bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are Formal and Informal Home Mindfulness Practice Quantities Associated With Outcomes? Results From a Pilot Study of a Four-Week Mindfulness Intervention for Chronic Pain Management
Authors: Brintz Carrie E. , Polser Geneva , Coronado Rogelio A. , French Benjamin , Faurot Keturah R. , Gaylord Susan A. 
Published: March 2024

Background The association between home mindfulness practice quantity in standard length mindfulness-based interventions (MBIs) and chronic pain outcomes is variable. Few studies focus on abbreviated MBIs (< 8 weeks) and distinguish between formal guided practices and informal practices in daily life. Objectives To characterize home mindfulness practice and explore associations between home practice quantity and pre-to-post-outcome changes after an MBI for chronic pain. Methods In this single-arm study, 21 adults with chronic pain (mean age = 54 years, 81% White, mean pain duration = 7 years) completed an MBI with four weekly group sessions. Pre and post self-report measures of pain intensity/interference, physical function, depression, anxiety, positive affect, sleep disturbance (all PROMIS measures), and pain acceptance, catastrophizing, perceived stress and mindfulness were completed, along with daily surveys of formal (mindfulness of breath, body scan) and informal (breathing space, mindfulness of daily activities) practice. Bivariate correlations and multivariable regression models were used to assess the association between days and minutes of practice and change in outcomes. Results On average, formal practice was completed on 4.3 days per week and 13.5 minutes per day. Informal practice was completed on 3.5 days per week and 8.6 minutes per day. Formal practice was not significantly correlated with outcomes (Spearman’s ρ = |.01|-|.32|), whereas informal practice was correlated with multiple outcomes (ρ = |.04|-|.66|). Number of days practiced informally was associated with improved pain interference, physical function, sleep disturbance, and catastrophizing ( p’s ≤ .05). Number of minutes practiced informally was associated with improved pain interference, anxiety, positive affect, and catastrophizing ( p’s ≤ .05). Conclusion Informal home practice quantity, but not formal practice quantity, is associated with improved outcomes during an abbreviated MBI for chronic pain. For these MBIs, it is important to evaluate the distinct roles of formal and informal practice. ClinicalTrials.gov Registration NCT03495856.
Density functional theory study of the atomic and electronic structures of trans-vacant 1M Al-rich illite
Authors: Gao Wei , Zhao Jian , He Man-Chao 
Published: March 2024

AbstractIllite is a common clay mineral that is found in a wide range of geological settings. The good thermal stability and non-swelling properties of illite make it valuable in ceramic materials, paints and coatings, drilling fluids, agriculture and geological studies. To gain a deeper understanding of the physical and chemical properties of illite, in the present paper the atomic and electronic structures of a typical trans-vacant 1M Al-rich illite were constructed and calculated using density functional theory. The calculated indirect band gap of Al-rich illite was 4.99 eV. The electronic analysis revealed that the interactions in the tetrahedral sheet were more stable than those in the octahedral sheet. The substitution of Al atoms noticeably reduced the stability of the tetrahedral sheet in Al-rich illite. Other properties of Al-rich illite, including the density of states, electron population/charge, electronic charge density and bonding interaction, are also discussed and analysed in detail.
Sickle cell disease iPSC-derived sensory neurons exhibit increased excitability and sensitization to patient plasma
Authors: Allison Reilly L. , Welby Emily , Ehlers Vanessa , Burand Anthony , Isaeva Olena , Nieves Torres Damaris , Highland Janelle , Brandow Amanda M. , Stucky Cheryl L. , Ebert Allison D. 
Published: March 2024

