bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale diet tracking data reveal disparate associations between food environment and diet
Authors: Althoff Tim , Nilforoshan Hamed , Hua Jenna , Leskovec Jure 
Published: January 2022

AbstractAn unhealthy diet is a major risk factor for chronic diseases including cardiovascular disease, type 2 diabetes, and cancer1–4. Limited access to healthy food options may contribute to unhealthy diets5,6. Studying diets is challenging, typically restricted to small sample sizes, single locations, and non-uniform design across studies, and has led to mixed results on the impact of the food environment7–23. Here we leverage smartphones to track diet health, operationalized through the self-reported consumption of fresh fruits and vegetables, fast food and soda, as well as body-mass index status in a country-wide observational study of 1,164,926 U.S. participants (MyFitnessPal app users) and 2.3 billion food entries to study the independent contributions of fast food and grocery store access, income and education to diet health outcomes. This study constitutes the largest nationwide study examining the relationship between the food environment and diet to date. We find that higher access to grocery stores, lower access to fast food, higher income and college education are independently associated with higher consumption of fresh fruits and vegetables, lower consumption of fast food and soda, and lower likelihood of being affected by overweight and obesity. However, these associations vary significantly across zip codes with predominantly Black, Hispanic or white populations. For instance, high grocery store access has a significantly larger association with higher fruit and vegetable consumption in zip codes with predominantly Hispanic populations (7.4% difference) and Black populations (10.2% difference) in contrast to zip codes with predominantly white populations (1.7% difference). Policy targeted at improving food access, income and education may increase healthy eating, but intervention allocation may need to be optimized for specific subpopulations and locations.
Combination of pre-adapted bacteriophage therapy and antibiotics for treatment of fracture-related infection due to pandrug-resistant Klebsiella pneumoniae
Authors: Eskenazi Anaïs , Lood Cédric , Wubbolts Julia , Hites Maya , Balarjishvili Nana , Leshkasheli Lika , Askilashvili Lia , Kvachadze Leila , van Noort Vera , Wagemans Jeroen , Jayankura Marc , Chanishvili Nina , de Boer Mark , Nibbering Peter , Kutateladze Mzia , Lavigne Rob , Merabishvili Maya , Pirnay Jean-Paul 
Published: January 2022

AbstractA 30-year-old bombing victim with a fracture-related pandrug-resistantKlebsiella pneumoniaeinfection after long-term (>700 days) antibiotic therapy is treated with a pre-adapted bacteriophage along with meropenem and colistin, followed by ceftazidime/avibactam. This salvage therapy results in objective clinical, microbiological and radiological improvement of the patient’s wounds and overall condition. In support, the bacteriophage and antibiotic combination is highly effective against the patient’sK. pneumoniaestrain in vitro, in 7-day mature biofilms and in suspensions.
An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes
Authors: Kratochwil Claudius F. , Kautt Andreas F. , Nater Alexander , Härer Andreas , Liang Yipeng , Henning Frederico , Meyer Axel 
Published: January 2022

AbstractPolymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remain elusive. Here, we aim to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (Amphilophus spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic “dark morph”, about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous “gold morph”. Using a new haplotype-resolved long-read assembly we discover an 8.2 kb, transposon-derived inverted repeat in an intron of an undescribed gene, which we term goldentouch in reference to the Greek myth of King Midas. The gene goldentouch is differentially expressed between morphs, presumably due to structural implications of inverted repeats in both DNA and/or RNA (cruciform and hairpin formation). The near-perfect association of the insertion with the phenotype across independent populations suggests that it likely underlies this trans-specific, stable polymorphism.
Decarbonising the iron and steel sector for a 2 °C target using inherent waste streams
Authors: Sun Yongqi , Tian Sicong , Ciais Philippe , Zeng Zhenzhong , Meng Jing , Zhang Zuotai 
Published: January 2022

