bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dopant triggered atomic configuration activates water splitting to hydrogen
Authors: Wu Rui , Xu Jie , Zhao Chuan-Lin , Su Xiao-Zhi , Zhang Xiao-Long , Zheng Ya-Rong , Yang Feng-Yi , Zheng Xu-Sheng , Zhu Jun-Fa , Luo Jun , Li Wei-Xue , Gao Min-Rui , Yu Shu-Hong 
Published: April 2023

AbstractFinding highly efficient hydrogen evolution reaction (HER) catalysts is pertinent to the ultimate goal of transformation into a net-zero carbon emission society. The design principles for such HER catalysts lie in the well-known structure-property relationship, which guides the synthesis procedure that creates catalyst with target properties such as catalytic activity. Here we report a general strategy to synthesize 10 kinds of single-atom-doped CoSe2-DETA (DETA = diethylenetriamine) nanobelts. By systematically analyzing these products, we demonstrate a volcano-shape correlation between HER activity and Co atomic configuration (ratio of Co-N bonds to Co-Se bonds). Specifically, Pb-CoSe2-DETA catalyst reaches current density of 10 mA cm−2 at 74 mV in acidic electrolyte (0.5 M H2SO4, pH ~0.35). This striking catalytic performance can be attributed to its optimized Co atomic configuration induced by single-atom doping.
Influenza virus mRNAs encode determinants for nuclear export via the cellular TREX-2 complex
Authors: Bhat Prasanna , Aksenova Vasilisa , Gazzara Matthew , Rex Emily A. , Aslam Sadaf , Haddad Christina , Gao Shengyan , Esparza Matthew , Cagatay Tolga , Batten Kimberly , El Zahed Sara S. , Arnaoutov Alexei , Zhong Hualin , Shay Jerry W. , Tolbert Blanton S. , Dasso Mary , Lynch Kristen W. , García-Sastre Adolfo , Fontoura Beatriz M. A. 
Published: April 2023

AbstractNuclear export of influenza A virus (IAV) mRNAs occurs through the nuclear pore complex (NPC). Using the Auxin-Induced Degron (AID) system to rapidly degrade proteins, we show that among the nucleoporins localized at the nucleoplasmic side of the NPC, TPR is the key nucleoporin required for nuclear export of influenza virus mRNAs. TPR recruits the TRanscription and EXport complex (TREX)−2 to the NPC for exporting a subset of cellular mRNAs. By degrading components of the TREX-2 complex (GANP, Germinal-center Associated Nuclear Protein; PCID2, PCI domain containing 2), we show that influenza mRNAs require the TREX-2 complex for nuclear export and replication. Furthermore, we found that cellular mRNAs whose export is dependent on GANP have a small number of exons, a high mean exon length, long 3’ UTR, and low GC content. Some of these features are shared by influenza virus mRNAs. Additionally, we identified a 45 nucleotide RNA signal from influenza virus HA mRNA that is sufficient to mediate GANP-dependent mRNA export. Thus, we report a role for the TREX-2 complex in nuclear export of influenza mRNAs and identified RNA determinants associated with the TREX-2-dependent mRNA export.
Transcription tuned by S-nitrosylation underlies a mechanism for Staphylococcus aureus to circumvent vancomycin killing
Authors: Shu Xueqin , Shi Yingying , Huang Yi , Yu Dan , Sun Baolin 
Published: April 2023

AbstractTreatment of Staphylococcus aureus infections is a constant challenge due to emerging resistance to vancomycin, a last-resort drug. S-nitrosylation, the covalent attachment of a nitric oxide (NO) group to a cysteine thiol, mediates redox-based signaling for eukaryotic cellular functions. However, its role in bacteria is largely unknown. Here, proteomic analysis revealed that S-nitrosylation is a prominent growth feature of vancomycin-intermediate S. aureus. Deletion of NO synthase (NOS) or removal of S-nitrosylation from the redox-sensitive regulator MgrA or WalR resulted in thinner cell walls and increased vancomycin susceptibility, which was due to attenuated promoter binding and released repression of genes involved in cell wall metabolism. These genes failed to respond to H2O2-induced oxidation, suggesting distinct transcriptional responses to alternative modifications of the cysteine residue. Furthermore, treatment with a NOS inhibitor significantly decreased vancomycin resistance in S. aureus. This study reveals that transcriptional regulation via S-nitrosylation underlies a mechanism for NO-mediated bacterial antibiotic resistance.
Enhanced osmotic transport in individual double-walled carbon nanotube
Authors: Cui Guandong , Xu Zhi , Li Han , Zhang Shuchen , Xu Luping , Siria Alessandro , Ma Ming 
Published: April 2023

