bluuebunny/crossref_metadata_2025 huggingface dataset:
Self‐reported snoring is associated with chronic kidney disease independent of metabolic syndrome in middle‐aged and elderly Chinese
Authors: Song Jun , Wang Chuan , Ma Aixia , Zheng Huizhen , Zheng Wenjian , Hou Xinguo , Hu Cheng , Chen Li , Jia Weiping
Published: April 2018

Aims/Introduction

To investigate the correlation between snoring and chronic kidney disease (CKD), and explore whether metabolic syndrome (MetS) plays an important role in this relationship among middle‐aged and elderly Chinese.

Materials and Methods

The participants included in the present study were categorized into three subgroups based on self‐reported snoring frequency (regularly [≥3 times per week], occasionally [between ‘regularly’ and ‘never’] or never [<1 time per month]). An estimated glomerular filtration rate <60 mL/min/1.73 m2 was considered as CKD. We diagnosed MetS based on the 2004 Chinese Diabetes Society criteria. We explored the relationship between snoring and CKD by using multiple logistic regressions.

Results

The frequency of MetS, MetS components and CKD was dramatically higher in regular snorers than in non‐snorers and occasional snorers. The odds ratios for MetS and all the MetS elements, except for hyperglycemia, increased progressively with the snoring frequency (P < 0.001). Upon additional adjustment for other MetS components, snoring was not significantly related with hypertension; however, the associations between snoring frequency and overweight/obesity and dyslipidemia became attenuated, but still remained statistically significant (P < 0.01). Interestingly, odds ratios for CKD also increasingly augmented with snoring frequency (P < 0.001). Upon further adjustment for individual MetS components or MetS, regular snoring also resulted in a significantly increased odds ratio for CKD (odds ratio 1.72; P = 0.034) relative to non‐snoring.

Conclusions

Self‐reported snoring is closely associated with CKD independent of MetS among middle‐aged and elderly Chinese.
Managing uncertainty in design flood magnitude: Flexible protection strategies versus safety factors
Authors: Dittes B. , Špačková O. , Straub D.
Published: April 2018

When planning flood protection, agencies are confronted with uncertainty in the design flood magnitude. In particular, the required capacity may increase in the future and render the protection insufficient. This problem can be adressed by applying a safety factor to the design capacity. We propose a Bayesian quantitative sequential decision model that identifies a cost‐optimal safety factor in the face of uncertainty. It takes into account the flexibility of the protection system, that is, how costly it is to adjust. We focus on the description of the decision model and on the concept of flexibility, investigating only the effect of uncertainty from the historic flood record. Extension to other types of uncertainty is possible. The model is implemented for a catchment in Germany. Various degrees of uncertainty are investigated by using different lengths of historic records. The optimal safety factor decreases with decreasing uncertainty and with increasing system flexibility.
The value components of contract farming in contemporary capitalism
Authors: Dubb Alex
Published: April 2018

Contract farming (CF) has generally been understood as, essentially, a market institution—by both (approving) “mainstream” and (critical) “radical” perspectives. Analyses of relations of production have, meanwhile, tended towards a problematic “peasantist” frame, where contracts undermine farmer “autonomy” in processes of “flexible” corporate agro‐industrial restructuring. This paper argues that a materialist analysis of CF from within capital–labour relations offers a stronger conceptual foundation for re‐synthesizing questions of market‐power. It first argues that radical notions of “peasant subsumation” conceptually mirror Marx's “formal subsumption of capital” but underplay dynamics of “real subsumption” accompanying capitalism's wider development. Drawing on the “petty commodity production” concept, it then argues that CF's “flexibility” rests in its differential content. CF's fungibility to contradictory movements of “integration” and “dispersion” enables it to emphasize different methods of surplus appropriation under shifting conditions; each corresponding to a different dominant social tendency. On the one hand, conditions of market expansion inspire integration for relative surplus appropriation through raised productivity, and CF tends to act as a “tool of proletarianization” in the wider centralization of capital. On the other, conditions of contraction motivate the dispersal of unvalorized capital, prompting efforts to raise absolute surplus appropriation, and CF tends to act as a “tool of differentiation” to concentrate agricultural capital.
Milk feeding and first complementary foods during the first year of life in the TEDDY study
Authors: Riikonen Anne , Hadley David , Uusitalo Ulla , Miller Nicole , Koletzko Sibylle , Yang Jimin , Andrén Aronsson Carin , Hummel Sandra , Norris Jill M. , Virtanen Suvi M. ,   on behalf of the TEDDY Study Group
Published: April 2018

The aim was to describe milk feeding patterns and first weaning foods during the first year of life in a large prospective birth cohort of infants with increased genetic risk for Type 1 diabetes (T1D) recruited in 4 different countries: the United States, Finland, Germany, and Sweden. All enrolled children with dietary information (n = 8,673) were included in the analyses; 1,307 (15%) children who dropped out before the first birthday were excluded from some analyses. Supplementary milk feeding in the first 3 days of life was common in all the four countries, although the type of the supplementary milk differed by country and by maternal T1D. Donated human milk was commonly used only in Finland. In all the countries, the most common first supplementary food was cow's milk‐based infant formula, especially among offspring of mothers with T1D. The use of specific types of infant formulas differed notably by country: Extensively hydrolysed formulas were most used in Finland, partially hydrolysed ones in the United States and in Germany, and soy formulas only in the United States. Infant formulas commonly included probiotics, prebiotics, and starches. During the first year of life, most of the infants received conventional cow's milk. Overall, milk feeding during the first 3 days of life and thereafter until the first birthday differed markedly by maternal T1D status and across countries. These descriptive data may be useful in understanding early infant feeding practices and in planning potential interventions, which affect infant feeding.
A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch
Authors: Meile Lukas , Croll Daniel , Brunner Patrick C. , Plissonneau Clémence , Hartmann Fanny E. , McDonald Bruce A. , Sánchez‐Vallet Andrea
Published: April 2018

Cultivar‐strain specificity in the wheat–Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, many of which have been identified. On the pathogen side, however, the molecular determinants of specificity remain largely unknown.

