bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diatom centromeres suggest a mechanism for nuclear DNA acquisition
Authors: Diner Rachel E. , Noddings Chari M. , Lian Nathan C. , Kang Anthony K. , McQuaid Jeffrey B. , Jablanovic Jelena , Espinoza Josh L. , Nguyen Ngocquynh A. , Anzelmatti Miguel A. , Jansson Jakob , Bielinski Vincent A. , Karas Bogumil J. , Dupont Christopher L. , Allen Andrew E. , Weyman Philip D. 
Published: July 2017

Significance
Centromeres are genomic sites facilitating chromosome segregation during cell division. We report our discovery of diatom centromeres and the description of centromere identity in the stramenopile protists. We also show that simple requirements for diatom centromeres permit ecologically relevant foreign DNA molecules to function as diatom centromeres by “hijacking” chromosome maintenance features. Because little is known at the molecular level about chromosome maintenance in diatoms, this paper provides experimental data with broad implications for cellular biology studies and biotechnology applications. The ability to maintain circular artificial chromosomes using foreign DNA sequences is unique among organisms with studied centromeres and opens up fascinating evolutionary questions about the mechanisms of nuclear gene acquisition from the multiple endosymbiotic events characterizing the stramenopile lineage.
Traffic is a major source of atmospheric nanocluster aerosol
Authors: Rönkkö Topi , Kuuluvainen Heino , Karjalainen Panu , Keskinen Jorma , Hillamo Risto , Niemi Jarkko V. , Pirjola Liisa , Timonen Hilkka J. , Saarikoski Sanna , Saukko Erkka , Järvinen Anssi , Silvennoinen Henna , Rostedt Antti , Olin Miska , Yli-Ojanperä Jaakko , Nousiainen Pekka , Kousa Anu , Dal Maso Miikka 
Published: July 2017

Significance
We report the significant presence of traffic-originated nanocluster aerosol (NCA) particles in a particle diameter range of 1.3–3.0 nm of urban air, determine the emission factors for the NCA, and evaluate its global importance. Our findings are important because they significantly update the current understanding of atmospheric aerosol in urban areas. They demonstrate that in urban air, extremely small particles form a significant fraction of the total particle number and are a direct result of anthropogenic emissions, that is, the emissions from road traffic. Thus, our findings also imply that in urban areas, an atmospheric nucleation process is not necessary for the formation of a large number of particles that affect population health and climate.
Polymorphism at a mimicry supergene maintained by opposing frequency-dependent selection pressures
Authors: Chouteau Mathieu , Llaurens Violaine , Piron-Prunier Florence , Joron Mathieu 
Published: July 2017

Significance
Although biological diversity is being lost at an alarming rate, a mimetic butterfly from the Amazon reveals a selective mechanism that can lead to rich adaptive diversity. In these toxic and vividly colored butterflies, several forms are maintained within populations, accurately mimicking distinct local butterflies, and controlled by differentiated alleles of a supergene. Such diversity is not expected because selection by predators promotes the fixation of a single morph. We show that the mating behavior favors pairings of dissimilar forms and boosts allelic diversity at the mimicry supergene. Therefore, sexual selection maintains a phenotypic diversity that predators channel and refine into a diversity of warning phenotypes, which correspond to the signals used by other defended species of butterflies in the local community.
Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex
Authors: Zhang Wen , Tam Chun Pong , Walton Travis , Fahrenbach Albert C. , Birrane Gabriel , Szostak Jack W. 
Published: July 2017

