bluuebunny/crossref_metadata_2025_split huggingface dataset:
RPLP1 restricts HIV-1 transcription by disrupting C/EBPβ binding to the LTR
Authors: Yang Weijing , Wang Hong , Li Zhaolong , Zhang Lihua , Liu Jianhui , Kirchhoff Frank , Huan Chen , Zhang Wenyan 
Published: June 2024

AbstractLong-term non-progressors (LTNPs) of HIV-1 infection may provide important insights into mechanisms involved in viral control and pathogenesis. Here, our results suggest that the ribosomal protein lateral stalk subunit P1 (RPLP1) is expressed at higher levels in LTNPs compared to regular progressors (RPs). Functionally, RPLP1 inhibits transcription of clade B HIV-1 strains by occupying the C/EBPβ binding sites in the viral long terminal repeat (LTR). This interaction requires the α-helixes 2 and 4 domains of RPLP1 and is evaded by HIV-1 group M subtype C and group N, O and P strains that do not require C/EBPβ for transcription. We further demonstrate that HIV-1-induced translocation of RPLP1 from the cytoplasm to the nucleus is essential for antiviral activity. Finally, knock-down of RPLP1 promotes reactivation of latent HIV-1 proviruses. Thus, RPLP1 may play a role in the maintenance of HIV-1 latency and resistance to RPLP1 restriction may contribute to the effective spread of clade C HIV-1 strains.
Sugar-based synthesis of an enantiomorphically pure zeolite
Authors: Sala Andrés , Jordá José L. , Sastre German , Llamas-Saiz Antonio L. , Rey Fernando , Valencia Susana 
Published: June 2024

AbstractZeolites, well-known by their high selectivities in catalytic and separation processes due to their porous nature, play a crucial role in various applications. One significant long-term objective is the synthesis of enantiopure zeolites, potentially enabling enantioselective processes. Earlier attempts result in partial success, yielding some enantiomorphically enriched zeolites. In this study, we introduce a zeolite synthesis approach utilizing chiral organic structure directing agents (ch-OSDAs) derived from sugars, guiding the crystallization process toward achieving enantiomorphically pure S-STW zeolite. The purity of the zeolite is confirmed through extensive analyses of individual crystals using single-crystal X-ray diffraction, extracting Flack parameters and space groups. Theoretical and structural investigations confirm that the sugar-derived ch-OSDA perfectly fits the characteristic helicoidal channel of the zeolite structure, featuring its efficacy in achieving enantiopure zeolites.
PJA1-mediated suppression of pyroptosis as a driver of docetaxel resistance in nasopharyngeal carcinoma
Authors: Huang Sheng-Yan , Gong Sha , Zhao Yin , Ye Ming-Liang , Li Jun-Yan , He Qing-Mei , Qiao Han , Tan Xi-Rong , Wang Jing-Yun , Liang Ye-Lin , Huang Sai-Wei , He Shi-Wei , Li Ying-Qin , Xu Sha , Li Ying-Qing , Liu Na 
Published: June 2024

AbstractChemoresistance is a main reason for treatment failure in patients with nasopharyngeal carcinoma, but the exact regulatory mechanism underlying chemoresistance in nasopharyngeal carcinoma remains to be elucidated. Here, we identify PJA1 as a key E3 ubiquitin ligase involved in nasopharyngeal carcinoma chemoresistance that is highly expressed in nasopharyngeal carcinoma patients with nonresponse to docetaxel-cisplatin-5-fluorouracil induction chemotherapy. We find that PJA1 facilitates docetaxel resistance by inhibiting GSDME-mediated pyroptosis in nasopharyngeal carcinoma cells. Mechanistically, PJA1 promotes the degradation of the mitochondrial protein PGAM5 by increasing its K48-linked ubiquitination at K88, which further facilitates DRP1 phosphorylation at S637 and reduced mitochondrial reactive oxygen species production, resulting in suppression of GSDME-mediated pyroptosis and the antitumour immune response. PGAM5 knockdown fully restores the docetaxel sensitization effect of PJA1 knockdown. Moreover, pharmacological targeting of PJA1 with the small molecule inhibitor RTA402 enhances the docetaxel sensitivity of nasopharyngeal carcinoma in vitro and in vivo. Clinically, high PJA1 expression indicates inferior survival and poor clinical efficacy of TPF IC in nasopharyngeal carcinoma patients. Our study emphasizes the essential role of E3 ligases in regulating chemoresistance and provides therapeutic strategies for nasopharyngeal carcinoma based on targeting the ubiquitin-proteasome system.
Physical exercise restores adult neurogenesis deficits induced by simulated microgravity
Authors: Gros Alexandra , Furlan Fandilla Marie , Rouglan Vanessa , Favereaux Alexandre , Bontempi Bruno , Morel Jean-Luc 
Published: June 2024

