bluuebunny/crossref_metadata_2025 huggingface dataset:
User Fee System Sebagai Bentuk Implementasi Kebijakan Tata Ruang Wilayah Pesisir Teluk Kendari
Authors: Imam Wahyudi Adi , Adrianto Luky , Bahri Agus Syamsul
Published: March 2024

Penelitian dilaksanakan mulai April hingga Mei 2015. Tujuan penelitian untuk mengestimasi nilai ekonomi dari wisata rekreasi dalam hal ini pantai dan mengetahui persepsi pengelolaan pantai Teluk Kendari serta mengetahui tingkat kepuasan wisatawan. Wisatawan yang melakukan aktivitas rekreasi di Teluk Kendari adalah responden yang dipilih. Metode sampling acak sederhana digunakan untuk mengumpulkan sampel dari responden. Mengumpulkan data awal responden melalui observasi langsung di lapangan melalui wawancara. Data sekunder dikumpulkan dengan melakukan penelitian literatur. Analisis data menggunakan metode Penilaian Kontingensi dan Biaya Perjalanan sebagai hasil dari kerelaan membayar (WTP) dan analisis persepsi pengelolaan pengunjung wisata menggunakan Expert Couplet Node melalui pendekatan kualitatif. Hasil penelitian menunjukkan bahwa besarnya kesediaan membayar (WTP) agregat sebesar Rp. 23.250,- individu-1 tahun-1. Hasil perhitungan nilai konsumen surplus sebesar Rp. 13.983,- individu-1 tahun-1 dengan total nilai konsumen surplus kunjungan di Teluk Kendari sebesar Rp. 624.720,- tahun-1. Persentase sebesar 62% menunjukkan kurangnya kepuasan pengunjung terhadap pengelolaan ruang wisata serta 68% responden menunjukkan kurangnya kepuasan terhadap upaya pelestarian lingkungan Teluk Kendari.
Analisis Mutu Kimia Pakan Ikan dari Tepung Ikan Julung-Julung (Hemiramphus sp.) Sebagai Sumber Protein Utama
Authors: Anwar Lely Okmawaty , Payama Wahyudi , Sari Sri Fatmah , Asjun  , Mustam
Published: March 2024

Pakan merupakan komponen penting dalam menunjang kelangsungan hidup ikan. Tepung ikan julung-julung dapat menjadi alternatif bahan baku pembuatan pakan ikan karena mengandung protein tinggi sebesar 57,80%. Tepung kedelai dapat digunakan sebagai bahan campuran alami untuk menunjang nutrisi pakan ikan dengan kandungan protein 40%. Penelitian bertujuan untuk menganalisis mutu pakan ikan dari tepung ikan julung-julung sebagai sumber protein utama. Formulasi pakan menggunakan perhitungan persegi pearson’s. Metode penelitian menggunakan Rancangan Acak Lengkap (RAL) dengan 3 formulasi. Formulasi J1 yaitu tepung ikan julung-julung 50% : tepung kedelai 50%, J2 yaitu tepung ikan julung-julung 75% : tepung kedelai 25%, dan J3 yaitu tepung ikan julung-julung 100% : tepung kedelai 0%. Parameter uji yaitu kadar air, protein, lemak, serat, dan abu, serta Penentuan harga pokok produksi (HPP). Hasil penelitian menunjukan bahwa pakan formulasi J1 memiliki nilai kadar air 10,08%, protein 34,97%, lemak 14,35%, kadar serat 3,42%, dan kadar abu 6,94% dengan harga pokok produksi sebesar Rp 23.562.00/kg. Formulasi J2 nilai kadar air 10,14%, protein 41,49%, lemak 7,91%, kadar serat 5,81%, dan kadar abu 8,58% dengan harga pokok produksi sebesar Rp 23.561.00/kg. Formulasi J3 nilai kadar air 11,01%, protein 43,03%, lemak 6,76%, kadar serat 1,63%, dan kadar abu 9,00% dengan harga pokok produksi sebesar Rp 23.562.00/kg.
DoE-based medium optimization for improved biosurfactant production with Aureobasidium pullulans
Authors: Haala Frederick , Dielentheis-Frenken Marie R. E. , Brandt Friedrich M. , Karmainski Tobias , Blank Lars M. , Tiso Till
Published: March 2024

Polyol lipids (a.k.a. liamocins) produced by the polyextremotolerant, yeast-like fungus Aureobasidium pullulans are amphiphilic molecules with high potential to serve as biosurfactants. So far, cultivations of A. pullulans have been performed in media with complex components, which complicates further process optimization due to their undefined composition. In this study, we developed and optimized a minimal medium, focusing on biosurfactant production. Firstly, we replaced yeast extract and peptone in the best-performing polyol lipid production medium to date with a vitamin solution, a trace-element solution, and a nitrogen source. We employed a design of experiments approach with a factor screening using a two-level-factorial design, followed by a central composite design. The polyol lipid titer was increased by 56% to 48 g L−1, and the space-time yield from 0.13 to 0.20 g L−1 h−1 in microtiter plate cultivations. This was followed by a successful transfer to a 1 L bioreactor, reaching a polyol lipid concentration of 41 g L−1. The final minimal medium allows the investigation of alternative carbon sources and the metabolic pathways involved, to pinpoint targets for genetic modifications. The results are discussed in the context of the industrial applicability of this robust and versatile fungus.
PEX1 is essential for glycosome biogenesis and trypanosomatid parasite survival
Authors: Mahadevan Lavanya , Arya Hemant , Droste Andrea , Schliebs Wolfgang , Erdmann Ralf , Kalel Vishal C.
Published: March 2024