Abstract
Individuals living with sickle cell disease (SCD) experience severe recurrent acute and chronic pain. Challenges to gaining mechanistic insight into pathogenic SCD pain processes include differential gene expression and function of sensory neurons between humans and mice with SCD, and extremely limited availability of neuronal tissues from patients with SCD. Here, we used induced pluripotent stem cells (iPSCs), derived from patients with SCD, differentiated into sensory neurons (SCD iSNs) to begin to overcome these challenges. We characterize key gene expression and function of SCD iSNs to establish a model to investigate intrinsic and extrinsic factors that may contribute to SCD pain. Despite similarities in receptor gene expression, SCD iSNs show pronounced excitability using patch clamp electrophysiology. Furthermore, we find that plasma taken from patients with SCD during acute pain associated with a vaso-occlusive event increases the calcium responses to the nociceptive stimulus capsaicin in SCD iSNs compared with those treated with paired plasma from patients with SCD at steady state baseline or healthy control plasma samples. We identified high levels of the polyamine spermine in baseline and acute pain states of plasma from patients with SCD, which sensitizes SCD iSNs to subthreshold concentrations of capsaicin. Together, these data identify potential intrinsic mechanisms within SCD iSNs that may extend beyond a blood-based pathology.
Platelet dysfunction reversal with cold-stored vs room temperature–stored platelet transfusions
Authors: Kogler Valery J. , Miles Jeffrey A. , Özpolat Tahsin , Bailey S. Lawrence , Byrne Daire A. , Bawcom-Randall Morgan , Wang Yi , Larsen Hannah J. , Reed Franklin , Fu Xiaoyun , Stolla Moritz 
Published: March 2024

Abstract
Platelets are stored at room temperature for 5 to 7 days (room temperature–stored platelets [RSPs]). Because of frequent and severe shortages, the US Food and Drug Administration recently approved up to 14-day cold-stored platelets (CSPs) in plasma. However, the posttransfusion function of CSPs is unknown and it is unclear which donors are best suited to provide either RSPs or CSPs. In this study, we sought to evaluate the posttransfusion platelet function and its predictors for platelets stored for the maximum approved storage times (7-day RSPs and 14-day CSPs) in healthy volunteers on acetylsalicylic acid (ASA). We conducted a randomized crossover study in 10 healthy humans. Individuals donated 1 platelet unit, stored at either 22°C or 4°C based on randomization. Before transfusion, participants ingested ASA to inhibit endogenous platelets. Transfusion recipients were tested for platelet function and lipid mediators. Platelet units were tested for lipid mediators only. A second round of transfusion with the alternative product was followed by an identical testing sequence. RSPs reversed platelet inhibition significantly better in αIIbβ3 integrin activation–dependent assays. In contrast, CSPs in recipients led to significantly more thrombin generation, which was independent of platelet microparticles. Lysophosphatidylcholine-O species levels predicted the procoagulant capacity of CSPs. In contrast, polyunsaturated fatty acid concentrations predicted the aggregation response of RSPs. In summary, we provide, to our knowledge, the first efficacy data of extended-stored CSPs in plasma. Our results suggest that identifying ideal RSP and CSP donors is possible, and pave the way for larger studies in the future. This trial is registered at www.ClinicalTrials.gov as #NCT0511102.
Smoldering multiple myeloma: taking the narrow over the wide path?
Authors: Avet-Loiseau Herve , Bahlis Nizar J. 
Published: March 2024

Abstract
Smoldering multiple myeloma (MM) is an asymptomatic clonal plasma cell condition considered as a premalignant entity that may evolve over time to symptomatic MM. Based on a “poorly defined” risk of progression, some well-intended investigators proposed prospective interventional trials for these individuals. We believe this may be a harmful intervention and favor a close “wait and watch” approach and rather enroll these patients in dedicated observational biological studies aiming to better identify patients who will evolve to MM, based on their plasma cells' biology, including genomics, epigenetics, and the immune microenvironment.
Proteomic analysis of plasma proteins from patients with cardiac rupture after acute myocardial infarction using TMT-based quantitative proteomics approach
Authors: Hou Jingyuan , Deng Qiaoting , Qiu Xiaohong , Liu Sudong , Li Youqian , Huang Changjing , Wang Xianfang , Zhang Qunji , Deng Xunwei , Zhong Zhixiong , Zhong Wei 
Published: March 2024

