bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of genes involved in enhanced membrane vesicle formation in Pseudomonas aeruginosa biofilms: surface sensing facilitates vesiculation
Authors: Kanno Mizuki , Shiota Takuya , Ueno So , Takahara Minato , Haneda Keisuke , Tahara Yuhei O. , Shintani Masaki , Nakao Ryoma , Miyata Makoto , Kimbara Kazuhide , Futamata Hiroyuki , Tashiro Yosuke
Published: December 2023

Membrane vesicles (MVs) are small spherical structures (20–400 nm) produced by most bacteria and have important biological functions including toxin delivery, signal transfer, biofilm formation, and immunomodulation of the host. Although MV formation is enhanced in biofilms of a wide range of bacterial species, the underlying mechanisms are not fully understood. An opportunistic pathogen, Pseudomonas aeruginosa, causes chronic infections that can be difficult to treat due to biofilm formation. Since MVs are abundant in biofilms, can transport virulence factors to the host, and have inflammation-inducing functions, the mechanisms of enhanced MV formation in biofilms needs to be elucidated to effectively treat infections. In this study, we evaluated the characteristics of MVs in P. aeruginosa PAO1 biofilms, and identified factors that contribute to enhanced MV formation. Vesiculation was significantly enhanced in the static culture; MVs were connected to filamentous substances in the biofilm, and separation between the outer and inner membranes and curvature of the membrane were observed in biofilm cells. By screening a transposon mutant library (8,023 mutants) for alterations in MV formation in biofilms, 66 mutants were identified as low-vesiculation strains (2/3 decrease relative to wild type), whereas no mutant was obtained that produced more MVs (twofold increase). Some transposons were inserted into genes related to biofilm formation, including flagellar motility (flg, fli, and mot) and extracellular polysaccharide synthesis (psl). ΔpelAΔpslA, which does not synthesize the extracellular polysaccharides Pel and Psl, showed reduced MV production in biofilms but not in planktonic conditions, suggesting that enhanced vesiculation is closely related to the synthesis of biofilm matrices in P. aeruginosa. Additionally, we found that blebbing occurred during bacterial attachment. Our findings indicate that biofilm-related factors are closely involved in enhanced MV formation in biofilms and that surface sensing facilitates vesiculation. Furthermore, this work expands the understanding of the infection strategy in P. aeruginosa biofilms.
A bibliometric analysis on discovering anti-quorum sensing agents against clinically relevant pathogens: current status, development, and future directions
Authors: Peng Bo , Li Yanqun , Yin Jiajia , Ding Wenping , Fazuo Wang , Xiao Zhihui , Yin Hao
Published: December 2023

Background

Quorum sensing is bacteria’s ability to communicate and regulate their behavior based on population density. Anti-quorum sensing agents (anti-QSA) is promising strategy to treat resistant infections, as well as reduce selective pressure that leads to antibiotic resistance of clinically relevant pathogens. This study analyzes the output, hotspots, and trends of research in the field of anti-QSA against clinically relevant pathogens.

Methods

The literature on anti-QSA from the Web of Science Core Collection database was retrieved and analyzed. Tools such as CiteSpace and Alluvial Generator were used to visualize and interpret the data.

Results

From 1998 to 2023, the number of publications related to anti-QAS research increased rapidly, with a total of 1,743 articles and reviews published in 558 journals. The United States was the largest contributor and the most influential country, with an H-index of 88, higher than other countries. Williams was the most productive author, and Hoiby N was the most cited author. Frontiers in Microbiology was the most prolific and the most cited journal. Burst detection indicated that the main frontier disciplines shifted from MICROBIOLOGY, CLINICAL, MOLECULAR BIOLOGY, and other biomedicine-related fields to FOOD, MATERIALS, NATURAL PRODUCTS, and MULTIDISCIPLINARY. In the whole research history, the strongest burst keyword was cystic-fibrosis patients, and the strongest burst reference was Lee and Zhang (2015). In the latest period (burst until 2023), the strongest burst keyword was silver nanoparticle, and the strongest burst reference was Whiteley et al. (2017). The co-citation network revealed that the most important interest and research direction was anti-biofilm/anti-virulence drug development, and timeline analysis suggested that this direction is also the most active. The key concepts alluvial flow visualization revealed seven terms with the longest time span and lasting until now, namely Escherichia coli, virulence, Pseudomonas aeruginosa, virulence factor, bacterial biofilm, gene expression, quorum sensing. Comprehensive analysis shows that nanomaterials, marine natural products, and artificial intelligence (AI) may become hotspots in the future.

