bluuebunny/crossref_metadata_2025 huggingface dataset:
Are people willing to pay for reusable bags? The case study in Yogyakarta and Surakarta
Authors: Herawati Dian Rachma , Gravitiani Evi , Ratnadewati Ainina
Published: December 2024

The purpose of this study is to determine the value of Willingness to pay (WTP) reusable bags in an effort to reduce the use of plastic bags and the variables that affect the value of Willingness to pay. This study uses the Contingent Valuation Method (CVM) analysis method and multiple linear regression analysis to determine the factors that affect the magnitude of WTP reusable bag value. The results showed that the characteristics of respondents in this study were dominated by respondents with female gender, in the age range of 20-24 years, with the last high school education (12 years), and at the income level of Rp1,000,000 - Rp5,000,000. As many as 77% of 400 respondents know how to limit the use of plastic bags to preserve the environment. The average WTP value of respondents was Rp4,485, with an economic value of Rp2,553,197,000 per month. Variables that have a significant effect on WTP are age, domicile, recent education, knowledge, and income. At the same time, the sex variable did not have a significant effect on WTP. The public needs to be educated about the purpose of the implementation of paid plastic bags and the use of reusable bags in consumption activities. In addition, there is a need for education about the urgency of the zero waste program in Indonesia.
Potrait on Regulation and Policy to Life on Land
Authors: Asriyani  , Maskun
Published: December 2024

Environmental problems are caused by environmental damage caused by massive deforestation. This happens because humans overuse natural resources without paying attention to the damage that occurs. The goal of maintaining the land ecosystem of life on land affects environmental protection policies so that no more ecological damage occurs in Indonesia. The method used is normative research using legislation and norm systems as the objects of study, such as ideal legal values, legal theories, legal principles, legal teachings, court decisions, and legal policies. Maintaining the land ecosystem of the Life on Land SDGs affects environmental protection policies in Indonesia. Therefore, it is necessary to implement environmental protection regulations, synchronize SDGs 15, and maintain land ecosystems. The SDGs affect environmental protection policies by maintaining and protecting the environment so that no more ecological damage occurs in Indonesia.
A Multiple Streams Analysis: The Policy Process Indonesia’s New Social Forestry Model
Authors: Rahayu Sari , Sakuntaladewi Niken , Fauzi Ridwan , Ramawati  , Nugroho Ardiyanto , Suhartono
Published: December 2024

Indonesia Social Forestry Program was first implemented on the island of Java in the area of the State Forestry Company (Perhutani). “Social forestry” initiatives are emerging to integrate local communities into forest governance. Perhutani implemented the Managing Forest with Community (PHBM) program and formed a Forest Village Community (LMDH) institution. The main aim of this program is to improve the welfare of forest farming communities through tree planting, intercropping, and animal husbandry activities. However, after four decades of implementing the social forestry program, up to fifteen years after the implementation of PHBM, it is considered that it has not answered the challenges of Java’s forests, such as access, poverty in communities around the forest, the ecological crisis, and conflicts over forest area management. In 2017, the Indonesian government introduced a new social forestry scheme in the Perhutani working area, known as the “Social Forestry Forest Utilization Permit” (IPHPS). This research utilizes a qualitative approach, collecting primary and secondary data. This study discusses why and how new social forestry (IPHPS) became part of the government policy agenda. Using the Multiple Streams Framework, this study found complex dynamics surrounding the policy formulation process, leading to the formulation of win-win policies that attempt to cover diverse interests. The political stream is dominant in converging problem and policy streams. The Ministry of Environment and Forestry, acting as a Policy Entrepreneur, utilized the policy window to formulate the IPHPS policy framework and sought to convince other policy actors. This study showed that public issues involving political interests tend to capture attention quickly. Furthermore, it showed that public policy formulation is fraught with contesting various stakeholders’ interests.
Predicting Water Discharge Using Model The Hydrologic Engineering Center Hydrologic Modeling System in the Mallusetasi Watershed
Authors: Wahyuni  , Damayanti Anisa Fitri , Soma Andang Suryana
Published: December 2024