AbstractThe decarbonisation of the iron and steel industry, contributing approximately 8% of current global anthropogenic CO2 emissions, is challenged by the persistently growing global steel demand and limitations of techno-economically feasible options for low-carbon steelmaking. Here we explore the inherent potential of recovering energy and re-using materials from waste streams, high-temperature slag, and re-investing the revenues for carbon capture and storage. In a pathway based on energy recovery and resource recycling of glassy blast furnace slag and crystalline steel slag, we show that a reduction of 28.5 ± 5.7% CO2 emissions to the sectoral 2 °C target requirements in the iron and steel industry could be realized in 2050 under strong decarbonization policy consistent with low warming targets. The technological schemes applied to engineer this high-potential pathway could generate a revenue of US$35 ± 16 and US$40 ± 18 billion globally in 2035 and 2050, respectively. If this revenue is used for carbon capture and storage implementation, equivalent CO2 emission to the 2 °C sectoral target requirements is expected to be reduced before 2050, without any external investments.
Emergent Sasaki-Einstein geometry and AdS/CFT
Authors: Berman Robert J. , Collins Tristan C. , Persson Daniel 
Published: January 2022

AbstractA central problem in any quantum theory of gravity is to explain the emergence of the classical spacetime geometry in some limit of a more fundamental, microscopic description of nature. The gauge/gravity-correspondence provides a framework in which this problem can, in principle, be addressed. This is a holographic correspondence which relates a supergravity theory in five-dimensional Anti-deSitter space to a strongly coupled superconformal gauge theory on its 4-dimensional flat Minkowski boundary. In particular, the classical geometry should therefore emerge from some quantum state of the dual gauge theory. Here we confirm this by showing how the classical metric emerges from a canonical state in the dual gauge theory. In particular, we obtain approximations to the Sasaki-Einstein metric underlying the supergravity geometry, in terms of an explicit integral formula involving the canonical quantum state in question. In the special case of toric quiver gauge theories we show that our results can be computationally simplified through a process of tropicalization.
Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases
Authors: Lim Kayeong , Cho Sung-Ik , Kim Jin-Soo 
Published: January 2022

AbstractBase editing in nuclear DNA and mitochondrial DNA (mtDNA) is broadly useful for biomedical research, medicine, and biotechnology. Here, we present a base editing platform, termed zinc finger deaminases (ZFDs), composed of custom-designed zinc-finger DNA-binding proteins, the split interbacterial toxin deaminase DddAtox, and a uracil glycosylase inhibitor (UGI), which catalyze targeted C-to-T base conversions without inducing unwanted small insertions and deletions (indels) in human cells. We assemble plasmids encoding ZFDs using publicly available zinc finger resources to achieve base editing at frequencies of up to 60% in nuclear DNA and 30% in mtDNA. Because ZFDs, unlike CRISPR-derived base editors, do not cleave DNA to yield single- or double-strand breaks, no unwanted indels caused by error-prone non-homologous end joining are produced at target sites. Furthermore, recombinant ZFD proteins, expressed in and purified from E. coli, penetrate cultured human cells spontaneously to induce targeted base conversions, demonstrating the proof-of-principle of gene-free gene therapy.
4polar-STORM polarized super-resolution imaging of actin filament organization in cells
Authors: Rimoli Caio Vaz , Valades-Cruz Cesar Augusto , Curcio Valentina , Mavrakis Manos , Brasselet Sophie 
Published: January 2022

AbstractSingle-molecule localization microscopy provides insights into the nanometer-scale spatial organization of proteins in cells, however it does not provide information on their conformation and orientation, which are key functional signatures. Detecting single molecules’ orientation in addition to their localization in cells is still a challenging task, in particular in dense cell samples. Here, we present a polarization-splitting scheme which combines Stochastic Optical Reconstruction Microscopy (STORM) with single molecule 2D orientation and wobbling measurements, without requiring a strong deformation of the imaged point spread function. This method called 4polar-STORM allows, thanks to a control of its detection numerical aperture, to determine both single molecules’ localization and orientation in 2D and to infer their 3D orientation. 4polar-STORM is compatible with relatively high densities of diffraction-limited spots in an image, and is thus ideally placed for the investigation of dense protein assemblies in cells. We demonstrate the potential of this method in dense actin filament organizations driving cell adhesion and motility.
Molecular mechanism of agonism and inverse agonism in ghrelin receptor
Authors: Qin Jiao , Cai Ye , Xu Zheng , Ming Qianqian , Ji Su-Yu , Wu Chao , Zhang Huibing , Mao Chunyou , Shen Dan-Dan , Hirata Kunio , Ma Yanbin , Yan Wei , Zhang Yan , Shao Zhenhua 
Published: January 2022