Conclusion

This bibliometric study reveals the current status and trends of anti-QSA research and may assist researchers in identifying hot topics and exploring new research directions.
Characterization of the probiotic properties of Lacticaseibacillus rhamnosus LR6 isolated from the vaginas of healthy Korean women against vaginal pathogens
Authors: Chung Yusook , Kang Seung Beom , Son Dooheon , Lee Ji Young , Chung Myung Jun , Lim Sanghyun
Published: December 2023

The human microbiome exhibits intricate populations across the body, with the vaginal tract serving as an ecosystem characterized by the prevalence of the genus Lactobacillus. Disruptions in the vaginal microbiota, which are frequently linked to variables such as sexual activity, hormonal fluctuations, and excessive use of antibiotics, can result in vaginal dysbiosis and the development of diseases such as bacterial vaginosis (BV) and candidiasis. Lactobacillus species, owing to their capacity to create an acidic environment through the production of lactic acid, have a key function within this complex microbial community: they inhibit the growth of harmful microorganisms. This study aimed to investigate the genomic characteristics of L. rhamnosus LR6, a newly discovered strain isolated from the vaginal microbiota of 20 healthy women to assess its potential as a vaginal probiotic. We performed a comparative investigation of the genetic traits of L. rhamnosus using 45 publicly available genomes from various sources. We evaluated the genetic characteristics related to carbohydrate utilization, adhesion to host cells, and the presence of bacteriocin clusters. A comprehensive study was conducted by integrating in silico evaluations with experimental techniques to authenticate the physiological characteristics of strain LR6. We further used a rat model to assess the impact of L. rhamnosus LR6 administration on the changes in the gastrointestinal tract and the vaginal microbiome. The assessments revealed a significantly high inhibitory activity against pathogens, enhanced adherence to host cells, and high lactic acid production. Rat experiments revealed changes in both the fecal and vaginal microbiota; in treated rats, Firmicutes increased in both; Lactobacillaceae increased in the fecal samples; and Enterobacteriaceae decreased but Enterococcaceae, Streptococcaceae, and Morganellaceae increased in the vaginal samples. The study results provide evidence of the genetic characteristics and probiotic properties of LR6, and suggest that oral administration of L. rhamnosus LR6 can alter both gut and vaginal microbiome. Collectively, these findings establish L. rhamnosus LR6 as a highly promising candidate for improving vaginal health.
Validation of potential RNA biomarkers for prostate cancer diagnosis and monitoring in plasma and urinary extracellular vesicles
Authors: Brokāne Agnese , Bajo-Santos Cristina , Zayakin Pawel , Belovs Alberts , Jansons Juris , Lietuvietis Vilnis , Martens-Uzunova Elena S. , Jenster Guido W. , Linē Aija
Published: December 2023

Introduction: Prostate cancer (PCa), one of the most prevalent malignancies affecting men worldwide, presents significant challenges in terms of early detection, risk stratification, and active surveillance. In recent years, liquid biopsies have emerged as a promising non-invasive approach to complement or even replace traditional tissue biopsies. Extracellular vesicles (EVs), nanosized membranous structures released by various cells into body fluids, have gained substantial attention as a source of cancer biomarkers due to their ability to encapsulate and transport a wide range of biological molecules, including RNA. In this study, we aimed to validate 15 potential RNA biomarkers, identified in a previous EV RNA sequencing study, using droplet digital PCR.

Methods: The candidate biomarkers were tested in plasma and urinary EVs collected before and after radical prostatectomy from 30 PCa patients and their diagnostic potential was evaluated in a test cohort consisting of 20 benign prostate hyperplasia (BPH) and 20 PCa patients’ plasma and urinary EVs. Next, the results were validated in an independent cohort of plasma EVs from 31 PCa and 31 BPH patients.

Results: We found that the levels of NKX3-1 (p = 0.0008) in plasma EVs, and tRF-Phe-GAA-3b (p < 0.0001) tRF-Lys-CTT-5c (p < 0.0327), piR-28004 (p = 0.0081) and miR-375-3p (p < 0.0001) in urinary EVs significantly decreased after radical prostatectomy suggesting that the main tissue source of these RNAs is prostate and/or PCa. Two mRNA biomarkers—GLO1 and NKX3-1 showed promising diagnostic potential in distinguishing between PCa and BPH with AUC of 0.68 and 0.82, respectively, in the test cohort and AUC of 0.73 and 0.65, respectively, in the validation cohort, when tested in plasma EVs. Combining these markers in a biomarker model yielded AUC of 0.85 and 0.71 in the test and validation cohorts, respectively. Although the PSA levels in the blood could not distinguish PCa from BPH in our cohort, adding PSA to the mRNA biomarker model increased AUC from 0.71 to 0.76.

Conclusion: This study identified two novel EV-enclosed RNA biomarkers–NKX3-1 and GLO1–for the detection of PCa, and highlights the complementary nature of GLO1, NKX3-1 and PSA as combined biomarkers in liquid biopsies of PCa.
Transient ischemic stroke triggers sustained damage of the choroid plexus blood-CSF barrier
Authors: Chen Yang , Lin Lin , Bhuiyan Mohammad Iqbal H. , He Kai , Jha Roshani , Song Shanshan , Fiesler Victoria M. , Begum Gulnaz , Yin Yan , Sun Dandan
Published: December 2023