The frequent occurrence of discharge in the watershed makes the Mallusetasi watershed a high contributor to the number of natural disasters in Barru Regency. This causes the need for research related to the discharge in the Mallusetasi watershed. This study aims to determine the magnitude of the Mallusetasi Watershed Flow Regime Coefficient (KRA) and determine the level of validation of the HEC-HMS model in predicting water discharge in the Mallusetasi Watershed in 2022. Factors that affect water discharge in the Year 2022 analysis in the Mallusetasi watershed are land cover, slope, soil type which includes soil hydrology group and soil texture, rainfall, and geology. Based on the results of analysis and simulation in the Year 2022 model, rainfall and soil type are the most influential factors on water discharge in the Mallusetasi watershed. The predicted maximum flow discharge produced by the model is 26.4 m3/s in December with a volume of 985,34 mm. The calibration results of the HEC-HMS model obtained an NSE value of 0,468 and an R2 value of 0,682. After the validation process, the NSE value obtained is 0,373 and R2 with a value of 0,672. The KRA value obtained from the results of the analysis carried out has the highest value of 1140 which is in Sub-basin 3 with a very high classification.
Identification of Mangrove Ecosystem Boundaries in the Coastal Area of Bontang City Based on Tides Using Geospatial Analysis
Authors: Pramono Dwi Agung , Karyati  , Suhardiman Ali , Kiswanto  , Widyasasi Dyah
Published: December 2024

Mangrove ecosystems in coastal areas are important in storing large amounts of carbon and preventing coastal erosion due to sea wave scouring. Mangrove areas have many advantages as examples of mangrove plants that provide good nutrition for the surrounding area. Mangrove plants and surrounding mangrove sediments act as carbon sinks and social benefits for coastal communities. This mangrove area is located between the beach and the river and is influenced by salt water tides. Mangroves play an important ecological role in coastal stabilization by minimizing the impact of wave and wind energy on shorelines and acting as excellent land structural protection. The existence of mangrove forest areas in Bontang City poses a threat of changes in mangrove forest areas caused by various factors, including anthropogenic and global environmental changes. With the development of geospatial science, it can be used to analyze land boundaries that are influenced by sea tides. The main objective of this study is to identify the boundaries of the mangrove ecosystem in the coastal area of Bontang City. This research uses geospatial analysis methods with Remote Sensing and also Geographic Information Systems (GIS). This research shows an overview of the boundaries of the mangrove ecosystem area on the coast of Bontang City along a coastline of 135.79 km and an estimated area of the mangrove ecosystem area of 2,413.14 Ha. The results of this research can be the basis for a rehabilitation program for mangrove ecosystem areas.
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

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

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

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

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

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

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

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

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

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

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

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

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, >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

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

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

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.
Centromeric localization of αKNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions
Authors: Yalagapati Surya Prakash , Ahmadli Ulkar , Sinha Aditya , Kalidass Manikandan , Dabravolski Siarhei , Zuo Sheng , Yadala Ramakrishna , Rutten Twan , Talbert Paul , Berr Alexandre , Lermontova Inna
Published: December 2024

In eukaryotes, accurate chromosome segregation during cell division relies on the centromeric histone H3 variant, CENH3. Our previous work identified KINETOCHORE NULL2 (αKNL2) as a plant CENH3 assembly factor, which contains a centromere-targeting motif, CENPC-k, analogous to the CENPC motif found in CENP-C. We also demonstrated that αKNL2 can bind DNA in vitro in a sequence-independent manner, without the involvement of its CENPC-k motif. In this study, we show that the CENPC-k and CENPC motifs alone are insufficient for centromere targeting in Nicotiana benthamiana and Arabidopsis thaliana. In silico analysis identified adjacent DNA-binding regions near the CENPC-k and CENPC motifs, suggesting their role in centromeric DNA interaction. We further demonstrated that protein fragments containing these motifs effectively target centromeres. Deletion of these DNA-binding domains reduced the centromeric localization of αKNL2-C, while fusing CENPC-k to the non-specific DNA-binding domain of histone-like nucleoid structuring protein from Escherichia coli successfully targeted it to centromeres. Our findings suggest that the centromeric targeting of αKNL2 and CENP-C proteins relies on the CENPC-k/CENPC motifs, and that their sequence-independent DNA-binding activity enhances their centromere anchoring. These insights into the mechanisms of αKNL2 and CENP-C targeting may facilitate the engineering of kinetochore structures by directing chromatin-modifying proteins to centromeres.
Towards next-generation DNA encryption via an expanded genetic system
Authors: Huang Xiaoluo , Hou Zhaohua , Qiang Wei , Wang Honglei , Wang Xiangxiang , Chen Xiaoxu , Hu Xin , Dai Junbiao , Li Lingjun , Zhao Guanghou
Published: December 2024

