bluuebunny/crossref_metadata_2025 huggingface dataset:
APEX: Automated Protein EXpression inEscherichia coli
Authors: Kasprzyk Martyna , Herrera Michael A. , Stracquadanio Giovanni
Published: August 2024

Heterologous protein expression is an indispensable strategy to generate significant amounts of recombinant proteins. To this end,Escherichia coli(E. coli) is one the most used microbial host for recombinant protein production due to its rapid growth, well-characterised genetics, and ability to produce recombinant proteins in high yields using modern recombinant DNA technology. However, while there is a plethora of robust protein expression protocols forE. coli, these methods are often unsuitable for high-throughput screening due to their significant resource and time consumption; these protocols are also susceptible to operator error and inconsistency.

To address these challenges, we have developed APEX, a robust and automated protocol for recombinant protein production inE. coli. APEX leverages the accessible, open-source Opentrons OT-2 platform to automate microbial handling and protein expression with high precision and repro-ducibility. APEX can be configured to perform heat shock transformation, colony selection, colony sampling, inoculation, subculturing and protein expression using a low-cost, minimal OT-2 hardware setup. We further demonstrate the efficacy of our automated transformation workflows using a variety of plasmids (2.7-17.7 kb), and exemplify the automated heterologous expression of a diverse array of proteins (27-222 kDa). Designed with customization, modularity and user-friendliness in mind, APEX can be easily adapted to the operator’s needs without requiring any coding expertise.

APEX is available athttps://github.com/stracquadaniolab/apex-nfunder the AGPL3 license.
A Light Sensitive Hyaluronic Acid-based Hydrogel for 3D Culturing, Differentiation, and Harvesting of Mesenchymal Stromal Cells
Authors: Palmieri Francesco , Gueye Marieme , Vicario del Rio Lucia , Bunschuh Saskia , Chopra Pradeep , Mihăilă Silvia , Vermonden Tina , Levato Riccardo , Boons Geert-Jan
Published: August 2024

Hydrogels derived from natural sources are commonly used for 3D cell culturing due to their favourable interactions with cells. However, these biomaterials (e.g. Matrigel) suffer from variations in composition, limited mechanical tunability, the presence of xenogenic components and difficulties of cell retrieval. Semi-synthetic hydrogels are emerging to address these limitations, making these attractive for drug delivery and tissue engineering. Here, we describe a hydrogel platform based on hyaluronic acid (HA) modified by (1R,8S,9S)-bicycle[6.1.0]non-4-yn-9-ylmethanol (BCN) and a cross-linker composed of light sensitiveo-nitrobenzyl moieties and polyethylene glycol (PEG) chains terminating in azides. The two components can undergo strain-promoted azide-alkyne cycloaddition (SPAAC) resulting in rapid gel formation. The stiffness of the hydrogel can be modulated by varying the crosslinker ratio and multi-functionalizing is possible by the incorporation of chemical cues modified by an azide. The fast hydrogelation enables easy encapsulation of cells and harvesting with preservation of viability is possible be short exposure to UV light. Moreover, it is demonstrated that visible light (405 nm) can soften the hydrogel resulting in phenotypical changes of human Mesenchymal Stromal Cells (hMSCs) co-cultured with endothelial colony-forming cells (ECFCs) with high viability. Our findings highlight that the photosensitive HA-based hydrogel provides a versatile and biocompatible platform for cell culture and tissue engineering applications, offering advantages over traditional 3D cell culturing platforms.
An extra-glycolytic function for hexokinase 2 as an RNA-binding protein regulatingSOX10mRNA translation in melanoma
Authors: Dian Ana Luisa , Moya-Plana Antoine , Claps Giuseppina , Labbé Céline M. , Quidville Virginie , Baille Dorothée , Roy Séverine , Raynal Virginie , Baulande Sylvain , Robert Caroline , Vagner Stéphan
Published: August 2024

Several studies have reported the importance of aerobic glycolysis in melanoma development. Although metabolic benefits of glycolysis have been extensively described in tumor cells, the extra-metabolic functions linked to this energetic pathway in melanoma growth and proliferation have not been clearly established yet. Recently, some key glycolytic enzymes, such as GAPDH and PKM2, were reported to regulate mRNA translation. Translational control of gene expression is considered as a critical effector in cancer biology, representing a highly promising area of research. Here, we report that Hexokinase 2 (HK2), a glucose kinase that catalyzes the first step of glycolysis, is an RNA binding protein (RBP) that regulates mRNA translation in melanoma. We show that siRNA-mediated HK2 depletion changes the translational landscape of melanoma cells. Polysome profiling experiments and RNA-Seq indicate that the translational regulation exerted by HK2 is partly independent of the metabolic status or the glycolytic pathway. We found that HK2 specifically regulates the translation of the mRNA encoding SOX10, a transcription factor implicated in the regulation of tumor initiation, maintenance and progression in melanoma. RNA-protein interaction assays, including crosslinking immunoprecipitation (CLIP), indicate that HK2 is an RBP whose interaction with RNA is independent of its hexokinase activity or subcellular localization. We also show that HK2 specifically associates with the 5’ untranslated region (5’UTR) of theSOX10mRNA, and that several deletions in this region decreases both HK2-SOX10mRNA association andSOX105’ UTR-mediated translation. We further show that HK2-dependent SOX10 translational regulation is involved in melanoma cell proliferation and colony formation. Collectively, our data highlight a non-metabolic function of HK2, indicating that melanoma cells may enhance glycolysis for purposes beyond simple anabolism.
TooT-PLM-P2S: Incorporating Secondary Structure Information into Protein Language Models
Authors: Ghazikhani Hamed , Butler Gregory
Published: August 2024

