journal
MENU ▼
Read by QxMD icon Read
search

PLoS Biology

journal
https://www.readbyqxmd.com/read/27906976/a-laboratory-critical-incident-and-error-reporting-system-for-experimental-biomedicine
#1
Ulrich Dirnagl, Ingo Przesdzing, Claudia Kurreck, Sebastian Major
We here propose the implementation of a simple and effective method to enhance the quality of basic and preclinical academic research: critical incident reporting (CIR). CIR has become a standard in clinical medicine but to our knowledge has never been implemented in the context of academic basic research. We provide a simple, free, open-source software tool for implementing a CIR system in research groups, laboratories, or large institutions (LabCIRS). LabCIRS was developed, tested, and implemented in our multidisciplinary and multiprofessional neuroscience research department...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27902690/decoding-the-interactions-regulating-the-active-state-mechanics-of-eukaryotic-protein-kinases
#2
Hiruy S Meharena, Xiaorui Fan, Lalima G Ahuja, Malik M Keshwani, Christopher L McClendon, Angela M Chen, Joseph A Adams, Susan S Taylor
Eukaryotic protein kinases regulate most cellular functions by phosphorylating targeted protein substrates through a highly conserved catalytic core. In the active state, the catalytic core oscillates between open, intermediate, and closed conformations. Currently, the intramolecular interactions that regulate the active state mechanics are not well understood. Here, using cAMP-dependent protein kinase as a representative model coupled with biochemical, biophysical, and computational techniques, we define a set of highly conserved electrostatic and hydrophobic interactions working harmoniously to regulate these mechanics...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27893764/virus-mediated-alterations-in-mirna-factors-and-degradation-of-viral-mirnas-by-mcpip1
#3
Christine Happel, Dhivya Ramalingam, Joseph M Ziegelbauer
Kaposi's sarcoma-associated herpesvirus (KSHV), the causative agent of Kaposi's sarcoma, encodes 25 mature viral miRNAs. MCP-1-induced protein-1 (MCPIP1), a critical regulator of immune homeostasis, has been shown to suppress miRNA biosynthesis via cleavage of precursor miRNAs through its RNase domain. We demonstrate that MCPIP1 can directly cleave KSHV and EBV precursor miRNAs and that MCPIP1 expression is repressed following de novo KSHV infection. In addition, repression with siRNAs to MCPIP1 in KSHV-infected cells increased IL-6 and KSHV miRNA expression, supporting a role for MCPIP1 in IL-6 and KSHV miRNA regulation...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27893754/cyp26-enzymes-facilitate-second-heart-field-progenitor-addition-and-maintenance-of-ventricular-integrity
#4
Ariel B Rydeen, Joshua S Waxman
Although retinoic acid (RA) teratogenicity has been investigated for decades, the mechanisms underlying RA-induced outflow tract (OFT) malformations are not understood. Here, we show zebrafish embryos deficient for Cyp26a1 and Cyp26c1 enzymes, which promote RA degradation, have OFT defects resulting from two mechanisms: first, a failure of second heart field (SHF) progenitors to join the OFT, instead contributing to the pharyngeal arch arteries (PAAs), and second, a loss of first heart field (FHF) ventricular cardiomyocytes due to disrupted cell polarity and extrusion from the heart tube...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27880767/distribution-of-misfolded-prion-protein-seeding-activity-alone-does-not-predict-regions-of-neurodegeneration
#5
James Alibhai, Richard A Blanco, Marcelo A Barria, Pedro Piccardo, Byron Caughey, V Hugh Perry, Tom C Freeman, Jean C Manson
Protein misfolding is common across many neurodegenerative diseases, with misfolded proteins acting as seeds for "prion-like" conversion of normally folded protein to abnormal conformations. A central hypothesis is that misfolded protein accumulation, spread, and distribution are restricted to specific neuronal populations of the central nervous system and thus predict regions of neurodegeneration. We examined this hypothesis using a highly sensitive assay system for detection of misfolded protein seeds in a murine model of prion disease...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27880766/sox2-and-pi3k-cooperate-to-induce-and-stabilize-a-squamous-committed-stem-cell-injury-state-during-lung-squamous-cell-carcinoma-pathogenesis
#6
Bo Ram Kim, Emily Van de Laar, Michael Cabanero, Shintaro Tarumi, Stefan Hasenoeder, Dennis Wang, Carl Virtanen, Takaya Suzuki, Bizhan Bandarchi, Shingo Sakashita, Nhu An Pham, Sharon Lee, Shaf Keshavjee, Thomas K Waddell, Ming-Sound Tsao, Nadeem Moghal
Although cancers are considered stem cell diseases, mechanisms involving stem cell alterations are poorly understood. Squamous cell carcinoma (SQCC) is the second most common lung cancer, and its pathogenesis appears to hinge on changes in the stem cell behavior of basal cells in the bronchial airways. Basal cells are normally quiescent and differentiate into mucociliary epithelia. Smoking triggers a hyperproliferative response resulting in progressive premalignant epithelial changes ranging from squamous metaplasia to dysplasia...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27870851/a-normalization-framework-for-emotional-attention
#7
Xilin Zhang, Shruti Japee, Zaid Safiullah, Nicole Mlynaryk, Leslie G Ungerleider
