bluuebunny/crossref_metadata_2025_split huggingface dataset:
Not‐XOR (NXOR) Logic Gate Realized with Enzyme‐Catalyzed Reactions: Optical and Electrochemical Signal Transduction
Authors: Filipov Yaroslav , Bollella Paolo , Katz Evgeny 
Published: June 2019

AbstractThe studied enzyme‐based biocatalytic system mimics NXOR Boolean logic gate, which is a logical operator that corresponds to equality in Boolean algebra. It gives the functional value true (1) if both functional arguments (input signals) have the same logical value (0,0 or 1,1), and false (0) if they are different (0,1 or 1,0). The output signal producing reaction is catalyzed by pyrroloquinoline quinone‐dependent glucose dehydrogenase (PQQ‐GDH), which is inhibited at acidic and basic pH values. Two other reactions catalyzed by esterase and urease produce acetic acid and ammonium hydroxide, respectively, shifting solution pH from the optimum pH for PQQ‐GDH to acidic and basic values (1,0 and 0,1 input combinations, respectively), thus switching the enzyme activity off (output 0). When the input signals are not applied (0,0 combination) or both applied compensating each other (1,1 combination) the optimum pH is preserved, thus keeping PQQ‐GDH running at the high rate (output 1). The biocatalytic cascade mimicking the NXOR gate was characterized optically and electrochemically. In the electrochemical experiments the PQQ‐GDH enzyme communicated electronically with a conducting electrode support, thus resulting in the electrocatalytic current when signal combinations 0,0 and 1,1 were applied. The logic gate operation, when it was realized electrochemically, was also extended to the biomolecular release controlled by the gate. The release system included two electrodes, one performing the NXOR gate and another one activated for the release upon electrochemically stimulated alginate hydrogel dissolution. The studied system represents a general approach to the biocatalytic realization of the NXOR logic gate, which can be included in different catalytic cascades mimicking operation of concatenated gates in sophisticated logic circuitries.
Evolution of vertebrate spinal cord patterning
Authors: Leung Brigid , Shimeld Sebastian M. 
Published: June 2019

AbstractThe vertebrate spinal cord is organized across three developmental axes, anterior‐posterior (AP), dorsal‐ventral (DV), and medial‐lateral (ML). Patterning of these axes is regulated by canonical intercellular signaling pathways: the AP axis by Wnt, fibroblast growth factor, and retinoic acid (RA), the DV axis by Hedgehog, Tgfβ, and Wnt, and the ML axis where proliferation is controlled by Notch. Developmental time plays an important role in which signal does what and when. Patterning across the three axes is not independent, but linked by interactions between signaling pathway components and their transcriptional targets. Combined this builds a sophisticated organ with many different types of cell in specific AP, DV, and ML positions. Two living lineages share phylum Chordata with vertebrates, amphioxus, and tunicates, while the jawless fish such as lampreys, survive as the most basally divergent vertebrate lineage. Genes and mechanisms shared between lampreys and other vertebrates tell us what predated vertebrates, while those also shared with other chordates tell us what evolved early in chordate evolution. Between these lie vertebrate innovations: genetic and developmental changes linked to evolution of new morphology. These include gene duplications, differences in how signals are received, and new regulatory connections between signaling pathways and their target genes.
The conservation value of cacao agroforestry for bird functional diversity in tropical agricultural landscapes
Authors: Rocha Joedison , Laps Rudi Ricardo , Machado Caio Graco , Campiolo Sofia 
Published: June 2019