In bioinformatics, modeling the protein space to better predict function and structure has benefitted from Protein Language Models (PLMs). Their basis is the protein’s amino acid sequence and self-supervised learning. Ankh is a prime example of such a PLM. While there has been some recent work on integrating structure with a PLM to enhance predictive performance, to date there has been no work on integrating secondary structure rather than three-dimensional structure. Here we present TooT-PLM-P2S that begins with the Ankh model pre-trained on 45 million proteins using self-supervised learning. TooT-PLM-P2S builds upon the Ankh model by initially using its pre-trained encoder and decoder. It then undergoes an additional training phase with approximately 10,000 proteins and their corresponding secondary structures. This retraining process modifies the encoder and decoder, resulting in the creation of TooT-PLM-P2S. We then assess the impact of integrating secondary structure information into the Ankh model by comparing Ankh and TooT-PLM-P2S on eight downstream tasks including fluorescence and solubility prediction, sub-cellular localization, and membrane protein classification. For both Ankh and TooT-PLM-P2S the downstream tasks required task-specific training. Few of the results showed statistically significant differences. Ankh outperformed on three of the eight tasks, TooT-PLM-P2S did not outperform on any task for the primary metric. TooT-PLM-P2S did outperform for the precision metric for the task of discriminating membrane proteins from non-membrane proteins. This study requires future work with expanded datasets and refined integration methods.
An Automated High-throughput Affinity Capture-Mass Spectrometry Platform with Data- Independent Acquisition
Authors: Jing Hui , Richardson Paul L. , Potts Gregory K. , Senaweera Sameera , Marin Violeta L , McClure Ryan , Banlasan Adam , Tang Hua , Kath James E. , Ma Renze , Williams Jon D.
Published: August 2024

Affinity capture (AC) combined with mass spectrometry (MS)-based proteomics is highly utilized throughout the drug discovery pipeline to determine small molecule target selectivity and engagement. However, the tedious sample preparation steps and time-consuming MS acquisition process has limited its use in high-throughput format. Here, we report an automated workflow employing biotinylated probes and streptavidin magnetic beads for small molecule target enrichment in 96-well plate format, ending with direct sampling from EvoSep Solid Phase Extraction tips for liquid chromatography (LC)-tandem mass spectrometry (MS/MS) analysis. The streamlined process significantly reduced both overall and hands-on time needed for sample preparation. Additionally, we developed a data-independent acquisition-mass spectrometry (DIA-MS) method to establish an efficient label-free quantitative chemical proteomic kinome profiling workflow. DIA-MS yielded coverage of ∼380 kinases, a >60% increase compared to using a data-dependent acquisition (DDA)-MS method and provided reproducible target profiling of the kinase inhibitor dasatinib. We further showcased the applicability of this AC-MS workflow for assessing the selectivity of two clinical-stage CDK9 inhibitors against ∼250 probe-enriched kinases. Our study here provides a roadmap for efficient target engagement and selectivity profiling in native cell or tissue lysates using AC-MS.
Identification of the Polo-like kinase substrate required for homologous synapsis inC. elegans
Authors: Gold Ariel L. , Hurlock Matthew E. , Guevara Alicia M. , Isenberg Lilah Y. Z. , Kim Yumi
Published: August 2024

The synaptonemal complex (SC) is a zipper-like protein structure that aligns homologous chromosome pairs and regulates recombination during meiosis. Despite its conserved appearance and function, how synapsis occurs between chromosome axes remains elusive. Here, we demonstrate that Polo-like kinases (PLKs) phosphorylate a single conserved residue in the disordered C-terminal tails of two paralogous SC subunits, SYP-5 and SYP-6, to establish an electrostatic interface between the SC central region and chromosome axes inC. elegans. While SYP-5/6 phosphorylation is dispensable for the ability of SC proteins to self-assemble, local phosphorylation by PLKs at the pairing center is crucial for SC elongation between homologous chromosome axes. Additionally, SYP-5/6 phosphorylation is essential for asymmetric SC disassembly and proper PLK-2 localization after crossover designation, which drives chromosome remodeling required for homolog separation during meiosis I. This work identifies a key regulatory mechanism by which localized PLK activity mediates the SC-axis interaction through phosphorylation of SYP-5/6, coupling synapsis initiation to homolog pairing.
Data-driven determination of plant growth stages for improved weather index insurance design
Authors: Zou Jing , Odening Martin , Okhrin Ostap
Published: August 2024

Purpose

This paper aims to improve the delimitation of plant growth stages in the context of weather index insurance design. We propose a data-driven phase division that minimizes estimation errors in the weather-yield relationship and investigate whether it can substitute an expert-based determination of plant growth phases. We combine this procedure with various statistical and machine learning estimation methods and compare their performance.

