bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Natural Trajectory of Smoking Cessation Among Cancer Patients Who Want to Quit “On Their Own”: A Mixed-Methods, Longitudinal Study
Authors: Borger Tia , Feather Abigayle R , Wakeman Kathleen E , Bowling William , Burris Jessica L 
Published: October 2023

Abstract

Introduction
Many cancer patients who smoke cigarettes want to quit. Unfortunately, many of these cancer patients prefer to quit without the aid of pharmacotherapy or behavioral counseling. The teachable moment of cancer diagnosis might still position these cancer patients to make meaningful changes in their smoking behavior, but no study has documented the trajectory of smoking cessation outcomes among cancer patients who want to quit “on their own.” This study aimed to fill this gap in the literature.

Methods
In this mixed-methods, longitudinal study, 35 cancer patients who declined tobacco treatment because of the desire to quit “on their own” provided data via three surveys and 1–2 semi-structured interviews. The observation period spanned 60 days. Participants were recently diagnosed at and recruited from outpatient cancer clinics.

Results
Participants were mostly female (68.57%), White, non-Hispanic (85.71%), unemployed due to disability (57.14%), and rural residents (54.29%). Across time, 43.76% of participants achieved 50% smoking reduction, 21.88% achieved 3-day floating abstinence, 18.75% achieved 7-day floating abstinence, and 12.50% achieved 30-day point-prevalence abstinence. Key themes that emerged from the interviews centered on intention and confidence to quit and types of tobacco treatment used/received.

Conclusions
This study with cancer patients who desired to quit smoking without assistance found some evidence of quit success, but success waned as criteria grew more stringent. Results showed participants’ initial intention to quit unassisted was quite strong, as few reported tobacco treatment use. Interventions to increase the uptake of evidence-based tobacco treatment among cancer patients are sorely needed.

Implications
The preference to quit smoking without assistance is common among cancer patients, even given lack of evidence supporting its effectiveness. This study is the first to explore the trajectory of smoking cessation outcomes among cancer patients who desire to quit without assistance. These data can be used to develop interventions to increase the uptake of tobacco treatment and increase quit success among cancer patients.
Evaluating Oncologists’ Practice Patterns and Decision-Making in Locally Advanced or Metastatic Urothelial Carcinoma: The US Physician PARADIGM Study
Authors: Gupta Shilpa , Costantino Halley , Ike Chiemeka , Gupta Shaloo , Bhanegaonkar Abhijeet , Su Cathy , Thakkar Sheena , Mackie deMauri S , Devgan Geeta , Katzenstein Howard M , Liu Frank X 
Published: October 2023

Abstract

Background
The treatment landscape for locally advanced/metastatic urothelial carcinoma (la/mUC) has evolved. This study examined US prescribing patterns and clinical decision-making for first-line (1L) and first-line maintenance (1LM) treatment.

Materials and Methods
US-based oncologists (N = 150) completed an online survey on patient demographics, practice patterns, and important factors considered in 1L/1LM selection. Multivariable logistic regression was used to assess factors associated with more vs less frequent 1L/1LM prescribing.

Results
Physician reports estimated that 23% of patients with la/mUC had not received any systemic therapy in the previous 6 months; however, 46% received 1L, 32% received second-line, and 22% received subsequent-line systemic treatments. Of patients who were receiving 1L treatment, 72% were estimated to be receiving 1L platinum-based chemotherapy. Around 69% of patients eligible for 1LM received the treatment. Physicians categorized as frequent prescribers reported overall survival (OS), disease control rate (DCR), and rate of grade 3/4 adverse events (AEs) as factors associated with 1L treatment selection (all P &lt; .05). OS, rate of grade 3/4 immune-mediated AEs, and inclusion in institutional guidelines were reported as attributes used in 1LM treatment selection (all P &lt; .05). Multivariable analysis revealed OS, DCR, and rate of grade 3/4 AEs as important factors in oncologists’ 1L treatment selection; academic practice setting and use of Response Evaluation Criteria in Solid Tumors version 1.1 were associated with 1LM use (all P &lt; .05).

