bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem
Authors: Suzuki Shino , Ishii Shun’ichi , Wu Angela , Cheung Andrea , Tenney Aaron , Wanger Greg , Kuenen J. Gijs , Nealson Kenneth H. 
Published: September 2013

Significance
The Cedars, in coastal northern California, is an active serpentinization site. The spring waters emerging from this system feature very high pH (≈11.5), low redox potential (≈−550 mV), and low ionic concentrations, making it an exceptionally challenging environment for life. The microbial communities are different in different springs, strongly correlated with the source of the serpentinizing groundwater feeding the springs (shallow or deep). The shallow groundwater community was similar to those described in other terrestrial serpentinizing sites, while the deep community was distinctly different from any other previously described terrestrial serpentinizing community. These communities have the potential to yield important insights into survival mechanisms in these challenging, early-earth analog environments.
Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases
Authors: Lee Shun-Hsiao , Siaw Grace Ee-Lu , Willcox Smaranda , Griffith Jack D. , Hsieh Tao-Shih 
Published: September 2013

Significance
A hemicatenane conjoins two DNA duplexes through a single-strand interlock. It has been proposed that hemicatenanes are important intermediates for replication, repair, and recombination. However, the biochemical analysis of hemicatenanes is hampered by the relative inaccessibility of such structures. We report here that a DNA topoisomerase III (Top3) from a hyperthermophilic archaeum can carry out synthesis and dissolution of hemicatenanes. We also show that a complex of human Top3α, Bloom helicase (Blm), and RecQ-mediated genome instability protein 1 and 2 has a biochemical function of reversing this hemicatenation. Our results demonstrate that type IA topoisomerases can regulate the formation of hemicatenane structures.
Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification
Authors: Zhou Pingzhu , Zhang Yijing , Ma Qing , Gu Fei , Day Daniel S. , He Aibin , Zhou Bin , Li Jing , Stevens Sean M. , Romo Daniel , Pu William T. 
Published: September 2013

Significance
We developed reagents and approaches to pull down ribosome-associated RNAs from Cre-labeled cells. We show that this strategy is useful to probe cell type-specific gene expression and the extent of transcript binding to ribosomes.
From extortion to generosity, evolution in the Iterated Prisoner’s Dilemma
Authors: Stewart Alexander J. , Plotkin Joshua B. 
Published: September 2013

Significance
Cooperative behavior seems at odds with the Darwinian principle of survival of the fittest, yet cooperation is abundant in nature. Scientists have used the Prisoner Dilemma game, in which players must choose to cooperate or defect, to study the emergence and stability of cooperation. Recent work has uncovered a remarkable class of extortion strategies that provide one player a disproportionate payoff when facing an unwitting opponent. Extortion strategies perform very well in head-to-head competitions, but they fare poorly in large, evolving populations. Rather we identify a closely related set of generous strategies, which cooperate with others and forgive defection, that replace extortionists and dominate in large populations. Our results help to explain the evolution of cooperation.
Drift and conservation of differential exon usage across tissues in primate species
Authors: Reyes Alejandro , Anders Simon , Weatheritt Robert J. , Gibson Toby J. , Steinmetz Lars M. , Huber Wolfgang 
Published: September 2013

Significance
In higher organisms, most genes consist of several disconnected regions (exons), which are combined in various ways to produce several different gene transcripts from the same gene. Such alternative exon usage is thought to contribute to the ability of organisms to generate different cell types and tissues from a single genome. However, recent evidence has also suggested that much alternative exon usage might be noise with no particular function. We reconcile these two views by comparing how exons are used in different tissues and for which exons these usage patterns across tissues change or stay similar (are “conserved”) in several primate species. The latter case is an indication that the pattern is of functional importance, and our analysis quantifies how widespread such cases are.
Pathogenic role of diabetes-induced PPAR-α down-regulation in microvascular dysfunction
Authors: Hu Yang , Chen Ying , Ding Lexi , He Xuemin , Takahashi Yusuke , Gao Yang , Shen Wei , Cheng Rui , Chen Qian , Qi Xiaoping , Boulton Michael E. , Ma Jian-xing 
Published: September 2013

