bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural Language Processing Approaches to Text Data Augmentation: A Computational Linguistic Analysis
Authors: Zaiton Hoda , Al-Ansary Sameh
Published: June 2024

In the context of Natural Language Processing (NLP) tasks, problems such as insufficient or skewed data are frequently encountered. One practical solution to this problem is to generate additional textual data. Text Data Augmentation (TDA) refers to small changes made to accessible text at the character, word, or sentence level to generate synthetic data that is subsequently inserted into data loaders to train the model. By producing synthetic data, models can learn from a larger range of instances and, hence, enhance their resilience and generalization skills. Despite the fact that the entire NLP community has extensively studied many NLP DA approaches, recent research on the subject suggests that the relationship between the several DA techniques now in use is not entirely known in practice. Therefore, this study applies and extends the advances of TDA to encounter and cover varied tools on multiple settings or contexts. To carry out a thorough practical implementation of NLP DA approaches, comparing the way they perform and highlighting some of the significant similarities and differences in these various scenarios, this work depends on different tools of easy data augmentation and neural-based augmentation. This study suggests that some typical DA techniques might not be suitable in some circumstances or text environments. Specifically, according to the initial results, the context and word count of a text may have a significant impact on the quality of the synthetic data.
Metaphors They Kill by: Dehumanization of Palestinians by Israeli Officials and Sympathizers
Authors: Maalej Zouheir A. , Zibin Aseel
Published: June 2024

Within the cognitive paradigm, metaphors are said to play a key role “not just in language but in thought and action” (Lakoff and Johnson 1980: p. 3). As a form of action, genocide in recent human history has been incited by metaphor, with Holocaust Jews as “parasites” (Musolff 2010), Iraqis as “rapists” (Lakoff 1991), Rwandan Tutsis as “cockroaches” (Hintjens 1999; Mowarin 2014), Bosnians as “Islamic fundamentalists” (Karčić 2022), etc. The aim of the present study is to investigate the ongoing genocide committed by Israel against the Palestinians in the Gaza Strip by bringing political ideology to bear on cognition both in thought and action (Gibbs 2017). In particular, it will be shown that the conceptual metaphor politics is religion (Charteris-Black 2004) in the Christian Zionists’ in-group’s socio-cultural cognition, acts in tandem with and motivates the “animalized dehumanization” (Sevillano and Fiske 2023) of Palestinians. Such an ideology, which is tainted by psychological essentialism (Leyens et al. 2001) of the Jews supremacy, is instrumentalizing the deliberate, superordinate conceptual metaphor (Steen 2023) humans are animals and other basic-level metaphors such as Palestinians are rats, ants and cockroaches, therefore stripping the Palestinian outgroup of their humanity (Leyens et al. 2000; Leyens et al. 2003; Haslam 23.2.2024, 2006; Haslam, Loughnan and Sun 2011; Harris and Fiske 2011) in order to legitimize the Palestinian genocide. Animalized dehumanization, which is a blue print for genocide, will be accounted for using Lakoff and Johnson’s (1980, 1999) Conceptual Theory of Metaphor together with Lakoff and Turner’s (1989) Great Chain of Being Metaphor.
Penetapan Titik Kendali Kritis (TKK) pada Proses Produksi Bakso di PT XYZ
Authors: Lesmana Angga , Uzwatania Fina , Ginantaka Aditia
Published: June 2024

Titik kendali kritis (TKK) merupakan salah satu prinsip yang ada dalam Hazard and Critical Control Points (HACCP) sebagai langkah dalam penetapan poin penting yang perlu dikendalaikan selama proses produksi. Penentuan TKK adalah upaya dalam pengurangan dan proses eliminasi bahaya yang sudah diidentifikasi ataupun mengurangi dampak bahaya hingga tingkat yang dapat diterima. PT XYZ adalah salah satu industri yang mengembangkan segmentasi pengolah makanan siap saji frozen food yaitu bakso. Perlunya penetapan TKK di PT XYZ memastikan bahwa bakso yang diberikan pada konsumen sehat dan aman. Penelitian ini bertujuan untuk mengidentifikasi, menganalisis serta mengendalikan bahaya yang mungkin terjadi pada proses pembuatan bakso. Metode yang digunakan dalam penelitian ini melalui pendekatan kualitatif berupa analisis proses dan Titik Kendali Kritis pada tahapan proses produksi bakso, serta menetapkan tindakan koreksi prosedur monitoring pada tahapan proses. Hasil penelitian menunjukan bahwa proses yang menjadi TKK atau critical control point (CCP) adalah proses perebusan dengan bentuk bahaya logam berat dan serangga serta benda asing. Tindakan koreksi yang dilakukan adalah penggunaan mesin metal detector untuk mengantisipasi cemaran logam berat dan pemantauan kembali kebersihan pekerja, penggunaan APD, dan kebersihan alat.
The journey of decellularized vessel: from laboratory to operating room
Authors: Kang Chenbin , Yang Hongji
Published: June 2024

