bluuebunny/crossref_metadata_2025 huggingface dataset:
Liver function may play an uneven role in haemorrhagic transformation for stroke subtypes after acute ischaemic stroke
Authors: Tan G. , Lei C. , Hao Z. , Chen Y. , Yuan R. , Liu M.
Published: November 2015

Background and purpose

Haemorrhagic transformation (HT) is common after acute ischaemic stroke. Whether liver function plays a role in HT remains an open question.

Methods

Acute ischaemic stroke patients within 7 days from stroke onset were included. Baseline data including liver function tests were collected. An independent association between liver function and HT was identified by multivariate regression analysis for stroke overall and stroke subtypes.

Results

A total of 2788 patients were included. HT occurred in 277 patients (9.9%), with 32 patients (1.1%) with symptomatic HT and 245 patients (8.8%) with asymptomatic HT. On multivariate regression analysis, aspartate aminotransferase (AST) and bilirubin (BILI) were independently associated with HT for stroke overall. In different stroke subtypes, AST was independently associated with HT for cardioembolic stroke, BILI for stroke of undetermined aetiology, and no liver function indicators for stroke of large‐artery atherosclerosis and small‐artery occlusion.

Conclusions

Liver function played an uneven role in HT for different stroke subtypes. Indicators of liver function independently associated with HT were AST for cardioembolic stroke, BILI for stroke of undetermined aetiology and none for stroke of large‐artery atherosclerosis and small‐artery occlusion.
Laryngeal motility alteration: A missing link between sleep apnea and vagus nerve stimulation for epilepsy
Authors: Zambrelli Elena , Saibene Alberto M. , Furia Francesca , Chiesa Valentina , Vignoli Aglaia , Pipolo Carlotta , Felisati Giovanni , Canevini Maria Paola
Published: November 2015

This study aimed to evaluate the prevalence and the relationship of sleep breathing disorders (SBDs) and laryngeal motility alterations in patients with drug‐resistant epilepsy after vagus nerve stimulator (VNS) implantation. Twenty‐three consecutive patients with medically refractory epilepsy underwent out‐of‐center sleep testing before and after VNS implantation. Eighteen eligible subjects underwent endoscopic laryngeal examination post‐VNS implantation. Statistical analysis was carried out to assess an association between laryngeal motility alterations and the onset/worsening of SBDs. After VNS implantation, 11 patients showed a new‐onset mild/moderate SBD. Half of the patients already affected by obstructive sleep apnea (OSA) showed worsening of SBD. All of the patients with a new‐onset OSA had a laryngeal pattern with left vocal cord adduction (LVCA) during VNS stimulation. The association between VNS‐induced LVCA and SBD was statistically significant. This study suggests an association between VNS and SBD, hinting to a pivotal role of laryngeal motility alterations. The relationship between SBD and VNS‐induced LVCA supports the need to routinely investigate sleep respiratory and laryngeal motility patterns before and after VNS implantation.
Are self‐etch adhesive systems effective in the retention of occlusal sealants? A systematic review and meta‐analysis
Authors: Botton Graziela , Morgental Caroline Sonego , Scherer Maitê Munhoz , Lenzi Tathiane Larissa , Montagner Anelise Fernandes , Rocha Rachel de Oliveira
Published: November 2015

Background

Occlusal sealants are an effective method for caries prevention, although the effectiveness of different application strategies has not been established yet.

Aim

This systematic review compared the retention rate of sealants placed on occlusal surfaces following the use of self‐etch adhesive systems and traditional acid etching, with or without the application of adhesive system.

Design

Literature searching was carried out until June 2015 in PubMed/MEDLINE, CENTRAL, and ClinicalTrials databases selecting randomized clinical trials that evaluated self‐etch adhesive systems associated with pit and fissure sealants in primary or permanent molars comprising retention as outcome. From 683 potentially eligible studies, 10 were selected for full‐text analysis and 5 were included in the meta‐analysis. Two reviewers independently selected the studies, extracted the data, and assessed the bias risk. Pooled‐effect estimates were obtained by comparing the retention failure rate between groups (self‐etch systems vs acid etching with or without adhesive systems).

Results

Significant difference was found between groups, favoring the control group (prior acid etching) (P < 0.05), which showed lower failure rate in the retention of occlusal sealants. High heterogeneity was found on the meta‐analysis. Most trials showed good evidence strength.

Conclusions

Occlusal sealants applied with self‐etch systems show lower retention throughout time than sealants applied in the conventional approach, regardless of the use of adhesive systems.
Use of a fluorescence‐based camera for monitoring occlusal surfaces of primary and permanent teeth
Authors: Jablonski‐Momeni Anahita , Heinzel‐Gutenbrunner Monika , Vill Gabriel
Published: November 2015

Background

Sound teeth and incipient lesions require regular monitoring to detect possible progression of caries early on.

Aim

To evaluate the ability of the VistaProof (VP) fluorescence‐based camera for monitoring occlusal surfaces.