We used genetic mapping, targeted gene disruption and allele swapping to characterise the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to characterise the evolutionary trajectory of Avr3D1.

Avr3D1 is specifically recognised by wheat cultivars harbouring the Stb7 resistance gene, triggering a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a genome region populated by independent transposable element insertions. The gene was present in all 132 investigated strains and is highly polymorphic, with 30 different protein variants identified. We demonstrated that specific amino acid substitutions in Avr3D1 led to evasion of recognition.

These results demonstrate that quantitative resistance and gene‐for‐gene interactions are not mutually exclusive. Localising avirulence genes in highly plastic genomic regions probably facilitates accelerated evolution that enables escape from recognition by resistance proteins.
The interaction between homatropine and optical blur on choroidal thickness
Authors: Sander Beata P. , Collins Michael J. , Read Scott A.
Published: April 2018

Purpose

To analyse the short‐term interaction between a short period of myopic and hyperopic defocus and the muscarinic antagonist homatropine upon the choroidal thickness and ocular biometrics of healthy subjects.

Methods

Thirty young adults (15 myopes and 15 emmetropes) aged 18–35 years had subfoveal choroidal thickness (ChT) and ocular biometry measurements taken before, 30 min, and 60 min following the introduction of monocular optical blur (0.00 D, +3.00 D and −3.00 D) combined with administration of either 2% homatropine or placebo (total of six conditions). Each combination of optical blur and drug was tested on different days, 2 days apart, in randomised order. For choroidal thickness, we captured three SD OCT images (5 mm, cross scans centred at the fovea with 999 A‐scans and 50 B‐scans) with the Copernicus SOCT HR instrument (www.optopol.com). A masked observer manually segmented the average B‐scan images to derive subfoveal choroidal thickness measurements from each measurement session.

Results

The choroid exhibited significant thinning after imposing hyperopic defocus (−3.00 D) combined with placebo (−11 ± 3 μm, p < 0.001). Homatropine prevented the significant choroidal thinning response with hyperopic defocus (+3 ± 2 μm), and the magnitude of ChT change was significantly different to placebo and hyperopic defocus (p < 0.001). There was a significant increase in ChT after the introduction of myopic defocus (+3.00 D) with placebo (+12 ± 3 μm, p < 0.0001) and homatropine combined with myopic defocus also caused a similar increase in ChT (+11 ± 3 μm; p < 0.001). Eyes treated with homatropine alone exhibited a significant increase in ChT (+14 ± 3 μm, p < 0.0001). There was no evidence of differences in choroidal response between refractive groups. Axial length also underwent small but significant changes (all p < 0.01 except homatropine/hyperopic blur and placebo) that were of similar magnitude, but of opposite direction to the changes in choroidal thickness.

Conclusions

Homatropine appears to block the thinning effect of hyperopic defocus on choroidal thickness but did not enhance the thickening effect of myopic defocus. The changes in the choroid may relate to the different pathways in the eye's response to myopic and hyperopic blur or reflect an upper limit on the capacity of the choroid to thicken in the short‐term.
Schlemm's canal and trabecular meshwork morphology in high myopia
Authors: Chen Zhiqi , Song Yinwei , Li Mu , Chen Wei , Liu Shiliang , Cai Zhen , Chen Liugui , Xiang Yan , Zhang Hong , Wang Junming
Published: April 2018

Purpose

Myopes have a higher risk for open‐angle glaucoma; however, the reason is not clear. This study aims to explore the morphologic alterations of Schlemm's canal and trabecular meshwork size in highly myopic eyes.

Methods

Forty myopic eyes from 40 patients with high myopia and 40 control eyes from 40 subjects with low myopia, emmetropia or low hyperopia were enrolled. Optical coherence tomography (OCT) was used to image Schlemm's canal and trabecular meshwork size. The correlations between the morphological alterations of Schlemm's canal and trabecular meshwork, spherical equivalent refractive error, axial length, and intraocular pressure were analysed.

Results

Subjects with high myopia had a significantly larger Schlemm's canal diameter in the nasal (188.1 ± 85.6 μm vs 127.4 ± 46.7 μm, P < 0.001), temporal (200.1 ± 7.2 μm vs 147.6 ± 68.1 μm, P = 0.001) quadrants and average value (173.1 ± 48.1 μm vs 137.3 ± 39.6 μm, P = 0.001), and larger Schlemm's canal area in the nasal (7333.2 ± 3877.7 μm2 vs 3833.2 ± 2094.7 μm2, P < 0.001), temporal (7274.8 ± 3247.4 μm2 vs 4631.1 ± 2431.9 μm2, P < 0.001) inferior (5512 ± 2504.9 μm2 vs 3922.6 ± 1935.6 μm2, P = 0.003) quadrants and average value(6165.4 ± 2080.5 μm2 vs 4044.4 ± 1581.1 μm2, P < 0.001). In the high myopia group, trabecular meshwork thickness of the nasal and temporal quadrants was significantly smaller (108.8 ± 31.6 μm vs 126 ± 42.2 μm, P = 0.045; 100.5 ± 15.4 μm vs 118.4 ± 26.8 μm, P = 0.001, respectively) compared with the control group, as well as the average value (106.4 ± 16.5 μm vs 120.9 ± 23.5 μm, P = 0.002). In the high myopia group, Schlemm's canal and trabecular meshwork size were not correlated with spherical equivalent refractive error and axial length (P > 0.05), while Schlemm's canal area showed a significant negative correlation with intraocular pressure (r = −0.33, P = 0.039).