AbstractCacao agroforestry have been considered as biodiversity‐friendly farming practices by maintaining habitats for a high diversity of species in tropical landscapes. However, little information is available to evaluate whether this agrosystem can maintain functional diversity, given that agricultural changes can affect the functional components, but not the taxonomic one (e.g., species richness). Thus, considering functional traits improve the understanding of the agricultural impacts on biodiversity. Here, we measured functional diversity (functional richness‐FD, functional evenness‐FEve, and functional divergence‐Rao) and taxonomic diversity (species richness and Simpson index) to evaluate changes of bird diversity in cacao agroforestry in comparison with nearby mature forests (old‐growth forests) in the Brazilian Atlantic Forest. We used data from two landscapes with constraining areas of mature forest (49% Una and 4.8% Ilhéus) and cacao agroforestry cover (6% and 82%, respectively). To remove any bias of species richness and to evaluate assembly processes (functional overdispersion or clustering), all functional indices were adjusted using null models. Our analyses considered the entire community, as well as separately for forest specialists, habitat generalists, and birds that contribute to seed dispersal (frugivores/granivores) or invertebrate removal (insectivores). Our findings showed that small cacao agroforestry in the forested landscape sustains functional diversity (FD and FEve) as diverse as nearby forests when considering the entire community, forest specialist, and habitat generalists. However, we observed declines for frugivores/granivores and insectivores (FD and Rao). These responses of bird communities differed from those observed by taxonomic diversity, suggesting that even species‐rich communities in agroforestry may capture lower functional diversity. Furthermore, communities in both landscapes showed either functional clustering or neutral processes as the main driver of functional assembly. Functional clustering may indicate that local conditions and resources were changed or lost, while neutral assemblies may reveal high functional redundancy at the landscape scale. In Ilhéus, the neutral assembly predominance suggests an effect of functional homogenization between habitats. Thus, the conservation value of cacao agroforestry to harbor species‐rich communities and ecosystem functions relies on smallholder production with reduced farm management in a forested landscape. Finally, we emphasize that seed dispersers and insectivores should be the priority conservation targets in cacao systems.
Modelling mitigation measures for smolt migration at dammed river sections
Authors: Szabo‐Meszaros Marcell , Forseth Torbjørn , Baktoft Henrik , Fjeldstad Hans‐Petter , Silva Ana T. , Gjelland Karl Øystein , Økland Finn , Uglem Ingebrigt , Alfredsen Knut 
Published: June 2019

AbstractThere is no generic solution to establish safe passage of downstream‐migrating fish passed hydropower facilities, and mitigation measures are species and site specific. Development of solutions is thus often based on “trial and error,” and modelling‐based approaches may significantly reduce cost and time to arrive at successful mitigation. Here, we explore such an approach by combining data on fish migration and hydraulic modelling. First, we performed a positional telemetry study at a dammed section of a Norwegian river, where 100 Atlantic salmon smolts were tagged to track their downstream movement at the vicinity of a hydropower intake channel and bypass gates. An explanatory model was developed to explore mechanisms of migration route, into the intake towards the turbines or through the bypass gates. Next, flow conditions during the smolt run was numerically modelled to explore the physical environment of the tracked smolts. The joint results from the two approaches supported the general assumption that downstream migration is strongly influenced by flow patterns and showed that fish entering the study site closer to the riverbank where the intake channel is located were more likely to enter the intake due to the strong currents towards the intake. Finally, a suite of measures to guide salmon smolts past the hydropower intake were proposed based on the findings and local conditions and tested by hydraulic modelling. We found that most of the measures that were likely candidates for field trials would most likely fail at improving safe passage, and only a rack‐type guiding boom was promising. The presented combination of telemetry migration data and hydraulic modelling illustrates the value of evaluation of mitigation measures prior to implementation.
Hydrophobic deep eutectic solvent‐based dispersive liquid–liquid microextraction for the simultaneous enantiomeric analysis of five β‐agonists in the environmental samples
Authors: Liu Yongjing , Xu Wen , Zhang Hua , Xu Wei 
Published: June 2019

AbstractIn this study, a simple and effective method was developed for the enantiomeric analysis of five β‐agonists (terbutaline, clorprenaline, tulobuterol, clenbuterol, and salbutamol) in water samples using deep eutectic solvent (DES) based dispersive liquid–liquid microextraction and chiral LC‐MS. In such a framework, different kinds of hydrophobic DESs were tailored to examine their extraction ability for five β‐agonists from aqueous sample. After an initial screening, the primary factors affecting the extraction recovery of DES based dispersive liquid–liquid microextraction, such as hydrogen‐bond acceptor/hydrogen‐bond donor ratio, DES volume, type and volume of disperser solvent and so on, were investigated and optimized. Finally, the established method was validated and found to be linear, precise, and accurate. The method was successfully applied to analyze the five β‐agonists in water samples, which will help better understand the behavior of individual enantiomer and make accurate risk assessment on the ecosystem.
Bioaccumulation in Functionally Different Species: Ongoing Input of PCBs with Sediment Deposition to Activated Carbon Remediated Bed Sediments
Authors: Gidley Philip T. , Kennedy Alan J. , Lotufo Guilherme R. , Wooley Allyson H. , Melby Nicolas L. , Ghosh Upal , Burgess Robert M. , Mayer Philipp , Fernandez Loretta A. , Schmidt Stine N. , Wang Alice P. , Bridges Todd S. , Ruiz Carlos E. 
Published: June 2019