Design

A total of 419 posterior teeth (205 primary molars, 145 permanent molars, and 69 premolars) of 35 patients were examined (average age: 9.1 years). The occlusal surfaces were classified visually according to the criteria of the International Caries Detection and Assessment System (ICDAS). VP measurements were performed at baseline (t1), and the examinations were repeated after six (t2) and twelve month (t3). Correlation between methods was calculated using Spearman's rank correlation coefficient (rs). Wilcoxon test was used to monitor whether VP identified changes as well as ICDAS (α = 0.05).

Results

Correlations between ICDAS and VP were significantly positive (rs: 0.66–0.73, P < 0.001). No significant differences were found between all times for the ICDAS findings. Significant differences for the VP were ascertained for t1/t2 (P = 0.03). Results based on cluster randomization showed significant differences between ICDAS and VistaProof concerning the absence/presence of changes in the finding (P < 0.0005).

Conclusion

Correlation between ICDAS and VP was strong. The VP supported the findings of visual examination for monitoring occlusal surfaces, although not all changes could be detected with respect to the visual findings.
Assessment of potential public health impact of a quadrivalent inactivated influenza vaccine inThailand
Authors: Kittikraisak Wanitchaya , Chittaganpitch Malinee , Gregory Christopher J. , Laosiritaworn Yongjua , Thantithaveewat Thanawadee , Dawood Fatimah S. , Lindblade Kim A.
Published: November 2015

Background

Each year, an influenza B strain representing only one influenza B lineage is included in the trivalent inactivated influenza vaccine (IIV3); a mismatch between the selected lineage and circulating viruses can result in suboptimal vaccine effectiveness. We modeled the added potential public health impact of a quadrivalent inactivated influenza vaccine (IIV4) that includes strains from both influenza B lineages compared toIIV3 on influenza‐associated morbidity and mortality in Thailand.

Methods

Using data on the incidence of influenza‐associated hospitalizations and deaths, vaccine effectiveness, and vaccine coverage from the 2007–2012 influenza seasons in Thailand, we estimated rates of influenza‐associated outcomes that might be averted usingIIV4 instead ofIIV3. We then applied these rates to national population estimates to calculate averted illnesses, hospitalizations, and deaths for each season. We assumed that the influenza B lineage included inIIV3 would provide a relative vaccine effectiveness of 75% against the other B lineage.

Results

Compared to use ofIIV3, use ofIIV4 might have led to an additional reduction ranging from 0·4 to 14·3 influenza‐associated illnesses per 100 000 population/year, <0·1 to 0·5 hospitalizations per 100 000/year, and <0·1 to 0·4 deaths per 1000/year. Based on extrapolation to national population estimates, replacement ofIIV3 withIIV4 might have averted an additional 267–9784 influenza‐associated illnesses, 9–320 hospitalizations, and 0–3 deaths.

Conclusion

Compared to use ofIIV3,IIV4 has the potential to further reduce the burden of influenza‐associated morbidity and mortality in Thailand.
MAIT cells are activated and accumulated in the inflamed mucosa of ulcerative colitis
Authors: Haga Keiichi , Chiba Asako , Shibuya Tomoyoshi , Osada Taro , Ishikawa Dai , Kodani Tomohiro , Nomura Osamu , Watanabe Sumio , Miyake Sachiko
Published: November 2015

Background and Aim:

Ulcerative colitis (UC) is a chronic, relapsing and remitting, inflammatory disorder of the large intestine. Mucosal associated invariant T (MAIT) cells are a member of innate‐like lymphocytes found abundantly in the mucosal tissue. The contribution of MAIT cells in the pathogenesis of UC is still unclear; therefore, this study aimed at investigating the role of these cells in patients with UC.

Methods:

The frequency of MAIT cells, as well as the production of cytokines and expression levels of activation markers by these cells in the peripheral blood of UC patients and healthy controls, was analyzed by flow cytometry. MAIT cells were also quantified in colon biopsies of UC patients using a confocal microscope.

Results:

There was a significant reduction in MAIT cell frequency in the peripheral blood of UC patients compared with healthy controls (P < 0.0001). MAIT cells from UC patients secreted more interleukin (IL)‐17 than healthy controls (P < 0.05). The expression levels of CD69 on these cells were correlated with disease activity and endoscopic scores and plasma levels of IL‐18. Furthermore, MAIT cells increased in the inflamed mucosa, and their frequency was correlated with clinical and endoscopic disease activity in UC patients.