Over the past few decades, there has been a remarkable advancement in the field of transplantation. But the shortage of donors is still an urgent problem that requires immediate attention. As with xenotransplantation, bioengineered organs are promising solutions to the current shortage situation. And decellularization is a unique technology in organ-bioengineering. However, at present, there is no unified decellularization method for different tissues, and there is no gold-standard for evaluating decellularization efficiency. Meanwhile, recellularization, re-endothelialization and modification are needed to form transplantable organs. With this mind, we can start with decellularization and re-endothelialization or modification of small blood vessels, which would serve to address the shortage of small-diameter vessels while simultaneously gathering the requisite data and inspiration for further recellularization of the whole organ-scale vascular network. In this review, we collect the related experiments of decellularization and post-decellularization approaches of small vessels in recent years. Subsequently, we summarize the experience in relation to the decellularization and post-decellularization combinations, and put forward obstacle we face and possible solutions.
Effects of different tooth movement patterns and aligner thicknesses on maxillary arch expansion with clear aligners: a three-dimensional finite element study
Authors: Li Na , Wang ChunJuan , Yang Min , Chen DingGen , Tang MingYuan , Li DaoKun , Qiu ShengLei , Chen Qi , Feng Yi
Published: June 2024

Objectives

The objective of this study was to investigate the biomechanical effects of different tooth movement patterns and aligner thicknesses on teeth and periodontal tissues during maxillary arch expansion with clear aligners, to facilitate more precise and efficient clinical orthodontic treatments.

Methods

Three-dimensional models including teeth, maxilla, periodontal ligament, and aligner were constructed and subjected to finite element analysis. Tooth displacement trends and periodontal ligament stresses were measured for seven tooth displacement patterns (divided into three categories including overall movement of premolars and molars with gradually increasing molar expansion in each step; distributed movement of premolars and molars; and alternating movement between premolars and molars at intervals) and two aligner thicknesses (0.5 mm and 0.75 mm) during maxillary arch expansion with clear aligners.

Results

When expanding the maxillary arch with clear aligners, the effective expansion of the target teeth mainly showed a tilting movement trend. Increasing the amount of molar expansion increased the buccal displacement of the first molar but decreased the buccal displacement of the premolars. The mean buccal displacement of the target teeth was greater in the posterior teeth interval alternating movement group (0.026 mm) than in the premolar/molar distributed movement group (0.016 mm) and the overall movement group (0.015 mm). Increasing aligner thickness resulted in greater buccal displacement of the crowns and increased stress on the periodontal ligaments.

Conclusion

Increasing the amount of molar expansion reduces the efficiency of premolar expansion. Alternating movement of premolars and molars at intervals achieves a higher arch expansion efficiency, but attention should be paid to the anchorage of adjacent teeth. Increasing the thickness of the aligner increases the expansion efficiency but may also increase the burden on the periodontal tissues.
Screening of potentially active compounds against rheumatoid arthritis in the Juan-Bi decoction using systems pharmacology and animal experiments
Authors: Liu Dahai , Fu Qiang , Liu Leyna G. , Li Wenwen , Qi Fei , Liu Justin , Shang Lifeng , Wang Xiu , Yang Fang , Li Jie , Lu Daoqiang , Feng Huiying , Zhang Ziwen , Chen Yiqing , Liang Junru , Yao Jiayi , Lv Hua , Li Riwang , Wang Jun , Wu Di , Liu Yuxi , Xia Chenglai , Li Wenxing
Published: June 2024

Background: The Juan-Bi decoction (JBD) is a classic traditional Chinese medicines (TCMs) prescription for the treatment of rheumatoid arthritis (RA). However, the active compounds of the JBD in RA treatment remain unclear.

Aim: The aim of this study is to screen effective compounds in the JBD for RA treatment using systems pharmacology and experimental approaches.

Method: Botanical drugs and compounds in the JBD were acquired from multiple public TCM databases. All compounds were initially screened using absorption, distribution, metabolism, excretion, and toxicity (ADMET) and physicochemical properties, and then a target prediction was performed. RA pathological genes were acquired from the DisGeNet database. Potential active compounds were screened by constructing a compound–target–pathogenic gene (C-T-P) network and calculating the cumulative interaction intensity of the compounds on pathogenic genes. The effectiveness of the compounds was verified using lipopolysaccharide (LPS)-induced RAW.264.7 cells and collagen-induced arthritis (CIA) mouse models.

Results: We screened 15 potentially active compounds in the JBD for RA treatment. These compounds primarily act on multiple metabolic pathways, immune pathways, and signaling transduction pathways. Furthermore, in vivo and in vitro experiments showed that bornyl acetate (BAC) alleviated joint damage, and inflammatory cells infiltrated and facilitated a smooth cartilage surface via the suppression of the steroid hormone biosynthesis.

