bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants
Authors: Ouamba Alexandre J. K. , Gagnon Mérilie , Varin Thibault , Chouinard P. Yvan , LaPointe Gisèle , Roy Denis
Published: November 2023

Introduction

The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.

Methods

We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.

Results and discussion

Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated byEnterobacteriaceae,Microbacteriaceae,Beijerinckiaceae, andSphingomonadaceae, the GL and GLICI communities showed high proportions ofLeuconostocaceaeandAcetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated byEnterobacteriaceaeand other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.
Biotechnological production of omega-3 fatty acids: current status and future perspectives
Authors: Qin Jiansong , Kurt Elif , LBassi Tyler , Sa Lucas , Xie Dongming
Published: November 2023

Omega-3 fatty acids, including alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), have shown major health benefits, but the human body’s inability to synthesize them has led to the necessity of dietary intake of the products. The omega-3 fatty acid market has grown significantly, with a global market from an estimated USD 2.10 billion in 2020 to a predicted nearly USD 3.61 billion in 2028. However, obtaining a sufficient supply of high-quality and stable omega-3 fatty acids can be challenging. Currently, fish oil serves as the primary source of omega-3 fatty acids in the market, but it has several drawbacks, including high cost, inconsistent product quality, and major uncertainties in its sustainability and ecological impact. Other significant sources of omega-3 fatty acids include plants and microalgae fermentation, but they face similar challenges in reducing manufacturing costs and improving product quality and sustainability. With the advances in synthetic biology, biotechnological production of omega-3 fatty acids via engineered microbial cell factories still offers the best solution to provide a more stable, sustainable, and affordable source of omega-3 fatty acids by overcoming the major issues associated with conventional sources. This review summarizes the current status, key challenges, and future perspectives for the biotechnological production of major omega-3 fatty acids.
Comparison of comprehensive quantitative EEG metrics between typically developing boys and girls in resting state eyes-open and eyes-closed conditions
Authors: Modarres Mo , Cochran David , Kennedy David N. , Frazier Jean A.
Published: November 2023

Introduction

A majority of published studies comparing quantitative EEG (qEEG) in typically developing (TD) children and children with neurodevelopmental or psychiatric disorders have used a control group (e.g., TD children) that combines boys and girls. This suggests a widespread supposition that typically developing boys and girls have similar brain activity at all locations and frequencies, allowing the data from TD boys and girls to be aggregated in a single group.

Methods

In this study, we have rigorously challenged this assumption by performing a comprehensive qEEG analysis on EEG recoding of TD boys (n = 84) and girls (n = 62), during resting state eyes-open and eyes-closed conditions (EEG recordings from Child Mind Institute’s Healthy Brain Network (HBN) initiative). Our qEEG analysis was performed over narrow-band frequencies (e.g., separating low α from high α, etc.), included sex, age, and head size as covariates in the analysis, and encompassed computation of a wide range of qEEG metrics that included both absolute and relative spectral power levels, regional hemispheric asymmetry, and inter- and intra-hemispheric magnitude coherences as well as phase coherency among cortical regions. We have also introduced a novel compact yet comprehensive visual presentation of the results that allows comparison of the qEEG metrics of boys and girls for the entire EEG locations, pairs, and frequencies in a single graph.

Results

Our results show there are wide-spread EEG locations and frequencies where TD boys and girls exhibit differences in their absolute and relative spectral powers, hemispheric power asymmetry, and magnitude coherence and phase synchrony.

Discussion

These findings strongly support the necessity of including sex, age, and head size as covariates in the analysis of qEEG of children, and argue against combining data from boys and girls. Our analysis also supports the utility of narrow-band frequencies, e.g., dividing α, β, and γ band into finer sub-scales. The results of this study can serve as a comprehensive normative qEEG database for resting state studies in children containing both eyes open and eyes closed paradigms.
A case report of jejunum transplantation in the treatment of severe cervical esophageal stricture in patients with dystrophic epidermolysis bullosa
Authors: Xu Zhen , Zhang Yong , Hu Yanjiao , Xiu Xia , Yang Bowen , Huang Tianqiao , Huang Yichuan
Published: November 2023

Epidermolysis bullosa (EB) is a rare disorder caused by autosomal genetic variation. Its main clinical features include skin and mucous membrane blisters, erosion, repeated ulcers and scar formation. The lesions mostly involve the skin, oral cavity, digestive system and urinary system. Epidermolysis bullosa complicated with esophageal stenosis is a common gastrointestinal manifestation of this disorder. Currently, there is no cure for EB, and thus symptomatic treatment is usually applied. Here we describe the case of a patient with recessive dystrophic EB complicated with severe esophageal stenosis. The narrow segment of esophagus was removed and the free part of jejunum was transplanted into the esophageal defect to reconstruct the esophagus and restore the patient’s normal swallowing. For patients with EB complicated with severe esophageal stenosis, surgical resection of the diseased esophagus and jejunal transplantation can be used to repair the esophageal and restore normal swallowing pathway, providing an effective treatment for this condition.
Use of comprehensive genomic profiling for biomarker discovery for the management of non-small cell lung cancer brain metastases
Authors: Abdulhaleem Mohammed , Hunting John C. , Wang Yuezhu , Smith Margaret R. , Agostino Ralph D’ jr. , Lycan Thomas , Farris Michael K. , Ververs James , Lo Hui-Wen , Watabe Kounosuke , Topaloglu Umit , Li Wencheng , Whitlow Christopher , Su Jing , Wang Ge , Chan Michael D. , Xing Fei , Ruiz Jimmy
Published: November 2023

Background

Clinical biomarkers for brain metastases remain elusive. Increased availability of genomic profiling has brought discovery of these biomarkers to the forefront of research interests.