Conclusions:

The findings from this study indicate that MAIT cells could be associated with UC and may serve as potential biomarkers or therapeutic targets in UC.
Pain management in photoepilation
Authors: Aimonetti Jean‐Marc , Ribot‐Ciscar Edith
Published: November 2015

The hair follicle is a complex, hormonally active structure with permanent and cyclically renewed parts which are highly innervated by myelinated and unmyelinated afferent fibers. Hair removal, a very ancient practice, affects this sensory network and causes both acute and diffuse pain associated with inflammatory reaction. Optic permanent hair removal is becoming a popular alternative to traditional methods such as shaving, waxing, among other methods. These optical removal devices thermally destroy the target chromophore, that is, melanin, without damaging the surrounding skin. The increase in the skin surface temperature causes mild‐to‐severe pain, and optical hair removal has to be combined with pain relieving devices. Pain management relies on topical anesthetic agents, cooling devices, or non‐noxious cutaneous stimulation whose mechanisms of action and efficiency are discussed in this article.
The effects of polymer carrier, hot melt extrusion process and downstream processing parameters on the moisture sorption properties of amorphous solid dispersions
Authors: Feng Xin , Vo Anh , Patil Hemlata , Tiwari Roshan V , Alshetaili Abdullah S , Pimparade Manjeet B , Repka Michael A
Published: November 2015

Objective

The aim of this study was to evaluate the effect of polymer carrier, hot melt extrusion and downstream processing parameters on the water uptake properties of amorphous solid dispersions.

Methods

Three polymers and a model drug were used to prepare amorphous solid dispersions utilizing the hot melt extrusion technology. The sorption–desorption isotherms of solid dispersions and their physical mixtures were measured by the dynamic vapour sorption system, and the effects of polymer hydrophobicity, hygroscopicity, molecular weight and the hot melt extrusion process were investigated. Fourier transform infrared (FTIR) imaging was performed to understand the phase separation driven by the moisture.

Key findings

Solid dispersions with polymeric carriers with lower hydrophilicity, hygroscopicity and higher molecular weight could sorb less moisture under the high relative humidity (RH) conditions. The water uptake ability of polymer–drug solid dispersion systems were decreased compared with the physical mixture after hot melt extrusion, which might be due to the decreased surface area and porosity. The FTIR imaging indicated that the homogeneity of the drug molecularly dispersed within the polymer matrix was changed after exposure to high RH.

Conclusion

Understanding the effect of formulation and processing on the moisture sorption properties of solid dispersions is essential for the development of drug products with desired physical and chemical stability.
Uricosuric agents decrease the plasma urate level in rats by concomitant treatment with topiroxostat, a novel xanthine oxidoreductase inhibitor
Authors: Taniguchi Tetsuya , Ashizawa Naoki , Matsumoto Koji , Iwanaga Takashi , Saitoh Kazuhiro
Published: November 2015

Objectives

The aim of this study was to establish the rat model for evaluating hypouricemic effects by some uricosuric agents.

Methods

Rats were made hyperuricemic by subcutaneous administration of potassium oxonate, a uricase inhibitor, or made hypouricemic by oral administration of topiroxostat, a xanthine oxidoreductase inhibitor. Furthermore, rats were co-treated with topiroxostat and inosine, a urate precursor. In each condition, hypouricemic effects by uricosuric agents were examined.

Key findings

In potassium oxonate-treated rats, treatment with uricosuric agents such as FYU-981, F12859 and probenecid showed no hypouricemic effect. On the other hand, in topiroxostat-treated rats, uricosuric agents remarkably lowered plasma urate level compared with topiroxostat treatment alone, with a dose dependency of 30 and 100 mg/kg for FYU-981 and F12859 each. The decrease in the plasma urate level observed in the topiroxostat-treated rats disappeared by further co-treatment with inosine.

Conclusions

Effects of uricosuric agents on the plasma urate level in rats were sensitive to the rate of urate formation. Induction of slower urate formation by topiroxostat provides valuable model for evaluation of hypouricemic effects by uricosuric agents in rats.
The role of marine reserves in the replenishment of a locally impacted population of anemonefish on the Great Barrier Reef
Authors: Bonin Mary C. , Harrison Hugo B. , Williamson David H. , Frisch Ashley J. , Saenz‐Agudelo Pablo , Berumen Michael L. , Jones Geoffrey P.
Published: November 2015

The development of parentage analysis to track the dispersal of juvenile offspring has given us unprecedented insight into the population dynamics of coral reef fishes. These tools now have the potential to inform fisheries management and species conservation, particularly for small fragmented populations under threat from exploitation and disturbance. In this study, we resolve patterns of larval dispersal for a population of the anemonefish Amphiprion melanopus in the Keppel Islands (southern Great Barrier Reef). Habitat loss and fishing appear to have impacted this population and a network of no‐take marine reserves currently protects 75% of the potential breeders. Using parentage analysis, we estimate that 21% of recruitment in the island group was generated locally and that breeding adults living in reserves were responsible for 79% (31 of 39) of these of locally produced juveniles. Overall, the network of reserves was fully connected via larval dispersal; however, one reserve was identified as a critical source of larvae for the island group. The population in the Keppel Islands also appears to be well‐connected to other source populations at least 60 km away, given that 79% (145 of 184) of the juveniles sampled remained unassigned in the parentage analysis. We estimated the effective size of the A. melanopus metapopulation to be 745 (582–993 95% CI) and recommend continued monitoring of its genetic status. Maintaining connectivity with populations beyond the Keppel Islands and recovery of local recruitment habitat, potentially through active restoration of host anemone populations, will be important for its long‐term persistence.
Cascading ecological effects of landscape moderated arthropod diversity
Authors: Smith Jeffrey R. , Schmitz Oswald J.
Published: November 2015

