bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Mangrove Forest Cover in Bontang City of East Kalimantan Province Using Normalized Difference Vegetation Index
Authors: Widyasasi Dyah , Karyati  , Kiswanto  , Ibrahim  , Pramono Dwi Agung 
Published: December 2024

Abstract
Mangrove ecosystems, commonly found in tropical states like Indonesia, are famous for their robust root systems that facilitate their survival in tidal habitats. Notwithstanding the importance and variety of mangroves, some 637,000 hectares, or 10-33 percent of Indonesia’s total mangrove area, have seen degradation and alteration in recent decades. The development of effective mangrove forest management strategies requires the backing of precise data and information. This research uses geographic information systems and remote sensing technologies to delineate mangrove forest cover according to stand density. The research site was chosen in Bontang City, East Kalimantan Province, to facilitate the analysis of Sentinel 2 satellite images via the Normalized Difference Vegetation Index method. The research findings indicated three NDVI classifications representing mangrove vegetation density: low density including 72,039 hectares (3%), medium density covering 209,044 hectares (9%), and high density spanning 2,119,287 hectares (88%). This study assists policymakers when creating sustainable management and restoration strategies for mangrove forests based on vegetation density.
Use of supernatants from extremophilic bacteria on the biocontrol of root knot nematodes Meloidogyne sp.
Authors: Vera-Morales Marcos , López-Medina Eloy , Avilés-Centeno Ángel , Sabando Cinthya , Ratti María F. 
Published: December 2024

Abstract
Plant-parasitic nematodes, particularly the root-knot nematodes (Meloidogyne spp.), pose a significant threat to crop yields, with potential losses ranging from 26.5% to 73.3% in solanaceous crops like tomatoes. Traditional chemical controls, such as methyl bromide and other soil fumigants, have been effective but pose environmental and health risks, prompting the need for alternative strategies. This study investigates the efficacy of extremophilic bacterial supernatants derived from Antarctic strains as biocontrol agents against Meloidogyne spp. in tomato plants, both in vitro and under greenhouse conditions. Bacteria were isolated from cold environments and identified through molecular characterization. The supernatants from Pseudomonas, Filibacter, Frondihabitans, and Psychrobacter were tested for their nematicidal activity at different concentrations. The results demonstrated that these bacterial supernatants effectively reduced nematode populations, with varying degrees of success, suggesting their potential as sustainable biocontrol agents. The use of extremophilic bacteria could offer a viable alternative for managing nematode infestations, particularly in mountainous and cold-climate agriculture.
Seasonal fluctuations in water temperature and dissolved oxygen: A comparative study of oxbow lakes along the Kapuas Riverine System
Authors: Subehi L , Uno H , Nomosatryo S , Yustiawati  , Sulastri  , Sulawesty F , Toruan R L , Afandi A Y , Rusydi A F , Julzarika A , Witasari Y , Ajie G S , Sunthari H 
Published: December 2024

Abstract
Lake Keliling and Lake Baru are oxbow lakes located along the Kapuas River, the largest river in West Kalimantan. This study aimed to analyze the variations in water temperature and dissolved oxygen (DO), and their relationship with fluctuations in the main river during the dry and wet seasons. We measured water temperature and DO parameters at Lake Keliling and Lake Baru in February and September 2023 for wet and dry seasons, respectively. Moreover, we installed a camera for monitoring the river water level fluctuations at both locations. In addition, we obtained the secondary data for water level and water quality data (2021 – 2022 and 2018 – 2022, respectively) close to both sites. The result showed during the wet season, the vertical distribution pattern of DO in Lake Keliling and Lake Baru showed a similar pattern to temperature. Anoxic conditions in Lake Keliling during the rainy season were observed at a depth of 2 meters, whereas in Lake Baru, these conditions were found at depths of 6 to 8 meters. During the dry season, the depth of the anoxic water column in Lake Keliling remained at 2 meters, while in Lake Baru, the anoxic layer shifted to a shallower depth of approximately 1.8 meters, except at Station Baru 3. This indicates the potential for sediments to store heat at shallow depths. It could be explained that the variability of water temperature and DO parameters, was likely various changes related to the water level conditions (dry and wet seasons).
Investigation of discharge regimes of silicon needle with short air gap
Authors: Wang Yanyi , Ge Yining , Chen Yong , Wang Li , Liu Xuandong 
Published: December 2024

