bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic constraints on the evolution of genetic codes: Did multiple 'preaerobic' ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Authors: Wallace Rodrick 
Published: July 2019

AbstractA spontaneous symmetry lifting model based on Tlusty's elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low fidelity quasi-equilibria consistent with the 'virus world' hypothesis of Koonin et al. (2006). A more detailed search for empirical evidence of 'preaerobic' ecosystem shifts in metabolic free energy availability or efficiency of use might be surprisingly fruitful.
Using MicroPET Imaging in Quantitative Verification of Acupuncture Effect in Ischemia Stroke Treatment
Authors: Shen Xiaoyan , Tang Hongtu , Li Jia , Xiang Ting , Liu Huafeng , Yu Weichuan 
Published: July 2019

AbstractWhile acupuncture has survived several thousand years’ evolution of medical practice, its function still remains as a myth from the view point of modern medicine. Our goal in this paper is to quantitatively understand the function of acupuncture in ischemia stroke treatment. We carried out a comparative study using the Sprague Dawley rat animal model. We induced the focal cerebral ischemia in the rats using the middle cerebral artery occlusion (MCAO) procedure. For each rat from the real acupuncture group (n = 40), sham acupoint treatment group (n = 54), and blank control group (n = 16), we acquired 3-D FDG-microPET images at baseline, after MCAO, and after treatment (i.e., real acupuncture, sham acupoint treatment, or resting according to the group assignment), respectively. After verifying that the injured area is in the right hemisphere of the cerebral cortex in the brain by using magnetic resonance imaging(MRI) and triphenyl tetrazolium cchloride (TTC)-staining, we directly compared the glucose metabolism in the right hemisphere of each rat. We carried out t-test and permutation test on the image data. Both tests demonstrated that acupuncture had a more positive effect than non-acupoint stimulus and blank control (P < 0.025) in increasing the glucose metabolic level in the stroke-injured area in the brain, while there was no statistically significant difference between non-acupoint stimulus and blank control (P>0.15). The immediate positive effect of acupuncture over sham acupoint treatment and blank control is verified using our experiments. The long-term benefit of acupuncture needs to be further studied.
On optical detection of densely labeled synapses in neuropil and mapping connectivity with combinatorially multiplexed fluorescent synaptic markers
Authors: Mishchenko Yuriy 
Published: July 2019

AbstractWe propose a new method for mapping neural connectivity optically, by utilizing Cre/Lox system Brainbow to tag synapses of different neurons with random mixtures of different fluorophores, such as GFP, YFP, etc., and then detecting patterns of fluorophores at different synapses using light microscopy (LM). Such patterns will immediately report the pre- and post-synaptic cells at each synaptic connection, without tracing neural projections from individual synapses to corresponding cell bodies. We simulate fluorescence from a population of densely labeled synapses in a block of hippocampal neuropil, completely reconstructed from electron microscopy data, and show that high-end LM is able to detect such patterns with over 95% accuracy. We conclude, therefore, that with the described approach neural connectivity in macroscopically large neural circuits can be mapped with great accuracy, in scalable manner, using fast optical tools, and straightforward image processing. Relying on an electron microscopy dataset, we also derive and explicitly enumerate the conditions that should be met to allow synaptic connectivity studies with high-resolution optical tools.
ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data
Authors: Khiabanian Hossein , Van Vlierberghe Pieter , Palomero Teresa , Ferrando Adolfo , Rabadan Raul 
Published: July 2019

AbstractNext-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants using partially mapped reads in nextgen sequencing data. We also report ParMap’s successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.
Exploitation, secondary extinction and the altered trophic structure of Jamaican coral reefs
Authors: Roopnarine Peter , Hertog Rachel 
Published: July 2019

AbstractCoral reef communities of the Greater Antilles in the Caribbean have a long history of anthropogenic disturbance, driven by the exploitation for food of both vertebrate and invertebrate species. Exploitation, coupled with region wide declines of coral environments has resulted in local and regional vertebrate extinctions. The impact of those extinctions on reef communities, however, remains largely unexplored. Here we show, using a highly resolved model coral reef-seagrass food web, that at least 40 of 188 expected vertebrate species are absent from Jamaican coral reefs. Twenty one of the absent species are of high trophic level and are exploited by humans. The remainder of the absent species are unexploited, and comprises a significantly high proportion of specialized reef foragers. Many of those species are also more trophically specialized than their closest trophic competitors. We conclude that the absence of unexploited species from Jamaica is caused by the overexploitation of high trophic level species, and consequent trophic cascades and secondary extinction among their prey in an increasingly degraded reef environment. The result is a reef community depauperate of both exploited high trophic level predators, and unexploited, specialized lower trophic level reef foragers.
Homeoprotein Hbx4 represses adhesion molecule governing cytokinesis and development
Authors: Kim Ji-Sun , Seo Ji-Hui , Yim Hyung-Soon , Kang Sa-Ouk 
Published: July 2019

