bluuebunny/crossref_metadata_2025_split huggingface dataset:
AK2 is an AMP-sensing negative regulator of BRAF in tumorigenesis
Authors: Kim Hyunjoo , Jeong Muhah , Na Do-Hyeong , Ryu Shin-Hyeon , Jeong Eun Il , Jung Kwangmin , Kang Jaemin , Lee Ho-June , Sim Taebo , Yu Dae-Yeul , Yu Hee Chul , Cho Baik-Hwan , Jung Yong-Keun 
Published: May 2022

AbstractThe RAS–BRAF signaling is a major pathway of cell proliferation and their mutations are frequently found in human cancers. Adenylate kinase 2 (AK2), which modulates balance of adenine nucleotide pool, has been implicated in cell death and cell proliferation independently of its enzyme activity. Recently, the role of AK2 in tumorigenesis was in part elucidated in some cancer types including lung adenocarcinoma and breast cancer, but the underlying mechanism is not clear. Here, we show that AK2 is a BRAF-suppressor. In in vitro assays and cell model, AK2 interacted with BRAF and inhibited BRAF activity and downstream ERK phosphorylation. Energy-deprived conditions in cell model and the addition of AMP to cell lysates strengthened the AK2-BRAF interaction, suggesting that AK2 is involved in the regulation of BRAF activity in response to cell metabolic state. AMP facilitated the AK2–BRAF complex formation through binding to AK2. In a panel of HCC cell lines, AK2 expression was inversely correlated with ERK/MAPK activation, and AK2-knockdown or -knockout increased BRAF activity and promoted cell proliferation. Tumors from HCC patients showed low-AK2 protein expression and increased ERK activation compared to non-tumor tissues and the downregulation of AK2 was also verified by two microarray datasets (TCGA-LIHC and GSE14520). Moreover, AK2/BRAF interaction was abrogated by RAS activation in in vitro assay and cell model and in a mouse model of HRASG12V-driven HCC, and AK2 ablation promoted tumor growth and BRAF activity. AK2 also bound to BRAF inhibitor-insensitive BRAF mutants and attenuated their activities. These findings indicate that AK2 monitoring cellular AMP levels is indeed a negative regulator of BRAF, linking the metabolic status to tumor growth.
A novel 3’tRNA-derived fragment tRF-Val promotes proliferation and inhibits apoptosis by targeting EEF1A1 in gastric cancer
Authors: Cui Huaiping , Li Han , Wu Hao , Du Fengying , Xie Xiaozhou , Zeng Shujie , Zhang Zihao , Dong Kangdi , Shang Liang , Jing Changqing , Li Leping 
Published: May 2022

AbstractAt present, it is commonly believed that tRFs and tiRNAs are formed by the specific and selective shear of tRNAs under certain pressure stimulation, rather than by random degradation of tRNA. tRFs and tiRNAs have been reported to contribute to the biological process of a variety of human cancers. However, the evidence for the mechanisms of tRFs and tiRNAs in the occurrence and development of gastric cancer (GC) is still insufficient. Here, we aimed to explore the carcinogenic roles of tRFs and tiRNAs in GC with RNA-sequencing technique, and found a novel 3’tRNA-derived fragment tRF-Val was significantly upregulated in GC tissues and cell lines. tRF-Val expression was positively correlated with tumor size and the depth of tumor invasion in GC tissues. Functionally, tRF-Val promoted proliferation and invasion, and inhibited apoptosis in GC cells. Mechanistically, tRF-Val directly bound to the chaperone molecule EEF1A1, mediated its transport into the nucleus and promoted its interaction with MDM2 (a specific p53 E3 ubiquitin ligase), thus inhibiting the downstream molecular pathway of p53 and promoting GC progression. These findings provided a new potential therapeutic target for GC and a new explanation for the occurrence of GC.
Visual barcodes for clonal-multiplexing of live microscopy-based assays
Authors: Kaufman Tom , Nitzan Erez , Firestein Nir , Ginzberg Miriam Bracha , Iyengar Seshu , Patel Nish , Ben-Hamo Rotem , Porat Ziv , Hunter Jaryd , Hilfinger Andreas , Rotter Varda , Kafri Ran , Straussman Ravid 
Published: May 2022