Neuroinflammation is a pathological event associated with many neurological disorders, including dementia and stroke. The choroid plexus (ChP) is a key structure in the ventricles of the brain that secretes cerebrospinal fluid (CSF), forms a blood-CSF barrier, and responds to disease conditions by recruiting immune cells and maintaining an immune microenvironment in the brain. Despite these critical roles, the exact structural and functional changes to the ChP over post-stroke time remain to be elucidated. We induced ischemic stroke in C57BL/6J mice via transient middle cerebral artery occlusion which led to reduction of cerebral blood flow and infarct stroke. At 1–7 days post-stroke, we detected time-dependent increase in the ChP blood-CSF barrier permeability to albumin, tight-junction damage, and dynamic changes of SPAK-NKCC1 protein complex, a key ion transport regulatory system for CSF production and clearance. A transient loss of SPAK protein complex but increased phosphorylation of the SPAK-NKCC1 complex was observed in both lateral ventricle ChPs. Most interestingly, stroke also triggered elevation of proinflammatory Lcn2 mRNA and its protein as well as infiltration of anti-inflammatory myeloid cells in ChP at day 5 post-stroke. These findings demonstrate that ischemic strokes cause significant damage to the ChP blood-CSF barrier, contributing to neuroinflammation in the subacute stage.
The predictive validity of a Brain Care Score for dementia and stroke: data from the UK Biobank cohort
Authors: Singh Sanjula D. , Oreskovic Tin , Carr Sinclair , Papier Keren , Conroy Megan , Senff Jasper R. , Chemali Zeina , Gutierrez-Martinez Leidys , Parodi Livia , Mayerhofer Ernst , Marini Sandro , Nunley Courtney , Newhouse Amy , Ouyang An , Brouwers H. Bart , Westover Brandon , Rivier Cyprien , Falcone Guido , Howard Virginia , Howard George , Pikula Aleksandra , Ibrahim Sarah , Sheth Kevin N. , Yechoor Nirupama , Lazar Ronald M. , Anderson Christopher D. , Tanzi Rudolph E. , Fricchione Gregory , Littlejohns Thomas , Rosand Jonathan
Published: December 2023

Introduction

The 21-point Brain Care Score (BCS) was developed through a modified Delphi process in partnership with practitioners and patients to promote behavior changes and lifestyle choices in order to sustainably reduce the risk of dementia and stroke. We aimed to assess the associations of the BCS with risk of incident dementia and stroke.

Methods

The BCS was derived from the United Kingdom Biobank (UKB) baseline evaluation for participants aged 40–69 years, recruited between 2006–2010. Associations of BCS and risk of subsequent incident dementia and stroke were estimated using Cox proportional hazard regressions, adjusted for sex assigned at birth and stratified by age groups at baseline.

Results

The BCS (median: 12; IQR:11–14) was derived for 398,990 UKB participants (mean age: 57; females: 54%). There were 5,354 incident cases of dementia and 7,259 incident cases of stroke recorded during a median follow-up of 12.5 years. A five-point higher BCS at baseline was associated with a 59% (95%CI: 40-72%) lower risk of dementia among participants aged <50. Among those aged 50–59, the figure was 32% (95%CI: 20-42%) and 8% (95%CI: 2-14%) for those aged >59 years. A five-point higher BCS was associated with a 48% (95%CI: 39-56%) lower risk of stroke among participants aged <50, 52% (95%CI, 47-56%) among those aged 50–59, and 33% (95%CI, 29-37%) among those aged >59.

Discussion

The BCS has clinically relevant and statistically significant associations with risk of dementia and stroke in approximately 0.4 million UK people. Future research includes investigating the feasibility, adaptability and implementation of the BCS for patients and providers worldwide.
A narrative review of antibody–drug conjugates in EGFR-mutated non-small cell lung cancer
Authors: Hsu Robert , Benjamin David J.
Published: December 2023

In the past 15 years, non-small cell lung cancer (NSCLC) treatment has changed with the discovery of mutations and the development of new targeted therapies and immune checkpoint inhibitors. Epidermal growth factor receptor (EGFR) was the first mutation in NSCLC to have a drug that was FDA-approved in 2013. Osimertinib, a third-generation tyrosine kinase inhibitor, is approved as first-line therapy for advanced NSCLC and in the adjuvant setting for Stage IB-IIIA resected NSCLC. However, resistance to osimertinib is inevitably an issue, and thus patterns of resistance to EGFR-mutated NSCLC have been studied, including MET amplification, EGFR C797X-acquired mutation, human epidermal growth factor 2 (HER2) amplification, and transformation to small cell and squamous cell lung cancer. Current management for EGFR-mutated NSCLC upon progression of EGFR TKI is limited at this time to chemotherapy and radiation therapy, sometimes in combination with the continuation of osimertinib. Antibody–drug conjugates (ADCs) are made up of a monoclonal antibody linked to a cytotoxic drug and are an increasingly popular class of drug being studied in NSCLC. Trastuzumab deruxtecan has received accelerated FDA approval in HER2-mutated NSCLC. ADCs offer a possible solution to finding a new treatment that could bypass the intracellular resistance mechanism. In this review article, we summarize the mechanism of ADCs and investigational ADCs for EGFR-mutated NSCLC, which include targets to MET amplification, HER3, Trop2, and EGFR, along with other ADC targets being investigated in NSCLC, and discuss future directions that may arise with ADCs in EGFR-mutated NSCLC.
Screening some pine species from North America and dried zones of western Asia for drought stress tolerance in terms of nutrients status, biochemical and physiological characteristics
Authors: Nouri Karim , Nikbakht Ali , Haghighi Maryam , Etemadi Nematollah , Rahimmalek Mehdi , Szumny Antoni
Published: December 2023

