bluuebunny/crossref_metadata_2025_split huggingface dataset:
A roadmap for global synthesis of the plant tree of life
Authors: Eiserhardt Wolf L. , Antonelli Alexandre , Bennett Dominic J. , Botigué Laura R. , Burleigh J. Gordon , Dodsworth Steven , Enquist Brian J. , Forest Félix , Kim Jan T. , Kozlov Alexey M. , Leitch Ilia J. , Maitner Brian S. , Mirarab Siavash , Piel William H. , Pérez‐Escobar Oscar A. , Pokorny Lisa , Rahbek Carsten , Sandel Brody , Smith Stephen A. , Stamatakis Alexandros , Vos Rutger A. , Warnow Tandy , Baker William J. 
Published: March 2018

AbstractProviding science and society with an integrated, up‐to‐date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree‐building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non‐experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re‐run at regular intervals, storing trees and their metadata long‐term. Providing the trees to a diverse global audience through user‐friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.
The Role of Neighborhood Context and School Climate in School‐Level Academic Achievement
Authors: Ruiz Linda D. , McMahon Susan D. , Jason Leonard A. 
Published: March 2018

AbstractIn recent years, the quality of education available to children has become increasingly dependent on the social and economic demographics of neighborhoods in which the children live. This study assesses the role of community violence in explaining the relation between socio‐economic status (SES) and academic outcomes and the potential of positive school climate to promote academic achievement. With a sample of 297 Chicago public elementary schools, we examine community‐level and school‐level data and use Geographic Information Systems (GIS) mapping to illustrate how school academic achievement coincides with neighborhood economics and crime statistics. Results support the hypothesized mediation, such that lowerSESwas associated with lower academic achievement, and violent crime partially mediated this relation. School climate was positively associated with academic achievement, and student safety significantly moderated the relation betweenSESand academic achievement. Implications for theory, research, and intervention are discussed.
Behavioral Self‐Regulation, Early Academic Achievement, and the Effectiveness of Urban Schools for Low‐Income Ethnic Minority Children
Authors: Caughy Margaret O. , Mills Britain , Brinkley Dawn , Owen Margaret T. 
Published: March 2018

AbstractThe independent and joint associations between child behavioral self‐regulation ability and school effectiveness in relation to academic achievement were examined in a sample of low‐income African American (n = 132) and Latino (n = 198) children attending kindergarten and first grade across a large metropolitan area. Child behavioral self‐regulation and school effectiveness were positively associated with both reading and mathematics performance. School effectiveness moderated the effect of behavioral self‐regulation on reading but not math achievement. Lower child behavioral self‐regulation during early elementary school was associated with lower reading achievement the following year but only among children attending less effective schools. Behavioral self‐regulation was not related to reading achievement among children attending more effective schools. Implications of these findings for policies addressing disparities in early academic achievement are discussed.
Treatment patterns and clinical outcomes in high‐risk newly diagnosed multiple myeloma patients carrying the 17p deletion: An observational multi‐center retrospective study
Authors: Cohen Yael C. , Saranga Avi , Gatt Moshe E. , Lavi Noa , Ganzel Chezi , Magen Hila , Avivi Irit , Tadmor Tamar , Suriu Celia , Jarchowsky Dolberg Osnat , Papushado Amitai , Trestman Svetlana , Ram Ron 
Published: March 2018

