bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aspirin-triggered proresolving mediators stimulate resolution in cancer
Authors: Gilligan Molly M. , Gartung Allison , Sulciner Megan L. , Norris Paul C. , Sukhatme Vikas P. , Bielenberg Diane R. , Huang Sui , Kieran Mark W. , Serhan Charles N. , Panigrahy Dipak 
Published: March 2019

Significance
Strong epidemiologic evidence indicates that aspirin is a powerful antitumorigenic agent. We now demonstrate that aspirin-triggered resolvins achieve the antitumor and chemopreventive activity of aspirin without toxicity, identifying a mechanism for aspirin’s anticancer activity. Our results suggest that differentiating between suppression and resolution of inflammation is highly relevant in cancer biology, revealing a class of endogenous antitumor mechanisms. These results have pivotal implications for cancer therapy and chemoprevention; unlike anti-inflammatory drugs, aspirin-triggered resolvins are active at nanogram doses and are not immunosuppressive. The antitumorigenic activity of aspirin-triggered resolvins may be harnessed to “mimic” aspirin without incurring aspirin-induced toxicity, such as bleeding, to contain minimal residual disease.
Polyandrous bee provides extended offspring care biparentally as an alternative to monandry based eusociality
Authors: Mikát Michael , Janošík Lukáš , Černá Kateřina , Matoušková Eva , Hadrava Jiří , Bureš Vít , Straka Jakub 
Published: March 2019

SignificanceBiparental care is a rare strategy of offspring protection in insects. We discovered a case of biparental care in bees, inCeratina nigrolabiata. Benefits of biparental care were identified for both males and females; yet, we found that an extraordinarily high proportion of offspring were unrelated to guard males. This is because females ofC. nigrolabiataare polyandrous and store sperm. Therefore, the most important benefit for males is increased mating opportunities. We suggest that female polyandry and prolonged female receptivity supported the origin and/or maintenance of biparental care concomitant with extended male lifespan. Biparental care is an alternative method of brood protection to eusociality, which provides similar benefits but arises under different female mating conditions.
Multiplexed profiling of single-cell extracellular vesicles secretion
Authors: Ji Yahui , Qi Dongyuan , Li Linmei , Su Haoran , Li Xiaojie , Luo Yong , Sun Bo , Zhang Fuyin , Lin Bingcheng , Liu Tingjiao , Lu Yao 
Published: March 2019

Significance
Extracellular vesicles (EVs) are cell-derived nanosized particles medicating cell−cell communication and transferring biology information molecules like nucleic acids to regulate human health and diseases. Conventional methods for EV surface marker profiling can’t tell the differences in the quantity and phenotypes of EV secretion between cells. To address this need, we developed a microchip platform for profiling an array of surface markers on EVs from large numbers of single cells, enabling more-comprehensive monitoring of cellular communications. Single-cell EV secretion assay led to previously unobserved cell heterogeneity underlying EV secretion, which might open up avenues for studying cell communication and cell microenvironment in both basic and clinical research.
Primitive Old World monkey from the earliest Miocene of Kenya and the evolution of cercopithecoid bilophodonty
Authors: Rasmussen D. Tab , Friscia Anthony R. , Gutierrez Mercedes , Kappelman John , Miller Ellen R. , Muteti Samuel , Reynoso Dawn , Rossie James B. , Spell Terry L. , Tabor Neil J. , Gierlowski-Kordesch Elizabeth , Jacobs Bonnie F. , Kyongo Benson , Macharwas Mathew , Muchemi Francis 
Published: March 2019

Significance
Almost nothing is known about the origin and evolution of Old World monkeys (cercopithecoids) because the first ∼12 million years of their fossil record is documented by only two isolated teeth. We describe a new primitive monkey from Kenya that dates from ∼22 million years ago and reveals a previously unknown stage of evolution. Comparisons between this monkey and other cercopithecoids offer detailed insights into the development of the novelties associated with the evolution of the cercopithecoid dentition, and particularly bilophodonty. Results suggest that this fossil monkey exhibited dental adaptations for frugivory and perhaps hard object feeding. Bilophodonty, the dental trait that unites all living cercopithecoids, evolved later, likely in response to the inclusion of leaves in the diet.
On, for, and with practitioners
Authors: Perrin Daniel 
Published: March 2019

