bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crustal‐Scale Seismic Reflection Profiling Constrains How the Paleo‐Asian Ocean Was Closed
Authors: Tan Xiao‐Miao , Zhou Jian‐Bo , Deng Xiao‐Fan , Wang Hai‐Yan , Hou He‐Sheng , Li Hui‐Lin , Qi Rui , Xie Fan , Gao Rui 
Published: September 2023

AbstractThe Central Asian Orogenic Belt (CAOB) is the most significant accretionary orogenic belt since the Phanerozoic and the most ideal site for studying continental growth evolution processes. A 460‐km‐long high‐resolution crustal‐scale seismic reflection study was conducted across the eastern CAOB in North‐Central China to constrain the closure mode and location of the Paleo‐Asian Ocean, that is, the previous ocean of the CAOB. The resultant seismic reflection profile revealed opposite‐dipping reflectors in the northern and southern parts of the profile, which converge at the profile center to form an inverted U‐shaped reflector pattern near the crust–mantle transition zone beneath the Solonker Suture. The dipping reflectors represent bidirectional fossil subduction zones sloping to the north and south, and the convergence reflector pattern represents the ocean closure location. Integration of these results with available geological data facilitated model construction whereby Paleo‐Asian Ocean closure was accomplished by divergent subduction of the Paleo‐Asian oceanic plate, with northward subduction beneath the southern margin of the Mongolian Block and southward subduction beneath the northern margin of the North China Craton. The oceanic lithosphere contracted and deformed, yielding the observed inverted U‐shaped reflector pattern, representing Paleo‐Asian Ocean closure. This subsurface location lies beneath the Solonker Suture surface exposure, suggesting that this suture marks the ocean closure location, rather than the previously proposed Hegenshan–Heihe Suture to the north or Xar Moron Suture to the south. Our study suggests that divergently dipping subduction and associated accretion and magmatism may constitute the primary continental growth mode for accretionary‐type orogens.
Light People: Professor Fan Wang
Authors: Guo Siqiu 
Published: September 2023

EditorialMy first encounter with Prof. Fan Wang left a profound impression on me. I felt that he was exactly the gentle and courteous scholar depicted in books, well-read in poetry and literature, and exceptionally talented. Through my interactions with Prof. Fan Wang, I deeply sensed his passion for academia and pursuit of knowledge, as well as his warm hospitality, kindness, and gentle demeanor.His thinking is profound and broad, capable of examining issues from various perspectives, and providing inspiration. Prof. Fan Wang is a leading young scientist who actively engages in various academic activities, concerns himself with cutting-edge technological issues, and dedicates himself to overcoming research challenges that can drive advancements and developments in optoelectronics, biophotonics and nanomaterials.Prof. Fan Wang’s talent, knowledge, character, and sense of family responsibility all fill me with admiration and respect. Now, let’s step into the world of Light People Prof. Fan Wang and together, appreciate the brilliance of his carefree and extraordinary life.
Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study
Authors: Wu Junqi , Li Chongwu , Gao Peigen , Zhang Chenhong , Zhang Pei , Zhang Lei , Dai Chenyang , Zhang Kunpeng , Shi Bowen , Liu Mengyang , Zheng Junmeng , Pan Bo , Chen Zhan , Zhang Chao , Liao Wanqing , Pan Weihua , Fang Wenjie , Chen Chang 
Published: September 2023