AbstractHomeobox genes encode proteins with a highly conserved DNA-binding motif and provoke morphological diversification of body segments by differentially controlling the expression of downstream targets. Here, we have identified hbx4, one of many homeobox genes in Dictyostelium discoideum and investigated its role during growth and development. In suspension, Hbx4-overexpressing cells, Hbx4^OE^, showed defects in cytokinesis and growth rate. During development, Hbx4^OE^ and hbx4-disrupting cells, hbx4&175; made differences in shape of mound and slug, cell-type proportioning from wild type KAx3 cells. These phenotypes were similar to those of mutant defective in cadA encoding Ca^2+^-dependent cell adhesion molecule so that we investigated the relationship between hbx4 and cadA. Overexpression of Hbx4 inhibited the expression of cadA and cAMP also failed to stimulate cadA in Hbx4^OE^. Furthermore, gel mobility shift assay showed the promoter of cadA contained Hbx4-binding site, indicating Hbx4 negatively regulates the expression of cadA. Proteome analysis revealed that overexpression of Hbx4 repressed the rdiA and abpB encoding rho guanine nucleotide dissociation inhibitor1, RhoGDI1 and actin bundling protein 34, ABP34, respectively. And the overexpression of cadA in Hbx4^OE^ cells rescued the defects and increased mRNA level of rdiA, abpB and one of Rho GTPase, rac1b. These results suggested that Hbx4 can modulate cytokinesis, cell sorting and cell-type proportioning by repressing cadA that regulates GTPase-dependent signaling pathway.
The response of two legume crops (hyacinth bean and Kidney bean) to the parasitism of field dodder (Cuscuta campestris)
Authors: Farah Awad 
Published: July 2019

AbstractAbstract: Microscopic examinations and chemical studies were performed to study the response of two legume crops, hyacinth bean (Lablab purpureus L.) Sweet and kidney bean (phaseolus vulgaris L.) to the filed dodder (FD) (Cuscuta campestris Yuncker) parasitism. Hyacinth bean, showing no effective resistance mechanisms,was found to be a highly susceptible host to FD. However, kidney bean, displaying resistant reactions towards the parasitism of FD,was found to be an incompatible host.The possible reasons for the resistance of kidney bean to FD were anatomical (hypersensitivity) and chemical (high contents of phenolic acids and lignin) stimulated defence mechanisms, which developed during the actual intrusion of FD haustorial cells inside its tissues.
Wikipedia as an encyclopaedia of life
Authors: Page Roderic 
Published: July 2019

AbstractIn his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision.
Whisker's Directional Selectivity: Orientation Columns in the Barrel Field?
Authors: Tsytsarev Vassiliy , Pope Daniel , Pumbo Elena , Yablonskii Alexander , Hofmann Michael 
Published: July 2019

AbstractUsing voltage-sensitive dye optical imaging methods, we visualized neural activity in the rat barrel cortex in response to the deflection of a single whisker in different directions. Obtained data indicates that fast movements of single whiskers in varying directions correlate with different patterns of activation in the somatosensory cortex. A functional map was created based on the voltage-sensitive dye optical signal. This supports prior research that vibrissae deflections cause responses in different cortical neurons within the barrel field according to the direction of the deflection. By analogy with the orientation columns in the visual cortex, directionally-biased single whisker responses to different directions of deflection could be a possible mechanism for the directional selectivity of this important sensory response.
A Fresh Look at Energy, Materials, and Labor in Agriculture
Authors: Baum Aaron , Patzek Tadeusz , Bender Martin , Renich Steve , Jackson Wes 
Published: July 2019