Method

In this single institution retrospective series, 130 patients presenting with brain metastasis secondary to Non-Small Cell Lung Cancer (NSCLC) underwent comprehensive genomic profiling conducted using next generation circulating tumor deoxyribonucleic acid (DNA) (Guardant Health, Redwood City, CA). A total of 77 genetic mutation identified and correlated with nine clinical outcomes using appropriate statistical tests (general linear models, Mantel-Haenzel Chi Square test, and Cox proportional hazard regression models). For each outcome, a genetic signature composite score was created by summing the total genes wherein genes predictive of a clinically unfavorable outcome assigned a positive score, and genes with favorable clinical outcome assigned negative score.

Results

Seventy-two genes appeared in at least one gene signature including: 14 genes had only unfavorable associations, 36 genes had only favorable associations, and 22 genes had mixed effects. Statistically significant associated signatures were found for the clinical endpoints of brain metastasis velocity, time to distant brain failure, lowest radiosurgery dose, extent of extracranial metastatic disease, concurrent diagnosis of brain metastasis and NSCLC, number of brain metastases at diagnosis as well as distant brain failure. Some genes were solely associated with multiple favorable or unfavorable outcomes.

Conclusion

Genetic signatures were derived that showed strong associations with different clinical outcomes in NSCLC brain metastases patients. While these data remain to be validated, they may have prognostic and/or therapeutic impact in the future.

Statement of translation relevance

Using Liquid biopsy in NSCLC brain metastases patients, the genetic signatures identified in this series are associated with multiple clinical outcomes particularly these ones that lead to early or more numerous metastases. These findings can be reverse-translated in laboratory studies to determine if they are part of the genetic pathway leading to brain metastasis formation.
Prognostic value analysis of cholesterol and cholesterol homeostasis related genes in breast cancer by Mendelian randomization and multi-omics machine learning
Authors: Wu Haodong , Wu Zhixuan , Ye Daijiao , Li Hongfeng , Dai Yinwei , Wang Ziqiong , Bao Jingxia , Xu Yiying , He Xiaofei , Wang Xiaowu , Dai Xuanxuan
Published: November 2023

Introduction

The high incidence of breast cancer (BC) prompted us to explore more factors that might affect its occurrence, development, treatment, and also recurrence. Dysregulation of cholesterol metabolism has been widely observed in BC; however, the detailed role of how cholesterol metabolism affects chemo-sensitivity, and immune response, as well as the clinical outcome of BC is unknown.

Methods

With Mendelian randomization (MR) analysis, the potential causal relationship between genetic variants of cholesterol and BC risk was assessed first. Then we analyzed 73 cholesterol homeostasis-related genes (CHGs) in BC samples and their expression patterns in the TCGA cohort with consensus clustering analysis, aiming to figure out the relationship between cholesterol homeostasis and BC prognosis. Based on the CHG analysis, we established a CAG_score used for predicting therapeutic response and overall survival (OS) of BC patients. Furthermore, a machine learning method was adopted to accurately predict the prognosis of BC patients by comparing multi-omics differences of different risk groups.

Results

We observed that the alterations in plasma cholesterol appear to be correlative with the venture of BC (MR Egger, OR: 0.54, 95% CI: 0.35-0.84, p<0.006). The expression patterns of CHGs were classified into two distinct groups(C1 and C2). Notably, the C1 group exhibited a favorable prognosis characterized by a suppressed immune response and enhanced cholesterol metabolism in comparison to the C2 group. In addition, high CHG score were accompanied by high performance of tumor angiogenesis genes. Interestingly, the expression of vascular genes (CDH5, CLDN5, TIE1, JAM2, TEK) is lower in patients with high expression of CHGs, which means that these patients have poorer vascular stability. The CAG_score exhibits robust predictive capability for the immune microenvironment characteristics and prognosis of patients(AUC=0.79). It can also optimize the administration of various first-line drugs, including AKT inhibitors VIII Imatinib, Crizotinib, Saracatinib, Erlotinib, Dasatinib, Rapamycin, Roscovitine and Shikonin in BC patients. Finally, we employed machine learning techniques to construct a multi-omics prediction model(Risklight),with an area under the feature curve (AUC) of up to 0.89.

