bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive impact of human papillomavirus circulating tumorDNAin treatment response monitoring ofHPV‐associated cancers; a meta‐analysis on recurrent event endpoints
Authors: Karimi Abbas , Jafari‐Koshki Tohid , Zehtabi Mojtaba , Kargar Farzaneh , Gheit Tarik 
Published: July 2023

AbstractBackgroundHPV infection can cause cancer, and standard treatments often result in recurrence. The extent to which liquid biopsy using HPV circulating tumor DNA (HPV ctDNA) can be used as a promising marker for predicting recurrence in HPV‐related cancers remains to be validated. Here we conducted a systematic review and meta‐analysis to assess its effectiveness in predicting treatment response.MethodsWe conducted a systematic literature search of online databases, including PubMed, Embase, Scopus, and the Cochrane Library, up to December 2022. The goal was to identify survival studies that evaluated the potential of plasma HPV ctDNA at baseline and end‐of‐treatment (EoT) in predicting recurrence of related cancers. Hazard ratios were estimated directly from models or extracted from Kaplan–Meier plots.ResultsThe pooled effect of HPV ctDNA presence on disease recurrence was estimated to be HR = 7.97 (95% CI: [3.74, 17.01]). Subgroup analysis showed that the risk of recurrence was HR = 2.17 (95% CI: [1.07, 4.41]) for baseline‐positive cases and HR = 13.21 (95% CI: [6.62, 26.36]) for EoT‐positive cases. Significant associations were also observed between recurrence of oropharyngeal squamous cell carcinoma (HR = 12.25 (95% CI: [2.62, 57.36])) and cervical cancer (HR = 4.60 (95% CI: [2.08, 10.17])) in plasma HPV ctDNA‐positive patients.ConclusionsThe study found that HPV ctDNA detection can predict the rate of relapse or recurrence after treatment, with post‐treatment measurement being more effective than baseline assessment. HPV ctDNA could be used as a surrogate or incorporated with other methods for detecting residual disease.
Community integration as reentry: Understanding functioning, vocational identity, and core self‐evaluations
Authors: Brehmer Chelsea E. , Strauser David R. 
Published: July 2023

AbstractIndividuals who have experienced incarceration are an underserved population in need of career development to reduce barriers to employment. Given the high rates of disability and health concerns for individuals who have been previously incarcerated, this study explored the relationships between individual health functioning, vocational identity, core self‐evaluations, and community integration. Using structural equation modeling structural regression, results showed that functional difficulties negatively impact vocational identity and core self‐evaluations. Conversely, core self‐evaluations significantly improve community integration and mediate a positive relationship between vocational identity and community integration. Career development activities aimed at core self‐evaluations and increasing meaning in employment may reduce some of the barriers experienced by individuals post incarceration.
Control valve stiction detection using Markov transition field and deep convolutional neural network
Authors: Memarian Amirreza , Damarla Seshu Kumar , Huang Biao 
Published: July 2023

AbstractControl valve stiction is an industrial problem that often causes oscillations in process control loops. Oscillating control loops are not capable of maintaining key process variables near or at their desired values, thus yielding low‐quality products, inducing economic loss, and increasing environmental impacts. Therefore, it is of vital importance to detect stiction in industrial control valves. In this regard, the present work proposes a new method based on the Markov transition field and convolutional neural network (CNN) to identify sticky control valves in industrial control loops. The Markov transition field is employed to convert process variable (PV) and controller output (OP) into two‐dimensional images, which are then utilized by CNN to learn to distinguish stiction induced oscillations from oscillations brought out by a non‐stiction condition. A transfer learning strategy is adopted to improve the stiction detection capability of the proposed method. Its performance is evaluated via its application to benchmark control loops taken from the chemical, paper, mining, and metal industries. Results demonstrate that the proposed method obtains the correct verdict for the majority of the control loops studied.
Cellular dynamics in tumour microenvironment along with lung cancer progression underscore spatial and evolutionary heterogeneity of neutrophil
Authors: Peng Haoxin , Wu Xiangrong , Liu Shaopeng , He Miao , Tang Chenshuo , Wen Yaokai , Xie Chao , Zhong Ran , Li Caichen , Xiong Shan , Liu Jun , Zheng Hongbo , He Jianxing , Lu Xu , Liang Wenhua 
Published: July 2023

