bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connectivity Problems on Heterogeneous Graphs
Authors: Wu Jimmy , Khodaverdian Alex , Weitz Benjamin , Yosef Nir 
Published: April 2018

AbstractBackgroundNetwork connectivity problems are abundant in computational biology research, where graphs are used to represent a range of phenomena: from physical interactions between molecules to more abstract relationships such as gene co-expression. One common challenge in studying biological networks is the need to extract meaningful, small subgraphs out of large databases of potential interactions. A useful abstraction for this task turned out to be the Steiner network problems: given a reference “database” graph, find a parsimonious subgraph that satisfies a given set of connectivity demands. While this formulation proved useful in a number of instances, the next challenge is to account for the fact that the reference graph may not be static. This can happen for instance, when studying protein measurements in single cells or at different time points, whereby different subsets of conditions can have different protein milieu.Results and DiscussionWe introduce the condition Steiner network problem in which we concomitantly consider a set of distinct biological conditions. Each condition is associated with a set of connectivity demands, as well as a set of edges that are assumed to be present in that condition. The goal of this problem is to find a minimal subgraph that satisfies all the demands through paths that are present in the respective condition. We show that introducing multiple conditions as an additional factor makes this problem much harder to approximate. Specifically, we prove that for C conditions, this new problem is NP-hard to approximate to a factor of C – ϵ, for every C ≥ 2 and ϵ > 0, and that this bound is tight. Moving beyond the worst case, we explore a special set of instances where the reference graph grows monotonically between conditions, and show that this problem admits substantially improved approximation algorithms. We also developed an integer linear programming solver for the general problem and demonstrate its ability to reach optimality with instances from the human protein interaction network.ConclusionOur results demonstrate that in contrast to most connectivity problems studied in computational biology, accounting for multiplicity of biological conditions adds considerable complexity, which we propose to address with a new solver. Importantly, our results extend to several network connectivity problems that are commonly used in computational biology, such as Prize-Collecting Steiner Tree, and provide insight into the theoretical guarantees for their applications in a multiple condition setting.AvailabilityOur solver for the general condition Steiner network problem is available at https://github.com/YosefLab/condition_connectivity_problems
Mathematical and ecological traits of above and belowground biomass production of beech (Fagus silvatica L.) trees growing in pure even-aged stands in north-east France
Authors: Goff Noël Le , Ottorini Jean-Marc 
Published: April 2018

AbstractTree biomass and biomass increment equations were specially developed in 1996–1997 to study the ecophysiological functioning of an experimental European beech stand, aged about 30 year-old, in the Hesse forest (NE France). In order to extend such a study to beech stands of different age classes, it was necessary to build biomass and biomass increment equations that could be used for any age; we call them generalized biomass equations.To build such generalized equations, trees were sampled in different forest plots covering the whole age range. Moreover, in each plot, several trees were chosen to represent the different crown classes (from dominant to suppressed). Sampled trees were felled down and the root system excavated for a sub-sample of trees, for biomass analysis by separating the main compartments of the above and belowground tree parts. When it was not possible to measure the total biomass of a given tree compartment (large trees), wood samples were taken in the concerned compartment. Moreover, equations were built to estimate the biomass of the missing parts of the root system and branch compartments that were likely to have suffered losses during root excavation and tree felling, respectively. Multivariate linear and non-linear models including possible random effects were tested to represent the biomass and biomass increment variations of each tree compartment and of their aggregation in the above and belowground parts of the tree.Compatible biomass and biomass increment equations for the different tree compartments and their combination in above and belowground tree parts were developed and fitted, allowing the analysis of the variations of the biomass distribution and allocation with tree age. Stem growth efficiency was also calculated and appeared dependent on tree age and tree social status.The biomass and biomass increment equations established for beech in this study allow the estimation of the biomass and carbon stocks and fluxes (NPP) for the even-aged beech stands of the Hesse forest, whatever the age of the stand; they could also be used to analyze the effects of different silvicultural treatments on the biomass and carbon stocks and fluxes of beech stands, using the available stand growth and yield models developed for beech in France.
Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers
Authors: Bergey Christina M. , Lopez Marie , Harrison Genelle F. , Patin Etienne , Cohen Jacob , Quintana-Murci Lluis , Barreiro Luis B. , Perry George H. 
Published: April 2018

