, maintenance of CRF was associated with 9% and 7% lower risk of CVD and all-cause admission, respectively. Increase in CRF reduced the risk by 13% and 11% and, for individuals with prior admission, by 20% and 14%. The burden of CVD and all-cause admission was 6% and 5% lower than if the whole cohort had declined CRF, with large potential cost savings.

Conclusion

Efforts to maintain or improve CRF should be included in disease-preventive strategies, regardless of change in other lifestyle-related risk factors. Preventing the age-associated decline in CRF can lessen healthcare utilization and costs.
Comparison of automated subcutaneous defibrillator screening between different pacing sites in cardiac pacing device carriers
Authors: Molina-Lerma Manuel , Cabrera-Borrego Eva , Rivera-Lopez Ricardo , Sánchez-Millán Pablo , Peña Mellado Jesús , Arriaga Jiménez Antonio , Álvarez Miguel
Published: November 2023

Aims

The compatibility of cardiac pacing with the presence of a subcutaneous implantable cardioverter-defibrillator (S-ICD) has been investigated, but S-ICD screening test results have not been compared among different pacing sites. The objective was to compare S-ICD screening results among different cardiac pacing sites and to assess the electrocardiographic predictors of success.

Methods and results

This prospective single-centre study conducted automated S-ICD screening in 102 carriers of cardiac pacing devices in conduction system (CSP), biventricular (BVP), right ventricular outflow tract (RVOT), or right ventricular apex (RVA) pacing sites. The study included 102 patients: 40 with CSP (20 left bundle pacing and 20 His bundle pacing), 21 with BVP, and 20 and 21 with RVOT and RVA pacing, respectively. The percentage of positive screenings was significantly higher for CSP (97.5%) than for the other patient groups (BVP 71.4%, RVOT 70%, and RVA 19%). In multivariate analysis, positive screening was associated with a narrower QRS (OR 0.95 [0.92–0.98] P = 0.001) and higher R/T ratio in precordial leads (1.76 [1.18–2.61]).

Conclusion

A higher S-ICD eligibility rate of cardiac pacing device carriers was obtained in CSP than in conventional pacing (RVA or RVOT) or BVP. The presence of narrower paced QRS width and paced corrected QT interval and of higher R/T ratio in precordial and limb leads are electrocardiographic predictors of a positive response to screening.
When and how can we predict adaptive responses to climate change?
Authors: Urban Mark C , Swaegers Janne , Stoks Robby , Snook Rhonda R , Otto Sarah P , Noble Daniel W A , Moiron Maria , Hällfors Maria H , Gómez-Llano Miguel , Fior Simone , Cote Julien , Charmantier Anne , Bestion Elvire , Berger David , Baur Julian , Alexander Jake M , Saastamoinen Marjo , Edelsparre Allan H , Teplitsky Celine
Published: November 2023

Predicting if, when, and how populations can adapt to climate change constitutes one of the greatest challenges in science today. Here, we build from contributions to the special issue on evolutionary adaptation to climate change, a survey of its authors, and recent literature to explore the limits and opportunities for predicting adaptive responses to climate change. We outline what might be predictable now, in the future, and perhaps never even with our best efforts. More accurate predictions are expected for traits characterized by a well-understood mapping between genotypes and phenotypes and traits experiencing strong, direct selection due to climate change. A meta-analysis revealed an overall moderate trait heritability and evolvability in studies performed under future climate conditions but indicated no significant change between current and future climate conditions, suggesting neither more nor less genetic variation for adapting to future climates. Predicting population persistence and evolutionary rescue remains uncertain, especially for the many species without sufficient ecological data. Still, when polled, authors contributing to this special issue were relatively optimistic about our ability to predict future evolutionary responses to climate change. Predictions will improve as we expand efforts to understand diverse organisms, their ecology, and their adaptive potential. Advancements in functional genomic resources, especially their extension to non-model species and the union of evolutionary experiments and “omics,” should also enhance predictions. Although predicting evolutionary responses to climate change remains challenging, even small advances will reduce the substantial uncertainties surrounding future evolutionary responses to climate change.
Substantial variation in species ages among vertebrate clades
Authors: Pie Marcio R , Caron Fernanda S
Published: November 2023