Conclusions

This study reports for the first time that eyes with high myopia have a larger Schlemm's canal diameter and area, as well as decreased trabecular meshwork thickness, which may help to understand the close association between high myopia and open‐angle glaucoma. Schlemm's canal and trabecular meshwork analysis by OCT images may help to characterise the underlying pathophysiological mechanisms involved in high myopia.
Hannah Arendt on the evil of not being a person
Authors: Shuster Martin
Published: April 2018

This article presents Hannah Arendt's novel conception of evil, arguing that what animates and undergirds this conception is an understanding of human agency, of what it means to be a person at all. The banality of evil that Arendt theorizes is exactly the failure to become a person in the first place—it is, in short, the evil of being a nobody. For Arendt, this evil becomes extreme when a mass of such nobodies becomes organized by totalitarianism. This article focuses on the connection between Arendt's understanding of personhood and her conception of evil, showing how Arendt falls into a Kantian tradition of prioritizing apperception—thinking—as central for human agency. In this way, the article shows that thinking—being a person—is central to Arendt's work, thereby prioritizing and making sense of her claim in The Human Condition that one is never “more active” than when thinking.
Marketplace, Reseller, or Hybrid: Strategic Analysis of an Emerging E‐Commerce Model
Authors: Tian Lin , Vakharia Asoo J. , Tan Yinliang (Ricky) , Xu Yifan
Published: April 2018

Traditionally, online retailers have acted as product resellers. Recently, these retailers have also started to serve as online marketplaces by providing a platform to directly connect sellers with buyers. Over and above re‐shaping the traditional e‐commerce market, conventional wisdom suggests that this new format will mitigate the double‐marginalization effect and benefit both the intermediary and suppliers through a revenue sharing scheme. However, we find that upstream competition between suppliers critically moderates this possibility. We also find that the interaction of order‐fulfillment costs and upstream competition intensity moderates the selection of an optimal mode for the intermediary. More specifically, when order‐fulfillment costs are large and when the supplier product offerings are similar (i.e., competition intensity is high), the pure reseller mode is the preferred choice; when order‐fulfillment costs are small and the supplier product offerings are highly differentiated (i.e., low competition intensity), the pure marketplace mode is the preferred choice. Finally, the hybrid mode is preferred when order‐fulfillment costs are moderate and suppliers’ products are somewhat similar (i.e., competition intensity is moderate). The intuition behind these results hinges on the trade‐off between transfer of pricing rights and the responsibility for order fulfillment. Our findings not only complement the emerging online marketplace literature but also provide testable empirical questions concerning the relationship and magnitude of different factors steering the mode choice.
Expanding the Political Philosophy Dimension of the RISP Model: Examining the Conditional Indirect Effects of Cultural Cognition
Authors: Hmielowski Jay D. , Wang Meredith Y. , Donaway Rebecca R.
Published: April 2018

This article attempts to connect literatures from the Risk Information Seeking and Processing (RISP) model and cultural cognition theory. We do this by assessing the relationship between the two prominent cultural cognition variables (i.e., group and grid) and risk perceptions. We then examine whether these risk perceptions are associated with three outcomes important to the RISP model: information seeking, systematic processing, and heuristic processing, through a serial mediation model. We used 2015 data collected from 10 communities across the United States to test our hypotheses. Our results show that people high on group and low on grid (egalitarian communitarians) show greater risk perceptions regarding water quality issues. Moreover, these higher levels of perceived risk translate into increased information seeking, systematic processing of information, and lower heuristic processing through intervening variables from the RISP model (e.g., negative emotions and information insufficiency). These results extend the extant literature by expanding on the treatment of political ideology within the RISP model literature and taking a more nuanced approach to political beliefs in accordance with the cultural cognitions literature. Our article also expands on the RISP literature by looking at information‐processing variables.
Assessing Transboundary Wildfire Exposure in the Southwestern United States
Authors: Ager Alan A. , Palaiologou Palaiologos , Evers Cody R. , Day Michelle A. , Barros Ana M. G.
Published: April 2018

We assessed transboundary wildfire exposure among federal, state, and private lands and 447 communities in the state of Arizona, southwestern United States. The study quantified the relative magnitude of transboundary (incoming, outgoing) versus nontransboundary (i.e., self‐burning) wildfire exposure based on land tenure or community of the simulated ignition and the resulting fire perimeter. We developed and described several new metrics to quantify and map transboundary exposure. We found that incoming transboundary fire accounted for 37% of the total area burned on large parcels of federal and state lands, whereas 63% of the area burned was burned by ignitions within the parcel. However, substantial parcel to parcel variation was observed for all land tenures for all metrics. We found that incoming transboundary fire accounted for 66% of the total area burned within communities versus 34% of the area burned by self‐burning ignitions. Of the total area burned within communities, private lands contributed the largest proportion (36.7%), followed by national forests (19.5%), and state lands (15.4%). On average seven land tenures contributed wildfire to individual communities. Annual wildfire exposure to structures was highest for wildfires ignited on state and national forest land, followed by tribal, private, and BLM. We mapped community firesheds, that is, the area where ignitions can spawn fires that can burn into communities, and estimated that they covered 7.7 million ha, or 26% of the state of Arizona. Our methods address gaps in existing wildfire risk assessments, and their implementation can help reduce fragmentation in governance systems and inefficiencies in risk planning.
Performance Ranking and Environmental Governance: An Empirical Study of the Mandatory Target System
Authors: Tang Xiao , Liu Zhengwen , Yi Hongtao
Published: April 2018

