bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive atrial fibrillation burden and symptom reduction post-ablation: insights from DECAAF II
Authors: Noujaim Charbel , Assaf Ala , Lim Chanho , Feng Han , Younes Hadi , Mekhael Mario , Chouman Nour , Shamaileh Ghaith , El Hajjar Abdel Hadi , Ayoub Tarek , Isakadze Nino , Chelu Mihail G , Marrouche Nassir , Donnellan Eoin
Published: April 2024

Aims

Traditional atrial fibrillation (AF) recurrence after catheter ablation is reported as a binary outcome. However, a paradigm shift towards a more granular definition, considering arrhythmic or symptomatic burden, is emerging. We hypothesize that ablation reduces AF burden independently of conventional recurrence status in patients with persistent AF, correlating with symptom burden reduction.

Methods and results

Ninety-eight patients with persistent AF from the DECAAF II trial with pre-ablation follow-up were included. Patients recorded daily single-lead electrocardiogram (ECG) strips, defining AF burden as the proportion of AF days among total submitted ECG days. The primary outcome was atrial arrhythmia recurrence. The AF severity scale was administered pre-ablation and at 12 months post-ablation. At follow-up, 69 patients had atrial arrhythmia recurrence and 29 remained in sinus rhythm. These patients were categorized into a recurrence (n = 69) and a no-recurrence group (n = 29). Both groups had similar baseline characteristics, but recurrence patients were older (P = 0.005), had a higher prevalence of hyperlipidaemia (P = 0.007), and had a larger left atrial (LA) volume (P = 0.01). There was a reduction in AF burden in the recurrence group when compared with their pre-ablation burden (65 vs. 15%, P < 0.0001). Utah Stage 4 fibrosis and diabetes predicted less improvement in AF burden. The symptom severity score at 12 months post-ablation was significantly reduced compared with the pre-ablation score in the recurrence group, and there was a significant correlation between the reduction in symptom severity score and the reduction in AF burden (R = 0.39, P = 0.001).

Conclusion

Catheter ablation reduces AF burden, irrespective of arrhythmia recurrence post-procedure. There is a strong correlation between AF burden reduction and symptom improvement post-ablation. Notably, elevated LA fibrosis impedes AF burden decrease following catheter ablation.
Pelagic zone is an evolutionary catalyst, but an ecological dead end, for North American minnows
Authors: Burress Edward D , Hart Pamela B
Published: April 2024

The colonization of a novel geographic area is a classic source of ecological opportunity. Likewise, complex microhabitats are thought to promote biodiversity. We sought to reconcile these two predictions when they are naturally opposing outcomes. We assess the macroevolutionary consequences of an ancestral shift from benthic to pelagic microhabitat zones on rates of speciation and phenotypic evolution in North American minnows. Pelagic species have more similar phenotypes and slower rates of phenotypic evolution, but faster speciation rates, than benthic species. These are likely two independent, opposing responses to specialization along the benthic-pelagic axis, as rates of phenotypic evolution and speciation are not directly correlated. The pelagic zone is more structurally homogenous and offers less ecological opportunity, acting as an ecological dead end for minnows. In contrast, pelagic species may be more mobile and prone to dispersal and subsequent geographic isolation and, consequently, experience elevated instances of allopatric speciation. Microhabitat shifts can have decoupled effects on different dimensions of biodiversity, highlighting the need for nuance when interpreting the macroevolutionary consequences of ecological opportunity.
Building physician wellness into the culture: evaluating a family physician well-being programme using the physician wellness inventory
Authors: Clay Tarin L , Mabachi Natabhona M , Callen Elisabeth F
Published: April 2024

Purpose

Family physicians have a higher incidence of burnout, dissatisfaction, and disengagement compared to other medical specialties. Addressing burnout on the individual and systemic level is important to promoting wellness and preventing deleterious effects on physicians and patients. We used the Physician Wellness Inventory (PWI) to assess the effects of a wellness programme designed to equip family physicians with skills to address burnout.

Methods

The PWI is a fourteen-item 5-point Likert scale broken down into 3 scores; (i) career purpose, (ii) cognitive flexibility, and (iii) distress. The PWI was distributed to a cohort of n = 111 family physician scholars at 3 time points: January 2021, May–June 2021, and October 2021. The response rate was 96.4% at baseline, and 72.1% overall. Demographic information was collected to assess differences. The survey was distributed online through Qualtrics (Provo, UT).