AbstractBackgroundThe cellular dynamics in the tumour microenvironment (TME) along with non‐small cell lung cancer (NSCLC) progression remain unclear.MethodsMultiplex immunofluorescence test detecting 10 immune‐related markers on 553 primary tumour (PT) samples of NSCLC was conducted and spatial information in TME was assessed by the StarDist depth learning model. The single‐cell transcriptomic atlas of PT (n = 4) and paired tumour‐draining lymph nodes (TDLNs) (n = 5 for tumour‐invaded, n = 3 for tumour‐free) microenvironment was profiled. Various bioinformatics analyses based on Gene Expression Omnibus, TCGA and Array‐Express databases were also used to validate the discoveries.ResultsSpatial distances of CD4+ T cells–CD38+ T cells, CD4+ T cells–neutrophils and CD38+ T cells–neutrophils prolonged and they were replaced by CD163+ macrophages in PT along with tumour progression. Neutrophils showed unique stage and location‐dependent prognostic effects. A high abundance of stromal neutrophils improved disease‐free survival in the early‐stage, whereas high intratumoural neutrophil infiltrates predicted poor prognosis in the mid‐to‐late‐stage. Significant molecular and functional reprogramming in PT and TDLN microenvironments was observed. Diverse interaction networks mediated by neutrophils were found between positive and negative TDLNs. Five phenotypically and functionally heterogeneous subtypes of tumour‐associated neutrophil (TAN) were further identified by pseudotime analysis, including TAN‐0 with antigen‐presenting function, TAN‐1 with strong expression of interferon (IFN)‐stimulated genes, the pro‐tumour TAN‐2 subcluster, the classical subset (TAN‐3) and the pro‐inflammatory subtype (TAN‐4). Loss of IFN‐stimulated signature and growing angiogenesis activity were discovered along the transitional trajectory. Eventually, a robust six neutrophil differentiation relevant genes‐based model was established, showing that low‐risk patients had longer overall survival time and may respond better to immunotherapy.ConclusionsThe cellular composition, spatial location, molecular and functional changes in PT and TDLN microenvironments along with NSCLC progression were deciphered, highlighting the immunoregulatory roles and evolutionary heterogeneity of TANs.
Joint channel estimation and data detection for high rate orthogonal time frequency space systems
Authors: Ouchikh Rabah , Chonavel Thierry , Aïssa‐El‐Bey Abdeldjalil , Djeddou Mustapha 
Published: July 2023

SummaryThis paper proposes a new pilot pattern in the delay‐Doppler (DD) domain for the orthogonal time frequency space (OTFS) system. In contrast to the embedded‐pilot schemes, guard intervals are not used so as increase the spectral efficiency. Also, compared to the superimposed design where data symbols and pilots are arranged on the entire DD grid, in the proposed rearrangement, the number of pilots used is only spread over a subgrid of the DD grid. Hence, the interference of pilots with data symbols is reduced. Afterwards, an algorithm for channel estimation (CE) and symbol detection in the DD domain benefiting from the sparsity of the DD channel is designed. The sparse CE step is formulated as a specific marginalization of the maximum a posteriori (MAP) criterion by providing a Bayesian approach via the mean‐field approximation that involves the variational Bayesian expectation maximization (VB‐EM) algorithm. Detection of data symbols is done using a low complexity MP algorithm. We also propose an interference cancellation (IC) scheme to mitigate contamination of data by pilots that is run after each CE step. To achieve a high CE accuracy, based on the mean mutual incoherence property (MIP), a pilot optimization problem for OTFS is formulated and develop a simulated annealing‐based algorithm to solve it. Finally, simulation results show that the proposed scheme achieves a good compromise between spectral efficiency, complexity, and performance in terms of bit error rate (BER) and normalized mean square error (NMSE) when compared to literature benchmarks.
Safety of full bowel preparation and colonoscopy in elderly patients with ulcerative colitis: A real‐world multicenter retrospective cohort study
Authors: Hashimoto Yu , Kuribayashi Shiko , Itoi Yuki , Satou Keigo , Nakata Kou , Kasuga Kengo , Tanaka Hirohito , Hosaka Hiroko , Masuo Takashige , Maruhashi Kyoko , Furuya Kensuke , Masuda Tomoyuki , Takahashi Kazuhiro , Yamazaki Setsuo , Iwamoto Atsuo , Uraoka Toshio 
Published: July 2023