AbstractDifferent human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The pygmy phenotype (small adult body size), a characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent vs. population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes (exomes) of two pairs of populations, Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda, and Andamanese rainforest hunter-gatherers (Jarawa and Onge) and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the Batwa and Andamanese rainforest hunter-gatherers across the set of genes with annotated ‘growth factor binding’ functions (p< 0.001). Unexpectedly, for the rainforest groups we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g. ‘cardiac muscle tissue development’;p= 0.001). We hypothesize that the growth hormone sub-responsiveness likely underlying the pygmy phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations we did not observe similar patterns of positive selection on sets of genes associated with either growth or cardiac development, indicating that our results most likely reflect a history of convergent adaptation to the similar ecology of rainforest hunter-gatherers rather than a more common or general evolutionary pattern for human populations.
Predicting influenza H3N2 vaccine efficacy from evolution of the dominant epitope
Authors: Bonomo Melia E. , Deem Michael W. 
Published: April 2018

AbstractWe predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to 20% observed. This tool assists candidate vaccine selection by predicting human protection against circulating strains.40-word summary of main pointOur pepitope model predicts the ability of the influenza vaccine to reduce the A(H3N2) disease attack rate, with an r^2=0.77. This fast, sequence-based method compliments strain-to-strain antigenic comparisons from ferret models and provides antigenic comparisons for all circulating sequences.
Monitoring Anti-Pythium insidiosum IgG Antibodies and (1->3)-β-D-Glucan in Vascular Pythiosis
Authors: Worasilchai Navaporn , Permpalung Nitipong , Chongsathidkiet Pakawat , Leelahavanichkul Asada , Mendoza Alberto Leonel , Palaga Tanapat , Reantragoon Rangsima , Finkelman Malcolm , Sutcharitchan Pranee , Chindamporn Ariya 
Published: April 2018

AbstractBackgroundDespite aggressive treatment, vascular pythiosis has a mortality rate of 40%. This is due to the delay in diagnosis and lack of effective monitoring tools. To overcome this drawback, serum beta-D-glucan (BG) and P. insidiosum specific antibody (Pi-Ab) were examined as potential monitoring markers in vascular pythiosis.MethodsA prospective cohort study of vascular pythiosis patients was carried on during January 2010-July 2016. Clinical information and blood samples were collected and evaluated by the BG and Pi-Ab assays. Linear mixed effect models were used to compare BG and Pi-Ab levels. The in vitro susceptibility test was performed in all P. insidiosum isolates from culture positive cases.ResultsA total of 50 patients were enrolled; 45 survived and 5 died during follow-up. The survivors had a significantly shorter time to medical care (p<0.0001) and a significantly shorter waiting time to the first surgery (p<0.0001). There were no differences in BG levels among the groups at diagnosis (p=0.17); however, BG levels among survivors were significantly lower than the deceased group at 0.5 months (p<0.0001) and became undetectable after 3 months. Survivors were able to maintain ELISA value (EV) of Pi-Ab above 8, whereas EV among deceased patients was less than 4. In vitro susceptibility results revealed no synergistic effects between itraconazole and terbinafine.ConclusionsThis study showed that BG and Pi-Ab were potentially valuable markers to monitor the disease after treatment initiation. An unchanged BG level at 2 weeks after surgery should prompt an evaluation for residual disease.
An important role for periplasmic storage inPseudomonas aeruginosacopper homeostasis revealed by a combined experimental and computational modeling study
Authors: Parmar Jignesh H. , Quintana Julia , Ramírez David , Laubenbacher Reinhard , Argüello José M. , Mendes Pedro 
Published: April 2018

SummaryBiological systems require precise copper homeostasis enabling metallation of cuproproteins while preventing metal toxicity. In bacteria, sensing, transport and storage molecules act in coordination to fulfill these roles. However, there is not yet a kinetic schema explaining the system integration. Here, we report a model emerging from experimental and computational approaches that describes the dynamics of copper distribution inPseudomonas aeruginosa. Based on copper uptake experiments, a minimal kinetic model describes well the copper distribution in the wild type bacteria but is unable to explain the behavior of the mutant strain lacking CopA1, a key Cu+efflux ATPase. The model was expanded through an iterative hypothesis-driven approach, arriving to a mechanism that considers the induction of compartmental pools and the parallel function of CopA and Cus efflux systems. Model simulations support the presence of a periplasmic copper storage with a crucial role under dyshomeostasis conditions inP. aeruginosa. Importantly, the model predicts not only the interplay of periplasmic and cytoplasmic pools but also the existence of a threshold in the concentration of external copper beyond which cells lose their ability to control copper levels.
Nicotinic modulation of hierarchal inhibitory control over prefrontal cortex resting state dynamics: modeling of genetic modification and schizophreniarelated pathology
Authors: Rooy Marie , Koukouli Fani , Maskos Uwe , Gutkin Boris 
Published: April 2018