Results

Cognitive Flexibility scores at the endpoint were higher for POC scholars than white scholars (P = 0.024). Distress scores for all groups decreased over time. Female scholars were more nervous, and anxious at the start than male scholars (P = 0.012), which decreased over time (P = 0.022). New career scholars were more likely than later career scholars to be distressed (P = 0.007), but both groups’ distress decreased over time (P = 0.003). Later career scholars’ feelings of being bothered by little interest or pleasure in doing things decreased more than new career scholars (endpoint: P = 0.022; overall: P = 0.023).

Conclusions

The wellness programme shows improvement in PWI scores, indicating the programme content should be evaluated further for system level improvements.
Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution
Authors: Iliopoulou Elisavet , Papadogiannis Vasileios , Tsigenopoulos Costas S , Manousaki Tereza
Published: April 2024

Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts.
On the ∂—-Equation with L2 Estimates on Singular Complex Spaces
Authors: Li Zhenqian , Li Zhi , Zhou Xiangyu
Published: April 2024

In this paper, we present the unsolvability of $\overline \partial $-equation with weighted $L^{2}$ estimates involved curvature terms on any singular normal complex space in general. Moreover, in the non-normal case, we also give a complete description on $L^{2}$-solvability of the $\overline \partial $-equation with weighted $L^{2}$ estimates for plane curve singularities and their variants in the higher dimension.
Rational Points in the Noether-Lefschetz Locus of Moduli Spaces of K3 Surfaces
Authors: Valloni Domenico
Published: April 2024

We give a characterization of rational points lying on the Noether-Lefschetz locus of moduli spaces of K3 surfaces by studying their lifting properties under some natural coverings of the ambient space. We then prove that the Bombieri-Lang conjecture implies non-density statements for the rational points in the Noether-Lefschetz locus, as predicted by a conjecture of Shafarevich.
Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates
Authors: Alvarez-Aponte Zoila I , Govindaraju Alekhya M , Hallberg Zachary F , Nicolas Alexa M , Green Myka A , Mok Kenny C , Fonseca-García Citlali , Coleman-Derr Devin , Brodie Eoin L , Carlson Hans K , Taga Michiko E
Published: April 2024

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
Extracorporeal Life Support Use in Mixed Distributive–Obstructive Shock Following an Electrical Injury: A Case Report
Authors: Blake Eva , Maqsood Hannan A , Dougherty Jacob M , Vercruysse Gary , Wang Stewart C , Hemmila Mark R , Sangji Naveen F
Published: April 2024

Electrical burn injuries can be catastrophic, threatening severe disability or mortality. We present a patient who suffered from electrical shock, requiring bilateral above-knee amputations, right trans-radial amputation, renal replacement therapy, and veno-arterial extracorporeal life support (VA ECLS) therapy. While there exist reports of cases that have demonstrated the potential use of ECLS in burn patients with cardiogenic shock or acute respiratory distress syndrome, this is a unique case of VA ECLS use for an electrical injury patient who developed mixed distributive–obstructive shock secondary to pulmonary embolism and sepsis. Given the wide variety of morbidities that can result from electrical burns, VA ECLS is a promising tool for those who require cardiopulmonary support refractory to traditional measures.
Single-cell RNA sequencing reveals that an imbalance in monocyte subsets rather than changes in gene expression patterns is a feature of postmenopausal osteoporosis
Authors: Tao Lin , Jiang Wen , Li Hao , Wang Xiaochuan , Tian Zixuan , Yang Keda , Zhu Yue
Published: April 2024