Conclusion

With the help of CAG_score and Risklight, we reveal the signature of cholesterol homeostasis-related genes for angiogenesis, immune responses, and the therapeutic response in breast cancer, which contributes to precision medicine and improved prognosis of BC.
The impact of liver abscess formation on prognosis of patients with malignant liver tumors after transarterial chemoembolization
Authors: Wang Yunan , Chang Zhihui , Zheng Jiahe , Liu Zhaoyu , Zhang Jun
Published: November 2023

Purpose

Liver abscess is a rare and serious complication after transarterial chemoembolization (TACE) for liver cancer; however, its impact on the prognosis is unclear. This retrospective study examined the outcomes of patients with liver abscess formation following TACE for malignant liver tumors to elucidate the impact of liver abscess formation on the prognosis of these patients.

Methods

From January 2017 to January 2022, 1,387 patients with malignant tumors underwent 3,341 sessions of TACE at our hospital. Clinical characteristics of patients at baseline and follow-up were examined, including treatment and outcome of liver abscess, tumor response to the TACE leading to liver abscess, and overall survival time.

Results

Of 1,387 patients, 15 (1.1%) patients with liver abscess complications after TACE resulted in a total of 16 (0.5%) cases of liver abscess after 3,341 TACE sessions (including one patient with two events). After antibiotic or percutaneous catheter drainage (PCD) treatment, all the infections associated with liver abscesses were controlled. In the PCD group, eight patients died before drainage tube removal, one retained the drainage tube until the end of follow-up, and five underwent drainage tube removal; the mean drainage tube removal time was 149.17 ± 134.19 days. The efficacy of TACE leading to liver abscess was evaluated as partial response (18.75%), stable disease (37.5%), and progressive disease (43.75%). Eleven patients died during the follow-up period owing to causes unrelated to infections caused by liver abscesses. The survival rates at 3 months, 6 months, 1 year, and 5 years were 86.7%, 50.9%, 25.5%, and 17%, respectively.

Conclusion

Patients with liver abscess formation following TACE for malignant liver tumors experienced prolonged drainage tube removal time after PCD; while this condition did not directly cause death, it indirectly contributed to a poor prognosis in these patients.
Cuproptosis: emerging biomarkers and potential therapeutics in cancers
Authors: Wang Min , Zheng Lianwen , Ma Shuai , Lin Ruixin , Li Jiahui , Yang Shuli
Published: November 2023

The sustenance of human life activities depends on copper, which also serves as a crucial factor for vital enzymes. Under typical circumstances, active homeostatic mechanisms keep the intracellular copper ion concentration low. Excess copper ions cause excessive cellular respiration, which causes cytotoxicity and cell death as levels steadily rise above a threshold. It is a novel cell death that depends on mitochondrial respiration, copper ions, and regulation. Cuproptosis is now understood to play a role in several pathogenic processes, including inflammation, oxidative stress, and apoptosis. Copper death is a type of regulatory cell death(RCD).Numerous diseases are correlated with the development of copper homeostasis imbalances. One of the most popular areas of study in the field of cancer is cuproptosis. It has been discovered that cancer angiogenesis, proliferation, growth, and metastasis are all correlated with accumulation of copper ions. Copper ion concentrations can serve as a crucial marker for cancer development. In order to serve as a reference for clinical research on the product, diagnosis, and treatment of cancer, this paper covers the function of copper ion homeostasis imbalance in malignant cancers and related molecular pathways.
Acquired aplastic anaemia after SARS-CoV-2 infection in China: a case report
Authors: Wu Xiyan , Mo Yi , Wen Kailiang , Ming Rui , Yin Xinyu , Hu Liang , Liu Gang , Lin Ge , Li Weina
Published: November 2023

Since the coronavirus disease 2019 (COVID-19) pandemic began, several research groups in different countries have described cases of aplastic anaemia (AA) after COVID-19 or COVID-19 vaccination. Here, we present the case of a patient with new-onset AA in Changsha, China, that was presumably associated with preceding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We conducted an epidemiological assessment of the incidence rate of blood system diseases from July 1, 2022, to May 31, 2023, in the haematology department of the Second Xiangya Hospital of Central South University and Hunan Children's Hospital. The detection rates of AA and leukaemia in the first two months after the epidemic outbreak were higher than those before and during the outbreak. However, only the difference in the detection rate of leukaemia was statistically significant.
Efficacy and safety of high-dose ilaprazole-amoxicillin dual therapy for Helicobacter pylori eradication: a prospective, single-center, randomized trial
Authors: Cheng Jianping , Fan Chanjuan , Huang Kun , Zhai Lili , Wang Hui , Xie Dongling , Cai Yong , Li Zhen , Bai Qixuan , Wang Pan , Ding Haiou
Published: November 2023

Background: Until now, there have been no randomized controlled trials directly evaluating the efficacy of high-dose ilaprazole-amoxicillin dual therapy (HT) in comparison to other standard treatments for H. pylori (Helicobacter pylori) infection. This study aimed to compare the effectiveness and safety of HT with bismuth quadruple therapy (BQT) as an initial treatment for H. pylori.