Ecological and evolutionary studies traditionally assume that species are comparable units of biodiversity. However, not only this assumption is rarely tested, but also there have been few attempts even to assess variation in most emergent, species-level traits and their corresponding underlying mechanisms. One such trait is species age, here defined as the time since the most recent common ancestor between a given species and its sister lineage. In this study, we demonstrate that different terrestrial vertebrate clades vary considerably in the age of their constituent species. In particular, species ages were youngest in mammals and birds as opposed to squamates and amphibians, although considerable variation was found within those clades as well. Sensitivity analyses showed that these results are unaffected by phylogenetic uncertainty or incomplete taxonomic sampling. Interestingly, there was little geographical correspondence in mean species age across taxa, as well as with temperature and precipitation stability over the past 21 000 years. We discuss candidate mechanisms that might explain differences in species ages among clades, and explore the implications of these findings in relation to recent advances in age-dependent speciation and extinction models of diversification.
A targeted approach to enrich host-associated bacteria for metagenomic sequencing
Authors: Dungan Ashley M , Tandon Kshitij , Jameson Vanta , Gotze Cecilie Ravn , Blackall Linda L , van Oppen Madeleine J H
Published: November 2023

Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67–91 M reads per sample, 55%–90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the ‘Endozoicomonas’ population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.
A Nonpharmacologic Treatment for Anxiety in Older Adults Based on Cognitive-Motor Training With Response-Generated Feedback
Authors: Lucia Stefania , Forte Roberta , Boccacci Luca , Grimandi Luca , Bittner Marion , Aydin Merve , Trentin Chiara , Tocci Nicoletta , Di Russo Francesco
Published: November 2023

Objectives

Simultaneous combinations of cognitive and physical exercises (cognitive-motor dual-task training [CMDT]) are more effective than physical and cognitive training alone in counteracting the decline of older adults and promoting physical and psychological well-being. The CMDT can be particularly effective in improving cognitive and functional abilities. Here, we validated an innovative nonpharmacologic intervention for anxiety and general well-being in older people by combining CMDT and response-generated feedback (RGF) principles. As outcomes, anxiety, cognitive functions, and functional mobility were evaluated. In addition, electroencephalographic methods were employed to investigate the neural basis of the possible intervention effects.

Methods

Thirty older adults were divided into an experimental group trained using a CMDT + RGF protocol and a control group using the CMDT only. The CMDT + RGF consisted of the simultaneous execution of whole-body exercises, cognitive tasks that were realized using interactive devices, and continuous feedback on every response.

Results

Results showed decreased anxiety and increased response speed in the experimental group, and both groups improved their functional ability and response accuracy after the intervention. According to electroencephalographic results, both groups showed an increase in the bilateral prefrontal cortex anticipatory activity, but the experimental group also showed a further increase in the left prefrontal cortex and in the premotor areas anticipatory functions.

Discussion

This study confirms the effectiveness of the proposed intervention on anxiety by adopting a nonpharmacology treatment that could affect public and individual health costs by proposing an alternative approach to expensive medications and psychotherapy and could significantly improve older adults’ quality of life.
Predicting streaming potential in reactive media: the role of pore geometry during dissolution and precipitation
Authors: Soldi M , Guarracino L , Jougnot D
Published: November 2023

