bluuebunny/crossref_metadata_2025_split huggingface dataset:
The E3 ubiquitin ligase c-IAP1 regulates PCSK9-mediated LDLR degradation: Linking the TNF-&x03B1; pathway to cholesterol uptake
Authors: Xu Weiming , Liu Lizhi 
Published: July 2019

AbstractProprotein convertase subtilisin/kexin type 9 (PCSK9), in addition to LDLR (low-density lipoprotein receptor) and APOB (apolipoprotein B), is one of three loci implicated in autosomal dominant hypercholesterolaemia (ADH)^1^. A number of PCSK9 gain-of-function mutations and loss-of-function mutations have been identified from families afflicted with ADH with hypercholesterolaemia or hypocholesterolaemia, respectively^1-4^. In humans, the main function of PCSK9 appears to be the post-transcriptional regulation of the number of cell-surface LDL receptors^5-7^. To date, only LDLR and its closest family members VLDLR and ApoER2 have been shown to bind with PCSK9^8,9^. To find new binding partners for PCSK9, we used a shotgun proteomic method to analyse the protein complex pulled down by immunoprecipitation against FLAG-tagged PCSK9 protein. Among 22 potential novel binding proteins identified, we found that the cellular inhibitor of apoptosis protein 1 (c-IAP1^10^) and the TNF receptor-associated factor 2 (TRAF2^11^) complex are regulated differently in different dominant PCSK9 mutations that occur naturally. Further immunoprecipitation analysis showed that c-IAP1 is a direct binding partner for PCSK9. One of the "gain-of-function" mutants, PCSK9-S127R, which has impaired autocatalytic activity, is defective in binding to c-IAP1. The other dominant mutation, PCSK9-D374Y^12^, which is 10-fold more potent in degrading the LDLR protein than wild-type PCSK9, can be significantly ubiquitinated by c-IAP1 in vitro. The ubiquitinated PCSK9-D374Y is unable to degrade LDLR, which is its main cause of hypercholesterolaemia in patients. These results indicate that there is a novel cholesterol uptake regulation pathway linking PCSK9/LDLR to the E3 ubiquitin ligase c-IAP1 in a TNF-[alpha] response pathway. This highlights the possibility of developing new treatments for human cardiovascular diseases through ubiquitin ligase-mediated ubiquitination of target proteins in cholesterol metabolism.
Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Authors: Bhardwaj Mohit , Bharadwaj Leena , Trigunayat Kritika , Trigunayat Madan Mohan 
Published: July 2019

AbstractThe paper reveals thermal characteristics of P.falciparum species specific proteins. These proteins determine why P. vivex species are dominant over P.falciparum in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of P.falciparum species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for Plasmodium falciparum can remain in native state between &8805;7 degree centigrade and &8804;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd protein were found more heat susceptible for temperature minima and maxima than Pvsd proteins of P. vivex causing all time high population ratio of P.falciparum species.
The Size-Weight Illusion Is Not an Illusion When Picking the Best Objects to Throw
Authors: Zhu Qin , Bingham Geoffrey 
Published: July 2019

AbstractHeaviness perception involves a misperception of weight known, since the 19th century, as the Size-Weight Illusion ^1^. The larger of two objects of equal mass is reported to be lighter than the smaller when they are lifted. The illusion has been found to be reliable and robust. It persists even when people know that the masses are equal and handle objects properly ^2^. It has been exhibited by children of only 2 years of age ^3,4^. All this suggests that the effect might be intrinsic to humans. Although different hypotheses have been advanced to account for the illusion over the 100+ years it has been studied ^5-11^, its origin remains unknown. More recently, people&apos;s perception of optimal objects for long distance throwing was found to exhibit a size-weight relation similar to the illusion ^12,13^, greater weights were picked for larger objects and they were indeed thrown to the greatest distances. Here we show that the perception of heaviness (including the illusion) and perception of optimal objects for long distance throwing are in fact equivalent. Thus, the size-weight illusion has a useful application: optimal objects for throwing are picked by a thrower as having a particular heaviness, which is the best heaviness learned when learning to throw ^14,15^. Long distance throwing is a uniquely human ability that is understood to have enabled our species to survive and even thrive during the ice ages ^16-22^. The fact that the illusion is a functional component of human throwing skill adds credence to the idea that it is intrinsic to the species.
TreeBASE2: Rise of the Machines
Authors: Vos Rutger , Lapp Hilmar , Piel William , Tannen Val 
Published: July 2019