The role of monocytes in postmenopausal osteoporosis is widely recognized; however, the mechanisms underlying monocyte reprogramming remain unknown. In this study, single-cell RNA sequencing (scRNA-seq) was conducted on CD14+ bone marrow monocytes obtained from 3 postmenopausal women with normal BMD and 3 women with postmenopausal osteoporosis (PMOP). Monocle2 was used to classify the monocytes into 7 distinct clusters. The proportion of cluster 1 significantly decreased in PMOP patients, while the proportion of cluster 7 increased. Further analysis via GSEA, transcription factor activity analysis, and sc-metabolic analysis revealed significant differences between clusters 1 and 7. Cluster 7 exhibited upregulated pathways associated with inflammation, immunity, and osteoclast differentiation, whereas cluster 1 demonstrated the opposite results. Monocle2, TSCAN, VECTOR, and scVelo data indicated that cluster 1 represented the initial subset and that cluster 7 represents one of the terminal subsets. BayesPrism and ssGSEA were employed to analyze the bulk transcriptome data obtained from the GEO database. The observed alterations in the proportions of 1 and 7 were validated and found to have diagnostic significance. CD16 serves as the marker gene for cluster 7, thus leading to an increased proportion of CD16+ monocytes in women with PMOP. Flow cytometry was used to assess the consistency of outcomes with those of the bioinformatic analysis. Subsequently, an additional scRNA-seq analysis was conducted on bone marrow mononuclear cells obtained from 3 patients with PMOP and 3 postmenopausal women with normal BMD. The differential proportions of cluster 1 and cluster 7 were once again confirmed, with the pathological effect of cluster 7 may attribute to cell–cell communication. The scRNA-seq findings suggest that an imbalance in monocyte subsets is a characteristic feature of PMOP. These findings elucidate the limitations of utilizing bulk transcriptome data for detecting alterations in monocytes, which may influence novel research inquiries.
Pre-Registered Interim Analysis Designs (PRIADs): Increasing the Cost-Effectiveness of Hypothesis Testing
Authors: André Quentin , Reinholtz Nicholas
Published: April 2024

The difficulty of determining how many observations to collect is a source of inefficiency in consumer behavior research. Group sequential designs, which allow researchers to perform interim analyses while data collection is ongoing, could offer a remedy. However, they are scarcely used in consumer behavior research, probably owing to low awareness, perceived complexity, or concerns about the validity of this approach. This article offers a tutorial on group sequential designs and introduces Pre-Registered Interim Analysis Designs (PRIADs): A practical five-step procedure to facilitate the adoption of these designs in marketing. We show that group sequential designs can be easily adopted by marketing researchers, and introduce a companion app to help researchers implement them. We demonstrate multiple benefits of PRIADs for researchers engaged in confirmatory hypothesis testing: They facilitate sample size decisions, allow researchers to achieve a desired level of statistical power with a smaller number of observations, and help conduct more efficient pilot studies. We validate this cost-saving potential through a comprehensive re-analysis of 212 studies published in the Journal of Consumer Research, which shows that using PRIADs would have reduced participant costs by 20–29%. We conclude with a discussion of limitations and possible alternatives to PRIADs.
Assessment of the efficacy of Piper methysticum (Micrembryeae: Piperaceae) as a bioinsecticide, and/or spinosad combined with attractive plant volatiles for a novel lure and kill strategy against Bactrocera tryoni (Diptera: Tephritidae) in laboratory
Authors: Horain Amélie , Leroy Lise , Pöllabauer Léa , Mas Flore , Mille Christian Gilbert
Published: April 2024

The Queensland fruit fly, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is a crop pest of global economic importance because of its wide range of hosts and its invasiveness capacities. To develop a novel integrated and sustainable crop protection, we have investigated the insecticidal properties of different varieties of kava (Piper methysticum [Frost]) extracted by two methods and the attractive effects of six plant volatiles identified from B. tryoni host plants to female, mated or not. We did not identify any significant insecticidal effect of the traditional Pacific kava plant at the tested concentrations. Among mated females, ethyl acetate compared to the no odor control elicited the highest attraction (87%, of which 60% for this odor), while ethyl butyrate was preferred compared with ethyl acetate in dual choice assays. Flies’ preferences for specific odors depended on their mating status and the odor landscape they were confronted with. Combination with the commercial ingestion insecticide (Success 4: spinosad, 480 g/l, Dow AgroSciences, Valbonne, France) with the plant volatiles were tested to detect an increase in mortality related to the addition of an attractant. The 2-heptanone slightly showed a tend to increase the attractiveness of mated females within 4-6 h to the food bait, but the results were not statistically significant after 8 h. Further tests should be performed with other concentrations or mixtures of the identified host plant volatiles to develop a strong lure and kill strategy.
Landscape and prognostic values of lymphocytes in patients with hepatocellular carcinoma undergoing transarterial embolization
Authors: Zhao Rui-dong , Liu Ding-jie , Li Jia-wei , Wang Yong , Lin Jun-hao , Zhang Yi-tian , Li Yong , Zhan Mei-xiao , Yin Zhi-nan , Lu Li-gong , Liu Bing
Published: April 2024

