bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnosis and management of atrial fibrillation in primary care: a case study
Authors: Willetts Christopher
Published: February 2024

This critically reflective case study will look at a 65-year-old male presenting with dyspnoea and an incidental diagnosis of atrial fibrillation (AF) in a primary care setting. The article critically analyses the diagnosis and management of the patient, considers potential differential diagnoses, current guidelines, and areas for service improvement. The author, a trainee advanced clinical practitioner (ACP) prescriber with a paramedic background, discusses the complexity of managing AF and the need for collaboration with a general practitioner. AF is a common cardiac arrhythmia associated with a significantly increased risk of stroke. The primary focus of AF management is stroke prevention. This article delves into the pathophysiology of AF, discussing its various causes and classifications, emphasising the role of left atrial appendage (LAA) in stroke risk. The limitations of AF screening methods, especially for paroxysmal AF, are also discussed. Recent advancements in opportunistic screening, including the use of artificial intelligence (AI) and smartwatches, show promise but require further research and validation. This article explores stroke risk assessment tools like CHA2DS2VASc and ATRIA, bleeding risk assessment using HAS-BLED and ORBIT scores, as well as rhythm control in newly diagnosed AF cases. Finally, the importance of lifestyle modifications and regular patient follow-up are underscored. AF diagnosis and management are multifaceted, involving stroke prevention, rate or rhythm control, and lifestyle modifications. Technological advancements hold promise in improving early AF detection. Collaborative efforts between healthcare providers and adherence to current guidelines are crucial in achieving optimal patient outcomes, while future practice may benefit from enhanced diagnostic screening and treatment options as further research unfolds.
Transcriptomic analyses and machine-learning methods reveal dysregulated key genes and potential pathogenesis in human osteoarthritic cartilage
Authors: Zhao Di , Zeng Ling-feng , Liang Gui-hong , Luo Ming-hui , Pan Jian-ke , Dou Yao-xing , Lin Fang-zheng , Huang He-tao , Yang Wei-yi , Liu Jun
Published: February 2024

Aims

This study aimed to explore the biological and clinical importance of dysregulated key genes in osteoarthritis (OA) patients at the cartilage level to find potential biomarkers and targets for diagnosing and treating OA.

Methods

Six sets of gene expression profiles were obtained from the Gene Expression Omnibus database. Differential expression analysis, weighted gene coexpression network analysis (WGCNA), and multiple machine-learning algorithms were used to screen crucial genes in osteoarthritic cartilage, and genome enrichment and functional annotation analyses were used to decipher the related categories of gene function. Single-sample gene set enrichment analysis was performed to analyze immune cell infiltration. Correlation analysis was used to explore the relationship among the hub genes and immune cells, as well as markers related to articular cartilage degradation and bone mineralization.

Results

A total of 46 genes were obtained from the intersection of significantly upregulated genes in osteoarthritic cartilage and the key module genes screened by WGCNA. Functional annotation analysis revealed that these genes were closely related to pathological responses associated with OA, such as inflammation and immunity. Four key dysregulated genes (cartilage acidic protein 1 (CRTAC1), iodothyronine deiodinase 2 (DIO2), angiopoietin-related protein 2 (ANGPTL2), and MAGE family member D1 (MAGED1)) were identified after using machine-learning algorithms. These genes had high diagnostic value in both the training cohort and external validation cohort (receiver operating characteristic > 0.8). The upregulated expression of these hub genes in osteoarthritic cartilage signified higher levels of immune infiltration as well as the expression of metalloproteinases and mineralization markers, suggesting harmful biological alterations and indicating that these hub genes play an important role in the pathogenesis of OA. A competing endogenous RNA network was constructed to reveal the underlying post-transcriptional regulatory mechanisms.

Conclusion

The current study explores and validates a dysregulated key gene set in osteoarthritic cartilage that is capable of accurately diagnosing OA and characterizing the biological alterations in osteoarthritic cartilage; this may become a promising indicator in clinical decision-making. This study indicates that dysregulated key genes play an important role in the development and progression of OA, and may be potential therapeutic targets.

Cite this article: Bone Joint Res 2024;13(2):66–82.
Antimicrobial and FAD synthetases modulating activities of leporins A-C isolated from the sponge-associated fungus Trichoderma sp.
Authors: LOSUNG FITJE , GINTING ELVY L. , ABDJUL BOBBY , KAPOJOS MAGIE M. , MAARISIT WILMAR , MENTANG FENY , SUMILAT DEISKE A. , BALANSA WALTER , MANGINDAAN REMY E. P.
Published: February 2024

