bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in the nature of environmental limitation in two forest herbs during two decades of forest succession
Authors: Baeten Lander , Verheyen Kris
Published: May 2017

Aims

The environmental legacies of past land use generally have an important impact on the establishment and persistence of forest understorey plant species in post‐agricultural forests. Here we studied how the nature of such environmental limitation changes during the first decades of forest development.

Location

Deciduous forest ‘Muizenbos’, northern Belgium.

Methods

Two forest herbs with comparable life‐history traits, but contrasting rates of post‐agricultural forest colonization (Primula elatior, Geum urbanum) were introduced 18 yr ago. Introduction sites were ancient or post‐agricultural forest; seeds or adults were added to permanent plots where the understorey vegetation was initially cleared or left undisturbed. We measured chemical soil conditions and recorded the understorey plant community to characterize the sites. The effects of the treatments (land use, vegetation clearing) were tested on the present‐day occurrence and abundance of the introduced species across the plots. We also quantified whether the temporal changes in the total number of individuals per site was different between the two land‐use types and consistent within land‐use types.

Results

Land use had an important effect on soil and vegetation. In post‐agricultural forest, the P availabilities were many times higher, the plant community diversity was lower and the competitive species were significantly more abundant compared with ancient forest. The present‐day abundance of P. elatior was significantly higher in the ancient forest sites, both for planted and seeded plots, while for G. urbanum land use had no effect. The initial vegetation clearing had a persistent effect on the establishment success of both species. The 18‐yr‐long time series showed consistent changes in the total population sizes in ancient forest: P. elatior has been expanding and G. urbanum initially increased and then declined over the past decade. In post‐agricultural forest, temporal patterns were more divergent and partly related to differences in dominant tree species: differences in acidification rates and changes in insolation caused by canopy dieback have put the populations on new and unforeseen trajectories.

Conclusions

The longer the experiment is running, the more the individual sites show separate dynamics. In general, we showed that environmental limitation affects plant colonization at least during the first two decades of secondary forest succession, but also that as the post‐agricultural forests develop, the nature of environmental limitation changes.
Dispersal‐driven homogenization of wetland vegetation revealed from local contributions to β‐diversity
Authors: Deane David C. , Fordham Damien A. , Stevens Alys K. , Bradshaw Corey J.A.
Published: May 2017

Questions

Within a meta‐community, what determines how local species composition differs from the regional community? How do local conditions and landscape context affect this differentiation in wetland vegetation?

Location

Fleurieu Peninsula, South Australia.

Methods

We sampled native vegetation across 26 hydrological gradients in a wetland meta‐community within a heavily cleared agricultural landscape. We used the local contribution to β‐diversity to quantify how species composition at each site differed from the average across all sites. We hypothesized that local contribution to β‐diversity would respond to assembly processes (niche, biological interactions, dispersal) through effects on the species turnover and richness difference components of β‐diversity. We used beta regression to model local contribution to β‐diversity, building a candidate set of 55 models, each incorporating one of the assembly processes. We used standardized regression coefficients to measure effect size, and null models to explore diversity patterns further.

Results

While variations in among‐site niche dimensions were influential, the strongest control on local contribution to β‐diversity was a negative association with the number of wetlands within 200 m. Null models showed this was because common species were over‐represented in well‐connected sites within the meta‐community, while rare species were under‐represented.

Conclusions

Our results demonstrate the homogenization of native plant species composition in well‐connected wetlands, consistent with theoretical predictions of declining β‐diversity when connectivity is high. We recommend comparative analysis of local species composition to regional average diversity to evaluate the role of wetland connectivity in homogenization of composition before conservation or restoration priorities are assigned.
The bicellular tensile force sorts the localization of LSRs in bicellular and tricellular junctions
Authors: Kohno Takayuki , Kikuchi Shin , Ninomiya Takafumi , Kojima Takashi
Published: May 2017

Lipolysis‐stimulated lipoprotein receptors (LSRs) localize to tricellular tight junctions. Recent studies have shown that changes in the localization and expression profiles of LSRs are associated with malignancy of endometrial carcinomas, although the precise mechanisms by which malignant progression induces changes in the localization of LSRs are still unknown. In this study, we found that changes in cell tension correlated with alterations in the junctional localization of LSRs in endometrial cancer Sawano cells. At high cell densities, myosin phosphatase target subunit 1 (MYPT1) localized to bicellular junctions, whereas activated myosin regulatory light chain 2 (MRLC2) was dislocated from these regions, suggesting that circumferential tensile forces decreased at high cell densities. Under these conditions, LSRs localized to tricellular junctions. In contrast, a phosphorylated form of MRLC2 localized to bicellular regions, while MYPT1 was excluded from these regions, suggesting that tensile forces formed along the circumferential edge at low cell densities. It is noteworthy that, when cells were cultured under these conditions, LSRs localized to bicellular regions. Upon treatment with a myosin inhibitor, LSR localization in bicellular junctions decreased at low cell densities. Overall, our results indicate that the modulation of cellular tension was involved in the translocation of LSRs from bicellular to tricellular tight junctions.
Carnivoran resource and habitat use in the context of a Late Miocene faunal turnover episode
Authors: Domingo Laura , Domingo M. Soledad , Koch Paul L. , Morales Jorge , Alberdi M. Teresa
Published: May 2017