AbstractMuch effort has been invested in the investigation of the structural basis of G protein-coupled receptors (GPCRs) activation. Inverse agonists, which can inhibit GPCRs with constitutive activity, are considered useful therapeutic agents, but the molecular mechanism of such ligands remains insufficiently understood. Here, we report a crystal structure of the ghrelin receptor bound to the inverse agonist PF-05190457 and a cryo-electron microscopy structure of the active ghrelin receptor-Go complex bound to the endogenous agonist ghrelin. Our structures reveal a distinct binding mode of the inverse agonist PF-05190457 in the ghrelin receptor, different from the binding mode of agonists and neutral antagonists. Combining the structural comparisons and cellular function assays, we find that a polar network and a notable hydrophobic cluster are required for receptor activation and constitutive activity. Together, our study provides insights into the detailed mechanism of ghrelin receptor binding to agonists and inverse agonists, and paves the way to design specific ligands targeting ghrelin receptors.
Algorithm-aided engineering of aliphatic halogenase WelO5* for the asymmetric late-stage functionalization of soraphens
Authors: Büchler Johannes , Malca Sumire Honda , Patsch David , Voss Moritz , Turner Nicholas J. , Bornscheuer Uwe T. , Allemann Oliver , Le Chapelain Camille , Lumbroso Alexandre , Loiseleur Olivier , Buller Rebecca 
Published: January 2022

AbstractLate-stage functionalization of natural products offers an elegant route to create novel entities in a relevant biological target space. In this context, enzymes capable of halogenating sp3carbons with high stereo- and regiocontrol under benign conditions have attracted particular attention. Enabled by a combination of smart library design and machine learning, we engineer the iron/α-ketoglutarate dependent halogenase WelO5* for the late-stage functionalization of the complex and chemically difficult to derivatize macrolides soraphen A and C, potent anti-fungal agents. While the wild type enzyme WelO5* does not accept the macrolide substrates, our engineering strategy leads to active halogenase variants and improves upon their apparentkcatand total turnover number by more than 90-fold and 300-fold, respectively. Notably, our machine-learning guided engineering approach is capable of predicting more active variants and allows us to switch the regio-selectivity of the halogenases facilitating the targeted analysis of the derivatized macrolides’ structure-function activity in biological assays.
Stiffness control in dual color tomographic volumetric 3D printing
Authors: Wang Bin , Engay Einstom , Stubbe Peter R. , Moghaddam Saeed Z. , Thormann Esben , Almdal Kristoffer , Islam Aminul , Yang Yi 
Published: January 2022

AbstractTomographic volumetric printing (TVP) physically reverses tomography to offer fast and auxiliary-free 3D printing. Here we show that wavelength-sensitive photoresins can be cured using visible ($$\bar{\lambda }=455$$

λ

¯

=
455
nm) and UV ($$\bar{\lambda }=365$$

λ

¯

=
365
nm) sources simultaneously in a TVP setup to generate internal mechanical property gradients with high precision. We develop solutions of mixed acrylate and epoxy monomers and utilize the orthogonal chemistry between free radical and cationic polymerization to realize fully 3D stiffness control. The radial resolution of stiffness control is 300 µm or better and an average modulus gradient of 5 MPa/µm is achieved. We further show that the reactive transport of radical inhibitors defines a workpiece’s shape and limits the achievable stiffness contrast to a range from 127 MPa to 201 MPa according to standard tensile tests after post-processing. Our result presents a strategy for controlling the stiffness of material spatially in light-based volumetric additive manufacturing.
Optical fibre taper-enabled waveguide photoactuators
Authors: Xiao Jianliang , Zhou Tao , Yao Ni , Ma Shuqi , Pan Chenxinyu , Wang Pan , Fu Haoran , Liu Haitao , Pan Jing , Yu Longteng , Wang Shipeng , Yang Wenzhen , Tong Limin , Zhang Lei 
Published: January 2022

