bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards Understanding Directed Evolution: More than Half of All Amino Acid Positions Contribute to Ionic Liquid Resistance of Bacillus subtilis Lipase A
Authors: Frauenkron‐Machedjou Victorine Josiane , Fulton Alexander , Zhu Leilei , Anker Carolin , Bocola Marco , Jaeger Karl‐Erich , Schwaneberg Ulrich 
Published: March 2015

AbstractIonic liquids (ILs) are attractive (co‐)solvents for biocatalysis. However, in high concentration (>10 % IL), enzymes usually show decreased activity. No general principles have been discovered to improve IL resistance of enzymes by protein engineering. We present a systematic study to elucidate general engineering principles by site saturation mutagenesis on the complete gene bsla. Screening in presence of four [BMIM]‐based ILs revealed two unexpected lessons on directed evolution: 1) resistance improvement was obtainable at 50–69 % of all amino acid positions, thus explaining the success of small sized random mutant libraries; 2) 6–13 % of substitutions led to improved resistance. Among these, 66–95 % were substitutions by chemically different amino acids (e.g., aromatic to polar/aliphatic/charged amino acids), thus indicating that mutagenesis methods introducing such changes should, at least for lipases like BSLA, be favored to improve IL resistance.
Genome Mining of the Hitachimycin Biosynthetic Gene Cluster: Involvement of a Phenylalanine‐2,3‐aminomutase in Biosynthesis
Authors: Kudo Fumitaka , Kawamura Koichi , Uchino Asuka , Miyanaga Akimasa , Numakura Mario , Takayanagi Ryuichi , Eguchi Tadashi 
Published: March 2015

AbstractHitachimycin is a macrolactam antibiotic with (S)‐β‐phenylalanine (β‐Phe) at the starter position of its polyketide skeleton. To understand the incorporation mechanism of β‐Phe and the modification mechanism of the unique polyketide skeleton, the biosynthetic gene cluster for hitachimycin in Streptomyces scabrisporus was identified by genome mining. The identified gene cluster contains a putative phenylalanine‐2,3‐aminomutase (PAM), five polyketide synthases, four β‐amino‐acid‐carrying enzymes, and a characteristic amidohydrolase. A hitA knockout mutant showed no hitachimycin production, but antibiotic production was restored by feeding with (S)‐β‐Phe. We also confirmed the enzymatic activity of the HitA PAM. The results suggest that the identified gene cluster is responsible for the biosynthesis of hitachimycin. A plausible biosynthetic pathway for hitachimycin, including a unique polyketide skeletal transformation mechanism, is proposed.
Chemical Speciation and Bond Lengths of Organic Solutes by Core‐Level Spectroscopy: pH and Solvent Influence on p‐Aminobenzoic Acid
Authors: Stevens Joanna S. , Gainar Adrian , Suljoti Edlira , Xiao Jie , Golnak Ronny , Aziz Emad F. , Schroeder Sven L. M. 
Published: March 2015

AbstractThrough X‐ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near‐edge X‐ray absorption fine structure (NEXAFS) and resonant inelastic X‐ray scattering (RIXS) measurements at the nitrogen K‐edge of para‐aminobenzoic acid reveal both pH‐ and solvent‐dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.
Synthesis, Characterisation and Reactivity of Copper(I) Amide Complexes and Studies on Their Role in the Modified Ullmann Amination Reaction
Authors: Sung Simon , Braddock D. Christopher , Armstrong Alan , Brennan Colin , Sale David , White Andrew J. P. , Davies Robert P. 
Published: March 2015

