bluuebunny/crossref_metadata_2025 huggingface dataset:
The labeling problem in syntactic bootstrapping
Authors: White Aaron Steven , Hacquard Valentine , Lidz Jeffrey
Published: July 2018

In English, the distinction between belief verbs, such as think, and desire verbs, such as want, is tracked by tense found in the subordinate clauses of those verbs. This suggests that subordinate clause tense might be a useful cue for learning the meanings of these verbs via syntactic bootstrapping. However, the correlation between tense and the belief v. desire distinction is not cross-linguistically robust; yet the acquisition profile of these verbs is similar cross-linguistically. Our proposal in this chapter is that, instead of using concrete cues like subordinate clause tense, learners may utilize more abstract syntactic cues that must be tuned to the syntactic distinctions present in a particular language. We present computational modeling evidence supporting the viability of this proposal.
Perspectives on truth
Authors: de Villiers Jill G.
Published: July 2018

Many theorists take language – vocabulary, mental verbs, syntax, counterfactuals, discourse – to be a significant help in the development of explicit Theory of Mind. Does conversation, with all its point-of-view indicators, betray another’s perspective? By comparing how different linguistic markers behave across clausal environments, I demonstrate that they fall into distinct classes, only one of which – tense – patterns with the truth of the clause in terms of perspective. Sentences with embedded finite complements thus have a special role in representing the truth or falsity of others’ beliefs. Children who master embedded sentential complements can then more readily reason about others’ false beliefs.
Four-year-old children compute scalar implicatures in absence of epistemic reasoning
Authors: Barner David , Hochstein Lara K. , Rubenson Miriam P. , Bale Alan
Published: July 2018

Children exhibit sophisticated mental state (epistemic) reasoning abilities from an early age, but it remains unclear what role these abilities play in the development of pragmatic inference in language acquisition. Here, we examined the role of epistemic reasoning in scalar implicature. Experiment 1 found that most 4-year-olds successfully computed a sub-type of scalar implicature (ad hoc implicatures), despite failing to compute so-called “ignorance implicatures”, a type of epistemic inference that Gricean models of pragmatics deem necessary for scalar implicature. In Experiment 2, we tested 4- and 5-year-old children, and replicated the finding that children compute ad hoc implicatures more readily than ignorance implicatures, and that children’s difficulties with ignorance implicature are unrelated to performance on Theory of Mind tasks.
Mechanical properties of low-transformation-temperature weld metals after low-temperature postweld heat treatment
Authors: Wu Shipin , Wang Dongpo , Zhang Zhi , Li Chengning , Liu Xiuguo , Meng Xianqun , Feng Zhongyuan , Di Xinjie
Published: July 2018

The as-welded low-transformation-temperature (LTT) weld metal with martensite/retained austenite (RA) dual phase exhibits high toughness and ductility, but the yield strength (YS) is very low. After low-temperature postweld heat treatment at 300°C, the YS, toughness and ductility of dual-phase LTT weld metal increase dramatically, while there is a slight effect on mechanical properties of full martensite LTT weld metal. During the low-temperature postweld heat treatment, carbon atoms diffuse from martensite into RA, which increases the stability of RA. The improvements of mechanical properties for dual-phase LTT weld metal after low-temperature postweld heat treatment are attributed to the increased stability of RA and enhanced transformation-induced plasticity effect.
Assessment of the degradation of aesthetics Beneficial Use Impairment in the Toronto and region Area of Concern
Authors: Dahmer S. C. , Matos L. , Jarvie S.
Published: July 2018

Toronto and Region was designated a Great Lakes Area of Concern in 1987 due to significant degradation of environmental quality and impaired beneficial uses, including Degradation of Aesthetics. Historically overflows of combined sewers, direct discharge of poorly treated industrial wastewater, contaminated storm water, and litter contributed to excessive floating debris, odour and unnatural turbidity along parts of the waterfront and in some sections of Area of Concern watersheds. Despite the perception of poor aesthetic quality of these waters, little to no monitoring was carried out to assess the Degradation of Aesthetics Beneficial Use Impairment due to the challenge of reporting aesthetics in a quantifiable, unbiased manner. Here we describe the qualitative monitoring program implemented in the Toronto region to assess the aesthetic condition of local watersheds. An Aesthetic Quality Index developed for use by Areas of Concern was adapted by taking advantage of existing monitoring programs and local expertise. Results of the assessment indicate that no persistent objectionable deposit, unnatural colour or turbidity, or unnatural odour was present in the Toronto region during the period of study.
Refugees in Greece: the Greeks as ‘refugees’
Authors: Velissariou Aspasia
Published: July 2018

