bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropsychological Profile of Children with Early and Continuously Treated Phenylketonuria: Systematic Review and Future Approaches
Authors: Canton Marie , Gall Didier Le , Feillet François , Bonnemains Chrystele , Roy Arnaud 
Published: April 2019

AbstractObjective:To provide a comprehensive systematic review of the literature by examining studies published on all cognitive aspects of children with early and continuously treated phenylketonuria (ECT-PKU) included in the databases Medline, PsycINFO, and PsycARTICLE.Method:In addition to a classical approach, we summarized methodology and results of each study in order to discuss current theoretical and methodological issues. We also examined recent advances in biochemical markers and treatments of PKU, with implications for future research on metabolic control and its role as a determinant of neuropsychological outcome.Results:Consistent with previous reviews, the hypothesis of a specific and central executive impairment in children with ECT-PKU was suggested. However, findings are inconclusive regarding the nature of executive impairments as well as their specificity, impact on everyday life, persistence over time, and etiology.Conclusion:Given the current state of the science, we suggest future directions for research that utilizes a developmental and integrative approach to examine the effects of recent advances in biochemical markers and treatment of PKU. (JINS, 2019,25, 624–643)
Lachenmann's Silent Voices (and the Speechless Echoes of Nono and Stockhausen)
Authors: LEIPERT TRENT 
Published: April 2019

AbstractIn order to assess Helmut Lachenmann's characterization of (his) music as an ‘existential experience’ this article focuses on a specific aspect of many of his compositions: stretches of near-silence and minimized musical activity such as reduced dynamics and gestures which contrasts the surrounding material. I argue that in the case of his early vocal compositions Consolation I and II (1967 and 1968) these ‘meta-musical fermatas’ relate to a key portion of each work's text in order to encourage self-reflection on the part of the listener. My analyses reveal the influence of Luigi Nono and Karlheinz Stockhausen, particularly in terms of word-setting and of the works’ spiritual and political messages. I further trace the changes undertaken in these compositions and in Lachenmann's commentaries for them over the following decade. I suggest these changes relate to political events in Germany occurring between 1968 and 1977 which also led to the conception of Lachenmann's ‘music with images’, Das Mädchen mit den Schwefelhölzern.
Germination ecology for Florida populations of carpetweed (Mollugo verticillata), Carolina geranium (Geranium carolinianum), eclipta (Eclipta prostrata), and goosegrass (Eleusine indica)
Authors: Sharpe Shaun M. , Boyd Nathan S. 
Published: April 2019

AbstractRow-middle weed control in Florida vegetable production is challenging and often necessitates several PRE and POST herbicide applications. Coordinating POST spray applications with emergence timings should increase herbicide efficacy by targeting susceptible growth stages. Most published emergence models were developed in temperate climates, and adapting them to subtropical climates can be complex and requires reductionist insights into seed ecology, particularly germination and dormancy. The study objective was to examine the influence of temperature and osmotic potential on seed germination of carpetweed (Mollugo verticillata L.), Carolina geranium (Geranium carolinianum L.), eclipta [Eclipta prostrata (L.) L.], and goosegrass [Eleusine indica (L.) Gaertn.]. Mollugo verticillata seed germination was positively photoblastic, with increased germination at high temperatures (≥35 C), more so with high fluctuating temperatures (35/20 and 35/25 C), and occurred at osmotic potentials as low as −0.5 MPa. Geranium carolinianum seed germinated between 10 and 20 C in light or darkness and at osmotic potentials as low as −0.4 MPa. Eclipta prostrata seed germination was entirely positively photoblastic, occurring optimally between 15 and 25 C and at osmotic potentials as low as −1 MPa. Eleusine indica seed germination demonstrated some degree of positive photoblasticity, with greater germination in the light, peak germination at 35 C, and germination occurring at osmotic potentials as low as −0.5 MPa. Described germination ecology for selected species will provide insights for building ecology-based growing degree-day accounting restrictions for empirically derived emergence models.
On the Regional and Seasonal Ozone Depletion Potential of Chlorinated Very Short‐Lived Substances
Authors: Claxton Tom , Hossaini Ryan , Wild Oliver , Chipperfield Martyn P. , Wilson Chris 
Published: April 2019