Trypanosomatid parasites are kinetoplastid protists that compartmentalize glycolytic enzymes in unique peroxisome-related organelles called glycosomes. The heterohexameric AAA-ATPase complex of PEX1-PEX6 is anchored to the peroxisomal membrane and functions in the export of matrix protein import receptor PEX5 from the peroxisomal membrane. Defects in PEX1, PEX6 or their membrane anchor causes dysfunction of peroxisomal matrix protein import cycle. In this study, we functionally characterized a putative Trypanosoma PEX1 orthologue by bioinformatic and experimental approaches and show that it is a true PEX1 orthologue. Using yeast two-hybrid analysis, we demonstrate that TbPEX1 can bind to TbPEX6. Endogenously tagged TbPEX1 localizes to glycosomes in the T. brucei parasites. Depletion of PEX1 gene expression by RNA interference causes lethality to the bloodstream form trypanosomes, due to a partial mislocalization of glycosomal enzymes to the cytosol and ATP depletion. TbPEX1 RNAi leads to a selective proteasomal degradation of both matrix protein import receptors TbPEX5 and TbPEX7. Unlike in yeast, PEX1 depletion did not result in an accumulation of ubiquitinated TbPEX5 in trypanosomes. As PEX1 turned out to be essential for trypanosomatid parasites, it could provide a suitable drug target for parasitic diseases. The results also suggest that these parasites possess a highly efficient quality control mechanism that exports the import receptors from glycosomes to the cytosol in the absence of a functional TbPEX1-TbPEX6 complex.
Validating the inactivation of viral pathogens with a focus on SARS-CoV-2 to safely transfer samples from high-containment laboratories
Authors: Chaki Sankar Prasad , Kahl-McDonagh Melissa M. , Neuman Benjamin W. , Zuelke Kurt A.
Published: March 2024

Introduction

Pathogen leak from a high-containment laboratory seriously threatens human safety, animal welfare, and environmental security. Transportation of pathogens from a higher (BSL4 or BSL3) to a lower (BSL2) containment laboratory for downstream experimentation requires complete pathogen inactivation. Validation of pathogen inactivation is necessary to ensure safety during transportation. This study established a validation strategy for virus inactivation.

Methods

SARS-CoV-2 wild type, delta, and omicron variants underwent heat treatment at 95°C for 10 minutes using either a hot water bath or a thermocycler. To validate the inactivation process, heat-treated viruses, and untreated control samples were incubated with A549-hACE2 and Vero E6-TMPRSS2-T2A-ACE2 cells. The cells were monitored for up to 72 hours for any cytopathic effects, visually and under a microscope, and for virus genome replication via RT-qPCR. The quality of post-treated samples was assessed for suitability in downstream molecular testing applications.

Results

Heat treatment at 95°C for 10 minutes effectively inactivated SARS-CoV-2 variants. The absence of cytopathic effects, coupled with the inability of virus genome replication, validated the efficacy of the inactivation process. Furthermore, the heat-treated samples proved to be qualified for COVID-19 antigen testing, RT-qPCR, and whole-genome sequencing.

Discussion

By ensuring the safety of sample transportation for downstream experimentation, this validation approach enhances biosecurity measures. Considerations for potential limitations, comparisons with existing inactivation methods, and broader implications of the findings are discussed.
Factor H-related protein 1 promotes complement-mediated opsonization of Pseudomonas aeruginosa
Authors: González-Alsina Alex , Martín-Merinero Héctor , Mateu-Borrás Margalida , Verd María , Doménech-Sánchez Antonio , Goldberg Joanna B. , Rodríguez de Córdoba Santiago , Albertí Sebastián
Published: March 2024

Pseudomonas aeruginosa is an important human opportunistic pathogen responsible for a wide range of infections. The complement system is the main early host defense mechanism to control these infections. P. aeruginosa counteracts complement attack by binding Factor H (FH), a complement regulator that inactivates C3b, preventing the formation of the C3-convertase and complement amplification on the bacterial surface. Factor H-related proteins (FHRs) are a group of plasma proteins evolutionarily related to FH that have been postulated to interfere in this bacterial mechanism of resisting complement. Here, we show that FHR-1 binds to P. aeruginosa via the outer membrane protein OprG in a lipopolysaccharide (LPS) O antigen-dependent manner. Binding assays with purified components or with FHR-1-deficient serum supplemented with FHR-1 show that FHR-1 competes with FH for binding to P. aeruginosa. Blockage of FH binding to C3b deposited on the bacteria reduces FH-mediated cofactor activity of C3b degradation, increasing the opsonization of the bacteria and the formation of the potent chemoattractant C5a. Overall, our findings indicate that FHR-1 is a host factor that promotes complement activation, facilitating clearance of P. aeruginosa by opsonophagocytosis.
Isolation and identification of Wickerhamiella tropicalis from blood culture by MALDI-MS
Authors: Takei Satomi , Teramoto Kanae , Fujimura Junya , Fujiwara Megumi , Suzuki Mai , Fukui Yukiko , Sekiguchi Yuji , Kawakami Takaaki , Chonan Masayoshi , Wakita Mitsuru , Horiuchi Yuki , Miida Takashi , Naito Toshio , Kirikae Teruo , Tada Tatsuya , Tabe Yoko
Published: March 2024