Significance
This study investigated the expression and function of peroxisome proliferator-activated receptor alpha (PPARα) in the retina and its role in diabetic retinopathy. In both type 1 and type 2 diabetes models, expression of PPARα was significantly down-regulated in the retina. PPARα knockout exacerbated diabetes-induced retinal vascular leakage and retinal inflammation, while over-expression of PPARα in the retina of diabetic rats significantly alleviated diabetic retinopathy. This study reveals that PPARα has an anti-inflammatory function in the retina. These findings also suggest that diabetes-induced down-regulation of PPARα plays an important role in diabetic retinopathy and represents a novel therapeutic target for diabetic retinopathy.
Unraveling the chromophoric disorder of poly(3-hexylthiophene)
Authors: Thiessen Alexander , Vogelsang Jan , Adachi Takuji , Steiner Florian , Vanden Bout David , Lupton John M. 
Published: September 2013

SignificanceIdeal photovoltaic cells would be black, absorbing all of the Sun’s radiation, whereas Nature’s machinery for solar energy harvesting—photosynthesis—looks green. Organic semiconductor devices, based on molecular building blocks, lie conceptionally between the extremes of inorganic and photosynthetic light harvesting. How can organic solar cells appear almost black if they are based on molecular units? Using single-molecule spectroscopy, we identify the fundamental electronic building blocks of organic solar cells and reveal that discrete molecule-like transitions scatter over the entire visible spectrum. The fundamental molecular unit is narrowband, but disorder induces a continuum reminiscent of that characterizing highly ordered inorganic crystals.
Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P
Authors: Peil Lauri , Starosta Agata L. , Lassak Jürgen , Atkinson Gemma C. , Virumäe Kai , Spitzer Michaela , Tenson Tanel , Jung Kirsten , Remme Jaanus , Wilson Daniel N. 
Published: September 2013

Significance
During protein synthesis, ribosomes catalyze peptide-bond formation between amino acids with differing efficiency. We show that two or more consecutive prolines induce ribosome stalling, and that stalling strength is influenced by the amino acid preceding and following the prolines. In bacteria, the elongation factor EF-P efficiently rescues the ribosome stalling irrespective of the XPP or PPX motif.
Diagnosis of tumors during tissue-conserving surgery with integrated autofluorescence and Raman scattering microscopy
Authors: Kong Kenny , Rowlands Christopher J. , Varma Sandeep , Perkins William , Leach Iain H. , Koloydenko Alexey A. , Williams Hywel C. , Notingher Ioan 
Published: September 2013

Significance
Histopathology is the standard method for diagnosis of cancer. However, this method requires time-consuming procedures for sectioning and staining of tissues, making histopathology impractical for use during surgery for most cancer types. We report a unique method based on two optical spectroscopy techniques—autofluorescence imaging and Raman scattering—that can accurately measure molecular differences between tumor cells and healthy tissue and allows diagnosis of tumors faster than histopathology, without requiring tissue sectioning or staining. Our study demonstrates the potential of this technique for diagnosis of tissues during cancer surgery, providing a quick and objective way to determine whether the tissue layers removed by the surgeon are clear of tumor.
Tissue- and cell-type–specific manifestations of heteroplasmic mtDNA 3243A>G mutation in human induced pluripotent stem cell-derived disease model
Authors: Hämäläinen Riikka H. , Manninen Tuula , Koivumäki Hanna , Kislin Mikhail , Otonkoski Timo , Suomalainen Anu 
Published: September 2013

