MDPI - Publisher of Open Access Journals

16 pages, 889 KiB

Open AccessReview

A Bioinformatics Toolkit for Next-Generation Sequencing in Clinical Oncology

by

Simon Cabello-Aguilar

,

Julie A. Vendrell

and

Jérôme Solassol

Curr. Issues Mol. Biol. 2023, 45(12), 9737-9752; https://doi.org/10.3390/cimb45120608 - 04 Dec 2023

Abstract

Next-generation sequencing (NGS) has taken on major importance in clinical oncology practice. With the advent of targeted therapies capable of effectively targeting specific genomic alterations in cancer patients, the development of bioinformatics processes has become crucial. Thus, bioinformatics pipelines play an essential role [...] Read more.

Next-generation sequencing (NGS) has taken on major importance in clinical oncology practice. With the advent of targeted therapies capable of effectively targeting specific genomic alterations in cancer patients, the development of bioinformatics processes has become crucial. Thus, bioinformatics pipelines play an essential role not only in the detection and in identification of molecular alterations obtained from NGS data but also in the analysis and interpretation of variants, making it possible to transform raw sequencing data into meaningful and clinically useful information. In this review, we aim to examine the multiple steps of a bioinformatics pipeline as used in current clinical practice, and we also provide an updated list of the necessary bioinformatics tools. This resource is intended to assist researchers and clinicians in their genetic data analyses, improving the precision and efficiency of these processes in clinical research and patient care. Full article

(This article belongs to the Special Issue Next-Generation Sequencing (NGS) Technique and Personalized Medicine)

15 pages, 1933 KiB

Open AccessReview

A Compendious Review on the Determination of Fundamental Site Period: Methods and Importance

by

Ahmet Güllü

Geotechnics 2023, 3(4), 1309-1323; https://doi.org/10.3390/geotechnics3040071 - 04 Dec 2023

Abstract

It is now well-known that ground motion characteristics can be influenced significantly by local site characteristics. In general, soil characteristics were classified by considering the time-average velocity down to 30 m (V_s30). However, recent studies have showed that the fundamental site [...] Read more.

It is now well-known that ground motion characteristics can be influenced significantly by local site characteristics. In general, soil characteristics were classified by considering the time-average velocity down to 30 m (V_s30). However, recent studies have showed that the fundamental site period is a better proxy than V_s30, or the most complementary parameter to V_s30, for this purpose. Recent earthquakes have also revealed that the largest amplifications occur at the fundamental site period and cause heavy damage or the collapse of structures when they have similar vibrational characteristics with the site’s fundamental period, i.e., resonance. Therefore, many studies in the literature have been performed to determine the fundamental periods of layered soil profiles using different analytical, approximate, and data-driven methods. However, there is a requirement to evaluate these methods by following a systematic procedure. Hence, the reader will receive a comprehensive review of the available procedures for determining the site’s fundamental period of layered soil profiles and their applications at different scales, along with an exploration of current research gaps. Full article

(This article belongs to the Special Issue Recent Advances in Geotechnical Engineering (2nd Edition))

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2 pages, 186 KiB

Open AccessEditorial

Inherited Arrhythmogenic Syndromes

by

Georgia Sarquella-Brugada

and

Oscar Campuzano

Cardiogenetics 2023, 13(4), 173-174; https://doi.org/10.3390/cardiogenetics13040016 - 04 Dec 2023

Abstract

Inherited arrhythmogenic syndromes (IASs) are a heterogeneous group of rare cardiac entities of genetic origin [...] Full article

(This article belongs to the Special Issue Genetics of Inherited Arrhythmogenic Syndromes Associated with Sudden Death)

13 pages, 844 KiB

Open AccessReview

Gene-Based Therapy: A New Approach to Feline Induced Sterilization?

by

Rita Payan-Carreira

Future Pharmacol. 2023, 3(4), 938-950; https://doi.org/10.3390/futurepharmacol3040057 - 04 Dec 2023

Abstract

Feline population control remains a concern as to whether it is intended for the short- or long-term. Induced sterilization of felids is critical in the case of feral, free-roaming cats, or the management of wild populations in Zoos or sanctuaries. This narrative review [...] Read more.

Feline population control remains a concern as to whether it is intended for the short- or long-term. Induced sterilization of felids is critical in the case of feral, free-roaming cats, or the management of wild populations in Zoos or sanctuaries. This narrative review explores the shifting paradigm in induced sterilization methods, driven by the development of gene editing approaches recently applied to control felid reproductive activity. Although gene therapy approaches have gained attention as alternatives to more traditional methods, their clinical applications remain in the realm of thought. The objective of this study was to provide a comprehensive overview of the current state and most recent advances in gene-based contraception options, consolidate current research and evidence, and share some considerations on its potential effectiveness, advantages or limitations, and implications for animal welfare and population control strategies. Gene-based contraception therapy tested in felines, targeting the AMH pathway, was unable to suppress the estrous cycle and follicular development. However, at an experimental level, preliminary results hint at the need to change towards different molecular targets. Moreover, their side effects remain largely unknown, and several questions remain unanswered, such as the regularity of treatment applications or cost. Full article

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12 pages, 420 KiB

Open AccessArticle

Mine Productivity Upper Bounds and Truck Dispatch Rules

by

Adriano Chaves Lisboa

,

Felipe Luz Barbosa Castro

and

Pedro Vinícius Almeida Borges de Venâncio

Mining 2023, 3(4), 786-797; https://doi.org/10.3390/mining3040043 - 04 Dec 2023

Abstract

This paper proposes an upper bound for mine productivity (useful for long-term planning) and also a simple truck dispatch rule (useful for short-term operations) that demonstrates how tight the upper bound can be using a simulation. It also proposes a greedy search to [...] Read more.