AbstractPhotoactuators have attracted significant interest for soft robot and gripper applications, yet most of them rely on free-space illumination, which requires a line-of-site low-loss optical path. While waveguide photoactuators can overcome this limitation, their actuating performances are fundamentally restricted by the nature of standard optical fibres. Herein, we demonstrated miniature photoactuators by embedding optical fibre taper in a polydimethylsiloxane/Au nanorod-graphene oxide photothermal film. The special geometric features of the taper endow the designed photoactuator with microscale active layer thickness, high energy density and optical coupling efficiency. Hence, our photoactuator show large bending angles (>270°), fast response (1.8 s for 180° bending), and low energy consumption (<0.55 mW/°), significantly exceeding the performance of state-of-the-art waveguide photoactuators. As a proof-of-concept study, one-arm and two-arm photoactuator-based soft grippers are demonstrated for capturing/moving small objects, which is challenging for free-space light-driven photoactuators.
C/EBPβ isoform-specific regulation of migration and invasion in triple-negative breast cancer cells
Authors: Sterken Britt A. , Ackermann Tobias , Müller Christine , Zuidhof Hidde R. , Kortman Gertrud , Hernandez-Segura Alejandra , Broekhuis Mathilde , Spierings Diana , Guryev Victor , Calkhoven Cornelis F. 
Published: January 2022

AbstractThe transcription factor C/EBPβ is a master regulator of mammary gland development and tissue remodelling during lactation. TheCEBPB-mRNA is translated into three distinct protein isoforms named C/EBPβ-LAP1, -LAP2 and -LIP that are functionally different. The smaller isoform LIP lacks the N-terminal transactivation domains and is considered to act as an inhibitor of the transactivating LAP1/2 isoforms by competitive binding for the same DNA recognition sequences. Aberrantly high expression of LIP is associated with mammary epithelial proliferation and is found in grade III, estrogen receptor (ER) and progesterone (PR) receptor-negative human breast cancer. Here, we show that reverting the high LIP/LAP ratios in triple-negative breast cancer (TNBC) cell lines into low LIP/LAP ratios by overexpression of LAP reduces migration and matrix invasion of these TNBC cells. In addition, in untransformed MCF10A human mammary epithelial cells overexpression of LIP stimulates migration. Knockout ofCEBPBin TNBC cells where LIP expression prevails, resulted in strongly reduced migration that was accompanied by a downregulation of genes involved in cell migration, extracellular matrix production and cytoskeletal remodelling, many of which are epithelial to mesenchymal transition (EMT) marker genes. Together, this study suggests that the LIP/LAP ratio is involved in regulating breast cancer cell migration and invasion. This study together with studies from others shows that understanding the functions the C/EBPβ-isoforms in breast cancer development may reveal new avenues of treatment.
HBXIP induces anoikis resistance by forming a reciprocal feedback loop with Nrf2 to maintain redox homeostasis and stabilize Prdx1 in breast cancer
Authors: Zhou Xiaolei , Li Li , Guo Xin , Zhang Chunxiao , Du Yanyan , Li Tianming , Tong Kaiqing , Zhu Chongyue , Wang Zijin 
Published: January 2022