AbstractA series of copper(I) alkylamide complexes have been synthesised; copper(I) dicyclohexylamide (1), copper(I) 2,2,6,6‐tetramethylpiperidide (2), copper(I) pyrrolidide (3), copper(I) piperidide (4), and copper(I) benzylamide (5). Their solid‐state structures and structures in [D6]benzene solution are characterised, with the aggregation state in solution determined by a combination of DOSY NMR spectroscopy and DFT calculations. Complexes 1, 2 and 4 are shown to exist as tetramers in the solid state by X‐ray crystallography. In [D6]benzene solution, complexes 1, 2 and 5 were found by using 1H DOSY NMR to exist in rapid equilibrium between aggregates with average aggregation numbers of 2.5, 2.4 and 3.3, respectively, at 0.05 M concentration. Conversely, distinct trimeric, tetrameric and pentameric forms of 3 and 4 were distinguishable by one‐dimensional 1H and 1H DOSY NMR spectroscopy. Complexes 3–5 are found to react stoichiometrically with iodobenzene, in the presence or absence of 1,10‐phenanthroline as an ancillary ligand, to give arylamine products indicative of their role as potential intermediates in the modified Ullmann reaction. The role of phenanthroline has also been explored both in the stoichiometric reaction and in the catalytic Ullmann protocol.
Ceramic Counterflow Reactor for Efficient Conversion of CO2 to Carbon‐Rich Syngas
Authors: Kelling René , Dubbe Hendrik , Eigenberger Gerhart , Nieken Ulrich 
Published: March 2015

AbstractCO2 is a suitable feedstock for syngas production. Possible co‐reactants to convert CO2 are hydrogen or methane. Hydrogen can be produced from electrolysis of water with renewable energy, whereby pure oxygen is obtained. Consequently, a simultaneous partial combustion of the energy‐rich co‐reactants (H2 or CH4) with oxygen is possible to compensate for the required heat of reaction and to achieve high temperatures. This is crucial for both, high CO2 conversion and the prevention of harmful coke formation. For this application a new, scalable reactor concept is proposed. A proof of concept is presented both experimentally and model‐based. The model predicts high CO2 conversion and syngas production in industrial scale while maintaining defined temperature limits so that coke formation is avoided.
Cytopathology of pulmonary adenocarcinoma with a single histological pattern using the proposed International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) classification
Authors: Rodriguez Erika F. , Dacic Sanja , Pantanowitz Liron , Khalbuss Walid E. , Monaco Sara E. 
Published: March 2015

BACKGROUNDGuidelines for histological subtyping in patients with surgically resected lung adenocarcinoma (ADC) were recently proposed by the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society. The objective of the current study was to investigate the cytomorphology of these subtypes of ADC in cases with matched histology specimens demonstrating a single pure subtype.METHODSThe authors reviewed their database for patients with histological diagnoses of primary lung ADC with a single histological pattern observed on surgical resection and investigated the cytological findings in 18 matched cytology specimens to eliminate sampling issues in cases of mixed ADC.RESULTSResections were classified as acinar (7 specimens), solid (6 specimens), lepidic (2 specimens), mucinous (2 specimens), and papillary (1 specimen). Cytology specimens demonstrating a solid pattern had a predominance of 3‐dimensional clusters (5 of 6 vs 0 of 12 specimens) (P = .0007, Fisher exact test), necrotic background (3 of 6 vs 0 of 12 specimens) (P = .02), pleomorphic nuclei (6 of 6 vs 1 of 12 specimens) (P = .0004), irregular nuclear contours (6 of 6 vs 3 of 12 specimens) (P = .009), and nuclear enlargement (5 of 6 vs 2 of 12 specimens) (P = .01) compared with the nonsolid patterns. Nuclear pseudoinclusions were present only in nonsolid patterns (5 of 12 specimens), although this finding was not statistically significant (P = .05)CONCLUSIONSCytological features of lung ADC subtypes proposed by the Study of Lung Cancer/American Thoracic Society/European Respiratory Society classification overlap. However, architectural and nuclear features may be helpful, particularly in distinguishing the prognostically adverse solid pattern from other patterns. Cancer (Cancer Cytopathol) 2015;123:306–17. © 2015 American Cancer Society.
Gonadectomy before puberty increases the number of neurons and glia in the medial prefrontal cortex of female, but not male, rats
Authors: Koss Wendy A. , Lloyd Madeline M. , Sadowski Renee N. , Wise Leslie M. , Juraska Janice M. 
Published: March 2015