Abstract. Losung F, Ginting EL, Abdjul B, Kapojos MM, Maarisit W, Mentang F, Sumilat DA, Balansa W, Mangindaan REP. 2023. Antimicrobial and FAD synthetases modulating activities of leporins A-C isolated from the sponge-associated fungus Trichoderma sp. Biodiversitas 24: 6502-6515. The emergence of microbial resistance poses a formidable threat to human health, requiring the discovery of new antibiotics. In this study, we investigated the antimicrobial potential and molecular structures of the metabolites produced by a sponge's symbiont fungal species, Trichoderma sp., in vitro against S. aureus IAM 12544T and Candida albicans IFM 4954 and in-silico against the emerging antibacterial target, prokaryotic bifunctional synthetases (FADS). The molecular structures were determined using spectroscopic techniques (1D, 2D NMR, HRESIMS), while the assessment of biological activities, physicochemical properties, and molecular modifications was performed through a slightly modified disk agar diffusion method, molecular docking, SwissAdme and pkCMS tools, and bioisosterism, respectively. The analysis of spectroscopic data supported the identification of leporins A-C (1-3) as the metabolites, which exhibited strong binding affinities against the 2X0K protein target (-8.9 to -9.4 kcal/mol). Despite their being slightly weaker than known FADS modulators such as compounds 4 (-10.5 kcal/mol) and 5 (-10.5 kcal/mol), leporins A-C demonstrated a stronger binding affinity than compound 6 (-9.6 to -10.5 kcal/mol). Notably, substituting a methyl group with a fluorine atom in 1-3 resulted in lepofluorins A-C (1a-3a), which exhibited enhanced binding affinities and improved physicochemical properties compared to the existing FADS modulators. These findings suggest that leporins A-C (1-3), particularly lepofluorins A-C (1a-3a), have potential as putative novel modulators of FADS. This study provides valuable insights into the design and development of new antibiotics to combat microbial resistance.
The characteristics of PUFAs-rich virgin fish oil as affected by size of tuna eye
Authors: TRILAKSANI WINI , RIYANTO BAMBANG , RAMADHAN WAHYU , SINULINGGA FAHRI , FAUZIAH SILVA
Published: February 2024

Abstract. Trilaksani W, Riyanto B, Ramadhan W, Sinulingga F, Fauziah S. 2023. The characteristics of PUFAs-rich virgin fish oil as affected by size of tuna eye. Biodiversitas 24: 6545-6556. The food supplement market expects growth in demand for long-chain omega-3 fatty acids, particularly Eicosapentaenoic Acid (EPA) and Docosahexaenoic Acid (DHA), which play crucial for brain development and can lower the chances of health issues like depression, Myocardial Infarction (MI), thromboembolism, and cardiac arrhythmias, and have anti-viral effects, boosting the immune system during the pandemic. Therefore, to meet this demand, exploring new sources is crucial. Tuna eyes have emerged as a potential source of DHA; however, quality and standardized sizes pose a challenge as they are by-products. The purpose of this research was to determine how the eye size of tuna affected the quality and yield of fish oil, which is a novel source of omega-3 fatty acids. This study determined the virgin oil profile of tuna eyes, which met the quality standards. The investigation covered morphology, chemical composition, heavy metal content, oil yield and quality, fatty acid composition, and related health lipid indices (Atherogenicity Index (AI) and Thrombogenicity Index (TI)). For the size specifications, tuna eyes were classified into three groups based on their diameter, namely 'small' (<6 cm), 'medium' (6-9 cm), and 'large' (>9 cm). The results showed that eye size directly influenced the weight, fat content, and oil yield, with negligible disparity in chemical composition except for the fat content; the larger the eyes, the higher the oil yield. Tuna eye oil had a safe composition for consumption with low or undetected heavy metals, the oil's oxidative level met CODEX standards, and the fatty acid profile revealed DHA as the most abundant fatty acid, reaching 36.95%. The predominance of n-3 series values in the fatty acid composition of tuna's eye was 9-12 times greater than that of n-6 fatty acid values. The values of AI and TI were 0.33 and 0.12; 0.47 and 0.20; 0.55 and 0.20 for large, small, and medium eyes, respectively. The study highlights tuna eyes' unique characteristics and potential applications in the food supplement industry.
Evaluation of antifungal activity against Corynespora cassiicola by bacteria isolated from soil in the root zone of cucumber plants
Authors: DUY LE QUOC
Published: February 2024

Abstract. Duy LQ. 2023. Evaluation of antifungal activity against Corynespora cassiicola by bacteria isolated from soil in the root zone of cucumber plants. Biodiversitas 24: 6584-6591. Target leaf spot caused by Corynespora cassiicola poses a major disease threat to cucumber cultivation worldwide. Reliance on chemical fungicides has raised resistance to environmental and health concerns. As cucumber production expands globally, sustainable solutions are needed. Plant Growth-Promoting Rhizobacteria (PGPR) show promise but remain underexplored against C. cassiicola in cucumber. This study aimed to assess the potency of rhizobacteria in antagonistic activity against C. cassiicola, causing cucumber target leaf spots under in vitro conditions. The present study isolated bacterial strains from cucumber soil rhizosphere and screened for antifungal activity against C. cassiicola using dual culture assays. Using quantitative assays, selected antagonistic strains were further assessed for key biocontrol traits, including ?-1,3-glucanase, chitinase, and siderophore production. Cell-free supernatants were tested for direct fungal growth inhibition using the environmental toxicity. Isolated PGPR strains showed robust C. cassiicola inhibition from 39.8% to 62.6% growth reduction. Most antagonistic isolates produced ?-1,3-glucanase, chitinase, and siderophores and suppressed pathogen growth via metabolites in their supernatants. These results demonstrate multiple biocontrol mechanisms, including enzymatic degradation of fungal cell walls, iron competition through siderophores, and antimicrobial compound secretion. Bacillus siamensis strain TV16 exhibited the strongest overall antagonism against C. cassiicola. These findings reveal the biocontrol potential of PGPR for managing cucumber-target leaf-spot disease, offering a sustainable alternative to chemical pesticides. With further optimization and field testing, PGPR-based biopesticides can be integrated into cucumber production to improve crop health while reducing fungicide reliance.
Seagrass diversity in Pulau Banyak, Aceh Singkil District, Indonesia
Authors: ERNIATI ERNIATI , ANDIKA YUDHO , IMANULLAH IMANULLAH , IMAMSHADIQIN IMAMSHADIQIN , ERLANGGA ERLANGGA , RAHMAD RAHMAD , TAULADAN TOHA ALI , SIREGAR FAUJIAH REZEKI , FITRI ANDIRA , RITONGA GARA HASONANGAN
Published: February 2024