Wickerhamiella is a genus of budding yeast that is mainly isolated from environmental samples, and 40 species have been detected. The yeast isolated from human clinical samples usually only contain three species: W. infanticola, W. pararugosa and W. sorbophila. In this study, we isolated W. tropicalis from a blood sample of a six-year-old female with a history of B-cell precursor lymphoblastic leukemia in Japan in 2022. Though the strain was morphologically identified as Candida species by routine microbiological examinations, it was subsequently identified as W. tropicalis by sequencing the internal transcribed spacer (ITS) of ribosomal DNA (rDNA). The isolate had amino acid substitutions in ERG11 and FKS1 associated with azole and echinocandin resistance, respectively, in Candida species and showed intermediate-resistant to fluconazole and micafungin. The patient was successfully treated with micafungin. Furthermore, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) detected three novel peaks that are specific for W. tropicalis, indicating that MALDI-MS analysis is useful for rapid detection of Wickerhamiella species in routine microbiological examinations.
OSPS-MicroNet: a distilled knowledge micro-CNN network for detecting rice diseases
Authors: Tharani Pavithra P. , Baranidharan B.
Published: March 2024

More than half of the world's population relies on rice as their primary food source. In India, it is a dominant cereal crop that plays a significant role in the national economy, contributing to almost 17% of the GDP and engaging 60% of the population. Still, the agricultural sector faces numerous challenges, including diseases that can cause significant losses. Convolutional neural networks (CNNs) have proven effective in identifying rice diseases based on visual characteristics. However, CNNs require millions of parameters, resulting in high computational complexity, so deploying these models on limited-resource devices can be difficult due to their computational complexity. In this research, a lightweight CNN model named Oryza Sativa Pathosis Spotter (OSPS)-MicroNet is proposed. OSPS-MicroNet is inspired by the teacher-student knowledge distillation mechanism. The experimental results demonstrate that OSPS-MicroNet achieves an accuracy of 92.02% with only 0.7% of the network size of the heavyweight model, RESNET152. This research aims to create a more streamlined and resource-efficient model to detect rice diseases while minimizing demands on computational resources.
Clinical significance of regional constructive and wasted work in patients receiving cardiac resynchronization therapy
Authors: Wang Chun-Li , Wu Lung-Sheng , Wu Chia-Tung , Yeh Yung-Hsin , Cheng Yu-Wen , Yen Kun-Chi , Chan Yi-Hsin , Chuang Chi , Kuo Chi-Tai , Chu Pao-Hsien
Published: March 2024

Background

Previous studies have shown that global constructive work (CW) and wasted work (WW) predict response to cardiac resynchronization therapy (CRT). This study evaluated the predictive value of regional CW and WW for reverse remodeling and clinical outcomes after CRT.

Methods

We performed a prospective study involving 134 CRT candidates with left bundle branch block and left ventricular ejection fraction ≤35%. Global and regional CW and WW were calculated using pressure-strain loop analysis. CRT response was defined by reverse remodeling as a reduction of ≥15% in left ventricular end-systolic volume after six months.

Results

At six-month follow-up, 92 (69%) patients responded to CRT. Of the regional CW and WW measures, lateral wall (LW) CW and septal WW were most strongly and significantly correlated with reverse remodeling. At multivariate analysis, LW CW and septal WW were both independent determinants of reverse remodeling. When LW CW and septal WW were included in the model, global CW and WW were not independently associated with reverse remodeling. LW CW and septal WW predicted reverse remodeling with an area under the curve (AUC) of 0.783 (95% CI: 0.700–0.866) and 0.737 (95% CI: 0.644–0.831), respectively. Using both variables increased the AUC to 0.832 (95% CI: 0.755–0.908). Both LW CW ≤878 mmHg% (HR 2.01; 95% CI: 1.07–3.79) and septal WW ≤181 mmHg% (HR 2.60; 95% CI: 1.38–4.90) were significant predictors of combined death and HF hospitalization at two-year follow-up.

Conclusion

LW CW and septal WW before CRT are important determinants of reverse remodeling and clinical outcomes.
Structural and chemical changes in hardwood cell walls during early stages of flash pyrolysis
Authors: Lindstrom Jake K. , Peterson Chad A. , Ciesielski Peter N. , Ralph John , Chen Mingjie , Jakes Joseph E. , Johnston Patrick A. , Rollag Sean A. , Brown Robert C.
Published: March 2024

Volatile products from thermal decomposition of lignocellulosic biomass have been well characterized, but the solid- and liquid-phase reactions during the early stages of decomposition are largely unknown. Here the initial solid-phase biomass thermal deconstruction reactions were analyzed in situ and with high particle heating rates, delineating how these processes occur. A variety of instrumentation was used to quantify the extent and relative rates of deconstruction, demonstrating that biopolymers resist the thermally energetic conditions to differing degrees, even when ensconced in biomass cell walls. Hemicellulose and the more frangible lignin components decompose and volatilize more readily than cellulose, which temporarily enriches biomass with cellulose. These chemical changes manifest in larger cell wall structural and mechanical property transformations. In all, this investigation concludes that these solid-phase reactions strongly influence the production rates of volatile species and will require additional study before these processes can be modeled precisely to improve yields of desired product.
Research on hydro-photovoltaic complementary analysis of Yangfanggou hydropower station on Yalong River
Authors: He Bin , Yin Weixuan , Liang Guohua , Jiang Lei
Published: March 2024

