bluuebunny/crossref_metadata_2025 huggingface dataset:
Slovenia and the European Union
Authors: Bojinović Fenko Ana , Svetličič Marjan
Published: September 2017

Despite having fought for their bare survival against hostile foreigners, after finally reaching their independence and international recognition in 1991–1992, paradoxically, even before fully assuming statehood Slovenians were eager to engage in yet another international integration—the European Union. This historical and societal wager, rather than merely political elites’ driven perspective, dominates as the prevailing reason for pursuing European Union (EU) membership; thus security assurance to a small geopolitically transit state, economic benefits of a larger common market in conditions of economic globalization, and cultural proximity of Slovenian to European society explain Slovenian general identity-related elements favoring membership in the EU. There is also a more immediate time-space related explanatory factor for this, namely, the collapsing of the socialist Yugoslavia starting by the end 1980s and a view of assuring the democratic political life and market-lead economy via integration with Western European countries rather than South Slavic nations or following other alternative scenarios like full liberalization with all partners’ strategy. Authors critically evaluate where and why during the effort of becoming an EU member state and performing excellently as one during the first four years, the state fell short of capability-building and/or seizing the opportunities of EU membership. As the latter has been most brutally exposed via the effects of the 2008–2014 economic and financial crisis, of key importance for Slovenians before the COVID-19 crisis stood a self-reflection of its development strategy and enhancing competitiveness. A novel problem introduced by the 2020–2022 government and revealed to the European and international public during the Slovenian 2021 Presidency to the Council of the EU was the country’s rapidly deteriorating performance in implementation of until-then unequivocal engagement toward EU values, particularly liberal democracy, rule of law, freedom of speech, and observation of human rights.. After the April 2022 general election, in which liberal democratic and social parties won a large majority, the central challenge remains how to overcome the small state hindrances and more effectively formulate and project national interest to the EU level. Some of the main questions of national interest within the EU concern assurance of social security to citizens; upgrading economic union to face more effectively global challenges, especially digitalization, the green transition, and interstate solidarity; refreshing enlargement policy for the remaining Western Balkans non-member states; and re-establishing Slovenian participation in the group of core states leading the European integration.
Defining and Operationalizing Context Through a Structural Political Geography for International Relations
Authors: Flint Colin , Dezzani Raymond J.
Published: September 2017

A structural understanding of the contextualized behavior of states is introduced and operationalized. Context is a central theme of the discipline of geography and identifies context specific, rather than universal, social behavior. Social behavior is both defined by and creates contexts in a constant recursive interaction. Context is defined through a geographic perspective on world-systems analysis, and we focus on the behavior of states. States are central actors because, through territorial sovereignty, they are able to define key social relations and economic flows. The idea of context is developed in a way that extends the key International Relations (IR) concepts of milieu and opportunity and willingness.

The recursive interaction between agency and context is conceptualized in a relational way as maneuver, the process by which the aggregate behavior of elites define state-level choices and behaviors that are made by considering the contextual position relative to all other states in the capitalist world-economy. In turn, the decision by any one state changes the behavior of other states so that context and state-level decisions interact and are constantly in flux. The elements of context include the position of a state in the hierarchy of the capitalist world-economy as well as regional and local interstate relations, some of which may display path dependency.

The operationalization of maneuver requires an understanding of states as signaling and learning entities and a set of modeling techniques that identify: (1) the degree of change within the system as a whole—or the degree of stability in the number and identity of states within particular positions in the hierarchy of the capitalist world-economy; (2) the maneuver of particular states—or which states change position (or not) within the hierarchy; and (3) the explanatory power of variables measuring political and economic interstate relations in explaining the maneuver behavior of particular states.
The Diverging Theory and Practice of International Law
Authors: Johns Leslie
Published: September 2017

Existing theories of international law are largely state-centric. While international cooperation can benefit all, states are often tempted to violate their promises in order to manage economic and political crises. States must accordingly balance enforcement against flexibility: legal institutions must provide enough enforcement that states comply most of the time yet also provide enough flexibility that states can violate during crises. Such a balance is possible when laws are crafted and enforced by unitary actors that will tolerate occasional violations by others in order to preserve their own right to occasionally violate.

However, the changing doctrine of sovereign immunity has dramatically transformed the actual practice of international law. Non-state actors and domestic courts play an increasingly important role in challenging state legal violations, generating a divergence between the theory and practice of contemporary international law. This divergence is apparent in many issue areas, including terrorism, human rights, sovereign debt, and foreign investment. This divergence suggests that political scientists and legal scholars must reconsider the limits of state-centric theories and examine the role of non-state actors and domestic courts.
Job and Work Design
Authors: Van den Broeck Anja , Parker Sharon K.
Published: September 2017