Drought due to climate change or reduced precipitation is one of the main factors limiting the growth and establishment of plants and is one of the most critical challenges facing humans. To investigate the effect of different levels of drought stress on some pine species, this research was carried out as a factorial experiment using two factors and a completely randomized design. It included five populations of four pine species (Pinus brutia Ten. var. eldarica, P. nigra Arnold, P. mugo, and P. banksiana Lamb (including populations 8310055 and 8960049), and three levels of irrigation (100%, 75%, or 50% FC, denoted as normal, mild or intense drought stress, respectively) with three replicates. The findings showed that, photosynthetic pigments, relative water content, visual quality, the content of nutrients, protein content, and fresh and dry weight all decreased significantly when plants were exposed to intense drought stress. However, raised proline levels, electrolyte leakage percentage, soluble sugars levels, and antioxidant enzyme activity. We detected a decline in most growth traits when comparing mild drought stress conditions to normal irrigation, yet acceptable quality seedlings when compared to intense drought stress. Intense drought stress had a substantial impact on many pine seedlings. PCA results showed that among different pine species, the level of resistance to drought is as follows: P. mugo> P. brutia var. eldarica> P. nigra> P. banksiana 8310055> P. banksiana 8960049. Our novel finding was that, P. mugo is a resistant species in arid and semi-arid regions, and P. banksiana species, especially its population of 8960049, is sensitive.
Sugarcane/soybean intercropping with reduced nitrogen addition promotes photosynthesized carbon sequestration in the soil
Authors: Zhang Tantan , Tang Hu , Peng Peng , Ge Shiqiang , Liu Yali , Feng Yuanjiao , Wang Jianwu
Published: December 2023

Introduction

Sugarcane/soybean intercropping with reduced nitrogen (N) addition has improved soil fertility and sustainable agricultural development in China. However, the effects of intercropping pattern and N fertilizer addition on the allocation of photosynthesized carbon (C) in plant-soil system were far less understood.

Methods

In this study, we performed an 13CO2 pulse labeling experiment to trace C footprints in plant-soil system under different cropping patterns [sugarcane monoculture (MS), sugarcane/soybean intercropping (SB)] and N addition levels [reduced N addition (N1) and conventional N addition (N2)].

Results and discussion

Our results showed that compared to sugarcane monoculture, sugarcane/soybean intercropping with N reduced addition increased sugarcane biomass and root/shoot ratio, which in turn led to 23.48% increase in total root biomass. The higher root biomass facilitated the flow of shoot fixed 13C to the soil in the form of rhizodeposits. More than 40% of the retained 13C in the soil was incorporated into the labile C pool [microbial biomass C (MBC) and dissolved organic C (DOC)] on day 1 after labeling. On day 27 after labeling, sugarcane/soybean intercropping with N reduced addition showed the highest 13C content in the MBC as well as in the soil, 1.89 and 1.14 times higher than the sugarcane monoculture, respectively. Moreover, intercropping pattern increased the content of labile C and labile N (alkaline N, ammonium N and nitrate N) in the soil. The structural equation model indicated that the cropping pattern regulated 13C sequestration in the soil mainly by driving changes in labile C, labile N content and root biomass in the soil. Our findings demonstrate that sugarcane/soybean intercropping with reduced N addition increases photosynthesized C sequestration in the soil, enhances the C sink capacity of agroecosystems.
Shedding light on neurofilament involvement in cognitive decline in obstructive sleep apnea and its possible role as a biomarker
Authors: Jaromirska Julia , Kaczmarski Piotr , Strzelecki Dominik , Sochal Marcin , Białasiewicz Piotr , Gabryelska Agata
Published: December 2023

Obstructive sleep apnea is one of the most common sleep disorders with a high estimated global prevalence and a large number of associated comorbidities in general as well as specific neuropsychiatric complications such as cognitive impairment. The complex pathogenesis and effects of the disorder including chronic intermittent hypoxia and sleep fragmentation may lead to enhanced neuronal damage, thereby contributing to neuropsychiatric pathologies. Obstructive sleep apnea has been described as an independent risk factor for several neurodegenerative diseases, including Alzheimer's disease and all-cause dementia. The influence of obstructive sleep apnea on cognitive deficits is still a topic of recent debate, and several mechanisms, including neurodegeneration and depression-related cognitive dysfunction, underlying this correlation are taken into consideration. The differentiation between both pathomechanisms of cognitive impairment in obstructive sleep apnea is a complex clinical issue, requiring the use of multiple and costly diagnostic methods. The studies conducted on neuroprotection biomarkers, such as brain-derived neurotrophic factors and neurofilaments, are recently gaining ground in the topic of cognition assessment in obstructive sleep apnea patients. Neurofilaments as neuron-specific cytoskeletal proteins could be useful non-invasive indicators of brain conditions and neurodegeneration, which already are observed in many neurological diseases leading to cognitive deficits. Additionally, neurofilaments play an important role as a biomarker in other sleep disorders such as insomnia. Thus, this review summarizes the current knowledge on the involvement of neurofilaments in cognitive decline and neurodegeneration in obstructive sleep apnea patients as well as discusses its possible role as a biomarker of these changes.
Genomic evolution of BA.5.2 and BF.7.14 derived lineages causing SARS-CoV-2 outbreak at the end of 2022 in China
Authors: Zhu Wentao , Wang Xiaoxia , Lin Yujin , He Lvfen , Zhang Rui , Wang Chuan , Zhu Xiong , Tang Tian , Gu Li
Published: December 2023