AbstractDel17p is a genomic imbalance occurring in ∼7%‐10% of myeloma at diagnosis newly diagnosed myeloma patients (NDMM) and comprises a poor prognostic factor. The goal of this study is to analyze real world data and outcomes among NDMM patients carrying 17p deletion. We report an observational, retrospective, multicenter study. Sixty consecutive patients diagnosed with multiple myeloma in the 8 participating centers diagnosed between 1/2008 and 1/2016 proven to carry 17p deletion by means of fluorescence in situ hybridization (FISH) were identified. Most received a bortezomib‐based induction, over half underwent autologous hematopoietic cell transplantation (HCT); 30% of the patients gained early access to new novel agents via clinical trials, access programs or private insurance. Overall response rate (ORR) after induction was 85%; 94% for transplant eligible (TE); and 75% for transplant ineligible (NTE), and declined in subsequent treatment lines, 64% achieved ≥ VGPR. Median overall survival (OS) was 43 months; median progression free survival (PFS) was 11 months, 19 months for TE and 7 for NTE. In multivariate analysis: higher M‐Spike, presence of extramedullary disease, and >50% of cells baring del17p were associated with adverse PFS; Autologous HCT and higher hemoglobin were associated with longer PFS; OS was 59 months for patients with early access to newer agents. Older age and higher M‐Spike levels were associated with adverse OS, Autologous HCT was associated with favorable OS, 59.7 vs 28.7 months for NTE patients. Despite the improvement achieved with autologous HCT and new novel agents, the prognosis of patients with 17p deletion is still inferior, emphasizing the need for novel approaches.
CXCR4 blockade improves leukemia eradication by allogeneic lymphocyte infusion
Authors: Jin Chun‐Hui , Li Yang , Xia Jinxing , Li Yuying , Chen Mo , Hu Zheng , Mapara Markus Y. , Li Wei , Yang Yong‐Guang 
Published: March 2018

AbstractPersistent low levels of disease in bone marrow, an immunoprivileged tissue, are responsible for relapse following allogeneic hematopoietic cell transplantation. Using mouse models carrying primary human acute lymphoblast leukemia derived from MLL‐AF9‐overexpressing human hematopoietic stem cells, we demonstrate that allogeneic lymphocyte infusion (ALI)‐mediated graft‐vs.‐leukemia effects selectively spare leukemia cells in the bone marrow. The resistance of leukemia cells to ALI within bone marrow is due to the immunosuppressive status of the tissue, as ALI achieved a significantly increased complete remission rate when leukemia cells were dislodged from bone marrow by treatment with a CXCR4 antagonist AMD3100. Adoptive transfer experiments confirmed that the frequency of leukemia‐initiating cells in bone marrow was significantly decreased in the recipients treated with ALI plus AMD3100 compared to those receiving ALI only. These findings indicate that the immunoprivileged nature of bone marrow is largely responsible for relapse after immunotherapies, and that treatment with AMD3100 may offer a clinically‐practical approach to improving the outcome of adoptive allogeneic cell therapy.
A prospective phase II study of low dose lenalidomide plus dexamethasone in patients with newly diagnosed polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes (POEMS) syndrome
Authors: Li Jian , Huang Xu‐Fei , Cai Qian‐Qian , Wang Chen , Cai Hao , Zhao Hao , Zhang Lu , Cao Xin‐Xin , Gale Robert Peter , Zhou Dao‐bin 
Published: March 2018

AbstractPolyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes (POEMS) syndrome is a rare plasma dyscrasia without standard treatment. This phase II prospective trial evaluates the safety and response of 12 cycles of low dose lenalidomide (10 mg) plus dexamethasone (Rdex) in patients with newly diagnosed POEMS syndrome. Forty‐one patients (28 men) were enrolled and the median age at diagnosis was 49 years (range, 21‐70 years). Twenty‐one patients (46%) achieved complete hematologic response and the neurologic response rate was 95%. The median serum vascular endothelial growth factor (VEGF) declined from 5155 pg/mL (range, 534‐14 328 pg/mL) to 832 pg/mL (95‐6254 pg/mL) after therapy. The overall VEGF response rate was 83%, and the median time to response was 2 months, with a mean VEGF reduction of 43% at the first month. In terms of clinical response, Rdex substantially relieved extravascular volume overload, organomegaly, and pulmonary hypertension. No treatment‐related deaths occurred and no patients suffered from lenalidomide‐related grade 3 or above adverse events. After a median follow‐up of 34 months, median overall survival (OS) and progression‐free survival (PFS) were not reached, with an estimated 3‐year OS and PFS of 90% and 75%, respectively. In conclusion, Rdex was active with high hematologic, VEGF and organ response rate and well tolerated for patients with newly diagnosed POEMS syndrome. This trial was registered at www.clinicaltrials.gov as #NCT01816620.
Copper‐Catalyzed Bis‐ or Trifunctionalization of Alkynyl Carboxylic Acids: An Efficient Route to Bis‐ and Tris‐selenide Alkenes
Authors: Chen Jing , Su Shi‐Xia , Hu Da‐Chao , Cui Fei‐Hu , Xu Yan‐Li , Chen Yan‐Yan , Ma Xian‐Li , Pan Ying‐Ming , Liang Ying 
Published: March 2018

