bluuebunny/crossref_metadata_2025_split huggingface dataset:
The 3′ Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies
Authors: Suzuki Hidefumi , Abe Ryota , Shimada Miho , Hirose Tomonori , Hirose Hiroko , Noguchi Keisuke , Ike Yoko , Yasui Nanami , Furugori Kazuki , Yamaguchi Yuki , Toyoda Atsushi , Suzuki Yutaka , Yamamoto Tatsuro , Saitoh Noriko , Sato Shigeo , Tomomori-Sato Chieri , Conaway Ronald C. , Conaway Joan W. , Takahashi Hidehisa 
Published: May 2022

AbstractNon-polyadenylated mRNAs of replication-dependent histones (RDHs) are synthesized by RNA polymerase II (Pol II) at histone locus bodies (HLBs). HLBs frequently associate with Cajal bodies (CBs), in which 3′-end processing factors for RDH genes are enriched; however, this association’s role in transcription termination of RDH genes remains unclear. Here, we show that Pol II pauses immediately upstream of transcript end sites of RDH genes and Mediator plays a role in this Pol II pausing through CBs’ association with HLBs. Disruption of the Mediator docking site for Little elongation complex (LEC)–Cap binding complex (CBC)–Negative elongation factor (NELF), components of CBs, interferes with CBs’ association with HLBs and 3′ Pol II pausing, resulting in increased aberrant unprocessed RDH gene transcripts. Our findings suggest Mediator’s involvement in CBs’ association with HLBs to facilitate 3′ Pol II pausing and subsequent 3′-end processing of RDH genes by supplying 3′-end processing factors.
Peptide nano-blanket impedes fibroblasts activation and subsequent formation of pre-metastatic niche
Authors: Zhou Yi , Ke Peng , Bao Xiaoyan , Wu Honghui , Xia Yiyi , Zhang Zhentao , Zhong Haiqing , Dai Qi , Wu Linjie , Wang Tiantian , Lin Mengting , Li Yaosheng , Jiang Xinchi , Yang Qiyao , Lu Yiying , Zhong Xincheng , Han Min , Gao Jianqing 
Published: May 2022

AbstractThere is evidence to suggest that the primary tumor induces the formation of a pre-metastatic niche in distal organs by stimulating the production of pro-metastatic factors. Given the fundamental role of the pre-metastatic niche in the development of metastases, interruption of its formation would be a promising strategy to take early action against tumor metastasis. Here we report an enzyme-activated assembled peptide FR17 that can serve as a “flame-retarding blanket” in the pre-metastatic niche specifically to extinguish the “fire” of tumor-supportive microenvironment adaption. We show that the in-situ assembled peptide nano-blanket inhibits fibroblasts activation, suppressing the remodeling of the metastasis-supportive host stromal tissue, and reversing vascular destabilization and angiogenesis. Furthermore, we demonstrate that the nano-blanket prevents the recruitment of myeloid cells to the pre-metastatic niche, regulating the immune-suppressive microenvironment. We show that FR17 administration effectively inhibits the formation of the pulmonary pre-metastatic niche and postoperative metastasis, offering a therapeutic strategy against pre-metastatic niche formation.
Seeking patterns of antibiotic resistance in ATLAS, an open, raw MIC database with patient metadata
Authors: Catalán Pablo , Wood Emily , Blair Jessica M. A. , Gudelj Ivana , Iredell Jonathan R. , Beardmore Robert E. 
Published: May 2022

AbstractAntibiotic resistance represents a growing medical concern where raw, clinical datasets are under-exploited as a means to track the scale of the problem. We therefore sought patterns of antibiotic resistance in the Antimicrobial Testing Leadership and Surveillance (ATLAS) database. ATLAS holds 6.5M minimal inhibitory concentrations (MICs) for 3,919 pathogen-antibiotic pairs isolated from 633k patients in 70 countries between 2004 and 2017. We show most pairs form coherent, although not stationary, timeseries whose frequencies of resistance are higher than other databases, although we identified no systematic bias towards including more resistant strains in ATLAS. We sought data anomalies whereby MICs could shift for methodological and not clinical or microbiological reasons and found artefacts in over 100 pathogen-antibiotic pairs. Using an information-optimal clustering methodology to classify pathogens into low and high antibiotic susceptibilities, we used ATLAS to predict changes in resistance. Dynamics of the latter exhibit complex patterns with MIC increases, and some decreases, whereby subpopulations’ MICs can diverge. We also identify pathogens at risk of developing clinical resistance in the near future.
Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes
Authors: Wang Chunyan , Hesketh Emma L. , Shamorkina Tatiana M. , Li Wentao , Franken Peter J. , Drabek Dubravka , van Haperen Rien , Townend Sarah , van Kuppeveld Frank J. M. , Grosveld Frank , Ranson Neil A. , Snijder Joost , de Groot Raoul J. , Hurdiss Daniel L. , Bosch Berend-Jan 
Published: May 2022

