bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human neuromaturation, juvenile extreme energy liability, and adult cognition/cooperation
Authors: Skoyles John 
Published: July 2019

AbstractHuman childhood and adolescence is the period in which adult cognitive competences (including those that create the unique cooperativeness of humans) are acquired. It is also a period when neural development puts a juvenile’s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses ≈50% of its total energy expenditure (TEE) (cf. adult ≈12%). This brain expensiveness is due to (1) the brain making up ≈6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is ≈100% greater in the gray matter of a child than in an adult (a result of the extra costs of synaptic neuromaturation). The high absolute number of neurons in the human brain requires as part of learning a prolonged neurodevelopment. This refines inter- and intraarea neural networks so they become structured with economical “small world” connectivity attributes (such as hub organization and high cross-brain differentiation/integration). Once acquired, this connectivity enables highly complex adult cognitive capacities. Humans evolved as hunter-gatherers. Contemporary hunter-gatherers (and it is also likely Middle Paleolithic ones) pool high energy foods in an egalitarian manner that reliably supported mothers and juveniles with high energy intake. This type of sharing unique to humans protects against energy shortage happening to the immature brain. This cooperation that protects neuromaturation arises from adults having the capacity to communicate and evaluate social reputation, cognitive skills that exist as a result of extended neuromaturation. Human biology is therefore characterized by a presently overlooked bioenergetic-cognition loop (called here the “HEBE ring”) by which extended neuromaturation creates the cooperative abilities in adults that support juveniles through the potentially vulnerable period of the neurodevelopment needed to become such adults.
Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Authors: Prisecaru V. , Baianu I 
Published: July 2019

AbstractA new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such 'dynamically inter-connected' biomolecules form numerous inter-related pathways referred to as 'molecular networks'. One such family of signaling pathways contains the cell cyclins. Cyclins are proteins that link several critical pro-apoptotic and other cell cycling/division components, including the tumor suppressor gene TP53 and its product, the Thomsen-Friedenreich antigen (T antigen), Rb, mdm2, c-Myc, p21, p27, Bax, Bad and Bcl-2, which play major roles in various neoplastic transformations of many tissues.The novel theoretical analysis presented here is based on recently published studies of arrested cell differentiation that normally leads to neural system formation during early developmental stages; the perturbed development may involve cyclin signaling and cell cycling responsible for rapidly induced cell proliferation without differentiation into neural cells in such experimental studies.
Generalized Theory of Life
Authors: Kalmykov Vyacheslav 
Published: July 2019

AbstractThe paper is mathematically, physically and biologically inspired - it is a deductive attempt of the biologist to find the most appropriate language for modelling of life. Applications of mathematical structures - groupoids, groups, categories, functors and monads, which are the most effective for the description of the complex objects, are discussed. Some new conceptions and interpretations were introduced: unified classification of complex systems; the generalized conception about stationary states of any autonomous agent ("Statology"); the total quantitative criterions of evolutionary direction; the generalized group of symmetry. The definitions of information, entropy, organization, behavior, evolution, creation, life, culture, cognition were formulated. An actually closed and potentially opened ecosystem was introduced as the elementary object of organization and evolution of life. Evolution considered as process of generating of a concrete group G of permutations of elements of ecosystems, which is based on activities of the intrinsic autonomous agents. Life was considered as the way of realization of extreme principles of physics through co-organizing of behavior of the ecosystem elements and through dilating borders of the ecosystem by an interiorization of an extrinsic environment.
Nonlinear Models of Neural and Genetic Network Dynamics
Authors: Baianu I. 
Published: July 2019

AbstractA categorical and Łukasiewicz-Topos framework for Łukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks.
On Asymmetry in Biology and Nature
Authors: Baianu I. 
Published: July 2019

AbstractSymmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by ‘perfect’ order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered ‘structure’ that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to anatomy- one often finds asymmetry to be present , although symmetries are also encountered whenever nature affords it. An important case is that of cell biomembranes that possess a marked structural and functional asymmetry which is essential to the survival of cells and microorganisms. Asymmetry both in time and selection ‘criteria’ plays a key role in the evolution of organisms and species.
Analysis of DTC nutrigenetic services in Italy: state of the art, agreement to the ESHG statement and future outlooks
Authors: Cocozza Sergio , Pinelli Michele , Cinque Vincenzo , Acquaviva Fabio , Vergara Paola , Cianflone Alessandra , Castaldo Imma , Monticelli Antonella 
Published: July 2019