The normalization model of attention proposes that attention can affect performance by response- or contrast-gain changes, depending on the size of the stimulus and attention field. Here, we manipulated the attention field by emotional valence, negative faces versus positive faces, while holding stimulus size constant in a spatial cueing task. We observed changes in the cueing effect consonant with changes in response gain for negative faces and contrast gain for positive faces. Neuroimaging experiments confirmed that subjects' attention fields were narrowed for negative faces and broadened for positive faces...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27861590/phylosymbiosis-relationships-and-functional-effects-of-microbial-communities-across-host-evolutionary-history
#8
Andrew W Brooks, Kevin D Kohl, Robert M Brucker, Edward J van Opstal, Seth R Bordenstein
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27855162/adamts5-is-a-critical-regulator-of-virus-specific-t-cell-immunity
#9
Meagan McMahon, Siying Ye, Leonard Izzard, Daniel Dlugolenski, Ralph A Tripp, Andrew G D Bean, Daniel R McCulloch, John Stambas
The extracellular matrix (ECM) provides physical scaffolding for cellular constituents and initiates biochemical and biomechanical cues that are required for physiological activity of living tissues. The ECM enzyme ADAMTS5, a member of the ADAMTS (A Disintegrin-like and Metalloproteinase with Thrombospondin-1 motifs) protein family, cleaves large proteoglycans such as aggrecan, leading to the destruction of cartilage and osteoarthritis. However, its contribution to viral pathogenesis and immunity is currently undefined...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27851749/the-machado-joseph-disease-deubiquitinase-ataxin-3-regulates-the-stability-and-apoptotic-function-of-p53
#10
Hongmei Liu, Xiaoling Li, Guozhu Ning, Shu Zhu, Xiaolu Ma, Xiuli Liu, Chunying Liu, Min Huang, Ina Schmitt, Ullrich Wüllner, Yamei Niu, Caixia Guo, Qiang Wang, Tie-Shan Tang
As a deubiquitinating enzyme (DUB), the physiological substrates of ataxin-3 (ATX-3) remain elusive, which limits our understanding of its normal cellular function and that of pathogenic mechanism of spinocerebellar ataxia type 3 (SCA3). Here, we identify p53 to be a novel substrate of ATX-3. ATX-3 binds to native and polyubiquitinated p53 and deubiquitinates and stabilizes p53 by repressing its degradation through the ubiquitin (Ub)-proteasome pathway. ATX-3 deletion destabilizes p53, resulting in deficiency of p53 activity and functions, whereas ectopic expression of ATX-3 induces selective transcription/expression of p53 target genes and promotes p53-dependent apoptosis in both mammalian cells and the central nervous system of zebrafish...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27846219/pharmacological-fingerprints-of-contextual-uncertainty
#11
Louise Marshall, Christoph Mathys, Diane Ruge, Archy O de Berker, Peter Dayan, Klaas E Stephan, Sven Bestmann
Successful interaction with the environment requires flexible updating of our beliefs about the world. By estimating the likelihood of future events, it is possible to prepare appropriate actions in advance and execute fast, accurate motor responses. According to theoretical proposals, agents track the variability arising from changing environments by computing various forms of uncertainty. Several neuromodulators have been linked to uncertainty signalling, but comprehensive empirical characterisation of their relative contributions to perceptual belief updating, and to the selection of motor responses, is lacking...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27846209/prediction-errors-but-not-sharpened-signals-simulate-multivoxel-fmri-patterns-during-speech-perception
#12
Helen Blank, Matthew H Davis
Successful perception depends on combining sensory input with prior knowledge. However, the underlying mechanism by which these two sources of information are combined is unknown. In speech perception, as in other domains, two functionally distinct coding schemes have been proposed for how expectations influence representation of sensory evidence. Traditional models suggest that expected features of the speech input are enhanced or sharpened via interactive activation (Sharpened Signals). Conversely, Predictive Coding suggests that expected features are suppressed so that unexpected features of the speech input (Prediction Errors) are processed further...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27832101/animal-study-registries-results-from-a-stakeholder-analysis-on-potential-strengths-weaknesses-facilitators-and-barriers
#13
Susanne Wieschowski, Diego S Silva, Daniel Strech
Publication bias in animal research, its extent, its predictors, and its potential countermeasures are increasingly discussed. Recent reports and conferences highlight the potential strengths of animal study registries (ASRs) in this regard. Others have warned that prospective registration of animal studies could diminish creativity, add administrative burdens, and complicate intellectual property issues in translational research. A literature review and 21 international key-informant interviews were conducted and thematically analyzed to develop a comprehensive matrix of main- and subcategories for potential ASR-related strengths, weaknesses, facilitators, and barriers (SWFBs)...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27832072/current-incentives-for-scientists-lead-to-underpowered-studies-with-erroneous-conclusions
