bluuebunny/crossref_metadata_2025_split huggingface dataset:
B-378 Cell-free Plasma Preparation Workflow Solution
Authors: Manley L , Lopez S , Kothandaramaswamy L , Saunders H , Cheng A 
Published: September 2023

Abstract

Background
Liquid biopsy for the study and monitoring of various cancers has become a growing area of study, pre-analytical sample handling can impact the quality and profile of the circulating tumor nucleic acid. Preparing samples like cell-free plasma for downstream assays is imperative to maintaining quality in downstream applications for clinical research in oncology. To obtain cell-free plasma, blood samples must undergo centrifugation at 2000g for 10 min at 4C followed by a second spin for 30 min at 4C. This two-step spin process presents an issue with labs that don’t have a refrigerated centrifuge suitable for higher speeds.

Methods
Here, we perform a series of studies to investigate the impact of various spin conditions on cell-free nucleic acid recovery and quality. Four plasma centrifugation methods encompassing variables attributing to speed, temperature, and number of centrifugations steps, were evaluated from whole blood tubes obtained from six donors in K2EDTA upfront of nucleic acid isolation with MagMAX™ cell-free TNA nucleic acid isolation chemistry on a KingFisher™ magnetic particle processor. Yield, quality, and functional performance was evaluated from the extracted cell-free nucleic acid and compared across all plasma spin-down methods.

Result
Study results indicated that centrifugation of plasma at lower speeds for a shorter period at room temperature had no negative impact to nucleic acid recovery and integrity.

Conclusion
Here, we offer a plasma spin workflow solution to mid- to high- throughput clinical research labs to allow versatility within the laboratory setup. Reducing the need for refrigerated centrifugation allows clinical researchers to obtain high-quality cfNA suitable for their downstream applications in clinical oncology and genomics research.
Percutaneous closure of ‘complex’ multi-fenestrated atrial septal aneurysm in visceral situs inversus using a multi-device approach: a case report
Authors: Scalera Silvia , Pizzuto Alessandra , Marchese Pietro , Santoro Giuseppe 
Published: September 2023

Abstract

Background
Percutaneous closure is nowadays still deemed challenging in patent forame ovale (PFO) associated to multi-fenestrated atrial septal aneurysm (ASA). This anatomic arrangement is still considered a significant risk factor for recurrence of paradoxical embolism. Theoretically, transcatheter approach could be theoretically even more complex in the case of dextrocardia and visceral situs inversus.

Case summary
A 59-year-old man with history of migraine with aura and multiple cryptogenic strokes was referred for percutaneous closure of a PFO with associated ASA. He had been previously submitted to repeat attempt of percutaneous closure with not self-centering and self-centering devices that failed due to unfavorable anatomic characteristics (dextrocardia with situs viscerum inversus, huge ASA, multiple fenestrations, large PFO). Based on this “complex” anatomy, a sequential 2-step interventional approach aiming to reduce size and mobility of the atrial septal aneurysm with a suture-based approach (Noblestich™ EL, HeartStitch, Fountain Valley, CA, USA) and to close any eventual accessory fenestrations with a not self-centering occluding device was planned. At the end of the procedure, the ASA completely disappeared and no residual shunt was imaged at TEE bubble test.

Discussion
We describe a very rare case of symptomatic ASA-PFO in dextrocardia with situs viscerum inversus as well as an innovative approach to treat such complex anatomic setting by using the suture-based closure of a PFO to reduce size and mobility of an ASA in order to deploy dedicated not-self-centering occluding devices.
Magnetic resonance detection of advanced atrial cardiomyopathy increases the risk for atypical atrial flutter occurrence following atrial fibrillation ablation
Authors: Ferró Elisenda , Pérez Núria , Althoff Till , Guasch Eduard , Prat Susana , Doltra Adelina , Borrás Roger , Tolosana José María , Arbelo Elena , Sitges Marta , Porta-Sánchez Andreu , Roca-Luque Ivo , Mont Lluís , Guichard Jean-Baptiste 
Published: September 2023

Abstract

Aims
Recurrence of arrhythmia after catheter ablation of atrial fibrillation (AF) in the form of atypical atrial flutter (AFL) is common among a significant number of patients and often requires redo ablation with limited success rates. Identifying patients at high risk of AFL after AF ablation could aid in patient selection and personalized ablation approach. The study aims to assess the relationship between pre-existing atrial cardiomyopathy and the occurrence of AFL following AF ablation.

