bluuebunny/crossref_metadata_2025_split huggingface dataset:
N-glycosylation of the CmeABC multidrug efflux pump is needed for optimal function in Campylobacter jejuni
Authors: Dubb Rajinder K , Nothaft Harald , Beadle Bernadette , Richards Michele R , Szymanski Christine M 
Published: October 2019

AbstractCampylobacter jejuni is a prevalent gastrointestinal pathogen associated with increasing rates of antimicrobial resistance development. It was also the first bacterium demonstrated to possess a general N-linked protein glycosylation pathway capable of modifying &gt; 80 different proteins, including the primary Campylobacter multidrug efflux pump, CmeABC. Here we demonstrate that N-glycosylation is necessary for the function of the efflux pump and may, in part, explain the evolutionary pressure to maintain this protein modification system. Mutants of cmeA in two common wildtype (WT) strains are highly susceptible to erythromycin (EM), ciprofloxacin and bile salts when compared to the isogenic parental strains. Complementation of the cmeA mutants with the native cmeA allele restores the WT phenotype, whereas expression of a cmeA allele with point mutations in both N-glycosylation sites is comparable to the cmeA mutants. Moreover, loss of CmeA glycosylation leads to reduced chicken colonization levels similar to the cmeA knock-out strain, while complementation fully restores colonization. Reconstitution of C. jejuni CmeABC into Escherichia coli together with the C. jejuni N-glycosylation pathway increases the EM minimum inhibitory concentration and decreases ethidium bromide accumulation when compared to cells lacking the pathway. Molecular dynamics simulations reveal that the protein structures of the glycosylated and non-glycosylated CmeA models do not vary from one another, and in vitro studies show no change in CmeA multimerization or peptidoglycan association. Therefore, we conclude that N-glycosylation has a broader influence on CmeABC function most likely playing a role in complex stability.
The RxHL study: community-responsive research to explore barriers to medication adherence
Authors: Shaw Susan J , Korchmaros Josephine D , Huebner Torres Cristina , Totman Molly S , Lee Jeannie K 
Published: October 2019

Abstract
This study aims to contribute to the development of community-responsive research approaches by describing the research methods used in the RxHL study and the interprofessional and community-based collaboration that produced them. The mixed-method RxHL study was developed in close consultation with staff and providers at our research site, a federally qualified health center in Springfield, MA. We utilized quantitative methods including chart review, manual pill counts and self-report surveys to assess factors associated with medication adherence in a diverse population of low-income patients with chronic disease. We triangulated these results with findings from qualitative methods that included in-depth interviews, home visits and chronic disease diaries. We used the constant comparison method and interdisciplinary, participatory team meetings to integrate quantitative and qualitative findings. A community-responsive approach facilitated the recruitment and retention of a diverse sample of patients. Self-report surveys revealed the widespread scope of barriers to care such as medication costs and transportation, and limited health literacy among diverse groups. Qualitative research methods offered a deeper understanding of the social and environmental contexts in which medication adherence takes place. Prioritizing the needs of community partners and research participants facilitates rigorous data collection in clinical settings with maximum participation from community partners.
Environmental controls and anthropogenic impacts on deep-sea sponge grounds in the Faroe-Shetland Channel, NE Atlantic: the importance of considering spatial scale to distinguish drivers of change
Authors: Vad J , Kazanidis G , Henry L-A , Jones D O B , Gates A R , Roberts J M 
Published: October 2019

