bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maintenance of quiescent oocytes by noradrenergic signals
Authors: Kim Jeongho , Hyun Moonjung , Hibi Masahiko , You Young-Jai 
Published: November 2021

AbstractAll females adopt an evolutionary conserved reproduction strategy; under unfavorable conditions such as scarcity of food or mates, oocytes remain quiescent. However, the signals to maintain oocyte quiescence are largely unknown. Here, we report that in four different species – Caenorhabditis elegans, Caenorhabditis remanei, Drosophila melanogaster, and Danio rerio – octopamine and norepinephrine play an essential role in maintaining oocyte quiescence. In the absence of mates, the oocytes of Caenorhabditis mutants lacking octopamine signaling fail to remain quiescent, but continue to divide and become polyploid. Upon starvation, the egg chambers of D. melanogaster mutants lacking octopamine signaling fail to remain at the previtellogenic stage, but grow to full-grown egg chambers. Upon starvation, D. rerio lacking norepinephrine fails to maintain a quiescent primordial follicle and activates an excessive number of primordial follicles. Our study reveals an evolutionarily conserved function of the noradrenergic signal in maintaining quiescent oocytes.
Temporal loss boundary engineered photonic cavity
Authors: Cong Longqing , Han Jiaguang , Zhang Weili , Singh Ranjan 
Published: November 2021

AbstractLosses are ubiquitous and unavoidable in nature inhibiting the performance of most optical processes. Manipulating losses to adjust the dissipation of photons is analogous to braking a running car that is as important as populating photons via a gain medium. Here, we introduce the transient loss boundary into a photon populated cavity that functions as a ‘photon brake’ and probe photon dynamics by engineering the ‘brake timing’ and ‘brake strength’. Coupled cavity photons can be distinguished by stripping one photonic mode through controlling the loss boundary, which enables the transition from a coupled to an uncoupled state. We interpret the transient boundary as a perturbation by considering both real and imaginary parts of permittivity, and the dynamic process is modeled with a temporal two-dipole oscillator: one with the natural resonant polarization and the other with a frequency-shift polarization. The model unravels the underlying mechanism of concomitant coherent spectral oscillations and generation of tone-tuning cavity photons in the braking process. By synthesizing the temporal loss boundary into a photon populated cavity, a plethora of interesting phenomena and applications are envisioned such as the observation of quantum squeezed states, low-loss nonreciprocal waveguides and ultrafast beam scanning devices.
Global warming-induced Asian hydrological climate transition across the Miocene–Pliocene boundary
Authors: Ao Hong , Rohling Eelco J. , Zhang Ran , Roberts Andrew P. , Holbourn Ann E. , Ladant Jean-Baptiste , Dupont-Nivet Guillaume , Kuhnt Wolfgang , Zhang Peng , Wu Feng , Dekkers Mark J. , Liu Qingsong , Liu Zhonghui , Xu Yong , Poulsen Christopher J. , Licht Alexis , Sun Qiang , Chiang John C. H. , Liu Xiaodong , Wu Guoxiong , Ma Chao , Zhou Weijian , Jin Zhangdong , Li Xinxia , Li Xinzhou , Peng Xianzhe , Qiang Xiaoke , An Zhisheng 
Published: November 2021

AbstractAcross the Miocene–Pliocene boundary (MPB; 5.3 million years ago, Ma), late Miocene cooling gave way to the early-to-middle Pliocene Warm Period. This transition, across which atmospheric CO2 concentrations increased to levels similar to present, holds potential for deciphering regional climate responses in Asia—currently home to more than half of the world’s population— to global climate change. Here we find that CO2-induced MPB warming both increased summer monsoon moisture transport over East Asia, and enhanced aridification over large parts of Central Asia by increasing evaporation, based on integration of our ~1–2-thousand-year (kyr) resolution summer monsoon records from the Chinese Loess Plateau aeolian red clay with existing terrestrial records, land-sea correlations, and climate model simulations. Our results offer palaeoclimate-based support for ‘wet-gets-wetter and dry-gets-drier’ projections of future regional hydroclimate responses to sustained anthropogenic forcing. Moreover, our high-resolution monsoon records reveal a dynamic response to eccentricity modulation of solar insolation, with predominant 405-kyr and ~100-kyr periodicities between 8.1 and 3.4 Ma.
Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes
Authors: Ansari-Pour Naser , Zheng Yonglan , Yoshimatsu Toshio F. , Sanni Ayodele , Ajani Mustapha , Reynier Jean-Baptiste , Tapinos Avraam , Pitt Jason J. , Dentro Stefan , Woodard Anna , Rajagopal Padma Sheila , Fitzgerald Dominic , Gruber Andreas J. , Odetunde Abayomi , Popoola Abiodun , Falusi Adeyinka G. , Babalola Chinedum Peace , Ogundiran Temidayo , Ibrahim Nasiru , Barretina Jordi , Van Loo Peter , Chen Mengjie , White Kevin P. , Ojengbede Oladosu , Obafunwa John , Huo Dezheng , Wedge David C. , Olopade Olufunmilayo I. 
Published: November 2021