Methods and results
We analysed a cohort of 1007 consecutive AF patients who underwent catheter ablation and were included in a prospective registry. Patients who did not have baseline cardiac magnetic resonance imaging and late gadolinium enhancement (LGE-CMR) or did not experience any recurrences were excluded. A total of 166 patients were included gathering 56 patients who underwent re-ablation due to AFL recurrences and 110 patients who underwent re-ablation due to AF recurrences (P = 0.11). A multiparametric assessment of atrial cardiomyopathy was based on basal LGE-CMR, including left atrial (LA) volume, LA sphericity, and global and segmental LA fibrosis using semiautomated post-processing software. Out of the initial cohort of 1007 patients, AFL and AF occurred in 56 and 110 patients, respectively. An age higher than 65 [odds ratio (OR) = 5.6, 95% confidence interval (CI): 2.2–14.4], the number of previous ablations (OR = 3.0, 95% CI: 1.2–7.8), and the management of ablation lines in the index procedure (OR = 2.5, 95% CI: 1.0–6.3) were independently associated with AFL occurrence. Furthermore, several characteristics assessed by LGE-CMR were identified as independent predictors of AFL recurrence after the index ablation for AF, such as enhanced LA sphericity (OR = 1.3, 95% CI: 1.1–1.6), LA global fibrosis (OR = 1.03, 95% CI: 1.01–1.07), and increased fibrosis in the lateral wall (OR = 1.03, 95% CI: 1.01–1.04).

Conclusion
Advanced atrial cardiomyopathy assessed by LGE-CMR, such as increased LA sphericity, global LA fibrosis, and fibrosis in the lateral wall, is independently associated with arrhythmia recurrence in the form of AFL following AF ablation.
Is use of a long-term proton pump inhibitor or histamine-2 receptor antagonist a risk factor for iron-deficiency anaemia in Taiwan? A neglected clinical drug-drug interaction
Authors: Wu Yi-Ting , Lu Ya-Ting , Chu Chao-Yu , Chao Horng-Jiun , Kuo Li-Na , Cheng Kuei-Ju , Chen Hsiang-Yin 
Published: September 2023

Abstract

Background
Proton pump inhibitors (PPIs) and histamine-2 receptor (H2) antagonists change the gastric pH and reduce the intestinal absorption of nonheme iron. Case reports and case-control studies have demonstrated that absorption of iron is affected by gastric acidity, but the clinical importance of these drug-drug interactions has remained uncertain.

Objectives
The present case-control study employed 2 million longitudinal claims in 2011–2018 in the Taiwan National Health Insurance Research Database to investigate the impact of PPIs/H2 antagonists on the occurrence of iron-deficiency anaemia (IDA).

Methods
The present study retrospectively compared exposure to PPIs/H2 antagonists for 1 year among 5,326 cases with IDA and 21,304 matched controls. The postdiagnosis prescribing pattern was also calculated to understand current practice.

Results
Long-term (≥2 month) use of PPIs/H2 antagonists resulted in a higher risk of developing IDA than noncontinuous use/nonuse of those drugs (adjusted odds ratio [aOR] = 2.36, 95% confidence interval [CI] = 1.94–2.86, P &lt; 0.001). There were significant changes in the postdiagnosis prescribing patterns of PPIs/H2 antagonists. The risk of developing IDA remained significant in the female subgroup (aOR = 2.16, 95% CI = 1.73–2.70, P &lt; 0.001) and was even more prominent in those aged ≥ 50 years (aOR = 2.68, 95% CI = 1.94–3.70, P &lt; 0.05).

Conclusions
This study found that long-term use of PPIs/H2 antagonists increased the risk of developing IDA, and there was strong evidence of prescription pattern adjustments postdiagnosis. Physicians and pharmacists should be aware of this risk when patients are expected to take or have been taking PPIs/H2 antagonists for the long term.
Assessing large-scale mantle compositional heterogeneity from machine learning analysis of 28 global P- and S-wave tomography models
Authors: Rahimzadeh Bajgiran Moloud , Colli Lorenzo , Wu Jonny 
Published: September 2023