Understanding the mechanisms regulating the diversity and distribution of arthropods is essential to understanding food web interactions and ecosystem functioning. Local arthropod diversity is known to be linked to features of surrounding landscapes, including the area of human‐developed land. Yet, how such landscape moderation of diversity affects processes within local sites remains understudied. We report on a study that 1) measured the impacts of human development surrounding old‐field habitats of arthropods on arthropod food web structure within those habitats and 2) determined if these shifts were associated with cascading impacts on the plant community. We sampled the arthropod community in 16 old‐fields that span an urban‐rural gradient throughout southern New England, USA. In each field, we also established paired mesocosms enclosing vegetation, one of which allowed arthropod herbivory while the other excluded such interactions, to isolate impacts of arthropod herbivory on three functional groups of plants: grasses, goldenrod and non‐goldenrod forbs. Biomass of both herbivorous and predatory arthropods were positively related to the proportion of natural area surrounding a field early in the growing season (June). This relationship persisted later into the season for predatory arthropods (through July), but not for herbivorous arthropods. We found no evidence that the biomass of predators was related to the abundance of herbivorous arthropods in a field; or that biomass of herbivores was correlated to change in plant biomass between the two types of mesocosms. We did, however, find that in fields with low predator abundance there was greater herbivory on grasses (nutritious host), but that in high predator fields goldenrod was increasingly impacted (safe host), as is predicted by past work in old‐field ecosystems. The findings support the generalizability of landscape moderated biodiversity to non‐agricultural systems and suggests that observed shifts in food webs have implications for community and ecosystem dynamics.
Toward an Effective Design of Behavioral Health Care Delivery: An Empirical Analysis of Care for Depression
Authors: Zepeda E. David , Sinha Kingshuk K.
Published: November 2015

A criticism of behavioral health care delivery is that it has largely missed the social determinants of behavioral health disorders and their diagnosis. Toward addressing this criticism, this study evaluates the delivery of behavioral health care as a part of primary care operations. Focusing on the treatment of depression, the study results show that: (i) primary care clinics operating in communities with superior social environment characteristics are associated with improved depression outcomes in the short term, and (ii) psychosocial resources (social and emotional support) and the built environment (man‐made resources and infrastructure to support human activity) of primary care clinics are associated with sustaining the improvement in depression outcome in the long term. Centering our attention on IT‐enabled, evidence‐based, and affordable primary care as mechanisms that can enable the integration of behavioral and medical care delivery, the results suggest that IT‐enabled and evidence‐based primary care are associated with improvements in depression outcomes. We also find that the effect of improving the affordability of behavioral health care delivery depends on the community's socioeconomic status. Primary care clinics in socioeconomically disadvantaged communities practicing cost‐containment are associated with improvements in depression outcomes, and, therefore, can contribute toward reducing disparities in behavioral health care delivery. Counter to our original expectations, we find that the effect of evidence‐based care on improvements on depression outcomes increases as the availability of medically trained behavioral health care specialists practicing in a community increases lending support to concerns that primary care clinics in resource‐rich communities obtain greater benefit from quality improvement interventions.
Robust Inference in Sample Selection Models
Authors: Zhelonkin Mikhail , Genton Marc G. , Ronchetti Elvezio
Published: November 2015

The problem of non-random sample selectivity often occurs in practice in many fields. The classical estimators introduced by Heckman are the backbone of the standard statistical analysis of these models. However, these estimators are very sensitive to small deviations from the distributional assumptions which are often not satisfied in practice. We develop a general framework to study the robustness properties of estimators and tests in sample selection models. We derive the influence function and the change-of-variance function of Heckman's two-stage estimator, and we demonstrate the non-robustness of this estimator and its estimated variance to small deviations from the model assumed. We propose a procedure for robustifying the estimator, prove its asymptotic normality and give its asymptotic variance. Both cases with and without an exclusion restriction are covered. This allows us to construct a simple robust alternative to the sample selection bias test. We illustrate the use of our new methodology in an analysis of ambulatory expenditures and we compare the performance of the classical and robust methods in a Monte Carlo simulation study.
Large eccentric strength increase using the Copenhagen Adduction exercise in football: A randomized controlled trial
Authors: Ishøi L. , Sørensen C. N. , Kaae N. M. , Jørgensen L. B. , Hölmich P. , Serner A.
Published: November 2015

