bluuebunny/crossref_metadata_2025 huggingface dataset:
Ulrich Beck ve Anthony Giddens’ın Düşünümsellik Analizi Bağlamında Yapay Zeka Tartışmalarına Uzanmak
Authors: Çelik Tuğçe Nur
Published: June 2024

Ulrich Beck ve Anthony Giddens, klasik modernleşmeden sonra artan bilim ve teknolojik gelişmeler ile oluşan günümüz toplumunun karşılığı niteliğinde olan düşünümsel modernite üzerine analizleriyle ön plana çıkmaktadırlar. Modernliğin bir devamı olarak ele aldıkları ikinci moderniteye “düşünümsellik” kavramıyla açıklık getiren bu iki düşünür, modern toplumun karmaşıklığını ve belirsizliğini ele alırken güçlü bir analitik çerçeve sunarak modern dünyanın karanlık yüzüne ışık tutmaktadırlar. Bu çalışma, Beck ve Giddens’ın düşünümsellik analizleriyle günümüz toplumunu yeniden şekillendirmeye başlayan “yapay zeka teknolojilerini” ilişkilendirme amacı taşımaktadır. Modernliğin ve beraberinde bireylerin düşünümsel bir özellik kazandığı, modernliğin kendi yapılarını yıkarak özellikle bilim ve teknoloji vasıtasıyla yenilerini inşa ettiği düşünümsel modernite analizlerinin yapay zeka teknolojilerinin yarattığı tartışmalara farklı bir perspektif yaratacağı düşünülmektedir. Zira yapay zeka teknolojileri bu teorik yaklaşımların ışığında incelendiğinde, modernliğin risk ve belirsizlik alanlarını, bireylerin kimlik oluşumlarını ve toplumsal yapıların bu teknolojiler tarafından nasıl etkilendiği konusunda derinlemesine bir anlayış sağlamaktadır. Dolayısıyla bu çalışmada, yapay zeka teknolojilerinin modern toplumun dinamiklerine nasıl entegre olduğu ve bireylerin bu teknolojilerle etkileşiminin nasıl şekillendiği incelenecek ve Beck ile Giddens’ın teorik çerçeveleri ışığında yapay zeka tartışmalarına yeni bir bakış açısı getirilecektir.
Using Arduino in Science, Technology, Engineering, and Mathematics (STEM) Education: Bibliometric Analysis
Authors:   Dokuz Eylul University, Turkey, Pabuçcu Akış Aybüke
Published: June 2024

The dramatic increase in science, technology, engineering, and mathematics (STEM) education studies has resulted in more authors promoting the use of Arduino in STEM education. Although there are educational research studies utilizing bibliometric procedures for the exploration of Arduino and STEM separately, there is a further need for research on their relationship. The current study utilizes several software tools (Vosviewer, Biblioshiny) and bibliometric procedures for this research domain. The documents were retrieved from the Scopus database from 2013 to 2022. Performance analysis was used to reveal publications and citation trends with the top contributors. Moreover, bibliographic mapping was used to comprehend the conceptual (co-occurrences), intellectual (bibliographic coupling), and social (collaboration network) structures of the retrieved data. The results revealed that the most prolific authors and institutes were addressed in Turkey. Besides, the most cited authors and institutes were from the USA. However, it seems this situation will change soon to the advantage of Turkey because of its highest annual growth rate and smallest document average age. This research also shows that there is a sign of the risk of monopolization in this area soon. Moreover, little cooperation was found within the dataset implying the importance and necessity of encouraging the mobility of researchers as well as increasing the collaboration between universities at both national and international levels. Overall, the study reveals that Arduino has great potential in using STEM activities in the future.
Investigating the Ability in Constructing Scientific Explanations of Thai Grade 10 Students: Insights from Learning Achievement, Attitude, and School Size
Authors:   Science Education Center, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand, Wannathai Piriya , Pruekpramool Chaninan ,   Science Education Center, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
Published: June 2024

The ability to construct scientific explanations is a vital goal of learning science at all levels. Students from different backgrounds are likely to have this ability differently. This research aimed to assess Thai grade 10 students’ ability to construct scientific explanations, examine differences based on learning achievement, attitude toward science, and school size, and find correlations among these variables. The study included 231 students from Phetchaburi province, Thailand, with 77.5% showing moderate ability levels. The research identified significant differences in students’ ability levels based on their learning achievement, attitude toward science, and school size. The levels of students’ ability correlated with their learning achievement, attitude toward science, and school size. In addition, students with high learning achievement, and positive attitudes, and who attended larger schools tended to have higher ability levels. However, there was no significant relationship between the levels of students’ attitudes toward science and school size. These findings highlight the importance of considering individual differences and backgrounds when teaching science, particularly in terms of learning achievement, attitude toward science, and school size.
UMA ANÁLISE DE THE STANLEY PARABLE
Authors: De Abreu Mendonça Bruno , Malveira Ícaro Lênin Maia , Matos Torquato Ana Laura
Published: June 2024