SUMMARY
Differences between P- and S-wave models have been frequently used as evidence for the presence of large-scale compositional heterogeneity in the Earth's mantle. Our two-step machine learning (ML) analysis of 28 P- and S-wave global tomographic models reveals that, on a global scale, such differences are for the most part not intrinsic and could be reduced by changing the models in their respective null spaces. In other words, P- and S-wave images of mantle structure are not necessarily distinct from each other. Thus, a purely thermal explanation for large-scale seismic structure is sufficient at present; significant mantle compositional heterogeneities do not need to be invoked. We analyse 28 widely used tomographic models based on various theoretical approximations ranging from ray theory (e.g. UU-P07 and MIT-P08), Born scattering (e.g. DETOX) and full-waveform techniques (e.g. CSEM and GLAD). We apply Varimax principal component analysis to reduce tomography model dimensionality by 83 percent, while preserving relevant information (94 percent of the original variance), followed by hierarchical clustering (HC) analysis using Ward's method to quantitatively categorize all models into hierarchical groups based on similarities. We found two main tomography model clusters: Cluster 1, which we called ‘Pure P wave’, is composed of six P-wave models that only use longitudinal body wave phases (e.g. P, PP and Pdiff); and Cluster 2, which we called ‘Mixed’, includes both P- and S-wave models. P-wave models in the ‘Mixed’ cluster use inversion methods that include inputs from other geophysical and geological data sources, and this causes them to be more similar to S-wave models than Pure P-wave models without significant loss of fitness to P-wave data. Given that inclusion of new data classes and seismic phases in more recent tomographic models significantly changes imaged seismic structure, our ML assessment of global tomography model similarity may improve selection of appropriate P- and S-wave models for future global tomography comparative studies.
Prevalence of parental supply of alcohol to minors: a systematic review
Authors: van der Kruk Shannen , Harrison Nathan J , Bartram Ashlea , Newton Skye , Miller Caroline , Room Robin , Olver Ian , Bowden Jacqueline 
Published: September 2023

Abstract
Parental supply of alcohol to minors (i.e. those under the legal drinking age) is often perceived by parents as protective against harms from drinking, despite evidence linking it with adverse alcohol-related outcomes. This systematic review describes the prevalence of parental supply of alcohol, as reported in the international literature. The review was registered with PROSPERO (CRD42020218754). We searched seven online databases (Medline, Embase, PsycINFO, CINAHL, Scopus, Web of Science and Public Health Database) and grey literature from January 2011 to December 2022 and assessed the risk of bias with the JBI Critical Appraisal Checklist. Among 58 articles included in narrative synthesis from 29 unique datasets, there was substantial variation in the definition and measurement of parental supply of alcohol. Overall prevalence rates ranged from 7.0 to 60.0% for minor-report samples, and from 24.0 to 48.0% for parent-report samples. Data indicate that parental supply prevalence is generally proportionately higher for older minors or later-stage students, for girls, and has increased over time among minors who report drinking. Literature on the prevalence of parental supply of alcohol is robust in quantity but inconsistent in quality and reported prevalence. Greater consistency in defining and measuring parental supply is needed to better inform health promotion initiatives aimed at increasing parents’ awareness.
Spatiotemporal miRNA and transcriptomic network dynamically regulate the developmental and senescence processes of poplar leaves
Authors: Du Kang , Jiang Shenxiu , Chen Hao , Xia Yufei , Guo Ruihua , Ling Aoyu , Liao Ting , Wu Wenqi , Kang Xiangyang 
Published: September 2023

Abstract
Poplar is an important afforestation and urban greening species. Poplar leaf development occurs in stages, from young to mature and then from mature to senescent; these are accompanied by various phenotypic and physiological changes. However, the associated transcriptional regulatory network is relatively unexplored. We first used principal component analysis to classify poplar leaves at different leaf positions into two stages: developmental maturity (the stage of maximum photosynthetic capacity); and the stage when photosynthetic capacity started to decline and gradually changed to senescence. The two stages were then further subdivided into five intervals by gene expression clustering analysis: young leaves, the period of cell genesis and functional differentiation (L1); young leaves, the period of development and initial formation of photosynthetic capacity (L3–L7); the period of maximum photosynthetic capacity of functional leaves (L9–L13); the period of decreasing photosynthetic capacity of functional leaves (L15–L27); and the period of senescent leaves (L29). Using a weighted co-expression gene network analysis of regulatory genes, high-resolution spatiotemporal transcriptional regulatory networks were constructed to reveal the core regulators that regulate leaf development. Spatiotemporal transcriptome data of poplar leaves revealed dynamic changes in genes and miRNAs during leaf development and identified several core regulators of leaf development, such as GRF5 and MYB5. This in-depth analysis of transcriptional regulation during leaf development provides a theoretical basis for exploring the biological basis of the transcriptional regulation of leaf development and the molecular design of breeding for delaying leaf senescence.
Development and validation of a bioanalytical assay for the measurement of total and unbound teicoplanin in human serum
Authors: Mouton J W A , Raaijmakers J , Botterblom M , Toonen M , ter Heine R , Smeets R L , Brüggemann R J M , te Brake L , Jager N G L 
Published: September 2023