AbstractDetermining the scale of anthropogenic impacts is critical in order to understand ecosystem effects of human activities, within the context of changes caused by natural environmental variability. We applied spatial eigenfunction analysis to disentangle effects of anthropogenic drivers from environmental factors on species assembly in the Faroe-Shetland Channel (FSC), in the northeast Atlantic. We found that the species assembly considered here was structured at both small and large spatial scales. Specifically, substrate types, distance to oil wells and pipelines, the presence of objects and demersal fishing (both static and mobile) appeared significant in explaining large spatial scale species assembly structures. Conversely, temperature and variance in temperature shaped the species community across smaller spatial scales. Mobile scavenger species were found in areas impacted by demersal fishing. Oil and gas structures seemed to provide a habitat for a range of species including the commercially important fishes Molva sp. and Sebastes sp. These results demonstrate how the benthic ecosystem in the FSC has been shaped by multiple human activities, at both small and large spatial scales. Only by sampling datasets covering several sites, like in this study, can the effects of anthropogenic activities be separated from natural environmental controls.
Ecological thresholds in forecast performance for key United States West Coast Chinook salmon stocks
Authors: Satterthwaite William H , Andrews Kelly S , Burke Brian J , Gosselin Jennifer L , Greene Correigh M , Harvey Chris J , Munsch Stuart H , O’Farrell Michael R , Samhouri Jameal F , Sobocinski Kathryn L 
Published: October 2019

AbstractPreseason abundance forecasts drive management of US West Coast salmon fisheries, yet little is known about how environmental variability influences forecast performance. We compared forecasts of Chinook salmon (Oncorhynchus tshawytscha) against returns for (i) key California-Oregon ocean fishery stocks and (ii) high priority prey stocks for endangered Southern Resident Killer Whales (Orcinus orca) in Puget Sound, Washington. We explored how well environmental indices (at multiple locations and time lags) explained performance of forecasts based on different methods (i.e. sibling-based, production-based, environment-based, or recent averages), testing for nonlinear threshold dynamics. For the California stocks, no index tested explained &gt;50% of the variation in forecast performance, but spring Pacific Decadal Oscillation and winter North Pacific Index during the year of return explained &gt;40% of the variation for the sibling-based Sacramento Fall Chinook forecast, with nonlinearity and apparent thresholds. This suggests that oceanic conditions experienced by adults (after younger siblings returned) have the most impact on sibling-based forecasts. For Puget Sound stocks, we detected nonlinear/threshold relationships explaining &gt;50% of the variation with multiple indices and lags. Environmental influences on preseason forecasts may create biases that render salmon fisheries management more or less conservative, and therefore could motivate the development of ecosystem-based risk assessments.
Comparisons of mean length-based mortality estimators and age-structured models for six southeastern US stocks
Authors: Huynh Quang C , Cummings Nancie J , Hoenig John M 
Published: October 2019

Abstract
Length-based mortality estimators have been developed as alternative assessment methods for data-limited stocks. We compared mortality estimates from three methodologically related mean length-based methods to those from an age-structured model (ASM). We estimated fishing mortality and determined overfishing status, i.e. if F/FMSY > 1, for six stocks which support important recreational and commercial fisheries in the southeastern United States. The similarities in historical fishing mortality between the length-based methods and the most recent assessments varied among the case studies, but the classification of overfishing status in the terminal year did not differ based on the choice of model for all six stocks. There was also high agreement in the number of overfishing years within different historical periods. Applications of length-based methods can be consistent with the results that might be obtained from an ASM. In one case, diagnostics were used to identify the problems with the length-based estimators. The potential for determining overfishing status from these methods can encourage data collection programmes for unassessed stocks.
Clinical significance of right atrial volume in patients with repaired tetralogy of Fallot
Authors: Kido Takashi , Ueno Takayoshi , Taira Masaki , Kanaya Tomomitsu , Okuda Naoki , Toda Koichi , Kuratani Toru , Sawa Yoshiki 
Published: October 2019

Abstract

OBJECTIVES
Atrial arrhythmia and right ventricular (RV) diastolic dysfunction are associated with increased morbidity and mortality in patients with repaired tetralogy of Fallot (TOF). This study was performed to determine whether the preoperative right atrial (RA) volume can predict the development of atrial arrhythmia after pulmonary valve replacement (PVR) in patients with TOF.

METHODS
Forty-seven consecutive adult patients with repaired TOF underwent PVR from 2003 to 2018. Seventeen patients showed preoperative atrial arrhythmia and underwent the Maze procedure concomitantly. The preoperative RA volume was evaluated with computed tomography and image analysis software.