Hip adductor injuries are frequent in football, and players with low adductor strength appear to be at increased risk of injury. High adductor muscle activity has been shown in the Copenhagen Adduction exercise (CA); however, an associated strength gain has not been investigated. This study aims to examine the eccentric hip adduction strength (EHAD) gain using the CA in‐season. Two U‐19 sub‐elite football teams, including 24 football players, were randomized to either an 8‐week supervised progressive training program in addition to the usual training (intervention) or to continue training as usual (control). EHAD, eccentric hip abduction strength (EHAB), and side‐bridge endurance were measured using reliable test procedures at baseline and follow‐up by a blinded tester. There was a significant interaction between group and time on EHAD, EHAB, and EHAD/EHAB ratio (P < 0.025). The intervention group demonstrated a 35.7% increase in EHAD (P < 0.001); a 20.3% increase in EHAB (P = 0.003), and 12.3% increase in EHAD/EHAB ratio (P = 0.019). No significant within‐group differences were found in the control group (P > 0.335). Compliance was 91.25%, and median muscle soreness ranged from 0 to 2. The CA implemented in‐season with an 8‐week progressive training program elicited a large significant increase in EHAD, EHAB, and EHAD/EHAB ratio.
Factors associated with playing football after anterior cruciate ligament reconstruction in female football players
Authors: Fältström A. , Hägglund M. , Kvist J.
Published: November 2015

This study investigated whether player‐related factors (demographic, personality, or psychological factors) or the characteristics of the anterior cruciate ligament (ACL) injury were associated with the return to playing football in females after ACL reconstruction (ACLR). We also compared current knee function, knee related quality of life and readiness to return to sport between females who returned to football and those who had not returned. Females who sustained a primary ACL rupture while playing football and underwent ACLR 6–36 months ago were eligible. Of the 460 contacted, 274 (60%) completed a battery of questionnaires, and 182 were included a median of 18 months (IQR 13) after ACLR. Of these, 94 (52%) returned to football and were currently playing, and 88 (48%) had not returned. Multiple logistic regression analysis identified two factors associated with returning to football: short time between injury and ACLR (0–3 months, OR 5.6; 3–12 months OR 4.7 vs reference group > 12 months) and high motivation. Current players showed higher ratings for current knee function, knee‐related quality of life, and psychological readiness to return to sport (P < 0.001). Undergoing ACLR sooner after injury and high motivation to return to sports may impact a player's return to football after ACLR.
The wheat TaGBF1 gene is involved in the blue‐light response and salt tolerance
Authors: Sun Yang , Xu Wei , Jia Yuebin , Wang Mengcheng , Xia Guangmin
Published: November 2015

Light and abiotic stress both strongly modulate plant growth and development. However, the effect of light‐responsive factors on growth and abiotic stress responses in wheat (Triticum aestivum) is unknown. G–box binding factors (GBFs) are blue light‐specific components, but their function in abiotic stress responses has not been studied. Here we identified a wheat GBF1 gene that mediated both the blue light‐ and abiotic stress‐responsive signaling pathways. TaGBF1 was inducible by blue light, salt and exposure to abscisic acid (ABA). TaGBF1 interacted with a G–box light‐responsive element in vitro and promoted a blue‐light response in wheat and Aradidopsis thaliana. Both TaGBF1 over‐expression in wheat and its heterologous expression in A. thaliana heighten sensitivity to salinity and ABA, but its knockdown in wheat conferred resistance to high salinity and ABA. The expression of AtABI5, a key component of the ABA signaling pathway in A. thaliana, and its homolog Wabi5 in wheat was increased by transgenic expression of TaGBF1. The hypersensitivity to salt and ABA caused by TaGBF1 was not observed in the abi5 mutant background, showing that ABI5 is the mediator in TaGBF1‐induced abiotic stress responses. However, the hypersensitivity to salt conferred by TaGBF1 is not dependent on light. This suggests that TaGBF1 is a common component of blue light‐ and abiotic stress‐responsive signaling pathways.
Thromboembolic outcomes after use of a four‐factor prothrombin complex concentrate for vitamin K antagonist reversal in a real‐world setting
Authors: Joseph Ranjit , Burner James , Yates Sean , Strickland Amanda , Tharpe William , Sarode Ravi
Published: November 2015

BACKGROUND

A four‐factor prothrombin complex concentrate (4F‐PCC) was recently licensed in the United States for urgent vitamin K antagonist (VKA) reversal based on two randomized clinical trials. These studies excluded patients at high risk of thrombosis; therefore, the risk of thrombotic complications in unselected patients remains a concern.

STUDY DESIGN AND METHODS

This study retrospectively evaluated the incidence of thromboembolic events (TEEs) and death in patients who received 4F‐PCC for VKA reversal. The study included 113 consecutive patients who were 18 years of age and older and were administered 4F‐PCC for VKA reversal. The incidence of TEE and deaths was evaluated for up to 60 days after PCC administration or until the end of hospitalization, whichever came later.

RESULTS

Seven (6.2%) patients developed TEEs and 17 (15%) patients died. PCC administration was probably related to TEE and subsequent death in two (1.8%) patients. Multivariate analysis revealed that a diagnosis of Factor V Leiden or antiphospholipid syndrome was predictive of TEE, and active malignancy was predictive of death.