Methods: This single-center, prospective, randomized clinical controlled trial recruited 225 consecutive patients. They were assigned to either HT group (ilaprazole, 10 mg, twice daily; amoxicillin 1,000 mg, three times daily) or BQT group (compound bismuth aluminate granules, 2.6 g, three times daily; ilaprazole, 5 mg, twice daily; amoxicillin, 1,000 mg, twice daily; clarithromycin, 500 mg, twice daily) for 14 days. The 13C-urea breath test assessed eradication success 4 weeks after treatment. The primary outcome focused on the eradication rate, with secondary outcomes including safety and compliance.

Results: From February 2023 to March 2023, 228 subjects were screened, and 225 were randomized. The HT and BQT groups showed eradication rates of 76.3% and 61.3% (p = 0.015) both by intention-to-treat (ITT) analysis and per-protocol (PP) analysis. HT was associated with fewer adverse events than BQT (27.2% vs. 81.8%, p = 0.002). The most commonly reported adverse events was bitter taste of mouth (3.5% vs. 60.4%, p < 0.001). There was no significant difference in compliance between the two groups (89.5% vs. 92.8%, p = 0.264).

Conclusion: The 14-day HT treatment demonstrates better efficacy in H. pylori eradication treatment and improved safety and compliance compared to BQT. The results provide supporting evidence for 14-day HT can be potentially considered as a first-line regimen for empirical treatment.

Clinical Trial Registration:https://www.chictr.org.cn/showproj.html?proj=186562, identifier ChiCTR2200066284
Vesicular CLC chloride/proton exchangers in health and diseases
Authors: Picollo Alessandra
Published: November 2023

Chloride is one of the most abundant anions in the human body; it is implicated in several physiological processes such as the transmission of action potentials, transepithelial salt transport, maintenance of cellular homeostasis, regulation of osmotic pressure and intracellular pH, and synaptic transmission. The balance between the extracellular and intracellular chloride concentrations is controlled by the interplay of ion channels and transporters embedded in the cellular membranes. Vesicular members of the CLC chloride protein family (vCLCs) are chloride/proton exchangers expressed in the membrane of the intracellular organelles, where they control vesicular acidification and luminal chloride concentration. It is well known that mutations in CLCs cause bone, kidney, and lysosomal genetic diseases. However, the role of CLC exchangers in neurological disorders is only now emerging with the identification of pathogenic CLCN gene variants in patients with severe neuronal and intellectual dysfunctions. This review will provide an overview of the recent advances in understanding the role of the vesicular CLC chloride/proton exchangers in human pathophysiology.
Let there be light to interact
Authors: Stibor Herwig , Stockenreiter Maria
Published: November 2023

Light plays a crucial role in ecological dynamics, both as a consumable resource and as an environmental factor. Prokaryotic and eukaryotic photoautotrophs use light as an energy source for photosynthesis, which forms the basis of food chains and determines the flow of energy and matter in ecosystems. Light availability and quality can influence resource complementarity and species coexistence, as well as the stoichiometry of primary producers and the transfer efficiency of food webs. In addition, light serves as an important source of information for organisms, influencing their activities and interactions with the environment. Light shapes biotic interactions, including competition, predator-prey relationships, and mutualistic and antagonistic relationships between photoautotrophs and heterotrophs. Anthropogenic activities affect these photoecological processes, with largely unknown consequences. Hence, understanding the ecological role and control of light is essential for understanding the functioning of ecosystems and biogeochemical cycles.
Internal and external load during on-field training drills with an aim of improving the physical performance of players in professional soccer: a retrospective observational study
Authors: Ammann Linda , Chmura Paweł
Published: November 2023

Extensive research has led to evidence-based methodological recommendations for appropriate prescription and implementation of different training drills to improve the physical performance of professional soccer players, while also pointing out limitations of drills. Less is known about the current methods used in an ecological context and the extent to which evidence-based considerations are applied. Knowledge of current practices might also enable to identify pitfalls in successful implementation and/or deficiencies in the communication of scientific knowledge. Thus, the aim of this study was to quantify and compare the load that players experience in an ecological context during drills that are frequently used, and in which there is an intention to improve the players’ physical capacities. Therefore, a retrospective observational cohort study was conducted over a 14-month period, analyzing 9 load measures during training drills of 39 players of a team competing in the highest Swiss league. The load experienced by players was statistically significant different between the assessed drill categories for each load measure (all p < .001). This indicates different drills provide different stimuli. HIIT drills proved to be a more powerful tool of getting players to cover distances at high-speed and to spend time at an intensity ≥90% HRmax compared to sided games. The sprint distance of players was very low in all sided games and in most cases also in HIIT drills, in the latter the players also hardly performed any deceleration. In small goal-oriented sided games, players covered a greater distance per minute when outside floaters were present. Particularly regarding an improvement of the players’ aerobic capacity, the present data emphasize the relevance for coaches to ensure an appropriate exposure. In general, the importance of individual load management in professional soccer is highlighted.
Nitric oxide synthase and its function in animal reproduction: an update
Authors: Zhang Wei , Chen Su juan , Guo Li ya , Zhang Zijing , Zhang Jia bin , Wang Xiao meng , Meng Xiang bo , Zhang Min ying , Zhang Ke ke , Chen Lin lin , Li Yi wei , Wen Yuliang , Wang Lei , Hu Jian he , Bai Yue yu , Zhang Xiao jian
Published: November 2023