Este artigo analisa o jogo de ficção interativa The Stanley Parable (2011), desenvolvido por Davey Wreden e William Pugh, à luz dos pressupostos da gamearte propostos por Saul e Stuckey (2007), Bruno Mendonça (2014) e Annelise Witt (2013). A análise tem como objetivo estabelecer relações entre a gamearte e as características narrativas e de mecânica no game, como o gameplay em primeira pessoa, metalinguagem, quebra da quarta parede e construção de tensões dramáticas. Desse modo, defende-se que The Stanley Parable pode ser considerado um produto de gamearte, contribuindo, assim, para a reflexão estética e teórica nesse campo de estudo.
Control motor y alteraciones de la marcha en la Enfermedad de Parkinson
Authors: Maldonado Cornejo Jorge Gabriel , Pilla Almeida Cynthia Natalia , Pérez Peñafiel Carolina Elizabeth , Remache Arias Diana Alexandra , PINZON BERNAL MONICA YAMILE
Published: June 2024

Introducción: La enfermedad de Parkinson (EP)es un trastorno neurodegenerativo asociado amuerte de las células productoras de dopamina delnúcleo estriado, afecta al control motor, causandosíntomas como rigidez muscular y temblores, asícomo alteraciones específicas en la marcha, comopasos arrastrados y reducción de la amplitud delbalanceo de los brazos. Estas dificultades en lalocomoción se agravan con la progresión de laenfermedad y aumentan el riesgo de caídas. Objetivo:Realizar una revisión de literatura relacionada conlas alteraciones del control motor y la marcha enpersonas mayores de 65 años con EP y las distintasalternativas de tratamiento. Metodología: Revisiónde la literatura basada en las recomendaciones deguías de revisiones sistemáticas para las revisionesde alcance. La búsqueda se realizó en bases dedatos como Medline/pubmed y PhysiotherapyEvidence Database PEDro, limitando la búsqueda aartículos en inglés publicados en los últimos cincoaños. Resultados: Se identificación 934 registrosde los cuales se incluyeron 21 que cumplían conlos criterios de elegibilidad que presentaban lasprincipales alteraciones del control motor y la marchaagrupados en cambios en la postura, bradicinesia,debilidad muscular y una zancada más corta.Conclusiones: La EP produce alteraciones notablesen el control motor y en la marcha de los pacientes.Estas alteraciones se caracterizan por dificultadesen la iniciación y mantenimiento de movimientos,así como en la coordinación de la marcha, lo queresulta en pasos arrastrados, disminución en laamplitud del balanceo de los brazos y problemascon la postura. Estos cambios no solo limitan lamovilidad y la independencia funcional, sino quetambién aumentan el riesgo de caídas y lesiones,impactando significativamente en la calidad de vidade los pacientes con esta enfermedad. Es crucialimplementar intervenciones terapéuticas específicasy adaptadas en donde se involucren ambientesenriquecidos para abordar estas alteraciones ymejorar su calidad de vida. Resultados: Se identificación 934 registros de los cuales se incluyeron 21 que cumplían con los criterios de elegibilidad que presentaban las principales alteraciones del control motor y la marcha agrupados en cambios en la postura, bradicinesia, debilidad muscular y una zancada más corta. Conclusiones: La marcha en EP está caracterizada por la alteración en el equilibrio y control postural, presentando signos comunes como reducción de la amplitud del balanceo de los brazos, longitud de la zancada y pasos arrastrados. Se identificó que al realizar un entrenamiento cognitivo con tareas duales disminuyó el tiempo de apoyo doble, mejora la velocidad y la longitud de la zancada. Las señales o claves auditivas y visuales, además de los ambientes enriquecidos son efectivos en el tratamiento enfocado en el aprendizaje motor de la marcha.
Degradation of specific glycosaminoglycans improves transfection efficiency and vector production in transient lentiviral vector manufacturing processes
Authors: Williams-Fegredo Thomas , Davies Lee , Knevelman Carol , Mitrophanous Kyriacos , Miskin James , Rafiq Qasim A.
Published: June 2024

Both cell surface and soluble extracellular glycosaminoglycans have been shown to interfere with the exogenous nucleic acid delivery efficiency of non-viral gene delivery, including lipoplex and polyplex-mediated transfection. Most gene therapy viral vectors used commercially and in clinical trials are currently manufactured using transient transfection-based bioprocesses. The growing demand for viral vector products, coupled with a global shortage in production capability, requires improved transfection technologies and processes to maximise process efficiency and productivity. Soluble extracellular glycosaminoglycans were found to accumulate in the conditioned cell culture medium of suspension adapted HEK293T cell cultures, compromising transfection performance and lentiviral vector production. The enzymatic degradation of specific, chondroitin sulphate-based, glycosaminoglycans with chondroitinase ABC was found to significantly enhance transfection performance. Additionally, we report significant improvements in functional lentiviral vector titre when cultivating cells at higher cell densities than those utilised in a control lentiviral vector bioprocess; an improvement that was further enhanced when cultures were supplemented with chondroitinase ABC prior to transfection. A 71.2% increase in functional lentiviral vector titre was calculated when doubling the cell density prior to transfection compared to the existing process and treatment of the high-density cell cultures with 0.1 U/mL chondroitinase ABC resulted in a further 18.6% increase in titre, presenting a method that can effectively enhance transfection performance.
Neural crest and sons: role of neural crest cells and Schwann cell precursors in development and gland embryogenesis
Authors: Knyazeva Aleksandra , Dyachuk Vyacheslav
Published: June 2024

