bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clonal integration systemically regulates leaf microstructure ofBouteloua dactyloidesinterconnected ramets to better adapt to different levels of simulated insect herbivory
Authors: Chai Xuxu , Sun Xiaoling , Cui Xinyi , Johnson Paul G , Fu Zhihui 
Published: December 2022

AbstractStolon connection of clonal plants can translocate resources and signalling molecules between interconnected ramets to enhance resistance. Plants are well known to enhance leaf anatomical structure and vein density to respond to insect herbivory. Herbivory signalling molecules are transferred through vascular system to alert distant undamaged leaves, which is called systemic defence induction. Here, we investigated how clonal integration modulates leaf vasculature and anatomical structure of Bouteloua dactyloides ramets to cope with different levels of simulated herbivory. Ramet pairs were subject to six treatments, daughter ramets were exposed to three defoliation levels (0 %, 40 % or 80 % leaf removal) and their stolon connections to mother ramets were either severed or kept intact. Local 40 % defoliation increased vein density and adaxial/abaxial cuticle thickness, decreased leaf width and areolar area of daughter ramets. However, such effects of 80 % defoliation were much smaller. Compared with remote 40 % defoliation, remote 80 % defoliation increased leaf width and areolar area and decreased vein density of interconnected undefoliated mother ramets. Without simulated herbivory, stolon connection negatively affected most leaf microstructural traits of both ramets except from denser veins of mother ramets and more bundle sheath cells of daughter ramets. The negative effect of stolon connection on leaf mechanical structures of daughter ramets was ameliorated in the 40 % defoliation treatment, but not in the 80 % defoliation treatment. Stolon connection increased vein density and decreased areolar area of daughter ramets in the 40 % defoliation treatment. In contrast, stolon connection increased areolar area and decreased bundle sheath cell number of 80 % defoliated daughter ramets. Defoliation signals were transmitted from younger ramets to older ramets to change their leaf biomechanical structure. Clonal integration can adjust leaf microstructure of younger ramets according to the degree of herbivory stress, especially leaf vasculature.
Sex differences in the predictability of risk-taking behavior
Authors: Brand Jack A , Henry Jason , Melo Gabriela C , Wlodkowic Donald , Wong Bob B M , Martin Jake M 
Published: December 2022

Abstract
Recent research has found that individuals often vary in how consistently they express their behavior over time (i.e., behavioral predictability) and suggested that these individual differences may be heritable. However, little is known about the intrinsic factors that drive variation in the predictability of behavior. Indeed, whether variation in behavioral predictability is sex-specific is not clear. This is important, as behavioral predictability has been associated with vulnerability to predation, suggesting that the predictability of behavioral traits may have key fitness implications. We investigated whether male and female eastern mosquitofish (Gambusia holbrooki) differed in the predictability of their risk-taking behavior. Specifically, over a total of 954 behavioral trials, we repeatedly measured risk-taking behavior with three commonly used assays—refuge-use, thigmotaxis, and foraging latency. We predicted that there would be consistent sex differences in both mean-level risk-taking behavior and behavioral predictability across the assays. We found that risk-taking behavior was repeatable within each assay, and that some individuals were consistently bolder than others across all three assays. There were also consistent sex differences in mean-level risk-taking behavior, with males being bolder across all three assays compared to females. In contrast, both the magnitude and direction of sex differences in behavioral predictability were assay-specific. Taken together, these results highlight that behavioral predictability may be independent from underlying mean-level behavioral traits and suggest that males and females may differentially adjust the consistency of their risk-taking behavior in response to subtle changes in environmental conditions.
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs
Authors: Moen Marcus T , Johnston Iain G 
Published: December 2022

Abstract

Motivation
The evolution of bacterial drug resistance and other features in biology, the progression of cancer and other diseases and a wide range of broader questions can often be viewed as the sequential stochastic acquisition of binary traits (e.g. genetic changes, symptoms or characters). Using potentially noisy or incomplete data to learn the sequences by which such traits are acquired is a problem of general interest. The problem is complicated for large numbers of traits, which may, individually or synergistically, influence the probability of further acquisitions both positively and negatively. Hypercubic inference approaches, based on hidden Markov models on a hypercubic transition network, address these complications, but previous Bayesian instances can consume substantial time for converged results, limiting their practical use.