Abstract. Erniati, Andika Y, Imanullah, Imamshadiqin, Erlangga, Rahmad, Tauladan TA, Siregar FR, Fitri A, Ritonga GH. 2023. Seagrass diversity in Pulau Banyak, Aceh Singkil District, Indonesia. Biodiversitas 24: 6621-6628. Seagrass is a high-level plant where life activities are submerged in seawater. Currently, the seagrass ecosystem is threatened with destruction and disappearance. The extent of seagrass ecosystems globally was estimated to have declined by about 58%. The solution to this problem is to balance local communities' utilization of biological resources and biodiversity maintenance. The biodiversity aspect of seagrass is key to the sustainability of seagrass ecosystems. Banyak Island is one of the sub-districts in Aceh Singkil Regency, which consists of a cluster of small islands and has rich fisheries and marine potential, one of them is seagrass, where station 1 is Balong Island, Stasion 2 is Balong Island, Stasion 3 is Lamun Island and Stasion 4 is Rago-Rago Island. This study aimed to assess the diversity of seagrass beds, including seagrass species composition, density, percentage cover, and water quality that affect the existence of seagrass ecosystems. This study used a purposive sampling method with 3 transect lines spaced 50 m perpendicular from the shoreline to the sea. Each transect line has 5 plots with a distance of 10 meters measuring 50 x 50 cm2, and the water quality parameters were measured in situ. This research found 5 seagrass species, namely T. hemprichii, C. rotundata, E. acroides, S. isoetifolium, and H. ovalis. C. rotundata is the species with the highest density on Matahari Island, but seagrass diversity is low, and no species were dominant in the groups. The results of PCA analysis showed that the environmental factors that most influenced the pattern of seagrass distribution and density were nitrate, phosphate, and substrate. The conclusion revealed that seagrass diversity on Banyak Islands is relatively low.
Comparative anatomical characters of the genus Aerides Lour. (Orchidaceae) in Thailand
Authors: TOKAEW WORACHAT , KRUBKRATOKE DUANGMANEE , PAYAKDET SAOWALAK , PHROMPRASIT PHUTSADEE
Published: February 2024

Abstract. Tokaew W, Krubkratoke D, Payakdet S, Phromprasit P. 2023. Comparative anatomical characters of the genus Aerides Lour. (Orchidaceae) in Thailand. Biodiversitas 24: 6641-6651. The genus Aerides Lour. belonging to the subfamily Epidendroideae (Orchidaceae), which are ornamental plants in Thailand. The identification of Thai Aerides is mostly based on the flower morphology which is a short period. The vegetative parts of Aerides species have similar characters. The anatomical data are also helpful for the identification of the Aerides species. Therefore, this study aimed to observe the vegetative stages (leaf and root) of seven species of Aerides in Thailand. Permanent slides of the leaf epidermis were prepared by epidermal peeling and stained with safranin. Transverse sections of leaf lamina and root were prepared using the paraffin method with a rotary microtome. They were then stained with safranin and fast green, examined using a light microscope, and their anatomical characteristics were described. The results showed that certain anatomical characteristics can be used for species identification, including distribution of stomata, presence of crystals, types of crystals, xylem arches in the root, shapes of the midrib and margin, and presence of starch grains. The key to species of Aerides species in Thailand based on anatomy characters is constructed. Anatomical features can be used for taxonomically important data and provide more information on the anatomical properties of Thai Aerides.
The diversity, distribution, biomass, and conservation status of ichthyofauna of the Singkil peat swamp in Aceh Province, Indonesia
Authors: RAZI NANDA MUHAMMAD , NASIR MUHAMMAD , KHALIDIN KHALIDIN , SAVIRA DEA , NAJMI ISTAFAN , MAHFUD MAHFUD , DERMAWAN FEBRI , FADLI NUR , MUCHLISIN ZAINAL A.
Published: February 2024

Abstract. Razi NM, Nasir M, Khalidin K, Savira D, Najmi I, Mahfud M, Dermawan F, Fadli N, Muchlisin ZA. 2023. The diversity, distribution, biomass, and conservation status of ichthyofauna of the Singkil peat swamp in Aceh Province, Indonesia. Biodiversitas 24: 6661-6674. The land conversion of the Singkil peat swamp into oil palm plantations poses a significant threat to the aquatic ecosystem, with potentially detrimental consequences for fish biodiversity. Several reports showed that there was no data on fish diversity in the Singkil peat swamp despite the damage occurring in the area. Therefore, this study aimed to analyze the diversity, distribution, biomass, and conservation status of Ichthyofauna in the Singkil peat swamp waters. Sampling was carried out at 13 locations from July 2023 to August 2023, and the samples were caught using gill nets, casting nets, fishing rods, and traps. A total of 934 samples were collected during the sampling, belonging to 39 species, 31 genera, and 26 families. The results showed that Cyprinidae was the most dominant family, with an average diversity index of 1.23, indicating the medium category. The average dominance index was 0.42, which was placed in the low category. Channa striata (Bloch, 1793) and Trichopodus trichopterus (Pallas, 1770) had the highest frequency of occurrence and were found in seven locations out of 13 surveyed. Furthermore, these species were categorized as frequently found based on their availability. The average fish biomass was 288.75 kg/ha, with C. striata having the largest value. Among the 39 fish species obtained, 3 species were classified as near threatened, including Anguilla bicolor (McClelland, 1844), Mystus bimaculatus (Volz, 1904), and Kryptopterus minor (Roberts, 1989), while 1 invasive sample was recorded, namely Oreochromis niloticus (Linnaeus, 1758) in one location.
Antibacterial activity of sea hare (Dolabella auricularia) egg string extracts against potentially pathogenic bacteria
Authors: LIGUEZ CHENCY GRACE O. , TABUGO SHARON ROSE
Published: February 2024