We investigate resource and habitat use by apex predators through stable isotope analysis at two Spanish Late Miocene localities: Los Valles de Fuentidueña (~9.6 Ma,LVF) and Cerro de los Batallones (~9.1 Ma,BAT). The temporal window represented byLVFandBATwas crucial in the shaping of the current Iberian mammalian structure because it corresponds to the initial stages of a faunal turnover episode and regional environmental change at ~9.5–8.5 Ma (Vallesian–Turolian transition), associated with an increase in the seasonality of precipitation. Herbivore and carnivore δ13C and δ18O values do not point to significant changes in either the vegetation cover (a woodland to mesic C3grassland) or the hydrological regime during the time lapse represented betweenLVFandBAT. This suggests that the environmental shift recorded around the Vallesian–Turolian boundary may have occurred later in time, sinceLVFandBATages are synchronic with the onset of the turnover event. From the standpoint of predator–prey evaluation by means of stable isotope analysis, statisticalpost hoctests, mixing model output, and the assessment of niche occupation byLVFandBATcarnivores point to high levels of interspecific competition among large active carnivores, albeit some genera, such as the amphicyonidMagericyonand specially the hyaenidLycyaena, seemed to avoid competition by taking prey from a more open habitat. Despite the drop in diversity and change in faunal components observed between theLVFandBATassemblages, a high degree of resource and habitat competition is evident from stable isotope data.
Domestication rewired gene expression and nucleotide diversity patterns in tomato
Authors: Sauvage Christopher , Rau Andrea , Aichholz Charlotte , Chadoeuf Joël , Sarah Gautier , Ruiz Manuel , Santoni Sylvain , Causse Mathilde , David Jacques , Glémin Sylvain
Published: May 2017

Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co‐expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co‐expressedDEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co‐expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific toDEG. Our study provides an extensive profiling of the rewiring of gene co‐expression induced by the domestication syndrome in one of the main crop species.
Comprehensive profiling of rhizome‐associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)
Authors: Wang Taotao , Wang Huiyuan , Cai Dawei , Gao Yubang , Zhang Hangxiao , Wang Yongsheng , Lin Chentao , Ma Liuyin , Gu Lianfeng
Published: May 2017

Moso bamboo (Phyllostachys edulis) represents one of the fastest‐spreading plants in the world, due in part to its well‐developed rhizome system. However, the post‐transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single‐molecule long‐read sequencing technology and polyadenylation site sequencing (PAS‐seq) to re‐annotate the bamboo genome, and identify genome‐wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full‐length non‐chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis‐annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron‐containing full‐length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome‐root system were identified. Taken together, these results suggest that post‐transcriptional regulation may potentially have a vital role in the underground rhizome‐root system.
Relationships between soil properties and the occurrence of the most agronomically important weed species in the field margins of eastern Arkansas – implications for weed management in field margins
Authors: Korres N E , Norsworthy J K , Brye K R , Skinner V , Mauromoustakos A
Published: May 2017

The work presented in this study adds to previous research on the occurrence, distribution and growth habitat of common weeds along roadsides in the Mississippi River Delta region of eastern Arkansas, USA. It addresses the relationships between soil properties (i.e. defined as a group of individual soil characteristics or attributes such as P, K, Ca, Mn and other nutrients) and the most agronomically important weeds of which the occurrence at field margins accounted for ≥ 10% of the total sampling sites. These were three broad‐leaved weeds (Amaranthus palmeri, Ipomoea spp. and Sida spinosa) and four grass weeds (Echinochloa crus‐galli, Urochloa platyphylla, Sorghum halepense and Digitaria sanguinalis). Soil properties were used as explanatory variables for weed occurrence (presence–absence) using partition analysis; the occurrences of the weeds under examination were partitioned by the application of a decision‐tree method. The most important soil properties explaining the occurrence of these weeds in field margins were extractable soil nutrients, specifically sodium, boron and copper content, as well as soil physical attributes, in order of importance, bulk density, silt content, field moisture capacity, hydraulic conductivity, wilting point, available water and clay content. Soil chemical properties proved least reliable in explaining weed occurrence at roadside field margins. Knowledge of the relationships between soil properties and weed occurrence can add to our understanding of weed biology and hence enhance the efficiency of weed management strategies. For example, the occurrence of A. palmeri, in soils with high bulk density (>1.4 g cm−3) and low organic matter content (<2.7%) and thus lower residual herbicide activity, will require integrated weed management of this species in field margins. This is of interest given the occurrence of herbicide resistance in roadside arable weeds, mainly A. palmeri, E. crus‐galli and S. halepense, in the Mississippi River Delta region of eastern Arkansas and other parts of the world.
First description of iolinid mites (Acari: Tydeoidea) from Brazil
Authors: Da Silva Guilherme Liberato , Da-Costa Tairis , Ferraz Célia Siqueira , Pallini Ângelo , Ferla Noeli Juarez
Published: May 2017

