bluuebunny/crossref_metadata_2025 huggingface dataset:
PRRX1-TOP2A interaction is a malignancy-promoting factor in human malignant peripheral nerve sheath tumours
Authors: Takihira Shota , Yamada Daisuke , Osone Tatsunori , Takao Tomoka , Sakaguchi Masakiyo , Hakozaki Michiyuki , Itano Takuto , Nakata Eiji , Fujiwara Tomohiro , Kunisada Toshiyuki , Ozaki Toshifumi , Takarada Takeshi
Published: March 2024

Background

Paired related-homeobox 1 (PRRX1) is a transcription factor in the regulation of developmental morphogenetic processes. There is growing evidence that PRRX1 is highly expressed in certain cancers and is critically involved in human survival prognosis. However, the molecular mechanism of PRRX1 in cancer malignancy remains to be elucidated.

Methods

PRRX1 expression in human Malignant peripheral nerve sheath tumours (MPNSTs) samples was detected immunohistochemically to evaluate survival prognosis. MPNST models with PRRX1 gene knockdown or overexpression were constructed in vitro and the phenotype of MPNST cells was evaluated. Bioinformatics analysis combined with co-immunoprecipitation, mass spectrometry, RNA-seq and structural prediction were used to identify proteins interacting with PRRX1.

Results

High expression of PRRX1 was associated with a poor prognosis for MPNST. PRRX1 knockdown suppressed the tumorigenic potential. PRRX1 overexpressed in MPNSTs directly interacts with topoisomerase 2 A (TOP2A) to cooperatively promote epithelial-mesenchymal transition and increase expression of tumour malignancy-related gene sets including mTORC1, KRAS and SRC signalling pathways. Etoposide, a TOP2A inhibitor used in the treatment of MPNST, may exhibit one of its anticancer effects by inhibiting the PRRX1–TOP2A interaction.

Conclusion

Targeting the PRRX1–TOP2A interaction in malignant tumours with high PRRX1 expression might provide a novel tumour-selective therapeutic strategy.
LSD1 modulates the bone metastasis of breast cancer cells through hnRNPA2B1-mediated sorting of exosomal miRNAs
Authors: Liu Ziyu , Xin Benkai , Zhang Nan , An Peipei , Shi Yueru , Yang Jingtong , Wan Youzhong , He Yuquan , Hu Xin
Published: March 2024

Bone metastasis is a key contributor to morbidity and mortality of breast cancer patients. We have previously shown that exosomal miRNAs derived from LSD1 knockdown (KD) breast cancer cells inhibit osteoblast differentiation and promote osteoclast differentiation. However, how LSD1 regulates exosomal miRNAs and whether miRNAs promote bone metastasis through the formation of pre-metastatic niches remains unclear. In vivo experiments demonstrates that exosomes derived from LSD1 KD breast cancer cells significantly promoted bone metastasis. To explore the mechanism underlying the effect of LSD1 on exosomes in breast cancer cells, exosomal and cellular miRNAs from control, LSD1 KD, and rescue cells were sequenced. Interestingly, approximately 80% of LSD1-associated miRNAs were downregulated in exosomes from LSD1 KD cells. The consensus sequence UAGGGC, was identified in many miRNAs downregulated in LSD1 KD exosomes. We found that hnRNPA2B1 regulated the exosomal sorting of miR-6881-3p and some other miRNAs. LSD1 deficiency reduced hnRNPA2B1 expression in breast cancer cells by decreasing the level of H3K9me2 demethylation in the promoter region of the hnRNPA2B1 gene. Our study revealed that LSD1 plays a crucial role in the regulation of exosomal sorting of miRNA.
The rapid proximity labeling system PhastID identifies ATP6AP1 as an unconventional GEF for Rheb
Authors: Feng Ran , Liu Feng , Li Ruofei , Zhou Zhifen , Lin Zhuoheng , Lin Song , Deng Shengcheng , Li Yingying , Nong Baoting , Xia Ying , Li Zhiyi , Zhong Xiaoqin , Yang Shuhan , Wan Gang , Ma Wenbin , Wu Su , Songyang Zhou
Published: March 2024

Rheb is a small G protein that functions as the direct activator of the mechanistic target of rapamycin complex 1 (mTORC1) to coordinate signaling cascades in response to nutrients and growth factors. Despite extensive studies, the guanine nucleotide exchange factor (GEF) that directly activates Rheb remains unclear, at least in part due to the dynamic and transient nature of protein–protein interactions (PPIs) that are the hallmarks of signal transduction. Here, we report the development of a rapid and robust proximity labeling system named Pyrococcus horikoshii biotin protein ligase (PhBPL)-assisted biotin identification (PhastID) and detail the insulin-stimulated changes in Rheb-proximity protein networks that were identified using PhastID. In particular, we found that the lysosomal V-ATPase subunit ATP6AP1 could dynamically interact with Rheb. ATP6AP1 could directly bind to Rheb through its last 12 amino acids and utilizes a tri-aspartate motif in its highly conserved C-tail to enhance Rheb GTP loading. In fact, targeting the ATP6AP1 C-tail could block Rheb activation and inhibit cancer cell proliferation and migration. Our findings highlight the versatility of PhastID in mapping transient PPIs in live cells, reveal ATP6AP1’s role as an unconventional GEF for Rheb, and underscore the importance of ATP6AP1 in integrating mTORC1 activation signals through Rheb, filling in the missing link in Rheb/mTORC1 activation.
Unconventional superconductivity in Cr-based compound Pr3Cr10−xN11
Authors: Chen C. S. , Wu Q. , Zou M. Y. , Zhu Z. H. , Yang Y. X. , Tan C. , Hillier A. D. , Chang J. , Luo J. L. , Wu W. , Shu L.
Published: March 2024