AbstractHuman coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1A domain, but, remarkably, also to S1B. The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1B epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2.
A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors
Authors: Koveal Dorothy , Rosen Paul C. , Meyer Dylan J. , Díaz-García Carlos Manlio , Wang Yongcheng , Cai Li-Heng , Chou Peter J. , Weitz David A. , Yellen Gary 
Published: May 2022

AbstractGenetically encoded fluorescent biosensors are powerful tools used to track chemical processes in intact biological systems. However, the development and optimization of biosensors remains a challenging and labor-intensive process, primarily due to technical limitations of methods for screening candidate biosensors. Here we describe a screening modality that combines droplet microfluidics and automated fluorescence imaging to provide an order of magnitude increase in screening throughput. Moreover, unlike current techniques that are limited to screening for a single biosensor feature at a time (e.g. brightness), our method enables evaluation of multiple features (e.g. contrast, affinity, specificity) in parallel. Because biosensor features can covary, this capability is essential for rapid optimization. We use this system to generate a high-performance biosensor for lactate that can be used to quantify intracellular lactate concentrations. This biosensor, named LiLac, constitutes a significant advance in metabolite sensing and demonstrates the power of our screening approach.
O-GlcNAc modification of leucyl-tRNA synthetase 1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine
Authors: Kim Kibum , Yoo Hee Chan , Kim Byung Gyu , Kim Sulhee , Sung Yulseung , Yoon Ina , Yu Ya Chun , Park Seung Joon , Kim Jong Hyun , Myung Kyungjae , Hwang Kwang Yeon , Kim Sunghoon , Han Jung Min 
Published: May 2022

AbstractAll living organisms have the ability to sense nutrient levels to coordinate cellular metabolism. Despite the importance of nutrient-sensing pathways that detect the levels of amino acids and glucose, how the availability of these two types of nutrients is integrated is unclear. Here, we show that glucose availability regulates the central nutrient effector mTORC1 through intracellular leucine sensor leucyl-tRNA synthetase 1 (LARS1). Glucose starvation results in O-GlcNAcylation of LARS1 on residue S1042. This modification inhibits the interaction of LARS1 with RagD GTPase and reduces the affinity of LARS1 for leucine by promoting phosphorylation of its leucine-binding site by the autophagy-activating kinase ULK1, decreasing mTORC1 activity. The lack of LARS1 O-GlcNAcylation constitutively activates mTORC1, supporting its ability to sense leucine, and deregulates protein synthesis and leucine catabolism under glucose starvation. This work demonstrates that LARS1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine.
Rhodium-catalyzed selective direct arylation of phosphines with aryl bromides
Authors: Wang Dingyi , Li Mingjie , Shuang Chengdong , Liang Yong , Zhao Yue , Wang Minyan , Shi Zhuangzhi 
Published: May 2022

AbstractThe widespread use of phosphine ligand libraries is frequently hampered by the challenges associated with their modular preparation. Here, we report a protocol that appends arenes to arylphosphines to access a series of biaryl monophosphines via rhodium-catalyzed P(III)-directedorthoC–H activation, enabling unprecedented one-fold, two-fold, and three-fold direct arylation. Our experimental and theoretical findings reveal a mechanism involving oxidative addition of aryl bromides to the Rh catalyst, furtherorthoC–H metalation viaafour-membered cyclometalated ring. Given the ready availability of substrates, our approach opens the door to developing more general methods for the construction of phosphine ligands.
The macular inner plexiform layer thickness as an early diagnostic indicator for Parkinson’s disease
Authors: Wang Xin , Jiao Bin , Jia Xiaoliang , Wang Yaqin , Liu Hui , Zhu Xiangyu , Hao Xiaoli , Zhu Yuan , Xu Bei , Zhang Sizhe , Xu Qian , Wang Junling , Guo Jifeng , Yan Xinxiang , Tang Beisha , Zhao Rongchang , Shen Lu 
Published: May 2022