AbstractNicotinic acetylcholine receptors (nAChRs) strongly modulate the cholinergic drive to a hierarchy of inhibitory neurons in the superficial layers of the PFC, critical to cognitive processes. Genetic deletion of various types of nAChRs, located on specific interneurons, impacts the properties of ultra-slow transitions between high and low activity states (H-states and L-states, respectively), recorded in mice during quiet wakefulness. In addition, recent data indicate that a genetic mutation of the α5 nAChR subunit located on vasoactive intestinal polypeptide (VIP) inhibitory neurons, the rs16969968 single nucleotide polymorphism (α5 SNP), appears to be responsible for “hypofrontality” observed in schizophrenia. Chronic nicotine application to α5 SNP mice restores neural activity to control levels. Using firing rate models of hierarchically organized neural populations, we showed that the change of activity patterns recorded in the genetically modified mice can be explained by a change of activity state stability, differentially modulated by cholinergic inputs to parvalbumin (PV), somatostatin (SOM) or VIP inhibitory populations. A change in amplitude, but not duration of H-states fully account for the lowered pyramidal (PYR) firing rates recorded in α5 SNP mice. We demonstrate that desensitization and upregulation of β2 nAChRs located on SOM interneurons, but not activation of α5 nAChRs located on VIP interneurons, by chronic nicotine application could account for activity normalization recorded in α5 SNP mice. The model implies that subsequent nicotine withdrawal should lead to PYR activity depression more severe than the original hypofrontality caused by SNP mutation.
Why talented athletes drop out from sport? The Portuguese and Czech case
Authors: Silva Dias Teresa , Novotná Katerina , Oliveira Helder Zimmermann , Azevedo Carlos , Corte-Real Nuno , Slepička Pavel , Fonseca António Manuel 
Published: April 2018

PurposeThe purpose of this paper is to perceive the perspective of Portuguese and Czech’ talented athletes regarding: the main reasons pointed to drop out of sport, putting into analysis motivational factors; the conciliation of School and Sport, and how the organization of schools and sports contexts are articulated in relation to the training and promotion of students, athletes and citizens; and the contributions (positive/negative) of sports to daily life and society.Design/methodology/approachThis study uses a qualitative approach to interview eight talented athletes from different sports that had to drop out the practice of sport and explores their narratives regarding experiences and the relational dynamics between sports contexts and schools.FindingsAthletes identify factors that led to drop out: the coach profile or the methodology and dynamics of practicing/training; time consuming; and the impossibility of reconciling sports with school/job. Athletes can identify the sport’s culture, self-development and health being as positive contributions of sports, whereas injuries were referred as the main negative factor of sport. As proposal of changes, athletes referred to the need of a more professional organization of the sport contexts and to more proximity between school policies and sport policies allowing conciliating both.Research limitations/implicationsOne limitation that could be pointed to this research is the difference between the Czech and Portuguese socio-cultural and political situation, not only in the concept and organization of sports activities (since scholar years) but also in the general society. This difference could have more visibility when interpreting the data that led to this fact referred above.Practical implicationsIt is recommended a more proximity relationship between researchers and the contexts of practice (sport contexts) being that it is important that these contexts should have feedback from the investigations carried out. Only in this way coaches, federations and confederations can be aware of the motivational factors that lead to talented athletes drop out, and make a greater investment in initial formation of the coaches and propose policies that try to establish partnerships with schools or professional contexts which could help the management of athletes’ times outside of sport.Originality/valueDeparting from the athletes’ feelings, concerns and motivations related to sport and the reasons that led to their drop out, we argue for the definition of public policies, in both countries, that promote non-discrimination of young people who wish to maintain a path linked to sports in articulation with other areas of their lives.
A novel method to solve sustainable economic power loading dispatch problem
Authors: Li Lingling , Yang Yanfang , Tseng Ming-Lang , Wang Ching-Hsin , Lim Ming K. 
Published: April 2018

Purpose
The purpose of this paper is to deal with the economic requirements of power system loading dispatch and reduce the fuel cost of generation units. In order to optimize the scheduling of power load, an improved chicken swarm optimization (ICSO) is proposed to be adopted, for solving economic load dispatch (ELD) problem.