In this review, we consider the multipotency of neural crest cells (NCCs), Schwann cell precursors (SCPs), and their role in embryogenesis base on genetic tracing and knock out model animals and single cell transcriptomic analysis. In particular, we summarize and analyze data on the contribution of NCCs and SCPs to the gland development and functions.
Scenarios—using the complexity frame of reference to inform the construction of available futures in the possibility space
Authors: Byrne David Sidney
Published: June 2024

The global socio-ecological system in the era of the Capitalocene—the world system created by the use of fossil fuels to provide energy for the development of a growth-oriented capitalist logic in all areas of production and consumption—is facing a set of interwoven sub-system crises that come together to make it extremely unlikely that the global system can continue in its present form. The whole system is in a state of crisis—a system state that cannot continue to exist and in which the system must either return to a previous system state—be resilient in the common usage of that word to mean “bouncing back”—or be transformed into a new relatively long-lasting but qualitatively different state. The most evident whole system crisis is, of course, a product of the impending climate transformation contingent upon global warming, but there are related crises of increasing social inequality, demographic structures, healthcare systems, fiscal and public expenditure processes, and urban systems in an urbanized world. These are all interwoven to constitute a polycrisis across the global socio-ecological world system. They are also manifested at all geographical levels and, in particular, at the level of city regions, which, in a predominantly urbanized world, are crucial levels for administration and action. The complex realist frame of reference can be used to inform the development of scenarios for the available alternative system states in the path-dependent possibility space. We have to start from where we are to get to where we want to go. Scenarios are not only descriptions of possible futures but also include a specification of the actions—the drivers—that shape the creation of specific kinds of futures in those available to us. The construction of scenarios should be done through a process of action research, involving a dialog among system scientists, key actors in governance systems, and civil society. The co-production of knowledge as a guide to action is essential.
Inflammaging, immunosenescence, and cardiovascular aging: insights into long COVID implications
Authors: Müller Ludmila , Di Benedetto Svetlana
Published: June 2024

Aging leads to physiological changes, including inflammaging—a chronic low-grade inflammatory state with significant implications for various physiological systems, particularly for cardiovascular health. Concurrently, immunosenescence—the age-related decline in immune function, exacerbates vulnerabilities to cardiovascular pathologies in older individuals. Examining the dynamic connections between immunosenescence, inflammation, and cardiovascular aging, this mini-review aims to disentangle some of these interactions for a better understanding of their complex interplay. In the context of cardiovascular aging, the chronic inflammatory state associated with inflammaging compromises vascular integrity and function, contributing to atherosclerosis, endothelial dysfunction, arterial stiffening, and hypertension. The aging immune system's decline amplifies oxidative stress, fostering an environment conducive to atherosclerotic plaque formation. Noteworthy inflammatory markers, such as the high-sensitivity C-reactive protein, interleukin-6, interleukin-1β, interleukin-18, and tumor necrosis factor-alpha emerge as key players in cardiovascular aging, triggering inflammatory signaling pathways and intensifying inflammaging and immunosenescence. In this review we aim to explore the molecular and cellular mechanisms underlying inflammaging and immunosenescence, shedding light on their nuanced contributions to cardiovascular diseases. Furthermore, we explore the reciprocal relationship between immunosenescence and inflammaging, revealing a self-reinforcing cycle that intensifies cardiovascular risks. This understanding opens avenues for potential therapeutic targets to break this cycle and mitigate cardiovascular dysfunction in aging individuals. Furthermore, we address the implications of Long COVID, introducing an additional layer of complexity to the relationship between aging, immunosenescence, inflammaging, and cardiovascular health. Our review aims to stimulate continued exploration and advance our understanding within the realm of aging and cardiovascular health.
The differential collapse–filling evolution process of the paleo-underground river in the Northern Uplift of the Tarim Basin
Authors: Dong Hong-Qi , Liang Jia-Peng , Zhang Qing-Yu , Li Jing-Rui , Wan Jun-Wei , Nie Guo-Quan , Li Yu-Lu
Published: June 2024

The characteristics and stages of collapse–filling in paleo-underground rivers vary in recharge–runoff–discharge zones, constraining the associated fracture-caved reservoirs in carbonate strata. This paper comprehensively uses core, fluid inclusion, and carbon–oxygen isotope to probe the evolution process and migration of collapse–filling in paleo-underground rivers in the Northern Uplift of the Tarim Basin. The results show that 1) more than three stages of collapse–filling were identified in recharge–runoff–discharge zones, and a four-stage differential collapse–filling process was proposed to summarize the evolution of paleo-underground rivers. 2) The collapse–filling process varies spatiotemporally in the recharge, runoff, and discharge zones. Hydrodynamic strength and filling capacity migrate gradually from the recharge zone to the discharge zone. 3) Collapse–filling mechanisms, including gravity, suffusion, and suction–erosion mechanisms, also vary along with the collapse–filling evolution process of paleo-underground rivers. The research provided a new insight to recognize and interpret the differential planar distribution and vertical filling of the paleo-underground river system, which can be further applied to investigate the fracture-caved karst reservoirs.
Voltage control strategy of a high-permeability photovoltaic distribution network based on cluster division
Authors: Li He , Song Kun , Meng Fanyu , Wang Zhenhao , Wang Chaobin
Published: June 2024