Nitric oxide (NO), a free radical labile gas, is involved in the regulation of various biological functions and physiological processes during animal reproduction. Recently, increasing evidence suggests that the biological role and chemical fate of NO is dependent on dynamic regulation of its biosynthetic enzyme, three distinct nitric oxide synthase (NOS) according to their structure, location and function. The impact of NOS isoforms on reproductive functions need to be timely elucidated. Here, we focus on and the basic background and latest studies on the development, structure, importance inhibitor, location pattern, complex functions. Moreover, we summarize the exactly mechanisms which involved some cell signal pathways in the regulation of NOS with cellular and molecular level in the animal reproduction. Therefore, this growing research area provides the new insight into the important role of NOS male and female reproduction system. It also provides the treatment evidence on targeting NOS of reproductive regulation and diseases.
Evaluation of relative pollen productivities in temperate China for reliable pollen-based quantitative reconstructions of Holocene plant cover
Authors: Li Furong , Gaillard Marie-José , Xie Siqi , Huang Kangyou , Cui Qiaoyu , Fyfe Ralph , Marquer Laurent , Sugita Shinya
Published: November 2023

The Landscape Reconstruction Algorithm (LRA) is regarded as the soundest approach for quantifying taxon-specific plant cover from pollen data. The reliability of relative pollen productivity (RPP) estimates is fundamental in the accuracy of quantitative vegetation reconstruction using the LRA approach. Inconsistent RPP estimates produced by different studies can cast doubt on the reliability and applicability of quantitative vegetation reconstruction. Therefore, it is crucial that the RPP estimates are evaluated before being applied for quantitative vegetation reconstruction. We have tested two alternative approaches, namely, a leave-one-out cross-validation (LOO) method and a splitting-by-subregion strategy, using surface pollen assemblages and the REVEALS model—the first step in the LRA—to evaluate the reliability of RPPs estimates of 10 target taxa obtained in the cultural landscape of Shandong. We compared the REVEALS estimates (RVs) with observations of regional vegetation abundance (OBVs) and pollen proportions (PPs). The RVs of all taxa are generally closer to OBVs than PPs, and the degree of similarity depends strongly on the abundance of individual taxa in plant and pollen; taxa dominant in the region show the highest similarity between RVs and OBVs, such as Artemisia, Poaceae, and Humulus. The RVs of all herb taxa except Humulus and Asteraceae SF Cichorioideae are slightly overrepresented, and the RVs of all tree taxa are underrepresented except for Castanea. The comparison of RVs with OBVs collected from different spatial extents shows that the RVs of all herb taxa are more similar to OBVs collected from shorter distances (100 km and 75 km for the entire region and the subregion, respectively), whereas the RVs of all tree taxa are more similar to OBVs collected from longer distances (150 km and 100 km for the entire region and the subregion, respectively). Furthermore, our findings highlight the importance to test different sizes of area for vegetation surveys for evaluation of the RVs given that the appropriate size of vegetation survey may vary between low pollen producers (mainly herbs) and high pollen producers (mainly trees). We consider that the LOO strategy is the best approach in this case study for evaluating the RPP estimates from surface moss polsters. The evaluation confirms the reliability of the obtained RPP estimates for their potential application in quantitative reconstruction of vegetation abundance in temperate China.
Harnessing the power of diffusion models for plant disease image augmentation
Authors: Muhammad Abdullah , Salman Zafar , Lee Kiseong , Han Dongil
Published: November 2023

Introduction

The challenges associated with data availability, class imbalance, and the need for data augmentation are well-recognized in the field of plant disease detection. The collection of large-scale datasets for plant diseases is particularly demanding due to seasonal and geographical constraints, leading to significant cost and time investments. Traditional data augmentation techniques, such as cropping, resizing, and rotation, have been largely supplanted by more advanced methods. In particular, the utilization of Generative Adversarial Networks (GANs) for the creation of realistic synthetic images has become a focal point of contemporary research, addressing issues related to data scarcity and class imbalance in the training of deep learning models. Recently, the emergence of diffusion models has captivated the scientific community, offering superior and realistic output compared to GANs. Despite these advancements, the application of diffusion models in the domain of plant science remains an unexplored frontier, presenting an opportunity for groundbreaking contributions.

Methods

In this study, we delve into the principles of diffusion technology, contrasting its methodology and performance with state-of-the-art GAN solutions, specifically examining the guided inference model of GANs, named InstaGAN, and a diffusion-based model, RePaint. Both models utilize segmentation masks to guide the generation process, albeit with distinct principles. For a fair comparison, a subset of the PlantVillage dataset is used, containing two disease classes of tomato leaves and three disease classes of grape leaf diseases, as results on these classes have been published in other publications.