The state of economic emergency under which Greece has been put for the past eight years throws into relief the basic antinomy inherent in democracy. This pertains to the exercise of national sovereignty on the basis of borders whose safeguarding, however, implements a network of state practices of control and selection of populations both ‘within’ and ‘outside’. In Greece, under the memoranda imposed by the Tetroika (involving four institutions: IMF, ECB, ESM and EC, not three as in Troika), extreme austerity has created ‘superfluous’ populations within their own country. The internal shifting of the borders that produces exclusion, sustained by parliamentary dictates and intense supervision because of the Tetroika's policies at the national level, goes along with the stiffening of external border control by the state in a strategy of deterrence against the entry of war refugees into the country. At the same time, the regulation of ‘superfluous’ refugee populations replicates the biopolitical model of EU governance introduced to the national ‘body’. Therefore, the Greek radical Left has to demonstrate that both dispossessed Greek subjects and refugees are victims of globalized capitalism, distance itself from humanitarianism and politicize solidarity by creating the terms for a common struggle.
Commons manifestos: a reply to Bauwens and Ramos
Authors: Murdock Graham
Published: July 2018

This reply piece is a response to the article by Michel Bauwens and Jose Ramos, “Re-imagining the Left through an ecology of the commons: Toward a post-capitalist commons transition”. In it, Graham Murdock argues that while developing a commons for contemporary conditions is a core requirement for a post-capitalist social order, it is not in itself sufficient. It is also necessary to confront the contradictory role the state has played in the development of capitalism, as both a force for enclosure and the defence of property rights and the prime guarantor of the public goods and social conditions that facilitate commoning. The rise of neoliberal economic polices has fuelled a new push to enclosure characterized by the privatisation of previously public resources, accelerated corporate concentration, widening income inequalities, and a deepening ecological crisis. The leading digital corporations have played a central role in cementing these processes. Consequently, mobilising digital technologies for commoning requires concerted state action to reverse them and restore the public resources and social conditions that support mutuality.
Neoliberalism as a historical stage
Authors: Karatani Kojin
Published: July 2018

Orthodox Marxist historical materialisms have viewed the history of social formations one-sidedly from the mode of production as base, which over-determines the political, ideological superstructure. In contrast, this article proposes an augmentation of historical materialism which has as its determinative base the mode of exchange. Specifically, through a lens of exchange, a spatial and territorial element is brought to an analysis and historicizing of imperialism. This article argues that the world entered into an imperialist stage of capitalism in the 1990s. Imperialism is inseparable from the capitalist economy. But it does not necessarily follow that imperialism can be explained away as a historical stage of the capitalist economy. Imperialism is a matter of politics among nations. To see this, we need to look at world history from the double axis, i.e. the state and capital. Modern imperialism is not necessarily expansionist in terms of territory. Rather, it aims at expanding through trade. By way of spreading the market economy, imperialism tries to gain surplus value. Thus, ‘neoliberalism’ by definition is imperialism. Its nature is to aim for global expansion of the market.
The force-sensitive protein Ajuba regulates cell adhesion during epithelial morphogenesis
Authors: Razzell William , Bustillo Maria E. , Zallen Jennifer A.
Published: July 2018

The reorganization of cells in response to mechanical forces converts simple epithelial sheets into complex tissues of various shapes and dimensions. Epithelial integrity is maintained throughout tissue remodeling, but the mechanisms that regulate dynamic changes in cell adhesion under tension are not well understood. In Drosophila melanogaster, planar polarized actomyosin forces direct spatially organized cell rearrangements that elongate the body axis. We show that the LIM-domain protein Ajuba is recruited to adherens junctions in a tension-dependent fashion during axis elongation. Ajuba localizes to sites of myosin accumulation at adherens junctions within seconds, and the force-sensitive localization of Ajuba requires its N-terminal domain and two of its three LIM domains. We demonstrate that Ajuba stabilizes adherens junctions in regions of high tension during axis elongation, and that Ajuba activity is required to maintain cell adhesion during cell rearrangement and epithelial closure. These results demonstrate that Ajuba plays an essential role in regulating cell adhesion in response to mechanical forces generated by epithelial morphogenesis.
Generality and Causal Interdependence in Ecology
Authors: Elliott-Graves Alkistis
Published: July 2018

A hallmark of ecological research is dealing with complexity in the systems under investigation. One strategy is to diminish this complexity by constructing models and theories that are general. Alternatively, ecologists can constrain the scope of their generalizations to particular phenomena or types of systems. However, research employing the second strategy is often met with scathing criticism. I offer a theoretical argument in support of moderate generalizations in ecological research, based on the notions of interdependence and causal heterogeneity and their effect on the trade-off between generality and realism.
The Time of Data: Timescales of Data Use in the Life Sciences
Authors: Leonelli Sabina
Published: July 2018

