bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature variability implies greater economic damages from climate change
Authors: Calel Raphael , Chapman Sandra C. , Stainforth David A. , Watkins Nicholas W. 
Published: October 2020

AbstractA number of influential assessments of the economic cost of climate change rely on just a small number of coupled climate–economy models. A central feature of these assessments is their accounting of the economic cost of epistemic uncertainty—that part of our uncertainty stemming from our inability to precisely estimate key model parameters, such as the Equilibrium Climate Sensitivity. However, these models fail to account for the cost of aleatory uncertainty—the irreducible uncertainty that remains even when the true parameter values are known. We show how to account for this second source of uncertainty in a physically well-founded and tractable way, and we demonstrate that even modest variability implies trillions of dollars of previously unaccounted for economic damages.
Millisecond dynamics of an unlabeled amino acid transporter
Authors: Matin Tina R. , Heath George R. , Huysmans Gerard H. M. , Boudker Olga , Scheuring Simon 
Published: October 2020

AbstractExcitatory amino acid transporters (EAATs) are important in many physiological processes and crucial for the removal of excitatory amino acids from the synaptic cleft. Here, we develop and apply high-speed atomic force microscopy line-scanning (HS-AFM-LS) combined with automated state assignment and transition analysis for the determination of transport dynamics of unlabeled membrane-reconstituted GltPh, a prokaryotic EAAT homologue, with millisecond temporal resolution. We find that GltPh transporters can operate much faster than previously reported, with state dwell-times in the 50 ms range, and report the kinetics of an intermediate transport state with height between the outward- and inward-facing states. Transport domains stochastically probe transmembrane motion, and reversible unsuccessful excursions to the intermediate state occur. The presented approach and analysis methodology are generally applicable to study transporter kinetics at system-relevant temporal resolution.
A system-level approach identifies HIF-2α as a critical regulator of chondrosarcoma progression
Authors: Kim Hyeonkyeong , Cho Yongsik , Kim Hyeon-Seop , Kang Donghyun , Cheon Donghyeon , Kim Yi-Jun , Chang Moon Jong , Lee Kyoung Min , Chang Chong Bum , Kang Seung-Baik , Kang Hyun Guy , Kim Jin-Hong 
Published: October 2020

AbstractChondrosarcomas, malignant cartilaginous neoplasms, are capable of transitioning to highly aggressive, metastatic, and treatment-refractory states, resulting in significant patient mortality. Here, we aim to uncover the transcriptional program directing such tumor progression in chondrosarcomas. We conduct weighted correlation network analysis to extract a characteristic gene module underlying chondrosarcoma malignancy. Hypoxia-inducible factor-2α (HIF-2α, encoded by EPAS1) is identified as an upstream regulator that governs the malignancy gene module. HIF-2α is upregulated in high-grade chondrosarcoma biopsies and EPAS1 gene amplification is associated with poor prognosis in chondrosarcoma patients. Using tumor xenograft mouse models, we demonstrate that HIF-2α confers chondrosarcomas the capacities required for tumor growth, local invasion, and metastasis. Meanwhile, pharmacological inhibition of HIF-2α, in conjunction with the chemotherapy agents, synergistically enhances chondrosarcoma cell apoptosis and abolishes malignant signatures of chondrosarcoma in mice. We expect that our insights into the pathogenesis of chondrosarcoma will provide guidelines for the development of molecular targeted therapeutics for chondrosarcoma.
Protease circuits for processing biological information
Authors: Holt Brandon Alexander , Kwong Gabriel A. 
Published: October 2020

AbstractEngineered biocircuits designed with biological components have the capacity to expand and augment living functions. Here we demonstrate that proteases can be integrated into digital or analog biocircuits to process biological information. We first construct peptide-caged liposomes that treat protease activity as two-valued (i.e., signal is 0 or 1) operations to construct the biological equivalent of Boolean logic gates, comparators and analog-to-digital converters. We use these modules to assemble a cell-free biocircuit that can combine with bacteria-containing blood, quantify bacteria burden, and then calculate and unlock a selective drug dose. By contrast, we treat protease activity as multi-valued (i.e., signal is between 0 and 1) by controlling the degree to which a pool of enzymes is shared between two target substrates. We perform operations on these analog values by manipulating substrate concentrations and combine these operations to solve the mathematical problem Learning Parity with Noise (LPN). These results show that protease activity can be used to process biological information by binary Boolean logic, or as multi-valued analog signals under conditions where substrate resources are shared.
The Rho-GEF PIX-1 directs assembly or stability of lateral attachment structures between muscle cells
Authors: Moody Jasmine C. , Qadota Hiroshi , Reedy April R. , Okafor C. Denise , Shanmugan Niveda , Matsunaga Yohei , Christian Courtney J. , Ortlund Eric A. , Benian Guy M. 
Published: October 2020