Conclusion
OS and AEs were found to be relevant factors associated with offering 1L and 1LM treatment. Variability exists in physicians’ decision-making in the real-world setting for la/mUC.
Genome-Wide Analysis of Cotton MYB Transcription Factors and the Functional Validation of GhMYB in Response to Drought Stress
Authors: Su Jiuchang , Zhan Na , Cheng Xiaoru , Song Shanglin , Dong Tianyu , Ge Xiaoyang , Duan Hongying 
Published: October 2023

Abstract
MYB transcription factors play important roles during abiotic stress responses in plants. However, little is known about the accurate systematic analysis of MYB genes in the four cotton species, Gossypium hirsutum, G. barbadense, G. arboreum and G. raimondii. Herein, we performed phylogenetic analysis and showed that cotton MYBs and Arabidopsis MYBs were clustered in the same subfamilies for each species. The identified cotton MYBs were distributed unevenly on chromosomes in various densities for each species, wherein genome-wide tandem and segment duplications were the main driving force of MYB family expansion. Synteny analysis suggested that the abundant collinearity pairs of MYBs were identified between G. hirsutum and the other three species, and that they might have undergone strong purification selection. Characteristics of conserved motifs, along with their consensus sequence, promoter cis elements and gene structure, revealed that MYB proteins might be highly conserved in the same subgroups for each species. Subsequent analysis of differentially expressed genes and expression patterns indicated that most GhMYBs might be involved in response to drought (especially) and salt stress, which was supported by the expression levels of nine GhMYBs using real-time quantitative PCR. Finally, we performed a workflow that combined virus-induced gene silencing and the heterologous transformation of Arabidopsis, which confirmed the positive roles of GhMYBs under drought conditions, as validated by determining the drought-tolerant phenotypes, damage index and/or water loss rate. Collectively, our findings not only expand our understanding of the relationships between evolution and function of MYB genes, but they also provide candidate genes for cotton breeding.
BBX21 Integrates Brassinosteroid Biosynthesis and Signaling in the Inhibition of Hypocotyl Growth under Shade
Authors: Gómez-Ocampo Gabriel , Crocco Carlos D , Cascales Jimena , Oklestkova Jana , Tarkowská Danuše , Strnad Miroslav , Mora-Garcia Santiago , Pruneda-Paz José L , Blazquez Miguel A , Botto Javier F 
Published: October 2023

Abstract
B-Box-containing zinc finger transcription factors (BBX) are involved in light-mediated growth, affecting processes such as hypocotyl elongation in Arabidopsis thaliana. However, the molecular and hormonal framework that regulates plant growth through BBX proteins is incomplete. Here, we demonstrate that BBX21 inhibits the hypocotyl elongation through the brassinosteroid (BR) pathway. BBX21 reduces the sensitivity to 24-epiBL, a synthetic active BR, principally at very low concentrations in simulated shade. The biosynthesis profile of BRs showed that two active BR—brassinolide and 28-homobrassinolide—and 8 of 11 intermediates can be repressed by BBX21 under white light (WL) or simulated shade. Furthermore, BBX21 represses the expression of CYTOCHROME P450 90B1 (DWF4/CYP90B1), BRASSINOSTEROID-6-OXIDASE 1 (BR6OX1, CYP85A1) and BR6OX2 (CYP85A2) genes involved in the BR biosynthesis in WL while specifically promoting DWF4 and PHYB ACTIVATION TAGGED SUPPRESSOR 1 (CYP2B1/BAS1) expression in WL supplemented with far-red (WL + FR), a treatment that simulates shade. In addition, BBX21 represses BR signaling genes, such as PACLOBUTRAZOL RESISTANCE1 (PRE1), PRE3 and ARABIDOPSIS MYB-LIKE 2 (MYBL2), and auxin-related and expansin genes, such as INDOLE-3-ACETIC ACID INDUCIBLE 1 (IAA1), IAA4 and EXPANSIN 11 in short-term shade. By a genetic approach, we found that BBX21 acts genetically upstream of BRASSINAZOLE-RESISTANT 1 (BZR1) for the promotion of DWF4 and BAS1 gene expression in shade. We propose that BBX21 integrates the BR homeostasis and shade-light signaling, allowing the fine-tuning of hypocotyl elongation in Arabidopsis.
Lipidomic and Metabolomic Analyses Reveal Changes of Lipid and Metabolite Profiles in Rapeseed during Nitrogen Deficiency
Authors: Peng Yan , Lou Hongxiang , Tan Zengdong , Ouyang Zhewen , Zhang Yuting , Lu Shaoping , Guo Liang , Yang Bao 
Published: October 2023