This article considers the temporal dimension of data processing and use and the ways in which it affects the production and interpretation of knowledge claims. I start by distinguishing the time at which data collection, dissemination, and analysis occur (Data time, or Dt) from the time in which the phenomena for which data serve as evidence operate (Phenomena time, or Pt). Building on the analysis of two examples of data reuse from modeling and experimental practices in biology, I then argue that Dt affects how researchers (1) select and interpret data as evidence and (2) identify and understand phenomena.
Broom: application for non-redundant storage of high throughput sequencing data
Authors: Albayrak Levent , Khanipov Kamil , Golovko George , Fofanov Yuriy
Published: July 2018

Motivation

The data generation capabilities of high throughput sequencing (HTS) instruments have exponentially increased over the last few years, while the cost of sequencing has dramatically decreased allowing this technology to become widely used in biomedical studies. For small labs and individual researchers, however, storage and transfer of large amounts of HTS data present a significant challenge. The recent trends in increased sequencing quality and genome coverage can be used to reconsider HTS data storage strategies.

Results

We present Broom, a stand-alone application designed to select and store only high-quality sequencing reads at extremely high compression rates. Written in C++, the application accepts single and paired-end reads in FASTQ and FASTA formats and decompresses data in FASTA format.

Availability and implementation

C++ code available at https://scsb.utmb.edu/labgroups/fofanov/broom.asp.

Supplementary information

Supplementary data are available at Bioinformatics online.
Matt: Unix tools for alternative splicing analysis
Authors: Gohr André , Irimia Manuel
Published: July 2018

Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality.

Availability and implementation

matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules/the R Base package simplifying its installation.

Supplementary information

Supplementary data are available at Bioinformatics online.
Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
Authors: Eriksson Olivia , Jauhiainen Alexandra , Maad Sasane Sara , Kramer Andrei , Nair Anu G , Sartorius Carolina , Hellgren Kotaleski Jeanette
Published: July 2018

Motivation

Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours.

Results

We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building.

Availability and implementation

Source code is freely available at https://github.com/alexjau/uqsa.

Supplementary information

Supplementary data are available at Bioinformatics online.
Metagenomic binning through low-density hashing
Authors: Luo Yunan , Yu Yun William , Zeng Jianyang , Berger Bonnie , Peng Jian
Published: July 2018

Motivation

Vastly greater quantities of microbial genome data are being generated where environmental samples mix together the DNA from many different species. Here, we present Opal for metagenomic binning, the task of identifying the origin species of DNA sequencing reads. We introduce ‘low-density’ locality sensitive hashing to bioinformatics, with the addition of Gallager codes for even coverage, enabling quick and accurate metagenomic binning.

Results

On public benchmarks, Opal halves the error on precision/recall (F1-score) as compared with both alignment-based and alignment-free methods for species classification. We demonstrate even more marked improvement at higher taxonomic levels, allowing for the discovery of novel lineages. Furthermore, the innovation of low-density, even-coverage hashing should itself prove an essential methodological advance as it enables the application of machine learning to other bioinformatic challenges.

Availability and implementation

Full source code and datasets are available at http://opal.csail.mit.edu and https://github.com/yunwilliamyu/opal.

Supplementary information

Supplementary data are available at Bioinformatics online.
CoMSA: compression of protein multiple sequence alignment files
Authors: Deorowicz Sebastian , Walczyszyn Joanna , Debudaj-Grabysz Agnieszka
Published: July 2018

Motivation

Bioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating hundreds of GB is multiple sequence alignments of protein families. Its largest database, i.e. Pfam, consumes 40–230 GB, depending of the variant. Storage and transfer of such massive data has become a challenge.

Results

We propose a novel compression algorithm, CoMSA, designed especially for aligned data. It is based on a generalization of the positional Burrows–Wheeler transform for non-binary alphabets. CoMSA handles FASTA, as well as Stockholm files. It offers up to six times better compression ratio than other commonly used compressors, i.e. gzip. Performed experiments resulted in an analysis of the influence of a protein family size on the compression ratio.

Availability and implementation

CoMSA is available for free at https://github.com/refresh-bio/comsa and http://sun.aei.polsl.pl/REFRESH/comsa.

