Processing Steps Research Articles

Sample Article for Pree Reviewer

Background Large research consortia can generate tremendous amounts of biological information, including high-resolution soil, vegetation, and climate data. While this knowledge stock holds invaluable potential for answering evolutionary and ecological questions, making these data exploitable for modelling remains a daunting task due to the many processing steps required for synthesis. This might result in many researchers to fall back to a handful of ready-to-use data sets, potentially at the expense of statistical power and scientific rigour. In a push for a more stringent approach, we introduce BEpipeR, an R pipeline that allows for the streamlined synthesis of plot-based Biodiversity Exploratories data. Methods BEpipeR was designed with flexibility and ease of use in mind. For instance, users simply choose between aggregating forest or grassland data, or a combination thereof, effectively allowing them to process any experimental plot data of this research consortium. Additionally, instead of coding, they parse most processing information in a user-friendly way through parameter sheets. Processing includes, among others, the creation of a spatially explicit plot-ID template, data wrangling, quality control, plot-wise aggregations, the calculation of derived metrics, data joining to a large composite data set, and metadata compilation. Results With BEpipeR, we provide a feature-rich pipeline that allows users to process Biodiversity Exploratories data in a flexible and reproducible way. This pipeline might serve as a starting point for aggregating the numerous data sets of this and potentially similar research consortia. In this way, it might be a primer for the construction of consortia-wide composite data sets that take full advantage of the consortia’s rich information stocks, ultimately boosting the visibility and participation of individual research projects. Conclusions The BEpipeR permits the user-friendly processing and plot-wise aggregation of Biodiversity Exploratories data. With modifications, this framework may be easily adopted by other research consortia.

Novel Insights into the Enrichment Pattern of Aroma and Taste in Cooked Marinated Meat Products of Black Pork via Typical Process Steps

This study aims to reveal the evolution mechanism of odour and taste active compounds in cooked marinated pork knuckles via typical process steps; among them, the brine soup stage was the most important part due to spices’ enriching flavours. These results revealed that the content and diversity of volatile compounds increased due to the addition of spices and heating temperature, imparting a unique aroma. Aldehydes played the main role in the overall odour. Benzaldehyde, hexanal, 1-octen-3-ol, levulinic acid, hydroxyacetone, ethyl octanoate, and 2-pentyl-furan were identified as the most important odour-active compounds. The key taste-active amino acids were glutamine, leucine, valine, and lysine. The IMP, AMP, and GMP provided a strong umami taste. Taste nucleotides and Val, Leu, Ile, and Phe were important precursor substances for aldehydes. The high responses of the electronic nose indicated that the gas component contained alkanes, alcohols, and aldehydes. The synergistic effects between umami-free amino acids and nucleotides correlated well with umami, as assessed by the electronic tongue. These results could be a starting point for the manufacturing industry, contributing to a better understanding of product performance.

Novel insights into RNA polymerase II transcription regulation: transcription factors, phase separation, and their roles in cardiovascular diseases.

Transcription factors (TFs) are specialized proteins that bind DNA in a sequence-specific manner and modulate RNA polymerase II (Pol II) in multiple steps of the transcription process. Phase separation is a spontaneous or driven process that can form membrane-less organelles called condensates. By creating different liquid phases at active transcription sites, the formation of transcription condensates can reduce the water content of the condensate and lower the dielectric constant in biological systems, which in turn alters the structure and function of proteins and nucleic acids in the condensate. In RNA Pol II transcription, phase separation formation shortens the time at which TFs bind to target DNA sites and promotes transcriptional bursting. RNA Pol II transcription is engaged in developing several diseases, such as cardiovascular disease, by regulating different TFs and mediating the occurrence of phase separation. This review aims to summarize the advances in the molecular mechanisms of RNA Pol II transcriptional regulation, in particular the effect of TFs and phase separation. The role of RNA Pol II transcriptional regulation in cardiovascular disease will be elucidated, providing potential therapeutic targets for the management and treatment of cardiovascular disease.