Abstract
Nitrogen is one of the most essential macronutrients for plant growth and its availability in soil is vital for agricultural sustainability and productivity. However, excessive nitrogen application could reduce the nitrogen use efficiency and produce environmental pollution. Here, we systematically determined the response in lipidome and metabolome in rapeseed during nitrogen starvation. Plant growth was severely retarded during nitrogen deficiency, while the levels of most amino acids were significantly decreased. The level of monogalactosyldiacyglycerol (MGDG) in leaves and roots was significantly decreased, while the level of digalactosyldiacylglycerol (DGDG) was significantly decreased in roots, resulting in a significant reduction of the MGDG/DGDG ratio during nitrogen starvation. Meanwhile, the levels of sulfoquinovosyl diacylglycerol, phosphatidylglycerol and glucuronosyl diacylglycerol were reduced to varying extents. Moreover, the levels of metabolites in the tricarboxylic acid cycle, Calvin cycle and energy metabolism were changed during nitrogen deficiency. These findings show that nitrogen deprivation alters the membrane lipid metabolism and carbon metabolism, and our study provides valuable information to further understand the response of rapeseed to nitrogen deficiency at the metabolism level.
Evolutionary trajectory of organelle-derived nuclear DNAs in the Triticum/Aegilops complex species
Authors: Zhang Zhibin , Zhao Jing , Li Juzuo , Yao Jinyang , Wang Bin , Ma Yiqiao , Li Ning , Wang Hongyan , Wang Tianya , Liu Bao , Gong Lei 
Published: October 2023

Abstract
Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.
Ethylene and jasmonate signaling converge on gibberellin catabolism during thigmomorphogenesis in Arabidopsis
Authors: Wang Lei , Ma Canrong , Wang Shuanghua , Yang Fei , Sun Yan , Tang Jinxiang , Luo Ji , Wu Jianqiang 
Published: October 2023

Abstract
Touch induces marked morphological changes in plants, including reduced rosette diameters and delayed flowering, a process called thigmomorphogenesis. Previous studies have revealed that thigmomorphogenesis in Arabidopsis (Arabidopsis thaliana) results from touch-induced accumulation of jasmonic acid (JA) and GIBBERELLIN 2-OXIDASE7 (GA2ox7) transcripts, which encode a gibberellin (GA) catabolism enzyme, leading to reduced levels of active GAs. However, the mechanisms underlying thigmomorphogenesis remain uncharacterized. Here, we showed that touch induces ethylene (ET) production in Arabidopsis. After touch treatment, ET biosynthesis and signaling mutants exhibited even greater thigmomorphogenic changes and more decreased GA4 contents than did wild-type (WT) plants. Biochemical analysis indicated that the transcription factor ETHYLENE INSENSITIVE3 (EIN3) of the ET pathway binds to the promoter of GA2ox8 (encoding another GA 2-oxidase performing the same GA modification as GA2ox7) and represses GA2ox8 transcription. Moreover, MYC2, the master regulator of JA signaling, directly promoted GA2ox7 expression by binding the G-box motif on GA2ox7 promoter. Further genetic analysis suggested that the ET and JA pathways independently control the expression of GA2ox8 and GA2ox7, respectively. This study reveals that the ET pathway is a novel repressor of touch-induced thigmomorphogenesis and highlights that the ET and JA pathways converge on GA catabolism but play opposite roles to fine-tune GA4 content during thigmomorphogenesis.
The effects of multifactorial stress combination on rice and maize
Authors: Sinha Ranjita , Peláez-Vico María Ángeles , Shostak Benjamin , Nguyen Thao Thi , Pascual Lidia S , Ogden Andrew M , Lyu Zhen , Zandalinas Sara I , Joshi Trupti , Fritschi Felix B , Mittler Ron 
Published: October 2023