Results
Here, we introduce HyperHMM, an adapted Baum–Welch (expectation–maximization) algorithm for hypercubic inference with resampling to quantify uncertainty, and show that it allows orders-of-magnitude faster inference while making few practical sacrifices compared to previous hypercubic inference approaches. We show that HyperHMM allows any combination of traits to exert arbitrary positive or negative influence on the acquisition of other traits, relaxing a common limitation of only independent trait influences. We apply this approach to synthetic and biological datasets and discuss its more general application in learning evolutionary and progressive pathways.

Availability and implementation
Code for inference and visualization, and data for example cases, is freely available at https://github.com/StochasticBiology/hypercube-hmm.

Supplementary information
Supplementary data are available at Bioinformatics online.
Benchmarking and integration of methods for deconvoluting spatial transcriptomic data
Authors: Yan Lulu , Sun Xiaoqiang 
Published: December 2022

Abstract

Motivation
The rapid development of spatial transcriptomics (ST) approaches has provided new insights into understanding tissue architecture and function. However, the gene expressions measured at a spot may contain contributions from multiple cells due to the low-resolution of current ST technologies. Although many computational methods have been developed to disentangle discrete cell types from spatial mixtures, the community lacks a thorough evaluation of the performance of those deconvolution methods.

Results
Here, we present a comprehensive benchmarking of 14 deconvolution methods on four datasets. Furthermore, we investigate the robustness of different methods to sequencing depth, spot size and the choice of normalization. Moreover, we propose a new ensemble learning-based deconvolution method (EnDecon) by integrating multiple individual methods for more accurate deconvolution. The major new findings include: (i) cell2loction, RCTD and spatialDWLS are more accurate than other ST deconvolution methods, based on the evaluation of three metrics: RMSE, PCC and JSD; (ii) cell2location and spatialDWLS are more robust to the variation of sequencing depth than RCTD; (iii) the accuracy of the existing methods tends to decrease as the spot size becomes smaller; (iv) most deconvolution methods perform best when they normalize ST data using the method described in their original papers; and (v) the integrative method, EnDecon, could achieve more accurate ST deconvolution. Our study provides valuable information and guideline for practically applying ST deconvolution tools and developing new and more effective methods.

Availability and implementation
The benchmarking pipeline is available at https://github.com/SunXQlab/ST-deconvoulution. An R package for EnDecon is available at https://github.com/SunXQlab/EnDecon.

Supplementary information
Supplementary data are available at Bioinformatics online.
Long-term survival in patients with node-positive breast cancer who undergo sentinel lymph node biopsy alone after neoadjuvant chemotherapy: meta-analysis
Authors: Keelan Stephen , Boland Michael R , Ryan Éanna J , Moran Laura R , Davey Matthew G , Lloyd Angus J , Elwahab Sami , Hill Arnold D K 
Published: December 2022

