bluuebunny/crossref_metadata_2025_split huggingface dataset:
Games and teams with shared constraints
Authors: Kulkarni Ankur A. 
Published: July 2017

Energy systems of the future are envisaged to encompass multiple interacting autonomous entities. The theory of games provides the foundations for the design and analysis of such systems. This paper reviews models and results that would be of use for such analysis. Classically, games have involved players whose strategies are coupled only through the dependence of utility functions on strategies of other players. However, in many practical settings in the energy domain, system-level limitations bind the choices players can make. In 1965, Rosen (Econometrica33, 520–534 (doi:10.2307/1911749)) pioneered the study of a class of games where there is a common constraint, called ashared constraint, that couples the strategies available to the players. We discuss how this seemingly benign extension has important ramifications, ranging from the very definition of an equilibrium concept, to other key issues such as existence, uniqueness and efficiency of equilibria. We show how the presence of a shared constraint naturally leads to notions of a price and forms the motivations for more recent models. Although most of the paper has the character of a survey, occasionally we also prove new results.This article is part of the themed issue ‘Energy management: flexibility, risk and optimization’.
The origin of animal multicellularity and cell differentiation
Authors: Brunet Thibaut , King Nicole 
Published: July 2017

AbstractHow animals evolved from their single-celled ancestors over 600 million years ago is poorly understood. Comparisons of genomes from animals and their closest relatives – choanoflagellates, filastereans and ichthyosporeans – have recently revealed the genomic landscape of animal origins. However, the cell and developmental biology of the first animals have been less well examined. Using principles from evolutionary cell biology, we reason that the last common ancestor of animals and choanoflagellates (the ‘Urchoanozoan’) used a collar complex - a flagellum surrounded by a microvillar collar – to capture bacterial prey. The origin of animal multicellularity likely occurred through the modification of pre-existing mechanisms for extracellular matrix synthesis and regulation of cytokinesis. The progenitors of animals likely developed clonally through serial division of flagellated cells, giving rise to sheets of cells that folded into spheres by a morphogenetic process comparable to that seen in modern choanoflagellate rosettes and calcareous sponge embryos. Finally, we infer that cell differentiation evolved in the animal stem-lineage by a combination of three mechanisms: division of labor from ancient plurifunctional cell types, conversion of temporally segregated phenotypes into spatially segregated cell types, and functional innovation.
5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages
Authors: Song Chun-Xiao , Yin Senlin , Ma Li , Wheeler Amanda , Chen Yu , Zhang Yan , Liu Bin , Xiong Junjie , Zhang Weihan , Hu Jiankun , Zhou Zongguang , Dong Biao , Tian Zhiqi , Jeffrey Stefanie S. , Chua Mei-Sze , So Samuel , Li Weimin , Wei Yuquan , Diao Jiajie , Xie Dan , Quake Stephen R. 
Published: July 2017

Abstract5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in circulating cell-free DNA (cfDNA) using a sensitive chemical labeling-based low-input shotgun sequencing approach. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that could be used to predict cancer types and stages with high accuracy. Specifically, we discovered that lung cancer leads to a progressive global loss of 5hmC in cfDNA, whereas hepatocellular carcinoma and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our proof of principle results suggest that cell-free 5hmC signatures may potentially be used not only to identify cancer types but also to track tumor stage in some cancers.One Sentence SummaryAnalyzing the epigenetic modification 5-hydroxymethylcysoine in circulating cell-free DNA reveals tumor tissue of origin and stages for cancer diagnostics.
Why Does the Neocortex Have Columns, A Theory of Learning the Structure of the World
Authors: Hawkins Jeff , Ahmad Subutai , Cui Yuwei 
Published: July 2017