We report results of specific heat and muon spin relaxation (μSR) measurements on a polycrystalline sample of Pr3Cr10−xN11, which shows superconducting state below Tc = 5.25 K, a large upper critical field Hc2 ~ 20 T and a residual Sommerfeld coefficient γ0. The field dependence of γ0(H) resembles γ of the U-based superconductors UTe2 and URhGe at low temperatures. The temperature-dependent superfluid density measured by transverse-field μSR experiments is consistent with a p-wave pairing symmetry. ZF-μSR experiment suggests a time-reversal symmetry broken superconducting transition, and temperature-independent spin fluctuations at low temperatures are revealed by LF-μSR experiments. These results indicate that Pr3Cr10−xN11 is a candidate of p-wave superconductor which breaks time-reversal symmetry.
Integrated optical frequency division for microwave and mmWave generation
Authors: Sun Shuman , Wang Beichen , Liu Kaikai , Harrington Mark W. , Tabatabaei Fatemehsadat , Liu Ruxuan , Wang Jiawei , Hanifi Samin , Morgan Jesse S. , Jahanbozorgi Mandana , Yang Zijiao , Bowers Steven M. , Morton Paul A. , Nelson Karl D. , Beling Andreas , Blumenthal Daniel J. , Yi Xu
Published: March 2024

The generation of ultra-low-noise microwave and mmWave in miniaturized, chip-based platforms can transform communication, radar and sensing systems1–3. Optical frequency division that leverages optical references and optical frequency combs has emerged as a powerful technique to generate microwaves with superior spectral purity than any other approaches4–7. Here we demonstrate a miniaturized optical frequency division system that can potentially transfer the approach to a complementary metal-oxide-semiconductor-compatible integrated photonic platform. Phase stability is provided by a large mode volume, planar-waveguide-based optical reference coil cavity8,9 and is divided down from optical to mmWave frequency by using soliton microcombs generated in a waveguide-coupled microresonator10–12. Besides achieving record-low phase noise for integrated photonic mmWave oscillators, these devices can be heterogeneously integrated with semiconductor lasers, amplifiers and photodiodes, holding the potential of large-volume, low-cost manufacturing for fundamental and mass-market applications13.
Near-ultraviolet photon-counting dual-comb spectroscopy
Authors: Xu Bingxin , Chen Zaijun , Hänsch Theodor W. , Picqué Nathalie
Published: March 2024

Ultraviolet spectroscopy provides unique insights into the structure of matter with applications ranging from fundamental tests to photochemistry in the Earth’s atmosphere and astronomical observations from space telescopes1–8. At longer wavelengths, dual-comb spectroscopy, using two interfering laser frequency combs, has become a powerful technique capable of simultaneously providing a broad spectral range and very high resolution9. Here we demonstrate a photon-counting approach that can extend the unique advantages of this method into ultraviolet regions where nonlinear frequency conversion tends to be very inefficient. Our spectrometer, based on two frequency combs with slightly different repetition frequencies, provides a wide-span, high-resolution frequency calibration within the accuracy of an atomic clock, and overall consistency of the spectra. We demonstrate a signal-to-noise ratio at the quantum limit and an optimal use of the measurement time, provided by the multiplexed recording of all spectral data on a single photon-counter10. Our initial experiments are performed in the near-ultraviolet and in the visible spectral ranges with alkali-atom vapour, with a power per comb line as low as a femtowatt. This crucial step towards precision broadband spectroscopy at short wavelengths paves the way for extreme-ultraviolet dual-comb spectroscopy, and, more generally, opens up a new realm of applications for photon-level diagnostics, as encountered, for example, when driving single atoms or molecules.
A concerted neuron–astrocyte program declines in ageing and schizophrenia
Authors: Ling Emi , Nemesh James , Goldman Melissa , Kamitaki Nolan , Reed Nora , Handsaker Robert E. , Genovese Giulio , Vogelgsang Jonathan S. , Gerges Sherif , Kashin Seva , Ghosh Sulagna , Esposito John M. , Morris Kiely , Meyer Daniel , Lutservitz Alyssa , Mullally Christopher D. , Wysoker Alec , Spina Liv , Neumann Anna , Hogan Marina , Ichihara Kiku , Berretta Sabina , McCarroll Steven A.
Published: March 2024

Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a relationship between people’s cortical neurons and cortical astrocytes. We used single-nucleus RNA sequencing to analyse the prefrontal cortex of 191 human donors aged 22–97 years, including healthy individuals and people with schizophrenia. Latent-factor analysis of these data revealed that, in people whose cortical neurons more strongly expressed genes encoding synaptic components, cortical astrocytes more strongly expressed distinct genes with synaptic functions and genes for synthesizing cholesterol, an astrocyte-supplied component of synaptic membranes. We call this relationship the synaptic neuron and astrocyte program (SNAP). In schizophrenia and ageing—two conditions that involve declines in cognitive flexibility and plasticity1,2—cells divested from SNAP: astrocytes, glutamatergic (excitatory) neurons and GABAergic (inhibitory) neurons all showed reduced SNAP expression to corresponding degrees. The distinct astrocytic and neuronal components of SNAP both involved genes in which genetic risk factors for schizophrenia were strongly concentrated. SNAP, which varies quantitatively even among healthy people of similar age, may underlie many aspects of normal human interindividual differences and may be an important point of convergence for multiple kinds of pathophysiology.
A vagal reflex evoked by airway closure
Authors: Schappe Michael S. , Brinn Philip A. , Joshi Narendra R. , Greenberg Rachel S. , Min Soohong , Alabi AbdulRasheed A. , Zhang Chuchu , Liberles Stephen D.
Published: March 2024

Airway integrity must be continuously maintained throughout life. Sensory neurons guard against airway obstruction and, on a moment-by-moment basis, enact vital reflexes to maintain respiratory function1,2. Decreased lung capacity is common and life-threatening across many respiratory diseases, and lung collapse can be acutely evoked by chest wall trauma, pneumothorax or airway compression. Here we characterize a neuronal reflex of the vagus nerve evoked by airway closure that leads to gasping. In vivo vagal ganglion imaging revealed dedicated sensory neurons that detect airway compression but not airway stretch. Vagal neurons expressing PVALB mediate airway closure responses and innervate clusters of lung epithelial cells called neuroepithelial bodies (NEBs). Stimulating NEBs or vagal PVALB neurons evoked gasping in the absence of airway threats, whereas ablating NEBs or vagal PVALB neurons eliminated gasping in response to airway closure. Single-cell RNA sequencing revealed that NEBs uniformly express the mechanoreceptor PIEZO2, and targeted knockout of Piezo2 in NEBs eliminated responses to airway closure. NEBs were dispensable for the Hering–Breuer inspiratory reflex, which indicated that discrete terminal structures detect airway closure and inflation. Similar to the involvement of Merkel cells in touch sensation3,4, NEBs are PIEZO2-expressing epithelial cells and, moreover, are crucial for an aspect of lung mechanosensation. These findings expand our understanding of neuronal diversity in the airways and reveal a dedicated vagal pathway that detects airway closure to help preserve respiratory function.
A global dataset on species occurrences and functional traits of Schizothoracinae fish
Authors: Du Tingqi , Ding Chengzhi , Yang Ke , Chen Jinnan , Liu Xingchen , Lv Wenna , Ding Liuyong , He Dekui , Tao Juan
Published: March 2024

The Schizothoracinae fish are a natural group of cyprinids widely distributed in rivers and lakes in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. These fish parallelly evolved with the QTP uplift and are thus important for uncovering geological history, the paleoclimatic environment, and the mechanisms of functional adaptation to environmental change. However, a dataset including species occurrences and functional traits, which are essential for resolving the above issues and guiding relevant conservation, remains unavailable. To fill this gap, we systematically compiled a comprehensive dataset on species occurrences and functional traits of Schizothoracinae fish from our long-term field samplings and various sources (e.g., publications and online databases). The dataset includes 7,333 occurrence records and 3,204 records of 32 functional traits covering all the genera and species of Schizothoracinae fish (i.e., 12 genera and 125 species or subspecies). Sampling records spanned over 180 years. This dataset will serve as a valuable resource for future research on the evolution, historical biogeography, responses to environmental change, and conservation of the Schizothoracinae fish.
Spatial and temporal assessment of snake encounters in urban Delhi, India
Authors: Barhadiya Gaurav , Purkayastha Jayaditya , Saha Ashis Kumar , Ghosh Chirashree
Published: March 2024

Delhi, the capital city of India is, highly urbanized and surrounded by remnant forest, farms, ridges, and other green areas experience regular snake encounters in and around residential, institutional, and industrial areas. A total of 41 months of sampling from January 2019 to May 2022 was conducted wherein we, studied the snake assemblage in Delhi to determine the species composition, encounter frequency, seasonal activity patterns, and probable encounter sites in an urban setup. We documented 372 individuals belonging to 15 species from seven families out of 23 species found in Delhi. Snakes were found inside forests, public parks, homes, drain networks, streets, office buildings, and even in school-college buildings. The most recorded species being Ptyas mucosa (37.37%, n = 139), Naja naja (19.62%, n = 73), and Lycodon aulicus (13.44%, n = 50). The highest numbers of incidents were reported in the month of July (22.04%, n = 82) and August (19.89%, n = 74) during the peak monsoon season, for identifying high encounter sites, we used a geostatistical modeling tool, Ordinary kriging to identify places having more snake occurrences. We further used a statistical spatial method called average nearest neighbor distance to detect the pattern distribution of snake species. Spatial interpolation done through Ordinary kriging highlighted two areas having concentrated snake encounters. The results of the average nearest neighbor distance analysis showed three species having clustered and two species having dispersed distribution. The incidence of snake encounters was found to be highly seasonal and appeared to be associated mainly with monthly rainfall, temperature, and humidity. The findings of this study on snakes’ distribution patterns provide valuable insights into the conservation of these species. Understanding their habitat preferences and spatial distribution is crucial for the implementation of effective conservation strategies.
Research on fabric surface defect detection algorithm based on improved Yolo_v4
Authors: Li Yuanyuan , Song Liyuan , Cai Yin , Fang Zhijun , Tang Ming
Published: March 2024

