bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphatidylserine polarization is required for proper Cdc42 localization and for development of cell polarity.
Authors: Fairn Gregory , Grinstein Sergio 
Published: July 2019

AbstractWe used genetically-encoded fluorescent probes to visualize the distribution of phosphatidylserine (PS) in live S. cerevisiae. The majority of the PS was found to reside in the cytosolic leaflet of the plasma membrane. Remarkably, PS was polarized, accumulating in bud necks, the bud cortex and the tips of mating projections. Polarization required vectorial delivery of PS-enriched secretory and recycling vesicles. Rapid dissipation of the PS gradient is prevented by the slow diffusion of lipids along the plasmalemmal inner leaflet, estimated by photobleaching recovery measurements to be over an order of magnitude slower than in mammalian cells. In mutants lacking PS-synthase the absence of PS was associated with, and likely responsible for impaired polarization of the Cdc42 complex, leading to inhibition of bud emergence, diminished growth rate and abolishment of mating. The results indicate that PS polarization is required for optimal Cdc42 targeting and activation during cell division and mating.
Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm
Authors: Jeevitesh M. , Behera Narayan , Jose Justin , Kant Krishna , Dey Alpana 
Published: July 2019

AbstractMultiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known individual bioinformatics tools. This PASA is statistically the most accurate protein alignment method today. It can have potential applications in drug discovery processes in the biotechnology industry.
Formulating MEDLINE queries for article retrieval based on PubMed exemplars
Authors: Garnett Alexander , Piwowar Heather , Rasmussen Edie , Illes Judy 
Published: July 2019

AbstractBibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process. In this paper, we describe a system to help with this task, given an example set of PubMed articles to retrieve and a corresponding set of articles to exclude. The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold. From this information and their knowledge of the domain, users can formulate a query and evaluate its performance. We apply the system to the task of distinguishing original research articles of functional magnetic resonance imaging (fMRI) of sensorimotor function from fMRI studies of higher cognitive functions.
A Rate Distortion approach to protein symmetry
Authors: Wallace Rodrick 
Published: July 2019

AbstractA spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein 'molten globule'. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty's (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Versatile Control System for Automated Single-Molecule Optical Tweezers Investigations
Authors: Koch Steven , Yeh Richard 
Published: July 2019

AbstractWe present a versatile control system to automate single-molecule biophysics experiments. This method combines low-level controls into various functional, user-configurable modules, which can be scripted in a domain-specific instruction language. The ease with which the high-level parameters can be changed accelerates the development of a durable experiment for the perishable single-molecule samples. Once the experimental parameters are tuned, the control system can be used to repeatedly manipulate other single molecules in the same way, which is necessary to accumulate the statistics needed to report results from single-molecule studies. This system has been implemented for an optical tweezers instrument for single-molecule manipulations, with real-time point-by-point feedback at a loop rate of 10-20 kHz.
Phagocytic Activity and Hexose Monophosphate Shunt Activity of Cultured Human Kupffer Cells upon Zymosan, Erythrocytes, Amoebic Trophozoits, Latex Beads and Nitroimidazole
Authors: Sharma Rakesh , Singh Vijay 
Published: July 2019

AbstractPhagocytic function of human Kupffer cells was altered by the addition of nitroimidazole and amoebic trophozoits. The hypothesis was that phagocytic activity was dependent on the nature of additives in culture. The Kupffer cells were fractionated and lysosomes were isolated for enzyme estimations in presence of additives. Phagocytic activity function of human Kupffer cells was altered by the addition of nitroimidazole and amoebic trophozoits in Kupffer cell culture. The human Kupffer cells showed take up of zymosan particles larger than 1 micron in diameter and inert interaction with latex particles. The liver endothelial cells or phagocytes constitute a second line of defense in the liver for the phagoctosis function. The nitroimidazole slowed down the Kupffer cells phagocytosis activity of engulfing beads, trophozoits and removing the foreign materials from the vicinity while Kupffer cell phagocytic function remained totally intact. The potential role of Kupffer cells was phagocytosis and nitroimidazole slowed down the further activated Kupffer cells under physiologic conditions when Kupffer cells are active in clearing foreign substance from the circulation. In conclusion, theses first Kupffer cell and trophozoits interaction in the presence of nitroimidazole suggested the synergistic interaction and this cellular interaction in liver.
A war-prone tribe migrated out of Africa to populate the world.
Authors: Moreno Eduardo 
Published: July 2019