Hydropower and photovoltaic power are widely used as clean energy sources around the world. Hydro-Photovoltaic complementary is precisely the use of the regulation performance of hydropower stations and the peak regulation performance of PV electric fields to improve the system’s power generation efficiency. The Yalong River basin as one of China’s clean energy bases, is rich in water and light resources. And now its midstream Yangfanggou hydropower station has just been completed, and the relevant PV electric field is in the construction planning stage. It is worth studying how to effectively utilize its hydropower and PV output resources. Therefore, Yangfanggou hydropower station and its PV electric field are taken as the research objects in this paper. The possibility of hydro-photovoltaic complementarity is analyzed within the year and day respectively. Then, a short-term scheduling model of hydro-photovoltaic complementarity is constructed according to the principle, and its operation mode and effect are optimized using the genetic algorithm NSGA-II. The results indicate that the annual power generation of the system is increased by about 1.4 billion kWh from the original hydropower through the hydro-photovoltaic complementary, and the annual guaranteed output is also increased with a large increase degree at the same time.
Composition and diversity of rhizosphere microorganisms of Suaeda salsa in the Yellow River Delta
Authors: Xu Hui , Li Na , Li Wenjuan , Wang Hongguo , Shao Yan , Liu Jingmei , Zhang Jiabo , Wang Jun , Shang Shuai
Published: March 2024

Introduction

Suaeda salsa is a typical wetland plant species in coastal areas that plays an important role in protecting the marine eco-environment. The rhizosphere microorganisms of S. salsa are responsible for its growth and development.

Method

Eighteen samples were collected from three areas, including the natural S. salsa-growing area (YDJ), artificial S. salsa restoration area (YDB), and nonrestoration area (BKS), and high-throughput sequencing technology was employed to explore the characteristics of the rhizosphere microorganisms of S. salsa in the Yellow River Delta.

Results

The results illustrated that the abundance and diversity of soil bacteria were highest in the YDJ group, fungal abundance was highest in the YDJ group, and fungal diversity was greatest in the YDB group. In total, 26,663 operational taxonomy units (OTUs) were found in soil bacteria, among which 9,095, 8,023, and 11,001 were detected in the BKS, YDB, and YDJ groups, respectively. 11,619 OTUs were found in soil fungi, among which 4,278, 4,552, and 5,100 were detected in the BKS, YDB, and YDJ groups, respectively. The YDJ group had the highest number of OTUs for bacteria and fungi among the three groups.

Discussion

S. salsa in natural wetland conditions tended to be similar to artificially restored S. salsa. The composition of fungi in the S. salsa rhizosphere had greater similarities than that of the bacteria. Proteobacteria had the highest abundance among bacterial communities, and Ascomycota, Basidiomycota, and Olpidiomycota were dominant in the fungal communities of the three groups. The correlation results found that power of hydrogen (pH) was significantly and negatively correlated with the abundance of Acidobacteriota and Proteobacteria. Meanwhile, electrical conductivity (EC) was significantly and positively correlated with the abundance of Firmicutes and negatively correlated with that of Proteobacteria. Regarding fungi, pH and EC were significantly and negatively correlated with the abundance of Chytridiomycota. Our findings provided some theoretical data for S. salsa conservation and wetland restoration.
Shrubs plays an important role in configuration of shelterbelt in windy and sandy areas
Authors: Zhang Shuai , Yuan Weijie , Yu Yi , Zhang Yaoxiang , Wang Weinan , Wang Luzhen , Yang Ying , Wang Haixia
Published: March 2024

Introduction

Planted forests are of great significance in reducing wind erosion and controlling degraded land, and are the main measure to improve the ecological environment in arid and semi-arid areas. Afforestation is mainly based on tall trees, but forest belts consume a large amount of water, bringing significant pressure to the environmental carrying capacity. While shrubs generally consume less water than do trees, it remains understudied what role shrubs play in configuration of shelterbelts in arid areas.

Methods

In this study, we conducted wind tunnel simulation experiments with the common used afforestation tree species Populus popularis and shrub species Salix psammophila. We set up single- or double-belt pure forest and mixed tree/shrub configurations, to analyze their effects on the wind speed, flow field, and wind prevention efficiency of different forest belt types.

Results

The results showed that: 1) the wind erosion resistance of the double-belt shelter forest was stronger than that of a single-belt forest. 2) Shelterbelts consisting of trees had a strong resistance to airflow disturbances, but their protective effect was reflected mainly in the canopy layer, with poor near-surface protection. 3) Shelterbelts consisting of shrubs had a good protective effect within effective height, and the wind speed in the double-shrub forest belt was 77% of that in the single-tree forest belt. 4) The wind prevention efficiency within the shrub forest belt was better than that of the tree forest belt, with wind prevention efficiency exceeding 40% in most double-shrub forests. Shrubs as a supplement to trees could increase the minimum wind prevention efficiency by up to 30%.

Discussion

Therefore, the role of shrubs should be emphasized in afforestation in arid areas, especially in areas that need near-surface protection.
Tree growth at the limits: the response of multiple conifers to opposing climatic constraints along an elevational gradient in the Alps
Authors: Obojes Nikolaus , Buscarini Serena , Meurer Armin Konrad , Tasser Erich , Oberhuber Walter , Mayr Stefan , Tappeiner Ulrike
Published: March 2024

Introduction

Climate change affects the vitality of mountain forests through increasing temperatures and decreasing water availability due to changing precipitation patterns, earlier snowmelt, and increasing evaporative demand. Depending on species characteristics, tree growth might therefore increase in cold habitats near the forest line but decrease in water-limited conditions at low elevation.