Design/methodology/approach

Using the example of winter barley, we divide the complete growth cycle into four sub-phases based on phenology reports and expert instructions and evaluate all combinations of start and end points of the various growth stages by their estimation errors of the respective yield models. Some of the most commonly used statistical and machine learning methods are employed to model the weather-yield relationship with each selected method we applied.

Findings

Our results confirm that the fit of crop-yield models can be improved by disaggregation of the vegetation period. Moreover, we find that the data-driven approach leads to similar division points as the expert-based approach. Regarding the statistical model, in terms of yield model prediction accuracy, Support Vector Machine ranks first and Polynomial Regression last; however, the performance across different methods exhibits only minor differences.

Originality/value

This research addresses the challenge of separating plant growth stages when phenology information is unavailable. Moreover, it evaluates the performance of statistical and machine learning methods in the context of crop yield prediction. The suggested phase-division in conjunction with advanced statistical methods offers promising avenues for improving weather index insurance design.
The art of deception: humanizing AI to outsmart detection
Authors: Ayub Taseef , Ahmad Malla Rayees , Khan Mashood Yousuf , Ganaie Shabir Ahmad
Published: August 2024

Purpose

The study aims to investigate the influence of HIX.AI, an artificial intelligence (AI) tool that humanizes the generated content, on the detection capabilities of AI-generated text detectors.

Design/methodology/approach

The study investigates the reliability of six AI-generated content detection tools by passing ten essays, five each generated using Chat Generative Pre-Trained Transformer (ChatGPT) and Bard (Gemini) before and after passing through HIX.AI, which humanizes the AI-generated content.

Findings

The study found that the selected AI-generated text detectors identified the generated content with inconsistencies. Some of the essays were falsely identified as human-written by a few detectors, indicating that the detectors are unreliable. Post-HIX.AI application found that all the essays were passed as human-written except two, which identified as AI-generated and mixed content by two separate detectors.

Practical implications

The findings present the evolving field of AI-generated text detectors and the tools that can bypass the detectors highlighting the difficulties in identifying the generated content in the presence of the humanization tool. Passing the generated content as human-written has serious consequences, especially in academics. Hence, the study recommends more robust detectors to distinguish human-written and AI-generated content accurately.

Originality/value

The study contributes to the existing literature on AI text detectors and highlights the challenges that humanization tools pose in identifying AI-generated text by AI text detectors.
Serial mediation effect of service innovation and word of mouth on mutual fund investment decision through mobile customer relationship management
Authors: Deb Suman Kumar , Jain Ruchi , Marwah Sanjiv , Deb Varsha
Published: August 2024

Purpose

The purpose of this paper is to examine the effect of mobile customer relationship management (mCRM), service innovation (SI) and word of mouth (WOM) on the investment decisions (IDs) of mutual fund investors.

Design/methodology/approach

This paper presents a new model for impacting the IDs of mutual fund investors. To verify the suggested model, Partial Least Squares with Structural Equation Modelling are used. For analysis, a survey questionnaire is designed, and data inputs were invited from more than 400 online mutual fund investors in Delhi NCR.

Findings

The outcomes reveal that the ID of mutual fund investors is significantly influenced by WOM. WOM, in turn, is significantly impacted by mCRM applications through SI playing a mediating role.

Research limitations/implications

The limitation with reference to survey respondents was that only online mutual fund investors using mCRM applications were considered. Moreover, this study was conducted in Delhi NRC, and a limited sample was considered.

Practical implications

The result from this research helps the financial organisation to consider SI in their mCRM application as one of the main concerned areas for increased WOM that directly influences the ID of mutual fund investors.

Originality/value

This study highlighted the impact of SI and WOM on the mutual fund investors’ decision, who use mCRM application. The outcome may contribute to the theoretical framework of IDs concerning mCRM applications. The results of this research offer practical implications for financial organisations in strategising their marketing and product development plans in the context of mutual funds. Also, the mutual fund ID through mCRM application is positively influenced by SI and WOM using both constructs as sequential mediating tools. This research offers new insights into mCRM application for mutual fund investors and financial organisations in India.
How to promote resilience in the supply chain in the context of COVID-19? An exploratory study using the Delphi method
Authors: Santos Devisson Mesquita dos , Lopes Fernanda Leandra Leal , Melo André Cristiano Silva , Nunes Denilson Ricardo de Lucena , Rampasso Izabela Simon , Martins Vitor William Batista
Published: August 2024

Purpose

This paper is dedicated to elaborating, proposing and validating an action plan to enhance the mitigation of risks generated by the COVID-19 pandemic in the electric sector supply chain, aiming to promote a more resilient supply chain.

Design/methodology/approach

For this, a systematic review of the literature was carried out to prepare an action plan that was validated by a group of experts, through the Delphi methodology.