Abstract
Activated carbon-amended bed sediments reduced total polychlorinated biphenyl (PCB) accumulation in 3 functionally different marine species, sandworms (Alitta virens), hard clams (Mercenaria mercenaria), and sheepshead minnows (Cyprinodon variegatus), during both clean and contaminated ongoing sediment inputs. Mesocosm experiments were conducted for 90 d to evaluate native, field-aged bed sediment PCBs, and ongoing input PCBs added 3 times a week. Simulated in situ remediation applied an activated carbon dose equal to the native organic carbon content that was premixed into the bed sediment for 1 mo. The highest bioaccumulation of native PCBs was in worms that remained in and directly ingested the sediment, whereas the highest bioaccumulation of the input PCBs was in fish that were exposed to the water column. When periodic PCB-contaminated sediment inputs were introduced to the water column, the activated carbon remedy had minimal effect on the input PCBs, whereas the native bed PCBs still dominated bioaccumulation in the control (no activated carbon). Therefore, remediation of only the local bedded sediment in environmental systems with ongoing contaminant inputs may have lower efficacy for fish and other pelagic and epibenthic organisms. While ongoing inputs continue to obscure remedial outcomes at contaminated sediment sites, the present study showed clear effectiveness of activated carbon amendment remediation on native PCBs despite these inputs but no remediation effectiveness for the input-associated PCBs (at least within the present study duration). Environ Toxicol Chem 2019;38:2326–2336. Published 2019 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
White matter plasticity and maturation in human cognition
Authors: Bells Sonya , Lefebvre Jérémie , Longoni Giulia , Narayanan Sridar , Arnold Douglas L. , Yeh Eleun Ann , Mabbott Donald J. 
Published: June 2019

AbstractWhite matter plasticity likely plays a critical role in supporting cognitive development. However, few studies have used the imaging methods specific to white matter tissue structure or experimental designs sensitive to change in white matter necessary to elucidate these relations. Here we briefly review novel imaging approaches that provide more specific information regarding white matter microstructure. Furthermore, we highlight recent studies that provide greater clarity regarding the relations between changes in white matter and cognition maturation in both healthy children and adolescents and those with white matter insult. Finally, we examine the hypothesis that white matter is linked to cognitive function via its impact on neural synchronization. We test this hypothesis in a population of children and adolescents with recurrent demyelinating syndromes. Specifically, we evaluate group differences in white matter microstructure within the optic radiation; and neural phase synchrony in visual cortex during a visual task between 25 patients and 28 typically developing age‐matched controls. Children and adolescents with demyelinating syndromes show evidence of myelin and axonal compromise and this compromise predicts reduced phase synchrony during a visual task compared to typically developing controls. We investigate one plausible mechanism at play in this relationship using a computational model of gamma generation in early visual cortical areas. Overall, our findings show a fundamental connection between white matter microstructure and neural synchronization that may be critical for cognitive processing. In the future, longitudinal or interventional studies can build upon our knowledge of these exciting relations between white matter, neural communication, and cognition.
Segmental tracheal resection (nine rings) and reconstruction for carcinoma showing thymus‐like differentiation (CASTLE) of the thyroid
Authors: Tran Justin , Zafereo Mark 
Published: June 2019