The use of distributed photovoltaics (PVs) on a large scale often causes voltage over-limit problems in distribution networks. This paper proposes a distributed photovoltaic cluster collaborative optimization voltage control strategy based on an improved community algorithm to address the issue of centralized control being unable to respond quickly to the randomness of distributed photovoltaics and the difficulty of achieving overall coordination with local control. First, by improving the community algorithm, the division of reactive and active clusters, considering the power balance and node coupling degree, is realized. Then, the cluster-coordinated voltage control strategy is proposed by making full use of the power control ability of a photovoltaic inverter. Finally, a voltage regulation ability evaluation index is proposed to assess the node regulation ability within the cluster and select key nodes. This effectively reduces the number of control nodes. The simulation analysis of the improved IEEE 69 distribution network shows that the proposed voltage control strategy can mitigate the issue of voltage over-limit in high-permeability distributed photovoltaic access distribution and enhance the photovoltaic consumption capacity.
Effects of ankylosing spondylitis on cardiovascular disease: aMendelian randomization study
Authors: Xiao Lu , Lin Shudian , Zhan Feng
Published: June 2024

Objective

Accumulating evidence suggests that patients with ankylosing spondylitis (AS) have an elevated risk for cardiovascular disease (CVD) and cardiovascular death, however, whether AS has causal effects on the risk of CVD is unclear.Two-sample Mendelian randomization (MR) was utilizedto examine the probable causal link between them.

Methods

Summary statistics from publicly released genome-wide association studies (GWAS) was used to perform MR analyses. Genetically predicted AS was selected as the exposure variable from published GWAS meta-analyses. CVD was adopted as the outcome variable. The inverse variant weighted method was employed to obtain the casual estimates. The robustness of the results was also examined by evaluating the pleiotropy and heterogeneity of single-nucleotide polymorphisms.

Results

According to MR analyses, genetic susceptibility to AS was associated with a high risk of heart failure and ischemic stroke, while negativelygenetic susceptibility was found between AS and peripheral atherosclerosis. No statistical relationship was found between AS and venous thromboembolism, atrial fibrillation, coronary atherosclerosis, and valvular heart disease. Sensitivity analysis showed no evidence of horizontal pleiotropy or heterogeneity.

Conclusion

The present study suggests that AS exerts causal effects on the risk of CVD, including heart failure, ischemic stroke, and peripheral atherosclerosis.
Identification of differentially expressed genes of blood leukocytes for Schizophrenia
Authors: Wang Feifan , Fan Yao , Li Yinghui , Zhou Yuan , Wang Xin , Zhu Mengya , Chen Xuefei , Xue Yong , Shen Chong
Published: June 2024

Background

Schizophrenia (SCZ) is a severe neurodevelopmental disorder with brain dysfunction. This study aimed to use bioinformatic analysis to identify candidate blood biomarkers for SCZ.

Methods

The study collected peripheral blood leukocyte samples of 9 SCZ patients and 20 healthy controls for RNA sequencing analysis. Bioinformatic analyses included differentially expressed genes (DEGs) analysis, pathway enrichment analysis, and weighted gene co-expression network analysis (WGCNA).

Results

This study identified 1,205 statistically significant DEGs, of which 623 genes were upregulated and 582 genes were downregulated. Functional enrichment analysis showed that DEGs were mainly enriched in cell chemotaxis, cell surface, and serine peptidase activity, as well as involved in Natural killer cell-mediated cytotoxicity. WGCNA identified 16 gene co-expression modules, and five modules were significantly correlated with SCZ (p < 0.05). There were 106 upregulated genes and 90 downregulated genes in the five modules. The top ten genes sorted by the Degree algorithm were RPS28, BRD4, FUS, PABPC1, PCBP1, PCBP2, RPL27A, RPS21, RAG1, and RPL27. RAG1 and the other nine genes belonged to the turquoise and pink module respectively. Pathway enrichment analysis indicated that these 10 genes were mainly involved in processes such as Ribosome, cytoplasmic translation, RNA binding, and protein binding.

Conclusion

This study finds that the gene functions in key modules and related enrichment pathways may help to elucidate the molecular pathogenesis of SCZ, and the potential of key genes to become blood biomarkers for SCZ warrants further validation.
Case report: Disitamab vedotin combined with immunotherapy demonstrated excellent efficacy in scrotal Paget’s disease with Her-2 overexpression
Authors: Wang Jia-Ling , Meng Wen-Jun , Hu Nian , Liu Ji-Yan
Published: June 2024

Background

Extramammary Paget’s disease (EMPD) is a rare epithelial malignancy, and approximately 30%–40% of EMPD patients overexpress human epidermal growth factor receptor 2 (Her-2). Currently, there are no established standard treatments for advanced EMPD while anti–Her-2 therapy is recommended for Her-2–positive cases.

