bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential of microwave soil heating for weed management and yield improvement in rice cropping
Authors: Khan Muhammad Jamal , Brodie Graham , Gupta Dorin
Published: March 2019

Herbicide-resistant weeds have prompted the development of non-chemical weed-control techniques for sustainable crop production. We examined the potential of pre-emergence microwave (MW) soil treatment to suppress weeds and enhance grain yield in rice (Oryza sativa L.) cropping in two agro-ecological zones of Australia. An experimental MW weed killer, which has four, independently controlled, 2-kW MW generators operating at 2.45 GHz, was used to treat the soil before cropping under field conditions. A once-off MW soil treatment (duration 60 s) and an untreated control were assigned in a randomised complete block design with five replicates at two study locations: Dookie (Victoria) and Jerilderie (New South Wales). Simpson’s numerical surface integral approximation estimated the applied energy density of ~500 J cm–2. This energy increased the soil’s temperature up to 70–75°C in top soil horizon (0–6 cm) as depicted by infrared thermal imaging. No statistically significant difference was detected for weed control between MW and untreated control plots at either study location. At Dookie, grain yield did not significantly increase in response to MW soil treatment, whereas at Jerilderie, grain yield was 20% higher (P < 0.05) with MW soil treatment than in control plots. At Jerilderie, the irrigation water use efficiency (t ML–1) was 21% higher in MW plots than control plots. In summary, MW exposure of 60 s appeared to be an insufficient heating duration for seedbank depletion. This suggests further treatment modification followed by rigorous testing under different soils conditions using the MW prototype.
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

Significance

Biparental 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.
Predictable hydrological and ecological responses to Holocene North Atlantic variability
Authors: Shuman Bryan N. , Marsicek Jeremiah , Oswald W. Wyatt , Foster David R.
Published: March 2019

Climate variations in the North Atlantic region can substantially impact surrounding continents. Notably, the Younger Dryas chronozone was named for the ecosystem effects of abrupt changes in the region at circa (ca.) 12.9–11.7 ka (millennia before 1950 AD). Holocene variations since then, however, have been hard to diagnose, and the responsiveness of terrestrial ecosystems continues to be debated. Here, we show that Holocene climate variations had spatial patterns consistent with changes in Atlantic overturning and repeatedly steepened the temperature gradient between Nova Scotia and Greenland since >8 ka. The multicentury changes correlated with hydrologic and vegetation changes in the northeast United States, including when an enhanced temperature gradient coincided with subregional droughts indicated by water-level changes at multiple coastal lakes at 4.9–4.6, 4.2–3.9, 2.8–2.1, and 1.3–1.2 ka. We assessed the variability and its effects by replicating signals across sites, using converging evidence from multiple methods, and applying forward models of the systems involved. We evaluated forest responses in the northeast United States and found that they tracked the regional climate shifts including the smallest magnitude (∼5% or 50 mm) changes in effective precipitation. Although a long-term increase in effective precipitation of >45% (>400 mm) could have prevented ecological communities from equilibrating to the continuously changing conditions, our comparisons confirm stable vegetation–climate relationships and support the use of fossil pollen records for quantitative paleoclimate reconstruction. Overall, the network of records indicates that centennial climate variability has repeatedly affected the North Atlantic region with predictable consequences.
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.
Saving endangered species using adaptive management
Authors: Serrouya Robert , Seip Dale R. , Hervieux Dave , McLellan Bruce N. , McNay R. Scott , Steenweg Robin , Heard Doug C. , Hebblewhite Mark , Gillingham Michael , Boutin Stan
Published: March 2019

Significance

A replicated management experiment was conducted across >90,000 km
2
to test recovery options for woodland caribou, a species that was functionally extirpated from the contiguous United States in March 2018. Recovery options were reductions of predators, reductions of overabundant prey, translocations, and creating fenced refuges from predators. Population growth was strongest where multiple recovery options were applied simultaneously. This adaptive management study was one of the largest predator-prey manipulations ever conducted and provided positive results for this endangered North American ungulate.
On, for, and with practitioners
Authors: Perrin Daniel
Published: March 2019

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

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.
Functionally graded structures of refractory metals by wire arc additive manufacturing
Authors: Marinelli Gianrocco , Martina Filomeno , Lewtas Heather , Hancock David , Ganguly Supriyo , Williams Stewart
Published: March 2019

Functionally graded components are usually preferred for severe and critical service conditions, thanks to the possibility of achieving different complementary material properties within the same structure. Wire + Arc Additive Manufacturing is an emerging technology which lends itself well to the production of sound graded structures. In this study, an integral structure of two functional gradients, namely tantalum to molybdenum, and molybdenum to tungsten, was successfully deposited. A linear gradient was observed in both composition and hardness. Microstructure, elemental composition and hardness were characterised as a function of position, and discussed. The study demonstrates that WAAM has the potential to successfully deposit functionally graded structures of refractory metals, obtaining controlled properties.
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

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 < .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 < .01) and information-processing speed (r = .30; p < .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

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

Motivation

In 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.