Conclusion: We screened potential compounds in the JBD for the treatment of RA using systems pharmacology approaches. In particular, BAC had an anti-rheumatic effect, and future studies are required to elucidate the underlying mechanisms.
Miconazole induces aneuploidy-mediated tolerance in Candida albicans that is dependent on Hsp90 and calcineurin
Authors: Guo Liangsheng , Zheng Lijun , Dong Yubo , Wang Chen , Deng Huijie , Wang Zongjie , Xu Yi
Published: June 2024

Antifungal resistance and antifungal tolerance are two distinct terms that describe different cellular responses to drugs. Antifungal resistance describes the ability of a fungus to grow above the minimal inhibitory concentration (MIC) of a drug. Antifungal tolerance describes the ability of drug susceptible strains to grow slowly at inhibitory drug concentrations. Recent studies indicate antifungal resistance and tolerance have distinct evolutionary trajectories. Superficial candidiasis bothers millions of people yearly. Miconazole has been used for topical treatment of yeast infections for over 40 years. Yet, fungal resistance to miconazole remains relatively low. Here we found different clinical isolates of Candida albicans had different profile of tolerance to miconazole, and the tolerance was modulated by physiological factors including temperature and medium composition. Exposure of non-tolerant strains with different genetic backgrounds to miconazole mainly induced development of tolerance, not resistance, and the tolerance was mainly due to whole chromosomal or segmental amplification of chromosome R. The efflux gene CDR1 was required for maintenance of tolerance in wild type strains but not required for gain of aneuploidy-mediated tolerance. Heat shock protein Hsp90 and calcineurin were essential for maintenance as well as gain of tolerance. Our study indicates development of aneuploidy-mediated tolerance, not resistance, is the predominant mechanism of rapid adaptation to miconazole in C. albicans, and the clinical relevance of tolerance deserves further investigations.
Impact of coronary collateralization on major adverse cardiovascular and cerebrovascular events after successful recanalization of chronic total occlusion
Authors: Sun Yurong , Zhang Bin , Zhang Xinyuan , Zhang Xiaojiao , Bao Wenqi , Bai Hangrui , Luan Bo
Published: June 2024

Aims

This study aims to investigate the effects of coronary collateral circulation (CCC) on the prognosis of chronic total occlusion (CTO) patients with or without metabolic syndrome (MetS).

Methods

The study included 342 CTO patients who underwent successful percutaneous coronary intervention at the People's Hospital of Liaoning Province between 1 February 2021 and 30 September 2023. The Rentrop score was used to assess the status of CCC. The outcome was major adverse cardiovascular and cerebrovascular events (MACCEs), defined as a composite of all-cause mortality, cardiac death, non-fatal myocardial infarction (MI), target vessel revascularization (TVR), and non-fatal stroke. Univariate and multivariate logistic analyses were used to investigate the association of CCC, MetS, and MACCEs with odds ratios (ORs) and 95% confidence intervals (CIs). The effect of CCC was further investigated in different MetS, diabetes mellitus (DM), and Syntax score groups.

Results

MACCEs were more common in patients with poor CCC compared to those with good CCC (38.74% vs. 16.56%). Statistical differences were found in MACCEs (OR = 3.33, 95% CI: 1.93–5.72), MI (OR = 3.11, 95% CI: 1.73–5.58), TVR (OR = 3.06, 95% CI: 1.70–5.53), and stent thrombosis (OR = 6.14, 95% CI: 2.76–13.65) between the good and poor CCC groups. Poor CCC patients with MetS had a higher incidence of MACCEs (OR = 4.21, 95% CI: 2.05–8.65), non-fatal MI (OR = 4.44, 95% CI: 2.01–9.83), TVR (OR = 3.28, 95% CI: 1.51–7.11), and stent thrombosis (OR = 10.80, 95% CI: 3.11–37.54). Similar findings were also observed in CTO patients with DM and a Syntax score ≥23.

Conclusion

Poor CCC could increase the risk of MACCEs in CTO patients, particularly those with MetS, DM, and a Syntax score ≥23. Further prospective, multicenter studies are needed to validate our findings and to explore potential therapeutic interventions.
Development and deployment of an adaptive national elementary reading screening test
Authors: Walgermo Bente Rigmor , Foldnes Njål , Uppstad Per Henning , Bakken Arild Michel , Lundetræ Kjersti
Published: June 2024

Increasingly over the past decade, there has been a demand of more thorough documentation of the quality of reading assessments. Yet, available documentation of high-quality measures are often restricted to general framework descriptions providing psychometric information as a token of test quality. In a modern view of validity, understanding what is being measured and how scores are calculated is a prerequisite for good interpretation and use of test scores. The present article aims to document the research and development process of a national adaptive screening test for reading difficulties, in which the envisioned interpretation and use of test scores is guiding the work. Given the mandatory nature of this test the sample consist of 49,828 third grade students aged 8. Significant outcomes from this design process involve detailed information on: (a) choice of sub-tests and item formats, (b) selection of high quality items, (c) choice and design of adaptive model, and finally, a statement on the challenges that are still to be met for such a test to function optimally. The present paper is among the first to, in an open and detailed manner, describe the development process as well as qualities and challenges of an adaptive reading screening test for students of this young age.
Heavy metals in wastewater and fish collected from waste stabilization pond and human health risks in southwestern Ethiopia
Authors: Berhanu Girma , Lemma Hailu , Mekonnen Seblework , Dadi Dessalegn
Published: June 2024

Introduction

This study aimed to measure the concentration of toxic heavy metals in wastewater samples and Nile tilapia (Oreochromis niloticus) species inhabiting wastewater (waste stabilization ponds) and evaluate their safety as a food source in southwestern Ethiopia. For this purpose, toxic metals like lead (Pb), cadmium (Cd), arsenic (As), and mercury (Hg) in wastewater samples and fish tissues (muscle, gill, and liver) were independently examined.