In industry, the task of defect classification and defect localization is an important part of defect detection system. However, existing studies only focus on one task and it is difficult to ensure the accuracy of both tasks. This paper proposes a defect detection system based on improved Yolo_v4, which greatly improves the detection ability of minor defects. For K_Means algorithm clustering prianchors question with strong subjectivity, the paper proposes the Density Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm to determine the number of Anchors. To solve the problem of low detection rate of small targets caused by insufficient reuse rate of low-level features in CSPDarknet53 feature extraction network, this paper proposes an ECA-DenseNet-BC-121 feature extraction network to improve it. And the Dual Channel Feature Enhancement (DCFE) module is proposed to improve the local information loss and gradient propagation obstruction caused by quad chain convolution in PANet networks to improve the robustness of the model. The experimental results on the fabric surface defect detection datasets show that the mAP of the improved Yolo_v4 is 98.97%, which is 7.67% higher than SSD, 3.75% higher than Faster_RCNN, 10.82% higher than Yolo_v4 tiny, and 5.35% higher than Yolo_v4, and the detection speed reaches 39.4 fps. It can meet the real-time monitoring needs of industrial sites.
Spatiotemporal optical vortex reconnections of multi-vortices
Authors: Adams Jordan , Agha Imad , Chong Andy
Published: March 2024

Vortex reconnections are ubiquitous events found in diverse media. Here we show that vortex reconnections also occur between spatiotemporal vortices in optical waves. Since vortices exhibit orbital angular momentum (OAM), the reconnections of optical vortices create a variety of connected OAM states. Dispersion and diffraction can cause different reconnection pairs, depending on the orientation of the vortices. The transverse crossing of two vortices with a topological charge of one can produce unique vortex loop reconnection patterns. Higher topological charges result in arrays of vortex loops and connection points. Crossing of three vortices produces spherical structures made of three symmetrical vortex arms. A three vortices reconnection with higher topological charges develops complicated patterns similar to turbulence cascade phenomena in other media. Studying optical vortex interactions may bring insight into vortex reconnections in other fields. We also provide experimental results of two-vortex loop interaction.
Americans misperceive the frequency and format of political debate
Authors: Bailey Erica R. , White Michael W. , Iyengar Sheena S. , Akinola Modupe
Published: March 2024

Disagreement over divergent viewpoints seems like an ever-present feature of American life—but how common is debate and with whom do debates most often occur? In the present research, we theorize that the landscape of debate is distorted by social media and the salience of negativity present in high-profile spats. To understand the true landscape of debate, we conducted three studies (N = 2985) across online and lab samples. In contrast to the high-profile nature of negative debates with strangers, we found that people most commonly debate close contacts, namely family members and good friends. In addition, they often report feeling positive after engaging in debate. We then directly measured misperceptions regarding debate in a representative sample of Americans (N = 1991). We found that Americans systematically overestimated how often others engage in debate. This overestimation extended across debate partners (family members, good friends, acquaintances, coworkers, and strangers) and contexts (in-person and online; p’s < 0.001, d’s > 0.98), most strongly overestimating how often Americans debate strangers online. This misprediction may be psychologically costly: overestimating how often Americans debate strangers online significantly predicted greater hopelessness in the future of America. Together, our findings suggest that Americans may experience a false reality about the landscape of debate which can unnecessarily undermine their hope about the future.
Seasonal changes of prokaryotic microbial community structure in Zhangjiayan Reservoir and its response to environmental factors
Authors: Yu Xintao , Li Yong , Wu Yue , Gao Hui , Liu Wei , Liu Huan , Gong Sidan , Wu Honglian
Published: March 2024

As a typical sub-deep reservoir in the upper reaches of the Yangtze River in the southwest region, Zhangjiayan Reservoir is also an important source of drinking water. Exploring the role of microorganisms in the material cycle of water bodies is of great significance for preventing the exacerbation of eutrophication in the reservoir. In this study, water samples from the overlying water of five points in the reservoir were collected four times in spring (April), summer (July), autumn (November), and winter (January) of 2022–2023 using a gas-tight water sampler. Physicochemical factors were measured, and the microbial community structure was analyzed by high-throughput MiSeq sequencing of the V3–V4 hypervariable region of 16S rRNA gene in order to explore the relationship between physicochemical factors and microbial community structure and the dominant microbial populations that affect eutrophication of the reservoir. The following results were obtained through analysis. Among the 20 overlying water samples from Zhangjiayan Reservoir, a total of 66 phyla, 202 classes, 499 orders, 835 families, 1716 genera, and 27,904 ASVs of the bacterial domain were detected. The phyla Proteobacteria and Actinobacteria were dominant in the microbial community of the overlying water in Zhangjiayan Reservoir. At the genus level, hgcI_clade and Actinobacteria had the highest abundance and was the dominant population. The microbial community in the water of Zhangjiayan Reservoir has a high level of diversity. The diversity index ranked by numerical order was winter > autumn > summer > spring. Significant differences were found in the composition and structure of the microbial community between the spring/summer and autumn/winter seasons (p < 0.05). Total phosphorus, dissolved total phosphorus, soluble reactive phosphorus, and dissolved oxygen have a significant impact on the composition and structure of the microbial community (p < 0.01). The bacterial community in the overlying water of Zhangjiayan Reservoir showed a mainly positive correlation. Sphingomonas, Brevundimonas, and Blastomonas were the central populations of the bacterial community in the overlying water of Zhangjiayan Reservoir. This study indicates that environmental factors, such as phosphorus and other nutrients, have a significant impact on the formation of the microbial community structure in different seasons. Sphingomonas, Brevundimonas, and Blastomonas are key populations that may have a significant impact on eutrophication in Zhangjiayan Reservoir.
An exploratory study of the effect of age and gender on face scanning during affect recognition in immersive virtual reality
Authors: González-Gualda Luz M. , Vicente-Querol Miguel A. , García Arturo S. , Molina José P. , Latorre José M. , Fernández-Sotos Patricia , Fernández-Caballero Antonio
Published: March 2024