Results

We 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 implementation

The C++ source code of SCL is freely available at http://dna.cs.miami.edu/SCL/.

Supplementary information

Supplementary 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

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

Osteoporosis 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

Sampling 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

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 < 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 < 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

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

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

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).
Family-centred oral health promotion through Victorian child-health services: a pilot
Authors: Heilbrunn-Lang Adina Y , Carpenter Lauren M , de Silva Andrea M , Meyenn Lisa K , Lang Gillian , Ridge Allison , Perry Amanda , Cole Deborah , Hegde Shalika
Published: March 2019

Maternal and Child Health Services (MCHS) provide ideal settings for oral disease prevention. In Victoria (Australia), child mouth-checks (Lift-the-Lip) and oral health promotion (OHP) occur during MCHS child visits. This study trialled Tooth-Packs (OHP resources, toothbrushes, toothpastes) distribution within MCHS to (i) assess the impacts of Tooth-Packs distribution on child and family oral health (OH) behaviours and knowledge, including Maternal and Child Health Nurses (MCHN) child referral practices to dental services, and (ii) determine the feasibility and acceptability of incorporating Tooth-Packs distribution into MCHN OHP practices. A mixed-methods evaluation design was employed. MCHN from four high-needs Victorian Local Government Areas distributed Tooth-Packs to families of children attending 18-month and/or 24-month MCHS visits (baseline). Families completed a questionnaire on OH and dietary practices at baseline and 30-month follow-up. Tooth-Packs distribution, Lift-the-lip mouth-checks and child OH referrals were conducted. Guided discussions with MCHN examined intervention feasibility. Overall, 1585 families received Tooth-Packs. Lift-the-lip was conducted on 1493 children (94.1%). Early childhood caries were identified in 142 children (9.5%) and these children were referred to dental services. Baseline to follow-up behavioural improvements (n = 230) included: increased odds of children having ever seen an OH professional (OR 28.0; 95% CI 7.40–236.88; p < 0.001), parent assisted toothbrushing twice/day (OR 1.76; 95% CI 1.05–3.00; p = 0.030) and toothpaste use >once/day (OR 2.82; 95% CI 1.59–5.24; p < 0.001). MCHN recommendations included distribution of Tooth-Packs to at-risk children <12-months of age. MCHS provide an ideal setting to enable timely family-centred OHP intervention and adoption of good OH behaviours at an early age.
Ketoacidosis related to sodium glucose cotransporter 2 inhibitors after emergency coronary surgery
Authors: Horikoshi Rihito , Kitamura Tadashi , Miyaji Kagami
Published: March 2019

Sodium glucose cotransporter 2 inhibitors are currently widely used antihyperglycaemic medications that are considered to be associated with euglycaemic diabetic ketoacidosis. We report 2 cases of patients who received sodium glucose cotransporter 2 inhibitors until emergency coronary artery bypass grafting (CABG) and developed euglycaemic ketoacidosis after surgery; they were treated with sugar replenishment and insulin infusion. In one case, coronary angiography revealed a spastic change of the bypass graft possibly due to severe acidosis. A rapid diagnosis and proper intervention are crucial to achieve better outcomes with CABG.
Can Rotational Fluxes Impede the Tendency Toward Spatial Homogeneity in Nutrient Taxis(-Stokes) Systems?
Authors: Winkler Michael
Published: March 2019