AbstractBlack women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast cancers, with RNA-seq in a subset, from women in Nigeria in comparison with The Cancer Genome Atlas (n = 76) reveal a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonalGATA3mutations with a 10.5-year younger age at diagnosis. We also find non-coding mutations in bona fide drivers (ZNF217andSYPL1) and a previously unreported INDEL signature strongly associated with African ancestry proportion, underscoring the need to expand inclusion of diverse populations in biomedical research. Finally, we demonstrate that characterizing tumors for homologous recombination deficiency has significant clinical relevance in stratifying patients for potentially life-saving therapies.
Coalescence and directed anisotropic growth of starch granule initials in subdomains of Arabidopsis thaliana chloroplasts
Authors: Bürgy Léo , Eicke Simona , Kopp Christophe , Jenny Camilla , Lu Kuan Jen , Escrig Stephane , Meibom Anders , Zeeman Samuel C. 
Published: November 2021

AbstractLiving cells orchestrate enzyme activities to produce myriads of biopolymers but cell-biological understanding of such processes is scarce. Starch, a plant biopolymer forming discrete, semi-crystalline granules within plastids, plays a central role in glucose storage, which is fundamental to life. Combining complementary imaging techniques and Arabidopsis genetics we reveal that, in chloroplasts, multiple starch granules initiate in stromal pockets between thylakoid membranes. These initials coalesce, then grow anisotropically to form lenticular granules. The major starch polymer, amylopectin, is synthesized at the granule surface, while the minor amylose component is deposited internally. The non-enzymatic domain of STARCH SYNTHASE 4, which controls the protein’s localization, is required for anisotropic growth. These results present us with a conceptual framework for understanding the biosynthesis of this key nutrient.
BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma
Authors: Laubscher Dominik , Gryder Berkley E. , Sunkel Benjamin D. , Andresson Thorkell , Wachtel Marco , Das Sudipto , Roschitzki Bernd , Wolski Witold , Wu Xiaoli S. , Chou Hsien-Chao , Song Young K. , Wang Chaoyu , Wei Jun S. , Wang Meng , Wen Xinyu , Ngo Quy Ai , Marques Joana G. , Vakoc Christopher R. , Schäfer Beat W. , Stanton Benjamin Z. , Khan Javed 
Published: November 2021

AbstractRhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage. The aggressive alveolar subtype is characterized by t(2;13) or t(1;13) translocations encoding for PAX3- or PAX7-FOXO1 chimeric transcription factors, respectively, and are referred to as fusion positive RMS (FP-RMS). The fusion gene alters the myogenic program and maintains the proliferative state while blocking terminal differentiation. Here, we investigated the contributions of chromatin regulatory complexes to FP-RMS tumor maintenance. We define the mSWI/SNF functional repertoire in FP-RMS. We find that SMARCA4 (encoding BRG1) is overexpressed in this malignancy compared to skeletal muscle and is essential for cell proliferation. Proteomic studies suggest proximity between PAX3-FOXO1 and BAF complexes, which is further supported by genome-wide binding profiles revealing enhancer colocalization of BAF with core regulatory transcription factors. Further, mSWI/SNF complexes localize to sites of de novo histone acetylation. Phenotypically, interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes, which is recapitulated by BRG1 targeting compounds. We conclude that inhibition of BRG1 overcomes the differentiation blockade of FP-RMS cells and may provide a therapeutic strategy for this lethal childhood tumor.
A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division
Authors: Martini Silvia , Davis Khalil , Faraway Rupert , Elze Lisa , Lockwood Nicola , Jones Andrew , Xie Xiao , McDonald Neil Q. , Mann David J. , Armstrong Alan , Ule Jernej , Parker Peter J. 
Published: November 2021