AbstractThe transport of fluid and ions across nanotubes or nanochannels has attracted great attention due to the ultrahigh energy power density and slip length, with applications in water purification, desalination, energy conversion and even ion-based neuromorphic computing. Investigation on individual nanotube or nanochannel is essential in revealing the fundamental mechanism as well as demonstrating the property unambiguously. Surprisingly, while carbon nanotube is the pioneering and one of the most attractive systems for nanofluidics, study on its response and performance under osmotic forcing is lacking. Here, we measure the osmotic energy conversion for individual double-walled carbon nanotube with an inner radius of 2.3 nm. By fabricating a nanofluidic device using photolithography, we find a giant power density (up to 22.5 kW/m2) for the transport of KCl, NaCl, and LiCl solutions across the tube. Further experiments show that such an extraordinary performance originates from the ultrahigh slip lengths (up to a few micrometers). Our results suggest that carbon nanotube is a good candidate for not only ultrafast transport, but also osmotic power harvesting under salinity gradients.
A DBHS family member regulates male determination in the filariasis vector Armigeres subalbatus
Authors: Liu Peiwen , Yang Wenqiang , Kong Ling , Zhao Siyu , Xie Zhensheng , Zhao Yijie , Wu Yang , Guo Yijia , Xie Yugu , Liu Tong , Jin Binbin , Gu Jinbao , Tu Zhijian Jake , James Anthony A. , Chen Xiao-Guang 
Published: April 2023

AbstractThe initial signals governing sex determination vary widely among insects. Here we show that Armigeres subalbatus M factor (AsuMf), a male-specific duplication of an autosomal gene of the Drosophila behaviour/human splicing (DBHS) gene family, is the potential primary signal for sex determination in the human filariasis vector mosquito, Ar. subalbatus. Our results show that AsuMf satisfies two fundamental requirements of an M factor: male-specific expression and early embryonic expression. Ablations of AsuMf result in a shift from male- to female-specific splicing of doublesex and fruitless, leading to feminization of males both in morphology and general transcription profile. These data support the conclusion that AsuMf is essential for male development in Ar. subalbatus and reveal a male-determining factor that is derived from duplication and subsequent neofunctionalization of a member of the conserved DBHS family.
Structural-disorder-driven critical quantum fluctuation and localization in two-dimensional semiconductors
Authors: Shin Bong Gyu , Park Ji-Hoon , Juo Jz-Yuan , Kong Jing , Jung Soon Jung 
Published: April 2023

