bluuebunny/crossref_metadata_2025 huggingface dataset:
The Manipulative Effects in the Technology-Facilitated Preservice Tipping Experience
Authors: Fan Alei , Wu Laurie , Ma Chang , Wang Peihao
Published: March 2024

Drawing on persuasion theory and persuasion knowledge theory, this research evaluates the technology-facilitated preservice tipping practices and tipping enhancement strategies currently employed by food ordering and delivery service platforms such as Uber Eats. The findings from two empirical experimental studies show that, in the technology-facilitated preservice tipping encounter, the presence of a reason to tip increases customers’ tipping amount and lowers their inferred manipulative intent of tipping. The lowered inferred manipulative intent of tipping reduces dissatisfaction with the payment experience and enhanced intention to use such a payment app for future service. However, the adoption of additional server personalization attenuates the positive impact of providing tipping reason on the inferred manipulative intent, dissatisfaction with the payment experience and intention to use such a payment app for future service. The research findings offer practical implications to contemporary hospitality practitioners when facing the emerging technology-facilitated preservice tipping encounters, reminding the marketers about customers’ awareness of and reactance toward firms’ persuasion efforts to make customer spend more.
Biomechanical Comparison of All-Suture, All-Inside Meniscus Repair Devices in a Human Cadaveric Meniscus Model
Authors: Massey Patrick A. , Scalisi Wayne , Montgomery Carver , Daily Drayton , Robinson James , Solitro Giovanni F.
Published: March 2024

Objective

Newer all-suture, all-inside meniscus repair devices utilize soft suture anchors. The purpose of this study was to compare the biomechanical performance of 4 meniscus repair devices in human cadaver menisci: the JuggerStitch (all-suture, all-inside), the FiberStitch (all-suture, all-inside), a polyether ether ketone (PEEK) all-inside, and an inside-out device.

Design

Forty human cadaver menisci were tested after creating 20 mm longitudinal tears in the posterior meniscus. Each knee was randomized to 1 of 4 meniscus repair groups: JuggerStitch (all-suture, all-inside), FiberStitch (all-suture, all-inside), FAST-FIX 360 (PEEK-based anchor all-inside), and inside-out (with BroadbandTM tape meniscus needles). For each meniscus, 2 devices were used to prepare vertical mattress repair construct. The specimens were tested by pre-conditioning 20 cycles between 5 N and 30 N and then the tear diastasis was measured, followed by distraction to failure phase after imposing a displacement at a rate of 0.5 mm/s.

Results

Ten menisci were tested in each of the 4 groups. After pre-conditioning, there was no significant difference in the gap formation among groups ( P = 0.212). The average failure load for the JuggerStitch, FiberStitch, PEEK all-inside, and inside-out was 384 N, 311 N, 207 N, and 261 N, respectively, with a significant difference between groups ( P = 0.034). Post hoc analysis showed the JuggerStitch failure load was higher than the PEEK all-inside and inside-out ( P = 0.005, and P = 0.045, respectively). There was no significant difference between the failure load of the JuggerStitch and FiberStitch ( P = 0.225).

Conclusion

The JuggerStitch all-suture device, FiberStitch all-suture device, PEEK all-inside, and inside-out devices have similar biomechanical properties for gapping and stiffness. The JuggerStitch all-suture, all-inside device has superior failure load compared with the PEEK all-inside and inside-out repair for longitudinal meniscus tear repair.
Phosphorylation of chitin and chitosan: A review on its significance and various synthesis routes
Authors: Geeta  , Kumar Satish , Shivani  , Shayoraj  , Saini Mohit , Dubey Santosh Kumar
Published: March 2024