AbstractWhether the alternated microbiota in the gut contribute to the risk of allograft rejection (AR) and pulmonary infection (PI) in the setting of lung transplant recipients (LTRs) remains unexplored. A prospective multicenter cohort of LTRs was identified in the four lung transplant centers. Paired fecal and serum specimens were collected and divided into AR, PI, and event-free (EF) groups according to the diagnosis at sampling. Fecal samples were determined by metagenomic sequencing. And metabolites and cytokines were detected in the paired serum to analyze the potential effect of the altered microbiota community. In total, we analyzed 146 paired samples (AR = 25, PI = 43, and EF = 78). Notably, we found that the gut microbiome of AR followed a major depletion pattern with decreased 487 species and compositional diversity. Further multi-omics analysis showed depleted serum metabolites and increased inflammatory cytokines in AR and PI. Bacteroides uniformis, which declined in AR (2.4% vs 0.6%) and was negatively associated with serum IL-1β and IL-12, was identified as a driven specie in the network of gut microbiome of EF. Functionally, the EF specimens were abundant in probiotics related to mannose and cationic antimicrobial peptide metabolism. Furthermore, a support-vector machine classifier based on microbiome, metabolome, and clinical parameters highly predicted AR (AUPRC = 0.801) and PI (AUPRC = 0.855), whereby the microbiome dataset showed a particularly high diagnostic power. In conclusion, a disruptive gut microbiota showed a significant association with allograft rejection and infection and with systemic cytokines and metabolites in LTRs.
The Neurod1/4-Ntrk3-Src pathway regulates gonadotrope cell adhesion and motility
Authors: Le Ciclé Charles , Pacini Vincent , Rama Nicolas , Tauszig-Delamasure Servane , Airaud Eloïse , Petit Florence , de Beco Simon , Cohen-Tannoudji Joëlle , L’hôte David 
Published: September 2023

AbstractPituitary gonadotrope cells are essential for the endocrine regulation of reproduction in vertebrates. These cells emerge early during embryogenesis, colonize the pituitary glands and organize in tridimensional networks, which are believed to be crucial to ensure proper regulation of fertility. However, the molecular mechanisms regulating the organization of gonadotrope cell population during embryogenesis remain poorly understood. In this work, we characterized the target genes of NEUROD1 and NEUROD4 transcription factors in the immature gonadotrope αT3-1 cell model by in silico functional genomic analyses. We demonstrated that NEUROD1/4 regulate genes belonging to the focal adhesion pathway. Using CRISPR/Cas9 knock-out approaches, we established a double NEUROD1/4 knock-out αT3-1 cell model and demonstrated that NEUROD1/4 regulate cell adhesion and cell motility. We then characterized, by immuno-fluorescence, focal adhesion number and signaling in the context of NEUROD1/4 insufficiency. We demonstrated that NEUROD1/4 knock-out leads to an increase in the number of focal adhesions associated with signaling abnormalities implicating the c-Src kinase. We further showed that the neurotrophin tyrosine kinase receptor 3 NTRK3, a target of NEUROD1/4, interacts physically with c-Src. Furthermore, using motility rescue experiments and time-lapse video microscopy, we demonstrated that NTRK3 is a major regulator of gonadotrope cell motility. Finally, using a Ntrk3 knock-out mouse model, we showed that NTRK3 regulates gonadotrope cells positioning in the developing pituitary, in vivo. Altogether our study demonstrates that the Neurod1/4-Ntrk3-cSrc pathway is a major actor of gonadotrope cell mobility, and thus provides new insights in the regulation of gonadotrope cell organization within the pituitary gland.
Knockdown of KIF15 suppresses proliferation of prostate cancer cells and induces apoptosis through PI3K/Akt signaling pathway
Authors: Bi Hai , Hou Xiaofei , Shen Qiyang , Liu Zenan , Zhu Xuehua , Ma Lulin , Lu Jian 
Published: September 2023

AbstractProstate cancer is one of the most common malignancies in men, which has been considered a public health threat. KIF15 is a kind of driver protein, and its abnormal expression is closely related to the occurrence and development of malignant tumors. The purpose of the study was to explore the significance and role of KIF15 in prostate cancer and to show some potential value for prostate cancer. Immunohistochemistry analysis showed that KIF15 was highly expressed in prostate cancer tissues, which was also positively correlated with T Infiltrate. The loss-of-function and gain-of-function assays based on prostate cancer cells indicated that the change in KIF15 expression could significantly affect cell proliferation, tumorigenesis, migration, and cell apoptosis. The inhibition of prostate cancer development by KIF15 knockdown was also assured in vivo. The Human Apoptosis Antibody Array showed that CD40L, cytoC, DR6, and p21 were up-regulated upon KIF15 knockdown, while IGF-I and Survivin were down-regulated. Moreover, the involvement of the PI3K/Akt pathway in the KIF15-mediated regulation of prostate cancer was preliminarily proved. In summary, KIF15 was identified to play an important role in the development or biological progress of prostate cancer and is considered to possess the potential to be used as a therapeutic target.
Transposable elements as tissue-specific enhancers in cancers of endodermal lineage
Authors: Karttunen Konsta , Patel Divyesh , Xia Jihan , Fei Liangru , Palin Kimmo , Aaltonen Lauri , Sahu Biswajyoti 
Published: September 2023

AbstractTransposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we utilize unbiased massively parallel reporter assay data using a whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identify distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.
Acquired miR-142 deficit in leukemic stem cells suffices to drive chronic myeloid leukemia into blast crisis
Authors: Zhang Bin , Zhao Dandan , Chen Fang , Frankhouser David , Wang Huafeng , Pathak Khyatiben V. , Dong Lei , Torres Anakaren , Garcia-Mansfield Krystine , Zhang Yi , Hoang Dinh Hoa , Chen Min-Hsuan , Tao Shu , Cho Hyejin , Liang Yong , Perrotti Danilo , Branciamore Sergio , Rockne Russell , Wu Xiwei , Ghoda Lucy , Li Ling , Jin Jie , Chen Jianjun , Yu Jianhua , Caligiuri Michael A. , Kuo Ya-Huei , Boldin Mark , Su Rui , Swiderski Piotr , Kortylewski Marcin , Pirrotte Patrick , Nguyen Le Xuan Truong , Marcucci Guido 
Published: September 2023

AbstractThe mechanisms underlying the transformation of chronic myeloid leukemia (CML) from chronic phase (CP) to blast crisis (BC) are not fully elucidated. Here, we show lower levels of miR-142 in CD34+CD38− blasts from BC CML patients than in those from CP CML patients, suggesting that miR-142 deficit is implicated in BC evolution. Thus, we create miR-142 knockout CML (i.e., miR-142−/−BCR-ABL) mice, which develop BC and die sooner than miR-142 wt CML (i.e., miR-142+/+BCR-ABL) mice, which instead remain in CP CML. Leukemic stem cells (LSCs) from miR-142−/−BCR-ABL mice recapitulate the BC phenotype in congenic recipients, supporting LSC transformation by miR-142 deficit. State-transition and mutual information analyses of “bulk” and single cell RNA-seq data, metabolomic profiling and functional metabolic assays identify enhanced fatty acid β-oxidation, oxidative phosphorylation and mitochondrial fusion in LSCs as key steps in miR-142-driven BC evolution. A synthetic CpG-miR-142 mimic oligodeoxynucleotide rescues the BC phenotype in miR-142−/−BCR-ABL mice and patient-derived xenografts.
Pressure evolution of electron dynamics in the superconducting kagome metal CsV3Sb5
Authors: Wenzel Maxim , Tsirlin Alexander A. , Capitani Francesco , Chan Yuk T. , Ortiz Brenden R. , Wilson Stephen D. , Dressel Martin , Uykur Ece 
Published: September 2023

AbstractThe coexistence of the charge-density wave (CDW) and superconducting phases and their tunability under external pressure remains one of the key points in understanding the electronic structure of AV3Sb5 (A = K, Rb, Cs) kagome metals. Here, we employ synchrotron-based infrared spectroscopy assisted by density-functional calculations to study the pressure evolution of the electronic structure at room temperature up to 17 GPa experimentally. The optical spectrum of CsV3Sb5 is characterized by the presence of localized carriers seen as a broad peak at finite frequencies in addition to the conventional metallic Drude response. The non-monotonic pressure dependence of this low-energy peak reflects the re-entrant behavior of superconductivity and may be interpreted in terms of electron-phonon coupling, varying with the growth and shrinkage of the Fermi surface under pressure. Moreover, drastic modifications in the low-energy interband absorptions are observed upon the suppression of CDW. These changes are related to the upward shift of the Sb2 px + py band that eliminates part of the Fermi surface around the M-point, whereas band saddle points do not move significantly. These observations shed new light on the mixed electronic and lattice origin of the CDW in CsV3Sb5.
Time of day and sleep effects on motor acquisition and consolidation
Authors: Truong Charlène , Ruffino Célia , Gaveau Jérémie , White Olivier , Hilt Pauline M. , Papaxanthis Charalambos 
Published: September 2023