Abstract

Background
The glycopeptide teicoplanin is considered first-line treatment for severe infections caused by Gram-positive bacteria. Individualized treatment of teicoplanin is gaining interest. As only protein-unbound drug is pharmacologically active, a sensitive assay measuring unbound and total teicoplanin is indispensable for pharmacological research and dose optimization.

Objectives
To develop and validate a UPLC-MS/MS method to quantify unbound and total teicoplanin in human serum.

Methods
The developed assay was validated according to the ICH guideline M10 on Bioanalytical Method Validation and study sample analysis. Unbound teicoplanin was obtained by ultrafiltration. The assay was cross-validated with a quantitative microsphere (QMS) immunoassay in a side-by-side comparison using 40 patient samples.

Results
With the developed and validated method, all main teicoplanin components (A2-1, A2-2/A2-3, A2-4/A2-5 and A3-1) can be quantified. Total run time was 5.5 min. Concentration range was 2.5–150 mg/L for total and 0.1–25 mg/L for unbound teicoplanin. Precision (coefficient of variation) and accuracy (bias) of total teicoplanin were 5.97% and 107%, respectively, and 7.17% and 108%, respectively, for unbound teicoplanin.
Bland–Altman analysis showed total concentrations measured with the UPLC-MS/MS method were equivalent to the results of the QMS immunoassay. A total of 188 samples from 30 patients admitted to the ICU and haematology department were measured; total concentrations ranged between 2.92 and 98.5 mg/L, and unbound concentrations ranged between 0.37 and 30.7 mg/L.

Conclusions
The developed method provided rapid, precise and accurate measurement of unbound and total teicoplanin. The developed method is now routinely applied in pharmacological research and clinical practice.
Telomeric DNA breaks in human induced pluripotent stem cells trigger ATR-mediated arrest and telomerase-independent telomere damage repair
Authors: Estep Katrina N , Tobias John W , Fernandez Rafael J , Beveridge Brinley M , Johnson F Brad 
Published: September 2023

Abstract
Although mechanisms of telomere protection are well-defined in differentiated cells, how stem cells sense and respond to telomere dysfunction, in particular telomeric double-strand breaks (DSBs), is poorly characterized. Here, we report the DNA damage signaling, cell cycle, and transcriptome changes in human induced pluripotent stem cells (iPSCs) in response to telomere-internal DSBs. We engineer human iPSCs with an inducible TRF1-FokI fusion protein to acutely induce DSBs at telomeres. Using this model, we demonstrate that TRF1-FokI DSBs activate an ATR-dependent DNA damage response, which leads to p53-independent cell cycle arrest in G2. Using CRISPR–Cas9 to cripple the catalytic domain of telomerase reverse transcriptase, we show that telomerase is largely dispensable for survival and lengthening of TRF1-FokI-cleaved telomeres, which instead are effectively repaired by robust homologous recombination (HR). In contrast to HR-based telomere maintenance in mouse embryonic stem cells, where HR causes ZSCAN4-dependent extension of telomeres beyond their initial lengths, HR-based repair of telomeric breaks is sufficient to maintain iPSC telomeres at a normal length, which is compatible with sustained survival of the cells over several days of TRF1-FokI induction. Our findings suggest a previously unappreciated role for HR in telomere maintenance in telomerase-positive iPSCs and reveal distinct iPSC-specific responses to targeted telomeric DNA damage.
Comparison of the Standard E TB-Feron ELISA and QuantiFERON-TB Gold PLUS assays: the advantageous use of whole recombinant protein antigens for latent tuberculosis diagnosis
Authors: Lee Da-Gyum , Kang Jihye , Jung Jihee , Kim Taeyoon , Kim Jiyeon , Lee Hyunjin , Lee Junghee , Won Youngsub , Ryoo Sungweon 
Published: September 2023