Abstract. Liguez CGO, Tabugo SR. 2023. Antibacterial activity of sea hare (Dolabella auricularia) egg string extracts against potentially pathogenic bacteria. Biodiversitas 24: 6675-6683. Pharmaceutical industries now recognize the vast variety of ocean organisms, each possessing distinct biological characteristics. Sea hares, for example, are marine organisms that use bioactive chemicals to defend against predators, including their eggs. To explore the potential antibacterial properties of sea hare species (Dolabella auricularia) found in Pujada Bay, Philippines, egg strings were collected and extracted using hexane and methanol solvents. The antibacterial activity of each fraction was then determined through Minimum Inhibitory Concentration (MIC) testing against four potentially pathogenic bacteria, two gram-positive strains (Staphylococcus aureus, Bacillus subtilis) and two gram-negative strains (Escherichia coli, Pseudomonas aeruginosa). The broth microdilution method was employed to assess the antibacterial activity of Dolabella auricularia egg strings. The results revealed the MIC values for the four bacterial strains. The hexane extracts of both extract 1 and extract 2 exhibited a MIC of 0. 23 and 0.33 mg/mL and a MIC of 0.52 and 0.125 mg/mL against P. aeruginosa, respectively. The methanolic extracts (1 and 2) displayed a MIC of 1.46 and 2.83 mg/mL against E. coli and an even more potent MIC of 1.33 and 0.79 mg/mL against P. aeruginosa. In the case of B. subtilis, the hexane extracts (1 and 2) had a MIC of 1.5 and 0.54 mg/mL, while the methanolic extracts (1 and 2) exhibited a MIC of 1.17 mg/mL and 0.83 mg/mL. Lastly, against S. aureus, hexane extracts (1 and 2) suppressed the growth with a MIC of 0.77 mg/mL and 0.25 mg/mL, respectively, while both methanolic extracts (1 and 2) demonstrated a MIC of 3.33 mg/mL. These findings showcase the promising antibacterial activity of Dolabella auricularia egg string extracts and highlight their potential for further investigation and development in the pharmaceutical field.
Short Communication: New records of Mactra clams (Bivalvia: Mactridae) from Madura Island, Indonesia
Authors: WIJAYA CATHERINE BERLIANA , AMBARWATI RENI , ISNANINGSIH NUR ROHMATIN
Published: February 2024

Abstract. Wijaya CB, Ambarwati R, Isnaningsih NR. 2023. Short Communication: New records of Mactra clams (Bivalvia: Mactridae) from Madura Island, Indonesia. Biodiversitas 24: 6684-6691. Mactridae is a family of bivalves found in shallow waters, such as living at high tide lines, in tidal areas, and below low tide lines. More mactrid bivalves could be discovered, and further studies are needed in Indonesian waters. Madura Island has a variety of bivalves, and Mactra clams could also be discovered on this island. Therefore, this study aimed to identify Mactra clams from Madura Island, Indonesia, and analyze their morphological characters. Samples were collected at Nepa and Badur Beaches during low tides, and then identified based on morphological characteristics. A stereo microscope observation and detailed descriptions were carried out to obtain the qualitative characteristics, while the quantitative ones, included shell length and height, palial line height, and diameter. The environmental parameters of this two-beach were also evaluated. Data were analyzed descriptively. The results showed two new records of Mactridae members at both beaches, namely Mactra luzonica Reeve, 1854, Mactra dissimilis Reeve, 1854. Mactra dissimilis revealed morphological variation, namely in the coloration on both the exterior and interior of the shell. There were three variations of M. dissimilis, namely bluish-white shell, brownish-white shell, and white shell. The findings of M. dissimilis and M. luzonica are regarded as new records for Madura Island, Indonesia.
Bone growth evaluation in collagen-hydroxyapatite implant locations using digital radiography: an animal model
Authors: Sari Laela , Julia Siti , Lubis Lukmanda Evan , Sihono Dwi Seno Kuncoro , Sari Yessie Widya , Soejoko Djarwani Soeharso
Published: February 2024

BACKGROUND Digital radiography has been used to evaluate the progress of bone growth with a collagen-hydroxyapatite implant in rabbit tibias. This study aimed to introduce digital radiography methods that provide comprehensive data availability for continuous information retrieval from the implant preparation to the cultivation period.

METHODS 38 digital radiographs were divided into 3 treatment groups, namely a single defect without implant (control), single-implant, and three-implant. Radiographic acquisitions were performed at preparation time and post-implantation from 0 to 56 days. Observations were concentrated on the implantation site, followed by creating a lateral profile. The prediction of implantation growth was determined using relative bone density (RBD) percentage.

RESULTS Based on the profile, the recovery process consisted of implant absorption and new bone tissue deposition. The absorption process was highly influenced by the defect size. In the control and single-implant groups, regardless of the different recovery processes, similar recovery results were observed 56 days post-implantation, with an RBD value of approximately 90%. Meanwhile, the three-implant group only had an RBD value of 62%.