Abstract
The complexity of environmental factors affecting crops in the field is gradually increasing due to climate change-associated weather events, such as droughts or floods combined with heat waves, coupled with the accumulation of different environmental and agricultural pollutants. The impact of multiple stress conditions on plants was recently termed “multifactorial stress combination” (MFSC) and defined as the occurrence of 3 or more stressors that impact plants simultaneously or sequentially. We recently reported that with the increased number and complexity of different MFSC stressors, the growth and survival of Arabidopsis (Arabidopsis thaliana) seedlings declines, even if the level of each individual stress is low enough to have no significant effect on plants. However, whether MFSC would impact commercial crop cultivars is largely unknown. Here, we reveal that a MFSC of 5 different low-level abiotic stresses (salinity, heat, the herbicide paraquat, phosphorus deficiency, and the heavy metal cadmium), applied in an increasing level of complexity, has a significant negative impact on the growth and biomass of a commercial rice (Oryza sativa) cultivar and a maize (Zea mays) hybrid. Proteomics, element content, and mixOmics analyses of MFSC in rice identified proteins that correlate with the impact of MFSC on rice seedlings, and analysis of 42 different rice genotypes subjected to MFSC revealed substantial genetic variability in responses to this unique state of stress combination. Taken together, our findings reveal that the impacts of MFSC on 2 different crop species are severe and that MFSC may substantially affect agricultural productivity.
Effectiveness, tolerability, and response predictors of preventive anti-CGRP mAbs for migraine in patients over 65 years old: a multicenter real-world case-control study
Authors: Gonzalez-Martinez Alicia , Sanz-García Ancor , García-Azorín David , Rodríguez-Vico Jaime , Jaimes Alex , Gómez García Andrea , Casas-Limón Javier , Díaz de Terán Javier , Sastre-Real María , Membrilla Javier , Latorre Germán , Calle de Miguel Carlos , Gil Luque Sendoa , Trevino-Peinado Cristina , Quintas Sonia , Heredia Patricia , Echavarría-Íñiguez Ana , Guerrero-Peral Ángel , Sierra Álvaro , González-García Nuria , Porta-Etessam Jesús , Gago-Veiga Ana Beatriz 
Published: October 2023

Abstract

Objective
To evaluate clinical characteristics, effectiveness, and tolerability of preventive anti- calcitonin gene-related peptide (CGRP) monoclonal antibodies (mAbs) in the elderly. Anti-CGRP mAbs have demonstrated efficacy and safety in patients with migraine although there is limited information regarding the elderly.

Design
We performed a multicenter case-control study of cases (patients over 65 years old) and controls (sex-matched patients under 55 years old) with migraine receiving anti-CGRP mAbs.

Methods
We included the demographic characteristics, effectiveness—reduction in the number of monthly headache days (MHD) and monthly migraine days (MMD), 30%, 50%, and 75% responder rates—and treatment emergent adverse events (TEAEs). The primary endpoint was the 50% response rate regarding MHD at weeks 20–24; exploratory 50% response predictors in the elderly were evaluated.

Results
In total, 228 patients were included: 114 cases , 114 controls-. Among cases 84.2% (96/114) were women, 79.8% (91/114) CM; mean age of cases 70.1 years old (range: 66–86); mean age of controls was 42.9 years old(range: 38–49). Cases had a higher percentage of vascular risk factors (P &lt; .05),older age of onset (P &lt; .001) and more reported prior preventive treatments (P &lt; .001). Regarding effectiveness in cases, 50% response rate was achieved by 57.5% (42/73) at 20–24 weeks, with lower reduction in the MHD at 8–12 weeks (5 [7.2], 8 [9.1]; P = .001) and a higher reduction in MMD at 20–24 weeks (10.7 [9.1], 9.2 [7.7]; P = .04) compared to the control group. The percentage of TEAEs was similar in the 2 groups. Diagnosis of episodic migraine (EM) (P = .03) and lower number of MHD at baseline (P = .001) were associated with a 50% response in the elderly in univariate analysis.

