bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking
Authors: Grasekamp Kyrie P. , Beaud Benyahia Basile , Taib Najwa , Audrain Bianca , Bardiaux Benjamin , Rossez Yannick , Izadi-Pruneyre Nadia , Lejeune Maylis , Trivelli Xavier , Chouit Zina , Guerardel Yann , Ghigo Jean-Marc , Gribaldo Simonetta , Beloin Christophe 
Published: November 2023

AbstractE. coli and most other diderm bacteria (those with two membranes) have an inner membrane enriched in glycerophospholipids (GPLs) and an asymmetric outer membrane (OM) containing GPLs in its inner leaflet and primarily lipopolysaccharides in its outer leaflet. In E. coli, this lipid asymmetry is maintained by the Mla system which consists of six proteins: the OM lipoprotein MlaA extracts GPLs from the outer leaflet, and the periplasmic chaperone MlaC transfers them across the periplasm to the inner membrane complex MlaBDEF. However, GPL trafficking still remains poorly understood, and has only been studied in a handful of model species. Here, we investigate GPL trafficking in Veillonella parvula, a diderm Firmicute with an Mla system that lacks MlaA and MlaC, but contains an elongated MlaD. V. parvula mla mutants display phenotypes characteristic of disrupted lipid asymmetry which can be suppressed by mutations in tamB, supporting that these two systems have opposite GPL trafficking functions across diverse bacterial lineages. Structural modelling and subcellular localisation assays suggest that V. parvula MlaD forms a transenvelope bridge, comprising a typical inner membrane-localised MCE domain and, in addition, an outer membrane ß-barrel. Phylogenomic analyses indicate that this elongated MlaD type is widely distributed across diderm bacteria and likely forms part of the ancestral functional core of the Mla system, which would be composed of MlaEFD only.
SLC35D3 promotes white adipose tissue browning to ameliorate obesity by NOTCH signaling
Authors: Wang Hongrui , Yu Liang , Wang Jin’e , Zhang Yaqing , Xu Mengchen , Lv Cheng , Cui Bing , Yuan Mengmeng , Zhang Yu , Yan Yupeng , Hui Rutai , Wang Yibo 
Published: November 2023

AbstractWhite adipose tissue browning can promote lipid burning to increase energy expenditure and improve adiposity. Here, we show that Slc35d3 expression is significantly lower in adipose tissues of obese mice. While adipocyte-specific Slc35d3 knockin is protected against diet-induced obesity, adipocyte-specific Slc35d3 knockout inhibits white adipose tissue browning and causes decreased energy expenditure and impaired insulin sensitivity in mice. Mechanistically, we confirm that SLC35D3 interacts with the NOTCH1 extracellular domain, which leads to the accumulation of NOTCH1 in the endoplasmic reticulum and thus inhibits the NOTCH1 signaling pathway. In addition, knockdown of Notch1 in mouse inguinal white adipose tissue mediated by orthotopic injection of AAV8-adiponectin-shNotch1 shows considerable improvement in obesity and glucolipid metabolism, which is more pronounced in adipocyte-specific Slc35d3 knockout mice than in knockin mice. Overall, in this study, we reveal that SLC35D3 is involved in obesity via NOTCH1 signaling, and low adipose SLC35D3 expression in obesity might be a therapeutic target for obesity and associated metabolic disorders.
Regulation of the physiology and virulence of Ralstonia solanacearum by the second messenger 2′,3′-cyclic guanosine monophosphate
Authors: Li Xia , Yin Wenfang , Lin Junjie Desmond , Zhang Yong , Guo Quan , Wang Gerun , Chen Xiayu , Cui Binbin , Wang Mingfang , Chen Min , Li Peng , He Ya-Wen , Qian Wei , Luo Haibin , Zhang Lian-Hui , Liu Xue-Wei , Song Shihao , Deng Yinyue 
Published: November 2023