We consider the spatially 2D version of the model $$\begin{equation*} \qquad\quad\left\{ \begin{array}{@{}rcll} n_t + u\cdot\nabla n &=& \Delta n - \nabla \cdot \big(nS(x,n,c) \cdot \nabla c \big), \qquad &\qquad x\in \Omega, \ t>0, \\ c_t + u\cdot \nabla c &=& \Delta c - n f(c), \qquad &\qquad x\in \Omega, \ t>0, \\ u_t &=& \Delta u + \nabla P + n\nabla\phi, \qquad \nabla\cdot u=0, \qquad &\qquad x\in \Omega, \ t>0, \end{array} \right. \qquad \qquad (\star) \end{equation*}$$for nutrient taxis processes, possibly interacting with liquid environments. Here the particular focus is on the situation when the chemotactic sensitivity $S$ is not a scalar function but rather attains general values in ${\mathbb{R}}^{2\times 2}$, thus accounting for rotational flux components in accordance with experimental findings and recent modeling approaches. Reflecting significant new challenges that mainly stem from apparent loss of energy-like structures, especially for initial data with large size, the knowledge on ($\star$) so far seems essentially restricted to results on global existence of certain generalized solutions with possibly quite poor boundedness and regularity properties; widely unaddressed seem aspects related to possible effects of such non-diagonal taxis mechanisms on the qualitative solution behavior, especially with regard to the fundamental question whether spatial structures may thereby be supported. The present work answers the latter in the negative in the following sense: under the assumptions that the initial data $(n_0,c_0,u_0)$ and the parameter functions $S$, $f$, and $\phi$ are sufficiently smooth, and that $S$ is bounded and $f$ is positive on $(0,\infty )$ with $f(0)=0$, it is shown that any nontrivial of these solutions eventually becomes smooth and satisfies $$\begin{equation*} n(\cdot,t)\to - \int_\Omega n_0, \quad c(\cdot,t)\to 0 \quad \text{and} \quad u(\cdot,t)\to 0 \qquad \text{as} \ t\to\infty, \end{equation*}$$uniformly with respect to $x\in \Omega$. By not requiring any smallness condition on the initial data, the latter seems new even in the corresponding fluid-free version obtained on letting $u\equiv 0$ in ($\star$).
Jejunal interposition for short bowel syndrome in a septuagenarian
Authors: Gee Tikfu , Lim Shu Yu , Sudhakaran Nadarajan , Hassan Muhammad Firdaus
Published: March 2019

Short bowel syndrome in adults occurs as a result of massive small intestinal resection commonly due to severe Crohn’s disease, volvulus or tumors. Diarrhea and weight loss are hallmarks of malabsorption which are aggravated if the colon is removed along with the small intestinal resection. Enteral nutrition autonomy is difficult to achieve in such cases of malabsorption where parenteral nutrition are required more often than not. We report a case of short bowel syndrome with severe malabsorption following extensive small bowel removal. The patient eventually underwent intestinal rehabilitation surgery and achieved independence from parenteral nutrition.
Thiol redox-regulation for efficient adjustment of sulfur metabolism in acclimation to abiotic stress
Authors: Telman Wilena , Dietz Karl-Josef
Published: March 2019

Sulfur assimilation and sulfur metabolism are tightly controlled at the transcriptional, post-transcriptional, and post-translational levels in order to meet the demand for reduced sulfur in growth and metabolism. These regulatory mechanisms coordinate the cellular sulfhydryl supply with carbon and nitrogen assimilation in particular. Redox homeostasis is an important cellular parameter intimately connected to sulfur by means of multiple thiol modifications. Post-translational thiol modifications such as disulfide formation, sulfenylation, S-nitrosylation, persulfidation, and S-glutathionylation allow for versatile switching and adjustment of protein functions. This review focuses on redox-regulation of enzymes involved in the sulfur assimilation pathway, namely adenosine 5´-phosphosulfate reductase (APR), adenosine 5´-phosphosulfate kinase (APSK), and γ-glutamylcysteine ligase (GCL). The activity of these enzymes is adjusted at the transcriptional and post-translational level depending on physiological requirements and the state of the redox and reactive oxygen species network, which are tightly linked to abiotic stress conditions. Hormone-dependent fine-tuning contributes to regulation of sulfur assimilation. Thus, the link between oxylipin signalling and sulfur assimilation has been substantiated by identification of the so-called COPS module in the chloroplast with its components cyclophilin 20–3, O-acetylserine thiol lyase, 2-cysteine peroxiredoxin, and serine acetyl transferase. We now have a detailed understanding of how regulation enables the fine-tuning of sulfur assimilation under both normal and abiotic stress conditions.
An Update on Hardening: A Qualitative Review
Authors: Hughes John R
Published: March 2019

Introduction

This review examines the evidence for the hardening hypothesis; that is, the prevalence of (1) becoming a former smoker is decreasing over time due to (2) decreased quit attempts, or (3) decreased success on a given quit attempt.

Methods

PubMed, EMBASE, PsychINFO, trial registries, and other databases were searched for population-based surveys that reported whether one of the aforementioned three outcomes decreased over time.

Results

None of the 26 studies found that conversion from current to former smoking, number of quit attempts, or success on a given quit attempt decreased over time and several found these increased over time. These results appeared to be similar across survey dates, duration of time examined, number of data points, data source, outcome definitions, and nationality.