A person with impaired emotion recognition is not able to correctly identify facial expressions represented by other individuals. The aim of the present study is to assess eyes gaze and facial emotion recognition in a healthy population using dynamic avatars in immersive virtual reality (IVR). For the first time, the viewing of each area of interest of the face in IVR is studied by gender and age. This work in healthy people is conducted to assess the future usefulness of IVR in patients with deficits in the recognition of facial expressions. Seventy-four healthy volunteers participated in the study. The materials used were a laptop computer, a game controller, and a head-mounted display. Dynamic virtual faces randomly representing the six basic emotions plus neutral expression were used as stimuli. After the virtual human represented an emotion, a response panel was displayed with the seven possible options. Besides storing the hits and misses, the software program internally divided the faces into different areas of interest (AOIs) and recorded how long participants looked at each AOI. As regards the overall accuracy of the participants’ responses, hits decreased from the youngest to the middle-aged and older adults. Also, all three groups spent the highest percentage of time looking at the eyes, but younger adults had the highest percentage. It is also noteworthy that attention to the face compared to the background decreased with age. Moreover, the hits between women and men were remarkably similar and, in fact, there were no statistically significant differences between them. In general, men paid more attention to the eyes than women, but women paid more attention to the forehead and mouth. In contrast to previous work, our study indicates that there are no differences between men and women in facial emotion recognition. Moreover, in line with previous work, the percentage of face viewing time for younger adults is higher than for older adults. However, contrary to earlier studies, older adults look more at the eyes than at the mouth.Consistent with other studies, the eyes are the AOI with the highest percentage of viewing time. For men the most viewed AOI is the eyes for all emotions in both hits and misses. Women look more at the eyes for all emotions, except for joy, fear, and anger on hits. On misses, they look more into the eyes for almost all emotions except surprise and fear.
Label-free nonlinear optical signatures of extracellular vesicles in liquid and tissue biopsies of human breast cancer
Authors: Sorrells Janet E. , Park Jaena , Aksamitiene Edita , Marjanovic Marina , Martin Elisabeth M. , Chaney Eric J. , Higham Anna M. , Cradock Kimberly A. , Liu Zheng G. , Boppart Stephen A.
Published: March 2024

Extracellular vesicles (EVs) have been implicated in metastasis and proposed as cancer biomarkers. However, heterogeneity and small size makes assessments of EVs challenging. Often, EVs are isolated from biofluids, losing spatial and temporal context and thus lacking the ability to access EVs in situ in their native microenvironment. This work examines the capabilities of label-free nonlinear optical microscopy to extract biochemical optical metrics of EVs in ex vivo tissue and EVs isolated from biofluids in cases of human breast cancer, comparing these metrics within and between EV sources. Before surgery, fresh urine and blood serum samples were obtained from human participants scheduled for breast tumor surgery (24 malignant, 6 benign) or healthy participants scheduled for breast reduction surgery (4 control). EVs were directly imaged both in intact ex vivo tissue that was removed during surgery and in samples isolated from biofluids by differential ultracentrifugation. Isolated EVs and freshly excised ex vivo breast tissue samples were imaged with custom nonlinear optical microscopes to extract single-EV optical metabolic signatures of NAD(P)H and FAD autofluorescence. Optical metrics were significantly altered in cases of malignant breast cancer in biofluid-derived EVs and intact tissue EVs compared to control samples. Specifically, urinary isolated EVs showed elevated NAD(P)H fluorescence lifetime in cases of malignant cancer, serum-derived isolated EVs showed decreased optical redox ratio in stage II cancer, but not earlier stages, and ex vivo breast tissue showed an elevated number of EVs in cases of malignant cancer. Results further indicated significant differences in the measured optical metabolic signature based on EV source (urine, serum and tissue) within individuals.
Genome-wide identification of WRKY transcription factor family members in Miscanthus sinensis (Miscanthus sinensis Anderss)
Authors: Yan Yongkang , Yan Zhanyou , Zhao Guofang
Published: March 2024