Dissolution and precipitation processes modify the structure of the porous media at microscale which significantly affects the macroscopic properties of the media. These variations in the pore geometry result in changes in the hydraulic properties that control the groundwater flow, and also modify the electrokinetic properties associated to the displacement of electrical charges carried by the flow which originates the streaming potential. Under the hypothesis of a uniform dissolution or precipitation of the pores and based on the effective excess charge density approach, we present a physically based theoretical model for estimating the effective excess charge density as a function of time. The model is based on the assumption that the pore structure can be represented by an ensemble of capillary tubes with a smooth periodic variation of their radius and a fractal pore size distribution. The analytical expressions obtained to describe the effective excess charge density depend on the chemical parameters of the fluid and the petrophysical properties of the medium. In addition, the periodic variations assumed in the pore geometry represent a more realistic description of a porous medium than considering the pores as constant radii capillaries. These irregularities allow us to include the hysteresis phenomenon in the electrokinetic properties. The expressions of the proposed model have been tested with experimental data consisting of sets of effective excess charge density-effective saturation, permeability-effective saturation, porosity-time and permeability-time values. In all cases, the model is able to satisfactorily reproduce the behaviour of the data.
DAS-N2N: machine learning distributed acoustic sensing (DAS) signal denoising without clean data
Authors: Lapins S , Butcher A , Kendall J-M , Hudson T S , Stork A L , Werner M J , Gunning J , Brisbourne A M
Published: November 2023

This paper presents a weakly supervised machine learning method, which we call DAS-N2N, for suppressing strong random noise in distributed acoustic sensing (DAS) recordings. DAS-N2N requires no manually produced labels (i.e. pre-determined examples of clean event signals or sections of noise) for training and aims to map random noise processes to a chosen summary statistic, such as the distribution mean, median or mode, whilst retaining the true underlying signal. This is achieved by splicing (joining together) two fibres hosted within a single optical cable, recording two noisy copies of the same underlying signal corrupted by different independent realizations of random observational noise. A deep learning model can then be trained using only these two noisy copies of the data to produce a near fully denoised copy. Once the model is trained, only noisy data from a single fibre is required. Using a data set from a DAS array deployed on the surface of the Rutford Ice Stream in Antarctica, we demonstrate that DAS-N2N greatly suppresses incoherent noise and enhances the signal-to-noise ratios (SNR) of natural microseismic icequake events. We further show that this approach is inherently more efficient and effective than standard stop/pass band and white noise (e.g. Wiener) filtering routines, as well as a comparable self-supervised learning method based on masking individual DAS channels. Our preferred model for this task is lightweight, processing 30 s of data recorded at a sampling frequency of 1000 Hz over 985 channels (approximately 1 km of fibre) in <1 s. Due to the high noise levels in DAS recordings, efficient data-driven denoising methods, such as DAS-N2N, will prove essential to time-critical DAS earthquake detection, particularly in the case of microseismic monitoring.
Multichannel coherence migration grid search (MCMgs) in locating microseismic events recorded by a surface array
Authors: Parastatidis E , Pytharouli S , Stankovic L , Stankovic V , Shi P , Hildyard M W
Published: November 2023

Microseismic monitoring has been used in geo-energy related activities, such as shale-gas exploitation, mining, deep geothermal exploitation, geotechnical and structural engineering, for detecting and locating fractures, rock failures and micro-earthquakes. The success of microseismic monitoring depends on reliable detection and location of the recorded microseismicity. Multichannel coherence migration (MCM) is a detection and location waveform migration-based approach which does not require phase picking, identification and association and performs well on noisy data. Its caveat is a high computational cost, which impedes its application of MCM on large data sets or for real-time monitoring. To address this issue, we propose an improved approach, the multichannel coherence migration grid search (MCMgs), by introducing an adaptive grid optimization technique. Based on results from synthetic and real data, we show that MCMgs reduces the computation time up to 64 times. In addition, MCMgs generates multiple maximum coherence values with various grid sizes instead of a single (maximum) coherence value that links to a single gridpoint and size, thus resulting in more accurate locations. Our simulation results on different deployment geometries demonstrate that MCMgs is effective even with a small number of recordings available—a minimum of seven. We conduct a sensitivity analysis to assess how the detectability of events is affected by the spatial arrangement of the deployed monitoring array. If a limited number of seismometers are available for deployment, our analysis favours a patch array deployment geometry. We show that 12 seismometers deployed at a patch array geometry can have similar detection and localization capability as a large rectangular array of more than 100 seismometers but at a much lower computational and deployment cost.
Vacuolar proteomic analysis reveals tonoplast transporters for accumulation of citric acid and sugar in citrus fruit
Authors: Mao Zuolin , Wang Yue , Li Mengdi , Zhang Shuhang , Zhao Zeqi , Xu Qiang , Liu Ji-Hong , Li Chunlong
Published: November 2023