Transarterial embolization, the first-line treatment for hepatocellular carcinoma, does not always lead to promising outcomes in all patients. A better understanding of how the immune lymphocyte changes after transarterial embolization might be the key to improve the efficacy of transarterial embolization. However, there are few studies evaluating immune lymphocytes in transarterial embolization patients. Therefore, we aimed to evaluate the short- and long-term effects of transarterial embolization on lymphocyte subsets in patients with hepatocellular carcinoma to identify those that predict transarterial embolization prognosis. Peripheral blood samples were collected from 44 patients with hepatocellular carcinoma at the following time points: 1 d before the initial transarterial embolization, 3 d after the initial transarterial embolization, and 1 mo after the initial transarterial embolization and subjected to peripheral blood mononuclear cell isolation and flow cytometry. Dynamic changes in 75 lymphocyte subsets were recorded, and their absolute counts were calculated. Tumor assessments were made every 4 to 6 wk via computed tomography or magnetic resonance imaging. Our results revealed that almost all lymphocyte subsets fluctuated 3 d after transarterial embolization, but only Tfh and B cells decreased 1 mo after transarterial embolization. Univariate and multivariate Cox regression showed that high levels of Th2 and conventional killer Vδ2 cells were associated with longer progressive-free survival after transarterial embolization. Longer overall survival after transarterial embolization was associated with high levels of Th17 and viral infection–specific Vδ1 cells and low levels of immature natural killer cells. In conclusion, transarterial embolization has a dynamic influence on the status of lymphocytes. Accordingly, several lymphocyte subsets can be used as prognostic markers for transarterial embolization.
The association of health-care contact days with physical function and survival in CCTG/AGITG CO.17
Authors: Gupta Arjun , O’Callaghan Christopher J , Zhu Liting , Jonker Derek J , Wong Ralph P W , Colwell Bruce , Moore Malcolm J , Karapetis Christos S , Tebbutt Niall C , Shapiro Jeremy D , Tu Dongsheng , Booth Christopher M
Published: April 2024

Introduction

Although contact days—days with health-care contact outside home—are increasingly adopted as a measure of time toxicity and treatment burden, they could also serve as a surrogate of treatment-related harm. We sought to assess the association between contact days and patient-reported outcomes and the prognostic ability of contact days.

Methods

We conducted a secondary analysis of CO.17 that evaluated cetuximab vs supportive care in patients with advanced colorectal cancer. CO.17 collected European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire C30 instrument data. We assessed the association between number of contact days in a window and changes in physical function and global health status and the association between number of contact days in the first 4 weeks with overall survival.

Results

There was a negative association between the number of contact days and change in physical function (per each additional contact day: at 4 weeks, 1.50-point decrease; 8 weeks, 1.06-point decrease; P < .0001 for both) but not with global health status. This negative association was seen in patients receiving cetuximab but not supportive care. More contact days in the first 4 weeks was associated with worse overall survival for all participants and patients receiving cetuximab (per each additional contact day: all participants, adjusted hazard ratio [HR] = 1.07, 95% confidence interval [CI] = 1.05 to 1.10; and cetuximab, adjusted HR = 1.08, 95% CI = 1.05 to 1.11; P < .0001 for both).

Conclusions

In this secondary analysis of a clinical trial, more contact days early in the course were associated with declines in physical function and worse survival in all participants and in participants receiving cancer-directed treatment.

Trial registration

ClinicalTrials.gov number, NCT00079066.
Systematic investigation of genetically determined plasma and urinary metabolites to discover potential interventional targets for colorectal cancer
Authors: Sun Jing , Zhao Jianhui , Zhou Siyun , Li Xinxuan , Li Tengfei , Wang Lijuan , Yuan Shuai , Chen Dong , Law Philip J , Larsson Susanna C , Farrington Susan M , Houlston Richard S , Dunlop Malcolm G , Theodoratou Evropi , Li Xue
Published: April 2024

Background

We aimed to identify plasma and urinary metabolites related to colorectal cancer (CRC) risk and elucidate their mediator role in the associations between modifiable risk factors and CRC.

Methods

Metabolite quantitative trait loci were derived from 2 published metabolomics genome-wide association studies, and summary-level data were extracted for 651 plasma metabolites and 208 urinary metabolites. Genetic associations with CRC were obtained from a large-scale genome-wide association study meta-analysis (100 204 cases, 154 587 controls) and the FinnGen cohort (4957 cases, 304 197 controls). Mendelian randomization and colocalization analyses were performed to evaluate the causal roles of metabolites in CRC. Druggability evaluation was employed to prioritize potential therapeutic targets. Multivariable Mendelian randomization and mediation estimation were conducted to elucidate the mediating effects of metabolites on the associations between modifiable risk factors and CRC.