#14
Andrew D Higginson, Marcus R Munafò
We can regard the wider incentive structures that operate across science, such as the priority given to novel findings, as an ecosystem within which scientists strive to maximise their fitness (i.e., publication record and career success). Here, we develop an optimality model that predicts the most rational research strategy, in terms of the proportion of research effort spent on seeking novel results rather than on confirmatory studies, and the amount of research effort per exploratory study. We show that, for parameter values derived from the scientific literature, researchers acting to maximise their fitness should spend most of their effort seeking novel results and conduct small studies that have only 10%-40% statistical power...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27832071/approach-induced-biases-in-human-information-sampling
#15
Laurence T Hunt, Robb B Rutledge, W M Nishantha Malalasekera, Steven W Kennerley, Raymond J Dolan
Information sampling is often biased towards seeking evidence that confirms one's prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27832066/modifiers-of-the-genotype-phenotype-map-hsp90-and-beyond
#16
Rachel Schell, Martin Mullis, Ian M Ehrenreich
Disruption of certain genes alters the heritable phenotypic variation among individuals. Research on the chaperone Hsp90 has played a central role in determining the genetic basis of this phenomenon, which may be important to evolution and disease. Key studies have shown that Hsp90 perturbation modifies the effects of many genetic variants throughout the genome. These modifications collectively transform the genotype-phenotype map, often resulting in a net increase or decrease in heritable phenotypic variation...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27832064/project-bioeyes-accessible-student-driven-science-for-k-12-students-and-teachers
#17
Jamie R Shuda, Valerie G Butler, Robert Vary, Steven A Farber
BioEYES, a nonprofit outreach program using zebrafish to excite and educate K-12 students about science and how to think and act like scientists, has been integrated into hundreds of under-resourced schools since 2002. During the week-long experiments, students raise zebrafish embryos to learn principles of development and genetics. We have analyzed 19,463 participating students' pre- and post-tests within the program to examine their learning growth and attitude changes towards science. We found that at all grade levels, BioEYES effectively increased students' content knowledge and produced favorable shifts in students' attitudes about science...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27828957/plasticity-in-single-axon-glutamatergic-connection-to-gabaergic-interneurons-regulates-complex-events-in-the-human-neocortex
#18
Viktor Szegedi, Melinda Paizs, Eszter Csakvari, Gabor Molnar, Pal Barzo, Gabor Tamas, Karri Lamsa
In the human neocortex, single excitatory pyramidal cells can elicit very large glutamatergic EPSPs (VLEs) in inhibitory GABAergic interneurons capable of triggering their firing with short (3-5 ms) delay. Similar strong excitatory connections between two individual neurons have not been found in nonhuman cortices, suggesting that these synapses are specific to human interneurons. The VLEs are crucial for generating neocortical complex events, observed as single pyramidal cell spike-evoked discharge of cell assemblies in the frontal and temporal cortices...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27824858/prefrontal-markers-and-cognitive-performance-are-dissociated-during-progressive-dopamine-lesion
#19
Charles R E Wilson, Julien Vezoli, Frederic M Stoll, Maïlys C M Faraut, Vincent Leviel, Kenneth Knoblauch, Emmanuel Procyk
Dopamine is thought to directly influence the neurophysiological mechanisms of both performance monitoring and cognitive control-two processes that are critically linked in the production of adapted behaviour. Changing dopamine levels are also thought to induce cognitive changes in several neurological and psychiatric conditions. But the working model of this system as a whole remains untested. Specifically, although many researchers assume that changing dopamine levels modify neurophysiological mechanisms and their markers in frontal cortex, and that this in turn leads to cognitive changes, this causal chain needs to be verified...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27814355/differences-in-collaboration-patterns-across-discipline-career-stage-and-gender
#20
Xiao Han T Zeng, Jordi Duch, Marta Sales-Pardo, João A G Moreira, Filippo Radicchi, Haroldo V Ribeiro, Teresa K Woodruff, Luís A Nunes Amaral
Collaboration plays an increasingly important role in promoting research productivity and impact. What remains unclear is whether female and male researchers in science, technology, engineering, and mathematical (STEM) disciplines differ in their collaboration propensity. Here, we report on an empirical analysis of the complete publication records of 3,980 faculty members in six STEM disciplines at select U.S. research universities. We find that female faculty have significantly fewer distinct co-authors over their careers than males, but that this difference can be fully accounted for by females' lower publication rate and shorter career lengths...
November 2016: PLoS Biology
journal
journal
40488
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"