AbstractA highly efficient copper‐catalyzed protocol for the synthesis of bis‐ and tris‐selenide alkenes from alkynyl carboxylic acids and diselenides has been developed. The reaction of alkynyl carboxylic acids and diselenides in the presence of CuI/Cs2CO3/toluene under white light LEDs only gave bis‐selenide alkenes, whereas tris‐selenide alkenes were obtained in the presence of a CuI/Cs2CO3/NMP system. This method provides a rapid access to bis‐ and tris‐selenide alkenes derivatives.
Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments
Authors: Nieves‐Colón Maria A. , Ozga Andrew T. , Pestle William J. , Cucina Andrea , Tiesler Vera , Stanton Travis W. , Stone Anne C. 
Published: March 2018

AbstractObjectivesThe tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi‐tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12).Materials and MethodsAll samples were extracted twice, built into double‐stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.ResultsNo significant difference was found in overall ancient DNA yields or post‐mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality‐filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.DiscussionBoth methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.
Permeability of the blood–brain barrier predicts no evidence of disease activity at 2 years after natalizumab or fingolimod treatment in relapsing–remitting multiple sclerosis
Authors: Cramer Stig P. , Simonsen Helle J. , Varatharaj Aravinthan , Galea Ian , Frederiksen Jette L. , Larsson Henrik B. W. 
Published: March 2018

ObjectiveTo investigate whether blood–brain barrier (BBB) permeability, as measured by dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI), can provide early detection of suboptimal treatment response in relapsing–remitting multiple sclerosis (RRMS).MethodsThirty‐five RRMS patients starting on fingolimod or natalizumab, drugs with a common effect of decreasing lymphocyte influx into the central nervous system, were scanned with DCE‐MRI at 3T prior to treatment and at 3 and 6 months posttreatment. We calculated the influx constant Ki, a measure of BBB permeability, using the Patlak model. Suboptimal treatment response was defined as loss of no evidence of disease activity (NEDA) status after 2 years of treatment.ResultsSubjects with loss of NEDA status at 2 years had a 51% higher mean Ki in normal‐appearing white matter (NAWM) measured after 6 months of treatment, compared to subjects with maintained NEDA status (mean difference = 0.06ml/100g/min, 95% confidence interval [CI] = 0.02–0.09, p = 0.002). Ki in NAWM at 6 months was a good predictor of loss of NEDA status at 2 years (area under the curve = 0.84, 95% CI = 0.70–0.99, p = 0.003), and a value above 0.136ml/100/g/min yielded an odds ratio of 12.4 for suboptimal treatment response at 2 years, with a sensitivity of 73% and a specificity of 82%.InterpretationOur results suggest that BBB permeability as measured by DCE‐MRI reliably predicts suboptimal treatment response and is a surrogate marker of the state of health of the BBB. We find a predictive threshold for disease activity, which is remarkably identical in clinically isolated syndrome as previously reported and established RRMS as investigated here. Ann Neurol 2018;83:902–914
Stem cell modeling of mitochondrial parkinsonism reveals key functions of OPA1
Authors: Jonikas Mindaugas , Madill Martin , Mathy Alexandre , Zekoll Theresa , Zois Christos E. , Wigfield Simon , Kurzawa‐Akanbi Marzena , Browne Cathy , Sims David , Chinnery Patrick F. , Cowley Sally A. , Tofaris George K. 
Published: March 2018