Abstract
This article explains how research “on” practitioners can be turned into research “for and with” practitioners
(Cameron, Frazer, Rampton, & Richardson, 1992, p. 22) by including these
practitioners in the research teams. Methodologically, it draws on two decades of multimethod research and knowledge
transformation at the interface of applied linguistics and transdisciplinary action research on professional communication (Perrin, 2013). Empirically, it is based on large corpora of data collected in
multilingual and multicultural workplaces. First, the article outlines transdisciplinary action research as a theoretical
framework that enables researchers and practitioners to collaboratively develop sustainable solutions to real-world problems in
which language use in general and text production in particular play a substantial role (Section 1). Then, Progression Analysis is explained as a multimethod approach to investigate text production practices
in natural environments such as workplaces (Section 2). Examples from four domains
(education, finance, translation, and journalism) illustrate what value transdisciplinary collaboration between academic
researchers and practitioners can add to knowledge generation in applied linguistics (Section 3). For the case of journalism in increasingly global contexts, in-depth analyses offer step-by-step
understanding of the trajectory from a real-world problem to a sustainable solution (Section 4). The article concludes by suggesting empirically-based measures for research that contribute to the
development of both theory and practice in applied linguistics (Section 5).
Applied linguistics as epistemic assemblage
Authors: Pennycook Alastair 
Published: March 2019

Abstract
Any discussion of transdisciplinary applied linguistics needs to engage with three central questions. First, while
interdisciplinarity may allow for disciplines to stay in place and engage with each other,
transdisciplinarity implies a space beyond or above disciplines. As a result, we have to consider whether
applied linguistics is seen as a discipline (in which case it is not transdisciplinary) or whether it is seen as a
transdisciplinary field of study (in which case it is not a discipline). Second, while applied linguists may engage with work from
other fields – sociology, geography, philosophy, cognitive science are common examples – this does not necessarily mean that we
engage with those fields as disciplines. Rather, the engagement with such work is often on the basis that relevant thinkers are
engaging themselves with broader epistemic shifts. Such work may therefore be seen as having to do with epistemes
rather than disciplines. Third, a focus on transdisciplinarity obscures broader concerns about unequal relations of knowledge
production, particularly between North and South. If applied linguistics is to become a responsible field of work, it needs to
engage with southern epistemologies. In order to do so, applied linguistic practices can be more usefully understood as temporary
assemblages of thought and action that come together at particular moments when language-related concerns need to be addressed.
This flexible account helps us see how applied linguistic practices are assemblages of different language-oriented projects,
epistemes and matters of concern.
The Reliability and Validity of the Action Fluency Test in Healthy College Students
Authors: Ross Thomas P , O’Connor Sydne , Holmes Graham , Fuller Brittany , Henrich Megan 
Published: March 2019

Abstract

Objective
This study examined the test–retest reliability and construct validity of the Action Fluency Test (AFT) as a measure of executive functioning.

Method
Using a correlational design, 128 healthy college students (M Age = 19.24, SD = 2.01; M education = 13.29 years, SD = 0.81) completed the AFT, and measures of verbal and figural fluency, executive functioning and other relevant constructs (e.g., vocabulary, working memory, and attention).

Results
Coefficients of stability were acceptable for AFT correct words (r = .76; p &lt; .01), but not for errors (r = .41) or perseverations (r = .14). No practice effects were observed upon repeat testing (M interval = 39.21 days). Divergent validity evidence was mixed. AFT scores were unrelated to working memory and perceptual-reasoning abilities; however, correlations with vocabulary (r = .32; p &lt; .01) and information-processing speed (r = .30; p &lt; .01) were greater than associations between AFT scores and executive measures. Regarding convergent validity, AFT scores correlated with other fluency tasks (r = .4 range), but correlations with measures of executive functioning were absent or small. Action and letter fluency correlated with measures of attentional control and inhibition; however, these associations were no longer significant after controlling for shared variance with information-processing speed.