Design/methodology/approach
The ICSO increased the self-foraging factor to the chicks whose activities were the highest. And the evolutionary operations of chicks capturing the rooster food were increased. Therefore, these helped the ICSO to jump out of the local extreme traps and obtain the global optimal solution. In this study, the generation capacity of the generation unit is regarded as a variable, and the fuel cost is regarded as the objective function. The particle swarm optimization (PSO), chicken swarm optimization (CSO), and ICSO were used to optimize the fuel cost of three different test systems.

Findings
The result showed that the convergence speed, global search ability, and total fuel cost of the ICSO were better than those of PSO and CSO under different test systems. The non-linearity of the input and output of the generating unit satisfied the equality constraints; the average ratio of the optimal solution obtained by PSO, CSO, and ICSO was 1:0.999994:0.999988. The result also presented the equality and inequality constraints; the average ratio of the optimal solution was 1:0.997200:0.996033. The third test system took the non-linearity of the input and output of the generating unit that satisfied both equality and inequality constraints; the average ratio was 1:0.995968:0.993564.

Practical implications
This study realizes the whole fuel cost minimization in which various types of intelligent algorithms have been applied to the field of load economic scheduling. With the continuous evolution of intelligent algorithms, they save a lot of fuel cost for the ELD problem.

Originality/value
The ICSO is applied to solve the ELD problem. The quality of the optimal solution and the convergence speed of ICSO are better than that of CSO and PSO. Compared with PSO and CSO, ICSO can dispatch the generator more reasonably, thus saving the fuel cost. This will help the power sector to achieve greater economic benefits. Hence, the ICSO has good performance and significant effectiveness in solving the ELD problem.
Process of innovation knowledge increase in supply chain network from the perspective of sustainable development
Authors: Zhang Dan , Wang Ching-Hsin , Zheng Dengpan , Yu Xianyun 
Published: April 2018

PurposeThe purpose of this paper is to extend prior supply chain research by describing the process of innovation knowledge increase in supply chain network. More specifically, this study investigates the role of network density, and views the knowledge increase as the process of knowledge diffusion and knowledge innovation.Design/methodology/approachA multi-agent model, which demonstrates the process of knowledge increase in supply chain network, was established, and simulated by using NetLogo simulation platform.FindingsThe results indicate that the network density will promote the knowledge increase of the supply chain when it is high or low. In the meantime, these results show that the inhibition of knowledge diffusion and knowledge innovation will appear when network density is moderate.Originality/valueAlthough previous research has identified the importance of knowledge increase in promoting sustainable development of supply chain, far less attention was given to the study of the effect of network structure on the knowledge increase in supply chain. This study thus fulfills the research gap by providing a description of the process of knowledge increase with the consideration of network density. The conclusion is of great significance for the choice of network density for sustainable development of supply chain.
Buying decision in the marketing ofSharialife insurance (evidence from Indonesia)
Authors: Amron Amron , Usman Usman , Mursid Ali 
Published: April 2018

PurposeThe purpose of this study is to examine the effect of satisfaction (SAT) and trust (TRS) on word of mouth (WOM) and buying decision (BD) forSharialife insurance in the Muslim society of Indonesia.Design/methodology/approachThe research design was taken from 386 Muslim customers who heldSharialife insurance policies using the approach of purposive sampling in four cities in Indonesia, namely, Jakarta, Surabaya, Makassar and Medan. The hypothesis testing used structural equation modeling.FindingsThe research results show SAT and TRS have effects on WOM. Moreover, WOM has a significant effect on the BD of the customers of theSharialife insurance product.Research limitations/implicationsThis study focused only BD of customers who boughtSharialife insurance products, so the results cannot be generalized to other types ofShariainsurance. Therefore, future research could consider otherShariainsurance products, such asShariageneral insurance.Practical implicationsIn relation to the testing of SAT and TRS on WOM, this study examined the influence of the two variables on WOM and BD. This study can serve as reference forSharialife insurance companies when formulating promotion strategy.Originality/valueThis study justified the strong association between SAT and TRS for WOM and BD inSharialife insurance in an integrated way.