Since the end of 2022, when China adjusted its COVID-19 response measures, the SARS-CoV-2 epidemic has rapidly grown in the country. It is very necessary to monitor the evolutionary dynamic of epidemic variants. However, detailed reports presenting viral genome characteristics in China during this period are limited. In this study, we examined the epidemiological, genomic, and evolutionary characteristics of the SARS-CoV-2 genomes from China. We analyzed nearly 20,000 genomes belonging to 17 lineages, predominantly including BF.7.14 (22.3%), DY.2 (17.3%), DY.4 (15.5%), and BA.5.2.48 (11.9%). The Rt value increased rapidly after mid-November 2022, reaching its peak at the end of the month. We identified forty-three core mutations in the S gene and forty-seven core mutations in the ORF1ab gene. The positive selection of all circulating lineages was primarily due to non-synonymous substitutions in the S1 region. These findings provide insights into the genomic characteristics of SARS-CoV-2 genomes in China following the relaxation of the ‘dynamic zero-COVID’ policy and emphasize the importance of ongoing genomic monitoring.
Policy implementation strategies to address rural disparities in access to care for stroke patients
Authors: Rasool Aysha , Bailey Moriah , Lue Brittany , Omeaku Nina , Popoola Adebola , Shantharam Sharada S. , Brown Amanda A. , Fulmer Erika B.
Published: December 2023

Context

Stroke systems of care (SSOC) promote access to stroke prevention, treatment, and rehabilitation and ensure patients receive evidence-based treatment. Stroke patients living in rural areas have disproportionately less access to emergency medical services (EMS). In the United States, rural counties have a 30% higher stroke mortality rate compared to urban counties. Many states have SSOC laws supported by evidence; however, there are knowledge gaps in how states implement these state laws to strengthen SSOC.

Objective

This study identifies strategies and potential challenges to implementing state policy interventions that require or encourage evidence-supported pre-hospital interventions for stroke pre-notification, triage and transport, and inter-facility transfer of patients to the most appropriate stroke facility.

Design

Researchers interviewed representatives engaged in implementing SSOC across six states. Informants (n = 34) included state public health agency staff and other public health and clinical practitioners.

Outcomes

This study examined implementation of pre-hospital SSOCs policies in terms of (1) development roles, processes, facilitators, and barriers; (2) implementation partners, challenges, and solutions; (3) EMS system structure, protocols, communication, and supervision; and (4) program improvement, outcomes, and sustainability.

Results

Challenges included unequal resource allocation and EMS and hospital services coverage, particularly in rural settings, lack of stroke registry usage, insufficient technologies, inconsistent use of standardized tools and protocols, collaboration gaps across SSOC, and lack of EMS stroke training. Strategies included addressing scarce resources, services, and facilities; disseminating, training on, and implementing standardized statewide SSOC protocols and tools; and utilizing SSOC quality and performance improvement systems and approaches.

Conclusions

This paper identifies several strategies that can be incorporated to enhance the implementation of evidence-based stroke policies to improve access to timely stroke care for all patient populations, particularly those experiencing disparities in rural communities.
DAMPs and alarmin gene expression patterns in aging healthy and diseased mucosal tissues
Authors: Gonzalez O. A. , Kirakodu S. S. , Ebersole J. L.
Published: December 2023

Introduction

Periodontitis is delineated by a dysbiotic microbiome at sites of lesions accompanied by a dysregulated persistent inflammatory response that undermines the integrity of the periodontium. The interplay of the altered microbial ecology and warning signals from host cells would be a critical feature for maintaining or re-establishing homeostasis in these tissues.

Methods

This study used a nonhuman primate model (Macaca mulatta) with naturally-occurring periodontitis (n = 34) and experimental ligature-induced periodontitis (n = 36) to describe the features of gene expression for an array of damage-associate molecular patterns (DAMPs) or alarmins within the gingival tissues. The animals were age stratified into: ≤3 years (Young), 7–12 years (Adolescent), 12–15 years (Adult) and 17–23 years (Aged). Gingival tissue biopsies were examined via microarray. The analysis focused on 51 genes representative of the DAMPs/alarmins family of host cell warning factors and 18 genes associated with tissue destructive processed in the gingival tissues. Bacterial plaque samples were collected by curette sampling and 16S rRNA gene sequences used to describe the oral microbiome.

Results

A subset of DAMPs/alarmins were expressed in healthy and naturally-occurring periodontitis tissues in the animals and suggested local effects on gingival tissues leading to altered levels of DAMPs/alarmins related to age and disease. Significant differences from adult healthy levels were most frequently observed in the young and adolescent animals with few representatives in this gene array altered in the healthy aged gingival tissues. Of the 51 target genes, only approximately ⅓ were altered by ≥1.5-fold in any of the age groups of animals during disease, with those increases observed during disease initiation. Distinctive positive and negative correlations were noted with the DAMP/alarmin gene levels and comparative expression changes of tissue destructive molecules during disease across the age groups. Finally, specific correlations of DAMP/alarmin genes and relative abundance of particular microbes were observed in health and resolution samples in younger animals, while increased correlations during disease in the older groups were noted.