Conclusions
Findings are consistent with previous research suggesting vocabulary and information-processing speed underlie effective fluency performance to a greater extent than executive functioning. The AFT measures unique variance not accounted for by semantic and letter fluency tasks, and therefore may be used for a variety of research and clinical purposes.
PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits
Authors: Gao X Raymond , Huang Hua 
Published: March 2019

Abstract

Summary
Pleiotropy plays an important role in furthering our understanding of the shared genetic architecture of different human diseases and traits. However, exploring and visualizing pleiotropic information with currently publicly available tools is limiting and challenging. To aid researchers in constructing and digesting pleiotropic networks, we present PleioNet, a web-based visualization tool for exploring this information across human diseases and traits. This program provides an intuitive and interactive web interface that seamlessly integrates large database queries with visualizations that enable users to quickly explore complex high-dimensional pleiotropic information. PleioNet works on all modern computer and mobile web browsers, making pleiotropic information readily available to a broad range of researchers and clinicians with diverse technical backgrounds. We expect that PleioNet will be an important tool for studying the underlying pleiotropic connections among human diseases and traits.

Availability and implementation
PleioNet is hosted on Google cloud and freely available at http://www.pleionet.com/.
SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data
Authors: Zhu Hao , Wang Zheng 
Published: March 2019

AbstractMotivationIn contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the 3D structures of chromosomes based on single-cell Hi-C data.ResultsWe developed single-cell lattice (SCL), a computational method to reconstruct 3D structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2 D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3 D cubic lattice. Metropolis–Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3 D structures (at both 500 and 50 kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3 D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topologically associating domains (TADs), and H3K4me3 enriched TADs by mapping data from previous studies onto the SCL-inferred 3 D structures.Availability and implementationThe C++ source code of SCL is freely available at http://dna.cs.miami.edu/SCL/.Supplementary informationSupplementary data are available at Bioinformatics online.
Methylation of global DNA repeat LINE-1 and subtelomeric DNA repeats D4Z4 in leukocytes is associated with biochemical recurrence in African American prostate cancer patients
Authors: Xu Junfeng , Tsai Chia-Wen , Chang Wen-Shin , Han Yuyan , Bau Da-Tian , Pettaway Curtis A , Gu Jian 
Published: March 2019

Abstract
Global DNA methylation may play important roles in cancer etiology and prognosis. The goal of this study is to investigate whether the methylation of long interspersed nucleotide elements (LINE-1) and subtelomeric DNA repeats D4Z4 in leukocyte DNA is associated with aggressive prostate cancer (PCa) in African Americans. We measured DNA methylation levels of LINE-1 and D4Z4 in 306 African American (AA) PCa patients using pyrosequencing and compared their methylation levels among clinical variables. We further applied multivariate Cox proportional hazards model and Kaplan–Meier survival function and log-rank tests to assess the association between DNA methylation and biochemical recurrence (BCR). Overall, there was no significant difference of the methylation levels of LINE-1 and D4Z4 among patients with different clinical and epidemiological characteristics. However, the methylation of LINE-1 and D4Z4 was associated with BCR. Patients with lower LINE-1 methylation and higher D4Z4 methylation exhibited markedly increased risks of BCR with adjusted hazard ratios of 3.34 (95% confidence interval, 1.32–8.45) and 4.12 (95% confidence interval, 1.32–12.86), respectively, and significantly shorter BCR-free survival times. Our results suggest that lower global DNA methylation and higher subtelomeric region methylation may predict worse prognosis in localized AA PCa patients.
Femur Bone Volumetric Estimation for Osteoporosis Classification Using Optimization-Based Deep Belief Network in X-Ray Images
Authors: Shankar N , Sathish Babu S , Viswanathan C 
Published: March 2019