Significance
Rudimentary mechanisms of genome replication are essential for the earliest RNA-based cellular life, yet it is unknown how RNA or related polymers could have replicated nonenzymatically. For decades, 2-methylimidazole–activated GMP (2-MeImpG) has been used as a model substrate. We recently showed that two 2-MeImpG monomers react to form an imidazolium-bridged dinucleotide, which then reacts rapidly with the RNA primer. To explore this mechanism, we cocrystallized an RNA primer–template complex with several 5ʹ-5ʹ–linked analogs of the imidazolium-bridged intermediate. The closest analog, GpppG, binds to RNA in a conformation that explains the high reactivity of the imidazolium-bridged intermediate, whereas the structures of other dinucleotide ligands appear less favorable. Our study provides insight into the fundamental mechanism of nonenzymatic RNA self-replication.
Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary
Authors: Feng Yan-Jie , Blackburn David C. , Liang Dan , Hillis David M. , Wake David B. , Cannatella David C. , Zhang Peng 
Published: July 2017

SignificanceFrogs are the dominant component of semiaquatic vertebrate faunas. How frogs originated and diversified has long attracted the attention of evolutionary biologists. Here, we recover their evolutionary history by extensive sampling of genes and species and present a hypothesis for frog evolution. In contrast to prior conclusions that the major frog clades were established in the Mesozoic, we find that ∼88% of living frogs originated from three principal lineages that arose at the end of the Mesozoic, coincident with the Cretaceous–Paleogene (K–Pg) mass extinction event that decimated nonavian dinosaurs 66 Mya. The K–Pg extinction events played a pivotal role in shaping the current diversity and geographic distribution of modern frogs.
Four-stranded mini microtubules formed by
Prosthecobacter
BtubAB show dynamic instability
Authors: Deng Xian , Fink Gero , Bharat Tanmay A. M. , He Shaoda , Kureisaite-Ciziene Danguole , Löwe Jan 
Published: July 2017

Significance
Microtubules, essential in eukaryotic cells, are wide and hollow tubes that are formed through the polymerisation of αβ-tubulin proteins. Microtubules provide tracks for motor-driven cellular transport. Dynamic instability of microtubules, the stochastic change between slow growth and rapid shrinkage, is important during mitotic DNA segregation. Although microtubules were thought to be unique to eukaryotes, certain bacteria are exceptions because they possess BtubAB proteins that are closely related to tubulins and form hollow tubes. We demonstrate with the atomic structure of bacterial BtubAB “mini microtubules” that they share many features with eukaryotic microtubules, and that they exhibit dynamic instability. Our work highlights deep conservation of structure and dynamics between bacterial and eukaryotic microtubules, providing clues about their evolution.
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution
Authors: Huang Ancheng C. , Kautsar Satria A. , Hong Young J. , Medema Marnix H. , Bond Andrew D. , Tantillo Dean J. , Osbourn Anne 
Published: July 2017

Significance
Sesterterpenoids are a rare terpene class with largely unexplored chemical diversity and bioactivities, representing a potential new drug source. Sesterterpene synthases catalyze the first committed biosynthesis step and shape sesterterpene structural diversity. Here, using a customized algorithm for systematically surveying plant genomes, we unearth a sesterterpene synthase gene repertoire in the Brassicaceae that synthesizes fungal-type sesterterpenes with diverse scaffolds, thus fueling the drug-discovery pipeline. Mechanistic studies shed light on the origin of structural diversification and offer insights for expanding nature’s diversity by protein engineering. Our work also supports the concept of convergent evolution in natural product biosynthesis.
Global priorities for conservation across multiple dimensions of mammalian diversity
Authors: Brum Fernanda T. , Graham Catherine H. , Costa Gabriel C. , Hedges S. Blair , Penone Caterina , Radeloff Volker C. , Rondinini Carlo , Loyola Rafael , Davidson Ana D. 
Published: July 2017