AbstractCognitive impairments have been reported in astronauts during spaceflights and documented in ground-based models of simulated microgravity (SMG) in animals. However, the neuronal causes of these behavioral effects remain largely unknown. We explored whether adult neurogenesis, known to be a crucial plasticity mechanism supporting memory processes, is altered by SMG. Adult male Long-Evans rats were submitted to the hindlimb unloading model of SMG. We studied the proliferation, survival and maturation of newborn cells in the following neurogenic niches: the subventricular zone (SVZ)/olfactory bulb (OB) and the dentate gyrus (DG) of the hippocampus, at different delays following various periods of SMG. SMG exposure for 7 days, but not shorter periods of 6 or 24 h, resulted in a decrease of newborn cell proliferation restricted to the DG. SMG also induced a decrease in short-term (7 days), but not long-term (21 days), survival of newborn cells in the SVZ/OB and DG. Physical exercise, used as a countermeasure, was able to reverse the decrease in newborn cell survival observed in the SVZ and DG. In addition, depending on the duration of SMG periods, transcriptomic analysis revealed modifications in gene expression involved in neurogenesis. These findings highlight the sensitivity of adult neurogenesis to gravitational environmental factors during a transient period, suggesting that there is a period of adaptation of physiological systems to this new environment.
A hybrid framework for estimating nonlinear functions of quantum states
Authors: Zhou You , Liu Zhenhuan 
Published: June 2024

AbstractEstimating nonlinear functions of quantum states, such as the moment $${{{\rm{tr}}}}({\rho }^{m})$$

tr

(

ρ

m

)

, is of fundamental and practical interest in quantum science and technology. Here we show a quantum-classical hybrid framework to measure them, where the quantum part is constituted by the generalized swap test, and the classical part is realized by postprocessing the result from randomized measurements. This hybrid framework utilizes the partial coherent power of the intermediate-scale quantum processor and, at the same time, dramatically reduces the number of quantum measurements and the cost of classical postprocessing. We demonstrate the advantage of our framework in the tasks of state-moment estimation and quantum error mitigation.
Sugar-sweetened beverage but not diluted cloudy apple juice consumption induces post-prandial endotoxemia in healthy adults
Authors: Staltner Raphaela , Valder Sarah , Wodak Maximilian F. , Köpsel Magdalena , Herdegen Volker , Esatbeyoglu Tuba , Kostov Tihomir , Diel Patrick , Bergheim Ina 
Published: June 2024

AbstractSugar beverages are discussed as critical in the development of metabolic endotoxemia. Here, employing a cross-over design study we assessed the effect of diluted cloudy apple juice (AJ), an iso-caloric and -sweetened placebo (P), or water (W) on post-prandial endotoxemia in healthy, normal weight adults. After obtaining fasting blood, 19 healthy men and women consumed 500 mL AJ, P, or W in a randomized order and blood was taken 120 and 180 min later. Caco-2 cells were incubated with the beverages. Markers of intestinal barrier function were assessed. The intake of P but not of AJ or W was associated with a significant increase in TLR2 ligands and bacterial endotoxin in serum after 120 min and 180 min, respectively. P but not AJ significantly increased bacterial toxin permeation in Caco-2 cells. Our results suggest that the effects of sugar-sweetened beverages on markers of intestinal barrier function markedly differ from those of fruit juices.
Ionospheric irregularities at Jupiter observed by JWST
Authors: Melin Henrik , O’Donoghue J. , Moore L. , Stallard T. S. , Fletcher L. N. , Roman M. T. , Harkett J. , King O. R. T. , Thomas E. M. , Wang R. , Tiranti P. I. , Knowles K. L. , de Pater I. , Fouchet T. , Fry P. H. , Wong M. H. , Holler B. J. , Hueso R. , James M. K. , Orton G. S. , Mura A. , Sánchez-Lavega A. , Lellouch E. , de Kleer K. , Showalter M. R. 
Published: June 2024