Case presentation

Here, we report a 51-year-old male diagnosed with advanced Her-2–positive EMPD, presenting with numerous lymph node metastases. This patient received disitamab vedotin (an antibody-drug conjugate, targeting Her-2) combined with serplulimab as first-line treatment. After seven cycles of combination therapy, the patient tolerated the treatment well and the lymph node lesions continued to shrink. However, the patient developed immunotherapy-related pneumonia following the eighth treatment. Hormone therapy was administered while all the anti-tumor therapies were halted. After the pneumonia improved, the patient underwent positron emission tomography-computed tomography, revealing a complete response to his tumor. To consolidate the effect, he received another five cycles of disitamab vedotin monotherapy as maintenance therapy, without experiencing any adverse events. To date, the patient has remained in good health without any recurrence 10 months after drug discontinuance.

Conclusion

Disitamab vedotin combined with immunotherapy demonstrated a long-term clinical benefit in advanced Her-2–positive EMPD. For rare solid tumors with Her-2 overexpression, disitamab vedotin combined with immunotherapy might offer a viable therapeutic choice.
Hypoxia within the glioblastoma tumor microenvironment: a master saboteur of novel treatments
Authors: Feldman Lisa
Published: June 2024

Glioblastoma (GBM) tumors are the most aggressive primary brain tumors in adults that, despite maximum treatment, carry a dismal prognosis. GBM tumors exhibit tissue hypoxia, which promotes tumor aggressiveness and maintenance of glioma stem cells and creates an overall immunosuppressive landscape. This article reviews how hypoxic conditions overlap with inflammatory responses, favoring the proliferation of immunosuppressive cells and inhibiting cytotoxic T cell development. Immunotherapies, including vaccines, immune checkpoint inhibitors, and CAR-T cell therapy, represent promising avenues for GBM treatment. However, challenges such as tumor heterogeneity, immunosuppressive TME, and BBB restrictiveness hinder their effectiveness. Strategies to address these challenges, including combination therapies and targeting hypoxia, are actively being explored to improve outcomes for GBM patients. Targeting hypoxia in combination with immunotherapy represents a potential strategy to enhance treatment efficacy.
A degranulation assay using Vγ9Vδ2 T cells for the rapid diagnosis of familial hemophagocytic syndromes
Authors: Jorisch-Mühlebach Olivia , Pitts Dina , Tinner Raphaela , Teh Hong Ying , Roelli Conrad , Prader Seraina , Vavassori Stefano , Pachlopnik Schmid Jana
Published: June 2024

Introduction

Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening immune disorder characterized by uncontrolled lymphocyte and macrophage activation and a subsequent cytokine storm. The timely initiation of immunosuppressive treatment is crucial for survival.

Methods

Here, we harnessed Vγ9Vδ2 T cell degranulation to develop a novel functional assay for the diagnosis of HLH. We compared the novel assay with the conventional natural killer (NK) cell stimulation method in terms of efficiency, specificity, and reliability. Our analysis involved 213 samples from 182 individuals, including 23 samples from 12 patients with degranulation deficiency (10 individuals with UNC13D deficiency, 1 with STXBP2 deficiency, and 1 with RAB27A deficiency).

Results

While both tests exhibited 100% sensitivity, the Vγ9Vδ2 T cell degranulation assay showed a superior specificity of 86.2% (n=70) compared to the NK cell degranulation assay, which achieved 78.9% specificity (n=213). The Vγ9Vδ2 T cell degranulation assay offered simpler technical requirements and reduced labor intensity, leading to decreased susceptibility to errors with faster processing times.

Discussion

This efficiency stemmed from the sole requirement of dissolving (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP) powder, contrasting with the intricate maintenance of K562 cells necessary for the NK cell degranulation assay. With its diminished susceptibility to errors, we anticipate that the assay will require fewer repetitions of analysis, rendering it particularly well-suited for testing infants.

Conclusion

The Vγ9Vδ2 T cell degranulation assay is a user-friendly, efficient diagnostic tool for HLH. It offers greater specificity, reliability, and practicality than established methods. We believe that our present findings will facilitate the prompt, accurate diagnosis of HLH and thus enable rapid treatment and better patient outcomes.
Microbiome-derived bacterial lipids regulate gene expression of proinflammatory pathway inhibitors in systemic monocytes
Authors: Mihori Saki , Nichols Frank , Provatas Anthony , Matz Alyssa , Zhou Beiyan , Blesso Christopher N. , Panier Hunter , Daddi Lauren , Zhou Yanjiao , Clark Robert B.
Published: June 2024