Job design or work design refers to the content, structure, and organization of tasks and activities. It is mostly studied in terms of job characteristics, such as autonomy, workload, role problems, and feedback. Throughout history, job design has moved away from a sole focus on efficiency and productivity to more motivational job designs, including the social approach toward work, Herzberg’s two-factor model, Hackman and Oldham’s job characteristics model, the job demand control model of Karasek, Warr’s vitamin model, and the job demands resources model of Bakker and Demerouti. The models make it clear that a variety of job characteristics make up the quality of job design that benefits employees and employers alike. Job design is crucial for a whole range of outcomes, including (a) employee health and well-being, (b) attitudes like job satisfaction and commitment, (c) employee cognitions and learning, and (d) behaviors like productivity, absenteeism, proactivity, and innovation. Employee personal characteristics play an important role in job design. They influence how employees themselves perceive and seek out particular job characteristics, help in understanding how job design exerts its influence, and have the potential to change the impact of job design.
The Formation and Evolution of the Solar System
Authors: Marov Mikhail
Published: September 2017

The formation and evolution of our solar system (and planetary systems around other stars) are among the most challenging and intriguing fields of modern science. As the product of a long history of cosmic matter evolution, this important branch of astrophysics is referred to as stellar-planetary cosmogony. Interdisciplinary by way of its content, it is based on fundamental theoretical concepts and available observational data on the processes of star formation. Modern observational data on stellar evolution, disc formation, and the discovery of extrasolar planets, as well as mechanical and cosmochemical properties of the solar system, place important constraints on the different scenarios developed, each supporting the basic cosmogony concept (as rooted in the Kant-Laplace hypothesis). Basically, the sequence of events includes fragmentation of an original interstellar molecular cloud, emergence of a primordial nebula, and accretion of a protoplanetary gas-dust disk around a parent star, followed by disk instability and break-up into primary solid bodies (planetesimals) and their collisional interactions, eventually forming a planet.

Recent decades have seen major advances in the field, due to in-depth theoretical and experimental studies. Such advances have clarified a new scenario, which largely supports simultaneous stellar-planetary formation. Here, the collapse of a protosolar nebula’s inner core gives rise to fusion ignition and star birth with an accretion disc left behind: its continuing evolution resulting ultimately in protoplanets and planetary formation. Astronomical observations have allowed us to resolve in great detail the turbulent structure of gas-dust disks and their dynamics in regard to solar system origin. Indeed radio isotope dating of chondrite meteorite samples has charted the age and the chronology of key processes in the formation of the solar system. Significant progress also has been made in the theoretical study and computer modeling of protoplanetary accretion disk thermal regimes; evaporation/condensation of primordial particles depending on their radial distance, mechanisms of clustering, collisions, and dynamics. However, these breakthroughs are yet insufficient to resolve many problems intrinsically related to planetary cosmogony. Significant new questions also have been posed, which require answers. Of great importance are questions on how contemporary natural conditions appeared on solar system planets: specifically, why the three neighbor inner planets—Earth, Venus, and Mars—reveal different evolutionary paths.
Human Exploration and Development in the Solar System
Authors: Mendell Wendell
Published: September 2017

Emergence of ballistic missile technology after World War II enabled human flight into the Earth’s orbit, fueling the imagination of those fascinated with science, technology, exploration, and adventure. The performance of astronauts in the early flights assuaged concerns about the functioning of “the human system” in the absence of the Earth’s gravity. However, researchers in space medicine have observed degradation of crews after longer exposure to the space environment and have developed countermeasures for most of them, although significant challenges remain. With the dawn of the 21st century, well-financed and technically competent commercial entities have begun to provide more affordable alternatives to historically expensive and risk-averse government-funded programs. The growing accessibility to space has encouraged entrepreneurs to pursue plans for potentially autarkic communities beyond the Earth, exploiting natural resources on other worlds. Should such dreams prove to be technically and economically feasible, a new era will open for humanity with concomitant societal issues of a revolutionary nature.
Women and Religion in Colonial North America and the United States
Authors: Brekus Catherine A.
Published: September 2017

Historically, women in colonial North America and the United States have been deeply influenced by their religious traditions. Even though world religions like Judaism, Christianity, Buddhism, Hinduism, and Islam are based on scriptural traditions that portray women as subordinate to men, women have made up the majority of most religious groups in America. While some Americans have used religious arguments to limit women’s legal, political, and economic rights, others have drawn on scripture to defend women’s dignity and equality. Women’s religious beliefs have shaped every aspect of their lives, including their choices about how to structure their time, their attitudes toward sexuality and the body, and their understanding of suffering. Unlike early American Catholic women, who saw their highest religious calling as the sisterhood, most white colonial women identified their primary religious vocation as ministering to their families. In the 19th century, however, white Protestant women become increasingly involved in reform movements like temperance, abolitionism, and women’s suffrage, and African-American, Native American, Asian-American, and Latina women used religious arguments to challenge assumptions about white racial supremacy. In the 20th century, growing numbers of women from many different religious traditions have served as religious leaders, and in some cases they have also demanded ordination. Despite these dramatic changes in religious life, however, many religiously conservative women opposed the Equal Rights Amendment during the 1970s and early 1980s, and in the first decades of the 21st century they have continued to identify feminism and religion as antithetical.
Evolution of Strategic Flood Risk Management in Support of Social Justice, Ecosystem Health, and Resilience
Authors: Sayers Paul
Published: September 2017

Throughout history, flood management practice has evolved in response to flood events. This heuristic approach has yielded some important incremental shifts in both policy and planning (from the need to plan at a catchment scale to the recognition that flooding arises from multiple sources and that defenses, no matter how reliable, fail). Progress, however, has been painfully slow and sporadic, but a new, more strategic, approach is now emerging.