AbstractTreeBASE is a public repository of peer-reviewed phylogenetic knowledge. Researchers submit their results to TreeBASE when they are writing a manuscript based on them for publication in a suitable journal. The submitted data are assigned permanent, unique identifiers and web addresses that authors can refer to in their article. Anyone can locate and access the data once the study has been published by TreeBASE and by the targeted journal.A prototype of this system has served the phylogenetics community well for a number of years, accumulating the results of thousands of studies. The usage model was that of a silo where data could only be accessed through a web browser, and only be downloaded in representations that omitted important associated metadata. A human with considerable expertise needed to read and interpret the web pages through which everything was served up to make sense out of what was available. This model is not always practical. For example, phyloinformatic research often uses so much data that automation is becoming necessary. Where human intervention is no longer feasible, machines – which are stupid – must be able to do the job instead; and they need to be told what is what. This has spurred more explicit standardization of the syntax and semantics of phylogenetic knowledge. The latest version of TreeBASE facilitates this by adopting a collection of community standards: * PhyloWS for automated searching using a contextual query language and retrieval using a clearly defined URL API. * NeXML for robust data syntax and flexible metadata annotation. * CDAO (and other ontologies) for defining the semantics of the metadata. We will present an overview of how these components work together to make phylogenetic knowledge accessible to machines on the semantic web. Using this new architecture, client side software (including off-the-shelve tools such as RSS readers) can query, transform and download TreeBASE data autonomously.
GMOD for Evolutionary Biology
Authors: Buels Robert , Clements Dave 
Published: July 2019

AbstractThe Generic Model Organism Database (GMOD, "http://gmod.org":http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data. GMOD is also a community of people addressing common challenges with biological data. Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.This talk will focus on three areas of particular interest to iEvoBio participants. 1) GBrowse_syn comparative genomics viewer2) Natural Diversity Module of the Chado database schema3) GMOD evolutionary biology hackathon The GBrowse_syn comparative genomics viewer displays synteny between a reference and any number of related species. It shows inversions, duplications, and indels, and can show synteny across non-contiguous regions. It is built on the widely used GBrowse genome viewer. The Natural Diversity Module is an extension to GMOD’s Chado database schema to enable Chado to support natural diversity, population genomics, individuals, breeding, phenotypes and geolocation information. This module is the first extension to Chado to be designed by the community, rather than at one institution. We will close by soliciting nominations and ideas for a GMOD Evolutionary Biology Hackathon. This hackathon will be held November 8-12, at NESCent, which is sponsoring the event. There will be an open call for participation in August.
Effective Phylogenetic Compression with TreeZip
Authors: Matthews Suzanne , Sul SeungJin , Williams Tiffani 
Published: July 2019

AbstractPhylogenetic trees are family trees that represent the relationships between a group of organisms, or taxa. The most popular techniques for reconstructing phylogenetic trees intelligently navigate an exponentially-sized tree space by solving NP-hard optimization problems that that best hypothesize the evolutionary history for a given set of taxa. Instead of reconstructing a single tree, these heuristics often return tens to hundreds of thousands of trees that represent equally-plausible hypotheses for how the taxa of interest evolved from a common ancestor. As biologists attempt to reconstruct increasingly larger phylogenies, these tree collections only continue to grow in size. To combat the cost of storage and to facilitate the transfer of these large tree files, we developed a new compression algorithm called TreeZip that reduces the requirements for storing large collections of evolutionary trees over standard compression methods. TreeZip is distributed under the GPL license and can be accessed at: "http://treezip.googlecode.com":http://treezip.googlecode.com.
From aptamer-based biomarker discovery to diagnostic and clinical applications: an aptamer-based, streamlined multiplex proteomic assay
Authors: Kraemer Stephan , Vaught Jonathon , Bock Christopher , Gold Larry , Katilius Evaldas , Keeney Tracy , Kim Nancy , Saccomano Nicholas , Wilcox Sheri , Zichi Dom , Sanders Glenn 
Published: July 2019

AbstractRecently, we reported an aptamer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated. We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community.
It is better than you think: fluid intelligence across the lifespan
Authors: Alloway Tracy Packiam , Alloway Ross 
Published: July 2019

AbstractThe growth and decline of fluid intelligence is associated with brain structural changes. For example, development of fluid IQ is associated with cortex thickness during the critical period between 6 to 12 years old. On the other end of the lifespan, poor performance in cognitive functioning is attributed to a decrease of frontal gray matter density in elderly populations. In particular, there is a sharp decline in fluid IQ scores after 65 years of age. There is substantial evidence that working memory and fluid intelligence (Gf) share neural substrates, such as the prefrontal and parietal cortices. However, very little research has examined whether the pattern of growth and decline in working memory mirrors that of fluid intelligence. For example, does the decline of working memory skills in elderly populations mirror fluid intelligence? Is the rate of working memory decline similar to the rate of growth?
Validation of a Multivariate Serum Profile for Epithelial Ovarian Cancer Using a Prospective Multi-Site Collection
Authors: Seshaiah Partha , Bertenshaw Greg , Chen Tzong-Hao , Bergstrom Katharine , Zhao Jinghua , Mapes James , Stephen Laurie , Amonkar Suraj , McCollum Michael , Miller Brigitte , Roman Lynda , Karlan Beth , Chalas Eva , DiSilvestro Paul , Barter James , Orr James , Bigsby Glenn , Holloway Robert , Alvarez Ronald , Yip Ping , Mansfield Brian 
Published: July 2019