How the microbiome regulates responses of systemic innate immune cells is unclear. In the present study, our purpose was to document a novel mechanism by which the microbiome mediates crosstalk with the systemic innate immune system. We have identified a family of microbiome Bacteroidota-derived lipopeptides—the serine-glycine (S/G) lipids, which are TLR2 ligands, access the systemic circulation, and regulate proinflammatory responses of splenic monocytes. To document the role of these lipids in regulating systemic immunity, we used oral gavage with an antibiotic to decrease the production of these lipids and administered exogenously purified lipids to increase the systemic level of these lipids. We found that decreasing systemic S/G lipids by decreasing microbiome Bacteroidota significantly enhanced splenic monocyte proinflammatory responses. Replenishing systemic levels of S/G lipids via exogenous administration returned splenic monocyte responses to control levels. Transcriptomic analysis demonstrated that S/G lipids regulate monocyte proinflammatory responses at the level of gene expression of a small set of upstream inhibitors of TLR and NF-κB pathways that include Trem2 and Irf4. Consistent with enhancement in proinflammatory cytokine responses, decreasing S/G lipids lowered gene expression of specific pathway inhibitors. Replenishing S/G lipids normalized gene expression of these inhibitors. In conclusion, our results suggest that microbiome-derived S/G lipids normally establish a level of buffered signaling activation necessary for well-regulated innate immune responses in systemic monocytes. By regulating gene expression of inflammatory pathway inhibitors such as Trem2, S/G lipids merit broader investigation into the potential dysfunction of other innate immune cells, such as microglia, in diseases such as Alzheimer’s disease.
Drone-based photogrammetry reveals differences in humpback whale body condition and mass across North Atlantic foraging grounds
Authors: Napoli Chelsi , Hirtle Nathan , Stepanuk Julia , Christiansen Fredrik , Heywood Eleanor I. , Grove Thomas J. , Stoller Alyssa , Dodds Flordespina , Glarou Maria , Rasmussen Marianne H. , Lonati Gina L. , Davies Kimberley T.A. , Videsen Simone , Simon Malene J. , Boye Tenna K. , Zoidis Ann , Todd Sean K. , Thorne Lesley H.
Published: June 2024

Baleen whales are key consumers in marine ecosystems and can serve as ecosystem sentinels. Body condition, defined as an individual’s energy stores relative to its structural size, can provide a useful proxy for health in baleen whales. As capital breeders, important life history events in baleen whales such as seasonal migrations and reproduction depend on having sufficient energy stores. Spatiotemporal variability of body condition of baleen whales can reflect differences in energy accumulated during the foraging season. Here we assess and compare the body condition and mass of humpback whales (Megaptera novaeangliae) across four different foraging areas from the West Indies distinct population segment in the Northwest Atlantic. Morphometric measurements of humpback whales were obtained using unoccupied aerial systems (UAS, or drones) from the New York Bight, the Gulf of Maine, Iceland, and Greenland. Uncertainty in morphometric estimates was incorporated and propagated using a bootstrapping approach. Measurements were used to estimate body volume and calculate a body condition index (BCI) for each individual whale. Since body mass is a key parameter for understanding animal physiology and bioenergetics, we further compared whale body mass to body size between foraging areas by converting body volume to body mass using estimates of tissue density from tagging studies. BCI showed significant differences between foraging areas with a large effect size (ANCOVA: mean η2 = 0.168; all p< 0.001) when incorporating day of year and year as covariates. Humpback whales in the Gulf of Maine showed significantly higher BCI than those in the New York Bight, Iceland, and Greenland. Standardized Major Axis (SMA) regressions comparing log-log relationships of both body volume and body mass, respectively, to total length reinforced these results. Humpback whales in the Gulf of Maine showed significantly higher elevation in the SMAs than those in the other study regions (p<0.001), implying that humpback whales foraging in the Gulf of Maine accumulated greater energy reserves for a given body size. Estimates of body mass indicate that for a given body length, humpback whales in the Gulf of Maine have an 18% greater body mass than those in the New York Bight, Iceland, or Greenland. Regional differences in prey availability or anthropogenic threats could contribute to the observed patterns in body condition. Our findings highlight the importance of regional environmental factors to the nutritional health of baleen whales.
Revealing macrozoobenthos diversity of Java coral reefs, Indonesia: a review on research trends and species assemblages
Authors: Aulia Elsa Dianita , Park Jinsoon , Lee Sang-kyu , Khim Jong Seong
Published: June 2024

Macrozoobenthos communities play significant ecological roles in coral reef ecosystems. However, they are frequently overlooked due to their cryptic appearance, and their diversity remains undiscovered, particularly in Indonesia. This comprehensive review of publications on the macrozoobenthos in the coral reef ecosystems of Java - the most populated island in Indonesia, was conducted to compile a species list and gain an overview of its community composition. We also assessed the existence of species that are frequently reported, endemic, protected, and threatened. Data analysis was performed with data from 53 publications appearing from the 1980s to 2022. In total, 482 species belonging to 4 phyla and 9 classes have been recorded. Mollusca is the most speciose phylum (n = 321), followed by Echinodermata (n = 106), Arthropoda (n = 49), and Platyhelminthes (n = 6). Generally, the northern part of Java is well studied and has larger numbers of recorded phyla and species. The highest species number (n = 266) has been recorded off the northern coast of West Java, while there are around 25–99 species in other regions. Echinoderms species such as Culcita novaeguineae, Diadema setosum, Echinothrix calamaris, and Holothuria atra had relatively higher occurrences than other taxa. We also noted the occurrence of giant clam Hippopus hippopus, which is protected by Indonesian law. This review provides fundamental knowledge of macrozoobenthic diversity in the coral reefs of Java, making it available to global audiences. However, it revealed a lack of research on benthic fauna in several areas with moderate to good coral cover conditions. Further research is needed to explore macrozoobenthic species richness in this region thoroughly, and periodic monitoring is essential to provide early warnings of possible changes and biodiversity loss.
Mendelian randomization based on genome-wide association studies and expression quantitative trait loci, predicting gene targets for the complexity of osteoarthritis as well as the clinical prognosis of the condition
Authors: Yan Yiqun , He Junyan , Xu Zelin , Wang Chen , Hu Zhongyao , Zhang Chun , Cheng Wendan
Published: June 2024

Background

Osteoarthritis (OA) entails a prevalent chronic ailment, marked by the widespread involvement of entire joints. Prolonged low-grade synovial inflammation serves as the key instigator for a cascade of pathological alterations in the joints.