AbstractWe investigated the influence of the time-of-day and sleep on skill acquisition (i.e., skill improvement immediately after a training-session) and consolidation (i.e., skill retention after a time interval including sleep). Three groups were trained at 10 a.m. (G10am), 3 p.m. (G3pm), or 8 p.m. (G8pm) on a finger-tapping task. We recorded the skill (i.e., the ratio between movement duration and accuracy) before and immediately after the training to evaluate acquisition, and after 24 h to measure consolidation. We did not observe any difference in acquisition according to the time of the day. Interestingly, we found a performance improvement 24 h after the evening training (G8pm), while the morning (G10am) and the afternoon (G3pm) groups deteriorated and stabilized their performance, respectively. Furthermore, two control experiments (G8awake and G8sleep) supported the idea that a night of sleep contributes to the skill consolidation of the evening group. These results show a consolidation when the training is carried out in the evening, close to sleep, and forgetting when the training is carried out in the morning, away from sleep. This finding may have an important impact on the planning of training programs in sports, clinical, or experimental domains.
“You did incredibly well!”: teachers’ inflated praise can make children from low-SES backgrounds seem less smart (but more hardworking)
Authors: Schoneveld Emiel , Brummelman Eddie 
Published: September 2023

AbstractCan teachers’ inflated praise make children from low socioeconomic status (SES) backgrounds seem less smart? We conducted two preregistered experiments to address this question. We used hypothetical scenarios to ensure experimental control. An experiment with primary school teachers (N = 106, ages 21–63) showed that when a child from a low-SES (vs. high-SES) background succeeded in school, teachers attributed this success more to hard work and delivered more inflated praise (e.g., “You did incredibly well!”) but less modest praise (e.g., “You did well!”). An experiment with primary school children (N = 63, ages 10–13) showed that when children learned that another child received inflated praise (while an equally performing classmate received modest praise or no praise), they perceived this child as less smart but more hardworking. These studies provide converging evidence that teachers’ inflated praise, although well-intentioned, can make children from low-SES backgrounds seem less smart, thereby reinforcing negative stereotypes about these children’s academic abilities.
Sub-arc mantle fugacity shifted by sediment recycling across the Great Oxidation Event
Authors: Moreira Hugo , Storey Craig , Bruand Emilie , Darling James , Fowler Mike , Cotte Marine , Villalobos-Portillo Edgar E. , Parat Fleurice , Seixas Luís , Philippot Pascal , Dhuime Bruno 
Published: August 2023

AbstractThe chemical exchange between the atmosphere, crust and mantle depends on sediment recycling via subduction. However, it remains unclear how atmospherically modified sediment may affect mantle oxygen fugacity through time. The Great Oxidation Event, among the most important atmospheric changes on Earth, offers an opportunity to investigate changes in magmatism related to surface–mantle interactions. Here we use sulfur K-edge micro X-ray absorption near-edge structure spectroscopy to measure the relative abundances of S6+, S4+ and S2− state in apatite inclusions hosted in 2.4–2.1-billion-year-old igneous zircons from the Mineiro Belt, Brazil. The host magmas record intracrustal melting of juvenile crust and the involvement of recycled sediments in the sub-arc mantle wedge. Unaltered apatite inclusions reveal a change from reduced to more oxidized magmas from pre- to post-Great Oxidation Event during the early Proterozoic. We argue that this change is a direct result of deep subduction of oxidized sediments and thus evidence of mantle–atmosphere interaction across the Great Oxidation Event. This suggests that the onset of sediment recycling in the Archaean provided atmospheric access to the mantle, and early ‘whiffs’ of oxygen may have already contributed to a localized increase of calc-alkaline magmatism and related ore deposits on Earth.
Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly
Authors: Aswal Manisha , Singhal Neelja , Kumar Manish 
Published: September 2023