This paper proposes an upper bound for mine productivity (useful for long-term planning) and also a simple truck dispatch rule (useful for short-term operations) that demonstrates how tight the upper bound can be using a simulation. It also proposes a greedy search to approximate the productivity upper bound, which is faster and often exact. Uncertainty is added to the simulation in order to verify how the productivity responds to it. Typically, the productivity’s upper bound is less tight close to its saturation point as a function of the number of trucks, where adding more trucks only increases queues. Furthermore, more uncertainty in the model typically leads to a less tight upper bound. The results conducted using real data from an open pit mine in Brazil show that the gap between the productivity upper bound and the productivity realization using the proposed dispatch rule for a homogeneous fleet can be less than

2%

, but it can be as large as

12%

near the productivity saturation point without uncertainty. Even though this gap seems to become arbitrarily small as the number of trucks and the simulation horizon increase, the productivity upper bound is never violated, which validates it as an upper bound and induces optimality for the dispatch rule. Full article

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11 pages, 344 KiB

Open AccessArticle

Perspectives of Hospitalized Mental Health Care Users Concerning the Involvement of Family Members in Their Care: A Qualitative Study

by

Mihloti E. Shimange

and

Hilda N. Shilubane

Nurs. Rep. 2023, 13(4), 1684-1694; https://doi.org/10.3390/nursrep13040139 - 04 Dec 2023

Abstract

The value of families and professionals in mental health care is well understood. Patient perspectives appear to have gotten less attention to date. This study investigated the perspectives of hospitalized mental health care users on the involvement of family members in their care [...] Read more.

The value of families and professionals in mental health care is well understood. Patient perspectives appear to have gotten less attention to date. This study investigated the perspectives of hospitalized mental health care users on the involvement of family members in their care using a qualitative phenomenological design. The participants with lived experience of family members being involved in their care were chosen using non-probability, purposive sampling. Individual interviews were carried out with the assistance of a voice recorder and observation notes. Because of data saturation, only fifteen people were interviewed. The interviews were transcribed verbatim and analyzed using Colaizzi’s method. It started with reading and reviewing the transcript to extract key statements about the phenomenon. The meaning was then determined by carefully studying the primary significant statements and phrases. The established meanings were then organized into themes and subthemes. The three themes that emerged from the data analysis are as follows: a wide variation in patients’ perspectives when family members remind them of their medicine, unpredictable visitation by family members, and a lack of support from family members. There were also the following five sub-themes: not visiting mental health care users in the hospital causes uncertainty about their future, mental health care users were concerned by fewer visits from relatives, friends were perceived as a contributory factor to no or limited visitation by family members, disappointment by a lack of financial support, and perceived lack of emotional support from family members. There is a need for family members to visit mental health care users to remove uncertainty about their future. Healthcare providers should listen to mental health care users to identify the challenges they are faced with, and hospital policies tailored to enhancing the involvement of family members should be formulated. Full article

14 pages, 1510 KiB

Open AccessArticle

Decay of Root Debris after Harvesting American Ginseng (Panax quinquefolius) and Changes in Soil Chemistry and Microbiology

by

Iván Darío Samur Suárez

,

Moez Valliani

,

Tom Hsiang

and

Paul H. Goodwin

Soil Syst. 2023, 7(4), 108; https://doi.org/10.3390/soilsystems7040108 - 04 Dec 2023

Abstract

Commercial harvesting of American ginseng (Panax quinquefolius) results in root debris in the soil, but the rate of decay is unknown. In this study, post-harvest root debris decayed mostly over the fall and winter, with almost no ginseng debris remaining in [...] Read more.

Commercial harvesting of American ginseng (Panax quinquefolius) results in root debris in the soil, but the rate of decay is unknown. In this study, post-harvest root debris decayed mostly over the fall and winter, with almost no ginseng debris remaining in the soil by late spring of the following year. However, a small number of intact pencil-shaped roots were able to survive after harvest and sprout the following spring without any evidence of root decay. Root rot lesions were observed, which included many associated with the root rot pathogen Ilyonectria mors-panacis, with disappearing root rot symptoms observed in the following spring. Ginsenosides in soil were highest just prior to harvest, declining until an increase the following spring. Soil bacterial and fungal populations changed over time after harvest with several peaks in bacterial populations mostly in the fall, but this was less clear for fungal populations, which were dominated by only a few taxa. Harvesting ginseng can leave considerable debris in the soil, impacting its chemistry and microbiota. Ginseng replant disease, where the second crop shows high levels of root rot due to I. mors-panacis infection compared to low levels in the first crop, could be related to the decay of post-harvest crop debris, but additional research is needed to demonstrate this. Full article

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15 pages, 309 KiB

Open AccessArticle

The Protein Composition of Bovine Milk from Once-a-Day and Twice-a-Day Milking Production Systems in New Zealand

by

Marit van der Zeijden

,

Ashling Ellis

,

Nicolas Lopez-Villalobos

,

Siqi Li

,

Nicole C. Roy

and

Warren McNabb

Dairy 2023, 4(4), 689-703; https://doi.org/10.3390/dairy4040047 - 04 Dec 2023

Abstract

An increasing number of dairy farmers in New Zealand (NZ) have adopted a once-a-day (OAD) milking production system, and little is known about the impact of this production system on milk protein composition. The objective of this study was to evaluate the effect [...] Read more.

