bluuebunny/crossref_metadata_2025_split huggingface dataset:
On biological homochirality
Authors: Wallace Rodrick 
Published: July 2019

AbstractGeneralizing Landau's spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to 'freeze' the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemistry, in contrast with a recent prediction of a racemic average.
MicroDNAs and Transcriptional Regulation
Authors: sheikhnejad Reza 
Published: July 2019

AbstractSynthetic &quot;microDNAs (MIDs)&quot;is a new class of ~ 20-25 nucleotide-long DNAs capable of repressing the activity of the target gene at the level of transcription by mechanisms that have not been clarified yet. However they are designed to target non-coding regions of the cancer causing genes, thus interfering with transcription. The inhibition might be possible through the direct binding of MIDs to cis-regulatory sites and/or to some Transcription Factors (TF) that normally activate transcription. Synthetic MIDs in some ways are similar to the newly discovered microRNAs a mechanism by which cell regulates its genetic activities at post-transcriptional level. Synthetic MIDs can provide a powerful tool to prevent massive production of mRNA by undesired gene activities. Therefore drugs are not required to interact with overwhelming number of mRNA and microRNA copies that may present unwanted side effects. In vitro studies suggest that the inhibition of the target gene starts after the first round of DNA replication, usually 24 hours after treatment depending on cell doubling time. Cell growth suppression maximizes at day 6 or 7 and the inhibition effect is sustained for weeks. We have shown that blocking of both bcl-2 and k-ras transcription by their specific microDNA Inhibitors induced apoptosis in HL60 leukemia cells and B-cell lymphomas.
Topological network alignment uncovers biological function and phylogeny
Authors: Kuchaiev Oleksii , Milenkovic Tijana , Memisevic Vesna , Hayes Wayne , Przulj Natasa 
Published: July 2019

AbstractSequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein-protein interaction networks of two very different species—yeast and human—indicate that even distant species share a surprising amount of network topology with each other, suggesting broad similarities in internal cellular wiring across all life on Earth.
Dyslexia and the assessment of visual attention
Authors: Skoyles John , Skottun Bernt 
Published: July 2019

AbstractVisual stream segregation has been proposed as a method to measure visual attention in dyslexia. Another task proposed to do this is the line-motion illusion. Both tasks, it is observed, can be carried out with spatially distributed stimuli. This, however, appears inconsistent with these tasks being linked speci?cally to attentional processes since this would require them to spatially focus cognitive resources. Also, both line-motion and visual stream segregation involve the perception of movement raising the possibility that what is actually measured by these tasks is not attention but some aspect of motion perception.
The land surface water and energy budgets over the Tibetan Plateau
Authors: Xu Li 
Published: July 2019

AbstractTibetan Plateau plays an important role in the Asian Monsoon and global general circulation system. Due to the lack of quantitative observations and complicated cold season processes in high elevation terrain, however, the land surface water and energy budgets are still unexplored over this special region. In this study, the water and energy balances are analyzed in detail based on recently released land surface “reanalysis” data produced by NASA Global Land Data Assimilation System by three different land models, which first ingest all available ground and satellite data into the data assimilation system over the Tibetan Plateau. The major land surface energy and water components in the annual variability are compared. The model and data assimilation skills and deficiencies are also discussed. The total heat fluxes in the transition from heat source to heat sink is observed at the west edge of the TP during winter. But, the area and intensity is far less than the previous hypothesized. The Budyko curve for hydrology indicates that the TP is a typical dry and arid climate where evaporation is mainly controlled by precipitation.
Spike processing model of the brain
Authors: Brown Robert 
Published: July 2019

AbstractThe timing of a spike within a specific time period is used to identify a place in space (input terminal) and/or sense changes in energy or position in the environment, and is used to determine the motion of an actuator or the activation of a place in space (output terminal). The timing of a spike is specified by a sensor or a time delay memory cell that is preset (predetermined) or set through experience (empirical). Time delay memory cells are arranged in decoding networks that activate specific output terminals based upon the timing of incoming spike trains, or arranged in encoding networks that generate spike trains from activated input terminals. These spike trains form semi-axes that can transmit large quantities of information in one direction through a single conductor, and are essential in the transmission of information from peripheral neurons to and from the brain through the spinal chord.
Chemotherapy effects on brain glucose metabolism at rest
Authors: Baudino Bruno , D’Agata Federico , Castellano Giancarlo , Caroppo Paola , Cauda Simona , Parente Antonella , Manfredi Matteo , Geda Elisabetta , Orsi Laura , Cauda Franco , Castelli Lorys , Sacco Katiuscia , Ardito Rita , Torta Riccardo , Bisi Gianni 
Published: July 2019

Abstract
Background:
A growing number of studies reports that chemotherapy may impair brain functions inducing cognitive changes which can persist in a subset of cancer survivors.Aims: To investigate the neural basis of the chemotherapy-induced neurobehavioral changes by means of metabolic imaging and voxel-based statistical parametric mapping analyses.