Abstract
The laboratory diagnosis of latent tuberculosis is often performed using interferon-gamma release assays. Here, we compared two enzyme-linked immunosorbent assay-based interferon-gamma release assays, namely, the newly developed Standard E TB-Feron enzyme-linked immunosorbent assay (STFE) and the QuantiFERON-TB Gold PLUS assay (QFT-GP), using samples from 155 participants. The STFE is based on using whole EAST6 and CFP10 recombinant antigens for latent tuberculosis diagnosis. The participants were classified into four groups and screened using both assays per the manufacturers’ instructions. Thereafter, two statistical analyses were conducted to compare the obtained results. First, the STFE results were compared with the QTF-GP results (used as the gold standard) to calculate the total concordance, sensitivity, and specificity of STFE. Second, positivity and negativity concordances were calculated to differentiate healthy participants from participants with tuberculosis. The STFE showed 97% and 94% sensitivity and specificity, respectively. Furthermore, its positivity and negativity concordances were 91% and 98%, respectively. These results indicate the coordinated clinical performance of STFE in detecting latent tuberculosis and its improved performance in targeting tuberculosis-infected participants. Based on the comparison of the latent tuberculosis diagnostic abilities of STFE and QFT-GP, we establish the suitability and superior performance of STFE as a diagnostic tool.
A biomarker framework for cardiac aging: the Aging Biomarker Consortium consensus statement
Authors:   Aging Biomarker Consortium, Zhang Weiwei , Che Yang , Tang Xiaoqiang , Chen Siqi , Song Moshi , Wang Li , Sun Ai-Jun , Chen Hou-Zao , Xu Ming , Wang Miao , Pu Jun , Li Zijian , Xiao Junjie , Cao Chun-Mei , Zhang Yan , Lu Yao , Zhao Yingxin , Wang Yan-Jiang , Zhang Cuntai , Shen Tao , Zhang Weiqi , Tao Ling , Qu Jing , Tang Yi-Da , Liu Guang-Hui , Pei Gang , Li Jian , Cao Feng 
Published: September 2023

AbstractCardiac aging constitutes a significant risk factor for cardiovascular diseases prevalent among the elderly population. Urgent attention is required to prioritize preventive and management strategies for age-related cardiovascular conditions to safeguard the well-being of elderly individuals. In response to this critical challenge, the Aging Biomarker Consortium (ABC) of China has formulated an expert consensus on cardiac aging biomarkers. This consensus draws upon the latest scientific literature and clinical expertise to provide a comprehensive assessment of biomarkers associated with cardiac aging. Furthermore, it presents a standardized methodology for characterizing biomarkers across three dimensions: functional, structural, and humoral. The functional dimension encompasses a broad spectrum of markers that reflect diastolic and systolic functions, sinus node pacing, neuroendocrine secretion, coronary microcirculation, and cardiac metabolism. The structural domain emphasizes imaging markers relevant to concentric cardiac remodeling, coronary artery calcification, and epicardial fat deposition. The humoral aspect underscores various systemic (N) and heart-specific (X) markers, including endocrine hormones, cytokines, and other plasma metabolites. The ABC’s primary objective is to establish a robust foundation for assessing cardiac aging, thereby furnishing a dependable reference for clinical applications and future research endeavors. This aims to contribute significantly to the enhancement of cardiovascular health and overall well-being among elderly individuals.
Secondary gas in debris discs released following the decay of long-lived radioactive nuclides, catastrophic, or resurfacing collisions
Authors: Bonsor Amy , Wyatt Mark C , Marino Sebastian , Davidsson Björn J R , Kral Quentin , Thebault Philippe 
Published: September 2023

ABSTRACT
Kuiper-like belts of planetesimals orbiting stars other than the Sun are most commonly detected from the thermal emission of small dust produced in collisions. Emission from gas, most notably CO, highlights the cometary nature of these planetesimals. Here, we present models for the release of gas from comet-like bodies in these belts, both due to their thermophysical evolution, most notably the decay of long-lived radioactive nuclides, and collisional evolution, including catastrophic and gentler resurfacing collisions. We show that the rate of gas release is not proportional to the rate of dust release, if non-catastrophic collisions or thermal evolution dominate the release of CO gas. In this case, care must be taken when inferring the composition of comets. Non-catastrophic collisions dominate the gas production at earlier times than catastrophic collisions, depending on the properties of the planetesimal belt. We highlight the importance of the thermal evolution of comets, including crucially the decay of long-lived radioactive nuclides, as a source of CO gas around young (&lt;50 Myr) planetary systems, if large (10–100 km) planetesimals are present.