Environmental study delays in Nepal: A comparison with India and Bangladesh and policy recommendations

This research examines the environmental approval process in Nepal and compares it with those in India and Bangladesh, focusing on the time taken to complete the assessment of environmental study reports. The study conducts three levels of analysis. First, the policy review outlines all relevant environmental policies and laws, highlighting key provisions related to approval timelines. While not every step of the environmental study process has a mandated time frame, the legal time limits for report forwarding and approval are explicitly defined. Second, statistical analysis reveals a significant discrepancy between the statutory and actual approval times. While the legal mandate is just 35 days for Environmental Impact Assessment (EIA), assessing a report actually takes 339 days on average. The trend line reveals that the average time taken is decreasing. However, it is still much higher than India’s average EIA approval time of 64 days. Third, through a comparative analysis of eighteen different components of the environmental assessment process, this paper identifies the possible factors contributing to the delays, such as ambiguous jurisdiction, lack of nodal agency, lack of integrated guidelines, high centralization, and no use of e-governance. This paper also compares the thresholds that trigger the environmental study across eight sectors for three countries and finds that Nepal’s thresholds are narrower than India’s and comparable to Bangladesh’s. Recommendations made include clarifying jurisdictional roles, developing integrated guidelines, establishing specialized nodal agencies, and implementing digital systems. Overall, this research attempts to address flaws in Nepal’s environmental assessment system, offering solutions for efficient environmental regulation and improving the business environment in Nepal.

Unintended Consequences of Data Sharing Under the Meaningful Use Program.

Interoperability has been designed to improve the quality and efficiency of health care. It allows the Centers for Medicare and Medicaid Services to collect data on quality measures as a part of the Meaningful Use program. Covered providers who fail to provide data have lower rates of reimbursement. Unintended consequences also arise at each step of the data collection process: (1) providers are not reimbursed for the extra time required to generate data; (2) patients do not have control over when and how their data are provided to or used by the government; and (3) large datasets increase the chances of an accidental data breach or intentional hacker attack. After detailing the issues, we describe several solutions, including an appropriate data use review board, which is designed to oversee certain aspects of the process and ensure accountability and transparency.

Acknowledging the role of loss in facilitating employee transition in a partial business acquisition

PurposeThe purpose of this paper is to explore the experience of a cohort of staff who transferred from a medium-sized Irish pharmaceutical company to a US multinational, while remaining in the same building as their original employers and colleagues. It highlights the role of acknowledging loss when facilitating employee transition and the co-development of a communication and integration strategy in transitioning to a new organisation.Design/methodology/approachAn exploratory qualitative case study captures the experiences of the senior manager responsible for the business unit transition and a cohort of 32 employees who moved to the US multinational. Conversations between the senior manager (author three) and his academic peers (authors one and two) trace the experience of this team as they transitioned to the new organisation.FindingsInsights are offered through the transition journey – from the unofficial partial-acquisition offer through to the due diligence period and onto the subsequent implementation of the communication and integration strategy. Findings exhibit a co-developed a communication and integration strategy, revealing a largely successful initial integration of the team into the new organisation.Originality/valueThe paper offers a first-hand account of the steps taken in a successful employee transition to a new organisation following a partial acquisition. It describes how acknowledging loss is a valuable first step in the transition process, enabled by the design and adoption of a co-created communication and integration strategy.

Hormonal interventions in skin wounds - a mini review.

The ability to heal from wounds is perhaps the most important biological function that ensures our survival and perpetuation. Cutaneous wound healing typically consists of four characteristic stages, namely hemostasis, inflammation, proliferation, and remodeling, which are carefully carried out by coordinated actions of various cells, cytokines, and hormones. Incoordination of these steps may impede complete and efficient reconstruction and functional recovery of wounds or even lead to worsened outcomes. Hormones, as powerful modulators of organ functions, participate in multiple steps of the wound healing process and play a pivotal role by choreographing the complex interplay of cellular and molecular events. Leveraging the regulatory effects of hormones to enhance the healing process, hormonal therapy has emerged as a promising approach in the clinical treatment of wounds. Current research has focused on determination of the optimal dosages, delivery methods, and combinations of hormonal therapies to maximize their therapeutic benefits while minimizing potential side effects. This review highlights the molecular mechanisms, clinical benefits and side effects of the most commonly used hormones in clinical treatment of wounds.