AbstractBackgroundTumors invading the trachea are rare, and although literature often suggests five tracheal rings as the maximum limit of tracheal resection with primary closure, longer tracheal resections and primary closure are possible in many patients. One such locally invasive tumor with propensity for tracheal invasion is carcinoma showing thymic‐like differentiation (CASTLE) of the thyroid.MethodsA 53‐year‐old woman presents with a 2‐year history of hoarseness, newly diagnosed right vocal cord paralysis, and a thyroid mass with significant tracheal and esophageal muscularis invasion. Pathology suggests CASTLE. Segmental nine‐ring tracheal resection with primary closure is illustrated, demonstrating important tracheal reconstructive techniques.ResultsAt the completion of total thyroidectomy and central compartment dissection (not illustrated), the area of tracheoesophageal tumor involvement is isolated. First, the disease is sharply dissected from the tracheal wall and esophagus, excising 4 cm of esophageal muscularis. Next, a plane is established between the membranous trachea and esophagus. The intact left recurrent laryngeal nerve is released from the left tracheoesophageal groove. Substernal thoracic tracheal attachments are released, and a suprahyoid muscle release is performed. Tracheal rings 1 through 9 are resected en bloc, and circumferential tracheal closure is illustrated, with careful attention to technique of tracheal closure and management of the endotracheal tube. Finally, given the degree of tracheoesophageal resection and indication for postoperative radiation therapy, a pectoralis muscle flap is rotated over the trachea and esophagus.ConclusionTo our knowledge, this is the first video demonstration of a segmental resection and reconstruction of a CASTLE of the thyroid in the peer‐reviewed literature. Unique to this case is the significant length of tracheal resection with primary closure, as well as demonstration of concurrent esophageal muscularis resection. Resection and reconstruction of longer segments of cervical trachea require stepwise surgical technique to safely preserve recurrent laryngeal nerve (s), while releasing the larynx and thoracic trachea to minimize tension on the tracheal closure.
Tax shocks with high and low uncertainty
Authors: Bertolotti Fabio , Marcellino Massimiliano 
Published: June 2019

SummaryWe assess whether the effects of fiscal policy depend on the extent of uncertainty in the economy. Focusing on tax shocks, identified by the narrative series by Romer and Romer (American Economic Review, 2010, 100(3), 763‐801), and various measures of uncertainty, we use a Threshold VAR model to allow for dependence of the effects of the tax shocks on both the level of uncertainty and the sign of the shock. We find that the economy responds more positively to tax cuts during periods of low uncertainty, while, in response to tax increases, the response of main aggregates is more negative in more uncertain times. We argue that controlling for monetary policy in fiscal VARs is important to avoid omitted variable bias. We interpret our empirical evidence in light of existing theoretical contributions.
Facile synthesis of zwitterionic organoaluminum complexes containing formally dianionic homoscorpionate ligands
Authors: Su Wei‐Jia , Hsu Yu‐Lin , Ruan Jian‐Wen , Liang Lan‐Chang 
Published: June 2019

AbstractA series of zwitterionic aluminum complexes of the type AlX[(2‐O‐3,5‐tBu2C6H2)3PZ] (AlX [O3PZ]; X = Cl, Me, Et, and iBu; Z = H, Me) containing C3‐symmetric, formally dianionic, facially tridentate ligands [O3PZ]2− were prepared and structurally characterized. Although serendipitous, these complexes can be readily synthesized by partial protonolysis of AlX3 with equal molar (2‐HO‐3,5‐tBu2C6H2)3P (H3[O3P]) or [(2‐HO‐3,5‐tBu2C6H2)3p.m.e](OTf) ({H3[O3PMe]}OTf) in THF at 25°C or elevated temperatures. Alcoholysis of AlMe[O3PMe] (2) with an excess amount of MeOH in refluxing toluene generates AlOMe[O3PMe] (10). Salt metathesis of AlCl[O3PMe] (6) with nBuM (M = Li, MgCl) and NaOR (R = tBu, Ph) in ethereal solutions affords AlnBu[O3PMe] (9) and AlOR[O3PMe] (R = tBu (11), Ph (12)), respectively. Reactivity of 10, 11, and 12 with respect to catalytic ring‐opening polymerization of ε‐caprolactone is assessed.
Co‐expression analysis provides important module and pathways of human dilated cardiomyopathy
Authors: Xiao Junhui , Li Fang , Yang Qianzhao , Zeng Xue‐Feng , Ke Zun‐Ping 
Published: June 2019