AbstractQuantum fluctuations of wavefunctions in disorder-driven quantum phase transitions (QPT) exhibit criticality, as evidenced by their multifractality and power law behavior. However, understanding the metal-insulator transition (MIT) as a continuous QPT in a disordered system has been challenging due to fundamental issues such as the lack of an apparent order parameter and its dynamical nature. Here, we elucidate the universal mechanism underlying the structural-disorder-driven MIT in 2D semiconductors through autocorrelation and multifractality of quantum fluctuations. The structural disorder causes curvature-induced band gap fluctuations, leading to charge localization and formation of band tails near band edges. As doping level increases, the localization-delocalization transition occurs when states above a critical energy become uniform due to unusual band bending by localized charge. Furthermore, curvature induces local variations in spin-orbit interactions, resulting in non-uniform ferromagnetic domains. Our findings demonstrate that the structural disorder in 2D materials is essential to understanding the intricate phenomena associated with localization-delocalization transition, charge percolation, and spin glass with both topological and magnetic disorders.
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma
Authors: Okonechnikov Konstantin , Camgöz Aylin , Chapman Owen , Wani Sameena , Park Donglim Esther , Hübner Jens-Martin , Chakraborty Abhijit , Pagadala Meghana , Bump Rosalind , Chandran Sahaana , Kraft Katerina , Acuna-Hidalgo Rocio , Reid Derek , Sikkink Kristin , Mauermann Monika , Juarez Edwin F. , Jenseit Anne , Robinson James T. , Pajtler Kristian W. , Milde Till , Jäger Natalie , Fiesel Petra , Morgan Ling , Sridhar Sunita , Coufal Nicole G. , Levy Michael , Malicki Denise , Hobbs Charlotte , Kingsmore Stephen , Nahas Shareef , Snuderl Matija , Crawford John , Wechsler-Reya Robert J. , Davidson Tom Belle , Cotter Jennifer , Michaiel George , Fleischhack Gudrun , Mundlos Stefan , Schmitt Anthony , Carter Hannah , Michealraj Kulandaimanuvel Antony , Kumar Sachin A. , Taylor Michael D. , Rich Jeremy , Buchholz Frank , Mesirov Jill P. , Pfister Stefan M. , Ay Ferhat , Dixon Jesse R. , Kool Marcel , Chavez Lukas 
Published: April 2023

AbstractEpendymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains (‘neo-TADs’) caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
The prognostic value and immune microenvironment association of AR in HER2+ nonmetastatic breast cancer
Authors: Zhou Danyang , Li Mei , Yasin Mohamed Hussein , Lu Qianyi , Fu Jia , Jiang Kuikui , Hong Ruoxi , Wang Shusen , Xu Fei 
Published: April 2023

AbstractThis study aimed to investigate the prognostic value of AR in HER2+ nonmetastatic breast invasive ductal carcinoma (IDC) and its relationship with the immune microenvironment. HER2+ nonmetastatic breast IDC patients diagnosed by pathology who underwent surgery at Sun Yat-sen University Cancer Center from 2016 to 2017 were included. AR+ and AR− breast IDC samples were matched 1:1 in age, T stage, and N stage for immune infiltration analysis. A total of 554 patients with HER2+ nonmetastatic breast cancer were included in this retrospective study, regardless of HR status. The cut-off value for AR was set at 10%. ER+ (p < 0.001) and PR+ (p < 0.001) were associated with positive AR expression. Kaplan–Meier survival curve analysis suggested that AR was closely correlated with overall survival (OS) (p = 0.001) but not disease-free survival (DFS) (p = 0.051). After eliminating the potential impact caused by HR, AR also predicted longer OS (p = 0.014) and was an independent predictive factor for OS of HER2+HR− nonmetastatic breast IDC patients, as revealed by multivariate analysis (p = 0.036). For AR+ and AR− matched HER2+HR− patients, TILs (p = 0.043) and PD-L1 (p = 0.027) levels were significantly lower in AR+ patients. The strongest negative correlation was observed between AR and PD-L1 (Pearson’s r = −0.299, p = 0.001). AR+ status was markedly related to better OS in HER2+HR− nonmetastatic breast cancer patients, while a negative correlation was observed between AR and PD-L1/TILs. We provide new insights into the prognostic value of AR and its association with the immune microenvironment to optimize treatment strategies in HER2+ nonmetastatic breast IDCs.
Putting hornets on the genomic map
Authors: Favreau Emeline , Cini Alessandro , Taylor Daisy , Câmara Ferreira Francisco , Bentley Michael A. , Cappa Federico , Cervo Rita , Privman Eyal , Schneider Jadesada , Thiéry Denis , Mashoodh Rahia , Wyatt Christopher D. R. , Brown Robert L. , Bodrug-Schepers Alexandrina , Stralis-Pavese Nancy , Dohm Juliane C. , Mead Daniel , Himmelbauer Heinz , Guigo Roderic , Sumner Seirian 
Published: April 2023

AbstractHornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets,Vespa crabroandVespa velutina.We compare their genomes with those of other social Hymenoptera, including the northern giant hornetVespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges.Vespa crabrohas experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.
Dendrites help mitigate the plasticity-stability dilemma
Authors: Wilmes Katharina A. , Clopath Claudia 
Published: April 2023

AbstractWith Hebbian learning ‘who fires together wires together’, well-known problems arise. Hebbian plasticity can cause unstable network dynamics and overwrite stored memories. Because the known homeostatic plasticity mechanisms tend to be too slow to combat unstable dynamics, it has been proposed that plasticity must be highly gated and synaptic strengths limited. While solving the issue of stability, gating and limiting plasticity does not solve the stability-plasticity dilemma. We propose that dendrites enable both stable network dynamics and considerable synaptic changes, as they allow the gating of plasticity in a compartment-specific manner. We investigate how gating plasticity influences network stability in plastic balanced spiking networks of neurons with dendrites. We compare how different ways to gate plasticity, namely via modulating excitability, learning rate, and inhibition increase stability. We investigate how dendritic versus perisomatic gating allows for different amounts of weight changes in stable networks. We suggest that the compartmentalisation of pyramidal cells enables dendritic synaptic changes while maintaining stability. We show that the coupling between dendrite and soma is critical for the plasticity-stability trade-off. Finally, we show that spatially restricted plasticity additionally improves stability.
Effect of distance measures on confidences of t-SNE embeddings and its implications on clustering for scRNA-seq data
Authors: Ozgode Yigin Busra , Saygili Gorkem 
Published: April 2023

AbstractArguably one of the most famous dimensionality reduction algorithms of today is t-distributed stochastic neighbor embedding (t-SNE). Although being widely used for the visualization of scRNA-seq data, it is prone to errors as any algorithm and may lead to inaccurate interpretations of the visualized data. A reasonable way to avoid misinterpretations is to quantify the reliability of the visualizations. The focus of this work is first to find the best possible way to predict sample-based confidence scores for t-SNE embeddings and next, to use these confidence scores to improve the clustering algorithms. We adopt an RF regression algorithm using seven distance measures as features for having the sample-based confidence scores with a variety of different distance measures. The best configuration is used to assess the clustering improvement using K-means and Density-Based Spatial Clustering of Applications with Noise (DBSCAN) based on Adjusted Rank Index (ARI), Normalized Mutual Information (NMI), and accuracy (ACC) scores. The experimental results show that distance measures have a considerable effect on the precision of confidence scores and clustering performance can be improved substantially if these confidence scores are incorporated before the clustering algorithm. Our findings reveal the usefulness of these confidence scores on downstream analyses for scRNA-seq data.
Positive maternal affect during mother–litter interaction is reduced in new mother rats exhibiting a depression-like phenotype
Authors: Tuncali Idil , Sorial Natalie , Torr Kali , Pereira Mariana 
Published: April 2023

AbstractThe experience of positive affect during new motherhood is considered essential for a healthy mother–infant relationship, with life-long consequences for both mother and child. Affective availability and contingent responsiveness are often compromised in mothers experiencing postpartum depression, yet how maternal affect impacts parenting is not fully understood. In this study, we used the Wistar-Kyoto (WKY) rat model of depression and ultrasonic vocalizations to examine the relationship between maternal affect and parenting. We examined the affective and behavioral response of WKY and control new mother rats during social interactions with their offspring. Our results show that WKY mothers displayed altered USV signaling accompanying substantial disturbances in their maternal caregiving. In addition, WKY mothers failed to adjust vocal frequency in coordination with offspring proximity and interaction compared to control mothers. A follow up experiment demonstrated that the administration of the adenosine A2A receptor antagonist MSX-3 ameliorated both maternal behavioral deficits and low positive affect in WKY mothers. Together, our results highlight the importance of maternal positive affect in the dyad relationship and suggest a role for the striatopallidal pathway in the affective processing of parenting.
Cr$$_2$$AlN and the search for the highest temperature superconductor in the M$$_2$$AX family
Authors: Karaca E. , Byrne P. J. P. , Hasnip P. J. , Probert M. I. J. 
Published: April 2023