Abstract
Semiconductor electronic devices are prone to charge accumulation during production and transportation, which usually causes device breakdown. Ionizers are widely used for electrostatic elimination, and utilizing semiconductor silicon for the discharge needle material in ionizers can effectively prevent metal contamination. To investigate the discharge characteristics of silicon needles and their mode modulation mechanism, this study has established an experimental platform for silicon needle-plate discharge under positive polarity voltage. Discharge pulse parameters and optical signals were measured at varying electrode spacings. The experimental results reveal that silicon needle discharge progresses through four regimes: the spontaneous streamer, the periodic streamer, the cluster streamer, and the glow discharge. Among these, the pulse amplitude is most uniform and stable in the periodic streamer regime. In addition, shorter-gap discharge exhibits higher pulse amplitude and repetition frequency but is easier to transition into the filament regime. The formation process of a single pulse is closely related to the field strength in the ionization region near the needle tip. Hence, parameters such as the pulse rising edge time and falling edge time show minimal variation with voltage. The amount of charge generated per unit time is primarily influenced by the repetition frequency. Consequently, the electrostatic ionizer produces the highest, most stable, and most uniform charges if it operates in the periodic streamer regime.
Investigation on spraying pressure in etching process of flexible printed circuit board (FPCB) with 18 μm line pitch
Authors: Sun Bin , Yu Dayang , Peng Weiping , Wang Yingjie , Ming Ruijian , Wang Jian 
Published: December 2024

Abstract
In the wet etching process of the flexible printed circuit board (FPCB), to obtain a better etching profile and improve the yield, it is necessary to control the etching spraying pressure and etching time as far as possible. In this paper, a numerical method implemented with the Euler multiphase flow model is proposed to investigate the impact of etching spraying pressure and etching time on the quality of FPCB. The FPCB sample with 18 μm line pitch is manufactured based on the process parameters obtained by simulations. A comparison between the microscopic analysis of actual structures and the cavity profiles predicted by the simulations validates the numerical simulation method. The results of simulations demonstrate that the average pressure on the upper surface of the FPCB is 2,510 Pa. The maximum etching cavity width and lateral etching width are about 10 μm and 1 μm, respectively. The cavity profiles extracted from simulation and experiments are in good agreement except upper left and right with a deviation less than 2 μm.
Assessment and optimization of biomedical waste management using Neutrosophic multi-criteria decision-making method
Authors: Pillai Nagarajan Deivanayagam , Parthasarathy Vellaichamy , Anbalagan Kanchana 
Published: December 2024

Abstract
This paper proposes a multicriteria decision-making (MCDM) framework based on Neutrosophic TOPSIS, considering factors such as cost-effectiveness, health and safety, regulatory compliance, environmental impact, and technological feasibility. The framework is informed by expert recommendations and recent literature. Next, in comparison with predetermined benchmarks. The results show that recycling is the best choice since it can minimise waste, recover resources, and save the environment. By taking subjectivity and uncertainties into consideration, this method aids decision-makers in selecting the best waste management solution while also enhancing the consistency and transparency of the process. The suggested strategy encourages eco-friendly waste management techniques in the biomedical sector and provides practitioners and policymakers with a useful tool to improve waste management systems. Recent literature and expert recommendations indicate a pressing need for an advanced multicriteria decision-making framework that can comprehensively evaluate biomedical waste management options. The Neutrosophic technique is particularly well-suited for this purpose, as it integrates linguistic assessments to handle uncertainties and subjective judgments. Given the significant environmental and public health impacts of improper waste disposal, this research aims to provide a robust and transparent decision-making tool that can guide practitioners and policymakers toward more sustainable waste management practices. By evaluating real data from a medical facility, this study demonstrates the practical applicability and effectiveness of the proposed Neutrosophic TOPSIS-based method.
Genal: a Python toolkit for genetic risk scoring and Mendelian randomization
Authors: Rivier Cyprien A , Clocchiatti-Tuozzo Santiago , Huo Shufan , Torres-Lopez Victor , Renedo Daniela , Sheth Kevin N , Falcone Guido J , Acosta Julian N 
Published: December 2024