Abstract
Background:
In both USA and Europe operate companies selling Direct-to-consumer genetic tests (DTC). These tests are offered to healthy people aiming to identify predispositions to complex diseases and to take preventive measures. Several DTC-nutrigenetic tests (DNTs) are available on the market. They propose the definition of a personalized diet, on the basis of the investigated genetic variants, which would reduce the risk of developing those diseases which have been associated to specific genetic markers. However, the risk/benefit balance of exposing unselected population to genetic testing without any medical surveillance is far from be established. Furthermore, it lacks an accepted procedure to select which genetic markers needs to be investigated, to evaluate their specific role and, as consequence, to define a personalized diet. Within this context, the European Society of Human Genetics (ESHG) released a statement regarding the DTC tests that has been ratified by several national societies including the Italian one.In the present study we analyzed the DNT offered in Italy, the state of the art and the abidance with the ESHG statement.

Methods:
We queried web search engine for the DNT offered to italian population, portraying a non-specialized customer. We examined the DNTs vendor websites and/or directly contacted the companies to collect information on: 1) genetic marker essayed, 2) diseases and phenotypes considered and 3) kind of dietary advices provided. Finally, we evaluated the abidance to the ESHG statement. The study was conducted between November, 2010 and May, 2011.

Results:
Six companies operate in Italy with a total of seven different DNTs offered. Both studied phenotypes and investigated genetic markers were very different among companies, with a relative higher level of agreement for phenotype than for genes. None of the companies described the methods used to select markers and to define diet advices. None of the companies showed a complete agreement to the statement of the ESHG.

Conclusion:
Although DNT companies' efforts are worthy, a standardization of methods and a more strictly agreement with ESHG statement should be encouraged.
Epigenetic reprogramming of primary pancreatic cancer cells counteracts their in vivo tumourigenicity
Authors: Khoshchehreh Reyhaneh , Totonchi Mehdi , Carlos Ramirez Juan , Torres Raul , Baharvand Hossein , Aicher Alexandra , Ebrahimi Marzieh , Heeschen Christopher 
Published: July 2019

Abstract
Pancreatic ductal adenocarcinoma (PDAC) arises through accumulation of multiple genetic alterations. However, cancer cells also acquire and depend on cancer-specific epigenetic changes. To conclusively demonstrate the crucial relevance of the epigenetic programme for the tumourigenicity of the cancer cells, we used cellular reprogramming technology to reverse these epigenetic changes. We reprogrammed human PDAC cultures using three different techniques – (1) lentivirally via induction of Yamanaka Factors (OSKM), (2) the pluripotency-associated gene OCT4 and the microRNA mir-302, or (3) using episomal vectors as a safer alternative without genomic integration. We found that induction with episomal vectors was the most efficient method to reprogram primary human PDAC cultures as well as primary human fibroblasts that served as positive controls. Successful reprogramming was evidenced by immunostaining, alkaline phosphatase staining, and real-time PCR. Intriguingly, reprogramming of primary human PDAC cultures drastically reduced their in vivo tumourigenicity, which appeared to be driven by the cells’ enhanced differentiation and loss of stemness upon transplantation. Our study demonstrates that reprogrammed primary PDAC cultures are functionally distinct from parental PDAC cells resulting in drastically reduced tumourigenicity in vitro and in vivo. Thus, epigenetic alterations account at least in part for the tumourigenicity and aggressiveness of pancreatic cancer, supporting the notion that epigenetic modulators could be a suitable approach to improve the dismal outcome of patients with pancreatic cancer.
Environmental conditions shape the nature of a minimal bacterial genome
Authors: Antczak Magdalena , Michaelis Martin , Wass Mark N. 
Published: July 2019

AbstractOf the 473 genes in the genome of the bacterium with the smallest genome generated to date, 149 genes have unknown function, emphasising a universal problem; less than 1% of proteins have experimentally determined annotations. Here, we combine the results from state-of-the-art in silico methods for functional annotation and assign functions to 66 of the 149 proteins. Proteins that are still not annotated lack orthologues, lack protein domains, and/ or are membrane proteins. Twenty-four likely transporter proteins are identified indicating the importance of nutrient uptake into and waste disposal out of the minimal bacterial cell in a nutrient-rich environment after removal of metabolic enzymes. Hence, the environment shapes the nature of a minimal genome. Our findings also show that the combination of multiple different state-of-the-art in silico methods for annotating proteins is able to predict functions, even for difficult to characterise proteins and identify crucial gaps for further development.
Apoptotic signalling targets the post-endocytic sorting machinery of the death receptor Fas/CD95
Authors: Sharma Shruti , Carmona Antonio , Skowronek Agnieszka , Yu Fangyan , Collins Mark O. , Naik Sindhu , Murzeau Claire M. , Tseng Pei-Li , Erdmann Kai S. 
Published: July 2019