AbstractEscherichia coli are highly diverse bacteria with different pathogenic types, serotypes and phylogenetic types/phylotypes. In recent years, infections with E. coli have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of E. coli. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-β-lactam resistant and the other was multi-drug resistant (resistant to multiple β-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the de-novo approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N50 value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.
Pre-neuronal processing of haptic sensory cues via dispersive high-frequency vibrational modes
Authors: Ding Yu , Vlasov Yurii 
Published: September 2023

AbstractSense of touch is one of the major perception channels. Neural coding of object textures conveyed by rodents’ whiskers has been a model to study early stages of haptic information uptake. While high-precision spike timing has been observed during whisker sweeping across textured surfaces, the exact nature of whisker micromotions that spikes encode remains elusive. Here, we discovered that a single micro-collision of a whisker with surface features generates vibrational eigenmodes spanning frequencies up to 10 kHz. While propagating along the whisker, these high-frequency modes can carry up to 80% of shockwave energy, exhibit 100× smaller damping ratio, and arrive at the follicle 10× faster than low frequency components. The mechano-transduction of these energy bursts into time-sequenced population spike trains may generate temporally unique “bar code” with ultra-high information capacity. This hypothesis of pre-neuronal processing of haptic signals based on dispersive temporal separation of the vibrational modal frequencies can shed light on neural coding of haptic signals in many whisker-like sensory organs across the animal world as well as in texture perception in primate’s glabrous skin.
Non-chemotherapy adjuvant agents in TP53 mutant Ewing sarcoma
Authors: Kim Jin-Ah , Crawford Kenneth A. , Spada Piero A. , Martin Leah R. , Zhang Jiaqi , Wong Rain , Reid Joel M. , Stewart Clinton F. , Frank Timothy M. , Liu Qianqian , Michalek Joel E. , Keller Charles 
Published: September 2023

AbstractEwing sarcoma (EWS) is a malignant tumor arising in bone or soft tissue that occurs in adolescent and young adult patients as well as adults later in life. Although non-metastatic EWS is typically responsive to treatment when newly diagnosed, relapsed cases have an unmet need for which no standard treatment approach exists. Recent phase III clinical trials for EWS comparing 7 vs 5 chemotherapy drugs have failed to improve survival. To extend the durability of remission for EWS, we investigated 3 non-chemotherapy adjuvant therapy drug candidates to be combined with chemotherapy. The efficacy of these adjuvant drugs was investigated via anchorage-dependent growth assays, anchorage-independent soft-agar colony formation assays and EWS xenograft mouse models. Enoxacin and entinostat were the most effective adjuvant drug in both long-term in vitro and in vivo adjuvant studies. In the context that enoxacin is an FDA-approved antibiotic, and that entinostat is an investigational agent not yet FDA-approved, we propose enoxacin as an adjuvant drug for further preclinical and clinical investigation in EWS patients.
Identification of growth years for Puerariae Thomsonii Radix based on hyperspectral imaging technology and deep learning algorithm
Authors: Zhang Lei , Guan Yu , Wang Ni , Ge Fei , Zhang Yan , Zhao Yuping 
Published: August 2023

AbstractPuerariae Thomsonii Radix (PTR) is not only widely used in disease prevention and treatment but is also an important raw material as a source of starch and other food. The growth years of PTR are closely related to its quality. The rapid and nondestructive identification of growth year is essential for the quality control of PTR and other traditional Chinese medicines. In this study, we proposed a convolutional neural network (CNN)-based classification framework in conjunction with hyperspectral imaging (HSI) technology for the rapid identification of the growth years of PTRs. Traditional treatment methods (i.e., multiplicative scatter correction, standard normal variate, and Savitzky-Golay smoothing) combined with machine learning algorithms (i.e., random forest, logistic regression, naive Bayes, and eXtreme gradient boost) were used as baseline models. Among them, the F1-score of CNN-based models based on PTRs’ outer surfaces was over 90%, outperforming all the other baseline models. These results showed that it was feasible to use a deep learning algorithm in conjunction with HSI technology to identify the growth years of PTR. This method provides a fast, nondestructive, and simple method of identifying the growth years of PTR. It can be easily applied to other scenarios, such as for the identification of the locality or years of growth for other traditional Chinese herbs.