AbstractWhether structural alterations of intraretinal layers are indicators for the early diagnosis of Parkinson’s disease (PD) remains unclear. We assessed the retinal layer thickness in different stages of PD and explored whether it can be an early diagnostic indicator for PD. In total, 397 [131, 146, and 120 with Hoehn-Yahr I (H-Y I), H-Y II, and H-Y III stages, respectively] patients with PD and 427 healthy controls (HCs) were enrolled. The peripapillary retinal nerve fiber layer (pRNFL), total macular retinal thickness (MRT), and macular volume (TMV) were measured by high-definition optical coherence tomography, and the macular intraretinal thickness was analyzed by the Iowa Reference Algorithms. As a result, the PD group had a significantly lower average, temporal quadrant pRNFL, MRT, and TMV than the HCs group (all p < 0.001). Moreover, the ganglion cell layer (GCL), inner plexiform layer (IPL), and outer nuclear layer were thinner in patients with PD with H-Y I, and significantly decreased as the H-Y stage increased. In addition, we observed that GCL and IPL thicknesses were both correlated with Movement Disorder Society-Unified Parkinson’s Disease Rating Scale III (MDS-UPDRS III) scores and non-motor symptoms assessment scores. Furthermore, macular IPL thickness in the superior inner (SI) quadrant (IPL-SI) had the best diagnostic performance in patients with PD with H-Y I versus HCs, with a sensitivity and specificity of 75.06% and 81.67%, respectively. In conclusion, we confirmed the retinal structure was significantly altered in patients with PD in different clinical stages, and that GCL and IPL changes occurred during early PD disease and were correlated with MDS-UPDRS III scores and non-motor symptoms assessment scores. Furthermore, macular IPL-SI thickness might be performed as an early diagnostic indicator for PD.
Dataset of solution-based inorganic materials synthesis procedures extracted from the scientific literature
Authors: Wang Zheren , Kononova Olga , Cruse Kevin , He Tanjin , Huo Haoyan , Fei Yuxing , Zeng Yan , Sun Yingzhi , Cai Zijian , Sun Wenhao , Ceder Gerbrand 
Published: May 2022

AbstractThe development of a materials synthesis route is usually based on heuristics and experience. A possible new approach would be to apply data-driven approaches to learn the patterns of synthesis from past experience and use them to predict the syntheses of novel materials. However, this route is impeded by the lack of a large-scale database of synthesis formulations. In this work, we applied advanced machine learning and natural language processing techniques to construct a dataset of 35,675 solution-based synthesis procedures extracted from the scientific literature. Each procedure contains essential synthesis information including the precursors and target materials, their quantities, and the synthesis actions and corresponding attributes. Every procedure is also augmented with the reaction formula. Through this work, we are making freely available the first large dataset of solution-based inorganic materials synthesis procedures.
Cross-reactive immunity potentially drives global oscillation and opposed alternation patterns of seasonal influenza A viruses
Authors: Gatti Lorenzo , Koenen Mischa H. , Zhang Jitao David , Anisimova Maria , Verhagen Lilly M. , Schutten Martin , Osterhaus Ab , van der Vries Erhard 
Published: May 2022