AbstractJupiter’s upper atmosphere is composed of a neutral thermosphere and charged ionosphere. In the latter, the dominant molecular ion H3+ emits in the near-infrared, allowing for the remote exploration of the physical properties of the upper atmosphere. However, the Jovian low-latitude ionosphere remains largely unexplored because H3+ emissions from this region are faint and spectrally entangled with bright neutral species, such as CH4. Here, we present James Webb Space Telescope H3+ observations of Jupiter’s low-latitude ionosphere in the region of the Great Red Spot, showing unexpected small-scale intensity features such as arcs, bands and spots. Our observations may imply that the low-latitude ionosphere of Jupiter is strongly coupled to the lower atmosphere via gravity waves that superimpose to produce this complex and intricate morphology.
Climate change to exacerbate the burden of water collection on women’s welfare globally
Authors: Carr Robert , Kotz Maximilian , Pichler Peter-Paul , Weisz Helga , Belmin Camille , Wenz Leonie 
Published: June 2024

AbstractClimate change is aggravating water scarcity worldwide. In rural households lacking access to running water, women often bear the responsibility for its collection, with adverse effects on their well being through long daily time commitments, physical strain and mental distress. Here we show that rising temperatures will exacerbate this water collection burden globally. Using fixed-effects regression, we analyse the effect of climate conditions on self-reported water collection times for 347 subnational regions across four continents from 1990 to 2019. Historically, a 1 °C temperature rise increased daily water collection times by 4 minutes. Reduced precipitation historically increased water collection time, most strongly where precipitation levels were low or fewer women employed. Accordingly, due to warming by 2050, daily water collection times for women without household access could increase by 30% globally and up to 100% regionally, under a high-emissions scenario. This underscores a gendered dimension of climate impacts, which undermines womens’ welfare.
Wave-momentum shaping for moving objects in heterogeneous and dynamic media
Authors: Orazbayev Bakhtiyar , Malléjac Matthieu , Bachelard Nicolas , Rotter Stefan , Fleury Romain 
Published: June 2024

AbstractLight and sound waves can move objects through the transfer of linear or angular momentum, which has led to the development of optical and acoustic tweezers, with applications ranging from biomedical engineering to quantum optics. Although impressive manipulation results have been achieved, the stringent requirement for a highly controlled, low-reverberant and static environment still hinders the applicability of these techniques in many scenarios. Here we overcome this challenge and demonstrate the manipulation of objects in disordered and dynamic media by optimally tailoring the momentum of sound waves iteratively in the far field. The method does not require information about the object’s physical properties or the spatial structure of the surrounding medium but relies only on a real-time scattering matrix measurement and a positional guide-star. Our experiment demonstrates the possibility of optimally moving and rotating objects to extend the reach of wave-based object manipulation to complex and dynamic scattering media. We envision new opportunities for biomedical applications, sensing and manufacturing.
Resource demands in telco data centers
Authors: Paranou Dimitra , Pentelas Angelos , Doukas George , Chondralis Konstantinos , Katsiros Dimitris , Angelou Evangelos , Anastopoulos Nikos , Giannopoulos Giorgos , Papastefanatos George 
Published: June 2024

AbstractTelecommunication (telco) cloud services have emerged as crucial components in the modern digital landscape, offering extensive capabilities for data management, connectivity, and service provision. However, research on telco clouds lacks comprehensive data on the characteristics of production workloads, which is fundamental for designing effective resource management systems, such as workload schedulers and power management mechanisms. To this end, this paper addresses a substantial gap in telco cloud research by creating a comprehensive dataset that encapsulates crucial information regarding the pattern demands of applications within telco data centers. In addition, the proposed dataset contributes to the field by enabling strategic network configuration, optimizing data center sizing, facilitating proactive decision-making for data center operations, but its applicability extends beyond these cases. These examples illustrate the practical value of the dataset in enhancing efficiency, reducing operational costs, and ensuring optimal performance within telecommunication data centers.
Chromosome-level genome assembly of Euphorbia tirucalli (Euphorbiaceae), a highly stress-tolerant oil plant
Authors: Wei Zuoying , Feng Chao , Xu Jiayun , Shi Xizuo , Kang Ming , Wang Jing 
Published: June 2024

