bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems Biology Graphical Notation: Process Diagram Level 1
Authors: Le Novere Nicolas , Moodie Stuart , Sorokin Anatoly , Hucka Michael , Schreiber Falk , Demir Emek , Mi Huaiyu , Matsuoka Yukiko , Wegner Katja , Kitano Hiroaki 
Published: July 2019

AbstractStandard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
Embedding machine-readable proteins interactions data in scientific articles for easy access and retrieval
Authors: Tieri Paolo , Termanini Alberto , Fariselli Piero , Franceschi Claudio 
Published: July 2019

AbstractExtraction of protein-protein interactions data from scientific literature remains a hard, time- and resource-consuming task. This task would be greatly simplified by embedding in the source, i.e. research articles, a standardized, synthetic, machine-readable codification for protein-protein interactions data description, to make the identification and the retrieval of such very valuable information easier, faster, and more reliable than now.We shortly discuss how this information can be easily encoded and embedded in research papers with the collaboration of authors and scientific publishers, and propose an online demonstrative tool that shows how to help and allow authors for the easy and fast conversion of such valuable biological data into an embeddable, accessible, computer-readable codification.
Cueing in a perceptual task causes long-lasting interference that generalizes across context to affect only late perceptual learning and is remediated by the passage of time
Authors: Rajan Ramesh 
Published: July 2019

AbstractPerceptual learning, the improvement in sensory discriminations with practise, is also subject to stimulus-specific interference from temporal jitter in a learning session or manipulations applied between or immediately after sessions. We demonstrate a novel form of perceptual interference where even a brief cueing exposure to a complex speech-in-noise task produces a forward interference on subsequent speech-in-noise learning. This potent interference generalizes across cueing context but specifically affects only late learning in the subsequent task, is resistant to the remediating effects of sleep and persists across an overnight delay involving sleep, and can be evoked by a single exposure 1 day before the learning. Learning in the speech-in-noise task is due to generalized improvements in discriminating and extracting signals (speech) from noise and we hypothesize that the forward interference represents interference with improvements in access to higher-level representations in rapid perception of ecologically-familiar complex signals such as speech from background noise.
Facile Synthesis and Versatilities of Polyanthraquinoylamine Nanofibril Bundles with Self Stability and High Carbon Yield
Authors: Li Xin-Gui , Huang Mei-Rong , Li Hu , Moloney Mark G. 
Published: July 2019

AbstractA facile synthesis for nanosized conducting polymers with inherent self-stability and multi-functionalities is a main challenge. Here we simply synthesize intrinsically self-stabilized nanofibril bundles of poly(1-anthraquinoylamine) (PAQ) by a template-free method. The critical polymerization parameters were studied to significantly optimize the synthesis, size, properties, and functionalities of the resulted fine nanofibrils with a diameter of ca. 30 nm and length of ~6 μm. The PAQ obtained with ammonium persulfate possesses higher polymerization yield, purer composition, higher conductivity, better melting behaviour, higher thermostability, lower burning enthalpy, and slower degradation than that with other oxidants. Furthermore, the polymer nanofibrils exhibit high self-stability, powerful redispersibility, high purity, and clean surface because of a complete avoidance of the contamination from external stabilizer. The PAQ exhibits widely controllable conductivity moving across ten orders of magnitudes from 10^-9^ to 50 S/cm, photoluminescence, lead-ion adsorbability, very high thermostability in air and extremely high char yield in nitrogen at 1000˚C. These materials would be useful as advanced materials including photoluminescent materials, highly cost-effective carbon precursors, sorbents of toxic metal ions, and cost-efficient conductive nanocomposite with low percolation threshold.
Detection of genetic diversity among Indian strains of Xanthomonas campestris pv. mangiferaeindicae using PCR-RAPD
Authors: Kishun Ram , Gupta Vijai Kumar 
Published: July 2019

AbstractThe randomly amplified polymorphic DNA (RAPD) technique was used to investigate the genetic diversity in 6 strains of Xanthomonas campestris pv. mangiferaeindicae (Xcmi), the causal pathogen of mango bacterial canker disease (MBCD). The RAPD analysis was also intended to identify molecular markers, specific to the species to develop PCR-based markers for detection of Xcmi in mango field and planting materials. Twenty RAPD primers (CP 1-CP 20) were evaluated to establish molecular characters and genetic variability in the genome of Xcmi. Among these, only 4 were found efficient for development of reproducible banding pattern. It has been observed that the largest and smallest amplified RAPD products were of 2.036 and 0.201 kbp. A total of 136 bands were scored against 6 strains of Xcmi. There was 7.66 per cent polymorphism in individual isolates which indicates significant polymorphism among the evaluated strains, with mean difference of 0.33 (Xcmi 2 vs. Xcmi 8) and 0.29 (Xcmi 10 vs. Xcmi 12). However, the single linkage euclidean distances were statistically significant (P>0.05), i.e., 0.58. The markers CP 5, 10, 16 and 19 were amplified in all the strains with polymorphic alleles, which indicates that these markers could be used for rapid detection of genetic variability in Xcmi strains.
Evidence of salt secretion at the stem of Melaleuca cuticularis Labill.
Authors: Twomey Amanda , Naidu Bodapati , Fukai Shu 
Published: July 2019