With the deterioration of the environment across the globe, environmental problems have attracted much attention from the public, academia, and governments. This study contributes to the understanding of environmental policy implementation by empirically testing the policy feedback theory and official ranking tournament theory in the Chinese context. In particular, it focuses on how prior environmental performance ranking transitions into future policy performance through the mandatory target system (MTS) in China. The results from this study show that provincial environmental performance ranking serves as an effective incentive for strengthening environmental governance. Low‐ranking provinces will improve their environmental policy performances in future years because of competition in the official tournament. Policy implications are drawn to improve the administrative design of environmental management.
The political economy of regulations and trade: Wine trade 1860–1970
Authors: Meloni Giulia , Swinnen Johan
Published: April 2018

Dramatic changes in the 1860–1970 wine trade provide insights on the political economy of regulations and policy instrument choice and trade. An invasion of Phylloxera in the 1870s turned France from the world's leading exporter to a massive importer of wine and grapes. When French production recovered a combination of tariffs, safety regulations and quality standards were introduced to protect its French producers, causing dramatic changes in global wine and grape production and trade, including in Spain, Italy, Turkey, Greece, Algeria, Tunisia and Morocco. Changes in wine regulations were caused by relative income and loss aversion factors in political economy. Tariffs were the preferred policy instruments as they directly restrict imports, bring in revenues, have low transaction costs and are preferred political instruments when there are information imperfections. Safety regulations and quality standards, including labelling and input prohibitions, reduce asymmetric information for consumers or undesirable externalities, and simultaneously protected domestic producers. Regulations were often targeted at imported products (wine and raisins) when tariffs were ineffective or constrained by institutions (such as on colonial wine). Hence, tariffs and quality regulations were jointly used in wine policy, both as complements and as substitutes in policy design.
Fluorescence enabled direct visual observation for diagnosis of ultrafiltration membrane fouling by bi‐disperse submicron particle suspensions
Authors: Autin O. , Sakar H. , McAdam E. J.
Published: April 2018

Whilst direct observation (DO) methodologies can describe back‐transport of supra‐micron particles, present technologies are unable to discriminate submicron particles, which are primarily responsible for membrane fouling. In this study, we therefore introduce a fluorescence enabled direct visual observation (RLF‐DVO) methodology to permit visual characterisation of submicron particle transport during cross‐flow filtration. Particle discrimination was achievable for particle diameters exceeding 0.25 µm; however, this was dependent upon particle concentration and the cross‐flow velocity employed. Nevertheless, this is considerably below the detection limit of current techniques (around 3 µm). During filtration of a binary dispersion comprised of submicron particles, deposition was observed before a change in transmembrane pressure was detected, which underpins the important role of DO for fouling diagnosis. Based on observations made during this study, recommendations are proposed that will further improve resolution. Importantly, this study demonstrates RLF‐DVO can provide real‐time description of submicron particle transport during cross‐flow filtration.
Reconquering the water: Evolution and systematics of South and Central American aquatic lizards (Gymnophthalmidae)
Authors: Marques‐Souza Sergio , Prates Ivan , Fouquet Antoine , Camacho Agustín , Kok Philippe J. R. , Nunes Pedro M. S. , Dal Vechio Francisco , Recoder Renato Sousa , Mejia Nathalia , Teixeira Junior Mauro , Barrio‐Amorós Cesar , Cassimiro José , Dias Lima Jucivaldo , Aurélio de Sena Marco , Rodrigues Miguel Trefaut
Published: April 2018

The Cercosaurini tribe stands out from other Gymnophthalmidae lizards for including several species with morphological adaptations to aquatic lifestyle (“Crocodile‐Like Morphology” – CLM). Recent molecular phylogenies of Cercosaurini demonstrated the paraphyly of CLM species, implicitly suggesting that adaptations to the aquatic life evolved more than once. However, CLM species have remained poorly sampled, and a number of uncertainties persist, such as the monophyly of Neusticurus and the placement of Potamites apodemus within the tribe. Based on a more extensive molecular and morphological data set, we propose a phylogenetic hypothesis for Neusticurus and investigate, for the first time, the phylogenetic position of P. apodemus. We recovered a monophyletic Neusticurus clade; however, Neusticurus rudis as currently understood was recovered as paraphyletic, with two lineages that also show consistent morphological diagnosis; as a result, we resurrect and provide a taxonomic redescription of Neusticurus surinamensis Müller, . Moreover, because P. apodemus was recovered as sister to all other Echinosaura, we propose a new combination for this species (Echinosaura apodema). We also review the distribution of Neusticurus species, offering a comprehensive view of their biogeography. Lastly, our ancestral character reconstruction and dating analyses indicate that the CLM phenotype evolved four times independently during Cercosaurini′s evolutionary history. We hypothesize that the CLM phenotype and subsequent adaptation to aquatic life may be linked to the development of the Pebas Lake in western Amazonia during the Miocene.
Public Health Law Perspectives: Nutritional Supplements and Doping In Sports
Authors: Atienza-Macías Elena
Published: April 2018