An increasing number of dairy farmers in New Zealand (NZ) have adopted a once-a-day (OAD) milking production system, and little is known about the impact of this production system on milk protein composition. The objective of this study was to evaluate the effect of OAD milking on the protein composition in milk from individual cows. Milk was sampled in early, mid-, and late lactation from cows kept at Massey University farms Dairy No. 1 (OAD milking) and Dairy No. 4 (TAD milking) in Palmerston North, NZ. The yields of total milk and milk solids, the proximate composition, and the protein composition were determined. Results showed that OAD milking yielded less milk and milk solids than TAD milking. However, no significant differences in protein, fat, and lactose contents were found. While the proportions of total casein (CN), total whey proteins, αs1-CN, β-CN, and β-lactoglobulin were not affected by the milking frequency, milk from a OAD milking system contained higher proportions of αs2-CN and κ-CN and lower proportions of α-lactalbumin. These proteins also changed differently throughout the milking season in a OAD milking system than in a TAD milking system. These changes in the protein composition of the milk observed in a OAD milking system could have implications for its processing properties and product quality. Full article

(This article belongs to the Section Dairy Farm System and Management)

10 pages, 398 KiB

Open AccessArticle

Cancer Treatment Closer to the Patient Reduces Travel Burden, Time Toxicity, and Improves Patient Satisfaction, Results of 546 Consecutive Patients in a Northern Italian District

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Medicina 2023, 59(12), 2121; https://doi.org/10.3390/medicina59122121 - 04 Dec 2023

Abstract

Background and Objectives: The distance to cancer facilities may cause disparities by creating barriers to oncologic diagnosis and treatment, and travel burden may cause time and financial toxicity. Materials and Methods: To relieve travel burden, a program to deliver oncologic treatment [...] Read more.

Background and Objectives: The distance to cancer facilities may cause disparities by creating barriers to oncologic diagnosis and treatment, and travel burden may cause time and financial toxicity. Materials and Methods: To relieve travel burden, a program to deliver oncologic treatment closer to the patient was initiated in the district of Piacenza (Northern Italy) several years ago. The oncologic activities are performed by oncologists and by nurses who travel from the oncologic ward of the city hospital to territorial centres to provide cancer patient management. This model is called Territorial Oncology Care (TOC): patients are managed near their home, in three territorial hospitals and in a health centre, named “Casa della Salute” (CDS). A retrospective study was performed and the records of patients with cancer managed in the TOC program were analysed. The primary endpoints were the km and time saved, the secondary endpoints: reduction of caregiver need for transport and patient satisfaction. Results: 546 cancer patients managed in the TOC program from 2 January 2021 to 30 June 2022 were included in this study. Primary endpoints: median km to reach the city hospital: 26 (range 11–79 km) median time: 44 min (range 32–116); median km to reach the territorial clinicians in the TOC program: 7 (range 1–35 km), median time: 16 minutes (range 6–54), p < 0.001. Secondary endpoints: 64.8% of patients who needed a caregiver for the city hospital could travel alone in the TOC program and 99.63% of patients were satisfied. Conclusions: The results of this retrospective study highlight the possibility of treating cancer patients near their residence, reducing travel burden and saving time. Full article

(This article belongs to the Section Oncology)

12 pages, 3233 KiB

Open AccessArticle

New Insight into the Effects of Gaseous CO₂ on Spherically Symmetric Droplet Flames

by

Ter-Ki Hong

and

Seul-Hyun Park

Fire 2023, 6(12), 461; https://doi.org/10.3390/fire6120461 - 04 Dec 2023

Abstract

This study investigated the effect of CO₂ on the burning behavior and radiative properties of a single ethanol droplet flame in microgravity. Measurements of the droplet burning rate, the flame size and temperature, and the radiative emissions were performed, under microgravity conditions [...] Read more.

This study investigated the effect of CO₂ on the burning behavior and radiative properties of a single ethanol droplet flame in microgravity. Measurements of the droplet burning rate, the flame size and temperature, and the radiative emissions were performed, under microgravity conditions for ethanol droplets burning in N₂ and CO₂ environments, using the 1.5 s drop tower facilities at the Korea Maritime and Ocean University (KMOU). The non-monotonic sooting behaviors (caused by the elevated O₂ concentrations) were found to have a significant influence on radiative heat losses in N₂ environments, resulting in non-linear droplet burning behaviors with O₂ concentrations. Due to the unique nature of CO₂ in microgravity, which absorbs radiative energy from the flame and raises the temperatures of the surrounding gases, the CO₂ environments suppressed the radiative heat losses from the flame, regardless of the non-monotonic sooting behavior observed at the higher O₂ concentrations. These experimental findings highlight the complicated physics of CO₂ gas radiation in microgravity, which has not been quantitatively explored. Full article

(This article belongs to the Special Issue Combustion Diagnostics)

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15 pages, 554 KiB

Open AccessArticle

Interstitial Lung Disease Is Associated with Sleep Disorders in Rheumatoid Arthritis Patients

by

Natalia Mena-Vázquez

,

Rocío Redondo-Rodriguez

,

Pablo Cabezudo-García

,

Aimara Garcia-Studer

,

Fernando Ortiz-Márquez

,

Paula Borregón-Garrido

,

Manuel Martín-Valverde

,

Inmaculada Ureña-Garnica

,

Sara Manrique-Arija

,

Laura Cano-García

and

Antonio Fernández-Nebro

Clocks & Sleep 2023, 5(4), 755-769; https://doi.org/10.3390/clockssleep5040049 - 04 Dec 2023

Abstract

Objective: To evaluate sleep disorders and associated factors in patients with rheumatoid-arthritis-associated interstitial lung disease (RA-ILD). Methods: We performed an observational study of 35 patients with RA-ILD (cases) and 35 age- and sex-matched RA patients without ILD (controls). We evaluated sleep disorders (Oviedo [...] Read more.