ABSTRACTNeocortical regions are organized into columns and layers. Connections between layers run mostly perpendicular to the surface suggesting a columnar functional organization. Some layers have long-range excitatory lateral connections suggesting interactions between columns. Similar patterns of connectivity exist in all regions but their exact role remain a mystery. In this paper, we propose a network model composed of columns and layers that performs robust object learning and recognition. Each column integrates its changing input over time to learn complete predictive models of observed objects. Excitatory lateral connections across columns allow the network to more rapidly infer objects based on the partial knowledge of adjacent columns. Because columns integrate input over time and space, the network learns models of complex objects that extend well beyond the receptive field of individual cells. Our network model introduces a new feature to cortical columns. We propose that a representation of location relative to the object being sensed is calculated within the sub-granular layers of each column. The location signal is provided as an input to the network, where it is combined with sensory data. Our model contains two layers and one or more columns. Simulations show that using Hebbian-like learning rules small single-column networks can learn to recognize hundreds of objects, with each object containing tens of features. Multi-column networks recognize objects with significantly fewer movements of the sensory receptors. Given the ubiquity of columnar and laminar connectivity patterns throughout the neocortex, we propose that columns and regions have more powerful recognition and modeling capabilities than previously assumed.
Attributing the variability in direction and magnitude of local-scale marine biodiversity change to human activities
Authors: Dunic Jillian C , Elahi Robin , Hensel Marc J. S. , Kearns Patrick J. , O’Connor Mary I. , Acuña Daniel , Honig Aaron , Wilson Alexa R. , Byrnes Jarrett E. K. 
Published: July 2017

AbstractIn recent decades, environmental drivers of community change have been associated with changes in biodiversity from local to global scales. Here we evaluate the role of anthropogenic drivers in marine ecosystems as drivers of change in local species richness with a meta-analysis of a novel dataset of temporal change in species richness. We paired biodiversity data from 144 sites with large-scale drivers derived from geospatial databases: human cumulative impact scores, sea surface temperature change, nutrient loading, and invasion potential. Three specific drivers (nutrient inputs, rate of linear temperature change, and non-native species invasion potential) explained patterns in local marine species richness change. We show that these drivers have opposing effects on biodiversity trends. In some cases, variability in drivers can create contrasting directions of change yielding observations of no net change when localities are pooled in an attempt to find a global average. Further, long-term studies reveal different effects of drivers that are not observed in short-term studies. These findings begin to explain high variability observed in species diversity trends at local scales. Formally attributing local species diversity change to human drivers is essential to understanding global patterns of local species diversity change and their consequences.
The relationship between the spatial scaling of biodiversity and ecosystem stability
Authors: Delsol Robin , Loreau Michel , Haegeman Bart 
Published: July 2017

AbstractEcosystem stability and its link with biodiversity have been mainly studied at the local scale. Here we present a simple theoretical model to address the joint dependence of diversity and stability on spatial scale, from local to continental. The notion of stability we use is based on the temporal variability of an ecosystem-level property, such as primary productivity. In this way, our model integrates the well-known species-area relationship (SAR) with a recent proposal to quantify the spatial scaling of stability, called the invariability-area relationship (IAR). To explore the possible links between the two relationships, we contrast two assumptions about the spatial decay of correlations. In case species differences determine spatial decorrelation, the IAR is a duplicate of the SAR; in case decorrelation is directly determined by spatial separation, the IAR is unrelated to the SAR. We apply the two model variants to explore the effects of species loss and habitat destruction on stability, and find a rich variety of multi-scale spatial dependencies. Our work emphasizes the importance of studying diversity and stability across spatial scales, and provides a point of reference for mechanistic models and data analyses.
New insights from Thailand into the maternal genetic history of Mainland Southeast Asia
Authors: Kutanan Wibhu , Kampuansai Jatupol , Brunelli Andrea , Ghirotto Silvia , Pittayaporn Pittayawat , Ruangchai Sukhum , Schröder Roland , Macholdt Enrico , Srikummool Metawee , Kangwanpong Daoroong , Hübner Alexander , Alvis Leonardo Arias , Stoneking Mark 
Published: July 2017

AbstractTai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1,234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA sequences from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the extension and expansion of TK people through MSEA, although there is also some support for an admixture model. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.
Blazing Signature Filter: a library for fast pairwise similarity comparisons
Authors: Lee Joon-Yong , Fujimoto Grant M. , Wilson Ryan , Wiley H. Steven , Payne Samuel H. 
Published: July 2017

AbstractIdentifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phenotype, the underlying computational task is often a multi-dimensional similarity test. As datasets continue to grow, improvements to the efficiency, sensitivity or specificity of such computation will have broad impacts as it allows scientists to more completely explore the wealth of scientific data. A significant practical drawback of large-scale data mining is that the vast majority of pairwise comparisons are unlikely to be relevant, meaning that they do not share a signature of interest. It is therefore essential to efficiently identify these unproductive comparisons as rapidly as possible and exclude them from more time-intensive similarity calculations. The Blazing Signature Filter (BSF) is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time. The algorithm transforms datasets into binary metrics, allowing it to utilize the computationally efficient bit operators and provide a coarse measure of similarity. As a result, the BSF can scale to high dimensionality and rapidly filter unproductive pairwise comparison. Two bioinformatics applications of the tool are presented to demonstrate the ability to scale to billions of pairwise comparisons and the usefulness of this approach.
Polioviruses that bind a chimeric Pvr–nectin-2 protein identify capsid residues involved in receptor interaction
Authors: Lin Yi , Racaniello Vincent R. 
Published: July 2017