AbstractWhile multiplexing samples using DNA barcoding revolutionized the pace of biomedical discovery, multiplexing of live imaging-based applications has been limited by the number of fluorescent proteins that can be deconvoluted using common microscopy equipment. To address this limitation, we develop visual barcodes that discriminate the clonal identity of single cells by different fluorescent proteins that are targeted to specific subcellular locations. We demonstrate that deconvolution of these barcodes is highly accurate and robust to many cellular perturbations. We then use visual barcodes to generate ‘Signalome’ cell-lines by mixing 12 clones of different live reporters into a single population, allowing simultaneous monitoring of the activity in 12 branches of signaling, at clonal resolution, over time. Using the ‘Signalome’ we identify two distinct clusters of signaling pathways that balance growth and proliferation, emphasizing the importance of growth homeostasis as a central organizing principle in cancer signaling. The ability to multiplex samples in live imaging applications, both in vitro and in vivo may allow better high-content characterization of complex biological systems.
Large-scale GWAS of food liking reveals genetic determinants and genetic correlations with distinct neurophysiological traits
Authors: May-Wilson Sebastian , Matoba Nana , Wade Kaitlin H. , Hottenga Jouke-Jan , Concas Maria Pina , Mangino Massimo , Grzeszkowiak Eryk J. , Menni Cristina , Gasparini Paolo , Timpson Nicholas J. , Veldhuizen Maria G. , de Geus Eco , Wilson James F. , Pirastu Nicola 
Published: May 2022

AbstractWe present the results of a GWAS of food liking conducted on 161,625 participants from the UK-Biobank. Liking was assessed over 139 specific foods using a 9-point scale. Genetic correlations coupled with structural equation modelling identified a multi-level hierarchical map of food-liking with three main dimensions: “Highly-palatable”, “Acquired” and “Low-caloric”. The Highly-palatable dimension is genetically uncorrelated from the other two, suggesting that independent processes underlie liking high reward foods. This is confirmed by genetic correlations with MRI brain traits which show with distinct associations. Comparison with the corresponding food consumption traits shows a high genetic correlation, while liking exhibits twice the heritability. GWAS analysis identified 1,401 significant food-liking associations which showed substantial agreement in the direction of effects with 11 independent cohorts. In conclusion, we created a comprehensive map of the genetic determinants and associated neurophysiological factors of food-liking.
Global diversity dynamics in the fossil record are regionally heterogeneous
Authors: Flannery-Sutherland Joseph T. , Silvestro Daniele , Benton Michael J. 
Published: May 2022

AbstractGlobal diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid these biases, yet diversity-through-time arises from the interplay of origination and extinction, the processes that shape macroevolutionary history. Here we present a subsampling algorithm to eliminate spatial sampling bias, coupled with advanced probabilistic methods for estimating origination and extinction rates and a Bayesian method for estimating sampling-corrected diversity. We then re-examine the Late Permian to Early Jurassic marine fossil record, an interval spanning several global biotic upheavals that shaped the origins of the modern marine biosphere. We find that origination and extinction rates are regionally heterogenous even during events that manifested globally, highlighting the need for spatially explicit views of macroevolutionary processes through geological time.
Breaking scaling relationships in alkynol semi-hydrogenation by manipulating interstitial atoms in Pd with d-electron gain
Authors: Yang Yang , Zhu Xiaojuan , Wang Lili , Lang Junyu , Yao Guohua , Qin Tian , Ren Zhouhong , Chen Liwei , Liu Xi , Li Wei , Wan Ying 
Published: May 2022

AbstractPd catalysts are widely used in alkynol semi-hydrogenation. However, due to the existence of scaling relationships of adsorption energies between the key adsorbed species, the increase in conversion is frequently accompanied by side reactions, thereby reducing the selectivity to alkenols. We report that the simultaneous increase in alkenol selectivity and alkynol conversion is achieved by manipulating interstitial atoms including B, P, C, S and N in Pd catalysts. A negative linear relationship is observed between the activation entropies of 2-methyl-3-butyn-2-ol and 2-methyl-3-buten-2-ol which is highly related to the filling of d-orbital of Pd catalysts by the modification of p-block elements. A catalyst co-modified by B and C atoms has the maximum d charge of Pd that achieves a 17-fold increase in the turn-over frequency values compared to the Lindlar catalysts in the semi-hydrogenation of 2-methyl-3-butyn-2-ol. When the conversion is close to 100%, the selectivity can be as high as 95%.
Uncovering material deformations via machine learning combined with four-dimensional scanning transmission electron microscopy
Authors: Shi Chuqiao , Cao Michael C. , Rehn Sarah M. , Bae Sang-Hoon , Kim Jeehwan , Jones Matthew R. , Muller David A. , Han Yimo 
Published: May 2022