Over the past few decades, chitin and chitosan, value-added biopolymers obtained majorly from seafood wastes, have been extensively evaluated and utilized for their application in plenty of domains such as biomedical, pharmaceutical, agricultural, food processing industries, fuel cells, wastewater curing, and flame retardants. A vast number of physical, chemical, and enzymatic approaches have been followed to improve the biological activities, biocompatibility, and physicochemical properties of chitin and chitosan. Among the innumerable modifications, this article focuses primarily on the importance of phosphorylation, as it intensifies not only water solubility but also tissue regeneration, flame retardation, ionic conductivity, metal chelation, and drug-carrying abilities. Furthermore, the aim of this review is to thoroughly assess various techniques that involve the use of phosphorylating agents such as phosphoric acid, phosphorus acid, phosphorus oxychloride, phosphorus pentoxide, and the grafting method to synthesize phosphorylated derivatives of chitin and chitosan, so that a clear vision can be provided to the reader aimed at choosing a best-fit method for phosphorylation.
A comprehensive review and update on the current state of computer-assisted rehabilitation in implant dentistry
Authors: Michelinakis George , Apostolakis Dimitrios , Nikolidakis Dimitrios , Blum Igor R.
Published: March 2024

Aim:

This paper provides a comprehensive review of the established concepts and newer developments related to computer-assisted implant rehabilitation.

Methods:

Two independent researchers searched the English literature published to 31st December 2023 in the PubMed/Medline database for primary and secondary research and related publications on computer-assisted implant planning, computer-assisted implant placement and computer-assisted implant restoration.

Results:

A total of 58,923 papers were identified, 198 relevant papers were read in full text and 110 studies were finally included. Computer-assisted implant rehabilitation was found to result in more precise implant positioning than freehand placement. Advantages include reduced trauma and surgery time; disadvantages include reduced primary implant stability and higher cost.

Conclusion:

Computer-assisted surgery is particularly indicated in cases of critical anatomy, but may encounter limitations in terms of cost, restricted mouth opening, visibility and adjustment of the surgical guides and the need for prior familiarisation with the procedure. Nonetheless, this surgical technique reduces the post-implant placement complication rate.
Consecutive Microsurgical Cases Performed by Single Surgeon at a Canadian Tertiary Care Center: A Retrospective Review
Authors: Chen Andrew T. , Gormley Jessica , Olaiya Oluwatobi , Voineskos Sophocles H. , Coroneos Christopher J. , Avram Ronen
Published: March 2024

Background: The practice of a microsurgeon evolves over time with experience, changes in clinical interest, and practice setting. Previous reports suggest that complication rates may be influenced by years of practice. The aim of this study was to analyze consecutive microsurgical cases performed by a single surgeon during the first half of their career in a broad microsurgical practice at a Canadian academic tertiary care center. Methods: A retrospective chart review of all free tissue transfers between 2007 and 2020 completed by a single academic plastic surgeon was performed. The primary outcomes were the odds of postoperative complications and free flap failure. The secondary outcomes included the annual number and type of free flap cases over time. Results: The surgeon performed 795 free flaps on 537 patients. There were a total of 131 postoperative complications. There was no statistically significant association between the years in practice and odds of a complication. Overall, there were 26 flap failures, yielding a 96.7% success rate. There was no association between flap failure and years in practice. The most common type of reconstruction was breast, followed by lower extremity and head and neck. There was a significant change in the type of reconstruction cases over time ( P < 0.005). Conclusion: The type and volume of free flap reconstruction conducted by the surgeon has changed over time. In this single surgeon career, surgical experience did not have a significant impact on free flap complications. At our center, free tissue transfer remains a valuable tool for reconstruction in both low and high-risk patients.
Methodological Complexity: A Both/And Approach to Address Tool Validity and Reliability for Assessment of Cultural Responsiveness in Indigenous Serving Schools
Authors: Joseph Darold H. , Keene Chesleigh N. , Castagno Angelina E. , Dass Pradeep M. , Macias Crystal
Published: March 2024

This article presents the first psychometric validation of the Culturally Responsive Assessment of Indigenous Schooling (CRAIS) tool, alongside a call for methodological complexity when engaged in research with and in Indigenous contexts. We examined the 23 culturally responsive schooling (CRS) principles underlying the newly created CRAIS tool in independent samples of curriculum units produced by teachers. Of these, 22 principles loaded into two factors. We further investigated the rationale for all 23 items through a review of the literature and robust discussions about the lived experiences of the authors and the Indigenous teachers with whom we work. We suggest that this both/and approach of quantitative and qualitative analysis results in a richer and more nuanced tool, as compared to what one single method would have rendered. Embracing this methodological complexity allows us to both center Indigenous lived experiences and maintain fidelity to the statistical implications of our work.
The Evolving Complexities of MAID Care in Canada From a Nursing Perspective
Authors: Pesut Barbara , Thorne Sally , Chambaere Kenneth , Hall Margaret , Schiller Catharine J.
Published: March 2024