Supplementary material

Supplementary data are available at Bioinformatics online.
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters
Authors: Lu Xinguo , Qian Xin , Li Xing , Miao Qiumai , Peng Shaoliang
Published: July 2018

Motivation

Functional somatic mutations within coding amino acid sequences confer growth advantage in pathogenic process. Most existing methods for identifying cancer-related mutations focus on the single amino acid or the entire gene level. However, gain-of-function mutations often cluster in specific protein regions instead of existing independently in the amino acid sequences. Some approaches for identifying mutation clusters with mutation density on amino acid chain have been proposed recently. But their performance in identification of mutation clusters remains to be improved.

Results

Here we present a Data-adaptive Mutation Clustering Method (DMCM), in which kernel density estimate (KDE) with a data-adaptive bandwidth is applied to estimate the mutation density, to find variable clusters with different lengths on amino acid sequences. We apply this approach in the mutation data of 571 genes in over twenty cancer types from The Cancer Genome Atlas (TCGA). We compare the DMCM with M2C, OncodriveCLUST and Pfam Domain and find that DMCM tends to identify more significant clusters. The cross-validation analysis shows DMCM is robust and cluster cancer type enrichment analysis shows that specific cancer types are enriched for specific mutation clusters.

Availability and implementation

DMCM is written in Python and analysis methods of DMCM are written in R. They are all released online, available through https://github.com/XinguoLu/DMCM.

Supplementary information

Supplementary data are available at Bioinformatics online.
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC
Authors: Cheng Xiang , Lin Wei-Zhong , Xiao Xuan , Chou Kuo-Chen
Published: July 2018

Motivation

A cell contains numerous protein molecules. One of the fundamental goals in cell biology is to determine their subcellular locations, which can provide useful clues about their functions. Knowledge of protein subcellular localization is also indispensable for prioritizing and selecting the right targets for drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization based on the sequence information alone. Recently, a predictor called ‘pLoc-mAnimal’ was developed for identifying the subcellular localization of animal proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with the multi-label systems in which some proteins, called ‘multiplex proteins’, may simultaneously occur in two or more subcellular locations. Although it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mAnimal was trained by an extremely skewed dataset in which some subset (subcellular location) was about 128 times the size of the other subsets. Accordingly, such an uneven training dataset will inevitably cause a biased consequence.

Results

To alleviate such biased consequence, we have developed a new and bias-reducing predictor called pLoc_bal-mAnimal by quasi-balancing the training dataset. Cross-validation tests on exactly the same experiment-confirmed dataset have indicated that the proposed new predictor is remarkably superior to pLoc-mAnimal, the existing state-of-the-art predictor, in identifying the subcellular localization of animal proteins.

Availability and implementation

To maximize the convenience for the vast majority of experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mAnimal/, by which users can easily get their desired results without the need to go through the complicated mathematics.

Supplementary information

Supplementary data are available at Bioinformatics online.
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios
Authors: Curis Emmanuel , Courtin Cindie , Geoffroy Pierre Alexis , Laplanche Jean-Louis , Saubaméa Bruno , Marie-Claire Cynthia
Published: July 2018

Motivation

RNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions.

Results

The methods is suited for qRT-PCR and RNA-Seq data analyses, and leads to easy-to-interpret, graphical results and the identification of set of genes that share a similar behavior when the studied condition changes. For qRT-PCR data, it has better statistical properties than the common ΔΔCq method.

Availability and implementation

Construction of all pairwise ratio analysis P-values matrix, and conversion into a graph was implemented in an R package, named SARP.compo. It is freely available for download on the CRAN repository. Example R script using the package are provided as Supplementary Material; the R package includes the data needed. One of these scripts reproduces the Figure 2 of this paper.

Supplementary information

Supplementary data are available at Bioinformatics online.
Precessional dynamics of black hole triples: binary mergers with near-zero effective spin
Authors: Antonini Fabio , Rodriguez Carl L , Petrovich Cristobal , Fischer Caitlin L
Published: July 2018

The binary black hole mergers detected by Advanced LIGO/Virgo have shown no evidence of large black hole spins. However, because LIGO/Virgo best measures the effective combination of the two spins along the orbital angular momentum (χeff), it is difficult to distinguish between binaries with slowly spinning black holes and binaries with spins lying in the orbital plane. Here, we study the spin dynamics for binaries with a distant black hole companion. For spins initially aligned with the orbital angular momentum of the binary, we find that χeff ‘freezes’ near zero as the orbit decays through the emission of gravitational waves. Through a population study, we show that this process predominantly leads to merging black hole binaries with near-zero χeff. We conclude that if the detected black hole binaries were formed in triples, then this would explain their low χeff without the need to invoke near-zero spins or initially large spin–orbit angles.
Coronal EUV, QFP, and kink waves simultaneously launched during the course of jet–loop interaction
Authors: Shen Yuandeng , Tang Zehao , Li Hongbo , Liu Yu
Published: July 2018