Methods

We analyzed the tree-ring widths of five conifers (Picea abies, Larix decidua, Pinus sylvestris, Pinus nigra, and Pinus cembra) along an elevational gradient from 1,000 m to 2,320 m above sea level (a.s.l.) in Vinschgau/Val Venosta Valley in Northern Italy, one of the driest regions of the Alps (mean annual precipitation of 682 mm at 1,310 m a.s.l.).

Results

Our aim was to estimate the species-specific growth response to changing climate conditions along an elevational gradient. At low elevations, we observed a significant response to water availability not only during the actual growing season but also throughout the previous autumn for all species present. At mid-elevation, the correlation coefficients to precipitation and drought indices (SPEI) were highest for Picea abies. At high elevations, the positive correlation of growth with temperature was smaller than expected for Pinus cembra. In contrast, Larix decidua responded positively to temperature and grew faster in recent decades.

Discussion

Considering that a further increase in temperatures will reduce plant water availability during the growing season, our space-for-time approach provides an outlook on future growth conditions of conifers in larger regions of the European Alps. Water limitation will affect tree growth and vitality not only at low elevation in the valleys but also at mid elevation on mountain slopes, potentially impacting timber production and protective and recreative functions of forests. Near the forest line, the different capabilities of tree species to benefit from higher temperatures might lead to changes in species composition.
Comparative stigmatic transcriptomics reveals self and cross pollination responses to heteromorphic incompatibility in Plumbago auriculata Lam.
Authors: Hu Di , Lin Di , Yi Shouli , Gao Suping , Lei Ting , Li Wenji , Xu Tingdan
Published: March 2024

“Heteromorphic self-incompatibility” (HetSI) in plants is a mechanism of defense to avoid self-pollination and promote outcrossing. However, the molecular mechanism underlying HetSI remains largely unknown. In this study, RNA-seq was conducted to explore the molecular mechanisms underlying self-compatible (SC, “T × P” and “P × T”) and self-incompatible (SI, “T × T” and “P × P”) pollination in the two types of flowers of Plumbago auriculata Lam. which is a representative HetSI plant. By comparing “T × P” vs. “T × T”, 3773 (1407 upregulated and 2366 downregulated) differentially expressed genes (DEGs) were identified, 1261 DEGs between “P × T” and “P × P” (502 upregulated and 759 downregulated). The processes in which these DEGs were significantly enriched were “MAPK (Mitogen-Activated Protein Kinases-plant) signaling pathway”, “plant-pathogen interaction”,“plant hormone signal transduction”, and “pentose and glucuronate interconversion” pathways. Surprisingly, we discovered that under various pollination conditions, multiple notable genes that may be involved in HetSI exhibited distinct regulation. We can infer that the HetSI strategy might be unique in P. auriculata. It was similar to “sporophytic self-incompatibility” (SSI) but the HetSI mechanisms in pin and thrum flowers are diverse. In this study, new hypotheses and inferences were proposed, which can provide a reference for crop production and breeding.
Functional significance of DNA methylation: epigenetic insights into Sjögren’s syndrome
Authors: Wang Yanqing , Riaz Farooq , Wang Wei , Pu Jincheng , Liang Yuanyuan , Wu Zhenzhen , Pan Shengnan , Song Jiamin , Yang Lufei , Zhang Youwei , Wu Huihong , Han Fang , Tang Jianping , Wang Xuan
Published: March 2024

Sjögren’s syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.
Rapid isolation of pan-neutralizing antibodies against Omicron variants from convalescent individuals infected with SARS-CoV-2
Authors: Yu Peng , Ran Jingping , Yang Ruiqi , Zhu Hang , Lu Song , Wu Yuzhang , Zhao Tingting , Xiong Tianchen
Published: March 2024

Introduction

The emergence of SARS-CoV-2 Omicron subvariants has presented a significant challenge to global health, as these variants show resistance to most antibodies developed early in the pandemic. Therapeutic antibodies with potent efficacy to the Omicron variants are urgently demanded.

Methods

Utilizing the rapid antibody discovery platform, Berkeley Lights Beacon, we isolated two monoclonal neutralizing antibodies, 2173-A6 and 3462-A4. These antibodies were isolated from individuals who recently recovered from Omicron infections.

Results

Both antibodies, 2173-A6 and 3462-A4, demonstrated high affinity for the RBD and effectively neutralized pseudoviruses from various Omicron lineages, including BA.4/5, XBB.1.16, XBB.1.5, and EG.5.1. This neutralization was achieved through binding to identical or overlapping epitopes.

Discussion

The use of the Beacon platform enabled the rapid isolation and identification of effective neutralizing antibodies within less than 10 days. This process significantly accelerates the development of novel therapeutic antibodies, potentially reducing the time required to respond to unknown infectious diseases in the future.
The effect of contextual factors on a health intervention against podoconiosis in Ethiopia
Authors: Engdawork Kibur , Tadele Getnet , Nahar Papreen , Davey Gail , Zaman Shahaduz
Published: March 2024

Introduction

Understanding contextual factors that influence the implementation and outcome of interventions is crucial to improving them. Outcome and process evaluation studies have to date focused on the successes and limitations of interventions with little consideration of external factors that could either facilitate or impede them. Guided by the Context and Implementation of Complex Intervention (CICI) framework, we evaluated the effect of contextual factors on a health intervention implemented against the neglected tropical disease (NTD) podoconiosis in Ethiopia.