Conclusions

Thus, using this human-like preclinical model of induced periodontitis, we demonstrated the dynamics of the activation of the DAMP/alarmin warning system in the gingival tissues that showed some specific differences based on age.
How Russia’s war in Ukraine can change gender studies
Authors: Johnson Janet Elise
Published: December 2023

The catastrophe of Russia’s war in Ukraine following on the heels of the COVID-19 pandemic and the Black Lives Matter-inspired protests raises the possibility of marked changes in people’s gendered experiences in Central-Eastern Europe and Eurasia (CEE&E). Drawing upon recent discussions, events, and publications—with particular attention to Ukrainian voices and reflexivity as to my position as a US-based political scientist mostly trained on Russia—I suggest ways that these developments have begun to, can, and should change gender studies. I raise three questions: (1) Does CEE&E still constitute a meaningful geopolitical context—or region—for understanding gender? (2) Who should have authority to speak about gender in CEE&E? and (3) Have the possibilities for solidarities among feminist activists across CEE&E and beyond CEE&E increased or decreased, and why? Considering these questions, I argue that there is still much to be gained from studying gender in CEE&E as a field if we incorporate intersectional and decolonial lenses and especially if we can keep pushing ourselves through the scholarly debates that have constituted the field. Incorporating this part of the world—elided since Soviet collapse—can help gender studies as a whole deepen and reconsider paradigmatic concepts such as intersectionality, colonialism, and solidarity.
Bundled climate-smart agricultural solutions for smallholder farmers in Sri Lanka
Authors: Amarnath Giriraj , Taron Avinandan , Alahacoon Niranga , Ghosh Surajit
Published: December 2023

Smallholder farmers are among the most vulnerable to climate shocks in Sri Lanka. Lack of education and technical skills, poverty, risks inherent to agricultural investments, limited assets, and financial capital are major reasons for low investments in enhancing adaptive capacity. The study explores the use of agricultural technologies in improving smallholder resilience to water-related disasters and their opportunities for recovery. We tested four bundled services to promote climate-smart agriculture practices namely weather index insurance (WII), agronomic advisories dissemination via SMS, weather services, and climate-resilient seeds of maize and rice. The integrated solutions are referred to as Bundled Solutions of Index Insurance with Climate Information and Seed Systems (BICSA) to manage agricultural risks in Sri Lanka. The study conducted the bundled solutions in three agroecological regions spread over five districts and covering more than 2,500 farmers in three cropping periods ofMahaandYalaseasons. The results demonstrate that providing bundled solutions significantly protects smallholders against moderate drought events. The satellite-based weather index insurance can offset the long-term consequences of severe yield losses and mitigate the long-term drop in farm productivity. Our findings demonstrate the importance of bundled insurance to mitigate financial risks associated with extreme weather events and enhance resilience to climate change among vulnerable smallholders. It is evident from the study promoting a viable business model among seed companies, insurance companies, and technological partners, along with public institutions such as agricultural extension services can help production-level improvements and develop strategies at both the farm and policy levels that will support a transition to a more resilient farming system.
Attitudes and practices on antibiotic use and its emerging threats among Lebanese dairy veterinarians: a case study from a developing country
Authors: Dankar Iman , Hassan Hussein F. , Serhan Mireille
Published: December 2023

Introduction

This study aimed to explore how veterinarians (vets) rationalized their prescribing decisions for antimicrobial (AM) uses, the barriers they perceived to implement proper farm management in Lebanon, and the consecutive threats that might arise concerning the emergent spread of antimicrobial resistance in animals and the population.

Methods

Amid the COVID-19 pandemic, phone call interviews were conducted with 34 veterinarians working in different demographic regions across the country. Data were analyzed qualitatively using an inductive thematic analysis.

Results and discussion

The majority of veterinarians called for responsible antibiotic use. The prescribing decision of veterinarians was based mainly on suspected disease from field examination, farmer’s reports via phone calls, and the ability of the farmer to cover antibiotic costs. Very few veterinarians referred to laboratory diagnosis before prescribing a specific AM due to many obstacles. This study uncovered the absence of a trust relationship between veterinarians and farmers in Lebanon. Veterinarians provided different insights into farming practices, reflecting that farmers, in general, lack proper knowledge and implementation of farm management and that they mainly treat the herd on their own, especially in light of the current unprecedented economic crisis that Lebanon has been facing in the last three years. Above all, veterinarians revealed that AM resistance in Lebanon is markedly spreading, which calls for a serious and instantaneous set of governmental policies and regulations.
Automatic Segmentation of Histological Images of Mouse Brains
Authors: Cisneros Juan , Lalande Alain , Yalcin Binnaz , Meriaudeau Fabrice , Collins Stephan
Published: December 2023