Objective

The study seeks to explore potential therapeutic targets for OA and investigate the associated mechanistic pathways.

Methods

Summary-level data for OA were downloaded from the genome-wide association studies (GWAS) database, expression quantitative trait loci (eQTL) data were acquired from the eQTLGen consortium, and synovial chip data for OA were obtained from the GEO database. Following the integration of data and subsequent Mendelian randomization analysis, differential analysis, and weighted gene co-expression network analysis (WGCNA) analysis, core genes that exhibit a significant causal relationship with OA traits were pinpointed. Subsequently, by employing three machine learning algorithms, additional identification of gene targets for the complexity of OA was achieved. Additionally, corresponding ROC curves and nomogram models were established for the assessment of clinical prognosis in patients. Finally, western blotting analysis and ELISA methodology were employed for the initial validation of marker genes and their linked pathways.

Results

Twenty-two core genes with a significant causal relationship to OA traits were obtained. Through the application of distinct machine learning algorithms, MAT2A and RBM6 emerged as diagnostic marker genes. ROC curves and nomogram models were utilized for evaluating both the effectiveness of the two identified marker genes associated with OA in diagnosis. MAT2A governs the synthesis of SAM within synovial cells, thereby thwarting synovial fibrosis induced by the TGF-β1-activated Smad3/4 signaling pathway.

Conclusion

The first evidence that MAT2A and RBM6 serve as robust diagnostic for OA is presented in this study. MAT2A, through its involvement in regulating the synthesis of SAM, inhibits the activation of the TGF-β1-induced Smad3/4 signaling pathway, thereby effectively averting the possibility of synovial fibrosis. Concurrently, the development of a prognostic risk model facilitates early OA diagnosis, functional recovery evaluation, and offers direction for further therapy.
Comparative genomic analysis of Bacillus atrophaeus HAB-5 reveals genes associated with antimicrobial and plant growth-promoting activities
Authors: Dahar Ghulam Yaseen , Wang Huan Wei , Rajer Faheem Uddin , Jin Pengfie , Xu Peidong , Abro Manzoor Ali , Qureshi Abdul Sattar , Karim Asad , Miao Weiguo
Published: June 2024

Bacillus atrophaeus HAB-5 is a plant growth-promoting rhizobacterium (PGPR) that exhibits several biotechnological traits, such as enhancing plant growth, colonizing the rhizosphere, and engaging in biocontrol activities. In this study, we conducted whole-genome sequencing of B. atrophaeus HAB-5 using the single-molecule real-time (SMRT) sequencing platform by Pacific Biosciences (PacBio; United States), which has a circular chromosome with a total length of 4,083,597 bp and a G + C content of 44.21%. The comparative genomic analysis of B. atrophaeus HAB-5 with other strains, Bacillus amyloliquefaciens DSM7, B. atrophaeus SRCM101359, Bacillus velezensis FZB42, B. velezensis HAB-2, and Bacillus subtilis 168, revealed that these strains share 2,465 CDSs, while 599 CDSs are exclusive to the B. atrophaeus HAB-5 strain. Many gene clusters in the B. atrophaeus HAB-5 genome are associated with the production of antimicrobial lipopeptides and polypeptides. These gene clusters comprise distinct enzymes that encode three NRPs, two Transat-Pks, one terpene, one lanthipeptide, one T3PKS, one Ripp, and one thiopeptide. In addition to the likely IAA-producing genes (trpA, trpB, trpC, trpD, trpE, trpS, ywkB, miaA, and nadE), there are probable genes that produce volatile chemicals (acoA, acoB, acoR, acuB, and acuC). Moreover, HAB-5 contained genes linked to iron transportation (fbpA, fetB, feuC, feuB, feuA, and fecD), sulfur metabolism (cysC, sat, cysK, cysS, and sulP), phosphorus solubilization (ispH, pstA, pstC, pstS, pstB, gltP, and phoH), and nitrogen fixation (nif3-like, gltP, gltX, glnR, glnA, nadR, nirB, nirD, nasD, narl, narH, narJ, and nark). In conclusion, this study provides a comprehensive genomic analysis of B. atrophaeus HAB-5, pinpointing the genes and genomic regions linked to the antimicrobial properties of the strain. These findings advance our knowledge of the genetic basis of the antimicrobial properties of B. atrophaeus and imply that HAB-5 may employ a variety of commercial biopesticides and biofertilizers as a substitute strategy to increase agricultural output and manage a variety of plant diseases.
Recent advances in the therapeutic potential of cathelicidins
Authors: Guerra Maria Eduarda Souza , Vieira Brenda , Calazans Ana Paula Carvalho Thiers , Destro Giulia Vicente , Melo Karina , Rodrigues Emilly , Waz Natalha Tedeschi , Girardello Raquel , Darrieux Michelle , Converso Thiago Rojas
Published: June 2024