AbstractChloroform (CHCl3), dichloromethane (CH2Cl2), perchloroethylene (C2Cl4), and 1,2‐dichloroethane (C2H4Cl2) are chlorinated Very Short‐Lived Substances (Cl‐VSLS) with a range of commercial/industrial applications. Recent studies highlight the increasing influence of Cl‐VSLS on the stratospheric chlorine budget and therefore their possible role in ozone depletion. Here we evaluate the ozone depletion potential (ODP) of these Cl‐VSLS using a three‐dimensional chemical transport model and investigate sensitivity to emission location/season. The seasonal dependence of the ODPs is small, but ODPs vary by a factor of 2–3 depending on the continent of emission: 0.0143–0.0264 (CHCl3), 0.0097–0.0208 (CH2Cl2), 0.0057–0.0198 (C2Cl4), and 0.0029–0.0119 (C2H4Cl2). Asian emissions produce the largest ODPs owing to proximity to the tropics and efficient troposphere‐to‐stratosphere transport of air originating from industrialized East Asia. The Cl‐VSLS ODPs are generally small, but the upper ends of the CHCl3 and CH2Cl2 ranges are comparable to the mean ODP of methyl chloride (0.02), a longer‐lived ozone‐depleting substance.
Changing Moho Beneath the Tibetan Plateau Revealed by GRACE Observations
Authors: Jiao Jiashuang , Zhang Yongzhi , Yin Peng , Zhang Kainan , Wang Yipeng , Bilker‐Koivula Mirjam 
Published: April 2019

AbstractA wide range of mass gain in the inland of the Tibetan Plateau (TP) has been observed by the Gravity Recovery and Climate Experiment (GRACE). But there are still controversies on how to understand this phenomenon. In this paper, satellite geodesy data and hydrological models are combined and applied for extracting signals caused by tectonic processes in the TP during the period from 2003 to 2009. We find that in the inland of the TP there are three regions with a significant signal that should be attributed to tectonic processes. The three prominent mass signals, each located in the western, central, and eastern TP, are estimated to be at the rate of 1.47 ± 0.43, −0.85 ± 0.53, and 1.51 ± 0.56 cm/year, respectively, in equivalent water height. However, the rate caused by Earth surface deformation constrained by GPS is 0.33 ± 0.15/0.30 ± 0.10/0.14 ± 0.24 cm/year in equivalent water height, which cannot explain the whole tectonic signals and indicates that a significant mass change occurs beneath the crust, that is, the deformation of the Moho interface. We estimate the Moho change rate in the inland of the TP and find that the Moho interface is suffering an uneven deformation. The Moho is uprising at a rate of 18.1 ± 7.2 mm/year in the west and 21.7 ± 9.7 mm/year in the east of the TP, while there is an obvious deepening rate of −18.3 ± 8.6 mm/year in the central TP.
Prediction Model for Solar Energetic Proton Events: Analysis and Verification
Authors: Zhong Qiuzhen , Wang Jingjing , Meng Xuejie , Liu Siqing , Gong Jiancun 
Published: April 2019

AbstractSolar energetic protons (SEPs) can cause radiation damage to satellites. The Space Environment Prediction Center of China defines the start of a SEP event as the time when three consecutive instances of the 5‐min‐averaged integral flux of >10 MeV protons equal or exceed the 10 proton flux unit threshold. In this study, we analyzed the 5‐min‐averaged soft X‐ray flux and the differential and integral proton flux obtained by the Geostationary Operational Environmental Satellites for the period from January 1990 to September 2017 and developed SEP prediction models and their products. The statistical models take one or two data products and the given thresholds as the predictor and predict whether a SEP event will occur or not in the next 24 hr. The quality of the forecast models was measured by comparing the model results against certain verification metrics. Our model taking the products of 5‐min‐averaged integral flux of >10 MeV protons and long wavelength of soft X‐ray flux as predictors can provide a probability of detection of 0.80 (152/190), a false alarm ratio of 0.26 (53/205), and an average warning time of 2.6 hr for the correctly predicted events. In addition, the model can provide a critical success index of 0.63, a Gilbert skill score of 0.62, and a Heidke skill score of 0.76.
Temperature-induced amorphization in CaCO3 at high pressure and implications for recycled CaCO3 in subduction zones
Authors: Hou Mingqiang , Zhang Qian , Tao Renbiao , Liu Hong , Kono Yoshio , Mao Ho-kwang , Yang Wenge , Chen Bin , Fei Yingwei 
Published: April 2019

