bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracing Snowmelt Paths in an Integrated Hydrological Model for Understanding Seasonal Snowmelt Contribution at Basin Scale
Authors: Li Hongyi , Li Xin , Yang Dawen , Wang Jian , Gao Bing , Pan Xiaoduo , Zhang Yanlin , Hao Xiaohua 
Published: July 2019

AbstractSnowmelt contributions to water resources in cold regions are receiving increasing attention. However, there are clear challenges to accurately distinguish the snowmelt contributions to different hydrological processes in seasonal snow regions. Here, we present an improved method to evaluate snowmelt contributions by tracing the snowmelt flow paths in different media based on a distributed geomorphology‐based ecohydrological model coupled with a physically based snow module. The calculated snowmelt contribution is not limited to river discharge but is also applicable to evaporation and soil storage. The study region, the upstream Heihe River (UHR) basin, is located in the northeastern Tibetan Plateau. Our results indicate that snowmelt can continuously contribute to hydrological processes throughout the year because most of the snowmelt remains in soil voids, even on snow‐free days. In UHR, the snowmelt contribution to total runoff on snow days accounts for a minor part of the total snowmelt contribution, and the snowmelt contribution on snow‐free days accounts for a major part of the total. There is notable snowmelt retention in the soil in each year, which continues to supply discharge into next year. Our results also indicate that the role of snowmelt contribution to annual discharge could be gradually weakened if rainfall more greatly increases the summer discharge in the UHR basin. The improved evaluation method will contribute to a more comprehensive assessment of snowmelt contributions to hydrological processes in seasonal snow regions.
DNA expression microarrays may be the wrong tool to identify biological pathways
Authors: Mondry Adrian , Loh Marie , Giuliani Alessandro 
Published: July 2019

AbstractDNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen’s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 < k < 0.79) between the analysis methods used. Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used.
Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems
Authors: Boline Jyl , Hawrylycz Michael , Williams Robert 
Published: July 2019

AbstractThe goal of this workshop was to survey current activities and plans related to development of mouse and rat brain digital atlasing systems. The workshop discussed needs for and types of coordinated action that will ensure rapid progress, compatibility, and dissemination with use of novel technological approaches. The report summarizes the state-of-the-art in the field and provides recommendations for actions.
Understanding and mapping water resources by multidimensional statistics and fuzzy logic: Missouri River basin case
Authors: Shmagin Boris , Chen Din 
Published: July 2019

AbstractTime series from 46 gauging station with drainage areas from 113 to 398 sq mi in the Upper Missouri River basin with mutual period of observation from 1963 to 1991 were used for analysis. Factor analysis of average annual flow revealed five patterns of river runoff within four distinct subregions of the territory (east, two carbonate karsts areas, uplands). This factor model reflected 62% variance of initial matrix. Each of four groups of watersheds obtained as a factor was presented by one gauging station with time series of annual and monthly discharges (I- 06218500, II- 06478690, III- 06412500, and IV- 06323000). Streams represented by patterns I, II and IV have increase of values and those represented by III have a decrease. The positive trend for pattern II is statistically significant. For four typical flow records, monthly average values were obtained from three to four seasons composed of different ensembles of months. The trends for seasonal components were analyzed for four typical watersheds and a significant increase was obtained for fall-winter season for type IV. Stream runoff is the most appropriate regional indicator for hydroclimatological processes. With multidimensional statistics this process can be considered as spatiotemporal structure of different scale of landscape properties and dynamics. Uncertainties of process originating stream runoff based on dynamic of regional meteorological system and diversity of local landscapes. Boundaries for domains with different annul and seasonal regimes of stream runoff were defined with factor loadings and fuzzy logic rules. With case of Missouri River basin presented that more complete decryption of real events in nature requires use probability and fuzzy logic together.
Proapoptotic Bid Association with Mre11-Rad50-Nbs1 Complex is Indispensable for Checkpoint Activation after DNA Damage
Authors: Ta Van B. T. , Bezstarosti Karel , Demmers Jeroen A. A. , Maculins Timurs , Schellekens Karlyn , van Gent Dik C. , Persengiev Stephan P. 
Published: July 2019