ABSTRACTThe human prefrontal cortex, important for executive functions, loses gray matter throughout the adolescent period. In rats, our laboratory demonstrated that a loss of neurons between adolescence and adulthood partially underlies the loss of volume, and this loss is greater in females than males. Here, we examine whether being deprived of gonadal hormones before puberty through adulthood influences the number of neurons in the medial prefrontal cortex (mPFC). Prior to puberty, the testes or ovaries were removed in male and female rats. In adulthood, the number of neurons and glia in the mPFC were quantified using unbiased stereology, and the volume of the frontal white matter was measured. Prepubertal ovariectomy resulted in a higher number of neurons and glia and a larger volume of white matter compared to sham control littermates. Castrated males were not different from sham males on any measure. Thus ovarian hormones secreted after puberty influence the cellular composition of the medial prefrontal cortex. © 2015 Wiley Periodicals, Inc. Dev Psychobiol 57: 305–312, 2015.
Early gait development in human infants: Plasticity and clinical applications
Authors: Teulier Caroline , Lee Do Kyeong , Ulrich Beverly D. 
Published: March 2015

ABSTRACTIn this paper we focus on how a developmental perspective on plasticity in the control of human movement can promote early therapy and improve gait acquisition in infants with developmental disabilities. Current knowledge about stepping development in healthy infants across the first year of life highlights strong plasticity, both in behavioral outcome and in underlying neuro‐muscular activation. These data show that stepping, like other motor skills, emerges from the interaction between infant's maturation and the environment. This view is reinforced by showing that infants with different internal resources (like genetic disorder or neural tube defect) show unique developmental trajectories when supported on a treadmill, yet do respond. Moreover, we will show that their behavior can be improved by context manipulations (mostly sensory stimulation) or practice. Overall, plasticity in the neural, skeletal, and muscle tissues create new opportunities for optimizing early intervention by creatively tapping into the same developmental processes experienced by healthy infants. © 2015 Wiley Periodicals, Inc. Dev Psychobiol 57: 447–458, 2015.
Exploration—exploitation strategy is dependent on early experience
Authors: Humphreys Kathryn L. , Lee Steve S. , Telzer Eva H. , Gabard‐Durnam Laurel J. , Goff Bonnie , Flannery Jessica , Tottenham Nim 
Published: March 2015

ABSTRACTTraditional conceptualizations of early adversity characterize behavioral outcomes as maladaptive. However, conditional adaptation theory proposes that differing behavioral phenotypes following early experience are appropriate for the expected environment (e.g., behaviors likely to result in the best outcome based on environmental expectations). In the present study, youth with (n = 46) and without (n = 91) a history of previous institutionalization completed a laboratory‐based experimental paradigm in which exploration—exploitation strategy was examined, a phenotype relevant to environmental expectations. Previous institutionalization was associated with decreased exploration and increased exploitation. A strategy favoring exploration resulted in greater success in the generous task condition whereas a strategy favoring exploitation produced greater success in the restricted task condition. These results suggest that exploration—exploitation strategy may be influenced by early experience, and the resulting success of strategy choice is context dependent and in line with expectations of the future environment based on early experience. © 2015 Wiley Periodicals, Inc. Dev Psychobiol 57: 313–321, 2015.
New era for chimpanzee research: Broad implications of chimpanzee research decisions
Authors: Bennett Allyson J. 
Published: March 2015

ABSTRACTThe unprecedented recent decision‐making about chimpanzees supported for biomedical science by the US National Institutes of Health attracted international attention and significantly changed many dimensions of chimpanzee research. Many public and media portrayals incorrectly generalized the NIH findings to conclude that chimpanzee research itself was no longer necessary. In fact, the broader question of the necessity and value of the full range of chimpanzee research was never asked, evaluated, or within the NIH's primary charge. The Institute of Medicine evaluative panel found that research with chimpanzees was necessary for some, but not all, purposes. The panel's findings also led the NIH to introduce new standards for the care and management of NIH‐supported chimpanzees and a new mechanism for ethical review of grant proposals involving chimpanzees. The NIH evaluation and decisions could not address all captive chimpanzees and all types of research. However, the process did underscore the need for a more expansive framework for continued ethical review and decision‐making to responsibly address the future of captive chimpanzee management and research. Among the broader considerations are extension of evidence‐informed standards to ensure equitable care and treatment of all chimpanzees; determining the global impact of limited captive populations; and balancing benefit and harm at individual, species, societal, and environmental levels. The breadth and longevity of impact from the current US decisions suggest the need for many voices, disciplines, and stakeholders to address the complex interplay between science, animal welfare, and global health. Summary © 2015Wiley Periodicals, Inc. Dev Psychobiol 57: 279–288, 2015.
Active touch in late‐preterm and early‐term neonates
Authors: Molina Michèle , Sann Coralie , David Morgane , Touré Yacine , Guillois Bernard , Jouen François 
Published: March 2015