ObjectiveDefective mitochondrial function attributed to optic atrophy 1 (OPA1) mutations causes primarily optic atrophy and, less commonly, neurodegenerative syndromes. The pathomechanism by which OPA1 mutations trigger diffuse loss of neurons in some, but not all, patients is unknown. Here, we used a tractable induced pluripotent stem cell (iPSC)‐based model to capture the biology of OPA1 haploinsufficiency in cases presenting with classic eye disease versus syndromic parkinsonism.MethodsiPSCs were generated from 2 patients with OPA1 haploinsufficiency and 2 controls and differentiated into dopaminergic neurons. Metabolic profile was determined by extracellular flux analysis, respiratory complex levels using immunoblotting, and complex I activity by a colorimetric assay. Mitochondria were examined by transmission electron microscopy. Mitochondrial DNA copy number and deletions were assayed using long‐range PCR. Mitochondrial membrane potential was measured by tetramethylrhodamine methyl ester uptake, and mitochondrial fragmentation was assessed by confocal microscopy. Exome sequencing was used to screen for pathogenic variants.ResultsOPA1 haploinsufficient iPSCs differentiated into dopaminergic neurons and exhibited marked reduction in OPA1 protein levels. Loss of OPA1 caused a late defect in oxidative phosphorylation, reduced complex I levels, and activity without a significant change in the ultrastructure of mitochondria. Loss of neurons in culture recapitulated dopaminergic degeneration in syndromic disease and correlated with mitochondrial fragmentation.InterpretationOPA1 levels maintain oxidative phosphorylation in iPSC‐derived neurons, at least in part, by regulating the stability of complex I. Severity of OPA1 disease associates primarily with the extent of OPA1‐mediated fusion, suggesting that activation of this mechanism or identification of its genetic modifiers may have therapeutic or prognostic value. Ann Neurol 2018;83:915–925
Coadsorbate‐Induced Reversal of Solid–Liquid Interface Dynamics
Authors: Rahn Björn , Wen Rui , Deuchler Lukas , Stremme Johannes , Franke Andreas , Pehlke Eckhard , Magnussen Olaf M. 
Published: March 2018

AbstractCoadsorbed anions are well‐known to influence surface reactivity and dynamics at solid–liquid interfaces. Here we demonstrate that the chemical nature of these spectator species can entirely determine the microscopic dynamic behavior. Quantitative in situ video‐STM data on the surface diffusion of adsorbed sulfur atoms on Cu(100) electrodes in aqueous solution covered by bromide and chloride spectators, respectively, reveal in both cases a strong exponential potential dependence, but with opposite sign. This reversal is highly surprising in view of the isostructural adsorbate arrangement in the two systems. Detailed DFT studies suggest an anion‐induced difference in the sulfur diffusion mechanism, specifically an exchange diffusion on the Br‐covered surface. Experimental evidence for the latter is provided by the observation of Cu vacancy formation in the Br system, which can be rationalized by a side reaction of the sulfur exchange diffusion.
Generation and Rearrangement of N,O‐Dialkenylhydroxylamines for the Synthesis of 2‐Aminotetrahydrofurans
Authors: Son Jongwoo , Reidl Tyler W. , Kim Ki Hwan , Wink Donald J. , Anderson Laura L. 
Published: March 2018

AbstractA new diastereoselective route to 2‐aminotetrahydrofurans has been developed from N,O‐dialkenylhydroxylamines. These intermediates undergo a spontaneous C−C bond‐forming [3,3]‐sigmatropic rearrangement followed by a C−O bond‐forming cyclization. A copper‐catalyzed N‐alkenylation of an N‐Boc‐hydroxylamine with alkenyl iodides, and a base‐promoted addition of the resulting N‐hydroxyenamines to an electron‐deficient allene, provide modular access to these novel rearrangement precursors. The scope of this de novo synthesis of simple nucleoside analogues has been explored to reveal trends in diastereoselectivity and reactivity. In addition, a base‐promoted ring‐opening and Mannich reaction has been discovered to covert 2‐aminotetrahydrofurans to cyclopentyl β‐aminoacid derivatives or cyclopentenones.
Two‐Dimensional Fullerene Assembly from an Exfoliated van der Waals Template
Authors: Lee Kihong , Choi Bonnie , Plante Ilan Jen‐La , Paley Maria V. , Zhong Xinjue , Crowther Andrew C. , Owen Jonathan S. , Zhu Xiaoyang , Roy Xavier 
Published: March 2018