AbstractAn understanding of agriculture's energy, material, and labor requirements is essential for achieving economic and ecological sustainability, and for assessing the effectiveness of relevant policy decisions (biofuel subsidies, regulations, labeling, etc.). Previous studies of energy, materials, and labor use in farming have been based on either unverified voluntary reporting or test plots, rather than on the high-resolution measurements of mass and energy flows. Here we present a recursive analysis of 1.25 million data points describing in unprecedented detail the resource transactions on a 60 ha farm functioning for over 6 years. This analysis highlights the importance of accounting for all types of materials, as well as capital equipment, non-field labor, and commuting. The superior energy efficiency of the farm&apos;s energy-saving methods, including green manure, crop rotation, composting, and short-duration grazing -- compared with conventional methods -- persists even when the higher labor requirements are taken into account. One of the farm's methods, however -- the use of horses for traction -- is shown to be highly inefficient compared with mechanical tractors.
A Roadmap of Cancer Systems Biology
Authors: Wang Edwin 
Published: July 2019

AbstractWhat is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed.
Processing of insect retrotransposons by self-cleaving ribozymes
Authors: Ruminski Dana , Webb Chiu-Ho , Riccitelli Nathan , Luptak Andrej 
Published: July 2019

AbstractWe show that several classes of insect non-LTR retrotransposons harbor self-cleaving ribozymes of the HDV family at their 5′ termini. In Drosophila the R2 ribozymes exhibit highly differential in vivo expression and robust in vitro activity, modulated by an upstream sequence originating from the insertion site. Our data suggest a role for self-cleaving ribozymes in co-transcriptional processing of retrotransposons with implications for downstream events, including translation and retrotransposition.
Tumor suppressors p53, p63, and p73 inhibit migrating cancer stem cells by increasing the expression of stem cell suppressing miRNAs
Authors: Boominathan Lakshmanane 
Published: July 2019

AbstractZEB1/2 has been shown to suppress the expression of the tumor suppressors E-cadherin, TA-p73, INK4b, CDKN1a, and thereby promotes epithelial to mesenchymal transition, invasion, and metastasis. I have recently shown that p53-dependent miRs, such as miR-192, 215, 145, 203, 200b/c, 183, suppress the expression of ZEB1/2. Another recent study showed that ZEB1/2 suppresses the expression of miR-200b/c, miR-203, & miR-183, which in turn, inhibit the expression of stem cell factors, such as Sox-2, Klf-4, and BMI. ZEB1/2, by inhibiting the expression of stem cell factors suppressing miRs, it up regulates the expression of stem cell factors. By up regulating the stem cell factors and down regulating metastasis suppressors, ZEB1/2 promotes both metastasis and migration of cancer stem cells. p53/p63/p73, by down regulating the expression of ZEB1/2 through its target miRNAs, it could activate the expression of stem cell suppressing miRNAs, such as miR-200b/c, miR-203 & miR-183. Thereby, it could inhibit the expression of stem cell factors, such as Sox-2, Klf-4 and BMI-1(an inhibitor of INK4a/ARF). In addition, p53/p63/p73 appears to inhibit the expression of other EMT inducers, such as Snail1/2 and Twist, expression through its target miRs. Remarkably, bioinformatics analysis of stem cell factors suppressing miRNAs, miR-200, miR-183, miR-141, and miR-203, promoters revealed a number of p53/p63/p73 responsive elements, indicating that they could be direct transcriptional targets of p53/TA-p63/p73. Together, these data suggest that p53/TA-p63/p73, by suppressing the expression of ZEB1/2, Snail1/2, and Twist through its target miRs, it could inhibit migration, metastasis, and proliferation of cancer stem cells. In conclusion, the data presented here provide mechanistic insights into how TA-p63/p73 and p53 function as metastasis suppressors.
The last Charrua Indian; (Uruguay): analysis of the remains of Chief Vaimaca Per&x00FA;.
Authors: Sans Monica , Figueiro Gonzalo , Sanguinetti Carlos , Echarte-Rafaelli Lourdes , Portela Cecilia , Taranto Luis , Pizzarossa Carlos , Oliver Roberto , Manikowski Rosana , Barreto Isabel , Hidalgo Pedro , Berro Guido 
Published: July 2019