AbstractThe proapoptotic protein Bid is phosphorylated by ATM after double strand breaks (DSBs) induction and induces S-phase arrest by a mechanism that remains to be elucidated. Here we show that in mammalian cells, Bid is associated with Mre11, a subunit of the Mre11-Rad50-Nbs1 (MRN) complex. We demonstrate that Bid activation is abrogated in Mre11 and Nbs1 deficient primary mouse fibroblasts and cells from patients with ataxia talangiectasia-like disorder. Bid depletion by RNA interference inhibited the S-phase checkpoint activation and G2/M arrest after genotoxic insult, but had no effect on MRN complex formation. Our results explain the mechanism of Bid phosphorylation by ATM in response to DNA damage and suggest that Bid functions as a link between the MRN complex and S-phase regulatory proteins.
Cell-free Embryonic Stem Cell Extract-mediated Derivation of Multi-potent Stem Cells from NIH3T3 Fibroblasts for Functional and Anatomical Ischemic Tissue Repair
Authors: Rajasingh Johnson , Hamada Hiromichi , Bord Evelyn , Thorne Tina , Goukassian Ilona , Lambers Erin , Krishnamurthy Prasanna , Qin Gangjian , Schlauch Karen , Rosen Kenneth , Ahluwalia Deepali , Zhu Yan , Losordo Douglas , Kishore Raj 
Published: July 2019

AbstractThe oocyte-independent generation of multipotent stem cells is one of the goals in regenerative medicine. We report that upon exposure to mouse ES cell (ESC) extracts, reversibly permeabilized NIH3T3 cells undergo de-differentiation followed by stimulus-induced re-differentiation into multiple lineage cell types. Genome-wide expression profiling revealed significant differences between NIH3T3 and ESC-extract treated NIH3T3 cells including re-activation of ESC specific transcripts. Epigenetically, ESC extracts induced CpG de-methylation of Oct4 promoter, hyper-acetylation of histones 3 and 4 and decreased lysine 9 (K-9) dimethylation of histone 3. In mouse models of surgically-induced hind limb ischemia (HLI) or acute myocardial infarction (AMI) transplantation of reprogrammed NIH3T3 cells significantly improved post-injury physiological functions and showed antomical evidence of engraftment and trans-differentiation into skeletal muscle, endothelial cell and cardiomyocytes. These data provide evidence for the generation of functional multi-potent stem like cells from terminally differentiated somatic cells without the introduction of trans-genes or ESC fusion.
The sound of concepts: The link between auditory and conceptual brain systems
Authors: Kiefer Markus , Sim Eun-Jin , Herrnberger Bärbel , Grothe Jo , Hoenig Klaus 
Published: July 2019