AbstractUnderstanding lattice deformations is crucial in determining the properties of nanomaterials, which can become more prominent in future applications ranging from energy harvesting to electronic devices. However, it remains challenging to reveal unexpected deformations that crucially affect material properties across a large sample area. Here, we demonstrate a rapid and semi-automated unsupervised machine learning approach to uncover lattice deformations in materials. Our method utilizes divisive hierarchical clustering to automatically unveil multi-scale deformations in the entire sample flake from the diffraction data using four-dimensional scanning transmission electron microscopy (4D-STEM). Our approach overcomes the current barriers of large 4D data analysis without a priori knowledge of the sample. Using this purely data-driven analysis, we have uncovered different types of material deformations, such as strain, lattice distortion, bending contour, etc., which can significantly impact the band structure and subsequent performance of nanomaterials-based devices. We envision that this data-driven procedure will provide insight into materials’ intrinsic structures and accelerate the discovery of materials.
Optically induced nuclear spin–spin couplings in GaAs manifested by spin echo decays under optical pumping
Authors: Goto Atsushi , Hashi Kenjiro , Ohki Shinobu , Shimizu Tadashi 
Published: May 2022

AbstractOptically induced nuclear spin–spin coupling in semiconductors is expected to serve for gate operations in nuclear-magnetic-resonance (NMR) quantum computations. However, not much is known about its characteristics. In this study, we investigate optically induced couplings in GaAs via double-resonance spin-echo decay experiments under optical pumping. The squared echo decay rate $$\left( {1/T_2} \right)^2$$

1
/

T

2

2

of 71Ga measured under various light powers revealed that optically induced couplings increase with increasing light power, and the sign of heteronuclear couplings between Ga–As pairs is opposite to that of dipolar couplings, which cancel each other out. Under higher light power, the optically induced “controllable” coupling is expected to eventually surpass the “uncontrollable” nuclear dipolar coupling, becoming dominant, which is preferable for the gate operation in NMR quantum computation.
Synergistic HNO3–H2SO4–NH3 upper tropospheric particle formation
Authors: Wang Mingyi , Xiao Mao , Bertozzi Barbara , Marie Guillaume , Rörup Birte , Schulze Benjamin , Bardakov Roman , He Xu-Cheng , Shen Jiali , Scholz Wiebke , Marten Ruby , Dada Lubna , Baalbaki Rima , Lopez Brandon , Lamkaddam Houssni , Manninen Hanna E. , Amorim António , Ataei Farnoush , Bogert Pia , Brasseur Zoé , Caudillo Lucía , De Menezes Louis-Philippe , Duplissy Jonathan , Ekman Annica M. L. , Finkenzeller Henning , Carracedo Loïc Gonzalez , Granzin Manuel , Guida Roberto , Heinritzi Martin , Hofbauer Victoria , Höhler Kristina , Korhonen Kimmo , Krechmer Jordan E. , Kürten Andreas , Lehtipalo Katrianne , Mahfouz Naser G. A. , Makhmutov Vladimir , Massabò Dario , Mathot Serge , Mauldin Roy L. , Mentler Bernhard , Müller Tatjana , Onnela Antti , Petäjä Tuukka , Philippov Maxim , Piedehierro Ana A. , Pozzer Andrea , Ranjithkumar Ananth , Schervish Meredith , Schobesberger Siegfried , Simon Mario , Stozhkov Yuri , Tomé António , Umo Nsikanabasi Silas , Vogel Franziska , Wagner Robert , Wang Dongyu S. , Weber Stefan K. , Welti André , Wu Yusheng , Zauner-Wieczorek Marcel , Sipilä Mikko , Winkler Paul M. , Hansel Armin , Baltensperger Urs , Kulmala Markku , Flagan Richard C. , Curtius Joachim , Riipinen Ilona , Gordon Hamish , Lelieveld Jos , El-Haddad Imad , Volkamer Rainer , Worsnop Douglas R. , Christoudias Theodoros , Kirkby Jasper , Möhler Ottmar , Donahue Neil M. 
Published: May 2022