Medical Assistance in Dying (MAID) legislation has evolved rapidly in Canada with significant impacts on nursing practice. The purpose of this paper is to describe evolving complexities in legislative context and practice standards that influence the experiences nurse practitioners and registered nurses have with MAID. Qualitative interviews were conducted with 25 registered nurses and 10 nurse practitioners from diverse contexts across Canada. Participants described their practices and considerations when discussing MAID as part of advance care planning; their use of, and challenges with, waivers of consent; their practice considerations in negotiating the complexities of clients for whom death is not reasonably foreseeable; and their moral wrestling with the inclusion of MAID for persons whose sole underlying medical condition is mental illness. Findings illustrate the moral complexities inherent in the evolving legislation and the importance of robust health and social care systems to the legal and ethical implementation of MAID in Canada.
Book review: Kevin Rudd, The Avoidable War: The Dangers of a Catastrophic Conflict between the US and Xi Jinping’s China
Authors: Koshy Sanoop Sajan
Published: March 2024

Kevin Rudd, The Avoidable War: The Dangers of a Catastrophic Conflict between the US and Xi Jinping’s China. New York: Public Affairs, 2022, 379 pp. (hardcover). ISBN: 9781541701298
Mexico: Territory of confinement during the pandemic
Authors: Castillo Ramírez Guillermo
Published: March 2024

Since the 1990s, Mexico has been a transit country par excellence in the Americas. However, since the beginning of the 2010s, Mexican territory has been configured as an extended and violent space of migratory containment. In the regional context of Mexico and the United States, the COVID-19 pandemic accentuated state processes of migratory control and criminalization that had been in place for years (such as zero tolerance policies and migrant protection protocols during the Trump administration). Unlike other countries on the American continent, this health emergency in Mexico did not imply the adoption of strict internal measures to limit mobility. Consequently, although the influx of global migrants in transit, mostly Northern Central Americans, slowed during the first months of the pandemic, it did not cease. In fact, since mid-2020, these transitions have multiplied. However, due to the health emergency, asylum seekers and other migrants could not cross the northern border of Mexico as a direct effect of the increase in controls and strict anti-immigrant policies implemented by the United States. The blockade of the northern border, together with the continued influx of even more global migrants (many from northern Central America), meant that Mexico, in a trend that had been going on for years, consolidated itself as a regional and global territory of spatial and temporal confinement (long waiting). Therefore, this article analyzes the geopolitical implications of these processes for Mexico in the midst of a triple health, political and social security crisis.
Better Constant Scores and Active Forward Elevation Using Deltopectoral Versus Anterosuperior Approach for Reverse Shoulder Arthroplasty: Matched Cohort Study
Authors: Nerot Cecile , Berhouet Julien , Garret Jérôme , Kany Jean ,   ReSurg, van Rooij Floris , Hibon Aude , Nover Luca , Saffarini Mo ,   SoFEC, Aswad Richard , Hubert Laurent , Mansat Pierre , Gallinet David , Guery Jacques , Josserand Laurent Nove , Sirveaux François , Peduzzi Lisa , Godenèche Arnaud
Published: March 2024

Purpose

To determine, from a sizable cohort of reverse shoulder arthroplasty (RSA), whether the deltopectoral (DP) or anterosuperior (AS) approach grant better outcomes at a minimum follow-up of 24 months.

Methods

The authors reviewed 743 RSAs in patients with primary osteoarthritis (OA) with or without rotator cuff lesions and secondary OA due to rotator cuff tears. The DP approach was used in 540 and the AS approach in 203. Pre- and post-operative constant scores (CSs) and shoulder range of motion were recorded.