Objective: To evaluate sleep disorders and associated factors in patients with rheumatoid-arthritis-associated interstitial lung disease (RA-ILD). Methods: We performed an observational study of 35 patients with RA-ILD (cases) and 35 age- and sex-matched RA patients without ILD (controls). We evaluated sleep disorders (Oviedo Sleep Questionnaire), positive psychological factors (resilience using the Wagnild and Young Resilience Scale, emotional intelligence using the 24-item Trait Meta-Mood Scale), anxiety and depression (Hospital Anxiety and Depression Scale), quality of life (36-item short-form survey), and fatigue (Functional Assessment of Chronic Illness Therapy Questionnaire). Other variables studied included the Charlson Comorbidity Index (CCI) and RA activity according to the DAS28-ESR. Results: Compared to the controls, the cases were characterized by poorer sleep quality with a higher prevalence of insomnia (42% vs. 20%; p = 0.039), greater severity of insomnia (p = 0.001), and lower sleep satisfaction (p = 0.033). They also had poorer resilience and emotional recovery and more severe anxiety and depression. A diagnosis of ILD was the only factor independently associated with the three dimensions of sleep quality. The predictors of poorer sleep satisfaction in patients with RA-ILD were age (β = −0.379), DAS28-ESR (β = −0.331), and usual interstitial pneumonia pattern (β = −0.438). The predictors of insomnia were DAS28-ESR (β = 0.294), resilience (β = −0.352), and CCI (β = 0.377). Conclusions: RA-ILD is associated with significant sleep disorders. RA-ILD seems to be an independent risk factor for sleep alterations, with a greater impact on insomnia. Age, disease activity, and comorbidity also play a role in sleep disorders in patients with RA-ILD. Full article

(This article belongs to the Section Disorders)

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20 pages, 2309 KiB

Open AccessArticle

Adaptive Fuzzy Fault-Tolerant Control of Uncertain Fractional-Order Nonlinear Systems with Sensor and Actuator Faults

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Fractal Fract. 2023, 7(12), 862; https://doi.org/10.3390/fractalfract7120862 - 04 Dec 2023

Abstract

In this work, an adaptive fuzzy backstepping fault-tolerant control (FTC) issue is tackled for uncertain fractional-order (FO) nonlinear systems with sensor and actuator faults. A fuzzy logic system is exploited to manage unknown nonlinearity. In addition, a novel FO nonlinear filter-based dynamic surface [...] Read more.

In this work, an adaptive fuzzy backstepping fault-tolerant control (FTC) issue is tackled for uncertain fractional-order (FO) nonlinear systems with sensor and actuator faults. A fuzzy logic system is exploited to manage unknown nonlinearity. In addition, a novel FO nonlinear filter-based dynamic surface control (DSC) method is constructed, effectively avoiding the inherent complexity explosion problem in the backstepping recursive process, and in the light of the construction of auxiliary functions, compensating the coupling term introduced by faults. On account of certain assumptions, the stability criterion of the FO Lyapunov function is applied to guarantee the stability of the closed-loop system. Finally, the simulation example verifies the validity of the presented control strategy. Full article

(This article belongs to the Special Issue Advances in Fractional-Order Multiagent Systems: Theory and Applications)

25 pages, 4925 KiB

Open AccessArticle

Understanding the Influence of Genre-Specific Music Using Network Analysis and Machine Learning Algorithms

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Big Data Cogn. Comput. 2023, 7(4), 180; https://doi.org/10.3390/bdcc7040180 - 04 Dec 2023

Abstract

This study analyzes a network of musical influence using machine learning and network analysis techniques. A directed network model is used to represent the influence relations between artists as nodes and edges. Network properties and centrality measures are analyzed to identify influential patterns. [...] Read more.

This study analyzes a network of musical influence using machine learning and network analysis techniques. A directed network model is used to represent the influence relations between artists as nodes and edges. Network properties and centrality measures are analyzed to identify influential patterns. In addition, influence within and outside the genre is quantified using in-genre and out-genre weights. Regression analysis is performed to determine the impact of musical attributes on influence. We find that speechiness, acousticness, and valence are the top features of the most influential artists. We also introduce the IRDI, an algorithm that provides an innovative approach to quantify an artist’s influence by capturing the degree of dominance among their followers. This approach underscores influential artists who drive the evolution of music, setting trends and significantly inspiring a new generation of artists. The independent cascade model is further employed to open up the temporal dynamics of influence propagation across the entire musical network, highlighting how initial seeds of influence can contagiously spread through the network. This multidisciplinary approach provides a nuanced understanding of musical influence that refines existing methods and sheds light on influential trends and dynamics. Full article

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19 pages, 1800 KiB

Open AccessArticle

Fan Stage Design and Performance Optimization for Low Specific Thrust Turbofans

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Int. J. Turbomach. Propuls. Power 2023, 8(4), 53; https://doi.org/10.3390/ijtpp8040053 - 04 Dec 2023

Abstract

In modern turbofan engines, the bypass section of the fan stage alone provides the majority of the total thrust required in cruise, and the size of the fan has a considerable effect on the overall engine weight and nacelle drag. Thrust requirements in [...] Read more.