AbstractPrevious studies have demonstrated that bis-(3',5')-cyclic diguanosine monophosphate (bis-3',5'-c-di-GMP) is a ubiquitous second messenger employed by bacteria. Here, we report that 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) controls the important biological functions, quorum sensing (QS) signaling systems and virulence in Ralstonia solanacearum through the transcriptional regulator RSp0980. This signal specifically binds to RSp0980 with high affinity and thus abolishes the interaction between RSp0980 and the promoters of target genes. In-frame deletion of RSp0334, which contains an evolved GGDEF domain with a LLARLGGDQF motif required to catalyze 2',3'-cGMP to (2',5')(3',5')-cyclic diguanosine monophosphate (2',3'-c-di-GMP), altered the abovementioned important phenotypes through increasing the intracellular 2',3'-cGMP levels. Furthermore, we found that 2',3'-cGMP, its receptor and the evolved GGDEF domain with a LLARLGGDEF motif also exist in the human pathogen Salmonella typhimurium. Together, our work provides insights into the unusual function of the GGDEF domain of RSp0334 and the special regulatory mechanism of 2',3'-cGMP signal in bacteria.
Stabilizing non-iridium active sites by non-stoichiometric oxide for acidic water oxidation at high current density
Authors: Zhou Lingxi , Shao Yangfan , Yin Fang , Li Jia , Kang Feiyu , Lv Ruitao 
Published: November 2023

AbstractStabilizing active sites of non-iridium-based oxygen evolution reaction (OER) electrocatalysts is crucial, but remains a big challenge for hydrogen production by acidic water splitting. Here, we report that non-stoichiometric Ti oxides (TiOx) can safeguard the Ru sites through structural-confinement and charge-redistribution, thereby extending the catalyst lifetime in acid by 10 orders of magnitude longer compared to that of the stoichiometric one (Ru/TiO2). By exploiting the redox interaction-engaged strategy, the in situ growth of TiOx on Ti foam and the loading of Ru nanoparticles are realized in one step. The as-synthesized binder-free Ru/TiOx catalyst exhibits low OER overpotentials of 174 and 265 mV at 10 and 500 mA cm−2, respectively. Experimental characterizations and theoretical calculations confirm that TiOx stabilizes the Ru active center, enabling operation at 10 mA cm−2 for over 37 days. This work opens an avenue of using non-stoichiometric compounds as stable and active materials for energy technologies.
Position error-free control of magnetic domain-wall devices via spin-orbit torque modulation
Authors: Lee Seong-Hyub , Kim Myeonghoe , Whang Hyun-Seok , Nam Yune-Seok , Park Jung-Hyun , Kim Kitae , Kim Minhwan , Shin Jiho , Yu Ji-Sung , Yoon Jaesung , Chang Jun-Young , Kim Duck-Ho , Choe Sug-Bong 
Published: November 2023

AbstractMagnetic domain-wall devices such as racetrack memory and domain-wall shift registers facilitate massive data storage as hard disk drives with low power portability as flash memory devices. The key issue to be addressed is how perfectly the domain-wall motion can be controlled without deformation, as it can replace the mechanical motion of hard disk drives. However, such domain-wall motion in real media is subject to the stochasticity of thermal agitation with quenched disorders, resulting in severe deformations with pinning and tilting. To sort out the problem, we propose and demonstrate a new concept of domain-wall control with a position error-free scheme. The primary idea involves spatial modulation of the spin-orbit torque along nanotrack devices, where the boundary of modulation possesses broken inversion symmetry. In this work, by showing the unidirectional motion of domain wall with position-error free manner, we provide an important missing piece in magnetic domain-wall device development.
Epidermal–dermal coupled spheroids are important for tissue pattern regeneration in reconstituted skin explant cultures
Authors: Lei Mingxing , Jiang Jingwei , Wang Mengyue , Wu Wang , Zhang Jinwei , Liu Wanqian , Zhou Wei , Lai Yung-Chih , Jiang Ting-Xin , Widelitz Randall B. , Harn Hans I-Chen , Yang Li , Chuong Cheng-Ming 
Published: November 2023