AbstractIn previous studies we described the use of a retrospective collection of ovarian cancer and benign disease samples, in combination with a large set of multiplexed immunoassays and a multivariate pattern recognition algorithm, to develop an 11-biomarker classification profile that is predictive for the presence of epithelial ovarian cancer. In this study, customized, Luminex-based multiplexed immunoassay kits were GMP-manufactured and the classification profile was refined from 11 to 8 biomarkers (CA-125, epidermal growth factor receptor, CA 19-9, C-reactive protein, tenascin C, apolipoprotein AI, apolipoprotein CIII, and myoglobin). The customized kits and the 8-biomarker profile were then validated in a double-blinded manner using prospective samples collected from women scheduled for surgery, with a gynecologic oncologist, for suspicion of having ovarian cancer. The performance observed in model development held in validation, demonstrating 81.1% sensitivity (95% CI 72.6 – 87.9%) for invasive epithelial ovarian cancer and 85.4% specificity (95% CI 81.1 – 88.9%) for benign ovarian conditions. The specificity for normal healthy women was 95.6% (95% CI 83.6 – 99.2%). These results have encouraged us to undertake a second validation study arm, currently in progress, to examine the performance of the 8-biomarker profile on the population of women not under the surgical care of a gynecologic oncologist.
Origin and diversification of steroids: Co-evolution of enzymes and nuclear receptors
Authors: Baker Michael 
Published: July 2019

AbstractRecent sequencing of amphioxus and sea urchin genomes has provided important data for understanding the origins of enzymes that synthesize adrenal and sex steroids and the receptors that mediate physiological response to these vertebrate steroids. Phylogenetic analyses reveal that CYP11A and CYP19, which are involved in the synthesis of adrenal and sex steroids, first appear in the common ancestor of amphioxus and vertebrates. This correlates with recent evidence for the first appearance in amphioxus of receptors with close similarity to vertebrate steroid receptors. Other CYP450 enzymes involved in steroid synthesis can be traced back to invertebrates, in which they have at least two functions: detoxifying xenobiotics and catalyzing the synthesis of sterols that activate nuclear receptors. CYP450 metabolism of hydrophobic xenobiotics may have been a key event in the origin of ligand-activated steroid receptors from constitutively active nuclear receptors.
Simple reverse genetics approach to elucidating the biosynthetic pathway of complex thiopeptide nocathiacin
Authors: Wei Maochen , Deng Jing , Wang Shuzhen , Liu Nan , Chen Yijun 
Published: July 2019

AbstractBiothythetic pathway of the most drugable thiopeptide nocathiacin has been elucidated by applying reverse genetics method based on its structural features. The present study provides an efficient approach for an easy access to the biosynthetic gene clusters of complex bioactive peptides that are ribosomally synthesized with extensive posttranslational modifications.
The Future of the Journal? Integrating research data with scientific discourse
Authors: de Waard Anita 
Published: July 2019

AbstractTo advance the pace of scientific discovery we propose a conceptual format that forms the basis of a truly new way of publishing science. In our proposal, all scientific communication objects (including experimental workflows, direct results, email conversations, and all drafted and published information artifacts) are labeled and stored in a great, big, distributed data store (or many distributed data stores that are all connected). Each item has a set of metadata attached to it, which includes (at least) the person and time it was created, the type of object it is, and the status of the object including intellectual property rights and ownership. Every researcher can (and must) deposit every knowledge item that is produced in the lab into this repository. With this deposition goes an essential metadata component that states who has the rights to see, use, distribute, buy or sell this item. Into this grand (and system-wise distributed, cloud-based) architecture, all items produced by a single lab, or several labs, are stored, labeled and connected.
Detection of MicroRNAs in Dried Serum Blots
Authors: Patnaik Santosh , Mallick Reema , Yendamuri Sai 
Published: July 2019