Miscanthus is an emerging sustainable bioenergy crop whose growing environment is subject to many abiotic and biological stresses. WRKY transcription factors play an important role in stress response and growth of biotic and abiotic. To clarify the distribution and expression of the WRKY genes in Miscanthus, it is necessary to classify and phylogenetically analyze the WRKY genes in Miscanthus. The v7.1 genome assembly of Miscanthus was analyzed by constructing an evolutionary tree. In Miscanthus, there are 179 WRKY genes were identified. The 179 MsWRKYs were classified into three groups with conserved gene structure and motif composition. The tissue expression profile of the WRKY genes showed that MsWRKY genes played an essential role in all growth stages of plants. At the early stage of plant development, the MsWRKY gene is mainly expressed in the rhizome of plants. In the middle stage, it is mainly expressed in the leaf. At the end stage, mainly in the stem. According to the results, it showed significant differences in the expression of the MsWRKY in different stages of Miscanthus sinensis. The results of the study contribute to a better understanding of the role of the MsWRKY gene in the growth and development of Miscanthus.
High methionine diet mediated oxidative stress and proteasome impairment causes toxicity in liver
Authors: Derouiche Faouzia , Djemil Randa , Sebihi Fatima Zohra , Douaouya Lilia , Maamar Hichem , Benjemana Katia
Published: March 2024

Methionine (Met) rich diet inducing oxidative stress is reported to alter many organs. Proteasome as a regulator of oxidative stress can be targeted. This study was performed to investigate if excessive methionine supplementation causes hepatotoxicity related to proteasome dysfunction under endogenous oxidative stress in rats. Male Wistar albino rats (n = 16) were divided into controls and treated groups. The treated rats (n = 08) received orally l-methionine (1 g/kg/day) for 21 days. Total homocysteine (tHcy), total oxidant status (TOS), total antioxidant status (TAS), hepatic enzymes levels: aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), alkaline phosphatase (ALP), with total bilirubin (TBil), albumin (Alb), and C-reactive protein (CRP) were determined in plasma by biochemical assays. Liver supernatants were used for malondialdehyde (MDA), protein carbonyls (PC), glutathione (GSH), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), 20S proteasome activities and their subunits expression, tumor necrosis factor-α (TNF-α), and interleukin 6 (IL-6) evaluation by appropriate methods and light microscopy for liver histological examination. Methionine treatment increased homocysteine, TOS, oxidative stress index (OSI), MDA and PC but decreased TAS, GSH, CAT, SOD, GPx with the 20S proteasome activities and their β subunits expression. Liver proteins: AST, ALT, LDH, ALP, TBil and CRP were increased but Alb was decreased. Liver histology was also altered. An increase in liver TNF-α and IL-6 levels were observed. These findings indicated that methionine supplementation associated oxidative stress and proteasome dysfunction, caused hepatotoxicity and inflammation in rat. Further investigations should be to better understand the relation between methionine, oxidative stress, proteasome, and liver injuries.
Characterization of polychaetes inhabiting estuaries and inner bays by composition analysis of amino acids and lactate enantiomers
Authors: Onozato Mayu , Shinohara Wataru , Osaka Yuichiro , Sakamoto Tatsuya , Umino Maho , Nishigaki Atsuko , Okoshi Kenji , Fukushima Takeshi
Published: March 2024

In this study, we investigated the composition of free amino acids and lactate (Lac) in polychaetes in river estuaries and inner bays using chromatographic techniques. Both l-amino acids and d-amino acids (d-asparagine, d-alanine (d-Ala), d-serine, d-aspartic acid, and d-proline (d-Pro)) were detected, indicating that polychaetes contain some d-amino acids. Some polychaete species exhibited notable amino acid levels, such as glycine in Capitellidae sp. and Thelepus sp., d-Pro in Glycera sp., and β-Ala in Scoletoma nipponica and Scoletoma sp.. High d-Lac levels were detected in Tylorrhynchus osawai and Hediste diadroma, (691 and 797 μmol/100 g-wet, respectively), with the d-form exceeding 98%. T. osawai was dominant in the upper tidal-sensitive zone, wherein other organisms were less abundant because of low salinity (3–8 PSU). Seasonal differences in the concentrations of components in T. osawai were observed, particularly a significant increase in d-Lac in the reproductive period. Notably, the d-Lac concentrations of T. osawai were higher upstream than downstream. Thus, d-Lac might be involved in strategies underlying adaptations to low salinity and reproductive activity. These results suggest that both the d-form of Lac and amino acids may play certain physiological roles in the life of polychaetes.
Complex hybrid weighted pruning method for accelerating convolutional neural networks
Authors: Geng Xu , Gao Jinxiong , Zhang Yonghui , Xu Dingtan
Published: March 2024

The increasing interest in filter pruning of convolutional neural networks stems from its inherent ability to effectively compress and accelerate these networks. Currently, filter pruning is mainly divided into two schools: norm-based and relation-based. These methods aim to selectively remove the least important filters according to predefined rules. However, the limitations of these methods lie in the inadequate consideration of filter diversity and the impact of batch normalization (BN) layers on the input of the next layer, which may lead to performance degradation. To address the above limitations of norm-based and similarity-based methods, this study conducts empirical analyses to reveal their drawbacks and subsequently introduces a groundbreaking complex hybrid weighted pruning method. By evaluating the correlations and norms between individual filters, as well as the parameters of the BN layer, our method effectively identifies and prunes the most redundant filters in a robust manner, thereby avoiding significant decreases in network performance. We conducted comprehensive and direct pruning experiments on different depths of ResNet using publicly available image classification datasets, ImageNet and CIFAR-10. The results demonstrate the significant efficacy of our approach. In particular, when applied to the ResNet-50 on the ImageNet dataset, achieves a significant reduction of 53.5% in floating-point operations, with a performance loss of only 0.6%.
Identified S100A9 as a target for diagnosis and treatment of ulcerative colitis by bioinformatics analysis
Authors: Tan Lulu , Li Xin , Qin Hong , Zhang Qingqing , Wang Jinfeng , Chen Tao , Zhang Chengwu , Zhang Xiaoying , Tan Yuyan
Published: March 2024