RESULTS
The median follow-up period after PVR was 6.8 years. Among 17 patients who underwent the Maze procedure, recurrent atrial arrhythmia developed in 8 patients. Among 30 patients without preoperative atrial arrhythmia, novel atrial arrhythmia developed in 2 patients. The RA volume index was a significant predictor according to the multivariate analysis (P = 0.003). The RA volume index showed a significant positive correlation with the RV end-diastolic pressure (P < 0.001).

CONCLUSIONS
The RA volume predicts the development of atrial arrhythmia after PVR in patients with repaired TOF. RA volume measurement is strongly recommended in the management of this patient population.

Clinical trial registration number
Institutional review board of Osaka University Hospital, number 16105.
The Role of User Comments in Estimation of the Public Opinion Climate and Perceived Support for One’s Opinion
Authors: Soffer Oren , Gordoni Galit 
Published: October 2019

Abstract
This article examines how user comments influence assessment of public opinion climate and perceived support for one’s opinion. The effects of user-comment sentiment (positive vs. negative) and of user-comment content (with or without personal exemplification) were tested with an online experiment (n = 1,510). Results show that user-comment effects on estimates of public opinion depend mainly on the sentiment of the comments and not on their framing as opinions with or without personal exemplification. Negative comments significantly reduce readers’ estimation of public opinion support of the issue dealt with by the article and affect the perceived support of one’s opinion. Study results refer to the possible dangers in user comments deliberate manipulation in democratic public discussion.
Toric Geometry of Spin(7)-Manifolds
Authors: Bruun Madsen Thomas , Swann Andrew 
Published: October 2019

Abstract
We study $ \operatorname{Spin}(7) $-manifolds with an effective multi-Hamiltonian action of a four-torus. On an open dense set, we provide a Gibbons–Hawking type ansatz that describes such geometries in terms of a symmetric $ 4\times 4 $-matrix of functions. This description leads to the 1st known $ \operatorname{Spin}(7) $-manifolds with a rank $ 4 $ symmetry group and full holonomy. We also show that the multi-moment map exhibits the full orbit space topologically as a smooth four-manifold, containing a trivalent graph in $ \mathbb{R}^4 $ as the image of the set of the special orbits.
2-torsion points on theta divisors
Authors: Pareschi Giuseppe , Salvati Manni Riccardo 
Published: October 2019

AbstractIn this note we prove a sharp bound for the number of 2-torsion points on a theta divisor and show that this is achieved only in the case of products of elliptic curves. This settles in the affirmative a conjecture of Marcucci and Pirola.
Hyperboloidal Similarity Coordinates and a Globally Stable Blowup Profile for Supercritical Wave Maps
Authors: Biernat Paweł , Donninger Roland , Schörkhuber Birgit 
Published: October 2019

Abstract
We consider co-rotational wave maps from (1+3)-dimensional Minkowski space into the three-sphere. This model exhibits an explicit blowup solution, and we prove the asymptotic nonlinear stability of this solution in the whole space under small perturbations of the initial data. The key ingredient is the introduction of a novel coordinate system that allows one to track the evolution past the blowup time and almost up to the Cauchy horizon of the singularity. As a consequence, we also obtain a result on continuation beyond blowup.
Dimensional Bounds for Ancient Caloric Functions on Graphs
Authors: Hua Bobo 
Published: October 2019

Abstract
We study ancient solutions of polynomial growth to heat equations on graphs and extend Colding and Minicozzi’s theorem [9] on manifolds to graphs: for a graph of polynomial volume growth, the dimension of the space of ancient solutions of polynomial growth is bounded by the product of the growth degree and the dimension of harmonic functions with the same growth.
Multiplicity of Asymptomatic Plasmodium falciparum Infections and Risk of Clinical Malaria: A Systematic Review and Pooled Analysis of Individual Participant Data
Authors: Eldh Martina , Hammar Ulf , Arnot David , Beck Hans-Peter , Garcia André , Liljander Anne , Mercereau-Puijalon Odile , Migot-Nabias Florence , Mueller Ivo , Ntoumi Francine , Ross Amanda , Smith Thomas , Sondén Klara , Vafa Homann Manijeh , Yman Victor , Felger Ingrid , Färnert Anna 
Published: October 2019

Abstract

Background
The malaria parasite Plasmodium falciparum holds an extensive genetic polymorphism. In this pooled analysis, we investigate how the multiplicity in asymptomatic P. falciparum infections—that is, the number of coinfecting clones—affects the subsequent risk of clinical malaria in populations living under different levels of transmission.