Vacuole largely dictates the fruit taste and flavor, as most of the sugars and organic acids are stored in the vacuoles of the fruit. However, difficulties associated with vacuole separation severely hinder identification and characterization of vacuolar proteins in fruit species. In this study, we established an effective approach for separating vacuoles and successfully purified vacuolar protein from six types of citrus fruit with varying patterns of sugar and organic acid contents. By using label-free LC–MS/MS proteomic analysis, 1443 core proteins were found to be associated with the essential functions of vacuole in citrus fruit. Correlation analysis of metabolite concentration with proteomic data revealed a transporter system for the accumulation of organic acid and soluble sugars in citrus. Furthermore, we characterized the physiological roles of selected key tonoplast transporters, ABCG15, Dict2.1, TMT2, and STP7 in the accumulation of citric acid and sugars. These findings provide a novel perspective and practical solution for investigating the transporters underlying the formation of citrus taste and flavor.
Semilinear optimal control with Dirac measures
Authors: Otárola Enrique
Published: November 2023

The purpose of this work is to study an optimal control problem for a semilinear elliptic partial differential equation with a linear combination of Dirac measures as a forcing term; the control variable corresponds to the amplitude of such singular sources. We analyze the existence of optimal solutions and derive first- and, necessary and sufficient, second-order optimality conditions. We develop a solution technique that discretizes the state and adjoint equations with continuous piecewise linear finite elements; the control variable is already discrete. We analyze the convergence properties of discretizations and obtain, in two dimensions, an a priori error estimate for the underlying approximation of an optimal control variable.
The Zoo of Opers and Dualities
Authors: Koroteev Peter , Zeitlin Anton M
Published: November 2023

We investigate various spaces of $SL(r+1)$-opers and their deformations. For each type of such opers, we study the quantum/classical duality, which relates quantum integrable spin chains with classical solvable many body systems. In this context, quantum/classical dualities serve as an interplay between two different coordinate systems on the space of opers. We also establish correspondences between the underlying oper spaces, which recently had multiple incarnations in symplectic duality and bispectral duality.
Current diagnosis and treatment of salivary gland-type tumors of the lung
Authors: Horio Yoshitsugu , Kuroda Hiroaki , Masago Katsuhiro , Matsushita Hirokazu , Sasaki Eiichi , Fujiwara Yutaka
Published: November 2023

Salivary gland-type tumors of the lung are thought to originate from the submucosal exocrine glands of the large airways. Due to their rare occurrence, reports of their study are limited to small-scale or case reports. Therefore, daily clinical practices often require a search for previous reports. In the last 20 years, several genetic rearrangements have been identified, such as MYB::NF1B rearrangements in adenoid cystic carcinoma, CRTC1::MAML2 rearrangements in mucoepidermoid carcinoma, EWSR1::ATF1 rearrangements in hyalinizing clear cell carcinoma and rearrangements of the EWSR1 locus or FUS (TLS) locus in myoepithelioma and myoepithelial carcinoma. These molecular alterations have been useful in diagnosing these tumors, although they have not yet been linked to molecularly targeted therapies. The morphologic, immunophenotypic, and molecular characteristics of these tumors are similar to those of their counterparts of extrapulmonary origin, so clinical and radiologic differential diagnosis is required to distinguish between primary and metastatic disease of other primary sites. However, these molecular alterations can be useful in differentiating them from other primary lung cancer histologic types. The management of these tumors requires broad knowledge of the latest diagnostics, surgery, radiotherapy, bronchoscopic interventions, chemotherapy, immunotherapy as well as therapeutic agents in development, including molecularly targeted agents. This review provides a comprehensive overview of the current diagnosis and treatment of pulmonary salivary gland tumors, with a focus on adenoid cystic carcinoma and mucoepidermoid carcinoma, which are the two most common subtypes.
Comprehensive X-ray and multiwavelength study of ULXs in NGC 1566
Authors: Allak Sinan
Published: November 2023