CONCLUSIONS Radiography can evaluate absorption and new bone growth during implantation in New Zealand white rabbits. Radiographs, which can be obtained at any time during cultivation, offered more information on the recovery implantation process than the other method that relies on data obtained after sacrificing the animals.
Hybrid electrode interface modification enhances OLEDs performance
Authors: Guo Yangyang , Li Xin , Li Bo , Wang Wenjun
Published: February 2024

Highly conductive transparent anodes based on graphene oxide (GO) functional material mixed with poly(3,4-ethylenedioxythiophene)-polystyrene sulfide (PEDOT:PSS) solution were prepared by spin-coating method, and the conductive properties of the anode mixture were further improved by interface treatment. The square resistance of the hybrid film at 36 nm film thickness was 62 Ω/□ and the transmittance at 550 nm was 89%. OLED devices using optimized GO/PEDOT:PSS hybrid films as anodes have lower turn-on voltages and the highest current efficiencies, with a maximum brightness that is 2.37 times that of pure PEDOT:PSS devices and 2.7 times that of ITO devices. Higher transmittance, conductivity, and better highest occupied molecular orbital (HOMO) level matching after hybrid electrode interface treatment contribute to the performance of GO/PEDOT:PSS hybrid anode OLED devices.
Massive Klein tunneling in topological photonic crystals
Authors: Nakatsugawa Keiji , Hu Xiao
Published: February 2024

Klein’s paradox refers to the transmission of a relativistic particle through a high potential barrier. Although it has a simple resolution in terms of particle-to-antiparticle tunneling (Klein tunneling), debates on its physical meaning seem lasting partially due to the lack of direct experimental verification. In this article, we point out that honeycomb-type photonic crystals (PhCs) provide an ideal platform to investigate the nature of Klein tunneling, where the effective Dirac mass can be tuned in a relatively easy way from a positive value (trivial PhC) to a negative value (topological PhC) via a zero-mass case (PhC graphene). Specifically, we show that analysis of the transmission between domains with opposite Dirac masses—a case hardly be treated within the scheme available so far—sheds new light on the understanding of the Klein tunneling.
Predicting cortical-thalamic connectivity using functional near-infrared spectroscopy and graph convolutional networks
Authors: Tang Lingkai , Kebaya Lilian , Vahidi Homa , Meyerink Paige , de Ribaupierre Sandrine , Bhattacharya Soume , St. Lawrence Keith , Duerden Emma
Published: February 2024

Functional near-infrared spectroscopy (fNIRS) measures cortical changes in hemoglobin concentrations, yet cannot collected this information from the subcortices. To address this drawback, we propose a machine-learning-based approach to predict cortical-thalamic functional connectivity using cortical fNIRS data. We applied graph convolutional networks (GCN) on two datasets obtained from adults and neonates, respectively. Each dataset contained fNIRS data as input to the predictive models and connectivities of functional magnetic resonance imaging (fMRI) as training targets. GCN models performed better compared to conventional methods, on both identifying the connections, and regressing the quantified strengths of connections. We also propose the addition of inter-subject connections into the GCN kernels could improve performance. Our results show it is feasible to indicate subcortical activity from cortical fNIRS recordings.
CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly
Authors: Sweeney Katelyn M. , Chantarawong Sapanna , Barbieri Edward M. , Cajka Greg , Liu Matthew , Spruce Lynn , Fazelinia Hossein , Portz Bede , Copley Katie , Lapidot Tomer , Duhamel Lauren , Greenwald Phoebe , Saida Naseeb , Shalgi Reut , Shorter James , Shalem Ophir
Published: February 2024

The presence of large protein inclusions is a hallmark of neurodegeneration, and yet the precise molecular factors that contribute to their formation remain poorly understood. Screens using aggregation-prone proteins have commonly relied on downstream toxicity as a readout rather than the direct formation of aggregates. Here, we combined a genome-wide CRISPR knockout screen with Pulse Shape Analysis, a FACS-based method for inclusion detection, to identify direct modifiers of TDP-43 aggregation in human cells. Our screen revealed both canonical and novel proteostasis genes, and unearthed SRRD, a poorly characterized protein, as a top regulator of protein inclusion formation. APEX biotin labeling reveals that SRRD resides in proximity to proteins that are involved in the formation and breakage of disulfide bonds and to intermediate filaments, suggesting a role in regulation of the spatial dynamics of the intermediate filament network. Indeed, loss of SRRD results in aberrant intermediate filament fibrils and the impaired formation of aggresomes, including blunted vimentin cage structure, during proteotoxic stress. Interestingly, SRRD also localizes to aggresomes and unfolded proteins, and rescues proteotoxicity in yeast whereby its N-terminal low complexity domain is sufficient to induce this affect. Altogether this suggests an unanticipated and broad role for SRRD in cytoskeletal organization and cellular proteostasis.
Endolysosomal trafficking controls yolk granule biogenesis in vitellogenic Drosophila oocytes
Authors: Yu Yue , Chen Dongsheng , Farmer Stephen M. , Xu Shiyu , Rios Beatriz , Solbach Amanda , Ye Xin , Ye Lili , Zhang Sheng
Published: February 2024