AbstractBackgroundSentinel lymph node biopsy (SLNB) after neoadjuvant chemotherapy (NACT) in patients with breast cancer who are initially node-positive but convert to clinically/radiologically node-negative remains controversial. The primary aim was to assess pooled 5-year disease-free (DFS) and overall (OS) survival for patients who are initially node-positive but have a negative SLNB after NACT, and do not proceed to axillary lymph node dissection (ALND).MethodsThe study was performed using PRISMA guidelines. A systematic literature search of relevant databases was conducted. The Der Simonian–Laird and Cochran–Mantel–Haenszel methods were used to calculate weighted pooled estimates for OS and DFS for this group compared with patients who had NACT and proceeded to ALND after a negative or positive SLNB.ResultsSeven studies involving 915 patients who had a negative SLNB after NACT were included. Pooled estimates of 5-year DFS and OS in patients with a negative SLNB after NACT were 86 (95 per cent c.i. 82.1 to 90.3) and 93.1 (87.8 to 97.0) per cent respectively. Patients with a positive SLNB who underwent ALND had reduced 5-year DFS (OR 0.49, 95 per cent c.i. 0.35 to 0.69; P &lt; 0.001) and OS (OR 0.41, 0.16 to 1.02; P = 0.06) compared with those who had a negative SLNB after NACT. There were no differences in DFS for patients who had a negative SLNB only compared with those undergoing ALND with a pCR (OR 1.65, 0.71 to 3.79; P = 0.24).ConclusionPatients who are initially node-positive and who achieve a complete clinical/radiological axillary response after NACT with a subsequent negative SLNB have high rates of DFS and OS after 5 years. Patients with residual disease have significantly reduced DFS and further axillary treatment may still be warranted.
Sleep and seizure risk in epilepsy: bed and wake times are more important than sleep duration
Authors: Stirling Rachel E , Hidajat Cindy M , Grayden David B , D’Souza Wendyl J , Naim-Feil Jodie , Dell Katrina L , Schneider Logan D , Nurse Ewan , Freestone Dean , Cook Mark J , Karoly Philippa J 
Published: December 2022

Abstract
Sleep duration, sleep deprivation and the sleep–wake cycle are thought to play an important role in the generation of epileptic activity and may also influence seizure risk. Hence, people diagnosed with epilepsy are commonly asked to maintain consistent sleep routines. However, emerging evidence paints a more nuanced picture of the relationship between seizures and sleep, with bidirectional effects between changes in sleep and seizure risk in addition to modulation by sleep stages and transitions between stages. We conducted a longitudinal study investigating sleep parameters and self-reported seizure occurrence in an ambulatory at-home setting using mobile and wearable monitoring.
Sixty subjects wore a Fitbit smartwatch for at least 28 days while reporting their seizure activity in a mobile app. Multiple sleep features were investigated, including duration, oversleep and undersleep, and sleep onset and offset times. Sleep features in participants with epilepsy were compared to a large (n = 37 921) representative population of Fitbit users, each with 28 days of data. For participants with at least 10 seizure days (n = 34), sleep features were analysed for significant changes prior to seizure days.
A total of 4956 reported seizures (mean = 83, standard deviation = 130) and 30 485 recorded sleep nights (mean = 508, standard deviation = 445) were included in the study. There was a trend for participants with epilepsy to sleep longer than the general population, although this difference was not significant. Just 5 of 34 participants showed a significant difference in sleep duration the night before seizure days compared to seizure-free days. However, 14 of 34 subjects showed significant differences between their sleep onset (bed) and/or offset (wake) times before seizure occurrence. In contrast to previous studies, the current study found undersleeping was associated with a marginal 2% decrease in seizure risk in the following 48 h (P &lt; 0.01). Nocturnal seizures were associated with both significantly longer sleep durations and increased risk of a seizure occurring in the following 48 h.
Overall, the presented results demonstrated that day-to-day changes in sleep duration had a minimal effect on reported seizures, while patient-specific changes in bed and wake times were more important for identifying seizure risk the following day. Nocturnal seizures were the only factor that significantly increased the risk of seizures in the following 48 h on a group level. Wearables can be used to identify these sleep–seizure relationships and guide clinical recommendations or improve seizure forecasting algorithms.
Patient selection, peri-procedural management, and ablation techniques for catheter ablation of atrial fibrillation: an EHRA survey
Authors: Iliodromitis Konstantinos , Lenarczyk Radoslaw , Scherr Daniel , Conte Giulio , Farkowski Michal M , Marin Francisco , Garcia-Seara Javier , Simovic Stefan , Potpara Tatjana 
Published: December 2022