Abstract

Motivation
The expansion of genetic association data from genome-wide association studies has increased the importance of methodologies like Polygenic Risk Scores (PRS) and Mendelian Randomization (MR) in genetic epidemiology. However, their application is often impeded by complex, multi-step workflows requiring specialized expertise and the use of disparate tools with varying data formatting requirements. Existing solutions are frequently standalone packages or command-line based—largely due to dependencies on tools like PLINK—limiting accessibility for researchers without computational experience. Given Python’s popularity and ease of use, there is a need for an integrated, user-friendly Python toolkit to streamline PRS and MR analyses.

Results
We introduce Genal, a Python package that consolidates SNP-level data handling, cleaning, clumping, PRS computation, and MR analyses into a single, cohesive toolkit. By eliminating the need for multiple R packages and for command-line interaction by wrapping around PLINK, Genal lowers the barrier for medical scientists to perform complex genetic epidemiology studies. Genal draws on concepts from several well-established tools, ensuring that users have access to rigorous statistical techniques in the intuitive Python environment. Additionally, Genal leverages parallel processing for MR methods, including MR-PRESSO, significantly reducing the computational time required for these analyses.

Availability and implementation
The package is available on Pypi (https://pypi.org/project/genal-python/), the code is openly available on Github with a tutorial: https://github.com/CypRiv/genal, and the documentation can be found on readthedocs: https://genal.rtfd.io.
CT-based liver peritumoural radiomics features predict hepatic metastases sources as gastrointestinal or non-gastrointestinal
Authors: Hou Chengshi , Wang Fang , Prince Martin , Yang Xin , Wang Wenjian , Ye Jing , Chen Lei , Luo Xianfu 
Published: December 2024

Abstract

Objectives
To investigate the feasibility of radiomics models for predicting the source of hepatic metastases from gastrointestinal (GI) vs non-gastrointestinal (non-GI) primary tumours on contrast-enhanced CT (CECT).

Methods
Three hundred and forty-seven patients with liver metastases (180 from GI and 167 from non-GI) and abdominal CECT including arterial, portal venous, and delayed phases were divided into training (221) and validation (96) sets at a ratio of 7:3 and an independent testing set (30). Radiomics features were extracted from volumes of interest (VOIs) including tumoural (Vtc) and peritumoural (Vpt) regions on CECT. Optimal radiomics features were used in logistic regression models using receiver operating curve (ROC) analysis to evaluate the diagnostic efficiency.

Results
The best single-phase model was a venous phase peritumoural VOI with 11 features. Area under the curve (AUC), sensitivity, and specificity were 0.817, 0.740, and 0.761, respectively in the validation set. While the best arterial phase tumoural VOI gave an AUC of 0.677 in the validation set. For the combined models, peritumoural VOI in arterial and venous phases (15 features) achieved the best prediction performance with an AUC of 0.926 in the validation set and 0.884 in the testing set.

Conclusion
Liver peritumoural radiomics features extracted from CECT were able to identify the source of hepatic metastases as GI vs non-GI.

Advances in knowledge
Peritumoural radiomics features showed a correlation with source of liver metastases. The radiomics features from liver peritumoural arterial and venous phases CT were promising in differentiating the source of hepatic metastases from GI vs non-GI primary tumours.
Left Ventricular Assist Device Versus Cardiac Implantable Electronic Device Infections: Distinct Entities, Distinct Suppression Strategies
Authors: Chesdachai Supavit , Baddour Larry M , DeSimone Daniel C 
Published: December 2024

Abstract
A distinction between infections of left ventricular assist devices and cardiac implantable electronic devices is warranted as they differ markedly in incidence, microbiologic profiles, clinical presentations, and extraction feasibility. These differences necessitate tailored suppressive antibiotic therapy (SAT) strategies. This commentary highlights the need for device-specific SAT approaches.
Severe tricuspid regurgitation after a horse kick: a case report of a rare cause of acquired valvulopathy
Authors: Dorge Michaël , Deleuse Remi , Pouleur Anne-Catherine , Badii Maria Chiara 
Published: December 2024

Abstract

Background
Many rare complications are associated with blunt chest trauma and right ventricular contusion. Among these, post-traumatic severe tricuspid regurgitation is a relatively rare clinical entity. Furthermore, only a few cases reported in the literature are associated with trauma due to kicking by a horse.