Information encryption based on DNA data archiving, referred to as DNA encryption, has been advocated for decades and has become highly appealing owing to its remarkable advantages, e.g., high storage capacity, complexity and programmability. Early DNA encryption schemes primarily leveraged the natural four-letter genetic alphabet for data storage, with message-storing DNA sequences easily decrypted by routine DNA sequencing, which is consequently vulnerable to attack and faces severe security challenges. Here, an unnatural base pair (UBP), dNaM-dTPT3, was introduced into the message and/or index DNA sequences, which can be stored either in vitro or in vivo; this approach achieved the bioorthogonal encryption of “secret” messages, where message DNAs could be selectively, faithfully and readily retrieved or read exclusively in the presence of unnatural bases. Furthermore, a separative computational algorithm, named IM-Codec, was developed to encrypt the data into a “key sequence” (KS) and an “information sequence” (IS) through UBP insertion. Finally, a UBP-based multilevel DNA encryption approach was developed and validated for data encryption and decryption. The employment of the UBP expanded genetic system for data encryption should provide valuable solutions for archiving highly confidential data and thus usher in a new era of DNA encryption.
The cytokinin efflux transporter ABCC4 participates in Arabidopsis root system development
Authors: Uragami Takuya , Kiba Takatoshi , Kojima Mikiko , Takebayashi Yumiko , Tozawa Yuzuru , Hayashi Yuki , Kinoshita Toshinori , Sakakibara Hitoshi
Published: December 2024

The directional and sequential flow of cytokinin in plants is organized by a complex network of transporters. Genes involved in several aspects of cytokinin transport have been characterized; however, much of the elaborate system remains elusive. In this study, we used a transient expression system in tobacco (Nicotiana benthamiana) leaves to screen Arabidopsis (Arabidopsis thaliana) transporter genes and isolated ATP-BINDING CASSETTE TRANSPORTER C4 (ABCC4). Validation through drug-induced expression in Arabidopsis and heterologous expression in budding yeast revealed that ABCC4 effluxes the active form of cytokinins. During the seedling stage, ABCC4 was highly expressed in roots, and its expression was upregulated in response to cytokinin application. Loss-of-function mutants of ABCC4 displayed enhanced primary root elongation, similar to mutants impaired in cytokinin biosynthesis or signaling, that was suppressed by exogenous trans-zeatin treatment. In contrast, overexpression of the gene led to suppression of root elongation. These results suggest that ABCC4 plays a role in the efflux of active cytokinin, thereby contributing to root growth regulation. Additionally, cytokinin-dependent enlargement of stomatal aperture was impaired in the loss-of-function and overexpression lines. Our findings contribute to unraveling the many complexities of cytokinin flow and enhance our understanding of the regulatory mechanisms underlying root system development and stomatal opening in plants.
The associations among platelet count, mean platelet volume, and erectile dysfunction: an observational and Mendelian randomization study
Authors: Peng Jingxuan , An Jinshun , Chen Yuxing , Zhou Jun , Xiang Boyu
Published: December 2024

Background

While previous studies have explored the associations and causalities among platelet count (PC), mean platelet volume (MPV), and erectile dysfunction (ED), further investigations are needed to clarify these relationships using advanced methodologies and analyzing specific populations.

Aim

To investigate the associations and causalities among PC, MPV, and ED using observational study and Mendelian randomization (MR) analysis.

Methods

A total of 114 patients with ED and 158 healthy control participants underwent a fasting blood draw to test for PC and MPV along with a comprehensive laboratory examination. The International Erectile Function Index was used to diagnose ED. Genetic variants of ED were obtained from individuals of European ancestry including 6175 ED cases and 217 630 controls. PC and MPV values were obtained from the UK Biobank and Investigating the effect of varying the whole blood inter-donation interval (INTERVAL) studies, encompassing a cohort of 173 480 individuals of European descent. Inverse-variant weighted (IVW), weighted median (WM), and MR-Egger methods were employed in MR analysis to explore the causal effects between variables to assess the impact of PC and MPV on ED. Various sensitivity analyses were employed to ensure the reliability of the results.