CONCLUSION

This study supports the safety of 4F‐PCC for urgent VKA reversal even in unselected patients. The underlying type of hypercoagulable state and the dose of PCC may influence the incidence of TEE.
Designing a sampling scheme to reveal correlations between weeds and soil properties at multiple spatial scales
Authors: Metcalfe H , Milne A E , Webster R , Lark R M , Murdoch A J , Storkey J
Published: November 2015

Weeds tend to aggregate in patches within fields, and there is evidence that this is partly owing to variation in soil properties. Because the processes driving soil heterogeneity operate at various scales, the strength of the relations between soil properties and weed density would also be expected to be scale‐dependent. Quantifying these effects of scale on weed patch dynamics is essential to guide the design of discrete sampling protocols for mapping weed distribution. We developed a general method that uses novel within‐field nested sampling and residual maximum‐likelihood (reml) estimation to explore scale‐dependent relations between weeds and soil properties. We validated the method using a case study of Alopecurus myosuroides in winter wheat. Using reml, we partitioned the variance and covariance into scale‐specific components and estimated the correlations between the weed counts and soil properties at each scale. We used variograms to quantify the spatial structure in the data and to map variables by kriging. Our methodology successfully captured the effect of scale on a number of edaphic drivers of weed patchiness. The overall Pearson correlations between A. myosuroides and soil organic matter and clay content were weak and masked the stronger correlations at >50 m. Knowing how the variance was partitioned across the spatial scales, we optimised the sampling design to focus sampling effort at those scales that contributed most to the total variance. The methods have the potential to guide patch spraying of weeds by identifying areas of the field that are vulnerable to weed establishment.
Sagging ropes demonstrate transversality conditions of variational problems
Authors: Bormashenko Edward , Whyman Gene , Bormashenko Yelena , Grynyov Roman , Shulzinger Evgeny , Kazachkov Alexander
Published: November 2015

We present an account of transversality conditions of variational problems and show how they give rise to essential results in the analysis of different physical phenomena. We find such conditions to be a powerful and elegant approach to a diverse number of variational problems with free endpoints. In this work, we illustrate such condition with the study of a heavy inextensible rope sagging both symmetrically and asymmetrically between two variously shaped, steering-guide wires without friction. In such a situation, the transversality conditions lead to the orthogonality of the rope to the wires at endpoints of the rope, which we confirm experimentally. Freeing the endpoints of the rope yields exact analytical equations that predict the tension of the rope. Heavy ropes whose endpoints are free to slip between arbitrarily shaped, steering wires are discussed.
The geometrical significance of the Laplacian
Authors: Styer Daniel F.
Published: November 2015

The Laplacian operator can be defined, not only as a differential operator, but also through its averaging properties. Such a definition lends geometric significance to the operator: a large Laplacian at a point reflects a “nonconformist” (i.e., different from average) character for the function there. This point of view is used to motivate the wave equation for a drumhead.
Transient episodes of mild environmental oxygenation and oxidative continental weathering during the late Archean
Authors: Kendall Brian , Creaser Robert A. , Reinhard Christopher T. , Lyons Timothy W. , Anbar Ariel D.
Published: November 2015

Osmium isotope data from black shales show that oxidative continental weathering likely occurred episodically in the late
Archean.
Quantum entanglement at ambient conditions in a macroscopic solid-state spin ensemble
Authors: Klimov Paul V. , Falk Abram L. , Christle David J. , Dobrovitski Viatcheslav V. , Awschalom David D.
Published: November 2015

On-demand generation of many maximally entangled Bell states in a room-temperature semiconductor at low magnetic field.
Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches
Authors: Yu Pingfeng , Mathieu Jacques , Li Mengyan , Dai Zhaoyi , Alvarez Pedro J. J.
Published: November 2015

Many studies on phage biology are based on isolation methods that may inadvertently select for narrow-host-range phages. Consequently, broad-host-range phages, whose ecological significance is largely unexplored, are consistently overlooked. To enhance research on such polyvalent phages, we developed two sequential multihost isolation methods and tested both culture-dependent and culture-independent phage libraries for broad infectivity. Lytic phages isolated from activated sludge were capable of interspecies or even interorder infectivity without a significant reduction in the efficiency of plating (0.45 to 1.15). Two polyvalent phages (PX1 of thePodoviridaefamily and PEf1 of theSiphoviridaefamily) were characterized in terms of adsorption rate (3.54 × 10−10to 8.53 × 10−10ml/min), latent time (40 to 55 min), and burst size (45 to 99 PFU/cell), using different hosts. These phages were enriched with a nonpathogenic host (Pseudomonas putidaF1 orEscherichia coliK-12) and subsequently used to infect model problematic bacteria. By using a multiplicity of infection of 10 in bacterial challenge tests, >60% lethality was observed forPseudomonas aeruginosarelative to uninfected controls. The corresponding lethality forPseudomonas syringaewas ∼50%. Overall, this work suggests that polyvalent phages may be readily isolated from the environment by using different sequential hosts, and this approach should facilitate the study of their ecological significance as well as enable novel applications.
Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater
Authors: Feld Louise , Nielsen Tue Kjærgaard , Hansen Lars Hestbjerg , Aamand Jens , Albers Christian Nyrop
Published: November 2015