We present the observations of an extreme ultraviolet (EUV) wave, a quasi-periodic fast-propagating (QFP) magnetosonic wave, and a kink wave that were simultaneously associated with the impingement of a coronal jet upon a group of coronal loops. After the interaction, the coronal loop showed obvious kink oscillation that had a period of about 428 s. In the meantime, a large-scale EUV wave and a QFP wave are observed on the west of the interaction position. It is interesting that the QFP wave showed refraction effect during its passing through two strong magnetic regions. The angular extent, speed, and lifetime of the EUV (QFP) wave were about 140° (40°), 423 (322) km s−1, and 6 (26) min, respectively. It is measured that the period of the QFP wave was about 390 ± 100. Based on the observational analysis results, we propose that the kink wave was probably excited by the interaction of the jet; the EUV was probably launched by the sudden expansion of the loop system due to the impingement of the coronal jet; and the QFP wave was possibly formed through the dispersive evolution of the disturbance caused by the jet–loop interaction.
On the [α/Fe]–[Fe/H] relations in early-type galaxies
Authors: Vincenzo Fiorenzo , Kobayashi Chiaki , Taylor Philip
Published: July 2018

We study how the predicted [α/Fe]–[Fe/H] relations in early-type galaxies vary as functions of their stellar masses, ages, and stellar velocity dispersions, by making use of cosmological chemodynamical simulations with feedback from active galactic nuclei. Our model includes a detailed treatment for the chemical enrichment from dying stars, core-collapse supernovae (both Type II and hypernovae) and Type Ia supernovae. At redshift $z$ = 0, we create a catalogue of 526 galaxies, among which we determine 80 early-type galaxies. From the analysis of our simulations, we find [α/Fe]–[Fe/H] relations similar to the Galactic bulge. We also find that, in the oldest galaxies, Type Ia supernovae start to contribute at higher [Fe/H] than in the youngest ones. On the average, early-type galaxies with larger stellar masses (and, equivalently, higher stellar velocity dispersions) have higher [α/Fe] ratios, at fixed [Fe/H]. This is qualitatively consistent with the recent observations of Sybilska et al., but quantitatively there are mismatches, which might require stronger feedback, sub-classes of Type Ia Supernovae, or a variable initial mass function to address.
Evolving paradigms in biological carbon cycling in the ocean
Authors: Zhang Chuanlun , Dang Hongyue , Azam Farooq , Benner Ronald , Legendre Louis , Passow Uta , Polimene Luca , Robinson Carol , Suttle Curtis A , Jiao Nianzhi
Published: July 2018

Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.
Impact of Smoking Cessation on Periodontitis: A Systematic Review and Meta-analysis of Prospective Longitudinal Observational and Interventional Studies
Authors: Leite Fábio R M , Nascimento Gustavo G , Baake Stina , Pedersen Lisa D , Scheutz Flemming , López Rodrigo
Published: July 2018

Aims

This systematic review aimed to estimate the effect of tobacco smoking cessation on the risk for periodontitis compared to the risk among never-smokers and to evaluate the effect of tobacco smoking cessation on the clinical outcomes of nonsurgical periodontal treatment.

Methods

Electronic searches were performed in PubMed, Scopus, and Embase. Search strategy included MeSH and free terms: periodontitis, periodontal diseases, smoking, tobacco use, tobacco, tobacco products, cigarette, pipe, and cigar. Only original prospective longitudinal observational and interventional studies that investigated the association between smoking cessation and periodontitis onset or progression were included. Meta-analyses were conducted to summarize the evidence.

Results

A total of 2743 articles were identified in electronic searches; out of which only six were included in the meta-analysis. Pooled estimates showed that the risk of periodontitis incidence or progression among those who quit smoking was not significantly different from the risk for never-smokers (risk ratio [RR] = 0.97; 95% confidence interval [CI] = 0.87% to 1.08%). Smokers had approximately 80% higher risk of periodontitis than quitters (RR = 1.79; 95% CI = 1.36% to 2.35%) and never-smokers (RR = 1.82; 95% CI = 1.43% to 2.31%). Periodontal therapy resulted in up to 0.2 mm (95% CI = −0.32% to −0.08%) higher gain in attachment level and extra 0.32 mm (95% CI = 0.07% to 0.52%) reduction in pocket depth among quitters over nonquitters after short follow-up (12–24 months).