AbstractOf the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder^1,2,3,4,5^. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve conflicts. This, in the light of the “recent out of Africa” hypothesis”^6,7^, suggests that the tribe that left Africa 80.000 years ago performed ritualized fights. In contrast to the more pacific tradition of non-L3 foragers, it may also have had a tendency towards combat. The data implicate that the entire human population outside Africa is descended from only two closely related sub-branches of L3 that practiced ritual fighting and probably had a higher propensity towards warfare and the use of murder for conflict resolution. This may have crucially influenced the subsequent history of the world.
Regulation of Phosphatase Homologue of Tensin Protein Expression by Bone Morphogenetic Proteins in Prostate Epithelial Cells
Authors: Jerde Travis , Wu Zhong , Theodorescu Dan , Bushman Wade 
Published: July 2019

AbstractPhosphatase homologue of tensin (PTEN) is the key endogenous inhibitor of phosphoinositide signaling and is the most commonly mutated gene in human prostate cancer. The bone morphogenetic proteins (BMPs) are secreted developmental signaling molecules known to promote differentiation in the prostate. BMP ligands have been shown to inhibit prostate cancer cell line proliferation and tumor growth and expression of BMPs, BMP ligands, receptors and signaling effectors are diminished in prostate cancer. A previous report in the colon led us to investigate the potential mechanistic relationship between PTEN and BMP signaling in prostate epithelial cells. We show here that BPM signaling positively regulates PTEN in normal and malignant prostate cells by increasing mRNA expression and stabilizing PTEN protein. Further, we show that BMP attenuates prostate cell growth at least in part through its effects on PTEN. BMP treatment did not further inhibit the growth of conditional PTEN over-expressing cells, and stable shRNA-PTEN transfectants were refractory to BMP-mediated growth inhibition. Loss-of-function of PTEN in prostate cancer cells may render them insensitive to the normal differentiating and growth-inhibitory effects of BMPs. These data are the first to identify a mechanistic linkage between BMP signaling and PTEN in normal prostate epithelial cells and to suggest coordinate dysregulation in prostate cancer.
Understanding Consciousness: An Online Workshop on Contemporary Theories
Authors: Pereira Jr Alfredo , Edwards Jonathan , Lehmann Dietrich , Nunn Chris , Trehub Arnold , Velmans Max 
Published: July 2019

AbstractAn invited workshop on ‘Theories of Consciousness’ was organized in the format of a Nature Network closed group during the second semester of 2009. There were presentations by each of 15 authors active in the field, followed by debate with other presenters and invitees. A week was allocated to each of the theories proposed; general discussion threads were also opened from time to time, as seemed appropriate. We (who had been participants in the workshop) offer here an account of the principal outcomes. It can be regarded as a contemporary, ‘state of the art’ snapshot of thinking in this field.
Improving cellular cancer vaccines
Authors: Lokhov Petr 
Published: July 2019

AbstractImmunization with cancer cells is of great demand in anti-cancer therapy. However, current cellular vaccines are inefficient and there are questions regarding their overall safety. We report a simple and straightforward approach for improving of cellular cancer vaccines. Through treatment of cancer cell cultures with purified protease, it is possible to make preparations of cell-surface antigens that are free of intracellular content and contain two orders-of-magnitude less protein than the whole lysate of an equivalent number of cancer cells. Despite this difference in total protein content, protease-generated preparations stimulate anti-cancer responses from immune cells better those stimulated with cancer cells themselves. The composition of collected cell-surface antigens, prior to vaccination, can be directly compared with antigenic profile of target cancer cells by the proteomic footprinting. Any contaminates (cell parasites, viruses, toxins, prions, etc.) are easily separated from antigens by means of ultrafiltration. Thus, current cellular vaccines may be improved by replacing whole cancer cells with their isolated cell-surface antigens. Vaccines prepared in this manner are potentially more qualified, purer, and safer.
Simulation of Two Dimensional Ultraviolet (2DUV) Spectroscopy of Amyloid Fibrils
Authors: Jiang Jun , Abramavicius Darius , Falvo Cyril , Bulheller Benjamin , Hirst Jonathan , Mukamel Shaul 
Published: July 2019