Results

The study identified 30 plasma metabolites and 4 urinary metabolites for CRC. Plasma sphingomyelin and urinary lactose, which were positively associated with CRC risk, could be modulated by drug interventions (ie, olipudase alfa, tilactase). Thirteen modifiable risk factors were associated with 9 metabolites, and 8 of these modifiable risk factors were associated with CRC risk. These 9 metabolites mediated the effect of modifiable risk factors (Actinobacteria, body mass index, waist to hip ratio, fasting insulin, smoking initiation) on CRC.

Conclusion

This study identified key metabolite biomarkers associated with CRC and elucidated their mediator roles in the associations between modifiable risk factors and CRC. These findings provide new insights into the etiology and potential therapeutic targets for CRC and the etiological pathways of modifiable environmental factors with CRC.
Burdens, bribes, and bureaucrats: the political economy of petty corruption and administrative burdens
Authors: Nieto-Morales Fernando , Peeters Rik , Lotta Gabriela
Published: April 2024

Bribery and other forms of petty corruption typically arise in bureaucratic encounters and are a common element of the everyday experience of the state in many countries, particularly in places with weak institutions. This type of corruption is especially troublesome because it creates direct costs for citizens when accessing services and benefits to which they are formally entitled. However, only a few studies deal with how situational attributes of bureaucratic interactions create incentives for citizens to pay bribes and opportunities for street-level bureaucrats to demand them. We contribute to filling this gap by providing evidence that administrative burdens increase the chance of bribery. We do so by analyzing the prevalence of (attempted) bribery in more than 63,000 interactions across 20 different types of bureaucratic encounters, ranging from paying taxes to accessing essential services, using multilevel logistic regression analysis. Our study contributes to understanding the possible consequences of administrative burdens and the factors conducive to petty corruption in specific citizen–state interactions.
How to use CRISPR/Cas9 in plants: from target site selection to DNA repair
Authors: Přibylová Adéla , Fischer Lukáš
Published: April 2024

A tool for precise, target-specific, efficient, and affordable genome editing is a dream for many researchers, from those who conduct basic research to those who use it for applied research. Since 2012, we have tool that almost fulfils such requirements; it is based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems. However, even CRISPR/Cas has limitations and obstacles that might surprise its users. In this review, we focus on the most frequently used variant, CRISPR/Cas9 from Streptococcus pyogenes, and highlight key factors affecting its mutagenesis outcomes: (i) factors affecting the CRISPR/Cas9 activity, such as the effect of the target sequence, chromatin state, or Cas9 variant, and how long it remains in place after cleavage; and (ii) factors affecting the follow-up DNA repair mechanisms including mostly the cell type and cell cycle phase, but also, for example, the type of DNA ends produced by Cas9 cleavage (blunt/staggered). Moreover, we note some differences between using CRISPR/Cas9 in plants, yeasts, and animals, as knowledge from individual kingdoms is not fully transferable. Awareness of these factors can increase the likelihood of achieving the expected results of plant genome editing, for which we provide detailed guidelines.
Time-course analysis system for leaf feeding marks reveals effects of Arabidopsis trichomes on insect herbivore feeding behavior
Authors: Sotta Naoyuki , Fujiwara Toru
Published: April 2024

Bioassay with an insect herbivore is a common approach to studying plant defense. While measuring insect growth rate as a negative indicator of plant defense levels is simple and straightforward, analysing more detailed feeding behavior parameters of insects, such as feeding rates, leaf area consumed per feeding event, intervals between feeding events, and spatio-temporal patterns of feeding sites on leaves, is more informative. However, such observations are generally time consuming and labor-intensive. Here, we provide a semi-automated system for quantifying feeding behavior parameters of insects feeding on plant leaves. Automated photo scanners record the time-course development of feeding marks on leaves. An image analysis pipeline processes the scanned images and extracts leaf area. By analysing changes in leaf area over time, it detects insect feeding events and calculates the leaf area consumed during each feeding event, providing quantitative parameters of the feeding behavior of insects. In addition, it visualizes spatio-temporal changes in feeding sites, providing a measure of the complex behavior of insects on leaves. Using this analysis pipeline, we demonstrate that Arabidopsis trichomes reduce insect feeding rate, but not feeding duration or intervals between feeding events. Our image acquisition system requires only a photo scanner and a laptop computer and does not require any specialized equipment. The analysis software is provided as an ImageJ macro and R package and is available at no cost. Taken together, our work provides a scalable method for quantitative assessment of the feeding behavior of insects on leaves, facilitating understanding of plant defense mechanisms.
A large population of neutron star low-mass X-ray binaries with long outburst recurrence time?
Authors: Meyer-Hofmeister E , Cheng H Q , Liu B F
Published: April 2024