AbstractMicroRNAs are short RNAs which can be utilized as biomarkers for a variety of conditions. They are detectable in serum, and changes in the levels of circulating microRNAs have been associated with different diseases. We tested for the presence of microRNAs in serum that is dried on paper and stored unrefrigerated instead of being kept frozen. MicroRNAs were readily detectable in such blots, and their detectability was improved by using paper made of cellulose instead of glass fiber, and by re-hydrating dried blots with Trizol™ instead of water, phosphate-buffered saline, or guanidine hydrochloride before RNA extraction. MicroRNA preservation was not diminished by drying of blots at 37, 45 or 60 ºC instead of room temperature or by storage of blots at 37, 45 or 60 ºC instead of room temperature, but was worse when blots were dried incompletely or exposed to high humidity during storage. Preservation of microRNAs in serum was not adversely affected if instead of being kept frozen at -80 ºC it was stored as dried blots at room temperature or 37 ºC for ten or eight and a half months, respectively. In a group of ten individuals, microRNA quantifications of -80 ºC-frozen or dried sera stored at room temperature correlated well. Dried blots may thus be a convenient and safer way to save, transport, and store serum without refrigeration for microRNA assays.
The Etiology of Depression in Parkinson's Disease
Authors: Sourani Dafhna , Eitan Renana , Oelman Gadi 
Published: July 2019

AbstractAlthough a high percentage of Parkinson&apos;s disease (PD) patients suffer from depression in addition to their motor disabilities, the etiology of this depression is unknown. Within the framework of the monoamine deficiency hypothesis of depression, we present a neuronal circuitry that accounts for depression in PD. Using behavioral and direct neuronal circuitry measurements we show that the habenula mediates the coupling between the dopaminergic and the serotonergic systems and argue that alterations in basal ganglia activity cause habenula hyperactivity that result with depression in PD. Behavioral results from novelty suppressed feeding and force swim tests, as well as direct circuitry measures with manganese enhanced MRI indicate (i) depressive-like behavior and reduced raphe nuclei connectivity/excitability in unilateral 6-hydroxydopamine injected rats, (ii) partial normalization of behavior and raphe connectivity after apomorphine treatment, and (iii) normalization of behavior after bilateral lesion of the habenula. These findings open up avenues for therapeutic intervention.
Without magic bullets: the biological basis for public health interventions against protein folding disorders
Authors: Wallace Rodrick 
Published: July 2019

AbstractProtein folding disorders of aging like Alzheimer's and Parkinson's diseases currently present intractable medical challenges. 'Small molecule' interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary 'physics' or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty's (2010a) elegant exploration of the genetic code. The formalism produces large-scale, quasi-equilibrium 'resilience' states representing normal and pathological protein folding regulation under a cellular-level cognitive paradigm similar to that proposed by Atlan and Cohen (1998) for the immune system. Generalization to long times produces diffusion models of protein folding disorders in which epigenetic or life history factors determine the rate of onset of regulatory failure, in essence, a premature aging driven by familiar synergisms between disjunctions of resource allocation and need in the context of socially or physiologically toxic exposures and chronic powerlessness at individual and group scales.
Beautifying Data in the Real World
Authors: Willighagen Egon , Bradley Jean-Claude , Guha Rajarshi , Lang Andrew , Lindenbaum Pierre , Neylon Cameron , Williams Antony 
Published: July 2019

AbstractThis chapter from the O'Reilly book "Beautiful Data" describes the use of Open Notebook Science to crowdsource solubility data. The use of GoogleDocs, wikis, ChemSpider, RDF, the Chemistry Development Kit and Second Life is described.
The association between having a household member with a cancer-related limitation and human papillomavirus vaccine uptake
Authors: Offutt-Powell Tabatha , Ojha Rohit , Tota Joseph , Singh Karan 
Published: July 2019

AbstractOBJECTIVE: To evaluate the association between having a household member with a cancer-related limitation (physical, mental, or emotional) and human papillomavirus (HPV) vaccine uptake among females aged 9 – 17 years.
METHODS:
We analyzed 2008 National Health Interview Survey for our cross-sectional analysis. All households with females aged 9 – 17 years were eligible for inclusion in our analysis. Our outcomes of interest included HPV vaccine initiation (≥1 dose) and series completion (full 3 doses). A dichotomous variable indicating a cancer-related limitation for a household member was created if at least one adult in the household responded to having a limitation caused by cancer. We used Firth’s bias-reducing penalized likelihood for logistic regression[11] to estimate prevalence odds ratios (ORs) and corresponding 95% profile penalized likelihood confidence intervals (CIs) for HPV vaccine uptake among young females who had a household member with a cancer-related limitation compared to young females who did not have a household member with a cancer-related limitation after adjusting for child’s age, race/ethnicity, and SES.

RESULTS:
HPV vaccine initiation and completion were higher among females aged 9-17 years who had a household member with a cancer-related limitation (Initiation: OR=1.42, 95%CI: 0.26, 5.18); Completion: OR=2.50, 95%CI: 0.26, 11.58).

CONCLUSION:
Our results suggest that females aged 9 – 17 years in the United States who have a household member with a cancer-related limitation (physical, mental, or emotional) may be more likely to initiate and complete the HPV vaccination. However, our point estimates lack precision (evident by wide confidence intervals) because of limited prevalence of the exposure in our study population.