Case summary
We present the case of a 56-year-old woman who was diagnosed with early massive tricuspid regurgitation caused by traumatic rupture of the anterior papillary muscle, which was successfully treated by surgical tricuspid repair. The patient had no symptoms suggestive of valvular dysfunction, which was incidentally detected on routine transthoracic echocardiogram following a horse kick.

Discussion
The most commonly cited mechanism is an anteroposterior compression of the chest, causing a sudden increase in right ventricular pressure during the end-diastolic phase. The mean interval to diagnosis of traumatic tricuspid regurgitation is usually long, leading to a progressive right ventricular remodelling and deterioration of right ventricular function. As a result, surgical repair of the valve is often not possible and an early tricuspid valve replacement is required.
Why usefulness is rarely useful
Authors: Wang Fangyi , Feldmann Mitchell J , Runcie Daniel E 
Published: December 2024

Abstract
Mate selection plays an important role in breeding programs. The Usefulness Criterion was proposed to improve mate selection, combining information on both the mean and standard deviation of the potential offspring of a cross, particularly in clonally propagated species where large family sizes are possible. Predicting the mean value of a cross is generally easier than predicting the standard deviation, especially in outbred species when the linkage of alleles is unknown and phasing is required. In this study, we developed a method for estimating phasing accuracy from unphased genotype data on possible parental lines and evaluated whether the accuracy was sufficient to predict family standard deviations of possible crosses. We used simulations spanning a wide range of genetic architectures and used genotypes from a real strawberry breeding population to evaluate the conditions when usefulness could be accurately predicted. We found that with highly accurate computational phasing, predicting family standard deviations and usefulness criteria for potential crosses yields benefit over simply selecting crosses based on predicted family means only at high selection intensity and high heritability and with small numbers of QTL. However, even then the gain from using the family usefulness is small.
Amino Acid Substitutions in the Fusion Protein of Respiratory Syncytial Virus in Fukushima, Japan, During 2008–2023 and Their Effects
Authors: Okabe Hisao , Hashimoto Koichi , Norito Sakurako , Asano Yuichiro , Sato Masatoki , Kume Yohei , Chishiki Mina , Maeda Hajime , Mashiyama Fumi , Takeyama Aya , Murai Hiromichi , Nemoto Kenji , Ito Masaki , Suzuki Shigeo , Sakuma Hiroko , Shirato Kazuya , Go Hayato , Hosoya Mitsuaki 
Published: December 2024

Abstract

Background
Amino acid (AA) substitutions in the fusion (F) protein of respiratory syncytial virus (RSV) and their effects on antibody susceptibility remain unclear. We analyzed AA substitutions in the main neutralizing epitopes of the F protein.

Methods
We analyzed F protein genes of 236 RSV strains isolated from children hospitalized with RSV infection in Fukushima, Japan (June 2008–February 2023). AA substitutions in antigenic sites II, V, and Ø were detected, and their effects on antibody susceptibility and viral replication were evaluated.

Results
Site II: The K272M (RSV-A) and the K272E (RSV-B) substitutions in strains from palivizumab-treated children reduced antibody susceptibility. Site V: In RSV-A, &gt;50% of strains isolated since 2022 harbored the V178I substitution; however, this did not change antibody susceptibility. In RSV-B, L172Q/S173L mutant strains became predominant around 2016, leading to reduced antibody susceptibility. Site Ø: No AA substitutions were detected in RSV-A. In RSV-B, the I206M/Q209R mutant strain became predominant around 2018, leading to improved antibody susceptibility and replicative ability. However, none of the substitutions reduced antibody susceptibility.

