bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Urban Representation on Simulation of Hurricane Rainfall
Authors: Patel Pratiman , Ankur Kumar , Jamshidi Sajad , Tiwari Alka , Nadimpalli Raghu , Busireddy N. K. R. , Safaee Samira , Osuri Krishna K. , Karmakar Subhankar , Ghosh Subimal , Aliaga Daniel , Smith James , Marks Frank , Yang Zong‐Liang , Niyogi Dev 
Published: November 2023

AbstractTaking the examples of Hurricane Florence (2018) over the Carolinas and Hurricane Harvey (2017) over the Texas Gulf Coast, the study attempts to understand the performance of slab, single‐layer Urban Canopy Model (UCM), and Building Environment Parameterization (BEP) in simulating hurricane rainfall using the Weather Research and Forecasting (WRF) model. The WRF model simulations showed that for an intense, large‐scale event such as a hurricane, the model quantitative precipitation forecast over the urban domain was sensitive to the model urban physics. The spatial and temporal verification using the modified Kling‐Gupta efficiency and Method for Object based Diagnostic and Evaluation in Time Domain suggests that UCM performance is superior to the BEP scheme. Additionally, using the BEP urban physics scheme over UCM for landfalling hurricane rainfall simulations has helped simulate heavy rainfall hotspots.
A Reappraisal of Subtropical Subsurface Water Ice Stability on Mars
Authors: Lange L. , Forget F. , Vincendon M. , Spiga A. , Vos E. , Aharonson O. , Millour E. , Bierjon A. , Vandemeulebrouck R. 
Published: November 2023

AbstractMassive reservoirs of subsurface water ice in equilibrium with atmospheric water vapor are found poleward of 45° latitude on Mars. The absence of CO2 frost on steep pole‐facing slopes and simulations of atmospheric‐soil water exchanges suggested that water ice could be stable underneath these slopes down to 25° latitude. We revisit these arguments with a new slope microclimate model. Our model shows that below 30° latitude, slopes are warmer than previously estimated as the air above is heated by warm surrounding plains. This additional heat prevents the formation of surface CO2 frost and subsurface water ice for most slopes. Our model suggests the presence of subsurface water ice beneath pole‐facing slopes down to 30° latitude, and possibly 25° latitude on sparse steep dusty slopes. While unstable ice deposits might be present, our results suggest that water ice is rarer than previously thought in the ±30° latitude range considered for human exploration.
Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges
Authors: Aihara Takaki , Araki Kyoko , Onuma Yunosuke , Cai Yihan , Paing Aye Myat Myat , Goto Susumu , Hisamoto Yoko , Tomaru Nobuhiro , Homma Kosuke , Takagi Masahiro , Yoshida Toshiya , Iio Atsuhiro , Nagamatsu Dai , Kobayashi Hajime , Hirota Mitsuru , Uchiyama Kentaro , Tsumura Yoshihiko 
Published: November 2023

AbstractThe reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species’ range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii’s distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations’ saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.
NULISA: a proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing
Authors: Feng Wei , Beer Joanne C. , Hao Qinyu , Ariyapala Ishara S. , Sahajan Aparna , Komarov Andrei , Cha Katie , Moua Mason , Qiu Xiaolei , Xu Xiaomei , Iyengar Shweta , Yoshimura Thu , Nagaraj Rajini , Wang Li , Yu Ming , Engel Kate , Zhen Lucas , Xue Wen , Lee Chen-jung , Park Chan Ho , Peng Cheng , Zhang Kaiyuan , Grzybowski Adrian , Hahm Johnnie , Schmidt Susanne V. , Odainic Alexandru , Spitzer Jasper , Buddika Kasun , Kuo Dwight , Fang Lei , Zhang Bingqing , Chen Steve , Latz Eicke , Yin Yiyuan , Luo Yuling , Ma Xiao-Jun 
Published: November 2023