Method

We purposefully selected a health intervention jointly implemented by two NGOs in podoconiosis-endemic districts in Northwestern Ethiopia. We employed an exploratory mixed methods approach, and data were collected between April and July 2022. We first conducted document analysis, observations, 4 focus group discussions, 32 in-depth interviews and 19 key informant interviews. Subsequently, we administered a survey to 369 rural residents, of whom 42 were affected by podoconiosis. The qualitative data were managed with NVivo version 12 software. The quantitative data were analyzed using Stata version 15 software.

Results

Most project activities were implemented as per the initial plan and the intervention reached patients that never had access to treatment services before. Contextual factors (geographical, epidemiological, socio-economic, socio-cultural, ethical, legal and political) and lived experience of patients influenced the implementation and outcome of the intervention. Most of the contextual factors pose constraints on implementation and affected the acceptability and sustainability of project activities. On the other hand, political context such the commitment of the government to rollout national programs and set up NTD structures at district level positively influenced the implementation of the intervention.

Conclusion

Health intervention implementors should be aware of the interactive effects of contextual factors wherein interventions are put into practice. Minimizing the constraining effects of these contextual factors while utilizing opportunities presented by them might help implement optimal strategies to improve the lives of individuals affected by podoconiosis and similar NTDs.
Ecology of arboviruses and their potential mosquito vectors in Benin, Côte d’Ivoire and Gabon: a mini review
Authors: Manouana Gédéon Prince , Sarah-Matio Elangwe-Milo , Hellhammer Fanny , Zahouli Julien Zahouli Bi , Tapé Aurélien Sery Bahi , Biré Yasmine Nandy , Dibo Jean-Denis Kacou , Houriaaidji Guiéno Edwige , Maganga Gaël Darren , Koumba Jumafra Perside , Zinsou Jeannot Frejus , Ongouta-Mafia Grace Cherile , Boussougou-Sambe Terence Stravensky , Djogbenou Luc Salako , Medjigbodo Adandé , Djihinto Oswald , Mavoungou Jacques F. , Mintsa-Nguema Rodrigue , Adegnika Ayola Akim , Borrmann Steffen , Becker Stefanie C.
Published: March 2024

Mosquito-borne arboviral zoonoses are an increasingly (re-)emerging threat for millions of people in endemic countries of Africa. Aedes-transmitted yellow fever (YF), dengue (DEN), chikungunya (CHIK), and Zika (ZIK) viruses, as well as Aedes- and Culex transmitted Rift Valley fever virus (RVFV) infections often go undiagnosed and as a result, accurate clinical reports for these viral diseases are lacking. The absence of evidence-based risk maps for arbovirus infections hinders the implementation of more suitable prevention/surveillance and control strategies in both non-endemic and endemic African countries. The vectorial capacity of arbovirus-transmitting vectors is highly complex mainly due to the interplay between biotic and abiotic factors that vary in time and space, explaining the differential patterns of arbovirus diseases between countries. Mapping the influential factors of arbovirus transmission, such as vector ecology, behavior, and biology in countries with different outcomes of arboviral diseases, will strongly help improve our understanding of local epidemiology and circulation of these diseases. Herein, we review up-to-date data on the distribution of arboviruses and their respective vectors from three sub-Saharan African countries (Benin, Côte d’Ivoire, and Gabon) presenting different patterns of arbovirus diseases. We pinpointed major knowledge gaps and potential research interests to increase knowledge of the distribution of arboviral diseases and their vectors through African countries to improve the strategies to successfully prevent, monitor, and control the disease outbreak.
Podocyte number and glomerulosclerosis indices are associated with the response to therapy for primary focal segmental glomerulosclerosis
Authors: de Zoysa Natasha , Haruhara Kotaro , Nikolic-Paterson David J. , Kerr Peter G. , Ling Jonathan , Gazzard Sarah E. , Puelles Victor G. , Bertram John F. , Cullen-McEwen Luise A.
Published: March 2024

Corticosteroid therapy, often in combination with inhibition of the renin-angiotensin system, is first-line therapy for primary focal and segmental glomerulosclerosis (FSGS) with nephrotic-range proteinuria. However, the response to treatment is variable, and therefore new approaches to indicate the response to therapy are required. Podocyte depletion is a hallmark of early FSGS, and here we investigated whether podocyte number, density and/or size in diagnostic biopsies and/or the degree of glomerulosclerosis could indicate the clinical response to first-line therapy. In this retrospective single center cohort study, 19 participants (13 responders, 6 non-responders) were included. Biopsies obtained at diagnosis were prepared for analysis of podocyte number, density and size using design-based stereology. Renal function and proteinuria were assessed 6 months after therapy commenced. Responders and non-responders had similar levels of proteinuria at the time of biopsy and similar kidney function. Patients who did not respond to treatment at 6 months had a significantly higher percentage of glomeruli with global sclerosis than responders (p < 0.05) and glomerulosclerotic index (p < 0.05). Podocyte number per glomerulus in responders was 279 (203–507; median, IQR), 50% greater than that of non-responders (186, 118–310; p < 0.05). These findings suggest that primary FSGS patients with higher podocyte number per glomerulus and less advanced glomerulosclerosis are more likely to respond to first-line therapy at 6 months. A podocyte number less than approximately 216 per glomerulus, a GSI greater than 1 and percentage global sclerosis greater than approximately 20% are associated with a lack of response to therapy. Larger, prospective studies are warranted to confirm whether these parameters may help inform therapeutic decision making at the time of diagnosis of primary FSGS.
Evaluation of serum and urine biomarkers for severe COVID-19
Authors: Shansky Yaroslav D. , Yanushevich Oleg O. , Gospodarik Alina V. , Maev Igor V. , Krikheli Natella I. , Levchenko Oleg V. , Zaborovsky Andrew V. , Evdokimov Vladimir V. , Solodov Alexander A. , Bely Petr A. , Andreev Dmitry N. , Serkina Anna N. , Esiev Sulejman S. , Komarova Anastacia V. , Sokolov Philip S. , Fomenko Aleksei K. , Devkota Mikhail K. , Tsaregorodtsev Sergei V. , Bespyatykh Julia A.
Published: March 2024