Results

Quantitatively, RePaint demonstrated superior performance over InstaGAN, with average Fréchet Inception Distance (FID) score of 138.28 and Kernel Inception Distance (KID) score of 0.089 ± (0.002), compared to InstaGAN’s average FID and KID scores of 206.02 and 0.159 ± (0.004) respectively. Additionally, RePaint’s FID scores for grape leaf diseases were 69.05, outperforming other published methods such as DCGAN (309.376), LeafGAN (178.256), and InstaGAN (114.28). For tomato leaf diseases, RePaint achieved an FID score of 161.35, surpassing other methods like WGAN (226.08), SAGAN (229.7233), and InstaGAN (236.61).

Discussion

This study offers valuable insights into the potential of diffusion models for data augmentation in plant disease detection, paving the way for future research in this promising field.
Impact of quantitative safety targets on road fatality reduction: an empirical support toward governance plan
Authors: Cui Haizhou , Guo Yuliang , Li Yuchen , Zhang Jianwei , Wang Yida , Yang Lin , Hu Jiayi , Wong Hak Kei , Bai Yuxuan , Ma Yang , Chen Faan
Published: November 2023

Introduction

The role of quantitative target setting has become an important topic in debates on the improvement of road safety performance. Specifically, there are questions regarding the relationship between quantitative safety targets and their actual effects. Although previous studies have provided important insights into this subject, their empirical findings have largely been equivocal, and research on this topic remains inadequate.

Methods

Based on panel data representing 20 years of observations from 34 OECD member states, we employed nonlinear and linear panel models to investigate whether and how the attributes of quantitative road safety targets (i.e., target ambition and duration) influence their success (i.e., target completion status and rate).

Results

The results indicate that a quantitative target with a higher level of ambition is associated with a lower likelihood and rate of completion, whereas there is no support for a connection between target duration and final completion rate. This suggests that an excessively ambitious target does not necessarily result in better road safety performance and is detrimental to achieving expected fatality reductions.

Conclusion

From an empirical perspective, this study revealed a potential interaction effect between quantitative road safety targets and practical fatality reduction performance, providing government officials and policymakers with essential references for future practices on target setting and governance planning in regard to public health.
Medical image analysis using deep learning algorithms
Authors: Li Mengfang , Jiang Yuanyuan , Zhang Yanzhou , Zhu Haisheng
Published: November 2023

In the field of medical image analysis within deep learning (DL), the importance of employing advanced DL techniques cannot be overstated. DL has achieved impressive results in various areas, making it particularly noteworthy for medical image analysis in healthcare. The integration of DL with medical image analysis enables real-time analysis of vast and intricate datasets, yielding insights that significantly enhance healthcare outcomes and operational efficiency in the industry. This extensive review of existing literature conducts a thorough examination of the most recent deep learning (DL) approaches designed to address the difficulties faced in medical healthcare, particularly focusing on the use of deep learning algorithms in medical image analysis. Falling all the investigated papers into five different categories in terms of their techniques, we have assessed them according to some critical parameters. Through a systematic categorization of state-of-the-art DL techniques, such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Generative Adversarial Networks (GANs), Long Short-term Memory (LSTM) models, and hybrid models, this study explores their underlying principles, advantages, limitations, methodologies, simulation environments, and datasets. Based on our results, Python was the most frequent programming language used for implementing the proposed methods in the investigated papers. Notably, the majority of the scrutinized papers were published in 2021, underscoring the contemporaneous nature of the research. Moreover, this review accentuates the forefront advancements in DL techniques and their practical applications within the realm of medical image analysis, while simultaneously addressing the challenges that hinder the widespread implementation of DL in image analysis within the medical healthcare domains. These discerned insights serve as compelling impetuses for future studies aimed at the progressive advancement of image analysis in medical healthcare research. The evaluation metrics employed across the reviewed articles encompass a broad spectrum of features, encompassing accuracy, sensitivity, specificity, F-score, robustness, computational complexity, and generalizability.
Why Are Phytoplankton in The Southern Ocean Starving for Iron?
Authors: van der Merwe Pier C. , Lannuzel Delphine
Published: November 2023

In one of Earth’s largest oceans, the Southern Ocean, tiny organisms called phytoplankton are starving! Not for spaghetti though. How would you like a dinner of iron soup? No? Well, phytoplankton love it. Luckily, these important little organisms can get their iron soup near melting ice, undersea volcanoes, and even near the rear ends of whales! Sounds gross, right? Well, not for tiny phytoplankton. When they are not starving, they multiply enough to be visible from space! They have two super-important jobs that they do for the Earth, for free. First, they produce oxygen for humans and other animals to breathe. Second, they change carbon dioxide into sugar-filled snacks that become food for an organism called krill. And krill are whale food! Phytoplankton do these two jobs while also slowing global warming. Read on to hear how iron soup for phytoplankton might help save our planet!
Electron cyclotron harmonic waves in Jovian magnetosphere as seen by Juno
Authors: Joseph J. , Jaynes A. N. , Kurth W. S. , Menietti J. D. , Connerney J. E. P. , Bolton S. J.
Published: November 2023