Significance
Mitochondrial DNA (mtDNA) mutations are a common cause of human inherited diseases and manifest with exceptional clinical heterogeneity and tissue specificity, the molecular basis of which are largely unknown. We produced induced pluripotent stem cells (iPSCs) from patients carrying the most common mtDNA mutation, m.3243A>G. During reprogramming, the cells underwent an mtDNA bottleneck, mimicking that in epiblast specification. We differentiated iPSCs to heteroplasmic human cells and tissues with isogenic nuclear background and show that the disease manifestation depends on cellular context. We show that upon neuronal differentiation, complex I is actively degraded by an autophagy-mediated mechanism. Our data indicate that cellular context actively modifies mtDNA segregation and manifestations, and that complex I is actively down-regulated in neurons with m.3243A>G mutation.
Young infants have biological expectations about animals
Authors: Setoh Peipei , Wu Di , Baillargeon Renée , Gelman Rochel 
Published: September 2013

Significance
We provide an experimental demonstration that young infants possess abstract biological expectations about animals. Our findings represent a major breakthrough in the study of the foundations of human knowledge. In four experiments, 8-mo-old infants expected novel objects they categorized as animals to have filled insides. Thus, infants detected a violation when objects that were self-propelled and agentive were revealed to be hollow, or when an object that was self-propelled and furry rattled when shaken, as though mostly hollow. We describe possible characterizations of infants’ expectations about animals’ insides, including a characterization that emphasizes human predator–prey adaptations. We also discuss how infants’ expectation that animals have insides lays a foundation for the development of more advanced biological knowledge.
Low-copy
piggyBac
transposon mutagenesis in mice identifies genes driving melanoma
Authors: Ni Thomas K. , Landrette Sean F. , Bjornson Robert D. , Bosenberg Marcus W. , Xu Tian 
Published: September 2013

Significance
Passenger mutation rates are highly elevated in many human cancers, posing a significant hurdle for the identification of cancer-driving genes. In this study, we screened for melanomas in mice using a unique, low-copy transposon mutagenesis system that can induce tumors with few somatic mutations. We show that our experimental system accurately recapitulated the genetic basis of human melanomas with only five somatic mutations, thus circumventing hundreds of unrelated passengers. Using cross-species comparative analyses and functional studies in human cells, we identified three previously undescribed genes involved in melanoma and several dozen candidate genes. Our study demonstrates that the low-copy transposon mutagenesis approach can facilitate the identification of cancer-driving genes that are masked by high passenger mutation rates.
Effect of relationship experience on trust recovery following a breach
Authors: Schilke Oliver , Reimann Martin , Cook Karen S. 
Published: September 2013

SignificanceWill people be more likely to forgive a breach of trust in an earlier or later stage of an interpersonal relationship? The present article reports behavioral and neurophysiological experiments that speak to this important question. Results show that trust recovery is facilitated with increasing relationship experience. Differential activation in the controlled social cognition system (C-system) and the automatic social cognition system (X-system) indicate that decision making is less controlled and more automatic following a later as opposed to an earlier trust breach. These findings have important implications for the study of trust recovery after a breach, as well as the neuroscience of trust.
Novel human lncRNA–disease association inference based on lncRNA expression profiles
Authors: Chen Xing , Yan Gui-Ying 
Published: September 2013

Abstract
Motivation: More and more evidences have indicated that long–non-coding RNAs (lncRNAs) play critical roles in many important biological processes. Therefore, mutations and dysregulations of these lncRNAs would contribute to the development of various complex diseases. Developing powerful computational models for potential disease-related lncRNAs identification would benefit biomarker identification and drug discovery for human disease diagnosis, treatment, prognosis and prevention.
Results: In this article, we proposed the assumption that similar diseases tend to be associated with functionally similar lncRNAs. Then, we further developed the method of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) in the semisupervised learning framework. Although known disease–lncRNA associations in the database are rare, LRLSLDA still obtained an AUC of 0.7760 in the leave-one-out cross validation, significantly improving the performance of previous methods. We also illustrated the performance of LRLSLDA is not sensitive (even robust) to the parameters selection and it can obtain a reliable performance in all the test classes. Plenty of potential disease–lncRNA associations were publicly released and some of them have been confirmed by recent results in biological experiments. It is anticipated that LRLSLDA could be an effective and important biological tool for biomedical research.
Availability: The code of LRLSLDA is freely available at http://asdcd.amss.ac.cn/Software/Details/2.
Contact: xingchen@amss.ac.cn or yangy@amt.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploiting disjointness axioms to improve semantic similarity measures
Authors: Ferreira João D. , Hastings Janna , Couto Francisco M. 
Published: September 2013