AbstractPIX proteins are guanine nucleotide exchange factors (GEFs) that activate Rac and Cdc42, and are known to have numerous functions in various cell types. Here, we show that a PIX protein has an important function in muscle. From a genetic screen in C. elegans, we found that pix-1 is required for the assembly of integrin adhesion complexes (IACs) at borders between muscle cells, and is required for locomotion of the animal. A pix-1 null mutant has a reduced level of activated Rac in muscle. PIX-1 localizes to IACs at muscle cell boundaries, M-lines and dense bodies. Mutations in genes encoding proteins at known steps of the PIX signaling pathway show defects at muscle cell boundaries. A missense mutation in a highly conserved residue in the RacGEF domain results in normal levels of PIX-1 protein, but a reduced level of activated Rac in muscle, and abnormal IACs at muscle cell boundaries.
Magic-angle semimetals
Authors: Fu Yixing , König Elio J. , Wilson Justin H. , Chou Yang-Zhi , Pixley Jedediah H. 
Published: October 2020

AbstractBreakthroughs in two-dimensional van der Waals heterostructures have revealed that twisting creates a moiré pattern that quenches the kinetic energy of electrons, allowing for exotic many-body states. We show that cold atomic, trapped ion, and metamaterial systems can emulate the effects of a twist in many models from one to three dimensions. Further, we demonstrate at larger angles (and argue at smaller angles) that by considering incommensurate effects, the magic-angle effect becomes a single-particle quantum phase transition (including in a model for twisted bilayer graphene in the chiral limit). We call these models “magic-angle semimetals”. Each contains nodes in the band structure and an incommensurate modulation. At magic-angle criticality, we report a nonanalytic density of states, flat bands, multifractal wave functions that Anderson delocalize in momentum space, and an essentially divergent effective interaction scale. As a particular example, we discuss how to observe this effect in an ultracold Fermi gas.
Unexpected differences between surface and bulk spectroscopic and implied Kondo properties of heavy fermion CeRh2Si2
Authors: Poelchen Georg , Schulz Susanne , Mende Max , Güttler Monika , Generalov Alexander , Fedorov Alexander V. , Caroca-Canales Nubia , Geibel Christoph , Kliemt Kristin , Krellner Cornelius , Danzenbächer Steffen , Usachov Dmitry Yu. , Dudin Pavel , Antonov Victor N. , Allen James W. , Laubschat Clemens , Kummer Kurt , Kucherenko Yuri , Vyalikh Denis V. 
Published: October 2020

AbstractUltra-violet angle-resolved photoemission spectroscopy (UV-ARPES) was used to explore the temperature dependence of the Ce-4f spectral responses for surface and bulk in the antiferromagnetic Kondo lattice CeRh2Si2. Spectra were taken from Ce- and Si-terminated surfaces in a wide temperature range, and reveal characteristic 4f patterns for weakly (surface) and strongly (bulk) hybridized Ce, respectively. The temperature dependence of the Fermi level peak differs strongly for both cases implying that the effective Kondo temperature at the surface and bulk can be rather distinct. The greatly reduced crystal–electric-field (CEF) splitting at the surface gives reason to believe that the surface may exhibit a larger effective Kondo temperature because of a higher local-moment effective degeneracy. Further, the hybridization processes could strongly affect the 4f peak intensity at the Fermi level. We derived the k-resolved dispersion of the Kondo peak which is also found to be distinct due to different sets of itinerant bands to which the 4f states of surface and bulk Ce are coupled. Overall our study brings into reach the ultimate goal of quantitatively testing many-body theories that link spectroscopy and transport properties, for both the bulk and the surface, separately. It also allows for a direct insight into the broader problem of Kondo lattices with two different local-moment sublattices, providing some understanding of why the cross-talking between the two Kondo effects is weak.
A novel speculum-free imaging strategy for visualization of the internal female lower reproductive system
Authors: Asiedu Mercy N. , Agudogo Júlia S. , Dotson Mary E. , Skerrett Erica , Krieger Marlee S. , Lam Christopher T. , Agyei Doris , Amewu Juliet , Asah-Opoku Kwaku , Huchko Megan , Schmitt John W. , Samba Ali , Srofenyoh Emmanuel , Ramanujam Nirmala 
Published: October 2020

AbstractFear of the speculum and feelings of vulnerability during the gynecologic exams are two of the biggest barriers to cervical cancer screening for women. To address these barriers, we have developed a novel, low-cost tool called the Callascope to reimagine the gynecological exam, enabling clinician and self-imaging of the cervix without the need for a speculum. The Callascope contains a 2 megapixel camera and contrast agent spray mechanism housed within a form factor designed to eliminate the need for a speculum during contrast agent administration and image capture. Preliminary bench testing for comparison of the Callascope camera to a $20,000 high-end colposcope demonstrated that the Callascope camera meets visual requirements for cervical imaging. Bench testing of the spray mechanism demonstrates that the contrast agent delivery enables satisfactory administration and cervix coverage. Clinical studies performed at Duke University Medical Center, Durham, USA and in Greater Accra Regional Hospital, Accra, Ghana assessed (1) the Callascope’s ability to visualize the cervix compared to the standard-of-care speculum exam, (2) the feasibility and willingness of women to use the Callascope for self-exams, and (3) the feasibility and willingness of clinicians and their patients to use the Callascope for clinician-based examinations. Cervix visualization was comparable between the Callascope and speculum (83% or 44/53 women vs. 100%) when performed by a clinician. Visualization was achieved in 95% (21/22) of women who used the Callascope for self-imaging. Post-exam surveys indicated that participants preferred the Callascope to a speculum-based exam. Our results indicate the Callascope is a viable option for clinician-based and self-exam speculum-free cervical imaging.Clinical study registration ClinicalTrials.gov https://clinicaltrials.gov/ct2/show/record/ NCT00900575, Pan African Clinical Trial Registry (PACTR) https://www.pactr.org/ PACTR201905806116817.
Spatial and temporal variations of air pollution over 41 cities of India during the COVID-19 lockdown period
Authors: Vadrevu Krishna Prasad , Eaturu Aditya , Biswas Sumalika , Lasko Kristofer , Sahu Saroj , Garg J. K. , Justice Chris 
Published: October 2020

AbstractIn this study, we characterize the impacts of COVID-19 on air pollution using NO2 and Aerosol Optical Depth (AOD) from TROPOMI and MODIS satellite datasets for 41 cities in India. Specifically, our results suggested a 13% NO2 reduction during the lockdown (March 25–May 3rd, 2020) compared to the pre-lockdown (January 1st–March 24th, 2020) period. Also, a 19% reduction in NO2 was observed during the 2020-lockdown as compared to the same period during 2019. The top cities where NO2 reduction occurred were New Delhi (61.74%), Delhi (60.37%), Bangalore (48.25%), Ahmedabad (46.20%), Nagpur (46.13%), Gandhinagar (45.64) and Mumbai (43.08%) with less reduction in coastal cities. The temporal analysis revealed a progressive decrease in NO2 for all seven cities during the 2020 lockdown period. Results also suggested spatial differences, i.e., as the distance from the city center increased, the NO2 levels decreased exponentially. In contrast, to the decreased NO2 observed for most of the cities, we observed an increase in NO2 for cities in Northeast India during the 2020 lockdown period and attribute it to vegetation fires. The NO2 temporal patterns matched the AOD signal; however, the correlations were poor. Overall, our results highlight COVID-19 impacts on NO2, and the results can inform pollution mitigation efforts across different cities of India.
A novel exchange method to access sulfated molecules
Authors: Alshehri Jaber A. , Benedetti Anna Mary , Jones Alan M. 
Published: October 2020

AbstractOrganosulfates and sulfamates are important classes of bioactive molecules but due to their polar nature, they are both difficult to prepare and purify. We report an operationally simple, double ion-exchange method to access organosulfates and sulfamates. Inspired by the novel sulfating reagent, TriButylSulfoAmmonium Betaine (TBSAB), we developed a 3-step procedure using tributylamine as the novel solubilising partner coupled to commercially available sulfating agents. Hence, in response to an increasing demand for complementary methods to synthesise organosulfates, we developed an alternative sulfation route based on an inexpensive, molecularly efficient and solubilising cation exchanging method using off-the-shelf reagents. The disclosed method is amenable to a range of differentially substituted benzyl alcohols, benzylamines and aniline and can also be performed at low temperature for sensitive substrates in good to excellent isolated yield.
High-purity foam-like micron-sized gold cage material with tunable plasmon properties
Authors: Dong Shuo , Yi Lin , Cheng Lexiao , Li Shijian , Yang Weiming , Wang Zhebin , Jiang Shaoen 
Published: October 2020

AbstractHerein, by growing mono dispersed gold nanoparticles (MNPAu) on the surface of polystyrene (PS)/nanogold (Au) core–shell composites (PS@Au), we successfully synthesized a micron-sized gold cage (2.6–10.7 μm), referred to as PS@Au@MNPAu for the first time. The new micron-gold cage materials exhibit broadband absorption range from near-ultraviolet to near-infrared, which is unlike the conventional nanogold core–shell structure. The uniform growth of MNPAu on the surface forms a new photonic crystal spectrum. The strong coupling of the spectra causes anomalous absorption in the ultraviolet-near infrared band (400–900 nm). Furthermore, by removing the PS core, a nanogold cavity structure referred to as Au@MNPAu was prepared. This structure demonstrated a high purity (> 97 wt%), low density (9–223 mg/cm3), and high specific surface area (854 m2/g). As the purification process progressed, the MNPAu coupling on the surface of the micro-gold cage strengthened, resulting in the formation of peaks around 370 nm, plasma resonant peaks around 495 nm, and structural bands of photonic crystal peaks around 850 nm. The micron-sized gold cage provides hybridized and tunable plasmonic systems. The theoretical simulations indicate that this plasmon anomalous absorption phenomena can be understood as the novel form of the topological structural transitions near the percolation threshold, which is consistent experimental measurements.
Oncogenic driver mutations predict outcome in a cohort of head and neck squamous cell carcinoma (HNSCC) patients within a clinical trial
Authors: Fernández-Mateos Javier , Pérez-García Jéssica , Seijas-Tamayo Raquel , Mesía Ricard , Rubió-Casadevall Jordi , García-Girón Carlos , Iglesias Lara , Carral Maseda Alberto , Adansa Klain Juan Carlos , Taberna Miren , Vazquez Silvia , Gómez María Asunción , del Barco Edel , Ocana Alberto , González-Sarmiento Rogelio , Cruz-Hernández Juan Jesús 
Published: October 2020

Abstract234 diagnostic formalin-fixed paraffin-embedded (FFPE) blocks from homogeneously treated patients with locally advanced head and neck squamous cell carcinoma (HNSCC) within a multicentre phase III clinical trial were characterised. The mutational spectrum was examined by next generation sequencing in the 26 most frequent oncogenic drivers in cancer and correlated with treatment response and survival. Human papillomavirus (HPV) status was measured by p16INK4a immunohistochemistry in oropharyngeal tumours. Clinicopathological features and response to treatment were measured and compared with the sequencing results. The results indicated TP53 as the most mutated gene in locally advanced HNSCC. HPV-positive oropharyngeal tumours were less mutated than HPV-negative tumours in TP53 (p < 0.01). Mutational and HPV status influences patient survival, being mutated or HPV-negative tumours associated with poor overall survival (p < 0.05). No association was found between mutations and clinicopathological features. This study confirmed and expanded previously published genomic characterization data in HNSCC. Survival analysis showed that non-mutated HNSCC tumours associated with better prognosis and lack of mutations can be identified as an important biomarker in HNSCC. Frequent alterations in PI3K pathway in HPV-positive HNSCC could define a promising pathway for pharmacological intervention in this group of tumours.
Exploring cyclic networks of multisite modification reveals origins of information processing characteristics
Authors: Suwanmajo Thapanar , Ramesh Vaidhiswaran , Krishnan J. 
Published: October 2020

AbstractMultisite phosphorylation (and generally multisite modification) is a basic way of encoding substrate function and circuits/networks of post-translational modifications (PTM) are ubiquitous in cell signalling. The information processing characteristics of PTM systems are a focal point of broad interest. The ordering of modifications is a key aspect of multisite modification, and a broad synthesis of the impact of ordering of modifications is still missing. We focus on a basic class of multisite modification circuits: the cyclic mechanism, which corresponds to the same ordering of phosphorylation and dephosphorylation, and examine multiple variants involving common/separate kinases and common/separate phosphatases. This is of interest both because it is encountered in concrete cellular contexts, and because it serves as a bridge between ordered (sequential) mechanisms (representing one type of ordering) and random mechanisms (which have no ordering). We show that bistability and biphasic dose response curves of the maximally modified phosphoform are ruled out for basic structural reasons independent of parameters, while oscillations can result with even just one shared enzyme. We then examine the effect of relaxing some basic assumptions about the ordering of modification. We show computationally and analytically how bistability, biphasic responses and oscillations can be generated by minimal augmentations to the cyclic mechanism even when these augmentations involved reactions operating in the unsaturated limit. All in all, using this approach we demonstrate (1) how the cyclic mechanism (with single augmentations) represents a modification circuit using minimal ingredients (in terms of shared enzymes and sequestration of enzymes) to generate bistability and oscillations, when compared to other mechanisms, (2) new design principles for rationally designing PTM systems for a variety of behaviour, (3) a basis and a necessary step for understanding the origins and robustness of behaviour observed in basic multisite modification systems.
Normal electric field enhanced light-induced polarizations and magnetic detection of valley polarization in silicene
Authors: Shahabi N. , Phirouznia A. 
Published: October 2020

AbstractThe role of staggered potential on light-induced spin and pseudo-spin polarization has been investigated in silicene. It has been shown that non-equilibrium spin and pseudo-spin polarizations are emerged in silicene sheet by applying an external perpendicular electric field in the presence of circularly polarized light emission. This electric field results in pseudo-spin resolved states very close to the Dirac points therefore could be considered as a pseudomagnetic field. It has been shown that staggered potential induced spin-valley locking and pseudo-spin resolved bands are responsible for the enhancement of the spin and pseudo-spin polarizations. Meanwhile, spin-valley locking suggests a coexistence of both spin and valley polarizations with nearly identical (or at least proportional) population imbalance at low Fermi energies which could be employed for magnetic detection of the valley polarization. It has been shown that spin-valley locking results in the protection of the spin polarizations against the relaxations in elastic scattering regime. In addition, the results indicate that the pseudo-spin current can be generated by the circularly polarized light which could be explained by asymmetric light absorption of the states in k-space.
LncRNA-AK149641 regulates the secretion of tumor necrosis factor-α in P815 mast cells by targeting the nuclear factor-kappa B signaling pathway
Authors: Zhou Yao , Gu Li-na , Zhang Jie , Pan Jing , Zhang Jia-min , Zhao De-yu , Liu Feng 
Published: October 2020

AbstractLong noncoding RNAs play important roles in various biological processes. However, not much is known about their roles in inflammatory response. Mast cells, involved in innate and adaptive immunity, are one of the major effector cells in allergic inflammatory reactions and contribute to the pathogenesis of disorders, including asthma. In the present study, we aimed to verify and elucidate the function and possible role of a novel lncRNA, called lncRNA-AK149641, in the mechanism of lipopolysaccharide (LPS)-induced inflammatory response in P815 mast cells. The results showed that downregulating lncRNA-AK149641 decreased secretion of tumor necrosis factor-α into the supernatants of LPS-stimulated mast cells. Mechanistically, the activity of nuclear factor-kappa B (NF-κB) decreased after downregulating lncRNA-AK149641, as shown by western blot and electrophoretic mobility shift assays. Moreover, RNA binding protein immunoprecipitation (RIP) verified that lncRNA-AK149641 was able to bind to NF-κB in the nucleus. In conclusion, we demonstrated that lncRNA-AK149641 regulated LPS-induced inflammatory response in mast cells through the NF-κB signaling pathway.