Endocytosis and endolysosomal trafficking are essential for almost all aspects of physiological functions of eukaryotic cells. As our understanding on these membrane trafficking events are mostly from studies in yeast and cultured mammalian cells, one challenge is to systematically evaluate the findings from these cell-based studies in multicellular organisms under physiological settings. One potentially valuable in vivo system to address this challenge is the vitellogenic oocyte in Drosophila, which undergoes extensive endocytosis by Yolkless (Yl), a low-density lipoprotein receptor (LDLR), to uptake extracellular lipoproteins into oocytes and package them into a specialized lysosome, the yolk granule, for storage and usage during later development. However, by now there is still a lack of sufficient understanding on the molecular and cellular processes that control yolk granule biogenesis. Here, by creating genome-tagging lines for Yl receptor and analyzing its distribution in vitellogenic oocytes, we observed a close association of different endosomal structures with distinct phosphoinositides and actin cytoskeleton dynamics. We further showed that Rab5 and Rab11, but surprisingly not Rab4 and Rab7, are essential for yolk granules biogenesis. Instead, we uncovered evidence for a potential role of Rab7 in actin regulation and observed a notable overlap of Rab4 and Rab7, two Rab GTPases that have long been proposed to have distinct spatial distribution and functional roles during endolysosomal trafficking. Through a small-scale RNA interference (RNAi) screen on a set of reported Rab5 effectors, we showed that yolk granule biogenesis largely follows the canonical endolysosomal trafficking and maturation processes. Further, the data suggest that the RAVE/V-ATPase complexes function upstream of or in parallel with Rab7, and are involved in earlier stages of endosomal trafficking events. Together, our study provides s novel insights into endolysosomal pathways and establishes vitellogenic oocyte in Drosophila as an excellent in vivo model for dissecting the highly complex membrane trafficking events in metazoan.
I did not scream. i could not; i was terrified. i just followed them. . .i blocked my mind. then they all raped me: A narrative inquiry on the onset of tonic immobility among women rape victims in Nigeria
Authors: Gbahabo Dooshima Dorothy , Duma Sinegugu Evidence
Published: February 2024

Tonic immobility (TI) is a common uncontrollable autonomic mammalian response to an extremely fearful situation. It is one of the most immediate devastating consequences of rape and remains poorly understood. While controversies over its definition persist among researchers, this also reflects on the care for and support to victims. The study aimed to explore and describe the onset of TI and the meaning attached to the experience among women raped victims in Nigeria. The study design was the qualitative narrative inquiry approach. Criterion and purposive sampling were conducted across four post-rape care facilities in Lagos, Nigeria, to recruit 13 participants. In-depth face-to-face interviews were conducted using a semi-structured interview guide to generate data that were thematically analysed. The findings of the study revealed five themes relating to the onset of TI as follows: the first two focused on the experience of TI: (1) the onset of TI prior to rape due to perceived imminent danger, (2) the onset of TI as a self-protection mechanism from further harm) while the last three relate to the meaning-making of the experience of TI (3) self-loathing as a meaning attached to TI, (4) suicidal ideations as a meaning attached to TI, and (5) divine intervention as a meaning attached to TI. Conclusion: The findings underscore the experiences and meanings that participants attach to TI following rape. There is a strong likelihood that tonic-immobility is not an uncommon experience amongst rape victims, but that in the absence of research, specialized care on the condition, and its associated consequences will haunt many women, affecting their psychological well-being and their entire quality of life. Describing the phenomenon as it is experienced by the participants is critical because understanding the condition is the first step toward effective appropriate management.
Nature Forest Reserves in Tanzania and their importance for conservation
Authors: Ract Claire , Burgess Neil D. , Dinesen Lars , Sumbi Peter , Malugu Isaac , Latham Julia , Anderson Lucy , Gereau Roy E. , Gonçalves de Lima Marcelo , Akida Amina , Nashanda Evarist , Shabani Zainabu , Tango Yusuph , Mteleka Someni , Santos Silayo Dos , Mwangi Juma , Lyatuu Gertrude , Platts Philip J. , Rovero Francesco
Published: February 2024

Since 1997 Tanzania has undertaken a process to identify and declare a network of Nature Forest Reserves (NFRs) with high biodiversity values, from within its existing portfolio of national Forest Reserves, with 16 new NFRs declared since 2015. The current network of 22 gazetted NFRs covered 948,871 hectares in 2023. NFRs now cover a range of Tanzanian habitat types, including all main forest types—wet, seasonal, and dry—as well as wetlands and grasslands. NFRs contain at least 178 of Tanzania’s 242 endemic vertebrate species, of which at least 50% are threatened with extinction, and 553 Tanzanian endemic plant taxa (species, subspecies, and varieties), of which at least 50% are threatened. NFRs also support 41 single-site endemic vertebrate species and 76 single-site endemic plant taxa. Time series analysis of management effectiveness tracking tool (METT) data shows that NFR management effectiveness is increasing, especially where donor funds have been available. Improved management and investment have resulted in measurable reductions of some critical threats in NFRs. Still, ongoing challenges remain to fully contain issues of illegal logging, charcoal production, firewood, pole-cutting, illegal hunting and snaring of birds and mammals, fire, wildlife trade, and the unpredictable impacts of climate change. Increased tourism, diversified revenue generation and investment schemes, involving communities in management, and stepping up control measures for remaining threats are all required to create a network of economically self-sustaining NFRs able to conserve critical biodiversity values.
First molecular detection and genetic characterization of porcine circovirus 4 in the Gansu Province of China
Authors: Fu Peng-Fei , Wang Yan-Hong , Liu Guo , Wang Dong-Mei , Huang Wei-Wei , Guo Duan-Qiang , Li Xin-Yang , Liu Ping , Wei Meng-Xiang , Lu Min , Hong Jun
Published: February 2024