Introduction

The new coronavirus disease, COVID-19, poses complex challenges exacerbated by several factors, with respiratory tissue lesions being notably significant among them. Consequently, there is a pressing need to identify informative biological markers that can indicate the severity of the disease. Several studies have highlighted the involvement of proteins such as APOA1, XPNPEP2, ORP150, CUBN, HCII, and CREB3L3 in these respiratory tissue lesions. However, there is a lack of information regarding antibodies to these proteins in the human body, which could potentially serve as valuable diagnostic markers for COVID-19. Simultaneously, it is relevant to select biological fluids that can be obtained without invasive procedures. Urine is one such fluid, but its effect on clinical laboratory analysis is not yet fully understood due to lack of study on its composition.

Methods

Methods used in this study are as follows: total serum protein analysis; ELISA on moderate and severe COVID-19 patients’ serum and urine; bioinformatic methods: ROC analysis, PCA, SVM.

Results and discussion

The levels of antiAPOA1, antiXPNPEP2, antiORP150, antiCUBN, antiHCII, and antiCREB3L3 exhibit gradual fluctuations ranging from moderate to severe in both the serum and urine of COVID-19 patients. However, the diagnostic value of individual anti-protein antibodies is low, in both blood serum and urine. On the contrary, joint detection of these antibodies in patients’ serum significantly increases the diagnostic value as demonstrated by the results of principal component analysis (PCA) and support vector machine (SVM). The non-linear regression model achieved an accuracy of 0.833. Furthermore, PCA aided in identifying serum protein markers that have the greatest impact on patient group discrimination. The study revealed that serum serves as a superior analyte for describing protein quantification due to its consistent composition and lack of organic salts and drug residues, which can otherwise affect protein stability.
Transcriptomic analysis and carbohydrate metabolism-related enzyme expression across different pH values in Rhizopus delemar
Authors: Liang Jinpeng , Chen Yulan , Li Sisi , Liu Dongyang , Tian Hong , Xiang Quanju , Zhao Ke , Yu Xiumei , Chen Qiang , Fan Hongzhu , Zhang Lingzi , Penttinen Petri , Gu Yunfu
Published: March 2024

Introduction

pH is one of the important factors affecting the growth and performance of microorganisms.

Methods

We studied the pH response and plant growth-promoting (PGP) ability of Rhizopus delemar using cultivation experiments and transcriptomics, and verified the expression profiles using quantitative real-time PCR.

Results

pH affected the growth and PGP properties of R. delemar. At pH 7, the growth rate of R. delemar was rapid, whereas pH 4 and 8 inhibited mycelial growth and PGP ability, respectively. In the pot experiment, the plant height was the highest at pH 7, 56 cm, and the lowest at pH 4 and pH 5, 46.6 cm and 47 cm, respectively. Enzyme activities were highest at pH 6 to pH 7. Enzyme activities were highest at pH 6 to pH 7. Among the 1,629 differentially expressed genes (DEGs), 1,033 genes were up-regulated and 596 were down-regulated. A total of 1,623 DEGs were annotated to carbohydrate-active enzyme coding genes.

Discussion

The PGP characteristics, e.g., Phosphorus solubilization ability, of R. delemar were strongest at pH 7. The results provide useful information regarding the molecular mechanism of R. delemar pH response.
Analysis on metabolic functions of rhizosphere microbial communities of Pinus massoniana provenances with different carbon storage by Biolog Eco microplates
Authors: Huang Zichen , Qin Yiyun , He Xin , Zhang Mengyang , Ren Xingyue , Yu Wenya , Ji Kongshu
Published: March 2024

Introduction

Rhizosphere microorganisms are influenced by vegetation. Meanwhile, they respond to vegetation through their own changes, developing an interactive feedback system between microorganisms and vegetation. However, it is still unclear whether the functional diversity of rhizosphere soil microorganisms varies with different carbon storage levels and what factors affect the functional diversity of rhizosphere soil microorganisms.

Methods

In this study, the Biolog-Eco microplate technique was used to analyze the metabolic diversity of carbon source of rhizosphere soil microorganisms from 6 Pinus massoniana provenances with three levels of high, medium and low carbon storage.