Methods

A laboratory-based cross-sectional study was performed to ascertain the levels of Pb, Cd, As, and Hg in the fish tissues ofO. niloticusand wastewater samples. Heavy metal levels were analyzed by microplasma atomic emission spectrometry (Agilent 4210 MP-AES) and hydrogen-generated atomic absorption spectrometry (HGAAS, novAA 400P, Germany).

Results

Heavy metal concentrations were measured in the following decreasing order (µg L−1): Cd > Pb > As > Hg in facultative and maturation ponds, with Cd (27.66 µg L−1) having the highest concentration and Hg (0.349 µg L−1) having the lowest concentration. Among the heavy metals detected in the wastewater samples, Hg showed a statistically significant difference between the sampling points (p = 0.023). The maximum metal concentration was measured for Pb (0.35 mg kg−1) and Cd (0.24 mg kg−1) in the muscle tissue ofO. niloticus. The value of arsenic (0.02 mg kg−1) detected in fish edible muscles exceeded the FAO/WHO maximum permissible limit (MPL = 0.01) for human consumption. The carcinogenic and non-carcinogenic health risks of consuming fish due to trace metals were relatively low and posed fewer potential threats to human health. According to this finding, children were more susceptible to heavy metal exposure than adults.

Conclusion

Due to the high quantities of these harmful heavy metals, wastewater from oxidation ponds should not be used for fishing to avoid bioaccumulation. The target carcinogenic risk (TR) and target hazard quotient (THQ) indicated that all heavy metals were below the safe threshold. This research will provide a baseline for monitoring trace metals in various edible aquatic creatures and for future research in artificial habitats and regulatory considerations.
Using adjusted local assortativity with Molecular Pixelation unveils colocalization of membrane proteins with immunological significance
Authors: Rhomberg-Kauert Jan , Karlsson Max , Thiagarajan Divya , Kallas Tomasz , Karlsson Filip , Fredriksson Simon , Dahlberg Johan , Martinez Barrio Alvaro
Published: June 2024

Advances in spatial proteomics and protein colocalization are a driving force in the understanding of cellular mechanisms and their influence on biological processes. New methods in the field of spatial proteomics call for the development of algorithms and open up new avenues of research. The newly introduced Molecular Pixelation (MPX) provides spatial information on surface proteins and their relationship with each other in single cells. This allows for in silico representation of neighborhoods of membrane proteins as graphs. In order to analyze this new data modality, we adapted local assortativity in networks of MPX single-cell graphs and created a method that is able to capture detailed information on the spatial relationships of proteins. The introduced method can evaluate the pairwise colocalization of proteins and access higher-order similarity to investigate the colocalization of multiple proteins at the same time. We evaluated the method using publicly available MPX datasets where T cells were treated with a chemokine to study uropod formation. We demonstrate that adjusted local assortativity detects the effects of the stimuli at both single- and multiple-marker levels, which enhances our understanding of the uropod formation. We also applied our method to treating cancerous B-cell lines using a therapeutic antibody. With the adjusted local assortativity, we recapitulated the effect of rituximab on the polarity of CD20. Our computational method together with MPX improves our understanding of not only the formation of cell polarity and protein colocalization under stimuli but also advancing the overall insight into immune reaction and reorganization of cell surface proteins, which in turn allows the design of novel therapies. We foresee its applicability to other types of biological spatial data when represented as undirected graphs.
Altered ontogeny and transcriptomic signatures of tissue-resident pulmonary interstitial macrophages ameliorate allergic airway hyperresponsiveness
Authors: Tighe Robert M. , Birukova Anastasiya , Malakhau Yuryi , Kobayashi Yoshihiko , Vose Aaron T. , Chandramohan Vidya , Cyphert-Daly Jaime M. , Cumming R. Ian , Fradin Kirshner Helene , Tata Purushothama R. , Ingram Jennifer L. , Gunn Michael D. , Que Loretta G. , Yu Yen-Rei A.
Published: June 2024

Introduction

Environmental exposures and experimental manipulations can alter the ontogenetic composition of tissue-resident macrophages. However, the impact of these alterations on subsequent immune responses, particularly in allergic airway diseases, remains poorly understood. This study aims to elucidate the significance of modified macrophage ontogeny resulting from environmental exposures on allergic airway responses to house dust mite (HDM) allergen.

Methods

We utilized embryonic lineage labeling to delineate the ontogenetic profile of tissue-resident macrophages at baseline and following the resolution of repeated lipopolysaccharide (LPS)-induced lung injury. We investigated differences in house dust mite (HDM)-induced allergy to assess the influence of macrophage ontogeny on allergic airway responses. Additionally, we employed single-cell RNA sequencing (scRNAseq) and immunofluorescent staining to characterize the pulmonary macrophage composition, associated pathways, and tissue localization.