A strategic approach does not, however, simply sustain an acceptable level of flood defence. Strategic Flood Risk Management (SFRM) is an approach that relies upon an adaptable portfolio of measures and policies to deliver outcomes that are socially just (when assessed against egalitarian, utilitarian, and Rawlsian principles), contribute positively to ecosystem services, and promote resilience. In doing so, SFRM offers a practical policy and planning framework to transform our understanding of risk and move toward a flood-resilient society. A strategic approach to flood management involves much more than simply reducing the chance of damage through the provision of “strong” structures and recognizes adaptive management as much more than simply “wait and see.” SFRM is inherently risk based and implemented through a continuous process of review and adaptation that seeks to actively manage future uncertainty, a characteristic that sets it apart from the linear flood defense planning paradigm based upon a more certain view of the future.

In doing so, SFRM accepts there is no silver bullet to flood issues and that people and economies cannot always be protected from flooding. It accepts flooding as an important ecosystem function and that a legitimate ecosystem service is its contribution to flood risk management. Perhaps most importantly, however, SFRM enables the inherent conflicts as well as opportunities that characterize flood management choices to be openly debated, priorities to be set, and difficult investment choices to be made.
How Environmental Degradation Impoverishes the Poor
Authors: Barbier Edward B.
Published: September 2017

Globally, around 1.5 billion people in developing countries, or approximately 35% of the rural population, can be found on less-favored agricultural land (LFAL), which is susceptible to low productivity and degradation because the agricultural potential is constrained biophysically by terrain, poor soil quality, or limited rainfall. Around 323 million people in such areas also live in locations that are highly remote, and thus have limited access to infrastructure and markets. The households in such locations often face a vicious cycle of declining livelihoods, increased ecological degradation and loss of resource commons, and declining ecosystem services on which they depend. In short, these poor households are prone to a poverty-environment trap. Policies to eradicate poverty, therefore, need to be targeted to improve the economic livelihood, productivity, and income of the households located on remote LFAL. The specific elements of such a strategy include involving the poor in paying for ecosystem service schemes and other measures that enhance the environments on which the poor depend; targeting investments directly to improving the livelihoods of the rural poor, thus reducing their dependence on exploiting environmental resources; and tackling the lack of access by the rural poor in less-favored areas to well-functioning and affordable markets for credit, insurance, and land, as well as the high transportation and transaction costs that prohibit the poorest households in remote areas to engage in off-farm employment and limit smallholder participation in national and global markets.
Structure-based prediction of protein– peptide binding regions using Random Forest
Authors: Taherzadeh Ghazaleh , Zhou Yaoqi , Liew Alan Wee-Chung , Yang Yuedong
Published: September 2017

Motivation

Protein–peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processes, functional mechanisms, and drug discovery. Protein–peptide interactions can be analyzed by studying the structures of protein–peptide complexes. However, only a small portion has known complex structures and experimental determination of protein–peptide interaction is costly and inefficient. Thus, predicting peptide-binding sites computationally will be useful to improve efficiency and cost effectiveness of experimental studies. Here, we established a machine learning method called SPRINT-Str (Structure-based prediction of protein–Peptide Residue-level Interaction) to use structural information for predicting protein–peptide binding residues. These predicted binding residues are then employed to infer the peptide-binding site by a clustering algorithm.

Results

SPRINT-Str achieves robust and consistent results for prediction of protein–peptide binding regions in terms of residues and sites. Matthews’ Correlation Coefficient (MCC) for 10-fold cross validation and independent test set are 0.27 and 0.293, respectively, as well as 0.775 and 0.782, respectively for area under the curve. The prediction outperforms other state-of-the-art methods, including our previously developed sequence-based method. A further spatial neighbor clustering of predicted binding residues leads to prediction of binding sites at 20–116% higher coverage than the next best method at all precision levels in the test set. The application of SPRINT-Str to protein binding with DNA, RNA and carbohydrate confirms the method‘s capability of separating peptide-binding sites from other functional sites. More importantly, similar performance in prediction of binding residues and sites is obtained when experimentally determined structures are replaced by unbound structures or quality model structures built from homologs, indicating its wide applicability.