Outcomes

Both observational study results and MR results revealed that elevated PC levels were associated with a heightened risk of ED, whereas reductions in MPV were linked to a decreased risk.

Results

Logistic regression analysis indicated that an increased PC was associated with a greater risk of ED, with an odds ratio (OR) of 1.14 (95% CI: 1.08, 1.22; P = .005), whereas decreased MPV was linked to an increased risk for ED, with an OR of 0.65 (95% CI: 0.48, 0.88; P = .003). Our MR analysis also revealed that genetically predicted PC was associated with a 1.09-fold increased risk of ED (95% CI: 1.01, 1.18; P = .016). Conversely, genetically predicted MPV was linked to a 0.93-fold increased risk of ED (95% CI: 0.88, 0.99; P = .014). The absence of heterogeneity (P > .05) and pleiotropy (P > .05) was confirmed through Cochran's Q tests and MR-Egger regression. Exclusion of individual single-nucleotide polymorphisms (SNPs) did not alter the robustness of the results.

Clinical implications

In clinical work, it is an important guide for the prevention, diagnosis, and treatment of ED.

Strengths and limitations

Our study employed a combination of observational studies and MR studies to strengthen our evidence. The observational study's sample size was relatively small, and MR was limited to individuals of European ancestry.

Conclusion

A high PC and a low MPV are associated with an increased risk of ED, highlighting the importance of addressing platelet parameters in ED management.
Race, homosexuality, and AIDS in London: the response of British AIDS voluntary organizations to Black gay men’s sexual health needs during the AIDS crisis (1980s–2000)
Authors: Cann Lucy
Published: December 2024

Focusing on three specific organizations—The Terrence Higgins Trust (THT), Blackliners, and The NAZ Project (Naz)—this article explores the different ways in which voluntary organizations responded to Black gay men (BGM) in Britain during the AIDS crisis from the 1980s to 2000. Illustrating how the place of BGM in Britain at this time was multidimensional and often contradictory, the first section demonstrates how they required safer-sex messaging that took account of the heterogeneous ways in which they experienced the intersection of racism and homophobia. Situated in this context, the second section explores for the first time the well-documented work of THT as it applied to BGM. It shows how although the Trust increasingly recognized the need to reach BGM, white activists struggled to grapple with issues of race. It demonstrates how their work on race was shaped by the broader context of changes to voluntary organizations’ relationship to the state. In doing so, it makes clear the challenges of intersectional activism with communities of colour for white-dominated organizations and sheds light on how the HIV/AIDS voluntary sector responded to communities with particular needs. Taking Black AIDS organizations as its focus, the final section uncovers how Blackliners and Naz centred gay men in their work and reveals their nuanced and culturally sensitive initiatives. By tracing the contrasting ways in which these organizations navigated contested understandings of race in the final decades of the twentieth century, this article demonstrates the real-world consequences of the fragmentation of political conceptions of Blackness.
Engineered Pine Endophytic Fungus Expressing dsRNA Targeting Lethal Genes to Control the Plant Parasitic Nematode Bursaphelenchus xylophilus
Authors: Zhang Wei , Wang Ruijiong , Li Yongxia , Li Dongzhen , Wang Xuan , Wen Xiaojian , Feng Yuqian , Liu Zhenkai , Ma Shuai , Zhang Xingyao
Published: December 2024