Results

Our findings demonstrate that the ontogeny of homeostatic alveolar and interstitial macrophages is altered after the resolution from repeated LPS-induced lung injury, leading to the replacement of embryonic-derived by bone marrow-derived macrophages. This shift in macrophage ontogeny is associated with reduced HDM-induced allergic airway responses. Through scRNAseq and immunofluorescent staining, we identified a distinct subset of resident-derived interstitial macrophages expressing genes associated with allergic airway diseases, localized adjacent to terminal bronchi, and diminished by prior LPS exposure.

Discussion

These results suggest a pivotal role for pulmonary macrophage ontogeny in modulating allergic airway responses. Moreover, our findings highlight the implications of prior environmental exposures in shaping future immune responses and influencing the development of allergies. By elucidating the mechanisms underlying these phenomena, this study provides valuable insights into potential therapeutic targets for allergic airway diseases and avenues for further research into immune modulation and allergic disease prevention.
Uptake of dissolved inorganic nitrogen and N2 fixation by Crocosphaera watsonii under climate change scenarios
Authors: Umbricht Jacqueline , Filella Alba , Klett Angelina , Vogts Angela , Benavides Mar , Voss Maren
Published: June 2024

The response of N2 fixation to projected future conditions in the ocean cannot be reliably predicted to date. We conducted a minicosm experiment with pre-acclimated cultures of the globally significant diazotroph Crocosphaera watsonii strain WH8501 (“Crocosphaera”). PH and temperature were altered simultaneously to match the RCP scenarios 4.5 and 6 and investigate a more realistic future scenario compared to studies that focus on changes of a single stressor only. The cell abundance and nitrogen metabolism of Crocosphaera was monitored over 5 days. Our results imply that Crocosphaera is able to simultaneously perform N2 fixation and assimilate dissolved inorganic nitrogen (DIN, i.e., nitrate and ammonium) under all the conditions tested and implies a competition with non-diazotrophic phytoplankton for DIN, which should be further investigated. Using NanoSIMS analysis of single cells, our results point towards a preference for DIN assimilation over N2 fixation under more acidic and warmer conditions. Overall, our results show that while the combined alteration of pH and temperature had a negative effect on the diazotroph’s growth and N2 fixation, Crocosphaera is likely to cope well with conditions in the future ocean. The high intra-population variability in nitrogen assimilation pathways may give this species the flexibility to quickly react to environmental changes.
Biodiversity and community structures across the Magellan seamounts and abyssal plains in the western Pacific Ocean revealed by environmental DNA metabarcoding analysis
Authors: Kim Eun-Bi , Ju Se-Jong , Suh Yeon Jee
Published: June 2024

Seamounts within deep-sea ecosystems are recognized as biodiversity hotspots, yet they are increasingly threatened by anthropogenic activities such as overfishing, resource exploitation, and climate change. To establish environmental baseline data and assess the impacts of current or future anthropogenic activities, we conducted environmental DNA (eDNA) metabarcoding analyses to comprehensively characterize prokaryotic and eukaryotic diversity across various water depths of the Magellan seamounts and the adjacent abyssal plains. Metabarcoding analysis revealed higher richness and diversity in both prokaryotic and eukaryotic communities within the seamounts compared to the abyssal plains. Overall, the analysis identified 9,068 prokaryotic amplicon sequence variants (ASVs), representing 39 phyla and 47 classes. Similarly, 4,569 eukaryotic ASVs were identified, spanning 34 phyla and 93 classes. Furthermore, our results revealed distinct community structures between the seamounts and abyssal plains, with turnover across different water depths. These findings are crucial as they indicate the unique ecological roles and potential vulnerability of seamount communities, emphasizing the need for targeted conservation strategies. Our study underscores the importance of conducting comprehensive long-term environmental assessments of the impacts of anthropogenic activities on seamount ecosystems and highlights the potential of eDNA metabarcoding as a powerful tool for guiding conservation and management efforts in remote and challenging marine environments.
Integrated assessment of trace elements in a marine ranching area based on multi-species and multi-level biomarkers: a case study in China’s national-level marine ranching demonstration area
Authors: Li Mingzhu , Chen Zhixu , Li Ming , Zhang Jiugang , Xu Bingqing , Yang Yanyan , Li Xiangfei , Fan Linlin , Liu Baojun , Zheng Tao , Fang Yan , Li Fan
Published: June 2024