SignificanceApproximately a quarter of all land mammals are currently threatened, mostly by human activities including habitat loss and harvesting. Here, we provide the first biological map of priority areas that captures all three dimensions of mammalian biodiversity: taxonomic, phylogenetic, and traits. We find limited overlap in priority regions across the three dimensions and with currently protected areas, indicating that conservation planning should consider multiple dimensions of biodiversity to maximize biodiversity conservation. Our complementarity-based prioritization provides a conservation solution that can be incorporated in future conservation planning efforts aimed at helping protect not only species but also evolutionary potential and ecosystem function.
Delineation of an immunosuppressive gradient in hepatocellular carcinoma using high-dimensional proteomic and transcriptomic analyses
Authors: Chew Valerie , Lai Liyun , Pan Lu , Lim Chun Jye , Li Juntao , Ong Raymond , Chua Camillus , Leong Jing Yao , Lim Kiat Hon , Toh Han Chong , Lee Ser Yee , Chan Chung Yip , Goh Brian K. P. , Chung Alexander , Chow Pierce K. H. , Albani Salvatore 
Published: July 2017

SignificanceThe roles of tumor-infiltrating leukocytes in mediating cancer progression are well recognized, but a multidimensional analysis of the entire cancer immune system is lacking. Here, we dissected the cancer-immune landscape in hepatocellular carcinoma (HCC) across tumor, nontumor, and peripheral blood cells using time-of-flight mass cytometry, multiplex immunofluorescence tissue staining, and NanoString analysis. We identified various immune subsets that were enriched in the tumor microenvironment and their potential impact on the tumor immunity based on their detailed phenotypes. This study has validated the concept of a cancer-immune gradient and demonstrated in primary HCC that immune-cell subsets become progressively suppressive as they traverse the nontumor to tumor microenvironment. These data have opened avenues for the design of immunotherapeutics in HCC.
Negative scope, temporality, fixedness, and right- and left-branching
Authors: Ono Tsuyoshi , Thompson Sandra 
Published: July 2017

Abstract
‘Negative scope’ concerns what it is that is negated in an utterance with a negative morpheme. With English and Japanese conversational data, we show that for an English speaker, calculating negative scope requires that recipients incrementally keep track of all the material in the clause that follows the negative morpheme, which comes early in the clause. In contrast, the negative morpheme comes late in the clause in Japanese; thus it would seem that recipients need to hold in memory all the material in the clause preceding the negative until the negative morpheme is produced. Several features of Japanese grammar, however, suggest that this characterization is not accurate. We argue that prosody, grammar, cognition, processing, and fixedness all interact with the grammar of clause organization to afford quite different real-time processing strategies for calculating the assignment of negative scope in languages with different ‘word order’ norms.
Agreement with the internal possessor in Chimane*
Authors: Ritchie Sandy 
Published: July 2017

AbstractThe paper examines a type of clausal construction in Chimane (or Tsimane’, unclassified, Bolivia) in which possessors which are apparently internal to patient- or recipient-like possessive phrases can control object agreement on the verb. Various aspects of the construction point to an analysis in which the internal possessor is doubled by an external representation or ‘proxy’ in the clause which mediates the agreement relation between the possessor and the verb. The construction bears some resemblance to external possessor constructions, albeit with the added complication that the possessor itself remains internal to the possessive phrase while its argument function is borne by the external proxy. The paper examines features of the construction and contrasts it with similar or related phenomena which have been identified in other languages.
Production of a novel wheat gluten hydrolysate containing dipeptidyl peptidase-IV inhibitory tripeptides using ginger protease
Authors: Taga Yuki , Hayashida Osamu , Kusubata Masashi , Ogawa-Goto Kiyoko , Hattori Shunji 
Published: July 2017