Methods:
We studied the resting brain [18]FDG-PET/CT images of 43 adult cancer patients with solid (n=12, 28%) or hematologic malignancies (n=31, 72%); 12 patients were studied prior to chemotherapy (No chemotherapy) while treated patients were divided into two matched subgroups: Early High (<9 months after chemotherapy, >6 chemotherapy cycles, n=10), and Late Low (>9 months after chemotherapy, <6 chemotherapy cycles, n=21).

Findings:
Compared to No chemotherapy, the Early High subgroup showed a significant bilateral (p<0.05) lower regional cerebral metabolic rate of glucose metabolism in both the prefrontal cortices and white matter, cerebellum, posterior medial cortices and limbic regions. A similar pattern emerged in the Early High versus Low Late comparison, while no significant result was obtained in the Low Late versus No chemotherapy comparison. The number of cycles and the post-chemotherapy time were negatively and positively correlated, respectively, with a set of these same brain regions.

Interpretation:
The present study shows that chemotherapy induces significant transient changes in the glucose metabolism of multiple cerebral cortical and white matter regions with a prevailing involvement of the prefrontal cortex. The severity of these changes are significantly related with the number of chemotherapy cycles and a subset of brain regions seems to present longer lasting, but more subtle, metabolic changes.
Expression cartography of human tissues using self organizing maps
Authors: Wirth Henry , Löffler Markus , von Bergen Martin , Binder Hans 
Published: July 2019

Abstract
Background:
The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.

Results:
The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues.

Conclusions:
The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.
Collective Animal Behavior from Bayesian Estimation and Probability Matching
Authors: Perez-Escudero Alfonso , de Polavieja Gonzalo 
Published: July 2019

AbstractAnimals living in groups make movement decisions that depend, among other factors, on social interactions with other group members. Our present understanding of social rules in animal collectives is mainly based on empirical fits to observations, with less emphasis in obtaining first-principles approaches that allow their derivation. Here we show that patterns of collective decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with two stages: Bayesian estimation and probabilistic matching.In the first stage, each animal makes a Bayesian estimation of which behavior is best to perform taking into account personal information about the environment and social information collected by observing the behaviors of other animals. In the probability matching stage, each animal chooses a behavior with a probability equal to the Bayesian-estimated probability that this behavior is the most appropriate one. This model derives very simple rules of interaction in animal collectives that depend only on two types of reliability parameters, one that each animal assigns to the other animals and another given by the quality of the non-social information. We test our model by obtaining theoretically a rich set of observed collective patterns of decisions in three-spined sticklebacks, Gasterosteus aculeatus, a shoaling fish species. The quantitative link shown between probabilistic estimation and collective rules of behavior allows a better contact with other fields such as foraging, mate selection, neurobiology and psychology, and gives predictions for experiments directly testing the relationship between estimation and collective behavior.
Efficient Replication of Over 180 Genetic Associations with Self-Reported Medical Data
Authors: Francke Uta , Naughton Brian , Mountain Joanna , Wojcicki Anne , Tung Joyce , Do Chuong , Hinds David , Kiefer Amy , Macpherson J. Michael , Eriksson Nicholas , Chowdry Arnab 
Published: July 2019

AbstractWhile the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for amassing large amounts of medical information in a recontactable cohort by assessing our ability to replicate genetic associations using these data. Using web-based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals. Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we expected to (based on the number of cases in our cohort and reported odds ratios, and excluding a set of associations with contradictory published evidence). Altogether we replicated over 180 previously reported associations, including many for type 2 diabetes, prostate cancer, cholesterol levels, and multiple sclerosis. We found significant variation across categories of conditions in the percentage of expected associations that we were able to replicate, which may reflect systematic inflation of the effects in some initial reports, or differences across diseases in the likelihood of misdiagnosis or misreport. We also demonstrated that we could improve replication success by taking advantage of our recontactable cohort, offering more in-depth questions to refine self-reported diagnoses. Our data suggests that online collection of self-reported data in a recontactable cohort may be a viable method for both broad and deep phenotyping in large populations.
Antimicrobial and Phytochemical Analysis of Centella asiatica (L.)
Authors: Perumal Samy Ramar , TK Chow Vincent 
Published: July 2019

AbstractIn vitro antibacterial studies were carried out using hexane, dichloromethane and methanol extract of leaves of Centella asiatica by disc-diffusion method against gram-positive and gram-negative bacteria. The methanol and dichloromethane extracts of leaf showed a broad spectrum antibacterial activity. Thus the results substantiate the traditional usage of this plant as a medicine.
3DScape: three dimensional visualization plug-in for Cytoscape
Authors: Wang Qi 
Published: July 2019

Abstract3DScape is the first plug-in which enables three-dimensional network visualization in Cytoscape. The extra dimension is useful in accommodating, visualizing, and distinguishing larger networks with multiple crossing connections.Special features in 3DScape include 3D layout algorithms, mapping onto 3D models and animation effects on a series of expression data. 3DScape is available at http://www.rendware.com
Complex Systems Analysis of Cell Cycling Models in Carcinogenesis
Authors: Baianu I. 
Published: July 2019