AbstractThe blood proteome holds great promise for precision medicine but poses substantial challenges due to the low abundance of most plasma proteins and the vast dynamic range of the plasma proteome. Here we address these challenges with NUcleic acid Linked Immuno-Sandwich Assay (NULISA™), which improves the sensitivity of traditional proximity ligation assays by ~10,000-fold to attomolar level, by suppressing assay background via a dual capture and release mechanism built into oligonucleotide-conjugated antibodies. Highly multiplexed quantification of both low- and high-abundance proteins spanning a wide dynamic range is achieved by attenuating signals from abundant targets with unconjugated antibodies and next-generation sequencing of barcoded reporter DNA. A 200-plex NULISA containing 124 cytokines and chemokines and other proteins demonstrates superior sensitivity to a proximity extension assay in detecting biologically important low-abundance biomarkers in patients with autoimmune diseases and COVID-19. Fully automated NULISA makes broad and in-depth proteomic analysis easily accessible for research and diagnostic applications.
A transcriptional network governing ceramide homeostasis establishes a cytokine-dependent developmental process
Authors: Liao Ruiqi , Babatunde Abiola , Qiu Stephanie , Harikumar Hamsini , Coon Joshua J. , Overmyer Katherine A. , Hannun Yusuf A. , Luberto Chiara , Bresnick Emery H. 
Published: November 2023

AbstractTranscriptional mechanisms controlling developmental processes establish and maintain proteomic networks, which can govern the levels of intracellular small molecules. Although dynamic changes in bioactive small molecules can link transcription factor and genome activity with cell state transitions, many mechanistic questions are unresolved. Using quantitative lipidomics and multiomics, we discover that the hematopoietic transcription factor GATA1 establishes ceramide homeostasis during erythroid differentiation by regulating genes encoding sphingolipid metabolic enzymes. Inhibiting a GATA1-induced sphingolipid biosynthetic enzyme, delta(4)-desaturase, or disrupting ceramide homeostasis with cell-permeable dihydroceramide or ceramide is detrimental to erythroid, but not myeloid, progenitor activity. Coupled with genetic editing-based rewiring of the regulatory circuitry, we demonstrate that ceramide homeostasis commissions vital stem cell factor and erythropoietin signaling by opposing an inhibitory protein phosphatase 2A-dependent, dual-component mechanism. Integrating bioactive lipids as essential components of GATA factor mechanisms to control cell state transitions has implications for diverse cell and tissue types.
EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes
Authors: Shinder Ida , Hu Richard , Ji Hyun Joo , Chao Kuan-Hao , Pertea Mihaela 
Published: November 2023

AbstractAccurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the basic sciences. We reveal that widely used splice-aware aligners, such as STAR and HISAT2, can introduce erroneous spliced alignments between repeated sequences, leading to the inclusion of falsely spliced transcripts in RNA-seq experiments. In some cases, the ‘phantom’ introns resulting from these errors make their way into widely-used genome annotation databases. To address this issue, we present EASTR (Emending Alignments of Spliced Transcript Reads), a software tool that detects and removes falsely spliced alignments or transcripts from alignment and annotation files. EASTR improves the accuracy of spliced alignments across diverse species, including human, maize, and Arabidopsis thaliana, by detecting sequence similarity between intron-flanking regions. We demonstrate that applying EASTR before transcript assembly substantially reduces false positive introns, exons, and transcripts, improving the overall accuracy of assembled transcripts. Additionally, we show that EASTR’s application to reference annotation databases can detect and correct likely cases of mis-annotated transcripts.
Reconciling Southern Ocean fronts equatorward migration with minor Antarctic ice volume change during Miocene cooling
Authors: Hou Suning , Stap Lennert B. , Paul Ryan , Nelissen Mei , Hoem Frida S. , Ziegler Martin , Sluijs Appy , Sangiorgi Francesca , Bijl Peter K. 
Published: November 2023

AbstractGradual climate cooling and CO2 decline in the Miocene were recently shown not to be associated with major ice volume expansion, challenging a fundamental paradigm in the functioning of the Antarctic cryosphere. Here, we explore Miocene ice-ocean-climate interactions by presenting a multi-proxy reconstruction of subtropical front migration, bottom water temperature and global ice volume change, using dinoflagellate cyst biogeography, benthic foraminiferal clumped isotopes from offshore Tasmania. We report an equatorward frontal migration and strengthening, concurrent with surface and deep ocean cooling but absence of ice volume change in the mid–late-Miocene. To reconcile these counterintuitive findings, we argue based on new ice sheet modelling that the Antarctic ice sheet progressively lowered in height while expanding seawards, to maintain a stable volume. This can be achieved with rigorous intervention in model precipitation regimes on Antarctica and ice-induced ocean cooling and requires rethinking the interactions between ice, ocean and climate.
Stepwise taming of triplet excitons via multiple confinements in intrinsic polymers for long-lived room-temperature phosphorescence
Authors: Gao Liang , Huang Jiayue , Qu Lunjun , Chen Xiaohong , Zhu Ying , Li Chen , Tian Quanchi , Zhao Yanli , Yang Chaolong 
Published: November 2023