AbstractFas plays a major role in regulating ligand-induced apoptosis in many cell types. It is well known that several cancers demonstrate reduced cell surface levels of Fas and thus escape a potential control system via ligand-induced apoptosis, although underlying mechanisms are unclear. Here we report that the endosome associated trafficking regulator 1 (ENTR1), controls cell surface levels of Fas and Fas-mediated apoptotic signalling. ENTR1 regulates, via binding to the coiled coil domain protein Dysbindin, the delivery of Fas from endosomes to lysosomes thereby controlling termination of Fas signal transduction. We demonstrate that ENTR1 is cleaved during Fas-induced apoptosis in a caspase-dependent manner revealing an unexpected interplay of apoptotic signalling and regulation of endolysosomal trafficking resulting in a positive feedback signalling-loop. Our data provide insights into the molecular mechanism of Fas post-endocytic trafficking and signalling, opening possible explanations on how cancer cells regulate cell surface levels of death receptors.
Mutation bias and GC content shape antimutator invasions
Authors: Couce Alejandro , Tenaillon Olivier 
Published: July 2019

AbstractMutators represent a successful strategy in rapidly adapting asexual populations, but theory predicts their eventual extinction due to their unsustainably large deleterious load. While antimutator invasions have been documented experimentally, important discrepancies among studies remain currently unexplained. Here we show that a largely neglected factor, the mutational idiosyncrasy displayed by different mutators, can play a major role in this process. Analysing phylogenetically diverse bacteria, we find marked and systematic differences in the protein-disruptive effects of mutations caused by different mutators in species with different GC compositions. Computer simulations show that these differences can account for order-of-magnitude changes in antimutator fitness for a realistic range of parameters. Overall, our results suggest that antimutator dynamics may be highly dependent on the specific genetic, ecological and evolutionary history of a given population. This context-dependency further complicates our understanding of mutators in clinical settings, as well as their role in shaping bacterial genome size and composition.
The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data
Authors: Xia Enhua , Li Fangdong , Tong Wei , Yang Hua , Wang Songbo , Zhao Jian , Liu Chun , Gao Liping , Tai Yuling , She Guangbiao , Sun Jun , Cao Haisheng , Gao Qiang , Li Yeyun , Deng Weiwei , Jiang Xiaolan , Wang Wenzhao , Chen Qi , Zhang Shihua , Li Haijing , Wu Junlan , Wang Ping , Li Penghui , Shi Chengying , Zheng Fengya , Jian Jianbo , Huang Bei , Shan Dai , Shi Mingming , Fang Congbing , Yue Yi , Wu Qiong , Ge Ruoheng , Zhao Huijuan , Li Daxiang , Wei Shu , Han Bin , Jiang Changjun , Yin Ye , Xia Tao , Zhang Zhengzhu , Zhao Shancen , Bennetzen Jeffrey L. , Wei Chaoling , Wan Xiaochun 
Published: July 2019

AbstractTea is a globally consumed non-alcohol beverage with great economic importance. However, lack of the reference genome has largely hampered the utilization of precious tea plant genetic resources towards breeding. To address this issue, we previously generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology, which produced a total of 2,124 Gb short and 125 Gb long read data, respectively. A hybrid strategy was employed to assemble the tea genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more comprehensive omics datasets with improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be utilized to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, thus help to breed new varieties with high yield and better quality in the future.
Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data
Authors: Bang Sohyun , Yoo DongAhn , Kim Soo-Jin , Jhang Soyun , Cho Seoae , Kim Heebal 
Published: July 2019

AbstractDiseases prediction has been performed by machine learning approaches with various biological data. One of the representative data is the gut microbial community, which interacts with the host’s immune system. The abundance of a few microorganisms has been used as markers to predict diverse diseases. In this study, we hypothesized that multi-classification using machine learning approach could distinguish the gut microbiome from following six diseases: multiple sclerosis, juvenile idiopathic arthritis, myalgic encephalomyelitis/chronic fatigue syndrome, acquired immune deficiency syndrome, stroke and colorectal cancer. We used the abundance of microorganisms at five taxonomy levels as features in 696 samples collected from different studies to establish the best prediction model. We built classification models based on four multi-class classifiers and two feature selection methods including a forward selection and a backward elimination. As a result, we found that the performance of classification is improved as we use the lower taxonomy levels of features; the highest performance was observed at the genus level. Among four classifiers, LogitBoost–based prediction model outperformed other classifiers. Also, we suggested the optimal feature subsets at the genus-level obtained by backward elimination. We believe the selected feature subsets could be used as markers to distinguish various diseases simultaneously. The finding in this study suggests the potential use of selected features for the diagnosis of several diseases.
HLA class II-Restricted CD8+ T cells in HIV-1 Virus Controllers
Authors: Nyanhete Tinashe E. , Frisbee Alyse L. , Bradley Todd , Faison William J. , Robins Elizabeth , Payne Tamika , Freel Stephanie A. , Sawant Sheetal , Weinhold Kent J. , Wiehe Kevin , Haynes Barton F. , Ferrari Guido , Li Qi-Jing , Moody M. Anthony , Tomaras Georgia D. 
Published: July 2019