The family Iolinidae is recorded from Brazil for the first time. Two new species: Pausia litchiae n. sp. and Pseudopronematulus nadirae n. sp. collected from leaves of Litchi chinensis Sonn. (Sapindaceae) at Viçosa County, Minas Gerais State are described and illustrated.
“Living” dynamics of filamentous bacteria on an adherent surface under hydrodynamic exposure
Authors: Jahnke Justin P. , Smith Austin M. , Zander Nicole E. , Wiedorn Victoria , Strawhecker Kenneth E. , Terrell Jessica L. , Stratis-Cullum Dimitra N. , Cheng Xuanhong
Published: May 2017

The potential advantages of cell-based biohybrid devices over conventional nonliving systems drive the interest to control the behavior of the underlying biological cells in microdevices. Here, the authors studied how shear influenced the geometry and elongation of fimbriated filaments on affinity substrates. The cells were engineered to express FimH, which binds to mannose with a high affinity. A microfluidic channel was functionalized with RNAse B, which is rich in mannose residues, and the device was used to control the hydrodynamic force on live Escherichia coli under filamentous growth. It was discovered that filamentous E. coli cells adopt buckled geometry when the shear rate is low, but assume an extended geometry at high shear and align with the flow direction. The extension moves from bidirectional to preferentially downstream as the shear rate increases. Furthermore, living filaments slide easily on the substrate, and detach from the substrates at a rate nearly ten times greater than unfilamented live E. coli at high shear conditions (1000–4000 s−1). The hydrodynamic force and binding force experienced by the cells are further analyzed by COMSOL simulation and atomic force microscopy measurements, respectively, to explore the mechanism behind the living cell dynamics. Knowledge from this work helps guide design of interfacial properties and shear environments to control the geometry of living filamentous bacteria.
Voltage-amplitude-controlled complementary and self-compliance bipolar resistive switching of slender filaments in Pt/HfO2/HfOx/Pt memory devices
Authors: Yang Mei , Wang Hong , Ma Xiaohua , Gao Haixia , Hao Yue
Published: May 2017

Complementary resistive switching (CRS) in single devices without internal electrodes is attractive in high-density memory applications because it simplifies fabrication and avoids the complicated controlling and matching needed when using two resistive switching (RS) devices, as in conventional CRS devices. To improve the performance of such devices, however, the CRS mechanism must be understood further. Here, the authors report on voltage-amplitude-controlled CRS and self-compliance opposite-polarity bipolar RS in Pt/HfO2/HfOx/Pt memory devices. In these devices, CRS showed an almost symmetrical current–voltage hysteresis loop. Both the set voltages and hopping conduction mechanism of the high resistance states in both the bipolar RS were consistent with those of the CRS. An excess current beyond Ohmic conduction appeared before the reset switching in the bipolar RS. To interpret the characteristics of the CRS and bipolar RS, the authors propose a slender conductive filament model. According to this model, a limited oxygen vacancy (Vo) source, high Vo diffusion barrier, small film thickness, and concentrated electric field all contribute to the formation of slender filaments and to CRS operations. The model also suggests that a slender filament might form in a layer of multilayer junctions, which allows for different layers to play specific roles and improve device performance.
Catalyst free growth of highly crystalline ZnO nanopillars on c-GaN/sapphire templates by chemical vapor deposition technique
Authors: Saroj Rajendra K. , Barick Barun K. , Dhar Shubhabrata
Published: May 2017

The catalyst free growth of a large density of highly oriented ZnO nanopillars on c-GaN/sapphire templates has been demonstrated through a chemical vapor deposition route. The pillars are found to have a narrow distribution of height and diameter. It has been observed that the morphology of the growth can be varied from entirely continuous epitaxial layer to oriented nanopillars by controlling the growth temperature and growth duration. These parameters can also be adjusted to control the average diameter and height of these pillars. The authors attribute the formation of nanopillars to a two dimension to three dimension transition of the growth mode as a result of an abrupt change of Zn to oxygen flux ratio upon the closure of oxygen flow into the reactor at the end of the growth.
Review Article: Unraveling synergistic effects in plasma-surface processes by means of beam experiments
Authors: von Keudell Achim , Corbella Carles
Published: May 2017