Conclusions
Our study provides real world evidence of effectiveness and safety of anti-CGRP mAbs for migraine in patients without upper age-limit and possible predictors of anti-CGRP response in the elderly.
Applications of genetic code expansion technology in eukaryotes
Authors: Guo Qiao-ru , Cao Yu J 
Published: October 2023

Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
Leaf trait coordination and variation of blue oak across topo-environmental scales
Authors: Wu Angelica , Anderegg Leander D L , Dawson Todd E , Trugman Anna T 
Published: October 2023

Abstract
Trees are arguably the most diverse and complex macro-organisms on Earth. The equally diverse functions of trees directly impact fluxes of carbon, water and energy from the land surface. A number of recent studies have shed light on the substantial within-species variability across plant traits, including aspects of leaf morphology and plant allocation of photosynthates to leaf biomass. Yet, within-tree variability in leaf traits due to microclimatic variations, leaf hydraulic coordination across traits at different physiological scales and variations in leaf traits over a growing season remain poorly studied. This knowledge gap is stymieing the fundamental understanding of what drives trait variation and covariation from tissues to trees to landscapes. Here, we present an extensive dataset measuring within-tree heterogeneity in leaf traits in California’s blue oak (Quercus douglasii) across an edaphic gradient and over the course of a growing season at an oak–grass savanna in Southern CA, USA. We found a high level of within-tree crown leaf area:sapwood area variation that was not attributable to sample height or aspect. We also found a higher level of trait integration at the tree level, rather than branch level, suggesting that trees optimize water use at the organismal level. Despite the large variance in traits within a tree crown and across trees, we did not find strong evidence for adaptive plasticity or acclimation in leaf morphological traits (e.g., changes to phenotype which increased fitness) across temporal and spatial water availability gradients. Collectively, our results highlight strong variation in drought-related physiology, but limited evidence for adaptive trait plasticity over shorter time scales.
Advances in gene therapy for inborn errors of immunity
Authors: Ott de Bruin Lisa M. , Lankester Arjan C. , Staal Frank J.T. 
Published: October 2023

Purpose of review
Provide an overview of the landmark accomplishments and state of the art of gene therapy for inborn errors of immunity (IEI).

Recent findings
Three decades after the first clinical application of gene therapy for IEI, there is one market authorized product available, while for several others efficacy has been demonstrated or is currently being tested in ongoing clinical trials. Gene editing approaches using programmable nucleases are being explored preclinically and could be beneficial for genes requiring tightly regulated expression, gain-of-function mutations and dominant-negative mutations.

Summary
Gene therapy by modifying autologous hematopoietic stem cells (HSCs) offers an attractive alternative to allogeneic hematopoietic stem cell transplantation (HSCT), the current standard of care to treat severe IEI. This approach does not require availability of a suitable allogeneic donor and eliminates the risk of graft versus host disease (GvHD). Gene therapy can be attempted by using a viral vector to add a copy of the therapeutic gene (viral gene addition) or by using programmable nucleases (gene editing) to precisely correct mutations, disrupt a gene or introduce an entire copy of a gene at a specific locus. However, gene therapy comes with its own challenges such as safety, therapeutic effectiveness and access. For viral gene addition, a major safety concern is vector-related insertional mutagenesis, although this has been greatly reduced with the introduction of safer vectors. For gene editing, the risk of off-site mutagenesis is a main driver behind the ongoing search for modified nucleases. For both approaches, HSCs have to be manipulated ex vivo, and doing this efficiently without losing stemness remains a challenge, especially for gene editing.