Ulcerative colitis (UC) is a chronic, recurrent inflammatory bowel disease. UC confronts with severe challenges including the unclear pathogenesis and lack of specific diagnostic markers, demanding for identifying predictive biomarkers for UC diagnosis and treatment. We perform immune infiltration and weighted gene co-expression network analysis on gene expression profiles of active UC, inactive UC, and normal controls to identify UC related immune cell and hub genes. Neutrophils, M1 macrophages, activated dendritic cells, and activated mast cells are significantly enriched in active UC. MMP-9, CHI3L1, CXCL9, CXCL10, CXCR2 and S100A9 are identified as hub genes in active UC. Specifically, S100A9 is significantly overexpressed in mice with colitis. The receiver operating characteristic curve demonstrates the excellent performance of S100A9 expression in diagnosing active UC. Inhibition of S100A9 expression reduces DSS-induced colonic inflammation. These identified biomarkers associated with activity in UC patients enlighten the new insights of UC diagnosis and treatment.
Sex-specific associations of serum cortisol with brain biomarkers of Alzheimer’s risk
Authors: Mosconi Lisa , Williams Schantel , Carlton Caroline , Zarate Camila , Boneu Camila , Fauci Francesca , Ajila Trisha , Nerattini Matilde , Jett Steven , Andy Caroline , Battista Michael , Pahlajani Silky , Osborne Joseph , Brinton Roberta Diaz , Dyke Jonathan P.
Published: March 2024

Emerging evidence implicates chronic psychological stress as a risk factor for Alzheimer’s disease (AD). Herein, we examined the relationships between serum cortisol and multimodality brain AD biomarkers in 277 cognitively normal midlife individuals at risk for AD. Overall, higher cortisol was associated with lower total brain volume, lower glucose metabolism (CMRglc) in frontal cortex, and higher β-amyloid (Aβ) load in AD-vulnerable regions; and marginally associated with phosphocreatine to ATP ratios (PCr/ATP) in precuneus and parietal regions. Sex-specific modification effects were noted: in women, cortisol exhibited stronger associations with Aβ load and frontal CMRglc, the latter being more pronounced postmenopause. In men, cortisol exhibited stronger associations with gray matter volume and PCr/ATP measures. Higher cortisol was associated with poorer delayed memory in men but not in women. Results were adjusted for age, Apolipoprotein E (APOE) epsilon 4 status, midlife health factors, and hormone therapy use. These results suggest sex-specific neurophysiological responses to stress, and support a role for stress reduction in AD prevention.
Fabrication of carbon black nanoparticles from green algae and sugarcane bagasse
Authors: Elmaghraby Nehad A. , Hassaan Mohamed A. , Zien Mohamed A. , Abedelrhim Elsayed M. , Ragab Safaa , Yılmaz Murat , El Nemr Ahmed
Published: March 2024

There are several industrial uses for carbon black (CB), an extremely fine powdered form of elemental carbon that is made up of coalesced particle aggregates and almost spherical colloidal particles. Most carbon black is produced from petroleum-derived feedstock, so there is a need to find an alternative method to produce CB, which relies on renewable resources such as algae and agricultural waste. A process involving hydrolysis, carbonization, and pyrolysis of green algae and sugarcane bagasse was developed, as the optimal hydrolysis conditions (16N sulfuric acid, 70 °C, 1 h, 1:30 g/ml GA or SC to sulfuric acid ratio), a hydrolysis ratio of 62% for SC and 85% for GA were achieved. The acidic solution was carbonized using a water bath, and the solid carbon was then further pyrolyzed at 900 °C. The obtained carbon black has a high carbon content of about 90% which is confirmed by EDX, XRD, and XPS analysis. By comparison carbon black from sugar cane bagasse (CBB) and carbon black from green algae Ulva lactuca (CBG) with commercial carbon black (CCB) it showed the same morphology which was confirmed by SEM analysis. The BET data, showed the high specific surface area of prepared CB, which was 605 (m2/g) for CBB and 424 (m2/g) for CBG compared with commercial carbon black (CBB) was 50 (m2/g), also the mean pore diameter of CBB, CBG and CCB indicated that CBB and CBG were rich in micropores, but CCB was rich in mesoporous according to IUPAC classification. This study might have created a technique that can be used to make carbon black from different kinds of biomass.
Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater
Authors: Ensor Katherine B. , Schedler Julia C. , Sun Thomas , Schneider Rebecca , Mulenga Anthony , Wu Jingjing , Stadler Lauren B. , Hopkins Loren
Published: March 2024