The interaction of plasmas with surfaces is dominated by synergistic effects between incident ions and radicals. Film growth is accelerated by the ions, providing adsorption sites for incoming radicals. Chemical etching is accelerated by incident ions when chemical etching products are removed from the surface by ion sputtering. The latter is the essence of anisotropic etching in microelectronics, as elucidated by the seminal paper of Coburn and Winters [J. Appl. Phys. 50, 3189 (1979)]. However, ion-radical-synergisms play also an important role in a multitude of other systems, which are described in this article: (1) hydrocarbon thin film growth from methyl radicals and hydrogen atoms; (2) hydrocarbon thin film etching by ions and reactive neutrals; (3) plasma inactivation of bacteria; (4) plasma treatment of polymers; and (5) oxidation mechanisms during reactive magnetron sputtering of metal targets. All these mechanisms are unraveled by using a particle beam experiment to mimic the plasma–surface interface with the advantage of being able to control the species fluxes independently. It clearly shows that the mechanisms in action that had been described by Coburn and Winters [J. Appl. Phys. 50, 3189 (1979)] are ubiquitous.
Noise exposure-response relationships established from repeated binary observations: Modeling approaches and applications
Authors: Schäffer Beat , Pieren Reto , Mendolia Franco , Basner Mathias , Brink Mark
Published: May 2017

Noise exposure-response relationships are used to estimate the effects of noise on individuals or a population. Such relationships may be derived from independent or repeated binary observations, and modeled by different statistical methods. Depending on the method by which they were established, their application in population risk assessment or estimation of individual responses may yield different results, i.e., predict “weaker” or “stronger” effects. As far as the present body of literature on noise effect studies is concerned, however, the underlying statistical methodology to establish exposure-response relationships has not always been paid sufficient attention. This paper gives an overview on two statistical approaches (subject-specific and population-averaged logistic regression analysis) to establish noise exposure-response relationships from repeated binary observations, and their appropriate applications. The considerations are illustrated with data from three noise effect studies, estimating also the magnitude of differences in results when applying exposure-response relationships derived from the two statistical approaches. Depending on the underlying data set and the probability range of the binary variable it covers, the two approaches yield similar to very different results. The adequate choice of a specific statistical approach and its application in subsequent studies, both depending on the research question, are therefore crucial.
Sound propagation in a continuously stratified laboratory ocean model
Authors: Zhang Likun , Swinney Harry L.
Published: May 2017

The propagation of sound in a density-stratified fluid is examined in an experiment with a tank of salty water whose density increases continuously from the fluid surface to the tank bottom. Measurements of the height dependence of the fluid density are used to calculate the height dependence of the fluid salinity and sound speed. The height-dependent sound speed is then used to calculate the refraction of sound rays. Sound propagation in the fluid is measured in three dimensions and compared with the ray analysis. This study provides a basis for laboratory modeling of underwater sound propagation in the fluctuating stratified oceans.
Marathon Specialization in Elites: A Head Start for Africans
Authors: Noble Tyler J. , Chapman Robert F.
Published: May 2017

Purpose: To assess differences in event-specific specialization between elite African and non-African male marathon runners based on age, performance, and career length. Methods: The top 90 African marathoners from 2001 to 2015 were compared with the top 90 non-African marathoners from the same time period across various markers related to specialization age, performance, and career length. Independent t tests were used to identify significant differences (P < .05) between the African and non-African groups. Linear regression was used to explore the relationship between first half-marathon and best full-marathon performance. A 1-way ANOVA and Bonferroni correction was used to assess differences in specialization age and rates of performance improvement and decline. Results: African marathoners were found to specialize, reach peak levels of performance, and retire at younger ages than non-African marathoners (P < .001). In addition, African marathoners were found to be faster at these same career time points and in half-marathon performance (P < .001). There was no significant difference in the number of career marathons run between groups, but African marathoners were found to race more frequently than non-African marathoners (P < .001). Half-marathon performance was positively correlated with marathon performance (r2 = .67). Marathon athletes who specialized at early ages experienced significantly higher rates of improvement than those who specialized at older ages. (P < .05). Conclusions: The findings suggest that elite African marathoners achieve a greater level of performance at younger ages than their non-African counterparts. Furthermore, current marathon talent-identification practice may benefit from using half-marathon performance.
Sex Differences in World-Record Performance: The Influence of Sport Discipline and Competition Duration
Authors: Sandbakk Øyvind , Solli Guro Strøm , Holmberg Hans-Christer
Published: May 2017