AbstractNew particle formation in the upper free troposphere is a major global source of cloud condensation nuclei (CCN)1–4. However, the precursor vapours that drive the process are not well understood. With experiments performed under upper tropospheric conditions in the CERN CLOUD chamber, we show that nitric acid, sulfuric acid and ammonia form particles synergistically, at rates that are orders of magnitude faster than those from any two of the three components. The importance of this mechanism depends on the availability of ammonia, which was previously thought to be efficiently scavenged by cloud droplets during convection. However, surprisingly high concentrations of ammonia and ammonium nitrate have recently been observed in the upper troposphere over the Asian monsoon region5,6. Once particles have formed, co-condensation of ammonia and abundant nitric acid alone is sufficient to drive rapid growth to CCN sizes with only trace sulfate. Moreover, our measurements show that these CCN are also highly efficient ice nucleating particles—comparable to desert dust. Our model simulations confirm that ammonia is efficiently convected aloft during the Asian monsoon, driving rapid, multi-acid HNO3–H2SO4–NH3nucleation in the upper troposphere and producing ice nucleating particles that spread across the mid-latitude Northern Hemisphere.
A trail of dark-matter-free galaxies from a bullet-dwarf collision
Authors: van Dokkum Pieter , Shen Zili , Keim Michael A. , Trujillo-Gomez Sebastian , Danieli Shany , Dutta Chowdhury Dhruba , Abraham Roberto , Conroy Charlie , Kruijssen J. M. Diederik , Nagai Daisuke , Romanowsky Aaron 
Published: May 2022

AbstractThe ultra-diffuse galaxies DF2 and DF4 in the NGC 1052 group share several unusual properties: they both have large sizes1, rich populations of overluminous and large globular clusters2–6, and very low velocity dispersions that indicate little or no dark matter7–10. It has been suggested that these galaxies were formed in the aftermath of high-velocity collisions of gas-rich galaxies11–13, events that resemble the collision that created the bullet cluster14 but on much smaller scales. The gas separates from the dark matter in the collision and subsequent star formation leads to the formation of one or more dark-matter-free galaxies12. Here we show that the present-day line-of-sight distances and radial velocities of DF2 and DF4 are consistent with their joint formation in the aftermath of a single bullet-dwarf collision, around eight billion years ago. Moreover, we find that DF2 and DF4 are part of an apparent linear substructure of seven to eleven large, low-luminosity objects. We propose that these all originated in the same event, forming a trail of dark-matter-free galaxies that is roughly more than two megaparsecs long and angled 7° ± 2° from the line of sight. We also tentatively identify the highly dark-matter-dominated remnants of the two progenitor galaxies that are expected11 at the leading edges of the trail.
The VISTA datasets, a combination of inertial sensors and depth cameras data for activity recognition
Authors: Fiorini Laura , Cornacchia Loizzo Federica Gabriella , Sorrentino Alessandra , Rovini Erika , Di Nuovo Alessandro , Cavallo Filippo 
Published: May 2022

AbstractThis paper makes the VISTA database, composed of inertial and visual data, publicly available for gesture and activity recognition. The inertial data were acquired with the SensHand, which can capture the movement of wrist, thumb, index and middle fingers, while the RGB-D visual data were acquired simultaneously from two different points of view, front and side. The VISTA database was acquired in two experimental phases: in the former, the participants have been asked to perform 10 different actions; in the latter, they had to execute five scenes of daily living, which corresponded to a combination of the actions of the selected actions. In both phase, Pepper interacted with participants. The two camera point of views mimic the different point of view of pepper. Overall, the dataset includes 7682 action instances for the training phase and 3361 action instances for the testing phase. It can be seen as a framework for future studies on artificial intelligence techniques for activity recognition, including inertial-only data, visual-only data, or a sensor fusion approach.
No alteration of back muscle oxygenation during isometric exercise in individuals with non-specific low back pain
Authors: Langenfeld Anke , Wirth Brigitte , Scherer-Vrana Andrea , Riner Fabienne , Gaehwiler Kyra , Valdivieso Paola , Humphreys B. Kim , Scholkmann Felix , Flueck Martin , Schweinhardt Petra 
Published: May 2022