AbstractEuphorbia, one of the largest genera of flowering plants, is well-known for containing many biofuel crops. Euphorbia tirucalli, an evergreen succulent mainly native to the Africa continent but cultivated worldwide, is a promising petroleum plant with high tolerance to drought and salt stress. However, the exploration of such an important plant resource is severely hampered by the lack of a reference genome. Here, we present the chromosome-level genome assembly of E. tirucalli using PacBio HiFi sequencing and Hi-C technology. Its genome size was approximately 745.62 Mb, with a contig N50 of 74.16 Mb. A total of 743.63 Mb (99.73%) of the assembled sequences were anchored to 10 chromosomes with a complete BUSCO score of 97.80%. Genome annotation revealed 26,304 protein-coding genes, and 76.37% of the genome was identified as repeat elements. The high-quality genome provides valuable genetic resources that would be useful for unraveling the genetic mechanisms of biofuel synthesis and evolutionary adaptation of E. tirucalli.
Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus
Authors: Yuan Yixin , Zhong Tianxing , Wang Yifei , Yang Jinquan , Gui Lang , Shen Yubang , Zhou Jiajun , Chung-Davidson Yu-Wen , Li Weiming , Xu Jinkai , Li Jiale , Li Mingyou , Ren Jianfeng 
Published: June 2024

AbstractAcrossocheilus fasciatus is a stream-dwelling fish species of the Barbinae subfamily. It is valued for its colorfully striped appearance and delicious meat. This species is also characterized by apparent sexual dimorphism and toxic ovum. Biology and aquaculture researches of A. fasciatus are hindered by the lack of a high-quality reference genome. Here, we report chromosome-level genome assemblies of the male and female A. fasciatus. The HiFi-only genome assemblies for both female and male individuals were 899.13 Mb (N50 length of 32.58 Mb) and 885.68 Mb (N50 length of 33.06 Mb), respectively. Notably, a substantial proportion of the assembled sequences, accounting for 96.15% and 98.35% for female and male genomes, respectively, were successfully anchored onto 25 chromosomes utilizing Hi-C data. We annotated the female assembly as a reference genome and identified a total of 400.62 Mb (44.56%) repetitive sequences, 27,392 protein-coding genes, and 35,869 ncRNAs. The high-quality male and female reference genomes will provide genomic resources for developing sex-specific molecular markers, inform single-sex breeding, and elucidate genetic mechanisms of sexual dimorphism.
A dataset of trophic state index for nation-scale lakes in China from 40-year Landsat observations
Authors: Hu Minqi , Ma Ronghua , Xue Kun , Cao Zhigang , Chen Xi , Xiong Junfeng , Xu Jinduo , Huang Zehui , Yu Zhengyang 
Published: June 2024

AbstractTrophic state index (TSI) serves as a key indicator for quantifying and understanding the lake eutrophication, which has not been fully explored for long-term water quality monitoring, especially for small and medium inland waters. Landsat satellites offer an effective complement to facilitate the temporal and spatial monitoring of multi-scale lakes. Landsat surface reflectance products were utilized to retrieve the annual average TSI for 2693 lakes over 1 km2 in China from 1984 to 2023. Our method first distinguishes lake types by pixels with a decision tree and then derives relationships between trophic state and algal biomass index. Validation with public reports and existing datasets confirmed the good consistency and reliability. The dataset provides reliable annual TSI results and credible trends for lakes under different area scales, which can serve as a reference for further research and provide convenience for lake sustainable management.
A dataset of high-resolution digital elevation models of the Skeiðarársandur kettle holes, Southern Iceland
Authors: Szafraniec Joanna Ewa 
Published: June 2024

AbstractIn studies of the relief evolution of smaller landforms, up to several dozen meters in width/diameter, digital elevation models (DEMs) freely accessible in different repositories may be insufficient in terms of resolution. Existing geophysical or photogrammetric equipment is not always available due to costs, conditions and regulations, especially for students or young researchers. An alternative may be the handy-held ground-based Structure from Motion technique. It allows us to obtain free high-resolution DEMs (~0.05 m) using open-source software. The method was tested on kettle holes of the glacial flood origin on Skeiðarársandur (S Iceland). The material was collected in 2022 at two outwash levels of different ages and vegetation cover. The dataset is available in the Zenodo repository; the first part is data processed in point clouds and DEMs, and the second includes original videos in MOV format. The data can be used as a reference to assess changes in the kettle hole relief in subsequent research seasons, as a methodological study for other projects, or for didactic purposes.
INSPIRE, a publicly available research dataset for perioperative medicine
Authors: Lim Leerang , Lee Hyeonhoon , Jung Chul-Woo , Sim Dayeon , Borrat Xavier , Pollard Tom J. , Celi Leo A. , Mark Roger G. , Vistisen Simon T. , Lee Hyung-Chul 
Published: June 2024