ABSTRACTAn infant‐controlled tactile habituation without visual control procedure was used to evaluate the ability of 32 late‐preterm neonates (mean gestational age: 34 weeks) and 32 early‐term neonates (mean gestational age: 38 weeks) to actively explore with hands objects varying in texture (smooth, granular). Holding time and Hand Pressure Frequency (HPF) were recorded. Holding time decreased as habituation progressed in both group of neonates. Holding time increased from habituation trials to test trials only in early‐term neonates. A reaction to novelty was only observed in early‐term neonates. During habituation, HPF remained unchanged in late‐preterm infants whereas HPF decreased in early‐term infants. HPF increased from habituation trials to test trials in early‐term neonates and in late‐preterm infants. However, reaction to novelty was only observed for early‐term infants. The significance of these results is discussed in reference to brain maturation in preterm infants. © 2015 Wiley Periodicals, Inc. Dev Psychobiol 57: 322–335, 2015.
Ear manipulations reveal a critical period for survival and dendritic development at the single‐cell level in Mauthner neurons
Authors: Elliott Karen L. , Houston Douglas W. , DeCook Rhonda , Fritzsch Bernd 
Published: March 2015

ABSTRACTSecond‐order sensory neurons are dependent on afferents from the sense organs during a critical period in development for their survival and differentiation. Past research has mostly focused on whole populations of neurons, hampering progress in understanding the mechanisms underlying these critical phases. To move toward a better understanding of the molecular and cellular basis of afferent‐dependent neuronal development, we developed a new model to study the effects of ear removal on a single identifiable cell in the hindbrain of a frog, the Mauthner cell. Ear extirpation at various stages of Xenopus laevis development defines a critical period of progressively‐reduced dependency of Mauthner cell survival/differentiation on the ear afferents. Furthermore, ear removal results in a progressively decreased reduction in the number of dendritic branches. Conversely, addition of an ear results in an increase in the number of dendritic branches. These results suggest that the duration of innervation and the number of inner ear afferents play a quantitative role in Mauthner cell survival/differentiation, including dendritic development. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 1339–1351, 2015
Spatial pattern of spontaneous retinal waves instructs retinotopic map refinement more than activity frequency
Authors: Xu Hong‐Ping , Burbridge Timothy J. , Chen Ming‐Gang , Ge Xinxin , Zhang Yueyi , Zhou Zhimin Jimmy , Crair Michael C. 
Published: March 2015

ABSTRACTSpontaneous activity during early development is necessary for the formation of precise neural connections, but it remains uncertain whether activity plays an instructive or permissive role in brain wiring. In the visual system, retinal ganglion cell (RGC) projections to the brain form two prominent sensory maps, one reflecting eye of origin and the other retinotopic location. Recent studies provide compelling evidence supporting an instructive role for spontaneous retinal activity in the development of eye‐specific projections, but evidence for a similarly instructive role in the development of retinotopy is more equivocal. Here, we report on experiments in which we knocked down the expression of β2‐containing nicotinic acetylcholine receptors (β2‐nAChRs) specifically in the retina through a Cre‐loxP recombination strategy. Overall levels of spontaneous retinal activity in retina‐specific β2‐nAChR mutant mice (Rx‐β2cKO), examined in vitro and in vivo, were reduced to a degree comparable to that observed in whole animal β2‐nAChR mouse mutants (β2KO). However, many residual spontaneous waves in Rx‐β2cKO mice displayed local propagating features with strong correlations between nearby but not distant RGCs typical of waves observed in wild‐type (WT) but not β2KO mice. We further observed that eye‐specific segregation was disrupted in Rx‐β2cKO mice, but retinotopy was spared in a competition‐dependent manner. These results suggest that propagating patterns of spontaneous retinal waves are essential for normal development of the retinotopic map, even while overall activity levels are significantly reduced, and support an instructive role for spontaneous retinal activity in both eye‐specific segregation and retinotopic refinement. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 621–640, 2015
Transient ipsilateral retinal ganglion cell projections to the brain: Extent, targeting, and disappearance
Authors: Soares Célia A. , Mason Carol A. 
Published: March 2015