AbstractTwo‐dimensional (2D) materials are commonly prepared by exfoliating bulk layered van der Waals crystals. The creation of synthetic 2D materials from bottom‐up methods is an important challenge as their structural flexibility will enable chemists to tune the materials properties. A 2D material was assembled using C60 as a polymerizable monomer. The C60 building blocks are first assembled into a layered solid using a molecular cluster as structure director. The resulting hierarchical crystal is used as a template to polymerize its C60 monolayers, which can be exfoliated down to 2D crystalline nanosheets. Derived from the parent template, the 2D structure is composed of a layer of inorganic cluster, sandwiched between two monolayers of polymerized C60. The nanosheets can be transferred onto solid substrates and depolymerized by heating. Electronic absorption spectroscopy reveals an optical gap of 0.25 eV, narrower than that of the bulk parent crystalline solid.
Tunable Pentapeptide Self‐Assembled β‐Sheet Hydrogels
Authors: Clarke David E. , Parmenter Christopher D. J. , Scherman Oren A. 
Published: March 2018

AbstractOligopeptide‐based supramolecular hydrogels hold promise in a range of applications. The gelation of these systems is hard to control, with minor alterations in the peptide sequence significantly influencing the self‐assembly process. We explored three pentapeptide sequences with different charge distributions and discovered that they formed robust, pH‐responsive hydrogels. By altering the concentration and charge distribution of the peptide sequence, the stiffness of the hydrogels could be tuned across two orders of magnitude (2–200 kPa). Also, through reassembly of the β‐sheet interactions the hydrogels could self‐heal and they demonstrated shear‐thin behavior. Using spectroscopic and cryo‐imaging techniques, we investigated the relationship between peptide sequence and molecular structure, and how these influence the mechanical properties of the hydrogel. These pentapeptide hydrogels with tunable morphology and mechanical properties have promise in tissue engineering, injectable delivery vectors, and 3D printing applications.
Dissipative Synthetic DNA‐Based Receptors for the Transient Loading and Release of Molecular Cargo
Authors: Del Grosso Erica , Amodio Alessia , Ragazzon Giulio , Prins Leonard J. , Ricci Francesco 
Published: March 2018

AbstractSupramolecular chemistry is moving into a direction in which the composition of a chemical equilibrium is no longer determined by thermodynamics but by the efficiency with which kinetic states can be populated by energy consuming processes. Herein, we show that DNA is ideally suited for programming chemically fueled dissipative self‐assembly processes. Advantages of the DNA‐based systems presented in this study include a perfect control over the activation site for the chemical fuel in terms of selectivity and affinity, highly selective fuel consumption that occurs exclusively in the activated complex, and a high tolerance for the presence of waste products. Finally, it is shown that chemical fuels can be used to selectively activate different functions in a system of higher complexity embedded with multiple response pathways.
Carbon‐Electrode‐Tailored All‐Inorganic Perovskite Solar Cells To Harvest Solar and Water‐Vapor Energy
Authors: Duan Jialong , Hu Tianyu , Zhao Yuanyuan , He Benlin , Tang Qunwei 
Published: March 2018

AbstractMoisture is the worst enemy for state‐of‐the‐art perovskite solar cells (PSCs). However, the flowing water vapor within nanoporous carbonaceous materials can create potentials. Therefore, it is a challenge to integrate water vapor and solar energies into a single PSC device. We demonstrate herein all‐inorganic cesium lead bromide (CsPbBr3) solar cells tailored with carbon electrodes to simultaneously harvest solar and water‐vapor energy. Upon interfacial modification and plasma treatment, the bifunctional PSCs yield a maximum power conversion efficiency up to 9.43 % under one sun irradiation according to photoelectric conversion principle and a power output of 0.158 μW with voltage of 0.35 V and current of 0.45 μA in 80 % relative humidity through the flowing potentials at the carbon/water interface. The initial efficiency is only reduced by 2 % on exposing the inorganic PSC with 80 % humidity over 40 days. The successful realization of physical proof‐of‐concept multi‐energy integrated solar cells provides new opportunities of maximizing overall power output.