Results

The results showed that the average well color development(AWCD) value of rhizosphere microorganisms was significantly positive correlated with carbon storage level of Pinus massoniana (p < 0.05). The AWCD value, Simpson and Shannon diversity of high carbon sequestrance provenances were 1.40 (144h incubation) 0.96 and 3.24, respectively, which were significantly higher (p < 0.05) than those of other P. massoniana provenances. The rhizosphere microbial AWCD, Shannon and Simpson diversity of the 6 provenances showed the same variation trend (SM>AY>QJ>SX>HF>SW). Similarly, microbial biomass carbon (MBC) content was positively correlated with carbon storage level, and there were significant differences among high, medium and low carbon storage provenances. The PCA results showed that the differences in the carbon source metabolism of rhizosphere microorganisms were mainly reflected in the utilization of amino acids, carboxylic acids and carbohydrates. Pearson correlation analysis showed that soil organic carbon (SOC), total nitrogen (TN) and pH were significantly correlated with rhizosphere AWCD (p < 0.05).

Conclusion

Soil properties are important factors affecting rhizosphere microbial carbon source metabolism. The study confirmed that the microorganisms of high carbon storage provenances had relatively high carbon metabolic activity. Among them, the carbon metabolic activity of rhizosphere microorganisms of SM provenance was the highest, which was the preferred provenances in effective ecological service function.
The mediating effect of 18F-FDG metabolism in right caudate between depressive symptoms and cognitive function in Alzheimer’s disease
Authors: Wang Bojun , Cui Chunlei , Chen Yifan , Liang Zhigang
Published: March 2024

Purpose

The objective of this study was to investigate the accumulation of 18F-fluorodeoxyglucose (18F-FDG) in the whole brain between Alzheimer’s disease (AD) with depressive (ADD) symptoms compared with AD without depressive (ADND) symptoms using positron emission tomography/magnetic resonance imaging (PET/MRI). Additionally, this study aimed to explore the associations among the accumulation of 18F-FDG in the brain, depressive symptoms, and cognitive function in ADD patients.

Methods

In this study, 25 AD patients and 22 healthy controls were enrolled. The AD patients were stratified into two groups, namely ADD and ADND, based on their scores of the Hamilton Depression Scale (HAMD). Both AD patients and healthy controls underwent an 18F-FDG PET/MRI scan. A standardized uptake value ratio (SUVR) was calculated to examine the accumulation of 18F-FDG in the brain. A simple mediation model was employed to examine the mediation effect between SUVR, depressive symptoms and cognitive function in ADD patients.

Results

The ADD group exhibited significant cognitive impairment compared to the ADND group (p < 0.001) and healthy controls (p < 0.001). The ADD patients exhibited the reduced SUVR (0.228 ± 0.126) in the right caudate (the voxel level p < 0.005, cluster level p < 0.05, after false discovery rate (FDR) correction) compared to ADND patients (0.459 ± 0.064) and healthy controls (0.706 ± 0.122). The SUVR of the right caudate was correlated with the HAMD scores (r = −0.792, p < 0.001) and mini-mental state examination (MMSE) (r = 0.738, p < 0.01). The relationship between depressive symptoms and the cognitive function in ADD patients is mediated by the right caudate SUVR (total effects = −0.385, direct effects = −0.02, total indirect effects = −0.405).

Conclusion

The ADD group exhibited the reduced SUVR in the right caudate compared to the ADND group and healthy controls. The relationship between depressive symptoms and the cognitive ability of AD patients was mediated by the right caudate SUVR. The results contribute to a deeper understanding of the neurobiological mechanisms related to AD with depressive symptoms.
Slowing Alzheimer’s disease progression through probiotic supplementation
Authors: Medeiros Destynie , McMurry Kristina , Pfeiffer Melissa , Newsome Kayla , Testerman Todd , Graf Joerg , Silver Adam C. , Sacchetti Paola
Published: March 2024

The lack of affordable and effective therapeutics against cognitive impairment has promoted research toward alternative approaches to the treatment of neurodegeneration. In recent years, a bidirectional pathway that allows the gut to communicate with the central nervous system has been recognized as the gut-brain axis. Alterations in the gut microbiota, a dynamic population of trillions of microorganisms residing in the gastrointestinal tract, have been implicated in a variety of pathological states, including neurodegenerative disorders such as Alzheimer’s disease (AD). However, probiotic treatment as an affordable and accessible adjuvant therapy for the correction of dysbiosis in AD has not been thoroughly explored. Here, we sought to correct the dysbiosis in an AD mouse model with probiotic supplementation, with the intent of exploring its effects on disease progression. Transgenic 3xTg-AD mice were fed a control or a probiotic diet (Lactobacillus plantarum KY1032 and Lactobacillus curvatus HY7601) for 12  weeks, with the latter leading to a significant increase in the relative abundance of Bacteroidetes. Cognitive functions were evaluated via Barnes Maze trials and improvements in memory performance were detected in probiotic-fed AD mice. Neural tissue analysis of the entorhinal cortex and hippocampus of 10-month-old 3xTg-AD mice demonstrated that astrocytic and microglial densities were reduced in AD mice supplemented with a probiotic diet, with changes more pronounced in probiotic-fed female mice. In addition, elevated numbers of neurons in the hippocampus of probiotic-fed 3xTg-AD mice suggested neuroprotection induced by probiotic supplementation. Our results suggest that probiotic supplementation could be effective in delaying or mitigating early stages of neurodegeneration in the 3xTg-AD animal model. It is vital to explore new possibilities for palliative care for neurodegeneration, and probiotic supplementation could provide an inexpensive and easily implemented adjuvant clinical treatment for AD.