bluuebunny/crossref_metadata_2025_split huggingface dataset:
A bird’s-eye view of Italian genomic variation through whole-genome sequencing
Authors: Cocca Massimiliano , Barbieri Caterina , Concas Maria Pina , Robino Antonietta , Brumat Marco , Gandin Ilaria , Trudu Matteo , Sala Cinzia Felicita , Vuckovic Dragana , Girotto Giorgia , Matullo Giuseppe , Polasek Ozren , Kolčić Ivana , Gasparini Paolo , Soranzo Nicole , Toniolo Daniela , Mezzavilla Massimo 
Published: November 2019

AbstractThe genomic variation of the Italian peninsula populations is currently under characterised: the only Italian whole-genome reference is represented by the Tuscans from the 1000 Genome Project. To address this issue, we sequenced a total of 947 Italian samples from three different geographical areas. First, we defined a new Italian Genome Reference Panel (IGRP1.0) for imputation, which improved imputation accuracy, especially for rare variants, and we tested it by GWAS analysis on red blood traits. Furthermore, we extended the catalogue of genetic variation investigating the level of population structure, the pattern of natural selection, the distribution of deleterious variants and occurrence of human knockouts (HKOs). Overall the results demonstrate a high level of genomic differentiation between cohorts, different signatures of natural selection and a distinctive distribution of deleterious variants and HKOs, confirming the necessity of distinct genome references for the Italian population.
Efficacy and safety of subthreshold micropulse laser compared with threshold conventional laser in central serous chorioretinopathy
Authors: Sun Zuhua , Huang Ying , Nie Chaochao , Wang Zhijie , Pei Junqing , Lin Bing , Zhou Rong , Zhang Junyan , Chong Victor , Liu Xiaoling 
Published: November 2019

AbstractPurposeTo compare the efficacy and safety of subthreshold micropulse laser (SML) with threshold conventional laser (TCL) in central serous chorioretinopathy (CSC).MethodsProspective, randomized, double-masked, non-inferiority, 12-week clinical trial. Patients were randomly assigned 1:1 to SML group or TCL group. Patients in the SML group were treated with 577 nm micropulse laser. The spot size was 160 µm, the duty cycle was 5% and exposure time was 0.2 s. The power was 50% threshold tested. Patients in the TCL group were treated with 577 nm continuous laser. The power was 100% threshold tested. The primary outcome was the mean change in best-corrected visual acuity (BCVA) at week 12, with a non-inferiority limit of five letters on the Early Treatment Diabetic Retinopathy Study (ETDRS) visual acuity charts.ResultsEighty-eight patients were enroled. Seventy-seven patients were male. Forty-four patients were in SML group and 44 in TCL group. At week 12, SML was equivalent to TCL with a gain of 6.23 ± 8.59 and 6.61 ± 6.35 letters, respectively, (SML–TCL difference: −0.38 letters; 95% confidence interval (CI):−3.58–2.81;Pnon-inferiority = 0.0026). There was no statistically significant difference between the two groups (t = 0.240,P = 0.811). At week 12, the proportion of patients whose SRF had been totally absorbed was 63.63 and 81.82% respectively for SML and TCL groups. There was no statistically significant difference between the two groups (χ2 = 3.67,P = 0.056).ConclusionsBoth SML and TCL can improve visual acuity in CSC. SML was non-inferior to TCL in the improvement of BCVA.
An open source automated tumor infiltrating lymphocyte algorithm for prognosis in melanoma
Authors: Acs Balazs , Ahmed Fahad Shabbir , Gupta Swati , Wong Pok Fai , Gartrell Robyn D. , Sarin Pradhan Jaya , Rizk Emanuelle M. , Gould Rothberg Bonnie , Saenger Yvonne M. , Rimm David L. 
Published: November 2019