This paper presents a comprehensive X-ray and multiwavelength study of ultraluminous X-ray sources (ULXs) in NGC 1566 using archival Chandra, Swift/XRT, JWST, and HST observations. The main results are, first, from the hardness ratio diagram, where spectral state transitions from hard to soft as seen in typical Galactic high-mass X-ray binaries for ULX-3 were observed. Secondly, a new transient ULX candidate (ULX-4) was identified, reaching a peak luminosity of ∼1040 erg s−1. Thirdly, the optical and NIR (near-infrared) counterparts of the ULXs were searched from the precise astrometric calculations. For ULX-1 and ULX-2, evidence was found that the observed NIR emission is due to the circumbinary disc/dust disrupted by X-rays. Lastly, the optical observations suggest that the possible donor star of ULX-3 is a B-type supergiant. In the case of ULX-4, the multiwavelength properties are not clear since many sources are detected within the astrometric error radius.
Revised ephemeris and orbital period derivative of the supersoft X-ray source CAL 87 based on 34 yr of observations
Authors: Stecchini P E , Jablonski F , Diaz M P , D’Amico F , Oliveira A S , Palivanas N , Saito R K
Published: November 2023

In this study, we present an analysis of over 34 yr of observational data from CAL 87, an eclipsing supersoft X-ray source. The primary aim of our study, which combines previously analysed measurements as well as unexplored publicly available data sets, is to examine the orbital period evolution of CAL 87. After meticulously and consistently determining the eclipse timings, we constructed an O − C (observed minus calculated) diagram using a total of 38 data points. Our results provide confirmation of a positive derivative in the system’s orbital period, with a determined value of $\dot{P}=+\, 8.18\pm 1.46\times 10^{-11}$ s s−1. We observe a noticeable jitter in the eclipse timings and additionally identify a systematic delay in the X-ray eclipses compared to those observed in longer wavelengths. We discuss the interplay of the pertinent factors that could contribute to a positive period derivative and the inherent variability in the eclipses.
The centroid speed as a characteristic of the group speed of solar coronal fast magnetoacoustic wave trains
Authors: Kolotkov Dmitrii Y , Nakariakov Valery M , Cloesen Maximilien
Published: November 2023

The highly filamented nature of the coronal plasma significantly influences dynamic processes in the corona such as magnetohydrodynamic waves and oscillations. Fast magnetoacoustic waves, guided by coronal plasma non-uniformities, exhibit strong geometric dispersion, forming quasi-periodic fast-propagating (QFP) wave trains. QFP wave trains are observed in extreme-ultraviolet imaging data and indirectly in microwaves and low-frequency radio, aiding in understanding the magnetic connectivity, energy, and mass transport in the corona. However, measuring the field-aligned group speed of QFP wave trains, as a key parameter for seismological analysis, is challenging due to strong dispersion and associated rapid evolution of the wave train envelope. We demonstrate that the group speed of QFP wave trains formed in plane low-β coronal plasma non-uniformities can be assessed through the propagation of the wave train’s effective centre of mass, referred to as the wave train’s centroid speed. This centroid speed, as a potential observable, is shown empirically to correspond to the group speed of the most energetic Fourier harmonic in the wave train. The centroid speed is found to be almost insensitive to the waveguide density contrast with the ambient corona, and to vary with the steepness of the transverse density profile. The discrepancy between the centroid speed as the group speed measure and the phase speed at the corresponding wavelength is shown to reach 70 per cent, which is crucial for the energy flux estimation and interpretation of observations.
Unravelling the dust attenuation scaling relations and their evolution
Authors: Maheson Gabriel , Maiolino Roberto , Curti Mirko , Sanders Ryan , Tacchella Sandro , Sandles Lester
Published: November 2023