Wastewater surveillance has proven a cost-effective key public health tool to understand a wide range of community health diseases and has been a strong source of information on community levels and spread for health departments throughout the SARS- CoV-2 pandemic. Studies spanning the globe demonstrate the strong association between virus levels observed in wastewater and quality clinical case information of the population served by the sewershed. Few of these studies incorporate the temporal dependence present in sampling over time, which can lead to estimation issues which in turn impact conclusions. We contribute to the literature for this important public health science by putting forward time series methods coupled with statistical process control that (1) capture the evolving trend of a disease in the population; (2) separate the uncertainty in the population disease trend from the uncertainty due to sampling and measurement; and (3) support comparison of sub-sewershed population disease dynamics with those of the population represented by the larger downstream treatment plant. Our statistical methods incorporate the fact that measurements are over time, ensuring correct statistical conclusions. We provide a retrospective example of how sub-sewersheds virus levels compare to the upstream wastewater treatment plant virus levels. An on-line algorithm supports real-time statistical assessment of deviations of virus level in a population represented by a sub-sewershed to the virus level in the corresponding larger downstream wastewater treatment plant. This information supports public health decisions by spotlighting segments of the population where outbreaks may be occurring.
Validation of numerical simulations and experiments on impulse characteristics induced by self-excited oscillation
Authors: Wu Qiang , Ji Guodong , Zhao Jian , Sun Liudang , Han Dapeng , Liu Li , Hu Huaigang , Yu Jinping , Chen Changchang , Sun Yuqi , Guo Jinyong
Published: March 2024

The high-frequency pulse flow, equivalent to the natural frequency of rocks, is generated by a self-excited oscillating cavity to achieve resonance rock-breaking. The flow field and oscillating mechanism of the self-excited oscillating cavity were simulated using the large eddy simulation method of Computational Fluid Dynamics (CFD). A field-scale testing apparatus was developed to investigate the impulse characteristics and verify the simulation results. The results show that the fluid at the outlet at the tool is deflected due to the pulse oscillation of the fluid. The size and shape of low-pressure vortices constantly change, leading to periodic changes in fluid impedance within the oscillating cavity. The impulse frequency reaches its highest point when the length–diameter ratio is 0.67. As the length–diameter ratio increases, the tool pressure loss also increases. Regarding the cavity thickness, the impulse frequency of the oscillating cavity initially decreases, then increases, and finally decreases again. Moreover, both the impulse frequency and pressure loss increase with an increase in displacement. The numerical simulation findings align with the experimental results, thus confirming the validity of the theoretical model. This research provides theoretical guidance for the practical application of resonance rock-breaking technology.
Multi-defect risk assessment in high-speed rail subgrade infrastructure in China
Authors: Wang Jinchen , Zhang Yinsheng , Wang Luqi , Sun Yifan , Zhang Jingyu , Li Jianlin , Li Sen
Published: March 2024

This study addresses the escalating risk of high-speed railway (HSR) infrastructure in China, amplified by climate warming, increased rainfall, frequent extreme weather, and geohazard events. Leveraging a georeferenced dataset of recent HSR defects obtained through an extensive literature review, we employ machine learning techniques for a quantitative multi-defect risk assessment. Climatic, geomorphological, geohydrological, and anthropogenic variables influencing HSR subgrade safety are identified and ranked. Climatic factors significantly impact frost damage and mud pumping, while geomorphological variables exhibit greater influence on settlement and uplift deformation defects. Notably, frost damage is prevalent in the northeast and northwest, mud pumping along the southeast coast, and settlement and uplift deformation in the northwest and central areas. The generated comprehensive risk map underscores high-risk zones, particularly the Menyuan Hui Autonomous and Minle County sections of the Lanzhou-Urumqi HSR, emphasizing the need for focused attention and preventive actions to mitigate potential losses and ensure operational continuity.
Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation
Authors: Sardzikova Sara , Andrijkova Kristina , Svec Peter , Beke Gabor , Klucar Lubos , Minarik Gabriel , Bielik Viktor , Kolenova Alexandra , Soltys Katarina
Published: March 2024

The gut microbiota of paediatric oncology patients undergoing a conditioning regimen before hematopoietic stem cell transplantation is recently considered to play role in febrile neutropenia. Disruption of commensal microbiota and evolution of opportune pathogens community carrying a plethora of antibiotic-resistance genes play crucial role. However, the impact, predictive role and association of patient´s gut resistome in the course of the therapy is still to be elucidated. We analysed gut microbiota composition and resistome of 18 paediatric oncology patients undergoing hematopoietic stem cell transplantation, including 12 patients developing febrile neutropenia, hospitalized at The Bone Marrow Transplantation Unit of the National Institute of Children´s disease in Slovak Republic and healthy individuals (n = 14). Gut microbiome of stool samples obtained in 3 time points, before hematopoietic stem cell transplantation (n = 16), one week after hematopoietic stem cell transplantation (n = 16) and four weeks after hematopoietic stem cell transplantation (n = 14) was investigated using shotgun metagenome sequencing and bioinformatical analysis. We identified significant decrease in alpha-diversity and nine antibiotic-resistance genes msr(C), dfrG, erm(T), VanHAX, erm(B), aac(6)-aph(2), aph(3)-III, ant(6)-Ia and aac(6)-Ii, one week after hematopoietic stem cell transplantation associated with febrile neutropenia. Multidrug-resistant opportune pathogens of ESKAPE, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli found in the gut carried the significant subset of patient’s resistome. Over 50% of patients treated with trimethoprim/sulfamethoxazole, piperacillin/tazobactam and amikacin carried antibiotic-resistance genes to applied treatment. The alpha diversity and the resistome of gut microbiota one week after hematopoietic stem cell transplantation is relevant predictor of febrile neutropenia outcome after hematopoietic stem cell transplantation. Furthermore, the interindividual diversity of multi-drug resistant opportunistic pathogens with variable portfolios of antibiotic-resistance genes indicates necessity of preventive, personalized approach.