Availability and implementation

http://sparks-lab.org/server/SPRINT-Str

Supplementary information

Supplementary data are available at Bioinformatics online.
Shared and Disorder-Specific Neurocomputational Mechanisms of Decision-Making in Autism Spectrum Disorder and Obsessive-Compulsive Disorder
Authors: Carlisi Christina O , Norman Luke , Murphy Clodagh M , Christakou Anastasia , Chantiluke Kaylita , Giampietro Vincent , Simmons Andrew , Brammer Michael , Murphy Declan G , Mataix-Cols David , Rubia Katya ,   MRC AIMS consortium
Published: September 2017

Autism spectrum disorder (ASD) and obsessive-compulsive disorder (OCD) often share phenotypes of repetitive behaviors, possibly underpinned by abnormal decision-making. To compare neural correlates underlying decision-making between these disorders, brain activation of boys with ASD (N = 24), OCD (N = 20) and typically developing controls (N = 20) during gambling was compared, and computational modeling compared performance. Patients were unimpaired on number of risky decisions, but modeling showed that both patient groups had lower choice consistency and relied less on reinforcement learning compared to controls. ASD individuals had disorder-specific choice perseverance abnormalities compared to OCD individuals. Neurofunctionally, ASD and OCD boys shared dorsolateral/inferior frontal underactivation compared to controls during decision-making. During outcome anticipation, patients shared underactivation compared to controls in lateral inferior/orbitofrontal cortex and ventral striatum. During reward receipt, ASD boys had disorder-specific enhanced activation in inferior frontal/insular regions relative to OCD boys and controls. Results showed that ASD and OCD individuals shared decision-making strategies that differed from controls to achieve comparable performance to controls. Patients showed shared abnormalities in lateral-(orbito)fronto-striatal reward circuitry, but ASD boys had disorder-specific lateral inferior frontal/insular overactivation, suggesting that shared and disorder-specific mechanisms underpin decision-making in these disorders. Findings provide evidence for shared neurobiological substrates that could serve as possible future biomarkers.
CD40L controls obesity-associated vascular inflammation, oxidative stress, and endothelial dysfunction in high fat diet-treated and db/db mice
Authors: Steven Sebastian , Dib Mobin , Hausding Michael , Kashani Fatemeh , Oelze Matthias , Kröller-Schön Swenja , Hanf Alina , Daub Steffen , Roohani Siyer , Gramlich Yves , Lutgens Esther , Schulz Eberhard , Becker Christian , Lackner Karl J , Kleinert Hartmut , Knosalla Christoph , Niesler Beate , Wild Philipp S , Münzel Thomas , Daiber Andreas
Published: September 2017

Aims

CD40 ligand (CD40L) signaling controls vascular oxidative stress and related dysfunction in angiotensin-II-induced arterial hypertension by regulating vascular immune cell recruitment and platelet activation. Here we investigated the role of CD40L in experimental hyperlipidemia.

Methods and results

Male wild type and CD40L−/− mice (C57BL/6 background) were subjected to high fat diet for sixteen weeks. Weight, cholesterol, HDL, and LDL levels, endothelial function (isometric tension recording), oxidative stress (NADPH oxidase expression, dihydroethidium fluorescence) and inflammatory parameters (inducible nitric oxide synthase, interleukin-6 expression) were assessed. CD40L expression, weight, leptin and lipids were increased, and endothelial dysfunction, oxidative stress and inflammation were more pronounced in wild type mice on a high fat diet, all of which was almost normalized by CD40L deficiency. Similar results were obtained in diabetic db/db mice with CD40/TRAF6 inhibitor (6877002) therapy. In a small human study higher serum sCD40L levels and an inflammatory phenotype were detected in the blood and Aorta ascendens of obese patients (body mass index > 35) that underwent by-pass surgery.

Conclusion

CD40L controls obesity-associated vascular inflammation, oxidative stress and endothelial dysfunction in mice and potentially humans. Thus, CD40L represents a therapeutic target in lipid metabolic disorders which is a leading cause in cardiovascular disease.
Discovering foodborne illness in online restaurant reviews
Authors: Effland Thomas , Lawson Anna , Balter Sharon , Devinney Katelynn , Reddy Vasudha , Waechter HaeNa , Gravano Luis , Hsu Daniel
Published: September 2017

Objective

We developed a system for the discovery of foodborne illness mentioned in online Yelp restaurant reviews using text classification. The system is used by the New York City Department of Health and Mental Hygiene (DOHMH) to monitor Yelp for foodborne illness complaints.

Materials and Methods

We built classifiers for 2 tasks: (1) determining if a review indicated a person experiencing foodborne illness and (2) determining if a review indicated multiple people experiencing foodborne illness. We first developed a prototype classifier in 2012 for both tasks using a small labeled dataset. Over years of system deployment, DOHMH epidemiologists labeled 13 526 reviews selected by this classifier. We used these biased data and a sample of complementary reviews in a principled bias-adjusted training scheme to develop significantly improved classifiers. Finally, we performed an error analysis of the best resulting classifiers.

Results

We found that logistic regression trained with bias-adjusted augmented data performed best for both classification tasks, with F1-scores of 87% and 66% for tasks 1 and 2, respectively.

Discussion

Our error analysis revealed that the inability of our models to account for long phrases caused the most errors. Our bias-adjusted training scheme illustrates how to improve a classification system iteratively by exploiting available biased labeled data.