In modern turbofan engines, the bypass section of the fan stage alone provides the majority of the total thrust required in cruise, and the size of the fan has a considerable effect on the overall engine weight and nacelle drag. Thrust requirements in different parts of the flight envelope must also be satisfied together with sufficient margins towards stalling. An accurate description of the interdependencies between the relevant performance and design attributes of the fan stage alone—such as efficiency, surge margin, fan-face Mach number, stage loading, flow coefficient, and aspect ratio—are therefore necessary to estimate system-level objectives such as mission fuel burn and the direct operating cost with enough confidence during the conceptual design phase. The contribution of this study is to apply a parametric optimization approach to the conceptual design of fan stages for low specific thrust turbofans based on the streamline curvature method. Trade-offs between fan stage attributes for Pareto-optimal solutions are modeled by training Kriging surrogate models on the results from the parametric optimization. A case study is provided in the end to demonstrate the potential implications of including a higher level of fan-stage parameter interdependency in an engine systems model. Results implied that being able to predict the rotor solidity required to maintain a given average blade loading—in addition to stage efficiency—is of significant importance when it comes to evaluating the trade-off between engine weight and thrust-specific fuel consumption. Full article

18 pages, 8348 KiB

Open AccessArticle

Numerical Modelling of the 3D Unsteady Flow of an Inlet Particle Separator for Turboshaft Engines

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Int. J. Turbomach. Propuls. Power 2023, 8(4), 52; https://doi.org/10.3390/ijtpp8040052 - 04 Dec 2023

Abstract

Helicopter and turboprop engines are susceptible to the ingestion of debris and other foreign objects, especially during take-off, landing, and hover. To avoid deleterious effects, filters such as Inlet Particle Separators (IPS) can be installed. However, the performance and limitations of these systems [...] Read more.

Helicopter and turboprop engines are susceptible to the ingestion of debris and other foreign objects, especially during take-off, landing, and hover. To avoid deleterious effects, filters such as Inlet Particle Separators (IPS) can be installed. However, the performance and limitations of these systems have to be investigated before the actual equipment can be installed in the aircraft powerplant. In this paper, we propose different numerical methods with increasing resolution in order to provide an aerodynamic characterization of the IPS, i.e., from a simple semi-empirical model to 3D large eddy simulation. We validate these numerical tools that could aid IPS design using experimental data in terms of global parameters such as separation efficiency and pressure losses. For each of those tools, we underline weaknesses and potential benefits in industry practices. Unsteady flow analysis reveals that detached eddy simulation is the trade-off choice that allows designers to most effectively plan experimental campaigns and mitigate risks. Full article

16 pages, 671 KiB

Open AccessReview

Recent Advances in the Effects of Biochar on Constructed Wetlands: Treatment Performance and Microorganisms

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Separations 2023, 10(12), 593; https://doi.org/10.3390/separations10120593 - 04 Dec 2023

Abstract

Constructed wetlands (CWs) are a kind of green environmental protection technology, which are widely used in sewage treatment. Traditional CWs are faced with the problem of a low treatment effect of high-concentration sewage. In recent years, biochar, as a new type of adsorption [...] Read more.

Constructed wetlands (CWs) are a kind of green environmental protection technology, which are widely used in sewage treatment. Traditional CWs are faced with the problem of a low treatment effect of high-concentration sewage. In recent years, biochar, as a new type of adsorption material, has been used in CWs because of its advantages of large specific surface area, strong adsorption capacity, and wide material sources. This paper systematically summarized the characteristics of biochar and the preparation of biochar by studying the changes in microorganisms added to CWs and compared the effects of different treatment methods coupled with biochar on the treatment performance of CWs. The effects of biochar coupled with CWs on enzyme activity, functional genes, metabolites, and microbial communities were investigated. This review summarizes how different preparation methods affect the properties of biochar and how these biochar properties cause changes in the microorganisms added to CWs. It provides a new theoretical basis for the treatment of pollutants in CWs. Full article

(This article belongs to the Special Issue Separation Technology in Bioprocess for Environmental Remediation)

20 pages, 512 KiB

Open AccessArticle

Flowing Time: Emergentism and Linguistic Diversity

by

Kasia M. Jaszczolt

Philosophies 2023, 8(6), 116; https://doi.org/10.3390/philosophies8060116 - 04 Dec 2023

Abstract

Humans are complex systems, ‘macro-entities’, whose existence, behaviour and consciousness stem out of the configurations of physical entities on the micro-level of the physical world. But an explanation of what humans do and think cannot be found through ‘tracking us back’, so to [...] Read more.

Humans are complex systems, ‘macro-entities’, whose existence, behaviour and consciousness stem out of the configurations of physical entities on the micro-level of the physical world. But an explanation of what humans do and think cannot be found through ‘tracking us back’, so to speak, to micro-particles. So, in explaining human behaviour, including linguistic behaviour on which this paper focuses, emergentism opens up a powerful opportunity to explain what it is exactly that emerged on that level, bearing in mind the end product in the form of the intra- and inter-cultural diversity. Currently there is a gap in emergentism research. On one hand, there are discussions in philosophy of the emergent human reality; on the other, there are discussions of social, cultural, or individual variation of these emergent aspects of humanity in the fields of anthropology, sociology, linguistics or psychology. What I do in this paper is look for a way to ‘trace’ some such diversified emergents from what is universal about their ‘coming to being’, all the way through to their diversification. My chosen emergent is human time, my domain of inquiry is natural-language discourse, and the drive behind this project is to understand the link between ‘real’ time of spacetime on the micro-level from which we emerged and the human time devised by us, paying close attention to the overwhelming diversity in which temporal reference is expressed in human languages. The main question is, where does this diversity fit in? Does understanding of this diversity, as well as of what lurks under the surface of this diversity, aid the emergentism story? My contribution to this volume on ‘the nature of structure and the structure of nature’ thus takes the following take on the title. The structure of human communication is at the same time uniform, universal, and relative to culture, in that it is emergent as a human characteristic, and as such compatible with the micro-level correlates in some essential ways, but also free to fly in different directions that are specific to societies and cultures. I explore here the grey area between the micro-level and the linguistic reflections of time—the middle ground that is emergent itself but that tends to be by-passed by those who approach the question of human flowing time from either end: metaphysics and the philosophy of time on the one hand, and contrastive linguistics, anthropological linguistics and language documentation on the other. I illustrate the debate with examples from tensed and tenseless languages from different language families, entertaining the possibility of a conceptual universal pertaining to time as degrees of epistemic modality. Needless to say, putting the question in this way also sets out my (not unassailable) methodology. Full article