AbstractDilated cardiomyopathy (DCM) is a heart disease that injured greatly to the people wordwide. Systemic co‐expression analysis for this cancer is still limited, although massive clinic experiments and gene profiling analyses had been well performed previously. Here, using the public RNA‐Seq data “GSE116250” and gene annotation of Ensembl database, we built the co‐expression modules for DCM by Weighted Gene Co‐Expression Network Analysis, and investigated the function enrichment and protein‐protein interaction (PPI) network of co‐expression genes of each module by Database for Annotation, Visualization, and Integrated Discovery and Search Tool for the Retrieval of Interacting Genes/Proteins database, respectively. First, 5,000 genes in the 37 samples were screened and 11 co‐expression modules were conducted. The number of genes for each module ranged from 77 to 936, with a mean of 455. Second, interaction relationships of hub‐genes between pairwise modules showed great differences, suggesting relatively high‐scale independence of the modules. Third, functional enrichments of the co‐expression modules exhibited great differences. We found that genes in module 3 were significantly enriched in the pathways of focal adhesion and ubiquitin‐mediated proteolysis. This module was inferred as the key module involved in DCM. In addition, PPI analysis revealed that the genes HSP90AA1, CTNNB1, MAPK1, GART, and PPP2CA owned the largest number of adjacency genes, unveiling that they may function importantly during the occurrence of DCM. Focal adhesion and ubiquitin‐mediated proteolysis play important roles in human DCM.
Morphology of the genital organs of the female red‐rumped agouti (Dasyprocta leporina, Linnaeus, 1758) during estrous cycle phases and in advanced pregnancy
Authors: de Oliveira Gleidson Benevides , de Araújo Júnior Hélio Noberto , dos Santos Sousa Rejane , Bezerra Ferdinando Vinícius Fernandes , dos Santos Amilton Cesar , de Moura Carlos Eduardo Bezerra , Silva Alexandre Rodrigues , de Oliveira Rocha Hugo Alexandre , de Oliveira Moacir Franco 
Published: June 2019

AbstractThe study investigated the gross and microscopic anatomy of the genital organs of 20 agoutis at different stages of the estrous cycle and four in the final trimester of pregnancy. Specimens were euthanized and their reproductive organs were fixed in a 4% paraformaldehyde or 2.5% glutaraldehyde solution and submitted to routine histological techniques for light and scanning electron microscopy. In the ovary, during the proestrus phase, we observed developing follicles and corpus luteum (CL) in regression; during estrus, there were Graafian follicles; during metestrus, there was a hemorrhagic corpus, whereas in diestrus, there was a mature CL. The uterus was partially double because the cervix was cranially septate but caudally, the septum disappeared, forming a single ostium that opened into the vagina. Changes occurred along the estrous cycle in the uterine and vaginal epithelia, that is, an increase in the uterine epithelium height accompanied by an increase of thickness of the vaginal epithelium during the follicular phase and a decrease of thickness of both epithelia during the luteal phase. The endometrial lining was composed of a simple cuboidal epithelium to simple columnar epithelium with basal nuclei. The vaginal mucosa consisted of epithelium that varied from nonkeratinized stratified squamous (luteal phase) to keratinized stratified squamous (follicular phase). The clitoris was external to the vagina. It presented two protruding lateral keratinized spicules and a centralized urethra, with no common parts between the urinary and genital tracts. Anatomical and histological changes were observed mainly in the cervix, vagina and spicules of the clitoris during the EC.
Physiological aging at striatal synapses
Authors: Walsh John P. , Akopian Garnik 
Published: June 2019

AbstractMike Levine's body of work guides thinking on how the basal ganglia process information to create coordinated movements and skill learning throughout the life span and in disease. This special issue is a nod to Mike's career and a well‐deserved gesture by the neuroscience community thanking him for the impact he has made on many people's careers and the field of basal ganglia physiology. This paper reviews how aging impacts basal ganglia processing with a focus on single cell and synaptic physiology. This review begins with the work Mike did with his collaborators Nat Buchwald, Chester Hull and Jay Schneider. These early studies paved the way for subsequent studies on changes in synaptic processing that occur with aging in the basal ganglia. The primary focus of this review is aging at corticostriatal synapses. Corticostriatal synapses show reduced expression of both short‐term and long‐term synaptic potentiation. The roles of age‐related changes in calcium homeostasis, vesicle cycling, dopamine modulation, and NMDA receptor function in aging's effect on synaptic plasticity are discussed. The article ends with a review of mitochondrial aging theory as it applies to age‐induced changes in corticostriatal synaptic function.