AbstractUruguay is the only Latin American country that at present lacks Native populations and little is known about its prehistoric populations. In the construction of National identity, the unique reference to Natives is about Charra Indians, one of the most important ethnic groups that lived in the territory and exterminated in the 1830s. In 1833, four survivors were taken to be exhibited and studied in France, becoming martyrs and a symbol of their nation. The skeletal remains of Chief Per&x00FA; were preserved and studied mainly by Rivet1; these are the only remains certainly identified as belonging to a Charr&x00FA;a. In 2002, the French government returned the remains to Uruguay, where they were buried with honours at the National Pantheon. Before the burial, we performed morphological studies as well as extracted samples for DNA analysis. Peru&apos;s morphology is coherent with the one of a nomadic warrior: robust body with strong muscular insertions, wounds, and healthy diet based mainly on meat. Here we show that metric and morphological data as well as maternal inherited mitochondrial DNA (mtDNA) hypervariable region I (HVRI) and restriction fragment length polymorphisms (RFLPs), indicate a close relationship with Pampa-Patagonian Indians, and specially, with prehistoric Natives buried in mounds from eastern Uruguay. This last finding is particularly important to understand Uruguayan prehistory and history, raising the debate about who the mound builders were, and showing continuity between them, historic Charr&x00FA;a Indians, and present populations.
Networks, Extinction and Paleocommunity Food Webs
Authors: Roopnarine Peter 
Published: July 2019

AbstractFood webs represent 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 the consideration of paleocommunity food webs. The fossil record presents challenges in this regard, but the problem can be approached with combinatoric analysis and network theory. This paper is an introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores a probabilistic and numerical approach.
Effect of Non-Coding RNA on Post-Transcriptional Gene Silencing of Alzheimer Disease
Authors: Namboori Krishnan , Mohan Arun , K.U. Radhagayathri , Gopal Varun , C.S. Vasavi , P Premkumar , Gopakumar Deepa , K.I. Ramachandran 
Published: July 2019

AbstractA large amount of hidden biological information is contained in the human genome, which is not expressed or revealed in the form of proteins; the usual end product form of gene expression. Instead, most of such information is in the form of non-coding RNAs (ncRNAs). ncRNAs correspond to genes that are transcribed, but do not get translated into proteins. This part of the genome was, till recently, considered as ‘junk’. The term ‘junk’ implied lack of any discernible function of these RNA. More than 98% of the human genomic size encompasses these non-coding RNAs. But, recent research has evidently brought out the indispensible contribution of non-coding RNA in controlling and regulating gene expression. ncRNA such as siRNAs and microRNAs have been reported to greatly help in causing post-transcriptional gene silencing (PTGS) in cells through RNA interference (RNAi) pathway. In this work, we have investigated the possibility of using siRNAs and microRNAs to aid in gene silencing of early onset Alzheimer’s disease genes. Alzheimer’s disease specific mutations and their corresponding positions in mRNA have been identified for six genes; Presenilin-1, Presenilin-2, APP (amyloid beta precursor protein), APBB3, BACE-1 and PSENEN. Small interfering RNAs (siRNAs) that can cause PTGS through RNA interference pathway have been designed. RNA analysis has been done to verify complementarity of antisense siRNA sequence with target mRNA sequence. Interaction studies have been done computationally between these antisense siRNA strands and seven Argonaute proteins. From the interaction studies, only one of the seven Argonaute proteins; 1Q8K, was found to have interaction with the siRNAs indicating the importance and uniqueness of this particular protein in RISC (RNA induced silencing complex). The interaction studies have been carried out for the microRNAs also. Out of the 700 mature human microRNAs collected, 394 microRNAs have been identified to show partial complementarity with their target sequence on PSEN-1 mRNA. Of these 394, five microRNAs have shown partial complementarity to early onset Alzheimer’s disease specific mutations in PSEN-1 mRNA. Interaction studies have been done between these microRNAs and Argonaute proteins. Thus, design, characterization and analysis of ncRNAs that contribute to post transcriptional gene silencing of Alzheimer’s disease have been achieved.
Death of human tumor endothelial cells in vitro through a probable calcium-associated mechanism induced by bevacizumab and detected via a novel method
Authors: Weisenthal Larry , Liu Haddy , Rueff-Weisenthal Constance 
Published: July 2019

AbstractWe isolated three dimensional cell clusters from fresh human solid tumors and also isolated human neoplastic and normal lymphatic cells. Cells were cultured for 96 hours with and without bevacizumab and other agents. At concentrations of bevacizumab which completely removed VEGF from the culture medium, dead microvascular cells were detected through Fast Green/H&E staining as previously described. These peculiar staining characteristics suggested the involvement of calcium, and this was confirmed through staining with Alizarin red S. Using Alizarin staining as a marker for endothelial cell death permitted the use of public domain image analysis software which resulted in a sensitive and specific system for identifying active pharmaceuticals which target the tumor microvasculature at the same time direct antitumor cell effects are determined. Our results suggest an important role for calcium in endothelial cell death mediated by bevacizumab and other agents and further suggest that agents promoting calcium influx may potentiate the activity of antiangiogenic agents.