(This article belongs to the Special Issue The Nature of Structure and the Structure of Nature)

15 pages, 2536 KiB

Open AccessArticle

Greenhouse Screening for pH Stress in Rhododendron Genotypes

by

Shusheng Wang

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Marie-Christine Van Labeke

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Emmy Dhooghe

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Johan Van Huylenbroeck

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Leen Leus

Horticulturae 2023, 9(12), 1302; https://doi.org/10.3390/horticulturae9121302 - 04 Dec 2023

Abstract

The genus Rhododendron is known for its preference for acidic soils, although some genotypes can tolerate a more neutral or alkaline pH. In this study, a greenhouse experiment was set up for 140 days to examine different parameters to assess pH stress in [...] Read more.

The genus Rhododendron is known for its preference for acidic soils, although some genotypes can tolerate a more neutral or alkaline pH. In this study, a greenhouse experiment was set up for 140 days to examine different parameters to assess pH stress in the progeny of R. fortunei and the cross combination R. ‘Pink Purple Dream’ x ‘Belami’. Additional cultivars ‘Gomer Waterer’ and ‘Cunningham’s White’ were included in the greenhouse test. The plants were divided into two groups. One group was planted in a substrate with a neutral pH (treatment, pH 6.3) and the other group of plants was planted in an acidic pH substrate (control, pH 4.5). Tolerance to pH stress was evaluated for the individual genotypes on both substrates 140 days after the start of the experiment. The following parameters were analyzed: shoot length, root development, chlorophyll fluorescence (Fv/Fm), leaf color and weight (fresh and dry). In intolerant genotypes, all parameters except for number of shoots were negatively affected by pH stress; especially, the development of roots was negatively impacted by the neutral pH, resulting in above-ground symptoms of pH stress, including decreased height and lower fresh and dry weight. The results show variation in pH tolerance within the genotypes tested and point to the potential for the selection of Rhododendron genotypes with improved tolerance to neutral pH. Full article

(This article belongs to the Special Issue Tolerance and Response of Ornamental Plants to Abiotic Stress)

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16 pages, 3499 KiB

Open AccessArticle

A Bioinspired Astrocyte-Derived Coating Promotes the In Vitro Proliferation of Human Neural Stem Cells While Maintaining Their Stemness

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Andrea C. Jimenez-Vergara

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Ana M. Díaz-Lasprilla

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Dany J. Munoz-Pinto

Biomimetics 2023, 8(8), 589; https://doi.org/10.3390/biomimetics8080589 - 04 Dec 2023

Abstract

The repair of neuronal tissue is a challenging process due to the limited proliferative capacity of neurons. Neural stem cells (NSCs) can aid in the regeneration process of neural tissue due to their high proliferation potential and capacity to differentiate into neurons. The [...] Read more.

The repair of neuronal tissue is a challenging process due to the limited proliferative capacity of neurons. Neural stem cells (NSCs) can aid in the regeneration process of neural tissue due to their high proliferation potential and capacity to differentiate into neurons. The therapeutic potential of these cells can only be achieved if sufficient cells are obtained without losing their differentiation potential. Toward this end, an astrocyte-derived coating (HAc) was evaluated as a promising substrate to promote the proliferation of NSCs. Mass spectroscopy and scanning electron microscopy were used to characterize the HAc. The proliferation rate and the expression of stemness and differentiation markers in NSCs cultured on the HAc were evaluated and compared to the responses of these cells to commonly used coating materials including Poly-L-Ornithine (PLO), and a Human Induced Pluripotent Stem Cell (HiPSC)-based coating. The use of the HAc promotes the in vitro cell growth of NSCs. The expression of the stemness markers Sox2 and Nestin, and the differentiation marker DCX in the HAc group was akin to the expression of these markers in the controls. In summary, HAc supported the proliferation of NSCs while maintaining their stemness and neural differentiation potential. Full article

(This article belongs to the Special Issue Biomaterials for Stem Cell Engineering)

14 pages, 5181 KiB

Open AccessArticle

Optimized Fertilization Shifted Soil Microbial Properties and Improved Vegetable Growth in Facility Soils with Obstacles

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Horticulturae 2023, 9(12), 1303; https://doi.org/10.3390/horticulturae9121303 - 04 Dec 2023

Abstract

Currently, facility cultivation produces almost a third of all vegetables in China. The intensive production style has led to serious soil problems that need to be tackled. In this paper, a pot experiment was set up to evaluate the effects of optimized fertilization [...] Read more.