Conclusions

These results convincingly indicate hardening is not occurring in the general population of smokers. On the other hand, the prevalence of smoking is declining less among older and women smokers, and smokers with low education, low income, psychological problems, alcohol or drug abuse, medical problems, and greater nicotine dependence, than among those without these characteristics, presumably due to less quitting. Why this has not lead to decreased success in stopping smoking in the general population is unclear.

Implications

Some have argued that a greater emphasis on harm reduction and more intensive or dependence-based treatments are needed because remaining smokers are those who are less likely to stop with current methods. This review finds no or little evidence for this assumption. Psychosocial factors, such as low education and psychiatric problems, predict less ability to quit and appear to becoming more prevalent among smokers. Why this is not leading to decreased quitting in the general population is an anomaly that may be worth trying to understand.
Let’s Join the Lane: The Role of Infectious Diseases Physicians in Preventing Gun Violence
Authors: Zheng Crystal , Mushatt David
Published: March 2019

On November 7, 2018, the National Rifle Association (NRA) issued a tweet advising “self-important anti-gun doctors to stay in their lane.” The tweet has galvanized physicians to share their experiences with gun violence through the grassroots #ThisISOurLane campaign. Infectious diseases physicians are regularly called upon to manage complications such as infected wounds and osteomyelitis in gunshot victims. Yet, Infectious Diseases as a specialty has been poorly represented in the national dialogue on gun violence. Over 80 medical societies have endorsed statements on gun violence, including the American College of Physicians (ACP) and the American College of Cardiology; the Infectious Diseases Society of America has not. We argue that gun violence does affect the Infectious Diseases community and issue a call to action to engage in the conversation, advocate for our patients, and join with other medical societies in affirming a commitment to gun violence prevention.
Novel Endovascular Neck Reconstruction and Coiling Technique for the Treatment of a Large Wide-Necked Basilar Apex Aneurysm Through a Radial Artery Approach: 2-Dimensional Operative Video
Authors: Sorenson Thomas J , Lanzino Giuseppe , Rangel Castilla Leonardo
Published: March 2019

Herein, we demonstrate a case of a large, wide-necked, basilar apex aneurysm (BAA) that was treated with neck reconstruction-assisted coil embolization using the PulseRider device (PulsarVascular, Los Gatos, California), a novel neck-reconstruction device. A 68-yr-old man was found to have large BAA during work-up for sinusitis. Computed tomography angiogram revealed an 11 × 10-mm BAA. Patient has history of coronary artery disease, atrial fibrillation (currently taking Warfarin), recent left hip replacement and right femoral bypass. Treatment of the aneurysm was advised due to its location and size. Microsurgical clip reconstruction was high risk for general anesthesia due to his medical comorbidities and anticoagulation. Wide-necked bifurcation aneurysms are challenging to treat with traditional balloon- or stent-assisted techniques. To mitigate these challenges, novel neck-reconstruction devices have been developed. The Pulsar is one of these neck-reconstruction devices that removes the need to selectively catheterize branch arteries; it is available in a “Y” and “T” configuration. Under conscious sedation and through a radial artery approach, the patient underwent endovascular reconstruction of BAA with Pulsar device and coils. A 6-Fr guide catheter, a 0.021" microcatheter for the Pulsar device and a 0.017" microcatheter for coil delivering were used. A 3 × 8.6 mm Pulsar device was selected based on aneurysm neck and basilar artery measurements. Complete embolization (Raymond-Roy 1 obliteration) of the aneurysm was successfully achieved with no complications. The patient remained neurologically intact and was discharged on postoperative day 1.

 Parts of this video were published in Intracranial Aneurysms (1st Edition), Ringer (Ed), online companion to chapter 33B, Copyright Elsevier (2018).
Brief Report: Higher Levels of Angiopoietin-1 Are Associated With Early and Sustained Viral Suppression in Children Living With Vertically Acquired HIV
Authors: Gulhati Vishrut , Soo Jeremy , Ransy Doris G. , Brophy Jason , Kakkar Fatima , Bitnun Ari , Samson Lindy , Read Stanley , Soudeyns Hugo , Hawkes Michael T. ,   for EPIC4 Study Group
Published: March 2019

Background:

Systemic inflammation, platelet dysfunction, and endothelial activation persist in people living with HIV despite sustained virologic suppression (SVS) with combined antiretroviral therapy (cART) and may lead to complications such as atherosclerosis and cardiovascular disease. Angiopoietin-1 (Ang-1) is a key regulator of angiogenesis and endothelial activation and has been studied as an objective biomarker in disease states such as atherosclerosis, sepsis, and severe malaria.