AbstractSeveral human pathogens exhibit distinct patterns of seasonality and circulate as pairs. For instance, influenza A virus subtypes oscillate and peak during winter seasons of the world’s temperate climate zones. Alternation of dominant strains in successive influenza seasons makes epidemic forecasting a major challenge. From the start of the 2009 influenza pandemic we enrolled influenza A virus infected patients (n = 2980) in a global prospective clinical study. Complete hemagglutinin sequences were obtained from 1078 A/H1N1 and 1033 A/H3N2 viruses. We used phylodynamics to construct high resolution spatio-temporal phylogenetic hemagglutinin trees and estimated global influenza A effective reproductive numbers (R) over time (2009–2013). We demonstrate that R oscillates around R = 1 with a clear opposed alternation pattern between phases of the A/H1N1 and A/H3N2 subtypes. Moreover, we find a similar alternation pattern for the number of global viral spread between the sampled geographical locations. Both observations suggest a between-strain competition for susceptible hosts on a global level. Extrinsic factors that affect person-to-person transmission are a major driver of influenza seasonality. The data presented here indicate that cross-reactive host immunity is also a key intrinsic driver of influenza seasonality, which determines the influenza A virus strain at the onset of each epidemic season.
Exploring 3D elastic-wave scattering at interfaces using high-resolution phased-array system
Authors: Ohara Yoshikazu , Remillieux Marcel C. , Ulrich Timothy James , Ozawa Serina , Tsunoda Kosuke , Tsuji Toshihiro , Mihara Tsuyoshi 
Published: May 2022

AbstractThe elastic-wave scattering at interfaces, such as cracks, is essential for nondestructive inspections, and hence, understanding the phenomenon is crucial. However, the elastic-wave scattering at cracks is very complex in three dimensions since microscopic asperities of crack faces can be multiple scattering sources. We propose a method for exploring 3D elastic-wave scattering based on our previously developed high-resolution 3D phased-array system, the piezoelectric and laser ultrasonic system (PLUS). We describe the principle of PLUS, which combines a piezoelectric transmitter and a 2D mechanical scan of a laser Doppler vibrometer, enabling us to resolve a crack into a collection of scattring sources. Subsequently, we show how the 3D elastic-wave scattering in the vicinity of each response can be extracted. Here, we experimentally applied PLUS to a fatigue-crack specimen. We found that diverse 3D elastic-wave scattering occurred in a manner depending on the responses within the fatigue crack. This is significant because access to such information will be useful for optimizing inspection conditions, designing ultrasonic measurement systems, and characterizing cracks. More importantly, the described methodology is very general and can be applied to not only metals but also other materials such as composites, concrete, and rocks, leading to progress in many fields.
Multiscale entropy analysis of retinal signals reveals reduced complexity in a mouse model of Alzheimer’s disease
Authors: Araya-Arriagada Joaquín , Garay Sebastián , Rojas Cristóbal , Duran-Aniotz Claudia , Palacios Adrián G. , Chacón Max , Medina Leonel E. 
Published: May 2022

AbstractAlzheimer’s disease (AD) is one of the most significant health challenges of our time, affecting a growing number of the elderly population. In recent years, the retina has received increased attention as a candidate for AD biomarkers since it appears to manifest the pathological signatures of the disease. Therefore, its electrical activity may hint at AD-related physiological changes. However, it is unclear how AD affects retinal electrophysiology and what tools are more appropriate to detect these possible changes. In this study, we used entropy tools to estimate the complexity of the dynamics of healthy and diseased retinas at different ages. We recorded microelectroretinogram responses to visual stimuli of different nature from retinas of young and adult, wild-type and 5xFAD—an animal model of AD—mice. To estimate the complexity of signals, we used the multiscale entropy approach, which calculates the entropy at several time scales using a coarse graining procedure. We found that young retinas had more complex responses to different visual stimuli. Further, the responses of young, wild-type retinas to natural-like stimuli exhibited significantly higher complexity than young, 5xFAD retinas. Our findings support a theory of complexity-loss with aging and disease and can have significant implications for early AD diagnosis.
Associations of body shape index (ABSI) and hip index with liver, metabolic, and inflammatory biomarkers in the UK Biobank cohort
Authors: Christakoudi Sofia , Riboli Elio , Evangelou Evangelos , Tsilidis Konstantinos K. 
Published: May 2022

AbstractAssociations of liver, metabolic, and inflammatory biomarkers in blood with body shape are unclear, because waist circumference (WC) and hip circumference (HC) are dependent on overall body size, resulting in bias. We have used the allometric “a body shape index” (ABSI = WC(mm)$$\,*\,$$

∗

Weight(kg)-2/3$$\,*\,$$

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Height(m)5/6) and hip index (HIwomen = HC(cm)$$\,*\,$$