AbstractCalcium carbonate (CaCO3) significantly affects the properties of upper mantle and plays a key role in deep carbon recycling. However, its phase relations above 3 GPa and 1000 K are controversial. Here we report a reversible temperature-induced aragonite-amorphization transition in CaCO3 at 3.9–7.5 GPa and temperature above 1000 K. Amorphous CaCO3 shares a similar structure as liquid CaCO3 but with much larger C-O and Ca-Ca bond lengths, indicating a lower density and a mechanism of lattice collapse for the temperature-induced amorphous phase. The less dense amorphous phase compared with the liquid provides an explanation for the observed CaCO3 melting curve overturn at about 6 GPa. Amorphous CaCO3 is stable at subduction zone conditions and could aid the recycling of carbon to the surface.
Macroscale cortical organization and a default-like apex transmodal network in the marmoset monkey
Authors: Buckner Randy L. , Margulies Daniel S. 
Published: April 2019

AbstractNetworks of widely distributed regions populate human association cortex. One network, often called the default network, is positioned at the apex of a gradient of sequential networks that radiate outward from primary cortex. Here, extensive anatomical data made available through the Marmoset Brain Architecture Project are explored to show a homologue exists in marmoset. Results reveal that a gradient of networks extend outward from primary cortex to progressively higher-order transmodal association cortex in both frontal and temporal cortex. The apex transmodal network comprises frontopolar and rostral temporal association cortex, parahippocampal areas TH / TF, the ventral posterior midline, and lateral parietal association cortex. The positioning of this network in the gradient and its composition of areas make it a candidate homologue to the human default network. That the marmoset, a physiologically- and genetically-accessible primate, might possess a default-network-like candidate creates opportunities for study of higher cognitive and social functions.
Regioselective radical α-borylation of α,β-unsaturated carbonyl compounds for direct synthesis of α-borylcarbonyl molecules
Authors: Ren Shi-Chao , Zhang Feng-Lian , Xu Ai-Qing , Yang Yinuo , Zheng Min , Zhou Xiaoguo , Fu Yao , Wang Yi-Feng 
Published: April 2019

AbstractOrganoboron compounds are highly valuable in synthetic chemistry. In particular, α-borylcarbonyl compounds have shown versatile synthetic applications, owing to fruitful chemistries of both the boryl and carbonyl moieties. However, the synthesis of these molecules still remains tedious and time-consuming. Here we report a straightforward and practical route to synthesize α-borylcarbonyl molecules based on a regioselective radical α-borylation of α,β-unsaturated carbonyl compounds. The reaction features unusual α-regioselectivity and high functional-group compatibility. Further synthetic applications of new α-borylated products were also demonstrated. DFT and kinetic studies implicated that the α-regioselectivity of β-aryl-α,β-unsaturated carbonyl compounds was determined by the thermodynamically more favorable radical α-addition step, whereas the formation of α-addition products from β-alkyl-α,β-unsaturated carbonyl compounds was driven by an energetically favored hydrogen atom transfer step. Given that α,β-unsaturated carbonyl compounds can be easily obtained in abundance and variety, this method enjoys great advantages in diverse and economical synthesis of valuable α-borylcarbonyl molecules.
Liquid-like behaviours of metallic glassy nanoparticles at room temperature
Authors: Cao C. R. , Huang K. Q. , Shi J. A. , Zheng D. N. , Wang W. H. , Gu L. , Bai H. Y. 
Published: April 2019

AbstractDirect atomic-scale observations and measurements on dynamics of amorphous metallic nanoparticles (a-NPs) are challenging owing to the insufficient consciousness to their striking characterizations and the difficulties in technological approaches. In this study, we observe coalescence process of the a-NPs at atomic scale. We measure the viscosity of the a-NPs through the particles coalescence by in situ method. We find that the a-NPs have fast dynamics, and the viscosity of the a-NPs exhibits a power law relationship with size of the a-NPs. The a-NPs with sizes smaller than 3 nm are in a supercooled liquid state and exhibit liquid-like behaviours with a decreased viscosity by four orders of magnitude lower than that of bulk glasses. These results reveal the intrinsic flow characteristics of glasses in low demension, and pave a way to understand the liquid-like behaviours of low dimension glass, and are also of key interest to develop size-controlled nanodevices.
Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression
Authors: Yamashita Seisuke , Nagaike Takashi , Tomita Kozo 
Published: April 2019