AbstractPolymeric materials exhibiting room temperature phosphorescence (RTP) show a promising application potential. However, the conventional ways of preparing such materials are mainly focused on doping, which may suffer from phase separation, poor compatibility, and lack of effective methods to promote intersystem crossing and suppress the nonradiative deactivation rates. Herein, we present an intrinsically polymeric RTP system producing long-lived phosphorescence, high quantum yields and multiple colors by stepwise structural confinement to tame triplet excitons. In this strategy, the performance of the materials is improved in two aspects simultaneously: the phosphorescence lifetime of one polymer (9VA-B) increased more than 4 orders of magnitude, and the maximum phosphorescence quantum yield reached 16.04% in halogen-free polymers. Moreover, crack detection is realized by penetrating steam through the materials exposed to humid surroundings as a special quenching effect, and the information storage is carried out by employing the Morse code and the variations in lifetimes. This study provides a different strategy for constructing intrinsically polymeric RTP materials toward targeted applications.
Co-option of a non-retroviral endogenous viral element in planthoppers
Authors: Huang Hai-Jian , Li Yi-Yuan , Ye Zhuang-Xin , Li Li-Li , Hu Qing-Ling , He Yu-Juan , Qi Yu-Hua , Zhang Yan , Li Ting , Lu Gang , Mao Qian-Zhuo , Zhuo Ji-Chong , Lu Jia-Bao , Xu Zhong-Tian , Sun Zong-Tao , Yan Fei , Chen Jian-Ping , Zhang Chuan-Xi , Li Jun-Min 
Published: November 2023

AbstractNon-retroviral endogenous viral elements (nrEVEs) are widely dispersed throughout the genomes of eukaryotes. Although nrEVEs are known to be involved in host antiviral immunity, it remains an open question whether they can be domesticated as functional proteins to serve cellular innovations in arthropods. In this study, we found that endogenous toti-like viral elements (ToEVEs) are ubiquitously integrated into the genomes of three planthopper species, with highly variable distributions and polymorphism levels in planthopper populations. Three ToEVEs display exon‒intron structures and active transcription, suggesting that they might have been domesticated by planthoppers. CRISPR/Cas9 experiments revealed that one ToEVE in Nilaparvata lugens, NlToEVE14, has been co-opted by its host and plays essential roles in planthopper development and fecundity. Large-scale analysis of ToEVEs in arthropod genomes indicated that the number of arthropod nrEVEs is currently underestimated and that they may contribute to the functional diversity of arthropod genes.
MAF amplification licenses ERα through epigenetic remodelling to drive breast cancer metastasis
Authors: Llorente Alicia , Blasco María Teresa , Espuny Irene , Guiu Marc , Ballaré Cecilia , Blanco Enrique , Caballé Adrià , Bellmunt Anna , Salvador Fernando , Morales Andrea , Nuñez Marc , Loren Guillem , Imbastari Francesca , Fidalgo Marta , Figueras-Puig Cristina , Gibler Patrizia , Graupera Mariona , Monteiro Freddy , Riera Antoni , Holen Ingunn , Avgustinova Alexandra , Di Croce Luciano , Gomis Roger R. 
Published: November 2023