AbstractBackgroundCardiac rupture (CR) is a rare but catastrophic mechanical complication of acute myocardial infarction (AMI) that seriously threatens human health. However, the reliable biomarkers for clinical diagnosis and the underlying signaling pathways insights of CR has yet to be elucidated.MethodsIn the present study, a quantitative approach with tandem mass tag (TMT) labeling and liquid chromatography–tandem mass spectrometry was used to characterize the differential protein expression profiles of patients with CR. Plasma samples were collected from patients with CR (n = 37), patients with AMI (n = 47), and healthy controls (n = 47). Candidate proteins were selected for validation by multiple reaction monitoring (MRM) and enzyme-linked immunosorbent assay (ELISA).ResultsIn total, 1208 proteins were quantified and 958 differentially expressed proteins (DEPs) were identified. The difference in the expression levels of the DEPs was more noticeable between the CR and Con groups than between the AMI and Con groups. Bioinformatics analysis showed most of the DEPs to be involved in numerous crucial biological processes and signaling pathways, such as RNA transport, ribosome, proteasome, and protein processing in the endoplasmic reticulum, as well as necroptosis and leukocyte transendothelial migration, which might play essential roles in the complex pathological processes associated with CR. MRM analysis confirmed the accuracy of the proteomic analysis results. Four proteins i.e., C-reactive protein (CRP), heat shock protein beta-1 (HSPB1), vinculin (VINC) and growth/differentiation factor 15 (GDF15), were further validated via ELISA. By receiver operating characteristic (ROC) analysis, combinations of these four proteins distinguished CR patients from AMI patients with a high area under the curve (AUC) value (0.895, 95% CI, 0.802–0.988,p < 0.001).ConclusionsOur study highlights the value of comprehensive proteomic characterization for identifying plasma proteome changes in patients with CR. This pilot study could serve as a valid foundation and initiation point for elucidation of the mechanisms of CR, which might aid in identifying effective diagnostic biomarkers in the future.
AStruct: detection of allele-specific RNA secondary structure in structuromic probing data
Authors: Xu Qingru , Bao Xiaoqiong , Lin Zhuobin , Tang Lin , He Li-na , Ren Jian , Zuo Zhixiang , Hu Kunhua 
Published: March 2024

Abstract
Background
Uncovering functional genetic variants from an allele-specific perspective is of paramount importance in advancing our understanding of gene regulation and genetic diseases. Recently, various allele-specific events, such as allele-specific gene expression, allele-specific methylation, and allele-specific binding, have been explored on a genome-wide scale due to the development of high-throughput sequencing methods. RNA secondary structure, which plays a crucial role in multiple RNA-associated processes like RNA modification, translation and splicing, has emerged as an essential focus of relevant research. However, tools to identify genetic variants associated with allele-specific RNA secondary structures are still lacking.

Results
Here, we develop a computational tool called ‘AStruct’ that enables us to detect allele-specific RNA secondary structure (ASRS) from RT-stop based structuromic probing data. AStruct shows robust performance in both simulated datasets and public icSHAPE datasets. We reveal that single nucleotide polymorphisms (SNPs) with higher AStruct scores are enriched in coding regions and tend to be functional. These SNPs are highly conservative, have the potential to disrupt sites involved in m6A modification or protein binding, and are frequently associated with disease.

Conclusions
AStruct is a tool dedicated to invoke allele-specific RNA secondary structure events at heterozygous SNPs in RT-stop based structuromic probing data. It utilizes allelic variants, base pairing and RT-stop information under different cell conditions to detect dynamic and functional ASRS. Compared to sequence-based tools, AStruct considers dynamic cell conditions and outperforms in detecting functional variants. AStruct is implemented in JAVA and is freely accessible at: https://github.com/canceromics/AStruct.
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models
Authors: Scharl Theresa , Grün Bettina 
Published: March 2024

AbstractRNA sequencing of time-course experiments results in three-way count data where the dimensions are the genes, the time points and the biological units. Clustering RNA-seq data allows to extract groups of co-expressed genes over time. After standardisation, the normalised counts of individual genes across time points and biological units have similar properties as compositional data. We propose the following procedure to suitably cluster three-way RNA-seq data: (1) pre-process the RNA-seq data by calculating the normalised expression profiles, (2) transform the data using the additive log ratio transform to map the composition in the D-part Aitchison simplex to a $$D-1$$

D
-
1

-dimensional Euclidean vector, (3) cluster the transformed RNA-seq data using matrix-variate Gaussian mixture models and (4) assess the quality of the overall cluster solution and of individual clusters based on cluster separation in the transformed space using density-based silhouette information and on compactness of the cluster in the original space using cluster maps as a suitable visualisation. The proposed procedure is illustrated on RNA-seq data from fission yeast and results are also compared to an analogous two-way approach after flattening out the biological units.
Genome-wide analysis and functional validation reveal the role of late embryogenesis abundant genes in strawberry (Fragaria × ananassa) fruit ripening
Authors: Lin Yuanxiu , She Musha , Zhao Mantong , Yu Hong , Xiao Wenfei , Zhang Yunting , Li Mengyao , Chen Qing , Zhang Yong , Wang Yan , He Wen , Wang Xiaorong , Tang Haoru , Luo Ya 
Published: March 2024