AbstractOsteoporosis classification is a significant requirement in the medical field to automatically classify the patients with skeleton disorder that occurs as a result of aging. The classification algorithms required improved accuracy and computationally less complexity. Accordingly, this paper proposes a classification method using the proposed gradient harmony search (GHS) optimization-based deep belief network. The GHS is developed by integrating the harmony search (HS) in the gradient descent (GD) algorithm. The osteoporosis classification is progressed as five major steps: preprocessing, segmentation using active shape model, geometric estimation using the proposed template search method, feature extraction for extracting the medical and image level features, and osteoporosis classification using the proposed GHS based deep belief network. The proposed template search method updates the geometric points of the femur segment effectively and automatically. Experimentation using the real-time database ensures the effectiveness of the proposed method in terms of accuracy, sensitivity, and specificity. The proposed method acquired the accuracy of 0.9539, proving that the osteoporosis classification using the proposed algorithm seems to be effective in taking accurate decisions regarding the patients.
Generating connected random graphs
Authors: Gray Caitlin , Mitchell Lewis , Roughan Matthew 
Published: March 2019

AbstractSampling random graphs is essential in many applications, and often algorithms use Markov chain Monte Carlo methods to sample uniformly from the space of graphs. However, often there is a need to sample graphs with some property that we are unable, or it is too inefficient, to sample using standard approaches. In this article, we are interested in sampling graphs from a conditional ensemble of the underlying graph model. We present an algorithm to generate samples from an ensemble of connected random graphs using a Metropolis–Hastings framework. The algorithm extends to a general framework for sampling from a known distribution of graphs, conditioned on a desired property. We demonstrate the method to generate connected spatially embedded random graphs, specifically the well-known Waxman network, and illustrate the convergence and practicalities of the algorithm.
Impact of pectus excavatum on cardiac morphology and function according to the site of maximum compression: effect of physical exertion and respiratory cycle
Authors: Rodriguez-Granillo Gaston A , Raggio Ignacio M , Deviggiano Alejandro , Bellia-Munzon Gaston , Capunay Carlos , Nazar Maximiliano , Martinez Jorge Luis , Carrascosa Patricia , Martinez-Ferro Marcelo 
Published: March 2019

Abstract

Aims
Previous studies have demonstrated diverse cardiac manifestations in patients with pectus excavatum (PEX), although mostly addressing morphological or physiological impact as separate findings. Using multimodality imaging, we evaluated the impact of PEX on cardiac morphology and function according to the site of maximum compression, and the effect of exertion and breathing.

Methods and results
All patients underwent chest computed tomography, cardiac magnetic resonance (CMR), and stress echocardiography (echo) in order to establish surgical candidacy. We evaluated diastolic function and trans-tricuspid gradient during stress (echo); and systolic function and respiratory-related septal wall motion abnormalities (CMR). Patients were classified according to the site of cardiac compression as type 0 (without cardiac compression); type 1 (right ventricle); and type 2 [right ventricle and atrioventricular (AV) groove]. Fifty-nine patients underwent multimodality imaging, with a mean age of 19.5 ± 5.9 years. Compared with a sex and age matched control group, peak exercise capacity was lower in patients with PEX (8.4 ± 2.0 METs vs. 15.1 ± 4.6 METs, P &lt; 0.0001). At stress, significant differences were found between groups regarding left ventricular E/A (P = 0.004) and e/a ratio (P = 0.005), right ventricular E/A ratio (P = 0.03), and trans-tricuspid gradient (P = 0.001). At CMR, only 9 (15%) patients with PEX had normal septal motion, whereas 17 (29%) had septal flattening during inspiration. Septal motion abnormalities were significantly related to the cardiac compression classification (P &lt; 0.0001).

Conclusions
The present study demonstrated that patients with PEX, particularly those with compression affecting the right ventricle and AV groove, manifest diverse cardiac abnormalities that are mostly related to exertion, inspiration, and diastolic function.
Concealing Collusion: The Suez Crisis, Political Memoirs and Official Secrecy, 1956–1969
Authors: Moran Christopher 
Published: March 2019