AbstractLin28-dependent oligo-uridylylation of precursor let-7 (pre-let-7) by terminal uridylyltransferase 4/7 (TUT4/7) represses let-7 expression by blocking Dicer processing, and regulates cell differentiation and proliferation. The interaction between the Lin28:pre-let-7 complex and the N-terminal Lin28-interacting module (LIM) of TUT4/7 is required for pre-let-7 oligo-uridylylation by the C-terminal catalytic module (CM) of TUT4/7. Here, we report crystallographic and biochemical analyses of the LIM of human TUT4. The LIM consists of the N-terminal Cys2His2-type zinc finger (ZF) and the non-catalytic nucleotidyltransferase domain (nc-NTD). The ZF of LIM adopts a distinct structural domain, and its structure is homologous to those of double-stranded RNA binding zinc fingers. The interaction between the ZF and pre-let-7 stabilizes the Lin28:pre-let-7:TUT4 ternary complex, and enhances the oligo-uridylylation reaction by the CM. Thus, the ZF in LIM and the zinc-knuckle in the CM, which interacts with the oligo-uridylylated tail, together facilitate Lin28-dependent pre-let-7 oligo-uridylylation.
CUT&Tag for efficient epigenomic profiling of small samples and single cells
Authors: Kaya-Okur Hatice S. , Wu Steven J. , Codomo Christine A. , Pledger Erica S. , Bryson Terri D. , Henikoff Jorja G. , Ahmad Kami , Henikoff Steven 
Published: April 2019

AbstractMany chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.
Changes in the Anterior Lamina Cribrosa Morphology with Glaucoma Severity
Authors: Tan Nicholas Y. Q. , Tham Yih-Chung , Thakku Sri Gowtham , Wang Xiaofei , Baskaran Mani , Tan Marcus C. L. , Mari Jean-Martial , Strouthidis Nicholas G. , Aung Tin , Girard Michaël J. A. , Cheng Ching-Yu 
Published: April 2019

AbstractThis study was designed to evaluate if primary open angle glaucoma (POAG) and its severity are associated with the shape of the lamina cribrosa (LC) as measured by a global shape index (LC-GSI), or other indices of LC curvature or depth. Optical coherence tomography (OCT) scans of the optic nerve head (OHN) were obtained from subjects with POAG (n = 99) and non-glaucomatous controls (n = 76). ONH structures were delineated, the anterior LC morphology reconstructed in 3D, and the LC-GSI calculated (more negative values denote greater posterior concavity). Anterior LC depth and 2D-curvature were also measured. Severity of glaucoma was defined by the extent of visual field loss, based on the Hodapp-Parrish-Anderson grading. Linear regression analyses compared LC characteristics between controls, mild-moderate, and advanced POAG groups. After adjusting for age, gender, ethnicity, intraocular pressure, axial length and corneal curvature, the LC-GSI was most negative in the advanced POAG group (mean [standard error] = −0.34 [0.05]), followed by the mild-moderate POAG group (−0.31 [0.02]) and then controls (−0.23 [0.02], PTrend = 0.01). There was also a significant trend of increasing LC depth and greater LC horizontal curvature with increasing severity of glaucoma (PTrend = 0.04 and 0.02, respectively). Therefore, with more severe glaucoma, the LC-GSI was increasingly more negative, and the anterior LC depth and curvature greater. These observations collectively correspond to greater cupping of the ONH at the level of the LC. As the LC-GSI describes the 3D anterior LC morphology, its potential usage may be complementary to existing ONH parameters measured on OCT.
A library of Neo Open Reading Frame peptides (NOPs) as a sustainable resource of common neoantigens in up to 50% of cancer patients
Authors: Koster Jan , Plasterk Ronald H. A. 
Published: April 2019