Findings

As a result, an action plan was obtained, with 18 actions subdivided into 13 resilience elements and related to 20 main risks arising from the pandemic. The actions oriented to the development of relationships among supply chain members, promotion of a culture oriented to learning and problem solving, contingency plan, safety stock and risk management were pointed as those capable of generating resilience in the chain analyzed in the moment of crisis.

Originality/value

The results achieved can contribute to the expansion of debates in the area of resilient supply chain management, as well as contribute to supply chain managers in their elaboration and definition of actions that aim to make the supply chain more resilient. It is noteworthy that no similar study was found in the literature considering the specificities of supply chain management in the Brazilian Amazon region.
To protect and to serve? Comparing students’ perceptions of the legitimacy of the campus police in urban and suburban contexts
Authors: Jacobsen Shannon K.
Published: August 2024

Purpose

Given that previous research examining students’ perceptions of the legitimacy of the campus police (CP) has largely taken place on a single campus and utilized quantitative methods, the purpose of this qualitative study was to understand how community context shapes students’ interactions with and perceptions of the CP in two distinct campus settings.

Design/methodology/approach

This study draws on in-depth interviews with 70 undergraduates, including 36 attending a university in a relatively safe, affluent suburban area and 34 attending a university in a high crime, disadvantaged urban area.

Findings

Although participants at both universities appreciated the presence and visibility of the CP, some Suburban U students felt that rather than being protected from outside threats, they were instead policed for engaging in behaviors that they deemed typical of the college experience. Alternatively, Urban U students expressed the opposite of their CP, providing evidence that brief and positive officer-initiated encounters can enhance perceptions of legitimacy, particularly in settings characterized by higher crime rates.

Research limitations/implications

These findings have implications for how the CP can build trust and legitimacy among students to enhance campus safety and foster future compliance and mutual respect.

Originality/value

This study extends the findings of previous research in two important ways. First, it compares two starkly different campus contexts to understand how community setting and local crime rates influence students’ perceptions of the CP, and second, it utilizes both a comparative and qualitative research design.
Food safety, voluntary recall and firm reputation
Authors: Yu Jianyu , Cai Dongling , Gong Qiang , Mo Jiaying
Published: August 2024

Product recalls are direct remedies for producers in case of food safety problems. Unlike in the United States or other developed countries, in China, voluntary recalls are rarely documented in the food sector. The purpose of this paper is to address two questions: (1) why do firms adopt different recall strategies in different countries; (2) under what circumstances can voluntary recall help firms build up their food safety reputation? Based on the theory of collective reputation, we develop a dynamic model to incorporate firms' recall strategy and investigate the impact of such a strategy on industry collective reputation. The model takes into account production hazards: producers' lapses in food safety despite good‐faith efforts. Our results show that voluntary recall helps a firm to maintain a good historical record. Hence, firms are likely to achieve a high level of collective reputation under voluntary recall. However, a firm is willing to initiate voluntary recall only if the collective reputation is high enough. This explains the current situation in China: as consumers show little trust (belief in collective reputation is low), firms cannot recover the recall loss and thus have no incentive to initiate a voluntary recall.
Leveraging NLP for crisis communication management: A case study of news media analysis of the COVID‐19 pandemic in two Nordic countries
Authors: Mykkänen Markus , Patron Anri , Badham Mark , Valentini Chiara
Published: August 2024

The news media plays a vital role in influencing public perceptions about topics, issues and crises. They also act as important intermediaries between organizations and public, enabling organizations to shape how people think about crisis topics and actors. Monitoring news coverage and assessing the news media's agenda‐setting role in a crisis can help organizations respond more effectively to emerging situations. When crises are prolonged and affect many countries, media analysis can become a tedious task for crisis managers. This study demonstrates how natural language processing (NLP) methods can be utilized in news media analysis of crisis situations, such as an extended cross‐national pandemic. Specifically, it demonstrates the possibilities of using NLP to identify and compare the salience of diverse crisis topics and how the media treat these topics and crisis actors (first‐ and second‐level agenda‐setting) across countries, news outlets, and time. The COVID‐19 pandemic serves as an illustrative case study to showcase the application of NLP techniques to provide insights into public perceptions of a major health crisis shaped by the news media in two Nordic countries (Finland and Sweden). Findings show the suitability of NLP methods to detect nuanced differences in news media coverage and offer relevant knowledge of how public perceptions and responsibility attribution fluctuate across time and countries.
A stepped wedge cluster randomized trial to evaluate the effectiveness of a multisite family caregiver skills training program
Authors: Van Houtven Courtney Harold , Coffman Cynthia J. , Decosimo Kasey , Grubber Janet M. , Dadolf Joshua , Sullivan Caitlin , Tucker Matthew , Bruening Rebecca , Sperber Nina R. , Stechuchak Karen M. , Shepherd‐Banigan Megan , Boucher Nathan , Ma Jessica E. , Kaufman Brystana G. , Colón‐Emeric Cathleen S. , Jackson George L. , Damush Teresa M. , Christensen Leah , Wang Virginia , Allen Kelli D. , Hastings Susan N.
Published: August 2024

Objective

To assess the effects of an evidence‐based family caregiver training program (implementation of Helping Invested Families Improve Veteran Experiences Study [iHI‐FIVES]) in the Veterans Affairs healthcare system on Veteran days not at home and family caregiver well‐being.