AbstractAssessment of tumor infiltrating lymphocytes (TILs) as a prognostic variable in melanoma has not seen broad adoption due to lack of standardization. Automation could represent a solution. Here, using open source software, we build an algorithm for image-based automated assessment of TILs on hematoxylin-eosin stained sections in melanoma. Using a retrospective collection of 641 melanoma patients comprising four independent cohorts; one training set (N = 227) and three validation cohorts (N = 137, N = 201, N = 76) from 2 institutions, we show that the automated TIL scoring algorithm separates patients into favorable and poor prognosis cohorts, where higher TILs scores were associated with favorable prognosis. In multivariable analyses, automated TIL scores show an independent association with disease-specific overall survival. Therefore, the open source, automated TIL scoring is an independent prognostic marker in melanoma. With further study, we believe that this algorithm could be useful to define a subset of patients that could potentially be spared immunotherapy.
Efficient upgrading of CO to C3 fuel using asymmetric C-C coupling active sites
Authors: Wang Xue , Wang Ziyun , Zhuang Tao-Tao , Dinh Cao-Thang , Li Jun , Nam Dae-Hyun , Li Fengwang , Huang Chun-Wei , Tan Chih-Shan , Chen Zitao , Chi Miaofang , Gabardo Christine M. , Seifitokaldani Ali , Todorović Petar , Proppe Andrew , Pang Yuanjie , Kirmani Ahmad R. , Wang Yuhang , Ip Alexander H. , Richter Lee J. , Scheffel Benjamin , Xu Aoni , Lo Shen-Chuan , Kelley Shana O. , Sinton David , Sargent Edward H. 
Published: November 2019

AbstractThe electroreduction of C1 feedgas to high-energy-density fuels provides an attractive avenue to the storage of renewable electricity. Much progress has been made to improve selectivity to C1 and C2 products, however, the selectivity to desirable high-energy-density C3 products remains relatively low. We reason that C3 electrosynthesis relies on a higher-order reaction pathway that requires the formation of multiple carbon-carbon (C-C) bonds, and thus pursue a strategy explicitly designed to couple C2 with C1 intermediates. We develop an approach wherein neighboring copper atoms having distinct electronic structures interact with two adsorbates to catalyze an asymmetric reaction. We achieve a record n-propanol Faradaic efficiency (FE) of (33 ± 1)% with a conversion rate of (4.5 ± 0.1) mA cm−2, and a record n-propanol cathodic energy conversion efficiency (EEcathodic half-cell) of 21%. The FE and EEcathodic half-cell represent a 1.3× improvement relative to previously-published CO-to-n-propanol electroreduction reports.
Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia
Authors: Braun Theodore P. , Okhovat Mariam , Coblentz Cody , Carratt Sarah A. , Foley Amy , Schonrock Zachary , Curtiss Brittany M. , Nevonen Kimberly , Davis Brett , Garcia Brianna , LaTocha Dorian , Weeder Benjamin R. , Grzadkowski Michal R. , Estabrook Joey C. , Manning Hannah G. , Watanabe-Smith Kevin , Jeng Sophia , Smith Jenny L. , Leonti Amanda R. , Ries Rhonda E. , McWeeney Shannon , Di Genua Cristina , Drissen Roy , Nerlov Claus , Meshinchi Soheil , Carbone Lucia , Druker Brian J. , Maxson Julia E. 
Published: November 2019

AbstractAcute Myeloid Leukemia (AML) develops due to the acquisition of mutations from multiple functional classes. Here, we demonstrate that activating mutations in the granulocyte colony stimulating factor receptor (CSF3R), cooperate with loss of function mutations in the transcription factor CEBPA to promote acute leukemia development. The interaction between these distinct classes of mutations occurs at the level of myeloid lineage enhancers where mutant CEBPA prevents activation of a subset of differentiation associated enhancers. To confirm this enhancer-dependent mechanism, we demonstrate that CEBPA mutations must occur as the initial event in AML initiation. This improved mechanistic understanding will facilitate therapeutic development targeting the intersection of oncogene cooperativity.
Bridging the gap between efficacy trials and model-based impact evaluation for new tuberculosis vaccines
Authors: Tovar Mario , Arregui Sergio , Marinova Dessislava , Martín Carlos , Sanz Joaquín , Moreno Yamir 
Published: November 2019

AbstractIn Tuberculosis (TB), given the complexity of its transmission dynamics, observations of reduced epidemiological risk associated with preventive interventions can be difficult to translate into mechanistic interpretations. Specifically, in clinical trials of vaccine efficacy, a readout of protection against TB disease can be mapped to multiple dynamical mechanisms, an issue that has been overlooked so far. Here, we describe this limitation and its effect on model-based evaluations of vaccine impact. Furthermore, we propose a methodology to analyze efficacy trials that circumvents it, leveraging a combination of compartmental models and stochastic simulations. Using our approach, we can disentangle the different possible mechanisms of action underlying vaccine protection effects against TB, conditioned to trial design, size, and duration. Our results unlock a deeper interpretation of the data emanating from efficacy trials of TB vaccines, which renders them more interpretable in terms of transmission models and translates into explicit recommendations for vaccine developers.
Benchmarking an 11-qubit quantum computer
Authors: Wright K. , Beck K. M. , Debnath S. , Amini J. M. , Nam Y. , Grzesiak N. , Chen J.-S. , Pisenti N. C. , Chmielewski M. , Collins C. , Hudek K. M. , Mizrahi J. , Wong-Campos J. D. , Allen S. , Apisdorf J. , Solomon P. , Williams M. , Ducore A. M. , Blinov A. , Kreikemeier S. M. , Chaplin V. , Keesan M. , Monroe C. , Kim J. 
Published: November 2019