Results

Of the initial cohort of 743 shoulders, 193 (25.7%) were lost to follow-up, 16 (2.1%) died, and 33 (4.4%) were revised; 540 shoulders were operated using DP approach (73%), of which 22 were revised (4.1%), while 203 were operated using the AS approach (27%), of which 11 were revised (5.4%). Propensity score matching resulted in two groups: 172 shoulders operated by DP approach, and 88 shoulders operated by AS approach. Comparing outcomes of the matched groups at 2 or more years also revealed that, compared to the AS approach, the DP approach resulted in significantly better post-operative CSs (67.3 ± 14.0° vs 60.8 ± 18.3, P = 0.017), active forward elevation (137° ± 27.4° vs 129° ± 29.8; P = 0.031).

Conclusion

At 2 or more years following RSA, the DP approach granted significantly better CS (by 6.5 points) and active forward elevation (by 8°) compared to the AS approach. The differences observed are clinically relevant and must be considered to manage patient expectations following RSA and for selecting surgical approach depending on their functional needs.

Level of evidence

III, comparative study
The coyote in the cloud
Authors: Niesner Chase A , Kelty Christopher , Robins Spencer
Published: March 2024

Coyotes (Canis latrans) exist throughout North America and increasingly thrive in dense urban spaces; they also cause controversies when they eat small pets or seem to pose a threat. Based on fieldwork in Los Angeles, and an archive of over 400 conversations collected from the online application Nextdoor (2015–2019), we theorize the emergence of what we call the cloud coyote. Cloud coyotes are not representations but lively actors in coyote politics animated by discussion, debate, and a settler logic of property relations in places like Los Angeles. They do this by performing a threat and justifying a response that includes various attempts at extermination, containment, and assimilation, all of which—even supposedly humane alternatives—further sediment forms of settler colonialism in urban Los Angeles. We diagnose this process, show how it works, and argue that anticolonial practices—in both Los Angeles and its cloudy territories like Nextdoor—are needed to escape from perpetuating its violence.
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

Illite 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

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

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

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

Background

Cardiac 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.

Methods

In 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).

Results

In 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).

Conclusions

Our 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

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

RNA 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

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

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

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

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.
Polymorphisms of IFN signaling genes and FOXP4 influence the severity of COVID-19
Authors: Zhang Feng , Zhou Pingping , Wang Liangliang , Liao Xinzhong , Liu Xuejie , Ke Changwen , Wen Simin , Shu Yuelong
Published: March 2024

Background

The clinical manifestations of COVID-19 range from asymptomatic, mild to moderate, severe, and critical disease. Host genetic variants were recognized to affect the disease severity. However, the genetic landscape differs among various populations. Therefore, we explored the variants associated with COVID-19 severity in the Guangdong population.

Methods

A total of 314 subjects were selected, of which the severe and critical COVID-19 patients were defined as “cases”, and the mild and moderate patients were defined as “control”. Twenty-two variants in interferon-related genes and FOXP4 were genotyped using the MassARRAY technology platform.

Results

IFN signaling gene MX1 rs17000900 CA + AA genotype was correlated with a reduced risk of severe COVID-19 in males (P = 0.001, OR = 0.050, 95%CI = 0.008–0.316). The AT haplotype comprised of MX1 rs17000900 and rs2071430 was more likely to protect against COVID-19 severity (P = 6.3E-03). FOXP4 rs1886814 CC genotype (P = 0.001, OR = 3.747, 95%CI = 1.746–8.043) and rs2894439 GA + AA genotype (P = 0.001, OR = 5.703, 95% CI = 2.045–15.903) were correlated with increased risk of severe COVID-19. Haplotype CA comprised of rs1886814 and rs2894439 was found to be correlated with adverse outcomes (P = 7.0E-04). FOXP4 rs1886814 CC (P = 0.0004) and rs2894439 GA + AA carriers had higher neutralizing antibody titers (P = 0.0018). The CA + AA genotype of MX1 rs17000900 tended to be correlated with lower neutralizing antibody titers than CC genotype (P = 0.0663), but the difference was not statistically significant.