Abstract
Background
Late embryogenesis abundant (LEA) proteins play important roles in plant growth and development, as well as stresses responsiveness. Nowadays, it has been found that LEAs also have function in fruit ripening. However, the comprehensive analysis on a genome-wide basis of LEA family remains limited, and the role of LEA in fruit ripening has not been fully explored yet, especially in strawberry, an economic important plant and ideal material for studying fruit ripening.

Results
In this study, a total of 266 putative LEA proteins were identified and characterized in strawberry genome. Subcellular localization prediction indicated that they were mostly localized in chloroplast, cytoplasm and nucleus. Duplication events detection revealed that whole genome duplication or segmental was the main driver for the expansion of LEA family in strawberry. The phylogenetic analysis suggested that FaLEAs were classified into eight groups, among which, LEA2 was the largest subgroup with 179 members, followed by LEA3, dehydrin (DHN), LEA4 and SMP (seed maturation protein). The LEA1 and DHN groups were speculated to play dominant roles in strawberry fruit development and ripening, according to their larger proportion of members detected as differentially expressed genes during such process. Notably, the expression of FaLEA167 belonging to LEA1 group was altered by strawberry maturation, and inhibited by overexpression of negative regulators of ripening (a cytosolic/plastid glyceraldehyde-3-phosphate dehydrogenase, FaGAPC2 and a cytosolic pyruvate kinase, FaPKc2.2). Subsequently, overexpression of FaLEA167 significantly increased the percentage of fruit at green stage, while reduced the full red fruit proportion. In consistent, the anthocyanins content and the fruit skin color variable reflecting a range from greenness to redness (a* value) were significantly reduced. Whereas, FaLEA167 overexpression apparently up-regulated citric acid, soluble protein and malondialdehyde content, but had no obvious effects on total soluble solids, sugar, flavonoids, phenolics content and antioxidant capacity.

Conclusions
These findings not only provided basic information of FaLEA family for further functional research, but also revealed the involvement of FaLEA167 in negatively regulating strawberry fruit ripening, giving new insights into understanding of FaLEA functions.
Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome
Authors: Chen HuiJuan , Zhang YiRan , Wang Bing , Liao Rui , Duan XiaoHong , Yang ChunYan , Chen Jing , Hao YanTong , Shu YingShuang , Cai LiLi , Leng Xue , Qian Nian-Song , Sun DaWei , Niu Beifang , Zhou Qiming 
Published: March 2024

Abstract
Background
Hybridization capture-based targeted next generation sequencing (NGS) is gaining importance in routine cancer clinical practice. DNA library preparation is a fundamental step to produce high-quality sequencing data. Numerous unexpected, low variant allele frequency calls were observed in libraries using sonication fragmentation and enzymatic fragmentation. In this study, we investigated the characteristics of the artifact reads induced by sonication and enzymatic fragmentation. We also developed a bioinformatic algorithm to filter these sequencing errors.

Results
We used pairwise comparisons of somatic single nucleotide variants (SNVs) and insertions and deletions (indels) of the same tumor DNA samples prepared using both ultrasonic and enzymatic fragmentation protocols. Our analysis revealed that the number of artifact variants was significantly greater in the samples generated using enzymatic fragmentation than using sonication. Most of the artifacts derived from the sonication-treated libraries were chimeric artifact reads containing both cis- and trans-inverted repeat sequences of the genomic DNA. In contrast, chimeric artifact reads of endonuclease-treated libraries contained palindromic sequences with mismatched bases. Based on these distinctive features, we proposed a mechanistic hypothesis model, PDSM (pairing of partial single strands derived from a similar molecule), by which these sequencing errors derive from ultrasonication and enzymatic fragmentation library preparation. We developed a bioinformatic algorithm to generate a custom mutation “blacklist” in the BED region to reduce errors in downstream analyses.