AbstractA paradigm shifting study demonstrated that induction of MHC class E and II-restricted CD8+ T cells was associated with the clearance of SIV infection in rhesus macaques. Another recent study highlighted the presence of HIV-1-specific class II-restricted CD8+ T cells in HIV-1 patients who naturally control infection (virus controllers; VCs). However, questions regarding class II-restricted CD8+ T cells ontogeny, distribution across different HIV-1 disease states and their role in viral control remain unclear. In this study, we investigated the distribution and anti-viral properties of HLA-DRB1*0701 and DQB1*0501 class II-restricted CD8+ T cells in different HIV-1 patient cohorts; and whether class II-restricted CD8+ T cells represent a unique T cell subset. We show that memory class II-restricted CD8+ T cell responses were more often detectable in VCs than in chronically infected patients, but not in healthy seronegative donors. We also demonstrate that VC CD8+ T cells inhibit virus replication in both a class I- and class II-dependent manner, and that in two VC patients the class II-restricted CD8+ T cells with an anti-viral gene signature expressed both CD4+ and CD8+ T cell lineage-specific genes. These data demonstrated that anti-viral memory class II-restricted CD8+ T cells with hybrid CD4+ and CD8+ features are present during natural HIV-1 infection.
Using weather radar to monitor the number, timing and directions of flying-foxes emerging from their roosts
Authors: Meade Jessica , van der Ree Rodney , Stepanian Phillip M. , Westcott David A. , Welbergen Justin A. 
Published: July 2019

AbstractKnowledge of species’ population trends is crucial when planning for conservation and management; however, this information can be difficult to obtain for extremely mobile species such as flying-foxes (Pteropus spp.; Chiroptera, Pteropodidae). In mainland Australia, flying-foxes are of particular management concern due their involvement in human-wildlife conflict, and their role as vectors of zoonotic diseases; and two species, the grey-headed flying-fox (Pteropus poliocephalus) and the spectacled flying-fox (P. conspicillatus), are currently threatened with extinction. Here we demonstrate that archival weather radar data over a period of ten years can be used to monitor a large colony of grey-headed flying-foxes near Melbourne. We show that radar estimates of colony size closely match those derived from traditional counting methods. Moreover, we show that radar data can be used to determine the timing and departure direction of flying-foxes emerging from the roost. Finally, we show that radar observations of flying-foxes can be used to identify signals of important ecological events, such as mass flowering and extreme heat events, and can inform human activities, e.g. the safe operation of airports and windfarms. As such, radar represents an extremely promising tool for the conservation and management of vulnerable flying-fox populations and for managing human interactions with these ecologically-important mammals.
Early evaluation of corneal collagen crosslinking in ex-vivo human corneas using two-photon imaging
Authors: Batista Ana , Breunig Hans Georg , Hager Tobias , Seitz Berthold , König Karsten 
Published: July 2019

AbstractThe clinical outcome of corneal collagen crosslinking (CXL) is typically evaluated several weeks after treatment. An earlier assessment of its outcome could lead to an optimization of the treatment, including an immediate re-intervention in case of failure, thereby, avoiding additional discomfort and pain to the patient. In this study, we propose two-photon imaging (TPI) as an earlier evaluation method. CXL was performed in human corneas by application of riboflavin followed by UVA irradiation. Autofluorescence (AF) intensity and lifetime images were acquired using a commercial clinically certified multiphoton tomograph prior to CXL and after 2h, 24h, 72h, and 144h storage in culture medium. The first monitoring point was determined as the minimum time required for riboflavin clearance from the cornea. As control, untreated samples and samples treated only with riboflavin (without UVA irradiation) were monitored at the same time points. Significant increases in the stroma AF intensity and lifetime were observed as soon as 2h after treatment. A depth-dependent TPI analysis showed higher AF lifetimes anteriorly corresponding to areas were CXL was most effective. No alterations were observed in the control groups. Using TPI, the outcome of CXL can be assessed non-invasively and label-free much sooner than with conventional clinical devices.