In this paper the author intends to set forth, briefly but rigorously, the mix of legal issues around the extended use of (incorrectly) so-called "food supplements", trying to express in full the complex inventory of problems arising from the lack of ad hoc regulation in the field of doping in sport.
Numerical and analytic modelling of elastodynamic scattering within polycrystalline materials
Authors: Van Pamel A. , Sha G. , Lowe M. J. S. , Rokhlin S. I.
Published: April 2018

The elastodynamic behavior of polycrystalline cubic materials is studied through the fundamental propagation properties, the attenuation and wave speed, of a longitudinal wave. Predictions made by different analytical models are compared to both numerical and experimental results. The numerical model is based on a three-dimensional Finite Element (FE) simulation which provides a full-physics solution to the scattering problem. The three main analytical models include the Far-Field Approximation (FFA), the Self-Consistent Approximation (SCA) to the reference medium, and the herein derived Second Order Approximation (SOA). The classic Stanke and Kino model is also included, which by comparison to the SOA, reveals the importance of the distribution of length-scales described in terms of the two-point correlation function in determining scattering behavior. Further comparison with the FE model demonstrates that the FFA provides a simple but satisfactory approximation, whereas the SOA shows all-around excellent agreement. The experimental wave velocity data evaluated against the SOA and SCA reveal a better agreement when the Voigt reference is used in second order models. The use of full-physics numerical simulations has enabled the study of wave behavior in these random media which will be important to inform the ongoing development of analytical models and the understanding of observations.
Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions
Authors: Wicks June K. , Smith Raymond F. , Fratanduono Dayne E. , Coppari Federica , Kraus Richard G. , Newman Matthew G. , Rygg J. Ryan , Eggert Jon H. , Duffy Thomas S.
Published: April 2018

This is the first direct determination of Fe-Si alloy structures at pressures found in the cores of super-Earth planets.
The delivery of water by impacts from planetary accretion to present
Authors: Daly R. Terik , Schultz Peter H.
Published: April 2018

Impact melts and breccias trap surprisingly large quantities of water carried by carbonaceous chondrite–like impactors.
Guns, germs, and trees determine density and distribution of gorillas and chimpanzees in Western Equatorial Africa
Authors: Strindberg Samantha , Maisels Fiona , Williamson Elizabeth A. , Blake Stephen , Stokes Emma J. , Aba’a Rostand , Abitsi Gaspard , Agbor Anthony , Ambahe Ruffin D. , Bakabana Parfait C. , Bechem Martha , Berlemont Antoine , Bokoto de Semboli Bruno , Boundja Patrick R. , Bout Nicolas , Breuer Thomas , Campbell Genevieve , De Wachter Pauwel , Ella Akou Marc , Esono Mba Fidel , Feistner Anna T. C. , Fosso Bernard , Fotso Roger , Greer David , Inkamba-Nkulu Clement , Iyenguet Calixte F. , Jeffery Kathryn J. , Kokangoye Max , Kühl Hjalmar S. , Latour Stephanie , Madzoke Bola , Makoumbou Calixte , Malanda Guy-Aimé F. , Malonga Richard , Mbolo Victor , Morgan David B. , Motsaba Prosper , Moukala Gabin , Mowawa Brice S. , Murai Mizuki , Ndzai Christian , Nishihara Tomoaki , Nzooh Zacharie , Pintea Lilian , Pokempner Amy , Rainey Hugo J. , Rayden Tim , Ruffler Heidi , Sanz Crickette M. , Todd Angelique , Vanleeuwe Hilde , Vosper Ashley , Warren Ymke , Wilkie David S.
Published: April 2018

We quantify the impacts of poaching, Ebola, and habitat degradation on western lowland gorillas and central chimpanzees.
Footprints preserve terminal Pleistocene hunt? Human-sloth interactions in North America
Authors: Bustos David , Jakeway Jackson , Urban Tommy M. , Holliday Vance T. , Fenerty Brendan , Raichlen David A. , Budka Marcin , Reynolds Sally C. , Allen Bruce D. , Love David W. , Santucci Vincent L. , Odess Daniel , Willey Patrick , McDonald H. Gregory , Bennett Matthew R.
Published: April 2018

Contemporaneous sloth and human footprints from the terminal Pleistocene at White Sands National Monument suggest stalking.
Fundamental science behind today’s important medicines
Authors: Spector Jonathan M. , Harrison Rosemary S. , Fishman Mark C.
Published: April 2018

Today’s most transformative medicines exist because of fundamental discoveries that were made without regard to practical outcome and with their relevance to therapeutics only appearing decades later.
First Penicillin-Binding Protein Occupancy Patterns of β-Lactams and β-Lactamase Inhibitors in Klebsiella pneumoniae
Authors: Sutaria Dhruvitkumar S. , Moya Bartolome , Green Kari B. , Kim Tae Hwan , Tao Xun , Jiao Yuanyuan , Louie Arnold , Drusano George L. , Bulitta Jürgen B.
Published: April 2018