Conclusions
We first proposed a mechanistic hypothesis model (PDSM) of sequencing errors caused by specific structures of inverted repeat sequences and palindromic sequences in the natural genome. This new hypothesis predicts the existence of chimeric reads that could not be explained by previous models, and provides a new direction for further improving NGS analysis accuracy. A bioinformatic algorithm, ArtifactsFinder, was developed and used to reduce the sequencing errors in libraries produced using sonication and enzymatic fragmentation.
Lipid mediated plant immunity in susceptible and tolerant soybean cultivars in response to Phytophthora sojae colonization and infection
Authors: Adigun Oludoyin Adeseun , Pham Thu Huong , Grapov Dmitry , Nadeem Muhammad , Jewell Linda Elizabeth , Galagedara Lakshman , Cheema Mumtaz , Thomas Raymond 
Published: March 2024

Abstract
Background
Soybean is one of the most cultivated crops globally and a staple food for much of the world's population. The annual global crop losses due to infection by Phytophthora sojae is currently estimated at $20B USD, yet we have limited understanding of the role of lipid mediators in the adaptative strategies used by the host plant to limit infection. Since root is the initial site of this infection, we examined the infection process in soybean root infected with Phytophthora sojae using scanning electron microscopy to observe the changes in root morphology and a multi-modal lipidomics approach to investigate how soybean cultivars remodel their lipid mediators to successfully limit infection by Phytophthora sojae.

Results
The results reveal the presence of elevated biogenic crystals and more severe damaged cells in the root morphology of the infected susceptible cultivar compared to the infected tolerant cultivars. Furthermore, induced accumulation of stigmasterol was observed in the susceptible cultivar whereas, induced accumulation of phospholipids and glycerolipids occurred in tolerant cultivar.

Conclusion
The altered lipidome reported in this study suggest diacylglycerol and phosphatidic acid mediated lipid signalling impacting phytosterol anabolism appears to be a strategy used by tolerant soybean cultivars to successfully limit infection and colonization by Phytophthora sojae.
Development and acceptability of PETS-Now, an electronic point-of-care tool to monitor treatment burden in patients with multiple chronic conditions: a multi-method study
Authors: Eton David T. , Yost Kathleen J. , Ridgeway Jennifer L. , Bucknell Bayly , Wambua Mike , Erbs Natalie C. , Allen Summer V. , Rogers Elizabeth A. , Anderson Roger T. , Linzer Mark 
Published: March 2024

Abstract

Background
The aim of this study was to develop a web-based tool for patients with multiple chronic conditions (MCC) to communicate concerns about treatment burden to their healthcare providers.

Methods
Patients and providers from primary-care clinics participated. We conducted focus groups to identify content for a prototype clinical tool to screen for treatment burden by reviewing domains and items from a previously validated measure, the Patient Experience with Treatment and Self-management (PETS). Following review of the prototype, a quasi-experimental pilot study determined acceptability of using the tool in clinical practice. The study protocol was modified to accommodate limitations due to the Covid-19 pandemic.

Results
Fifteen patients with MCC and 18 providers participated in focus groups to review existing PETS content. The pilot tool (named PETS-Now) consisted of eight domains (Living Healthy, Health Costs, Monitoring Health, Medicine, Personal Relationships, Getting Healthcare, Health Information, and Medical Equipment) with each domain represented by a checklist of potential concerns. Administrative burden was minimized by limiting patients to selection of one domain. To test acceptability, 17 primary-care providers first saw 92 patients under standard care (control) conditions followed by another 90 patients using the PETS-Now tool (intervention). Each treatment burden domain was selected at least once by patients in the intervention. No significant differences were observed in overall care quality between patients in the control and intervention conditions with mean care quality rated high in both groups (9.3 and 9.2, respectively, out of 10). There were no differences in provider impressions of patient encounters under the two conditions with providers reporting that patient concerns were addressed in 95% of the visits in both conditions. Most intervention group patients (94%) found that the PETS-Now was easy to use and helped focus the conversation with the provider on their biggest concern (98%). Most providers (81%) felt they had learned something new about the patient from the PETS-Now.

Conclusion
The PETS-Now holds promise for quickly screening and monitoring treatment burden in people with MCC and may provide information for care planning. While acceptable to patients and clinicians, integration of information into the electronic medical record should be prioritized.