Electron cyclotron harmonic (ECH) waves along with whistler mode waves are suggested to be responsible for causing the persistent diffuse aurora in Jupiter. In this work, for the first time we systematically analyze the ECH waves in the Jovian inner magnetosphere, which was surveyed by Juno during the later orbits (>25). We find that in the Jovian inner magnetosphere, ECH waves occur in two specific regions—one equatorial and the other off-equatorial, just outside the Io torus. Equatorial ECH waves have higher intensity compared to their off-equatorial counterpart. We also notice an overlap between the region of mid-latitude hot injections and the region of off-equatorial ECH wave occurrence. Finally, we show an event to describe the complex nature of ECH wave growth/damping varying with particle density structures of the injection region at mid-latitude.
Recent research patterns and factors influencing eating behaviour amongst Malaysian youths: a scoping review
Authors: Abang Brian Chen , Stephenson Marcus L. , Tan Ai Ling
Published: November 2023

Introduction

This scoping review focuses on the eating behaviour of Malaysian youths and the way in which their eating behaviour has been studied in recent years. There is a continuous need to comprehend the nature and structure of eating behaviour acquired during young adulthood as it is linked to the increasing number of adults who are overweight and obese. Past research has been employed using various methodologies in the analysis of different dimensions of eating behaviour amongst Malaysian youths. This enquiry reviewed recent studies to collate and map out the methodologies, areas of research and factors associated with eating behaviour amongst this target group.

Methods

The “preferred reporting items for systematic reviews and meta-analyses extension for scoping reviews” (PRISMA-ScR) was adopted for this scoping review which utilised the EBSCOhost discovery platform and other such databases as Sage, ProQuest and Clinical Key™.

Results

The search resulted in a total of 34 articles which were then analysed. This gave rise to the identification of four main dimensions of eating behaviour amongst Malaysian youth, namely: “general adequacy and frequency of consumption of food groups”; “consumption of specific food groups”; “eating disorders”; and “weight control.”

Conclusion

The majority of the recent studies focused on the general adequacy and frequency of consumption of food groups studied using quantitative approaches across multi-ethnic target groups within the central region of Malaysia. This leaves room for more studies on the consumption of specific food groups, eating disorders and weight control that could be more ethnic-centric within other geographical areas within Malaysia. Many studies suggested the need to apply qualitative measures to investigate the contradictions arising from current research concerning the interplay between interpersonal, intrapersonal and environmental factors affecting eating behaviour amongst Malaysian youths.
Safety profile of magnetic sphincter augmentation for gastroesophageal reflux disease
Authors: Froiio Caterina , Aiolfi Alberto , Bona Davide , Bonavina Luigi
Published: November 2023

Background

The magnetic sphincter augmentation (MSA) procedure is an effective treatment for gastroesophageal reflux disease (GERD). Adverse events requiring MSA device removal are rare, but the true prevalence and incidence may be underestimated.

Methods

Retrospective study on a prospectively collected database. Patients who underwent MSA procedure between March 2007 and September 2021 in two tertiary-care referral centers for esophageal surgery were included. The trend of MSA explant, the changes in the sizing technique and crura repair over the years, the technique of explant, and the clinical outcomes of the revisional procedure were reviewed.

Results

Out of 397 consecutive patients, 50 (12.4%) underwent MSA removal, with a median time to explant of 39.5 [IQR = 53.7] months. Main symptoms leading to removal were dysphagia (43.2%), heartburn (25%), and epigastric pain (13.6%). Erosion occurred in 2.5% of patients. Smaller (12- and 13-bead) devices were the ones most frequently explanted. The majority of the explants were performed laparoscopically with endoscopic assistance. There was no perioperative morbidity, and the median length of stay was 2.8 ± 1.4 days. After 2014, changes in sizing technique and crura repair resulted in a decreased incidence of explants from 23% to 5% (p < 0.0001). Multivariate analysis confirmed the protective role of added bead units [HR 0.06 (95% CI = 0.001–0.220); p < 0.000].