AbstractIt has been observed that Melaleuca cuticularis Labill. has the ability to secrete salt solution to the surface of its stem. No literature has been found to illustrate other species' capacity to secrete salts at the stem and with what little literature there is on M. cuticularis under saline conditions ^1, 2^, there was no evidence documented by those authors to have witnessed salt secreting at the stem. Most recorded observations of salt secretion by plants has usually been on leaf salt secretion through specialized glands or bladders often in mangroves, salt bushes and grass species, among others ^3-8^. This observation is the first known record of a plant species capable of secreting salts mostly at the stem.
Striatal Enriched Protein Tyrosine Phosphatase mediates Ethanol inhibition of NMDA Receptor Activity
Authors: Wu Peter , Freund Ronald , Procotor William , Goebel-Goody Susan , Browning Michael , Lombroso Paul 
Published: July 2019

AbstractWe demonstrated previously that ethanol inhibition of NMDA receptor (NMDAR) function is accompanied by a reduction in tyrosine phosphorylation of Tyr^1472^ on the NR2B subunit, and this action of ethanol is attenuated by a broad spectrum tyrosine phosphatase inhibitor. Here we examined whether this ethanol inhibition of NMDAR activity was due to the actions of STriatal Enriched protein tyrosine Phosphatase (STEP) which has been shown to regulate NMDAR internalization by dephosphorylating Tyr^1472^ on the NR2B subunit. Using whole-cell recordings of pharmacologically isolated NMDAR-mediated excitatory post-synaptic currents (NMDA EPSCs) from hippocampal CA1 pyramidal neurons, we show that intracellular infusion of a substrate-trapping inactive form of STEP (TAT-STEP C/S) significantly blocks ethanol inhibition of NMDA EPSCs. Ethanol does not inhibit NMDA EPSCs or LTP in neurons from STEP knockout mice, but its effect is restored after acute intracellular delivery of wild type TAT-STEP, suggesting that STEP mediates ethanol inhibition of NMDAR function.
Electrocortical activity can predict pianist's proficiency
Authors: Mills Malcolm 
Published: July 2019

AbstractElectro-cortical changes associated with learning and performing were investigated in eighteen pianists over three closely-spaced performances of sight-reading a novel music score. Six musical criteria were assessed: right hand errors, left hand errors, rhythmic errors, speed accuracy, fluency, and musical expression. These skills correlated specifically to electrical rhythms of 8.5-10.5 cycles per second near the sensory-motor cortex and the supplementary area. The correlations progressively reduced with each performance as it improved and learning occurred. Further, these electro-cortical potentials can predict the quality of performer and performance at the same or later occasion based on the same or different skill. Understanding this physiology will help to improve the rate, and success, of learning or detect loss of performance-related attention long before sleep onset measures indicate the persistence of loss of vehicle control from exhaustion or drug action. This knowledge can be used in electromechanical coupling allowing direct brain control of devices.
Relation Ontology II
Authors: Cocos Cristian 
Published: July 2019

AbstractConceived as follow-up to recent efforts destined to supply .owl ontologies with relational tools of greater complexity, the present article focuses on four main paths, all of them consisting in providing biomedical ontologies with formal means to express (1) deviations from normality, (2) topological connectedness, (3) inherence and (4) causality and function.
Carbon Finance Schemes - Incentives for Forest and Agroforestry Systems
Authors: Seeberg-Elverfeldt Christina , Schwarze Stefan , Zeller Manfred 
Published: July 2019

AbstractDeforestation contributes a quarter of all anthropogenic greenhouse gas emissions. On the island of Sulawesi in the vicinity of the Lore Lindu National Park, smallholders contribute to deforestation processes with their agricultural practices, specifically with cocoa plantations. This study assesses the impact of carbon sequestration payments for forest management systems on the prevailing land use systems. Additionally, the level of incentives which induces farmers to adopt sustainable agroforestry practices is determined. We show that low carbon credit prices have a small impact on household income. However, with rising prices, the poorest households can realise an increase of 18 percent. The majority of the households have an incentive to adopt the more sustainable shade intensive agroforestry system and stop deforestation activities with prices observed on markets. The cost-efficiency of avoided deforestation, compared to biofuels, is demonstrated. The study shows that forestry activities provide an important opportunity as climate mitigation strategies.
A functional dissociation of conflict processing within anterior cingulate cortex
Authors: Kim Chobok , Kroger James , Kim Jeounghoon 
Published: July 2019