Prospects of Improving Efficiency and Stability of Hybrid Perovskite Solar Cells by Alumina Ultrathin Films.

Over the last few years, the influence of low temperature (≤80 °C) and, in particular, of room temperature, atomic layer deposited alumina (ALD-Al2O3) on the properties of the underlying hybrid perovskites of different compositions and on the efficiency and stability of the corresponding perovskite solar cells (PSCs) is extensively investigated. The main conclusion is that most probably thanks to the presence of intrinsic defect states in the ALD-Al2O3 and in the perovskite layers, charge transfer and neutralization are possible and the entire lifetime of the PSCs is thus improved. Moreover, the migration of mobile ions between the layers is blocked by the ALD-Al2O3 layer and thus the occurrence of hysteresis in the current density-voltage characteristics of the PSCs is suppressed. Considering the uniform and nondestructive surface coverage, low thermal budget, small amount of material required, and short duration of the established ALD-Al2O3 deposition on top of hybrid perovskites, this additional, but fully solar cell technology-compatible, process step is most likely the most effective, cheapest, and fastest way to improve the efficiency and long-term stability of PSCs and thus increase their marketability.

Targeting Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2): Latest Insights on Synthetic Strategies

Vascular endothelial growth factor receptor 2 (VEGFR-2) is a crucial mediator of angiogenesis, playing a pivotal role in both normal physiological processes and cancer progression. Tumors harness VEGFR-2 signaling to promote abnormal blood vessel growth, which is a key step in the metastasis process, making it a valuable target for anticancer drug development. While there are VEGFR-2 inhibitors approved for therapeutic use, they face challenges like drug resistance, off-target effects, and adverse side effects, limiting their effectiveness. The quest for new drug candidates with VEGFR-2 inhibitory activity often starts with the selection of key structural motifs present in molecules currently used in clinical practice, expanding the chemical space by generating novel derivatives bearing one or more of these moieties. This review provides an overview of recent advances in the development of novel VEGFR-2 inhibitors, focusing on the synthesis of new drug candidates with promising antiproliferative and VEGFR-2 inhibition activities, organizing them by relevant structural features.

Velocity-independent NMO correction based on multi-scale dynamic time warping

Normal moveout (NMO) correction is one of the common steps of seismic data processing. Conventional NMO correction is generally based on a velocity function, but velocity analysis is considered time-consuming and labor-intensive. Moreover, the field seismic data observed in complex areas can have low signal-to-noise ratio (SNR), resulting in inaccurate picked up velocity parameters and poor NMO correction. The conventional NMO correction has stretching issues, most significantly at shallow and large offset areas. To address these problems, a new multi-scale dynamic time warping (MSD) algorithm for velocity-independent stretch-free NMO correction is investigated. This algorithm has higher accuracy and stronger noise resistance, as our comparisons with other applications of DTW show. In our algorithm, the original seismic data is decomposed into multiple morphological scales (using mathematical morphology theory), and alignment errors are calculated separately at each scale, followed by further adaptive weighted summation. Accumulation and backtracking operations based on alignment errors produce time shift sequences for automatic flattening of the gathers. The effectiveness of the presented approach is tested on both synthetic and field data. The results demonstrate that compared with traditional velocity-based NMO correction methods, the proposed method can accurately flatten seismic gathers without the NMO stretch and is robust to strong noise.

Aging Dynamics of Polyvinyl Chloride Microplastics in Three Soils with Different Properties.

Microplastic (MP) contamination in soil has been of great concern, but the dynamic aging process and potential pathways of MPs in natural soil systems remain poorly understood. Herein, poly(vinyl chloride) microplastics (5% w/w) were weathered for 12 months in sandy soil, silty clay, and silt loam. The results showed that the continuous increase of C═O and O-H groups (rate constant, k = 0.080-0.424 m-1) with time was observed on the surface of MPs aging in sandy soil due to the leading role of •OH induced by light irradiation. In the loam soil, the abundant coating of aluminosilicates and iron oxides on the MP surface by the formation of mineral-hydroxyl groups inhibited the generation of the C═O group (k < 0.165 m-1). The k of the characteristic bond C-Cl during the first 9 months was 9.51 and 1.93 times higher in clay compared to that in sandy and loam soil, respectively, revealing that dechlorination triggered the first step of the aging process for MPs in clay owing to the participation of degrading bacteria (Phenylobacterium and Caulobacteraceae). The results provide important insights into the aging dynamics of MPs in environmentally realistic circumstance, which account for understanding the different aging processes of MPs in different soils.