Conclusion

Oversizing and full mediastinal dissection with posterior hiatoplasty may improve the outcomes of the MSA procedure and possibly reduce removal rates.
Transcriptome and metabolome profiling to elucidate the mechanism underlying the poor growth of Streptococcus suis serotype 2 after orphan response regulator CovR deletion
Authors: Zong Bingbing , Xiao Yong , Li Rui , Li Huanhuan , Wang Peiyi , Yang Xiaopei , Zhang Yanyan
Published: November 2023

The deletion of orphan response regulator CovR reduces the growth rate ofStreptococcus suisserotype 2 (S. suis2). In this study, metabolome and transcriptome profiling were performed to study the mechanisms underlying the poor growth ofS. suis2 caused by the deletion of orphan response regulator CovR. By comparingS. suis2 (ΔcovR) andS. suis2 (SC19), 146 differentially accumulated metabolites (upregulated: 83 and downregulated: 63) and 141 differentially expressed genes (upregulated: 86 and downregulated: 55) were identified. Metabolome and functional annotation analysis revealed that the growth of ΔcovRwas inhibited by the imbalance aminoacyl tRNA biosynthesis (the low contents of L-lysine, L-aspartic acid, L-glutamine, and L-glutamic acid, and the high content of L-methionine). These results provide a new insight into the underlying poor growth ofS. suis2 caused by the deletion of orphan response regulator CovR. Metabolites and candidate genes regulated by the orphan response regulator CovR and involved in the growth ofS. suis2 were reported in this study.
Current investigations for liver fibrosis treatment: between repurposing the FDA-approved drugs and the other emerging approaches
Authors: Mohammed Omima S. , Attia Hany G. , Mohamed Bassim M. S. A. , Elbaset Marawan A. , Fayed Hany M.
Published: November 2023

Long-term liver injuries lead to hepatic fibrosis, often progressing into cirrhosis, liver failure, portal hypertension, and hepatocellular carcinoma. There is currently no effective therapy available for liver fibrosis. Thus, continuous investigations for anti-fibrotic therapy are ongoing. The main theme of anti-fibrotic investigation during recent years is the rationale-based selection of treatment molecules according to the current understanding of the pathology of the disease. The research efforts are mainly toward repurposing current FDA-approved drugs targeting etiological molecular factors involved in developing liver fibrosis. In parallel, investigations also focus on experimental small molecules with evidence to hinder or reverse the fibrosis. Natural compounds, immunological, and genetic approaches have shown significant encouraging effects. This review summarizes the efficacy and safety of current under-investigation antifibrosis medications targeting various molecular targets, as well as the properties of antifibrosis medications, mainly in phase II and III clinical trials.
High-Altitude Hypoxia Induces Excessive Erythrocytosis in Mice via Upregulation of the Intestinal HIF2a/Iron-Metabolism Pathway
Authors: Zhou Sisi , Yan Jun , Song Kang , Ge Ri-Li
Published: November 2023

Excessive erythrocytosis (EE) is a preclinical form of chronic mountain sickness (CMS). The dysregulation of iron metabolism in high-altitude hypoxia may induce EE. The intestinal hypoxia-inducible factor 2 alpha (HIF2a) regulates the genes involved in iron metabolism. Considering these findings, we aimed to investigate the function and mechanism of intestinal HIF2α and the iron metabolism pathway in high-altitude EE mice. C57BL/6J mice were randomized into four groups: the low-altitude group, the high-altitude group, the high-altitude + HIF2α inhibitor group, and the high-altitude + vehicle group. In-vitro experiments were performed using the human intestinal cell line HCT116 cultured under hypoxic conditions for 24 h. Results showed that high-altitude hypoxia significantly increased the expression of intestinal HIF2α and iron metabolism-related genes, including Dmt1, Dcytb, Fpn, Tfrc, and Fth in EE mice. Genetic blockade of the intestinal HIF2α-iron metabolism pathway decreased iron availability in HCT116 cells during hypoxia. The HIF2α inhibitor PT2385 suppressed intestinal HIF2α expression, decreased iron hypermetabolism, and reduced excessive erythrocytosis in mice. These data support the hypothesis that exposure to high-altitude hypoxia can lead to iron hypermetabolism by activating intestinal HIF2α transcriptional regulation, and reduced iron availability improves EE by inhibiting intestinal HIF2α signaling.
The Unmet Needs of Pancreatic Cancer Carers Are Associated with Anxiety and Depression in Patients and Carers
Authors: Huynh Thi N. T. , Hartel Gunter , Janda Monika , Wyld David , Merrett Neil , Gooden Helen , Neale Rachel E. , Beesley Vanessa L.
Published: November 2023

Pancreatic cancer has one of the lowest survival rates, and patients experience debilitating symptoms. Family carers provide essential daily care. This study determined the prevalence of and risk factors for unmet supportive care needs among carers for pancreatic cancer patients and examined which carer needs were associated with anxiety and depression in carers and patients. Eighty-four pancreatic cancer patients and their carers were recruited. The carers completed a needs survey (SCNS-P&C). Both carers and patients completed the Hospital Anxiety and Depression Scale. Log binomial regression was used to identify associations between carer needs and anxiety and depression among carers and patients. The top 10 moderate-to-high unmet needs reported by ≥28% of carers were related to healthcare (e.g., discussing concerns with doctors) and information need domains (e.g., information about a patient’s physical needs), plus one other item related to hospital parking. Being male or caring for a patient within 4 months of their diagnosis were associated with greater unmet needs. Some unmet needs, including ‘accessing information about treatments’ and ‘being involved in patient care’, were associated with both carers and patients having anxiety and depression. Carers should be involved in health care consultations and provided with information and opportunities to discuss concerns.