AbstractMAF amplification increases the risk of breast cancer (BCa) metastasis through mechanisms that are still poorly understood yet have important clinical implications. Oestrogen-receptor-positive (ER+) BCa requires oestrogen for both growth and metastasis, albeit by ill-known mechanisms. Here we integrate proteomics, transcriptomics, epigenomics, chromatin accessibility and functional assays from human and syngeneic mouse BCa models to show that MAF directly interacts with oestrogen receptor alpha (ERα), thereby promoting a unique chromatin landscape that favours metastatic spread. We identify metastasis-promoting genes that are de novo licensed following oestrogen exposure in a MAF-dependent manner. The histone demethylase KDM1A is key to the epigenomic remodelling that facilitates the expression of the pro-metastatic MAF/oestrogen-driven gene expression program, and loss of KDM1A activity prevents this metastasis. We have thus determined that the molecular basis underlying MAF/oestrogen-mediated metastasis requires genetic, epigenetic and hormone signals from the systemic environment, which influence the ability of BCa cells to metastasize.
Most large structural variants in cancer genomes can be detected without long reads
Authors: Choo Zi-Ning , Behr Julie M. , Deshpande Aditya , Hadi Kevin , Yao Xiaotong , Tian Huasong , Takai Kaori , Zakusilo George , Rosiene Joel , Da Cruz Paula Arnaud , Weigelt Britta , Setton Jeremy , Riaz Nadeem , Powell Simon N. , Busam Klaus , Shoushtari Alexander N. , Ariyan Charlotte , Reis-Filho Jorge , de Lange Titia , Imieliński Marcin 
Published: November 2023

AbstractShort-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole genomes, we analyzed ‘loose ends’—local violations of mass balance between adjacent DNA segments. In the landscape of loose ends across 1,330 high-purity cancer whole genomes, most large (>10-kb) clonal SVs were fully resolved by short reads in the 87% of the human genome where copy number could be reliably measured. Some loose ends represent neotelomeres, which we propose as a hallmark of the alternative lengthening of telomeres phenotype. These pan-cancer findings were confirmed by long-molecule profiles of 38 breast cancer and melanoma cases. Our results indicate that aberrant homologous recombination is unlikely to drive the majority of large cancer SVs. Furthermore, analysis of mass balance in short-read whole genome data provides a surprisingly complete picture of cancer chromosomal structure.
Topological analysis of sharp-wave ripple waveforms reveals input mechanisms behind feature variations
Authors: Sebastian Enrique R. , Quintanilla Juan P. , Sánchez-Aguilera Alberto , Esparza Julio , Cid Elena , de la Prida Liset M. 
Published: November 2023

AbstractThe reactivation of experience-based neural activity patterns in the hippocampus is crucial for learning and memory. These reactivation patterns and their associated sharp-wave ripples (SWRs) are highly variable. However, this variability is missed by commonly used spectral methods. Here, we use topological and dimensionality reduction techniques to analyze the waveform of ripples recorded at the pyramidal layer of CA1. We show that SWR waveforms distribute along a continuum in a low-dimensional space, which conveys information about the underlying layer-specific synaptic inputs. A decoder trained in this space successfully links individual ripples with their expected sinks and sources, demonstrating how physiological mechanisms shape SWR variability. Furthermore, we found that SWR waveforms segregated differently during wakefulness and sleep before and after a series of cognitive tasks, with striking effects of novelty and learning. Our results thus highlight how the topological analysis of ripple waveforms enables a deeper physiological understanding of SWRs.
Transcriptionally defined amygdala subpopulations play distinct roles in innate social behaviors
Authors: Lischinsky Julieta E. , Yin Luping , Shi Chenxi , Prakash Nandkishore , Burke Jared , Shekaran Govind , Grba Maria , Corbin Joshua G. , Lin Dayu 
Published: November 2023

AbstractSocial behaviors are innate and supported by dedicated neural circuits, but the molecular identities of these circuits and how they are established developmentally and shaped by experience remain unclear. Here we show that medial amygdala (MeA) cells originating from two embryonically parcellated developmental lineages have distinct response patterns and functions in social behavior in male mice. MeA cells expressing the transcription factor Foxp2 (MeAFoxp2) are specialized for processing male conspecific cues and are essential for adult inter-male aggression. By contrast, MeA cells derived from the Dbx1 lineage (MeADbx1) respond broadly to social cues, respond strongly during ejaculation and are not essential for male aggression. Furthermore, MeAFoxp2 and MeADbx1 cells show differential anatomical and functional connectivity. Altogether, our results suggest a developmentally hardwired aggression circuit at the MeA level and a lineage-based circuit organization by which a cell’s embryonic transcription factor profile determines its social information representation and behavioral relevance during adulthood.
Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor
Authors: Noddings Chari M. , Johnson Jill L. , Agard David A. 
Published: November 2023