Conclusion

Our study found a possible association between MX1 and FOXP4 polymorphisms and the severity of COVID-19. Distinguishing high-risk patients who develop severe COVID-19 will provide clues for early intervention and individual treatment strategies.
Evaluation of post-dilatation on longitudinal stent deformation and postprocedural stent malapposition in the left main artery by optical coherence tomography (OCT): an in vitro study
Authors: He Qing , Fan Yuqi , Xu Zuojun , Zhang Junfeng
Published: March 2024

Background

The diameter of the ostial and proximal left main coronary artery can be greater than 5.0 mm. However, the diameters of the mostly available coronary drug-eluting stents (DESs) are ≤ 4.0 mm. Whether high-pressure dilatation can increase the diameter of stents from 4.0 to 5.0 mm and whether post-dilatation leads to longitudinal stent deformation (LSD) of 4.0-mm-diameter stents have rarely been studied. Therefore, this study aims to evaluate LSD and stent malapposition of six types of commercially available 4.0-mm-diameter stents in China in a 5.0-mm-diameter artificial blood vessel model by optical coherence tomography (OCT) in vitro.

Methods

The left main coronary artery was simulated by a truncated cone-shaped silicone tube. The internal diameters were 4.0 mm at one end of the silicone tube and 5.0 mm at the other end. Six different types of coronary stents widely used in China were selected for this study. Each stent was respectively implanted into the simulated blood vessel and dilated to a diameter of 4.2 mm according to the stent-balloon pressure compliance table. The stents were subjected to post-dilatation with a 5.0 × 15-mm noncompliant balloon. The LSD ratio of the longitudinal axis of each stent and stent malapposition were measured through OCT, and any fractures of the stents were determined.

Results

None of the six types of stents fractured following post-dilatation. The longitudinal axes of the BuMA and Excrossal stents were slightly shortened, while the other stents were elongated after high-pressure post-dilatation. All stents expanded to a diameter of 5.0 mm without incomplete stent apposition, except for the Nano Plus stent, which remained malapposed after high-pressure post-dilatation.

Conclusion

All 4.0-mm-diameter stents can be expanded to a diameter of 5.0 mm by noncompliant balloon post-dilatation without stent strut fracture. Most stents were found to be well apposed after high-pressure post-dilatation. However, LSD was observed after post-balloon dilatation. Stent malapposition might be positively correlated with the percentage change in stent length.
Comparison of cognitive workload and surgical outcomes between a three-dimensional and conventional microscope macular hole surgery
Authors: Kelkar Aditya , Natarajan S. , Kothari Akshay , Bolisetty Mounika
Published: March 2024

Background

Performing a surgical task subjects the surgeon to multitudinal stressors, especially with the newer 3D technology. The quantum of cognitive workload using this modern surgical system in comparison to the Conventional microscope system remains unexplored. We evaluate the surgeon’s cognitive workload and the surgical outcomes of macular hole(MH) surgery performed on a 3D versus a Conventional microscope operating system.

Methods

50 eyes of 50 patients with MH undergoing surgery using the 3D or Conventional microscope visualization system. Cognitive workload assessment was done by real-time tools(Surgeons’ heart rate [HR] and oxygen saturation[SPO2]) and self-report tool(Surgery Task Load Index[SURG-TLX] questionnaire) of three Vitreoretinal surgeons. Based on the SURG-TLX questionnaire, an assessment of the workload was performed.

Results

Of the 50 eyes, 30 eyes and 20 eyes underwent surgery with the Conventional microscope and the 3D system, respectively. No difference was noted in the MH basal-diameter(p = 0.128), total surgical-duration(p = 0.299), internal-limiting membrane(ILM) peel time(p = 0.682), and the final visual acuity (VA; p = 0.515) between the two groups. Both groups showed significant improvement in VA(p < 0.001) with a 90% closure rate at one-month post-surgery. Cognitive workload comparison, the intraoperative HR(p = 0.024), total workload score(P = 0.005), and temporal-demand dimension(p = 0.004) were significantly more in Conventional microscope group as compared to 3D group. In both the groups, the HR increased significantly from the baseline while performing ILM peeling and at the end.

Conclusion

The surgeon’s cognitive workload is markedly reduced while performing macular hole surgery with a 3D viewing system. Moreover, duration of surgery including ILM peel time, MH closure rates, and visual outcomes remains unaffected irrespective of the operating microscope system.