Penicillin-binding proteins (PBPs) are the high-affinity target sites of all β-lactam antibiotics in bacteria. It is well known that each β-lactam covalently binds to and thereby inactivates different PBPs with various affinities. Despite β-lactams serving as the cornerstone of our therapeutic armamentarium against
Klebsiella pneumoniae
, PBP binding data are missing for this pathogen. We aimed to generate the first PBP binding data on 13 chemically diverse and clinically relevant β-lactams and β-lactamase inhibitors in
K. pneumoniae
. PBP binding was determined using isolated membrane fractions from
K. pneumoniae
strains ATCC 43816 and ATCC 13883. Binding reactions were conducted using β-lactam concentrations from 0.0075 to 256 mg/liter (or 128 mg/liter). After β-lactam exposure, unbound PBPs were labeled by Bocillin FL. Binding affinities (50% inhibitory concentrations [IC
50
]) were reported as the β-lactam concentrations that half-maximally inhibited Bocillin FL binding. PBP occupancy patterns by β-lactams were consistent across both strains. Carbapenems bound to all PBPs, with PBP2 and PBP4 as the highest-affinity targets (IC
50
, <0.0075 mg/liter). Preferential PBP2 binding was observed by mecillinam (amdinocillin; IC
50
, <0.0075 mg/liter) and avibactam (IC
50
, 2 mg/liter). Aztreonam showed high affinity for PBP3 (IC
50
, 0.06 to 0.12 mg/liter). Ceftazidime bound PBP3 at low concentrations (IC
50
, 0.06 to 0.25 mg/liter) and PBP1a/b at higher concentrations (4 mg/liter), whereas cefepime bound PBPs 1 to 4 at more even concentrations (IC
50
, 0.015 to 2 mg/liter). These PBP binding data on a comprehensive set of 13 clinically relevant β-lactams and β-lactamase inhibitors in
K. pneumoniae
enable, for the first time, the rational design and optimization of double β-lactam and β-lactam–β-lactamase inhibitor combinations.
Complete Genome Sequences of Two Novel Staphylococcus aureus Podoviruses of Potential Therapeutic Use, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9
Authors: Gozdek Agnieszka , Głowacka-Rutkowska Aleksandra , Gawor Jan , Empel Joanna , Gromadka Robert , Łobocka Małgorzata B.
Published: April 2018

Here, we report the genome sequences of two
Staphylococcus aureus
phages belonging to the family
Podoviridae
and subfamily
Picovirinae
, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9, which were isolated from Warsaw sewage. Analysis of their genomes provides valuable information about the diversity of phages belonging to the genus
Rosenblumvirus
and their genes that undergo evolutionary adaptation to cells of different host strains.
Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa
Authors: Naranjo-Ortíz Miguel A. , Rodríguez-Píres Silvia , Torres Rosario , De Cal Antonieta , Usall Josep , Gabaldón Toni
Published: April 2018

Monilinia laxa
(phylum
Ascomycota
) is a plant pathogen responsible for the brown rot blossom blight disease in stone fruit trees of the
Rosaceae
family, such as apricots. We report here the genome sequence of strain 8L of this species, which was assembled into 618 scaffolds, having a total size of 40.799 Mb and encoding 9,567 unique protein-coding genes.
Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1
Authors: Puente-Sánchez Fernando , González-Silva Carlos , Parro Victor , Tamames Javier , Azua-Bustos Armando
Published: April 2018

Gloeocapsopsis
sp. strain AAB1 is an extremely desiccation-tolerant cyanobacterium isolated from translucent quartz stones from the Atacama Desert (Chile). Here, we report its draft genome sequence, which consists of 137 contigs with an ∼5.4-Mb genome size. The annotation revealed 5,641 coding DNA sequences, 38 tRNA genes, and 5 rRNA genes.
Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252
Authors: Naquin Delphine , Panozzo Cristina , Dujardin Geneviève , van Dijk Erwin , d’Aubenton-Carafa Yves , Thermes Claude
Published: April 2018

The mitochondrial genomes of
Saccharomyces cerevisiae
strains contain up to 13 introns. An intronless recombinant genome introduced into the nuclear background of
S. cerevisiae
strain W303 gave the
S. cerevisiae
CW252 strain, which is used to model mitochondrial respiratory pathologies. The complete sequence of this mitochondrial genome was obtained using a hybrid assembling methodology.
Complete Chromosome and Plasmid Sequences of Two Plant Pathogens, Dickeya solani Strains D s0432-1 and PPO 9019
Authors: Khayi Slimane , Blin Pauline , Chong Teik Min , Chan Kok-Gan , Faure Denis
Published: April 2018

Dickeya solani
species are emerging bacterial pathogens of
Solanum tuberosum
. Here, we announce the complete genome sequences of two strains,
Dickeya solani
D s0432-1 and PPO 9019. Strain PPO 9019 represents the first described member of the genus
Dickeya
with an extrachromosomal genetic element.
Complete Genome Sequences of Six Human Bocavirus Strains from Patients with Acute Gastroenteritis in the North Region of Brazil
Authors: Watanabe Aripuanã Sakurada Aranha , Luchs Adriana , Leal Élcio , Milagres Flavio Augusto de Pádua , Komninakis Shirley Vasconcelos , Gill Danielle Elise , Lobato Márcia Cristina Alves Brito Sayão , Brustulin Rafael , das Chagas Rogério Togisaki , Abrão Maria de Fátima Neves dos Santos , Soares Cassia Vitória de Deus Alves , Deng Xutao , Sabino Ester Cerdeira , Delwart Eric , da Costa Antonio Charlys
Published: April 2018

Human bocavirus (HBoV) is commonly associated with acute respiratory tract illness and gastroenteritis. We report six complete genomic sequences of HBoV strains from patients with gastroenteritis in Belém do Pará and Tocantins in the North Region of Brazil. Phylogenetic analysis indicated that the six HBoV strains belong to genotypes 1, 2, and 3.
Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus)
Authors: Lee Yoonhang , Nguyen Thanh Luan , Kim Ahran , Kim Nameun , Roh Heyong Jin , Han Hyun-Ja , Jung Sung-Hee , Cho Mi-Young , Kang Ho Young , Kim Do-Hyung
Published: April 2018