ABSTRACTDuring development of the mammalian eye, the first retinal ganglion cells (RGCs) that extend to the brain are located in the dorsocentral (DC) retina. These RGCs extend to either ipsilateral or contralateral targets, but the ipsilateral projections do not survive into postnatal periods. The function and means of disappearance of the transient ipsilateral projection are not known. We have followed the course of this transient early ipsilateral cohort of RGCs, paying attention to how far they extend, whether they enter targets and if so, which ones, and the time course of their disappearance. The DC ipsilateral RGC axons were traced using DiI labeling at E13.5 and E15.5 to compare the proportion of ipsi‐ versus contralateral projections during the first period of growth. In utero electroporation of E12.5 retina with GFP constructs was used to label axons that could be visualized at succeeding time points into postnatal ages. Our results show that the earliest ipsilateral axons grow along the cellular border of the brain, and are segregated from the laterally positioned contralateral axons from the same retinal origin. In agreement with previous reports, although many early RGCs extend ipsilaterally, after E16 their number rapidly declines. Nonetheless, some ipsilateral axons from the DC retina enter the superior colliculus and arborize minimally, but very few enter the dorsal lateral geniculate nucleus and those that do extend only short branches. While the mechanism of selective axonal disappearance remains elusive, these data give further insight into establishment of the visual pathways. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 1385–1401, 2015
Extended Flocking Algorithm for Self‐parameter Tuning
Authors: YAMAUCHI SHO , KAWAMURA HIDENORI , SUZUKI KEIJI 
Published: March 2015

SUMMARYFlocking algorithms for a multiagent system are distributed algorithms that only have simple rules for each agent but generate complex formational movement. These algorithms are known as swarm intelligence and are robust and disaster tolerant for most cases. We consider that flocking algorithms that have these characteristics are the way to generate homeostasis in a system. We expect that by making use of this algorithm the system can tune its self‐parameters and thus maintain a high performance. First, to apply a flocking algorithm to a system, we extended the flocking algorithm to form an arbitrary lattice for further flexibility. We then applied the extended flocking algorithm to position tracking camera system as an example.
Application of Directed Self‐Assembly Lithography to Semiconductor Device Manufacturing Process
Authors: SEINO YURIKO , KATO HIROKAZU , YONEMITSU HIROKI , SATO HIRONOBU , KANNO MASAHIRO , KOBAYASHI KATSUTOSHI , KAWANISHI AYAKO , AZUMA TSUKASA 
Published: March 2015

SUMMARYDirected self‐assembly (DSA) lithography has recently entered the spotlight as one of the most promising new generation lithography candidates, with the potential for fabrication of semiconductor device patterns down to sub‐30 nm. In this report, the latest experimental and simulation results on the contact hole shrinking process using DSA are demonstrated.
Synthesis of 5‐Iodo‐4H‐1,3‐oxazine‐4‐ones Through a [3+3] Reaction of Amides and Propiolates Induced by N‐Iodosuccinimide (NIS) and Cu(CF3SO3)2
Authors: Li Chen , Liu Nan , Qi Qing‐Rong , Chen Yue , He Ling 
Published: March 2015

AbstractA series of novel trisubstituted 5‐iodo‐4H‐1,3‐oxazine‐4‐ones were prepared in moderate to excellent yields induced by NIS and Cu(CF3SO3)2through a [3+3] reaction of amides and propiolates. The reaction proceeds in a one‐pot manner under mild conditions and gives rise to a new strategy for the formation of trisubstituted 5‐iodo‐4H‐1,3‐oxazine‐4‐ones and their derivatives.