Behavior and flow of microplastics during sludge treatment in Japan.

Microplastic (MP) pollution is a growing public and scientific concern. In urban environments, wastewater treatment plants (WWTPs) are major sources of MPs. This study sampled sludge and separated water from each sludge treatment unit in two WWTPs in Osaka, Japan. Analyzing method for MPs in sewage sludge was optimized, ultrasonic pretreatment and double digestion were introduced into the analyzing method of MPs in sewage sludge, recovering test of standard MPs proved its high efficiency. Then MPs larger than 100 μm were extracted and analyzed, their size and type were recorded, the MP concentration was calculated, and the MP flow in the sludge treatment system was estimated. MPs were detected at every step of the sludge treatment process, and 13 types of MPs were identified. The MP concentration in sludge ranged from 81 ± 48 to 6470 ± 1490 particles/kg dry sludge (DS). In the separated water, MP concentrations were much lower, ranging from 0 to 1740 ± 794 particles/kg DS. During the thickening and dewatering processes, nearly all MPs were transferred into thickened or dewatered sludge; only 5-10 % of MPs returned to the primary sedimentation pond with the separated water. The most common types of MPs were PMMA, PE, and PS. No significant differences in MP type distributions were observed among sampling batches; however, significant differences in a few types of MPs were detected between treatment units, which requires further investigation. All detected MPs were smaller than 1000 μm; larger MPs might have been removed in the grit chamber before reaching the primary or secondary sedimentation ponds. Overall, the particle size distribution did not substantially change during sludge treatment.

Efficient Selective CO2 Composite Sorbent from Amino Acid Ionic Liquids and Silica Gel: 2H NMR Spectroscopy Provides Insight on the CO2-Binding Mechanism and in-Pore Microscopic Viscosity.

A promising CO2 sorbent based on the [Emim][Gly] (1-ethyl-3-methylimidazolium glycinate)/silica gel composite has been studied. CO2 sorption experiments have shown that the optimum loading of [Emim][Gly] ionic liquid in silica gel is 40 wt.%. The 2-step process CO2 binding mechanism in [Emim][Gly] has been proposed based on the results of sorption experiments, 2H NMR spectroscopy and ab-initio calculations. The impact of CO2 on the microscopic viscosity and the dynamical melting of ionic liquid has been thoroughly investigated. 2H NMR spectroscopy has revealed that CO2 strongly binds cation and anion in [Emim][Gly], forcing them to move in a correlated fashion.

Integrating gene expression and imaging data across Visium capture areas with visiumStitched.

Visium is a widely-used spatially-resolved transcriptomics assay available from 10x Genomics. Standard Visium capture areas (6.5mm by 6.5mm) limit the survey of larger tissue structures, but combining overlapping images and associated gene expression data allow for more complex study designs. Current software can handle nested or partial image overlaps, but is designed for merging up to two capture areas, and cannot account for some technical scenarios related to capture area alignment. We generated Visium data from a postmortem human tissue sample such that two capture areas were partially overlapping and a third one was adjacent. We developed the R/Bioconductor package visiumStitched, which facilitates stitching the images together with Fiji (ImageJ), and constructing SpatialExperiment R objects with the stitched images and gene expression data. visiumStitched constructs an artificial hexagonal array grid which allows seamless downstream analyses such as spatially-aware clustering without discarding data from overlapping spots. Data stitched with visiumStitched can then be interactively visualized with spatialLIBD. visiumStitched provides a simple, but flexible framework to handle various multi-capture area study design scenarios. Specifically, it resolves a data processing step without disrupting analysis workflows and without discarding data from overlapping spots. visiumStitched relies on affine transformations by Fiji, which have limitations and are less accurate when aligning against an atlas or other situations. visiumStitched provides an easy-to-use solution which expands possibilities for designing multi-capture area study designs.