AbstractSomatic mutations in cancer can result in neoantigens against which patients can be vaccinated. The quest for tumor specific neoantigens has yielded no targets that are common to all tumors, yet foreign to healthy cells. Single base pair substitutions (SNVs) at best can alter 1 amino acid which can result in a neoantigen; with the exception of rare site-specific oncogenic driver mutations (such as RAS) such mutations are private. Here, we describe a source of common neoantigens induced by frame shift mutations, based on analysis of 10,186 TCGA tumor samples. We find that these frame shift mutations can produce long neoantigens. These are completely new to the body, and indeed recent evidence suggests that frame shifts can be highly immunogenic. We report that many different frame shift mutations converge to the same small set of 3′ neo open reading frame peptides (NOPs), all encoded by the Neo-ORFeome. We find that a fixed set of only 1,244 neo-peptides in as much as 30% of all TCGA cancer patients. For some tumor classes this is higher; e.g. for colon and cervical cancer, peptides derived from only ten genes (saturated at 90 peptides) can be applied to 39% of all patients. 50% of all TCGA patients can be achieved at saturation (using all those peptides in the library found more than once). A pre-fabricated library of vaccines (peptide, RNA or DNA) based on this set can provide off the shelf, quality certified, ‘personalized’ vaccines within hours, saving months of vaccine preparation. This is crucial for critically ill cancer patients with short average survival expectancy after diagnosis.
Characterization of the Phosphorylation Site of GRTH/DDX25 and Protein Kinase A Binding Interface Provides Structural Basis for the Design of a Non-Hormonal Male Contraceptive
Authors: Raju Murugananthkumar , Hassan Sergio A. , Kavarthapu Raghuveer , Anbazhagan Rajakumar , Dufau Maria L. 
Published: April 2019

AbstractGonadotropin Regulated Testicular Helicase (GRTH/DDX25), expressed in the male gonad, is essential for the completion of spermatogenesis. Our early studies revealed a missense mutation (R242H) of GRTH in 5.8% of Japanese patient population with azoospermia. Transfection of the mutant GRTH construct in COS-1 cells leads to loss of the 61 kDa cytoplasmic phospho-species. Mice with knock-in of the human GRTH mutation are sterile and lack sperm with normal androgen and mating behavior. These findings provide an avenue for the development of a non-hormonal male contraceptive. Using site directed mutagenesis and a site-specific phospho-antibody, we have identified T239, structurally adjacent to the patient’s mutant site as the GRTH phospho-site. Molecular modelling provided structural basis for the role of R242 and other critical solvent-exposed residues at the GRTH/PKA interface (E165/K240/D237), on the control of GRTH phosphorylation at T239. Single or double mutations of these residues caused marked reduction or abolition of the phospho-form. These effects can be ascribed to critical disruptions of intramolecular H-bonds at the GRTH/PKA interface, which leads to modest but consequential structural changes that can affect PKA catalytic efficiency. Inhibition of phosphorylation may be achieved by small, drug-like molecules that bind to GRTH and reconfigure the GRTH/PKA interface.
SPARK-MSNA: Efficient algorithm on Apache Spark for aligning multiple similar DNA/RNA sequences with supervised learning
Authors: Vineetha V. , Biji C. L. , Nair Achuthsankar S. 
Published: April 2019

AbstractMultiple sequence alignment (MSA) is an integral part of molecular biology. But handling massive number of large sequences is still a bottleneck for most of the state-of-the-art software tools. Knowledge driven algorithms utilizing features of input sequences, such as high similarity in case of DNA sequences, can help in improving the efficiency of DNA MSA to assist in phylogenetic tree construction, comparative genomics etc. This article showcases the benefit of utilizing similarity features while performing the alignment. The algorithm uses suffix tree for identifying common substrings and uses a modified Needleman-Wunsch algorithm for pairwise alignments. In order to improve the efficiency of pairwise alignments, a knowledge base is created and a supervised learning with nearest neighbor algorithm is used to guide the alignment. The algorithm provided linear complexityO(m)compared toO(m2). Comparing with state-of-the-art algorithms (e.g., HAlign II), SPARK-MSNA provided 50% improvement in memory utilization in processing human mitochondrial genome (mt. genomes, 100x, 1.1. GB) with a better alignment accuracy in terms of average SP score and comparable execution time. The algorithm is implemented on big data framework Apache Spark in order to improve the scalability. The source code & test data are available at:https://sourceforge.net/projects/spark-msna/.