Here, we report the complete genome sequence of multiple-antibiotic-resistant
Streptococcus parauberis
strain SPOF3K, isolated from the kidney of a diseased olive flounder in South Korea in 2013. Sequencing using a PacBio platform yielded a circular chromosome of 2,128,740 bp and a plasmid of 23,538 bp, harboring 2,123 and 24 protein-coding genes, respectively.
Complete Genome Sequence of Sphingobium sp. Strain YG1, a Lignin Model Dimer-Metabolizing Bacterium Isolated from Sediment in Kagoshima Bay, Japan
Authors: Ohta Yukari , Shimane Yasuhiro , Nishi Shinro , Ichikawa Junko , Kurosawa Kanako , Tsubouchi Taishi , Ishii Shun'ichi
Published: April 2018

Sphingobium
sp. strain YG1 is a lignin model dimer-metabolizing bacterium newly isolated from sediment in Kagoshima, Japan, at a depth of 102 m. Here, we report the complete genome nucleotide sequence of strain YG1.
Complete Genome Sequence of a Novel Porcine Circovirus Type 3 Strain, CH/GX/1776D/2017, Isolated from Guangxi, China
Authors: Lu Bingxia , Qin Yibin , He Ying , Liu Lei , Duan Qunpeng , Zhou Yingning , Li Bin , Chen Zhongwei , Liang Jiaxing , Su Qianlian , Bi Bingfen , Jiang Dongfu , Lu Jingzhuan , Zhao Wu
Published: April 2018

Porcine circovirus type 3 (PCV3) was first described in 2016 in U.S. swine herds as a pathogenic agent for pigs. To date, PCV3 has been reported to be widely circulating in the United States, China, South Korea, Brazil, Italy, and Poland. Here, we report the genome sequence of a PCV3 strain (CH/GX/1776D/2017) isolated from Guangxi Province in southern China. The sequence data presented in this study will help us better understand the molecular characteristics and genetic diversity of PCV3 in China.
Whole-Genome Sequences of 18 Bovine Alphaherpesvirus 1 Field Isolates from Pennsylvania and Minnesota
Authors: Chothe Shubhada K. , Sebastian Aswathy , Thomas Asha , Nissly Ruth , Byukusenge Maurice , Wolfgang David , Mor Sunil Kumar , Goyal Sagar , Albert Istvan , Jayarao Bhushan , Kuchipudi Suresh V.
Published: April 2018

Bovine alphaherpesvirus 1 (BHV-1), a member of the
Herpesviridae
family, causes respiratory and reproductive tract infections in cattle. Here, we report complete genome sequences of 18 field isolates of BHV-1 from Pennsylvania and Minnesota.
Reevaluation of the Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1 with Single-Molecule Real-Time Sequencing Data
Authors: Uebe René , Schüler Dirk , Jogler Christian , Wiegand Sandra
Published: April 2018

Magnetospirillum gryphiswaldense
is a key organism for understanding magnetosome formation and magnetotaxis. As earlier studies suggested a high genomic plasticity, we (re)sequenced the type strain MSR-1 and the laboratory strain R3/S1. Both sequences differ by only 11 point mutations, but organization of the magnetosome island deviates from that of previous genome sequences.
Genome Sequences of RIGVIR Oncolytic Virotherapy Virus and Five Other Echovirus 7 Isolates
Authors: Hietanen Eero , Smura Teemu , Hakanen Marika , Chansaenroj Jira , Merilahti Pirjo , Nevalainen Janne , Pandey Sunita , Koskinen Satu , Tripathi Lav , Poovorawan Yong , Pursiheimo Juha , Susi Petri
Published: April 2018

We report here the nearly complete Illumina-sequenced consensus genome sequences of six isolates of echovirus 7 (E7), including oncolytic virotherapy virus RIGVIR and the Wallace prototype. Amino acid identities within the coding region were highly conserved across all isolates, ranging from 95.31% to 99.73%.
Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing
Authors: Tondini Federico , Jiranek Vladimir , Grbin Paul R. , Onetto Cristobal A.
Published: April 2018

Here, we report the first sequenced genome of an indigenous Australian wine isolate of
Torulaspora delbrueckii
using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes.
Draft Genome Sequences of the Obligatory Marine Myxobacterial Strains Enhygromyxa salina SWB005 and SWB007
Authors: Amiri Moghaddam Jamshid , Poehlein Anja , Fisch Katja , Alanjary Mohammad , Daniel Rolf , König Gabriele M. , Schäberle Till F.
Published: April 2018

The two marine myxobacterial strains
Enhygromyxa salina
SWB005 and SWB007 were isolated from coastal soil samples using
Escherichia coli
as bait for these predatory strains. These strains produce unique specialized metabolites. Genomes were assembled into 312 contigs for
E. salina
SWB005 (9.0 Mbp) and 192 contigs for
E. salina
SWB007 (10.6 Mbp).
Whole-Genome Sequence of Infectious Pancreatic Necrosis Virus Isolated from Farmed Brook Trout (Salvelinus fontinalis) in Pennsylvania
Authors: Palchak Kay , Chothe Shubhada K. , Sebastian Aswathy , Nissly Ruth H. , Barry Rhiannon , Albert Istvan , Jayarao Bhushan M. , Kuchipudi Suresh V.
Published: April 2018