Conclusions

Our system has been instrumental in the identification of 10 outbreaks and 8523 complaints of foodborne illness associated with New York City restaurants since July 2012. Our evaluation has identified strong classifiers for both tasks, whose deployment will allow DOHMH epidemiologists to more effectively monitor Yelp for foodborne illness investigations.
Postdiagnosis Changes in Cigarette Smoking and Survival Following Breast Cancer
Authors: Parada Humberto , Bradshaw Patrick T. , Steck Susan E. , Engel Lawrence S. , Conway Kathleen , Teitelbaum Susan L. , Neugut Alfred I. , Santella Regina M. , Gammon Marilie D.
Published: September 2017

Background

The purpose of this study was to examine whether at-diagnosis smoking and postdiagnosis changes in smoking within five years after breast cancer were associated with long-term all-cause and breast cancer-specific mortality.

Methods

A population-based cohort of 1508 women diagnosed with first primary in situ or invasive breast cancer in 1996 to 1997 were interviewed shortly after diagnosis and again approximately five years later to assess smoking history. Participants were followed for vital status through December 31, 2014. After 18+ years of follow-up, 597 deaths were identified, 237 of which were breast cancer related. Multivariable Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs).

Results

Compared with never smokers, risk of all-cause mortality was elevated among the 19% of at-diagnosis smokers (HR = 1.69, 95% CI = 1.36 to 2.11), those who smoked 20 or more cigarettes per day (HR = 1.85, 95% CI = 1.42 to 2.40), women who had smoked for 30 or more years (HR = 1.62, 95% CI = 1.28 to 2.05), and women who had smoked 30 or more pack-years (HR = 1.82, 95% CI = 1.39 to 2.37). Risk of all-cause mortality was further increased among the 8% of women who were at-/postdiagnosis smokers (HR = 2.30, 95% CI = 1.56 to 3.39) but was attenuated among the 11% women who quit smoking after diagnosis (HR = 1.83, 95% CI = 1.32 to 2.52). Compared with never smokers, breast cancer–specific mortality risk was elevated 60% (HR = 1.60, 95% CI = 0.79 to 3.23) among at-/postdiagnosis current smokers, but the confidence interval included the null value and elevated 175% (HR = 2.75, 95% CI = 1.26 to 5.99) when we considered postdiagnosis cumulative pack-years.

Conclusions

Smoking negatively impacts long-term survival after breast cancer. Postdiagnosis cessation of smoking may reduce the risk of all-cause mortality. Breast cancer survivors may benefit from aggressive smoking cessation programs starting as early as the time of diagnosis.
Minimizing Retraction by Pia-Arachnoidal 10-0 Sutures in Intrasulcal Dissection
Authors: Uluc Kutluay , Cikla Ulas , Morkan Deniz B , Sirin Alperen , Ahmed Azam S , Swanson Kyle , Baskaya Mustafa K
Published: September 2017

BACKGROUND

In contemporary microneurosurgery reducing retraction-induced injury to the brain is essential. Self-retaining retractor systems are commonly used to improve visualization and decrease the repetitive microtrauma, but sometimes self-retaining retractor systems can be cumbersome and the force applied can cause focal ischemia or contusions. This may increase the morbidity and mortality. Here, we describe a technique of retraction using 10-0 sutures in the arachnoid.

OBJECTIVE

To evaluate the imaging and clinical results in patients where 10-0 suture retraction was used to aid the surgical procedure.

METHODS

Adjacent cortex was retracted by placing 10-0 nylon suture in the arachnoid of the bank or banks of the sulcus. The suture was secured to the adjacent dural edge by using aneurysm clips, allowing for easy adjustability of the amount of retraction. We retrospectively analyzed the neurological outcome, signal changes in postoperative imaging, and ease of performing surgery in 31 patients with various intracranial lesions including intracranial aneurysms, intra- and extra-axial tumors, and cerebral ischemia requiring arterial bypass.

RESULTS

Clinically, there were no injuries, vascular events, or neurological deficits referable to the relevant cortex. Postoperative imaging did not show changes consistent with ischemia or contusion due to the retraction. This technique improved the visualization and illumination of the surgical field in all cases.

CONCLUSION

Retraction of the arachnoid can be used safely in cases where trans-sulcal dissection is required. This technique may improve initial visualization and decrease the need for dynamic or static retraction.
Specific Hypersensitive Response–Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato
Authors: Mesarich Carl H. , Ӧkmen Bilal , Rovenich Hanna , Griffiths Scott A. , Wang Changchun , Karimi Jashni Mansoor , Mihajlovski Aleksandar , Collemare Jérôme , Hunziker Lukas , Deng Cecilia H. , van der Burgt Ate , Beenen Henriek G. , Templeton Matthew D. , Bradshaw Rosie E. , de Wit Pierre J. G. M.
Published: September 2017

Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged. To combat these strains, new Cf genes are required. An effectoromics approach was employed to identify wild tomato accessions carrying new Cf genes. Proteomics and transcriptome sequencing were first used to identify 70 apoplastic in planta–induced C. fulvum SSPs. Based on sequence homology, 61 of these SSPs were novel or lacked known functional domains. Seven, however, had predicted structural homology to antimicrobial proteins, suggesting a possible role in mediating antagonistic microbe-microbe interactions in planta. Wild tomato accessions were then screened for HR-associated recognition of 41 SSPs, using the Potato virus X–based transient expression system. Nine SSPs were recognized by one or more accessions, suggesting that these plants carry new Cf genes available for incorporation into cultivated tomato.
Spatiotemporal Attributes and Crop Loss Associated with Tan Spot Epidemics in Baby Lima Bean in New York
Authors: Pethybridge Sarah J. , Hay Frank S. , Gorny Adrienne , Kikkert Julie R.
Published: September 2017

Tan spot, caused by the pycnidial fungi Didymella americana and Boeremia exigua var. exigua, is a foliar disease affecting processing baby lima bean production in New York. Tan spot epidemics are prevalent, occur annually, and may result in substantial defoliation. The disease is controlled by the prophylactic application of fungicides to maximize green leaf area. Information on yield losses due to tan spot on baby lima bean yield and the benefits of fungicide applications is needed to justify investments in disease management. Four small-plot, replicated trials were conducted over 2 years in commercial baby lima bean fields to evaluate the efficacy of fungicides for tan spot control at Piffard and Leicester, NY. Applications of pyraclostrobin or boscalid significantly reduced tan spot incidence and severity compared with nontreated plots, and increased the number of leaves per stem. In 2016, the increase in green leaf area associated with fungicide application was also documented in canopy reflectance values at 830 nm. Despite the decrease in tan spot incidence and corresponding increase in crop health obtained from fungicides, this effect did not translate into significant increases in pod yield. This finding suggested that the relationship between green leaf area and yield is highly variable in baby lima bean. The spatial and spatiotemporal patterns of naturally occurring tan spot epidemics were also characterized in baby lima bean fields across western New York using disease incidence data collected in transects and grids. The spatial pattern of data collected in transects was analyzed using median runs analysis. Disease incidence data collected in two-dimensional grids were analyzed to quantify spatial pattern using spatial analysis by distance indices (SADIE). The association function of SADIE was used to quantify the spatiotemporal patterns of tan spot epidemics after crop emergence and at harvest. These findings suggested that tan spot is likely to initiate at relatively frequent, randomly positioned foci, and that subsequent, limited spread results in significant local aggregation. Hypotheses for inoculum sources and recommendations for tan spot control in baby lima bean fields in New York are discussed.
A Rapid Diagnostic for Detection ofAphelenchoides besseyiandA. fujianensisBased on Real-Time PCR
Authors: Buonicontro Dalila Sêni , Roberts David Mark , Oliveira Claudio Marcelo Gonçalves , Blok Vivian Carol , Neilson Roy , Oliveira Rosângela D’arc De Lima
Published: September 2017

Aphelenchoides besseyi and A. fujianensis have been frequently found in mixed populations associated with forage grass seed in Brazil. The morphological similarity between both species has previously led A. fujianensis to be erroneously identified as A. besseyi. A. besseyi is a quarantine pest in many countries that import Brazilian forage seed; however, there is no current evidence suggesting that A. fujianensis is a plant-parasitic species. Two real-time polymerase chain reaction (qPCR) diagnostics were developed to detect each species and an operational envelope was established. A set of primers and hydrolysis probes for each species was designed targeting the large subunit (LSU) region. To assess their specificity, primers and probes sets were tested with samples of nontarget Aphelenchoides and Paraphelenchus sp. also frequently associated with forage seed. Experiments using dilutions of purified plasmid standards underpinned the sensitivity of the qPCR assays, which detected as few as 10 copies of target nematode ribosomal DNA. Thus, the developed diagnostics were sufficiently sensitive to detect DNA extracted from a fragment of a single target nematode. There was a positive correlation between copy number of the target species and nematode abundance, suggesting the potential of this method for quantification. Evidence of intra-individual variability among cloned sequences of the LSU region in a single A. besseyi population is also reported.
Molecular Diversity of Phytoplasmas Associated with Grapevine Yellows Disease in North-Eastern Italy
Authors: Zambon Yuri , Canel Alessandro , Bertaccini Assunta , Contaldo Nicoletta
Published: September 2017