AbstractA new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments that form numerous inter-related pathways referred to as networks.The variable biotopology of such dynamic networks is highly complex, and has a number of interesting properties that can be formally characterized at one level of organization by mathematical structures called 'biogroupoids'.One such family of 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 all play major roles in carcinogenesis of many cancers. A novel theoretical analysis is thus possible based on recently published studies of cyclin signaling, with special emphasis placed on the roles of cyclins D1 and E, suggests novel clinical trials and rational therapies of cancer through reestablishment of cell cycling inhibition in metastatic cancer cells.
Early Diagnosis of Alzheimer's disease by NIRF Spectroscopy and Nuclear Medicine
Authors: Baianu I. 
Published: July 2019

AbstractThere is an urgent need for the early detection of diseases such as Alzheimer’s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image resolution, as well as patient irradiation in the case of CAT/CT and PET. On the other hand, Near Infrared Chemical Imaging Microspectroscopy and certain Fluorescence spectroscopic techniques are capable of single cancer cell and/or single molecule detection and/or imaging. Such powerful capabilities, combined with low cost of diagnostics, make these novel techniques very attractive means for early detection of diseases such as cancer and Alzheimer’s, that are promising to reduce the fatality rate of patients through adequate diagnosis and treatment of such diseases at early stages.Currently NIH provides only inadequate funding for the clinical and research aspects of these novel investigation and clinical diagnostic techniques by FT-NIRS and Fluorescence spectrocopy for early detection of Alzheimer's and Cancers.
Berberine induces caspase-independent cell death in colon tumor cells through activation of apoptosis-inducing factor
Authors: Wilson Keith , Polk D. Brent , Yan Fang , Wang Lihong , Liu Liping , Shi Yan , Cao Hamwei , Chaturvedi Rupesh , Hu Tianhui 
Published: July 2019

AbstractBerberine, an isoquinoline alkaloid derived from plants, is a traditional medicine for treating bacterial diarrhea and intestinal parasite infections. Although berberine has recently been shown to suppress growth of several tumor cell lines, information regarding the effect of berberine on colon tumor growth is limited. Here, we investigated the mechanisms underlying the effects of berberine on regulating the fate of colon tumor cells, specifically the immorto Min mouse colonic epithelial (IMCE) cells carrying the Apcmin mutation, and of normal colon epithelial cells, namely young adult mouse colon (YAMC) epithelial cells. Berberine decreased colon tumor colony formation in agar, and induced cell death and LDH release in a time- and concentration-dependent manner in IMCE cells. In contrast, YAMC cells were not sensitive to berberine-induced cell death. Berberine did not stimulate caspase activation, and PARP cleavage and berberine-induced cell death were not affected by a caspase inhibitor in IMCE cells. Rather, berberine stimulated a caspase-independent cell death mediator, apoptosis-inducing factor (AIF) release from mitochondria and nuclear translocation in a ROS production-dependent manner. Amelioration of berberine-stimulated ROS production or suppression of AIF expression blocked berberine-induced cell death and LDH release in IMCE cells. Furthermore, two targets of ROS production in cells, cathepsin B release from lysosomes and PARP activation were induced by berberine. Blockage of either of these pathways decreased berberine-induced AIF activation and cell death in IMCE cells. Thus, berberine-stimulated ROS production leads to cathepsin B release and PARP activation-dependent AIF activation, resulting in caspase-independent cell death in colon tumor cells. Notably, normal colon epithelial cells are less susceptible to berberine-induced cell death, which suggests the specific inhibitory effects of berberine on colon tumor cell growth.
Transcriptional memory emerges from cooperative histone modifications
Authors: Binder Hans , Steiner Lydia , Rohlf Thimo , Prohaska Sonja , Galle Joerg 
Published: July 2019

Abstract
Background
Transcriptional regulation in cells makes use of diverse mechanisms to ensure that functional states can be maintained and adapted to variable environments; among them are chromatin-related mechanisms. While mathematical models of transcription factor networks controlling development are well established, models of transcriptional regulation by chromatin states are rather rare despite they appear to be a powerful regulatory mechanism.

Results
We here introduce a mathematical model of transcriptional regulation governed by histone modifications. This model describes binding of protein complexes to chromatin which are capable of reading and writing histone marks. Molecular interactions between these complexes and DNA or histones create a regulatory switch of transcriptional activity possessing a regulatory memory. The regulatory states of the switch depend on the activity of histone (de-) methylases, the structure of the DNA-binding regions of the complexes, and the number of histones contributing to binding.We apply our model to transcriptional regulation by trithorax- and polycomb- complex binding. By analyzing data on pluripotent and lineage-committed cells we verify basic model assumptions and provide evidence for a positive effect of the length of the modified regions on the stability of the induced regulatory states and thus on the transcriptional memory.

Conclusions
Our results provide new insights into epigenetic modes of transcriptional regulation. Moreover, they implicate well-founded hypotheses on cooperative histone modifications, proliferation induced epigenetic changes and higher order folding of chromatin which await experimental validation. Our approach represents a basic step towards multi-scale models of transcriptional control during development and lineage specification.