Currently, facility cultivation produces almost a third of all vegetables in China. The intensive production style has led to serious soil problems that need to be tackled. In this paper, a pot experiment was set up to evaluate the effects of optimized fertilization on vegetable growth and soil properties. Specifically, calcium, magnesium, boron and molybdenum were added on the basis of soil testing. The results showed that the growth of Chinese cabbage was significantly increased by optimized fertilization. The soil pH increased (by 3.82%), and EC decreased (by 8.54%). The abundance of culturable bacteria increased by 33.86%, whereas that of fungi decreased by 70.7%. The optimized fertilization increased the richness but not the evenness of soil microorganisms, increased the relative abundance of Proteobacteria, Firmicutes, Bacillus and Bacteroidetes, and decreased the relative abundance of Actinobacteria, Chloroflexi, and superphyla. Optimized fertilization inhibited the growth of Chytridiomycota and Mortierellomycota, especially the plant pathogen Fusarium. Moreover, balanced fertilization was beneficial in promoting various metabolic processes of soil bacteria. Soil water-soluble Ca, Mg, and available Mo might be the main factors driving the change in microbial groups. Full article

(This article belongs to the Section Plant Nutrition)

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23 pages, 2512 KiB

Open AccessReview

Peptide-Hydrogel Nanocomposites for Anti-Cancer Drug Delivery

by

Farid Hajareh Haghighi

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Gels 2023, 9(12), 953; https://doi.org/10.3390/gels9120953 - 04 Dec 2023

Abstract

Cancer is the second leading cause of death globally, but conventional anticancer drugs have side effects, mainly due to their non-specific distribution in the body in both cancerous and healthy cells. To address this relevant issue and improve the efficiency of anticancer drugs, [...] Read more.

Cancer is the second leading cause of death globally, but conventional anticancer drugs have side effects, mainly due to their non-specific distribution in the body in both cancerous and healthy cells. To address this relevant issue and improve the efficiency of anticancer drugs, increasing attention is being devoted to hydrogel drug-delivery systems for different kinds of cancer treatment due to their high biocompatibility and stability, low side effects, and ease of modifications. To improve the therapeutic efficiency and provide multi-functionality, different types of nanoparticles (NPs) can be incorporated within the hydrogels to form smart hydrogel nanocomposites, benefiting the advantages of both counterparts and suitable for advanced anticancer applications. Despite many papers on non-peptide hydrogel nanocomposites, there is limited knowledge about peptide-based nanocomposites, specifically in anti-cancer drug delivery. The aim of this short but comprehensive review is, therefore, to focus attention on the synergies resulting from the combination of NPs with peptide-based hydrogels. This review, which includes a survey of recent advances in this kind of material, does not aim to be an exhaustive review of hydrogel technology, but it instead highlights recent noteworthy publications and discusses novel perspectives to provide valuable insights into the promising synergic combination of peptide hydrogels and NPs for the design of novel anticancer drug delivery systems. Full article

(This article belongs to the Special Issue Functional Gels Applied in Cancer Therapy)

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18 pages, 4760 KiB

Open AccessArticle

The Advantages of Non-Adhesive Gel-like Embolic Materials in the Endovascular Treatment of Benign Hypervascularized Lesions of the Head and Neck

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Gels 2023, 9(12), 954; https://doi.org/10.3390/gels9120954 - 04 Dec 2023

Abstract

Objectives: The use of non-adhesive gel-like embolic materials (NAGLEMs) in the endovascular treatment of hypervascularized formations in the head and neck is gaining in popularity because of a number of important characteristics involved. Their primary benefits are their capacity to penetrate diseased vasculature, [...] Read more.

Objectives: The use of non-adhesive gel-like embolic materials (NAGLEMs) in the endovascular treatment of hypervascularized formations in the head and neck is gaining in popularity because of a number of important characteristics involved. Their primary benefits are their capacity to penetrate diseased vasculature, effectively distribute, and, most importantly, remain controllable during the process. We reviewed the literature and evaluated the results of using NAGLEMs in comparison to other embolizing substances (namely, coils, glue, and particles) as alternative embolizing agents for patients receiving care at our clinic. The process comprised evaluating the safety, effectiveness, and technological elements of endovascular therapy used to treat two categories of hypervascular pathological abnormalities that were surgically corrected between 2015 and 2023. Arteriovenous malformations (AVMs) located in the head, neck, and paragangliomas with jugular/carotid body localization are combined by intense shunting blood flow and shared requirements for the embolic agent used in endovascular treatment (such as penetration, distribution, delayed polymerization, and controllability). An analysis of the literature was also conducted. Results showed 18 patients diagnosed with neck paragangliomas of the carotid body and jugular type. Five patients with arteriovenous malformation (AVM) of the face and neck were included, consisting of sixteen females and seven males with an average age of 55 ± 13 years. Endovascular procedures were performed using NAGLEMs (ONYX (Medtronic, Irvine, CA, USA), SQUID (Balt, Montmorency, France), and PHIL (Microvention, Tustin, CA, USA)) and dimethyl sulfoxide (DMSO)-compatible balloon catheters. All patients achieved complete or partial embolization of hypervascularized formations using one or more stages of endovascular treatment. Additionally, three AVMs of the face and two paragangliomas of the neck were surgically excised following embolization. In other instances, formations were not deemed necessary to be removed. The patients’ condition upon discharge was assessed by the modified Rankin Scale (mRs) and rated between 0 and 2. Conclusion: Currently, NAGLEMs are predominantly used to treat hypervascularized formations in the neck and head due to their fundamental properties. These properties include a lack of adhesion and a delay in predictable polymerization (after 30–40 min). NAGLEMs also exhibit excellent distribution and penetration throughout the vascular bed of the formation. Adequate controllability of the process is largely achieved through the presence of embolism forms of different viscosity, as well as excellent X-ray visualization. Full article

(This article belongs to the Special Issue Functional Gel Materials and Applications)

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30 pages, 1518 KiB

Open AccessArticle

Obesity during Pregnancy in the Horse: Effect on Term Placental Structure and Gene Expression, as Well as Colostrum and Milk Fatty Acid Concentration

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Morgane Robles

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Delphine Rousseau-Ralliard

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Anne Couturier-Tarrade

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Pascale Chavatte-Palmer

Vet. Sci. 2023, 10(12), 691; https://doi.org/10.3390/vetsci10120691 - 04 Dec 2023

Abstract

In horses, the prevalence of obesity is high and associated with serious metabolic pathologies. Being a broodmare has been identified as a risk factor for obesity. In other species, maternal obesity is known to affect the development of the offspring. This article is [...] Read more.