AbstractThe PKCε-regulated genome protective pathway provides transformed cells a failsafe to successfully complete mitosis. Despite the necessary role for Aurora B in this programme, it is unclear whether its requirement is sufficient or if other PKCε cell cycle targets are involved. To address this, we developed a trapping strategy using UV-photocrosslinkable amino acids encoded in the PKCε kinase domain. The validation of the mRNA binding protein SERBP1 as a PKCε substrate revealed a series of mitotic events controlled by the catalytic form of PKCε. PKCε represses protein translation, altering SERBP1 binding to the 40 S ribosomal subunit and promoting the assembly of ribonucleoprotein granules containing SERBP1, termed M-bodies. Independent of Aurora B, SERBP1 is shown to be necessary for chromosome segregation and successful cell division, correlating with M-body formation. This requirement for SERBP1 demonstrates that Aurora B acts in concert with translational regulation in the PKCε-controlled pathway exerting genome protection.
Pattern transfer of large-scale thin membranes with controllable self-delamination interface for integrated functional systems
Authors: Park Jun Kyu , Zhang Yue , Xu Baoxing , Kim Seok 
Published: November 2021

AbstractDirect transfer of pre-patterned device-grade nano-to-microscale materials highly benefits many existing and potential, high performance, heterogeneously integrated functional systems over conventional lithography-based microfabrication. We present, in combined theory and experiment, a self-delamination-driven pattern transfer of a single crystalline silicon thin membrane via well-controlled interfacial design in liquid media. This pattern transfer allows the usage of an intermediate or mediator substrate where both front and back sides of a thin membrane are capable of being integrated with standard lithographical processing, thereby achieving deterministic assembly of the thin membrane into a multi-functional system. Implementations of these capabilities are demonstrated in broad variety of applications ranging from electronics to microelectromechanical systems, wetting and filtration, and metamaterials.
Multi-decadal increase of forest burned area in Australia is linked to climate change
Authors: Canadell Josep G. , Meyer C. P. , Cook Garry D. , Dowdy Andrew , Briggs Peter R. , Knauer Jürgen , Pepler Acacia , Haverd Vanessa 
Published: November 2021

AbstractFire activity in Australia is strongly affected by high inter-annual climate variability and extremes. Through changes in the climate, anthropogenic climate change has the potential to alter fire dynamics. Here we compile satellite (19 and 32 years) and ground-based (90 years) burned area datasets, climate and weather observations, and simulated fuel loads for Australian forests. Burned area in Australia’s forests shows a linear positive annual trend but an exponential increase during autumn and winter. The mean number of years since the last fire has decreased consecutively in each of the past four decades, while the frequency of forest megafire years (>1 Mha burned) has markedly increased since 2000. The increase in forest burned area is consistent with increasingly more dangerous fire weather conditions, increased risk factors associated with pyroconvection, including fire-generated thunderstorms, and increased ignitions from dry lightning, all associated to varying degrees with anthropogenic climate change.
Stroke subtype-dependent synapse elimination by reactive gliosis in mice
Authors: Shi Xiaojing , Luo Longlong , Wang Jixian , Shen Hui , Li Yongfang , Mamtilahun Muyassar , Liu Chang , Shi Rubing , Lee Joon-Hyuk , Tian Hengli , Zhang Zhijun , Wang Yongting , Chung Won-Suk , Tang Yaohui , Yang Guo-Yuan 
Published: November 2021