AbstractBackgroundThe number of elderly patients with ulcerative colitis (UC) has been increasing worldwide. Complications are common in elderly patients who undergo colonoscopy, raising doubts about whether colonoscopy should be performed in the same way in this age group as in younger patients. The aim of this study was to determine the safety of full bowel preparation and colonoscopy in elderly patients with UC.MethodsWe retrospectively reviewed a cohort of patients with UC who had visited any of the 12 hospitals and were registered in our inflammatory bowel disease database. We compared complications associated with colonoscopy and bowel preparation and relapse of UC after colonoscopy in 133 patients aged ≥65 years with UC (the elderly group) and 116 randomly selected patients aged <65 years with UC (the non‐elderly group).ResultsNine elderly patients were not referred for colonoscopy by their physicians because of poor performance status or advanced age. There was no significant between‐group difference in the complication rate (p = 0.57) or frequency of relapse of UC after colonoscopy (p = 0.67).ConclusionsThe findings of this study indicate that colonoscopy can be performed as safely in elderly patients with UC as in their younger counterparts. However, our results also indicate that colonoscopy is often avoided in elderly patients, possibly because of concerns about safety.
Transmission of a bumblebee parasite is robust despite parasite exposure to extreme temperatures
Authors: Wolmuth‐Gordon Hannah S. , Brown Mark J. F. 
Published: July 2023

AbstractAll organisms are exposed to fluctuating environmental conditions, such as temperature. How individuals respond to temperature affects their interactions with one another. Changes to the interaction between parasites and their hosts can have a large effect on disease dynamics. The gut parasite, Crithidia bombi, can be highly prevalent in the bumblebee, Bombus terrestris, and is an established epidemiological model. The parasite is transmitted between bumblebees via flowers, exposing it to a range of environmental temperatures prior to infection. We investigated whether incubation duration and temperature exposure, prior to infection, affects parasite infectivity. Prior to inoculation in B. terrestris, C. bombi was incubated at 10, 20, 30, 40 or 50°C for either 10 or 60 min. These times were chosen to reflect the length of time that the parasite remains infective when outside the host and the rate of floral visitation in bumblebees. Prevalence and infection intensity were measured in bees 1 week later. Incubation duration and the interaction between incubation temperature and duration affected the prevalence of C. bombi at 50°C, resulting in no infections after 60 min. Below 50°C, C. bombi prevalence was not affected by incubation temperature or duration. Extreme temperatures induced morphological changes in C. bombi cells; however, infection intensity was not affected by incubation duration or temperature. These results highlight that this parasite is robust to a wide range of temperatures. The parasite was not infective after being exposed to 50°C for 60 min, such temperatures likely exceed the flight abilities of bumblebees, and thus the potential for transmission. This study shows the importance of understanding the effects of environmental conditions on both hosts and parasites, which is needed to predict transmission under different environmental conditions.
Trait‐based and multi‐scale approach provides insight on responses of freshwater mussels to environmental heterogeneity
Authors: Mitchell Zachary A. , Cottenie Karl , Schwalb Astrid N. 
Published: July 2023