Using a high-throughput neuroanatomical screen of histological brain sections developed in collaboration with the International Mouse Phenotyping Consortium, we previously reported a list of 198 genes whose inactivation leads to neuroanatomical phenotypes. To achieve this milestone, tens of thousands of hours of manual image segmentation were necessary. The present work involved developing a full pipeline to automate the application of deep learning methods for the automated segmentation of 24 anatomical regions used in the aforementioned screen. The dataset includes 2000 annotated parasagittal slides (24,000 × 14,000 pixels). Our approach consists of three main parts: the conversion of images (.ROI to .PNG), the training of the deep learning approach on the compressed images (512 × 256 and 2048 × 1024 pixels of the deep learning approach) to extract the regions of interest using either the U-Net or Attention U-Net architectures, and finally the transformation of the identified regions (.PNG to .ROI), enabling visualization and editing within the Fiji/ImageJ 1.54 software environment. With an image resolution of 2048 × 1024, the Attention U-Net provided the best results with an overall Dice Similarity Coefficient (DSC) of 0.90 ± 0.01 for all 24 regions. Using one command line, the end-user is now able to pre-analyze images automatically, then runs the existing analytical pipeline made of ImageJ macros to validate the automatically generated regions of interest resulting. Even for regions with low DSC, expert neuroanatomists rarely correct the results. We estimate a time savings of 6 to 10 times.
Classification of Plenodomus lingam and Plenodomus biglobosus in Co-Occurring Samples Using Reflectance Spectroscopy
Authors: Wójtowicz Andrzej , Piekarczyk Jan , Wójtowicz Marek , Jasiewicz Jarosław , Królewicz Sławomir , Starzycka-Korbas Elżbieta
Published: December 2023

Under natural conditions, mixed infections are often observed when two or more species of plant pathogens are present on one host. Thus, the detection and characterization of co-occurring pest species is a challenge of great importance. In this study, we focused on the development of a spectral unmixing method for the discrimination of two fungi species, Plenodomus lingam and Plenodomus biglobosus, the pathogens of oilseed rape. Over 24 days, spectral reflectance measurements from Petri dishes inoculated with fungi were conducted. Four experimental combinations were used: the first two were pure fungal samples, while the other two were co-occurring fungal samples. The results of the study show the possibility of distinguishing, based on spectral characteristics, between P. lingam and P. biglobosus not only in pure but also in co-occurring samples. We observed the changes in the reflectance of electromagnetic radiation from the tested fungi over time and a strong correlation between the reflectance and changes in the areas of the mycelia on the Petri dishes. Moreover, the wavelengths most useful for spectral classification of the tested fungal mycelia were selected. Finally, a spectral unmixing model was proposed, which enables the estimation of the areas of two pathogens in co-occurring samples based on the spectral characteristics of the entire plate with an error smaller than 0.2. To our knowledge, the present study is the first report examining the use of reflectance spectroscopy methods for classifying pathogens on the same Petri dish. The study results indicate the feasibility of reflectance spectroscopy as a nondestructive sampling method for plant pathogen detection and classification.
Design and Experiment of Bionic Straw-Cutting Blades Based on Locusta Migratoria Manilensis
Authors: Hu Jinpeng , Xu Lizhang , Yu Yang , Lu Jin , Han Dianlei , Chai Xiaoyu , Wu Qinhao , Zhu Linjun
Published: December 2023

Aimed at addressing the problems of the existing straw choppers on combine harvesters, such as a large cutting resistance and poor cutting effect, combined with bionic engineering technology and biological characteristics, a bionic model was used to extract the characteristics of the cutting blades of locusta migratoria manilensis’s upper jaw. A 3D point cloud reconstruction and machine vision methods were used to fit the polynomial curve of the blade edge using Matlab 2016. A straw-cutting process was simulated using the discrete element method, and the cutting effect of the bionic blade was verified. Cutting experiments with rice straws were conducted using a physical property tester, and the cutting resistance of straw to bionic blades and general blades was compared. On the whole, the average cutting force of the bionic blades was lower than that of the general blades. The average cutting force of the bionic blade was 18.74~38.23% lower than that of a smooth blade and 1.63~25.23% lower than that of a serrated blade. Similarly, the maximum instantaneous cutting force of the bionic blade was reduced by 2.30~2.89% compared with the general blade, which had a significant drag reduction effect. By comparing the time–force curves of different blades’ cutting processes, it was determined that the drag-reducing effect of the bionic blade lies in shortening the straw rupture time. The larger the contact area between the blade and the straw, the more uniform the cutting morphology of the straw after cutting. Field experiment results indicate that the average power consumption of a straw chopper partially installed with bionic blades was 5.48% lower than one with smooth blades, measured using a wireless torque analysis module. In this research study, the structure of the straw chopper of an existing combine harvester was improved based on the bionic principle, which reduced resistance when cutting crop straw, thus reducing the power consumption required by the straw chopper and improving the effectiveness and stability of the blades.
Indication of Light Stress in Ficus elastica Using Hyperspectral Imaging
Authors: Dmitriev Pavel A. , Kozlovsky Boris L. , Dmitrieva Anastasiya A. , Lysenko Vladimir S. , Chokheli Vasily A. , Varduni Tatyana V.
Published: December 2023

Hyperspectral imaging techniques are widely used to remotely assess the vegetation and physiological condition of plants. Usually, such studies are carried out without taking into account the light history of the objects (for example, direct sunlight or light scattered by clouds), including light-stress conditions (photoinhibition). In addition, strong photoinhibitory lighting itself can cause stress. Until now, it is unknown how light history influences the physiologically meaningful spectral indices of reflected light. In the present work, shifts in the spectral reflectance characteristics of Ficus elastica leaves caused by 10 h exposure to photoinhibitory white LED light, 200 μmol photons m−2 s−1 (light stress), and moderate natural light, 50 μmol photons m−2 s−1 (shade) are compared to dark-adapted plants. Measurements were performed with a Cubert UHD-185 hyperspectral camera in discrete spectral bands centred on wavelengths from 450 to 950 nm with a 4 nm step. It was shown that light stress leads to an increase in reflection in the range of 522–594 nm and a decrease in reflection at 666–682 nm. The physiological causes of the observed spectral shifts are discussed. Based on empirical data, the light-stress index (LSI) = mean(R666:682)/mean(R552:594) was calculated and tested. The data obtained suggest the possibility of identifying plant light stress using spectral sensors that remotely fix passive reflection with the need to take light history into account when analysing hyperspectral data.
Linkages of Enzymatic Activity and Stoichiometry with Soil Physical-Chemical Properties under Long-Term Manure Application to Saline-Sodic Soil on the Songnen Plain
Authors: Zhai Cheyu , Feng Xiaotong , Liu Changjie , Li Yang , Fan Jiaming , Zhang Juan , Meng Qingfeng
Published: December 2023