Methods
A systematic search of the literature was performed to identify studies in which P. falciparum infections were genotyped in asymptomatic individuals who were followed up prospectively regarding the incidence of clinical malaria. Individual participant data were pooled from 15 studies (n = 3736 individuals).

Results
Multiclonal asymptomatic infections were associated with a somewhat increased subsequent risk of clinical malaria in the youngest children, followed by an initial declining risk with age irrespective of transmission intensity. At approximately 5 years of age, the risk continued the gradual decline with age in high-transmission settings. However, in older children in moderate-, low-, and seasonal-transmission settings, multiclonal infections were either not significantly associated with the risk of subsequent febrile malaria or were associated with an increased risk.

Conclusions
The number of clones in asymptomatic P. falciparum infections is associated with different risks of subsequent clinical malaria depending on age and transmission intensity.
A randomized, double-blind trial investigating the efficacy of caspofungin versus amphotericin B deoxycholate in the treatment of invasive candidiasis in neonates and infants younger than 3 months of age
Authors: Kim Jason , Nakwa Firdose Lambey , Araujo Motta Fábio , Liu Hong , Dorr Mary Beth , Anderson Leah J , Kartsonis Nicholas 
Published: October 2019

Abstract

Objectives
Investigate the efficacy of caspofungin in participants &lt;3 months of age with invasive Candida infection (ICI).

Methods
This multicentre, randomized, double-blind, comparator-controlled, Phase 2 study (protocol MK0991-064; NCT01945281) enrolled participants &lt;3 months of age with culture-confirmed ICI within 96 h of study entry. Participants were randomly assigned 2:1 to once-daily intravenous 2 mg/kg caspofungin or intravenous 1 mg/kg amphotericin B deoxycholate (dAMB). The primary endpoint was fungal-free survival (FFS) 2 weeks after treatment in the full-analysis-set (FAS) population, defined as participants with culture-confirmed ICI who received ≥1 dose of therapy. Planned enrolment was 90 participants.

Results
Fifty-one participants were enrolled; 49 received treatment (caspofungin, n=33; dAMB, n=16); 2 additional participants did not have confirmed infections at study entry. The study was terminated after ∼ 3.5 years because of low enrolment. Forty-seven participants were included in the FAS population (caspofungin, n=31; dAMB, n=16). FFS rate at 2 weeks after treatment was 71.0% (22/31) in the caspofungin arm and 68.8% (11/16) in the dAMB arm [difference, stratified by weight, − 0.9% (95% CI, − 24.3%–27.7%)]. Adverse events developed in 84.8% (28/33) of participants in the caspofungin arm and 100% (16/16) in the dAMB arm.

Conclusions
Among neonates and infants with confirmed ICI, FFS at 2 weeks was similar in the caspofungin and dAMB treatment arms. A smaller proportion of participants who received caspofungin experienced adverse events.
Adaptive Radiation Genomics of Two Ecologically Divergent Hawai‘ian Honeycreepers: The ‘akiapōlā‘au and the Hawai‘i ‘amakihi
Authors: Campana Michael G , Corvelo André , Shelton Jennifer , Callicrate Taylor E , Bunting Karen L , Riley-Gillis Bridget , Wos Frank , DeGrazia Justin , Jarvis Erich D , Fleischer Robert C 
Published: October 2019