AbstractHsp90 is an essential molecular chaperone responsible for the folding and activation of hundreds of ‘client’ proteins, including the glucocorticoid receptor (GR). Previously, we revealed that Hsp70 and Hsp90 remodel the conformation of GR to regulate ligand binding, aided by co-chaperones. In vivo, the co-chaperones FKBP51 and FKBP52 antagonistically regulate GR activity, but a molecular understanding is lacking. Here we present a 3.01 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP52 complex, revealing how FKBP52 integrates into the GR chaperone cycle and directly binds to the active client, potentiating GR activity in vitro and in vivo. We also present a 3.23 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP51 complex, revealing how FKBP51 competes with FKBP52 for GR:Hsp90 binding and demonstrating how FKBP51 can act as a potent antagonist to FKBP52. Altogether, we demonstrate how FKBP51 and FKBP52 integrate into the GR chaperone cycle to advance GR to the next stage of maturation.
ADORA2A promotes proliferation and inhibits apoptosis through PI3K/AKT pathway activation in colorectal carcinoma
Authors: Ran Longyan , Mou Xiao , Peng Zhenglin , Li Xiaochen , Li Meirong , Xu Duo , Yang Zixi , Sun Xingwang , Yin Tao 
Published: November 2023

AbstractThe third most often diagnosed disease globally and the second most prevalent cause of cancer-related death is colorectal cancer (CRC). Numerous human malignancies have been identified to have high expression of ADORA2A. However, it is still ambiguous about its function in CRC. RNA-seq with stable transfected SETDB1 knockdown cells was used to identify differentially expressed genes. Further, knockdown of ADORA2A in CRC cell lines SW620 and HCT116 was performed with siRNA and over expression of ADORA2A in SW480 cells was conducted with plasmids. CCK8, colony formation, wound healing, and transwell assay were used to detect the effects of cell proliferation, migration, and invasion after knockdown and over expression of ADORA2A. Also, apoptosis was analyzed by flow cytometry, apoptosis-related proteins and key PI3K/AKT pathway proteins were detected using Western blotting. ADORA2A was identified after RNA-seq analysis and played an important role in CRC prognosis. ADORA2A was relatively high in SW620 and HCT116 cell lines compared to SW480 cell lines. ADORA2A knockdown in SW620 and HCT116 inhibited cell proliferation, migration, and invasion, while ADORA2A overexpression had the opposite effect. In addition, ADORA2A also impacted the expression of apoptosis-related proteins, including Bcl-2, Bax, Cleaved caspase-3 and Cleaved caspase-9, and reduced apoptosis. Furthermore, this process may include the PI3K/AKT signaling pathway. ADORA2A promotes CRC progression and inhibits apoptosis by the PI3K/AKT signaling pathway. It may contribute to the management and treatment of CRC.
Antiproliferative effects of D-allose associated with reduced cell division frequency in glioblastoma
Authors: Suzuki Kenta , Ogawa Daisuke , Kanda Takahiro , Fujimori Takeshi , Shibayama Yuki , Rahman Asadur , Ye Juanjuan , Ohsaki Hiroyuki , Akimitsu Kazuya , Izumori Ken , Tamiya Takashi , Nishiyama Akira , Miyake Keisuke 
Published: November 2023

AbstractRecent studies have shown that D-allose, a rare sugar, elicits antitumor effects on different types of solid cancers, such as hepatocellular carcinoma, non-small-cell lung cancer, and squamous cell carcinoma of the head and neck. In this study, we examined the effects of D-allose on the proliferation of human glioblastoma (GBM) cell lines (i.e., U251MG and U87MG) in vitro and in vivo and the underlying mechanisms. D-allose treatment inhibited the proliferation of U251MG and U87MG cells in a dose-dependent manner (3–50 mM). However, D-allose treatment did not affect cell cycles or apoptosis in these cells but significantly decreased the cell division frequency in both GBM cell lines. In a subcutaneous U87MG cell xenograft model, intraperitoneal injection of D-allose (100 mg/kg/day) significantly reduced the tumor volume in 28 days. These data indicate that D-allose-induced reduction in cell proliferation is associated with a subsequent decrease in the number of cell divisions, independent of cell-cycle arrest and apoptosis. Thus, D-allose could be an attractive additive to therapeutic strategies for GBM.