Infectious pancreatic necrosis (IPN) is an acute contagious systemic disease affecting several fish species and a critical disease in the salmonid fish farming industry. Here, we report the complete genome sequence of IPN virus (IPNV) RNA segments A and B, isolated from a farmed brook trout in Pennsylvania.
Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan
Authors: Ito Toshihiro , Maruyama Fumito , Sawai Kotaro , Nozaki Keiko , Otsu Keiko , Ohya Kenji
Published: April 2018

Mycobacterium virginiense
, a newly described species of the
Mycobacterium terrae
complex, is a cause of tenosynovitis and osteomyelitis in the United States. Here, we report the 4,849,424-bp draft genome sequence of
M. virginiense
strain GF75, isolated from a mud sample taken from a Japanese swine farm.
Developing a
Bacteroides
System for Function-Based Screening of DNA from the Human Gut Microbiome
Authors: Lam Kathy N. , Martens Eric C. , Charles Trevor C.
Published: April 2018

Human gut microbiome research has been supported by advances in DNA sequencing that make it possible to obtain gigabases of sequence data from metagenomes but is limited by a lack of knowledge of gene function that leads to incomplete annotation of these data sets. There is a need for the development of methods that can provide experimental data regarding microbial gene function. Functional metagenomics is one such method, but functional screens are often carried out using hosts that may not be able to express the bulk of the environmental DNA being screened. We expand the range of current screening hosts and demonstrate that human gut-derived metagenomic libraries can be introduced into the gut microbe
Bacteroides thetaiotaomicron
to identify genes based on activity screening. Our results support the continuing development of genetically tractable systems to obtain information about gene function.
luxRHomolog-Linked Biosynthetic Gene Clusters inProteobacteria
Authors: Brotherton Carolyn A. , Medema Marnix H. , Greenberg E. Peter
Published: April 2018

Bacteria biosynthesize specialized metabolites with a variety of ecological functions, including defense against other microbes. Genes that code for specialized metabolite biosynthetic enzymes are frequently clustered together. These BGCs are often regulated by a transcription factor encoded within the cluster itself. These pathway-specific regulators respond to a signal or indirectly through other means of environmental sensing. Many specialized metabolites are not produced under laboratory growth conditions, and one reason for this issue is that laboratory growth media lack environmental cues necessary for BGC expression. Here, we report a bioinformatics study that reveals that BGCs are frequently linked to genes coding for LuxR family QS-responsive transcription factors in the phylumProteobacteria. The products of theseluxRhomolog-associated gene clusters may serve as a practical source of bioactive metabolites.
Quantifying the mechanical and histological properties of thrombus analog made from human blood for the creation of synthetic thrombus for thrombectomy device testing
Authors: Merritt William , Holter Anne Marie , Beahm Sharna , Gonzalez Connor , Becker Timothy A , Tabor Aaron , Ducruet Andrew F , Bonsmann Laura S , Cotter Trevor R , Frenklakh Sergey
Published: April 2018

Background

Untreated ischemic stroke can lead to severe morbidity and death, and as such, there are numerous endovascular blood-clot removal (thrombectomy) devices approved for human use. Human thrombi types are highly variable and are typically classified in qualitative terms – ‘soft/red,’ ‘hard/white,’ or ‘aged/calcified.’ Quantifying human thrombus properties can accelerate the development of thrombus analogs for the study of thrombectomy outcomes, which are often inconsistent among treated patients.

Methods

‘Soft’human thrombi were created from blood samples ex vivo (ie, human blood clotted in sample vials) and tested for mechanical properties using a hybrid rheometer material testing system. Synthetic thrombus materials were also mechanically tested and compared with the ‘soft’ human blood clots.

Results

Mechanical testing quantified the shear modulus and dynamic (elastic) modulus of volunteer human thrombus samples. This data was used to formulate a synthetic blood clot made from a composite polymer hydrogel of polyacrylamide and alginate (PAAM-Alg). The PAAM-Alg interpenetrating network of covalently and ionically cross-linked polymers had tunable elastic and shear moduli properties and shape memory characteristics.

Conclusions

Due to its adjustable properties, PAAM-Alg can be modified to mimic various thrombi classifications. Future studies will include obtaining and quantitatively classifying patient thrombectomy samples and altering the PAAM-Alg to mimic the results for use with in vitro thrombectomy studies.
Vatican beats Italy 1–0 in the tobacco endgame
Authors: Gallus Silvano , Cattaruzza Maria Sofia , Gorini Giuseppe , Faggiano Fabrizio
Published: April 2018

‘The Holy See cannot be cooperating with a practice that is clearly harming the health of people’. This is the reason behind Pope Francis banning the sale of tobacco products inside the Vatican in January 2018. Just outside the Holy See, in Italy, cigarette sales produce around €13 billion of fiscal revenues every year. In Italy, proposals to increase tobacco taxation are systematically rejected and new tobacco company plants have been officially inaugurated in recent years by representatives of State. The national branch of the Red Cross also shows ambivalent attitudes towards the tobacco industry, from which it has accepted significant funding in disregard of the recommendations of the International Federation of Red Cross. Against this backdrop, it is wishful thinking to imagine that tobacco sales and consumption in Italy will be substantially reduced in the near future. To counteract this situation, more than 30 Italian scientific associations/organisations launched a Manifesto, so far ignored by public authorities, indicating a set of measures whose gradual implementation at country level may lead to a tobacco endgame within the next few decades. Authors of this article would like to express their support for Pope Francis’ enlightened decision and plead with politicians worldwide to follow his example, thus acting more decisively against tobacco.