AbstractTissue patterning is critical for the development and regeneration of organs. To advance the use of engineered reconstituted skin organs, we study cardinal features important for tissue patterning and hair regeneration. We find they spontaneously form spheroid configurations, with polarized epidermal cells coupled with dermal cells through a newly formed basement membrane. Functionally, the spheroid becomes competent morphogenetic units (CMU) that promote regeneration of tissue patterns. The emergence of new cell types and molecular interactions during CMU formation was analyzed using scRNA-sequencing. Surprisingly, in newborn skin explants, IFNr signaling can induce apical-basal polarity in epidermal cell aggregates. Dermal-Tgfb induces basement membrane formation. Meanwhile, VEGF signaling mediates dermal cell attachment to the epidermal cyst shell, thus forming a CMU. Adult mouse and human fetal scalp cells fail to form a CMU but can be restored by adding IFNr or VEGF to achieve hair regeneration. We find different multi-cellular configurations and molecular pathways are used to achieve morphogenetic competence in developing skin, wound-induced hair neogenesis, and reconstituted explant cultures. Thus, multiple paths can be used to achieve tissue patterning. These insights encourage more studies of “in vitro morphogenesis” which may provide novel strategies to enhance regeneration.
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates
Authors: Yada Yuichiro , Naoki Honda 
Published: November 2023

AbstractThe pair-wise observation of the input and target values obtained from the same sample is mandatory in any prediction problem. In the biomarker discovery of Alzheimer’s disease (AD), however, obtaining such paired data is laborious and often avoided. Accumulation of amyloid-beta (Aβ) in the brain precedes neurodegeneration in AD, and the quantitative accumulation level may reflect disease progression in the very early phase. Nevertheless, the direct observation of Aβ is rarely paired with the observation of other biomarker candidates. To this end, we established a method that quantitatively predicts Aβ accumulation from biomarker candidates by integrating the mostly unpaired observations via a few-shot learning approach. When applied to 5xFAD mouse behavioral data, the proposed method predicted the accumulation level that conformed to the observed amount of Aβ in the samples with paired data. The results suggest that the proposed model can contribute to discovering Aβ predictability-based biomarkers.
Community forest governance and synergies among carbon, biodiversity and livelihoods
Authors: Fischer Harry W. , Chhatre Ashwini , Duddu Apurva , Pradhan Nabin , Agrawal Arun 
Published: November 2023

AbstractForest landscape restoration has emerged as a key strategy to sequester atmospheric carbon and conserve biodiversity while providing livelihood co-benefits for indigenous peoples and local communities. Using a dataset of 314 forest commons in human-dominated landscapes in 15 tropical countries in Africa, Asia and Latin America, we examine the relationships among carbon sequestered in above-ground woody biomass, tree species richness and forest livelihoods. We find five distinct clusters of forest commons, with co-benefits and trade-offs on multiple dimensions. The presence of a formal community management association and local participation in rule-making are consistent predictors of multiple positive outcomes. These findings, drawn from a range of contexts globally, suggest that empowered local forest governance may support multiple objectives of forest restoration. Our analysis advances understanding of institutional aspects of restoration while underscoring the importance of analysing the interconnections among multiple forest benefits to inform effective interventions for multifunctional tropical forests.
Defensive behavior is linked to altered surface chemistry following infection in a termite society
Authors: Esparza-Mora M. Alejandra , Mazumdar Tilottama , Jiang Shixiong , Radek Renate , Thiem Julian N. , Feng Linshan , Petrašiūnaitė Vesta , Banasiak Ronald , Golian Marek , Gleske Melanie , Lucas Christophe , Springer Andreas , Buellesbach Jan , McMahon Dino P. 
Published: November 2023