Abstract
Wheat gluten is a Pro-rich protein complex comprising glutenins and gliadins. Previous studies have reported that oral intake of enzymatic hydrolysates of gluten has beneficial effects, such as suppression of muscle injury and improvement of hepatitis. Here, we utilized ginger protease that preferentially cleaves peptide bonds with Pro at the P2 position to produce a novel type of wheat gluten hydrolysate. Ginger protease efficiently hydrolyzed gluten, particularly under weak acidic conditions, to peptides with an average molecular weight of &lt;600 Da. In addition, the gluten hydrolysate contained substantial amounts of tripeptides, including Gln-Pro-Gln, Gln-Pro-Gly, Gln-Pro-Phe, Leu-Pro-Gln, and Ser-Pro-Gln (e.g. 40.7 mg/g at pH 5.2). These gluten-derived tripeptides showed high inhibitory activity on dipeptidyl peptidase-IV with IC50 values of 79.8, 70.9, 71.7, 56.7, and 78.9 μM, respectively, suggesting that the novel gluten hydrolysate prepared using ginger protease can be used as a functional food for patients with type 2 diabetes.
ISEScan: automated identification of insertion sequence elements in prokaryotic genomes
Authors: Xie Zhiqun , Tang Haixu 
Published: July 2017

Abstract

Motivation
The insertion sequence (IS) elements are the smallest but most abundant autonomous transposable elements in prokaryotic genomes, which play a key role in prokaryotic genome organization and evolution. With the fast growing genomic data, it is becoming increasingly critical for biology researchers to be able to accurately and automatically annotate ISs in prokaryotic genome sequences. The available automatic IS annotation systems are either providing only incomplete IS annotation or relying on the availability of existing genome annotations. Here, we present a new IS elements annotation pipeline to address these issues.

Results
ISEScan is a highly sensitive software pipeline based on profile hidden Markov models constructed from manually curated IS elements. ISEScan performs better than existing IS annotation systems when tested on prokaryotic genomes with curated annotations of IS elements. Applying it to 2784 prokaryotic genomes, we report the global distribution of IS families across taxonomic clades in Archaea and Bacteria.

Availability and implementation
ISEScan is implemented in Python and released as an open source software at https://github.com/xiezhq/ISEScan.

Supplementary information
Supplementary data are available at Bioinformatics online.
nandb—number and brightness in R with a novel automatic detrending algorithm
Authors: Nolan Rory , Alvarez Luis A J , Elegheert Jonathan , Iliopoulou Maro , Jakobsdottir G Maria , Rodriguez-Muñoz Marina , Aricescu A Radu , Padilla-Parra Sergi 
Published: July 2017

Abstract

Summary
An R package for performing number and brightness image analysis, with the implementation of a novel automatic detrending algorithm.

Availability and implementation
Available at https://github.com/rorynolan/nandb for all platforms.

Contact
rnolan@well.ox.ac.uk or spadilla@well.ox.ac.uk

Supplementary information
Supplementary data are available at Bioinformatics online.
powsimR: power analysis for bulk and single cell RNA-seq experiments
Authors: Vieth Beate , Ziegenhain Christoph , Parekh Swati , Enard Wolfgang , Hellmann Ines 
Published: July 2017

Abstract

Summary
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

Availability and implementation
The R package and associated tutorial are freely available at https://github.com/bvieth/powsimR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Defending the IASP Definition of Pain
Authors: Aydede Murat 
Published: July 2017

Abstract
The official definition of ‘pain’ by the International Association for the Study of Pain (IASP) hasn’t seen much revision since its publication in 1979. There have been various criticisms of the definition in the literature from different quarters. In my view, most of these criticisms depend on misunderstandings or on uncharitable interpretations. My aim is to go over the definition, clarify some potential ambiguities, and argue that these criticisms don’t cut much ice. At the end, I will present a few slightly reworded versions of the definition that I claim are more felicitous and capture the original intended meaning by the members of the taxonomic committee in a much better and transparent way that avoids all the major extant criticisms in the literature.
A National Longitudinal Survey of Medical Students’ Intentions to Practice Among the Underserved
Authors: O’Connell Thomas F. , Ham Sandra A. , Hart Theodore G. , Curlin Farr A. , Yoon John D. 
Published: July 2017

Purpose
To explore students’ intentions to practice in medically underserved areas.