Abstract
The Suez crisis in 1956 has long been recognised as a watershed in British history—precipitating the fall of Anthony Eden’s government, accelerating the end of empire, and underscoring how weak Britain had become on the international stage, especially in relation to the United States, which emerged from the episode as undeniably the senior partner in the ‘Special Relationship’. Less understood is the important role that the crisis played in weakening the foundations of official secrecy in Britain, especially what might be described as the social underpinnings of secrecy. This article explores how sensitive details about Suez eventually came to light in the period 1956 to 1969, despite concerted and sometimes cunning efforts by the Whitehall machine to prevent disclosure. Contrary to conventional wisdom, which suggests that socialist parliamentary firebrands like Michael Foot proved the most difficult to control, it is argued that the greatest challenge to secret-keepers came from senior conservative politicians writing memoirs—chief among them Eden himself—who were headstrong, not easily intimidated, and unafraid to bypass rules and codes of discretion to vindicate their careers. Fascinatingly, memoir writers not only ignored legal mechanisms such as the much-feared Official Secrets Act, but, against the backdrop of profound social and cultural change, they also dismissed attempts by mandarins to exploit gentlemanly bonds and loyalties, which in the past had been an effective method of promoting self-censorship by members of the elite.
Incidence, predictors and cerebrovascular consequences of leaflet thrombosis after transcatheter aortic valve implantation: a systematic review and meta-analysis
Authors: D’Ascenzo Fabrizio , Salizzoni Stefano , Saglietto Andrea , Cortese Martina , Latib Azeem , Franzone Anna , Barbanti Marco , Nietlispach Fabian , Holy Erik W , Burriesci Gaetano , De Paoli Alessandro , Fonio Paolo , Atzeni Francesco , Moretti Claudio , Perl Leor , D’Amico Maurizio , Rinaldi Mauro , Conrotto Federico 
Published: March 2019

Abstract

OBJECTIVES
We examined the incidence, the impact of subsequent cerebrovascular events and the clinical or procedural predictors of leaflet thrombosis (LT) in patients undergoing transcatheter aortic valve implantation (TAVI).

METHODS
MEDLINE/PubMed was systematically screened for studies reporting on LT in TAVI patients. Incidence [both clinical and subclinical, i.e. detected with computed tomography (CT)] of LT was the primary end point of the study. Predictors of LT evaluated at multivariable analysis and impact of LT on stroke were the secondary ones.

RESULTS
Eighteen studies encompassing 11 124 patients evaluating incidence of LT were included. Pooled incidence of LT was 0.43% per month [5.16% per year, 95% confidence interval (CI) 0.21–0.72, I2 = 98%]. Pooled incidence of subclinical LT was 1.36% per month (16.32% per year, 95% CI 0.71–2.19, I2 = 94%). Clinical LT was less frequent (0.04% per month, 0.48% per year, 95% CI 0.00–0.19, I2 = 93%). LT increased the risk of stroke [odds ratio (OR) 4.21, 95% CI 1.27–13.98], and was more frequent in patients with a valve diameter of 28-mm (OR 2.89: 1.55–5.8), for balloon-expandable (OR 8: 2.1–9.7) or after valve-in-valve procedures (OR 17.1: 3.1–84.9). Oral anticoagulation therapy reduced the risk of LT (OR 0.43, 95% CI: 0.22–0.84, I2 = 64%), as well as the mean transvalvular gradient.

CONCLUSIONS
LT represents an infrequent event after TAVI, despite increasing risk of stroke. Given its full reversal with warfarin, in high-risk patients (those with valve-in-valve procedures, balloon expandable or large-sized devices), a protocol which includes a control CT appears reasonable.
A unique methylation pattern by a type I HsdM methyltransferase prepares for DpnI rare cutting sites in the Pseudomonas aeruginosa PAO1 genome
Authors: Fischer Sebastian , Römling Ute , Tümmler Burkhard 
Published: March 2019

ABSTRACT
A physical genome map of Pseudomonas aeruginosa PAO1 had been constructed in the late 1980s by combinatorial SpeI/DpnI long-range restriction mapping. Whereas SpeI was known to cleave within the infrequent 5′-ACTAGT hexanucleotide, the rare recognition site 5′-Gm6ATC for the methylation-sensitive 4-cutter DpnI in the PAO1 genome remained elusive. Resequencing the PAO1 genome with the methylation-sensitive Single Molecule Real-Time (SMRT) sequencing technology identified DpnI to cleave the PAO1 genome at 15 palindromic GAC(N)6Gm6ATC(N)6GTC recognition sites with the central Gm6ATC palindrome to be methylated on both strands by the clone PAO1-specific type I HsdM superfamily methyltransferase M.PaePAOI (PA2735).