Conclusions

Few studies on the topic were identified. Smoking cessation reduced the risk for periodontitis onset and progression, and improved the outcomes of nonsurgical periodontal therapy.

Implications

This review provides the first quantitative evidence of the impact of smoking cessation on the risk for periodontitis onset and progression. The findings have demonstrated that the risk for periodontitis becomes comparable to that of never-smokers and that nonsurgical periodontal treatment outcomes improve after smoking cessation. Dental professionals ought to consider smoking cessation interventions as a relevant component of the periodontal therapy.
Clinical Outcomes Associated With Linezolid Resistance in Leukemia Patients With Linezolid-Resistant Staphylococcus epidermidis Bacteremia
Authors: Folan Stephanie A , Marx Kayleigh R , Tverdek Frank P , Raad Issam , Mulanovich Victor E , Tarrand Jeffrey J , Shelburne Samuel A , Aitken Samuel L
Published: July 2018

Background

Coagulase-negative staphylococci, including Staphylococcus epidermidis, are the most common cause of bloodstream infection in cancer patients. Linezolid resistance is increasingly identified in S. epidermidis, but whether such resistance alters the clinical course of S. epidermidis infections is unknown. The purpose of this study was to assess the clinical impact of linezolid resistance in leukemia patients with S. epidermidis bloodstream infection.

Methods

This was a retrospective, single-center cohort study of all adult leukemia patients with S. epidermidis bacteremia treated with empiric linezolid between 2012 and 2015. The primary end point was adverse clinical outcome on day 3, defined as a composite of persistent bacteremia, fever, intensive care unit admission, or death. Fourteen- and 30-day mortality were also assessed.

Results

Eighty-two unique leukemia patients with S. epidermidis were identified. Linezolid resistance was identified in 33/82 (40%). Patients with linezolid-resistant S. epidermidis were significantly more likely to have persistent bacteremia (41% vs 7%; adjusted relative risk [aRR], 5.15; 95% confidence interval [CI], 1.63–16.30; P = .005); however, adverse short-term clinical outcomes overall were not more common among patients with linezolid-resistant S. epidermidis (61% vs 33%; aRR, 1.46; 95% CI, 0.92–2.32; P = .108). No differences were observed in 14- or 30-day mortality.

Conclusions

Leukemia patients with linezolid-resistant S. epidermidis bacteremia who were treated with linezolid were significantly more likely to have persistent bacteremia compared with those with linezolid-sensitive isolates. Interventions to limit the clinical impact of linezolid-resistant S. epidermidis are warranted.
Operative Management of Idiopathic Spinal Cord Herniation: Case Series and Novel Technique for Repair of Recurrent Herniation
Authors: Hlubek Randall J , Xu David S , Mulholland Celene B , Gilson Jourdan , Theodore Nicholas , Turner Jay D , Kakarla U Kumar
Published: July 2018

BACKGROUND

Idiopathic spinal cord herniation (ISCH) is a rare pathology of the spine defined by herniation of the spinal cord through a dural defect.

OBJECTIVE

To highlight the operative management of ISCH and the surgical nuances of ISCH repairs conducted at our institution.

METHODS

This retrospective review examines consecutive patients with ISCH who were treated surgically between January 1, 2010, and July 31, 2017, at Barrow Neurological Institute, Phoenix, Arizona.

RESULTS

Four patients with ISCH presented with thoracic myelopathy and lower extremity weakness during the study period. Treatment consisted of reduction of the herniated spinal cord and filling of the dural defect with a collagen-based dural regeneration matrix. In 3 patients the dural edges were covered with a collagen-matrix intradural sling, and in 1 patient they were repaired primarily with interrupted sutures. Three of the 4 patients experienced improvement in myelopathic symptoms; the fourth patient suffered neurological decline in the immediate postoperative period.

CONCLUSION

ISCH is a complex pathological condition likely to result in progressive myelopathy. Surgery offers patients the possibility of stabilizing the progression of the spinal cord dysfunction and perhaps restoring neurological function. However, extreme care must be taken during surgery to minimize manipulation of the fragile herniated cord.
Supracerebellar Infratentorial and Occipital Transtentorial Approaches to the Pulvinar: Ipsilateral Versus Contralateral Corridors
Authors: Cohen-Cohen Salomon , Cohen-Gadol Aaron A , Gomez-Amador Juan L , Alves-Belo Joao T , Shah Kushal J , Fernandez-Miranda Juan C
Published: July 2018

BACKGROUND

Due to the critical neurovascular structures that surround the pulvinar, deciding the best surgical approach can be challenging, with multiple options available.