AbstractThe pathological role of reactive gliosis in CNS repair remains controversial. In this study, using murine ischemic and hemorrhagic stroke models, we demonstrated that microglia/macrophages and astrocytes are differentially involved in engulfing synapses in the reactive gliosis region. By specifically deleting MEGF10 and MERTK phagocytic receptors, we determined that inhibiting phagocytosis of microglia/macrophages or astrocytes in ischemic stroke improved neurobehavioral outcomes and attenuated brain damage. In hemorrhagic stroke, inhibiting phagocytosis of microglia/macrophages but not astrocytes improved neurobehavioral outcomes. Single-cell RNA sequencing revealed that phagocytosis related biological processes and pathways were downregulated in astrocytes of the hemorrhagic brain compared to the ischemic brain. Together, these findings suggest that reactive microgliosis and astrogliosis play individual roles in mediating synapse engulfment in pathologically distinct murine stroke models and preventing this process could rescue synapse loss.
Towards non-blind optical tweezing by finding 3D refractive index changes through off-focus interferometric tracking
Authors: Landenberger Benjamin , Yatish  , Rohrbach Alexander 
Published: November 2021

AbstractIn modern 3D microscopy, holding and orienting arbitrary biological objects with optical forces instead of using coverslips and gel cylinders is still a vision. Although optical trapping forces are strong enough and related photodamage is acceptable, the precise (re-) orientation of large specimen with multiple optical traps is difficult, since they grab blindly at the object and often slip off. Here, we present an approach to localize and track regions with increased refractive index using several holographic optical traps with a single camera in an off-focus position. We estimate the 3D grabbing positions around several trapping foci in parallel through analysis of the beam deformations, which are continuously measured by defocused camera images of cellular structures inside cell clusters. Although non-blind optical trapping is still a vision, this is an important step towards fully computer-controlled orientation and feature-optimized laser scanning of sub-mm sized biological specimen for future 3D light microscopy.
Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites
Authors: Mullins Elwood A. , Dorival Jonathan , Tang Gong-Li , Boger Dale L. , Eichman Brandt F. 
Published: November 2021

AbstractMicrobes produce a broad spectrum of antibiotic natural products, including many DNA-damaging genotoxins. Among the most potent of these are DNA alkylating agents in the spirocyclopropylcyclohexadienone (SCPCHD) family, which includes the duocarmycins, CC-1065, gilvusmycin, and yatakemycin. The yatakemycin biosynthesis cluster inStreptomycessp. TP-A0356 contains an AlkD-related DNA glycosylase, YtkR2, that serves as a self-resistance mechanism against yatakemycin toxicity. We previously reported that AlkD, which is not present in an SCPCHD producer, provides only limited resistance against yatakemycin. We now show that YtkR2 and C10R5, a previously uncharacterized homolog found in the CC-1065 biosynthetic gene cluster ofStreptomyces zelensis, confer far greater resistance against their respective SCPCHD natural products. We identify a structural basis for substrate specificity across gene clusters and show a correlation between in vivo resistance and in vitro enzymatic activity indicating that reduced product affinity—not enhanced substrate recognition—is the evolutionary outcome of selective pressure to provide self-resistance against yatakemycin and CC-1065.
Optimal verification of the Bell state and Greenberger–Horne–Zeilinger states in untrusted quantum networks
Authors: Han Yun-Guang , Li Zihao , Wang Yukun , Zhu Huangjun 
Published: November 2021

AbstractBipartite and multipartite entangled states are basic ingredients for constructing quantum networks and their accurate verification is crucial to the functioning of the networks, especially for untrusted networks. Here we propose a simple approach for verifying the Bell state in an untrusted network in which one party is not honest. Only local projective measurements are required for the honest party. It turns out each verification protocol is tied to a probability distribution on the Bloch sphere and its performance has an intuitive geometric meaning. This geometric picture enables us to construct the optimal and simplest verification protocols, which are also very useful to detecting entanglement in the untrusted network. Moreover, we show that our verification protocols can achieve almost the same sample efficiencies as protocols tailored to standard quantum state verification. Furthermore, we establish an intimate connection between the verification of Greenberger–Horne–Zeilinger states and the verification of the Bell state. By virtue of this connection we construct the optimal protocol for verifying Greenberger–Horne–Zeilinger states and for detecting genuine multipartite entanglement.
A database of global coastal conditions
Authors: Castaneda-Guzman Mariana , Mantilla-Saltos Gabriel , Murray Kris A. , Settlage Robert , Escobar Luis E. 
Published: November 2021