AbstractThe field of quantum computing has grown from concept to demonstration devices over the past 20 years. Universal quantum computing offers efficiency in approaching problems of scientific and commercial interest, such as factoring large numbers, searching databases, simulating intractable models from quantum physics, and optimizing complex cost functions. Here, we present an 11-qubit fully-connected, programmable quantum computer in a trapped ion system composed of 13 171Yb+ ions. We demonstrate average single-qubit gate fidelities of 99.5$$\%$$%, average two-qubit-gate fidelities of 97.5$$\%$$%, and SPAM errors of 0.7$$\%$$%. To illustrate the capabilities of this universal platform and provide a basis for comparison with similarly-sized devices, we compile the Bernstein-Vazirani and Hidden Shift algorithms into our native gates and execute them on the hardware with average success rates of 78$$\%$$% and 35$$\%$$%, respectively. These algorithms serve as excellent benchmarks for any type of quantum hardware, and show that our system outperforms all other currently available hardware.
Fine mapping and identification of serum urate loci in American Indians: The Strong Heart Family Study
Authors: Chittoor Geetha , Haack Karin , Balakrishnan Poojitha , Bizon Christopher , Laston Sandra , Best Lyle G. , MacCluer Jean W. , North Kari E. , Umans Jason G. , Franceschini Nora , Prasad Gauri , Macias-Kauffer Luis , Villarreal-Molina Teresa , Bharadwaj Dwaipayan , Canizales-Quinteros Samuel , Navas-Acien Ana , Cole Shelley A. , Voruganti V. S. 
Published: November 2019

AbstractWhile studies have reported genetic loci affecting serum urate (SU) concentrations, few studies have been conducted in minority populations. Our objective for this study was to identify genetic loci regulating SU in a multigenerational family-based cohort of American Indians, the Strong Heart Family Study (SHFS). We genotyped 162,718 single nucleotide polymorphisms (SNPs) in 2000 SHFS participants using an Illumina MetaboChip array. A genome-wide association analysis of SU was conducted using measured genotype analysis approach accounting for kinships in SOLAR, and meta-analysis in METAL. Our results showed strong association of SU with rs4481233, rs9998811, rs7696092 and rs13145758 (minor allele frequency (MAF) = 25–44%; P < 3 × 10−14) of solute carrier family 2, member 9 (SLC2A9) and rs41481455, rs2231142 and rs1481012 (MAF = 29%; p < 3 × 10−9) of ATP-binding cassette protein, subfamily G, member 2 (ABCG2). Carriers of G alleles of rs9998811, rs4148155 and rs1481012 and A alleles of rs4481233, rs7696092 and rs13145758 and rs2231142 had lower SU concentrations as compared to non-carriers. Genetic analysis of SU conditional on significant SLC2A9 and ABCG2 SNPs revealed new loci, nucleobindin 1 (NUCB1) and neuronal PAS domain protein 4 (NPAS4) (p <6× 10−6). To identify American Indian-specific SNPs, we conducted targeted sequencing of key regions of SLC2A9. A total of 233 SNPs were identified of which 89 were strongly associated with SU (p < 7.1 × 10−10) and 117 were American Indian specific. Analysis of key SNPs in cohorts of Mexican-mestizos, European, Indian and East Asian ancestries showed replication of common SNPs, including our lead SNPs. Our results demonstrate the association of SU with uric acid transporters in a minority population of American Indians and potential novel associations of SU with neuronal-related genes which warrant further investigation.
Sorting Fermionization from Crystallization in Many-Boson Wavefunctions
Authors: Bera S. , Chakrabarti B. , Gammal A. , Tsatsos M. C. , Lekala M. L. , Chatterjee B. , Lévêque C. , Lode A. U. J. 
Published: November 2019