The goal of this study was to evaluate the trace element pollution in a marine ranching area in China based on molecular responses (expression of metallothionein and antioxidant enzyme genes), and biochemical biomarkers (metallothionein content, antioxidant enzyme activities, and malonaldehyde level) in four indicator species. We collected samples of two fish (Lateolabrax maculatus and Sebastes schlegelii), one crustacean (Charybdis japonica), and one gastropod (Rapana venosa) from the western Furong Island marine ranching area and from an adjacent area in March 2022 and measured the trace element content in these indicator species as well as in the seawater and sediment. We found that the bioaccumulation characteristics of trace elements and the response patterns of biomarkers were species specific. Moreover, not every biomarker was significantly correlated with environmental trace element content. We then established two biomarker combinations indicative of trace element pollution in seawater and sediment, respectively, based on the correlation between biomarkers and trace element contents. The selected biomarkers were integrated using integrated biomarker response version 2 (IBRv2). IBRv2 values in the studied marine ranching area were lower than those in the adjacent area. Additionally, these values were consistent with the bioaccumulation of trace elements in the indicator species, the integrated trace element pollution index for seawater, and the potential risk index for sediment. These results show that this multi-biomarker and multi-species IBRv2 approach provided a comprehensive diagnosis of trace element pollution in the marine ranching area. Therefore, its application may be beneficial for marine environmental monitoring and management in view of the ecotoxicological impact of pollutants on organisms.
Impact of ocean acidification on microzooplankton grazing dynamics
Authors: Shi Wenting , Fu Xiaoting , Han Yabo , Qin Jiahui , Sun Jun
Published: June 2024

This study examines the potential impacts of projected atmospheric carbon dioxide (pCO2) levels reaching 800 ppm by the end of the century, focusing on ocean acidification effects on marine ecosystems in the coastal areas of Bohai. We investigated how acidification affects the grazing patterns of microzooplankton using dilution techniques and ecophysiological methods. Our findings indicate that acidic conditions shift the phytoplankton community structure, changing dominant species. Elevated CO2 concentrations reduced grazing pressure on phytoplankton, with less steep declines in growth rates at 800 ppm CO2 (spring: 2.43 d−1 vs. 2.16 d−1, summer: −0.46 d−1 vs. −0.73 d−1, autumn: −0.45 d−1 vs. −0.90 d−1) and significant decreases in grazing pressure percentages (%Pp from 0.84 to 0.58 and %Pi from 0.64 to 0.46). Short-term acid exposure significantly increased superoxide dismutase activity in both microplankton (from 0.03 to 0.08 U mg−1, p<0.01) and nanoplankton (from 0.05 to 0.09 U mg−1, p<0.001), indicating an adaptive response to oxidative stress. These results highlight that elevated CO2 levels primarily boost phytoplankton growth by reducing microzooplankton grazing pressure, resulting in higher growth rates and a shift towards smaller-sized phytoplankton, reflecting complex short-term ecological responses to acidification. Further research is needed to understand the long-term effects of ocean acidification on microzooplankton and their role in marine secondary productivity.
Effect of gradation on macro-meso shear properties of the alluvial-diluvial soil-rock mixture (ADSRM)
Authors: Liu Longqi , Fan Zhenhao , Yao Linhu , Yang Yunshu
Published: June 2024

Alluvial-diluvial soil-rock mixture (ADSRM) is a unique geological material primarily consisting of pebbles, gravel, and soil. Gradation design significantly enhances the shear strength of ADSRM, offering significant implications for sustainable construction of transportation infrastructure in mountainous regions. Hence, the N-method of gradation theory was employed for the gradation design of ADSRM fillers in this study. Macro-mechanical testing reveals that the graded sample exhibits significantly higher shear strength, equivalent cohesion, and friction angle compared to the ungraded sample, with more pronounced shear dilatancy. Meso-shear properties suggest that the graded sample has a lower percentage of pore area compared to the ungraded sample, but a higher percentage of small pores relative to total pores, and more crushed rock blocks under the same normal stress conditions. Pore abundance indicates that the majority of pores on the shear plane are oblate in shape. The findings from the equivalent diameter and fractal dimension of the rock block contour suggest improved grinding roundness of rock blocks in the graded sample post-shearing. In summary, the quantity of pores and broken rock blocks primarily impacts the strength and equivalent cohesion of the filler, while the abundance, roundness, shape coefficient, and fractal dimension of rock block contour mainly affects the internal friction angle.
Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity
Authors: Chin Hong Soon , Ravi Varadharajulu Narendrakumar , Lin Zhi-Han , Chen Wen-Yu , Zhang Zong-Han , Arumugam Sankar , Lai Ching-Yen , Yu Steve S.-F.
Published: June 2024

The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.
Exploring the role of anticipatory postural adjustment duration within APA2 subphase as a potential mediator between clinical disease severity and fall risk in Parkinson’s disease
Authors: Hu Cheng-Hao , Lai Yun-Ru , Huang Chih-Cheng , Lien Chia-Yi , Chen Yueh-Sheng , Yu Chiun-Chieh , Lee Sieh-Yang , Lin Wei-Che , Cheng Ben-Chung , Chiu Wen-Chan , Chiang Yi-Fang , Kung Chien-Feng , Lu Cheng-Hsien
Published: June 2024

Introduction

People with Parkinson’s Disease (PD) often show reduced anticipatory postural adjustments (APAs) before voluntary steps, impacting their stability. The specific subphase within the APA stage contributing significantly to fall risk remains unclear.