AbstractConcepts in long-term memory are important building blocks of human cognition and are the basis for object recognition, language and thought. While it is well accepted that concepts are comprised of features related to sensory object attributes, it is still unclear how these features are represented in the brain. Of central interest is whether concepts are essentially grounded in perception. This would imply a common neuroanatomical substrate for perceptual and conceptual processing. Here we show using functional magnetic resonance imaging and recordings of event-related potentials that acoustic conceptual features rapidly recruit auditory areas even when implicitly presented through visual words. Recognizing words denoting objects for which acoustic features are highly relevant (e.g. "telephone") suffices to ignite cell assemblies in the posterior superior and middle temporal gyrus (pSTG/MTG) that were also activated by listening to real sounds. Activity in pSTG/MTG had an onset of 150 ms and increased parametrically as a function of acoustic feature relevance. Both findings suggest a conceptual origin of this effect rather than post-conceptual strategies such as imagery. The presently demonstrated link between auditory and conceptual brain systems parallels observations in other memory systems suggesting that modality-specificity represents a general organizational principle in cortical memory representation. The understanding of concepts as a partial reinstatement of brain activity during perception stresses the necessity of rich sensory experiences for concept acquisition. The modality-specific nature of concepts could also explain the difficulties in achieving a consensus about overall definitions of abstract concepts such as freedom or justice unless embedded in a concrete, experienced situation.
A database of naturally occurring human urinary peptides and proteins for use in clinical applications
Authors: Zürbig Petra , Coon Joshua , Bauer Hartwig , Behrens Georg , Dakna Mohammed , Dominiczak Anna , Decramer Stephane , Ehrich Jochen , Fliser Danilo , Frommberger Moritz , Ganser Arnold , Giolami Mark , Golovko Igor , Good David , Gwinner Wilfried , Haubitz Marion , Herget-Rosenthal Stefan , Jahn Holger , Jerums George , Julian Bruce , Kellmann Markus , Kliem Volker , Kolch Walter , Krolewski Andrzej , Luppi Mario , Massy Ziad , Melter Michael , Neusüss Christian , Novak Jan , Peter Karlheinz , Rossing Kasper , Rupprecht Harald , Schanstra Joost , Schiffer Eric , Stolzenburg Jens-Uwe , Tarnow Lise , Theodorescu Dan , Thongboonkerd Visith , Vanholder Raymond , Weissinger Eva , Mischak Harald , Schmitt-Kopplin Philippe 
Published: July 2019

AbstractOwing to its availability, ease of collection and correlation with (patho-) physiology, urine is an attractive source for clinical proteomics. However, the lack of comparable datasets from large cohorts has greatly hindered development in this field. Here we report the establishment of a high resolution proteome database of naturally occurring human urinary peptides and proteins - ranging from 800-17,000 Da - from over 3,600 individual samples using capillary electrophoresis coupled to mass spectrometry, yielding an average of 1,500 peptides per sample. All processed data were deposited in an SQL database, currently containing 5,010 relevant unique urinary peptides that serve as classifiers for diagnosis and monitoring of diseases, including kidney and vascular diseases. Of these, 352 have been sequenced to date. To demonstrate the applicability of this database, two examples of disease diagnosis were provided: For renal damage diagnosis, patients with a specific renal disease were identified with high specificity and sensitivity in a blinded cohort of 131 individuals. We further show definition of biomarkers specific for immunosuppression and complications after transplantation (Kaposi’s sarcoma). Due to its high information content, this database will be a powerful tool for the validation of biomarkers for both renal and non-renal diseases.
An intelligent liposome that may deliver drug molecules in a well controlled fashion
Authors: Popescu Dumitru , Popescu Alin Gabriel 
Published: July 2019

AbstractThe passage of molecules, especially large ones, through the cellular membrane is a very important problem for some biotechnological applications, such as drug delivery. The appearance of pores in the lipid bilayer following some controlled mechanisms may be an adequate and interesting way. Some pores, named stochastic pores, can appear due to structural and dynamic properties of lipid bilayer, but others may be favored by mechanical tension induced by different ways. Recently, a sequence of 30-40 pores was observed in the same vesicle, a pore at a time, which can appear in vesicles stretched by optical induced mechanical tension. There are two very interesting biotechnological applications that require the increase of membrane permeability: gene therapy and targeted drug delivery. In the first one, the transport of DNA fragments through cellular and nuclear membranes is required. The second application uses drug molecules encapsulated in vesicles, which have to be transported to a target place. Having reached that point, one supposes that the liposome discharges its content by its breakdown. In this paper, we will write about how a lipid vesicle has to release the drug molecules in a well-controlled fashion. Such liposomes are named pulsatory liposomes and they induce cyclic activity. We will demonstrate that this liposome may be programmed to work a certain number of cycles, settled in advance. Also, we will calculate the amount of drug delivered during each cycle. In fact, a pulsatory liposome may be conceived as a drug dose micro device, which works according to a medical prescription established a priori.
Semiotic Dynamics Solves the Symbol Grounding Problem
Authors: Steels Luc , Loetzsch Martin , Spranger Michael 
Published: July 2019