AbstractThe aim of our study was (I) To compare back muscle oxygenation and perfusion as well as Biering–Sorensen muscle endurance (BSME) test holding times between chronic non-specific low back pain (CNSLBP) patients and asymptomatic controls matched for age, body mass index (BMI), sex and physical activity, and (II) to investigate factors associated with BSME holding times. Muscle perfusion (tHb) and oxygenation (SmO2) were measured by near-infrared spectroscopy (NIRS) based oximetry in three back muscles during the BSME. Reliability of tHb and SmO2 was assessed in a separate sample. BSME holding time and SmO2 were compared between patients (n = 45) and controls (n = 45) and factors associated with BSME holding time were assessed using multiple linear regression. Reliability for SmO2 was excellent (ICC = 0.87–0.99). THb showed poor to moderate reliability and was not further used. Groups differed for BSME holding time (P = 0.03), pain intensity (P ≤ 0.0005) and subcutaneous tissue thickness (P = 0.01) but not for NIRS measures. Physical activity and BMI were associated with BSME holding times. Insufficient muscle oxygenation does not seem to be a major factor contributing to CNSLBP. Future investigation should evaluate other determinants of BSME holding times, such as motivation and recruitment of auxiliary muscles.
Efficiency in the evolution of metro networks
Authors: Pei Aihui , Xiao Feng , Yu Senbin , Li Lili 
Published: May 2022

AbstractMetro systems extended rapidly in China, especially in the last decade, developing over a half-century. This work explores the dynamical evolution of the structural efficiency of metro systems interpreted as complex networks for 14 large cities in mainland China. Based on the empirical observations, we find that the global efficiencies scale with the number of stations and counter-intuitively decreases as the metro networks expand, which shows a long-tail characteristic. The evolution of metro networks is, in essence, the improvement of the relative ratio of average nodal efficiency in the core compared to global efficiency. These relationships are in good agreement with the temporal structure of metro networks. Besides, we find that the metro stations with the higher efficiencies are those surrounding the urban center, and most of them dwell within the core and gradually expand the branches in space. Our findings suggest that the evolution properties of metro systems influenced by numerous geographical, historical, and social activities suggest that underlying, universal mechanisms are at play during their evolution in the spatial–temporal dimension.
Changes in global DNA methylation under climatic stress in two related grasses suggest a possible role of epigenetics in the ecological success of polyploids
Authors: Tomczyk Przemysław P. , Kiedrzyński Marcin , Forma Ewa , Zielińska Katarzyna M. , Kiedrzyńska Edyta 
Published: May 2022

AbstractPolyploidization drives the evolution of grasses and can result in epigenetic changes, which may have a role in the creation of new evolutionary lineages and ecological speciation. As such changes may be inherited, they can also influence adaptation to the environment. Populations from different regions and climates may also differ epigenetically; however, this phenomenon is poorly understood. The present study analyzes the effect of climatic stress on global DNA methylation based on a garden collection of two related mountain grasses (the narrow endemic diploid Festuca tatrae and the more widely distributed mixed-ploidy F. amethystina) with different geographic ranges and ecological niches. A lower level of DNA methylation was observed for F. tatrae, while a higher mean level was obtained for the diploid and tetraploid of F. amethystina; with the tetraploids having a higher level of global methylated DNA than the diploids. The weather conditions (especially insolation) measured 24 h prior to sampling appeared to have a closer relationship with global DNA methylation level than those observed seven days before sampling. Our findings suggest that the level of methylation during stress conditions (drought, high temperature and high insolation) may be significantly influenced by the ploidy level and bioclimatic provenance of specimens; however an important role may also be played by the intensity of stress conditions in a given year.
Discovery of Late Triassic bivalves from Jurassic deep-water deposits in Riganpeicuo area, Tibet and their geological significance
Authors: Xiao Hongji , Luo Shenglong , Gao Jinhan , Wang Genhou 
Published: May 2022

AbstractThe Jurassic sequences in the South Qiangtang Basin of Tibet are essential for understanding the paleogeography and tectonic evolution of this basin and the Bangong-Nujiang Meso-Tethys Ocean (BNMO). However, the partial absence of fossils hinders the study of the stratigraphic distribution and tectonic paleogeography of the basin. Late Triassic bivalves, including nine species in nine genera, were identified for the first time in olistostromes from the Sêwa Formation in the Riganpeicuo area. Based on detailed geological field surveys and sedimentary facies analysis, the lower-middle part of the Rigenco section is a deep-water turbidite fan deposit and the upper part is a shallow sea mixed shelf deposit, which differs distinctively from the carbonate platform facies of the Jiebuqu Formation. Therefore, the strata formerly assigned to the Jiebuqu Formation (Rigenco section) is formally reassigned to the Lower-Middle Jurassic Sêwa Formation and Middle Jurassic Shaqiaomu Formation. These results not only provide further understanding of the sedimentary infill history of the South Qiangtang Basin, but also further support that the BNMO was already open in the Late Triassic and formed a mature ocean in the Early-Middle Jurassic, with subsequent rapid subduction. Both the opening and subduction processes were completed in a relatively short time interval with a large number of attendant olistostromes.