Low-mass X-ray binaries (LMXBs) with neutron stars show quite different features that depend on the rate of mass transfer from the donor star. With a high transfer rate, the Z sources are in a persistent soft spectral state, and with a moderate transfer rate the transient Atoll sources have outburst cycles like the black hole X-ray binaries. The observations document very long outburst recurrence times for quite a number of sources. We follow with our computations the evolution of the accretion disc until the onset of the ionization instability. For sources with a low mass transfer rate, the accumulation of matter in the disc is essentially reduced due to the continuous evaporation of matter from the disc to the coronal flow. Different mass transfer rates result in nearly the same amount of matter accumulated for the outburst, which means that the outburst properties are similar for sources with short outburst cycles and sources with long outburst cycles, contrary to some expectations. Then, for systems with long recurrence time, less sources will be detected and the total population of LMXBs could be larger than it appears. This would relieve the apparent problem that the observed number of LMXBs as progenitors of millisecond pulsars (MSPs) is too small compared to the number of MSPs. Concerning the few quasi-persistent sources with year-long soft states, we argue that these states are not outbursts, but quasi-stationary hot states as in Z sources.
IGM damping wing constraints on the tail end of reionization from the enlarged XQR-30 sample
Authors: Greig B , Mesinger A , Bañados E , Becker G D , Bosman S E I , Chen H , Davies F B , D’Odorico V , Eilers A -C , Gallerani S , Haehnelt M G , Keating L , Lai S , Qin Y , Ryan-Weber E , Satyavolu S , Wang F , Yang J , Zhu Y
Published: April 2024

The attenuation of Lyα photons by neutral hydrogen in the intergalactic medium (IGM) at z ≳ 5 continues to be a powerful probe for studying the epoch of reionization. Given a framework to estimate the intrinsic (true) Lyα emission of high-z sources, one can infer the ionization state of the IGM during reionization. In this work, we use the enlarged XQR-30 sample of 42 high-resolution and high signal-to-noise quasar spectra between $5.8\lesssim \, z\lesssim \, 6.6$ obtained with VLT/X-shooter to place constraints on the IGM neutral fraction. This is achieved using our existing Bayesian QSO reconstruction framework which accounts for uncertainties such as the: (i) posterior distribution of predicted intrinsic Lyα emission profiles (obtained via covariance matrix reconstruction of the Lyα and N v emission lines from unattenuated high-ionization emission line profiles; C iv, Si iv  + O iv], and C iii]) and (ii) distribution of ionized regions within the IGM using synthetic damping wing profiles drawn from a 1.63 Gpc3 reionization simulation. Following careful quality control, we used 23 of the 42 available QSOs to obtain constraints/limits on the IGM neutral fraction during the tail-end of reionization. Our median and 68th percentile constraints on the IGM neutral fraction are: $0.20\substack{+0.14 -0.12}$ and $0.29\substack{+0.14 -0.13}$ at z = 6.15 and 6.35. Further, we also report 68th percentile upper limits of $\bar{x}_{\mathrm{H\, {\small I}}{}} \lt 0.21$, 0.20, 0.21, and 0.18 at z = 5.8, 5.95, 6.05, and 6.55. These results imply reionization is still ongoing at $5.8\lesssim \, z\lesssim \, 6.55$, consistent with previous results from XQR-30 (dark fraction and Lyα forest) along with other observational probes considered in the literature.
Improving and extending non-Poissonian distributions for satellite galaxies sampling in HOD: applications to eBOSS ELGs
Authors: Vos-Ginés Bernhard , Avila Santiago , Gonzalez-Perez Violeta , Yepes Gustavo
Published: April 2024