AbstractRevealing the structure and aggregation mechanism of amyloid fibrils is essential for the treatment of over 20 diseases related to protein misfolding. Coherent two dimensional (2D) infrared spectroscopy is a novel tool that provides a wealth of new insight into the structure and dynamics of biomolecular systems. Recently developed ultrafast laser sources are extending multidimensional spectroscopy into the ultraviolet (UV), and this opens up new opportunities for probing fibrils. In a simulation study, we show that 2DUV spectra of the backbone of a 32-residue &x03B2;-amyloid (A&x03B2;(9-40)) fibril associated with Alzheimer&apos;s disease, and two intermediate prefibrillar structures carry characteristic signatures of fibril size and geometry that could be used to monitor its formation kinetics. The dominant features of the &x03B2;-amyloid fibril spectra are determined by intramolecular interactions within a single A&x03B2;(9-40), while intermolecular interactions at the &quot;external interface&quot; have clear signatures in the fine details of these signals.
Studies of Histidine, Phenylalanine Complexes of Oxovanadium(IV) Derived from Acetylacetone
Authors: Singh Yadav Rajeev 
Published: July 2019

AbstractSchiff base complexes of oxovanadium(IV) with amino acids and acetylacetone were synthesized and characterized by elemental analysis, conductivity measurements, spectral and magnetic data. The complexes were found to be non-electrolytes and stoichiometry shown 1:1. The spectral and magnetic data were suggesting the square pyramidal geometry
The architecture of predator-prey and the relationship between complexity and stability
Authors: Burgoa Rosso Karen Luz , Nogales Vera Jose Alberto , Faria Lucas , Charret Iraziet , Paixao Chrystian 
Published: July 2019

AbstractTheoretical studies predict that the stability of an ecosystem is negatively correlated with its complexity, measured by the number of interacting species. On the other hand, empirical evidence indicates that food webs are highly interconnected. In this manuscript we present results on the stability two-level predator-prey food webs. We analyzed exhaustively all possible topologies of connections among species. Our findings show that those food webs fall into two classes with clearly distinct stability properties. In one of them stability is negatively correlated with complexity, and in the other group stability is positively correlated. For a positive relationship our results reveals highly structured food webs. The positive or negative relationship is related only to the topological structure of the food web. It is independent of the number of connections, strengths of predator-prey interactions or number of species. We review empirical evidence that corroborates our results.
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Authors: Csermely Peter , Palotai Robin , Nussinov Ruth 
Published: July 2019

AbstractSingle molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond-types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein (‘discrete breathers’) can govern conformational transitions and allosteric propagation that accompany binding processes, and as such may be more sensitive to mutational events. Additionally, we highlight the dynamic complexity of binding scenarios as they relate to events such as aggregation and signalling, and the crowded cellular environment.
In-Vivo Lipidomics using Single-Cell Raman Spectroscopy
Authors: Wu Huawen , Volponi Joanne , Oliver Ann , Parikh Atul , Simmons Blake , Singh Seema 
Published: July 2019

AbstractWe describe a method for direct, quantitative, in vivo lipid profiling of oil producing microalgae using single-cell laser-trapping Raman spectroscopy (LTRS). This approach is demonstrated in the quantitative determination of the degree of unsaturation and transition temperatures of constituent lipids within microalgae. These properties are important markers for determining engine compatibility and performance metrics of algal biodiesel. We show that these factors can be directly measured from a single living microalgal cell held in place with an optical trap while simultaneously collecting Raman data. Cellular response to different growth conditions is monitored in real time. Our approach circumvents the need for lipid extraction and analysis that is both slow and invasive. Furthermore, this technique yields real-time chemical information in a label-free manner, thus eliminating the limitations of impermeability, toxicity and specificity of the fluorescent probes used in other common protocols. Although the single-cell Raman spectroscopy demonstrated here is focused on the study of the microalgal lipids with biofuel applications, the analytical capability and quantitation algorithms demonstrated are applicable to many different organisms, and should prove useful for a diverse range of applications in lipidomics.
How and why physicists and chemists use blogs
Authors: Pikas Christina 
Published: July 2019