The current review summarizes scientific knowledge concerning sex differences in world-record performance and the influence of sport discipline and competition duration. In addition, the way that physiological factors relate to sex dimorphism is discussed. While cultural factors played a major role in the rapid improvement of performance of women relative to men up until the 1990s, sex differences between the world’s best athletes in most events have remained relatively stable at approximately 8–12%. The exceptions are events in which upper-body power is a major contributor, where this difference is more than 12%, and ultraendurance swimming, where the gap is now less than 5%. The physiological advantages in men include a larger body size with more skeletal-muscle mass, a lower percentage of body fat, and greater maximal delivery of anaerobic and aerobic energy. The greater strength and anaerobic capacity in men normally disappear when normalized for fat-free body mass, whereas the higher hemoglobin concentrations lead to 5–10% greater maximal oxygen uptake in men with such normalization. The higher percentage of muscle mass in the upper body of men results in a particularly large sex difference in power production during upper-body exercise. While the exercise efficiency of men and women is usually similar, women have a better capacity to metabolize fat and demonstrate better hydrodynamics and more even pacing, which may be advantageous, in particular during long-lasting swimming competitions.
Sound Intensity Levels of Volume Settings on Cardiovascular Entertainment Systems in a University Wellness Center
Authors: Nathan Garrett , Britten Frederick , Burnett Jeffrey
Published: May 2017

As wellness centers across the nation continue to expand and entertain its patrons, a potential serious health issue may become more prevalent. When using the integrated entertainment systems within the cardiovascular equipment, intensity levels are able to reach levels that could contribute to noise-induced hearing loss. This research discovered that volume settings that are a part of the integrated entertainment systems of this equipment can reach intensity levels that exceed a safe listening level. In addition, the manufacturer default volume settings were found to be borderline at safe listening levels. This research identified excessive sound intensity levels at specific volume settings on three different types of cardiovascular equipment. Fitness administrators, professionals in hearing science, and wellness center patrons should collaborate to understand the potential impact for hearing loss when listening to this equipment at excessive sound intensity levels.
Recreation Center Utilization Affects Academic Outcomes
Authors: Roddy LesleyAnne , Pohle-Krauza Rachael J. , Geltz Becky
Published: May 2017

This study described the association between students' use of a university recreation center and concomitant achieved cumulative grade point average (GPA). Data were derived retrospectively from undergraduate student records from 12 consecutive months ( N = 6,098). Results showed that in general, use of the recreation center on campus was beneficial to a student's academic performance, where female students who visited the facility more often had higher GPAs on average. When GPAs were considered categorically for all students, however, those with the very lowest academic performance were characterized by a very high pattern of use, indicating that there may be a threshold benefit to center utilization.
Deciphering MCR-2 Colistin Resistance
Authors: Sun Jian , Xu Yongchang , Gao Rongsui , Lin Jingxia , Wei Wenhui , Srinivas Swaminath , Li Defeng , Yang Run-Shi , Li Xing-Ping , Liao Xiao-Ping , Liu Ya-Hong , Feng Youjun
Published: May 2017

Antibiotic resistance is a prevalent problem in public health worldwide. In general, the carbapenem β-lactam antibiotics are considered a final resort against lethal infections by multidrug-resistant bacteria. Colistin is a cationic polypeptide antibiotic and acts as the last line of defense for treatment of carbapenem-resistant bacteria. Very recently, a new plasmid-borne colistin resistance gene,
mcr-2
, was revealed soon after the discovery of the paradigm gene
mcr-1
, which has disseminated globally. However, the molecular mechanisms for MCR-2 colistin resistance are poorly understood. Here we show a unique transposon unit that facilitates the acquisition and transfer of
mcr-2
. Evolutionary analyses suggested that both MCR-2 and MCR-1 might be traced to their cousin phosphoethanolamine (PEA) lipid A transferase from a known polymyxin producer,
Paenibacillus
. Transcriptional analyses showed that the level of
mcr-2
transcripts is relatively higher than that of
mcr-1
. Genetic deletions revealed that the transmembrane regions (TM1 and TM2) of both MCR-1 and MCR-2 are critical for their location and function in bacterial periplasm, and domain swapping indicated that the TM2 is more efficient than TM1. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) confirmed that all four MCR proteins (MCR-1, MCR-2, and two chimeric versions [TM1-MCR-2 and TM2-MCR-1]) can catalyze chemical modification of lipid A moiety anchored on lipopolysaccharide (LPS) with the addition of phosphoethanolamine to the phosphate group at the 4′ position of the sugar. Structure-guided site-directed mutagenesis defined an essential 6-residue-requiring zinc-binding/catalytic motif for MCR-2 colistin resistance. The results further our mechanistic understanding of transferable colistin resistance, providing clues to improve clinical therapeutics targeting severe infections by MCR-2-containing pathogens.