AbstractWe present the INSPIRE dataset, a publicly available research dataset in perioperative medicine, which includes approximately 130,000 surgical operations at an academic institution in South Korea over a ten-year period between 2011 and 2020. This comprehensive dataset includes patient characteristics such as age, sex, American Society of Anesthesiologists physical status classification, diagnosis, surgical procedure code, department, and type of anaesthesia. The dataset also includes vital signs in the operating theatre, general wards, and intensive care units (ICUs), laboratory results from six months before admission to six months after discharge, and medication during hospitalisation. Complications include total hospital and ICU length of stay and in-hospital death. We hope this dataset will inspire collaborative research and development in perioperative medicine and serve as a reproducible external validation dataset to improve surgical outcomes.
Exploration on OCT biomarker candidate related to macular edema caused by diabetic retinopathy and retinal vein occlusion in SD-OCT images
Authors: Tao Yuhui , Ge Lexin , Su Na , Li Mingchao , Fan Wen , Jiang Lin , Yuan Songtao , Chen Qiang 
Published: June 2024

AbstractTo improve the understanding of potential pathological mechanisms of macular edema (ME), we try to discover biomarker candidates related to ME caused by diabetic retinopathy (DR) and retinal vein occlusion (RVO) in spectral-domain optical coherence tomography images by means of deep learning (DL). 32 eyes of 26 subjects with non-proliferative DR (NPDR), 77 eyes of 61 subjects with proliferative DR (PDR), 120 eyes of 116 subjects with branch RVO (BRVO), and 17 eyes of 15 subjects with central RVO (CRVO) were collected. A DL model was implemented to guide biomarker candidate discovery. The disorganization of the retinal outer layers (DROL), i.e., the gray value of the retinal tissues between the external limiting membrane (ELM) and retinal pigment epithelium (RPE), the disrupted and obscured rate of the ELM, ellipsoid zone (EZ), and RPE, was measured. In addition, the occurrence, number, volume, and projected area of hyperreflective foci (HRF) were recorded. ELM, EZ, and RPE are more likely to be obscured in RVO group and HRFs are observed more frequently in DR group (all P ≤ 0.001). In conclusion, the features of DROL and HRF can be possible biomarkers related to ME caused by DR and RVO in OCT modality.
Pseudomonas flavocrustae sp. nov., an endophyte with plant growth promoting traits isolated from Passiflora incarnata
Authors: Cueva-Yesquén Luis Gabriel , Sartoratto Adilson , da Silva Santos Adriana , de Melo Itamar Soares , Fantinatti-Garboggini Fabiana 
Published: June 2024

AbstractA polyphasic approach was applied to characterize taxonomically a novel endophytic bacterial strain, designated as EP178T, which was previously isolated from Passiflora incarnata leaves and characterized as plant-growth promoter. The strain EP178T forms Gram stain-negative and rod-shaped cells, and circular and yellow-pigmented colonies. Its growth occurs at 10–37 °C, at pH 6.0–8.0, and tolerates up to 7% (w/v) NaCl. The major cellular fatty acids found were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω6c /C16:1 ω7c), and C16:0, and the predominant ubiquinone was Q-9. The phylogenetic and nucleotide-similarity analysis with 16S rRNA gene sequences showed that strain EP178T belongs to Pseudomonas genus. The genomic-based G + C content was 65.5%. The average nucleotide identity and digital DNA-DNA hybridization values between strains EP178T and the closest type strain, P. oryzihabitans DSM 6835T, were 92.6% and 52.2%, respectively. Various genes associated with plant-growth promoting mechanisms were annotated from genome sequences. Based on the phenotypic, genomic, phylogeny and chemotaxonomic data, strain EP178T represents a new species of the genus Pseudomonas, for which the name Pseudomonas flavocrustae sp. nov. was proposed. The type strain is EP178T (= CBMAI 2609T = ICMP 24844T = MUM 23.01T).