Data Sources and Study Setting

Participants included Veterans referred to home‐ and community‐based services with an identified caregiver across 8 medical centers and confirmed family caregivers of eligible Veterans.

Study Design

In a stepped wedge cluster randomized trial, sites were randomized to a 6‐month time interval for starting iHI‐FIVES and received standardized implementation support. The primary outcome, number of Veteran “days not at home,” and secondary outcomes, changes over 3 months in measures of caregiver well‐being, were compared between pre‐ and post‐iHI‐FIVES intervals using generalized linear models including covariates.

Data Collection/Extraction Methods

Patient data were extracted from the electronic health record. Caregiver data were collected from 2 telephone‐based surveys.

Principal Findings

Overall, n = 898 eligible Veterans were identified across pre‐iHI‐FIVES (n = 327) and post‐iHI‐FIVES intervals (n = 571). Just under one fifth (17%) of Veterans in post‐iHI‐FIVES intervals had a caregiver enroll in iHI‐FIVES. Veteran and caregiver demographics in pre‐iHI‐FIVES intervals were similar to those in post‐iHI‐FIVES intervals. In adjusted models, the estimated rate of days not at home over 6‐months was 42% lower (rate ratio = 0.58 [95% confidence interval: 0.31–1.09; p = 0.09]) post‐iHI‐FIVES compared with pre‐iHI‐FIVES. The estimated mean days not at home over a 6‐month period was 13.0 days pre‐iHI‐FIVES and 7.5 post‐iHI‐FIVES. There were no differences between pre‐ and post‐iHI‐FIVES in change over 3 months in caregiver well‐being measures.

Conclusions

Reducing days not at home is consistent with effectiveness because more time at home increases quality of life. In this study, after adjusting for Veteran characteristics, we did not find evidence that implementation of a caregiver training program yielded a reduction in Veteran's days not at home.
Assessing and supporting children and young people with probable or diagnosed fetal alcohol spectrum disorder: The experience of clinicians working within child and adolescent mental health services
Authors: Tanfield Yasmin , Burrows Kathy , Middlemiss Megan
Published: August 2024

Background

Fetal alcohol spectrum disorders (FASD) are a group of conditions that occur due to prenatal alcohol exposure (PAE), which impacts physical, behavioral, and cognitive ability. The literature demonstrates that healthcare professionals lack knowledge and understanding of FASD, resulting in children and young people (CYP) often getting misdiagnosed with neurodevelopmental disorders or the diagnosis of FASD missed, increasing their risk of experiencing secondary mental health difficulties. Child and Adolescent Mental Health Services (CAMHS) are the commissioned service to diagnose neurodevelopmental conditions and support CYP with mental health difficulties, therefore, it is likely that CYP with probable or diagnosed FASD will present in CAMHS. There is currently no research exploring the awareness and understanding of FASD within these services.

Methods

Constructivist grounded theory was utilized to explore the barriers and facilitators clinicians experience when assessing and supporting CYP with probable or diagnosed FASD within CAMHS. A sample of 12 CAMHS clinicians from an NHS Mental Health Trust situated in the Northeast of England were interviewed. Interviews were transcribed and analyzed and grounded theory techniques were utilized to generate an end model.

Results

The end model was developed on a box analogy with four categories. ‘Unable to Open the Box’ captures barriers CAMHS clinicians experience when exploring FASD, ‘Things that Help Open the Box’ captures facilitators CAMHS clinicians experience when exploring FASD, ‘Asking Others About the Box’ captures systemic influences CAMHS clinicians may experience when exploring FASD, and ‘Making the Box Easier to Open in Future’ captures how we can support CAMHS clinicians moving forward to explore FASD.

Conclusions

This model provides new insights into the barriers and facilitators CAMHS clinicians experience when assessing and supporting CYP with probable or diagnosed FASD, highlighting key clinical implications. Recommendations for future research are outlined to expand the knowledge base for this area.
Prognostic mutations identified by whole‐exome sequencing and validation of the Molecular International Prognostic Scoring System in myelodysplastic syndromes after allogeneic haematopoietic stem cell transplantation
Authors: Wang Hong , Li Xueqian , Qi Jiaqian , Liu Hong , Chu Tiantian , Xu Xiaoyan , Qiu Huiying , Fu Chengcheng , Tang Xiaowen , Ruan Changgeng , Wu Depei , Han Yue
Published: August 2024