In this study, we investigated the establishment of natural bacterial degraders in a sand filter treating groundwater contaminated with the phenoxypropionate herbicides (
RS
)-2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) and (
RS
)-2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and the associated impurity/catabolite 4-chlorophenoxypropanoic acid (4-CPP). A pilot facility was set up in a contaminated landfill site. Anaerobic groundwater was pumped up and passed through an aeration basin and subsequently through a rapid sand filter, which is characterized by a short residence time of the water in the filter. For 3 months, the degradation of DCPP, MCPP, and 4-CPP in the sand filter increased to 15 to 30% of the inlet concentration. A significant selection for natural bacterial herbicide degraders also occurred in the sand filter. Using a most-probable-number (MPN) method, we found a steady increase in the number of culturable phenoxypropionate degraders, reaching approximately 5 × 10
5
degraders per g sand by the end of the study. Using a quantitative PCR targeting the two phenoxypropionate degradation genes,
rdpA
and
sdpA
, encoding stereospecific dioxygenases, a parallel increase was observed, but with the gene copy numbers being about 2 to 3 log units higher than the MPN. In general, the
sdpA
gene was more abundant than the
rdpA
gene, and the establishment of a significant population of bacteria harboring
sdpA
occurred faster than the establishment of an
rdpA
gene-carrying population. The identities of the specific herbicide degraders in the sand filter were assessed by Illumina MiSeq sequencing of 16S rRNA genes from sand filter samples and from selected MPN plate wells. We propose a list of potential degrader bacteria involved in herbicide degradation, including representatives belonging to the
Comamonadaceae
and
Sphingomonadales
.
Diversity and Ecology of Viruses in Hyperarid Desert Soils
Authors: Zablocki Olivier , Adriaenssens Evelien M. , Cowan Don
Published: November 2015

In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.
A Livestock-Associated, Multidrug-Resistant, Methicillin-Resistant Staphylococcus aureus Clonal Complex 97 Lineage Spreading in Dairy Cattle and Pigs in Italy
Authors: Feltrin Fabiola , Alba Patricia , Kraushaar Britta , Ianzano Angela , Argudín María Angeles , Di Matteo Paola , Porrero María Concepción , Aarestrup Frank M. , Butaye Patrick , Franco Alessia , Battisti Antonio
Published: November 2015

Pandemic methicillin-resistant
Staphylococcus aureus
(MRSA) clonal complex 97 (CC97) lineages originated from livestock-to-human host jumps. In recent years, CC97 has become one of the major MRSA lineages detected in Italian farmed animals. The aim of this study was to characterize and analyze differences in MRSA and methicillin-susceptible
S. aureus
(MSSA) mainly of swine and bovine origins. Forty-seven CC97 isolates, 35 MRSA isolates, and 6 MSSA isolates from different Italian pig and cattle holdings; 5 pig MRSA isolates from Germany; and 1 human MSSA isolate from Spain were characterized by macrorestriction pulsed-field gel electrophoresis (PFGE) analysis, multilocus sequence typing (MLST),
spa
typing, staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and antimicrobial resistance pattern analysis. Virulence and resistance genes were investigated by PCR and microarray analysis. Most of the isolates were of SCC
mec
type V (SCC
mec
V), except for two German MRSA isolates (SCC
mec
III). Five main clusters were identified by PFGE, with the German isolates (clusters I and II) showing 60.5% similarity with the Italian isolates, most of which (68.1%) grouped into cluster V. All CC97 isolates were Panton-Valentine leukocidin (PVL) negative, and a few (
n
= 7) tested positive for
sak
or
scn
. All MRSA isolates were multidrug resistant (MDR), and the main features were
erm
(B)- or
erm
(C)-mediated (
n
= 18) macrolide-lincosamide-streptogramin B resistance,
vga
(A)-mediated (
n
= 37) pleuromutilin resistance, fluoroquinolone resistance (
n
= 33),
tet
(K) in 32/37
tet
(M)-positive isolates, and
blaZ
in almost all MRSA isolates. Few host-associated differences were detected among CC97 MRSA isolates: their extensive MDR nature in both pigs and dairy cattle may be a consequence of a spillback from pigs of a MRSA lineage that originated in cattle as MSSA and needs further investigation. Measures should be implemented at the farm level to prevent spillover to humans in intensive farming areas.
MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently
Authors: Yun Choong-Soo , Takahashi Yurika , Shintani Masaki , Takeda Toshiharu , Suzuki-Minakuchi Chiho , Okada Kazunori , Yamane Hisakazu , Nojiri Hideaki
Published: November 2015