Excess Na+ and high pH result in poor structures in Saline-Sodic soils, which reduces extracellular enzyme activity (EEA) and causes nutrient limitations. The application of manure improved the Physical-Chemical properties of soil and balanced the soil nutrient supply, which was reflected in the soil EEAs and stoichiometry. Five experimental treatments were designed according to the manure application duration as follows: manure application for 11 years (11a), 16 years (16a), 22 years (22a), and 27 years (27a) and a control treatment with no manure application (CK). The results of the redundancy analysis (RDA) showed that physical properties (mean weight diameter (MWD)) and EEA (β–glucosidase (BG)) significantly increased and bulk density (ρb) significantly decreased when the nutrient content increased. Additionally, soil pH, electrical conductivity (EC), exchangeable sodium percentage (ESP) and sodium adsorption ratio (SAR) significantly decreased after manure application. Based on stepwise multiple linear regression models (SMLR), total nitrogen (TN) was the dominant variable that significantly increased EEA, and the Mantel test showed that soil C:N significantly influenced enzyme stoichiometry. Furthermore, RDA showed that pH, soil C:N and TN were the main factors influencing EEAs and enzyme stoichiometry. Soil EEAs significantly increased with TN and decreased with pH and soil C:N, which affected enzyme stoichiometry. The enzyme stoichiometry increased from 1:2.1:1.2 and 1:2.7:1.5 to 1:1.7:1.2, and the vector angle (vector A) increased, which showed that the N limitation was relieved after the application of manure. The vector length (vector L) showed no significant difference in the C limitation at depths of 0–20 cm and significantly increased at depths of 20–40 cm. In conclusion, soil EEAs and stoichiometry improved with changes in TN and soil C:N, and pH decreased with changes in the soil structure after the application of manure, which accelerated the soil nutrient cycle and balanced the soil nutrient supply.
Evaluating Scald Reactions of Some Turkish Barley (Hordeum vulgare L.) Varieties Using GGE Biplot Analysis
Authors: Akan Kadir , Cat Ahmet , Hocaoglu Onur , Tekin Mehmet
Published: December 2023

Scald caused by the fungal pathogen Rhynchosporium commune is a significant foliar disease affecting barley production on a global scale, and it leads to substantial reductions in both yield and quality of barley. In the current study, the reactions of 40 Turkish barley (Hordeum vulgare L.) varieties to scald were evaluated under natural conditions in Çanakkale and Kırşehir in 2021–2022, and Antalya and Siirt locations in 2022–2023 growing seasons. Field trials were conducted according to randomized block design with three replications in each year; the spore concentration was 1 × 106 spores per mL, and it was applied to the varieties three times at different growth stages. The reactions of barley varieties were assessed using a newly designed two-digit scale ranging from 11 to 99. Based on their scale values, the varieties were categorized as immune (0), resistant (11–35), moderately resistant (36–55), moderately susceptible (56–75), and susceptible (76–99). In addition, genotype plus genotype-by-environment (GGE) interactions of scale values were analyzed through GGE Biplot and explained 97.65% of the total variation. The ranking of genotypes based on scale groups generally showed consistency with GGE Biplot results, but GGE Biplot offered a more detailed classification, especially for moderately susceptible varieties. The relationship between the two methods indicated the relative stability of variety reactions, as GGE Biplot analysis also considered genotype stability. In conclusion, the use of the newly developed scale for evaluating scald reactions in barley gives reliable results. In addition, identified resistant varieties can serve as valuable genetic resources for further breeding studies.
Machine Learning Applications in Agriculture: Current Trends, Challenges, and Future Perspectives
Authors: Araújo Sara Oleiro , Peres Ricardo Silva , Ramalho José Cochicho , Lidon Fernando , Barata José
Published: December 2023

Progress in agricultural productivity and sustainability hinges on strategic investments in technological research. Evolving technologies such as the Internet of Things, sensors, robotics, Artificial Intelligence, Machine Learning, Big Data, and Cloud Computing are propelling the agricultural sector towards the transformative Agriculture 4.0 paradigm. The present systematic literature review employs the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology to explore the usage of Machine Learning in agriculture. The study investigates the foremost applications of Machine Learning, including crop, water, soil, and animal management, revealing its important role in revolutionising traditional agricultural practices. Furthermore, it assesses the substantial impacts and outcomes of Machine Learning adoption and highlights some challenges associated with its integration in agricultural systems. This review not only provides valuable insights into the current landscape of Machine Learning applications in agriculture, but it also outlines promising directions for future research and innovation in this rapidly evolving field.