IMPORTANCE
Carbapenem and colistin are the last line of refuge in fighting multidrug-resistant Gram-negative pathogens. MCR-2 is a newly emerging variant of the mobilized colistin resistance protein MCR-1, posing a potential challenge to public health. Here we report transfer of the
mcr-2
gene by a unique transposal event and its possible origin. Distribution of MCR-2 in bacterial periplasm is proposed to be a prerequisite for its role in the context of biochemistry and the colistin resistance. We also define the genetic requirement of a zinc-binding/catalytic motif for MCR-2 colistin resistance. This represents a glimpse of transferable colistin resistance by MCR-2.
The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals
Authors: Franco-Obregón Alfredo , Gilbert Jack A.
Published: May 2017

Lynn Margulis in the 1960s elegantly proposed a shared phylogenetic history between bacteria and mitochondria; this relationship has since become a cornerstone of modern cellular biology. Yet, an interesting facet of the interaction between the microbiome and mitochondria has been mostly ignored, that of the systems biology relationship that underpins host health and longevity.
Do outcomes after kidney transplantation differ for black patients in England versus New York State? A comparative, population-cohort analysis
Authors: Tahir Sanna , Gillott Holly , Jackson-Spence Francesca , Nath Jay , Mytton Jemma , Evison Felicity , Sharif Adnan
Published: May 2017

Objectives

Inferior outcomes for black kidney transplant recipients in the USA may not be generalisable elsewhere. In this population cohort analysis, we compared outcomes for black kidney transplant patients in England versus New York State.

Design

Retrospective, comparative, population cohort study utilising administrative data registries.

Settings and participants

English data were derived from Hospital Episode Statistics, while New York State data were derived from Statewide Planning and Research Cooperative System. All adults receiving their first kidney-alone allograft between 2003 and 2013 were eligible for inclusion.

Measures

The primary outcome measure was mortality post kidney transplantation (including inhospital death, 30-day mortality and 1-year mortality). Secondary outcome measures included postoperative admission length of stay, risk of rehospitalisation, development of cardiac events, stroke, cancer or fracture and finally transplant rejection/failure. Cox proportional hazards regression was used to investigate relationship between ethnicity, country and outcome.

Results

Black patients comprised 6.5% of the English cohort (n=1215/18 493) and 23.0% of the New York State cohort (n=2660/11 602). Compared with New York State, black kidney transplant recipients in England were more likely younger, male, living-donor kidney recipients and had dissimilar medical comorbidities. Inpatient mortality was not statistically different, but death within 30 days, 1 year or kidney transplant rejection/failure was lower among black patients in England versus black patients in New York State. In adjusted regression analysis, with black ethnicity the reference group, white patients had reduced risk for 30-day mortality (OR 0.62 (95% CI 0.44 to 0.86)) and 1-year mortality (OR 0.79 (95% CI 0.63 to 0.99)) in New York State but no difference was observed in England. Compared with England, black kidney transplant patients in New York State had increased HR for kidney transplant rejection rejection/failure by median follow-up (HR 2.15, 95% CI 1.91 to 2.43).

Conclusions

Outcomes after kidney transplantation for black patients may not be translatable between countries.
Association of endotoxaemia with serum free fatty acids in metabolically healthy and unhealthy abdominally obese individuals: a case–control study in northwest of Iran
Authors: Saghafi-Asl Maryam , Amiri Parichehr , Naghizadeh Mahsa , Ghavami Seyed Mostafa , Karamzad Nahid
Published: May 2017

Objectives

This study aimed to compare serum free fatty acids (FFAs) and lipopolysaccharide-binding protein (LBP) between metabolically healthy abdominally obese (MHAO) and metabolically unhealthy abdominally obese (MUAO) individuals. We also examined the association between serum FFAs and LBP in the participants.

Methods

In this age-matched and gender-matched case–control study, 164 abdominally obese subjects were recruited from June to November 2015 in the northwest of Iran. Demographic data, dietary intake, body composition, anthropometric indices and physical activity (PA) were assessed. Basal blood samples were collected to determine serum metabolic parameters, FFAs and LBP. Abdominal obesity was defined as having waist circumference ≥95 cm. Those with three or more metabolic alterations were defined as MUAO and those having two or less were classified as MHAO. Data were analysed using SPSS V.17.0.