We explore the dependence of dust attenuation, as traced by the $\rm H_{\alpha }/\rm H_{\beta }$ Balmer decrement, on galactic properties by using a large sample of Sloan Digital Sky Survey spectra. We use both partial correlation coefficients and random forest analysis to distinguish those galactic parameters that directly and primarily drive dust attenuation in galaxies, from parameters that are only indirectly correlated through secondary dependencies. We find that, once galactic inclination is controlled for, dust attenuation depends primarily on stellar mass, followed by metallicity and velocity dispersion. Once the dependence on these quantities is taken into account, there is no dependence on the star formation rate. While the dependence on stellar mass and metallicity was expected based on simple analytical equations for the interstellar medium, the dependence on velocity dispersion was not predicted, and we discuss possible scenarios to explain it. We identify a projection of this multidimensional parameters space which minimizes the dispersion in terms of the Balmer decrement and which encapsulates the primary and secondary dependences of the Balmer decrement into a single parameter defined as the reduced mass μ = log M⋆ + 3.67[O/H] + 2.96log (σv/100 km s−1). We show that the dependence of the Balmer decrement on this single parameter also holds at high redshift, suggesting that the processes regulating dust production and distribution do not change significantly through cosmic epochs at least out to z ∼ 2.
The intrinsic X-ray luminosity distribution of an optically selected SDSS quasar population
Authors: Rankine Amy L , Aird James , Ruiz Angel , Georgakakis Antonis
Published: November 2023

In active galactic nuclei, the relationship between UV and X-ray luminosity is well studied (often characterised by αox) but often with heterogeneous samples. We have parametrized the intrinsic distribution of X-ray luminosity, LX, for the optically selected sample of SDSS quasars in the Stripe 82 and XXL fields across redshifts 0.5–3.5. We make use of the available XMM observations and a custom pipeline to produce Bayesian sensitivity curves that are used to derive the intrinsic X-ray distribution in a hierarchical Bayesian framework. We find that the X-ray luminosity distribution is well described by a Gaussian function in log10 LX space with a mean that is dependent on the monochromatic 2500 Å UV luminosity, L2500. We also observe some redshift dependence of the distribution. The mean of the LX distribution increases with redshift while the width decreases. This weak but significant redshift dependence leads to L2500–LX and L2500–αox relations that evolve with redshift, and we produce a redshift- and L2500-dependent αox equation. Neither black hole mass nor Eddington ratio appear to be potential drivers of the redshift evolution.
Modelling the spectra of the kilonova AT2017gfo – II. Beyond the photospheric epochs
Authors: Gillanders J H , Sim S A , Smartt S J , Goriely S , Bauswein A
Published: November 2023