The alarming increase in antimicrobial resistance in the last decades has prompted the search for alternatives to control infectious diseases. Antimicrobial peptides (AMPs) represent a heterogeneous class of molecules with ample antibacterial, antiviral, and antifungal effects. They can be found in many organisms, including all classes of vertebrates, providing a valuable source of new antimicrobial agents. The unique properties of AMPs make it harder for microbes develop resistance, while their immunomodulatory properties and target diversity reinforce their translational use in multiple diseases, from autoimmune disorders to different types of cancer. The latest years have witnessed a vast number of studies evaluating the use of AMPs in therapy, with many progressing to clinical trials. The present review explores the recent developments in the medicinal properties of cathelicidins, a vast family of AMPs with potent antimicrobial and immunomodulatory effects. Cathelicidins from several organisms have been tested in disease models of viral and bacterial infections, inflammatory diseases, and tumors, with encouraging results. Combining nanomaterials with active, natural antimicrobial peptides, including LL-37 and synthetic analogs like ceragenins, leads to the creation of innovative nanoagents with significant clinical promise. However, there are still important limitations, such as the toxicity of many cathelicidins to healthy host cells and low stability in vivo. The recent advances in nanomaterials and synthetic biology may help overcome the current limitations, enabling the use of cathelicidins in future therapeutics. Furthermore, a better understanding of the mechanisms of cathelicidin action in vivo and their synergy with other host molecules will contribute to the development of safer, highly effective therapies.
Genomic and biological insights of bacteriophages JNUWH1 and JNUWD in the arms race against bacterial resistance
Authors: Zhang Hengwei , You Jiajia , Pan Xuewei , Hu Yanglu , Zhang Zan , Zhang Xian , Zhang Weiguo , Rao Zhiming
Published: June 2024

The coevolution of bacteria and bacteriophages has created a great diversity of mechanisms by which bacteria fight phage infection, and an equivalent diversity of mechanisms by which phages subvert bacterial immunity. Effective and continuous evolution by phages is necessary to deal with coevolving bacteria. In this study, to better understand the connection between phage genes and host range, we examine the isolation and genomic characterization of two bacteriophages, JNUWH1 and JNUWD, capable of infecting Escherichia coli. Sourced from factory fermentation pollutants, these phages were classified within the Siphoviridae family through TEM and comparative genomic analysis. Notably, the phages exhibited a viral burst size of 500 and 1,000 PFU/cell, with latent periods of 15 and 20 min, respectively. They displayed stability over a pH range of 5 to 10, with optimal activity at 37°C. The complete genomes of JNUWH1 and JNUWD were 44,785 bp and 43,818 bp, respectively. Phylogenetic analysis revealed their close genetic relationship to each other. Antibacterial assays demonstrated the phages’ ability to inhibit E. coli growth for up to 24 h. Finally, through laboratory-driven adaptive evolution, we successfully identified strains for both JNUWH1 and JNUWD with mutations in receptors specifically targeting lipopolysaccharides (LPS) and the lptD gene. Overall, these phages hold promise as additives in fermentation products to counter E. coli, offering potential solutions in the context of evolving bacterial resistance.
Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium
Authors: Wei Xinxiang , Chen Hongliang , Zhu Fangfang , Li Jiang
Published: June 2024

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.
Acinetobacter pittii: the emergence of a hospital-acquired pathogen analyzed from the genomic perspective
Authors: Bello-López Elena , Escobedo-Muñoz Ana Sofía , Guerrero Gabriela , Cruz-Córdova Ariadnna , Garza-González Elvira , Hernández-Castro Rigoberto , Zarain Patricia Lozano , Morfín-Otero Rayo , Volkow Patricia , Xicohtencatl-Cortes Juan , Cevallos Miguel A.
Published: June 2024

Acinetobacter pittii has increasingly been associated with several types of hospital-acquired severe infections. Genes implicated in carbapenem resistance, tigecycline resistance, or genes encoding extended spectrum cephalosporinases, such as blaADC, are commonly found in isolates implicated in these infections. A. pittii strains that are pandrug resistant have occasionally been identified. Food for human consumption, animals and plants are environmental sources of this pathogen. An alarming situation is that A. pitti has been identified as responsible for outbreaks in different regions worldwide. In this study, 384 genomes of A. pittii were analyzed, comprising sequences from clinical and non-clinical origins from 32 countries. The objective was to investigate if clinical strains possess genetic traits facilitating hospital adaptation. Results indicate significant genomic variability in terms of size and gene content among A. pittii isolates. The core genome represents a small portion (25–36%) of each isolate’s genome, while genes associated with antibiotic resistance and virulence predominantly belong to the accessory genome. Notably, antibiotic resistance genes are encoded by a diverse array of plasmids. As the core genome between environmental and hospital isolates is the same, we can assume that hospital isolates acquired ARGs due to a high selective pressure in these settings. The strain’s phylogeographic distribution indicates that there is no geographical bias in the isolate distribution; isolates from different geographic regions are dispersed throughout a core genome phylogenetic tree. A single clade may include isolates from extremely distant geographical areas. Furthermore, strains isolated from the environment or animal, or plant sources frequently share the same clade as hospital isolates. Our analysis showed that the clinical isolates do not already possess specific genes, other than antibiotic-resistant genes, to thrive in the hospital setting.