AbstractThe care-kill response determines whether a sick individual will be treated or eliminated from an insect society, but little is known about the physiological underpinnings of this process. We exploited the stepwise infection dynamics of an entomopathogenic fungus in a termite to explore how care-kill transitions occur, and identify the chemical cues behind these shifts. We found collective responses towards pathogen-injected individuals to vary according to severity and timing of pathogen challenge, with elimination, via cannibalism, occurring sooner in response to a severe active infection. However, injection with inactivated fungal blastospores also resulted in increased albeit delayed cannibalism, even though it did not universally cause host death. This indicates that the decision to eliminate an individual is triggered before pathogen viability or terminal disease status has been established. We then compared the surface chemistry of differently challenged individuals, finding increased amounts of long-chained methyl-branched alkanes with similar branching patterns in individuals injected with both dead and viable fungal blastospores, with the latter showing the largest increase. This coincided with the highest amounts of observed cannibalism as well as signs of severe moribundity. Our study provides new mechanistic insight into the emergent collective behaviors involved in the disease defense of a termite society.
Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns
Authors: Francisconi Ana Flávia , Marroquín Jonathan Andre Morales , Cauz-Santos Luiz Augusto , van den Berg Cássio , Martins Kauanne Karolline Moreno , Costa Marcones Ferreira , Picanço-Rodrigues Doriane , de Alencar Luciano Delmodes , Zanello Cesar Augusto , Colombo Carlos Augusto , Hernández Brenda Gabriela Díaz , Amaral Danilo Trabuco , Lopes Maria Teresa Gomes , Veasey Elizabeth Ann , Zucchi Maria Imaculada 
Published: November 2023

AbstractThe Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
The effects of precipitation change on urban meadows in different design models and substrates
Authors: Jiang Yarong , Yuan Tao 
Published: November 2023

AbstractClimate change, such as temperature and precipitation changes, is becoming increasingly obvious, and in this context, planting designs need to urgently consider future climate change in advance. A field experiment was conducted in Beijing, China, where the future precipitation is predicted to increase, and extra irrigation was used to simulate the future precipitation increase. The species richness of sown meadows, including spontaneous plants and sown plants, and the adaptive strategies of the communities were recorded under different types of design models and substrates. The results showed that precipitation increased the diversity of sown plants and resource-demanding spontaneous plants but had no significant effect on the dry matter content of the entire community of species. Moreover, the interactions among precipitation and substrate, especially the design models, were significant. Of the models, the three-layer model had the highest species richness and least invasive plants. In addition, increased precipitation significantly changed the functional strategy of the plant community away from ruderals and towards competitor-stress tolerant species. This study provides guidance for the design and management of naturalistic plant communities under climate change.
PTPRC functions as a prognosis biomarker in the tumor microenvironment of cutaneous melanoma
Authors: Li Xuemei , Yue Zhanghui , Wang Dan , Zhou Lu 
Published: November 2023

AbstractCutaneous melanoma is one of the most malignant types of skin cancer, with an extremely poor prognosis. Immune cells infiltrated in the tumor microenvironment (TME) affects melanoma initiation, progression, prognosis and immunotherapy strategies in melanoma. The potential utility of TME-related genes as a prognostic model for melanoma and as a predictor of immunotherapeutic response merits further exploration. In this study, we determined that an immune-related gene, protein tyrosine phosphatase receptor type C (PTPRC), was positively correlated with the positive prognosis of melanoma patients. Integration of this gene with TNM classification created a predictive model that showed better performance in determining overall survival than others. PTPRC expression was positively correlated with the levels of immune checkpoint molecules, and PTPRC knockdown significantly enhanced the migration, invasion, and proliferation of melanoma cells. Finally, immunohistochemical results from HPA and Real-time quantitative PCR of clinical tissues confirmed that PTPRC expression was higher in melanoma than in normal skin. In conclusion, PTPRC served as a potential predictor of survival and response to immunotherapy in melanoma patients. The risk model combining the PTPRC and TNM classifications holds the potential to be a promising tool for prognostic prediction of cutaneous melanoma. This will help in the effective clinical management of melanoma patients.
Proximate composition of Vitex doniana and Saba comorensis fruits
Authors: Charles Dominic , Mgina Clarence 
Published: November 2023