AbstractCatheter ablation (CA) of atrial fibrillation (AF) is the therapy of choice for the maintenance of sinus rhythm in patients with symptomatic AF. Time towards interventional treatment and peri-procedural management of patients undergoing AF ablation may vary in daily practice. The scope of this European Heart Rhythm Association (EHRA) survey was to report the current clinical practice regarding the management of patients undergoing AF ablation and physician’s adherence to the European Society of Cardiology Guidelines and the EHRA/HRS/ECAS expert consensus statement on the CA for AF. This physician-based survey was conducted among EHRA members, using an internet-based questionnaire developed by the EHRA Scientific Initiatives Committee. A total of 258 physicians participated in the survey. In patients with paroxysmal or persistent AF, 42 and 9% of the physicians would routinely perform AF ablation as first-line therapy respectively, whereas 71% of physicians would consider ablation as first-line therapy in patients with symptomatic AF and left ventricular ejection fraction &lt;35%. Only 14% of the respondents manage cardiovascular risk factors in patients referred for CA using a dedicated AF risk factor management programme. Radiofrequency CA is the preferred technology for first-time AF (56%), followed by cryo-balloon CA (40%). This EHRA survey demonstrated a considerable variation in the management of patients undergoing AF ablation in routine practice and deviations between guideline recommendations and clinical practice.
Subjective Well-Being and Active Life Expectancy in Japan: Evidence From a Longitudinal Study
Authors: Minagawa Yuka , Saito Yasuhiko 
Published: December 2022

AbstractBackground and ObjectivesExisting research has suggested that older adults in Japan enjoy phenomenal physical health status, but they have poor subjective well-being (SWB). Limited empirical evidence exists, however, on how physical health and SWB intersect and are linked to the lives of older men and women in Japan. Using the concept of health expectancy, this study examines the role of SWB, as measured by life satisfaction, in the mortality and morbidity experiences of Japanese adults aged 65 years and older.Research Design and MethodsWe used the nationally representative Nihon University Japanese Longitudinal Study of Aging, 1999–2009. Our measurement of morbidity is disability, based on difficulty in activities in daily living (ADLs) and instrumental ADLs. We use the Interpolation of Markov Chains approach to compute life expectancy (LE), LE without disability (active LE), and LE with differing severity of disability for those who are satisfied with life and for those who are not.ResultsWe documented significant differences in LE and active LE by the state of life satisfaction among older adults in Japan. Men and women who are satisfied with life are expected to live longer and spend more years without having disability compared to those who are not satisfied. We found no differences in the length of life with disability of differing severity by the state of life satisfaction.Discussion and ImplicationsOur results highlight the important role of SWB at older ages in Japan, because it is directly related to the physical health of its aging population. Fully understanding the health of the older population requires research that focuses on both objective and subjective dimensions of well-being.
Using 3-D seismic data to estimate stress based on the curvature attribute integrated mechanical earth model
Authors: Shuai Da , Xian Chenggang , Zhao Yang , Chen Gang , Ge Hongkui , Cao Huan 
Published: December 2022

SUMMARY
The current state of the technology for unconventional gas and oil development integrates geology, geophysics and engineering into a comprehensive reservoir description. To construct a mechanical earth model (MEM) which takes the geological structure influence into account, we introduce the curvature attribute to express the horizontal strains and extend the classical uniform horizontal strains MEM. The horizontal strains are derived based on the theory of plates and depend on the curvature attributes which reflect the geological structure influence. To take seismic data into the unconventional reservoir characterization, we design a geophysical workflow to estimate the in-situ stress. Amplitude Versus Offset (AVO) inversion produces the elastic parameters and the finite-difference method calculates the curvature attributes. The Bowers’ method computes the pore pressure and the in-situ stresses computed from the well-log data are used for the calibration. Real data from the shale gas pilot development areas in the Zhaotong National Demonstration Zone are used to demonstrate the method and compare the new MEM results with the MEM modelling technique results. The curvature attribute integrated MEM shows its advantage.
Linezolid resistance: detection of the cfr(B) gene in French clinical MRSA strains
Authors: Youenou Benjamin , Martins Simoes Patricia , Tristan Anne , Farfour Eric , Beauruelle Clémence , Kolenda Camille , Ranc Anne-Gaëlle , Vandenesch François , Laurent Frédéric , Dupieux Céline 
Published: December 2022

Abstract

Objectives
To describe two linezolid-resistant MRSA strains carrying the cfr(B) gene detected in the French National Reference Centre for staphylococci.