Methods

We analyzed center of pressure (CoP) trajectory parameters, including duration, length, and velocity, throughout gait initiation. This examination encompassed both the postural phase, referred to as anticipatory postural adjustment (APA) (APA1, APA2a, APA2b), and the subsequent locomotor phases (LOC). Participants were instructed to initiate a step and then stop (initiating a single step). Furthermore, we conducted assessments of clinical disease severity using the Unified Parkinson’s Disease Rating Scale (UPDRS) and evaluated fall risk using Tinetti gait and balance scores during off-medication periods.

Results

Freezing of gait (FOG) was observed in 18 out of 110 participants during the measurement of CoP trajectories. The Ramer-Douglas-Peucker algorithm successfully identified CoP displacement trajectories in 105 participants (95.5%), while the remaining 5 cases could not be identified due to FOG. Tinetti balance and gait score showed significant associations with levodopa equivalent daily dose, UPDRS total score, disease duration, duration (s) in APA2a (s) and LOC (s), length in APA1 (cm) and APA2b (cm), mediolateral velocity in APA1 (X) (cm/s), APA2a (X) (cm/s), APA2b (X) (cm/s) and LOC (X) (cm/s), and anterior–posterior velocity in APA2a (Z) (cm/s) and APA2b (Z) (cm/s). Multiple linear regression revealed that only duration (s) in APA2a and UPDRS total score was independently associated with Tinetti gait and balance score. Further mediation analysis showed that the duration (s) in APA2a served as a mediator between UPDRS total score and Tinetti balance and gait score (Sobel test, p = 0.047).

Conclusion

APA2 subphase duration mediates the link between disease severity and fall risk in PD, suggesting that longer APA2a duration may indicate reduced control during gait initiation, thereby increasing fall risk.
Validation and refinement of a predictive nomogram using artificial intelligence: assessing in-hospital mortality in patients with large hemispheric cerebral infarction
Authors: Ding Jian , Ma Xiaoming , Huang Wendie , Yue Chunxian , Xu Geman , Wang Yumei , Sheng Shiying , Liu Meng , Ren Yi
Published: June 2024

Background

Large Hemispheric Infarction (LHI) poses significant mortality and morbidity risks, necessitating predictive models for in-hospital mortality. Previous studies have explored LHI progression to malignant cerebral edema (MCE) but have not comprehensively addressed in-hospital mortality risk, especially in non-decompressive hemicraniectomy (DHC) patients.

Methods

Demographic, clinical, risk factor, and laboratory data were gathered. The population was randomly divided into Development and Validation Groups at a 3:1 ratio, with no statistically significant differences observed. Variable selection utilized the Bonferroni-corrected Boruta technique (p < 0.01). Logistic Regression retained essential variables, leading to the development of a nomogram. ROC and DCA curves were generated, and calibration was conducted based on the Validation Group.

Results

This study included 314 patients with acute anterior-circulating LHI, with 29.6% in the Death group (n = 93). Significant variables, including Glasgow Coma Score, Collateral Score, NLR, Ventilation, Non-MCA territorial involvement, and Midline Shift, were identified through the Boruta algorithm. The final Logistic Regression model led to a nomogram creation, exhibiting excellent discriminative capacity. Calibration curves in the Validation Group showed a high degree of conformity with actual observations. DCA curve analysis indicated substantial clinical net benefit within the 5 to 85% threshold range.

Conclusion

We have utilized NIHSS score, Collateral Score, NLR, mechanical ventilation, non-MCA territorial involvement, and midline shift to develop a highly accurate, user-friendly nomogram for predicting in-hospital mortality in LHI patients. This nomogram serves as valuable reference material for future studies on LHI patient prognosis and mortality prevention, while addressing previous research limitations.
Artificial sweeteners and their implications in diabetes: a review
Authors: Angelin Matcha , Kumar Janardhanan , Vajravelu Leela Kakithakara , Satheesan Abhishek , Chaithanya Venkata , Murugesan Ria
Published: June 2024

Diabetes is a significant global health concern, highlighting the critical role of dietary strategies in its management and prevention. Artificial sweeteners (ASs), due to their capacity to provide sweetness without contributing to caloric intake, have emerged as a potential tool in diabetes management. This review thoroughly examines the nuanced relationship between artificial sweeteners and diabetes, addressing their benefits and potential risks. ASs have been shown to aid in weight management, a key factor in reducing diabetes risk, and do not impact immediate blood glucose levels, offering improved glucose control for individuals with diabetes. Beyond these benefits, however, artificial sweeteners may interact complexly with gut microbiota, potentially altering its composition and affecting metabolic health. This interaction introduces concerns regarding insulin sensitivity and the risk of insulin resistance, with studies reporting conflicting findings. This comprehensive review highlights the importance of a nuanced approach to understanding the implications of artificial sweeteners in diabetes management. Given the mixed evidence on their health effects, there is a clear need for further research to fully elucidate the role of artificial sweeteners in metabolic health and their suitability as part of dietary interventions for diabetes.
Evaluation of the diagnostic and prognostic clinical values of circulating tumor DNA and cell-free DNA in pancreatic malignancies: a comprehensive meta-analysis
Authors: Arayici Mehmet Emin , İnal Abdullah , Basbinar Yasemin , Olgun Nur
Published: June 2024

Background

The diagnostic and prognostic clinical value of circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) in pancreatic malignancies are unclear. Herein, we aimed to perform a meta-analysis to evaluate ctDNA and cfDNA as potential diagnostic and prognostic biomarkers.