Processing, evaluating, and understanding FMRI data with afni_proc.py

Abstract FMRI data are noisy, complicated to acquire, and typically go through many steps of processing before they are used in a study or clinical practice. Being able to visualize and understand the data from the start through the completion of processing, while being confident that each intermediate step was successful, is challenging. AFNI’s afni_proc.py is a tool to create and run a processing pipeline for FMRI data. With its flexible features, afni_proc.py allows users to both control and evaluate their processing at a detailed level. It has been designed to keep users informed about all processing steps: it does not just process the data, but also first outputs a fully commented processing script that the users can read, query, interpret, and refer back to. Having this full provenance is important for being able to understand each step of processing; it also promotes transparency and reproducibility by keeping the record of individual-level processing and modeling specifics in a single, shareable place. Additionally, afni_proc.py creates pipelines that contain several automatic self-checks for potential problems during runtime. The output directory contains a dictionary of relevant quantities that can be programmatically queried for potential issues and a systematic, interactive quality control (QC) HTML. All of these features help users evaluate and understand their data and processing in detail. We describe these and other aspects of afni_proc.py here using a set of task-based and resting-state FMRI example commands.

Application of deep learning algorithms for identifying deterioration in the ushnisha (Head Bun) of the Leshan Giant Buddha

AbstractThe Leshan Giant Buddha’s ushnisha (Head Bun) has suffered from loss of lime plaster, cracks, and biological damage, compromising its structural integrity and reducing the effectiveness of the drainage system in the Buddha's head. The infiltration of moisture has led to water damage within the statue, significantly accelerating its weathering. This situation urgently requires protection and reinforcement measures. Detecting deterioration in the ushnisha is a crucial step in the preservation process. In this study, we utilized two deep learning models for pixel-level semantic segmentation of the damage. Due to the small size of the cracks, a weighted loss function was applied to improve both the training speed of the model and the efficiency of crack identification. This weighting strategy proved effective for both models. The weighted K-Net model achieved a mean accuracy (mAcc) of 90.23% and a mean intersection-over-union (mIoU) of 69.55%, with a damage segmentation speed of 7 images per second, which is 1309 times faster than manual segmentation. By applying the trained deep learning models to re-examine the ushnisha, we successfully identified damage that had been overlooked during manual annotation. Using the model’s enhanced results, we conducted a comprehensive quantification of the damage across all ushnisha and identified the most severely affected areas. Additionally, we performed a model interpretability analysis to explain the decision-making process and principles of the deep learning models. This research provides significant practical value for detecting and quantifying damage in the Leshan Giant Buddha.

Physiological and pathological roles of the transcriptional kinases CDK12 and CDK13 in the central nervous system.

The cyclin-dependent kinases 12 (CDK12) and 13 (CDK13) govern several steps of gene expression, including transcription, RNA processing and translation. The main target of CDK12/13 is the serine 2 residue of the carboxy-terminal domain of RNA polymerase II (RNAPII), thus influencing the directionality, elongation rate and processivity of the enzyme. The CDK12/13-dependent regulation of RNAPII activity influences the expression of selected target genes with important functional roles in the proliferation and viability of all eukaryotic cells. Neuronal cells are particularly affected by the loss of CDK12/13, as result of the high dependency of neuronal genes on RNAPII processivity for their expression. Deregulation of CDK12/13 activity strongly affects brain physiology by influencingthe stemness potential and differentiation properties of neuronal precursor cells. Moreover, mounting evidence also suggest the involvement of CDK12/13 in brain tumours. Herein, we discuss the functional role(s) of CDK12 and CDK13 in gene expression regulation and highlight similarities and differences between these highly homologous kinases, with particular attention to their impact on brain physiology and pathology. Lastly, we provide an overview of CDK12/13 inhibitors and of their efficacy in brain tumours and other neoplastic diseases.