AbstractThe wild fruits of Vitex doniana and Saba comorensis were randomly collected from Pwani and Tanga regions. Laboratory analysis was done using the methods described by the Association of Official Analytical Chemists AOAC (1995 and 2000). The amount of protein was 7.13 ± 0.04% and 21.73 ± 0.02% in V. doniana fruits while the fat contents were 2.4 ± 0.00% and 1.9 ± 0.10% in V. doniana fruits. The amount of fats in S. comorensis fruits ranged from 0.00 to 0.01% for the fruit samples from both Pwani and Tanga regions, however the differences was not statistically significant (P > 0.05). The amounts of carbohydrates in V. doniana 23.98 ± 0.20% and in S. comorensis fruit samples (23.81 ± 0.38%) from Pwani Region were not statistically difference. The differences can be attributed to environmental and soil factors. S. comorensis fruit samples from Tanga had ash 4.20 ± 0.01% and moisture content 70.97 ± 0.04%. These values were higher than those observed for S. comorensis fruit samples from Pwani. The amount of ash is indicative of potential elements like sodium and potassium which are beneficial in human health for the development of bones. These fruits have significant amounts of carbohydrate and protein and hence healthy for consumption as part of human diet.
Computer-aided diagnosis of keratoconus through VAE-augmented images using deep learning
Authors: Agharezaei Zhila , Firouzi Reza , Hassanzadeh Samira , Zarei-Ghanavati Siamak , Bahaadinbeigy Kambiz , Golabpour Amin , Akbarzadeh Reyhaneh , Agharezaei Laleh , Bakhshali Mohamad Amin , Sedaghat Mohammad Reza , Eslami Saeid 
Published: November 2023

AbstractDetecting clinical keratoconus (KCN) poses a challenging and time-consuming task. During the diagnostic process, ophthalmologists are required to review demographic and clinical ophthalmic examinations in order to make an accurate diagnosis. This study aims to develop and evaluate the accuracy of deep convolutional neural network (CNN) models for the detection of keratoconus (KCN) using corneal topographic maps. We retrospectively collected 1758 corneal images (978 normal and 780 keratoconus) from 1010 subjects of the KCN group with clinically evident keratoconus and the normal group with regular astigmatism. To expand the dataset, we developed a model using Variational Auto Encoder (VAE) to generate and augment images, resulting in a dataset of 4000 samples. Four deep learning models were used to extract and identify deep corneal features of original and synthesized images. We demonstrated that the utilization of synthesized images during training process increased classification performance. The overall average accuracy of the deep learning models ranged from 99% for VGG16 to 95% for EfficientNet-B0. All CNN models exhibited sensitivity and specificity above 0.94, with the VGG16 model achieving an AUC of 0.99. The customized CNN model achieved satisfactory results with an accuracy and AUC of 0.97 at a much faster processing speed compared to other models. In conclusion, the DL models showed high accuracy in screening for keratoconus based on corneal topography images. This is a development toward the potential clinical implementation of a more enhanced computer-aided diagnosis (CAD) system for KCN detection, which would aid ophthalmologists in validating the clinical decision and carrying out prompt and precise KCN treatment.
Long-term continuous cultivation of Kenyan infant fecal microbiota using the host adapted PolyFermS model
Authors: Rachmühl Carole , Lacroix Christophe , Cabrera Paula Momo , Geirnaert Annelies 
Published: November 2023

AbstractAppropriate in vitro models to investigate the impact of novel nutritional strategies on the gut microbiota of infants living in rural Africa are scarce. Here, we aimed to develop such a continuous gut fermentation model based on the PolyFermS platform, which allows controlled and stable long-term cultivation of colon microbiota in conditions akin the host. Nine immobilized Kenyan infant fecal microbiota were used as inoculum for continuous PolyFermS colon models fed with medium mimicking the weaning infant diet. Fructo-oligosaccharides (FOS) supplementation (1, 4 and 8 g/L) and cultivation pH (5.8 and 6.3) were investigated stepwise. Conditions providing a close match between fecal and in vitro microbiota (pH 5.8 with 1 g/L FOS) were selected for investigating long-term stability of four Kenyan infant PolyFermS microbiota. The shared fraction of top bacterial genera between fecal and in vitro microbiota was high (74–89%) and stable during 107 days of continuous cultivation. Community diversity was maintained and two distinct fermentation metabolite profiles of infant fecal microbiota were observed. Three propiogenic and one butyrogenic metabolite profile of infant fecal microbiota established from day 8 onwards and stayed stable. We present here the first rationally designed continuous cultivation model of African infant gut microbiota. This model will be important to assess the effect of dietary or environmental factors on the gut microbiota of African infants with high enteropathogen exposure.