AbstractRemote sensing satellite imagery has the potential to monitor and understand dynamic environmental phenomena by retrieving information about Earth’s surface. Marine ecosystems, however, have been studied with less intensity than terrestrial ecosystems due, in part, to data limitations. Data on sea surface temperature (SST) and Chlorophyll-a(Chlo-a) can provide quantitative information of environmental conditions in coastal regions at a high spatial and temporal resolutions. Using the exclusive economic zone of coastal regions as the study area, we compiled monthly and annual statistics of SST and Chlo-aglobally for 2003 to 2020. This ready-to-use dataset aims to reduce the computational time and costs for local-, regional-, continental-, and global-level studies of coastal areas. Data may be of interest to researchers in the areas of ecology, oceanography, biogeography, fisheries, and global change. Target applications of the database include environmental monitoring of biodiversity and marine microorganisms, and environmental anomalies.
A computer-aided method for controlling chemical resistance of drugs using RRKM theory in the liquid phase
Authors: Douroudgari Hamed , Vahedpour Morteza 
Published: November 2021

AbstractThe chemical resistance of drugs against any change in their composition and studying the rate of multiwell-multichannel reactions in the liquid phase, respectively, are the important challenges of pharmacology and chemistry. In this article, we investigate two challenges together through studying drug stability against its unimolecular reactions in the liquid phase. Accordingly, multiwell-multichannel reactions based on 1,4-H shifts are designed for simplified drugs such as 3-hydroxyl-1H-pyrrol-2(5H)-one, 3-hydroxyfuran-2(5H)-one, and 3-hydroxythiophen-2(5H)-one. After that, the reverse and forward rate constants are calculated by using the Rice Ramsperger Kassel Marcus theory (RRKM) and Eckart tunneling correction over the 298–360 K temperature range. Eventually, using the obtained rate constants, we can judge drug resistance versus structural changes. To attain the goals, the potential energy surfaces of all reactions are computed by the complete basis set-quadratic Becke3 composite method, CBS-QB3, and the high-performance meta hybrid density functional method, M06-2X, along with the universal Solvation Model based on solute electron Density, SMD, due to providing more precise and efficient results for the barrier heights and thermodynamic studies. To find the main reaction pathway of the intramolecular 1,4-H shifts in the target molecules, all possible reaction pathways are considered mechanistically in the liquid phase. Also, the direct dynamics calculations that carry out by RRKM theory on the modeled pathways are used to distinguish the main reaction pathway. As the main finding of this research, the results of quantum chemical calculations accompanied by the RRKM/Eckart rate constants are used to predict the stability of drugs. This study proposes a new way to examine drug stability by the computer-aided reaction design of target drugs. Our results show that 3-hydroxyfuran-2(5H)-one based drugs are the most stable and 3-hydroxythiophen-2(5H)-one based drugs are more stable than 3-hydroxy-1H-pyrrol-2 (5H)-one based drugs in water solution.
Dual electrochemical sensing of spiked virus and SARS-CoV-2 using natural bed-receptor (MV-gal1)
Authors: Ghazizadeh E. , Neshastehriz Ali , Firoozabadi Ali Dehghani , Yazdi Mohammad Kaji , Saievar-Iranizad Esmail , Einali Samira 
Published: November 2021

AbstractIt has been necessary to use methods that can detect the specificity of a virus during virus screening. In this study, we use a dual platform to identify any spiked virus and specific SARS-CoV-2 antigen, sequentially. We introduce a natural bed-receptor surface as Microparticle Vesicle-Galactins1 (MV-gal1) with the ability of glycan binding to screen every spiked virus. MV are the native vesicles which may have the gal-1 receptor. Gal-1 is the one of lectin receptor which can bind to glycan. After dropping the MV-gal1 on the SCPE/GNP, the sensor is turned on due to the increased electrochemical exchange with [Fe(CN)6]−3/−4 probe. Dropping the viral particles of SARS-CoV-2 cause to turn off the sensor with covering the sugar bond (early screening). Then, with the addition of Au/Antibody-SARS-CoV-2 on the MV-gal1@SARS-CoV-2 Antigen, the sensor is turned on again due to the electrochemical amplifier of AuNP (specific detection).For the first time, our sensor has the capacity of screening of any spike virus, and the specific detection of COVID-19 (LOD: 4.57 × 102 copies/mL) by using the natural bed-receptor and a specific antibody in the point of care test.