Results

There were no significant differences in dietary intake, anthropometric indices, body composition and PA between the two groups. The odds of MUAO significantly increased by increments in serum fasting blood sugar (OR 3.79, 95% CI 2.25 to 6.40), triglycerides (OR 1.10, 95% CI 1.05 to 1.15), systolic blood pressure (OR 1.02, 95% CI 1.00 to 1.04) and diastolic blood pressure (OR 1.03, 95% CI 1.01 to 1.06) and decreased by increase in serum high-density lipoprotein cholesterol (OR 0.32, 95% CI 0.20 to 0.52). The levels of LBP and FFAs showed no significant differences between the two groups. However, significant correlations were found between LBP and FFAs in pooled population (r=0.712; p<0.001) as well as in cases (r=0.717; p<0.001) and controls (r=0.704; p<0.001). Neither FFAs nor LBP were significantly correlated with dietary intake or metabolic parameters (p>0.05).

Conclusion

The results indicated that serum LBP and FFAs are highly correlated both in MHAO and MUAO states. In addition, the levels of LBP and FFAs seem to be more related to abdominal obesity than to the presence or absence of metabolic health.
Staying connected: Service-specific orientation can be successfully achieved using a mobile application for onboarding care providers
Authors: Chreiman Kristen M , Prakash Priya S , Martin Niels D , Kim Patrick K , Mehta Samir , McGinnis Kelly , Gallagher John J , Reilly Patrick M
Published: May 2017

Communicating service-specific practice patterns, guidelines, and provider information to a new team of learners that rotate frequently can be challenging. Leveraging individual and healthcare electronic resources, a mobile device platform was implemented into a newly revised resident onboarding process. We hypothesized that offering an easy-to-use mobile application would improve communication across multiple disciplines as well as improve provider experiences when transitioning to a new rotation. A mobile platform was created and deployed to assist with enhancing communication within a trauma service and its resident onboarding process. The platform had resource materials such as: divisional policies, Clinical Practice Guidelines (CMGs), and onboarding manuals along with allowing for the posting of divisional events, a divisional directory that linked to direct dialing, text or email messaging, as well as on-call schedules. A mixed-methods study, including an anonymous survey, aimed at providing information on team member's impressions and usage of the mobile application was performed. Usage statistics over a 3-month period were analyzed on those providers who completed the survey. After rotation on the trauma service, trainees were asked to complete an anonymous, online survey addressing both the experience with, as well as the utility of, the mobile app. Thirty of the 37 (81%) residents and medical students completed the survey. Twenty-five (83%) trainees stated that this was their first experience rotating on the trauma service and 6 (20%) were from outside of the health system. According to those surveyed, the most useful function of the app were access to the directory (15, 50%), the divisional calendar (4, 13.3%), and the on-call schedules (3, 10%). Overall, the app was felt to be easy to use (27, 90%) and was accessed an average of 7 times per day (1–50, SD 9.67). Over half the survey respondents felt that the mobile app was helpful in completing their everyday tasks (16, 53.3%). Fifteen (50%) of the respondents stated that the app made the transition to the trauma service easier. Twenty-five (83.3%) stated it was valuable knowing about departmental events and announcements, and 17 (56.7%) felt more connected to the division. The evolution of mobile technology is rapidly becoming fundamental in medical education and training. We found that integrating a service-specific mobile application improved the learner's experience when transitioning to a new service and was a valuable onboarding instrument.

Level of evidenceIV.
Application of one-class support vector machine to quickly identify multivariate anomalies from geochemical exploration data
Authors: Chen Yongliang , Wu Wei
Published: May 2017

Identifying multivariate anomalies from geochemical exploration data in a complex geological setting is very challenging because the complex geological setting may lead to an unknown high-dimensional distribution of the geochemical exploration data. One-class support vector machine (OCSVM) can give useful results in outlier detection in high-dimension or without any assumptions on the distribution of data. Thus, we applied the OCSVM model to identify multivariate geochemical anomalies from stream sediment survey data of the Lalingzaohuo district, an area with complex geological setting, in Qinghai Province, China. The performance of the OCSVM model was compared with that of continuous restricted Boltzmann machine (CRBM) in terms of receiver operating characteristic (ROC) curve, area under curve (
AUC
) and data-processing efficiency. The results show that the two models perform similarly well in terms of ROC and
AUC
; while their data-modeling processes spent 6.06 and 279.36 s, respectively. The anomalies identified by the OCSVM model occupy 19% of the study area and contain 82% of the known mineral deposits; and the anomalies identified by the CRBM model occupy 35% of the study area and contain 88% of the known mineral deposits.
A Load-Balancing Divide-and-Conquer SVM Solver
Authors: Chen Xiaogang , Wang Z. Jane , Ji Xiangyang
Published: May 2017