AbstractWe have developed a high-throughput computational method to predict the superconducting transition temperature in stable hexagonal M$$_2$$

2

AX phases, and applied it to all the known possible choices for M (M: Sc, Ti, V, Cr, Mn, Fe, Y, Zr, Nb, Mo, Lu, Hf and Ta). We combine this with the best candidates for A (A: Al, Cu, Ge and Sn ) and X (X: C and N) from our previous work, and predict T$$_c$$

c

for 60 M$$_2$$

2

AX-phase materials, 53 of which have never been studied before. From all of these, we identify Cr$$_2$$

2

AlN as the best candidate for the highest T$$_c$$

c

, and confirm its high T$$_c$$

c

with more detailed density functional theory electron-phonon coupling calculations. Our detailed calculations predict $$T_c$$

T
c

= 14.8 K for Cr$$_2$$

2

AlN, which is significantly higher than any $$T_c$$

T
c

value known or predicted for any material in the M$$_2$$

2

AX family to date.
Outcomes for an arboreal folivore after rehabilitation and implications for management
Authors: Leigh Kellie A. , Hofweber Lacey N. , Sloggett Brienna K. , Inman Victoria L. , Pettit Lachlan J. , Sriram Aditi , Haering Ron 
Published: April 2023

AbstractWildlife rehabilitation is a critical part of animal welfare that contributes to species conservation. Despite the resources that go into rehabilitation, how animals fare after release from care is unknown. This is particularly true for cryptic arboreal species where specialist diets in care and low detectability in the wild present challenges for both care and post-release monitoring. We evaluated post-release outcomes for koalas and assessed if koalas were fed appropriately while in care. We monitored 36 koalas that had experienced one of three categories of medical intervention (none, minor, major) during rehabilitation. We examined the drivers of (i) koala survival and (ii) movements post-release, and (iii) evaluated variation between the species of browse fed in care versus browse selected by koalas in-situ. Overall, the post release survival rate of koalas was 58.5%, with only koalas that received medical intervention experiencing mortality. A critical threshold for mortality occurred at two weeks post-release and mortality was related to the measurable indicators of low body condition and poor climbing ability at time of release. In the month following their release, animals translocated furthest from their capture point moved the furthest. There was poor overlap between the tree species that koalas were fed in care and those they utilized post-release. We provide recommendations to address critical gaps in rehabilitation practices, as well as priorities for monitoring animals post-release to improve outcomes for arboreal folivores.
Degeneration of muscle spindles in a murine model of Pompe disease
Authors: Watkins Bridgette , Schultheiß Jürgen , Rafuna Andi , Hintze Stefan , Meinke Peter , Schoser Benedikt , Kröger Stephan 
Published: April 2023

AbstractPompe disease is a debilitating medical condition caused by a functional deficiency of lysosomal acid alpha-glucosidase (GAA). In addition to muscle weakness, people living with Pompe disease experience motor coordination deficits including an instable gait and posture. We reasoned that an impaired muscle spindle function might contribute to these deficiencies and therefore analyzed proprioception as well as muscle spindle structure and function in 4- and 8-month-old Gaa−/− mice. Gait analyses showed a reduced inter-limb and inter-paw coordination in Gaa−/− mice. Electrophysiological analyses of single-unit muscle spindle proprioceptive afferents revealed an impaired sensitivity of the dynamic and static component of the stretch response. Finally, a progressive degeneration of the sensory neuron and of the intrafusal fibers was detectable in Gaa−/− mice. We observed an increased abundance and size of lysosomes, a fragmentation of the inner and outer connective tissue capsule and a buildup of autophagic vacuoles in muscle spindles from 8-month-old Gaa−/− mice, indicating lysosomal defects and an impaired autophagocytosis. These results demonstrate a structural and functional degeneration of muscle spindles and an altered motor coordination in Gaa−/− mice. Similar changes could contribute to the impaired motor coordination in patients living with Pompe disease.