AbstractOur understanding of the factors driving the distribution of metacommunities at different scales can be obscured by high variation in species composition between sites and a lack of fine‐scale distribution data. Trait‐based approaches have long been used to better identify and examine ecological patterns. Most recent studies of riverine metacommunities examining trait‐based patterns have focused on shorter lived organisms. Here we focused on a group of longer lived, sedentary riverine organisms, unionid freshwater mussels. The objective of this study was to examine how (1) the distribution of mussels with different life history strategies (trait‐based approach) and (2) the relative importance of environmental and spatial factors (as a proxy for dispersal) would differ with spatial scale and position in the river; and to (3) further compare this with patterns derived from a taxonomic approach. Fine‐scale distribution data of mussels and environmental factors were collected every 100 m in spatially extensive surveys in an upstream and downstream segment (200 sites/20‐km segment) of a semiarid river, making them some of the most spatially intensive surveys documented to date. A combination of redundancy analysis, asymmetric eigenvector mapping, and variation partitioning analyses revealed that more variation was explained by environmental factors where more environmental differences occur between sites. Where environmental heterogeneity was lower, the amount of variation explained by smaller scale spatial factors was higher, likely mostly associated with stochastic rather than dispersal processes. A higher amount of unexplained variation at the taxonomic level suggests that stochasticity may also play an important role in determining species composition. In contrast, different life history groups had a highly predictable distribution pattern driven by environmental heterogeneity, especially between river segments and mesohabitat, which was associated with different flow conditions. The role we predict for environmental heterogeneity and stochasticity in shaping the distribution of mussels in our study river likely also applies to other taxa and ecosystems at a spatial scale at which neither dispersal limitation nor mass effects occur. Thus, understanding the magnitude and extent of dispersal relative to the amount of environmental heterogeneity may be key for predicting metacommunity structure and dynamics for different organisms.
Tree species size class patterns portend compositional shifts and low resilience in managed northern hardwood forests
Authors: Henry Catherine R. , Walters Michael B. 
Published: July 2023

AbstractDeclining temperate forest biodiversity is a global challenge to future sustainability and resilience. Canopy tree diversity has declined in northern hardwood forests (NHFs) of the Great Lakes region since European colonization, with current tree regeneration patterns suggesting this trend may continue. However, regional (106 ha) patterns and drivers are underexplored. We used data from 141 managed NHF stands, Michigan, USA, to examine diversity indices across tree size classes (seedling, sapling, and canopy); stand‐level drivers of regeneration (seedling and sapling) diversity and individual species density; and patterns among species in relative abundances across size classes. Diversity was similar across size classes (mean asymptotic species richness of 6–7 species and <3 effective common species); however, some species contributing to sapling diversity are unlikely to contribute to future canopy diversity (Fraxinus americanaandFagus grandifolia, insect/pathogen limited;Ostrya virginiana, small maximum size). For the 11 most common species, conspecific canopy density (+, seedlings, significant for 10 species) and stand basal area (−, saplings, 3 species) most consistently associated with density; deer use, site quality, and substrate were less predictive. Patterns of relative density by size class among 18 species present on >10% of sites were consistent with species life history strategy and/or establishment/recruitment barriers. For seven species (includingTsuga canadensis,Betula alleghaniensis), relative density was lowest in the seedling layer, suggesting seedling establishment substrate and/or early shade mortality limitations. For two species (Acer saccharum,Quercus rubra), reduced sapling relative density compared with seedling or canopy strata suggests a sapling recruitment bottleneck from deer browsing/shade, whereas six species (e.g.,F. grandifolia,O. virginiana,Pinus strobus) had highest relative density for saplings, suggesting sapling to canopy recruitment limitations. Lastly, seedlings were relatively most dense forAcer rubrumandPrunusspp., indicating disproportionally high seedling establishment, if not sapling or canopy recruitment, and forF. americana, consistent with recent pest‐related canopy mortality. Collectively our analyses suggest sustained low diversity and shifting composition are driven by limited local seed availability, limited seedling establishment substrate, deep shading, and abundant deer. Management aimed at overcoming these limitations may be necessary to promote future NHF resilience.
Modeling uncertainty of specimens employing spines and force‐limiting connections tested at E‐defense shake table
Authors: Astudillo Bryam , Rivera David , Duke Jessica , Simpson Barbara , Fahnestock Larry A. , Sause Richard , Ricles James , Kurata Masahiro , Okazaki Taichiro , Kawamata Yohsuke , Tao Zhuoqi , Qie Yi 
Published: July 2023