Abstract
Motivation: Representing domain knowledge in biology has traditionally been accomplished by creating simple hierarchies of classes with textual annotations. Recently, expressive ontology languages, such as Web Ontology Language, have become more widely adopted, supporting axioms that express logical relationships other than class–subclass, e.g. disjointness. This is improving the coverage and validity of the knowledge contained in biological ontologies. However, current semantic tools still need to adapt to this more expressive information. In this article, we propose a method to integrate disjointness axioms, which are being incorporated in real-world ontologies, such as the Gene Ontology and the chemical entities of biological interest ontology, into semantic similarity, the measure that estimates the closeness in meaning between classes.
Results: We present a modification of the measure of shared information content, which extends the base measure to allow the incorporation of disjointness information. To evaluate our approach, we applied it to several randomly selected datasets extracted from the chemical entities of biological interest ontology. In 93.8% of these datasets, our measure performed better than the base measure of shared information content. This supports the idea that semantic similarity is more accurate if it extends beyond the hierarchy of classes of the ontology.
Contact: joao.ferreira@lasige.di.fc.ul.pt
Supplementary information: Supplementary data are available at Bioinformatics online.
Metriculator: quality assessment for mass spectrometry-based proteomics
Authors: Taylor Ryan M. , Dance Jamison , Taylor Russ J. , Prince John T. 
Published: September 2013

Abstract
Summary: Quality control in mass spectrometry-based proteomics remains subjective, labor-intensive and inconsistent between laboratories. We introduce Metriculator, a software designed to facilitate long-term storage of extensive performance metrics as introduced by NIST in 2010. Metriculator features a web interface that generates interactive comparison plots for contextual understanding of metric values and an automated metric generation toolkit. The comparison plots are designed for at-a-glance determination of outliers and trends in the datasets, together with relevant statistical comparisons. Easy-to-use quantitative comparisons and a framework for integration plugins will encourage a culture of quality assurance within the proteomics community.
Availability and Implementation: Available under the MIT license at http://github.com/princelab/metriculator.
Contact: jtprince@chem.byu.edu
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure
Authors: Suddala Krishna C. , Rinaldi Arlie J. , Feng Jun , Mustoe Anthony M. , Eichhorn Catherine D. , Liberman Joseph A. , Wedekind Joseph E. , Al-Hashimi Hashim M. , Brooks Charles L. , Walter Nils G. 
Published: September 2013

Abstract
Riboswitches are structural elements in the 5′ untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ1 (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ1 riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at near-physiological Mg2+ concentration and pH, both ligand-free aptamers adopt similar pre-folded state ensembles that differ in their ligand-mediated folding. Structure-based Gō-model simulations of the two aptamers suggest that the ligand binds late (Bacillus subtilis) and early (Thermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the principal distinction between the two riboswitches lies in their relative tendencies to fold via mechanisms of conformational selection and induced fit, respectively. These mechanistic insights are put to the test by rationally designing a single nucleotide swap distal from the ligand binding pocket that we find to predictably control the aptamers′ pre-folded states and their ligand binding affinities.
The Role of Oxytocin in Psychiatric Disorders
Authors: Cochran David M. , Fallon Daniel , Hill Michael , Frazier Jean A. 
Published: September 2013