Methods
Two linezolid-resistant MRSA strains isolated from cystic fibrosis patients in two different French hospitals in 2017 and 2019 were examined to explore the mechanisms of linezolid resistance. Antimicrobial susceptibility was tested using broth microdilution and gradient strips. The genetic determinants of linezolid resistance were assessed by a multiplex PCR targeting cfr/cfr(B), optrA and poxtA genes, by amplification and sequencing of individual 23S rRNA genes and by WGS using both Illumina and Nanopore technologies.

Results
The two MRSA strains were resistant to linezolid but susceptible to tedizolid, and PCR-positive for cfr/cfr(B). The WGS analysis indicated that they belonged to two different STs (ST8-MRSA-IV and ST5382-MRSA-IV) and that they both harboured the cfr(B) gene on the same 9.7 kb Tn6218-like chromosomal transposon, a finding only previously reported in Enterococcus sp. and Clostridioides difficile.

Conclusions
To the best of our knowledge, this is the first description of the presence of cfr(B) in staphylococci, more specifically in linezolid-resistant MRSA strains. This finding illustrates the risk of horizontal intergenus transfer of oxazolidinone resistance genes in Staphylococcus aureus and highlights the need to monitor such emergence in this species.
Pharmacology of boosted and unboosted integrase strand transfer inhibitors for two-dose event-driven HIV prevention regimens among men
Authors: Haaland Richard E , Fountain Jeffrey , Martin Amy , Dinh Chuong , Holder Angela , Edwards Tiancheng E , Lupo L Davis , Hall LaShonda , Conway-Washington Christopher , Massud Ivana , García-Lerma J Gerardo , Kelley Colleen F , Heneine Walid M 
Published: December 2022

Abstract

Background
Event-driven HIV prevention strategies are a priority for users who do not require daily pre-exposure prophylaxis (PrEP). Regimens containing integrase strand transfer inhibitors (INSTIs) are under evaluation as alternatives to daily PrEP. To better understand INSTI distribution and inform dosing selection we compared the pharmacology of two-dose boosted elvitegravir and unboosted bictegravir regimens in MSM.

Materials and methods
Blood, rectal and penile secretions and rectal biopsies were collected from 63 HIV-negative MSM aged 18–49 years. Specimens were collected up to 96 h after two oral doses of tenofovir alafenamide and emtricitabine with elvitegravir boosted by cobicistat or unboosted bictegravir given 24 h apart. Antiretroviral drugs were measured by LC-MS.

Results
Mean bictegravir plasma concentrations remained above the 95% protein-adjusted effective concentration 96 h after dosing [273 (95% CI: 164–456) ng/mL] whereas elvitegravir plasma concentrations became undetectable 48 h after the second dose. Bictegravir and elvitegravir reached rectal tissues within 2 h after the first dose, and elvitegravir tissue concentrations [1.07 (0.38–13.51) ng/mg] were greater than bictegravir concentrations [0.27 (0.15–0.70) ng/mg]. Both INSTIs became undetectable in tissues within 96 h. Elvitegravir and bictegravir were not consistently detected in penile secretions.

Conclusions
Whereas bictegravir plasma concentrations persist at least 4 days after a two-oral-dose HIV prophylaxis regimen, elvitegravir accumulates in mucosal tissues. Differing elvitegravir and bictegravir distribution may result in variable mucosal and systemic antiviral activity and can inform dosing strategies for event-driven HIV prevention.