AbstractIn light of the significant damage observed after earthquakes in Japan and New Zealand, enhanced performing seismic force‐resisting systems and energy dissipation devices are increasingly being utilized in buildings. Numerical models are needed to estimate the seismic response of these systems for seismic design or assessment. While there have been studies on modeling uncertainty, selecting the model features most important to response can remain ambiguous, especially if the structure employs less well‐established lateral force‐resisting systems and components. Herein, a global sensitivity analysis was used to address modeling uncertainty in specimens with elastic spines and force‐limiting connections (FLCs) physically tested at full‐scale at the E‐Defense shake table in Japan. Modeling uncertainty was addressed for both model class and model parameter uncertainty by varying primary models to develop several secondary models according to pre‐established uncertainty groups. Numerical estimates of peak story drift ratio and floor acceleration were compared to the results from the experimental testing program using confidence intervals and root‐mean‐square error. Metrics such as the coefficient of variation, variance, linear Pearson correlation coefficient, and Sobol index were used to gain intuition about each model feature's contribution to the dispersion in estimates of the engineering demands. Peak floor acceleration was found to be more sensitive to modeling uncertainty compared to story drift ratio. Assumptions for the spine‐to‐frame connection significantly impacted estimates of peak floor accelerations, which could influence future design methods for spines and FLC in enhanced lateral‐force resisting systems.
Selection of rhizobial strains differing in their nodulation kinetics under low temperature in four temperate legume species
Authors: D'Amours Emmanuelle , Bertrand Annick , Cloutier Jean , Chalifour François‐Philippe , Claessens Annie , Rocher Solen , Bipfubusa Marie , Giroux Chantal , Beauchamp Chantal J. 
Published: July 2023

AbstractBackgroundWinter climate change including frequent freeze‐thaw episodes and shallow snow cover will have major impacts on the spring regrowth of perennial crops. Non‐bloating perennial forage legume species including sainfoin, birdsfoot trefoil, red clover, and alsike clover have been bred for their adaptation to harsh winter conditions. In parallel, the selection of cold‐tolerant rhizobial strains could allow earlier symbiotic nitrogen (N) fixation to hasten spring regrowth of legumes.MethodsTo identify strains forming nodules rapidly and showing high N‐fixing potential, 60 rhizobial strains in association with four temperate legume species were evaluated over 11 weeks under spring soil temperatures for kinetics of nodule formation, nitrogenase activity, and host yield.ResultsStrains differed in their capacity to form efficient nodules on legume hosts over time. Strains showing higher nitrogenase activity were arctic strain N10 with sainfoin and strain L2 with birdsfoot trefoil. For clovers, nitrogenase activity was similar for control and inoculated plants, likely due to formation of effective nodules in controls by endophyte rhizobia present in seeds.ConclusionsSelection based on nodulation kinetics at low temperature, nitrogenase activity, and yield was effective to identify performant rhizobial strains for legume crops. The use of cold‐tolerant strains could help mitigate winter climatic changes.
Phonological and morphological literacy skills in English and Chinese: A cross‐linguistic neuroimaging comparison of Chinese–English bilingual and monolingual English children
Authors: Zhang Kehui , Sun Xin , Yu Chi‐Lin , Eggleston Rachel L. , Marks Rebecca A. , Nickerson Nia , Caruso Valeria C. , Hu Xiao‐Su , Tardif Twila , Chou Tai‐Li , Booth James R. , Kovelman Ioulia 
Published: July 2023

AbstractOver the course of literacy development, children learn to recognize word sounds and meanings in print. Yet, they do so differently across alphabetic and character‐based orthographies such as English and Chinese. To uncover cross‐linguistic influences on children's literacy, we asked young Chinese–English simultaneous bilinguals and English monolinguals (N = 119, ages 5–10) to complete phonological and morphological awareness (MA) literacy tasks. Children completed the tasks in the auditory modality in each of their languages during functional near‐infrared spectroscopy neuroimaging. Cross‐linguistically, comparisons between bilinguals' two languages revealed that the task that was more central to reading in a given orthography, such as phonological awareness (PA) in English and MA in Chinese, elicited less activation in the left inferior frontal and parietal regions. Group comparisons between bilinguals and monolinguals in English, their shared language of academic instruction, revealed that the left inferior frontal was less active during phonology but more active during morphology in bilinguals relative to monolinguals. MA skills are generally considered to have greater language specificity than PA skills. Bilingual literacy training in a skill that is maximally similar across languages, such as PA, may therefore yield greater automaticity for this skill, as reflected in the lower activation in bilinguals relative to monolinguals. This interpretation is supported by negative correlations between proficiency and brain activation. Together, these findings suggest that both the structural characteristics and literacy experiences with a given language can exert specific influences on bilingual and monolingual children's emerging brain networks for learning to read.