Setting:

Eight pediatric HIV care centers across Canada.

Methods:

Cross-sectional study of 61 children living with vertically acquired HIV on cART with undetectable RNA viral load. Plasma levels of Ang-1 were measured by ELISA and analyzed in relation to clinical characteristics abstracted from medical records.

Results:

Ang-1 levels were directly correlated with clinical indices of virologic control: cumulative proportion of life on effective cART (ρ = +0.35, P = 0.0078) and cumulative proportion of life with SVS (ρ = +0.36, P = 0.0049). Furthermore, higher Ang-1 levels were associated with younger age at SVS (ρ = −0.56, P < 0.0001). These associations remained statistically significant in multivariable linear regression models adjusting for potential confounders (P < 0.05 for all associations).

Conclusions:

Early effective cART and SVS were associated with higher Ang-1 levels in children living with vertically acquired HIV-1.
Chaperone-Mediated Reflux of Secretory Proteins to the Cytosol During Endoplasmic Reticulum Stress
Authors: Igbaria Aeid , Merksamer Philip I. , Trusina Ala , Tilahun Firehiwot , Johnson Jefferey R. , Brandman Onn , Krogan Nevan J. , Weissman Jonathan S. , Papa Feroz R.
Published: March 2019

Diverse perturbations to endoplasmic reticulum (ER) functions compromise the proper folding and structural maturation of secretory proteins. To study secretory pathway physiology during such “ER stress”, we employed an ER-targeted, redox-responsive, green fluorescent protein—eroGFP—that reports on ambient changes in oxidizing potential. Here we find that diverse ER stress agents cause properly folded, ER-resident eroGFP (and other ER luminal proteins) to “reflux” back to the reducing environment of the cytosol as intact, folded proteins. By utilizing eroGFP in a comprehensive genetic screen inS. cerevisiae, we show that ER protein reflux during ER stress requires specific chaperones and co-chaperones residing in both the ER and the cytosol. Chaperone-mediated ER protein reflux does not require E3 ligase activity, and proceeds even more vigorously when these ER-associated degradation (ERAD) factors are crippled, suggesting that reflux may work in parallel with ERAD. In summary, chaperone-mediated ER-protein reflux may be a conserved protein quality control process that evolved to maintain secretory pathway homeostasis during ER protein-folding stress.

SIGNIFICANCE

Approximately one third of eukaryotic proteins are synthesized on ribosomes attached to the endoplasmic reticulum (ER) membrane. Many of these polypeptides co- or post-translationally translocate into the ER, wherein they fold and mature. An ER quality-control system proofreads these proteins by facilitating their folding and modification, while eliminating misfolded proteins through ER-associated degradation (ERAD). Yet, the fate of many secretory proteins during ER stress is not completely understood. Here, we uncovered an ER-stress induced “protein reflux” system that delivers intact, folded ER luminal proteins back to the cytosol without degrading them. We found that ER protein reflux works in parallel to ERAD and requires distinct ER-resident and cytosolic chaperones and co-chaperones.
Endothelial PKA targets ATG16L1 to regulate angiogenesis by limiting autophagy
Authors: Zhao Xiaocheng , Nedvetsky Pavel , Vion Anne-Clemence , Popp Oliver , Zühlke Kerstin , Dittmar Gunnar , Klussmann Enno , Gerhardt Holger
Published: March 2019

The cAMP-dependent protein kinase A (PKA) regulates a plethora of cellular functions in health and disease. During angiogenesis, PKA activity in endothelial cells controls the transition from sprouting to vessel maturation and limits tip cell formation independently of Notch signaling. The molecular PKA targets mediating these effects remain unknown. We report a chemical genetics screen identifying endothelial-specific substrates of PKA in human umbilical vein endothelial cells (HUVEC). We identified ATG16L1, a regulator of autophagy, as novel target of PKA. Biochemical validation, mass spectrometry and peptide spot arrays revealed that PKA phosphorylates ATG16L1α at Ser268 and ATG16L1β at Ser269. The phosphorylations drive degradation of ATG16L1 protein. Knocking down PKA or inhibiting its activity increased ATG16L1 protein levels and endothelial autophagy.In vivogenetics and pharmacological experiments demonstrated that autophagy inhibition partially rescues vascular hypersprouting caused by PKA deficiency. We propose that endothelial PKA activity restricts active sprouting by reducing endothelial autophagy through phosphorylation of ATG16L1.