The pine wood nematode (PWN), Bursaphelenchus xylophilus, is one of the most serious invasive forest pests, responsible for pine wilt disease (PWD). Currently, there are no effective, environmentally friendly control methods available. RNA interference (RNAi) technology has been extensively utilized to screen functional genes in eukaryotes and to explore sustainable pest management approaches through genetic engineering. In this study, we identified 353 predicted lethal genes in PWN by comparing its genome with those of lethal genes from Caenorhabditis elegans. We selected five predicted lethal genes (Bxy1177, Bxy1239, Bxy1104, Bxy667, and BxyAK1) with identification values exceeding 60% to evaluate their nematicidal effects on PWN. We tested the double-stranded RNA (dsRNA) of these genes using two methods: firstly, soaking in a synthesized dsRNA solution in vitro, or secondly, feeding on a dsRNA-engineered endophytic fungus, Fusarium babinda. Following dsRNA ingestion, either through soaking or fungal feeding, the expression of genes Bxy1177, Bxy667, Bxy1104, and BxyAK1 was significantly suppressed. Notably, nematode populations that consumed fungi expressing dsL1177 and dsAK1 showed substantial declines over time. These findings provide novel insights and a practical foundation for employing endophytic fungi-expressed dsRNA in sustainable pest management strategies.
Pediatric orthopedic all-terrain vehicle injury patterns, surgeries, and complications: appreciating the true morbidity and impact
Authors: Willis Chad B. , Rabenhorst Brien M. , Johnston Kirsten , Bumpass David B.
Published: December 2024

All-terrain vehicle (ATV) accidents frequently cause orthopedic injuries. Previous studies have reported the frequency of fractures in ATV injuries. No studies have provided detailed assessments of fracture patterns, types of operative intervention, or risks for multiple surgeries. A total of 489 patients with ATV-related injuries were treated at one tertiary Level 1 pediatric hospital from January 2011 to December 2016. Medical records were retrospectively reviewed to define orthopedic injuries and treatment. Data were organized to identify fracture patterns, surgeries, and complications. Three age groups were utilized (0–6, 7–12, and ≥13 years). A total of 270 pelvic and extremity fractures occurred in 215 patients (44%); 136 patients (63%) required surgical intervention; 47 patients (22%) required multiple trips to the operating room; 16% of fractures (43/270) were open, and seven developed deep infections. Three patients required amputations, and one death was recorded. No significant differences were found between age and fracture frequency or need for surgery. Surgical rates of supracondylar humerus (97%) and tibial shaft fractures (87%) were higher than historical norms (16–24% and 5–74%, respectively). To date, this is one of the largest single-institution cohorts of ATV-related pediatric orthopedic injuries. Nearly half of ATV-related pediatric trauma patients sustained orthopedic injuries. The majority required surgical treatment, and nearly 1/4 of patients required multiple surgeries. Younger patients were as likely to require surgery as older patients. Supracondylar humerus fractures and tibial shaft fractures from ATVs required surgery at a higher rate than historical norms. The surgical morbidity of pediatric ATV fractures is substantial and should influence safety and prevention education.
Accuracy of breath tests for colorectal neoplasms diagnosis: a meta-analysis
Authors: Tian Lei , Wei Yizhe , Shi Yue , Zhao Yiming , Chen Jiang , Liu Xuan , Lin Bencheng
Published: December 2024

Early noninvasive and rapid screening for colorectal cancer critically influences treatment outcomes. Breath testing, as an emerging screening technology, allows for noninvasive and convenient screening for different biomarkers and is a reliable screening method for various diseases. In this study, a meta-analysis of the accuracy and current status of volatile organic compounds present in exhaled breath for colorectal cancer detection was performed. PubMed, Cochrane Library, and CNKI were searched for relevant studies. The quality of the studies was assessed using the QUADAS-2 criteria, and meta-analysis was performed using RevMan 5.3 and Stata 16. The pooled sensitivity is 90% [95% confidence interval (CI), 85–94%], the pooled specificity is 86% (95% CI, 72–93%), the pooled positive likelihood ratio is 6.3 (95% CI, 3.1–12.6), the negative likelihood ratio is 0.11 (95% CI, 0.07–0.17), and the diagnostic odds ratio is 56 (95% CI, 23–133). Summary receiver operating characteristic analysis revealed an area under the curve of 0.94 (95% CI, 0.91–0.95). The alteration of specific components of exhaled breath is associated with colorectal cancer development, and the selection of biomarkers and detection instruments influence the diagnostic value. What this paper adds to the literature: this meta-analysis provides a comprehensive evaluation of the diagnostic accuracy of volatile organic compounds in breath tests for colorectal cancer, highlighting the influence of biomarker selection and detection methods on screening efficacy.