Method
In January 2011, 960 third-year medical students from 24 MD-granting U.S. medical schools were invited to participate in a survey on their intention to practice in a medically underserved area. A follow-up survey was sent to participants in September 2011. Covariates included student demographics, medical school characteristics, environmental exposures, work experiences, sense of calling, and religious characteristics.

Results
Adjusted response rates were 564/919 (61.4%, first survey) and 474/564 (84.0%, follow-up survey). Among fourth-year medical students, an estimated 34.3% had an intention to practice among the underserved. In multivariate logistic regression modeling, predictors for intentions to practice among the underserved included growing up in an underserved setting (odds ratio [OR] range: 2.96–4.81), very strong sense of calling (OR range: 1.86–3.89), and high medical school social mission score (in fourth year: OR = 2.34 [95% confidence interval (CI), 1.31–4.21]). International experience was associated with favorable change of mind in the fourth year (OR = 2.86 [95% CI, 1.13–7.24]). High intrinsic religiosity was associated with intentions to practice primary care in underserved settings (in fourth year: OR = 2.29 [95% CI = 1.13–4.64]).

Conclusions
Growing up in medically underserved settings, work experience in religiously affiliated organizations, very strong sense of calling, and high medical school social mission score were associated with intentions to practice in underserved areas. Lack of formative educational experiences may dissuade students from considering underserved practice.
Cantonese Tone Perception for Children Who Use a Hearing Aid and a Cochlear Implant in Opposite Ears
Authors: Mok Mansze , Holt Colleen M. , Lee Kathy Y. S. , Dowell Richard C. , Vogel Adam P. 
Published: July 2017

Objectives:
The ability to recognize tones is vital for speech perception in tonal languages. Cantonese has six tones, which are differentiated almost exclusively by pitch cues (tones 1 to 6). The differences in pitch contours among the tones are subtle, making Cantonese a challenging language for cochlear implant users. The addition of a hearing aid has been shown to improve speech perception in nontonal languages and in Mandarin Chinese. This study (1) investigates the Cantonese tone perception ability of children who use a cochlear implant and a hearing aid in opposite ears; (2) evaluates the effect of varying pitch height and pitch contour cues on Cantonese tone perception for these children; and (3) compares the Cantonese tone perception ability for using a hearing aid and a cochlear implant together versus an implant alone.

Design:
Eight native Cantonese speaking children using a cochlear implant and a hearing aid in opposite ears were assessed for tone perception and word identification. The tone perception test involved discriminating and ranking tone pairs from natural and artificially manipulated Cantonese tones with various pitch heights and/or pitch contours. The word identification test involved identifying Cantonese words in a four-alternative forced-choice task. All tests were performed in two device conditions: (1) cochlear implant and hearing aid together and (2) implant alone.

Results:
Seven of the 8 subjects performed significantly above chance in both tests using the cochlear implant alone. Results showed that both pitch height and/or pitch direction were important perceptual cues for implant users. Perception for some tones was improved by increasing the pitch height differences between the tones. The ability to discriminate and rank the tone 2/tone 5 contrast and the tone 4/tone 6 contrast was poor, as the tones in these contrasts are similar in pitch contours and onset frequencies. No significant improvement was observed after artificially increasing the pitch offset differences between the tones in the tone 2/tone 5 and the tone 4/tone 6 contrasts. Tone perception results were significantly better with the addition of the hearing aid in the nonimplanted ear compared with using the implant alone; however, word identification results were not significantly different between using the implant alone and using both the hearing aid and the implant together. None of the subjects performed worse in tone perception or in word identification when the hearing aid was added.

Conclusions:
Reduced ability to perceive pitch contour cues, even when artificially exaggerated, may explain some of the difficulties in Cantonese word recognition for implant users. The addition of a contralateral hearing aid could be beneficial for Cantonese tone perception for some individuals with a unilateral implant. The results encouraged Cantonese speakers to trial a hearing aid in the nonimplanted ear when using a cochlear implant.