AbstractLanguage requires the capacity to link symbols (words, sentences) through the intermediary of internal representations to the physical world, a process known as symbol grounding. One of the biggest debates in the cognitive sciences concerns the question how human brains are able to do this. Do we need a material explanation or a system explanation? John Searle’s well known Chinese Room thought experiment, which continues to generate a vast polemic literature of arguments and counter-arguments, has argued that autonomously establishing internal representations of the world (called ’intentionality’ in philosophical parlance) is based on special properties of human neural tissue and that consequently an artificial system, such as an autonomous physical robot, can never achieve this. Here we study the Grounded Naming Game as a particular example of symbolic interaction and investigate a dynamical system that autonomously builds up and uses the semiotic networks necessary for performance in the game. We demonstrate in real experiments with physical robots that such a dynamical system indeed leads to a successful emergent communication system and hence that symbol grounding and intentionality can be explained in terms of a particular kind of system dynamics. The human brain has obviously the right mechanisms to participate in this kind of dynamics but the same dynamics can also be embodied in other types of physical systems.
On Real-Time Synthetic Primate Vision
Authors: Dankers Andrew , Barnes Nick , Bischof Walter , Zelinsky Alex 
Published: July 2019

AbstractThe primate vision system exhibits numerous capabilities. Some important basic visual competencies include: 1) a consistent representation of visual space across eye movements; 2) egocentric spatial perception; 3) coordinated stereo fixation upon and pursuit of dynamic objects; and 4) attentional gaze deployment. We present a synthetic vision system that incorporates these competencies.We hypothesize that similarities between the underlying synthetic system model and that of the primate vision system elicit accordingly similar gaze behaviors. Psychophysical trials were conducted to record human gaze behavior when free-viewing a reproducible, dynamic, 3D scene. Identical trials were conducted with the synthetic system. A statistical comparison of synthetic and human gaze behavior has shown that the two are remarkably similar.
Artificial Antigen Presenting Cells With Preclustered anti-CD28/-CD3/-LFA-1 Monoclonal Antibodies Are Highly Effective To Induce The Ex-Vivo Expansion Of Functional Human Antitumor T Cells
Authors: Zappasodi Roberta , Di Nicola Massimo , Carlo-Stella Carmelo , Mortarini Roberta , Molla Alessandra , Vegetti Claudia , Passoni Lorena , Albani Salvatore , Anichini Andrea , Gianni Alessandro 
Published: July 2019

AbstractEffective adoptive T cell therapy requires the ex vivo generation of functional T lymphocytes with a long lifespan in vivo. We evaluated in vitro T cell expansion by artificial antigen presenting cells (aAPC) generated with activating (human anti-CD3), co-stimulating (human anti-CD28) and adhesion (human anti-LFA-1) monoclonal antibodies pre-clustered in microdomains (MDs) held by a liposome scaffold. The co-localization of T cell ligands in MDs and the targeting of an adhesion protein, increasing the efficiency of immunological synapse formations, represent the novelties of our system. These aAPCs allowed increased expansion of polyclonal CD4^+^ and CD8^+^ T cells and of tumor antigen-specific CD8^+^ T cells compared to anti-CD28- and anti-CD3-coated microbeads and to immobilized anti-CD3. These aAPCs allowed the generation of T cells displaying an immunophenotype consistent with long-term in vivo persistence, without increasing the frequency of regulatory T cells. Finally, our aAPCs proved to be suitable for large scale T cell expansion required in immunotherapy trials.
Neural activity dissociation between thought-based and perception-based response conflict
Authors: Chen Antao , Lei Xu , Huang Xiting , Zhang Qinglin , Liu Qiang , Lai Yongxiu , Yao Dezhong , Li Hong 
Published: July 2019