AbstractThis study examined how and why chemists and physicists blog. Two qualitative methods were used: content analysis of blog and “about” pages and in-depth responsive interviews with chemists and physicists who maintain blogs. Analysis of the data yielded several cross-cutting themes that provide a window into how physicists and chemists use their blogs and what value they receive from maintaining a blog and participating in a blogging community. The article concludes with a discussion of implications for supporting scientists’ work.
Graphs, Networks, Extinction and Paleocommunity Food Webs
Authors: Roopnarine Peter 
Published: July 2019

AbstractFood webs represent the trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for proper reconstruction and analysis of paleocommunity food webs. The fossil record presents many challenges, but the problem may be approached with combinatoric analysis, and graph and network theories. This paper is a brief introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores several probabilistic and numerical approaches.
EAG K+ channel joins the p53&x2212;miR-34&x2212;E2F1 signaling pathway as a terminal effecter component for its oncogenic overexpression and action
Authors: Wang Zhiguo , Chen Chang , Li Zhe , Luo Xiaobin , Xiao Jiening , Lin Huixian , Zhang Jianchun , Dong Deli , Lu Yanjie , Yang Baofeng 
Published: July 2019

AbstractThe human ether-&x00E0;-go-go-1 (h-eag1) voltage-dependent K+ channel is necessary for cell cycle progression and its overexpression stimulates tumorigenesis; specific inhibition of h-eag1 expression leads to a reduction in tumor cell proliferation in vitro and in vivo. On the other hand, the tumor-suppressor gene p53 and its downstream genes consist of a complex molecular signaling network and p53 is at the center of this network regulating diverse physiological responses to cancer-related stresses. We report here that h-eag1 expression is controlled by the p53&x2212;miR-34&x2212;E2F1 pathway through a negative feed-forward mechanism. We first established E2F1 as a transactivator of h-eag1 gene. We then revealed that miR-34, a known transcriptional target of p53, is an important negative regulator of h-eag1 through dual mechanisms by directly repressing h-eag1 at the post-transcriptional level and indirectly silencing h-eag1 at the transcriptional level via repressing E2F1. The antisense against h-eag1 antagonized the growth-stimulating effects and the upregulation of h-eag1 expression in SHSY5Y cells, induced by E2F1 overexpression, inhibition of p53 activity, or knockdown of miR-34. Thus, negative regulation of p53 causes oncogenic overexpression of h-eag1 by relieving the negative feed-forward regulation of the p53&x2212;miR-34&x2212;E2F1 pathway or overexpression of h-eag1 fulfills the oncogenic cell growth-stimulating effect of p53 inactivation.
CFP and YFP photostabilities are differentially affected by common mounting fluids
Authors: Schmid Johannes 
Published: July 2019

AbstractThe use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking and tracing of specific proteins or cells or to determine protein interactions. In the later case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is visualized by specific microscopy techniques. When we applied a commonly used FRET microscopy technique - the increase in CFP-fluorescence after bleaching of YFP, we noticed that it worked well for live cells, but that most of the FRET-signal was lost in fixed cells mounted in commercial microscopy mounting fluids. Subsequently, we could show that CFP bleached much faster in the mounting medium than in live cells, while the opposite effect was observed for YFP. This change in photostability was not caused by the fixation but directly dependent on the mounting fluid. Furthermore we made the interesting observation that the CFP-fluorescence intensity increased in live cells after illumination at the YFP-excitation wavelength – a phenomenon, which might cause a false-positive signal in the FRET-microscopy technique that is based on bleaching of YFP. All together our results show that it is problematic to use commercially available mounting fluids for fluorescent proteins due to their differential effects on the bleaching kinetics and that the FRET microscopy technique based on bleaching of the acceptor is prone to artefacts at least for the CFP/YFP pair.