Conclusions
The RSV F protein in Fukushima has naturally undergone AA substitutions with corresponding changes in antibody susceptibility, including unique regional patterns. Monitoring substitutions and antibody susceptibility is essential.
Microcystin shapes the Microcystis phycosphere through community filtering and by influencing cross-feeding interactions
Authors: Große Rebecca , Heuser Markus , Teikari Jonna E , Ramakrishnan Dinesh K , Abdelfattah Ahmed , Dittmann Elke 
Published: December 2024

Abstract
The cyanobacterium Microcystis causes harmful algal blooms that pose a major threat to human health and ecosystem services, particularly due to the prevalence of the potent hepatotoxin microcystin (MC). With their pronounced EPS layer, Microcystis colonies also serve as a hub for heterotrophic phycosphere bacteria. Here, we tested the hypothesis that the genotypic plasticity in its ability to produce MC influences the composition and assembly of the Microcystis phycosphere microbiome. In an analysis of individual colonies of a natural Microcystis bloom, we observed a significantly reduced richness of the community in the presence of MC biosynthesis genes. A subsequent synthetic community experiment with 21 heterotrophic bacterial strains in co-cultivation with either the wild-type strain Microcystis aeruginosa PCC 7806 or the MC-free mutant ΔmcyB revealed not only a tug-of-war between phototrophic and heterotrophic bacteria, but also a reciprocal dominance of two isolates of the genus Sphingomonas and Flavobacterium. In contrast, an Agrobacterium isolate thrived equally well in both consortia. In substrate utilization tests, Sphingomonas showed the strongest dependence on Microcystis exudates with a clear preference for the wild-type strain. Genome sequencing revealed a high potential for complementary cross-feeding, particularly for the Agrobacterium and Sphingomonas isolates but no potential for MC degradation. We postulate that strain-specific functional traits, such as the ability to perform glycolate oxidation, play a crucial role in the cross-feeding interactions, and that MC is one of the determining factors in the Microcystis phycosphere due to its interference with inorganic carbon metabolism.
Inhibition of EphA2 by syndecan-4 in wounded skin regulates clustering of fibroblasts
Authors: Brooks Rebecca , Wei Xianhui , Lei Mang Leng , Cid Francisca Cisterna , Roper James A , Williamson Rosalind C , Bass Mark D 
Published: December 2024

Abstract
Upon injury, fibroblasts in the surrounding tissue become activated, migrating into the wound in a controlled manner. Once they arrive, they contract the wound and remodel the stroma. While certain cell surface receptors promote fibroblast migration, others cause repulsion between fibroblasts upon contact, seemingly opposing their clustering within the wound bed. Eph receptor–ephrin interactions on colliding cells trigger this repulsion, but how fibroblasts transition to clustering behaviour during healing remains unclear. Syndecan-4 modulates transmembrane receptors involved in wound healing, including receptors for the extracellular matrix and growth factors. As a result, Sdc4–/– mice experience delayed healing due to impaired fibroblast recruitment. In this study, we report that syndecan-4 also regulates fibroblast repulsion during wound healing. We discover that syndecan-4 inhibits the expression and signalling of EphA2 by activating PKCα. Changes in syndecan-4 expression, such as those observed during wound healing, alter fibroblast behaviour from repulsion to adhesion upon cell collision by modulating EphA2 levels. Moreover, we find that EphA2 expression is suppressed in wound bed fibroblasts in a syndecan-4-dependent manner, explaining how fibroblast clustering is achieved during wound healing.
SP140 represses specific loci by recruiting polycomb repressive complex 2 and NuRD complex
Authors: Tamburri Simone , Zucchelli Chiara , Matafora Vittoria , Zapparoli Ettore , Jevtic Zivojin , Farris Francesco , Iannelli Fabio , Musco Giovanna , Bachi Angela 
Published: December 2024

Abstract
SP140, a lymphocytic-restricted protein, is an epigenetic reader working as a corepressor of genes implicated in inflammation and orchestrating macrophage transcriptional programs to maintain cellular identity. Reduced SP140 expression is associated both to autoimmune diseases and blood cancers. However, the molecular mechanisms that link SP140 altered protein levels to detrimental effects on the immune response and cellular growth, as well as the interactors through which SP140 promotes gene silencing, remain elusive. In this work, we have applied a multi-omics approach (i.e. interactomics, ChIP-seq and proteomics) in two Burkitt lymphoma cell lines to identify both interactors and target genes of endogenous SP140. We found that SP140 interacts with the PRC2 and NuRD complexes, and we showed that these interactions are functional as SP140 directs H3K27me3 deposition and NuRD binding on a set of target genes implicated in cellular growth and leukemia progression.