MvaT proteins are members of the H-NS family of proteins in pseudomonads. The IncP-7 conjugative plasmid pCAR1 carries an
mvaT
-homologous gene,
pmr
. In
Pseudomonas putida
KT2440 bearing pCAR1,
pmr
and the chromosomally carried homologous genes,
turA
and
turB
, are transcribed at high levels, and Pmr interacts with TurA and TurB
in vitro
. In the present study, we clarified how the three MvaT proteins regulate the transcriptome of
P. putida
KT2440(pCAR1). Analyses performed by a modified chromatin immunoprecipitation assay with microarray technology (ChIP-chip) suggested that the binding regions of Pmr, TurA, and TurB in the
P. putida
KT2440(pCAR1) genome are almost identical; nevertheless, transcriptomic analyses using mutants with deletions of the genes encoding the MvaT proteins during the log and early stationary growth phases clearly suggested that their regulons were different. Indeed, significant regulon dissimilarity was found between Pmr and the other two proteins. Transcription of a larger number of genes was affected by Pmr deletion during early stationary phase than during log phase, suggesting that Pmr ameliorates the effects of pCAR1 on host fitness more effectively during the early stationary phase. Alternatively, the similarity of the TurA and TurB regulons implied that they might play complementary roles as global transcriptional regulators in response to plasmid carriage.
Validation of a Previously Developed Geospatial Model That Predicts the Prevalence of Listeria monocytogenes in New York State Produce Fields
Authors: Weller Daniel , Shiwakoti Suvash , Bergholz Peter , Grohn Yrjo , Wiedmann Martin , Strawn Laura K.
Published: November 2015

Technological advancements, particularly in the field of geographic information systems (GIS), have made it possible to predict the likelihood of foodborne pathogen contamination in produce production environments using geospatial models. Yet, few studies have examined the validity and robustness of such models. This study was performed to test and refine the rules associated with a previously developed geospatial model that predicts the prevalence of
Listeria monocytogenes
in produce farms in New York State (NYS). Produce fields for each of four enrolled produce farms were categorized into areas of high or low predicted
L. monocytogenes
prevalence using rules based on a field's available water storage (AWS) and its proximity to water, impervious cover, and pastures. Drag swabs (
n
= 1,056) were collected from plots assigned to each risk category. Logistic regression, which tested the ability of each rule to accurately predict the prevalence of
L. monocytogenes
, validated the rules based on water and pasture. Samples collected near water (odds ratio [OR], 3.0) and pasture (OR, 2.9) showed a significantly increased likelihood of
L. monocytogenes
isolation compared to that for samples collected far from water and pasture. Generalized linear mixed models identified additional land cover factors associated with an increased likelihood of
L. monocytogenes
isolation, such as proximity to wetlands. These findings validated a subset of previously developed rules that predict
L. monocytogenes
prevalence in produce production environments. This suggests that GIS and geospatial models can be used to accurately predict
L. monocytogenes
prevalence on farms and can be used prospectively to minimize the risk of preharvest contamination of produce.
Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis
Authors: Morganti Marina , Scaltriti Erika , Cozzolino Paolo , Bolzoni Luca , Casadei Gabriele , Pierantoni Marco , Foni Emanuela , Pongolini Stefano
Published: November 2015

The quantitative and qualitative patterns of environmental contamination by
Listeria monocytogenes
were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for
L. monocytogenes
, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of
L. monocytogenes
within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of
L. monocytogenes
within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.
Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae
Authors: Ji Shi-Qi , Wang Bing , Lu Ming , Li Fu-Li
Published: November 2015

Brown algae are one of the largest groups of oceanic primary producers for CO
2
removal and carbon sinks for coastal regions. However, the mechanism for brown alga assimilation remains largely unknown in thermophilic microorganisms. In this work, a thermophilic alginolytic community was enriched from coastal sediment, from which an obligate anaerobic and thermophilic bacterial strain, designated Alg1, was isolated. Alg1 shared a 16S rRNA gene identity of 94.6% with
Defluviitalea saccharophila
LIND6LT2
T
. Phenotypic, chemotaxonomic, and phylogenetic studies suggested strain Alg1 represented a novel species of the genus
Defluviitalea
, for which the name
Defluviitalea phaphyphila
sp. nov. is proposed. Alg1 exhibited an intriguing ability to convert carbohydrates of brown algae, including alginate, laminarin, and mannitol, to ethanol and acetic acid. Three gene clusters participating in this process were predicted to be in the genome, and candidate enzymes were successfully expressed, purified, and characterized. Six alginate lyases were demonstrated to synergistically deconstruct alginate into unsaturated monosaccharide, followed by one uronic acid reductase and two 2-keto-3-deoxy-
d
-gluconate (KDG) kinases to produce pyruvate. A nonclassical mannitol 1-phosphate dehydrogenase, catalyzing
d
-mannitol 1-phosphate to fructose 1-phosphate in the presence of NAD
+
, and one laminarase also were disclosed. This work revealed that a thermophilic brown alga-decomposing system containing numerous novel thermophilic alginate lyases and a unique mannitol 1-phosphate dehydrogenase was adopted by the natural ethanologenic strain Alg1 during the process of evolution in hostile habitats.