Binary neutron star mergers are the first confirmed site of element nucleosynthesis by the rapid neutron-capture process (r-process). The kilonova AT2017gfo is the only electromagnetic counterpart of a neutron star merger spectroscopically observed. We analyse the entire spectral sequence of AT2017gfo (from merger to +10.4 d) and identify seven emission-like features. We confirm that the prominent 1.08 $\mu{\text{m}}$ feature can be explained by the Sr ii near-infrared triplet evolving from a P-Cygni profile through to pure emission. We calculate the expected strength of the [Sr ii] doublet and show that its absence requires highly clumped ejecta. Near-infrared features at 1.58 and 2.07 $\mu {\text{m}}$ emerge after three days and become more prominent as the spectra evolve. We model these as optically thick P-Cygni profiles and alternatively as pure emission features (with FWHM ≃ 35 600 ± 6600 km s−1) and favour the latter interpretation. The profile of the strong 2.07 $\mu {\text{m}}$ emission feature is best reproduced with two lines, centred at 2.059 and 2.135 $\mu {\text{m}}$. We search for candidate ions for all prominent features in the spectra. Strong, permitted transitions of La iii, Ce iii, Gd iii, Ra ii, and Ac i are plausible candidates for the emission features. If any of these features are produced by intrinsically weak, forbidden transitions, we highlight candidate ions spanning the three r-process peaks. The second r-process peak elements Te and I have plausible matches to multiple features. We highlight the need for more detailed and quantitative atomic line transition data.
Photoevaporation obfuscates the distinction between wind and viscous angular momentum transport in protoplanetary discs
Authors: Coleman Gavin A L , Mroueh Joseph K , Haworth Thomas J
Published: November 2023

How protoplanetary discs evolve remains an unanswered question. Competing theories of viscosity and magnetohydrodynamic disc winds have been put forward as the drivers of angular momentum transport in protoplanetary discs. These two models predict distinct differences in the disc mass, radius, and accretion rates over time, that could be used to distinguish them. However that expectation is built on models that do not include another important process – photoevaporation, both internally by the host star and externally by neighbouring stars. In this work we produce numerical models of protoplanetary discs including viscosity, magnetohydrodynamic disc winds, and internal and external photoevaporation. We find that even weak levels of external photoevaporation can significantly affect the evolution of protoplanetary discs, influencing the observable features such as disc radii, that might otherwise distinguish between viscous and wind driven discs. Including internal photoevaporation further suppresses differences in evolution between viscous and wind driven discs. This makes it much more difficult than previously anticipated, to use observations of nearby star forming regions to determine whether discs are viscous or wind driven. Interestingly we find that evolved protoplanetary discs in intermediate FUV environments may be the best cases for differentiating whether they evolve through viscosity or magnetohydrodynamic disc winds. Ultimately this work demonstrates the importance of understanding what are the key evolutionary processes and including as many of those as possible when exploring the evolution of protoplanetary discs.
Narrow absorption line outflow in Seyfert 1 galaxy J1429+4518: outflow’s distance from the central source and its energetics
Authors: Dehghanian M , Arav N , Byun D , Walker G , Sharma M
Published: November 2023

In the Hubble Space Telescope/Cosmic Origins Spectrograph spectrum of the Seyfert 1 galaxy 2MASX J14292507+4518318, we have identified a narrow absorption line outflow system with a velocity of −151 km s−1. This outflow exhibits absorption troughs from the resonance states of ions like C iv, N v, S iv, and Si ii, as well as excited states from C ii* and Si ii*. Our investigation of the outflow involved measuring ionic column densities and conducting photoionization analysis. These allow the total column density of the outflow to be estimated as log NH = 19.84 cm−2, its ionization parameter to be log UH = −2.0, and its electron number density to be log ne = 2.75 cm−3. These measurements enabled us to determine the mass-loss rate and the kinetic luminosity of the outflow system to be $\dot{M}$ = 0.22 $\mathrm{ M}_{\odot } \, \mathrm{ yr}^{-1}$ and $\log \dot{E_{\mathrm{ K}}}$ = 39.3 erg s−1, respectively. We have also measured the location of the outflow system to be at ∼275 pc from the central source. This outflow does not contribute to the active galactic nucleus (AGN) feedback processes due to the low ratio of the outflow’s kinetic luminosity to the AGN’s Eddington luminosity ($\dot{E_{\mathrm{ K}}}/{L_{\mathrm{ Edd}}}\approx 0.00025 {{\, \rm per\, cent}}$). This outflow is remarkably similar to the two bipolar lobe outflows observed in the Milky Way by XMM–Newton and Chandra.