In this study, we used the whole‐exome sequencing (WES) approach to obtain genomic profiles from 92 marrow samples of myelodysplastic syndrome (MDS) patients before haematopoietic stem cell transplantation. We identified 129 mutations in 45 driver genes. Fifty‐five patients (59.8%) carried at least 1 driver mutation. The splicing factor U2AF1 was the most frequently mutated in the cohort (21 cases, 23%), followed by BCOR (9 cases, 10%), ASXL1 (8 cases, 9%), TET2 (6 cases, 7%), NPM1 (5 cases, 5%), RUNX1 (5 cases, 5%), and SETBP1 (5 cases, 5%). WES also identified 49 possible oncogenic variants in six genes (PIEZO1, LOXHD1, MYH13, DNAH5, DPH1, and USH2A) that were associated with overall survival (OS) or relapse‐free survival (RFS) in MDS after transplantation. Multivariate analysis showed mutations in DNAH5 and USH2A to be independent risk factors for OS. Mutations in DNAH5 and LOXHD1 were risk factors for worse RFS. The Molecular International Prognostic Scoring System retained its independent prognostic significance for RFS after multivariate analysis.
The plasticisation model of dye diffusion: Part 2
Authors: Burkinshaw Stephen M.
Published: August 2024

Temperature dependent equilibrium dye adsorption data reported forChlorazol Fast Scarlet 8B, Durazol Red 2BandChrysophenine Gon cotton, CV and CUP fibres andDurazol Grey RGon cotton and CV fibres in the presence of a constant amount of added inorganic electrolyte between 60°C and 90°C, as well asChrysophenine Gon cellophane sheet in the presence of varying amounts of added inorganic electrolyte, between 60°C and 97.5°C, was re‐evaluated using the Williams‐Landel‐Ferry equation. The results obtained suggest that the plasticisation model of dye diffusion appears to offer a reasonable explanation of the temperature dependent equilibrium adsorption of direct dyes on cellulosic fibres/polymers.
Preference changes and index number theory
Authors: Le Thu Huyen , Yu Kam
Published: August 2024

The economic approach to the cost of living index assumes that consumer preferences remain constant over time. This assumption poses little risk in calculating a short‐run intertemporal bilateral price index. The assumption, however, breaks down in the case of a fixed‐based time series index spanning a long period and in the context of international comparison. The economic analysis of preference changes, however, is not well‐established. In this paper, we review the economic approach in index numbers under preference changes. Suggestions are made on how to approach the problem and their implications for the measurement of price and quantity indices.
Plant species and associated root nutritional traits influence soil dominant bacteria in coastal wetlands across China
Authors: Li Jing , Cui Lijuan , Delgado‐Baquerizo Manuel , Wang Juntao , Wang Shaokun , Wang Rumiao , Zhu Yinuo , Li Wei , Singh Brajesh K.
Published: August 2024

Climate and edaphic properties drive the biogeographic distribution of dominant soil microbial phylotypes in terrestrial ecosystems. However, the impact of plant species and their root nutritional traits on microbial distribution in coastal wetlands remains unclear.

Here, we investigated the nutritional traits of 100 halophyte root samples and the bacterial communities in the corresponding soil samples from coastal wetlands across eastern China. This study spans 22° of latitude, covering over 2500 km from north to south.

We found that 1% of soil bacterial phylotypes accounted for nearly 30% of the soil bacterial community abundance, suggesting that a few bacterial phylotypes dominated the coastal wetlands. These dominated phylotypes could be grouped into three ecological clusters as per their preference over climatic (temperature and precipitation), edaphic (soil carbon and nitrogen), and plant factors (halophyte vegetation, root carbon, and nitrogen). We further provide novel evidence that plant root nutritional traits, especially root C and N, can strongly influence the distribution of these ecological clusters.

Taken together, our study provides solid evidence of revealing the dominance of specific bacterial phylotypes and the complex interactions with their environment, highlighting the importance of plant root nutritional traits on biogeographic distribution of soil microbiome in coastal wetland ecosystems.
Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots
Authors: Guo Jing , Luo Dan , Chen Yamao , Li Fengjiao , Gong Jiajia , Yu Fen , Zhang Wengen , Qi Ji , Guo Chunce
Published: August 2024

Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy.

We employed both spatial and single‐nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development.

Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots.

The single‐nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.
Life criticism and De Quincey's ethical concern over the aestheticiability of murder
Authors: Duan Yingjie , Tian Junwu
Published: August 2024

The self‐reflexive tendency in De Quincey's seemingly Kantian aestheticization of murder allows some leeway in deciphering his underlying ethical concerns. As “On the knocking at the gate in Macbeth” shows, De Quincey engages in a special kind of life writing that can be termed “life criticism,” which is not naively referential but revelatory, translating the autobiographical records of memories, experiences, and emotions into mediatory possibilities for argumentative assessments of literary and aesthetic questions. James Wood's critiques function as a compelling touchstone of De Quincey's life criticism, exhibiting how self‐referential episodes, as both the starting and end points for literary criticism, can be incorporated into serious and illuminating theoretical interrogations. Through the new prism of De Quincey's habitual mode of life criticism, his aesthetics of murder can be interpreted as a meta‐reflection upon his literary experiences with Westmorland Gazette and Blackwood's Magazine. His awareness of the facile aestheticiability of murder in the periodical press has an obvious moral implication: it shows his self‐reflexive concern over the commercialized public taste that makes him torn between insisting upon classical highbrow culture and contributing sensational magazine reading matter.
Immunocytochemical evaluation of aquaporins and cell wall components and their influence on foliar water uptake in Andean Melastomataceae
Authors: Boanares D. , Posada‐Herrera J. M. , Bragança G. P. P. , Arriola I. A. , Caldeira C. F. , da Costa L. E. N. , Gastauer M. , França M. G. C. , Isaias R. M. d. S.
Published: August 2024

Andean ecosystems are characterized by high humidity, mainly from rain and fog events. Because of differences in altitude two Andean ecosystems – sub‐Andean forest and Páramo –face different environmental pressures that affect leaf anatomy and cell wall composition and, consequently, species foliar water uptake (FWU) capacity.