AbstractGoal-directed behavior requires cognitive control to regulate neural processing when conflict is encountered. The dorsal anterior cingulate cortex (dACC) has been associated with detecting response conflict during conflict tasks. However, recent findings have indicated not only that two distinct subregions of dACC are involved in conflict processing but also that the conflict occurs at both perceptual and response levels. We clarified a functional dissociation of the caudal dACC (cdACC) and the rostral dACC (rdACC) in responding to different sources of conflict. The cdACC was selectively engaged in perceptual conflict whereas the rdACC was more active in response conflict. Further, the dorsolateral prefrontal cortex (DLPFC) was coactivated not with cdACC but with rdACC. We suggest that cdACC plays an important role in regulative processing of perceptual conflict whereas rdACC is involved in detecting response conflict.
Substrate entering and product leaving trajectories predict an engulfing dynamic for the major conformational change of the &946;-lactam acylase
Authors: Huang Xi , Yin Jun , Jiang Wei-Hong , Deng Zixin , Zhao Guo-Ping 
Published: July 2019

AbstractIt is still a major challenge to acquire insight into the conformational changes between the ground state and the transition state of an enzyme, although conformational fluctuation within interconverting conformers has been widely investigated (1-4). Here, we utilize different enzymatic reactions in b-lactam acylase to figure out the substrate/product trajectories in the enzyme, thereby probing the overall conformational changes in transition state. First, an auto-proteolytic intermediate of cephalosporin acylase (EC 3.5.1.11) with partial spacer segment was identified. As a final proteolytic step, the deletion of this spacer segment was revealed to be a first-order reaction, suggesting an intramolecular Ntn mechanism for the auto-proteolysis. Accordingly, the different proteolytic sites in the acylase precursor indicate a substrate entering pathway along the spacer peptide. Second, bromoacyl-7ACA can interact with penicillin G acylase (EC 3.5.1.11) in two distinguish aspects, to be hydrolyzed as a substrate analogue and to affinity alkylate the conserved Trpb4 as a product analogue. The kinetic correlation between these two reactions suggests a channel opening from Serb1 to Trpb4, responsible for the main product leaving. These two reaction trajectories relaying at the active centre, together with the crystal structures (5-10), predict an engulfing dynamic involving pocket constriction and channel opening.
Leaping and Accelerometry: A Theoretical Approach
Authors: Sellers William 
Published: July 2019

AbstractAccelerometry has always been a popular method of monitoring locomotor activity but its use is becoming more widespread due to the easy availability of low cost, low power sensors. However one of the major problems with interpreting accelerometer data is that rotation of the sensor alters the output and obtaining independent orientation information is currently difficult. For the specific case of leaping locomotion full orientation information is unecessary as long as an independent measure of height change is available such as can be obtained from a sensitive pressure sensor. Therefore a 4 channel logging system recording 3 accelerometry axes combined with a channel measuring pressure could be used to accurately assess leaping locomotion. This approach should also work for any locomotion where acceleration is limited to the vertical plane but in practice it may be restricted by the sensitivity and acquisition characteristics of the pressure measurement system. Ultimately it should be a useful addition to the range of measurements available for remote locomotor monitoring particularly for leaping species such as lemurs and other non-human primates.
Items on the Left Are Better Remembered
Authors: Della Sala Sergio , Darling Stephen , Logie Robert 
Published: July 2019

AbstractWe report evidence of a new phenomenon from three experiments: a leftward bias when people try to remember visually presented information. Experiments 1 and 2 showed lateral leftward biases in memory in a large (total N&gt;60000) sample of participants, with data collected via the British Broadcasting Corporation (BBC) web site. Experiment 3 replicated the findings of a leftwards bias in short-term memory with a more intensive data collection.
Is Sustainable Development of Deserts Feasible?
Authors: Polyakov Yuriy , Eimicke William , Musaev Ibrahim , Polyakov Sergey 
Published: July 2019

AbstractHot deserts that presently cover about one-fifth of the land area of our planet are rapidly devouring more and more arable lands mostly due to anthropogenic causes. We propose an interdisciplinary approach to revitalizing and commercializing hot deserts, which is based on systems thinking and Russian and NASA space technology experience in designing life-support systems for long-duration flights. We formulate ten principles for the design of sustainable life support systems in deserts, which can make the development of the deserts feasible. It is discussed how the principles can be employed to design and operate desert’s eco-industrial parks with greenhouses in which the transpired and evaporated moisture is collected and condensed. The potential benefits of setting up the eco-industrial parks in deserts include the slowdown and eventual reversal of the desertification trend, the migration of many industrial production facilities from mild-climate regions to deserts, the increased availability of potable water and food in deserts, the development of poor African countries, and the emergence of new investment markets.
Energy or chow, that’s a question: “two-bottle” may be more suitable than “one-bottle” in modeling nutritional obesity
Authors: Zhang JG , Sun XW , Gao P , Xie L , Liu WQ , Xiao HT , Ai H 
Published: July 2019