OBJECTIVE

To analyze and compare the ipsilateral vs the contralateral version of the 2 main approaches to the cisternal pulvinar surface: paramedian supracerebellar infratentorial (PSCI) and interhemispheric occipital transtentorial (IOT).

METHODS

The PSCI and IOT approaches were performed on 7 formalin-fixed adult cadaveric heads to evaluate qualitatively and quantitatively the microsurgical exposure of relevant anatomic structures. We quantitatively measured the corridor distance to our target with each approach.

RESULTS

The ipsilateral PSCI approach provided an easier access and a better exposure of the anteromedial portion of the cisternal pulvinar surface. The contralateral approach provided a wider and more accessible exposure of the posterolateral portion of the cisternal pulvinar surface. When protrusion of the posterior parahippocampal gyrus above the free edge of the tentorium was present, the contralateral PSCI approach provided an unobstructed view to both areas. The IOT approach provided a better view of the anteromedial portion of the cisternal pulvinar surface, especially with a contralateral approach.

CONCLUSION

Multiple approaches to the pulvinar have been described, modified, and improved. Based on this anatomic study we believe that although the corridor distance with a contralateral approach is longer, the surgical view and access can be better. We recommend the use of a PSCI contralateral approach especially when a significant protrusion of the posterior parahippocampal gyrus is present.
Terminology of Pelvic Floor Muscle Function in Women With and Without Urinary Incontinence: A Systematic Review
Authors: Saltiel Fernanda , Miranda-Gazzola Ana Paula G , Vitória Rayane O , Figueiredo Elyonara M
Published: July 2018

Background

Pelvic floor muscle function (PFMF) is a target of the physical therapist intervention for women with urinary incontinence (UI). However, possible variations in PFMF terminology might hamper communication among researchers and health care professionals in Women's Health.

Objective

The objective of this study was to investigate the terminology of PFMF regarding clear terms, conceptual definitions, and operational definitions.

Data Sources

Data sources include PUBMED, CINAHL, LILACS, and SCIELO.

Study Selection

Observational studies investigating any PFMF in women with or without UI, published in English, Spanish, or Portuguese from 2005 through 2017, were considered.

Data Extraction

The risk of bias was assessed by a questionnaire on the quality of observational studies. Data on terminology were extracted as terms, conceptual definitions, and operational definitions of PFMF and were synthesized according to key words, key ideas, and key operationalization, respectively. Consistencies and variations were identified for the most frequently investigated PFMF.

Data Synthesis

Sixty-four studies were included, and a low risk of bias was identified. All studies presented terms and operational definitions of PFMF, but only 29.7% presented conceptual definitions of those terms. One hundred ninety-six different terms referred to PFMF. According to similarities in terminology, 161 PFMF terms could be grouped under 26 terms; the other 35 were left ungrouped. Therefore, a total of 61 different PFMF terms were identified in the literature.

Limitations

A limitation in the study was that only observational studies were included.

Conclusions

A large variation in PFMF terminology was identified, precluding data gathering and meta-analysis. The lack of use of standardized terminology delays the progress of scientific knowledge and evidence-based practice dissemination. Efforts toward creating a collaborative, consensual terminology based on a sound framework are necessary.
Childhood obesity prevention: priority areas for future research and barriers and facilitators to knowledge translation, coproduced using the nominal group technique
Authors: Hennessy Marita , Byrne Molly , Laws Rachel , Mc Sharry Jenny , O’Malley Grace , Heary Caroline
Published: July 2018

Childhood obesity is a significant public health challenge, yet research priorities for childhood obesity prevention are not established. Coproduction of priorities leads to research which may be more translatable to the domains of policy and practice. The aim of the present study was to identify knowledge gaps and research priorities in addition to facilitators and barriers to knowledge translation in childhood obesity prevention. The nominal group technique involving consensus building with researchers, policymakers, and practitioners was employed during workshops at a national obesity conference held over 2 days in May 2017. Seventy-seven people participated in the first round of research prioritization on Day 1, while 14 stakeholders participated on Day 2. The top five research priorities identified were as follows: (i) Evaluate (including economic evaluation) current programs to inform practice and policy; (ii) How to change culture toward addressing the determinants of health; (iii) Implementation science: process; (iv) How to integrate obesity prevention into existing service structures; (v) How to enhance opportunities for habitual physical activity, including free play and active travel. Key themes emerging from this research prioritization exercise were the importance of funding and resources, coproduction of research, and a focus on both implementation research and social determinants within the field of childhood obesity prevention. The coproduced research priorities may help to shape the research agendas of funders and researchers, and aid in the conduct of policy-relevant research and the translation of research into practice in childhood obesity prevention.
Leveraging RNA-Seq to Characterize Resistance to Brown Stem Rot and the Rbs3 Locus in Soybean
Authors: McCabe Chantal E. , Cianzio Silvia R. , O’Rourke Jamie A. , Graham Michelle A.
Published: July 2018