In horses, the prevalence of obesity is high and associated with serious metabolic pathologies. Being a broodmare has been identified as a risk factor for obesity. In other species, maternal obesity is known to affect the development of the offspring. This article is a follow-up study of previous work showing that Obese mares (O, n = 10, body condition score > 4.25 at insemination) were more insulin resistant and presented increased systemic inflammation during pregnancy compared to Normal mares (N, n = 14, body condition score < 4 at insemination). Foals born to O mares were more insulin-resistant, presented increased systemic inflammation, and were more affected by osteoarticular lesions. The objective of the present study was to investigate the effect of maternal obesity on placental structure and function, as well as the fatty acid profile in the plasma of mares and foals, colostrum, and milk until 90 days of lactation, which, to our knowledge, has been poorly studied in the horse. Mares from both groups were fed the same diet during pregnancy and lactation. During lactation, mares were housed in pasture. A strong heat wave, followed by a drought, occurred during their 2nd and 3rd months of lactation (summer of 2016 in the Limousin region, France). In the present article, term placental morphometry, structure (stereology), and gene expression (RT-qPCR, genes involved in nutrient transport, growth, and development, as well as vascularization) were studied. Plasma of mares and their foals, as well as colostrum and milk, were sampled at birth, 30 days, and 90 days of lactation. The fatty acid composition of these samples was measured using gas chromatography. No differences between the N and O groups were observed for term placental morphometry, structure, or gene expression. No difference in plasma fatty acid composition was observed between groups in mares. The plasma fatty acid profile of O foals was more pro-inflammatory and indicated an altered placental lipid metabolism between birth and 90 days of age. These results are in line with the increased systemic inflammation and altered glucose metabolism observed until 18 months of age in this group. The colostrum fatty acid profile of O mares was more pro-inflammatory and indicated an increased transfer and/or desaturation of long-chain fatty acids. Moreover, O foals received a colostrum poorer in medium-chain saturated fatty acid, a source of immediate energy for the newborn that can also play a role in immunity and gut microbiota development. Differences in milk fatty acid composition indicated a decreased ability to adapt to heat stress in O mares, which could have further affected the metabolic development of their foals. In conclusion, maternal obesity affected the fatty acid composition of milk, thus also influencing the foal’s plasma fatty acid composition and likely participating in the developmental programming observed in growing foals. Full article

(This article belongs to the Special Issue Placentation in Mammals: Development, Function and Pathology)

22 pages, 3376 KiB

Open AccessArticle

Leaf Mustard (Brassica juncea) Germplasm Resources Showed Diverse Characteristics in Agro-Morphological Traits and Glucosinolate Levels

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Awraris Derbie Assefa

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Seong-Hoon Kim

,

Ho Chul Ko

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Nayoung Ro

,

Parthiban Subramanian

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and

Foods 2023, 12(23), 4374; https://doi.org/10.3390/foods12234374 - 04 Dec 2023

Abstract

Leaf mustard, characterized by its purple/red/green leaves with a green/white midrib, is known for its thick, tender, and spicy leaves with a unique taste and flavor. There were only a few studies reported on leaf mustard for its morphological and biochemical traits from [...] Read more.

Leaf mustard, characterized by its purple/red/green leaves with a green/white midrib, is known for its thick, tender, and spicy leaves with a unique taste and flavor. There were only a few studies reported on leaf mustard for its morphological and biochemical traits from Korea. A total of 355 leaf mustard accessions stored at the GenBank of the National Agrobiodiversity Center were evaluated for 25 agro-morphological traits and seven intact glucosinolates (GSLs). The accessions showed a wide variation in terms of most of the traits. The quantitative agro-morphological traits varied from 16.0 (leaf length) to 48.7% (petiole width) of the coefficient of variation (CV). The highest variation was observed in glucoiberin (299.5%, CV), while the total GSL showed a CV of 66.1%. Sinigrin, followed by gluconapin and gluconasturtiin, was the most abundant GSL, accounting for as high as 75% of the total GSLs, while glucobrassicanapin and glucoiberin were the least abundant, contributing 0.7% and 0.1% on average, respectively. Sinigrin had a positive significant correlation with all GSLs but gluconasturtiin, while glucobarbarin and gluconasturtiin were highly positively correlated to each other, but least correlated with other GSLs. The leaf length was negatively correlated with sinigrin and glucoiberin. The width of the petiole showed a positive correlation with gluconapin, glucobrassicanapin, and glucobrassicin, while the length of the petiole had a negative correlation with sinigrin, glucobrassicanapin, glucoiberin, glucobrassicin, and the total GSLs. A higher width of the midrib was associated with higher contents of gluconapin, glucobrassicanapin, and glucobrassicin. A PCA analysis based on the agro-morphological traits showed that the first and second principal components accounted for 65.2% of the overall variability. Accessions that form a head tend to exhibit a longer leaf length, a larger plant weight, a thicker midrib, and higher widths of the midrib, petiole, and leaf. The GSLs showed inconsistent inter-and intra-leaf variation. Accessions that identified for various traits in their performance, such as, for example, Yeosu66 and IT259487 (highest total glucosinolates) and IT228984 (highest plant weight), would be promising lines for developing new varieties. Full article

(This article belongs to the Special Issue Extracts from Plant Foods: Biological Characterization and Application)

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