Methods

PRISMA reporting guidelines were followed closely for conducting the current meta-analysis. The PubMed/Medline, Scopus, and Web of Science (WoS) databases were scanned in detail to identify eligible papers for the study. A quality assessment was performed in accordance with the REMARK criteria. The risk ratios (RRs) of the diagnostic accuracy of ctDNA compared to that of carbohydrate antigen 19.9 (CA 19.9) in all disease stages and the hazard ratios (HRs) of the prognostic role of ctDNA in overall survival (OS) were calculated with 95% confidence intervals (CIs).

Results

A total of 18 papers were evaluated to assess the diagnostic accuracy and prognostic value of biomarkers related to pancreatic malignancies. The pooled analysis indicated that CA19.9 provides greater diagnostic accuracy across all disease stages than ctDNA or cfDNA (RR = 0.64, 95% CI: 0.50–0.82, p < 0.001). Additionally, in a secondary analysis focusing on prognosis, patients who were ctDNA-positive were found to have significantly worse OS (HR = 2.00, 95% CI: 1.51–2.66, p < 0.001).

Conclusion

The findings of this meta-analysis demonstrated that CA19-9 still has greater diagnostic accuracy across all disease stages than KRAS mutations in ctDNA or cfDNA. Nonetheless, the presence of detectable levels of ctDNA was associated with worse patient outcomes regarding OS. There is a growing need for further research on this topic.

Systematic review registration

https://doi.org/10.37766/inplasy2023.12.0092, identifier INPLASY2023120092.
The growth-promoting and disease-suppressing mechanisms of Trichoderma inoculation on peanut seedlings
Authors: Wang Xingqiang , Zhao Zhongjuan , Li Hongmei , Wei Yanli , Hu Jindong , Yang Han , Zhou Yi , Li Jishun
Published: June 2024

Trichoderma spp. is known for its ability to enhance plant growth and suppress disease, but the mechanisms for its interaction with host plants and pathogens remain unclear. This study investigated the transcriptomics and metabolomics of peanut plants (Arachis hypogaea L.) inoculated with Trichoderma harzianum QT20045, in the absence and presence of the stem rot pathogen Sclerotium rolfsii JN3011. Under the condition without pathogen stress, the peanut seedlings inoculated with QT20045 showed improved root length and plant weight, increased indole acetic acid (IAA) production, and reduced ethylene level, with more active 1-aminocyclopropane-1-carboxylate acid (ACC) synthase (ACS) and ACC oxidase (ACO), compared with the non-inoculated control. Under the pathogen stress, the biocontrol efficacy of QT20045 against S. rolfsii was 78.51%, with a similar effect on plant growth, and IAA and ethylene metabolisms to the condition with no biotic stress. Transcriptomic analysis of peanut root revealed that Trichoderma inoculation upregulated the expression of certain genes in the IAA family but downregulated the genes in the ACO family (AhACO1 and AhACO) and ACS family (AhACS3 and AhACS1) consistently in the absence and presence of pathogens. During pathogen stress, QT20045 inoculation leads to the downregulation of the genes in the pectinesterase family to keep the host plant’s cell wall stable, along with upregulation of the AhSUMM2 gene to activate plant defense responses. In vitro antagonistic test confirmed that QT20045 suppressed S. rolfsii growth through mechanisms of mycelial entanglement, papillary protrusions, and decomposition. Our findings highlight that Trichoderma inoculation is a promising tool for sustainable agriculture, offering multiple benefits from pathogen control to enhanced plant growth and soil health.
Consistent decrease in conifer embolism resistance from the stem apex to base resulting from axial trends in tracheid and pit traits
Authors: Zambonini Dario , Savi Tadeja , Rosner Sabine , Petit Giai
Published: June 2024

Introduction

Drought-induced embolism formation in conifers is associated with several tracheid and pit traits, which vary in parallel from stem apex to base. We tested whether this axial anatomical variability is associated with a progressive variation in embolism vulnerability along the stem from apex to base.

Methods

We assessed the tracheid hydraulic diameter (Dh), mean pit membrane area (PMA) and the xylem pressure at 50% loss of conductivity (P50) on longitudinal stem segments extracted at different distances from the stem apex (DFA) in a Picea abies and an Abies alba tree.

Results

In both trees, Dh and PMA scaled with DFA0.2. P50 varied for more than 3 MPa from the treetop to the stem base, according to a scaling of -P50 with DFA-0.2. The largest Dh, PMA and P50 variation occurred for DFA<1.5 m. PMA and Dh scaled more than isometrically (exponent b=1.2). Pit traits vary proportionally with tracheid lumen diameter.

Discussion and conclusions

Apex-to-base trends in tracheid and pit traits, along with variations in P50, suggest a strong structure-function relationship that is influenced by DFA. Although the effect of DFA on P50 has not been extensively explored previously, we propose that analyzing the relationship between P50 and DFA could be crucial for a comprehensive assessment of embolism vulnerability at the individual level.