In Situ Fluorescent Visualization of the Interfacial Layer of Induced Crystallization in Polyvinyl Chloride

Despite the remarkable progress in the modification and application of polyvinyl chloride (PVC), developing processing aids for the induced crystallization of PVC and characterizing its interfacial layer remain challenges. Herein, we propose a new polymeric nucleating agent, polyamidea12-graft-styrene–maleic anhydride copolymer (PA12-g-SMA), which possesses high compatibility and crystallinity, effectively improving the crystallinity to 15.1%, the impact strength to 61.03 kJ/m2, and the degradation temperature of PVC to 267 °C through a single and straightforward processing step. Additionally, after the introduction of two different fluorescent sensors in PA12-g-SMA and PVC, the interfacial layer of the induced crystallization can be monitored in situ via a confocal laser scanning microscope (CLSM). This study highlights a rare strategy for significantly enhancing the physical properties of rigid PVC through simply adding a polymeric nucleating agent during processing, while also emphasizing the importance of visualizing the interfacial layer to understand various polymer crystallization processes.

A Scoping Study of Cultural Adaptation Frameworks.

Translating evidence-based intervention in public health is important to improve health behaviors and other outcomes and reduce health disparities. Culturally adapting intervention is one approach to reaching different cultural groups. The goals of this paper were to compile definitions of program adaptations, identify processes and steps in cultural adaptations, and pose recommendations for future research related to cultural adaptations. We performed a scoping review of cultural adaptation frameworks or models for public health. Studies were coded for definitions of adaptation, cultural adaptation, other cultural concepts, process steps, community engagement, and public health topic. We found 15 frameworks that described cultural adaptation concepts and processes, and nine had varying definitions of cultural adaptations. All frameworks included tasks of information gathering about the community and developing a preliminary adapted program; over 50% had making refinements to the adapted program after some pilot testing. Only one framework mentioned the role of experts in the adaptation or enhancement process, and one mentioned dissemination. Thirteen articles (86.7%) reported the inclusion of community engagement in the adaptation process. These data present key definitions related to cultural adaptation and themes related to the process of cultural adaptation. We also report on key steps for conducting cultural adaptations. Findings can be utilized to guide future adaptations of evidence-based interventions to ensure culturally competent research and practice.

Methods Used in Co-Creation Within the Health CASCADE Co-Creation Database and Gray Literature: Systematic Methods Overview.

Co-creation is increasingly recognized for its potential to generate innovative solutions, particularly in addressing complex and wicked problems in public health. Despite this growing recognition, there are no standards or recommendations for method use in co-creation, leading to confusion and inconsistency. While some studies have examined specific methods, a comprehensive overview is lacking, limiting the collective understanding and ability to make informed decisions about the most appropriate methods for different contexts and research objectives. This study aimed to systematically compile and analyze methods used in co-creation to enhance transparency and deepen understanding of how co-creation is practiced. To enhance transparency and deepen understanding of how co-creation is practiced, this study systematically inventoried and analyzed methods used in co-creation. We conducted a systematic methods overview, applying 2 parallel processes: one within the peer-reviewed Health CASCADE Co-Creation Database and another within gray literature. An artificial intelligence-assisted recursive search strategy, coupled with a 2-step screening process, ensured that we captured relevant methods. We then extracted method names and conducted textual, comparative, and bibliometric analyses to assess the content, relationship between methods, fields of research, and the methodological underpinnings of the included sources. We examined a total of 2627 academic papers and gray literature sources, with the literature primarily drawn from health sciences, medical research, and health services research. The dominant methodologies identified were co-creation, co-design, coproduction, participatory research methodologies, and public and patient involvement. From these sources, we extracted and analyzed 956 co-creation methods, noting that only 10% (n=97) of the methods overlap between academic and gray literature. Notably, 91.3% (230/252) of the methods in academic literature co-occurred, often involving combinations of multiple qualitative methods. The most frequently used methods in academic literature included surveys, focus groups, photo voice, and group discussion, whereas gray literature highlighted methods such as world café, focus groups, role-playing, and persona. This study presents the first systematic overview of co-creation methods, providing a clear understanding of the diverse methods currently in use. Our findings reveal a significant methodological gap between researchers and practitioners, offering insights into the relative prevalence and combinations of methods. By shedding light on these methods, this study helps bridge the gap and supports researchers in making informed decisions about which methods to apply in their work. Additionally, it offers a foundation for further investigation into method use in co-creation. This systematic investigation is a valuable resource for anyone engaging in co-creation or similar participatory methodologies, helping to navigate the diverse landscape of methods.