ABSTRACTAmino acid changes in the C’C”D region in poliovirus receptor domain 1 disrupt poliovirus binding. To examine further the role of the C’C”D region in poliovirus infection, we substituted this region of Pvr into the corresponding region of a murine homolog, nectin-2. The chimeric receptor, nectin-2Pvr(c'c"d), rendered transformed L cells susceptible to infection with poliovirus P1/Mahoney, but not with polioviruses P2/Lansing and P3/Leon, due to lack of binding. Twenty-four variants of P2/Lansing were selected that replicate in nectin-2Pvr(c'c"d)producing cell lines. Sequence analysis revealed 30 amino acid changes at 28 capsid residues. One change, K1103R, is found in nearly all isolates and is located at one end of the VP1 BC loop. Other alterations are located on the canyon surface, at the protomer interface, and along the perimeter of the canyon south wall. Unlike poliovirus-Pvr binding, the VP1 BC loop is required for infection of cells producing nectin-2Pvr(c'c"d).
Sensory discrimination by isolated feeding tentacles inSanderia malayensis
Authors: Mori Kazuo , Sullivan Matthew , Ayers Joseph ,   Northeastern University, Marine Science Center, East Point, Nahant, MA 01908
Published: July 2017

AbstractDespite having only a diffuse neural network, tentacles of scyphomedusae exhibit a variety of distinct behavioral acts. One such behavior in tentacles is the capture and subsequent transfer of prey to the mouth. Interaction with prey consists of a variety of distinct stimuli—mechanical contact with the organism, chemical stimulation from the prey, and once captured by the tentacle, the weight of the food particles stretching the tentacle. By isolating and observing these individual stimuli in intact and isolated tentacles of the scyphomedusa,Sanderia malayensis, two separate reflexes have been distinguished. The tentacle feeding response observations suggest that the tentacle has two sensing networks, a bi-directional network for withdrawal and a proximally directed network for feeding.Summary StatementTwo separate reflexes have been distinguished isolated tentacles of the scyphomedusa,Sanderia malayensis, a bi-directional network for withdrawal and a proximally directed network for feeding.
Integral mindflow
Authors: Cacioppe Ron Lewis 
Published: July 2017

Purpose
This paper aims to examine the differences in mindfulness, meditation and flow and the conditions in which each occurs. It summarizes research that demonstrates positive benefits of these three for employee and organizational learning. While mindfulness focuses awareness on what is occurring in the moment, flow involves total immersion in an activity and loss of awareness of one’s self and the environment. This paper discusses if and how mindfulness can be incorporated into flow and how this relates to organizational learning.

Design/methodology/approach
A mindfulness-in-flow process, called mindflow, is described as one that includes open awareness at the “integral point”. Pilot programmes were conducted that integrated mindfulness, meditation and flow for three companies and participants that reported personal physical and psychological benefits and development of mindfulness-in-flow skills.

Findings
This paper suggests that conducting workplace programmes and environments that incorporate mindfulness, meditation and flow has considerable potential to improve culture, responsiveness and learning.

Research limitations/implications
For mindflow to be a useful process to enhance individual and organizational learning, conditions need to be embedded which encourage mindfulness and flow in the organization. Further research is needed into the study of the integration of mindfulness in flow versus mindfulness, the workplace conditions necessary to support mindflow and how these translate into organizational learning.

Practical implications
Organizations need to provide workplace conditions, resources and systems that support mindful flow. Leaders also need to be models and coaches to guide individuals and teams to work in a mind-flow way.

Social implications
The process and practice of mindflow provides greater fulfillment for workers as well as greater alignment between the organization’s products and services and the well being of society.