Since its initial discovery in the Hunan province of China, genomic DNA of porcine circovirus 4 (PCV4) has been detected in pigs across multiple provinces in China, as well as in South Korea. However, the prevalence of porcine circovirus type 4 in Gansu Province, China, remains unknown. To address this gap, we undertook an extensive study where we gathered 121 clinical samples displaying diverse clinical manifestations from pig farms in Gansu Province between 2022 and 2023. Employing a real-time fluorescence quantification method, we identified the presence of PCV4 genome. Out of the 121 clinical samples analyzed, 13 samples tested positive for PCV4, resulting in a positive rate of 10.74% (13/121). This finding confirms the presence of PCV4 in pig farms within Gansu Province, China. Furthermore, we successfully sequenced and analyzed the complete genomes of two distinct PCV4 strains, comparing them with 60 reference sequences archived in the GenBank database. The results revealed a high nucleotide homology (98.2–98.8%) between the strains obtained in this study and the PCV4 reference strains, indicating a relatively low evolutionary rate of the PCV4 genome. Phylogenetic analysis revealed that two strains in this study belong to PCV4a and PCV4c. As far as we know, this study marks the inaugural report on the molecular identification and genomic attributes of PCV4 in Gansu Province, China, offering valuable insights for devising preventive and control strategies against this emerging virus.
Transcriptome sequencing and screening of genes related to the MADS-box gene family in Clematis courtoisii
Authors: Chen Mingjian , Li Linfang , Wang Shu’an , Wang Peng , Li Ya
Published: February 2024

The MADS-box gene family controls plant flowering and floral organ development; therefore, it is particularly important in ornamental plants. To investigate the genes associated with the MADS-box family in Clematis courtoisii, we performed full-length transcriptome sequencing on C. courtoisii using the PacBio Sequel third-generation sequencing platform, as no reference genome data was available. A total of 12.38 Gb of data, containing 9,476,585 subreads and 50,439 Unigenes were obtained. According to functional annotation, a total of 37,923 Unigenes (75.18% of the total) were assigned with functional annotations, and 50 Unigenes were identified as MADS-box related genes. Subsequently, we employed hmmerscan to perform protein sequence similarity search for the translated Unigene sequences and successfully identified 19 Unigenes associated with the MADS-box gene family, including MIKC*(1) and MIKCC (18) genes. Furthermore, within the MIKCC group, six subclasses can be further distinguished.
Assessment of differentially private synthetic data for utility and fairness in end-to-end machine learning pipelines for tabular data
Authors: Pereira Mayana , Kshirsagar Meghana , Mukherjee Sumit , Dodhia Rahul , Lavista Ferres Juan , de Sousa Rafael
Published: February 2024

Differentially private (DP) synthetic datasets are a solution for sharing data while preserving the privacy of individual data providers. Understanding the effects of utilizing DP synthetic data in end-to-end machine learning pipelines impacts areas such as health care and humanitarian action, where data is scarce and regulated by restrictive privacy laws. In this work, we investigate the extent to which synthetic data can replace real, tabular data in machine learning pipelines and identify the most effective synthetic data generation techniques for training and evaluating machine learning models. We systematically investigate the impacts of differentially private synthetic data on downstream classification tasks from the point of view of utility as well as fairness. Our analysis is comprehensive and includes representatives of the two main types of synthetic data generation algorithms: marginal-based and GAN-based. To the best of our knowledge, our work is the first that: (i) proposes a training and evaluation framework that does not assume that real data is available for testing the utility and fairness of machine learning models trained on synthetic data; (ii) presents the most extensive analysis of synthetic dataset generation algorithms in terms of utility and fairness when used for training machine learning models; and (iii) encompasses several different definitions of fairness. Our findings demonstrate that marginal-based synthetic data generators surpass GAN-based ones regarding model training utility for tabular data. Indeed, we show that models trained using data generated by marginal-based algorithms can exhibit similar utility to models trained using real data. Our analysis also reveals that the marginal-based synthetic data generated using AIM and MWEM PGM algorithms can train models that simultaneously achieve utility and fairness characteristics close to those obtained by models trained with real data.
Numerical investigation of seismic amplification characteristics in loess ridge region of Xiji, northwest China
Authors: Peng Da , Bo Jingshan , Chang Chaoyu , Qi Wenhao , Li Xiaobo
Published: February 2024

The seismic effects on sloped terrain, which are of paramount importance for engineering design and earthquake risk mitigation, have always been a central focus of earthquake engineering research. In this study, generalized geometric models of loess ridges at varying heights were created, and a three-dimensional nonlinear numerical model was established using FLAC3D. Seismic ground motion time histories at different frequencies and actual earthquake ground motion records were input into the model to analyze the peak acceleration amplification effects experienced by the surface of loess ridges when subjected to SV waves. The study’s outcomes reveal that seismic amplification on the slopes of loess ridges is characterized by non-linearity with respect to slope height. Instead, it exhibits rhythmic variations, with the rate of change in these rhythms increasing in correspondence with the frequency of seismic motion and the height of the slope. Under low-intensity seismic motion, a linear increase in acceleration amplification is observed at the ridge’s crest concerning the height of the loess ridge. However, under high-intensity seismic motion, the relationship between amplification and slope height becomes less significant. Typically, the peak acceleration at the ridge’s crest is reported to be 1.5 to 2.5 times that observed at the slope’s base. The amplification effect at the ridge’s crest is more pronounced in the low-frequency and high-frequency segments when compared to the mid-frequency range. Conversely, significant amplification is observed in the high-frequency range in the lower sections of the slope near the base. It is further noted that the amplification effect at the ridge’s crest displays distinct behavior at different frequencies, characterized by narrow frequency bands of maximum amplification, with peak amplification factors exceeding 10 in some cases. These research findings have practical significance and provide valuable references for engineering construction and seismic risk mitigation planning in loess regions.
Comparative evaluation of iStent versus iStent inject W combined with phacoemulsification in open angle glaucoma
Authors: Morita Shuu , Sakanishi Yoshihito , Riyu Ikari , Watanabe Satoshi , Ebihara Nobuyuki
Published: February 2024