Brown stem rot, caused by the fungus Phialophora gregata, reduces soybean yield by up to 38%. Although three dominant resistance loci have been identified (Rbs1 to Rbs3), the gene networks responsible for pathogen recognition and defense remain unknown. Further, identification and characterization of resistant and susceptible germplasm remains difficult. We conducted RNA-Seq of infected and mock-infected leaf, stem, and root tissues of a resistant (PI 437970, Rbs3) and susceptible (Corsoy 79) genotype. Combining historical mapping data with genotype expression differences allowed us to identify a cluster of receptor-like proteins that are candidates for the Rbs3 resistance gene. Reads mapping to the Rbs3 locus were used to identify potential novel single-nucleotide polymorphisms within candidate genes that could improve phenotyping and breeding efficiency. Comparing responses to infection revealed little overlap in differential gene expression between genotypes or tissues. Gene networks associated with defense, DNA replication, and iron homeostasis are hallmarks of resistance to P. gregata. This novel research demonstrates the utility of combining contrasting genotypes, gene expression, and classical genetic studies to characterize complex disease resistance loci.
Evaluation of Rice Responses to the Blast Fungus Magnaporthe oryzae at Different Growth Stages
Authors: Chen Xinglong , Jia Yulin , Wu Bo Ming
Published: July 2018

Rice blast, caused by the fungus Magnaporthe oryzae, is the most damaging disease for rice worldwide. However, the reactions of rice to M. oryzae at different growth stages are largely unknown. In the present study, two temperate japonica rice cultivars, M-202 and Nipponbare, were inoculated synchronously at different vegetative growth stages, V1 to V10. Plants of M-202 at each stage from V1 to reproductive stage R8 were inoculated with M. oryzae race (isolate) IB-49 (ZN61) under controlled conditions. Disease reactions were recorded 7 days postinoculation by measuring the percentage of diseased area of all leaves, excluding the youngest leaf. The results showed that the plants were significantly susceptible at the V1 to V4 stages with a disease severity of 26.7 to 46.8% and disease index of 18.62 to 37.76 for M-202. At the V1 to V2 stages, the plants were significantly susceptible with a disease a severity of 28.6 to 39.3% and disease index of 23.65 to 29.82 for Nipponbare. Similar results were observed when plants of M-202 were inoculated at each growth stage with a disease severity of 29.7 to 60.6% and disease index of 21.93 to 59.25 from V1 to V4. Susceptibility decreased after the V5 stage (severity 4.6% and index 2.17) and became completely resistant at the V9 to V10 stages and after the reproductive stages, suggesting that plants have enhanced disease resistance at later growth stages. These findings are useful for managing rice blast disease in commercial rice production worldwide.
Ectopic expression of recipient CD47 inhibits mouse macrophage‐mediated immune rejection against human stem cell transplants
Authors: Leung Cherry S. , Li Jiatao , Xu Feng , Wong Alan S. L. , Lui Kathy O.
Published: July 2018

Like conventional transplants, immunosuppression is required to facilitate survival and function of human embryonic stem cell (hESC) derivatives after implantation into xenogeneic recipients. We have previously reported that T cells alone are sufficient to reject allogeneic murine ESC derivatives; and strategies that inhibit T‐cell activation, including coreceptor and costimulation blockade, prevent hESC derivatives from being rejected. This study aimed to investigate, in addition to T cells, whether macrophages contribute to transplant rejection of hESC xenografts with nonobese diabetic (NOD)/SCID mice that lack functional T and B cells but have macrophages. We show that acute rejection against hESC‐derived endothelial cells (hESC‐ECs) was mediated, to some degree, by infiltrating macrophages that phagocytosed them. Transgenic expression of murine CD47 on cell surface of hESC‐ECs mitigates macrophage‐mediated phagocytosis and improves their survival after transplantation. Our results highlight that innate immune cells, such as macrophages, can reject hESC derivatives, raising concern against the use of NOD/SCID as transplant recipients for testing in vivo function of hESC‐derived tissues. Augmenting CD47 signaling promotes survival and function of hESC derivatives after xenogeneic transplantation.—Leung, C. S., Li, J., Xu, F., Wong, A. S. L., Lui, K. O. Ectopic expression of recipient CD47 inhibits mouse macrophage‐mediated immune rejection against human stem cell transplants. FASEB J. 33, 484–193 (2019). www.fasebj.org