Originality/value
This paper suggests that conducting workplace programmes and providing organizational conditions that incorporate mindfulness, meditation and flow will increase organizational learning and provide an essential culture for a learning organization.
Cross double‐difference inversion for simultaneous velocity model update and microseismic event location
Authors: Tian Xiao , Zhang Wei , Zhang Jie 
Published: July 2017

ABSTRACTMicroseismic monitoring is an approach for mapping hydraulic fracturing. Detecting the accurate locations of microseismic events relies on an accurate velocity model. The one‐dimensional layered velocity model is generally obtained by model calibration from inverting perforation data. However, perforation shots may only illuminate the layers between the perforation shots and the recording receivers with limited raypath coverage in a downhole monitoring problem. Some of the microseismic events may occur outside of the depth range of these layers. To derive an accurate velocity model covering all of the microseismic events and locating events at the same time, we apply the cross double‐difference method for the simultaneous inversion of a velocity model and event locations using both perforation shots and microseismic data. The cross double‐difference method could provide accurate locations in both the relative and absolute sense, utilizing cross traveltime differences between P and S phases over different events. At the downhole monitoring scale, the number of cross traveltime differences is sufficiently large to constrain events locations and velocity model as well. In this study, we assume that the layer thickness is known, and velocities of P‐ and S‐wave are inverted. Different simultaneous inversion methods based on the Geiger's, double‐difference, and cross double‐difference algorithms have been compared with the same input data. Synthetic and field data experiments suggest that combining both perforation shots and microseismic data for the simultaneous cross double‐difference inversion of the velocity model and event locations is available for overcoming the trade‐offs in solutions and producing reliable results.
The emerging role of alternative splicing in senescence and aging
Authors: Deschênes Mathieu , Chabot Benoit 
Published: July 2017

SummaryDeregulation of precursor mRNA splicing is associated with many illnesses and has been linked to age‐related chronic diseases. Here we review recent progress documenting how defects in the machinery that performs intron removal and controls splice site selection contribute to cellular senescence and organismal aging. We discuss the functional association linking p53, IGF‐1, SIRT1, and ING‐1 splice variants with senescence and aging, and review a selection of splicing defects occurring in accelerated aging (progeria), vascular aging, and Alzheimer's disease. Overall, it is becoming increasingly clear that changes in the activity of splicing factors and in the production of key splice variants can impact cellular senescence and the aging phenotype.
Do long‐term institutional investors foster corporate innovation?
Authors: Kim Hyun‐Dong , Park Kwangwoo , Roy Song Kyojik 
Published: July 2017

AbstractThis article examines the effect of institutional investors’ investment horizons on firms’ innovation activities. We conjecture that the presence of long‐term institutional investors mitigates managerial myopia, prompting firms to generate greater corporate innovation outputs. Using data on patents and patent citations for US firms, we find that institutions’ investment horizons are positively related to the number of patents and patent citations. We also document that long‐term (short‐term) institutional ownership is positively (negatively) related to the innovation outputs. This article makes an additional contribution to the corporate innovation literature by addressing the positive role of long‐term institutional investors.
A comparative proteomic analysis of blood serum for developmental stages in pigs
Authors: Srikanth K. , Lee E. , Kwon A. , Shin J. , Chung H. 
Published: July 2017

SummaryThis study aimed to differentiate genes at developmental stages of pigs from 0 to 150 days of age, to build up a protein database and to find candidate genetic markers for growth traits. The analysis of two‐dimensional electrophoresis and matrix‐assisted laser‐desorption/ionization mass spectrometry separated 252 protein segments. After successfully blasting the peptide sequences, the analysis confirmed 37 differentially expressed proteins that increased from birth to 150 days of age (type A), whereas the type B proteins presented the inverse pattern. The type C proteins included proteins that were expressed continuously throughout the developmental periods. A total of 319 primer sets for 33 genes were designed to find genetic variants using pooled DNA samples of Yorkshire pigs. Amplification products for all primer sets produced approximately 20 000 clones that were sequenced, and 48 candidate SNP sites were finalized for genotyping. A total of 475 animals were used for high throughput genotyping analysis. Among these, phenotype data of all 475 animals were collected for average daily gain, backfat thickness and days to 90 kg, whereas feed conversion data were collected for 300 animals and body measurement traits (starting weight, ending weight, body length, wither height and chest depth) were collected for 209 animals. Association analysis found significant statistical differences between the animals having genotypes of 13 SNPs (g.78935883C>T, g.147629986C>T, g.98266037T>C, g.214707340G>A, g.88350299C>T, g.17180956C>T, g.17181024C>T, g.2350283A>G, g.138361311C>T, g.44996379C>T, g.44996247A>C, g.107715245C>T, g.4149631C>T) for the various measured traits. The identified genetic polymorphisms, of which one was novel (g.214707340G>A), may serve as candidate molecular markers to change population means for the targeted growth traits.