Scaling up kernel support vector machine (SVM) training has been an important topic in recent years. Despite its theoretical elegance, training kernel SVM is impractical when facing millions of data. The divide-and-conquer (DC) strategy is a natural framework of handling gigantic problems, and the divide-and-conquer solver for kernel SVM (DC-SVM) is able to train kernel SVM with millions of data with limited time cost. However, there are some drawbacks of the DC-SVM approach. First, it used an unsupervised clustering method to partition the whole problem, which is prone to construct singular subsets, and, second, it is hard to balance the computation load between sub-problems. To address these issues, this article proposed a load-balancing partition method for kernel SVM. First, it clusters sample from one class and then assigns data samples to the cluster centers by a distance measure and construct sub-problems; in this way, it is able to control the computation load and avoid singular problems. Experimental results show that the proposed method has better load-balancing performance than DC-SVM, which implies that it is suitable for distributed and embedding systems.
Simulation and Experimentation Platforms for Underwater Acoustic Sensor Networks
Authors: Luo Hanjiang , Wu Kaishun , Ruby Rukhsana , Hong Feng , Guo Zhongwen , Ni Lionel M.
Published: May 2017

Ocean and water basically cover the major parts of our planet. To obtain the best utilization of the underlying resources on these parts of the Earth, people have made some research advancements. Specifically, the research on underwater wireless acoustic sensor networks (UWA-SNs) has made great progress. However, wide deployment of UWA-SNs is far from a reality due to several reasons. One important reason is that offshore deployment and field-level experiments of ocean-centric applications are both expensive and labor intensive. Other alternatives to attain this objective are to conduct simulation or experimentation that can reduce cost and accelerate the research activities and their outcomes. However, designing efficient and reliable simulation and experimentation platforms have proven to be more challenging beyond the expectation. In this article, we explore the main techniques (including their pros and cons) and components to develop simulation and experimentation platforms and provide a comprehensive survey report in this area. We classify simulation and experimentation platforms based on some typical criteria and then provide useful guidelines for researchers on choosing suitable platforms in accordance with their requirements. Finally, we address some open and un-resolved issues in this context and provide some suggestions on future research.
An Indexing Framework for Queries on Probabilistic Graphs
Authors: Maniu Silviu , Cheng Reynold , Senellart Pierre
Published: May 2017

Information in many applications, such as mobile wireless systems, social networks, and road networks, is captured by graphs. In many cases, such information is uncertain. We study the problem of querying a probabilistic graph, in which vertices are connected to each other probabilistically. In particular, we examine “source-to-target” queries (ST-queries), such as computing the shortest path between two vertices. The major difference with the deterministic setting is that query answers are enriched with probabilistic annotations. Evaluating ST-queries over probabilistic graphs is #P-hard, as it requires examining an exponential number of “possible worlds”—database instances generated from the probabilistic graph. Existing solutions to the ST-query problem, which sample possible worlds, have two downsides: (i) a possible world can be very large and (ii) many samples are needed for reasonable accuracy. To tackle these issues, we study the
ProbTree
, a data structure that stores a succinct, or
indexed
, version of the possible worlds of the graph. Existing ST-query solutions are executed on top of this structure, with the number of samples and sizes of the possible worlds reduced. We examine lossless and lossy methods for generating the ProbTree, which reflect the tradeoff between the accuracy and efficiency of query evaluation. We analyze the correctness and complexity of these approaches. Our extensive experiments on real datasets show that the ProbTree is fast to generate and small in size. It also enhances the accuracy and efficiency of existing ST-query algorithms significantly.
A Survey of Techniques for Cache Partitioning in Multicore Processors
Authors: Mittal Sparsh
Published: May 2017

As the number of on-chip cores and memory demands of applications increase, judicious management of cache resources has become not merely attractive but imperative. Cache partitioning, that is, dividing cache space between applications based on their memory demands, is a promising approach to provide capacity benefits of shared cache with performance isolation of private caches. However, naively partitioning the cache may lead to performance loss, unfairness, and lack of quality-of-service guarantees. It is clear that intelligent techniques are required for realizing the full potential of cache partitioning. In this article, we present a survey of techniques for partitioning shared caches in multicore processors. We categorize the techniques based on important characteristics and provide a bird’s eye view of the field of cache partitioning.
A Single-Molecule View of Genome Editing Proteins: Biophysical Mechanisms for TALEs and CRISPR/Cas9
Authors: Cuculis Luke , Schroeder Charles M.
Published: May 2017

Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In this review, we discuss the application of single-molecule techniques to uncover the mechanisms behind two premier classes of genome editing proteins: transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). These technologies have facilitated a striking number of gene editing applications in a variety of organisms; however, we are only beginning to understand the molecular mechanisms governing the DNA editing properties of these systems. Here, we discuss the DNA search and recognition process for TALEs and Cas9 that have been revealed by recent single-molecule experiments.
Ecology and Genomic Insights into Plant-Pathogenic and Plant-Nonpathogenic Endophytes
Authors: Brader Günter , Compant Stéphane , Vescio Kathryn , Mitter Birgit , Trognitz Friederike , Ma Li-Jun , Sessitsch Angela
Published: May 2017

Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.