AbstractFermionization is what happens to the state of strongly interacting repulsive bosons interacting with contact interactions in one spatial dimension. Crystallization is what happens for sufficiently strongly interacting repulsive bosons with dipolar interactions in one spatial dimension. Crystallization and fermionization resemble each other: in both cases – due to their repulsion – the bosons try to minimize their spatial overlap. We trace these two hallmark phases of strongly correlated one-dimensional bosonic systems by exploring their ground state properties using the one- and two-body density matrix. We solve the N-body Schrödinger equation accurately and from first principles using the multiconfigurational time-dependent Hartree for bosons (MCTDHB) and for fermions (MCTDHF) methods. Using the one- and two-body density, fermionization can be distinguished from crystallization in position space. For N interacting bosons, a splitting into an N-fold pattern in the one-body and two-body density is a unique feature of both, fermionization and crystallization. We demonstrate that this splitting is incomplete for fermionized bosons and restricted by the confinement potential. This incomplete splitting is a consequence of the convergence of the energy in the limit of infinite repulsion and is in agreement with complementary results that we obtain for fermions using MCTDHF. For crystalline bosons, in contrast, the splitting is complete: the interaction energy is capable of overcoming the confinement potential. Our results suggest that the spreading of the density as a function of the dipolar interaction strength diverges as a power law. We describe how to distinguish fermionization from crystallization experimentally from measurements of the one- and two-body density.
Evolution of large area TiS2-TiO2 heterostructures and S-doped TiO2 nano-sheets on titanium foils
Authors: Etghani S. Ahmad , Ansari E. , Mohajerzadeh S. 
Published: November 2019

AbstractWe report a novel and facile method to synthesize sulfur-doped titanium oxide sheets and realize TiS2-TiO2 heterostructures by means of a sequential sulfurization and oxidation step in a dual-zone chemical vapor deposition furnace. The inclusion of chlorine and argon gases during the growth of such titanium-based compounds plays a critical role in the formation of desired geometries and crystalline structures. These heterostructures possess nano-whisker and nanosheet configurations, controlled by adjusting the growth parameters such as temperature, carrier gas and the sequencing between different steps of the growth. The evolution of these complex heterostructures has been investigated using Raman spectroscopy and EDS characterization. The presence of chlorine gas during the growth results in local TiS2 formation as well as faceted growth of TiO2 nanosheets through anatase to rutile phase change prohibition. The electron microscopy (TEM) images and diffraction pattern (SAED) characterization reveal the crystallinity and layered nature of grown structures, further demonstrating the 2D characteristics of S-doped nanosheets. The evolution of TiO2 on TiS2 heterostructures has also has been verified using XPS analysis. These highly featured nanostructures are suitable candidates to enhance the photocatalytic behavior of TiO2 nanostructures.
Misinterpreting carbon accumulation rates in records from near-surface peat
Authors: Young Dylan M. , Baird Andy J. , Charman Dan J. , Evans Chris D. , Gallego-Sala Angela V. , Gill Peter J. , Hughes Paul D. M. , Morris Paul J. , Swindles Graeme T. 
Published: November 2019

AbstractPeatlands are globally important stores of carbon (C) that contain a record of how their rates of C accumulation have changed over time. Recently, near-surface peat has been used to assess the effect of current land use practices on C accumulation rates in peatlands. However, the notion that accumulation rates in recently formed peat can be compared to those from older, deeper, peat is mistaken – continued decomposition means that the majority of newly added material will not become part of the long-term C store. Palaeoecologists have known for some time that high apparent C accumulation rates in recently formed peat are an artefact and take steps to account for it. Here we show, using a model, how the artefact arises. We also demonstrate that increased C accumulation rates in near-surface peat cannot be used to infer that a peatland as a whole is accumulating more C – in fact the reverse can be true because deep peat can be modified by events hundreds of years after it was formed. Our findings highlight that care is needed when evaluating recent C addition to peatlands especially because these interpretations could be wrongly used to inform land use policy and decisions.
Recycling Waste Circuit Board Efficiently and Environmentally Friendly through Small-Molecule Assisted Dissolution
Authors: Chen Zhiqiang , Yang Meng , Shi Qian , Kuang Xiao , Qi H. Jerry , Wang Tiejun 
Published: November 2019