Abstract
*Objective:*
To model nutritional obesity in rats with two-bottle-feeding method according to human eating feature. *Design:* Animals were grouped into control and model randomly according to their initial body weight. The control rats fed with standard chow singly and the model rats fed with the standard chow and a high fat (HF) diet simultaneously for 20 weeks. Lee’s index of control was used as the reference of obesity identification. The inducing effect of this method and animals’ eating features were studied. *Subjects:* 142 weaned male Sprague-Dawley (SD) rats (body weight: 43.95±4.0g). *Measurements:* Body weight (BW), body length (BL), and food accumulation were measured weekly, and Lee’s index was calculated for obesity evaluation.

*Results:*
This modeling process based on human eating feature facilitated the production and evaluation to HF diet, and showed an effective inducing effect. At the end of 14th week, about 51% rats (by Lee’s index) or 70.6% rats (by body weight) developed obesity and all developed fatty liver. Animals’ preference to HF diet was proved to be varied greatly. Its influence on obesity and obesity resistance (OR) rats can be balanced by two-bottle-feeding method, p=0.42. Obesity rats ate more HF diet than OR rats, but they ate same amount of chow. On the other hand, Lee’s index of the animals was not well related to energy intake, r2=0.48. Thus, animal’s preference to HF diet and their own metabolic feature were potential influence factors, except for these factors, animals’ food intake and energy efficiency are key factors deciding obesity.

*Conclusions:*
Two-bottle-feeding method is an effective way to modeling nutritional obesity as well as fatty liver in rats. Food-intake and energy efficiency are inner key factors deciding obesity or obesity resistance.
Weight change and quality of life in a community-based population
Authors: Verkleij Saskia , Adriaanse Marcel , Wendel-Vos Gerrie , Schuit Albertine 
Published: July 2019

Abstract
*Objectives:*
This study investigates the longitudinal association between 5-year weight change and quality of life (QoL) in Dutch men and women.*Design:* A prospective cohort study (1998, 2000, 2003) in a population based sample. Subjects: 2,414 men and women from the Maastricht region of the Netherlands.*Measurements:* QoL outcomes were measured by the RAND-36 (eight subscales and two overall composite scores, physical and mental health (PCS and MCS)). Weight was measured on a scale. Weight change was calculated as change in weight between 1998 and 2003. In addition, 5-year weight change was also categorized in three groups: weight losers, weight maintainers, and weight gainers. All analyses were stratified for gender.

*Results:*
A total of 598 men (50%) and 646 women (54%) maintained their weight, 177 men (15%) and 163 women (14%) lost more than 2.5 kg, and 410 men (35%) and 379 women (32%) gained more than 2.5 kg. Associations between 5-year weight change and QoL were found for MCS ([beta] = 0.13, 95% CI: 0.02∣0.24) in women, and PCS ([beta] = -0.09, 95% CI: -0.17∣-0.00; [beta] = -0.10, 95% CI: -0.19∣-0.01) in men and women respectively. Moreover, associations between weight change and QoL were most pronounced for women of normal weight and obese men. Furthermore, in both genders, weight gainers showed a greater reduction on all physical components of QoL compared with weight maintainers. However, after 5-years weight gainers and weight losers did not significantly differ from weight maintainers in the mean change of MCS and PCS.*Conclusion:* Weight gain was inversely associated with the physical domains of QoL in women and obese men. Conversely, in women, weight gain was positively associated with the mental domains of QoL. No differences between weight losers and weight gainers were found in mean change of QoL compared with weight maintainers.
Fibromyalgia: A Unifying Neuroendocrinologic Model for Understanding Its Pathophysiology
Authors: Dorsher Peter 
Published: July 2019

AbstractFibromyalgia is believed to affect at least 2% of the population. Despite advances in the scientific understanding of the derangements of central and peripheral pain processing mechanisms in fibromyalgia, no current models of its pathophysiology account for the other clinical conditions associated with it such as fatigue, migraine headache, irritable bowel syndrome, and sleep cycle abnormalities. A neuroendocrinologic model of fibromyalgia is presented that accommodates both its known central and peripheral pain mechanisms as well as the myriad of hormonal, visceral, and psychological symptoms associated with that disorder. This model also provides a unifying pathophysiologic basis of fibromyalgia and chronic muscle pain, and offers the potential for developing new avenues of research and treatment for these enigmatic, frequently disabling medical conditions.