AbstractThe Hawai‘ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, demographic history, and genes involved in bill morphology phenotypes in 2 honeycreepers: the ‘akiapōlā‘au (Hemignathus wilsoni) and the Hawai‘i ‘amakihi (Chlorodrepanis virens). The ‘akiapōlā‘au is an endangered island endemic, filling the “woodpecker” niche by using a unique bill morphology, while the Hawai‘i ‘amakihi is a dietary generalist common on the islands of Hawai‘i and Maui. We de novo sequenced the ‘akiapōlā‘au genome and compared it to the previously sequenced ‘amakihi genome. The ‘akiapōlā‘au is far less heterozygous and has a smaller effective population size than the ‘amakihi, which matches expectations due to its smaller census population and restricted ecological niche. Our investigation revealed genomic islands of divergence, which may be involved in the honeycreeper radiation. Within these islands of divergence, we identified candidate genes (including DLK1, FOXB1, KIF6, MAML3, PHF20, RBP1, and TIMM17A) that may play a role in honeycreeper adaptations. The gene DLK1, previously shown to influence Darwin’s finch bill size, may be related to honeycreeper bill morphology evolution, while the functions of the other candidates remain unknown.
Beyond Rational Choice: International Trade Law and The Behavioral Political Economy of Protectionism
Authors: van Aaken Anne , Kurtz Jürgen 
Published: October 2019

ABSTRACT
The classic political economy of trade models state behavior on the international plane by reference to the formation of domestic interests. Voters, interest groups, and politicians are rational actors in this model, pursuing their economic preferences without cognitive or motivational distortions. This article questions the sufficiency of the rational choice model in the formation of contemporary trade policy. Starting from the classic political economy story, this article explores real-world deviations from rationally expected outcomes by drawing on cognitive psychology. Using both theoretical and empirical analysis, we seek to identify key distortions that can better explain voter and politician behavior in the current trade wars. We begin with loss aversion in that individuals have asymmetrical attitudes towards gains and losses. Rising inequality within the rich world amounts to a perceived relative loss particularly for middle-class citizens. Combined with the absolute rise of equality between countries, this can trigger a double loss frame—both as an individual loss and a national loss—that can profoundly shape anti-trade preferences in certain countries. Framing trade as a security threat also invokes powerful hawkish biases. Lastly, the availability bias can be provoked by social media mechanisms making people tend to focus on particular risks and overweight their import.
Atomistic and dynamic structural characterizations in low-dimensional materials: recent applications of in situ transmission electron microscopy
Authors: Zheng He , Cao Fan , Zhao Ligong , Jiang Renhui , Zhao Peili , Zhang Ying , Wei Yanjie , Meng Shuang , Li Kaixuan , Jia Shuangfeng , Li Luying , Wang Jianbo 
Published: October 2019

Abstract
In situ transmission electron microscopy has achieved remarkable advances for atomic-scale dynamic analysis in low-dimensional materials and become an indispensable tool in view of linking a material’s microstructure to its properties and performance. Here, accompanied with some cutting-edge researches worldwide, we briefly review our recent progress in dynamic atomistic characterization of low-dimensional materials under external mechanical stress, thermal excitations and electrical field. The electron beam irradiation effects in metals and metal oxides are also discussed. We conclude by discussing the likely future developments in this area.
Mapping the Global Cancer Research Funding Landscape
Authors: Schmutz Anna , Salignat Claire , Plotkina Daria , Devouassoux Amandine , Lee Teresa , Arnold Melina , Ervik Morten , Kelm Olaf 
Published: October 2019

Abstract

Background
Global investment in research on noncommunicable diseases is on the rise. Cancer as primus inter pares draws particular interest from a wide spectrum of research funders. Next to the private, governmental, and academic sectors, philanthropy has carved out a sizeable area in the funding landscape over the last 25 years. Previous reports describing cancer research funding have looked at the volume of investment in cancer research but have paid little attention to building strategic intelligence on funders. Moreover, these efforts have focused primarily on well-resourced organizations, neglecting a large number of players with less-developed finances.

Methods
In this article, we combined gnostic data acquisition with agnostic bibliometrics to establish a comprehensive map of the global cancer research funding landscape. The analysis of funding acknowledgments from cancer research papers used in this exercise is a “bottom-up” method that provides a broader perspective on the variety of actors involved. It does not rely on a priori knowledge, nor does it require funders’ support for access to the data.

Results
Using this approach, we have identified a total of 4693 organizations from 107 countries engaged in funding cancer research today.

Conclusions
This is the largest mapping exercise performed to date and should serve as a knowledge base for future analyses and comparisons aimed at understanding the dynamics and priorities of global cancer research funding.