AbstractWith the increasing amount of electronic waste (e-waste) generated globally, it is an enormous challenge to recycle printed circuit boards (PCBs) efficiently and environmentally friendly. However, conventional recycling technologies have low efficiency and require tough treatment such as high temperature (>200 °C) and high pressure. In this paper, a small-molecule assisted approach based on dynamic reaction was proposed to dissolve thermosetting polymers containing ester groups and recycle electronic components from PCBs. This effective approach operates below 200 °C and the polymer could be dissolved in a short time. It has a remarkable ability to recycle a wide range of commercial PCBs, including boards made of typical anhydride epoxy or polyester substrate. Besides, it is environmentally friendly as even the recycling solution could be reused multiple times. In addition, the wasted solution after recycling could be used for board bonding and damage repair. This work also demonstrates the advantage of using polymers containing ester groups as the PCB substrate in consideration of eco-friendly and efficient recycling.
Simultaneous measurement of p53:Mdm2 and p53:Mdm4 protein-protein interactions in whole cells using fluorescence labelled foci
Authors: Frosi Y. , Inoue K. , Ramlan Siti Radhiah , Lane D. P. , Watanabe T. , Brown C. J. 
Published: November 2019

AbstractIn this report we describe the development of a Fluorescent Protein-Protein Interaction-visualization (FLUOPPI) to enable the simultaneous measurement of both Mdm2:p53 and Mdm4:p53 interactions in order to assess the relative efficiencies of mimetic molecules of the p53 peptide helix against both PPIs. Mdm2 and Mdm4 overexpression frequently leads to the inactivation of non-mutated p53 in human cancers, via inhibition of its transcriptional activity, enhancing its degradation by the proteasome or by preventing its nuclear import. Development of inhibitors to disrupt the binding of one or both of these protein interactions have been the subject of intensive pharmaceutical development for anti-cancer therapies. Using the bimodal FLUOPPI system we have characterised compounds that were either monospecific for Mdm2 or bispecific for both Mdm2 and Mdm4. We have also demonstrated that the FLUOPPI assay can reliably differentiate between specific and non-specific disruption of these protein complexes via accurate assessment and normalization to the cell population under measurement. We envision that this methodology will increase the efficiency of identifying compounds that are either specific against a single PPI from a closely related family of interactions or compounds that interact across multiple related PPI pairs, depending on which is more desirable.
A Model Falsification Approach to Learning in Non-Stationary Environments for Experimental Design
Authors: Murari Andrea , Lungaroni Michele , Peluso Emmanuele , Craciunescu Teddy , Gelfusa Michela 
Published: November 2019

AbstractThe application of data driven machine learning and advanced statistical tools to complex physics experiments, such as Magnetic Confinement Nuclear Fusion, can be problematic, due the varying conditions of the systems to be studied. In particular, new experiments have to be planned in unexplored regions of the operational space. As a consequence, care must be taken because the input quantities used to train and test the performance of the analysis tools are not necessarily sampled by the same probability distribution as in the final applications. The regressors and dependent variables cannot therefore be assumed to verify the i.i.d. (independent and identical distribution) hypothesis and learning has therefore to take place under non stationary conditions. In the present paper, a new data driven methodology is proposed to guide planning of experiments, to explore the operational space and to optimise performance. The approach is based on the falsification of existing models. The deployment of Symbolic Regression via Genetic Programming to the available data is used to identify a set of candidate models, using the method of the Pareto Frontier. The confidence intervals for the predictions of such models are then used to find the best region of the parameter space for their falsification, where the next set of experiments can be most profitably carried out. Extensive numerical tests and applications to the scaling laws in Tokamaks prove the viability of the proposed methodology.
Assembly along lines in boundary-driven dynamical system
Authors: Singh Kulveer , Rabin Yitzhak 
Published: November 2019

AbstractWe introduce a simple dynamical rule in which each particle locates a particle that is farthest from it and moves towards it. Repeated application of this algorithm results in the formation of unusual dynamical patterns: during the process of assembly the system self-organizes into slices of low particle density separated by lines of increasingly high particle density along which most particles move. As the process proceeds, pairs of lines meet and merge with each other until a single line remains and particles move along it towards the zone of assembly. We show that this pattern is governed by particles (attractors) situated on the instantaneous outer boundary of the system and that both in two and in three dimensions the lines are formed by zigzag motion of a particle towards a pair of nearly equidistant attractors. This novel line-dominated assembly is very different from the local assembly in which particles that move towards their nearest neighbors produce point-like clusters that coalesce into new point-like clusters, etc.