AbstractBased on the idea that intentions have different penetrability to perception and thought (Fodor, 1983), four Stroop-like tasks, AA, AW, WA, and WW are used, where the A represents an arrow and the CPPR (closest processing prior to response) is perception, and the W represents a word and the CPPR is thought. Event-related brain potentials were recorded as participants completed these tasks, and sLORETA (standardized low resolution brain electromagnetic tomography) was used to localize the sources at specific time points. These results showed that there is an interference effect in the AA and WA tasks, but not in the AW or WW tasks. The activated brain areas related to the interference effect in the AA task were the PFC and ACC, and PFC activation took place prior to ACC activation; but only PFC in WA task. Combined with previous results, a new neural mechanism of cognitive control is proposed.
Age and origin of enigmatic megaherbs from the subantarctic islands
Authors: Wagstaff Steven J. , Breitwieser Ilse , Quinn Christopher , Ito Motomi 
Published: July 2019

AbstractBiogeographic relationships in the southern hemisphere have puzzled biologists for the last two centuries. Once joined to form the supercontinent Gondwana, Africa, Antarctica, Australia, New Zealand and South America are widely separated by the Pacific and Indian oceans. Sir Joseph Hooker was the first to suggest that Antarctica served as a corridor for plant migration not unlike the land-bridges in the northern hemisphere. While the Antarctic flora was largely erased by glaciation during the Pleistocene, at least some of these Antarctic plant communities found refuge on the subantarctic islands. Here we provide support for the hypothesis that giant herbs persisted in the subantactic islands prior to the onset of Pleistocene glaciation, then dispersed northward in response to glacial advance. Our findings provide further evidence that Antarctica has played a pivotal role in shaping southern hemisphere biogeography.
French birds lag behind climate warming
Authors: Devictor Vincent , Julliard Romain , Couvet Denis , Jiguet Frédéric 
Published: July 2019

AbstractBiodiversity responses to climate warming have been documented through the study of changes in distributions, abundances or phenologies of individual species or in more integrated measures such as species community richness and composition. However, whether these observed population and community changes are occurring fast enough to cope with new climatic conditions remain uncertain and hardly quantifiable. Here, using spatial and temporal trends from the French breeding bird survey, we show that although bird assemblages are strongly responding to climate warming, this response is slower than expected for catching up with the current temperature increase. During the last two decades, French birds have only achieved 54% of the response required to follow temperature increase, and have accumulated, in 18 years, a 97 km delay in their northward shift. We thus developed a framework to measure both the observed and predicted response of species assemblage to climate change, an approach which is flexible enough to be applicable to any taxa with large-scale survey data, using either abundance or distribution data. For example, it can be further used to test if different delays are found across groups or if, for a given group, the delay depends on the land-use contexts.
Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans
Authors: Farrell Philip , Le Marechal Cedric , Ferec Claude , Siker Malika , Teschler-Nicola Maria 
Published: July 2019

AbstractThe most common, life-threatening autosomal recessive disease of Europeans and Euro-Americans, cystic fibrosis (CF), occurs predominately in patients with the F508del mutation.1 Although F508del is currently detectable as a single allele in 1/30-1/40 Europeans2-4 and Euro-Americans,5 it has not been determined what heterozygote selective advantage(s) might account for its relatively high prevalence. Indirect evidence6 suggests that this mutation was present in Brittany at least 3000 years ago, but no direct analyses of ancient DNA have been reported to identify F508del and clarify its frequency in prehistoric inhabitants of Europe. Here we show that F508del was present in 3 of 32 Iron Age inhabitants of Austria from whom DNA could be recovered from molar teeth using procedures that fulfill authenticity criteria.7 Because these individuals, who were buried in cemeteries along the Danube river, were shown by radiocarbon dating of isolated bone collagen to have lived there during 544-255 BC, this indicates that the F508del mutation is definitely more than 2000 years old and that CF (the disease) was present among them. More generally, the apparent enrichment of this Iron Age population in F508del suggests an evolutionary advantage in their environment that can be investigated by interdisciplinary strategies of paleoepidemiology.