∗

Weight(kg)-0.482$$\,*\,$$

∗

Height(cm)0.310, HImen = HC(cm)$$\,*\,$$

∗

Weight(kg)-2/5$$\,*\,$$

∗

Height(cm)1/5), which are independent of body mass index (BMI) by design, in multivariable linear regression models for 121,879 UK Biobank men and 135,559 women. Glucose, glycated haemoglobin (HbA1c), triglycerides, low-density-lipoprotein cholesterol, apolipoprotein-B, alanine aminotransferase (ALT), gamma-glutamyltransferase, and lymphocytes were associated positively with BMI and ABSI but inversely with HI. High-density-lipoprotein cholesterol and apolipoprotein-A1 were associated inversely with BMI and ABSI but positively with HI. Lipid-related biomarkers and ALT were associated only with HI in obese men. C-reactive protein, neutrophils, monocytes, and alkaline phosphatase were associated positively, while bilirubin was associated inversely, with BMI and ABSI but not with HI. Associations were consistent within the clinical reference ranges but were lost or changed direction for low or high biomarker levels. Our study confirms associations with waist and hip size, independent of BMI, for metabolic biomarkers but only with waist size for inflammatory biomarkers, suggesting different contribution of the mechanistic pathways related to body shape.
Common gene expression patterns are observed in rice roots during associations with plant growth-promoting bacteria, Herbaspirillum seropedicae and Azospirillum brasilense
Authors: Wiggins Grant , Thomas Jacklyn , Rahmatallah Yasir , Deen Connor , Haynes Allee , Degon Zachariah , Glazko Galina , Mukherjee Arijit 
Published: May 2022

AbstractNon-legume plants such as rice and maize can form beneficial associations with plant growth-promoting bacteria (PGPB) such as Herbaspirillum seropedicae and Azospirillum brasilense. Several studies have shown that these PGPB promote plant growth via multiple mechanisms. Our current understanding of the molecular aspects and signaling between plants like rice and PGPB like Herbaspirillum seropedicae is limited. In this study, we used an experimental system where H. seropedicae could colonize the plant roots and promote growth in wild-type rice. Using this experimental setup, we identified 1688 differentially expressed genes (DEGs) in rice roots, 1 day post-inoculation (dpi) with H. seropedicae. Several of these DEGs encode proteins involved in the flavonoid biosynthetic pathway, defense, hormone signaling pathways, and nitrate and sugar transport. We validated the expression pattern of some genes via RT-PCR. Next, we compared the DEGs identified in this study to those we previously identified in rice roots during associations with another PGPB, Azospirillum brasilense. We identified 628 genes that were differentially expressed during both associations. The expression pattern of these genes suggests that some of these are likely to play a significant role(s) during associations with both H. seropedicae and A. brasilense and are excellent targets for future studies.
Prussian blue technique is prone to yield false negative results in magnetoreception research
Authors: Curdt Franziska , Haase Katrin , Ziegenbalg Laura , Greb Helena , Heyers Dominik , Winklhofer Michael 
Published: May 2022

AbstractPerls’s Prussian blue staining technique has been used in magnetoreception research to screen tissues for iron-rich structures as proxies for putative magnetoreceptor structures based on magnetic particles. However, seemingly promising structural candidates in the upper beak of birds detected with Prussian blue turned out to be either irreproducible or located in non-neuronal cells, which has spurred a controversy that has not been settled yet. Here we identify possible pitfalls in the previous works and apply the Prussian blue technique to tissues implicated in magnetic-particle-based magnetoreception, in an effort to reassess its suitability for staining single-domain magnetite, i.e., the proposed magnetic substrate for the interaction with the external magnetic field. In the upper beak of night-migratory songbirds, we found staining products in great numbers, but not remotely associated with fiber terminals of the traced ophthalmic branch of the trigeminal nerve. Surprisingly, staining products were absent from the lamina propria in the olfactory rosette of rainbow trout where candidate magnetoreceptor structures were identified with different techniques earlier. Critically, magnetosome chains in whole cells of magnetotactic bacteria remained unstained. The failure to label single-domain magnetite in positive control samples is a serious limitation of the technique and suggests that two most influential but antipodal studies conducted previously stood little chances of obtaining correct positive results under the assumption that magnetosome-like particles were present in the tissues. Nonetheless, the staining technique appears suitable to identify tissue contamination with iron-rich fine dust trapped in epithelia already in vivo.