Abstract

Learning Objectives
After participating in this educational activity, the physician should be better able to
Oxytocin is a peptide hormone integral in parturition, milk letdown, and maternal behaviors that has been demonstrated in animal studies to be important in the formation of pair bonds and in social behaviors. This hormone is increasingly recognized as an important regulator of human social behaviors, including social decision making, evaluating and responding to social stimuli, mediating social interactions, and forming social memories. In addition, oxytocin is intricately involved in a broad array of neuropsychiatric functions and may be a common factor important in multiple psychiatric disorders such as autism, schizophrenia, and mood and anxiety disorders. This review article examines the extant literature on the evidence for oxytocin dysfunction in a variety of psychiatric disorders and highlights the need for further research to understand the complex role of the oxytocin system in psychiatric disease and thus pave the way for developing new therapeutic modalities. Articles were selected that involved human participants with various psychiatric disorders and that either compared oxytocin biology to healthy controls or examined the effects of exogenous oxytocin administration.
Curriculum Development and Implementation of a National Interprofessional Fellowship in Patient Safety
Authors: Watts Bradley V. , Williams Linda , Mills Peter D. , Paull Douglas E. , Cully Jeffrey A. , Gilman Stuart C. , Hemphill Robin R. 
Published: September 2013

Objectives
Developing a workforce skilled in improving the safety of medical care has often been cited as an important means to achieve safer care. Although some educational programs geared toward patient safety have been developed, few advanced training programs have been described in the literature. We describe the development of a patient safety fellowship program.

Methods
We describe the development and curriculum of an Interprofessional Fellowship in Patient Safety. The 1-year in residence fellowship focuses on domains such as leadership, spreading innovations, medical improvement, patient safety culture, reliability science, and understanding errors.

Results
Specific training in patient safety is available and has been delivered to 48 fellows from a wide range of backgrounds. Fellows have accomplished much in terms of improvement projects, educational innovations, and publications. After completing the fellowship program, fellows are obtaining positions within health-care quality and safety and are likely to make long-term contributions.

Conclusions
We offer a curriculum and fellowship design for the topic of patient safety. Available evidence suggests that the fellowship results in the development of patient safety professionals.
Biofilm formation and antibiotic production in Ruegeria mobilis are influenced by intracellular concentrations of cyclic dimeric guanosinmonophosphate
Authors: D'Alvise Paul W. , Magdenoska Olivera , Melchiorsen Jette , Nielsen Kristian F. , Gram Lone 
Published: September 2013

SummaryIn many species of the marine Roseobacter clade, periods of attached life, in association with phytoplankton or particles, are interspersed with planktonic phases. The purpose of this study was to determine whether shifts between motile and sessile life in the globally abundant Roseobacter clade species Ruegeria mobilis are associated with intracellular concentrations of the signal compound cyclic dimeric guanosinmonophosphate (c‐di‐GMP), which in bacteria regulates transitions between motile and sessile life stages. Genes for diguanylate cyclases and phosphodiesterases, which are involved in c‐di‐GMP signalling, were found in the genome of R. mobilis strain F1926. Ion pair chromatography‐tandem mass spectrometry revealed 20‐fold higher c‐di‐GMP concentrations per cell in biofilm‐containing cultures than in planktonic cells. An introduced diguanylate cyclase gene increased c‐di‐GMP and enhanced biofilm formation and production of the potent antibiotic tropodithietic acid (TDA). An introduced phosphodiesterase gene decreased c‐di‐GMP and reduced biofilm formation and TDA production. tdaC, a key gene for TDA biosynthesis, was expressed only in attached or biofilm‐forming cells, and expression was induced immediately after initial attachment. In conclusion, c‐di‐GMP signalling controls biofilm formation and biofilm‐associated traits in R. mobilis and, as suggested by presence of GGDEF and EAL domain protein genes, also in other Roseobacter clade species.