Purpose

The study aimed to compare the 12-month post-operative outcomes of iStent and iStent inject W (inject W), and the factors associated with their success in open-angle glaucoma.

Methods

This single-center, retrospective comparative case series evaluated the medical records of patients who underwent iStent (comprising 1 stent) or inject W (comprising 2 stents) implantation with cataract surgery for primary open-angle glaucoma and normal tension glaucoma between January 2019 and March 2022. The 12-month post-operative efficacy outcomes included intraocular pressure (IOP), glaucoma medications, and survival analysis of the probability of success. “Failure” was defined as any of the following conditions compared to baseline: 1) IOP elevation, 2) increased glaucoma medication, or 3) IOP decline not exceeding 20% when glaucoma medication scores were comparable, and 4) need for additional glaucoma surgery. The safety outcomes included intra- and post-operative adverse events and changes in the best-corrected visual acuity and visual field.

Results

The study comprised 55 eyes in the iStent and 105 in the inject W groups. At 12 months, treatment success was achieved in 66.0% of iStent and 78.4% of inject W eyes. The mean IOP was lower, and the percent reduction from baseline was equal in iStent-treated eyes (8.0% reduction, 14.8 mmHg to 13.7 mmHg, P<0.01) and inject W-treated eyes (11.9% reduction, 15.0 mmHg to 13.8 mmHg, P<0.01) (between-group comparison, P = 0.23). The mean medication burden decreased significantly from 2.5 to 1.1 for iStent (55.0% reduction, P<0.01) and 2.9 to 1.7 for iStent inject (46.8% reduction, P<0.01), with no significant differences between the two groups (P = 0.17). Both devices exhibited excellent safety.

Conclusions

Both devices significantly reduced IOP and glaucoma medication 12 months post-operatively. The outcome measures did not differ significantly between the two groups, and lower baseline IOP was predictive of surgical failure.
Low-cost soil moisture sensor calibration
Authors: Duarte Jean Rodrigues , Nuñez Daniel Noe Coaguila
Published: February 2024

Brazil has been experiencing several instabilities regarding the climate. There is a great climatological variation in the cultures that have been suffering drastically from this stress, mainly water. Therefore, it is necessary to quickly and efficiently check the soil moisture rate, before any operation in the field, avoiding production losses and unnecessary extra expenses for the producer. Methods for measuring soil moisture are extremely important for carrying out adequate irrigation, thus optimizing water resources and saving water. Humidity directly affects seed quality, germination rate and crop yield, other unit operations. In this study the low-cost WeMos sensor was evaluated regarding its efficiency and possible calibration in comparison to high-cost equipment with an average of US$: 405,75 dollars. The gravimetric method was used to calibrate the sensor, which consists of sample preparation, drying, determination of its mass and evaluation calculation. The gravimetric method was used to calibrate the sensor, which consists of sample preparation, drying, determination of its mass and evaluation calculation. From the data obtained, the equation was used, which was first inserted into the programming carried out in the Arduino system transmitted to the WeMos sensor. The results obtained by the WeMos sensor were consistent with the gravimetric humidity results obtained. It is concluded that the WeMos Arduino sensor presents reliability in sampled data and that it is an economically viable option for rural producers who need to obtain an answer regarding the humidity of the planting soil.
High Prevalence of Elevated Alanine Aminotransferase in American Indian Children Seen in a Pediatric Weight Management Clinic
Authors: Parashette Kalyan Ray , Coakley Kathryn E. , Kong Alberta S. , Jimenez Elizabeth Y. , Negrete Sylvia
Published: February 2024

INTRODUCTION:

Elevated alanine aminotransferase (ALT) can indicate risk of metabolic dysfunction–associated steatotic liver disease. However, there is little data about the prevalence of elevated ALT in American Indian (AI) children.

METHODS:

Baseline data from children attending the pediatric weight management clinic were used to describe the prevalence of elevated ALT, stratified by race and ethnicity.

RESULTS:

The prevalence of elevated ALT was higher among children who were male, were older, had higher body mass index Z scores, and were non-Hispanic and AI.

DISCUSSION:

In this clinic, AI children with overweight and obesity had a disproportionately high prevalence of elevated ALT; root causes of this disparity should be identified.
Musikvermittlung zwischen Publikumsentwicklung und sozialer Verantwortung
Authors: Petri-Preis Axel
Published: February 2024

In diesem Artikel widmet sich Axel Petri-Preis Musikvermittlung im Spannungsfeld von Publikumsentwicklung und sozialer Verantwortung. Er geht zunächst auf mögliche Ziele von Musikvermittlung im Hinblick auf Audience Development und Community Engagement ein und plädiert am Ende dafür, Musikvermittlung als eine Arbeit am gemeinsam Geteilten im Sinne eines doing universality zu betrachten.