Here, FWU capacity of eight species in the Melastomataceae was evaluated and found to be related to proportions of cell wall components and aquaporins in the two ecosystems. Cellulose was labelled with Calcofluor white, and aquaporin and pectins were labelled with monoclonal antibodies.

There were differences in plant FWU capacity in both ecosystems, with higher FWU capacity in sub‐Andean forest species than in Páramo forest species. Cell wall components were positively related to FWU, with increased FWU related to pectin and aquaporin content of the plasma membrane.

Differences in water availability in the two analysed environments led to differences in FWU capacity that are associated with leaf anatomical traits and cell wall composition. In these two environments, plants with similar traits are selected to respond to given environmental pressures. Traits that favour FWU in sub‐Andean forest species may lead to further advances of these species in this environments.
Development of a biomarker‐based platform for comprehensive skin characterization using minimally invasive skin sampling and quantitative real‐time PCR
Authors: Kim Seo Hyeong , Kim Ji Hye , Choi Yoon Mi , Seo Su Min , Jang Eun Young , Lee Sung Jae , Zhang Hyun‐Soo , Roh Yunho , Jung Yeon Woo , Park Chang Ook , Jeong Do Hyeon , Lee Kwang Hoon
Published: August 2024

Background

Classifying diverse skin types is crucial for promoting skin health. However, efficiently identifying and analyzing relevant biomarkers from a vast array of available genetic data is challenging. Therefore, this study aimed to develop a precise and efficient platform for analyzing specific skin biomarkers using quantitative real‐time PCR (qRT‐PCR) with the minimal invasive skin sampling method (MISSM).

Materials and methods

MISSM was used for RNA extraction from skin samples, followed by qRT‐PCR analysis to quantify the expression of 20 biomarkers associated with skin characteristics (four biomarkers each for five skin characteristics). Noninvasive measurements from 299 Korean participants were utilized to correlate biomarker expression with skin parameters. Statistical analyses were conducted between biomarker expression levels and noninvasive skin measurements to select the relatively best‐performing biomarker for each skin characteristic.

Results

Collagen type 1 alpha 1 (COL1A1) and moesin (MSN) were identified as skin aging biomarkers. Krüppel‐like factor 4 (KLF4) and serine peptidase inhibitor Kazal type 5 (SPINK5) were identified as skin dryness biomarkers, whereas melan‐A (MLANA) was selected as a biomarker for understanding pigmentation dynamics. Myelin protein zero like 3 (MPZL3) and high mobility group box 2 (HMGB2) were identified as markers of oily skin and skin sensitivity, respectively. Statistically significant correlations were found between the biomarker expression levels and noninvasive skin characteristic measurements.

Conclusion

This study successfully developed a platform for the precise evaluation of individual skin characteristics using MISSM and qRT‐PCR biomarker analysis. By selecting biomarkers that correlate with noninvasive measurements of skin characteristics, we demonstrated the platform's efficacy in assessing diverse skin conditions.
Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing
Authors: Zhang Hui , Li Feng
Published: August 2024

The accessory proteins Hyponastic‐like 1 (HYL1) and Serrated (SE) enhance the precise and efficient processing of miRNAs by Dicer‐like 1 (DCL1), which is important for proper miRNA function. However, other factors determining the precision and efficiency of miRNA biogenesis are not well‐known. Here, we found that an asymmetric bulge (AB) at the 3′ end of miR‐5p (produced from the 5′ arm of the pre‐miRNA) reduced the precision of the second cleavage, whereas an AB at other sites of miR‐5p mainly affected the accumulation level of miR‐5p in transient expression in Nicotiana benthamiana. In contrast, many ABs in miR‐3p (produced from the 3′ arm of the pre‐miRNA) impose strong negative impact on the processing precision and the accumulation level of miR‐5p in N. benthamiana. Arabidopsis DCL1/SE/HYL1 complex‐mediated miRNA processing was reconstituted in Saccharomyces cerevisiae to further investigate AB‐mediated interference with DCL1 processing. With this system, the positional effect of AB on miRNA processing was tested. The results showed that ABs on the middle of miR‐5p have less of an impact on DCL1 cleavage efficiency and precision, whereas those on miR‐3p or near the ends of miR‐5p strongly reduce DCL1 cleavage activity, precision or both. Studies using the yeast miRNA processing system and transgenic Arabidopsis also revealed the importance of the interaction between the 2‐nt 3′ overhang of pre‐miRNA and the 3′ overhang binding pocket (3′BP) on the precision of the second cleavage reaction for many endogenous miRNAs. These findings provide new insights into the mechanism of miRNA biogenesis.
Therapeutic efficacy of cold atmospheric plasma in four golden retrievers with acute otitis externa
Authors: Bakır Alanur , Nett‐Mettler Claudia Susanne , Ulutas Bulent
Published: August 2024

Background

Cold atmospheric plasma (CAP) is a new therapeutic tool used to treat various skin diseases in humans and animals.