A 3-year survey was conducted in Northern Italy to verify the presence and diversity of phytoplasmas in selected vineyards showing symptoms of severe yellows. Symptomatic and asymptomatic grapevines were sampled, and insects were collected using yellow sticky traps. The phytoplasmas detected in grapevine samples were different according to the years: “flavescence dorée” (16SrV-C/D) was detected together with other phytoplasmas such as 16SrXII-A (‘Candidatus Phytoplasma solani’-related, bois noir), 16SrI-B (‘Ca. P. asteris’-related, aster yellows), 16SrX-B (‘Ca. P. prunorum’-related, European stone fruit yellows), and 16SrV-A (‘Ca. P. ulmi’-related, elm yellows). Moreover, phytoplasmas belonging to 16SrVII-A (‘Ca. P. fraxini’-related) and 16SrVI (‘Ca. P. trifolii’-related) subgroups were also identified. Identification of phytoplasmas was also carried out from insects and showed the presence of some of these phytoplasmas in Scaphoideus titanus and Orientus ishidae: 16SrXII-A, 16SrVII, and 16SrVI phytoplasmas were detected in specimens of both species, while 16SrXII-A and 16SrI-B phytoplasma strains were identified in Orientus ishidae and Hyalesthes obsoletus, and 16SrX-B in S. titanus. Direct sequencing of selected amplicons obtained from 16S rRNA, rp, and tuf genes from grapevine and insect samples confirmed the phytoplasma identification. The 16SrVII-A and 16SrVI phytoplasmas were never detected before in grapevine, S. titanus and Orientus ishidae in Europe and their epidemiological importance is being monitored.
Effect of Tranexamic Acid on Transfusion: A Randomized Clinical Trial in Acetabular Fracture Surgery
Authors: Lack William D. , Crist Brett D. , Seymour Rachel B. , Harvin William , Karunakar Madhav A. ,   the TXA Study Group‖
Published: September 2017

Objectives:

Given the increasing evidence that minimizing blood loss and limiting allogeneic transfusion can improve patient outcome, we are performing a randomized controlled trial of the use of tranexamic acid (TXA) during acetabular fracture surgery.

Design:

Prospective, multicenter, and randomized.

Setting:

Two level I trauma centers.

Participants:

Eighty-eight patients underwent randomization, with 42 assigned to the TXA group and 46 assigned to the placebo group.

Intervention:

The use of TXA during acetabular fracture surgery.

Main Outcome Measurements:

The primary outcome was allogeneic blood transfusion. Secondary outcomes consisted of estimate blood loss (EBL) and venous thromboembolism (VTE).

Results:

The overall transfusion rate was 40.9% (36 of 88), and the average estimated blood loss was 635 mL. There were no significant differences between groups for transfusion incidence, number of units transfused, EBL, or incidence of VTE. There was no difference in transfusion rate for the TXA group (0.097). Transfusion was significantly more likely in cases with low preoperative hemoglobin levels, higher rates of intraoperative blood loss, and longer surgical times.

Conclusions:

There was no significant difference in transfusion rate, EBL, or VTE for TXA versus placebo. Any potential benefit seems to be overwhelmed by other factors, specifically preoperative anemia and surgical time, which are highly variable in trauma surgery. These findings do not support the routine use of TXA in the setting of open reduction and internal fixation of acetabular fractures.

Level of Evidence:

Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.
Shortening and Angulation Strategies to Address Composite Bone and Soft Tissue Defects
Authors: Pierrie Sarah N. , Hsu Joseph R.
Published: September 2017

Gustilo–Anderson IIIB tibial fractures and infected tibial nonunions represent particular challenges for the orthopaedic trauma surgeon. Debridement of dysvascular bone and soft tissues can create composite bone and soft tissue defects. Restoring the soft tissue envelope is a critical step in preventing or treating ongoing infection and in restoring local blood supply. Shortening and angulation techniques, including the gradual expansion muscle flap, rely on distraction histogenesis to address composite bone and soft tissue loss. These strategies can be used to treat large soft tissue defects when flap coverage or free tissue transfer is not available.
Critical-Sized Bone Defects: Sequence and Planning
Authors: Toogood Paul , Miclau Theodore
Published: September 2017

Bone defects associated with open fractures require a careful approach and planning. At initial presentation, an emergent irrigation and debridement is required. Immediate definitive fixation is frequently safe, with the exception of those injuries that normally require staged management or very severe type IIIB and IIIC injuries. Traumatic wounds that can be approximated primarily should be closed at the time of initial presentation. Wounds that cannot be closed should have a negative pressure wound therapy dressing applied. The need for subsequent debridements remains a clinical judgment, but all nonviable tissue should be removed before definitive coverage. Cefazolin remains the standard of care for all open fractures, and type III injuries also require gram-negative coverage. Both induced membrane technique with staged bone grafting and distraction osteogenesis are excellent options for bony reconstruction. Soft tissue coverage within 1 week of injury seems critical.
Ring Keratitis From Topical Anesthetic Abuse After Laser Epithelial Keratomileusis
Authors: Mergen Burak , Ozdamar Akif , Sarici Ahmet Murat
Published: September 2017

A 28-year-old man underwent laser epithelial keratomileusis for the correction of myopia in both eyes. The patient subsequently had delayed corneal epithelial healing in both eyes and ring infiltrate in the left eye (LE). Corneal scrapings were obtained from the ocular surface and subjected to microscopic examination and culture. On identifying and preventing the use of topical proparacaine, the corneal epithelium healed in both eyes after the use of eye pressure patches. The ring infiltrate resolved in the patient's LE, leaving minor opacity at the inferior cornea. Refractive surgeons should consider the possibility of topical anesthetic abuse in cases of corneal ring infiltrates. The resulting prognosis can be excellent after the rapid removal of inciting agents and the application of appropriate treatments.
Genome-guided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin
Authors: van Heel Auke J. , Montalban-Lopez Manuel , Oliveau Quentin , Kuipers Oscar P.
Published: September 2017