AbstractAnoikis resistance is an essential prerequisite for tumor metastasis, but the underlying molecular mechanisms remain unknown. Herein, we report that the oncoprotein hepatitis B X-interacting protein (HBXIP) is prominently upregulated in breast cancer cells following ECM detachment. Altering HBXIP expression can impair the anchorage-independent growth ability of tumor cells. Mechanistically, HBXIP, which binds to Kelch-like ECH-associated protein 1 (Keap1) to activate nuclear factor E2-related factor 2 (Nrf2), contains a cis-acting antioxidant response element (ARE) in the gene promoter and is a target gene of Nrf2. The HBXIP/Nrf2 axis forms a reciprocal positive feedback loop that reinforces the expression and tumor-promoting actions of each protein. In response to ECM detachment, Nrf2 reduces reactive oxygen species (ROS) accumulation, protects the mitochondrial membrane potential and increases cellular ATP, GSH and NADPH levels to maintain breast cancer cell survival. Meanwhile, the reinforcement of HBXIP induced by Nrf2 inhibits JNK1 activation by inhibiting ubiquitin-mediated degradation of Prdx1, which also plays an essential role in promoting ECM-detached cell survival. Furthermore, a strong positive correlation was identified between HBXIP expression and Prdx1 expression in clinical breast cancer tissues and TCGA Pan-Cancer Atlas clinical data of breast invasive carcinoma based on the cBioPortal cancer genomics database. Co-expression of HBXIP and Prdx1 predicts a poor prognosis for breast cancer patients. Collectively, our findings reveal a significant mechanism by which the HBXIP/Nrf2 feedback loop contributes to anoikis resistance by maintaining redox homeostasis and inhibiting JNK1 activation and support the likely therapeutic value of the HBXIP/Nrf2 axis in breast cancer patients.
Relativistic domain-wall dynamics in van der Waals antiferromagnet MnPS3
Authors: Alliati Ignacio M. , Evans Richard F. L. , Novoselov Kostya S. , Santos Elton J. G. 
Published: January 2022

AbstractThe discovery of two-dimensional (2D) magnetic van der Waals (vdW) materials has flourished an endeavor for fundamental problems as well as potential applications in computing, sensing and storage technologies. Of particular interest are antiferromagnets, which due to their intrinsic exchange coupling show several advantages in relation to ferromagnets such as robustness against external magnetic perturbations. Here we show that, despite of this cornerstone, the magnetic domains of recently discovered 2D vdW MnPS3 antiferromagnet can be controlled via magnetic fields and electric currents. We achieve ultrafast domain-wall dynamics with velocities up to ~3000 m s−1 within a relativistic kinematic. Lorentz contraction and emission of spin-waves in the terahertz gap are observed with dependence on the edge termination of the layers. Our results indicate that the implementation of 2D antiferromagnets in real applications can be further controlled through edge engineering which sets functional characteristics for ultrathin device platforms with relativistic features.
Cross-condition and cross-platform remaining useful life estimation via adversarial-based domain adaptation
Authors: Zhao Dongdong , Liu Feng 
Published: January 2022

AbstractSupervised machine learning is a traditionally remaining useful life (RUL) estimation tool, which requires a lot of prior knowledge. For the situation lacking labeled data, supervised methods are invalid for the issue of domain shift in data distribution. In this paper, a adversarial-based domain adaptation (ADA) architecture with convolution neural networks (CNN) for RUL estimation of bearings under different conditions and platforms, referred to as ADACNN, is proposed. Specifically, ADACNN is trained in source labeled data and fine-tunes to similar target unlabeled data via an adversarial training and parameters shared mechanism. Besides a feature extractor and source domain regressive predictor, ADACNN also includes a domain classifier that tries to guide feature extractor find some domain-invariant features, which differents with traditional methods and belongs to a unsupervised learning in target domain, which has potential application value and far-reaching significance in academia. In addition, according to different first predictive time (FPT) detection mechanisms, we also explores the impact of different FPT detection mechanisms on RUL estimation performance. Finally, according to extensive experiments, the results of RUL estimation of bearing in cross-condition and cross-platform prove that ADACNN architecture has satisfactory generalization performance and great practical value in industry.
Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering
Authors: Sy Mouhamad , Deme Awa B. , Warren Joshua L. , Early Angela , Schaffner Stephen , Daniels Rachel F. , Dieye Baba , Ndiaye Ibrahima Mbaye , Diedhiou Younous , Mbaye Amadou Moctar , Volkman Sarah K. , Hartl Daniel L. , Wirth Dyann F. , Ndiaye Daouda , Bei Amy K. 
Published: January 2022

AbstractMolecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate less than 1). Genetic identity (identity by state, IBS) was established using a 24-single nucleotide polymorphism molecular barcode, identity by descent was calculated from whole genome sequence data, and a hierarchical Bayesian regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts.