bluuebunny/crossref_metadata_2025_split huggingface dataset:
ADP binding by the Culex quinquefasciatus mosquito D7 salivary protein enhances blood feeding on mammals
Authors: Martin-Martin Ines , Paige Andrew , Valenzuela Leon Paola Carolina , Gittis Apostolos G. , Kern Olivia , Bonilla Brian , Chagas Andrezza Campos , Ganesan Sundar , Smith Leticia Barion , Garboczi David N. , Calvo Eric 
Published: June 2020

AbstractDuring blood-feeding, mosquito saliva is injected into the skin to facilitate blood meal acquisition. D7 proteins are among the most abundant components of the mosquito saliva. Here we report the ligand binding specificity and physiological relevance of two D7 long proteins from Culex quinquefasciatus mosquito, the vector of filaria parasites or West Nile viruses. CxD7L2 binds biogenic amines and eicosanoids. CxD7L1 exhibits high affinity for ADP and ATP, a binding capacity not reported in any D7. We solve the crystal structure of CxD7L1 in complex with ADP to 1.97 Å resolution. The binding pocket lies between the two protein domains, whereas all known D7s bind ligands either within the N- or the C-terminal domains. We demonstrate that these proteins inhibit hemostasis in ex vivo and in vivo experiments. Our results suggest that the ADP-binding function acquired by CxD7L1 evolved to enhance blood-feeding in mammals, where ADP plays a key role in platelet aggregation.
Structural distortion and electron redistribution in dual-emitting gold nanoclusters
Authors: Li Qi , Zhou Dongming , Chai Jinsong , So Woong Young , Cai Tong , Li Mingxing , Peteanu Linda A. , Chen Ou , Cotlet Mircea , Wendy Gu X. , Zhu Haiming , Jin Rongchao 
Published: June 2020

AbstractDeciphering the complicated excited-state process is critical for the development of luminescent materials with controllable emissions in different applications. Here we report the emergence of a photo-induced structural distortion accompanied by an electron redistribution in a series of gold nanoclusters. Such unexpected slow process of excited-state transformation results in near-infrared dual emission with extended photoluminescent lifetime. We demonstrate that this dual emission exhibits highly sensitive and ratiometric response to solvent polarity, viscosity, temperature and pressure. Thus, a versatile luminescent nano-sensor for multiple environmental parameters is developed based on this strategy. Furthermore, we fully unravel the atomic-scale structural origin of this unexpected excited-state transformation, and demonstrate control over the transition dynamics by tailoring the bi-tetrahedral core structures of gold nanoclusters. Overall, this work provides a substantial advance in the excited-state physical chemistry of luminescent nanoclusters and a general strategy for the rational design of next-generation nano-probes, sensors and switches.
Quantifying the drivers and predictability of seasonal changes in African fire
Authors: Yu Yan , Mao Jiafu , Thornton Peter E. , Notaro Michael , Wullschleger Stan D. , Shi Xiaoying , Hoffman Forrest M. , Wang Yaoping 
Published: June 2020

AbstractAfrica contains some of the most vulnerable ecosystems to fires. Successful seasonal prediction of fire activity over these fire-prone regions remains a challenge and relies heavily on in-depth understanding of various driving mechanisms underlying fire evolution. Here, we assess the seasonal environmental drivers and predictability of African fire using the analytical framework of Stepwise Generalized Equilibrium Feedback Assessment (SGEFA) and machine learning techniques (MLTs). The impacts of sea-surface temperature, soil moisture, and leaf area index are quantified and found to dominate the fire seasonal variability by regulating regional burning condition and fuel supply. Compared with previously-identified atmospheric and socioeconomic predictors, these slowly evolving oceanic and terrestrial predictors are further identified to determine the seasonal predictability of fire activity in Africa. Our combined SGEFA-MLT approach achieves skillful prediction of African fire one month in advance and can be generalized to provide seasonal estimates of regional and global fire risk.
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
Authors: Liu Miao , Lu Yanfang , Yang Bing , Chen Yanbo , Radda Jonathan S. D. , Hu Mengwei , Katz Samuel G. , Wang Siyuan 
Published: June 2020

AbstractThe three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and lamina- and nucleolus-associated regions, have been discovered. However, how these structures are arranged in the same cell and how they are mutually correlated in different cell types in mammalian tissue are largely unknown. Here, we develop Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We apply this method in mouse fetal liver, and identify de novo cell-type-specific chromatin architectures associated with gene expression, as well as cell-type-independent principles of chromatin organization. Polymer simulation shows that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our results illustrate a multi-faceted picture and physical principles of chromatin organization.
Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen
Authors: Wu Daichao , Gallagher D. Travis , Gowthaman Ragul , Pierce Brian G. , Mariuzza Roy A. 
Published: June 2020

AbstractAdoptive cell therapy (ACT) with tumor-specific T cells can mediate cancer regression. The main target of tumor-specific T cells are neoantigens arising from mutations in self-proteins. Although the majority of cancer neoantigens are unique to each patient, and therefore not broadly useful for ACT, some are shared. We studied oligoclonal T-cell receptors (TCRs) that recognize a shared neoepitope arising from a driver mutation in the p53 oncogene (p53R175H) presented by HLA-A2. Here we report structures of wild-type and mutant p53–HLA-A2 ligands, as well as structures of three tumor-specific TCRs bound to p53R175H–HLA-A2. These structures reveal how a driver mutation in p53 rendered a self-peptide visible to T cells. The TCRs employ structurally distinct strategies that are highly focused on the mutation to discriminate between mutant and wild-type p53. The TCR–p53R175H–HLA-A2 complexes provide a framework for designing TCRs to improve potency for ACT without sacrificing specificity.
Synthesis and versatile reactivity of scandium phosphinophosphinidene complexes
Authors: Feng Bin , Xiang Li , McCabe Karl N. , Maron Laurent , Leng Xuebing , Chen Yaofeng 
Published: June 2020

AbstractM=E/M≡E multiple bonds (M = transition metal, E = main group element) are of significant fundamental scientific importance and have widespread applications. Expanding the ranges of M and E represents grand challenges for synthetic chemists and will bring new horizons for the chemistry. There have been reports of M=E/M≡E multiple bonds for the majority of the transition metals, and even some actinide metals. In stark contrast, as the largest subgroup in the periodic table, rare-earth metals (Ln) were scarcely involved in Ln=E/Ln≡E multiple bonds. Until recently, there were a few examples of rare-earth monometallic alkylidene, imido and oxo complexes, featuring Ln=C/N/O bonds. What are in absence are rare-earth monometallic phosphinidene complexes with Ln=P bonds. Herein, we report synthesis and structure of rare-earth monometallic phosphinidene complexes, namely scandium phosphinophosphinidene complexes. Reactivity of scandium phosphinophosphinidene complexes is also mapped out, and appears to be easily tuned by the supporting ligand.
Deep Learning for Improved Risk Prediction in Surgical Outcomes
Authors: Jalali Ali , Lonsdale Hannah , Do Nhue , Peck Jacquelin , Gupta Monesha , Kutty Shelby , Ghazarian Sharon R. , Jacobs Jeffrey P. , Rehman Mohamed , Ahumada Luis M. 
Published: June 2020

AbstractThe Norwood surgical procedure restores functional systemic circulation in neonatal patients with single ventricle congenital heart defects, but this complex procedure carries a high mortality rate. In this study we address the need to provide an accurate patient specific risk prediction for one-year postoperative mortality or cardiac transplantation and prolonged length of hospital stay with the purpose of assisting clinicians and patients’ families in the preoperative decision making process. Currently available risk prediction models either do not provide patient specific risk factors or only predict in-hospital mortality rates. We apply machine learning models to predict and calculate individual patient risk for mortality and prolonged length of stay using the Pediatric Heart Network Single Ventricle Reconstruction trial dataset. We applied a Markov Chain Monte-Carlo simulation method to impute missing data and then fed the selected variables to multiple machine learning models. The individual risk of mortality or cardiac transplantation calculation produced by our deep neural network model demonstrated 89 ± 4% accuracy and 0.95 ± 0.02 area under the receiver operating characteristic curve (AUROC). The C-statistics results for prediction of prolonged length of stay were 85 ± 3% accuracy and AUROC 0.94 ± 0.04. These predictive models and calculator may help to inform clinical and organizational decision making.
Jasmonic acid and methyl jasmonate modulate growth, photosynthetic activity and expression of photosystem II subunit genes in Brassica oleracea L
Authors: Sirhindi Geetika , Mushtaq Ruqia , Gill Sarvajeet Singh , Sharma Poonam , Abd_Allah Elsayed F. , Ahmad Parvaiz 
Published: June 2020

AbstractThe effects of jasmonic acid (JA) and methyl jasmonate (Me-JA) on photosynthetic efficiency and expression of some photosystem (PSII) related in different cultivars of Brassica oleracea L. (var. italica, capitata, and botrytis) were investigated. Plants raised from seeds subjected to a pre-sowing soaking treatment of varying concentrations of JA and Me-JA showed enhanced photosynthetic efficiency in terms of qP and chlorophyll fluorescence. Maximum quantum efficiency of PSII (Fv/Fm) was increased over that in the control seedlings. This enhancement was more pronounced in the Me-JA-treated seedlings compared to that in JA-treated ones. The expression of PSII genes was differentially regulated among the three varieties of B. oleracea. The gene PsbI up-upregulated in var. botrytis after treatment of JA and Me-JA, whereas PsbL up-regulated in capitata and botrytis after supplementation of JA. The gene PsbM showed many fold enhancements in these expressions in italica and botrytis after treatment with JA. However, the expression of the gene PsbM increased by both JA and Me-JA treatments. PsbTc(p) and PsbTc(n) were also found to be differentially expressed which revealed specificity with the variety chosen as well as JA or Me-JA treatments. The RuBP carboxylase activity remained unaffected by either JA or Me-JA supplementation in all three varieties of B. oleracea L. The data suggest that exogenous application of JA and Me-JA to seeds before germination could influence the assembly, stability, and repair of PS II in the three varieties of B. oleracea examined. Furthermore, this improvement in the PS II machinery enhanced the photosynthetic efficiency of the system and improved the photosynthetic productivity in terms of saccharides accumulation.
A novel culture medium with reduced nutrient concentrations supports the development and viability of mouse embryos
Authors: Ermisch Alison F. , Herrick Jason R. , Pasquariello Rolando , Dyer McKenna C. , Lyons Sarah M. , Broeckling Corey D. , Rajput Sandeep K. , Schoolcraft William B. , Krisher Rebecca L. 
Published: June 2020

AbstractFurther refinement of culture media is needed to improve the quality of embryos generated in vitro. Previous results from our laboratory demonstrated that uptake of nutrients by the embryo is significantly less than what is supplied in traditional culture media. Our objective was to determine the impact of reduced nutrient concentrations in culture medium on mouse embryo development, metabolism, and quality as a possible platform for next generation medium formulation. Concentrations of carbohydrates, amino acids, and vitamins could be reduced by 50% with no detrimental effects, but blastocyst development was impaired at 25% of standard nutrient provision (reduced nutrient medium; RN). Addition of pyruvate and L-lactate (+PL) to RN at 50% of standard concentrations restored blastocyst development, hatching, and cell number. In addition, blastocysts produced in RN + PL contained more ICM cells and ATP than blastocysts cultured in our control (100% nutrient) medium; however, metabolic activity was altered. Similarly, embryos produced in the RN medium with elevated (50% control) concentrations of pyruvate and lactate in the first step medium and EAA and Glu in the second step medium were competent to implant and develop into fetuses at a similar rate as embryos produced in the control medium. This novel approach to culture medium formulation could help define the optimal nutrient requirements of embryos in culture and provide a means of shifting metabolic activity towards the utilization of specific metabolic pathways that may be beneficial for embryo viability.
Association of body surface scanner-based abdominal volume with parameters of the Metabolic Syndrome and comparison with manually measured waist circumference
Authors: Jaeschke Lina , Steinbrecher Astrid , Hansen Guido , Sommer Stefan , Adler Carolin , Janke Jürgen , Pischon Tobias 
Published: June 2020

AbstractTo investigate abdominal volume determined by a new body scanner algorithm as anthropometric marker for Metabolic Syndrome (MetS) and its parameters compared to manually measured waist circumference (WC), we performed body scans in 411 participants (38% men, 20-81 years). WC and triglyceride, HDL-cholesterol, and fasting glucose concentrations, and blood pressure were assessed as MetS parameters. We used Spearman correlations and linear regression to investigate associations and goodness-of-fit (R², BIC) of abdominal volume and WC with MetS parameters, and logistic regression to analyse the discriminative power of WC and abdominal volume to assess likelihoods of MetS components and MetS. Correlations with triglyceride, HDL-cholesterol, and glucose concentration were slightly stronger for abdominal volume (r; 0.32, −0.32, and 0.34, respectively) than for WC (0.28, −0.28, and 0.29, respectively). Explained variances in MetS parameters were slightly higher and goodness-of-fit slightly better for abdominal volume than for WC, but differences were small. Exemplarily, glucose levels were 0.28 mmol/L higher (R² = 0.25; BIC = 945.5) per 1-SD higher WC, and 0.35 mmol/L higher (R² = 0.28; BIC = 929.1) per 1-SD higher abdominal volume. The discriminative power to estimate MetS components was similar for WC and abdominal volume. Our data show that abdominal volume allows metabolic characterization comparable to established WC.
Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy
Authors: Cavicchio L. , Tassoni L. , Laconi A. , Cunial G. , Gagliazzo L. , Milani A. , Campalto M. , Di Martino G. , Forzan M. , Monne I. , Beato M. S. 
Published: June 2020

AbstractNoroviruses (NoVs) are one of the major causative agents of non-bacterial gastroenteritis in humans worldwide. NoVs, belonging to Caliciviridae, are classified into ten genogroups (G) and eight P-groups based on major capsid protein (VP1) and of the RNA-dependent-RNA-polymerase (RdRp), respectively. In swine, the main genogroup and P-group identified are GII and GII.P; which can infect humans too. To date, only one case of GIIP.11 have been identified in swine in Italy while the circulation of other P-types is currently unknown. In the present study, 225 swine faecal samples were collected from 74 swine herds in Veneto region through on-farm monitoring. NoV circulation was particularly high in older pigs. The phylogenetic analysis showed the co-circulation of NoVs belonging to two different P-types: GII.P11 and GII.P18, here described for the first time in Italy, presenting an extensive genetic diversity, never described before worldwide. Distinct NoV genetic subgroups and unique amino acid mutations were identified for each P-type for the first time. This study demonstrated the co-circulation of diverse swine NoVs subgroups in Italy, raising questions on the origin of such diversity and suggesting that continuous monitoring of swine NoVs is needed to track the emergence of potentially zoonotic viruses by recombination events.
Identifying the role of PrimPol in TDF-induced toxicity and implications of its loss of function mutation in an HIV+ patient
Authors: Duong Vincent N. , Zhou Lei , Martínez-Jiménez María I. , He Linh , Cosme Moises , Blanco Luis , Paintsil Elijah , Anderson Karen S. 
Published: June 2020

AbstractA key component of antiretroviral therapy (ART) for HIV patients is the nucleoside reverse transcriptase inhibitor (NRTI) is tenofovir. Recent reports of tenofovir toxicity in patients taking ART for HIV cannot be explained solely on the basis of off-target inhibition of mitochondrial DNA polymerase gamma (Polγ). PrimPol was discovered as a primase-polymerase localized to the mitochondria with repriming and translesion synthesis capabilities and, therefore, a potential contributor to mitochondrial toxicity. We established a possible role of PrimPol in tenofovir-induced toxicity in vitro and show that tenofovir-diphosphate incorporation by PrimPol is dependent on the n-1 nucleotide. We identified and characterized a PrimPol mutation, D114N, in an HIV+ patient on tenofovir-based ART with mitochondrial toxicity. This mutant form of PrimPol, targeting a catalytic metal ligand, was unable to synthesize primers, likely due to protein instability and weakened DNA binding. We performed cellular respiration and toxicity assays using PrimPol overexpression and shRNA knockdown strains in renal proximal tubular epithelial cells. The PrimPol-knockdown strain was hypersensitive to tenofovir treatment, indicating that PrimPol protects against tenofovir-induced mitochondrial toxicity. We show that a major cellular role of PrimPol is protecting against toxicity caused by ART and individuals with inactivating mutations may be predisposed to these effects.
Frontoparietal connectivity correlates with working memory performance in multiple sclerosis
Authors: Figueroa-Vargas Alejandra , Cárcamo Claudia , Henríquez-Ch Rodrigo , Zamorano Francisco , Ciampi Ethel , Uribe-San-Martin Reinaldo , Vásquez Macarena , Aboitiz Francisco , Billeke Pablo 
Published: June 2020

AbstractWorking Memory (WM) impairment is the most common cognitive deficit of patients with Multiple Sclerosis (MS). However, evidence of its neurobiological mechanisms is scarce. Here we recorded electroencephalographic activity of twenty patients with relapsing-remitting MS and minimal cognitive deficit, and 20 healthy control (HC) subjects while they solved a WM task. In spite of similar performance, the HC group demonstrated both a correlation between temporoparietal theta activity and memory load, and a correlation between medial frontal theta activity and successful memory performances. MS patients did not show theses correlations leading significant differences between groups. Moreover, cortical connectivity analyses using granger causality and phase-amplitude coupling between theta and gamma revealed that HC group, but not MS group, presented a load-modulated progression of the frontal-to-parietal connectivity. This connectivity correlated with working memory capacity in MS groups. This early alterations in the oscillatory dynamics underlaying working memory could be useful for plan therapeutic interventions.
Light-enhanced incoherence of electronic transport in quantum cascade lasers
Authors: Kolek Andrzej 
Published: June 2020

AbstractSince their invention in the middle of the 1990s, quantum cascade lasers (QCLs) attract increasing theoretical interest stimulated by their widening applications. One of the key theoretical issues is the optimization of electronic transport which in most of these devices is governed by the injection barrier of QCL heterostructure. In the paper, the nonequilibrium Green’s function formalism is used to study electronic transition through the injection barrier as a function of laser field in the cavity; for the increasing field, a crossover is observed from the strong coupling regime, in which electronic transport through the barrier is coherent, to the weak coupling regime, in which electronic transport gets incoherent. This crossover is characterized by gain recovery time, τrec, which takes sub-picosecond values for mid-IR QCLs operating at room temperature. This time is also important for the performance of devices under steady-state conditions; the maximum output power is obtained when the figure of merit, FOM = (g(0)/gth − 1)/gcτrec [g(0) is the linear response gain, gth is the threshold gain needed to compensate all losses, gc is the gain cross-section], reaches maximum. It is shown that the use of this optimization criterion can result in the structures essentially different from those which can be obtained when the optimized quantity is the linear response gain, g(0).
Discovery of new boron-rich chalcogenides: orthorhombic B6X (X=S, Se)
Authors: Cherednichenko Kirill A. , Mukhanov Vladimir A. , Wang Zhenhai , Oganov Artem R. , Kalinko Aleksandr , Dovgaliuk Iurii , Solozhenko Vladimir L. 
Published: June 2020

AbstractNew boron-rich sulfide B6S and selenide B6Se have been discovered by combination of high pressure – high temperature synthesis and ab initio evolutionary crystal structure prediction, and studied by synchrotron X-ray diffraction and Raman spectroscopy at ambient conditions. As it follows from Rietveld refinement of powder X-ray diffraction data, both chalcogenides have orthorhombic symmetry and belong to Pmna space group. All experimentally observed Raman bands have been attributed to the theoretically calculated phonon modes, and the mode assignment has been performed. Prediction of mechanical properties (hardness and elastic moduli) of new boron-rich chalcogenides has been made using ab initio calculations, and both compounds were found to be members of a family of hard phases.