bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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 &lt; .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 &lt; .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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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.