Objective

To evaluate the effect of CAP in the treatment of canine acute otitis externa (AOE).

Animals

Four client‐owned golden retriever dogs with bilateral AOE.

Methods and Materials

After cleaning with a commercial ear cleanser, right ears (STANDARD group) were treated with an antibiotic/antifungal/corticosteroid combination and left ears (CAP group) were treated with CAP every three days for a total of four treatments. Cytological score and otitis index score (OTIS)3 were recorded for each ear on Day (D)0, D10 and D15. At D10 and D15, owners and investigators recorded an overall assessment.

Results

In both groups, OTIS3 and cytological score decreased over the study period. The overall assessment scale ranged from moderate to excellent in both groups.

Conclusions and Clinical Relevance

Cold atmospheric plasma treatment showed equal therapeutic effect compared with a commercial topical anti‐inflammatory and antimicrobial ear treatment.
Cardiac sympathetic neurons are additional cells affected in genetically determined arrhythmogenic cardiomyopathy
Authors: Vanaja Induja Perumal , Scalco Arianna , Ronfini Marco , Bona Anna Di , Olianti Camilla , Rizzo Stefania , Chelko Stephen P. , Corrado Domenico , Sacconi Leonardo , Basso Cristina , Mongillo Marco , Zaglia Tania
Published: August 2024

Arrhythmogenic cardiomyopathy (AC) is a familial cardiac disease, mainly caused by mutations in desmosomal genes, which accounts for most cases of stress‐related arrhythmic sudden death, in young and athletes. AC hearts display fibro‐fatty lesions that generate the arrhythmic substrate and cause contractile dysfunction. A correlation between physical/emotional stresses and arrhythmias supports the involvement of sympathetic neurons (SNs) in the disease, but this has not been confirmed previously. Here, we combined molecular, in vitro and ex vivo analyses to determine the role of AC‐linked DSG2 downregulation on SN biology and assess cardiac sympathetic innervation in desmoglein‐2 mutant (Dsg2mut/mut) mice. Molecular assays showed that SNs express DSG2, implying that DSG2‐mutation carriers would harbour the mutant protein in SNs. Confocal immunofluorescence of heart sections and 3‐D reconstruction of SN network in clarified heart blocks revealed significant changes in the physiologialc SN topology, with massive hyperinnervation of the intact subepicardial layers and heterogeneous distribution of neurons in fibrotic areas. Cardiac SNs isolated from Dsg2mut/mut neonatal mice, prior to the establishment of cardiac innervation, show alterations in axonal sprouting, process development and distribution of varicosities. Consistently, virus‐assisted DSG2 downregulation replicated, in PC12‐derived SNs, the phenotypic alterations displayed by Dsg2mut/mut primary neurons, corroborating that AC‐linked Dsg2 variants may affect SNs. Our results reveal that altered sympathetic innervation is an unrecognized feature of AC hearts, which may result from the combination of cell‐autonomous and context‐dependent factors implicated in myocardial remodelling. Our results favour the concept that AC is a disease of multiple cell types also hitting cardiac SNs.

image

Key points

Arrhythmogenic cardiomyopathy is a genetically determined cardiac disease, which accounts for most cases of stress‐related arrhythmic sudden death.

Arrhythmogenic cardiomyopathy linked to mutations in desmoglein‐2 (DSG2) is frequent and leads to a left‐dominant form of the disease.

Arrhythmogenic cardiomyopathy has been approached thus far as a disease of cardiomyocytes, but we here unveil that DSG2 is expressed, in addition to cardiomyocytes, by cardiac and extracardiac sympathetic neurons, although not organized into desmosomes.

AC‐linked DSG2 downregulation primarily affect sympathetic neurons, resulting in the significant increase in cardiac innervation density, accompanied by alterations in sympathetic neuron distribution.

Our data supports the notion that AC develops with the contribution of several ‘desmosomal protein‐carrying’ cell types and systems.
Stress-Induced Syncope: A Case Study
Authors: Albrecht Alyssa
Published: August 2024

Four adolescent female athletes across four grades were diagnosed with either psychogenic nonepileptic seizures or conversion disorder. The females underwent thorough evaluations with their primary care providers and episode and symptom tracking by their athletic trainer. Through different applications of cognitive behavioral therapy and one-on-one counseling, the disorders resolved. Teaching athletes the importance of choosing healthy coping mechanisms to stress is vital to quality mental health. It is recommended that more research be done on psychogenic nonepileptic seizures and provide an understanding to those working with the adolescent population on triggers and treatments for psychogenic nonepileptic seizures.