Halo occupation distribution (HOD) models help us to connect observations and theory, by assigning galaxies to dark matter haloes. In this work, we study one of the components of HOD models: the probability distribution function (PDF), which is used to assign a discrete number of galaxies to a halo, given a mean number of galaxies. For satellite galaxies, the most commonly used PDF is a Poisson Distribution. PDFs with super-Poisson variances have also been studied, allowing for continuous values of variances. This has not been the case for sub-Poisson variances, for which only the nearest integer distribution, with a single variance, has been used in the past. In this work, we propose a distribution based on the binomial one, which provides continuous sub-Poisson variances. We have generated mock galaxy catalogues from two dark-matter only simulations, unit and outerrim, with HOD models assuming different PDFs. We show that the variance of the PDF for satellite galaxies affects the one-halo term of the projected correlation function, and the count-in-cells (CIC) one point statistics. We fit the clustering of eBOSS emission line galaxies, finding results consistent with the literature, when we only vary the parameter controlling the PDF variance and the fraction of satellites. Using a mock catalogue as a reference, we have also included both the clustering and CIC to constrain the parameters of the HOD model. CIC can provide strong constraints to the PDF variance of satellite galaxies.
A covariant formulation for cosmological radiative transfer of the 21-cm line
Authors: Chan Jennifer Y H , Han Qin , Wu Kinwah , McEwen Jason D
Published: April 2024

The 21-cm hyperfine line of neutral hydrogen is a useful tool to probe the conditions of the Universe during the Dark Ages, Cosmic Dawn, and the Epoch of Reionization. In most of the current calculations, the 21-cm line signals at given frequencies are computed, using an integrated line-of-sight line opacity, with the correction for cosmological expansion. These calculations have not fully captured the line and continuum interactions in the radiative transfer, in response to evolution of the radiation field and the variations of thermal and dynamic properties of the line-of-sight medium. We construct a covariant formulation for the radiative transfer of the 21-cm line and derive the cosmological 21-cm line radiative transfer (C21LRT) equation. The formulation properly accounts for local emission and absorption processes and the interaction between the line and continuum when the radiation propagates across the expanding Universe to the present observer. Our C21LRT calculations show that methods simply summing the line optical depth could lead to error of 5  per cent in the 21-cm signals for redshift z ∼ 12–35 and of $\gt 10~{{\ \rm per\ cent}}$ for redshift z ≲ 8. Proper covariant radiative transfer is therefore necessary for producing correct theoretical templates for extracting information of the structural evolution of the Universe through the Epoch of Reionization from the 21-cm tomographic data.
The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees
Authors: Lin Qianying , Goldberg Emma E , Leitner Thomas , Molina-París Carmen , King Aaron A , Romero-Severson Ethan O
Published: April 2024

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.
Comprehensive profiling of L1 retrotransposons in mouse
Authors: Zhang Xuanming , Celic Ivana , Mitchell Hannah , Stuckert Sam , Vedula Lalitha , Han Jeffrey S
Published: April 2024

L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here, we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200 000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single-cell level in vivo.
RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET
Authors: Banerjee Tithi , Rothenberg Eli , Belasco Joel G
Published: April 2024

The ability of obstacles in cellular transcripts to protect downstream but not upstream sites en masse from attack by RNase E has prompted the hypothesis that this mRNA-degrading endonuclease may scan 5′-monophosphorylated RNA linearly for cleavage sites, starting at the 5′ end. However, despite its proposed regulatory importance, the migration of RNase E on RNA has never been directly observed. We have now used single-molecule FRET to monitor the dynamics of this homotetrameric enzyme on RNA. Our findings reveal that RNase E slides along unpaired regions of RNA without consuming a molecular source of energy such as ATP and that its forward progress can be impeded when it encounters a large structural discontinuity. This movement, which is bidirectional, occurs in discrete steps of variable length and requires an RNA ligand much longer than needed to occupy a single RNase E subunit. These results indicate that RNase E scans for cleavage sites by one-dimensional diffusion and suggest a possible molecular mechanism.
Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control
Authors: Chen Katharine Y , Park Heungwon , Subramaniam Arvind Rasi
Published: April 2024

Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
High-density generation of spatial transcriptomics with STAGE
Authors: Li Shang , Gai Kuo , Dong Kangning , Zhang Yiyang , Zhang Shihua
Published: April 2024

Spatial transcriptome technologies have enabled the measurement of gene expression while maintaining spatial location information for deciphering the spatial heterogeneity of biological tissues. However, they were heavily limited by the sparse spatial resolution and low data quality. To this end, we develop a spatial location-supervised auto-encoder generator STAGE for generating high-density spatial transcriptomics (ST). STAGE takes advantage of the customized supervised auto-encoder to learn continuous patterns of gene expression in space and generate high-resolution expressions for given spatial coordinates. STAGE can improve the low quality of spatial transcriptome data and smooth the generated manifold of gene expression through the de-noising function on the latent codes of the auto-encoder. Applications to four ST datasets, STAGE has shown better recovery performance for down-sampled data than existing methods, revealed significant tissue structure specificity, and enabled robust identification of spatially informative genes and patterns. In addition, STAGE can be extended to three-dimensional (3D) stacked ST data for generating gene expression at any position between consecutive sections for shaping high-density 3D ST configuration.
Awake pediatric brain-MRI: a fast multi-sequence scan augmented with motion compensated single-shot 2D acquisitions
Authors: van Niekerk Adam , Svoboda Jan , Aspelin Åsa , Sprenger Tim , Rydén Henric , Norbeck Ola , Avventi Enrico , Johansson Katarina , Rygaard Natalie , Lindberg Peter , Wickström Ronny , Delgado Anna Falk , Skare Stefan
Published: April 2024

Background

Magnetic resonance imaging (MRI) is susceptible to motion artifacts, a particular challenge in pediatric imaging. External motion tracking devices and navigator techniques have been previously explored, but challenges persist necessitating sedation.

Purpose

To establish a new awake brain-MRI exam tolerated by children with diagnostic quality images.

Materials and Methods

Participants were prospectively recruited and investigated using an in-house developed multi-sequence scan called NeuroMix that produces T1-weighted, T2-weighted, T2*-weighted, T2-FLAIR, and diffusion-weighted images in under 3 minutes. Additionally, a self-created motion tracking device was attached to participants' foreheads to perform prospective motion correction (PMC) on 2D single-shot sequences that produce higher resolution images of the same contrasts as NeuroMix.

Three neuroradiologists scored the completed series for artifacts. The effects of age group (<5 vs ≥5 years) and sequence type (NeuroMix vs PMC) were evaluated with a Chi2-test.

Results

Of the 64 participants recruited (mean age 6.7 years [2.7 standard deviation]) 58 completed their examination. Head motion recorded during PMC sequences revealed prevalent superior-inferior displacements [25% (67/293) exceeding 13.2 mm], and chin-up/down rotations [25% (67/293) exceeding 13.7°]. Sequence redundancy through NeuroMix and PMC scans resulted in 93% (54/58) of completed examinations having all series essential for producing an MRI-report rated as artifact-free, and therefore a report of high confidence in 84% (54/64) of participants. 22% (13/58) of completed exam reports could have been written using NeuroMix alone, the remaining required PMC- T2-weighted or T2-FLAIR sequences.

Conclusion

This protocol reliably provided diagnostic quality images and reports with high radiologist confidence and could reduce the use of procedure sedation in children.
Longitudinal study of patients with anti-SAE antibody-positive dermatomyositis: a multicenter cohort study in China
Authors: Zhang Yingfang , Liu Lei , Duan Xinwang , Pi Hui , Jiang Lili , Li Jiang , Wang Guochun , Shu Xiaoming
Published: April 2024

Objectives

To describe the longitudinal study and long-term prognosis of a multicentre large inception cohort of patients with anti-SAE positive DM.

Methods

We retrospectively recruited patients with anti-SAE+DM in four tertiary referral centres from China between March 2005 and December 2022. Long-term survival analysis was performed on the enrolled patients. The Myositis Damage Index and Cutaneous Disease Area and Severity Index were used to evaluate the degree of different organ damage and the extent of skin rashes. Longitudinal CT patterns were analysed. Phenotypes were characterized using unsupervised cluster analysis.

Results

All-cause death occurred in 10.5% (4/38) of all patients, in which three patients succumbed to malignancies at 13, 18 and 36 months. Most patients had favourable long-term outcomes, 35.3% of them were in drug-free remission. Skin rashes showed significant improvement evaluated by Cutaneous Disease Area and Severity Index with time. However, damage to different systems was observed in 70.6% of the surviving patients using the Myositis Damage Index, which mainly consisted of skin damage, accounting for 47.1%. Nine patients with anti-SAE+DM-associated interstitial lung disease underwent repeat CT showed marked radiological improvement at 6 months or being stable after 12 months. In further, different characteristics and outcomes were also showed in three clusters identified by unsupervised analysis.

Conclusions

Anti-SAE+DM is characterized with a lower mortality rate and the development of malignancies being the primary cause of death. Patients who survived showed notable cutaneous damage, while the interstitial lung disease tends to stabilize. Clusters identified with unsupervised analysis could assist physicians in identifying a higher risk of mortality.