The need for novel antibiotics in an era where antimicrobial resistance is on the rise, and the number of new approved antimicrobial drugs reaching the market is declining, is evident. The underused potential of post-translationally modified peptides for clinical use makes this class of peptides interesting candidates. In this study, we made use of the vast amounts of available genomic data and screened all publicly available prokaryotic genomes (~3000) to identify 394 novel head-to-tail cyclized antimicrobial peptides. To verify these in silico results, we isolated and characterized a novel antimicrobial peptide from Bacillus pumilus that we named pumilarin. Pumilarin was demonstrated to have a circular structure and showed antimicrobial activity against several indicator strains, including pathogens.
Enterococcus faecalis and pathogenic streptococci inactivate daptomycin by releasing phospholipids
Authors: Ledger Elizabeth V. K. , Pader Vera , Edwards Andrew M.
Published: September 2017

Daptomycin is a lipopeptide antibiotic with activity against Gram-positive bacteria. We showed previously that Staphylococcus aureus can survive daptomycin exposure by releasing membrane phospholipids that inactivate the antibiotic. To determine whether other pathogens possess this defence mechanism, phospholipid release and daptomycin activity were measured after incubation of Staphylococcus epidermidis, group A or B streptococci, Streptococcus gordonii or Enterococcus faecalis with the antibiotic. All bacteria released phospholipids in response to daptomycin, which resulted in at least partial inactivation of the antibiotic. However, E. faecalis showed the highest levels of lipid release and daptomycin inactivation. As shown previously for S. aureus, phospholipid release by E. faecalis was inhibited by the lipid biosynthesis inhibitor platensimycin. In conclusion, several pathogenic Gram-positive bacteria, including E. faecalis, inactivate daptomycin by releasing phospholipids, which may contribute to the failure of daptomycin to resolve infections caused by these pathogens.
In vivo, chromatin is a fluctuating polymer chain at equilibrium constrained by internal friction
Authors: Socol M. , Wang R. , Jost D. , Carrivain P. , Dahirel V. , Zedek A. , Normand C. , Bystricky K. , Victor J.M. , Gadal O. , Bancaud A.
Published: September 2017

Chromosome mechanical properties determine DNA folding and dynamics, and underlie all major nuclear functions. Here we combine modeling and real-time motion tracking experiments to infer the physical parameters describing chromatin fibers.In vitro,motion of nucleosome arrays can be accurately modeled by assuming a Kuhn length of 35-55 nm.In vivo, the amplitude of chromosome fluctuations is drastically reduced, and depends on transcription. Transcription activation increases chromatin dynamics only if it involves gene relocalization, while global transcriptional inhibition augments the fluctuations, yet without relocalization. Chromatin fiber motion is accounted for by a model of equilibrium fluctuations of a polymer chain, in which random contacts along the chromosome contour induce an excess of internal friction. Simulations that reproduce chromosome conformation capture and imaging data corroborate this hypothesis. This model unravels the transient nature of chromosome contacts, characterized by a life time of ∼2 seconds and a free energy of formation of ∼1 kBT.
Insights into Hepatitis C Transmission in Young Persons who Inject Drugs: Results From a Dynamic Modeling Approach Informed by State-Level Public Health Surveillance Data
Authors: Gicquelais Rachel E , Foxman Betsy , Coyle Joseph , Eisenberg Marisa C
Published: September 2017

Rising use of heroin and prescription opioids are major contributors to increases in Hepatitis C Virus (HCV) incidence in US young adults since the late 1990s. How best to interrupt transmission and decrease HCV prevalence in young persons who inject drugs (PWID) is uncertain, but modeling studies in older populations support interventions that increase HCV treatment among all PWID. We developed a transmission model of young (aged 15-30 years) PWID, which we fit to state-level US HCV surveillance data, and simulated the potential impact of primary (reducing injection initiation), secondary (increasing cessation, reducing injection partners, or reducing injection drug use relapse), and tertiary (HCV treatment) interventions on incident and prevalent HCV cases. Interventions with primary prevention initiatives (reducing injection initiation) yielded concurrent reductions to HCV incidence and prevalence. Treatment of former PWID led to prevalence reductions but did not reduce incidence. Treatment of current and former PWID without other interventions led to incidence reductions in scenarios with high injection initiation rates, high syringe sharing, and low relapse rates after injection cessation. While these results are specific to Michigan, our approach could be applied in other states conducting HCV surveillance to identify local-level intervention opportunities.
Whole Genome Bisulphite Sequencing Using the Illumina Hiseq X System
Authors: Suzuki M. , Liao W. , Wos F. , Johnston A.D. , DeGrazia J. , Ishii J. , Bloom T. , Zody M.C. , Germer S. , Greally J.M.
Published: September 2017

The Illumina HiSeq X platform has helped to reduce the cost of whole genome sequencing substantially, but its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and the elimination of a previously unrecognized artefact affecting several percent of bisulphite sequencing reads.